merge upstream/master

811 files changed, 24421 insertions, 143435 deletions

diff --git a/.gitignore b/.gitignore
index 4c40fe81..aa2e64eb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,44 +1,128 @@
-*.log
-*.bbl
+*.a
 *.aux
+*.bbl
 *.blg
+*.dvi
 *.idx
+*.log
+*.o
 *.pdf
-*.dvi
 *.ps
-*.toc
-*.so
 *.pyc
+*.so
+*.toc
 *swp
-*.o
-*.a
 *~
 .*
 ./cdec/
+Makefile
+Makefile.in
+aclocal.m4
+autom4te.cache/
+config.guess
+config.h
+config.h.in
+config.h.in~
+config.log
+config.status
+config.sub
+configure
+decoder/Makefile
+decoder/Makefile.in
 decoder/bin/
+decoder/cdec
+decoder/dict_test
+decoder/ff_test
+decoder/grammar_test
+decoder/hg_test
+decoder/logval_test
+decoder/parser_test
+decoder/rule_lexer.cc
+decoder/small_vector_test
+decoder/trule_test
+decoder/weights_test
+depcomp
+dist
+dpmert/Makefile
+dpmert/Makefile.in
+dpmert/fast_score
+dpmert/lo_test
+dpmert/mr_dpmert_generate_mapper_input
+dpmert/mr_dpmert_map
+dpmert/mr_dpmert_reduce
+dpmert/scorer_test
+dpmert/sentclient
+dpmert/sentserver
+dpmert/union_forests
+dtrain/dtrain
+extools/build_lexical_translation
+extools/extractor
+extools/extractor_monolingual
+extools/featurize_grammar
+extools/filter_grammar
+extools/filter_score_grammar
+extools/mr_stripe_rule_reduce
+extools/score_grammar
+extools/sg_lexer.cc
+gi/clda/src/clda
+gi/markov_al/ml
+gi/pf/align-lexonly
+gi/pf/align-lexonly-pyp
 gi/pf/align-tl
 gi/pf/bayes_lattice_score
+gi/pf/brat
+gi/pf/cbgi
+gi/pf/condnaive
+gi/pf/dpnaive
+gi/pf/itg
+gi/pf/learn_cfg
 gi/pf/nuisance_test
 gi/pf/pf_test
+gi/pf/pfbrat
+gi/pf/pfdist
+gi/pf/pfnaive
 gi/pf/pyp_lm
+gi/posterior-regularisation/prjava/build/
+gi/posterior-regularisation/prjava/lib/*.jar
+gi/posterior-regularisation/prjava/lib/prjava-20100713.jar
+gi/posterior-regularisation/prjava/lib/prjava-20100715.jar
+gi/posterior-regularisation/prjava/prjava.jar
+gi/pyp-topics/src/contexts_lexer.cc
+gi/pyp-topics/src/pyp-contexts-train
+gi/pyp-topics/src/pyp-topics-train
+install-sh
 jam-files/bjam
 jam-files/engine/bin.*
 jam-files/engine/bootstrap/
 klm/lm/bin/
+klm/lm/build_binary
 klm/lm/query
 klm/util/bin/
+libtool
+ltmain.sh
+m4/libtool.m4
+m4/ltoptions.m4
+m4/ltsugar.m4
+m4/ltversion.m4
+m4/lt~obsolete.m4
+minrisk/minrisk_optimize
+mira/kbest_mira
+missing
 mteval/bin/
+mteval/fast_score
+mteval/mbr_kbest
+mteval/scorer_test
+phrasinator/gibbs_train_plm
+phrasinator/gibbs_train_plm_notables
+previous.sh
+pro-train/mr_pro_map
+pro-train/mr_pro_reduce
+python/setup.py
 rampion/rampion_cccp
 rst_parser/mst_train
+rst_parser/random_tree
 rst_parser/rst_parse
 rst_parser/rst_train
-training/liblbfgs/bin/
-training/liblbfgs/ll_test
-utils/atools
-utils/bin/
-utils/crp_test
-mira/kbest_mira
-utils/m_test
 sa-extract/calignment.c
 sa-extract/cdat.c
 sa-extract/cfloatlist.c
@@ -52,126 +136,44 @@ sa-extract/precomputation.c
 sa-extract/rule.c
 sa-extract/rulefactory.c
 sa-extract/sym.c
-training/lbl_model
-training/mpi_flex_optimize
-training/test_ngram
-utils/dict_test
-utils/logval_test
-utils/mfcr_test
-utils/phmt
-utils/small_vector_test
-utils/ts
-utils/weights_test
-pro-train/mr_pro_map
-pro-train/mr_pro_reduce
-utils/reconstruct_weights
+stamp-h1
+tests/system_tests/hmm/foo.src
+training/Makefile
+training/Makefile.in
+training/atools
 training/augment_grammar
+training/cllh_filter_grammar
+training/collapse_weights
+training/grammar_convert
+training/lbfgs_test
+training/lbl_model
+training/liblbfgs/bin/
+training/liblbfgs/ll_test
+training/model1
 training/mpi_batch_optimize
 training/mpi_compute_cllh
 training/mpi_em_optimize
 training/mpi_extract_features
 training/mpi_extract_reachable
-klm/lm/build_binary
-extools/extractor_monolingual
-gi/pf/learn_cfg
-gi/pf/brat
-gi/pf/cbgi
-gi/pf/dpnaive
-gi/pf/itg
-gi/pf/pfbrat
-gi/pf/pfdist
-gi/pf/pfnaive
-gi/markov_al/ml
-gi/posterior-regularisation/prjava/lib/*.jar
-tests/system_tests/hmm/foo.src
-training/cllh_filter_grammar
-mteval/fast_score
-mteval/mbr_kbest
+training/mpi_flex_optimize
 training/mpi_online_optimize
-dpmert/sentserver
-dpmert/sentclient
-gi/pyp-topics/src/contexts_lexer.cc
-config.guess
-config.sub
-libtool
-ltmain.sh
-config.h.in~
-decoder/ff_test
-decoder/grammar_test
-decoder/hg_test
-decoder/parser_test
-decoder/small_vector_test
-decoder/rule_lexer.cc
-training/atools
-training/collapse_weights
-training/lbfgs_test
-training/mr_optimize_reduce
 training/mr_em_adapted_reduce
 training/mr_em_map_adapter
+training/mr_optimize_reduce
 training/mr_reduce_to_weights
 training/optimize_test
 training/plftools
-dpmert/fast_score
-dpmert/lo_test
-dpmert/mr_dpmert_map
-dpmert/mr_dpmert_reduce
-dpmert/scorer_test
-dpmert/union_forests
-minrisk/minrisk_optimize
-Makefile
-Makefile.in
-aclocal.m4
-autom4te.cache/
-config.h
-config.h.in
-config.log
-config.status
-configure
-depcomp
-install-sh
-missing
-extools/extractor
-extools/mr_stripe_rule_reduce
-decoder/Makefile
-decoder/Makefile.in
-decoder/cdec
-decoder/dict_test
-decoder/trule_test
-decoder/weights_test
-stamp-h1
-training/Makefile
-training/Makefile.in
-training/grammar_convert
-training/model1
-dpmert/Makefile
-dpmert/Makefile.in
-dpmert/mr_dpmert_generate_mapper_input
-decoder/logval_test
-dtrain/dtrain
-extools/build_lexical_translation
-extools/filter_grammar
-extools/score_grammar
-gi/clda/src/clda
-gi/pyp-topics/src/pyp-topics-train
-m4/libtool.m4
-m4/ltoptions.m4
-m4/ltsugar.m4
-m4/ltversion.m4
-m4/lt~obsolete.m4
-extools/featurize_grammar
-extools/filter_score_grammar
-gi/posterior-regularisation/prjava/build/
-gi/posterior-regularisation/prjava/lib/prjava-20100713.jar
-gi/posterior-regularisation/prjava/prjava.jar
-gi/pyp-topics/src/pyp-contexts-train
-extools/sg_lexer.cc
-gi/posterior-regularisation/prjava/lib/prjava-20100715.jar
-gi/pf/align-lexonly
-gi/pf/align-lexonly-pyp
-gi/pf/condnaive
-mteval/scorer_test
-phrasinator/gibbs_train_plm
-phrasinator/gibbs_train_plm_notables
-previous.sh
-dist
-python/build/
+training/test_ngram
+utils/atools
+utils/bin/
+utils/crp_test
+utils/dict_test
+utils/logval_test
+utils/m_test
+utils/mfcr_test
+utils/phmt
+utils/reconstruct_weights
+utils/small_vector_test
+utils/ts
+utils/weights_test
+utils/unigram_pyp_lm
diff --git a/.travis.yml b/.travis.yml
index 326609d2..43d32b92 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -2,9 +2,11 @@ before_script:
  - sudo apt-get install libboost-program-options-dev
  - sudo apt-get install libboost-regex-dev
  - sudo apt-get install libboost-test-dev
+ - sudo apt-get install libboost-system-dev
  - sudo apt-get install flex
  - autoreconf -ifv
  - ./configure
 script: make
 after_script:
+ - make check
  - ./tests/run-system-tests.pl
diff --git a/Jamroot b/Jamroot
deleted file mode 100644
index 87a5a53d..00000000
--- a/Jamroot
+++ /dev/null
@@ -1,45 +0,0 @@
-#cdec compilation with bjam
-#
-#--with-boost=/usr/include
-#--with-google-hash=/usr/include so that $with-google-hash/google/dense_hash_map exists
-#
-#-a forces the build to run from scratch
-#-jN parallelizes just like make
-#
-#Respects CXXFLAGS, CFLAGS, and LDFLAGS environment variables.  
-
-path-constant TOP : . ;
-include $(TOP)/jam-files/sanity.jam ;
-boost 104400 ;
-external-lib z ;
-
-with-google-hash = [ option.get "with-google-hash" ] ;
-if [ test_header google/dense_hash_map ] || $(with-google-hash) {
-  requirements += <define>HAVE_SPARSEHASH <include>$(with-google-hash) ;
-}
-
-if [ test_header cmph.h ] || $(with-cmph) {
-  requirements += <define>HAVE_CMPH <include>$(with-cmph) ;
-}
-
-if [ test_header boost/serialization/map.hpp ] && [ test_library boost_serialization ] {
-  requirements += <define>HAVE_BOOST_ARCHIVE_TEXT_OARCHIVE_HPP ;
-}
-
-project : requirements $(requirements) <toolset>darwin:<link>static ;
-project : default-build <warnings>on <variant>release ;
-
-install-bin-libs dpmert//programs utils//programs mteval//programs klm/lm//programs training//liblbfgs decoder//cdec phrasinator//programs mira//kbest_mira ;
-
-install perl-scripts : dpmert//dpmert.pl : <location>$(bindir) ;
-
-build-projects mteval decoder dpmert klm/lm training/liblbfgs ;
-
-#Compile everything ending with _test.cc into a test and run it.
-rule all_tests ( targets * : dependencies : properties * ) {
-  targets ?= [ glob *_test.cc ] ;
-  for t in $(targets) {
-    local base = [ MATCH "^(.*).cc$" : $(t) ] ;
-    unit-test $(base) : $(t) $(dependencies) ..//boost_unit_test_framework : $(properties) ;
-  }
-}
diff --git a/Makefile.am b/Makefile.am
index 332542c4..fefc470d 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -6,8 +6,8 @@ SUBDIRS = \
   mteval \
   klm/util \
   klm/lm \
+  klm/search \
   decoder \
-  phrasinator \
   training \
   training/liblbfgs \
   mira \
@@ -16,13 +16,11 @@ SUBDIRS = \
   pro-train \
   rampion \
   minrisk \
-  extools \
-  gi/pf \
-  gi/markov_al \
-  rst_parser
+  example_extff
 
 #gi/pyp-topics/src gi/clda/src gi/posterior-regularisation/prjava
 
 AUTOMAKE_OPTIONS = foreign
 ACLOCAL_AMFLAGS = -I m4
-AM_CPPFLAGS =  -D_GLIBCXX_PARALLEL -march=native -mtune=native -O2 -pipe -fomit-frame-pointer -Wall
+AM_CPPFLAGS =  -D_GLIBCXX_PARALLEL
+
diff --git a/README b/README
deleted file mode 100644
index 47b52355..00000000
--- a/README
+++ /dev/null
@@ -1,57 +0,0 @@
-cdec is a fast decoder.
-
-SPEED COMPARISON
-------------------------------------------------------------------------------
-
-Here is a comparison with a couple of other decoders doing SCFG decoding:
-
-  Decoder  Lang.   BLEU    Run-Time        Memory
-  cdec     c++     31.47   0.37 sec/sent   1.0-1.1GB
-  Joshua   Java    31.55   2.34 sec/sent   4.0-4.8GB
-  Hiero    Python  31.22   27.2 sec/sent   1.7-1.9GB
-
-The maximum number of pops from candidate heap at each node is k=30, no other
-pruning, 3gm LM, Chinese-English translation task.
-
-
-GETTING STARTED
-------------------------------------------------------------------------------
-
-See the BUILDING file for instructions on how to build the software.  To
-explore the decoder's features, the best way to get started is to look
-at cdec's command line options or to have a look at the test cases in
-the tests/system_tests/ directory.  Each of these can be run with a command
-like ./cdec -c cdec.ini -i input.txt -w weights .  The files should be
-self explanatory.
-
-
-EXTRACTING A SYNCHRONOUS GRAMMAR / PHRASE TABLE
-------------------------------------------------------------------------------
-cdec does not include code for generating grammars.  To build these, you will
-need to write your own software or use an existing package like Joshua, Hiero,
-or Moses.
-
-
-OPTIMIZING / TRAINING MODELS
-------------------------------------------------------------------------------
-cdec does include code for optimizing models, according to a number of
-training criteria, including training models as CRFs (with latent derivation
-variables), MERT (over hypergraphs) to opimize BLEU, TER, etc.
-
-Eventually, I will provide documentation for this.
-
-
-ALIGNMENT / SYNCHRONOUS PARSING / CONSTRAINED DECODING
-------------------------------------------------------------------------------
-cdec can be used as an aligner.  For examples, see the test cases.
-
-
-COPYRIGHT AND LICENSE
-------------------------------------------------------------------------------
-Copyright (c) 2009 by Chris Dyer <redpony@gmail.com>
-
-See the file LICENSE.txt for the licensing terms that this software is
-released under. This software also includes the file m4/boost.m4 which is
-licensed under the LGPL v3, for more information refer to the comments
-in that file.
-
diff --git a/README.md b/README.md
new file mode 100644
index 00000000..d89e9558
--- /dev/null
+++ b/README.md
@@ -0,0 +1,24 @@
+`cdec` is a research platform for machine translation and similar structured prediction problems.
+
+## Installation
+
+Build `cdec`:
+
+	autoreconf -ifv
+	./configure
+	make
+	./tests/run-system-tests.pl
+
+You will need the following libraries / tools:
+
+- [Autoconf / Automake / Libtool](http://www.gnu.org/software/autoconf/)
+    - Older versions of GNU autotools may not work properly.
+- [Boost C++ libraries (version 1.44 or later)](http://www.boost.org/)
+    - If you build your own boost, you _must install it_ using `bjam install`.
+    - Older versions of Boost _may_ work, but problems have been reported with command line option parsing on some platforms with older versions.
+- [GNU Flex](http://flex.sourceforge.net/)
+
+## Further information
+
+[For more information, refer to the cdec documentation](http://www.cdec-decoder.org)
+
diff --git a/bjam b/bjam
deleted file mode 100755
index d1ac8a55..00000000
--- a/bjam
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/bin/bash
-set -e
-if
-  bjam="$(which bjam 2>/dev/null)" && #exists
-  [ ${#bjam} != 0 ] && #paranoia about which printing nothing then returning true
-  ! grep UFIHGUFIHBDJKNCFZXAEVA "${bjam}" </dev/null >/dev/null && #bjam in path isn't this script
-  "${bjam}" --help >/dev/null 2>/dev/null && #bjam in path isn't broken (i.e. has boost-build)
-  "${bjam}" --version |grep "Boost.Build 201" >/dev/null 2>/dev/null #It's recent enough.  
-then
-  #Delegate to system bjam
-  exec "${bjam}" "$@"
-fi
-
-top="$(dirname "$0")"
-if [ ! -x "$top"/jam-files/bjam ]; then
-  pushd "$top/jam-files/engine"
-  ./build.sh
-  cp -f bin.*/bjam ../bjam
-  popd
-fi
-
-export BOOST_BUILD_PATH="$top"/jam-files/boost-build 
-exec "$top"/jam-files/bjam "$@"
diff --git a/configure.ac b/configure.ac
index eb2f4aaa..cb132d66 100644
--- a/configure.ac
+++ b/configure.ac
@@ -12,7 +12,12 @@ AC_PROG_CXX
 AC_LANG_CPLUSPLUS
 BOOST_REQUIRE([1.44])
 BOOST_PROGRAM_OPTIONS
+BOOST_SYSTEM
 BOOST_TEST
+AM_PATH_PYTHON
+AC_CHECK_HEADER(dlfcn.h,AC_DEFINE(HAVE_DLFCN_H))
+AC_CHECK_LIB(dl, dlopen)
+
 AC_ARG_ENABLE(mpi,
  [ --enable-mpi  Build MPI binaries, assumes mpi.h is present ],
  [ mpi=yes
@@ -69,9 +74,9 @@ fi
 
 #BOOST_THREADS
 CPPFLAGS="$CPPFLAGS $BOOST_CPPFLAGS"
-LDFLAGS="$LDFLAGS $BOOST_PROGRAM_OPTIONS_LDFLAGS"
+LDFLAGS="$LDFLAGS $BOOST_PROGRAM_OPTIONS_LDFLAGS $BOOST_SYSTEM_LDFLAGS"
 # $BOOST_THREAD_LDFLAGS"
-LIBS="$LIBS $BOOST_PROGRAM_OPTIONS_LIBS"
+LIBS="$LIBS $BOOST_PROGRAM_OPTIONS_LIBS $BOOST_SYSTEM_LIBS"
 # $BOOST_THREAD_LIBS"
 
 AC_CHECK_HEADER(google/dense_hash_map,
@@ -79,13 +84,6 @@ AC_CHECK_HEADER(google/dense_hash_map,
 
 AC_PROG_INSTALL
 
-AM_CONDITIONAL([RAND_LM], false)
-AC_ARG_WITH(randlm,
-            [AC_HELP_STRING([--with-randlm=PATH], [(optional) path to RandLM toolkit])],
-            [with_randlm=$withval],
-            [with_randlm=no]
-           )
-
 AM_CONDITIONAL([GLC], false)
 AC_ARG_WITH(glc,
             [AC_HELP_STRING([--with-glc=PATH], [(optional) path to Global Lexical Coherence package (Context CRF)])],
@@ -94,24 +92,6 @@ AC_ARG_WITH(glc,
            )
 FF_GLC=""
 
-if test "x$with_randlm" != 'xno'
-then
-  SAVE_CPPFLAGS="$CPPFLAGS"
-  CPPFLAGS="$CPPFLAGS -I${with_randlm}/include"
-
-  AC_CHECK_HEADER(RandLM.h,
-                 [AC_DEFINE([HAVE_RANDLM], [], [flag for RandLM])],
-                 [AC_MSG_ERROR([Cannot find RandLM!])])
-
-
-  LIB_RANDLM="-lrandlm"
-  LDFLAGS="$LDFLAGS -L${with_randlm}/lib"
-  LIBS="$LIBS $LIB_RANDLM"
-  FMTLIBS="$FMTLIBS librandlm.a"
-  AM_CONDITIONAL([RAND_LM], true)
-fi
-
-
 if test "x$with_glc" != 'xno'
 then
   SAVE_CPPFLAGS="$CPPFLAGS"
@@ -132,4 +112,24 @@ fi
 
 CPPFLAGS="-DPIC -fPIC $CPPFLAGS -DHAVE_CONFIG_H"
 
-AC_OUTPUT(Makefile rst_parser/Makefile utils/Makefile mteval/Makefile extools/Makefile decoder/Makefile phrasinator/Makefile training/Makefile training/liblbfgs/Makefile dpmert/Makefile pro-train/Makefile rampion/Makefile minrisk/Makefile klm/util/Makefile klm/lm/Makefile mira/Makefile dtrain/Makefile gi/pyp-topics/src/Makefile gi/clda/src/Makefile gi/pf/Makefile gi/markov_al/Makefile)
+AC_CONFIG_FILES([Makefile])
+AC_CONFIG_FILES([utils/Makefile])
+AC_CONFIG_FILES([mteval/Makefile])
+AC_CONFIG_FILES([decoder/Makefile])
+AC_CONFIG_FILES([training/Makefile])
+AC_CONFIG_FILES([training/liblbfgs/Makefile])
+AC_CONFIG_FILES([dpmert/Makefile])
+AC_CONFIG_FILES([pro-train/Makefile])
+AC_CONFIG_FILES([rampion/Makefile])
+AC_CONFIG_FILES([minrisk/Makefile])
+AC_CONFIG_FILES([klm/util/Makefile])
+AC_CONFIG_FILES([klm/lm/Makefile])
+AC_CONFIG_FILES([klm/search/Makefile])
+AC_CONFIG_FILES([mira/Makefile])
+AC_CONFIG_FILES([dtrain/Makefile])
+AC_CONFIG_FILES([example_extff/Makefile])
+
+AC_CONFIG_FILES([python/setup.py])
+
+AC_OUTPUT
+
diff --git a/corpus/add-self-translations.pl b/corpus/add-self-translations.pl
new file mode 100755
index 00000000..153bc454
--- /dev/null
+++ b/corpus/add-self-translations.pl
@@ -0,0 +1,29 @@
+#!/usr/bin/perl -w
+use strict;
+
+# ADDS SELF-TRANSLATIONS OF POORLY ATTESTED WORDS TO THE PARALLEL DATA
+
+my %df;
+my %def;
+while(<>) {
+  print;
+  chomp;
+  my ($sf, $se) = split / \|\|\| /;
+  die "Format error: $_\n" unless defined $sf && defined $se;
+  my @fs = split /\s+/, $sf;
+  my @es = split /\s+/, $se;
+  for my $f (@fs) {
+    $df{$f}++;
+    for my $e (@es) {
+      if ($f eq $e) { $def{$f}++; }
+    }
+  }
+}
+
+for my $k (sort keys %def) {
+  next if $df{$k} > 4;
+  print "$k ||| $k\n";
+  print "$k ||| $k\n";
+  print "$k ||| $k\n";
+}
+
diff --git a/decoder/Jamfile b/decoder/Jamfile
deleted file mode 100644
index 06c5bfda..00000000
--- a/decoder/Jamfile
+++ /dev/null
@@ -1,78 +0,0 @@
-import testing ;
-import lex ;
-import option ;
-
-if [ option.get "with-glc" ] {
-  glc = ff_glc.cc string_util.cc feature-factory.cc ;
-}
-
-lib decoder : 
-  forest_writer.cc
-  maxtrans_blunsom.cc
-  cdec_ff.cc
-  cfg.cc
-  dwarf.cc
-  ff_dwarf.cc
-  rule_lexer.ll
-  fst_translator.cc
-  csplit.cc
-  translator.cc
-  scfg_translator.cc
-  hg.cc
-  hg_io.cc
-  decoder.cc
-  hg_intersect.cc
-  hg_sampler.cc
-  factored_lexicon_helper.cc
-  viterbi.cc
-  lattice.cc
-  aligner.cc
-  apply_models.cc
-  earley_composer.cc
-  phrasetable_fst.cc
-  trule.cc
-  ff.cc
-  ff_rules.cc
-  ff_wordset.cc
-  ff_context.cc
-  ff_charset.cc
-  ff_lm.cc
-  ff_klm.cc
-  ff_ngrams.cc
-  ff_spans.cc
-  ff_ruleshape.cc
-  ff_wordalign.cc
-  ff_csplit.cc
-  ff_tagger.cc
-  ff_source_syntax.cc
-  ff_bleu.cc
-  ff_factory.cc
-  lexalign.cc
-  lextrans.cc
-  tagger.cc
-  bottom_up_parser.cc
-  phrasebased_translator.cc
-  JSON_parser.c
-  json_parse.cc
-  grammar.cc
-  $(glc)
-  ..//utils
-  ..//mteval
-  ../klm/lm//kenlm
-  ..//boost_program_options
-  : <include>.
-  : :
-  <library>..//utils
-  <library>..//mteval
-  <library>../klm/lm//kenlm
-  <library>..//boost_program_options
-  <include>.
-  ;
-
-exe cdec : cdec.cc decoder ..//utils ..//mteval ../klm/lm//kenlm ..//boost_program_options ;
-
-all_tests [ glob *_test.cc : cfg_test.cc ] : decoder : <testing.arg>$(TOP)/decoder/test_data ;
-
-install legacy : cdec
-  : <location>$(TOP)/cdec <install-type>EXE <install-dependencies>on <link>shared:<dll-path>$(TOP)/cdec <link>shared:<install-type>LIB ;
-
diff --git a/decoder/Makefile.am b/decoder/Makefile.am
index 0a792549..f8f427d3 100644
--- a/decoder/Makefile.am
+++ b/decoder/Makefile.am
@@ -17,7 +17,7 @@ trule_test_SOURCES = trule_test.cc
 trule_test_LDADD = $(BOOST_UNIT_TEST_FRAMEWORK_LDFLAGS) $(BOOST_UNIT_TEST_FRAMEWORK_LIBS) libcdec.a ../mteval/libmteval.a ../utils/libutils.a -lz
 
 cdec_SOURCES = cdec.cc
-cdec_LDADD = libcdec.a ../mteval/libmteval.a ../utils/libutils.a ../klm/lm/libklm.a ../klm/util/libklm_util.a -lz
+cdec_LDADD = libcdec.a ../mteval/libmteval.a ../utils/libutils.a ../klm/search/libksearch.a ../klm/lm/libklm.a ../klm/util/libklm_util.a -lz
 
 AM_CPPFLAGS = -DBOOST_TEST_DYN_LINK -W -Wno-sign-compare $(GTEST_CPPFLAGS) -I.. -I../mteval -I../utils -I../klm
 
@@ -33,6 +33,7 @@ libcdec_a_SOURCES = \
   cfg.cc \
   dwarf.cc \
   ff_dwarf.cc \
+  ff_external.cc \
   rule_lexer.cc \
   fst_translator.cc \
   csplit.cc \
@@ -44,6 +45,7 @@ libcdec_a_SOURCES = \
   hg_remove_eps.cc \
   decoder.cc \
   hg_intersect.cc \
+  hg_union.cc \
   hg_sampler.cc \
   factored_lexicon_helper.cc \
   viterbi.cc \
@@ -54,6 +56,8 @@ libcdec_a_SOURCES = \
   phrasetable_fst.cc \
   trule.cc \
   ff.cc \
+  ffset.cc \
+  ff_basic.cc \
   ff_rules.cc \
   ff_wordset.cc \
   ff_context.cc \
@@ -69,6 +73,7 @@ libcdec_a_SOURCES = \
   ff_source_syntax.cc \
   ff_bleu.cc \
   ff_factory.cc \
+  incremental.cc \
   lexalign.cc \
   lextrans.cc \
   tagger.cc \
diff --git a/decoder/apply_models.cc b/decoder/apply_models.cc
index 9ba59d1b..330de9e2 100644
--- a/decoder/apply_models.cc
+++ b/decoder/apply_models.cc
@@ -16,6 +16,7 @@
 #include "verbose.h"
 #include "hg.h"
 #include "ff.h"
+#include "ffset.h"
 
 #define NORMAL_CP 1
 #define FAST_CP 2
diff --git a/decoder/cdec.cc b/decoder/cdec.cc
index c671af57..cc3fcff1 100644
--- a/decoder/cdec.cc
+++ b/decoder/cdec.cc
@@ -4,6 +4,8 @@
 #include "decoder.h"
 #include "ff_register.h"
 #include "verbose.h"
+#include "timing_stats.h"
+#include "util/usage.hh"
 
 using namespace std;
 
@@ -27,6 +29,7 @@ int main(int argc, char** argv) {
     if (buf.empty()) continue;
     decoder.Decode(buf);
   }
+  Timer::Summarize();
 #ifdef CP_TIME
     cerr << "Time required for Cube Pruning execution: "
     << CpTime::Get()
@@ -38,6 +41,7 @@ int main(int argc, char** argv) {
       cout << FD::Convert(i) << endl;
     }
   }
+  util::PrintUsage(std::cerr);
   return 0;
 }
 
diff --git a/decoder/cdec_ff.cc b/decoder/cdec_ff.cc
index d64bdada..3ab0f9f6 100644
--- a/decoder/cdec_ff.cc
+++ b/decoder/cdec_ff.cc
@@ -1,6 +1,7 @@
 #include <boost/shared_ptr.hpp>
 
 #include "ff.h"
+#include "ff_basic.h"
 #include "ff_context.h"
 #include "ff_spans.h"
 #include "ff_lm.h"
@@ -18,6 +19,7 @@
 #include "ff_charset.h"
 #include "ff_wordset.h"
 #include "ff_dwarf.h"
+#include "ff_external.h"
 
 #ifdef HAVE_GLC
 #include <cdec/ff_glc.h>
@@ -70,6 +72,7 @@ void register_feature_functions() {
   ff_registry.Register("WordPairFeatures", new FFFactory<WordPairFeatures>);
   ff_registry.Register("WordSet", new FFFactory<WordSet>);
   ff_registry.Register("Dwarf", new FFFactory<Dwarf>);
+  ff_registry.Register("External", new FFFactory<ExternalFeature>);
 #ifdef HAVE_GLC
   ff_registry.Register("ContextCRF", new FFFactory<Model1Features>);
 #endif
diff --git a/decoder/cfg.h b/decoder/cfg.h
index 8cb29bb9..aeeacb83 100644
--- a/decoder/cfg.h
+++ b/decoder/cfg.h
@@ -130,7 +130,7 @@ struct CFG {
     int lhs; // index into nts
     RHS rhs;
     prob_t p; // h unused for now (there's nothing admissable, and p is already using 1st pass inside as pushed toward top)
-    FeatureVector f; // may be empty, unless copy_features on Init
+    SparseVector<double> f; // may be empty, unless copy_features on Init
     IF_CFG_TRULE(TRulePtr rule;)
     int size() const { // for stats only
       return rhs.size();
diff --git a/decoder/cfg_format.h b/decoder/cfg_format.h
index 2f40d483..d12da261 100644
--- a/decoder/cfg_format.h
+++ b/decoder/cfg_format.h
@@ -100,7 +100,7 @@ struct CFGFormat {
     }
   }
 
-  void print_features(std::ostream &o,prob_t p,FeatureVector const& fv=FeatureVector()) const {
+  void print_features(std::ostream &o,prob_t p,SparseVector<double> const& fv=SparseVector<double>()) const {
     bool logp=(logprob_feat && p!=prob_t::One());
     if (features || logp) {
       o << partsep;
diff --git a/decoder/cfg_test.cc b/decoder/cfg_test.cc
index b8f4cf11..316c6d16 100644
--- a/decoder/cfg_test.cc
+++ b/decoder/cfg_test.cc
@@ -25,9 +25,9 @@ struct CFGTest : public TestWithParam<HgW> {
   Hypergraph hg;
   CFG cfg;
   CFGFormat form;
-  FeatureVector weights;
+  SparseVector<double> weights;
 
-  static void JsonFN(Hypergraph &hg,CFG &cfg,FeatureVector &featw,std::string file
+  static void JsonFN(Hypergraph &hg,CFG &cfg,SparseVector<double> &featw,std::string file
                      ,std::string const& wts="Model_0 1 EgivenF 1 f1 1")
   {
     istringstream ws(wts);
diff --git a/decoder/decoder.cc b/decoder/decoder.cc
index a6f7b1ce..b5f4b9b6 100644
--- a/decoder/decoder.cc
+++ b/decoder/decoder.cc
@@ -4,6 +4,7 @@
 #include <boost/program_options.hpp>
 #include <boost/program_options/variables_map.hpp>
 #include <boost/make_shared.hpp>
+#include <boost/scoped_ptr.hpp>
 
 #include "program_options.h"
 #include "stringlib.h"
@@ -24,10 +25,12 @@
 #include "hg.h"
 #include "sentence_metadata.h"
 #include "hg_intersect.h"
+#include "hg_union.h"
 
 #include "oracle_bleu.h"
 #include "apply_models.h"
 #include "ff.h"
+#include "ffset.h"
 #include "ff_factory.h"
 #include "viterbi.h"
 #include "kbest.h"
@@ -37,6 +40,7 @@
 #include "sampler.h"
 
 #include "forest_writer.h" // TODO this section should probably be handled by an Observer
+#include "incremental.h"
 #include "hg_io.h"
 #include "aligner.h"
 
@@ -89,11 +93,6 @@ inline void ShowBanner() {
   cerr << "cdec v1.0 (c) 2009-2011 by Chris Dyer\n";
 }
 
-inline void show_models(po::variables_map const& conf,ModelSet &ms,char const* header) {
-  cerr<<header<<": ";
-  ms.show_features(cerr,cerr,conf.count("warn_0_weight"));
-}
-
 inline string str(char const* name,po::variables_map const& conf) {
   return conf[name].as<string>();
 }
@@ -131,7 +130,7 @@ inline boost::shared_ptr<FeatureFunction> make_ff(string const& ffp,bool verbose
   }
   boost::shared_ptr<FeatureFunction> pf = ff_registry.Create(ff, param);
   if (!pf) exit(1);
-  int nbyte=pf->NumBytesContext();
+  int nbyte=pf->StateSize();
   if (verbose_feature_functions && !SILENT)
     cerr<<"State is "<<nbyte<<" bytes for "<<pre<<"feature "<<ffp<<endl;
   return pf;
@@ -327,6 +326,8 @@ struct DecoderImpl {
   bool feature_expectations; // TODO Observer
   bool output_training_vector; // TODO Observer
   bool remove_intersected_rule_annotations;
+  boost::scoped_ptr<IncrementalBase> incremental;
+
 
   static void ConvertSV(const SparseVector<prob_t>& src, SparseVector<double>* trg) {
     for (SparseVector<prob_t>::const_iterator it = src.begin(); it != src.end(); ++it)
@@ -414,6 +415,7 @@ DecoderImpl::DecoderImpl(po::variables_map& conf, int argc, char** argv, istream
         ("show_conditional_prob", "Output the conditional log prob to STDOUT instead of a translation")
         ("show_cfg_search_space", "Show the search space as a CFG")
         ("show_target_graph", po::value<string>(), "Directory to write the target hypergraphs to")
+        ("incremental_search", po::value<string>(), "Run lazy search with this language model file")
         ("coarse_to_fine_beam_prune", po::value<double>(), "Prune paths from coarse parse forest before fine parse, keeping paths within exp(alpha>=0)")
         ("ctf_beam_widen", po::value<double>()->default_value(2.0), "Expand coarse pass beam by this factor if no fine parse is found")
         ("ctf_num_widenings", po::value<int>()->default_value(2), "Widen coarse beam this many times before backing off to full parse")
@@ -641,8 +643,6 @@ DecoderImpl::DecoderImpl(po::variables_map& conf, int argc, char** argv, istream
       prev_weights = rp.weight_vector;
     }
     rp.models.reset(new ModelSet(*rp.weight_vector, rp.ffs));
-    string ps = "Pass1 "; ps[4] += pass;
-    if (!SILENT) show_models(conf,*rp.models,ps.c_str());
   }
 
   // show configuration of rescoring passes
@@ -730,6 +730,10 @@ DecoderImpl::DecoderImpl(po::variables_map& conf, int argc, char** argv, istream
   sent_id = -1;
   acc_obj = 0; // accumulate objective
   g_count = 0;    // number of gradient pieces computed
+
+  if (conf.count("incremental_search")) {
+    incremental.reset(IncrementalBase::Load(conf["incremental_search"].as<string>().c_str(), CurrentWeightVector()));
+  }
 }
 
 Decoder::Decoder(istream* cfg) { pimpl_.reset(new DecoderImpl(conf,0,0,cfg)); }
@@ -831,6 +835,12 @@ bool DecoderImpl::Decode(const string& input, DecoderObserver* o) {
   if (conf.count("show_target_graph"))
     HypergraphIO::WriteTarget(conf["show_target_graph"].as<string>(), sent_id, forest);
 
+  if (conf.count("incremental_search")) {
+    incremental->Search(pop_limit, forest);
+    o->NotifyDecodingComplete(smeta);
+    return true;
+  }
+
   for (int pass = 0; pass < rescoring_passes.size(); ++pass) {
     const RescoringPass& rp = rescoring_passes[pass];
     const vector<weight_t>& cur_weights = *rp.weight_vector;
@@ -870,13 +880,13 @@ bool DecoderImpl::Decode(const string& input, DecoderObserver* o) {
     if (rp.fid_summary) {
       if (summary_feature_type == kEDGE_PROB) {
         const prob_t z = forest.PushWeightsToGoal(1.0);
-        if (!isfinite(log(z)) || isnan(log(z))) {
+        if (!std::isfinite(log(z)) || std::isnan(log(z))) {
           cerr << "  " << passtr << " !!! Invalid partition detected, abandoning.\n";
         } else {
           for (int i = 0; i < forest.edges_.size(); ++i) {
             const double log_prob_transition = log(forest.edges_[i].edge_prob_); // locally normalized by the edge
                                                                               // head node by forest.PushWeightsToGoal
-            if (!isfinite(log_prob_transition) || isnan(log_prob_transition)) {
+            if (!std::isfinite(log_prob_transition) || std::isnan(log_prob_transition)) {
               cerr << "Edge: i=" << i << " got bad inside prob: " << *forest.edges_[i].rule_ << endl;
               abort();
             }
@@ -888,7 +898,7 @@ bool DecoderImpl::Decode(const string& input, DecoderObserver* o) {
       } else if (summary_feature_type == kNODE_RISK) {
         Hypergraph::EdgeProbs posts;
         const prob_t z = forest.ComputeEdgePosteriors(1.0, &posts);
-        if (!isfinite(log(z)) || isnan(log(z))) {
+        if (!std::isfinite(log(z)) || std::isnan(log(z))) {
           cerr << "  " << passtr << " !!! Invalid partition detected, abandoning.\n";
         } else {
           for (int i = 0; i < forest.nodes_.size(); ++i) {
@@ -897,7 +907,7 @@ bool DecoderImpl::Decode(const string& input, DecoderObserver* o) {
             for (int j = 0; j < in_edges.size(); ++j)
               node_post += (posts[in_edges[j]] / z);
             const double log_np = log(node_post);
-            if (!isfinite(log_np) || isnan(log_np)) {
+            if (!std::isfinite(log_np) || std::isnan(log_np)) {
               cerr << "got bad posterior prob for node " << i << endl;
               abort();
             }
@@ -912,13 +922,13 @@ bool DecoderImpl::Decode(const string& input, DecoderObserver* o) {
       } else if (summary_feature_type == kEDGE_RISK) {
         Hypergraph::EdgeProbs posts;
         const prob_t z = forest.ComputeEdgePosteriors(1.0, &posts);
-        if (!isfinite(log(z)) || isnan(log(z))) {
+        if (!std::isfinite(log(z)) || std::isnan(log(z))) {
           cerr << "  " << passtr << " !!! Invalid partition detected, abandoning.\n";
         } else {
           assert(posts.size() == forest.edges_.size());
           for (int i = 0; i < posts.size(); ++i) {
             const double log_np = log(posts[i] / z);
-            if (!isfinite(log_np) || isnan(log_np)) {
+            if (!std::isfinite(log_np) || std::isnan(log_np)) {
               cerr << "got bad posterior prob for node " << i << endl;
               abort();
             }
@@ -958,7 +968,7 @@ bool DecoderImpl::Decode(const string& input, DecoderObserver* o) {
 
   // Oracle Rescoring
   if(get_oracle_forest) {
-    assert(!"this is broken"); FeatureVector dummy; // = last_weights
+    assert(!"this is broken"); SparseVector<double> dummy; // = last_weights
     Oracle oc=oracle.ComputeOracle(smeta,&forest,dummy,10,conf["forest_output"].as<std::string>());
     if (!SILENT) cerr << "  +Oracle BLEU forest (nodes/edges): " << forest.nodes_.size() << '/' << forest.edges_.size() << endl;
     if (!SILENT) cerr << "  +Oracle BLEU (paths): " << forest.NumberOfPaths() << endl;
@@ -980,7 +990,7 @@ bool DecoderImpl::Decode(const string& input, DecoderObserver* o) {
         bool succeeded = HypergraphIO::ReadFromJSON(rf.stream(), &new_hg);
         if (!succeeded) abort();
       }
-      new_hg.Union(forest);
+      HG::Union(forest, &new_hg);
       bool succeeded = writer.Write(new_hg, false);
       if (!succeeded) abort();
     } else {
@@ -1067,7 +1077,7 @@ bool DecoderImpl::Decode(const string& input, DecoderObserver* o) {
             bool succeeded = HypergraphIO::ReadFromJSON(rf.stream(), &new_hg);
             if (!succeeded) abort();
           }
-          new_hg.Union(forest);
+          HG::Union(forest, &new_hg);
           bool succeeded = writer.Write(new_hg, false);
           if (!succeeded) abort();
         } else {
@@ -1089,7 +1099,7 @@ bool DecoderImpl::Decode(const string& input, DecoderObserver* o) {
           cerr << "DIFF. ERR! log_z < log_ref_z: " << log_z << " " << log_ref_z << endl;
           exit(1);
         }
-        assert(!isnan(log_ref_z));
+        assert(!std::isnan(log_ref_z));
         ref_exp -= full_exp;
         acc_vec += ref_exp;
         acc_obj += (log_z - log_ref_z);
diff --git a/decoder/decoder.h b/decoder/decoder.h
index bef2ff5e..79c7a602 100644
--- a/decoder/decoder.h
+++ b/decoder/decoder.h
@@ -24,7 +24,7 @@ private:
 #endif
 
 class SentenceMetadata;
-struct Hypergraph;
+class Hypergraph;
 struct DecoderImpl;
 
 struct DecoderObserver {
diff --git a/decoder/exp_semiring.h b/decoder/exp_semiring.h
index 111eaaf1..2a9034bb 100644
--- a/decoder/exp_semiring.h
+++ b/decoder/exp_semiring.h
@@ -59,7 +59,7 @@ struct PRWeightFunction {
   explicit PRWeightFunction(const PWeightFunction& pwf = PWeightFunction(),
                             const RWeightFunction& rwf = RWeightFunction()) :
     pweight(pwf), rweight(rwf) {}
-  PRPair<P,R> operator()(const Hypergraph::Edge& e) const {
+  PRPair<P,R> operator()(const HG::Edge& e) const {
     const P p = pweight(e);
     const R r = rweight(e);
     return PRPair<P,R>(p, r * p);
diff --git a/decoder/ff.cc b/decoder/ff.cc
index 557e0b5f..a6a035b5 100644
--- a/decoder/ff.cc
+++ b/decoder/ff.cc
@@ -1,9 +1,3 @@
-//TODO: non-sparse vector for all feature functions?  modelset applymodels keeps track of who has what features?  it's nice having FF that could generate a handful out of 10000 possible feats, though.
-
-//TODO: actually score rule_feature()==true features once only, hash keyed on rule or modify TRule directly?  need to keep clear in forest which features come from models vs. rules; then rescoring could drop all the old models features at once
-
-#include "fast_lexical_cast.hpp"
-#include <stdexcept>
 #include "ff.h"
 
 #include "tdict.h"
@@ -16,8 +10,7 @@ FeatureFunction::~FeatureFunction() {}
 void FeatureFunction::PrepareForInput(const SentenceMetadata&) {}
 
 void FeatureFunction::FinalTraversalFeatures(const void* /* ant_state */,
-                                             SparseVector<double>* /* features */) const {
-}
+                                             SparseVector<double>* /* features */) const {}
 
 string FeatureFunction::usage_helper(std::string const& name,std::string const& params,std::string const& details,bool sp,bool sd) {
   string r=name;
@@ -32,188 +25,14 @@ string FeatureFunction::usage_helper(std::string const& name,std::string const&
   return r;
 }
 
-Features FeatureFunction::single_feature(WordID feat) {
-  return Features(1,feat);
-}
-
-Features ModelSet::all_features(std::ostream *warn,bool warn0) {
-  //return ::all_features(models_,weights_,warn,warn0);
-}
-
-void show_features(Features const& ffs,DenseWeightVector const& weights_,std::ostream &out,std::ostream &warn,bool warn_zero_wt) {
-  out << "Weight  Feature\n";
-  for (unsigned i=0;i<ffs.size();++i) {
-    WordID fid=ffs[i];
-    string const& fname=FD::Convert(fid);
-    double wt=weights_[fid];
-    if (warn_zero_wt && wt==0)
-      warn<<"WARNING: "<<fname<<" has 0 weight."<<endl;
-    out << wt << "  " << fname<<endl;
-  }
-}
-
-void ModelSet::show_features(std::ostream &out,std::ostream &warn,bool warn_zero_wt)
-{
-//  ::show_features(all_features(),weights_,out,warn,warn_zero_wt);
-  //show_all_features(models_,weights_,out,warn,warn_zero_wt,warn_zero_wt);
-}
-
-// Hiero and Joshua use log_10(e) as the value, so I do to
-WordPenalty::WordPenalty(const string& param) :
-  fid_(FD::Convert("WordPenalty")),
-    value_(-1.0 / log(10)) {
-  if (!param.empty()) {
-    cerr << "Warning WordPenalty ignoring parameter: " << param << endl;
-  }
-}
-
-void FeatureFunction::TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                        const Hypergraph::Edge& edge,
-                                        const std::vector<const void*>& ant_states,
-                                        SparseVector<double>* features,
-                                        SparseVector<double>* estimated_features,
-                                        void* state) const {
-  throw std::runtime_error("TraversalFeaturesImpl not implemented - override it or TraversalFeaturesLog.\n");
+void FeatureFunction::TraversalFeaturesImpl(const SentenceMetadata&,
+                                        const Hypergraph::Edge&,
+                                        const std::vector<const void*>&,
+                                        SparseVector<double>*,
+                                        SparseVector<double>*,
+                                        void*) const {
+  cerr << "TraversalFeaturesImpl not implemented - override it or TraversalFeaturesLog\n";
   abort();
 }
 
 
-void WordPenalty::TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                        const Hypergraph::Edge& edge,
-                                        const std::vector<const void*>& ant_states,
-                                        SparseVector<double>* features,
-                                        SparseVector<double>* estimated_features,
-                                        void* state) const {
-  (void) smeta;
-  (void) ant_states;
-  (void) state;
-  (void) estimated_features;
-  features->set_value(fid_, edge.rule_->EWords() * value_);
-}
-
-SourceWordPenalty::SourceWordPenalty(const string& param) :
-    fid_(FD::Convert("SourceWordPenalty")),
-    value_(-1.0 / log(10)) {
-  if (!param.empty()) {
-    cerr << "Warning SourceWordPenalty ignoring parameter: " << param << endl;
-  }
-}
-
-Features SourceWordPenalty::features() const {
-  return single_feature(fid_);
-}
-
-Features WordPenalty::features() const {
-  return single_feature(fid_);
-}
-
-
-void SourceWordPenalty::TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                        const Hypergraph::Edge& edge,
-                                        const std::vector<const void*>& ant_states,
-                                        SparseVector<double>* features,
-                                        SparseVector<double>* estimated_features,
-                                        void* state) const {
-  (void) smeta;
-  (void) ant_states;
-  (void) state;
-  (void) estimated_features;
-  features->set_value(fid_, edge.rule_->FWords() * value_);
-}
-
-ArityPenalty::ArityPenalty(const std::string& param) :
-    value_(-1.0 / log(10)) {
-  string fname = "Arity_";
-  unsigned MAX=DEFAULT_MAX_ARITY;
-  using namespace boost;
-  if (!param.empty())
-    MAX=lexical_cast<unsigned>(param);
-  for (unsigned i = 0; i <= MAX; ++i) {
-    WordID fid=FD::Convert(fname+lexical_cast<string>(i));
-    fids_.push_back(fid);
-  }
-  while (!fids_.empty() && fids_.back()==0) fids_.pop_back(); // pretty up features vector in case FD was frozen.  doesn't change anything
-}
-
-Features ArityPenalty::features() const {
-  return Features(fids_.begin(),fids_.end());
-}
-
-void ArityPenalty::TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                         const Hypergraph::Edge& edge,
-                                         const std::vector<const void*>& ant_states,
-                                         SparseVector<double>* features,
-                                         SparseVector<double>* estimated_features,
-                                         void* state) const {
-  (void) smeta;
-  (void) ant_states;
-  (void) state;
-  (void) estimated_features;
-  unsigned a=edge.Arity();
-  features->set_value(a<fids_.size()?fids_[a]:0, value_);
-}
-
-ModelSet::ModelSet(const vector<double>& w, const vector<const FeatureFunction*>& models) :
-    models_(models),
-    weights_(w),
-    state_size_(0),
-    model_state_pos_(models.size()) {
-  for (int i = 0; i < models_.size(); ++i) {
-    model_state_pos_[i] = state_size_;
-    state_size_ += models_[i]->NumBytesContext();
-  }
-}
-
-void ModelSet::PrepareForInput(const SentenceMetadata& smeta) {
-  for (int i = 0; i < models_.size(); ++i)
-    const_cast<FeatureFunction*>(models_[i])->PrepareForInput(smeta);
-}
-
-void ModelSet::AddFeaturesToEdge(const SentenceMetadata& smeta,
-                                 const Hypergraph& /* hg */,
-                                 const FFStates& node_states,
-                                 Hypergraph::Edge* edge,
-                                 FFState* context,
-                                 prob_t* combination_cost_estimate) const {
-  edge->reset_info();
-  context->resize(state_size_);
-  if (state_size_ > 0) {
-    memset(&(*context)[0], 0, state_size_);
-  }
-  SparseVector<double> est_vals;  // only computed if combination_cost_estimate is non-NULL
-  if (combination_cost_estimate) *combination_cost_estimate = prob_t::One();
-  for (int i = 0; i < models_.size(); ++i) {
-    const FeatureFunction& ff = *models_[i];
-    void* cur_ff_context = NULL;
-    vector<const void*> ants(edge->tail_nodes_.size());
-    bool has_context = ff.NumBytesContext() > 0;
-    if (has_context) {
-      int spos = model_state_pos_[i];
-      cur_ff_context = &(*context)[spos];
-      for (int i = 0; i < ants.size(); ++i) {
-        ants[i] = &node_states[edge->tail_nodes_[i]][spos];
-      }
-    }
-    ff.TraversalFeatures(smeta, *edge, ants, &edge->feature_values_, &est_vals, cur_ff_context);
-  }
-  if (combination_cost_estimate)
-    combination_cost_estimate->logeq(est_vals.dot(weights_));
-  edge->edge_prob_.logeq(edge->feature_values_.dot(weights_));
-}
-
-void ModelSet::AddFinalFeatures(const FFState& state, Hypergraph::Edge* edge,SentenceMetadata const& smeta) const {
-  assert(1 == edge->rule_->Arity());
-  edge->reset_info();
-  for (int i = 0; i < models_.size(); ++i) {
-    const FeatureFunction& ff = *models_[i];
-    const void* ant_state = NULL;
-    bool has_context = ff.NumBytesContext() > 0;
-    if (has_context) {
-      int spos = model_state_pos_[i];
-      ant_state = &state[spos];
-    }
-    ff.FinalTraversalFeatures(smeta, *edge, ant_state, &edge->feature_values_);
-  }
-  edge->edge_prob_.logeq(edge->feature_values_.dot(weights_));
-}
-
diff --git a/decoder/ff.h b/decoder/ff.h
index 6c22d39f..3280592e 100644
--- a/decoder/ff.h
+++ b/decoder/ff.h
@@ -1,79 +1,47 @@
 #ifndef _FF_H_
 #define _FF_H_
 
-#define DEBUG_INIT 0
-#if DEBUG_INIT
-# include <iostream>
-# define DBGINIT(a) do { std::cerr<<a<<"\n"; } while(0)
-#else
-# define DBGINIT(a)
-#endif
-
-#include <stdint.h>
+#include <string>
 #include <vector>
-#include <cstring>
-#include "fdict.h"
-#include "hg.h"
-#include "feature_vector.h"
-#include "value_array.h"
+#include "sparse_vector.h"
 
+namespace HG { struct Edge; struct Node; }
+class Hypergraph;
 class SentenceMetadata;
-class FeatureFunction;  // see definition below
-
-typedef std::vector<WordID> Features; // set of features ids
 
 // if you want to develop a new feature, inherit from this class and
 // override TraversalFeaturesImpl(...).  If it's a feature that returns /
 // depends on context, you may also need to implement
 // FinalTraversalFeatures(...)
 class FeatureFunction {
+  friend class ExternalFeature;
  public:
   std::string name_; // set by FF factory using usage()
-  bool debug_; // also set by FF factory checking param for immediate initial "debug"
-  //called after constructor, but before name_ and debug_ have been set
-  virtual void Init() { DBGINIT("default FF::Init name="<<name_); }
-  virtual void init_name_debug(std::string const& n,bool debug) {
-    name_=n;
-    debug_=debug;
-  }
-  bool debug() const { return debug_; }
   FeatureFunction() : state_size_() {}
   explicit FeatureFunction(int state_size) : state_size_(state_size) {}
   virtual ~FeatureFunction();
   bool IsStateful() const { return state_size_ > 0; }
+  int StateSize() const { return state_size_; }
 
   // override this.  not virtual because we want to expose this to factory template for help before creating a FF
   static std::string usage(bool show_params,bool show_details) {
     return usage_helper("FIXME_feature_needs_name","[no parameters]","[no documentation yet]",show_params,show_details);
   }
   static std::string usage_helper(std::string const& name,std::string const& params,std::string const& details,bool show_params,bool show_details);
-  static Features single_feature(int feat);
-public:
-
-  // stateless feature that doesn't depend on source span: override and return true.  then your feature can be precomputed over rules.
-  virtual bool rule_feature() const { return false; }
 
   // called once, per input, before any feature calls to TraversalFeatures, etc.
   // used to initialize sentence-specific data structures
   virtual void PrepareForInput(const SentenceMetadata& smeta);
 
-  //OVERRIDE THIS:
-  virtual Features features() const { return single_feature(FD::Convert(name_)); }
-  // returns the number of bytes of context that this feature function will
-  // (maximally) use.  By default, 0 ("stateless" models in Hiero/Joshua).
-  // NOTE: this value is fixed for the instance of your class, you cannot
-  // use different amounts of memory for different nodes in the forest.  this will be read as soon as you create a ModelSet, then fixed forever on
-  inline int NumBytesContext() const { return state_size_; }
-
   // Compute the feature values and (if this applies) the estimates of the
   // feature values when this edge is used incorporated into a larger context
   inline void TraversalFeatures(const SentenceMetadata& smeta,
-                                Hypergraph::Edge& edge,
+                                const HG::Edge& edge,
                                 const std::vector<const void*>& ant_contexts,
-                                FeatureVector* features,
-                                FeatureVector* estimated_features,
+                                SparseVector<double>* features,
+                                SparseVector<double>* estimated_features,
                                 void* out_state) const {
-    TraversalFeaturesLog(smeta, edge, ant_contexts,
+    TraversalFeaturesImpl(smeta, edge, ant_contexts,
                           features, estimated_features, out_state);
     // TODO it's easy for careless feature function developers to overwrite
     // the end of their state and clobber someone else's memory.  These bugs
@@ -83,21 +51,10 @@ public:
   }
 
   // if there's some state left when you transition to the goal state, score
-  // it here.  For example, the language model computes the cost of adding
+  // it here.  For example, a language model might the cost of adding
   // <s> and </s>.
-
-protected:
   virtual void FinalTraversalFeatures(const void* residual_state,
-                                      FeatureVector* final_features) const;
-public:
-  //override either this or one of above.
-  virtual void FinalTraversalFeatures(const SentenceMetadata& /* smeta */,
-                                      Hypergraph::Edge& /* edge */, // so you can log()
-                                      const void* residual_state,
-                                      FeatureVector* final_features) const {
-    FinalTraversalFeatures(residual_state,final_features);
-  }
-
+                                      SparseVector<double>* final_features) const;
 
  protected:
   // context is a pointer to a buffer of size NumBytesContext() that the
@@ -107,191 +64,19 @@ public:
   // of the particular FeatureFunction class.  There is one exception:
   // equality of the contents (i.e., memcmp) is required to determine whether
   // two states can be combined.
-
-  // by Log, I mean that the edge is non-const only so you can log to it with INFO_EDGE(edge,msg<<"etc.").  most features don't use this so implement the below.  it has a different name to allow a default implementation without name hiding when inheriting + overriding just 1.
-  virtual void TraversalFeaturesLog(const SentenceMetadata& smeta,
-                                    Hypergraph::Edge& edge, // this is writable only so you can use log()
-                                     const std::vector<const void*>& ant_contexts,
-                                     FeatureVector* features,
-                                     FeatureVector* estimated_features,
-                                     void* context) const {
-    TraversalFeaturesImpl(smeta,edge,ant_contexts,features,estimated_features,context);
-  }
-
-  // override above or below.
   virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     Hypergraph::Edge const& edge,
+                                     const HG::Edge& edge,
                                      const std::vector<const void*>& ant_contexts,
-                                     FeatureVector* features,
-                                     FeatureVector* estimated_features,
+                                     SparseVector<double>* features,
+                                     SparseVector<double>* estimated_features,
                                      void* context) const;
 
   // !!! ONLY call this from subclass *CONSTRUCTORS* !!!
   void SetStateSize(size_t state_size) {
     state_size_ = state_size;
   }
-  int StateSize() const { return state_size_; }
- private:
-  int state_size_;
-};
-
-
-// word penalty feature, for each word on the E side of a rule,
-// add value_
-class WordPenalty : public FeatureFunction {
- public:
-  Features features() const;
-  WordPenalty(const std::string& param);
-  static std::string usage(bool p,bool d) {
-    return usage_helper("WordPenalty","","number of target words (local feature)",p,d);
-  }
-  bool rule_feature() const { return true; }
- protected:
-  virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
-                                     const std::vector<const void*>& ant_contexts,
-                                     FeatureVector* features,
-                                     FeatureVector* estimated_features,
-                                     void* context) const;
- private:
-  const int fid_;
-  const double value_;
-};
-
-class SourceWordPenalty : public FeatureFunction {
- public:
-  bool rule_feature() const { return true; }
-  Features features() const;
-  SourceWordPenalty(const std::string& param);
-  static std::string usage(bool p,bool d) {
-    return usage_helper("SourceWordPenalty","","number of source words (local feature, and meaningless except when input has non-constant number of source words, e.g. segmentation/morphology/speech recognition lattice)",p,d);
-  }
- protected:
-  virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
-                                     const std::vector<const void*>& ant_contexts,
-                                     FeatureVector* features,
-                                     FeatureVector* estimated_features,
-                                     void* context) const;
- private:
-  const int fid_;
-  const double value_;
-};
-
-#define DEFAULT_MAX_ARITY 9
-#define DEFAULT_MAX_ARITY_STRINGIZE(x) #x
-#define DEFAULT_MAX_ARITY_STRINGIZE_EVAL(x) DEFAULT_MAX_ARITY_STRINGIZE(x)
-#define DEFAULT_MAX_ARITY_STR DEFAULT_MAX_ARITY_STRINGIZE_EVAL(DEFAULT_MAX_ARITY)
-
-class ArityPenalty : public FeatureFunction {
- public:
-  bool rule_feature() const { return true; }
-  Features features() const;
-  ArityPenalty(const std::string& param);
-  static std::string usage(bool p,bool d) {
-    return usage_helper("ArityPenalty","[MaxArity(default " DEFAULT_MAX_ARITY_STR ")]","Indicator feature Arity_N=1 for rule of arity N (local feature).  0<=N<=MaxArity(default " DEFAULT_MAX_ARITY_STR ")",p,d);
-  }
-
- protected:
-  virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
-                                     const std::vector<const void*>& ant_contexts,
-                                     FeatureVector* features,
-                                     FeatureVector* estimated_features,
-                                     void* context) const;
- private:
-  std::vector<WordID> fids_;
-  const double value_;
-};
-
-void show_features(Features const& features,DenseWeightVector const& weights,std::ostream &out,std::ostream &warn,bool warn_zero_wt=true); //show features and weights
-
-template <class FFp>
-Features all_features(std::vector<FFp> const& models_,DenseWeightVector &weights_,std::ostream *warn=0,bool warn_fid_0=false) {
-  using namespace std;
-  Features ffs;
-#define WARNFF(x) do { if (warn) { *warn << "WARNING: "<< x << endl; } } while(0)
-  typedef map<WordID,string> FFM;
-  FFM ff_from;
-  for (unsigned i=0;i<models_.size();++i) {
-    string const& ffname=models_[i]->name_;
-    Features si=models_[i]->features();
-    if (si.empty()) {
-      WARNFF(ffname<<" doesn't yet report any feature IDs - either supply feature weight, or use --no_freeze_feature_set, or implement features() method");
-    }
-    unsigned n0=0;
-    for (unsigned j=0;j<si.size();++j) {
-      WordID fid=si[j];
-      if (!fid) ++n0;
-      if (fid >= weights_.size())
-        weights_.resize(fid+1);
-      if (warn_fid_0 || fid) {
-        pair<FFM::iterator,bool> i_new=ff_from.insert(FFM::value_type(fid,ffname));
-        if (i_new.second) {
-          if (fid)
-            ffs.push_back(fid);
-          else
-            WARNFF("Feature id 0 for "<<ffname<<" (models["<<i<<"]) - probably no weight provided.  Don't freeze feature ids to see the name");
-        } else {
-          WARNFF(ffname<<" (models["<<i<<"]) tried to define feature "<<FD::Convert(fid)<<" already defined earlier by "<<i_new.first->second);
-        }
-      }
-    }
-    if (n0)
-      WARNFF(ffname<<" (models["<<i<<"]) had "<<n0<<" unused features (--no_freeze_feature_set to see them)");
-  }
-  return ffs;
-#undef WARNFF
-}
-
-template <class FFp>
-void show_all_features(std::vector<FFp> const& models_,DenseWeightVector &weights_,std::ostream &out,std::ostream &warn,bool warn_fid_0=true,bool warn_zero_wt=true) {
-  return show_features(all_features(models_,weights_,&warn,warn_fid_0),weights_,out,warn,warn_zero_wt);
-}
-
-typedef ValueArray<uint8_t> FFState; // this is about 10% faster than string.
-//typedef std::string FFState;
-
-//FIXME: only context.data() is required to be contiguous, and it becomes invalid after next string operation.  use ValueArray instead? (higher performance perhaps, save a word due to fixed size)
-typedef std::vector<FFState> FFStates;
-
-// this class is a set of FeatureFunctions that can be used to score, rescore,
-// etc. a (translation?) forest
-class ModelSet {
- public:
-  ModelSet(const std::vector<double>& weights,
-           const std::vector<const FeatureFunction*>& models);
-
-  // sets edge->feature_values_ and edge->edge_prob_
-  // NOTE: edge must not necessarily be in hg.edges_ but its TAIL nodes
-  // must be.  edge features are supposed to be overwritten, not added to (possibly because rule features aren't in ModelSet so need to be left alone
-  void AddFeaturesToEdge(const SentenceMetadata& smeta,
-                         const Hypergraph& hg,
-                         const FFStates& node_states,
-                         Hypergraph::Edge* edge,
-                         FFState* residual_context,
-                         prob_t* combination_cost_estimate = NULL) const;
-
-  //this is called INSTEAD of above when result of edge is goal (must be a unary rule - i.e. one variable, but typically it's assumed that there are no target terminals either (e.g. for LM))
-  void AddFinalFeatures(const FFState& residual_context,
-                        Hypergraph::Edge* edge,
-                        SentenceMetadata const& smeta) const;
-
-  // this is called once before any feature functions apply to a hypergraph
-  // it can be used to initialize sentence-specific data structures
-  void PrepareForInput(const SentenceMetadata& smeta);
-
-  bool empty() const { return models_.empty(); }
-
-  bool stateless() const { return !state_size_; }
-  Features all_features(std::ostream *warnings=0,bool warn_fid_zero=false); // this will warn about duplicate features as well (one function overwrites the feature of another).  also resizes weights_ so it is large enough to hold the (0) weight for the largest reported feature id.  since 0 is a NULL feature id, it's never included.  if warn_fid_zero, then even the first 0 id is
-  void show_features(std::ostream &out,std::ostream &warn,bool warn_zero_wt=true);
-
  private:
-  std::vector<const FeatureFunction*> models_;
-  const std::vector<double>& weights_;
   int state_size_;
-  std::vector<int> model_state_pos_;
 };
 
 #endif
diff --git a/decoder/ff_basic.cc b/decoder/ff_basic.cc
new file mode 100644
index 00000000..f9404d24
--- /dev/null
+++ b/decoder/ff_basic.cc
@@ -0,0 +1,80 @@
+#include "ff_basic.h"
+
+#include "fast_lexical_cast.hpp"
+#include "hg.h"
+
+using namespace std;
+
+// Hiero and Joshua use log_10(e) as the value, so I do to
+WordPenalty::WordPenalty(const string& param) :
+  fid_(FD::Convert("WordPenalty")),
+    value_(-1.0 / log(10)) {
+  if (!param.empty()) {
+    cerr << "Warning WordPenalty ignoring parameter: " << param << endl;
+  }
+}
+
+void WordPenalty::TraversalFeaturesImpl(const SentenceMetadata& smeta,
+                                        const Hypergraph::Edge& edge,
+                                        const std::vector<const void*>& ant_states,
+                                        SparseVector<double>* features,
+                                        SparseVector<double>* estimated_features,
+                                        void* state) const {
+  (void) smeta;
+  (void) ant_states;
+  (void) state;
+  (void) estimated_features;
+  features->set_value(fid_, edge.rule_->EWords() * value_);
+}
+
+
+SourceWordPenalty::SourceWordPenalty(const string& param) :
+    fid_(FD::Convert("SourceWordPenalty")),
+    value_(-1.0 / log(10)) {
+  if (!param.empty()) {
+    cerr << "Warning SourceWordPenalty ignoring parameter: " << param << endl;
+  }
+}
+
+void SourceWordPenalty::TraversalFeaturesImpl(const SentenceMetadata& smeta,
+                                        const Hypergraph::Edge& edge,
+                                        const std::vector<const void*>& ant_states,
+                                        SparseVector<double>* features,
+                                        SparseVector<double>* estimated_features,
+                                        void* state) const {
+  (void) smeta;
+  (void) ant_states;
+  (void) state;
+  (void) estimated_features;
+  features->set_value(fid_, edge.rule_->FWords() * value_);
+}
+
+
+ArityPenalty::ArityPenalty(const std::string& param) :
+    value_(-1.0 / log(10)) {
+  string fname = "Arity_";
+  unsigned MAX=DEFAULT_MAX_ARITY;
+  using namespace boost;
+  if (!param.empty())
+    MAX=lexical_cast<unsigned>(param);
+  for (unsigned i = 0; i <= MAX; ++i) {
+    WordID fid=FD::Convert(fname+lexical_cast<string>(i));
+    fids_.push_back(fid);
+  }
+  while (!fids_.empty() && fids_.back()==0) fids_.pop_back(); // pretty up features vector in case FD was frozen.  doesn't change anything
+}
+
+void ArityPenalty::TraversalFeaturesImpl(const SentenceMetadata& smeta,
+                                         const Hypergraph::Edge& edge,
+                                         const std::vector<const void*>& ant_states,
+                                         SparseVector<double>* features,
+                                         SparseVector<double>* estimated_features,
+                                         void* state) const {
+  (void) smeta;
+  (void) ant_states;
+  (void) state;
+  (void) estimated_features;
+  unsigned a=edge.Arity();
+  features->set_value(a<fids_.size()?fids_[a]:0, value_);
+}
+
diff --git a/decoder/ff_basic.h b/decoder/ff_basic.h
new file mode 100644
index 00000000..901c0110
--- /dev/null
+++ b/decoder/ff_basic.h
@@ -0,0 +1,68 @@
+#ifndef _FF_BASIC_H_
+#define _FF_BASIC_H_
+
+#include "ff.h"
+
+// word penalty feature, for each word on the E side of a rule,
+// add value_
+class WordPenalty : public FeatureFunction {
+ public:
+  WordPenalty(const std::string& param);
+  static std::string usage(bool p,bool d) {
+    return usage_helper("WordPenalty","","number of target words (local feature)",p,d);
+  }
+ protected:
+  virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
+                                     const HG::Edge& edge,
+                                     const std::vector<const void*>& ant_contexts,
+                                     SparseVector<double>* features,
+                                     SparseVector<double>* estimated_features,
+                                     void* context) const;
+ private:
+  const int fid_;
+  const double value_;
+};
+
+class SourceWordPenalty : public FeatureFunction {
+ public:
+  SourceWordPenalty(const std::string& param);
+  static std::string usage(bool p,bool d) {
+    return usage_helper("SourceWordPenalty","","number of source words (local feature, and meaningless except when input has non-constant number of source words, e.g. segmentation/morphology/speech recognition lattice)",p,d);
+  }
+ protected:
+  virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
+                                     const HG::Edge& edge,
+                                     const std::vector<const void*>& ant_contexts,
+                                     SparseVector<double>* features,
+                                     SparseVector<double>* estimated_features,
+                                     void* context) const;
+ private:
+  const int fid_;
+  const double value_;
+};
+
+#define DEFAULT_MAX_ARITY 9
+#define DEFAULT_MAX_ARITY_STRINGIZE(x) #x
+#define DEFAULT_MAX_ARITY_STRINGIZE_EVAL(x) DEFAULT_MAX_ARITY_STRINGIZE(x)
+#define DEFAULT_MAX_ARITY_STR DEFAULT_MAX_ARITY_STRINGIZE_EVAL(DEFAULT_MAX_ARITY)
+
+class ArityPenalty : public FeatureFunction {
+ public:
+  ArityPenalty(const std::string& param);
+  static std::string usage(bool p,bool d) {
+    return usage_helper("ArityPenalty","[MaxArity(default " DEFAULT_MAX_ARITY_STR ")]","Indicator feature Arity_N=1 for rule of arity N (local feature).  0<=N<=MaxArity(default " DEFAULT_MAX_ARITY_STR ")",p,d);
+  }
+
+ protected:
+  virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
+                                     const HG::Edge& edge,
+                                     const std::vector<const void*>& ant_contexts,
+                                     SparseVector<double>* features,
+                                     SparseVector<double>* estimated_features,
+                                     void* context) const;
+ private:
+  std::vector<WordID> fids_;
+  const double value_;
+};
+
+#endif
diff --git a/decoder/ff_bleu.h b/decoder/ff_bleu.h
index 5544920e..344dc788 100644
--- a/decoder/ff_bleu.h
+++ b/decoder/ff_bleu.h
@@ -20,7 +20,7 @@ class BLEUModel : public FeatureFunction {
   static std::string usage(bool param,bool verbose);
  protected:
   virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
+                                     const HG::Edge& edge,
                                      const std::vector<const void*>& ant_contexts,
                                      SparseVector<double>* features,
                                      SparseVector<double>* estimated_features,
diff --git a/decoder/ff_charset.cc b/decoder/ff_charset.cc
index 33afc1a7..6429088b 100644
--- a/decoder/ff_charset.cc
+++ b/decoder/ff_charset.cc
@@ -1,5 +1,7 @@
 #include "ff_charset.h"
 
+#include "tdict.h"
+#include "hg.h"
 #include "fdict.h"
 #include "stringlib.h"
 
@@ -7,9 +9,9 @@ using namespace std;
 
 NonLatinCount::NonLatinCount(const string& param) : FeatureFunction(), fid_(FD::Convert("NonLatinCount")) {}
 
-bool ContainsNonLatin(const char* word) {
-  int cur = 0;
-  while(word[cur]) {
+bool ContainsNonLatin(const string& word) {
+  unsigned cur = 0;
+  while(cur < word.size()) {
     const int size = UTF8Len(word[cur]);
     if (size > 1) return true;
     cur += size;  
@@ -20,8 +22,8 @@ bool ContainsNonLatin(const char* word) {
 void NonLatinCount::TraversalFeaturesImpl(const SentenceMetadata& smeta,
                                           const Hypergraph::Edge& edge,
                                           const std::vector<const void*>& ant_contexts,
-                                          FeatureVector* features,
-                                          FeatureVector* estimated_features,
+                                          SparseVector<double>* features,
+                                          SparseVector<double>* estimated_features,
                                           void* context) const {
   const vector<WordID>& e = edge.rule_->e();
   int count = 0;
diff --git a/decoder/ff_charset.h b/decoder/ff_charset.h
index b1ad537e..267ef65d 100644
--- a/decoder/ff_charset.h
+++ b/decoder/ff_charset.h
@@ -13,10 +13,10 @@ class NonLatinCount : public FeatureFunction {
   NonLatinCount(const std::string& param);
  protected:
   virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
+                                     const HG::Edge& edge,
                                      const std::vector<const void*>& ant_contexts,
-                                     FeatureVector* features,
-                                     FeatureVector* estimated_features,
+                                     SparseVector<double>* features,
+                                     SparseVector<double>* estimated_features,
                                      void* context) const;
  private:
   mutable std::map<WordID, bool> is_non_latin_;
diff --git a/decoder/ff_context.cc b/decoder/ff_context.cc
index 9de4d737..f2b0e67c 100644
--- a/decoder/ff_context.cc
+++ b/decoder/ff_context.cc
@@ -5,12 +5,14 @@
 #include <cassert>
 #include <cmath>
 
+#include "hg.h"
 #include "filelib.h"
 #include "stringlib.h"
 #include "sentence_metadata.h"
 #include "lattice.h"
 #include "fdict.h"
 #include "verbose.h"
+#include "tdict.h"
 
 RuleContextFeatures::RuleContextFeatures(const string& param) {
   //  cerr << "initializing RuleContextFeatures with parameters: " << param;
diff --git a/decoder/ff_context.h b/decoder/ff_context.h
index 89bcb557..19198ec3 100644
--- a/decoder/ff_context.h
+++ b/decoder/ff_context.h
@@ -14,7 +14,7 @@ class RuleContextFeatures : public FeatureFunction {
   RuleContextFeatures(const string& param);
  protected:
   virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
+                                     const HG::Edge& edge,
                                      const vector<const void*>& ant_contexts,
                                      SparseVector<double>* features,
                                      SparseVector<double>* estimated_features,
diff --git a/decoder/ff_csplit.cc b/decoder/ff_csplit.cc
index c9ed996c..e6f78f84 100644
--- a/decoder/ff_csplit.cc
+++ b/decoder/ff_csplit.cc
@@ -5,6 +5,7 @@
 
 #include "klm/lm/model.hh"
 
+#include "hg.h"
 #include "sentence_metadata.h"
 #include "lattice.h"
 #include "tdict.h"
@@ -88,7 +89,7 @@ void BasicCSplitFeaturesImpl::TraversalFeaturesImpl(
   features->set_value(letters_sq_, (edge.j_ - edge.i_) * (edge.j_ - edge.i_));
   features->set_value(letters_sqrt_, sqrt(edge.j_ - edge.i_));
   const WordID word = edge.rule_->e_[1];
-  const char* sword = TD::Convert(word);
+  const char* sword = TD::Convert(word).c_str();
   const int len = strlen(sword);
   int cur = 0;
   int chars = 0;
diff --git a/decoder/ff_csplit.h b/decoder/ff_csplit.h
index 38c0c5b8..64d42526 100644
--- a/decoder/ff_csplit.h
+++ b/decoder/ff_csplit.h
@@ -12,7 +12,7 @@ class BasicCSplitFeatures : public FeatureFunction {
   BasicCSplitFeatures(const std::string& param);
  protected:
   virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
+                                     const HG::Edge& edge,
                                      const std::vector<const void*>& ant_contexts,
                                      SparseVector<double>* features,
                                      SparseVector<double>* estimated_features,
@@ -27,7 +27,7 @@ class ReverseCharLMCSplitFeature : public FeatureFunction {
   ReverseCharLMCSplitFeature(const std::string& param);
  protected:
   virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
+                                     const HG::Edge& edge,
                                      const std::vector<const void*>& ant_contexts,
                                      SparseVector<double>* features,
                                      SparseVector<double>* estimated_features,
diff --git a/decoder/ff_dwarf.cc b/decoder/ff_dwarf.cc
index 43528405..fe7a472e 100644
--- a/decoder/ff_dwarf.cc
+++ b/decoder/ff_dwarf.cc
@@ -4,6 +4,7 @@
 #include <string>
 #include <iostream>
 #include <map>
+#include "hg.h"
 #include "ff_dwarf.h"
 #include "dwarf.h"
 #include "wordid.h"
diff --git a/decoder/ff_dwarf.h b/decoder/ff_dwarf.h
index 083fcc7c..3d6a7da6 100644
--- a/decoder/ff_dwarf.h
+++ b/decoder/ff_dwarf.h
@@ -56,7 +56,7 @@ class Dwarf : public FeatureFunction {
         function word alignments set by 3.
   */ 
   void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
+                                     const HG::Edge& edge,
                                      const std::vector<const void*>& ant_contexts,
                                      SparseVector<double>* features,
                                      SparseVector<double>* estimated_features,
diff --git a/decoder/ff_external.cc b/decoder/ff_external.cc
new file mode 100644
index 00000000..dea0e20f
--- /dev/null
+++ b/decoder/ff_external.cc
@@ -0,0 +1,60 @@
+#include "ff_external.h"
+
+#include <dlfcn.h>
+
+#include "stringlib.h"
+#include "hg.h"
+
+using namespace std;
+
+ExternalFeature::ExternalFeature(const string& param) {
+  size_t pos = param.find(' ');
+  string nparam;
+  string file = param;
+  if (pos < param.size()) {
+    nparam = Trim(param.substr(pos + 1));
+    file = param.substr(0, pos);
+  }
+  if (file.size() < 1) {
+    cerr << "External requires a path to a dynamic library!\n";
+    abort();
+  }
+  lib_handle = dlopen(file.c_str(), RTLD_LAZY);
+  if (!lib_handle) {
+    cerr << "dlopen reports: " << dlerror() << endl;
+    cerr << "Did you provide a full path to the dynamic library?\n";
+    abort();
+  }
+  FeatureFunction* (*fn)(const string&) =
+    (FeatureFunction* (*)(const string&))(dlsym(lib_handle, "create_ff"));
+  if (!fn) {
+    cerr << "dlsym reports: " << dlerror() << endl;
+    abort();
+  }
+  ff_ext = (*fn)(nparam);
+  SetStateSize(ff_ext->StateSize());
+}
+
+ExternalFeature::~ExternalFeature() {
+  delete ff_ext;
+  dlclose(lib_handle);
+}
+
+void ExternalFeature::PrepareForInput(const SentenceMetadata& smeta) {
+  ff_ext->PrepareForInput(smeta);
+}
+
+void ExternalFeature::FinalTraversalFeatures(const void* context,
+                                             SparseVector<double>* features) const {
+  ff_ext->FinalTraversalFeatures(context, features);
+}
+
+void ExternalFeature::TraversalFeaturesImpl(const SentenceMetadata& smeta,
+                                     const Hypergraph::Edge& edge,
+                                     const std::vector<const void*>& ant_contexts,
+                                     SparseVector<double>* features,
+                                     SparseVector<double>* estimated_features,
+                                     void* context) const {
+  ff_ext->TraversalFeaturesImpl(smeta, edge, ant_contexts, features, estimated_features, context);
+}
+
diff --git a/decoder/ff_external.h b/decoder/ff_external.h
new file mode 100644
index 00000000..3e2bee51
--- /dev/null
+++ b/decoder/ff_external.h
@@ -0,0 +1,26 @@
+#ifndef _FFEXTERNAL_H_
+#define _FFEXTERNAL_H_
+
+#include "ff.h"
+
+// dynamically loaded feature function
+class ExternalFeature : public FeatureFunction {
+ public:
+  ExternalFeature(const std::string& param);
+  ~ExternalFeature();
+  virtual void PrepareForInput(const SentenceMetadata& smeta);
+  virtual void FinalTraversalFeatures(const void* context,
+                                      SparseVector<double>* features) const;
+ protected:
+  virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
+                                     const HG::Edge& edge,
+                                     const std::vector<const void*>& ant_contexts,
+                                     SparseVector<double>* features,
+                                     SparseVector<double>* estimated_features,
+                                     void* context) const;
+ private:
+  void* lib_handle;
+  FeatureFunction* ff_ext;
+};
+
+#endif
diff --git a/decoder/ff_factory.h b/decoder/ff_factory.h
index 5eb68c8b..bfdd3257 100644
--- a/decoder/ff_factory.h
+++ b/decoder/ff_factory.h
@@ -43,7 +43,6 @@ template<class FF>
 struct FFFactory : public FactoryBase<FeatureFunction> {
   FP Create(std::string param) const {
     FF *ret=new FF(param);
-    ret->Init();
     return FP(ret);
   }
   virtual std::string usage(bool params,bool verbose) const {
@@ -57,7 +56,6 @@ template<class FF>
 struct FsaFactory : public FactoryBase<FsaFeatureFunction> {
   FP Create(std::string param) const {
     FF *ret=new FF(param);
-    ret->Init();
     return FP(ret);
   }
   virtual std::string usage(bool params,bool verbose) const {
@@ -98,8 +96,6 @@ struct FactoryRegistry : public UntypedFactoryRegistry {
     if (debug)
       cerr<<"debug enabled for "<<ffname<< " - remaining options: '"<<param<<"'\n";
     FP res = dynamic_cast<FB const&>(*it->second).Create(param);
-    res->init_name_debug(ffname,debug);
-    // could add a res->Init() here instead of in Create if we wanted feature id to potentially differ based on the registered name rather than static usage() - of course, specific feature ids can be computed on the basis of feature param as well; this only affects the default single feature id=name
     return res;
   }
 };
diff --git a/decoder/ff_klm.cc b/decoder/ff_klm.cc
index 09ef282c..fefa90bd 100644
--- a/decoder/ff_klm.cc
+++ b/decoder/ff_klm.cc
@@ -327,11 +327,6 @@ KLanguageModel<Model>::KLanguageModel(const string& param) {
 }
 
 template <class Model>
-Features KLanguageModel<Model>::features() const {
-  return single_feature(fid_);
-}
-
-template <class Model>
 KLanguageModel<Model>::~KLanguageModel() {
   delete pimpl_;
 }
@@ -362,7 +357,6 @@ void KLanguageModel<Model>::FinalTraversalFeatures(const void* ant_state,
 
 template <class Model> boost::shared_ptr<FeatureFunction> CreateModel(const std::string &param) {
   KLanguageModel<Model> *ret = new KLanguageModel<Model>(param);
-  ret->Init();
   return boost::shared_ptr<FeatureFunction>(ret);
 }
 
diff --git a/decoder/ff_klm.h b/decoder/ff_klm.h
index 6efe50f6..b5ceffd0 100644
--- a/decoder/ff_klm.h
+++ b/decoder/ff_klm.h
@@ -20,10 +20,9 @@ class KLanguageModel : public FeatureFunction {
   virtual void FinalTraversalFeatures(const void* context,
                                       SparseVector<double>* features) const;
   static std::string usage(bool param,bool verbose);
-  Features features() const;
  protected:
   virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
+                                     const HG::Edge& edge,
                                      const std::vector<const void*>& ant_contexts,
                                      SparseVector<double>* features,
                                      SparseVector<double>* estimated_features,
diff --git a/decoder/ff_lm.cc b/decoder/ff_lm.cc
index 5e16d4e3..6ec7b4f3 100644
--- a/decoder/ff_lm.cc
+++ b/decoder/ff_lm.cc
@@ -519,10 +519,6 @@ LanguageModel::LanguageModel(const string& param) {
   SetStateSize(LanguageModelImpl::OrderToStateSize(order));
 }
 
-Features LanguageModel::features() const {
-  return single_feature(fid_);
-}
-
 LanguageModel::~LanguageModel() {
   delete pimpl_;
 }
diff --git a/decoder/ff_lm.h b/decoder/ff_lm.h
index ccee4268..94e18f00 100644
--- a/decoder/ff_lm.h
+++ b/decoder/ff_lm.h
@@ -55,10 +55,9 @@ class LanguageModel : public FeatureFunction {
                                       SparseVector<double>* features) const;
   std::string DebugStateToString(const void* state) const;
   static std::string usage(bool param,bool verbose);
-  Features features() const;
  protected:
   virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
+                                     const HG::Edge& edge,
                                      const std::vector<const void*>& ant_contexts,
                                      SparseVector<double>* features,
                                      SparseVector<double>* estimated_features,
@@ -81,7 +80,7 @@ class LanguageModelRandLM : public FeatureFunction {
   std::string DebugStateToString(const void* state) const;
  protected:
   virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
+                                     const HG::Edge& edge,
                                      const std::vector<const void*>& ant_contexts,
                                      SparseVector<double>* features,
                                      SparseVector<double>* estimated_features,
diff --git a/decoder/ff_ngrams.h b/decoder/ff_ngrams.h
index 064dbb49..4965d235 100644
--- a/decoder/ff_ngrams.h
+++ b/decoder/ff_ngrams.h
@@ -17,7 +17,7 @@ class NgramDetector : public FeatureFunction {
                                       SparseVector<double>* features) const;
  protected:
   virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
+                                     const HG::Edge& edge,
                                      const std::vector<const void*>& ant_contexts,
                                      SparseVector<double>* features,
                                      SparseVector<double>* estimated_features,
diff --git a/decoder/ff_rules.cc b/decoder/ff_rules.cc
index 3d0e514a..6716d3da 100644
--- a/decoder/ff_rules.cc
+++ b/decoder/ff_rules.cc
@@ -10,6 +10,8 @@
 #include "lattice.h"
 #include "fdict.h"
 #include "verbose.h"
+#include "tdict.h"
+#include "hg.h"
 
 using namespace std;
 
diff --git a/decoder/ff_rules.h b/decoder/ff_rules.h
index 08b168b0..dc9a15d5 100644
--- a/decoder/ff_rules.h
+++ b/decoder/ff_rules.h
@@ -3,6 +3,7 @@
 
 #include <vector>
 #include <map>
+#include "trule.h"
 #include "ff.h"
 #include "array2d.h"
 #include "wordid.h"
@@ -12,7 +13,7 @@ class RuleIdentityFeatures : public FeatureFunction {
   RuleIdentityFeatures(const std::string& param);
  protected:
   virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
+                                     const HG::Edge& edge,
                                      const std::vector<const void*>& ant_contexts,
                                      SparseVector<double>* features,
                                      SparseVector<double>* estimated_features,
@@ -42,7 +43,7 @@ class RuleTargetBigramFeatures : public FeatureFunction {
   RuleTargetBigramFeatures(const std::string& param);
  protected:
   virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
+                                     const HG::Edge& edge,
                                      const std::vector<const void*>& ant_contexts,
                                      SparseVector<double>* features,
                                      SparseVector<double>* estimated_features,
diff --git a/decoder/ff_ruleshape.cc b/decoder/ff_ruleshape.cc
index f56ccfa9..7bb548c4 100644
--- a/decoder/ff_ruleshape.cc
+++ b/decoder/ff_ruleshape.cc
@@ -1,5 +1,7 @@
 #include "ff_ruleshape.h"
 
+#include "trule.h"
+#include "hg.h"
 #include "fdict.h"
 #include <sstream>
 
diff --git a/decoder/ff_ruleshape.h b/decoder/ff_ruleshape.h
index 23c9827e..9f20faf3 100644
--- a/decoder/ff_ruleshape.h
+++ b/decoder/ff_ruleshape.h
@@ -9,7 +9,7 @@ class RuleShapeFeatures : public FeatureFunction {
   RuleShapeFeatures(const std::string& param);
  protected:
   virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
+                                     const HG::Edge& edge,
                                      const std::vector<const void*>& ant_contexts,
                                      SparseVector<double>* features,
                                      SparseVector<double>* estimated_features,
diff --git a/decoder/ff_source_syntax.cc b/decoder/ff_source_syntax.cc
index 035132b4..a1997695 100644
--- a/decoder/ff_source_syntax.cc
+++ b/decoder/ff_source_syntax.cc
@@ -3,6 +3,7 @@
 #include <sstream>
 #include <stack>
 
+#include "hg.h"
 #include "sentence_metadata.h"
 #include "array2d.h"
 #include "filelib.h"
diff --git a/decoder/ff_source_syntax.h b/decoder/ff_source_syntax.h
index 279563e1..a8c7150a 100644
--- a/decoder/ff_source_syntax.h
+++ b/decoder/ff_source_syntax.h
@@ -11,7 +11,7 @@ class SourceSyntaxFeatures : public FeatureFunction {
   ~SourceSyntaxFeatures();
  protected:
   virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
+                                     const HG::Edge& edge,
                                      const std::vector<const void*>& ant_contexts,
                                      SparseVector<double>* features,
                                      SparseVector<double>* estimated_features,
@@ -28,7 +28,7 @@ class SourceSpanSizeFeatures : public FeatureFunction {
   ~SourceSpanSizeFeatures();
  protected:
   virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
+                                     const HG::Edge& edge,
                                      const std::vector<const void*>& ant_contexts,
                                      SparseVector<double>* features,
                                      SparseVector<double>* estimated_features,
diff --git a/decoder/ff_spans.cc b/decoder/ff_spans.cc
index 0483517b..0ccac69b 100644
--- a/decoder/ff_spans.cc
+++ b/decoder/ff_spans.cc
@@ -4,6 +4,8 @@
 #include <cassert>
 #include <cmath>
 
+#include "hg.h"
+#include "tdict.h"
 #include "filelib.h"
 #include "stringlib.h"
 #include "sentence_metadata.h"
diff --git a/decoder/ff_spans.h b/decoder/ff_spans.h
index 24e0dede..d2f5e84c 100644
--- a/decoder/ff_spans.h
+++ b/decoder/ff_spans.h
@@ -12,7 +12,7 @@ class SpanFeatures : public FeatureFunction {
   SpanFeatures(const std::string& param);
  protected:
   virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
+                                     const HG::Edge& edge,
                                      const std::vector<const void*>& ant_contexts,
                                      SparseVector<double>* features,
                                      SparseVector<double>* estimated_features,
@@ -49,7 +49,7 @@ class CMR2008ReorderingFeatures : public FeatureFunction {
   CMR2008ReorderingFeatures(const std::string& param);
  protected:
   virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
+                                     const HG::Edge& edge,
                                      const std::vector<const void*>& ant_contexts,
                                      SparseVector<double>* features,
                                      SparseVector<double>* estimated_features,
diff --git a/decoder/ff_tagger.cc b/decoder/ff_tagger.cc
index fd9210fa..7f9af9cd 100644
--- a/decoder/ff_tagger.cc
+++ b/decoder/ff_tagger.cc
@@ -2,6 +2,7 @@
 
 #include <sstream>
 
+#include "hg.h"
 #include "tdict.h"
 #include "sentence_metadata.h"
 #include "stringlib.h"
diff --git a/decoder/ff_tagger.h b/decoder/ff_tagger.h
index bd5b62c0..46418b0c 100644
--- a/decoder/ff_tagger.h
+++ b/decoder/ff_tagger.h
@@ -18,7 +18,7 @@ class Tagger_BigramIndicator : public FeatureFunction {
   Tagger_BigramIndicator(const std::string& param);
  protected:
   virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
+                                     const HG::Edge& edge,
                                      const std::vector<const void*>& ant_contexts,
                                      SparseVector<double>* features,
                                      SparseVector<double>* estimated_features,
@@ -39,7 +39,7 @@ class LexicalPairIndicator : public FeatureFunction {
   virtual void PrepareForInput(const SentenceMetadata& smeta);
  protected:
   virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
+                                     const HG::Edge& edge,
                                      const std::vector<const void*>& ant_contexts,
                                      SparseVector<double>* features,
                                      SparseVector<double>* estimated_features,
@@ -59,7 +59,7 @@ class OutputIndicator : public FeatureFunction {
   OutputIndicator(const std::string& param);
  protected:
   virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
+                                     const HG::Edge& edge,
                                      const std::vector<const void*>& ant_contexts,
                                      SparseVector<double>* features,
                                      SparseVector<double>* estimated_features,
diff --git a/decoder/ff_wordalign.cc b/decoder/ff_wordalign.cc
index decdf9bc..1491819d 100644
--- a/decoder/ff_wordalign.cc
+++ b/decoder/ff_wordalign.cc
@@ -549,7 +549,7 @@ void IdentityCycleDetector::TraversalFeaturesImpl(const SentenceMetadata& smeta,
       static map<WordID, bool> big_enough;
       map<WordID,bool>::iterator it = big_enough_.find(word);
       if (it == big_enough_.end()) {
-        out_is_identity = big_enough_[word] = strlen(TD::Convert(word)) >= length_min_;
+        out_is_identity = big_enough_[word] = TD::Convert(word).size() >= length_min_;
       } else {
         out_is_identity = it->second;
       }
diff --git a/decoder/ff_wordalign.h b/decoder/ff_wordalign.h
index d7a2dda8..ba3d0b9b 100644
--- a/decoder/ff_wordalign.h
+++ b/decoder/ff_wordalign.h
@@ -13,7 +13,7 @@ class RelativeSentencePosition : public FeatureFunction {
   RelativeSentencePosition(const std::string& param);
  protected:
   virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
+                                     const HG::Edge& edge,
                                      const std::vector<const void*>& ant_contexts,
                                      SparseVector<double>* features,
                                      SparseVector<double>* estimated_features,
@@ -36,7 +36,7 @@ class SourceBigram : public FeatureFunction {
   void PrepareForInput(const SentenceMetadata& smeta);
  protected:
   virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
+                                     const HG::Edge& edge,
                                      const std::vector<const void*>& ant_contexts,
                                      SparseVector<double>* features,
                                      SparseVector<double>* estimated_features,
@@ -55,7 +55,7 @@ class LexNullJump : public FeatureFunction {
   LexNullJump(const std::string& param);
  protected:
   virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
+                                     const HG::Edge& edge,
                                      const std::vector<const void*>& ant_contexts,
                                      SparseVector<double>* features,
                                      SparseVector<double>* estimated_features,
@@ -72,7 +72,7 @@ class NewJump : public FeatureFunction {
   NewJump(const std::string& param);
  protected:
   virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
+                                     const HG::Edge& edge,
                                      const std::vector<const void*>& ant_contexts,
                                      SparseVector<double>* features,
                                      SparseVector<double>* estimated_features,
@@ -109,7 +109,7 @@ class LexicalTranslationTrigger : public FeatureFunction {
   LexicalTranslationTrigger(const std::string& param);
  protected:
   virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
+                                     const HG::Edge& edge,
                                      const std::vector<const void*>& ant_contexts,
                                      SparseVector<double>* features,
                                      SparseVector<double>* estimated_features,
@@ -132,14 +132,14 @@ class BlunsomSynchronousParseHack : public FeatureFunction {
   BlunsomSynchronousParseHack(const std::string& param);
  protected:
   virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
+                                     const HG::Edge& edge,
                                      const std::vector<const void*>& ant_contexts,
                                      SparseVector<double>* features,
                                      SparseVector<double>* estimated_features,
                                      void* out_context) const;
  private:
   inline bool DoesNotBelong(const void* state) const {
-    for (int i = 0; i < NumBytesContext(); ++i) {
+    for (int i = 0; i < StateSize(); ++i) {
       if (*(static_cast<const unsigned char*>(state) + i)) return false;
     }
     return true;
@@ -148,9 +148,9 @@ class BlunsomSynchronousParseHack : public FeatureFunction {
   inline void AppendAntecedentString(const void* state, std::vector<WordID>* yield) const {
     int i = 0;
     int ind = 0;
-    while (i < NumBytesContext() && !(*(static_cast<const unsigned char*>(state) + i))) { ++i; ind += 8; }
-    // std::cerr << i << " " << NumBytesContext() << std::endl;
-    assert(i != NumBytesContext());
+    while (i < StateSize() && !(*(static_cast<const unsigned char*>(state) + i))) { ++i; ind += 8; }
+    // std::cerr << i << " " << StateSize() << std::endl;
+    assert(i != StateSize());
     assert(ind < cur_ref_->size());
     int cur = *(static_cast<const unsigned char*>(state) + i);
     int comp = 1;
@@ -171,7 +171,7 @@ class BlunsomSynchronousParseHack : public FeatureFunction {
   }
 
   inline void SetStateMask(int start, int end, void* state) const {
-    assert((end / 8) < NumBytesContext());
+    assert((end / 8) < StateSize());
     int i = 0;
     int comp = 1;
     for (int j = 0; j < start; ++j) {
@@ -209,7 +209,7 @@ class WordPairFeatures : public FeatureFunction {
   WordPairFeatures(const std::string& param);
  protected:
   virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
+                                     const HG::Edge& edge,
                                      const std::vector<const void*>& ant_contexts,
                                      SparseVector<double>* features,
                                      SparseVector<double>* estimated_features,
@@ -226,7 +226,7 @@ class IdentityCycleDetector : public FeatureFunction {
   IdentityCycleDetector(const std::string& param);
  protected:
   virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
+                                     const HG::Edge& edge,
                                      const std::vector<const void*>& ant_contexts,
                                      SparseVector<double>* features,
                                      SparseVector<double>* estimated_features,
@@ -242,7 +242,7 @@ class InputIndicator : public FeatureFunction {
   InputIndicator(const std::string& param);
  protected:
   virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
+                                     const HG::Edge& edge,
                                      const std::vector<const void*>& ant_contexts,
                                      SparseVector<double>* features,
                                      SparseVector<double>* estimated_features,
@@ -258,7 +258,7 @@ class Fertility : public FeatureFunction {
   Fertility(const std::string& param);
  protected:
   virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
+                                     const HG::Edge& edge,
                                      const std::vector<const void*>& ant_contexts,
                                      SparseVector<double>* features,
                                      SparseVector<double>* estimated_features,
diff --git a/decoder/ff_wordset.cc b/decoder/ff_wordset.cc
index 44468899..70cea7de 100644
--- a/decoder/ff_wordset.cc
+++ b/decoder/ff_wordset.cc
@@ -1,5 +1,6 @@
 #include "ff_wordset.h"
 
+#include "hg.h"
 #include "fdict.h"
 #include <sstream>
 #include <iostream>
diff --git a/decoder/ff_wordset.h b/decoder/ff_wordset.h
index 7c9a3fb7..639e1514 100644
--- a/decoder/ff_wordset.h
+++ b/decoder/ff_wordset.h
@@ -2,6 +2,7 @@
 #define _FF_WORDSET_H_
 
 #include "ff.h"
+#include "tdict.h"
 
 #include <tr1/unordered_set>
 #include <boost/algorithm/string.hpp>
@@ -32,11 +33,9 @@ class WordSet : public FeatureFunction {
   ~WordSet() {
   }
 
-  Features features() const { return single_feature(fid_); }
-
  protected:
   virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
+                                     const HG::Edge& edge,
                                      const std::vector<const void*>& ant_contexts,
                                      SparseVector<double>* features,
                                      SparseVector<double>* estimated_features,
diff --git a/decoder/ffset.cc b/decoder/ffset.cc
new file mode 100644
index 00000000..5820f421
--- /dev/null
+++ b/decoder/ffset.cc
@@ -0,0 +1,72 @@
+#include "ffset.h"
+
+#include "ff.h"
+#include "tdict.h"
+#include "hg.h"
+
+using namespace std;
+
+ModelSet::ModelSet(const vector<double>& w, const vector<const FeatureFunction*>& models) :
+    models_(models),
+    weights_(w),
+    state_size_(0),
+    model_state_pos_(models.size()) {
+  for (int i = 0; i < models_.size(); ++i) {
+    model_state_pos_[i] = state_size_;
+    state_size_ += models_[i]->StateSize();
+  }
+}
+
+void ModelSet::PrepareForInput(const SentenceMetadata& smeta) {
+  for (int i = 0; i < models_.size(); ++i)
+    const_cast<FeatureFunction*>(models_[i])->PrepareForInput(smeta);
+}
+
+void ModelSet::AddFeaturesToEdge(const SentenceMetadata& smeta,
+                                 const Hypergraph& /* hg */,
+                                 const FFStates& node_states,
+                                 HG::Edge* edge,
+                                 FFState* context,
+                                 prob_t* combination_cost_estimate) const {
+  //edge->reset_info();
+  context->resize(state_size_);
+  if (state_size_ > 0) {
+    memset(&(*context)[0], 0, state_size_);
+  }
+  SparseVector<double> est_vals;  // only computed if combination_cost_estimate is non-NULL
+  if (combination_cost_estimate) *combination_cost_estimate = prob_t::One();
+  for (int i = 0; i < models_.size(); ++i) {
+    const FeatureFunction& ff = *models_[i];
+    void* cur_ff_context = NULL;
+    vector<const void*> ants(edge->tail_nodes_.size());
+    bool has_context = ff.StateSize() > 0;
+    if (has_context) {
+      int spos = model_state_pos_[i];
+      cur_ff_context = &(*context)[spos];
+      for (int i = 0; i < ants.size(); ++i) {
+        ants[i] = &node_states[edge->tail_nodes_[i]][spos];
+      }
+    }
+    ff.TraversalFeatures(smeta, *edge, ants, &edge->feature_values_, &est_vals, cur_ff_context);
+  }
+  if (combination_cost_estimate)
+    combination_cost_estimate->logeq(est_vals.dot(weights_));
+  edge->edge_prob_.logeq(edge->feature_values_.dot(weights_));
+}
+
+void ModelSet::AddFinalFeatures(const FFState& state, HG::Edge* edge,SentenceMetadata const& smeta) const {
+  assert(1 == edge->rule_->Arity());
+  //edge->reset_info();
+  for (int i = 0; i < models_.size(); ++i) {
+    const FeatureFunction& ff = *models_[i];
+    const void* ant_state = NULL;
+    bool has_context = ff.StateSize() > 0;
+    if (has_context) {
+      int spos = model_state_pos_[i];
+      ant_state = &state[spos];
+    }
+    ff.FinalTraversalFeatures(ant_state, &edge->feature_values_);
+  }
+  edge->edge_prob_.logeq(edge->feature_values_.dot(weights_));
+}
+
diff --git a/decoder/ffset.h b/decoder/ffset.h
new file mode 100644
index 00000000..28aef667
--- /dev/null
+++ b/decoder/ffset.h
@@ -0,0 +1,57 @@
+#ifndef _FFSET_H_
+#define _FFSET_H_
+
+#include <vector>
+#include "value_array.h"
+#include "prob.h"
+
+namespace HG { struct Edge; struct Node; }
+class Hypergraph;
+class FeatureFunction;
+class SentenceMetadata;
+class FeatureFunction;  // see definition below
+
+// TODO let states be dynamically sized
+typedef ValueArray<uint8_t> FFState; // this is a fixed array, but about 10% faster than string
+
+//FIXME: only context.data() is required to be contiguous, and it becomes invalid after next string operation.  use ValueArray instead? (higher performance perhaps, save a word due to fixed size)
+typedef std::vector<FFState> FFStates;
+
+// this class is a set of FeatureFunctions that can be used to score, rescore,
+// etc. a (translation?) forest
+class ModelSet {
+ public:
+  ModelSet(const std::vector<double>& weights,
+           const std::vector<const FeatureFunction*>& models);
+
+  // sets edge->feature_values_ and edge->edge_prob_
+  // NOTE: edge must not necessarily be in hg.edges_ but its TAIL nodes
+  // must be.  edge features are supposed to be overwritten, not added to (possibly because rule features aren't in ModelSet so need to be left alone
+  void AddFeaturesToEdge(const SentenceMetadata& smeta,
+                         const Hypergraph& hg,
+                         const FFStates& node_states,
+                         HG::Edge* edge,
+                         FFState* residual_context,
+                         prob_t* combination_cost_estimate = NULL) const;
+
+  //this is called INSTEAD of above when result of edge is goal (must be a unary rule - i.e. one variable, but typically it's assumed that there are no target terminals either (e.g. for LM))
+  void AddFinalFeatures(const FFState& residual_context,
+                        HG::Edge* edge,
+                        SentenceMetadata const& smeta) const;
+
+  // this is called once before any feature functions apply to a hypergraph
+  // it can be used to initialize sentence-specific data structures
+  void PrepareForInput(const SentenceMetadata& smeta);
+
+  bool empty() const { return models_.empty(); }
+
+  bool stateless() const { return !state_size_; }
+
+ private:
+  std::vector<const FeatureFunction*> models_;
+  const std::vector<double>& weights_;
+  int state_size_;
+  std::vector<int> model_state_pos_;
+};
+
+#endif
diff --git a/decoder/grammar.cc b/decoder/grammar.cc
index d1fe53af..ee43f537 100644
--- a/decoder/grammar.cc
+++ b/decoder/grammar.cc
@@ -127,48 +127,3 @@ bool TextGrammar::HasRuleForSpan(int /* i */, int /* j */, int distance) const {
   return (max_span_ >= distance);
 }
 
-GlueGrammar::GlueGrammar(const string& file) : TextGrammar(file) {}
-
-void RefineRule(TRulePtr pt, const unsigned int ctf_level){
-  for (unsigned int i=0; i<ctf_level; ++i){
-    TRulePtr r(new TRule(*pt));
-    pt->fine_rules_.reset(new vector<TRulePtr>);
-    pt->fine_rules_->push_back(r);
-    pt = r;
-  }
-}
-
-GlueGrammar::GlueGrammar(const string& goal_nt, const string& default_nt, const unsigned int ctf_level) {
-  TRulePtr stop_glue(new TRule("[" + goal_nt + "] ||| [" + default_nt + ",1] ||| [1]"));
-  AddRule(stop_glue);
-  RefineRule(stop_glue, ctf_level);
-  TRulePtr glue(new TRule("[" + goal_nt + "] ||| [" + goal_nt + ",1] ["+ default_nt + ",2] ||| [1] [2] ||| Glue=1"));
-  AddRule(glue);
-  RefineRule(glue, ctf_level);
-}
-
-bool GlueGrammar::HasRuleForSpan(int i, int /* j */, int /* distance */) const {
-  return (i == 0);
-}
-
-PassThroughGrammar::PassThroughGrammar(const Lattice& input, const string& cat, const unsigned int ctf_level) {
-  unordered_set<WordID> ss;
-  for (int i = 0; i < input.size(); ++i) {
-    const vector<LatticeArc>& alts = input[i];
-    for (int k = 0; k < alts.size(); ++k) {
-      const int j = alts[k].dist2next + i;
-      const string& src = TD::Convert(alts[k].label);
-      if (ss.count(alts[k].label) == 0) {
-        TRulePtr pt(new TRule("[" + cat + "] ||| " + src + " ||| " + src + " ||| PassThrough=1"));
-        pt->a_.push_back(AlignmentPoint(0,0));
-        AddRule(pt);
-        RefineRule(pt, ctf_level);
-        ss.insert(alts[k].label);
-      }
-    }
-  }
-}
-
-bool PassThroughGrammar::HasRuleForSpan(int, int, int distance) const {
-  return (distance < 2);
-}
diff --git a/decoder/grammar.h b/decoder/grammar.h
index e6a15a69..add1a235 100644
--- a/decoder/grammar.h
+++ b/decoder/grammar.h
@@ -81,18 +81,4 @@ struct TextGrammar : public Grammar {
 
 };
 
-struct GlueGrammar : public TextGrammar {
-  // read glue grammar from file
-  explicit GlueGrammar(const std::string& file);
-  GlueGrammar(const std::string& goal_nt, const std::string& default_nt, const unsigned int ctf_level=0);  // "S", "X"
-  virtual bool HasRuleForSpan(int i, int j, int distance) const;
-};
-
-struct PassThroughGrammar : public TextGrammar {
-  PassThroughGrammar(const Lattice& input, const std::string& cat, const unsigned int ctf_level=0);
-  virtual bool HasRuleForSpan(int i, int j, int distance) const;
-};
-
-void RefineRule(TRulePtr pt, const unsigned int ctf_level);
-
 #endif
diff --git a/decoder/grammar_test.cc b/decoder/grammar_test.cc
index 4500490a..912f4f12 100644
--- a/decoder/grammar_test.cc
+++ b/decoder/grammar_test.cc
@@ -10,7 +10,9 @@
 #include "tdict.h"
 #include "grammar.h"
 #include "bottom_up_parser.h"
+#include "hg.h"
 #include "ff.h"
+#include "ffset.h"
 #include "weights.h"
 
 using namespace std;
diff --git a/decoder/hg.h b/decoder/hg.h
index 591e98ce..3d8cd9bc 100644
--- a/decoder/hg.h
+++ b/decoder/hg.h
@@ -33,47 +33,20 @@
 // slow
 #undef HG_EDGES_TOPO_SORTED
 
-class Hypergraph;
-typedef boost::shared_ptr<Hypergraph> HypergraphP;
-
-// class representing an acyclic hypergraph
-//  - edges have 1 head, 0..n tails
-class Hypergraph {
-public:
-  Hypergraph() : is_linear_chain_(false) {}
+// SmallVector is a fast, small vector<int> implementation for sizes <= 2
+typedef SmallVectorUnsigned TailNodeVector; // indices in nodes_
+typedef std::vector<int> EdgesVector; // indices in edges_
 
-  // SmallVector is a fast, small vector<int> implementation for sizes <= 2
-  typedef SmallVectorUnsigned TailNodeVector; // indices in nodes_
-  typedef std::vector<int> EdgesVector; // indices in edges_
-
-  // TODO get rid of cat_?
-  // TODO keep cat_ and add span and/or state? :)
-  struct Node {
-    Node() : id_(), cat_() {}
-    int id_; // equal to this object's position in the nodes_ vector
-    WordID cat_;  // non-terminal category if <0, 0 if not set
-    WordID NT() const { return -cat_; }
-    EdgesVector in_edges_;   // an in edge is an edge with this node as its head.  (in edges come from the bottom up to us)  indices in edges_
-    EdgesVector out_edges_;  // an out edge is an edge with this node as its tail.  (out edges leave us up toward the top/goal). indices in edges_
-    void copy_fixed(Node const& o) { // nonstructural fields only - structural ones are managed by sorting/pruning/subsetting
-      cat_=o.cat_;
-    }
-    void copy_reindex(Node const& o,indices_after const& n2,indices_after const& e2) {
-      copy_fixed(o);
-      id_=n2[id_];
-      e2.reindex_push_back(o.in_edges_,in_edges_);
-      e2.reindex_push_back(o.out_edges_,out_edges_);
-    }
-  };
+enum {
+  NONE=0,CATEGORY=1,SPAN=2,PROB=4,FEATURES=8,RULE=16,RULE_LHS=32,PREV_SPAN=64,ALL=0xFFFFFFFF
+};
 
+namespace HG {
 
-  // TODO get rid of edge_prob_? (can be computed on the fly as the dot
-  // product of the weight vector and the feature values)
   struct Edge {
-//    int poplimit; //TODO: cube pruning per edge limit?  per node didn't work well at all.  also, inside cost + outside(node) is the same information i'd use to set a per-edge limit anyway - and nonmonotonicity in cube pruning may mean it's good to favor edge (in same node) w/ relatively worse score
     Edge() : i_(-1), j_(-1), prev_i_(-1), prev_j_(-1) {}
     Edge(int id,Edge const& copy_pod_from) : id_(id) { copy_pod(copy_pod_from); } // call copy_features yourself later.
-    Edge(int id,Edge const& copy_from,TailNodeVector const& tail) // fully inits - probably more expensive when push_back(Edge(...)) than setting after
+    Edge(int id,Edge const& copy_from,TailNodeVector const& tail) // fully inits - probably more expensive when push_back(Edge(...)) than sett
       : tail_nodes_(tail),id_(id) { copy_pod(copy_from);copy_features(copy_from); }
     inline int Arity() const { return tail_nodes_.size(); }
     int head_node_;               // refers to a position in nodes_
@@ -83,8 +56,6 @@ public:
     prob_t edge_prob_;             // dot product of weights and feat_values
     int id_;   // equal to this object's position in the edges_ vector
 
-    //FIXME: these span ids belong in Node, not Edge, right?  every node should have the same spans.
-
     // span info. typically, i_ and j_ refer to indices in the source sentence.
     // In synchronous parsing, i_ and j_ will refer to target sentence/lattice indices
     // while prev_i_ prev_j_ will refer to positions in the source.
@@ -97,54 +68,6 @@ public:
     short int j_;
     short int prev_i_;
     short int prev_j_;
-
-    void copy_info(Edge const& o) {
-#if USE_INFO_EDGE
-      set_info(o.info_.str()); // by convention, each person putting info here starts with a separator (e.g. space).  it's empty if nobody put any info there.
-#else
-      (void) o;
-#endif
-    }
-    void copy_pod(Edge const& o) {
-      rule_=o.rule_;
-      i_ = o.i_; j_ = o.j_; prev_i_ = o.prev_i_; prev_j_ = o.prev_j_;
-    }
-    void copy_features(Edge const& o) {
-      feature_values_=o.feature_values_;
-      copy_info(o);
-    }
-    void copy_fixed(Edge const& o) {
-      copy_pod(o);
-      copy_features(o);
-      edge_prob_ = o.edge_prob_;
-    }
-    void copy_reindex(Edge const& o,indices_after const& n2,indices_after const& e2) {
-      copy_fixed(o);
-      head_node_=n2[o.head_node_];
-      id_=e2[o.id_];
-      n2.reindex_push_back(o.tail_nodes_,tail_nodes_);
-    }
-
-#if USE_INFO_EDGE
-    std::ostringstream info_;
-    void set_info(std::string const& s) {
-      info_.str(s);
-      info_.seekp(0,std::ios_base::end);
-    }
-    Edge(Edge const& o) : head_node_(o.head_node_),tail_nodes_(o.tail_nodes_),rule_(o.rule_),feature_values_(o.feature_values_),edge_prob_(o.edge_prob_),id_(o.id_),i_(o.i_),j_(o.j_),prev_i_(o.prev_i_),prev_j_(o.prev_j_), info_(o.info_.str(),std::ios_base::ate) {
-//      info_.seekp(0,std::ios_base::end);
- }
-    void operator=(Edge const& o) {
-      head_node_ = o.head_node_; tail_nodes_ = o.tail_nodes_; rule_ = o.rule_; feature_values_ = o.feature_values_; edge_prob_ = o.edge_prob_; id_ = o.id_; i_ = o.i_; j_ = o.j_; prev_i_ = o.prev_i_; prev_j_ = o.prev_j_;
-      set_info(o.info_.str());
-    }
-    std::string info() const { return info_.str(); }
-    void reset_info() { info_.str(""); info_.clear(); }
-#else
-    std::string info() const { return std::string(); }
-    void reset_info() {  }
-    void set_info(std::string const& ) {  }
-#endif
     void show(std::ostream &o,unsigned mask=SPAN|RULE) const {
       o<<'{';
       if (mask&CATEGORY)
@@ -159,10 +82,6 @@ public:
         o<<' '<<feature_values_;
       if (mask&RULE)
         o<<' '<<rule_->AsString(mask&RULE_LHS);
-      if (USE_INFO_EDGE) {
-        std::string const& i=info();
-        if (mask&&!i.empty()) o << " |||"<<i; // remember, the initial space is expected as part of i
-      }
       o<<'}';
     }
     std::string show(unsigned mask=SPAN|RULE) const {
@@ -170,12 +89,28 @@ public:
       show(o,mask);
       return o.str();
     }
-    /* generic recursion re: child_handle=re(tail_nodes_[i],i,parent_handle)
-
-       FIXME: make kbest create a simple derivation-tree structure (could be a
-       hg), and replace the list-of-edges viterbi.h with a tree-structured one.
-       CreateViterbiHypergraph can do for 1best, though.
-    */
+    void copy_pod(Edge const& o) {
+      rule_=o.rule_;
+      i_ = o.i_; j_ = o.j_; prev_i_ = o.prev_i_; prev_j_ = o.prev_j_;
+    }
+    void copy_features(Edge const& o) {
+      feature_values_=o.feature_values_;
+    }
+    void copy_fixed(Edge const& o) {
+      copy_pod(o);
+      copy_features(o);
+      edge_prob_ = o.edge_prob_;
+    }
+    void copy_reindex(Edge const& o,indices_after const& n2,indices_after const& e2) {
+      copy_fixed(o);
+      head_node_=n2[o.head_node_];
+      id_=e2[o.id_];
+      n2.reindex_push_back(o.tail_nodes_,tail_nodes_);
+    }
+    // generic recursion re: child_handle=re(tail_nodes_[i],i,parent_handle)
+    //   FIXME: make kbest create a simple derivation-tree structure (could be a
+    //   hg), and replace the list-of-edges viterbi.h with a tree-structured one.
+    //   CreateViterbiHypergraph can do for 1best, though.
     template <class EdgeRecurse,class TEdgeHandle>
     std::string derivation_tree(EdgeRecurse const& re,TEdgeHandle const& eh,bool indent=true,int show_mask=SPAN|RULE,int maxdepth=0x7FFFFFFF,int depth=0) const {
       std::ostringstream o;
@@ -203,7 +138,43 @@ public:
     }
   };
 
-  // all this info ought to live in Node, but for some reason it's on Edges.
+  // TODO get rid of cat_?
+  // TODO keep cat_ and add span and/or state? :)
+  struct Node {
+    Node() : id_(), cat_() {}
+    int id_; // equal to this object's position in the nodes_ vector
+    WordID cat_;  // non-terminal category if <0, 0 if not set
+    WordID NT() const { return -cat_; }
+    EdgesVector in_edges_;   // an in edge is an edge with this node as its head.  (in edges come from the bottom up to us)  indices in edges_
+    EdgesVector out_edges_;  // an out edge is an edge with this node as its tail.  (out edges leave us up toward the top/goal). indices in edges_
+    void copy_fixed(Node const& o) { // nonstructural fields only - structural ones are managed by sorting/pruning/subsetting
+      cat_=o.cat_;
+    }
+    void copy_reindex(Node const& o,indices_after const& n2,indices_after const& e2) {
+      copy_fixed(o);
+      id_=n2[id_];
+      e2.reindex_push_back(o.in_edges_,in_edges_);
+      e2.reindex_push_back(o.out_edges_,out_edges_);
+    }
+  };
+
+} // namespace HG
+
+class Hypergraph;
+typedef boost::shared_ptr<Hypergraph> HypergraphP;
+// class representing an acyclic hypergraph
+//  - edges have 1 head, 0..n tails
+class Hypergraph {
+public:
+  Hypergraph() : is_linear_chain_(false) {}
+  typedef HG::Node Node;
+  typedef HG::Edge Edge;
+  typedef SmallVectorUnsigned TailNodeVector; // indices in nodes_
+  typedef std::vector<int> EdgesVector; // indices in edges_
+  enum {
+    NONE=0,CATEGORY=1,SPAN=2,PROB=4,FEATURES=8,RULE=16,RULE_LHS=32,PREV_SPAN=64,ALL=0xFFFFFFFF
+  };
+
   // except for stateful models that have split nt,span, this should identify the node
   void SetNodeOrigin(int nodeid,NTSpan &r) const {
     Node const &n=nodes_[nodeid];
@@ -230,18 +201,9 @@ public:
     }
     return s;
   }
-  // 0 if none, -TD index otherwise (just like in rule)
   WordID NodeLHS(int nodeid) const {
     Node const &n=nodes_[nodeid];
     return n.NT();
-    /*
-    if (!n.in_edges_.empty()) {
-      Edge const& e=edges_[n.in_edges_.front()];
-      if (e.rule_)
-        return -e.rule_->lhs_;
-    }
-    return 0;
-    */
   }
 
   typedef std::vector<prob_t> EdgeProbs;
@@ -250,14 +212,8 @@ public:
   typedef std::vector<bool> NodeMask;
 
   std::string show_viterbi_tree(bool indent=true,int show_mask=SPAN|RULE,int maxdepth=0x7FFFFFFF,int depth=0) const;
-// builds viterbi hg and returns it formatted as a pretty string
-
-  enum {
-    NONE=0,CATEGORY=1,SPAN=2,PROB=4,FEATURES=8,RULE=16,RULE_LHS=32,PREV_SPAN=64,ALL=0xFFFFFFFF
-  };
 
   std::string show_first_tree(bool indent=true,int show_mask=SPAN|RULE,int maxdepth=0x7FFFFFFF,int depth=0) const;
-  // same as above, but takes in_edges_[0] all the way down - to make it viterbi cost (1-best), call ViterbiSortInEdges() first
 
   typedef Edge const* EdgeHandle;
   EdgeHandle operator()(int tailn,int /*taili*/,EdgeHandle /*parent*/) const {
@@ -334,7 +290,7 @@ public:
   Edge* AddEdge(Edge const& in_edge, const TailNodeVector& tail) {
     edges_.push_back(Edge(edges_.size(),in_edge));
     Edge* edge = &edges_.back();
-    edge->copy_features(in_edge);
+    edge->feature_values_ = in_edge.feature_values_;
     edge->tail_nodes_ = tail; // possibly faster than copying to Edge() constructed above then copying via push_back.  perhaps optimized it's the same.
     index_tails(*edge);
     return edge;
@@ -503,9 +459,9 @@ public:
 
   template <class V>
   void visit_edges_topo(V &v) {
-    for (int i = 0; i < nodes_.size(); ++i) {
+    for (unsigned i = 0; i < nodes_.size(); ++i) {
       EdgesVector const& in=nodes_[i].in_edges_;
-      for (int j=0;j<in.size();++j) {
+      for (unsigned j=0;j<in.size();++j) {
         int e=in[j];
         v(i,e,edges_[e]);
       }
@@ -534,14 +490,14 @@ private:
 // for generic Viterbi/Inside algorithms
 struct EdgeProb {
   typedef prob_t Weight;
-  inline const prob_t& operator()(const Hypergraph::Edge& e) const { return e.edge_prob_; }
+  inline const prob_t& operator()(const HG::Edge& e) const { return e.edge_prob_; }
 };
 
 struct EdgeSelectEdgeWeightFunction {
   typedef prob_t Weight;
   typedef std::vector<bool> EdgeMask;
   EdgeSelectEdgeWeightFunction(const EdgeMask& v) : v_(v) {}
-  inline prob_t operator()(const Hypergraph::Edge& e) const {
+  inline prob_t operator()(const HG::Edge& e) const {
     if (v_[e.id_]) return prob_t::One();
     else return prob_t::Zero();
   }
@@ -551,7 +507,7 @@ private:
 
 struct ScaledEdgeProb {
   ScaledEdgeProb(const double& alpha) : alpha_(alpha) {}
-  inline prob_t operator()(const Hypergraph::Edge& e) const { return e.edge_prob_.pow(alpha_); }
+  inline prob_t operator()(const HG::Edge& e) const { return e.edge_prob_.pow(alpha_); }
   const double alpha_;
   typedef prob_t Weight;
 };
@@ -560,7 +516,7 @@ struct ScaledEdgeProb {
 struct EdgeFeaturesAndProbWeightFunction {
   typedef SparseVector<prob_t> Weight;
   typedef Weight Result; //TODO: change Result->Weight everywhere?
-  inline const Weight operator()(const Hypergraph::Edge& e) const {
+  inline const Weight operator()(const HG::Edge& e) const {
     SparseVector<prob_t> res;
     for (SparseVector<double>::const_iterator it = e.feature_values_.begin();
          it != e.feature_values_.end(); ++it)
@@ -571,7 +527,7 @@ struct EdgeFeaturesAndProbWeightFunction {
 
 struct TransitionCountWeightFunction {
   typedef double Weight;
-  inline double operator()(const Hypergraph::Edge& e) const { (void)e; return 1.0; }
+  inline double operator()(const HG::Edge& e) const { (void)e; return 1.0; }
 };
 
 #endif
diff --git a/decoder/hg_intersect.cc b/decoder/hg_intersect.cc
index 6e3bfee6..ad5b701a 100644
--- a/decoder/hg_intersect.cc
+++ b/decoder/hg_intersect.cc
@@ -79,7 +79,9 @@ static bool FastLinearIntersect(const Lattice& target, Hypergraph* hg) {
   return (cov.size() == target.size());
 }
 
-bool HG::Intersect(const Lattice& target, Hypergraph* hg) {
+namespace HG {
+
+bool Intersect(const Lattice& target, Hypergraph* hg) {
   // there are a number of faster algorithms available for restricted
   // classes of hypergraph and/or target.
   if (hg->IsLinearChain() && target.IsSentence())
@@ -101,7 +103,7 @@ bool HG::Intersect(const Lattice& target, Hypergraph* hg) {
   // grammar, create the labels here
   const string kSEP = "_";
   for (unsigned i = 0; i < nnodes; ++i) {
-    const char* pstr = "CAT";
+    string pstr = "CAT";
     if (hg->nodes_[i].cat_ < 0)
       pstr = TD::Convert(-hg->nodes_[i].cat_);
     cats[i] = TD::Convert(pstr + kSEP + lexical_cast<string>(i)) * -1;
@@ -160,3 +162,5 @@ bool HG::Intersect(const Lattice& target, Hypergraph* hg) {
   return true;
 }
 
+}
+
diff --git a/decoder/hg_intersect.h b/decoder/hg_intersect.h
index 826bdaae..29a5ea2a 100644
--- a/decoder/hg_intersect.h
+++ b/decoder/hg_intersect.h
@@ -1,13 +1,11 @@
 #ifndef _HG_INTERSECT_H_
 #define _HG_INTERSECT_H_
 
-#include <vector>
-
 #include "lattice.h"
 
 class Hypergraph;
-struct HG {
-  static bool Intersect(const Lattice& target, Hypergraph* hg);
+namespace HG {
+  bool Intersect(const Lattice& target, Hypergraph* hg);
 };
 
 #endif
diff --git a/decoder/hg_io.cc b/decoder/hg_io.cc
index 8bd40387..64c6663e 100644
--- a/decoder/hg_io.cc
+++ b/decoder/hg_io.cc
@@ -28,7 +28,7 @@ struct HGReader : public JSONParser {
       hg.ConnectEdgeToHeadNode(&hg.edges_[in_edges[i]], node);
     }
   }
-  void CreateEdge(const TRulePtr& rule, FeatureVector* feats, const SmallVectorUnsigned& tail) {
+  void CreateEdge(const TRulePtr& rule, SparseVector<double>* feats, const SmallVectorUnsigned& tail) {
     Hypergraph::Edge* edge = hg.AddEdge(rule, tail);
     feats->swap(edge->feature_values_);
     edge->i_ = spans[0];
@@ -392,8 +392,8 @@ string HypergraphIO::AsPLF(const Hypergraph& hg, bool include_global_parentheses
         const Hypergraph::Edge& e = hg.edges_[hg.nodes_[i].out_edges_[j]];
         const string output = e.rule_->e_.size() ==2 ? Escape(TD::Convert(e.rule_->e_[1])) : EPS;
         double prob = log(e.edge_prob_);
-        if (isinf(prob)) { prob = -9e20; }
-        if (isnan(prob)) { prob = 0; }
+        if (std::isinf(prob)) { prob = -9e20; }
+        if (std::isnan(prob)) { prob = 0; }
         os << "('" << output << "'," << prob << "," << e.head_node_ - i << "),";
       }
       os << "),";
@@ -600,7 +600,7 @@ void HypergraphIO::WriteAsCFG(const Hypergraph& hg) {
   // grammar, create the labels here
   const string kSEP = "_";
   for (int i = 0; i < hg.nodes_.size(); ++i) {
-    const char* pstr = "CAT";
+    string pstr = "CAT";
     if (hg.nodes_[i].cat_ < 0)
       pstr = TD::Convert(-hg.nodes_[i].cat_);
     cats[i] = TD::Convert(pstr + kSEP + boost::lexical_cast<string>(i)) * -1;
diff --git a/decoder/hg_sampler.cc b/decoder/hg_sampler.cc
index cdf0ec3c..8e520871 100644
--- a/decoder/hg_sampler.cc
+++ b/decoder/hg_sampler.cc
@@ -71,3 +71,58 @@ void HypergraphSampler::sample_hypotheses(const Hypergraph& hg,
     Viterbi(hg, &hyp.words, ESentenceTraversal(), SampledDerivationWeightFunction(sampled_edges));
   }
 }
+
+void HypergraphSampler::sample_trees(const Hypergraph& hg,
+                                     unsigned n,
+                                     MT19937* rng,
+                                     vector<string>* trees) {
+  trees->clear();
+  trees->resize(n);
+
+  // compute inside probabilities
+  vector<prob_t> node_probs;
+  Inside<prob_t, EdgeProb>(hg, &node_probs, EdgeProb());
+
+  vector<bool> sampled_edges(hg.edges_.size());
+  queue<unsigned> q;
+  SampleSet<prob_t> ss;
+  for (unsigned i = 0; i < n; ++i) {
+    fill(sampled_edges.begin(), sampled_edges.end(), false);
+    // sample derivation top down
+    assert(q.empty());
+    q.push(hg.nodes_.size() - 1);
+    prob_t model_score = prob_t::One();
+    while(!q.empty()) {
+      unsigned cur_node_id = q.front();
+      q.pop();
+      const Hypergraph::Node& node = hg.nodes_[cur_node_id];
+      const unsigned num_in_edges = node.in_edges_.size();
+      unsigned sampled_edge_idx = 0;
+      if (num_in_edges == 1) {
+        sampled_edge_idx = node.in_edges_[0];
+      } else {
+        assert(num_in_edges > 1);
+        ss.clear();
+        for (unsigned j = 0; j < num_in_edges; ++j) {
+          const Hypergraph::Edge& edge = hg.edges_[node.in_edges_[j]];
+          prob_t p = edge.edge_prob_;   // edge weight
+          for (unsigned k = 0; k < edge.tail_nodes_.size(); ++k)
+            p *= node_probs[edge.tail_nodes_[k]];  // tail node inside weight
+          ss.add(p);
+        }
+        sampled_edge_idx = node.in_edges_[rng->SelectSample(ss)];
+      }
+      sampled_edges[sampled_edge_idx] = true;
+      const Hypergraph::Edge& sampled_edge = hg.edges_[sampled_edge_idx];
+      model_score *= sampled_edge.edge_prob_;
+      //sampled_deriv->push_back(sampled_edge_idx);
+      for (unsigned j = 0; j < sampled_edge.tail_nodes_.size(); ++j) {
+        q.push(sampled_edge.tail_nodes_[j]);
+      }
+    }
+    vector<WordID> tmp;
+    Viterbi(hg, &tmp, ETreeTraversal(), SampledDerivationWeightFunction(sampled_edges));
+    (*trees)[i] = TD::GetString(tmp);
+  }
+}
+
diff --git a/decoder/hg_sampler.h b/decoder/hg_sampler.h
index bf4e1eb0..6ac39a20 100644
--- a/decoder/hg_sampler.h
+++ b/decoder/hg_sampler.h
@@ -3,6 +3,7 @@
 
 
 #include <vector>
+#include <string>
 #include "sparse_vector.h"
 #include "sampler.h"
 #include "wordid.h"
@@ -22,6 +23,12 @@ struct HypergraphSampler {
                     unsigned n,   // how many samples to draw
                     MT19937* rng,
                     std::vector<Hypothesis>* hypos);
+
+  static void
+  sample_trees(const Hypergraph& hg,
+               unsigned n,
+               MT19937* rng,
+               std::vector<std::string>* trees);
 };
 
 #endif
diff --git a/decoder/hg_test.cc b/decoder/hg_test.cc
index 92ed98b2..37469748 100644
--- a/decoder/hg_test.cc
+++ b/decoder/hg_test.cc
@@ -6,6 +6,7 @@
 
 #include "json_parse.h"
 #include "hg_intersect.h"
+#include "hg_union.h"
 #include "viterbi.h"
 #include "kbest.h"
 #include "inside_outside.h"
@@ -52,7 +53,7 @@ BOOST_AUTO_TEST_CASE(Union) {
   int l2 = ViterbiPathLength(hg2);
   cerr << c1 << "\t" << TD::GetString(t1) << endl;
   cerr << c2 << "\t" << TD::GetString(t2) << endl;
-  hg1.Union(hg2);
+  HG::Union(hg2, &hg1);
   hg1.Reweight(wts);
   c3 = ViterbiESentence(hg1, &t3);
   int l3 = ViterbiPathLength(hg1);
@@ -121,8 +122,8 @@ BOOST_AUTO_TEST_CASE(InsideScore) {
   vector<prob_t> post;
   inside = hg.ComputeBestPathThroughEdges(&post);
   BOOST_CHECK_CLOSE(-0.3, log(inside), 1e-4);  // computed by hand
-  BOOST_CHECK_EQUAL(post.size(), 4);
-  for (int i = 0; i < 4; ++i) {
+  BOOST_CHECK_EQUAL(post.size(), 5);
+  for (int i = 0; i < 5; ++i) {
     cerr << "edge post: " << log(post[i]) << '\t' << hg.edges_[i].rule_->AsString() << endl;
   }
 }
@@ -139,12 +140,15 @@ BOOST_AUTO_TEST_CASE(PruneInsideOutside) {
   cerr << TD::GetString(trans) << "\n";
   cerr << "cost: " << cost << "\n";
   hg.PrintGraphviz();
+#if 0
   hg.DensityPruneInsideOutside(0.5, false, 2.0);
   hg.BeamPruneInsideOutside(0.5, false, 0.5);
   cost = ViterbiESentence(hg, &trans);
   cerr << "Ncst: " << cost << endl;
   cerr << TD::GetString(trans) << "\n";
   hg.PrintGraphviz();
+#endif
+  cerr << "FIX PLEASE\n";
 }
 
 BOOST_AUTO_TEST_CASE(TestPruneEdges) {
diff --git a/decoder/hg_test.h b/decoder/hg_test.h
index 2e308c37..e96cb0b1 100644
--- a/decoder/hg_test.h
+++ b/decoder/hg_test.h
@@ -64,12 +64,21 @@ Name HGjsons[]= {
 
 }
 
+void AddNullEdge(Hypergraph* hg) {
+  TRule x;
+  x.arity_ = 0;
+  hg->nodes_[0].in_edges_.push_back(hg->AddEdge(TRulePtr(new TRule(x)), Hypergraph::TailNodeVector())->id_);
+  hg->edges_.back().head_node_ = 0;
+}
+
 void HGSetup::CreateTinyLatticeHG(Hypergraph* hg) {
     Json(hg,HGjsons[TinyLatticeHG]);
+  AddNullEdge(hg);
 }
 
 void HGSetup::CreateLatticeHG(Hypergraph* hg) {
   Json(hg,HGjsons[LatticeHG]);
+  AddNullEdge(hg);
 }
 
 void HGSetup::CreateHG_tiny(Hypergraph* hg) {
diff --git a/decoder/hg_union.cc b/decoder/hg_union.cc
new file mode 100644
index 00000000..37082976
--- /dev/null
+++ b/decoder/hg_union.cc
@@ -0,0 +1,58 @@
+#include "hg_union.h"
+
+#include "hg.h"
+
+using namespace std;
+
+namespace HG {
+
+void Union(const Hypergraph& in, Hypergraph* out) {
+  if (&in == out) return;
+  if (out->nodes_.empty()) {
+    out->nodes_ = in.nodes_;
+    out->edges_ = in.edges_; return;
+  }
+  unsigned noff = out->nodes_.size();
+  unsigned eoff = out->edges_.size();
+  int ogoal = in.nodes_.size() - 1;
+  int cgoal = noff - 1;
+  // keep a single goal node, so add nodes.size - 1
+  out->nodes_.resize(out->nodes_.size() + ogoal);
+  // add all edges
+  out->edges_.resize(out->edges_.size() + in.edges_.size());
+
+  for (int i = 0; i < ogoal; ++i) {
+    const Hypergraph::Node& on = in.nodes_[i];
+    Hypergraph::Node& cn = out->nodes_[i + noff];
+    cn.id_ = i + noff;
+    cn.in_edges_.resize(on.in_edges_.size());
+    for (unsigned j = 0; j < on.in_edges_.size(); ++j)
+      cn.in_edges_[j] = on.in_edges_[j] + eoff;
+
+    cn.out_edges_.resize(on.out_edges_.size());
+    for (unsigned j = 0; j < on.out_edges_.size(); ++j)
+      cn.out_edges_[j] = on.out_edges_[j] + eoff;
+  }
+
+  for (unsigned i = 0; i < in.edges_.size(); ++i) {
+    const Hypergraph::Edge& oe = in.edges_[i];
+    Hypergraph::Edge& ce = out->edges_[i + eoff];
+    ce.id_ = i + eoff;
+    ce.rule_ = oe.rule_;
+    ce.feature_values_ = oe.feature_values_;
+    if (oe.head_node_ == ogoal) {
+      ce.head_node_ = cgoal;
+      out->nodes_[cgoal].in_edges_.push_back(ce.id_);
+    } else {
+      ce.head_node_ = oe.head_node_ + noff;
+    }
+    ce.tail_nodes_.resize(oe.tail_nodes_.size());
+    for (unsigned j = 0; j < oe.tail_nodes_.size(); ++j)
+      ce.tail_nodes_[j] = oe.tail_nodes_[j] + noff;
+  }
+
+  out->TopologicallySortNodesAndEdges(cgoal);
+}
+
+}
+
diff --git a/decoder/hg_union.h b/decoder/hg_union.h
new file mode 100644
index 00000000..34624246
--- /dev/null
+++ b/decoder/hg_union.h
@@ -0,0 +1,9 @@
+#ifndef _HG_UNION_H_
+#define _HG_UNION_H_
+
+class Hypergraph;
+namespace HG {
+  void Union(const Hypergraph& in, Hypergraph* out);
+};
+
+#endif
diff --git a/decoder/incremental.cc b/decoder/incremental.cc
new file mode 100644
index 00000000..46615b0b
--- /dev/null
+++ b/decoder/incremental.cc
@@ -0,0 +1,167 @@
+#include "incremental.h"
+
+#include "hg.h"
+#include "fdict.h"
+#include "tdict.h"
+
+#include "lm/enumerate_vocab.hh"
+#include "lm/model.hh"
+#include "search/config.hh"
+#include "search/context.hh"
+#include "search/edge.hh"
+#include "search/edge_generator.hh"
+#include "search/rule.hh"
+#include "search/vertex.hh"
+#include "search/vertex_generator.hh"
+#include "util/exception.hh"
+
+#include <boost/scoped_ptr.hpp>
+#include <boost/scoped_array.hpp>
+
+#include <iostream>
+#include <vector>
+
+namespace {
+
+struct MapVocab : public lm::EnumerateVocab {
+  public:
+    MapVocab() {}
+
+    // Do not call after Lookup.  
+    void Add(lm::WordIndex index, const StringPiece &str) {
+      const WordID cdec_id = TD::Convert(str.as_string());
+      if (cdec_id >= out_.size()) out_.resize(cdec_id + 1);
+      out_[cdec_id] = index;
+    }
+
+    // Assumes Add has been called and will never be called again.  
+    lm::WordIndex FromCDec(WordID id) const {
+      return out_[out_.size() > id ? id : 0];
+    }
+
+  private:
+    std::vector<lm::WordIndex> out_;
+};
+
+template <class Model> class Incremental : public IncrementalBase {
+  public:
+    Incremental(const char *model_file, const std::vector<weight_t> &weights) :
+      IncrementalBase(weights), 
+      m_(model_file, GetConfig()),
+      weights_(
+          weights[FD::Convert("KLanguageModel")],
+          weights[FD::Convert("KLanguageModel_OOV")],
+          weights[FD::Convert("WordPenalty")]) {
+      std::cerr << "Weights KLanguageModel " << weights_.LM() << " KLanguageModel_OOV " << weights_.OOV() << " WordPenalty " << weights_.WordPenalty() << std::endl;
+    }
+    void Search(unsigned int pop_limit, const Hypergraph &hg) const;
+
+  private:
+    void ConvertEdge(const search::Context<Model> &context, bool final, search::Vertex *vertices, const Hypergraph::Edge &in, search::EdgeGenerator &gen) const;
+
+    lm::ngram::Config GetConfig() {
+      lm::ngram::Config ret;
+      ret.enumerate_vocab = &vocab_;
+      return ret;
+    }
+
+    MapVocab vocab_;
+
+    const Model m_;
+
+    const search::Weights weights_;
+};
+
+void PrintFinal(const Hypergraph &hg, const search::Final final) {
+  const std::vector<WordID> &words = static_cast<const Hypergraph::Edge*>(final.GetNote().vp)->rule_->e();
+  const search::Final *child(final.Children());
+  for (std::vector<WordID>::const_iterator i = words.begin(); i != words.end(); ++i) {
+    if (*i > 0) {
+      std::cout << TD::Convert(*i) << ' ';
+    } else {
+      PrintFinal(hg, *child++);
+    }
+  }
+}
+
+template <class Model> void Incremental<Model>::Search(unsigned int pop_limit, const Hypergraph &hg) const {
+  boost::scoped_array<search::Vertex> out_vertices(new search::Vertex[hg.nodes_.size()]);
+  search::Config config(weights_, pop_limit);
+  search::Context<Model> context(config, m_);
+
+  for (unsigned int i = 0; i < hg.nodes_.size() - 1; ++i) {
+    search::EdgeGenerator gen;
+    const Hypergraph::EdgesVector &down_edges = hg.nodes_[i].in_edges_;
+    for (unsigned int j = 0; j < down_edges.size(); ++j) {
+      unsigned int edge_index = down_edges[j];
+      ConvertEdge(context, i == hg.nodes_.size() - 2, out_vertices.get(), hg.edges_[edge_index], gen);
+    }
+    search::VertexGenerator vertex_gen(context, out_vertices[i]);
+    gen.Search(context, vertex_gen);
+  }
+  const search::Final top = out_vertices[hg.nodes_.size() - 2].BestChild();
+  if (!top.Valid()) {
+    std::cout << "NO PATH FOUND" << std::endl;
+  } else {
+    PrintFinal(hg, top);
+    std::cout << "||| " << top.GetScore() << std::endl;
+  }
+}
+
+template <class Model> void Incremental<Model>::ConvertEdge(const search::Context<Model> &context, bool final, search::Vertex *vertices, const Hypergraph::Edge &in, search::EdgeGenerator &gen) const {
+  const std::vector<WordID> &e = in.rule_->e();
+  std::vector<lm::WordIndex> words;
+  words.reserve(e.size());
+  std::vector<search::PartialVertex> nts;
+  unsigned int terminals = 0;
+  float score = 0.0;
+  for (std::vector<WordID>::const_iterator word = e.begin(); word != e.end(); ++word) {
+    if (*word <= 0) {
+      nts.push_back(vertices[in.tail_nodes_[-*word]].RootPartial());
+      if (nts.back().Empty()) return;
+      score += nts.back().Bound();
+      words.push_back(lm::kMaxWordIndex);
+    } else {
+      ++terminals;
+      words.push_back(vocab_.FromCDec(*word));
+    }
+  }
+
+  if (final) {
+    words.push_back(m_.GetVocabulary().EndSentence());
+  }
+
+  search::PartialEdge out(gen.AllocateEdge(nts.size()));
+
+  memcpy(out.NT(), &nts[0], sizeof(search::PartialVertex) * nts.size());
+
+  search::Note note;
+  note.vp = &in;
+  out.SetNote(note);
+
+  score += in.rule_->GetFeatureValues().dot(cdec_weights_);
+  score -= static_cast<float>(terminals) * context.GetWeights().WordPenalty() / M_LN10;
+  score += search::ScoreRule(context, words, final, out.Between());
+  out.SetScore(score);
+
+  gen.AddEdge(out);
+}
+
+} // namespace
+
+IncrementalBase *IncrementalBase::Load(const char *model_file, const std::vector<weight_t> &weights) {
+  lm::ngram::ModelType model_type;
+  if (!lm::ngram::RecognizeBinary(model_file, model_type)) model_type = lm::ngram::PROBING;
+  switch (model_type) {
+    case lm::ngram::PROBING:
+      return new Incremental<lm::ngram::ProbingModel>(model_file, weights);
+    case lm::ngram::REST_PROBING:
+      return new Incremental<lm::ngram::RestProbingModel>(model_file, weights);
+    default:
+      UTIL_THROW(util::Exception, "Sorry this lm type isn't supported yet.");
+  }
+}
+
+IncrementalBase::~IncrementalBase() {}
+
+IncrementalBase::IncrementalBase(const std::vector<weight_t> &weights) : cdec_weights_(weights) {}
diff --git a/decoder/incremental.h b/decoder/incremental.h
new file mode 100644
index 00000000..f791a626
--- /dev/null
+++ b/decoder/incremental.h
@@ -0,0 +1,23 @@
+#ifndef _INCREMENTAL_H_
+#define _INCREMENTAL_H_
+
+#include "weights.h"
+#include <vector>
+
+class Hypergraph;
+
+class IncrementalBase {
+  public:
+    static IncrementalBase *Load(const char *model_file, const std::vector<weight_t> &weights);
+
+    virtual ~IncrementalBase();
+
+    virtual void Search(unsigned int pop_limit, const Hypergraph &hg) const = 0;
+
+  protected:
+    IncrementalBase(const std::vector<weight_t> &weights);
+
+    const std::vector<weight_t> &cdec_weights_;
+};
+
+#endif // _INCREMENTAL_H_
diff --git a/decoder/inside_outside.h b/decoder/inside_outside.h
index f73a1d3f..c0377fe8 100644
--- a/decoder/inside_outside.h
+++ b/decoder/inside_outside.h
@@ -42,7 +42,7 @@ WeightType Inside(const Hypergraph& hg,
     Hypergraph::EdgesVector const& in=hg.nodes_[i].in_edges_;
     const unsigned num_in_edges = in.size();
     for (unsigned j = 0; j < num_in_edges; ++j) {
-      const Hypergraph::Edge& edge = hg.edges_[in[j]];
+      const HG::Edge& edge = hg.edges_[in[j]];
       WeightType score = weight(edge);
       for (unsigned k = 0; k < edge.tail_nodes_.size(); ++k) {
         const int tail_node_index = edge.tail_nodes_[k];
@@ -74,7 +74,7 @@ void Outside(const Hypergraph& hg,
     Hypergraph::EdgesVector const& in=hg.nodes_[i].in_edges_;
     const int num_in_edges = in.size();
     for (int j = 0; j < num_in_edges; ++j) {
-      const Hypergraph::Edge& edge = hg.edges_[in[j]];
+      const HG::Edge& edge = hg.edges_[in[j]];
       WeightType head_and_edge_weight = weight(edge);
       head_and_edge_weight *= head_node_outside_score;
       const int num_tail_nodes = edge.tail_nodes_.size();
@@ -138,7 +138,7 @@ struct InsideOutsides {
       Hypergraph::EdgesVector const& in=hg.nodes_[i].in_edges_;
       const int num_in_edges = in.size();
       for (int j = 0; j < num_in_edges; ++j) {
-        const Hypergraph::Edge& edge = hg.edges_[in[j]];
+        const HG::Edge& edge = hg.edges_[in[j]];
         KType kbar_e = outside[i];
         const int num_tail_nodes = edge.tail_nodes_.size();
         for (int k = 0; k < num_tail_nodes; ++k)
@@ -156,7 +156,7 @@ struct InsideOutsides {
       const int num_in_edges = in.size();
       for (int j = 0; j < num_in_edges; ++j) {
         int edgei=in[j];
-        const Hypergraph::Edge& edge = hg.edges_[edgei];
+        const HG::Edge& edge = hg.edges_[edgei];
         V x=weight(edge)*outside[i];
         const int num_tail_nodes = edge.tail_nodes_.size();
         for (int k = 0; k < num_tail_nodes; ++k)
diff --git a/decoder/kbest.h b/decoder/kbest.h
index 9af3a20e..9a55f653 100644
--- a/decoder/kbest.h
+++ b/decoder/kbest.h
@@ -48,7 +48,7 @@ namespace KBest {
     }
 
     struct Derivation {
-      Derivation(const Hypergraph::Edge& e,
+      Derivation(const HG::Edge& e,
                  const SmallVectorInt& jv,
                  const WeightType& w,
                  const SparseVector<double>& f) :
@@ -58,11 +58,11 @@ namespace KBest {
         feature_values(f) {}
 
       // dummy constructor, just for query
-      Derivation(const Hypergraph::Edge& e,
+      Derivation(const HG::Edge& e,
                  const SmallVectorInt& jv) : edge(&e), j(jv) {}
 
       T yield;
-      const Hypergraph::Edge* const edge;
+      const HG::Edge* const edge;
       const SmallVectorInt j;
       const WeightType score;
       const SparseVector<double> feature_values;
@@ -82,8 +82,8 @@ namespace KBest {
       Derivation const* d;
       explicit EdgeHandle(Derivation const* d) : d(d) {  }
 //      operator bool() const { return d->edge; }
-      operator Hypergraph::Edge const* () const { return d->edge; }
-//      Hypergraph::Edge const * operator ->() const { return d->edge; }
+      operator HG::Edge const* () const { return d->edge; }
+//      HG::Edge const * operator ->() const { return d->edge; }
     };
 
     EdgeHandle operator()(unsigned t,unsigned taili,EdgeHandle const& parent) const {
@@ -158,7 +158,7 @@ namespace KBest {
     // the yield is computed in LazyKthBest before the derivation is added to D
     // returns NULL if j refers to derivation numbers larger than the
     // antecedent structure define
-    Derivation* CreateDerivation(const Hypergraph::Edge& e, const SmallVectorInt& j) {
+    Derivation* CreateDerivation(const HG::Edge& e, const SmallVectorInt& j) {
       WeightType score = w(e);
       SparseVector<double> feats = e.feature_values_;
       for (int i = 0; i < e.Arity(); ++i) {
@@ -177,7 +177,7 @@ namespace KBest {
 
       const Hypergraph::Node& node = g.nodes_[v];
       for (unsigned i = 0; i < node.in_edges_.size(); ++i) {
-        const Hypergraph::Edge& edge = g.edges_[node.in_edges_[i]];
+        const HG::Edge& edge = g.edges_[node.in_edges_[i]];
         SmallVectorInt jv(edge.Arity(), 0);
         Derivation* d = CreateDerivation(edge, jv);
         assert(d);
diff --git a/decoder/oracle_bleu.h b/decoder/oracle_bleu.h
index b603e27a..d2c4715c 100644
--- a/decoder/oracle_bleu.h
+++ b/decoder/oracle_bleu.h
@@ -12,6 +12,7 @@
 #include "scorer.h"
 #include "hg.h"
 #include "ff_factory.h"
+#include "ffset.h"
 #include "ff_bleu.h"
 #include "sparse_vector.h"
 #include "viterbi.h"
@@ -26,7 +27,7 @@
 struct Translation {
   typedef std::vector<WordID> Sentence;
   Sentence sentence;
-  FeatureVector features;
+  SparseVector<double> features;
   Translation() {  }
   Translation(Hypergraph const& hg,WeightVector *feature_weights=0)
   {
@@ -57,14 +58,14 @@ struct Oracle {
   }
   // feature 0 will be the error rate in fear and hope
   // move toward hope
-  FeatureVector ModelHopeGradient() const {
-    FeatureVector r=hope.features-model.features;
+  SparseVector<double> ModelHopeGradient() const {
+    SparseVector<double> r=hope.features-model.features;
     r.set_value(0,0);
     return r;
   }
   // move toward hope from fear
-  FeatureVector FearHopeGradient() const {
-    FeatureVector r=hope.features-fear.features;
+  SparseVector<double> FearHopeGradient() const {
+    SparseVector<double> r=hope.features-fear.features;
     r.set_value(0,0);
     return r;
   }
diff --git a/decoder/program_options.h b/decoder/program_options.h
index 87afb320..3cd7649a 100644
--- a/decoder/program_options.h
+++ b/decoder/program_options.h
@@ -94,7 +94,7 @@ struct any_printer  : public boost::function<void (Ostream &,boost::any const&)>
   {}
 
   template <class T>
-  explicit any_printer(T const* tag) : F(typed_print<T>()) {
+  explicit any_printer(T const*) : F(typed_print<T>()) {
   }
 
   template <class T>
diff --git a/decoder/scfg_translator.cc b/decoder/scfg_translator.cc
index a978cfc2..3b43b586 100644
--- a/decoder/scfg_translator.cc
+++ b/decoder/scfg_translator.cc
@@ -15,13 +15,73 @@
 #include "tdict.h"
 #include "viterbi.h"
 #include "verbose.h"
+#include <tr1/unordered_map>
 
 #define foreach         BOOST_FOREACH
 #define reverse_foreach BOOST_REVERSE_FOREACH
 
 using namespace std;
+using namespace std::tr1;
 static bool printGrammarsUsed = false;
 
+struct GlueGrammar : public TextGrammar {
+  // read glue grammar from file
+  explicit GlueGrammar(const std::string& file);
+  GlueGrammar(const std::string& goal_nt, const std::string& default_nt, const unsigned int ctf_level=0);  // "S", "X"
+  virtual bool HasRuleForSpan(int i, int j, int distance) const;
+};
+
+struct PassThroughGrammar : public TextGrammar {
+  PassThroughGrammar(const Lattice& input, const std::string& cat, const unsigned int ctf_level=0);
+  virtual bool HasRuleForSpan(int i, int j, int distance) const;
+};
+
+GlueGrammar::GlueGrammar(const string& file) : TextGrammar(file) {}
+
+static void RefineRule(TRulePtr pt, const unsigned int ctf_level){
+  for (unsigned int i=0; i<ctf_level; ++i){
+    TRulePtr r(new TRule(*pt));
+    pt->fine_rules_.reset(new vector<TRulePtr>);
+    pt->fine_rules_->push_back(r);
+    pt = r;
+  }
+}
+
+GlueGrammar::GlueGrammar(const string& goal_nt, const string& default_nt, const unsigned int ctf_level) {
+  TRulePtr stop_glue(new TRule("[" + goal_nt + "] ||| [" + default_nt + ",1] ||| [1]"));
+  AddRule(stop_glue);
+  RefineRule(stop_glue, ctf_level);
+  TRulePtr glue(new TRule("[" + goal_nt + "] ||| [" + goal_nt + ",1] ["+ default_nt + ",2] ||| [1] [2] ||| Glue=1"));
+  AddRule(glue);
+  RefineRule(glue, ctf_level);
+}
+
+bool GlueGrammar::HasRuleForSpan(int i, int /* j */, int /* distance */) const {
+  return (i == 0);
+}
+
+PassThroughGrammar::PassThroughGrammar(const Lattice& input, const string& cat, const unsigned int ctf_level) {
+  unordered_set<WordID> ss;
+  for (int i = 0; i < input.size(); ++i) {
+    const vector<LatticeArc>& alts = input[i];
+    for (int k = 0; k < alts.size(); ++k) {
+      const int j = alts[k].dist2next + i;
+      const string& src = TD::Convert(alts[k].label);
+      if (ss.count(alts[k].label) == 0) {
+        TRulePtr pt(new TRule("[" + cat + "] ||| " + src + " ||| " + src + " ||| PassThrough=1"));
+        pt->a_.push_back(AlignmentPoint(0,0));
+        AddRule(pt);
+        RefineRule(pt, ctf_level);
+        ss.insert(alts[k].label);
+      }
+    }
+  }
+}
+
+bool PassThroughGrammar::HasRuleForSpan(int, int, int distance) const {
+  return (distance < 2);
+}
+
 struct SCFGTranslatorImpl {
   SCFGTranslatorImpl(const boost::program_options::variables_map& conf) :
       max_span_limit(conf["scfg_max_span_limit"].as<int>()),
diff --git a/decoder/tromble_loss.h b/decoder/tromble_loss.h
index 599a2d54..fde33100 100644
--- a/decoder/tromble_loss.h
+++ b/decoder/tromble_loss.h
@@ -28,7 +28,7 @@ class TrombleLossComputer : private boost::base_from_member<boost::scoped_ptr<Tr
 
  protected:
   virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
-                                     const Hypergraph::Edge& edge,
+                                     const HG::Edge& edge,
                                      const std::vector<const void*>& ant_contexts,
                                      SparseVector<double>* features,
                                      SparseVector<double>* estimated_features,
diff --git a/decoder/viterbi.cc b/decoder/viterbi.cc
index 1b9c6665..9e381ac6 100644
--- a/decoder/viterbi.cc
+++ b/decoder/viterbi.cc
@@ -139,8 +139,8 @@ inline bool close_enough(double a,double b,double epsilon)
     return diff<=epsilon*fabs(a) || diff<=epsilon*fabs(b);
 }
 
-FeatureVector ViterbiFeatures(Hypergraph const& hg,WeightVector const* weights,bool fatal_dotprod_disagreement) {
-  FeatureVector r;
+SparseVector<double> ViterbiFeatures(Hypergraph const& hg,WeightVector const* weights,bool fatal_dotprod_disagreement) {
+  SparseVector<double> r;
   const prob_t p = Viterbi<FeatureVectorTraversal>(hg, &r);
   if (weights) {
     double logp=log(p);
diff --git a/decoder/viterbi.h b/decoder/viterbi.h
index 03e961a2..a8a0ea7f 100644
--- a/decoder/viterbi.h
+++ b/decoder/viterbi.h
@@ -14,10 +14,10 @@ std::string viterbi_stats(Hypergraph const& hg, std::string const& name="forest"
 //TODO: make T a typename inside Traversal and WeightType a typename inside WeightFunction?
 // Traversal must implement:
 //  typedef T Result;
-//  void operator()(Hypergraph::Edge const& e,const vector<const Result*>& ants, Result* result) const;
+//  void operator()(HG::Edge const& e,const vector<const Result*>& ants, Result* result) const;
 // WeightFunction must implement:
 //  typedef prob_t Weight;
-//  Weight operator()(Hypergraph::Edge const& e) const;
+//  Weight operator()(HG::Edge const& e) const;
 template<class Traversal,class WeightFunction>
 typename WeightFunction::Weight Viterbi(const Hypergraph& hg,
                    typename Traversal::Result* result,
@@ -39,9 +39,9 @@ typename WeightFunction::Weight Viterbi(const Hypergraph& hg,
       *cur_node_best_weight = WeightType(1);
       continue;
     }
-    Hypergraph::Edge const* edge_best=0;
+    HG::Edge const* edge_best=0;
     for (unsigned j = 0; j < num_in_edges; ++j) {
-      const Hypergraph::Edge& edge = hg.edges_[cur_node.in_edges_[j]];
+      const HG::Edge& edge = hg.edges_[cur_node.in_edges_[j]];
       WeightType score = weight(edge);
       for (unsigned k = 0; k < edge.tail_nodes_.size(); ++k)
         score *= vit_weight[edge.tail_nodes_[k]];
@@ -51,7 +51,7 @@ typename WeightFunction::Weight Viterbi(const Hypergraph& hg,
       }
     }
     assert(edge_best);
-    Hypergraph::Edge const& edgeb=*edge_best;
+    HG::Edge const& edgeb=*edge_best;
     std::vector<const T*> antsb(edgeb.tail_nodes_.size());
     for (unsigned k = 0; k < edgeb.tail_nodes_.size(); ++k)
       antsb[k] = &vit_result[edgeb.tail_nodes_[k]];
@@ -98,7 +98,7 @@ prob_t Viterbi(const Hypergraph& hg,
 
 struct PathLengthTraversal {
   typedef int Result;
-  void operator()(const Hypergraph::Edge& edge,
+  void operator()(const HG::Edge& edge,
                   const std::vector<const int*>& ants,
                   int* result) const {
     (void) edge;
@@ -109,7 +109,7 @@ struct PathLengthTraversal {
 
 struct ESentenceTraversal {
   typedef std::vector<WordID> Result;
-  void operator()(const Hypergraph::Edge& edge,
+  void operator()(const HG::Edge& edge,
                   const std::vector<const Result*>& ants,
                   Result* result) const {
     edge.rule_->ESubstitute(ants, result);
@@ -118,7 +118,7 @@ struct ESentenceTraversal {
 
 struct ELengthTraversal {
   typedef int Result;
-  void operator()(const Hypergraph::Edge& edge,
+  void operator()(const HG::Edge& edge,
                   const std::vector<const int*>& ants,
                   int* result) const {
     *result = edge.rule_->ELength() - edge.rule_->Arity();
@@ -128,7 +128,7 @@ struct ELengthTraversal {
 
 struct FSentenceTraversal {
   typedef std::vector<WordID> Result;
-  void operator()(const Hypergraph::Edge& edge,
+  void operator()(const HG::Edge& edge,
                   const std::vector<const Result*>& ants,
                   Result* result) const {
     edge.rule_->FSubstitute(ants, result);
@@ -142,7 +142,7 @@ struct ETreeTraversal {
   const std::string space;
   const std::string right;
   typedef std::vector<WordID> Result;
-  void operator()(const Hypergraph::Edge& edge,
+  void operator()(const HG::Edge& edge,
                   const std::vector<const Result*>& ants,
                   Result* result) const {
     Result tmp;
@@ -162,7 +162,7 @@ struct FTreeTraversal {
   const std::string space;
   const std::string right;
   typedef std::vector<WordID> Result;
-  void operator()(const Hypergraph::Edge& edge,
+  void operator()(const HG::Edge& edge,
                   const std::vector<const Result*>& ants,
                   Result* result) const {
     Result tmp;
@@ -177,8 +177,8 @@ struct FTreeTraversal {
 };
 
 struct ViterbiPathTraversal {
-  typedef std::vector<Hypergraph::Edge const*> Result;
-  void operator()(const Hypergraph::Edge& edge,
+  typedef std::vector<HG::Edge const*> Result;
+  void operator()(const HG::Edge& edge,
                   std::vector<Result const*> const& ants,
                   Result* result) const {
     for (unsigned i = 0; i < ants.size(); ++i)
@@ -189,8 +189,8 @@ struct ViterbiPathTraversal {
 };
 
 struct FeatureVectorTraversal {
-  typedef FeatureVector Result;
-  void operator()(Hypergraph::Edge const& edge,
+  typedef SparseVector<double> Result;
+  void operator()(HG::Edge const& edge,
                   std::vector<Result const*> const& ants,
                   Result* result) const {
     for (unsigned i = 0; i < ants.size(); ++i)
@@ -210,6 +210,6 @@ int ViterbiELength(const Hypergraph& hg);
 int ViterbiPathLength(const Hypergraph& hg);
 
 /// if weights supplied, assert viterbi prob = features.dot(*weights) (exception if fatal, cerr warn if not).  return features (sum over all edges in viterbi derivation)
-FeatureVector ViterbiFeatures(Hypergraph const& hg,WeightVector const* weights=0,bool fatal_dotprod_disagreement=false);
+SparseVector<double> ViterbiFeatures(Hypergraph const& hg,WeightVector const* weights=0,bool fatal_dotprod_disagreement=false);
 
 #endif
diff --git a/dpmert/Jamfile b/dpmert/Jamfile
deleted file mode 100644
index bc4b079b..00000000
--- a/dpmert/Jamfile
+++ /dev/null
@@ -1,32 +0,0 @@
-import testing ;
-import lex ;
-import option ;
-
-lib dpmert : 
-  ces.cc
-  error_surface.cc
-  line_optimizer.cc
-  mert_geometry.cc
-  ..//utils
-  ..//mteval
-  ..//decoder
-  ../klm/lm//kenlm
-  ..//boost_program_options
-  : <include>.
-  : :
-  <library>..//utils
-  <library>..//mteval
-  <library>../klm/lm//kenlm
-  <library>..//boost_program_options
-  <include>.
-  ;
-
-all_tests [ glob *_test.cc ] : dpmert : <testing.arg>$(TOP)/dpmert/test_data ;
-
-exe sentserver : sentserver.c : <threading>multi ;
-exe sentclient : sentclient.c ;
-exe mr_dpmert_generate_mapper_input : mr_dpmert_generate_mapper_input.cc dpmert ..//boost_program_options ;
-exe mr_dpmert_map : mr_dpmert_map.cc dpmert ..//boost_program_options ;
-exe mr_dpmert_reduce : mr_dpmert_reduce.cc dpmert ..//boost_program_options ;
-
-alias programs : sentserver sentclient mr_dpmert_generate_mapper_input mr_dpmert_map mr_dpmert_reduce ;
diff --git a/dpmert/line_optimizer.cc b/dpmert/line_optimizer.cc
index 49443fbe..9cf33502 100644
--- a/dpmert/line_optimizer.cc
+++ b/dpmert/line_optimizer.cc
@@ -56,7 +56,10 @@ double LineOptimizer::LineOptimize(
 	//cerr << "NEW BEST: " << pos << "  (score=" << cur_best_score << ")\n";
       }
       // string xx = metric->DetailedScore(acc); cerr << "---- " << xx;
-      // cerr << "---- s=" << sco << "\n";
+#undef SHOW_ERROR_SURFACES
+#ifdef SHOW_ERROR_SURFACES
+      cerr << "x=" << seg.x << "\ts=" << sco << "\n";
+#endif
       last_boundary = seg.x;
     }
     // cerr << "x-boundary=" << seg.x << "\n";
diff --git a/dpmert/lo_test.cc b/dpmert/lo_test.cc
index 2daf87bb..95a08d3d 100644
--- a/dpmert/lo_test.cc
+++ b/dpmert/lo_test.cc
@@ -36,7 +36,7 @@ BOOST_AUTO_TEST_CASE( TestCheckNaN) {
   double x = 0;
   double y = 0;
   double z = x / y;
-  BOOST_CHECK_EQUAL(true, isnan(z));
+  BOOST_CHECK_EQUAL(true, std::isnan(z));
 }
 
 BOOST_AUTO_TEST_CASE(TestConvexHull) {
diff --git a/dtrain/Makefile.am b/dtrain/Makefile.am
index 64fef489..ca9581f5 100644
--- a/dtrain/Makefile.am
+++ b/dtrain/Makefile.am
@@ -1,7 +1,7 @@
 bin_PROGRAMS = dtrain
 
 dtrain_SOURCES = dtrain.cc score.cc
-dtrain_LDADD   = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a ../klm/lm/libklm.a ../klm/util/libklm_util.a -lz
+dtrain_LDADD   = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/klm/search/libksearch.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a ../klm/lm/libklm.a ../klm/util/libklm_util.a -lz
 
 AM_CPPFLAGS = -W -Wall -Wno-sign-compare -I$(top_srcdir)/utils -I$(top_srcdir)/decoder -I$(top_srcdir)/mteval
 
diff --git a/dtrain/parallelize.rb b/dtrain/parallelize.rb
index e88d9eef..1d277ff6 100755
--- a/dtrain/parallelize.rb
+++ b/dtrain/parallelize.rb
@@ -7,7 +7,7 @@ if ARGV.size != 5
   exit
 end
 
-dtrain_bin = '/home/pks/mt/cdec-dtrain/dtrain/dtrain_local_new_f'
+dtrain_bin = '/home/pks/bin/dtrain_local'
 ruby       = '/usr/bin/ruby'
 lplp_rb    = '/home/pks/mt/cdec-dtrain/dtrain/hstreaming/lplp.rb'
 lplp_args  = 'l2 select_k 100000'
diff --git a/example_extff/Makefile.am b/example_extff/Makefile.am
new file mode 100644
index 00000000..ac2694ca
--- /dev/null
+++ b/example_extff/Makefile.am
@@ -0,0 +1,5 @@
+AM_CPPFLAGS = -DBOOST_TEST_DYN_LINK -W -Wno-sign-compare $(GTEST_CPPFLAGS) -I.. -I../mteval -I../utils -I../klm -I../decoder
+
+lib_LTLIBRARIES = libff_example.la
+libff_example_la_SOURCES = ff_example.cc
+libff_example_la_LDFLAGS = -version-info 1:0:0 -module
diff --git a/example_extff/README.md b/example_extff/README.md
new file mode 100644
index 00000000..f2aba487
--- /dev/null
+++ b/example_extff/README.md
@@ -0,0 +1,8 @@
+This is an example of an _external_ feature function which is loaded as a dynamically linked library at run time to compute feature functions over derivations in a hypergraph. To load feature external feature functions, you can specify them in your `cdec.ini` configuration file as follows:
+
+	feature_function=External /path/to/libmy_feature.so
+
+Any extra options are passed to the external library.
+
+*Note*: the build system uses [GNU Libtool](http://www.gnu.org/software/libtool/) to create the shared library. This may be placed in a hidden directory called `./libs`.
+
diff --git a/example_extff/ff_example.cc b/example_extff/ff_example.cc
new file mode 100644
index 00000000..4e478ecd
--- /dev/null
+++ b/example_extff/ff_example.cc
@@ -0,0 +1,58 @@
+#include "ff.h"
+#include <iostream>
+#include <sstream>
+
+#include "hg.h"
+
+using namespace std;
+
+// example of a "stateful" feature made available as an external library
+// This feature looks nodes and their daughters and fires an indicator based
+// on the arities of the rules involved.
+// (X (X a) b (X c)) - this is a 2 arity parent with children of 0 and 0 arity
+//                     so you get MAF_2_0_0=1
+class ParentChildrenArityFeatures : public FeatureFunction {
+ public:
+  ParentChildrenArityFeatures(const string& param) : fids(16, vector<int>(256, -1)) {
+    SetStateSize(1); // number of bytes extra state required by this Feature
+  }
+  virtual void FinalTraversalFeatures(const void* context,
+                                      SparseVector<double>* features) const {
+    // Goal always is arity 1, so there's no discriminative value of
+    // computing a feature
+  }
+ protected:
+  virtual void TraversalFeaturesImpl(const SentenceMetadata& smeta,
+                                     const Hypergraph::Edge& edge,
+                                     const std::vector<const void*>& ant_contexts,
+                                     FeatureVector* features,
+                                     FeatureVector* estimated_features,
+                                     void* context) const {
+    unsigned child_arity_code = 0;
+    for (unsigned j = 0; j < ant_contexts.size(); ++j) {
+      child_arity_code <<= 4;
+      child_arity_code |= *reinterpret_cast<const unsigned char*>(ant_contexts[j]);
+    }
+    int& fid = fids[edge.Arity()][child_arity_code]; // reference!
+    if (fid < 0) {
+      ostringstream feature_string;
+      feature_string << "MAF_" << edge.Arity();
+      for (unsigned j = 0; j < ant_contexts.size(); ++j)
+        feature_string << '_' << 
+          static_cast<int>(*reinterpret_cast<const unsigned char*>(ant_contexts[j]));
+      fid = FD::Convert(feature_string.str());
+    }
+    features->set_value(fid, 1.0);
+    *reinterpret_cast<unsigned char*>(context) = edge.Arity(); // save state
+  }
+ private:
+  mutable vector<vector<int> > fids;
+};
+
+// IMPORTANT: this function must be implemented by any external FF library
+// if your library has multiple features, you can use str to configure things
+extern "C" FeatureFunction* create_ff(const string& str) {
+  return new ParentChildrenArityFeatures(str);
+}
+
+
diff --git a/extools/Makefile.am b/extools/Makefile.am
deleted file mode 100644
index ee363264..00000000
--- a/extools/Makefile.am
+++ /dev/null
@@ -1,30 +0,0 @@
-bin_PROGRAMS = \
-  extractor \
-  mr_stripe_rule_reduce \
-  filter_grammar \
-  featurize_grammar \
-  extractor_monolingual
-
-noinst_PROGRAMS =
-
-sg_lexer.cc: sg_lexer.l
-	$(LEX) -s -CF -8 -o$@ $<
-
-filter_grammar_SOURCES = filter_grammar.cc extract.cc sentence_pair.cc striped_grammar.cc sg_lexer.cc
-filter_grammar_LDADD = $(top_srcdir)/utils/libutils.a -lz
-#filter_grammar_LDFLAGS = -all-static
-
-featurize_grammar_SOURCES = featurize_grammar.cc extract.cc sentence_pair.cc sg_lexer.cc striped_grammar.cc
-featurize_grammar_LDADD = $(top_srcdir)/utils/libutils.a -lz
-
-mr_stripe_rule_reduce_SOURCES = mr_stripe_rule_reduce.cc extract.cc sentence_pair.cc striped_grammar.cc sg_lexer.cc
-mr_stripe_rule_reduce_LDADD = $(top_srcdir)/utils/libutils.a -lz
-
-extractor_SOURCES = sentence_pair.cc extract.cc extractor.cc striped_grammar.cc
-extractor_LDADD = $(top_srcdir)/utils/libutils.a -lz
-
-extractor_monolingual_SOURCES = extractor_monolingual.cc
-extractor_monolingual_LDADD = $(top_srcdir)/utils/libutils.a -lz
-
-AM_CPPFLAGS = -W -Wall -Wno-sign-compare $(GTEST_CPPFLAGS) -I$(top_srcdir)/utils
-
diff --git a/extools/README b/extools/README
deleted file mode 100644
index af91ce79..00000000
--- a/extools/README
+++ /dev/null
@@ -1,32 +0,0 @@
-
-Categories have the format i-j:CAT where i and j are the indices of the spaces
-between words in the TARGET language.  For example, slash categories can be written:
-
-  the blue house
-  0-1:DT 1-2:JJ 2-3:NN 1-3:NBAR 0-2:NP/NN 0-3:NP
-
-
-You may multiply label each span, e.g.
-
-  NP
-   |
- NBAR
-   |
-  NN
-   |
- John
-  0-1:NP 0-1:NBAR 0-1:NP
-
-However, this may result in a very large number of rules being extracted.
-
-
-****
-* Filtering and Scoring of Unscored and Unfiltered Grammars
-****
-
-Take the unfiltered grammar, and a test set, and run:
-./filter_grammar <test set> < unfiltered.grammar > filter.grammar
-
-Then, to score the new filtered grammar, run:
-./score_grammar <alignment> < filtered.grammar > scored.grammar
-
diff --git a/extools/coarsen_grammar.pl b/extools/coarsen_grammar.pl
deleted file mode 100755
index f2dd6689..00000000
--- a/extools/coarsen_grammar.pl
+++ /dev/null
@@ -1,133 +0,0 @@
-#!/usr/bin/perl
-
-# dumb grammar coarsener that maps every nonterminal to X (except S).
-
-use strict;
-
-unless (@ARGV > 1){ 
-  die "Usage: $0 <weight file> <grammar file> [<grammar file> ... <grammar file>] \n";
-}
-my $weight_file = shift @ARGV;
-
-$ENV{"LC_ALL"} = "C";
-local(*GRAMMAR, *OUT_GRAMMAR, *WEIGHTS);
-
-my %weights;
-unless (open(WEIGHTS, $weight_file)) {die "Could not open weight file $weight_file\n" }
-while (<WEIGHTS>){
-  if (/(.+) (.+)$/){
-    $weights{$1} = $2;
-  } 
-}
-close(WEIGHTS);
-unless (keys(%weights)){
-  die "Could not find any PhraseModel features in weight file (perhaps you specified the wrong file?)\n\n".
-    "Usage: $0 <weight file> <grammar file> [<grammar file> ... <grammar file>] \n";
-}
-
-sub cleanup_and_die;
-$SIG{INT} = "cleanup_and_die";
-$SIG{TERM} = "cleanup_and_die"; 
-$SIG{HUP} = "cleanup_and_die";
-
-open(OUT_GRAMMAR, ">grammar.tmp");
-while (my $grammar_file = shift @ARGV){
-  unless (open(GRAMMAR, $grammar_file)) {die "Could not open grammar file $grammar_file\n"}
-  while (<GRAMMAR>){
-    if (/^((.*\|{3}){3})(.*)$/){
-      my $rule = $1;
-      my $rest = $3;
-      my $coarse_rule = $rule;
-      $coarse_rule =~ s/\[X[^\],]*/[X/g;
-      print OUT_GRAMMAR "$coarse_rule $rule $rest\n";
-    } else {
-      die "Unrecognized rule format: $_\n";
-    }
-  }
-  close(GRAMMAR);
-}
-close(OUT_GRAMMAR);
-
-`sort grammar.tmp > grammar.tmp.sorted`;
-sub dump_rules;
-sub compute_score;
-unless (open(GRAMMAR, "grammar.tmp.sorted")){ die "Something went wrong; could not open intermediate file grammar.tmp.sorted\n"};
-my $prev_coarse_rule = "";
-my $best_features = "";
-my $best_score = 0;
-my @rules = ();
-while (<GRAMMAR>){
-  if (/^\s*((\S.*\|{3}\s*){3})((\S.*\|{3}\s*){3})(.*)$/){
-    my $coarse_rule = $1;
-    my $fine_rule = $3;
-    my $features = $5;  # This code does not correctly handle rules with other info (e.g. alignments)
-    if ($coarse_rule eq $prev_coarse_rule){
-      my $score = compute_score($features, %weights);
-      if ($score > $best_score){
-        $best_score = $score;
-        $best_features = $features;
-      }
-    } else {
-      dump_rules($prev_coarse_rule, $best_features, @rules);
-      $prev_coarse_rule = $coarse_rule;
-      $best_features = $features;
-      $best_score = compute_score($features, %weights);
-      @rules = ();
-    }
-    push(@rules, "$fine_rule$features\n");
-  } else {
-    die "Something went wrong during grammar projection: $_\n";
-  }
-}
-dump_rules($prev_coarse_rule, $best_features, @rules);
-close(GRAMMAR);
-cleanup();
-
-sub compute_score {
-  my($features, %weights) = @_;
-  my $score = 0;
-  if ($features =~ s/^\s*(\S.*\S)\s*$/$1/) { 
-    my @features = split(/\s+/, $features);
-    my $pm=0;
-    for my $feature (@features) {
-      my $feature_name; 
-      my $feature_val;
-      if ($feature =~ /(.*)=(.*)/){
-        $feature_name = $1;
-        $feature_val= $2;
-      } else {
-        $feature_name = "PhraseModel_" . $pm;
-        $feature_val= $feature;
-      }
-      $pm++;
-      if ($weights{$feature_name}){
-        $score += $weights{$feature_name} * $feature_val;
-      } 
-    }  
-  } else {
-    die "Unexpected feature value format: $features\n";
-  }
-  return $score;
-}
-
-sub dump_rules {
-  my($coarse_rule, $coarse_rule_scores, @fine_rules) = @_;
-  unless($coarse_rule){ return; }
-  print "$coarse_rule $coarse_rule_scores\n";
-  for my $rule (@fine_rules){
-    print "\t$rule";
-  }
-}
-
-sub cleanup_and_die {
-  cleanup();
-  die "\n";
-}
-
-sub cleanup {
- `rm -rf grammar.tmp grammar.tmp.sorted`;
-}
-
-
-
-
diff --git a/extools/extract.cc b/extools/extract.cc
deleted file mode 100644
index 49542fed..00000000
--- a/extools/extract.cc
+++ /dev/null
@@ -1,336 +0,0 @@
-#include "extract.h"
-
-#include <queue>
-#include <vector>
-#include <utility>
-#include <tr1/unordered_map>
-#include <set>
-#include <boost/tuple/tuple_comparison.hpp>
-
-#include <boost/functional/hash.hpp>
-#include <boost/tuple/tuple.hpp>
-
-#include "sentence_pair.h"
-#include "tdict.h"
-#include "wordid.h"
-#include "array2d.h"
-
-using namespace std;
-using namespace boost;
-using std::tr1::unordered_map;
-using boost::tuple;
-
-namespace {
-  inline bool IsWhitespace(char c) { return c == ' ' || c == '\t'; }
-
-  inline void SkipWhitespace(const char* buf, int* ptr) {
-    while (buf[*ptr] && IsWhitespace(buf[*ptr])) { ++(*ptr); }
-  }
-}
-
-Extract::RuleObserver::~RuleObserver() {
-  cerr << "Rules extracted: " << count << endl;
-}
-
-void Extract::ExtractBasePhrases(const int max_base_phrase_size,
-                        const AnnotatedParallelSentence& sentence,
-                        vector<ParallelSpan>* phrases) {
-  phrases->clear();
-
-  vector<pair<int,int> > f_spans(sentence.f_len, pair<int,int>(sentence.e_len, 0));
-  vector<pair<int,int> > e_spans(sentence.e_len, pair<int,int>(sentence.f_len, 0));
-  // for each alignment point in e, precompute the minimal consistent phrases in f
-  // for each alignment point in f, precompute the minimal consistent phrases in e
-  for (int i = 0; i < sentence.f_len; ++i) {
-    for (int j = 0; j < sentence.e_len; ++j) {
-      if (sentence.aligned(i,j)) {
-        if (j < f_spans[i].first) f_spans[i].first = j;
-        f_spans[i].second = j+1;
-        if (i < e_spans[j].first) e_spans[j].first = i;
-        e_spans[j].second = i+1;
-      }
-    }
-  }
-
-  for (int i1 = 0; i1 < sentence.f_len; ++i1) {
-    if (sentence.f_aligned[i1] == 0) continue;
-    int j1 = sentence.e_len;
-    int j2 = 0;
-    const int i_limit = min(sentence.f_len, i1 + max_base_phrase_size);
-    for (int i2 = i1 + 1; i2 <= i_limit; ++i2) {
-      if (sentence.f_aligned[i2-1] == 0) continue;
-      // cerr << "F has aligned span " << i1 << " to " << i2 << endl;
-      j1 = min(j1, f_spans[i2-1].first);
-      j2 = max(j2, f_spans[i2-1].second);
-      if (j1 >= j2) continue;
-      if (j2 - j1 > max_base_phrase_size) continue;
-      int condition = 0;
-      for (int j = j1; j < j2; ++j) {
-        if (e_spans[j].first < i1) { condition = 1; break; }
-        if (e_spans[j].second > i2) { condition = 2; break; }
-      }
-      if (condition == 1) break;
-      if (condition == 2) continue;
-      // category types added later!
-      phrases->push_back(ParallelSpan(i1, i2, j1, j2));
-      // cerr << i1 << " " << i2 << " : " << j1 << " " << j2 << endl;
-    }
-  }
-}
-
-void Extract::LoosenPhraseBounds(const AnnotatedParallelSentence& sentence,
-                                 const int max_base_phrase_size,
-                                 vector<ParallelSpan>* phrases) {
-  const int num_phrases = phrases->size();
-  map<int, map<int, map<int, map<int, bool> > > > marker;
-  for (int i = 0; i < num_phrases; ++i) {
-    const ParallelSpan& cur = (*phrases)[i];
-    marker[cur.i1][cur.i2][cur.j1][cur.j2] = true;
-  }
-  for (int i = 0; i < num_phrases; ++i) {
-    const ParallelSpan& cur = (*phrases)[i];
-    const int i1_max = cur.i1;
-    const int i2_min = cur.i2;
-    const int j1_max = cur.j1;
-    const int j2_min = cur.j2;
-    int i1_min = i1_max;
-    while (i1_min > 0 && sentence.f_aligned[i1_min-1] == 0) { --i1_min; }
-    int j1_min = j1_max;
-    while (j1_min > 0 && sentence.e_aligned[j1_min-1] == 0) { --j1_min; }
-    int i2_max = i2_min;
-    while (i2_max < sentence.f_len && sentence.f_aligned[i2_max] == 0) { ++i2_max; }
-    int j2_max = j2_min;
-    while (j2_max < sentence.e_len && sentence.e_aligned[j2_max] == 0) { ++j2_max; }
-    for (int i1 = i1_min; i1 <= i1_max; ++i1) {
-      const int ilim = min(i2_max, i1 + max_base_phrase_size);
-      for (int i2 = max(i1+1,i2_min); i2 <= ilim; ++i2) {
-        for (int j1 = j1_min; j1 <= j1_max; ++j1) {
-          const int jlim = std::min(j2_max, j1 + max_base_phrase_size);
-          for (int j2 = std::max(j1+1, j2_min); j2 <= jlim; ++j2) {
-            bool& seen = marker[i1][i2][j1][j2];
-            if (!seen)
-              phrases->push_back(ParallelSpan(i1,i2,j1,j2));
-            seen = true;
-          }
-        }
-      }
-    }
-  }
-}
-
-template <typename K, typename V>
-void
-lookup_and_append(const map<K, V> &dict, const K &key, V &output)
-{
-    typename map<K, V>::const_iterator found = dict.find(key);
-    if (found != dict.end())
-        copy(found->second.begin(), found->second.end(), back_inserter(output));
-}
-
-// this uses the TARGET span (i,j) to annotate phrases, will copy
-// phrases if there is more than one annotation.
-// TODO: support source annotation
-void Extract::AnnotatePhrasesWithCategoryTypes(const WordID default_cat,
-                                      const map< boost::tuple<short,short,short,short>, vector<WordID> > &types,
-                                      vector<ParallelSpan>* phrases) {
-  const int num_unannotated_phrases = phrases->size();
-  // have to use num_unannotated_phrases since we may grow the vector
-  for (int i = 0; i < num_unannotated_phrases; ++i) {
-    ParallelSpan& phrase = (*phrases)[i];
-    vector<WordID> cats;
-    lookup_and_append(types, boost::make_tuple(phrase.i1, phrase.i2, phrase.j1, phrase.j2), cats);
-    lookup_and_append(types, boost::make_tuple((short)-1, (short)-1, phrase.j1, phrase.j2), cats);
-    lookup_and_append(types, boost::make_tuple(phrase.i1, phrase.i2, (short)-1, (short)-1), cats);
-    if (cats.empty() && default_cat != 0) {
-      cats = vector<WordID>(1, default_cat);
-    }
-    if (cats.empty()) {
-      cerr << "ERROR span " << phrase.i1 << "," << phrase.i2 << "-"
-           << phrase.j1 << "," << phrase.j2 << " has no type. "
-              "Did you forget --default_category?\n";
-    }
-    phrase.cat = cats[0];
-    for (int ci = 1; ci < cats.size(); ++ci) {
-      ParallelSpan new_phrase = phrase;
-      new_phrase.cat = cats[ci];
-      phrases->push_back(new_phrase);
-    }
-  }
-}
-
-// a partially complete (f-side) of a rule
-struct RuleItem {
-  vector<ParallelSpan> f;
-  int i,j,syms,vars;
-  explicit RuleItem(int pi) : i(pi), j(pi), syms(), vars() {}
-  void Extend(const WordID& fword) {
-    f.push_back(ParallelSpan(fword));
-    ++j;
-    ++syms;
-  }
-  void Extend(const ParallelSpan& subphrase) {
-    f.push_back(subphrase);
-    j += subphrase.i2 - subphrase.i1;
-    ++vars;
-    ++syms;
-  }
-  bool RuleFEndsInVariable() const {
-    if (f.size() > 0) {
-      return f.back().IsVariable();
-    } else { return false; }
-  }
-};
-
-void Extract::ExtractConsistentRules(const AnnotatedParallelSentence& sentence,
-                          const vector<ParallelSpan>& phrases,
-                          const int max_vars,
-                          const int max_syms,
-                          const bool permit_adjacent_nonterminals,
-                          const bool require_aligned_terminal,
-                          RuleObserver* observer,
-                          vector<WordID>* all_cats) {
-  const char bkoff_mrkr = '_';
-  queue<RuleItem> q;  // agenda for BFS
-  int max_len = -1;
-  unordered_map<pair<short, short>, vector<ParallelSpan>, boost::hash<pair<short, short> > > fspans;
-  vector<vector<ParallelSpan> > spans_by_start(sentence.f_len);
-  set<int> starts;
-  WordID bkoff;
-  for (int i = 0; i < phrases.size(); ++i) {
-    fspans[make_pair(phrases[i].i1,phrases[i].i2)].push_back(phrases[i]);
-    max_len = max(max_len, phrases[i].i2 - phrases[i].i1);
-    // have we already added a rule item starting at phrases[i].i1?
-    if (starts.insert(phrases[i].i1).second)
-      q.push(RuleItem(phrases[i].i1));
-    spans_by_start[phrases[i].i1].push_back(phrases[i]);
-  }
-  starts.clear();
-  vector<pair<int,int> > next_e(sentence.e_len);
-  vector<WordID> cur_rhs_f, cur_rhs_e;
-  vector<pair<short, short> > cur_terminal_align;
-  vector<int> cur_es, cur_fs;
-  while(!q.empty()) {
-    const RuleItem& rule = q.front();
-
-    // extend the partial rule
-    if (rule.j < sentence.f_len && (rule.j - rule.i) < max_len && rule.syms < max_syms) {
-      RuleItem ew = rule;
-
-      // extend with a word
-      ew.Extend(sentence.f[ew.j]);
-      q.push(ew);
-
-      // with variables
-      if (rule.vars < max_vars &&
-          !spans_by_start[rule.j].empty() &&
-          ((!rule.RuleFEndsInVariable()) || permit_adjacent_nonterminals)) {
-        const vector<ParallelSpan>& sub_phrases = spans_by_start[rule.j];
-        for (int it = 0; it < sub_phrases.size(); ++it) {
-          if (sub_phrases[it].i2 - sub_phrases[it].i1 + rule.j - rule.i <= max_len) {
-            RuleItem ev = rule;
-            ev.Extend(sub_phrases[it]);
-            q.push(ev);
-            assert(ev.j <= sentence.f_len);
-          }
-        }
-      }
-    }
-    // determine if rule is consistent
-    if (rule.syms > 0 &&
-        fspans.count(make_pair(rule.i,rule.j)) &&
-        (!rule.RuleFEndsInVariable() || rule.syms > 1)) {
-      const vector<ParallelSpan>& orig_spans = fspans[make_pair(rule.i,rule.j)];
-      for (int s = 0; s < orig_spans.size(); ++s) {
-        const ParallelSpan& orig_span = orig_spans[s];
-        const WordID lhs = orig_span.cat;
-        for (int j = orig_span.j1; j < orig_span.j2; ++j) next_e[j].first = -1;
-        int nt_index_e = 0;
-        for (int i = 0; i < rule.f.size(); ++i) {
-          const ParallelSpan& cur = rule.f[i];
-          if (cur.IsVariable())
-            next_e[cur.j1] = pair<int,int>(cur.j2, ++nt_index_e);
-        }
-        cur_rhs_f.clear();
-        cur_rhs_e.clear();
-        cur_terminal_align.clear();
-        cur_fs.clear();
-        cur_es.clear();
-
-        const int elen = orig_span.j2 - orig_span.j1;
-        vector<int> isvar(elen, 0);
-        int fbias = rule.i;
-        bool bad_rule = false;
-        bool has_aligned_terminal = false;
-        for (int i = 0; i < rule.f.size(); ++i) {
-          const ParallelSpan& cur = rule.f[i];
-          cur_rhs_f.push_back(cur.cat);
-          if (cur.cat > 0) {   // terminal
-            if (sentence.f_aligned[fbias + i]) has_aligned_terminal = true;
-            cur_fs.push_back(fbias + i);
-          } else {             // non-terminal
-            int subj1 = cur.j1 - orig_span.j1;
-            int subj2 = cur.j2 - orig_span.j1;
-            if (subj1 < 0 || subj2 > elen) { bad_rule = true; break; }
-            for (int j = subj1; j < subj2 && !bad_rule; ++j) {
-              int& isvarj = isvar[j];
-              isvarj = true;
-            }
-            if (bad_rule) break;
-            cur_fs.push_back(-1);
-            fbias += cur.i2 - cur.i1 - 1;
-          }
-        }
-        if (require_aligned_terminal && !has_aligned_terminal) bad_rule = true;
-        if (!bad_rule) {
-          for (int j = orig_span.j1; j < orig_span.j2; ++j) {
-            if (next_e[j].first < 0) {
-              cur_rhs_e.push_back(sentence.e[j]);
-              cur_es.push_back(j);
-            } else {
-              cur_rhs_e.push_back(1 - next_e[j].second);  // next_e[j].second is NT gap index
-              cur_es.push_back(-1);
-              j = next_e[j].first - 1;
-            }
-          }
-          for (short i = 0; i < cur_fs.size(); ++i)
-            if (cur_fs[i] >= 0)
-              for (short j = 0; j < cur_es.size(); ++j)
-                if (cur_es[j] >= 0 && sentence.aligned(cur_fs[i],cur_es[j]))
-                  cur_terminal_align.push_back(make_pair(i,j));
-          //observer->CountRule(lhs, cur_rhs_f, cur_rhs_e, cur_terminal_align);
-          
-          if(!all_cats->empty()) {
-            //produce the backoff grammar if the category wordIDs are available
-          for (int i = 0; i < cur_rhs_f.size(); ++i) {
-            if(cur_rhs_f[i] < 0) {
-              //cerr << cur_rhs_f[i] << ": (cats,f) |" << TD::Convert(-cur_rhs_f[i]) << endl;
-              string nonterm = TD::Convert(-cur_rhs_f[i]);
-              nonterm+=bkoff_mrkr;
-              bkoff = -TD::Convert(nonterm);
-              cur_rhs_f[i]=bkoff;
-              /*vector<WordID> rhs_f_bkoff;
-              vector<WordID> rhs_e_bkoff;
-              vector<pair<short,short> > bkoff_align;
-              bkoff_align.clear();
-              bkoff_align.push_back(make_pair(0,0));
-              
-              for (int cat = 0; cat < all_cats->size(); ++cat) {
-                rhs_f_bkoff.clear();
-                rhs_e_bkoff.clear();
-                rhs_f_bkoff.push_back(-(*all_cats)[cat]);
-                rhs_e_bkoff.push_back(0);
-                observer->CountRule(bkoff,rhs_f_bkoff,rhs_e_bkoff,bkoff_align);
-                
-              }*/
-            }
-          }
-           
-          } 
-          observer->CountRule(lhs, cur_rhs_f, cur_rhs_e, cur_terminal_align);
-        }
-      }
-    }
-    q.pop();
-  }
-}
-
diff --git a/extools/extract.h b/extools/extract.h
deleted file mode 100644
index e9ea5e65..00000000
--- a/extools/extract.h
+++ /dev/null
@@ -1,94 +0,0 @@
-#ifndef _EXTRACT_H_
-#define _EXTRACT_H_
-
-#include <iostream>
-#include <utility>
-#include <vector>
-#include <boost/tuple/tuple.hpp>
-#include "array2d.h"
-#include "wordid.h"
-#include "sparse_vector.h"
-
-struct AnnotatedParallelSentence;
-
-// usually represents a consistent phrase, which may
-// be annotated with a type (cat)
-// inside the rule extractor, this class is also used to represent a word
-// in a partial rule.
-struct ParallelSpan {
-  // i1 = i of f side
-  // i2 = j of f side
-  // j1 = i of e side
-  // j2 = j of e side
-  short i1,i2,j1,j2;
-  // cat is set by AnnotatePhrasesWithCategoryTypes, otherwise it's 0
-  WordID cat;  // category type of span (also overloaded by RuleItem class
-               //                        to be a word ID)
-  ParallelSpan() : i1(-1), i2(-1), j1(-1), j2(-1), cat() {}
-  // used by Rule class to represent a terminal symbol:
-  explicit ParallelSpan(WordID w) : i1(-1), i2(-1), j1(-1), j2(-1), cat(w) {}
-  ParallelSpan(int pi1, int pi2, int pj1, int pj2) : i1(pi1), i2(pi2), j1(pj1), j2(pj2), cat() {}
-  ParallelSpan(int pi1, int pi2, int pj1, int pj2, WordID c) : i1(pi1), i2(pi2), j1(pj1), j2(pj2), cat(c) {}
-
-  // ParallelSpan is used in the Rule class where it is
-  // overloaded to also represent terminal symbols
-  inline bool IsVariable() const { return i1 != -1; }
-};
-
-// rule extraction logic lives here. this has no data, it's just got
-// static member functions.
-struct Extract {
-  // RuleObserver's CountRule is called for each rule extracted
-  // implement CountRuleImpl to do things like count the rules,
-  // write them to a file, etc.
-  struct RuleObserver {
-    RuleObserver() : count() {}
-    virtual void CountRule(WordID lhs,
-                           const std::vector<WordID>& rhs_f,
-                           const std::vector<WordID>& rhs_e,
-                           const std::vector<std::pair<short, short> >& fe_terminal_alignments) {
-      ++count;
-      CountRuleImpl(lhs, rhs_f, rhs_e, fe_terminal_alignments);
-    }
-    virtual ~RuleObserver();
-
-   protected:
-    virtual void CountRuleImpl(WordID lhs,
-                           const std::vector<WordID>& rhs_f,
-                           const std::vector<WordID>& rhs_e,
-                           const std::vector<std::pair<short, short> >& fe_terminal_alignments) = 0;
-   private:
-    int count;
-  };
-
-  // given a set of "tight" phrases and the aligned sentence they were
-  // extracted from, "loosen" them
-  static void LoosenPhraseBounds(const AnnotatedParallelSentence& sentence,
-                                 const int max_base_phrase_size,
-                                 std::vector<ParallelSpan>* phrases);
-
-  // extract all consistent phrase pairs, up to size max_base_phrase_size
-  // (on the source side). these phrases will be "tight".
-  static void ExtractBasePhrases(const int max_base_phrase_size,
-                        const AnnotatedParallelSentence& sentence,
-                        std::vector<ParallelSpan>* phrases);
-
-  // this uses the TARGET span (i,j) to annotate phrases, will copy
-  // phrases if there is more than one annotation.
-  static void AnnotatePhrasesWithCategoryTypes(const WordID default_cat,
-                                      const std::map< boost::tuple<short,short,short,short>, std::vector<WordID> > &types,
-                                      std::vector<ParallelSpan>* phrases);
-
-  // use the Chiang (2007) extraction logic to extract consistent subphrases
-  // observer->CountRule is called once for each rule extracted
-  static void ExtractConsistentRules(const AnnotatedParallelSentence& sentence,
-                          const std::vector<ParallelSpan>& phrases,
-                          const int max_vars,
-                          const int max_syms,
-                          const bool permit_adjacent_nonterminals,
-                          const bool require_aligned_terminal,
-                          RuleObserver* observer,
-                          std::vector<WordID>* all_cats);
-};
-
-#endif
diff --git a/extools/extractor.cc b/extools/extractor.cc
deleted file mode 100644
index 1e4154ef..00000000
--- a/extools/extractor.cc
+++ /dev/null
@@ -1,439 +0,0 @@
-#include <iostream>
-#include <vector>
-#include <utility>
-#include <tr1/unordered_map>
-
-#include <boost/functional/hash.hpp>
-#include <boost/program_options.hpp>
-#include <boost/program_options/variables_map.hpp>
-#include <boost/lexical_cast.hpp>
-
-#include "sparse_vector.h"
-#include "sentence_pair.h"
-#include "extract.h"
-#include "tdict.h"
-#include "fdict.h"
-#include "wordid.h"
-#include "array2d.h"
-#include "filelib.h"
-#include "striped_grammar.h"
-
-using namespace std;
-using namespace std::tr1;
-namespace po = boost::program_options;
-
-static const size_t MAX_LINE_LENGTH = 100000;
-WordID kBOS, kEOS, kDIVIDER, kGAP, kSPLIT;
-int kCOUNT;
-
-void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
-  po::options_description opts("Configuration options");
-  opts.add_options()
-        ("input,i", po::value<string>()->default_value("-"), "Input file")
-        ("default_category,d", po::value<string>(), "Default span type (use X for 'Hiero')")
-        ("x_cdyer_pos,x", "Extract monolingual POS contexts (cdyer experimental)")
-        ("loose", "Use loose phrase extraction heuristic for base phrases")
-        ("base_phrase,B", "Write base phrases")
-        ("base_phrase_spans", "Write base sentences and phrase spans")
-        ("phrase_language", po::value<string>()->default_value("target"), "Extract phrase strings in source, target or both languages")
-        ("context_language", po::value<string>()->default_value("target"), "Extract context strings in source, target or both languages")
-        ("bidir,b", "Extract bidirectional rules (for computing p(f|e) in addition to p(e|f))")
-        ("combiner_size,c", po::value<size_t>()->default_value(800000), "Number of unique items to store in cache before writing rule counts. Set to 1 to disable cache. Set to 0 for no limit.")
-        ("silent", "Write nothing to stderr except errors")
-        ("phrase_context,C", "Write base phrase contexts")
-        ("phrase_context_size,S", po::value<int>()->default_value(2), "Use this many words of context on left and write when writing base phrase contexts")
-        ("max_base_phrase_size,L", po::value<int>()->default_value(10), "Maximum starting phrase size")
-        ("max_syms,l", po::value<int>()->default_value(5), "Maximum number of symbols in final phrase size")
-        ("max_vars,v", po::value<int>()->default_value(2), "Maximum number of nonterminal variables in final phrase size")
-        ("permit_adjacent_nonterminals,A", "Permit adjacent nonterminals in source side of rules")
-        ("no_required_aligned_terminal,n", "Do not require an aligned terminal")
-        ("topics,t", po::value<int>()->default_value(50), "Number of categories assigned during clustering")
-        ("backoff,g","Produce a backoff grammar")
-        ("help,h", "Print this help message and exit");
-  po::options_description clo("Command line options");
-  po::options_description dcmdline_options;
-  dcmdline_options.add(opts);
-
-  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
-  po::notify(*conf);
-
-  if (conf->count("help") || conf->count("input") == 0) {
-    cerr << "\nUsage: extractor [-options]\n";
-    cerr << dcmdline_options << endl;
-    exit(1);
-  }
-}
-
-// TODO how to handle alignment information?
-void WriteBasePhrases(const AnnotatedParallelSentence& sentence,
-                      const vector<ParallelSpan>& phrases) {
-  vector<WordID> e,f;
-  for (int it = 0; it < phrases.size(); ++it) {
-    const ParallelSpan& phrase = phrases[it];
-    e.clear();
-    f.clear();
-    for (int i = phrase.i1; i < phrase.i2; ++i)
-      f.push_back(sentence.f[i]);
-    for (int j = phrase.j1; j < phrase.j2; ++j)
-      e.push_back(sentence.e[j]);
-    cout << TD::GetString(f) << " ||| " << TD::GetString(e) << endl;
-  }
-}
-
-void WriteBasePhraseSpans(const AnnotatedParallelSentence& sentence,
-                          const vector<ParallelSpan>& phrases) {
-  cout << TD::GetString(sentence.f) << " ||| " << TD::GetString(sentence.e) << " |||";
-  for (int it = 0; it < phrases.size(); ++it) {
-    const ParallelSpan& phrase = phrases[it];
-    cout << " " << phrase.i1 << "-" << phrase.i2
-      << "-" << phrase.j1 << "-" << phrase.j2;
-  }
-  cout << endl;
-}
-
-struct CountCombiner {
-  CountCombiner(const size_t& csize) : combiner_size(csize) {
-    if (csize == 0) { cerr << "Using unlimited combiner cache.\n"; }
-  }
-  ~CountCombiner() {
-    if (!cache.empty()) WriteAndClearCache();
-  }
-
-  void Count(const vector<WordID>& key,
-             const vector<WordID>& val,
-             const int count_type,
-             const vector<pair<short,short> >& aligns) {
-    if (combiner_size != 1) {
-      RuleStatistics& v = cache[key][val];
-      float newcount = v.counts.add_value(count_type, 1.0f);
-      // hack for adding alignments
-      if (newcount < 7.0f && aligns.size() > v.aligns.size())
-        v.aligns = aligns;
-      if (combiner_size > 1 && cache.size() > combiner_size)
-        WriteAndClearCache();
-    } else {
-      cout << TD::GetString(key) << '\t' << TD::GetString(val) << " ||| ";
-      cout << RuleStatistics(count_type, 1.0f, aligns) << endl;
-    }
-  }
-
- private:
-  void WriteAndClearCache() {
-    for (unordered_map<vector<WordID>, Vec2PhraseCount, boost::hash<vector<WordID> > >::iterator it = cache.begin();
-         it != cache.end(); ++it) {
-      cout << TD::GetString(it->first) << '\t';
-      const Vec2PhraseCount& vals = it->second;
-      bool needdiv = false;
-      for (Vec2PhraseCount::const_iterator vi = vals.begin(); vi != vals.end(); ++vi) {
-        if (needdiv) cout << " ||| "; else needdiv = true;
-        cout << TD::GetString(vi->first) << " ||| " << vi->second;
-      }
-      cout << endl;
-    }
-    cache.clear();
-  }
-
-  const size_t combiner_size;
-  typedef unordered_map<vector<WordID>, RuleStatistics, boost::hash<vector<WordID> > > Vec2PhraseCount;
-  unordered_map<vector<WordID>, Vec2PhraseCount, boost::hash<vector<WordID> > > cache;
-};
-
-// TODO optional source context
-// output <k, v> : k = phrase "document" v = context "term"
-void WritePhraseContexts(const AnnotatedParallelSentence& sentence,
-                         const vector<ParallelSpan>& phrases,
-                         const int ctx_size,
-                         bool phrase_s, bool phrase_t,
-                         bool context_s, bool context_t,
-                         CountCombiner* o) {
-  vector<WordID> context, context_f;
-  if (context_t)
-  {
-      context.resize(ctx_size * 2 + 1);
-      context[ctx_size] = kGAP;
-  }
-  if (context_s)
-  {
-      context_f.resize(ctx_size * 2 + 1);
-      context_f[ctx_size] = kGAP;
-  }
-  vector<WordID> key, key_f;
-  if (phrase_t) key.reserve(100);
-  if (phrase_s) key_f.reserve(100);
-
-  for (int it = 0; it < phrases.size(); ++it) {
-    const ParallelSpan& phrase = phrases[it];
-
-    key.clear();
-    for (int j = phrase.j1; j < phrase.j2 && phrase_t; ++j)
-      key.push_back(sentence.e[j]);
-
-    if (context_t)
-    {
-        context.resize(ctx_size * 2 + 1);
-        for (int i = 0; i < ctx_size && context_t; ++i) {
-          int epos = phrase.j1 - 1 - i;
-          const WordID left_ctx = (epos < 0) ? kBOS : sentence.e[epos];
-          context[ctx_size - i - 1] = left_ctx;
-          epos = phrase.j2 + i;
-          const WordID right_ctx = (epos >= sentence.e_len) ? kEOS : sentence.e[epos];
-          context[ctx_size + i + 1] = right_ctx;
-        }
-    }
-    else
-        context.clear();
-
-    if (phrase_s)
-    {
-        key_f.clear();
-        for (int i = phrase.i1; i < phrase.i2; ++i)
-          key_f.push_back(sentence.f[i]);
-        if (phrase_t) key.push_back(kSPLIT);
-        copy(key_f.begin(), key_f.end(), back_inserter(key));
-    }
-
-    if (context_s)
-    {
-        for (int i = 0; i < ctx_size; ++i) {
-          int fpos = phrase.i1 - 1 - i;
-          const WordID left_ctx = (fpos < 0) ? kBOS : sentence.f[fpos];
-          context_f[ctx_size - i - 1] = left_ctx;
-          fpos = phrase.i2 + i;
-          const WordID right_ctx = (fpos >= sentence.f_len) ? kEOS : sentence.f[fpos];
-          context_f[ctx_size + i + 1] = right_ctx;
-        }
-        if (context_t) context.push_back(kSPLIT);
-        copy(context_f.begin(), context_f.end(), back_inserter(context));
-    }
-
-    o->Count(key, context, kCOUNT, vector<pair<short,short> >());
-  }
-}
-
-struct SimpleRuleWriter : public Extract::RuleObserver {
- protected:
-  virtual void CountRuleImpl(WordID lhs,
-                             const vector<WordID>& rhs_f,
-                             const vector<WordID>& rhs_e,
-                             const vector<pair<short,short> >& fe_terminal_alignments) {
-    cout << "[" << TD::Convert(-lhs) << "] |||";
-    for (int i = 0; i < rhs_f.size(); ++i) {
-      if (rhs_f[i] < 0) cout << " [" << TD::Convert(-rhs_f[i]) << ']';
-      else cout << ' ' << TD::Convert(rhs_f[i]);
-    }
-    cout << " |||";
-    for (int i = 0; i < rhs_e.size(); ++i) {
-      if (rhs_e[i] <= 0) cout << " [" << (1-rhs_e[i]) << ']';
-      else cout << ' ' << TD::Convert(rhs_e[i]);
-    }
-    cout << " |||";
-    for (int i = 0; i < fe_terminal_alignments.size(); ++i) {
-      cout << ' ' << fe_terminal_alignments[i].first << '-' << fe_terminal_alignments[i].second;
-    }
-    cout << endl;
-  }
-};
-
-struct HadoopStreamingRuleObserver : public Extract::RuleObserver {
-  HadoopStreamingRuleObserver(CountCombiner* cc, bool bidir_flag) :
-     bidir(bidir_flag),
-     kF(TD::Convert("F")),
-     kE(TD::Convert("E")),
-     kDIVIDER(TD::Convert("|||")),
-     kLB("["), kRB("]"),
-     combiner(*cc),
-     kEMPTY(),
-     kCFE(FD::Convert("CFE")) {
-   for (int i=1; i < 50; ++i)
-     index2sym[1-i] = TD::Convert(kLB + boost::lexical_cast<string>(i) + kRB);
-   fmajor_key.resize(10, kF);
-   emajor_key.resize(10, kE);
-   if (bidir)
-     fmajor_key[2] = emajor_key[2] = kDIVIDER;
-   else
-     fmajor_key[1] = kDIVIDER;
- }
-
- protected:
-  virtual void CountRuleImpl(WordID lhs,
-                             const vector<WordID>& rhs_f,
-                             const vector<WordID>& rhs_e,
-                             const vector<pair<short,short> >& fe_terminal_alignments) {
-    if (bidir) { // extract rules in "both directions" E->F and F->E
-      fmajor_key.resize(3 + rhs_f.size());
-      emajor_key.resize(3 + rhs_e.size());
-      fmajor_val.resize(rhs_e.size());
-      emajor_val.resize(rhs_f.size());
-      emajor_key[1] = fmajor_key[1] = MapSym(lhs);
-      int nt = 1;
-      for (int i = 0; i < rhs_f.size(); ++i) {
-        const WordID id = rhs_f[i];
-        if (id < 0) {
-          fmajor_key[3 + i] = MapSym(id, nt);
-          emajor_val[i] = MapSym(id, nt);
-          ++nt;
-        } else {
-          fmajor_key[3 + i] = id;
-          emajor_val[i] = id;
-        }
-      }
-      for (int i = 0; i < rhs_e.size(); ++i) {
-        WordID id = rhs_e[i];
-        if (id <= 0) {
-          fmajor_val[i] = index2sym[id];
-          emajor_key[3 + i] = index2sym[id];
-        } else {
-          fmajor_val[i] = id;
-          emajor_key[3 + i] = id;
-        }
-      }
-      combiner.Count(fmajor_key, fmajor_val, kCFE, fe_terminal_alignments);
-      combiner.Count(emajor_key, emajor_val, kCFE, kEMPTY);
-    } else { // extract rules only in F->E
-      fmajor_key.resize(2 + rhs_f.size());
-      fmajor_val.resize(rhs_e.size());
-      fmajor_key[0] = MapSym(lhs);
-      int nt = 1;
-      for (int i = 0; i < rhs_f.size(); ++i) {
-        const WordID id = rhs_f[i];
-        if (id < 0)
-          fmajor_key[2 + i] = MapSym(id, nt++);
-        else
-          fmajor_key[2 + i] = id;
-      }
-      for (int i = 0; i < rhs_e.size(); ++i) {
-        const WordID id = rhs_e[i];
-        if (id <= 0)
-          fmajor_val[i] = index2sym[id];
-        else
-          fmajor_val[i] = id;
-      }
-      combiner.Count(fmajor_key, fmajor_val, kCFE, fe_terminal_alignments);
-    }
-  }
-
- private:
-  WordID MapSym(WordID sym, int ind = 0) {
-    WordID& r = cat2ind2sym[sym][ind];
-    if (!r) {
-      if (ind == 0)
-        r = TD::Convert(kLB + TD::Convert(-sym) + kRB);
-      else
-        r = TD::Convert(kLB + TD::Convert(-sym) + "," + boost::lexical_cast<string>(ind) + kRB);
-    }
-    return r;
-  }
-
-  const bool bidir;
-  const WordID kF, kE, kDIVIDER;
-  const string kLB, kRB;
-  CountCombiner& combiner;
-  const vector<pair<short,short> > kEMPTY;
-  const int kCFE;
-  map<WordID, map<int, WordID> > cat2ind2sym;
-  map<int, WordID> index2sym;
-  vector<WordID> emajor_key, emajor_val, fmajor_key, fmajor_val;
-};
-
-int main(int argc, char** argv) {
-  po::variables_map conf;
-  InitCommandLine(argc, argv, &conf);
-  kBOS = TD::Convert("<s>");
-  kEOS = TD::Convert("</s>");
-  kDIVIDER = TD::Convert("|||");
-  kGAP = TD::Convert("<PHRASE>");
-  kCOUNT = FD::Convert("C");
-  kSPLIT = TD::Convert("<SPLIT>");
-
-  WordID default_cat = 0;  // 0 means no default- extraction will
-                           // fail if a phrase is extracted without a
-                           // category
-  const bool backoff = (conf.count("backoff") ? true : false);
-  if (conf.count("default_category")) {
-    string sdefault_cat = conf["default_category"].as<string>();
-    default_cat = -TD::Convert(sdefault_cat);
-    cerr << "Default category: " << sdefault_cat << endl;
-  }
-  ReadFile rf(conf["input"].as<string>());
-  istream& in = *rf.stream();
-
-  char buf[MAX_LINE_LENGTH];
-  AnnotatedParallelSentence sentence;
-  vector<ParallelSpan> phrases;
-  vector<WordID> all_cats;
-  int max_base_phrase_size = conf["max_base_phrase_size"].as<int>();
-  bool write_phrase_contexts = conf.count("phrase_context") > 0;
-  const bool write_base_phrases = conf.count("base_phrase") > 0;
-  const bool write_base_phrase_spans = conf.count("base_phrase_spans") > 0;
-  const bool loose_phrases = conf.count("loose") > 0;
-  const bool silent = conf.count("silent") > 0;
-  const int max_syms = conf["max_syms"].as<int>();
-  const int max_vars = conf["max_vars"].as<int>();
-  const int ctx_size = conf["phrase_context_size"].as<int>();
-  const int num_categories = conf["topics"].as<int>();
-  const bool permit_adjacent_nonterminals = conf.count("permit_adjacent_nonterminals") > 0;
-  const bool require_aligned_terminal = conf.count("no_required_aligned_terminal") == 0;
-  const string ps = conf["phrase_language"].as<string>();
-  const bool phrase_s = ps == "source" || ps == "both";
-  const bool phrase_t = ps == "target" || ps == "both";
-  const string cs = conf["context_language"].as<string>();
-  const bool context_s = cs == "source" || cs == "both";
-  const bool context_t = cs == "target" || cs == "both";
-  const bool x_cdyer_pos = conf.count("x_cdyer_pos");
-  int line = 0;
-  CountCombiner cc(conf["combiner_size"].as<size_t>());
-  HadoopStreamingRuleObserver o(&cc,
-                                conf.count("bidir") > 0);
-
-  assert(phrase_s || phrase_t);
-  assert(context_s || context_t);
-
-  if(backoff) {
-    for (int i=0;i < num_categories;++i)
-        all_cats.push_back(TD::Convert("X"+boost::lexical_cast<string>(i)));
-  }
-
-  //SimpleRuleWriter o;
-  while(in) {
-    ++line;
-    in.getline(buf, MAX_LINE_LENGTH);
-    if (buf[0] == 0) continue;
-    //cerr << "line #" << line << " = " << buf << endl;
-    if (!silent) {
-      if (line % 200 == 0) cerr << '.';
-      if (line % 8000 == 0) cerr << " [" << line << "]\n" << flush;
-    }
-    sentence.ParseInputLine(buf);
-    if (x_cdyer_pos) {
-      sentence.e = sentence.f;
-      sentence.AllocateForAlignment();
-      for (int i = 0; i < sentence.e.size(); ++i) sentence.Align(i,i);
-      max_base_phrase_size = 1;
-      write_phrase_contexts = true;
-    }
-    phrases.clear();
-    Extract::ExtractBasePhrases(max_base_phrase_size, sentence, &phrases);
-    if (loose_phrases)
-      Extract::LoosenPhraseBounds(sentence, max_base_phrase_size, &phrases);
-    if (phrases.empty()) {
-      cerr << "WARNING no phrases extracted line: " << line << endl;
-      continue;
-    }
-    if (write_phrase_contexts) {
-      WritePhraseContexts(sentence, phrases, ctx_size, phrase_s, phrase_t, context_s, context_t, &cc);
-      continue;
-    }
-    if (write_base_phrases) {
-      WriteBasePhrases(sentence, phrases);
-      continue;
-    }
-    if (write_base_phrase_spans) {
-      WriteBasePhraseSpans(sentence, phrases);
-      continue;
-    }
-    Extract::AnnotatePhrasesWithCategoryTypes(default_cat, sentence.span_types, &phrases);
-    Extract::ExtractConsistentRules(sentence, phrases, max_vars, max_syms, permit_adjacent_nonterminals, require_aligned_terminal, &o, &all_cats);
-  }
-  if (!silent) cerr << endl;
-  return 0;
-}
diff --git a/extools/extractor_monolingual.cc b/extools/extractor_monolingual.cc
deleted file mode 100644
index 049ebc85..00000000
--- a/extools/extractor_monolingual.cc
+++ /dev/null
@@ -1,256 +0,0 @@
-#include <iostream>
-#include <vector>
-#include <utility>
-#include <tr1/unordered_map>
-
-#include <boost/functional/hash.hpp>
-#include <boost/program_options.hpp>
-#include <boost/program_options/variables_map.hpp>
-#include <boost/lexical_cast.hpp>
-
-#include "tdict.h"
-#include "fdict.h"
-#include "wordid.h"
-#include "filelib.h"
-
-using namespace std;
-using namespace std::tr1;
-namespace po = boost::program_options;
-
-static const size_t MAX_LINE_LENGTH = 100000;
-WordID kBOS, kEOS, kDIVIDER, kGAP;
-int kCOUNT;
-
-void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
-  po::options_description opts("Configuration options");
-  opts.add_options()
-        ("input,i", po::value<string>()->default_value("-"), "Input file")
-        ("phrases,p", po::value<string>(), "File contatining phrases of interest")
-        ("phrase_context_size,S", po::value<int>()->default_value(2), "Use this many words of context on left and write when writing base phrase contexts")
-        ("combiner_size,c", po::value<size_t>()->default_value(30000), "Number of unique items to store in cache before writing rule counts. Set to 1 to disable cache. Set to 0 for no limit.")
-        ("prune", po::value<size_t>()->default_value(0), "Prune items with count less than threshold; applies each time the cache is dumped.")
-        ("silent", "Write nothing to stderr except errors")
-        ("help,h", "Print this help message and exit");
-  po::options_description clo("Command line options");
-  po::options_description dcmdline_options;
-  dcmdline_options.add(opts);
-
-  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
-  po::notify(*conf);
-
-  if (conf->count("help") || conf->count("input") != 1 || conf->count("phrases") != 1) {
-    cerr << "\nUsage: extractor_monolingual [-options]\n";
-    cerr << dcmdline_options << endl;
-    exit(1);
-  }
-}
-
-struct TrieNode
-{
-  TrieNode(int l) : finish(false), length(l) {};
-  ~TrieNode()
-  {
-    for (unordered_map<int, TrieNode*>::iterator
-         it = next.begin(); it != next.end(); ++it)
-      delete it->second;
-    next.clear();
-  }
-
-  TrieNode *follow(int token)
-  {
-    unordered_map<int, TrieNode*>::iterator
-      found = next.find(token);
-    if (found != next.end())
-      return found->second;
-    else
-      return 0;
-  }
-
-  void insert(const vector<int> &tokens)
-  {
-    insert(tokens.begin(), tokens.end());
-  }
-
-  void insert(vector<int>::const_iterator begin, vector<int>::const_iterator end)
-  {
-    if (begin == end)
-      finish = true;
-    else
-    {
-      int token = *begin;
-      unordered_map<int, TrieNode*>::iterator 
-        nit = next.find(token);
-      if (nit == next.end())
-        nit = next.insert(make_pair(token, new TrieNode(length+1))).first;
-      ++begin;
-      nit->second->insert(begin, end);
-    }
-  }
-
-  bool finish;
-  int length;
-  unordered_map<int, TrieNode*> next;
-};
-
-struct CountCombiner {
-  CountCombiner(const size_t& csize, const size_t& prune) : combiner_size(csize), threshold(prune) {
-    if (csize == 0) { cerr << "Using unlimited combiner cache.\n"; }
-  }
-  ~CountCombiner() {
-    if (!cache.empty()) WriteAndClearCache();
-  }
-
-  void Count(const vector<WordID>& key,
-             const vector<WordID>& val,
-             const int count_type)
-  {
-    if (combiner_size != 1) {
-      cache[key][val] += count_type;
-      if (combiner_size > 1 && cache.size() > combiner_size)
-        WriteAndClearCache();
-    } else {
-      cout << TD::GetString(key) << '\t' << TD::GetString(val) << " ||| C=" << count_type << "\n";
-    }
-  }
-
- private:
-  void WriteAndClearCache() {
-    for (unordered_map<vector<WordID>, Vec2PhraseCount, boost::hash<vector<WordID> > >::iterator it = cache.begin();
-         it != cache.end(); ++it) {
-      const Vec2PhraseCount& vals = it->second;
-      bool first = true;
-      for (Vec2PhraseCount::const_iterator vi = vals.begin(); vi != vals.end(); ++vi) 
-      {
-        if (threshold > 1 && combiner_size != 1 && vi->second < threshold)
-            continue;
-
-        if (!first) cout << " ||| "; 
-        else 
-        {
-            cout << TD::GetString(it->first) << '\t';
-            first = false;
-        }
-        cout << TD::GetString(vi->first) << " ||| C=" << vi->second;
-       }
-      if (!first)
-          cout << '\n';
-    }
-    cout << flush;
-    cache.clear();
-  }
-
-  const size_t combiner_size, threshold;
-  typedef unordered_map<vector<WordID>, int, boost::hash<vector<WordID> > > Vec2PhraseCount;
-  unordered_map<vector<WordID>, Vec2PhraseCount, boost::hash<vector<WordID> > > cache;
-};
-
-void WriteContext(const vector<int>& sentence, int start, int end, int ctx_size, CountCombiner &combiner) 
-{
-  vector<WordID> phrase, context;
-  for (int i = start; i < end; ++i)
-      phrase.push_back(sentence[i]);
-
-  for (int i = ctx_size; i > 0; --i)
-    context.push_back(sentence[start-i]);
-  context.push_back(kGAP);
-  for (int i = 0; i < ctx_size; ++i)
-    context.push_back(sentence[end+i]);
-
-  combiner.Count(phrase, context, 1);
-}
-
-inline bool IsWhitespace(char c) { 
-    return c == ' ' || c == '\t'; 
-}
-
-inline void SkipWhitespace(const char* buf, int* ptr) {
-  while (buf[*ptr] && IsWhitespace(buf[*ptr])) { ++(*ptr); }
-}
-
-vector<int> ReadSentence(const char *buf, int padding)
-{
-  int ptr = 0;
-  SkipWhitespace(buf, &ptr);
-  int start = ptr;
-  vector<int> sentence;
-  for (int i = 0; i < padding; ++i)
-    sentence.push_back(kBOS);
-
-  while (char c = buf[ptr])
-  {
-    if (!IsWhitespace(c)) 
-      ++ptr; 
-    else {
-      sentence.push_back(TD::Convert(string(buf, start, ptr-start)));
-      SkipWhitespace(buf, &ptr);
-      start = ptr;
-    }
-  }
-  for (int i = 0; i < padding; ++i)
-    sentence.push_back(kEOS);
-
-  return sentence;
-}
-
-int main(int argc, char** argv) 
-{
-  po::variables_map conf;
-  InitCommandLine(argc, argv, &conf);
-  kBOS = TD::Convert("<s>");
-  kEOS = TD::Convert("</s>");
-  kDIVIDER = TD::Convert("|||");
-  kGAP = TD::Convert("<PHRASE>");
-  kCOUNT = FD::Convert("C");
-
-  bool silent = conf.count("silent") > 0;
-  const int ctx_size = conf["phrase_context_size"].as<int>();
-  CountCombiner cc(conf["combiner_size"].as<size_t>(), conf["prune"].as<size_t>());
-
-  char buf[MAX_LINE_LENGTH];
-  TrieNode phrase_trie(0);
-  ReadFile rpf(conf["phrases"].as<string>());
-  istream& pin = *rpf.stream();
-  while (pin) {
-      pin.getline(buf, MAX_LINE_LENGTH);
-      phrase_trie.insert(ReadSentence(buf, 0));
-  }
-
-  ReadFile rif(conf["input"].as<string>());
-  istream &iin = *rif.stream();
-  int line = 0;
-  while (iin) {
-    ++line;
-    iin.getline(buf, MAX_LINE_LENGTH);
-    //cout << "line: " << line << " '" << buf << "'" << endl;
-    if (buf[0] == 0) continue;
-    if (!silent) {
-      if (line % 200 == 0) cerr << '.';
-      if (line % 8000 == 0) cerr << " [" << line << "]\n" << flush;
-    }
-
-    vector<int> sentence = ReadSentence(buf, ctx_size);
-    //cout << "sentence: " << TD::GetString(sentence) << endl;
-    vector<TrieNode*> tries;
-    for (int i = ctx_size; i < (int)sentence.size() - ctx_size; ++i)
-    {
-      //cout << "i: " << i << " token: " << TD::Convert(sentence[i]) << " tries: " << tries.size() << endl;
-      vector<TrieNode*> tries_prime;
-      tries.push_back(&phrase_trie);
-      for (vector<TrieNode*>::iterator tit = tries.begin(); tit != tries.end(); ++tit)
-      {
-        TrieNode* next = (*tit)->follow(sentence[i]);
-        if (next != 0)
-        {
-          //cout << "\tfollowed edge: " << next->finish << endl;
-          if (next->finish)
-            WriteContext(sentence, i + 1 - next->length, i + 1, ctx_size, cc);
-          tries_prime.push_back(next);
-        }
-      }
-      swap(tries, tries_prime);
-    }
-    //cout << "/sentence" << endl;
-  }
-  if (!silent) cerr << endl;
-  return 0;
-}
diff --git a/extools/featurize_grammar.cc b/extools/featurize_grammar.cc
deleted file mode 100644
index 78175202..00000000
--- a/extools/featurize_grammar.cc
+++ /dev/null
@@ -1,716 +0,0 @@
-/*
- * Featurize a grammar in striped format
- */
-#include <iostream>
-#include <sstream>
-#include <string>
-#include <map>
-#include <vector>
-#include <utility>
-#include <cstdlib>
-#include <tr1/unordered_map>
-
-#include "lex_trans_tbl.h"
-#include "sparse_vector.h"
-#include "sentence_pair.h"
-#include "extract.h"
-#include "fdict.h"
-#include "tdict.h"
-#include "filelib.h"
-#include "striped_grammar.h"
-
-#include <boost/tuple/tuple.hpp>
-#include <boost/shared_ptr.hpp>
-#include <boost/functional/hash.hpp>
-#include <boost/program_options.hpp>
-#include <boost/program_options/variables_map.hpp>
-
-using namespace std;
-using namespace std::tr1;
-using boost::shared_ptr;
-namespace po = boost::program_options;
-
-static string aligned_corpus;
-static const size_t MAX_LINE_LENGTH = 64000000;
-
-// Data structures for indexing and counting rules
-//typedef boost::tuple< WordID, vector<WordID>, vector<WordID> > RuleTuple;
-struct RuleTuple {
-  RuleTuple(const WordID& lhs, const vector<WordID>& s, const vector<WordID>& t)
-  : m_lhs(lhs), m_source(s), m_target(t) {
-    hash_value();
-    m_dirty = false;
-  }
-
-  size_t hash_value() const {
-//    if (m_dirty) {
-      size_t hash = 0;
-      boost::hash_combine(hash, m_lhs);
-      boost::hash_combine(hash, m_source);
-      boost::hash_combine(hash, m_target);
-//    }
-//    m_dirty = false;
-    return hash;
-  }
-
-  bool operator==(RuleTuple const& b) const
-  { return m_lhs == b.m_lhs && m_source == b.m_source && m_target == b.m_target; }
-
-  WordID& lhs() { m_dirty=true; return m_lhs; }
-  vector<WordID>& source() { m_dirty=true; return m_source; }
-  vector<WordID>& target() { m_dirty=true; return m_target; }
-  const WordID& lhs() const { return m_lhs; }
-  const vector<WordID>& source() const { return m_source; }
-  const vector<WordID>& target() const { return m_target; }
-
-//  mutable size_t m_hash;
-private:
-  WordID m_lhs;
-  vector<WordID> m_source, m_target;
-  mutable bool m_dirty;
-};
-std::size_t hash_value(RuleTuple const& b) { return b.hash_value(); }
-bool operator<(RuleTuple const& l, RuleTuple const& r) {
-  if (l.lhs() < r.lhs()) return true;
-  else if (l.lhs() == r.lhs()) {
-    if (l.source() < r.source()) return true;
-    else if (l.source() == r.source()) {
-      if (l.target() < r.target()) return true;
-    }
-  }
-  return false;
-}
-
-ostream& operator<<(ostream& o, RuleTuple const& r) {
-  o << "(" << r.lhs() << "-->" << "<";
-  for (vector<WordID>::const_iterator it=r.source().begin(); it!=r.source().end(); ++it)
-    o << TD::Convert(*it) << " ";
-  o << "|||";
-  for (vector<WordID>::const_iterator it=r.target().begin(); it!=r.target().end(); ++it)
-    o << " " << TD::Convert(*it);
-  o << ">)";
-  return o;
-}
-
-template <typename Key>
-struct FreqCount {
-  //typedef unordered_map<Key, int, boost::hash<Key> > Counts;
-  typedef map<Key, int> Counts;
-  Counts counts;
-
-  int inc(const Key& r, int c=1) {
-    pair<typename Counts::iterator,bool> itb
-      = counts.insert(make_pair(r,c));
-    if (!itb.second)
-      itb.first->second += c;
-    return itb.first->second;
-  }
-
-  int inc_if_exists(const Key& r, int c=1) {
-    typename Counts::iterator it = counts.find(r);
-    if (it != counts.end())
-      it->second += c;
-    return it->second;
-  }
-
-  int count(const Key& r) const {
-    typename Counts::const_iterator it = counts.find(r);
-    if (it == counts.end()) return 0;
-    return it->second;
-  }
-
-  int operator()(const Key& r) const { return count(r); }
-};
-typedef FreqCount<RuleTuple> RuleFreqCount;
-
-class FeatureExtractor;
-class FERegistry;
-struct FEFactoryBase {
-  virtual ~FEFactoryBase() {}
-  virtual boost::shared_ptr<FeatureExtractor> Create() const = 0;
-};
-
-
-class FERegistry {
-  friend class FEFactoryBase;
- public:
-  FERegistry() {}
-  boost::shared_ptr<FeatureExtractor> Create(const std::string& ffname) const {
-    map<string, boost::shared_ptr<FEFactoryBase> >::const_iterator it = reg_.find(ffname);
-    boost::shared_ptr<FeatureExtractor> res;
-    if (it == reg_.end()) {
-      cerr << "I don't know how to create feature " << ffname << endl;
-    } else {
-      res = it->second->Create();
-    }
-    return res;
-  }
-  void DisplayList(ostream* out) const {
-    bool first = true;
-    for (map<string, boost::shared_ptr<FEFactoryBase> >::const_iterator it = reg_.begin();
-        it != reg_.end(); ++it) {
-      if (first) {first=false;} else {*out << ' ';}
-      *out << it->first;
-    }
-  }
-
-  void Register(const std::string& ffname, FEFactoryBase* factory) {
-    if (reg_.find(ffname) != reg_.end()) {
-      cerr << "Duplicate registration of FeatureExtractor with name " << ffname << "!\n";
-      exit(1);
-    }
-    reg_[ffname].reset(factory);
-  }
-
- private:
-  std::map<std::string, boost::shared_ptr<FEFactoryBase> > reg_;
-};
-
-template<class FE>
-class FEFactory : public FEFactoryBase {
-  boost::shared_ptr<FeatureExtractor> Create() const {
-    return boost::shared_ptr<FeatureExtractor>(new FE);
-  }
-};
-
-void InitCommandLine(const FERegistry& r, int argc, char** argv, po::variables_map* conf) {
-  po::options_description opts("Configuration options");
-  ostringstream feats;
-  feats << "[multiple] Features to extract (";
-  r.DisplayList(&feats);
-  feats << ")";
-  opts.add_options()
-        ("filtered_grammar,g", po::value<string>(), "Grammar to add features to")
-        ("list_features,L", "List extractable features")
-        ("feature,f", po::value<vector<string> >()->composing(), feats.str().c_str())
-        ("aligned_corpus,c", po::value<string>(), "Aligned corpus (single line format)")
-        ("help,h", "Print this help message and exit");
-  po::options_description clo("Command line options");
-  po::options_description dcmdline_options;
-  dcmdline_options.add(opts);
-
-  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
-  po::notify(*conf);
-
-  if (conf->count("help") || conf->count("aligned_corpus")==0 || conf->count("feature") == 0) {
-    cerr << "\nUsage: featurize_grammar -g FILTERED-GRAMMAR.gz -c ALIGNED_CORPUS.fr-en-al -f Feat1 -f Feat2 ... < UNFILTERED-GRAMMAR\n";
-    cerr << dcmdline_options << endl;
-    exit(1);
-  }
-}
-
-static const bool DEBUG = false;
-
-void LexTranslationTable::createTTable(const char* buf){
-  AnnotatedParallelSentence sent;
-  sent.ParseInputLine(buf);
-
-  //iterate over the alignment to compute aligned words
-
-  for(int i =0;i<sent.aligned.width();i++)
-    {
-      for (int j=0;j<sent.aligned.height();j++)
-        {
-          if (DEBUG) cerr << sent.aligned(i,j) << " ";
-          if( sent.aligned(i,j))
-            {
-              if (DEBUG) cerr << TD::Convert(sent.f[i])  << " aligned to " << TD::Convert(sent.e[j]);
-              ++word_translation[pair<WordID,WordID> (sent.f[i], sent.e[j])];
-              ++total_foreign[sent.f[i]];
-              ++total_english[sent.e[j]];
-            }
-        }
-      if (DEBUG)  cerr << endl;
-    }
-  if (DEBUG) cerr << endl;
-
-  const WordID NULL_ = TD::Convert("NULL");
-  //handle unaligned words - align them to null
-  for (int j =0; j < sent.e_len; j++) {
-    if (sent.e_aligned[j]) continue;
-    ++word_translation[pair<WordID,WordID> (NULL_, sent.e[j])];
-    ++total_foreign[NULL_];
-    ++total_english[sent.e[j]];
-  }
-
-  for (int i =0; i < sent.f_len; i++) {
-    if (sent.f_aligned[i]) continue;
-    ++word_translation[pair<WordID,WordID> (sent.f[i], NULL_)];
-    ++total_english[NULL_];
-    ++total_foreign[sent.f[i]];
-  }
-}
-
-inline float safenlog(float v) {
-  if (v == 1.0f) return 0.0f;
-  float res = -log(v);
-  if (res > 100.0f) res = 100.0f;
-  return res;
-}
-
-static bool IsZero(float f) { return (f > 0.999 && f < 1.001); }
-
-struct FeatureExtractor {
-  // create any keys necessary
-  virtual void ObserveFilteredRule(const WordID /* lhs */,
-                                   const vector<WordID>& /* src */,
-                                   const vector<WordID>& /* trg */) {}
-
-  // compute statistics over keys, the same lhs-src-trg tuple may be seen
-  // more than once
-  virtual void ObserveUnfilteredRule(const WordID /* lhs */,
-                                     const vector<WordID>& /* src */,
-                                     const vector<WordID>& /* trg */,
-                                     const RuleStatistics& /* info */) {}
-
-  // compute features, a unique lhs-src-trg tuple will be seen exactly once
-  virtual void ExtractFeatures(const WordID lhs,
-                               const vector<WordID>& src,
-                               const vector<WordID>& trg,
-                               const RuleStatistics& info,
-                               SparseVector<float>* result) const = 0;
-
-  virtual ~FeatureExtractor() {}
-};
-
-struct LogRuleCount : public FeatureExtractor {
-  LogRuleCount() :
-    fid_(FD::Convert("LogRuleCount")),
-    sfid_(FD::Convert("SingletonRule")),
-    kCFE(FD::Convert("CFE")) {}
-  virtual void ExtractFeatures(const WordID lhs,
-                               const vector<WordID>& src,
-                               const vector<WordID>& trg,
-                               const RuleStatistics& info,
-                               SparseVector<float>* result) const {
-    (void) lhs; (void) src; (void) trg;
-    //result->set_value(fid_, log(info.counts.get(kCFE)));
-    result->set_value(fid_, log(info.counts.get(kCFE)));
-    if (IsZero(info.counts.get(kCFE)))
-      result->set_value(sfid_, 1);
-  }
-  const int fid_;
-  const int sfid_;
-  const int kCFE;
-};
-
-struct RulePenalty : public FeatureExtractor {
-  RulePenalty() : fid_(FD::Convert("RulePenalty")) {}
-  virtual void ExtractFeatures(const WordID /*lhs*/,
-                               const vector<WordID>& /*src*/,
-                               const vector<WordID>& /*trg*/,
-                               const RuleStatistics& /*info*/,
-                               SparseVector<float>* result) const
-  { result->set_value(fid_, 1); }
-
-  const int fid_;
-};
-
-// The negative log of the condition rule probs
-// ignoring the identities of the  non-terminals.
-// i.e. the prob Hiero would assign.
-// Also extracts Labelled features.
-struct XFeatures: public FeatureExtractor {
-  XFeatures() :
-    fid_xfe(FD::Convert("XFE")),
-    fid_xef(FD::Convert("XEF")),
-    fid_labelledfe(FD::Convert("LabelledFE")),
-    fid_labelledef(FD::Convert("LabelledEF")),
-    fid_xesingleton(FD::Convert("XE_Singleton")),
-    fid_xfsingleton(FD::Convert("XF_Singleton")),
-    kCFE(FD::Convert("CFE")) {}
-  virtual void ObserveFilteredRule(const WordID /*lhs*/,
-                                   const vector<WordID>& src,
-                                   const vector<WordID>& trg) {
-    RuleTuple r(-1, src, trg);
-    map_rule(r);
-    rule_counts.inc(r, 0);
-    source_counts.inc(r.source(), 0);
-    target_counts.inc(r.target(), 0);
-  }
-
-  virtual void ObserveUnfilteredRule(const WordID /*lhs*/,
-                                     const vector<WordID>& src,
-                                     const vector<WordID>& trg,
-                                     const RuleStatistics& info) {
-    RuleTuple r(-1, src, trg);
-    map_rule(r);
-    const int count = info.counts.get(kCFE);
-    assert(count > 0);
-    rule_counts.inc_if_exists(r, count);
-    source_counts.inc_if_exists(r.source(), count);
-    target_counts.inc_if_exists(r.target(), count);
-  }
-
-  virtual void ExtractFeatures(const WordID /*lhs*/,
-                               const vector<WordID>& src,
-                               const vector<WordID>& trg,
-                               const RuleStatistics& info,
-                               SparseVector<float>* result) const {
-    RuleTuple r(-1, src, trg);
-    map_rule(r);
-    double l_r_freq = log(rule_counts(r));
-
-    const int t_c = target_counts(r.target());
-    assert(t_c > 0);
-    result->set_value(fid_xfe, log(t_c) - l_r_freq);
-    result->set_value(fid_labelledfe, log(t_c) - log(info.counts.get(kCFE)));
-//    if (t_c == 1)
-//      result->set_value(fid_xesingleton, 1.0);
-
-    const int s_c = source_counts(r.source());
-    assert(s_c > 0);
-    result->set_value(fid_xef, log(s_c) - l_r_freq);
-    result->set_value(fid_labelledef, log(s_c) - log(info.counts.get(kCFE)));
-//    if (s_c == 1)
-//      result->set_value(fid_xfsingleton, 1.0);
-  }
-
-  void map_rule(RuleTuple& r) const {
-    vector<WordID> indexes; int i=0;
-    for (vector<WordID>::iterator it = r.target().begin(); it != r.target().end(); ++it) {
-      if (*it <= 0)
-        indexes.push_back(*it);
-    }
-    for (vector<WordID>::iterator it = r.source().begin(); it != r.source().end(); ++it) {
-      if (*it <= 0)
-        *it = indexes.at(i++);
-    }
-  }
-
-  const int fid_xfe, fid_xef;
-  const int fid_labelledfe, fid_labelledef;
-  const int fid_xesingleton, fid_xfsingleton;
-  const int kCFE;
-  RuleFreqCount rule_counts;
-  FreqCount< vector<WordID> > source_counts, target_counts;
-};
-
-
-struct LabelledRuleConditionals: public FeatureExtractor {
-  LabelledRuleConditionals() :
-    fid_fe(FD::Convert("LabelledFE")),
-    fid_ef(FD::Convert("LabelledEF")),
-    kCFE(FD::Convert("CFE")) {}
-  virtual void ObserveFilteredRule(const WordID lhs,
-                                   const vector<WordID>& src,
-                                   const vector<WordID>& trg) {
-    RuleTuple r(lhs, src, trg);
-    rule_counts.inc(r, 0);
-    source_counts.inc(r.source(), 0);
-
-    target_counts.inc(r.target(), 0);
-  }
-
-  virtual void ObserveUnfilteredRule(const WordID lhs,
-                                     const vector<WordID>& src,
-                                     const vector<WordID>& trg,
-                                     const RuleStatistics& info) {
-    RuleTuple r(lhs, src, trg);
-    rule_counts.inc_if_exists(r, info.counts.get(kCFE));
-    source_counts.inc_if_exists(r.source(), info.counts.get(kCFE));
-
-    target_counts.inc_if_exists(r.target(), info.counts.get(kCFE));
-  }
-
-  virtual void ExtractFeatures(const WordID lhs,
-                               const vector<WordID>& src,
-                               const vector<WordID>& trg,
-                               const RuleStatistics& /*info*/,
-                               SparseVector<float>* result) const {
-    RuleTuple r(lhs, src, trg);
-    double l_r_freq = log(rule_counts(r));
-    result->set_value(fid_fe, log(target_counts(r.target())) - l_r_freq);
-    result->set_value(fid_ef, log(source_counts(r.source())) - l_r_freq);
-  }
-
-  const int fid_fe, fid_ef;
-  const int kCFE;
-  RuleFreqCount rule_counts;
-  FreqCount< vector<WordID> > source_counts, target_counts;
-};
-
-struct LHSProb: public FeatureExtractor {
-  LHSProb() : fid_(FD::Convert("LHSProb")), kCFE(FD::Convert("CFE")), total_count(0) {}
-
-  virtual void ObserveUnfilteredRule(const WordID lhs,
-                                     const vector<WordID>& /*src*/,
-                                     const vector<WordID>& /*trg*/,
-                                     const RuleStatistics& info) {
-    int count = info.counts.get(kCFE);
-    total_count += count;
-    lhs_counts.inc(lhs, count);
-  }
-
-  virtual void ExtractFeatures(const WordID lhs,
-                               const vector<WordID>& /*src*/,
-                               const vector<WordID>& /*trg*/,
-                               const RuleStatistics& /*info*/,
-                               SparseVector<float>* result) const {
-    double lhs_log_prob =  log(total_count) - log(lhs_counts(lhs));
-    result->set_value(fid_, lhs_log_prob);
-  }
-
-  const int fid_;
-  const int kCFE;
-  int total_count;
-  FreqCount<WordID> lhs_counts;
-};
-
-// Proper rule generative probability: p( s,t | lhs)
-struct GenerativeProb: public FeatureExtractor {
-  GenerativeProb() :
-    fid_(FD::Convert("GenerativeProb")),
-    kCFE(FD::Convert("CFE")) {}
-
-  virtual void ObserveUnfilteredRule(const WordID lhs,
-                                     const vector<WordID>& /*src*/,
-                                     const vector<WordID>& /*trg*/,
-                                     const RuleStatistics& info)
-  { lhs_counts.inc(lhs, info.counts.get(kCFE)); }
-
-  virtual void ExtractFeatures(const WordID lhs,
-                               const vector<WordID>& /*src*/,
-                               const vector<WordID>& /*trg*/,
-                               const RuleStatistics& info,
-                               SparseVector<float>* result) const {
-    double log_prob = log(lhs_counts(lhs)) - log(info.counts.get(kCFE));
-    result->set_value(fid_, log_prob);
-  }
-
-  const int fid_;
-  const int kCFE;
-  FreqCount<WordID> lhs_counts;
-};
-
-// remove terminals from the rules before estimating the conditional prob
-struct LabellingShape: public FeatureExtractor {
-  LabellingShape() : fid_(FD::Convert("LabellingShape")), kCFE(FD::Convert("CFE")) {}
-
-  virtual void ObserveFilteredRule(const WordID /*lhs*/,
-                                   const vector<WordID>& src,
-                                   const vector<WordID>& trg) {
-    RuleTuple r(-1, src, trg);
-    map_rule(r);
-    rule_counts.inc(r, 0);
-    source_counts.inc(r.source(), 0);
-  }
-
-  virtual void ObserveUnfilteredRule(const WordID /*lhs*/,
-                                     const vector<WordID>& src,
-                                     const vector<WordID>& trg,
-                                     const RuleStatistics& info) {
-    RuleTuple r(-1, src, trg);
-    map_rule(r);
-    rule_counts.inc_if_exists(r, info.counts.get(kCFE));
-    source_counts.inc_if_exists(r.source(), info.counts.get(kCFE));
-  }
-
-  virtual void ExtractFeatures(const WordID /*lhs*/,
-                               const vector<WordID>& src,
-                               const vector<WordID>& trg,
-                               const RuleStatistics& /*info*/,
-                               SparseVector<float>* result) const {
-    RuleTuple r(-1, src, trg);
-    map_rule(r);
-    double l_r_freq = log(rule_counts(r));
-    result->set_value(fid_, log(source_counts(r.source())) - l_r_freq);
-  }
-
-  // Replace all terminals with generic -1
-  void map_rule(RuleTuple& r) const {
-    for (vector<WordID>::iterator it = r.target().begin(); it != r.target().end(); ++it)
-      if (*it <= 0) *it = -1;
-    for (vector<WordID>::iterator it = r.source().begin(); it != r.source().end(); ++it)
-      if (*it <= 0) *it = -1;
-  }
-
-  const int fid_, kCFE;
-  RuleFreqCount rule_counts;
-  FreqCount< vector<WordID> > source_counts;
-};
-
-
-// this extracts the lexical translation prob features
-// in BOTH directions.
-struct LexProbExtractor : public FeatureExtractor {
-  LexProbExtractor() :
-      e2f_(FD::Convert("LexE2F")), f2e_(FD::Convert("LexF2E")) {
-    ReadFile rf(aligned_corpus);
-    //create lexical translation table
-    cerr << "Computing lexical translation probabilities from " << aligned_corpus << "..." << endl;
-    char* buf = new char[MAX_LINE_LENGTH];
-    istream& alignment = *rf.stream();
-    while(alignment) {
-      alignment.getline(buf, MAX_LINE_LENGTH);
-      if (buf[0] == 0) continue;
-      table.createTTable(buf);
-    }
-    delete[] buf;
-  }
-
-  virtual void ExtractFeatures(const WordID /*lhs*/,
-                               const vector<WordID>& src,
-                               const vector<WordID>& trg,
-                               const RuleStatistics& info,
-                               SparseVector<float>* result) const {
-    map <WordID, pair<int, float> > foreign_aligned;
-    map <WordID, pair<int, float> > english_aligned;
-
-    //Loop over all the alignment points to compute lexical translation probability
-    const vector< pair<short,short> >& al = info.aligns;
-    vector< pair<short,short> >::const_iterator ita;
-    for (ita = al.begin(); ita != al.end(); ++ita) {
-            if (DEBUG) {
-              cerr << "\nA:" << ita->first << "," << ita->second << "::";
-              cerr <<  TD::Convert(src[ita->first]) << "-" << TD::Convert(trg[ita->second]);
-            }
-
-            //Lookup this alignment probability in the table
-            int temp = table.word_translation[pair<WordID,WordID> (src[ita->first],trg[ita->second])];
-            float f2e=0, e2f=0;
-            if ( table.total_foreign[src[ita->first]] != 0)
-              f2e = (float) temp / table.total_foreign[src[ita->first]];
-            if ( table.total_english[trg[ita->second]] !=0 )
-              e2f = (float) temp / table.total_english[trg[ita->second]];
-            if (DEBUG) printf (" %d %E %E\n", temp, f2e, e2f);
-
-            //local counts to keep track of which things haven't been aligned, to later compute their null alignment
-            if (foreign_aligned.count(src[ita->first])) {
-              foreign_aligned[ src[ita->first] ].first++;
-              foreign_aligned[ src[ita->first] ].second += e2f;
-            } else {
-              foreign_aligned[ src[ita->first] ] = pair<int,float> (1,e2f);
-            }
-
-            if (english_aligned.count( trg[ ita->second] )) {
-               english_aligned[ trg[ ita->second] ].first++;
-               english_aligned[ trg[ ita->second] ].second += f2e;
-            } else {
-               english_aligned[ trg[ ita->second] ] = pair<int,float> (1,f2e);
-            }
-          }
-
-          float final_lex_f2e=1, final_lex_e2f=1;
-          static const WordID NULL_ = TD::Convert("NULL");
-
-          //compute lexical weight P(F|E) and include unaligned foreign words
-           for(int i=0;i<src.size(); i++) {
-               if (!table.total_foreign.count(src[i])) continue;      //if we dont have it in the translation table, we won't know its lexical weight
-
-               if (foreign_aligned.count(src[i]))
-                 {
-                   pair<int, float> temp_lex_prob = foreign_aligned[src[i]];
-                   final_lex_e2f *= temp_lex_prob.second / temp_lex_prob.first;
-                 }
-               else //dealing with null alignment
-                 {
-                   int temp_count = table.word_translation[pair<WordID,WordID> (src[i],NULL_)];
-                   float temp_e2f = (float) temp_count / table.total_english[NULL_];
-                   final_lex_e2f *= temp_e2f;
-                 }
-
-             }
-
-           //compute P(E|F) unaligned english words
-           for(int j=0; j< trg.size(); j++) {
-               if (!table.total_english.count(trg[j])) continue;
-
-               if (english_aligned.count(trg[j]))
-                 {
-                   pair<int, float> temp_lex_prob = english_aligned[trg[j]];
-                   final_lex_f2e *= temp_lex_prob.second / temp_lex_prob.first;
-                 }
-               else //dealing with null
-                 {
-                   int temp_count = table.word_translation[pair<WordID,WordID> (NULL_,trg[j])];
-                   float temp_f2e = (float) temp_count / table.total_foreign[NULL_];
-                   final_lex_f2e *= temp_f2e;
-                 }
-           }
-     result->set_value(e2f_, safenlog(final_lex_e2f));
-     result->set_value(f2e_, safenlog(final_lex_f2e));
-  }
-  const int e2f_, f2e_;
-  mutable LexTranslationTable table;
-};
-
-struct Featurizer {
-  Featurizer(const vector<boost::shared_ptr<FeatureExtractor> >& ex) : extractors(ex) {
-  }
-  void Callback1(WordID lhs, const vector<WordID>& src, const ID2RuleStatistics& trgs) {
-    for (ID2RuleStatistics::const_iterator it = trgs.begin(); it != trgs.end(); ++it) {
-      for (int i = 0; i < extractors.size(); ++i)
-        extractors[i]->ObserveFilteredRule(lhs, src, it->first);
-    }
-  }
-  void Callback2(WordID lhs, const vector<WordID>& src, const ID2RuleStatistics& trgs) {
-    for (ID2RuleStatistics::const_iterator it = trgs.begin(); it != trgs.end(); ++it) {
-      for (int i = 0; i < extractors.size(); ++i)
-        extractors[i]->ObserveUnfilteredRule(lhs, src, it->first, it->second);
-    }
-  }
-  void Callback3(WordID lhs, const vector<WordID>& src, const ID2RuleStatistics& trgs) {
-    for (ID2RuleStatistics::const_iterator it = trgs.begin(); it != trgs.end(); ++it) {
-      SparseVector<float> feats;
-      for (int i = 0; i < extractors.size(); ++i)
-        extractors[i]->ExtractFeatures(lhs, src, it->first, it->second, &feats);
-      cout << '[' << TD::Convert(-lhs) << "] ||| ";
-      WriteNamed(src, &cout);
-      cout << " ||| ";
-      WriteAnonymous(it->first, &cout);
-      cout << " ||| ";
-      print(cout,feats,"=");
-      cout << endl;
-    }
-  }
- private:
-  vector<boost::shared_ptr<FeatureExtractor> > extractors;
-};
-
-void cb1(WordID lhs, const vector<WordID>& src_rhs, const ID2RuleStatistics& rules, void* extra) {
-  static_cast<Featurizer*>(extra)->Callback1(lhs, src_rhs, rules);
-}
-
-void cb2(WordID lhs, const vector<WordID>& src_rhs, const ID2RuleStatistics& rules, void* extra) {
-  static_cast<Featurizer*>(extra)->Callback2(lhs, src_rhs, rules);
-}
-
-void cb3(WordID lhs, const vector<WordID>& src_rhs, const ID2RuleStatistics& rules, void* extra) {
-  static_cast<Featurizer*>(extra)->Callback3(lhs, src_rhs, rules);
-}
-
-int main(int argc, char** argv){
-  FERegistry reg;
-  reg.Register("LogRuleCount", new FEFactory<LogRuleCount>);
-  reg.Register("LexProb", new FEFactory<LexProbExtractor>);
-  reg.Register("XFeatures", new FEFactory<XFeatures>);
-  reg.Register("LabelledRuleConditionals", new FEFactory<LabelledRuleConditionals>);
-  reg.Register("RulePenalty", new FEFactory<RulePenalty>);
-  reg.Register("LHSProb", new FEFactory<LHSProb>);
-  reg.Register("LabellingShape", new FEFactory<LabellingShape>);
-  reg.Register("GenerativeProb", new FEFactory<GenerativeProb>);
-  po::variables_map conf;
-  InitCommandLine(reg, argc, argv, &conf);
-  aligned_corpus = conf["aligned_corpus"].as<string>();  // GLOBAL VAR
-  ReadFile fg1(conf["filtered_grammar"].as<string>());
-
-  vector<string> feats = conf["feature"].as<vector<string> >();
-  vector<boost::shared_ptr<FeatureExtractor> > extractors(feats.size());
-  for (int i = 0; i < feats.size(); ++i)
-    extractors[i] = reg.Create(feats[i]);
-  Featurizer fizer(extractors);
-
-  cerr << "Reading filtered grammar to detect keys..." << endl;
-  StripedGrammarLexer::ReadStripedGrammar(fg1.stream(), cb1, &fizer);
-
-  cerr << "Reading unfiltered grammar..." << endl;
-  StripedGrammarLexer::ReadStripedGrammar(&cin, cb2, &fizer);
-
-  ReadFile fg2(conf["filtered_grammar"].as<string>());
-  cerr << "Reading filtered grammar and adding features..." << endl;
-  StripedGrammarLexer::ReadStripedGrammar(fg2.stream(), cb3, &fizer);
-
-  return 0;
-}
-
diff --git a/extools/filter_grammar.cc b/extools/filter_grammar.cc
deleted file mode 100644
index cafcc923..00000000
--- a/extools/filter_grammar.cc
+++ /dev/null
@@ -1,135 +0,0 @@
-/*
- * Filter a grammar in striped format
- */
-#include <iostream>
-#include <string>
-#include <map>
-#include <vector>
-#include <utility>
-#include <tr1/unordered_map>
-
-#include "suffix_tree.h"
-#include "sparse_vector.h"
-#include "sentence_pair.h"
-#include "extract.h"
-#include "fdict.h"
-#include "tdict.h"
-#include "filelib.h"
-#include "striped_grammar.h"
-
-#include <boost/shared_ptr.hpp>
-#include <boost/functional/hash.hpp>
-#include <boost/program_options.hpp>
-#include <boost/program_options/variables_map.hpp>
-
-using namespace std;
-using namespace std::tr1;
-namespace po = boost::program_options;
-
-static const size_t MAX_LINE_LENGTH = 64000000;
-
-void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
-  po::options_description opts("Configuration options");
-  opts.add_options()
-        ("test_set,t", po::value<string>(), "Filter for this test set")
-        ("top_e_given_f,n", po::value<size_t>()->default_value(30), "Keep top N rules, according to p(e|f). 0 for all")
-        ("help,h", "Print this help message and exit");
-  po::options_description clo("Command line options");
-  po::options_description dcmdline_options;
-  dcmdline_options.add(opts);
-
-  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
-  po::notify(*conf);
-
-  if (conf->count("help") || conf->count("test_set")==0) {
-    cerr << "\nUsage: filter_grammar -t TEST-SET.fr [-options] < grammar\n";
-    cerr << dcmdline_options << endl;
-    exit(1);
-  }
-}
-
-struct SourceFilter {
-  // return true to keep the rule, otherwise false
-  virtual bool Matches(const vector<WordID>& key) const = 0;
-  virtual ~SourceFilter() {}
-};
-
-struct DumbSuffixTreeFilter : SourceFilter {
-  DumbSuffixTreeFilter(const string& corpus) {
-    cerr << "Build suffix tree from test set in " << corpus << endl;
-    assert(FileExists(corpus));
-    ReadFile rfts(corpus);
-    istream& testSet = *rfts.stream();
-    char* buf = new char[MAX_LINE_LENGTH];
-    AnnotatedParallelSentence sent;
-
-    /* process the data set to build suffix tree
-     */
-    while(!testSet.eof()) {
-      testSet.getline(buf, MAX_LINE_LENGTH);
-      if (buf[0] == 0) continue;
-
-      //hack to read in the test set using AnnotatedParallelSentence
-      strcat(buf," ||| fake ||| 0-0");
-      sent.ParseInputLine(buf);
-
-      //add each successive suffix to the tree
-      for(int i=0; i<sent.f_len; i++)
-        root.InsertPath(sent.f, i, sent.f_len - 1);
-    }
-    delete[] buf;
-  }
-  virtual bool Matches(const vector<WordID>& src_rhs) const {
-    const Node<int>* curnode = &root;
-    for(int i=0; i < src_rhs.size(); i++) {
-      if (src_rhs[i] <= 0) {
-        curnode = &root;
-      } else if (curnode) {
-        curnode = curnode->Extend(src_rhs[i]);
-        if (!curnode) return false;
-      }
-    }
-    return true;
-  }
-  Node<int> root;
-};
-
-boost::shared_ptr<SourceFilter> filter;
-multimap<float, ID2RuleStatistics::const_iterator> options;
-int kCOUNT;
-int max_options;
-
-void cb(WordID lhs, const vector<WordID>& src_rhs, const ID2RuleStatistics& rules, void*) {
-  options.clear();
-  if (!filter || filter->Matches(src_rhs)) {
-    for (ID2RuleStatistics::const_iterator it = rules.begin(); it != rules.end(); ++it) {
-      options.insert(make_pair(-it->second.counts.get(kCOUNT), it));
-    }
-    int ocount = 0;
-    cout << '[' << TD::Convert(-lhs) << ']' << " ||| ";
-    WriteNamed(src_rhs, &cout);
-    cout << '\t';
-    bool first = true;
-    for (multimap<float,ID2RuleStatistics::const_iterator>::iterator it = options.begin(); it != options.end(); ++it) {
-      if (first) { first = false; } else { cout << " ||| "; }
-      WriteAnonymous(it->second->first, &cout);
-      cout << " ||| " << it->second->second;
-      ++ocount;
-      if (ocount == max_options) break;
-    }
-    cout << endl;
-  }
-}
-
-int main(int argc, char** argv){
-  po::variables_map conf;
-  InitCommandLine(argc, argv, &conf);
-  max_options = conf["top_e_given_f"].as<size_t>();;
-  kCOUNT = FD::Convert("CFE");
-  istream& unscored_grammar = cin;
-  cerr << "Loading test set " << conf["test_set"].as<string>() << "...\n";
-  filter.reset(new DumbSuffixTreeFilter(conf["test_set"].as<string>()));
-  cerr << "Filtering...\n";
-  StripedGrammarLexer::ReadStripedGrammar(&unscored_grammar, cb, NULL);
-}
-
diff --git a/extools/lex_trans_tbl.h b/extools/lex_trans_tbl.h
deleted file mode 100644
index 161b4a0d..00000000
--- a/extools/lex_trans_tbl.h
+++ /dev/null
@@ -1,25 +0,0 @@
-/*
- * lex_trans_tbl.h
- *
- *  Created on: May 25, 2010
- *      Author: Vlad
- */
-
-#ifndef LEX_TRANS_TBL_H_
-#define LEX_TRANS_TBL_H_
-
-#include "wordid.h"
-#include <map>
-
-class LexTranslationTable
-{
- public:
-
-  std::map < std::pair<WordID,WordID>,int > word_translation;
-  std::map <WordID, int> total_foreign;
-  std::map <WordID, int> total_english;
-  void createTTable(const char* buf);
-  
-};
-
-#endif /* LEX_TRANS_TBL_H_ */
diff --git a/extools/merge_lines.pl b/extools/merge_lines.pl
deleted file mode 100755
index 8711e4ce..00000000
--- a/extools/merge_lines.pl
+++ /dev/null
@@ -1,43 +0,0 @@
-#!/usr/bin/perl -w
-use strict;
-
-if (scalar @ARGV < 2) {
-  die "Usage: $0 file1.txt file2.txt ...\n\n  Concatenate the nth line of each input file. All files\n  must be the same length.\n\n";
-}
-
-my @fhs=();
-for my $file (@ARGV) {
-  my $fh;
-  open $fh, "<$file" or die "Can't read $file: $!\n";
-  push @fhs, $fh;
-}
-
-my $first = shift @fhs;
-
-while(my $x = <$first>) {
-  my $ind = 0;
-  chomp $x;
-  my @fields = ($x);
-  for my $fh (@fhs) {
-    $ind++;
-    $x = <$fh>;
-    die "ERROR: Mismatched number of lines: $ARGV[$ind]\n" unless $x;
-    chomp $x;
-    push @fields, $x;
-  }
-  print join ' ||| ', @fields;
-  print "\n";
-}
-my $ind = 0;
-for my $fh (@fhs) {
-  $ind++;
-  my $x=<$fh>;
-  die "ERROR: $ARGV[$ind] has extra lines!\n" if $x;
-}
-
-exit 0;
-
-for my $fh (@fhs) {
-  close $fh;
-}
-
diff --git a/extools/mr_stripe_rule_reduce.cc b/extools/mr_stripe_rule_reduce.cc
deleted file mode 100644
index c9b2eb2a..00000000
--- a/extools/mr_stripe_rule_reduce.cc
+++ /dev/null
@@ -1,172 +0,0 @@
-#include <iostream>
-#include <vector>
-#include <utility>
-#include <cstdlib>
-#include <tr1/unordered_map>
-
-#include <boost/functional/hash.hpp>
-#include <boost/program_options.hpp>
-#include <boost/program_options/variables_map.hpp>
-
-#include "striped_grammar.h"
-#include "tdict.h"
-#include "sentence_pair.h"
-#include "fdict.h"
-#include "extract.h"
-
-using namespace std;
-using namespace std::tr1;
-namespace po = boost::program_options;
-
-static const size_t MAX_LINE_LENGTH = 64000000;
-
-bool use_hadoop_counters = false;
-
-void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
-  po::options_description opts("Configuration options");
-  opts.add_options()
-        ("phrase_marginals,p", "Compute phrase marginals")
-	("use_hadoop_counters,C", "Enable this if running inside Hadoop")
-        ("bidir,b", "Rules are tagged as being F->E or E->F, invert E rules in output")
-        ("help,h", "Print this help message and exit");
-  po::options_description clo("Command line options");
-  po::options_description dcmdline_options;
-  dcmdline_options.add(opts);
-
-  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
-  po::notify(*conf);
-
-  if (conf->count("help")) {
-    cerr << "\nUsage: mr_stripe_rule_reduce [-options]\n";
-    cerr << dcmdline_options << endl;
-    exit(1);
-  }
-}
-
-void PlusEquals(const ID2RuleStatistics& v, ID2RuleStatistics* self) {
-  for (ID2RuleStatistics::const_iterator it = v.begin(); it != v.end(); ++it) {
-    RuleStatistics& dest = (*self)[it->first];
-    dest += it->second;
-    // TODO - do something smarter about alignments?
-    if (dest.aligns.empty() && !it->second.aligns.empty())
-      dest.aligns = it->second.aligns;
-  }
-}
-
-void WriteKeyValue(const vector<WordID>& key, const ID2RuleStatistics& val) {
-  cout << TD::GetString(key) << '\t';
-  bool needdiv = false;
-  for (ID2RuleStatistics::const_iterator it = val.begin(); it != val.end(); ++it) {
-    if (needdiv) cout << " ||| "; else needdiv = true;
-    cout << TD::GetString(it->first) << " ||| " << it->second;
-  }
-  cout << endl;
-  if (use_hadoop_counters) cerr << "reporter:counter:UserCounters,RuleCount," << val.size() << endl;
-}
-
-void DoPhraseMarginals(const vector<WordID>& key, const bool bidir, ID2RuleStatistics* val) {
-  static const WordID kF = TD::Convert("F");
-  static const WordID kE = TD::Convert("E");
-  static const int kCF = FD::Convert("CF");
-  static const int kCE = FD::Convert("CE");
-  static const int kCFE = FD::Convert("CFE");
-  assert(key.size() > 0);
-  int cur_marginal_id = kCF;
-  if (bidir) {
-    if (key[0] != kF && key[0] != kE) {
-      cerr << "DoPhraseMarginals expects keys to have the from 'F|E [NT] word word word'\n";
-      cerr << "  but got: " << TD::GetString(key) << endl;
-      exit(1);
-    }
-    if (key[0] == kE) cur_marginal_id = kCE;
-  }
-  double tot = 0;
-  for (ID2RuleStatistics::iterator it = val->begin(); it != val->end(); ++it)
-    tot += it->second.counts.get(kCFE);
-  for (ID2RuleStatistics::iterator it = val->begin(); it != val->end(); ++it) {
-    it->second.counts.set_value(cur_marginal_id, tot);
-
-    // prevent double counting of the joint
-    if (cur_marginal_id == kCE) it->second.counts.erase(kCFE);
-  }
-}
-
-void WriteWithInversions(const vector<WordID>& key, const ID2RuleStatistics& val) {
-  static const WordID kE = TD::Convert("E");
-  static const WordID kDIV = TD::Convert("|||");
-  vector<WordID> new_key(key.size() - 1);
-  for (int i = 1; i < key.size(); ++i)
-    new_key[i - 1] = key[i];
-  const bool do_invert = (key[0] == kE);
-  if (!do_invert) {
-    WriteKeyValue(new_key, val);
-  } else {
-    ID2RuleStatistics inv;
-    assert(new_key.size() > 2);
-    vector<WordID> tk(new_key.size() - 2);
-    for (int i = 0; i < tk.size(); ++i)
-      tk[i] = new_key[2 + i];
-    RuleStatistics& inv_stats = inv[tk];
-    for (ID2RuleStatistics::const_iterator it = val.begin(); it != val.end(); ++it) {
-      inv_stats.counts = it->second.counts;
-      vector<WordID> ekey(2 + it->first.size());
-      ekey[0] = key[1];
-      ekey[1] = kDIV;
-      for (int i = 0; i < it->first.size(); ++i)
-        ekey[2+i] = it->first[i];
-      WriteKeyValue(ekey, inv);
-    }
-  }
-}
-
-struct Reducer {
-  Reducer(bool phrase_marginals, bool bidir) : pm_(phrase_marginals), bidir_(bidir) {}
-
-  void ProcessLine(const vector<WordID>& key, const ID2RuleStatistics& rules) {
-    if (cur_key_ != key) {
-      if (cur_key_.size() > 0) Emit();
-      acc_.clear();
-      cur_key_ = key;
-    }
-    PlusEquals(rules, &acc_);
-  }
-
-  ~Reducer() {
-    Emit();
-  }
-
-  void Emit() {
-    if (pm_)
-      DoPhraseMarginals(cur_key_, bidir_, &acc_);
-    if (bidir_)
-      WriteWithInversions(cur_key_, acc_);
-    else
-      WriteKeyValue(cur_key_, acc_);
-  }
-
-  const bool pm_;
-  const bool bidir_;
-  vector<WordID> cur_key_;
-  ID2RuleStatistics acc_;
-};
-
-void cb(const vector<WordID>& key, const ID2RuleStatistics& contexts, void* red) {
-  static_cast<Reducer*>(red)->ProcessLine(key, contexts);
-}
-
-
-int main(int argc, char** argv) {
-  po::variables_map conf;
-  InitCommandLine(argc, argv, &conf);
-
-  char* buf = new char[MAX_LINE_LENGTH];
-  vector<WordID> key, cur_key;
-  int line = 0;
-  use_hadoop_counters = conf.count("use_hadoop_counters") > 0;
-  const bool phrase_marginals = conf.count("phrase_marginals") > 0;
-  const bool bidir = conf.count("bidir") > 0;
-  Reducer reducer(phrase_marginals, bidir);
-  StripedGrammarLexer::ReadContexts(&cin, cb, &reducer);
-  return 0;
-}
-
diff --git a/extools/score_grammar.cc b/extools/score_grammar.cc
deleted file mode 100644
index 0945e018..00000000
--- a/extools/score_grammar.cc
+++ /dev/null
@@ -1,352 +0,0 @@
-/*
- * Score a grammar in striped format
- * ./score_grammar <alignment> < filtered.grammar > scored.grammar
- */
-#include <iostream>
-#include <string>
-#include <map>
-#include <vector>
-#include <utility>
-#include <cstdlib>
-#include <fstream>
-#include <tr1/unordered_map>
-
-#include "sentence_pair.h"
-#include "extract.h"
-#include "fdict.h"
-#include "tdict.h"
-#include "lex_trans_tbl.h"
-#include "filelib.h"
-
-#include <boost/functional/hash.hpp>
-#include <boost/program_options.hpp>
-#include <boost/program_options/variables_map.hpp>
-
-using namespace std;
-using namespace std::tr1;
-
-
-static const size_t MAX_LINE_LENGTH = 64000000;
-
-typedef unordered_map<vector<WordID>, RuleStatistics, boost::hash<vector<WordID> > > ID2RuleStatistics;
-
-
-namespace {
-  inline bool IsWhitespace(char c) { return c == ' ' || c == '\t'; }
-  inline bool IsBracket(char c){return c == '[' || c == ']';}
-  inline void SkipWhitespace(const char* buf, int* ptr) {
-    while (buf[*ptr] && IsWhitespace(buf[*ptr])) { ++(*ptr); }
-  }
-}
-
-int ReadPhraseUntilDividerOrEnd(const char* buf, const int sstart, const int end, vector<WordID>* p) {
-  static const WordID kDIV = TD::Convert("|||");
-  int ptr = sstart;
-  while(ptr < end) {
-    while(ptr < end && IsWhitespace(buf[ptr])) { ++ptr; }
-    int start = ptr;
-    while(ptr < end && !IsWhitespace(buf[ptr])) { ++ptr; }
-    if (ptr == start) {cerr << "Warning! empty token.\n"; return ptr; }
-    const WordID w = TD::Convert(string(buf, start, ptr - start));
-
-    if((IsBracket(buf[start]) and IsBracket(buf[ptr-1])) or( w == kDIV))
-      p->push_back(1 * w);
-    else {
-      if (w == kDIV) return ptr;
-      p->push_back(w);
-    }
-  }
-  return ptr;
-}
-
-
-void ParseLine(const char* buf, vector<WordID>* cur_key, ID2RuleStatistics* counts) {
-  static const WordID kDIV = TD::Convert("|||");
-  counts->clear();
-  int ptr = 0;
-  while(buf[ptr] != 0 && buf[ptr] != '\t') { ++ptr; }
-  if (buf[ptr] != '\t') {
-    cerr << "Missing tab separator between key and value!\n INPUT=" << buf << endl;
-    exit(1);
-  }
-  cur_key->clear();
-  // key is: "[X] ||| word word word"
-  int tmpp = ReadPhraseUntilDividerOrEnd(buf, 0, ptr, cur_key);
-  cur_key->push_back(kDIV);
-  ReadPhraseUntilDividerOrEnd(buf, tmpp, ptr, cur_key);
-  ++ptr;
-  int start = ptr;
-  int end = ptr;
-  int state = 0; // 0=reading label, 1=reading count
-  vector<WordID> name;
-  while(buf[ptr] != 0) {
-    while(buf[ptr] != 0 && buf[ptr] != '|') { ++ptr; }
-    if (buf[ptr] == '|') {
-      ++ptr;
-      if (buf[ptr] == '|') {
-        ++ptr;
-        if (buf[ptr] == '|') {
-          ++ptr;
-          end = ptr - 3;
-          while (end > start && IsWhitespace(buf[end-1])) { --end; }
-          if (start == end) {
-            cerr << "Got empty token!\n  LINE=" << buf << endl;
-            exit(1);
-          }
-          switch (state) {
-            case 0: ++state; name.clear(); ReadPhraseUntilDividerOrEnd(buf, start, end, &name); break;
-            case 1: --state; (*counts)[name].ParseRuleStatistics(buf, start, end); break;
-            default: cerr << "Can't happen\n"; abort();
-          }
-          SkipWhitespace(buf, &ptr);
-          start = ptr;
-        }
-      }
-    }
-  }
-  end=ptr;
-  while (end > start && IsWhitespace(buf[end-1])) { --end; }
-  if (end > start) {
-    switch (state) {
-      case 0: ++state; name.clear(); ReadPhraseUntilDividerOrEnd(buf, start, end, &name); break;
-      case 1: --state; (*counts)[name].ParseRuleStatistics(buf, start, end); break;
-      default: cerr << "Can't happen\n"; abort();
-    }
-  }
-}
-
-
-
-void LexTranslationTable::createTTable(const char* buf){
-
-  bool DEBUG = false;
-
-  AnnotatedParallelSentence sent;
-      
-  sent.ParseInputLine(buf);
-      
-  //iterate over the alignment to compute aligned words
-  
-  for(int i =0;i<sent.aligned.width();i++)
-    {
-      for (int j=0;j<sent.aligned.height();j++)
-	{
-	  if (DEBUG) cerr << sent.aligned(i,j) << " ";
-	  if( sent.aligned(i,j))
-	    {
-	      if (DEBUG) cerr << TD::Convert(sent.f[i])  << " aligned to " << TD::Convert(sent.e[j]);
-	      ++word_translation[pair<WordID,WordID> (sent.f[i], sent.e[j])];
-	      ++total_foreign[sent.f[i]];
-	      ++total_english[sent.e[j]];
-	    }
-	}
-      if (DEBUG)  cerr << endl;
-    }
-  if (DEBUG) cerr << endl;
-  
-  static const WordID NULL_ = TD::Convert("NULL");
-  //handle unaligned words - align them to null
-  for (int j =0; j < sent.e_len; j++)
-    {
-      if (sent.e_aligned[j]) continue;
-      ++word_translation[pair<WordID,WordID> (NULL_, sent.e[j])];
-      ++total_foreign[NULL_];
-      ++total_english[sent.e[j]];
-    }
-  
-  for (int i =0; i < sent.f_len; i++)
-    {
-      if (sent.f_aligned[i]) continue;
-      ++word_translation[pair<WordID,WordID> (sent.f[i], NULL_)];
-      ++total_english[NULL_];
-      ++total_foreign[sent.f[i]];
-    }
- 
-}
-
-
-inline float safenlog(float v) {
-  if (v == 1.0f) return 0.0f;
-  float res = -log(v);
-  if (res > 100.0f) res = 100.0f;
-  return res;
-}
-
-int main(int argc, char** argv){
-  bool DEBUG= false;
-  if (argc != 2) {
-    cerr << "Usage: " << argv[0] << " corpus.al < filtered.grammar\n";
-    return 1;
-  }
-  ifstream alignment (argv[1]);
-  istream& unscored_grammar = cin;
-  ostream& scored_grammar = cout;
-
-  //create lexical translation table
-  cerr << "Creating table..." << endl;
-  char* buf = new char[MAX_LINE_LENGTH];
-
-  LexTranslationTable table;
-
-  while(!alignment.eof())
-    {
-      alignment.getline(buf, MAX_LINE_LENGTH);
-      if (buf[0] == 0) continue;
-      
-      table.createTTable(buf);      	
-    }
-  
-  bool PRINT_TABLE=false;
-  if (PRINT_TABLE)
-    {
-      ofstream trans_table;
-      trans_table.open("lex_trans_table.out");
-      for(map < pair<WordID,WordID>,int >::iterator it = table.word_translation.begin(); it != table.word_translation.end(); ++it)
-      {
-	trans_table <<  TD::Convert(it->first.first) <<  "|||" << TD::Convert(it->first.second) << "==" << it->second << "//" << table.total_foreign[it->first.first] << "//" << table.total_english[it->first.second] << endl;
-      } 
-
-      trans_table.close();
-    }
-  
- 
-  //score unscored grammar
-  cerr <<"Scoring grammar..." << endl;
-
-  ID2RuleStatistics acc, cur_counts;
-  vector<WordID> key, cur_key,temp_key;
-  vector< pair<short,short> > al;
-  vector< pair<short,short> >::iterator ita;
-  int line = 0;
-
-  static const int kCF = FD::Convert("CF");
-  static const int kCE = FD::Convert("CE");
-  static const int kCFE = FD::Convert("CFE");	
-
-  while(!unscored_grammar.eof())
-    {
-      ++line;
-      unscored_grammar.getline(buf, MAX_LINE_LENGTH);
-      if (buf[0] == 0) continue;
-      ParseLine(buf, &cur_key, &cur_counts);
-      
-      //loop over all the Target side phrases that this source aligns to
-      for (ID2RuleStatistics::const_iterator it = cur_counts.begin(); it != cur_counts.end(); ++it)
-	{
-	  
-	 /*Compute phrase translation prob.
-	   Print out scores in this format:
-	   Phrase trnaslation prob P(F|E)
-	   Phrase translation prob P(E|F)
-	   Lexical weighting prob lex(F|E)
-	   Lexical weighting prob lex(E|F)
-	 */      
-	  
-	  float pEF_ = it->second.counts.value(kCFE) / it->second.counts.value(kCF);
-	  float pFE_ = it->second.counts.value(kCFE) / it->second.counts.value(kCE);
-
-	  map <WordID, pair<int, float> > foreign_aligned;
-	  map <WordID, pair<int, float> > english_aligned;
-
-	  //Loop over all the alignment points to compute lexical translation probability
-	  al = it->second.aligns;	  
-	  for(ita = al.begin(); ita != al.end(); ++ita)
-	    {
-	     
-	      if (DEBUG)
-		{
-		  cerr << "\nA:" << ita->first << "," << ita->second << "::";
-		  cerr <<  TD::Convert(cur_key[ita->first + 2]) << "-" << TD::Convert(it->first[ita->second]);
-		}
-
-
-	      //Lookup this alignment probability in the table
-	      int temp = table.word_translation[pair<WordID,WordID> (cur_key[ita->first+2],it->first[ita->second])];
-	      float f2e=0, e2f=0;
-	      if ( table.total_foreign[cur_key[ita->first+2]] != 0)
-		f2e = (float) temp / table.total_foreign[cur_key[ita->first+2]];
-	      if ( table.total_english[it->first[ita->second]] !=0 )
-		e2f = (float) temp / table.total_english[it->first[ita->second]];
-	      if (DEBUG) printf (" %d %E %E\n", temp, f2e, e2f);
-	      
-	      
-	      //local counts to keep track of which things haven't been aligned, to later compute their null alignment	      
-	      if (foreign_aligned.count(cur_key[ita->first+2]))
-		{
-		  foreign_aligned[ cur_key[ita->first+2] ].first++;
-		  foreign_aligned[ cur_key[ita->first+2] ].second += e2f;
-		}
-	      else
-		foreign_aligned [ cur_key[ita->first+2] ] = pair<int,float> (1,e2f);
-		
-	      
-
-	      if (english_aligned.count( it->first[ ita->second] ))
-		{
-		  english_aligned[ it->first[ ita->second ]].first++;
-		  english_aligned[  it->first[ ita->second] ].second += f2e;
-		}
-	      else
-		english_aligned [ it->first[ ita->second] ] = pair<int,float> (1,f2e);
-		
-	      
-	    
-	   	      
-	    }
-
-	  float final_lex_f2e=1, final_lex_e2f=1;
-	  static const WordID NULL_ = TD::Convert("NULL");
-
-	  //compute lexical weight P(F|E) and include unaligned foreign words
-	   for(int i=0;i<cur_key.size(); i++)
-	     {
-	       
-	       if (!table.total_foreign.count(cur_key[i])) continue;      //if we dont have it in the translation table, we won't know its lexical weight
-	       
-	       if (foreign_aligned.count(cur_key[i])) 
-		 {
-		   pair<int, float> temp_lex_prob = foreign_aligned[cur_key[i]];
-		   final_lex_e2f *= temp_lex_prob.second / temp_lex_prob.first;
-		 }
-	       else //dealing with null alignment
-		 {
-		   int temp_count = table.word_translation[pair<WordID,WordID> (cur_key[i],NULL_)];
-		   float temp_e2f = (float) temp_count / table.total_english[NULL_];
-		   final_lex_e2f *= temp_e2f;
-		 }	       	       
-
-	     }
-
-	   //compute P(E|F) unaligned english words
-	   for(int j=0; j< it->first.size(); j++)
-	     {
-	       if (!table.total_english.count(it->first[j])) continue;
-	       
-	       if (english_aligned.count(it->first[j]))
-		 {
-		   pair<int, float> temp_lex_prob = english_aligned[it->first[j]];
-		   final_lex_f2e *= temp_lex_prob.second / temp_lex_prob.first;
-		 }
-	       else //dealing with null
-		 {
-		   int temp_count = table.word_translation[pair<WordID,WordID> (NULL_,it->first[j])];
-		   float temp_f2e = (float) temp_count / table.total_foreign[NULL_];
-		   final_lex_f2e *= temp_f2e;
-		 }
-	     }
-	   
-	   
-       scored_grammar << TD::GetString(cur_key);
-       string lhs = TD::Convert(cur_key[0]);
-	   scored_grammar << " " << TD::GetString(it->first) << " |||";
-	   if(lhs.find('_')!=string::npos) {
-	       scored_grammar << " Bkoff=" << safenlog(3.0f);
-	   } else {
-	       scored_grammar << " FGivenE=" << safenlog(pFE_) << " EGivenF=" << safenlog(pEF_);
-	       scored_grammar << " LexE2F=" << safenlog(final_lex_e2f) << " LexF2E=" << safenlog(final_lex_f2e);
-	   }  
-	   scored_grammar << endl;
-	}  
-    }
-}
-
diff --git a/extools/sentence_pair.cc b/extools/sentence_pair.cc
deleted file mode 100644
index 7d60715a..00000000
--- a/extools/sentence_pair.cc
+++ /dev/null
@@ -1,198 +0,0 @@
-#include "sentence_pair.h"
-
-#include <queue>
-#include <iostream>
-#include <string>
-#include <vector>
-#include <utility>
-#include <set>
-#include <boost/tuple/tuple_comparison.hpp>
-
-#include "tdict.h"
-#include "wordid.h"
-#include "array2d.h"
-
-using namespace std;
-using namespace boost;
-
-namespace {
-  inline bool IsWhitespace(char c) { return c == ' ' || c == '\t'; }
-
-  inline void SkipWhitespace(const char* buf, int* ptr) {
-    while (buf[*ptr] && IsWhitespace(buf[*ptr])) { ++(*ptr); }
-  }
-}
-
-void AnnotatedParallelSentence::Reset() {
-  f.clear();
-  e.clear();
-  e_aligned.clear();
-  f_aligned.clear();
-  aligns_by_fword.clear();
-  aligned.clear();
-  span_types.clear();
-}
-
-void AnnotatedParallelSentence::AllocateForAlignment() {
-  f_len = f.size();
-  e_len = e.size();
-  aligned.resize(f_len, e_len, false);
-  f_aligned.resize(f_len, 0);
-  e_aligned.resize(e_len, 0);
-  aligns_by_fword.resize(f_len);
-}
-
-// read an alignment point of the form X-Y where X and Y are strings
-// of digits. if permit_col is true, the right edge will be determined
-// by the presence of a colon
-int AnnotatedParallelSentence::ReadAlignmentPoint(const char* buf,
-                                                  const int start,
-                                                  const int end,
-                                                  const bool permit_col,
-                                                  short* a, short* b, short* c, short* d) {
-  if (end - start < 3) {
-    cerr << "Alignment point badly formed 1: " << string(buf, start, end-start) << endl << buf << endl;
-    exit(1);
-  }
-  int ch = start;
-  *a = 0;
-  while(ch < end && buf[ch] != '-') {
-    if (buf[ch] < '0' || buf[ch] > '9') {
-      cerr << "Alignment point badly formed 2: " << string(buf, start, end-start) << endl << buf << endl;
-      exit(1);
-    }
-    (*a) *= 10;
-    (*a) += buf[ch] - '0';
-    ++ch;
-  }
-  ++ch;
-  if (ch >= end) {
-    cerr << "Alignment point badly formed 3: " << string(buf, start, end-start) << endl << buf << endl;
-    exit(1);
-  }
-  (*b) = 0;
-  while((ch < end) && (c == 0 && (!permit_col || (permit_col && buf[ch] != ':')) || c != 0 && buf[ch] != '-')) {
-    if ((buf[ch] < '0') || (buf[ch] > '9')) {
-      cerr << "Alignment point badly formed 4: " << string(buf, start, end-start) << endl << buf << endl << buf[ch] << endl;
-      exit(1);
-    }
-    (*b) *= 10;
-    (*b) += buf[ch] - '0';
-    ++ch;
-  }
-  if (c != 0)
-  {
-      ++ch;
-      if (ch >= end) {
-        cerr << "Alignment point badly formed 5: " << string(buf, start, end-start) << endl << buf << endl;
-        exit(1);
-      }
-      (*c) = 0;
-      while(ch < end && buf[ch] != '-') {
-        if (buf[ch] < '0' || buf[ch] > '9') {
-          cerr << "Alignment point badly formed 6: " << string(buf, start, end-start) << endl << buf << endl;
-          exit(1);
-        }
-        (*c) *= 10;
-        (*c) += buf[ch] - '0';
-        ++ch;
-      }
-      ++ch;
-      if (ch >= end) {
-        cerr << "Alignment point badly formed 7: " << string(buf, start, end-start) << endl << buf << endl;
-        exit(1);
-      }
-      (*d) = 0;
-      while(ch < end && (!permit_col || (permit_col && buf[ch] != ':'))) {
-        if (buf[ch] < '0' || buf[ch] > '9') {
-          cerr << "Alignment point badly formed 8: " << string(buf, start, end-start) << endl << buf << endl;
-          exit(1);
-        }
-        (*d) *= 10;
-        (*d) += buf[ch] - '0';
-        ++ch;
-      }
-  }
-  return ch;
-}
-
-void AnnotatedParallelSentence::Align(const short a, const short b) {
-  aligned(a,b) = true;
-  ++f_aligned[a];
-  ++e_aligned[b];
-  aligns_by_fword[a].push_back(make_pair(a,b));
-  // cerr << a << " " << b << endl;
-}
-
-void AnnotatedParallelSentence::ParseAlignmentPoint(const char* buf, int start, int end) {
-  short a, b;
-  ReadAlignmentPoint(buf, start, end, false, &a, &b, 0, 0);
-  if (a >= f_len || b >= e_len) {
-    cerr << "(" << a << ',' << b << ") is out of bounds. INPUT=\n" << buf << endl;
-    exit(1);
-  }
-  Align(a,b);
-}
-
-void AnnotatedParallelSentence::ParseSpanLabel(const char* buf, int start, int end) {
-  short a,b,c,d;
-  int ch = ReadAlignmentPoint(buf, start, end, true, &a, &b, &c, &d) + 1;
-  if (buf[ch-1] != ':' || ch >= end) {
-    cerr << "Span badly formed: " << string(buf, start, end-start) << endl << buf << endl;
-    exit(1);
-  }
-  if (a >= f_len || b > f_len) {
-    cerr << "(" << a << ',' << b << ") is out of bounds in labeled span. INPUT=\n" << buf << endl;
-    exit(1);
-  }
-  if (c >= e_len || d > e_len) {
-    cerr << "(" << c << ',' << d << ") is out of bounds in labeled span. INPUT=\n" << buf << endl;
-    exit(1);
-  }
-  // cerr << a << " " << b << " " << string(buf,c,end-c) << endl;
-  span_types[boost::make_tuple(a,b,c,d)].push_back(-TD::Convert(string(buf, ch, end-ch)));
-}
-
-// INPUT FORMAT
-// ein haus ||| a house ||| 0-0 1-1 ||| 0-0:DT 1-1:NN 0-1:NP
-void AnnotatedParallelSentence::ParseInputLine(const char* buf) {
-  Reset();
-  int ptr = 0;
-  SkipWhitespace(buf, &ptr);
-  int start = ptr;
-  int state = 0;  // 0 = French, 1 = English, 2 = Alignment, 3 = Spans
-  while(char c = buf[ptr]) {
-    if (!IsWhitespace(c)) { ++ptr; continue; } else {
-      if (ptr - start == 3 && buf[start] == '|' && buf[start+1] == '|' && buf[start+2] == '|') {
-        ++state;
-        if (state == 4) { cerr << "Too many fields (ignoring):\n  " << buf << endl; return; }
-        if (state == 2) {
-          // cerr << "FLEN=" << f->size() << " ELEN=" << e->size() << endl;
-          AllocateForAlignment();
-        }
-        SkipWhitespace(buf, &ptr);
-        start = ptr;
-        continue;
-      }
-      switch (state) {
-        case 0:  f.push_back(TD::Convert(string(buf, start, ptr-start))); break;
-        case 1:  e.push_back(TD::Convert(string(buf, start, ptr-start))); break;
-        case 2:  ParseAlignmentPoint(buf, start, ptr); break;
-        case 3:  ParseSpanLabel(buf, start, ptr); break;
-        default: cerr << "Can't happen\n"; abort();
-      }
-      SkipWhitespace(buf, &ptr);
-      start = ptr;
-    }
-  }
-  if (ptr > start) {
-    switch (state) {
-      case 0:  f.push_back(TD::Convert(string(buf, start, ptr-start))); break;
-      case 1:  e.push_back(TD::Convert(string(buf, start, ptr-start))); break;
-      case 2:  ParseAlignmentPoint(buf, start, ptr); break;
-      case 3:  ParseSpanLabel(buf, start, ptr); break;
-      default: cerr << "Can't happen\n"; abort();
-    }
-  }
-}
-
diff --git a/extools/sentence_pair.h b/extools/sentence_pair.h
deleted file mode 100644
index a05275e7..00000000
--- a/extools/sentence_pair.h
+++ /dev/null
@@ -1,43 +0,0 @@
-#ifndef _SENTENCE_PAIR_H_
-#define _SENTENCE_PAIR_H_
-
-#include <map>
-#include <utility>
-#include <vector>
-#include <boost/tuple/tuple.hpp>
-#include "wordid.h"
-#include "array2d.h"
-
-// represents a parallel sentence with a word alignment and category
-// annotations over subspans (currently in terms of f)
-// you should read one using ParseInputLine and then use the public
-// member variables to query things about it
-struct AnnotatedParallelSentence {
-  // read annotated parallel sentence from string
-  void ParseInputLine(const char* buf);
-
-  std::vector<WordID> f, e;  // words in f and e
-
-  // word alignment information
-  std::vector<int> e_aligned, f_aligned; // counts the number of times column/row x is aligned
-  Array2D<bool> aligned;
-  std::vector<std::vector<std::pair<short, short> > > aligns_by_fword;
-
-  // span type information
-  std::map< boost::tuple<short,short,short,short>, std::vector<WordID> > span_types;
-  // span_types(i,j,k,l) is the list of category span (i,j) in source and (k,l) in the target language.
-
-  int f_len, e_len;
-
-  void Align(const short a, const short b);
-  void AllocateForAlignment();
-
-  static int ReadAlignmentPoint(const char* buf, int start, int end, bool permit_col, short* a, short* b, short* c, short* d);
-
- private:
-  void Reset();
-  void ParseAlignmentPoint(const char* buf, int start, int end);
-  void ParseSpanLabel(const char* buf, int start, int end);
-};
-
-#endif
diff --git a/extools/sg_lexer.l b/extools/sg_lexer.l
deleted file mode 100644
index c85cdea7..00000000
--- a/extools/sg_lexer.l
+++ /dev/null
@@ -1,294 +0,0 @@
-%{
-#include <string>
-#include <iostream>
-#include <sstream>
-#include <cstring>
-#include <cassert>
-#include "tdict.h"
-#include "fdict.h"
-#include "striped_grammar.h"
-
-int lex_line = 0;
-int read_contexts = 0;
-std::istream* sglex_stream = NULL;
-StripedGrammarLexer::GrammarCallback grammar_callback = NULL;
-StripedGrammarLexer::ContextCallback context_callback = NULL;
-void* grammar_callback_extra = NULL;
-void* context_callback_extra = NULL;
-
-#undef YY_INPUT
-#define YY_INPUT(buf, result, max_size) (result = sglex_stream->read(buf, max_size).gcount())
-
-#define YY_SKIP_YYWRAP 1
-int num_rules = 0;
-int yywrap() { return 1; }
-bool fl = true;
-#define MAX_TOKEN_SIZE 255
-std::string sglex_tmp_token(MAX_TOKEN_SIZE, '\0');
-
-#define MAX_RULE_SIZE 48
-WordID sglex_src_rhs[MAX_RULE_SIZE];
-WordID sglex_trg_rhs[MAX_RULE_SIZE];
-int sglex_src_rhs_size;
-int sglex_trg_rhs_size;
-WordID sglex_lhs;
-int sglex_src_arity;
-int sglex_trg_arity;
-
-#define MAX_FEATS 100
-int sglex_feat_ids[MAX_FEATS];
-double sglex_feat_vals[MAX_FEATS];
-int sglex_num_feats;
-
-#define MAX_ARITY 20
-int sglex_nt_sanity[MAX_ARITY];
-int sglex_src_nts[MAX_ARITY];
-float sglex_nt_size_means[MAX_ARITY];
-float sglex_nt_size_vars[MAX_ARITY];
-
-std::vector<WordID> cur_src_rhs;
-std::vector<WordID> cur_trg_rhs;
-ID2RuleStatistics cur_options;
-RuleStatistics* cur_stats = NULL;
-int sglex_cur_fid = 0;
-
-static void sanity_check_trg_index(int index) {
-  if (index > sglex_src_arity) {
-    std::cerr << "Target index " << index << " exceeds source arity " << sglex_src_arity << std::endl;
-    abort();
-  }
-  int& flag = sglex_nt_sanity[index - 1];
-  if (flag) {
-    std::cerr << "Target index " << index << " used multiple times!" << std::endl;
-    abort();
-  }
-  flag = 1;
-}
-
-static void sglex_reset() {
-  sglex_src_arity = 0;
-  sglex_trg_arity = 0;
-  sglex_num_feats = 0;
-  sglex_src_rhs_size = 0;
-  sglex_trg_rhs_size = 0;
-}
-
-%}
-
-REAL [\-+]?[0-9]+(\.[0-9]*([eE][-+]*[0-9]+)?)?|inf|[\-+]inf
-NT [^\t \[\],]+
-ALIGN [0-9]+-[0-9]+
-
-%x LHS_END SRC TRG FEATS FEATVAL ALIGNS
-%%
-
-<INITIAL>[ ]	;
-<INITIAL>[\t]	{
-		if (read_contexts) {
-			cur_options.clear();
-			BEGIN(TRG);
-		} else {
-			std::cerr << "Unexpected tab while reading striped grammar\n";
-			exit(1);
-		}
-		}
-
-<INITIAL>\[{NT}\]   {
-		if (read_contexts) {
-			sglex_tmp_token.assign(yytext, yyleng);
-			sglex_src_rhs[sglex_src_rhs_size] = TD::Convert(sglex_tmp_token);
-			++sglex_src_rhs_size;
-		} else {
-			sglex_tmp_token.assign(yytext + 1, yyleng - 2);
-			sglex_lhs = -TD::Convert(sglex_tmp_token);
-			// std::cerr << sglex_tmp_token << "\n";
-  			BEGIN(LHS_END);
-			}
-		}
-
-<INITIAL>[^ \t]+ {
-		if (read_contexts) {
-			// std::cerr << "Context: " << yytext << std::endl;
-			sglex_tmp_token.assign(yytext, yyleng);
-			sglex_src_rhs[sglex_src_rhs_size] = TD::Convert(sglex_tmp_token);
-			++sglex_src_rhs_size;
-		} else {
-			std::cerr << "Unexpected input: " << yytext << " when NT expected\n";
-			exit(1);
-		}
-		}
-
-<SRC>\[{NT}\]   {
-		sglex_tmp_token.assign(yytext + 1, yyleng - 2);
-		sglex_src_nts[sglex_src_arity] = sglex_src_rhs[sglex_src_rhs_size] = -TD::Convert(sglex_tmp_token);
-		++sglex_src_arity;
-		++sglex_src_rhs_size;
-		}
-
-<LHS_END>[ ] { ; }
-<LHS_END>\|\|\|	{
-		sglex_reset();
-		BEGIN(SRC);
-		}
-
-<LHS_END>.	{
-		std::cerr << "Line " << lex_line << ": unexpected input in LHS: " << yytext << std::endl;
-		exit(1);
-		}
-
-
-<SRC>\[{NT},[1-9][0-9]?\]   {
-		int index = yytext[yyleng - 2] - '0';
-		if (yytext[yyleng - 3] == ',') {
-		  sglex_tmp_token.assign(yytext + 1, yyleng - 4);
-		} else {
-		  sglex_tmp_token.assign(yytext + 1, yyleng - 5);
-		  index += 10 * (yytext[yyleng - 3] - '0');
-		}
-		if ((sglex_src_arity+1) != index) {
-			std::cerr << "Src indices must go in order: expected " << sglex_src_arity << " but got " << index << std::endl;
-			abort();
-		}
-		sglex_src_nts[sglex_src_arity] = sglex_src_rhs[sglex_src_rhs_size] = -TD::Convert(sglex_tmp_token);
-		++sglex_src_rhs_size;
-		++sglex_src_arity;
-		}
-
-<SRC>[^ \t]+	{ 
-		sglex_tmp_token.assign(yytext, yyleng);
-		sglex_src_rhs[sglex_src_rhs_size] = TD::Convert(sglex_tmp_token);
-		++sglex_src_rhs_size;
-		}
-<SRC>[ ]	{ ; }
-<SRC>\t		{
-		//std::cerr << "LHS=" << TD::Convert(-sglex_lhs) << " ";
-		//std::cerr << "  src_size: " << sglex_src_rhs_size << std::endl;
-		//std::cerr << "  src_arity: " << sglex_src_arity << std::endl;
-		cur_options.clear();
-		memset(sglex_nt_sanity, 0, sglex_src_arity * sizeof(int));
-		sglex_trg_rhs_size = 0;
-		BEGIN(TRG);
-		}
-
-<TRG>\[[1-9][0-9]?\]   {
-		if (read_contexts) {
-			sglex_tmp_token.assign(yytext, yyleng);
-			sglex_trg_rhs[sglex_trg_rhs_size] = TD::Convert(sglex_tmp_token);
-			++sglex_trg_rhs_size;
-		} else {
-			int index = yytext[yyleng - 2] - '0';
-			if (yyleng == 4) {
-			  index += 10 * (yytext[yyleng - 3] - '0');
-			}
-			++sglex_trg_arity;
-			sanity_check_trg_index(index);
-			sglex_trg_rhs[sglex_trg_rhs_size] = 1 - index;
-			++sglex_trg_rhs_size;
-		}
-}
-
-<TRG>\|\|\|	{
-		//std::cerr << "  trg_size: " << sglex_trg_rhs_size << std::endl;
-		//std::cerr << "  trg_arity: " << sglex_trg_arity << std::endl;
-		assert(sglex_trg_rhs_size > 0);
-		cur_trg_rhs.resize(sglex_trg_rhs_size);
-		for (int i = 0; i < sglex_trg_rhs_size; ++i)
-			cur_trg_rhs[i] = sglex_trg_rhs[i];
-		cur_stats = &cur_options[cur_trg_rhs];
-		BEGIN(FEATS);
-		}
-
-<TRG>[^ ]+	{
-		sglex_tmp_token.assign(yytext, yyleng);
-		sglex_trg_rhs[sglex_trg_rhs_size] = TD::Convert(sglex_tmp_token);
-		
-		++sglex_trg_rhs_size;
-		}
-<TRG>[ ]+	{ ; }
-
-<FEATS>\n	{
-		assert(sglex_src_rhs_size > 0);
-		cur_src_rhs.resize(sglex_src_rhs_size);
-		for (int i = 0; i < sglex_src_rhs_size; ++i)
-			cur_src_rhs[i] = sglex_src_rhs[i];
-		if (read_contexts) {
-			context_callback(cur_src_rhs, cur_options, context_callback_extra);
-		} else {
-			assert(sglex_lhs < 0);
-			grammar_callback(sglex_lhs, cur_src_rhs, cur_options, grammar_callback_extra);
-		}
-		cur_options.clear();
-		sglex_reset();
-		BEGIN(INITIAL);
-		}
-<FEATS>[ ]+	{ ; }
-<FEATS>\|\|\|	{
-		memset(sglex_nt_sanity, 0, sglex_src_arity * sizeof(int));
-		sglex_trg_rhs_size = 0;
-		BEGIN(TRG);
-		}
-<FEATS>[A-Z][A-Z_0-9]*=	{
-		// std::cerr << "FV: " << yytext << std::endl;
-		sglex_tmp_token.assign(yytext, yyleng - 1);
-		sglex_cur_fid = FD::Convert(sglex_tmp_token);
-		static const int Afid = FD::Convert("A");
-		if (sglex_cur_fid == Afid) {
-			BEGIN(ALIGNS);
-		} else {
-			BEGIN(FEATVAL);
-		}
-		}
-<FEATVAL>{REAL}	{
-		// std::cerr << "Feature val input: " << yytext << std::endl;
-		cur_stats->counts.add_value(sglex_cur_fid, strtod(yytext, NULL));
-		BEGIN(FEATS);
-		}
-<FEATVAL>.	{
-		std::cerr << "Feature val unexpected input: " << yytext << std::endl;
-		exit(1);
-		}
-<FEATS>.	{
-		std::cerr << "Features unexpected input: " << yytext << std::endl;
-		exit(1);
-		}
-<ALIGNS>{ALIGN}(,{ALIGN})*	{
-		assert(cur_stats->aligns.empty());
-		int i = 0;
-		while(i < yyleng) {
-			short a = 0;
-			short b = 0;
-			while (yytext[i] != '-') { a *= 10; a += yytext[i] - '0'; ++i; }
-			++i;
-			while (yytext[i] != ',' && i < yyleng) { b *= 10; b += yytext[i] - '0'; ++i; }
-			++i;
-			cur_stats->aligns.push_back(std::make_pair(a,b));
-		}
-		BEGIN(FEATS);
-		}
-<ALIGNS>.	{
-		std::cerr << "Aligns unexpected input: " << yytext << std::endl;
-		exit(1);
-		}
-%%
-
-#include "filelib.h"
-
-void StripedGrammarLexer::ReadStripedGrammar(std::istream* in, GrammarCallback func, void* extra) {
-  read_contexts = 0;
-  lex_line = 1;
-  sglex_stream = in;
-  grammar_callback_extra = extra;
-  grammar_callback = func;
-  yylex();
-}
-
-void StripedGrammarLexer::ReadContexts(std::istream* in, ContextCallback func, void* extra) {
-  read_contexts = 1;
-  lex_line = 1;
-  sglex_stream = in;
-  context_callback_extra = extra;
-  context_callback = func;
-  yylex();
-}
-
-
diff --git a/extools/simple-extract-context.sh b/extools/simple-extract-context.sh
deleted file mode 100755
index 17487b1c..00000000
--- a/extools/simple-extract-context.sh
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/bin/bash
-
-MYDIR=$(dirname $0)
-
-export LANG=C
-date 1>&2
-$MYDIR/extractor -i $1 -c 500000 -L 12 -C | sort -t $'\t' -k 1 | $MYDIR/mr_stripe_rule_reduce
-date 1>&2
-
diff --git a/extools/simple-extract.sh b/extools/simple-extract.sh
deleted file mode 100755
index ec5c5276..00000000
--- a/extools/simple-extract.sh
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/bin/bash
-
-export LANG=C
-date
-./extractor -i $1 -d X -c 500000 -L 12 -b | sort -t $'\t' -k 1 | gzip > ex.output.gz
-date
-# -p = compute phrase marginals
-# -b = bidirectional rules (starting with F or E) were extracted
-zcat ex.output.gz | ./mr_stripe_rule_reduce -p -b | sort -t $'\t' -k 1 | ./mr_stripe_rule_reduce | gzip > phrase-table.gz
-date
-
diff --git a/extools/striped_grammar.cc b/extools/striped_grammar.cc
deleted file mode 100644
index 785f4bbe..00000000
--- a/extools/striped_grammar.cc
+++ /dev/null
@@ -1,67 +0,0 @@
-#include "striped_grammar.h"
-
-#include <iostream>
-
-#include "sentence_pair.h"
-
-using namespace std;
-
-namespace {
-  inline bool IsWhitespace(char c) { return c == ' ' || c == '\t'; }
-
-  inline void SkipWhitespace(const char* buf, int* ptr) {
-    while (buf[*ptr] && IsWhitespace(buf[*ptr])) { ++(*ptr); }
-  }
-}
-
-void RuleStatistics::ParseRuleStatistics(const char* buf, int start, int end) {
-  int ptr = start;
-  counts.clear();
-  aligns.clear();
-  while (ptr < end) {
-    SkipWhitespace(buf, &ptr);
-    int vstart = ptr;
-    while(ptr < end && buf[ptr] != '=') ++ptr;
-    assert(buf[ptr] == '=');
-    assert(ptr > vstart);
-    if (buf[vstart] == 'A' && buf[vstart+1] == '=') {
-      ++ptr;
-      while (ptr < end && !IsWhitespace(buf[ptr])) {
-        while(ptr < end && buf[ptr] == ',') { ++ptr; }
-        assert(ptr < end);
-        vstart = ptr;
-        while(ptr < end && buf[ptr] != ',' && !IsWhitespace(buf[ptr])) { ++ptr; }
-        if (ptr > vstart) {
-          short a, b;
-          AnnotatedParallelSentence::ReadAlignmentPoint(buf, vstart, ptr, false, &a, &b, 0, 0);
-          aligns.push_back(make_pair(a,b));
-        }
-      }
-    } else {
-      int name = FD::Convert(string(buf,vstart,ptr-vstart));
-      ++ptr;
-      vstart = ptr;
-      while(ptr < end && !IsWhitespace(buf[ptr])) { ++ptr; }
-      assert(ptr > vstart);
-      counts.set_value(name, strtod(buf + vstart, NULL));
-    }
-  }
-}
-
-ostream& operator<<(ostream& os, const RuleStatistics& s) {
-  bool needspace = false;
-  for (SparseVector<float>::const_iterator it = s.counts.begin(); it != s.counts.end(); ++it) {
-    if (needspace) os << ' '; else needspace = true;
-    os << FD::Convert(it->first) << '=' << it->second;
-  }
-  if (s.aligns.size() > 0) {
-    os << " A=";
-    needspace = false;
-    for (int i = 0; i < s.aligns.size(); ++i) {
-      if (needspace) os << ','; else needspace = true;
-      os << s.aligns[i].first << '-' << s.aligns[i].second;
-    }
-  }
-  return os;
-}
-
diff --git a/extools/striped_grammar.h b/extools/striped_grammar.h
deleted file mode 100644
index bf3aec7d..00000000
--- a/extools/striped_grammar.h
+++ /dev/null
@@ -1,56 +0,0 @@
-#ifndef _STRIPED_GRAMMAR_H_
-#define _STRIPED_GRAMMAR_H_
-
-#include <iostream>
-#include <boost/functional/hash.hpp>
-#include <vector>
-#include <tr1/unordered_map>
-#include "sparse_vector.h"
-#include "wordid.h"
-#include "tdict.h"
-
-// represents statistics / information about a rule pair
-struct RuleStatistics {
-  SparseVector<float> counts;
-  std::vector<std::pair<short,short> > aligns;
-  RuleStatistics() {}
-  RuleStatistics(int name, float val, const std::vector<std::pair<short,short> >& al) :
-      aligns(al) {
-    counts.set_value(name, val);
-  }
-  void ParseRuleStatistics(const char* buf, int start, int end);
-  RuleStatistics& operator+=(const RuleStatistics& rhs) {
-    counts += rhs.counts;
-    return *this;
-  }
-};
-std::ostream& operator<<(std::ostream& os, const RuleStatistics& s);
-
-inline void WriteNamed(const std::vector<WordID>& v, std::ostream* os) {
-  bool first = true;
-  for (int i = 0; i < v.size(); ++i) {
-    if (first) { first = false; } else { (*os) << ' '; }
-    if (v[i] < 0) { (*os) << '[' << TD::Convert(-v[i]) << ']'; }
-    else (*os) << TD::Convert(v[i]);
-  }
-}
-
-inline void WriteAnonymous(const std::vector<WordID>& v, std::ostream* os) {
-  bool first = true;
-  for (int i = 0; i < v.size(); ++i) {
-    if (first) { first = false; } else { (*os) << ' '; }
-    if (v[i] <= 0) { (*os) << '[' << (1-v[i]) << ']'; }
-    else (*os) << TD::Convert(v[i]);
-  }
-}
-
-typedef std::tr1::unordered_map<std::vector<WordID>, RuleStatistics, boost::hash<std::vector<WordID> > > ID2RuleStatistics;
-
-struct StripedGrammarLexer {
-  typedef void (*GrammarCallback)(WordID lhs, const std::vector<WordID>& src_rhs, const ID2RuleStatistics& rules, void *extra);
-  static void ReadStripedGrammar(std::istream* in, GrammarCallback func, void* extra);
-  typedef void (*ContextCallback)(const std::vector<WordID>& phrase, const ID2RuleStatistics& rules, void *extra);
-  static void ReadContexts(std::istream* in, ContextCallback func, void* extra);
-};
-
-#endif
diff --git a/extools/suffix_tree.h b/extools/suffix_tree.h
deleted file mode 100644
index f62f53f4..00000000
--- a/extools/suffix_tree.h
+++ /dev/null
@@ -1,46 +0,0 @@
-/*
- * suffix_tree.h
- *
- *  Created on: May 17, 2010
- *      Author: Vlad
-
-NOTE (graehl): this seems to be a (forward) trie of the suffixes (of sentences).
-so O(m*n^2) for m sentences of length n.
-
-For a real suffix tree (linear size/time), see:
-http://en.wikipedia.org/wiki/Suffix_tree
-http://www.cs.helsinki.fi/u/ukkonen/SuffixT1withFigs.pdf
-
- */
-
-#ifndef SUFFIX_TREE_H_
-#define SUFFIX_TREE_H_
-
-#include <string>
-#include <map>
-#include <vector>
-
-template <class T>
-class Node {
-	public:
-		std::map<T, Node> edge_list_;
-		int InsertPath(const std::vector<T>& p, int start, int end);
-		const Node* Extend(const T& e) const {
-			typename std::map<T, Node>::const_iterator it = edge_list_.find(e);
-			if (it == edge_list_.end()) return NULL;
-			return &it->second;
-		}
-};
-
-bool DEBUG = false;
-
-template <class T>
-int Node<T>::InsertPath(const std::vector<T>& p, int start, int end){
-	Node* currNode = this;
-	for(int i=start;i<= end; i++ ) {
-		currNode = &(currNode->edge_list_)[p[i]];
-	}
-	return 1;
-}
-
-#endif /* SUFFIX_TRIE_H_ */
diff --git a/extools/test_data/README b/extools/test_data/README
deleted file mode 100644
index e368cffc..00000000
--- a/extools/test_data/README
+++ /dev/null
@@ -1,10 +0,0 @@
-The following was used to create the test data.  The real inputs
-were corpus.fr, corpus.en, and corpus.aligned.  The generated files
-were corpus.len_cats and fr-en.al.len.
-
-
-  ./make_len_cats.pl corpus.en > corpus.len_cats
-
-  ../merge_lines.pl corpus.fr corpus.en corpus.aligned corpus.len_cats > fr-en.al.len
-
-
diff --git a/extools/test_data/corpus.aligned b/extools/test_data/corpus.aligned
deleted file mode 100644
index aa09e9ab..00000000
--- a/extools/test_data/corpus.aligned
+++ /dev/null
@@ -1,5 +0,0 @@
-0-0 1-2 2-1
-0-0 1-1
-0-0 0-1 1-0 1-1 2-0 2-1 3-2 4-3
-0-0
-0-0 1-1
diff --git a/extools/test_data/corpus.en b/extools/test_data/corpus.en
deleted file mode 100644
index 2d4751bf..00000000
--- a/extools/test_data/corpus.en
+++ /dev/null
@@ -1,5 +0,0 @@
-the blue house
-the hat
-there is a hat
-cap
-the cat
diff --git a/extools/test_data/corpus.fr b/extools/test_data/corpus.fr
deleted file mode 100644
index 75b5e127..00000000
--- a/extools/test_data/corpus.fr
+++ /dev/null
@@ -1,5 +0,0 @@
-la maison bleue
-le chapeau
-il y a un chapeau
-chapeau
-le chat
diff --git a/extools/test_data/corpus.len_cats b/extools/test_data/corpus.len_cats
deleted file mode 100644
index 18d321de..00000000
--- a/extools/test_data/corpus.len_cats
+++ /dev/null
@@ -1,5 +0,0 @@
-0-1:SHORT 0-2:SHORT 0-3:MID 1-2:SHORT 1-3:SHORT 2-3:SHORT
-0-1:SHORT 0-2:SHORT 1-2:SHORT
-0-1:SHORT 0-2:SHORT 0-3:MID 0-4:MID 1-2:SHORT 1-3:SHORT 1-4:MID 2-3:SHORT 2-4:SHORT 3-4:SHORT
-0-1:SHORT
-0-1:SHORT 0-2:SHORT 1-2:SHORT
diff --git a/extools/test_data/fr-en.al.len b/extools/test_data/fr-en.al.len
deleted file mode 100644
index 7ee6b85d..00000000
--- a/extools/test_data/fr-en.al.len
+++ /dev/null
@@ -1,5 +0,0 @@
-la maison bleue ||| the blue house ||| 0-0 1-2 2-1 ||| 0-1:SHORT 0-2:SHORT 0-3:MID 1-2:SHORT 1-3:SHORT 2-3:SHORT
-le chapeau ||| the hat ||| 0-0 1-1 ||| 0-1:SHORT 0-2:SHORT 1-2:SHORT
-il y a un chapeau ||| there is a hat ||| 0-0 0-1 1-0 1-1 2-0 2-1 3-2 4-3 ||| 0-1:SHORT 0-2:SHORT 0-3:MID 0-4:MID 1-2:SHORT 1-3:SHORT 1-4:MID 2-3:SHORT 2-4:SHORT 3-4:SHORT
-chapeau ||| cap ||| 0-0 ||| 0-1:SHORT
-le chat ||| the cat ||| 0-0 1-1 ||| 0-1:SHORT 0-2:SHORT 1-2:SHORT
diff --git a/extools/test_data/make_len_cats.pl b/extools/test_data/make_len_cats.pl
deleted file mode 100755
index 25ef75fa..00000000
--- a/extools/test_data/make_len_cats.pl
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/usr/bin/perl -w
-use strict;
-
-my $max_len = 15;
-my @cat_names = qw( NULL SHORT SHORT MID MID MID LONG LONG LONG LONG LONG VLONG VLONG VLONG VLONG VLONG );
-
-while(<>) {
-  chomp;
-  my @words = split /\s+/;
-  my $len = scalar @words;
-  my @spans;
-  for (my $i =0; $i < $len; $i++) {
-    for (my $k = 1; $k <= $max_len; $k++) {
-      my $j = $i + $k;
-      next if ($j > $len);
-      my $cat = $cat_names[$k];
-      die unless $cat;
-      push @spans, "$i-$j:$cat";
-    }
-  }
-  print "@spans\n";
-}
-
diff --git a/gi/clda/src/Makefile.am b/gi/clda/src/Makefile.am
deleted file mode 100644
index cdca1f97..00000000
--- a/gi/clda/src/Makefile.am
+++ /dev/null
@@ -1,6 +0,0 @@
-bin_PROGRAMS = clda
-
-clda_SOURCES = clda.cc
-
-AM_CPPFLAGS = -W -Wall -Wno-sign-compare -funroll-loops -I$(top_srcdir)/utils $(GTEST_CPPFLAGS)
-AM_LDFLAGS = $(top_srcdir)/utils/libutils.a -lz
diff --git a/gi/clda/src/ccrp.h b/gi/clda/src/ccrp.h
deleted file mode 100644
index a7c2825c..00000000
--- a/gi/clda/src/ccrp.h
+++ /dev/null
@@ -1,291 +0,0 @@
-#ifndef _CCRP_H_
-#define _CCRP_H_
-
-#include <numeric>
-#include <cassert>
-#include <cmath>
-#include <list>
-#include <iostream>
-#include <vector>
-#include <tr1/unordered_map>
-#include <boost/functional/hash.hpp>
-#include "sampler.h"
-#include "slice_sampler.h"
-
-// Chinese restaurant process (Pitman-Yor parameters) with table tracking.
-
-template <typename Dish, typename DishHash = boost::hash<Dish> >
-class CCRP {
- public:
-  CCRP(double disc, double conc) :
-    num_tables_(),
-    num_customers_(),
-    discount_(disc),
-    concentration_(conc),
-    discount_prior_alpha_(std::numeric_limits<double>::quiet_NaN()),
-    discount_prior_beta_(std::numeric_limits<double>::quiet_NaN()),
-    concentration_prior_shape_(std::numeric_limits<double>::quiet_NaN()),
-    concentration_prior_rate_(std::numeric_limits<double>::quiet_NaN()) {}
-
-  CCRP(double d_alpha, double d_beta, double c_shape, double c_rate, double d = 0.1, double c = 10.0) :
-    num_tables_(),
-    num_customers_(),
-    discount_(d),
-    concentration_(c),
-    discount_prior_alpha_(d_alpha),
-    discount_prior_beta_(d_beta),
-    concentration_prior_shape_(c_shape),
-    concentration_prior_rate_(c_rate) {}
-
-  double discount() const { return discount_; }
-  double concentration() const { return concentration_; }
-
-  bool has_discount_prior() const {
-    return !std::isnan(discount_prior_alpha_);
-  }
-
-  bool has_concentration_prior() const {
-    return !std::isnan(concentration_prior_shape_);
-  }
-
-  void clear() {
-    num_tables_ = 0;
-    num_customers_ = 0;
-    dish_locs_.clear();
-  }
-
-  unsigned num_tables(const Dish& dish) const {
-    const typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator it = dish_locs_.find(dish);
-    if (it == dish_locs_.end()) return 0;
-    return it->second.table_counts_.size();
-  }
-
-  unsigned num_customers() const {
-    return num_customers_;
-  }
-
-  unsigned num_customers(const Dish& dish) const {
-    const typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator it = dish_locs_.find(dish);
-    if (it == dish_locs_.end()) return 0;
-    return it->total_dish_count_;
-  }
-
-  // returns +1 or 0 indicating whether a new table was opened
-  int increment(const Dish& dish, const double& p0, MT19937* rng) {
-    DishLocations& loc = dish_locs_[dish];
-    bool share_table = false;
-    if (loc.total_dish_count_) {
-      const double p_empty = (concentration_ + num_tables_ * discount_) * p0;
-      const double p_share = (loc.total_dish_count_ - loc.table_counts_.size() * discount_);
-      share_table = rng->SelectSample(p_empty, p_share);
-    }
-    if (share_table) {
-      double r = rng->next() * (loc.total_dish_count_ - loc.table_counts_.size() * discount_);
-      for (typename std::list<unsigned>::iterator ti = loc.table_counts_.begin();
-           ti != loc.table_counts_.end(); ++ti) {
-        r -= (*ti - discount_);
-        if (r <= 0.0) {
-          ++(*ti);
-          break;
-        }
-      }
-      if (r > 0.0) {
-        std::cerr << "Serious error: r=" << r << std::endl;
-        Print(&std::cerr);
-        assert(r <= 0.0);
-      }
-    } else {
-      loc.table_counts_.push_back(1u);
-      ++num_tables_;
-    }
-    ++loc.total_dish_count_;
-    ++num_customers_;
-    return (share_table ? 0 : 1);
-  }
-
-  // returns -1 or 0, indicating whether a table was closed
-  int decrement(const Dish& dish, MT19937* rng) {
-    DishLocations& loc = dish_locs_[dish];
-    assert(loc.total_dish_count_);
-    if (loc.total_dish_count_ == 1) {
-      dish_locs_.erase(dish);
-      --num_tables_;
-      --num_customers_;
-      return -1;
-    } else {
-      int delta = 0;
-      // sample customer to remove UNIFORMLY. that is, do NOT use the discount
-      // here. if you do, it will introduce (unwanted) bias!
-      double r = rng->next() * loc.total_dish_count_;
-      --loc.total_dish_count_;
-      for (typename std::list<unsigned>::iterator ti = loc.table_counts_.begin();
-           ti != loc.table_counts_.end(); ++ti) {
-        r -= *ti;
-        if (r <= 0.0) {
-          if ((--(*ti)) == 0) {
-            --num_tables_;
-            delta = -1;
-            loc.table_counts_.erase(ti);
-          }
-          break;
-        }
-      }
-      if (r > 0.0) {
-        std::cerr << "Serious error: r=" << r << std::endl;
-        Print(&std::cerr);
-        assert(r <= 0.0);
-      }
-      --num_customers_;
-      return delta;
-    }
-  }
-
-  double prob(const Dish& dish, const double& p0) const {
-    const typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator it = dish_locs_.find(dish);
-    const double r = num_tables_ * discount_ + concentration_;
-    if (it == dish_locs_.end()) {
-      return r * p0 / (num_customers_ + concentration_);
-    } else {
-      return (it->second.total_dish_count_ - discount_ * it->second.table_counts_.size() + r * p0) /
-               (num_customers_ + concentration_);
-    }
-  }
-
-  double log_crp_prob() const {
-    return log_crp_prob(discount_, concentration_);
-  }
-
-  static double log_beta_density(const double& x, const double& alpha, const double& beta) {
-    assert(x > 0.0);
-    assert(x < 1.0);
-    assert(alpha > 0.0);
-    assert(beta > 0.0);
-    const double lp = (alpha-1)*log(x)+(beta-1)*log(1-x)+lgamma(alpha+beta)-lgamma(alpha)-lgamma(beta);
-    return lp;
-  }
-
-  static double log_gamma_density(const double& x, const double& shape, const double& rate) {
-    assert(x >= 0.0);
-    assert(shape > 0.0);
-    assert(rate > 0.0);
-    const double lp = (shape-1)*log(x) - shape*log(rate) - x/rate - lgamma(shape);
-    return lp;
-  }
-
-  // taken from http://en.wikipedia.org/wiki/Chinese_restaurant_process
-  // does not include P_0's
-  double log_crp_prob(const double& discount, const double& concentration) const {
-    double lp = 0.0;
-    if (has_discount_prior())
-      lp = log_beta_density(discount, discount_prior_alpha_, discount_prior_beta_);
-    if (has_concentration_prior())
-      lp += log_gamma_density(concentration, concentration_prior_shape_, concentration_prior_rate_);
-    assert(lp <= 0.0);
-    if (num_customers_) {
-      if (discount > 0.0) {
-        const double r = lgamma(1.0 - discount);
-        lp += lgamma(concentration) - lgamma(concentration + num_customers_)
-             + num_tables_ * log(discount) + lgamma(concentration / discount + num_tables_)
-             - lgamma(concentration / discount);
-        assert(std::isfinite(lp));
-        for (typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator it = dish_locs_.begin();
-             it != dish_locs_.end(); ++it) {
-          const DishLocations& cur = it->second;
-          for (std::list<unsigned>::const_iterator ti = cur.table_counts_.begin(); ti != cur.table_counts_.end(); ++ti) {
-            lp += lgamma(*ti - discount) - r;
-          }
-        }
-      } else {
-        assert(!"not implemented yet");
-      }
-    }
-    assert(std::isfinite(lp));
-    return lp;
-  }
-
-  void resample_hyperparameters(MT19937* rng) {
-    assert(has_discount_prior() || has_concentration_prior());
-    DiscountResampler dr(*this);
-    ConcentrationResampler cr(*this);
-    const int niterations = 10;
-    double gamma_upper = std::numeric_limits<double>::infinity();
-    for (int iter = 0; iter < 5; ++iter) {
-      if (has_concentration_prior()) {
-        concentration_ = slice_sampler1d(cr, concentration_, *rng, 0.0,
-                               gamma_upper, 0.0, niterations, 100*niterations);
-      }
-      if (has_discount_prior()) {
-        discount_ = slice_sampler1d(dr, discount_, *rng, std::numeric_limits<double>::min(),
-                               1.0, 0.0, niterations, 100*niterations);
-      }
-    }
-    concentration_ = slice_sampler1d(cr, concentration_, *rng, 0.0,
-                             gamma_upper, 0.0, niterations, 100*niterations);
-  }
-
-  struct DiscountResampler {
-    DiscountResampler(const CCRP& crp) : crp_(crp) {}
-    const CCRP& crp_;
-    double operator()(const double& proposed_discount) const {
-      return crp_.log_crp_prob(proposed_discount, crp_.concentration_);
-    }
-  };
-
-  struct ConcentrationResampler {
-    ConcentrationResampler(const CCRP& crp) : crp_(crp) {}
-    const CCRP& crp_;
-    double operator()(const double& proposed_concentration) const {
-      return crp_.log_crp_prob(crp_.discount_, proposed_concentration);
-    }
-  };
-
-  struct DishLocations {
-    DishLocations() : total_dish_count_() {}
-    unsigned total_dish_count_;        // customers at all tables with this dish
-    std::list<unsigned> table_counts_; // list<> gives O(1) deletion and insertion, which we want
-                                       // .size() is the number of tables for this dish
-  };
-
-  void Print(std::ostream* out) const {
-    for (typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator it = dish_locs_.begin();
-         it != dish_locs_.end(); ++it) {
-      (*out) << it->first << " (" << it->second.total_dish_count_ << " on " << it->second.table_counts_.size() << " tables): ";
-      for (typename std::list<unsigned>::const_iterator i = it->second.table_counts_.begin();
-           i != it->second.table_counts_.end(); ++i) {
-        (*out) << " " << *i;
-      }
-      (*out) << std::endl;
-    }
-  }
-
-  typedef typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator const_iterator;
-  const_iterator begin() const {
-    return dish_locs_.begin();
-  }
-  const_iterator end() const {
-    return dish_locs_.end();
-  }
-
-  unsigned num_tables_;
-  unsigned num_customers_;
-  std::tr1::unordered_map<Dish, DishLocations, DishHash> dish_locs_;
-
-  double discount_;
-  double concentration_;
-
-  // optional beta prior on discount_ (NaN if no prior)
-  double discount_prior_alpha_;
-  double discount_prior_beta_;
-
-  // optional gamma prior on concentration_ (NaN if no prior)
-  double concentration_prior_shape_;
-  double concentration_prior_rate_;
-};
-
-template <typename T,typename H>
-std::ostream& operator<<(std::ostream& o, const CCRP<T,H>& c) {
-  c.Print(&o);
-  return o;
-}
-
-#endif
diff --git a/gi/clda/src/clda.cc b/gi/clda/src/clda.cc
deleted file mode 100644
index f548997f..00000000
--- a/gi/clda/src/clda.cc
+++ /dev/null
@@ -1,148 +0,0 @@
-#include <iostream>
-#include <vector>
-#include <map>
-#include <string>
-
-#include "timer.h"
-#include "crp.h"
-#include "ccrp.h"
-#include "sampler.h"
-#include "tdict.h"
-const size_t MAX_DOC_LEN_CHARS = 10000000;
-
-using namespace std;
-
-void ShowTopWordsForTopic(const map<WordID, int>& counts) {
-  multimap<int, WordID> ms;
-  for (map<WordID,int>::const_iterator it = counts.begin(); it != counts.end(); ++it)
-    ms.insert(make_pair(it->second, it->first));
-  int cc = 0;
-  for (multimap<int, WordID>::reverse_iterator it = ms.rbegin(); it != ms.rend(); ++it) {
-    cerr << it->first << ':' << TD::Convert(it->second) << " ";
-    ++cc;
-    if (cc==20) break;
-  }
-  cerr << endl;
-}
-
-int main(int argc, char** argv) {
-  if (argc != 3) {
-    cerr << "Usage: " << argv[0] << " num-classes num-samples\n";
-    return 1;
-  }
-  const int num_classes = atoi(argv[1]);
-  const int num_iterations = atoi(argv[2]);
-  const int burnin_size = num_iterations * 0.9;
-  if (num_classes < 2) {
-    cerr << "Must request more than 1 class\n";
-    return 1;
-  }
-  if (num_iterations < 5) {
-    cerr << "Must request more than 5 iterations\n";
-    return 1;
-  }
-  cerr << "CLASSES: " << num_classes << endl;
-  char* buf = new char[MAX_DOC_LEN_CHARS];
-  vector<vector<int> > wji;   // w[j][i] - observed word i of doc j
-  vector<vector<int> > zji;   // z[j][i] - topic assignment for word i of doc j
-  cerr << "READING DOCUMENTS\n";
-  while(cin) {
-    cin.getline(buf, MAX_DOC_LEN_CHARS);
-    if (buf[0] == 0) continue;
-    wji.push_back(vector<WordID>());
-    TD::ConvertSentence(buf, &wji.back());
-  }
-  cerr << "READ " << wji.size() << " DOCUMENTS\n";
-  MT19937 rng;
-  cerr << "INITIALIZING RANDOM TOPIC ASSIGNMENTS\n";
-  zji.resize(wji.size());
-  double disc = 0.1;
-  double beta = 10.0;
-  double alpha = 50.0;
-  const double uniform_topic = 1.0 / num_classes;
-  const double uniform_word = 1.0 / TD::NumWords();
-  vector<CCRP<int> > dr(zji.size(), CCRP<int>(1,1,1,1,disc, beta)); // dr[i] describes the probability of using a topic in document i
-  vector<CCRP<int> > wr(num_classes, CCRP<int>(1,1,1,1,disc, alpha)); // wr[k] describes the probability of generating a word in topic k
-  for (int j = 0; j < zji.size(); ++j) {
-    const size_t num_words = wji[j].size();
-    vector<int>& zj = zji[j];
-    const vector<int>& wj = wji[j];
-    zj.resize(num_words);
-    for (int i = 0; i < num_words; ++i) {
-      int random_topic = rng.next() * num_classes;
-      if (random_topic == num_classes) { --random_topic; }
-      zj[i] = random_topic;
-      const int word = wj[i];
-      dr[j].increment(random_topic, uniform_topic, &rng);
-      wr[random_topic].increment(word, uniform_word, &rng);
-    }
-  }
-  cerr << "SAMPLING\n";
-  vector<map<WordID, int> > t2w(num_classes);
-  Timer timer;
-  SampleSet<double> ss;
-  ss.resize(num_classes);
-  double total_time = 0;
-  for (int iter = 0; iter < num_iterations; ++iter) {
-    cerr << '.';
-    if (iter && iter % 10 == 0) {
-      total_time += timer.Elapsed();
-      timer.Reset();
-      double llh = 0;
-#if 1
-      for (int j = 0; j < dr.size(); ++j)
-        dr[j].resample_hyperparameters(&rng);
-      for (int j = 0; j < wr.size(); ++j)
-        wr[j].resample_hyperparameters(&rng);
-#endif
-
-      for (int j = 0; j < dr.size(); ++j)
-        llh += dr[j].log_crp_prob();
-      for (int j = 0; j < wr.size(); ++j)
-        llh += wr[j].log_crp_prob();
-      cerr << " [LLH=" << llh << " I=" << iter << "]\n";
-    }
-    for (int j = 0; j < zji.size(); ++j) {
-      const size_t num_words = wji[j].size();
-      vector<int>& zj = zji[j];
-      const vector<int>& wj = wji[j];
-      for (int i = 0; i < num_words; ++i) {
-        const int word = wj[i];
-        const int cur_topic = zj[i];
-        dr[j].decrement(cur_topic, &rng);
-        wr[cur_topic].decrement(word, &rng);
- 
-        for (int k = 0; k < num_classes; ++k) {
-          ss[k]= dr[j].prob(k, uniform_topic) * wr[k].prob(word, uniform_word);
-        }
-        const int new_topic = rng.SelectSample(ss);
-        dr[j].increment(new_topic, uniform_topic, &rng);
-        wr[new_topic].increment(word, uniform_word, &rng);
-        zj[i] = new_topic;
-        if (iter > burnin_size) {
-          ++t2w[cur_topic][word];
-        }
-      }
-    }
-  }
-  for (int i = 0; i < num_classes; ++i) {
-    cerr << "---------------------------------\n";
-    cerr << " final PYP(" << wr[i].discount() << "," << wr[i].concentration() << ")\n";
-    ShowTopWordsForTopic(t2w[i]);
-  }
-  cerr << "-------------\n";
-#if 0
-  for (int j = 0; j < zji.size(); ++j) {
-    const size_t num_words = wji[j].size();
-    vector<int>& zj = zji[j];
-    const vector<int>& wj = wji[j];
-    zj.resize(num_words);
-    for (int i = 0; i < num_words; ++i) {
-      cerr << TD::Convert(wji[j][i]) << '(' << zj[i] << ") ";
-    }
-    cerr << endl;
-  }
-#endif
-  return 0;
-}
-
diff --git a/gi/clda/src/crp.h b/gi/clda/src/crp.h
deleted file mode 100644
index 9d35857e..00000000
--- a/gi/clda/src/crp.h
+++ /dev/null
@@ -1,50 +0,0 @@
-#ifndef _CRP_H_
-#define _CRP_H_
-
-// shamelessly adapted from code by Phil Blunsom and Trevor Cohn
-
-#include <boost/functional/hash.hpp>
-#include <tr1/unordered_map>
-
-#include "prob.h"
-
-template <typename DishType, typename Hash = boost::hash<DishType> >
-class CRP {
- public:
-  CRP(double alpha) : alpha_(alpha), palpha_(alpha), total_customers_() {}
-  void increment(const DishType& dish);
-  void decrement(const DishType& dish);
-  void erase(const DishType& dish) {
-    counts_.erase(dish);
-  }
-  inline int count(const DishType& dish) const {
-    const typename MapType::const_iterator i = counts_.find(dish);
-    if (i == counts_.end()) return 0; else return i->second;
-  }
-  inline prob_t prob(const DishType& dish, const prob_t& p0) const {
-    return (prob_t(count(dish)) + palpha_ * p0) / prob_t(total_customers_ + alpha_);
-  }
- private:
-  typedef std::tr1::unordered_map<DishType, int, Hash> MapType;
-  MapType counts_;
-  const double alpha_;
-  const prob_t palpha_;
-  int total_customers_;
-};
-
-template <typename Dish, typename Hash>
-void CRP<Dish,Hash>::increment(const Dish& dish) {
-  ++counts_[dish];
-  ++total_customers_;
-}
-
-template <typename Dish, typename Hash>
-void CRP<Dish,Hash>::decrement(const Dish& dish) {
-  typename MapType::iterator i = counts_.find(dish);
-  assert(i != counts_.end());
-  if (--i->second == 0)
-    counts_.erase(i);
-  --total_customers_;
-}
-
-#endif
diff --git a/gi/clda/src/slice_sampler.h b/gi/clda/src/slice_sampler.h
deleted file mode 100644
index aa48a169..00000000
--- a/gi/clda/src/slice_sampler.h
+++ /dev/null
@@ -1,191 +0,0 @@
-//! slice-sampler.h is an MCMC slice sampler
-//!
-//! Mark Johnson, 1st August 2008
-
-#ifndef SLICE_SAMPLER_H
-#define SLICE_SAMPLER_H
-
-#include <algorithm>
-#include <cassert>
-#include <cmath>
-#include <iostream>
-#include <limits>
-
-//! slice_sampler_rfc_type{} returns the value of a user-specified
-//! function if the argument is within range, or - infinity otherwise
-//
-template <typename F, typename Fn, typename U>
-struct slice_sampler_rfc_type {
-  F min_x, max_x;
-  const Fn& f;
-  U max_nfeval, nfeval;
-  slice_sampler_rfc_type(F min_x, F max_x, const Fn& f, U max_nfeval) 
-    : min_x(min_x), max_x(max_x), f(f), max_nfeval(max_nfeval), nfeval(0) { }
-    
-  F operator() (F x) {
-    if (min_x < x && x < max_x) {
-      assert(++nfeval <= max_nfeval);
-      F fx = f(x);
-      assert(std::isfinite(fx));
-      return fx;
-    }
-      return -std::numeric_limits<F>::infinity();
-  }
-};  // slice_sampler_rfc_type{}
-
-//! slice_sampler1d() implements the univariate "range doubling" slice sampler
-//! described in Neal (2003) "Slice Sampling", The Annals of Statistics 31(3), 705-767.
-//
-template <typename F, typename LogF, typename Uniform01>
-F slice_sampler1d(const LogF& logF0,               //!< log of function to sample
-		  F x,                             //!< starting point
-		  Uniform01& u01,                  //!< uniform [0,1) random number generator
-		  F min_x = -std::numeric_limits<F>::infinity(),  //!< minimum value of support
-		  F max_x = std::numeric_limits<F>::infinity(),   //!< maximum value of support
-		  F w = 0.0,                       //!< guess at initial width
-		  unsigned nsamples=1,             //!< number of samples to draw
-		  unsigned max_nfeval=200)         //!< max number of function evaluations
-{
-  typedef unsigned U;
-  slice_sampler_rfc_type<F,LogF,U> logF(min_x, max_x, logF0, max_nfeval);
-
-  assert(std::isfinite(x));
-
-  if (w <= 0.0) {                           // set w to a default width 
-    if (min_x > -std::numeric_limits<F>::infinity() && max_x < std::numeric_limits<F>::infinity())
-      w = (max_x - min_x)/4;
-    else
-      w = std::max(((x < 0.0) ? -x : x)/4, (F) 0.1);
-  }
-  assert(std::isfinite(w));
-
-  F logFx = logF(x);
-  for (U sample = 0; sample < nsamples; ++sample) {
-    F logY = logFx + log(u01()+1e-100);     //! slice logFx at this value
-    assert(std::isfinite(logY));
-
-    F xl = x - w*u01();                     //! lower bound on slice interval
-    F logFxl = logF(xl);
-    F xr = xl + w;                          //! upper bound on slice interval
-    F logFxr = logF(xr);
-
-    while (logY < logFxl || logY < logFxr)  // doubling procedure
-      if (u01() < 0.5) 
-	logFxl = logF(xl -= xr - xl);
-      else
-	logFxr = logF(xr += xr - xl);
-	
-    F xl1 = xl;
-    F xr1 = xr;
-    while (true) {                          // shrinking procedure
-      F x1 = xl1 + u01()*(xr1 - xl1);
-      if (logY < logF(x1)) {
-	F xl2 = xl;                         // acceptance procedure
-	F xr2 = xr; 
-	bool d = false;
-	while (xr2 - xl2 > 1.1*w) {
-	  F xm = (xl2 + xr2)/2;
-	  if ((x < xm && x1 >= xm) || (x >= xm && x1 < xm))
-	    d = true;
-	  if (x1 < xm)
-	    xr2 = xm;
-	  else
-	    xl2 = xm;
-	  if (d && logY >= logF(xl2) && logY >= logF(xr2))
-	    goto unacceptable;
-	}
-	x = x1;
-	goto acceptable;
-      }
-      goto acceptable;
-    unacceptable:
-      if (x1 < x)                           // rest of shrinking procedure
-	xl1 = x1;
-      else 
-	xr1 = x1;
-    }
-  acceptable:
-    w = (4*w + (xr1 - xl1))/5;              // update width estimate
-  }
-  return x;
-}
-
-/*
-//! slice_sampler1d() implements a 1-d MCMC slice sampler.
-//! It should be correct for unimodal distributions, but
-//! not for multimodal ones.
-//
-template <typename F, typename LogP, typename Uniform01>
-F slice_sampler1d(const LogP& logP,     //!< log of distribution to sample
-		  F x,                  //!< initial sample
-		  Uniform01& u01,       //!< uniform random number generator
-		  F min_x = -std::numeric_limits<F>::infinity(),  //!< minimum value of support
-		  F max_x = std::numeric_limits<F>::infinity(),   //!< maximum value of support
-		  F w = 0.0,            //!< guess at initial width
-		  unsigned nsamples=1,  //!< number of samples to draw
-		  unsigned max_nfeval=200)  //!< max number of function evaluations
-{
-  typedef unsigned U;
-  assert(std::isfinite(x));
-  if (w <= 0.0) {
-    if (min_x > -std::numeric_limits<F>::infinity() && max_x < std::numeric_limits<F>::infinity())
-      w = (max_x - min_x)/4;
-    else
-      w = std::max(((x < 0.0) ? -x : x)/4, 0.1);
-  }
-  // TRACE4(x, min_x, max_x, w);
-  F logPx = logP(x);
-  assert(std::isfinite(logPx));
-  U nfeval = 1;
-  for (U sample = 0; sample < nsamples; ++sample) {
-    F x0 = x;
-    F logU = logPx + log(u01()+1e-100);
-    assert(std::isfinite(logU));
-    F r = u01();
-    F xl = std::max(min_x, x - r*w);
-    F xr = std::min(max_x, x + (1-r)*w);
-    // TRACE3(x, logPx, logU);
-    while (xl > min_x && logP(xl) > logU) {
-      xl -= w;
-      w *= 2;
-      ++nfeval;
-      if (nfeval >= max_nfeval)
-	std::cerr << "## Error: nfeval = " << nfeval << ", max_nfeval = " << max_nfeval << ", sample = " << sample << ", nsamples = " << nsamples << ", r = " << r << ", w = " << w << ", xl = " << xl << std::endl;
-      assert(nfeval < max_nfeval);
-    }
-    xl = std::max(xl, min_x);
-    while (xr < max_x && logP(xr) > logU) {
-      xr += w;
-      w *= 2;
-      ++nfeval;
-      if (nfeval >= max_nfeval)
-	std::cerr << "## Error: nfeval = " << nfeval << ", max_nfeval = " << max_nfeval << ", sample = " << sample << ", nsamples = " << nsamples << ", r = " << r << ", w = " << w << ", xr = " << xr << std::endl;
-      assert(nfeval < max_nfeval);
-    }
-    xr = std::min(xr, max_x);
-    while (true) {
-      r = u01();
-      x = r*xl + (1-r)*xr;
-      assert(std::isfinite(x));
-      logPx = logP(x);
-      // TRACE4(logPx, x, xl, xr);
-      assert(std::isfinite(logPx));
-      ++nfeval;
-      if (nfeval >= max_nfeval)
-	std::cerr << "## Error: nfeval = " << nfeval << ", max_nfeval = " << max_nfeval << ", sample = " << sample << ", nsamples = " << nsamples << ", r = " << r << ", w = " << w << ", xl = " << xl << ", xr = " << xr << ", x = " << x << std::endl;
-      assert(nfeval < max_nfeval);
-      if (logPx > logU)
-        break;
-      else if (x > x0)
-          xr = x;
-        else
-          xl = x;
-    }
-    // w = (4*w + (xr-xl))/5;   // gradually adjust w
-  }
-  // TRACE2(logPx, x);
-  return x;
-}  // slice_sampler1d()
-*/
-
-#endif  // SLICE_SAMPLER_H
diff --git a/gi/clda/src/timer.h b/gi/clda/src/timer.h
deleted file mode 100644
index 123d9a94..00000000
--- a/gi/clda/src/timer.h
+++ /dev/null
@@ -1,20 +0,0 @@
-#ifndef _TIMER_STATS_H_
-#define _TIMER_STATS_H_
-
-#include <ctime>
-
-struct Timer {
-  Timer() { Reset(); }
-  void Reset() {
-    start_t = clock();
-  }
-  double Elapsed() const {
-    const clock_t end_t = clock();
-    const double elapsed = (end_t - start_t) / 1000000.0;
-    return elapsed;
-  }
- private:
-  std::clock_t start_t;
-};
-
-#endif
diff --git a/gi/evaluation/conditional_entropy.py b/gi/evaluation/conditional_entropy.py
deleted file mode 100644
index 356d3b1d..00000000
--- a/gi/evaluation/conditional_entropy.py
+++ /dev/null
@@ -1,61 +0,0 @@
-#!/usr/bin/env python
-
-import sys, math, itertools, getopt
-
-def usage():
-    print >>sys.stderr, 'Usage:', sys.argv[0], '[-s slash_threshold] input-1 input-2'
-    sys.exit(0)
-
-optlist, args = getopt.getopt(sys.argv[1:], 'hs:')
-slash_threshold = None
-for opt, arg in optlist:
-    if opt == '-s':
-        slash_threshold = int(arg)
-    else:
-        usage()
-if len(args) != 2:
-    usage()
-
-ginfile = open(args[0])
-pinfile = open(args[1])
-
-# evaluating: H(G | P) = sum_{g,p} p(g,p) log { p(p) / p(g,p) }
-#                      = sum_{g,p} c(g,p)/N { log c(p) - log N - log c(g,p) + log N }
-#                      = 1/N sum_{g,p} c(g,p) { log c(p) - log c(g,p) }
-# where G = gold, P = predicted, N = number of events
-
-N = 0
-gold_frequencies = {}
-predict_frequencies = {}
-joint_frequencies = {}
-
-for gline, pline in itertools.izip(ginfile, pinfile):
-    gparts = gline.split('||| ')[1].split()
-    pparts = pline.split('||| ')[1].split()
-    assert len(gparts) == len(pparts)
-
-    for gpart, ppart in zip(gparts, pparts):
-        gtag = gpart.split(':',1)[1]
-        ptag = ppart.split(':',1)[1]
-
-        if slash_threshold == None or gtag.count('/') + gtag.count('\\') <= slash_threshold:
-            joint_frequencies.setdefault((gtag, ptag), 0)
-            joint_frequencies[gtag,ptag] += 1
-
-            predict_frequencies.setdefault(ptag, 0)
-            predict_frequencies[ptag] += 1
-
-            gold_frequencies.setdefault(gtag, 0)
-            gold_frequencies[gtag] += 1
-
-            N += 1
-
-hg2p = 0
-hp2g = 0
-for (gtag, ptag), cgp in joint_frequencies.items():
-    hp2g += cgp * (math.log(predict_frequencies[ptag], 2) - math.log(cgp, 2))
-    hg2p += cgp * (math.log(gold_frequencies[gtag], 2) - math.log(cgp, 2))
-hg2p /= N
-hp2g /= N
-
-print 'H(P|G)', hg2p, 'H(G|P)', hp2g, 'VI', hg2p + hp2g
diff --git a/gi/evaluation/confusion_matrix.py b/gi/evaluation/confusion_matrix.py
deleted file mode 100644
index 2dd7aa47..00000000
--- a/gi/evaluation/confusion_matrix.py
+++ /dev/null
@@ -1,123 +0,0 @@
-#!/usr/bin/env python
-
-import sys, math, itertools, getopt
-
-def usage():
-    print >>sys.stderr, 'Usage:', sys.argv[0], '[-s slash_threshold] [-p output] [-m] input-1 input-2'
-    sys.exit(0)
-
-optlist, args = getopt.getopt(sys.argv[1:], 'hs:mp:')
-slash_threshold = None
-output_fname = None
-show_matrix = False
-for opt, arg in optlist:
-    if opt == '-s':
-        slash_threshold = int(arg)
-    elif opt == '-p':
-        output_fname = arg
-    elif opt == '-m':
-        show_matrix = True
-    else:
-        usage()
-if len(args) != 2 or (not show_matrix and not output_fname):
-    usage()
-
-ginfile = open(args[0])
-pinfile = open(args[1])
-
-if output_fname:
-    try:
-        import Image, ImageDraw
-    except ImportError:
-        print >>sys.stderr, "Error: Python Image Library not available. Did you forget to set your PYTHONPATH environment variable?" 
-        sys.exit(1)
-
-N = 0
-gold_frequencies = {}
-predict_frequencies = {}
-joint_frequencies = {}
-
-for gline, pline in itertools.izip(ginfile, pinfile):
-    gparts = gline.split('||| ')[1].split()
-    pparts = pline.split('||| ')[1].split()
-    assert len(gparts) == len(pparts)
-
-    for gpart, ppart in zip(gparts, pparts):
-        gtag = gpart.split(':',1)[1]
-        ptag = ppart.split(':',1)[1]
-
-        if slash_threshold == None or gtag.count('/') + gtag.count('\\') <= slash_threshold:
-            joint_frequencies.setdefault((gtag, ptag), 0)
-            joint_frequencies[gtag,ptag] += 1
-
-            predict_frequencies.setdefault(ptag, 0)
-            predict_frequencies[ptag] += 1
-
-            gold_frequencies.setdefault(gtag, 0)
-            gold_frequencies[gtag] += 1
-
-            N += 1
-
-# find top tags
-gtags = gold_frequencies.items()
-gtags.sort(lambda x,y: x[1]-y[1])
-gtags.reverse()
-#gtags = gtags[:50]
-
-preds = predict_frequencies.items()
-preds.sort(lambda x,y: x[1]-y[1])
-preds.reverse()
-
-if show_matrix:
-    print '%7s %7s' % ('pred', 'cnt'),
-    for gtag, gcount in gtags: print '%7s' % gtag,
-    print
-    print '=' * 80
-
-    for ptag, pcount in preds:
-        print '%7s %7d' % (ptag, pcount),
-        for gtag, gcount in gtags:
-            print '%7d' % joint_frequencies.get((gtag, ptag), 0),
-        print
-
-    print '%7s %7d' % ('total', N),
-    for gtag, gcount in gtags: print '%7d' % gcount,
-    print
-
-if output_fname:
-    offset=10
-
-    image = Image.new("RGB", (len(preds), len(gtags)), (255, 255, 255))
-    #hsl(hue, saturation%, lightness%)
-
-    # re-sort preds to get a better diagonal
-    ptags=[]
-    if True:
-        ptags = map(lambda (p,c): p, preds)
-    else:
-        remaining = set(predict_frequencies.keys())
-        for y, (gtag, gcount) in enumerate(gtags):
-            best = (None, 0)
-            for ptag in remaining:
-                #pcount = predict_frequencies[ptag]
-                p = joint_frequencies.get((gtag, ptag), 0)# / float(pcount)
-                if p > best[1]: best = (ptag, p)
-            ptags.append(ptag)
-            remaining.remove(ptag)
-            if not remaining: break
-
-    print 'Predicted tag ordering:', ' '.join(ptags)
-    print 'Gold tag ordering:', ' '.join(map(lambda (t,c): t, gtags))
-    
-    draw = ImageDraw.Draw(image)
-    for x, ptag in enumerate(ptags):
-        pcount = predict_frequencies[ptag]
-        minval = math.log(offset)
-        maxval = math.log(pcount + offset)
-        for y, (gtag, gcount) in enumerate(gtags):
-            f = math.log(offset + joint_frequencies.get((gtag, ptag), 0))
-            z = int(240. * (maxval - f) / float(maxval - minval))
-            #print x, y, z, f, maxval
-            draw.point([(x,y)], fill='hsl(%d, 100%%, 50%%)' % z)
-    del draw
-    image.save(output_fname)
diff --git a/gi/evaluation/entropy.py b/gi/evaluation/entropy.py
deleted file mode 100644
index ec1ef502..00000000
--- a/gi/evaluation/entropy.py
+++ /dev/null
@@ -1,38 +0,0 @@
-#!/usr/bin/env python
-
-import sys, math, itertools, getopt
-
-def usage():
-    print >>sys.stderr, 'Usage:', sys.argv[0], '[-s slash_threshold] input file'
-    sys.exit(0)
-
-optlist, args = getopt.getopt(sys.argv[1:], 'hs:')
-slash_threshold = None
-for opt, arg in optlist:
-    if opt == '-s':
-        slash_threshold = int(arg)
-    else:
-        usage()
-if len(args) != 1:
-    usage()
-
-infile = open(args[0])
-N = 0
-frequencies = {}
-
-for line in infile:
-
-    for part in line.split('||| ')[1].split():
-        tag = part.split(':',1)[1]
-
-        if slash_threshold == None or tag.count('/') + tag.count('\\') <= slash_threshold:
-            frequencies.setdefault(tag, 0)
-            frequencies[tag] += 1
-            N += 1
-
-h = 0
-for tag, c in frequencies.items():
-    h -= c * (math.log(c, 2) - math.log(N, 2))
-h /= N
-
-print 'entropy', h
diff --git a/gi/evaluation/extract_ccg_labels.py b/gi/evaluation/extract_ccg_labels.py
deleted file mode 100644
index e0034648..00000000
--- a/gi/evaluation/extract_ccg_labels.py
+++ /dev/null
@@ -1,129 +0,0 @@
-#!/usr/bin/env python
-
-#
-# Takes spans input along with treebank and spits out CG style categories for each span.
-#   spans = output from CDEC's extools/extractor with --base_phrase_spans option
-#   treebank = PTB format, one tree per line
-# 
-# Output is in CDEC labelled-span format
-#
-
-import sys, itertools, tree
-
-tinfile = open(sys.argv[1])
-einfile = open(sys.argv[2])
-
-def number_leaves(node, next=0):
-    left, right = None, None
-    for child in node.children:
-        l, r = number_leaves(child, next)
-        next = max(next, r+1)
-        if left == None or l < left:
-            left = l
-        if right == None or r > right:
-            right = r
-
-    #print node, left, right, next
-    if left == None or right == None:
-        assert not node.children
-        left = right = next
-
-    node.left = left
-    node.right = right
-
-    return left, right
-
-def ancestor(node, indices):
-    #print node, node.left, node.right, indices
-    # returns the deepest node covering all the indices
-    if min(indices) >= node.left and max(indices) <= node.right:
-        # try the children
-        for child in node.children:
-            x = ancestor(child, indices)
-            if x: return x
-        return node
-    else:
-        return None
-
-def frontier(node, indices):
-    #print 'frontier for node', node, 'indices', indices
-    if node.left > max(indices) or node.right < min(indices):
-        #print '\toutside'
-        return [node]
-    elif node.children:
-        #print '\tcovering at least part'
-        ns = []
-        for child in node.children:
-            n = frontier(child, indices)
-            ns.extend(n)
-        return ns
-    else:
-        return [node]
-
-def project_heads(node):
-    #print 'project_heads', node
-    is_head = node.data.tag.endswith('-HEAD')
-    if node.children:
-        found = 0
-        for child in node.children:
-            x = project_heads(child)
-            if x:
-                node.data.tag = x
-                found += 1
-        assert found == 1
-    elif is_head:
-        node.data.tag = node.data.tag[:-len('-HEAD')]
-
-    if is_head:
-        return node.data.tag
-    else:
-        return None
-
-for tline, eline in itertools.izip(tinfile, einfile):
-    if tline.strip() != '(())':
-        if tline.startswith('( '):
-            tline = tline[2:-1].strip()
-        tr = tree.parse_PST(tline)
-	if tr != None:
-		number_leaves(tr)
-		#project_heads(tr) # assumes Bikel-style head annotation for the input trees
-    else:
-        tr = None
-    
-    parts = eline.strip().split(" ||| ")
-    zh, en = parts[:2]
-    spans = parts[-1]
-    print '|||',
-    for span in spans.split():
-        sps = span.split(":")
-        i, j, x, y = map(int, sps[0].split("-"))
-
-        if tr:
-            a = ancestor(tr, range(x,y))
-	    try:
-		fs = frontier(a, range(x,y))
-	    except:
-		print >>sys.stderr, "problem with line", tline.strip(), "--", eline.strip()
-		raise
-
-            #print x, y
-            #print 'ancestor', a
-            #print 'frontier', fs
-
-            cat = a.data.tag
-            for f in fs:
-                if f.right < x:
-                    cat += '\\' + f.data.tag
-                else:
-                    break
-            fs.reverse()
-            for f in fs:
-                if f.left >= y:
-                    cat += '/' + f.data.tag
-                else:
-                    break
-        else:
-            cat = 'FAIL'
-            
-        print '%d-%d:%s' % (x, y, cat),
-    print
diff --git a/gi/evaluation/tree.py b/gi/evaluation/tree.py
deleted file mode 100644
index 702d80b6..00000000
--- a/gi/evaluation/tree.py
+++ /dev/null
@@ -1,485 +0,0 @@
-import re, sys
-
-class Symbol:
-    def __init__(self, nonterm, term=None, var=None):
-        assert not (term != None and var != None)
-        self.tag = nonterm
-        self.token = term
-        self.variable = var
-
-    def is_variable(self):
-        return self.variable != None
-
-    def __eq__(self, other):
-        return self.tag == other.tag and self.token == other.token and self.variable == other.variable
-
-    def __ne__(self, other):
-        return not (self == other)
-
-    def __hash__(self):
-        return hash((self.tag, self.token, self.variable))
-
-    def __repr__(self):
-        return str(self)
-
-    def __cmp__(self, other):
-        return cmp((self.tag, self.token, self.variable),
-                   (other.tag, other.token, other.variable))
-
-    def __str__(self):
-        parts = []
-	if False: # DEPENDENCY
-	    if self.token:
-		parts.append(str(self.token))
-	    elif self.variable != None:
-		parts.append('#%d' % self.variable)
-	    if self.tag:
-		parts.append(str(self.tag))
-	    return '/'.join(parts)
-	else:
-	    if self.tag:
-		parts.append(str(self.tag))
-	    if self.token:
-		parts.append(str(self.token))
-	    elif self.variable != None:
-		parts.append('#%d' % self.variable)
-	    return ' '.join(parts)
-
-class TreeNode:
-    def __init__(self, data, children=None, order=-1):
-        self.data = data
-        self.children = []
-        self.order = order
-        self.parent = None
-        if children: self.children = children
-
-    def insert(self, child):
-        self.children.append(child)
-        child.parent = self
-
-    def leaves(self):
-        ls = []
-        for node in self.xtraversal():
-            if not node.children:
-                ls.append(node.data)
-        return ls
-
-    def leaf_nodes(self):
-        ls = []
-        for node in self.xtraversal():
-            if not node.children:
-                ls.append(node)
-        return ls
-
-    def max_depth(self):
-        d = 1
-        for child in self.children:
-            d = max(d, 1 + child.max_depth())
-        if not self.children and self.data.token:
-            d = 2
-        return d
-
-    def max_width(self):
-        w = 0
-        for child in self.children:
-           w += child.max_width()
-        return max(1, w)
-
-    def num_internal_nodes(self):
-        if self.children:
-            n = 1
-            for child in self.children:
-                n += child.num_internal_nodes()
-            return n
-        elif self.data.token:
-            return 1
-        else:
-            return 0
-
-    def postorder_traversal(self, visit):
-        """
-	Postorder traversal; no guarantee that terminals will be read in the
-	correct order for dep. trees.
-        """
-        for child in self.children:
-            child.traversal(visit)
-	visit(self)
-
-    def traversal(self, visit):
-        """
-        Preorder for phrase structure trees, and inorder for dependency trees.
-        In both cases the terminals will be read off in the correct order.
-        """
-        visited_self = False
-        if self.order <= 0:
-            visited_self = True
-            visit(self)
-
-        for i, child in enumerate(self.children):
-            child.traversal(visit)
-            if i + 1 == self.order:
-                visited_self = True
-                visit(self)
-
-        assert visited_self
-
-    def xpostorder_traversal(self):
-        for child in self.children:
-            for node in child.xpostorder_traversal():
-                yield node
-        yield self
-
-    def xtraversal(self):
-        visited_self = False
-        if self.order <= 0:
-            visited_self = True
-            yield self
-
-        for i, child in enumerate(self.children):
-            for d in child.xtraversal():
-                yield d
-
-            if i + 1 == self.order:
-                visited_self = True
-                yield self
-
-        assert visited_self
-
-    def xpostorder_traversal(self):
-        for i, child in enumerate(self.children):
-            for d in child.xpostorder_traversal():
-                yield d
-        yield self
-
-    def edges(self):
-        es = []
-        self.traverse_edges(lambda h,c: es.append((h,c)))
-        return es
-
-    def traverse_edges(self, visit):
-        for child in self.children:
-            visit(self.data, child.data)
-            child.traverse_edges(visit)
-
-    def subtrees(self, include_self=False):
-        st = []
-        if include_self:
-            stack = [self]
-        else:
-            stack = self.children[:]
-
-        while stack:
-            node = stack.pop()
-            st.append(node)
-            stack.extend(node.children)
-        return st
-
-    def find_parent(self, node):
-        try:
-            index = self.children.index(node)
-            return self, index
-        except ValueError:
-            for child in self.children:
-                if isinstance(child, TreeNode):
-                    r = child.find_parent(node)
-                    if r: return r
-        return None
-
-    def is_ancestor_of(self, node):
-        if self == node:
-            return True
-        for child in self.children:
-            if child.is_ancestor_of(child):
-                return True
-        return False
-
-    def find(self, node):
-        if self == node:
-            return self
-        for child in self.children:
-            if isinstance(child, TreeNode):
-                r = child.find(node)
-                if r: return r
-            else:
-                if child == node:
-                   return r
-        return None
-
-    def equals_ignorecase(self, other):
-        if not isinstance(other, TreeNode):
-            return False
-        if self.data != other.data:
-            return False
-        if len(self.children) != len(other.children):
-            return False
-        for mc, oc in zip(self.children, other.children):
-            if isinstance(mc, TreeNode):
-                if not mc.equals_ignorecase(oc):
-                    return False
-            else:
-                if mc.lower() != oc.lower():
-                    return False
-        return True
-
-    def node_number(self, numbering, next=0):
-        if self.order <= 0:
-            numbering[id(self)] = next
-            next += 1
-
-        for i, child in enumerate(self.children):
-            next = child.node_number(numbering, next)
-            if i + 1 == self.order:
-                numbering[id(self)] = next
-                next += 1
-
-        return next
-
-    def display_conll(self, out):
-        numbering = {}
-        self.node_number(numbering)
-        next = 0
-        self.children[0].traversal(lambda x: \
-            out.write('%d\t%s\t%s\t%s\t%s\t_\t%d\tLAB\n' \
-             % (numbering[id(x)], x.data.token, x.data.token, 
-                x.data.tag, x.data.tag, numbering[id(x.parent)])))
-        out.write('\n')
-
-    def size(self):
-        sz = 1 
-        for child in self.children:
-            sz += child.size()
-        return sz
-
-    def __eq__(self, other):
-        if isinstance(other, TreeNode) and self.data == other.data \
-                and self.children == other.children:
-            return True
-        return False
-
-    def __cmp__(self, other):
-        if not isinstance(other, TreeNode): return 1
-        n = cmp(self.data, other.data)
-        if n != 0: return n
-        n = len(self.children) - len(other.children)
-        if n != 0: return n
-        for sc, oc in zip(self.children, other.children):
-            n = cmp(sc, oc)
-            if n != 0: return n
-        return 0
-
-    def __ne__(self, other):
-        return not self.__eq__(other)
-
-    def __hash__(self):
-        return hash((self.data, tuple(self.children)))
-
-    def __repr__(self):
-        return str(self)
-
-    def __str__(self):
-        s = '('
-        space = False
-        if self.order <= 0:
-            s += str(self.data)
-            space = True
-        for i, child in enumerate(self.children):
-            if space: s += ' '
-            s += str(child)
-            space = True
-            if i+1 == self.order:
-                s += ' ' + str(self.data)
-        return s + ')'
-
-def read_PSTs(fname):
-    infile = open(fname)
-    trees = []
-    for line in infile:
-        trees.append(parse_PST(line.strip()))
-    infile.close()
-    return trees
-
-def parse_PST_multiline(infile, hash_is_var=True):
-    buf = ''
-    num_open = 0
-    while True:
-        line = infile.readline()
-        if not line:
-            return None
-        buf += ' ' + line.rstrip()
-        num_open += line.count('(') - line.count(')')
-        if num_open == 0:
-            break
-
-    return parse_PST(buf, hash_is_var)
-
-def parse_PST(line, hash_is_var=True):
-    line = line.rstrip()
-    if not line or line.lower() == 'null':
-        return None
-
-    # allow either (a/DT) or (DT a)
-    #parts_re = re.compile(r'(\(*)([^/)]*)(?:/([^)]*))?(\)*)$')
-
-    # only allow (DT a)
-    parts_re = re.compile(r'(\(*)([^)]*)(\)*)$')
-
-    root = TreeNode(Symbol('TOP'))
-    stack = [root]
-    for part in line.rstrip().split():
-        m = parts_re.match(part)
-        #opening, tok_or_tag, tag, closing = m.groups()
-        opening, tok_or_tag, closing = m.groups()
-	tag = None
-        #print 'token', part, 'bits', m.groups()
-        for i in opening:
-            node = TreeNode(Symbol(None))
-            stack[-1].insert(node)
-            stack.append(node)
-
-        if tag:
-            stack[-1].data.tag = tag
-            if hash_is_var and tok_or_tag.startswith('#'):
-                stack[-1].data.variable = int(tok_or_tag[1:])
-            else:
-                stack[-1].data.token = tok_or_tag
-        else:
-            if stack[-1].data.tag == None:
-                stack[-1].data.tag = tok_or_tag
-            else:
-                if hash_is_var and tok_or_tag.startswith('#'):
-                    try:
-                        stack[-1].data.variable = int(tok_or_tag[1:])
-                    except ValueError: # it's really a token!
-                        #print >>sys.stderr, 'Warning: # used for token:', tok_or_tag
-                        stack[-1].data.token = tok_or_tag
-                else:
-                    stack[-1].data.token = tok_or_tag
-        
-        for i in closing:
-            stack.pop()
-
-    #assert str(root.children[0]) == line
-    return root.children[0]
-
-def read_DTs(fname):
-    infile = open(fname)
-    trees = []
-    while True:
-        t = parse_DT(infile)
-        if t: trees.append(t)
-        else: break
-    infile.close()
-    return trees
-
-def read_bracketed_DTs(fname):
-    infile = open(fname)
-    trees = []
-    for line in infile:
-        trees.append(parse_bracketed_DT(line))
-    infile.close()
-    return trees
-
-def parse_DT(infile):
-    tokens = [Symbol('ROOT')]
-    children = {}
-
-    for line in infile:
-        parts = line.rstrip().split()
-        #print parts
-        if not parts: break
-        index = len(tokens)
-        token = parts[1]
-        tag = parts[3]
-        parent = int(parts[6])
-        if token.startswith('#'):
-            tokens.append(Symbol(tag, var=int(token[1:])))
-        else:
-            tokens.append(Symbol(tag, token))
-        children.setdefault(parent, set()).add(index)
-
-    if len(tokens) == 1: return None
-
-    root = TreeNode(Symbol('ROOT'), [], 0)
-    schedule = []
-    for child in sorted(children[0]):
-        schedule.append((root, child))
-
-    while schedule:
-        parent, index = schedule[0]
-        del schedule[0]
-    
-        node = TreeNode(tokens[index])
-        node.order = 0
-        parent.insert(node)
-
-        for child in sorted(children.get(index, [])):
-            schedule.append((node, child))
-            if child < index:
-                node.order += 1
-
-    return root
-
-_bracket_split_re = re.compile(r'([(]*)([^)/]*)(?:/([^)]*))?([)]*)')
-
-def parse_bracketed_DT(line, insert_root=True):
-    line = line.rstrip()
-    if not line or line == 'NULL': return None
-    #print line
-
-    root = TreeNode(Symbol('ROOT'))
-    stack = [root]
-    for part in line.rstrip().split():
-        m = _bracket_split_re.match(part)
-
-        for c in m.group(1):
-            node = TreeNode(Symbol(None))
-            stack[-1].insert(node)
-            stack.append(node)
-
-        if m.group(3) != None:
-            if m.group(2).startswith('#'):
-                stack[-1].data.variable = int(m.group(2)[1:])
-            else:
-                stack[-1].data.token = m.group(2)
-            stack[-1].data.tag = m.group(3)
-        else:
-            stack[-1].data.tag = m.group(2)
-        stack[-1].order = len(stack[-1].children)
-        # FIXME: also check for vars
-
-        for c in m.group(4):
-            stack.pop()
-
-    assert len(stack) == 1
-    if not insert_root or root.children[0].data.tag == 'ROOT':
-        return root.children[0]
-    else:
-        return root
-
-_bracket_split_notag_re = re.compile(r'([(]*)([^)/]*)([)]*)')
-
-def parse_bracketed_untagged_DT(line):
-    line = line.rstrip()
-    if not line or line == 'NULL': return None
-
-    root = TreeNode(Symbol('TOP'))
-    stack = [root]
-    for part in line.rstrip().split():
-        m = _bracket_split_notag_re.match(part)
-
-        for c in m.group(1):
-            node = TreeNode(Symbol(None))
-            stack[-1].insert(node)
-            stack.append(node)
-
-        if stack[-1].data.token == None:
-            stack[-1].data.token = m.group(2)
-            stack[-1].order = len(stack[-1].children)
-        else:
-            child = TreeNode(Symbol(nonterm=None, term=m.group(2)))
-            stack[-1].insert(child)
-
-        for c in m.group(3):
-            stack.pop()
-
-    return root.children[0]
diff --git a/gi/markov_al/Makefile.am b/gi/markov_al/Makefile.am
deleted file mode 100644
index fe3e3349..00000000
--- a/gi/markov_al/Makefile.am
+++ /dev/null
@@ -1,6 +0,0 @@
-bin_PROGRAMS = ml
-
-ml_SOURCES = ml.cc
-
-AM_CPPFLAGS = -W -Wall -Wno-sign-compare -funroll-loops -I$(top_srcdir)/utils $(GTEST_CPPFLAGS) -I$(top_srcdir)/decoder
-AM_LDFLAGS = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/utils/libutils.a -lz
diff --git a/gi/markov_al/README b/gi/markov_al/README
deleted file mode 100644
index 9c10f7cd..00000000
--- a/gi/markov_al/README
+++ /dev/null
@@ -1,2 +0,0 @@
-Experimental translation models with Markovian dependencies.
-
diff --git a/gi/markov_al/ml.cc b/gi/markov_al/ml.cc
deleted file mode 100644
index 1e71edd6..00000000
--- a/gi/markov_al/ml.cc
+++ /dev/null
@@ -1,470 +0,0 @@
-#include <iostream>
-#include <tr1/unordered_map>
-
-#include <boost/shared_ptr.hpp>
-#include <boost/functional.hpp>
-#include <boost/program_options.hpp>
-#include <boost/program_options/variables_map.hpp>
-
-#include "tdict.h"
-#include "filelib.h"
-#include "sampler.h"
-#include "ccrp_onetable.h"
-#include "array2d.h"
-
-using namespace std;
-using namespace std::tr1;
-namespace po = boost::program_options;
-
-void PrintTopCustomers(const CCRP_OneTable<WordID>& crp) {
-  for (CCRP_OneTable<WordID>::const_iterator it = crp.begin(); it != crp.end(); ++it) {
-    cerr << "  " << TD::Convert(it->first) << " = " << it->second << endl;
-  }
-}
-
-void PrintAlignment(const vector<WordID>& src, const vector<WordID>& trg, const vector<unsigned char>& a) {
-  cerr << TD::GetString(src) << endl << TD::GetString(trg) << endl;
-  Array2D<bool> al(src.size(), trg.size());
-  for (int i = 0; i < a.size(); ++i)
-    if (a[i] != 255) al(a[i], i) = true;
-  cerr << al << endl;
-}
-
-void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
-  po::options_description opts("Configuration options");
-  opts.add_options()
-        ("samples,s",po::value<unsigned>()->default_value(1000),"Number of samples")
-        ("input,i",po::value<string>(),"Read parallel data from")
-        ("random_seed,S",po::value<uint32_t>(), "Random seed");
-  po::options_description clo("Command line options");
-  clo.add_options()
-        ("config", po::value<string>(), "Configuration file")
-        ("help,h", "Print this help message and exit");
-  po::options_description dconfig_options, dcmdline_options;
-  dconfig_options.add(opts);
-  dcmdline_options.add(opts).add(clo);
-  
-  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
-  if (conf->count("config")) {
-    ifstream config((*conf)["config"].as<string>().c_str());
-    po::store(po::parse_config_file(config, dconfig_options), *conf);
-  }
-  po::notify(*conf);
-
-  if (conf->count("help") || (conf->count("input") == 0)) {
-    cerr << dcmdline_options << endl;
-    exit(1);
-  }
-}
-
-struct Unigram;
-struct Bigram {
-  Bigram() : trg(), cond() {}
-  Bigram(WordID prev, WordID cur, WordID t) : trg(t) { cond.first = prev; cond.second = cur; }
-  const pair<WordID,WordID>& ConditioningPair() const {
-    return cond;
-  }
-  WordID& prev_src() { return cond.first; }
-  WordID& cur_src() { return cond.second; }
-  const WordID& prev_src() const { return cond.first; }
-  const WordID& cur_src() const { return cond.second; }
-  WordID trg;
- private:
-  pair<WordID, WordID> cond;
-};
-
-struct Unigram {
-  Unigram() : cur_src(), trg() {}
-  Unigram(WordID s, WordID t) : cur_src(s), trg(t) {}
-  WordID cur_src;
-  WordID trg;
-};
-
-ostream& operator<<(ostream& os, const Bigram& b) {
-  os << "( " << TD::Convert(b.trg) << " | " << TD::Convert(b.prev_src()) << " , " << TD::Convert(b.cur_src()) << " )";
-  return os;
-}
-
-ostream& operator<<(ostream& os, const Unigram& u) {
-  os << "( " << TD::Convert(u.trg) << " | " << TD::Convert(u.cur_src) << " )";
-  return os;
-}
-
-bool operator==(const Bigram& a, const Bigram& b) {
-  return a.trg == b.trg && a.cur_src() == b.cur_src() && a.prev_src() == b.prev_src();
-}
-
-bool operator==(const Unigram& a, const Unigram& b) {
-  return a.trg == b.trg && a.cur_src == b.cur_src;
-}
-
-size_t hash_value(const Bigram& b) {
-  size_t h = boost::hash_value(b.prev_src());
-  boost::hash_combine(h, boost::hash_value(b.cur_src()));
-  boost::hash_combine(h, boost::hash_value(b.trg));
-  return h;
-}
-
-size_t hash_value(const Unigram& u) {
-  size_t h = boost::hash_value(u.cur_src);
-  boost::hash_combine(h, boost::hash_value(u.trg));
-  return h;
-}
-
-void ReadParallelCorpus(const string& filename,
-                vector<vector<WordID> >* f,
-                vector<vector<WordID> >* e,
-                set<WordID>* vocab_f,
-                set<WordID>* vocab_e) {
-  f->clear();
-  e->clear();
-  vocab_f->clear();
-  vocab_e->clear();
-  istream* in;
-  if (filename == "-")
-    in = &cin;
-  else
-    in = new ifstream(filename.c_str());
-  assert(*in);
-  string line;
-  const WordID kDIV = TD::Convert("|||");
-  vector<WordID> tmp;
-  while(*in) {
-    getline(*in, line);
-    if (line.empty() && !*in) break;
-    e->push_back(vector<int>());
-    f->push_back(vector<int>());
-    vector<int>& le = e->back();
-    vector<int>& lf = f->back();
-    tmp.clear();
-    TD::ConvertSentence(line, &tmp);
-    bool isf = true;
-    for (unsigned i = 0; i < tmp.size(); ++i) {
-      const int cur = tmp[i];
-      if (isf) {
-        if (kDIV == cur) { isf = false; } else {
-          lf.push_back(cur);
-          vocab_f->insert(cur);
-        }
-      } else {
-        assert(cur != kDIV);
-        le.push_back(cur);
-        vocab_e->insert(cur);
-      }
-    }
-    assert(isf == false);
-  }
-  if (in != &cin) delete in;
-}
-
-struct UnigramModel {
-  UnigramModel(size_t src_voc_size, size_t trg_voc_size) :
-    unigrams(TD::NumWords() + 1, CCRP_OneTable<WordID>(1,1,1,1)),
-    p0(1.0 / trg_voc_size) {}
-
-  void increment(const Bigram& b) {
-    unigrams[b.cur_src()].increment(b.trg);
-  }
-
-  void decrement(const Bigram& b) {
-    unigrams[b.cur_src()].decrement(b.trg);
-  }
-
-  double prob(const Bigram& b) const {
-    const double q0 = unigrams[b.cur_src()].prob(b.trg, p0);
-    return q0;
-  }
-
-  double LogLikelihood() const {
-    double llh = 0;
-    for (unsigned i = 0; i < unigrams.size(); ++i) {
-      const CCRP_OneTable<WordID>& crp = unigrams[i];
-      if (crp.num_customers() > 0) {
-        llh += crp.log_crp_prob();
-        llh += crp.num_tables() * log(p0);
-      }
-    }
-    return llh;
-  }
-
-  void ResampleHyperparameters(MT19937* rng) {
-    for (unsigned i = 0; i < unigrams.size(); ++i)
-      unigrams[i].resample_hyperparameters(rng);
-  }
-
-  vector<CCRP_OneTable<WordID> > unigrams;  // unigrams[src].prob(trg, p0) = p(trg|src)
-
-  const double p0;
-};
-
-struct BigramModel {
-  BigramModel(size_t src_voc_size, size_t trg_voc_size) :
-    unigrams(TD::NumWords() + 1, CCRP_OneTable<WordID>(1,1,1,1)),
-    p0(1.0 / trg_voc_size) {}
-
-  void increment(const Bigram& b) {
-    BigramMap::iterator it = bigrams.find(b.ConditioningPair());
-    if (it == bigrams.end()) {
-      it = bigrams.insert(make_pair(b.ConditioningPair(), CCRP_OneTable<WordID>(1,1,1,1))).first;
-    }
-    if (it->second.increment(b.trg))
-      unigrams[b.cur_src()].increment(b.trg);
-  }
-
-  void decrement(const Bigram& b) {
-    BigramMap::iterator it = bigrams.find(b.ConditioningPair());
-    assert(it != bigrams.end());
-    if (it->second.decrement(b.trg)) {
-      unigrams[b.cur_src()].decrement(b.trg);
-      if (it->second.num_customers() == 0)
-        bigrams.erase(it);
-    }
-  }
-
-  double prob(const Bigram& b) const {
-    const double q0 = unigrams[b.cur_src()].prob(b.trg, p0);
-    const BigramMap::const_iterator it = bigrams.find(b.ConditioningPair());
-    if (it == bigrams.end()) return q0;
-    return it->second.prob(b.trg, q0);
-  }
-
-  double LogLikelihood() const {
-    double llh = 0;
-    for (unsigned i = 0; i < unigrams.size(); ++i) {
-      const CCRP_OneTable<WordID>& crp = unigrams[i];
-      if (crp.num_customers() > 0) {
-        llh += crp.log_crp_prob();
-        llh += crp.num_tables() * log(p0);
-      }
-    }
-    for (BigramMap::const_iterator it = bigrams.begin(); it != bigrams.end(); ++it) {
-      const CCRP_OneTable<WordID>& crp = it->second;
-      const WordID cur_src = it->first.second;
-      llh += crp.log_crp_prob();
-      for (CCRP_OneTable<WordID>::const_iterator bit = crp.begin(); bit != crp.end(); ++bit) {
-        llh += log(unigrams[cur_src].prob(bit->second, p0));
-      }
-    }
-    return llh;
-  }
-
-  void ResampleHyperparameters(MT19937* rng) {
-    for (unsigned i = 0; i < unigrams.size(); ++i)
-      unigrams[i].resample_hyperparameters(rng);
-    for (BigramMap::iterator it = bigrams.begin(); it != bigrams.end(); ++it)
-      it->second.resample_hyperparameters(rng);
-  }
-
-  typedef unordered_map<pair<WordID,WordID>, CCRP_OneTable<WordID>, boost::hash<pair<WordID,WordID> > > BigramMap;
-  BigramMap bigrams;  // bigrams[(src-1,src)].prob(trg, q0) = p(trg|src,src-1)
-  vector<CCRP_OneTable<WordID> > unigrams;  // unigrams[src].prob(trg, p0) = p(trg|src)
-
-  const double p0;
-};
-
-struct BigramAlignmentModel {
-  BigramAlignmentModel(size_t src_voc_size, size_t trg_voc_size) : bigrams(TD::NumWords() + 1, CCRP_OneTable<WordID>(1,1,1,1)), p0(1.0 / src_voc_size) {}
-  void increment(WordID prev, WordID next) {
-    bigrams[prev].increment(next);  // hierarchy?
-  }
-  void decrement(WordID prev, WordID next) {
-    bigrams[prev].decrement(next);  // hierarchy?
-  }
-  double prob(WordID prev, WordID next) {
-    return bigrams[prev].prob(next, p0);
-  }
-  double LogLikelihood() const {
-    double llh = 0;
-    for (unsigned i = 0; i < bigrams.size(); ++i) {
-      const CCRP_OneTable<WordID>& crp = bigrams[i];
-      if (crp.num_customers() > 0) {
-        llh += crp.log_crp_prob();
-        llh += crp.num_tables() * log(p0);
-      }
-    }
-    return llh;
-  }
-
-  vector<CCRP_OneTable<WordID> > bigrams;  // bigrams[prev].prob(next, p0) = p(next|prev)
-  const double p0;
-};
-
-struct Alignment {
-  vector<unsigned char> a;
-};
-
-int main(int argc, char** argv) {
-  po::variables_map conf;
-  InitCommandLine(argc, argv, &conf);
-  const unsigned samples = conf["samples"].as<unsigned>();
-
-  boost::shared_ptr<MT19937> prng;
-  if (conf.count("random_seed"))
-    prng.reset(new MT19937(conf["random_seed"].as<uint32_t>()));
-  else
-    prng.reset(new MT19937);
-  MT19937& rng = *prng;
-
-  vector<vector<WordID> > corpuse, corpusf;
-  set<WordID> vocabe, vocabf;
-  cerr << "Reading corpus...\n";
-  ReadParallelCorpus(conf["input"].as<string>(), &corpusf, &corpuse, &vocabf, &vocabe);
-  cerr << "F-corpus size: " << corpusf.size() << " sentences\t (" << vocabf.size() << " word types)\n";
-  cerr << "E-corpus size: " << corpuse.size() << " sentences\t (" << vocabe.size() << " word types)\n";
-  assert(corpusf.size() == corpuse.size());
-  const size_t corpus_len = corpusf.size();
-  const WordID kNULL = TD::Convert("<eps>");
-  const WordID kBOS = TD::Convert("<s>");
-  const WordID kEOS = TD::Convert("</s>");
-  Bigram TT(kBOS, TD::Convert("我"), TD::Convert("i"));
-  Bigram TT2(kBOS, TD::Convert("�"), TD::Convert("i"));
-
-  UnigramModel model(vocabf.size(), vocabe.size());
-  vector<Alignment> alignments(corpus_len);
-  for (unsigned ci = 0; ci < corpus_len; ++ci) {
-    const vector<WordID>& src = corpusf[ci];
-    const vector<WordID>& trg = corpuse[ci];
-    vector<unsigned char>& alg = alignments[ci].a;
-    alg.resize(trg.size());
-    int lenp1 = src.size() + 1;
-    WordID prev_src = kBOS;
-    for (int j = 0; j < trg.size(); ++j) {
-      int samp = lenp1 * rng.next();
-      --samp;
-      if (samp < 0) samp = 255;
-      alg[j] = samp;
-      WordID cur_src = (samp == 255 ? kNULL : src[alg[j]]);
-      Bigram b(prev_src, cur_src, trg[j]);
-      model.increment(b);
-      prev_src = cur_src;
-    }
-    Bigram b(prev_src, kEOS, kEOS);
-    model.increment(b);
-  }
-  cerr << "Initial LLH: " << model.LogLikelihood() << endl;
-
-  SampleSet<double> ss;
-  for (unsigned si = 0; si < 50; ++si) {
-    for (unsigned ci = 0; ci < corpus_len; ++ci) {
-      const vector<WordID>& src = corpusf[ci];
-      const vector<WordID>& trg = corpuse[ci];
-      vector<unsigned char>& alg = alignments[ci].a;
-      WordID prev_src = kBOS;
-      for (unsigned j = 0; j < trg.size(); ++j) {
-        unsigned char& a_j = alg[j];
-        WordID cur_e_a_j = (a_j == 255 ? kNULL : src[a_j]);
-        Bigram b(prev_src, cur_e_a_j, trg[j]);
-        //cerr << "DEC: " << b << "\t" << nextb << endl;
-        model.decrement(b);
-        ss.clear();
-        for (unsigned i = 0; i <= src.size(); ++i) {
-          const WordID cur_src = (i ? src[i-1] : kNULL);
-          b.cur_src() = cur_src;
-          ss.add(model.prob(b));
-        }
-        int sampled_a_j = rng.SelectSample(ss);
-        a_j = (sampled_a_j ? sampled_a_j - 1 : 255);
-        cur_e_a_j = (a_j == 255 ? kNULL : src[a_j]);
-        b.cur_src() = cur_e_a_j;
-        //cerr << "INC: " << b << "\t" << nextb << endl;
-        model.increment(b);
-        prev_src = cur_e_a_j;
-      }
-    }
-    cerr << '.' << flush;
-    if (si % 10 == 9) {
-      cerr << "[LLH prev=" << model.LogLikelihood();
-      //model.ResampleHyperparameters(&rng);
-      cerr << " new=" << model.LogLikelihood() << "]\n";
-      //pair<WordID,WordID> xx = make_pair(kBOS, TD::Convert("我"));
-      //PrintTopCustomers(model.bigrams.find(xx)->second);
-      cerr << "p(" << TT << ") = " << model.prob(TT) << endl;
-      cerr << "p(" << TT2 << ") = " << model.prob(TT2) << endl;
-      PrintAlignment(corpusf[0], corpuse[0], alignments[0].a);
-    }
-  }
-  {
-  // MODEL 2
-  BigramModel model(vocabf.size(), vocabe.size());
-  BigramAlignmentModel amodel(vocabf.size(), vocabe.size());
-  for (unsigned ci = 0; ci < corpus_len; ++ci) {
-    const vector<WordID>& src = corpusf[ci];
-    const vector<WordID>& trg = corpuse[ci];
-    vector<unsigned char>& alg = alignments[ci].a;
-    WordID prev_src = kBOS;
-    for (int j = 0; j < trg.size(); ++j) {
-      WordID cur_src = (alg[j] == 255 ? kNULL : src[alg[j]]);
-      Bigram b(prev_src, cur_src, trg[j]);
-      model.increment(b);
-      amodel.increment(prev_src, cur_src);
-      prev_src = cur_src;
-    }
-    amodel.increment(prev_src, kEOS);
-    Bigram b(prev_src, kEOS, kEOS);
-    model.increment(b);
-  }
-  cerr << "Initial LLH: " << model.LogLikelihood() << " " << amodel.LogLikelihood() << endl;
-
-  SampleSet<double> ss;
-  for (unsigned si = 0; si < samples; ++si) {
-    for (unsigned ci = 0; ci < corpus_len; ++ci) {
-      const vector<WordID>& src = corpusf[ci];
-      const vector<WordID>& trg = corpuse[ci];
-      vector<unsigned char>& alg = alignments[ci].a;
-      WordID prev_src = kBOS;
-      for (unsigned j = 0; j < trg.size(); ++j) {
-        unsigned char& a_j = alg[j];
-        WordID cur_e_a_j = (a_j == 255 ? kNULL : src[a_j]);
-        Bigram b(prev_src, cur_e_a_j, trg[j]);
-        WordID next_src = kEOS;
-        WordID next_trg = kEOS;
-        if (j < (trg.size() - 1)) {
-          next_src = (alg[j+1] == 255 ? kNULL : src[alg[j + 1]]);
-          next_trg = trg[j + 1];
-        }
-        Bigram nextb(cur_e_a_j, next_src, next_trg);
-        //cerr << "DEC: " << b << "\t" << nextb << endl;
-        model.decrement(b);
-        model.decrement(nextb);
-        amodel.decrement(prev_src, cur_e_a_j);
-        amodel.decrement(cur_e_a_j, next_src);
-        ss.clear();
-        for (unsigned i = 0; i <= src.size(); ++i) {
-          const WordID cur_src = (i ? src[i-1] : kNULL);
-          b.cur_src() = cur_src;
-          ss.add(model.prob(b) * model.prob(nextb) * amodel.prob(prev_src, cur_src) * amodel.prob(cur_src, next_src));
-          //cerr << log(ss[ss.size() - 1]) << "\t" << b << endl;
-        }
-        int sampled_a_j = rng.SelectSample(ss);
-        a_j = (sampled_a_j ? sampled_a_j - 1 : 255);
-        cur_e_a_j = (a_j == 255 ? kNULL : src[a_j]);
-        b.cur_src() = cur_e_a_j;
-        nextb.prev_src() = cur_e_a_j;
-        //cerr << "INC: " << b << "\t" << nextb << endl;
-        //exit(1);
-        model.increment(b);
-        model.increment(nextb);
-        amodel.increment(prev_src, cur_e_a_j);
-        amodel.increment(cur_e_a_j, next_src);
-        prev_src = cur_e_a_j;
-      }
-    }
-    cerr << '.' << flush;
-    if (si % 10 == 9) {
-      cerr << "[LLH prev=" << (model.LogLikelihood() + amodel.LogLikelihood());
-      //model.ResampleHyperparameters(&rng);
-      cerr << " new=" << model.LogLikelihood() << "]\n";
-      pair<WordID,WordID> xx = make_pair(kBOS, TD::Convert("我"));
-      cerr << "p(" << TT << ") = " << model.prob(TT) << endl;
-      cerr << "p(" << TT2 << ") = " << model.prob(TT2) << endl;
-      pair<WordID,WordID> xx2 = make_pair(kBOS, TD::Convert("�"));
-      PrintTopCustomers(model.bigrams.find(xx)->second);
-      //PrintTopCustomers(amodel.bigrams[TD::Convert("<s>")]);
-      //PrintTopCustomers(model.unigrams[TD::Convert("<eps>")]);
-      PrintAlignment(corpusf[0], corpuse[0], alignments[0].a);
-    }
-  }
-  }
-  return 0;
-}
-
diff --git a/gi/morf-segmentation/filter_docs.pl b/gi/morf-segmentation/filter_docs.pl
deleted file mode 100755
index a78575da..00000000
--- a/gi/morf-segmentation/filter_docs.pl
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/usr/bin/perl
-
-#Filters the phrase&cluster document set to retain only documents that correspond to words or morphs, i.e. not crossing word boundaries.
-
-#Usage: filter_docs.pl [mark]
-#  STDIN: data in the doc.txt format (i.e. phrase\t blahblah ), most likely from cdec extractor
-#  STDOUT: the matching subset, same format
-
-use utf8;
-my $letter=qr/\p{L}\p{M}*/; # see http://www.regular-expressions.info/unicode.html
-
-my $morph=qr/$letter+/;
-
-my $m = "##"; # marker used to indicate morphemes
-if ((scalar @ARGV) >= 1) {
-   $m = $ARGV[0];
-   shift;
-}
-print STDERR "Using $m to filter for morphemes\n";
-
-my $expr = qr/^($morph\Q$m\E)? ?(\Q$m\E$morph\Q$m\E)* ?(\Q$m\E$morph)?\t/; #\Q and \E bounded sections are escaped
-while(<>) {
-   /$expr/ && print;
-}
diff --git a/gi/morf-segmentation/invalid_vocab.patterns b/gi/morf-segmentation/invalid_vocab.patterns
deleted file mode 100644
index 473ce1b1..00000000
--- a/gi/morf-segmentation/invalid_vocab.patterns
+++ /dev/null
@@ -1,6 +0,0 @@
-[[:digit:]]
-[] !"#$%&()*+,./:;<=>?@[\^_`{|}~]
-^'$
--$
-^-
-^$
diff --git a/gi/morf-segmentation/linestripper.py b/gi/morf-segmentation/linestripper.py
deleted file mode 100755
index 04e9044a..00000000
--- a/gi/morf-segmentation/linestripper.py
+++ /dev/null
@@ -1,40 +0,0 @@
-#!/usr/bin/python
-
-import sys
-
-#linestripper   file file maxlen [numlines]
-
-if len(sys.argv) < 3:
-  print "linestripper   file1 file2 maxlen [numlines]" 
-  print " outputs subset of file1 to stdout, ..of file2 to stderr"
-  sys.exit(1)
-
-
-f1 = open(sys.argv[1],'r')
-f2 = open(sys.argv[2],'r')
-
-maxlen=int(sys.argv[3])
-numlines = 0
-
-if len(sys.argv) > 4:
-  numlines = int(sys.argv[4])
-
-count=0
-for line1 in f1:
-  line2 = f2.readline()
-  
-  w1 = len(line1.strip().split())
-  w2 = len(line2.strip().split())
-
-  if w1 <= maxlen and w2 <= maxlen:
-    count = count + 1
-    sys.stdout.write(line1)
-    sys.stderr.write(line2)
- 
-  if numlines > 0 and count >= numlines:
-    break
-
-f1.close()
-f2.close()
-  
-
diff --git a/gi/morf-segmentation/morf-pipeline.pl b/gi/morf-segmentation/morf-pipeline.pl
deleted file mode 100755
index 46eb5b46..00000000
--- a/gi/morf-segmentation/morf-pipeline.pl
+++ /dev/null
@@ -1,486 +0,0 @@
-#!/usr/bin/perl -w
-use strict;
-use File::Copy;
-
-
-# Preprocessing pipeline to take care of word segmentation
-# Learns a segmentation model for each/either side of the parallel corpus using all train/dev/test data
-# Applies the segmentation where necessary.
-# Learns word alignments on the preprocessed training data.
-# Outputs script files used later to score output.
-
-
-my $SCRIPT_DIR; BEGIN { use Cwd qw/ abs_path cwd /; use File::Basename; $SCRIPT_DIR = dirname(abs_path($0)); push @INC, $SCRIPT_DIR; }
-
-use Getopt::Long "GetOptions";
-
-my $GZIP = 'gzip';
-my $ZCAT = 'gunzip -c';
-my $SED = 'sed -e';
-
-my $MORF_TRAIN = "$SCRIPT_DIR/morftrain.sh";
-my $MORF_SEGMENT = "$SCRIPT_DIR/morfsegment.py";
-
-my $LINESTRIPPER = "$SCRIPT_DIR/linestripper.py";
-my $ALIGNER = "/export/ws10smt/software/berkeleyaligner/berkeleyaligner.jar";
-#java -d64 -Xmx10g -jar $ALIGNER ++word-align.conf >> aligner.log
-assert_exec($MORF_TRAIN, $LINESTRIPPER, $MORF_SEGMENT, $ALIGNER);
-
-my $OUTPUT = './morfwork';
-my $PPL_SRC = 50;
-my $PPL_TRG = 50;
-my $MARKER = "#";
-my $MAX_WORDS = 40;
-my $SENTENCES;# = 100000;
-my $SPLIT_TYPE = ""; #possible values: s, t, st, or (empty string)
-my $NAME_SHORTCUT;
-
-usage() unless &GetOptions('max_words=i' => \$MAX_WORDS,
-                           'output=s' => \$OUTPUT,
-                           'ppl_src=i' => \$PPL_SRC,
-                           'ppl_trg=i' => \$PPL_TRG,
-                           'sentences=i' => \$SENTENCES,
-                           'marker=s' => \$MARKER,
-                           'split=s' => \$SPLIT_TYPE,
-                           'get_name_only' => \$NAME_SHORTCUT,
-                          );
-
-usage() unless scalar @ARGV >= 2;
-
-my %CORPUS; # for (src,trg) it has (orig, name, filtered, final)
-
-$CORPUS{'src'}{'orig'} = $ARGV[0];
-open F, "<$CORPUS{'src'}{'orig'}" or die "Can't read $CORPUS{'src'}{'orig'}: $!"; close F;
-$CORPUS{'src'}{'name'} = get_basename($CORPUS{'src'}{'orig'});
-
-$CORPUS{'trg'}{'orig'} = $ARGV[1];
-open F, "<$CORPUS{'trg'}{'orig'}" or die "Can't read $CORPUS{'trg'}{'orig'}: $!"; close F;
-$CORPUS{'trg'}{'name'} = get_basename($CORPUS{'trg'}{'orig'});
-
-my %DEV; # for (src,trg) has (orig, final.split final.unsplit
-if (@ARGV >= 4) {
-  $DEV{'src'}{'orig'} = $ARGV[2];
-  open F, "<$DEV{'src'}{'orig'}" or die "Can't read $DEV{'src'}{'orig'}: $!"; close F;
-  $DEV{'src'}{'name'} = get_basename($DEV{'src'}{'orig'});
-  $DEV{'trg'}{'orig'} = $ARGV[3];
-  open F, "<$DEV{'trg'}{'orig'}" or die "Can't read $DEV{'trg'}{'orig'}: $!"; close F;
-  $DEV{'trg'}{'name'} = get_basename($DEV{'trg'}{'orig'});
-}
-
-my %TEST; # for (src,trg) has (orig, name) 
-if (@ARGV >= 6) {
-  $TEST{'src'}{'orig'} = $ARGV[4];
-  open F, "<$TEST{'src'}{'orig'}" or die "Can't read $TEST{'src'}{'orig'}: $!"; close F;
-  $TEST{'src'}{'name'} = get_basename($TEST{'src'}{'orig'});
-  $TEST{'trg'}{'orig'} = $ARGV[5];
-  open F, "<$TEST{'trg'}{'orig'}" or die "Can't read $TEST{'trg'}{'orig'}: $!"; close F;
-  $TEST{'trg'}{'name'} = get_basename($TEST{'trg'}{'orig'});
-}
-
-my $SPLIT_SRC; #use these to check whether that part is being split
-my $SPLIT_TRG;
-
-#OUTPUT WILL GO IN THESE
-my $CORPUS_DIR = $OUTPUT . '/' . corpus_dir();            #subsampled corpus
-my $MODEL_SRC_DIR = $OUTPUT . '/' . model_dir("src"); #splitting..
-my $MODEL_TRG_DIR = $OUTPUT . '/' . model_dir("trg"); # .. models
-my $PROCESSED_DIR = $OUTPUT . '/' . processed_dir();      #segmented copora+alignments
-my $ALIGNMENT_DIR = $PROCESSED_DIR . '/alignments';
-
-$CORPUS{'src'}{'filtered'} = $CORPUS_DIR . "/$CORPUS{'src'}{'name'}";
-$CORPUS{'trg'}{'filtered'} = $CORPUS_DIR . "/$CORPUS{'trg'}{'name'}";
-
-print STDERR "Output: $OUTPUT\n";
-print STDERR "Corpus: $CORPUS_DIR\n";
-print STDERR "Model-src: $MODEL_SRC_DIR\n";
-print STDERR "Model-trg: $MODEL_TRG_DIR\n";
-print STDERR "Finaldir: $PROCESSED_DIR\n";
-
-safemkdir($OUTPUT) or die "Couldn't create output directory $OUTPUT: $!";
-safemkdir($CORPUS_DIR) or die "Couldn't create output directory $CORPUS_DIR: $!";
-filter_corpus();
-
-safemkdir($PROCESSED_DIR);
-safemkdir($ALIGNMENT_DIR);
-
-if ($SPLIT_SRC) {
-  safemkdir($MODEL_SRC_DIR) or die "Couldn't create output directory $MODEL_SRC_DIR: $!";
-  learn_segmentation("src");
-  apply_segmentation_side("src", $MODEL_SRC_DIR);  
-}
-
-#assume that unsplit hypotheses will be scored against an aritificially split target test set; thus obtain a target splitting model  
-#TODO: add a flag to override this behaviour
-safemkdir($MODEL_TRG_DIR) or die "Couldn't create output directory $MODEL_TRG_DIR: $!";
-learn_segmentation("trg");
-$TEST{'trg'}{'finalunsplit'} = "$PROCESSED_DIR/$TEST{'trg'}{'name'}";
-copy($TEST{'trg'}{'orig'}, $TEST{'trg'}{'finalunsplit'}) or die "Could not copy unsegmented test set";  
-
-if ($SPLIT_TRG) {
-  apply_segmentation_side("trg", $MODEL_TRG_DIR);  
-  } else {
-  $TEST{'trg'}{'finalsplit'} = "$PROCESSED_DIR/$TEST{'trg'}{'name'}.split";
-  apply_segmentation_any($MODEL_TRG_DIR, $TEST{'trg'}{'finalunsplit'}, $TEST{'trg'}{'finalsplit'});  
-}
-
-write_eval_sh("$PROCESSED_DIR/eval-devtest.sh");
-
-#copy corpora if they haven't been put in place by splitting operations
-place_missing_data_side('src');
-place_missing_data_side('trg');
-
-do_align();
-
-if ($CORPUS{'src'}{'orig'} && $DEV{'src'}{'orig'} && $TEST{'src'}{'orig'}) {
-  print STDERR "Putting the config file entry in $PROCESSED_DIR/exp.config\n";
-#format is:
-  # nlfr100k_unsplit /export/ws10smt/jan/nlfr/morfwork/s100k.w40.sp_0 corpus.nl-fr.al fr-3.lm.gz dev.nl dev.fr test2008.nl eval-devtest.sh
-  my $line = split_name() . " $PROCESSED_DIR corpus.src-trg.al LMFILE.lm.gz";
-  $line = $line . " $DEV{'src'}{'name'} $DEV{'trg'}{'name'}";
-  $line = $line . " " . get_basename($TEST{'src'}{$SPLIT_SRC ? "finalsplit" : "finalunsplit"}) . " eval-devtest.sh";
-  safesystem("echo '$line' > $PROCESSED_DIR/exp.config");
-}
-
-system("date");
-print STDERR "All done. You now need to train a language model (if target split), put it in the right dir and update the config file.\n\n";
-
-############################## BILINGUAL ###################################
-
-sub filter_corpus {
-  print STDERR "\n!!!FILTERING TRAINING COPRUS!!!\n";
-  if ( -f $CORPUS{'src'}{'filtered'} && -f $CORPUS{'trg'}{'filtered'}) {
-    print STDERR "$CORPUS{'src'}{'filtered'} and $CORPUS{'trg'}{'filtered'} exist, reusing...\n";
-    return;
-  }
-  my $args = "$CORPUS{'src'}{'orig'} $CORPUS{'trg'}{'orig'} $MAX_WORDS";
-  if ($SENTENCES) { $args = $args . " $SENTENCES"; } 
-  safesystem("$LINESTRIPPER $args 1> $CORPUS{'src'}{'filtered'} 2> $CORPUS{'trg'}{'filtered'}") or die "Failed to filter training corpus for length.";
-}
-
-sub learn_segmentation
-{
-  my $WHICH = shift;
-  my $corpus; my $dev; my $test; my $moddir;  my $ppl;
-
-  $corpus = $CORPUS{$WHICH}{'filtered'};
-  $dev = $DEV{$WHICH}{'orig'};
-  $test = $TEST{$WHICH}{'orig'};
-
-  if ($WHICH eq "src") {
-    $moddir = $MODEL_SRC_DIR;
-    $ppl = $PPL_SRC;
-  } else {
-    $moddir = $MODEL_TRG_DIR;
-    $ppl = $PPL_TRG;
-  }
-  my $cmd = "cat $corpus";
-  if ($dev) { $cmd = "$cmd $dev"; }
-  if ($test) { $cmd = "$cmd $test"; }
-  my $tmpfile = "$CORPUS_DIR/all.tmp.gz";
-  safesystem("$cmd | $GZIP > $tmpfile") or die "Failed to concatenate data for model learning..";
-  assert_marker($tmpfile);
-
-  learn_segmentation_side($tmpfile, $moddir, $ppl, $WHICH);
-  safesystem("rm $tmpfile");
-}
-
-sub do_align {
-  print STDERR "\n!!!WORD ALIGNMENT!!!\n";
-  system("date");
-
-  my $ALIGNMENTS = "$ALIGNMENT_DIR/training.align";
-  if ( -f $ALIGNMENTS ) {
-    print STDERR "$ALIGNMENTS  exists, reusing...\n";
-    return;
-  } 
-  my $conf_file = "$ALIGNMENT_DIR/word-align.conf";
-    
-  #decorate training files with identifiers to stop the aligner from training on dev and test when rerun in future.
-  safesystem("cd $PROCESSED_DIR && ln -s $CORPUS{'src'}{'name'} corpus.src") or die "Failed to symlink: $!";
-  safesystem("cd $PROCESSED_DIR && ln -s $CORPUS{'trg'}{'name'} corpus.trg") or die "Failed to symlink: $!";
-
-  write_wconf($conf_file, $PROCESSED_DIR);  
-  system("java -d64 -Xmx24g -jar $ALIGNER ++$conf_file > $ALIGNMENT_DIR/aligner.log");
-
-  if (! -f $ALIGNMENTS) { die "Failed to run word alignment.";}
-
-  my $cmd = "paste $PROCESSED_DIR/corpus.src $PROCESSED_DIR/corpus.trg $ALIGNMENTS";
-  $cmd = $cmd . " | sed 's/\\t/ \|\|\| /g' > $PROCESSED_DIR/corpus.src-trg.al";
-  safesystem($cmd) or die "Failed to paste into aligned corpus file.";
-
-}
-
-############################# MONOLINGUAL #################################
-
-#copy the necessary data files that weren't place by segmentation
-sub place_missing_data_side {
-  my $side = shift;
-
-  ifne_copy($CORPUS{$side}{'filtered'}, "$PROCESSED_DIR/$CORPUS{$side}{'name'}") ;
-
-  if ($DEV{$side}{'orig'} && ! -f "$PROCESSED_DIR/$DEV{$side}{'name'}") {
-    $DEV{$side}{'final'} = "$PROCESSED_DIR/$DEV{$side}{'name'}";
-    copy($DEV{$side}{'orig'}, $DEV{$side}{'final'}) or die "Copy failed: $!";
-  }
-
-  if ($TEST{$side}{'orig'} && ! -f "$PROCESSED_DIR/$TEST{$side}{'name'}" && ! $TEST{$side}{'finalunsplit'}) {
-    $TEST{$side}{'finalunsplit'} = "$PROCESSED_DIR/$TEST{$side}{'name'}";
-    copy($TEST{$side}{'orig'}, $TEST{$side}{'finalunsplit'}) or die "Copy failed: $!";
-  }
-
-}
-
-sub apply_segmentation_side {
-  my ($side, $moddir) = @_;
- 
-  print STDERR "\n!!!APPLYING SEGMENTATION MODEL ($side)!!!\n";
-  apply_segmentation_any($moddir, $CORPUS{$side}{'filtered'}, "$PROCESSED_DIR/$CORPUS{$side}{'name'}");
-  if ($DEV{$side}{'orig'}) {
-     $DEV{$side}{'final'} = "$PROCESSED_DIR/$DEV{$side}{'name'}";
-    apply_segmentation_any($moddir, $DEV{$side}{'orig'}, "$DEV{$side}{'final'}");
-  }
-  if ($TEST{$side}{'orig'}) {
-    $TEST{$side}{'finalsplit'} = "$PROCESSED_DIR/$TEST{$side}{'name'}.split";
-    apply_segmentation_any($moddir, $TEST{$side}{'orig'}, $TEST{$side}{'finalsplit'} );
-  } 
-
-}
-
-sub learn_segmentation_side {
-  my($INPUT_FILE, $SEGOUT_DIR, $PPL, $LANG) = @_;
-
-  print STDERR "\n!!!LEARNING SEGMENTATION MODEL ($LANG)!!!\n";
-  system("date");
-  my $SEG_FILE = $SEGOUT_DIR . "/segmentation.ready";
-   if ( -f $SEG_FILE) {
-    print STDERR "$SEG_FILE exists, reusing...\n";
-    return;
-  }
-  my $cmd = "$MORF_TRAIN $INPUT_FILE $SEGOUT_DIR $PPL \"$MARKER\"";
-  safesystem($cmd) or die "Failed to learn segmentation model";
-}
-
-sub apply_segmentation_any {
-  my($moddir, $datfile, $outfile) = @_;
-  if ( -f $outfile) {
-    print STDERR "$outfile exists, reusing...\n";
-    return;
-  }
-  
-  my $args = "$moddir/inputvocab.gz $moddir/segmentation.ready \"$MARKER\"";
-  safesystem("cat $datfile | $MORF_SEGMENT $args &> $outfile") or die "Could not segment $datfile";
-}
-
-##################### PATH FUNCTIONS ##########################
-
-sub beautify_numlines {
-  return ($SENTENCES ? $SENTENCES : "_all");
-}
-
-sub corpus_dir {
-  return "s" . beautify_numlines() . ".w" . $MAX_WORDS;
-}
-
-sub model_dir {
-  my $lang = shift;
-  if ($lang eq "src") { 
-    return corpus_dir() . ".PPL" . $PPL_SRC . ".src";
-  } elsif ($lang eq "trg") {
-    return corpus_dir() .  ".PPL" . $PPL_TRG . ".trg";
-  } else {
-    return "PPLundef";
-  }    
-}
-
-sub processed_dir {
-  return corpus_dir() . "." . split_name();
-}
-
-########################## HELPER FUNCTIONS ############################
-
-sub ifne_copy {
-  my ($src, $dest) = @_;
-  if (! -f $dest) {
-    copy($src, $dest) or die "Copy failed: $!";
-  }
-}
-
-sub split_name {
-  #parses SPLIT_TYPE, which can have the following values
-  # t|s|ts|st (last 2 are equiv)
-  # or is undefined when no splitting is done
-  my $name = "";
-  
-  if ($SPLIT_TYPE) { 
-    $SPLIT_SRC = lc($SPLIT_TYPE) =~ /s/;
-    $SPLIT_TRG = lc($SPLIT_TYPE) =~ /t/;
-    $name = $name . ($SPLIT_SRC ? $PPL_SRC : "0");
-    $name = $name . "_" . ($SPLIT_TRG ? $PPL_TRG : "0"); 
-  } else {
-    #no splitting
-    $name = "0";
-  }
-
-  return "sp_" . $name;
-  
-}
-
-sub usage {
-  print <<EOT;
-
-Usage: $0 [OPTIONS] corpus.src corpus.trg [dev.src dev.trg [test.src test.trg]]
-
-Learns a segmentation model and splits up corpora as necessary. Word alignments are trained on a specified subset of the training corpus.
-
-EOT
-  exit 1;
-};
-
-sub safemkdir {
-  my $dir = shift;
-  if (-d $dir) { return 1; }
-  return mkdir($dir);
-}
-
-sub assert_exec {
-  my @files = @_;
-  for my $file (@files) {
-    die "Can't find $file - did you run make?\n" unless -e $file;
-    die "Can't execute $file" unless -e $file;
-  }
-};
-sub safesystem {
-  print STDERR "Executing: @_\n";
-  system(@_);
-  if ($? == -1) {
-      print STDERR "ERROR: Failed to execute: @_\n  $!\n";
-      exit(1);
-  }
-  elsif ($? & 127) {
-      printf STDERR "ERROR: Execution of: @_\n  died with signal %d, %s coredump\n",
-          ($? & 127),  ($? & 128) ? 'with' : 'without';
-      exit(1);
-  }
-  else {
-    my $exitcode = $? >> 8;
-    print STDERR "Exit code: $exitcode\n" if $exitcode;
-    return ! $exitcode;
-  }
-}
-
-sub get_basename
-{
-  my $x = shift;
-  $x = `basename $x`;
-  $x =~ s/\n//;
-  return $x;
-}
-
-sub assert_marker {
-  my $file = shift;
-  my $result = `zcat $file| grep '$MARKER' | wc -l` or die "Cannot read $file: $!";
-  print $result; 
-  if (scalar($result) != 0) { die "Data contains marker '$MARKER'; use something else.";}
-}
-########################### Dynamic config files ##############################
-
-sub write_wconf {
-  my ($filename, $train_dir) = @_;
-  open WCONF, ">$filename" or die "Can't write $filename: $!";
-
-  print WCONF <<EOT;
-## ----------------------
-## This is an example training script for the Berkeley
-## word aligner.  In this configuration it uses two HMM
-## alignment models trained jointly and then decoded
-## using the competitive thresholding heuristic.
-
-##########################################
-# Training: Defines the training regimen
-##########################################
-forwardModels   MODEL1 HMM
-reverseModels   MODEL1 HMM
-mode    JOINT JOINT
-iters   5 5
-
-###############################################
-# Execution: Controls output and program flow
-###############################################
-execDir $ALIGNMENT_DIR
-create
-overwriteExecDir
-saveParams  true
-numThreads  1
-msPerLine   10000
-alignTraining
-
-#################
-# Language/Data
-#################
-foreignSuffix   src
-englishSuffix   trg
-
-# Choose the training sources, which can either be directories or files that list files/directories
-trainSources    $train_dir/
-#trainSources     $train_dir/sources
-testSources     
-sentences   MAX
-
-#################
-# 1-best output
-#################
-competitiveThresholding
-
-EOT
-  close WCONF;
-}
-
-sub write_eval_sh
-{
-  my ($filename) = @_;
-  open EVALFILE, ">$filename" or die "Can't write $filename: $!";
-
-  print EVALFILE <<EOT;
-#!/bin/bash
-
-EVAL_MAIN=/export/ws10smt/data/eval.sh
-marker="$MARKER"
-EOT
-
-  if ($SPLIT_TRG) {
-    print EVALFILE <<EOT;
-echo "OUTPUT EVALUATION"
-echo "-----------------"
-\$EVAL_MAIN "\$1" $TEST{'trg'}{'finalsplit'}
-
-echo "RECOMBINED OUTPUT EVALUATION"
-echo "----------------------------"
-cat "\$1" | sed -e "s/\$marker \$marker//g" -e "s/\$marker//g" > "\$1.recombined"
-
-\$EVAL_MAIN "\$1.recombined" $TEST{'trg'}{'finalunsplit'}
-EOT
-
-  } else {
-    print EVALFILE <<EOT;
-echo "ARTIFICIAL SPLIT EVALUATION"
-echo "--------------------------"
-
-#split the output translation
-cat "\$1" | $MORF_SEGMENT $MODEL_TRG_DIR/inputvocab.gz $MODEL_TRG_DIR/segmentation.ready "\$MARKER" > "\$1.split"
-
-\$EVAL_MAIN "\$1.split" $TEST{'trg'}{'finalsplit'}
-
-echo "DIRECT EVALUATION"
-echo "--------------------------"
-\$EVAL_MAIN "\$1" $TEST{'trg'}{'finalunsplit'}
-  
-EOT
-
-  }
-  close EVALFILE;
-
-}
-
-
-
-
diff --git a/gi/morf-segmentation/morfsegment.py b/gi/morf-segmentation/morfsegment.py
deleted file mode 100755
index 85b9d4fb..00000000
--- a/gi/morf-segmentation/morfsegment.py
+++ /dev/null
@@ -1,50 +0,0 @@
-#!/usr/bin/python
-
-import sys
-import gzip
-
-#usage: morfsegment.py inputvocab.gz segmentation.ready
-#  stdin: the data to segment
-#  stdout: the segmented data
-
-if len(sys.argv) < 3:
-  print "usage: morfsegment.py inputvocab.gz segmentation.ready [marker]"
-  print "  stdin: the data to segment"
-  print "  stdout: the segmented data"
-  sys.exit()
-
-#read index:
-split_index={}
-
-marker="##"
-
-if len(sys.argv) > 3:
-  marker=sys.argv[3]
-
-word_vocab=gzip.open(sys.argv[1], 'rb') #inputvocab.gz
-seg_vocab=open(sys.argv[2], 'r') #segm.ready..
-
-for seg in seg_vocab:
-  #seg = ver# #wonder\n
-  #wordline = 1 verwonder\n
-  word = word_vocab.readline().strip().split(' ')
-  assert(len(word) == 2)
-  word = word[1]
-  seg=seg.strip()
-
-  if seg != word:
-    split_index[word] = seg
-
-word_vocab.close()
-seg_vocab.close()
-
-for line in sys.stdin:
-  words = line.strip().split()
-
-  newsent = []
-  for word in words:
-    splitword = split_index.get(word, word)
-    newsent.append(splitword)
-
-  print ' '.join(newsent)
-
diff --git a/gi/morf-segmentation/morftrain.sh b/gi/morf-segmentation/morftrain.sh
deleted file mode 100755
index 9004922f..00000000
--- a/gi/morf-segmentation/morftrain.sh
+++ /dev/null
@@ -1,110 +0,0 @@
-#!/bin/bash
-
-if [[ $# -lt 3 ]]; then
-	echo "Trains a morfessor model and places the result in writedir"
-	echo
-	echo "Usage: `basename $0` corpus_input_file writedir [PPL] [marker] [lines]"
-	echo -e "\tcorpus_input_file contains a sentence per line."
-	exit 1
-fi
-
-MORFESSOR_DIR="/export/ws10smt/software/morfessor_catmap0.9.2"
-SCRIPT_DIR=$(dirname `readlink -f $0`)
-
-MORFBINDIR="$MORFESSOR_DIR/bin"
-MORFMAKEFILE_TRAIN="$MORFESSOR_DIR/train/Makefile"
-VOCABEXT="$SCRIPT_DIR/vocabextractor.sh"
-
-MARKER="#"
-
-if [[ ! -f $VOCABEXT ]]; then
-  echo "$VOCABEXT doesn't exist!"
-  exit 1
-fi
-if [[ ! -f $MORFMAKEFILE_TRAIN ]]; then
-  echo "$MORFMAKEFILE_TRAIN doesn't exist!"
-  exit 1
-fi
-
-
-CORPUS="$1"
-WRITETODIR=$2
-
-if [[ ! -f $CORPUS ]]; then
-  echo "$CORPUS doesn't exist!"
-  exit 1
-fi
-
-PPL=10
-LINES=0
-if [[ $# -gt 2 ]]; then
-  PPL=$3
-fi
-if [[ $# -gt 3 ]]; then
-  MARKER="$4"
-fi
-if [[ $# -gt 4 ]]; then
-  LINES=$5
-fi
-
-mkdir -p $WRITETODIR
-
-#extract vocabulary to train on
-echo "Extracting vocabulary..."
-if [[ -f $WRITETODIR/inputvocab.gz ]]; then
-  echo " ....$WRITETODIR/inputvocab.gz exists, reusing."
-else
-  if [[ $LINES -gt 0 ]]; then
-    $VOCABEXT $CORPUS $LINES | gzip > $WRITETODIR/inputvocab.gz
-  else
-    $VOCABEXT $CORPUS | gzip > $WRITETODIR/inputvocab.gz
-  fi
-fi
-
-
-#train it
-echo "Training morf model..."
-if [[ -f $WRITETODIR/segmentation.final.gz ]]; then
-  echo " ....$WRITETODIR/segmentation.final.gz exists, reusing.."
-else
-  OLDPWD=`pwd`
-  cd $WRITETODIR
-  
-  #put the training Makefile in place, with appropriate modifications
-  sed -e "s/^GZIPPEDINPUTDATA = .*$/GZIPPEDINPUTDATA = inputvocab.gz/"  \
-    -e "s/^PPLTHRESH = .*$/PPLTHRESH = $PPL/" \
-    -e "s;^BINDIR = .*$;BINDIR = $MORFBINDIR;" \
-    $MORFMAKEFILE_TRAIN > ./Makefile
-
-  date
-  make > ./trainmorf.log 2>&1
-  cd $OLDPWD
-  
-  
-  echo "Post processing..."
-  #remove comments, counts and morph types
-  #mark morphs
-  
-  if [[ ! -f $WRITETODIR/segmentation.final.gz ]]; then
-     echo "Failed to learn segmentation model: $WRITETODIR/segmentation.final.gz not written"
-     exit 1
-  fi
-
-  zcat $WRITETODIR/segmentation.final.gz | \
-    awk '$1 !~ /^#/ {print}' | \
-    cut -d ' ' --complement -f 1 | \
-    sed -e "s/\/...//g" -e "s/ + /$MARKER $MARKER/g" \
-    > $WRITETODIR/segmentation.ready
-
-  if [[ ! -f $WRITETODIR/segmentation.ready ]]; then
-     echo "Failed to learn segmentation model: $WRITETODIR/segmentation.final.gz not written"
-     exit 1
-  fi
-
-
-
-  echo "Done training."
-  date
-fi
-echo "Segmentation model is $WRITETODIR/segmentation.ready."
-
diff --git a/gi/morf-segmentation/vocabextractor.sh b/gi/morf-segmentation/vocabextractor.sh
deleted file mode 100755
index 00ae7109..00000000
--- a/gi/morf-segmentation/vocabextractor.sh
+++ /dev/null
@@ -1,40 +0,0 @@
-#!/bin/bash
-
-d=$(dirname `readlink -f $0`)
-if [ $# -lt 1 ]; then
-	echo "Extracts unique words and their frequencies from a subset of a corpus."
-	echo
-	echo "Usage: `basename $0` input_file [number_of_lines] > output_file"
-	echo -e "\tinput_file contains a sentence per line."
-	echo
-	echo "Script also removes words from the vocabulary if they contain a digit or a special character. Output is printed to stdout in a format suitable for use with Morfessor."
-	echo
-	exit
-fi
-
-srcname=$1
-reallen=0
-
-if [[ $# -gt 1 ]]; then
-  reallen=$2
-fi
-
-pattern_file=$d/invalid_vocab.patterns
-
-if [[ ! -f $pattern_file ]]; then
-  echo "Pattern file missing"
-  exit 1 
-fi
-
-#this awk strips entries from the vocabulary if they contain invalid characters
-#invalid characters are digits and punctuation marks, and words beginning or ending with a dash
-#uniq -c extracts the unique words and counts the occurrences
-
-if [[ $reallen -eq 0 ]]; then
-	#when a zero is passed, use the whole file
-  zcat -f $srcname | sed 's/ /\n/g' | egrep -v -f $pattern_file | sort | uniq -c | sed 's/^  *//' 
-
-else
-	zcat -f $srcname | head -n $reallen | sed 's/ /\n/g' | egrep -v -f $pattern_file | sort | uniq -c | sed 's/^  *//'
-fi
-
diff --git a/gi/pf/Makefile.am b/gi/pf/Makefile.am
deleted file mode 100644
index 86f8e07b..00000000
--- a/gi/pf/Makefile.am
+++ /dev/null
@@ -1,44 +0,0 @@
-bin_PROGRAMS = cbgi brat dpnaive pfbrat pfdist itg pfnaive condnaive align-lexonly-pyp learn_cfg pyp_lm nuisance_test align-tl pf_test bayes_lattice_score
-
-noinst_LIBRARIES = libpf.a
-
-libpf_a_SOURCES = base_distributions.cc reachability.cc cfg_wfst_composer.cc corpus.cc unigrams.cc ngram_base.cc transliterations.cc backward.cc hpyp_tm.cc pyp_tm.cc
-
-bayes_lattice_score_SOURCES = bayes_lattice_score.cc
-bayes_lattice_score_LDADD = libpf.a $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a $(top_srcdir)/klm/lm/libklm.a $(top_srcdir)/klm/util/libklm_util.a -lz
-
-pf_test_SOURCES = pf_test.cc
-pf_test_LDADD = libpf.a $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a $(top_srcdir)/klm/lm/libklm.a $(top_srcdir)/klm/util/libklm_util.a -lz
-
-nuisance_test_SOURCES = nuisance_test.cc
-nuisance_test_LDADD = libpf.a $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a $(top_srcdir)/klm/lm/libklm.a $(top_srcdir)/klm/util/libklm_util.a -lz
-
-align_lexonly_pyp_SOURCES = align-lexonly-pyp.cc
-align_lexonly_pyp_LDADD = libpf.a $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a $(top_srcdir)/klm/lm/libklm.a $(top_srcdir)/klm/util/libklm_util.a -lz
-
-align_tl_SOURCES = align-tl.cc
-align_tl_LDADD = libpf.a $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a $(top_srcdir)/klm/lm/libklm.a $(top_srcdir)/klm/util/libklm_util.a -lz
-
-itg_SOURCES = itg.cc
-
-pyp_lm_SOURCES = pyp_lm.cc
-
-learn_cfg_SOURCES = learn_cfg.cc
-
-condnaive_SOURCES = condnaive.cc
-
-dpnaive_SOURCES = dpnaive.cc
-
-pfdist_SOURCES = pfdist.cc
-
-pfnaive_SOURCES = pfnaive.cc
-
-cbgi_SOURCES = cbgi.cc
-
-brat_SOURCES = brat.cc
-
-pfbrat_SOURCES = pfbrat.cc
-
-AM_CPPFLAGS = -W -Wall -Wno-sign-compare -funroll-loops -I$(top_srcdir)/utils $(GTEST_CPPFLAGS) -I$(top_srcdir)/decoder -I$(top_srcdir)/klm
-
-AM_LDFLAGS = libpf.a $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/klm/lm/libklm.a $(top_srcdir)/klm/util/libklm_util.a $(top_srcdir)/utils/libutils.a -lz
diff --git a/gi/pf/README b/gi/pf/README
deleted file mode 100644
index 62e47541..00000000
--- a/gi/pf/README
+++ /dev/null
@@ -1,2 +0,0 @@
-Experimental Bayesian alignment tools. Nothing to see here.
-
diff --git a/gi/pf/align-lexonly-pyp.cc b/gi/pf/align-lexonly-pyp.cc
deleted file mode 100644
index e7509f57..00000000
--- a/gi/pf/align-lexonly-pyp.cc
+++ /dev/null
@@ -1,243 +0,0 @@
-#include <iostream>
-#include <queue>
-
-#include <boost/program_options.hpp>
-#include <boost/program_options/variables_map.hpp>
-
-#include "tdict.h"
-#include "stringlib.h"
-#include "filelib.h"
-#include "array2d.h"
-#include "sampler.h"
-#include "corpus.h"
-#include "pyp_tm.h"
-#include "hpyp_tm.h"
-#include "quasi_model2.h"
-
-using namespace std;
-namespace po = boost::program_options;
-
-void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
-  po::options_description opts("Configuration options");
-  opts.add_options()
-        ("samples,s",po::value<unsigned>()->default_value(1000),"Number of samples")
-        ("infer_alignment_hyperparameters,I", "Infer alpha and p_null, otherwise fixed values will be assumed")
-        ("p_null,0", po::value<double>()->default_value(0.08), "probability of aligning to null")
-        ("align_alpha,a", po::value<double>()->default_value(4.0), "how 'tight' is the bias toward be along the diagonal?")
-        ("input,i",po::value<string>(),"Read parallel data from")
-        ("random_seed,S",po::value<uint32_t>(), "Random seed");
-  po::options_description clo("Command line options");
-  clo.add_options()
-        ("config", po::value<string>(), "Configuration file")
-        ("help,h", "Print this help message and exit");
-  po::options_description dconfig_options, dcmdline_options;
-  dconfig_options.add(opts);
-  dcmdline_options.add(opts).add(clo);
-  
-  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
-  if (conf->count("config")) {
-    ifstream config((*conf)["config"].as<string>().c_str());
-    po::store(po::parse_config_file(config, dconfig_options), *conf);
-  }
-  po::notify(*conf);
-
-  if (conf->count("help") || (conf->count("input") == 0)) {
-    cerr << dcmdline_options << endl;
-    exit(1);
-  }
-}
-
-MT19937* prng;
-
-struct LexicalAlignment {
-  unsigned char src_index;
-  bool is_transliteration;
-  vector<pair<short, short> > derivation;
-};
-
-struct AlignedSentencePair {
-  vector<WordID> src;
-  vector<WordID> trg;
-  vector<LexicalAlignment> a;
-  Array2D<short> posterior;
-};
-
-template <class LexicalTranslationModel>
-struct Aligner {
-  Aligner(const vector<vector<WordID> >& lets,
-          int vocab_size,
-          int num_letters,
-          const po::variables_map& conf,
-          vector<AlignedSentencePair>* c) :
-      corpus(*c),
-      paj_model(conf["align_alpha"].as<double>(), conf["p_null"].as<double>()),
-      infer_paj(conf.count("infer_alignment_hyperparameters") > 0),
-      model(lets, vocab_size, num_letters),
-      kNULL(TD::Convert("NULL")) {
-    assert(lets[kNULL].size() == 0);
-  }
-
-  vector<AlignedSentencePair>& corpus;
-  QuasiModel2 paj_model;
-  const bool infer_paj;
-  LexicalTranslationModel model;
-  const WordID kNULL;
-
-  void ResampleHyperparameters() {
-    model.ResampleHyperparameters(prng);
-    if (infer_paj) paj_model.ResampleHyperparameters(prng);
-  }
-
-  void InitializeRandom() {
-    cerr << "Initializing with random alignments ...\n";
-    for (unsigned i = 0; i < corpus.size(); ++i) {
-      AlignedSentencePair& asp = corpus[i];
-      asp.a.resize(asp.trg.size());
-      for (unsigned j = 0; j < asp.trg.size(); ++j) {
-        unsigned char& a_j = asp.a[j].src_index;
-        a_j = prng->next() * (1 + asp.src.size());
-        const WordID f_a_j = (a_j ? asp.src[a_j - 1] : kNULL);
-        model.Increment(f_a_j, asp.trg[j], &*prng);
-        paj_model.Increment(a_j, j, asp.src.size(), asp.trg.size());
-      }
-    }
-    cerr << "Corpus intialized randomly." << endl;
-    cerr << "LLH = " << Likelihood() << "    \t(Amodel=" << paj_model.Likelihood()
-         << " TModel=" << model.Likelihood() << ") contexts=" << model.UniqueConditioningContexts() << endl;
-  }
-
-  void ResampleCorpus() {
-    for (unsigned i = 0; i < corpus.size(); ++i) {
-      AlignedSentencePair& asp = corpus[i];
-      SampleSet<prob_t> ss; ss.resize(asp.src.size() + 1);
-      for (unsigned j = 0; j < asp.trg.size(); ++j) {
-        unsigned char& a_j = asp.a[j].src_index;
-        const WordID e_j = asp.trg[j];
-        WordID f_a_j = (a_j ? asp.src[a_j - 1] : kNULL);
-        model.Decrement(f_a_j, e_j, prng);
-        paj_model.Decrement(a_j, j, asp.src.size(), asp.trg.size());
-
-        for (unsigned prop_a_j = 0; prop_a_j <= asp.src.size(); ++prop_a_j) {
-          const WordID prop_f = (prop_a_j ? asp.src[prop_a_j - 1] : kNULL);
-          ss[prop_a_j] = model.Prob(prop_f, e_j);
-          ss[prop_a_j] *= paj_model.Prob(prop_a_j, j, asp.src.size(), asp.trg.size());
-        }
-        a_j = prng->SelectSample(ss);
-        f_a_j = (a_j ? asp.src[a_j - 1] : kNULL);
-        model.Increment(f_a_j, e_j, prng);
-        paj_model.Increment(a_j, j, asp.src.size(), asp.trg.size());
-      }
-    }
-  }
-
-  prob_t Likelihood() const {
-    return model.Likelihood() * paj_model.Likelihood();
-  }
-};
-
-void ExtractLetters(const set<WordID>& v, vector<vector<WordID> >* l, set<WordID>* letset = NULL) {
-  for (set<WordID>::const_iterator it = v.begin(); it != v.end(); ++it) {
-    vector<WordID>& letters = (*l)[*it];
-    if (letters.size()) continue;   // if e and f have the same word
-
-    const string& w = TD::Convert(*it);
-    
-    size_t cur = 0;
-    while (cur < w.size()) {
-      const size_t len = UTF8Len(w[cur]);
-      letters.push_back(TD::Convert(w.substr(cur, len)));
-      if (letset) letset->insert(letters.back());
-      cur += len;
-    }
-  }
-}
-
-void Debug(const AlignedSentencePair& asp) {
-  cerr << TD::GetString(asp.src) << endl << TD::GetString(asp.trg) << endl;
-  Array2D<bool> a(asp.src.size(), asp.trg.size());
-  for (unsigned j = 0; j < asp.trg.size(); ++j) {
-    assert(asp.a[j].src_index <= asp.src.size());
-    if (asp.a[j].src_index) a(asp.a[j].src_index - 1, j) = true;
-  }
-  cerr << a << endl;
-}
-
-void AddSample(AlignedSentencePair* asp) {
-  for (unsigned j = 0; j < asp->trg.size(); ++j)
-    asp->posterior(asp->a[j].src_index, j)++;
-}
-
-void WriteAlignments(const AlignedSentencePair& asp) {
-  bool first = true;
-  for (unsigned j = 0; j < asp.trg.size(); ++j) {
-    int src_index = -1;
-    int mc = -1;
-    for (unsigned i = 0; i <= asp.src.size(); ++i) {
-      if (asp.posterior(i, j) > mc) {
-        mc = asp.posterior(i, j);
-        src_index = i;
-      }
-    }
-
-    if (src_index) {
-      if (first) first = false; else cout << ' ';
-      cout << (src_index - 1) << '-' << j;
-    }
-  }
-  cout << endl;
-}
-
-int main(int argc, char** argv) {
-  po::variables_map conf;
-  InitCommandLine(argc, argv, &conf);
-
-  if (conf.count("random_seed"))
-    prng = new MT19937(conf["random_seed"].as<uint32_t>());
-  else
-    prng = new MT19937;
-
-  vector<vector<int> > corpuse, corpusf;
-  set<int> vocabe, vocabf;
-  corpus::ReadParallelCorpus(conf["input"].as<string>(), &corpusf, &corpuse, &vocabf, &vocabe);
-  cerr << "f-Corpus size: " << corpusf.size() << " sentences\n";
-  cerr << "f-Vocabulary size: " << vocabf.size() << " types\n";
-  cerr << "f-Corpus size: " << corpuse.size() << " sentences\n";
-  cerr << "f-Vocabulary size: " << vocabe.size() << " types\n";
-  assert(corpusf.size() == corpuse.size());
-
-  vector<AlignedSentencePair> corpus(corpuse.size());
-  for (unsigned i = 0; i < corpuse.size(); ++i) {
-    corpus[i].src.swap(corpusf[i]);
-    corpus[i].trg.swap(corpuse[i]);
-    corpus[i].posterior.resize(corpus[i].src.size() + 1, corpus[i].trg.size());
-  }
-  corpusf.clear(); corpuse.clear();
-
-  vocabf.insert(TD::Convert("NULL"));
-  vector<vector<WordID> > letters(TD::NumWords());
-  set<WordID> letset;
-  ExtractLetters(vocabe, &letters, &letset);
-  ExtractLetters(vocabf, &letters, NULL);
-  letters[TD::Convert("NULL")].clear();
-
-  //Aligner<PYPLexicalTranslation> aligner(letters, vocabe.size(), letset.size(), conf, &corpus);
-  Aligner<HPYPLexicalTranslation> aligner(letters, vocabe.size(), letset.size(), conf, &corpus);
-  aligner.InitializeRandom();
-
-  const unsigned samples = conf["samples"].as<unsigned>();
-  for (int i = 0; i < samples; ++i) {
-    for (int j = 65; j < 67; ++j) Debug(corpus[j]);
-    if (i % 10 == 9) {
-      aligner.ResampleHyperparameters();
-      cerr << "LLH = " << aligner.Likelihood() << "    \t(Amodel=" << aligner.paj_model.Likelihood()
-           << " TModel=" << aligner.model.Likelihood() << ") contexts=" << aligner.model.UniqueConditioningContexts() << endl;
-    }
-    aligner.ResampleCorpus();
-    if (i > (samples / 5) && (i % 6 == 5)) for (int j = 0; j < corpus.size(); ++j) AddSample(&corpus[j]);
-  }
-  for (unsigned i = 0; i < corpus.size(); ++i)
-    WriteAlignments(corpus[i]);
-  aligner.model.Summary();
-
-  return 0;
-}
diff --git a/gi/pf/align-tl.cc b/gi/pf/align-tl.cc
deleted file mode 100644
index f6608f1d..00000000
--- a/gi/pf/align-tl.cc
+++ /dev/null
@@ -1,339 +0,0 @@
-#include <iostream>
-#include <tr1/memory>
-#include <queue>
-
-#include <boost/multi_array.hpp>
-#include <boost/program_options.hpp>
-#include <boost/program_options/variables_map.hpp>
-
-#include "backward.h"
-#include "array2d.h"
-#include "base_distributions.h"
-#include "monotonic_pseg.h"
-#include "conditional_pseg.h"
-#include "trule.h"
-#include "tdict.h"
-#include "stringlib.h"
-#include "filelib.h"
-#include "dict.h"
-#include "sampler.h"
-#include "mfcr.h"
-#include "corpus.h"
-#include "ngram_base.h"
-#include "transliterations.h"
-
-using namespace std;
-using namespace tr1;
-namespace po = boost::program_options;
-
-void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
-  po::options_description opts("Configuration options");
-  opts.add_options()
-        ("samples,s",po::value<unsigned>()->default_value(1000),"Number of samples")
-        ("input,i",po::value<string>(),"Read parallel data from")
-        ("s2t", po::value<string>(), "character level source-to-target prior transliteration probabilities")
-        ("t2s", po::value<string>(), "character level target-to-source prior transliteration probabilities")
-        ("max_src_chunk", po::value<unsigned>()->default_value(4), "Maximum size of translitered chunk in source")
-        ("max_trg_chunk", po::value<unsigned>()->default_value(4), "Maximum size of translitered chunk in target")
-        ("expected_src_to_trg_ratio", po::value<double>()->default_value(1.0), "If a word is transliterated, what is the expected length ratio from source to target?")
-        ("random_seed,S",po::value<uint32_t>(), "Random seed");
-  po::options_description clo("Command line options");
-  clo.add_options()
-        ("config", po::value<string>(), "Configuration file")
-        ("help,h", "Print this help message and exit");
-  po::options_description dconfig_options, dcmdline_options;
-  dconfig_options.add(opts);
-  dcmdline_options.add(opts).add(clo);
-  
-  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
-  if (conf->count("config")) {
-    ifstream config((*conf)["config"].as<string>().c_str());
-    po::store(po::parse_config_file(config, dconfig_options), *conf);
-  }
-  po::notify(*conf);
-
-  if (conf->count("help") || (conf->count("input") == 0)) {
-    cerr << dcmdline_options << endl;
-    exit(1);
-  }
-}
-
-boost::shared_ptr<MT19937> prng;
-
-struct LexicalAlignment {
-  unsigned char src_index;
-  bool is_transliteration;
-  vector<pair<short, short> > derivation;
-};
-
-struct AlignedSentencePair {
-  vector<WordID> src;
-  vector<WordID> trg;
-  vector<LexicalAlignment> a;
-  Array2D<short> posterior;
-};
-
-struct HierarchicalWordBase {
-  explicit HierarchicalWordBase(const unsigned vocab_e_size) :
-      base(prob_t::One()), r(1,1,1,1,0.66,50.0), u0(-log(vocab_e_size)), l(1,prob_t::One()), v(1, prob_t::Zero()) {}
-
-  void ResampleHyperparameters(MT19937* rng) {
-    r.resample_hyperparameters(rng);
-  }
-
-  inline double logp0(const vector<WordID>& s) const {
-    return Md::log_poisson(s.size(), 7.5) + s.size() * u0;
-  }
-
-  // return p0 of rule.e_
-  prob_t operator()(const TRule& rule) const {
-    v[0].logeq(logp0(rule.e_));
-    return r.prob(rule.e_, v.begin(), l.begin());
-  }
-
-  void Increment(const TRule& rule) {
-    v[0].logeq(logp0(rule.e_));
-    if (r.increment(rule.e_, v.begin(), l.begin(), &*prng).count) {
-      base *= v[0] * l[0];
-    }
-  }
-
-  void Decrement(const TRule& rule) {
-    if (r.decrement(rule.e_, &*prng).count) {
-      base /= prob_t(exp(logp0(rule.e_)));
-    }
-  }
-
-  prob_t Likelihood() const {
-    prob_t p; p.logeq(r.log_crp_prob());
-    p *= base;
-    return p;
-  }
-
-  void Summary() const {
-    cerr << "NUMBER OF CUSTOMERS: " << r.num_customers() << "  (d=" << r.discount() << ",s=" << r.strength() << ')' << endl;
-    for (MFCR<1,vector<WordID> >::const_iterator it = r.begin(); it != r.end(); ++it)
-      cerr << "   " << it->second.total_dish_count_ << " (on " << it->second.table_counts_.size() << " tables) " << TD::GetString(it->first) << endl;
-  }
-
-  prob_t base;
-  MFCR<1,vector<WordID> > r;
-  const double u0;
-  const vector<prob_t> l;
-  mutable vector<prob_t> v;
-};
-
-struct BasicLexicalAlignment {
-  explicit BasicLexicalAlignment(const vector<vector<WordID> >& lets,
-                                 const unsigned words_e,
-                                 const unsigned letters_e,
-                                 vector<AlignedSentencePair>* corp) :
-      letters(lets),
-      corpus(*corp),
-      //up0(words_e),
-      //up0("en.chars.1gram", letters_e),
-      //up0("en.words.1gram"),
-      up0(letters_e),
-      //up0("en.chars.2gram"),
-      tmodel(up0) {
-  }
-
-  void InstantiateRule(const WordID src,
-                       const WordID trg,
-                       TRule* rule) const {
-    static const WordID kX = TD::Convert("X") * -1;
-    rule->lhs_ = kX;
-    rule->e_ = letters[trg];
-    rule->f_ = letters[src];
-  }
-
-  void InitializeRandom() {
-    const WordID kNULL = TD::Convert("NULL");
-    cerr << "Initializing with random alignments ...\n";
-    for (unsigned i = 0; i < corpus.size(); ++i) {
-      AlignedSentencePair& asp = corpus[i];
-      asp.a.resize(asp.trg.size());
-      for (unsigned j = 0; j < asp.trg.size(); ++j) {
-        const unsigned char a_j = prng->next() * (1 + asp.src.size());
-        const WordID f_a_j = (a_j ? asp.src[a_j - 1] : kNULL);
-        TRule r;
-        InstantiateRule(f_a_j, asp.trg[j], &r);
-        asp.a[j].is_transliteration = false;
-        asp.a[j].src_index = a_j;
-        if (tmodel.IncrementRule(r, &*prng))
-          up0.Increment(r);
-      }
-    }
-    cerr << "  LLH = " << Likelihood() << endl;
-  }
-
-  prob_t Likelihood() const {
-    prob_t p = tmodel.Likelihood();
-    p *= up0.Likelihood();
-    return p;
-  }
-
-  void ResampleHyperparemeters() {
-    tmodel.ResampleHyperparameters(&*prng);
-    up0.ResampleHyperparameters(&*prng);
-    cerr << "  (base d=" << up0.r.discount() << ",s=" << up0.r.strength() << ")\n";
-  }
-
-  void ResampleCorpus();
-
-  const vector<vector<WordID> >& letters; // spelling dictionary
-  vector<AlignedSentencePair>& corpus;
-  //PhraseConditionalUninformativeBase up0;
-  //PhraseConditionalUninformativeUnigramBase up0;
-  //UnigramWordBase up0;
-  //HierarchicalUnigramBase up0;
-  HierarchicalWordBase up0;
-  //CompletelyUniformBase up0;
-  //FixedNgramBase up0;
-  //ConditionalTranslationModel<PhraseConditionalUninformativeBase> tmodel;
-  //ConditionalTranslationModel<PhraseConditionalUninformativeUnigramBase> tmodel;
-  //ConditionalTranslationModel<UnigramWordBase> tmodel;
-  //ConditionalTranslationModel<HierarchicalUnigramBase> tmodel;
-  MConditionalTranslationModel<HierarchicalWordBase> tmodel;
-  //ConditionalTranslationModel<FixedNgramBase> tmodel;
-  //ConditionalTranslationModel<CompletelyUniformBase> tmodel;
-};
-
-void BasicLexicalAlignment::ResampleCorpus() {
-  static const WordID kNULL = TD::Convert("NULL");
-  for (unsigned i = 0; i < corpus.size(); ++i) {
-    AlignedSentencePair& asp = corpus[i];
-    SampleSet<prob_t> ss; ss.resize(asp.src.size() + 1);
-    for (unsigned j = 0; j < asp.trg.size(); ++j) {
-      TRule r;
-      unsigned char& a_j = asp.a[j].src_index;
-      WordID f_a_j = (a_j ? asp.src[a_j - 1] : kNULL);
-      InstantiateRule(f_a_j, asp.trg[j], &r);
-      if (tmodel.DecrementRule(r, &*prng))
-        up0.Decrement(r);
-
-      for (unsigned prop_a_j = 0; prop_a_j <= asp.src.size(); ++prop_a_j) {
-        const WordID prop_f = (prop_a_j ? asp.src[prop_a_j - 1] : kNULL);
-        InstantiateRule(prop_f, asp.trg[j], &r);
-        ss[prop_a_j] = tmodel.RuleProbability(r);
-      }
-      a_j = prng->SelectSample(ss);
-      f_a_j = (a_j ? asp.src[a_j - 1] : kNULL);
-      InstantiateRule(f_a_j, asp.trg[j], &r);
-      if (tmodel.IncrementRule(r, &*prng))
-        up0.Increment(r);
-    }
-  }
-  cerr << "  LLH = " << Likelihood() << endl;
-}
-
-void ExtractLetters(const set<WordID>& v, vector<vector<WordID> >* l, set<WordID>* letset = NULL) {
-  for (set<WordID>::const_iterator it = v.begin(); it != v.end(); ++it) {
-    vector<WordID>& letters = (*l)[*it];
-    if (letters.size()) continue;   // if e and f have the same word
-
-    const string& w = TD::Convert(*it);
-    
-    size_t cur = 0;
-    while (cur < w.size()) {
-      const size_t len = UTF8Len(w[cur]);
-      letters.push_back(TD::Convert(w.substr(cur, len)));
-      if (letset) letset->insert(letters.back());
-      cur += len;
-    }
-  }
-}
-
-void Debug(const AlignedSentencePair& asp) {
-  cerr << TD::GetString(asp.src) << endl << TD::GetString(asp.trg) << endl;
-  Array2D<bool> a(asp.src.size(), asp.trg.size());
-  for (unsigned j = 0; j < asp.trg.size(); ++j)
-    if (asp.a[j].src_index) a(asp.a[j].src_index - 1, j) = true;
-  cerr << a << endl;
-}
-
-void AddSample(AlignedSentencePair* asp) {
-  for (unsigned j = 0; j < asp->trg.size(); ++j)
-    asp->posterior(asp->a[j].src_index, j)++;
-}
-
-void WriteAlignments(const AlignedSentencePair& asp) {
-  bool first = true;
-  for (unsigned j = 0; j < asp.trg.size(); ++j) {
-    int src_index = -1;
-    int mc = -1;
-    for (unsigned i = 0; i <= asp.src.size(); ++i) {
-      if (asp.posterior(i, j) > mc) {
-        mc = asp.posterior(i, j);
-        src_index = i;
-      }
-    }
-
-    if (src_index) {
-      if (first) first = false; else cout << ' ';
-      cout << (src_index - 1) << '-' << j;
-    }
-  }
-  cout << endl;
-}
-
-int main(int argc, char** argv) {
-  po::variables_map conf;
-  InitCommandLine(argc, argv, &conf);
-
-  if (conf.count("random_seed"))
-    prng.reset(new MT19937(conf["random_seed"].as<uint32_t>()));
-  else
-    prng.reset(new MT19937);
-//  MT19937& rng = *prng;
-
-  vector<vector<int> > corpuse, corpusf;
-  set<int> vocabe, vocabf;
-  corpus::ReadParallelCorpus(conf["input"].as<string>(), &corpusf, &corpuse, &vocabf, &vocabe);
-  cerr << "f-Corpus size: " << corpusf.size() << " sentences\n";
-  cerr << "f-Vocabulary size: " << vocabf.size() << " types\n";
-  cerr << "f-Corpus size: " << corpuse.size() << " sentences\n";
-  cerr << "f-Vocabulary size: " << vocabe.size() << " types\n";
-  assert(corpusf.size() == corpuse.size());
-
-  vector<AlignedSentencePair> corpus(corpuse.size());
-  for (unsigned i = 0; i < corpuse.size(); ++i) {
-    corpus[i].src.swap(corpusf[i]);
-    corpus[i].trg.swap(corpuse[i]);
-    corpus[i].posterior.resize(corpus[i].src.size() + 1, corpus[i].trg.size());
-  }
-  corpusf.clear(); corpuse.clear();
-
-  vocabf.insert(TD::Convert("NULL"));
-  vector<vector<WordID> > letters(TD::NumWords() + 1);
-  set<WordID> letset;
-  ExtractLetters(vocabe, &letters, &letset);
-  ExtractLetters(vocabf, &letters, NULL);
-  letters[TD::Convert("NULL")].clear();
-
-  // TODO configure this
-  const int max_src_chunk = conf["max_src_chunk"].as<unsigned>();
-  const int max_trg_chunk = conf["max_trg_chunk"].as<unsigned>();
-  const double s2t_rat = conf["expected_src_to_trg_ratio"].as<double>();
-  const BackwardEstimator be(conf["s2t"].as<string>(), conf["t2s"].as<string>());
-  Transliterations tl(max_src_chunk, max_trg_chunk, s2t_rat, be); 
-
-  cerr << "Initializing transliteration graph structures ...\n";
-  for (int i = 0; i < corpus.size(); ++i) {
-    const vector<int>& src = corpus[i].src;
-    const vector<int>& trg = corpus[i].trg;
-    for (int j = 0; j < src.size(); ++j) {
-      const vector<int>& src_let = letters[src[j]];
-      for (int k = 0; k < trg.size(); ++k) {
-        const vector<int>& trg_let = letters[trg[k]];
-        tl.Initialize(src[j], src_let, trg[k], trg_let);
-        //if (src_let.size() < min_trans_src)
-        //  tl.Forbid(src[j], src_let, trg[k], trg_let);
-      }
-    }
-  }
-  cerr << endl;
-  tl.GraphSummary();
-
-  return 0;
-}
diff --git a/gi/pf/backward.cc b/gi/pf/backward.cc
deleted file mode 100644
index b92629fd..00000000
--- a/gi/pf/backward.cc
+++ /dev/null
@@ -1,89 +0,0 @@
-#include "backward.h"
-
-#include <queue>
-#include <utility>
-
-#include "array2d.h"
-#include "reachability.h"
-#include "base_distributions.h"
-
-using namespace std;
-
-BackwardEstimator::BackwardEstimator(const string& s2t,
-                    const string& t2s) : m1(new Model1(s2t)), m1inv(new Model1(t2s)) {}
-
-BackwardEstimator::~BackwardEstimator() {
-  delete m1; m1 = NULL;
-  delete m1inv; m1inv = NULL;
-}
-
-float BackwardEstimator::ComputeBackwardProb(const std::vector<WordID>& src,
-                                             const std::vector<WordID>& trg,
-                                             unsigned src_covered,
-                                             unsigned trg_covered,
-                                             double s2t_ratio) const {
-  if (src_covered == src.size() || trg_covered == trg.size()) {
-    assert(src_covered == src.size());
-    assert(trg_covered == trg.size());
-    return 0;
-  }
-  static const WordID kNULL = TD::Convert("<eps>");
-  const prob_t uniform_alignment(1.0 / (src.size() - src_covered + 1));
-  // TODO factor in expected length ratio
-  prob_t e; e.logeq(Md::log_poisson(trg.size() - trg_covered, (src.size() - src_covered) * s2t_ratio)); // p(trg len remaining | src len remaining)
-  for (unsigned j = trg_covered; j < trg.size(); ++j) {
-    prob_t p = (*m1)(kNULL, trg[j]) + prob_t(1e-12);
-    for (unsigned i = src_covered; i < src.size(); ++i)
-      p += (*m1)(src[i], trg[j]);
-    if (p.is_0()) {
-      cerr << "ERROR: p(" << TD::Convert(trg[j]) << " | " << TD::GetString(src) << ") = 0!\n";
-      assert(!"failed");
-    }
-    p *= uniform_alignment;
-    e *= p;
-  }
-  // TODO factor in expected length ratio
-  const prob_t inv_uniform(1.0 / (trg.size() - trg_covered + 1.0));
-  prob_t inv;
-  inv.logeq(Md::log_poisson(src.size() - src_covered, (trg.size() - trg_covered) / s2t_ratio));
-  for (unsigned i = src_covered; i < src.size(); ++i) {
-    prob_t p = (*m1inv)(kNULL, src[i]) + prob_t(1e-12);
-    for (unsigned j = trg_covered; j < trg.size(); ++j)
-      p += (*m1inv)(trg[j], src[i]);
-    if (p.is_0()) {
-      cerr << "ERROR: p_inv(" << TD::Convert(src[i]) << " | " << TD::GetString(trg) << ") = 0!\n";
-      assert(!"failed");
-    }
-    p *= inv_uniform;
-    inv *= p;
-  }
-  return (log(e) + log(inv)) / 2;
-}
-
-void BackwardEstimator::InitializeGrid(const vector<WordID>& src,
-                      const vector<WordID>& trg,
-                      const Reachability& r,
-                      double s2t_ratio,
-                      float* grid) const {
-  queue<pair<int,int> > q;
-  q.push(make_pair(0,0));
-  Array2D<bool> done(src.size()+1, trg.size()+1, false);
-  //cerr << TD::GetString(src) << " ||| " << TD::GetString(trg) << endl;
-  while(!q.empty()) {
-    const pair<int,int> n = q.front();
-    q.pop();
-    if (done(n.first,n.second)) continue;
-    done(n.first,n.second) = true;
-
-    float lp = ComputeBackwardProb(src, trg, n.first, n.second, s2t_ratio);
-    if (n.first == 0 && n.second == 0) grid[0] = lp;
-    //cerr << "  " << n.first << "," << n.second << "\t" << lp << endl;
-
-    if (n.first == src.size() || n.second == trg.size()) continue;
-    const vector<pair<short,short> >& edges = r.valid_deltas[n.first][n.second];
-    for (int i = 0; i < edges.size(); ++i)
-      q.push(make_pair(n.first + edges[i].first, n.second + edges[i].second));
-  }
-  //static int cc = 0; ++cc; if (cc == 80) exit(1);
-}
-
diff --git a/gi/pf/backward.h b/gi/pf/backward.h
deleted file mode 100644
index e67eff0c..00000000
--- a/gi/pf/backward.h
+++ /dev/null
@@ -1,33 +0,0 @@
-#ifndef _BACKWARD_H_
-#define _BACKWARD_H_
-
-#include <vector>
-#include <string>
-#include "wordid.h"
-
-struct Reachability;
-struct Model1;
-
-struct BackwardEstimator {
-  BackwardEstimator(const std::string& s2t,
-                    const std::string& t2s);
-  ~BackwardEstimator();
-
-  void InitializeGrid(const std::vector<WordID>& src,
-                      const std::vector<WordID>& trg,
-                      const Reachability& r,
-                      double src2trg_ratio,
-                      float* grid) const;
-
- private:
-  float ComputeBackwardProb(const std::vector<WordID>& src,
-                            const std::vector<WordID>& trg,
-                            unsigned src_covered,
-                            unsigned trg_covered,
-                            double src2trg_ratio) const;
-
-  Model1* m1;
-  Model1* m1inv;
-};
-
-#endif
diff --git a/gi/pf/base_distributions.cc b/gi/pf/base_distributions.cc
deleted file mode 100644
index d9761005..00000000
--- a/gi/pf/base_distributions.cc
+++ /dev/null
@@ -1,241 +0,0 @@
-#include "base_distributions.h"
-
-#include <iostream>
-
-#include "filelib.h"
-
-using namespace std;
-
-TableLookupBase::TableLookupBase(const string& fname) {
-  cerr << "TableLookupBase reading from " << fname << " ..." << endl;
-  ReadFile rf(fname);
-  istream& in = *rf.stream();
-  string line;
-  unsigned lc = 0;
-  const WordID kDIV = TD::Convert("|||");
-  vector<WordID> tmp;
-  vector<int> le, lf;
-  TRule x;
-  x.lhs_ = -TD::Convert("X");
-  bool flag = false;
-  while(getline(in, line)) {
-    ++lc;
-    if (lc % 1000000 == 0) { cerr << " [" << lc << ']' << endl; flag = false; }
-    else if (lc % 25000 == 0) { cerr << '.' << flush; flag = true; }
-    tmp.clear();
-    TD::ConvertSentence(line, &tmp);
-    x.f_.clear();
-    x.e_.clear();
-    size_t pos = 0;
-    int cc = 0;
-    while(pos < tmp.size()) {
-      const WordID cur = tmp[pos++];
-      if (cur == kDIV) {
-        ++cc;
-      } else if (cc == 0) {
-        x.f_.push_back(cur);    
-      } else if (cc == 1) {
-        x.e_.push_back(cur);
-      } else if (cc == 2) {
-        table[x].logeq(atof(TD::Convert(cur)));
-        ++cc;
-      } else {
-        if (flag) cerr << endl;
-        cerr << "Bad format in " << lc << ": " << line << endl; abort();
-      }
-    }
-    if (cc != 3) {
-      if (flag) cerr << endl;
-      cerr << "Bad format in " << lc << ": " << line << endl; abort();
-    }
-  }
-  if (flag) cerr << endl;
-  cerr << " read " << lc << " entries\n";
-}
-
-prob_t PhraseConditionalUninformativeUnigramBase::p0(const vector<WordID>& vsrc,
-                                                     const vector<WordID>& vtrg,
-                                                     int start_src, int start_trg) const {
-  const int flen = vsrc.size() - start_src;
-  const int elen = vtrg.size() - start_trg;
-  prob_t p;
-  p.logeq(Md::log_poisson(elen, flen + 0.01));       // elen | flen          ~Pois(flen + 0.01)
-  //p.logeq(log_poisson(elen, 1));       // elen | flen          ~Pois(flen + 0.01)
-  for (int i = 0; i < elen; ++i)
-    p *= u(vtrg[i + start_trg]);                        // draw e_i             ~Uniform
-  return p;
-}
-
-prob_t PhraseConditionalUninformativeBase::p0(const vector<WordID>& vsrc,
-                                              const vector<WordID>& vtrg,
-                                              int start_src, int start_trg) const {
-  const int flen = vsrc.size() - start_src;
-  const int elen = vtrg.size() - start_trg;
-  prob_t p;
-  //p.logeq(log_poisson(elen, flen + 0.01));       // elen | flen          ~Pois(flen + 0.01)
-  p.logeq(Md::log_poisson(elen, 1));       // elen | flen          ~Pois(flen + 0.01)
-  for (int i = 0; i < elen; ++i)
-    p *= kUNIFORM_TARGET;                        // draw e_i             ~Uniform
-  return p;
-}
-
-void Model1::LoadModel1(const string& fname) {
-  cerr << "Loading Model 1 parameters from " << fname << " ..." << endl;
-  ReadFile rf(fname);
-  istream& in = *rf.stream();
-  string line;
-  unsigned lc = 0;
-  while(getline(in, line)) {
-    ++lc;
-    int cur = 0;
-    int start = 0;
-    while(cur < line.size() && line[cur] != ' ') { ++cur; }
-    assert(cur != line.size());
-    line[cur] = 0;
-    const WordID src = TD::Convert(&line[0]);
-    ++cur;
-    start = cur;
-    while(cur < line.size() && line[cur] != ' ') { ++cur; }
-    assert(cur != line.size());
-    line[cur] = 0;
-    WordID trg = TD::Convert(&line[start]);
-    const double logprob = strtod(&line[cur + 1], NULL);
-    if (src >= ttable.size()) ttable.resize(src + 1);
-    ttable[src][trg].logeq(logprob);
-  }
-  cerr << "  read " << lc << " parameters.\n";
-}
-
-prob_t PhraseConditionalBase::p0(const vector<WordID>& vsrc,
-                                 const vector<WordID>& vtrg,
-                                 int start_src, int start_trg) const {
-  const int flen = vsrc.size() - start_src;
-  const int elen = vtrg.size() - start_trg;
-  prob_t uniform_src_alignment; uniform_src_alignment.logeq(-log(flen + 1));
-  prob_t p;
-  p.logeq(Md::log_poisson(elen, flen + 0.01));       // elen | flen          ~Pois(flen + 0.01)
-  for (int i = 0; i < elen; ++i) {               // for each position i in e-RHS
-    const WordID trg = vtrg[i + start_trg];
-    prob_t tp = prob_t::Zero();
-    for (int j = -1; j < flen; ++j) {
-      const WordID src = j < 0 ? 0 : vsrc[j + start_src];
-      tp += kM1MIXTURE * model1(src, trg);
-      tp += kUNIFORM_MIXTURE * kUNIFORM_TARGET;
-    }
-    tp *= uniform_src_alignment;                 //     draw a_i         ~uniform
-    p *= tp;                                     //     draw e_i         ~Model1(f_a_i) / uniform
-  }
-  if (p.is_0()) {
-    cerr << "Zero! " << vsrc << "\nTRG=" << vtrg << endl;
-    abort();
-  }
-  return p;
-}
-
-prob_t PhraseJointBase::p0(const vector<WordID>& vsrc,
-                           const vector<WordID>& vtrg,
-                           int start_src, int start_trg) const {
-  const int flen = vsrc.size() - start_src;
-  const int elen = vtrg.size() - start_trg;
-  prob_t uniform_src_alignment; uniform_src_alignment.logeq(-log(flen + 1));
-  prob_t p;
-  p.logeq(Md::log_poisson(flen, 1.0));               // flen                 ~Pois(1)
-                                                 // elen | flen          ~Pois(flen + 0.01)
-  prob_t ptrglen; ptrglen.logeq(Md::log_poisson(elen, flen + 0.01));
-  p *= ptrglen;
-  p *= kUNIFORM_SOURCE.pow(flen);                // each f in F ~Uniform
-  for (int i = 0; i < elen; ++i) {               // for each position i in E
-    const WordID trg = vtrg[i + start_trg];
-    prob_t tp = prob_t::Zero();
-    for (int j = -1; j < flen; ++j) {
-      const WordID src = j < 0 ? 0 : vsrc[j + start_src];
-      tp += kM1MIXTURE * model1(src, trg);
-      tp += kUNIFORM_MIXTURE * kUNIFORM_TARGET;
-    }
-    tp *= uniform_src_alignment;                 //     draw a_i         ~uniform
-    p *= tp;                                     //     draw e_i         ~Model1(f_a_i) / uniform
-  }
-  if (p.is_0()) {
-    cerr << "Zero! " << vsrc << "\nTRG=" << vtrg << endl;
-    abort();
-  }
-  return p;
-}
-
-prob_t PhraseJointBase_BiDir::p0(const vector<WordID>& vsrc,
-                                 const vector<WordID>& vtrg,
-                                 int start_src, int start_trg) const {
-  const int flen = vsrc.size() - start_src;
-  const int elen = vtrg.size() - start_trg;
-  prob_t uniform_src_alignment; uniform_src_alignment.logeq(-log(flen + 1));
-  prob_t uniform_trg_alignment; uniform_trg_alignment.logeq(-log(elen + 1));
-
-  prob_t p1;
-  p1.logeq(Md::log_poisson(flen, 1.0));               // flen                 ~Pois(1)
-                                                 // elen | flen          ~Pois(flen + 0.01)
-  prob_t ptrglen; ptrglen.logeq(Md::log_poisson(elen, flen + 0.01));
-  p1 *= ptrglen;
-  p1 *= kUNIFORM_SOURCE.pow(flen);                // each f in F ~Uniform
-  for (int i = 0; i < elen; ++i) {               // for each position i in E
-    const WordID trg = vtrg[i + start_trg];
-    prob_t tp = prob_t::Zero();
-    for (int j = -1; j < flen; ++j) {
-      const WordID src = j < 0 ? 0 : vsrc[j + start_src];
-      tp += kM1MIXTURE * model1(src, trg);
-      tp += kUNIFORM_MIXTURE * kUNIFORM_TARGET;
-    }
-    tp *= uniform_src_alignment;                 //     draw a_i         ~uniform
-    p1 *= tp;                                     //     draw e_i         ~Model1(f_a_i) / uniform
-  }
-  if (p1.is_0()) {
-    cerr << "Zero! " << vsrc << "\nTRG=" << vtrg << endl;
-    abort();
-  }
-
-  prob_t p2;
-  p2.logeq(Md::log_poisson(elen, 1.0));               // elen                 ~Pois(1)
-                                                 // flen | elen          ~Pois(flen + 0.01)
-  prob_t psrclen; psrclen.logeq(Md::log_poisson(flen, elen + 0.01));
-  p2 *= psrclen;
-  p2 *= kUNIFORM_TARGET.pow(elen);                // each f in F ~Uniform
-  for (int i = 0; i < flen; ++i) {               // for each position i in E
-    const WordID src = vsrc[i + start_src];
-    prob_t tp = prob_t::Zero();
-    for (int j = -1; j < elen; ++j) {
-      const WordID trg = j < 0 ? 0 : vtrg[j + start_trg];
-      tp += kM1MIXTURE * invmodel1(trg, src);
-      tp += kUNIFORM_MIXTURE * kUNIFORM_SOURCE;
-    }
-    tp *= uniform_trg_alignment;                 //     draw a_i         ~uniform
-    p2 *= tp;                                     //     draw e_i         ~Model1(f_a_i) / uniform
-  }
-  if (p2.is_0()) {
-    cerr << "Zero! " << vsrc << "\nTRG=" << vtrg << endl;
-    abort();
-  }
-
-  static const prob_t kHALF(0.5);
-  return (p1 + p2) * kHALF;
-}
-
-JumpBase::JumpBase() : p(200) {
-  for (unsigned src_len = 1; src_len < 200; ++src_len) {
-    map<int, prob_t>& cpd = p[src_len];
-    int min_jump = 1 - src_len;
-    int max_jump = src_len;
-    prob_t z;
-    for (int j = min_jump; j <= max_jump; ++j) {
-      prob_t& cp = cpd[j];
-      if (j < 0)
-        cp.logeq(Md::log_poisson(1.5-j, 1));
-      else if (j > 0)
-        cp.logeq(Md::log_poisson(j, 1));
-      cp.poweq(0.2);
-      z += cp;
-    }
-    for (int j = min_jump; j <= max_jump; ++j) {
-      cpd[j] /= z;
-    }
-  }
-}
-
diff --git a/gi/pf/base_distributions.h b/gi/pf/base_distributions.h
deleted file mode 100644
index 41b513f8..00000000
--- a/gi/pf/base_distributions.h
+++ /dev/null
@@ -1,238 +0,0 @@
-#ifndef _BASE_MEASURES_H_
-#define _BASE_MEASURES_H_
-
-#include <vector>
-#include <map>
-#include <string>
-#include <cmath>
-#include <iostream>
-#include <cassert>
-
-#include "unigrams.h"
-#include "trule.h"
-#include "prob.h"
-#include "tdict.h"
-#include "sampler.h"
-#include "m.h"
-#include "os_phrase.h"
-
-struct Model1 {
-  explicit Model1(const std::string& fname) :
-      kNULL(TD::Convert("<eps>")),
-      kZERO() {
-    LoadModel1(fname);
-  }
-
-  void LoadModel1(const std::string& fname);
-
-  // returns prob 0 if src or trg is not found
-  const prob_t& operator()(WordID src, WordID trg) const {
-    if (src == 0) src = kNULL;
-    if (src < ttable.size()) {
-      const std::map<WordID, prob_t>& cpd = ttable[src];
-      const std::map<WordID, prob_t>::const_iterator it = cpd.find(trg);
-      if (it != cpd.end())
-        return it->second;
-    }
-    return kZERO;
-  }
-
-  const WordID kNULL;
-  const prob_t kZERO;
-  std::vector<std::map<WordID, prob_t> > ttable;
-};
-
-struct PoissonUniformUninformativeBase {
-  explicit PoissonUniformUninformativeBase(const unsigned ves) : kUNIFORM(1.0 / ves) {}
-  prob_t operator()(const TRule& r) const {
-    prob_t p; p.logeq(Md::log_poisson(r.e_.size(), 1.0));
-    prob_t q = kUNIFORM; q.poweq(r.e_.size());
-    p *= q;
-    return p;
-  }
-  void Summary() const {}
-  void ResampleHyperparameters(MT19937*) {}
-  void Increment(const TRule&) {}
-  void Decrement(const TRule&) {}
-  prob_t Likelihood() const { return prob_t::One(); }
-  const prob_t kUNIFORM;
-};
-
-struct CompletelyUniformBase {
-  explicit CompletelyUniformBase(const unsigned ves) : kUNIFORM(1.0 / ves) {}
-  prob_t operator()(const TRule&) const {
-    return kUNIFORM;
-  }
-  void Summary() const {}
-  void ResampleHyperparameters(MT19937*) {}
-  void Increment(const TRule&) {}
-  void Decrement(const TRule&) {}
-  prob_t Likelihood() const { return prob_t::One(); }
-  const prob_t kUNIFORM;
-};
-
-struct UnigramWordBase {
-  explicit UnigramWordBase(const std::string& fname) : un(fname) {}
-  prob_t operator()(const TRule& r) const {
-    return un(r.e_);
-  }
-  const UnigramWordModel un;
-};
-
-struct RuleHasher {
-  size_t operator()(const TRule& r) const {
-    return hash_value(r);
-  }
-};
-
-struct TableLookupBase {
-  TableLookupBase(const std::string& fname);
-
-  prob_t operator()(const TRule& rule) const {
-    const std::tr1::unordered_map<TRule,prob_t,RuleHasher>::const_iterator it = table.find(rule);
-    if (it == table.end()) {
-      std::cerr << rule << " not found\n";
-      abort();
-    }
-    return it->second;
-  }
-
-  void ResampleHyperparameters(MT19937*) {}
-  void Increment(const TRule&) {}
-  void Decrement(const TRule&) {}
-  prob_t Likelihood() const { return prob_t::One(); }
-  void Summary() const {}
-
-  std::tr1::unordered_map<TRule,prob_t,RuleHasher> table;
-};
-
-struct PhraseConditionalUninformativeBase {
-  explicit PhraseConditionalUninformativeBase(const unsigned vocab_e_size) :
-      kUNIFORM_TARGET(1.0 / vocab_e_size) {
-    assert(vocab_e_size > 0);
-  }
-
-  // return p0 of rule.e_ | rule.f_
-  prob_t operator()(const TRule& rule) const {
-    return p0(rule.f_, rule.e_, 0, 0);
-  }
-
-  prob_t p0(const std::vector<WordID>& vsrc, const std::vector<WordID>& vtrg, int start_src, int start_trg) const;
-
-  void Summary() const {}
-  void ResampleHyperparameters(MT19937*) {}
-  void Increment(const TRule&) {}
-  void Decrement(const TRule&) {}
-  prob_t Likelihood() const { return prob_t::One(); }
-  const prob_t kUNIFORM_TARGET;
-};
-
-struct PhraseConditionalUninformativeUnigramBase {
-  explicit PhraseConditionalUninformativeUnigramBase(const std::string& file, const unsigned vocab_e_size) : u(file, vocab_e_size) {}
-
-  // return p0 of rule.e_ | rule.f_
-  prob_t operator()(const TRule& rule) const {
-    return p0(rule.f_, rule.e_, 0, 0);
-  }
-
-  prob_t p0(const std::vector<WordID>& vsrc, const std::vector<WordID>& vtrg, int start_src, int start_trg) const;
-
-  const UnigramModel u;
-};
-
-struct PhraseConditionalBase {
-  explicit PhraseConditionalBase(const Model1& m1, const double m1mixture, const unsigned vocab_e_size) :
-      model1(m1),
-      kM1MIXTURE(m1mixture),
-      kUNIFORM_MIXTURE(1.0 - m1mixture),
-      kUNIFORM_TARGET(1.0 / vocab_e_size) {
-    assert(m1mixture >= 0.0 && m1mixture <= 1.0);
-    assert(vocab_e_size > 0);
-  }
-
-  // return p0 of rule.e_ | rule.f_
-  prob_t operator()(const TRule& rule) const {
-    return p0(rule.f_, rule.e_, 0, 0);
-  }
-
-  prob_t p0(const std::vector<WordID>& vsrc, const std::vector<WordID>& vtrg, int start_src, int start_trg) const;
-
-  const Model1& model1;
-  const prob_t kM1MIXTURE;  // Model 1 mixture component
-  const prob_t kUNIFORM_MIXTURE; // uniform mixture component
-  const prob_t kUNIFORM_TARGET;
-};
-
-struct PhraseJointBase {
-  explicit PhraseJointBase(const Model1& m1, const double m1mixture, const unsigned vocab_e_size, const unsigned vocab_f_size) :
-      model1(m1),
-      kM1MIXTURE(m1mixture),
-      kUNIFORM_MIXTURE(1.0 - m1mixture),
-      kUNIFORM_SOURCE(1.0 / vocab_f_size),
-      kUNIFORM_TARGET(1.0 / vocab_e_size) {
-    assert(m1mixture >= 0.0 && m1mixture <= 1.0);
-    assert(vocab_e_size > 0);
-  }
-
-  // return p0 of rule.e_ , rule.f_
-  prob_t operator()(const TRule& rule) const {
-    return p0(rule.f_, rule.e_, 0, 0);
-  }
-
-  prob_t p0(const std::vector<WordID>& vsrc, const std::vector<WordID>& vtrg, int start_src, int start_trg) const;
-
-  const Model1& model1;
-  const prob_t kM1MIXTURE;  // Model 1 mixture component
-  const prob_t kUNIFORM_MIXTURE; // uniform mixture component
-  const prob_t kUNIFORM_SOURCE;
-  const prob_t kUNIFORM_TARGET;
-};
-
-struct PhraseJointBase_BiDir {
-  explicit PhraseJointBase_BiDir(const Model1& m1,
-                                 const Model1& im1,
-                                 const double m1mixture,
-                                 const unsigned vocab_e_size,
-                                 const unsigned vocab_f_size) :
-      model1(m1),
-      invmodel1(im1),
-      kM1MIXTURE(m1mixture),
-      kUNIFORM_MIXTURE(1.0 - m1mixture),
-      kUNIFORM_SOURCE(1.0 / vocab_f_size),
-      kUNIFORM_TARGET(1.0 / vocab_e_size) {
-    assert(m1mixture >= 0.0 && m1mixture <= 1.0);
-    assert(vocab_e_size > 0);
-  }
-
-  // return p0 of rule.e_ , rule.f_
-  prob_t operator()(const TRule& rule) const {
-    return p0(rule.f_, rule.e_, 0, 0);
-  }
-
-  prob_t p0(const std::vector<WordID>& vsrc, const std::vector<WordID>& vtrg, int start_src, int start_trg) const;
-
-  const Model1& model1;
-  const Model1& invmodel1;
-  const prob_t kM1MIXTURE;  // Model 1 mixture component
-  const prob_t kUNIFORM_MIXTURE; // uniform mixture component
-  const prob_t kUNIFORM_SOURCE;
-  const prob_t kUNIFORM_TARGET;
-};
-
-// base distribution for jump size multinomials
-// basically p(0) = 0 and then, p(1) is max, and then
-// you drop as you move to the max jump distance
-struct JumpBase {
-  JumpBase();
-
-  const prob_t& operator()(int jump, unsigned src_len) const {
-    assert(jump != 0);
-    const std::map<int, prob_t>::const_iterator it = p[src_len].find(jump);
-    assert(it != p[src_len].end());
-    return it->second;
-  }
-  std::vector<std::map<int, prob_t> > p;
-};
-
-
-#endif
diff --git a/gi/pf/bayes_lattice_score.cc b/gi/pf/bayes_lattice_score.cc
deleted file mode 100644
index 70cb8dc2..00000000
--- a/gi/pf/bayes_lattice_score.cc
+++ /dev/null
@@ -1,309 +0,0 @@
-#include <iostream>
-#include <queue>
-
-#include <boost/functional.hpp>
-#include <boost/program_options.hpp>
-#include <boost/program_options/variables_map.hpp>
-
-#include "inside_outside.h"
-#include "hg.h"
-#include "hg_io.h"
-#include "bottom_up_parser.h"
-#include "fdict.h"
-#include "grammar.h"
-#include "m.h"
-#include "trule.h"
-#include "tdict.h"
-#include "filelib.h"
-#include "dict.h"
-#include "sampler.h"
-#include "ccrp.h"
-#include "ccrp_onetable.h"
-
-using namespace std;
-using namespace tr1;
-namespace po = boost::program_options;
-
-boost::shared_ptr<MT19937> prng;
-
-void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
-  po::options_description opts("Configuration options");
-  opts.add_options()
-        ("samples,s",po::value<unsigned>()->default_value(1000),"Number of samples")
-        ("input,i",po::value<string>(),"Read parallel data from")
-        ("random_seed,S",po::value<uint32_t>(), "Random seed");
-  po::options_description clo("Command line options");
-  clo.add_options()
-        ("config", po::value<string>(), "Configuration file")
-        ("help", "Print this help message and exit");
-  po::options_description dconfig_options, dcmdline_options;
-  dconfig_options.add(opts);
-  dcmdline_options.add(opts).add(clo);
-  
-  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
-  if (conf->count("config")) {
-    ifstream config((*conf)["config"].as<string>().c_str());
-    po::store(po::parse_config_file(config, dconfig_options), *conf);
-  }
-  po::notify(*conf);
-
-  if (conf->count("help") || (conf->count("input") == 0)) {
-    cerr << dcmdline_options << endl;
-    exit(1);
-  }
-}
-
-unsigned ReadCorpus(const string& filename,
-                    vector<Lattice>* e,
-                    set<WordID>* vocab_e) {
-  e->clear();
-  vocab_e->clear();
-  ReadFile rf(filename);
-  istream* in = rf.stream();
-  assert(*in);
-  string line;
-  unsigned toks = 0;
-  while(*in) {
-    getline(*in, line);
-    if (line.empty() && !*in) break;
-    e->push_back(Lattice());
-    Lattice& le = e->back();
-    LatticeTools::ConvertTextOrPLF(line, & le);
-    for (unsigned i = 0; i < le.size(); ++i)
-      for (unsigned j = 0; j < le[i].size(); ++j)
-        vocab_e->insert(le[i][j].label);
-    toks += le.size();
-  }
-  return toks;
-}
-
-struct BaseModel {
-  explicit BaseModel(unsigned tc) :
-      unif(1.0 / tc), p(prob_t::One()) {}
-  prob_t prob(const TRule& r) const {
-    return unif;
-  }
-  void increment(const TRule& r, MT19937* rng) {
-    p *= prob(r);
-  }
-  void decrement(const TRule& r, MT19937* rng) {
-    p /= prob(r);
-  }
-  prob_t Likelihood() const {
-    return p;
-  }
-  const prob_t unif;
-  prob_t p;
-};
-
-struct UnigramModel {
-  explicit UnigramModel(unsigned tc) : base(tc), crp(1,1,1,1), glue(1,1,1,1) {}
-  BaseModel base;
-  CCRP<TRule> crp;
-  CCRP<TRule> glue;
-
-  prob_t Prob(const TRule& r) const {
-    if (r.Arity() != 0) {
-      return glue.prob(r, prob_t(0.5));
-    }
-    return crp.prob(r, base.prob(r));
-  }
-
-  int Increment(const TRule& r, MT19937* rng) {
-    if (r.Arity() != 0) {
-      glue.increment(r, 0.5, rng);
-      return 0;
-    } else {
-      if (crp.increment(r, base.prob(r), rng)) {
-        base.increment(r, rng);
-        return 1;
-      }
-      return 0;
-    }
-  }
-
-  int Decrement(const TRule& r, MT19937* rng) {
-    if (r.Arity() != 0) {
-      glue.decrement(r, rng);
-      return 0;
-    } else {
-      if (crp.decrement(r, rng)) {
-        base.decrement(r, rng);
-        return -1;
-      }
-      return 0;
-    }
-  }
-
-  prob_t Likelihood() const {
-    prob_t p;
-    p.logeq(crp.log_crp_prob() + glue.log_crp_prob());
-    p *= base.Likelihood();
-    return p;
-  }
-
-  void ResampleHyperparameters(MT19937* rng) {
-    crp.resample_hyperparameters(rng);
-    glue.resample_hyperparameters(rng);
-    cerr << " d=" << crp.discount() << ", s=" << crp.strength() << "\t STOP d=" << glue.discount() << ", s=" << glue.strength() << endl;
-  }
-};
-
-UnigramModel* plm;
-
-void SampleDerivation(const Hypergraph& hg, MT19937* rng, vector<unsigned>* sampled_deriv) {
-  vector<prob_t> node_probs;
-  Inside<prob_t, EdgeProb>(hg, &node_probs);
-  queue<unsigned> q;
-  q.push(hg.nodes_.size() - 2);
-  while(!q.empty()) {
-    unsigned cur_node_id = q.front();
-//    cerr << "NODE=" << cur_node_id << endl;
-    q.pop();
-    const Hypergraph::Node& node = hg.nodes_[cur_node_id];
-    const unsigned num_in_edges = node.in_edges_.size();
-    unsigned sampled_edge = 0;
-    if (num_in_edges == 1) {
-      sampled_edge = node.in_edges_[0];
-    } else {
-      //prob_t z;
-      assert(num_in_edges > 1);
-      SampleSet<prob_t> ss;
-      for (unsigned j = 0; j < num_in_edges; ++j) {
-        const Hypergraph::Edge& edge = hg.edges_[node.in_edges_[j]];
-        prob_t p = edge.edge_prob_;
-        for (unsigned k = 0; k < edge.tail_nodes_.size(); ++k)
-          p *= node_probs[edge.tail_nodes_[k]];
-        ss.add(p);
-//        cerr << log(ss[j]) << " ||| " << edge.rule_->AsString() << endl;
-        //z += p;
-      }
-//      for (unsigned j = 0; j < num_in_edges; ++j) {
-//        const Hypergraph::Edge& edge = hg.edges_[node.in_edges_[j]];
-//        cerr << exp(log(ss[j] / z)) << " ||| " << edge.rule_->AsString() << endl;
-//      }
-//      cerr << " --- \n";
-      sampled_edge = node.in_edges_[rng->SelectSample(ss)];
-    }
-    sampled_deriv->push_back(sampled_edge);
-    const Hypergraph::Edge& edge = hg.edges_[sampled_edge];
-    for (unsigned j = 0; j < edge.tail_nodes_.size(); ++j) {
-      q.push(edge.tail_nodes_[j]);
-    }
-  }
-//  for (unsigned i = 0; i < sampled_deriv->size(); ++i) {
-//    cerr << *hg.edges_[(*sampled_deriv)[i]].rule_ << endl;
-//  }
-}
-
-void IncrementDerivation(const Hypergraph& hg, const vector<unsigned>& d, UnigramModel* plm, MT19937* rng) {
-  for (unsigned i = 0; i < d.size(); ++i)
-    plm->Increment(*hg.edges_[d[i]].rule_, rng);
-}
-
-void DecrementDerivation(const Hypergraph& hg, const vector<unsigned>& d, UnigramModel* plm, MT19937* rng) {
-  for (unsigned i = 0; i < d.size(); ++i)
-    plm->Decrement(*hg.edges_[d[i]].rule_, rng);
-}
-
-prob_t TotalProb(const Hypergraph& hg) {
-  return Inside<prob_t, EdgeProb>(hg);
-}
-
-void IncrementLatticePath(const Hypergraph& hg, const vector<unsigned>& d, Lattice* pl) {
-  Lattice& lat = *pl;
-  for (int i = 0; i < d.size(); ++i) {
-    const Hypergraph::Edge& edge = hg.edges_[d[i]];
-    if (edge.rule_->Arity() != 0) continue;
-    WordID sym = edge.rule_->e_[0];
-    vector<LatticeArc>& las = lat[edge.i_];
-    int dist = edge.j_ - edge.i_;
-    assert(dist > 0);
-    for (int j = 0; j < las.size(); ++j) {
-      if (las[j].dist2next == dist &&
-          las[j].label == sym) {
-        las[j].cost += 1;
-      }
-    }
-  }
-}
-
-int main(int argc, char** argv) {
-  po::variables_map conf;
-
-  InitCommandLine(argc, argv, &conf);
-  vector<GrammarPtr> grammars(2);
-  grammars[0].reset(new GlueGrammar("S","X"));
-  const unsigned samples = conf["samples"].as<unsigned>();
-
-  if (conf.count("random_seed"))
-    prng.reset(new MT19937(conf["random_seed"].as<uint32_t>()));
-  else
-    prng.reset(new MT19937);
-  MT19937& rng = *prng;
-  vector<Lattice> corpuse;
-  set<WordID> vocabe;
-  cerr << "Reading corpus...\n";
-  const unsigned toks = ReadCorpus(conf["input"].as<string>(), &corpuse, &vocabe);
-  cerr << "E-corpus size: " << corpuse.size() << " lattices\t (" << vocabe.size() << " word types)\n";
-  UnigramModel lm(vocabe.size());
-  vector<Hypergraph> hgs(corpuse.size());
-  vector<vector<unsigned> > derivs(corpuse.size());
-  for (int i = 0; i < corpuse.size(); ++i) {
-    grammars[1].reset(new PassThroughGrammar(corpuse[i], "X"));
-    ExhaustiveBottomUpParser parser("S", grammars);
-    bool res = parser.Parse(corpuse[i], &hgs[i]);  // exhaustive parse
-    assert(res);
-  }
-
-  double csamples = 0;
-  for (int SS=0; SS < samples; ++SS) {
-    const bool is_last = ((samples - 1) == SS);
-    prob_t dlh = prob_t::One();
-    bool record_sample = (SS > (samples * 1 / 3) && (SS % 5 == 3));
-    if (record_sample) csamples++;
-    for (int ci = 0; ci < corpuse.size(); ++ci) {
-      Lattice& lat = corpuse[ci];
-      Hypergraph& hg = hgs[ci];
-      vector<unsigned>& d = derivs[ci];
-      if (!is_last) DecrementDerivation(hg, d, &lm, &rng);
-      for (unsigned i = 0; i < hg.edges_.size(); ++i) {
-        TRule& r = *hg.edges_[i].rule_;
-        if (r.Arity() != 0)
-          hg.edges_[i].edge_prob_ = prob_t::One();
-        else
-          hg.edges_[i].edge_prob_ = lm.Prob(r);
-      }
-      if (!is_last) {
-        d.clear();
-        SampleDerivation(hg, &rng, &d);
-        IncrementDerivation(hg, derivs[ci], &lm, &rng);
-      } else {
-        prob_t p = TotalProb(hg);
-        dlh *= p;
-        cerr << " p(sentence) = " << log(p) << "\t" << log(dlh) << endl;
-      }
-      if (record_sample) IncrementLatticePath(hg, derivs[ci], &lat);
-    }
-    double llh = log(lm.Likelihood());
-    cerr << "LLH=" << llh << "\tENTROPY=" << (-llh / log(2) / toks) << "\tPPL=" << pow(2, -llh / log(2) / toks) << endl;
-    if (SS % 10 == 9) lm.ResampleHyperparameters(&rng);
-    if (is_last) {
-      double z = log(dlh);
-      cerr << "TOTAL_PROB=" << z << "\tENTROPY=" << (-z / log(2) / toks) << "\tPPL=" << pow(2, -z / log(2) / toks) << endl;
-    }
-  }
-  cerr << lm.crp << endl;
-  cerr << lm.glue << endl;
-  for (int i = 0; i < corpuse.size(); ++i) {
-    for (int j = 0; j < corpuse[i].size(); ++j)
-      for (int k = 0; k < corpuse[i][j].size(); ++k) {
-        corpuse[i][j][k].cost /= csamples;
-        corpuse[i][j][k].cost += 1e-3;
-        corpuse[i][j][k].cost = log(corpuse[i][j][k].cost);
-      }
-    cout << HypergraphIO::AsPLF(corpuse[i]) << endl;
-  }
-  return 0;
-}
-
diff --git a/gi/pf/brat.cc b/gi/pf/brat.cc
deleted file mode 100644
index 832f22cf..00000000
--- a/gi/pf/brat.cc
+++ /dev/null
@@ -1,543 +0,0 @@
-#include <iostream>
-#include <tr1/memory>
-#include <queue>
-
-#include <boost/functional.hpp>
-#include <boost/multi_array.hpp>
-#include <boost/program_options.hpp>
-#include <boost/program_options/variables_map.hpp>
-
-#include "viterbi.h"
-#include "hg.h"
-#include "trule.h"
-#include "tdict.h"
-#include "filelib.h"
-#include "dict.h"
-#include "sampler.h"
-#include "ccrp_nt.h"
-#include "cfg_wfst_composer.h"
-
-using namespace std;
-using namespace tr1;
-namespace po = boost::program_options;
-
-static unsigned kMAX_SRC_PHRASE;
-static unsigned kMAX_TRG_PHRASE;
-struct FSTState;
-
-double log_poisson(unsigned x, const double& lambda) {
-  assert(lambda > 0.0);
-  return log(lambda) * x - lgamma(x + 1) - lambda;
-}
-
-struct ConditionalBase {
-  explicit ConditionalBase(const double m1mixture, const unsigned vocab_e_size, const string& model1fname) :
-      kM1MIXTURE(m1mixture),
-      kUNIFORM_MIXTURE(1.0 - m1mixture),
-      kUNIFORM_TARGET(1.0 / vocab_e_size),
-      kNULL(TD::Convert("<eps>")) {
-    assert(m1mixture >= 0.0 && m1mixture <= 1.0);
-    assert(vocab_e_size > 0);
-    LoadModel1(model1fname);
-  }
-
-  void LoadModel1(const string& fname) {
-    cerr << "Loading Model 1 parameters from " << fname << " ..." << endl;
-    ReadFile rf(fname);
-    istream& in = *rf.stream();
-    string line;
-    unsigned lc = 0;
-    while(getline(in, line)) {
-      ++lc;
-      int cur = 0;
-      int start = 0;
-      while(cur < line.size() && line[cur] != ' ') { ++cur; }
-      assert(cur != line.size());
-      line[cur] = 0;
-      const WordID src = TD::Convert(&line[0]);
-      ++cur;
-      start = cur;
-      while(cur < line.size() && line[cur] != ' ') { ++cur; }
-      assert(cur != line.size());
-      line[cur] = 0;
-      WordID trg = TD::Convert(&line[start]);
-      const double logprob = strtod(&line[cur + 1], NULL);
-      if (src >= ttable.size()) ttable.resize(src + 1);
-      ttable[src][trg].logeq(logprob);
-    }
-    cerr << "  read " << lc << " parameters.\n";
-  }
-
-  // return logp0 of rule.e_ | rule.f_
-  prob_t operator()(const TRule& rule) const {
-    const int flen = rule.f_.size();
-    const int elen = rule.e_.size();
-    prob_t uniform_src_alignment; uniform_src_alignment.logeq(-log(flen + 1));
-    prob_t p;
-    p.logeq(log_poisson(elen, flen + 0.01));       // elen | flen          ~Pois(flen + 0.01)
-    for (int i = 0; i < elen; ++i) {               // for each position i in e-RHS
-      const WordID trg = rule.e_[i];
-      prob_t tp = prob_t::Zero();
-      for (int j = -1; j < flen; ++j) {
-        const WordID src = j < 0 ? kNULL : rule.f_[j];
-        const map<WordID, prob_t>::const_iterator it = ttable[src].find(trg);
-        if (it != ttable[src].end()) {
-          tp += kM1MIXTURE * it->second;
-        }
-        tp += kUNIFORM_MIXTURE * kUNIFORM_TARGET;
-      }
-      tp *= uniform_src_alignment;                 //     draw a_i         ~uniform
-      p *= tp;                                     //     draw e_i         ~Model1(f_a_i) / uniform
-    }
-    return p;
-  }
-
-  const prob_t kM1MIXTURE;  // Model 1 mixture component
-  const prob_t kUNIFORM_MIXTURE; // uniform mixture component
-  const prob_t kUNIFORM_TARGET;
-  const WordID kNULL;
-  vector<map<WordID, prob_t> > ttable;
-};
-
-void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
-  po::options_description opts("Configuration options");
-  opts.add_options()
-        ("samples,s",po::value<unsigned>()->default_value(1000),"Number of samples")
-        ("input,i",po::value<string>(),"Read parallel data from")
-        ("max_src_phrase",po::value<unsigned>()->default_value(3),"Maximum length of source language phrases")
-        ("max_trg_phrase",po::value<unsigned>()->default_value(3),"Maximum length of target language phrases")
-        ("model1,m",po::value<string>(),"Model 1 parameters (used in base distribution)")
-        ("model1_interpolation_weight",po::value<double>()->default_value(0.95),"Mixing proportion of model 1 with uniform target distribution")
-        ("random_seed,S",po::value<uint32_t>(), "Random seed");
-  po::options_description clo("Command line options");
-  clo.add_options()
-        ("config", po::value<string>(), "Configuration file")
-        ("help,h", "Print this help message and exit");
-  po::options_description dconfig_options, dcmdline_options;
-  dconfig_options.add(opts);
-  dcmdline_options.add(opts).add(clo);
-  
-  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
-  if (conf->count("config")) {
-    ifstream config((*conf)["config"].as<string>().c_str());
-    po::store(po::parse_config_file(config, dconfig_options), *conf);
-  }
-  po::notify(*conf);
-
-  if (conf->count("help") || (conf->count("input") == 0)) {
-    cerr << dcmdline_options << endl;
-    exit(1);
-  }
-}
-
-void ReadParallelCorpus(const string& filename,
-                vector<vector<WordID> >* f,
-                vector<vector<int> >* e,
-                set<int>* vocab_f,
-                set<int>* vocab_e) {
-  f->clear();
-  e->clear();
-  vocab_f->clear();
-  vocab_e->clear();
-  istream* in;
-  if (filename == "-")
-    in = &cin;
-  else
-    in = new ifstream(filename.c_str());
-  assert(*in);
-  string line;
-  const WordID kDIV = TD::Convert("|||");
-  vector<WordID> tmp;
-  while(*in) {
-    getline(*in, line);
-    if (line.empty() && !*in) break;
-    e->push_back(vector<int>());
-    f->push_back(vector<int>());
-    vector<int>& le = e->back();
-    vector<int>& lf = f->back();
-    tmp.clear();
-    TD::ConvertSentence(line, &tmp);
-    bool isf = true;
-    for (unsigned i = 0; i < tmp.size(); ++i) {
-      const int cur = tmp[i];
-      if (isf) {
-        if (kDIV == cur) { isf = false; } else {
-          lf.push_back(cur);
-          vocab_f->insert(cur);
-        }
-      } else {
-        assert(cur != kDIV);
-        le.push_back(cur);
-        vocab_e->insert(cur);
-      }
-    }
-    assert(isf == false);
-  }
-  if (in != &cin) delete in;
-}
-
-struct UniphraseLM {
-  UniphraseLM(const vector<vector<int> >& corpus,
-              const set<int>& vocab,
-              const po::variables_map& conf) :
-    phrases_(1,1),
-    gen_(1,1),
-    corpus_(corpus),
-    uniform_word_(1.0 / vocab.size()),
-    gen_p0_(0.5),
-    p_end_(0.5),
-    use_poisson_(conf.count("poisson_length") > 0) {}
-
-  void ResampleHyperparameters(MT19937* rng) {
-    phrases_.resample_hyperparameters(rng);
-    gen_.resample_hyperparameters(rng);
-    cerr << " " << phrases_.alpha();
-  }
-
-  CCRP_NoTable<vector<int> > phrases_;
-  CCRP_NoTable<bool> gen_;
-  vector<vector<bool> > z_;   // z_[i] is there a phrase boundary after the ith word
-  const vector<vector<int> >& corpus_;
-  const double uniform_word_;
-  const double gen_p0_;
-  const double p_end_; // in base length distribution, p of the end of a phrase
-  const bool use_poisson_;
-};
-
-struct Reachability {
-  boost::multi_array<bool, 4> edges;  // edges[src_covered][trg_covered][x][trg_delta] is this edge worth exploring?
-  boost::multi_array<short, 2> max_src_delta; // msd[src_covered][trg_covered] -- the largest src delta that's valid
-
-  Reachability(int srclen, int trglen, int src_max_phrase_len, int trg_max_phrase_len) :
-      edges(boost::extents[srclen][trglen][src_max_phrase_len+1][trg_max_phrase_len+1]),
-      max_src_delta(boost::extents[srclen][trglen]) {
-    ComputeReachability(srclen, trglen, src_max_phrase_len, trg_max_phrase_len);
-  }
-
- private:
-  struct SState {
-    SState() : prev_src_covered(), prev_trg_covered() {}
-    SState(int i, int j) : prev_src_covered(i), prev_trg_covered(j) {}
-    int prev_src_covered;
-    int prev_trg_covered;
-  };
-
-  struct NState {
-    NState() : next_src_covered(), next_trg_covered() {}
-    NState(int i, int j) : next_src_covered(i), next_trg_covered(j) {}
-    int next_src_covered;
-    int next_trg_covered;
-  };
-
-  void ComputeReachability(int srclen, int trglen, int src_max_phrase_len, int trg_max_phrase_len) {
-    typedef boost::multi_array<vector<SState>, 2> array_type;
-    array_type a(boost::extents[srclen + 1][trglen + 1]);
-    a[0][0].push_back(SState());
-    for (int i = 0; i < srclen; ++i) {
-      for (int j = 0; j < trglen; ++j) {
-        if (a[i][j].size() == 0) continue;
-        const SState prev(i,j);
-        for (int k = 1; k <= src_max_phrase_len; ++k) {
-          if ((i + k) > srclen) continue;
-          for (int l = 1; l <= trg_max_phrase_len; ++l) {
-            if ((j + l) > trglen) continue;
-            a[i + k][j + l].push_back(prev);
-          }
-        }
-      }
-    }
-    a[0][0].clear();
-    cerr << "Final cell contains " << a[srclen][trglen].size() << " back pointers\n";
-    assert(a[srclen][trglen].size() > 0);
-
-    typedef boost::multi_array<bool, 2> rarray_type;
-    rarray_type r(boost::extents[srclen + 1][trglen + 1]);
-//    typedef boost::multi_array<vector<NState>, 2> narray_type;
-//    narray_type b(boost::extents[srclen + 1][trglen + 1]);
-    r[srclen][trglen] = true;
-    for (int i = srclen; i >= 0; --i) {
-      for (int j = trglen; j >= 0; --j) {
-        vector<SState>& prevs = a[i][j];
-        if (!r[i][j]) { prevs.clear(); }
-//        const NState nstate(i,j);
-        for (int k = 0; k < prevs.size(); ++k) {
-          r[prevs[k].prev_src_covered][prevs[k].prev_trg_covered] = true;
-          int src_delta = i - prevs[k].prev_src_covered;
-          edges[prevs[k].prev_src_covered][prevs[k].prev_trg_covered][src_delta][j - prevs[k].prev_trg_covered] = true;
-          short &msd = max_src_delta[prevs[k].prev_src_covered][prevs[k].prev_trg_covered];
-          if (src_delta > msd) msd = src_delta;
-//          b[prevs[k].prev_src_covered][prevs[k].prev_trg_covered].push_back(nstate);
-        }
-      }
-    }
-    assert(!edges[0][0][1][0]);
-    assert(!edges[0][0][0][1]);
-    assert(!edges[0][0][0][0]);
-    cerr << "  MAX SRC DELTA[0][0] = " << max_src_delta[0][0] << endl;
-    assert(max_src_delta[0][0] > 0);
-    //cerr << "First cell contains " << b[0][0].size() << " forward pointers\n";
-    //for (int i = 0; i < b[0][0].size(); ++i) {
-    //  cerr << "  -> (" << b[0][0][i].next_src_covered << "," << b[0][0][i].next_trg_covered << ")\n";
-    //}
-  }
-};
-
-ostream& operator<<(ostream& os, const FSTState& q);
-struct FSTState {
-  explicit FSTState(int src_size) :
-      trg_covered_(),
-      src_covered_(),
-      src_coverage_(src_size) {}
-
-  FSTState(short trg_covered, short src_covered, const vector<bool>& src_coverage, const vector<short>& src_prefix) :
-      trg_covered_(trg_covered),
-      src_covered_(src_covered),
-      src_coverage_(src_coverage),
-      src_prefix_(src_prefix) {
-    if (src_coverage_.size() == src_covered) {
-      assert(src_prefix.size() == 0);
-    }
-  }
-
-  // if we extend by the word at src_position, what are
-  // the next states that are reachable and lie on a valid
-  // path to the final state?
-  vector<FSTState> Extensions(int src_position, int src_len, int trg_len, const Reachability& r) const {
-    assert(src_position < src_coverage_.size());
-    if (src_coverage_[src_position]) {
-      cerr << "Trying to extend " << *this << " with position " << src_position << endl;
-      abort();
-    }
-    vector<bool> ncvg = src_coverage_;
-    ncvg[src_position] = true;
-
-    vector<FSTState> res;
-    const int trg_remaining = trg_len - trg_covered_;
-    if (trg_remaining <= 0) {
-      cerr << "Target appears to have been covered: " << *this << " (trg_len=" << trg_len << ",trg_covered=" << trg_covered_ << ")" << endl;
-      abort();
-    }
-    const int src_remaining = src_len - src_covered_;
-    if (src_remaining <= 0) {
-      cerr << "Source appears to have been covered: " << *this << endl;
-      abort();
-    }
-
-    for (int tc = 1; tc <= kMAX_TRG_PHRASE; ++tc) {
-      if (r.edges[src_covered_][trg_covered_][src_prefix_.size() + 1][tc]) {
-        int nc = src_prefix_.size() + 1 + src_covered_;
-        res.push_back(FSTState(trg_covered_ + tc, nc, ncvg, vector<short>()));
-      }
-    }
-
-    if ((src_prefix_.size() + 1) < r.max_src_delta[src_covered_][trg_covered_]) {
-      vector<short> nsp = src_prefix_;
-      nsp.push_back(src_position);
-      res.push_back(FSTState(trg_covered_, src_covered_, ncvg, nsp));
-    }
-
-    if (res.size() == 0) {
-      cerr << *this << " can't be extended!\n";
-      abort();
-    }
-    return res;
-  }
-
-  short trg_covered_, src_covered_;
-  vector<bool> src_coverage_;
-  vector<short> src_prefix_;
-};
-bool operator<(const FSTState& q, const FSTState& r) {
-  if (q.trg_covered_ != r.trg_covered_) return q.trg_covered_ < r.trg_covered_;
-  if (q.src_covered_!= r.src_covered_) return q.src_covered_ < r.src_covered_;
-  if (q.src_coverage_ != r.src_coverage_) return q.src_coverage_ < r.src_coverage_;
-  return q.src_prefix_ < r.src_prefix_;
-}
-
-ostream& operator<<(ostream& os, const FSTState& q) {
-  os << "[" << q.trg_covered_ << " : ";
-  for (int i = 0; i < q.src_coverage_.size(); ++i)
-    os << q.src_coverage_[i];
-  os << " : <";
-  for (int i = 0; i < q.src_prefix_.size(); ++i) {
-    if (i != 0) os << ' ';
-    os << q.src_prefix_[i];
-  }
-  return os << ">]";
-}
-
-struct MyModel {
-  MyModel(ConditionalBase& rcp0) : rp0(rcp0) {}
-  typedef unordered_map<vector<WordID>, CCRP_NoTable<TRule>, boost::hash<vector<WordID> > > SrcToRuleCRPMap;
-
-  void DecrementRule(const TRule& rule) {
-    SrcToRuleCRPMap::iterator it = rules.find(rule.f_);
-    assert(it != rules.end());
-    it->second.decrement(rule);
-    if (it->second.num_customers() == 0) rules.erase(it);
-  }
-
-  void IncrementRule(const TRule& rule) {
-    SrcToRuleCRPMap::iterator it = rules.find(rule.f_);
-    if (it == rules.end()) {
-      CCRP_NoTable<TRule> crp(1,1);
-      it = rules.insert(make_pair(rule.f_, crp)).first;
-    }
-    it->second.increment(rule);
-  }
-
-  // conditioned on rule.f_
-  prob_t RuleConditionalProbability(const TRule& rule) const {
-    const prob_t base = rp0(rule);
-    SrcToRuleCRPMap::const_iterator it = rules.find(rule.f_);
-    if (it == rules.end()) {
-      return base;
-    } else {
-      const double lp = it->second.logprob(rule, log(base));
-      prob_t q; q.logeq(lp);
-      return q;
-    }
-  }
-
-  const ConditionalBase& rp0;
-  SrcToRuleCRPMap rules;
-};
-
-struct MyFST : public WFST {
-  MyFST(const vector<WordID>& ssrc, const vector<WordID>& strg, MyModel* m) :
-      src(ssrc), trg(strg),
-      r(src.size(),trg.size(),kMAX_SRC_PHRASE, kMAX_TRG_PHRASE),
-      model(m) {
-    FSTState in(src.size());
-    cerr << " INIT: " << in << endl;
-    init = GetNode(in);
-    for (int i = 0; i < in.src_coverage_.size(); ++i) in.src_coverage_[i] = true;
-    in.src_covered_ = src.size();
-    in.trg_covered_ = trg.size();
-    cerr << "FINAL: " << in << endl;
-    final = GetNode(in);
-  }
-  virtual const WFSTNode* Final() const;
-  virtual const WFSTNode* Initial() const;
-
-  const WFSTNode* GetNode(const FSTState& q);
-  map<FSTState, boost::shared_ptr<WFSTNode> > m;
-  const vector<WordID>& src;
-  const vector<WordID>& trg;
-  Reachability r;
-  const WFSTNode* init;
-  const WFSTNode* final;
-  MyModel* model;
-};
-
-struct MyNode : public WFSTNode {
-  MyNode(const FSTState& q, MyFST* fst) : state(q), container(fst) {}
-  virtual vector<pair<const WFSTNode*, TRulePtr> > ExtendInput(unsigned srcindex) const;
-  const FSTState state;
-  mutable MyFST* container;
-};
-
-vector<pair<const WFSTNode*, TRulePtr> > MyNode::ExtendInput(unsigned srcindex) const {
-  cerr << "EXTEND " << state << " with " << srcindex << endl;
-  vector<FSTState> ext = state.Extensions(srcindex, container->src.size(), container->trg.size(), container->r);
-  vector<pair<const WFSTNode*,TRulePtr> > res(ext.size());
-  for (unsigned i = 0; i < ext.size(); ++i) {
-    res[i].first = container->GetNode(ext[i]);
-    if (ext[i].src_prefix_.size() == 0) {
-      const unsigned trg_from = state.trg_covered_;
-      const unsigned trg_to = ext[i].trg_covered_;
-      const unsigned prev_prfx_size = state.src_prefix_.size();
-      res[i].second.reset(new TRule);
-      res[i].second->lhs_ = -TD::Convert("X");
-      vector<WordID>& src = res[i].second->f_;
-      vector<WordID>& trg = res[i].second->e_;
-      src.resize(prev_prfx_size + 1);
-      for (unsigned j = 0; j < prev_prfx_size; ++j)
-        src[j] = container->src[state.src_prefix_[j]];
-      src[prev_prfx_size] = container->src[srcindex];
-      for (unsigned j = trg_from; j < trg_to; ++j)
-        trg.push_back(container->trg[j]);
-      res[i].second->scores_.set_value(FD::Convert("Proposal"), log(container->model->RuleConditionalProbability(*res[i].second)));
-    }
-  }
-  return res;
-}
-
-const WFSTNode* MyFST::GetNode(const FSTState& q) {
-  boost::shared_ptr<WFSTNode>& res = m[q];
-  if (!res) {
-    res.reset(new MyNode(q, this));
-  }
-  return &*res;
-}
-
-const WFSTNode* MyFST::Final() const {
-  return final;
-}
-
-const WFSTNode* MyFST::Initial() const {
-  return init;
-}
-
-int main(int argc, char** argv) {
-  po::variables_map conf;
-  InitCommandLine(argc, argv, &conf);
-  kMAX_TRG_PHRASE = conf["max_trg_phrase"].as<unsigned>();
-  kMAX_SRC_PHRASE = conf["max_src_phrase"].as<unsigned>();
-
-  if (!conf.count("model1")) {
-    cerr << argv[0] << "Please use --model1 to specify model 1 parameters\n";
-    return 1;
-  }
-  boost::shared_ptr<MT19937> prng;
-  if (conf.count("random_seed"))
-    prng.reset(new MT19937(conf["random_seed"].as<uint32_t>()));
-  else
-    prng.reset(new MT19937);
-  MT19937& rng = *prng;
-
-  vector<vector<int> > corpuse, corpusf;
-  set<int> vocabe, vocabf;
-  ReadParallelCorpus(conf["input"].as<string>(), &corpusf, &corpuse, &vocabf, &vocabe);
-  cerr << "f-Corpus size: " << corpusf.size() << " sentences\n";
-  cerr << "f-Vocabulary size: " << vocabf.size() << " types\n";
-  cerr << "f-Corpus size: " << corpuse.size() << " sentences\n";
-  cerr << "f-Vocabulary size: " << vocabe.size() << " types\n";
-  assert(corpusf.size() == corpuse.size());
-
-  ConditionalBase lp0(conf["model1_interpolation_weight"].as<double>(),
-                      vocabe.size(),
-                      conf["model1"].as<string>());
-  MyModel m(lp0);
-
-  TRule x("[X] ||| kAnwntR myN ||| at the convent ||| 0");
-  m.IncrementRule(x);
-  TRule y("[X] ||| nY dyN ||| gave ||| 0");
-  m.IncrementRule(y);
-
-
-  MyFST fst(corpusf[0], corpuse[0], &m);
-  ifstream in("./kimura.g");
-  assert(in);
-  CFG_WFSTComposer comp(fst);
-  Hypergraph hg;
-  bool succeed = comp.Compose(&in, &hg);
-  hg.PrintGraphviz();
-  if (succeed) { cerr << "SUCCESS.\n"; } else { cerr << "FAILURE REPORTED.\n"; }
-
-#if 0
-  ifstream in2("./amnabooks.g");
-  assert(in2);
-  MyFST fst2(corpusf[1], corpuse[1], &m);
-  CFG_WFSTComposer comp2(fst2);
-  Hypergraph hg2;
-  bool succeed2 = comp2.Compose(&in2, &hg2);
-  if (succeed2) { cerr << "SUCCESS.\n"; } else { cerr << "FAILURE REPORTED.\n"; }
-#endif
-
-  SparseVector<double> w; w.set_value(FD::Convert("Proposal"), 1.0);
-  hg.Reweight(w);
-  cerr << ViterbiFTree(hg) << endl;
-  return 0;
-}
-
diff --git a/gi/pf/cbgi.cc b/gi/pf/cbgi.cc
deleted file mode 100644
index 97f1ba34..00000000
--- a/gi/pf/cbgi.cc
+++ /dev/null
@@ -1,330 +0,0 @@
-#include <queue>
-#include <sstream>
-#include <iostream>
-
-#include <boost/unordered_map.hpp>
-#include <boost/functional/hash.hpp>
-
-#include "sampler.h"
-#include "filelib.h"
-#include "hg_io.h"
-#include "hg.h"
-#include "ccrp_nt.h"
-#include "trule.h"
-#include "inside_outside.h"
-
-using namespace std;
-using namespace std::tr1;
-
-double log_poisson(unsigned x, const double& lambda) {
-  assert(lambda > 0.0);
-  return log(lambda) * x - lgamma(x + 1) - lambda;
-}
-
-double log_decay(unsigned x, const double& b) {
-  assert(b > 1.0);
-  assert(x > 0);
-  return log(b - 1) - x * log(b);
-}
-
-struct SimpleBase {
-  SimpleBase(unsigned esize, unsigned fsize, unsigned ntsize = 144) :
-    uniform_e(-log(esize)),
-    uniform_f(-log(fsize)),
-    uniform_nt(-log(ntsize)) {
-  }
-
-  // binomial coefficient
-  static double choose(unsigned n, unsigned k) {
-    return exp(lgamma(n + 1) - lgamma(k + 1) - lgamma(n - k + 1));
-  }
-
-  // count the number of patterns of terminals and NTs in the rule, given elen and flen
-  static double log_number_of_patterns(const unsigned flen, const unsigned elen) {
-    static vector<vector<double> > counts;
-    if (elen >= counts.size()) counts.resize(elen + 1);
-    if (flen >= counts[elen].size()) counts[elen].resize(flen + 1);
-    double& count = counts[elen][flen];
-    if (count) return log(count);
-    const unsigned max_arity = min(elen, flen);
-    for (unsigned a = 0; a <= max_arity; ++a)
-      count += choose(elen, a) * choose(flen, a);
-    return log(count);
-  }
-
-  // return logp0 of rule | LHS
-  double operator()(const TRule& rule) const {
-    const unsigned flen = rule.f_.size();
-    const unsigned elen = rule.e_.size();
-#if 0
-    double p = 0;
-    p += log_poisson(flen, 0.5);                   // flen                 ~Pois(0.5)
-    p += log_poisson(elen, flen);                  // elen | flen          ~Pois(flen)
-    p -= log_number_of_patterns(flen, elen);       // pattern | flen,elen  ~Uniform
-    for (unsigned i = 0; i < flen; ++i) {          // for each position in f-RHS
-      if (rule.f_[i] <= 0)                         //   according to pattern
-        p += uniform_nt;                           //     draw NT          ~Uniform
-      else
-        p += uniform_f;                            //     draw f terminal  ~Uniform
-    }
-    p -= lgamma(rule.Arity() + 1);                 // draw permutation     ~Uniform 
-    for (unsigned i = 0; i < elen; ++i) {          // for each position in e-RHS
-      if (rule.e_[i] > 0)                          //   according to pattern
-        p += uniform_e;                            //     draw e|f term    ~Uniform
-        // TODO this should prob be model 1
-    }
-#else
-    double p = 0;
-    bool is_abstract = rule.f_[0] <= 0;
-    p += log(0.5);
-    if (is_abstract) {
-      if (flen == 2) p += log(0.99); else p += log(0.01);
-    } else {
-      p += log_decay(flen, 3);
-    }
-
-    for (unsigned i = 0; i < flen; ++i) {          // for each position in f-RHS
-      if (rule.f_[i] <= 0)                         //   according to pattern
-        p += uniform_nt;                           //     draw NT          ~Uniform
-      else
-        p += uniform_f;                            //     draw f terminal  ~Uniform
-    }
-#endif
-    return p;
-  }
-  const double uniform_e;
-  const double uniform_f;
-  const double uniform_nt;
-  vector<double> arities;
-};
-
-MT19937* rng = NULL;
-
-template <typename Base>
-struct MHSamplerEdgeProb {
-  MHSamplerEdgeProb(const Hypergraph& hg,
-                  const map<int, CCRP_NoTable<TRule> >& rdp,
-                  const Base& logp0,
-                  const bool exclude_multiword_terminals) : edge_probs(hg.edges_.size()) {
-    for (int i = 0; i < edge_probs.size(); ++i) {
-      const TRule& rule = *hg.edges_[i].rule_;
-      const map<int, CCRP_NoTable<TRule> >::const_iterator it = rdp.find(rule.lhs_);
-      assert(it != rdp.end());
-      const CCRP_NoTable<TRule>& crp = it->second;
-      edge_probs[i].logeq(crp.logprob(rule, logp0(rule)));
-      if (exclude_multiword_terminals && rule.f_[0] > 0 && rule.f_.size() > 1)
-        edge_probs[i] = prob_t::Zero();
-    }
-  }
-  inline prob_t operator()(const Hypergraph::Edge& e) const {
-    return edge_probs[e.id_];
-  }
-  prob_t DerivationProb(const vector<int>& d) const {
-    prob_t p = prob_t::One();
-    for (unsigned i = 0; i < d.size(); ++i)
-      p *= edge_probs[d[i]];
-    return p;
-  }
-  vector<prob_t> edge_probs;
-};
-
-template <typename Base>
-struct ModelAndData {
-  ModelAndData() :
-     base_lh(prob_t::One()),
-     logp0(10000, 10000),
-     mh_samples(),
-     mh_rejects() {}
-
-  void SampleCorpus(const string& hgpath, int i);
-  void ResampleHyperparameters() {
-    for (map<int, CCRP_NoTable<TRule> >::iterator it = rules.begin(); it != rules.end(); ++it)
-      it->second.resample_hyperparameters(rng);
-  }
-
-  CCRP_NoTable<TRule>& RuleCRP(int lhs) {
-    map<int, CCRP_NoTable<TRule> >::iterator it = rules.find(lhs);
-    if (it == rules.end()) {
-      rules.insert(make_pair(lhs, CCRP_NoTable<TRule>(1,1)));
-      it = rules.find(lhs);
-    }
-    return it->second;
-  }
-
-  void IncrementRule(const TRule& rule) {
-    CCRP_NoTable<TRule>& crp = RuleCRP(rule.lhs_);
-    if (crp.increment(rule)) {
-      prob_t p; p.logeq(logp0(rule));
-      base_lh *= p;
-    }
-  }
-
-  void DecrementRule(const TRule& rule) {
-    CCRP_NoTable<TRule>& crp = RuleCRP(rule.lhs_);
-    if (crp.decrement(rule)) {
-      prob_t p; p.logeq(logp0(rule));
-      base_lh /= p;
-    }
-  }
-
-  void DecrementDerivation(const Hypergraph& hg, const vector<int>& d) {
-    for (unsigned i = 0; i < d.size(); ++i) {
-      const TRule& rule = *hg.edges_[d[i]].rule_;
-      DecrementRule(rule);
-    }
-  }
-
-  void IncrementDerivation(const Hypergraph& hg, const vector<int>& d) {
-    for (unsigned i = 0; i < d.size(); ++i) {
-      const TRule& rule = *hg.edges_[d[i]].rule_;
-      IncrementRule(rule);
-    }
-  }
-
-  prob_t Likelihood() const {
-    prob_t p = prob_t::One();
-    for (map<int, CCRP_NoTable<TRule> >::const_iterator it = rules.begin(); it != rules.end(); ++it) {
-      prob_t q; q.logeq(it->second.log_crp_prob());
-      p *= q;
-    }
-    p *= base_lh;
-    return p;
-  }
-
-  void ResampleDerivation(const Hypergraph& hg, vector<int>* sampled_derivation);
-
-  map<int, CCRP_NoTable<TRule> > rules;  // [lhs] -> distribution over RHSs
-  prob_t base_lh;
-  SimpleBase logp0;
-  vector<vector<int> > samples;   // sampled derivations
-  unsigned int mh_samples;
-  unsigned int mh_rejects;
-};
-
-template <typename Base>
-void ModelAndData<Base>::SampleCorpus(const string& hgpath, int n) {
-  vector<Hypergraph> hgs(n); hgs.clear();
-  boost::unordered_map<TRule, unsigned> acc;
-  map<int, unsigned> tot;
-  for (int i = 0; i < n; ++i) {
-    ostringstream os;
-    os << hgpath << '/' << i << ".json.gz";
-    if (!FileExists(os.str())) continue;
-    hgs.push_back(Hypergraph());
-    ReadFile rf(os.str());
-    HypergraphIO::ReadFromJSON(rf.stream(), &hgs.back());
-  }
-  cerr << "Read " << hgs.size() << " alignment hypergraphs.\n";
-  samples.resize(hgs.size());
-  const unsigned SAMPLES = 2000;
-  const unsigned burnin = 3 * SAMPLES / 4;
-  const unsigned every = 20;
-  for (unsigned s = 0; s < SAMPLES; ++s) {
-    if (s % 10 == 0) {
-      if (s > 0) { cerr << endl; ResampleHyperparameters(); }
-      cerr << "[" << s << " LLH=" << log(Likelihood()) << " REJECTS=" << ((double)mh_rejects / mh_samples) << " LHS's=" << rules.size() << " base=" << log(base_lh) << "] ";
-    }
-    cerr << '.';
-    for (unsigned i = 0; i < hgs.size(); ++i) {
-      ResampleDerivation(hgs[i], &samples[i]);
-      if (s > burnin && s % every == 0) {
-        for (unsigned j = 0; j < samples[i].size(); ++j) {
-          const TRule& rule = *hgs[i].edges_[samples[i][j]].rule_;
-          ++acc[rule];
-          ++tot[rule.lhs_];
-        }
-      }
-    }
-  }
-  cerr << endl;
-  for (boost::unordered_map<TRule,unsigned>::iterator it = acc.begin(); it != acc.end(); ++it) {
-    cout << it->first << " MyProb=" << log(it->second)-log(tot[it->first.lhs_]) << endl;
-  }
-}
-
-template <typename Base>
-void ModelAndData<Base>::ResampleDerivation(const Hypergraph& hg, vector<int>* sampled_deriv) {
-  vector<int> cur;
-  cur.swap(*sampled_deriv);
-
-  const prob_t p_cur = Likelihood();
-  DecrementDerivation(hg, cur);
-  if (cur.empty()) {
-    // first iteration, create restaurants
-    for (int i = 0; i < hg.edges_.size(); ++i)
-      RuleCRP(hg.edges_[i].rule_->lhs_);
-  }
-  MHSamplerEdgeProb<SimpleBase> wf(hg, rules, logp0, cur.empty());
-//  MHSamplerEdgeProb<SimpleBase> wf(hg, rules, logp0, false);
-  const prob_t q_cur = wf.DerivationProb(cur);
-  vector<prob_t> node_probs;
-  Inside<prob_t, MHSamplerEdgeProb<SimpleBase> >(hg, &node_probs, wf);
-  queue<unsigned> q;
-  q.push(hg.nodes_.size() - 3);
-  while(!q.empty()) {
-    unsigned cur_node_id = q.front();
-//    cerr << "NODE=" << cur_node_id << endl;
-    q.pop();
-    const Hypergraph::Node& node = hg.nodes_[cur_node_id];
-    const unsigned num_in_edges = node.in_edges_.size();
-    unsigned sampled_edge = 0;
-    if (num_in_edges == 1) {
-      sampled_edge = node.in_edges_[0];
-    } else {
-      prob_t z;
-      assert(num_in_edges > 1);
-      SampleSet<prob_t> ss;
-      for (unsigned j = 0; j < num_in_edges; ++j) {
-        const Hypergraph::Edge& edge = hg.edges_[node.in_edges_[j]];
-        prob_t p = wf.edge_probs[edge.id_];             // edge proposal prob
-        for (unsigned k = 0; k < edge.tail_nodes_.size(); ++k)
-          p *= node_probs[edge.tail_nodes_[k]];
-        ss.add(p);
-//        cerr << log(ss[j]) << " ||| " << edge.rule_->AsString() << endl;
-        z += p;
-      }
-//      for (unsigned j = 0; j < num_in_edges; ++j) {
-//        const Hypergraph::Edge& edge = hg.edges_[node.in_edges_[j]];
-//        cerr << exp(log(ss[j] / z)) << " ||| " << edge.rule_->AsString() << endl;
-//      }
-//      cerr << " --- \n";
-      sampled_edge = node.in_edges_[rng->SelectSample(ss)];
-    }
-    sampled_deriv->push_back(sampled_edge);
-    const Hypergraph::Edge& edge = hg.edges_[sampled_edge];
-    for (unsigned j = 0; j < edge.tail_nodes_.size(); ++j) {
-      q.push(edge.tail_nodes_[j]);
-    }
-  }
-  IncrementDerivation(hg, *sampled_deriv);
-
-//  cerr << "sampled derivation contains " << sampled_deriv->size() << " edges\n";
-//  cerr << "DERIV:\n";
-//  for (int i = 0; i < sampled_deriv->size(); ++i) {
-//    cerr << "  " << hg.edges_[(*sampled_deriv)[i]].rule_->AsString() << endl;
-//  }
-
-  if (cur.empty()) return;  // accept first sample
-
-  ++mh_samples;
-  // only need to do MH if proposal is different to current state
-  if (cur != *sampled_deriv) {
-    const prob_t q_prop = wf.DerivationProb(*sampled_deriv);
-    const prob_t p_prop = Likelihood();
-    if (!rng->AcceptMetropolisHastings(p_prop, p_cur, q_prop, q_cur)) {
-      ++mh_rejects;
-      DecrementDerivation(hg, *sampled_deriv);
-      IncrementDerivation(hg, cur);
-      swap(cur, *sampled_deriv);
-    }
-  }
-}
-
-int main(int argc, char** argv) {
-  rng = new MT19937;
-  ModelAndData<SimpleBase> m;
-  m.SampleCorpus("./hgs", 50);
-  // m.SampleCorpus("./btec/hgs", 5000);
-  return 0;
-}
-
diff --git a/gi/pf/cfg_wfst_composer.cc b/gi/pf/cfg_wfst_composer.cc
deleted file mode 100644
index 19c0875d..00000000
--- a/gi/pf/cfg_wfst_composer.cc
+++ /dev/null
@@ -1,731 +0,0 @@
-#include "cfg_wfst_composer.h"
-
-#include <iostream>
-#include <fstream>
-#include <map>
-#include <queue>
-#include <tr1/unordered_map>
-#include <tr1/unordered_set>
-
-#include <boost/shared_ptr.hpp>
-#include <boost/program_options.hpp>
-#include <boost/program_options/variables_map.hpp>
-#include "fast_lexical_cast.hpp"
-
-#include "phrasetable_fst.h"
-#include "sparse_vector.h"
-#include "tdict.h"
-#include "hg.h"
-#include "hg_remove_eps.h"
-
-namespace po = boost::program_options;
-using namespace std;
-using namespace std::tr1;
-
-WFSTNode::~WFSTNode() {}
-WFST::~WFST() {}
-
-// Define the following macro if you want to see lots of debugging output
-// when you run the chart parser
-#undef DEBUG_CHART_PARSER
-
-// A few constants used by the chart parser ///////////////
-static const int kMAX_NODES = 2000000;
-static const string kPHRASE_STRING = "X";
-static bool constants_need_init = true;
-static WordID kUNIQUE_START;
-static WordID kPHRASE;
-static TRulePtr kX1X2;
-static TRulePtr kX1;
-static WordID kEPS;
-static TRulePtr kEPSRule;
-
-static void InitializeConstants() {
-  if (constants_need_init) {
-    kPHRASE = TD::Convert(kPHRASE_STRING) * -1;
-    kUNIQUE_START = TD::Convert("S") * -1;
-    kX1X2.reset(new TRule("[X] ||| [X,1] [X,2] ||| [X,1] [X,2]"));
-    kX1.reset(new TRule("[X] ||| [X,1] ||| [X,1]"));
-    kEPSRule.reset(new TRule("[X] ||| <eps> ||| <eps>"));
-    kEPS = TD::Convert("<eps>");
-    constants_need_init = false;
-  }
-}
-////////////////////////////////////////////////////////////
-
-class EGrammarNode {
-  friend bool CFG_WFSTComposer::Compose(const Hypergraph& src_forest, Hypergraph* trg_forest);
-  friend void AddGrammarRule(const string& r, map<WordID, EGrammarNode>* g);
- public:
-#ifdef DEBUG_CHART_PARSER
-  string hint;
-#endif
-  EGrammarNode() : is_some_rule_complete(false), is_root(false) {}
-  const map<WordID, EGrammarNode>& GetTerminals() const { return tptr; }
-  const map<WordID, EGrammarNode>& GetNonTerminals() const { return ntptr; }
-  bool HasNonTerminals() const { return (!ntptr.empty()); }
-  bool HasTerminals() const { return (!tptr.empty()); }
-  bool RuleCompletes() const {
-    return (is_some_rule_complete || (ntptr.empty() && tptr.empty()));
-  }
-  bool GrammarContinues() const {
-    return !(ntptr.empty() && tptr.empty());
-  }
-  bool IsRoot() const {
-    return is_root;
-  }
-  // these are the features associated with the rule from the start
-  // node up to this point.  If you use these features, you must
-  // not Extend() this rule.
-  const SparseVector<double>& GetCFGProductionFeatures() const {
-    return input_features;
-  }
-
-  const EGrammarNode* Extend(const WordID& t) const {
-    if (t < 0) {
-      map<WordID, EGrammarNode>::const_iterator it = ntptr.find(t);
-      if (it == ntptr.end()) return NULL;
-      return &it->second;
-    } else {
-      map<WordID, EGrammarNode>::const_iterator it = tptr.find(t);
-      if (it == tptr.end()) return NULL;
-      return &it->second;
-    }
-  }
-
- private:
-  map<WordID, EGrammarNode> tptr;
-  map<WordID, EGrammarNode> ntptr;
-  SparseVector<double> input_features;
-  bool is_some_rule_complete;
-  bool is_root;
-};
-typedef map<WordID, EGrammarNode> EGrammar;    // indexed by the rule LHS
-
-// edges are immutable once created
-struct Edge {
-#ifdef DEBUG_CHART_PARSER
-  static int id_count;
-  const int id;
-#endif
-  const WordID cat;                   // lhs side of rule proved/being proved
-  const EGrammarNode* const dot;      // dot position
-  const WFSTNode* const q;             // start of span
-  const WFSTNode* const r;             // end of span
-  const Edge* const active_parent;    // back pointer, NULL for PREDICT items
-  const Edge* const passive_parent;   // back pointer, NULL for SCAN and PREDICT items
-  TRulePtr tps;   // translations
-  boost::shared_ptr<SparseVector<double> > features; // features from CFG rule
-
-  bool IsPassive() const {
-    // when a rule is completed, this value will be set
-    return static_cast<bool>(features);
-  }
-  bool IsActive() const { return !IsPassive(); }
-  bool IsInitial() const {
-    return !(active_parent || passive_parent);
-  }
-  bool IsCreatedByScan() const {
-    return active_parent && !passive_parent && !dot->IsRoot();
-  }
-  bool IsCreatedByPredict() const {
-    return dot->IsRoot();
-  }
-  bool IsCreatedByComplete() const {
-    return active_parent && passive_parent;
-  }
-
-  // constructor for PREDICT
-  Edge(WordID c, const EGrammarNode* d, const WFSTNode* q_and_r) :
-#ifdef DEBUG_CHART_PARSER
-    id(++id_count),
-#endif
-    cat(c), dot(d), q(q_and_r), r(q_and_r), active_parent(NULL), passive_parent(NULL), tps() {}
-  Edge(WordID c, const EGrammarNode* d, const WFSTNode* q_and_r, const Edge* act_parent) :
-#ifdef DEBUG_CHART_PARSER
-    id(++id_count),
-#endif
-    cat(c), dot(d), q(q_and_r), r(q_and_r), active_parent(act_parent), passive_parent(NULL), tps() {}
-
-  // constructors for SCAN
-  Edge(WordID c, const EGrammarNode* d, const WFSTNode* i, const WFSTNode* j,
-       const Edge* act_par, const TRulePtr& translations) :
-#ifdef DEBUG_CHART_PARSER
-    id(++id_count),
-#endif
-    cat(c), dot(d), q(i), r(j), active_parent(act_par), passive_parent(NULL), tps(translations) {}
-
-  Edge(WordID c, const EGrammarNode* d, const WFSTNode* i, const WFSTNode* j,
-       const Edge* act_par, const TRulePtr& translations,
-       const SparseVector<double>& feats) :
-#ifdef DEBUG_CHART_PARSER
-    id(++id_count),
-#endif
-    cat(c), dot(d), q(i), r(j), active_parent(act_par), passive_parent(NULL), tps(translations),
-    features(new SparseVector<double>(feats)) {}
-
-  // constructors for COMPLETE
-  Edge(WordID c, const EGrammarNode* d, const WFSTNode* i, const WFSTNode* j,
-       const Edge* act_par, const Edge *pas_par) :
-#ifdef DEBUG_CHART_PARSER
-    id(++id_count),
-#endif
-    cat(c), dot(d), q(i), r(j), active_parent(act_par), passive_parent(pas_par), tps() {
-      assert(pas_par->IsPassive());
-      assert(act_par->IsActive());
-    }
-
-  Edge(WordID c, const EGrammarNode* d, const WFSTNode* i, const WFSTNode* j,
-       const Edge* act_par, const Edge *pas_par, const SparseVector<double>& feats) :
-#ifdef DEBUG_CHART_PARSER
-    id(++id_count),
-#endif
-    cat(c), dot(d), q(i), r(j), active_parent(act_par), passive_parent(pas_par), tps(),
-    features(new SparseVector<double>(feats)) {
-      assert(pas_par->IsPassive());
-      assert(act_par->IsActive());
-    }
-
-  // constructor for COMPLETE query
-  Edge(const WFSTNode* _r) :
-#ifdef DEBUG_CHART_PARSER
-    id(0),
-#endif
-    cat(0), dot(NULL), q(NULL),
-    r(_r), active_parent(NULL), passive_parent(NULL), tps() {}
-  // constructor for MERGE quere
-  Edge(const WFSTNode* _q, int) :
-#ifdef DEBUG_CHART_PARSER
-    id(0),
-#endif
-    cat(0), dot(NULL), q(_q),
-    r(NULL), active_parent(NULL), passive_parent(NULL), tps() {}
-};
-#ifdef DEBUG_CHART_PARSER
-int Edge::id_count = 0;
-#endif
-
-ostream& operator<<(ostream& os, const Edge& e) {
-  string type = "PREDICT";
-  if (e.IsCreatedByScan())
-    type = "SCAN";
-  else if (e.IsCreatedByComplete())
-    type = "COMPLETE";
-  os << "["
-#ifdef DEBUG_CHART_PARSER
-     << '(' << e.id << ") "
-#else
-     << '(' << &e << ") "
-#endif
-     << "q=" << e.q << ", r=" << e.r
-     << ", cat="<< TD::Convert(e.cat*-1) << ", dot="
-     << e.dot
-#ifdef DEBUG_CHART_PARSER
-     << e.dot->hint
-#endif
-     << (e.IsActive() ? ", Active" : ", Passive")
-     << ", " << type;
-#ifdef DEBUG_CHART_PARSER
-  if (e.active_parent) { os << ", act.parent=(" << e.active_parent->id << ')'; }
-  if (e.passive_parent) { os << ", psv.parent=(" << e.passive_parent->id << ')'; }
-#endif
-  if (e.tps) { os << ", tps=" << e.tps->AsString(); }
-  return os << ']';
-}
-
-struct Traversal {
-  const Edge* const edge;      // result from the active / passive combination
-  const Edge* const active;
-  const Edge* const passive;
-  Traversal(const Edge* me, const Edge* a, const Edge* p) : edge(me), active(a), passive(p) {}
-};
-
-struct UniqueTraversalHash {
-  size_t operator()(const Traversal* t) const {
-    size_t x = 5381;
-    x = ((x << 5) + x) ^ reinterpret_cast<size_t>(t->active);
-    x = ((x << 5) + x) ^ reinterpret_cast<size_t>(t->passive);
-    x = ((x << 5) + x) ^ t->edge->IsActive();
-    return x;
-  }
-};
-
-struct UniqueTraversalEquals {
-  size_t operator()(const Traversal* a, const Traversal* b) const {
-    return (a->passive == b->passive && a->active == b->active && a->edge->IsActive() == b->edge->IsActive());
-  }
-};
-
-struct UniqueEdgeHash {
-  size_t operator()(const Edge* e) const {
-    size_t x = 5381;
-    if (e->IsActive()) {
-      x = ((x << 5) + x) ^ reinterpret_cast<size_t>(e->dot);
-      x = ((x << 5) + x) ^ reinterpret_cast<size_t>(e->q);
-      x = ((x << 5) + x) ^ reinterpret_cast<size_t>(e->r);
-      x = ((x << 5) + x) ^ static_cast<size_t>(e->cat);
-      x += 13;
-    } else {  // with passive edges, we don't care about the dot
-      x = ((x << 5) + x) ^ reinterpret_cast<size_t>(e->q);
-      x = ((x << 5) + x) ^ reinterpret_cast<size_t>(e->r);
-      x = ((x << 5) + x) ^ static_cast<size_t>(e->cat);
-    }
-    return x;
-  }
-};
-
-struct UniqueEdgeEquals {
-  bool operator()(const Edge* a, const Edge* b) const {
-    if (a->IsActive() != b->IsActive()) return false;
-    if (a->IsActive()) {
-      return (a->cat == b->cat) && (a->dot == b->dot) && (a->q == b->q) && (a->r == b->r);
-    } else {
-      return (a->cat == b->cat) && (a->q == b->q) && (a->r == b->r);
-    }
-  }
-};
-
-struct REdgeHash {
-  size_t operator()(const Edge* e) const {
-    size_t x = 5381;
-    x = ((x << 5) + x) ^ reinterpret_cast<size_t>(e->r);
-    return x;
-  }
-};
-
-struct REdgeEquals {
-  bool operator()(const Edge* a, const Edge* b) const {
-    return (a->r == b->r);
-  }
-};
-
-struct QEdgeHash {
-  size_t operator()(const Edge* e) const {
-    size_t x = 5381;
-    x = ((x << 5) + x) ^ reinterpret_cast<size_t>(e->q);
-    return x;
-  }
-};
-
-struct QEdgeEquals {
-  bool operator()(const Edge* a, const Edge* b) const {
-    return (a->q == b->q);
-  }
-};
-
-struct EdgeQueue {
-  queue<const Edge*> q;
-  EdgeQueue() {}
-  void clear() { while(!q.empty()) q.pop(); }
-  bool HasWork() const { return !q.empty(); }
-  const Edge* Next() { const Edge* res = q.front(); q.pop(); return res; }
-  void AddEdge(const Edge* s) { q.push(s); }
-};
-
-class CFG_WFSTComposerImpl {
- public:
-  CFG_WFSTComposerImpl(WordID start_cat,
-                       const WFSTNode* q_0,
-                       const WFSTNode* q_final) : start_cat_(start_cat), q_0_(q_0), q_final_(q_final) {}
-
-  // returns false if the intersection is empty
-  bool Compose(const EGrammar& g, Hypergraph* forest) {
-    goal_node = NULL;
-    EGrammar::const_iterator sit = g.find(start_cat_);
-    forest->ReserveNodes(kMAX_NODES);
-    assert(sit != g.end());
-    Edge* init = new Edge(start_cat_, &sit->second, q_0_);
-    assert(IncorporateNewEdge(init));
-    while (exp_agenda.HasWork() || agenda.HasWork()) {
-      while(exp_agenda.HasWork()) {
-        const Edge* edge = exp_agenda.Next();
-        FinishEdge(edge, forest);
-      }
-      if (agenda.HasWork()) {
-        const Edge* edge = agenda.Next();
-#ifdef DEBUG_CHART_PARSER
-        cerr << "processing (" << edge->id << ')' << endl;
-#endif
-        if (edge->IsActive()) {
-          if (edge->dot->HasTerminals())
-            DoScan(edge);
-          if (edge->dot->HasNonTerminals()) {
-            DoMergeWithPassives(edge);
-            DoPredict(edge, g);
-          }
-        } else {
-          DoComplete(edge);
-        }
-      }
-    }
-    if (goal_node) {
-      forest->PruneUnreachable(goal_node->id_);
-      RemoveEpsilons(forest, kEPS);
-    }
-    FreeAll();
-    return goal_node;
-  }
-
-  void FreeAll() {
-    for (int i = 0; i < free_list_.size(); ++i)
-      delete free_list_[i];
-    free_list_.clear();
-    for (int i = 0; i < traversal_free_list_.size(); ++i)
-      delete traversal_free_list_[i];
-    traversal_free_list_.clear();
-    all_traversals.clear();
-    exp_agenda.clear();
-    agenda.clear();
-    tps2node.clear();
-    edge2node.clear();
-    all_edges.clear();
-    passive_edges.clear();
-    active_edges.clear();
-  }
-
-  ~CFG_WFSTComposerImpl() {
-    FreeAll();
-  }
-
-  // returns the total number of edges created during composition
-  int EdgesCreated() const {
-    return free_list_.size();
-  }
-
- private:
-  void DoScan(const Edge* edge) {
-    // here, we assume that the FST will potentially have many more outgoing
-    // edges than the grammar, which will be just a couple.  If you want to
-    // efficiently handle the case where both are relatively large, this code
-    // will need to change how the intersection is done.  The best general
-    // solution would probably be the Baeza-Yates double binary search.
-
-    const EGrammarNode* dot = edge->dot;
-    const WFSTNode* r = edge->r;
-    const map<WordID, EGrammarNode>& terms = dot->GetTerminals();
-    for (map<WordID, EGrammarNode>::const_iterator git = terms.begin();
-         git != terms.end(); ++git) {
-
-      if (!(TD::Convert(git->first)[0] >= '0' && TD::Convert(git->first)[0] <= '9')) {
-        std::cerr << "TERMINAL SYMBOL: " << TD::Convert(git->first) << endl;
-        abort();
-      }
-      std::vector<std::pair<const WFSTNode*, TRulePtr> > extensions = r->ExtendInput(atoi(TD::Convert(git->first)));
-      for (unsigned nsi = 0; nsi < extensions.size(); ++nsi) {
-        const WFSTNode* next_r = extensions[nsi].first;
-        const EGrammarNode* next_dot = &git->second;
-        const bool grammar_continues = next_dot->GrammarContinues();
-        const bool rule_completes    = next_dot->RuleCompletes();
-        if (extensions[nsi].second)
-          cerr << "!!! " << extensions[nsi].second->AsString() << endl;
-        // cerr << "  rule completes: " << rule_completes << " after consuming " << TD::Convert(git->first) << endl;
-        assert(grammar_continues || rule_completes);
-        const SparseVector<double>& input_features = next_dot->GetCFGProductionFeatures();
-        if (rule_completes)
-          IncorporateNewEdge(new Edge(edge->cat, next_dot, edge->q, next_r, edge, extensions[nsi].second, input_features));
-        if (grammar_continues)
-          IncorporateNewEdge(new Edge(edge->cat, next_dot, edge->q, next_r, edge, extensions[nsi].second));
-      }
-    }
-  }
-
-  void DoPredict(const Edge* edge, const EGrammar& g) {
-    const EGrammarNode* dot = edge->dot;
-    const map<WordID, EGrammarNode>& non_terms = dot->GetNonTerminals();
-    for (map<WordID, EGrammarNode>::const_iterator git = non_terms.begin();
-         git != non_terms.end(); ++git) {
-      const WordID nt_to_predict = git->first;
-      //cerr << edge->id << " -- " << TD::Convert(nt_to_predict*-1) << endl;
-      EGrammar::const_iterator egi = g.find(nt_to_predict);
-      if (egi == g.end()) {
-        cerr << "[ERROR] Can't find any grammar rules with a LHS of type "
-             << TD::Convert(-1*nt_to_predict) << '!' << endl;
-        continue;
-      }
-      assert(edge->IsActive());
-      const EGrammarNode* new_dot = &egi->second;
-      Edge* new_edge = new Edge(nt_to_predict, new_dot, edge->r, edge);
-      IncorporateNewEdge(new_edge);
-    }
-  }
-
-  void DoComplete(const Edge* passive) {
-#ifdef DEBUG_CHART_PARSER
-    cerr << "  complete: " << *passive << endl;
-#endif
-    const WordID completed_nt = passive->cat;
-    const WFSTNode* q = passive->q;
-    const WFSTNode* next_r = passive->r;
-    const Edge query(q);
-    const pair<unordered_multiset<const Edge*, REdgeHash, REdgeEquals>::iterator,
-         unordered_multiset<const Edge*, REdgeHash, REdgeEquals>::iterator > p =
-      active_edges.equal_range(&query);
-    for (unordered_multiset<const Edge*, REdgeHash, REdgeEquals>::iterator it = p.first;
-         it != p.second; ++it) {
-      const Edge* active = *it;
-#ifdef DEBUG_CHART_PARSER
-      cerr << "    pos: " << *active << endl;
-#endif
-      const EGrammarNode* next_dot = active->dot->Extend(completed_nt);
-      if (!next_dot) continue;
-      const SparseVector<double>& input_features = next_dot->GetCFGProductionFeatures();
-      // add up to 2 rules
-      if (next_dot->RuleCompletes())
-        IncorporateNewEdge(new Edge(active->cat, next_dot, active->q, next_r, active, passive, input_features));
-      if (next_dot->GrammarContinues())
-        IncorporateNewEdge(new Edge(active->cat, next_dot, active->q, next_r, active, passive));
-    }
-  }
-
-  void DoMergeWithPassives(const Edge* active) {
-    // edge is active, has non-terminals, we need to find the passives that can extend it
-    assert(active->IsActive());
-    assert(active->dot->HasNonTerminals());
-#ifdef DEBUG_CHART_PARSER
-    cerr << "  merge active with passives: ACT=" << *active << endl;
-#endif
-    const Edge query(active->r, 1);
-    const pair<unordered_multiset<const Edge*, QEdgeHash, QEdgeEquals>::iterator,
-         unordered_multiset<const Edge*, QEdgeHash, QEdgeEquals>::iterator > p =
-      passive_edges.equal_range(&query);
-    for (unordered_multiset<const Edge*, QEdgeHash, QEdgeEquals>::iterator it = p.first;
-         it != p.second; ++it) {
-      const Edge* passive = *it;
-      const EGrammarNode* next_dot = active->dot->Extend(passive->cat);
-      if (!next_dot) continue;
-      const WFSTNode* next_r = passive->r;
-      const SparseVector<double>& input_features = next_dot->GetCFGProductionFeatures();
-      if (next_dot->RuleCompletes())
-        IncorporateNewEdge(new Edge(active->cat, next_dot, active->q, next_r, active, passive, input_features));
-      if (next_dot->GrammarContinues())
-        IncorporateNewEdge(new Edge(active->cat, next_dot, active->q, next_r, active, passive));
-    }
-  }
-
-  // take ownership of edge memory, add to various indexes, etc
-  // returns true if this edge is new
-  bool IncorporateNewEdge(Edge* edge) {
-    free_list_.push_back(edge);
-    if (edge->passive_parent && edge->active_parent) {
-      Traversal* t = new Traversal(edge, edge->active_parent, edge->passive_parent);
-      traversal_free_list_.push_back(t);
-      if (all_traversals.find(t) != all_traversals.end()) {
-        return false;
-      } else {
-        all_traversals.insert(t);
-      }
-    }
-    exp_agenda.AddEdge(edge);
-    return true;
-  }
-
-  bool FinishEdge(const Edge* edge, Hypergraph* hg) {
-    bool is_new = false;
-    if (all_edges.find(edge) == all_edges.end()) {
-#ifdef DEBUG_CHART_PARSER
-      cerr << *edge << " is NEW\n";
-#endif
-      all_edges.insert(edge);
-      is_new = true;
-      if (edge->IsPassive()) passive_edges.insert(edge);
-      if (edge->IsActive()) active_edges.insert(edge);
-      agenda.AddEdge(edge);
-    } else {
-#ifdef DEBUG_CHART_PARSER
-      cerr << *edge << " is NOT NEW.\n";
-#endif
-    }
-    AddEdgeToTranslationForest(edge, hg);
-    return is_new;
-  }
-
-  // build the translation forest
-  void AddEdgeToTranslationForest(const Edge* edge, Hypergraph* hg) {
-    assert(hg->nodes_.size() < kMAX_NODES);
-    Hypergraph::Node* tps = NULL;
-    // first add any target language rules
-    if (edge->tps) {
-      Hypergraph::Node*& node = tps2node[(size_t)edge->tps.get()];
-      if (!node) {
-        // cerr << "Creating phrases for " << edge->tps << endl;
-        const TRulePtr& rule = edge->tps;
-        node = hg->AddNode(kPHRASE);
-        Hypergraph::Edge* hg_edge = hg->AddEdge(rule, Hypergraph::TailNodeVector());
-        hg_edge->feature_values_ += rule->GetFeatureValues();
-        hg->ConnectEdgeToHeadNode(hg_edge, node);
-      }
-      tps = node;
-    }
-    Hypergraph::Node*& head_node = edge2node[edge];
-    if (!head_node)
-      head_node = hg->AddNode(kPHRASE);
-    if (edge->cat == start_cat_ && edge->q == q_0_ && edge->r == q_final_ && edge->IsPassive()) {
-      assert(goal_node == NULL || goal_node == head_node);
-      goal_node = head_node;
-    }
-    Hypergraph::TailNodeVector tail;
-    SparseVector<double> extra;
-    if (edge->IsCreatedByPredict()) {
-      // extra.set_value(FD::Convert("predict"), 1);
-    } else if (edge->IsCreatedByScan()) {
-      tail.push_back(edge2node[edge->active_parent]->id_);
-      if (tps) {
-        tail.push_back(tps->id_);
-      }
-      //extra.set_value(FD::Convert("scan"), 1);
-    } else if (edge->IsCreatedByComplete()) {
-      tail.push_back(edge2node[edge->active_parent]->id_);
-      tail.push_back(edge2node[edge->passive_parent]->id_);
-      //extra.set_value(FD::Convert("complete"), 1);
-    } else {
-      assert(!"unexpected edge type!");
-    }
-    //cerr << head_node->id_ << "<--" << *edge << endl;
-
-#ifdef DEBUG_CHART_PARSER
-      for (int i = 0; i < tail.size(); ++i)
-        if (tail[i] == head_node->id_) {
-          cerr << "ERROR: " << *edge << "\n   i=" << i << endl;
-          if (i == 1) { cerr << "\tP: " << *edge->passive_parent << endl; }
-          if (i == 0) { cerr << "\tA: " << *edge->active_parent << endl; }
-          assert(!"self-loop found!");
-        }
-#endif
-    Hypergraph::Edge* hg_edge = NULL;
-    if (tail.size() == 0) {
-      hg_edge = hg->AddEdge(kEPSRule, tail);
-    } else if (tail.size() == 1) {
-      hg_edge = hg->AddEdge(kX1, tail);
-    } else if (tail.size() == 2) {
-      hg_edge = hg->AddEdge(kX1X2, tail);
-    }
-    if (edge->features)
-      hg_edge->feature_values_ += *edge->features;
-    hg_edge->feature_values_ += extra;
-    hg->ConnectEdgeToHeadNode(hg_edge, head_node);
-  }
-
-  Hypergraph::Node* goal_node;
-  EdgeQueue exp_agenda;
-  EdgeQueue agenda;
-  unordered_map<size_t, Hypergraph::Node*> tps2node;
-  unordered_map<const Edge*, Hypergraph::Node*, UniqueEdgeHash, UniqueEdgeEquals> edge2node;
-  unordered_set<const Traversal*, UniqueTraversalHash, UniqueTraversalEquals> all_traversals;
-  unordered_set<const Edge*, UniqueEdgeHash, UniqueEdgeEquals> all_edges;
-  unordered_multiset<const Edge*, QEdgeHash, QEdgeEquals> passive_edges;
-  unordered_multiset<const Edge*, REdgeHash, REdgeEquals> active_edges;
-  vector<Edge*> free_list_;
-  vector<Traversal*> traversal_free_list_;
-  const WordID start_cat_;
-  const WFSTNode* const q_0_;
-  const WFSTNode* const q_final_;
-};
-
-#ifdef DEBUG_CHART_PARSER
-static string TrimRule(const string& r) {
-  size_t start = r.find(" |||") + 5;
-  size_t end = r.rfind(" |||");
-  return r.substr(start, end - start);
-}
-#endif
-
-void AddGrammarRule(const string& r, EGrammar* g) {
-  const size_t pos = r.find(" ||| ");
-  if (pos == string::npos || r[0] != '[') {
-    cerr << "Bad rule: " << r << endl;
-    return;
-  }
-  const size_t rpos = r.rfind(" ||| ");
-  string feats;
-  string rs = r;
-  if (rpos != pos) {
-    feats = r.substr(rpos + 5);
-    rs = r.substr(0, rpos);
-  }
-  string rhs = rs.substr(pos + 5);
-  string trule = rs + " ||| " + rhs + " ||| " + feats;
-  TRule tr(trule);
-  cerr << "X: " << tr.e_[0] << endl;
-#ifdef DEBUG_CHART_PARSER
-  string hint_last_rule;
-#endif
-  EGrammarNode* cur = &(*g)[tr.GetLHS()];
-  cur->is_root = true;
-  for (int i = 0; i < tr.FLength(); ++i) {
-    WordID sym = tr.f()[i];
-#ifdef DEBUG_CHART_PARSER
-    hint_last_rule = TD::Convert(sym < 0 ? -sym : sym);
-    cur->hint += " <@@> (*" + hint_last_rule + ") " + TrimRule(tr.AsString());
-#endif
-    if (sym < 0)
-      cur = &cur->ntptr[sym];
-    else
-      cur = &cur->tptr[sym];
-  }
-#ifdef DEBUG_CHART_PARSER
-  cur->hint += " <@@> (" + hint_last_rule + "*) " + TrimRule(tr.AsString());
-#endif
-  cur->is_some_rule_complete = true;
-  cur->input_features = tr.GetFeatureValues();
-}
-
-CFG_WFSTComposer::~CFG_WFSTComposer() {
-  delete pimpl_;
-}
-
-CFG_WFSTComposer::CFG_WFSTComposer(const WFST& wfst) {
-  InitializeConstants();
-  pimpl_ = new CFG_WFSTComposerImpl(kUNIQUE_START, wfst.Initial(), wfst.Final());
-}
-
-bool CFG_WFSTComposer::Compose(const Hypergraph& src_forest, Hypergraph* trg_forest) {
-  // first, convert the src forest into an EGrammar
-  EGrammar g;
-  const int nedges = src_forest.edges_.size();
-  const int nnodes = src_forest.nodes_.size();
-  vector<int> cats(nnodes);
-  bool assign_cats = false;
-  for (int i = 0; i < nnodes; ++i)
-    if (assign_cats) {
-      cats[i] = TD::Convert("CAT_" + boost::lexical_cast<string>(i)) * -1;
-    } else {
-      cats[i] = src_forest.nodes_[i].cat_;
-    }
-  // construct the grammar
-  for (int i = 0; i < nedges; ++i) {
-    const Hypergraph::Edge& edge = src_forest.edges_[i];
-    const vector<WordID>& src = edge.rule_->f();
-    EGrammarNode* cur = &g[cats[edge.head_node_]];
-    cur->is_root = true;
-    int ntc = 0;
-    for (int j = 0; j < src.size(); ++j) {
-      WordID sym = src[j];
-      if (sym <= 0) {
-        sym = cats[edge.tail_nodes_[ntc]];
-        ++ntc;
-        cur = &cur->ntptr[sym];
-      } else {
-        cur = &cur->tptr[sym];
-      }
-    }
-    cur->is_some_rule_complete = true;
-    cur->input_features = edge.feature_values_;
-  }
-  EGrammarNode& goal_rule = g[kUNIQUE_START];
-  assert((goal_rule.ntptr.size() == 1 && goal_rule.tptr.size() == 0) ||
-         (goal_rule.ntptr.size() == 0 && goal_rule.tptr.size() == 1));
-
-  return pimpl_->Compose(g, trg_forest);
-}
-
-bool CFG_WFSTComposer::Compose(istream* in, Hypergraph* trg_forest) {
-  EGrammar g;
-  while(*in) {
-    string line;
-    getline(*in, line);
-    if (line.empty()) continue;
-    AddGrammarRule(line, &g);
-  }
-
-  return pimpl_->Compose(g, trg_forest);
-}
diff --git a/gi/pf/cfg_wfst_composer.h b/gi/pf/cfg_wfst_composer.h
deleted file mode 100644
index cf47f459..00000000
--- a/gi/pf/cfg_wfst_composer.h
+++ /dev/null
@@ -1,46 +0,0 @@
-#ifndef _CFG_WFST_COMPOSER_H_
-#define _CFG_WFST_COMPOSER_H_
-
-#include <iostream>
-#include <vector>
-#include <utility>
-
-#include "trule.h"
-#include "wordid.h"
-
-class CFG_WFSTComposerImpl;
-class Hypergraph;
-
-struct WFSTNode {
-  virtual ~WFSTNode();
-  // returns the next states reachable by consuming srcindex (which identifies a word)
-  // paired with the output string generated by taking that transition.
-  virtual std::vector<std::pair<const WFSTNode*,TRulePtr> > ExtendInput(unsigned srcindex) const = 0;
-};
-
-struct WFST {
-  virtual ~WFST();
-  virtual const WFSTNode* Final() const = 0;
-  virtual const WFSTNode* Initial() const = 0;
-};
-
-class CFG_WFSTComposer {
- public:
-  ~CFG_WFSTComposer();
-  explicit CFG_WFSTComposer(const WFST& wfst);
-  bool Compose(const Hypergraph& in_forest, Hypergraph* trg_forest);
-
-  // reads the grammar from a file. There must be a single top-level
-  // S -> X rule.  Anything else is possible. Format is:
-  // [S] ||| [SS,1]
-  // [SS] ||| [NP,1] [VP,2] ||| Feature1=0.2 Feature2=-2.3
-  // [SS] ||| [VP,1] [NP,2] ||| Feature1=0.8
-  // [NP] ||| [DET,1] [N,2] ||| Feature3=2
-  // ...
-  bool Compose(std::istream* grammar_file, Hypergraph* trg_forest);
-
- private:
-  CFG_WFSTComposerImpl* pimpl_;
-};
-
-#endif
diff --git a/gi/pf/conditional_pseg.h b/gi/pf/conditional_pseg.h
deleted file mode 100644
index 81ddb206..00000000
--- a/gi/pf/conditional_pseg.h
+++ /dev/null
@@ -1,275 +0,0 @@
-#ifndef _CONDITIONAL_PSEG_H_
-#define _CONDITIONAL_PSEG_H_
-
-#include <vector>
-#include <tr1/unordered_map>
-#include <boost/functional/hash.hpp>
-#include <iostream>
-
-#include "m.h"
-#include "prob.h"
-#include "ccrp_nt.h"
-#include "mfcr.h"
-#include "trule.h"
-#include "base_distributions.h"
-#include "tdict.h"
-
-template <typename ConditionalBaseMeasure>
-struct MConditionalTranslationModel {
-  explicit MConditionalTranslationModel(ConditionalBaseMeasure& rcp0) :
-    rp0(rcp0), d(0.5), strength(1.0), lambdas(1, prob_t::One()), p0s(1) {}
-
-  void Summary() const {
-    std::cerr << "Number of conditioning contexts: " << r.size() << std::endl;
-    for (RuleModelHash::const_iterator it = r.begin(); it != r.end(); ++it) {
-      std::cerr << TD::GetString(it->first) << "   \t(d=" << it->second.discount() << ",s=" << it->second.strength() << ") --------------------------" << std::endl;
-      for (MFCR<1,TRule>::const_iterator i2 = it->second.begin(); i2 != it->second.end(); ++i2)
-        std::cerr << "   " << i2->second.total_dish_count_ << '\t' << i2->first << std::endl;
-    }
-  }
-
-  double log_likelihood(const double& dd, const double& aa) const {
-    if (aa <= -dd) return -std::numeric_limits<double>::infinity();
-    //double llh = Md::log_beta_density(dd, 10, 3) + Md::log_gamma_density(aa, 1, 1);
-    double llh = Md::log_beta_density(dd, 1, 1) +
-                 Md::log_gamma_density(dd + aa, 1, 1);
-    typename std::tr1::unordered_map<std::vector<WordID>, MFCR<1,TRule>, boost::hash<std::vector<WordID> > >::const_iterator it;
-    for (it = r.begin(); it != r.end(); ++it)
-      llh += it->second.log_crp_prob(dd, aa);
-    return llh;
-  }
-
-  struct DiscountResampler {
-    DiscountResampler(const MConditionalTranslationModel& m) : m_(m) {}
-    const MConditionalTranslationModel& m_;
-    double operator()(const double& proposed_discount) const {
-      return m_.log_likelihood(proposed_discount, m_.strength);
-    }
-  };
-
-  struct AlphaResampler {
-    AlphaResampler(const MConditionalTranslationModel& m) : m_(m) {}
-    const MConditionalTranslationModel& m_;
-    double operator()(const double& proposed_strength) const {
-      return m_.log_likelihood(m_.d, proposed_strength);
-    }
-  };
-
-  void ResampleHyperparameters(MT19937* rng) {
-    typename std::tr1::unordered_map<std::vector<WordID>, MFCR<1,TRule>, boost::hash<std::vector<WordID> > >::iterator it;
-#if 1
-    for (it = r.begin(); it != r.end(); ++it) {
-      it->second.resample_hyperparameters(rng);
-    }
-#else
-    const unsigned nloop = 5;
-    const unsigned niterations = 10;
-    DiscountResampler dr(*this);
-    AlphaResampler ar(*this);
-    for (int iter = 0; iter < nloop; ++iter) {
-      strength = slice_sampler1d(ar, strength, *rng, -d + std::numeric_limits<double>::min(),
-                              std::numeric_limits<double>::infinity(), 0.0, niterations, 100*niterations);
-      double min_discount = std::numeric_limits<double>::min();
-      if (strength < 0.0) min_discount -= strength;
-      d = slice_sampler1d(dr, d, *rng, min_discount,
-                          1.0, 0.0, niterations, 100*niterations);
-    }
-    strength = slice_sampler1d(ar, strength, *rng, -d,
-                            std::numeric_limits<double>::infinity(), 0.0, niterations, 100*niterations);
-    std::cerr << "MConditionalTranslationModel(d=" << d << ",s=" << strength << ") = " << log_likelihood(d, strength) << std::endl;
-    for (it = r.begin(); it != r.end(); ++it) {
-      it->second.set_discount(d);
-      it->second.set_strength(strength);
-    }
-#endif
-  }
-
-  int DecrementRule(const TRule& rule, MT19937* rng) {
-    RuleModelHash::iterator it = r.find(rule.f_);
-    assert(it != r.end());
-    const TableCount delta = it->second.decrement(rule, rng);
-    if (delta.count) {
-      if (it->second.num_customers() == 0) r.erase(it);
-    }
-    return delta.count;
-  }
-
-  int IncrementRule(const TRule& rule, MT19937* rng) {
-    RuleModelHash::iterator it = r.find(rule.f_);
-    if (it == r.end()) {
-      //it = r.insert(make_pair(rule.f_, MFCR<1,TRule>(d, strength))).first;
-      it = r.insert(make_pair(rule.f_, MFCR<1,TRule>(1,1,1,1,0.6, -0.12))).first;
-    }
-    p0s[0] = rp0(rule); 
-    TableCount delta = it->second.increment(rule, p0s.begin(), lambdas.begin(), rng);
-    return delta.count;
-  }
-
-  prob_t RuleProbability(const TRule& rule) const {
-    prob_t p;
-    RuleModelHash::const_iterator it = r.find(rule.f_);
-    if (it == r.end()) {
-      p = rp0(rule);
-    } else {
-      p0s[0] = rp0(rule);
-      p = it->second.prob(rule, p0s.begin(), lambdas.begin());
-    }
-    return p;
-  }
-
-  prob_t Likelihood() const {
-    prob_t p; p.logeq(log_likelihood(d, strength));
-    return p;
-  }
-
-  const ConditionalBaseMeasure& rp0;
-  typedef std::tr1::unordered_map<std::vector<WordID>,
-                                  MFCR<1, TRule>,
-                                  boost::hash<std::vector<WordID> > > RuleModelHash;
-  RuleModelHash r;
-  double d, strength;
-  std::vector<prob_t> lambdas;
-  mutable std::vector<prob_t> p0s;
-};
-
-template <typename ConditionalBaseMeasure>
-struct ConditionalTranslationModel {
-  explicit ConditionalTranslationModel(ConditionalBaseMeasure& rcp0) :
-    rp0(rcp0) {}
-
-  void Summary() const {
-    std::cerr << "Number of conditioning contexts: " << r.size() << std::endl;
-    for (RuleModelHash::const_iterator it = r.begin(); it != r.end(); ++it) {
-      std::cerr << TD::GetString(it->first) << "   \t(\\alpha = " << it->second.alpha() << ") --------------------------" << std::endl;
-      for (CCRP_NoTable<TRule>::const_iterator i2 = it->second.begin(); i2 != it->second.end(); ++i2)
-        std::cerr << "   " << i2->second << '\t' << i2->first << std::endl;
-    }
-  }
-
-  void ResampleHyperparameters(MT19937* rng) {
-    for (RuleModelHash::iterator it = r.begin(); it != r.end(); ++it)
-      it->second.resample_hyperparameters(rng);
-  } 
-
-  int DecrementRule(const TRule& rule) {
-    RuleModelHash::iterator it = r.find(rule.f_);
-    assert(it != r.end());    
-    int count = it->second.decrement(rule);
-    if (count) {
-      if (it->second.num_customers() == 0) r.erase(it);
-    }
-    return count;
-  }
-
-  int IncrementRule(const TRule& rule) {
-    RuleModelHash::iterator it = r.find(rule.f_);
-    if (it == r.end()) {
-      it = r.insert(make_pair(rule.f_, CCRP_NoTable<TRule>(1.0, 1.0, 8.0))).first;
-    } 
-    int count = it->second.increment(rule);
-    return count;
-  }
-
-  void IncrementRules(const std::vector<TRulePtr>& rules) {
-    for (int i = 0; i < rules.size(); ++i)
-      IncrementRule(*rules[i]);
-  }
-
-  void DecrementRules(const std::vector<TRulePtr>& rules) {
-    for (int i = 0; i < rules.size(); ++i)
-      DecrementRule(*rules[i]);
-  }
-
-  prob_t RuleProbability(const TRule& rule) const {
-    prob_t p;
-    RuleModelHash::const_iterator it = r.find(rule.f_);
-    if (it == r.end()) {
-      p.logeq(log(rp0(rule)));
-    } else {
-      p.logeq(it->second.logprob(rule, log(rp0(rule))));
-    }
-    return p;
-  }
-
-  prob_t Likelihood() const {
-    prob_t p = prob_t::One();
-    for (RuleModelHash::const_iterator it = r.begin(); it != r.end(); ++it) {
-      prob_t q; q.logeq(it->second.log_crp_prob());
-      p *= q;
-      for (CCRP_NoTable<TRule>::const_iterator i2 = it->second.begin(); i2 != it->second.end(); ++i2)
-        p *= rp0(i2->first);
-    }
-    return p;
-  }
-
-  const ConditionalBaseMeasure& rp0;
-  typedef std::tr1::unordered_map<std::vector<WordID>,
-                                  CCRP_NoTable<TRule>,
-                                  boost::hash<std::vector<WordID> > > RuleModelHash;
-  RuleModelHash r;
-};
-
-template <typename ConditionalBaseMeasure>
-struct ConditionalParallelSegementationModel {
-  explicit ConditionalParallelSegementationModel(ConditionalBaseMeasure& rcp0) :
-    tmodel(rcp0), base(prob_t::One()), aligns(1,1) {}
-
-  ConditionalTranslationModel<ConditionalBaseMeasure> tmodel;
-
-  void DecrementRule(const TRule& rule) {
-    tmodel.DecrementRule(rule);
-  }
-
-  void IncrementRule(const TRule& rule) {
-    tmodel.IncrementRule(rule);
-  }
-
-  void IncrementRulesAndAlignments(const std::vector<TRulePtr>& rules) {
-    tmodel.IncrementRules(rules);
-    for (int i = 0; i < rules.size(); ++i) {
-      IncrementAlign(rules[i]->f_.size());
-    }
-  }
-
-  void DecrementRulesAndAlignments(const std::vector<TRulePtr>& rules) {
-    tmodel.DecrementRules(rules);
-    for (int i = 0; i < rules.size(); ++i) {
-      DecrementAlign(rules[i]->f_.size());
-    }
-  }
-
-  prob_t RuleProbability(const TRule& rule) const {
-    return tmodel.RuleProbability(rule);
-  }
-
-  void IncrementAlign(unsigned span) {
-    if (aligns.increment(span)) {
-      // TODO
-    }
-  }
-
-  void DecrementAlign(unsigned span) {
-    if (aligns.decrement(span)) {
-      // TODO
-    }
-  }
-
-  prob_t AlignProbability(unsigned span) const {
-    prob_t p;
-    p.logeq(aligns.logprob(span, Md::log_poisson(span, 1.0)));
-    return p;
-  }
-
-  prob_t Likelihood() const {
-    prob_t p; p.logeq(aligns.log_crp_prob());
-    p *= base;
-    p *= tmodel.Likelihood();
-    return p;
-  }
-
-  prob_t base;
-  CCRP_NoTable<unsigned> aligns;
-};
-
-#endif
-
diff --git a/gi/pf/condnaive.cc b/gi/pf/condnaive.cc
deleted file mode 100644
index 419731ac..00000000
--- a/gi/pf/condnaive.cc
+++ /dev/null
@@ -1,298 +0,0 @@
-#include <iostream>
-#include <tr1/memory>
-#include <queue>
-
-#include <boost/multi_array.hpp>
-#include <boost/program_options.hpp>
-#include <boost/program_options/variables_map.hpp>
-
-#include "base_distributions.h"
-#include "monotonic_pseg.h"
-#include "conditional_pseg.h"
-#include "trule.h"
-#include "tdict.h"
-#include "filelib.h"
-#include "dict.h"
-#include "sampler.h"
-#include "ccrp_nt.h"
-#include "corpus.h"
-
-using namespace std;
-using namespace std::tr1;
-namespace po = boost::program_options;
-
-static unsigned kMAX_SRC_PHRASE;
-static unsigned kMAX_TRG_PHRASE;
-
-void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
-  po::options_description opts("Configuration options");
-  opts.add_options()
-        ("samples,s",po::value<unsigned>()->default_value(1000),"Number of samples")
-        ("input,i",po::value<string>(),"Read parallel data from")
-        ("max_src_phrase",po::value<unsigned>()->default_value(4),"Maximum length of source language phrases")
-        ("max_trg_phrase",po::value<unsigned>()->default_value(4),"Maximum length of target language phrases")
-        ("model1,m",po::value<string>(),"Model 1 parameters (used in base distribution)")
-        ("model1_interpolation_weight",po::value<double>()->default_value(0.95),"Mixing proportion of model 1 with uniform target distribution")
-        ("random_seed,S",po::value<uint32_t>(), "Random seed");
-  po::options_description clo("Command line options");
-  clo.add_options()
-        ("config", po::value<string>(), "Configuration file")
-        ("help,h", "Print this help message and exit");
-  po::options_description dconfig_options, dcmdline_options;
-  dconfig_options.add(opts);
-  dcmdline_options.add(opts).add(clo);
-  
-  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
-  if (conf->count("config")) {
-    ifstream config((*conf)["config"].as<string>().c_str());
-    po::store(po::parse_config_file(config, dconfig_options), *conf);
-  }
-  po::notify(*conf);
-
-  if (conf->count("help") || (conf->count("input") == 0)) {
-    cerr << dcmdline_options << endl;
-    exit(1);
-  }
-}
-
-boost::shared_ptr<MT19937> prng;
-
-struct ModelAndData {
-  explicit ModelAndData(ConditionalParallelSegementationModel<PhraseConditionalBase>& m, const vector<vector<int> >& ce, const vector<vector<int> >& cf, const set<int>& ve, const set<int>& vf) :
-     model(m),
-     rng(&*prng),
-     corpuse(ce),
-     corpusf(cf),
-     vocabe(ve),
-     vocabf(vf),
-     mh_samples(),
-     mh_rejects(),
-     kX(-TD::Convert("X")),
-     derivations(corpuse.size()) {}
-
-  void ResampleHyperparameters() {
-  }
-
-  void InstantiateRule(const pair<short,short>& from,
-                       const pair<short,short>& to,
-                       const vector<int>& sentf,
-                       const vector<int>& sente,
-                       TRule* rule) const {
-    rule->f_.clear();
-    rule->e_.clear();
-    rule->lhs_ = kX;
-    for (short i = from.first; i < to.first; ++i)
-      rule->f_.push_back(sentf[i]);
-    for (short i = from.second; i < to.second; ++i)
-      rule->e_.push_back(sente[i]);
-  }
-
-  void DecrementDerivation(const vector<pair<short,short> >& d, const vector<int>& sentf, const vector<int>& sente) {
-    if (d.size() < 2) return;
-    TRule x;
-    for (int i = 1; i < d.size(); ++i) {
-      InstantiateRule(d[i], d[i-1], sentf, sente, &x);
-      model.DecrementRule(x);
-      model.DecrementAlign(x.f_.size());
-    }
-  }
-
-  void PrintDerivation(const vector<pair<short,short> >& d, const vector<int>& sentf, const vector<int>& sente) {
-    if (d.size() < 2) return;
-    TRule x;
-    for (int i = 1; i < d.size(); ++i) {
-      InstantiateRule(d[i], d[i-1], sentf, sente, &x);
-      cerr << i << '/' << (d.size() - 1) << ": " << x << endl;
-    }
-  }
-
-  void IncrementDerivation(const vector<pair<short,short> >& d, const vector<int>& sentf, const vector<int>& sente) {
-    if (d.size() < 2) return;
-    TRule x;
-    for (int i = 1; i < d.size(); ++i) {
-      InstantiateRule(d[i], d[i-1], sentf, sente, &x);
-      model.IncrementRule(x);
-      model.IncrementAlign(x.f_.size());
-    }
-  }
-
-  prob_t Likelihood() const {
-    return model.Likelihood();
-  }
-
-  prob_t DerivationProposalProbability(const vector<pair<short,short> >& d, const vector<int>& sentf, const vector<int>& sente) const {
-    prob_t p = prob_t::One();
-    TRule x;
-    for (int i = 1; i < d.size(); ++i) {
-      InstantiateRule(d[i], d[i-1], sentf, sente, &x);
-      p *= model.RuleProbability(x);
-      p *= model.AlignProbability(x.f_.size());
-    }
-    return p;
-  }
-
-  void Sample();
-
-  ConditionalParallelSegementationModel<PhraseConditionalBase>& model;
-  MT19937* rng;
-  const vector<vector<int> >& corpuse, corpusf;
-  const set<int>& vocabe, vocabf;
-  unsigned mh_samples, mh_rejects;
-  const int kX;
-  vector<vector<pair<short, short> > > derivations;
-};
-
-void ModelAndData::Sample() {
-  unsigned MAXK = kMAX_SRC_PHRASE;
-  unsigned MAXL = kMAX_TRG_PHRASE;
-  TRule x;
-  x.lhs_ = -TD::Convert("X");
-
-  for (int samples = 0; samples < 1000; ++samples) {
-    if (samples % 1 == 0 && samples > 0) {
-      //ResampleHyperparameters();
-      cerr << " [" << samples << " LLH=" << log(Likelihood()) << " MH=" << ((double)mh_rejects / mh_samples) << "]\n";
-      for (int i = 0; i < 10; ++i) {
-        cerr << "SENTENCE: " << TD::GetString(corpusf[i]) << " ||| " << TD::GetString(corpuse[i]) << endl;
-        PrintDerivation(derivations[i], corpusf[i], corpuse[i]);
-      }
-      static TRule xx("[X] ||| w n ||| s h ||| X=0");
-      const CCRP_NoTable<TRule>& dcrp = model.tmodel.r.find(xx.f_)->second;
-      for (CCRP_NoTable<TRule>::const_iterator it = dcrp.begin(); it != dcrp.end(); ++it) {
-        cerr << "\t" << it->second << "\t" << it->first << endl;
-      }
-    }
-    cerr << '.' << flush;
-    for (int s = 0; s < corpuse.size(); ++s) {
-      const vector<int>& sentf = corpusf[s];
-      const vector<int>& sente = corpuse[s];
-//      cerr << "  CUSTOMERS: " << rules.num_customers() << endl;
-//      cerr << "SENTENCE: " << TD::GetString(sentf) << " ||| " << TD::GetString(sente) << endl;
-
-      vector<pair<short, short> >& deriv = derivations[s];
-      const prob_t p_cur = Likelihood();
-      DecrementDerivation(deriv, sentf, sente);
-
-      boost::multi_array<prob_t, 2> a(boost::extents[sentf.size() + 1][sente.size() + 1]);
-      boost::multi_array<prob_t, 4> trans(boost::extents[sentf.size() + 1][sente.size() + 1][MAXK][MAXL]);
-      a[0][0] = prob_t::One();
-      for (int i = 0; i < sentf.size(); ++i) {
-        for (int j = 0; j < sente.size(); ++j) {
-          const prob_t src_a = a[i][j];
-          x.f_.clear();
-          for (int k = 1; k <= MAXK; ++k) {
-            if (i + k > sentf.size()) break;
-            x.f_.push_back(sentf[i + k - 1]);
-            x.e_.clear();
-            const prob_t p_span = model.AlignProbability(k);  // prob of consuming this much source
-            for (int l = 1; l <= MAXL; ++l) {
-              if (j + l > sente.size()) break;
-              x.e_.push_back(sente[j + l - 1]);
-              trans[i][j][k - 1][l - 1] = model.RuleProbability(x) * p_span;
-              a[i + k][j + l] += src_a * trans[i][j][k - 1][l - 1];
-            }
-          }
-        }
-      }
-//      cerr << "Inside: " << log(a[sentf.size()][sente.size()]) << endl;
-      const prob_t q_cur = DerivationProposalProbability(deriv, sentf, sente);
-
-      vector<pair<short,short> > newderiv;
-      int cur_i = sentf.size();
-      int cur_j = sente.size();
-      while(cur_i > 0 && cur_j > 0) {
-        newderiv.push_back(pair<short,short>(cur_i, cur_j));
-//        cerr << "NODE: (" << cur_i << "," << cur_j << ")\n";
-        SampleSet<prob_t> ss;
-        vector<pair<short,short> > nexts;
-        for (int k = 1; k <= MAXK; ++k) {
-          const int hyp_i = cur_i - k;
-          if (hyp_i < 0) break;
-          for (int l = 1; l <= MAXL; ++l) {
-            const int hyp_j = cur_j - l;
-            if (hyp_j < 0) break;
-            const prob_t& inside = a[hyp_i][hyp_j];
-            if (inside == prob_t::Zero()) continue;
-            const prob_t& transp = trans[hyp_i][hyp_j][k - 1][l - 1];
-            if (transp == prob_t::Zero()) continue;
-            const prob_t p = inside * transp;
-            ss.add(p);
-            nexts.push_back(pair<short,short>(hyp_i, hyp_j));
-//            cerr << "    (" << hyp_i << "," << hyp_j << ")  <--- " << log(p) << endl;
-          }
-        }
-//        cerr << "  sample set has " << nexts.size() << " elements.\n";
-        const int selected = rng->SelectSample(ss);
-        cur_i = nexts[selected].first;
-        cur_j = nexts[selected].second;
-      }
-      newderiv.push_back(pair<short,short>(0,0));
-      const prob_t q_new = DerivationProposalProbability(newderiv, sentf, sente);
-      IncrementDerivation(newderiv, sentf, sente);
-//      cerr << "SANITY: " << q_new << "  " <<log(DerivationProposalProbability(newderiv, sentf, sente)) << endl;
-      if (deriv.empty()) { deriv = newderiv; continue; }
-      ++mh_samples;
-
-      if (deriv != newderiv) {
-        const prob_t p_new = Likelihood();
-//        cerr << "p_cur=" << log(p_cur) << "\t p_new=" << log(p_new) << endl;
-//        cerr << "q_cur=" << log(q_cur) << "\t q_new=" << log(q_new) << endl;
-        if (!rng->AcceptMetropolisHastings(p_new, p_cur, q_new, q_cur)) {
-          ++mh_rejects;
-          DecrementDerivation(newderiv, sentf, sente);
-          IncrementDerivation(deriv, sentf, sente);
-        } else {
-//          cerr << "  ACCEPT\n";
-          deriv = newderiv;
-        }
-      }
-    }
-  }
-}
-
-int main(int argc, char** argv) {
-  po::variables_map conf;
-  InitCommandLine(argc, argv, &conf);
-  kMAX_TRG_PHRASE = conf["max_trg_phrase"].as<unsigned>();
-  kMAX_SRC_PHRASE = conf["max_src_phrase"].as<unsigned>();
-
-  if (!conf.count("model1")) {
-    cerr << argv[0] << "Please use --model1 to specify model 1 parameters\n";
-    return 1;
-  }
-  if (conf.count("random_seed"))
-    prng.reset(new MT19937(conf["random_seed"].as<uint32_t>()));
-  else
-    prng.reset(new MT19937);
-//  MT19937& rng = *prng;
-
-  vector<vector<int> > corpuse, corpusf;
-  set<int> vocabe, vocabf;
-  corpus::ReadParallelCorpus(conf["input"].as<string>(), &corpusf, &corpuse, &vocabf, &vocabe);
-  cerr << "f-Corpus size: " << corpusf.size() << " sentences\n";
-  cerr << "f-Vocabulary size: " << vocabf.size() << " types\n";
-  cerr << "f-Corpus size: " << corpuse.size() << " sentences\n";
-  cerr << "f-Vocabulary size: " << vocabe.size() << " types\n";
-  assert(corpusf.size() == corpuse.size());
-
-  Model1 m1(conf["model1"].as<string>());
-
-  PhraseConditionalBase pcb0(m1, conf["model1_interpolation_weight"].as<double>(), vocabe.size());
-  ConditionalParallelSegementationModel<PhraseConditionalBase> x(pcb0);  
-
-  ModelAndData posterior(x, corpuse, corpusf, vocabe, vocabf);
-  posterior.Sample();
-
-  TRule r1("[X] ||| x ||| l e ||| X=0");
-  TRule r2("[X] ||| A ||| a d ||| X=0");
-  TRule r3("[X] ||| n ||| e r ||| X=0");
-  TRule r4("[X] ||| x A n ||| b l a g ||| X=0");
-
-  PhraseConditionalUninformativeBase u0(vocabe.size());
-
-  cerr << (pcb0(r1)*pcb0(r2)*pcb0(r3)) << endl;
-  cerr << (u0(r4)) << endl;
-
-  return 0;
-}
-
diff --git a/gi/pf/corpus.cc b/gi/pf/corpus.cc
deleted file mode 100644
index cb6e4ed7..00000000
--- a/gi/pf/corpus.cc
+++ /dev/null
@@ -1,62 +0,0 @@
-#include "corpus.h"
-
-#include <set>
-#include <vector>
-#include <string>
-
-#include "tdict.h"
-#include "filelib.h"
-
-using namespace std;
-
-namespace corpus {
-
-void ReadParallelCorpus(const string& filename,
-                vector<vector<WordID> >* f,
-                vector<vector<WordID> >* e,
-                set<WordID>* vocab_f,
-                set<WordID>* vocab_e) {
-  f->clear();
-  e->clear();
-  vocab_f->clear();
-  vocab_e->clear();
-  ReadFile rf(filename);
-  istream* in = rf.stream();
-  assert(*in);
-  string line;
-  unsigned lc = 0;
-  const WordID kDIV = TD::Convert("|||");
-  vector<WordID> tmp;
-  while(getline(*in, line)) {
-    ++lc;
-    e->push_back(vector<int>());
-    f->push_back(vector<int>());
-    vector<int>& le = e->back();
-    vector<int>& lf = f->back();
-    tmp.clear();
-    TD::ConvertSentence(line, &tmp);
-    bool isf = true;
-    for (unsigned i = 0; i < tmp.size(); ++i) {
-      const int cur = tmp[i];
-      if (isf) {
-        if (kDIV == cur) {
-          isf = false;
-        } else {
-          lf.push_back(cur);
-          vocab_f->insert(cur);
-        }
-      } else {
-        if (cur == kDIV) {
-          cerr << "ERROR in " << lc << ": " << line << endl << endl;
-          abort();
-        }
-        le.push_back(cur);
-        vocab_e->insert(cur);
-      }
-    }
-    assert(isf == false);
-  }
-}
-
-}
-
diff --git a/gi/pf/corpus.h b/gi/pf/corpus.h
deleted file mode 100644
index e7febdb7..00000000
--- a/gi/pf/corpus.h
+++ /dev/null
@@ -1,19 +0,0 @@
-#ifndef _CORPUS_H_
-#define _CORPUS_H_
-
-#include <string>
-#include <vector>
-#include <set>
-#include "wordid.h"
-
-namespace corpus {
-
-void ReadParallelCorpus(const std::string& filename,
-                std::vector<std::vector<WordID> >* f,
-                std::vector<std::vector<WordID> >* e,
-                std::set<WordID>* vocab_f,
-                std::set<WordID>* vocab_e);
-
-}
-
-#endif
diff --git a/gi/pf/dpnaive.cc b/gi/pf/dpnaive.cc
deleted file mode 100644
index 75ccad72..00000000
--- a/gi/pf/dpnaive.cc
+++ /dev/null
@@ -1,301 +0,0 @@
-#include <iostream>
-#include <tr1/memory>
-#include <queue>
-
-#include <boost/multi_array.hpp>
-#include <boost/program_options.hpp>
-#include <boost/program_options/variables_map.hpp>
-
-#include "base_distributions.h"
-#include "monotonic_pseg.h"
-#include "trule.h"
-#include "tdict.h"
-#include "filelib.h"
-#include "dict.h"
-#include "sampler.h"
-#include "ccrp_nt.h"
-#include "corpus.h"
-
-using namespace std;
-using namespace std::tr1;
-namespace po = boost::program_options;
-
-static unsigned kMAX_SRC_PHRASE;
-static unsigned kMAX_TRG_PHRASE;
-
-void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
-  po::options_description opts("Configuration options");
-  opts.add_options()
-        ("samples,s",po::value<unsigned>()->default_value(1000),"Number of samples")
-        ("input,i",po::value<string>(),"Read parallel data from")
-        ("max_src_phrase",po::value<unsigned>()->default_value(4),"Maximum length of source language phrases")
-        ("max_trg_phrase",po::value<unsigned>()->default_value(4),"Maximum length of target language phrases")
-        ("model1,m",po::value<string>(),"Model 1 parameters (used in base distribution)")
-        ("inverse_model1,M",po::value<string>(),"Inverse Model 1 parameters (used in base distribution)")
-        ("model1_interpolation_weight",po::value<double>()->default_value(0.95),"Mixing proportion of model 1 with uniform target distribution")
-        ("random_seed,S",po::value<uint32_t>(), "Random seed");
-  po::options_description clo("Command line options");
-  clo.add_options()
-        ("config", po::value<string>(), "Configuration file")
-        ("help,h", "Print this help message and exit");
-  po::options_description dconfig_options, dcmdline_options;
-  dconfig_options.add(opts);
-  dcmdline_options.add(opts).add(clo);
-  
-  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
-  if (conf->count("config")) {
-    ifstream config((*conf)["config"].as<string>().c_str());
-    po::store(po::parse_config_file(config, dconfig_options), *conf);
-  }
-  po::notify(*conf);
-
-  if (conf->count("help") || (conf->count("input") == 0)) {
-    cerr << dcmdline_options << endl;
-    exit(1);
-  }
-}
-
-boost::shared_ptr<MT19937> prng;
-
-template <typename Base>
-struct ModelAndData {
-  explicit ModelAndData(MonotonicParallelSegementationModel<PhraseJointBase_BiDir>& m, const Base& b, const vector<vector<int> >& ce, const vector<vector<int> >& cf, const set<int>& ve, const set<int>& vf) :
-     model(m),
-     rng(&*prng),
-     p0(b),
-     baseprob(prob_t::One()),
-     corpuse(ce),
-     corpusf(cf),
-     vocabe(ve),
-     vocabf(vf),
-     mh_samples(),
-     mh_rejects(),
-     kX(-TD::Convert("X")),
-     derivations(corpuse.size()) {}
-
-  void ResampleHyperparameters() {
-  }
-
-  void InstantiateRule(const pair<short,short>& from,
-                       const pair<short,short>& to,
-                       const vector<int>& sentf,
-                       const vector<int>& sente,
-                       TRule* rule) const {
-    rule->f_.clear();
-    rule->e_.clear();
-    rule->lhs_ = kX;
-    for (short i = from.first; i < to.first; ++i)
-      rule->f_.push_back(sentf[i]);
-    for (short i = from.second; i < to.second; ++i)
-      rule->e_.push_back(sente[i]);
-  }
-
-  void DecrementDerivation(const vector<pair<short,short> >& d, const vector<int>& sentf, const vector<int>& sente) {
-    if (d.size() < 2) return;
-    TRule x;
-    for (int i = 1; i < d.size(); ++i) {
-      InstantiateRule(d[i], d[i-1], sentf, sente, &x);
-      model.DecrementRule(x);
-      model.DecrementContinue();
-    }
-    model.DecrementStop();
-  }
-
-  void PrintDerivation(const vector<pair<short,short> >& d, const vector<int>& sentf, const vector<int>& sente) {
-    if (d.size() < 2) return;
-    TRule x;
-    for (int i = 1; i < d.size(); ++i) {
-      InstantiateRule(d[i], d[i-1], sentf, sente, &x);
-      cerr << i << '/' << (d.size() - 1) << ": " << x << endl;
-    }
-  }
-
-  void IncrementDerivation(const vector<pair<short,short> >& d, const vector<int>& sentf, const vector<int>& sente) {
-    if (d.size() < 2) return;
-    TRule x;
-    for (int i = 1; i < d.size(); ++i) {
-      InstantiateRule(d[i], d[i-1], sentf, sente, &x);
-      model.IncrementRule(x);
-      model.IncrementContinue();
-    }
-    model.IncrementStop();
-  }
-
-  prob_t Likelihood() const {
-    return model.Likelihood();
-  }
-
-  prob_t DerivationProposalProbability(const vector<pair<short,short> >& d, const vector<int>& sentf, const vector<int>& sente) const {
-    prob_t p = model.StopProbability();
-    if (d.size() < 2) return p;
-    TRule x;
-    const prob_t p_cont = model.ContinueProbability();
-    for (int i = 1; i < d.size(); ++i) {
-      InstantiateRule(d[i], d[i-1], sentf, sente, &x);
-      p *= p_cont;
-      p *= model.RuleProbability(x);
-    }
-    return p;
-  }
-
-  void Sample();
-
-  MonotonicParallelSegementationModel<PhraseJointBase_BiDir>& model;
-  MT19937* rng;
-  const Base& p0;
-  prob_t baseprob; // cached value of generating the table table labels from p0
-                   // this can't be used if we go to a hierarchical prior!
-  const vector<vector<int> >& corpuse, corpusf;
-  const set<int>& vocabe, vocabf;
-  unsigned mh_samples, mh_rejects;
-  const int kX;
-  vector<vector<pair<short, short> > > derivations;
-};
-
-template <typename Base>
-void ModelAndData<Base>::Sample() {
-  unsigned MAXK = kMAX_SRC_PHRASE;
-  unsigned MAXL = kMAX_TRG_PHRASE;
-  TRule x;
-  x.lhs_ = -TD::Convert("X");
-  for (int samples = 0; samples < 1000; ++samples) {
-    if (samples % 1 == 0 && samples > 0) {
-      //ResampleHyperparameters();
-      cerr << " [" << samples << " LLH=" << log(Likelihood()) << " MH=" << ((double)mh_rejects / mh_samples) << "]\n";
-      for (int i = 0; i < 10; ++i) {
-        cerr << "SENTENCE: " << TD::GetString(corpusf[i]) << " ||| " << TD::GetString(corpuse[i]) << endl;
-        PrintDerivation(derivations[i], corpusf[i], corpuse[i]);
-      }
-    }
-    cerr << '.' << flush;
-    for (int s = 0; s < corpuse.size(); ++s) {
-      const vector<int>& sentf = corpusf[s];
-      const vector<int>& sente = corpuse[s];
-//      cerr << "  CUSTOMERS: " << rules.num_customers() << endl;
-//      cerr << "SENTENCE: " << TD::GetString(sentf) << " ||| " << TD::GetString(sente) << endl;
-
-      vector<pair<short, short> >& deriv = derivations[s];
-      const prob_t p_cur = Likelihood();
-      DecrementDerivation(deriv, sentf, sente);
-
-      boost::multi_array<prob_t, 2> a(boost::extents[sentf.size() + 1][sente.size() + 1]);
-      boost::multi_array<prob_t, 4> trans(boost::extents[sentf.size() + 1][sente.size() + 1][MAXK][MAXL]);
-      a[0][0] = prob_t::One();
-      const prob_t q_stop = model.StopProbability();
-      const prob_t q_cont = model.ContinueProbability();
-      for (int i = 0; i < sentf.size(); ++i) {
-        for (int j = 0; j < sente.size(); ++j) {
-          const prob_t src_a = a[i][j];
-          x.f_.clear();
-          for (int k = 1; k <= MAXK; ++k) {
-            if (i + k > sentf.size()) break;
-            x.f_.push_back(sentf[i + k - 1]);
-            x.e_.clear();
-            for (int l = 1; l <= MAXL; ++l) {
-              if (j + l > sente.size()) break;
-              x.e_.push_back(sente[j + l - 1]);
-              const bool stop_now = ((j + l) == sente.size()) && ((i + k) == sentf.size());
-              const prob_t& cp = stop_now ? q_stop : q_cont;
-              trans[i][j][k - 1][l - 1] = model.RuleProbability(x) * cp;
-              a[i + k][j + l] += src_a * trans[i][j][k - 1][l - 1];
-            }
-          }
-        }
-      }
-//      cerr << "Inside: " << log(a[sentf.size()][sente.size()]) << endl;
-      const prob_t q_cur = DerivationProposalProbability(deriv, sentf, sente);
-
-      vector<pair<short,short> > newderiv;
-      int cur_i = sentf.size();
-      int cur_j = sente.size();
-      while(cur_i > 0 && cur_j > 0) {
-        newderiv.push_back(pair<short,short>(cur_i, cur_j));
-//        cerr << "NODE: (" << cur_i << "," << cur_j << ")\n";
-        SampleSet<prob_t> ss;
-        vector<pair<short,short> > nexts;
-        for (int k = 1; k <= MAXK; ++k) {
-          const int hyp_i = cur_i - k;
-          if (hyp_i < 0) break;
-          for (int l = 1; l <= MAXL; ++l) {
-            const int hyp_j = cur_j - l;
-            if (hyp_j < 0) break;
-            const prob_t& inside = a[hyp_i][hyp_j];
-            if (inside == prob_t::Zero()) continue;
-            const prob_t& transp = trans[hyp_i][hyp_j][k - 1][l - 1];
-            if (transp == prob_t::Zero()) continue;
-            const prob_t p = inside * transp;
-            ss.add(p);
-            nexts.push_back(pair<short,short>(hyp_i, hyp_j));
-//            cerr << "    (" << hyp_i << "," << hyp_j << ")  <--- " << log(p) << endl;
-          }
-        }
-//        cerr << "  sample set has " << nexts.size() << " elements.\n";
-        const int selected = rng->SelectSample(ss);
-        cur_i = nexts[selected].first;
-        cur_j = nexts[selected].second;
-      }
-      newderiv.push_back(pair<short,short>(0,0));
-      const prob_t q_new = DerivationProposalProbability(newderiv, sentf, sente);
-      IncrementDerivation(newderiv, sentf, sente);
-//      cerr << "SANITY: " << q_new << "  " <<log(DerivationProposalProbability(newderiv, sentf, sente)) << endl;
-      if (deriv.empty()) { deriv = newderiv; continue; }
-      ++mh_samples;
-
-      if (deriv != newderiv) {
-        const prob_t p_new = Likelihood();
-//        cerr << "p_cur=" << log(p_cur) << "\t p_new=" << log(p_new) << endl;
-//        cerr << "q_cur=" << log(q_cur) << "\t q_new=" << log(q_new) << endl;
-        if (!rng->AcceptMetropolisHastings(p_new, p_cur, q_new, q_cur)) {
-          ++mh_rejects;
-          DecrementDerivation(newderiv, sentf, sente);
-          IncrementDerivation(deriv, sentf, sente);
-        } else {
-//          cerr << "  ACCEPT\n";
-          deriv = newderiv;
-        }
-      }
-    }
-  }
-}
-
-int main(int argc, char** argv) {
-  po::variables_map conf;
-  InitCommandLine(argc, argv, &conf);
-  kMAX_TRG_PHRASE = conf["max_trg_phrase"].as<unsigned>();
-  kMAX_SRC_PHRASE = conf["max_src_phrase"].as<unsigned>();
-
-  if (!conf.count("model1")) {
-    cerr << argv[0] << "Please use --model1 to specify model 1 parameters\n";
-    return 1;
-  }
-  if (!conf.count("inverse_model1")) {
-    cerr << argv[0] << "Please use --inverse_model1 to specify inverse model 1 parameters\n";
-    return 1;
-  }
-  if (conf.count("random_seed"))
-    prng.reset(new MT19937(conf["random_seed"].as<uint32_t>()));
-  else
-    prng.reset(new MT19937);
-//  MT19937& rng = *prng;
-
-  vector<vector<int> > corpuse, corpusf;
-  set<int> vocabe, vocabf;
-  corpus::ReadParallelCorpus(conf["input"].as<string>(), &corpusf, &corpuse, &vocabf, &vocabe);
-  cerr << "f-Corpus size: " << corpusf.size() << " sentences\n";
-  cerr << "f-Vocabulary size: " << vocabf.size() << " types\n";
-  cerr << "f-Corpus size: " << corpuse.size() << " sentences\n";
-  cerr << "f-Vocabulary size: " << vocabe.size() << " types\n";
-  assert(corpusf.size() == corpuse.size());
-
-  Model1 m1(conf["model1"].as<string>());
-  Model1 invm1(conf["inverse_model1"].as<string>());
-//  PhraseJointBase lp0(m1, conf["model1_interpolation_weight"].as<double>(), vocabe.size(), vocabf.size());
-  PhraseJointBase_BiDir alp0(m1, invm1, conf["model1_interpolation_weight"].as<double>(), vocabe.size(), vocabf.size());
-  MonotonicParallelSegementationModel<PhraseJointBase_BiDir> m(alp0);
-
-  ModelAndData<PhraseJointBase_BiDir> posterior(m, alp0, corpuse, corpusf, vocabe, vocabf);
-  posterior.Sample();
-
-  return 0;
-}
-
diff --git a/gi/pf/guess-translits.pl b/gi/pf/guess-translits.pl
deleted file mode 100755
index d00c2168..00000000
--- a/gi/pf/guess-translits.pl
+++ /dev/null
@@ -1,72 +0,0 @@
-#!/usr/bin/perl -w
-use strict;
-use utf8;
-
-my $MIN_PMI = -3;
-
-my %fs;
-my %es;
-my %ef;
-
-die "Usage: $0 < input.utf8.txt\n" if scalar @ARGV > 0;
-
-binmode(STDIN,":utf8");
-binmode(STDOUT,":utf8");
-binmode(STDERR,":utf8");
-
-my $tot = 0;
-print STDERR "Reading alignments from STDIN ...\n";
-while(<STDIN>) {
-  chomp;
-  my ($fsent, $esent, $alsent) = split / \|\|\| /;
-  die "Format should be 'foreign sentence ||| english sentence ||| 0-0 1-1 ...'\n" unless defined $fsent && defined $esent && defined $alsent;
-
-  my @fws = split /\s+/, $fsent;  
-  my @ews = split /\s+/, $esent;
-  my @as = split /\s+/, $alsent;
-  my %a2b;
-  my %b2a;
-  for my $ap (@as) {
-    my ($a,$b) = split /-/, $ap;
-    die "BAD INPUT: $_\n" unless defined $a && defined $b;
-    $a2b{$a}->{$b} = 1;
-    $b2a{$b}->{$a} = 1;
-  }
-  for my $a (keys %a2b) {
-    my $bref = $a2b{$a};
-    next unless scalar keys %$bref < 2;
-    my $b = (keys %$bref)[0];
-    next unless scalar keys %{$b2a{$b}} < 2;
-    my $f = $fws[$a];
-    next unless defined $f;
-    next unless length($f) > 3;
-    my $e = $ews[$b];
-    next unless defined $e;
-    next unless length($e) > 3;
-
-    $ef{$f}->{$e}++;
-    $es{$e}++;
-    $fs{$f}++;
-    $tot++;
-  }  
-}
-my $ltot = log($tot);
-my $num = 0;
-print STDERR "Extracting pairs for PMI > $MIN_PMI ...\n";
-for my $f (keys %fs) {
-  my $logf = log($fs{$f});
-  my $esref = $ef{$f};
-  for my $e (keys %$esref) {
-    my $loge = log($es{$e});
-    my $ef = $esref->{$e};
-    my $logef = log($ef);
-    my $pmi = $logef - ($loge + $logf);
-    next if $pmi < $MIN_PMI;
-    my @flets = split //, $f;
-    my @elets = split //, $e;
-    print "@flets ||| @elets\n";
-    $num++;
-  }
-}
-print STDERR "Extracted $num pairs.\n";
-print STDERR "Recommend running:\n   ../../training/model1 -v -d -t -99999 output.txt\n";
diff --git a/gi/pf/hpyp_tm.cc b/gi/pf/hpyp_tm.cc
deleted file mode 100644
index 784f9958..00000000
--- a/gi/pf/hpyp_tm.cc
+++ /dev/null
@@ -1,133 +0,0 @@
-#include "hpyp_tm.h"
-
-#include <tr1/unordered_map>
-#include <iostream>
-#include <queue>
-
-#include "tdict.h"
-#include "ccrp.h"
-#include "pyp_word_model.h"
-#include "tied_resampler.h"
-
-using namespace std;
-using namespace std::tr1;
-
-struct FreqBinner {
-  FreqBinner(const std::string& fname) { fd_.Load(fname); }
-  unsigned NumberOfBins() const { return fd_.Max() + 1; }
-  unsigned Bin(const WordID& w) const { return fd_.LookUp(w); }
-  FreqDict<unsigned> fd_;
-};
-
-template <typename Base, class Binner = FreqBinner>
-struct ConditionalPYPWordModel {
-  ConditionalPYPWordModel(Base* b, const Binner* bnr = NULL) :
-      base(*b),
-      binner(bnr),
-      btr(binner ? binner->NumberOfBins() + 1u : 2u) {}
-
-  void Summary() const {
-    cerr << "Number of conditioning contexts: " << r.size() << endl;
-    for (RuleModelHash::const_iterator it = r.begin(); it != r.end(); ++it) {
-      cerr << TD::Convert(it->first) << "   \tPYP(d=" << it->second.discount() << ",s=" << it->second.strength() << ") --------------------------" << endl;
-      for (CCRP<vector<WordID> >::const_iterator i2 = it->second.begin(); i2 != it->second.end(); ++i2)
-        cerr << "   " << i2->second.total_dish_count_ << '\t' << TD::GetString(i2->first) << endl;
-    }
-  }
-
-  void ResampleHyperparameters(MT19937* rng) {
-    btr.ResampleHyperparameters(rng);
-  } 
-
-  prob_t Prob(const WordID src, const vector<WordID>& trglets) const {
-    RuleModelHash::const_iterator it = r.find(src);
-    if (it == r.end()) {
-      return base(trglets);
-    } else {
-      return it->second.prob(trglets, base(trglets));
-    }
-  }
-
-  void Increment(const WordID src, const vector<WordID>& trglets, MT19937* rng) {
-    RuleModelHash::iterator it = r.find(src);
-    if (it == r.end()) {
-      it = r.insert(make_pair(src, CCRP<vector<WordID> >(0.5,1.0))).first;
-      static const WordID kNULL = TD::Convert("NULL");
-      unsigned bin = (src == kNULL ? 0 : 1);
-      if (binner && bin) { bin = binner->Bin(src) + 1; }
-      btr.Add(bin, &it->second);
-    }
-    if (it->second.increment(trglets, base(trglets), rng))
-      base.Increment(trglets, rng);
-  }
-
-  void Decrement(const WordID src, const vector<WordID>& trglets, MT19937* rng) {
-    RuleModelHash::iterator it = r.find(src);
-    assert(it != r.end());
-    if (it->second.decrement(trglets, rng)) {
-      base.Decrement(trglets, rng);
-    }
-  }
-
-  prob_t Likelihood() const {
-    prob_t p = prob_t::One();
-    for (RuleModelHash::const_iterator it = r.begin(); it != r.end(); ++it) {
-      prob_t q; q.logeq(it->second.log_crp_prob());
-      p *= q;
-    }
-    return p;
-  }
-
-  unsigned UniqueConditioningContexts() const {
-    return r.size();
-  }
-
-  // TODO tie PYP hyperparameters based on source word frequency bins
-  Base& base;
-  const Binner* binner;
-  BinTiedResampler<CCRP<vector<WordID> > > btr;
-  typedef unordered_map<WordID, CCRP<vector<WordID> > > RuleModelHash;
-  RuleModelHash r;
-};
-
-HPYPLexicalTranslation::HPYPLexicalTranslation(const vector<vector<WordID> >& lets,
-                                               const unsigned vocab_size,
-                                               const unsigned num_letters) :
-    letters(lets),
-    base(vocab_size, num_letters, 5),
-    up0(new PYPWordModel<PoissonUniformWordModel>(&base)),
-    tmodel(new ConditionalPYPWordModel<PYPWordModel<PoissonUniformWordModel> >(up0, new FreqBinner("10k.freq"))),
-    kX(-TD::Convert("X")) {}
-
-void HPYPLexicalTranslation::Summary() const {
-  tmodel->Summary();
-  up0->Summary();
-}
-
-prob_t HPYPLexicalTranslation::Likelihood() const {
-  prob_t p = up0->Likelihood();
-  p *= tmodel->Likelihood();
-  return p;
-}
-
-void HPYPLexicalTranslation::ResampleHyperparameters(MT19937* rng) {
-  tmodel->ResampleHyperparameters(rng);
-  up0->ResampleHyperparameters(rng);
-}
-
-unsigned HPYPLexicalTranslation::UniqueConditioningContexts() const {
-  return tmodel->UniqueConditioningContexts();
-}
-
-prob_t HPYPLexicalTranslation::Prob(WordID src, WordID trg) const {
-  return tmodel->Prob(src, letters[trg]);
-}
-
-void HPYPLexicalTranslation::Increment(WordID src, WordID trg, MT19937* rng) {
-  tmodel->Increment(src, letters[trg], rng);
-}
-
-void HPYPLexicalTranslation::Decrement(WordID src, WordID trg, MT19937* rng) {
-  tmodel->Decrement(src, letters[trg], rng);
-}
-
diff --git a/gi/pf/hpyp_tm.h b/gi/pf/hpyp_tm.h
deleted file mode 100644
index af3215ba..00000000
--- a/gi/pf/hpyp_tm.h
+++ /dev/null
@@ -1,38 +0,0 @@
-#ifndef HPYP_LEX_TRANS
-#define HPYP_LEX_TRANS
-
-#include <vector>
-#include "wordid.h"
-#include "prob.h"
-#include "sampler.h"
-#include "freqdict.h"
-#include "poisson_uniform_word_model.h"
-
-struct FreqBinner;
-template <class B> struct PYPWordModel;
-template <typename T, class B> struct ConditionalPYPWordModel;
-
-struct HPYPLexicalTranslation {
-  explicit HPYPLexicalTranslation(const std::vector<std::vector<WordID> >& lets,
-                                 const unsigned vocab_size,
-                                 const unsigned num_letters);
-
-  prob_t Likelihood() const;
-
-  void ResampleHyperparameters(MT19937* rng);
-  prob_t Prob(WordID src, WordID trg) const;  // return p(trg | src)
-  void Summary() const;
-  void Increment(WordID src, WordID trg, MT19937* rng);
-  void Decrement(WordID src, WordID trg, MT19937* rng);
-  unsigned UniqueConditioningContexts() const;
-
- private:
-  const std::vector<std::vector<WordID> >& letters;   // spelling dictionary
-  PoissonUniformWordModel base;  // "generator" of English types
-  PYPWordModel<PoissonUniformWordModel>* up0;  // model English lexicon
-  ConditionalPYPWordModel<PYPWordModel<PoissonUniformWordModel>, FreqBinner>* tmodel;  // translation distributions
-                      // (model English word | French word)
-  const WordID kX;
-};
-
-#endif
diff --git a/gi/pf/itg.cc b/gi/pf/itg.cc
deleted file mode 100644
index 29ec3860..00000000
--- a/gi/pf/itg.cc
+++ /dev/null
@@ -1,275 +0,0 @@
-#include <iostream>
-#include <tr1/memory>
-#include <queue>
-
-#include <boost/functional.hpp>
-#include <boost/program_options.hpp>
-#include <boost/program_options/variables_map.hpp>
-
-#include "viterbi.h"
-#include "hg.h"
-#include "trule.h"
-#include "tdict.h"
-#include "filelib.h"
-#include "dict.h"
-#include "sampler.h"
-#include "ccrp_nt.h"
-#include "ccrp_onetable.h"
-
-using namespace std;
-using namespace tr1;
-namespace po = boost::program_options;
-
-ostream& operator<<(ostream& os, const vector<WordID>& p) {
-  os << '[';
-  for (int i = 0; i < p.size(); ++i)
-    os << (i==0 ? "" : " ") << TD::Convert(p[i]);
-  return os << ']';
-}
-
-struct UnigramModel {
-  explicit UnigramModel(const string& fname, unsigned vocab_size, double p0null = 0.05) :
-      use_uniform_(fname.size() == 0),
-      p0null_(p0null),
-      uniform_((1.0 - p0null) / vocab_size),
-      probs_(TD::NumWords() + 1) {
-    if (fname.size() > 0) LoadUnigrams(fname);
-    probs_[0] = p0null_;
-  }
-
-// 
-// \data\
-// ngram 1=9295
-// 
-// \1-grams:
-// -3.191193	"
-
-  void LoadUnigrams(const string& fname) {
-    cerr << "Loading unigram probabilities from " << fname << " ..." << endl;
-    ReadFile rf(fname);
-    string line;
-    istream& in = *rf.stream();
-    assert(in);
-    getline(in, line);
-    assert(line.empty());
-    getline(in, line);
-    assert(line == "\\data\\");
-    getline(in, line);
-    size_t pos = line.find("ngram 1=");
-    assert(pos == 0);
-    assert(line.size() > 8);
-    const size_t num_unigrams = atoi(&line[8]);
-    getline(in, line);
-    assert(line.empty());
-    getline(in, line);
-    assert(line == "\\1-grams:");
-    for (size_t i = 0; i < num_unigrams; ++i) {
-      getline(in, line);
-      assert(line.size() > 0);
-      pos = line.find('\t');
-      assert(pos > 0);
-      assert(pos + 1 < line.size());
-      const WordID w = TD::Convert(line.substr(pos + 1));
-      line[pos] = 0;
-      float p = atof(&line[0]);
-      const prob_t pnon_null(1.0 - p0null_.as_float());
-      if (w < probs_.size()) probs_[w].logeq(p * log(10) + log(pnon_null)); else abort();
-    }
-  }
-
-  const prob_t& operator()(const WordID& w) const {
-    if (!w) return p0null_;
-    if (use_uniform_) return uniform_;
-    return probs_[w];
-  }
-
-  const bool use_uniform_;
-  const prob_t p0null_;
-  const prob_t uniform_;
-  vector<prob_t> probs_;
-};
-
-struct Model1 {
-  explicit Model1(const string& fname) :
-      kNULL(TD::Convert("<eps>")),
-      kZERO() {
-    LoadModel1(fname);
-  }
-
-  void LoadModel1(const string& fname) {
-    cerr << "Loading Model 1 parameters from " << fname << " ..." << endl;
-    ReadFile rf(fname);
-    istream& in = *rf.stream();
-    string line;
-    unsigned lc = 0;
-    while(getline(in, line)) {
-      ++lc;
-      int cur = 0;
-      int start = 0;
-      while(cur < line.size() && line[cur] != ' ') { ++cur; }
-      assert(cur != line.size());
-      line[cur] = 0;
-      const WordID src = TD::Convert(&line[0]);
-      ++cur;
-      start = cur;
-      while(cur < line.size() && line[cur] != ' ') { ++cur; }
-      assert(cur != line.size());
-      line[cur] = 0;
-      WordID trg = TD::Convert(&line[start]);
-      const double logprob = strtod(&line[cur + 1], NULL);
-      if (src >= ttable.size()) ttable.resize(src + 1);
-      ttable[src][trg].logeq(logprob);
-    }
-    cerr << "  read " << lc << " parameters.\n";
-  }
-
-  // returns prob 0 if src or trg is not found!
-  const prob_t& operator()(WordID src, WordID trg) const {
-    if (src == 0) src = kNULL;
-    if (src < ttable.size()) {
-      const map<WordID, prob_t>& cpd = ttable[src];
-      const map<WordID, prob_t>::const_iterator it = cpd.find(trg);
-      if (it != cpd.end())
-        return it->second;
-    }
-    return kZERO;
-  }
-
-  const WordID kNULL;
-  const prob_t kZERO;
-  vector<map<WordID, prob_t> > ttable;
-};
-
-void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
-  po::options_description opts("Configuration options");
-  opts.add_options()
-        ("samples,s",po::value<unsigned>()->default_value(1000),"Number of samples")
-        ("particles,p",po::value<unsigned>()->default_value(25),"Number of particles")
-        ("input,i",po::value<string>(),"Read parallel data from")
-        ("model1,m",po::value<string>(),"Model 1 parameters (used in base distribution)")
-        ("inverse_model1,M",po::value<string>(),"Inverse Model 1 parameters (used in backward estimate)")
-        ("model1_interpolation_weight",po::value<double>()->default_value(0.95),"Mixing proportion of model 1 with uniform target distribution")
-        ("src_unigram,u",po::value<string>()->default_value(""),"Source unigram distribution; empty for uniform")
-        ("trg_unigram,U",po::value<string>()->default_value(""),"Target unigram distribution; empty for uniform")
-        ("random_seed,S",po::value<uint32_t>(), "Random seed");
-  po::options_description clo("Command line options");
-  clo.add_options()
-        ("config", po::value<string>(), "Configuration file")
-        ("help,h", "Print this help message and exit");
-  po::options_description dconfig_options, dcmdline_options;
-  dconfig_options.add(opts);
-  dcmdline_options.add(opts).add(clo);
-  
-  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
-  if (conf->count("config")) {
-    ifstream config((*conf)["config"].as<string>().c_str());
-    po::store(po::parse_config_file(config, dconfig_options), *conf);
-  }
-  po::notify(*conf);
-
-  if (conf->count("help") || (conf->count("input") == 0)) {
-    cerr << dcmdline_options << endl;
-    exit(1);
-  }
-}
-
-void ReadParallelCorpus(const string& filename,
-                vector<vector<WordID> >* f,
-                vector<vector<WordID> >* e,
-                set<WordID>* vocab_f,
-                set<WordID>* vocab_e) {
-  f->clear();
-  e->clear();
-  vocab_f->clear();
-  vocab_e->clear();
-  istream* in;
-  if (filename == "-")
-    in = &cin;
-  else
-    in = new ifstream(filename.c_str());
-  assert(*in);
-  string line;
-  const WordID kDIV = TD::Convert("|||");
-  vector<WordID> tmp;
-  while(*in) {
-    getline(*in, line);
-    if (line.empty() && !*in) break;
-    e->push_back(vector<int>());
-    f->push_back(vector<int>());
-    vector<int>& le = e->back();
-    vector<int>& lf = f->back();
-    tmp.clear();
-    TD::ConvertSentence(line, &tmp);
-    bool isf = true;
-    for (unsigned i = 0; i < tmp.size(); ++i) {
-      const int cur = tmp[i];
-      if (isf) {
-        if (kDIV == cur) { isf = false; } else {
-          lf.push_back(cur);
-          vocab_f->insert(cur);
-        }
-      } else {
-        assert(cur != kDIV);
-        le.push_back(cur);
-        vocab_e->insert(cur);
-      }
-    }
-    assert(isf == false);
-  }
-  if (in != &cin) delete in;
-}
-
-int main(int argc, char** argv) {
-  po::variables_map conf;
-  InitCommandLine(argc, argv, &conf);
-  const unsigned particles = conf["particles"].as<unsigned>();
-  const unsigned samples = conf["samples"].as<unsigned>();
-  TD::Convert("<s>");
-  TD::Convert("</s>");
-  TD::Convert("<unk>");
-  if (!conf.count("model1")) {
-    cerr << argv[0] << "Please use --model1 to specify model 1 parameters\n";
-    return 1;
-  }
-  boost::shared_ptr<MT19937> prng;
-  if (conf.count("random_seed"))
-    prng.reset(new MT19937(conf["random_seed"].as<uint32_t>()));
-  else
-    prng.reset(new MT19937);
-  MT19937& rng = *prng;
-
-  vector<vector<WordID> > corpuse, corpusf;
-  set<WordID> vocabe, vocabf;
-  cerr << "Reading corpus...\n";
-  ReadParallelCorpus(conf["input"].as<string>(), &corpusf, &corpuse, &vocabf, &vocabe);
-  cerr << "F-corpus size: " << corpusf.size() << " sentences\t (" << vocabf.size() << " word types)\n";
-  cerr << "E-corpus size: " << corpuse.size() << " sentences\t (" << vocabe.size() << " word types)\n";
-  assert(corpusf.size() == corpuse.size());
-  UnigramModel src_unigram(conf["src_unigram"].as<string>(), vocabf.size());
-  UnigramModel trg_unigram(conf["trg_unigram"].as<string>(), vocabe.size());
-  const prob_t kHALF(0.5);
-
-  const string kEMPTY = "NULL";
-  const int kLHS = -TD::Convert("X");
-  Model1 m1(conf["model1"].as<string>());
-  Model1 invm1(conf["inverse_model1"].as<string>());
-  for (int si = 0; si < conf["samples"].as<unsigned>(); ++si) {
-    cerr << '.' << flush;
-    for (int ci = 0; ci < corpusf.size(); ++ci) {
-      const vector<WordID>& trg = corpuse[ci];
-      const vector<WordID>& src = corpusf[ci];
-      for (int i = 0; i <= trg.size(); ++i) {
-        const WordID e_i = i > 0 ? trg[i-1] : 0;
-        for (int j = 0; j <= src.size(); ++j) {
-          const WordID f_j = j > 0 ? src[j-1] : 0;
-          if (e_i == 0 && f_j == 0) continue;
-          prob_t je = kHALF * src_unigram(f_j) * m1(f_j,e_i) + kHALF * trg_unigram(e_i) * invm1(e_i,f_j);
-          cerr << "p( " << (e_i ? TD::Convert(e_i) : kEMPTY) << " , " << (f_j ? TD::Convert(f_j) : kEMPTY) << " ) = " << log(je) << endl;
-          if (e_i && f_j)
-            cout << "[X] ||| " << TD::Convert(f_j) << " ||| " << TD::Convert(e_i) << " ||| LogProb=" << log(je) << endl;
-        }
-      }
-    }
-  }
-}
-
diff --git a/gi/pf/learn_cfg.cc b/gi/pf/learn_cfg.cc
deleted file mode 100644
index 44eaa162..00000000
--- a/gi/pf/learn_cfg.cc
+++ /dev/null
@@ -1,428 +0,0 @@
-#include <iostream>
-#include <tr1/memory>
-#include <queue>
-
-#include <boost/functional.hpp>
-#include <boost/program_options.hpp>
-#include <boost/program_options/variables_map.hpp>
-
-#include "inside_outside.h"
-#include "hg.h"
-#include "bottom_up_parser.h"
-#include "fdict.h"
-#include "grammar.h"
-#include "m.h"
-#include "trule.h"
-#include "tdict.h"
-#include "filelib.h"
-#include "dict.h"
-#include "sampler.h"
-#include "ccrp.h"
-#include "ccrp_onetable.h"
-
-using namespace std;
-using namespace tr1;
-namespace po = boost::program_options;
-
-boost::shared_ptr<MT19937> prng;
-vector<int> nt_vocab;
-vector<int> nt_id_to_index;
-static unsigned kMAX_RULE_SIZE = 0;
-static unsigned kMAX_ARITY = 0;
-static bool kALLOW_MIXED = true;  // allow rules with mixed terminals and NTs
-static bool kHIERARCHICAL_PRIOR = false;
-
-void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
-  po::options_description opts("Configuration options");
-  opts.add_options()
-        ("samples,s",po::value<unsigned>()->default_value(1000),"Number of samples")
-        ("input,i",po::value<string>(),"Read parallel data from")
-        ("max_rule_size,m", po::value<unsigned>()->default_value(0), "Maximum rule size (0 for unlimited)")
-        ("max_arity,a", po::value<unsigned>()->default_value(0), "Maximum number of nonterminals in a rule (0 for unlimited)")
-        ("no_mixed_rules,M", "Do not mix terminals and nonterminals in a rule RHS")
-        ("nonterminals,n", po::value<unsigned>()->default_value(1), "Size of nonterminal vocabulary")
-        ("hierarchical_prior,h", "Use hierarchical prior")
-        ("random_seed,S",po::value<uint32_t>(), "Random seed");
-  po::options_description clo("Command line options");
-  clo.add_options()
-        ("config", po::value<string>(), "Configuration file")
-        ("help", "Print this help message and exit");
-  po::options_description dconfig_options, dcmdline_options;
-  dconfig_options.add(opts);
-  dcmdline_options.add(opts).add(clo);
-  
-  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
-  if (conf->count("config")) {
-    ifstream config((*conf)["config"].as<string>().c_str());
-    po::store(po::parse_config_file(config, dconfig_options), *conf);
-  }
-  po::notify(*conf);
-
-  if (conf->count("help") || (conf->count("input") == 0)) {
-    cerr << dcmdline_options << endl;
-    exit(1);
-  }
-}
-
-unsigned ReadCorpus(const string& filename,
-                    vector<vector<WordID> >* e,
-                    set<WordID>* vocab_e) {
-  e->clear();
-  vocab_e->clear();
-  istream* in;
-  if (filename == "-")
-    in = &cin;
-  else
-    in = new ifstream(filename.c_str());
-  assert(*in);
-  string line;
-  unsigned toks = 0;
-  while(*in) {
-    getline(*in, line);
-    if (line.empty() && !*in) break;
-    e->push_back(vector<int>());
-    vector<int>& le = e->back();
-    TD::ConvertSentence(line, &le);
-    for (unsigned i = 0; i < le.size(); ++i)
-      vocab_e->insert(le[i]);
-    toks += le.size();
-  }
-  if (in != &cin) delete in;
-  return toks;
-}
-
-struct Grid {
-  // a b c d e
-  // 0 - 0 - -
-  vector<int> grid;
-};
-
-struct BaseRuleModel {
-  explicit BaseRuleModel(unsigned term_size,
-                         unsigned nonterm_size = 1) :
-      unif_term(1.0 / term_size),
-      unif_nonterm(1.0 / nonterm_size) {}
-  prob_t operator()(const TRule& r) const {
-    prob_t p; p.logeq(Md::log_poisson(1.0, r.f_.size()));
-    const prob_t term_prob((2.0 + 0.01*r.f_.size()) / (r.f_.size() + 2));
-    const prob_t nonterm_prob(1.0 - term_prob.as_float());
-    for (unsigned i = 0; i < r.f_.size(); ++i) {
-      if (r.f_[i] <= 0) {     // nonterminal
-        if (kALLOW_MIXED) p *= nonterm_prob;
-        p *= unif_nonterm;
-      } else {                // terminal
-        if (kALLOW_MIXED) p *= term_prob;
-        p *= unif_term;
-      }
-    }
-    return p;
-  }
-  const prob_t unif_term, unif_nonterm;
-};
-
-struct HieroLMModel {
-  explicit HieroLMModel(unsigned vocab_size, unsigned num_nts = 1) :
-      base(vocab_size, num_nts),
-      q0(1,1,1,1),
-      nts(num_nts, CCRP<TRule>(1,1,1,1)) {}
-
-  prob_t Prob(const TRule& r) const {
-    return nts[nt_id_to_index[-r.lhs_]].prob(r, p0(r));
-  }
-
-  inline prob_t p0(const TRule& r) const {
-    if (kHIERARCHICAL_PRIOR)
-      return q0.prob(r, base(r));
-    else
-      return base(r);
-  }
-
-  int Increment(const TRule& r, MT19937* rng) {
-    const int delta = nts[nt_id_to_index[-r.lhs_]].increment(r, p0(r), rng);
-    if (kHIERARCHICAL_PRIOR && delta)
-      q0.increment(r, base(r), rng);
-    return delta;
-    // return x.increment(r);
-  }
-
-  int Decrement(const TRule& r, MT19937* rng) {
-    const int delta = nts[nt_id_to_index[-r.lhs_]].decrement(r, rng);
-    if (kHIERARCHICAL_PRIOR && delta)
-      q0.decrement(r, rng);
-    return delta;
-    //return x.decrement(r);
-  }
-
-  prob_t Likelihood() const {
-    prob_t p = prob_t::One();
-    for (unsigned i = 0; i < nts.size(); ++i) {
-      prob_t q; q.logeq(nts[i].log_crp_prob());
-      p *= q;
-      for (CCRP<TRule>::const_iterator it = nts[i].begin(); it != nts[i].end(); ++it) {
-        prob_t tp = p0(it->first);
-        tp.poweq(it->second.table_counts_.size());
-        p *= tp;
-      }
-    }
-    if (kHIERARCHICAL_PRIOR) {
-      prob_t q; q.logeq(q0.log_crp_prob());
-      p *= q;
-      for (CCRP<TRule>::const_iterator it = q0.begin(); it != q0.end(); ++it) {
-        prob_t tp = base(it->first);
-        tp.poweq(it->second.table_counts_.size());
-        p *= tp;
-      }
-    }
-    //for (CCRP_OneTable<TRule>::const_iterator it = x.begin(); it != x.end(); ++it)
-    //    p *= base(it->first);
-    return p;
-  }
-
-  void ResampleHyperparameters(MT19937* rng) {
-    for (unsigned i = 0; i < nts.size(); ++i)
-      nts[i].resample_hyperparameters(rng);
-    if (kHIERARCHICAL_PRIOR) {
-      q0.resample_hyperparameters(rng);
-      cerr << "[base d=" << q0.discount() << ", s=" << q0.strength() << "]";
-    }
-    cerr << " d=" << nts[0].discount() << ", s=" << nts[0].strength() << endl;
-  }
-
-  const BaseRuleModel base;
-  CCRP<TRule> q0;
-  vector<CCRP<TRule> > nts;
-  //CCRP_OneTable<TRule> x;
-};
-
-vector<GrammarIter* > tofreelist;
-
-HieroLMModel* plm;
-
-struct NPGrammarIter : public GrammarIter, public RuleBin {
-  NPGrammarIter() : arity() { tofreelist.push_back(this); }
-  NPGrammarIter(const TRulePtr& inr, const int a, int symbol) : arity(a) {
-    if (inr) {
-      r.reset(new TRule(*inr));
-    } else {
-      r.reset(new TRule);
-    }
-    TRule& rr = *r;
-    rr.lhs_ = nt_vocab[0];
-    rr.f_.push_back(symbol);
-    rr.e_.push_back(symbol < 0 ? (1-int(arity)) : symbol);
-    tofreelist.push_back(this);
-  }
-  inline static unsigned NextArity(int cur_a, int symbol) {
-    return cur_a + (symbol <= 0 ? 1 : 0);
-  }
-  virtual int GetNumRules() const {
-    if (r) return nt_vocab.size(); else return 0;
-  }
-  virtual TRulePtr GetIthRule(int i) const {
-    if (i == 0) return r;
-    TRulePtr nr(new TRule(*r));
-    nr->lhs_ = nt_vocab[i];
-    return nr;
-  }
-  virtual int Arity() const {
-    return arity;
-  }
-  virtual const RuleBin* GetRules() const {
-    if (!r) return NULL; else return this;
-  }
-  virtual const GrammarIter* Extend(int symbol) const {
-    const int next_arity = NextArity(arity, symbol);
-    if (kMAX_ARITY && next_arity > kMAX_ARITY)
-      return NULL;
-    if (!kALLOW_MIXED && r) {
-      bool t1 = r->f_.front() <= 0;
-      bool t2 = symbol <= 0;
-      if (t1 != t2) return NULL;
-    }
-    if (!kMAX_RULE_SIZE || !r || (r->f_.size() < kMAX_RULE_SIZE))
-      return new NPGrammarIter(r, next_arity, symbol);
-    else
-      return NULL;
-  }
-  const unsigned char arity;
-  TRulePtr r;
-};
-
-struct NPGrammar : public Grammar {
-  virtual const GrammarIter* GetRoot() const {
-    return new NPGrammarIter;
-  }
-};
-
-prob_t TotalProb(const Hypergraph& hg) {
-  return Inside<prob_t, EdgeProb>(hg);
-}
-
-void SampleDerivation(const Hypergraph& hg, MT19937* rng, vector<unsigned>* sampled_deriv) {
-  vector<prob_t> node_probs;
-  Inside<prob_t, EdgeProb>(hg, &node_probs);
-  queue<unsigned> q;
-  q.push(hg.nodes_.size() - 2);
-  while(!q.empty()) {
-    unsigned cur_node_id = q.front();
-//    cerr << "NODE=" << cur_node_id << endl;
-    q.pop();
-    const Hypergraph::Node& node = hg.nodes_[cur_node_id];
-    const unsigned num_in_edges = node.in_edges_.size();
-    unsigned sampled_edge = 0;
-    if (num_in_edges == 1) {
-      sampled_edge = node.in_edges_[0];
-    } else {
-      //prob_t z;
-      assert(num_in_edges > 1);
-      SampleSet<prob_t> ss;
-      for (unsigned j = 0; j < num_in_edges; ++j) {
-        const Hypergraph::Edge& edge = hg.edges_[node.in_edges_[j]];
-        prob_t p = edge.edge_prob_;
-        for (unsigned k = 0; k < edge.tail_nodes_.size(); ++k)
-          p *= node_probs[edge.tail_nodes_[k]];
-        ss.add(p);
-//        cerr << log(ss[j]) << " ||| " << edge.rule_->AsString() << endl;
-        //z += p;
-      }
-//      for (unsigned j = 0; j < num_in_edges; ++j) {
-//        const Hypergraph::Edge& edge = hg.edges_[node.in_edges_[j]];
-//        cerr << exp(log(ss[j] / z)) << " ||| " << edge.rule_->AsString() << endl;
-//      }
-//      cerr << " --- \n";
-      sampled_edge = node.in_edges_[rng->SelectSample(ss)];
-    }
-    sampled_deriv->push_back(sampled_edge);
-    const Hypergraph::Edge& edge = hg.edges_[sampled_edge];
-    for (unsigned j = 0; j < edge.tail_nodes_.size(); ++j) {
-      q.push(edge.tail_nodes_[j]);
-    }
-  }
-  for (unsigned i = 0; i < sampled_deriv->size(); ++i) {
-    cerr << *hg.edges_[(*sampled_deriv)[i]].rule_ << endl;
-  }
-}
-
-void IncrementDerivation(const Hypergraph& hg, const vector<unsigned>& d, HieroLMModel* plm, MT19937* rng) {
-  for (unsigned i = 0; i < d.size(); ++i)
-    plm->Increment(*hg.edges_[d[i]].rule_, rng);
-}
-
-void DecrementDerivation(const Hypergraph& hg, const vector<unsigned>& d, HieroLMModel* plm, MT19937* rng) {
-  for (unsigned i = 0; i < d.size(); ++i)
-    plm->Decrement(*hg.edges_[d[i]].rule_, rng);
-}
-
-int main(int argc, char** argv) {
-  po::variables_map conf;
-
-  InitCommandLine(argc, argv, &conf);
-  nt_vocab.resize(conf["nonterminals"].as<unsigned>());
-  assert(nt_vocab.size() > 0);
-  assert(nt_vocab.size() < 26);
-  {
-    string nt = "X";
-    for (unsigned i = 0; i < nt_vocab.size(); ++i) {
-      if (nt_vocab.size() > 1) nt[0] = ('A' + i);
-      int pid = TD::Convert(nt);
-      nt_vocab[i] = -pid;
-      if (pid >= nt_id_to_index.size()) {
-        nt_id_to_index.resize(pid + 1, -1);
-      }
-      nt_id_to_index[pid] = i;
-    }
-  }
-  vector<GrammarPtr> grammars;
-  grammars.push_back(GrammarPtr(new NPGrammar));
-
-  const unsigned samples = conf["samples"].as<unsigned>();
-  kMAX_RULE_SIZE = conf["max_rule_size"].as<unsigned>();
-  if (kMAX_RULE_SIZE == 1) {
-    cerr << "Invalid maximum rule size: must be 0 or >1\n";
-    return 1;
-  }
-  kMAX_ARITY = conf["max_arity"].as<unsigned>();
-  if (kMAX_ARITY == 1) {
-    cerr << "Invalid maximum arity: must be 0 or >1\n";
-    return 1;
-  }
-  kALLOW_MIXED = !conf.count("no_mixed_rules");
-
-  kHIERARCHICAL_PRIOR = conf.count("hierarchical_prior");
-
-  if (conf.count("random_seed"))
-    prng.reset(new MT19937(conf["random_seed"].as<uint32_t>()));
-  else
-    prng.reset(new MT19937);
-  MT19937& rng = *prng;
-  vector<vector<WordID> > corpuse;
-  set<WordID> vocabe;
-  cerr << "Reading corpus...\n";
-  const unsigned toks = ReadCorpus(conf["input"].as<string>(), &corpuse, &vocabe);
-  cerr << "E-corpus size: " << corpuse.size() << " sentences\t (" << vocabe.size() << " word types)\n";
-  HieroLMModel lm(vocabe.size(), nt_vocab.size());
-
-  plm = &lm;
-  ExhaustiveBottomUpParser parser(TD::Convert(-nt_vocab[0]), grammars);
-
-  Hypergraph hg;
-  const int kGoal = -TD::Convert("Goal");
-  const int kLP = FD::Convert("LogProb");
-  SparseVector<double> v; v.set_value(kLP, 1.0);
-  vector<vector<unsigned> > derivs(corpuse.size());
-  vector<Lattice> cl(corpuse.size());
-  for (int ci = 0; ci < corpuse.size(); ++ci) {
-    vector<int>& src = corpuse[ci];
-    Lattice& lat = cl[ci];
-    lat.resize(src.size());
-    for (unsigned i = 0; i < src.size(); ++i)
-      lat[i].push_back(LatticeArc(src[i], 0.0, 1));
-  }
-  for (int SS=0; SS < samples; ++SS) {
-    const bool is_last = ((samples - 1) == SS);
-    prob_t dlh = prob_t::One();
-    for (int ci = 0; ci < corpuse.size(); ++ci) {
-      const vector<int>& src = corpuse[ci];
-      const Lattice& lat = cl[ci];
-      cerr << TD::GetString(src) << endl;
-      hg.clear();
-      parser.Parse(lat, &hg);  // exhaustive parse
-      vector<unsigned>& d = derivs[ci];
-      if (!is_last) DecrementDerivation(hg, d, &lm, &rng);
-      for (unsigned i = 0; i < hg.edges_.size(); ++i) {
-        TRule& r = *hg.edges_[i].rule_;
-        if (r.lhs_ == kGoal)
-          hg.edges_[i].edge_prob_ = prob_t::One();
-        else
-          hg.edges_[i].edge_prob_ = lm.Prob(r);
-      }
-      if (!is_last) {
-        d.clear();
-        SampleDerivation(hg, &rng, &d);
-        IncrementDerivation(hg, derivs[ci], &lm, &rng);
-      } else {
-        prob_t p = TotalProb(hg);
-        dlh *= p;
-        cerr << " p(sentence) = " << log(p) << "\t" << log(dlh) << endl;
-      }
-      if (tofreelist.size() > 200000) {
-        cerr << "Freeing ... ";
-        for (unsigned i = 0; i < tofreelist.size(); ++i)
-          delete tofreelist[i];
-        tofreelist.clear();
-        cerr << "Freed.\n";
-      }
-    }
-    double llh = log(lm.Likelihood());
-    cerr << "LLH=" << llh << "\tENTROPY=" << (-llh / log(2) / toks) << "\tPPL=" << pow(2, -llh / log(2) / toks) << endl;
-    if (SS % 10 == 9) lm.ResampleHyperparameters(&rng);
-    if (is_last) {
-      double z = log(dlh);
-      cerr << "TOTAL_PROB=" << z << "\tENTROPY=" << (-z / log(2) / toks) << "\tPPL=" << pow(2, -z / log(2) / toks) << endl;
-    }
-  }
-  for (unsigned i = 0; i < nt_vocab.size(); ++i)
-    cerr << lm.nts[i] << endl;
-  return 0;
-}
-
diff --git a/gi/pf/make-freq-bins.pl b/gi/pf/make-freq-bins.pl
deleted file mode 100755
index fdcd3555..00000000
--- a/gi/pf/make-freq-bins.pl
+++ /dev/null
@@ -1,26 +0,0 @@
-#!/usr/bin/perl -w
-use strict;
-
-my $BASE = 6;
-my $CUTOFF = 3;
-
-my %d;
-my $num = 0;
-while(<>){
- chomp;
- my @words = split /\s+/;
- for my $w (@words) {$d{$w}++; $num++;}
-}
-
-my @vocab = sort {$d{$b} <=> $d{$a}} keys %d;
-
-for (my $i=0; $i<scalar @vocab; $i++) {
-  my $most = $d{$vocab[$i]};
-  my $least = 1;
-
-  my $nl = -int(log($most / $num) / log($BASE) + $CUTOFF);
-  if ($nl < 0) { $nl = 0; }
-  print "$vocab[$i] $nl\n"
-}
-
-
diff --git a/gi/pf/mh_test.cc b/gi/pf/mh_test.cc
deleted file mode 100644
index 296e7285..00000000
--- a/gi/pf/mh_test.cc
+++ /dev/null
@@ -1,148 +0,0 @@
-#include "ccrp.h"
-
-#include <vector>
-#include <iostream>
-
-#include "tdict.h"
-#include "transliterations.h"
-
-using namespace std;
-
-MT19937 rng;
-
-static bool verbose = false;
-
-struct Model {
-
-  Model() : bp(), base(0.2, 0.6) , ccrps(5, CCRP<int>(0.8, 0.5)) {}
-
-  double p0(int x) const {
-    assert(x > 0);
-    assert(x < 5);
-    return 1.0/4.0;
-  }
-
-  double llh() const {
-    double lh = bp + base.log_crp_prob();
-    for (int ctx = 1; ctx < 5; ++ctx)
-      lh += ccrps[ctx].log_crp_prob();
-    return lh;
-  }
-
-  double prob(int ctx, int x) const {
-    assert(ctx > 0 && ctx < 5);
-    return ccrps[ctx].prob(x, base.prob(x, p0(x)));
-  }
-
-  void increment(int ctx, int x) {
-    assert(ctx > 0 && ctx < 5);
-    if (ccrps[ctx].increment(x, base.prob(x, p0(x)), &rng)) {
-      if (base.increment(x, p0(x), &rng)) {
-        bp += log(1.0 / 4.0);
-      }
-    }
-  }
-
-  // this is just a biased estimate
-  double est_base_prob(int x) {
-    return (x + 1) * x / 40.0;
-  }
-
-  void increment_is(int ctx, int x) {
-    assert(ctx > 0 && ctx < 5);
-    SampleSet<double> ss;
-    const int PARTICLES = 25;
-    vector<CCRP<int> > s1s(PARTICLES, CCRP<int>(0.5,0.5));
-    vector<CCRP<int> > sbs(PARTICLES, CCRP<int>(0.5,0.5));
-    vector<double> sp0s(PARTICLES);
-
-    CCRP<int> s1 = ccrps[ctx];
-    CCRP<int> sb = base;
-    double sp0 = bp;
-    for (int pp = 0; pp < PARTICLES; ++pp) {
-      if (pp > 0) {
-        ccrps[ctx] = s1;
-        base = sb;
-        bp = sp0;
-      }
-
-      double q = 1;
-      double gamma = 1;
-      double est_p = est_base_prob(x);
-      //base.prob(x, p0(x)) + rng.next() * 0.1;
-      if (ccrps[ctx].increment(x, est_p, &rng, &q)) {
-        gamma = q * base.prob(x, p0(x));
-        q *= est_p;
-        if (verbose) cerr << "(DP-base draw) ";
-        double qq = -1;
-        if (base.increment(x, p0(x), &rng, &qq)) {
-          if (verbose) cerr << "(G0 draw) ";
-          bp += log(p0(x));
-          qq *= p0(x);
-        }
-      } else { gamma = q; }
-      double w = gamma / q;
-      if (verbose)
-        cerr << "gamma=" << gamma << " q=" << q << "\tw=" << w << endl;
-      ss.add(w);
-      s1s[pp] = ccrps[ctx];
-      sbs[pp] = base;
-      sp0s[pp] = bp;
-    }
-    int ps = rng.SelectSample(ss);
-    ccrps[ctx] = s1s[ps];
-    base = sbs[ps];
-    bp = sp0s[ps];
-    if (verbose) {
-      cerr << "SELECTED: " << ps << endl;
-      static int cc = 0; cc++; if (cc ==10) exit(1);
-    }
-  }
-
-  void decrement(int ctx, int x) {
-    assert(ctx > 0 && ctx < 5);
-    if (ccrps[ctx].decrement(x, &rng)) {
-      if (base.decrement(x, &rng)) {
-        bp -= log(p0(x));
-      }
-    }
-  }
-
-  double bp;
-  CCRP<int> base;
-  vector<CCRP<int> > ccrps;
-
-};
-
-int main(int argc, char** argv) {
-  if (argc > 1) { verbose = true; }
-  vector<int> counts(15, 0);
-  vector<int> tcounts(15, 0);
-  int points[] = {1,2, 2,2, 3,2, 4,1, 3, 4, 3, 3, 2, 3, 4, 1, 4, 1, 3, 2, 1, 3, 1, 4, 0, 0};
-  double tlh = 0;
-  double tt = 0;
-  for (int n = 0; n < 1000; ++n) {
-    if (n % 10 == 0) cerr << '.';
-    if ((n+1) % 400 == 0) cerr << " [" << (n+1) << "]\n";
-    Model m;
-    for (int *x = points; *x; x += 2)
-      m.increment(x[0], x[1]);
-
-    for (int j = 0; j < 24; ++j) {
-      for (int *x = points; *x; x += 2) {
-        if (rng.next() < 0.8) {
-          m.decrement(x[0], x[1]);
-          m.increment_is(x[0], x[1]);
-        }
-      }
-    }
-    counts[m.base.num_customers()]++;
-    tcounts[m.base.num_tables()]++;
-    tlh += m.llh();
-    tt += 1.0;
-  }
-  cerr << "mean LLH = " << (tlh / tt) << endl;
-  for (int i = 0; i < 15; ++i)
-    cerr << i << ": " << (counts[i] / tt) << "\t" << (tcounts[i] / tt) << endl;
-}
-
diff --git a/gi/pf/monotonic_pseg.h b/gi/pf/monotonic_pseg.h
deleted file mode 100644
index 10d171fe..00000000
--- a/gi/pf/monotonic_pseg.h
+++ /dev/null
@@ -1,89 +0,0 @@
-#ifndef _MONOTONIC_PSEG_H_
-#define _MONOTONIC_PSEG_H_
-
-#include <vector>
-
-#include "prob.h"
-#include "ccrp_nt.h"
-#include "trule.h"
-#include "base_distributions.h"
-
-template <typename BaseMeasure>
-struct MonotonicParallelSegementationModel {
-  explicit MonotonicParallelSegementationModel(BaseMeasure& rcp0) :
-    rp0(rcp0), base(prob_t::One()), rules(1,1), stop(1.0) {}
-
-  void DecrementRule(const TRule& rule) {
-    if (rules.decrement(rule))
-      base /= rp0(rule);
-  }
-
-  void IncrementRule(const TRule& rule) {
-    if (rules.increment(rule))
-      base *= rp0(rule);
-  }
-
-  void IncrementRulesAndStops(const std::vector<TRulePtr>& rules) {
-    for (int i = 0; i < rules.size(); ++i)
-      IncrementRule(*rules[i]);
-    if (rules.size()) IncrementContinue(rules.size() - 1);
-    IncrementStop();
-  }
-
-  void DecrementRulesAndStops(const std::vector<TRulePtr>& rules) {
-    for (int i = 0; i < rules.size(); ++i)
-      DecrementRule(*rules[i]);
-    if (rules.size()) {
-      DecrementContinue(rules.size() - 1);
-      DecrementStop();
-    }
-  }
-
-  prob_t RuleProbability(const TRule& rule) const {
-    prob_t p; p.logeq(rules.logprob(rule, log(rp0(rule))));
-    return p;
-  }
-
-  prob_t Likelihood() const {
-    prob_t p = base;
-    prob_t q; q.logeq(rules.log_crp_prob());
-    p *= q;
-    q.logeq(stop.log_crp_prob());
-    p *= q;
-    return p;
-  }
-
-  void IncrementStop() {
-    stop.increment(true);
-  }
-
-  void IncrementContinue(int n = 1) {
-    for (int i = 0; i < n; ++i)
-      stop.increment(false);
-  }
-
-  void DecrementStop() {
-    stop.decrement(true);
-  }
-
-  void DecrementContinue(int n = 1) {
-    for (int i = 0; i < n; ++i)
-      stop.decrement(false);
-  }
-
-  prob_t StopProbability() const {
-    return prob_t(stop.prob(true, 0.5));
-  }
-
-  prob_t ContinueProbability() const {
-    return prob_t(stop.prob(false, 0.5));
-  }
-
-  const BaseMeasure& rp0;
-  prob_t base;
-  CCRP_NoTable<TRule> rules;
-  CCRP_NoTable<bool> stop;
-};
-
-#endif
-
diff --git a/gi/pf/ngram_base.cc b/gi/pf/ngram_base.cc
deleted file mode 100644
index 1299f06f..00000000
--- a/gi/pf/ngram_base.cc
+++ /dev/null
@@ -1,69 +0,0 @@
-#include "ngram_base.h"
-
-#include "lm/model.hh"
-#include "tdict.h"
-
-using namespace std;
-
-namespace {
-struct GICSVMapper : public lm::EnumerateVocab {
-  GICSVMapper(vector<lm::WordIndex>* out) : out_(out), kLM_UNKNOWN_TOKEN(0) { out_->clear(); }
-  void Add(lm::WordIndex index, const StringPiece &str) {
-    const WordID cdec_id = TD::Convert(str.as_string());
-    if (cdec_id >= out_->size())
-      out_->resize(cdec_id + 1, kLM_UNKNOWN_TOKEN);
-    (*out_)[cdec_id] = index;
-  }
-  vector<lm::WordIndex>* out_;
-  const lm::WordIndex kLM_UNKNOWN_TOKEN;
-};
-}
-
-struct FixedNgramBaseImpl {
-  FixedNgramBaseImpl(const string& param) {
-    GICSVMapper vm(&cdec2klm_map_);
-    lm::ngram::Config conf;
-    conf.enumerate_vocab = &vm;
-    cerr << "Reading character LM from " << param << endl;
-    model = new lm::ngram::ProbingModel(param.c_str(), conf);
-    order = model->Order();
-    kEOS = MapWord(TD::Convert("</s>"));
-    assert(kEOS > 0);
-  }
-
-  lm::WordIndex MapWord(const WordID w) const {
-    if (w < cdec2klm_map_.size()) return cdec2klm_map_[w];
-    return 0;
-  }
-
-  ~FixedNgramBaseImpl() { delete model; }
-
-  prob_t StringProbability(const vector<WordID>& s) const {
-    lm::ngram::State state = model->BeginSentenceState();
-    double prob = 0;
-    for (unsigned i = 0; i < s.size(); ++i) {
-      const lm::ngram::State scopy(state);
-      prob += model->Score(scopy, MapWord(s[i]), state);
-    }
-    const lm::ngram::State scopy(state);
-    prob += model->Score(scopy, kEOS, state);
-    prob_t p; p.logeq(prob * log(10));
-    return p;
-  }
-
-  lm::ngram::ProbingModel* model;
-  unsigned order;
-  vector<lm::WordIndex> cdec2klm_map_;
-  lm::WordIndex kEOS;
-};
-
-FixedNgramBase::~FixedNgramBase() { delete impl; }
-
-FixedNgramBase::FixedNgramBase(const string& lmfname) {
-  impl = new FixedNgramBaseImpl(lmfname);
-}
-
-prob_t FixedNgramBase::StringProbability(const vector<WordID>& s) const {
-  return impl->StringProbability(s);
-}
-
diff --git a/gi/pf/ngram_base.h b/gi/pf/ngram_base.h
deleted file mode 100644
index 4ea999f3..00000000
--- a/gi/pf/ngram_base.h
+++ /dev/null
@@ -1,25 +0,0 @@
-#ifndef _NGRAM_BASE_H_
-#define _NGRAM_BASE_H_
-
-#include <string>
-#include <vector>
-#include "trule.h"
-#include "wordid.h"
-#include "prob.h"
-
-struct FixedNgramBaseImpl;
-struct FixedNgramBase {
-  FixedNgramBase(const std::string& lmfname);
-  ~FixedNgramBase();
-  prob_t StringProbability(const std::vector<WordID>& s) const;
-
-  prob_t operator()(const TRule& rule) const {
-    return StringProbability(rule.e_);
-  }
-
- private:
-  FixedNgramBaseImpl* impl;
-
-};
-
-#endif
diff --git a/gi/pf/nuisance_test.cc b/gi/pf/nuisance_test.cc
deleted file mode 100644
index fc0af9cb..00000000
--- a/gi/pf/nuisance_test.cc
+++ /dev/null
@@ -1,161 +0,0 @@
-#include "ccrp.h"
-
-#include <vector>
-#include <iostream>
-
-#include "tdict.h"
-#include "transliterations.h"
-
-using namespace std;
-
-MT19937 rng;
-
-ostream& operator<<(ostream&os, const vector<int>& v) {
-  os << '[' << v[0];
-  if (v.size() == 2) os << ' ' << v[1];
-  return os << ']';
-}
-
-struct Base {
-  Base() : llh(), v(2), v1(1), v2(1), crp(0.25, 0.5) {}
-  inline double p0(const vector<int>& x) const {
-    double p = 0.75;
-    if (x.size() == 2) p = 0.25;
-    p *= 1.0 / 3.0;
-    if (x.size() == 2) p *= 1.0 / 3.0;
-    return p;
-  }
-  double est_deriv_prob(int a, int b, int seg) const {
-    assert(a > 0 && a < 4);  // a \in {1,2,3}
-    assert(b > 0 && b < 4);  // b \in {1,2,3}
-    assert(seg == 0 || seg == 1);   // seg \in {0,1}
-    if (seg == 0) {
-      v[0] = a;
-      v[1] = b;
-      return crp.prob(v, p0(v));
-    } else {
-      v1[0] = a;
-      v2[0] = b;
-      return crp.prob(v1, p0(v1)) * crp.prob(v2, p0(v2));
-    }
-  }
-  double est_marginal_prob(int a, int b) const {
-    return est_deriv_prob(a,b,0) + est_deriv_prob(a,b,1);
-  }
-  int increment(int a, int b, double* pw = NULL) {
-    double p1 = est_deriv_prob(a, b, 0);
-    double p2 = est_deriv_prob(a, b, 1);
-    //p1 = 0.5; p2 = 0.5;
-    int seg = rng.SelectSample(p1,p2);
-    double tmp = 0;
-    if (!pw) pw = &tmp;
-    double& w = *pw;
-    if (seg == 0) {
-      v[0] = a;
-      v[1] = b;
-      w = crp.prob(v, p0(v)) / p1;
-      if (crp.increment(v, p0(v), &rng)) {
-        llh += log(p0(v));
-      }
-    } else {
-      v1[0] = a;
-      w = crp.prob(v1, p0(v1)) / p2;
-      if (crp.increment(v1, p0(v1), &rng)) {
-        llh += log(p0(v1));
-      }
-      v2[0] = b;
-      w *= crp.prob(v2, p0(v2));
-      if (crp.increment(v2, p0(v2), &rng)) {
-        llh += log(p0(v2));
-      }
-    }
-    return seg;
-  }
-  void increment(int a, int b, int seg) {
-    if (seg == 0) {
-      v[0] = a;
-      v[1] = b;
-      if (crp.increment(v, p0(v), &rng)) {
-        llh += log(p0(v));
-      }
-    } else {
-      v1[0] = a;
-      if (crp.increment(v1, p0(v1), &rng)) {
-        llh += log(p0(v1));
-      }
-      v2[0] = b;
-      if (crp.increment(v2, p0(v2), &rng)) {
-        llh += log(p0(v2));
-      }
-    }
-  }
-  void decrement(int a, int b, int seg) {
-    if (seg == 0) {
-      v[0] = a;
-      v[1] = b;
-      if (crp.decrement(v, &rng)) {
-        llh -= log(p0(v));
-      }
-    } else {
-      v1[0] = a;
-      if (crp.decrement(v1, &rng)) {
-        llh -= log(p0(v1));
-      }
-      v2[0] = b;
-      if (crp.decrement(v2, &rng)) {
-        llh -= log(p0(v2));
-      }
-    }
-  }
-  double log_likelihood() const {
-    return llh + crp.log_crp_prob();
-  }
-  double llh;
-  mutable vector<int> v, v1, v2;
-  CCRP<vector<int> > crp;
-};
-
-int main(int argc, char** argv) {
-  double tl = 0;
-  const int ITERS = 1000;
-  const int PARTICLES = 20;
-  const int DATAPOINTS = 50;
-  WordID x = TD::Convert("souvenons");
-  WordID y = TD::Convert("remember");
-  vector<WordID> src; TD::ConvertSentence("s o u v e n o n s", &src);
-  vector<WordID> trg; TD::ConvertSentence("r e m e m b e r", &trg);
-//  Transliterations xx;
-//  xx.Initialize(x, src, y, trg);
-//  return 1;
-
- for (int j = 0; j < ITERS; ++j) {
-  Base b;
-  vector<int> segs(DATAPOINTS);
-  SampleSet<double> ss;
-  vector<int> sss;
-  for (int i = 0; i < DATAPOINTS; i++) {
-    ss.clear();
-    sss.clear();
-    int x = ((i / 10) % 3) + 1;
-    int y = (i % 3) + 1;
-    //double ep = b.est_marginal_prob(x,y);
-    //cerr << "est p(" << x << "," << y << ") = " << ep << endl;
-    for (int n = 0; n < PARTICLES; ++n) {
-      double w;
-      int seg = b.increment(x,y,&w);
-      //cerr << seg << " w=" << w << endl;
-      ss.add(w);
-      sss.push_back(seg);
-      b.decrement(x,y,seg);
-    }
-    int seg = sss[rng.SelectSample(ss)];
-    b.increment(x, y, seg);
-    //cerr << "Selected: " << seg << endl;
-    //return 1;
-    segs[i] = seg;
-  }
-  tl += b.log_likelihood();
- }
-  cerr << "LLH=" << tl / ITERS << endl;
-}
-
diff --git a/gi/pf/os_phrase.h b/gi/pf/os_phrase.h
deleted file mode 100644
index dfe40cb1..00000000
--- a/gi/pf/os_phrase.h
+++ /dev/null
@@ -1,15 +0,0 @@
-#ifndef _OS_PHRASE_H_
-#define _OS_PHRASE_H_
-
-#include <iostream>
-#include <vector>
-#include "tdict.h"
-
-inline std::ostream& operator<<(std::ostream& os, const std::vector<WordID>& p) {
-  os << '[';
-  for (int i = 0; i < p.size(); ++i)
-    os << (i==0 ? "" : " ") << TD::Convert(p[i]);
-  return os << ']';
-}
-
-#endif
diff --git a/gi/pf/pf.h b/gi/pf/pf.h
deleted file mode 100644
index ede7cda8..00000000
--- a/gi/pf/pf.h
+++ /dev/null
@@ -1,84 +0,0 @@
-#ifndef _PF_H_
-#define _PF_H_
-
-#include <cassert>
-#include <vector>
-#include "sampler.h"
-#include "prob.h"
-
-template <typename ParticleType>
-struct ParticleRenormalizer {
-  void operator()(std::vector<ParticleType>* pv) const {
-    if (pv->empty()) return;
-    prob_t z = prob_t::Zero();
-    for (unsigned i = 0; i < pv->size(); ++i)
-      z += (*pv)[i].weight;
-    assert(z > prob_t::Zero());
-    for (unsigned i = 0; i < pv->size(); ++i)
-      (*pv)[i].weight /= z;
-  }
-};
-
-template <typename ParticleType>
-struct MultinomialResampleFilter {
-  explicit MultinomialResampleFilter(MT19937* rng) : rng_(rng) {}
-
-  void operator()(std::vector<ParticleType>* pv) {
-    if (pv->empty()) return;
-    std::vector<ParticleType>& ps = *pv;
-    SampleSet<prob_t> ss;
-    for (int i = 0; i < ps.size(); ++i)
-      ss.add(ps[i].weight);
-    std::vector<ParticleType> nps; nps.reserve(ps.size());
-    const prob_t uniform_weight(1.0 / ps.size());
-    for (int i = 0; i < ps.size(); ++i) {
-      nps.push_back(ps[rng_->SelectSample(ss)]);
-      nps[i].weight = uniform_weight;
-    }
-    nps.swap(ps);
-  }
-
- private:
-  MT19937* rng_;
-};
-
-template <typename ParticleType>
-struct SystematicResampleFilter {
-  explicit SystematicResampleFilter(MT19937* rng) : rng_(rng), renorm_() {}
-
-  void operator()(std::vector<ParticleType>* pv) {
-    if (pv->empty()) return;
-    renorm_(pv);
-    std::vector<ParticleType>& ps = *pv;
-    std::vector<ParticleType> nps; nps.reserve(ps.size());
-    double lower = 0, upper = 0;
-    const double skip = 1.0 / ps.size();
-    double u_j = rng_->next() * skip;
-    //std::cerr << "u_0: " << u_j << std::endl;
-    int j = 0;
-    for (unsigned i = 0; i < ps.size(); ++i) {
-      upper += ps[i].weight.as_float();
-      //std::cerr << "lower: " << lower << " upper: " << upper << std::endl;
-      // how many children does ps[i] have?
-      while (u_j < lower) { u_j += skip; ++j; }
-      while (u_j >= lower && u_j <= upper) {
-        assert(j < ps.size());
-        nps.push_back(ps[i]);
-        u_j += skip;
-        //std::cerr << " add u_j=" << u_j << std::endl;
-        ++j;
-      }
-      lower = upper;
-    }
-    //std::cerr << ps.size() << " " << nps.size() << "\n";
-    assert(ps.size() == nps.size());
-    //exit(1);
-    ps.swap(nps);
-  }
-
- private:
-  MT19937* rng_;
-  ParticleRenormalizer<ParticleType> renorm_;
-};
-
-#endif
diff --git a/gi/pf/pf_test.cc b/gi/pf/pf_test.cc
deleted file mode 100644
index 296e7285..00000000
--- a/gi/pf/pf_test.cc
+++ /dev/null
@@ -1,148 +0,0 @@
-#include "ccrp.h"
-
-#include <vector>
-#include <iostream>
-
-#include "tdict.h"
-#include "transliterations.h"
-
-using namespace std;
-
-MT19937 rng;
-
-static bool verbose = false;
-
-struct Model {
-
-  Model() : bp(), base(0.2, 0.6) , ccrps(5, CCRP<int>(0.8, 0.5)) {}
-
-  double p0(int x) const {
-    assert(x > 0);
-    assert(x < 5);
-    return 1.0/4.0;
-  }
-
-  double llh() const {
-    double lh = bp + base.log_crp_prob();
-    for (int ctx = 1; ctx < 5; ++ctx)
-      lh += ccrps[ctx].log_crp_prob();
-    return lh;
-  }
-
-  double prob(int ctx, int x) const {
-    assert(ctx > 0 && ctx < 5);
-    return ccrps[ctx].prob(x, base.prob(x, p0(x)));
-  }
-
-  void increment(int ctx, int x) {
-    assert(ctx > 0 && ctx < 5);
-    if (ccrps[ctx].increment(x, base.prob(x, p0(x)), &rng)) {
-      if (base.increment(x, p0(x), &rng)) {
-        bp += log(1.0 / 4.0);
-      }
-    }
-  }
-
-  // this is just a biased estimate
-  double est_base_prob(int x) {
-    return (x + 1) * x / 40.0;
-  }
-
-  void increment_is(int ctx, int x) {
-    assert(ctx > 0 && ctx < 5);
-    SampleSet<double> ss;
-    const int PARTICLES = 25;
-    vector<CCRP<int> > s1s(PARTICLES, CCRP<int>(0.5,0.5));
-    vector<CCRP<int> > sbs(PARTICLES, CCRP<int>(0.5,0.5));
-    vector<double> sp0s(PARTICLES);
-
-    CCRP<int> s1 = ccrps[ctx];
-    CCRP<int> sb = base;
-    double sp0 = bp;
-    for (int pp = 0; pp < PARTICLES; ++pp) {
-      if (pp > 0) {
-        ccrps[ctx] = s1;
-        base = sb;
-        bp = sp0;
-      }
-
-      double q = 1;
-      double gamma = 1;
-      double est_p = est_base_prob(x);
-      //base.prob(x, p0(x)) + rng.next() * 0.1;
-      if (ccrps[ctx].increment(x, est_p, &rng, &q)) {
-        gamma = q * base.prob(x, p0(x));
-        q *= est_p;
-        if (verbose) cerr << "(DP-base draw) ";
-        double qq = -1;
-        if (base.increment(x, p0(x), &rng, &qq)) {
-          if (verbose) cerr << "(G0 draw) ";
-          bp += log(p0(x));
-          qq *= p0(x);
-        }
-      } else { gamma = q; }
-      double w = gamma / q;
-      if (verbose)
-        cerr << "gamma=" << gamma << " q=" << q << "\tw=" << w << endl;
-      ss.add(w);
-      s1s[pp] = ccrps[ctx];
-      sbs[pp] = base;
-      sp0s[pp] = bp;
-    }
-    int ps = rng.SelectSample(ss);
-    ccrps[ctx] = s1s[ps];
-    base = sbs[ps];
-    bp = sp0s[ps];
-    if (verbose) {
-      cerr << "SELECTED: " << ps << endl;
-      static int cc = 0; cc++; if (cc ==10) exit(1);
-    }
-  }
-
-  void decrement(int ctx, int x) {
-    assert(ctx > 0 && ctx < 5);
-    if (ccrps[ctx].decrement(x, &rng)) {
-      if (base.decrement(x, &rng)) {
-        bp -= log(p0(x));
-      }
-    }
-  }
-
-  double bp;
-  CCRP<int> base;
-  vector<CCRP<int> > ccrps;
-
-};
-
-int main(int argc, char** argv) {
-  if (argc > 1) { verbose = true; }
-  vector<int> counts(15, 0);
-  vector<int> tcounts(15, 0);
-  int points[] = {1,2, 2,2, 3,2, 4,1, 3, 4, 3, 3, 2, 3, 4, 1, 4, 1, 3, 2, 1, 3, 1, 4, 0, 0};
-  double tlh = 0;
-  double tt = 0;
-  for (int n = 0; n < 1000; ++n) {
-    if (n % 10 == 0) cerr << '.';
-    if ((n+1) % 400 == 0) cerr << " [" << (n+1) << "]\n";
-    Model m;
-    for (int *x = points; *x; x += 2)
-      m.increment(x[0], x[1]);
-
-    for (int j = 0; j < 24; ++j) {
-      for (int *x = points; *x; x += 2) {
-        if (rng.next() < 0.8) {
-          m.decrement(x[0], x[1]);
-          m.increment_is(x[0], x[1]);
-        }
-      }
-    }
-    counts[m.base.num_customers()]++;
-    tcounts[m.base.num_tables()]++;
-    tlh += m.llh();
-    tt += 1.0;
-  }
-  cerr << "mean LLH = " << (tlh / tt) << endl;
-  for (int i = 0; i < 15; ++i)
-    cerr << i << ": " << (counts[i] / tt) << "\t" << (tcounts[i] / tt) << endl;
-}
-
diff --git a/gi/pf/pfbrat.cc b/gi/pf/pfbrat.cc
deleted file mode 100644
index 832f22cf..00000000
--- a/gi/pf/pfbrat.cc
+++ /dev/null
@@ -1,543 +0,0 @@
-#include <iostream>
-#include <tr1/memory>
-#include <queue>
-
-#include <boost/functional.hpp>
-#include <boost/multi_array.hpp>
-#include <boost/program_options.hpp>
-#include <boost/program_options/variables_map.hpp>
-
-#include "viterbi.h"
-#include "hg.h"
-#include "trule.h"
-#include "tdict.h"
-#include "filelib.h"
-#include "dict.h"
-#include "sampler.h"
-#include "ccrp_nt.h"
-#include "cfg_wfst_composer.h"
-
-using namespace std;
-using namespace tr1;
-namespace po = boost::program_options;
-
-static unsigned kMAX_SRC_PHRASE;
-static unsigned kMAX_TRG_PHRASE;
-struct FSTState;
-
-double log_poisson(unsigned x, const double& lambda) {
-  assert(lambda > 0.0);
-  return log(lambda) * x - lgamma(x + 1) - lambda;
-}
-
-struct ConditionalBase {
-  explicit ConditionalBase(const double m1mixture, const unsigned vocab_e_size, const string& model1fname) :
-      kM1MIXTURE(m1mixture),
-      kUNIFORM_MIXTURE(1.0 - m1mixture),
-      kUNIFORM_TARGET(1.0 / vocab_e_size),
-      kNULL(TD::Convert("<eps>")) {
-    assert(m1mixture >= 0.0 && m1mixture <= 1.0);
-    assert(vocab_e_size > 0);
-    LoadModel1(model1fname);
-  }
-
-  void LoadModel1(const string& fname) {
-    cerr << "Loading Model 1 parameters from " << fname << " ..." << endl;
-    ReadFile rf(fname);
-    istream& in = *rf.stream();
-    string line;
-    unsigned lc = 0;
-    while(getline(in, line)) {
-      ++lc;
-      int cur = 0;
-      int start = 0;
-      while(cur < line.size() && line[cur] != ' ') { ++cur; }
-      assert(cur != line.size());
-      line[cur] = 0;
-      const WordID src = TD::Convert(&line[0]);
-      ++cur;
-      start = cur;
-      while(cur < line.size() && line[cur] != ' ') { ++cur; }
-      assert(cur != line.size());
-      line[cur] = 0;
-      WordID trg = TD::Convert(&line[start]);
-      const double logprob = strtod(&line[cur + 1], NULL);
-      if (src >= ttable.size()) ttable.resize(src + 1);
-      ttable[src][trg].logeq(logprob);
-    }
-    cerr << "  read " << lc << " parameters.\n";
-  }
-
-  // return logp0 of rule.e_ | rule.f_
-  prob_t operator()(const TRule& rule) const {
-    const int flen = rule.f_.size();
-    const int elen = rule.e_.size();
-    prob_t uniform_src_alignment; uniform_src_alignment.logeq(-log(flen + 1));
-    prob_t p;
-    p.logeq(log_poisson(elen, flen + 0.01));       // elen | flen          ~Pois(flen + 0.01)
-    for (int i = 0; i < elen; ++i) {               // for each position i in e-RHS
-      const WordID trg = rule.e_[i];
-      prob_t tp = prob_t::Zero();
-      for (int j = -1; j < flen; ++j) {
-        const WordID src = j < 0 ? kNULL : rule.f_[j];
-        const map<WordID, prob_t>::const_iterator it = ttable[src].find(trg);
-        if (it != ttable[src].end()) {
-          tp += kM1MIXTURE * it->second;
-        }
-        tp += kUNIFORM_MIXTURE * kUNIFORM_TARGET;
-      }
-      tp *= uniform_src_alignment;                 //     draw a_i         ~uniform
-      p *= tp;                                     //     draw e_i         ~Model1(f_a_i) / uniform
-    }
-    return p;
-  }
-
-  const prob_t kM1MIXTURE;  // Model 1 mixture component
-  const prob_t kUNIFORM_MIXTURE; // uniform mixture component
-  const prob_t kUNIFORM_TARGET;
-  const WordID kNULL;
-  vector<map<WordID, prob_t> > ttable;
-};
-
-void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
-  po::options_description opts("Configuration options");
-  opts.add_options()
-        ("samples,s",po::value<unsigned>()->default_value(1000),"Number of samples")
-        ("input,i",po::value<string>(),"Read parallel data from")
-        ("max_src_phrase",po::value<unsigned>()->default_value(3),"Maximum length of source language phrases")
-        ("max_trg_phrase",po::value<unsigned>()->default_value(3),"Maximum length of target language phrases")
-        ("model1,m",po::value<string>(),"Model 1 parameters (used in base distribution)")
-        ("model1_interpolation_weight",po::value<double>()->default_value(0.95),"Mixing proportion of model 1 with uniform target distribution")
-        ("random_seed,S",po::value<uint32_t>(), "Random seed");
-  po::options_description clo("Command line options");
-  clo.add_options()
-        ("config", po::value<string>(), "Configuration file")
-        ("help,h", "Print this help message and exit");
-  po::options_description dconfig_options, dcmdline_options;
-  dconfig_options.add(opts);
-  dcmdline_options.add(opts).add(clo);
-  
-  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
-  if (conf->count("config")) {
-    ifstream config((*conf)["config"].as<string>().c_str());
-    po::store(po::parse_config_file(config, dconfig_options), *conf);
-  }
-  po::notify(*conf);
-
-  if (conf->count("help") || (conf->count("input") == 0)) {
-    cerr << dcmdline_options << endl;
-    exit(1);
-  }
-}
-
-void ReadParallelCorpus(const string& filename,
-                vector<vector<WordID> >* f,
-                vector<vector<int> >* e,
-                set<int>* vocab_f,
-                set<int>* vocab_e) {
-  f->clear();
-  e->clear();
-  vocab_f->clear();
-  vocab_e->clear();
-  istream* in;
-  if (filename == "-")
-    in = &cin;
-  else
-    in = new ifstream(filename.c_str());
-  assert(*in);
-  string line;
-  const WordID kDIV = TD::Convert("|||");
-  vector<WordID> tmp;
-  while(*in) {
-    getline(*in, line);
-    if (line.empty() && !*in) break;
-    e->push_back(vector<int>());
-    f->push_back(vector<int>());
-    vector<int>& le = e->back();
-    vector<int>& lf = f->back();
-    tmp.clear();
-    TD::ConvertSentence(line, &tmp);
-    bool isf = true;
-    for (unsigned i = 0; i < tmp.size(); ++i) {
-      const int cur = tmp[i];
-      if (isf) {
-        if (kDIV == cur) { isf = false; } else {
-          lf.push_back(cur);
-          vocab_f->insert(cur);
-        }
-      } else {
-        assert(cur != kDIV);
-        le.push_back(cur);
-        vocab_e->insert(cur);
-      }
-    }
-    assert(isf == false);
-  }
-  if (in != &cin) delete in;
-}
-
-struct UniphraseLM {
-  UniphraseLM(const vector<vector<int> >& corpus,
-              const set<int>& vocab,
-              const po::variables_map& conf) :
-    phrases_(1,1),
-    gen_(1,1),
-    corpus_(corpus),
-    uniform_word_(1.0 / vocab.size()),
-    gen_p0_(0.5),
-    p_end_(0.5),
-    use_poisson_(conf.count("poisson_length") > 0) {}
-
-  void ResampleHyperparameters(MT19937* rng) {
-    phrases_.resample_hyperparameters(rng);
-    gen_.resample_hyperparameters(rng);
-    cerr << " " << phrases_.alpha();
-  }
-
-  CCRP_NoTable<vector<int> > phrases_;
-  CCRP_NoTable<bool> gen_;
-  vector<vector<bool> > z_;   // z_[i] is there a phrase boundary after the ith word
-  const vector<vector<int> >& corpus_;
-  const double uniform_word_;
-  const double gen_p0_;
-  const double p_end_; // in base length distribution, p of the end of a phrase
-  const bool use_poisson_;
-};
-
-struct Reachability {
-  boost::multi_array<bool, 4> edges;  // edges[src_covered][trg_covered][x][trg_delta] is this edge worth exploring?
-  boost::multi_array<short, 2> max_src_delta; // msd[src_covered][trg_covered] -- the largest src delta that's valid
-
-  Reachability(int srclen, int trglen, int src_max_phrase_len, int trg_max_phrase_len) :
-      edges(boost::extents[srclen][trglen][src_max_phrase_len+1][trg_max_phrase_len+1]),
-      max_src_delta(boost::extents[srclen][trglen]) {
-    ComputeReachability(srclen, trglen, src_max_phrase_len, trg_max_phrase_len);
-  }
-
- private:
-  struct SState {
-    SState() : prev_src_covered(), prev_trg_covered() {}
-    SState(int i, int j) : prev_src_covered(i), prev_trg_covered(j) {}
-    int prev_src_covered;
-    int prev_trg_covered;
-  };
-
-  struct NState {
-    NState() : next_src_covered(), next_trg_covered() {}
-    NState(int i, int j) : next_src_covered(i), next_trg_covered(j) {}
-    int next_src_covered;
-    int next_trg_covered;
-  };
-
-  void ComputeReachability(int srclen, int trglen, int src_max_phrase_len, int trg_max_phrase_len) {
-    typedef boost::multi_array<vector<SState>, 2> array_type;
-    array_type a(boost::extents[srclen + 1][trglen + 1]);
-    a[0][0].push_back(SState());
-    for (int i = 0; i < srclen; ++i) {
-      for (int j = 0; j < trglen; ++j) {
-        if (a[i][j].size() == 0) continue;
-        const SState prev(i,j);
-        for (int k = 1; k <= src_max_phrase_len; ++k) {
-          if ((i + k) > srclen) continue;
-          for (int l = 1; l <= trg_max_phrase_len; ++l) {
-            if ((j + l) > trglen) continue;
-            a[i + k][j + l].push_back(prev);
-          }
-        }
-      }
-    }
-    a[0][0].clear();
-    cerr << "Final cell contains " << a[srclen][trglen].size() << " back pointers\n";
-    assert(a[srclen][trglen].size() > 0);
-
-    typedef boost::multi_array<bool, 2> rarray_type;
-    rarray_type r(boost::extents[srclen + 1][trglen + 1]);
-//    typedef boost::multi_array<vector<NState>, 2> narray_type;
-//    narray_type b(boost::extents[srclen + 1][trglen + 1]);
-    r[srclen][trglen] = true;
-    for (int i = srclen; i >= 0; --i) {
-      for (int j = trglen; j >= 0; --j) {
-        vector<SState>& prevs = a[i][j];
-        if (!r[i][j]) { prevs.clear(); }
-//        const NState nstate(i,j);
-        for (int k = 0; k < prevs.size(); ++k) {
-          r[prevs[k].prev_src_covered][prevs[k].prev_trg_covered] = true;
-          int src_delta = i - prevs[k].prev_src_covered;
-          edges[prevs[k].prev_src_covered][prevs[k].prev_trg_covered][src_delta][j - prevs[k].prev_trg_covered] = true;
-          short &msd = max_src_delta[prevs[k].prev_src_covered][prevs[k].prev_trg_covered];
-          if (src_delta > msd) msd = src_delta;
-//          b[prevs[k].prev_src_covered][prevs[k].prev_trg_covered].push_back(nstate);
-        }
-      }
-    }
-    assert(!edges[0][0][1][0]);
-    assert(!edges[0][0][0][1]);
-    assert(!edges[0][0][0][0]);
-    cerr << "  MAX SRC DELTA[0][0] = " << max_src_delta[0][0] << endl;
-    assert(max_src_delta[0][0] > 0);
-    //cerr << "First cell contains " << b[0][0].size() << " forward pointers\n";
-    //for (int i = 0; i < b[0][0].size(); ++i) {
-    //  cerr << "  -> (" << b[0][0][i].next_src_covered << "," << b[0][0][i].next_trg_covered << ")\n";
-    //}
-  }
-};
-
-ostream& operator<<(ostream& os, const FSTState& q);
-struct FSTState {
-  explicit FSTState(int src_size) :
-      trg_covered_(),
-      src_covered_(),
-      src_coverage_(src_size) {}
-
-  FSTState(short trg_covered, short src_covered, const vector<bool>& src_coverage, const vector<short>& src_prefix) :
-      trg_covered_(trg_covered),
-      src_covered_(src_covered),
-      src_coverage_(src_coverage),
-      src_prefix_(src_prefix) {
-    if (src_coverage_.size() == src_covered) {
-      assert(src_prefix.size() == 0);
-    }
-  }
-
-  // if we extend by the word at src_position, what are
-  // the next states that are reachable and lie on a valid
-  // path to the final state?
-  vector<FSTState> Extensions(int src_position, int src_len, int trg_len, const Reachability& r) const {
-    assert(src_position < src_coverage_.size());
-    if (src_coverage_[src_position]) {
-      cerr << "Trying to extend " << *this << " with position " << src_position << endl;
-      abort();
-    }
-    vector<bool> ncvg = src_coverage_;
-    ncvg[src_position] = true;
-
-    vector<FSTState> res;
-    const int trg_remaining = trg_len - trg_covered_;
-    if (trg_remaining <= 0) {
-      cerr << "Target appears to have been covered: " << *this << " (trg_len=" << trg_len << ",trg_covered=" << trg_covered_ << ")" << endl;
-      abort();
-    }
-    const int src_remaining = src_len - src_covered_;
-    if (src_remaining <= 0) {
-      cerr << "Source appears to have been covered: " << *this << endl;
-      abort();
-    }
-
-    for (int tc = 1; tc <= kMAX_TRG_PHRASE; ++tc) {
-      if (r.edges[src_covered_][trg_covered_][src_prefix_.size() + 1][tc]) {
-        int nc = src_prefix_.size() + 1 + src_covered_;
-        res.push_back(FSTState(trg_covered_ + tc, nc, ncvg, vector<short>()));
-      }
-    }
-
-    if ((src_prefix_.size() + 1) < r.max_src_delta[src_covered_][trg_covered_]) {
-      vector<short> nsp = src_prefix_;
-      nsp.push_back(src_position);
-      res.push_back(FSTState(trg_covered_, src_covered_, ncvg, nsp));
-    }
-
-    if (res.size() == 0) {
-      cerr << *this << " can't be extended!\n";
-      abort();
-    }
-    return res;
-  }
-
-  short trg_covered_, src_covered_;
-  vector<bool> src_coverage_;
-  vector<short> src_prefix_;
-};
-bool operator<(const FSTState& q, const FSTState& r) {
-  if (q.trg_covered_ != r.trg_covered_) return q.trg_covered_ < r.trg_covered_;
-  if (q.src_covered_!= r.src_covered_) return q.src_covered_ < r.src_covered_;
-  if (q.src_coverage_ != r.src_coverage_) return q.src_coverage_ < r.src_coverage_;
-  return q.src_prefix_ < r.src_prefix_;
-}
-
-ostream& operator<<(ostream& os, const FSTState& q) {
-  os << "[" << q.trg_covered_ << " : ";
-  for (int i = 0; i < q.src_coverage_.size(); ++i)
-    os << q.src_coverage_[i];
-  os << " : <";
-  for (int i = 0; i < q.src_prefix_.size(); ++i) {
-    if (i != 0) os << ' ';
-    os << q.src_prefix_[i];
-  }
-  return os << ">]";
-}
-
-struct MyModel {
-  MyModel(ConditionalBase& rcp0) : rp0(rcp0) {}
-  typedef unordered_map<vector<WordID>, CCRP_NoTable<TRule>, boost::hash<vector<WordID> > > SrcToRuleCRPMap;
-
-  void DecrementRule(const TRule& rule) {
-    SrcToRuleCRPMap::iterator it = rules.find(rule.f_);
-    assert(it != rules.end());
-    it->second.decrement(rule);
-    if (it->second.num_customers() == 0) rules.erase(it);
-  }
-
-  void IncrementRule(const TRule& rule) {
-    SrcToRuleCRPMap::iterator it = rules.find(rule.f_);
-    if (it == rules.end()) {
-      CCRP_NoTable<TRule> crp(1,1);
-      it = rules.insert(make_pair(rule.f_, crp)).first;
-    }
-    it->second.increment(rule);
-  }
-
-  // conditioned on rule.f_
-  prob_t RuleConditionalProbability(const TRule& rule) const {
-    const prob_t base = rp0(rule);
-    SrcToRuleCRPMap::const_iterator it = rules.find(rule.f_);
-    if (it == rules.end()) {
-      return base;
-    } else {
-      const double lp = it->second.logprob(rule, log(base));
-      prob_t q; q.logeq(lp);
-      return q;
-    }
-  }
-
-  const ConditionalBase& rp0;
-  SrcToRuleCRPMap rules;
-};
-
-struct MyFST : public WFST {
-  MyFST(const vector<WordID>& ssrc, const vector<WordID>& strg, MyModel* m) :
-      src(ssrc), trg(strg),
-      r(src.size(),trg.size(),kMAX_SRC_PHRASE, kMAX_TRG_PHRASE),
-      model(m) {
-    FSTState in(src.size());
-    cerr << " INIT: " << in << endl;
-    init = GetNode(in);
-    for (int i = 0; i < in.src_coverage_.size(); ++i) in.src_coverage_[i] = true;
-    in.src_covered_ = src.size();
-    in.trg_covered_ = trg.size();
-    cerr << "FINAL: " << in << endl;
-    final = GetNode(in);
-  }
-  virtual const WFSTNode* Final() const;
-  virtual const WFSTNode* Initial() const;
-
-  const WFSTNode* GetNode(const FSTState& q);
-  map<FSTState, boost::shared_ptr<WFSTNode> > m;
-  const vector<WordID>& src;
-  const vector<WordID>& trg;
-  Reachability r;
-  const WFSTNode* init;
-  const WFSTNode* final;
-  MyModel* model;
-};
-
-struct MyNode : public WFSTNode {
-  MyNode(const FSTState& q, MyFST* fst) : state(q), container(fst) {}
-  virtual vector<pair<const WFSTNode*, TRulePtr> > ExtendInput(unsigned srcindex) const;
-  const FSTState state;
-  mutable MyFST* container;
-};
-
-vector<pair<const WFSTNode*, TRulePtr> > MyNode::ExtendInput(unsigned srcindex) const {
-  cerr << "EXTEND " << state << " with " << srcindex << endl;
-  vector<FSTState> ext = state.Extensions(srcindex, container->src.size(), container->trg.size(), container->r);
-  vector<pair<const WFSTNode*,TRulePtr> > res(ext.size());
-  for (unsigned i = 0; i < ext.size(); ++i) {
-    res[i].first = container->GetNode(ext[i]);
-    if (ext[i].src_prefix_.size() == 0) {
-      const unsigned trg_from = state.trg_covered_;
-      const unsigned trg_to = ext[i].trg_covered_;
-      const unsigned prev_prfx_size = state.src_prefix_.size();
-      res[i].second.reset(new TRule);
-      res[i].second->lhs_ = -TD::Convert("X");
-      vector<WordID>& src = res[i].second->f_;
-      vector<WordID>& trg = res[i].second->e_;
-      src.resize(prev_prfx_size + 1);
-      for (unsigned j = 0; j < prev_prfx_size; ++j)
-        src[j] = container->src[state.src_prefix_[j]];
-      src[prev_prfx_size] = container->src[srcindex];
-      for (unsigned j = trg_from; j < trg_to; ++j)
-        trg.push_back(container->trg[j]);
-      res[i].second->scores_.set_value(FD::Convert("Proposal"), log(container->model->RuleConditionalProbability(*res[i].second)));
-    }
-  }
-  return res;
-}
-
-const WFSTNode* MyFST::GetNode(const FSTState& q) {
-  boost::shared_ptr<WFSTNode>& res = m[q];
-  if (!res) {
-    res.reset(new MyNode(q, this));
-  }
-  return &*res;
-}
-
-const WFSTNode* MyFST::Final() const {
-  return final;
-}
-
-const WFSTNode* MyFST::Initial() const {
-  return init;
-}
-
-int main(int argc, char** argv) {
-  po::variables_map conf;
-  InitCommandLine(argc, argv, &conf);
-  kMAX_TRG_PHRASE = conf["max_trg_phrase"].as<unsigned>();
-  kMAX_SRC_PHRASE = conf["max_src_phrase"].as<unsigned>();
-
-  if (!conf.count("model1")) {
-    cerr << argv[0] << "Please use --model1 to specify model 1 parameters\n";
-    return 1;
-  }
-  boost::shared_ptr<MT19937> prng;
-  if (conf.count("random_seed"))
-    prng.reset(new MT19937(conf["random_seed"].as<uint32_t>()));
-  else
-    prng.reset(new MT19937);
-  MT19937& rng = *prng;
-
-  vector<vector<int> > corpuse, corpusf;
-  set<int> vocabe, vocabf;
-  ReadParallelCorpus(conf["input"].as<string>(), &corpusf, &corpuse, &vocabf, &vocabe);
-  cerr << "f-Corpus size: " << corpusf.size() << " sentences\n";
-  cerr << "f-Vocabulary size: " << vocabf.size() << " types\n";
-  cerr << "f-Corpus size: " << corpuse.size() << " sentences\n";
-  cerr << "f-Vocabulary size: " << vocabe.size() << " types\n";
-  assert(corpusf.size() == corpuse.size());
-
-  ConditionalBase lp0(conf["model1_interpolation_weight"].as<double>(),
-                      vocabe.size(),
-                      conf["model1"].as<string>());
-  MyModel m(lp0);
-
-  TRule x("[X] ||| kAnwntR myN ||| at the convent ||| 0");
-  m.IncrementRule(x);
-  TRule y("[X] ||| nY dyN ||| gave ||| 0");
-  m.IncrementRule(y);
-
-
-  MyFST fst(corpusf[0], corpuse[0], &m);
-  ifstream in("./kimura.g");
-  assert(in);
-  CFG_WFSTComposer comp(fst);
-  Hypergraph hg;
-  bool succeed = comp.Compose(&in, &hg);
-  hg.PrintGraphviz();
-  if (succeed) { cerr << "SUCCESS.\n"; } else { cerr << "FAILURE REPORTED.\n"; }
-
-#if 0
-  ifstream in2("./amnabooks.g");
-  assert(in2);
-  MyFST fst2(corpusf[1], corpuse[1], &m);
-  CFG_WFSTComposer comp2(fst2);
-  Hypergraph hg2;
-  bool succeed2 = comp2.Compose(&in2, &hg2);
-  if (succeed2) { cerr << "SUCCESS.\n"; } else { cerr << "FAILURE REPORTED.\n"; }
-#endif
-
-  SparseVector<double> w; w.set_value(FD::Convert("Proposal"), 1.0);
-  hg.Reweight(w);
-  cerr << ViterbiFTree(hg) << endl;
-  return 0;
-}
-
diff --git a/gi/pf/pfdist.cc b/gi/pf/pfdist.cc
deleted file mode 100644
index a3e46064..00000000
--- a/gi/pf/pfdist.cc
+++ /dev/null
@@ -1,598 +0,0 @@
-#include <iostream>
-#include <tr1/memory>
-#include <queue>
-
-#include <boost/functional.hpp>
-#include <boost/program_options.hpp>
-#include <boost/program_options/variables_map.hpp>
-
-#include "pf.h"
-#include "base_distributions.h"
-#include "reachability.h"
-#include "viterbi.h"
-#include "hg.h"
-#include "trule.h"
-#include "tdict.h"
-#include "filelib.h"
-#include "dict.h"
-#include "sampler.h"
-#include "ccrp_nt.h"
-#include "ccrp_onetable.h"
-
-using namespace std;
-using namespace tr1;
-namespace po = boost::program_options;
-
-boost::shared_ptr<MT19937> prng;
-
-void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
-  po::options_description opts("Configuration options");
-  opts.add_options()
-        ("samples,s",po::value<unsigned>()->default_value(1000),"Number of samples")
-        ("particles,p",po::value<unsigned>()->default_value(30),"Number of particles")
-        ("filter_frequency,f",po::value<unsigned>()->default_value(5),"Number of time steps between filterings")
-        ("input,i",po::value<string>(),"Read parallel data from")
-        ("max_src_phrase",po::value<unsigned>()->default_value(5),"Maximum length of source language phrases")
-        ("max_trg_phrase",po::value<unsigned>()->default_value(5),"Maximum length of target language phrases")
-        ("model1,m",po::value<string>(),"Model 1 parameters (used in base distribution)")
-        ("inverse_model1,M",po::value<string>(),"Inverse Model 1 parameters (used in backward estimate)")
-        ("model1_interpolation_weight",po::value<double>()->default_value(0.95),"Mixing proportion of model 1 with uniform target distribution")
-        ("random_seed,S",po::value<uint32_t>(), "Random seed");
-  po::options_description clo("Command line options");
-  clo.add_options()
-        ("config", po::value<string>(), "Configuration file")
-        ("help,h", "Print this help message and exit");
-  po::options_description dconfig_options, dcmdline_options;
-  dconfig_options.add(opts);
-  dcmdline_options.add(opts).add(clo);
-  
-  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
-  if (conf->count("config")) {
-    ifstream config((*conf)["config"].as<string>().c_str());
-    po::store(po::parse_config_file(config, dconfig_options), *conf);
-  }
-  po::notify(*conf);
-
-  if (conf->count("help") || (conf->count("input") == 0)) {
-    cerr << dcmdline_options << endl;
-    exit(1);
-  }
-}
-
-void ReadParallelCorpus(const string& filename,
-                vector<vector<WordID> >* f,
-                vector<vector<WordID> >* e,
-                set<WordID>* vocab_f,
-                set<WordID>* vocab_e) {
-  f->clear();
-  e->clear();
-  vocab_f->clear();
-  vocab_e->clear();
-  istream* in;
-  if (filename == "-")
-    in = &cin;
-  else
-    in = new ifstream(filename.c_str());
-  assert(*in);
-  string line;
-  const WordID kDIV = TD::Convert("|||");
-  vector<WordID> tmp;
-  while(*in) {
-    getline(*in, line);
-    if (line.empty() && !*in) break;
-    e->push_back(vector<int>());
-    f->push_back(vector<int>());
-    vector<int>& le = e->back();
-    vector<int>& lf = f->back();
-    tmp.clear();
-    TD::ConvertSentence(line, &tmp);
-    bool isf = true;
-    for (unsigned i = 0; i < tmp.size(); ++i) {
-      const int cur = tmp[i];
-      if (isf) {
-        if (kDIV == cur) { isf = false; } else {
-          lf.push_back(cur);
-          vocab_f->insert(cur);
-        }
-      } else {
-        assert(cur != kDIV);
-        le.push_back(cur);
-        vocab_e->insert(cur);
-      }
-    }
-    assert(isf == false);
-  }
-  if (in != &cin) delete in;
-}
-
-#if 0
-struct MyConditionalModel {
-  MyConditionalModel(PhraseConditionalBase& rcp0) : rp0(&rcp0), base(prob_t::One()), src_phrases(1,1), src_jumps(200, CCRP_NoTable<int>(1,1)) {}
-
-  prob_t srcp0(const vector<WordID>& src) const {
-    prob_t p(1.0 / 3000.0);
-    p.poweq(src.size());
-    prob_t lenp; lenp.logeq(log_poisson(src.size(), 1.0));
-    p *= lenp;
-    return p;
-  }
-
-  void DecrementRule(const TRule& rule) {
-    const RuleCRPMap::iterator it = rules.find(rule.f_);
-    assert(it != rules.end());
-    if (it->second.decrement(rule)) {
-      base /= (*rp0)(rule);
-      if (it->second.num_customers() == 0)
-        rules.erase(it);
-    }
-    if (src_phrases.decrement(rule.f_))
-      base /= srcp0(rule.f_);
-  }
-
-  void IncrementRule(const TRule& rule) {
-    RuleCRPMap::iterator it = rules.find(rule.f_);
-    if (it == rules.end())
-      it = rules.insert(make_pair(rule.f_, CCRP_NoTable<TRule>(1,1))).first;
-    if (it->second.increment(rule)) {
-      base *= (*rp0)(rule);
-    }
-    if (src_phrases.increment(rule.f_))
-      base *= srcp0(rule.f_);
-  }
-
-  void IncrementRules(const vector<TRulePtr>& rules) {
-    for (int i = 0; i < rules.size(); ++i)
-      IncrementRule(*rules[i]);
-  }
-
-  void DecrementRules(const vector<TRulePtr>& rules) {
-    for (int i = 0; i < rules.size(); ++i)
-      DecrementRule(*rules[i]);
-  }
-
-  void IncrementJump(int dist, unsigned src_len) {
-    assert(src_len > 0);
-    if (src_jumps[src_len].increment(dist))
-      base *= jp0(dist, src_len);
-  }
-
-  void DecrementJump(int dist, unsigned src_len) {
-    assert(src_len > 0);
-    if (src_jumps[src_len].decrement(dist))
-      base /= jp0(dist, src_len);
-  }
-
-  void IncrementJumps(const vector<int>& js, unsigned src_len) {
-    for (unsigned i = 0; i < js.size(); ++i)
-      IncrementJump(js[i], src_len);
-  }
-
-  void DecrementJumps(const vector<int>& js, unsigned src_len) {
-    for (unsigned i = 0; i < js.size(); ++i)
-      DecrementJump(js[i], src_len);
-  }
-
-  // p(jump = dist | src_len , z)
-  prob_t JumpProbability(int dist, unsigned src_len) {
-    const prob_t p0 = jp0(dist, src_len);
-    const double lp = src_jumps[src_len].logprob(dist, log(p0));
-    prob_t q; q.logeq(lp);
-    return q;
-  }
-
-  // p(rule.f_ | z) * p(rule.e_ | rule.f_ , z)
-  prob_t RuleProbability(const TRule& rule) const {
-    const prob_t p0 = (*rp0)(rule);
-    prob_t srcp; srcp.logeq(src_phrases.logprob(rule.f_, log(srcp0(rule.f_))));
-    const RuleCRPMap::const_iterator it = rules.find(rule.f_);
-    if (it == rules.end()) return srcp * p0;
-    const double lp = it->second.logprob(rule, log(p0));
-    prob_t q; q.logeq(lp);
-    return q * srcp;
-  }
-
-  prob_t Likelihood() const {
-    prob_t p = base;
-    for (RuleCRPMap::const_iterator it = rules.begin();
-         it != rules.end(); ++it) {
-      prob_t cl; cl.logeq(it->second.log_crp_prob());
-      p *= cl;
-    }
-    for (unsigned l = 1; l < src_jumps.size(); ++l) {
-      if (src_jumps[l].num_customers() > 0) {
-        prob_t q;
-        q.logeq(src_jumps[l].log_crp_prob());
-        p *= q;
-      }
-    }
-    return p;
-  }
-
-  JumpBase jp0;
-  const PhraseConditionalBase* rp0;
-  prob_t base;
-  typedef unordered_map<vector<WordID>, CCRP_NoTable<TRule>, boost::hash<vector<WordID> > > RuleCRPMap;
-  RuleCRPMap rules;
-  CCRP_NoTable<vector<WordID> > src_phrases;
-  vector<CCRP_NoTable<int> > src_jumps;
-};
-
-#endif
-
-struct MyJointModel {
-  MyJointModel(PhraseJointBase& rcp0) :
-    rp0(rcp0), base(prob_t::One()), rules(1,1), src_jumps(200, CCRP_NoTable<int>(1,1)) {}
-
-  void DecrementRule(const TRule& rule) {
-    if (rules.decrement(rule))
-      base /= rp0(rule);
-  }
-
-  void IncrementRule(const TRule& rule) {
-    if (rules.increment(rule))
-      base *= rp0(rule);
-  }
-
-  void IncrementRules(const vector<TRulePtr>& rules) {
-    for (int i = 0; i < rules.size(); ++i)
-      IncrementRule(*rules[i]);
-  }
-
-  void DecrementRules(const vector<TRulePtr>& rules) {
-    for (int i = 0; i < rules.size(); ++i)
-      DecrementRule(*rules[i]);
-  }
-
-  void IncrementJump(int dist, unsigned src_len) {
-    assert(src_len > 0);
-    if (src_jumps[src_len].increment(dist))
-      base *= jp0(dist, src_len);
-  }
-
-  void DecrementJump(int dist, unsigned src_len) {
-    assert(src_len > 0);
-    if (src_jumps[src_len].decrement(dist))
-      base /= jp0(dist, src_len);
-  }
-
-  void IncrementJumps(const vector<int>& js, unsigned src_len) {
-    for (unsigned i = 0; i < js.size(); ++i)
-      IncrementJump(js[i], src_len);
-  }
-
-  void DecrementJumps(const vector<int>& js, unsigned src_len) {
-    for (unsigned i = 0; i < js.size(); ++i)
-      DecrementJump(js[i], src_len);
-  }
-
-  // p(jump = dist | src_len , z)
-  prob_t JumpProbability(int dist, unsigned src_len) {
-    const prob_t p0 = jp0(dist, src_len);
-    const double lp = src_jumps[src_len].logprob(dist, log(p0));
-    prob_t q; q.logeq(lp);
-    return q;
-  }
-
-  // p(rule.f_ | z) * p(rule.e_ | rule.f_ , z)
-  prob_t RuleProbability(const TRule& rule) const {
-    prob_t p; p.logeq(rules.logprob(rule, log(rp0(rule))));
-    return p;
-  }
-
-  prob_t Likelihood() const {
-    prob_t p = base;
-    prob_t q; q.logeq(rules.log_crp_prob());
-    p *= q;
-    for (unsigned l = 1; l < src_jumps.size(); ++l) {
-      if (src_jumps[l].num_customers() > 0) {
-        prob_t q;
-        q.logeq(src_jumps[l].log_crp_prob());
-        p *= q;
-      }
-    }
-    return p;
-  }
-
-  JumpBase jp0;
-  const PhraseJointBase& rp0;
-  prob_t base;
-  CCRP_NoTable<TRule> rules;
-  vector<CCRP_NoTable<int> > src_jumps;
-};
-
-struct BackwardEstimate {
-  BackwardEstimate(const Model1& m1, const vector<WordID>& src, const vector<WordID>& trg) :
-      model1_(m1), src_(src), trg_(trg) {
-  }
-  const prob_t& operator()(const vector<bool>& src_cov, unsigned trg_cov) const {
-    assert(src_.size() == src_cov.size());
-    assert(trg_cov <= trg_.size());
-    prob_t& e = cache_[src_cov][trg_cov];
-    if (e.is_0()) {
-      if (trg_cov == trg_.size()) { e = prob_t::One(); return e; }
-      vector<WordID> r(src_.size() + 1); r.clear();
-      r.push_back(0);  // NULL word
-      for (int i = 0; i < src_cov.size(); ++i)
-        if (!src_cov[i]) r.push_back(src_[i]);
-      const prob_t uniform_alignment(1.0 / r.size());
-      e.logeq(Md::log_poisson(trg_.size() - trg_cov, r.size() - 1)); // p(trg len remaining | src len remaining)
-      for (unsigned j = trg_cov; j < trg_.size(); ++j) {
-        prob_t p;
-        for (unsigned i = 0; i < r.size(); ++i)
-          p += model1_(r[i], trg_[j]);
-        if (p.is_0()) {
-          cerr << "ERROR: p(" << TD::Convert(trg_[j]) << " | " << TD::GetString(r) << ") = 0!\n";
-          abort();
-        }
-        p *= uniform_alignment;
-        e *= p;
-      }
-    }
-    return e;
-  }
-  const Model1& model1_;
-  const vector<WordID>& src_;
-  const vector<WordID>& trg_;
-  mutable unordered_map<vector<bool>, map<unsigned, prob_t>, boost::hash<vector<bool> > > cache_;
-};
-
-struct BackwardEstimateSym {
-  BackwardEstimateSym(const Model1& m1,
-                      const Model1& invm1, const vector<WordID>& src, const vector<WordID>& trg) :
-      model1_(m1), invmodel1_(invm1), src_(src), trg_(trg) {
-  }
-  const prob_t& operator()(const vector<bool>& src_cov, unsigned trg_cov) const {
-    assert(src_.size() == src_cov.size());
-    assert(trg_cov <= trg_.size());
-    prob_t& e = cache_[src_cov][trg_cov];
-    if (e.is_0()) {
-      if (trg_cov == trg_.size()) { e = prob_t::One(); return e; }
-      vector<WordID> r(src_.size() + 1); r.clear();
-      for (int i = 0; i < src_cov.size(); ++i)
-        if (!src_cov[i]) r.push_back(src_[i]);
-      r.push_back(0);  // NULL word
-      const prob_t uniform_alignment(1.0 / r.size());
-      e.logeq(Md::log_poisson(trg_.size() - trg_cov, r.size() - 1)); // p(trg len remaining | src len remaining)
-      for (unsigned j = trg_cov; j < trg_.size(); ++j) {
-        prob_t p;
-        for (unsigned i = 0; i < r.size(); ++i)
-          p += model1_(r[i], trg_[j]);
-        if (p.is_0()) {
-          cerr << "ERROR: p(" << TD::Convert(trg_[j]) << " | " << TD::GetString(r) << ") = 0!\n";
-          abort();
-        }
-        p *= uniform_alignment;
-        e *= p;
-      }
-      r.pop_back();
-      const prob_t inv_uniform(1.0 / (trg_.size() - trg_cov + 1.0));
-      prob_t inv;
-      inv.logeq(Md::log_poisson(r.size(), trg_.size() - trg_cov));
-      for (unsigned i = 0; i < r.size(); ++i) {
-        prob_t p;
-        for (unsigned j = trg_cov - 1; j < trg_.size(); ++j)
-          p += invmodel1_(j < trg_cov ? 0 : trg_[j], r[i]);
-        if (p.is_0()) {
-          cerr << "ERROR: p_inv(" << TD::Convert(r[i]) << " | " << TD::GetString(trg_) << ") = 0!\n";
-          abort();
-        }
-        p *= inv_uniform;
-        inv *= p;
-      }
-      prob_t x = pow(e * inv, 0.5);
-      e = x;
-      //cerr << "Forward: " << log(e) << "\tBackward: " << log(inv) << "\t prop: " << log(x) << endl;
-    }
-    return e;
-  }
-  const Model1& model1_;
-  const Model1& invmodel1_;
-  const vector<WordID>& src_;
-  const vector<WordID>& trg_;
-  mutable unordered_map<vector<bool>, map<unsigned, prob_t>, boost::hash<vector<bool> > > cache_;
-};
-
-struct Particle {
-  Particle() : weight(prob_t::One()), src_cov(), trg_cov(), prev_pos(-1) {}
-  prob_t weight;
-  prob_t gamma_last;
-  vector<int> src_jumps;
-  vector<TRulePtr> rules;
-  vector<bool> src_cv;
-  int src_cov;
-  int trg_cov;
-  int prev_pos;
-};
-
-ostream& operator<<(ostream& o, const vector<bool>& v) {
-  for (int i = 0; i < v.size(); ++i)
-    o << (v[i] ? '1' : '0');
-  return o;
-}
-ostream& operator<<(ostream& o, const Particle& p) {
-  o << "[cv=" << p.src_cv << "  src_cov=" << p.src_cov << " trg_cov=" << p.trg_cov << " last_pos=" << p.prev_pos << " num_rules=" << p.rules.size() << "  w=" << log(p.weight) << ']';
-  return o;
-}
-
-int main(int argc, char** argv) {
-  po::variables_map conf;
-  InitCommandLine(argc, argv, &conf);
-  const unsigned kMAX_TRG_PHRASE = conf["max_trg_phrase"].as<unsigned>();
-  const unsigned kMAX_SRC_PHRASE = conf["max_src_phrase"].as<unsigned>();
-  const unsigned particles = conf["particles"].as<unsigned>();
-  const unsigned samples = conf["samples"].as<unsigned>();
-  const unsigned rejuv_freq = conf["filter_frequency"].as<unsigned>();
-
-  if (!conf.count("model1")) {
-    cerr << argv[0] << "Please use --model1 to specify model 1 parameters\n";
-    return 1;
-  }
-  if (conf.count("random_seed"))
-    prng.reset(new MT19937(conf["random_seed"].as<uint32_t>()));
-  else
-    prng.reset(new MT19937);
-  MT19937& rng = *prng;
-
-  vector<vector<WordID> > corpuse, corpusf;
-  set<WordID> vocabe, vocabf;
-  cerr << "Reading corpus...\n";
-  ReadParallelCorpus(conf["input"].as<string>(), &corpusf, &corpuse, &vocabf, &vocabe);
-  cerr << "F-corpus size: " << corpusf.size() << " sentences\t (" << vocabf.size() << " word types)\n";
-  cerr << "E-corpus size: " << corpuse.size() << " sentences\t (" << vocabe.size() << " word types)\n";
-  assert(corpusf.size() == corpuse.size());
-
-  const int kLHS = -TD::Convert("X");
-  Model1 m1(conf["model1"].as<string>());
-  Model1 invm1(conf["inverse_model1"].as<string>());
-
-#if 0
-  PhraseConditionalBase lp0(m1, conf["model1_interpolation_weight"].as<double>(), vocabe.size());
-  MyConditionalModel m(lp0);
-#else
-  PhraseJointBase lp0(m1, conf["model1_interpolation_weight"].as<double>(), vocabe.size(), vocabf.size());
-  MyJointModel m(lp0);
-#endif
-
-  MultinomialResampleFilter<Particle> filter(&rng);
-  cerr << "Initializing reachability limits...\n";
-  vector<Particle> ps(corpusf.size());
-  vector<Reachability> reaches; reaches.reserve(corpusf.size());
-  for (int ci = 0; ci < corpusf.size(); ++ci)
-    reaches.push_back(Reachability(corpusf[ci].size(),
-                                   corpuse[ci].size(),
-                                   kMAX_SRC_PHRASE,
-                                   kMAX_TRG_PHRASE));
-  cerr << "Sampling...\n"; 
-  vector<Particle> tmp_p(10000);  // work space
-  SampleSet<prob_t> pfss;
-  for (int SS=0; SS < samples; ++SS) {
-    for (int ci = 0; ci < corpusf.size(); ++ci) {
-      vector<int>& src = corpusf[ci];
-      vector<int>& trg = corpuse[ci];
-      m.DecrementRules(ps[ci].rules);
-      m.DecrementJumps(ps[ci].src_jumps, src.size());
-
-      //BackwardEstimate be(m1, src, trg);
-      BackwardEstimateSym be(m1, invm1, src, trg);
-      const Reachability& r = reaches[ci];
-      vector<Particle> lps(particles);
-
-      for (int pi = 0; pi < particles; ++pi) {
-        Particle& p = lps[pi];
-        p.src_cv.resize(src.size(), false);
-      }
-
-      bool all_complete = false;
-      while(!all_complete) {
-        SampleSet<prob_t> ss;
-
-        // all particles have now been extended a bit, we will reweight them now
-        if (lps[0].trg_cov > 0)
-          filter(&lps);
-
-        // loop over all particles and extend them
-        bool done_nothing = true;
-        for (int pi = 0; pi < particles; ++pi) {
-          Particle& p = lps[pi];
-          int tic = 0;
-          while(p.trg_cov < trg.size() && tic < rejuv_freq) {
-            ++tic;
-            done_nothing = false;
-            ss.clear();
-            TRule x; x.lhs_ = kLHS;
-            prob_t z;
-            int first_uncovered = src.size();
-            int last_uncovered = -1;
-            for (int i = 0; i < src.size(); ++i) {
-              const bool is_uncovered = !p.src_cv[i];
-              if (i < first_uncovered && is_uncovered) first_uncovered = i;
-              if (is_uncovered && i > last_uncovered) last_uncovered = i;
-            }
-            assert(last_uncovered > -1);
-            assert(first_uncovered < src.size());
-
-            for (int trg_len = 1; trg_len <= kMAX_TRG_PHRASE; ++trg_len) {
-              x.e_.push_back(trg[trg_len - 1 + p.trg_cov]);
-              for (int src_len = 1; src_len <= kMAX_SRC_PHRASE; ++src_len) {
-                if (!r.edges[p.src_cov][p.trg_cov][src_len][trg_len]) continue;
-
-                const int last_possible_start = last_uncovered - src_len + 1;
-                assert(last_possible_start >= 0);
-                //cerr << src_len << "," << trg_len << " is allowed. E=" << TD::GetString(x.e_) << endl;
-                //cerr << "  first_uncovered=" << first_uncovered << "  last_possible_start=" << last_possible_start << endl;
-                for (int i = first_uncovered; i <= last_possible_start; ++i) {
-                  if (p.src_cv[i]) continue;
-                  assert(ss.size() < tmp_p.size());  // if fails increase tmp_p size
-                  Particle& np = tmp_p[ss.size()];
-                  np = p;
-                  x.f_.clear();
-                  int gap_add = 0;
-                  bool bad = false;
-                  prob_t jp = prob_t::One();
-                  int prev_pos = p.prev_pos;
-                  for (int j = 0; j < src_len; ++j) {
-                    if ((j + i + gap_add) == src.size()) { bad = true; break; }
-                    while ((i+j+gap_add) < src.size() && p.src_cv[i + j + gap_add]) { ++gap_add; }
-                    if ((j + i + gap_add) == src.size()) { bad = true; break; }
-                    np.src_cv[i + j + gap_add] = true;
-                    x.f_.push_back(src[i + j + gap_add]);
-                    jp *= m.JumpProbability(i + j + gap_add - prev_pos, src.size());
-                    int jump = i + j + gap_add - prev_pos;
-                    assert(jump != 0);
-                    np.src_jumps.push_back(jump);
-                    prev_pos = i + j + gap_add;
-                  }
-                  if (bad) continue;
-                  np.prev_pos = prev_pos;
-                  np.src_cov += x.f_.size();
-                  np.trg_cov += x.e_.size();
-                  if (x.f_.size() != src_len) continue;
-                  prob_t rp = m.RuleProbability(x);
-                  np.gamma_last = rp * jp;
-                  const prob_t u = pow(np.gamma_last * be(np.src_cv, np.trg_cov), 0.2);
-                  //cerr << "**rule=" << x << endl;
-                  //cerr << "  u=" << log(u) << "  rule=" << rp << " jump=" << jp << endl;
-                  ss.add(u);
-                  np.rules.push_back(TRulePtr(new TRule(x)));
-                  z += u;
-
-                  const bool completed = (p.trg_cov == trg.size());
-                  if (completed) {
-                    int last_jump = src.size() - p.prev_pos;
-                    assert(last_jump > 0);
-                    p.src_jumps.push_back(last_jump);
-                    p.weight *= m.JumpProbability(last_jump, src.size());
-                  }
-                }
-              }
-            }
-            cerr << "number of edges to consider: " << ss.size() << endl;
-            const int sampled = rng.SelectSample(ss);
-            prob_t q_n = ss[sampled] / z;
-            p = tmp_p[sampled];
-            //m.IncrementRule(*p.rules.back());
-            p.weight *= p.gamma_last / q_n;
-            cerr << "[w=" << log(p.weight) << "]\tsampled rule: " << p.rules.back()->AsString() << endl;
-            cerr << p << endl;
-          }
-        } // loop over particles (pi = 0 .. particles)
-        if (done_nothing) all_complete = true;
-      }
-      pfss.clear();
-      for (int i = 0; i < lps.size(); ++i)
-        pfss.add(lps[i].weight);
-      const int sampled = rng.SelectSample(pfss);
-      ps[ci] = lps[sampled];
-      m.IncrementRules(lps[sampled].rules);
-      m.IncrementJumps(lps[sampled].src_jumps, src.size());
-      for (int i = 0; i < lps[sampled].rules.size(); ++i) { cerr << "S:\t" << lps[sampled].rules[i]->AsString() << "\n"; }
-      cerr << "tmp-LLH: " << log(m.Likelihood()) << endl;
-    }
-    cerr << "LLH: " << log(m.Likelihood()) << endl;
-    for (int sni = 0; sni < 5; ++sni) {
-      for (int i = 0; i < ps[sni].rules.size(); ++i) { cerr << "\t" << ps[sni].rules[i]->AsString() << endl; }
-    }
-  }
-  return 0;
-}
-
diff --git a/gi/pf/pfdist.new.cc b/gi/pf/pfdist.new.cc
deleted file mode 100644
index 3169eb75..00000000
--- a/gi/pf/pfdist.new.cc
+++ /dev/null
@@ -1,620 +0,0 @@
-#include <iostream>
-#include <tr1/memory>
-#include <queue>
-
-#include <boost/functional.hpp>
-#include <boost/program_options.hpp>
-#include <boost/program_options/variables_map.hpp>
-
-#include "base_measures.h"
-#include "reachability.h"
-#include "viterbi.h"
-#include "hg.h"
-#include "trule.h"
-#include "tdict.h"
-#include "filelib.h"
-#include "dict.h"
-#include "sampler.h"
-#include "ccrp_nt.h"
-#include "ccrp_onetable.h"
-
-using namespace std;
-using namespace tr1;
-namespace po = boost::program_options;
-
-shared_ptr<MT19937> prng;
-
-size_t hash_value(const TRule& r) {
-  size_t h = boost::hash_value(r.e_);
-  boost::hash_combine(h, -r.lhs_);
-  boost::hash_combine(h, boost::hash_value(r.f_));
-  return h;
-}
-
-bool operator==(const TRule& a, const TRule& b) {
-  return (a.lhs_ == b.lhs_ && a.e_ == b.e_ && a.f_ == b.f_);
-}
-
-void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
-  po::options_description opts("Configuration options");
-  opts.add_options()
-        ("samples,s",po::value<unsigned>()->default_value(1000),"Number of samples")
-        ("particles,p",po::value<unsigned>()->default_value(25),"Number of particles")
-        ("input,i",po::value<string>(),"Read parallel data from")
-        ("max_src_phrase",po::value<unsigned>()->default_value(5),"Maximum length of source language phrases")
-        ("max_trg_phrase",po::value<unsigned>()->default_value(5),"Maximum length of target language phrases")
-        ("model1,m",po::value<string>(),"Model 1 parameters (used in base distribution)")
-        ("inverse_model1,M",po::value<string>(),"Inverse Model 1 parameters (used in backward estimate)")
-        ("model1_interpolation_weight",po::value<double>()->default_value(0.95),"Mixing proportion of model 1 with uniform target distribution")
-        ("random_seed,S",po::value<uint32_t>(), "Random seed");
-  po::options_description clo("Command line options");
-  clo.add_options()
-        ("config", po::value<string>(), "Configuration file")
-        ("help,h", "Print this help message and exit");
-  po::options_description dconfig_options, dcmdline_options;
-  dconfig_options.add(opts);
-  dcmdline_options.add(opts).add(clo);
-  
-  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
-  if (conf->count("config")) {
-    ifstream config((*conf)["config"].as<string>().c_str());
-    po::store(po::parse_config_file(config, dconfig_options), *conf);
-  }
-  po::notify(*conf);
-
-  if (conf->count("help") || (conf->count("input") == 0)) {
-    cerr << dcmdline_options << endl;
-    exit(1);
-  }
-}
-
-void ReadParallelCorpus(const string& filename,
-                vector<vector<WordID> >* f,
-                vector<vector<WordID> >* e,
-                set<WordID>* vocab_f,
-                set<WordID>* vocab_e) {
-  f->clear();
-  e->clear();
-  vocab_f->clear();
-  vocab_e->clear();
-  istream* in;
-  if (filename == "-")
-    in = &cin;
-  else
-    in = new ifstream(filename.c_str());
-  assert(*in);
-  string line;
-  const WordID kDIV = TD::Convert("|||");
-  vector<WordID> tmp;
-  while(*in) {
-    getline(*in, line);
-    if (line.empty() && !*in) break;
-    e->push_back(vector<int>());
-    f->push_back(vector<int>());
-    vector<int>& le = e->back();
-    vector<int>& lf = f->back();
-    tmp.clear();
-    TD::ConvertSentence(line, &tmp);
-    bool isf = true;
-    for (unsigned i = 0; i < tmp.size(); ++i) {
-      const int cur = tmp[i];
-      if (isf) {
-        if (kDIV == cur) { isf = false; } else {
-          lf.push_back(cur);
-          vocab_f->insert(cur);
-        }
-      } else {
-        assert(cur != kDIV);
-        le.push_back(cur);
-        vocab_e->insert(cur);
-      }
-    }
-    assert(isf == false);
-  }
-  if (in != &cin) delete in;
-}
-
-#if 0
-struct MyConditionalModel {
-  MyConditionalModel(PhraseConditionalBase& rcp0) : rp0(&rcp0), base(prob_t::One()), src_phrases(1,1), src_jumps(200, CCRP_NoTable<int>(1,1)) {}
-
-  prob_t srcp0(const vector<WordID>& src) const {
-    prob_t p(1.0 / 3000.0);
-    p.poweq(src.size());
-    prob_t lenp; lenp.logeq(log_poisson(src.size(), 1.0));
-    p *= lenp;
-    return p;
-  }
-
-  void DecrementRule(const TRule& rule) {
-    const RuleCRPMap::iterator it = rules.find(rule.f_);
-    assert(it != rules.end());
-    if (it->second.decrement(rule)) {
-      base /= (*rp0)(rule);
-      if (it->second.num_customers() == 0)
-        rules.erase(it);
-    }
-    if (src_phrases.decrement(rule.f_))
-      base /= srcp0(rule.f_);
-  }
-
-  void IncrementRule(const TRule& rule) {
-    RuleCRPMap::iterator it = rules.find(rule.f_);
-    if (it == rules.end())
-      it = rules.insert(make_pair(rule.f_, CCRP_NoTable<TRule>(1,1))).first;
-    if (it->second.increment(rule)) {
-      base *= (*rp0)(rule);
-    }
-    if (src_phrases.increment(rule.f_))
-      base *= srcp0(rule.f_);
-  }
-
-  void IncrementRules(const vector<TRulePtr>& rules) {
-    for (int i = 0; i < rules.size(); ++i)
-      IncrementRule(*rules[i]);
-  }
-
-  void DecrementRules(const vector<TRulePtr>& rules) {
-    for (int i = 0; i < rules.size(); ++i)
-      DecrementRule(*rules[i]);
-  }
-
-  void IncrementJump(int dist, unsigned src_len) {
-    assert(src_len > 0);
-    if (src_jumps[src_len].increment(dist))
-      base *= jp0(dist, src_len);
-  }
-
-  void DecrementJump(int dist, unsigned src_len) {
-    assert(src_len > 0);
-    if (src_jumps[src_len].decrement(dist))
-      base /= jp0(dist, src_len);
-  }
-
-  void IncrementJumps(const vector<int>& js, unsigned src_len) {
-    for (unsigned i = 0; i < js.size(); ++i)
-      IncrementJump(js[i], src_len);
-  }
-
-  void DecrementJumps(const vector<int>& js, unsigned src_len) {
-    for (unsigned i = 0; i < js.size(); ++i)
-      DecrementJump(js[i], src_len);
-  }
-
-  // p(jump = dist | src_len , z)
-  prob_t JumpProbability(int dist, unsigned src_len) {
-    const prob_t p0 = jp0(dist, src_len);
-    const double lp = src_jumps[src_len].logprob(dist, log(p0));
-    prob_t q; q.logeq(lp);
-    return q;
-  }
-
-  // p(rule.f_ | z) * p(rule.e_ | rule.f_ , z)
-  prob_t RuleProbability(const TRule& rule) const {
-    const prob_t p0 = (*rp0)(rule);
-    prob_t srcp; srcp.logeq(src_phrases.logprob(rule.f_, log(srcp0(rule.f_))));
-    const RuleCRPMap::const_iterator it = rules.find(rule.f_);
-    if (it == rules.end()) return srcp * p0;
-    const double lp = it->second.logprob(rule, log(p0));
-    prob_t q; q.logeq(lp);
-    return q * srcp;
-  }
-
-  prob_t Likelihood() const {
-    prob_t p = base;
-    for (RuleCRPMap::const_iterator it = rules.begin();
-         it != rules.end(); ++it) {
-      prob_t cl; cl.logeq(it->second.log_crp_prob());
-      p *= cl;
-    }
-    for (unsigned l = 1; l < src_jumps.size(); ++l) {
-      if (src_jumps[l].num_customers() > 0) {
-        prob_t q;
-        q.logeq(src_jumps[l].log_crp_prob());
-        p *= q;
-      }
-    }
-    return p;
-  }
-
-  JumpBase jp0;
-  const PhraseConditionalBase* rp0;
-  prob_t base;
-  typedef unordered_map<vector<WordID>, CCRP_NoTable<TRule>, boost::hash<vector<WordID> > > RuleCRPMap;
-  RuleCRPMap rules;
-  CCRP_NoTable<vector<WordID> > src_phrases;
-  vector<CCRP_NoTable<int> > src_jumps;
-};
-
-#endif
-
-struct MyJointModel {
-  MyJointModel(PhraseJointBase& rcp0) :
-    rp0(rcp0), base(prob_t::One()), rules(1,1), src_jumps(200, CCRP_NoTable<int>(1,1)) {}
-
-  void DecrementRule(const TRule& rule) {
-    if (rules.decrement(rule))
-      base /= rp0(rule);
-  }
-
-  void IncrementRule(const TRule& rule) {
-    if (rules.increment(rule))
-      base *= rp0(rule);
-  }
-
-  void IncrementRules(const vector<TRulePtr>& rules) {
-    for (int i = 0; i < rules.size(); ++i)
-      IncrementRule(*rules[i]);
-  }
-
-  void DecrementRules(const vector<TRulePtr>& rules) {
-    for (int i = 0; i < rules.size(); ++i)
-      DecrementRule(*rules[i]);
-  }
-
-  void IncrementJump(int dist, unsigned src_len) {
-    assert(src_len > 0);
-    if (src_jumps[src_len].increment(dist))
-      base *= jp0(dist, src_len);
-  }
-
-  void DecrementJump(int dist, unsigned src_len) {
-    assert(src_len > 0);
-    if (src_jumps[src_len].decrement(dist))
-      base /= jp0(dist, src_len);
-  }
-
-  void IncrementJumps(const vector<int>& js, unsigned src_len) {
-    for (unsigned i = 0; i < js.size(); ++i)
-      IncrementJump(js[i], src_len);
-  }
-
-  void DecrementJumps(const vector<int>& js, unsigned src_len) {
-    for (unsigned i = 0; i < js.size(); ++i)
-      DecrementJump(js[i], src_len);
-  }
-
-  // p(jump = dist | src_len , z)
-  prob_t JumpProbability(int dist, unsigned src_len) {
-    const prob_t p0 = jp0(dist, src_len);
-    const double lp = src_jumps[src_len].logprob(dist, log(p0));
-    prob_t q; q.logeq(lp);
-    return q;
-  }
-
-  // p(rule.f_ | z) * p(rule.e_ | rule.f_ , z)
-  prob_t RuleProbability(const TRule& rule) const {
-    prob_t p; p.logeq(rules.logprob(rule, log(rp0(rule))));
-    return p;
-  }
-
-  prob_t Likelihood() const {
-    prob_t p = base;
-    prob_t q; q.logeq(rules.log_crp_prob());
-    p *= q;
-    for (unsigned l = 1; l < src_jumps.size(); ++l) {
-      if (src_jumps[l].num_customers() > 0) {
-        prob_t q;
-        q.logeq(src_jumps[l].log_crp_prob());
-        p *= q;
-      }
-    }
-    return p;
-  }
-
-  JumpBase jp0;
-  const PhraseJointBase& rp0;
-  prob_t base;
-  CCRP_NoTable<TRule> rules;
-  vector<CCRP_NoTable<int> > src_jumps;
-};
-
-struct BackwardEstimate {
-  BackwardEstimate(const Model1& m1, const vector<WordID>& src, const vector<WordID>& trg) :
-      model1_(m1), src_(src), trg_(trg) {
-  }
-  const prob_t& operator()(const vector<bool>& src_cov, unsigned trg_cov) const {
-    assert(src_.size() == src_cov.size());
-    assert(trg_cov <= trg_.size());
-    prob_t& e = cache_[src_cov][trg_cov];
-    if (e.is_0()) {
-      if (trg_cov == trg_.size()) { e = prob_t::One(); return e; }
-      vector<WordID> r(src_.size() + 1); r.clear();
-      r.push_back(0);  // NULL word
-      for (int i = 0; i < src_cov.size(); ++i)
-        if (!src_cov[i]) r.push_back(src_[i]);
-      const prob_t uniform_alignment(1.0 / r.size());
-      e.logeq(log_poisson(trg_.size() - trg_cov, r.size() - 1)); // p(trg len remaining | src len remaining)
-      for (unsigned j = trg_cov; j < trg_.size(); ++j) {
-        prob_t p;
-        for (unsigned i = 0; i < r.size(); ++i)
-          p += model1_(r[i], trg_[j]);
-        if (p.is_0()) {
-          cerr << "ERROR: p(" << TD::Convert(trg_[j]) << " | " << TD::GetString(r) << ") = 0!\n";
-          abort();
-        }
-        p *= uniform_alignment;
-        e *= p;
-      }
-    }
-    return e;
-  }
-  const Model1& model1_;
-  const vector<WordID>& src_;
-  const vector<WordID>& trg_;
-  mutable unordered_map<vector<bool>, map<unsigned, prob_t>, boost::hash<vector<bool> > > cache_;
-};
-
-struct BackwardEstimateSym {
-  BackwardEstimateSym(const Model1& m1,
-                      const Model1& invm1, const vector<WordID>& src, const vector<WordID>& trg) :
-      model1_(m1), invmodel1_(invm1), src_(src), trg_(trg) {
-  }
-  const prob_t& operator()(const vector<bool>& src_cov, unsigned trg_cov) const {
-    assert(src_.size() == src_cov.size());
-    assert(trg_cov <= trg_.size());
-    prob_t& e = cache_[src_cov][trg_cov];
-    if (e.is_0()) {
-      if (trg_cov == trg_.size()) { e = prob_t::One(); return e; }
-      vector<WordID> r(src_.size() + 1); r.clear();
-      for (int i = 0; i < src_cov.size(); ++i)
-        if (!src_cov[i]) r.push_back(src_[i]);
-      r.push_back(0);  // NULL word
-      const prob_t uniform_alignment(1.0 / r.size());
-      e.logeq(log_poisson(trg_.size() - trg_cov, r.size() - 1)); // p(trg len remaining | src len remaining)
-      for (unsigned j = trg_cov; j < trg_.size(); ++j) {
-        prob_t p;
-        for (unsigned i = 0; i < r.size(); ++i)
-          p += model1_(r[i], trg_[j]);
-        if (p.is_0()) {
-          cerr << "ERROR: p(" << TD::Convert(trg_[j]) << " | " << TD::GetString(r) << ") = 0!\n";
-          abort();
-        }
-        p *= uniform_alignment;
-        e *= p;
-      }
-      r.pop_back();
-      const prob_t inv_uniform(1.0 / (trg_.size() - trg_cov + 1.0));
-      prob_t inv;
-      inv.logeq(log_poisson(r.size(), trg_.size() - trg_cov));
-      for (unsigned i = 0; i < r.size(); ++i) {
-        prob_t p;
-        for (unsigned j = trg_cov - 1; j < trg_.size(); ++j)
-          p += invmodel1_(j < trg_cov ? 0 : trg_[j], r[i]);
-        if (p.is_0()) {
-          cerr << "ERROR: p_inv(" << TD::Convert(r[i]) << " | " << TD::GetString(trg_) << ") = 0!\n";
-          abort();
-        }
-        p *= inv_uniform;
-        inv *= p;
-      }
-      prob_t x = pow(e * inv, 0.5);
-      e = x;
-      //cerr << "Forward: " << log(e) << "\tBackward: " << log(inv) << "\t prop: " << log(x) << endl;
-    }
-    return e;
-  }
-  const Model1& model1_;
-  const Model1& invmodel1_;
-  const vector<WordID>& src_;
-  const vector<WordID>& trg_;
-  mutable unordered_map<vector<bool>, map<unsigned, prob_t>, boost::hash<vector<bool> > > cache_;
-};
-
-struct Particle {
-  Particle() : weight(prob_t::One()), src_cov(), trg_cov(), prev_pos(-1) {}
-  prob_t weight;
-  prob_t gamma_last;
-  vector<int> src_jumps;
-  vector<TRulePtr> rules;
-  vector<bool> src_cv;
-  int src_cov;
-  int trg_cov;
-  int prev_pos;
-};
-
-ostream& operator<<(ostream& o, const vector<bool>& v) {
-  for (int i = 0; i < v.size(); ++i)
-    o << (v[i] ? '1' : '0');
-  return o;
-}
-ostream& operator<<(ostream& o, const Particle& p) {
-  o << "[cv=" << p.src_cv << "  src_cov=" << p.src_cov << " trg_cov=" << p.trg_cov << " last_pos=" << p.prev_pos << " num_rules=" << p.rules.size() << "  w=" << log(p.weight) << ']';
-  return o;
-}
-
-void FilterCrapParticlesAndReweight(vector<Particle>* pps) {
-  vector<Particle>& ps = *pps;
-  SampleSet<prob_t> ss;
-  for (int i = 0; i < ps.size(); ++i)
-    ss.add(ps[i].weight);
-  vector<Particle> nps; nps.reserve(ps.size());
-  const prob_t uniform_weight(1.0 / ps.size());
-  for (int i = 0; i < ps.size(); ++i) {
-    nps.push_back(ps[prng->SelectSample(ss)]);
-    nps[i].weight = uniform_weight;
-  }
-  nps.swap(ps);
-}
-
-int main(int argc, char** argv) {
-  po::variables_map conf;
-  InitCommandLine(argc, argv, &conf);
-  const unsigned kMAX_TRG_PHRASE = conf["max_trg_phrase"].as<unsigned>();
-  const unsigned kMAX_SRC_PHRASE = conf["max_src_phrase"].as<unsigned>();
-  const unsigned particles = conf["particles"].as<unsigned>();
-  const unsigned samples = conf["samples"].as<unsigned>();
-
-  if (!conf.count("model1")) {
-    cerr << argv[0] << "Please use --model1 to specify model 1 parameters\n";
-    return 1;
-  }
-  if (conf.count("random_seed"))
-    prng.reset(new MT19937(conf["random_seed"].as<uint32_t>()));
-  else
-    prng.reset(new MT19937);
-  MT19937& rng = *prng;
-
-  vector<vector<WordID> > corpuse, corpusf;
-  set<WordID> vocabe, vocabf;
-  cerr << "Reading corpus...\n";
-  ReadParallelCorpus(conf["input"].as<string>(), &corpusf, &corpuse, &vocabf, &vocabe);
-  cerr << "F-corpus size: " << corpusf.size() << " sentences\t (" << vocabf.size() << " word types)\n";
-  cerr << "E-corpus size: " << corpuse.size() << " sentences\t (" << vocabe.size() << " word types)\n";
-  assert(corpusf.size() == corpuse.size());
-
-  const int kLHS = -TD::Convert("X");
-  Model1 m1(conf["model1"].as<string>());
-  Model1 invm1(conf["inverse_model1"].as<string>());
-
-#if 0
-  PhraseConditionalBase lp0(m1, conf["model1_interpolation_weight"].as<double>(), vocabe.size());
-  MyConditionalModel m(lp0);
-#else
-  PhraseJointBase lp0(m1, conf["model1_interpolation_weight"].as<double>(), vocabe.size(), vocabf.size());
-  MyJointModel m(lp0);
-#endif
-
-  cerr << "Initializing reachability limits...\n";
-  vector<Particle> ps(corpusf.size());
-  vector<Reachability> reaches; reaches.reserve(corpusf.size());
-  for (int ci = 0; ci < corpusf.size(); ++ci)
-    reaches.push_back(Reachability(corpusf[ci].size(),
-                                   corpuse[ci].size(),
-                                   kMAX_SRC_PHRASE,
-                                   kMAX_TRG_PHRASE));
-  cerr << "Sampling...\n"; 
-  vector<Particle> tmp_p(10000);  // work space
-  SampleSet<prob_t> pfss;
-  for (int SS=0; SS < samples; ++SS) {
-    for (int ci = 0; ci < corpusf.size(); ++ci) {
-      vector<int>& src = corpusf[ci];
-      vector<int>& trg = corpuse[ci];
-      m.DecrementRules(ps[ci].rules);
-      m.DecrementJumps(ps[ci].src_jumps, src.size());
-
-      //BackwardEstimate be(m1, src, trg);
-      BackwardEstimateSym be(m1, invm1, src, trg);
-      const Reachability& r = reaches[ci];
-      vector<Particle> lps(particles);
-
-      for (int pi = 0; pi < particles; ++pi) {
-        Particle& p = lps[pi];
-        p.src_cv.resize(src.size(), false);
-      }
-
-      bool all_complete = false;
-      while(!all_complete) {
-        SampleSet<prob_t> ss;
-
-        // all particles have now been extended a bit, we will reweight them now
-        if (lps[0].trg_cov > 0)
-          FilterCrapParticlesAndReweight(&lps);
-
-        // loop over all particles and extend them
-        bool done_nothing = true;
-        for (int pi = 0; pi < particles; ++pi) {
-          Particle& p = lps[pi];
-          int tic = 0;
-          const int rejuv_freq = 1;
-          while(p.trg_cov < trg.size() && tic < rejuv_freq) {
-            ++tic;
-            done_nothing = false;
-            ss.clear();
-            TRule x; x.lhs_ = kLHS;
-            prob_t z;
-            int first_uncovered = src.size();
-            int last_uncovered = -1;
-            for (int i = 0; i < src.size(); ++i) {
-              const bool is_uncovered = !p.src_cv[i];
-              if (i < first_uncovered && is_uncovered) first_uncovered = i;
-              if (is_uncovered && i > last_uncovered) last_uncovered = i;
-            }
-            assert(last_uncovered > -1);
-            assert(first_uncovered < src.size());
-
-            for (int trg_len = 1; trg_len <= kMAX_TRG_PHRASE; ++trg_len) {
-              x.e_.push_back(trg[trg_len - 1 + p.trg_cov]);
-              for (int src_len = 1; src_len <= kMAX_SRC_PHRASE; ++src_len) {
-                if (!r.edges[p.src_cov][p.trg_cov][src_len][trg_len]) continue;
-
-                const int last_possible_start = last_uncovered - src_len + 1;
-                assert(last_possible_start >= 0);
-                //cerr << src_len << "," << trg_len << " is allowed. E=" << TD::GetString(x.e_) << endl;
-                //cerr << "  first_uncovered=" << first_uncovered << "  last_possible_start=" << last_possible_start << endl;
-                for (int i = first_uncovered; i <= last_possible_start; ++i) {
-                  if (p.src_cv[i]) continue;
-                  assert(ss.size() < tmp_p.size());  // if fails increase tmp_p size
-                  Particle& np = tmp_p[ss.size()];
-                  np = p;
-                  x.f_.clear();
-                  int gap_add = 0;
-                  bool bad = false;
-                  prob_t jp = prob_t::One();
-                  int prev_pos = p.prev_pos;
-                  for (int j = 0; j < src_len; ++j) {
-                    if ((j + i + gap_add) == src.size()) { bad = true; break; }
-                    while ((i+j+gap_add) < src.size() && p.src_cv[i + j + gap_add]) { ++gap_add; }
-                    if ((j + i + gap_add) == src.size()) { bad = true; break; }
-                    np.src_cv[i + j + gap_add] = true;
-                    x.f_.push_back(src[i + j + gap_add]);
-                    jp *= m.JumpProbability(i + j + gap_add - prev_pos, src.size());
-                    int jump = i + j + gap_add - prev_pos;
-                    assert(jump != 0);
-                    np.src_jumps.push_back(jump);
-                    prev_pos = i + j + gap_add;
-                  }
-                  if (bad) continue;
-                  np.prev_pos = prev_pos;
-                  np.src_cov += x.f_.size();
-                  np.trg_cov += x.e_.size();
-                  if (x.f_.size() != src_len) continue;
-                  prob_t rp = m.RuleProbability(x);
-                  np.gamma_last = rp * jp;
-                  const prob_t u = pow(np.gamma_last * be(np.src_cv, np.trg_cov), 0.2);
-                  //cerr << "**rule=" << x << endl;
-                  //cerr << "  u=" << log(u) << "  rule=" << rp << " jump=" << jp << endl;
-                  ss.add(u);
-                  np.rules.push_back(TRulePtr(new TRule(x)));
-                  z += u;
-
-                  const bool completed = (p.trg_cov == trg.size());
-                  if (completed) {
-                    int last_jump = src.size() - p.prev_pos;
-                    assert(last_jump > 0);
-                    p.src_jumps.push_back(last_jump);
-                    p.weight *= m.JumpProbability(last_jump, src.size());
-                  }
-                }
-              }
-            }
-            cerr << "number of edges to consider: " << ss.size() << endl;
-            const int sampled = rng.SelectSample(ss);
-            prob_t q_n = ss[sampled] / z;
-            p = tmp_p[sampled];
-            //m.IncrementRule(*p.rules.back());
-            p.weight *= p.gamma_last / q_n;
-            cerr << "[w=" << log(p.weight) << "]\tsampled rule: " << p.rules.back()->AsString() << endl;
-            cerr << p << endl;
-          }
-        } // loop over particles (pi = 0 .. particles)
-        if (done_nothing) all_complete = true;
-      }
-      pfss.clear();
-      for (int i = 0; i < lps.size(); ++i)
-        pfss.add(lps[i].weight);
-      const int sampled = rng.SelectSample(pfss);
-      ps[ci] = lps[sampled];
-      m.IncrementRules(lps[sampled].rules);
-      m.IncrementJumps(lps[sampled].src_jumps, src.size());
-      for (int i = 0; i < lps[sampled].rules.size(); ++i) { cerr << "S:\t" << lps[sampled].rules[i]->AsString() << "\n"; }
-      cerr << "tmp-LLH: " << log(m.Likelihood()) << endl;
-    }
-    cerr << "LLH: " << log(m.Likelihood()) << endl;
-    for (int sni = 0; sni < 5; ++sni) {
-      for (int i = 0; i < ps[sni].rules.size(); ++i) { cerr << "\t" << ps[sni].rules[i]->AsString() << endl; }
-    }
-  }
-  return 0;
-}
-
diff --git a/gi/pf/pfnaive.cc b/gi/pf/pfnaive.cc
deleted file mode 100644
index 958ec4e2..00000000
--- a/gi/pf/pfnaive.cc
+++ /dev/null
@@ -1,284 +0,0 @@
-#include <iostream>
-#include <tr1/memory>
-#include <queue>
-
-#include <boost/functional.hpp>
-#include <boost/program_options.hpp>
-#include <boost/program_options/variables_map.hpp>
-
-#include "pf.h"
-#include "base_distributions.h"
-#include "monotonic_pseg.h"
-#include "reachability.h"
-#include "viterbi.h"
-#include "hg.h"
-#include "trule.h"
-#include "tdict.h"
-#include "filelib.h"
-#include "dict.h"
-#include "sampler.h"
-#include "ccrp_nt.h"
-#include "ccrp_onetable.h"
-#include "corpus.h"
-
-using namespace std;
-using namespace tr1;
-namespace po = boost::program_options;
-
-boost::shared_ptr<MT19937> prng;
-
-void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
-  po::options_description opts("Configuration options");
-  opts.add_options()
-        ("samples,s",po::value<unsigned>()->default_value(1000),"Number of samples")
-        ("particles,p",po::value<unsigned>()->default_value(30),"Number of particles")
-        ("filter_frequency,f",po::value<unsigned>()->default_value(5),"Number of time steps between filterings")
-        ("input,i",po::value<string>(),"Read parallel data from")
-        ("max_src_phrase",po::value<unsigned>()->default_value(5),"Maximum length of source language phrases")
-        ("max_trg_phrase",po::value<unsigned>()->default_value(5),"Maximum length of target language phrases")
-        ("model1,m",po::value<string>(),"Model 1 parameters (used in base distribution)")
-        ("inverse_model1,M",po::value<string>(),"Inverse Model 1 parameters (used in backward estimate)")
-        ("model1_interpolation_weight",po::value<double>()->default_value(0.95),"Mixing proportion of model 1 with uniform target distribution")
-        ("random_seed,S",po::value<uint32_t>(), "Random seed");
-  po::options_description clo("Command line options");
-  clo.add_options()
-        ("config", po::value<string>(), "Configuration file")
-        ("help,h", "Print this help message and exit");
-  po::options_description dconfig_options, dcmdline_options;
-  dconfig_options.add(opts);
-  dcmdline_options.add(opts).add(clo);
-  
-  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
-  if (conf->count("config")) {
-    ifstream config((*conf)["config"].as<string>().c_str());
-    po::store(po::parse_config_file(config, dconfig_options), *conf);
-  }
-  po::notify(*conf);
-
-  if (conf->count("help") || (conf->count("input") == 0)) {
-    cerr << dcmdline_options << endl;
-    exit(1);
-  }
-}
-
-struct BackwardEstimateSym {
-  BackwardEstimateSym(const Model1& m1,
-                      const Model1& invm1, const vector<WordID>& src, const vector<WordID>& trg) :
-      model1_(m1), invmodel1_(invm1), src_(src), trg_(trg) {
-  }
-  const prob_t& operator()(unsigned src_cov, unsigned trg_cov) const {
-    assert(src_cov <= src_.size());
-    assert(trg_cov <= trg_.size());
-    prob_t& e = cache_[src_cov][trg_cov];
-    if (e.is_0()) {
-      if (trg_cov == trg_.size()) { e = prob_t::One(); return e; }
-      vector<WordID> r(src_.size() + 1); r.clear();
-      for (int i = src_cov; i < src_.size(); ++i)
-        r.push_back(src_[i]);
-      r.push_back(0);  // NULL word
-      const prob_t uniform_alignment(1.0 / r.size());
-      e.logeq(Md::log_poisson(trg_.size() - trg_cov, r.size() - 1)); // p(trg len remaining | src len remaining)
-      for (unsigned j = trg_cov; j < trg_.size(); ++j) {
-        prob_t p;
-        for (unsigned i = 0; i < r.size(); ++i)
-          p += model1_(r[i], trg_[j]);
-        if (p.is_0()) {
-          cerr << "ERROR: p(" << TD::Convert(trg_[j]) << " | " << TD::GetString(r) << ") = 0!\n";
-          abort();
-        }
-        p *= uniform_alignment;
-        e *= p;
-      }
-      r.pop_back();
-      const prob_t inv_uniform(1.0 / (trg_.size() - trg_cov + 1.0));
-      prob_t inv;
-      inv.logeq(Md::log_poisson(r.size(), trg_.size() - trg_cov));
-      for (unsigned i = 0; i < r.size(); ++i) {
-        prob_t p;
-        for (unsigned j = trg_cov - 1; j < trg_.size(); ++j)
-          p += invmodel1_(j < trg_cov ? 0 : trg_[j], r[i]);
-        if (p.is_0()) {
-          cerr << "ERROR: p_inv(" << TD::Convert(r[i]) << " | " << TD::GetString(trg_) << ") = 0!\n";
-          abort();
-        }
-        p *= inv_uniform;
-        inv *= p;
-      }
-      prob_t x = pow(e * inv, 0.5);
-      e = x;
-      //cerr << "Forward: " << log(e) << "\tBackward: " << log(inv) << "\t prop: " << log(x) << endl;
-    }
-    return e;
-  }
-  const Model1& model1_;
-  const Model1& invmodel1_;
-  const vector<WordID>& src_;
-  const vector<WordID>& trg_;
-  mutable unordered_map<unsigned, map<unsigned, prob_t> > cache_;
-};
-
-struct Particle {
-  Particle() : weight(prob_t::One()), src_cov(), trg_cov() {}
-  prob_t weight;
-  prob_t gamma_last;
-  vector<TRulePtr> rules;
-  int src_cov;
-  int trg_cov;
-};
-
-ostream& operator<<(ostream& o, const vector<bool>& v) {
-  for (int i = 0; i < v.size(); ++i)
-    o << (v[i] ? '1' : '0');
-  return o;
-}
-ostream& operator<<(ostream& o, const Particle& p) {
-  o << "[src_cov=" << p.src_cov << " trg_cov=" << p.trg_cov << " num_rules=" << p.rules.size() << "  w=" << log(p.weight) << ']';
-  return o;
-}
-
-int main(int argc, char** argv) {
-  po::variables_map conf;
-  InitCommandLine(argc, argv, &conf);
-  const unsigned kMAX_TRG_PHRASE = conf["max_trg_phrase"].as<unsigned>();
-  const unsigned kMAX_SRC_PHRASE = conf["max_src_phrase"].as<unsigned>();
-  const unsigned particles = conf["particles"].as<unsigned>();
-  const unsigned samples = conf["samples"].as<unsigned>();
-  const unsigned rejuv_freq = conf["filter_frequency"].as<unsigned>();
-
-  if (!conf.count("model1")) {
-    cerr << argv[0] << "Please use --model1 to specify model 1 parameters\n";
-    return 1;
-  }
-  if (conf.count("random_seed"))
-    prng.reset(new MT19937(conf["random_seed"].as<uint32_t>()));
-  else
-    prng.reset(new MT19937);
-  MT19937& rng = *prng;
-
-  vector<vector<WordID> > corpuse, corpusf;
-  set<WordID> vocabe, vocabf;
-  cerr << "Reading corpus...\n";
-  corpus::ReadParallelCorpus(conf["input"].as<string>(), &corpusf, &corpuse, &vocabf, &vocabe);
-  cerr << "F-corpus size: " << corpusf.size() << " sentences\t (" << vocabf.size() << " word types)\n";
-  cerr << "E-corpus size: " << corpuse.size() << " sentences\t (" << vocabe.size() << " word types)\n";
-  assert(corpusf.size() == corpuse.size());
-
-  const int kLHS = -TD::Convert("X");
-  Model1 m1(conf["model1"].as<string>());
-  Model1 invm1(conf["inverse_model1"].as<string>());
-
-  PhraseJointBase lp0(m1, conf["model1_interpolation_weight"].as<double>(), vocabe.size(), vocabf.size());
-  PhraseJointBase_BiDir alp0(m1, invm1, conf["model1_interpolation_weight"].as<double>(), vocabe.size(), vocabf.size());
-  MonotonicParallelSegementationModel<PhraseJointBase_BiDir> m(alp0);
-  TRule xx("[X] ||| ms. kimura ||| MS. KIMURA ||| X=0");
-  cerr << xx << endl << lp0(xx) << " " << alp0(xx) << endl;
-  TRule xx12("[X] ||| . ||| PHARMACY . ||| X=0");
-  TRule xx21("[X] ||| pharmacy . ||| . ||| X=0");
-//  TRule xx22("[X] ||| . ||| . ||| X=0");
-  TRule xx22("[X] ||| . ||| THE . ||| X=0");
-  cerr << xx12 << "\t" << lp0(xx12) << " " << alp0(xx12) << endl;
-  cerr << xx21 << "\t" << lp0(xx21) << " " << alp0(xx21) << endl;
-  cerr << xx22 << "\t" << lp0(xx22) << " " << alp0(xx22) << endl;
-
-  cerr << "Initializing reachability limits...\n";
-  vector<Particle> ps(corpusf.size());
-  vector<Reachability> reaches; reaches.reserve(corpusf.size());
-  for (int ci = 0; ci < corpusf.size(); ++ci)
-    reaches.push_back(Reachability(corpusf[ci].size(),
-                                   corpuse[ci].size(),
-                                   kMAX_SRC_PHRASE,
-                                   kMAX_TRG_PHRASE));
-  cerr << "Sampling...\n"; 
-  vector<Particle> tmp_p(10000);  // work space
-  SampleSet<prob_t> pfss;
-  SystematicResampleFilter<Particle> filter(&rng);
-  // MultinomialResampleFilter<Particle> filter(&rng);
-  for (int SS=0; SS < samples; ++SS) {
-    for (int ci = 0; ci < corpusf.size(); ++ci) {
-      vector<int>& src = corpusf[ci];
-      vector<int>& trg = corpuse[ci];
-      m.DecrementRulesAndStops(ps[ci].rules);
-      const prob_t q_stop = m.StopProbability();
-      const prob_t q_cont = m.ContinueProbability();
-      cerr << "P(stop)=" << q_stop << "\tP(continue)=" <<q_cont << endl;
-
-      BackwardEstimateSym be(m1, invm1, src, trg);
-      const Reachability& r = reaches[ci];
-      vector<Particle> lps(particles);
-
-      bool all_complete = false;
-      while(!all_complete) {
-        SampleSet<prob_t> ss;
-
-        // all particles have now been extended a bit, we will reweight them now
-        if (lps[0].trg_cov > 0)
-          filter(&lps);
-
-        // loop over all particles and extend them
-        bool done_nothing = true;
-        for (int pi = 0; pi < particles; ++pi) {
-          Particle& p = lps[pi];
-          int tic = 0;
-          while(p.trg_cov < trg.size() && tic < rejuv_freq) {
-            ++tic;
-            done_nothing = false;
-            ss.clear();
-            TRule x; x.lhs_ = kLHS;
-            prob_t z;
-
-            for (int trg_len = 1; trg_len <= kMAX_TRG_PHRASE; ++trg_len) {
-              x.e_.push_back(trg[trg_len - 1 + p.trg_cov]);
-              for (int src_len = 1; src_len <= kMAX_SRC_PHRASE; ++src_len) {
-                if (!r.edges[p.src_cov][p.trg_cov][src_len][trg_len]) continue;
-
-                int i = p.src_cov;
-                assert(ss.size() < tmp_p.size());  // if fails increase tmp_p size
-                Particle& np = tmp_p[ss.size()];
-                np = p;
-                x.f_.clear();
-                for (int j = 0; j < src_len; ++j)
-                  x.f_.push_back(src[i + j]);
-                np.src_cov += x.f_.size();
-                np.trg_cov += x.e_.size();
-                const bool stop_now = (np.src_cov == src_len && np.trg_cov == trg_len);
-                prob_t rp = m.RuleProbability(x) * (stop_now ? q_stop : q_cont);
-                np.gamma_last = rp;
-                const prob_t u = pow(np.gamma_last * pow(be(np.src_cov, np.trg_cov), 1.2), 0.1);
-                //cerr << "**rule=" << x << endl;
-                //cerr << "  u=" << log(u) << "  rule=" << rp << endl;
-                ss.add(u);
-                np.rules.push_back(TRulePtr(new TRule(x)));
-                z += u;
-              }
-            }
-            //cerr << "number of edges to consider: " << ss.size() << endl;
-            const int sampled = rng.SelectSample(ss);
-            prob_t q_n = ss[sampled] / z;
-            p = tmp_p[sampled];
-            //m.IncrementRule(*p.rules.back());
-            p.weight *= p.gamma_last / q_n;
-            //cerr << "[w=" << log(p.weight) << "]\tsampled rule: " << p.rules.back()->AsString() << endl;
-            //cerr << p << endl;
-          }
-        } // loop over particles (pi = 0 .. particles)
-        if (done_nothing) all_complete = true;
-        prob_t wv = prob_t::Zero();
-        for (int pp = 0; pp < lps.size(); ++pp)
-          wv += lps[pp].weight;
-        for (int pp = 0; pp < lps.size(); ++pp)
-          lps[pp].weight /= wv;
-      }
-      pfss.clear();
-      for (int i = 0; i < lps.size(); ++i)
-        pfss.add(lps[i].weight);
-      const int sampled = rng.SelectSample(pfss);
-      ps[ci] = lps[sampled];
-      m.IncrementRulesAndStops(lps[sampled].rules);
-      for (int i = 0; i < lps[sampled].rules.size(); ++i) { cerr << "S:\t" << lps[sampled].rules[i]->AsString() << "\n"; }
-      cerr << "tmp-LLH: " << log(m.Likelihood()) << endl;
-    }
-    cerr << "LLH: " << log(m.Likelihood()) << endl;
-  }
-  return 0;
-}
-
diff --git a/gi/pf/poisson_uniform_word_model.h b/gi/pf/poisson_uniform_word_model.h
deleted file mode 100644
index 76204a0e..00000000
--- a/gi/pf/poisson_uniform_word_model.h
+++ /dev/null
@@ -1,50 +0,0 @@
-#ifndef _POISSON_UNIFORM_WORD_MODEL_H_
-#define _POISSON_UNIFORM_WORD_MODEL_H_
-
-#include <cmath>
-#include <vector>
-#include "prob.h"
-#include "m.h"
-
-// len ~ Poisson(lambda)
-//   for (1..len)
-//     e_i ~ Uniform({Vocabulary})
-struct PoissonUniformWordModel {
-  explicit PoissonUniformWordModel(const unsigned vocab_size,
-                                   const unsigned alphabet_size,
-                                   const double mean_len = 5) :
-    lh(prob_t::One()),
-    v0(-std::log(vocab_size)),
-    u0(-std::log(alphabet_size)),
-    mean_length(mean_len) {}
-
-  void ResampleHyperparameters(MT19937*) {}
-
-  inline prob_t operator()(const std::vector<WordID>& s) const {
-    prob_t p;
-    p.logeq(Md::log_poisson(s.size(), mean_length) + s.size() * u0);
-    //p.logeq(v0);
-    return p;
-  }
-
-  inline void Increment(const std::vector<WordID>& w, MT19937*) {
-    lh *= (*this)(w);
-  }
-
-  inline void Decrement(const std::vector<WordID>& w, MT19937 *) {
-    lh /= (*this)(w);
-  }
-
-  inline prob_t Likelihood() const { return lh; }
-
-  void Summary() const {}
-
- private:
-
-  prob_t lh;  // keeps track of the draws from the base distribution
-  const double v0;  // uniform log prob of generating a word
-  const double u0;  // uniform log prob of generating a letter
-  const double mean_length;  // mean length of a word in the base distribution
-};
-
-#endif
diff --git a/gi/pf/pyp_lm.cc b/gi/pf/pyp_lm.cc
deleted file mode 100644
index e2b67e17..00000000
--- a/gi/pf/pyp_lm.cc
+++ /dev/null
@@ -1,209 +0,0 @@
-#include <iostream>
-#include <tr1/memory>
-#include <queue>
-
-#include <boost/functional.hpp>
-#include <boost/program_options.hpp>
-#include <boost/program_options/variables_map.hpp>
-
-#include "corpus_tools.h"
-#include "m.h"
-#include "tdict.h"
-#include "sampler.h"
-#include "ccrp.h"
-#include "tied_resampler.h"
-
-// A not very memory-efficient implementation of an N-gram LM based on PYPs
-// as described in Y.-W. Teh. (2006) A Hierarchical Bayesian Language Model
-// based on Pitman-Yor Processes. In Proc. ACL.
-
-// I use templates to handle the recursive formalation of the prior, so
-// the order of the model has to be specified here, at compile time:
-#define kORDER 3
-
-using namespace std;
-using namespace tr1;
-namespace po = boost::program_options;
-
-boost::shared_ptr<MT19937> prng;
-
-void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
-  po::options_description opts("Configuration options");
-  opts.add_options()
-        ("samples,n",po::value<unsigned>()->default_value(300),"Number of samples")
-        ("train,i",po::value<string>(),"Training data file")
-        ("test,T",po::value<string>(),"Test data file")
-        ("discount_prior_a,a",po::value<double>()->default_value(1.0), "discount ~ Beta(a,b): a=this")
-        ("discount_prior_b,b",po::value<double>()->default_value(1.0), "discount ~ Beta(a,b): b=this")
-        ("strength_prior_s,s",po::value<double>()->default_value(1.0), "strength ~ Gamma(s,r): s=this")
-        ("strength_prior_r,r",po::value<double>()->default_value(1.0), "strength ~ Gamma(s,r): r=this")
-        ("random_seed,S",po::value<uint32_t>(), "Random seed");
-  po::options_description clo("Command line options");
-  clo.add_options()
-        ("config", po::value<string>(), "Configuration file")
-        ("help", "Print this help message and exit");
-  po::options_description dconfig_options, dcmdline_options;
-  dconfig_options.add(opts);
-  dcmdline_options.add(opts).add(clo);
-  
-  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
-  if (conf->count("config")) {
-    ifstream config((*conf)["config"].as<string>().c_str());
-    po::store(po::parse_config_file(config, dconfig_options), *conf);
-  }
-  po::notify(*conf);
-
-  if (conf->count("help") || (conf->count("train") == 0)) {
-    cerr << dcmdline_options << endl;
-    exit(1);
-  }
-}
-
-template <unsigned N> struct PYPLM;
-
-// uniform base distribution (0-gram model)
-template<> struct PYPLM<0> {
-  PYPLM(unsigned vs, double, double, double, double) : p0(1.0 / vs), draws() {}
-  void increment(WordID, const vector<WordID>&, MT19937*) { ++draws; }
-  void decrement(WordID, const vector<WordID>&, MT19937*) { --draws; assert(draws >= 0); }
-  double prob(WordID, const vector<WordID>&) const { return p0; }
-  void resample_hyperparameters(MT19937*) {}
-  double log_likelihood() const { return draws * log(p0); }
-  const double p0;
-  int draws;
-};
-
-// represents an N-gram LM
-template <unsigned N> struct PYPLM {
-  PYPLM(unsigned vs, double da, double db, double ss, double sr) :
-      backoff(vs, da, db, ss, sr),
-      tr(da, db, ss, sr, 0.8, 1.0),
-      lookup(N-1) {}
-  void increment(WordID w, const vector<WordID>& context, MT19937* rng) {
-    const double bo = backoff.prob(w, context);
-    for (unsigned i = 0; i < N-1; ++i)
-      lookup[i] = context[context.size() - 1 - i];
-    typename unordered_map<vector<WordID>, CCRP<WordID>, boost::hash<vector<WordID> > >::iterator it = p.find(lookup);
-    if (it == p.end()) {
-      it = p.insert(make_pair(lookup, CCRP<WordID>(0.5,1))).first;
-      tr.Add(&it->second);  // add to resampler
-    }
-    if (it->second.increment(w, bo, rng))
-      backoff.increment(w, context, rng);
-  }
-  void decrement(WordID w, const vector<WordID>& context, MT19937* rng) {
-    for (unsigned i = 0; i < N-1; ++i)
-      lookup[i] = context[context.size() - 1 - i];
-    typename unordered_map<vector<WordID>, CCRP<WordID>, boost::hash<vector<WordID> > >::iterator it = p.find(lookup);
-    assert(it != p.end());
-    if (it->second.decrement(w, rng))
-      backoff.decrement(w, context, rng);
-  }
-  double prob(WordID w, const vector<WordID>& context) const {
-    const double bo = backoff.prob(w, context);
-    for (unsigned i = 0; i < N-1; ++i)
-      lookup[i] = context[context.size() - 1 - i];
-    typename unordered_map<vector<WordID>, CCRP<WordID>, boost::hash<vector<WordID> > >::const_iterator it = p.find(lookup);
-    if (it == p.end()) return bo;
-    return it->second.prob(w, bo);
-  }
-
-  double log_likelihood() const {
-    double llh = backoff.log_likelihood();
-    typename unordered_map<vector<WordID>, CCRP<WordID>, boost::hash<vector<WordID> > >::const_iterator it;
-    for (it = p.begin(); it != p.end(); ++it)
-      llh += it->second.log_crp_prob();
-    llh += tr.LogLikelihood();
-    return llh;
-  }
-
-  void resample_hyperparameters(MT19937* rng) {
-    tr.ResampleHyperparameters(rng);
-    backoff.resample_hyperparameters(rng);
-  }
-
-  PYPLM<N-1> backoff;
-  TiedResampler<CCRP<WordID> > tr;
-  double discount_a, discount_b, strength_s, strength_r;
-  double d, strength;
-  mutable vector<WordID> lookup;  // thread-local
-  unordered_map<vector<WordID>, CCRP<WordID>, boost::hash<vector<WordID> > > p;
-};
-
-int main(int argc, char** argv) {
-  po::variables_map conf;
-
-  InitCommandLine(argc, argv, &conf);
-  const unsigned samples = conf["samples"].as<unsigned>();
-  if (conf.count("random_seed"))
-    prng.reset(new MT19937(conf["random_seed"].as<uint32_t>()));
-  else
-    prng.reset(new MT19937);
-  MT19937& rng = *prng;
-  vector<vector<WordID> > corpuse;
-  set<WordID> vocabe;
-  const WordID kEOS = TD::Convert("</s>");
-  cerr << "Reading corpus...\n";
-  CorpusTools::ReadFromFile(conf["train"].as<string>(), &corpuse, &vocabe);
-  cerr << "E-corpus size: " << corpuse.size() << " sentences\t (" << vocabe.size() << " word types)\n";
-  vector<vector<WordID> > test;
-  if (conf.count("test"))
-    CorpusTools::ReadFromFile(conf["test"].as<string>(), &test);
-  else
-    test = corpuse;
-  PYPLM<kORDER> lm(vocabe.size(),
-                   conf["discount_prior_a"].as<double>(),
-                   conf["discount_prior_b"].as<double>(),
-                   conf["strength_prior_s"].as<double>(),
-                   conf["strength_prior_r"].as<double>());
-  vector<WordID> ctx(kORDER - 1, TD::Convert("<s>"));
-  for (int SS=0; SS < samples; ++SS) {
-    for (int ci = 0; ci < corpuse.size(); ++ci) {
-      ctx.resize(kORDER - 1);
-      const vector<WordID>& s = corpuse[ci];
-      for (int i = 0; i <= s.size(); ++i) {
-        WordID w = (i < s.size() ? s[i] : kEOS);
-        if (SS > 0) lm.decrement(w, ctx, &rng);
-        lm.increment(w, ctx, &rng);
-        ctx.push_back(w);
-      }
-      if (SS > 0) lm.decrement(kEOS, ctx, &rng);
-      lm.increment(kEOS, ctx, &rng);
-    }
-    if (SS % 10 == 9) {
-      cerr << " [LLH=" << lm.log_likelihood() << "]" << endl;
-      if (SS % 20 == 19) lm.resample_hyperparameters(&rng);
-    } else { cerr << '.' << flush; }
-  }
-  double llh = 0;
-  unsigned cnt = 0;
-  unsigned oovs = 0;
-  for (int ci = 0; ci < test.size(); ++ci) {
-    ctx.resize(kORDER - 1);
-    const vector<WordID>& s = test[ci];
-    for (int i = 0; i <= s.size(); ++i) {
-      WordID w = (i < s.size() ? s[i] : kEOS);
-      double lp = log(lm.prob(w, ctx)) / log(2);
-      if (i < s.size() && vocabe.count(w) == 0) {
-        cerr << "**OOV ";
-        ++oovs;
-        lp = 0;
-      }
-      cerr << "p(" << TD::Convert(w) << " |";
-      for (int j = ctx.size() + 1 - kORDER; j < ctx.size(); ++j)
-        cerr << ' ' << TD::Convert(ctx[j]);
-      cerr << ") = " << lp << endl;
-      ctx.push_back(w);
-      llh -= lp;
-      cnt++;
-    }
-  }
-  cerr << "  Log_10 prob: " << (-llh * log(2) / log(10)) << endl;
-  cerr << "        Count: " << cnt << endl;
-  cerr << "         OOVs: " << oovs << endl;
-  cerr << "Cross-entropy: " << (llh / cnt) << endl;
-  cerr << "   Perplexity: " << pow(2, llh / cnt) << endl;
-  return 0;
-}
-
-
diff --git a/gi/pf/pyp_tm.cc b/gi/pf/pyp_tm.cc
deleted file mode 100644
index 6bc8a5bf..00000000
--- a/gi/pf/pyp_tm.cc
+++ /dev/null
@@ -1,128 +0,0 @@
-#include "pyp_tm.h"
-
-#include <tr1/unordered_map>
-#include <iostream>
-#include <queue>
-
-#include "tdict.h"
-#include "ccrp.h"
-#include "pyp_word_model.h"
-#include "tied_resampler.h"
-
-using namespace std;
-using namespace std::tr1;
-
-struct FreqBinner {
-  FreqBinner(const std::string& fname) { fd_.Load(fname); }
-  unsigned NumberOfBins() const { return fd_.Max() + 1; }
-  unsigned Bin(const WordID& w) const { return fd_.LookUp(w); }
-  FreqDict<unsigned> fd_;
-};
-
-template <typename Base, class Binner = FreqBinner>
-struct ConditionalPYPWordModel {
-  ConditionalPYPWordModel(Base* b, const Binner* bnr = NULL) :
-      base(*b),
-      binner(bnr),
-      btr(binner ? binner->NumberOfBins() + 1u : 2u) {}
-
-  void Summary() const {
-    cerr << "Number of conditioning contexts: " << r.size() << endl;
-    for (RuleModelHash::const_iterator it = r.begin(); it != r.end(); ++it) {
-      cerr << TD::Convert(it->first) << "   \tPYP(d=" << it->second.discount() << ",s=" << it->second.strength() << ") --------------------------" << endl;
-      for (CCRP<vector<WordID> >::const_iterator i2 = it->second.begin(); i2 != it->second.end(); ++i2)
-        cerr << "   " << i2->second.total_dish_count_ << '\t' << TD::GetString(i2->first) << endl;
-    }
-  }
-
-  void ResampleHyperparameters(MT19937* rng) {
-    btr.ResampleHyperparameters(rng);
-  } 
-
-  prob_t Prob(const WordID src, const vector<WordID>& trglets) const {
-    RuleModelHash::const_iterator it = r.find(src);
-    if (it == r.end()) {
-      return base(trglets);
-    } else {
-      return it->second.prob(trglets, base(trglets));
-    }
-  }
-
-  void Increment(const WordID src, const vector<WordID>& trglets, MT19937* rng) {
-    RuleModelHash::iterator it = r.find(src);
-    if (it == r.end()) {
-      it = r.insert(make_pair(src, CCRP<vector<WordID> >(0.5,1.0))).first;
-      static const WordID kNULL = TD::Convert("NULL");
-      unsigned bin = (src == kNULL ? 0 : 1);
-      if (binner && bin) { bin = binner->Bin(src) + 1; }
-      btr.Add(bin, &it->second);
-    }
-    if (it->second.increment(trglets, base(trglets), rng))
-      base.Increment(trglets, rng);
-  }
-
-  void Decrement(const WordID src, const vector<WordID>& trglets, MT19937* rng) {
-    RuleModelHash::iterator it = r.find(src);
-    assert(it != r.end());
-    if (it->second.decrement(trglets, rng)) {
-      base.Decrement(trglets, rng);
-    }
-  }
-
-  prob_t Likelihood() const {
-    prob_t p = prob_t::One();
-    for (RuleModelHash::const_iterator it = r.begin(); it != r.end(); ++it) {
-      prob_t q; q.logeq(it->second.log_crp_prob());
-      p *= q;
-    }
-    return p;
-  }
-
-  unsigned UniqueConditioningContexts() const {
-    return r.size();
-  }
-
-  // TODO tie PYP hyperparameters based on source word frequency bins
-  Base& base;
-  const Binner* binner;
-  BinTiedResampler<CCRP<vector<WordID> > > btr;
-  typedef unordered_map<WordID, CCRP<vector<WordID> > > RuleModelHash;
-  RuleModelHash r;
-};
-
-PYPLexicalTranslation::PYPLexicalTranslation(const vector<vector<WordID> >& lets,
-                                             const unsigned vocab_size,
-                                             const unsigned num_letters) :
-    letters(lets),
-    base(vocab_size, num_letters, 5),
-    tmodel(new ConditionalPYPWordModel<PoissonUniformWordModel>(&base, new FreqBinner("10k.freq"))),
-    kX(-TD::Convert("X")) {}
-
-void PYPLexicalTranslation::Summary() const {
-  tmodel->Summary();
-}
-
-prob_t PYPLexicalTranslation::Likelihood() const {
-  return tmodel->Likelihood() * base.Likelihood();
-}
-
-void PYPLexicalTranslation::ResampleHyperparameters(MT19937* rng) {
-  tmodel->ResampleHyperparameters(rng);
-}
-
-unsigned PYPLexicalTranslation::UniqueConditioningContexts() const {
-  return tmodel->UniqueConditioningContexts();
-}
-
-prob_t PYPLexicalTranslation::Prob(WordID src, WordID trg) const {
-  return tmodel->Prob(src, letters[trg]);
-}
-
-void PYPLexicalTranslation::Increment(WordID src, WordID trg, MT19937* rng) {
-  tmodel->Increment(src, letters[trg], rng);
-}
-
-void PYPLexicalTranslation::Decrement(WordID src, WordID trg, MT19937* rng) {
-  tmodel->Decrement(src, letters[trg], rng);
-}
-
diff --git a/gi/pf/pyp_tm.h b/gi/pf/pyp_tm.h
deleted file mode 100644
index 2b076a25..00000000
--- a/gi/pf/pyp_tm.h
+++ /dev/null
@@ -1,36 +0,0 @@
-#ifndef PYP_LEX_TRANS
-#define PYP_LEX_TRANS
-
-#include <vector>
-#include "wordid.h"
-#include "prob.h"
-#include "sampler.h"
-#include "freqdict.h"
-#include "poisson_uniform_word_model.h"
-
-struct FreqBinner;
-template <typename T, class B> struct ConditionalPYPWordModel;
-
-struct PYPLexicalTranslation {
-  explicit PYPLexicalTranslation(const std::vector<std::vector<WordID> >& lets,
-                                 const unsigned vocab_size,
-                                 const unsigned num_letters);
-
-  prob_t Likelihood() const;
-
-  void ResampleHyperparameters(MT19937* rng);
-  prob_t Prob(WordID src, WordID trg) const;  // return p(trg | src)
-  void Summary() const;
-  void Increment(WordID src, WordID trg, MT19937* rng);
-  void Decrement(WordID src, WordID trg, MT19937* rng);
-  unsigned UniqueConditioningContexts() const;
-
- private:
-  const std::vector<std::vector<WordID> >& letters;   // spelling dictionary
-  PoissonUniformWordModel base;  // "generator" of English types
-  ConditionalPYPWordModel<PoissonUniformWordModel, FreqBinner>* tmodel;  // translation distributions
-                      // (model English word | French word)
-  const WordID kX;
-};
-
-#endif
diff --git a/gi/pf/pyp_word_model.h b/gi/pf/pyp_word_model.h
deleted file mode 100644
index 224a9034..00000000
--- a/gi/pf/pyp_word_model.h
+++ /dev/null
@@ -1,62 +0,0 @@
-#ifndef _PYP_WORD_MODEL_H_
-#define _PYP_WORD_MODEL_H_
-
-#include <iostream>
-#include <cmath>
-#include <vector>
-#include "prob.h"
-#include "ccrp.h"
-#include "m.h"
-#include "tdict.h"
-#include "os_phrase.h"
-
-// PYP(d,s,poisson-uniform) represented as a CRP
-template <class Base>
-struct PYPWordModel {
-  explicit PYPWordModel(Base* b) :
-      base(*b),
-      r(1,1,1,1,0.66,50.0)
-    {}
-
-  void ResampleHyperparameters(MT19937* rng) {
-    r.resample_hyperparameters(rng);
-    std::cerr << " PYPWordModel(d=" << r.discount() << ",s=" << r.strength() << ")\n";
-  }
-
-  inline prob_t operator()(const std::vector<WordID>& s) const {
-    return r.prob(s, base(s));
-  }
-
-  inline void Increment(const std::vector<WordID>& s, MT19937* rng) {
-    if (r.increment(s, base(s), rng))
-      base.Increment(s, rng);
-  }
-
-  inline void Decrement(const std::vector<WordID>& s, MT19937 *rng) {
-    if (r.decrement(s, rng))
-      base.Decrement(s, rng);
-  }
-
-  inline prob_t Likelihood() const {
-    prob_t p; p.logeq(r.log_crp_prob());
-    p *= base.Likelihood();
-    return p;
-  }
-
-  void Summary() const {
-    std::cerr << "PYPWordModel: generations=" << r.num_customers()
-         << " PYP(d=" << r.discount() << ",s=" << r.strength() << ')' << std::endl;
-    for (typename CCRP<std::vector<WordID> >::const_iterator it = r.begin(); it != r.end(); ++it) {
-      std::cerr << "   " << it->second.total_dish_count_
-                << " (on " << it->second.table_counts_.size() << " tables) "
-                << TD::GetString(it->first) << std::endl;
-    }
-  }
-
- private:
-
-  Base& base;  // keeps track of the draws from the base distribution
-  CCRP<std::vector<WordID> > r;
-};
-
-#endif
diff --git a/gi/pf/quasi_model2.h b/gi/pf/quasi_model2.h
deleted file mode 100644
index 4075affe..00000000
--- a/gi/pf/quasi_model2.h
+++ /dev/null
@@ -1,177 +0,0 @@
-#ifndef _QUASI_MODEL2_H_
-#define _QUASI_MODEL2_H_
-
-#include <vector>
-#include <cmath>
-#include <tr1/unordered_map>
-#include "boost/functional.hpp"
-#include "prob.h"
-#include "array2d.h"
-#include "slice_sampler.h"
-#include "m.h"
-#include "have_64_bits.h"
-
-struct AlignmentObservation {
-  AlignmentObservation() : src_len(), trg_len(), j(), a_j() {}
-  AlignmentObservation(unsigned sl, unsigned tl, unsigned tw, unsigned sw) :
-      src_len(sl), trg_len(tl), j(tw), a_j(sw) {}
-  unsigned short src_len;
-  unsigned short trg_len;
-  unsigned short j;
-  unsigned short a_j;
-};
-
-#ifdef HAVE_64_BITS
-inline size_t hash_value(const AlignmentObservation& o) {
-  return reinterpret_cast<const size_t&>(o);
-}
-inline bool operator==(const AlignmentObservation& a, const AlignmentObservation& b) {
-  return hash_value(a) == hash_value(b);
-}
-#else
-inline size_t hash_value(const AlignmentObservation& o) {
-  size_t h = 1;
-  boost::hash_combine(h, o.src_len);
-  boost::hash_combine(h, o.trg_len);
-  boost::hash_combine(h, o.j);
-  boost::hash_combine(h, o.a_j);
-  return h;
-}
-#endif
-
-struct QuasiModel2 {
-  explicit QuasiModel2(double alpha, double pnull = 0.1) :
-      alpha_(alpha),
-      pnull_(pnull),
-      pnotnull_(1 - pnull) {}
-
-  // a_j = 0 => NULL; src_len does *not* include null
-  prob_t Prob(unsigned a_j, unsigned j, unsigned src_len, unsigned trg_len) const {
-    if (!a_j) return pnull_;
-    return pnotnull_ *
-       prob_t(UnnormalizedProb(a_j, j, src_len, trg_len, alpha_) / GetOrComputeZ(j, src_len, trg_len));
-  }
-
-  void Increment(unsigned a_j, unsigned j, unsigned src_len, unsigned trg_len) {
-    assert(a_j <= src_len);
-    assert(j < trg_len);
-    ++obs_[AlignmentObservation(src_len, trg_len, j, a_j)];
-  }
-
-  void Decrement(unsigned a_j, unsigned j, unsigned src_len, unsigned trg_len) {
-    const AlignmentObservation ao(src_len, trg_len, j, a_j);
-    int &cc = obs_[ao];
-    assert(cc > 0);
-    --cc;
-    if (!cc) obs_.erase(ao);
-  }
-
-  struct PNullResampler {
-    PNullResampler(const QuasiModel2& m) : m_(m) {}
-    const QuasiModel2& m_;
-    double operator()(const double& proposed_pnull) const {
-      return log(m_.Likelihood(m_.alpha_, proposed_pnull));
-    }
-  };
-
-  struct AlphaResampler {
-    AlphaResampler(const QuasiModel2& m) : m_(m) {}
-    const QuasiModel2& m_;
-    double operator()(const double& proposed_alpha) const {
-      return log(m_.Likelihood(proposed_alpha, m_.pnull_.as_float()));
-    }
-  };
-
-  void ResampleHyperparameters(MT19937* rng, const unsigned nloop = 5, const unsigned niterations = 10) {
-    const PNullResampler dr(*this);
-    const AlphaResampler ar(*this);
-    for (unsigned i = 0; i < nloop; ++i) {
-      double pnull = slice_sampler1d(dr, pnull_.as_float(), *rng, 0.00000001,
-                            1.0, 0.0, niterations, 100*niterations);
-      pnull_ = prob_t(pnull);
-      alpha_ = slice_sampler1d(ar, alpha_, *rng, 0.00000001,
-                              std::numeric_limits<double>::infinity(), 0.0, niterations, 100*niterations);
-    }
-    std::cerr << "QuasiModel2(alpha=" << alpha_ << ",p_null="
-              << pnull_.as_float() << ") = " << Likelihood() << std::endl;
-    zcache_.clear();
-  }
-
-  prob_t Likelihood() const {
-    return Likelihood(alpha_, pnull_.as_float());
-  }
-
-  prob_t Likelihood(double alpha, double ppnull) const {
-    const prob_t pnull(ppnull);
-    const prob_t pnotnull(1 - ppnull);
-
-    prob_t p;
-    p.logeq(Md::log_gamma_density(alpha, 0.1, 25));  // TODO configure
-    assert(!p.is_0());
-    prob_t prob_of_ppnull; prob_of_ppnull.logeq(Md::log_beta_density(ppnull, 2, 10));
-    assert(!prob_of_ppnull.is_0());
-    p *= prob_of_ppnull;
-    for (ObsCount::const_iterator it = obs_.begin(); it != obs_.end(); ++it) {
-      const AlignmentObservation& ao = it->first;
-      if (ao.a_j) {
-        prob_t u = XUnnormalizedProb(ao.a_j, ao.j, ao.src_len, ao.trg_len, alpha);
-        prob_t z = XComputeZ(ao.j, ao.src_len, ao.trg_len, alpha);
-        prob_t pa(u / z);
-        pa *= pnotnull;
-        pa.poweq(it->second);
-        p *= pa;
-      } else {
-        p *= pnull.pow(it->second);
-      }
-    }
-    return p;
-  }
-
- private:
-  static prob_t XUnnormalizedProb(unsigned a_j, unsigned j, unsigned src_len, unsigned trg_len, double alpha) {
-    prob_t p;
-    p.logeq(-fabs(double(a_j - 1) / src_len - double(j) / trg_len) * alpha);
-    return p;
-  }
-
-  static prob_t XComputeZ(unsigned j, unsigned src_len, unsigned trg_len, double alpha) {
-    prob_t z = prob_t::Zero();
-    for (int a_j = 1; a_j <= src_len; ++a_j)
-      z += XUnnormalizedProb(a_j, j, src_len, trg_len, alpha);
-    return z;
-  }
-
-  static double UnnormalizedProb(unsigned a_j, unsigned j, unsigned src_len, unsigned trg_len, double alpha) {
-    return exp(-fabs(double(a_j - 1) / src_len - double(j) / trg_len) * alpha);
-  }
-
-  static double ComputeZ(unsigned j, unsigned src_len, unsigned trg_len, double alpha) {
-    double z = 0;
-    for (int a_j = 1; a_j <= src_len; ++a_j)
-      z += UnnormalizedProb(a_j, j, src_len, trg_len, alpha);
-    return z;
-  }
-
-  const double& GetOrComputeZ(unsigned j, unsigned src_len, unsigned trg_len) const {
-    if (src_len >= zcache_.size())
-      zcache_.resize(src_len + 1);
-    if (trg_len >= zcache_[src_len].size())
-      zcache_[src_len].resize(trg_len + 1);
-    std::vector<double>& zv = zcache_[src_len][trg_len];
-    if (zv.size() == 0)
-      zv.resize(trg_len);
-    double& z = zv[j];
-    if (!z)
-      z = ComputeZ(j, src_len, trg_len, alpha_);
-    return z;
-  }
-
-  double alpha_;
-  prob_t pnull_;
-  prob_t pnotnull_;
-  mutable std::vector<std::vector<std::vector<double> > > zcache_;
-  typedef std::tr1::unordered_map<AlignmentObservation, int, boost::hash<AlignmentObservation> > ObsCount;
-  ObsCount obs_;
-};
-
-#endif
diff --git a/gi/pf/reachability.cc b/gi/pf/reachability.cc
deleted file mode 100644
index 7d0d04ac..00000000
--- a/gi/pf/reachability.cc
+++ /dev/null
@@ -1,74 +0,0 @@
-#include "reachability.h"
-
-#include <vector>
-#include <iostream>
-
-using namespace std;
-
-struct SState {
-  SState() : prev_src_covered(), prev_trg_covered() {}
-  SState(int i, int j) : prev_src_covered(i), prev_trg_covered(j) {}
-  int prev_src_covered;
-  int prev_trg_covered;
-};
-
-void Reachability::ComputeReachability(int srclen, int trglen, int src_max_phrase_len, int trg_max_phrase_len) {
-    typedef boost::multi_array<vector<SState>, 2> array_type;
-    array_type a(boost::extents[srclen + 1][trglen + 1]);
-    a[0][0].push_back(SState());
-    for (int i = 0; i < srclen; ++i) {
-      for (int j = 0; j < trglen; ++j) {
-        if (a[i][j].size() == 0) continue;
-        const SState prev(i,j);
-        for (int k = 1; k <= src_max_phrase_len; ++k) {
-          if ((i + k) > srclen) continue;
-          for (int l = 1; l <= trg_max_phrase_len; ++l) {
-            if ((j + l) > trglen) continue;
-            a[i + k][j + l].push_back(prev);
-          }
-        }
-      }
-    }
-    a[0][0].clear();
-    //cerr << srclen << "," << trglen << ": Final cell contains " << a[srclen][trglen].size() << " back pointers\n";
-    if (a[srclen][trglen].empty()) {
-      cerr << "Sequence pair with lengths (" << srclen << ',' << trglen << ") violates reachability constraints\n";
-      nodes = 0;
-      return;
-    }
-
-    typedef boost::multi_array<bool, 2> rarray_type;
-    rarray_type r(boost::extents[srclen + 1][trglen + 1]);
-    r[srclen][trglen] = true;
-    nodes = 0;
-    for (int i = srclen; i >= 0; --i) {
-      for (int j = trglen; j >= 0; --j) {
-        vector<SState>& prevs = a[i][j];
-        if (!r[i][j]) { prevs.clear(); }
-        for (int k = 0; k < prevs.size(); ++k) {
-          r[prevs[k].prev_src_covered][prevs[k].prev_trg_covered] = true;
-          int src_delta = i - prevs[k].prev_src_covered;
-          edges[prevs[k].prev_src_covered][prevs[k].prev_trg_covered][src_delta][j - prevs[k].prev_trg_covered] = true;
-          valid_deltas[prevs[k].prev_src_covered][prevs[k].prev_trg_covered].push_back(make_pair<short,short>(src_delta,j - prevs[k].prev_trg_covered));
-          short &msd = max_src_delta[prevs[k].prev_src_covered][prevs[k].prev_trg_covered];
-          if (src_delta > msd) msd = src_delta;
-        }
-      }
-    }
-    assert(!edges[0][0][1][0]);
-    assert(!edges[0][0][0][1]);
-    assert(!edges[0][0][0][0]);
-    assert(max_src_delta[0][0] > 0);
-    nodes = 0;
-    for (int i = 0; i < srclen; ++i) {
-      for (int j = 0; j < trglen; ++j) {
-        if (valid_deltas[i][j].size() > 0) {
-          node_addresses[i][j] = nodes++;
-        } else {
-          node_addresses[i][j] = -1;
-        }
-      }
-    }
-    cerr << "Sequence pair with lengths (" << srclen << ',' << trglen << ") has " << valid_deltas[0][0].size() << " out edges in its root node, " << nodes << " nodes in total, and outside estimate matrix will require " << sizeof(float)*nodes << " bytes\n";
-  }
-
diff --git a/gi/pf/reachability.h b/gi/pf/reachability.h
deleted file mode 100644
index 1e22c76a..00000000
--- a/gi/pf/reachability.h
+++ /dev/null
@@ -1,34 +0,0 @@
-#ifndef _REACHABILITY_H_
-#define _REACHABILITY_H_
-
-#include "boost/multi_array.hpp"
-
-// determines minimum and maximum lengths of outgoing edges from all
-// coverage positions such that the alignment path respects src and
-// trg maximum phrase sizes
-//
-// runs in O(n^2 * src_max * trg_max) time but should be relatively fast
-//
-// currently forbids 0 -> n and n -> 0 alignments
-
-struct Reachability {
-  unsigned nodes;
-  boost::multi_array<bool, 4> edges;  // edges[src_covered][trg_covered][src_delta][trg_delta] is this edge worth exploring?
-  boost::multi_array<short, 2> max_src_delta; // msd[src_covered][trg_covered] -- the largest src delta that's valid
-  boost::multi_array<short, 2> node_addresses; // na[src_covered][trg_covered] -- the index of the node in a one-dimensional array (of size "nodes")
-  boost::multi_array<std::vector<std::pair<short,short> >, 2> valid_deltas; // valid_deltas[src_covered][trg_covered] list of valid transitions leaving a particular node
-
-  Reachability(int srclen, int trglen, int src_max_phrase_len, int trg_max_phrase_len) :
-      nodes(),
-      edges(boost::extents[srclen][trglen][src_max_phrase_len+1][trg_max_phrase_len+1]),
-      max_src_delta(boost::extents[srclen][trglen]),
-      node_addresses(boost::extents[srclen][trglen]),
-      valid_deltas(boost::extents[srclen][trglen]) {
-    ComputeReachability(srclen, trglen, src_max_phrase_len, trg_max_phrase_len);
-  }
-
- private:
-  void ComputeReachability(int srclen, int trglen, int src_max_phrase_len, int trg_max_phrase_len);
-};
-
-#endif
diff --git a/gi/pf/tied_resampler.h b/gi/pf/tied_resampler.h
deleted file mode 100644
index a4f4af36..00000000
--- a/gi/pf/tied_resampler.h
+++ /dev/null
@@ -1,122 +0,0 @@
-#ifndef _TIED_RESAMPLER_H_
-#define _TIED_RESAMPLER_H_
-
-#include <set>
-#include <vector>
-#include "sampler.h"
-#include "slice_sampler.h"
-#include "m.h"
-
-template <class CRP>
-struct TiedResampler {
-  explicit TiedResampler(double da, double db, double ss, double sr, double d=0.5, double s=1.0) :
-      d_alpha(da),
-      d_beta(db),
-      s_shape(ss),
-      s_rate(sr),
-      discount(d),
-      strength(s) {}
-
-  void Add(CRP* crp) {
-    crps.insert(crp);
-    crp->set_discount(discount);
-    crp->set_strength(strength);
-    assert(!crp->has_discount_prior());
-    assert(!crp->has_strength_prior());
-  }
-
-  void Remove(CRP* crp) {
-    crps.erase(crp);
-  }
-
-  size_t size() const {
-    return crps.size();
-  }
-
-  double LogLikelihood(double d, double s) const {
-    if (s <= -d) return -std::numeric_limits<double>::infinity();
-    double llh = Md::log_beta_density(d, d_alpha, d_beta) +
-                 Md::log_gamma_density(d + s, s_shape, s_rate);
-    for (typename std::set<CRP*>::iterator it = crps.begin(); it != crps.end(); ++it)
-      llh += (*it)->log_crp_prob(d, s);
-    return llh;
-  }
-
-  double LogLikelihood() const {
-    return LogLikelihood(discount, strength);
-  }
-
-  struct DiscountResampler {
-    DiscountResampler(const TiedResampler& m) : m_(m) {}
-    const TiedResampler& m_;
-    double operator()(const double& proposed_discount) const {
-      return m_.LogLikelihood(proposed_discount, m_.strength);
-    }
-  };
-
-  struct AlphaResampler {
-    AlphaResampler(const TiedResampler& m) : m_(m) {}
-    const TiedResampler& m_;
-    double operator()(const double& proposed_strength) const {
-      return m_.LogLikelihood(m_.discount, proposed_strength);
-    }
-  };
-
-  void ResampleHyperparameters(MT19937* rng, const unsigned nloop = 5, const unsigned niterations = 10) {
-    if (size() == 0) { std::cerr << "EMPTY - not resampling\n"; return; }
-    const DiscountResampler dr(*this);
-    const AlphaResampler ar(*this);
-    for (int iter = 0; iter < nloop; ++iter) {
-      strength = slice_sampler1d(ar, strength, *rng, -discount + std::numeric_limits<double>::min(),
-                              std::numeric_limits<double>::infinity(), 0.0, niterations, 100*niterations);
-      double min_discount = std::numeric_limits<double>::min();
-      if (strength < 0.0) min_discount -= strength;
-      discount = slice_sampler1d(dr, discount, *rng, min_discount,
-                          1.0, 0.0, niterations, 100*niterations);
-    }
-    strength = slice_sampler1d(ar, strength, *rng, -discount + std::numeric_limits<double>::min(),
-                            std::numeric_limits<double>::infinity(), 0.0, niterations, 100*niterations);
-    std::cerr << "TiedCRPs(d=" << discount << ",s="
-              << strength << ") = " << LogLikelihood(discount, strength) << std::endl;
-    for (typename std::set<CRP*>::iterator it = crps.begin(); it != crps.end(); ++it)
-      (*it)->set_hyperparameters(discount, strength);
-  }
- private:
-  std::set<CRP*> crps;
-  const double d_alpha, d_beta, s_shape, s_rate;
-  double discount, strength;
-};
-
-// split according to some criterion
-template <class CRP>
-struct BinTiedResampler {
-  explicit BinTiedResampler(unsigned nbins) :
-      resamplers(nbins, TiedResampler<CRP>(1,1,1,1)) {}
-
-  void Add(unsigned bin, CRP* crp) {
-    resamplers[bin].Add(crp);
-  }
-
-  void Remove(unsigned bin, CRP* crp) {
-    resamplers[bin].Remove(crp);
-  }
-
-  void ResampleHyperparameters(MT19937* rng) {
-    for (unsigned i = 0; i < resamplers.size(); ++i) {
-      std::cerr << "BIN " << i << " (" << resamplers[i].size() << " CRPs): " << std::flush;
-      resamplers[i].ResampleHyperparameters(rng);
-    }
-  }
-
-  double LogLikelihood() const {
-    double llh = 0;
-    for (unsigned i = 0; i < resamplers.size(); ++i)
-      llh += resamplers[i].LogLikelihood();
-    return llh;
-  }
-
- private:
-  std::vector<TiedResampler<CRP> > resamplers;
-};
-
-#endif
diff --git a/gi/pf/tpf.cc b/gi/pf/tpf.cc
deleted file mode 100644
index 7348d21c..00000000
--- a/gi/pf/tpf.cc
+++ /dev/null
@@ -1,99 +0,0 @@
-#include <iostream>
-#include <tr1/memory>
-#include <queue>
-
-#include "sampler.h"
-
-using namespace std;
-using namespace tr1;
-
-shared_ptr<MT19937> prng;
-
-struct Particle {
-  Particle() : weight(prob_t::One()) {}
-  vector<int> states;
-  prob_t weight;
-  prob_t gamma_last;
-};
-
-ostream& operator<<(ostream& os, const Particle& p) {
-  os << "[";
-  for (int i = 0; i < p.states.size(); ++i) os << p.states[i] << ' ';
-  os << "| w=" << log(p.weight) << ']';
-  return os;
-}
-
-void Rejuvenate(vector<Particle>& pps) {
-  SampleSet<prob_t> ss;
-  vector<Particle> nps(pps.size());
-  for (int i = 0; i < pps.size(); ++i) {
-//    cerr << pps[i] << endl;
-    ss.add(pps[i].weight);
-  }
-//  cerr << "REJUVINATING...\n";
-  for (int i = 0; i < pps.size(); ++i) {
-    nps[i] = pps[prng->SelectSample(ss)];
-    nps[i].weight = prob_t(1.0 / pps.size());
-//    cerr << nps[i] << endl;
-  }
-  nps.swap(pps);
-//  exit(1);
-}
-
-int main(int argc, char** argv) {
-  const unsigned particles = 100;
-  prng.reset(new MT19937);
-  MT19937& rng = *prng;
-
-  // q(a) = 0.8
-  // q(b) = 0.8
-  // q(c) = 0.4
-  SampleSet<double> ssq;
-  ssq.add(0.4);
-  ssq.add(0.6);
-  ssq.add(0);
-  double qz = 1;
-
-  // p(a) = 0.2
-  // p(b) = 0.8
-  vector<double> p(3);
-  p[0] = 0.2;
-  p[1] = 0.8;
-  p[2] = 0;
-
-  vector<int> counts(3);
-  int tot = 0;
-
-  vector<Particle> pps(particles);
-  SampleSet<prob_t> ppss;
-  int LEN = 12;
-  int PP = 1;
-  while (pps[0].states.size() < LEN) {
-    for (int pi = 0; pi < particles; ++pi) {
-      Particle& prt = pps[pi];
-
-      bool redo = true;
-      const Particle savedp = prt;
-      while (redo) {
-        redo = false;
-        for (int i = 0; i < PP; ++i) {
-          int s = rng.SelectSample(ssq);
-          double gamma_last = p[s];
-          if (!gamma_last) { redo = true; break; }
-          double q = ssq[s] / qz;
-          prt.states.push_back(s);
-          prt.weight *= prob_t(gamma_last / q);
-        }
-        if (redo) { prt = savedp; continue; }
-      }
-    }
-    Rejuvenate(pps);
-  }
-  ppss.clear();
-  for (int i = 0; i < particles; ++i) { ppss.add(pps[i].weight); }
-  int sp = rng.SelectSample(ppss);
-  cerr << pps[sp] << endl;
-
-  return 0;
-}
-
diff --git a/gi/pf/transliterations.cc b/gi/pf/transliterations.cc
deleted file mode 100644
index b2996f65..00000000
--- a/gi/pf/transliterations.cc
+++ /dev/null
@@ -1,334 +0,0 @@
-#include "transliterations.h"
-
-#include <iostream>
-#include <vector>
-
-#include "boost/shared_ptr.hpp"
-
-#include "backward.h"
-#include "filelib.h"
-#include "tdict.h"
-#include "trule.h"
-#include "filelib.h"
-#include "ccrp_nt.h"
-#include "m.h"
-#include "reachability.h"
-
-using namespace std;
-using namespace std::tr1;
-
-struct TruncatedConditionalLengthModel {
-  TruncatedConditionalLengthModel(unsigned max_src_size, unsigned max_trg_size, double expected_src_to_trg_ratio) :
-      plens(max_src_size+1, vector<prob_t>(max_trg_size+1, 0.0)) {
-    for (unsigned i = 1; i <= max_src_size; ++i) {
-      prob_t z = prob_t::Zero();
-      for (unsigned j = 1; j <= max_trg_size; ++j)
-        z += (plens[i][j] = prob_t(0.01 + exp(Md::log_poisson(j, i * expected_src_to_trg_ratio))));
-      for (unsigned j = 1; j <= max_trg_size; ++j)
-        plens[i][j] /= z;
-      //for (unsigned j = 1; j <= max_trg_size; ++j)
-      //  cerr << "P(trg_len=" << j << " | src_len=" << i << ") = " << plens[i][j] << endl;
-    }
-  }
-
-  // return p(tlen | slen) for *chunks* not full words
-  inline const prob_t& operator()(int slen, int tlen) const {
-    return plens[slen][tlen];
-  }
-
-  vector<vector<prob_t> > plens;
-};
-
-struct CondBaseDist {
-  CondBaseDist(unsigned max_src_size, unsigned max_trg_size, double expected_src_to_trg_ratio) :
-    tclm(max_src_size, max_trg_size, expected_src_to_trg_ratio) {}
-
-  prob_t operator()(const vector<WordID>& src, unsigned sf, unsigned st,
-                    const vector<WordID>& trg, unsigned tf, unsigned tt) const {
-    prob_t p = tclm(st - sf, tt - tf);  // target len | source length ~ TCLM(source len)
-    assert(!"not impl");
-    return p;
-  }
-  inline prob_t operator()(const vector<WordID>& src, const vector<WordID>& trg) const {
-    return (*this)(src, 0, src.size(), trg, 0, trg.size());
-  }
-  TruncatedConditionalLengthModel tclm;
-};
-
-// represents transliteration phrase probabilities, e.g.
-//   p( a l - | A l ) , p( o | A w ) , ...
-struct TransliterationChunkConditionalModel {
-  explicit TransliterationChunkConditionalModel(const CondBaseDist& pp0) :
-      d(0.0),
-      strength(1.0),
-      rp0(pp0) {
-  }
-
-  void Summary() const {
-    std::cerr << "Number of conditioning contexts: " << r.size() << std::endl;
-    for (RuleModelHash::const_iterator it = r.begin(); it != r.end(); ++it) {
-      std::cerr << TD::GetString(it->first) << "   \t(\\alpha = " << it->second.alpha() << ") --------------------------" << std::endl;
-      for (CCRP_NoTable<TRule>::const_iterator i2 = it->second.begin(); i2 != it->second.end(); ++i2)
-        std::cerr << "   " << i2->second << '\t' << i2->first << std::endl;
-    }
-  }
-
-  int DecrementRule(const TRule& rule) {
-    RuleModelHash::iterator it = r.find(rule.f_);
-    assert(it != r.end());    
-    int count = it->second.decrement(rule);
-    if (count) {
-      if (it->second.num_customers() == 0) r.erase(it);
-    }
-    return count;
-  }
-
-  int IncrementRule(const TRule& rule) {
-    RuleModelHash::iterator it = r.find(rule.f_);
-    if (it == r.end()) {
-      it = r.insert(make_pair(rule.f_, CCRP_NoTable<TRule>(strength))).first;
-    } 
-    int count = it->second.increment(rule);
-    return count;
-  }
-
-  void IncrementRules(const std::vector<TRulePtr>& rules) {
-    for (int i = 0; i < rules.size(); ++i)
-      IncrementRule(*rules[i]);
-  }
-
-  void DecrementRules(const std::vector<TRulePtr>& rules) {
-    for (int i = 0; i < rules.size(); ++i)
-      DecrementRule(*rules[i]);
-  }
-
-  prob_t RuleProbability(const TRule& rule) const {
-    prob_t p;
-    RuleModelHash::const_iterator it = r.find(rule.f_);
-    if (it == r.end()) {
-      p = rp0(rule.f_, rule.e_);
-    } else {
-      p = it->second.prob(rule, rp0(rule.f_, rule.e_));
-    }
-    return p;
-  }
-
-  double LogLikelihood(const double& dd, const double& aa) const {
-    if (aa <= -dd) return -std::numeric_limits<double>::infinity();
-    //double llh = Md::log_beta_density(dd, 10, 3) + Md::log_gamma_density(aa, 1, 1);
-    double llh = //Md::log_beta_density(dd, 1, 1) +
-                 Md::log_gamma_density(dd + aa, 1, 1);
-    std::tr1::unordered_map<std::vector<WordID>, CCRP_NoTable<TRule>, boost::hash<std::vector<WordID> > >::const_iterator it;
-    for (it = r.begin(); it != r.end(); ++it)
-      llh += it->second.log_crp_prob(aa);
-    return llh;
-  }
-
-  struct AlphaResampler {
-    AlphaResampler(const TransliterationChunkConditionalModel& m) : m_(m) {}
-    const TransliterationChunkConditionalModel& m_;
-    double operator()(const double& proposed_strength) const {
-      return m_.LogLikelihood(m_.d, proposed_strength);
-    }
-  };
-
-  void ResampleHyperparameters(MT19937* rng) {
-    std::tr1::unordered_map<std::vector<WordID>, CCRP_NoTable<TRule>, boost::hash<std::vector<WordID> > >::iterator it;
-    //const unsigned nloop = 5;
-    const unsigned niterations = 10;
-    //DiscountResampler dr(*this);
-    AlphaResampler ar(*this);
-#if 0
-    for (int iter = 0; iter < nloop; ++iter) {
-      strength = slice_sampler1d(ar, strength, *rng, -d + std::numeric_limits<double>::min(),
-                              std::numeric_limits<double>::infinity(), 0.0, niterations, 100*niterations);
-      double min_discount = std::numeric_limits<double>::min();
-      if (strength < 0.0) min_discount -= strength;
-      d = slice_sampler1d(dr, d, *rng, min_discount,
-                          1.0, 0.0, niterations, 100*niterations);
-    }
-#endif
-    strength = slice_sampler1d(ar, strength, *rng, -d,
-                            std::numeric_limits<double>::infinity(), 0.0, niterations, 100*niterations);
-    std::cerr << "CTMModel(alpha=" << strength << ") = " << LogLikelihood(d, strength) << std::endl;
-    for (it = r.begin(); it != r.end(); ++it) {
-#if 0
-      it->second.set_discount(d);
-#endif
-      it->second.set_alpha(strength);
-    }
-  }
-
-  prob_t Likelihood() const {
-    prob_t p; p.logeq(LogLikelihood(d, strength));
-    return p;
-  }
-
-  const CondBaseDist& rp0;
-  typedef std::tr1::unordered_map<std::vector<WordID>,
-                                  CCRP_NoTable<TRule>,
-                                  boost::hash<std::vector<WordID> > > RuleModelHash;
-  RuleModelHash r;
-  double d, strength;
-};
-
-struct GraphStructure {
-  GraphStructure() : r() {}
-  // leak memory - these are basically static
-  const Reachability* r;
-  bool IsReachable() const { return r->nodes > 0; }
-};
-
-struct ProbabilityEstimates {
-  ProbabilityEstimates() : gs(), backward() {}
-  explicit ProbabilityEstimates(const GraphStructure& g) :
-      gs(&g), backward() {
-    if (g.r->nodes > 0)
-      backward = new float[g.r->nodes];
-  }
-  // leak memory, these are static
-
-  // returns an estimate of the marginal probability
-  double MarginalEstimate() const {
-    if (!backward) return 0;
-    return backward[0];
-  }
-
-  // returns an backward estimate
-  double Backward(int src_covered, int trg_covered) const {
-    if (!backward) return 0;
-    int ind = gs->r->node_addresses[src_covered][trg_covered];
-    if (ind < 0) return 0;
-    return backward[ind];
-  }
-
-  prob_t estp;
-  float* backward;
- private:
-  const GraphStructure* gs;
-};
-
-struct TransliterationsImpl {
-  TransliterationsImpl(int max_src, int max_trg, double sr, const BackwardEstimator& b) :
-      cp0(max_src, max_trg, sr),
-      tccm(cp0),
-      be(b),
-      kMAX_SRC_CHUNK(max_src),
-      kMAX_TRG_CHUNK(max_trg),
-      kS2T_RATIO(sr),
-      tot_pairs(), tot_mem() {
-  }
-  const CondBaseDist cp0;
-  TransliterationChunkConditionalModel tccm;
-  const BackwardEstimator& be;
-
-  void Initialize(WordID src, const vector<WordID>& src_lets, WordID trg, const vector<WordID>& trg_lets) {
-    const size_t src_len = src_lets.size();
-    const size_t trg_len = trg_lets.size();
-
-    // init graph structure
-    if (src_len >= graphs.size()) graphs.resize(src_len + 1);
-    if (trg_len >= graphs[src_len].size()) graphs[src_len].resize(trg_len + 1);
-    GraphStructure& gs = graphs[src_len][trg_len];
-    if (!gs.r) {
-      double rat = exp(fabs(log(trg_len / (src_len * kS2T_RATIO))));
-      if (rat > 1.5 || (rat > 2.4 && src_len < 6)) {
-        cerr << " ** Forbidding transliterations of size " << src_len << "," << trg_len << ": " << rat << endl;
-        gs.r = new Reachability(src_len, trg_len, 0, 0);
-      } else {
-        gs.r = new Reachability(src_len, trg_len, kMAX_SRC_CHUNK, kMAX_TRG_CHUNK);
-      }
-    }
-
-    const Reachability& r = *gs.r;
-
-    // init backward estimates
-    if (src >= ests.size()) ests.resize(src + 1);
-    unordered_map<WordID, ProbabilityEstimates>::iterator it = ests[src].find(trg);
-    if (it != ests[src].end()) return; // already initialized
-
-    it = ests[src].insert(make_pair(trg, ProbabilityEstimates(gs))).first;
-    ProbabilityEstimates& est = it->second;
-    if (!gs.r->nodes) return;  // not derivable subject to length constraints
-
-    be.InitializeGrid(src_lets, trg_lets, r, kS2T_RATIO, est.backward);
-    cerr << TD::GetString(src_lets) << " ||| " << TD::GetString(trg_lets) << " ||| " << (est.backward[0] / trg_lets.size()) << endl;
-    tot_pairs++;
-    tot_mem += sizeof(float) * gs.r->nodes;
-  }
-
-  void Forbid(WordID src, const vector<WordID>& src_lets, WordID trg, const vector<WordID>& trg_lets) {
-    const size_t src_len = src_lets.size();
-    const size_t trg_len = trg_lets.size();
-    // TODO
-  }
-
-  prob_t EstimateProbability(WordID s, const vector<WordID>& src, WordID t, const vector<WordID>& trg) const {
-    assert(src.size() < graphs.size());
-    const vector<GraphStructure>& tv = graphs[src.size()];
-    assert(trg.size() < tv.size());
-    const GraphStructure& gs = tv[trg.size()];
-    if (gs.r->nodes == 0)
-      return prob_t::Zero();
-    const unordered_map<WordID, ProbabilityEstimates>::const_iterator it = ests[s].find(t);
-    assert(it != ests[s].end());
-    return it->second.estp;
-  }
-
-  void GraphSummary() const {
-    double to = 0;
-    double tn = 0;
-    double tt = 0;
-    for (int i = 0; i < graphs.size(); ++i) {
-      const vector<GraphStructure>& vt = graphs[i];
-      for (int j = 0; j < vt.size(); ++j) {
-        const GraphStructure& gs = vt[j];
-        if (!gs.r) continue;
-        tt++;
-        for (int k = 0; k < i; ++k) {
-          for (int l = 0; l < j; ++l) {
-            size_t c = gs.r->valid_deltas[k][l].size();
-            if (c) {
-              tn += 1;
-              to += c;
-            }
-          }
-        }
-      }
-    }
-    cerr << "     Average nodes = " << (tn / tt) << endl;
-    cerr << "Average out-degree = " << (to / tn) << endl;
-    cerr << " Unique structures = " << tt << endl;
-    cerr << "      Unique pairs = " << tot_pairs << endl;
-    cerr << "          BEs size = " << (tot_mem / (1024.0*1024.0)) << " MB" << endl;
-  }
-
-  const int kMAX_SRC_CHUNK;
-  const int kMAX_TRG_CHUNK;
-  const double kS2T_RATIO;
-  unsigned tot_pairs;
-  size_t tot_mem;
-  vector<vector<GraphStructure> > graphs; // graphs[src_len][trg_len]
-  vector<unordered_map<WordID, ProbabilityEstimates> > ests; // ests[src][trg]
-};
-
-Transliterations::Transliterations(int max_src, int max_trg, double sr, const BackwardEstimator& be) :
-    pimpl_(new TransliterationsImpl(max_src, max_trg, sr, be)) {}
-Transliterations::~Transliterations() { delete pimpl_; }
-
-void Transliterations::Initialize(WordID src, const vector<WordID>& src_lets, WordID trg, const vector<WordID>& trg_lets) {
-  pimpl_->Initialize(src, src_lets, trg, trg_lets);
-}
-
-prob_t Transliterations::EstimateProbability(WordID s, const vector<WordID>& src, WordID t, const vector<WordID>& trg) const {
-  return pimpl_->EstimateProbability(s, src,t, trg);
-}
-
-void Transliterations::Forbid(WordID src, const vector<WordID>& src_lets, WordID trg, const vector<WordID>& trg_lets) {
-  pimpl_->Forbid(src, src_lets, trg, trg_lets);
-}
-
-void Transliterations::GraphSummary() const {
-  pimpl_->GraphSummary();
-}
-
diff --git a/gi/pf/transliterations.h b/gi/pf/transliterations.h
deleted file mode 100644
index 49d14684..00000000
--- a/gi/pf/transliterations.h
+++ /dev/null
@@ -1,24 +0,0 @@
-#ifndef _TRANSLITERATIONS_H_
-#define _TRANSLITERATIONS_H_
-
-#include <vector>
-#include "wordid.h"
-#include "prob.h"
-
-struct BackwardEstimator;
-struct TransliterationsImpl;
-struct Transliterations {
-  // max_src and max_trg indicate how big the transliteration phrases can be
-  // see reachability.h for information about filter_ratio
-  explicit Transliterations(int max_src, int max_trg, double s2t_rat, const BackwardEstimator& be);
-  ~Transliterations();
-  void Initialize(WordID src, const std::vector<WordID>& src_lets, WordID trg, const std::vector<WordID>& trg_lets);
-  void Forbid(WordID src, const std::vector<WordID>& src_lets, WordID trg, const std::vector<WordID>& trg_lets);
-  void GraphSummary() const;
-  prob_t EstimateProbability(WordID s, const std::vector<WordID>& src, WordID t, const std::vector<WordID>& trg) const;
- private:
-  TransliterationsImpl* pimpl_;
-};
-
-#endif
-
diff --git a/gi/pf/unigrams.cc b/gi/pf/unigrams.cc
deleted file mode 100644
index 40829775..00000000
--- a/gi/pf/unigrams.cc
+++ /dev/null
@@ -1,80 +0,0 @@
-#include "unigrams.h"
-
-#include <string>
-#include <cmath>
-
-#include "stringlib.h"
-#include "filelib.h"
-
-using namespace std;
-
-void UnigramModel::LoadUnigrams(const string& fname) {
-  cerr << "Loading unigram probabilities from " << fname << " ..." << endl;
-  ReadFile rf(fname);
-  string line;
-  istream& in = *rf.stream();
-  assert(in);
-  getline(in, line);
-  assert(line.empty());
-  getline(in, line);
-  assert(line == "\\data\\");
-  getline(in, line);
-  size_t pos = line.find("ngram 1=");
-  assert(pos == 0);
-  assert(line.size() > 8);
-  const size_t num_unigrams = atoi(&line[8]);
-  getline(in, line);
-  assert(line.empty());
-  getline(in, line);
-  assert(line == "\\1-grams:");
-  for (size_t i = 0; i < num_unigrams; ++i) {
-    getline(in, line);
-    assert(line.size() > 0);
-    pos = line.find('\t');
-    assert(pos > 0);
-    assert(pos + 1 < line.size());
-    const WordID w = TD::Convert(line.substr(pos + 1));
-    line[pos] = 0;
-    float p = atof(&line[0]);
-    if (w < probs_.size()) probs_[w].logeq(p * log(10)); else cerr << "WARNING: don't know about '" << TD::Convert(w) << "'\n";
-  }
-}
-
-void UnigramWordModel::LoadUnigrams(const string& fname) {
-  cerr << "Loading unigram probabilities from " << fname << " ..." << endl;
-  ReadFile rf(fname);
-  string line;
-  istream& in = *rf.stream();
-  assert(in);
-  getline(in, line);
-  assert(line.empty());
-  getline(in, line);
-  assert(line == "\\data\\");
-  getline(in, line);
-  size_t pos = line.find("ngram 1=");
-  assert(pos == 0);
-  assert(line.size() > 8);
-  const size_t num_unigrams = atoi(&line[8]);
-  getline(in, line);
-  assert(line.empty());
-  getline(in, line);
-  assert(line == "\\1-grams:");
-  for (size_t i = 0; i < num_unigrams; ++i) {
-    getline(in, line);
-    assert(line.size() > 0);
-    pos = line.find('\t');
-    assert(pos > 0);
-    assert(pos + 1 < line.size());
-    size_t cur = pos + 1;
-    vector<WordID> w;
-    while (cur < line.size()) {
-      const size_t len = UTF8Len(line[cur]);
-      w.push_back(TD::Convert(line.substr(cur, len)));
-      cur += len;
-    }
-    line[pos] = 0;
-    float p = atof(&line[0]);
-    probs_[w].logeq(p * log(10.0));
-  }
-}
-
diff --git a/gi/pf/unigrams.h b/gi/pf/unigrams.h
deleted file mode 100644
index 1660d1ed..00000000
--- a/gi/pf/unigrams.h
+++ /dev/null
@@ -1,69 +0,0 @@
-#ifndef _UNIGRAMS_H_
-#define _UNIGRAMS_H_
-
-#include <vector>
-#include <string>
-#include <tr1/unordered_map>
-#include <boost/functional.hpp>
-
-#include "wordid.h"
-#include "prob.h"
-#include "tdict.h"
-
-struct UnigramModel {
-  explicit UnigramModel(const std::string& fname, unsigned vocab_size) :
-      use_uniform_(fname.size() == 0),
-      uniform_(1.0 / vocab_size),
-      probs_() {
-    if (fname.size() > 0) {
-      probs_.resize(TD::NumWords() + 1);
-      LoadUnigrams(fname);
-    }
-  }
-
-  const prob_t& operator()(const WordID& w) const {
-    assert(w);
-    if (use_uniform_) return uniform_;
-    return probs_[w];
-  }
-
- private:
-  void LoadUnigrams(const std::string& fname);
-
-  const bool use_uniform_;
-  const prob_t uniform_;
-  std::vector<prob_t> probs_;
-};
-
-
-// reads an ARPA unigram file and converts words like 'cat' into a string 'c a t'
-struct UnigramWordModel {
-  explicit UnigramWordModel(const std::string& fname) :
-      use_uniform_(false),
-      uniform_(1.0),
-      probs_() {
-    LoadUnigrams(fname);
-  }
-
-  explicit UnigramWordModel(const unsigned vocab_size) :
-      use_uniform_(true),
-      uniform_(1.0 / vocab_size),
-      probs_() {}
-
-  const prob_t& operator()(const std::vector<WordID>& s) const {
-    if (use_uniform_) return uniform_;
-    const VectorProbHash::const_iterator it = probs_.find(s);
-    assert(it != probs_.end());
-    return it->second;
-  }
-
- private:
-  void LoadUnigrams(const std::string& fname);
-
-  const bool use_uniform_;
-  const prob_t uniform_;
-  typedef std::tr1::unordered_map<std::vector<WordID>, prob_t, boost::hash<std::vector<WordID> > > VectorProbHash;
-  VectorProbHash probs_;
-};
-
-#endif
diff --git a/gi/pipeline/OLD.clsp.config b/gi/pipeline/OLD.clsp.config
deleted file mode 100644
index cd0f9d65..00000000
--- a/gi/pipeline/OLD.clsp.config
+++ /dev/null
@@ -1,9 +0,0 @@
-# THIS FILE GIVES THE LOCATIONS OF THE CORPORA USED
-# name path aligned-corpus LM xfeats.grammar dev dev-refs test1 testt-eval.sh ...
-btec /export/ws10smt/data/btec/ split.zh-en.al lm/en.3gram.lm.gz xgrammar/grammar.gz devtest/devset1_2.zh devtest/devset1_2.lc.en* devtest/devset3.zh eval-devset3.sh
-fbis /export/ws10smt/data/chinese-english.fbis corpus.zh-en.al
-zhen /export/ws10smt/data/chinese-english corpus.zh-en.al
-aren /export/ws10smt/data/arabic-english corpus.ar-en.al
-uren /export/ws10smt/data/urdu-english corpus.ur-en.al
-nlfr /export/ws10smt/data/dutch-french corpus.nl-fr.al
-
diff --git a/gi/pipeline/OLD.evaluation-pipeline.pl b/gi/pipeline/OLD.evaluation-pipeline.pl
deleted file mode 100755
index 49c303eb..00000000
--- a/gi/pipeline/OLD.evaluation-pipeline.pl
+++ /dev/null
@@ -1,277 +0,0 @@
-#!/usr/bin/perl -w
-use strict;
-use Getopt::Long;
-use Cwd;
-my $CWD = getcwd;
-
-my $SCRIPT_DIR; BEGIN { use Cwd qw/ abs_path /; use File::Basename; $SCRIPT_DIR = dirname(abs_path($0)); push @INC, $SCRIPT_DIR; }
-
-my @DEFAULT_FEATS = qw(
-  LogRuleCount SingletonRule LexE2F LexF2E WordPenalty
-  LogFCount LanguageModel Glue GlueTop PassThrough SingletonF
-);
-
-my %init_weights = qw(
-  LogRuleCount 0.2
-  LexE2F -0.3
-  LexF2E -0.3
-  LogFCount 0.1
-  WordPenalty -1.5
-  LanguageModel 1.2
-  Glue -1.0
-  GlueTop 0.00001
-  PassThrough -10.0
-  SingletonRule -0.1
-  X_EGivenF -0.3
-  X_FGivenE -0.3
-  X_LogECount -1
-  X_LogFCount -0.1
-  X_LogRuleCount 0.3
-  X_SingletonE -0.1
-  X_SingletonF -0.1
-  X_SingletonRule -0.5
-);
-
-my $CDEC = "$SCRIPT_DIR/../../decoder/cdec";
-my $PARALLELIZE = "$SCRIPT_DIR/../../vest/parallelize.pl";
-my $EXTOOLS = "$SCRIPT_DIR/../../extools";
-die "Can't find extools: $EXTOOLS" unless -e $EXTOOLS && -d $EXTOOLS;
-my $VEST = "$SCRIPT_DIR/../../vest";
-die "Can't find vest: $VEST" unless -e $VEST && -d $VEST;
-my $DISTVEST = "$VEST/dist-vest.pl";
-my $FILTSCORE = "$EXTOOLS/filter_score_grammar";
-my $ADDXFEATS = "$SCRIPT_DIR/scripts/xfeats.pl";
-assert_exec($CDEC, $PARALLELIZE, $FILTSCORE, $DISTVEST, $ADDXFEATS);
-
-my $config = "$SCRIPT_DIR/OLD.clsp.config";
-print STDERR "CORPORA CONFIGURATION: $config\n";
-open CONF, "<$config" or die "Can't read $config: $!";
-my %paths;
-my %corpora;
-my %lms;
-my %devs;
-my %devrefs;
-my %tests;
-my %testevals;
-my %xgrammars;
-print STDERR "       LANGUAGE PAIRS:";
-while(<CONF>) {
-  chomp;
-  next if /^#/;
-  next if /^\s*$/;
-  s/^\s+//;
-  s/\s+$//;
-  my ($name, $path, $corpus, $lm, $xgrammar, $dev, $devref, @xtests) = split /\s+/;
-  $paths{$name} = $path;
-  $corpora{$name} = $corpus;
-  $lms{$name} = $lm;
-  $xgrammars{$name} = $xgrammar;
-  $devs{$name} = $dev;
-  $devrefs{$name} = $devref;
-  $tests{$name} = $xtests[0];
-  $testevals{$name} = $xtests[1];
-  print STDERR " $name";
-}
-print STDERR "\n";
-
-my %langpairs = map { $_ => 1 } qw( btec zhen fbis aren uren nlfr );
-
-my $outdir = "$CWD/exp";
-my $help;
-my $XFEATS;
-my $EXTRA_FILTER = '';
-my $dataDir = '/export/ws10smt/data';
-if (GetOptions(
-        "data=s" => \$dataDir,
-        "xfeats" => \$XFEATS,
-) == 0 || @ARGV!=2 || $help) {
-        print_help();
-        exit;
-}
-my $lp = $ARGV[0];
-my $grammar = $ARGV[1];
-print STDERR "   CORPUS REPO: $dataDir\n";
-print STDERR " LANGUAGE PAIR: $lp\n";
-die "I don't know about that language pair\n" unless $paths{$lp};
-my $corpdir = "$dataDir";
-if ($paths{$lp} =~ /^\//) { $corpdir = $paths{$lp}; } else { $corpdir .= '/' . $paths{$lp}; }
-die "I can't find the corpora directory: $corpdir" unless -d $corpdir;
-print STDERR "       GRAMMAR: $grammar\n";
-my $LANG_MODEL = mydircat($corpdir, $lms{$lp});
-print STDERR "            LM: $LANG_MODEL\n";
-my $CORPUS = mydircat($corpdir, $corpora{$lp});
-die "Can't find corpus: $CORPUS" unless -f $CORPUS;
-
-my $dev = mydircat($corpdir, $devs{$lp});
-my $drefs = $devrefs{$lp};
-die "Can't find dev: $dev\n" unless -f $dev;
-die "Dev refs not set" unless $drefs;
-$drefs = mydircat($corpdir, $drefs);
-
-my $test = mydircat($corpdir, $tests{$lp});
-my $teval = mydircat($corpdir, $testevals{$lp});
-die "Can't find test: $test\n" unless -f $test;
-assert_exec($teval);
-
-if ($XFEATS) {
-  my $xgram = mydircat($corpdir, $xgrammars{$lp});
-  die "Can't find x-grammar: $xgram" unless -f $xgram;
-  $EXTRA_FILTER = "$ADDXFEATS $xgram |";
-  print STDERR "ADDING X-FEATS FROM $xgram\n";
-}
-
-# MAKE DEV
-print STDERR "\nFILTERING FOR dev...\n";
-print STDERR "DEV: $dev (REFS=$drefs)\n";
-`mkdir -p $outdir`;
-my $devgrammar = filter($grammar, $dev, 'dev', $outdir);
-my $devini = mydircat($outdir, "cdec-dev.ini");
-write_cdec_ini($devini, $devgrammar);
-
-
-# MAKE TEST
-print STDERR "\nFILTERING FOR test...\n";
-print STDERR "TEST: $test (EVAL=$teval)\n";
-`mkdir -p $outdir`;
-my $testgrammar = filter($grammar, $test, 'test', $outdir);
-my $testini = mydircat($outdir, "cdec-test.ini");
-write_cdec_ini($testini, $testgrammar);
-
-
-# CREATE INIT WEIGHTS
-print STDERR "\nCREATING INITIAL WEIGHTS FILE: weights.init\n";
-my $weights = mydircat($outdir, "weights.init");
-write_random_weights_file($weights);
-
-
-# VEST
-print STDERR "\nMINIMUM ERROR TRAINING\n";
-my $tuned_weights = mydircat($outdir, 'weights.tuned');
-if (-f $tuned_weights) {
-  print STDERR "TUNED WEIGHTS $tuned_weights EXISTS: REUSING\n";
-} else {
-  my $cmd = "$DISTVEST --ref-files=$drefs --source-file=$dev --weights $weights $devini";
-  print STDERR "MERT COMMAND: $cmd\n";
-  `rm -rf $outdir/vest 2> /dev/null`;
-  chdir $outdir or die "Can't chdir to $outdir: $!";
-  $weights = `$cmd`;
-  die "MERT reported non-zero exit code" unless $? == 0;
-  chomp $weights;
-  safesystem($tuned_weights, "cp $weights $tuned_weights");
-  print STDERR "TUNED WEIGHTS: $tuned_weights\n";
-  die "$tuned_weights is missing!" unless -f $tuned_weights;
-}
-
-# DECODE
-print STDERR "\nDECODE TEST SET\n";
-my $decolog = mydircat($outdir, "test-decode.log");
-my $testtrans = mydircat($outdir, "test.trans");
-my $cmd = "cat $test | $PARALLELIZE -j 20 -e $decolog -- $CDEC -c $testini -w $tuned_weights > $testtrans";
-safesystem($testtrans, $cmd) or die "Failed to decode test set!";
-
-
-# EVALUATE
-print STDERR "\nEVALUATE TEST SET\n";
-print STDERR "TEST: $testtrans\n";
-$cmd = "$teval $testtrans";
-safesystem(undef, $cmd) or die "Failed to evaluate!";
-exit 0;
-
-
-sub write_random_weights_file {
-  my ($file, @extras) = @_;
-  open F, ">$file" or die "Can't write $file: $!";
-  my @feats = (@DEFAULT_FEATS, @extras);
-  if ($XFEATS) {
-    my @xfeats = qw(
-      X_LogRuleCount X_LogECount X_LogFCount X_EGivenF X_FGivenE X_SingletonRule X_SingletonE X_SingletonF
-    );
-    @feats = (@feats, @xfeats);
-  }
-  for my $feat (@feats) {
-    my $r = rand(1.6);
-    my $w = $init_weights{$feat} * $r;
-    if ($w == 0) { $w = 0.0001; print STDERR "WARNING: $feat had no initial weight!\n"; }
-    print F "$feat $w\n";
-  }
-  close F;
-}
-
-sub filter {
-  my ($grammar, $set, $name, $outdir) = @_;
-  my $outgrammar = mydircat($outdir, "$name.scfg.gz");
-  if (-f $outgrammar) { print STDERR "$outgrammar exists - REUSING!\n"; } else {
-    my $cmd = "gunzip -c $grammar | $FILTSCORE -c $CORPUS -t $set | $EXTRA_FILTER gzip > $outgrammar";
-    safesystem($outgrammar, $cmd) or die "Can't filter and score grammar!";
-  }
-  return $outgrammar;
-}
-
-sub mydircat {
- my ($base, $suffix) = @_;
- if ($suffix =~ /^\//) { return $suffix; }
- my $res = $base . '/' . $suffix;
- $res =~ s/\/\//\//g;
- return $res;
-}
-
-sub write_cdec_ini {
-  my ($filename, $grammar_path) = (@_);
-  open CDECINI, ">$filename" or die "Can't write $filename: $!";
-  print CDECINI <<EOT;
-formalism=scfg
-cubepruning_pop_limit=100
-add_pass_through_rules=true
-scfg_extra_glue_grammar=/export/ws10smt/data/glue/glue.scfg.gz
-grammar=$grammar_path
-feature_function=WordPenalty
-feature_function=LanguageModel -o 3 $LANG_MODEL
-EOT
-  close CDECINI;
-};
-
-sub print_help {
-  print STDERR<<EOT;
-
-Usage: $0 [OPTIONS] language-pair unfiltered-grammar.gz
-
-Given an induced grammar for an entire corpus (i.e., generated by
-local-gi-pipeline.pl), filter and featurize it for a dev and test set,
-run MERT, report scores.
-
-EOT
-}
-
-sub safesystem {
-  my $output = shift @_;
-  print STDERR "Executing: @_\n";
-  system(@_);
-  if ($? == -1) {
-      print STDERR "ERROR: Failed to execute: @_\n  $!\n";
-      if (defined $output && -e $output) { printf STDERR "Removing $output\n"; `rm -rf $output`; }
-      exit(1);
-  }
-  elsif ($? & 127) {
-      printf STDERR "ERROR: Execution of: @_\n  died with signal %d, %s coredump\n",
-          ($? & 127),  ($? & 128) ? 'with' : 'without';
-      if (defined $output && -e $output) { printf STDERR "Removing $output\n"; `rm -rf $output`; }
-      exit(1);
-  }
-  else {
-    my $exitcode = $? >> 8;
-    if ($exitcode) {
-      print STDERR "Exit code: $exitcode\n";
-      if (defined $output && -e $output) { printf STDERR "Removing $output\n"; `rm -rf $output`; }
-    }
-    return ! $exitcode;
-  }
-}
-
-sub assert_exec {
-  my @files = @_;
-  for my $file (@files) {
-    die "Can't find $file - did you run make?\n" unless -e $file;
-    die "Can't execute $file" unless -e $file;
-  }
-};
-
diff --git a/gi/pipeline/backoff-pipe.pl b/gi/pipeline/backoff-pipe.pl
deleted file mode 100644
index ac103c8b..00000000
--- a/gi/pipeline/backoff-pipe.pl
+++ /dev/null
@@ -1,215 +0,0 @@
-#!/usr/bin/perl -w
-use strict;
-
-use Getopt::Long "GetOptions";
-
-my @grammars;
-my $OUTPUTPREFIX = './giwork/bo.hier.grammar';
-safemkdir($OUTPUTPREFIX);
-my $backoff_levels = 1;
-my $glue_levels = 1;
-
-usage() unless &GetOptions('grmr=s@' => \ @grammars,
-                           'outprefix=s' => \ $OUTPUTPREFIX,
-                           'bo-lvls=i' => \ $backoff_levels,
-                           'glue-lvls=i' => \ $glue_levels,
-);
-                           
-my $OUTDIR = $OUTPUTPREFIX . '/hier';
-print STDERR "@grammars\n";
-
-
-my %grmr = ();
-foreach my $grammar (@grammars) {
-    $grammar =~ m/\/[^\/]*\.t(\d+)\.[^\/]*/;
-    $grmr{$1} = $grammar;
-}
-
-my @index = sort keys %grmr;
-$OUTDIR = $OUTDIR . join('-',@index);
-safemkdir($OUTDIR);
-my $BACKOFF_GRMR = $OUTDIR . '/backoff.hier.gz';
-safesystem("echo \"\" | gzip > $BACKOFF_GRMR");
-my $GLUE_GRMR = $OUTDIR . '/glue.hier.gz';
-safesystem("echo \"\" | gzip > $GLUE_GRMR");
-my $joinedgrammars = $OUTDIR . '/grammar.hier.gz';
-
-join_grammars();
-
-for my $i (0..(scalar @index)-2) {
-    my $freqs = extract_freqs($index[$i], $index[$i+1]);
-    if ($i < $backoff_levels) {
-        create_backoff_rules($index[$i],$index[$i+1],$freqs);
-    }
-    if ($i < $glue_levels) {
-        add_glue_rules($index[$i]);
-    }
-}
-
-output_grammar_info();
-
-
-sub usage {
-  print <<EOT;
-
-Usage: $0 [OPTIONS] corpus.fr-en-al
-
-Induces a grammar using Pitman-Yor topic modeling or Posterior Regularisation.
-
-EOT
-  exit 1;
-};
-
-sub safemkdir {
-  my $dir = shift;
-  if (-d $dir) { return 1; }
-  return mkdir($dir);
-}
-
-
-sub safesystem {
-  print STDERR "Executing: @_\n";
-  system(@_);
-  if ($? == -1) {
-      print STDERR "ERROR: Failed to execute: @_\n  $!\n";
-      exit(1);
-  }
-  elsif ($? & 127) {
-      printf STDERR "ERROR: Execution of: @_\n  died with signal %d, %s coredump\n",
-          ($? & 127),  ($? & 128) ? 'with' : 'without';
-      exit(1);
-  }
-  else {
-    my $exitcode = $? >> 8;
-    print STDERR "Exit code: $exitcode\n" if $exitcode;
-    return ! $exitcode;
-  }
-}
-
-
-sub join_grammars {
-    print STDERR "\n!!! JOINING GRAMMARS\n";
-    if(-e $joinedgrammars) {
-        print STDERR "$joinedgrammars exists, reusing...\n";
-        return;
-    }
-    safesystem("echo \"\" | gzip > $joinedgrammars");
-    foreach my $i (@index) {
-        my $g = $grmr{$i};
-        safesystem("zcat $g | sed -r -e 's/X([0-9]+)/X$i\\1/g' - | gzip > $g.2.gz");
-        safesystem("zcat $joinedgrammars $g.2.gz | gzip > $joinedgrammars.2.gz");
-        safesystem("mv $joinedgrammars.2.gz $joinedgrammars");
-    }
-}
-
-
-sub extract_freqs {
-    my($grmr1,$grmr2) = @_;
-    print STDERR "\n!!!EXTRACTING FREQUENCIES: $grmr1->$grmr2\n";
-    my $IN_COARSE = substr($grmr{$grmr1},0,index($grmr{$grmr1},".grammar/")) . "/labeled_spans.txt";
-    my $IN_FINE = substr($grmr{$grmr2},0,index($grmr{$grmr2},".grammar/")) . "/labeled_spans.txt";
-    my $OUT_SPANS = "$OUTDIR/labeled_spans.hier$grmr1-$grmr2.txt";
-    my $FREQS = "$OUTDIR/label_freq.hier$grmr1-$grmr2.txt";
-    if(-e $OUT_SPANS && -e $FREQS) {
-        print STDERR "$OUT_SPANS exists, reusing...\n";
-        print STDERR "$FREQS exists, reusing...\n";
-        return $FREQS;
-    }
-    
-    safesystem("paste -d ' ' $IN_COARSE $IN_FINE > $OUT_SPANS");
-    
-    my %FREQ_HIER = ();
-    my %finehier = ();
-    
-    open SPANS, $OUT_SPANS or die $!;
-    while (<SPANS>) {
-        my ($tmp, $coarse, $fine) = split /\|\|\|/;
-        my @coarse_spans = $coarse =~ /\d+-\d+:X(\d+)/g;
-        my @fine_spans = $fine =~ /\d+-\d+:X(\d+)/g;
-        
-        foreach my $i (0..(scalar @coarse_spans)-1) {
-            my $coarse_cat = $coarse_spans[$i];
-            my $fine_cat = $fine_spans[$i];
-            
-            $FREQ_HIER{$coarse_cat}{$fine_cat}++;
-        }
-    }
-    close SPANS;
-    foreach (values %FREQ_HIER) {
-        my $coarse_freq = $_;
-        my $total = 0;
-        $total+=$_ for (values %{ $coarse_freq });
-        $coarse_freq->{$_}=log($coarse_freq->{$_}/$total) for (keys %{ $coarse_freq });
-    }
-    open FREQS, ">", $FREQS or die $!;
-    foreach my $coarse_cat (keys %FREQ_HIER) {
-        print FREQS "$coarse_cat |||";
-        foreach my $fine_cat (keys %{$FREQ_HIER{$coarse_cat}}) {
-            my $freq = $FREQ_HIER{$coarse_cat}{$fine_cat};
-            print FREQS " $fine_cat:$freq";
-            if(! exists $finehier{$fine_cat} || $finehier{$fine_cat} < $freq) {
-               $finehier{$fine_cat} = $coarse_cat;
-            }  
-        }
-        print FREQS "\n";
-    }
-#    foreach my $fine_cat (keys %finehier) {
-#        print FREQS "$fine_cat -> $finehier{$fine_cat}\n";
-#    }
-    close FREQS;
-    return $FREQS;
-}
-
-
-sub create_backoff_rules {
-    print STDERR "\n!!! CREATING BACKOFF RULES\n";
-    my ($grmr1, $grmr2, $freq) = @_;
-    my $OUTFILE = "$OUTDIR/backoff.hier$grmr1-$grmr2.txt";
-    if(-e $OUTFILE) {
-        print STDERR "$OUTFILE exists, reusing...\n";
-        return;
-    }
-    open FREQS, $freq or die $!;
-    open TMP, ">", $OUTFILE or die $!;
-    while (<FREQS>) {
-        my $line = $_;
-        $line = m/^(\d+) \|\|\| (.+)$/;
-        my $coarse = $1;
-        $line = $2;
-        my @finefreq = $line =~ m/(\d+):(\S+)/g;
-        for(my $i = 0; $i < scalar @finefreq; $i+=2) {
-            my $finecat = $finefreq[$i];
-            my $finefreq = $finefreq[$i+1];
-            print TMP "[X$grmr1$coarse] ||| [X$grmr2$finecat,1]\t[1] ||| BackoffRule=$finefreq A=0-0\n";
-        }
-    }
-    close TMP;
-    close FREQS;
-    safesystem("zcat $BACKOFF_GRMR | cat - $OUTFILE | gzip > $BACKOFF_GRMR.2.gz");
-    safesystem("mv $BACKOFF_GRMR.2.gz $BACKOFF_GRMR");
-}
-
-sub add_glue_rules {
-    print STDERR "\n!!! CREATING GLUE RULES\n";
-    my ($grmr) = @_;
-    my $OUTFILE = "$OUTDIR/glue.$grmr.gz";
-    if (-e $OUTFILE) {
-        print STDERR "$OUTFILE exists, reusing...\n";
-        return;
-    }
-    open TMP, ">", $OUTFILE or die $!;
-    for my $i (0..($grmr-1)) {
-        print TMP "[S] ||| [S,1] [X$grmr$i,2] ||| [1] [2] ||| Glue=1\n";
-        print TMP "[S] ||| [X$grmr$i,1] ||| [1] ||| GlueTop=1\n";
-    }
-    close TMP;
-    safesystem("zcat $GLUE_GRMR | cat - $OUTFILE | gzip > $GLUE_GRMR.2.gz");
-    safesystem("mv $GLUE_GRMR.2.gz $GLUE_GRMR");
-}
-
-sub output_grammar_info {
-    print STDERR "\n!!! GRAMMAR INFORMATION\n";
-    print STDOUT "GRAMMAR: \t$joinedgrammars\n";
-    print STDOUT "GLUE: \t$GLUE_GRMR\n";
-    print STDOUT "BACKOFF: \t$BACKOFF_GRMR\n";
-}
diff --git a/gi/pipeline/blacklight.config b/gi/pipeline/blacklight.config
deleted file mode 100644
index fc59a604..00000000
--- a/gi/pipeline/blacklight.config
+++ /dev/null
@@ -1,9 +0,0 @@
-# THIS FILE GIVES THE LOCATIONS OF THE CORPORA USED
-# name path aligned-corpus LM dev dev-refs test1 testt-eval.sh ...
-/usr/users/0/cdyer/ws10smt/data
-btec /home/cdyer/ws10smt-data/btec/ split.zh-en.al lm/en.3gram.lm.gz devtest/devset1_2.zh devtest/devset1_2.lc.en* devtest/devset3.zh eval-devset3.sh
-zhen /home/cdyer/ws10smt-data/chinese-english corpus.zh-en.al lm/c2e.3gram.lm.gz dev_and_test/mt02.src.txt dev_and_test/mt02.ref.* dev_and_test/mt03.src.txt eval-mt03.sh
-aren /home/cdyer/ws10smt-data/arabic-english corpus.ar-en-al lm/a2e.3gram.lm.gz dev_and_test/dev.src.txt dev_and_test/dev.ref.txt.* dev_and_test/mt05.src.txt eval-mt05.sh
-uren /usr/users/0/cdyer/ws10smt/data/urdu-english corpus.ur-en.al lm/u2e.en.lm.gz dev/dev.ur dev/dev.en* devtest/devtest.ur eval-devtest.sh
-nlfr /home/cdyer/ws10smt-data/dutch-french corpus.nl-fr.al
-
diff --git a/gi/pipeline/clsp.config b/gi/pipeline/clsp.config
deleted file mode 100644
index c23d409f..00000000
--- a/gi/pipeline/clsp.config
+++ /dev/null
@@ -1,10 +0,0 @@
-# THIS FILE GIVES THE LOCATIONS OF THE CORPORA USED
-# name path aligned-corpus LM dev dev-refs test1 testt-eval.sh ...
-/export/ws10smt/data
-btec /export/ws10smt/data/btec/ split.zh-en.al lm/en.3gram.lm.gz devtest/devset1_2.zh devtest/devset1_2.lc.en* devtest/devset3.zh eval-devset3.sh
-fbis /export/ws10smt/data/chinese-english.fbis corpus.zh-en.al
-zhen /export/ws10smt/data/chinese-english corpus.zh-en.al lm/c2e.3gram.lm.gz dev_and_test/mt02.src.txt dev_and_test/mt02.ref.* dev_and_test/mt03.src.txt eval-mt03.sh
-aren /export/ws10smt/data/arabic-english corpus.ar-en-al lm/a2e.3gram.lm.gz dev_and_test/dev.src.txt dev_and_test/dev.ref.txt.* dev_and_test/mt05.src.txt eval-mt05.sh
-uren /export/ws10smt/data/urdu-english corpus.ur-en.al lm/u2e.en.lm.gz dev/dev.ur dev/dev.en* devtest/devtest.ur eval-devtest.sh
-nlfr /export/ws10smt/data/dutch-french corpus.nl-fr.al
-
diff --git a/gi/pipeline/evaluation-pipeline.pl b/gi/pipeline/evaluation-pipeline.pl
deleted file mode 100755
index 4b4529d9..00000000
--- a/gi/pipeline/evaluation-pipeline.pl
+++ /dev/null
@@ -1,364 +0,0 @@
-#!/usr/bin/perl -w
-use strict;
-use Getopt::Long;
-use Cwd;
-my $CWD = getcwd;
-
-my $SCRIPT_DIR; BEGIN { use Cwd qw/ abs_path /; use File::Basename; $SCRIPT_DIR = dirname(abs_path($0)); push @INC, $SCRIPT_DIR, "$SCRIPT_DIR/../../environment"; }
-use LocalConfig;
-
-my $JOBS = 15;
-my $PMEM = "9G";
-my $NUM_TRANSLATIONS = 50;
-my $GOAL = "S";
-
-# featurize_grammar may add multiple features from a single feature extractor
-# the key in this map is the extractor name, the value is a list of the extracted features
-my $feat_map = {
-  "LogRuleCount" => [ "LogRuleCount", "SingletonRule" ] ,
-#  "XFeatures" => [ "XFE","XEF" ] ,
-  "XFeatures" => [ "XFE","XEF","LabelledEF","LabelledFE"], # ,"XE_Singleton","XF_Singleton"] ,
-  "LabelledRuleConditionals" => [ "LabelledFE","LabelledEF" ] ,
-  "LexProb" => [ "LexE2F", "LexF2E" ] ,
-  "BackoffRule" => [ "BackoffRule" ] ,
-  "RulePenalty" => [ "RulePenalty" ] ,
-  "LHSProb" => [ "LHSProb" ] ,
-  "LabellingShape" => [ "LabellingShape" ] ,
-  "GenerativeProb" => [ "GenerativeProb" ] ,
-};
-
-my %init_weights = qw(
-  EGivenF -0.735245
-  FGivenE -0.219391
-  Glue -0.306709
-  GlueTop 0.0473331
-  LanguageModel 2.40403
-  LexE2F -0.266989
-  LexF2E -0.550373
-  LogECount -0.129853
-  LogFCount -0.194037
-  LogRuleCount 0.256706
-  BackoffRule 0.5
-  XFE -0.256706
-  XEF -0.256706
-  XF_Singleton -0.05
-  XE_Singleton -0.8
-  LabelledFE -0.256706
-  LabelledEF -0.256706
-  PassThrough -0.9304905
-  SingletonE -3.04161
-  SingletonF 0.0714027
-  SingletonRule -0.889377
-  WordPenalty -1.99495
-  RulePenalty -0.1
-  LabellingShape -0.1
-  LHSProb -0.1
-  GenerativeProb -0.1
-);
-
-
-# these features are included by default
-my @DEFAULT_FEATS = qw( PassThrough Glue GlueTop LanguageModel WordPenalty );
-
-
-
-my $FILTERBYF = "$SCRIPT_DIR/scripts/filter-by-f.pl";
-my $CDEC = "$SCRIPT_DIR/../../decoder/cdec";
-my $PARALLELIZE = "$SCRIPT_DIR/../../vest/parallelize.pl";
-my $EXTOOLS = "$SCRIPT_DIR/../../extools";
-die "Can't find extools: $EXTOOLS" unless -e $EXTOOLS && -d $EXTOOLS;
-my $VEST = "$SCRIPT_DIR/../../vest";
-die "Can't find vest: $VEST" unless -e $VEST && -d $VEST;
-my $DISTVEST = "$VEST/dist-vest.pl";
-my $FILTER = "$EXTOOLS/filter_grammar";
-my $FEATURIZE = "$EXTOOLS/featurize_grammar";
-assert_exec($CDEC, $PARALLELIZE, $FILTER, $FEATURIZE, $DISTVEST, $FILTERBYF);
-
-my $numtopics = 25;
-
-my $config = "$SCRIPT_DIR/" . (lc environment_name()) . '.config';
-print STDERR "CORPORA CONFIGURATION: $config\n";
-open CONF, "<$config" or die "Can't read $config: $!";
-my %paths;
-my %corpora;
-my %lms;
-my %devs;
-my %devrefs;
-my %tests;
-my %testevals;
-my $datadir;
-print STDERR "       LANGUAGE PAIRS:";
-while(<CONF>) {
-  chomp;
-  next if /^#/;
-  next if /^\s*$/;
-  s/^\s+//;
-  s/\s+$//;
-  if (! defined $datadir) { $datadir = $_; next; }
-  my ($name, $path, $corpus, $lm, $dev, $devref, @xtests) = split /\s+/;
-  $paths{$name} = $path;
-  $corpora{$name} = $corpus;
-  $lms{$name} = $lm;
-  $devs{$name} = $dev;
-  $devrefs{$name} = $devref;
-  $tests{$name} = $xtests[0];
-  $testevals{$name} = $xtests[1];
-  print STDERR " $name";
-}
-print STDERR "\n";
-
-my %langpairs = map { $_ => 1 } qw( btec zhen fbis aren uren nlfr );
-
-my $outdir = "$CWD/exp";
-my $help;
-my $FEATURIZER_OPTS = '';
-my $dataDir = '/export/ws10smt/data';
-my @features;
-my $bkoffgram;
-my $gluegram;
-my $oovgram;
-my $usefork;
-my $lmorder = 3;
-my $density;
-if (GetOptions(
-        "backoff-grammar=s" => \$bkoffgram,
-        "density-prune=f" => \$density,
-        "glue-grammar=s" => \$gluegram,
-        "oov-grammar=s" => \$oovgram,
-        "data=s" => \$dataDir,
-        "pmem=s" => \$PMEM,
-        "n=i" => \$NUM_TRANSLATIONS,
-        "features=s@" => \@features,
-        "use-fork" => \$usefork,
-        "jobs=i" => \$JOBS,
-        "out-dir=s" => \$outdir,
-        "lmorder=i" => \$lmorder,
-        "goal=s" => \$GOAL,
-) == 0 || @ARGV!=2 || $help) {
-        print_help();
-        exit;
-}
-my $DENSITY_PRUNE = '';
-if ($density) {
-  $DENSITY_PRUNE = "--density-prune $density";
-}
-if ($usefork) { $usefork="--use-fork"; } else { $usefork = ''; }
-my @fkeys = keys %$feat_map;
-die "You must specify one or more features with -f. Known features: @fkeys\n" unless scalar @features > 0;
-my @xfeats;
-for my $feat (@features) {
-  my $rs = $feat_map->{$feat};
-  if (!defined $rs) { die "DON'T KNOW ABOUT FEATURE $feat\n"; }
-  my @xfs = @$rs;
-  @xfeats = (@xfeats, @xfs);
-  $FEATURIZER_OPTS .= " -f $feat" unless $feat eq "BackoffRule";
-}
-print STDERR "X-FEATS: @xfeats\n";
-
-my $lp = $ARGV[0];
-my $grammar = $ARGV[1];
-print STDERR "   CORPUS REPO: $dataDir\n";
-print STDERR " LANGUAGE PAIR: $lp\n";
-die "I don't know about that language pair\n" unless $paths{$lp};
-my $corpdir = "$dataDir";
-if ($paths{$lp} =~ /^\//) { $corpdir = $paths{$lp}; } else { $corpdir .= '/' . $paths{$lp}; }
-die "I can't find the corpora directory: $corpdir" unless -d $corpdir;
-print STDERR "       GRAMMAR: $grammar\n";
-my $LANG_MODEL = mydircat($corpdir, $lms{$lp});
-print STDERR "            LM: $LANG_MODEL\n";
-my $CORPUS = mydircat($corpdir, $corpora{$lp});
-die "Can't find corpus: $CORPUS" unless -f $CORPUS;
-
-my $dev = mydircat($corpdir, $devs{$lp});
-my $drefs = $devrefs{$lp};
-die "Can't find dev: $dev\n" unless -f $dev;
-die "Dev refs not set" unless $drefs;
-$drefs = mydircat($corpdir, $drefs);
-
-my $test = mydircat($corpdir, $tests{$lp});
-my $teval = mydircat($corpdir, $testevals{$lp});
-#die "Can't find test: $test\n" unless -f $test;
-#assert_exec($teval);
-
-`mkdir -p $outdir`;
-
-# CREATE INIT WEIGHTS
-print STDERR "\nCREATING INITIAL WEIGHTS FILE: weights.init\n";
-my $weights = mydircat($outdir, "weights.init");
-write_random_weights_file($weights, @xfeats);
-
-my $bkoff_grmr;
-my $glue_grmr;
-if($bkoffgram) {
-    print STDERR "Placing backoff grammar…\n";
-    $bkoff_grmr = mydircat($outdir, "backoff.scfg.gz");
-    print STDERR "cp $bkoffgram $bkoff_grmr\n";
-    safesystem(undef,"cp $bkoffgram $bkoff_grmr");
-}
-if($gluegram) {
-    print STDERR "Placing glue grammar…\n";
-    $glue_grmr = mydircat($outdir, "glue.bo.scfg.gz");
-    print STDERR "cp $gluegram $glue_grmr\n";
-    safesystem(undef,"cp $gluegram $glue_grmr");
-}
-
-# MAKE DEV
-print STDERR "\nFILTERING FOR dev...\n";
-print STDERR "DEV: $dev (REFS=$drefs)\n";
-my $devgrammar = filter($grammar, $dev, 'dev', $outdir);
-my $devini = mydircat($outdir, "cdec-dev.ini");
-write_cdec_ini($devini, $devgrammar);
-
-
-# MAKE TEST
-print STDERR "\nFILTERING FOR test...\n";
-print STDERR "TEST: $test (EVAL=$teval)\n";
-`mkdir -p $outdir`;
-my $testgrammar = filter($grammar, $test, 'test', $outdir);
-my $testini = mydircat($outdir, "cdec-test.ini");
-write_cdec_ini($testini, $testgrammar);
-
-
-# VEST
-print STDERR "\nMINIMUM ERROR TRAINING\n";
-my $tuned_weights = mydircat($outdir, 'weights.tuned');
-if (-f $tuned_weights) {
-  print STDERR "TUNED WEIGHTS $tuned_weights EXISTS: REUSING\n";
-} else {
-  my $cmd = "$DISTVEST $usefork $DENSITY_PRUNE --decode-nodes $JOBS --pmem=$PMEM --ref-files=$drefs --source-file=$dev --weights $weights $devini";
-  print STDERR "MERT COMMAND: $cmd\n";
-  `rm -rf $outdir/vest 2> /dev/null`;
-  chdir $outdir or die "Can't chdir to $outdir: $!";
-  $weights = `$cmd`;
-  die "MERT reported non-zero exit code" unless $? == 0;
-  chomp $weights;
-  safesystem($tuned_weights, "cp $weights $tuned_weights");
-  print STDERR "TUNED WEIGHTS: $tuned_weights\n";
-  die "$tuned_weights is missing!" unless -f $tuned_weights;
-}
-
-# DECODE
-print STDERR "\nDECODE TEST SET\n";
-my $decolog = mydircat($outdir, "test-decode.log");
-my $testtrans = mydircat($outdir, "test.trans");
-my $cmd = "cat $test | $PARALLELIZE $usefork -j $JOBS -e $decolog -- $CDEC -c $testini -w $tuned_weights > $testtrans";
-safesystem($testtrans, $cmd) or die "Failed to decode test set!";
-
-
-# EVALUATE
-print STDERR "\nEVALUATE TEST SET\n";
-print STDERR "TEST: $testtrans\n";
-$cmd = "$teval $testtrans";
-safesystem(undef, $cmd) or die "Failed to evaluate!";
-exit 0;
-
-
-sub write_random_weights_file {
-  my ($file, @extras) = @_;
-  if (-f $file) {
-    print STDERR "$file exists - REUSING!\n";
-    return;
-  }
-  open F, ">$file" or die "Can't write $file: $!";
-  my @feats = (@DEFAULT_FEATS, @extras);
-  for my $feat (@feats) {
-    my $r = rand(0.4) + 0.8;
-    my $w = $init_weights{$feat} * $r;
-    if ($w == 0) { $w = 0.0001; print STDERR "WARNING: $feat had no initial weight!\n"; }
-    print F "$feat $w\n";
-  }
-  close F;
-}
-
-sub filter {
-  my ($grammar, $set, $name, $outdir) = @_;
-  my $out1 = mydircat($outdir, "$name.filt.gz");
-  my $out2 = mydircat($outdir, "$name.f_feat.gz");
-  my $outgrammar = mydircat($outdir, "$name.scfg.gz");
-  if (-f $outgrammar) { print STDERR "$outgrammar exists - REUSING!\n"; } else {
-    my $cmd = "gunzip -c $grammar | $FILTER -t $set | gzip > $out1";
-    safesystem($out1, $cmd) or die "Filtering failed.";
-    $cmd = "gunzip -c $out1 | $FEATURIZE $FEATURIZER_OPTS -g $out1 -c $CORPUS | gzip > $out2";
-    safesystem($out2, $cmd) or die "Featurizing failed";
-    $cmd = "$FILTERBYF $NUM_TRANSLATIONS $out2 $outgrammar";
-    safesystem($outgrammar, $cmd) or die "Secondary filtering failed";
-  }
-  return $outgrammar;
-}  
-
-sub mydircat {
- my ($base, $suffix) = @_;
- if ($suffix =~ /^\//) { return $suffix; }
- my $res = $base . '/' . $suffix;
- $res =~ s/\/\//\//g;
- return $res;
-}
-
-sub write_cdec_ini {
-  my ($filename, $grammar_path) = (@_);
-  open CDECINI, ">$filename" or die "Can't write $filename: $!";
-  my $glue = ($gluegram ? "$glue_grmr" : "$datadir/glue/glue.scfg.gz");
-  my $oov = ($oovgram ? "$oovgram" : "$datadir/oov.scfg.gz");
-  print CDECINI <<EOT;
-formalism=scfg
-cubepruning_pop_limit=100
-add_pass_through_rules=true
-scfg_extra_glue_grammar=$glue
-grammar=$oov
-grammar=$grammar_path
-scfg_default_nt=OOV
-scfg_no_hiero_glue_grammar=true
-feature_function=WordPenalty
-feature_function=LanguageModel -o $lmorder $LANG_MODEL
-goal=$GOAL
-EOT
-  print CDECINI "grammar=$bkoff_grmr\n" if $bkoffgram;
-  close CDECINI;
-};
-
-sub print_help {
-  print STDERR<<EOT;
-
-Usage: $0 [-c data-config-file] [-n N] language-pair grammar.bidir.gz [OPTIONS]
-
-Given an induced grammar for an entire corpus (i.e., generated by
-local-gi-pipeline.pl), filter and featurize it for a dev and test set,
-run MERT, report scores. Use -n to specify the number of translations
-to keep for a given source (30 is default).
-
-EOT
-}
-
-sub safesystem {
-  my $output = shift @_;
-  print STDERR "Executing: @_\n";
-  system(@_);
-  if ($? == -1) {
-      print STDERR "ERROR: Failed to execute: @_\n  $!\n";
-      if (defined $output && -e $output) { printf STDERR "Removing $output\n"; `rm -rf $output`; }
-      exit(1);
-  }
-  elsif ($? & 127) {
-      printf STDERR "ERROR: Execution of: @_\n  died with signal %d, %s coredump\n",
-          ($? & 127),  ($? & 128) ? 'with' : 'without';
-      if (defined $output && -e $output) { printf STDERR "Removing $output\n"; `rm -rf $output`; }
-      exit(1);
-  }
-  else {
-    my $exitcode = $? >> 8;
-    if ($exitcode) {
-      print STDERR "Exit code: $exitcode\n";
-      if (defined $output && -e $output) { printf STDERR "Removing $output\n"; `rm -rf $output`; }
-    }
-    return ! $exitcode;
-  }
-}
-
-sub assert_exec {
-  my @files = @_;
-  for my $file (@files) {
-    die "Can't find $file - did you run make?\n" unless -e $file;
-    die "Can't execute $file" unless -e $file;
-  }
-};
-
diff --git a/gi/pipeline/local-gi-pipeline.pl b/gi/pipeline/local-gi-pipeline.pl
deleted file mode 100755
index e31167a2..00000000
--- a/gi/pipeline/local-gi-pipeline.pl
+++ /dev/null
@@ -1,465 +0,0 @@
-#!/usr/bin/perl -w
-use strict;
-use File::Copy;
-
-my $SCRIPT_DIR; BEGIN { use Cwd qw/ abs_path cwd /; use File::Basename; $SCRIPT_DIR = dirname(abs_path($0)); push @INC, $SCRIPT_DIR; }
-
-use Getopt::Long "GetOptions";
-
-my $GZIP = 'gzip';
-my $ZCAT = 'gunzip -c';
-my $SED = 'sed -e';
-my $BASE_PHRASE_MAX_SIZE = 10;
-my $COMPLETE_CACHE = 1;
-my $ITEMS_IN_MEMORY = 10000000;  # cache size in extractors
-my $NUM_TOPICS = 50;
-my $NUM_TOPICS_COARSE;
-my $NUM_TOPICS_FINE = $NUM_TOPICS;
-my $NUM_SAMPLES = 1000;
-my $CONTEXT_SIZE = 1;
-my $BIDIR = 0;
-my $TOPICS_CONFIG = "pyp-topics.conf";
-my $LANGUAGE = "target";
-my $LABEL_THRESHOLD = "0";
-my $PRESERVE_PHRASES;
-
-my $MODEL = "pyp";
-my $NUM_ITERS = 100;
-my $PR_SCALE_P = 0;
-my $PR_SCALE_C = 0;
-my $PR_FLAGS = "";
-my $MORFMARK = "";
-
-my $EXTOOLS = "$SCRIPT_DIR/../../extools";
-die "Can't find extools: $EXTOOLS" unless -e $EXTOOLS && -d $EXTOOLS;
-my $PYPTOOLS = "$SCRIPT_DIR/../pyp-topics/src";
-die "Can't find pyp-topics: $PYPTOOLS" unless -e $PYPTOOLS && -d $PYPTOOLS;
-my $PYPSCRIPTS = "$SCRIPT_DIR/../pyp-topics/scripts";
-die "Can't find pyp-topics: $PYPSCRIPTS" unless -e $PYPSCRIPTS && -d $PYPSCRIPTS;
-my $PRTOOLS = "$SCRIPT_DIR/../posterior-regularisation";
-die "Can't find posterior-regularisation: $PRTOOLS" unless -e $PRTOOLS && -d $PRTOOLS;
-my $REDUCER = "$EXTOOLS/mr_stripe_rule_reduce";
-my $C2D = "$PYPSCRIPTS/contexts2documents.py";
-my $S2L = "$PYPSCRIPTS/spans2labels.py";
-my $SPLIT = "$SCRIPT_DIR/../posterior-regularisation/split-languages.py";
-
-my $PREM_TRAIN="$PRTOOLS/prjava/train-PR-cluster.sh";
-
-my $SORT_KEYS = "$SCRIPT_DIR/scripts/sort-by-key.sh";
-my $PATCH_CORPUS = "$SCRIPT_DIR/scripts/patch-corpus.pl";
-my $REMOVE_TAGS_CORPUS = "$SCRIPT_DIR/scripts/remove-tags-from-corpus.pl";
-my $REMOVE_TAGS_CONTEXT = "$SCRIPT_DIR/scripts/remove-tags-from-contexts.pl";
-my $EXTRACTOR = "$EXTOOLS/extractor";
-my $TOPIC_TRAIN = "$PYPTOOLS/pyp-contexts-train";
-my $MORF_DOC_FILTER = "$SCRIPT_DIR/../morf-segmentation/filter_docs.pl";
-
-assert_exec($PATCH_CORPUS, $SORT_KEYS, $REDUCER, $EXTRACTOR,
-            $S2L, $C2D, $TOPIC_TRAIN, $SPLIT, $REMOVE_TAGS_CONTEXT, $REMOVE_TAGS_CORPUS, $MORF_DOC_FILTER);
-
-my $BACKOFF_GRAMMAR;
-my $DEFAULT_CAT;
-my $HIER_CAT;
-my %FREQ_HIER = ();
-my $TAGGED_CORPUS;
-
-my $NAME_SHORTCUT;
-
-my $OUTPUT = './giwork';
-usage() unless &GetOptions('base_phrase_max_size=i' => \$BASE_PHRASE_MAX_SIZE,
-                           'backoff_grammar' => \$BACKOFF_GRAMMAR,
-                           'output=s' => \$OUTPUT,
-                           'model=s' => \$MODEL,
-                           'topics=i' => \$NUM_TOPICS_FINE,
-                           'coarse_topics=i' => \$NUM_TOPICS_COARSE,
-                           'trg_context=i' => \$CONTEXT_SIZE,
-                           'samples=i' => \$NUM_SAMPLES,
-                           'label_threshold=f' => \$LABEL_THRESHOLD,
-                           'use_default_cat' => \$DEFAULT_CAT,
-                           'topics-config=s' => \$TOPICS_CONFIG,
-                           'iterations=i' => \$NUM_ITERS,
-                           'pr-scale-phrase=f' => \$PR_SCALE_P,
-                           'pr-scale-context=f' => \$PR_SCALE_C,
-                           'pr-flags=s' => \$PR_FLAGS,
-                           'tagged_corpus=s' => \$TAGGED_CORPUS,
-                           'language=s' => \$LANGUAGE,
-                           'get_name_only' => \$NAME_SHORTCUT,
-                           'preserve_phrases' => \$PRESERVE_PHRASES,
-                           'morf=s' => \$MORFMARK,
-                          );
-if ($NAME_SHORTCUT) {
-  $NUM_TOPICS = $NUM_TOPICS_FINE;
-  print STDERR labeled_dir();
-  exit 0;
-}
-usage() unless scalar @ARGV == 1;
-my $CORPUS = $ARGV[0];
-open F, "<$CORPUS" or die "Can't read $CORPUS: $!"; close F;
-
-$NUM_TOPICS = $NUM_TOPICS_FINE;
-
-$HIER_CAT = ( $NUM_TOPICS_COARSE ? 1 : 0 );
-
-print STDERR "   Output: $OUTPUT\n";
-my $DATA_DIR = $OUTPUT . '/corpora';
-my $LEX_NAME = "corpus.f_e_a.$LANGUAGE.lex";
-my $CORPUS_LEX = $DATA_DIR . '/' . $LEX_NAME;  # corpus used to extract rules
-my $CORPUS_CLUSTER = $DATA_DIR . "/corpus.f_e_a.$LANGUAGE.cluster"; # corpus used for clustering (often identical)
-
-my $CONTEXT_DIR = $OUTPUT . '/' . context_dir();
-my $CLUSTER_DIR = $OUTPUT . '/' . cluster_dir();
-my $LABELED_DIR = $OUTPUT . '/' . labeled_dir();
-my $CLUSTER_DIR_C;
-my $CLUSTER_DIR_F;
-my $LABELED_DIR_C;
-my $LABELED_DIR_F;
-if($HIER_CAT) {
-    $CLUSTER_DIR_F = $CLUSTER_DIR;
-    $LABELED_DIR_F = $LABELED_DIR;
-    $NUM_TOPICS = $NUM_TOPICS_COARSE;
-    $CLUSTER_DIR_C = $OUTPUT . '/' . cluster_dir();
-    $LABELED_DIR_C = $OUTPUT . '/' . labeled_dir();
-    $NUM_TOPICS = $NUM_TOPICS_FINE;
-}
-my $GRAMMAR_DIR = $OUTPUT . '/' . grammar_dir();
-print STDERR "  Context: $CONTEXT_DIR\n  Cluster: $CLUSTER_DIR\n  Labeled: $LABELED_DIR\n  Grammar: $GRAMMAR_DIR\n";
-safemkdir($OUTPUT) or die "Couldn't create output directory $OUTPUT: $!";
-safemkdir($DATA_DIR) or die "Couldn't create output directory $DATA_DIR: $!";
-safemkdir($CONTEXT_DIR) or die "Couldn't create output directory $CONTEXT_DIR: $!";
-safemkdir($CLUSTER_DIR) or die "Couldn't create output directory $CLUSTER_DIR: $!";
-if($HIER_CAT) {
-    safemkdir($CLUSTER_DIR_C) or die "Couldn't create output directory $CLUSTER_DIR_C: $!";
-    safemkdir($LABELED_DIR_C) or die "Couldn't create output directory $LABELED_DIR_C: $!";
-}
-safemkdir($LABELED_DIR) or die "Couldn't create output directory $LABELED_DIR: $!";
-safemkdir($GRAMMAR_DIR) or die "Couldn't create output directory $GRAMMAR_DIR: $!";
-if(-e $TOPICS_CONFIG) {
-    copy($TOPICS_CONFIG, $CLUSTER_DIR) or die "Copy failed: $!";
-}
-
-setup_data();
-
-if (lc($MODEL) eq "blagree") {
-    extract_bilingual_context();
-} else {
-    extract_context();
-}
-
-if (lc($MODEL) eq "pyp") {
-    if($HIER_CAT) {
-        $NUM_TOPICS = $NUM_TOPICS_COARSE;
-        $CLUSTER_DIR = $CLUSTER_DIR_C;
-        topic_train();
-        $NUM_TOPICS = $NUM_TOPICS_FINE;
-        $CLUSTER_DIR = $CLUSTER_DIR_F;
-        topic_train();
-    } else {
-        topic_train();
-    }
-} elsif (lc($MODEL) =~ /pr|em|agree/) {
-    prem_train();
-} else { die "Unsupported model type: $MODEL. Must be one of PYP or PREM.\n"; }
-if($HIER_CAT) {
-    $NUM_TOPICS = $NUM_TOPICS_COARSE;
-    $CLUSTER_DIR = $CLUSTER_DIR_C;
-    $LABELED_DIR = $LABELED_DIR_C;
-    label_spans_with_topics();
-    $NUM_TOPICS = $NUM_TOPICS_FINE;
-    $CLUSTER_DIR = $CLUSTER_DIR_F;
-    $LABELED_DIR = $LABELED_DIR_F;
-    label_spans_with_topics();
-    extract_freqs();
-} else {
-    label_spans_with_topics();
-}
-my $res;
-if ($BIDIR) {
-  $res = grammar_extract_bidir();
-} else {
-  $res = grammar_extract();
-}
-print STDERR "\n!!!COMPLETE!!!\n";
-print STDERR "GRAMMAR: $res\nYou should probably run: $SCRIPT_DIR/evaluation-pipeline.pl LANGPAIR giwork/ct1s0.L10.PYP.t4.s20.grammar/grammar.gz -f FEAT1 -f FEAT2\n\n";
-exit 0;
-
-sub setup_data {
-  print STDERR "\n!!!PREPARE CORPORA!!!\n";
-  if (-f $CORPUS_LEX && $CORPUS_CLUSTER) {
-    print STDERR "$CORPUS_LEX and $CORPUS_CLUSTER exist, reusing...\n";
-    return;
-  }
-  copy($CORPUS, $CORPUS_LEX);
-  if ($TAGGED_CORPUS) {
-    die "Can't find $TAGGED_CORPUS" unless -f $TAGGED_CORPUS;
-    my $opt="";
-    $opt = "-s" if ($LANGUAGE eq "source");
-    $opt = $opt . " -a" if ($PRESERVE_PHRASES);
-    my $cmd="$PATCH_CORPUS $opt $TAGGED_CORPUS $CORPUS_LEX > $CORPUS_CLUSTER";
-    safesystem($cmd) or die "Failed to extract contexts.";
-  } else {
-    symlink($LEX_NAME, $CORPUS_CLUSTER);
-  }
-}
-
-sub context_dir {
-  return "ct${CONTEXT_SIZE}s0.L$BASE_PHRASE_MAX_SIZE.l$LANGUAGE";
-}
-
-sub cluster_dir {
-    if (lc($MODEL) eq "pyp") {
-        return context_dir() . ".PYP.t$NUM_TOPICS.s$NUM_SAMPLES";
-    } elsif (lc($MODEL) eq "em") {
-        return context_dir() . ".EM.t$NUM_TOPICS.i$NUM_ITERS";
-    } elsif (lc($MODEL) eq "pr") {
-        return context_dir() . ".PR.t$NUM_TOPICS.i$NUM_ITERS.sp$PR_SCALE_P.sc$PR_SCALE_C";
-    } elsif (lc($MODEL) eq "agree") {
-        return context_dir() . ".AGREE.t$NUM_TOPICS.i$NUM_ITERS";
-    } elsif (lc($MODEL) eq "blagree") {
-        return context_dir() . ".BLAGREE.t$NUM_TOPICS.i$NUM_ITERS";
-    }
-}
-
-sub labeled_dir {
-  if (lc($MODEL) eq "pyp" && $LABEL_THRESHOLD ne "0") {
-    return cluster_dir() . "_lt$LABEL_THRESHOLD";
-  } else {
-    return cluster_dir();
-  }
-}
-
-sub grammar_dir {
-  # TODO add grammar config options -- adjacent NTs, etc
-  if($HIER_CAT) {
-    return cluster_dir() . ".hier$NUM_TOPICS_COARSE-$NUM_TOPICS_FINE.grammar";
-  } else {
-    return labeled_dir() . ".grammar";
-  }
-}
-
-
-
-sub safemkdir {
-  my $dir = shift;
-  if (-d $dir) { return 1; }
-  return mkdir($dir);
-}
-
-sub usage {
-  print <<EOT;
-
-Usage: $0 [OPTIONS] corpus.fr-en-al
-
-Induces a grammar using Pitman-Yor topic modeling or Posterior Regularisation.
-
-EOT
-  exit 1;
-};
-
-sub assert_exec {
-  my @files = @_;
-  for my $file (@files) {
-    die "Can't find $file - did you run make?\n" unless -e $file;
-    die "Can't execute $file" unless -e $file;
-  }
-};
-
-sub extract_context {
- print STDERR "\n!!!CONTEXT EXTRACTION\n"; 
- my $OUT_CONTEXTS = "$CONTEXT_DIR/context.txt.gz";
- if (-e $OUT_CONTEXTS) {
-   print STDERR "$OUT_CONTEXTS exists, reusing...\n";
- } else {
-   my $ccopt = "-c $ITEMS_IN_MEMORY";
-   my $postsort = "| $REDUCER ";
-   if ($COMPLETE_CACHE) {
-     print STDERR "COMPLETE_CACHE is set: removing memory limits on cache.\n";
-     $ccopt = "-c 0";
-     $postsort = "" unless ($PRESERVE_PHRASES);
-   }
-
-   my $presort = ($PRESERVE_PHRASES ? "| $REMOVE_TAGS_CONTEXT --phrase=tok --context=tag " : "");
-
-   if ($MORFMARK ne "") { 
-     $presort = $presort . "| $MORF_DOC_FILTER \"$MORFMARK\" "; 
-   }
-
-   my $cmd = "$EXTRACTOR -i $CORPUS_CLUSTER $ccopt -L $BASE_PHRASE_MAX_SIZE -C -S $CONTEXT_SIZE --phrase_language $LANGUAGE --context_language $LANGUAGE $presort | $SORT_KEYS $postsort | $GZIP > $OUT_CONTEXTS";
-   safesystem($cmd) or die "Failed to extract contexts.";
-  }
-}
-
-sub extract_bilingual_context {
- print STDERR "\n!!!CONTEXT EXTRACTION\n"; 
- my $OUT_SRC_CONTEXTS = "$CONTEXT_DIR/context.source";
- my $OUT_TGT_CONTEXTS = "$CONTEXT_DIR/context.target";
-
- if (-e $OUT_SRC_CONTEXTS . ".gz" and -e $OUT_TGT_CONTEXTS . ".gz") {
-   print STDERR "$OUT_SRC_CONTEXTS.gz and $OUT_TGT_CONTEXTS.gz exist, reusing...\n";
- } else {
-   my $OUT_BI_CONTEXTS = "$CONTEXT_DIR/context.bilingual.txt.gz";
-   my $cmd = "$EXTRACTOR -i $CORPUS_CLUSTER -c $ITEMS_IN_MEMORY -L $BASE_PHRASE_MAX_SIZE -C -S $CONTEXT_SIZE --phrase_language both --context_language both | $SORT_KEYS | $REDUCER | $GZIP > $OUT_BI_CONTEXTS";
-   if ($COMPLETE_CACHE) {
-     print STDERR "COMPLETE_CACHE is set: removing memory limits on cache.\n";
-     $cmd = "$EXTRACTOR -i $CORPUS_CLUSTER -c 0 -L $BASE_PHRASE_MAX_SIZE -C -S $CONTEXT_SIZE  --phrase_language both --context_language both  | $SORT_KEYS | $GZIP > $OUT_BI_CONTEXTS";
-   }
-   safesystem($cmd) or die "Failed to extract contexts.";
-
-   safesystem("$ZCAT $OUT_BI_CONTEXTS | $SPLIT $OUT_SRC_CONTEXTS $OUT_TGT_CONTEXTS") or die "Failed to split contexts.\n";
-   safesystem("$GZIP -f $OUT_SRC_CONTEXTS") or die "Failed to zip output contexts.\n";
-   safesystem("$GZIP -f $OUT_TGT_CONTEXTS") or die "Failed to zip output contexts.\n";
- }
-}
-
-
-sub topic_train {
-  print STDERR "\n!!!TRAIN PYP TOPICS\n";
-  my $IN_CONTEXTS = "$CONTEXT_DIR/context.txt.gz";
-  my $OUT_CLUSTERS = "$CLUSTER_DIR/docs.txt.gz";
-  if (-e $OUT_CLUSTERS) {
-    print STDERR "$OUT_CLUSTERS exists, reusing...\n";
-  } else {
-    safesystem("$TOPIC_TRAIN --data $IN_CONTEXTS --backoff-type simple -t $NUM_TOPICS -s $NUM_SAMPLES -o $OUT_CLUSTERS -c $TOPICS_CONFIG -w /dev/null") or die "Topic training failed.\n";
-  }
-}
-
-sub prem_train {
-  print STDERR "\n!!!TRAIN PR/EM model\n";
-  my $OUT_CLUSTERS = "$CLUSTER_DIR/docs.txt.gz";
-  if (-e $OUT_CLUSTERS) {
-    print STDERR "$OUT_CLUSTERS exists, reusing...\n";
-  } else {
-    my $in = "--in $CONTEXT_DIR/context.txt.gz";
-    my $opts = "";
-    if (lc($MODEL) eq "pr") {
-        $opts = "--scale-phrase $PR_SCALE_P --scale-context $PR_SCALE_C";
-    } elsif (lc($MODEL) eq "agree") {
-        $opts = "--agree-direction";
-    } elsif (lc($MODEL) eq "blagree") {
-        $in = "--in $CONTEXT_DIR/context.source.gz --in1 $CONTEXT_DIR/context.target.gz";
-        $opts = "--agree-language";
-    }
-    safesystem("$PREM_TRAIN $in --topics $NUM_TOPICS --out $OUT_CLUSTERS --iterations $NUM_ITERS $opts $PR_FLAGS") or die "Topic training failed.\n";
-  }
-}
-
-sub label_spans_with_topics {
-  my ($file) = (@_);
-  print STDERR "\n!!!LABEL SPANS\n";
-  my $IN_CLUSTERS = "$CLUSTER_DIR/docs.txt.gz";
-  my $OUT_SPANS = "$LABELED_DIR/labeled_spans.txt";
-  if (-e $OUT_SPANS) {
-    print STDERR "$OUT_SPANS exists, reusing...\n";
-  } else {
-    my $extra = "tt";
-    if ($LANGUAGE eq "source") {
-        $extra = "ss";
-    } elsif ($LANGUAGE eq "both") {
-        $extra = "bb";
-    } else { die "Invalid language specifier $LANGUAGE\n" unless $LANGUAGE eq "target" };
-    $extra = $extra . " tok,tag" if ($PRESERVE_PHRASES);
-    safesystem("$ZCAT $IN_CLUSTERS > $CLUSTER_DIR/clusters.txt") or die "Failed to unzip";
-    safesystem("$EXTRACTOR --base_phrase_spans -i $CORPUS_CLUSTER -c $ITEMS_IN_MEMORY -L $BASE_PHRASE_MAX_SIZE -S $CONTEXT_SIZE | $S2L $CLUSTER_DIR/clusters.txt $CONTEXT_SIZE $LABEL_THRESHOLD $extra > $OUT_SPANS") or die "Failed to label spans";
-    unlink("$CLUSTER_DIR/clusters.txt") or warn "Failed to remove $CLUSTER_DIR/clusters.txt";
-    safesystem("paste -d ' ' $CORPUS_LEX $OUT_SPANS | sed 's/ *||| *\$//'  > $LABELED_DIR/corpus.src_trg_al_label") or die "Couldn't paste";
-  }
-}
-
-sub extract_freqs {
-    print STDERR "\n!!!EXTRACTING FREQUENCIES\n";
-    my $IN_COARSE = "$LABELED_DIR_C/labeled_spans.txt";
-    my $IN_FINE = "$LABELED_DIR_F/labeled_spans.txt";
-    my $OUT_SPANS = "$LABELED_DIR_F/labeled_spans.hier$NUM_TOPICS_COARSE-$NUM_TOPICS_FINE.txt";
-    my $FREQS = "$LABELED_DIR_F/label_freq.hier$NUM_TOPICS_COARSE-$NUM_TOPICS_FINE.txt";
-    my $COARSE_EXPR = "\'s/\\(X[0-9][0-9]*\\)/\\1c/g\'"; #'
-    my $FINE_EXPR = "\'s/\\(X[0-9][0-9]*\\)/\\1f/g\'"; #'
-    my %finehier = ();
-    if (-e $OUT_SPANS) {
-        print STDERR "$OUT_SPANS exists, reusing...\n";
-    } else {
-        safesystem("paste -d ' ' $IN_COARSE $IN_FINE > $OUT_SPANS");
-    }
-    open SPANS, $OUT_SPANS or die $!;
-    while (<SPANS>) {
-        my ($tmp, $coarse, $fine) = split /\|\|\|/;
-        my @coarse_spans = $coarse =~ /\d+-\d+:X(\d+)/g;
-        my @fine_spans = $fine =~ /\d+-\d+:X(\d+)/g;
-        
-        foreach my $i (0..(scalar @coarse_spans)-1) {
-            my $coarse_cat = $coarse_spans[$i];
-            my $fine_cat = $fine_spans[$i];
-            
-            $FREQ_HIER{$coarse_cat}{$fine_cat}++;
-        }
-    }
-    close SPANS;
-    foreach (values %FREQ_HIER) {
-        my $coarse_freq = $_;
-        my $total = 0;
-        $total+=$_ for (values %{ $coarse_freq });
-        $coarse_freq->{$_}=log($coarse_freq->{$_}/$total) for (keys %{ $coarse_freq });
-    }
-    open FREQS, ">", $FREQS or die $!;
-    foreach my $coarse_cat (keys %FREQ_HIER) {
-        print FREQS "$coarse_cat |||";
-        foreach my $fine_cat (keys %{$FREQ_HIER{$coarse_cat}}) {
-            my $res = $FREQ_HIER{$coarse_cat}{$fine_cat};
-            print FREQS " $fine_cat:$res";
-            if(! exists $finehier{$fine_cat} || $finehier{$fine_cat} < $res) {
-               $finehier{$fine_cat} = $coarse_cat;
-            }  
-        }
-        print FREQS "\n";
-    }
-#    foreach my $fine_cat (keys %finehier) {
-#        print FREQS "$fine_cat -> $finehier{$fine_cat}\n";
-#    }
-    close FREQS;
-    $CLUSTER_DIR = $CLUSTER_DIR_F;
-}
-
-sub grammar_extract {
-  my $LABELED = "$LABELED_DIR/corpus.src_trg_al_label";
-  print STDERR "\n!!!EXTRACTING GRAMMAR\n";
-  my $OUTGRAMMAR = "$GRAMMAR_DIR/grammar.gz";
-  if (-e $OUTGRAMMAR) {
-    print STDERR "$OUTGRAMMAR exists, reusing...\n";
-  } else {
-    my $BACKOFF_ARG = ($BACKOFF_GRAMMAR ? "-g" : "");
-    my $DEFAULT_CAT_ARG = ($DEFAULT_CAT ? "-d X" : "");
-    safesystem("$EXTRACTOR -i $LABELED -c $ITEMS_IN_MEMORY -L $BASE_PHRASE_MAX_SIZE -t $NUM_TOPICS $BACKOFF_ARG $DEFAULT_CAT_ARG | $SORT_KEYS | $REDUCER -p | $GZIP > $OUTGRAMMAR") or die "Couldn't extract grammar";
-  }
-  return $OUTGRAMMAR;
-}
-
-sub grammar_extract_bidir {
-#gzcat ex.output.gz | ./mr_stripe_rule_reduce -p -b | sort -t $'\t' -k 1 | ./mr_stripe_rule_reduce | gzip > phrase-table.gz
-  my $LABELED = "$LABELED_DIR/corpus.src_trg_al_label";
-  print STDERR "\n!!!EXTRACTING GRAMMAR\n";
-  my $OUTGRAMMAR = "$GRAMMAR_DIR/grammar.bidir.gz";
-  if (-e $OUTGRAMMAR) {
-    print STDERR "$OUTGRAMMAR exists, reusing...\n";
-  } else {
-    my $BACKOFF_ARG = ($BACKOFF_GRAMMAR ? "-g" : "");
-    safesystem("$EXTRACTOR -i $LABELED -c $ITEMS_IN_MEMORY -L $BASE_PHRASE_MAX_SIZE -b -t $NUM_TOPICS $BACKOFF_ARG | $SORT_KEYS | $REDUCER -p -b | $SORT_KEYS | $REDUCER | $GZIP > $OUTGRAMMAR") or die "Couldn't extract grammar";
-  }
-  return $OUTGRAMMAR;
-}
-
-sub safesystem {
-  print STDERR "Executing: @_\n";
-  system(@_);
-  if ($? == -1) {
-      print STDERR "ERROR: Failed to execute: @_\n  $!\n";
-      exit(1);
-  }
-  elsif ($? & 127) {
-      printf STDERR "ERROR: Execution of: @_\n  died with signal %d, %s coredump\n",
-          ($? & 127),  ($? & 128) ? 'with' : 'without';
-      exit(1);
-  }
-  else {
-    my $exitcode = $? >> 8;
-    print STDERR "Exit code: $exitcode\n" if $exitcode;
-    return ! $exitcode;
-  }
-}
-
diff --git a/gi/pipeline/lticluster.config b/gi/pipeline/lticluster.config
deleted file mode 100644
index 3e23c8cb..00000000
--- a/gi/pipeline/lticluster.config
+++ /dev/null
@@ -1,9 +0,0 @@
-# THIS FILE GIVES THE LOCATIONS OF THE CORPORA USED
-# name path aligned-corpus LM dev dev-refs test1 testt-eval.sh ...
-/home/cdyer/ws10smt-data
-btec /home/cdyer/ws10smt-data/btec/ split.zh-en.al lm/en.3gram.lm.gz devtest/devset1_2.zh devtest/devset1_2.lc.en* devtest/devset3.zh eval-devset3.sh
-zhen /home/cdyer/ws10smt-data/chinese-english corpus.zh-en.al lm/c2e.3gram.lm.gz dev_and_test/mt02.src.txt dev_and_test/mt02.ref.* dev_and_test/mt03.src.txt eval-mt03.sh
-aren /home/cdyer/ws10smt-data/arabic-english corpus.ar-en-al lm/a2e.3gram.lm.gz dev_and_test/dev.src.txt dev_and_test/dev.ref.txt.* dev_and_test/mt05.src.txt eval-mt05.sh
-uren /home/cdyer/ws10smt-data/urdu-english corpus.ur-en.al lm/u2e.en.lm.gz dev/dev.ur dev/dev.en* devtest/devtest.ur eval-devtest.sh
-nlfr /home/cdyer/ws10smt-data/dutch-french corpus.nl-fr.al
-
diff --git a/gi/pipeline/scripts/filter-by-f.pl b/gi/pipeline/scripts/filter-by-f.pl
deleted file mode 100755
index 0cef0606..00000000
--- a/gi/pipeline/scripts/filter-by-f.pl
+++ /dev/null
@@ -1,56 +0,0 @@
-#!/usr/bin/perl -w
-use strict;
-
-my $SCRIPT_DIR; BEGIN { use Cwd qw/ abs_path /; use File::Basename; $SCRIPT_DIR = dirname(abs_path($0)); push @INC, $SCRIPT_DIR; }
-
-my $REKEY="$SCRIPT_DIR/rekey.pl";
-my $REFILTER="$SCRIPT_DIR/refilter.pl";
-my $SORT="$SCRIPT_DIR/sort-by-key.sh";
-assert_exec($REKEY, $REFILTER, $SORT);
-
-
-die "Usage: $0 NUM-TRANSLATIONS ingrammar.gz outgrammar.gz\n" unless scalar @ARGV == 3;
-my $translations = shift @ARGV;
-die "Need number: $translations" unless $translations > 0;
-die unless $ARGV[0] =~ /\.gz$/;
-die unless $ARGV[1] =~ /\.gz$/;
-die if $ARGV[0] eq $ARGV[1];
-die "Can't find $ARGV[0]" unless -f $ARGV[0];
-
-my $cmd = "gunzip -c $ARGV[0] | $REKEY | $SORT | $REFILTER $translations | gzip > $ARGV[1]";
-safesystem($ARGV[1], $cmd) or die "Filtering failed";
-exit 0;
-
-sub assert_exec {
-  my @files = @_;
-  for my $file (@files) {
-    die "Can't find $file - did you run make?\n" unless -e $file;
-    die "Can't execute $file" unless -e $file;
-  }
-};
-
-sub safesystem {
-  my $output = shift @_;
-  print STDERR "Executing: @_\n";
-  system(@_);
-  if ($? == -1) {
-      print STDERR "ERROR: Failed to execute: @_\n  $!\n";
-      if (defined $output && -e $output) { printf STDERR "Removing $output\n"; `rm -rf $output`; }
-      exit(1);
-  }
-  elsif ($? & 127) {
-      printf STDERR "ERROR: Execution of: @_\n  died with signal %d, %s coredump\n",
-          ($? & 127),  ($? & 128) ? 'with' : 'without';
-      if (defined $output && -e $output) { printf STDERR "Removing $output\n"; `rm -rf $output`; }
-      exit(1);
-  }
-  else {
-    my $exitcode = $? >> 8;
-    if ($exitcode) {
-      print STDERR "Exit code: $exitcode\n";
-      if (defined $output && -e $output) { printf STDERR "Removing $output\n"; `rm -rf $output`; }
-    }
-    return ! $exitcode;
-  }
-}
-
diff --git a/gi/pipeline/scripts/patch-corpus.pl b/gi/pipeline/scripts/patch-corpus.pl
deleted file mode 100755
index c0eec43e..00000000
--- a/gi/pipeline/scripts/patch-corpus.pl
+++ /dev/null
@@ -1,65 +0,0 @@
-#!/usr/bin/perl -w
-use strict;
-
-my $PATCH = shift @ARGV;
-my $TGT = 1;
-my $APPEND;
-while ($PATCH eq "-s" || $PATCH eq "-a") {
-    if ($PATCH eq "-s") {
-        undef $TGT;
-    } else {
-        $APPEND = 1;
-    }
-    $PATCH = shift @ARGV;
-}
-
-die "Usage: $0 [-s] [-a] tagged.en[_fr] < lexical.en_fr_al[_...]\n" unless $PATCH;
-
-open P, "<$PATCH" or die "Can't read tagged corpus $PATCH: $!";
-my $first=<P>; close P;
-my @fields = split / \|\|\| /, $first;
-die "Bad format!" if (scalar @fields > 2);
-
-if (scalar @fields != 1) {
-  # TODO support this
-  die "Patching source and target not supported yet!";
-}
-
-my $line = 0;
-open P, "<$PATCH" or die "Can't read tagged corpus $PATCH: $!";
-while(my $pline = <P>) {
-  chomp $pline;
-  $line++;
-  my $line = <>;
-  die "Too few lines in lexical corpus!" unless $line;
-  chomp $line;
-  @fields = split / \|\|\| /, $line;
-  my @pwords = split /\s+/, $pline;
-  if ($TGT) {
-      my @lwords = split /\s+/, $fields[1];
-      die "Length mismatch in line $line!\n" unless (scalar @pwords == scalar @lwords);
-      if ($APPEND) {
-          foreach my $i (0..(scalar @pwords-1)) {
-              $lwords[$i] = $lwords[$i] . '_' . $pwords[$i];
-          }
-          $fields[1] = join ' ', @lwords;
-      } else {
-          $fields[1] = $pline;
-      }
-  } else { # source side
-      my @lwords = split /\s+/, $fields[0];
-      die "Length mismatch in line $line!\n" unless (scalar @pwords == scalar @lwords);
-      if ($APPEND) {
-          foreach my $i (0..(scalar @pwords-1)) {
-              $lwords[$i] = $lwords[$i] . '_' . $pwords[$i];
-          }
-          $fields[0] = join ' ', @lwords;
-      } else {
-          $fields[0] = $pline;
-      }
-  }
-  print join ' ||| ', @fields;
-  print "\n";
-}
-
-
diff --git a/gi/pipeline/scripts/refilter.pl b/gi/pipeline/scripts/refilter.pl
deleted file mode 100755
index a783eb4e..00000000
--- a/gi/pipeline/scripts/refilter.pl
+++ /dev/null
@@ -1,40 +0,0 @@
-#!/usr/bin/perl -w
-use strict;
-
-my $NUM_TRANSLATIONS = shift @ARGV;
-unless ($NUM_TRANSLATIONS) { $NUM_TRANSLATIONS=30; }
-print STDERR "KEEPING $NUM_TRANSLATIONS TRANSLATIONS FOR SOURCE\n";
-
-my $pk = '';
-my %dict;
-while(<>) {
-  s/^(.+)\t//;
-  my $key = $1;
-  if ($key ne $pk) {
-    if ($pk) {
-      emit_dict();
-    }
-    %dict = ();
-    $pk = $key;
-  }
-  my ($lhs, $f, $e, $s) = split / \|\|\| /;
-  my $score = 0;
-  if ($s =~ /XEF=([^ ]+)/) {
-    $score += $1;
-  } else { die; }
-  if ($s =~ /GenerativeProb=([^ ]+)/) {
-    $score += ($1 / 10);
-  } else { die; }
-  $dict{"$lhs ||| $f ||| $e ||| $s"} = $score;
-}
-emit_dict();
-
-sub emit_dict {
-  my $cc = 0;
-  for my $k (sort { $dict{$a} <=> $dict{$b} } keys %dict) {
-    print "$k";
-    $cc++;
-    if ($cc >= $NUM_TRANSLATIONS) { last; }
-  }
-}
-
diff --git a/gi/pipeline/scripts/rekey.pl b/gi/pipeline/scripts/rekey.pl
deleted file mode 100755
index 31eb86b8..00000000
--- a/gi/pipeline/scripts/rekey.pl
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/usr/bin/perl
-
-while(<>) {
-  my ($lhs, $f, $e, $s) = split / \|\|\| /;
-  $f =~ s/\[X[0-9]+\]/\[X\]/g;
-  print "$f\t$_";
-}
-
diff --git a/gi/pipeline/scripts/remove-tags-from-contexts.pl b/gi/pipeline/scripts/remove-tags-from-contexts.pl
deleted file mode 100755
index 20698816..00000000
--- a/gi/pipeline/scripts/remove-tags-from-contexts.pl
+++ /dev/null
@@ -1,53 +0,0 @@
-#!/usr/bin/perl -w
-use strict;
-
-use Getopt::Long "GetOptions";
-
-my $PHRASE = 'tok';
-my $CONTEXT = 'tag';
-
-die "Usage: $0 [--phrase=tok|tag] [--context=tok|tag] < corpus" 
-    unless &GetOptions('phrase=s' => \$PHRASE, 'context=s' => \$CONTEXT);
-
-my $lno = 0;
-while(my $line = <>) {
-    $lno++;
-    chomp $line;
-    my @top = split /\t/, $line;
-    die unless (scalar @top == 2); 
-
-    my @pwords = split /\s+/, $top[0];
-    foreach my $token (@pwords) {
-        #print $token . "\n";
-        my @parts = split /_(?!.*_)/, $token;
-        die unless (scalar @parts == 2); 
-        if ($PHRASE eq "tok") {
-            $token = $parts[0]
-        } elsif ($PHRASE eq "tag") {
-            $token = $parts[1]
-        }
-    }
-
-    my @fields = split / \|\|\| /, $top[1];
-    foreach my $i (0..((scalar @fields) / 2 - 1)) {
-        #print $i . ": " . $fields[2*$i] . " of " . (scalar @fields) . "\n";
-        my @cwords = split /\s+/, $fields[2*$i];
-        foreach my $token (@cwords) {
-            #print $i . ": " . $token . "\n";
-            my @parts = split /_(?!.*_)/, $token;
-            if (scalar @parts == 2) {
-                if ($CONTEXT eq "tok") {
-                    $token = $parts[0]
-                } elsif ($CONTEXT eq "tag") {
-                    $token = $parts[1]
-                }
-            }
-        }
-        $fields[2*$i] = join ' ', @cwords;
-    }
-
-    print join ' ', @pwords;
-    print "\t";
-    print join ' ||| ', @fields;
-    print "\n";
-}
diff --git a/gi/pipeline/scripts/remove-tags-from-corpus.pl b/gi/pipeline/scripts/remove-tags-from-corpus.pl
deleted file mode 100755
index be3e97c0..00000000
--- a/gi/pipeline/scripts/remove-tags-from-corpus.pl
+++ /dev/null
@@ -1,44 +0,0 @@
-#!/usr/bin/perl -w
-use strict;
-
-use Getopt::Long "GetOptions";
-
-my $LANGUAGE = shift @ARGV;
-$LANGUAGE = 'target' unless ($LANGUAGE);
-
-my $lno = 0;
-while(my $line = <>) {
-    $lno++;
-    chomp $line;
-
-    my @fields = split / \|\|\| /, $line;
-
-    if ($LANGUAGE eq "source" or $LANGUAGE eq "both") {
-        my @cwords = split /\s+/, $fields[0];
-        foreach my $token (@cwords) {
-            my @parts = split /_(?!.*_)/, $token;
-            if (scalar @parts == 2) {
-                $token = $parts[0]
-            } else {
-                print STDERR "WARNING: invalid tagged token $token\n";
-            }
-        }
-        $fields[0] = join ' ', @cwords;
-    }
-
-    if ($LANGUAGE eq "target" or $LANGUAGE eq "both") {
-        my @cwords = split /\s+/, $fields[1];
-        foreach my $token (@cwords) {
-            my @parts = split /_(?!.*_)/, $token;
-            if (scalar @parts == 2) {
-                $token = $parts[1]
-            } else {
-                print STDERR "WARNING: invalid tagged token $token\n";
-            }
-        }
-        $fields[0] = join ' ', @cwords;
-    }
-
-    print join ' ||| ', @fields;
-    print "\n";
-}
diff --git a/gi/pipeline/scripts/sort-by-key.sh b/gi/pipeline/scripts/sort-by-key.sh
deleted file mode 100755
index 7ae33e03..00000000
--- a/gi/pipeline/scripts/sort-by-key.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/bin/bash
-
-export LANG=C
-sort -t $'\t' -k 1 -T /tmp -S 6000000000
-
diff --git a/gi/pipeline/scripts/xfeats.pl b/gi/pipeline/scripts/xfeats.pl
deleted file mode 100755
index dc578513..00000000
--- a/gi/pipeline/scripts/xfeats.pl
+++ /dev/null
@@ -1,39 +0,0 @@
-#!/usr/bin/perl -w
-use strict;
-
-die "Usage: $0 x-grammar.scfg[.gz] < cat-grammar.scfg\n" unless scalar @ARGV > 0;
-
-my $xgrammar = shift @ARGV;
-die "Can't find $xgrammar" unless -f $xgrammar;
-my $fh;
-if ($xgrammar =~ /\.gz$/) {
-  open $fh, "gunzip -c $xgrammar|" or die "Can't fork: $!";
-} else {
-  open $fh, "<$xgrammar" or die "Can't read $xgrammar: $!";
-}
-print STDERR "Reading X-feats from $xgrammar...\n";
-my %dict;
-while(<$fh>) {
-  chomp;
-  my ($lhs, $f, $e, $feats) = split / \|\|\| /;
-  my $xfeats;
-  my $cc = 0;
-  my @xfeats = ();
-  while ($feats =~ /(EGivenF|FGivenE|LogRuleCount|LogECount|LogFCount|SingletonRule|SingletonE|SingletonF)=([^ ]+)( |$)/og) {
-    push @xfeats, "X_$1=$2";
-  }
-  #print "$lhs ||| $f ||| $e ||| @xfeats\n";
-  $dict{"$lhs ||| $f ||| $e"} = "@xfeats";
-}
-close $fh;
-
-print STDERR "Add features...\n";
-while(<>) {
-  chomp;
-  my ($lhs, $f, $e) = split / \|\|\| /;
-  $f=~ s/\[[^]]+,([12])\]/\[X,$1\]/g;
-  my $xfeats = $dict{"[X] ||| $f ||| $e"};
-  die "Can't find x features for: $_\n" unless $xfeats;
-  print "$_ $xfeats\n";
-}
-
diff --git a/gi/pipeline/valhalla.config b/gi/pipeline/valhalla.config
deleted file mode 100644
index e00a8485..00000000
--- a/gi/pipeline/valhalla.config
+++ /dev/null
@@ -1,9 +0,0 @@
-# THIS FILE GIVES THE LOCATIONS OF THE CORPORA USED
-# name path aligned-corpus LM dev dev-refs test1 testt-eval.sh ...
-/home/chris/ws10smt/data
-btec /home/chris/ws10smt/data/btec/ split.zh-en.al lm/en.3gram.lm.gz devtest/devset1_2.zh devtest/devset1_2.lc.en* devtest/devset3.zh eval-devset3.sh
-fbis /home/chris/ws10smt/data/chinese-english.fbis corpus.zh-en.al
-zhen /home/chris/ws10smt/data/chinese-english corpus.zh-en.al
-aren /home/chris/ws10smt/data/arabic-english corpus.ar-en.al
-uren /home/chris/ws10smt/data/urdu-english corpus.ur-en.al lm/u2e.en.lm.gz dev/dev.ur dev/dev.en* devtest/devtest.ur eval-devtest.sh
-nlfr /home/chris/ws10smt/data/dutch-french corpus.nl-fr.al
diff --git a/gi/posterior-regularisation/Corpus.java b/gi/posterior-regularisation/Corpus.java
deleted file mode 100644
index 07b27387..00000000
--- a/gi/posterior-regularisation/Corpus.java
+++ /dev/null
@@ -1,167 +0,0 @@
-import gnu.trove.TIntArrayList;
-
-import java.io.*;
-import java.util.*;
-import java.util.regex.Pattern;
-
-public class Corpus
-{
-	private Lexicon<String> tokenLexicon = new Lexicon<String>();
-	private Lexicon<TIntArrayList> phraseLexicon = new Lexicon<TIntArrayList>();
-	private Lexicon<TIntArrayList> contextLexicon = new Lexicon<TIntArrayList>();
-	private List<Edge> edges = new ArrayList<Edge>();
-	private List<List<Edge>> phraseToContext = new ArrayList<List<Edge>>();
-	private List<List<Edge>> contextToPhrase = new ArrayList<List<Edge>>();
-	
-	public class Edge
-	{
-		Edge(int phraseId, int contextId, int count)
-		{
-			this.phraseId = phraseId;
-			this.contextId = contextId;
-			this.count = count;
-		}
-		public int getPhraseId()
-		{
-			return phraseId;
-		}
-		public TIntArrayList getPhrase()
-		{
-			return phraseLexicon.lookup(phraseId);
-		}
-		public String getPhraseString()
-		{
-			StringBuffer b = new StringBuffer();
-			for (int tid: getPhrase().toNativeArray())
-			{
-				if (b.length() > 0)
-					b.append(" ");
-				b.append(tokenLexicon.lookup(tid));
-			}
-			return b.toString();
-		}		
-		public int getContextId()
-		{
-			return contextId;
-		}
-		public TIntArrayList getContext()
-		{
-			return contextLexicon.lookup(contextId);
-		}
-		public String getContextString()
-		{
-			StringBuffer b = new StringBuffer();
-			for (int tid: getContext().toNativeArray())
-			{
-				if (b.length() > 0)
-					b.append(" ");
-				b.append(tokenLexicon.lookup(tid));
-			}
-			return b.toString();
-		}
-		public int getCount()
-		{
-			return count;
-		}
-		private int phraseId;
-		private int contextId;
-		private int count;
-	}
-
-	List<Edge> getEdges()
-	{
-		return edges;
-	}
-	
-	int getNumEdges()
-	{
-		return edges.size();
-	}
-
-	int getNumPhrases()
-	{
-		return phraseLexicon.size();
-	}
-	
-	List<Edge> getEdgesForPhrase(int phraseId)
-	{
-		return phraseToContext.get(phraseId);
-	}
-	
-	int getNumContexts()
-	{
-		return contextLexicon.size();
-	}
-	
-	List<Edge> getEdgesForContext(int contextId)
-	{
-		return contextToPhrase.get(contextId);
-	}
-	
-	int getNumTokens()
-	{
-		return tokenLexicon.size();
-	}
-	
-	static Corpus readFromFile(Reader in) throws IOException
-	{
-		Corpus c = new Corpus();
-		
-		// read in line-by-line
-		BufferedReader bin = new BufferedReader(in);
-		String line;
-		Pattern separator = Pattern.compile(" \\|\\|\\| ");
-
-		while ((line = bin.readLine()) != null)
-		{
-			// split into phrase and contexts
-			StringTokenizer st = new StringTokenizer(line, "\t");
-			assert (st.hasMoreTokens());
-			String phraseToks = st.nextToken();
-			assert (st.hasMoreTokens());
-			String rest = st.nextToken();
-			assert (!st.hasMoreTokens());
-
-			// process phrase	
-			st = new StringTokenizer(phraseToks, " ");
-			TIntArrayList ptoks = new TIntArrayList();
-			while (st.hasMoreTokens())
-				ptoks.add(c.tokenLexicon.insert(st.nextToken()));
-			int phraseId = c.phraseLexicon.insert(ptoks);
-			if (phraseId == c.phraseToContext.size())
-				c.phraseToContext.add(new ArrayList<Edge>());
-			
-			// process contexts
-			String[] parts = separator.split(rest);
-			assert (parts.length % 2 == 0);
-			for (int i = 0; i < parts.length; i += 2)
-			{
-				// process pairs of strings - context and count
-				TIntArrayList ctx = new TIntArrayList();
-				String ctxString = parts[i];
-				String countString = parts[i + 1];
-				StringTokenizer ctxStrtok = new StringTokenizer(ctxString, " ");
-				while (ctxStrtok.hasMoreTokens())
-				{
-					String token = ctxStrtok.nextToken();
-					if (!token.equals("<PHRASE>"))
-						ctx.add(c.tokenLexicon.insert(token));
-				}
-				int contextId = c.contextLexicon.insert(ctx);
-				if (contextId == c.contextToPhrase.size())
-					c.contextToPhrase.add(new ArrayList<Edge>());
-
-				assert (countString.startsWith("C="));
-				Edge e = c.new Edge(phraseId, contextId, 
-						Integer.parseInt(countString.substring(2).trim()));
-				c.edges.add(e);
-				
-				// index the edge for fast phrase, context lookup
-				c.phraseToContext.get(phraseId).add(e);
-				c.contextToPhrase.get(contextId).add(e);
-			}
-		}
-		
-		return c;
-	}	
-}
diff --git a/gi/posterior-regularisation/Lexicon.java b/gi/posterior-regularisation/Lexicon.java
deleted file mode 100644
index 9f0245ee..00000000
--- a/gi/posterior-regularisation/Lexicon.java
+++ /dev/null
@@ -1,32 +0,0 @@
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-public class Lexicon<T>
-{
-	public int insert(T word)
-	{
-		Integer i = wordToIndex.get(word);
-		if (i == null)
-		{
-			i = indexToWord.size();
-			wordToIndex.put(word, i);
-			indexToWord.add(word);
-		}
-		return i;
-	}
-
-	public T lookup(int index)
-	{
-		return indexToWord.get(index);
-	}
-
-	public int size()
-	{
-		return indexToWord.size();
-	}
-
-	private Map<T, Integer> wordToIndex = new HashMap<T, Integer>();
-	private List<T> indexToWord = new ArrayList<T>();
-}
\ No newline at end of file
diff --git a/gi/posterior-regularisation/PhraseContextModel.java b/gi/posterior-regularisation/PhraseContextModel.java
deleted file mode 100644
index 85bcfb89..00000000
--- a/gi/posterior-regularisation/PhraseContextModel.java
+++ /dev/null
@@ -1,466 +0,0 @@
-// Input of the form:
-// " the phantom of the opera "    tickets for <PHRASE> tonight ? ||| C=1 ||| seats for <PHRASE> ? </s> ||| C=1 ||| i see <PHRASE> ? </s> ||| C=1
-//                      phrase TAB [context]+
-// where    context =   phrase ||| C=...        which are separated by |||
-
-// Model parameterised as follows:
-// - each phrase, p, is allocated a latent state, t
-// - this is used to generate the contexts, c
-// - each context is generated using 4 independent multinomials, one for each position LL, L, R, RR
-
-// Training with EM:
-// - e-step is estimating q(t) = P(t|p,c) for all x,c
-// - m-step is estimating model parameters P(c,t|p) = P(t) P(c|t)
-// - PR uses alternate e-step, which first optimizes lambda 
-//      min_q KL(q||p) + delta sum_pt max_c E_q[phi_ptc]
-//   where
-//      q(t|p,c) propto p(t,c|p) exp( -phi_ptc )
-//   Then q is used to obtain expectations for vanilla M-step.
-
-// Sexing it up:
-// - learn p-specific conditionals P(t|p)
-// - or generate phrase internals, e.g., generate edge words from
-//   different distribution to central words
-// - agreement between phrase->context model and context->phrase model
-
-import java.io.*;
-import optimization.gradientBasedMethods.*;
-import optimization.gradientBasedMethods.stats.OptimizerStats;
-import optimization.gradientBasedMethods.stats.ProjectedOptimizerStats;
-import optimization.linesearch.ArmijoLineSearchMinimizationAlongProjectionArc;
-import optimization.linesearch.GenericPickFirstStep;
-import optimization.linesearch.InterpolationPickFirstStep;
-import optimization.linesearch.LineSearchMethod;
-import optimization.linesearch.WolfRuleLineSearch;
-import optimization.projections.SimplexProjection;
-import optimization.stopCriteria.CompositeStopingCriteria;
-import optimization.stopCriteria.NormalizedProjectedGradientL2Norm;
-import optimization.stopCriteria.NormalizedValueDifference;
-import optimization.stopCriteria.ProjectedGradientL2Norm;
-import optimization.stopCriteria.StopingCriteria;
-import optimization.stopCriteria.ValueDifference;
-import optimization.util.MathUtils;
-import java.util.*;
-import java.util.regex.*;
-import gnu.trove.TDoubleArrayList;
-import gnu.trove.TIntArrayList;
-import static java.lang.Math.*;
-
-class PhraseContextModel
-{
-	// model/optimisation configuration parameters
-	int numTags;
-	boolean posteriorRegularisation = true;
-	double constraintScale = 3; // FIXME: make configurable
-	
-	// copied from L1LMax in depparsing code
-	final double c1= 0.0001, c2=0.9, stoppingPrecision = 1e-5, maxStep = 10;
-	final int maxZoomEvals = 10, maxExtrapolationIters = 200;
-	int maxProjectionIterations = 200;
-	int minOccurrencesForProjection = 0;
-
-	// book keeping
-	int numPositions;
-	Random rng = new Random();
-
-	// training set
-	Corpus training;
-
-	// model parameters (learnt)
-	double emissions[][][]; // position in 0 .. 3 x tag x word Pr(word | tag, position)
-	double prior[][]; // phrase x tag Pr(tag | phrase)
-	double lambda[]; // edge = (phrase, context) x tag flattened lagrange multipliers
-
-	PhraseContextModel(Corpus training, int tags)
-	{
-		this.training = training;
-		this.numTags = tags;
-		assert (!training.getEdges().isEmpty());
-		assert (numTags > 1);
-
-		// now initialise emissions
-		numPositions = training.getEdges().get(0).getContext().size();
-		assert (numPositions > 0);
-
-		emissions = new double[numPositions][numTags][training.getNumTokens()];
-		prior = new double[training.getNumEdges()][numTags];
-		if (posteriorRegularisation)
-			lambda = new double[training.getNumEdges() * numTags];
-
-		for (double[][] emissionTW : emissions)
-		{
-			for (double[] emissionW : emissionTW)
-			{
-				randomise(emissionW);
-//				for (int i = 0; i < emissionW.length; ++i)
-//					emissionW[i] = i+1;
-//				normalise(emissionW);
-			}
-		}
-					
-		for (double[] priorTag : prior)
-		{
-			randomise(priorTag);
-//			for (int i = 0; i < priorTag.length; ++i)
-//				priorTag[i] = i+1;
-//			normalise(priorTag);
-		}
-	}
-
-	void expectationMaximisation(int numIterations)
-	{
-		double lastLlh = Double.NEGATIVE_INFINITY;
-
-		for (int iteration = 0; iteration < numIterations; ++iteration)
-		{
-			double emissionsCounts[][][] = new double[numPositions][numTags][training.getNumTokens()];
-			double priorCounts[][] = new double[training.getNumPhrases()][numTags];
-			
-			// E-step
-			double llh = 0;
-			if (posteriorRegularisation)
-			{
-				EStepDualObjective objective = new EStepDualObjective();
-				
-				// copied from x2y2withconstraints
-//				LineSearchMethod ls = new ArmijoLineSearchMinimizationAlongProjectionArc(new InterpolationPickFirstStep(1));				
-//				OptimizerStats stats = new OptimizerStats();
-//				ProjectedGradientDescent optimizer = new ProjectedGradientDescent(ls);
-//				CompositeStopingCriteria compositeStop = new CompositeStopingCriteria();
-//				compositeStop.add(new ProjectedGradientL2Norm(0.001));
-//				compositeStop.add(new ValueDifference(0.001));
-//				optimizer.setMaxIterations(50);
-//				boolean succeed = optimizer.optimize(objective,stats,compositeStop);
-				
-				// copied from depparser l1lmaxobjective
-				ProjectedOptimizerStats stats = new ProjectedOptimizerStats();
-				GenericPickFirstStep pickFirstStep = new GenericPickFirstStep(1);
-				LineSearchMethod linesearch = new WolfRuleLineSearch(pickFirstStep, c1, c2);
-				ProjectedGradientDescent optimizer = new ProjectedGradientDescent(linesearch);
-				optimizer.setMaxIterations(maxProjectionIterations);
-		        CompositeStopingCriteria stop = new CompositeStopingCriteria();
-		        stop.add(new NormalizedProjectedGradientL2Norm(stoppingPrecision));
-		        stop.add(new NormalizedValueDifference(stoppingPrecision));
-		        boolean succeed = optimizer.optimize(objective, stats, stop);
-
-				System.out.println("Ended optimzation Projected Gradient Descent\n" + stats.prettyPrint(1));
-				//System.out.println("Solution: " + objective.parameters);
-				if (!succeed)
-					System.out.println("Failed to optimize");
-				//System.out.println("Ended optimization in " + optimizer.getCurrentIteration());				
-
-				//lambda = objective.getParameters();
-				llh = objective.primal();
-				
-				for (int i = 0; i < training.getNumPhrases(); ++i)
-				{
-					List<Corpus.Edge> edges = training.getEdgesForPhrase(i);
-					for (int j = 0; j < edges.size(); ++j)
-					{
-						Corpus.Edge e = edges.get(j);
-						for (int t = 0; t < numTags; t++)
-						{
-							double p = objective.q.get(i).get(j).get(t);
-							priorCounts[i][t] += e.getCount() * p;
-							TIntArrayList tokens = e.getContext();
-							for (int k = 0; k < tokens.size(); ++k)
-								emissionsCounts[k][t][tokens.get(k)] += e.getCount() * p;
-						}
-					}
-				}
-			}
-			else
-			{
-				for (int i = 0; i < training.getNumPhrases(); ++i)
-				{
-					List<Corpus.Edge> edges = training.getEdgesForPhrase(i);
-					for (int j = 0; j < edges.size(); ++j)
-					{
-						Corpus.Edge e = edges.get(j);
-						double probs[] = posterior(i, e);			
-						double z = normalise(probs);
-						llh += log(z) * e.getCount();
-						
-						TIntArrayList tokens = e.getContext();
-						for (int t = 0; t < numTags; ++t)
-						{
-							priorCounts[i][t] += e.getCount() * probs[t];
-							for (int k = 0; k < tokens.size(); ++k)
-								emissionsCounts[j][t][tokens.get(k)] += e.getCount() * probs[t];
-						}
-					}
-				}
-			}
-
-			// M-step: normalise
-			for (double[][] emissionTW : emissionsCounts)
-				for (double[] emissionW : emissionTW)
-					normalise(emissionW);
-
-			for (double[] priorTag : priorCounts)
-				normalise(priorTag);
-
-			emissions = emissionsCounts;
-			prior = priorCounts;
-
-			System.out.println("Iteration " + iteration + " llh " + llh);
-
-//			if (llh - lastLlh < 1e-4)
-//				break;
-//			else
-//				lastLlh = llh;
-		}
-	}
-
-	static double normalise(double probs[])
-	{
-		double z = 0;
-		for (double p : probs)
-			z += p;
-		for (int i = 0; i < probs.length; ++i)
-			probs[i] /= z;
-		return z;
-	}
-
-	void randomise(double probs[])
-	{
-		double z = 0;
-		for (int i = 0; i < probs.length; ++i)
-		{
-			probs[i] = 10 + rng.nextDouble();
-			z += probs[i];
-		}
-
-		for (int i = 0; i < probs.length; ++i)
-			probs[i] /= z;
-	}
-
-	static int argmax(double probs[])
-	{
-		double m = Double.NEGATIVE_INFINITY;
-		int mi = -1;
-		for (int i = 0; i < probs.length; ++i)
-		{
-			if (probs[i] > m)
-			{
-				m = probs[i];
-				mi = i;
-			}
-		}
-		return mi;
-	}
-
-	double[] posterior(int phraseId, Corpus.Edge e) // unnormalised
-	{
-		double probs[] = new double[numTags];
-		TIntArrayList tokens = e.getContext();
-		for (int t = 0; t < numTags; ++t)
-		{
-			probs[t] = prior[phraseId][t];
-			for (int k = 0; k < tokens.size(); ++k)
-				probs[t] *= emissions[k][t][tokens.get(k)];
-		}
-		return probs;
-	}
-
-	void displayPosterior()
-	{
-		for (int i = 0; i < training.getNumPhrases(); ++i)
-		{
-			List<Corpus.Edge> edges = training.getEdgesForPhrase(i);
-			for (Corpus.Edge e: edges)
-			{
-				double probs[] = posterior(i, e);
-				normalise(probs);
-
-				// emit phrase
-				System.out.print(e.getPhraseString());
-				System.out.print("\t");
-				System.out.print(e.getContextString());
-				System.out.print("||| C=" + e.getCount() + " |||");
-
-				int t = argmax(probs);
-				System.out.print(" " + t + " ||| " + probs[t]);
-				// for (int t = 0; t < numTags; ++t)
-				// System.out.print(" " + probs[t]);
-				System.out.println();
-			}
-		}
-	}
-
-	public static void main(String[] args)
-	{
-		assert (args.length >= 2);
-		try
-		{
-			Corpus corpus = Corpus.readFromFile(new FileReader(new File(args[0])));
-			PhraseContextModel model = new PhraseContextModel(corpus, Integer.parseInt(args[1]));
-			model.expectationMaximisation(Integer.parseInt(args[2]));
-			model.displayPosterior();
-		} 
-		catch (IOException e)
-		{
-			System.out.println("Failed to read input file: " + args[0]);
-			e.printStackTrace();
-		}
-	}
-
-	class EStepDualObjective extends ProjectedObjective
-	{
-		List<List<TDoubleArrayList>> conditionals; // phrase id x context # x tag - precomputed
-		List<List<TDoubleArrayList>> q; // ditto, but including exp(-lambda) terms
-		double objective = 0; // log(z)
-		// Objective.gradient = d log(z) / d lambda = E_q[phi]
-		double llh = 0;
-
-		public EStepDualObjective()
-		{
-			super();
-			// compute conditionals p(context, tag | phrase) for all training instances
-			conditionals = new ArrayList<List<TDoubleArrayList>>(training.getNumPhrases());
-			q = new ArrayList<List<TDoubleArrayList>>(training.getNumPhrases());
-			for (int i = 0; i < training.getNumPhrases(); ++i)
-			{
-				List<Corpus.Edge> edges = training.getEdgesForPhrase(i);
-
-				conditionals.add(new ArrayList<TDoubleArrayList>(edges.size()));
-				q.add(new ArrayList<TDoubleArrayList>(edges.size()));
-
-				for (int j = 0; j < edges.size(); ++j)
-				{
-					Corpus.Edge e = edges.get(j);
-					double probs[] = posterior(i, e);
-					double z = normalise(probs);
-					llh += log(z) * e.getCount();
-					conditionals.get(i).add(new TDoubleArrayList(probs));
-					q.get(i).add(new TDoubleArrayList(probs));
-				}
-			}
-			
-			gradient = new double[training.getNumEdges()*numTags];
-			setInitialParameters(lambda);
-			computeObjectiveAndGradient();
-		}
-
-		@Override
-		public double[] projectPoint(double[] point)
-		{
-			SimplexProjection p = new SimplexProjection(constraintScale);
-
-			double[] newPoint = point.clone();
-			int edgeIndex = 0;
-			for (int i = 0; i < training.getNumPhrases(); ++i)
-			{
-				List<Corpus.Edge> edges = training.getEdgesForPhrase(i);
-
-				for (int t = 0; t < numTags; t++)
-				{
-					double[] subPoint = new double[edges.size()];
-					for (int j = 0; j < edges.size(); ++j)
-						subPoint[j] = point[edgeIndex+j*numTags+t];
-				
-					p.project(subPoint);
-					for (int j = 0; j < edges.size(); ++j)
-						newPoint[edgeIndex+j*numTags+t] = subPoint[j];
-				}
-				
-				edgeIndex += edges.size() * numTags;
-			}
-//			System.out.println("Proj from: " + Arrays.toString(point)); 
-//			System.out.println("Proj to:   " + Arrays.toString(newPoint)); 
-			return newPoint;
-		}
-
-		@Override
-		public void setParameters(double[] params)
-		{
-			super.setParameters(params);
-			computeObjectiveAndGradient();
-		}
-
-		@Override
-		public double[] getGradient()
-		{
-			gradientCalls += 1;
-			return gradient;
-		}
-
-		@Override
-		public double getValue()
-		{
-			functionCalls += 1;
-			return objective;
-		}
-
-		public void computeObjectiveAndGradient()
-		{
-			int edgeIndex = 0;
-			objective = 0;
-			Arrays.fill(gradient, 0);
-			for (int i = 0; i < training.getNumPhrases(); ++i)
-			{
-				List<Corpus.Edge> edges = training.getEdgesForPhrase(i);
-
-				for (int j = 0; j < edges.size(); ++j)
-				{
-					Corpus.Edge e = edges.get(j);
-					
-					double z = 0;
-					for (int t = 0; t < numTags; t++)
-					{
-						double v = conditionals.get(i).get(j).get(t) * exp(-parameters[edgeIndex+t]);
-						q.get(i).get(j).set(t, v);
-						z += v;
-					}
-					objective += log(z) * e.getCount();
-
-					for (int t = 0; t < numTags; t++)
-					{
-						double v = q.get(i).get(j).get(t) / z; 
-						q.get(i).get(j).set(t, v);
-						gradient[edgeIndex+t] -= e.getCount() * v;
-					}
-					
-					edgeIndex += numTags;
-				}
-			}			
-//			System.out.println("computeObjectiveAndGradient logz=" + objective);
-//			System.out.println("lambda=  " + Arrays.toString(parameters));
-//			System.out.println("gradient=" + Arrays.toString(gradient));
-		}
-
-		public String toString()
-		{
-			StringBuilder sb = new StringBuilder();
-			sb.append(getClass().getCanonicalName()).append(" with ");
-			sb.append(parameters.length).append(" parameters and ");
-			sb.append(training.getNumPhrases() * numTags).append(" constraints");
-			return sb.toString();
-		}
-				
-		double primal()
-		{
-			// primal = llh + KL(q||p) + scale * sum_pt max_c E_q[phi_pct]
-			// kl = sum_Y q(Y) log q(Y) / p(Y|X)
-			//    = sum_Y q(Y) { -lambda . phi(Y) - log Z }
-			//    = -log Z - lambda . E_q[phi]
-			//    = -objective + lambda . gradient
-			
-			double kl = -objective + MathUtils.dotProduct(parameters, gradient);
-			double l1lmax = 0;
-			for (int i = 0; i < training.getNumPhrases(); ++i)
-			{
-				List<Corpus.Edge> edges = training.getEdgesForPhrase(i);
-				for (int t = 0; t < numTags; t++)
-				{
-					double lmax = Double.NEGATIVE_INFINITY;
-					for (int j = 0; j < edges.size(); ++j)
-						lmax = max(lmax, q.get(i).get(j).get(t));
-					l1lmax += lmax;
-				}
-			}
-
-			return llh + kl + constraintScale * l1lmax;
-		}
-	}
-}
diff --git a/gi/posterior-regularisation/README b/gi/posterior-regularisation/README
deleted file mode 100644
index a3d54ffc..00000000
--- a/gi/posterior-regularisation/README
+++ /dev/null
@@ -1,3 +0,0 @@
-  557  ./cdec_extools/extractor -i btec/split.zh-en.al -c 500000 -L 12 -C  | sort -t $'\t' -k 1 | ./cdec_extools/mr_stripe_rule_reduce > btec.concordance
-  559  wc -l btec.concordance 
-  588  cat btec.concordance  | sed  's/.*	//' | awk '{ for (i=1; i < NF; i++) { x=substr($i, 1, 2); if (x == "C=") printf "\n"; else if (x != "||") printf "%s ", $i; }; printf "\n"; }' | sort | uniq | wc -l
diff --git a/gi/posterior-regularisation/alphabet.hh b/gi/posterior-regularisation/alphabet.hh
deleted file mode 100644
index 1db928da..00000000
--- a/gi/posterior-regularisation/alphabet.hh
+++ /dev/null
@@ -1,61 +0,0 @@
-#ifndef _alphabet_hh
-#define _alphabet_hh
-
-#include <cassert>
-#include <iosfwd>
-#include <map>
-#include <string>
-#include <vector>
-
-// Alphabet: indexes a set of types 
-template <typename T>
-class Alphabet: protected std::map<T, int>
-{
-public:
-    Alphabet() {};
-
-    bool empty() const { return std::map<T,int>::empty(); }
-    int size() const { return std::map<T,int>::size(); }
-
-    int operator[](const T &k) const
-    {
-        typename std::map<T,int>::const_iterator cit = find(k);
-        if (cit != std::map<T,int>::end())
-            return cit->second;
-        else
-            return -1;
-    }
-
-    int lookup(const T &k) const { return (*this)[k]; }
-
-    int insert(const T &k) 
-    {
-        int sz = size();
-        assert((unsigned) sz == _items.size());
-
-        std::pair<typename std::map<T,int>::iterator, bool>
-            ins = std::map<T,int>::insert(make_pair(k, sz));
-
-        if (ins.second) 
-            _items.push_back(k);
-
-        return ins.first->second;
-    }
-
-    const T &type(int i) const
-    {
-        assert(i >= 0);
-        assert(i < size());
-        return _items[i];
-    }
-
-    std::ostream &display(std::ostream &out, int i) const
-    {
-        return out << type(i);
-    }
-
-private:
-    std::vector<T> _items;
-};
-
-#endif
diff --git a/gi/posterior-regularisation/canned.concordance b/gi/posterior-regularisation/canned.concordance
deleted file mode 100644
index 710973ff..00000000
--- a/gi/posterior-regularisation/canned.concordance
+++ /dev/null
@@ -1,4 +0,0 @@
-a	0 0 <PHRASE> 0 0 ||| C=1 ||| 1 1 <PHRASE> 1 1 ||| C=1 ||| 2 2 <PHRASE> 2 2 ||| C=1
-b	0 0 <PHRASE> 0 0 ||| C=1 ||| 1 1 <PHRASE> 1 1 ||| C=1 
-c	2 2 <PHRASE> 2 2 ||| C=1 ||| 4 4 <PHRASE> 4 4 ||| C=1 ||| 5 5 <PHRASE> 5 5 ||| C=1
-d	4 4 <PHRASE> 4 4 ||| C=1 ||| 5 5 <PHRASE> 5 5 ||| C=1
diff --git a/gi/posterior-regularisation/em.cc b/gi/posterior-regularisation/em.cc
deleted file mode 100644
index f6c9fd68..00000000
--- a/gi/posterior-regularisation/em.cc
+++ /dev/null
@@ -1,830 +0,0 @@
-// Input of the form:
-// " the phantom of the opera "    tickets for <PHRASE> tonight ? ||| C=1 ||| seats for <PHRASE> ? </s> ||| C=1 ||| i see <PHRASE> ? </s> ||| C=1
-//                      phrase TAB [context]+
-// where    context =   phrase ||| C=...        which are separated by |||
-
-// Model parameterised as follows:
-// - each phrase, p, is allocated a latent state, t
-// - this is used to generate the contexts, c
-// - each context is generated using 4 independent multinomials, one for each position LL, L, R, RR
-
-// Training with EM:
-// - e-step is estimating P(t|p,c) for all x,c
-// - m-step is estimating model parameters P(p,c,t) = P(t) P(p|t) P(c|t)
-
-// Sexing it up:
-// - constrain the posteriors P(t|c) and P(t|p) to have few high-magnitude entries
-// - improve the generation of phrase internals, e.g., generate edge words from
-//   different distribution to central words
-
-#include "alphabet.hh"
-#include "log_add.hh"
-#include <algorithm>
-#include <fstream>
-#include <iostream>
-#include <iterator>
-#include <map>
-#include <sstream>
-#include <stdexcept>
-#include <vector>
-#include <tr1/random>
-#include <tr1/tuple>
-#include <nlopt.h>
-
-using namespace std;
-using namespace std::tr1;
-
-const int numTags = 5;
-const int numIterations = 100;
-const bool posterior_regularisation = true;
-const double PHRASE_VIOLATION_WEIGHT = 10;
-const double CONTEXT_VIOLATION_WEIGHT = 0;
-const bool includePhraseProb = false;
-
-// Data structures:
-Alphabet<string> lexicon;
-typedef vector<int> Phrase;
-typedef tuple<int, int, int, int> Context;
-Alphabet<Phrase> phrases;
-Alphabet<Context> contexts;
-
-typedef map<int, int> ContextCounts;
-typedef map<int, int> PhraseCounts;
-typedef map<int, ContextCounts> PhraseToContextCounts;
-typedef map<int, PhraseCounts> ContextToPhraseCounts;
-
-PhraseToContextCounts concordancePhraseToContexts;
-ContextToPhraseCounts concordanceContextToPhrases;
-
-typedef vector<double> Dist;
-typedef vector<Dist> ConditionalDist;
-Dist prior; // class -> P(class)
-vector<ConditionalDist> probCtx; // word -> class -> P(word | class), for each position of context word
-ConditionalDist probPhrase; // class -> P(word | class)
-Dist probPhraseLength; // class -> P(length | class) expressed as geometric distribution parameter
-
-mt19937 randomGenerator((size_t) time(NULL));
-uniform_real<double> uniDist(0.0, 1e-1);
-variate_generator< mt19937, uniform_real<double> > rng(randomGenerator, uniDist);
-
-void addRandomNoise(Dist &d);
-void normalise(Dist &d);
-void addTo(Dist &d, const Dist &e);
-int argmax(const Dist &d);
-
-map<Phrase, map<Context, int> > lambda_indices;
-
-Dist conditional_probs(const Phrase &phrase, const Context &context, double *normalisation = 0);
-template <typename T>
-Dist
-penalised_conditionals(const Phrase &phrase, const Context &context, 
-                       const T &lambda, double *normalisation);
-//Dist penalised_conditionals(const Phrase &phrase, const Context &context, const double *lambda, double *normalisation = 0);
-double penalised_log_likelihood(int n, const double *lambda, double *gradient, void *data);
-void optimise_lambda(double delta, double gamma, vector<double> &lambda);
-double expected_violation_phrases(const double *lambda);
-double expected_violation_contexts(const double *lambda);
-double primal_kl_divergence(const double *lambda);
-double dual(const double *lambda);
-void print_primal_dual(const double *lambda, double delta, double gamma);
-
-ostream &operator<<(ostream &, const Phrase &);
-ostream &operator<<(ostream &, const Context &);
-ostream &operator<<(ostream &, const Dist &);
-ostream &operator<<(ostream &, const ConditionalDist &);
-
-int
-main(int argc, char *argv[])
-{
-    randomGenerator.seed(time(NULL));
-
-    int edges = 0;
-    istream &input = cin;
-    while (input.good())
-    {
-        // read the phrase
-        string phraseString;
-        Phrase phrase;
-        getline(input, phraseString, '\t');
-        istringstream pinput(phraseString);
-        string token;
-        while (pinput >> token)
-            phrase.push_back(lexicon.insert(token));
-        int phraseId = phrases.insert(phrase);
-
-        // read the rest, storing each context
-        string remainder;
-        getline(input, remainder, '\n');
-        istringstream rinput(remainder);
-        Context context(-1, -1, -1, -1);
-        int index = 0;
-        while (rinput >> token)
-        {
-            if (token != "|||" && token != "<PHRASE>")
-            {
-                if (index < 4)
-                {
-                    // eugh! damn templates
-                    switch (index)
-                    {
-                        case 0: get<0>(context) = lexicon.insert(token); break;
-                        case 1: get<1>(context) = lexicon.insert(token); break;
-                        case 2: get<2>(context) = lexicon.insert(token); break;
-                        case 3: get<3>(context) = lexicon.insert(token); break;
-                        default: assert(false);
-                    }
-                    index += 1;
-                }
-                else if (token.find("C=") == 0)
-                {
-                    int contextId = contexts.insert(context);
-                    int count = atoi(token.substr(strlen("C=")).c_str());
-                    concordancePhraseToContexts[phraseId][contextId] += count;
-                    concordanceContextToPhrases[contextId][phraseId] += count;
-                    index = 0;
-                    context = Context(-1, -1, -1, -1);
-                    edges += 1;
-                }
-            }
-        }
-
-        // trigger EOF
-        input >> ws;
-    }
-
-    cout << "Read in " << phrases.size() << " phrases"
-         << " and " << contexts.size() << " contexts"
-         << " and " << edges << " edges"
-         << " and " << lexicon.size() << " word types\n";
-
-    // FIXME: filter out low count phrases and low count contexts (based on individual words?)
-    // now populate model parameters with uniform + random noise
-    prior.resize(numTags, 1.0);
-    addRandomNoise(prior);
-    normalise(prior);
-
-    probCtx.resize(4, ConditionalDist(numTags, Dist(lexicon.size(), 1.0)));
-    if (includePhraseProb)
-        probPhrase.resize(numTags, Dist(lexicon.size(), 1.0));
-    for (int t = 0; t < numTags; ++t)
-    {
-        for (int j = 0; j < 4; ++j)
-        {
-            addRandomNoise(probCtx[j][t]);
-            normalise(probCtx[j][t]);
-        }
-        if (includePhraseProb)
-        {
-            addRandomNoise(probPhrase[t]);
-            normalise(probPhrase[t]);
-        }
-    }
-    if (includePhraseProb)
-    {
-        probPhraseLength.resize(numTags, 0.5); // geometric distribution p=0.5
-        addRandomNoise(probPhraseLength);
-    }
-
-    cout << "\tprior:     " << prior << "\n";
-    //cout << "\tcontext:   " << probCtx << "\n";
-    //cout << "\tphrase:    " << probPhrase << "\n";
-    //cout << "\tphraseLen: " << probPhraseLength << endl;
-
-    vector<double> lambda;
-
-    // now do EM training
-    for (int iteration = 0; iteration < numIterations; ++iteration)
-    {
-        cout << "EM iteration " << iteration << endl;
-
-        if (posterior_regularisation)
-            optimise_lambda(PHRASE_VIOLATION_WEIGHT, CONTEXT_VIOLATION_WEIGHT, lambda);
-        //cout << "\tlambda " << lambda << endl;
-
-        Dist countsPrior(numTags, 0.0);
-        vector<ConditionalDist> countsCtx(4, ConditionalDist(numTags, Dist(lexicon.size(), 1e-10)));
-        ConditionalDist countsPhrase(numTags, Dist(lexicon.size(), 1e-10));
-        Dist countsPhraseLength(numTags, 0.0);
-        Dist nPhrases(numTags, 0.0);
-
-        double llh = 0;
-        for (PhraseToContextCounts::iterator pcit = concordancePhraseToContexts.begin();
-             pcit != concordancePhraseToContexts.end(); ++pcit)
-        {
-            const Phrase &phrase = phrases.type(pcit->first);
-
-            // e-step: estimate latent class probs; compile (class,word) stats for m-step
-            for (ContextCounts::iterator ccit = pcit->second.begin();
-                 ccit != pcit->second.end(); ++ccit)
-            {
-                const Context &context = contexts.type(ccit->first);
-
-                double z = 0;
-                Dist tagCounts;
-                if (!posterior_regularisation)
-                    tagCounts = conditional_probs(phrase, context, &z);
-                else
-                    tagCounts = penalised_conditionals(phrase, context, lambda, &z);
-
-                llh += log(z) * ccit->second;
-                addTo(countsPrior, tagCounts); // FIXME: times ccit->secon
-
-                for (int t = 0; t < numTags; ++t)
-                {
-                    for (int j = 0; j < 4; ++j)
-                        countsCtx[j][t][get<0>(context)] += tagCounts[t] * ccit->second;
-
-                    if (includePhraseProb)
-                    {
-                        for (Phrase::const_iterator pit = phrase.begin(); pit != phrase.end(); ++pit)
-                            countsPhrase[t][*pit] += tagCounts[t] * ccit->second;
-                        countsPhraseLength[t] += phrase.size() * tagCounts[t] * ccit->second;
-                        nPhrases[t] += tagCounts[t] * ccit->second;
-                    }
-                }
-            }
-        }
-
-        cout << "M-step\n";
-
-        // m-step: normalise prior and (class,word) stats and assign to model parameters
-        normalise(countsPrior);
-        prior = countsPrior;
-        for (int t = 0; t < numTags; ++t)
-        {
-            //cout << "\t\tt " << t << " prior " << countsPrior[t] << "\n";
-            for (int j = 0; j < 4; ++j)
-                normalise(countsCtx[j][t]);
-            if (includePhraseProb)
-            {
-                normalise(countsPhrase[t]);
-                countsPhraseLength[t] = nPhrases[t] / countsPhraseLength[t];
-            }
-        }
-        probCtx = countsCtx;
-        if (includePhraseProb)
-        {
-            probPhrase = countsPhrase;
-            probPhraseLength = countsPhraseLength;
-        }
-
-        double *larray = new double[lambda.size()];
-        copy(lambda.begin(), lambda.end(), larray);
-        print_primal_dual(larray, PHRASE_VIOLATION_WEIGHT, CONTEXT_VIOLATION_WEIGHT);
-        delete [] larray;
-
-        //cout << "\tllh " << llh << endl;
-        //cout << "\tprior:     " << prior << "\n";
-        //cout << "\tcontext:   " << probCtx << "\n";
-        //cout << "\tphrase:    " << probPhrase << "\n";
-        //cout << "\tphraseLen: " << probPhraseLength << "\n";
-    }
-
-    // output class membership
-    for (PhraseToContextCounts::iterator pcit = concordancePhraseToContexts.begin();
-         pcit != concordancePhraseToContexts.end(); ++pcit)
-    {
-        const Phrase &phrase = phrases.type(pcit->first);
-        for (ContextCounts::iterator ccit = pcit->second.begin();
-             ccit != pcit->second.end(); ++ccit)
-        {
-            const Context &context = contexts.type(ccit->first);
-            Dist tagCounts = conditional_probs(phrase, context, 0);
-            cout << phrase << " ||| " << context << " ||| " << argmax(tagCounts) << "\n";
-        }
-    }
-
-    return 0;
-}
-
-void addRandomNoise(Dist &d)
-{
-    for (Dist::iterator dit = d.begin(); dit != d.end(); ++dit)
-        *dit += rng();
-}
-
-void normalise(Dist &d)
-{
-    double z = 0;
-    for (Dist::iterator dit = d.begin(); dit != d.end(); ++dit)
-        z += *dit;
-    for (Dist::iterator dit = d.begin(); dit != d.end(); ++dit)
-        *dit /= z;
-}
-
-void addTo(Dist &d, const Dist &e)
-{
-    assert(d.size() == e.size());
-    for (int i = 0; i < (int) d.size(); ++i)
-        d[i] += e[i];
-}
-
-int argmax(const Dist &d)
-{
-    double best = d[0];
-    int index = 0;
-    for (int i = 1; i < (int) d.size(); ++i)
-    {
-        if (d[i] > best)
-        {
-            best = d[i];
-            index = i;
-        }
-    }
-    return index;
-}
-
-ostream &operator<<(ostream &out, const Phrase &phrase)
-{
-    for (Phrase::const_iterator pit = phrase.begin(); pit != phrase.end(); ++pit)
-        lexicon.display(((pit == phrase.begin()) ? out : out << " "), *pit);
-    return out;
-}
-
-ostream &operator<<(ostream &out, const Context &context)
-{
-    lexicon.display(out, get<0>(context));
-    lexicon.display(out << " ", get<1>(context));
-    lexicon.display(out << " <PHRASE> ", get<2>(context));
-    lexicon.display(out << " ", get<3>(context));
-    return out;
-}
-
-ostream &operator<<(ostream &out, const Dist &dist)
-{
-    for (Dist::const_iterator dit = dist.begin(); dit != dist.end(); ++dit)
-        out << ((dit == dist.begin()) ? "" : " ") << *dit;
-    return out;
-}
-
-ostream &operator<<(ostream &out, const ConditionalDist &dist)
-{
-    for (ConditionalDist::const_iterator dit = dist.begin(); dit != dist.end(); ++dit)
-        out << ((dit == dist.begin()) ? "" : "; ") << *dit;
-    return out;
-}
-
-// FIXME: slow - just use the phrase index, context index to do the mapping
-// (n.b. it's a sparse setup, not just equal to 3d array index)
-int
-lambda_index(const Phrase &phrase, const Context &context, int tag)
-{
-    return lambda_indices[phrase][context] + tag;
-}
-
-template <typename T>
-Dist
-penalised_conditionals(const Phrase &phrase, const Context &context, 
-                       const T &lambda, double *normalisation)
-{
-    Dist d = conditional_probs(phrase, context, 0);
-
-    double z = 0;
-    for (int t = 0; t < numTags; ++t)
-    {
-        d[t] *= exp(-lambda[lambda_index(phrase, context, t)]);
-        z += d[t];
-    }
-
-    if (normalisation)
-        *normalisation = z;
-
-    for (int t = 0; t < numTags; ++t)
-        d[t] /= z;
-
-    return d;
-}
-
-Dist 
-conditional_probs(const Phrase &phrase, const Context &context, double *normalisation)
-{
-    Dist tagCounts(numTags, 0.0);
-    double z = 0;
-    for (int t = 0; t < numTags; ++t)
-    {
-        double prob = prior[t];
-        prob *= (probCtx[0][t][get<0>(context)] * probCtx[1][t][get<1>(context)] *
-                 probCtx[2][t][get<2>(context)] * probCtx[3][t][get<3>(context)]);
-
-        if (includePhraseProb)
-        {
-            prob *= pow(1 - probPhraseLength[t], phrase.size() - 1) * probPhraseLength[t];
-            for (Phrase::const_iterator pit = phrase.begin(); pit != phrase.end(); ++pit)
-                prob *= probPhrase[t][*pit];
-        }
-
-        tagCounts[t] = prob;
-        z += prob;
-    }
-    if (normalisation)
-        *normalisation = z;
-
-    for (int t = 0; t < numTags; ++t)
-        tagCounts[t] /= z;
-
-    return tagCounts;
-}
-
-double 
-penalised_log_likelihood(int n, const double *lambda, double *grad, void *)
-{
-    // return log Z(lambda, theta) over the corpus
-    // where theta are the global parameters (prior, probCtx*, probPhrase*) 
-    // and lambda are lagrange multipliers for the posterior sparsity constraints
-    //
-    // this is formulated as: 
-    // f = log Z(lambda) = sum_i log ( sum_i p_theta(t_i|p_i,c_i) exp [-lambda_{t_i,p_i,c_i}] )
-    // where i indexes the training examples - specifying the (p, c) pair (which may occur with count > 1)
-    //
-    // with derivative:
-    // f'_{tpc} = frac { - count(t,p,c) p_theta(t|p,c) exp (-lambda_{t,p,c}) }
-    //                 { sum_t' p_theta(t'|p,c) exp (-lambda_{t',p,c}) }
-
-    //cout << "penalised_log_likelihood with lambda ";
-    //copy(lambda, lambda+n, ostream_iterator<double>(cout, " "));
-    //cout << "\n";
-
-    double f = 0;
-    if (grad)
-    {
-        for (int i = 0; i < n; ++i)
-            grad[i] = 0.0;
-    }
-
-    for (int p = 0; p < phrases.size(); ++p)
-    {
-        const Phrase &phrase = phrases.type(p);
-        PhraseToContextCounts::const_iterator pcit = concordancePhraseToContexts.find(p);
-        for (ContextCounts::const_iterator ccit = pcit->second.begin();
-             ccit != pcit->second.end(); ++ccit)
-        {
-            const Context &context = contexts.type(ccit->first);
-            double z = 0;
-            Dist scores = penalised_conditionals(phrase, context, lambda, &z);
-
-            f += ccit->second * log(z);
-            //cout << "\tphrase: " << phrase << " context: " << context << " count: " << ccit->second << " z " << z << endl;
-            //cout << "\t\tscores: " << scores << "\n";
-
-            if (grad)
-            {
-                for (int t = 0; t < numTags; ++t)
-                {
-                    int i = lambda_index(phrase, context, t); // FIXME: redundant lookups
-                    assert(grad[i] == 0.0);
-                    grad[i] = - ccit->second * scores[t];
-                }
-            }
-        }
-    }
-
-    //cout << "penalised_log_likelihood returning " << f;
-    //if (grad)
-    //{
-        //cout << "\ngradient: ";
-        //copy(grad, grad+n, ostream_iterator<double>(cout, " "));
-    //}
-    //cout << "\n";
-
-    return f;
-}
-
-typedef struct 
-{
-    // one of p or c should be set to -1, in which case it will be marginalised out 
-    // i.e. sum_p' lambda_{p'ct} <= threshold
-    //   or sum_c' lambda_{pc't} <= threshold
-    int p, c, t, threshold;
-} constraint_data;
-
-double 
-constraint_and_gradient(int n, const double *lambda, double *grad, void *data)
-{
-    constraint_data *d = (constraint_data *) data;
-    assert(d->t >= 0);
-    assert(d->threshold >= 0);
-
-    //cout << "constraint_and_gradient: t " << d->t << " p " << d->p << " c " << d->c << " tau " << d->threshold << endl;
-    //cout << "\tlambda ";
-    //copy(lambda, lambda+n, ostream_iterator<double>(cout, " "));
-    //cout << "\n";
-
-    // FIXME: it's crazy to use a dense gradient here => will only have a handful of non-zero entries
-    if (grad)
-    {
-        for (int i = 0; i < n; ++i)
-            grad[i] = 0.0;
-    }
-
-    //cout << "constraint_and_gradient: " << d->p << "; " << d->c << "; " << d->t << "; " << d->threshold << endl;
-
-    if (d->p >= 0)
-    {
-        assert(d->c < 0);
-        //    sum_c lambda_pct          <= delta [a.k.a. threshold]
-        // => sum_c lambda_pct - delta  <= 0
-        // derivative_pct = { 1, if p and t match; 0, otherwise }
-
-        double val = -d->threshold;
-
-        const Phrase &phrase = phrases.type(d->p);
-        PhraseToContextCounts::const_iterator pcit = concordancePhraseToContexts.find(d->p);
-        assert(pcit != concordancePhraseToContexts.end());
-        for (ContextCounts::const_iterator ccit = pcit->second.begin();
-             ccit != pcit->second.end(); ++ccit)
-        {
-            const Context &context = contexts.type(ccit->first);
-            int i = lambda_index(phrase, context, d->t);
-            val += lambda[i];
-            if (grad) grad[i] = 1;
-        }
-        //cout << "\treturning " << val << endl;
-
-        return val;
-    }
-    else
-    {
-        assert(d->c >= 0);
-        assert(d->p < 0);
-        //    sum_p lambda_pct          <= gamma [a.k.a. threshold]
-        // => sum_p lambda_pct - gamma  <= 0
-        // derivative_pct = { 1, if c and t match; 0, otherwise }
-
-        double val = -d->threshold;
-
-        const Context &context = contexts.type(d->c);
-        ContextToPhraseCounts::iterator cpit = concordanceContextToPhrases.find(d->c);
-        assert(cpit != concordanceContextToPhrases.end());
-        for (PhraseCounts::iterator pcit = cpit->second.begin();
-             pcit != cpit->second.end(); ++pcit)
-        {
-            const Phrase &phrase = phrases.type(pcit->first);
-            int i = lambda_index(phrase, context, d->t);
-            val += lambda[i];
-            if (grad) grad[i] = 1;
-        }
-        //cout << "\treturning " << val << endl;
-
-        return val;
-    }
-}
-
-void
-optimise_lambda(double delta, double gamma, vector<double> &lambdav)
-{
-    int num_lambdas = lambdav.size();
-    if (lambda_indices.empty() || lambdav.empty())
-    {
-        lambda_indices.clear();
-        lambdav.clear();
-
-        int i = 0;
-        for (int p = 0; p < phrases.size(); ++p)
-        {
-            const Phrase &phrase = phrases.type(p);
-            PhraseToContextCounts::iterator pcit = concordancePhraseToContexts.find(p);
-            for (ContextCounts::iterator ccit = pcit->second.begin();
-                 ccit != pcit->second.end(); ++ccit)
-            {
-                const Context &context = contexts.type(ccit->first);
-                lambda_indices[phrase][context] = i;
-                i += numTags;
-            }
-        }
-        num_lambdas = i;
-        lambdav.resize(num_lambdas);
-    }
-    //cout << "optimise_lambda: #langrange multipliers " << num_lambdas << endl;
-
-    // FIXME: better to work with an implicit representation to save memory usage
-    int num_constraints = (((delta > 0) ? phrases.size() : 0) + ((gamma > 0) ? contexts.size() : 0)) * numTags;
-    //cout << "optimise_lambda: #constraints " << num_constraints << endl;
-    constraint_data *data = new constraint_data[num_constraints];
-    int i = 0;
-    if (delta > 0)
-    {
-        for (int p = 0; p < phrases.size(); ++p)
-        {
-            for (int t = 0; t < numTags; ++t, ++i)
-            {
-                constraint_data &d = data[i];
-                d.p = p;
-                d.c = -1;
-                d.t = t;
-                d.threshold = delta;
-            }
-        }
-    }
-
-    if (gamma > 0)
-    {
-        for (int c = 0; c < contexts.size(); ++c)
-        {
-            for (int t = 0; t < numTags; ++t, ++i)
-            {
-                constraint_data &d = data[i];
-                d.p = -1;
-                d.c = c;
-                d.t = t;
-                d.threshold = gamma;
-            }
-        }
-    }
-    assert(i == num_constraints);
-
-    double lambda[num_lambdas];
-    double lb[num_lambdas], ub[num_lambdas];
-    for (i = 0; i < num_lambdas; ++i)
-    {
-        lambda[i] = lambdav[i]; // starting value
-        lb[i] = 0;              // lower bound
-        if (delta <= 0)         // upper bound
-            ub[i] = gamma;      
-        else if (gamma <= 0)
-            ub[i] = delta;
-        else
-            assert(false);
-    }
-
-    //print_primal_dual(lambda, delta, gamma);
-   
-    double minf;
-    int error_code = nlopt_minimize_constrained(NLOPT_LN_COBYLA, num_lambdas, penalised_log_likelihood, NULL,
-                                                num_constraints, constraint_and_gradient, data, sizeof(constraint_data),
-                                                lb, ub, lambda, &minf, -HUGE_VAL, 0.0, 0.0, 1e-4, NULL, 0, 0.0);
-    //cout << "optimise error code " << error_code << endl;
-
-    //print_primal_dual(lambda, delta, gamma);
-
-    delete [] data;
-
-    if (error_code < 0)
-        cout << "WARNING: optimisation failed with error code: " << error_code << endl;
-    //else
-    //{
-        //cout << "success; minf " << minf << endl;
-        //print_primal_dual(lambda, delta, gamma);
-    //}
-
-    lambdav = vector<double>(&lambda[0], &lambda[0] + num_lambdas);
-}
-
-// FIXME: inefficient - cache the scores
-double
-expected_violation_phrases(const double *lambda)
-{
-    // sum_pt max_c E_q[phi_pct]
-    double violation = 0;
-
-    for (int p = 0; p < phrases.size(); ++p)
-    {
-        const Phrase &phrase = phrases.type(p);
-        PhraseToContextCounts::const_iterator pcit = concordancePhraseToContexts.find(p);
-
-        for (int t = 0; t < numTags; ++t)
-        {
-            double best = 0;
-            for (ContextCounts::const_iterator ccit = pcit->second.begin();
-                 ccit != pcit->second.end(); ++ccit)
-            {
-                const Context &context = contexts.type(ccit->first);
-                Dist scores = penalised_conditionals(phrase, context, lambda, 0);
-                best = max(best, scores[t]);
-            }
-            violation += best;
-        }
-    }
-
-    return violation;
-}
-
-// FIXME: inefficient - cache the scores
-double
-expected_violation_contexts(const double *lambda)
-{
-    // sum_ct max_p E_q[phi_pct]
-    double violation = 0;
-
-    for (int c = 0; c < contexts.size(); ++c)
-    {
-        const Context &context = contexts.type(c);
-        ContextToPhraseCounts::iterator cpit = concordanceContextToPhrases.find(c);
-
-        for (int t = 0; t < numTags; ++t)
-        {
-            double best = 0;
-            for (PhraseCounts::iterator pit = cpit->second.begin();
-                 pit != cpit->second.end(); ++pit)
-            {
-                const Phrase &phrase = phrases.type(pit->first);
-                Dist scores = penalised_conditionals(phrase, context, lambda, 0);
-                best = max(best, scores[t]);
-            }
-            violation += best;
-        }
-    }
-
-    return violation;
-}
-
-// FIXME: possibly inefficient
-double 
-primal_likelihood() // FIXME: primal evaluation needs to use lambda and calculate l1linf terms
-{
-    double llh = 0;
-    for (int p = 0; p < phrases.size(); ++p)
-    {
-        const Phrase &phrase = phrases.type(p);
-        PhraseToContextCounts::const_iterator pcit = concordancePhraseToContexts.find(p);
-        for (ContextCounts::const_iterator ccit = pcit->second.begin();
-             ccit != pcit->second.end(); ++ccit)
-        {
-            const Context &context = contexts.type(ccit->first);
-            double z = 0;
-            Dist scores = conditional_probs(phrase, context, &z);
-            llh += ccit->second * log(z);
-        }
-    }
-    return llh;
-}
-
-// FIXME: inefficient - cache the scores
-double 
-primal_kl_divergence(const double *lambda)
-{
-    // return KL(q || p) = sum_y q(y) { log q(y) - log p(y | x) }
-    //                   = sum_y q(y) { log p(y | x) - lambda . phi(x, y) - log Z - log p(y | x) }
-    //                   = sum_y q(y) { - lambda . phi(x, y) } - log Z
-    // and q(y) factors with each edge, ditto for Z
-    
-    double feature_sum = 0, log_z = 0;
-    for (int p = 0; p < phrases.size(); ++p)
-    {
-        const Phrase &phrase = phrases.type(p);
-        PhraseToContextCounts::const_iterator pcit = concordancePhraseToContexts.find(p);
-        for (ContextCounts::const_iterator ccit = pcit->second.begin();
-             ccit != pcit->second.end(); ++ccit)
-        {
-            const Context &context = contexts.type(ccit->first);
-
-            double local_z = 0;
-            double local_f = 0;
-            Dist d = conditional_probs(phrase, context, 0);
-            for (int t = 0; t < numTags; ++t)
-            {
-                int i = lambda_index(phrase, context, t);
-                double s = d[t] * exp(-lambda[i]);
-                local_f += lambda[i] * s;
-                local_z += s;
-            }
-
-            log_z += ccit->second * log(local_z);
-            feature_sum += ccit->second * (local_f / local_z);
-        }
-    }
-
-    return -feature_sum - log_z;
-}
-
-// FIXME: inefficient - cache the scores
-double 
-dual(const double *lambda)
-{
-    // return log(Z) = - log { sum_y p(y | x) exp( - lambda . phi(x, y) }
-    // n.b. have flipped the sign as we're minimising
-    
-    double z = 0;
-    for (int p = 0; p < phrases.size(); ++p)
-    {
-        const Phrase &phrase = phrases.type(p);
-        PhraseToContextCounts::const_iterator pcit = concordancePhraseToContexts.find(p);
-        for (ContextCounts::const_iterator ccit = pcit->second.begin();
-             ccit != pcit->second.end(); ++ccit)
-        {
-            const Context &context = contexts.type(ccit->first);
-            double lz = 0;
-            Dist scores = penalised_conditionals(phrase, context, lambda, &z);
-            z += lz * ccit->second;
-        }
-    }
-    return log(z);
-}
-
-void
-print_primal_dual(const double *lambda, double delta, double gamma)
-{
-    double likelihood = primal_likelihood();
-    double kl = primal_kl_divergence(lambda);
-    double sum_pt = expected_violation_phrases(lambda);
-    double sum_ct = expected_violation_contexts(lambda);
-    //double d = dual(lambda);
-
-    cout << "\tllh=" << likelihood
-         << " kl=" << kl
-         << " violations phrases=" << sum_pt
-         << " contexts=" << sum_ct
-         //<< " primal=" << (kl + delta * sum_pt + gamma * sum_ct) 
-         //<< " dual=" << d
-         << " objective=" << (likelihood - kl + delta * sum_pt + gamma * sum_ct) 
-         << endl;
-}
diff --git a/gi/posterior-regularisation/invert.hh b/gi/posterior-regularisation/invert.hh
deleted file mode 100644
index d06356e9..00000000
--- a/gi/posterior-regularisation/invert.hh
+++ /dev/null
@@ -1,45 +0,0 @@
-// The following code inverts the matrix input using LU-decomposition with
-// backsubstitution of unit vectors. Reference: Numerical Recipies in C, 2nd
-// ed., by Press, Teukolsky, Vetterling & Flannery. 
-// Code written by Fredrik Orderud.
-// http://www.crystalclearsoftware.com/cgi-bin/boost_wiki/wiki.pl?LU_Matrix_Inversion
-
-#ifndef INVERT_MATRIX_HPP
-#define INVERT_MATRIX_HPP
-
-// REMEMBER to update "lu.hpp" header includes from boost-CVS
-#include <boost/numeric/ublas/vector.hpp>
-#include <boost/numeric/ublas/vector_proxy.hpp>
-#include <boost/numeric/ublas/matrix.hpp>
-#include <boost/numeric/ublas/triangular.hpp>
-#include <boost/numeric/ublas/lu.hpp>
-#include <boost/numeric/ublas/io.hpp>
-
-namespace ublas = boost::numeric::ublas;
-
-/* Matrix inversion routine.
-   Uses lu_factorize and lu_substitute in uBLAS to invert a matrix */
-template<class T>
-bool invert_matrix(const ublas::matrix<T>& input, ublas::matrix<T>& inverse) 
-{
-    using namespace boost::numeric::ublas;
-    typedef permutation_matrix<std::size_t> pmatrix;
-    // create a working copy of the input
-    matrix<T> A(input);
-    // create a permutation matrix for the LU-factorization
-    pmatrix pm(A.size1());
-
-    // perform LU-factorization
-    int res = lu_factorize(A,pm);
-    if( res != 0 ) return false;
-
-    // create identity matrix of "inverse"
-    inverse.assign(ublas::identity_matrix<T>(A.size1()));
-
-    // backsubstitute to get the inverse
-    lu_substitute(A, pm, inverse);
-    
-    return true;
-}
-
-#endif //INVERT_MATRIX_HPP
diff --git a/gi/posterior-regularisation/linesearch.py b/gi/posterior-regularisation/linesearch.py
deleted file mode 100644
index 5a3f2e9c..00000000
--- a/gi/posterior-regularisation/linesearch.py
+++ /dev/null
@@ -1,58 +0,0 @@
-## Automatically adapted for scipy Oct 07, 2005 by convertcode.py
-
-from scipy.optimize import minpack2
-import numpy
-
-import __builtin__
-pymin = __builtin__.min
-
-def line_search(f, myfprime, xk, pk, gfk, old_fval, old_old_fval,
-                args=(), c1=1e-4, c2=0.9, amax=50):
-
-    fc = 0
-    gc = 0
-    phi0 = old_fval
-    derphi0 = numpy.dot(gfk,pk)
-    alpha1 = pymin(1.0,1.01*2*(phi0-old_old_fval)/derphi0)
-    # trevor: added this test
-    alpha1 = pymin(alpha1,amax)
-
-    if isinstance(myfprime,type(())):
-        eps = myfprime[1]
-        fprime = myfprime[0]
-        newargs = (f,eps) + args
-        gradient = False
-    else:
-        fprime = myfprime
-        newargs = args
-        gradient = True
-
-    xtol = 1e-14
-    amin = 1e-8
-    isave = numpy.zeros((2,), numpy.intc)
-    dsave = numpy.zeros((13,), float)
-    task = 'START'
-    fval = old_fval
-    gval = gfk
-
-    while 1:
-        stp,fval,derphi,task = minpack2.dcsrch(alpha1, phi0, derphi0, c1, c2,
-                                               xtol, task, amin, amax,isave,dsave)
-        #print 'minpack2.dcsrch', alpha1, phi0, derphi0, c1, c2, xtol, task, amin, amax,isave,dsave
-        #print 'returns', stp,fval,derphi,task
-
-        if task[:2] == 'FG':
-            alpha1 = stp
-            fval = f(xk+stp*pk,*args)
-            fc += 1
-            gval = fprime(xk+stp*pk,*newargs)
-            if gradient: gc += 1
-            else: fc += len(xk) + 1
-            phi0 = fval
-            derphi0 = numpy.dot(gval,pk)
-        else:
-            break
-
-    if task[:5] == 'ERROR' or task[1:4] == 'WARN':
-        stp = None  # failed
-    return stp, fc, gc, fval, old_fval, gval
diff --git a/gi/posterior-regularisation/log_add.hh b/gi/posterior-regularisation/log_add.hh
deleted file mode 100644
index e0620c5a..00000000
--- a/gi/posterior-regularisation/log_add.hh
+++ /dev/null
@@ -1,30 +0,0 @@
-#ifndef log_add_hh
-#define log_add_hh
-
-#include <limits>
-#include <iostream>
-#include <cassert>
-#include <cmath>
-
-template <typename T>
-struct Log
-{
-    static T zero() { return -std::numeric_limits<T>::infinity(); } 
-
-    static T add(T l1, T l2)
-    {
-        if (l1 == zero()) return l2;
-        if (l1 > l2) 
-            return l1 + std::log(1 + exp(l2 - l1));
-        else
-            return l2 + std::log(1 + exp(l1 - l2));
-    }
-
-    static T subtract(T l1, T l2)
-    {
-        //std::assert(l1 >= l2);
-        return l1 + log(1 - exp(l2 - l1));
-    }
-};
-
-#endif
diff --git a/gi/posterior-regularisation/prjava.jar b/gi/posterior-regularisation/prjava.jar
deleted file mode 120000
index da8bf761..00000000
--- a/gi/posterior-regularisation/prjava.jar
+++ /dev/null
@@ -1 +0,0 @@
-prjava/prjava-20100708.jar
\ No newline at end of file
diff --git a/gi/posterior-regularisation/prjava/Makefile b/gi/posterior-regularisation/prjava/Makefile
deleted file mode 100755
index bd3bfca0..00000000
--- a/gi/posterior-regularisation/prjava/Makefile
+++ /dev/null
@@ -1,8 +0,0 @@
-all:
-	ant dist
-
-check:
-	echo no tests
-
-clean:
-	ant clean
diff --git a/gi/posterior-regularisation/prjava/build.xml b/gi/posterior-regularisation/prjava/build.xml
deleted file mode 100644
index 7222b3c8..00000000
--- a/gi/posterior-regularisation/prjava/build.xml
+++ /dev/null
@@ -1,38 +0,0 @@
-<project name="prjava" default="dist" basedir=".">
-  <!-- set global properties for this build -->
-  <property name="src" location="src"/>
-  <property name="build" location="build"/>
-  <property name="dist" location="lib"/>
-  <path id="classpath">
-      <pathelement location="lib/trove-2.0.2.jar"/>
-      <pathelement location="lib/optimization.jar"/>
-      <pathelement location="lib/jopt-simple-3.2.jar"/>
-      <pathelement location="lib/commons-math-2.1.jar"/>
-  </path>
-
-  <target name="init">
-    <!-- Create the time stamp -->
-    <tstamp/>
-    <!-- Create the build directory structure used by compile -->
-    <mkdir dir="${build}"/>
-  </target>
-
-  <target name="compile" depends="init"
-        description="compile the source " >
-    <!-- Compile the java code from ${src} into ${build} -->
-    <javac srcdir="${src}" destdir="${build}" includeantruntime="false">
-            <classpath refid="classpath"/>
-    </javac>
-  </target>
-
-  <target name="dist" depends="compile"
-        description="generate the distribution" >
-    <jar jarfile="${dist}/prjava-${DSTAMP}.jar" basedir="${build}"/>
-    <symlink link="./prjava.jar" resource="${dist}/prjava-${DSTAMP}.jar" overwrite="true"/>
-  </target>
-
-  <target name="clean"
-        description="clean up" >
-    <delete dir="${build}"/>
-  </target>
-</project>
diff --git a/gi/posterior-regularisation/prjava/lib/commons-math-2.1.jar b/gi/posterior-regularisation/prjava/lib/commons-math-2.1.jar
deleted file mode 100644
index 43b4b369..00000000
--- a/gi/posterior-regularisation/prjava/lib/commons-math-2.1.jar
+++ /dev/null
diff --git a/gi/posterior-regularisation/prjava/lib/jopt-simple-3.2.jar b/gi/posterior-regularisation/prjava/lib/jopt-simple-3.2.jar
deleted file mode 100644
index 56373621..00000000
--- a/gi/posterior-regularisation/prjava/lib/jopt-simple-3.2.jar
+++ /dev/null
diff --git a/gi/posterior-regularisation/prjava/lib/trove-2.0.2.jar b/gi/posterior-regularisation/prjava/lib/trove-2.0.2.jar
deleted file mode 100644
index 3e59fbf3..00000000
--- a/gi/posterior-regularisation/prjava/lib/trove-2.0.2.jar
+++ /dev/null
diff --git a/gi/posterior-regularisation/prjava/src/arr/F.java b/gi/posterior-regularisation/prjava/src/arr/F.java
deleted file mode 100644
index be0a6ed6..00000000
--- a/gi/posterior-regularisation/prjava/src/arr/F.java
+++ /dev/null
@@ -1,99 +0,0 @@
-package arr;

-

-import java.util.Arrays;

-import java.util.Random;

-

-public class F {

-	public static Random rng = new Random();

-

-	public static void randomise(double probs[])

-	{

-		randomise(probs, true);

-	}

-

-	public static void randomise(double probs[], boolean normalise)

-	{

-		double z = 0;

-		for (int i = 0; i < probs.length; ++i)

-		{

-			probs[i] = 10 + rng.nextDouble();

-			if (normalise)

-				z += probs[i];

-		}

-

-		if (normalise)

-			for (int i = 0; i < probs.length; ++i)

-				probs[i] /= z;

-	}

-	

-	public static void uniform(double probs[])

-	{

-		for (int i = 0; i < probs.length; ++i)

-			probs[i] = 1.0 / probs.length;

-	}

-	

-	public static void l1normalize(double [] a){

-		double sum=0;

-		for(int i=0;i<a.length;i++){

-			sum+=a[i];

-		}

-		if(sum==0)

-			Arrays.fill(a, 1.0/a.length);

-		else

-		{

-			for(int i=0;i<a.length;i++){

-				a[i]/=sum;

-			}

-		}

-	}

-	

-	public  static void l1normalize(double [][] a){

-		double sum=0;

-		for(int i=0;i<a.length;i++){

-			for(int j=0;j<a[i].length;j++){

-				sum+=a[i][j];

-			}

-		}

-		if(sum==0){

-			return;

-		}

-		for(int i=0;i<a.length;i++){

-			for(int j=0;j<a[i].length;j++){

-				a[i][j]/=sum;

-			}

-		}

-	}

-	

-	public static double l1norm(double a[]){

-		// FIXME: this isn't the l1 norm for a < 0

-		double norm=0;

-		for(int i=0;i<a.length;i++){

-			norm += a[i];

-		}

-		return norm;

-	}

-	

-	public static double l2norm(double a[]){

-		double norm=0;

-		for(int i=0;i<a.length;i++){

-			norm += a[i]*a[i];

-		}

-		return Math.sqrt(norm);

-	}

-	

-	public static int argmax(double probs[])

-	{

-		double m = Double.NEGATIVE_INFINITY;

-		int mi = -1;

-		for (int i = 0; i < probs.length; ++i)

-		{

-			if (probs[i] > m)

-			{

-				m = probs[i];

-				mi = i;

-			}

-		}

-		return mi;

-	}

-	

-}

diff --git a/gi/posterior-regularisation/prjava/src/data/Corpus.java b/gi/posterior-regularisation/prjava/src/data/Corpus.java
deleted file mode 100644
index 425ede11..00000000
--- a/gi/posterior-regularisation/prjava/src/data/Corpus.java
+++ /dev/null
@@ -1,233 +0,0 @@
-package data;

-

-import java.util.ArrayList;

-import java.util.Arrays;

-import java.util.HashMap;

-import java.util.Scanner;

-

-public class Corpus {

-

-	public static final String alphaFilename="../posdata/corpus.alphabet";

-	public static final String tagalphaFilename="../posdata/corpus.tag.alphabet";

-	

-//	public static final String START_SYM="<s>";

-	public static final String END_SYM="<e>";

-	public static final String NUM_TOK="<NUM>";

-	

-	public static final String UNK_TOK="<unk>";

-	

-	private ArrayList<String[]>sent;

-	private ArrayList<int[]>data;

-	

-	public ArrayList<String[]>tag;

-	public  ArrayList<int[]>tagData;

-	

-	public static boolean convertNumTok=true;

-	

-	private HashMap<String,Integer>freq;

-	public HashMap<String,Integer>vocab;

-	

-	public HashMap<String,Integer>tagVocab;

-	private int tagV;

-	

-	private int V;

-	

-	public static void main(String[] args) {

-		Corpus c=new Corpus("../posdata/en_test.conll");

-		System.out.println(

-			Arrays.toString(c.get(0))	

-		);

-		System.out.println(

-				Arrays.toString(c.getInt(0))	

-			);

-		

-		System.out.println(

-				Arrays.toString(c.get(1))	

-			);

-			System.out.println(

-					Arrays.toString(c.getInt(1))	

-				);

-	}

-

-	public Corpus(String filename,HashMap<String,Integer>dict){

-		V=0;

-		tagV=0;

-		freq=new HashMap<String,Integer>();

-		tagVocab=new HashMap<String,Integer>();

-		vocab=dict;

-		

-		sent=new ArrayList<String[]>();

-		tag=new ArrayList<String[]>();

-		

-		Scanner sc=io.FileUtil.openInFile(filename);

-		ArrayList<String>s=new ArrayList<String>();

-	//	s.add(START_SYM);

-		while(sc.hasNextLine()){

-			String line=sc.nextLine();

-			String toks[]=line.split("\t");

-			if(toks.length<2){

-				s.add(END_SYM);

-				sent.add(s.toArray(new String[0]));

-				s=new ArrayList<String>();

-		//		s.add(START_SYM);

-				continue;

-			}

-			String tok=toks[1].toLowerCase();

-			s.add(tok);

-		}

-		sc.close();

-

-		buildData();

-	}

-	

-	public Corpus(String filename){

-		V=0;

-		freq=new HashMap<String,Integer>();

-		vocab=new HashMap<String,Integer>();

-		tagVocab=new HashMap<String,Integer>();

-		

-		sent=new ArrayList<String[]>();

-		tag=new ArrayList<String[]>();

-		

-		System.out.println("Reading:"+filename);

-		

-		Scanner sc=io.FileUtil.openInFile(filename);

-		ArrayList<String>s=new ArrayList<String>();

-		ArrayList<String>tags=new ArrayList<String>();

-		//s.add(START_SYM);

-		while(sc.hasNextLine()){

-			String line=sc.nextLine();

-			String toks[]=line.split("\t");

-			if(toks.length<2){

-				s.add(END_SYM);

-				tags.add(END_SYM);

-				if(s.size()>2){

-					sent.add(s.toArray(new String[0]));

-					tag.add(tags.toArray(new String [0]));

-				}

-				s=new ArrayList<String>();

-				tags=new ArrayList<String>();

-			//	s.add(START_SYM);

-				continue;

-			}

-			

-			String tok=toks[1].toLowerCase();

-			if(convertNumTok && tok.matches(".*\\d.*")){

-				tok=NUM_TOK;

-			}

-			s.add(tok);

-			

-			if(toks.length>3){

-				tok=toks[3].toLowerCase();

-			}else{

-				tok="_";

-			}

-			tags.add(tok);

-			

-		}

-		sc.close();

-		

-		for(int i=0;i<sent.size();i++){

-			String[]toks=sent.get(i);

-			for(int j=0;j<toks.length;j++){

-				addVocab(toks[j]);

-				addTag(tag.get(i)[j]);

-			}

-		}

-		

-		buildVocab();

-		buildData();

-		System.out.println(data.size()+"sentences, "+vocab.keySet().size()+" word types");

-	}

-

-	public String[] get(int idx){

-		return sent.get(idx);

-	}

-	

-	private void addVocab(String s){

-		Integer integer=freq.get(s);

-		if(integer==null){

-			integer=0;

-		}

-		freq.put(s, integer+1);

-	}

-	

-	public int tokIdx(String tok){

-		Integer integer=vocab.get(tok);

-		if(integer==null){

-			return V;

-		}

-		return integer;

-	}

-	

-	public int tagIdx(String tok){

-		Integer integer=tagVocab.get(tok);

-		if(integer==null){

-			return tagV;

-		}

-		return integer;

-	}

-	

-	private void buildData(){

-		data=new ArrayList<int[]>();

-		for(int i=0;i<sent.size();i++){

-			String s[]=sent.get(i);

-			data.add(new int [s.length]);

-			for(int j=0;j<s.length;j++){

-				data.get(i)[j]=tokIdx(s[j]);

-			}

-		}

-		

-		tagData=new ArrayList<int[]>();

-		for(int i=0;i<tag.size();i++){

-			String s[]=tag.get(i);

-			tagData.add(new int [s.length]);

-			for(int j=0;j<s.length;j++){

-				tagData.get(i)[j]=tagIdx(s[j]);

-			}

-		}

-		sent=null;

-		tag=null;

-		System.gc();

-	}

-	

-	public int [] getInt(int idx){

-		return data.get(idx);

-	}

-	

-	/**

-	 * 

-	 * @return size of vocabulary 

-	 */

-	public int getVocabSize(){

-		return V;

-	}

-	

-	public int [][]getAllData(){

-		return data.toArray(new int [0][]);

-	}

-	

-	public int [][]getTagData(){

-		return tagData.toArray(new int [0][]);

-	}

-	

-	private void buildVocab(){

-		for (String key:freq.keySet()){

-			if(freq.get(key)>2){

-				vocab.put(key, V);

-				V++;

-			}

-		}

-		io.SerializedObjects.writeSerializedObject(vocab, alphaFilename);

-		io.SerializedObjects.writeSerializedObject(tagVocab,tagalphaFilename);

-	}

-

-	private void addTag(String tag){

-		Integer i=tagVocab.get(tag);

-		if(i==null){

-			tagVocab.put(tag, tagV);

-			tagV++;

-		}

-	}

-	

-}

diff --git a/gi/posterior-regularisation/prjava/src/hmm/HMM.java b/gi/posterior-regularisation/prjava/src/hmm/HMM.java
deleted file mode 100644
index 17a4679f..00000000
--- a/gi/posterior-regularisation/prjava/src/hmm/HMM.java
+++ /dev/null
@@ -1,579 +0,0 @@
-package hmm;

-

-import java.io.File;

-import java.io.FileNotFoundException;

-import java.io.IOException;

-import java.io.PrintStream;

-import java.util.ArrayList;

-import java.util.Scanner;

-

-public class HMM {

-

-	

-	//trans[i][j]=prob of going FROM i to j

-	double [][]trans;

-	double [][]emit;

-	double []pi;

-	int  [][]data;

-	int [][]tagdata;

-	

-	double logtrans[][];

-	

-	public HMMObjective o;

-	

-	public static void main(String[] args) {

-	

-	}

-	

-	public HMM(int n_state,int n_emit,int [][]data){

-		trans=new double [n_state][n_state];

-		emit=new double[n_state][n_emit];

-		pi=new double [n_state];

-		System.out.println(" random initial parameters");

-		fillRand(trans);

-		fillRand(emit);

-		fillRand(pi);

-

-		this.data=data;

-		

-	}

-	

-	private void fillRand(double [][] a){

-		for(int i=0;i<a.length;i++){

-			for(int j=0;j<a[i].length;j++){

-				a[i][j]=Math.random();

-			}

-			l1normalize(a[i]);

-		}

-	}

-	private void fillRand(double []a){

-		for(int i=0;i<a.length;i++){

-				a[i]=Math.random();

-		}

-		l1normalize(a);

-	}

-	

-	private double loglikely=0;

-	

-	public void EM(){

-		double trans_exp_cnt[][]=new double [trans.length][trans.length];

-		double emit_exp_cnt[][]=new double[trans.length][emit[0].length];

-		double start_exp_cnt[]=new double[trans.length];

-		loglikely=0;

-		

-		//E

-		for(int i=0;i<data.length;i++){

-			

-			double [][][] post=forwardBackward(data[i]);

-			incrementExpCnt(post, data[i], 

-					trans_exp_cnt,

-					emit_exp_cnt,

-					start_exp_cnt);

-			

-			

-			if(i%100==0){

-				System.out.print(".");

-			}

-			if(i%1000==0){

-				System.out.println(i);

-			}

-			

-		}

-		System.out.println("Log likelihood: "+loglikely);

-		

-		//M

-		addOneSmooth(emit_exp_cnt);

-		for(int i=0;i<trans.length;i++){

-		

-			//transition probs

-			double sum=0;

-			for(int j=0;j<trans.length;j++){

-				sum+=trans_exp_cnt[i][j];

-			}

-			//avoid NAN

-			if(sum==0){

-				sum=1;

-			}

-			for(int j=0;j<trans[i].length;j++){

-				trans[i][j]=trans_exp_cnt[i][j]/sum;

-			}

-			

-			//emission probs

-			

-			sum=0;

-			for(int j=0;j<emit[i].length;j++){

-				sum+=emit_exp_cnt[i][j];

-			}

-			//avoid NAN

-			if(sum==0){

-				sum=1;

-			}

-			for(int j=0;j<emit[i].length;j++){

-				emit[i][j]=emit_exp_cnt[i][j]/sum;

-			}

-			

-			

-			//initial probs

-			for(int j=0;j<pi.length;j++){

-				pi[j]=start_exp_cnt[j];

-			}

-			l1normalize(pi);

-		}

-	}

-	

-	private double [][][]forwardBackward(int [] seq){

-		double a[][]=new double [seq.length][trans.length];

-		double b[][]=new double [seq.length][trans.length];

-		

-		int len=seq.length;

-		//initialize the first step

-		for(int i=0;i<trans.length;i++){

-			a[0][i]=emit[i][seq[0]]*pi[i];

-			b[len-1][i]=1;

-		}

-		

-		//log of denominator for likelyhood

-		double c=Math.log(l1norm(a[0]));

-		

-		l1normalize(a[0]);

-		l1normalize(b[len-1]);

-		

-		

-		

-		//forward

-		for(int n=1;n<len;n++){

-			for(int i=0;i<trans.length;i++){

-				for(int j=0;j<trans.length;j++){

-					a[n][i]+=trans[j][i]*a[n-1][j];

-				}

-				a[n][i]*=emit[i][seq[n]];

-			}

-			c+=Math.log(l1norm(a[n]));

-			l1normalize(a[n]);

-		}

-		

-		loglikely+=c;

-		

-		//backward

-		for(int n=len-2;n>=0;n--){

-			for(int i=0;i<trans.length;i++){

-				for(int j=0;j<trans.length;j++){

-					b[n][i]+=trans[i][j]*b[n+1][j]*emit[j][seq[n+1]];

-				}

-			}

-			l1normalize(b[n]);

-		}

-		

-		

-		//expected transition 

-		double p[][][]=new double [seq.length][trans.length][trans.length];

-		for(int n=0;n<len-1;n++){

-			for(int i=0;i<trans.length;i++){

-				for(int j=0;j<trans.length;j++){

-					p[n][i][j]=a[n][i]*trans[i][j]*emit[j][seq[n+1]]*b[n+1][j];

-					

-				}

-			}

-

-			l1normalize(p[n]);

-		}

-		return p;

-	}

-	

-	private void incrementExpCnt(

-			double post[][][],int [] seq, 

-			double trans_exp_cnt[][],

-			double emit_exp_cnt[][],

-			double start_exp_cnt[])

-	{

-		

-		for(int n=0;n<post.length;n++){

-			for(int i=0;i<trans.length;i++){

-				double py=0;

-				for(int j=0;j<trans.length;j++){

-					py+=post[n][i][j];

-					trans_exp_cnt[i][j]+=post[n][i][j];

-				}

-

-				emit_exp_cnt[i][seq[n]]+=py;				

-				

-			}

-		}

-		

-		//the first state

-		for(int i=0;i<trans.length;i++){

-			double py=0;

-			for(int j=0;j<trans.length;j++){

-				py+=post[0][i][j];

-			}

-			start_exp_cnt[i]+=py;	

-		}

-		

-		

-		//the last state

-		int len=post.length;

-		for(int i=0;i<trans.length;i++){

-			double py=0;

-			for(int j=0;j<trans.length;j++){

-				py+=post[len-2][j][i];

-			}

-			emit_exp_cnt[i][seq[len-1]]+=py;	

-		}

-	}

-	

-	public void l1normalize(double [] a){

-		double sum=0;

-		for(int i=0;i<a.length;i++){

-			sum+=a[i];

-		}

-		if(sum==0){

-			return ;

-		}

-		for(int i=0;i<a.length;i++){

-			a[i]/=sum;

-		}

-	}

-	

-	public  void l1normalize(double [][] a){

-		double sum=0;

-		for(int i=0;i<a.length;i++){

-			for(int j=0;j<a[i].length;j++){

-				sum+=a[i][j];

-			}

-		}

-		if(sum==0){

-			return;

-		}

-		for(int i=0;i<a.length;i++){

-			for(int j=0;j<a[i].length;j++){

-				a[i][j]/=sum;

-			}

-		}

-	}

-	

-	public void writeModel(String modelFilename) throws FileNotFoundException, IOException{

-		PrintStream ps=io.FileUtil.printstream(new File(modelFilename));

-		ps.println(trans.length);

-		ps.println("Initial Probabilities:");

-		for(int i=0;i<pi.length;i++){

-			ps.print(pi[i]+"\t");

-		}

-		ps.println();

-		ps.println("Transition Probabilities:");

-		for(int i=0;i<trans.length;i++){

-			for(int j=0;j<trans[i].length;j++){

-				ps.print(trans[i][j]+"\t");

-			}

-			ps.println();

-		}

-		ps.println("Emission Probabilities:");

-		ps.println(emit[0].length);

-		for(int i=0;i<trans.length;i++){

-			for(int j=0;j<emit[i].length;j++){

-				ps.println(emit[i][j]);

-			}

-			ps.println();

-		}

-		ps.close();

-	}

-	

-	public HMM(){

-	

-	}

-	

-	public void readModel(String modelFilename){

-		Scanner sc=io.FileUtil.openInFile(modelFilename);

-	

-		int n_state=sc.nextInt();

-		sc.nextLine();

-		sc.nextLine();

-		pi=new double [n_state];

-		for(int i=0;i<n_state;i++){

-			pi[i]=sc.nextDouble();

-		}

-		sc.nextLine();

-		sc.nextLine();

-		trans=new double[n_state][n_state];

-		for(int i=0;i<trans.length;i++){

-			for(int j=0;j<trans[i].length;j++){

-				trans[i][j]=sc.nextDouble();

-			}

-		}

-		sc.nextLine();

-		sc.nextLine();

-		

-		int n_obs=sc.nextInt();

-		emit=new double[n_state][n_obs];

-		for(int i=0;i<trans.length;i++){

-			for(int j=0;j<emit[i].length;j++){

-				emit[i][j]=sc.nextDouble();

-			}

-		}

-		sc.close();

-	}

-	

-	public int []viterbi(int [] seq){

-		double [][]p=new double [seq.length][trans.length];

-		int backp[][]=new int [seq.length][trans.length];

-		

-		for(int i=0;i<trans.length;i++){

-			p[0][i]=Math.log(emit[i][seq[0]]*pi[i]);

-		}

-		

-		double a[][]=logtrans;

-		if(logtrans==null){

-			a=new double [trans.length][trans.length];

-			for(int i=0;i<trans.length;i++){

-				for(int j=0;j<trans.length;j++){

-					a[i][j]=Math.log(trans[i][j]);

-				}

-			}

-			logtrans=a;

-		}

-		

-		double maxprob=0;

-		for(int n=1;n<seq.length;n++){

-			for(int i=0;i<trans.length;i++){

-				maxprob=p[n-1][0]+a[0][i];

-				backp[n][i]=0;

-				for(int j=1;j<trans.length;j++){

-					double prob=p[n-1][j]+a[j][i];

-					if(maxprob<prob){

-						backp[n][i]=j;

-						maxprob=prob;

-					}

-				}

-				p[n][i]=maxprob+Math.log(emit[i][seq[n]]);

-			}

-		}

-		

-		maxprob=p[seq.length-1][0];

-		int maxIdx=0;

-		for(int i=1;i<trans.length;i++){

-			if(p[seq.length-1][i]>maxprob){

-				maxprob=p[seq.length-1][i];

-				maxIdx=i;

-			}

-		}

-		int ans[]=new int [seq.length];

-		ans[seq.length-1]=maxIdx;

-		for(int i=seq.length-2;i>=0;i--){

-			ans[i]=backp[i+1][ans[i+1]];

-		}

-		return ans;

-	}

-	

-	public double l1norm(double a[]){

-		double norm=0;

-		for(int i=0;i<a.length;i++){

-			norm += a[i];

-		}

-		return norm;

-	}

-	

-	public double [][]getEmitProb(){

-		return emit;

-	}

-	

-	public int [] sample(int terminalSym){

-		ArrayList<Integer > s=new ArrayList<Integer>();

-		int state=sample(pi);

-		int sym=sample(emit[state]);

-		while(sym!=terminalSym){

-			s.add(sym);

-			state=sample(trans[state]);

-			sym=sample(emit[state]);

-		}

-		

-		int ans[]=new int [s.size()];

-		for(int i=0;i<ans.length;i++){

-			ans[i]=s.get(i);

-		}

-		return ans;

-	}

-	

-	public int sample(double p[]){

-		double r=Math.random();

-		double sum=0;

-		for(int i=0;i<p.length;i++){

-			sum+=p[i];

-			if(sum>=r){

-				return i;

-			}

-		}

-		return p.length-1;

-	}

-	

-	public void train(int tagdata[][]){

-		double trans_exp_cnt[][]=new double [trans.length][trans.length];

-		double emit_exp_cnt[][]=new double[trans.length][emit[0].length];

-		double start_exp_cnt[]=new double[trans.length];

-		

-		for(int i=0;i<tagdata.length;i++){

-			start_exp_cnt[tagdata[i][0]]++;

-			

-			for(int j=0;j<tagdata[i].length;j++){

-				if(j+1<tagdata[i].length){

-					trans_exp_cnt[ tagdata[i][j] ] [ tagdata[i][j+1] ]++;

-				}

-				emit_exp_cnt[tagdata[i][j]][data[i][j]]++;

-			}

-			

-		}

-		

-		//M

-		addOneSmooth(emit_exp_cnt);

-		for(int i=0;i<trans.length;i++){

-		

-			//transition probs

-			double sum=0;

-			for(int j=0;j<trans.length;j++){

-				sum+=trans_exp_cnt[i][j];

-			}

-			if(sum==0){

-				sum=1;

-			}

-			for(int j=0;j<trans[i].length;j++){

-				trans[i][j]=trans_exp_cnt[i][j]/sum;

-			}

-			

-			//emission probs

-

-			sum=0;

-			for(int j=0;j<emit[i].length;j++){

-				sum+=emit_exp_cnt[i][j];

-			}

-			if(sum==0){

-				sum=1;

-			}

-			for(int j=0;j<emit[i].length;j++){

-				emit[i][j]=emit_exp_cnt[i][j]/sum;

-			}

-

-			

-			//initial probs

-			for(int j=0;j<pi.length;j++){

-				pi[j]=start_exp_cnt[j];

-			}

-			l1normalize(pi);

-		}

-	}

-	

-	private void addOneSmooth(double a[][]){

-		for(int i=0;i<a.length;i++){

-			for(int j=0;j<a[i].length;j++){

-				a[i][j]+=0.01;

-			}

-			//l1normalize(a[i]);

-		}

-	}

-	

-	public void PREM(){

-		

-		o.optimizeWithProjectedGradientDescent();

-		

-		double trans_exp_cnt[][]=new double [trans.length][trans.length];

-		double emit_exp_cnt[][]=new double[trans.length][emit[0].length];

-		double start_exp_cnt[]=new double[trans.length];

-		

-		o.loglikelihood=0;

-		//E

-		for(int sentNum=0;sentNum<data.length;sentNum++){

-			

-			double [][][] post=o.forwardBackward(sentNum);

-			incrementExpCnt(post, data[sentNum], 

-					trans_exp_cnt,

-					emit_exp_cnt,

-					start_exp_cnt);

-			

-			

-			if(sentNum%100==0){

-				System.out.print(".");

-			}

-			if(sentNum%1000==0){

-				System.out.println(sentNum);

-			}

-			

-		}

-		

-		System.out.println("Log likelihood: "+o.getValue());

-		

-		//M

-		addOneSmooth(emit_exp_cnt);

-		for(int i=0;i<trans.length;i++){

-		

-			//transition probs

-			double sum=0;

-			for(int j=0;j<trans.length;j++){

-				sum+=trans_exp_cnt[i][j];

-			}

-			//avoid NAN

-			if(sum==0){

-				sum=1;

-			}

-			for(int j=0;j<trans[i].length;j++){

-				trans[i][j]=trans_exp_cnt[i][j]/sum;

-			}

-			

-			//emission probs

-			

-			sum=0;

-			for(int j=0;j<emit[i].length;j++){

-				sum+=emit_exp_cnt[i][j];

-			}

-			//avoid NAN

-			if(sum==0){

-				sum=1;

-			}

-			for(int j=0;j<emit[i].length;j++){

-				emit[i][j]=emit_exp_cnt[i][j]/sum;

-			}

-			

-			

-			//initial probs

-			for(int j=0;j<pi.length;j++){

-				pi[j]=start_exp_cnt[j];

-			}

-			l1normalize(pi);

-		}

-		

-	}

-	

-	public void computeMaxwt(double[][]maxwt, int[][] d){

-

-		for(int sentNum=0;sentNum<d.length;sentNum++){

-			double post[][][]=forwardBackward(d[sentNum]);

-			

-			for(int n=0;n<post.length;n++){

-				for(int i=0;i<trans.length;i++){

-					double py=0;

-					for(int j=0;j<trans.length;j++){

-						py+=post[n][i][j];

-					}

-

-					if(py>maxwt[i][d[sentNum][n]]){

-						maxwt[i][d[sentNum][n]]=py;

-					}

-					

-				}

-			}

-			

-			//the last state

-			int len=post.length;

-			for(int i=0;i<trans.length;i++){

-				double py=0;

-				for(int j=0;j<trans.length;j++){

-					py+=post[len-2][j][i];

-				}

-				

-				if(py>maxwt[i][d[sentNum][len-1]]){

-					maxwt[i][d[sentNum][len-1]]=py;

-				}

-				

-			}

-			

-		}

-	

-	}

-	

-}//end of class

diff --git a/gi/posterior-regularisation/prjava/src/hmm/HMMObjective.java b/gi/posterior-regularisation/prjava/src/hmm/HMMObjective.java
deleted file mode 100644
index 70b6c966..00000000
--- a/gi/posterior-regularisation/prjava/src/hmm/HMMObjective.java
+++ /dev/null
@@ -1,351 +0,0 @@
-package hmm;

-

-import gnu.trove.TIntArrayList;

-import optimization.gradientBasedMethods.ProjectedGradientDescent;

-import optimization.gradientBasedMethods.ProjectedObjective;

-import optimization.gradientBasedMethods.stats.OptimizerStats;

-import optimization.linesearch.ArmijoLineSearchMinimizationAlongProjectionArc;

-import optimization.linesearch.InterpolationPickFirstStep;

-import optimization.linesearch.LineSearchMethod;

-import optimization.projections.SimplexProjection;

-import optimization.stopCriteria.CompositeStopingCriteria;

-import optimization.stopCriteria.ProjectedGradientL2Norm;

-import optimization.stopCriteria.StopingCriteria;

-import optimization.stopCriteria.ValueDifference;

-

-public class HMMObjective extends ProjectedObjective{

-

-	

-	private static final double GRAD_DIFF = 3;

-	public static double INIT_STEP_SIZE=10;

-	public static double VAL_DIFF=1000;

-	

-	private HMM hmm;

-	double[] newPoint  ;

-	

-	//posterior[sent num][tok num][tag]=index into lambda

-	private int posteriorMap[][][];

-	//projection[word][tag].get(occurence)=index into lambda

-	private TIntArrayList projectionMap[][];

-

-	//Size of the simplex

-	public double scale=10;

-	private SimplexProjection projection;

-	

-	private int wordFreq[];

-	private static int MIN_FREQ=10;

-	private int numWordsToProject=0;

-	

-	private int n_param;

-	

-	public  double loglikelihood;

-	

-	public HMMObjective(HMM h){

-		hmm=h;

-		

-		countWords();

-		buildMap();

-

-		gradient=new double [n_param];

-		projection = new SimplexProjection(scale);

-		newPoint  = new double[n_param];

-		setInitialParameters(new double[n_param]);

-		

-	}

-	

-	/**@brief counts word frequency in the corpus

-	 * 

-	 */

-	private void countWords(){

-		wordFreq=new int [hmm.emit[0].length];

-		for(int i=0;i<hmm.data.length;i++){

-			for(int j=0;j<hmm.data[i].length;j++){

-				wordFreq[hmm.data[i][j]]++;

-			}

-		}

-	}

-	

-	/**@brief build posterior and projection indices

-	 * 

-	 */

-	private void buildMap(){

-		//number of sentences hidden states and words

-		int n_states=hmm.trans.length;

-		int n_words=hmm.emit[0].length;

-		int n_sents=hmm.data.length;

-		

-		n_param=0;

-		posteriorMap=new int[n_sents][][];

-		projectionMap=new TIntArrayList[n_words][];

-		for(int sentNum=0;sentNum<n_sents;sentNum++){

-			int [] data=hmm.data[sentNum];

-			posteriorMap[sentNum]=new int[data.length][n_states];

-			numWordsToProject=0;

-			for(int i=0;i<data.length;i++){

-				int word=data[i];

-				for(int state=0;state<n_states;state++){

-					if(wordFreq[word]>MIN_FREQ){

-						if(projectionMap[word]==null){

-							projectionMap[word]=new TIntArrayList[n_states];

-						}

-			//			if(posteriorMap[sentNum][i]==null){

-			//				posteriorMap[sentNum][i]=new int[n_states];

-			//			}

-						

-						posteriorMap[sentNum][i][state]=n_param;

-						if(projectionMap[word][state]==null){

-							projectionMap[word][state]=new TIntArrayList();

-							numWordsToProject++;

-						}

-						projectionMap[word][state].add(n_param);

-						n_param++;

-					}

-					else{

-						posteriorMap[sentNum][i][state]=-1;

-					}

-				}

-			}

-		}

-	}

-	

-	@Override

-	public double[] projectPoint(double[] point) {

-		// TODO Auto-generated method stub

-		for(int i=0;i<projectionMap.length;i++){

-			

-			if(projectionMap[i]==null){

-				//this word is not constrained

-				continue;

-			}

-			

-			for(int j=0;j<projectionMap[i].length;j++){

-				TIntArrayList instances=projectionMap[i][j];

-				double[] toProject = new double[instances.size()];

-				

-				for (int k = 0; k < toProject.length; k++) {

-					//	System.out.print(instances.get(k) + " ");

-						toProject[k] = point[instances.get(k)];

-				}

-				

-				projection.project(toProject);

-				for (int k = 0; k < toProject.length; k++) {

-					newPoint[instances.get(k)]=toProject[k];

-				}

-			}

-		}

-		return newPoint;

-	}

-

-	@Override

-	public double[] getGradient() {

-		// TODO Auto-generated method stub

-		gradientCalls++;

-		return gradient;

-	}

-

-	@Override

-	public double getValue() {

-		// TODO Auto-generated method stub

-		functionCalls++;

-		return loglikelihood;

-	}

-	

-

-	@Override

-	public String toString() {

-		// TODO Auto-generated method stub

-		StringBuffer sb = new StringBuffer();

-		for (int i = 0; i < parameters.length; i++) {

-			sb.append(parameters[i]+" ");

-			if(i%100==0){

-				sb.append("\n");

-			}

-		}

-		sb.append("\n");

-		/*

-		for (int i = 0; i < gradient.length; i++) {

-			sb.append(gradient[i]+" ");

-			if(i%100==0){

-				sb.append("\n");

-			}

-		}

-		sb.append("\n");

-		*/

-		return sb.toString();

-	}

-

-	

-	/**

-	 * @param seq

-	 * @return posterior probability of each transition

-	 */

-	public double [][][]forwardBackward(int sentNum){

-		int [] seq=hmm.data[sentNum];

-		int n_states=hmm.trans.length;

-		double a[][]=new double [seq.length][n_states];

-		double b[][]=new double [seq.length][n_states];

-		

-		int len=seq.length;

-		

-		boolean  constrained=

-			(projectionMap[seq[0]]!=null);

-

-		//initialize the first step

-		for(int i=0;i<n_states;i++){

-			a[0][i]=hmm.emit[i][seq[0]]*hmm.pi[i];

-			if(constrained){

-				a[0][i]*=

-					Math.exp(- parameters[ posteriorMap[sentNum][0][i] ] );

-			}

-			b[len-1][i]=1;

-		}

-		

-		loglikelihood+=Math.log(hmm.l1norm(a[0]));		

-		hmm.l1normalize(a[0]);

-		hmm.l1normalize(b[len-1]);

-		

-		//forward

-		for(int n=1;n<len;n++){

-			

-			constrained=

-				(projectionMap[seq[n]]!=null);

-			

-			for(int i=0;i<n_states;i++){

-				for(int j=0;j<n_states;j++){

-					a[n][i]+=hmm.trans[j][i]*a[n-1][j];

-				}

-				a[n][i]*=hmm.emit[i][seq[n]];

-				

-				if(constrained){

-					a[n][i]*=

-						Math.exp(- parameters[ posteriorMap[sentNum][n][i] ] );

-				}

-				

-			}

-			loglikelihood+=Math.log(hmm.l1norm(a[n]));

-			hmm.l1normalize(a[n]);

-		}

-		

-		//temp variable for e^{-\lambda}

-		double factor=1;

-		//backward

-		for(int n=len-2;n>=0;n--){

-			

-			constrained=

-				(projectionMap[seq[n+1]]!=null);

-			

-			for(int i=0;i<n_states;i++){

-				for(int j=0;j<n_states;j++){

-					

-					if(constrained){

-						factor=

-							Math.exp(- parameters[ posteriorMap[sentNum][n+1][j] ] );

-					}else{

-						factor=1;

-					}

-					

-					b[n][i]+=hmm.trans[i][j]*b[n+1][j]*hmm.emit[j][seq[n+1]]*factor;

-					

-				}

-			}

-			hmm.l1normalize(b[n]);

-		}

-		

-		//expected transition 

-		double p[][][]=new double [seq.length][n_states][n_states];

-		for(int n=0;n<len-1;n++){

-			

-			constrained=

-				(projectionMap[seq[n+1]]!=null);

-			

-			for(int i=0;i<n_states;i++){

-				for(int j=0;j<n_states;j++){

-					

-					if(constrained){

-						factor=

-							Math.exp(- parameters[ posteriorMap[sentNum][n+1][j] ] );

-					}else{

-						factor=1;

-					}

-					

-					p[n][i][j]=a[n][i]*hmm.trans[i][j]*

-						hmm.emit[j][seq[n+1]]*b[n+1][j]*factor;

-					

-				}

-			}

-

-			hmm.l1normalize(p[n]);

-		}

-		return p;

-	}

-

-	public void optimizeWithProjectedGradientDescent(){

-		LineSearchMethod ls =

-			new ArmijoLineSearchMinimizationAlongProjectionArc

-				(new InterpolationPickFirstStep(INIT_STEP_SIZE));

-		

-		OptimizerStats stats = new OptimizerStats();

-		

-		

-		ProjectedGradientDescent optimizer = new ProjectedGradientDescent(ls);

-		StopingCriteria stopGrad = new ProjectedGradientL2Norm(GRAD_DIFF);

-		StopingCriteria stopValue = new ValueDifference(VAL_DIFF);

-		CompositeStopingCriteria compositeStop = new CompositeStopingCriteria();

-		compositeStop.add(stopGrad);

-		compositeStop.add(stopValue);

-		

-		optimizer.setMaxIterations(10);

-		updateFunction();

-		boolean succed = optimizer.optimize(this,stats,compositeStop);

-		System.out.println("Ended optimzation Projected Gradient Descent\n" + stats.prettyPrint(1));

-		if(succed){

-			System.out.println("Ended optimization in " + optimizer.getCurrentIteration());

-		}else{

-			System.out.println("Failed to optimize");

-		}

-	}

-	

-	@Override

-	public void setParameters(double[] params) {

-		super.setParameters(params);

-		updateFunction();

-	}

-	

-	private void updateFunction(){

-		

-		updateCalls++;

-		loglikelihood=0;

-	

-		for(int sentNum=0;sentNum<hmm.data.length;sentNum++){

-			double [][][]p=forwardBackward(sentNum);

-			

-			for(int n=0;n<p.length-1;n++){

-				for(int i=0;i<p[n].length;i++){

-					if(projectionMap[hmm.data[sentNum][n]]!=null){

-						double posterior=0;

-						for(int j=0;j<p[n][i].length;j++){

-							posterior+=p[n][i][j];

-						}

-						gradient[posteriorMap[sentNum][n][i]]=-posterior;

-					}

-				}

-			}

-			

-			//the last state

-			int n=p.length-2;

-			for(int i=0;i<p[n].length;i++){

-				if(projectionMap[hmm.data[sentNum][n+1]]!=null){

-					

-					double posterior=0;

-					for(int j=0;j<p[n].length;j++){

-						posterior+=p[n][j][i];

-					}

-					gradient[posteriorMap[sentNum][n+1][i]]=-posterior;

-				

-				}

-			}	

-		}

-		

-	}

-	

-}

diff --git a/gi/posterior-regularisation/prjava/src/hmm/POS.java b/gi/posterior-regularisation/prjava/src/hmm/POS.java
deleted file mode 100644
index bdcbc683..00000000
--- a/gi/posterior-regularisation/prjava/src/hmm/POS.java
+++ /dev/null
@@ -1,120 +0,0 @@
-package hmm;

-

-import java.io.File;

-import java.io.FileNotFoundException;

-import java.io.IOException;

-import java.io.PrintStream;

-import java.util.HashMap;

-

-import data.Corpus;

-

-public class POS {

-

-	//public String trainFilename="../posdata/en_train.conll";

-	public static String trainFilename="../posdata/small_train.txt";

-//	public static String trainFilename="../posdata/en_test.conll";

-//	public static String trainFilename="../posdata/trial1.txt";

-	

-	public static String testFilename="../posdata/en_test.conll";

-	//public static String testFilename="../posdata/trial1.txt";

-	

-	public static String predFilename="../posdata/en_test.predict.conll";

-	public static String modelFilename="../posdata/posModel.out";

-	public static final int ITER=20;

-	public static final int N_STATE=30;

-	

-	public static void main(String[] args) {

-		//POS p=new POS();

-		//POS p=new POS(true);

-		try {

-			PRPOS();

-		} catch (FileNotFoundException e) {

-			e.printStackTrace();

-		} catch (IOException e) {

-			e.printStackTrace();

-		}

-	}

-

-	

-	public POS() throws FileNotFoundException, IOException{

-		Corpus c= new Corpus(trainFilename);

-		//size of vocabulary +1 for unknown tokens

-		HMM hmm =new HMM(N_STATE, c.getVocabSize()+1,c.getAllData());

-		for(int i=0;i<ITER;i++){

-			System.out.println("Iter"+i);

-			hmm.EM();

-			if((i+1)%10==0){

-				hmm.writeModel(modelFilename+i);

-			}

-		}

-

-		hmm.writeModel(modelFilename);

-		

-		Corpus test=new Corpus(testFilename,c.vocab);

-		

-		PrintStream ps= io.FileUtil.printstream(new File(predFilename));

-		

-		int [][]data=test.getAllData();

-		for(int i=0;i<data.length;i++){

-			int []tag=hmm.viterbi(data[i]);

-			String sent[]=test.get(i);

-			for(int j=0;j<data[i].length;j++){

-				ps.println(sent[j]+"\t"+tag[j]);

-			}

-			ps.println();

-		}

-		ps.close();

-	}

-	

-	//POS induction with L1/Linf constraints

-	public static void PRPOS() throws FileNotFoundException, IOException{

-		Corpus c= new Corpus(trainFilename);

-		//size of vocabulary +1 for unknown tokens

-		HMM hmm =new HMM(N_STATE, c.getVocabSize()+1,c.getAllData());

-		hmm.o=new HMMObjective(hmm);

-		for(int i=0;i<ITER;i++){

-			System.out.println("Iter: "+i);

-			hmm.PREM();

-			if((i+1)%10==0){

-				hmm.writeModel(modelFilename+i);

-			}

-		}

-

-		hmm.writeModel(modelFilename);

-	}

-	

-	

-	public POS(boolean supervised) throws FileNotFoundException, IOException{

-		Corpus c= new Corpus(trainFilename);

-		//size of vocabulary +1 for unknown tokens

-		HMM hmm =new HMM(c.tagVocab.size() , c.getVocabSize()+1,c.getAllData());

-		hmm.train(c.getTagData());

-

-		hmm.writeModel(modelFilename);

-		

-		Corpus test=new Corpus(testFilename,c.vocab);

-		

-		HashMap<String, Integer>tagVocab=

-			(HashMap<String, Integer>) io.SerializedObjects.readSerializedObject(Corpus.tagalphaFilename);

-		String [] tagdict=new String [tagVocab.size()+1];

-		for(String key:tagVocab.keySet()){

-			tagdict[tagVocab.get(key)]=key;

-		}

-		tagdict[tagdict.length-1]=Corpus.UNK_TOK;

-		

-		System.out.println(c.vocab.get("<e>"));

-		

-		PrintStream ps= io.FileUtil.printstream(new File(predFilename));

-		

-		int [][]data=test.getAllData();

-		for(int i=0;i<data.length;i++){

-			int []tag=hmm.viterbi(data[i]);

-			String sent[]=test.get(i);

-			for(int j=0;j<data[i].length;j++){

-				ps.println(sent[j]+"\t"+tagdict[tag[j]]);

-			}

-			ps.println();

-		}

-		ps.close();

-	}

-}

diff --git a/gi/posterior-regularisation/prjava/src/io/FileUtil.java b/gi/posterior-regularisation/prjava/src/io/FileUtil.java
deleted file mode 100644
index 6720d087..00000000
--- a/gi/posterior-regularisation/prjava/src/io/FileUtil.java
+++ /dev/null
@@ -1,48 +0,0 @@
-package io;

-import java.util.*;

-import java.util.zip.GZIPInputStream;

-import java.util.zip.GZIPOutputStream;

-import java.io.*;

-public class FileUtil 

-{

-	public static BufferedReader reader(File file) throws FileNotFoundException, IOException

-	{

-		if (file.getName().endsWith(".gz"))

-			return new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(file)), "UTF8"));

-		else

-			return new BufferedReader(new InputStreamReader(new FileInputStream(file), "UTF8"));

-	}

-	

-	public static PrintStream printstream(File file) throws FileNotFoundException, IOException

-	{

-		if (file.getName().endsWith(".gz"))

-			return new PrintStream(new GZIPOutputStream(new FileOutputStream(file)), true, "UTF8");

-		else

-			return new PrintStream(new FileOutputStream(file), true, "UTF8");

-	}

-

-	public static Scanner openInFile(String filename)

-	{

-		Scanner localsc=null;

-		try

-		{

-			localsc=new Scanner(new FileInputStream(filename), "UTF8");

-

-		}catch(IOException ioe){

-			System.out.println(ioe.getMessage());

-		}

-		return localsc;

-	}

-	

-	public static FileInputStream openInputStream(String infilename)

-	{

-		FileInputStream fis=null;

-		try {

-			fis = new FileInputStream(infilename);

-			

-		} catch (IOException ioe) {

-			System.out.println(ioe.getMessage());

-		}

-		return fis;

-	}

-}

diff --git a/gi/posterior-regularisation/prjava/src/io/SerializedObjects.java b/gi/posterior-regularisation/prjava/src/io/SerializedObjects.java
deleted file mode 100644
index d1631b51..00000000
--- a/gi/posterior-regularisation/prjava/src/io/SerializedObjects.java
+++ /dev/null
@@ -1,83 +0,0 @@
-package io;
-
-
-
-import java.io.BufferedInputStream;
-import java.io.BufferedOutputStream;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.ObjectInput;
-import java.io.ObjectInputStream;
-import java.io.ObjectOutput;
-import java.io.ObjectOutputStream;
-import java.io.OutputStream;
-
-public class SerializedObjects
-{
-	public static void writeSerializedObject(Object object, String outFile)
-	{
-		ObjectOutput output = null;
-	    try{
-	      //use buffering
-	      OutputStream file = new FileOutputStream(outFile);
-	      OutputStream buffer = new BufferedOutputStream( file );
-	      output = new ObjectOutputStream( buffer );
-	      output.writeObject(object);
-	      buffer.close();
-	      file.close();
-	    }
-	    catch(IOException ex){
-	    	ex.printStackTrace();
-	    }
-	    finally{
-	      try {
-	        if (output != null) {
-	          //flush and close "output" and its underlying streams
-	          output.close();
-	        }
-	      }
-	      catch (IOException ex ){
-	    	  ex.printStackTrace();
-	      }
-	    }
-	}
-	
-	public static Object readSerializedObject(String inputFile)
-	{
-		ObjectInput input = null;
-	    Object recoveredObject=null;
-		try{
-	      //use buffering
-	      InputStream file = new FileInputStream(inputFile);
-	      InputStream buffer = new BufferedInputStream(file);
-	      input = new ObjectInputStream(buffer);
-	      //deserialize the List
-	      recoveredObject = input.readObject();
-	    }
-	    catch(IOException ex){
-	    	ex.printStackTrace();
-	    }
-	    catch (ClassNotFoundException ex){
-	    	ex.printStackTrace();
-	    }
-	    catch(Exception ex)
-	    {
-	    	ex.printStackTrace();
-	    }
-	    finally{
-	      try {
-	        if ( input != null ) {
-	          //close "input" and its underlying streams
-	          input.close();
-	        }
-	      }
-	      catch (IOException ex){
-	    	  ex.printStackTrace();
-	      }
-	    }
-	    return recoveredObject;
-	 }
-	
-}
\ No newline at end of file
diff --git a/gi/posterior-regularisation/prjava/src/optimization/examples/GeneralizedRosenbrock.java b/gi/posterior-regularisation/prjava/src/optimization/examples/GeneralizedRosenbrock.java
deleted file mode 100644
index 25fa7f09..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/examples/GeneralizedRosenbrock.java
+++ /dev/null
@@ -1,110 +0,0 @@
-package optimization.examples;
-
-
-import optimization.gradientBasedMethods.ConjugateGradient;
-import optimization.gradientBasedMethods.GradientDescent;
-import optimization.gradientBasedMethods.LBFGS;
-import optimization.gradientBasedMethods.Objective;
-import optimization.gradientBasedMethods.Optimizer;
-import optimization.gradientBasedMethods.stats.OptimizerStats;
-import optimization.linesearch.ArmijoLineSearchMinimization;
-import optimization.linesearch.LineSearchMethod;
-import optimization.stopCriteria.GradientL2Norm;
-import optimization.stopCriteria.StopingCriteria;
-import optimization.util.MathUtils;
-
-/**
- * 
- * @author javg
- * f(x) = \sum_{i=1}^{N-1} \left[ (1-x_i)^2+ 100 (x_{i+1} - x_i^2 )^2 \right] \quad \forall x\in\mathbb{R}^N.
- */
-public class GeneralizedRosenbrock extends Objective{
-
-	
-	
-	public GeneralizedRosenbrock(int dimensions){
-		parameters = new double[dimensions];		
-		java.util.Arrays.fill(parameters, 0);
-		gradient = new double[dimensions];
-		
-	}
-	
-	public GeneralizedRosenbrock(int dimensions, double[] params){
-		parameters = params;	
-		gradient = new double[dimensions];
-	}
-	
-	
-	public double getValue() {
-		functionCalls++;
-		double value = 0;
-		for(int i = 0; i < parameters.length-1; i++){
-			value += MathUtils.square(1-parameters[i]) + 100*MathUtils.square(parameters[i+1] - MathUtils.square(parameters[i]));
-		}
-		
-		return value;
-	}
-
-	/**
-	 * gx = -2(1-x) -2x200(y-x^2)
-	 * gy = 200(y-x^2)
-	 */
-	public double[] getGradient() {
-		gradientCalls++;
-		java.util.Arrays.fill(gradient,0);
-		for(int i = 0; i < parameters.length-1; i++){
-			gradient[i]+=-2*(1-parameters[i]) - 400*parameters[i]*(parameters[i+1] - MathUtils.square(parameters[i]));
-			gradient[i+1]+=200*(parameters[i+1] - MathUtils.square(parameters[i]));
-		}	
-		return gradient;
-	}
-
-	
-
-	
-
-	
-	
-	public String toString(){
-		String  res ="";
-		for(int i = 0; i < parameters.length; i++){
-			res += "P" + i+ " " + parameters[i];
-		}
-		res += " Value " + getValue();
-		return res;
-	}
-	
-	public static void main(String[] args) {
-		
-		GeneralizedRosenbrock o = new GeneralizedRosenbrock(2);
-		System.out.println("Starting optimization " + " x0 " + o.parameters[0]+ " x1 " + o.parameters[1]);
-		;
-
-		System.out.println("Doing Gradient descent");
-		//LineSearchMethod wolfe = new WolfRuleLineSearch(new InterpolationPickFirstStep(1),100,0.001,0.1);
-		StopingCriteria stop = new GradientL2Norm(0.001);		
-		LineSearchMethod ls = new ArmijoLineSearchMinimization();
-		Optimizer optimizer = new GradientDescent(ls);		
-		OptimizerStats stats = new OptimizerStats();
-		optimizer.setMaxIterations(1000);
-		boolean succed = optimizer.optimize(o,stats, stop);
-		System.out.println("Suceess " + succed + "/n"+stats.prettyPrint(1));
-		System.out.println("Doing Conjugate Gradient descent");
-		o = new GeneralizedRosenbrock(2);
-	//	wolfe = new WolfRuleLineSearch(new InterpolationPickFirstStep(1),100,0.001,0.1);
-		optimizer = new ConjugateGradient(ls);
-		stats = new OptimizerStats();
-		optimizer.setMaxIterations(1000);
-		succed = optimizer.optimize(o,stats,stop);
-		System.out.println("Suceess " + succed + "/n"+stats.prettyPrint(1));
-		System.out.println("Doing Quasi newton descent");
-		o = new GeneralizedRosenbrock(2);
-		optimizer = new LBFGS(ls,10);
-		stats = new OptimizerStats();
-		optimizer.setMaxIterations(1000);
-		succed = optimizer.optimize(o,stats,stop);
-		System.out.println("Suceess " + succed + "/n"+stats.prettyPrint(1));
-
-	}
-	
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/examples/x2y2.java b/gi/posterior-regularisation/prjava/src/optimization/examples/x2y2.java
deleted file mode 100644
index f087681e..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/examples/x2y2.java
+++ /dev/null
@@ -1,128 +0,0 @@
-package optimization.examples;
-
-
-import optimization.gradientBasedMethods.ConjugateGradient;
-
-import optimization.gradientBasedMethods.GradientDescent;
-import optimization.gradientBasedMethods.LBFGS;
-import optimization.gradientBasedMethods.Objective;
-import optimization.gradientBasedMethods.stats.OptimizerStats;
-import optimization.linesearch.GenericPickFirstStep;
-import optimization.linesearch.LineSearchMethod;
-import optimization.linesearch.WolfRuleLineSearch;
-import optimization.stopCriteria.GradientL2Norm;
-import optimization.stopCriteria.StopingCriteria;
-
-
-/**
- * @author javg
- *
- */
-public class x2y2 extends Objective{
-
-	
-	//Implements function ax2+ by2 
-	double a, b;
-	public x2y2(double a, double b){
-		this.a = a;
-		this.b = b;
-		parameters = new double[2];
-		parameters[0] = 4;
-		parameters[1] = 4;
-		gradient = new double[2];
-	}
-	
-	public double getValue() {
-		functionCalls++;
-		return a*parameters[0]*parameters[0]+b*parameters[1]*parameters[1];
-	}
-
-	public double[] getGradient() {
-		gradientCalls++;
-		gradient[0]=2*a*parameters[0];
-		gradient[1]=2*b*parameters[1];
-		return gradient;
-//		if(debugLevel >=2){
-//			double[] numericalGradient = DebugHelpers.getNumericalGradient(this, parameters, 0.000001);
-//			for(int i = 0; i < parameters.length; i++){
-//				double diff = Math.abs(gradient[i]-numericalGradient[i]);
-//				if(diff > 0.00001){
-//					System.out.println("Numerical Gradient does not match");
-//					System.exit(1);
-//				}
-//			}
-//		}
-	}
-
-	
-	
-	public void optimizeWithGradientDescent(LineSearchMethod ls, OptimizerStats stats, x2y2 o){
-		GradientDescent optimizer = new GradientDescent(ls);
-		StopingCriteria stop = new GradientL2Norm(0.001);
-//		optimizer.setGradientConvergenceValue(0.001);
-		optimizer.setMaxIterations(100);
-		boolean succed = optimizer.optimize(o,stats,stop);
-		System.out.println("Ended optimzation Gradient Descent\n" + stats.prettyPrint(1));
-		System.out.println("Solution: " + " x0 " + o.parameters[0]+ " x1 " + o.parameters[1]);
-		if(succed){
-			System.out.println("Ended optimization in " + optimizer.getCurrentIteration());
-		}else{
-			System.out.println("Failed to optimize");
-		}
-	}
-	
-	public void optimizeWithConjugateGradient(LineSearchMethod ls, OptimizerStats stats, x2y2 o){
-		ConjugateGradient optimizer = new ConjugateGradient(ls);
-		StopingCriteria stop = new GradientL2Norm(0.001);
-
-		optimizer.setMaxIterations(10);
-		boolean succed = optimizer.optimize(o,stats,stop);
-		System.out.println("Ended optimzation Conjugate Gradient\n" + stats.prettyPrint(1));
-		System.out.println("Solution: " + " x0 " + o.parameters[0]+ " x1 " + o.parameters[1]);
-		if(succed){
-			System.out.println("Ended optimization in " + optimizer.getCurrentIteration());
-		}else{
-			System.out.println("Failed to optimize");
-		}
-	}
-	
-	public void optimizeWithLBFGS(LineSearchMethod ls, OptimizerStats stats, x2y2 o){
-		LBFGS optimizer = new LBFGS(ls,10);
-		StopingCriteria stop = new GradientL2Norm(0.001);
-		optimizer.setMaxIterations(10);
-		boolean succed = optimizer.optimize(o,stats,stop);
-		System.out.println("Ended optimzation LBFGS\n" + stats.prettyPrint(1));
-		System.out.println("Solution: " + " x0 " + o.parameters[0]+ " x1 " + o.parameters[1]);
-		if(succed){
-			System.out.println("Ended optimization in " + optimizer.getCurrentIteration());
-		}else{
-			System.out.println("Failed to optimize");
-		}
-	}
-	
-	public static void main(String[] args) {
-		x2y2 o = new x2y2(1,10);
-		System.out.println("Starting optimization " + " x0 " + o.parameters[0]+ " x1 " + o.parameters[1]);
-		o.setDebugLevel(4);
-		LineSearchMethod wolfe = new WolfRuleLineSearch(new GenericPickFirstStep(1),0.001,0.9);;
-//		LineSearchMethod ls = new ArmijoLineSearchMinimization();
-		OptimizerStats stats = new OptimizerStats();
-		o.optimizeWithGradientDescent(wolfe, stats, o);
-		o = new x2y2(1,10);
-		System.out.println("Starting optimization " + " x0 " + o.parameters[0]+ " x1 " + o.parameters[1]);
-//		ls = new ArmijoLineSearchMinimization();
-		stats = new OptimizerStats();
-		o.optimizeWithConjugateGradient(wolfe, stats, o);
-		o = new x2y2(1,10);
-		System.out.println("Starting optimization " + " x0 " + o.parameters[0]+ " x1 " + o.parameters[1]);
-//		ls = new ArmijoLineSearchMinimization();
-		stats = new OptimizerStats();
-		o.optimizeWithLBFGS(wolfe, stats, o);	
-	}
-	
-	public String toString(){
-		return "P1: " + parameters[0] + " P2: " + parameters[1] + " value " + getValue();
-	}
-	
-	
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/examples/x2y2WithConstraints.java b/gi/posterior-regularisation/prjava/src/optimization/examples/x2y2WithConstraints.java
deleted file mode 100644
index 391775b7..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/examples/x2y2WithConstraints.java
+++ /dev/null
@@ -1,127 +0,0 @@
-package optimization.examples;
-
-
-import optimization.gradientBasedMethods.ProjectedGradientDescent;
-import optimization.gradientBasedMethods.ProjectedObjective;
-import optimization.gradientBasedMethods.stats.OptimizerStats;
-import optimization.linesearch.ArmijoLineSearchMinimizationAlongProjectionArc;
-import optimization.linesearch.InterpolationPickFirstStep;
-import optimization.linesearch.LineSearchMethod;
-import optimization.projections.BoundsProjection;
-import optimization.projections.Projection;
-import optimization.projections.SimplexProjection;
-import optimization.stopCriteria.CompositeStopingCriteria;
-import optimization.stopCriteria.GradientL2Norm;
-import optimization.stopCriteria.ProjectedGradientL2Norm;
-import optimization.stopCriteria.StopingCriteria;
-import optimization.stopCriteria.ValueDifference;
-
-
-/**
- * @author javg
- * 
- * 
- *ax2+ b(y2 -displacement)
- */
-public class x2y2WithConstraints extends ProjectedObjective{
-
-
-	double a, b;
-	double dx;
-	double dy;
-	Projection projection;
-	
-	
-	public x2y2WithConstraints(double a, double b, double[] params, double dx, double dy, Projection proj){
-		//projection = new BoundsProjection(0.2,Double.MAX_VALUE);
-		super();
-		projection = proj;	
-		this.a = a;
-		this.b = b;
-		this.dx = dx;
-		this.dy = dy;
-		setInitialParameters(params);
-		System.out.println("Function " +a+"(x-"+dx+")^2 + "+b+"(y-"+dy+")^2");
-		System.out.println("Gradient " +(2*a)+"(x-"+dx+") ; "+(b*2)+"(y-"+dy+")");
-		printParameters();
-		projection.project(parameters);
-		printParameters();
-		gradient = new double[2];
-	}
-	
-	public double getValue() {
-		functionCalls++;
-		return a*(parameters[0]-dx)*(parameters[0]-dx)+b*((parameters[1]-dy)*(parameters[1]-dy));
-	}
-
-	public double[] getGradient() {
-		if(gradient == null){
-			gradient = new double[2];
-		}
-		gradientCalls++;
-		gradient[0]=2*a*(parameters[0]-dx);
-		gradient[1]=2*b*(parameters[1]-dy);
-		return gradient;
-	}
-	
-	
-	public double[] projectPoint(double[] point) {
-		double[] newPoint = point.clone();
-		projection.project(newPoint);
-		return newPoint;
-	}	
-	
-	public void optimizeWithProjectedGradientDescent(LineSearchMethod ls, OptimizerStats stats, x2y2WithConstraints o){
-		ProjectedGradientDescent optimizer = new ProjectedGradientDescent(ls);
-		StopingCriteria stopGrad = new ProjectedGradientL2Norm(0.001);
-		StopingCriteria stopValue = new ValueDifference(0.001);
-		CompositeStopingCriteria compositeStop = new CompositeStopingCriteria();
-		compositeStop.add(stopGrad);
-		compositeStop.add(stopValue);
-		
-		optimizer.setMaxIterations(5);
-		boolean succed = optimizer.optimize(o,stats,compositeStop);
-		System.out.println("Ended optimzation Projected Gradient Descent\n" + stats.prettyPrint(1));
-		System.out.println("Solution: " + " x0 " + o.parameters[0]+ " x1 " + o.parameters[1]);
-		if(succed){
-			System.out.println("Ended optimization in " + optimizer.getCurrentIteration());
-		}else{
-			System.out.println("Failed to optimize");
-		}
-	}
-	
-	
-	
-	public String toString(){
-		
-		return "P1: " + parameters[0] + " P2: " + parameters[1] + " value " + getValue() + " grad (" + getGradient()[0] + ":" + getGradient()[1]+")";
-	}
-	
-	public static void main(String[] args) {
-		double a = 1;
-		double b=1;
-		double x0 = 0;
-		double y0  =1;
-		double dx = 0.5;
-		double dy = 0.5	;
-		double [] parameters = new double[2];
-		parameters[0] = x0;
-		parameters[1] = y0;
-		x2y2WithConstraints o = new x2y2WithConstraints(a,b,parameters,dx,dy, new SimplexProjection(0.5));
-		System.out.println("Starting optimization " + " x0 " + o.parameters[0]+ " x1 " + o.parameters[1] + " a " + a + " b "+b );
-		o.setDebugLevel(4);
-		
-		LineSearchMethod ls = new ArmijoLineSearchMinimizationAlongProjectionArc(new InterpolationPickFirstStep(1));
-		
-		OptimizerStats stats = new OptimizerStats();
-		o.optimizeWithProjectedGradientDescent(ls, stats, o);
-		
-//		o = new x2y2WithConstraints(a,b,x0,y0,dx,dy);
-//		stats = new OptimizerStats();
-//		o.optimizeWithSpectralProjectedGradientDescent(stats, o);
-	}
-	
-	
-	
-	
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/AbstractGradientBaseMethod.java b/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/AbstractGradientBaseMethod.java
deleted file mode 100644
index 2fcb7990..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/AbstractGradientBaseMethod.java
+++ /dev/null
@@ -1,120 +0,0 @@
-package optimization.gradientBasedMethods;
-
-import optimization.gradientBasedMethods.stats.OptimizerStats;
-import optimization.linesearch.DifferentiableLineSearchObjective;
-import optimization.linesearch.LineSearchMethod;
-import optimization.stopCriteria.StopingCriteria;
-import optimization.util.MathUtils;
-
-/**
- * 
- * @author javg
- *
- */
-public abstract class AbstractGradientBaseMethod implements Optimizer{
-	
-	protected int maxNumberOfIterations=10000;
-	
-	
-	
-	protected int currentProjectionIteration;
-	protected double currValue;	
-	protected double previousValue = Double.MAX_VALUE;;
-	protected double step;
-	protected double[] gradient;
-	public double[] direction;
-	
-	//Original values
-	protected double originalGradientL2Norm;
-	
-	protected LineSearchMethod lineSearch;
-	DifferentiableLineSearchObjective lso;
-	
-	
-	public void reset(){
-		direction = null;
-		gradient = null;
-		previousValue = Double.MAX_VALUE;
-		currentProjectionIteration = 0;
-		originalGradientL2Norm = 0;
-		step = 0;
-		currValue = 0;
-	}
-	
-	public void initializeStructures(Objective o,OptimizerStats stats, StopingCriteria stop){
-		lso =   new DifferentiableLineSearchObjective(o);
-	}
-	public void updateStructuresBeforeStep(Objective o,OptimizerStats stats, StopingCriteria stop){
-	}
-	
-	public void updateStructuresAfterStep(Objective o,OptimizerStats stats, StopingCriteria stop){
-	}
-	
-	public boolean optimize(Objective o,OptimizerStats stats, StopingCriteria stop){
-		//Initialize structures
-			
-		stats.collectInitStats(this, o);
-		direction = new double[o.getNumParameters()];
-		initializeStructures(o, stats, stop);
-		for (currentProjectionIteration = 1; currentProjectionIteration < maxNumberOfIterations; currentProjectionIteration++){
-			//System.out.println("\tgradient descent iteration " + currentProjectionIteration);
-			//System.out.print("\tparameters:" );
-			//o.printParameters();
-			previousValue = currValue;
-			currValue = o.getValue();
-			gradient = o.getGradient();
-			if(stop.stopOptimization(o)){
-				stats.collectFinalStats(this, o);
-				return true;
-			}	
-			
-			getDirection();
-			if(MathUtils.dotProduct(gradient, direction) > 0){
-				System.out.println("Not a descent direction");
-				System.out.println(" current stats " + stats.prettyPrint(1));
-				System.exit(-1);
-			}
-			updateStructuresBeforeStep(o, stats, stop);
-			lso.reset(direction);
-			step = lineSearch.getStepSize(lso);
-			//System.out.println("\t\tLeave with step: " + step);
-			if(step==-1){
-				System.out.println("Failed to find step");
-				stats.collectFinalStats(this, o);
-				return false;		
-			}
-			updateStructuresAfterStep( o, stats,  stop);
-//			previousValue = currValue;
-//			currValue = o.getValue();
-//			gradient = o.getGradient();
-			stats.collectIterationStats(this, o);
-		}
-		stats.collectFinalStats(this, o);
-		return false;
-	}
-	
-	
-	public int getCurrentIteration() {
-		return currentProjectionIteration;
-	}
-
-	
-	/**
-	 * Method specific
-	 */
-	public abstract double[] getDirection();
-
-	public double getCurrentStep() {
-		return step;
-	}
-
-
-
-	public void setMaxIterations(int max) {
-		maxNumberOfIterations = max;
-	}
-
-	public double getCurrentValue() {
-		return currValue;
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/ConjugateGradient.java b/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/ConjugateGradient.java
deleted file mode 100644
index 28295729..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/ConjugateGradient.java
+++ /dev/null
@@ -1,92 +0,0 @@
-package optimization.gradientBasedMethods;
-
-import optimization.gradientBasedMethods.stats.OptimizerStats;
-import optimization.linesearch.DifferentiableLineSearchObjective;
-import optimization.linesearch.LineSearchMethod;
-import optimization.stopCriteria.StopingCriteria;
-import optimization.util.MathUtils;
-
-
-
-public class ConjugateGradient extends AbstractGradientBaseMethod{
-	
-	
-	double[] previousGradient;
-	double[] previousDirection;
-
-	public ConjugateGradient(LineSearchMethod lineSearch) {
-		this.lineSearch = lineSearch;
-	}
-	
-	public void reset(){
-		super.reset();
-		java.util.Arrays.fill(previousDirection, 0);
-		java.util.Arrays.fill(previousGradient, 0);
-	}
-	
-	public void initializeStructures(Objective o,OptimizerStats stats, StopingCriteria stop){
-		super.initializeStructures(o, stats, stop);
-		previousGradient = new double[o.getNumParameters()];
-		previousDirection = new double[o.getNumParameters()];
-	}
-	public void updateStructuresBeforeStep(Objective o,OptimizerStats stats, StopingCriteria stop){
-		System.arraycopy(gradient, 0, previousGradient, 0, gradient.length);
-		System.arraycopy(direction, 0, previousDirection, 0, direction.length);	
-	}
-	
-//	public boolean optimize(Objective o,OptimizerStats stats, StopingCriteria stop){
-//		DifferentiableLineSearchObjective lso = new DifferentiableLineSearchObjective(o);
-//		stats.collectInitStats(this, o);
-//		direction = new double[o.getNumParameters()];
-//		initializeStructures(o, stats, stop);
-//		for (currentProjectionIteration = 0; currentProjectionIteration < maxNumberOfIterations; currentProjectionIteration++){
-//			previousValue = currValue;
-//			currValue = o.getValue();
-//			gradient =o.getGradient();
-//			if(stop.stopOptimization(gradient)){
-//				stats.collectFinalStats(this, o);
-//				return true;
-//			}
-//			getDirection();
-//			updateStructures(o, stats, stop);
-//			lso.reset(direction);
-//			step = lineSearch.getStepSize(lso);	
-//			if(step==-1){
-//				System.out.println("Failed to find a step size");
-//				System.out.println("Failed to find step");
-//				stats.collectFinalStats(this, o);
-//				return false;	
-//			}
-//			
-//			stats.collectIterationStats(this, o);
-//		}
-//		stats.collectFinalStats(this, o);
-//		return false;
-//	}
-	
-	public double[] getDirection(){
-		direction = MathUtils.negation(gradient);
-		if(currentProjectionIteration != 1){
-			//Using Polak-Ribiere method (book equation 5.45)
-			double b = MathUtils.dotProduct(gradient, MathUtils.arrayMinus(gradient, previousGradient))
-			/MathUtils.dotProduct(previousGradient, previousGradient);
-			if(b<0){
-				System.out.println("Defaulting to gradient descent");
-				b = Math.max(b, 0);
-			}
-			MathUtils.plusEquals(direction, previousDirection, b);
-			//Debug code
-			if(MathUtils.dotProduct(direction, gradient) > 0){
-				System.out.println("Not an descent direction reseting to gradien");
-				direction = MathUtils.negation(gradient);
-			}
-		}
-		return direction;
-	}
-	
-	
-	
-
-
-
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/DebugHelpers.java b/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/DebugHelpers.java
deleted file mode 100644
index 6dc4ef6c..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/DebugHelpers.java
+++ /dev/null
@@ -1,65 +0,0 @@
-package optimization.gradientBasedMethods;
-
-import java.util.ArrayList;
-
-import optimization.util.MathUtils;
-
-
-
-public class DebugHelpers {
-	public static void getLineSearchGraph(Objective o, double[] direction, 
-			double[] parameters, double originalObj,
-			double originalDot, double c1, double c2){
-		ArrayList<Double> stepS = new ArrayList<Double>();
-		ArrayList<Double> obj = new ArrayList<Double>();
-		ArrayList<Double> norm = new ArrayList<Double>();
-		double[] gradient = new double[o.getNumParameters()];
-		double[] newParameters = parameters.clone();
-		MathUtils.plusEquals(newParameters,direction,0);
-		o.setParameters(newParameters);
-		double minValue = o.getValue();
-		int valuesBiggerThanMax = 0;
-		for(double step = 0; step < 2; step +=0.01 ){
-			newParameters = parameters.clone();
-			MathUtils.plusEquals(newParameters,direction,step);
-			o.setParameters(newParameters);
-			double newValue = o.getValue();
-			gradient = o.getGradient();
-			double newgradDirectionDot = MathUtils.dotProduct(gradient,direction);
-			stepS.add(step);
-			obj.add(newValue);
-			norm.add(newgradDirectionDot);
-			if(newValue <= minValue){
-				minValue = newValue;
-			}else{
-				valuesBiggerThanMax++;
-			}
-			
-			if(valuesBiggerThanMax > 10){
-				break;
-			}
-			
-		}
-		System.out.println("step\torigObj\tobj\tsuffdec\tnorm\tcurvature1");
-		for(int i = 0; i < stepS.size(); i++){
-			double cnorm= norm.get(i); 
-			System.out.println(stepS.get(i)+"\t"+originalObj +"\t"+obj.get(i) + "\t" + 
-					(originalObj + originalDot*((Double)stepS.get(i))*c1) +"\t"+Math.abs(cnorm) +"\t"+c2*Math.abs(originalDot));
-		}
-	}
-	
-	public static double[] getNumericalGradient(Objective o, double[] parameters, double epsilon){
-		int nrParameters = o.getNumParameters();
-		double[] gradient = new double[nrParameters];
-		double[] newParameters;
-		double originalValue = o.getValue();
-		for(int parameter = 0; parameter < nrParameters; parameter++){
-			newParameters = parameters.clone();
-			newParameters[parameter]+=epsilon;
-			o.setParameters(newParameters);
-			double newValue = o.getValue();
-			gradient[parameter]=(newValue-originalValue)/epsilon;
-		}	
-		return gradient;
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/GradientDescent.java b/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/GradientDescent.java
deleted file mode 100644
index 9a53cef4..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/GradientDescent.java
+++ /dev/null
@@ -1,19 +0,0 @@
-package optimization.gradientBasedMethods;
-
-import optimization.linesearch.LineSearchMethod;
-
-
-
-public class GradientDescent extends AbstractGradientBaseMethod{
-	
-	public GradientDescent(LineSearchMethod lineSearch) {
-		this.lineSearch = lineSearch;
-	}
-		
-	public double[] getDirection(){
-		for(int i = 0; i< gradient.length; i++){
-			direction[i] = -gradient[i];
-		}
-		return direction;
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/LBFGS.java b/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/LBFGS.java
deleted file mode 100644
index dedbc942..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/LBFGS.java
+++ /dev/null
@@ -1,234 +0,0 @@
-package optimization.gradientBasedMethods;
-
-
-import optimization.gradientBasedMethods.stats.OptimizerStats;
-import optimization.linesearch.DifferentiableLineSearchObjective;
-import optimization.linesearch.LineSearchMethod;
-import optimization.stopCriteria.StopingCriteria;
-import optimization.util.MathUtils;
-
-public class LBFGS extends AbstractGradientBaseMethod{
-
-	//How many previous values are being saved
-	int history;
-	double[][] skList;
-	double[][] ykList;
-	double initialHessianParameters;
-	double[] previousGradient;
-	double[] previousParameters;
-	
-	//auxiliar structures
-	double q[];
-	double[] roi;
-	double[] alphai;
-	
-	public LBFGS(LineSearchMethod ls, int history) {
-		lineSearch = ls;
-		this.history = history;
-		skList = new double[history][];
-		ykList = new double[history][];
-
-	}
-	
-	public void reset(){
-		super.reset();
-		initialHessianParameters = 0;
-		previousParameters = null;
-		previousGradient = null;
-		skList = new double[history][];
-		ykList = new double[history][];
-		q = null;
-		roi = null;
-		alphai = null;
-	}
-	
-	public double[] LBFGSTwoLoopRecursion(double hessianConst){
-		//Only create array once
-		if(q == null){
-			 q = new double[gradient.length];
-		}
-		System.arraycopy(gradient, 0, q, 0, gradient.length);
-		//Only create array once
-		if(roi == null){
-			roi = new double[history]; 
-		}
-		//Only create array once
-		if(alphai == null){
-			alphai = new double[history];
-		}
-		
-		for(int i = history-1; i >=0 && skList[i]!= null && ykList[i]!=null; i-- ){			
-		//	System.out.println("New to Old proj " + currentProjectionIteration + " history "+history + " index " + i);
-			double[] si =  skList[i];
-			double[] yi = ykList[i];
-			roi[i]= 1.0/MathUtils.dotProduct(yi,si);
-			alphai[i] = MathUtils.dotProduct(si, q)*roi[i];
-			MathUtils.plusEquals(q, yi, -alphai[i]);
-		}
-		//Initial Hessian is just a constant
-		MathUtils.scalarMultiplication(q, hessianConst);
-		for(int i = 0; i <history && skList[i]!= null && ykList[i]!=null; i++ ){
-		//	System.out.println("Old to New proj " + currentProjectionIteration + " history "+history + " index " + i);
-			double beta = MathUtils.dotProduct(ykList[i], q)*roi[i];
-			MathUtils.plusEquals(q, skList[i], (alphai[i]-beta));
-		}
-		return q;
-	}
-	
-	
-	
-	
-	@Override
-	public double[] getDirection() {
-		
-		calculateInitialHessianParameter();
-//		System.out.println("Initial hessian " + initialHessianParameters);
-		return direction = MathUtils.negation(LBFGSTwoLoopRecursion(initialHessianParameters));		
-	}
-	
-	public void calculateInitialHessianParameter(){
-		if(currentProjectionIteration == 1){
-			//Use gradient
-			initialHessianParameters = 1;
-		}else if(currentProjectionIteration <= history){
-			double[] sk = skList[currentProjectionIteration-2];
-			double[] yk = ykList[currentProjectionIteration-2];
-			initialHessianParameters = MathUtils.dotProduct(sk, yk)/MathUtils.dotProduct(yk, yk);
-		}else{
-			//get the last one
-			double[] sk = skList[history-1];
-			double[] yk = ykList[history-1];
-			initialHessianParameters = MathUtils.dotProduct(sk, yk)/MathUtils.dotProduct(yk, yk);
-		}
-	}
-	
-	//TODO if structures exit just reset them to zero
-	public void initializeStructures(Objective o,OptimizerStats stats, StopingCriteria stop){
-		super.initializeStructures(o, stats, stop);
-		previousParameters = new double[o.getNumParameters()];
-		previousGradient = new double[o.getNumParameters()];
-	}
-	public void updateStructuresBeforeStep(Objective o,OptimizerStats stats, StopingCriteria stop){	
-		super.initializeStructures(o, stats, stop);
-		System.arraycopy(o.getParameters(), 0, previousParameters, 0, previousParameters.length);
-		System.arraycopy(gradient, 0, previousGradient, 0, gradient.length);
-	}
-
-	public void 	updateStructuresAfterStep( Objective o,OptimizerStats stats, StopingCriteria stop){
-		double[] diffX = MathUtils.arrayMinus(o.getParameters(), previousParameters);
-		double[] diffGrad = MathUtils.arrayMinus(gradient, previousGradient);
-		//Save new values and discard new ones
-		if(currentProjectionIteration > history){
-			for(int i = 0; i < history-1;i++){
-				skList[i]=skList[i+1];
-				ykList[i]=ykList[i+1];
-			}
-			skList[history-1]=diffX;
-			ykList[history-1]=diffGrad;
-		}else{
-			skList[currentProjectionIteration-1]=diffX;
-			ykList[currentProjectionIteration-1]=diffGrad;
-		}	
-	}
-	
-//	public boolean optimize(Objective o, OptimizerStats stats, StopingCriteria stop) {		
-//		DifferentiableLineSearchObjective lso = new DifferentiableLineSearchObjective(o);		
-//		gradient = o.getGradient();
-//		direction = new double[o.getNumParameters()];
-//		previousGradient = new double[o.getNumParameters()];
-//		
-//		previousParameters = new double[o.getNumParameters()];
-//	
-//		stats.collectInitStats(this, o);
-//		previousValue = Double.MAX_VALUE;
-//		currValue= o.getValue();
-//		//Used for stopping criteria
-//		double[] originalGradient = o.getGradient();
-//		
-//		originalGradientL2Norm = MathUtils.L2Norm(originalGradient);
-//		if(stop.stopOptimization(originalGradient)){
-//			stats.collectFinalStats(this, o);
-//			return true;
-//		}
-//		for (currentProjectionIteration = 1; currentProjectionIteration < maxNumberOfIterations; currentProjectionIteration++){
-//			
-//			
-//			currValue = o.getValue();
-//			gradient  = o.getGradient();
-//			currParameters = o.getParameters();
-//			
-//			
-//			if(currentProjectionIteration == 1){
-//				//Use gradient
-//				initialHessianParameters = 1;
-//			}else if(currentProjectionIteration <= history){
-//				double[] sk = skList[currentProjectionIteration-2];
-//				double[] yk = ykList[currentProjectionIteration-2];
-//				initialHessianParameters = MathUtils.dotProduct(sk, yk)/MathUtils.dotProduct(yk, yk);
-//			}else{
-//				//get the last one
-//				double[] sk = skList[history-1];
-//				double[] yk = ykList[history-1];
-//				initialHessianParameters = MathUtils.dotProduct(sk, yk)/MathUtils.dotProduct(yk, yk);
-//			}
-//			
-//			getDirection();
-//			
-//			//MatrixOutput.printDoubleArray(direction, "direction");
-//			double dot = MathUtils.dotProduct(direction, gradient);
-//			if(dot > 0){				
-//				throw new RuntimeException("Not a descent direction");
-//			} if (Double.isNaN(dot)){
-//				throw new RuntimeException("dot is not a number!!");
-//			}
-//			System.arraycopy(currParameters, 0, previousParameters, 0, currParameters.length);
-//			System.arraycopy(gradient, 0, previousGradient, 0, gradient.length);
-//			lso.reset(direction);
-//			step = lineSearch.getStepSize(lso);
-//			if(step==-1){
-//				System.out.println("Failed to find a step size");
-////				lso.printLineSearchSteps();
-////				System.out.println(stats.prettyPrint(1));
-//				stats.collectFinalStats(this, o);
-//				return false;	
-//			}
-//			stats.collectIterationStats(this, o);
-//			
-//			//We are not updating the alpha since it is done in line search already
-//			currParameters = o.getParameters();
-//			gradient = o.getGradient();
-//			
-//			if(stop.stopOptimization(gradient)){
-//				stats.collectFinalStats(this, o);
-//				return true;
-//			}
-//			double[] diffX = MathUtils.arrayMinus(currParameters, previousParameters);
-//			double[] diffGrad = MathUtils.arrayMinus(gradient, previousGradient);
-//			//Save new values and discard new ones
-//			if(currentProjectionIteration > history){
-//				for(int i = 0; i < history-1;i++){
-//					skList[i]=skList[i+1];
-//					ykList[i]=ykList[i+1];
-//				}
-//				skList[history-1]=diffX;
-//				ykList[history-1]=diffGrad;
-//			}else{
-//				skList[currentProjectionIteration-1]=diffX;
-//				ykList[currentProjectionIteration-1]=diffGrad;
-//			}		
-//			previousValue = currValue;
-//		}
-//		stats.collectFinalStats(this, o);
-//		return false;	
-//	}
-	
-
-
-	
-
-	
-
-	
-	
-
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/Objective.java b/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/Objective.java
deleted file mode 100644
index 6be01bf9..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/Objective.java
+++ /dev/null
@@ -1,87 +0,0 @@
-package optimization.gradientBasedMethods;
-
-
-/**
- * Defines an optimization objective:
- * 
- * 
- * @author javg
- *
- */
-public abstract  class Objective {
-
-	protected int functionCalls = 0;
-	protected int gradientCalls = 0;
-	protected int updateCalls = 0;
-	
-	protected double[] parameters;
-	
-	//Contains a cache with the gradient
-	public double[] gradient;
-	int debugLevel = 0;
-	
-	public void setDebugLevel(int level){
-		debugLevel = level;
-	}
-	
-	public int getNumParameters() {
-		return parameters.length;
-	}
-
-	public double getParameter(int index) {
-		return parameters[index];
-	}
-
-	public double[] getParameters() {
-		return parameters;
-	}
-
-	public abstract double[] getGradient( );
-	
-	public void setParameter(int index, double value) {
-		parameters[index]=value;
-	}
-
-	public void setParameters(double[] params) {
-		if(parameters == null){
-			parameters = new double[params.length];
-		}
-		updateCalls++;
-		System.arraycopy(params, 0, parameters, 0, params.length);
-	}
-
-	
-	public int getNumberFunctionCalls() {
-		return functionCalls;
-	}
-
-	public int getNumberGradientCalls() {
-		return gradientCalls;
-	}
-	
-	public int getNumberUpdateCalls() {
-		return updateCalls;
-	}
-	
-	public String finalInfoString() {
-		return "FE: " + functionCalls + " GE " + gradientCalls + " Params updates" +
-		updateCalls;
-	}
-	public void printParameters() {
-		System.out.println(toString());
-	}	
-	
-	public abstract String toString();	
-	public abstract double getValue ();
-	
-	/**
-	 * Sets the initial objective parameters
-	 * For unconstrained models this just sets the objective params = argument no copying
-	 * For a constrained objective project the parameters and then set
-	 * @param params
-	 */
-	public  void setInitialParameters(double[] params){
-		parameters = params;
-	}
-
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/Optimizer.java b/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/Optimizer.java
deleted file mode 100644
index 96fce5b0..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/Optimizer.java
+++ /dev/null
@@ -1,19 +0,0 @@
-package optimization.gradientBasedMethods;
-
-import optimization.gradientBasedMethods.stats.OptimizerStats;
-import optimization.stopCriteria.StopingCriteria;
-
-public interface Optimizer {
-	public boolean optimize(Objective o,OptimizerStats stats, StopingCriteria stoping);
-	
-	
-	public double[] getDirection();
-	public double getCurrentStep();
-	public double getCurrentValue();
-	public int getCurrentIteration();
-	public void reset();
-	
-	public void setMaxIterations(int max);
-	
-		
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/ProjectedAbstractGradientBaseMethod.java b/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/ProjectedAbstractGradientBaseMethod.java
deleted file mode 100644
index afb29d04..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/ProjectedAbstractGradientBaseMethod.java
+++ /dev/null
@@ -1,11 +0,0 @@
-package optimization.gradientBasedMethods;
-
-
-/**
- * 
- * @author javg
- *
- */
-public abstract class ProjectedAbstractGradientBaseMethod extends AbstractGradientBaseMethod implements ProjectedOptimizer{
-	
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/ProjectedGradientDescent.java b/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/ProjectedGradientDescent.java
deleted file mode 100644
index 0186e945..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/ProjectedGradientDescent.java
+++ /dev/null
@@ -1,154 +0,0 @@
-package optimization.gradientBasedMethods;
-
-import java.io.IOException;
-
-import optimization.gradientBasedMethods.stats.OptimizerStats;
-import optimization.linesearch.DifferentiableLineSearchObjective;
-import optimization.linesearch.LineSearchMethod;
-import optimization.linesearch.ProjectedDifferentiableLineSearchObjective;
-import optimization.stopCriteria.StopingCriteria;
-import optimization.util.MathUtils;
-
-
-/**
- * This class implements the projected gradiend
- * as described in Bertsekas "Non Linear Programming"
- * section 2.3.
- * 
- * The update is given by:
- * x_k+1 = x_k + alpha^k(xbar_k-x_k)
- * Where xbar is:
- * xbar = [x_k -s_k grad(f(x_k))]+
- * where []+ is the projection into the feasibility set
- * 
- * alpha is the step size 
- * s_k - is a positive scalar which can be view as a step size as well, by 
- * setting alpha to 1, then x_k+1 = [x_k -s_k grad(f(x_k))]+
- * This is called taking a step size along the projection arc (Bertsekas) which
- * we will use by default.
- * 
- * Note that the only place where we actually take a step size is on pick a step size
- * so this is going to be just like a normal gradient descent but use a different 
- * armijo line search where we project after taking a step.
- * 
- * 
- * @author javg
- *
- */
-public class ProjectedGradientDescent extends ProjectedAbstractGradientBaseMethod{
-	
-
-	
-	
-	public ProjectedGradientDescent(LineSearchMethod lineSearch) {
-		this.lineSearch = lineSearch;
-	}
-	
-	//Use projected differential objective instead
-	public void initializeStructures(Objective o, OptimizerStats stats, StopingCriteria stop) {
-		lso = new ProjectedDifferentiableLineSearchObjective(o);
-	};
-	
-	
-	ProjectedObjective obj;
-	public boolean optimize(ProjectedObjective o,OptimizerStats stats, StopingCriteria stop){
-		obj = o;
-		return super.optimize(o, stats, stop);
-	}
-	
-	public double[] getDirection(){
-		for(int i = 0; i< gradient.length; i++){
-			direction[i] = -gradient[i];
-		}
-		return direction;
-	}
-	
-	
-
-		
-}
-
-
-
-
-
-
-
-///OLD CODE
-
-//Use projected gradient norm
-//public boolean stopCriteria(double[] gradient){
-//	if(originalDirenctionL2Norm == 0){
-//		System.out.println("Leaving original direction norm is zero");
-//		return true;	
-//	}
-//	if(MathUtils.L2Norm(direction)/originalDirenctionL2Norm < gradientConvergenceValue){
-//		System.out.println("Leaving projected gradient Norm smaller than epsilon");
-//		return true;	
-//	}
-//	if((previousValue - currValue)/Math.abs(previousValue) < valueConvergenceValue) {
-//		System.out.println("Leaving value change below treshold " + previousValue + " - " + currValue);
-//		System.out.println(previousValue/currValue + " - " + currValue/currValue 
-//				+ " = " + (previousValue - currValue)/Math.abs(previousValue));
-//		return true;
-//	}
-//	return false;
-//}
-//
-
-//public boolean optimize(ProjectedObjective o,OptimizerStats stats, StopingCriteria stop){
-//		stats.collectInitStats(this, o);
-//		obj = o;
-//		step = 0;
-//		currValue = o.getValue();
-//		previousValue = Double.MAX_VALUE;
-//		gradient = o.getGradient();
-//		originalGradientL2Norm = MathUtils.L2Norm(gradient);
-//		parameterChange = new double[gradient.length];
-//		getDirection();
-//		ProjectedDifferentiableLineSearchObjective lso = new ProjectedDifferentiableLineSearchObjective(o,direction);
-//		
-//		originalDirenctionL2Norm = MathUtils.L2Norm(direction);
-//		//MatrixOutput.printDoubleArray(currParameters, "parameters");
-//		for (currentProjectionIteration = 0; currentProjectionIteration < maxNumberOfIterations; currentProjectionIteration++){		
-//		//	System.out.println("Iter " + currentProjectionIteration);
-//			//o.printParameters();
-//			
-//			
-//			
-//			if(stop.stopOptimization(gradient)){
-//				stats.collectFinalStats(this, o);
-//				lastStepUsed = step;
-//				return true;
-//			}			
-//			lso.reset(direction);
-//			step = lineSearch.getStepSize(lso);
-//			if(step==-1){
-//				System.out.println("Failed to find step");
-//				stats.collectFinalStats(this, o);
-//				return false;	
-//				
-//			}
-//			
-//			//Update the direction for stopping criteria
-//			previousValue = currValue;
-//			currValue = o.getValue();
-//			gradient = o.getGradient();
-//			direction = getDirection();		
-//			if(MathUtils.dotProduct(gradient, direction) > 0){
-//				System.out.println("Not a descent direction");
-//				System.out.println(" current stats " + stats.prettyPrint(1));
-//				System.exit(-1);
-//			}
-//			stats.collectIterationStats(this, o);
-//		}
-//		lastStepUsed = step;
-//		stats.collectFinalStats(this, o);
-//		return false;
-//	}
-
-//public boolean optimize(Objective o,OptimizerStats stats, StopingCriteria stop){
-//	System.out.println("Objective is not a projected objective");
-//	throw new RuntimeException();
-//}
-
diff --git a/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/ProjectedObjective.java b/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/ProjectedObjective.java
deleted file mode 100644
index c3d21393..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/ProjectedObjective.java
+++ /dev/null
@@ -1,29 +0,0 @@
-package optimization.gradientBasedMethods;
-
-import optimization.util.MathUtils;
-
-
-/**
- * Computes a projected objective
- * When we tell it to set some parameters it automatically projects the parameters back into the simplex:
- * 
- * 
- * When we tell it to get the gradient in automatically returns the projected gradient:
- * @author javg
- *
- */
-public abstract class ProjectedObjective extends Objective{
-	
-	public abstract double[] projectPoint (double[] point);
-	
-	public double[] auxParameters;
-	
-	
-	public  void setInitialParameters(double[] params){
-		setParameters(projectPoint(params));
-	}
-	
-	
-	
-	
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/ProjectedOptimizer.java b/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/ProjectedOptimizer.java
deleted file mode 100644
index 81d8403e..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/ProjectedOptimizer.java
+++ /dev/null
@@ -1,10 +0,0 @@
-package optimization.gradientBasedMethods;
-
-
-
-public interface ProjectedOptimizer extends Optimizer{
-	
-	
-	
-	
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/stats/OptimizerStats.java b/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/stats/OptimizerStats.java
deleted file mode 100644
index 6340ef73..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/stats/OptimizerStats.java
+++ /dev/null
@@ -1,86 +0,0 @@
-package optimization.gradientBasedMethods.stats;
-
-import java.util.ArrayList;
-
-import optimization.gradientBasedMethods.Objective;
-import optimization.gradientBasedMethods.Optimizer;
-import optimization.util.MathUtils;
-import optimization.util.StaticTools;
-
-
-public class OptimizerStats {
-	
-	double start = 0;
-	double totalTime = 0;
-	
-	String objectiveFinalStats;
-	
-	ArrayList<Double> gradientNorms = new ArrayList<Double>();
-	ArrayList<Double> steps = new ArrayList<Double>();
-	ArrayList<Double> value = new ArrayList<Double>();
-	ArrayList<Integer> iterations = new ArrayList<Integer>();
-	double prevValue =0;
-	
-	public void reset(){
-		start = 0;
-		totalTime = 0;
-		
-		objectiveFinalStats="";
-		
-		gradientNorms.clear();
-		steps.clear();
-		value.clear();
-		iterations.clear();
-		prevValue =0;
-	}
-	
-	public void startTime() {
-		start = System.currentTimeMillis();
-	}
-	public void stopTime() {
-		totalTime += System.currentTimeMillis() - start;
-	}
-	
-	public String prettyPrint(int level){
-		StringBuffer res = new StringBuffer();
-		res.append("Total time " + totalTime/1000 + " seconds \n" + "Iterations " + iterations.size() + "\n");
-		res.append(objectiveFinalStats+"\n");
-		if(level > 0){
-			if(iterations.size() > 0){
-			res.append("\tIteration"+iterations.get(0)+"\tstep: "+StaticTools.prettyPrint(steps.get(0), "0.00E00", 6)+ "\tgradientNorm "+ 
-					StaticTools.prettyPrint(gradientNorms.get(0), "0.00000E00", 10)+ "\tvalue "+ StaticTools.prettyPrint(value.get(0), "0.000000E00",11)+"\n");
-			}
-			for(int i = 1; i < iterations.size(); i++){
-			res.append("\tIteration:\t"+iterations.get(i)+"\tstep:"+StaticTools.prettyPrint(steps.get(i), "0.00E00", 6)+ "\tgradientNorm "+ 
-					StaticTools.prettyPrint(gradientNorms.get(i), "0.00000E00", 10)+ 
-					"\tvalue:\t"+ StaticTools.prettyPrint(value.get(i), "0.000000E00",11)+
-					"\tvalueDiff:\t"+ StaticTools.prettyPrint((value.get(i-1)-value.get(i)), "0.000000E00",11)+
-					"\n");
-			}
-		}
-		return res.toString();
-	}
-	
-	
-	public void collectInitStats(Optimizer optimizer, Objective objective){
-		startTime();
-		iterations.add(-1);
-		gradientNorms.add(MathUtils.L2Norm(objective.getGradient()));
-		steps.add(0.0);
-		value.add(objective.getValue());
-	}
-	
-	public void collectIterationStats(Optimizer optimizer, Objective objective){
-		iterations.add(optimizer.getCurrentIteration());
-		gradientNorms.add(MathUtils.L2Norm(objective.getGradient()));
-		steps.add(optimizer.getCurrentStep());
-		value.add(optimizer.getCurrentValue());
-	}
-	
-	
-	public void collectFinalStats(Optimizer optimizer, Objective objective){
-		stopTime();
-		objectiveFinalStats = objective.finalInfoString();
-	}
-	
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/stats/ProjectedOptimizerStats.java b/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/stats/ProjectedOptimizerStats.java
deleted file mode 100644
index d65a1267..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/gradientBasedMethods/stats/ProjectedOptimizerStats.java
+++ /dev/null
@@ -1,70 +0,0 @@
-package optimization.gradientBasedMethods.stats;
-
-import java.util.ArrayList;
-
-import optimization.gradientBasedMethods.Objective;
-import optimization.gradientBasedMethods.Optimizer;
-import optimization.gradientBasedMethods.ProjectedObjective;
-import optimization.gradientBasedMethods.ProjectedOptimizer;
-import optimization.util.MathUtils;
-import optimization.util.StaticTools;
-
-
-public class ProjectedOptimizerStats extends OptimizerStats{
-	
-	
-	
-	public void reset(){
-		super.reset();
-		projectedGradientNorms.clear();
-	}
-	
-	ArrayList<Double> projectedGradientNorms = new ArrayList<Double>();
-
-	public String prettyPrint(int level){
-		StringBuffer res = new StringBuffer();
-		res.append("Total time " + totalTime/1000 + " seconds \n" + "Iterations " + iterations.size() + "\n");
-		res.append(objectiveFinalStats+"\n");
-		if(level > 0){
-			if(iterations.size() > 0){
-			res.append("\tIteration"+iterations.get(0)+"\tstep: "+
-					StaticTools.prettyPrint(steps.get(0), "0.00E00", 6)+ "\tgradientNorm "+ 
-					StaticTools.prettyPrint(gradientNorms.get(0), "0.00000E00", 10)
-					+ "\tdirection"+
-					StaticTools.prettyPrint(projectedGradientNorms.get(0), "0.00000E00", 10)+
-					"\tvalue "+ StaticTools.prettyPrint(value.get(0), "0.000000E00",11)+"\n");
-			}
-			for(int i = 1; i < iterations.size(); i++){
-			res.append("\tIteration"+iterations.get(i)+"\tstep: "+StaticTools.prettyPrint(steps.get(i), "0.00E00", 6)+ "\tgradientNorm "+ 
-					StaticTools.prettyPrint(gradientNorms.get(i), "0.00000E00", 10)+ 
-					"\t direction "+
-					StaticTools.prettyPrint(projectedGradientNorms.get(i), "0.00000E00", 10)+
-					"\tvalue "+ StaticTools.prettyPrint(value.get(i), "0.000000E00",11)+
-					"\tvalueDiff "+ StaticTools.prettyPrint((value.get(i-1)-value.get(i)), "0.000000E00",11)+
-					"\n");
-			}
-		}
-		return res.toString();
-	}
-	
-	
-	public void collectInitStats(Optimizer optimizer, Objective objective){
-		startTime();
-	}
-	
-	public void collectIterationStats(Optimizer optimizer, Objective objective){		
-		iterations.add(optimizer.getCurrentIteration());
-		gradientNorms.add(MathUtils.L2Norm(objective.getGradient()));
-		projectedGradientNorms.add(MathUtils.L2Norm(optimizer.getDirection()));
-		steps.add(optimizer.getCurrentStep());
-		value.add(optimizer.getCurrentValue());
-	}
-	
-	
-	
-	public void collectFinalStats(Optimizer optimizer, Objective objective){
-		stopTime();
-		objectiveFinalStats = objective.finalInfoString();
-	}
-	
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/linesearch/ArmijoLineSearchMinimization.java b/gi/posterior-regularisation/prjava/src/optimization/linesearch/ArmijoLineSearchMinimization.java
deleted file mode 100644
index c9f9b8df..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/linesearch/ArmijoLineSearchMinimization.java
+++ /dev/null
@@ -1,102 +0,0 @@
-package optimization.linesearch;
-
-import optimization.util.Interpolation;
-
-
-/**
- * Implements Back Tracking Line Search as described on page 37 of Numerical Optimization.
- * Also known as armijo rule
- * @author javg
- *
- */
-public class ArmijoLineSearchMinimization implements LineSearchMethod{
-
-	/**
-	 * How much should the step size decrease at each iteration.
-	 */
-	double contractionFactor = 0.5;
-	double c1 = 0.0001;
-	
-	double sigma1 = 0.1;
-	double sigma2 = 0.9;
-
-
-	
-	double initialStep;
-	int maxIterations = 10;
-	
-			
-	public ArmijoLineSearchMinimization(){
-		this.initialStep = 1;
-	}
-	
-	//Experiment
-	double previousStepPicked = -1;;
-	double previousInitGradientDot = -1;
-	double currentInitGradientDot = -1;
-	
-	
-	public void reset(){
-		previousStepPicked = -1;;
-		previousInitGradientDot = -1;
-		currentInitGradientDot = -1;
-	}
-	
-	public void setInitialStep(double initial){
-		initialStep = initial;
-	}
-	
-	/**
-	 * 
-	 */
-	
-	public double getStepSize(DifferentiableLineSearchObjective o) {	
-		currentInitGradientDot = o.getInitialGradient();
-		//Should update all in the objective
-		o.updateAlpha(initialStep);	
-		int nrIterations = 0;
-		//System.out.println("tried alpha" + initialStep + " value " + o.getCurrentValue());
-		while(!WolfeConditions.suficientDecrease(o,c1)){			
-			if(nrIterations >= maxIterations){
-				o.printLineSearchSteps();	
-				return -1;
-			}
-			double alpha=o.getAlpha();
-			double alphaTemp = 
-				Interpolation.quadraticInterpolation(o.getOriginalValue(), o.getInitialGradient(), alpha, o.getCurrentValue());
-			if(alphaTemp >= sigma1 || alphaTemp <= sigma2*o.getAlpha()){
-//				System.out.println("using alpha temp " + alphaTemp);
-				alpha = alphaTemp;
-			}else{
-//				System.out.println("Discarding alpha temp " + alphaTemp);
-				alpha = alpha*contractionFactor;
-			}
-//			double alpha =o.getAlpha()*contractionFactor;
-
-			o.updateAlpha(alpha);
-			//System.out.println("tried alpha" + alpha+ " value " + o.getCurrentValue());
-			nrIterations++;			
-		}
-		
-		//System.out.println("Leavning line search used:");
-		//o.printLineSearchSteps();	
-		
-		previousInitGradientDot = currentInitGradientDot;
-		previousStepPicked = o.getAlpha();
-		return o.getAlpha();
-	}
-
-	public double getInitialGradient() {
-		return currentInitGradientDot;
-		
-	}
-
-	public double getPreviousInitialGradient() {
-		return previousInitGradientDot;
-	}
-
-	public double getPreviousStepUsed() {
-		return previousStepPicked;
-	}
-		
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/linesearch/ArmijoLineSearchMinimizationAlongProjectionArc.java b/gi/posterior-regularisation/prjava/src/optimization/linesearch/ArmijoLineSearchMinimizationAlongProjectionArc.java
deleted file mode 100644
index e153f2da..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/linesearch/ArmijoLineSearchMinimizationAlongProjectionArc.java
+++ /dev/null
@@ -1,141 +0,0 @@
-package optimization.linesearch;
-
-import optimization.gradientBasedMethods.ProjectedObjective;
-import optimization.util.Interpolation;
-import optimization.util.MathUtils;
-
-
-
-
-
-/**
- * Implements Armijo Rule Line search along the projection arc (Non-Linear Programming page 230)
- * To be used with Projected gradient Methods.
- * 
- * Recall that armijo tries successive step sizes alpha until the sufficient decrease is satisfied:
- * f(x+alpha*direction) < f(x) + alpha*c1*grad(f)*direction
- * 
- * In this case we are optimizing over a convex set X so we must guarantee that the new point stays inside the 
- * constraints.
- * First the direction as to be feasible (inside constraints) and will be define as:
- * d = (x_k_f - x_k) where x_k_f is a feasible point.
- * so the armijo condition can be rewritten as:
- * f(x+alpha(x_k_f - x_k)) < f(x) + c1*grad(f)*(x_k_f - x_k)
- * and x_k_f is defined as:
- * [x_k-alpha*grad(f)]+
- * where []+ mean a projection to the feasibility set.
- * So this means that we take a step on the negative gradient (gradient descent) and then obtain then project
- * that point to the feasibility set. 
- * Note that if the point is already feasible then we are back to the normal armijo rule.
- * 
- * @author javg
- *
- */
-public class ArmijoLineSearchMinimizationAlongProjectionArc implements LineSearchMethod{
-
-	/**
-	 * How much should the step size decrease at each iteration.
-	 */
-	double contractionFactor = 0.5;
-	double c1 = 0.0001;
-	
-	
-	double initialStep;
-	int maxIterations = 100;
-			
-	
-	double sigma1 = 0.1;
-	double sigma2 = 0.9;
-	
-	//Experiment
-	double previousStepPicked = -1;;
-	double previousInitGradientDot = -1;
-	double currentInitGradientDot = -1;
-	
-	GenericPickFirstStep strategy;
-	
-	
-	public void reset(){
-		previousStepPicked = -1;;
-		previousInitGradientDot = -1;
-		currentInitGradientDot = -1;
-	}
-
-	
-	public ArmijoLineSearchMinimizationAlongProjectionArc(){
-		this.initialStep = 1;
-	}
-	
-	public ArmijoLineSearchMinimizationAlongProjectionArc(GenericPickFirstStep strategy){
-		this.strategy = strategy;
-		this.initialStep = strategy.getFirstStep(this);
-	}
-	
-	
-	public void setInitialStep(double initial){
-		this.initialStep = initial;
-	}
-	
-	/**
-	 * 
-	 */
-	
-	public double getStepSize(DifferentiableLineSearchObjective o) {	
-
-		
-		//Should update all in the objective
-		initialStep = strategy.getFirstStep(this);
-		o.updateAlpha(initialStep);	
-		previousInitGradientDot=currentInitGradientDot;
-		currentInitGradientDot=o.getCurrentGradient();
-		int nrIterations = 0;
-	
-		//Armijo rule, the current value has to be smaller than the original value plus a small step of the gradient
-		while(o.getCurrentValue()  >
-			o.getOriginalValue() + c1*(o.getCurrentGradient())){			
-//			System.out.println("curr value "+o.getCurrentValue());
-//			System.out.println("original value "+o.getOriginalValue());
-//			System.out.println("GRADIENT decrease" +(MathUtils.dotProduct(o.o.gradient,
-//					MathUtils.arrayMinus(o.originalParameters,((ProjectedObjective)o.o).auxParameters))));
-//			System.out.println("GRADIENT SAVED" + o.getCurrentGradient());
-			if(nrIterations >= maxIterations){
-				System.out.println("Could not find a step leaving line search with -1");
-				o.printLineSearchSteps();
-				return -1;
-			}
-			double alpha=o.getAlpha();
-			double alphaTemp = 
-				Interpolation.quadraticInterpolation(o.getOriginalValue(), o.getInitialGradient(), alpha, o.getCurrentValue());
-			if(alphaTemp >= sigma1 || alphaTemp <= sigma2*o.getAlpha()){
-				alpha = alphaTemp;
-			}else{
-				alpha = alpha*contractionFactor;
-			}
-//			double alpha =obj.getAlpha()*contractionFactor;
-			o.updateAlpha(alpha);
-			nrIterations++;			
-		}
-//		System.out.println("curr value "+o.getCurrentValue());
-//		System.out.println("original value "+o.getOriginalValue());
-//		System.out.println("sufficient decrease" +c1*o.getCurrentGradient());
-//		System.out.println("Leavning line search used:");
-//		o.printSmallLineSearchSteps();	
-		
-		previousStepPicked = o.getAlpha();
-		return o.getAlpha();
-	}
-	
-	public double getInitialGradient() {
-		return currentInitGradientDot;
-		
-	}
-
-	public double getPreviousInitialGradient() {
-		return previousInitGradientDot;
-	}
-
-	public double getPreviousStepUsed() {
-		return previousStepPicked;
-	}
-		
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/linesearch/DifferentiableLineSearchObjective.java b/gi/posterior-regularisation/prjava/src/optimization/linesearch/DifferentiableLineSearchObjective.java
deleted file mode 100644
index a5bc958e..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/linesearch/DifferentiableLineSearchObjective.java
+++ /dev/null
@@ -1,185 +0,0 @@
-package optimization.linesearch;
-
-import gnu.trove.TDoubleArrayList;
-import gnu.trove.TIntArrayList;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Comparator;
-
-import optimization.gradientBasedMethods.Objective;
-import optimization.util.MathUtils;
-import optimization.util.StaticTools;
-
-
-
-import util.MathUtil;
-import util.Printing;
-
-
-/**
- * A wrapper class for the actual objective in order to perform 
- * line search.  The optimization code assumes that this does a lot 
- * of caching in order to simplify legibility.  For the applications 
- * we use it for, caching the entire history of evaluations should be 
- * a win. 
- * 
- * Note: the lastEvaluatedAt value is very important, since we will use
- * it to avoid doing an evaluation of the gradient after the line search.  
- * 
- * The differentiable line search objective defines a search along the ray
- * given by a direction of the main objective.
- * It defines the following function, 
- * where f is the original objective function:
- * g(alpha) = f(x_0 + alpha*direction)
- * g'(alpha) = f'(x_0 + alpha*direction)*direction
- * 
- * @author joao
- *
- */
-public class DifferentiableLineSearchObjective {
-
-	
-	
-	Objective o;
-	int nrIterations;
-	TDoubleArrayList steps;
-	TDoubleArrayList values;
-	TDoubleArrayList gradients;
-	
-	//This variables cannot change
-	public double[] originalParameters;
-	public double[] searchDirection;
-
-	
-	/**
-	 * Defines a line search objective:
-	 * Receives:
-	 * Objective to each we are performing the line search, is used to calculate values and gradients
-	 * Direction where to do the ray search, note that the direction does not depend of the 
-	 * objective but depends from the method.
-	 * @param o
-	 * @param direction
-	 */
-	public DifferentiableLineSearchObjective(Objective o) {
-		this.o = o;
-		originalParameters = new double[o.getNumParameters()];
-		searchDirection = new double[o.getNumParameters()];
-		steps = new TDoubleArrayList();
-		values = new TDoubleArrayList();
-		gradients = new TDoubleArrayList();
-	}
-	/**
-	 * Called whenever we start a new iteration. 
-	 * Receives the ray where we are searching for and resets all values
-	 * 
-	 */
-	public void reset(double[] direction){
-		//Copy initial values
-		System.arraycopy(o.getParameters(), 0, originalParameters, 0, o.getNumParameters());
-		System.arraycopy(direction, 0, searchDirection, 0, o.getNumParameters());
-		
-		//Initialize variables
-		nrIterations = 0;
-		steps.clear();
-		values.clear();
-		gradients.clear();
-	
-		values.add(o.getValue());
-		gradients.add(MathUtils.dotProduct(o.getGradient(),direction));	
-		steps.add(0);
-	}
-	
-	
-	/**
-	 * update the current value of alpha.
-	 * Takes a step with that alpha in direction
-	 * Get the real objective value and gradient and calculate all required information.
-	 */
-	public void updateAlpha(double alpha){
-		if(alpha < 0){
-			System.out.println("alpha may not be smaller that zero");
-			throw new RuntimeException();
-		}
-		nrIterations++;
-		steps.add(alpha);
-		//x_t+1 = x_t + alpha*direction
-		System.arraycopy(originalParameters,0, o.getParameters(), 0, originalParameters.length);
-		MathUtils.plusEquals(o.getParameters(), searchDirection, alpha);
-		o.setParameters(o.getParameters());
-//		System.out.println("Took a step of " + alpha + " new value " + o.getValue());
-		values.add(o.getValue());
-		gradients.add(MathUtils.dotProduct(o.getGradient(),searchDirection));		
-	}
-
-	
-	
-	public int getNrIterations(){
-		return nrIterations;
-	}
-	
-	/**
-	 * return g(alpha) for the current value of alpha
-	 * @param iter
-	 * @return
-	 */
-	public double getValue(int iter){
-		return values.get(iter);
-	}
-	
-	public double getCurrentValue(){
-		return values.get(nrIterations);
-	}
-	
-	public double getOriginalValue(){
-		return values.get(0);
-	}
-
-	/**
-	 * return g'(alpha) for the current value of alpha
-	 * @param iter
-	 * @return
-	 */
-	public double getGradient(int iter){
-		return gradients.get(iter);
-	}
-	
-	public double getCurrentGradient(){
-		return gradients.get(nrIterations);
-	}
-	
-	public double getInitialGradient(){
-		return gradients.get(0);
-	}
-	
-	
-	
-	
-	public double getAlpha(){
-		return steps.get(nrIterations);
-	}
-	
-	public void printLineSearchSteps(){
-		System.out.println(
-				" Steps size "+steps.size() + 
-				"Values size "+values.size() +
-				"Gradeients size "+gradients.size());
-		for(int i =0; i < steps.size();i++){
-			System.out.println("Iter " + i + " step " + steps.get(i) +
-					" value " + values.get(i) + " grad "  + gradients.get(i));
-		}
-	}
-	
-	public void printSmallLineSearchSteps(){
-		for(int i =0; i < steps.size();i++){
-			System.out.print(StaticTools.prettyPrint(steps.get(i), "0.0000E00",8) + " ");
-		}
-		System.out.println();
-	}
-	
-	public static void main(String[] args) {
-		
-	}
-	
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/linesearch/GenericPickFirstStep.java b/gi/posterior-regularisation/prjava/src/optimization/linesearch/GenericPickFirstStep.java
deleted file mode 100644
index a33eb311..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/linesearch/GenericPickFirstStep.java
+++ /dev/null
@@ -1,20 +0,0 @@
-package optimization.linesearch;
-
-
-public class GenericPickFirstStep{
-	double _initValue;
-	public GenericPickFirstStep(double initValue) {
-		_initValue = initValue;
-	}
-	
-	public double getFirstStep(LineSearchMethod ls){
-		return _initValue;
-	}
-	public void collectInitValues(LineSearchMethod ls){
-		
-	}
-	
-	public void collectFinalValues(LineSearchMethod ls){
-		
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/linesearch/InterpolationPickFirstStep.java b/gi/posterior-regularisation/prjava/src/optimization/linesearch/InterpolationPickFirstStep.java
deleted file mode 100644
index 0deebcdb..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/linesearch/InterpolationPickFirstStep.java
+++ /dev/null
@@ -1,25 +0,0 @@
-package optimization.linesearch;
-
-
-public class InterpolationPickFirstStep extends GenericPickFirstStep{
-	public InterpolationPickFirstStep(double initValue) {
-		super(initValue);
-	}
-	
-	public double getFirstStep(LineSearchMethod ls){
-		if(ls.getPreviousStepUsed() != -1 && ls.getPreviousInitialGradient()!=0){
-			double newStep = Math.min(300, 1.02*ls.getPreviousInitialGradient()*ls.getPreviousStepUsed()/ls.getInitialGradient());
-		//	System.out.println("proposing " + newStep);
-			return newStep;
-			
-		}
-		return _initValue;
-	}
-	public void collectInitValues(WolfRuleLineSearch ls){
-		
-	}
-	
-	public void collectFinalValues(WolfRuleLineSearch ls){
-		
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/linesearch/LineSearchMethod.java b/gi/posterior-regularisation/prjava/src/optimization/linesearch/LineSearchMethod.java
deleted file mode 100644
index 80cd7f39..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/linesearch/LineSearchMethod.java
+++ /dev/null
@@ -1,14 +0,0 @@
-package optimization.linesearch;
-
-
-public interface LineSearchMethod {
-	
-	double getStepSize(DifferentiableLineSearchObjective o);
-	
-	public double getInitialGradient();
-	public double getPreviousInitialGradient();
-	public double getPreviousStepUsed();
-	
-	public void setInitialStep(double initial);
-	public void reset();
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/linesearch/NonNewtonInterpolationPickFirstStep.java b/gi/posterior-regularisation/prjava/src/optimization/linesearch/NonNewtonInterpolationPickFirstStep.java
deleted file mode 100644
index 4b354fd9..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/linesearch/NonNewtonInterpolationPickFirstStep.java
+++ /dev/null
@@ -1,33 +0,0 @@
-package optimization.linesearch;
-
-/**
- * Non newtwon since we don't always try 1...
- * Not sure if that is even usefull for newton
- * @author javg
- *
- */
-public class NonNewtonInterpolationPickFirstStep extends GenericPickFirstStep{
-	public NonNewtonInterpolationPickFirstStep(double initValue) {
-		super(initValue);
-	}
-	
-	public double getFirstStep(LineSearchMethod ls){
-//		System.out.println("Previous step used " + ls.getPreviousStepUsed());
-//		System.out.println("PreviousGradinebt " + ls.getPreviousInitialGradient());
-//		System.out.println("CurrentGradinebt " + ls.getInitialGradient());
-		if(ls.getPreviousStepUsed() != -1 && ls.getPreviousInitialGradient()!=0){
-			double newStep = 1.01*ls.getPreviousInitialGradient()*ls.getPreviousStepUsed()/ls.getInitialGradient();
-			//System.out.println("Suggesting " + newStep);
-			return newStep;
-			
-		}
-		return _initValue;
-	}
-	public void collectInitValues(WolfRuleLineSearch ls){
-		
-	}
-	
-	public void collectFinalValues(WolfRuleLineSearch ls){
-		
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/linesearch/ProjectedDifferentiableLineSearchObjective.java b/gi/posterior-regularisation/prjava/src/optimization/linesearch/ProjectedDifferentiableLineSearchObjective.java
deleted file mode 100644
index 29ccbc32..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/linesearch/ProjectedDifferentiableLineSearchObjective.java
+++ /dev/null
@@ -1,137 +0,0 @@
-package optimization.linesearch;
-
-import optimization.gradientBasedMethods.Objective;
-import optimization.gradientBasedMethods.ProjectedObjective;
-import optimization.util.MathUtils;
-import optimization.util.MatrixOutput;
-
-
-/**
- * See ArmijoLineSearchMinimizationAlongProjectionArc for description
- * @author javg
- *
- */
-public class ProjectedDifferentiableLineSearchObjective extends DifferentiableLineSearchObjective{
-
-	
-	
-	ProjectedObjective obj;
-	public ProjectedDifferentiableLineSearchObjective(Objective o) {
-		super(o);
-		if(!(o instanceof ProjectedObjective)){
-			System.out.println("Must receive a projected objective");
-			throw new RuntimeException();
-		}
-		obj = (ProjectedObjective) o;
-	}
-
-	
-	
-	public double[] projectPoint (double[] point){
-		return ((ProjectedObjective)o).projectPoint(point);
-	}
-	public void updateAlpha(double alpha){
-		if(alpha < 0){
-			System.out.println("alpha may not be smaller that zero");
-			throw new RuntimeException();
-		}
-		
-		if(obj.auxParameters == null){
-			obj.auxParameters = new double[obj.getParameters().length];
-		}
-		
-		nrIterations++;
-		
-		steps.add(alpha);		
-		System.arraycopy(originalParameters, 0, obj.auxParameters, 0, obj.auxParameters.length);
-		
-		//Take a step into the search direction
-		
-//		MatrixOutput.printDoubleArray(obj.getGradient(), "gradient");
-		
-//		alpha=gradients.get(0)*alpha/(gradients.get(gradients.size()-1));
-	
-		//x_t+1 = x_t - alpha*gradient = x_t + alpha*direction
-		MathUtils.plusEquals(obj.auxParameters, searchDirection, alpha);
-//		MatrixOutput.printDoubleArray(obj.auxParameters, "before projection");
-		obj.auxParameters = projectPoint(obj.auxParameters);
-//		MatrixOutput.printDoubleArray(obj.auxParameters, "after projection");
-		o.setParameters(obj.auxParameters);
-//		System.out.println("new parameters");
-//		o.printParameters();
-		values.add(o.getValue());
-		//Computes the new gradient x_k-[x_k-alpha*Gradient(x_k)]+ 
-		MathUtils.minusEqualsInverse(originalParameters,obj.auxParameters,1);
-//		MatrixOutput.printDoubleArray(obj.auxParameters, "new gradient");
-		//Dot product between the new direction and the new gradient
-		double gradient = MathUtils.dotProduct(obj.auxParameters,searchDirection);
-		gradients.add(gradient);	
-		if(gradient > 0){
-			System.out.println("Gradient on line search has to be smaller than zero");
-			System.out.println("Iter: " + nrIterations);
-			MatrixOutput.printDoubleArray(obj.auxParameters, "new direction");
-			MatrixOutput.printDoubleArray(searchDirection, "search direction");
-			throw new RuntimeException();
-			
-		}
-		
-	}
-	
-	/**
-	 * 
-	 */
-//	public void updateAlpha(double alpha){
-//		
-//		if(alpha < 0){
-//			System.out.println("alpha may not be smaller that zero");
-//			throw new RuntimeException();
-//		}
-//		
-//		nrIterations++;
-//		steps.add(alpha);
-//		//x_t+1 = x_t - alpha*direction
-//		System.arraycopy(originalParameters, 0, parametersChange, 0, parametersChange.length);
-////		MatrixOutput.printDoubleArray(parametersChange, "parameters before step");
-////		System.out.println("Step" + alpha);
-//		MatrixOutput.printDoubleArray(originalGradient, "gradient + " + alpha);
-//
-//		MathUtils.minusEquals(parametersChange, originalGradient, alpha);
-//		
-//		//Project the points into the feasibility set
-////		MatrixOutput.printDoubleArray(parametersChange, "before projection");
-//		//x_k(alpha) = [x_k - alpha*grad f(x_k)]+
-//		parametersChange = projectPoint(parametersChange);
-////		MatrixOutput.printDoubleArray(parametersChange, "after projection");
-//		o.setParameters(parametersChange);
-//		values.add(o.getValue());
-//		//Computes the new direction x_k-[x_k-alpha*Gradient(x_k)]+
-//		
-//		direction=MathUtils.arrayMinus(parametersChange,originalParameters);
-////		MatrixOutput.printDoubleArray(direction, "new direction");
-//		
-//		double gradient = MathUtils.dotProduct(originalGradient,direction);
-//		gradients.add(gradient);		
-//		if(gradient > 1E-10){
-//			System.out.println("cosine " + gradient/(MathUtils.L2Norm(originalGradient)*MathUtils.L2Norm(direction)));
-//			
-//			
-//			System.out.println("not a descent direction for alpha " + alpha);
-//			System.arraycopy(originalParameters, 0, parametersChange, 0, parametersChange.length);
-//			MathUtils.minusEquals(parametersChange, originalGradient, 1E-20);
-//			
-//			parametersChange = projectPoint(parametersChange);
-//			direction=MathUtils.arrayMinus(parametersChange,originalParameters);
-//			gradient = MathUtils.dotProduct(originalGradient,direction);
-//			if(gradient > 0){
-//				System.out.println("Direction is really non-descent evern for small alphas:" + gradient);
-//			}
-//			System.out.println("ProjecteLineSearchObjective: Should be a descent direction at " + nrIterations + ": "+ gradient);
-////			System.out.println(Printing.doubleArrayToString(originalGradient, null,"Original gradient"));
-////			System.out.println(Printing.doubleArrayToString(originalParameters, null,"Original parameters"));
-////			System.out.println(Printing.doubleArrayToString(parametersChange, null,"Projected parameters"));
-////			System.out.println(Printing.doubleArrayToString(direction, null,"Direction"));
-//			throw new RuntimeException();
-//		}
-//	}
-	
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/linesearch/WolfRuleLineSearch.java b/gi/posterior-regularisation/prjava/src/optimization/linesearch/WolfRuleLineSearch.java
deleted file mode 100644
index 5489f2d0..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/linesearch/WolfRuleLineSearch.java
+++ /dev/null
@@ -1,300 +0,0 @@
-package optimization.linesearch;
-
-import java.io.PrintStream;
-import java.util.ArrayList;
-
-import optimization.util.Interpolation;
-
-
-
-
-/**
- * 
- * @author javg
- *
- */
-public class WolfRuleLineSearch implements LineSearchMethod{
-
-	GenericPickFirstStep pickFirstStep;
-	
-	double c1 = 1.0E-4;
-	double c2 = 0.9;
-	
-	//Application dependent
-	double maxStep=100;
-	
-	int extrapolationIteration;
-	int maxExtrapolationIteration = 1000;
-	
-	
-	double minZoomDiffTresh = 10E-10;
-
-	
-	ArrayList<Double> steps;
-	ArrayList<Double> gradientDots;
-	ArrayList<Double> functionVals;
-	
-	int debugLevel = 0;
-	boolean foudStep = false;
-	
-	public WolfRuleLineSearch(GenericPickFirstStep pickFirstStep){
-		this.pickFirstStep = pickFirstStep;
-		
-	}
-	
-	
-
-	
-	public WolfRuleLineSearch(GenericPickFirstStep pickFirstStep,  double c1, double c2){
-		this.pickFirstStep = pickFirstStep;
-		initialStep = pickFirstStep.getFirstStep(this);
-		this.c1 = c1;
-		this.c2 = c2;
-	}
-	
-	public void setDebugLevel(int level){
-		debugLevel = level;
-	}
-	
-	//Experiment
-	double previousStepPicked = -1;;
-	double previousInitGradientDot = -1;
-	double currentInitGradientDot = -1;
-	
-	double initialStep;
-
-	
-	public void reset(){
-		previousStepPicked = -1;;
-		previousInitGradientDot = -1;
-		currentInitGradientDot = -1;
-		if(steps != null)
-			steps.clear();
-		if(gradientDots != null)
-			gradientDots.clear();
-		if(functionVals != null)
-			functionVals.clear();
-	}
-	
-	public void setInitialStep(double initial){
-		initialStep = pickFirstStep.getFirstStep(this);
-	}
-	
-	
-	
-	/**
-	 * Implements Wolf Line search as described in nocetal.
-	 * This process consists in two stages. The first stage we try to satisfy the
-	 * biggest step size that still satisfies the curvature condition. We keep increasing
-	 * the initial step size until we find a step satisfying the curvature condition, we return 
-	 * success, we failed the sufficient increase so we cannot increase more and we can call zoom with 
-	 * that maximum step, or we pass the minimum in which case we can call zoom the same way. 
-	 * 
-	 */
-	public double getStepSize(DifferentiableLineSearchObjective objective){
-		//System.out.println("entering line search");
-		
-		foudStep = false;
-		if(debugLevel >= 1){
-			steps = new ArrayList<Double>();
-			gradientDots = new ArrayList<Double>();
-			functionVals  =new ArrayList<Double>();
-		}
-		
-		//test
-		currentInitGradientDot = objective.getInitialGradient();
-		
-		
-		double previousValue = objective.getCurrentValue();
-		double previousStep = 0;
-		double currentStep =pickFirstStep.getFirstStep(this);
-		for(extrapolationIteration = 0; 
-		extrapolationIteration < maxExtrapolationIteration; extrapolationIteration++){	
-			
-			objective.updateAlpha(currentStep);
-			double currentValue = objective.getCurrentValue();
-			if(debugLevel >= 1){
-				steps.add(currentStep);
-				functionVals.add(currentValue);
-				gradientDots.add(objective.getCurrentGradient());
-			}
-			
-			
-			//The current step does not satisfy the sufficient decrease condition anymore
-			// so we cannot get bigger than that calling zoom.
-			if(!WolfeConditions.suficientDecrease(objective,c1)||					
-					(extrapolationIteration > 0 && currentValue >= previousValue)){
-				currentStep = zoom(objective,previousStep,currentStep,objective.nrIterations-1,objective.nrIterations);
-				break;
-			}
-			
-			//Satisfying both conditions ready to leave
-			if(WolfeConditions.sufficientCurvature(objective,c1,c2)){
-				//Found step
-				foudStep = true;
-				break;
-			}
-			
-			/**
-			 * This means that we passed the minimum already since the dot product that should be 
-			 * negative (descent direction) is now positive. So we cannot increase more. On the other hand
-			 * since we know the direction is a descent direction the value the objective at the current step
-			 * is for sure smaller than the preivous step so we change the order.
-			 */
-			if(objective.getCurrentGradient() >= 0){
-				currentStep =  zoom(objective,currentStep,previousStep,objective.nrIterations,objective.nrIterations-1);
-				break;
-			}
-			
-			
-			//Ok, so we can still get a bigger step, 
-			double aux = currentStep;
-			//currentStep = currentStep*2;
-			if(Math.abs(currentStep-maxStep)>1.1e-2){
-				currentStep = (currentStep+maxStep)/2;
-			}else{
-				currentStep = currentStep*2;
-			}
-			previousStep = aux;
-			previousValue = currentValue;
-			//Could be done better
-			if(currentStep >= maxStep){
-				System.out.println("Excedded max step...calling zoom with maxStepSize");
-				currentStep = zoom(objective,previousStep,currentStep,objective.nrIterations-1,objective.nrIterations);
-			}
-		}
-		if(!foudStep){
-			System.out.println("Wolfe Rule exceed number of iterations");
-			if(debugLevel >= 1){
-				printSmallWolfeStats(System.out);
-//				System.out.println("Line search values");
-//				DebugHelpers.getLineSearchGraph(o,  direction, originalParameters,origValue, origGradDirectionDot,c1,c2);			
-			}
-			return -1;
-		}
-		if(debugLevel >= 1){
-			printSmallWolfeStats(System.out);
-		}
-
-		previousStepPicked = currentStep;
-		previousInitGradientDot = currentInitGradientDot;
-//		objective.printLineSearchSteps();
-		return currentStep;
-	}
-	
-	
-	
-	
-	
-	public void printWolfeStats(PrintStream out){
-		for(int i = 0; i < steps.size(); i++){		
-			out.println("Step " + steps.get(i) + " value " + functionVals.get(i) + " dot " + gradientDots.get(i));
-		}
-	}
-	
-	public void printSmallWolfeStats(PrintStream out){
-		for(int i = 0; i < steps.size(); i++){		
-			out.print(steps.get(i) + ":"+functionVals.get(i)+":"+gradientDots.get(i)+" ");
-		}
-		System.out.println();
-	}
-	
-	
-	
-	/**
-	 * Pick a step satisfying the strong wolfe condition from an given from lowerStep and higherStep
-	 * picked on the routine above.
-	 * 
-	 * Both lowerStep and higherStep have been evaluated, so we only need to pass the iteration where they have
-	 * been evaluated and save extra evaluations.
-	 * 
-	 * We know that lowerStepValue as to be smaller than higherStepValue, and that a point 
-	 * satisfying both conditions exists in such interval.
-	 * 
-	 * LowerStep always satisfies at least the sufficient decrease
-	 * @return
-	 */
-	public double zoom(DifferentiableLineSearchObjective o, double lowerStep, double higherStep,
-			int lowerStepIter, int higherStepIter){
-		
-		if(debugLevel >=2){
-			System.out.println("Entering zoom with " + lowerStep+"-"+higherStep);
-		}
-		
-		double currentStep=-1;
-		
-		int zoomIter = 0;
-		while(zoomIter < 1000){		
-			if(Math.abs(lowerStep-higherStep) < minZoomDiffTresh){
-				o.updateAlpha(lowerStep);
-				if(debugLevel >= 1){
-					steps.add(lowerStep);
-					functionVals.add(o.getCurrentValue());
-					gradientDots.add(o.getCurrentGradient());
-				}
-				foudStep = true;
-				return lowerStep;
-			}	
-	
-			//Cubic interpolation
-			currentStep = 
-				Interpolation.cubicInterpolation(lowerStep, o.getValue(lowerStepIter), o.getGradient(lowerStepIter), 
-						higherStep, o.getValue(higherStepIter), o.getGradient(higherStepIter));
-			
-			//Safeguard.... should not be required check in what condtions it is required
-			if(currentStep < 0 ){
-				currentStep = (lowerStep+higherStep)/2;
-			}
-			if(Double.isNaN(currentStep) || Double.isInfinite(currentStep)){
-				currentStep = (lowerStep+higherStep)/2;
-			}
-//			currentStep = (lowerStep+higherStep)/2;
-//			System.out.println("Trying "+currentStep);
-			o.updateAlpha(currentStep);
-			if(debugLevel >=1){
-				steps.add(currentStep);
-				functionVals.add(o.getCurrentValue());
-				gradientDots.add(o.getCurrentGradient());
-			}
-			if(!WolfeConditions.suficientDecrease(o,c1)
-					|| o.getCurrentValue() >= o.getValue(lowerStepIter)){
-				higherStepIter = o.nrIterations;
-				higherStep = currentStep;
-			}
-			//Note when entering here the new step satisfies the sufficent decrease and
-			// or as a function value that is better than the previous best (lowerStepFunctionValues)
-			// so we either leave or change the value of the alpha low.
-			else{
-				if(WolfeConditions.sufficientCurvature(o,c1,c2)){
-					//Satisfies the both wolf conditions
-					foudStep = true;
-					break;
-				}
-				//If does not satisfy curvature 
-				if(o.getCurrentGradient()*(higherStep-lowerStep) >= 0){
-					higherStep = lowerStep;
-					higherStepIter = lowerStepIter;
-				}
-				lowerStep = currentStep;
-				lowerStepIter = o.nrIterations;
-			}
-			zoomIter++;
-		}
-		return currentStep;
-	}
-
-	public double getInitialGradient() {
-		return currentInitGradientDot;
-		
-	}
-
-	public double getPreviousInitialGradient() {
-		return previousInitGradientDot;
-	}
-
-	public double getPreviousStepUsed() {
-		return previousStepPicked;
-	}
-	
-	
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/linesearch/WolfeConditions.java b/gi/posterior-regularisation/prjava/src/optimization/linesearch/WolfeConditions.java
deleted file mode 100644
index dcc704eb..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/linesearch/WolfeConditions.java
+++ /dev/null
@@ -1,45 +0,0 @@
-package optimization.linesearch;
-
-
-public class WolfeConditions {
-	
-	/**
-	 * Sufficient Increase number. Default constant
-	 */
-	
-	
-	/**
-	 * Value for suficient curvature:
-	 * 0.9 - For newton and quase netwon methods
-	 * 0.1 - Non linear conhugate gradient
-	 */
-	
-	int debugLevel = 0;
-	public void setDebugLevel(int level){
-		debugLevel = level;
-	}
-	
-	public  static boolean suficientDecrease(DifferentiableLineSearchObjective o, double c1){	
-		double value = o.getOriginalValue()+c1*o.getAlpha()*o.getInitialGradient();
-//		System.out.println("Sufficient Decrease original "+value+" new "+  o.getCurrentValue());
-		return o.getCurrentValue() <= value;
-	}
-	
-	
-
-
-	public static boolean sufficientCurvature(DifferentiableLineSearchObjective o, double c1, double c2){
-//		if(debugLevel >= 2){
-//			double current = Math.abs(o.getCurrentGradient());
-//			double orig = -c2*o.getInitialGradient();
-//			if(current <= orig){
-//				return true;
-//			}else{
-//				System.out.println("Not satistfying curvature condition curvature " + current + " wants " + orig);
-//				return false;
-//			}
-//		}
-		return Math.abs(o.getCurrentGradient()) <= -c2*o.getInitialGradient();
-	}
-	
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/projections/BoundsProjection.java b/gi/posterior-regularisation/prjava/src/optimization/projections/BoundsProjection.java
deleted file mode 100644
index 0429d531..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/projections/BoundsProjection.java
+++ /dev/null
@@ -1,104 +0,0 @@
-package optimization.projections;
-
-
-import java.util.Random;
-
-import optimization.util.MathUtils;
-import optimization.util.MatrixOutput;
-
-/**
- * Implements a projection into a box set defined by a and b.
- * If either a or b are infinity then that bound is ignored.
- * @author javg
- *
- */
-public class BoundsProjection extends Projection{
-
-	double a,b;
-	boolean ignoreA = false;
-	boolean ignoreB = false;
-	public BoundsProjection(double lowerBound, double upperBound) {
-		if(Double.isInfinite(lowerBound)){
-			this.ignoreA = true;
-		}else{
-			this.a =lowerBound;
-		}
-		if(Double.isInfinite(upperBound)){
-			this.ignoreB = true;
-		}else{
-			this.b =upperBound;
-		}
-	}
-	
-	
-	
-	/**
-	* Projects into the bounds
-	* a <= x_i <=b
-	 */
-	public void project(double[] original){
-		for (int i = 0; i < original.length; i++) {
-			if(!ignoreA && original[i] < a){
-				original[i] = a;
-			}else if(!ignoreB && original[i]>b){
-				original[i]=b;
-			}
-		}
-	}
-	
-	/**
-	 * Generates a random number between a and b.
-	 */
-
-	Random r = new Random();
-	
-	public double[] samplePoint(int numParams) {
-		double[] point = new double[numParams];
-		for (int i = 0; i < point.length; i++) {
-			double rand = r.nextDouble();
-			if(ignoreA && ignoreB){
-				//Use const to avoid number near overflow
-				point[i] = rand*(1.E100+1.E100)-1.E100;
-			}else if(ignoreA){
-				point[i] = rand*(b-1.E100)-1.E100;
-			}else if(ignoreB){
-				point[i] = rand*(1.E100-a)-a;
-			}else{
-				point[i] = rand*(b-a)-a;
-			}
-		}
-		return point;
-	}
-	
-	public static void main(String[] args) {
-		BoundsProjection sp = new BoundsProjection(0,Double.POSITIVE_INFINITY);
-		
-		
-		MatrixOutput.printDoubleArray(sp.samplePoint(3), "random 1");
-		MatrixOutput.printDoubleArray(sp.samplePoint(3), "random 2");
-		MatrixOutput.printDoubleArray(sp.samplePoint(3), "random 3");
-		
-		double[] d = {-1.1,1.2,1.4};
-		double[] original = d.clone();
-		MatrixOutput.printDoubleArray(d, "before");
-		
-		sp.project(d);
-		MatrixOutput.printDoubleArray(d, "after");
-		System.out.println("Test projection: " + sp.testProjection(original, d));
-	}
-	
-	double epsilon = 1.E-10;
-	public double[] perturbePoint(double[] point, int parameter){
-		double[] newPoint = point.clone();
-		if(!ignoreA && MathUtils.almost(point[parameter], a)){
-			newPoint[parameter]+=epsilon;
-		}else if(!ignoreB && MathUtils.almost(point[parameter], b)){
-			newPoint[parameter]-=epsilon;
-		}else{
-			newPoint[parameter]-=epsilon;
-		}
-		return newPoint;
-	}
-
-	
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/projections/Projection.java b/gi/posterior-regularisation/prjava/src/optimization/projections/Projection.java
deleted file mode 100644
index b5a9f92f..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/projections/Projection.java
+++ /dev/null
@@ -1,72 +0,0 @@
-package optimization.projections;
-
-import optimization.util.MathUtils;
-import optimization.util.MatrixOutput;
-import util.ArrayMath;
-import util.Printing;
-
-
-
-public abstract class Projection {
-
-	
-	public abstract void project(double[] original);
-	
-	
-	/**
-	 *  From the projection theorem "Non-Linear Programming" page
-	 *  201 fact 2.
-	 *  
-	 *  Given some z in R, and a vector x* in X;
-	 *  x* = z+ iif for all x in X 
-	 *  (z-x*)'(x-x*) <= 0 where 0 is when x*=x
-	 *  See figure 2.16 in book
-	 *  
-	 * @param original
-	 * @param projected
-	 * @return
-	 */
-	public boolean testProjection(double[] original, double[] projected){
-		double[] original1 = original.clone();
-		//System.out.println(Printing.doubleArrayToString(original1, null, "original"));
-		//System.out.println(Printing.doubleArrayToString(projected, null, "projected"));
-		MathUtils.minusEquals(original1, projected, 1);
-		//System.out.println(Printing.doubleArrayToString(original1, null, "minus1"));
-		for(int i = 0; i < 10; i++){
-			double[] x = samplePoint(original.length);
-		//	System.out.println(Printing.doubleArrayToString(x, null, "sample"));
-			//If the same this returns zero so we are there.	
-			MathUtils.minusEquals(x, projected, 1);
-		//	System.out.println(Printing.doubleArrayToString(x, null, "minus2"));
-			double dotProd = MathUtils.dotProduct(original1, x);
-			
-		//	System.out.println("dot " + dotProd);
-			if(dotProd > 0) return false;
-		}
-		
-		//Perturbs the point a bit in all possible directions
-		for(int i = 0; i < original.length; i++){
-			double[] x = perturbePoint(projected,i);
-		//	System.out.println(Printing.doubleArrayToString(x, null, "perturbed"));
-			//If the same this returns zero so we are there.	
-			MathUtils.minusEquals(x, projected, 1);
-		//	System.out.println(Printing.doubleArrayToString(x, null, "minus2"));
-			double dotProd = MathUtils.dotProduct(original1, x);
-			
-		//	System.out.println("dot " + dotProd);
-			if(dotProd > 0) return false;
-		}
-		
-		
-		
-		return true;
-	}
-
-	//Samples a point from the constrained set
-	public abstract double[] samplePoint(int dimensions);
-	
-	//Perturbs a point a bit still leaving it at the constraints set
-	public abstract double[] perturbePoint(double[] point, int parameter);
-	
-	
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/projections/SimplexProjection.java b/gi/posterior-regularisation/prjava/src/optimization/projections/SimplexProjection.java
deleted file mode 100644
index f22afcaf..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/projections/SimplexProjection.java
+++ /dev/null
@@ -1,127 +0,0 @@
-package optimization.projections;
-
-
-
-import java.util.Random;
-
-import optimization.util.MathUtils;
-import optimization.util.MatrixOutput;
-
-public class SimplexProjection extends Projection{
-
-	double scale;
-	public SimplexProjection(double scale) {
-		this.scale = scale;
-	}
-	
-	/**
-	 * projects the numbers of the array 
-	 * into a simplex of size. 
-	 * We follow the description of the paper
-	 * "Efficient Projetions onto the l1-Ball
-	 * for learning in high dimensions"
-	 */
-	public void project(double[] original){
-		double[] ds = new double[original.length];
-		System.arraycopy(original, 0, ds, 0, ds.length);
-		//If sum is smaller then zero then its ok
-		for (int i = 0; i < ds.length; i++) ds[i] = ds[i]>0? ds[i]:0;
-		double sum = MathUtils.sum(ds);
-		if (scale - sum >=  -1.E-10 ){
-			System.arraycopy(ds, 0, original, 0, ds.length);
-			//System.out.println("Not projecting");
-			return;
-		}
-		//System.out.println("projecting " + sum + " scontraints " + scale);	
-		util.Array.sortDescending(ds);
-		double currentSum = 0;
-		double previousTheta = 0;
-		double theta = 0;
-		for (int i = 0; i < ds.length; i++) {
-			currentSum+=ds[i];
-			theta = (currentSum-scale)/(i+1);
-			if(ds[i]-theta < -1e-10){
-				break;
-			}
-			previousTheta = theta;
-		}
-		//DEBUG
-		if(previousTheta < 0){
-			System.out.println("Simple Projection: Theta is smaller than zero: " + previousTheta);
-			System.exit(-1);
-		}
-		for (int i = 0; i < original.length; i++) {
-			original[i] = Math.max(original[i]-previousTheta, 0);
-		}
-	}
-	
-	
-	
-	
-	
-
-	/**
-	 * Samples a point from the simplex of scale. Just sample
-	 * random number from 0-scale and then if
-	 * their sum is bigger then sum make them normalize.
-	 * This is probably not sampling uniformly from the simplex but it is
-	 * enough for our goals in here.
-	 */
-	Random r = new Random();
-	public double[] samplePoint(int dimensions) {
-		double[] newPoint = new double[dimensions];
-		double sum =0;
-		for (int i = 0; i < newPoint.length; i++) {
-			double rand = r.nextDouble()*scale;
-			sum+=rand;
-			newPoint[i]=rand;
-		}
-		//Normalize
-		if(sum > scale){
-			for (int i = 0; i < newPoint.length; i++) {
-				newPoint[i]=scale*newPoint[i]/sum;
-			}
-		}
-		return newPoint;
-	}
-	
-	public static void main(String[] args) {
-		SimplexProjection sp = new SimplexProjection(1);
-		
-		
-		double[] point = sp.samplePoint(3);
-		MatrixOutput.printDoubleArray(point , "random 1 sum:" + MathUtils.sum(point));
-		point = sp.samplePoint(3);
-		MatrixOutput.printDoubleArray(point , "random 2 sum:" + MathUtils.sum(point));
-		point = sp.samplePoint(3);
-		MatrixOutput.printDoubleArray(point , "random 3 sum:" + MathUtils.sum(point));
-		
-		double[] d = {0,1.1,-10};
-		double[] original = d.clone();
-		MatrixOutput.printDoubleArray(d, "before");
-		
-		sp.project(d);
-		MatrixOutput.printDoubleArray(d, "after");
-		System.out.println("Test projection: " + sp.testProjection(original, d));
-		
-	}
-	
-	
-	double epsilon = 1.E-10;
-	public double[] perturbePoint(double[] point, int parameter){
-		double[] newPoint = point.clone();
-		if(MathUtils.almost(MathUtils.sum(point), scale)){
-			newPoint[parameter]-=epsilon;
-		}
-		else if(point[parameter]==0){
-			newPoint[parameter]+=epsilon;
-		}else if(MathUtils.almost(point[parameter], scale)){
-			newPoint[parameter]-=epsilon;
-		}
-		else{
-			newPoint[parameter]-=epsilon;
-		}
-		return newPoint;
-	}
-	
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/CompositeStopingCriteria.java b/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/CompositeStopingCriteria.java
deleted file mode 100644
index 15760f18..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/CompositeStopingCriteria.java
+++ /dev/null
@@ -1,33 +0,0 @@
-package optimization.stopCriteria;
-
-import java.util.ArrayList;
-
-import optimization.gradientBasedMethods.Objective;
-
-public class CompositeStopingCriteria implements StopingCriteria {
-	
-	ArrayList<StopingCriteria> criterias;
-	
-	public CompositeStopingCriteria() {
-		criterias = new ArrayList<StopingCriteria>();
-	}
-	
-	public void add(StopingCriteria criteria){
-		criterias.add(criteria);
-	}
-	
-	public boolean stopOptimization(Objective obj){
-		for(StopingCriteria criteria: criterias){
-			if(criteria.stopOptimization(obj)){
-				return true;
-			}
-		}
-		return false;
-	}
-	
-	public void reset(){
-		for(StopingCriteria criteria: criterias){
-			criteria.reset();
-		}
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/GradientL2Norm.java b/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/GradientL2Norm.java
deleted file mode 100644
index 534ff833..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/GradientL2Norm.java
+++ /dev/null
@@ -1,30 +0,0 @@
-package optimization.stopCriteria;
-
-import optimization.gradientBasedMethods.Objective;
-import optimization.util.MathUtils;
-
-public class GradientL2Norm implements StopingCriteria{
-	
-	/**
-	 * Stop if gradientNorm/(originalGradientNorm) smaller
-	 * than gradientConvergenceValue
-	 */
-	protected double gradientConvergenceValue;
-	
-	
-	public GradientL2Norm(double gradientConvergenceValue){
-		this.gradientConvergenceValue = gradientConvergenceValue;
-	}
-	
-	public void reset(){}
-	
-	public boolean stopOptimization(Objective obj){
-		double norm = MathUtils.L2Norm(obj.gradient);
-		if(norm < gradientConvergenceValue){
-			System.out.println("Gradient norm below treshold");
-			return true;
-		}
-		return false;
-		
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/NormalizedGradientL2Norm.java b/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/NormalizedGradientL2Norm.java
deleted file mode 100644
index 4a489641..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/NormalizedGradientL2Norm.java
+++ /dev/null
@@ -1,48 +0,0 @@
-package optimization.stopCriteria;
-
-import optimization.gradientBasedMethods.Objective;
-import optimization.gradientBasedMethods.ProjectedObjective;
-import optimization.util.MathUtils;
-
-/**
- * Divides the norm by the norm at the begining of the iteration
- * @author javg
- *
- */
-public class NormalizedGradientL2Norm extends GradientL2Norm{
-	
-	/**
-	 * Stop if gradientNorm/(originalGradientNorm) smaller
-	 * than gradientConvergenceValue
-	 */
-	protected double originalGradientNorm = -1;
-	
-	public void reset(){
-		originalGradientNorm = -1;
-	}
-	public NormalizedGradientL2Norm(double gradientConvergenceValue){
-		super(gradientConvergenceValue);
-	}
-	
-	
-	 
-	
-	public boolean stopOptimization(Objective obj){
-			double norm = MathUtils.L2Norm(obj.gradient);
-			if(originalGradientNorm == -1){
-				originalGradientNorm = norm;
-			}
-			if(originalGradientNorm < 1E-10){
-				System.out.println("Gradient norm is zero " +  originalGradientNorm);
-				return true;
-			}
-			double normalizedNorm = 1.0*norm/originalGradientNorm;
-			if( normalizedNorm < gradientConvergenceValue){
-				System.out.println("Gradient norm below normalized normtreshold: " + norm + " original: " + originalGradientNorm + " normalized norm: " + normalizedNorm);
-				return true;
-			}else{
-//				System.out.println("projected gradient norm: " + norm);
-				return false;
-			}
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/NormalizedProjectedGradientL2Norm.java b/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/NormalizedProjectedGradientL2Norm.java
deleted file mode 100644
index 5ae554c2..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/NormalizedProjectedGradientL2Norm.java
+++ /dev/null
@@ -1,60 +0,0 @@
-package optimization.stopCriteria;
-
-import optimization.gradientBasedMethods.Objective;
-import optimization.gradientBasedMethods.ProjectedObjective;
-import optimization.util.MathUtils;
-
-/**
- * Divides the norm by the norm at the begining of the iteration
- * @author javg
- *
- */
-public class NormalizedProjectedGradientL2Norm extends ProjectedGradientL2Norm{
-	
-	/**
-	 * Stop if gradientNorm/(originalGradientNorm) smaller
-	 * than gradientConvergenceValue
-	 */
-	double originalProjectedNorm = -1;
-	
-	public NormalizedProjectedGradientL2Norm(double gradientConvergenceValue){
-		super(gradientConvergenceValue);
-	}
-	
-	public void reset(){
-		originalProjectedNorm = -1;
-	}
-	
-	
-	 double[] projectGradient(ProjectedObjective obj){
-		
-		if(obj.auxParameters == null){
-			obj.auxParameters = new double[obj.getNumParameters()];
-		}
-		System.arraycopy(obj.getParameters(), 0, obj.auxParameters, 0, obj.getNumParameters());
-		MathUtils.minusEquals(obj.auxParameters, obj.gradient, 1);
-		obj.auxParameters = obj.projectPoint(obj.auxParameters);
-		MathUtils.minusEquals(obj.auxParameters,obj.getParameters(),1);
-		return obj.auxParameters;
-	}
-	
-	public boolean stopOptimization(Objective obj){
-		if(obj instanceof ProjectedObjective) {
-			ProjectedObjective o = (ProjectedObjective) obj;
-			double norm = MathUtils.L2Norm(projectGradient(o));
-			if(originalProjectedNorm == -1){
-				originalProjectedNorm = norm;
-			}
-			double normalizedNorm = 1.0*norm/originalProjectedNorm;
-			if( normalizedNorm < gradientConvergenceValue){
-				System.out.println("Gradient norm below normalized normtreshold: " + norm + " original: " + originalProjectedNorm + " normalized norm: " + normalizedNorm);
-				return true;
-			}else{
-//				System.out.println("projected gradient norm: " + norm);
-				return false;
-			}
-		}
-		System.out.println("Not a projected objective");
-		throw new RuntimeException();
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/NormalizedValueDifference.java b/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/NormalizedValueDifference.java
deleted file mode 100644
index 6dbbc50d..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/NormalizedValueDifference.java
+++ /dev/null
@@ -1,54 +0,0 @@
-package optimization.stopCriteria;
-
-import optimization.gradientBasedMethods.Objective;
-import optimization.util.MathUtils;
-
-public class NormalizedValueDifference implements StopingCriteria{
-	
-	/**
-	 * Stop if the different between values is smaller than a treshold
-	 */
-	protected double valueConvergenceValue=0.01;
-	protected double previousValue = Double.NaN;
-	protected double currentValue = Double.NaN;
-	
-	public NormalizedValueDifference(double valueConvergenceValue){
-		this.valueConvergenceValue = valueConvergenceValue;
-	}
-	
-	public void reset(){
-		previousValue = Double.NaN;
-		currentValue = Double.NaN;
-	}
-
-	
-	public boolean stopOptimization(Objective obj){
-		if(Double.isNaN(currentValue)){
-			currentValue = obj.getValue();
-			return false;
-		}else {
-			previousValue = currentValue;
-			currentValue = obj.getValue();
-			if(previousValue != 0){
-				double valueDiff = Math.abs(previousValue - currentValue)/Math.abs(previousValue);
-				if( valueDiff  < valueConvergenceValue){
-					System.out.println("Leaving different in values is to small: Prev " 
-							+ (previousValue/previousValue) + " Curr: " + (currentValue/previousValue) 
-							+ " diff: " + valueDiff);
-					return true;
-				}
-			}else{
-				double valueDiff = Math.abs(previousValue - currentValue);
-				if( valueDiff  < valueConvergenceValue){
-					System.out.println("Leaving different in values is to small: Prev " 
-							+ (previousValue) + " Curr: " + (currentValue) 
-							+ " diff: " + valueDiff);
-					return true;
-				}
-			}
-
-			return false;
-		}
-		
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/ProjectedGradientL2Norm.java b/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/ProjectedGradientL2Norm.java
deleted file mode 100644
index aadf1fd5..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/ProjectedGradientL2Norm.java
+++ /dev/null
@@ -1,51 +0,0 @@
-package optimization.stopCriteria;
-
-import optimization.gradientBasedMethods.Objective;
-import optimization.gradientBasedMethods.ProjectedObjective;
-import optimization.util.MathUtils;
-
-public class ProjectedGradientL2Norm implements StopingCriteria{
-	
-	/**
-	 * Stop if gradientNorm/(originalGradientNorm) smaller
-	 * than gradientConvergenceValue
-	 */
-	protected double gradientConvergenceValue;
-	
-	
-	public ProjectedGradientL2Norm(double gradientConvergenceValue){
-		this.gradientConvergenceValue = gradientConvergenceValue;
-	}
-	
-	public void reset(){
-		
-	}
-	
-	 double[] projectGradient(ProjectedObjective obj){
-		
-		if(obj.auxParameters == null){
-			obj.auxParameters = new double[obj.getNumParameters()];
-		}
-		System.arraycopy(obj.getParameters(), 0, obj.auxParameters, 0, obj.getNumParameters());
-		MathUtils.minusEquals(obj.auxParameters, obj.gradient, 1);
-		obj.auxParameters = obj.projectPoint(obj.auxParameters);
-		MathUtils.minusEquals(obj.auxParameters,obj.getParameters(),1);
-		return obj.auxParameters;
-	}
-	
-	public boolean stopOptimization(Objective obj){
-		if(obj instanceof ProjectedObjective) {
-			ProjectedObjective o = (ProjectedObjective) obj;
-			double norm = MathUtils.L2Norm(projectGradient(o));
-			if(norm < gradientConvergenceValue){
-	//			System.out.println("Gradient norm below treshold: " + norm);
-				return true;
-			}else{
-//				System.out.println("projected gradient norm: " + norm);
-				return false;
-			}
-		}
-		System.out.println("Not a projected objective");
-		throw new RuntimeException();
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/StopingCriteria.java b/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/StopingCriteria.java
deleted file mode 100644
index 10cf0522..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/StopingCriteria.java
+++ /dev/null
@@ -1,8 +0,0 @@
-package optimization.stopCriteria;
-
-import optimization.gradientBasedMethods.Objective;
-
-public interface StopingCriteria {
-	public boolean stopOptimization(Objective obj);
-	public void reset();
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/ValueDifference.java b/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/ValueDifference.java
deleted file mode 100644
index e5d07229..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/ValueDifference.java
+++ /dev/null
@@ -1,41 +0,0 @@
-package optimization.stopCriteria;
-
-import optimization.gradientBasedMethods.Objective;
-import optimization.util.MathUtils;
-
-public class ValueDifference implements StopingCriteria{
-	
-	/**
-	 * Stop if the different between values is smaller than a treshold
-	 */
-	protected double valueConvergenceValue=0.01;
-	protected double previousValue = Double.NaN;
-	protected double currentValue = Double.NaN;
-	
-	public ValueDifference(double valueConvergenceValue){
-		this.valueConvergenceValue = valueConvergenceValue;
-	}
-	
-	public void reset(){
-		previousValue = Double.NaN;
-		currentValue = Double.NaN;
-	}
-	
-	public boolean stopOptimization(Objective obj){
-		if(Double.isNaN(currentValue)){
-			currentValue = obj.getValue();
-			return false;
-		}else {
-			previousValue = currentValue;
-			currentValue = obj.getValue();
-			if(previousValue - currentValue   < valueConvergenceValue){
-//				System.out.println("Leaving different in values is to small: Prev " 
-//						+ previousValue + " Curr: " + currentValue 
-//						+ " diff: " + (previousValue - currentValue));
-				return true;
-			}
-			return false;
-		}
-		
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/util/Interpolation.java b/gi/posterior-regularisation/prjava/src/optimization/util/Interpolation.java
deleted file mode 100644
index cdbdefc6..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/util/Interpolation.java
+++ /dev/null
@@ -1,37 +0,0 @@
-package optimization.util;
-
-public class Interpolation {
-
-	/**
-	 * Fits a cubic polinomyal to a function given two points,
-	 * such that either gradB is bigger than zero or funcB >= funcA
-	 * 
-	 * NonLinear Programming appendix C
-	 * @param funcA
-	 * @param gradA
-	 * @param funcB
-	 * @param gradB
-	 */
-	public final static double cubicInterpolation(double a, 
-			double funcA, double gradA, double b,double funcB, double gradB ){
-		if(gradB < 0 && funcA > funcB){
-			System.out.println("Cannot call cubic interpolation");
-			return -1;
-		}
-		
-		double z = 3*(funcA-funcB)/(b-a) + gradA + gradB;
-		double w = Math.sqrt(z*z - gradA*gradB);
-		double min = b -(gradB+w-z)*(b-a)/(gradB-gradA+2*w);
-		return min;
-	}
-	
-	public final static double quadraticInterpolation(double initFValue, 
-			double initGrad, double point,double pointFValue){
-				double min = -1*initGrad*point*point/(2*(pointFValue-initGrad*point-initFValue));
-		return min;
-	}
-	
-	public static void main(String[] args) {
-		
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/util/Logger.java b/gi/posterior-regularisation/prjava/src/optimization/util/Logger.java
deleted file mode 100644
index 5343a39b..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/util/Logger.java
+++ /dev/null
@@ -1,7 +0,0 @@
-package optimization.util;
-
-public class Logger {
-	
-	
-	
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/util/MathUtils.java b/gi/posterior-regularisation/prjava/src/optimization/util/MathUtils.java
deleted file mode 100644
index af66f82c..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/util/MathUtils.java
+++ /dev/null
@@ -1,339 +0,0 @@
-package optimization.util;
-
-import java.util.Arrays;
-
-
-
-public class MathUtils {
-	
-	/**
-	 * 
-	 * @param vector
-	 * @return
-	 */
-	public static double L2Norm(double[] vector){
-		double value = 0;
-		for(int i = 0; i < vector.length; i++){
-			double v = vector[i];
-			value+=v*v;
-		}
-		return Math.sqrt(value);
-	}
-	
-	public static double sum(double[] v){
-		double sum = 0;
-		for (int i = 0; i < v.length; i++) {
-			sum+=v[i];
-		}
-		return sum;
-	}
-	
-	
-	
-	
-	/**
-	 * w = w + v
-	 * @param w
-	 * @param v
-	 */
-	public static void plusEquals(double[] w, double[] v) {
-		for(int i=0; i<w.length;i++){
-			w[i] += w[i] + v[i];
-		}		
-	}
-	
-	/**
-	 * w[i] = w[i] + v
-	 * @param w
-	 * @param v
-	 */
-	public static void plusEquals(double[] w, double v) {
-		for(int i=0; i<w.length;i++){
-			w[i] += w[i] + v;
-		}		
-	}
-	
-	/**
-	 * w[i] = w[i] - v
-	 * @param w
-	 * @param v
-	 */
-	public static void minusEquals(double[] w, double v) {
-		for(int i=0; i<w.length;i++){
-			w[i] -= w[i] + v;
-		}		
-	}
-	
-	/**
-	 * w = w + a*v
-	 * @param w
-	 * @param v
-	 * @param a
-	 */
-	public static void plusEquals(double[] w, double[] v, double a) {
-		for(int i=0; i<w.length;i++){
-			w[i] += a*v[i];
-		}		
-	}
-	
-	/**
-	 * w = w - a*v
-	 * @param w
-	 * @param v
-	 * @param a
-	 */
-	public static void minusEquals(double[] w, double[] v, double a) {
-		for(int i=0; i<w.length;i++){
-			w[i] -= a*v[i];
-		}		
-	}
-	/**
-	 * v = w - a*v
-	 * @param w
-	 * @param v
-	 * @param a
-	 */
-	public static void minusEqualsInverse(double[] w, double[] v, double a) {
-		for(int i=0; i<w.length;i++){
-			v[i] = w[i] - a*v[i];
-		}		
-	}
-	
-	public static double dotProduct(double[] w, double[] v){
-		double accum = 0;
-		for(int i=0; i<w.length;i++){
-			accum += w[i]*v[i];
-		}
-		return accum;
-	}
-	
-	public static double[] arrayMinus(double[]w, double[]v){
-		double result[] = w.clone();
-		for(int i=0; i<w.length;i++){
-			result[i] -= v[i];
-		}
-		return result;
-	}
-	
-	public static double[] arrayMinus(double[] result , double[]w, double[]v){
-		for(int i=0; i<w.length;i++){
-			result[i] = w[i]-v[i];
-		}
-		return result;
-	}
-	
-	public static double[] negation(double[]w){
-		double result[]  = new double[w.length];
-		for(int i=0; i<w.length;i++){
-			result[i] = -w[i];
-		}
-		return result;
-	}
-	
-	public static double square(double value){
-		return value*value;
-	}
-	public static double[][] outerProduct(double[] w, double[] v){
-		double[][] result = new double[w.length][v.length];
-		for(int i = 0; i < w.length; i++){
-			for(int j = 0; j < v.length; j++){
-				result[i][j] = w[i]*v[j];
-			}
-		}
-		return result;
-	}
-	/**
-	 * results = a*W*V
-	 * @param w
-	 * @param v
-	 * @param a
-	 * @return
-	 */
-	public static double[][] weightedouterProduct(double[] w, double[] v, double a){
-		double[][] result = new double[w.length][v.length];
-		for(int i = 0; i < w.length; i++){
-			for(int j = 0; j < v.length; j++){
-				result[i][j] = a*w[i]*v[j];
-			}
-		}
-		return result;
-	}
-	
-	public static double[][] identity(int size){
-		double[][] result = new double[size][size];
-		for(int i = 0; i < size; i++){
-			result[i][i] = 1;
-		}
-		return result;
-	}
-	
-	/**
-	 * v -= w
-	 * @param v
-	 * @param w
-	 */
-	public static void minusEquals(double[][] w, double[][] v){
-		for(int i = 0; i < w.length; i++){
-			for(int j = 0; j < w[0].length; j++){
-				w[i][j] -= v[i][j];
-			}
-		}
-	}
-	
-	/**
-	 * v[i][j] -= a*w[i][j]
-	 * @param v
-	 * @param w
-	 */
-	public static void minusEquals(double[][] w, double[][] v, double a){
-		for(int i = 0; i < w.length; i++){
-			for(int j = 0; j < w[0].length; j++){
-				w[i][j] -= a*v[i][j];
-			}
-		}
-	}
-	
-	/**
-	 * v += w
-	 * @param v
-	 * @param w
-	 */
-	public static void plusEquals(double[][] w, double[][] v){
-		for(int i = 0; i < w.length; i++){
-			for(int j = 0; j < w[0].length; j++){
-				w[i][j] += v[i][j];
-			}
-		}
-	}
-	
-	/**
-	 * v[i][j] += a*w[i][j]
-	 * @param v
-	 * @param w
-	 */
-	public static void plusEquals(double[][] w, double[][] v, double a){
-		for(int i = 0; i < w.length; i++){
-			for(int j = 0; j < w[0].length; j++){
-				w[i][j] += a*v[i][j];
-			}
-		}
-	}
-	
-	
-	/**
-	 * results = w*v
-	 * @param w
-	 * @param v
-	 * @return
-	 */
-	public static  double[][] matrixMultiplication(double[][] w,double[][] v){
-		int w1 = w.length;
-		int w2 = w[0].length;
-		int v1 = v.length;
-		int v2 = v[0].length;
-		
-		if(w2 != v1){
-			System.out.println("Matrix dimensions do not agree...");
-			System.exit(-1);
-		}
-		
-		double[][] result = new double[w1][v2];
-		for(int w_i1 = 0; w_i1 < w1; w_i1++){
-			for(int v_i2 = 0; v_i2 < v2; v_i2++){
-				double sum = 0;
-				for(int w_i2 = 0; w_i2 < w2; w_i2++){
-						sum += w[w_i1 ][w_i2]*v[w_i2][v_i2];	
-				}
-				result[w_i1][v_i2] = sum;
-			}
-		}
-		return result;
-	}
-	
-	/**
-	 * w = w.*v
-	 * @param w
-	 * @param v
-	 */
-	public static  void matrixScalarMultiplication(double[][] w,double v){
-		int w1 = w.length;
-		int w2 = w[0].length;	
-		for(int w_i1 = 0; w_i1 < w1; w_i1++){
-				for(int w_i2 = 0; w_i2 < w2; w_i2++){
-						w[w_i1 ][w_i2] *= v;	
-				}
-		}
-	}
-	
-	public static  void scalarMultiplication(double[] w,double v){
-		int w1 = w.length;
-		for(int w_i1 = 0; w_i1 < w1; w_i1++){
-			w[w_i1 ] *= v;	
-		}
-		
-	}
-	
-	public static  double[] matrixVector(double[][] w,double[] v){
-		int w1 = w.length;
-		int w2 = w[0].length;
-		int v1 = v.length;
-		
-		if(w2 != v1){
-			System.out.println("Matrix dimensions do not agree...");
-			System.exit(-1);
-		}
-		
-		double[] result = new double[w1];
-		for(int w_i1 = 0; w_i1 < w1; w_i1++){
-				double sum = 0;
-				for(int w_i2 = 0; w_i2 < w2; w_i2++){
-						sum += w[w_i1 ][w_i2]*v[w_i2];	
-				}
-				result[w_i1] = sum;
-		}
-		return result;
-	}
-	
-	public static boolean allPositive(double[] array){
-		for (int i = 0; i < array.length; i++) {
-			if(array[i] < 0) return false;
-		}
-		return true;
-	}
-	
-	
-	
-	
-	
-		public static void main(String[] args) {
-			double[][] m1 = new double[2][2];
-			m1[0][0]=2;
-			m1[1][0]=2;
-			m1[0][1]=2;
-			m1[1][1]=2;
-			MatrixOutput.printDoubleArray(m1, "m1");
-			double[][] m2 = new double[2][2];
-			m2[0][0]=3;
-			m2[1][0]=3;
-			m2[0][1]=3;
-			m2[1][1]=3;
-			MatrixOutput.printDoubleArray(m2, "m2");
-			double[][] result = matrixMultiplication(m1, m2);
-			MatrixOutput.printDoubleArray(result, "result");
-			matrixScalarMultiplication(result, 3);
-			MatrixOutput.printDoubleArray(result, "result after multiply by 3");
-		}
-	
-		public static boolean almost(double a, double b, double prec){
-			return Math.abs(a-b)/Math.abs(a+b) <= prec || (almostZero(a) && almostZero(b));
-		}
-
-		public static boolean almost(double a, double b){
-			return Math.abs(a-b)/Math.abs(a+b) <= 1e-10 || (almostZero(a) && almostZero(b));
-		}
-
-		public static boolean almostZero(double a) {
-			return Math.abs(a) <= 1e-30;
-		}
-	
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/util/MatrixOutput.java b/gi/posterior-regularisation/prjava/src/optimization/util/MatrixOutput.java
deleted file mode 100644
index 9fbdf955..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/util/MatrixOutput.java
+++ /dev/null
@@ -1,28 +0,0 @@
-package optimization.util;
-
-
-public class MatrixOutput {
-	public static void printDoubleArray(double[][] array, String arrayName) {
-		int size1 = array.length;
-		int size2 = array[0].length;
-		System.out.println(arrayName);
-		for (int i = 0; i < size1; i++) {
-			for (int j = 0; j < size2; j++) {
-				System.out.print(" " + StaticTools.prettyPrint(array[i][j],
-						"00.00E00", 4) + " ");
-
-			}
-			System.out.println();
-		}
-		System.out.println();
-	}
-	
-	public static void printDoubleArray(double[] array, String arrayName) {
-		System.out.println(arrayName);
-		for (int i = 0; i < array.length; i++) {
-				System.out.print(" " + StaticTools.prettyPrint(array[i],
-						"00.00E00", 4) + " ");
-		}
-		System.out.println();
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/util/StaticTools.java b/gi/posterior-regularisation/prjava/src/optimization/util/StaticTools.java
deleted file mode 100644
index bcabee06..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/util/StaticTools.java
+++ /dev/null
@@ -1,180 +0,0 @@
-package optimization.util;
-
-
-import java.io.File;
-import java.io.PrintStream;
-
-public class StaticTools {
-
-	static java.text.DecimalFormat fmt = new java.text.DecimalFormat();
-
-	public static void createDir(String directory) {
-
-		File dir = new File(directory);
-		if (!dir.isDirectory()) {
-			boolean success = dir.mkdirs();
-			if (!success) {
-				System.out.println("Unable to create directory " + directory);
-				System.exit(0);
-			}
-			System.out.println("Created directory " + directory);
-		} else {
-			System.out.println("Reusing directory " + directory);
-		}
-	}
-
-	/*
-	 * q and p are indexed by source/foreign Sum_S(q) = 1 the same for p KL(q,p) =
-	 * Eq*q/p
-	 */
-	public static double KLDistance(double[][] p, double[][] q, int sourceSize,
-			int foreignSize) {
-		double totalKL = 0;
-		// common.StaticTools.printMatrix(q, sourceSize, foreignSize, "q",
-		// System.out);
-		// common.StaticTools.printMatrix(p, sourceSize, foreignSize, "p",
-		// System.out);
-		for (int i = 0; i < sourceSize; i++) {
-			double kl = 0;
-			for (int j = 0; j < foreignSize; j++) {
-				assert !Double.isNaN(q[i][j]) : "KLDistance q:  prob is NaN";
-				assert !Double.isNaN(p[i][j]) : "KLDistance p:  prob is NaN";
-				if (p[i][j] == 0 || q[i][j] == 0) {
-					continue;
-				} else {
-					kl += q[i][j] * Math.log(q[i][j] / p[i][j]);
-				}
-
-			}
-			totalKL += kl;
-		}
-		assert !Double.isNaN(totalKL) : "KLDistance: prob is NaN";
-		if (totalKL < -1.0E-10) {
-			System.out.println("KL Smaller than zero " + totalKL);
-			System.out.println("Source Size" + sourceSize);
-			System.out.println("Foreign Size" + foreignSize);
-			StaticTools.printMatrix(q, sourceSize, foreignSize, "q",
-					System.out);
-			StaticTools.printMatrix(p, sourceSize, foreignSize, "p",
-					System.out);
-			System.exit(-1);
-		}
-		return totalKL / sourceSize;
-	}
-
-	/*
-	 * indexed the by [fi][si]
-	 */
-	public static double KLDistancePrime(double[][] p, double[][] q,
-			int sourceSize, int foreignSize) {
-		double totalKL = 0;
-		for (int i = 0; i < sourceSize; i++) {
-			double kl = 0;
-			for (int j = 0; j < foreignSize; j++) {
-				assert !Double.isNaN(q[j][i]) : "KLDistance q:  prob is NaN";
-				assert !Double.isNaN(p[j][i]) : "KLDistance p:  prob is NaN";
-				if (p[j][i] == 0 || q[j][i] == 0) {
-					continue;
-				} else {
-					kl += q[j][i] * Math.log(q[j][i] / p[j][i]);
-				}
-
-			}
-			totalKL += kl;
-		}
-		assert !Double.isNaN(totalKL) : "KLDistance: prob is NaN";
-		return totalKL / sourceSize;
-	}
-
-	public static double Entropy(double[][] p, int sourceSize, int foreignSize) {
-		double totalE = 0;
-		for (int i = 0; i < foreignSize; i++) {
-			double e = 0;
-			for (int j = 0; j < sourceSize; j++) {
-				e += p[i][j] * Math.log(p[i][j]);
-			}
-			totalE += e;
-		}
-		return totalE / sourceSize;
-	}
-
-	public static double[][] copyMatrix(double[][] original, int sourceSize,
-			int foreignSize) {
-		double[][] result = new double[sourceSize][foreignSize];
-		for (int i = 0; i < sourceSize; i++) {
-			for (int j = 0; j < foreignSize; j++) {
-				result[i][j] = original[i][j];
-			}
-		}
-		return result;
-	}
-
-	public static void printMatrix(double[][] matrix, int sourceSize,
-			int foreignSize, String info, PrintStream out) {
-
-		java.text.DecimalFormat fmt = new java.text.DecimalFormat();
-		fmt.setMaximumFractionDigits(3);
-		fmt.setMaximumIntegerDigits(3);
-		fmt.setMinimumFractionDigits(3);
-		fmt.setMinimumIntegerDigits(3);
-
-		out.println(info);
-
-		for (int i = 0; i < foreignSize; i++) {
-			for (int j = 0; j < sourceSize; j++) {
-				out.print(prettyPrint(matrix[j][i], ".00E00", 6) + " ");
-			}
-			out.println();
-		}
-		out.println();
-		out.println();
-	}
-
-	public static void printMatrix(int[][] matrix, int sourceSize,
-			int foreignSize, String info, PrintStream out) {
-
-		out.println(info);
-		for (int i = 0; i < foreignSize; i++) {
-			for (int j = 0; j < sourceSize; j++) {
-				out.print(matrix[j][i] + " ");
-			}
-			out.println();
-		}
-		out.println();
-		out.println();
-	}
-
-	public static String formatTime(long duration) {
-		StringBuilder sb = new StringBuilder();
-		double d = duration / 1000;
-		fmt.applyPattern("00");
-		sb.append(fmt.format((int) (d / (60 * 60))) + ":");
-		d -= ((int) d / (60 * 60)) * 60 * 60;
-		sb.append(fmt.format((int) (d / 60)) + ":");
-		d -= ((int) d / 60) * 60;
-		fmt.applyPattern("00.0");
-		sb.append(fmt.format(d));
-		return sb.toString();
-	}
-
-	public static String prettyPrint(double d, String patt, int len) {
-		fmt.applyPattern(patt);
-		String s = fmt.format(d);
-		while (s.length() < len) {
-			s = " " + s;
-		}
-		return s;
-	}
-	
-	
-	public static long getUsedMemory(){
-		System.gc();
-		return (Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory())/ (1024 * 1024);
-	}
-	
-	public final static boolean compareDoubles(double d1, double d2){
-		return Math.abs(d1-d2) <= 1.E-10;
-	}
-	
-	
-}
diff --git a/gi/posterior-regularisation/prjava/src/phrase/Agree.java b/gi/posterior-regularisation/prjava/src/phrase/Agree.java
deleted file mode 100644
index 8f7b499e..00000000
--- a/gi/posterior-regularisation/prjava/src/phrase/Agree.java
+++ /dev/null
@@ -1,204 +0,0 @@
-package phrase;

-

-import gnu.trove.TIntArrayList;

-

-import io.FileUtil;

-

-import java.io.File;

-import java.io.IOException;

-import java.io.PrintStream;

-import java.util.List;

-

-import phrase.Corpus.Edge;

-

-public class Agree {

-	PhraseCluster model1;

-	C2F model2;

-	Corpus c;

-	private int K,n_phrases, n_words, n_contexts, n_positions1,n_positions2;

-	

-	/**@brief sum of loglikelihood of two

-	 * individual models

-	 */

-	public double llh;

-	/**@brief Bhattacharyya distance

-	 * 

-	 */

-	public double bdist; 

-	/**

-	 * 

-	 * @param numCluster

-	 * @param corpus

-	 */

-	public Agree(int numCluster, Corpus corpus){

-		

-		model1=new PhraseCluster(numCluster, corpus);

-		model2=new C2F(numCluster,corpus);

-		c=corpus;

-		n_words=c.getNumWords();

-		n_phrases=c.getNumPhrases();

-		n_contexts=c.getNumContexts();

-		n_positions1=c.getNumContextPositions();

-		n_positions2=2;

-		K=numCluster;

-		

-	}

-	

-	/**@brief test

-	 * 

-	 */

-	public static void main(String args[]){

-		//String in="../pdata/canned.con";

-		String in="../pdata/btec.con";

-		String out="../pdata/posterior.out";

-		int numCluster=25;

-		Corpus corpus = null;

-		File infile = new File(in);

-		try {

-			System.out.println("Reading concordance from " + infile);

-			corpus = Corpus.readFromFile(FileUtil.reader(infile));

-			corpus.printStats(System.out);

-		} catch (IOException e) {

-			System.err.println("Failed to open input file: " + infile);

-			e.printStackTrace();

-			System.exit(1);

-		}

-		

-		Agree agree=new Agree(numCluster, corpus);

-		int iter=20;

-		for(int i=0;i<iter;i++){

-			agree.EM();

-			System.out.println("Iter"+i+", llh: "+agree.llh+

-					", divergence:"+agree.bdist+

-							" sum: "+(agree.llh+agree.bdist));

-		}

-		

-		File outfile = new File (out);

-		try {

-			PrintStream ps = FileUtil.printstream(outfile);

-			agree.displayPosterior(ps);

-		//	ps.println();

-		//	c2f.displayModelParam(ps);

-			ps.close();

-		} catch (IOException e) {

-			System.err.println("Failed to open output file: " + outfile);

-			e.printStackTrace();

-			System.exit(1);

-		}

-		

-	}

-	

-	public double EM(){

-		

-		double [][][]exp_emit1=new double [K][n_positions1][n_words];

-		double [][]exp_pi1=new double[n_phrases][K];

-		

-		double [][][]exp_emit2=new double [K][n_positions2][n_words];

-		double [][]exp_pi2=new double[n_contexts][K];

-		

-		llh=0;

-		bdist=0;

-		//E

-		for(int context=0; context< n_contexts; context++){

-			

-			List<Edge> contexts = c.getEdgesForContext(context);

-

-			for (int ctx=0; ctx<contexts.size(); ctx++){

-				Edge edge = contexts.get(ctx);

-				int phrase=edge.getPhraseId();

-				double p[]=posterior(edge);

-				double z = arr.F.l1norm(p);

-				assert z > 0;

-				bdist += edge.getCount() * Math.log(z);

-				arr.F.l1normalize(p);

-				

-				double count = edge.getCount();

-				//increment expected count

-				TIntArrayList phraseToks = edge.getPhrase();

-				TIntArrayList contextToks = edge.getContext();

-				for(int tag=0;tag<K;tag++){

-

-					for(int position=0;position<n_positions1;position++){

-						exp_emit1[tag][position][contextToks.get(position)]+=p[tag]*count;

-					}

-					

-					exp_emit2[tag][0][phraseToks.get(0)]+=p[tag]*count;

-					exp_emit2[tag][1][phraseToks.get(phraseToks.size()-1)]+=p[tag]*count;

-					

-					exp_pi1[phrase][tag]+=p[tag]*count;

-					exp_pi2[context][tag]+=p[tag]*count;

-				}

-			}

-		}

-		

-		//System.out.println("Log likelihood: "+loglikelihood);

-		

-		//M

-		for(double [][]i:exp_emit1){

-			for(double []j:i){

-				arr.F.l1normalize(j);

-			}

-		}

-		

-		for(double []j:exp_pi1){

-			arr.F.l1normalize(j);

-		}

-		

-		for(double [][]i:exp_emit2){

-			for(double []j:i){

-				arr.F.l1normalize(j);

-			}

-		}

-		

-		for(double []j:exp_pi2){

-			arr.F.l1normalize(j);

-		}

-		

-		model1.emit=exp_emit1;

-		model1.pi=exp_pi1;

-		model2.emit=exp_emit2;

-		model2.pi=exp_pi2;

-		

-		return llh;

-	}

-

-	public double[] posterior(Corpus.Edge edge) 

-	{

-		double[] prob1=model1.posterior(edge);

-		double[] prob2=model2.posterior(edge);

-		

-		llh+=edge.getCount()*Math.log(arr.F.l1norm(prob1));

-		llh+=edge.getCount()*Math.log(arr.F.l1norm(prob2));

-		arr.F.l1normalize(prob1);

-		arr.F.l1normalize(prob2);

-		

-		for(int i=0;i<prob1.length;i++){

-			prob1[i]*=prob2[i];

-			prob1[i]=Math.sqrt(prob1[i]);

-		}

-		

-		return prob1;

-	}

-	

-	public void displayPosterior(PrintStream ps)

-	{	

-		displayPosterior(ps, c.getEdges());

-	}

-	

-	public void displayPosterior(PrintStream ps, List<Edge> test)

-	{	

-		for (Edge edge : test)

-		{

-			double probs[] = posterior(edge);

-			arr.F.l1normalize(probs);

-

-			// emit phrase

-			ps.print(edge.getPhraseString());

-			ps.print("\t");

-			ps.print(edge.getContextString(true));

-			int t=arr.F.argmax(probs);

-			ps.println(" ||| C=" + t);

-		}

-	}

-	

-}

diff --git a/gi/posterior-regularisation/prjava/src/phrase/Agree2Sides.java b/gi/posterior-regularisation/prjava/src/phrase/Agree2Sides.java
deleted file mode 100644
index 031f887f..00000000
--- a/gi/posterior-regularisation/prjava/src/phrase/Agree2Sides.java
+++ /dev/null
@@ -1,197 +0,0 @@
-package phrase;

-

-import gnu.trove.TIntArrayList;

-

-import io.FileUtil;

-

-import java.io.File;

-import java.io.IOException;

-import java.io.PrintStream;

-import java.util.List;

-

-import phrase.Corpus.Edge;

-

-public class Agree2Sides {

-	PhraseCluster model1,model2;

-	Corpus c1,c2;

-	private int K;

-	

-	/**@brief sum of loglikelihood of two

-	 * individual models

-	 */

-	public double llh;

-	/**@brief Bhattacharyya distance

-	 * 

-	 */

-	public double bdist; 

-	/**

-	 * 

-	 * @param numCluster

-	 * @param corpus

-	 */

-	public Agree2Sides(int numCluster, Corpus corpus1 , Corpus corpus2 ){

-		

-		model1=new PhraseCluster(numCluster, corpus1);

-		model2=new PhraseCluster(numCluster,corpus2);

-		c1=corpus1;

-		c2=corpus2;

-		K=numCluster;

-		

-	}

-	

-	/**@brief test

-	 * 

-	 */

-	public static void main(String args[]){

-		//String in="../pdata/canned.con";

-	//	String in="../pdata/btec.con";

-		String in1="../pdata/source.txt";

-		String in2="../pdata/target.txt";

-		String out="../pdata/posterior.out";

-		int numCluster=25;

-		Corpus corpus1 = null,corpus2=null;

-		File infile1 = new File(in1),infile2=new File(in2);

-		try {

-			System.out.println("Reading concordance from " + infile1);

-			corpus1 = Corpus.readFromFile(FileUtil.reader(infile1));

-			System.out.println("Reading concordance from " + infile2);

-			corpus2 = Corpus.readFromFile(FileUtil.reader(infile2));

-			corpus1.printStats(System.out);

-		} catch (IOException e) {

-			System.err.println("Failed to open input file: " + infile1);

-			e.printStackTrace();

-			System.exit(1);

-		}

-		

-		Agree2Sides agree=new Agree2Sides(numCluster, corpus1,corpus2);

-		int iter=20;

-		for(int i=0;i<iter;i++){

-			agree.EM();

-			System.out.println("Iter"+i+", llh: "+agree.llh+

-					", divergence:"+agree.bdist+

-							" sum: "+(agree.llh+agree.bdist));

-		}

-		

-		File outfile = new File (out);

-		try {

-			PrintStream ps = FileUtil.printstream(outfile);

-			agree.displayPosterior(ps);

-		//	ps.println();

-		//	c2f.displayModelParam(ps);

-			ps.close();

-		} catch (IOException e) {

-			System.err.println("Failed to open output file: " + outfile);

-			e.printStackTrace();

-			System.exit(1);

-		}

-		

-	}

-	

-	public double EM(){

-		

-		double [][][]exp_emit1=new double [K][c1.getNumContextPositions()][c1.getNumWords()];

-		double [][]exp_pi1=new double[c1.getNumPhrases()][K];

-		

-		double [][][]exp_emit2=new double [K][c2.getNumContextPositions()][c2.getNumWords()];

-		double [][]exp_pi2=new double[c2.getNumPhrases()][K];

-		

-		llh=0;

-		bdist=0;

-		//E

-		for(int i=0;i<c1.getEdges().size();i++){

-			Edge edge1=c1.getEdges().get(i);

-			Edge edge2=c2.getEdges().get(i);

-			double p[]=posterior(i);

-			double z = arr.F.l1norm(p);

-			assert z > 0;

-			bdist += edge1.getCount() * Math.log(z);

-			arr.F.l1normalize(p);

-			double count = edge1.getCount();

-				//increment expected count

-			TIntArrayList contextToks1 = edge1.getContext();

-			TIntArrayList contextToks2 = edge2.getContext();

-			int phrase1=edge1.getPhraseId();

-			int phrase2=edge2.getPhraseId();

-			for(int tag=0;tag<K;tag++){

-				for(int position=0;position<c1.getNumContextPositions();position++){

-					exp_emit1[tag][position][contextToks1.get(position)]+=p[tag]*count;

-				}

-				for(int position=0;position<c2.getNumContextPositions();position++){

-					exp_emit2[tag][position][contextToks2.get(position)]+=p[tag]*count;

-				}

-				exp_pi1[phrase1][tag]+=p[tag]*count;

-				exp_pi2[phrase2][tag]+=p[tag]*count;

-			}

-		}

-		

-		//System.out.println("Log likelihood: "+loglikelihood);

-		

-		//M

-		for(double [][]i:exp_emit1){

-			for(double []j:i){

-				arr.F.l1normalize(j);

-			}

-		}

-		

-		for(double []j:exp_pi1){

-			arr.F.l1normalize(j);

-		}

-		

-		for(double [][]i:exp_emit2){

-			for(double []j:i){

-				arr.F.l1normalize(j);

-			}

-		}

-		

-		for(double []j:exp_pi2){

-			arr.F.l1normalize(j);

-		}

-		

-		model1.emit=exp_emit1;

-		model1.pi=exp_pi1;

-		model2.emit=exp_emit2;

-		model2.pi=exp_pi2;

-		

-		return llh;

-	}

-

-	public double[] posterior(int edgeIdx) 

-	{

-		return posterior(c1.getEdges().get(edgeIdx), c2.getEdges().get(edgeIdx));

-	}

-	

-	public double[] posterior(Edge e1, Edge e2) 

-	{

-		double[] prob1=model1.posterior(e1);

-		double[] prob2=model2.posterior(e2);

-		

-		llh+=e1.getCount()*Math.log(arr.F.l1norm(prob1));

-		llh+=e2.getCount()*Math.log(arr.F.l1norm(prob2));

-		arr.F.l1normalize(prob1);

-		arr.F.l1normalize(prob2);

-		

-		for(int i=0;i<prob1.length;i++){

-			prob1[i]*=prob2[i];

-			prob1[i]=Math.sqrt(prob1[i]);

-		}

-		

-		return prob1;

-	}

-	

-	public void displayPosterior(PrintStream ps)

-	{	

-		for (int i=0;i<c1.getEdges().size();i++)

-		{

-			Edge edge=c1.getEdges().get(i);

-			double probs[] = posterior(i);

-			arr.F.l1normalize(probs);

-

-			// emit phrase

-			ps.print(edge.getPhraseString());

-			ps.print("\t");

-			ps.print(edge.getContextString(true));

-			int t=arr.F.argmax(probs);

-			ps.println(" ||| C=" + t);

-		}

-	}

-}

diff --git a/gi/posterior-regularisation/prjava/src/phrase/C2F.java b/gi/posterior-regularisation/prjava/src/phrase/C2F.java
deleted file mode 100644
index e8783950..00000000
--- a/gi/posterior-regularisation/prjava/src/phrase/C2F.java
+++ /dev/null
@@ -1,216 +0,0 @@
-package phrase;

-

-import gnu.trove.TIntArrayList;

-

-import io.FileUtil;

-

-import java.io.File;

-import java.io.IOException;

-import java.io.PrintStream;

-import java.util.Arrays;

-import java.util.List;

-

-import phrase.Corpus.Edge;

-

-/**

- * @brief context generates phrase

- * @author desaic

- *

- */

-public class C2F {

-	public int K;

-	private int n_words, n_contexts, n_positions;

-	public Corpus c;

-	

-	/**@brief

-	 *  emit[tag][position][word] = p(word | tag, position in phrase)

-	 */

-	public double emit[][][];

-	/**@brief

-	 *  pi[context][tag] = p(tag | context)

-	 */

-	public double pi[][];

-	

-	public C2F(int numCluster, Corpus corpus){

-		K=numCluster;

-		c=corpus;

-		n_words=c.getNumWords();

-		n_contexts=c.getNumContexts();

-		

-		//number of words in a phrase to be considered

-		//currently the first and last word in source and target

-		//if the phrase has length 1 in either dimension then

-		//we use the same word for two positions

-		n_positions=c.phraseEdges(c.getEdges().get(0).getPhrase()).size();

-		

-		emit=new double [K][n_positions][n_words];

-		pi=new double[n_contexts][K];

-		

-		for(double [][]i:emit){

-			for(double []j:i){

-				arr.F.randomise(j);

-			}

-		}

-		

-		for(double []j:pi){

-			arr.F.randomise(j);

-		}

-	}

-	

-	/**@brief test

-	 * 

-	 */

-	public static void main(String args[]){

-		String in="../pdata/canned.con";

-		String out="../pdata/posterior.out";

-		int numCluster=25;

-		Corpus corpus = null;

-		File infile = new File(in);

-		try {

-			System.out.println("Reading concordance from " + infile);

-			corpus = Corpus.readFromFile(FileUtil.reader(infile));

-			corpus.printStats(System.out);

-		} catch (IOException e) {

-			System.err.println("Failed to open input file: " + infile);

-			e.printStackTrace();

-			System.exit(1);

-		}

-		

-		C2F c2f=new C2F(numCluster,corpus);

-		int iter=20;

-		double llh=0;

-		for(int i=0;i<iter;i++){

-			llh=c2f.EM();

-			System.out.println("Iter"+i+", llh: "+llh);

-		}

-		

-		File outfile = new File (out);

-		try {

-			PrintStream ps = FileUtil.printstream(outfile);

-			c2f.displayPosterior(ps);

-		//	ps.println();

-		//	c2f.displayModelParam(ps);

-			ps.close();

-		} catch (IOException e) {

-			System.err.println("Failed to open output file: " + outfile);

-			e.printStackTrace();

-			System.exit(1);

-		}

-		

-	}

-	

-	public double EM(){

-		double [][][]exp_emit=new double [K][n_positions][n_words];

-		double [][]exp_pi=new double[n_contexts][K];

-		

-		double loglikelihood=0;

-		

-		//E

-		for(int context=0; context< n_contexts; context++){

-			

-			List<Edge> contexts = c.getEdgesForContext(context);

-

-			for (int ctx=0; ctx<contexts.size(); ctx++){

-				Edge edge = contexts.get(ctx);

-				double p[]=posterior(edge);

-				double z = arr.F.l1norm(p);

-				assert z > 0;

-				loglikelihood += edge.getCount() * Math.log(z);

-				arr.F.l1normalize(p);

-				

-				double count = edge.getCount();

-				//increment expected count

-				TIntArrayList phrase= edge.getPhrase();

-				for(int tag=0;tag<K;tag++){

-

-					exp_emit[tag][0][phrase.get(0)]+=p[tag]*count;

-					exp_emit[tag][1][phrase.get(phrase.size()-1)]+=p[tag]*count;

-					

-					exp_pi[context][tag]+=p[tag]*count;

-				}

-			}

-		}

-		

-		//System.out.println("Log likelihood: "+loglikelihood);

-		

-		//M

-		for(double [][]i:exp_emit){

-			for(double []j:i){

-				arr.F.l1normalize(j);

-			}

-		}

-		

-		emit=exp_emit;

-		

-		for(double []j:exp_pi){

-			arr.F.l1normalize(j);

-		}

-		

-		pi=exp_pi;

-		

-		return loglikelihood;

-	}

-

-	public double[] posterior(Corpus.Edge edge) 

-	{

-		double[] prob=Arrays.copyOf(pi[edge.getContextId()], K);

-		

-		TIntArrayList phrase = edge.getPhrase();

-		TIntArrayList offsets = c.phraseEdges(phrase);

-		for(int tag=0;tag<K;tag++)

-		{

-			for (int i=0; i < offsets.size(); ++i)

-				prob[tag]*=emit[tag][i][phrase.get(offsets.get(i))];

-		}

-			

-		return prob;

-	}

-

-	public void displayPosterior(PrintStream ps)

-	{	

-		for (Edge edge : c.getEdges())

-		{

-			double probs[] = posterior(edge);

-			arr.F.l1normalize(probs);

-

-			// emit phrase

-			ps.print(edge.getPhraseString());

-			ps.print("\t");

-			ps.print(edge.getContextString(true));

-			int t=arr.F.argmax(probs);

-			ps.println(" ||| C=" + t);

-		}

-	}

-	

-	public void displayModelParam(PrintStream ps)

-	{

-		final double EPS = 1e-6;

-		

-		ps.println("P(tag|context)");

-		for (int i = 0; i < n_contexts; ++i)

-		{

-			ps.print(c.getContext(i));

-			for(int j=0;j<pi[i].length;j++){

-				if (pi[i][j] > EPS)

-					ps.print("\t" + j + ": " + pi[i][j]);

-			}

-			ps.println();

-		}

-		

-		ps.println("P(word|tag,position)");

-		for (int i = 0; i < K; ++i)

-		{

-			for(int position=0;position<n_positions;position++){

-				ps.println("tag " + i + " position " + position);

-				for(int word=0;word<emit[i][position].length;word++){

-					if (emit[i][position][word] > EPS)

-						ps.print(c.getWord(word)+"="+emit[i][position][word]+"\t");

-				}

-				ps.println();

-			}

-			ps.println();

-		}

-		

-	}

-	

-}

diff --git a/gi/posterior-regularisation/prjava/src/phrase/Corpus.java b/gi/posterior-regularisation/prjava/src/phrase/Corpus.java
deleted file mode 100644
index 4b1939cd..00000000
--- a/gi/posterior-regularisation/prjava/src/phrase/Corpus.java
+++ /dev/null
@@ -1,288 +0,0 @@
-package phrase;
-
-import gnu.trove.TIntArrayList;
-
-import java.io.*;
-import java.util.*;
-import java.util.regex.Pattern;
-
-
-public class Corpus
-{
-	private Lexicon<String> wordLexicon = new Lexicon<String>();
-	private Lexicon<TIntArrayList> phraseLexicon = new Lexicon<TIntArrayList>();
-	private Lexicon<TIntArrayList> contextLexicon = new Lexicon<TIntArrayList>();
-	private List<Edge> edges = new ArrayList<Edge>();
-	private List<List<Edge>> phraseToContext = new ArrayList<List<Edge>>();
-	private List<List<Edge>> contextToPhrase = new ArrayList<List<Edge>>();
-	public int splitSentinel;
-	public int phraseSentinel;
-	public int rareSentinel;
-
-	public Corpus()
-	{
-		splitSentinel = wordLexicon.insert("<SPLIT>");
-		phraseSentinel = wordLexicon.insert("<PHRASE>");		
-		rareSentinel = wordLexicon.insert("<RARE>");
-	}
-	
-	public class Edge
-	{
-		
-		Edge(int phraseId, int contextId, double count,int tag)
-		{
-			this.phraseId = phraseId;
-			this.contextId = contextId;
-			this.count = count;
-			fixTag=tag;
-		}
-		
-		Edge(int phraseId, int contextId, double count)
-		{
-			this.phraseId = phraseId;
-			this.contextId = contextId;
-			this.count = count;
-			fixTag=-1;
-		}
-		public int getTag(){
-			return fixTag;
-		}
-		
-		public int getPhraseId()
-		{
-			return phraseId;
-		}
-		public TIntArrayList getPhrase()
-		{
-			return Corpus.this.getPhrase(phraseId);
-		}
-		public String getPhraseString()
-		{
-			return Corpus.this.getPhraseString(phraseId);
-		}		
-		public int getContextId()
-		{
-			return contextId;
-		}
-		public TIntArrayList getContext()
-		{
-			return Corpus.this.getContext(contextId);
-		}
-		public String getContextString(boolean insertPhraseSentinel)
-		{
-			return Corpus.this.getContextString(contextId, insertPhraseSentinel);
-		}
-		public double getCount()
-		{
-			return count;
-		}
-		public boolean equals(Object other)
-		{
-			if (other instanceof Edge) 
-			{
-				Edge oe = (Edge) other;
-				return oe.phraseId == phraseId && oe.contextId == contextId; 
-			}
-			else return false;
-		}
-		public int hashCode()
-		{   // this is how boost's hash_combine does it
-			int seed = phraseId;
-			seed ^= contextId + 0x9e3779b9 + (seed << 6) + (seed >> 2);
-			return seed;
-		}
-		public String toString()
-		{
-			return getPhraseString() + "\t" + getContextString(true);
-		}
-		
-		private int phraseId;
-		private int contextId;
-		private double count;
-		private int fixTag;
-	}
-
-	List<Edge> getEdges()
-	{
-		return edges;
-	}
-	
-	int getNumEdges()
-	{
-		return edges.size();
-	}
-
-	int getNumPhrases()
-	{
-		return phraseLexicon.size();
-	}
-	
-	int getNumContextPositions()
-	{
-		return contextLexicon.lookup(0).size();
-	}
-	
-	List<Edge> getEdgesForPhrase(int phraseId)
-	{
-		return phraseToContext.get(phraseId);
-	}
-	
-	int getNumContexts()
-	{
-		return contextLexicon.size();
-	}
-	
-	List<Edge> getEdgesForContext(int contextId)
-	{
-		return contextToPhrase.get(contextId);
-	}
-	
-	int getNumWords()
-	{
-		return wordLexicon.size();
-	}
-	
-	String getWord(int wordId)
-	{
-		return wordLexicon.lookup(wordId);
-	}
-	
-	public TIntArrayList getPhrase(int phraseId)
-	{
-		return phraseLexicon.lookup(phraseId);
-	}
-	
-	public String getPhraseString(int phraseId)
-	{
-		StringBuffer b = new StringBuffer();
-		for (int tid: getPhrase(phraseId).toNativeArray())
-		{
-			if (b.length() > 0)
-				b.append(" ");
-			b.append(wordLexicon.lookup(tid));
-		}
-		return b.toString();
-	}		
-	
-	public TIntArrayList getContext(int contextId)
-	{
-		return contextLexicon.lookup(contextId);
-	}
-	
-	public String getContextString(int contextId, boolean insertPhraseSentinel)
-	{
-		StringBuffer b = new StringBuffer();
-		TIntArrayList c = getContext(contextId);
-		for (int i = 0; i < c.size(); ++i)
-		{
-			if (i > 0) b.append(" ");
-			//if (i == c.size() / 2) b.append("<PHRASE> ");
-			b.append(wordLexicon.lookup(c.get(i)));
-		}
-		return b.toString();
-	}
-	
-	public boolean isSentinel(int wordId)
-	{
-		return wordId == splitSentinel || wordId == phraseSentinel;
-	}
-	
-	List<Edge> readEdges(Reader in) throws IOException
-	{	
-		// read in line-by-line
-		BufferedReader bin = new BufferedReader(in);
-		String line;
-		Pattern separator = Pattern.compile(" \\|\\|\\| ");
-		
-		List<Edge> edges = new ArrayList<Edge>();
-		while ((line = bin.readLine()) != null)
-		{
-			// split into phrase and contexts
-			StringTokenizer st = new StringTokenizer(line, "\t");
-			assert (st.hasMoreTokens());
-			String phraseToks = st.nextToken();
-			assert (st.hasMoreTokens());
-			String rest = st.nextToken();
-			assert (!st.hasMoreTokens());
-
-			// process phrase	
-			st = new StringTokenizer(phraseToks, " ");
-			TIntArrayList ptoks = new TIntArrayList();
-			while (st.hasMoreTokens())
-				ptoks.add(wordLexicon.insert(st.nextToken()));
-			int phraseId = phraseLexicon.insert(ptoks);
-			
-			// process contexts
-			String[] parts = separator.split(rest);
-			assert (parts.length % 2 == 0);
-			for (int i = 0; i < parts.length; i += 2)
-			{
-				// process pairs of strings - context and count
-				String ctxString = parts[i];
-				String countString = parts[i + 1];
-
-				assert (countString.startsWith("C="));
-
-				String []countToks=countString.split(" ");
-				
-				double count = Double.parseDouble(countToks[0].substring(2).trim());
-				
-				TIntArrayList ctx = new TIntArrayList();
-				StringTokenizer ctxStrtok = new StringTokenizer(ctxString, " ");
-				while (ctxStrtok.hasMoreTokens())
-				{
-					String token = ctxStrtok.nextToken();
-					ctx.add(wordLexicon.insert(token));
-				}
-				int contextId = contextLexicon.insert(ctx);
-
-
-				if(countToks.length<2){
-					edges.add(new Edge(phraseId, contextId, count));
-				}
-				else{
-					int tag=Integer.parseInt(countToks[1].substring(2));
-					edges.add(new Edge(phraseId, contextId, count,tag));
-				}
-			}
-		}
-		return edges;
-	}
-	
-	static Corpus readFromFile(Reader in) throws IOException
-	{	
-		Corpus c = new Corpus();
-		c.edges = c.readEdges(in);
-		for (Edge edge: c.edges)
-		{
-			while (edge.getPhraseId() >= c.phraseToContext.size())
-				c.phraseToContext.add(new ArrayList<Edge>());
-			while (edge.getContextId() >= c.contextToPhrase.size())
-				c.contextToPhrase.add(new ArrayList<Edge>());
-			
-			// index the edge for fast phrase, context lookup
-			c.phraseToContext.get(edge.getPhraseId()).add(edge);
-			c.contextToPhrase.get(edge.getContextId()).add(edge);
-		}
-		return c;
-	}
-		
-	TIntArrayList phraseEdges(TIntArrayList phrase)
-	{
-		TIntArrayList r = new TIntArrayList(4);
-		for (int p = 0; p < phrase.size(); ++p)
-		{
-			if (p == 0 || phrase.get(p-1) == splitSentinel) 				
-				r.add(p);
-			if (p == phrase.size() - 1 || phrase.get(p+1) == splitSentinel) 
-				r.add(p);
-		}
-		return r;
-	}
-
-	public void printStats(PrintStream out) 
-	{
-		out.println("Corpus has " + edges.size() + " edges " + phraseLexicon.size() + " phrases " 
-				+ contextLexicon.size() + " contexts and " + wordLexicon.size() + " word types");
-	}
-}
\ No newline at end of file
diff --git a/gi/posterior-regularisation/prjava/src/phrase/Lexicon.java b/gi/posterior-regularisation/prjava/src/phrase/Lexicon.java
deleted file mode 100644
index a386e4a3..00000000
--- a/gi/posterior-regularisation/prjava/src/phrase/Lexicon.java
+++ /dev/null
@@ -1,34 +0,0 @@
-package phrase;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-public class Lexicon<T>
-{
-	public int insert(T word)
-	{
-		Integer i = wordToIndex.get(word);
-		if (i == null)
-		{
-			i = indexToWord.size();
-			wordToIndex.put(word, i);
-			indexToWord.add(word);
-		}
-		return i;
-	}
-
-	public T lookup(int index)
-	{
-		return indexToWord.get(index);
-	}
-
-	public int size()
-	{
-		return indexToWord.size();
-	}
-
-	private Map<T, Integer> wordToIndex = new HashMap<T, Integer>();
-	private List<T> indexToWord = new ArrayList<T>();
-}
\ No newline at end of file
diff --git a/gi/posterior-regularisation/prjava/src/phrase/PhraseCluster.java b/gi/posterior-regularisation/prjava/src/phrase/PhraseCluster.java
deleted file mode 100644
index c032bb2b..00000000
--- a/gi/posterior-regularisation/prjava/src/phrase/PhraseCluster.java
+++ /dev/null
@@ -1,540 +0,0 @@
-package phrase;

-

-import gnu.trove.TIntArrayList;

-import org.apache.commons.math.special.Gamma;

-

-import java.io.BufferedReader;

-import java.io.IOException;

-import java.io.PrintStream;

-import java.util.ArrayList;

-import java.util.Arrays;

-import java.util.List;

-import java.util.concurrent.Callable;

-import java.util.concurrent.ExecutionException;

-import java.util.concurrent.ExecutorService;

-import java.util.concurrent.Executors;

-import java.util.concurrent.Future;

-import java.util.concurrent.LinkedBlockingQueue;

-import java.util.concurrent.atomic.AtomicInteger;

-import java.util.concurrent.atomic.AtomicLong;

-import java.util.regex.Pattern;

-

-import phrase.Corpus.Edge;

-

-

-public class PhraseCluster {

-	

-	public int K;

-	private int n_phrases, n_words, n_contexts, n_positions;

-	public Corpus c;

-	public ExecutorService pool; 

-

-	double[] lambdaPTCT;

-	double[][] lambdaPT;

-	boolean cacheLambda = true;

-

-	// emit[tag][position][word] = p(word | tag, position in context)

-	double emit[][][];

-	// pi[phrase][tag] = p(tag | phrase)

-	double pi[][];

-	

-	public PhraseCluster(int numCluster, Corpus corpus)

-	{

-		K=numCluster;

-		c=corpus;

-		n_words=c.getNumWords();

-		n_phrases=c.getNumPhrases();

-		n_contexts=c.getNumContexts();

-		n_positions=c.getNumContextPositions();

-

-		emit=new double [K][n_positions][n_words];

-		pi=new double[n_phrases][K];

-		

-		for(double [][]i:emit)

-			for(double []j:i)

-				arr.F.randomise(j, true);

-

-		for(double []j:pi)

-			arr.F.randomise(j, true);

-	}

-	

-	void useThreadPool(ExecutorService pool)

-	{

-		this.pool = pool;

-	}

-

-	public double EM(int phraseSizeLimit)

-	{

-		double [][][]exp_emit=new double [K][n_positions][n_words];

-		double []exp_pi=new double[K];

-		

-		for(double [][]i:exp_emit)

-			for(double []j:i)

-				Arrays.fill(j, 1e-10);

-		

-		double loglikelihood=0;

-		

-		//E

-		for(int phrase=0; phrase < n_phrases; phrase++)

-		{

-			if (phraseSizeLimit >= 1 && c.getPhrase(phrase).size() > phraseSizeLimit)

-				continue;

-

-			Arrays.fill(exp_pi, 1e-10);

-			

-			List<Edge> contexts = c.getEdgesForPhrase(phrase);

-

-			for (int ctx=0; ctx<contexts.size(); ctx++)

-			{

-				Edge edge = contexts.get(ctx);

-				

-				double p[]=posterior(edge);

-				double z = arr.F.l1norm(p);

-				assert z > 0;

-				loglikelihood += edge.getCount() * Math.log(z);

-				arr.F.l1normalize(p);

-				

-				double count = edge.getCount();

-				//increment expected count

-				TIntArrayList context = edge.getContext();

-				for(int tag=0;tag<K;tag++)

-				{

-					for(int pos=0;pos<n_positions;pos++){

-						exp_emit[tag][pos][context.get(pos)]+=p[tag]*count;

-					}

-					exp_pi[tag]+=p[tag]*count;

-				}

-			}

-			arr.F.l1normalize(exp_pi);

-			System.arraycopy(exp_pi, 0, pi[phrase], 0, K);

-		}

-

-		//M

-		for(double [][]i:exp_emit)

-			for(double []j:i)

-				arr.F.l1normalize(j);

-			

-		emit=exp_emit;

-

-		return loglikelihood;

-	}

-	

-	public double PREM(double scalePT, double scaleCT, int phraseSizeLimit)

-	{

-		if (scaleCT == 0)

-		{

-			if (pool != null)

-				return PREM_phrase_constraints_parallel(scalePT, phraseSizeLimit);

-			else

-				return PREM_phrase_constraints(scalePT, phraseSizeLimit);

-		}

-		else // FIXME: ignores phraseSizeLimit

-			return this.PREM_phrase_context_constraints(scalePT, scaleCT);

-	}

-

-	

-	public double PREM_phrase_constraints(double scalePT, int phraseSizeLimit)

-	{

-		double [][][]exp_emit=new double[K][n_positions][n_words];

-		double []exp_pi=new double[K];

-		

-		for(double [][]i:exp_emit)

-			for(double []j:i)

-				Arrays.fill(j, 1e-10);

-		

-		if (lambdaPT == null && cacheLambda)

-			lambdaPT = new double[n_phrases][];

-		

-		double loglikelihood=0, kl=0, l1lmax=0, primal=0;

-		int failures=0, iterations=0;

-		long start = System.currentTimeMillis();

-		//E

-		for(int phrase=0; phrase<n_phrases; phrase++)

-		{

-			if (phraseSizeLimit >= 1 && c.getPhrase(phrase).size() > phraseSizeLimit)

-			{

-				//System.arraycopy(pi[phrase], 0, exp_pi[phrase], 0, K);

-				continue;

-			}

-			

-			Arrays.fill(exp_pi, 1e-10);

-			

-			// FIXME: add rare edge check to phrase objective & posterior processing

-			PhraseObjective po = new PhraseObjective(this, phrase, scalePT, (cacheLambda) ? lambdaPT[phrase] : null);

-			boolean ok = po.optimizeWithProjectedGradientDescent();

-			if (!ok) ++failures;

-			if (cacheLambda) lambdaPT[phrase] = po.getParameters();

-			iterations += po.getNumberUpdateCalls();

-			double [][] q=po.posterior();

-			loglikelihood += po.loglikelihood();

-			kl += po.KL_divergence();

-			l1lmax += po.l1lmax();

-			primal += po.primal(scalePT);

-			List<Edge> edges = c.getEdgesForPhrase(phrase);

-

-			for(int edge=0;edge<q.length;edge++){

-				Edge e = edges.get(edge);

-				TIntArrayList context = e.getContext();

-				double contextCnt = e.getCount();

-				//increment expected count

-				for(int tag=0;tag<K;tag++){

-					for(int pos=0;pos<n_positions;pos++){

-						exp_emit[tag][pos][context.get(pos)]+=q[edge][tag]*contextCnt;

-					}

-					

-					exp_pi[tag]+=q[edge][tag]*contextCnt;

-					

-				}

-			}

-			arr.F.l1normalize(exp_pi);

-			System.arraycopy(exp_pi, 0, pi[phrase], 0, K);

-		}

-		

-		long end = System.currentTimeMillis();

-		if (failures > 0)

-			System.out.println("WARNING: failed to converge in " + failures + "/" + n_phrases + " cases");

-		System.out.println("\tmean iters:     " + iterations/(double)n_phrases + " elapsed time " + (end - start) / 1000.0);

-		System.out.println("\tllh:            " + loglikelihood);

-		System.out.println("\tKL:             " + kl);

-		System.out.println("\tphrase l1lmax:  " + l1lmax);

-		

-		//M

-		for(double [][]i:exp_emit)

-			for(double []j:i)

-				arr.F.l1normalize(j);

-		emit=exp_emit;

-		

-		return primal;

-	}

-

-	public double PREM_phrase_constraints_parallel(final double scalePT, int phraseSizeLimit)

-	{

-		assert(pool != null);

-		

-		final LinkedBlockingQueue<PhraseObjective> expectations 

-			= new LinkedBlockingQueue<PhraseObjective>();

-		

-		double [][][]exp_emit=new double [K][n_positions][n_words];

-		double [][]exp_pi=new double[n_phrases][K];

-		

-		for(double [][]i:exp_emit)

-			for(double []j:i)

-				Arrays.fill(j, 1e-10);

-		for(double []j:exp_pi)

-			Arrays.fill(j, 1e-10);

-		

-		double loglikelihood=0, kl=0, l1lmax=0, primal=0;

-		final AtomicInteger failures = new AtomicInteger(0);

-		final AtomicLong elapsed = new AtomicLong(0l);

-		int iterations=0;

-		long start = System.currentTimeMillis();

-		List<Future<PhraseObjective>> results = new ArrayList<Future<PhraseObjective>>();

-		

-		if (lambdaPT == null && cacheLambda)

-			lambdaPT = new double[n_phrases][];

-

-		//E

-		for(int phrase=0;phrase<n_phrases;phrase++) {

-			if (phraseSizeLimit >= 1 && c.getPhrase(phrase).size() > phraseSizeLimit) {

-				System.arraycopy(pi[phrase], 0, exp_pi[phrase], 0, K);

-				continue;

-			}

-

-			final int p=phrase;

-			results.add(pool.submit(new Callable<PhraseObjective>() {

-				public PhraseObjective call() {

-					//System.out.println("" + Thread.currentThread().getId() + " optimising lambda for " + p);

-					long start = System.currentTimeMillis();

-					PhraseObjective po = new PhraseObjective(PhraseCluster.this, p, scalePT, (cacheLambda) ? lambdaPT[p] : null);

-					boolean ok = po.optimizeWithProjectedGradientDescent();

-					if (!ok) failures.incrementAndGet();

-					long end = System.currentTimeMillis();

-					elapsed.addAndGet(end - start);

-					//System.out.println("" + Thread.currentThread().getId() + " done optimising lambda for " + p);

-					return po;

-				}

-			}));

-		}

-		

-		// aggregate the expectations as they become available

-		for (Future<PhraseObjective> fpo : results)

-		{

-			try {

-				//System.out.println("" + Thread.currentThread().getId() + " reading queue #" + count);

-

-				// wait (blocking) until something is ready

-				PhraseObjective po = fpo.get();

-				// process

-				int phrase = po.phrase;

-				if (cacheLambda) lambdaPT[phrase] = po.getParameters();

-				//System.out.println("" + Thread.currentThread().getId() + " taken phrase " + phrase);

-				double [][] q=po.posterior();

-				loglikelihood += po.loglikelihood();

-				kl += po.KL_divergence();

-				l1lmax += po.l1lmax();

-				primal += po.primal(scalePT);

-				iterations += po.getNumberUpdateCalls();

-

-				List<Edge> edges = c.getEdgesForPhrase(phrase);

-				for(int edge=0;edge<q.length;edge++){

-					Edge e = edges.get(edge);

-					TIntArrayList context = e.getContext();

-					double contextCnt = e.getCount();

-					//increment expected count

-					for(int tag=0;tag<K;tag++){

-						for(int pos=0;pos<n_positions;pos++){

-							exp_emit[tag][pos][context.get(pos)]+=q[edge][tag]*contextCnt;

-						}

-						exp_pi[phrase][tag]+=q[edge][tag]*contextCnt;

-					}

-				}

-			} catch (InterruptedException e) {

-				System.err.println("M-step thread interrupted. Probably fatal!");

-				throw new RuntimeException(e);

-			} catch (ExecutionException e) {

-				System.err.println("M-step thread execution died. Probably fatal!");

-				throw new RuntimeException(e);

-			}

-		}

-		

-		long end = System.currentTimeMillis();

-		

-		if (failures.get() > 0)

-			System.out.println("WARNING: failed to converge in " + failures.get() + "/" + n_phrases + " cases");

-		System.out.println("\tmean iters:     " + iterations/(double)n_phrases + " walltime " + (end-start)/1000.0 + " threads " + elapsed.get() / 1000.0);

-		System.out.println("\tllh:            " + loglikelihood);

-		System.out.println("\tKL:             " + kl);

-		System.out.println("\tphrase l1lmax:  " + l1lmax);

-		

-		//M

-		for(double [][]i:exp_emit)

-			for(double []j:i)

-				arr.F.l1normalize(j);

-		emit=exp_emit;

-		

-		for(double []j:exp_pi)

-			arr.F.l1normalize(j);

-		pi=exp_pi;

-		

-		return primal;

-	}

-	

-	public double PREM_phrase_context_constraints(double scalePT, double scaleCT)

-	{	

-		double[][][] exp_emit = new double [K][n_positions][n_words];

-		double[][] exp_pi = new double[n_phrases][K];

-

-		//E step

-		PhraseContextObjective pco = new PhraseContextObjective(this, lambdaPTCT, pool, scalePT, scaleCT);

-		boolean ok = pco.optimizeWithProjectedGradientDescent();

-		if (cacheLambda) lambdaPTCT = pco.getParameters();

-

-		//now extract expectations

-		List<Corpus.Edge> edges = c.getEdges();

-		for(int e = 0; e < edges.size(); ++e)

-		{

-			double [] q = pco.posterior(e);

-			Corpus.Edge edge = edges.get(e);

-

-			TIntArrayList context = edge.getContext();

-			double contextCnt = edge.getCount();

-			//increment expected count

-			for(int tag=0;tag<K;tag++)

-			{

-				for(int pos=0;pos<n_positions;pos++)

-					exp_emit[tag][pos][context.get(pos)]+=q[tag]*contextCnt;

-				exp_pi[edge.getPhraseId()][tag]+=q[tag]*contextCnt;

-			}

-		}

-		

-		System.out.println("\tllh:            " + pco.loglikelihood());

-		System.out.println("\tKL:             " + pco.KL_divergence());

-		System.out.println("\tphrase l1lmax:  " + pco.phrase_l1lmax());

-		System.out.println("\tcontext l1lmax: " + pco.context_l1lmax());

-		

-		//M step

-		for(double [][]i:exp_emit)

-			for(double []j:i)

-				arr.F.l1normalize(j);

-		emit=exp_emit;

-		

-		for(double []j:exp_pi)

-			arr.F.l1normalize(j);

-		pi=exp_pi;

-		

-		return pco.primal();

-	}	

-		

-	/**

-	 * @param phrase index of phrase

-	 * @param ctx array of context

-	 * @return unnormalized posterior

-	 */

-	public double[] posterior(Corpus.Edge edge) 

-	{

-		double[] prob;

-		

-		if(edge.getTag()>=0){

-			prob=new double[K];

-			prob[edge.getTag()]=1;

-			return prob;

-		}

-		

-		if (edge.getPhraseId() < n_phrases)

-			prob = Arrays.copyOf(pi[edge.getPhraseId()], K);

-		else

-		{

-			prob = new double[K];

-			Arrays.fill(prob, 1.0);

-		}

-		

-		TIntArrayList ctx = edge.getContext();

-		for(int tag=0;tag<K;tag++)

-		{

-			for(int c=0;c<n_positions;c++)

-			{

-				int word = ctx.get(c);

-				if (!this.c.isSentinel(word) && word < n_words)

-					prob[tag]*=emit[tag][c][word];

-			}

-		}

-		

-		return prob;

-	}

-	

-	public void displayPosterior(PrintStream ps, List<Edge> testing)

-	{	

-		for (Edge edge : testing)

-		{

-			double probs[] = posterior(edge);

-			arr.F.l1normalize(probs);

-

-			// emit phrase

-			ps.print(edge.getPhraseString());

-			ps.print("\t");

-			ps.print(edge.getContextString(true));

-			int t=arr.F.argmax(probs);

-			ps.println(" ||| C=" + t + " T=" + edge.getCount() + " P=" + probs[t]);

-			//ps.println("# probs " + Arrays.toString(probs));

-		}

-	}

-	

-	public void displayModelParam(PrintStream ps)

-	{

-		final double EPS = 1e-6;

-		ps.println("phrases " + n_phrases + " tags " + K + " positions " + n_positions);

-		

-		for (int i = 0; i < n_phrases; ++i)

-			for(int j=0;j<pi[i].length;j++)

-				if (pi[i][j] > EPS)

-					ps.println(i + " " + j + " " + pi[i][j]);

-

-		ps.println();

-		for (int i = 0; i < K; ++i)

-		{

-			for(int position=0;position<n_positions;position++)

-			{

-				for(int word=0;word<emit[i][position].length;word++)

-				{

-					if (emit[i][position][word] > EPS)

-						ps.println(i + " " + position + " " + word + " " + emit[i][position][word]);

-				}

-			}

-		}

-	}

-	

-	double phrase_l1lmax()

-	{

-		double sum=0;

-		for(int phrase=0; phrase<n_phrases; phrase++)

-		{

-			double [] maxes = new double[K];

-			for (Edge edge : c.getEdgesForPhrase(phrase))

-			{

-				double p[] = posterior(edge);

-				arr.F.l1normalize(p);

-				for(int tag=0;tag<K;tag++)

-					maxes[tag] = Math.max(maxes[tag], p[tag]);

-			}

-			for(int tag=0;tag<K;tag++)

-				sum += maxes[tag];

-		}

-		return sum;

-	}

-

-	double context_l1lmax()

-	{

-		double sum=0;

-		for(int context=0; context<n_contexts; context++)

-		{

-			double [] maxes = new double[K];

-			for (Edge edge : c.getEdgesForContext(context))

-			{

-				double p[] = posterior(edge);

-				arr.F.l1normalize(p);

-				for(int tag=0;tag<K;tag++)

-					maxes[tag] = Math.max(maxes[tag], p[tag]);

-			}

-			for(int tag=0;tag<K;tag++)

-				sum += maxes[tag];

-		}

-		return sum;

-	}

-

-	public void loadParameters(BufferedReader input) throws IOException

-	{	

-		final double EPS = 1e-50;

-		

-		// overwrite pi, emit with ~zeros

-		for(double [][]i:emit)

-			for(double []j:i)

-				Arrays.fill(j, EPS);

-

-		for(double []j:pi)

-			Arrays.fill(j, EPS);

-

-		String line = input.readLine();

-		assert line != null;

-

-		Pattern space = Pattern.compile(" +");

-		String[] parts = space.split(line);

-		assert parts.length == 6;

-

-		assert parts[0].equals("phrases");

-		int phrases = Integer.parseInt(parts[1]);

-		int tags = Integer.parseInt(parts[3]);

-		int positions = Integer.parseInt(parts[5]);

-		

-		assert phrases == n_phrases;

-		assert tags == K;

-		assert positions == n_positions;

-

-		// read in pi

-		while ((line = input.readLine()) != null)

-		{

-			line = line.trim();

-			if (line.isEmpty()) break;

-			

-			String[] tokens = space.split(line);

-			assert tokens.length == 3;

-			int p = Integer.parseInt(tokens[0]);

-			int t = Integer.parseInt(tokens[1]);

-			double v = Double.parseDouble(tokens[2]);

-

-			pi[p][t] = v;

-		}

-		

-		// read in emissions

-		while ((line = input.readLine()) != null)

-		{

-			String[] tokens = space.split(line);

-			assert tokens.length == 4;

-			int t = Integer.parseInt(tokens[0]);

-			int p = Integer.parseInt(tokens[1]);

-			int w = Integer.parseInt(tokens[2]);

-			double v = Double.parseDouble(tokens[3]);

-

-			emit[t][p][w] = v;

-		}

-	}

-}

diff --git a/gi/posterior-regularisation/prjava/src/phrase/PhraseContextObjective.java b/gi/posterior-regularisation/prjava/src/phrase/PhraseContextObjective.java
deleted file mode 100644
index 646ff392..00000000
--- a/gi/posterior-regularisation/prjava/src/phrase/PhraseContextObjective.java
+++ /dev/null
@@ -1,436 +0,0 @@
-package phrase;

-

-import java.util.ArrayList;

-import java.util.Arrays;

-import java.util.HashMap;

-import java.util.List;

-import java.util.Map;

-import java.util.concurrent.ExecutionException;

-import java.util.concurrent.ExecutorService;

-import java.util.concurrent.Future;

-

-import optimization.gradientBasedMethods.ProjectedGradientDescent;

-import optimization.gradientBasedMethods.ProjectedObjective;

-import optimization.gradientBasedMethods.stats.OptimizerStats;

-import optimization.linesearch.ArmijoLineSearchMinimizationAlongProjectionArc;

-import optimization.linesearch.InterpolationPickFirstStep;

-import optimization.linesearch.LineSearchMethod;

-import optimization.projections.SimplexProjection;

-import optimization.stopCriteria.CompositeStopingCriteria;

-import optimization.stopCriteria.ProjectedGradientL2Norm;

-import optimization.stopCriteria.StopingCriteria;

-import optimization.stopCriteria.ValueDifference;

-import optimization.util.MathUtils;

-import phrase.Corpus.Edge;

-

-public class PhraseContextObjective extends ProjectedObjective

-{

-	private static final double GRAD_DIFF = 0.00002;

-	private static double INIT_STEP_SIZE = 300;

-	private static double VAL_DIFF = 1e-8;

-	private static int ITERATIONS = 20;

-	boolean debug = false;

-	

-	private PhraseCluster c;

-	

-	// un-regularized unnormalized posterior, p[edge][tag]

-	// P(tag|edge) \propto P(tag|phrase)P(context|tag)

-	private double p[][];

-

-	// regularized unnormalized posterior 

-	// q[edge][tag] propto p[edge][tag]*exp(-lambda)

-	private double q[][];

-	private List<Corpus.Edge> data;

-	

-	// log likelihood under q

-	private double loglikelihood;

-	private SimplexProjection projectionPhrase;

-	private SimplexProjection projectionContext;

-	

-	double[] newPoint;

-	private int n_param;

-	

-	// likelihood under p

-	public double llh;

-	

-	private static Map<Corpus.Edge, Integer> edgeIndex;

-	

-	private long projectionTime;

-	private long objectiveTime;

-	private long actualProjectionTime;

-	private ExecutorService pool;

-	

-	double scalePT;

-	double scaleCT;

-	

-	public PhraseContextObjective(PhraseCluster cluster, double[] startingParameters, ExecutorService pool,

-			double scalePT, double scaleCT)

-	{

-		c=cluster;

-		data=c.c.getEdges();

-		n_param=data.size()*c.K*2;

-		this.pool=pool;

-		this.scalePT = scalePT;

-		this.scaleCT = scaleCT;

-		

-		parameters = startingParameters;

-		if (parameters == null)

-			parameters = new double[n_param];

-		

-		System.out.println("Num parameters " + n_param);

-		newPoint = new double[n_param];

-		gradient = new double[n_param];

-		initP();

-		projectionPhrase = new SimplexProjection(scalePT);

-		projectionContext = new SimplexProjection(scaleCT);

-		q=new double [data.size()][c.K];

-		

-		if (edgeIndex == null) {

-			edgeIndex = new HashMap<Edge, Integer>();

-			for (int e=0; e<data.size(); e++)

-			{

-				edgeIndex.put(data.get(e), e);

-				//if (debug) System.out.println("Edge " + data.get(e) + " index " + e);

-			}

-		}

-		

-		setParameters(parameters);

-	}

-

-	private void initP(){

-		p=new double[data.size()][];

-		for(int edge=0;edge<data.size();edge++)

-		{

-			p[edge]=c.posterior(data.get(edge));

-			llh += data.get(edge).getCount() * Math.log(arr.F.l1norm(p[edge]));

-			arr.F.l1normalize(p[edge]);

-		}

-	}

-	

-	@Override

-	public void setParameters(double[] params) {

-		//System.out.println("setParameters " + Arrays.toString(parameters));

-		// TODO: test if params have changed and skip update otherwise

-		super.setParameters(params);

-		updateFunction();

-	}

-	

-	private void updateFunction()

-	{

-		updateCalls++;

-		loglikelihood=0;

-

-		System.out.print(".");

-		System.out.flush();

-

-		long begin = System.currentTimeMillis();

-		for (int e=0; e<data.size(); e++) 

-		{

-			Edge edge = data.get(e);

-			for(int tag=0; tag<c.K; tag++)

-			{

-				int ip = index(e, tag, true);

-				int ic = index(e, tag, false);

-				q[e][tag] = p[e][tag]*

-					Math.exp((-parameters[ip]-parameters[ic]) / edge.getCount());

-				//if (debug)

-					//System.out.println("\tposterior " + edge + " with tag " + tag + " p " + p[e][tag] + " params " + parameters[ip] + " and " + parameters[ic] + " q " + q[e][tag]);

-			}

-		}

-	

-		for(int edge=0;edge<data.size();edge++) {

-			loglikelihood+=data.get(edge).getCount() * Math.log(arr.F.l1norm(q[edge]));

-			arr.F.l1normalize(q[edge]);

-		}

-		

-		for (int e=0; e<data.size(); e++) 

-		{

-			for(int tag=0; tag<c.K; tag++)

-			{

-				int ip = index(e, tag, true);

-				int ic = index(e, tag, false);

-				gradient[ip]=-q[e][tag];

-				gradient[ic]=-q[e][tag];

-			}

-		}

-		//if (debug) {

-			//System.out.println("objective " + loglikelihood + " ||gradient||_2: " + arr.F.l2norm(gradient));		

-			//System.out.println("gradient " + Arrays.toString(gradient));

-		//}

-		objectiveTime += System.currentTimeMillis() - begin;

-	}

-	

-	@Override

-	public double[] projectPoint(double[] point) 

-	{

-		long begin = System.currentTimeMillis();

-		List<Future<?>> tasks = new ArrayList<Future<?>>();

-		

-		System.out.print(",");

-		System.out.flush();

-

-		Arrays.fill(newPoint, 0, newPoint.length, 0);

-		

-		// first project using the phrase-tag constraints,

-		// for all p,t: sum_c lambda_ptc < scaleP 

-		if (pool == null)

-		{

-			for (int p = 0; p < c.c.getNumPhrases(); ++p)

-			{

-				List<Edge> edges = c.c.getEdgesForPhrase(p);

-				double[] toProject = new double[edges.size()];

-				for(int tag=0;tag<c.K;tag++)

-				{

-					// FIXME: slow hash lookup for e (twice)

-					for(int e=0; e<edges.size(); e++) 						

-						toProject[e] = point[index(edges.get(e), tag, true)];

-					long lbegin = System.currentTimeMillis();

-					projectionPhrase.project(toProject);

-					actualProjectionTime += System.currentTimeMillis() - lbegin;

-					for(int e=0; e<edges.size(); e++)

-						newPoint[index(edges.get(e), tag, true)] = toProject[e];

-				}

-			}

-		}

-		else // do above in parallel using thread pool

-		{	

-			for (int p = 0; p < c.c.getNumPhrases(); ++p)

-			{

-				final int phrase = p;

-				final double[] inPoint = point;

-				Runnable task = new Runnable()

-				{

-					public void run()

-					{

-						List<Edge> edges = c.c.getEdgesForPhrase(phrase);

-						double toProject[] = new double[edges.size()];

-						for(int tag=0;tag<c.K;tag++)

-						{

-							// FIXME: slow hash lookup for e

-							for(int e=0; e<edges.size(); e++)

-								toProject[e] = inPoint[index(edges.get(e), tag, true)];

-							projectionPhrase.project(toProject);

-							for(int e=0; e<edges.size(); e++)

-								newPoint[index(edges.get(e), tag, true)] = toProject[e];

-						}

-					}		

-				};

-				tasks.add(pool.submit(task));

-			}

-		}

-		//System.out.println("after PT " + Arrays.toString(newPoint));

-	

-		// now project using the context-tag constraints,

-		// for all c,t: sum_p omega_pct < scaleC

-		if (pool == null)

-		{

-			for (int ctx = 0; ctx < c.c.getNumContexts(); ++ctx)

-			{

-				List<Edge> edges = c.c.getEdgesForContext(ctx);

-				double toProject[] = new double[edges.size()];

-				for(int tag=0;tag<c.K;tag++)

-				{

-					// FIXME: slow hash lookup for e

-					for(int e=0; e<edges.size(); e++)

-						toProject[e] = point[index(edges.get(e), tag, false)];

-					long lbegin = System.currentTimeMillis();

-					projectionContext.project(toProject);

-					actualProjectionTime += System.currentTimeMillis() - lbegin;

-					for(int e=0; e<edges.size(); e++)

-						newPoint[index(edges.get(e), tag, false)] = toProject[e];

-				}

-			}

-		}

-		else

-		{

-			// do above in parallel using thread pool

-			for (int ctx = 0; ctx < c.c.getNumContexts(); ++ctx)

-			{

-				final int context = ctx;

-				final double[] inPoint = point;

-				Runnable task = new Runnable()

-				{

-					public void run()

-					{

-						List<Edge> edges = c.c.getEdgesForContext(context);

-						double toProject[] = new double[edges.size()];

-						for(int tag=0;tag<c.K;tag++)

-						{

-							// FIXME: slow hash lookup for e

-							for(int e=0; e<edges.size(); e++)

-								toProject[e] = inPoint[index(edges.get(e), tag, false)];

-							projectionContext.project(toProject);

-							for(int e=0; e<edges.size(); e++)

-								newPoint[index(edges.get(e), tag, false)] = toProject[e];

-						}

-					}

-				};

-				tasks.add(pool.submit(task));

-			}

-		}

-		

-		if (pool != null)

-		{

-			// wait for all the jobs to complete

-			Exception failure = null;

-			for (Future<?> task: tasks)

-			{

-				try {

-					task.get();

-				} catch (InterruptedException e) {

-					System.err.println("ERROR: Projection thread interrupted");

-					e.printStackTrace();

-					failure = e;

-				} catch (ExecutionException e) {

-					System.err.println("ERROR: Projection thread died");

-					e.printStackTrace();

-					failure = e;

-				}

-			}

-			// rethrow the exception

-			if (failure != null)

-			{

-				pool.shutdownNow();

-				throw new RuntimeException(failure);

-			}

-		}

-		

-		double[] tmp = newPoint;

-		newPoint = point;

-		projectionTime += System.currentTimeMillis() - begin;

-		

-		//if (debug)

-			//System.out.println("\t\treturning " + Arrays.toString(tmp));

-		return tmp;

-	}

-	

-	private int index(Edge edge, int tag, boolean phrase)

-	{

-		// NB if indexing changes must also change code in updateFunction and constructor

-		if (phrase)

-			return tag * edgeIndex.size() + edgeIndex.get(edge);

-		else

-			return (c.K + tag) * edgeIndex.size() + edgeIndex.get(edge);

-	}

-

-	private int index(int e, int tag, boolean phrase)

-	{

-		// NB if indexing changes must also change code in updateFunction and constructor

-		if (phrase)

-			return tag * edgeIndex.size() + e;

-		else

-			return (c.K + tag) * edgeIndex.size() + e;

-	}

-	

-	@Override

-	public double[] getGradient() {

-		gradientCalls++;

-		return gradient;

-	}

-

-	@Override

-	public double getValue() {

-		functionCalls++;

-		return loglikelihood;

-	}

-

-	@Override

-	public String toString() {

-		return "No need for pointless toString";

-	}

-

-	public double []posterior(int edgeIndex){

-		return q[edgeIndex];

-	}

-	

-	public boolean optimizeWithProjectedGradientDescent()

-	{

-		projectionTime = 0;

-		actualProjectionTime = 0;

-		objectiveTime = 0;

-		long start = System.currentTimeMillis();

-

-		LineSearchMethod ls =

-			new ArmijoLineSearchMinimizationAlongProjectionArc

-				(new InterpolationPickFirstStep(INIT_STEP_SIZE));

-		//LineSearchMethod  ls = new WolfRuleLineSearch(

-		//		(new InterpolationPickFirstStep(INIT_STEP_SIZE)), c1, c2);

-		OptimizerStats stats = new OptimizerStats();

-		

-		

-		ProjectedGradientDescent optimizer = new ProjectedGradientDescent(ls);

-		StopingCriteria stopGrad = new ProjectedGradientL2Norm(GRAD_DIFF);

-		StopingCriteria stopValue = new ValueDifference(VAL_DIFF*(-llh));

-		CompositeStopingCriteria compositeStop = new CompositeStopingCriteria();

-		compositeStop.add(stopGrad);

-		compositeStop.add(stopValue);

-		optimizer.setMaxIterations(ITERATIONS);

-		updateFunction();

-		boolean success = optimizer.optimize(this,stats,compositeStop);

-

-		System.out.println();

-		System.out.println(stats.prettyPrint(1));

-		

-		if (success)

-			System.out.print("\toptimization took " + optimizer.getCurrentIteration() + " iterations");

-	 	else

-			System.out.print("\toptimization failed to converge");

-		long total = System.currentTimeMillis() - start;

-		System.out.println(" and " + total + " ms: projection " + projectionTime + 

-				" actual " + actualProjectionTime + " objective " + objectiveTime);

-

-		return success;

-	}

-	

-	double loglikelihood()

-	{

-		return llh;

-	}

-	

-	double KL_divergence()

-	{

-		return -loglikelihood + MathUtils.dotProduct(parameters, gradient);

-	}

-	

-	double phrase_l1lmax()

-	{

-		// \sum_{tag,phrase} max_{context} P(tag|context,phrase)

-		double sum=0;

-		for (int p = 0; p < c.c.getNumPhrases(); ++p)

-		{

-			List<Edge> edges = c.c.getEdgesForPhrase(p);

-			for(int tag=0;tag<c.K;tag++)

-			{

-				double max=0;

-				for (Edge edge: edges)

-					max = Math.max(max, q[edgeIndex.get(edge)][tag]);

-				sum+=max;

-			}	

-		}

-		return sum;

-	}

-	

-	double context_l1lmax()

-	{

-		// \sum_{tag,context} max_{phrase} P(tag|context,phrase)

-		double sum=0;

-		for (int ctx = 0; ctx < c.c.getNumContexts(); ++ctx)

-		{

-			List<Edge> edges = c.c.getEdgesForContext(ctx);

-			for(int tag=0; tag<c.K; tag++)

-			{

-				double max=0;

-				for (Edge edge: edges)

-					max = Math.max(max, q[edgeIndex.get(edge)][tag]);

-				sum+=max;

-			}	

-		}

-		return sum;

-	}

-	

-	// L - KL(q||p) - scalePT * l1lmax_phrase - scaleCT * l1lmax_context

-	public double primal()

-	{

-		return loglikelihood() - KL_divergence() - scalePT * phrase_l1lmax() - scaleCT * context_l1lmax();

-	}

-}
\ No newline at end of file
diff --git a/gi/posterior-regularisation/prjava/src/phrase/PhraseCorpus.java b/gi/posterior-regularisation/prjava/src/phrase/PhraseCorpus.java
deleted file mode 100644
index 0cf31c1c..00000000
--- a/gi/posterior-regularisation/prjava/src/phrase/PhraseCorpus.java
+++ /dev/null
@@ -1,193 +0,0 @@
-package phrase;

-

-import io.FileUtil;

-

-import java.io.BufferedInputStream;

-import java.io.BufferedReader;

-import java.io.File;

-import java.io.FileNotFoundException;

-import java.io.IOException;

-import java.io.PrintStream;

-import java.util.ArrayList;

-import java.util.HashMap;

-import java.util.Scanner;

-

-public class PhraseCorpus 

-{

-	public HashMap<String,Integer>wordLex;

-	public HashMap<String,Integer>phraseLex;

-	

-	public String wordList[];

-	public String phraseList[];

-	

-	//data[phrase][num context][position]

-	public int data[][][];

-	public int numContexts;	

-

-	public PhraseCorpus(String filename) throws FileNotFoundException, IOException

-	{

-		BufferedReader r = FileUtil.reader(new File(filename));

-		

-		phraseLex=new HashMap<String,Integer>();

-		wordLex=new HashMap<String,Integer>();

-		

-		ArrayList<int[][]>dataList=new ArrayList<int[][]>();

-		String line=null;

-		numContexts = 0;

-		

-		while((line=readLine(r))!=null){

-			

-			String toks[]=line.split("\t");

-			String phrase=toks[0];

-			addLex(phrase,phraseLex);

-			

-			toks=toks[1].split(" \\|\\|\\| ");

-			

-			ArrayList <int[]>ctxList=new ArrayList<int[]>();

-			

-			for(int i=0;i<toks.length;i+=2){

-				String ctx=toks[i];

-				String words[]=ctx.split(" ");

-				if (numContexts == 0)

-					numContexts = words.length - 1;

-				else

-					assert numContexts == words.length - 1;

-				

-				int []context=new int [numContexts+1];

-				int idx=0;

-				for(String word:words){

-					if(word.equals("<PHRASE>")){

-						continue;

-					}

-					addLex(word,wordLex);

-					context[idx]=wordLex.get(word);

-					idx++;

-				}

-				

-				String count=toks[i+1];

-				context[idx]=Integer.parseInt(count.trim().substring(2));

-				

-				ctxList.add(context);

-			}

-			

-			dataList.add(ctxList.toArray(new int [0][]));

-			

-		}

-		try{

-			r.close();

-		}catch(IOException ioe){

-			ioe.printStackTrace();

-		}

-		data=dataList.toArray(new int[0][][]);

-	}

-

-	private void addLex(String key, HashMap<String,Integer>lex){

-		Integer i=lex.get(key);

-		if(i==null){

-			lex.put(key, lex.size());

-		}

-	}

-	

-	//for debugging

-	public void saveLex(String lexFilename) throws FileNotFoundException, IOException

-	{

-		PrintStream ps = FileUtil.printstream(new File(lexFilename));

-		ps.println("Phrase Lexicon");

-		ps.println(phraseLex.size());

-		printDict(phraseLex,ps);

-		

-		ps.println("Word Lexicon");

-		ps.println(wordLex.size());

-		printDict(wordLex,ps);

-		ps.close();

-	}

-	

-	private static void printDict(HashMap<String,Integer>lex,PrintStream ps){

-		String []dict=buildList(lex);

-		for(int i=0;i<dict.length;i++){

-			ps.println(dict[i]);

-		}

-	}

-	

-	public void loadLex(String lexFilename){

-		Scanner sc=io.FileUtil.openInFile(lexFilename);

-		

-		sc.nextLine();

-		int size=sc.nextInt();

-		sc.nextLine();

-		String[]dict=new String[size];

-		for(int i=0;i<size;i++){

-			dict[i]=sc.nextLine();

-		}

-		phraseLex=buildMap(dict);

-

-		sc.nextLine();

-		size=sc.nextInt();

-		sc.nextLine();

-		dict=new String[size];

-		for(int i=0;i<size;i++){

-			dict[i]=sc.nextLine();

-		}

-		wordLex=buildMap(dict);

-		sc.close();

-	}

-	

-	private HashMap<String, Integer> buildMap(String[]dict){

-		HashMap<String,Integer> map=new HashMap<String,Integer>();

-		for(int i=0;i<dict.length;i++){

-			map.put(dict[i], i);

-		}

-		return map;

-	}

-	

-	public void buildList(){

-		if(wordList==null){

-			wordList=buildList(wordLex);

-			phraseList=buildList(phraseLex);

-		}

-	}

-	

-	private static String[]buildList(HashMap<String,Integer>lex){

-		String dict[]=new String [lex.size()];

-		for(String key:lex.keySet()){

-			dict[lex.get(key)]=key;

-		}

-		return dict;

-	}

-	

-	public String getContextString(int context[], boolean addPhraseMarker)

-	{

-		StringBuffer b = new StringBuffer();

-		for (int i=0;i<context.length-1;i++)

-		{

-			if (b.length() > 0)

-				b.append(" ");

-

-			if (i == context.length/2)

-				b.append("<PHRASE> ");

-			

-			b.append(wordList[context[i]]);

-		}

-		return b.toString();

-	}

-	

-	public static String readLine(BufferedReader r){

-		try{

-			return r.readLine();

-		}

-		catch(IOException ioe){

-			ioe.printStackTrace();

-		}

-		return null;

-	}

-

-	public static void main(String[] args) throws Exception 

-	{

-		String LEX_FILENAME="../pdata/lex.out";

-		String DATA_FILENAME="../pdata/btec.con";

-		PhraseCorpus c=new PhraseCorpus(DATA_FILENAME);

-		c.saveLex(LEX_FILENAME);

-		c.loadLex(LEX_FILENAME);

-		c.saveLex(LEX_FILENAME);

-	}

-}

diff --git a/gi/posterior-regularisation/prjava/src/phrase/PhraseObjective.java b/gi/posterior-regularisation/prjava/src/phrase/PhraseObjective.java
deleted file mode 100644
index ac73a075..00000000
--- a/gi/posterior-regularisation/prjava/src/phrase/PhraseObjective.java
+++ /dev/null
@@ -1,224 +0,0 @@
-package phrase;

-

-import java.util.Arrays;

-import java.util.List;

-

-import optimization.gradientBasedMethods.ProjectedGradientDescent;

-import optimization.gradientBasedMethods.ProjectedObjective;

-import optimization.gradientBasedMethods.stats.OptimizerStats;

-import optimization.linesearch.ArmijoLineSearchMinimizationAlongProjectionArc;

-import optimization.linesearch.InterpolationPickFirstStep;

-import optimization.linesearch.LineSearchMethod;

-import optimization.linesearch.WolfRuleLineSearch;

-import optimization.projections.SimplexProjection;

-import optimization.stopCriteria.CompositeStopingCriteria;

-import optimization.stopCriteria.ProjectedGradientL2Norm;

-import optimization.stopCriteria.StopingCriteria;

-import optimization.stopCriteria.ValueDifference;

-import optimization.util.MathUtils;

-

-public class PhraseObjective extends ProjectedObjective

-{

-	static final double GRAD_DIFF = 0.00002;

-	static double INIT_STEP_SIZE = 300;

-	static double VAL_DIFF = 1e-8; // tuned to BTEC subsample

-	static int ITERATIONS = 100;

-	private PhraseCluster c;

-	

-	/**@brief

-	 *  for debugging purposes

-	 */

-	//public static PrintStream ps;

-	

-	/**@brief current phrase being optimzed*/

-	public int phrase;

-

-	/**@brief un-regularized posterior

-	 * unnormalized

-	 * p[edge][tag]

-	*  P(tag|edge) \propto P(tag|phrase)P(context|tag)

-	 */

-	private double[][]p;

-

-	/**@brief regularized posterior

-	 * q[edge][tag] propto p[edge][tag]*exp(-lambda)

-	 */

-	private double q[][];

-	private List<Corpus.Edge> data;

-	

-	/**@brief log likelihood of the associated phrase

-	 * 

-	 */

-	private double loglikelihood;

-	private SimplexProjection projection;

-	

-	double[] newPoint  ;

-	

-	private int n_param;

-	

-	/**@brief likelihood under p

-	 * 

-	 */

-	public double llh;

-	

-	public PhraseObjective(PhraseCluster cluster, int phraseIdx, double scale, double[] lambda){

-		phrase=phraseIdx;

-		c=cluster;

-		data=c.c.getEdgesForPhrase(phrase);

-		n_param=data.size()*c.K;

-		//System.out.println("Num parameters " + n_param + " for phrase #" + phraseIdx);

-		

-		if (lambda==null) 

-			lambda=new double[n_param];

-		

-		parameters = lambda;

-		newPoint = new double[n_param];

-		gradient = new double[n_param];

-		initP();

-		projection=new SimplexProjection(scale);

-		q=new double [data.size()][c.K];

-

-		setParameters(parameters);

-	}

-

-	private void initP(){

-		p=new double[data.size()][];

-		for(int edge=0;edge<data.size();edge++){

-			p[edge]=c.posterior(data.get(edge));

-			llh += data.get(edge).getCount() * Math.log(arr.F.l1norm(p[edge])); // Was bug here - count inside log!

-			arr.F.l1normalize(p[edge]);

-		}

-	}

-	

-	@Override

-	public void setParameters(double[] params) {

-		super.setParameters(params);

-		updateFunction();

-	}

-	

-	private void updateFunction(){

-		updateCalls++;

-		loglikelihood=0;

-

-		for(int tag=0;tag<c.K;tag++){

-			for(int edge=0;edge<data.size();edge++){

-				q[edge][tag]=p[edge][tag]*

-					Math.exp(-parameters[tag*data.size()+edge]/data.get(edge).getCount());

-			}

-		}

-	

-		for(int edge=0;edge<data.size();edge++){

-			loglikelihood+=data.get(edge).getCount() * Math.log(arr.F.l1norm(q[edge]));

-			arr.F.l1normalize(q[edge]);

-		}

-		

-		for(int tag=0;tag<c.K;tag++){

-			for(int edge=0;edge<data.size();edge++){

-				gradient[tag*data.size()+edge]=-q[edge][tag];

-			}

-		}

-	}

-	

-	@Override

-	public double[] projectPoint(double[] point) 

-	{

-		double toProject[]=new double[data.size()];

-		for(int tag=0;tag<c.K;tag++){

-			for(int edge=0;edge<data.size();edge++){

-				toProject[edge]=point[tag*data.size()+edge];

-			}

-			projection.project(toProject);

-			for(int edge=0;edge<data.size();edge++){

-				newPoint[tag*data.size()+edge]=toProject[edge];

-			}

-		}

-		return newPoint;

-	}

-

-	@Override

-	public double[] getGradient() {

-		gradientCalls++;

-		return gradient;

-	}

-

-	@Override

-	public double getValue() {

-		functionCalls++;

-		return loglikelihood;

-	}

-

-	@Override

-	public String toString() {

-		return Arrays.toString(parameters);

-	}

-

-	public double [][]posterior(){

-		return q;

-	}

-	

-	long optimizationTime;

-	

-	public boolean optimizeWithProjectedGradientDescent(){

-		long start = System.currentTimeMillis();

-		

-		LineSearchMethod ls =

-			new ArmijoLineSearchMinimizationAlongProjectionArc

-				(new InterpolationPickFirstStep(INIT_STEP_SIZE));

-		//LineSearchMethod  ls = new WolfRuleLineSearch(

-		//		(new InterpolationPickFirstStep(INIT_STEP_SIZE)), c1, c2);

-		OptimizerStats stats = new OptimizerStats();

-		

-		

-		ProjectedGradientDescent optimizer = new ProjectedGradientDescent(ls);

-		StopingCriteria stopGrad = new ProjectedGradientL2Norm(GRAD_DIFF);

-		StopingCriteria stopValue = new ValueDifference(VAL_DIFF*(-llh));

-		CompositeStopingCriteria compositeStop = new CompositeStopingCriteria();

-		compositeStop.add(stopGrad);

-		compositeStop.add(stopValue);

-		optimizer.setMaxIterations(ITERATIONS);

-		updateFunction();

-		boolean success = optimizer.optimize(this,stats,compositeStop);

-		//System.out.println("Ended optimzation Projected Gradient Descent\n" + stats.prettyPrint(1));

-		//if(succed){

-			//System.out.println("Ended optimization in " + optimizer.getCurrentIteration());

-		//}else{

-//			System.out.println("Failed to optimize");

-		//}

-		//System.out.println(Arrays.toString(parameters));

-		

-		//	for(int edge=0;edge<data.getSize();edge++){

-		//	ps.println(Arrays.toString(q[edge]));

-		//	}

-

-		return success;

-	}

-	

-	public double KL_divergence()

-	{

-		return -loglikelihood + MathUtils.dotProduct(parameters, gradient);

-	}

-	

-	public double loglikelihood()

-	{

-		return llh;

-	}

-	

-	public double l1lmax()

-	{

-		double sum=0;

-		for(int tag=0;tag<c.K;tag++){

-			double max=0;

-			for(int edge=0;edge<data.size();edge++){

-				if(q[edge][tag]>max)

-					max=q[edge][tag];

-			}

-			sum+=max;

-		}

-		return sum;

-	}

-

-	public double primal(double scale)

-	{

-		return loglikelihood() - KL_divergence() - scale * l1lmax();	

-	}

-}

diff --git a/gi/posterior-regularisation/prjava/src/phrase/Trainer.java b/gi/posterior-regularisation/prjava/src/phrase/Trainer.java
deleted file mode 100644
index 6f302b20..00000000
--- a/gi/posterior-regularisation/prjava/src/phrase/Trainer.java
+++ /dev/null
@@ -1,257 +0,0 @@
-package phrase;
-
-import io.FileUtil;
-import joptsimple.OptionParser;
-import joptsimple.OptionSet;
-import java.io.File;
-import java.io.IOException;
-import java.io.PrintStream;
-import java.util.List;
-import java.util.Random;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-
-import phrase.Corpus.Edge;
-
-import arr.F;
-
-public class Trainer 
-{
-	public static void main(String[] args) 
-	{
-        OptionParser parser = new OptionParser();
-        parser.accepts("help");
-        parser.accepts("in").withRequiredArg().ofType(File.class);
-        parser.accepts("in1").withRequiredArg().ofType(File.class);
-        parser.accepts("test").withRequiredArg().ofType(File.class);
-        parser.accepts("out").withRequiredArg().ofType(File.class);
-        parser.accepts("start").withRequiredArg().ofType(File.class);
-        parser.accepts("parameters").withRequiredArg().ofType(File.class);
-        parser.accepts("topics").withRequiredArg().ofType(Integer.class).defaultsTo(5);
-        parser.accepts("iterations").withRequiredArg().ofType(Integer.class).defaultsTo(10);
-        parser.accepts("threads").withRequiredArg().ofType(Integer.class).defaultsTo(0);
-        parser.accepts("scale-phrase").withRequiredArg().ofType(Double.class).defaultsTo(0.0);
-        parser.accepts("scale-context").withRequiredArg().ofType(Double.class).defaultsTo(0.0);
-        parser.accepts("seed").withRequiredArg().ofType(Long.class).defaultsTo(0l);
-        parser.accepts("convergence-threshold").withRequiredArg().ofType(Double.class).defaultsTo(1e-6);
-        parser.accepts("variational-bayes");
-        parser.accepts("alpha-emit").withRequiredArg().ofType(Double.class).defaultsTo(0.1);
-        parser.accepts("alpha-pi").withRequiredArg().ofType(Double.class).defaultsTo(0.0001);
-        parser.accepts("agree-direction");
-        parser.accepts("agree-language");
-        parser.accepts("no-parameter-cache");
-        parser.accepts("skip-large-phrases").withRequiredArg().ofType(Integer.class).defaultsTo(5);
-        OptionSet options = parser.parse(args);
-
-        if (options.has("help") || !options.has("in"))
-        {
-        	try {
-				parser.printHelpOn(System.err);
-			} catch (IOException e) {
-				System.err.println("This should never happen.");
-				e.printStackTrace();
-			}
-        	System.exit(1);     
-        }
-		
-		int tags = (Integer) options.valueOf("topics");
-		int iterations = (Integer) options.valueOf("iterations");
-		double scale_phrase = (Double) options.valueOf("scale-phrase");
-		double scale_context = (Double) options.valueOf("scale-context");
-		int threads = (Integer) options.valueOf("threads");
-		double threshold = (Double) options.valueOf("convergence-threshold");
-		boolean vb = options.has("variational-bayes");
-		double alphaEmit = (vb) ? (Double) options.valueOf("alpha-emit") : 0;
-		double alphaPi = (vb) ? (Double) options.valueOf("alpha-pi") : 0;
-		int skip = (Integer) options.valueOf("skip-large-phrases");
-		
-		if (options.has("seed"))
-			F.rng = new Random((Long) options.valueOf("seed"));
-		
-		ExecutorService threadPool = null;
-		if (threads > 0)
-			threadPool = Executors.newFixedThreadPool(threads);			
-		
-		if (tags <= 1 || scale_phrase < 0 || scale_context < 0 || threshold < 0)
-		{
-			System.err.println("Invalid arguments. Try again!");
-			System.exit(1);
-		}
-		
-		Corpus corpus = null;
-		File infile = (File) options.valueOf("in");
-		Corpus corpus1 = null;
-		File infile1 = (File) options.valueOf("in1");
-		try {
-			System.out.println("Reading concordance from " + infile);
-			corpus = Corpus.readFromFile(FileUtil.reader(infile));
-			corpus.printStats(System.out);
-			if(options.has("in1")){
-				corpus1 = Corpus.readFromFile(FileUtil.reader(infile1));
-				corpus1.printStats(System.out);
-			}
-		} catch (IOException e) {
-			System.err.println("Failed to open input file: " + infile);
-			e.printStackTrace();
-			System.exit(1);
-		}
-				
-		if (!(options.has("agree-direction")||options.has("agree-language")))
-			System.out.println("Running with " + tags + " tags " +
-					"for " + iterations + " iterations " +
-					((skip > 0) ? "skipping large phrases for first " + skip + " iterations " : "") +
-					"with scale " + scale_phrase + " phrase and " + scale_context + " context " +
-					"and " + threads + " threads");
-		else
-			System.out.println("Running agreement model with " + tags + " tags " +
-	 				"for " + iterations);
-
-	 	System.out.println();
-		
- 		PhraseCluster cluster = null;
- 		Agree2Sides agree2sides = null;
- 		Agree agree= null;
- 		VB vbModel=null;
- 		if (options.has("agree-language"))
- 			agree2sides = new Agree2Sides(tags, corpus,corpus1);
- 		else if (options.has("agree-direction"))
- 			agree = new Agree(tags, corpus);
- 		else
- 		{
- 			if (vb)	
- 			{
- 				vbModel=new VB(tags,corpus);
- 				vbModel.alpha=alphaPi;
- 				vbModel.lambda=alphaEmit;
- 	 			if (threadPool != null) vbModel.useThreadPool(threadPool);
- 			} 
- 			else 
- 			{
- 				cluster = new PhraseCluster(tags, corpus);
- 	 			if (threadPool != null) cluster.useThreadPool(threadPool);
- 				
-	 			if (options.has("no-parameter-cache")) 
-	 				cluster.cacheLambda = false;
-	 			if (options.has("start"))
-	 			{
-	 				try {
-						System.err.println("Reading starting parameters from " + options.valueOf("start"));
-						cluster.loadParameters(FileUtil.reader((File)options.valueOf("start")));
-					} catch (IOException e) {
-						System.err.println("Failed to open input file: " + options.valueOf("start"));
-						e.printStackTrace();
-					}
-	 			}
- 			}
- 		}
-				
-		double last = 0;
-		for (int i=0; i < iterations; i++)
-		{
-			double o;
-			if (agree != null)
-				o = agree.EM();
-			else if(agree2sides!=null)
-				o = agree2sides.EM();
-			else
-			{
-				if (i < skip)
-					System.out.println("Skipping phrases of length > " + (i+1));
-				
-				if (scale_phrase <= 0 && scale_context <= 0)
-				{
-					if (!vb)
-						o = cluster.EM((i < skip) ? i+1 : 0);
-					else
-						o = vbModel.EM();	
-				}
-				else
-					o = cluster.PREM(scale_phrase, scale_context, (i < skip) ? i+1 : 0);
-			}
-			
-			System.out.println("ITER: "+i+" objective: " + o);
-			
-			// sometimes takes a few iterations to break the ties
-			if (i > 5 && Math.abs((o - last) / o) < threshold)
-			{
-				last = o;
-				break;
-			}
-			last = o;
-		}
-		
-		double pl1lmax = 0, cl1lmax = 0;
-		if (cluster != null)
-		{
-			pl1lmax = cluster.phrase_l1lmax();
-			cl1lmax = cluster.context_l1lmax();
-		}
-		else if (agree != null)
-		{
-			// fairly arbitrary choice of model1 cf model2
-			pl1lmax = agree.model1.phrase_l1lmax();
-			cl1lmax = agree.model1.context_l1lmax();
-		}
-		else if (agree2sides != null)
-		{
-			// fairly arbitrary choice of model1 cf model2
-			pl1lmax = agree2sides.model1.phrase_l1lmax();
-			cl1lmax = agree2sides.model1.context_l1lmax();
-		}
-
-		System.out.println("\nFinal posterior phrase l1lmax " + pl1lmax + " context l1lmax " + cl1lmax);
-		
-		if (options.has("out"))
-		{
-			File outfile = (File) options.valueOf("out");
-			try {
-				PrintStream ps = FileUtil.printstream(outfile);
-				List<Edge> test;
-				if (!options.has("test")) // just use the training
-					test = corpus.getEdges();
-				else
-				{	// if --test supplied, load up the file
-					infile = (File) options.valueOf("test");
-					System.out.println("Reading testing concordance from " + infile);
-					test = corpus.readEdges(FileUtil.reader(infile));
-				}
-				if(vb) {
-					assert !options.has("test");
-					vbModel.displayPosterior(ps);
-				} else if (cluster != null) 
-					cluster.displayPosterior(ps, test);
-				else if (agree != null) 
-					agree.displayPosterior(ps, test);
-				else if (agree2sides != null) {
-					assert !options.has("test");
-					agree2sides.displayPosterior(ps);
-				}
-				
-				ps.close();
-			} catch (IOException e) {
-				System.err.println("Failed to open either testing file or output file");
-				e.printStackTrace();
-				System.exit(1);
-			}
-		}
-
-		if (options.has("parameters"))
-		{
-			assert !vb;
-			File outfile = (File) options.valueOf("parameters");
-			PrintStream ps;
-			try {
-				ps = FileUtil.printstream(outfile);
-				cluster.displayModelParam(ps);
-				ps.close();
-			} catch (IOException e) {
-				System.err.println("Failed to open output parameters file: " + outfile);
-				e.printStackTrace();
-				System.exit(1);
-			}
-		}
-		
-		if (cluster != null && cluster.pool != null)
-			cluster.pool.shutdown();
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/phrase/VB.java b/gi/posterior-regularisation/prjava/src/phrase/VB.java
deleted file mode 100644
index cd3f4966..00000000
--- a/gi/posterior-regularisation/prjava/src/phrase/VB.java
+++ /dev/null
@@ -1,419 +0,0 @@
-package phrase;

-

-import gnu.trove.TIntArrayList;

-

-import io.FileUtil;

-

-import java.io.File;

-import java.io.IOException;

-import java.io.PrintStream;

-import java.util.ArrayList;

-import java.util.Arrays;

-import java.util.List;

-import java.util.concurrent.Callable;

-import java.util.concurrent.ExecutionException;

-import java.util.concurrent.ExecutorService;

-import java.util.concurrent.Future;

-

-import org.apache.commons.math.special.Gamma;

-

-import phrase.Corpus.Edge;

-

-public class VB {

-

-	public static int MAX_ITER=400;

-	

-	/**@brief

-	 * hyper param for beta

-	 * where beta is multinomial

-	 * for generating words from a topic

-	 */

-	public double lambda=0.1;

-	/**@brief

-	 * hyper param for theta

-	 * where theta is dirichlet for z

-	 */

-	public double alpha=0.0001;

-	/**@brief

-	 * variational param for beta

-	 */

-	private double rho[][][];

-	private double digamma_rho[][][];

-	private double rho_sum[][];

-	/**@brief

-	 * variational param for z

-	 */

-	//private double phi[][];

-	/**@brief

-	 * variational param for theta

-	 */

-	private double gamma[];

-	private static double VAL_DIFF_RATIO=0.005;

-	

-	private int n_positions;

-	private int n_words;

-	private int K;

-	private ExecutorService pool;

-	

-	private Corpus c;

-	public static void main(String[] args) {

-	//	String in="../pdata/canned.con";

-		String in="../pdata/btec.con";

-		String out="../pdata/vb.out";

-		int numCluster=25;

-		Corpus corpus = null;

-		File infile = new File(in);

-		try {

-			System.out.println("Reading concordance from " + infile);

-			corpus = Corpus.readFromFile(FileUtil.reader(infile));

-			corpus.printStats(System.out);

-		} catch (IOException e) {

-			System.err.println("Failed to open input file: " + infile);

-			e.printStackTrace();

-			System.exit(1);

-		}

-		

-		VB vb=new VB(numCluster, corpus);

-		int iter=20;

-		for(int i=0;i<iter;i++){

-			double obj=vb.EM();

-			System.out.println("Iter "+i+": "+obj);

-		}

-		

-		File outfile = new File (out);

-		try {

-			PrintStream ps = FileUtil.printstream(outfile);

-			vb.displayPosterior(ps);

-		//	ps.println();

-		//	c2f.displayModelParam(ps);

-			ps.close();

-		} catch (IOException e) {

-			System.err.println("Failed to open output file: " + outfile);

-			e.printStackTrace();

-			System.exit(1);

-		}

-	}

-

-	public VB(int numCluster, Corpus corpus){

-		c=corpus;

-		K=numCluster;

-		n_positions=c.getNumContextPositions();

-		n_words=c.getNumWords();

-		rho=new double[K][n_positions][n_words];

-		//to init rho

-		//loop through data and count up words

-		double[] phi_tmp=new double[K];

-		for(int i=0;i<K;i++){

-			for(int pos=0;pos<n_positions;pos++){

-				Arrays.fill(rho[i][pos], lambda);

-			}

-		}

-		for(int d=0;d<c.getNumPhrases();d++){

-			List<Edge>doc=c.getEdgesForPhrase(d);

-			for(int n=0;n<doc.size();n++){

-				TIntArrayList context=doc.get(n).getContext();

-				arr.F.randomise(phi_tmp);

-				for(int i=0;i<K;i++){

-					for(int pos=0;pos<n_positions;pos++){

-						rho[i][pos][context.get(pos)]+=phi_tmp[i];

-					}

-				}

-			}

-		}

-		

-	}

-	

-	private double inference(int phraseID, double[][] phi, double[] gamma)

-	{

-		List<Edge > doc=c.getEdgesForPhrase(phraseID);

-		for(int i=0;i<phi.length;i++){

-			for(int j=0;j<phi[i].length;j++){

-				phi[i][j]=1.0/K;

-			}

-		}

-		Arrays.fill(gamma,alpha+1.0/K);

-		

-		double digamma_gamma[]=new double[K];

-		

-		double gamma_sum=digamma(arr.F.l1norm(gamma));

-		for(int i=0;i<K;i++){

-			digamma_gamma[i]=digamma(gamma[i]);

-		}

-		double gammaSum[]=new double [K];

-		double prev_val=0;

-		double obj=0;

-		

-		for(int iter=0;iter<MAX_ITER;iter++){

-			prev_val=obj;

-			obj=0;

-			Arrays.fill(gammaSum,0.0);

-			for(int n=0;n<doc.size();n++){

-				TIntArrayList context=doc.get(n).getContext();

-				double phisum=0;

-				for(int i=0;i<K;i++){

-					double sum=0;

-					for(int pos=0;pos<n_positions;pos++){

-						int word=context.get(pos);

-						sum+=digamma_rho[i][pos][word]-rho_sum[i][pos];

-					}

-					sum+= digamma_gamma[i]-gamma_sum;

-					phi[n][i]=sum;

-					

-					if (i > 0){

-	                    phisum = log_sum(phisum, phi[n][i]);

-					}

-	                else{

-	                    phisum = phi[n][i];

-	                }

-					

-				}//end of  a word

-				

-				for(int i=0;i<K;i++){

-					phi[n][i]=Math.exp(phi[n][i]-phisum);

-					gammaSum[i]+=phi[n][i];

-				}

-				

-			}//end of doc

-			

-			for(int i=0;i<K;i++){

-				gamma[i]=alpha+gammaSum[i];

-			}

-			gamma_sum=digamma(arr.F.l1norm(gamma));

-			for(int i=0;i<K;i++){

-				digamma_gamma[i]=digamma(gamma[i]);

-			}

-			//compute objective for reporting

-

-			obj=0;

-			

-			for(int i=0;i<K;i++){

-				obj+=(alpha-1)*(digamma_gamma[i]-gamma_sum);

-			}

-			

-			

-			for(int n=0;n<doc.size();n++){

-				TIntArrayList context=doc.get(n).getContext();

-				

-				for(int i=0;i<K;i++){

-					//entropy of phi + expected log likelihood of z

-					obj+=phi[n][i]*(digamma_gamma[i]-gamma_sum);

-					

-					if(phi[n][i]>1e-10){

-						obj+=phi[n][i]*Math.log(phi[n][i]);

-					}

-					

-					double beta_sum=0;

-					for(int pos=0;pos<n_positions;pos++){

-						int word=context.get(pos);

-						beta_sum+=(digamma(rho[i][pos][word])-rho_sum[i][pos]);

-					}

-					obj+=phi[n][i]*beta_sum;

-				}

-			}

-			

-			obj-=log_gamma(arr.F.l1norm(gamma));

-			for(int i=0;i<K;i++){

-				obj+=Gamma.logGamma(gamma[i]);

-				obj-=(gamma[i]-1)*(digamma_gamma[i]-gamma_sum);

-			}

-			

-//			System.out.println(phraseID+": "+obj);

-			if(iter>0 && (obj-prev_val)/Math.abs(obj)<VAL_DIFF_RATIO){

-				break;

-			}

-		}//end of inference loop

-		

-		return obj;

-	}//end of inference

-	

-	/**

-	 * @return objective of this iteration

-	 */

-	public double EM(){

-		double emObj=0;

-		if(digamma_rho==null){

-			digamma_rho=new double[K][n_positions][n_words];

-		}

-		for(int i=0;i<K;i++){

-			for (int pos=0;pos<n_positions;pos++){

-				for(int j=0;j<n_words;j++){

-					digamma_rho[i][pos][j]= digamma(rho[i][pos][j]);

-				}

-			}

-		}

-		

-		if(rho_sum==null){

-			rho_sum=new double [K][n_positions];

-		}

-		for(int i=0;i<K;i++){

-			for(int pos=0;pos<n_positions;pos++){

-				rho_sum[i][pos]=digamma(arr.F.l1norm(rho[i][pos]));

-			}

-		}

-

-		//E

-		double exp_rho[][][]=new double[K][n_positions][n_words];

-		if (pool == null)

-		{

-			for (int d=0;d<c.getNumPhrases();d++)

-			{		

-				List<Edge > doc=c.getEdgesForPhrase(d);

-				double[][] phi = new double[doc.size()][K];

-				double[] gamma = new double[K];

-				

-				emObj += inference(d, phi, gamma);

-				

-				for(int n=0;n<doc.size();n++){

-					TIntArrayList context=doc.get(n).getContext();

-					for(int pos=0;pos<n_positions;pos++){

-						int word=context.get(pos);

-						for(int i=0;i<K;i++){	

-							exp_rho[i][pos][word]+=phi[n][i];

-						}

-					}

-				}

-				//if(d!=0 && d%100==0)  System.out.print(".");

-				//if(d!=0 && d%1000==0) System.out.println(d);

-			}

-		}

-		else // multi-threaded version of above loop

-		{

-			class PartialEStep implements Callable<PartialEStep>

-			{

-				double[][] phi;

-				double[] gamma;

-				double obj;

-				int d;

-				PartialEStep(int d) { this.d = d; }

-

-				public PartialEStep call()

-				{

-					phi = new double[c.getEdgesForPhrase(d).size()][K];

-					gamma = new double[K];

-					obj = inference(d, phi, gamma);

-					return this;

-				}			

-			}

-

-			List<Future<PartialEStep>> jobs = new ArrayList<Future<PartialEStep>>();

-			for (int d=0;d<c.getNumPhrases();d++)

-				jobs.add(pool.submit(new PartialEStep(d)));

-		

-			for (Future<PartialEStep> job: jobs)

-			{

-				try {

-					PartialEStep e = job.get();

-					

-					emObj += e.obj;				

-					List<Edge> doc = c.getEdgesForPhrase(e.d);

-					for(int n=0;n<doc.size();n++){

-						TIntArrayList context=doc.get(n).getContext();

-						for(int pos=0;pos<n_positions;pos++){

-							int word=context.get(pos);

-							for(int i=0;i<K;i++){	

-								exp_rho[i][pos][word]+=e.phi[n][i];

-							}

-						}

-					}

-				} catch (ExecutionException e) {

-					System.err.println("ERROR: E-step thread execution failed.");

-					throw new RuntimeException(e);

-				} catch (InterruptedException e) {

-					System.err.println("ERROR: Failed to join E-step thread.");

-					throw new RuntimeException(e);

-				}

-			}

-		}	

-	//	System.out.println("EM Objective:"+emObj);

-		

-		//M

-		for(int i=0;i<K;i++){

-			for(int pos=0;pos<n_positions;pos++){

-				for(int j=0;j<n_words;j++){

-					rho[i][pos][j]=lambda+exp_rho[i][pos][j];

-				}

-			}

-		}

-		

-		//E[\log p(\beta|\lambda)] - E[\log q(\beta)]

-		for(int i=0;i<K;i++){

-			double rhoSum=0;

-			for(int pos=0;pos<n_positions;pos++){

-				for(int j=0;j<n_words;j++){

-					rhoSum+=rho[i][pos][j];

-				}

-				double digamma_rhoSum=Gamma.digamma(rhoSum);

-				emObj-=Gamma.logGamma(rhoSum);

-				for(int j=0;j<n_words;j++){

-					emObj+=(lambda-rho[i][pos][j])*(Gamma.digamma(rho[i][pos][j])-digamma_rhoSum);

-					emObj+=Gamma.logGamma(rho[i][pos][j]);

-				}

-			}

-		}

-		

-		return emObj;

-	}//end of EM

-	

-	public void displayPosterior(PrintStream ps)

-	{	

-		for(int d=0;d<c.getNumPhrases();d++){

-			List<Edge > doc=c.getEdgesForPhrase(d);

-			double[][] phi = new double[doc.size()][K];

-			for(int i=0;i<phi.length;i++)

-				for(int j=0;j<phi[i].length;j++)

-					phi[i][j]=1.0/K;

-			double[] gamma = new double[K];

-

-			inference(d, phi, gamma);

-

-			for(int n=0;n<doc.size();n++){

-				Edge edge=doc.get(n);

-				int tag=arr.F.argmax(phi[n]);

-				ps.print(edge.getPhraseString());

-				ps.print("\t");

-				ps.print(edge.getContextString(true));

-

-				ps.println(" ||| C=" + tag);

-			}

-		}

-	}

-

-	double log_sum(double log_a, double log_b)

-	{

-	  double v;

-

-	  if (log_a < log_b)

-	      v = log_b+Math.log(1 + Math.exp(log_a-log_b));

-	  else

-	      v = log_a+Math.log(1 + Math.exp(log_b-log_a));

-	  return(v);

-	}

-		

-	double digamma(double x)

-	{

-	    double p;

-	    x=x+6;

-	    p=1/(x*x);

-	    p=(((0.004166666666667*p-0.003968253986254)*p+

-		0.008333333333333)*p-0.083333333333333)*p;

-	    p=p+Math.log(x)-0.5/x-1/(x-1)-1/(x-2)-1/(x-3)-1/(x-4)-1/(x-5)-1/(x-6);

-	    return p;

-	}

-	

-	double log_gamma(double x)

-	{

-	     double z=1/(x*x);

-

-	    x=x+6;

-	    z=(((-0.000595238095238*z+0.000793650793651)

-		*z-0.002777777777778)*z+0.083333333333333)/x;

-	    z=(x-0.5)*Math.log(x)-x+0.918938533204673+z-Math.log(x-1)-

-	    Math.log(x-2)-Math.log(x-3)-Math.log(x-4)-Math.log(x-5)-Math.log(x-6);

-	    return z;

-	}

-

-	public void useThreadPool(ExecutorService threadPool) 

-	{

-		pool = threadPool;

-	}

-}//End of  class

diff --git a/gi/posterior-regularisation/prjava/src/test/CorpusTest.java b/gi/posterior-regularisation/prjava/src/test/CorpusTest.java
deleted file mode 100644
index b4c3041f..00000000
--- a/gi/posterior-regularisation/prjava/src/test/CorpusTest.java
+++ /dev/null
@@ -1,60 +0,0 @@
-package test;

-

-import java.util.Arrays;

-import java.util.HashMap;

-

-import data.Corpus;

-import hmm.POS;

-

-public class CorpusTest {

-

-	public static void main(String[] args) {

-		Corpus c=new Corpus(POS.trainFilename);

-

-		

-		int idx=30;

-		

-		

-		HashMap<String, Integer>vocab=

-			(HashMap<String, Integer>) io.SerializedObjects.readSerializedObject(Corpus.alphaFilename);

-		

-		HashMap<String, Integer>tagVocab=

-			(HashMap<String, Integer>) io.SerializedObjects.readSerializedObject(Corpus.tagalphaFilename);

-		

-		

-		String [] dict=new String [vocab.size()+1];

-		for(String key:vocab.keySet()){

-			dict[vocab.get(key)]=key;

-		}

-		dict[dict.length-1]=Corpus.UNK_TOK;

-		

-		String [] tagdict=new String [tagVocab.size()+1];

-		for(String key:tagVocab.keySet()){

-			tagdict[tagVocab.get(key)]=key;

-		}

-		tagdict[tagdict.length-1]=Corpus.UNK_TOK;

-		

-		String[] sent=c.get(idx);

-		int []data=c.getInt(idx);

-		

-		

-		String []roundtrip=new String [sent.length];

-		for(int i=0;i<sent.length;i++){

-			roundtrip[i]=dict[data[i]];

-		}

-		System.out.println(Arrays.toString(sent));

-		System.out.println(Arrays.toString(roundtrip));

-		

-		sent=c.tag.get(idx);

-		data=c.tagData.get(idx);

-		

-		

-		roundtrip=new String [sent.length];

-		for(int i=0;i<sent.length;i++){

-			roundtrip[i]=tagdict[data[i]];

-		}

-		System.out.println(Arrays.toString(sent));

-		System.out.println(Arrays.toString(roundtrip));

-	}

-

-}

diff --git a/gi/posterior-regularisation/prjava/src/test/HMMModelStats.java b/gi/posterior-regularisation/prjava/src/test/HMMModelStats.java
deleted file mode 100644
index d54525c8..00000000
--- a/gi/posterior-regularisation/prjava/src/test/HMMModelStats.java
+++ /dev/null
@@ -1,105 +0,0 @@
-package test;

-

-import hmm.HMM;

-import hmm.POS;

-

-import java.io.File;

-import java.io.FileNotFoundException;

-import java.io.IOException;

-import java.io.PrintStream;

-import java.util.ArrayList;

-import java.util.Collections;

-import java.util.HashMap;

-

-import data.Corpus;

-

-public class HMMModelStats {

-

-	public static String modelFilename="../posdata/posModel.out";

-	public static String alphaFilename="../posdata/corpus.alphabet";

-	public static String statsFilename="../posdata/model.stats";

-

-	public static final int NUM_WORD=50;

-	

-	public static String testFilename="../posdata/en_test.conll";

-	

-	public static double [][]maxwt;

-	

-	public static void main(String[] args) {

-		HashMap<String, Integer>vocab=

-			(HashMap<String, Integer>) io.SerializedObjects.readSerializedObject(alphaFilename);

-		

-		Corpus test=new Corpus(testFilename,vocab);

-		

-		String [] dict=new String [vocab.size()+1];

-		for(String key:vocab.keySet()){

-			dict[vocab.get(key)]=key;

-		}

-		dict[dict.length-1]=Corpus.UNK_TOK;

-		

-		HMM hmm=new HMM();

-		hmm.readModel(modelFilename);

-

-		

-		

-		PrintStream ps = null;

-		try {

-			ps = io.FileUtil.printstream(new File(statsFilename));

-		} catch (IOException e) {

-			e.printStackTrace();

-			System.exit(1);

-		}

-		

-		double [][] emit=hmm.getEmitProb();

-		for(int i=0;i<emit.length;i++){

-			ArrayList<IntDoublePair>l=new ArrayList<IntDoublePair>();

-			for(int j=0;j<emit[i].length;j++){

-				l.add(new IntDoublePair(j,emit[i][j]));

-			}

-			Collections.sort(l);

-			ps.println(i);

-			for(int j=0;j<NUM_WORD;j++){

-				if(j>=dict.length){

-					break;

-				}

-				ps.print(dict[l.get(j).idx]+"\t");

-				if((1+j)%10==0){

-					ps.println();

-				}

-			}

-			ps.println("\n");

-		}

-		

-		checkMaxwt(hmm,ps,test.getAllData());

-		

-		int terminalSym=vocab.get(Corpus .END_SYM);

-		//sample 10 sentences

-		for(int i=0;i<10;i++){

-			int []sent=hmm.sample(terminalSym);

-			for(int j=0;j<sent.length;j++){

-				ps.print(dict[sent[j]]+"\t");

-			}

-			ps.println();

-		}

-		

-		ps.close();

-		

-	}

-	

-	public static void checkMaxwt(HMM hmm,PrintStream ps,int [][]data){

-		double [][]emit=hmm.getEmitProb();

-		maxwt=new double[emit.length][emit[0].length];

-		

-		hmm.computeMaxwt(maxwt,data);

-		double sum=0;

-		for(int i=0;i<maxwt.length;i++){

-			for(int j=0;j<maxwt.length;j++){

-				sum+=maxwt[i][j];

-			}

-		}

-		

-		ps.println("max w t P(w_i|t): "+sum);

-		

-	}

-	

-}

diff --git a/gi/posterior-regularisation/prjava/src/test/IntDoublePair.java b/gi/posterior-regularisation/prjava/src/test/IntDoublePair.java
deleted file mode 100644
index 3f9f0ad7..00000000
--- a/gi/posterior-regularisation/prjava/src/test/IntDoublePair.java
+++ /dev/null
@@ -1,23 +0,0 @@
-package test;

-

-public class IntDoublePair implements Comparable{

-	double val;

-	int idx;

-	public int compareTo(Object o){

-		if(o instanceof IntDoublePair){

-			IntDoublePair pair=(IntDoublePair)o;

-			if(pair.val>val){

-				return 1;

-			}

-			if(pair.val<val){

-				return -1;

-			}

-			return 0;

-		}

-		return -1;

-	}

-	public IntDoublePair(int i,double v){

-		val=v;

-		idx=i;

-	}

-}

diff --git a/gi/posterior-regularisation/prjava/src/test/X2y2WithConstraints.java b/gi/posterior-regularisation/prjava/src/test/X2y2WithConstraints.java
deleted file mode 100644
index 9059a59e..00000000
--- a/gi/posterior-regularisation/prjava/src/test/X2y2WithConstraints.java
+++ /dev/null
@@ -1,131 +0,0 @@
-package test;

-

-

-

-import optimization.gradientBasedMethods.ProjectedGradientDescent;

-import optimization.gradientBasedMethods.ProjectedObjective;

-import optimization.gradientBasedMethods.stats.OptimizerStats;

-import optimization.linesearch.ArmijoLineSearchMinimizationAlongProjectionArc;

-import optimization.linesearch.InterpolationPickFirstStep;

-import optimization.linesearch.LineSearchMethod;

-import optimization.projections.BoundsProjection;

-import optimization.projections.Projection;

-import optimization.projections.SimplexProjection;

-import optimization.stopCriteria.CompositeStopingCriteria;

-import optimization.stopCriteria.GradientL2Norm;

-import optimization.stopCriteria.ProjectedGradientL2Norm;

-import optimization.stopCriteria.StopingCriteria;

-import optimization.stopCriteria.ValueDifference;

-

-

-/**

- * @author javg

- * 

- * 

- *ax2+ b(y2 -displacement)

- */

-public class X2y2WithConstraints extends ProjectedObjective{

-

-

-	double a, b;

-	double dx;

-	double dy;

-	Projection projection;

-	

-	

-	public X2y2WithConstraints(double a, double b, double[] params, double dx, double dy, Projection proj){

-		//projection = new BoundsProjection(0.2,Double.MAX_VALUE);

-		super();

-		projection = proj;	

-		this.a = a;

-		this.b = b;

-		this.dx = dx;

-		this.dy = dy;

-		setInitialParameters(params);

-		System.out.println("Function " +a+"(x-"+dx+")^2 + "+b+"(y-"+dy+")^2");

-		System.out.println("Gradient " +(2*a)+"(x-"+dx+") ; "+(b*2)+"(y-"+dy+")");

-		printParameters();

-		projection.project(parameters);

-		printParameters();

-		gradient = new double[2];

-	}

-	

-	public double getValue() {

-		functionCalls++;

-		return a*(parameters[0]-dx)*(parameters[0]-dx)+b*((parameters[1]-dy)*(parameters[1]-dy));

-	}

-

-	public double[] getGradient() {

-		if(gradient == null){

-			gradient = new double[2];

-		}

-		gradientCalls++;

-		gradient[0]=2*a*(parameters[0]-dx);

-		gradient[1]=2*b*(parameters[1]-dy);

-		return gradient;

-	}

-	

-	

-	public double[] projectPoint(double[] point) {

-		double[] newPoint = point.clone();

-		projection.project(newPoint);

-		return newPoint;

-	}	

-	

-	public void optimizeWithProjectedGradientDescent(LineSearchMethod ls, OptimizerStats stats, X2y2WithConstraints o){

-		ProjectedGradientDescent optimizer = new ProjectedGradientDescent(ls);

-		StopingCriteria stopGrad = new ProjectedGradientL2Norm(0.001);

-		StopingCriteria stopValue = new ValueDifference(0.001);

-		CompositeStopingCriteria compositeStop = new CompositeStopingCriteria();

-		compositeStop.add(stopGrad);

-		compositeStop.add(stopValue);

-		

-		optimizer.setMaxIterations(5);

-		boolean succed = optimizer.optimize(o,stats,compositeStop);

-		System.out.println("Ended optimzation Projected Gradient Descent\n" + stats.prettyPrint(1));

-		System.out.println("Solution: " + " x0 " + o.parameters[0]+ " x1 " + o.parameters[1]);

-		if(succed){

-			System.out.println("Ended optimization in " + optimizer.getCurrentIteration());

-		}else{

-			System.out.println("Failed to optimize");

-		}

-	}

-	

-	

-	

-	public String toString(){

-		

-		return "P1: " + parameters[0] + " P2: " + parameters[1] + " value " + getValue() + " grad (" + getGradient()[0] + ":" + getGradient()[1]+")";

-	}

-	

-	public static void main(String[] args) {

-		double a = 1;

-		double b=1;

-		double x0 = 0;

-		double y0  =1;

-		double dx = 0.5;

-		double dy = 0.2	;

-		double [] parameters = new double[2];

-		parameters[0] = x0;

-		parameters[1] = y0;

-		X2y2WithConstraints o = new X2y2WithConstraints(a,b,parameters,dx,dy, 

-				new SimplexProjection(0.5)

-				//new BoundsProjection(0.0,0.4)

-		);

-		System.out.println("Starting optimization " + " x0 " + o.parameters[0]+ " x1 " + o.parameters[1] + " a " + a + " b "+b );

-		o.setDebugLevel(4);

-		

-		LineSearchMethod ls = new ArmijoLineSearchMinimizationAlongProjectionArc(new InterpolationPickFirstStep(1));

-		

-		OptimizerStats stats = new OptimizerStats();

-		o.optimizeWithProjectedGradientDescent(ls, stats, o);

-		

-//		o = new x2y2WithConstraints(a,b,x0,y0,dx,dy);

-//		stats = new OptimizerStats();

-//		o.optimizeWithSpectralProjectedGradientDescent(stats, o);

-	}

-	

-	

-	

-	

-}

diff --git a/gi/posterior-regularisation/prjava/src/util/Array.java b/gi/posterior-regularisation/prjava/src/util/Array.java
deleted file mode 100644
index cc4725af..00000000
--- a/gi/posterior-regularisation/prjava/src/util/Array.java
+++ /dev/null
@@ -1,41 +0,0 @@
-package util;
-
-import java.util.Arrays;
-
-public class Array {
-
-	
-	
-	public  static void sortDescending(double[] ds){
-		for (int i = 0; i < ds.length; i++) ds[i] = -ds[i];
-		Arrays.sort(ds);
-		for (int i = 0; i < ds.length; i++) ds[i] = -ds[i];
-	}
-	
-	/** 
-	 * Return a new reversed array
-	 * @param array
-	 * @return
-	 */
-	public static int[] reverseIntArray(int[] array){
-		int[] reversed = new int[array.length];
-		for (int i = 0; i < reversed.length; i++) {
-			reversed[i] = array[reversed.length-1-i];
-		}
-		return reversed;
-	}
-	
-	public static String[] sumArray(String[] in, int from){
-		String[] res = new String[in.length-from];
-		for (int i = from; i < in.length; i++) {
-			res[i-from] = in[i];
-		}
-		return res;
-	}
-	
-	public static void main(String[] args) {
-		int[] i = {1,2,3,4};
-		util.Printing.printIntArray(i, null, "original");
-		util.Printing.printIntArray(reverseIntArray(i), null, "reversed");
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/util/ArrayMath.java b/gi/posterior-regularisation/prjava/src/util/ArrayMath.java
deleted file mode 100644
index 398a13a2..00000000
--- a/gi/posterior-regularisation/prjava/src/util/ArrayMath.java
+++ /dev/null
@@ -1,186 +0,0 @@
-package util;
-
-import java.util.Arrays;
-
-public class ArrayMath {
-
-	public static double dotProduct(double[] v1, double[] v2) {
-		assert(v1.length == v2.length);
-		double result = 0;
-		for(int i = 0; i < v1.length; i++)
-			result += v1[i]*v2[i];
-		return result;
-	}
-
-	public static double twoNormSquared(double[] v) {
-		double result = 0;
-		for(double d : v)
-			result += d*d;
-		return result;
-	}
-
-	public static boolean containsInvalid(double[] v) {
-		for(int i = 0; i < v.length; i++)
-			if(Double.isNaN(v[i]) || Double.isInfinite(v[i]))
-				return true;
-		return false;
-	}
-
-
-	
-	public static double safeAdd(double[] toAdd) {
-		// Make sure there are no positive infinities
-		double sum = 0;
-		for(int i = 0; i < toAdd.length; i++) {
-			assert(!(Double.isInfinite(toAdd[i]) && toAdd[i] > 0));
-			assert(!Double.isNaN(toAdd[i]));
-			sum += toAdd[i];
-		}
-		
-		return sum;
-	}
-
-	/* Methods for filling integer and double arrays (of up to four dimensions) with the given value. */
-	
-	public static void set(int[][][][] array, int value) {
-		for(int i = 0; i < array.length; i++) {
-			set(array[i], value);
-		}
-	}
-	
-	public static void set(int[][][] array, int value) {
-		for(int i = 0; i < array.length; i++) {
-			set(array[i], value);
-		}
-	}
-	
-	public static void set(int[][] array, int value) {
-		for(int i = 0; i < array.length; i++) {
-			set(array[i], value);
-		}
-	}
-	
-	public static void set(int[] array, int value) {
-		Arrays.fill(array, value);
-	}
-	
-	
-	public static void set(double[][][][] array, double value) {
-		for(int i = 0; i < array.length; i++) {
-			set(array[i], value);
-		}
-	}
-	
-	public static void set(double[][][] array, double value) {
-		for(int i = 0; i < array.length; i++) {
-			set(array[i], value);
-		}
-	}
-	
-	public static void set(double[][] array, double value) {
-		for(int i = 0; i < array.length; i++) {
-			set(array[i], value);
-		}
-	}
-	
-	public static void set(double[] array, double value) {
-		Arrays.fill(array, value);
-	}
-
-	public static void setEqual(double[][][][] dest, double[][][][] source){
-		for (int i = 0; i < source.length; i++) {
-			setEqual(dest[i],source[i]);
-		}
-	}
-
-	
-	public static void setEqual(double[][][] dest, double[][][] source){
-		for (int i = 0; i < source.length; i++) {
-			set(dest[i],source[i]);
-		}
-	}
-
-	
-	public static void set(double[][] dest, double[][] source){
-		for (int i = 0; i < source.length; i++) {
-			setEqual(dest[i],source[i]);
-		}
-	}
-
-	public static void setEqual(double[] dest, double[] source){
-		System.arraycopy(source, 0, dest, 0, source.length);
-	}
-
-	public static void plusEquals(double[][][][] array, double val){
-		for (int i = 0; i < array.length; i++) {
-			plusEquals(array[i], val);
-		}
-	}	
-	
-	public static void plusEquals(double[][][] array, double val){
-		for (int i = 0; i < array.length; i++) {
-			plusEquals(array[i], val);
-		}
-	}	
-	
-	public static void plusEquals(double[][] array, double val){
-		for (int i = 0; i < array.length; i++) {
-			plusEquals(array[i], val);
-		}
-	}	
-	
-	public static void plusEquals(double[] array, double val){
-		for (int i = 0; i < array.length; i++) {
-			array[i] += val;
-		}
-	}
-
-	
-	public static double sum(double[] array) {
-		double res = 0;
-		for (int i = 0; i < array.length; i++) res += array[i];
-		return res;
-	}
-
-
-	
-	public static  double[][] deepclone(double[][] in){
-		double[][] res = new double[in.length][];
-		for (int i = 0; i < res.length; i++) {
-			res[i] = in[i].clone();
-		}
-		return res;
-	}
-
-	
-	public static  double[][][] deepclone(double[][][] in){
-		double[][][] res = new double[in.length][][];
-		for (int i = 0; i < res.length; i++) {
-			res[i] = deepclone(in[i]);
-		}
-		return res;
-	}
-
-	public static double cosine(double[] a,
-			double[] b) {
-		return (dotProduct(a, b)+1e-5)/(Math.sqrt(dotProduct(a, a)+1e-5)*Math.sqrt(dotProduct(b, b)+1e-5));
-	}
-
-	public static double max(double[] ds) {
-		double max = Double.NEGATIVE_INFINITY;
-		for(double d:ds) max = Math.max(d,max);
-		return max;
-	}
-
-	public static void exponentiate(double[] a) {
-		for (int i = 0; i < a.length; i++) {
-			a[i] = Math.exp(a[i]);
-		}
-	}
-
-	public static int sum(int[] array) {
-		int res = 0;
-		for (int i = 0; i < array.length; i++) res += array[i];
-		return res;
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/util/DifferentiableObjective.java b/gi/posterior-regularisation/prjava/src/util/DifferentiableObjective.java
deleted file mode 100644
index 1ff1ae4a..00000000
--- a/gi/posterior-regularisation/prjava/src/util/DifferentiableObjective.java
+++ /dev/null
@@ -1,14 +0,0 @@
-package util;
-
-public interface DifferentiableObjective {
-
-	public double getValue();
-
-	public void getGradient(double[] gradient);
-
-	public void getParameters(double[] params);
-
-	public void setParameters(double[] newParameters);
-
-	public int getNumParameters();
-}
diff --git a/gi/posterior-regularisation/prjava/src/util/DigammaFunction.java b/gi/posterior-regularisation/prjava/src/util/DigammaFunction.java
deleted file mode 100644
index ff1478ad..00000000
--- a/gi/posterior-regularisation/prjava/src/util/DigammaFunction.java
+++ /dev/null
@@ -1,21 +0,0 @@
-package util;
-
-public class DigammaFunction {
-	public static double expDigamma(double number){
-		if(number==0)return number;
-		return Math.exp(digamma(number));
-	}
-	
-	public static double digamma(double number){
-		if(number > 7){
-			return digammApprox(number-0.5);
-		}else{
-			return digamma(number+1) - 1.0/number;
-		}
-	}
-	
-	private static double digammApprox(double value){
-		return Math.log(value) + 0.04167*Math.pow(value, -2) - 0.00729*Math.pow(value, -4) 
-		+  0.00384*Math.pow(value, -6) - 0.00413*Math.pow(value, -8);
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/util/FileSystem.java b/gi/posterior-regularisation/prjava/src/util/FileSystem.java
deleted file mode 100644
index d7812e40..00000000
--- a/gi/posterior-regularisation/prjava/src/util/FileSystem.java
+++ /dev/null
@@ -1,21 +0,0 @@
-package util;
-
-import java.io.File;
-
-public class FileSystem {
-	public static boolean createDir(String directory) {
-
-		File dir = new File(directory);
-		if (!dir.isDirectory()) {
-			boolean success = dir.mkdirs();
-			if (!success) {
-				System.out.println("Unable to create directory " + directory);
-				return false;
-			}
-			System.out.println("Created directory " + directory);
-		} else {
-			System.out.println("Reusing directory " + directory);
-		}
-		return true;
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/util/InputOutput.java b/gi/posterior-regularisation/prjava/src/util/InputOutput.java
deleted file mode 100644
index da7f71bf..00000000
--- a/gi/posterior-regularisation/prjava/src/util/InputOutput.java
+++ /dev/null
@@ -1,67 +0,0 @@
-package util;
-
-import java.io.BufferedReader;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.OutputStream;
-import java.io.PrintStream;
-import java.io.UnsupportedEncodingException;
-import java.util.Properties;
-import java.util.zip.GZIPInputStream;
-import java.util.zip.GZIPOutputStream;
-
-public class InputOutput {
-
-	/**
-	 * Opens a file either compress with gzip or not compressed.
-	 */
-	public static BufferedReader openReader(String fileName) throws UnsupportedEncodingException, FileNotFoundException, IOException{
-		System.out.println("Reading: " + fileName);
-		BufferedReader reader;
-		fileName = fileName.trim();
-		if(fileName.endsWith("gz")){
-			reader = new BufferedReader(
-			new InputStreamReader(new GZIPInputStream(new FileInputStream(fileName)),"UTF8"));
-		}else{
-			reader = new BufferedReader(new InputStreamReader(
-					new FileInputStream(fileName), "UTF8"));
-		}
-		
-		return reader;
-	}
-	
-	
-	public static PrintStream openWriter(String fileName) 
-	throws UnsupportedEncodingException, FileNotFoundException, IOException{
-		System.out.println("Writting to file: " + fileName);
-		PrintStream writter;
-		fileName = fileName.trim();
-		if(fileName.endsWith("gz")){
-			writter = new PrintStream(new GZIPOutputStream(new FileOutputStream(fileName)),
-					true, "UTF-8");
-
-		}else{
-			writter = new PrintStream(new FileOutputStream(fileName),
-					true, "UTF-8");
-
-		}
-		
-		return writter;
-	}
-	
-	public static Properties readPropertiesFile(String fileName) {
-		Properties properties = new Properties();
-		try {
-			properties.load(new FileInputStream(fileName));
-		} catch (IOException e) {
-			e.printStackTrace();
-			throw new AssertionError("Wrong properties file " + fileName);
-		}
-		System.out.println(properties.toString());
-		
-		return properties;
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/util/LogSummer.java b/gi/posterior-regularisation/prjava/src/util/LogSummer.java
deleted file mode 100644
index 117393b9..00000000
--- a/gi/posterior-regularisation/prjava/src/util/LogSummer.java
+++ /dev/null
@@ -1,86 +0,0 @@
-package util;
-
-import java.lang.Math;
-
-/*
- * Math tool for computing logs of sums, when the terms of the sum are already in log form.
- * (Useful if the terms of the sum are very small numbers.)
- */
-public class LogSummer {
-	
-	private LogSummer() {
-	}
-		
-	/**
-	 * Given log(a) and log(b), computes log(a + b).
-	 * 
-	 * @param  loga log of first sum term
-	 * @param  logb log of second sum term
-	 * @return     log(sum), where sum = a + b
-	 */
-	public static double sum(double loga, double logb) {
-		assert(!Double.isNaN(loga));
-		assert(!Double.isNaN(logb));
-		
-		if(Double.isInfinite(loga))
-			return logb;
-		if(Double.isInfinite(logb))
-			return loga;
-
-		double maxLog;
-		double difference;
-		if(loga > logb) {
-			difference = logb - loga;
-			maxLog = loga;
-		}
-		else {
-			difference = loga - logb;
-			maxLog = logb;
-		}
-
-		return Math.log1p(Math.exp(difference)) + maxLog;
-	}
-
-	/**
-	 * Computes log(exp(array[index]) + b), and
-	 * modifies array[index] to contain this new value.
-	 * 
-	 * @param array array to modify
-	 * @param index index at which to modify
-	 * @param logb  log of the second sum term
-	 */
-	public static void sum(double[] array, int index, double logb) {
-		array[index] = sum(array[index], logb);
-	}
-	
-	/**
-	 * Computes log(a + b + c + ...) from log(a), log(b), log(c), ...
-	 * by recursively splitting the input and delegating to the sum method.
-	 * 
-	 * @param  terms an array containing the log of all the terms for the sum
-	 * @return log(sum), where sum = exp(terms[0]) + exp(terms[1]) + ...
-	 */
-	public static double sumAll(double... terms) {
-		return sumAllHelper(terms, 0, terms.length);
-	}
-	
-	/**
-	 * Computes log(a_0 + a_1 + ...) from a_0 = exp(terms[begin]),
-	 * a_1 = exp(terms[begin + 1]), ..., a_{end - 1 - begin} = exp(terms[end - 1]).
-	 * 
-	 * @param  terms an array containing the log of all the terms for the sum,
-	 *               and possibly some other terms that will not go into the sum
-	 * @return log of the sum of the elements in the [begin, end) region of the terms array
-	 */
-	private static double sumAllHelper(final double[] terms, final int begin, final int end) {
-		int length = end - begin;
-		switch(length) {
-			case 0: return Double.NEGATIVE_INFINITY;
-			case 1: return terms[begin];
-			default:
-				int midIndex = begin + length/2;
-				return sum(sumAllHelper(terms, begin, midIndex), sumAllHelper(terms, midIndex, end));
-		}
-	}
-
-}
\ No newline at end of file
diff --git a/gi/posterior-regularisation/prjava/src/util/MathUtil.java b/gi/posterior-regularisation/prjava/src/util/MathUtil.java
deleted file mode 100644
index 799b1faf..00000000
--- a/gi/posterior-regularisation/prjava/src/util/MathUtil.java
+++ /dev/null
@@ -1,148 +0,0 @@
-package util;
-
-import java.util.Random;
-
-public class MathUtil {
-	public static final boolean closeToOne(double number){
-		return Math.abs(number-1) < 1.E-10;
-	}
-	
-	public static final boolean closeToZero(double number){
-		return Math.abs(number) < 1.E-5;
-	}
-	
-	/**
-	 * Return a ramdom multinominal distribution.
-	 * 
-	 * @param size
-	 * @return
-	 */
-	public static final double[] randomVector(int size, Random r){
-		double[] random = new double[size];
-		double sum=0;
-		for(int i = 0; i < size; i++){
-			double number = r.nextDouble();
-			random[i] = number;
-			sum+=number;
-		}
-		for(int i = 0; i < size; i++){
-			random[i] = random[i]/sum;
-		}
-		return random;
-	}
-	
-	
-
-	public static double sum(double[] ds) {
-		double res = 0;
-		for (int i = 0; i < ds.length; i++) {
-			res+=ds[i];
-		}
-		return res;
-	}
-
-	public static double max(double[] ds) {
-		double res = Double.NEGATIVE_INFINITY;
-		for (int i = 0; i < ds.length; i++) {
-			res = Math.max(res, ds[i]);
-		}
-		return res;
-	}
-
-	public static double min(double[] ds) {
-		double res = Double.POSITIVE_INFINITY;
-		for (int i = 0; i < ds.length; i++) {
-			res = Math.min(res, ds[i]);
-		}
-		return res;
-	}
-
-	
-	public static double KLDistance(double[] p, double[] q) {
-		int len = p.length;
-		double kl = 0;
-		for (int j = 0; j < len; j++) {
-				if (p[j] == 0 || q[j] == 0) {
-					continue;
-				} else {
-					kl += q[j] * Math.log(q[j] / p[j]);
-				}
-
-		}
-		return kl;
-	}
-	
-	public static double L2Distance(double[] p, double[] q) {
-		int len = p.length;
-		double l2 = 0;
-		for (int j = 0; j < len; j++) {
-				if (p[j] == 0 || q[j] == 0) {
-					continue;
-				} else {
-					l2 += (q[j] - p[j])*(q[j] - p[j]);
-				}
-
-		}
-		return Math.sqrt(l2);
-	}
-	
-	public static double L1Distance(double[] p, double[] q) {
-		int len = p.length;
-		double l1 = 0;
-		for (int j = 0; j < len; j++) {
-				if (p[j] == 0 || q[j] == 0) {
-					continue;
-				} else {
-					l1 += Math.abs(q[j] - p[j]);
-				}
-
-		}
-		return l1;
-	}
-
-	public static double dot(double[] ds, double[] ds2) {
-		double res = 0;
-		for (int i = 0; i < ds2.length; i++) {
-			res+= ds[i]*ds2[i];
-		}
-		return res;
-	}
-	
-	public static double expDigamma(double number){
-		return Math.exp(digamma(number));
-	}
-	
-	public static double digamma(double number){
-		if(number > 7){
-			return digammApprox(number-0.5);
-		}else{
-			return digamma(number+1) - 1.0/number;
-		}
-	}
-	
-	private static double digammApprox(double value){
-		return Math.log(value) + 0.04167*Math.pow(value, -2) - 0.00729*Math.pow(value, -4) 
-		+  0.00384*Math.pow(value, -6) - 0.00413*Math.pow(value, -8);
-	}
-
-	public static double eulerGamma = 0.57721566490152386060651209008240243;
-	// FIXME -- so far just the initialization from Minka's paper "Estimating a Dirichlet distribution". 
-	public static double invDigamma(double y) {
-		if (y>= -2.22) return Math.exp(y)+0.5;
-		return -1.0/(y+eulerGamma);
-	}
-
-	
-	
-	public static void main(String[] args) {
-		for(double i = 0; i < 10 ; i+=0.1){
-			System.out.println(i+"\t"+expDigamma(i)+"\t"+(i-0.5));
-		}
-//		double gammaValue = (expDigamma(3)/expDigamma(10) + expDigamma(3)/expDigamma(10) + expDigamma(4)/expDigamma(10));
-//		double normalValue = 3/10+3/4+10/10;
-//		System.out.println("Gamma " + gammaValue + " normal " + normalValue);
-	}
-
-	
-	
-}
diff --git a/gi/posterior-regularisation/prjava/src/util/Matrix.java b/gi/posterior-regularisation/prjava/src/util/Matrix.java
deleted file mode 100644
index 8fb6d911..00000000
--- a/gi/posterior-regularisation/prjava/src/util/Matrix.java
+++ /dev/null
@@ -1,16 +0,0 @@
-package util;
-
-public class Matrix {
-	int x;
-	int y;
-	double[][] values;
-	
-	public Matrix(int x, int y){
-		this.x = x;
-		this.y=y;
-		values = new double[x][y];
-	}
-	
-	
-	
-}
diff --git a/gi/posterior-regularisation/prjava/src/util/MemoryTracker.java b/gi/posterior-regularisation/prjava/src/util/MemoryTracker.java
deleted file mode 100644
index 83a65611..00000000
--- a/gi/posterior-regularisation/prjava/src/util/MemoryTracker.java
+++ /dev/null
@@ -1,47 +0,0 @@
-package util;
-
-
-public class MemoryTracker {
-	
-	double initM,finalM;
-	boolean start = false,finish = false;
-	
-	public MemoryTracker(){
-		
-	}
-	
-	public void start(){
-		System.gc();
-	    System.gc();
-	    System.gc();
-	    initM = (Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory())/(1024*1024);  
-	    start = true;
-	}
-	
-	public void finish(){
-		if(!start){
-			throw new RuntimeException("Canot stop before starting");
-		}
-		System.gc();
-	    System.gc();
-	    System.gc();
-	    finalM = (Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory())/(1024*1024);  
-	    finish = true;
-	}
-	
-	public String print(){
-		if(!finish){
-			throw new RuntimeException("Canot print before stopping");
-		}
-		return "Used: " + (finalM - initM) + "MB";
-	}
-	
-	public void clear(){
-		initM = 0;
-		finalM = 0;
-		finish = false;
-		start = false;
-	}
-	
-	
-}
diff --git a/gi/posterior-regularisation/prjava/src/util/Pair.java b/gi/posterior-regularisation/prjava/src/util/Pair.java
deleted file mode 100644
index 7b1f108d..00000000
--- a/gi/posterior-regularisation/prjava/src/util/Pair.java
+++ /dev/null
@@ -1,31 +0,0 @@
-package util;
-
-public class Pair<O1, O2> {
-	public O1 _first;
-	public O2 _second;
-
-	public final O1 first() {
-		return _first;
-	}
-
-	public final O2 second() {
-		return _second;
-	}
-
-	public final void setFirst(O1 value){
-		_first = value;
-	}
-	
-	public final void setSecond(O2 value){
-		_second = value;
-	}
-	
-	public Pair(O1 first, O2 second) {
-		_first = first;
-		_second = second;
-	}
-
-	public String toString(){
-		return _first + " " + _second; 
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/util/Printing.java b/gi/posterior-regularisation/prjava/src/util/Printing.java
deleted file mode 100644
index 14fcbe91..00000000
--- a/gi/posterior-regularisation/prjava/src/util/Printing.java
+++ /dev/null
@@ -1,158 +0,0 @@
-package util;
-
-public class Printing {
-	static java.text.DecimalFormat fmt = new java.text.DecimalFormat();
-
-	public static String padWithSpace(String s, int len){
-		StringBuffer sb = new StringBuffer();
-		while(sb.length() +s.length() < len){
-			sb.append(" ");
-		}
-		sb.append(s);
-		return sb.toString();
-	}
-	
-	public static String prettyPrint(double d, String patt, int len) {
-		fmt.applyPattern(patt);
-		String s = fmt.format(d);
-		while (s.length() < len) {
-			s = " " + s;
-		}
-		return s;
-	}
-	
-	public static  String formatTime(long duration) {
-		StringBuilder sb = new StringBuilder();
-		double d = duration / 1000;
-		fmt.applyPattern("00");
-		sb.append(fmt.format((int) (d / (60 * 60))) + ":");
-		d -= ((int) d / (60 * 60)) * 60 * 60;
-		sb.append(fmt.format((int) (d / 60)) + ":");
-		d -= ((int) d / 60) * 60;
-		fmt.applyPattern("00.0");
-		sb.append(fmt.format(d));
-		return sb.toString();
-	}
-	
-	
-	public static String doubleArrayToString(double[] array, String[] labels, String arrayName) {
-		StringBuffer res = new StringBuffer();
-		res.append(arrayName);
-		res.append("\n");
-		for (int i = 0; i < array.length; i++) {
-			if (labels == null){
-				res.append(i+"       \t");
-			}else{
-				res.append(labels[i]+     "\t");
-			}
-		}
-		res.append("sum\n");
-		double sum = 0;
-		for (int i = 0; i < array.length; i++) {
-			res.append(prettyPrint(array[i],
-					"0.00000E00", 8) + "\t");
-			sum+=array[i];
-		}
-		res.append(prettyPrint(sum,
-				"0.00000E00", 8)+"\n");
-		return res.toString();
-	}
-	
-	
-	
-	public static void printDoubleArray(double[] array, String labels[], String arrayName) {
-		System.out.println(doubleArrayToString(array, labels,arrayName));
-	}
-	
-	
-	public static String doubleArrayToString(double[][] array, String[] labels1, String[] labels2,
-			String arrayName){
-		StringBuffer res = new StringBuffer();
-		res.append(arrayName);
-		res.append("\n\t");
-		//Calculates the column sum to keeps the sums
-		double[] sums = new double[array[0].length+1];
-		//Prints rows headings
-		for (int i = 0; i < array[0].length; i++) {
-			if (labels1 == null){
-				res.append(i+"        \t");
-			}else{
-				res.append(labels1[i]+"        \t");
-			}
-		}
-		res.append("sum\n");
-		double sum = 0;
-		//For each row print heading
-		for (int i = 0; i < array.length; i++) {
-			if (labels2 == null){
-				res.append(i+"\t");
-			}else{
-				res.append(labels2[i]+"\t");
-			}
-			//Print values for that row
-			for (int j = 0; j < array[0].length; j++) {
-				res.append(" " + prettyPrint(array[i][j],
-						"0.00000E00", 8) + "\t");
-				sums[j] += array[i][j]; 
-				sum+=array[i][j]; //Sum all values of that row
-			}
-			//Print row sum
-			res.append(prettyPrint(sum,"0.00000E00", 8)+"\n");
-			sums[array[0].length]+=sum;
-			sum=0;
-		}
-		res.append("sum\t");
-		//Print values for colums sum
-		for (int i = 0; i < array[0].length+1; i++) {
-			res.append(prettyPrint(sums[i],"0.00000E00", 8)+"\t");
-		}
-		res.append("\n");
-		return res.toString();
-	}
-	
-	public static void printDoubleArray(double[][] array, String[] labels1, String[] labels2
-			, String arrayName) {
-		System.out.println(doubleArrayToString(array, labels1,labels2,arrayName));
-	}
-	
-	
-	public static void printIntArray(int[][] array, String[] labels1, String[] labels2, String arrayName,
-			int size1, int size2) {
-		System.out.println(arrayName);
-		for (int i = 0; i < size1; i++) {
-			for (int j = 0; j < size2; j++) {
-				System.out.print(" " + array[i][j] +  " ");
-
-			}
-			System.out.println();
-		}
-		System.out.println();
-	}
-	
-	public static String intArrayToString(int[] array, String[] labels, String arrayName) {
-		StringBuffer res = new StringBuffer();
-		res.append(arrayName);
-		for (int i = 0; i < array.length; i++) {
-			res.append(" " + array[i] + " ");
-			
-		}
-		res.append("\n");
-		return res.toString();
-	}
-	
-	public static void printIntArray(int[] array, String[] labels, String arrayName) {
-		System.out.println(intArrayToString(array, labels,arrayName));
-	}
-	
-	public static String toString(double[][] d){
-		StringBuffer sb = new StringBuffer();
-		for (int i = 0; i < d.length; i++) {
-			for (int j = 0; j < d[0].length; j++) {
-				sb.append(prettyPrint(d[i][j], "0.00E0", 10));
-			}
-			sb.append("\n");
-		}
-		return sb.toString();
-	}
-	
-}
diff --git a/gi/posterior-regularisation/prjava/src/util/Sorters.java b/gi/posterior-regularisation/prjava/src/util/Sorters.java
deleted file mode 100644
index 836444e5..00000000
--- a/gi/posterior-regularisation/prjava/src/util/Sorters.java
+++ /dev/null
@@ -1,39 +0,0 @@
-package util;
-
-import java.util.Comparator;
-
-public class Sorters {
-	public static class sortWordsCounts implements Comparator{
-		
-		/**
-		 * Sorter for a pair of word id, counts. Sort ascending by counts
-		 */
-		public int compare(Object arg0, Object arg1) {
-			Pair<Integer,Integer> p1 = (Pair<Integer,Integer>)arg0;
-			Pair<Integer,Integer> p2 = (Pair<Integer,Integer>)arg1;
-			if(p1.second() > p2.second()){
-				return 1;
-			}else{
-				return -1;
-			}
-		}
-		
-	}
-	
-public static class sortWordsDouble implements Comparator{
-		
-		/**
-		 * Sorter for a pair of word id, counts. Sort by counts
-		 */
-		public int compare(Object arg0, Object arg1) {
-			Pair<Integer,Double> p1 = (Pair<Integer,Double>)arg0;
-			Pair<Integer,Double> p2 = (Pair<Integer,Double>)arg1;
-			if(p1.second() < p2.second()){
-				return 1;
-			}else{
-				return -1;
-			}
-		}
-		
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/train-PR-cluster.sh b/gi/posterior-regularisation/prjava/train-PR-cluster.sh
deleted file mode 100755
index 67552c00..00000000
--- a/gi/posterior-regularisation/prjava/train-PR-cluster.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/bin/sh
-
-d=`dirname $0`
-java -ea -Xmx30g -cp $d/prjava.jar:$d/lib/trove-2.0.2.jar:$d/lib/optimization.jar:$d/lib/jopt-simple-3.2.jar:$d/lib/commons-math-2.1.jar phrase.Trainer $*
diff --git a/gi/posterior-regularisation/projected_gradient.cc b/gi/posterior-regularisation/projected_gradient.cc
deleted file mode 100644
index f7c39817..00000000
--- a/gi/posterior-regularisation/projected_gradient.cc
+++ /dev/null
@@ -1,87 +0,0 @@
-//
-// Minimises given functional using the projected gradient method. Based on
-// algorithm and demonstration example in Linear and Nonlinear Programming,
-// Luenberger and Ye, 3rd ed., p 370.
-//
-
-#include "invert.hh"
-#include <iostream>
-
-using namespace std;
-
-double 
-f(double x1, double x2, double x3, double x4)
-{
-    return x1 * x1 + x2 * x2 + x3 * x3 + x4 * x4 - 2 * x1 - 3 * x4;
-}
-
-ublas::vector<double> 
-g(double x1, double x2, double x3, double x4)
-{
-    ublas::vector<double> v(4);
-    v(0) = 2 * x1 - 2;
-    v(1) = 2 * x2;
-    v(2) = 2 * x3;
-    v(3) = 2 * x4 - 3;
-    return v;
-}
-
-ublas::matrix<double> 
-activeConstraints(double x1, double x2, double x3, double x4)
-{
-    int n = 2;
-    if (x1 == 0) ++n;
-    if (x2 == 0) ++n;
-    if (x3 == 0) ++n;
-    if (x4 == 0) ++n;
-
-    ublas::matrix<double> a(n,4);
-    a(0, 0) = 2; a(0, 1) = 1; a(0, 2) = 1; a(0, 3) = 4;
-    a(1, 0) = 1; a(1, 1) = 1; a(1, 2) = 2; a(1, 3) = 1;
-
-    int c = 2;
-    if (x1 == 0) a(c++, 0) = 1;
-    if (x2 == 0) a(c++, 1) = 1;
-    if (x3 == 0) a(c++, 2) = 1;
-    if (x4 == 0) a(c++, 3) = 1;
-
-    return a;
-}
-
-ublas::matrix<double>
-projection(const ublas::matrix<double> &a)
-{
-    ublas::matrix<double> aT = ublas::trans(a);
-    ublas::matrix<double> inv(a.size1(), a.size1());
-    bool ok = invert_matrix(ublas::matrix<double>(ublas::prod(a, aT)), inv);
-    assert(ok && "Failed to invert matrix");
-    return ublas::identity_matrix<double>(4) - 
-        ublas::prod(aT, ublas::matrix<double>(ublas::prod(inv, a)));
-}
-
-int main(int argc, char *argv[])
-{
-    double x1 = 2, x2 = 2, x3 = 1, x4 = 0;
-
-    double fval = f(x1, x2, x3, x4);
-    cout << "f = " << fval << endl;
-    ublas::vector<double> grad = g(x1, x2, x3, x4);
-    cout << "g = " << grad << endl;
-    ublas::matrix<double> A = activeConstraints(x1, x2, x3, x4);
-    cout << "A = " << A << endl;
-    ublas::matrix<double> P = projection(A);
-    cout << "P = " << P << endl;
-    // the direction of movement
-    ublas::vector<double> d = prod(P, grad);
-    cout << "d = " << (d / d(0)) << endl;
-
-    // special case for d = 0
-
-    // next solve for limits on the line search
-
-    // then use golden rule technique between these values (if bounded)
-
-    // or simple Armijo's rule technique
-
-    return 0;
-}
diff --git a/gi/posterior-regularisation/simplex_pg.py b/gi/posterior-regularisation/simplex_pg.py
deleted file mode 100644
index 5da796d3..00000000
--- a/gi/posterior-regularisation/simplex_pg.py
+++ /dev/null
@@ -1,55 +0,0 @@
-#
-# Following Leunberger and Ye, Linear and Nonlinear Progamming, 3rd ed. p367
-# "The gradient projection method"
-# applied to an equality constraint for a simplex.
-#
-#   min f(x)
-#   s.t. x >= 0, sum_i x = d
-#
-# FIXME: enforce the positivity constraint - a limit on the line search?
-#
-
-from numpy import *
-from scipy import *
-from linesearch import line_search
-# local copy of scipy's Amijo line_search - wasn't enforcing alpha max correctly
-import sys
-
-dims = 4
-
-def f(x):
-    fv = x[0]*x[0] + x[1]*x[1] + x[2]*x[2] + x[3]*x[3] - 2*x[0] - 3*x[3]
-    # print 'evaluating f at', x, 'value', fv
-    return fv
-
-def g(x):
-    return array([2*x[0] - 2, 2*x[1], 2*x[2], 2*x[3]-3])
-
-def pg(x):
-    gv = g(x)
-    return gv - sum(gv) / dims
-
-x = ones(dims) / dims
-old_fval = None
-
-while True:
-    fv = f(x)
-    gv = g(x)
-    dv = pg(x)
-
-    print 'x', x, 'f', fv, 'g', gv, 'd', dv
-
-    if old_fval == None:
-        old_fval = fv + 0.1
-
-    # solve for maximum step size i.e. when positivity constraints kick in
-    # x - alpha d = 0   => alpha = x/d
-    amax = max(x/dv)
-    if amax < 1e-8: break
-
-    stuff = line_search(f, pg, x, -dv, dv, fv, old_fval, amax=amax)
-    alpha = stuff[0] # Nb. can avoid next evaluation of f,g,d using 'stuff'
-    if alpha < 1e-8: break
-    x -= alpha * dv
-
-    old_fval = fv
diff --git a/gi/posterior-regularisation/split-languages.py b/gi/posterior-regularisation/split-languages.py
deleted file mode 100755
index 206da661..00000000
--- a/gi/posterior-regularisation/split-languages.py
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/usr/bin/python
-
-import sys
-
-sout = open(sys.argv[1], 'w')
-tout = open(sys.argv[2], 'w')
-for line in sys.stdin:
-	phrase, contexts = line.rstrip().split('\t')
-	sp, tp = phrase.split(' <SPLIT> ')
-	sout.write('%s\t' % sp)
-	tout.write('%s\t' % tp)
-	parts = contexts.split(' ||| ')
-	for i in range(0, len(parts), 2):
-		sc, tc = parts[i].split(' <SPLIT> ')
-		if i != 0:
-			sout.write(' ||| ')
-			tout.write(' ||| ')
-		sout.write('%s ||| %s' % (sc, parts[i+1]))
-		tout.write('%s ||| %s' % (tc, parts[i+1]))
-	sout.write('\n')
-	tout.write('\n')
-sout.close()
-tout.close()
diff --git a/gi/posterior-regularisation/train_pr_agree.py b/gi/posterior-regularisation/train_pr_agree.py
deleted file mode 100644
index 9d41362d..00000000
--- a/gi/posterior-regularisation/train_pr_agree.py
+++ /dev/null
@@ -1,400 +0,0 @@
-import sys
-import scipy.optimize
-from scipy.stats import geom
-from numpy import *
-from numpy.random import random, seed
-
-style = sys.argv[1]
-if len(sys.argv) >= 3:
-     seed(int(sys.argv[2]))
-
-#
-# Step 1: load the concordance counts
-# 
-
-edges = []
-word_types = {}
-phrase_types = {}
-context_types = {}
-
-for line in sys.stdin:
-    phrase, rest = line.strip().split('\t')
-    ptoks = tuple(map(lambda t: word_types.setdefault(t, len(word_types)), phrase.split()))
-    pid = phrase_types.setdefault(ptoks, len(phrase_types))
-
-    parts = rest.split('|||')
-    for i in range(0, len(parts), 2):
-        context, count = parts[i:i+2]
-
-        ctx = filter(lambda x: x != '<PHRASE>', context.split())
-        ctoks = tuple(map(lambda t: word_types.setdefault(t, len(word_types)), ctx))
-        cid = context_types.setdefault(ctoks, len(context_types))
-
-        cnt = int(count.strip()[2:])
-        edges.append((pid, cid, cnt))
-
-word_type_list = [None] * len(word_types)
-for typ, index in word_types.items():
-    word_type_list[index] = typ
-
-phrase_type_list = [None] * len(phrase_types)
-for typ, index in phrase_types.items():
-    phrase_type_list[index] = typ
-
-context_type_list = [None] * len(context_types)
-for typ, index in context_types.items():
-    context_type_list[index] = typ
-
-num_tags = 5
-num_types = len(word_types)
-num_phrases = len(phrase_types)
-num_contexts = len(context_types)
-num_edges = len(edges)
-
-print 'Read in', num_edges, 'edges', num_phrases, 'phrases', num_contexts, 'contexts and', num_types, 'word types'
-
-#
-# Step 2:  expectation maximisation 
-#
-
-def normalise(a):
-    return a / float(sum(a))
-
-class PhraseToContextModel:
-    def __init__(self):
-        # Pr(tag | phrase)
-        self.tagDist = [normalise(random(num_tags)+1) for p in range(num_phrases)]
-        # Pr(context at pos i = w | tag) indexed by i, tag, word
-        self.contextWordDist = [[normalise(random(num_types)+1) for t in range(num_tags)] for i in range(4)]
-
-    def prob(self, pid, cid):
-        # return distribution p(tag, context | phrase) as vector of length |tags|
-        context = context_type_list[cid]
-        dist = zeros(num_tags)
-        for t in range(num_tags):
-            prob = self.tagDist[pid][t]
-            for k, tokid in enumerate(context):
-                prob *= self.contextWordDist[k][t][tokid]
-            dist[t] = prob
-        return dist
-
-    def expectation_maximisation_step(self, lamba=None):
-        tagCounts = zeros((num_phrases, num_tags))
-        contextWordCounts = zeros((4, num_tags, num_types))
-
-        # E-step
-        llh = 0
-        for pid, cid, cnt in edges:
-            q = self.prob(pid, cid)
-            z = sum(q)
-            q /= z
-            llh += log(z)
-            context = context_type_list[cid]
-            if lamba != None:
-                q *= exp(lamba)
-                q /= sum(q)
-            for t in range(num_tags):
-                tagCounts[pid][t] += cnt * q[t]
-            for i in range(4):
-                for t in range(num_tags):
-                    contextWordCounts[i][t][context[i]] += cnt * q[t]
-
-        # M-step
-        for p in range(num_phrases):
-            self.tagDist[p] = normalise(tagCounts[p])
-        for i in range(4):
-            for t in range(num_tags):
-                self.contextWordDist[i][t] = normalise(contextWordCounts[i,t])
-
-        return llh
-
-class ContextToPhraseModel:
-    def __init__(self):
-        # Pr(tag | context) = Multinomial
-        self.tagDist = [normalise(random(num_tags)+1) for p in range(num_contexts)]
-        # Pr(phrase = w | tag) = Multinomial
-        self.phraseSingleDist = [normalise(random(num_types)+1) for t in range(num_tags)]
-        # Pr(phrase_1 = w | tag) = Multinomial
-        self.phraseLeftDist = [normalise(random(num_types)+1) for t in range(num_tags)]
-        # Pr(phrase_-1 = w | tag) = Multinomial
-        self.phraseRightDist = [normalise(random(num_types)+1) for t in range(num_tags)]
-        # Pr(|phrase| = l | tag) = Geometric
-        self.phraseLengthDist = [0.5] * num_tags
-        # n.b. internal words for phrases of length >= 3 are drawn from uniform distribution
-
-    def prob(self, pid, cid):
-        # return distribution p(tag, phrase | context) as vector of length |tags|
-        phrase = phrase_type_list[pid]
-        dist = zeros(num_tags)
-        for t in range(num_tags):
-            prob = self.tagDist[cid][t]
-            f = self.phraseLengthDist[t]
-            prob *= geom.pmf(len(phrase), f)
-            if len(phrase) == 1:
-                prob *= self.phraseSingleDist[t][phrase[0]]
-            else:
-                prob *= self.phraseLeftDist[t][phrase[0]]
-                prob *= self.phraseRightDist[t][phrase[-1]]
-            dist[t] = prob
-        return dist
-
-    def expectation_maximisation_step(self, lamba=None):
-        tagCounts = zeros((num_contexts, num_tags))
-        phraseSingleCounts = zeros((num_tags, num_types))
-        phraseLeftCounts = zeros((num_tags, num_types))
-        phraseRightCounts = zeros((num_tags, num_types))
-        phraseLength = zeros(num_types)
-
-        # E-step
-        llh = 0
-        for pid, cid, cnt in edges:
-            q = self.prob(pid, cid)
-            z = sum(q)
-            q /= z
-            llh += log(z)
-            if lamba != None:
-                q *= exp(lamba)
-                q /= sum(q)
-            #print 'p', phrase_type_list[pid], 'c', context_type_list[cid], 'q', q
-            phrase = phrase_type_list[pid]
-            for t in range(num_tags):
-                tagCounts[cid][t] += cnt * q[t]
-                phraseLength[t] += cnt * len(phrase) * q[t]
-                if len(phrase) == 1:
-                    phraseSingleCounts[t][phrase[0]] += cnt * q[t]
-                else:
-                    phraseLeftCounts[t][phrase[0]] += cnt * q[t]
-                    phraseRightCounts[t][phrase[-1]] += cnt * q[t]
-
-        # M-step
-        for t in range(num_tags):
-            self.phraseLengthDist[t] = min(max(sum(tagCounts[:,t]) / phraseLength[t], 1e-6), 1-1e-6)
-            self.phraseSingleDist[t] = normalise(phraseSingleCounts[t])
-            self.phraseLeftDist[t] = normalise(phraseLeftCounts[t])
-            self.phraseRightDist[t] = normalise(phraseRightCounts[t])
-        for c in range(num_contexts):
-            self.tagDist[c] = normalise(tagCounts[c])
-
-        #print 't', self.tagDist
-        #print 'l', self.phraseLengthDist
-        #print 's', self.phraseSingleDist
-        #print 'L', self.phraseLeftDist
-        #print 'R', self.phraseRightDist
-
-        return llh
-
-class ProductModel:
-    """
-    WARNING: I haven't verified the maths behind this model. It's quite likely to be incorrect.
-    """
-
-    def __init__(self):
-        self.pcm = PhraseToContextModel()
-        self.cpm = ContextToPhraseModel()
-
-    def prob(self, pid, cid):
-        p1 = self.pcm.prob(pid, cid)
-        p2 = self.cpm.prob(pid, cid)
-        return (p1 / sum(p1)) * (p2 / sum(p2))
-
-    def expectation_maximisation_step(self):
-        tagCountsGivenPhrase = zeros((num_phrases, num_tags))
-        contextWordCounts = zeros((4, num_tags, num_types))
-
-        tagCountsGivenContext = zeros((num_contexts, num_tags))
-        phraseSingleCounts = zeros((num_tags, num_types))
-        phraseLeftCounts = zeros((num_tags, num_types))
-        phraseRightCounts = zeros((num_tags, num_types))
-        phraseLength = zeros(num_types)
-
-        kl = llh1 = llh2 = 0
-        for pid, cid, cnt in edges:
-            p1 = self.pcm.prob(pid, cid)
-            llh1 += log(sum(p1)) * cnt
-            p2 = self.cpm.prob(pid, cid)
-            llh2 += log(sum(p2)) * cnt
-
-            q = (p1 / sum(p1)) * (p2 / sum(p2))
-            kl += log(sum(q)) * cnt
-            qi = sqrt(q)
-            qi /= sum(qi)
-
-            phrase = phrase_type_list[pid]
-            context = context_type_list[cid]
-            for t in range(num_tags):
-                tagCountsGivenPhrase[pid][t] += cnt * qi[t]
-                tagCountsGivenContext[cid][t] += cnt * qi[t]
-                phraseLength[t] += cnt * len(phrase) * qi[t]
-                if len(phrase) == 1:
-                    phraseSingleCounts[t][phrase[0]] += cnt * qi[t]
-                else:
-                    phraseLeftCounts[t][phrase[0]] += cnt * qi[t]
-                    phraseRightCounts[t][phrase[-1]] += cnt * qi[t]
-                for i in range(4):
-                    contextWordCounts[i][t][context[i]] += cnt * qi[t]
-
-        kl *= -2
-
-        for t in range(num_tags):
-            for i in range(4):
-                self.pcm.contextWordDist[i][t] = normalise(contextWordCounts[i,t])
-            self.cpm.phraseLengthDist[t] = min(max(sum(tagCountsGivenContext[:,t]) / phraseLength[t], 1e-6), 1-1e-6)
-            self.cpm.phraseSingleDist[t] = normalise(phraseSingleCounts[t])
-            self.cpm.phraseLeftDist[t] = normalise(phraseLeftCounts[t])
-            self.cpm.phraseRightDist[t] = normalise(phraseRightCounts[t])
-        for p in range(num_phrases):
-            self.pcm.tagDist[p] = normalise(tagCountsGivenPhrase[p])
-        for c in range(num_contexts):
-            self.cpm.tagDist[c] = normalise(tagCountsGivenContext[c])
-
-        # return the overall objective
-        return llh1 + llh2 + kl
-
-class RegularisedProductModel:
-    # as above, but with a slack regularisation term which kills the
-    # closed-form solution for the E-step
-
-    def __init__(self, epsilon):
-        self.pcm = PhraseToContextModel()
-        self.cpm = ContextToPhraseModel()
-        self.epsilon = epsilon
-        self.lamba = zeros(num_tags)
-
-    def prob(self, pid, cid):
-        p1 = self.pcm.prob(pid, cid)
-        p2 = self.cpm.prob(pid, cid)
-        return (p1 / sum(p1)) * (p2 / sum(p2))
-
-    def dual(self, lamba):
-        return self.logz(lamba) + self.epsilon * dot(lamba, lamba) ** 0.5
-
-    def dual_gradient(self, lamba):
-        return self.expected_features(lamba) + self.epsilon * 2 * lamba
-
-    def expectation_maximisation_step(self):
-        # PR-step: optimise lambda to minimise log(z_lambda) + eps ||lambda||_2
-        self.lamba = scipy.optimize.fmin_slsqp(self.dual, self.lamba,
-                                bounds=[(0, 1e100)] * num_tags,
-                                fprime=self.dual_gradient, iprint=1)
-
-        # E,M-steps: collect expected counts under q_lambda and normalise
-        llh1 = self.pcm.expectation_maximisation_step(self.lamba)
-        llh2 = self.cpm.expectation_maximisation_step(-self.lamba)
-
-        # return the overall objective: llh - KL(q||p1.p2)
-        # llh = llh1 + llh2
-        # kl = sum q log q / p1 p2 = sum q { lambda . phi } - log Z
-        return llh1 + llh2 + self.logz(self.lamba) \
-            - dot(self.lamba, self.expected_features(self.lamba))
-
-    def logz(self, lamba):
-        lz = 0
-        for pid, cid, cnt in edges:
-            p1 = self.pcm.prob(pid, cid)
-            z1 = dot(p1 / sum(p1), exp(lamba))
-            lz += log(z1) * cnt
-
-            p2 = self.cpm.prob(pid, cid)
-            z2 = dot(p2 / sum(p2), exp(-lamba))
-            lz += log(z2) * cnt
-        return lz
-
-    def expected_features(self, lamba):
-        fs = zeros(num_tags)
-        for pid, cid, cnt in edges:
-            p1 = self.pcm.prob(pid, cid)
-            q1 = (p1 / sum(p1)) * exp(lamba)
-            fs += cnt * q1 / sum(q1)
-
-            p2 = self.cpm.prob(pid, cid)
-            q2 = (p2 / sum(p2)) * exp(-lamba)
-            fs -= cnt * q2 / sum(q2)
-        return fs
-
-
-class InterpolatedModel:
-    def __init__(self, epsilon):
-        self.pcm = PhraseToContextModel()
-        self.cpm = ContextToPhraseModel()
-        self.epsilon = epsilon
-        self.lamba = zeros(num_tags)
-
-    def prob(self, pid, cid):
-        p1 = self.pcm.prob(pid, cid)
-        p2 = self.cpm.prob(pid, cid)
-        return (p1 + p2) / 2
-
-    def dual(self, lamba):
-        return self.logz(lamba) + self.epsilon * dot(lamba, lamba) ** 0.5
-
-    def dual_gradient(self, lamba):
-        return self.expected_features(lamba) + self.epsilon * 2 * lamba
-
-    def expectation_maximisation_step(self):
-        # PR-step: optimise lambda to minimise log(z_lambda) + eps ||lambda||_2
-        self.lamba = scipy.optimize.fmin_slsqp(self.dual, self.lamba,
-                                bounds=[(0, 1e100)] * num_tags,
-                                fprime=self.dual_gradient, iprint=2)
-
-        # E,M-steps: collect expected counts under q_lambda and normalise
-        llh1 = self.pcm.expectation_maximisation_step(self.lamba)
-        llh2 = self.cpm.expectation_maximisation_step(self.lamba)
-
-        # return the overall objective: llh1 + llh2 - KL(q||p1.p2)
-        # kl = sum_y q log q / 0.5 * (p1 + p2) = sum_y q(y) { -lambda . phi(y) } - log Z
-        #    = -log Z + lambda . (E_q1[-phi] + E_q2[-phi]) / 2
-        kl = -self.logz(self.lamba) + dot(self.lamba, self.expected_features(self.lamba))
-        return llh1 + llh2 - kl, llh1, llh2, kl
-        # FIXME: KL comes out negative...
-
-    def logz(self, lamba):
-        lz = 0
-        for pid, cid, cnt in edges:
-            p1 = self.pcm.prob(pid, cid)
-            q1 = p1 / sum(p1) * exp(-lamba)
-            q1z = sum(q1)
-
-            p2 = self.cpm.prob(pid, cid)
-            q2 = p2 / sum(p2) * exp(-lamba)
-            q2z = sum(q2)
-
-            lz += log(0.5 * (q1z + q2z)) * cnt
-        return lz
-
-    # z = 1/2 * (sum_y p1(y|x) exp (-lambda . phi(y)) + sum_y p2(y|x) exp (-lambda . phi(y)))
-    #   = 1/2 (z1 + z2)
-    # d (log z) / dlambda = 1/2 (E_q1 [ -phi ] + E_q2 [ -phi ] )
-    def expected_features(self, lamba):
-        fs = zeros(num_tags)
-        for pid, cid, cnt in edges:
-            p1 = self.pcm.prob(pid, cid)
-            q1 = (p1 / sum(p1)) * exp(-lamba)
-            fs -= 0.5 * cnt * q1 / sum(q1)
-
-            p2 = self.cpm.prob(pid, cid)
-            q2 = (p2 / sum(p2)) * exp(-lamba)
-            fs -= 0.5 * cnt * q2 / sum(q2)
-        return fs
-
-if style == 'p2c':
-    m = PhraseToContextModel()
-elif style == 'c2p':
-    m = ContextToPhraseModel()
-elif style == 'prod':
-    m = ProductModel()
-elif style == 'prodslack':
-    m = RegularisedProductModel(0.5)
-elif style == 'sum':
-    m = InterpolatedModel(0.5)
-
-for iteration in range(30):
-    obj = m.expectation_maximisation_step()
-    print 'iteration', iteration, 'objective', obj
-
-for pid, cid, cnt in edges:
-    p = m.prob(pid, cid)
-    phrase = phrase_type_list[pid]
-    phrase_str = ' '.join(map(word_type_list.__getitem__, phrase))
-    context = context_type_list[cid]
-    context_str = ' '.join(map(word_type_list.__getitem__, context))
-    print '%s\t%s ||| C=%d' % (phrase_str, context_str, argmax(p))
diff --git a/gi/posterior-regularisation/train_pr_global.py b/gi/posterior-regularisation/train_pr_global.py
deleted file mode 100644
index 8521bccb..00000000
--- a/gi/posterior-regularisation/train_pr_global.py
+++ /dev/null
@@ -1,296 +0,0 @@
-import sys
-import scipy.optimize
-from numpy import *
-from numpy.random import random
-
-#
-# Step 1: load the concordance counts
-# 
-
-edges_phrase_to_context = []
-edges_context_to_phrase = []
-types = {}
-context_types = {}
-num_edges = 0
-
-for line in sys.stdin:
-    phrase, rest = line.strip().split('\t')
-    parts = rest.split('|||')
-    edges_phrase_to_context.append((phrase, []))
-    for i in range(0, len(parts), 2):
-        context, count = parts[i:i+2]
-
-        ctx = tuple(filter(lambda x: x != '<PHRASE>', context.split()))
-        cnt = int(count.strip()[2:])
-        edges_phrase_to_context[-1][1].append((ctx, cnt))
-
-        cid = context_types.get(ctx, len(context_types))
-        if cid == len(context_types):
-            context_types[ctx] = cid
-            edges_context_to_phrase.append((ctx, []))
-        edges_context_to_phrase[cid][1].append((phrase, cnt))
-
-        for token in ctx:
-            types.setdefault(token, len(types))
-        for token in phrase.split():
-            types.setdefault(token, len(types))
-
-        num_edges += 1
-
-print 'Read in', num_edges, 'edges and', len(types), 'word types'
-
-print 'edges_phrase_to_context', edges_phrase_to_context
-
-#
-# Step 2: initialise the model parameters
-#
-
-num_tags = 10
-num_types = len(types)
-num_phrases = len(edges_phrase_to_context)
-num_contexts = len(edges_context_to_phrase)
-delta = int(sys.argv[1])
-gamma = int(sys.argv[2])
-
-def normalise(a):
-    return a / float(sum(a))
-
-# Pr(tag | phrase)
-tagDist = [normalise(random(num_tags)+1) for p in range(num_phrases)]
-#tagDist = [normalise(array(range(1,num_tags+1))) for p in range(num_phrases)]
-# Pr(context at pos i = w | tag) indexed by i, tag, word
-#contextWordDist = [[normalise(array(range(1,num_types+1))) for t in range(num_tags)] for i in range(4)]
-contextWordDist = [[normalise(random(num_types)+1) for t in range(num_tags)] for i in range(4)]
-# PR langrange multipliers
-lamba = zeros(2 * num_edges * num_tags)
-omega_offset = num_edges * num_tags
-lamba_index = {}
-next = 0
-for phrase, ccs in edges_phrase_to_context:
-    for context, count in ccs:
-        lamba_index[phrase,context] = next
-        next += num_tags
-#print lamba_index
-
-#
-# Step 3: expectation maximisation
-#
-
-for iteration in range(20):
-    tagCounts = [zeros(num_tags) for p in range(num_phrases)]
-    contextWordCounts = [[zeros(num_types) for t in range(num_tags)] for i in range(4)]
-
-    #print 'tagDist', tagDist
-    #print 'contextWordCounts[0][0]', contextWordCounts[0][0]
-
-    # Tune lambda
-    # dual: min log Z(lamba) s.t. lamba >= 0;
-    # sum_c lamba_pct <= delta; sum_p lamba_pct <= gamma
-    def dual(ls):
-        logz = 0
-        for p, (phrase, ccs) in enumerate(edges_phrase_to_context):
-            for context, count in ccs:
-                conditionals = zeros(num_tags)
-                for t in range(num_tags):
-                    prob = tagDist[p][t]
-                    for i in range(4):
-                        prob *= contextWordDist[i][t][types[context[i]]]
-                    conditionals[t] = prob
-                cz = sum(conditionals)
-                conditionals /= cz
-
-                #print 'dual', phrase, context, count, 'p =', conditionals
-
-                local_z = 0
-                for t in range(num_tags):
-                    li = lamba_index[phrase,context] + t
-                    local_z += conditionals[t] * exp(-ls[li] - ls[omega_offset+li])
-                logz += log(local_z) * count
-
-        #print 'ls', ls
-        #print 'lambda', list(ls)
-        #print 'dual', logz
-        return logz
-
-    def loglikelihood():
-        llh = 0
-        for p, (phrase, ccs) in enumerate(edges_phrase_to_context):
-            for context, count in ccs:
-                conditionals = zeros(num_tags)
-                for t in range(num_tags):
-                    prob = tagDist[p][t]
-                    for i in range(4):
-                        prob *= contextWordDist[i][t][types[context[i]]]
-                    conditionals[t] = prob
-                cz = sum(conditionals)
-                llh += log(cz) * count
-        return llh
-
-    def primal(ls):
-        # FIXME: returns negative values for KL (impossible)
-        logz = dual(ls)
-        expectations = -dual_deriv(ls)
-        kl = -logz - dot(ls, expectations)
-        llh = loglikelihood()
-
-        pt_l1linf = 0
-        for phrase, ccs in edges_phrase_to_context:
-            for t in range(num_tags):
-                best = -1e500
-                for context, count in ccs:
-                    li = lamba_index[phrase,context] + t
-                    s = expectations[li]
-                    if s > best: best = s
-                pt_l1linf += best
-
-        ct_l1linf = 0
-        for context, pcs in edges_context_to_phrase:
-            for t in range(num_tags):
-                best = -1e500
-                for phrase, count in pcs:
-                    li = omega_offset + lamba_index[phrase,context] + t
-                    s = expectations[li]
-                    if s > best: best = s
-                ct_l1linf += best
-
-        return llh, kl, pt_l1linf, ct_l1linf, llh - kl - delta * pt_l1linf - gamma * ct_l1linf
-
-    def dual_deriv(ls):
-        # d/dl log(z) = E_q[phi]
-        deriv = zeros(2 * num_edges * num_tags)
-        for p, (phrase, ccs) in enumerate(edges_phrase_to_context):
-            for context, count in ccs:
-                conditionals = zeros(num_tags)
-                for t in range(num_tags):
-                    prob = tagDist[p][t]
-                    for i in range(4):
-                        prob *= contextWordDist[i][t][types[context[i]]]
-                    conditionals[t] = prob
-                cz = sum(conditionals)
-                conditionals /= cz
-
-                scores = zeros(num_tags)
-                for t in range(num_tags):
-                    li = lamba_index[phrase,context] + t
-                    scores[t] = conditionals[t] * exp(-ls[li] - ls[omega_offset + li])
-                local_z = sum(scores)
-
-                #print 'ddual', phrase, context, count, 'q =', scores / local_z
-
-                for t in range(num_tags):
-                    deriv[lamba_index[phrase,context] + t] -= count * scores[t] / local_z
-                    deriv[omega_offset + lamba_index[phrase,context] + t] -= count * scores[t] / local_z
-
-        #print 'ddual', list(deriv)
-        return deriv
-
-    def constraints(ls):
-        cons = zeros(num_phrases * num_tags + num_edges * num_tags)
-
-        index = 0
-        for phrase, ccs in edges_phrase_to_context:
-            for t in range(num_tags):
-                if delta > 0:
-                    total = delta
-                    for cprime, count in ccs:
-                        total -= ls[lamba_index[phrase, cprime] + t]
-                    cons[index] = total
-                index += 1
-
-        for context, pcs in edges_context_to_phrase:
-            for t in range(num_tags):
-                if gamma > 0:
-                    total = gamma
-                    for pprime, count in pcs:
-                        total -= ls[omega_offset + lamba_index[pprime, context] + t]
-                    cons[index] = total
-                index += 1
-
-        #print 'cons', cons
-        return cons
-
-    def constraints_deriv(ls):
-        cons = zeros((num_phrases * num_tags + num_edges * num_tags, 2 * num_edges * num_tags))
-
-        index = 0
-        for phrase, ccs in edges_phrase_to_context:
-            for t in range(num_tags):
-                if delta > 0:
-                    d = cons[index,:]#zeros(num_edges * num_tags)
-                    for cprime, count in ccs:
-                        d[lamba_index[phrase, cprime] + t] = -1
-                    #cons[index] = d
-                index += 1
-
-        for context, pcs in edges_context_to_phrase:
-            for t in range(num_tags):
-                if gamma > 0:
-                    d = cons[index,:]#d = zeros(num_edges * num_tags)
-                    for pprime, count in pcs:
-                        d[omega_offset + lamba_index[pprime, context] + t] = -1
-                    #cons[index] = d
-                index += 1
-        #print 'dcons', cons
-        return cons
-
-    print 'Pre lambda optimisation dual', dual(lamba), 'primal', primal(lamba)
-    #print 'lambda', lamba, lamba.shape
-    #print 'bounds', [(0, max(delta, gamma))] * (2 * num_edges * num_tags)
-
-    lamba = scipy.optimize.fmin_slsqp(dual, lamba,
-                            bounds=[(0, max(delta, gamma))] * (2 * num_edges * num_tags),
-                            f_ieqcons=constraints,
-                            fprime=dual_deriv,
-                            fprime_ieqcons=constraints_deriv,
-                            iprint=0)
-    print 'Post lambda optimisation dual', dual(lamba), 'primal', primal(lamba)
-
-    # E-step
-    llh = log_z = 0
-    for p, (phrase, ccs) in enumerate(edges_phrase_to_context):
-        for context, count in ccs:
-            conditionals = zeros(num_tags)
-            for t in range(num_tags):
-                prob = tagDist[p][t]
-                for i in range(4):
-                    prob *= contextWordDist[i][t][types[context[i]]]
-                conditionals[t] = prob
-            cz = sum(conditionals)
-            conditionals /= cz
-            llh += log(cz) * count
-
-            q = zeros(num_tags)
-            li = lamba_index[phrase, context]
-            for t in range(num_tags):
-                q[t] = conditionals[t] * exp(-lamba[li + t] - lamba[omega_offset + li + t])
-            qz = sum(q)
-            log_z += count * log(qz)
-
-            for t in range(num_tags):
-                tagCounts[p][t] += count * q[t] / qz
-
-            for i in range(4):
-                for t in range(num_tags):
-                    contextWordCounts[i][t][types[context[i]]] += count * q[t] / qz
-
-    print 'iteration', iteration, 'llh', llh, 'logz', log_z
-
-    # M-step
-    for p in range(num_phrases):
-        tagDist[p] = normalise(tagCounts[p])
-    for i in range(4):
-        for t in range(num_tags):
-            contextWordDist[i][t] = normalise(contextWordCounts[i][t])
-
-for p, (phrase, ccs) in enumerate(edges_phrase_to_context):
-    for context, count in ccs:
-        conditionals = zeros(num_tags)
-        for t in range(num_tags):
-            prob = tagDist[p][t]
-            for i in range(4):
-                prob *= contextWordDist[i][t][types[context[i]]]
-            conditionals[t] = prob
-        cz = sum(conditionals)
-        conditionals /= cz
-
-        print '%s\t%s ||| C=%d |||' % (phrase, context, argmax(conditionals)), conditionals
diff --git a/gi/posterior-regularisation/train_pr_parallel.py b/gi/posterior-regularisation/train_pr_parallel.py
deleted file mode 100644
index 3b9cefed..00000000
--- a/gi/posterior-regularisation/train_pr_parallel.py
+++ /dev/null
@@ -1,333 +0,0 @@
-import sys
-import scipy.optimize
-from numpy import *
-from numpy.random import random, seed
-
-#
-# Step 1: load the concordance counts
-# 
-
-edges_phrase_to_context = []
-edges_context_to_phrase = []
-types = {}
-context_types = {}
-num_edges = 0
-
-for line in sys.stdin:
-    phrase, rest = line.strip().split('\t')
-    parts = rest.split('|||')
-    edges_phrase_to_context.append((phrase, []))
-    for i in range(0, len(parts), 2):
-        context, count = parts[i:i+2]
-
-        ctx = tuple(filter(lambda x: x != '<PHRASE>', context.split()))
-        cnt = int(count.strip()[2:])
-        edges_phrase_to_context[-1][1].append((ctx, cnt))
-
-        cid = context_types.get(ctx, len(context_types))
-        if cid == len(context_types):
-            context_types[ctx] = cid
-            edges_context_to_phrase.append((ctx, []))
-        edges_context_to_phrase[cid][1].append((phrase, cnt))
-
-        for token in ctx:
-            types.setdefault(token, len(types))
-        for token in phrase.split():
-            types.setdefault(token, len(types))
-
-        num_edges += 1
-
-#
-# Step 2: initialise the model parameters
-#
-
-num_tags = 25
-num_types = len(types)
-num_phrases = len(edges_phrase_to_context)
-num_contexts = len(edges_context_to_phrase)
-delta = float(sys.argv[1])
-assert sys.argv[2] in ('local', 'global')
-local = sys.argv[2] == 'local'
-if len(sys.argv) >= 2:
-     seed(int(sys.argv[3]))
-
-print 'Read in', num_edges, 'edges', num_phrases, 'phrases', num_contexts, 'contexts and', len(types), 'word types'
-
-def normalise(a):
-    return a / float(sum(a))
-
-# Pr(tag | phrase)
-tagDist = [normalise(random(num_tags)+1) for p in range(num_phrases)]
-# Pr(context at pos i = w | tag) indexed by i, tag, word
-contextWordDist = [[normalise(random(num_types)+1) for t in range(num_tags)] for i in range(4)]
-
-#
-# Step 3: expectation maximisation
-#
-
-class GlobalDualObjective:
-    """
-    Objective, log(z), for all phrases s.t. lambda >= 0, sum_c lambda_pct <= scale 
-    """
-
-    def __init__(self, scale):
-        self.scale = scale
-        self.posterior = zeros((num_edges, num_tags))
-        self.q = zeros((num_edges, num_tags))
-        self.llh = 0
-
-        index = 0
-        for j, (phrase, edges) in enumerate(edges_phrase_to_context):
-            for context, count in edges:
-                for t in range(num_tags):
-                    prob = tagDist[j][t]
-                    for k, token in enumerate(context):
-                        prob *= contextWordDist[k][t][types[token]]
-                    self.posterior[index,t] = prob
-                z = sum(self.posterior[index,:])
-                self.posterior[index,:] /= z
-                self.llh += log(z) * count
-                index += 1
-
-    def objective(self, ls):
-        ls = ls.reshape((num_edges, num_tags))
-        logz = 0
-
-        index = 0
-        for j, (phrase, edges) in enumerate(edges_phrase_to_context):
-            for context, count in edges:
-                for t in range(num_tags):
-                    self.q[index,t] = self.posterior[index,t] * exp(-ls[index,t])
-                local_z = sum(self.q[index,:])
-                self.q[index,:] /= local_z
-                logz += log(local_z) * count
-                index += 1
-
-        return logz
-
-    # FIXME: recomputes q many more times than necessary
-
-    def gradient(self, ls):
-        ls = ls.reshape((num_edges, num_tags))
-        gradient = zeros((num_edges, num_tags))
-
-        index = 0
-        for j, (phrase, edges) in enumerate(edges_phrase_to_context):
-            for context, count in edges:
-                for t in range(num_tags):
-                    self.q[index,t] = self.posterior[index,t] * exp(-ls[index,t])
-                local_z = sum(self.q[index,:])
-                self.q[index,:] /= local_z
-                for t in range(num_tags):
-                    gradient[index,t] -= self.q[index,t] * count
-                index += 1
-
-        return gradient.ravel()
-
-    def constraints(self, ls):
-        ls = ls.reshape((num_edges, num_tags))
-        cons = ones((num_phrases, num_tags)) * self.scale
-        index = 0
-        for j, (phrase, edges) in enumerate(edges_phrase_to_context):
-            for i, (context, count) in enumerate(edges):
-                for t in range(num_tags):
-                    cons[j,t] -= ls[index,t] * count
-                index += 1
-        return cons.ravel()
-
-    def constraints_gradient(self, ls):
-        ls = ls.reshape((num_edges, num_tags))
-        gradient = zeros((num_phrases, num_tags, num_edges, num_tags))
-        index = 0
-        for j, (phrase, edges) in enumerate(edges_phrase_to_context):
-            for i, (context, count) in enumerate(edges):
-                for t in range(num_tags):
-                    gradient[j,t,index,t] -= count
-                index += 1
-        return gradient.reshape((num_phrases*num_tags, num_edges*num_tags))
-
-    def optimize(self):
-        ls = zeros(num_edges * num_tags)
-        #print '\tpre lambda optimisation dual', self.objective(ls) #, 'primal', primal(lamba)
-        ls = scipy.optimize.fmin_slsqp(self.objective, ls,
-                                bounds=[(0, self.scale)] * num_edges * num_tags,
-                                f_ieqcons=self.constraints,
-                                fprime=self.gradient,
-                                fprime_ieqcons=self.constraints_gradient,
-                                iprint=0) # =2 for verbose
-        #print '\tpost lambda optimisation dual', self.objective(ls) #, 'primal', primal(lamba)
-
-        # returns llh, kl and l1lmax contribution
-        l1lmax = 0
-        index = 0
-        for j, (phrase, edges) in enumerate(edges_phrase_to_context):
-            for t in range(num_tags):
-                lmax = None
-                for i, (context, count) in enumerate(edges):
-                    lmax = max(lmax, self.q[index+i,t])
-                l1lmax += lmax
-            index += len(edges)
-
-        return self.llh, -self.objective(ls) + dot(ls, self.gradient(ls)), l1lmax
-
-class LocalDualObjective:
-    """
-    Local part of objective, log(z) relevant to lambda_p**.
-    Optimised subject to lambda >= 0, sum_c lambda_pct <= scale forall t 
-    """
-
-    def __init__(self, phraseId, scale):
-        self.phraseId = phraseId
-        self.scale = scale
-        edges = edges_phrase_to_context[self.phraseId][1]
-        self.posterior = zeros((len(edges), num_tags))
-        self.q = zeros((len(edges), num_tags))
-        self.llh = 0
-
-        for i, (context, count) in enumerate(edges):
-            for t in range(num_tags):
-                prob = tagDist[phraseId][t]
-                for j, token in enumerate(context):
-                    prob *= contextWordDist[j][t][types[token]]
-                self.posterior[i,t] = prob
-            z = sum(self.posterior[i,:])
-            self.posterior[i,:] /= z
-            self.llh += log(z) * count
-
-    def objective(self, ls):
-        edges = edges_phrase_to_context[self.phraseId][1]
-        ls = ls.reshape((len(edges), num_tags))
-        logz = 0
-
-        for i, (context, count) in enumerate(edges):
-            for t in range(num_tags):
-                self.q[i,t] = self.posterior[i,t] * exp(-ls[i,t])
-            local_z = sum(self.q[i,:])
-            self.q[i,:] /= local_z
-            logz += log(local_z) * count
-
-        return logz
-
-    # FIXME: recomputes q many more times than necessary
-
-    def gradient(self, ls):
-        edges = edges_phrase_to_context[self.phraseId][1]
-        ls = ls.reshape((len(edges), num_tags))
-        gradient = zeros((len(edges), num_tags))
-
-        for i, (context, count) in enumerate(edges):
-            for t in range(num_tags):
-                self.q[i,t] = self.posterior[i,t] * exp(-ls[i,t])
-            local_z = sum(self.q[i,:])
-            self.q[i,:] /= local_z
-            for t in range(num_tags):
-                gradient[i,t] -= self.q[i,t] * count
-
-        return gradient.ravel()
-
-    def constraints(self, ls):
-        edges = edges_phrase_to_context[self.phraseId][1]
-        ls = ls.reshape((len(edges), num_tags))
-        cons = ones(num_tags) * self.scale
-        for t in range(num_tags):
-            for i, (context, count) in enumerate(edges):
-                cons[t] -= ls[i,t] * count
-        return cons
-
-    def constraints_gradient(self, ls):
-        edges = edges_phrase_to_context[self.phraseId][1]
-        ls = ls.reshape((len(edges), num_tags))
-        gradient = zeros((num_tags, len(edges), num_tags))
-        for t in range(num_tags):
-            for i, (context, count) in enumerate(edges):
-                gradient[t,i,t] -= count
-        return gradient.reshape((num_tags, len(edges)*num_tags))
-
-    def optimize(self, ls=None):
-        edges = edges_phrase_to_context[self.phraseId][1]
-        if ls == None:
-            ls = zeros(len(edges) * num_tags)
-        #print '\tpre lambda optimisation dual', self.objective(ls) #, 'primal', primal(lamba)
-        ls = scipy.optimize.fmin_slsqp(self.objective, ls,
-                                bounds=[(0, self.scale)] * len(edges) * num_tags,
-                                f_ieqcons=self.constraints,
-                                fprime=self.gradient,
-                                fprime_ieqcons=self.constraints_gradient,
-                                iprint=0) # =2 for verbose
-        #print '\tlambda', list(ls)
-        #print '\tpost lambda optimisation dual', self.objective(ls) #, 'primal', primal(lamba)
-
-        # returns llh, kl and l1lmax contribution
-        l1lmax = 0
-        for t in range(num_tags):
-            lmax = None
-            for i, (context, count) in enumerate(edges):
-                lmax = max(lmax, self.q[i,t])
-            l1lmax += lmax
-
-        return self.llh, -self.objective(ls) + dot(ls, self.gradient(ls)), l1lmax, ls
-
-ls = [None] * num_phrases
-for iteration in range(20):
-    tagCounts = [zeros(num_tags) for p in range(num_phrases)]
-    contextWordCounts = [[zeros(num_types) for t in range(num_tags)] for i in range(4)]
-
-    # E-step
-    llh = kl = l1lmax = 0
-    if local:
-        for p in range(num_phrases):
-            o = LocalDualObjective(p, delta)
-            #print '\toptimising lambda for phrase', p, '=', edges_phrase_to_context[p][0]
-            #print '\toptimising lambda for phrase', p, 'ls', ls[p]
-            obj = o.optimize(ls[p])
-            #print '\tphrase', p, 'deltas', obj
-            llh += obj[0]
-            kl += obj[1]
-            l1lmax += obj[2]
-            ls[p] = obj[3]
-
-            edges = edges_phrase_to_context[p][1]
-            for j, (context, count) in enumerate(edges):
-                for t in range(num_tags):
-                    tagCounts[p][t] += count * o.q[j,t]
-                for i in range(4):
-                    for t in range(num_tags):
-                        contextWordCounts[i][t][types[context[i]]] += count * o.q[j,t]
-
-        #print 'iteration', iteration, 'LOCAL objective', (llh + kl + delta * l1lmax), 'llh', llh, 'kl', kl, 'l1lmax', l1lmax
-    else:
-        o = GlobalDualObjective(delta)
-        obj = o.optimize()
-        llh, kl, l1lmax = o.optimize()
-
-        index = 0
-        for p, (phrase, edges) in enumerate(edges_phrase_to_context):
-            for context, count in edges:
-                for t in range(num_tags):
-                    tagCounts[p][t] += count * o.q[index,t]
-                for i in range(4):
-                    for t in range(num_tags):
-                        contextWordCounts[i][t][types[context[i]]] += count * o.q[index,t]
-                index += 1
-
-    print 'iteration', iteration, 'objective', (llh - kl - delta * l1lmax), 'llh', llh, 'kl', kl, 'l1lmax', l1lmax
-
-    # M-step
-    for p in range(num_phrases):
-        tagDist[p] = normalise(tagCounts[p])
-    for i in range(4):
-        for t in range(num_tags):
-            contextWordDist[i][t] = normalise(contextWordCounts[i][t])
-
-for p, (phrase, ccs) in enumerate(edges_phrase_to_context):
-    for context, count in ccs:
-        conditionals = zeros(num_tags)
-        for t in range(num_tags):
-            prob = tagDist[p][t]
-            for i in range(4):
-                prob *= contextWordDist[i][t][types[context[i]]]
-            conditionals[t] = prob
-        cz = sum(conditionals)
-        conditionals /= cz
-
-        print '%s\t%s ||| C=%d |||' % (phrase, context, argmax(conditionals)), conditionals
diff --git a/gi/pyp-topics/scripts/contexts2documents.py b/gi/pyp-topics/scripts/contexts2documents.py
deleted file mode 100755
index 9be4ebbb..00000000
--- a/gi/pyp-topics/scripts/contexts2documents.py
+++ /dev/null
@@ -1,37 +0,0 @@
-#!/usr/bin/python
-
-import sys
-from operator import itemgetter
-
-if len(sys.argv) > 3:
-  print "Usage: contexts2documents.py [contexts_index_out] [phrases_index_out]"
-  exit(1)
-
-context_index = {} 
-phrase_index = {}
-for line in sys.stdin:
-  phrase, line_tail = line.split('\t')
-
-  raw_contexts = line_tail.split('|||')
-  contexts = [c.strip() for x,c in enumerate(raw_contexts) if x%2 == 0]
-  counts   = [int(c.split('=')[1].strip()) for x,c in enumerate(raw_contexts) if x%2 != 0]
-  phrase_index.setdefault(phrase, len(phrase_index))
-  print len(contexts),
-  for context,count in zip(contexts,counts): 
-    c = context_index.setdefault(context, len(context_index))
-    print "%d:%d" % (c,count),
-  print
-if 1 < len(sys.argv) < 4:
-  contexts_out = open(sys.argv[1],'w')
-  contexts = context_index.items()
-  contexts.sort(key = itemgetter(1))
-  for context in contexts: 
-    print >>contexts_out, context[0]
-  contexts_out.close()
-if len(sys.argv) == 3:
-  phrases_out = open(sys.argv[2],'w')
-  phrases = phrase_index.items()
-  phrases.sort(key = itemgetter(1))
-  for phrase in phrases: 
-    print >>phrases_out, phrase[0]
-  phrases_out.close()
diff --git a/gi/pyp-topics/scripts/extract_contexts.py b/gi/pyp-topics/scripts/extract_contexts.py
deleted file mode 100755
index b2723f2a..00000000
--- a/gi/pyp-topics/scripts/extract_contexts.py
+++ /dev/null
@@ -1,144 +0,0 @@
-#!/usr/bin/python
-
-import sys,collections
-
-def extract_backoff(context_list, order):
-  assert len(context_list) == (2*order)
-  backoffs = []
-  for i in range(1,order+1):
-    if i == order:
-      backoffs.append(([context_list[i-1]+"|"], ["|"+context_list[i]]))
-    else:
-      right_limit = 2*order-i
-      core = context_list[i:right_limit]
-      left = [context_list[i-1]+"|"*(order-i+1)]
-      right = ["|"*(order-i+1)+context_list[right_limit]]
-      backoffs.append((core, left, right))
-# print context_list, backoffs
-  return backoffs
-
-def tuple_to_str(t):
-  s=""
-  for i,x in enumerate(t):
-    if i > 0: s += "|"
-    s += str(x)
-  return s
-
-if len(sys.argv) < 3:
-  print "Usage: extract-contexts.py output_filename order cutoff lowercase"
-  exit(1)
-
-output_filename = sys.argv[1]
-order = int(sys.argv[2])
-cutoff = 0
-if len(sys.argv) > 3:
-  cutoff = int(sys.argv[3])
-lowercase = False
-if len(sys.argv) > 4:
-  lowercase = bool(sys.argv[4])
-
-contexts_dict={}
-contexts_list=[]
-contexts_freq=collections.defaultdict(int)
-contexts_backoff={}
-
-token_dict={}
-token_list=[]
-documents_dict=collections.defaultdict(dict)
-
-contexts_at_order = [i for i in range(order+1)]
-
-prefix = ["<s%d>|<s>"%i for i in range(order)]
-suffix = ["</s%d>|</s>"%i for i in range(order)]
-
-for line in sys.stdin:
-  tokens = list(prefix)
-  tokens.extend(line.split())
-  tokens.extend(suffix)
-  if lowercase:
-    tokens = map(lambda x: x.lower(), tokens)
-
-  for i in range(order, len(tokens)-order):
-    context_list = []
-    term=""
-    for j in range(i-order, i+order+1):
-      token,tag = tokens[j].rsplit('|',2)
-      if j != i:
-        context_list.append(token)
-      else:
-        if token not in token_dict: 
-          token_dict[token] = len(token_dict)
-          token_list.append(token)
-        term = token_dict[token] 
-
-    context = tuple_to_str(tuple(context_list))
-
-    if context not in contexts_dict: 
-      context_index = len(contexts_dict)
-      contexts_dict[context] = context_index
-      contexts_list.append(context)
-      contexts_at_order[0] += 1
-
-      # handle backoff
-      backoff_contexts = extract_backoff(context_list, order)
-      bo_indexes=[(context_index,)]
-#     bo_indexes=[(context,)]
-      for i,bo in enumerate(backoff_contexts):
-        factor_indexes=[]
-        for factor in bo:
-          bo_tuple = tuple_to_str(tuple(factor))
-          if bo_tuple not in contexts_dict:
-            contexts_dict[bo_tuple] = len(contexts_dict)
-            contexts_list.append(bo_tuple)
-            contexts_at_order[i+1] += 1
-#         factor_indexes.append(bo_tuple)
-          factor_indexes.append(contexts_dict[bo_tuple])
-        bo_indexes.append(tuple(factor_indexes))
-      
-      for i in range(len(bo_indexes)-1):
-        contexts_backoff[bo_indexes[i][0]] = bo_indexes[i+1]
-
-    context_index = contexts_dict[context]
-    contexts_freq[context_index] += 1
-
-    if context_index not in documents_dict[term]:
-      documents_dict[term][context_index] = 1
-    else:
-      documents_dict[term][context_index] += 1
-
-term_file = open(output_filename+".terms",'w')
-for t in token_list: print >>term_file, t
-term_file.close()
-
-contexts_file = open(output_filename+".contexts",'w')
-for c in contexts_list: 
-  print >>contexts_file, c
-contexts_file.close()
-
-data_file = open(output_filename+".data",'w')
-for t in range(len(token_list)): 
-  line=""
-  num_active=0
-  for c in documents_dict[t]:
-    count = documents_dict[t][c]
-    if contexts_freq[c] >= cutoff:
-      line += (' ' + str(c) + ':' + str(count))
-      num_active += 1
-  if num_active > 0:
-    print >>data_file, "%d%s" % (num_active,line)
-data_file.close()
-
-contexts_backoff_file = open(output_filename+".contexts_backoff",'w')
-print >>contexts_backoff_file, len(contexts_list), order,
-#for x in contexts_at_order: 
-#  print >>contexts_backoff_file, x,
-#print >>contexts_backoff_file
-for x in range(order-1):
-  print >>contexts_backoff_file, 3,
-print >>contexts_backoff_file, 2
-
-for x in contexts_backoff: 
-  print >>contexts_backoff_file, x, 
-  for y in contexts_backoff[x]: print >>contexts_backoff_file, y,
-  print >>contexts_backoff_file 
-contexts_backoff_file.close()
diff --git a/gi/pyp-topics/scripts/extract_contexts_test.py b/gi/pyp-topics/scripts/extract_contexts_test.py
deleted file mode 100755
index 693b6e0b..00000000
--- a/gi/pyp-topics/scripts/extract_contexts_test.py
+++ /dev/null
@@ -1,72 +0,0 @@
-#!/usr/bin/python
-
-import sys,collections
-
-def tuple_to_str(t):
-  s=""
-  for i,x in enumerate(t):
-    if i > 0: s += "|"
-    s += str(x)
-  return s
-
-if len(sys.argv) < 5:
-  print "Usage: extract-contexts_test.py output_filename vocab contexts order lowercase"
-  exit(1)
-
-output_filename = sys.argv[1]
-output = open(output_filename+".test_data",'w')
-
-unk_term="-UNK-"
-vocab_dict={}
-for i,x in enumerate(file(sys.argv[2], 'r').readlines()): 
-  vocab_dict[x.strip()]=i
-
-contexts_dict={}
-contexts_list=[]
-for i,x in enumerate(file(sys.argv[3], 'r').readlines()): 
-  contexts_dict[x.strip()]=i
-  contexts_list.append(x.strip())
-
-order = int(sys.argv[4])
-
-lowercase = False
-if len(sys.argv) > 5:
-  lowercase = bool(sys.argv[5])
-if lowercase: unk_term = unk_term.lower()
-
-prefix = ["<s%d>|<s>"%i for i in range(order)]
-suffix = ["</s%d>|</s>"%i for i in range(order)]
-
-assert unk_term in vocab_dict
-for line in sys.stdin:
-  tokens = list(prefix)
-  tokens.extend(line.split())
-  tokens.extend(suffix)
-  if lowercase:
-    tokens = map(lambda x: x.lower(), tokens)
-
-  for i in range(order, len(tokens)-order):
-    context_list=[]
-    term=""
-    for j in range(i-order, i+order+1):
-      token,tag = tokens[j].rsplit('|',2)
-      if j != i:
-        context_list.append(token)
-      else:
-        if token not in vocab_dict: 
-          term = vocab_dict[unk_term] 
-        else:
-          term = vocab_dict[token] 
-    context = tuple_to_str(context_list)
-    if context not in contexts_dict: 
-      contexts_dict[context] = len(contexts_dict)
-      contexts_list.append(context)
-    context_index = contexts_dict[context]
-    print >>output, "%d:%d" % (term,context_index),
-  print >>output
-output.close()
-
-contexts_file = open(output_filename+".test_contexts",'w')
-for c in contexts_list: 
-  print >>contexts_file, c
-contexts_file.close()
diff --git a/gi/pyp-topics/scripts/extract_leaves.py b/gi/pyp-topics/scripts/extract_leaves.py
deleted file mode 100755
index 14783b36..00000000
--- a/gi/pyp-topics/scripts/extract_leaves.py
+++ /dev/null
@@ -1,49 +0,0 @@
-#!/usr/bin/python
-
-import nltk
-import nltk.probability
-import sys
-import getopt 
-
-lexicalise=False
-rm_traces=False
-cutoff=100
-length_cutoff=10000
-try:                                
-  opts, args = getopt.getopt(sys.argv[1:], "hs:c:l", ["help", "lexicalise", "cutoff","sentence-length","remove-traces"])
-except getopt.GetoptError:          
-  print "Usage: extract_leaves.py [-lsc]"                        
-  sys.exit(2)                     
-for opt, arg in opts:                
-  if opt in ("-h", "--help"):      
-    print "Usage: extract_leaves.py [-lsc]"                        
-    sys.exit()                  
-  elif opt in ("-l", "--lexicalise"):                
-    lexicalise = True                 
-  elif opt in ("-c", "--cutoff"):                
-    cutoff = int(arg) 
-  elif opt in ("-s", "--sentence-length"):                
-    length_cutoff = int(arg) 
-  elif opt in ("--remove-traces"):                
-    rm_traces = True                 
-
-token_freq = nltk.probability.FreqDist()
-lines = []
-for line in sys.stdin:
-  t = nltk.Tree.parse(line)
-  pos = t.pos()
-  if len(pos) <= length_cutoff:
-    lines.append(pos)
-    for token, tag in pos:
-      token_freq.inc(token)  
-
-for line in lines:
-  for token,tag in line:
-    if not (rm_traces and tag == "-NONE-"):
-      if lexicalise:
-        if token_freq[token] < cutoff:
-          token = '-UNK-'
-        print '%s|%s' % (token,tag),
-      else:
-        print '%s' % tag,
-  print
diff --git a/gi/pyp-topics/scripts/map-documents.py b/gi/pyp-topics/scripts/map-documents.py
deleted file mode 100755
index 703de312..00000000
--- a/gi/pyp-topics/scripts/map-documents.py
+++ /dev/null
@@ -1,20 +0,0 @@
-#!/usr/bin/python
-
-import sys
-
-if len(sys.argv) != 2:
-  print "Usage: map-documents.py vocab-file"
-  exit(1)
-
-vocab = file(sys.argv[1], 'r').readlines()
-term_dict = map(lambda x: x.strip(), vocab)
-
-for line in sys.stdin:
-  tokens = line.split()
-  for token in tokens:
-    elements = token.split(':')
-    if len(elements) == 1:
-      print "%s" % (term_dict[int(elements[0])]),
-    else:
-      print "%s:%s" % (term_dict[int(elements[0])], elements[1]),
-  print
diff --git a/gi/pyp-topics/scripts/map-terms.py b/gi/pyp-topics/scripts/map-terms.py
deleted file mode 100755
index eb0298d7..00000000
--- a/gi/pyp-topics/scripts/map-terms.py
+++ /dev/null
@@ -1,20 +0,0 @@
-#!/usr/bin/python
-
-import sys
-
-if len(sys.argv) != 2:
-  print "Usage: map-terms.py vocab-file"
-  exit(1)
-
-vocab = file(sys.argv[1], 'r').readlines()
-term_dict = map(lambda x: x.strip().replace(' ','_'), vocab)
-
-for line in sys.stdin:
-  tokens = line.split()
-  for token in tokens:
-    elements = token.split(':')
-    if len(elements) == 1:
-      print "%s" % (term_dict[int(elements[0])]),
-    else:
-      print "%s:%s" % (term_dict[int(elements[0])], elements[1]),
-  print
diff --git a/gi/pyp-topics/scripts/run.sh b/gi/pyp-topics/scripts/run.sh
deleted file mode 100644
index 19e625b1..00000000
--- a/gi/pyp-topics/scripts/run.sh
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/bin/sh
-
-
-./simple-extract-context.sh ~/workspace/clsp2010/jhuws2010/data/btec/split.zh-en.al 1 | ~/workspace/pyp-topics/scripts/contexts2documents.py > split.zh-en.data
-
-~/workspace/pyp-topics/bin/pyp-topics-train -d split.zh-en.data -t 50 -s 100 -o split.zh-en.documents.gz -w split.zh-en.topics.gz
-gunzip split.zh-en.documents.gz
-
-~/workspace/cdec/extools/extractor -i ../jhuws2010/data/btec/split.zh-en.al -S 1 -c 500000 -L 12 --base_phrase_spans | ~/workspace/pyp-topics/scripts/spans2labels.py split.zh-en.phrases split.zh-en.contexts split.zh-en.documents > corpus.zh-en.labelled_spans
-
-paste -d " " ~/workspace/clsp2010/jhuws2010/data/btec/split.zh-en.al corpus.labelled_spans > split.zh-en.labelled_spans
-
-./simple-extract.sh ~/workspace/clsp2010/scratch/split.zh-en.labelled_spans
diff --git a/gi/pyp-topics/scripts/score-mkcls.py b/gi/pyp-topics/scripts/score-mkcls.py
deleted file mode 100755
index 6bd33fc5..00000000
--- a/gi/pyp-topics/scripts/score-mkcls.py
+++ /dev/null
@@ -1,61 +0,0 @@
-#!/usr/bin/python
-
-import sys
-from collections import defaultdict
-
-def dict_max(d):
-  max_val=-1
-  max_key=None
-  for k in d:
-    if d[k] > max_val: 
-      max_val = d[k]
-      max_key = k
-  assert max_key
-  return max_key
-
-if len(sys.argv) != 3:
-  print "Usage: score-mkcls.py gold classes"
-  exit(1)
-
-gold_file=open(sys.argv[1],'r')
-
-term_to_topics = {}
-for line in open(sys.argv[2],'r'):
-  term,cls = line.split()
-  term_to_topics[term] = cls
-
-gold_to_topics = defaultdict(dict)
-topics_to_gold = defaultdict(dict)
-
-for gold_line in gold_file:
-  gold_tokens = gold_line.split()
-  for gold_token in gold_tokens:
-    gold_term,gold_tag = gold_token.rsplit('|',1)
-    pred_token = term_to_topics[gold_term]
-    gold_to_topics[gold_tag][pred_token] \
-      = gold_to_topics[gold_tag].get(pred_token, 0) + 1
-    topics_to_gold[pred_token][gold_tag] \
-      = topics_to_gold[pred_token].get(gold_tag, 0) + 1
-
-pred=0
-correct=0
-gold_file=open(sys.argv[1],'r')
-for gold_line in gold_file:
-  gold_tokens = gold_line.split()
-
-  for gold_token in gold_tokens:
-    gold_term,gold_tag = gold_token.rsplit('|',1)
-    pred_token = term_to_topics[gold_term]
-    print "%s|%s|%s" % (gold_token, pred_token, dict_max(topics_to_gold[pred_token])),
-    pred += 1
-    if gold_tag == dict_max(topics_to_gold[pred_token]):
-      correct += 1
-  print
-print >>sys.stderr, "Many-to-One Accuracy = %f" % (float(correct) / pred)
-#for x in gold_to_topics: 
-#  print x,dict_max(gold_to_topics[x])
-#print "###################################################"
-#for x in range(len(topics_to_gold)): 
-#  print x,dict_max(topics_to_gold[str(x)])
-#  print x,topics_to_gold[str(x)]
-#print term_to_topics
diff --git a/gi/pyp-topics/scripts/score-topics.py b/gi/pyp-topics/scripts/score-topics.py
deleted file mode 100755
index 1d8a1fcd..00000000
--- a/gi/pyp-topics/scripts/score-topics.py
+++ /dev/null
@@ -1,64 +0,0 @@
-#!/usr/bin/python
-
-import sys
-from collections import defaultdict
-
-def dict_max(d):
-  max_val=-1
-  max_key=None
-  for k in d:
-    if d[k] > max_val: 
-      max_val = d[k]
-      max_key = k
-  assert max_key
-  return max_key
-
-if len(sys.argv) != 3:
-  print "Usage: score-topics.py gold pred"
-  exit(1)
-
-gold_file=open(sys.argv[1],'r')
-pred_file=open(sys.argv[2],'r')
-
-gold_to_topics = defaultdict(dict)
-topics_to_gold = defaultdict(dict)
-term_to_topics = defaultdict(dict)
-
-for gold_line,pred_line in zip(gold_file,pred_file):
-  gold_tokens = gold_line.split()
-  pred_tokens = pred_line.split()
-  assert len(gold_tokens) == len(pred_tokens)
-
-  for gold_token,pred_token in zip(gold_tokens,pred_tokens):
-    gold_term,gold_tag = gold_token.rsplit('|',1)
-    gold_to_topics[gold_tag][pred_token] \
-      = gold_to_topics[gold_tag].get(pred_token, 0) + 1
-    term_to_topics[gold_term][pred_token] \
-      = term_to_topics[gold_term].get(pred_token, 0) + 1
-    topics_to_gold[pred_token][gold_tag] \
-      = topics_to_gold[pred_token].get(gold_tag, 0) + 1
-
-pred=0
-correct=0
-gold_file=open(sys.argv[1],'r')
-pred_file=open(sys.argv[2],'r')
-for gold_line,pred_line in zip(gold_file,pred_file):
-  gold_tokens = gold_line.split()
-  pred_tokens = pred_line.split()
-
-  for gold_token,pred_token in zip(gold_tokens,pred_tokens):
-    gold_term,gold_tag = gold_token.rsplit('|',1)
-#   print "%s|%s" % (gold_token, dict_max(gold_to_topics[gold_tag])),
-    print "%s|%s|%s" % (gold_token, pred_token, dict_max(topics_to_gold[pred_token])),
-    pred += 1
-    if gold_tag == dict_max(topics_to_gold[pred_token]):
-      correct += 1
-  print
-print >>sys.stderr, "Many-to-One Accuracy = %f" % (float(correct) / pred)
-#for x in gold_to_topics: 
-#  print x,dict_max(gold_to_topics[x])
-#print "###################################################"
-#for x in range(len(topics_to_gold)): 
-#  print x,dict_max(topics_to_gold[str(x)])
-#  print x,topics_to_gold[str(x)]
-#print term_to_topics
diff --git a/gi/pyp-topics/scripts/spans2labels.py b/gi/pyp-topics/scripts/spans2labels.py
deleted file mode 100755
index 50fa8106..00000000
--- a/gi/pyp-topics/scripts/spans2labels.py
+++ /dev/null
@@ -1,137 +0,0 @@
-#!/usr/bin/python
-
-import sys
-from operator import itemgetter
-
-if len(sys.argv) <= 2:
-  print "Usage: spans2labels.py phrase_context_index [order] [threshold] [languages={s,t,b}{s,t,b}] [type={tag,tok,both},{tag,tok,both}]"
-  exit(1)
-
-order=1
-threshold = 0
-cutoff_cat = "<UNK>"
-if len(sys.argv) > 2:
-  order = int(sys.argv[2])
-if len(sys.argv) > 3:
-  threshold = float(sys.argv[3])
-phr=ctx='t'
-if len(sys.argv) > 4:
-  phr, ctx = sys.argv[4]
-  assert phr in 'stb'
-  assert ctx in 'stb'
-phr_typ = ctx_typ = 'both'
-if len(sys.argv) > 5:
-  phr_typ, ctx_typ = sys.argv[5].split(',')
-  assert phr_typ in ('tag', 'tok', 'both')
-  assert ctx_typ in ('tag', 'tok', 'both')
-
-#print >>sys.stderr, "Loading phrase index"
-phrase_context_index = {}
-for line in file(sys.argv[1], 'r'):
-  phrase,tail= line.split('\t')
-  contexts = tail.split(" ||| ")
-  try: # remove Phil's bizarre integer pair
-       x,y = contexts[0].split()
-       x=int(x); y=int(y)
-       contexts = contexts[1:]
-  except:
-       pass
-  if len(contexts) == 1: continue
-  assert len(contexts) % 2 == 0
-  for i in range(0, len(contexts), 2):
-    #parse contexts[i+1] = " C=1 P=0.8 ... "
-    features=dict([ keyval.split('=') for keyval in contexts[i+1].split()])
-    category = features['C']    
-    if features.has_key('P') and float(features['P']) < threshold:
-	category = cutoff_cat
-    
-    phrase_context_index[(phrase,contexts[i])] = category 
-    #print (phrase,contexts[i]), category
-
-#print >>sys.stderr, "Labelling spans"
-for line in sys.stdin:
-  #print >>sys.stderr, "line", line.strip()
-  line_segments = line.split(' ||| ')
-  assert len(line_segments) >= 3
-  source = ['<s>' for x in range(order)] + line_segments[0].split() + ['</s>' for x in range(order)]
-  target = ['<s>' for x in range(order)] + line_segments[1].split() + ['</s>' for x in range(order)]
-  phrases = [ [int(i) for i in x.split('-')] for x in line_segments[2].split()]
-
-  if phr_typ != 'both' or ctx_typ != 'both':
-    if phr in 'tb' or ctx in 'tb':
-        target_toks = ['<s>' for x in range(order)] + map(lambda x: x.rsplit('_', 1)[0], line_segments[1].split()) + ['</s>' for x in range(order)]
-        target_tags = ['<s>' for x in range(order)] + map(lambda x: x.rsplit('_', 1)[-1], line_segments[1].split()) + ['</s>' for x in range(order)]
-
-        if phr in 'tb':
-            if phr_typ == 'tok':
-                targetP = target_toks
-            elif phr_typ == 'tag':
-                targetP = target_tags
-        if ctx in 'tb':
-            if ctx_typ == 'tok':
-                targetC = target_toks
-            elif ctx_typ == 'tag':
-                targetC = target_tags
-
-    if phr in 'sb' or ctx in 'sb':
-        source_toks = ['<s>' for x in range(order)] + map(lambda x: x.rsplit('_', 1)[0], line_segments[0].split()) + ['</s>' for x in range(order)]
-        source_tags = ['<s>' for x in range(order)] + map(lambda x: x.rsplit('_', 1)[-1], line_segments[0].split()) + ['</s>' for x in range(order)]
-
-        if phr in 'sb':
-            if phr_typ == 'tok':
-                sourceP = source_toks
-            elif phr_typ == 'tag':
-                sourceP = source_tags
-        if ctx in 'sb':
-            if ctx_typ == 'tok':
-                sourceC = source_toks
-            elif ctx_typ == 'tag':
-                sourceC = source_tags
-  else:
-    sourceP = sourceC = source
-    targetP = targetC = target
-
-  #print >>sys.stderr, "line", source, '---', target, 'phrases', phrases
-
-  print "|||",
-
-  for s1,s2,t1,t2 in phrases:
-    s1 += order
-    s2 += order
-    t1 += order
-    t2 += order
-
-    phraset = phrases = contextt = contexts = ''
-    if phr in 'tb':
-        phraset = reduce(lambda x, y: x+y+" ", targetP[t1:t2], "").strip()
-    if phr in 'sb':
-        phrases = reduce(lambda x, y: x+y+" ", sourceP[s1:s2], "").strip()
-
-    if ctx in 'tb':
-        left_context = reduce(lambda x, y: x+y+" ", targetC[t1-order:t1], "")
-        right_context = reduce(lambda x, y: x+y+" ", targetC[t2:t2+order], "").strip()
-        contextt = "%s<PHRASE> %s" % (left_context, right_context)
-    if ctx in 'sb':
-        left_context = reduce(lambda x, y: x+y+" ", sourceC[s1-order:s1], "")
-        right_context = reduce(lambda x, y: x+y+" ", sourceC[s2:s2+order], "").strip()
-        contexts = "%s<PHRASE> %s" % (left_context, right_context)
-
-    if phr == 'b':
-        phrase = phraset + ' <SPLIT> ' + phrases
-    elif phr == 's':
-        phrase = phrases
-    else:
-        phrase = phraset
-
-    if ctx == 'b':
-        context = contextt + ' <SPLIT> ' + contexts
-    elif ctx == 's':
-        context = contexts
-    else:
-        context = contextt
-
-    #print "%d-%d-%d-%d looking up" % (s1-order,s2-order,t1-order,t2-order), (phrase, context)
-    label = phrase_context_index.get((phrase,context), cutoff_cat)
-    if label != cutoff_cat: #cutoff'd spans are left unlabelled
-      print "%d-%d-%d-%d:X%s" % (s1-order,s2-order,t1-order,t2-order,label),
-  print
diff --git a/gi/pyp-topics/scripts/tokens2classes.py b/gi/pyp-topics/scripts/tokens2classes.py
deleted file mode 100755
index 33df255f..00000000
--- a/gi/pyp-topics/scripts/tokens2classes.py
+++ /dev/null
@@ -1,27 +0,0 @@
-#!/usr/bin/python
-
-import sys
-
-if len(sys.argv) != 3:
-  print "Usage: tokens2classes.py source_classes target_classes"
-  exit(1)
-
-source_to_topics = {}
-for line in open(sys.argv[1],'r'):
-  term,cls = line.split()
-  source_to_topics[term] = cls
-
-target_to_topics = {}
-for line in open(sys.argv[2],'r'):
-  term,cls = line.split()
-  target_to_topics[term] = cls
-
-for line in sys.stdin:
-  source, target, tail = line.split(" ||| ")
-
-  for token in source.split():
-    print source_to_topics[token],
-  print "|||",
-  for token in target.split():
-    print target_to_topics[token],
-  print "|||", tail,
diff --git a/gi/pyp-topics/scripts/topics.py b/gi/pyp-topics/scripts/topics.py
deleted file mode 100755
index 0db1af71..00000000
--- a/gi/pyp-topics/scripts/topics.py
+++ /dev/null
@@ -1,20 +0,0 @@
-#!/usr/bin/python
-
-import sys
-
-if len(sys.argv) != 2:
-  print "Usage: topics.py words-per-topic"
-  exit(1)
-
-for t,line in enumerate(sys.stdin):
-  tokens = line.split()
-  terms = []
-  for token in tokens:
-    elements = token.rsplit(':',1)
-    terms.append((int(elements[1]),elements[0]))
-  terms.sort()
-  terms.reverse()
-
-  print "Topic %d:" % t
-  map(lambda (x,y) : sys.stdout.write("   %s:%s\n" % (y,x)), terms[:int(sys.argv[1])])
-  print
diff --git a/gi/pyp-topics/src/Makefile.am b/gi/pyp-topics/src/Makefile.am
deleted file mode 100644
index d3f95d0b..00000000
--- a/gi/pyp-topics/src/Makefile.am
+++ /dev/null
@@ -1,16 +0,0 @@
-bin_PROGRAMS = pyp-topics-train pyp-contexts-train #mpi-pyp-contexts-train
-
-contexts_lexer.cc: contexts_lexer.l
-	$(LEX) -s -CF -8 -o$@ $<
-
-pyp_topics_train_SOURCES = mt19937ar.c corpus.cc gzstream.cc pyp-topics.cc train.cc contexts_lexer.cc contexts_corpus.cc
-pyp_topics_train_LDADD = $(top_srcdir)/utils/libutils.a -lz
-
-pyp_contexts_train_SOURCES = mt19937ar.c corpus.cc gzstream.cc pyp-topics.cc contexts_lexer.cc contexts_corpus.cc train-contexts.cc
-pyp_contexts_train_LDADD = $(top_srcdir)/utils/libutils.a -lz
-
-#mpi_pyp_contexts_train_SOURCES = mt19937ar.c corpus.cc gzstream.cc mpi-pyp-topics.cc contexts_lexer.cc contexts_corpus.cc mpi-train-contexts.cc
-#mpi_pyp_contexts_train_LDADD = $(top_srcdir)/utils/libutils.a -lz
-
-AM_CPPFLAGS = -W -Wall -Wno-sign-compare -funroll-loops -I../../../utils
-
diff --git a/gi/pyp-topics/src/Makefile.mpi b/gi/pyp-topics/src/Makefile.mpi
deleted file mode 100644
index b7b8a290..00000000
--- a/gi/pyp-topics/src/Makefile.mpi
+++ /dev/null
@@ -1,26 +0,0 @@
-BLD_ARCH=$(shell uname -s)
--include macros.${BLD_ARCH}
-
-local_objs = mt19937ar.o corpus.o gzstream.o mpi-pyp-topics.o contexts_lexer.o contexts_corpus.o mpi-train-contexts.o
-
-all: mpi-pyp-contexts-train
-
--include makefile.depend
-
-#-----------------------#
-# Local stuff
-#-----------------------#
-
-mpi-pyp-contexts-train: mpi-train-contexts.o $(local_objs)
-	$(CXX) -o $@ $^ $(LDFLAGS)
-
-.PHONY: depend echo
-depend:
-#$(CXX) -MM $(CXXFLAGS) *.cc *.c | sed 's/^\(.*\.o:\)/obj\/\1/' > makefile.depend
-	$(CXX) -MM $(CXXFLAGS) *.cc *.c > makefile.depend
-
-clean:
-	rm -f *.o
-
-#clobber: clean
-#	rm makefile.depend ../bin/${ARCH}/*
diff --git a/gi/pyp-topics/src/clock_gettime_stub.c b/gi/pyp-topics/src/clock_gettime_stub.c
deleted file mode 100644
index 4883b7c1..00000000
--- a/gi/pyp-topics/src/clock_gettime_stub.c
+++ /dev/null
@@ -1,141 +0,0 @@
-/*
- * Copyright (c), MM Weiss
- * All rights reserved.
- * 
- * Redistribution and use in source and binary forms, with or without modification, 
- * are permitted provided that the following conditions are met:
- * 
- *     1. Redistributions of source code must retain the above copyright notice, 
- *     this list of conditions and the following disclaimer.
- *     
- *     2. Redistributions in binary form must reproduce the above copyright notice, 
- *     this list of conditions and the following disclaimer in the documentation 
- *     and/or other materials provided with the distribution.
- *     
- *     3. Neither the name of the MM Weiss nor the names of its contributors 
- *     may be used to endorse or promote products derived from this software without 
- *     specific prior written permission.
- * 
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY 
- * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES 
- * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT 
- * SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, 
- * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT 
- * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) 
- * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR 
- * TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, 
- * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- */
-
-/*
- *  clock_gettime_stub.c
- *  gcc -Wall -c clock_gettime_stub.c
- *  posix realtime functions; MacOS user space glue
- */
- 
-/*  @comment
- *  other possible implementation using intel builtin rdtsc
- *  rdtsc-workaround: http://www.mcs.anl.gov/~kazutomo/rdtsc.html
- *  
- *  we could get the ticks by doing this
- * 
- *  __asm __volatile("mov %%ebx, %%esi\n\t"
- *  		"cpuid\n\t"
- *  		"xchg %%esi, %%ebx\n\t"
- *  		"rdtsc"
- *  		: "=a" (a),
- *  		  "=d" (d)
- * 	);
- 
- *  we could even replace our tricky sched_yield call by assembly code to get a better accurency,
- *  anyway the following C stub will satisfy 99% of apps using posix clock_gettime call, 
- *  moreover, the setter version (clock_settime) could be easly written using mach primitives:
- *  http://www.opensource.apple.com/source/xnu/xnu-${VERSION}/osfmk/man/ (clock_[set|get]_time)
- *  
- *  hackers don't be crackers, don't you use a flush toilet?
- * 
- *
- *  @see draft: ./posix-realtime-stub/posix-realtime-stub.c
- *
- */
- 
-
-#ifdef __APPLE__
-
-#pragma weak clock_gettime
-
-#include <sys/time.h>
-#include <sys/resource.h>
-#include <mach/mach.h>
-#include <mach/clock.h>
-#include <mach/mach_time.h>
-#include <errno.h>
-#include <unistd.h>
-#include <sched.h>
-
-typedef enum {
-	CLOCK_REALTIME,
-	CLOCK_MONOTONIC,
-	CLOCK_PROCESS_CPUTIME_ID,
-	CLOCK_THREAD_CPUTIME_ID
-} clockid_t;
-
-static mach_timebase_info_data_t __clock_gettime_inf;
-
-static int clock_gettime(clockid_t clk_id, struct timespec *tp) {
-	kern_return_t   ret;
-	clock_serv_t    clk;
-	clock_id_t clk_serv_id;
-	mach_timespec_t tm;
-	
-	uint64_t start, end, delta, nano;
-	
-	//task_basic_info_data_t tinfo;
-	//task_thread_times_info_data_t ttinfo;
-	//mach_msg_type_number_t tflag;
-	
-	int retval = -1;
-	switch (clk_id) {
-		case CLOCK_REALTIME:
-		case CLOCK_MONOTONIC:
-			clk_serv_id = clk_id == CLOCK_REALTIME ? CALENDAR_CLOCK : SYSTEM_CLOCK;
-			if (KERN_SUCCESS == (ret = host_get_clock_service(mach_host_self(), clk_serv_id, &clk))) {
-				if (KERN_SUCCESS == (ret = clock_get_time(clk, &tm))) {
-					tp->tv_sec  = tm.tv_sec;
-					tp->tv_nsec = tm.tv_nsec;
-					retval = 0;
-				}
-			}
-			if (KERN_SUCCESS != ret) {
-				errno = EINVAL;
-				retval = -1;
-			}
-		break;
-		case CLOCK_PROCESS_CPUTIME_ID:
-		case CLOCK_THREAD_CPUTIME_ID:
-			start = mach_absolute_time();
-			if (clk_id == CLOCK_PROCESS_CPUTIME_ID) {
-				getpid();
-			} else {
-				sched_yield();
-			}
-			end = mach_absolute_time();
-			delta = end - start;	
-			if (0 == __clock_gettime_inf.denom) {
-				mach_timebase_info(&__clock_gettime_inf);
-			}
-			nano = delta * __clock_gettime_inf.numer / __clock_gettime_inf.denom;
-			tp->tv_sec = nano * 1e-9;  
-			tp->tv_nsec = nano - (tp->tv_sec * 1e9);
-			retval = 0;
-		break;
-		default:
-			errno = EINVAL;
-			retval = -1;
-	}
-	return retval;
-}
-
-#endif // __APPLE__
-
-/* EOF */
diff --git a/gi/pyp-topics/src/contexts_corpus.cc b/gi/pyp-topics/src/contexts_corpus.cc
deleted file mode 100644
index 92b1b34c..00000000
--- a/gi/pyp-topics/src/contexts_corpus.cc
+++ /dev/null
@@ -1,164 +0,0 @@
-#include <sstream>
-#include <iostream>
-#include <set>
-
-#include "contexts_corpus.hh"
-#include "gzstream.hh"
-#include "contexts_lexer.h"
-
-#include <boost/tuple/tuple.hpp>
-
-
-using namespace std;
-
-//////////////////////////////////////////////////
-// ContextsCorpus
-//////////////////////////////////////////////////
-
-bool read_callback_binary_contexts = false;
-
-void read_callback(const ContextsLexer::PhraseContextsType& new_contexts, void* extra) {
-  assert(new_contexts.contexts.size() == new_contexts.counts.size());
-
-  boost::tuple<ContextsCorpus*, BackoffGenerator*, map<string,int>* >* extra_pair
-    = static_cast< boost::tuple<ContextsCorpus*, BackoffGenerator*, map<string,int>* >* >(extra);
-
-  ContextsCorpus* corpus_ptr = extra_pair->get<0>();
-  BackoffGenerator* backoff_gen = extra_pair->get<1>();
-  //map<string,int>* counts = extra_pair->get<2>();
-
-  Document* doc(new Document());
-
-  //cout << "READ: " << new_contexts.phrase << "\t";
-  for (int i=0; i < (int)new_contexts.counts.size(); ++i) {
-    int cache_word_count = corpus_ptr->m_dict.max();
-
-    //string context_str = corpus_ptr->m_dict.toString(new_contexts.contexts[i]);
-    int context_index = new_contexts.counts.at(i).first;
-    string context_str = corpus_ptr->m_dict.toString(new_contexts.contexts[context_index]);
-
-    // filter out singleton contexts
-    //if (!counts->empty()) {
-    //  map<string,int>::const_iterator find_it = counts->find(context_str);
-    //  if (find_it == counts->end() || find_it->second < 2)
-    //    continue;
-    //}
-
-    WordID id = corpus_ptr->m_dict.Convert(context_str);
-    if (cache_word_count != corpus_ptr->m_dict.max()) {
-      corpus_ptr->m_backoff->terms_at_level(0)++;
-      corpus_ptr->m_num_types++;
-    }
-
-    //int count = new_contexts.counts[i];
-    int count = new_contexts.counts.at(i).second;
-    if (read_callback_binary_contexts) {
-      doc->push_back(id);
-      corpus_ptr->m_num_terms++;
-    }
-    else {
-      for (int j=0; j<count; ++j)
-        doc->push_back(id);
-      corpus_ptr->m_num_terms += count;
-    }
-
-    // generate the backoff map
-    if (backoff_gen) {
-      int order = 1;
-      WordID backoff_id = id;
-      //ContextsLexer::Context backedoff_context = new_contexts.contexts[i];
-      ContextsLexer::Context backedoff_context = new_contexts.contexts[context_index];
-      while (true) {
-        if (!corpus_ptr->m_backoff->has_backoff(backoff_id)) {
-          //cerr << "Backing off from " << corpus_ptr->m_dict.Convert(backoff_id) << " to ";
-          backedoff_context = (*backoff_gen)(backedoff_context);
-
-          if (backedoff_context.empty()) {
-            //cerr << "Nothing." << endl;
-            (*corpus_ptr->m_backoff)[backoff_id] = -1;
-            break;
-          }
-
-          if (++order > corpus_ptr->m_backoff->order())
-            corpus_ptr->m_backoff->order(order);
-
-          int cache_word_count = corpus_ptr->m_dict.max();
-          int new_backoff_id = corpus_ptr->m_dict.Convert(backedoff_context);
-          if (cache_word_count != corpus_ptr->m_dict.max())
-            corpus_ptr->m_backoff->terms_at_level(order-1)++;
-
-          //cerr << corpus_ptr->m_dict.Convert(new_backoff_id) << " ." << endl;
-
-          backoff_id = ((*corpus_ptr->m_backoff)[backoff_id] = new_backoff_id);
-        }
-        else break;
-      }
-    }
-    //cout << context_str << " (" << id << ") ||| C=" << count << " ||| ";
-  }
-  //cout << endl;
-
-  //if (!doc->empty()) {
-    corpus_ptr->m_documents.push_back(doc);
-    corpus_ptr->m_keys.push_back(new_contexts.phrase);
-  //}
-}
-
-void filter_callback(const ContextsLexer::PhraseContextsType& new_contexts, void* extra) {
-  assert(new_contexts.contexts.size() == new_contexts.counts.size());
-
-  map<string,int>* context_counts = (static_cast<map<string,int>*>(extra));
-
-  for (int i=0; i < (int)new_contexts.counts.size(); ++i) {
-    int context_index = new_contexts.counts.at(i).first;
-    int count = new_contexts.counts.at(i).second;
-    //if (read_callback_binary_contexts) count = 1;
-    //int count = new_contexts.counts[i];
-    pair<map<string,int>::iterator,bool> result 
-      = context_counts->insert(make_pair(Dict::toString(new_contexts.contexts[context_index]),count));
-      //= context_counts->insert(make_pair(Dict::toString(new_contexts.contexts[i]),count));
-    if (!result.second)
-      result.first->second += count;
-  }
-}
-
-
-unsigned ContextsCorpus::read_contexts(const string &filename, 
-                                       BackoffGenerator* backoff_gen_ptr,
-                                       bool /*filter_singeltons*/,
-                                       bool binary_contexts) {
-  read_callback_binary_contexts = binary_contexts;
-
-  map<string,int> counts;
-  //if (filter_singeltons) 
-  {
-  //  cerr << "--- Filtering singleton contexts ---" << endl;
-
-    igzstream in(filename.c_str());
-    ContextsLexer::ReadContexts(&in, filter_callback, &counts);
-  }
-
-  m_num_terms = 0;
-  m_num_types = 0;
-
-  igzstream in(filename.c_str());
-  boost::tuple<ContextsCorpus*, BackoffGenerator*, map<string,int>* > extra_pair(this,backoff_gen_ptr,&counts);
-  ContextsLexer::ReadContexts(&in, read_callback, &extra_pair);
-
-  //m_num_types = m_dict.max();
-
-  cerr << "Read backoff with order " << m_backoff->order() << "\n";
-  for (int o=0; o<m_backoff->order(); o++)
-    cerr << "  Terms at " << o << " = " << m_backoff->terms_at_level(o) << endl;
-  //cerr << endl;
-
-  int i=0; double av_freq=0;
-  for (map<string,int>::const_iterator it=counts.begin(); it != counts.end(); ++it, ++i) {
-    WordID id = m_dict.Convert(it->first);
-    m_context_counts[id] = it->second;
-    av_freq += it->second;
-  }
-  cerr << "  Average term frequency = " << av_freq / (double) i << endl;
-
-  return m_documents.size();
-}
diff --git a/gi/pyp-topics/src/contexts_corpus.hh b/gi/pyp-topics/src/contexts_corpus.hh
deleted file mode 100644
index 2527f655..00000000
--- a/gi/pyp-topics/src/contexts_corpus.hh
+++ /dev/null
@@ -1,90 +0,0 @@
-#ifndef _CONTEXTS_CORPUS_HH
-#define _CONTEXTS_CORPUS_HH
-
-#include <vector>
-#include <string>
-#include <map>
-#include <tr1/unordered_map>
-
-#include <boost/ptr_container/ptr_vector.hpp>
-
-#include "corpus.hh"
-#include "contexts_lexer.h"
-#include "dict.h"
-
-
-class BackoffGenerator {
-public:
-  virtual ContextsLexer::Context
-    operator()(const ContextsLexer::Context& c) = 0;
-
-protected:
-  ContextsLexer::Context strip_edges(const ContextsLexer::Context& c) {
-    if (c.size() <= 1) return ContextsLexer::Context();
-    assert(c.size() % 2 == 1);
-    return ContextsLexer::Context(c.begin() + 1, c.end() - 1);
-  }
-};
-
-class NullBackoffGenerator : public BackoffGenerator {
-  virtual ContextsLexer::Context
-    operator()(const ContextsLexer::Context&) 
-    { return ContextsLexer::Context(); }
-};
-
-class SimpleBackoffGenerator : public BackoffGenerator {
-  virtual ContextsLexer::Context
-    operator()(const ContextsLexer::Context& c) { 
-      if (c.size() <= 3)
-        return ContextsLexer::Context();
-      return strip_edges(c); 
-    }
-};
-
-
-////////////////////////////////////////////////////////////////
-// ContextsCorpus
-////////////////////////////////////////////////////////////////
-
-class ContextsCorpus : public Corpus {
-  friend void read_callback(const ContextsLexer::PhraseContextsType&, void*);
-
-public:
-    ContextsCorpus() : m_backoff(new TermBackoff) {}
-    virtual ~ContextsCorpus() {}
-
-    virtual unsigned read_contexts(const std::string &filename, 
-                                   BackoffGenerator* backoff_gen=0,
-                                   bool filter_singeltons=false,
-                                   bool binary_contexts=false);
-
-    TermBackoffPtr backoff_index() {
-      return m_backoff;
-    }
-
-    std::vector<std::string> context2string(const WordID& id) const {
-      std::vector<std::string> res;
-      assert (id >= 0);
-      m_dict.AsVector(id, &res);
-      return res;
-    }
-
-    virtual int context_count(const WordID& id) const {
-      return m_context_counts.find(id)->second;
-    }
-
-
-    const std::string& key(const int& i) const {
-      return m_keys.at(i);
-    }
-
-    const Dict& dict() const { return m_dict; }
-
-protected:
-    TermBackoffPtr m_backoff;
-    Dict m_dict;
-    std::vector<std::string> m_keys;
-    std::tr1::unordered_map<int,int> m_context_counts;
-};
-
-#endif // _CONTEXTS_CORPUS_HH
diff --git a/gi/pyp-topics/src/contexts_lexer.h b/gi/pyp-topics/src/contexts_lexer.h
deleted file mode 100644
index 66004990..00000000
--- a/gi/pyp-topics/src/contexts_lexer.h
+++ /dev/null
@@ -1,22 +0,0 @@
-#ifndef _CONTEXTS_LEXER_H_
-#define _CONTEXTS_LEXER_H_ 
-
-#include <iostream>
-#include <vector>
-#include <string>
-
-#include "dict.h" 
-
-struct ContextsLexer {
-  typedef std::vector<std::string> Context;
-  struct PhraseContextsType {
-    std::string          phrase;
-    std::vector<Context> contexts;
-    std::vector< std::pair<int,int> >     counts;
-  };
-
-  typedef void (*ContextsCallback)(const PhraseContextsType& new_contexts, void* extra);
-  static void ReadContexts(std::istream* in, ContextsCallback func, void* extra);
-};
-
-#endif
diff --git a/gi/pyp-topics/src/contexts_lexer.l b/gi/pyp-topics/src/contexts_lexer.l
deleted file mode 100644
index 64cd7ca3..00000000
--- a/gi/pyp-topics/src/contexts_lexer.l
+++ /dev/null
@@ -1,113 +0,0 @@
-%{
-#include "contexts_lexer.h"
-
-#include <string>
-#include <iostream>
-#include <sstream>
-#include <cstring>
-#include <cassert>
-#include <algorithm>
-
-int lex_line = 0;
-std::istream* contextslex_stream = NULL;
-ContextsLexer::ContextsCallback contexts_callback = NULL;
-void* contexts_callback_extra = NULL;
-
-#undef YY_INPUT
-#define YY_INPUT(buf, result, max_size) (result = contextslex_stream->read(buf, max_size).gcount())
-
-#define YY_SKIP_YYWRAP 1
-int num_phrases = 0;
-int yywrap() { return 1; }
-
-#define MAX_TOKEN_SIZE 255
-std::string contextslex_tmp_token(MAX_TOKEN_SIZE, '\0');
-ContextsLexer::PhraseContextsType current_contexts;
-
-#define MAX_CONTEXT_SIZE 255
-//std::string tmp_context[MAX_CONTEXT_SIZE];
-ContextsLexer::Context tmp_context;
-
-
-void contextslex_reset() {
-  current_contexts.phrase.clear();
-  current_contexts.contexts.clear();
-  current_contexts.counts.clear();
-  tmp_context.clear();
-}
-
-%}
-
-INT [\-+]?[0-9]+|inf|[\-+]inf
-
-%x CONTEXT COUNT COUNT_END
-%%
-
-<INITIAL>[^\t]+	{ 
-    contextslex_reset();
-    current_contexts.phrase.assign(yytext, yyleng);
-    BEGIN(CONTEXT);
-  }
-<INITIAL>\t	{ 
-    ; 
-  }
-
-<INITIAL,CONTEXT,COUNT>\n	{
-    std::cerr << "ERROR: contexts_lexer.l: unexpected newline while trying to read phrase|context|count." << std::endl;
-    abort();
-  }
-
-<CONTEXT>\|\|\|	{
-    current_contexts.contexts.push_back(tmp_context);
-    tmp_context.clear();
-		BEGIN(COUNT);
-	}
-<CONTEXT>[^ \t]+	{ 
-		contextslex_tmp_token.assign(yytext, yyleng);
-    tmp_context.push_back(contextslex_tmp_token);
-  }
-<CONTEXT>[ \t]+	{ ; }
-
-<COUNT>[ \t]+	{ ; }
-<COUNT>C={INT} { 
-		current_contexts.counts.push_back(std::make_pair(current_contexts.counts.size(), atoi(yytext+2)));
-    BEGIN(COUNT_END);
-  }
-<COUNT>.	{ 
-    std::cerr << "ERROR: contexts_lexer.l: unexpected content while reading count." << std::endl;
-    abort();
-  }
-
-<COUNT_END>[ \t]+  { ; }
-<COUNT_END>\|\|\|	{
-		BEGIN(CONTEXT);
-  }
-<COUNT_END>\n {
-    //std::cerr << "READ:" << current_contexts.phrase << " with " << current_contexts.contexts.size() 
-    //  << " contexts, and " << current_contexts.counts.size() << " counts." << std::endl;
-    std::sort(current_contexts.counts.rbegin(), current_contexts.counts.rend()); 
-
-		contexts_callback(current_contexts, contexts_callback_extra);
-    current_contexts.phrase.clear();
-    current_contexts.contexts.clear();
-    current_contexts.counts.clear();
-		BEGIN(INITIAL);
-  }
-<COUNT_END>.  { 
-		contextslex_tmp_token.assign(yytext, yyleng);
-    std::cerr << "ERROR: contexts_lexer.l: unexpected content while looking for ||| closing count." << std::endl;
-    abort();
-  }
-
-%%
-
-#include "filelib.h" 
-
-void ContextsLexer::ReadContexts(std::istream* in, ContextsLexer::ContextsCallback func, void* extra) {
-  lex_line = 1;
-  contextslex_stream = in;
-  contexts_callback_extra = extra,
-  contexts_callback = func;
-  yylex();
-}
-
diff --git a/gi/pyp-topics/src/corpus.cc b/gi/pyp-topics/src/corpus.cc
deleted file mode 100644
index f182381f..00000000
--- a/gi/pyp-topics/src/corpus.cc
+++ /dev/null
@@ -1,104 +0,0 @@
-#include <sstream>
-#include <iostream>
-#include <set>
-
-#include "corpus.hh"
-#include "gzstream.hh"
-
-using namespace std;
-
-//////////////////////////////////////////////////
-// Corpus
-//////////////////////////////////////////////////
-
-Corpus::Corpus() : m_num_terms(0), m_num_types(0) {}
-
-unsigned Corpus::read(const std::string &filename) {
-  m_num_terms = 0;
-  m_num_types = 0;
-  std::set<int> seen_types;
-
-  igzstream in(filename.c_str());
-
-  string buf;
-  int token;
-  unsigned doc_count=0;
-  while (getline(in, buf)) {
-    Document* doc(new Document());
-    istringstream ss(buf);
-
-    ss >> token; // the number of unique terms
-
-    char delimeter;
-    int count;
-    while(ss >> token >> delimeter >> count) {
-      for (int i=0; i<count; ++i)
-        doc->push_back(token);
-      m_num_terms += count;
-      seen_types.insert(token);
-    }
-
-    m_documents.push_back(doc);
-    doc_count++;
-  }
-
-  m_num_types = seen_types.size();
-
-  return doc_count;
-}
-
-
-//////////////////////////////////////////////////
-// TestCorpus
-//////////////////////////////////////////////////
-
-TestCorpus::TestCorpus() {}
-
-void TestCorpus::read(const std::string &filename) {
-  igzstream in(filename.c_str());
-
-  string buf;
-  Term term;
-  DocumentId doc;
-  char delimeter;
-  while (getline(in, buf)) {
-    DocumentTerms* line(new DocumentTerms());
-    istringstream ss(buf);
-
-    while(ss >> doc >> delimeter >> term)
-      line->push_back(DocumentTerm(doc, term));
-
-    m_lines.push_back(line);
-  }
-}
-
-//////////////////////////////////////////////////
-// TermBackoff
-//////////////////////////////////////////////////
-
-void TermBackoff::read(const std::string &filename) {
-  igzstream in(filename.c_str());
-
-  string buf;
-  int num_terms;
-  getline(in, buf);
-  istringstream ss(buf); 
-  ss >> num_terms >> m_backoff_order;
-
-  m_dict.resize(num_terms, -1);
-  for (int i=0; i<m_backoff_order; ++i) {
-    int count; ss >> count;
-    m_terms_at_order.push_back(count);
-  }
-
-  Term term, backoff;
-  while (getline(in, buf)) {
-    istringstream ss(buf);
-    ss >> term >> backoff;
-
-    assert(term < num_terms);
-    assert(term >= 0);
-
-    m_dict[term] = backoff;
-  }
-}
diff --git a/gi/pyp-topics/src/corpus.hh b/gi/pyp-topics/src/corpus.hh
deleted file mode 100644
index 2aa03527..00000000
--- a/gi/pyp-topics/src/corpus.hh
+++ /dev/null
@@ -1,133 +0,0 @@
-#ifndef _CORPUS_HH
-#define _CORPUS_HH
-
-#include <vector>
-#include <string>
-#include <map>
-#include <limits>
-
-#include <boost/shared_ptr.hpp>
-#include <boost/ptr_container/ptr_vector.hpp>
-
-////////////////////////////////////////////////////////////////
-// Corpus
-////////////////////////////////////////////////////////////////
-typedef int Term;
-
-typedef std::vector<Term> Document;
-typedef std::vector<Term> Terms;
-
-class Corpus {
-public:
-    typedef boost::ptr_vector<Document>::const_iterator const_iterator;
-
-public:
-    Corpus();
-    virtual ~Corpus() {}
-
-    virtual unsigned read(const std::string &filename);
-
-    const_iterator begin() const { return m_documents.begin(); }
-    const_iterator end() const { return m_documents.end(); }
-
-    const Document& at(size_t i) const { return m_documents.at(i); }
-
-    int num_documents() const { return m_documents.size(); }
-    int num_terms() const { return m_num_terms; }
-    int num_types() const { return m_num_types; }
-
-    virtual int context_count(const int&) const {
-      return std::numeric_limits<int>::max();
-    }
-
-protected:
-    int m_num_terms, m_num_types;
-    boost::ptr_vector<Document> m_documents; 
-};
-
-typedef int DocumentId;
-struct DocumentTerm {
-  DocumentTerm(DocumentId d, Term t) : term(t), doc(d) {}
-  Term term;
-  DocumentId doc;
-};
-typedef std::vector<DocumentTerm> DocumentTerms;
-
-class TestCorpus {
-public:
-    typedef boost::ptr_vector<DocumentTerms>::const_iterator const_iterator;
-
-public:
-    TestCorpus();
-    ~TestCorpus() {}
-
-    void read(const std::string &filename);
-
-    const_iterator begin() const { return m_lines.begin(); }
-    const_iterator end() const { return m_lines.end(); }
-
-    int num_instances() const { return m_lines.size(); }
-
-protected:
-    boost::ptr_vector<DocumentTerms> m_lines; 
-};
-
-class TermBackoff {
-public:
-    typedef std::vector<Term> dictionary_type;
-    typedef dictionary_type::const_iterator const_iterator;
-    const static int NullBackoff=-1;
-
-public:
-    TermBackoff() { order(1); }
-    ~TermBackoff() {}
-
-    void read(const std::string &filename);
-
-    const_iterator begin() const { return m_dict.begin(); }
-    const_iterator end() const { return m_dict.end(); }
-
-    const Term& operator[](const Term& t) const {
-      assert(t < static_cast<int>(m_dict.size()));
-      return m_dict[t];
-    }
-
-    Term& operator[](const Term& t) {
-      if (t >= static_cast<int>(m_dict.size()))
-        m_dict.resize(t+1, -1);
-      return m_dict[t];
-    }
-
-    bool has_backoff(const Term& t) {
-      return t >= 0 && t < static_cast<int>(m_dict.size()) && m_dict[t] >= 0;
-    }
-
-    int order() const { return m_backoff_order; }
-    void order(int o) { 
-      if (o >= (int)m_terms_at_order.size())
-        m_terms_at_order.resize(o, 0);
-      m_backoff_order = o; 
-    }
-
-//    int levels() const { return m_terms_at_order.size(); }
-    bool is_null(const Term& term) const { return term < 0; }
-    int terms_at_level(int level) const { 
-      assert (level < (int)m_terms_at_order.size());
-      return m_terms_at_order.at(level);
-    }
-
-    int& terms_at_level(int level) { 
-      assert (level < (int)m_terms_at_order.size());
-      return m_terms_at_order.at(level);
-    }
-
-    int size() const { return m_dict.size(); }
-
-protected:
-    dictionary_type m_dict; 
-    int m_backoff_order;
-    std::vector<int> m_terms_at_order;
-};
-typedef boost::shared_ptr<TermBackoff> TermBackoffPtr;
-
-#endif // _CORPUS_HH
diff --git a/gi/pyp-topics/src/gammadist.c b/gi/pyp-topics/src/gammadist.c
deleted file mode 100644
index 4e260db8..00000000
--- a/gi/pyp-topics/src/gammadist.c
+++ /dev/null
@@ -1,247 +0,0 @@
-/* gammadist.c -- computes probability of samples under / produces samples from a Gamma distribution
- *
- * Mark Johnson, 22nd March 2008
- *
- * WARNING: you need to set the flag -std=c99 to compile
- *
- * gammavariate() was translated from random.py in Python library
- *
- * The Gamma distribution is:
- *
- *   Gamma(x | alpha, beta) = pow(x/beta, alpha-1) * exp(-x/beta) / (gamma(alpha)*beta)
- *
- * shape parameter alpha > 0 (also called c), scale parameter beta > 0 (also called s); 
- * mean is alpha*beta, variance is alpha*beta**2
- *
- * Note that many parameterizations of the Gamma function are in terms of an _inverse_
- * scale parameter beta, which is the inverse of the beta given here.
- *
- * To define a main() that tests the routines, uncomment the following #define:
- */
-/* #define GAMMATEST */
-
-#include <assert.h>
-#include <math.h> 
-
-#include "gammadist.h"
-#include "mt19937ar.h"
-
-/* gammadist() returns the probability density of x under a Gamma(alpha,beta) 
- * distribution
- */
-
-long double gammadist(long double x, long double alpha, long double beta) {
-  assert(alpha > 0);
-  assert(beta > 0);
-  return  pow(x/beta, alpha-1) * exp(-x/beta) / (tgamma(alpha)*beta);
-}
-
-/* lgammadist() returns the log probability density of x under a Gamma(alpha,beta)
- * distribution
- */
-
-long double lgammadist(long double x, long double alpha, long double beta) {
-  assert(alpha > 0);
-  assert(beta > 0);
-  return (alpha-1)*log(x) - alpha*log(beta) - x/beta - lgamma(alpha);
-}
-
-/* This definition of gammavariate is from Python code in
- * the Python random module.
- */
-
-long double gammavariate(long double alpha, long double beta) {
-
-  assert(alpha > 0);
-  assert(beta > 0);
-
-  if (alpha > 1.0) {
-    
-    /* Uses R.C.H. Cheng, "The generation of Gamma variables with
-       non-integral shape parameters", Applied Statistics, (1977), 26,
-       No. 1, p71-74 */
-
-    long double ainv = sqrt(2.0 * alpha - 1.0);
-    long double bbb = alpha - log(4.0);
-    long double ccc = alpha + ainv;
-    
-    while (1) {
-      long double u1 = mt_genrand_real3();
-      if (u1 > 1e-7  || u1 < 0.9999999) {
-	long double u2 = 1.0 - mt_genrand_real3();
-	long double v = log(u1/(1.0-u1))/ainv;
-	long double x = alpha*exp(v);
-	long double z = u1*u1*u2;
-	long double r = bbb+ccc*v-x;
-	if (r + (1.0+log(4.5)) - 4.5*z >= 0.0 || r >= log(z))
-	  return x * beta;
-      }
-    }
-  }
-  else if (alpha == 1.0) {
-    long double u = mt_genrand_real3();
-    while (u <= 1e-7)
-      u = mt_genrand_real3();
-    return -log(u) * beta;
-  }
-  else { 
-    /* alpha is between 0 and 1 (exclusive) 
-       Uses ALGORITHM GS of Statistical Computing - Kennedy & Gentle */
-    
-    while (1) {
-      long double u = mt_genrand_real3();
-      long double b = (exp(1) + alpha)/exp(1);
-      long double p = b*u;
-      long double x = (p <= 1.0) ? pow(p, 1.0/alpha) : -log((b-p)/alpha);
-      long double u1 = mt_genrand_real3();
-      if (! (((p <= 1.0) && (u1 > exp(-x))) ||
-	     ((p > 1.0)  &&  (u1 > pow(x, alpha - 1.0)))))
-	return x * beta;
-    }
-  }
-}
-
-/* betadist() returns the probability density of x under a Beta(alpha,beta)
- * distribution.
- */
-
-long double betadist(long double x, long double alpha, long double beta) {
-  assert(x >= 0);
-  assert(x <= 1);
-  assert(alpha > 0);
-  assert(beta > 0);
-  return pow(x,alpha-1)*pow(1-x,beta-1)*tgamma(alpha+beta)/(tgamma(alpha)*tgamma(beta));
-}
-
-/* lbetadist() returns the log probability density of x under a Beta(alpha,beta)
- * distribution.
- */
-
-long double lbetadist(long double x, long double alpha, long double beta) {
-  assert(x > 0);
-  assert(x < 1);
-  assert(alpha > 0);
-  assert(beta > 0);
-  return (alpha-1)*log(x)+(beta-1)*log(1-x)+lgamma(alpha+beta)-lgamma(alpha)-lgamma(beta);
-}
-
-/* betavariate() generates a sample from a Beta distribution with
- * parameters alpha and beta.
- *
- * 0 < alpha < 1, 0 < beta < 1, mean is alpha/(alpha+beta)
- */
-
-long double betavariate(long double alpha, long double beta) {
-  long double x = gammavariate(alpha, 1);
-  long double y = gammavariate(beta, 1);
-  return x/(x+y);
-}
-
-#ifdef GAMMATEST
-#include <stdio.h>
-
-int main(int argc, char **argv) {
-  int iteration, niterations = 1000;
-
-  for (iteration = 0; iteration < niterations; ++iteration) {
-    long double alpha = 100*mt_genrand_real3();
-    long double gv = gammavariate(alpha, 1);
-    long double pgv = gammadist(gv, alpha, 1);
-    long double pgvl = exp(lgammadist(gv, alpha, 1));
-    fprintf(stderr, "iteration = %d, gammavariate(%lg,1) = %lg, gammadist(%lg,%lg,1) = %lg, exp(lgammadist(%lg,%lg,1) = %lg\n",
-	    iteration, alpha, gv, gv, alpha, pgv, gv, alpha, pgvl);
-  }
-  return 0;
-}
-
-#endif /* GAMMATEST */
-
-
-/* Other routines I tried, but which weren't as good as the ones above */
-
-#if 0
-
-/*! gammavariate() returns samples from a Gamma distribution
- *! where alpha is the shape parameter and beta is the scale 
- *! parameter, using the algorithm described on p. 94 of 
- *! Gentle (1998) Random Number Generation and Monte Carlo Methods, 
- *! Springer.
- */
-
-long double gammavariate(long double alpha) {
-
-  assert(alpha > 0); 
-  
-  if (alpha > 1.0) {
-    while (1) {
-      long double u1 = mt_genrand_real3();
-      long double u2 = mt_genrand_real3();
-      long double v = (alpha - 1/(6*alpha))*u1/(alpha-1)*u2;
-      if (2*(u2-1)/(alpha-1) + v + 1/v <= 2 
-         || 2*log(u2)/(alpha-1) - log(v) + v <= 1)
-	return (alpha-1)*v;
-    }
-  } else if (alpha < 1.0) {  
-    while (1) {
-      long double t = 0.07 + 0.75*sqrt(1-alpha);
-      long double b = alpha + exp(-t)*alpha/t;
-      long double u1 = mt_genrand_real3();
-      long double u2 = mt_genrand_real3();
-      long double v = b*u1;
-      if (v <= 1) {
-	long double x = t*pow(v, 1/alpha);
-	if (u2 <= (2 - x)/(2 + x))
-	  return x;
-	if (u2 <= exp(-x))
-	  return x;
-      }
-      else {
-	long double x = log(t*(b-v)/alpha);
-	long double y = x/t;
-	if (u2*(alpha + y*(1-alpha)) <= 1)
-	  return x;
-	if (u2 <= pow(y,alpha-1))
-	  return x;
-      }
-    }
-  }
-  else  
-    return -log(mt_genrand_real3());
-} 
-
-
-/*! gammavariate() returns a deviate distributed as a gamma
- *! distribution of order alpha, beta, i.e., a waiting time to the alpha'th
- *! event in a Poisson process of unit mean.
- *!
- *! Code from Numerical Recipes
- */
-
-long double nr_gammavariate(long double ia) {
-  int j;
-  long double am,e,s,v1,v2,x,y;
-  assert(ia > 0);
-  if (ia < 10) { 
-    x=1.0; 
-    for (j=1;j<=ia;j++) 
-      x *= mt_genrand_real3();
-    x = -log(x);
-  } else { 
-    do {
-      do {
-	do { 
-	  v1=mt_genrand_real3();
-	  v2=2.0*mt_genrand_real3()-1.0;
-	} while (v1*v1+v2*v2 > 1.0); 
-	y=v2/v1;
-	am=ia-1;
-	s=sqrt(2.0*am+1.0);
-	x=s*y+am;
-      } while (x <= 0.0);
-      e=(1.0+y*y)*exp(am*log(x/am)-s*y);
-    } while (mt_genrand_real3() > e);
-  }
-  return x;
-} 
-
-#endif
diff --git a/gi/pyp-topics/src/gammadist.h b/gi/pyp-topics/src/gammadist.h
deleted file mode 100644
index b6ad6c40..00000000
--- a/gi/pyp-topics/src/gammadist.h
+++ /dev/null
@@ -1,72 +0,0 @@
-/* gammadist.h -- computes probability of samples under / produces samples from a Gamma distribution
- *
- * Mark Johnson, 22nd March 2008
- *
- * gammavariate() was translated from random.py in Python library
- *
- * The Gamma distribution is:
- *
- *   Gamma(x | alpha, beta) = pow(x/beta, alpha-1) * exp(-x/beta) / (gamma(alpha)*beta)
- *
- * shape parameter alpha > 0 (also called c), scale parameter beta > 0 (also called s); 
- * mean is alpha*beta, variance is alpha*beta**2
- *
- * Note that many parameterizations of the Gamma function are in terms of an _inverse_
- * scale parameter beta, which is the inverse of the beta given here.
- */
-
-#ifndef GAMMADIST_H
-#define GAMMADIST_H
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-  
-  /* gammadist() returns the probability density of x under a Gamma(alpha,beta) 
-   * distribution
-   */
-
-  long double gammadist(long double x, long double alpha, long double beta);
-
-  /* lgammadist() returns the log probability density of x under a Gamma(alpha,beta)
-   * distribution
-   */
-
-  long double lgammadist(long double x, long double alpha, long double beta);
-
-  /* gammavariate() generates samples from a Gamma distribution
-   * conditioned on the parameters alpha and beta.
-   * 
-   * alpha > 0, beta > 0, mean is alpha*beta, variance is alpha*beta**2
-   *
-   * Warning: a few older sources define the gamma distribution in terms
-   * of alpha > -1.0
-   */
-
-  long double gammavariate(long double alpha, long double beta);
-
-  /* betadist() returns the probability density of x under a Beta(alpha,beta)
-   * distribution.
-   */
-
-  long double betadist(long double x, long double alpha, long double beta);
-
-  /* lbetadist() returns the log probability density of x under a Beta(alpha,beta)
-   * distribution.
-   */
-  
-  long double lbetadist(long double x, long double alpha, long double beta);
-
-  /* betavariate() generates a sample from a Beta distribution with
-   * parameters alpha and beta.
-   *
-   * 0 < alpha < 1, 0 < beta < 1, mean is alpha/(alpha+beta)
-   */
-
-  long double betavariate(long double alpha, long double beta);
-
-#ifdef __cplusplus
-};
-#endif
-
-#endif /* GAMMADIST_H */
diff --git a/gi/pyp-topics/src/gzstream.cc b/gi/pyp-topics/src/gzstream.cc
deleted file mode 100644
index 7c4d3a12..00000000
--- a/gi/pyp-topics/src/gzstream.cc
+++ /dev/null
@@ -1,165 +0,0 @@
-// ============================================================================
-// gzstream, C++ iostream classes wrapping the zlib compression library.
-// Copyright (C) 2001  Deepak Bandyopadhyay, Lutz Kettner
-//
-// This library is free software; you can redistribute it and/or
-// modify it under the terms of the GNU Lesser General Public
-// License as published by the Free Software Foundation; either
-// version 2.1 of the License, or (at your option) any later version.
-//
-// This library is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-// Lesser General Public License for more details.
-//
-// You should have received a copy of the GNU Lesser General Public
-// License along with this library; if not, write to the Free Software
-// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
-// ============================================================================
-//
-// File          : gzstream.C
-// Revision      : $Revision: 1.1 $
-// Revision_date : $Date: 2006/03/30 04:05:52 $
-// Author(s)     : Deepak Bandyopadhyay, Lutz Kettner
-// 
-// Standard streambuf implementation following Nicolai Josuttis, "The 
-// Standard C++ Library".
-// ============================================================================
-
-#include "gzstream.hh"
-#include <iostream>
-#include <string.h>  // for memcpy
-
-#ifdef GZSTREAM_NAMESPACE
-namespace GZSTREAM_NAMESPACE {
-#endif
-
-// ----------------------------------------------------------------------------
-// Internal classes to implement gzstream. See header file for user classes.
-// ----------------------------------------------------------------------------
-
-// --------------------------------------
-// class gzstreambuf:
-// --------------------------------------
-
-gzstreambuf* gzstreambuf::open( const char* name, int open_mode) {
-    if ( is_open())
-        return (gzstreambuf*)0;
-    mode = open_mode;
-    // no append nor read/write mode
-    if ((mode & std::ios::ate) || (mode & std::ios::app)
-        || ((mode & std::ios::in) && (mode & std::ios::out)))
-        return (gzstreambuf*)0;
-    char  fmode[10];
-    char* fmodeptr = fmode;
-    if ( mode & std::ios::in)
-        *fmodeptr++ = 'r';
-    else if ( mode & std::ios::out)
-        *fmodeptr++ = 'w';
-    *fmodeptr++ = 'b';
-    *fmodeptr = '\0';
-    file = gzopen( name, fmode);
-    if (file == 0)
-        return (gzstreambuf*)0;
-    opened = 1;
-    return this;
-}
-
-gzstreambuf * gzstreambuf::close() {
-    if ( is_open()) {
-        sync();
-        opened = 0;
-        if ( gzclose( file) == Z_OK)
-            return this;
-    }
-    return (gzstreambuf*)0;
-}
-
-int gzstreambuf::underflow() { // used for input buffer only
-    if ( gptr() && ( gptr() < egptr()))
-        return * reinterpret_cast<unsigned char *>( gptr());
-
-    if ( ! (mode & std::ios::in) || ! opened)
-        return EOF;
-    // Josuttis' implementation of inbuf
-    int n_putback = gptr() - eback();
-    if ( n_putback > 4)
-        n_putback = 4;
-    memcpy( buffer + (4 - n_putback), gptr() - n_putback, n_putback);
-
-    int num = gzread( file, buffer+4, bufferSize-4);
-    if (num <= 0) // ERROR or EOF
-        return EOF;
-
-    // reset buffer pointers
-    setg( buffer + (4 - n_putback),   // beginning of putback area
-          buffer + 4,                 // read position
-          buffer + 4 + num);          // end of buffer
-
-    // return next character
-    return * reinterpret_cast<unsigned char *>( gptr());    
-}
-
-int gzstreambuf::flush_buffer() {
-    // Separate the writing of the buffer from overflow() and
-    // sync() operation.
-    int w = pptr() - pbase();
-    if ( gzwrite( file, pbase(), w) != w)
-        return EOF;
-    pbump( -w);
-    return w;
-}
-
-int gzstreambuf::overflow( int c) { // used for output buffer only
-    if ( ! ( mode & std::ios::out) || ! opened)
-        return EOF;
-    if (c != EOF) {
-        *pptr() = c;
-        pbump(1);
-    }
-    if ( flush_buffer() == EOF)
-        return EOF;
-    return c;
-}
-
-int gzstreambuf::sync() {
-    // Changed to use flush_buffer() instead of overflow( EOF)
-    // which caused improper behavior with std::endl and flush(),
-    // bug reported by Vincent Ricard.
-    if ( pptr() && pptr() > pbase()) {
-        if ( flush_buffer() == EOF)
-            return -1;
-    }
-    return 0;
-}
-
-// --------------------------------------
-// class gzstreambase:
-// --------------------------------------
-
-gzstreambase::gzstreambase( const char* name, int mode) {
-    init( &buf);
-    open( name, mode);
-}
-
-gzstreambase::~gzstreambase() {
-    buf.close();
-}
-
-void gzstreambase::open( const char* name, int open_mode) {
-    if ( ! buf.open( name, open_mode))
-        clear( rdstate() | std::ios::badbit);
-}
-
-void gzstreambase::close() {
-    if ( buf.is_open())
-        if ( ! buf.close())
-            clear( rdstate() | std::ios::badbit);
-}
-
-#ifdef GZSTREAM_NAMESPACE
-} // namespace GZSTREAM_NAMESPACE
-#endif
-
-// ============================================================================
-// EOF //
diff --git a/gi/pyp-topics/src/gzstream.hh b/gi/pyp-topics/src/gzstream.hh
deleted file mode 100644
index ad9785fd..00000000
--- a/gi/pyp-topics/src/gzstream.hh
+++ /dev/null
@@ -1,121 +0,0 @@
-// ============================================================================
-// gzstream, C++ iostream classes wrapping the zlib compression library.
-// Copyright (C) 2001  Deepak Bandyopadhyay, Lutz Kettner
-//
-// This library is free software; you can redistribute it and/or
-// modify it under the terms of the GNU Lesser General Public
-// License as published by the Free Software Foundation; either
-// version 2.1 of the License, or (at your option) any later version.
-//
-// This library is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-// Lesser General Public License for more details.
-//
-// You should have received a copy of the GNU Lesser General Public
-// License along with this library; if not, write to the Free Software
-// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
-// ============================================================================
-//
-// File          : gzstream.h
-// Revision      : $Revision: 1.1 $
-// Revision_date : $Date: 2006/03/30 04:05:52 $
-// Author(s)     : Deepak Bandyopadhyay, Lutz Kettner
-// 
-// Standard streambuf implementation following Nicolai Josuttis, "The 
-// Standard C++ Library".
-// ============================================================================
-
-#ifndef GZSTREAM_H
-#define GZSTREAM_H 1
-
-// standard C++ with new header file names and std:: namespace
-#include <iostream>
-#include <fstream>
-#include <zlib.h>
-
-#ifdef GZSTREAM_NAMESPACE
-namespace GZSTREAM_NAMESPACE {
-#endif
-
-// ----------------------------------------------------------------------------
-// Internal classes to implement gzstream. See below for user classes.
-// ----------------------------------------------------------------------------
-
-class gzstreambuf : public std::streambuf {
-private:
-    static const int bufferSize = 47+256;    // size of data buff
-    // totals 512 bytes under g++ for igzstream at the end.
-
-    gzFile           file;               // file handle for compressed file
-    char             buffer[bufferSize]; // data buffer
-    char             opened;             // open/close state of stream
-    int              mode;               // I/O mode
-
-    int flush_buffer();
-public:
-    gzstreambuf() : opened(0) {
-        setp( buffer, buffer + (bufferSize-1));
-        setg( buffer + 4,     // beginning of putback area
-              buffer + 4,     // read position
-              buffer + 4);    // end position      
-        // ASSERT: both input & output capabilities will not be used together
-    }
-    int is_open() { return opened; }
-    gzstreambuf* open( const char* name, int open_mode);
-    gzstreambuf* close();
-    ~gzstreambuf() { close(); }
-    
-    virtual int     overflow( int c = EOF);
-    virtual int     underflow();
-    virtual int     sync();
-};
-
-class gzstreambase : virtual public std::ios {
-protected:
-    gzstreambuf buf;
-public:
-    gzstreambase() { init(&buf); }
-    gzstreambase( const char* name, int open_mode);
-    ~gzstreambase();
-    void open( const char* name, int open_mode);
-    void close();
-    gzstreambuf* rdbuf() { return &buf; }
-};
-
-// ----------------------------------------------------------------------------
-// User classes. Use igzstream and ogzstream analogously to ifstream and
-// ofstream respectively. They read and write files based on the gz* 
-// function interface of the zlib. Files are compatible with gzip compression.
-// ----------------------------------------------------------------------------
-
-class igzstream : public gzstreambase, public std::istream {
-public:
-    igzstream() : std::istream( &buf) {} 
-    igzstream( const char* name, int open_mode = std::ios::in)
-        : gzstreambase( name, open_mode), std::istream( &buf) {}  
-    gzstreambuf* rdbuf() { return gzstreambase::rdbuf(); }
-    void open( const char* name, int open_mode = std::ios::in) {
-        gzstreambase::open( name, open_mode);
-    }
-};
-
-class ogzstream : public gzstreambase, public std::ostream {
-public:
-    ogzstream() : std::ostream( &buf) {}
-    ogzstream( const char* name, int mode = std::ios::out)
-        : gzstreambase( name, mode), std::ostream( &buf) {}  
-    gzstreambuf* rdbuf() { return gzstreambase::rdbuf(); }
-    void open( const char* name, int open_mode = std::ios::out) {
-        gzstreambase::open( name, open_mode);
-    }
-};
-
-#ifdef GZSTREAM_NAMESPACE
-} // namespace GZSTREAM_NAMESPACE
-#endif
-
-#endif // GZSTREAM_H
-// ============================================================================
-// EOF //
-
diff --git a/gi/pyp-topics/src/log_add.h b/gi/pyp-topics/src/log_add.h
deleted file mode 100644
index e0620c5a..00000000
--- a/gi/pyp-topics/src/log_add.h
+++ /dev/null
@@ -1,30 +0,0 @@
-#ifndef log_add_hh
-#define log_add_hh
-
-#include <limits>
-#include <iostream>
-#include <cassert>
-#include <cmath>
-
-template <typename T>
-struct Log
-{
-    static T zero() { return -std::numeric_limits<T>::infinity(); } 
-
-    static T add(T l1, T l2)
-    {
-        if (l1 == zero()) return l2;
-        if (l1 > l2) 
-            return l1 + std::log(1 + exp(l2 - l1));
-        else
-            return l2 + std::log(1 + exp(l1 - l2));
-    }
-
-    static T subtract(T l1, T l2)
-    {
-        //std::assert(l1 >= l2);
-        return l1 + log(1 - exp(l2 - l1));
-    }
-};
-
-#endif
diff --git a/gi/pyp-topics/src/macros.Linux b/gi/pyp-topics/src/macros.Linux
deleted file mode 100644
index 7c6e7fa7..00000000
--- a/gi/pyp-topics/src/macros.Linux
+++ /dev/null
@@ -1,18 +0,0 @@
-CC = /home/pblunsom/software/bin/mpicc
-CXX = /home/pblunsom/software/bin/mpicxx
-LD = /home/pblunsom/software/bin/mpicxx
-FC = /home/pblunsom/software/bin/mpif77
-
-SOFTWARE_DIR=/export/ws10smt/software
-
-CXXFLAGS = -Wall -I${SOFTWARE_DIR}/include
-CFLAGS = -Wall -I${SOFTWARE_DIR}/include
-FFLAGS = -Wall
-LDFLAGS = -lm -lz -L${SOFTWARE_DIR}/lib \
-	-lboost_program_options -lboost_mpi -lboost_serialization \
-  -lboost_regex -L../../../decoder -lcdec
-
-FFLAGS += -g -O6  -march=native
-CFLAGS += -g -O6  -march=native
-CXXFLAGS += -g -O6  -march=native
-LDFLAGS += -g -O6  -march=native
diff --git a/gi/pyp-topics/src/makefile.darwin b/gi/pyp-topics/src/makefile.darwin
deleted file mode 100644
index af608fd8..00000000
--- a/gi/pyp-topics/src/makefile.darwin
+++ /dev/null
@@ -1,15 +0,0 @@
-CC = /usr/bin/gcc
-CXX = /usr/bin/g++
-LD = /usr/bin/g++
-FC=/usr/bin/g77
-
-ARCH=i686-m64
-CXXFLAGS = -m64 -Wall -I/Users/pblunsom/packages/include 
-CFLAGS = -m64 -Wall -I/Users/pblunsom/packages/include 
-FFLAGS = -m64 -Wall
-LDFLAGS = -L/Users/pblunsom/packages/lib -lboost_program_options -lm -lz
-
-FFLAGS += -g -O3 -funroll-loops #-pg
-CFLAGS += -g -O3 -funroll-loops #-pg
-CXXFLAGS += -g -O3 -funroll-loops #-pg
-LDFLAGS += -g -O3 -funroll-loops #-pg
diff --git a/gi/pyp-topics/src/makefile.depend b/gi/pyp-topics/src/makefile.depend
deleted file mode 100644
index 9b8e306c..00000000
--- a/gi/pyp-topics/src/makefile.depend
+++ /dev/null
@@ -1,4042 +0,0 @@
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- /home/pblunsom/packages/include/boost/smart_ptr/scoped_array.hpp \
- /home/pblunsom/packages/include/boost/checked_delete.hpp \
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- /home/pblunsom/packages/include/boost/pointee.hpp \
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- /home/pblunsom/packages/include/boost/ptr_container/detail/void_ptr_iterator.hpp \
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- /home/pblunsom/packages/include/boost/random/detail/config.hpp \
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- /home/pblunsom/packages/include/boost/random/uniform_01.hpp \
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- /home/pblunsom/packages/include/boost/random/detail/const_mod.hpp \
- /home/pblunsom/packages/include/boost/random/detail/seed.hpp pyp.hh \
- slice-sampler.h log_add.h mt19937ar.h corpus.hh workers.hh \
- /home/pblunsom/packages/include/boost/bind.hpp \
- /home/pblunsom/packages/include/boost/bind/bind.hpp \
- /home/pblunsom/packages/include/boost/is_placeholder.hpp \
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- /home/pblunsom/packages/include/boost/bind/bind_mf_cc.hpp \
- /home/pblunsom/packages/include/boost/bind/bind_mf2_cc.hpp \
- /home/pblunsom/packages/include/boost/bind/placeholders.hpp \
- /home/pblunsom/packages/include/boost/thread/thread.hpp \
- /home/pblunsom/packages/include/boost/thread/detail/platform.hpp \
- /home/pblunsom/packages/include/boost/config/requires_threads.hpp \
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- /home/pblunsom/packages/include/boost/thread/detail/platform.hpp \
- /home/pblunsom/packages/include/boost/thread/exceptions.hpp \
- /home/pblunsom/packages/include/boost/config/abi_prefix.hpp \
- /home/pblunsom/packages/include/boost/config/abi_suffix.hpp \
- /home/pblunsom/packages/include/boost/enable_shared_from_this.hpp \
- /home/pblunsom/packages/include/boost/smart_ptr/enable_shared_from_this.hpp \
- /home/pblunsom/packages/include/boost/smart_ptr/weak_ptr.hpp \
- /home/pblunsom/packages/include/boost/thread/mutex.hpp \
- /home/pblunsom/packages/include/boost/thread/pthread/mutex.hpp \
- /home/pblunsom/packages/include/boost/thread/locks.hpp \
- /home/pblunsom/packages/include/boost/thread/detail/move.hpp \
- /home/pblunsom/packages/include/boost/thread/thread_time.hpp \
- /home/pblunsom/packages/include/boost/date_time/microsec_time_clock.hpp \
- /home/pblunsom/packages/include/boost/date_time/compiler_config.hpp \
- /home/pblunsom/packages/include/boost/date_time/locale_config.hpp \
- /home/pblunsom/packages/include/boost/date_time/c_time.hpp \
- /home/pblunsom/packages/include/boost/date_time/time_clock.hpp \
- /home/pblunsom/packages/include/boost/date_time/filetime_functions.hpp \
- /home/pblunsom/packages/include/boost/date_time/posix_time/posix_time_types.hpp \
- /home/pblunsom/packages/include/boost/date_time/posix_time/ptime.hpp \
- /home/pblunsom/packages/include/boost/date_time/posix_time/posix_time_system.hpp \
- /home/pblunsom/packages/include/boost/date_time/posix_time/posix_time_config.hpp \
- /home/pblunsom/packages/include/boost/config/no_tr1/cmath.hpp \
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- /home/pblunsom/packages/include/boost/date_time/time_resolution_traits.hpp \
- /home/pblunsom/packages/include/boost/date_time/int_adapter.hpp \
- /home/pblunsom/packages/include/boost/date_time/gregorian/gregorian_types.hpp \
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- /home/pblunsom/packages/include/boost/date_time/year_month_day.hpp \
- /home/pblunsom/packages/include/boost/date_time/period.hpp \
- /home/pblunsom/packages/include/boost/date_time/gregorian/greg_calendar.hpp \
- /home/pblunsom/packages/include/boost/date_time/gregorian/greg_weekday.hpp \
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- /home/pblunsom/packages/include/boost/type_traits/is_fundamental.hpp \
- /home/pblunsom/packages/include/boost/thread/condition.hpp timing.h \
- clock_gettime_stub.c contexts_corpus.hh contexts_lexer.h \
- ../../../decoder/dict.h \
- /home/pblunsom/packages/include/boost/functional/hash.hpp \
- /home/pblunsom/packages/include/boost/functional/hash/hash.hpp \
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- /home/pblunsom/packages/include/boost/functional/hash/extensions.hpp \
- /home/pblunsom/packages/include/boost/detail/container_fwd.hpp \
- ../../../decoder/wordid.h gzstream.hh
-clock_gettime_stub.o: clock_gettime_stub.c
-gammadist.o: gammadist.c gammadist.h mt19937ar.h
-mt19937ar.o: mt19937ar.c mt19937ar.h
diff --git a/gi/pyp-topics/src/mpi-corpus.hh b/gi/pyp-topics/src/mpi-corpus.hh
deleted file mode 100644
index f5c478a9..00000000
--- a/gi/pyp-topics/src/mpi-corpus.hh
+++ /dev/null
@@ -1,69 +0,0 @@
-#ifndef _MPI_CORPUS_HH
-#define _MPI_CORPUS_HH
-
-#include <vector>
-#include <string>
-#include <map>
-#include <tr1/unordered_map>
-
-#include <boost/ptr_container/ptr_vector.hpp>
-#include <boost/mpi/environment.hpp>
-#include <boost/mpi/communicator.hpp>
-
-#include "contexts_corpus.hh"
-
-
-////////////////////////////////////////////////////////////////
-// MPICorpus
-////////////////////////////////////////////////////////////////
-
-class MPICorpus : public ContextsCorpus {
-public:
-  MPICorpus() : ContextsCorpus() {
-    boost::mpi::communicator world;
-    m_rank = world.rank();
-    m_size = world.size();
-    m_start = -1;
-    m_end = -1;
-  }
-  virtual ~MPICorpus() {}
-
-  virtual unsigned read_contexts(const std::string &filename, 
-                                 BackoffGenerator* backoff_gen=0,
-                                 bool filter_singeltons=false,
-                                 bool binary_contexts=false) {
-    unsigned result = ContextsCorpus::read_contexts(filename, backoff_gen, filter_singeltons, binary_contexts);
-
-    if (m_rank == 0) std::cerr << "\tLoad balancing terms per mpi segment:" << std::endl;
-    float segment_size = num_terms() / m_size;
-    float term_threshold = segment_size;
-    int seen_terms = 0;
-    std::vector<int> end_points;
-    for (int i=0; i < num_documents(); ++i) {
-      seen_terms += m_documents.at(i).size();
-      if (seen_terms >= term_threshold) {
-        end_points.push_back(i+1);
-        term_threshold += segment_size;
-        if (m_rank == 0) std::cerr << "\t\t" << i+1 << ": " <<  seen_terms << " terms, " << 100*seen_terms / (float)num_terms() << "%" << std::endl;
-      }
-    }
-    m_start = (m_rank == 0 ? 0 : end_points.at(m_rank-1));
-    m_end = (m_rank == m_size-1 ? num_documents() : end_points.at(m_rank));
-
-    return result;
-  }
-
-  void
-  bounds(int* start, int* end) const {
-    *start = m_start;
-    *end = m_end;
-  }
-
-
-
-protected:
-  int m_rank, m_size;
-  int m_start, m_end;
-};
-
-#endif // _MPI_CORPUS_HH
diff --git a/gi/pyp-topics/src/mpi-pyp-topics.cc b/gi/pyp-topics/src/mpi-pyp-topics.cc
deleted file mode 100644
index d6e22af6..00000000
--- a/gi/pyp-topics/src/mpi-pyp-topics.cc
+++ /dev/null
@@ -1,466 +0,0 @@
-#include <boost/mpi/communicator.hpp>
-
-#include "timing.h"
-#include "mpi-pyp-topics.hh"
-
-//#include <boost/date_time/posix_time/posix_time_types.hpp>
-void MPIPYPTopics::sample_corpus(const MPICorpus& corpus, int samples,
-                              int freq_cutoff_start, int freq_cutoff_end,
-                              int freq_cutoff_interval,
-                              int max_contexts_per_document) {
-  Timer timer;
-
-  //int documents = corpus.num_documents();
-  /*
-  m_mpi_start = 0;
-  m_mpi_end = documents;
-  if (m_size != 1) {
-      assert(documents < std::numeric_limits<int>::max());
-      m_mpi_start = (documents / m_size) * m_rank;
-      if (m_rank == m_size-1) m_mpi_end = documents;
-      else m_mpi_end = (documents / m_size)*(m_rank+1);
-  }
-  */
-  corpus.bounds(&m_mpi_start, &m_mpi_end);
-  int local_documents = m_mpi_end - m_mpi_start;
-
-  if (!m_backoff.get()) {
-    m_word_pyps.clear();
-    m_word_pyps.push_back(MPIPYPs());
-  }
-
-  if (m_am_root) std::cerr << "\n Training with " << m_word_pyps.size()-1 << " backoff level"
-    << (m_word_pyps.size()>1 ? ":" : "s:") << std::endl;
-
-  for (int i=0; i<(int)m_word_pyps.size(); ++i) {
-    m_word_pyps.at(i).reserve(m_num_topics);
-    for (int j=0; j<m_num_topics; ++j)
-      m_word_pyps.at(i).push_back(new MPIPYP<int>(0.5, 1.0));
-  }
-  if (m_am_root) std::cerr << std::endl;
-
-  m_document_pyps.reserve(local_documents);
-  //m_document_pyps.reserve(corpus.num_documents());
-  //for (int j=0; j<corpus.num_documents(); ++j)
-  for (int j=0; j<local_documents; ++j)
-    m_document_pyps.push_back(new PYP<int>(0.5, 1.0));
-
-  m_topic_p0 = 1.0/m_num_topics;
-  m_term_p0 = 1.0/corpus.num_types();
-  m_backoff_p0 = 1.0/corpus.num_documents();
-
-  if (m_am_root) std::cerr << " Documents: " << corpus.num_documents() << "(" 
-    << local_documents << ")" << " Terms: " << corpus.num_types() << std::endl;
-
-  int frequency_cutoff = freq_cutoff_start;
-  if (m_am_root) std::cerr << " Context frequency cutoff set to " << frequency_cutoff << std::endl;
-
-  timer.Reset();
-  // Initialisation pass
-  int document_id=0, topic_counter=0;
-  for (int i=0; i<local_documents; ++i) {
-    document_id = i+m_mpi_start;
-
-  //for (Corpus::const_iterator corpusIt=corpus.begin();
-  //     corpusIt != corpus.end(); ++corpusIt, ++document_id) {
-    m_corpus_topics.push_back(DocumentTopics(corpus.at(document_id).size(), 0));
-
-    int term_index=0;
-    for (Document::const_iterator docIt=corpus.at(document_id).begin();
-         docIt != corpus.at(document_id).end(); ++docIt, ++term_index) {
-      topic_counter++;
-      Term term = *docIt;
-
-      // sample a new_topic
-      //int new_topic = (topic_counter % m_num_topics);
-      int freq = corpus.context_count(term);
-      int new_topic = -1;
-      if (freq > frequency_cutoff
-          && (!max_contexts_per_document || term_index < max_contexts_per_document)) {
-        new_topic = sample(i, term);
-        //new_topic = document_id % m_num_topics;
-
-        // add the new topic to the PYPs
-        increment(term, new_topic);
-
-        if (m_use_topic_pyp) {
-          F p0 = m_topic_pyp.prob(new_topic, m_topic_p0);
-          int table_delta = m_document_pyps.at(i).increment(new_topic, p0);
-          if (table_delta)
-            m_topic_pyp.increment(new_topic, m_topic_p0, rnd);
-        }
-        else m_document_pyps.at(i).increment(new_topic, m_topic_p0);
-      }
-
-      m_corpus_topics.at(i).at(term_index) = new_topic;
-    }
-  }
-
-  // Synchronise the topic->word counds across the processes.
-  synchronise();
-
-  if (m_am_root) std::cerr << "  Initialized in " << timer.Elapsed() << " seconds\n";
-
-  int* randomDocIndices = new int[local_documents];
-  for (int i = 0; i < local_documents; ++i)
-	  randomDocIndices[i] = i;
-
-  // Sampling phase
-  for (int curr_sample=0; curr_sample < samples; ++curr_sample) {
-    if (freq_cutoff_interval > 0 && curr_sample != 1
-        && curr_sample % freq_cutoff_interval == 1
-        && frequency_cutoff > freq_cutoff_end) {
-      frequency_cutoff--;
-      if (m_am_root) std::cerr << "\n Context frequency cutoff set to " << frequency_cutoff << std::endl;
-    }
-
-    if (m_am_root) std::cerr << "\n  -- Sample " << curr_sample << " "; std::cerr.flush();
-
-    // Randomize the corpus indexing array
-    int tmp;
-    int processed_terms=0;
-    for (int i = (local_documents-1); i > 0; --i) {
-      //i+1 since j \in [0,i] but rnd() \in [0,1)
-    	int j = (int)(rnd() * (i+1));
-      assert(j >= 0 && j <= i);
-     	tmp = randomDocIndices[i];
-    	randomDocIndices[i] = randomDocIndices[j];
-    	randomDocIndices[j] = tmp;
-    }
-
-    // for each document in the corpus
-    for (int rand_doc=0; rand_doc<local_documents; ++rand_doc) {
-    	int doc_index = randomDocIndices[rand_doc];
-    	int document_id = doc_index + m_mpi_start;
-      const Document& doc = corpus.at(document_id);
-
-      // for each term in the document
-      int term_index=0;
-      Document::const_iterator docEnd = doc.end();
-      for (Document::const_iterator docIt=doc.begin();
-           docIt != docEnd; ++docIt, ++term_index) {
-
-        if (max_contexts_per_document && term_index > max_contexts_per_document)
-          break;
-        
-        Term term = *docIt;
-        int freq = corpus.context_count(term);
-        if (freq < frequency_cutoff)
-          continue;
-
-        processed_terms++;
-
-        // remove the prevous topic from the PYPs
-        int current_topic = m_corpus_topics.at(doc_index).at(term_index);
-        // a negative label mean that term hasn't been sampled yet
-        if (current_topic >= 0) {
-          decrement(term, current_topic);
-
-          int table_delta = m_document_pyps.at(doc_index).decrement(current_topic);
-          if (m_use_topic_pyp && table_delta < 0)
-            m_topic_pyp.decrement(current_topic, rnd);
-        }
-
-        // sample a new_topic
-        int new_topic = sample(doc_index, term);
-
-        // add the new topic to the PYPs
-        m_corpus_topics.at(doc_index).at(term_index) = new_topic;
-        increment(term, new_topic);
-
-        if (m_use_topic_pyp) {
-          F p0 = m_topic_pyp.prob(new_topic, m_topic_p0);
-          int table_delta = m_document_pyps.at(doc_index).increment(new_topic, p0);
-          if (table_delta)
-            m_topic_pyp.increment(new_topic, m_topic_p0, rnd);
-        }
-        else m_document_pyps.at(doc_index).increment(new_topic, m_topic_p0);
-      }
-      if (document_id && document_id % 10000 == 0) {
-        if (m_am_root) std::cerr << "."; std::cerr.flush();
-      }
-    }
-    std::cerr << "|"; std::cerr.flush();  
-
-    // Synchronise the topic->word counds across the processes.
-    synchronise();
-
-    if (m_am_root) std::cerr << " ||| sampled " << processed_terms << " terms.";
-
-    if (curr_sample != 0 && curr_sample % 10 == 0) {
-      if (m_am_root) std::cerr << " ||| time=" << (timer.Elapsed() / 10.0) << " sec/sample" << std::endl;
-      timer.Reset();
-      if (m_am_root) std::cerr << "     ... Resampling hyperparameters"; std::cerr.flush();
-
-      // resample the hyperparamters
-      F log_p=0.0;
-      for (std::vector<MPIPYPs>::iterator levelIt=m_word_pyps.begin();
-           levelIt != m_word_pyps.end(); ++levelIt) {
-        for (MPIPYPs::iterator pypIt=levelIt->begin();
-             pypIt != levelIt->end(); ++pypIt) {
-          pypIt->resample_prior(rnd);
-          log_p += pypIt->log_restaurant_prob();
-        }
-      }
-
-      for (PYPs::iterator pypIt=m_document_pyps.begin();
-           pypIt != m_document_pyps.end(); ++pypIt) {
-        pypIt->resample_prior(rnd);
-        log_p += pypIt->log_restaurant_prob();
-      }
-
-      if (m_use_topic_pyp) {
-        m_topic_pyp.resample_prior(rnd);
-        log_p += m_topic_pyp.log_restaurant_prob();
-      }
-
-      std::cerr.precision(10);
-      if (m_am_root) std::cerr << " ||| LLH=" << log_p << " ||| resampling time=" << timer.Elapsed() << " sec" << std::endl;
-      timer.Reset();
-
-      int k=0;
-      if (m_am_root) std::cerr << "Topics distribution: ";
-      std::cerr.precision(2);
-      for (MPIPYPs::iterator pypIt=m_word_pyps.front().begin();
-           pypIt != m_word_pyps.front().end(); ++pypIt, ++k) {
-        if (m_am_root && k % 5 == 0) std::cerr << std::endl << '\t';
-        if (m_am_root) std::cerr << "<" << k << ":" << pypIt->num_customers() << ","
-          << pypIt->num_types() << "," << m_topic_pyp.prob(k, m_topic_p0) << "> ";
-      }
-      std::cerr.precision(4);
-      if (m_am_root) std::cerr << std::endl;
-    }
-  }
-  delete [] randomDocIndices;
-}
-
-void MPIPYPTopics::synchronise() {
-  // Synchronise the topic->word counds across the processes.
-  //for (std::vector<MPIPYPs>::iterator levelIt=m_word_pyps.begin();
-  //     levelIt != m_word_pyps.end(); ++levelIt) {
-//  std::vector<MPIPYPs>::iterator levelIt=m_word_pyps.begin(); 
-//  {
-//    for (MPIPYPs::iterator pypIt=levelIt->begin(); pypIt != levelIt->end(); ++pypIt) {
-    for (size_t label=0; label < m_word_pyps.at(0).size(); ++label) {
-      MPIPYP<int>& pyp = m_word_pyps.at(0).at(label);
-
-      //if (!m_am_root) boost::mpi::communicator().barrier();
-      //std::cerr << "Before Sync Process " << m_rank << ":";
-      //pyp.debug_info(std::cerr); std::cerr << std::endl;
-      //if (m_am_root) boost::mpi::communicator().barrier();
-
-      MPIPYP<int>::dish_delta_type delta;
-      pyp.synchronise(&delta);
-
-      for (MPIPYP<int>::dish_delta_type::const_iterator it=delta.begin(); it != delta.end(); ++it) {
-        int count = it->second;
-        if (count > 0)
-          for (int i=0; i < count; ++i) increment(it->first, label);
-        if (count < 0)
-          for (int i=0; i > count; --i) decrement(it->first, label);
-      }
-      pyp.reset_deltas();
-
-      //if (!m_am_root) boost::mpi::communicator().barrier();
-      //std::cerr << "After Sync Process " << m_rank << ":";
-      //pyp.debug_info(std::cerr); std::cerr << std::endl;
-      //if (m_am_root) boost::mpi::communicator().barrier();
-    }
-//  }
-    // Synchronise the hierarchical topic pyp
-    MPIPYP<int>::dish_delta_type topic_delta;
-    m_topic_pyp.synchronise(&topic_delta);
-    for (MPIPYP<int>::dish_delta_type::const_iterator it=topic_delta.begin(); it != topic_delta.end(); ++it) {
-      int count = it->second;
-      if (count > 0)
-        for (int i=0; i < count; ++i) 
-          m_topic_pyp.increment(it->first, m_topic_p0, rnd);
-      if (count < 0)
-        for (int i=0; i > count; --i) 
-          m_topic_pyp.decrement(it->first, rnd);
-    }
-    m_topic_pyp.reset_deltas();
-}
-
-void MPIPYPTopics::decrement(const Term& term, int topic, int level) {
-  //std::cerr << "MPIPYPTopics::decrement(" << term << "," << topic << "," << level << ")" << std::endl;
-  m_word_pyps.at(level).at(topic).decrement(term, rnd);
-  if (m_backoff.get()) {
-    Term backoff_term = (*m_backoff)[term];
-    if (!m_backoff->is_null(backoff_term))
-      decrement(backoff_term, topic, level+1);
-  }
-}
-
-void MPIPYPTopics::increment(const Term& term, int topic, int level) {
-  //std::cerr << "MPIPYPTopics::increment(" << term << "," << topic << "," << level << ")" << std::endl;
-  m_word_pyps.at(level).at(topic).increment(term, word_pyps_p0(term, topic, level), rnd);
-
-  if (m_backoff.get()) {
-    Term backoff_term = (*m_backoff)[term];
-    if (!m_backoff->is_null(backoff_term))
-      increment(backoff_term, topic, level+1);
-  }
-}
-
-int MPIPYPTopics::sample(const DocumentId& doc, const Term& term) {
-  // First pass: collect probs
-  F sum=0.0;
-  std::vector<F> sums;
-  for (int k=0; k<m_num_topics; ++k) {
-    F p_w_k = prob(term, k);
-
-    F topic_prob = m_topic_p0;
-    if (m_use_topic_pyp) topic_prob = m_topic_pyp.prob(k, m_topic_p0);
-
-    //F p_k_d = m_document_pyps[doc].prob(k, topic_prob);
-    F p_k_d = m_document_pyps.at(doc).unnormalised_prob(k, topic_prob);
-
-    sum += (p_w_k*p_k_d);
-    sums.push_back(sum);
-  }
-  // Second pass: sample a topic
-  F cutoff = rnd() * sum;
-  for (int k=0; k<m_num_topics; ++k) {
-    if (cutoff <= sums[k])
-      return k;
-  }
-  std::cerr << cutoff << " " << sum << std::endl;
-  assert(false);
-}
-
-MPIPYPTopics::F MPIPYPTopics::word_pyps_p0(const Term& term, int topic, int level) const {
-  //for (int i=0; i<level+1; ++i) std::cerr << "  ";
-  //std::cerr << "MPIPYPTopics::word_pyps_p0(" << term << "," << topic << "," << level << ")" << std::endl;
-
-  F p0 = m_term_p0;
-  if (m_backoff.get()) {
-    //static F fudge=m_backoff_p0; // TODO
-
-    Term backoff_term = (*m_backoff)[term];
-    if (!m_backoff->is_null(backoff_term)) {
-      assert (level < m_backoff->order());
-      //p0 = (1.0/(double)m_backoff->terms_at_level(level))*prob(backoff_term, topic, level+1);
-      p0 = prob(backoff_term, topic, level+1);
-    }
-    else
-      p0 = m_term_p0;
-  }
-  //for (int i=0; i<level+1; ++i) std::cerr << "  ";
-  //std::cerr << "MPIPYPTopics::word_pyps_p0(" << term << "," << topic << "," << level << ") = " << p0 << std::endl;
-  return p0;
-}
-
-MPIPYPTopics::F MPIPYPTopics::prob(const Term& term, int topic, int level) const {
-  //for (int i=0; i<level+1; ++i) std::cerr << "  ";
-  //std::cerr << "MPIPYPTopics::prob(" << term << "," << topic << "," << level << " " << factor << ")" << std::endl;
-
-  F p0 = word_pyps_p0(term, topic, level);
-  F p_w_k = m_word_pyps.at(level).at(topic).prob(term, p0);
-
-  //for (int i=0; i<level+1; ++i) std::cerr << "  ";
-  //std::cerr << "MPIPYPTopics::prob(" << term << "," << topic << "," << level << ") = " << p_w_k << std::endl;
-
-  return p_w_k;
-}
-
-int MPIPYPTopics::max_topic() const {
-  if (!m_use_topic_pyp)
-    return -1;
-
-  F current_max=0.0;
-  int current_topic=-1;
-  for (int k=0; k<m_num_topics; ++k) {
-    F prob = m_topic_pyp.prob(k, m_topic_p0);
-    if (prob > current_max) {
-      current_max = prob;
-      current_topic = k;
-    }
-  }
-  assert(current_topic >= 0);
-  assert(current_max >= 0);
-  return current_max;
-}
-
-std::pair<int,MPIPYPTopics::F> MPIPYPTopics::max(const DocumentId& true_doc) const {
-  //std::cerr << "MPIPYPTopics::max(" << doc << "," << term << ")" << std::endl;
-  // collect probs
-  F current_max=0.0;
-  DocumentId local_doc = true_doc - m_mpi_start;
-  int current_topic=-1;
-  for (int k=0; k<m_num_topics; ++k) {
-    //F p_w_k = prob(term, k);
-
-    F topic_prob = m_topic_p0;
-    if (m_use_topic_pyp)
-      topic_prob = m_topic_pyp.prob(k, m_topic_p0);
-
-    F prob = 0;
-    if (local_doc < 0) prob = topic_prob;
-    else               prob = m_document_pyps.at(local_doc).prob(k, topic_prob);
-
-    if (prob > current_max) {
-      current_max = prob;
-      current_topic = k;
-    }
-  }
-  assert(current_topic >= 0);
-  assert(current_max >= 0);
-  return std::make_pair(current_topic, current_max);
-}
-
-std::pair<int,MPIPYPTopics::F> MPIPYPTopics::max(const DocumentId& true_doc, const Term& term) const {
-  //std::cerr << "MPIPYPTopics::max(" << doc << "," << term << ")" << std::endl;
-  // collect probs
-  F current_max=0.0;
-  DocumentId local_doc = true_doc - m_mpi_start;
-  int current_topic=-1;
-  for (int k=0; k<m_num_topics; ++k) {
-    F p_w_k = prob(term, k);
-
-    F topic_prob = m_topic_p0;
-    if (m_use_topic_pyp)
-      topic_prob = m_topic_pyp.prob(k, m_topic_p0);
-
-    F p_k_d = 0;
-    if (local_doc < 0) p_k_d = topic_prob;
-    else               p_k_d = m_document_pyps.at(local_doc).prob(k, topic_prob);
-
-    F prob = (p_w_k*p_k_d);
-    if (prob > current_max) {
-      current_max = prob;
-      current_topic = k;
-    }
-  }
-  assert(current_topic >= 0);
-  assert(current_max >= 0);
-  return std::make_pair(current_topic, current_max);
-}
-
-std::ostream& MPIPYPTopics::print_document_topics(std::ostream& out) const {
-  for (CorpusTopics::const_iterator corpusIt=m_corpus_topics.begin();
-       corpusIt != m_corpus_topics.end(); ++corpusIt) {
-    int term_index=0;
-    for (DocumentTopics::const_iterator docIt=corpusIt->begin();
-         docIt != corpusIt->end(); ++docIt, ++term_index) {
-      if (term_index) out << " ";
-      out << *docIt;
-    }
-    out << std::endl;
-  }
-  return out;
-}
-
-std::ostream& MPIPYPTopics::print_topic_terms(std::ostream& out) const {
-  for (PYPs::const_iterator pypsIt=m_word_pyps.front().begin();
-       pypsIt != m_word_pyps.front().end(); ++pypsIt) {
-    int term_index=0;
-    for (PYP<int>::const_iterator termIt=pypsIt->begin();
-         termIt != pypsIt->end(); ++termIt, ++term_index) {
-      if (term_index) out << " ";
-      out << termIt->first << ":" << termIt->second;
-    }
-    out << std::endl;
-  }
-  return out;
-}
diff --git a/gi/pyp-topics/src/mpi-pyp-topics.hh b/gi/pyp-topics/src/mpi-pyp-topics.hh
deleted file mode 100644
index d96bc4e5..00000000
--- a/gi/pyp-topics/src/mpi-pyp-topics.hh
+++ /dev/null
@@ -1,106 +0,0 @@
-#ifndef MPI_PYP_TOPICS_HH
-#define MPI_PYP_TOPICS_HH
-
-#include <vector>
-#include <iostream>
-
-#include <boost/ptr_container/ptr_vector.hpp>
-#include <boost/random/uniform_real.hpp>
-#include <boost/random/variate_generator.hpp>
-#include <boost/random/mersenne_twister.hpp>
-#include <boost/random/inversive_congruential.hpp>
-#include <boost/random/linear_congruential.hpp>
-#include <boost/random/lagged_fibonacci.hpp>
-#include <boost/mpi/environment.hpp>
-#include <boost/mpi/communicator.hpp>
-
-
-#include "mpi-pyp.hh"
-#include "mpi-corpus.hh"
-
-class MPIPYPTopics {
-public:
-  typedef std::vector<int> DocumentTopics;
-  typedef std::vector<DocumentTopics> CorpusTopics;
-  typedef double F;
-
-public:
-  MPIPYPTopics(int num_topics, bool use_topic_pyp=false, unsigned long seed = 0) 
-    : m_num_topics(num_topics), m_word_pyps(1), 
-    m_topic_pyp(0.5,1.0), m_use_topic_pyp(use_topic_pyp),
-    m_seed(seed),
-    uni_dist(0,1), rng(seed == 0 ? (unsigned long)this : seed), 
-    rnd(rng, uni_dist), m_mpi_start(-1), m_mpi_end(-1) {
-      boost::mpi::communicator m_world;
-      m_rank = m_world.rank(); 
-      m_size = m_world.size();
-      m_am_root = (m_rank == 0);
-    }
-
-  void sample_corpus(const MPICorpus& corpus, int samples,
-                     int freq_cutoff_start=0, int freq_cutoff_end=0, 
-                     int freq_cutoff_interval=0,
-                     int max_contexts_per_document=0);
-
-  int sample(const DocumentId& doc, const Term& term);
-  std::pair<int,F> max(const DocumentId& doc, const Term& term) const;
-  std::pair<int,F> max(const DocumentId& doc) const;
-  int max_topic() const;
-
-  void set_backoff(const std::string& filename) {
-    m_backoff.reset(new TermBackoff);
-    m_backoff->read(filename);
-    m_word_pyps.clear();
-    m_word_pyps.resize(m_backoff->order(), MPIPYPs());
-  }
-  void set_backoff(TermBackoffPtr backoff) {
-    m_backoff = backoff;
-    m_word_pyps.clear();
-    m_word_pyps.resize(m_backoff->order(), MPIPYPs());
-  }
-
-  F prob(const Term& term, int topic, int level=0) const;
-  void decrement(const Term& term, int topic, int level=0);
-  void increment(const Term& term, int topic, int level=0);
-
-  std::ostream& print_document_topics(std::ostream& out) const;
-  std::ostream& print_topic_terms(std::ostream& out) const;
-
-  void synchronise();
-
-private:
-  F word_pyps_p0(const Term& term, int topic, int level) const;
-
-  int m_num_topics;
-  F m_term_p0, m_topic_p0, m_backoff_p0;
-
-  CorpusTopics m_corpus_topics;
-  typedef boost::ptr_vector< PYP<int> > PYPs;
-  typedef boost::ptr_vector< MPIPYP<int> > MPIPYPs;
-  PYPs m_document_pyps;
-  std::vector<MPIPYPs> m_word_pyps;
-  MPIPYP<int> m_topic_pyp;
-  bool m_use_topic_pyp;
-
-  unsigned long m_seed;
-
-  //typedef boost::mt19937 base_generator_type;
-  //typedef boost::hellekalek1995 base_generator_type;
-  typedef boost::lagged_fibonacci607 base_generator_type;
-  typedef boost::uniform_real<> uni_dist_type;
-  typedef boost::variate_generator<base_generator_type&, uni_dist_type> gen_type;
-
-  uni_dist_type uni_dist;
-  base_generator_type rng; //this gets the seed
-  gen_type rnd; //instantiate: rnd(rng, uni_dist)
-                //call: rnd() generates uniform on [0,1)
-
-  TermBackoffPtr m_backoff;
-
-  boost::mpi::communicator m_world;
-  bool m_am_root;
-  int m_rank, m_size;
-  int m_mpi_start, m_mpi_end;
-};
-
-#endif // PYP_TOPICS_HH
diff --git a/gi/pyp-topics/src/mpi-pyp.hh b/gi/pyp-topics/src/mpi-pyp.hh
deleted file mode 100644
index c2341b9e..00000000
--- a/gi/pyp-topics/src/mpi-pyp.hh
+++ /dev/null
@@ -1,447 +0,0 @@
-#ifndef _mpipyp_hh
-#define _mpipyp_hh
-
-#include <math.h>
-#include <map>
-#include <tr1/unordered_map>
-//#include <google/sparse_hash_map>
-
-#include <boost/random/uniform_real.hpp>
-#include <boost/random/variate_generator.hpp>
-#include <boost/random/mersenne_twister.hpp>
-#include <boost/tuple/tuple.hpp>
-#include <boost/serialization/map.hpp>
-#include <boost/mpi.hpp>
-#include <boost/mpi/environment.hpp>
-#include <boost/mpi/communicator.hpp>
-#include <boost/mpi/operations.hpp>
-
-
-#include "pyp.hh"
-
-//
-// Pitman-Yor process with customer and table tracking
-//
-
-template <typename Dish, typename Hash=std::tr1::hash<Dish> >
-class MPIPYP : public PYP<Dish, Hash> {
-public:
-  typedef std::map<Dish, int> dish_delta_type;
-
-  MPIPYP(double a, double b, Hash hash=Hash());
-
-  template < typename Uniform01 >
-    int increment(Dish d, double p0, Uniform01& rnd);
-  template < typename Uniform01 >
-    int decrement(Dish d, Uniform01& rnd);
-
-  void clear();
-  void reset_deltas();
-
-  void synchronise(dish_delta_type* result);
-
-private:
-  typedef std::map<Dish, typename PYP<Dish,Hash>::TableCounter> table_delta_type;
-
-  dish_delta_type m_count_delta;
-  table_delta_type m_table_delta;
-};
-
-template <typename Dish, typename Hash>
-MPIPYP<Dish,Hash>::MPIPYP(double a, double b, Hash h)
-: PYP<Dish,Hash>(a, b, 0, h) {}
-
-template <typename Dish, typename Hash>
-  template <typename Uniform01>
-int 
-MPIPYP<Dish,Hash>::increment(Dish dish, double p0, Uniform01& rnd) {
-  //std::cerr << "-----INCREMENT DISH " << dish << std::endl;
-  int delta = 0;
-  int table_joined=-1;
-  typename PYP<Dish,Hash>::TableCounter &tc = PYP<Dish,Hash>::_dish_tables[dish];
-
-  // seated on a new or existing table?
-  int c = PYP<Dish,Hash>::count(dish); 
-  int t = PYP<Dish,Hash>::num_tables(dish); 
-  int T = PYP<Dish,Hash>::num_tables();
-  double& a = PYP<Dish,Hash>::_a;
-  double& b = PYP<Dish,Hash>::_b;
-  double pshare = (c > 0) ? (c - a*t) : 0.0;
-  double pnew = (b + a*T) * p0;
-  if (pshare < 0.0) {
-    std::cerr << pshare << " " << c << " " << a << " " << t << std::endl;
-    assert(false);
-  }
-
-  if (rnd() < pnew / (pshare + pnew)) {
-    // assign to a new table
-    tc.tables += 1;
-    tc.table_histogram[1] += 1;
-    PYP<Dish,Hash>::_total_tables += 1;
-    delta = 1;
-    table_joined = 1;
-  }
-  else {
-    // randomly assign to an existing table
-    // remove constant denominator from inner loop
-    double r = rnd() * (c - a*t);
-    for (std::map<int,int>::iterator
-         hit = tc.table_histogram.begin();
-         hit != tc.table_histogram.end(); ++hit) {
-      r -= ((hit->first - a) * hit->second);
-      if (r <= 0) {
-        tc.table_histogram[hit->first+1] += 1;
-        hit->second -= 1;
-        table_joined = hit->first+1;
-        if (hit->second == 0)
-          tc.table_histogram.erase(hit);
-        break;
-      }
-    }
-    if (r > 0) {
-      std::cerr << r << " " << c << " " << a << " " << t << std::endl;
-      assert(false);
-    }
-    delta = 0;
-  }
-
-  std::tr1::unordered_map<Dish,int,Hash>::operator[](dish) += 1;
-  //google::sparse_hash_map<Dish,int,Hash>::operator[](dish) += 1;
-  PYP<Dish,Hash>::_total_customers += 1;
-
-  // MPI Delta handling
-  // track the customer entering
-  typename dish_delta_type::iterator customer_it; 
-  bool customer_insert_result; 
-  boost::tie(customer_it, customer_insert_result) 
-    = m_count_delta.insert(std::make_pair(dish,0)); 
-
-  customer_it->second += 1;
-  if (customer_it->second == 0)
-    m_count_delta.erase(customer_it);
-
-  // increment the histogram bar for the table joined
-  /*
-  typename PYP<Dish,Hash>::TableCounter &delta_tc = m_table_delta[dish];
-
-  std::map<int,int> &histogram = delta_tc.table_histogram;
-  assert (table_joined > 0);
-
-  typename std::map<int,int>::iterator table_it; bool table_insert_result; 
-  boost::tie(table_it, table_insert_result) = histogram.insert(std::make_pair(table_joined,0)); 
-  table_it->second += 1;
-  if (delta == 0) {
-    // decrement the histogram bar for the table left 
-    typename std::map<int,int>::iterator left_table_it; 
-    boost::tie(left_table_it, table_insert_result) 
-      = histogram.insert(std::make_pair(table_joined-1,0)); 
-    left_table_it->second -= 1;
-    if (left_table_it->second == 0) histogram.erase(left_table_it);
-  }
-  else delta_tc.tables += 1;
-
-  if (table_it->second == 0) histogram.erase(table_it);
-
-    //std::cerr << "Added (" << delta << ") " << dish << " to table " << table_joined << "\n"; 
-    //std::cerr << "Dish " << dish << " has " << count(dish) << " customers, and is sitting at " << PYP<Dish,Hash>::num_tables(dish) << " tables.\n"; 
-    //for (std::map<int,int>::const_iterator 
-    //     hit = delta_tc.table_histogram.begin();
-    //     hit != delta_tc.table_histogram.end(); ++hit) {
-    //  std::cerr << "    " << hit->second << " tables with " << hit->first << " customers." << std::endl; 
-    //}
-    //std::cerr << "Added (" << delta << ") " << dish << " to table " << table_joined << "\n"; 
-    //std::cerr << "Dish " << dish << " has " << count(dish) << " customers, and is sitting at " << PYP<Dish,Hash>::num_tables(dish) << " tables.\n"; 
-    int x_num_customers=0, x_num_table=0;
-    for (std::map<int,int>::const_iterator 
-         hit = delta_tc.table_histogram.begin();
-         hit != delta_tc.table_histogram.end(); ++hit) {
-      x_num_table += hit->second;
-      x_num_customers += (hit->second*hit->first);
-    }
-    int tmp_c = PYP<Dish,Hash>::count(dish);
-    int tmp_t = PYP<Dish,Hash>::num_tables(dish);
-    assert (x_num_customers <= tmp_c); 
-    assert (x_num_table <= tmp_t); 
-
-  if (delta_tc.table_histogram.empty()) {
-    assert (delta_tc.tables == 0);
-    m_table_delta.erase(dish);
-  }
-  */
-
-  //PYP<Dish,Hash>::debug_info(std::cerr);
-  //std::cerr << "   Dish " << dish << " has count " << PYP<Dish,Hash>::count(dish) << " tables " << PYP<Dish,Hash>::num_tables(dish) << std::endl;
-
-  return delta;
-}
-
-template <typename Dish, typename Hash>
-  template <typename Uniform01>
-int 
-MPIPYP<Dish,Hash>::decrement(Dish dish, Uniform01& rnd)
-{
-  //std::cerr << "-----DECREMENT DISH " << dish << std::endl;
-  typename std::tr1::unordered_map<Dish, int>::iterator dcit = find(dish);
-  //typename google::sparse_hash_map<Dish, int>::iterator dcit = find(dish);
-  if (dcit == PYP<Dish,Hash>::end()) {
-    std::cerr << dish << std::endl;
-    assert(false);
-  } 
-
-  int delta = 0, table_left=-1;
-
-  typename std::tr1::unordered_map<Dish, typename PYP<Dish,Hash>::TableCounter>::iterator dtit 
-    = PYP<Dish,Hash>::_dish_tables.find(dish);
-  //typename google::sparse_hash_map<Dish, TableCounter>::iterator dtit = _dish_tables.find(dish);
-  if (dtit == PYP<Dish,Hash>::_dish_tables.end()) {
-    std::cerr << dish << std::endl;
-    assert(false);
-  } 
-  typename PYP<Dish,Hash>::TableCounter &tc = dtit->second;
-
-  double r = rnd() * PYP<Dish,Hash>::count(dish);
-  for (std::map<int,int>::iterator hit = tc.table_histogram.begin();
-       hit != tc.table_histogram.end(); ++hit) {
-    r -= (hit->first * hit->second);
-    if (r <= 0) {
-      table_left = hit->first;
-      if (hit->first > 1) {
-        tc.table_histogram[hit->first-1] += 1;
-      }
-      else {
-        delta = -1;
-        tc.tables -= 1;
-        PYP<Dish,Hash>::_total_tables -= 1;
-      }
-
-      hit->second -= 1;
-      if (hit->second == 0) tc.table_histogram.erase(hit);
-      break;
-    }
-  }
-  if (r > 0) {
-    std::cerr << r << " " << PYP<Dish,Hash>::count(dish) << " " << PYP<Dish,Hash>::_a << " " 
-      << PYP<Dish,Hash>::num_tables(dish) << std::endl;
-    assert(false);
-  }
-
-  // remove the customer
-  dcit->second -= 1;
-  PYP<Dish,Hash>::_total_customers -= 1;
-  assert(dcit->second >= 0);
-  if (dcit->second == 0) {
-    PYP<Dish,Hash>::erase(dcit);
-    PYP<Dish,Hash>::_dish_tables.erase(dtit);
-  }
-
-  // MPI Delta processing
-  typename dish_delta_type::iterator it; 
-  bool insert_result; 
-  boost::tie(it, insert_result) = m_count_delta.insert(std::make_pair(dish,0)); 
-  it->second -= 1;
-  if (it->second == 0) m_count_delta.erase(it);
-
-  assert (table_left > 0);
-  typename PYP<Dish,Hash>::TableCounter& delta_tc = m_table_delta[dish];
-  if (table_left > 1) {
-    std::map<int,int>::iterator tit;
-    boost::tie(tit, insert_result) = delta_tc.table_histogram.insert(std::make_pair(table_left-1,0));
-    tit->second += 1;
-    if (tit->second == 0) delta_tc.table_histogram.erase(tit);
-  }
-  else delta_tc.tables -= 1;
-
-  std::map<int,int>::iterator tit;
-  boost::tie(tit, insert_result) = delta_tc.table_histogram.insert(std::make_pair(table_left,0));
-  tit->second -= 1;
-  if (tit->second == 0) delta_tc.table_histogram.erase(tit);
-
-  //  std::cerr << "Dish " << dish << " has " << count(dish) << " customers, and is sitting at " << PYP<Dish,Hash>::num_tables(dish) << " tables.\n"; 
-  //  for (std::map<int,int>::const_iterator 
-  //       hit = delta_tc.table_histogram.begin();
-  //       hit != delta_tc.table_histogram.end(); ++hit) {
-  //    std::cerr << "    " << hit->second << " tables with " << hit->first << " customers." << std::endl; 
-  //  }
-    int x_num_customers=0, x_num_table=0;
-    for (std::map<int,int>::const_iterator 
-         hit = delta_tc.table_histogram.begin();
-         hit != delta_tc.table_histogram.end(); ++hit) {
-      x_num_table += hit->second;
-      x_num_customers += (hit->second*hit->first);
-    }
-    int tmp_c = PYP<Dish,Hash>::count(dish);
-    int tmp_t = PYP<Dish,Hash>::num_tables(dish);
-    assert (x_num_customers <= tmp_c); 
-    assert (x_num_table <= tmp_t); 
-
-  if (delta_tc.table_histogram.empty()) {
-  //  std::cerr << "   DELETING " << dish << std::endl;
-    assert (delta_tc.tables == 0);
-    m_table_delta.erase(dish);
-  }
-
-  //PYP<Dish,Hash>::debug_info(std::cerr);
-  //std::cerr << "   Dish " << dish << " has count " << PYP<Dish,Hash>::count(dish) << " tables " << PYP<Dish,Hash>::num_tables(dish) << std::endl;
-  return delta;
-}
-
-template <typename Dish, typename Hash>
-void 
-MPIPYP<Dish,Hash>::clear() {
-  PYP<Dish,Hash>::clear();
-  reset_deltas();
-}
-
-template <typename Dish, typename Hash>
-void 
-MPIPYP<Dish,Hash>::reset_deltas() { 
-  m_count_delta.clear(); 
-  m_table_delta.clear();
-}
-
-template <typename Dish>
-struct sum_maps {
-  typedef std::map<Dish,int> map_type;
-  map_type& operator() (map_type& l, map_type const & r) const {
-    for (typename map_type::const_iterator it=r.begin(); it != r.end(); it++)
-      l[it->first] += it->second;
-    return l;
-  }
-};
-
-template <typename Dish>
-struct subtract_maps {
-  typedef std::map<Dish,int> map_type;
-  map_type& operator() (map_type& l, map_type const & r) const {
-    for (typename map_type::const_iterator it=r.begin(); it != r.end(); it++)
-      l[it->first] -= it->second;
-    return l;
-  }
-};
-
-// Needed Boost definitions
-namespace boost { 
-  namespace mpi {
-    template <>
-    struct is_commutative< sum_maps<int>, std::map<int,int> > : mpl::true_ {};
-  }
-
-  namespace serialization {
-    template<class Archive>
-    void serialize(Archive & ar, PYP<int>::TableCounter& t, const unsigned int version) {
-      ar & t.table_histogram;
-      ar & t.tables;
-    }
-
-  } // namespace serialization
-} // namespace boost
-
-template <typename A, typename B, typename C>
-struct triple {
-  triple() {}
-  triple(const A& a, const B& b, const C& c) : first(a), second(b), third(c) {}
-  A first;
-  B second;
-  C third;
-
-  template<class Archive>
-  void serialize(Archive &ar, const unsigned int version){
-      ar & first;
-      ar & second;
-      ar & third;
-  }
-};
-
-BOOST_IS_BITWISE_SERIALIZABLE(MPIPYP<int>::dish_delta_type)
-BOOST_CLASS_TRACKING(MPIPYP<int>::dish_delta_type,track_never)
-
-template <typename Dish, typename Hash>
-void 
-MPIPYP<Dish,Hash>::synchronise(dish_delta_type* result) {
-  boost::mpi::communicator world; 
-  //int rank = world.rank(), size = world.size();
-
-  boost::mpi::all_reduce(world, m_count_delta, *result, sum_maps<Dish>());
-  subtract_maps<Dish>()(*result, m_count_delta);
- 
-/*
-  // communicate the customer count deltas
-  dish_delta_type global_dish_delta;
-  boost::mpi::all_reduce(world, m_count_delta, global_dish_delta, sum_maps<Dish>());
-
-  // update this restaurant
-  for (typename dish_delta_type::const_iterator it=global_dish_delta.begin(); 
-       it != global_dish_delta.end(); ++it) {
-    int global_delta = it->second - m_count_delta[it->first];
-    if (global_delta == 0) continue;
-    typename std::tr1::unordered_map<Dish,int,Hash>::iterator dit; bool inserted;
-    boost::tie(dit, inserted) 
-      = std::tr1::unordered_map<Dish,int,Hash>::insert(std::make_pair(it->first, 0));
-    dit->second += global_delta;
-    assert(dit->second >= 0);
-    if (dit->second == 0) {
-      std::tr1::unordered_map<Dish,int,Hash>::erase(dit);
-    }
-
-    PYP<Dish,Hash>::_total_customers += (it->second - m_count_delta[it->first]);
-    int tmp = PYP<Dish,Hash>::_total_customers;
-    assert(tmp >= 0);
-    //std::cerr << "Process " << rank << " adding " <<  (it->second - m_count_delta[it->first]) << " of customer " << it->first << std::endl;
-  }
-*/
-/*
-  // communicate the table count deltas
-  for (int process = 0; process < size; ++process) {
-    typename std::vector< triple<Dish, int, int> > message;
-    if (rank == process) {
-      // broadcast deltas
-      for (typename table_delta_type::const_iterator dish_it=m_table_delta.begin(); 
-           dish_it != m_table_delta.end(); ++dish_it) {
-        //assert (dish_it->second.tables > 0);
-        for (std::map<int,int>::const_iterator it=dish_it->second.table_histogram.begin(); 
-             it != dish_it->second.table_histogram.end(); ++it) {
-          triple<Dish, int, int> m(dish_it->first, it->first, it->second);
-          message.push_back(m);
-        }
-        // append a special message with the total table delta for this dish
-        triple<Dish, int, int> m(dish_it->first, -1, dish_it->second.tables);
-        message.push_back(m);
-      }
-      boost::mpi::broadcast(world, message, process);
-    }
-    else {
-      // receive deltas
-      boost::mpi::broadcast(world, message, process);
-      for (typename std::vector< triple<Dish, int, int> >::const_iterator it=message.begin(); it != message.end(); ++it) {
-        typename PYP<Dish,Hash>::TableCounter& tc = PYP<Dish,Hash>::_dish_tables[it->first];
-        if (it->second >= 0) {
-          std::map<int,int>::iterator tit; bool inserted;
-          boost::tie(tit, inserted) = tc.table_histogram.insert(std::make_pair(it->second, 0));
-          tit->second += it->third;
-          if (tit->second < 0) {
-            std::cerr << tit->first << " " << tit->second << " " << it->first << " " << it->second << " " << it->third << std::endl;
-            assert(tit->second >= 0);
-          }
-          if (tit->second == 0) {
-            tc.table_histogram.erase(tit);
-          }
-        }
-        else {
-          tc.tables += it->third;
-          PYP<Dish,Hash>::_total_tables += it->third;
-          assert(tc.tables >= 0);
-          if (tc.tables == 0) assert(tc.table_histogram.empty());
-          if (tc.table_histogram.empty()) {
-            assert (tc.tables == 0);
-            PYP<Dish,Hash>::_dish_tables.erase(it->first);
-          }
-        }
-      }
-    }
-  }
-*/
-
-//  reset_deltas();
-}
-
-#endif
diff --git a/gi/pyp-topics/src/mpi-train-contexts.cc b/gi/pyp-topics/src/mpi-train-contexts.cc
deleted file mode 100644
index e05e0eac..00000000
--- a/gi/pyp-topics/src/mpi-train-contexts.cc
+++ /dev/null
@@ -1,201 +0,0 @@
-// STL
-#include <iostream>
-#include <fstream>
-#include <algorithm>
-#include <iterator>
-
-// Boost
-#include <boost/program_options/parsers.hpp>
-#include <boost/program_options/variables_map.hpp>
-#include <boost/scoped_ptr.hpp>
-#include <boost/mpi/environment.hpp>
-#include <boost/mpi/communicator.hpp>
-#include <boost/lexical_cast.hpp>
-
-// Local
-#include "mpi-pyp-topics.hh"
-#include "corpus.hh"
-#include "mpi-corpus.hh"
-#include "gzstream.hh"
-
-static const char *REVISION = "$Rev: 170 $";
-
-// Namespaces
-using namespace boost;
-using namespace boost::program_options;
-using namespace std;
-
-int main(int argc, char **argv)
-{
-  mpi::environment env(argc, argv);
-  mpi::communicator world;
-  int rank = world.rank();
-  bool am_root = (rank==0);
-  if (am_root) cout << "Pitman Yor topic models: Copyright 2010 Phil Blunsom\n";
-  if (am_root) std::cout << "I am process " << world.rank() << " of " << world.size() << "." << std::endl;
-  if (am_root) cout << REVISION << '\n' <<endl;
-
-  ////////////////////////////////////////////////////////////////////////////////////////////
-  // Command line processing
-  variables_map vm; 
-
-  // Command line processing
-  {
-    options_description cmdline_specific("Command line specific options");
-    cmdline_specific.add_options()
-      ("help,h", "print help message")
-      ("config,c", value<string>(), "config file specifying additional command line options")
-      ;
-    options_description config_options("Allowed options");
-    config_options.add_options()
-      ("help,h", "print help message")
-      ("data,d", value<string>(), "file containing the documents and context terms")
-      ("topics,t", value<int>()->default_value(50), "number of topics")
-      ("document-topics-out,o", value<string>(), "file to write the document topics to")
-      ("default-topics-out", value<string>(), "file to write default term topic assignments.")
-      ("topic-words-out,w", value<string>(), "file to write the topic word distribution to")
-      ("samples,s", value<int>()->default_value(10), "number of sampling passes through the data")
-      ("backoff-type", value<string>(), "backoff type: none|simple")
-//      ("filter-singleton-contexts", "filter singleton contexts")
-      ("hierarchical-topics", "Use a backoff hierarchical PYP as the P0 for the document topics distribution.")
-      ("binary-counts,b", "Use binary rather than integer counts for contexts.")
-      ("freq-cutoff-start", value<int>()->default_value(0), "initial frequency cutoff.")
-      ("freq-cutoff-end", value<int>()->default_value(0), "final frequency cutoff.")
-      ("freq-cutoff-interval", value<int>()->default_value(0), "number of iterations between frequency decrement.")
-      ("max-contexts-per-document", value<int>()->default_value(0), "Only sample the n most frequent contexts for a document.")
-      ;
-
-    cmdline_specific.add(config_options);
-
-    store(parse_command_line(argc, argv, cmdline_specific), vm); 
-    notify(vm);
-
-    if (vm.count("config") > 0) {
-      ifstream config(vm["config"].as<string>().c_str());
-      store(parse_config_file(config, config_options), vm); 
-    }
-
-    if (vm.count("help")) { 
-      cout << cmdline_specific << "\n"; 
-      return 1; 
-    }
-  }
-  ////////////////////////////////////////////////////////////////////////////////////////////
-
-  if (!vm.count("data")) {
-    cerr << "Please specify a file containing the data." << endl;
-    return 1;
-  }
-
-  // seed the random number generator: 0 = automatic, specify value otherwise
-  unsigned long seed = 0; 
-  MPIPYPTopics model(vm["topics"].as<int>(), vm.count("hierarchical-topics"), seed);
-
-  // read the data
-  BackoffGenerator* backoff_gen=0;
-  if (vm.count("backoff-type")) {
-    if (vm["backoff-type"].as<std::string>() == "none") {
-      backoff_gen = 0;
-    }
-    else if (vm["backoff-type"].as<std::string>() == "simple") {
-      backoff_gen = new SimpleBackoffGenerator();
-    }
-    else {
-     cerr << "Backoff type (--backoff-type) must be one of none|simple." <<endl;
-      return(1);
-    }
-  }
-
-  //ContextsCorpus contexts_corpus;
-  MPICorpus contexts_corpus;
-  contexts_corpus.read_contexts(vm["data"].as<string>(), backoff_gen, /*vm.count("filter-singleton-contexts")*/ false, vm.count("binary-counts"));
-  int mpi_start = 0, mpi_end = 0;
-  contexts_corpus.bounds(&mpi_start, &mpi_end);
-  std::cerr << "\tProcess " << rank << " has documents " << mpi_start << " -> " << mpi_end << "." << std::endl;
-
-  model.set_backoff(contexts_corpus.backoff_index());
-
-  if (backoff_gen) 
-    delete backoff_gen;
-
-  // train the sampler
-  model.sample_corpus(contexts_corpus, vm["samples"].as<int>(),
-                      vm["freq-cutoff-start"].as<int>(),
-                      vm["freq-cutoff-end"].as<int>(),
-                      vm["freq-cutoff-interval"].as<int>(),
-                      vm["max-contexts-per-document"].as<int>());
-
-  if (vm.count("document-topics-out")) {
-    std::ofstream documents_out((vm["document-topics-out"].as<string>() + ".pyp-process-" + boost::lexical_cast<std::string>(rank)).c_str());
-    //int documents = contexts_corpus.num_documents();
-    /*
-    int mpi_start = 0, mpi_end = documents;
-    if (world.size() != 1) {
-      mpi_start = (documents / world.size()) * rank;
-      if (rank == world.size()-1) mpi_end = documents;
-      else mpi_end = (documents / world.size())*(rank+1);
-    }
-    */
-
-    map<int,int> all_terms;
-    for (int document_id=mpi_start; document_id<mpi_end; ++document_id) {
-      assert (document_id < contexts_corpus.num_documents());
-      const Document& doc = contexts_corpus.at(document_id);
-      vector<int> unique_terms;
-      for (Document::const_iterator docIt=doc.begin(); docIt != doc.end(); ++docIt) {
-        if (unique_terms.empty() || *docIt != unique_terms.back())
-          unique_terms.push_back(*docIt);
-        // increment this terms frequency
-        pair<map<int,int>::iterator,bool> insert_result = all_terms.insert(make_pair(*docIt,1));
-        if (!insert_result.second) 
-          all_terms[*docIt] = all_terms[*docIt] + 1;
-      }
-      documents_out << contexts_corpus.key(document_id) << '\t';
-      documents_out << model.max(document_id).first << " " << doc.size() << " ||| ";
-      for (std::vector<int>::const_iterator termIt=unique_terms.begin(); termIt != unique_terms.end(); ++termIt) {
-        if (termIt != unique_terms.begin())
-          documents_out << " ||| ";
-        vector<std::string> strings = contexts_corpus.context2string(*termIt);
-        copy(strings.begin(), strings.end(),ostream_iterator<std::string>(documents_out, " "));
-        std::pair<int,MPIPYPTopics::F> maxinfo = model.max(document_id, *termIt);
-        documents_out << "||| C=" << maxinfo.first << " P=" << maxinfo.second;
-      }
-      documents_out <<endl;
-    }
-    documents_out.close();
-    world.barrier();
-
-    if (am_root) {
-      ogzstream root_documents_out(vm["document-topics-out"].as<string>().c_str());
-      for (int p=0; p < world.size(); ++p) {
-        std::string rank_p_prefix((vm["document-topics-out"].as<string>() + ".pyp-process-" + boost::lexical_cast<std::string>(p)).c_str());
-        std::ifstream rank_p_trees_istream(rank_p_prefix.c_str(), std::ios_base::binary);
-        root_documents_out << rank_p_trees_istream.rdbuf();
-        rank_p_trees_istream.close();
-        remove((rank_p_prefix).c_str());
-      }
-      root_documents_out.close();
-    }
-
-    if (am_root && vm.count("default-topics-out")) {
-      ofstream default_topics(vm["default-topics-out"].as<string>().c_str());
-      default_topics << model.max_topic() <<endl;
-      for (std::map<int,int>::const_iterator termIt=all_terms.begin(); termIt != all_terms.end(); ++termIt) {
-        vector<std::string> strings = contexts_corpus.context2string(termIt->first);
-        default_topics << model.max(-1, termIt->first).first << " ||| " << termIt->second << " ||| ";
-        copy(strings.begin(), strings.end(),ostream_iterator<std::string>(default_topics, " "));
-        default_topics <<endl;
-      }
-    }
-  }
-
-  if (am_root && vm.count("topic-words-out")) {
-    ogzstream topics_out(vm["topic-words-out"].as<string>().c_str());
-    model.print_topic_terms(topics_out);
-    topics_out.close();
-  }
-
-  cout <<endl;
-
-  return 0;
-}
diff --git a/gi/pyp-topics/src/mt19937ar.c b/gi/pyp-topics/src/mt19937ar.c
deleted file mode 100644
index 6551ea39..00000000
--- a/gi/pyp-topics/src/mt19937ar.c
+++ /dev/null
@@ -1,194 +0,0 @@
-/* 
-   A C-program for MT19937, with initialization improved 2002/1/26.
-   Coded by Takuji Nishimura and Makoto Matsumoto.
-
-   Before using, initialize the state by using mt_init_genrand(seed)  
-   or mt_init_by_array(init_key, key_length).
-
-   Copyright (C) 1997 - 2002, Makoto Matsumoto and Takuji Nishimura,
-   All rights reserved.                          
-
-   Redistribution and use in source and binary forms, with or without
-   modification, are permitted provided that the following conditions
-   are met:
-
-     1. Redistributions of source code must retain the above copyright
-        notice, this list of conditions and the following disclaimer.
-
-     2. Redistributions in binary form must reproduce the above copyright
-        notice, this list of conditions and the following disclaimer in the
-        documentation and/or other materials provided with the distribution.
-
-     3. The names of its contributors may not be used to endorse or promote 
-        products derived from this software without specific prior written 
-        permission.
-
-   THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-   "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-   LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
-   A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR
-   CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-   EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-   PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
-   PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
-   LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
-   NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-   SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-
-   Any feedback is very welcome.
-   http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/emt.html
-   email: m-mat @ math.sci.hiroshima-u.ac.jp (remove space)
-*/
-
-#include "mt19937ar.h"   /* XXX MJ 17th March 2006 */
-
-/* Period parameters */  
-#define N 624
-#define M 397
-#define MATRIX_A 0x9908b0dfUL   /* constant vector a */
-#define UPPER_MASK 0x80000000UL /* most significant w-r bits */
-#define LOWER_MASK 0x7fffffffUL /* least significant r bits */
-
-static unsigned long mt[N]; /* the array for the state vector  */
-static int mti=N+1; /* mti==N+1 means mt[N] is not initialized */
-
-/* initializes mt[N] with a seed */
-void mt_init_genrand(unsigned long s)
-{
-    mt[0]= s & 0xffffffffUL;
-    for (mti=1; mti<N; mti++) {
-        mt[mti] = 
-	    (1812433253UL * (mt[mti-1] ^ (mt[mti-1] >> 30)) + mti); 
-        /* See Knuth TAOCP Vol2. 3rd Ed. P.106 for multiplier. */
-        /* In the previous versions, MSBs of the seed affect   */
-        /* only MSBs of the array mt[].                        */
-        /* 2002/01/09 modified by Makoto Matsumoto             */
-        mt[mti] &= 0xffffffffUL;
-        /* for >32 bit machines */
-    }
-}
-
-/* initialize by an array with array-length */
-/* init_key is the array for initializing keys */
-/* key_length is its length */
-/* slight change for C++, 2004/2/26 */
-void mt_init_by_array(unsigned long init_key[], int key_length)
-{
-    int i, j, k;
-    mt_init_genrand(19650218UL);
-    i=1; j=0;
-    k = (N>key_length ? N : key_length);
-    for (; k; k--) {
-        mt[i] = (mt[i] ^ ((mt[i-1] ^ (mt[i-1] >> 30)) * 1664525UL))
-          + init_key[j] + j; /* non linear */
-        mt[i] &= 0xffffffffUL; /* for WORDSIZE > 32 machines */
-        i++; j++;
-        if (i>=N) { mt[0] = mt[N-1]; i=1; }
-        if (j>=key_length) j=0;
-    }
-    for (k=N-1; k; k--) {
-        mt[i] = (mt[i] ^ ((mt[i-1] ^ (mt[i-1] >> 30)) * 1566083941UL))
-          - i; /* non linear */
-        mt[i] &= 0xffffffffUL; /* for WORDSIZE > 32 machines */
-        i++;
-        if (i>=N) { mt[0] = mt[N-1]; i=1; }
-    }
-
-    mt[0] = 0x80000000UL; /* MSB is 1; assuring non-zero initial array */ 
-}
-
-/* generates a random number on [0,0xffffffff]-interval */
-unsigned long mt_genrand_int32(void)
-{
-    unsigned long y;
-    static unsigned long mag01[2]={0x0UL, MATRIX_A};
-    /* mag01[x] = x * MATRIX_A  for x=0,1 */
-
-    if (mti >= N) { /* generate N words at one time */
-        int kk;
-
-        if (mti == N+1)   /* if mt_init_genrand() has not been called, */
-            mt_init_genrand(5489UL); /* a default initial seed is used */
-
-        for (kk=0;kk<N-M;kk++) {
-            y = (mt[kk]&UPPER_MASK)|(mt[kk+1]&LOWER_MASK);
-            mt[kk] = mt[kk+M] ^ (y >> 1) ^ mag01[y & 0x1UL];
-        }
-        for (;kk<N-1;kk++) {
-            y = (mt[kk]&UPPER_MASK)|(mt[kk+1]&LOWER_MASK);
-            mt[kk] = mt[kk+(M-N)] ^ (y >> 1) ^ mag01[y & 0x1UL];
-        }
-        y = (mt[N-1]&UPPER_MASK)|(mt[0]&LOWER_MASK);
-        mt[N-1] = mt[M-1] ^ (y >> 1) ^ mag01[y & 0x1UL];
-
-        mti = 0;
-    }
-  
-    y = mt[mti++];
-
-    /* Tempering */
-    y ^= (y >> 11);
-    y ^= (y << 7) & 0x9d2c5680UL;
-    y ^= (y << 15) & 0xefc60000UL;
-    y ^= (y >> 18);
-
-    return y;
-}
-
-/* generates a random number on [0,0x7fffffff]-interval */
-long mt_genrand_int31(void)
-{
-    return (long)( mt_genrand_int32()>>1);
-}
-
-/* generates a random number on [0,1]-real-interval */
-double mt_genrand_real1(void)
-{
-    return mt_genrand_int32()*(1.0/4294967295.0); 
-    /* divided by 2^32-1 */ 
-}
-
-/* generates a random number on [0,1)-real-interval */
-double mt_genrand_real2(void)
-{
-    return mt_genrand_int32()*(1.0/4294967296.0); 
-    /* divided by 2^32 */
-}
-
-/* generates a random number on (0,1)-real-interval */
-double mt_genrand_real3(void)
-{
-    return (((double) mt_genrand_int32()) + 0.5)*(1.0/4294967296.0); 
-    /* divided by 2^32 */
-}
-
-/* generates a random number on [0,1) with 53-bit resolution*/
-double mt_genrand_res53(void) 
-{ 
-    unsigned long a=mt_genrand_int32()>>5, b=mt_genrand_int32()>>6; 
-    return(a*67108864.0+b)*(1.0/9007199254740992.0); 
-} 
-/* These real versions are due to Isaku Wada, 2002/01/09 added */
-
-/*
-#include <stdio.h>
-
-int main(void)
-{
-    int i;
-    unsigned long init[4]={0x123, 0x234, 0x345, 0x456}, length=4;
-    mt_init_by_array(init, length);
-    printf("1000 outputs of genrand_int32()\n");
-    for (i=0; i<1000; i++) {
-      printf("%10lu ", mt_genrand_int32());
-      if (i%5==4) printf("\n");
-    }
-    printf("\n1000 outputs of genrand_real2()\n");
-    for (i=0; i<1000; i++) {
-      printf("%10.8f ", mt_genrand_real2());
-      if (i%5==4) printf("\n");
-    }
-    return 0;
-}
-*/
diff --git a/gi/pyp-topics/src/mt19937ar.h b/gi/pyp-topics/src/mt19937ar.h
deleted file mode 100644
index caab4045..00000000
--- a/gi/pyp-topics/src/mt19937ar.h
+++ /dev/null
@@ -1,44 +0,0 @@
-/* mt19937ar.h
- *
- * Mark Johnson, 17th March 2006
- */
-
-#ifndef MT19937AR_H
-#define MT19937AR_H
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-  /* initializes mt[N] with a seed */
-  void mt_init_genrand(unsigned long s);
-
-  /* initialize by an array with array-length */
-  /* init_key is the array for initializing keys */
-  /* key_length is its length */
-  /* slight change for C++, 2004/2/26 */
-  void mt_init_by_array(unsigned long init_key[], int key_length);
-
-  /* generates a random number on [0,0xffffffff]-interval */
-  unsigned long mt_genrand_int32(void);
-
-  /* generates a random number on [0,0x7fffffff]-interval */
-  long mt_genrand_int31(void);
-
-  /* generates a random number on [0,1]-real-interval */
-  double mt_genrand_real1(void);
-
-  /* generates a random number on [0,1)-real-interval */
-  double mt_genrand_real2(void);
-
-  /* generates a random number on (0,1)-real-interval */
-  double mt_genrand_real3(void);
-
-  /* generates a random number on [0,1) with 53-bit resolution*/
-  double mt_genrand_res53(void);
-
-#ifdef __cplusplus
-};
-#endif
-
-#endif /* MT19937AR_H */
diff --git a/gi/pyp-topics/src/pyp-topics.cc b/gi/pyp-topics/src/pyp-topics.cc
deleted file mode 100644
index 4de52fd7..00000000
--- a/gi/pyp-topics/src/pyp-topics.cc
+++ /dev/null
@@ -1,499 +0,0 @@
-#include "timing.h"
-#include "pyp-topics.hh"
-#include "contexts_corpus.hh"
-
-//Dict const *dict;
-
-//#include <boost/date_time/posix_time/posix_time_types.hpp>
-void PYPTopics::sample_corpus(const Corpus& corpus, int samples,
-                              int freq_cutoff_start, int freq_cutoff_end,
-                              int freq_cutoff_interval,
-                              int max_contexts_per_document,
-                              F temp_start, F temp_end) {
-  Timer timer;
-  //dict = &((ContextsCorpus*) &corpus)->dict();
-
-  if (!m_backoff.get()) {
-    m_word_pyps.clear();
-    m_word_pyps.push_back(PYPs());
-  }
-
-  std::cerr << "\n Training with " << m_word_pyps.size()-1 << " backoff level"
-    << (m_word_pyps.size()==2 ? ":" : "s:") << std::endl;
-
-
-  for (int i=0; i<(int)m_word_pyps.size(); ++i)
-  {
-    m_word_pyps.at(i).reserve(m_num_topics);
-    for (int j=0; j<m_num_topics; ++j)
-      m_word_pyps.at(i).push_back(new PYP<int>(0.01, 1.0, m_seed));
-  }
-  std::cerr << std::endl;
-
-  m_document_pyps.reserve(corpus.num_documents());
-  for (int j=0; j<corpus.num_documents(); ++j)
-    m_document_pyps.push_back(new PYP<int>(0.01, 1.0, m_seed));
-
-  m_topic_p0 = 1.0/m_num_topics;
-  m_term_p0 = 1.0/(F)m_backoff->terms_at_level(m_word_pyps.size()-1);
-  //m_term_p0 = 1.0/corpus.num_types();
-  m_backoff_p0 = 1.0/corpus.num_documents();
-
-  std::cerr << " Documents: " << corpus.num_documents() << " Terms: "
-    << corpus.num_types() << std::endl;
-
-  int frequency_cutoff = freq_cutoff_start;
-  std::cerr << " Context frequency cutoff set to " << frequency_cutoff << std::endl;
-
-  timer.Reset();
-  // Initialisation pass
-  int document_id=0, topic_counter=0;
-  for (Corpus::const_iterator corpusIt=corpus.begin();
-       corpusIt != corpus.end(); ++corpusIt, ++document_id) {
-    m_corpus_topics.push_back(DocumentTopics(corpusIt->size(), 0));
-
-    int term_index=0;
-    for (Document::const_iterator docIt=corpusIt->begin();
-         docIt != corpusIt->end(); ++docIt, ++term_index) {
-      topic_counter++;
-      Term term = *docIt;
-
-      // sample a new_topic
-      //int new_topic = (topic_counter % m_num_topics);
-      int freq = corpus.context_count(term);
-      int new_topic = -1;
-      if (freq > frequency_cutoff
-          && (!max_contexts_per_document || term_index < max_contexts_per_document)) {
-        //new_topic = sample(document_id, term);
-        //new_topic = document_id % m_num_topics;
-        new_topic = (int) (rnd() * m_num_topics);
-
-        // add the new topic to the PYPs
-        increment(term, new_topic);
-
-        if (m_use_topic_pyp) {
-          F p0 = m_topic_pyp.prob(new_topic, m_topic_p0);
-          int table_delta = m_document_pyps[document_id].increment(new_topic, p0);
-          if (table_delta)
-            m_topic_pyp.increment(new_topic, m_topic_p0);
-        }
-        else m_document_pyps[document_id].increment(new_topic, m_topic_p0);
-      }
-
-      m_corpus_topics[document_id][term_index] = new_topic;
-    }
-  }
-  std::cerr << "  Initialized in " << timer.Elapsed() << " seconds\n";
-
-  int* randomDocIndices = new int[corpus.num_documents()];
-  for (int i = 0; i < corpus.num_documents(); ++i)
-	  randomDocIndices[i] = i;
-
-  if (num_jobs < max_threads)
-    num_jobs = max_threads;
-  int job_incr = (int) ( (float)m_document_pyps.size() / float(num_jobs) );
-
-  // Sampling phase
-  for (int curr_sample=0; curr_sample < samples; ++curr_sample) {
-    if (freq_cutoff_interval > 0 && curr_sample != 1
-        && curr_sample % freq_cutoff_interval == 1
-        && frequency_cutoff > freq_cutoff_end) {
-      frequency_cutoff--;
-      std::cerr << "\n Context frequency cutoff set to " << frequency_cutoff << std::endl;
-    }
-
-    F temp = 1.0 / (temp_start - curr_sample*(temp_start-temp_end)/samples);
-    std::cerr << "\n  -- Sample " << curr_sample << " (T=" << temp << ") "; std::cerr.flush();
-
-    // Randomize the corpus indexing array
-    int tmp;
-    int processed_terms=0;
-    /*
-    for (int i = corpus.num_documents()-1; i > 0; --i)
-    {
-        //i+1 since j \in [0,i] but rnd() \in [0,1)
-    	int j = (int)(rnd() * (i+1));
-      assert(j >= 0 && j <= i);
-     	tmp = randomDocIndices[i];
-    	randomDocIndices[i] = randomDocIndices[j];
-    	randomDocIndices[j] = tmp;
-    }
-    */
-
-    // for each document in the corpus
-    int document_id;
-    for (int i=0; i<corpus.num_documents(); ++i) {
-    	document_id = randomDocIndices[i];
-
-      // for each term in the document
-      int term_index=0;
-      Document::const_iterator docEnd = corpus.at(document_id).end();
-      for (Document::const_iterator docIt=corpus.at(document_id).begin();
-           docIt != docEnd; ++docIt, ++term_index) {
-        if (max_contexts_per_document && term_index > max_contexts_per_document)
-          break;
-        
-        Term term = *docIt;
-
-        int freq = corpus.context_count(term);
-        if (freq < frequency_cutoff)
-          continue;
-
-        processed_terms++;
-
-        // remove the prevous topic from the PYPs
-        int current_topic = m_corpus_topics[document_id][term_index];
-        // a negative label mean that term hasn't been sampled yet
-        if (current_topic >= 0) {
-          decrement(term, current_topic);
-
-          int table_delta = m_document_pyps[document_id].decrement(current_topic);
-          if (m_use_topic_pyp && table_delta < 0)
-            m_topic_pyp.decrement(current_topic);
-        }
-
-        // sample a new_topic
-        int new_topic = sample(document_id, term, temp);
-        //std::cerr << "TERM: " << dict->Convert(term) << " (" << term << ") " << " Old Topic: " 
-        //  << current_topic << " New Topic: " << new_topic << "\n" << std::endl;
-
-        // add the new topic to the PYPs
-        m_corpus_topics[document_id][term_index] = new_topic;
-        increment(term, new_topic);
-
-        if (m_use_topic_pyp) {
-          F p0 = m_topic_pyp.prob(new_topic, m_topic_p0);
-          int table_delta = m_document_pyps[document_id].increment(new_topic, p0);
-          if (table_delta)
-            m_topic_pyp.increment(new_topic, m_topic_p0);
-        }
-        else m_document_pyps[document_id].increment(new_topic, m_topic_p0);
-      }
-      if (document_id && document_id % 10000 == 0) {
-        std::cerr << "."; std::cerr.flush();
-      }
-    }
-    std::cerr << " ||| LLH= " << log_likelihood();
-
-    if (curr_sample != 0 && curr_sample % 10 == 0) {
-    //if (true) {
-      std::cerr << " ||| time=" << (timer.Elapsed() / 10.0) << " sec/sample" << std::endl;
-      timer.Reset();
-      std::cerr << "     ... Resampling hyperparameters (";
-      
-      // resample the hyperparamters
-      F log_p=0.0;
-      if (max_threads == 1)
-      { 
-        std::cerr << "1 thread)" << std::endl; std::cerr.flush();
-        log_p += hresample_topics();
-        log_p += hresample_docs(0, m_document_pyps.size());
-      }
-      else
-      { //parallelize
-        std::cerr << max_threads << " threads, " << num_jobs << " jobs)" << std::endl; std::cerr.flush();
-        
-        WorkerPool<JobReturnsF, F> pool(max_threads); 
-        int i=0, sz = m_document_pyps.size();
-        //documents...
-        while (i <= sz - 2*job_incr)
-        {    
-          JobReturnsF job = boost::bind(&PYPTopics::hresample_docs, this, i, i+job_incr);
-          pool.addJob(job);
-          i += job_incr;
-        }
-        //  do all remaining documents
-        JobReturnsF job = boost::bind(&PYPTopics::hresample_docs, this, i,sz);
-        pool.addJob(job);
-        
-        //topics...
-        JobReturnsF topics_job = boost::bind(&PYPTopics::hresample_topics, this);
-        pool.addJob(topics_job);
-
-        log_p += pool.get_result(); //blocks
-
-      }
-
-      if (m_use_topic_pyp) {
-        m_topic_pyp.resample_prior(rnd);
-        log_p += m_topic_pyp.log_restaurant_prob();
-      }
-
-      std::cerr.precision(10);
-      std::cerr << " ||| LLH=" << log_likelihood() << " ||| resampling time=" << timer.Elapsed() << " sec" << std::endl;
-      timer.Reset();
-
-      int k=0;
-      std::cerr << "Topics distribution: ";
-      std::cerr.precision(2);
-      for (PYPs::iterator pypIt=m_word_pyps.front().begin();
-           pypIt != m_word_pyps.front().end(); ++pypIt, ++k) {
-        if (k % 5 == 0) std::cerr << std::endl << '\t';
-        std::cerr << "<" << k << ":" << pypIt->num_customers() << ","
-          << pypIt->num_types() << "," << m_topic_pyp.prob(k, m_topic_p0) << "> ";
-      }
-      std::cerr.precision(10);
-      std::cerr << std::endl;
-    }
-  }
-  delete [] randomDocIndices;
-}
-
-PYPTopics::F PYPTopics::hresample_docs(int start, int end)
-{
-  int resample_counter=0;
-  F log_p = 0.0;
-  assert(start >= 0);
-  assert(end >= 0);
-  assert(start <= end);
-  for (int i=start; i < end; ++i)
-  {
-    m_document_pyps[i].resample_prior(rnd);
-    log_p += m_document_pyps[i].log_restaurant_prob();
-    if (resample_counter++ % 5000 == 0) {
-      std::cerr << "."; std::cerr.flush();
-    }
-  }
-  return log_p;
-}
-
-PYPTopics::F PYPTopics::hresample_topics()
-{
-  F log_p = 0.0;
-  for (std::vector<PYPs>::iterator levelIt=m_word_pyps.begin();
-      levelIt != m_word_pyps.end(); ++levelIt) {
-    for (PYPs::iterator pypIt=levelIt->begin();
-        pypIt != levelIt->end(); ++pypIt) {
-
-      pypIt->resample_prior(rnd);
-      log_p += pypIt->log_restaurant_prob();
-    }
-    std::cerr << log_p << std::endl;
-  }
-  return log_p;
-}
-
-PYPTopics::F PYPTopics::log_likelihood() const 
-{
-  F log_p = 0.0;
-
-  // LLH of topic term distribution
-  size_t i=0;
-  for (std::vector<PYPs>::const_iterator levelIt=m_word_pyps.begin();
-      levelIt != m_word_pyps.end(); ++levelIt, ++i) {
-    for (PYPs::const_iterator pypIt=levelIt->begin();
-        pypIt != levelIt->end(); ++pypIt, ++i) {
-      log_p += pypIt->log_restaurant_prob();
-
-      if (i == m_word_pyps.size()-1)
-        log_p += (pypIt->num_tables() * -log(m_backoff->terms_at_level(i)));
-      else
-        log_p += (pypIt->num_tables() * log(m_term_p0));
-    }
-  }
-  std::cerr << " TERM LLH: " << log_p << " "; //std::endl;
-
-  // LLH of document topic distribution
-  for (size_t i=0; i < m_document_pyps.size(); ++i) {
-    log_p += m_document_pyps[i].log_restaurant_prob();
-    if (!m_use_topic_pyp) log_p += (m_document_pyps[i].num_tables() * m_topic_p0);
-  }
-  if (m_use_topic_pyp) {
-    log_p += m_topic_pyp.log_restaurant_prob();
-    log_p += (m_topic_pyp.num_tables() * log(m_topic_p0));
-  }
-
-  return log_p;
-}
-
-void PYPTopics::decrement(const Term& term, int topic, int level) {
-  //std::cerr << "PYPTopics::decrement(" << term << "," << topic << "," << level << ")" << std::endl;
-  int table_delta = m_word_pyps.at(level).at(topic).decrement(term);
-  if (table_delta && m_backoff.get()) {
-    Term backoff_term = (*m_backoff)[term];
-    if (!m_backoff->is_null(backoff_term))
-      decrement(backoff_term, topic, level+1);
-  }
-}
-
-void PYPTopics::increment(const Term& term, int topic, int level) {
-  //std::cerr << "PYPTopics::increment(" << term << "," << topic << "," << level << ")" << std::endl;
-  int table_delta = m_word_pyps.at(level).at(topic).increment(term, word_pyps_p0(term, topic, level));
-
-  if (table_delta && m_backoff.get()) {
-    Term backoff_term = (*m_backoff)[term];
-    if (!m_backoff->is_null(backoff_term))
-      increment(backoff_term, topic, level+1);
-  }
-}
-
-int PYPTopics::sample(const DocumentId& doc, const Term& term, F inv_temp) {
-  // First pass: collect probs
-  F sum=0.0;
-  std::vector<F> sums;
-  for (int k=0; k<m_num_topics; ++k) {
-    F p_w_k = prob(term, k);
-
-    F topic_prob = m_topic_p0;
-    if (m_use_topic_pyp) topic_prob = m_topic_pyp.prob(k, m_topic_p0);
-
-    //F p_k_d = m_document_pyps[doc].prob(k, topic_prob);
-    F p_k_d = m_document_pyps[doc].unnormalised_prob(k, topic_prob);
-
-    F prob = p_w_k*p_k_d;
-    /*
-    if (prob < 0.0) { std::cerr << "\n\n" << prob << " " << p_w_k << " " << p_k_d << std::endl; assert(false); }
-    if (prob > 1.0) { std::cerr << "\n\n" << prob << " " << p_w_k << " " << p_k_d << std::endl; assert(false); }
-    assert (pow(prob, inv_temp) >= 0.0);
-    assert (pow(prob, inv_temp) <= 1.0);
-    */
-    sum += pow(prob, inv_temp);
-    sums.push_back(sum);
-  }
-  // Second pass: sample a topic
-  F cutoff = rnd() * sum;
-  for (int k=0; k<m_num_topics; ++k) {
-    if (cutoff <= sums[k])
-      return k;
-  }
-  assert(false);
-}
-
-PYPTopics::F PYPTopics::word_pyps_p0(const Term& term, int topic, int level) const {
-  //for (int i=0; i<level+1; ++i) std::cerr << "  ";
-  //std::cerr << "PYPTopics::word_pyps_p0(" << term << "," << topic << "," << level << ")" << std::endl;
-
-  F p0 = m_term_p0;
-  if (m_backoff.get()) {
-    //static F fudge=m_backoff_p0; // TODO
-
-    Term backoff_term = (*m_backoff)[term];
-    //std::cerr << "T: " << term << " BO: " << backoff_term << std::endl;
-    if (!m_backoff->is_null(backoff_term)) {
-      assert (level < m_backoff->order());
-      //p0 = (1.0/(F)m_backoff->terms_at_level(level))*prob(backoff_term, topic, level+1);
-      p0 = m_term_p0*prob(backoff_term, topic, level+1);
-      p0 = prob(backoff_term, topic, level+1);
-    }
-    else
-      p0 = (1.0/(F) m_backoff->terms_at_level(level));
-      //p0 = m_term_p0;
-  }
-  //for (int i=0; i<level+1; ++i) std::cerr << "  ";
-  //std::cerr << "PYPTopics::word_pyps_p0(" << term << "," << topic << "," << level << ") = " << p0 << std::endl;
-  return p0;
-}
-
-PYPTopics::F PYPTopics::prob(const Term& term, int topic, int level) const {
-  //for (int i=0; i<level+1; ++i) std::cerr << "  ";
-  //std::cerr << "PYPTopics::prob(" << dict->Convert(term) << "," << topic << "," << level << ")" << std::endl;
-
-  F p0 = word_pyps_p0(term, topic, level);
-  F p_w_k = m_word_pyps.at(level).at(topic).prob(term, p0);
-
-  /*
-  for (int i=0; i<level+1; ++i) std::cerr << "  ";
-  std::cerr << "PYPTopics::prob(" << dict->Convert(term) << "," << topic << "," << level << ") = " << p_w_k << std::endl;
-  for (int i=0; i<level+1; ++i) std::cerr << "  ";
-  m_word_pyps.at(level).at(topic).debug_info(std::cerr);
-  */
-  return p_w_k;
-}
-
-int PYPTopics::max_topic() const {
-  if (!m_use_topic_pyp)
-    return -1;
-
-  F current_max=0.0;
-  int current_topic=-1;
-  for (int k=0; k<m_num_topics; ++k) {
-    F prob = m_topic_pyp.prob(k, m_topic_p0);
-    if (prob > current_max) {
-      current_max = prob;
-      current_topic = k;
-    }
-  }
-  assert(current_topic >= 0);
-  return current_topic;
-}
-
-std::pair<int,PYPTopics::F> PYPTopics::max(const DocumentId& doc) const {
-  //std::cerr << "PYPTopics::max(" << doc << "," << term << ")" << std::endl;
-  // collect probs
-  F current_max=0.0;
-  int current_topic=-1;
-  for (int k=0; k<m_num_topics; ++k) {
-    //F p_w_k = prob(term, k);
-
-    F topic_prob = m_topic_p0;
-    if (m_use_topic_pyp)
-      topic_prob = m_topic_pyp.prob(k, m_topic_p0);
-
-    F prob = 0;
-    if (doc < 0) prob = topic_prob;
-    else         prob = m_document_pyps[doc].prob(k, topic_prob);
-
-    if (prob > current_max) {
-      current_max = prob;
-      current_topic = k;
-    }
-  }
-  assert(current_topic >= 0);
-  assert(current_max >= 0);
-  return std::make_pair(current_topic, current_max);
-}
-
-std::pair<int,PYPTopics::F> PYPTopics::max(const DocumentId& doc, const Term& term) const {
-  //std::cerr << "PYPTopics::max(" << doc << "," << term << ")" << std::endl;
-  // collect probs
-  F current_max=0.0;
-  int current_topic=-1;
-  for (int k=0; k<m_num_topics; ++k) {
-    F p_w_k = prob(term, k);
-
-    F topic_prob = m_topic_p0;
-    if (m_use_topic_pyp)
-      topic_prob = m_topic_pyp.prob(k, m_topic_p0);
-
-    F p_k_d = 0;
-    if (doc < 0) p_k_d = topic_prob;
-    else         p_k_d = m_document_pyps[doc].prob(k, topic_prob);
-
-    F prob = (p_w_k*p_k_d);
-    if (prob > current_max) {
-      current_max = prob;
-      current_topic = k;
-    }
-  }
-  assert(current_topic >= 0);
-  assert(current_max >= 0);
-  return std::make_pair(current_topic,current_max);
-}
-
-std::ostream& PYPTopics::print_document_topics(std::ostream& out) const {
-  for (CorpusTopics::const_iterator corpusIt=m_corpus_topics.begin();
-       corpusIt != m_corpus_topics.end(); ++corpusIt) {
-    int term_index=0;
-    for (DocumentTopics::const_iterator docIt=corpusIt->begin();
-         docIt != corpusIt->end(); ++docIt, ++term_index) {
-      if (term_index) out << " ";
-      out << *docIt;
-    }
-    out << std::endl;
-  }
-  return out;
-}
-
-std::ostream& PYPTopics::print_topic_terms(std::ostream& out) const {
-  for (PYPs::const_iterator pypsIt=m_word_pyps.front().begin();
-       pypsIt != m_word_pyps.front().end(); ++pypsIt) {
-    int term_index=0;
-    for (PYP<int>::const_iterator termIt=pypsIt->begin();
-         termIt != pypsIt->end(); ++termIt, ++term_index) {
-      if (term_index) out << " ";
-      out << termIt->first << ":" << termIt->second;
-    }
-    out << std::endl;
-  }
-  return out;
-}
diff --git a/gi/pyp-topics/src/pyp-topics.hh b/gi/pyp-topics/src/pyp-topics.hh
deleted file mode 100644
index 3a910540..00000000
--- a/gi/pyp-topics/src/pyp-topics.hh
+++ /dev/null
@@ -1,98 +0,0 @@
-#ifndef PYP_TOPICS_HH
-#define PYP_TOPICS_HH
-
-#include <vector>
-#include <iostream>
-#include <boost/ptr_container/ptr_vector.hpp>
-
-#include <boost/random/uniform_real.hpp>
-#include <boost/random/variate_generator.hpp>
-#include <boost/random/mersenne_twister.hpp>
-
-#include "pyp.hh"
-#include "corpus.hh"
-#include "workers.hh"
-
-class PYPTopics {
-public:
-  typedef std::vector<int> DocumentTopics;
-  typedef std::vector<DocumentTopics> CorpusTopics;
-  typedef long double F;
-
-public:
-  PYPTopics(int num_topics, bool use_topic_pyp=false, unsigned long seed = 0,
-        int max_threads = 1, int num_jobs = 1) 
-    : m_num_topics(num_topics), m_word_pyps(1), 
-    m_topic_pyp(0.5,1.0,seed), m_use_topic_pyp(use_topic_pyp),
-    m_seed(seed),
-    uni_dist(0,1), rng(seed == 0 ? (unsigned long)this : seed), 
-    rnd(rng, uni_dist), max_threads(max_threads), num_jobs(num_jobs) {}
-
-  void sample_corpus(const Corpus& corpus, int samples,
-                     int freq_cutoff_start=0, int freq_cutoff_end=0, 
-                     int freq_cutoff_interval=0,
-                     int max_contexts_per_document=0,
-                     F temp_start=1.0, F temp_end=1.0);
-
-  int sample(const DocumentId& doc, const Term& term, F inv_temp=1.0);
-  std::pair<int,F> max(const DocumentId& doc, const Term& term) const;
-  std::pair<int,F> max(const DocumentId& doc) const;
-  int max_topic() const;
-
-  void set_backoff(const std::string& filename) {
-    m_backoff.reset(new TermBackoff);
-    m_backoff->read(filename);
-    m_word_pyps.clear();
-    m_word_pyps.resize(m_backoff->order(), PYPs());
-  }
-  void set_backoff(TermBackoffPtr backoff) {
-    m_backoff = backoff;
-    m_word_pyps.clear();
-    m_word_pyps.resize(m_backoff->order(), PYPs());
-  }
-
-  F prob(const Term& term, int topic, int level=0) const;
-  void decrement(const Term& term, int topic, int level=0);
-  void increment(const Term& term, int topic, int level=0);
-
-  F log_likelihood() const;
-
-  std::ostream& print_document_topics(std::ostream& out) const;
-  std::ostream& print_topic_terms(std::ostream& out) const;
-
-private:
-  F word_pyps_p0(const Term& term, int topic, int level) const;
-
-  int m_num_topics;
-  F m_term_p0, m_topic_p0, m_backoff_p0;
-
-  CorpusTopics m_corpus_topics;
-  typedef boost::ptr_vector< PYP<int> > PYPs;
-  PYPs m_document_pyps;
-  std::vector<PYPs> m_word_pyps;
-  PYP<int> m_topic_pyp;
-  bool m_use_topic_pyp;
-
-  unsigned long m_seed;
-
-  typedef boost::mt19937 base_generator_type;
-  typedef boost::uniform_real<> uni_dist_type;
-  typedef boost::variate_generator<base_generator_type&, uni_dist_type> gen_type;
-
-  uni_dist_type uni_dist;
-  base_generator_type rng; //this gets the seed
-  gen_type rnd; //instantiate: rnd(rng, uni_dist)
-                //call: rnd() generates uniform on [0,1)
-
-  typedef boost::function<F()> JobReturnsF;
-
-  F hresample_docs(int start, int end); //does i in [start, end)
-
-  F hresample_topics();
-  
-  int max_threads;
-  int num_jobs;
-  TermBackoffPtr m_backoff;
-};
-
-#endif // PYP_TOPICS_HH
diff --git a/gi/pyp-topics/src/pyp.hh b/gi/pyp-topics/src/pyp.hh
deleted file mode 100644
index b1cb62be..00000000
--- a/gi/pyp-topics/src/pyp.hh
+++ /dev/null
@@ -1,566 +0,0 @@
-#ifndef _pyp_hh
-#define _pyp_hh
-
-#include "slice-sampler.h"
-#include <math.h>
-#include <map>
-#include <tr1/unordered_map>
-//#include <google/sparse_hash_map>
-
-#include <boost/random/uniform_real.hpp>
-#include <boost/random/variate_generator.hpp>
-#include <boost/random/mersenne_twister.hpp>
-
-#include "log_add.h"
-#include "mt19937ar.h"
-
-//
-// Pitman-Yor process with customer and table tracking
-//
-
-template <typename Dish, typename Hash=std::tr1::hash<Dish> >
-class PYP : protected std::tr1::unordered_map<Dish, int, Hash>
-//class PYP : protected google::sparse_hash_map<Dish, int, Hash>
-{
-public:
-  using std::tr1::unordered_map<Dish,int>::const_iterator;
-  using std::tr1::unordered_map<Dish,int>::iterator;
-  using std::tr1::unordered_map<Dish,int>::begin;
-  using std::tr1::unordered_map<Dish,int>::end;
-//  using google::sparse_hash_map<Dish,int>::const_iterator;
-//  using google::sparse_hash_map<Dish,int>::iterator;
-//  using google::sparse_hash_map<Dish,int>::begin;
-//  using google::sparse_hash_map<Dish,int>::end;
-
-  PYP(double a, double b, unsigned long seed = 0, Hash hash=Hash());
-
-  virtual int increment(Dish d, double p0);
-  virtual int decrement(Dish d);
-
-  // lookup functions
-  int count(Dish d) const;
-  double prob(Dish dish, double p0) const;
-  double prob(Dish dish, double dcd, double dca, 
-              double dtd, double dta, double p0) const;
-  double unnormalised_prob(Dish dish, double p0) const;
-
-  int num_customers() const { return _total_customers; }
-  int num_types() const { return std::tr1::unordered_map<Dish,int>::size(); }
-  //int num_types() const { return google::sparse_hash_map<Dish,int>::size(); }
-  bool empty() const { return _total_customers == 0; }
-
-  double log_prob(Dish dish, double log_p0) const;
-  // nb. d* are NOT logs
-  double log_prob(Dish dish, double dcd, double dca, 
-                       double dtd, double dta, double log_p0) const;
-
-  int num_tables(Dish dish) const;
-  int num_tables() const;
-
-  double a() const { return _a; }
-  void set_a(double a) { _a = a; }
-
-  double b() const { return _b; }
-  void set_b(double b) { _b = b; }
-
-  virtual void clear();
-  std::ostream& debug_info(std::ostream& os) const;
-
-  double log_restaurant_prob() const;
-  double log_prior() const;
-  static double log_prior_a(double a, double beta_a, double beta_b);
-  static double log_prior_b(double b, double gamma_c, double gamma_s);
-
-  template <typename Uniform01>
-    void resample_prior(Uniform01& rnd);
-  template <typename Uniform01>
-    void resample_prior_a(Uniform01& rnd);
-  template <typename Uniform01>
-    void resample_prior_b(Uniform01& rnd);
-
-protected:
-  double _a, _b; // parameters of the Pitman-Yor distribution
-  double _a_beta_a, _a_beta_b; // parameters of Beta prior on a
-  double _b_gamma_s, _b_gamma_c; // parameters of Gamma prior on b
-
-  struct TableCounter {
-    TableCounter() : tables(0) {};
-    int tables;
-    std::map<int, int> table_histogram; // num customers at table -> number tables
-  };
-  typedef std::tr1::unordered_map<Dish, TableCounter, Hash> DishTableType;
-  //typedef google::sparse_hash_map<Dish, TableCounter, Hash> DishTableType;
-  DishTableType _dish_tables;
-  int _total_customers, _total_tables;
-
-  typedef boost::mt19937 base_generator_type;
-  typedef boost::uniform_real<> uni_dist_type;
-  typedef boost::variate_generator<base_generator_type&, uni_dist_type> gen_type;
-
-//  uni_dist_type uni_dist;
-//  base_generator_type rng; //this gets the seed
-//  gen_type rnd; //instantiate: rnd(rng, uni_dist)
-                //call: rnd() generates uniform on [0,1)
-
-  // Function objects for calculating the parts of the log_prob for 
-  // the parameters a and b
-  struct resample_a_type {
-    int n, m; double b, a_beta_a, a_beta_b;
-    const DishTableType& dish_tables;
-    resample_a_type(int n, int m, double b, double a_beta_a, 
-                    double a_beta_b, const DishTableType& dish_tables)
-      : n(n), m(m), b(b), a_beta_a(a_beta_a), a_beta_b(a_beta_b), dish_tables(dish_tables) {}
-
-    double operator() (double proposed_a) const {
-      double log_prior = log_prior_a(proposed_a, a_beta_a, a_beta_b);
-      double log_prob = 0.0;
-      double lgamma1a = lgamma(1.0 - proposed_a);
-      for (typename DishTableType::const_iterator dish_it=dish_tables.begin(); dish_it != dish_tables.end(); ++dish_it) 
-        for (std::map<int, int>::const_iterator table_it=dish_it->second.table_histogram.begin(); 
-             table_it !=dish_it->second.table_histogram.end(); ++table_it) 
-          log_prob += (table_it->second * (lgamma(table_it->first - proposed_a) - lgamma1a));
-
-      log_prob += (proposed_a == 0.0 ? (m-1.0)*log(b) 
-                   : ((m-1.0)*log(proposed_a) + lgamma((m-1.0) + b/proposed_a) - lgamma(b/proposed_a)));
-      assert(std::isfinite(log_prob));
-      return log_prob + log_prior;
-    }
-  };
-
-  struct resample_b_type {
-    int n, m; double a, b_gamma_c, b_gamma_s;
-    resample_b_type(int n, int m, double a, double b_gamma_c, double b_gamma_s)
-      : n(n), m(m), a(a), b_gamma_c(b_gamma_c), b_gamma_s(b_gamma_s) {}
-
-    double operator() (double proposed_b) const {
-      double log_prior = log_prior_b(proposed_b, b_gamma_c, b_gamma_s);
-      double log_prob = 0.0;
-      log_prob += (a == 0.0  ? (m-1.0)*log(proposed_b) 
-                  : ((m-1.0)*log(a) + lgamma((m-1.0) + proposed_b/a) - lgamma(proposed_b/a)));
-      log_prob += (lgamma(1.0+proposed_b) - lgamma(n+proposed_b));
-      return log_prob + log_prior;
-    }
-  };
-   
-  /* lbetadist() returns the log probability density of x under a Beta(alpha,beta)
-   * distribution. - copied from Mark Johnson's gammadist.c
-   */
-  static long double lbetadist(long double x, long double alpha, long double beta);
-
-  /* lgammadist() returns the log probability density of x under a Gamma(alpha,beta)
-   * distribution - copied from Mark Johnson's gammadist.c
-   */
-  static long double lgammadist(long double x, long double alpha, long double beta);
-
-};
-
-template <typename Dish, typename Hash>
-PYP<Dish,Hash>::PYP(double a, double b, unsigned long seed, Hash)
-: std::tr1::unordered_map<Dish, int, Hash>(10), _a(a), _b(b), 
-//: google::sparse_hash_map<Dish, int, Hash>(10), _a(a), _b(b), 
-  _a_beta_a(1), _a_beta_b(1), _b_gamma_s(1), _b_gamma_c(1),
-  //_a_beta_a(1), _a_beta_b(1), _b_gamma_s(10), _b_gamma_c(0.1),
-  _total_customers(0), _total_tables(0)//,
-  //uni_dist(0,1), rng(seed == 0 ? (unsigned long)this : seed), rnd(rng, uni_dist)
-{
-//  std::cerr << "\t##PYP<Dish,Hash>::PYP(a=" << _a << ",b=" << _b << ")" << std::endl;
-  //set_deleted_key(-std::numeric_limits<Dish>::max());
-}
-
-template <typename Dish, typename Hash>
-double 
-PYP<Dish,Hash>::prob(Dish dish, double p0) const
-{
-  int c = count(dish), t = num_tables(dish);
-  double r = num_tables() * _a + _b;
-  //std::cerr << "\t\t\t\tPYP<Dish,Hash>::prob(" << dish << "," << p0 << ") c=" << c << " r=" << r << std::endl;
-  if (c > 0)
-    return (c - _a * t + r * p0) / (num_customers() + _b);
-  else
-    return r * p0 / (num_customers() + _b);
-}
-
-template <typename Dish, typename Hash>
-double 
-PYP<Dish,Hash>::unnormalised_prob(Dish dish, double p0) const
-{
-  int c = count(dish), t = num_tables(dish);
-  double r = num_tables() * _a + _b;
-  if (c > 0) return (c - _a * t + r * p0);
-  else       return r * p0;
-}
-
-template <typename Dish, typename Hash>
-double 
-PYP<Dish,Hash>::prob(Dish dish, double dcd, double dca, 
-                     double dtd, double dta, double p0)
-const
-{
-  int c = count(dish) + dcd, t = num_tables(dish) + dtd;
-  double r = (num_tables() + dta) * _a + _b;
-  if (c > 0)
-    return (c - _a * t + r * p0) / (num_customers() + dca + _b);
-  else
-    return r * p0 / (num_customers() + dca + _b);
-}
-
-template <typename Dish, typename Hash>
-double 
-PYP<Dish,Hash>::log_prob(Dish dish, double log_p0) const
-{
-  using std::log;
-  int c = count(dish), t = num_tables(dish);
-  double r = log(num_tables() * _a + b);
-  if (c > 0)
-    return Log<double>::add(log(c - _a * t), r + log_p0)
-      - log(num_customers() + _b);
-  else
-    return r + log_p0 - log(num_customers() + b);
-}
-
-template <typename Dish, typename Hash>
-double 
-PYP<Dish,Hash>::log_prob(Dish dish, double dcd, double dca, 
-                         double dtd, double dta, double log_p0)
-const
-{
-  using std::log;
-  int c = count(dish) + dcd, t = num_tables(dish) + dtd;
-  double r = log((num_tables() + dta) * _a + b);
-  if (c > 0)
-    return Log<double>::add(log(c - _a * t), r + log_p0)
-      - log(num_customers() + dca + _b);
-  else
-    return r + log_p0 - log(num_customers() + dca + b);
-}
-
-template <typename Dish, typename Hash>
-int 
-PYP<Dish,Hash>::increment(Dish dish, double p0) {
-  int delta = 0;
-  TableCounter &tc = _dish_tables[dish];
-
-  // seated on a new or existing table?
-  int c = count(dish), t = num_tables(dish), T = num_tables();
-  double pshare = (c > 0) ? (c - _a*t) : 0.0;
-  double pnew = (_b + _a*T) * p0;
-  assert (pshare >= 0.0);
-  //assert (pnew > 0.0);
-
-  //if (rnd() < pnew / (pshare + pnew)) {
-  if (mt_genrand_res53() < pnew / (pshare + pnew)) {
-    // assign to a new table
-    tc.tables += 1;
-    tc.table_histogram[1] += 1;
-    _total_tables += 1;
-    delta = 1;
-  }
-  else {
-    // randomly assign to an existing table
-    // remove constant denominator from inner loop
-    //double r = rnd() * (c - _a*t);
-    double r = mt_genrand_res53() * (c - _a*t);
-    for (std::map<int,int>::iterator
-         hit = tc.table_histogram.begin();
-         hit != tc.table_histogram.end(); ++hit) {
-      r -= ((hit->first - _a) * hit->second);
-      if (r <= 0) {
-        tc.table_histogram[hit->first+1] += 1;
-        hit->second -= 1;
-        if (hit->second == 0)
-          tc.table_histogram.erase(hit);
-        break;
-      }
-    }
-    if (r > 0) {
-      std::cerr << r << " " << c << " " << _a << " " << t << std::endl;
-      assert(false);
-    }
-    delta = 0;
-  }
-
-  std::tr1::unordered_map<Dish,int,Hash>::operator[](dish) += 1;
-  //google::sparse_hash_map<Dish,int,Hash>::operator[](dish) += 1;
-  _total_customers += 1;
-
-  return delta;
-}
-
-template <typename Dish, typename Hash>
-int 
-PYP<Dish,Hash>::count(Dish dish) const
-{
-  typename std::tr1::unordered_map<Dish, int>::const_iterator 
-  //typename google::sparse_hash_map<Dish, int>::const_iterator 
-    dcit = find(dish);
-  if (dcit != end())
-    return dcit->second;
-  else
-    return 0;
-}
-
-template <typename Dish, typename Hash>
-int 
-PYP<Dish,Hash>::decrement(Dish dish)
-{
-  typename std::tr1::unordered_map<Dish, int>::iterator dcit = find(dish);
-  //typename google::sparse_hash_map<Dish, int>::iterator dcit = find(dish);
-  if (dcit == end()) {
-    std::cerr << dish << std::endl;
-    assert(false);
-  } 
-
-  int delta = 0;
-
-  typename std::tr1::unordered_map<Dish, TableCounter>::iterator dtit = _dish_tables.find(dish);
-  //typename google::sparse_hash_map<Dish, TableCounter>::iterator dtit = _dish_tables.find(dish);
-  if (dtit == _dish_tables.end()) {
-    std::cerr << dish << std::endl;
-    assert(false);
-  } 
-  TableCounter &tc = dtit->second;
-
-  //std::cerr << "\tdecrement for " << dish << "\n";
-  //std::cerr << "\tBEFORE histogram: " << tc.table_histogram << " ";
-  //std::cerr << "count: " << count(dish) << " ";
-  //std::cerr << "tables: " << tc.tables << "\n";
-
-  //double r = rnd() * count(dish);
-  double r = mt_genrand_res53() * count(dish);
-  for (std::map<int,int>::iterator hit = tc.table_histogram.begin();
-       hit != tc.table_histogram.end(); ++hit)
-  {
-    //r -= (hit->first - _a) * hit->second;
-    r -= (hit->first) * hit->second;
-    if (r <= 0)
-    {
-      if (hit->first > 1)
-        tc.table_histogram[hit->first-1] += 1;
-      else
-      {
-        delta = -1;
-        tc.tables -= 1;
-        _total_tables -= 1;
-      }
-
-      hit->second -= 1;
-      if (hit->second == 0) tc.table_histogram.erase(hit);
-      break;
-    }
-  }
-  if (r > 0) {
-    std::cerr << r << " " << count(dish) << " " << _a << " " << num_tables(dish) << std::endl;
-    assert(false);
-  }
-
-  // remove the customer
-  dcit->second -= 1;
-  _total_customers -= 1;
-  assert(dcit->second >= 0);
-  if (dcit->second == 0) {
-    erase(dcit);
-    _dish_tables.erase(dtit);
-    //std::cerr << "\tAFTER histogram: Empty\n";
-  }
-  else {
-    //std::cerr << "\tAFTER histogram: " << _dish_tables[dish].table_histogram << " ";
-    //std::cerr << "count: " << count(dish) << " ";
-    //std::cerr << "tables: " << _dish_tables[dish].tables << "\n";
-  }
-
-  return delta;
-}
-
-template <typename Dish, typename Hash>
-int 
-PYP<Dish,Hash>::num_tables(Dish dish) const
-{
-  typename std::tr1::unordered_map<Dish, TableCounter, Hash>::const_iterator 
-  //typename google::sparse_hash_map<Dish, TableCounter, Hash>::const_iterator 
-    dtit = _dish_tables.find(dish);
-
-  //assert(dtit != _dish_tables.end());
-  if (dtit == _dish_tables.end())
-    return 0;
-
-  return dtit->second.tables;
-}
-
-template <typename Dish, typename Hash>
-int 
-PYP<Dish,Hash>::num_tables() const
-{
-  return _total_tables;
-}
-
-template <typename Dish, typename Hash>
-std::ostream&
-PYP<Dish,Hash>::debug_info(std::ostream& os) const
-{
-  int hists = 0, tables = 0;
-  for (typename std::tr1::unordered_map<Dish, TableCounter, Hash>::const_iterator 
-  //for (typename google::sparse_hash_map<Dish, TableCounter, Hash>::const_iterator 
-       dtit = _dish_tables.begin(); dtit != _dish_tables.end(); ++dtit)
-  {
-    hists += dtit->second.table_histogram.size();
-    tables += dtit->second.tables;
-
-//    if (dtit->second.tables <= 0)
-//      std::cerr << dtit->first << " " << count(dtit->first) << std::endl;
-    assert(dtit->second.tables > 0);
-    assert(!dtit->second.table_histogram.empty());
-
-//    os << "Dish " << dtit->first << " has " << count(dtit->first) << " customers, and is sitting at " << dtit->second.tables << " tables.\n"; 
-    for (std::map<int,int>::const_iterator 
-         hit = dtit->second.table_histogram.begin();
-         hit != dtit->second.table_histogram.end(); ++hit) {
-//      os << "    " << hit->second << " tables with " << hit->first << " customers." << std::endl; 
-      assert(hit->second > 0);
-    }
-  }
-
-  os << "restaurant has " 
-    << _total_customers << " customers; "
-    << _total_tables << " tables; " 
-    << tables << " tables'; " 
-    << num_types() << " dishes; "
-    << _dish_tables.size() << " dishes'; and "
-    << hists << " histogram entries\n";
-
-  return os;
-}
-
-template <typename Dish, typename Hash>
-void 
-PYP<Dish,Hash>::clear()
-{
-  this->std::tr1::unordered_map<Dish,int,Hash>::clear();
-  //this->google::sparse_hash_map<Dish,int,Hash>::clear();
-  _dish_tables.clear();
-  _total_tables = _total_customers = 0;
-}
-
-// log_restaurant_prob returns the log probability of the PYP table configuration.
-// Excludes Hierarchical P0 term which must be calculated separately.
-template <typename Dish, typename Hash>
-double 
-PYP<Dish,Hash>::log_restaurant_prob() const {
-  if (_total_customers < 1)
-    return (double)0.0;
-
-  double log_prob = 0.0;
-  double lgamma1a = lgamma(1.0-_a);
-
-  //std::cerr << "-------------------\n" << std::endl;
-  for (typename DishTableType::const_iterator dish_it=_dish_tables.begin(); 
-       dish_it != _dish_tables.end(); ++dish_it) {
-    for (std::map<int, int>::const_iterator table_it=dish_it->second.table_histogram.begin(); 
-         table_it !=dish_it->second.table_histogram.end(); ++table_it) {
-      log_prob += (table_it->second * (lgamma(table_it->first - _a) - lgamma1a));
-      //std::cerr << "|" << dish_it->first->parent << " --> " << dish_it->first->rhs << " " << table_it->first << " " << table_it->second << " " << log_prob;
-    }
-  }
-  //std::cerr << std::endl;
-
-  log_prob += (_a == (double)0.0 ? (_total_tables-1.0)*log(_b) : (_total_tables-1.0)*log(_a) + lgamma((_total_tables-1.0) + _b/_a) - lgamma(_b/_a));
-  //std::cerr << "\t\t" << log_prob << std::endl;
-  log_prob += (lgamma(1.0 + _b) - lgamma(_total_customers + _b));
-
-  //std::cerr << _total_customers << " " << _total_tables << " " << log_prob << " " << log_prior() << std::endl;
-  //std::cerr << _a << " " << _b << std::endl;
-  if (!std::isfinite(log_prob)) {
-    assert(false);
-  }
-  //return log_prob;
-  if (log_prob > 0.0)
-    std::cerr << log_prob << std::endl;
-  return log_prob;// + log_prior();
-}
-
-template <typename Dish, typename Hash>
-double 
-PYP<Dish,Hash>::log_prior() const {
-  double prior = 0.0;
-  if (_a_beta_a > 0.0 && _a_beta_b > 0.0 && _a > 0.0)
-    prior += log_prior_a(_a, _a_beta_a, _a_beta_b);
-  if (_b_gamma_s > 0.0 && _b_gamma_c > 0.0)
-    prior += log_prior_b(_b, _b_gamma_c, _b_gamma_s);
-
-  return prior;
-}
-
-template <typename Dish, typename Hash>
-double 
-PYP<Dish,Hash>::log_prior_a(double a, double beta_a, double beta_b) {
-  return lbetadist(a, beta_a, beta_b); 
-}
-
-template <typename Dish, typename Hash>
-double 
-PYP<Dish,Hash>::log_prior_b(double b, double gamma_c, double gamma_s) {
-  return lgammadist(b, gamma_c, gamma_s); 
-}
-
-template <typename Dish, typename Hash>
-long double PYP<Dish,Hash>::lbetadist(long double x, long double alpha, long double beta) {
-  assert(x > 0);
-  assert(x < 1);
-  assert(alpha > 0);
-  assert(beta > 0);
-  return (alpha-1)*log(x)+(beta-1)*log(1-x)+lgamma(alpha+beta)-lgamma(alpha)-lgamma(beta);
-//boost::math::lgamma
-}
-
-template <typename Dish, typename Hash>
-long double PYP<Dish,Hash>::lgammadist(long double x, long double alpha, long double beta) {
-  assert(alpha > 0);
-  assert(beta > 0);
-  return (alpha-1)*log(x) - alpha*log(beta) - x/beta - lgamma(alpha);
-}
-
-
-template <typename Dish, typename Hash>
-  template <typename Uniform01>
-void 
-PYP<Dish,Hash>::resample_prior(Uniform01& rnd) {
-  for (int num_its=5; num_its >= 0; --num_its) {
-    resample_prior_b(rnd);
-    resample_prior_a(rnd);
-  }
-  resample_prior_b(rnd);
-}
-
-template <typename Dish, typename Hash>
-  template <typename Uniform01>
-void 
-PYP<Dish,Hash>::resample_prior_b(Uniform01& rnd) {
-  if (_total_tables == 0) 
-    return;
-
-  //int niterations = 10;   // number of resampling iterations
-  int niterations = 5;   // number of resampling iterations
-  //std::cerr << "\n## resample_prior_b(), initial a = " << _a << ", b = " << _b << std::endl;
-  resample_b_type b_log_prob(_total_customers, _total_tables, _a, _b_gamma_c, _b_gamma_s);
-  _b = slice_sampler1d(b_log_prob, _b, rnd, (double) 0.0, std::numeric_limits<double>::infinity(), 
-  //_b = slice_sampler1d(b_log_prob, _b, mt_genrand_res53, (double) 0.0, std::numeric_limits<double>::infinity(), 
-                       (double) 0.0, niterations, 100*niterations);
-  //std::cerr << "\n## resample_prior_b(), final a = " << _a << ", b = " << _b << std::endl;
-}
-
-template <typename Dish, typename Hash>
-  template <typename Uniform01>
-void 
-PYP<Dish,Hash>::resample_prior_a(Uniform01& rnd) {
-  if (_total_tables == 0) 
-    return;
-
-  //int niterations = 10;
-  int niterations = 5;
-  //std::cerr << "\n## Initial a = " << _a << ", b = " << _b << std::endl;
-  resample_a_type a_log_prob(_total_customers, _total_tables, _b, _a_beta_a, _a_beta_b, _dish_tables);
-  _a = slice_sampler1d(a_log_prob, _a, rnd, std::numeric_limits<double>::min(), 
-  //_a = slice_sampler1d(a_log_prob, _a, mt_genrand_res53, std::numeric_limits<double>::min(), 
-                       (double) 1.0, (double) 0.0, niterations, 100*niterations);
-}
-
-#endif
diff --git a/gi/pyp-topics/src/slice-sampler.h b/gi/pyp-topics/src/slice-sampler.h
deleted file mode 100644
index 3108a0f7..00000000
--- a/gi/pyp-topics/src/slice-sampler.h
+++ /dev/null
@@ -1,192 +0,0 @@
-//! slice-sampler.h is an MCMC slice sampler
-//!
-//! Mark Johnson, 1st August 2008
-
-#ifndef SLICE_SAMPLER_H
-#define SLICE_SAMPLER_H
-
-#include <algorithm>
-#include <cassert>
-#include <cmath>
-#include <iostream>
-#include <limits>
-
-//! slice_sampler_rfc_type{} returns the value of a user-specified
-//! function if the argument is within range, or - infinity otherwise
-//
-template <typename F, typename Fn, typename U>
-struct slice_sampler_rfc_type {
-  F min_x, max_x;
-  const Fn& f;
-  U max_nfeval, nfeval;
-  slice_sampler_rfc_type(F min_x, F max_x, const Fn& f, U max_nfeval) 
-    : min_x(min_x), max_x(max_x), f(f), max_nfeval(max_nfeval), nfeval(0) { }
-    
-  F operator() (F x) {
-    if (min_x < x && x < max_x) {
-      assert(++nfeval <= max_nfeval);
-      F fx = f(x);
-      assert(std::isfinite(fx));
-      return fx;
-    }
-    else
-      return -std::numeric_limits<F>::infinity();
-  }
-};  // slice_sampler_rfc_type{}
-
-//! slice_sampler1d() implements the univariate "range doubling" slice sampler
-//! described in Neal (2003) "Slice Sampling", The Annals of Statistics 31(3), 705-767.
-//
-template <typename F, typename LogF, typename Uniform01>
-F slice_sampler1d(const LogF& logF0,               //!< log of function to sample
-		  F x,                             //!< starting point
-		  Uniform01& u01,                  //!< uniform [0,1) random number generator
-		  F min_x = -std::numeric_limits<F>::infinity(),  //!< minimum value of support
-		  F max_x = std::numeric_limits<F>::infinity(),   //!< maximum value of support
-		  F w = 0.0,                       //!< guess at initial width
-		  unsigned nsamples=1,             //!< number of samples to draw
-		  unsigned max_nfeval=200)         //!< max number of function evaluations
-{
-  typedef unsigned U;
-  slice_sampler_rfc_type<F,LogF,U> logF(min_x, max_x, logF0, max_nfeval);
-
-  assert(std::isfinite(x));
-
-  if (w <= 0.0) {                           // set w to a default width 
-    if (min_x > -std::numeric_limits<F>::infinity() && max_x < std::numeric_limits<F>::infinity())
-      w = (max_x - min_x)/4;
-    else
-      w = std::max(((x < 0.0) ? -x : x)/4, (F) 0.1);
-  }
-  assert(std::isfinite(w));
-
-  F logFx = logF(x);
-  for (U sample = 0; sample < nsamples; ++sample) {
-    F logY = logFx + log(u01()+1e-100);     //! slice logFx at this value
-    assert(std::isfinite(logY));
-
-    F xl = x - w*u01();                     //! lower bound on slice interval
-    F logFxl = logF(xl);
-    F xr = xl + w;                          //! upper bound on slice interval
-    F logFxr = logF(xr);
-
-    while (logY < logFxl || logY < logFxr)  // doubling procedure
-      if (u01() < 0.5) 
-	logFxl = logF(xl -= xr - xl);
-      else
-	logFxr = logF(xr += xr - xl);
-	
-    F xl1 = xl;
-    F xr1 = xr;
-    while (true) {                          // shrinking procedure
-      F x1 = xl1 + u01()*(xr1 - xl1);
-      if (logY < logF(x1)) {
-	F xl2 = xl;                         // acceptance procedure
-	F xr2 = xr; 
-	bool d = false;
-	while (xr2 - xl2 > 1.1*w) {
-	  F xm = (xl2 + xr2)/2;
-	  if ((x < xm && x1 >= xm) || (x >= xm && x1 < xm))
-	    d = true;
-	  if (x1 < xm)
-	    xr2 = xm;
-	  else
-	    xl2 = xm;
-	  if (d && logY >= logF(xl2) && logY >= logF(xr2))
-	    goto unacceptable;
-	}
-	x = x1;
-	goto acceptable;
-      }
-      goto acceptable;
-    unacceptable:
-      if (x1 < x)                           // rest of shrinking procedure
-	xl1 = x1;
-      else 
-	xr1 = x1;
-    }
-  acceptable:
-    w = (4*w + (xr1 - xl1))/5;              // update width estimate
-  }
-  return x;
-}
-
-/*
-//! slice_sampler1d() implements a 1-d MCMC slice sampler.
-//! It should be correct for unimodal distributions, but
-//! not for multimodal ones.
-//
-template <typename F, typename LogP, typename Uniform01>
-F slice_sampler1d(const LogP& logP,     //!< log of distribution to sample
-		  F x,                  //!< initial sample
-		  Uniform01& u01,       //!< uniform random number generator
-		  F min_x = -std::numeric_limits<F>::infinity(),  //!< minimum value of support
-		  F max_x = std::numeric_limits<F>::infinity(),   //!< maximum value of support
-		  F w = 0.0,            //!< guess at initial width
-		  unsigned nsamples=1,  //!< number of samples to draw
-		  unsigned max_nfeval=200)  //!< max number of function evaluations
-{
-  typedef unsigned U;
-  assert(std::isfinite(x));
-  if (w <= 0.0) {
-    if (min_x > -std::numeric_limits<F>::infinity() && max_x < std::numeric_limits<F>::infinity())
-      w = (max_x - min_x)/4;
-    else
-      w = std::max(((x < 0.0) ? -x : x)/4, 0.1);
-  }
-  // TRACE4(x, min_x, max_x, w);
-  F logPx = logP(x);
-  assert(std::isfinite(logPx));
-  U nfeval = 1;
-  for (U sample = 0; sample < nsamples; ++sample) {
-    F x0 = x;
-    F logU = logPx + log(u01()+1e-100);
-    assert(std::isfinite(logU));
-    F r = u01();
-    F xl = std::max(min_x, x - r*w);
-    F xr = std::min(max_x, x + (1-r)*w);
-    // TRACE3(x, logPx, logU);
-    while (xl > min_x && logP(xl) > logU) {
-      xl -= w;
-      w *= 2;
-      ++nfeval;
-      if (nfeval >= max_nfeval)
-	std::cerr << "## Error: nfeval = " << nfeval << ", max_nfeval = " << max_nfeval << ", sample = " << sample << ", nsamples = " << nsamples << ", r = " << r << ", w = " << w << ", xl = " << xl << std::endl;
-      assert(nfeval < max_nfeval);
-    }
-    xl = std::max(xl, min_x);
-    while (xr < max_x && logP(xr) > logU) {
-      xr += w;
-      w *= 2;
-      ++nfeval;
-      if (nfeval >= max_nfeval)
-	std::cerr << "## Error: nfeval = " << nfeval << ", max_nfeval = " << max_nfeval << ", sample = " << sample << ", nsamples = " << nsamples << ", r = " << r << ", w = " << w << ", xr = " << xr << std::endl;
-      assert(nfeval < max_nfeval);
-    }
-    xr = std::min(xr, max_x);
-    while (true) {
-      r = u01();
-      x = r*xl + (1-r)*xr;
-      assert(std::isfinite(x));
-      logPx = logP(x);
-      // TRACE4(logPx, x, xl, xr);
-      assert(std::isfinite(logPx));
-      ++nfeval;
-      if (nfeval >= max_nfeval)
-	std::cerr << "## Error: nfeval = " << nfeval << ", max_nfeval = " << max_nfeval << ", sample = " << sample << ", nsamples = " << nsamples << ", r = " << r << ", w = " << w << ", xl = " << xl << ", xr = " << xr << ", x = " << x << std::endl;
-      assert(nfeval < max_nfeval);
-      if (logPx > logU)
-        break;
-      else if (x > x0)
-          xr = x;
-        else
-          xl = x;
-    }
-    // w = (4*w + (xr-xl))/5;   // gradually adjust w
-  }
-  // TRACE2(logPx, x);
-  return x;
-}  // slice_sampler1d()
-*/
-
-#endif  // SLICE_SAMPLER_H
diff --git a/gi/pyp-topics/src/timing.h b/gi/pyp-topics/src/timing.h
deleted file mode 100644
index 08360b0f..00000000
--- a/gi/pyp-topics/src/timing.h
+++ /dev/null
@@ -1,37 +0,0 @@
-#ifndef TIMING_H
-#define TIMING_H
-
-#ifdef __CYGWIN__
-# ifndef _POSIX_MONOTONIC_CLOCK
-#  define _POSIX_MONOTONIC_CLOCK
-// this modifies <time.h>
-# endif
-// in case someone included <time.h> before we got here (this is lifted from time.h>)
-# ifndef CLOCK_MONOTONIC
-#  define CLOCK_MONOTONIC (clockid_t)4
-# endif
-#endif
-
-
-#include <time.h>
-#include <sys/time.h>
-#include "clock_gettime_stub.c"
-
-struct Timer {
-  Timer() { Reset(); }
-  void Reset()
-  {
-    clock_gettime(CLOCK_MONOTONIC, &start_t);
-  }
-  double Elapsed() const {
-    timespec end_t;
-    clock_gettime(CLOCK_MONOTONIC, &end_t);
-    const double elapsed = (end_t.tv_sec - start_t.tv_sec)
-                + (end_t.tv_nsec - start_t.tv_nsec) / 1000000000.0;
-    return elapsed;
-  }
- private:
-  timespec start_t;
-};
-
-#endif
diff --git a/gi/pyp-topics/src/train-contexts.cc b/gi/pyp-topics/src/train-contexts.cc
deleted file mode 100644
index 9463f9fc..00000000
--- a/gi/pyp-topics/src/train-contexts.cc
+++ /dev/null
@@ -1,174 +0,0 @@
-// STL
-#include <iostream>
-#include <fstream>
-#include <algorithm>
-#include <iterator>
-
-// Boost
-#include <boost/program_options/parsers.hpp>
-#include <boost/program_options/variables_map.hpp>
-#include <boost/scoped_ptr.hpp>
-
-// Local
-#include "pyp-topics.hh"
-#include "corpus.hh"
-#include "contexts_corpus.hh"
-#include "gzstream.hh"
-
-static const char *REVISION = "$Rev$";
-
-// Namespaces
-using namespace boost;
-using namespace boost::program_options;
-using namespace std;
-
-int main(int argc, char **argv)
-{
- cout << "Pitman Yor topic models: Copyright 2010 Phil Blunsom\n";
- cout << REVISION << '\n' <<endl;
-
-  ////////////////////////////////////////////////////////////////////////////////////////////
-  // Command line processing
-  variables_map vm; 
-
-  // Command line processing
-  {
-    options_description cmdline_specific("Command line specific options");
-    cmdline_specific.add_options()
-      ("help,h", "print help message")
-      ("config,c", value<string>(), "config file specifying additional command line options")
-      ;
-    options_description config_options("Allowed options");
-    config_options.add_options()
-      ("data,d", value<string>(), "file containing the documents and context terms")
-      ("topics,t", value<int>()->default_value(50), "number of topics")
-      ("document-topics-out,o", value<string>(), "file to write the document topics to")
-      ("default-topics-out", value<string>(), "file to write default term topic assignments.")
-      ("topic-words-out,w", value<string>(), "file to write the topic word distribution to")
-      ("samples,s", value<int>()->default_value(10), "number of sampling passes through the data")
-      ("backoff-type", value<string>(), "backoff type: none|simple")
-//      ("filter-singleton-contexts", "filter singleton contexts")
-      ("hierarchical-topics", "Use a backoff hierarchical PYP as the P0 for the document topics distribution.")
-      ("freq-cutoff-start", value<int>()->default_value(0), "initial frequency cutoff.")
-      ("freq-cutoff-end", value<int>()->default_value(0), "final frequency cutoff.")
-      ("freq-cutoff-interval", value<int>()->default_value(0), "number of iterations between frequency decrement.")
-      ("max-threads", value<int>()->default_value(1), "maximum number of simultaneous threads allowed")
-      ("max-contexts-per-document", value<int>()->default_value(0), "Only sample the n most frequent contexts for a document.")
-      ("num-jobs", value<int>()->default_value(1), "allows finer control over parallelization")
-      ("temp-start", value<double>()->default_value(1.0), "starting annealing temperature.")
-      ("temp-end", value<double>()->default_value(1.0), "end annealing temperature.")
-      ;
-
-    cmdline_specific.add(config_options);
-
-    store(parse_command_line(argc, argv, cmdline_specific), vm); 
-    notify(vm);
-
-    if (vm.count("config") > 0) {
-      ifstream config(vm["config"].as<string>().c_str());
-      store(parse_config_file(config, config_options), vm); 
-    }
-
-    if (vm.count("help")) { 
-      cout << cmdline_specific << "\n"; 
-      return 1; 
-    }
-  }
-  ////////////////////////////////////////////////////////////////////////////////////////////
-
-  if (!vm.count("data")) {
-    cerr << "Please specify a file containing the data." << endl;
-    return 1;
-  }
-  assert(vm["max-threads"].as<int>() > 0);
-  assert(vm["num-jobs"].as<int>() > -1);
-  // seed the random number generator: 0 = automatic, specify value otherwise
-  unsigned long seed = 0; 
-  PYPTopics model(vm["topics"].as<int>(), vm.count("hierarchical-topics"), seed, vm["max-threads"].as<int>(), vm["num-jobs"].as<int>());
-
-  // read the data
-  BackoffGenerator* backoff_gen=0;
-  if (vm.count("backoff-type")) {
-    if (vm["backoff-type"].as<std::string>() == "none") {
-      backoff_gen = 0;
-    }
-    else if (vm["backoff-type"].as<std::string>() == "simple") {
-      backoff_gen = new SimpleBackoffGenerator();
-    }
-    else {
-     cerr << "Backoff type (--backoff-type) must be one of none|simple." <<endl;
-      return(1);
-    }
-  }
-
-  ContextsCorpus contexts_corpus;
-  contexts_corpus.read_contexts(vm["data"].as<string>(), backoff_gen, /*vm.count("filter-singleton-contexts")*/ false);
-  model.set_backoff(contexts_corpus.backoff_index());
-
-  if (backoff_gen) 
-    delete backoff_gen;
-
-  // train the sampler
-  model.sample_corpus(contexts_corpus, vm["samples"].as<int>(),
-                      vm["freq-cutoff-start"].as<int>(),
-                      vm["freq-cutoff-end"].as<int>(),
-                      vm["freq-cutoff-interval"].as<int>(),
-                      vm["max-contexts-per-document"].as<int>(),
-                      vm["temp-start"].as<double>(), vm["temp-end"].as<double>());
-
-  if (vm.count("document-topics-out")) {
-    ogzstream documents_out(vm["document-topics-out"].as<string>().c_str());
-
-    int document_id=0;
-    map<int,int> all_terms;
-    for (Corpus::const_iterator corpusIt=contexts_corpus.begin(); 
-         corpusIt != contexts_corpus.end(); ++corpusIt, ++document_id) {
-      vector<int> unique_terms;
-      for (Document::const_iterator docIt=corpusIt->begin();
-           docIt != corpusIt->end(); ++docIt) {
-        if (unique_terms.empty() || *docIt != unique_terms.back())
-          unique_terms.push_back(*docIt);
-        // increment this terms frequency
-        pair<map<int,int>::iterator,bool> insert_result = all_terms.insert(make_pair(*docIt,1));
-        if (!insert_result.second) 
-          all_terms[*docIt] = all_terms[*docIt] + 1;
-          //insert_result.first++;
-      }
-      documents_out << contexts_corpus.key(document_id) << '\t';
-      documents_out << model.max(document_id).first << " " << corpusIt->size() << " ||| ";
-      for (std::vector<int>::const_iterator termIt=unique_terms.begin();
-           termIt != unique_terms.end(); ++termIt) {
-        if (termIt != unique_terms.begin())
-          documents_out << " ||| ";
-       vector<std::string> strings = contexts_corpus.context2string(*termIt);
-       copy(strings.begin(), strings.end(),ostream_iterator<std::string>(documents_out, " "));
-        std::pair<int,PYPTopics::F> maxinfo = model.max(document_id, *termIt);
-        documents_out << "||| C=" << maxinfo.first << " P=" << maxinfo.second;
-
-      }
-      documents_out <<endl;
-    }
-    documents_out.close();
-
-    if (vm.count("default-topics-out")) {
-      ofstream default_topics(vm["default-topics-out"].as<string>().c_str());
-      default_topics << model.max_topic() <<endl;
-      for (std::map<int,int>::const_iterator termIt=all_terms.begin(); termIt != all_terms.end(); ++termIt) {
-       vector<std::string> strings = contexts_corpus.context2string(termIt->first);
-        default_topics << model.max(-1, termIt->first).first << " ||| " << termIt->second << " ||| ";
-       copy(strings.begin(), strings.end(),ostream_iterator<std::string>(default_topics, " "));
-        default_topics <<endl;
-      }
-    }
-  }
-
-  if (vm.count("topic-words-out")) {
-    ogzstream topics_out(vm["topic-words-out"].as<string>().c_str());
-    model.print_topic_terms(topics_out);
-    topics_out.close();
-  }
-
- cout <<endl;
-
-  return 0;
-}
diff --git a/gi/pyp-topics/src/train.cc b/gi/pyp-topics/src/train.cc
deleted file mode 100644
index db7ca46e..00000000
--- a/gi/pyp-topics/src/train.cc
+++ /dev/null
@@ -1,135 +0,0 @@
-// STL
-#include <iostream>
-#include <fstream>
-
-// Boost
-#include <boost/program_options/parsers.hpp>
-#include <boost/program_options/variables_map.hpp>
-#include <boost/scoped_ptr.hpp>
-
-// Local
-#include "pyp-topics.hh"
-#include "corpus.hh"
-#include "contexts_corpus.hh"
-#include "gzstream.hh"
-
-static const char *REVISION = "$Rev$";
-
-// Namespaces
-using namespace boost;
-using namespace boost::program_options;
-using namespace std;
-
-int main(int argc, char **argv)
-{
-  std::cout << "Pitman Yor topic models: Copyright 2010 Phil Blunsom\n";
-  std::cout << REVISION << '\n' << std::endl;
-
-  ////////////////////////////////////////////////////////////////////////////////////////////
-  // Command line processing
-  variables_map vm; 
-
-  // Command line processing
-  options_description cmdline_specific("Command line specific options");
-  cmdline_specific.add_options()
-    ("help,h", "print help message")
-    ("config,c", value<string>(), "config file specifying additional command line options")
-    ;
-  options_description generic("Allowed options");
-  generic.add_options()
-    ("documents,d", value<string>(), "file containing the documents")
-    ("topics,t", value<int>()->default_value(50), "number of topics")
-    ("document-topics-out,o", value<string>(), "file to write the document topics to")
-    ("topic-words-out,w", value<string>(), "file to write the topic word distribution to")
-    ("samples,s", value<int>()->default_value(10), "number of sampling passes through the data")
-    ("test-corpus", value<string>(), "file containing the test data")
-    ("backoff-paths", value<string>(), "file containing the term backoff paths")
-    ;
-  options_description config_options, cmdline_options;
-  config_options.add(generic);
-  cmdline_options.add(generic).add(cmdline_specific);
-
-  store(parse_command_line(argc, argv, cmdline_options), vm); 
-  if (vm.count("config") > 0) {
-    ifstream config(vm["config"].as<string>().c_str());
-    store(parse_config_file(config, cmdline_options), vm); 
-  }
-  notify(vm);
-  ////////////////////////////////////////////////////////////////////////////////////////////
-
-  if (vm.count("documents") == 0) {
-    cerr << "Please specify a file containing the documents." << endl;
-    cout << cmdline_options << "\n"; 
-    return 1;
-  }
-
-  if (vm.count("help")) { 
-    cout << cmdline_options << "\n"; 
-    return 1; 
-  }
-
-  // seed the random number generator: 0 = automatic, specify value otherwise
-  unsigned long seed = 0; 
-  PYPTopics model(vm["topics"].as<int>(), false, seed);
-
-  // read the data
-  Corpus corpus;
-  corpus.read(vm["documents"].as<string>());
-
-  // read the backoff dictionary
-  if (vm.count("backoff-paths"))
-    model.set_backoff(vm["backoff-paths"].as<string>());
-
-  // train the sampler
-  model.sample_corpus(corpus, vm["samples"].as<int>());
-
-  if (vm.count("document-topics-out")) {
-    ogzstream documents_out(vm["document-topics-out"].as<string>().c_str());
-    //model.print_document_topics(documents_out);
-
-    int document_id=0;
-    for (Corpus::const_iterator corpusIt=corpus.begin(); 
-         corpusIt != corpus.end(); ++corpusIt, ++document_id) {
-      std::vector<int> unique_terms;
-      for (Document::const_iterator docIt=corpusIt->begin();
-           docIt != corpusIt->end(); ++docIt) {
-        if (unique_terms.empty() || *docIt != unique_terms.back())
-          unique_terms.push_back(*docIt);
-      }
-      documents_out << unique_terms.size();
-      for (std::vector<int>::const_iterator termIt=unique_terms.begin();
-           termIt != unique_terms.end(); ++termIt)
-        documents_out << " " << *termIt << ":" << model.max(document_id, *termIt).first;
-      documents_out << std::endl;
-    }
-    documents_out.close();
-  }
-
-  if (vm.count("topic-words-out")) {
-    ogzstream topics_out(vm["topic-words-out"].as<string>().c_str());
-    model.print_topic_terms(topics_out);
-    topics_out.close();
-  }
-
-  if (vm.count("test-corpus")) {
-    TestCorpus test_corpus;
-    test_corpus.read(vm["test-corpus"].as<string>());
-    ogzstream topics_out((vm["test-corpus"].as<string>() + ".topics.gz").c_str());
-
-    for (TestCorpus::const_iterator corpusIt=test_corpus.begin(); 
-         corpusIt != test_corpus.end(); ++corpusIt) {
-      int index=0;
-      for (DocumentTerms::const_iterator instanceIt=corpusIt->begin();
-           instanceIt != corpusIt->end(); ++instanceIt, ++index) {
-        int topic = model.max(instanceIt->doc, instanceIt->term).first;
-        if (index != 0) topics_out << " ";
-        topics_out << topic;
-      }
-      topics_out << std::endl;
-    }
-    topics_out.close();
-  }
-  std::cout << std::endl;
-
-  return 0;
-}
diff --git a/gi/pyp-topics/src/utility.h b/gi/pyp-topics/src/utility.h
deleted file mode 100644
index 405a5b0a..00000000
--- a/gi/pyp-topics/src/utility.h
+++ /dev/null
@@ -1,962 +0,0 @@
-// utility.h
-//
-// (c) Mark Johnson, 24th January 2005
-//
-// modified 6th May 2002 to ensure write/read consistency, fixed 18th July 2002
-// modified 14th July 2002 to include insert() (generic inserter)
-// modified 26th September 2003 to use mapped_type instead of data_type
-// 25th August 2004 added istream >> const char*
-// 24th January 2005 added insert_newkey()
-//
-// Defines:
-//  loop macros foreach, cforeach
-//  dfind (default find function)
-//  afind (find function that asserts key exists)
-//  insert_newkey (inserts a new key into a map)
-//  insert (generic inserter into standard data structures)
-//  disjoint (set operation)
-//  first_lessthan and second_lessthan (compares elements of pairs)
-//
-// Simplified interfaces to STL routines:
-//
-//  includes (simplified interface)
-//  set_intersection (simplified interface)
-//  inserter (simplified interface)
-//  max_element (simplified interface)
-//  min_element (simplified interface)
-//  hash functions for pairs, vectors, lists, slists and maps
-//  input and output for pairs and vectors
-//  resource_usage (interface improved)
-
-
-#ifndef UTILITY_H
-#define UTILITY_H
-
-#include <algorithm>
-// #include <boost/smart_ptr.hpp>    // Comment out this line if boost is not used
-#include <cassert>
-#include <cmath>
-#include <cctype>
-#include <cstdio>
-#include <unordered_map>
-#include <unordered_set>
-#include <ext/slist>
-#include <iostream>
-#include <iterator>
-#include <list>
-#include <map>
-#include <set>
-#include <string>
-#include <utility>
-#include <vector>
-#include <memory>
-
-#if (__GNUC__ > 3) || (__GNUC__ >= 3 && __GNUC_MINOR__ >= 1)
-#define EXT_NAMESPACE __gnu_cxx
-#else
-#define EXT_NAMESPACE std
-#endif
-
-namespace ext = EXT_NAMESPACE;
-
-inline float power(float x, float y) { return powf(x, y); }
-inline double power(double x, double y) { return pow(x, y); }
-inline long double power(long double x, long double y) { return powl(x, y); }
-
-typedef unsigned U;
-typedef long double F;  // slower than double, but underflows less
-
-///////////////////////////////////////////////////////////////////////////
-//                                                                       //
-//                              Looping constructs                       //
-//                                                                       //
-///////////////////////////////////////////////////////////////////////////
-
-// foreach is a simple loop construct
-//
-//   STORE should be an STL container
-//   TYPE is the typename of STORE
-//   VAR will be defined as a local variable of type TYPE::iterator
-//
-#define foreach(TYPE, VAR, STORE) \
-  for (TYPE::iterator VAR = (STORE).begin(); VAR != (STORE).end(); ++VAR)
-
-// cforeach is just like foreach, except that VAR is a const_iterator
-//
-//   STORE should be an STL container
-//   TYPE is the typename of STORE
-//   VAR will be defined as a local variable of type TYPE::const_iterator
-//
-#define cforeach(TYPE, VAR, STORE) \
-  for (TYPE::const_iterator VAR = (STORE).begin(); VAR != (STORE).end(); ++VAR)
-
-
-///////////////////////////////////////////////////////////////////////////
-//                                                                       //
-//                             Map searching                             //
-//                                                                       //
-// dfind(map, key) returns the key's value in map, or map's default      //
-//   value if no such key exists (the default value is not inserted)     //
-//                                                                       //
-// afind(map, key) returns a reference to the key's value in map, and    //
-//    asserts that this value exists                                     //
-//                                                                       //
-///////////////////////////////////////////////////////////////////////////
-
-// dfind(Map, Key) returns the value Map associates with Key, or the
-//  Map's default value if no such Key exists
-//
-template <class Map, class Key>
-inline typename Map::mapped_type dfind(Map& m, const Key& k)
-{
-  typename Map::iterator i = m.find(k);
-  if (i == m.end())
-    return typename Map::mapped_type();
-  else
-    return i->second;
-}
-
-template <class Map, class Key>
-inline const typename Map::mapped_type dfind(const Map& m, const Key& k)
-{
-  typename Map::const_iterator i = m.find(k);
-  if (i == m.end())
-    return typename Map::mapped_type();
-  else
-    return i->second;
-}
-
-
-// afind(map, key) returns a reference to the value associated
-//  with key in map.  It uses assert to check that the key's value
-//  is defined.
-//
-template <class Map, class Key>
-inline typename Map::mapped_type& afind(Map& m, const Key& k)
-{
-  typename Map::iterator i = m.find(k);
-  assert(i != m.end());
-  return i->second;
-}
-
-template <class Map, class Key>
-inline const typename Map::mapped_type& afind(const Map& m, const Key& k)
-{
-  typename Map::const_iterator i = m.find(k);
-  assert(i != m.end());
-  return i->second;
-}
-
-//! insert_newkey(map, key, value) checks that map does not contain
-//! key, and binds key to value.
-//
-template <class Map, class Key, class Value>
-inline typename Map::value_type& 
-insert_newkey(Map& m, const Key& k,const Value& v) 
-{
-  std::pair<typename Map::iterator, bool> itb 
-    = m.insert(Map::value_type(k, v));
-  assert(itb.second);
-  return *(itb.first);
-}  // insert_newkey()
-
-
-///////////////////////////////////////////////////////////////////////////
-//                                                                       //
-//                        Insert operations                              //
-//                                                                       //
-///////////////////////////////////////////////////////////////////////////
-
-
-template <typename T>
-void insert(std::list<T>& xs, const T& x) {
-  xs.push_back(x);
-}
-
-template <typename T>
-void insert(std::set<T>& xs, const T& x) {
-  xs.insert(x);
-}
-
-template <typename T>
-void insert(std::vector<T>& xs, const T& x) {
-  xs.push_back(x);
-}
-
-
-///////////////////////////////////////////////////////////////////////////
-//                                                                       //
-//                Additional versions of standard algorithms             //
-//                                                                       //
-///////////////////////////////////////////////////////////////////////////
-
-template <typename Set1, typename Set2>
-inline bool includes(const Set1& set1, const Set2& set2)
-{
-  return std::includes(set1.begin(), set1.end(), set2.begin(), set2.end());
-}
-
-template <typename Set1, typename Set2, typename Compare>
-inline bool includes(const Set1& set1, const Set2& set2, Compare comp)
-{
-  return std::includes(set1.begin(), set1.end(), set2.begin(), set2.end(), comp);
-}
-
-
-template <typename InputIter1, typename InputIter2>
-bool disjoint(InputIter1 first1, InputIter1 last1,
-              InputIter2 first2, InputIter2 last2)
-{
-  while (first1 != last1 && first2 != last2)
-    if (*first1 < *first2)
-      ++first1;
-    else if (*first2 < *first1)
-      ++first2;
-    else // *first1 == *first2
-      return false;
-  return true;
-}
-
-template <typename InputIter1, typename InputIter2, typename Compare>
-bool disjoint(InputIter1 first1, InputIter1 last1,
-              InputIter2 first2, InputIter2 last2, Compare comp)
-{
-  while (first1 != last1 && first2 != last2)
-    if (comp(*first1, *first2))
-      ++first1;
-    else if (comp(*first2, *first1))
-      ++first2;
-    else // *first1 == *first2
-      return false;
-  return true;
-}
-
-template <typename Set1, typename Set2>
-inline bool disjoint(const Set1& set1, const Set2& set2)
-{
-  return disjoint(set1.begin(), set1.end(), set2.begin(), set2.end());
-}
-
-template <typename Set1, typename Set2, typename Compare>
-inline bool disjoint(const Set1& set1, const Set2& set2, Compare comp)
-{
-  return disjoint(set1.begin(), set1.end(), set2.begin(), set2.end(), comp);
-}
-
-
-template <typename Set1, typename Set2, typename OutputIterator>
-inline OutputIterator set_intersection(const Set1& set1, const Set2& set2, 
-                                       OutputIterator result)
-{
-  return set_intersection(set1.begin(), set1.end(), set2.begin(), set2.end(), result);
-}
-
-template <typename Set1, typename Set2, typename OutputIterator, typename Compare>
-inline OutputIterator set_intersection(const Set1& set1, const Set2& set2, 
-                                       OutputIterator result, Compare comp)
-{
-  return set_intersection(set1.begin(), set1.end(), set2.begin(), set2.end(), result, comp);
-}
-
-
-template <typename Container>
-inline std::insert_iterator<Container> inserter(Container& container)
-{
-  return std::inserter(container, container.begin());
-}
-
-// max_element
-//
-template <class Es> inline typename Es::iterator max_element(Es& es)
-{
-  return std::max_element(es.begin(), es.end());
-}
-
-template <class Es> inline typename Es::const_iterator max_element(const Es& es)
-{
-  return std::max_element(es.begin(), es.end());
-}
-
-template <class Es, class BinaryPredicate> 
-inline typename Es::iterator max_element(Es& es, BinaryPredicate comp)
-{
-  return std::max_element(es.begin(), es.end(), comp);
-}
-
-template <class Es, class BinaryPredicate> 
-inline typename Es::const_iterator max_element(const Es& es, BinaryPredicate comp)
-{
-  return std::max_element(es.begin(), es.end(), comp);
-}
-
-// min_element
-//
-template <class Es> inline typename Es::iterator min_element(Es& es)
-{
-  return std::min_element(es.begin(), es.end());
-}
-
-template <class Es> inline typename Es::const_iterator min_element(const Es& es)
-{
-  return std::min_element(es.begin(), es.end());
-}
-
-template <class Es, class BinaryPredicate> 
-inline typename Es::iterator min_element(Es& es, BinaryPredicate comp)
-{
-  return std::min_element(es.begin(), es.end(), comp);
-}
-
-template <class Es, class BinaryPredicate> 
-inline typename Es::const_iterator min_element(const Es& es, BinaryPredicate comp)
-{
-  return std::min_element(es.begin(), es.end(), comp);
-}
-
-// first_lessthan and second_lessthan
-//
-struct first_lessthan {
-  template <typename T1, typename T2>
-    bool operator() (const T1& e1, const T2& e2) {
-      return e1.first < e2.first;
-    }
-};
-
-struct second_lessthan {
-  template <typename T1, typename T2>
-    bool operator() (const T1& e1, const T2& e2) {
-      return e1.second < e2.second;
-    }
-};
-
-// first_greaterthan and second_greaterthan
-//
-struct first_greaterthan {
-  template <typename T1, typename T2>
-    bool operator() (const T1& e1, const T2& e2) {
-      return e1.first > e2.first;
-    }
-};
-
-struct second_greaterthan {
-  template <typename T1, typename T2>
-    bool operator() (const T1& e1, const T2& e2) {
-      return e1.second > e2.second;
-    }
-};
-
-
-///////////////////////////////////////////////////////////////////////////
-//                                                                       //
-//                          hash<> specializations                       //
-//                                                                       //
-// These must be in namespace std.   They permit the corresponding STL   //
-// container to be used as a key in an STL hash table.                   //
-//                                                                       //
-///////////////////////////////////////////////////////////////////////////
-
-//namespace EXT_NAMESPACE {
-namespace std {
-  /*
-  // hash function for bool
-  //
-  template <> struct hash<bool>
-  {
-  size_t operator() (bool b) const 
-  {
-  return b;
-  } // operator()
-  }; // hash<bool>{}
-
-  // hash function for double
-  //
-  template <> struct hash<double>
-  {
-  size_t operator() (double d) const 
-  {
-  int exponent;
-  double fraction = frexp(d, &exponent);
-  return size_t(exponent) ^ size_t(1000000.0*(fabs(fraction-0.5)));
-  } // operator()
-  }; // hash<double>{}
-
-  // hash function for strings
-  //
-  template <> struct hash<std::string> 
-  {
-  size_t operator()(const std::string& s) const 
-  {
-  typedef std::string::const_iterator CI;
-
-  unsigned long h = 0; 
-  unsigned long g;
-  CI p = s.begin();
-  CI end = s.end();
-
-  while (p!=end) {
-  h = (h << 4) + (*p++);
-  if ((g = h&0xf0000000)) {
-  h = h ^ (g >> 24);
-  h = h ^ g;
-  }}
-  return size_t(h);
-  }  // operator()
-  };  // hash<string>{}
-
-*/
-  // hash function for arbitrary pairs
-  //
-  template<class T1, class T2> struct hash<std::pair<T1,T2> > {
-    size_t operator()(const std::pair<T1,T2>& p) const
-    {
-      size_t h1 = hash<T1>()(p.first);
-      size_t h2 = hash<T2>()(p.second);
-      return h1 ^ (h1 >> 1) ^ h2 ^ (h2 << 1);
-    }
-  };
-
-
-  // hash function for vectors
-  //
-  template<class T> struct hash<std::vector<T> > 
-  { //  This is the fn hashpjw of Aho, Sethi and Ullman, p 436.
-    size_t operator()(const std::vector<T>& s) const 
-    {
-      typedef typename std::vector<T>::const_iterator CI;
-
-      unsigned long h = 0; 
-      unsigned long g;
-      CI p = s.begin();
-      CI end = s.end();
-
-      while (p!=end) {
-        h = (h << 5) + hash<T>()(*p++);
-        if ((g = h&0xff000000)) {
-          h = h ^ (g >> 23);
-          h = h ^ g;
-        }}
-        return size_t(h);
-    }
-  };
-
-  // hash function for slists
-  //
-  template<class T> struct hash<ext::slist<T> > 
-  { //  This is the fn hashpjw of Aho, Sethi and Ullman, p 436.
-    size_t operator()(const ext::slist<T>& s) const 
-    {
-      typedef typename ext::slist<T>::const_iterator CI;
-
-      unsigned long h = 0; 
-      unsigned long g;
-      CI p = s.begin();
-      CI end = s.end();
-
-      while (p!=end) {
-        h = (h << 7) + hash<T>()(*p++);
-        if ((g = h&0xff000000)) {
-          h = h ^ (g >> 23);
-          h = h ^ g;
-        }}
-        return size_t(h);
-    }
-  };
-
-  // hash function for maps
-  //
-  template<typename T1, typename T2> struct hash<std::map<T1,T2> >
-  {
-    size_t operator()(const std::map<T1,T2>& m) const
-    {
-      typedef typename std::map<T1,T2> M;
-      typedef typename M::const_iterator CI;
-
-      unsigned long h = 0;
-      unsigned long g;
-      CI p = m.begin();
-      CI end = m.end();
-
-      while (p != end) {
-        h = (h << 11) + hash<typename M::value_type>()(*p++);
-        if ((g = h&0xff000000)) {
-          h = h ^ (g >> 23);
-          h = h ^ g;
-        }}
-        return size_t(h);
-    }
-  };
-
-} // namespace EXT_NAMESPACE
-
-
-
-///////////////////////////////////////////////////////////////////////////
-//                                                                       //
-//                           Write/Read code                             //
-//                                                                       //
-// These routines should possess write/read invariance IF their elements //
-// also have write-read invariance.  Whitespace, '(' and ')' are used as //
-// delimiters.                                                           //
-//                                                                       //
-///////////////////////////////////////////////////////////////////////////
-
-
-// Define istream >> const char* so that it consumes the characters from the
-// istream.  Just as in scanf, a space consumes an arbitrary amount of whitespace.
-//
-inline std::istream& operator>> (std::istream& is, const char* cp)
-{
-  if (*cp == '\0')
-    return is;
-  else if (*cp == ' ') {
-    char c;
-    if (is.get(c)) {
-      if (isspace(c))
-        return is >> cp;
-      else {
-        is.unget();
-        return is >> (cp+1);
-      }
-    }
-    else {
-      is.clear(is.rdstate() & ~std::ios::failbit);  // clear failbit
-      return is >> (cp+1);
-    }
-  }
-  else {
-    char c;
-    if (is.get(c)) {
-      if (c == *cp)
-        return is >> (cp+1);
-      else {
-        is.unget();
-        is.setstate(std::ios::failbit);
-      }
-    }
-    return is;
-  }
-}
-
-
-// Write out an auto_ptr object just as you would write out the pointer object
-//
-template <typename T> 
-inline std::ostream& operator<<(std::ostream& os, const std::auto_ptr<T>& sp)
-{
-  return os << sp.get();
-}
-
-
-// Pairs
-//
-template <class T1, class T2> 
-std::ostream& operator<< (std::ostream& os, const std::pair<T1,T2>& p)
-{
-  return os << '(' << p.first << ' ' << p.second << ')';
-}
-
-template <class T1, class T2>
-std::istream& operator>> (std::istream& is, std::pair<T1,T2>& p)
-{
-  char c;
-  if (is >> c) {
-    if (c == '(') {
-      if (is >> p.first >> p.second >> c && c == ')')
-        return is;
-      else 
-        is.setstate(std::ios::badbit);
-    }
-    else
-      is.putback(c);
-  }
-  is.setstate(std::ios::failbit);
-  return is;
-}
-
-// Lists
-//
-template <class T>
-std::ostream& operator<< (std::ostream& os, const std::list<T>& xs)
-{
-  os << '(';
-  for (typename std::list<T>::const_iterator xi = xs.begin(); xi != xs.end(); ++xi) {
-    if (xi != xs.begin())
-      os << ' ';
-    os << *xi;
-  }
-  return os << ')';
-}
-
-template <class T>
-std::istream& operator>> (std::istream& is, std::list<T>& xs)
-{
-  char c;                          // This code avoids unnecessary copy
-  if (is >> c) {                   // read the initial '('
-    if (c == '(') {
-      xs.clear();                  // clear the list
-      do {
-        xs.push_back(T());         // create a new elt in list
-        is >> xs.back();           // read element
-      }
-      while (is.good());           // read as long as possible
-      xs.pop_back();               // last read failed; pop last elt
-      is.clear(is.rdstate() & ~std::ios::failbit);  // clear failbit
-      if (is >> c && c == ')')     // read terminating ')'
-        return is;                 // successful return
-      else 
-        is.setstate(std::ios::badbit); // something went wrong, set badbit
-    }
-    else                           // c is not '('
-      is.putback(c);               //  put c back into input
-  }
-  is.setstate(std::ios::failbit);  // read failed, set failbit
-  return is;
-}
-
-// Vectors
-//
-template <class T>
-std::ostream& operator<< (std::ostream& os, const std::vector<T>& xs)
-{
-  os << '(';
-  for (typename std::vector<T>::const_iterator xi = xs.begin(); xi != xs.end(); ++xi) {
-    if (xi != xs.begin())
-      os << ' ';
-    os << *xi;
-  }
-  return os << ')';
-}
-
-template <class T>
-std::istream& operator>> (std::istream& is, std::vector<T>& xs)
-{
-  char c;                          // This code avoids unnecessary copy
-  if (is >> c) {                   // read the initial '('
-    if (c == '(') {
-      xs.clear();                  // clear the list
-      do {
-        xs.push_back(T());         // create a new elt in list
-        is >> xs.back();           // read element
-      }
-      while (is.good());           // read as long as possible
-      xs.pop_back();               // last read failed; pop last elt
-      is.clear(is.rdstate() & ~std::ios::failbit);  // clear failbit
-      if (is >> c && c == ')')     // read terminating ')'
-        return is;                 // successful return
-      else 
-        is.setstate(std::ios::badbit); // something went wrong, set badbit
-    }
-    else                           // c is not '('
-      is.putback(c);               //  put c back into input
-  }
-  is.setstate(std::ios::failbit);  // read failed, set failbit
-  return is;
-}
-
-// Slists
-//
-template <class T>
-std::ostream& operator<< (std::ostream& os, const ext::slist<T>& xs)
-{
-  os << '(';
-  for (typename ext::slist<T>::const_iterator xi = xs.begin(); xi != xs.end(); ++xi) {
-    if (xi != xs.begin())
-      os << ' ';
-    os << *xi;
-  }
-  return os << ')';
-}
-
-template <class T>
-std::istream& operator>> (std::istream& is, ext::slist<T>& xs)
-{
-  char c; 
-  if (is >> c) { 
-    if (c == '(') {
-      xs.clear();
-      T e;
-      if (is >> e) {   
-        xs.push_front(e);
-        typename ext::slist<T>::iterator xi = xs.begin();
-        while (is >> e)
-          xi = xs.insert_after(xi, e);
-        is.clear(is.rdstate() & ~std::ios::failbit);
-        if (is >> c && c == ')')
-          return is;
-        else 
-          is.setstate(std::ios::badbit); 
-      }
-      else { // empty list
-        is.clear(is.rdstate() & ~std::ios::failbit);
-        if (is >> c && c == ')')
-          return is;
-        else  // didn't see closing ')'
-          is.setstate(std::ios::badbit);
-      }
-    }
-    else  // didn't read '('
-      is.putback(c);
-  }
-  is.setstate(std::ios::failbit);
-  return is;
-}
-
-// Sets
-//
-template <class T>
-std::ostream& operator<< (std::ostream& os, const std::set<T>& s)
-{
-  os << '(';
-  for (typename std::set<T>::const_iterator i = s.begin(); i != s.end(); ++i) {
-    if (i != s.begin())
-      os << ' ';
-    os << *i;
-  }
-  return os << ')';
-}
-
-template <class T>
-std::istream& operator>> (std::istream& is, std::set<T>& s)
-{
-  char c;
-  if (is >> c) {
-    if (c == '(') {
-      s.clear();
-      T e;
-      while (is >> e)
-        s.insert(e);
-      is.clear(is.rdstate() & ~std::ios::failbit);
-      if (is >> c && c == ')')
-        return is;
-      else
-        is.setstate(std::ios::badbit);
-    }
-    else
-      is.putback(c);
-  }
-  is.setstate(std::ios::failbit);
-  return is;
-}
-
-// Hash_sets
-//
-template <class T>
-std::ostream& operator<< (std::ostream& os, const std::unordered_set<T>& s)
-{
-  os << '(';
-  for (typename std::unordered_set<T>::const_iterator i = s.begin(); i != s.end(); ++i) {
-    if (i != s.begin())
-      os << ' ';
-    os << *i;
-  }
-  return os << ')';
-}
-
-template <class T>
-std::istream& operator>> (std::istream& is, std::unordered_set<T>& s)
-{
-  char c;
-  if (is >> c) {
-    if (c == '(') {
-      s.clear();
-      T e;
-      while (is >> e)
-        s.insert(e);
-      is.clear(is.rdstate() & ~std::ios::failbit);
-      if (is >> c && c == ')')
-        return is;
-      else
-        is.setstate(std::ios::badbit);
-    }
-    else
-      is.putback(c);
-  }
-  is.setstate(std::ios::failbit);
-  return is;
-}
-
-
-// Maps
-//
-template <class Key, class Value>
-std::ostream& operator<< (std::ostream& os, const std::map<Key,Value>& m)
-{
-  typedef std::map<Key,Value> M;
-  os << '(';
-  for (typename M::const_iterator it = m.begin(); it != m.end(); ++it) {
-    if (it != m.begin())
-      os << ' ';
-    os << *it;
-  }
-  return os << ")";
-}
-
-template <class Key, class Value>
-std::istream& operator>> (std::istream& is, std::map<Key,Value>& m)
-{
-  char c;
-  if (is >> c) {
-    if (c == '(') {
-      m.clear();
-      std::pair<Key,Value> e;
-      while (is >> e)
-        m.insert(e);
-      is.clear(is.rdstate() & ~std::ios::failbit);
-      if (is >> c && c == ')')
-        return is;
-      else
-        is.setstate(std::ios::badbit);
-    }
-    else
-      is.putback(c);
-  }
-  is.setstate(std::ios::failbit);
-  return is;
-}
-
-// Hash_maps
-//
-template <class Key, class Value>
-std::ostream& operator<< (std::ostream& os, const std::unordered_map<Key,Value>& m)
-{
-  typedef std::unordered_map<Key,Value> M;
-  os << '(';
-  for (typename M::const_iterator it = m.begin(); it != m.end(); ++it) {
-    if (it != m.begin())
-      os << ' ';
-    os << *it;
-  }
-  return os << ")";
-}
-
-template <class Key, class Value>
-std::istream& operator>> (std::istream& is, std::unordered_map<Key,Value>& m)
-{
-  char c;
-  if (is >> c) {
-    if (c == '(') {
-      m.clear();
-      std::pair<Key,Value> e;
-      while (is >> e)
-        m.insert(e);
-      is.clear(is.rdstate() & ~std::ios::failbit);
-      if (is >> c && c == ')')
-        return is;
-      else
-        is.setstate(std::ios::badbit);
-    }
-    else
-      is.putback(c);
-  }
-  is.setstate(std::ios::failbit);
-  return is;
-}
-
-
-///////////////////////////////////////////////////////////////////////////
-//                                                                       //
-//                       Boost library additions                         //
-//                                                                       //
-///////////////////////////////////////////////////////////////////////////
-
-#ifdef BOOST_SHARED_PTR_HPP_INCLUDED
-
-// enhancements to boost::shared_ptr so it can be used with hash
-//
-namespace std {
-  template <typename T> struct equal_to<boost::shared_ptr<T> > 
-    : public binary_function<boost::shared_ptr<T>, boost::shared_ptr<T>, bool> {
-      bool operator() (const boost::shared_ptr<T>& p1, const boost::shared_ptr<T>& p2) const {
-        return equal_to<T*>()(p1.get(), p2.get());
-      }
-    };
-}  // namespace std
-
-//namespace EXT_NAMESPACE {
-namespace std {
-  template <typename T> struct hash<boost::shared_ptr<T> > {
-    size_t operator() (const boost::shared_ptr<T>& a) const {
-      return hash<T*>()(a.get());
-    }
-  };
-}  // namespace ext
-
-template <typename T> 
-inline std::ostream& operator<< (std::ostream& os, const boost::shared_ptr<T>& sp)
-{
-  return os << sp.get();
-}
-
-#endif  // BOOST_SHARED_PTR_HPP_INCLUDED
-
-struct resource_usage { };
-
-#ifndef __i386
-inline std::ostream& operator<< (std::ostream& os, resource_usage r)
-{
-  return os;
-}
-#else // Assume we are on a 586 linux
-inline std::ostream& operator<< (std::ostream& os, resource_usage r)
-{
-  FILE* fp = fopen("/proc/self/stat", "r");
-  assert(fp);
-  int utime;
-  int stime;
-  unsigned int vsize;
-  unsigned int rss;
-  int result = 
-    fscanf(fp, "%*d %*s %*c %*d %*d %*d %*d %*d %*u %*u %*u %*u %*u %d %d %*d %*d %*d %*d"
-           "%*u %*u %*d %u %u", &utime, &stime, &vsize, &rss);
-  assert(result == 4);
-  fclose(fp);
-  // s << "utime = " << utime << ", stime = " << stime << ", vsize = " << vsize << ", rss = " << rss
-  ;
-  // return s << "utime = " << utime << ", vsize = " << vsize;
-  return os << "utime " << float(utime)/1.0e2 << "s, vsize " 
-    << float(vsize)/1048576.0 << " Mb.";
-}
-#endif
-
-//! A default_value_type{} object is used to read an object from a stream,
-//! assigning a default value if the read fails.  Users should not need to
-//! construct such objects, but should use default_value() instead.
-//
-template <typename object_type, typename default_type>
-struct default_value_type {
-  object_type& object;
-  const default_type defaultvalue;
-  default_value_type(object_type& object, const default_type defaultvalue)
-    : object(object), defaultvalue(defaultvalue) { }
-};
-
-//! default_value() is used to read an object from a stream, assigning a
-//! default value if the read fails.  It returns a default_value_type{}
-//! object, which does the actual reading.
-//
-template <typename object_type, typename default_type>
-default_value_type<object_type,default_type>
-default_value(object_type& object, const default_type defaultvalue=default_type()) {
-  return default_value_type<object_type,default_type>(object, defaultvalue);
-}
-
-//! This version of operator>>() reads default_value_type{} from an input stream.
-//
-template <typename object_type, typename default_type>
-std::istream& operator>> (std::istream& is, 
-                          default_value_type<object_type, default_type> dv) {
-  if (is) {
-    if (is >> dv.object)
-      ;
-    else {
-      is.clear(is.rdstate() & ~std::ios::failbit);  // clear failbit
-      dv.object = dv.defaultvalue;
-    }
-  }
-  return is;
-}
-
-// inline F random1() { return rand()/(RAND_MAX+1.0); }
-inline F random1() { return mt_genrand_res53(); }
-
-#endif  // UTILITY_H
diff --git a/gi/pyp-topics/src/workers.hh b/gi/pyp-topics/src/workers.hh
deleted file mode 100644
index 95b18947..00000000
--- a/gi/pyp-topics/src/workers.hh
+++ /dev/null
@@ -1,275 +0,0 @@
-/**
-  Basic thread-pool tools using Boost.Thread.
-  (Jan Botha, 7/2010)
-
-  --Simple usage--
-  Use SimpleWorker.
-    Example, call a function that returns an int in a new thread:
-    typedef boost::function<int()> JobType;
-    JobType job = boost::bind(funcname);
-      //or boost::bind(&class::funcname, this) for a member function
-    SimpleWorker<JobType, int> worker(job);
-    int result = worker.getResult(); //blocks until result is ready
-
-  --Extended usage--
-  Use WorkerPool, which uses Queuemt (a synchronized queue) and Worker.
-  Example:
-    (same context and typedef
-    WorkerPool<JobType, int> pool(num_threads);
-    JobType job = ...
-    pool.addJob(job);
-    ...
-    pool.get_result(); //blocks until all workers are done, returns the some of their results.  
-    
-    Jobs added to a WorkerPool need to be the same type. A WorkerPool instance should not be reused (e.g. adding jobs) after calling get_result(). 
-*/
-
-#ifndef WORKERS_HH
-#define WORKERS_HH
-
-#include <iostream>
-#include <boost/bind.hpp>
-#include <boost/function.hpp>
-#include <queue>
-#include <boost/ptr_container/ptr_vector.hpp>
-#include <boost/thread/thread.hpp>
-#include <boost/thread/mutex.hpp>
-#include <boost/thread/shared_mutex.hpp>
-#include <boost/thread/future.hpp>
-#include <boost/thread/condition.hpp>
-
-#include <boost/date_time/posix_time/posix_time_types.hpp>
-#include "timing.h"
-
-/** Implements a synchronized queue*/
-template<typename J>
-class Queuemt
-{
-
-public:
-    boost::condition_variable_any cond;
-    const bool& running;
-
-    Queuemt() { }
-    Queuemt(const bool& running) : running(running), maxsize(0), qsize(0) 
-    { 
-    }
-
-    ~Queuemt() { 
-     }
-
-    J pop()
-    {
-        J job;
-        {
-            boost::unique_lock<boost::shared_mutex> qlock(q_mutex);
-            while (running && qsize == 0)
-                cond.wait(qlock);
-
-            if (qsize > 0)
-            {
-                job = q.front();
-                q.pop();
-                --qsize;      
-            }
-        }
-        if (job)
-            cond.notify_one();
-        return job;
-
-    }
-
-    void push(J job)
-    {
-        {
-            boost::unique_lock<boost::shared_mutex> lock(q_mutex);
-            q.push(job);
-            ++qsize;
-        }
-        if (qsize > maxsize)
-            maxsize = qsize;
-        
-        cond.notify_one();
-    }
-
-    int getMaxsize()
-    {
-        return maxsize;
-    }
-
-    int size()
-    {
-        return qsize;
-    }
-
-private:
-    boost::shared_mutex q_mutex;
-    std::queue<J> q;
-    int maxsize;
-    volatile int qsize;
-};
-
-
-template<typename J, typename R>
-class Worker
-{
-typedef boost::packaged_task<R> PackagedTask;
-public:
-    Worker(Queuemt<J>& queue, int id, int num_workers) :  
-      q(queue), tasktime(0.0), id(id), num_workers(num_workers)
-    {
-        PackagedTask task(boost::bind(&Worker<J, R>::run, this));
-        future = task.get_future();
-        boost::thread t(boost::move(task));
-    }
-
-    R run() //this is called upon thread creation
-    {
-        R wresult = 0;
-        while (isRunning())
-        {
-            J job = q.pop();
-
-            if (job)
-            {
-                timer.Reset();
-                wresult += job();
-                tasktime += timer.Elapsed();
-            }
-        }
-        return wresult;
-    }
-
-    R getResult()
-    {
-        if (!future.is_ready())
-            future.wait();
-        assert(future.is_ready());
-        return future.get();
-    }
-
-    double getTaskTime()
-    {
-        return tasktime;
-    }
-
-private:
-
-    Queuemt<J>& q;
-
-    boost::unique_future<R> future;
-
-    bool isRunning()
-    {
-        return q.running || q.size() > 0;
-    }
-    
-    Timer timer;
-    double tasktime;
-    int id;
-    int num_workers;
-};
-
-template<typename J, typename R>
-class WorkerPool
-{
-typedef boost::packaged_task<R> PackagedTask;
-typedef Worker<J,R> WJR;
-typedef boost::ptr_vector<WJR> WorkerVector;
-public:
-
-    WorkerPool(int num_workers)
-    {
-        q.reset(new Queuemt<J>(running));
-        running = true;
-        for (int i = 0; i < num_workers; ++i)
-            workers.push_back( new Worker<J, R>(*q, i, num_workers) );
-    }
-
-    ~WorkerPool()
-    {
-    }
-
-    R get_result()
-    {
-        running = false;
-        q->cond.notify_all();
-        R tmp = 0;
-        double tasktime = 0.0;
-        for (typename WorkerVector::iterator it = workers.begin(); it != workers.end(); it++)
-        {
-            R res = it->getResult();
-            tmp += res;
-            //std::cerr << "tasktime: " << it->getTaskTime() << std::endl; 
-            tasktime += it->getTaskTime();
-        }
-//        std::cerr << " maxQ = " << q->getMaxsize() << std::endl;
-        return tmp;
-    }
-
-    void addJob(J job)
-    {
-        q->push(job);
-    }
-
-private:
-
-    WorkerVector workers;
-
-    boost::shared_ptr<Queuemt<J> > q;
-
-    bool running;
-};
-
-///////////////////
-template <typename J, typename R>
-class SimpleWorker
-{
-typedef boost::packaged_task<R> PackagedTask;
-public:
-    SimpleWorker(J& job) : job(job), tasktime(0.0)
-    {
-        PackagedTask task(boost::bind(&SimpleWorker<J, R>::run, this));
-        future = task.get_future();
-        boost::thread t(boost::move(task));
-    }
-
-    R run() //this is called upon thread creation
-    {
-        R wresult = 0;
-
-        assert(job);
-        timer.Reset();
-        wresult = job();
-        tasktime = timer.Elapsed();
-        std::cerr << tasktime << " s" << std::endl; 
-        return wresult;
-    }
-
-    R getResult()
-    {
-        if (!future.is_ready())
-            future.wait();
-        assert(future.is_ready());
-        return future.get();
-    }
-
-    double getTaskTime()
-    {
-        return tasktime;
-    }
-
-private:
-
-    J job;
-
-    boost::unique_future<R> future;
-
-    Timer timer;
-    double tasktime;
-
-};
-
-
-
-#endif 
diff --git a/gi/scripts/buck2utf8.pl b/gi/scripts/buck2utf8.pl
deleted file mode 100755
index 1acfae8d..00000000
--- a/gi/scripts/buck2utf8.pl
+++ /dev/null
@@ -1,87 +0,0 @@
-#!/usr/bin/perl -w
-use strict;
-use utf8;
-binmode(STDOUT, ":utf8");
-while(<>) {
-  chomp;
-  my @words = split /\s+/;
-  for my $w (@words) {
-    $_ = $w;
-    if ($w =~ /^__NTK__/o) {
-      s/__NTK__//go;
-      next if /^$/;
-      print STDOUT "$_ ";
-      next;
-    }
-s/tR/\x{0679}/g;  # retroflex t
-s/dR/\x{0688}/g;  # retroflex d
-s/rR/\x{0691}/g;  # retroflex r
-s/p/\x{067E}/g;   # peh
-s/c/\x{0686}/g;   # tcheh
-s/g/\x{06AF}/g;   # geh (G=ghain)
-s/@/\x{06BE}/g;   # heh doachashmee
-s/h'/\x{06c2}/g;  # heh goal + hamza
-s/h/\x{06c1}/g;   # heh goal
-s/J/\x{0698}/g;   # zheh (rare, usually persian loan words)
-s/k/\x{06A9}/g;   # k
-s/Y'/\x{06d3}/g;  # yeh barree + hamza above (ligature)
-s/y/\x{06cc}/g;   # same as ya' in arabic
-s/Y/\x{06d2}/g;   # yeh barree
-s/N/\x{06BA}/g;  # Ghunna
-
-    s/\'/\x{0621}/g;
-    s/\|/\x{0622}/g;
-    s/\>/\x{0623}/g;
-    s/\&/\x{0624}/g;
-    s/\</\x{0625}/g;
-    s/\}/\x{0626}/g;
-    s/A/\x{0627}/g;
-    s/b/\x{0628}/g;
-    s/t/\x{062A}/g;
-    s/v/\x{062B}/g;
-    s/j/\x{062C}/g;
-    s/H/\x{062D}/g;
-    s/x/\x{062E}/g;
-    s/d/\x{062F}/g;
-    s/\*/\x{0630}/g;
-    s/r/\x{0631}/g;
-    s/z/\x{0632}/g;
-    s/s/\x{0633}/g;
-    s/\$/\x{0634}/g;
-    s/S/\x{0635}/g;
-    s/D/\x{0636}/g;
-    s/T/\x{0637}/g;
-    s/Z/\x{0638}/g;
-    s/E/\x{0639}/g;
-    s/g/\x{063A}/g;
-    s/_/\x{0640}/g;
-    s/f/\x{0641}/g;
-    s/q/\x{0642}/g;
-    s/k/\x{0643}/g;
-    s/l/\x{0644}/g;
-    s/m/\x{0645}/g;
-    s/n/\x{0646}/g;
-    s/h/\x{0647}/g;
-    s/w/\x{0648}/g;
-    s/Y/\x{0649}/g;
-    s/y/\x{064A}/g;
-    s/F/\x{064B}/g;
-    s/N/\x{064C}/g;
-    s/K/\x{064D}/g;
-    s/a/\x{064E}/g;
-    s/u/\x{064F}/g;
-    s/i/\x{0650}/g;
-    s/\~/\x{0651}/g;
-    s/o/\x{0652}/g;
-    s/\`/\x{0670}/g;
-    s/\{/\x{0671}/g;
-    s/P/\x{067E}/g;
-    s/J/\x{0686}/g;
-    s/V/\x{06A4}/g;
-    s/G/\x{06AF}/g;
-
-
-print STDOUT "$_ ";
-  }
-  print STDOUT "\n";
-}
diff --git a/jam-files/LICENSE_1_0.txt b/jam-files/LICENSE_1_0.txt
deleted file mode 100644
index 36b7cd93..00000000
--- a/jam-files/LICENSE_1_0.txt
+++ /dev/null
@@ -1,23 +0,0 @@
-Boost Software License - Version 1.0 - August 17th, 2003
-
-Permission is hereby granted, free of charge, to any person or organization
-obtaining a copy of the software and accompanying documentation covered by
-this license (the "Software") to use, reproduce, display, distribute,
-execute, and transmit the Software, and to prepare derivative works of the
-Software, and to permit third-parties to whom the Software is furnished to
-do so, all subject to the following:
-
-The copyright notices in the Software and this entire statement, including
-the above license grant, this restriction and the following disclaimer,
-must be included in all copies of the Software, in whole or in part, and
-all derivative works of the Software, unless such copies or derivative
-works are solely in the form of machine-executable object code generated by
-a source language processor.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT
-SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
-FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
-ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
-DEALINGS IN THE SOFTWARE.
diff --git a/jam-files/boost-build/boost-build.jam b/jam-files/boost-build/boost-build.jam
deleted file mode 100644
index 73db0497..00000000
--- a/jam-files/boost-build/boost-build.jam
+++ /dev/null
@@ -1,8 +0,0 @@
-# Copyright 2001, 2002 Dave Abrahams
-# Copyright 2002 Rene Rivera
-# Copyright 2003 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-
-boost-build kernel ;
diff --git a/jam-files/boost-build/bootstrap.jam b/jam-files/boost-build/bootstrap.jam
deleted file mode 100644
index af3e8bf5..00000000
--- a/jam-files/boost-build/bootstrap.jam
+++ /dev/null
@@ -1,18 +0,0 @@
-#  Copyright (c) 2003 Vladimir Prus.
-#
-#  Use, modification and distribution is subject to the Boost Software
-#  License Version 1.0. (See accompanying file LICENSE_1_0.txt or
-#  http://www.boost.org/LICENSE_1_0.txt)
-
-# This file handles initial phase of Boost.Build loading.
-# Boost.Jam has already figured out where Boost.Build is
-# and loads this file, which is responsible for initialization
-# of basic facilities such a module system and loading the
-# main Boost.Build module, build-system.jam.
-#
-# Exact operation of this module is not interesting, it makes
-# sense to look at build-system.jam right away.
-
-# Load the kernel/bootstrap.jam, which does all the work.
-.bootstrap-file = $(.bootstrap-file:D)/kernel/bootstrap.jam ;
-include $(.bootstrap-file) ;
\ No newline at end of file
diff --git a/jam-files/boost-build/build-system.jam b/jam-files/boost-build/build-system.jam
deleted file mode 100644
index 9f9c884c..00000000
--- a/jam-files/boost-build/build-system.jam
+++ /dev/null
@@ -1,1008 +0,0 @@
-# Copyright 2003, 2005, 2007 Dave Abrahams
-# Copyright 2006, 2007 Rene Rivera
-# Copyright 2003, 2004, 2005, 2006 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-# This file is part of Boost Build version 2. You can think of it as forming the
-# main() routine. It is invoked by the bootstrapping code in bootstrap.jam.
-
-import build-request ;
-import builtin ;
-import "class" : new ;
-import errors ;
-import feature ;
-import make ;
-import modules ;
-import os ;
-import path ;
-import project ;
-import property-set ;
-import regex ;
-import sequence ;
-import targets ;
-import toolset ;
-import utility ;
-import version ;
-import virtual-target ;
-import generators ;
-import configure ;
-
-################################################################################
-#
-# Module global data.
-#
-################################################################################
-
-# Shortcut used in this module for accessing used command-line parameters.
-.argv = [ modules.peek : ARGV ] ;
-
-# Flag indicating we should display additional debugging information related to
-# locating and loading Boost Build configuration files.
-.debug-config = [ MATCH ^(--debug-configuration)$ : $(.argv) ] ;
-
-# Legacy option doing too many things, some of which are not even documented.
-# Should be phased out.
-#   * Disables loading site and user configuration files.
-#   * Disables auto-configuration for toolsets specified explicitly on the
-#     command-line.
-#   * Causes --toolset command-line options to be ignored.
-#   * Prevents the default toolset from being used even if no toolset has been
-#     configured at all.
-.legacy-ignore-config = [ MATCH ^(--ignore-config)$ : $(.argv) ] ;
-
-# The cleaning is tricky. Say, if user says 'bjam --clean foo' where 'foo' is a
-# directory, then we want to clean targets which are in 'foo' as well as those
-# in any children Jamfiles under foo but not in any unrelated Jamfiles. To
-# achieve this we collect a list of projects under which cleaning is allowed.
-.project-targets = ;
-
-# Virtual targets obtained when building main targets references on the command
-# line. When running 'bjam --clean main_target' we want to clean only files
-# belonging to that main target so we need to record which targets are produced
-# for it.
-.results-of-main-targets = ;
-
-# Was an XML dump requested?
-.out-xml = [ MATCH ^--out-xml=(.*)$ : $(.argv) ] ;
-
-# Default toolset & version to be used in case no other toolset has been used
-# explicitly by either the loaded configuration files, the loaded project build
-# scripts or an explicit toolset request on the command line. If not specified,
-# an arbitrary default will be used based on the current host OS. This value,
-# while not strictly necessary, has been added to allow testing Boost-Build's
-# default toolset usage functionality.
-.default-toolset = ;
-.default-toolset-version = ;
-
-
-################################################################################
-#
-# Public rules.
-#
-################################################################################
-
-# Returns the property set with the free features from the currently processed
-# build request.
-#
-rule command-line-free-features ( )
-{
-    return $(.command-line-free-features) ;
-}
-
-
-# Returns the location of the build system. The primary use case is building
-# Boost where it is sometimes needed to get the location of other components
-# (e.g. BoostBook files) and it is convenient to use locations relative to the
-# Boost Build path.
-#
-rule location ( )
-{
-    local r = [ modules.binding build-system ] ;
-    return $(r:P) ;
-}
-
-
-# Sets the default toolset & version to be used in case no other toolset has
-# been used explicitly by either the loaded configuration files, the loaded
-# project build scripts or an explicit toolset request on the command line. For
-# more detailed information see the comment related to used global variables.
-#
-rule set-default-toolset ( toolset : version ? )
-{
-    .default-toolset = $(toolset) ;
-    .default-toolset-version = $(version) ;
-}
-
-rule set-pre-build-hook ( function )
-{
-    .pre-build-hook = $(function) ;
-}
-
-rule set-post-build-hook ( function )
-{
-    .post-build-hook = $(function) ;
-}
-
-################################################################################
-#
-# Local rules.
-#
-################################################################################
-
-# Returns actual Jam targets to be used for executing a clean request.
-#
-local rule actual-clean-targets ( )
-{
-    # Construct a list of projects explicitly detected as targets on this build
-    # system run. These are the projects under which cleaning is allowed.
-    for local t in $(targets)
-    {
-        if [ class.is-a $(t) : project-target ]
-        {
-            .project-targets += [ $(t).project-module ] ;
-        }
-    }
-
-    # Construct a list of targets explicitly detected on this build system run
-    # as a result of building main targets.
-    local targets-to-clean ;
-    for local t in $(.results-of-main-targets)
-    {
-        # Do not include roots or sources.
-        targets-to-clean += [ virtual-target.traverse $(t) ] ;
-    }
-    targets-to-clean = [ sequence.unique $(targets-to-clean) ] ;
-
-    local to-clean ;
-    for local t in [ virtual-target.all-targets ]
-    {
-        local p = [ $(t).project ] ;
-
-        # Remove only derived targets.
-        if [ $(t).action ]
-        {
-            if $(t) in $(targets-to-clean) ||
-                [ should-clean-project [ $(p).project-module ] ] = true
-            {
-                to-clean += $(t) ;
-            }
-        }
-    }
-
-    local to-clean-actual ;
-    for local t in $(to-clean)
-    {
-        to-clean-actual += [ $(t).actualize ] ;
-    }
-    return $(to-clean-actual) ;
-}
-
-
-# Given a target id, try to find and return the corresponding target. This is
-# only invoked when there is no Jamfile in ".". This code somewhat duplicates
-# code in project-target.find but we can not reuse that code without a
-# project-targets instance.
-#
-local rule find-target ( target-id )
-{
-    local split = [ MATCH (.*)//(.*) : $(target-id) ] ;
-
-    local pm ;
-    if $(split)
-    {
-        pm = [ project.find $(split[1]) : "." ] ;
-    }
-    else
-    {
-        pm = [ project.find $(target-id) : "." ] ;
-    }
-
-    local result ;
-    if $(pm)
-    {
-        result = [ project.target $(pm) ] ;
-    }
-
-    if $(split)
-    {
-        result = [ $(result).find $(split[2]) ] ;
-    }
-
-    return $(result) ;
-}
-
-
-# Initializes a new configuration module.
-#
-local rule initialize-config-module ( module-name : location ? )
-{
-    project.initialize $(module-name) : $(location) ;
-    if USER_MODULE in [ RULENAMES ]
-    {
-        USER_MODULE $(module-name) ;
-    }
-}
-
-
-# Helper rule used to load configuration files. Loads the first configuration
-# file with the given 'filename' at 'path' into module with name 'module-name'.
-# Not finding the requested file may or may not be treated as an error depending
-# on the must-find parameter. Returns a normalized path to the loaded
-# configuration file or nothing if no file was loaded.
-#
-local rule load-config ( module-name : filename : path + : must-find ? )
-{
-    if $(.debug-config)
-    {
-        ECHO "notice: Searching" "$(path)" "for" "$(module-name)"
-            "configuration file" "$(filename)" "." ;
-    }
-    local where = [ GLOB $(path) : $(filename) ] ;
-    if $(where)
-    {
-        where = [ NORMALIZE_PATH $(where[1]) ] ;
-        if $(.debug-config)
-        {
-            ECHO "notice: Loading" "$(module-name)" "configuration file"
-                "$(filename)" "from" $(where) "." ;
-        }
-
-        # Set source location so that path-constant in config files
-        # with relative paths work. This is of most importance
-        # for project-config.jam, but may be used in other
-        # config files as well.
-        local attributes = [ project.attributes $(module-name) ] ;
-        $(attributes).set source-location : $(where:D) : exact ;
-        modules.load $(module-name) : $(filename) : $(path) ;
-        project.load-used-projects $(module-name) ;
-    }
-    else
-    {
-        if $(must-find)
-        {
-            errors.user-error "Configuration file" "$(filename)" "not found in"
-                "$(path)" "." ;
-        }
-        if $(.debug-config)
-        {
-            ECHO "notice:" "Configuration file" "$(filename)" "not found in"
-                "$(path)" "." ;
-        }
-    }
-    return $(where) ;
-}
-
-
-# Loads all the configuration files used by Boost Build in the following order:
-#
-#   -- test-config --
-#   Loaded only if specified on the command-line using the --test-config
-# command-line parameter. It is ok for this file not to exist even if specified.
-# If this configuration file is loaded, regular site and user configuration
-# files will not be. If a relative path is specified, file is searched for in
-# the current folder.
-#
-#   -- site-config --
-#   Always named site-config.jam. Will only be found if located on the system
-# root path (Windows), /etc (non-Windows), user's home folder or the Boost Build
-# path, in that order. Not loaded in case the test-config configuration file is
-# loaded or either the --ignore-site-config or the --ignore-config command-line
-# option is specified.
-#
-#   -- user-config --
-#   Named user-config.jam by default or may be named explicitly using the
-# --user-config command-line option or the BOOST_BUILD_USER_CONFIG environment
-# variable. If named explicitly the file is looked for from the current working
-# directory and if the default one is used then it is searched for in the
-# user's home directory and the Boost Build path, in that order. Not loaded in
-# case either the test-config configuration file is loaded, --ignore-config
-# command-line option is specified or an empty file name is explicitly
-# specified. If the file name has been given explicitly then the file must
-# exist.
-#
-# Test configurations have been added primarily for use by Boost Build's
-# internal unit testing system but may be used freely in other places as well.
-#
-local rule load-configuration-files
-{
-    # Flag indicating that site configuration should not be loaded.
-    local ignore-site-config =
-        [ MATCH ^(--ignore-site-config)$ : $(.argv) ] ;
-
-    if $(.legacy-ignore-config) && $(.debug-config)
-    {
-        ECHO "notice: Regular site and user configuration files will be ignored" ;
-        ECHO "notice: due to the --ignore-config command-line option." ;
-    }
-
-    initialize-config-module test-config ;
-    local test-config = [ MATCH ^--test-config=(.*)$ : $(.argv) ] ;
-    local uq = [ MATCH \"(.*)\" : $(test-config) ] ;
-    if $(uq)
-    {
-        test-config = $(uq) ;
-    }
-    if $(test-config)
-    {
-        local where =
-            [ load-config test-config : $(test-config:BS) : $(test-config:D) ] ;
-        if $(where)
-        {
-            if $(.debug-config) && ! $(.legacy-ignore-config)
-            {
-                ECHO "notice: Regular site and user configuration files will" ;
-                ECHO "notice: be ignored due to the test configuration being"
-                    "loaded." ;
-            }
-        }
-        else
-        {
-            test-config = ;
-        }
-    }
-
-    local user-path = [ os.home-directories ] [ os.environ BOOST_BUILD_PATH ] ;
-    local site-path = /etc $(user-path) ;
-    if [ os.name ] in NT CYGWIN
-    {
-        site-path = [ modules.peek : SystemRoot ] $(user-path) ;
-    }
-
-    if $(ignore-site-config) && !$(.legacy-ignore-config)
-    {
-        ECHO "notice: Site configuration files will be ignored due to the" ;
-        ECHO "notice: --ignore-site-config command-line option." ;
-    }
-
-    initialize-config-module site-config ;
-    if ! $(test-config) && ! $(ignore-site-config) && ! $(.legacy-ignore-config)
-    {
-        load-config site-config : site-config.jam : $(site-path) ;
-    }
-
-    initialize-config-module user-config ;
-    if ! $(test-config) && ! $(.legacy-ignore-config)
-    {
-        local user-config = [ MATCH ^--user-config=(.*)$ : $(.argv) ] ;
-        user-config = $(user-config[-1]) ;
-        user-config ?= [ os.environ BOOST_BUILD_USER_CONFIG ] ;
-        # Special handling for the case when the OS does not strip the quotes
-        # around the file name, as is the case when using Cygwin bash.
-        user-config = [ utility.unquote $(user-config) ] ;
-        local explicitly-requested = $(user-config) ;
-        user-config ?= user-config.jam ;
-
-        if $(user-config)
-        {
-            if $(explicitly-requested)
-            {
-                # Treat explicitly entered user paths as native OS path
-                # references and, if non-absolute, root them at the current
-                # working directory.
-                user-config = [ path.make $(user-config) ] ;
-                user-config = [ path.root $(user-config) [ path.pwd ] ] ;
-                user-config = [ path.native $(user-config) ] ;
-
-                if $(.debug-config)
-                {
-                    ECHO "notice: Loading explicitly specified user"
-                        "configuration file:" ;
-                    ECHO "    $(user-config)" ;
-                }
-
-                load-config user-config : $(user-config:BS) : $(user-config:D)
-                    : must-exist ;
-            }
-            else
-            {
-                load-config user-config : $(user-config) : $(user-path) ;
-            }
-        }
-        else if $(.debug-config)
-        {
-            ECHO "notice: User configuration file loading explicitly disabled." ;
-        }
-    }
-        
-    # We look for project-config.jam from "." upward.
-    # I am not sure this is 100% right decision, we might as well check for
-    # it only alonside the Jamroot file. However:
-    #
-    # - We need to load project-root.jam before Jamroot
-    # - We probably would need to load project-root.jam even if there's no
-    #   Jamroot - e.g. to implement automake-style out-of-tree builds.
-    local file = [ path.glob "." : project-config.jam ] ;
-    if ! $(file)
-    {
-        file = [ path.glob-in-parents "." : project-config.jam ] ;
-    }
-    if $(file)
-    {
-        initialize-config-module project-config : $(file:D) ;
-        load-config project-config : project-config.jam : $(file:D) ;        
-    }   
-}
-
-
-# Autoconfigure toolsets based on any instances of --toolset=xx,yy,...zz or
-# toolset=xx,yy,...zz in the command line. May return additional properties to
-# be processed as if they had been specified by the user.
-#
-local rule process-explicit-toolset-requests
-{
-    local extra-properties ;
-
-    local option-toolsets  = [ regex.split-list [ MATCH ^--toolset=(.*)$ : $(.argv) ] : "," ] ;
-    local feature-toolsets = [ regex.split-list [ MATCH   ^toolset=(.*)$ : $(.argv) ] : "," ] ;
-
-    for local t in $(option-toolsets) $(feature-toolsets)
-    {
-        # Parse toolset-version/properties.
-        local (t-v,t,v) = [ MATCH (([^-/]+)-?([^/]+)?)/?.* : $(t) ] ;
-        local toolset-version = $((t-v,t,v)[1]) ;
-        local toolset = $((t-v,t,v)[2]) ;
-        local version = $((t-v,t,v)[3]) ;
-
-        if $(.debug-config)
-        {
-            ECHO notice: [cmdline-cfg] Detected command-line request for
-                $(toolset-version): "toolset=" $(toolset) "version="
-                $(version) ;
-        }
-
-        # If the toolset is not known, configure it now.
-        local known ;
-        if $(toolset) in [ feature.values <toolset> ]
-        {
-            known = true ;
-        }
-        if $(known) && $(version) && ! [ feature.is-subvalue toolset
-            : $(toolset) : version : $(version) ]
-        {
-            known = ;
-        }
-        # TODO: we should do 'using $(toolset)' in case no version has been
-        # specified and there are no versions defined for the given toolset to
-        # allow the toolset to configure its default version. For this we need
-        # to know how to detect whether a given toolset has any versions
-        # defined. An alternative would be to do this whenever version is not
-        # specified but that would require that toolsets correctly handle the
-        # case when their default version is configured multiple times which
-        # should be checked for all existing toolsets first.
-
-        if ! $(known)
-        {
-            if $(.debug-config)
-            {
-                ECHO "notice: [cmdline-cfg] toolset $(toolset-version) not"
-                    "previously configured; attempting to auto-configure now" ;
-            }
-            toolset.using $(toolset) : $(version) ;
-        }
-        else
-        {
-            if $(.debug-config)
-            {
-                ECHO notice: [cmdline-cfg] toolset $(toolset-version) already
-                    configured ;
-            }
-        }
-
-        # Make sure we get an appropriate property into the build request in
-        # case toolset has been specified using the "--toolset=..." command-line
-        # option form.
-        if ! $(t) in $(.argv) && ! $(t) in $(feature-toolsets)
-        {
-            if $(.debug-config)
-            {
-                ECHO notice: [cmdline-cfg] adding toolset=$(t) to the build
-                    request. ;
-            }
-            extra-properties += toolset=$(t) ;
-        }
-    }
-
-    return $(extra-properties) ;
-}
-
-
-# Returns 'true' if the given 'project' is equal to or is a (possibly indirect)
-# child to any of the projects requested to be cleaned in this build system run.
-# Returns 'false' otherwise. Expects the .project-targets list to have already
-# been constructed.
-#
-local rule should-clean-project ( project )
-{
-    if ! $(.should-clean-project.$(project))
-    {
-        local r = false ;
-        if $(project) in $(.project-targets)
-        {
-            r = true ;
-        }
-        else
-        {
-            local parent = [ project.attribute $(project) parent-module ] ;
-            if $(parent) && $(parent) != user-config
-            {
-                r = [ should-clean-project $(parent) ] ;
-            }
-        }
-        .should-clean-project.$(project) = $(r) ;
-    }
-
-    return $(.should-clean-project.$(project)) ;
-}
-
-
-################################################################################
-#
-# main()
-# ------
-#
-################################################################################
-
-{    
-    if --version in $(.argv)
-    {
-        version.print ;
-        EXIT ;
-    }
-    
-    version.verify-engine-version ;    
-    
-    load-configuration-files ;
-
-    local extra-properties ;
-    # Note that this causes --toolset options to be ignored if --ignore-config
-    # is specified.
-    if ! $(.legacy-ignore-config)
-    {
-        extra-properties = [ process-explicit-toolset-requests ] ;
-    }
-
-
-    # We always load project in "." so that 'use-project' directives have any
-    # chance of being seen. Otherwise, we would not be able to refer to
-    # subprojects using target ids.
-    local current-project ;
-    if [ project.find "." : "." ]
-    {
-        current-project = [ project.target [ project.load "." ] ] ;
-    }
-
-
-    # In case there are no toolsets currently defined makes the build run using
-    # the default toolset.
-    if ! $(.legacy-ignore-config) && ! [ feature.values <toolset> ]
-    {
-        local default-toolset = $(.default-toolset) ;
-        local default-toolset-version = ;
-        if $(default-toolset)
-        {
-            default-toolset-version = $(.default-toolset-version) ;
-        }
-        else
-        {
-            default-toolset = gcc ;
-            if [ os.name ] = NT
-            {
-                default-toolset = msvc ;
-            }
-            else if [ os.name ] = MACOSX
-            {
-                default-toolset = darwin ;
-            }                        
-        }
-
-        ECHO "warning: No toolsets are configured." ;
-        ECHO "warning: Configuring default toolset" \"$(default-toolset)\". ;
-        ECHO "warning: If the default is wrong, your build may not work correctly." ;
-        ECHO "warning: Use the \"toolset=xxxxx\" option to override our guess." ;
-        ECHO "warning: For more configuration options, please consult" ;
-        ECHO "warning: http://boost.org/boost-build2/doc/html/bbv2/advanced/configuration.html" ;
-
-        toolset.using $(default-toolset) : $(default-toolset-version) ;
-    }
-
-
-    # Parse command line for targets and properties. Note that this requires
-    # that all project files already be loaded.
-    local build-request = [ build-request.from-command-line $(.argv)
-        $(extra-properties) ] ;
-    local target-ids = [ $(build-request).get-at 1 ] ;
-    local properties = [ $(build-request).get-at 2 ] ;
-
-
-    # Expand properties specified on the command line into multiple property
-    # sets consisting of all legal property combinations. Each expanded property
-    # set will be used for a single build run. E.g. if multiple toolsets are
-    # specified then requested targets will be built with each of them.
-    if $(properties)
-    {
-        expanded = [ build-request.expand-no-defaults $(properties) ] ;
-        local xexpanded ;
-        for local e in $(expanded)
-        {
-            xexpanded += [ property-set.create [ feature.split $(e) ] ] ;
-        }
-        expanded = $(xexpanded) ;
-    }
-    else
-    {
-        expanded = [ property-set.empty ] ;
-    }
-
-
-    # Check that we actually found something to build.
-    if ! $(current-project) && ! $(target-ids)
-    {
-        errors.user-error "error: no Jamfile in current directory found, and no"
-            "target references specified." ;
-        EXIT ;
-    }
-
-
-    # Flags indicating that this build system run has been started in order to
-    # clean existing instead of create new targets. Note that these are not the
-    # final flag values as they may get changed later on due to some special
-    # targets being specified on the command line.
-    local clean    ; if "--clean"     in $(.argv) { clean    = true ; }
-    local cleanall ; if "--clean-all" in $(.argv) { cleanall = true ; }
-
-
-    # List of explicitly requested files to build. Any target references read
-    # from the command line parameter not recognized as one of the targets
-    # defined in the loaded Jamfiles will be interpreted as an explicitly
-    # requested file to build. If any such files are explicitly requested then
-    # only those files and the targets they depend on will be built and they
-    # will be searched for among targets that would have been built had there
-    # been no explicitly requested files.
-    local explicitly-requested-files
-
-
-    # List of Boost Build meta-targets, virtual-targets and actual Jam targets
-    # constructed in this build system run.
-    local targets ;
-    local virtual-targets ;
-    local actual-targets ;
-
-
-    # Process each target specified on the command-line and convert it into
-    # internal Boost Build target objects. Detect special clean target. If no
-    # main Boost Build targets were explictly requested use the current project
-    # as the target.
-    for local id in $(target-ids)
-    {
-        if $(id) = clean
-        {
-            clean = true ;
-        }
-        else
-        {
-            local t ;
-            if $(current-project)
-            {
-                t = [ $(current-project).find $(id) : no-error ] ;
-            }
-            else
-            {
-                t = [ find-target $(id) ] ;
-            }
-
-            if ! $(t)
-            {
-                ECHO "notice: could not find main target" $(id) ;
-                ECHO "notice: assuming it is a name of file to create." ;
-                explicitly-requested-files += $(id) ;
-            }
-            else
-            {
-                targets += $(t) ;
-            }
-        }
-    }
-    if ! $(targets)
-    {
-        targets += [ project.target [ project.module-name "." ] ] ;
-    }
-    
-    if [ option.get dump-generators : : true ] 
-    {
-        generators.dump ;
-    }
-    
-    # We wish to put config.log in the build directory corresponding
-    # to Jamroot, so that the location does not differ depending on
-    # directory where we do build.  The amount of indirection necessary
-    # here is scary.
-    local first-project = [ $(targets[0]).project ] ;
-    local first-project-root-location = [ $(first-project).get project-root ] ;
-    local first-project-root-module = [ project.load $(first-project-root-location) ] ;
-    local first-project-root = [ project.target  $(first-project-root-module) ] ;
-    local first-build-build-dir = [ $(first-project-root).build-dir ] ;
-    configure.set-log-file $(first-build-build-dir)/config.log ;
-    
-    # Now that we have a set of targets to build and a set of property sets to
-    # build the targets with, we can start the main build process by using each
-    # property set to generate virtual targets from all of our listed targets
-    # and any of their dependants.
-    for local p in $(expanded)
-    {
-        .command-line-free-features = [ property-set.create [ $(p).free ] ] ;
-        for local t in $(targets)
-        {
-            local g = [ $(t).generate $(p) ] ;
-            if ! [ class.is-a $(t) : project-target ]
-            {
-                .results-of-main-targets += $(g[2-]) ;
-            }
-            virtual-targets += $(g[2-]) ;
-        }
-    }
-
-
-    # Convert collected virtual targets into actual raw Jam targets.
-    for t in $(virtual-targets)
-    {
-        actual-targets += [ $(t).actualize ] ;
-    }
-
-
-    # If XML data output has been requested prepare additional rules and targets
-    # so we can hook into Jam to collect build data while its building and have
-    # it trigger the final XML report generation after all the planned targets
-    # have been built.
-    if $(.out-xml)
-    {
-        # Get a qualified virtual target name.
-        rule full-target-name ( target )
-        {
-            local name = [ $(target).name ] ;
-            local project = [ $(target).project ] ;
-            local project-path = [ $(project).get location ] ;
-            return $(project-path)//$(name) ;
-        }
-
-        # Generate an XML file containing build statistics for each constituent.
-        #
-        rule out-xml ( xml-file : constituents * )
-        {
-            # Prepare valid XML header and footer with some basic info.
-            local nl = "
-" ;
-            local os        = [ modules.peek : OS OSPLAT JAMUNAME ] "" ;
-            local timestamp = [ modules.peek : JAMDATE ] ;
-            local cwd       = [ PWD ] ;
-            local command   = $(.argv) ;
-            local bb-version = [ version.boost-build ] ;
-            .header on $(xml-file) =
-                "<?xml version=\"1.0\" encoding=\"utf-8\"?>"
-                "$(nl)<build format=\"1.0\" version=\"$(bb-version)\">"
-                "$(nl)  <os name=\"$(os[1])\" platform=\"$(os[2])\"><![CDATA[$(os[3-]:J= )]]></os>"
-                "$(nl)  <timestamp><![CDATA[$(timestamp)]]></timestamp>"
-                "$(nl)  <directory><![CDATA[$(cwd)]]></directory>"
-                "$(nl)  <command><![CDATA[\"$(command:J=\" \")\"]]></command>"
-                ;
-            .footer on $(xml-file) =
-                "$(nl)</build>" ;
-
-            # Generate the target dependency graph.
-            .contents on $(xml-file) +=
-                "$(nl)  <targets>" ;
-            for local t in [ virtual-target.all-targets ]
-            {
-                local action = [ $(t).action ] ;
-                if $(action)
-                    # If a target has no action, it has no dependencies.
-                {
-                    local name = [ full-target-name $(t) ] ;
-                    local sources = [ $(action).sources ] ;
-                    local dependencies ;
-                    for local s in $(sources)
-                    {
-                        dependencies += [ full-target-name $(s) ] ;
-                    }
-
-                    local path = [ $(t).path ] ;
-                    local jam-target = [ $(t).actual-name ] ;
-
-                    .contents on $(xml-file) +=
-                        "$(nl)    <target>"
-                        "$(nl)      <name><![CDATA[$(name)]]></name>"
-                        "$(nl)      <dependencies>"
-                        "$(nl)        <dependency><![CDATA[$(dependencies)]]></dependency>"
-                        "$(nl)      </dependencies>"
-                        "$(nl)      <path><![CDATA[$(path)]]></path>"
-                        "$(nl)      <jam-target><![CDATA[$(jam-target)]]></jam-target>"
-                        "$(nl)    </target>"
-                        ;
-                }
-            }
-            .contents on $(xml-file) +=
-                "$(nl)  </targets>" ;
-
-            # Build $(xml-file) after $(constituents). Do so even if a
-            # constituent action fails and regenerate the xml on every bjam run.
-            INCLUDES $(xml-file) : $(constituents) ;
-            ALWAYS $(xml-file) ;
-            __ACTION_RULE__ on $(xml-file) = build-system.out-xml.generate-action ;
-            out-xml.generate $(xml-file) ;
-        }
-
-        # The actual build actions are here; if we did this work in the actions
-        # clause we would have to form a valid command line containing the
-        # result of @(...) below (the name of the XML file).
-        #
-        rule out-xml.generate-action ( args * : xml-file
-            : command status start end user system : output ? )
-        {
-            local contents =
-                [ on $(xml-file) return $(.header) $(.contents) $(.footer) ] ;
-            local f = @($(xml-file):E=$(contents)) ;
-        }
-
-        # Nothing to do here; the *real* actions happen in
-        # out-xml.generate-action.
-        actions quietly out-xml.generate { }
-
-        # Define the out-xml file target, which depends on all the targets so
-        # that it runs the collection after the targets have run.
-        out-xml $(.out-xml) : $(actual-targets) ;
-
-        # Set up a global __ACTION_RULE__ that records all the available
-        # statistics about each actual target in a variable "on" the --out-xml
-        # target.
-        #
-        rule out-xml.collect ( xml-file : target : command status start end user
-            system : output ? )
-        {
-            local nl = "
-" ;
-            # Open the action with some basic info.
-            .contents on $(xml-file) +=
-                "$(nl)  <action status=\"$(status)\" start=\"$(start)\" end=\"$(end)\" user=\"$(user)\" system=\"$(system)\">" ;
-
-            # If we have an action object we can print out more detailed info.
-            local action = [ on $(target) return $(.action) ] ;
-            if $(action)
-            {
-                local action-name    = [ $(action).action-name ] ;
-                local action-sources = [ $(action).sources     ] ;
-                local action-props   = [ $(action).properties  ] ;
-
-                # The qualified name of the action which we created the target.
-                .contents on $(xml-file) +=
-                    "$(nl)    <name><![CDATA[$(action-name)]]></name>" ;
-
-                # The sources that made up the target.
-                .contents on $(xml-file) +=
-                    "$(nl)    <sources>" ;
-                for local source in $(action-sources)
-                {
-                    local source-actual = [ $(source).actual-name ] ;
-                    .contents on $(xml-file) +=
-                        "$(nl)      <source><![CDATA[$(source-actual)]]></source>" ;
-                }
-                .contents on $(xml-file) +=
-                    "$(nl)    </sources>" ;
-
-                # The properties that define the conditions under which the
-                # target was built.
-                .contents on $(xml-file) +=
-                    "$(nl)    <properties>" ;
-                for local prop in [ $(action-props).raw ]
-                {
-                    local prop-name = [ MATCH ^<(.*)>$ : $(prop:G) ] ;
-                    .contents on $(xml-file) +=
-                        "$(nl)      <property name=\"$(prop-name)\"><![CDATA[$(prop:G=)]]></property>" ;
-                }
-                .contents on $(xml-file) +=
-                    "$(nl)    </properties>" ;
-            }
-
-            local locate = [ on $(target) return $(LOCATE) ] ;
-            locate ?= "" ;
-            .contents on $(xml-file) +=
-                "$(nl)    <jam-target><![CDATA[$(target)]]></jam-target>"
-                "$(nl)    <path><![CDATA[$(target:G=:R=$(locate))]]></path>"
-                "$(nl)    <command><![CDATA[$(command)]]></command>"
-                "$(nl)    <output><![CDATA[$(output)]]></output>" ;
-            .contents on $(xml-file) +=
-                "$(nl)  </action>" ;
-        }
-
-        # When no __ACTION_RULE__ is set "on" a target, the search falls back to
-        # the global module.
-        module
-        {
-            __ACTION_RULE__ = build-system.out-xml.collect
-                [ modules.peek build-system : .out-xml ] ;
-        }
-        
-        IMPORT
-            build-system :
-            out-xml.collect
-            out-xml.generate-action
-            : :
-            build-system.out-xml.collect
-            build-system.out-xml.generate-action
-            ;
-    }
-
-    local j = [ option.get jobs ] ;
-    if $(j)
-    {
-        modules.poke : PARALLELISM : $(j) ;
-    }
-    
-    local k = [ option.get keep-going : true : true ] ;
-    if $(k) in "on" "yes" "true"
-    {
-        modules.poke : KEEP_GOING : 1 ;
-    }
-    else if $(k) in "off" "no" "false"
-    {
-        modules.poke : KEEP_GOING : 0 ;
-    }
-    else
-    {
-        ECHO "error: Invalid value for the --keep-going option" ;
-        EXIT ;
-    }
-                
-    # The 'all' pseudo target is not strictly needed expect in the case when we
-    # use it below but people often assume they always have this target
-    # available and do not declare it themselves before use which may cause
-    # build failures with an error message about not being able to build the
-    # 'all' target.
-    NOTFILE all ;
-
-    # And now that all the actual raw Jam targets and all the dependencies
-    # between them have been prepared all that is left is to tell Jam to update
-    # those targets.
-    if $(explicitly-requested-files)
-    {
-        # Note that this case can not be joined with the regular one when only
-        # exact Boost Build targets are requested as here we do not build those
-        # requested targets but only use them to construct the dependency tree
-        # needed to build the explicitly requested files.
-        UPDATE $(explicitly-requested-files:G=e) $(.out-xml) ;
-    }
-    else if $(cleanall)
-    {
-        UPDATE clean-all ;
-    }
-    else if $(clean)
-    {
-        common.Clean clean : [ actual-clean-targets ] ;
-        UPDATE clean ;
-    }
-    else
-    {      
-        configure.print-configure-checks-summary ;        
-        
-        if $(.pre-build-hook)
-        {
-            $(.pre-build-hook) ;
-        }
-        
-        DEPENDS all : $(actual-targets) ;
-        if UPDATE_NOW in [ RULENAMES ]
-        {            
-            local ok = [ UPDATE_NOW all $(.out-xml) ] ;
-            if $(.post-build-hook)
-            {
-                $(.post-build-hook) $(ok) ;
-            }
-            # Prevent automatic update of the 'all' target, now that
-            # we have explicitly updated what we wanted.
-            UPDATE ;
-        }
-        else
-        {
-            UPDATE all $(.out-xml) ;
-        }            
-    }
-}
diff --git a/jam-files/boost-build/build/__init__.py b/jam-files/boost-build/build/__init__.py
deleted file mode 100644
index e69de29b..00000000
--- a/jam-files/boost-build/build/__init__.py
+++ /dev/null
diff --git a/jam-files/boost-build/build/ac.jam b/jam-files/boost-build/build/ac.jam
deleted file mode 100644
index 6768f358..00000000
--- a/jam-files/boost-build/build/ac.jam
+++ /dev/null
@@ -1,198 +0,0 @@
-# Copyright (c) 2010 Vladimir Prus.
-#
-# Use, modification and distribution is subject to the Boost Software
-# License Version 1.0. (See accompanying file LICENSE_1_0.txt or
-# http://www.boost.org/LICENSE_1_0.txt)
-
-import property-set ;
-import path ;
-import modules ;
-import "class" ; 
-import errors ;
-import configure ;
-
-rule find-include-path ( variable : properties : header 
-    : provided-path ? )
-{
-    # FIXME: document which properties affect this function by
-    # default.
-    local target-os = [ $(properties).get <target-os> ] ;
-    properties = [ property-set.create <target-os>$(toolset) ] ;    
-    if $($(variable)-$(properties))
-    {
-        return $($(variable)-$(properties)) ;
-    }
-    else
-    {
-        provided-path ?= [ modules.peek : $(variable) ] ;
-        includes = $(provided-path) ;
-        includes += [ $(properties).get <include> ] ;
-        if [ $(properties).get <target-os> ] != windows
-        {
-            # FIXME: use sysroot
-            includes += /usr/include ;
-        }
-        
-        local result ;
-        while ! $(result) && $(includes)
-        {            
-            local f = [ path.root $(header) $(includes[1]) ] ;
-            ECHO "Checking " $(f) ;
-            if [ path.exists $(f) ]
-            {
-                result = $(includes[1]) ;
-            }
-            else if $(provided-path)
-            {
-                errors.user-error "Could not find header" $(header)
-                  : "in the user-specified directory" $(provided-path) ;
-            }            
-            includes = $(includes[2-]) ;                
-        }        
-        $(variable)-$(properties) = $(result) ;
-        return $(result) ;
-    }        
-}
-
-rule find-library ( variable : properties : names + : provided-path ? )
-{
-    local target-os = [ $(properties).get <target-os> ] ;
-    properties = [ property-set.create <target-os>$(toolset) ] ;
-    if $($(variable)-$(properties))
-    {
-        return $($(variable)-$(properties)) ;
-    }
-    else
-    {
-        provided-path ?= [ modules.peek : $(variable) ] ;
-        paths = $(provided-path) ;
-        paths += [ $(properties).get <library-path> ] ;
-        if [ $(properties).get <target-os> ] != windows
-        {
-            paths += /usr/lib /usr/lib32 /usr/lib64 ;
-        }
-        
-        local result ;               
-        while ! $(result) && $(paths)
-        {   
-            while ! $(result) && $(names)
-            {
-                local f ;
-                if $(target-os) = windows
-                {         
-                    f = $(paths[1])/$(names[1]).lib ;                
-                    if [ path.exists $(f) ] 
-                    {
-                        result = $(f) ;
-                    }
-                }
-                else
-                {
-                    # FIXME: check for .a as well, depending on
-                    # the 'link' feature.
-                    f = $(paths[1])/lib$(names[1]).so ;                
-                    ECHO "CHECKING $(f) " ;
-                    if [ path.exists $(f) ] 
-                    {
-                        result = $(f) ;
-                    }
-                }
-                if ! $(result) && $(provided-path)
-                {
-                    errors.user-error "Could not find either of: " $(names)
-                      : "in the user-specified directory" $(provided-path) ;
-                    
-                }                
-                names = $(names[2-]) ;
-            }
-            paths = $(paths[2-]) ;
-        }        
-        $(variable)-$(properties) = $(result) ;
-        return $(result) ;
-    }
-}
-
-class ac-library : basic-target
-{
-    import errors ;
-    import indirect ;
-    import virtual-target ;
-    import ac ;
-    import configure ;
-
-    rule __init__ ( name : project : * : * )
-    {
-        basic-target.__init__ $(name) : $(project) : $(sources)
-          : $(requirements) ;
-        
-        reconfigure $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ; 
-    }
-    
-    rule set-header ( header )
-    {
-        self.header = $(header) ; 
-    }
-        
-    rule set-default-names ( names + )
-    {
-        self.default-names = $(names) ;
-    }
-        
-    rule reconfigure ( * : * )
-    {
-        ECHO "XXX" $(1) ;
-        if ! $(1)
-        {
-            # This is 'using xxx ;'. Nothing to configure, really.
-        }
-        else
-        {
-            for i in 1 2 3 4 5 6 7 8 9             
-            {
-                # FIXME: this naming is inconsistent with XXX_INCLUDE/XXX_LIBRARY
-                if ! ( $($(i)[1]) in root include-path library-path library-name condition )
-                {
-                    errors.user-error "Invalid named parameter" $($(i)[1]) ;
-                }   
-                local name = $($(i)[1]) ;
-                local value = $($(i)[2-]) ;
-                if $($(name)) && $($(name)) != $(value)
-                {
-                    errors.user-error "Attempt to change value of '$(name)'" ;
-                }
-                $(name) = $(value) ;
-            }
-            
-            include-path ?= $(root)/include ;
-            library-path ?= $(root)/lib ;            
-        }        
-    }
-    
-    rule construct ( name : sources * : property-set )
-    {
-        # FIXME: log results.
-        local libnames = $(library-name) ;
-        if ! $(libnames) && ! $(include-path) && ! $(library-path)
-        {
-            libnames = [ modules.peek : $(name:U)_NAME ] ;
-            # Backward compatibility only.
-            libnames ?= [ modules.peek : $(name:U)_BINARY ] ;
-        }
-        libnames ?= $(self.default-names) ;
-                        
-        local includes = [ 
-          ac.find-include-path $(name:U)_INCLUDE : $(property-set) : $(self.header) : $(include-path) ] ;
-        local library = [ ac.find-library $(name:U)_LIBRARY : $(property-set) : $(libnames) : $(library-path) ] ;
-        if $(includes) && $(library)
-        {
-            library = [ virtual-target.from-file $(library) : . : $(self.project) ] ;
-            configure.log-library-search-result $(name) : "found" ;
-            return [ property-set.create <include>$(includes) <source>$(library) ] ;
-        }
-        else
-        {
-            configure.log-library-search-result $(name) : "no found" ;
-        }        
-    }
-}
-
diff --git a/jam-files/boost-build/build/alias.jam b/jam-files/boost-build/build/alias.jam
deleted file mode 100644
index 48019cb9..00000000
--- a/jam-files/boost-build/build/alias.jam
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 2003, 2004, 2006 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-# This module defines the 'alias' rule and the associated target class.
-#
-# Alias is just a main target which returns its source targets without any
-# processing. For example:
-#
-#   alias bin : hello test_hello ;
-#   alias lib : helpers xml_parser ;
-#
-# Another important use of 'alias' is to conveniently group source files:
-#
-#   alias platform-src : win.cpp : <os>NT ;
-#   alias platform-src : linux.cpp : <os>LINUX ;
-#   exe main : main.cpp platform-src ;
-#
-# Lastly, it is possible to create a local alias for some target, with different
-# properties:
-#
-#   alias big_lib : : @/external_project/big_lib/<link>static ;
-#
-
-import "class" : new ;
-import project ;
-import property-set ;
-import targets ;
-
-
-class alias-target-class : basic-target
-{
-    rule __init__ ( name : project : sources * : requirements *
-        : default-build * : usage-requirements * )
-    {
-        basic-target.__init__ $(name) : $(project) : $(sources) :
-            $(requirements) : $(default-build) : $(usage-requirements) ;
-    }
-
-    rule construct ( name : source-targets * : property-set )
-    {
-        return [ property-set.empty ] $(source-targets) ;
-    }
-
-    rule compute-usage-requirements ( subvariant )
-    {
-        local base = [ basic-target.compute-usage-requirements $(subvariant) ] ;
-        return [ $(base).add [ $(subvariant).sources-usage-requirements ] ] ;
-    }
-}
-
-
-# Declares the 'alias' target. It will process its sources virtual-targets by
-# returning them unaltered as its own constructed virtual-targets.
-#
-rule alias ( name : sources * : requirements * : default-build * :
-    usage-requirements * )
-{
-    local project = [ project.current ] ;
-
-    targets.main-target-alternative
-        [ new alias-target-class $(name) : $(project)
-            : [ targets.main-target-sources $(sources) : $(name) : no-renaming ]
-            : [ targets.main-target-requirements $(requirements) : $(project) ]
-            : [ targets.main-target-default-build $(default-build) : $(project)
-                ]
-            : [ targets.main-target-usage-requirements $(usage-requirements) :
-                $(project) ]
-        ] ;
-}
-
-
-IMPORT $(__name__) : alias : : alias ;
diff --git a/jam-files/boost-build/build/alias.py b/jam-files/boost-build/build/alias.py
deleted file mode 100644
index 575e5360..00000000
--- a/jam-files/boost-build/build/alias.py
+++ /dev/null
@@ -1,63 +0,0 @@
-# Copyright 2003, 2004, 2006 Vladimir Prus 
-# Distributed under the Boost Software License, Version 1.0. 
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt) 
-
-# Status: ported (danielw)
-# Base revision: 56043
-
-#  This module defines the 'alias' rule and associated class.
-#
-#  Alias is just a main target which returns its source targets without any 
-#  processing. For example::
-#
-#    alias bin : hello test_hello ;
-#    alias lib : helpers xml_parser ;
-#
-#  Another important use of 'alias' is to conveniently group source files::
-#
-#    alias platform-src : win.cpp : <os>NT ;
-#    alias platform-src : linux.cpp : <os>LINUX ;
-#    exe main : main.cpp platform-src ;
-# 
-#  Lastly, it's possible to create local alias for some target, with different
-#  properties::
-#
-#    alias big_lib : : @/external_project/big_lib/<link>static ;
-#
-
-import targets
-import property_set
-from b2.manager import get_manager
-
-from b2.util import metatarget
-
-class AliasTarget(targets.BasicTarget):
-
-    def __init__(self, *args):
-        targets.BasicTarget.__init__(self, *args)
-
-    def construct(self, name, source_targets, properties):
-        return [property_set.empty(), source_targets]
-
-    def compute_usage_requirements(self, subvariant):
-        base = targets.BasicTarget.compute_usage_requirements(self, subvariant)
-        # Add source's usage requirement. If we don't do this, "alias" does not
-        # look like 100% alias.
-        return base.add(subvariant.sources_usage_requirements())
-
-@metatarget
-def alias(name, sources=[], requirements=[], default_build=[], usage_requirements=[]):
-
-    project = get_manager().projects().current()
-    targets = get_manager().targets()
-
-    targets.main_target_alternative(AliasTarget(
-        name, project,
-        targets.main_target_sources(sources, name, no_renaming=True),
-        targets.main_target_requirements(requirements or [], project),
-        targets.main_target_default_build(default_build, project),
-        targets.main_target_usage_requirements(usage_requirements or [], project)))
-
-# Declares the 'alias' target. It will build sources, and return them unaltered.
-get_manager().projects().add_rule("alias", alias)
-
diff --git a/jam-files/boost-build/build/build-request.jam b/jam-files/boost-build/build/build-request.jam
deleted file mode 100644
index 8a1f7b0e..00000000
--- a/jam-files/boost-build/build/build-request.jam
+++ /dev/null
@@ -1,322 +0,0 @@
-# Copyright 2002 Dave Abrahams
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-import "class" : new ;
-import sequence ;
-import set ;
-import regex ;
-import feature ;
-import property ;
-import container ;
-import string ;
-
-
-# Transform property-set by applying f to each component property.
-#
-local rule apply-to-property-set ( f property-set )
-{
-    local properties = [ feature.split $(property-set) ] ;
-    return [ string.join [ $(f) $(properties) ] : / ] ;
-}
-
-
-# Expand the given build request by combining all property-sets which do not
-# specify conflicting non-free features. Expects all the project files to
-# already be loaded.
-#
-rule expand-no-defaults ( property-sets * )
-{
-    # First make all features and subfeatures explicit.
-    local expanded-property-sets = [ sequence.transform apply-to-property-set
-        feature.expand-subfeatures : $(property-sets) ] ;
-
-    # Now combine all of the expanded property-sets
-    local product = [ x-product $(expanded-property-sets) : $(feature-space) ] ;
-
-    return $(product) ;
-}
-
-
-# Implementation of x-product, below. Expects all the project files to already
-# be loaded.
-#
-local rule x-product-aux ( property-sets + )
-{
-    local result ;
-    local p = [ feature.split $(property-sets[1]) ] ;
-    local f = [ set.difference $(p:G) : [ feature.free-features ] ] ;
-    local seen ;
-    # No conflict with things used at a higher level?
-    if ! [ set.intersection $(f) : $(x-product-used) ]
-    {
-        local x-product-seen ;
-        {
-            # Do not mix in any conflicting features.
-            local x-product-used = $(x-product-used) $(f) ;
-
-            if $(property-sets[2])
-            {
-                local rest = [ x-product-aux $(property-sets[2-]) : $(feature-space) ] ;
-                result = $(property-sets[1])/$(rest) ;
-            }
-
-            result ?= $(property-sets[1]) ;
-        }
-
-        # If we did not encounter a conflicting feature lower down, do not
-        # recurse again.
-        if ! [ set.intersection $(f) : $(x-product-seen) ]
-        {
-            property-sets = ;
-        }
-
-        seen = $(x-product-seen) ;
-    }
-
-    if $(property-sets[2])
-    {
-        result += [ x-product-aux $(property-sets[2-]) : $(feature-space) ] ;
-    }
-
-    # Note that we have seen these features so that higher levels will recurse
-    # again without them set.
-    x-product-seen += $(f) $(seen) ;
-    return $(result) ;
-}
-
-
-# Return the cross-product of all elements of property-sets, less any that would
-# contain conflicting values for single-valued features. Expects all the project
-# files to already be loaded.
-#
-local rule x-product ( property-sets * )
-{
-    if $(property-sets).non-empty
-    {
-        # Prepare some "scoped globals" that can be used by the implementation
-        # function, x-product-aux.
-        local x-product-seen x-product-used ;
-        return [ x-product-aux $(property-sets) : $(feature-space) ] ;
-    }
-    # Otherwise return empty.
-}
-
-
-# Returns true if either 'v' or the part of 'v' before the first '-' symbol is
-# an implicit value. Expects all the project files to already be loaded.
-#
-local rule looks-like-implicit-value ( v )
-{
-    if [ feature.is-implicit-value $(v) ]
-    {
-        return true ;
-    }
-    else
-    {
-        local split = [ regex.split $(v) - ] ;
-        if [ feature.is-implicit-value $(split[1]) ]
-        {
-            return true ;
-        }
-    }
-}
-
-
-# Takes the command line tokens (such as taken from the ARGV rule) and
-# constructs a build request from them. Returns a vector of two vectors (where
-# "vector" means container.jam's "vector"). First is the set of targets
-# specified in the command line, and second is the set of requested build
-# properties. Expects all the project files to already be loaded.
-#
-rule from-command-line ( command-line * )
-{
-    local targets ;
-    local properties ;
-
-    command-line = $(command-line[2-]) ;
-    local skip-next = ;
-    for local e in $(command-line)
-    {
-        if $(skip-next)
-        {
-            skip-next = ;
-        }
-        else if ! [ MATCH "^(-).*" : $(e) ]
-        {
-            # Build request spec either has "=" in it or completely consists of
-            # implicit feature values.
-            local fs = feature-space ;
-            if [ MATCH "(.*=.*)" : $(e) ]
-                || [ looks-like-implicit-value $(e:D=) : $(feature-space) ]
-            {
-                properties += [ convert-command-line-element $(e) :
-                    $(feature-space) ] ;
-            }
-            else
-            {
-                targets += $(e) ;
-            }
-        }
-        else if [ MATCH "^(-[-ldjfsto])$" : $(e) ]
-        {
-            skip-next = true ;
-        }
-    }
-    return [ new vector
-        [ new vector $(targets) ]
-        [ new vector $(properties) ] ] ;
-}
-
-
-# Converts one element of command line build request specification into internal
-# form. Expects all the project files to already be loaded.
-#
-local rule convert-command-line-element ( e )
-{
-    local result ;
-    local parts = [ regex.split $(e) "/" ] ;
-    while $(parts)
-    {
-        local p = $(parts[1]) ;
-        local m = [ MATCH "([^=]*)=(.*)" : $(p) ] ;
-        local lresult ;
-        local feature ;
-        local values ;
-        if $(m)
-        {
-            feature = $(m[1]) ;
-            values = [ regex.split $(m[2]) "," ] ;
-            lresult = <$(feature)>$(values) ;
-        }
-        else
-        {
-            lresult = [ regex.split $(p) "," ] ;
-        }
-        
-        if $(feature) && free in [ feature.attributes $(feature) ]
-        {
-            # If we have free feature, then the value is everything
-            # until the end of the command line token. Slashes in
-            # the following string are not taked to mean separation
-            # of properties. Commas are also not interpreted specially.
-            values = $(values:J=,) ;
-            values = $(values) $(parts[2-]) ;
-            values = $(values:J=/) ;
-            lresult = <$(feature)>$(values) ;
-            parts = ;
-        }
-        
-        if ! [ MATCH (.*-.*) : $(p) ]
-        {
-            # property.validate cannot handle subfeatures, so we avoid the check
-            # here.
-            for local p in $(lresult)
-            {
-                property.validate $(p) : $(feature-space) ;
-            }
-        }
-
-        if ! $(result)
-        {
-            result = $(lresult) ;
-        }
-        else
-        {
-            result = $(result)/$(lresult) ;
-        }
-        
-        parts = $(parts[2-]) ;
-    }
-
-    return $(result) ;
-}
-
-
-rule __test__ ( )
-{
-    import assert ;
-    import feature ;
-
-    feature.prepare-test build-request-test-temp ;
-
-    import build-request ;
-    import build-request : expand-no-defaults : build-request.expand-no-defaults ;
-    import errors : try catch ;
-    import feature : feature subfeature ;
-
-    feature toolset : gcc msvc borland : implicit ;
-    subfeature toolset gcc : version : 2.95.2 2.95.3 2.95.4
-      3.0 3.0.1 3.0.2 : optional ;
-
-    feature variant : debug release : implicit composite ;
-    feature inlining : on off ;
-    feature "include" : : free ;
-
-    feature stdlib : native stlport : implicit ;
-
-    feature runtime-link : dynamic static : symmetric ;
-
-    # Empty build requests should expand to empty.
-    assert.result
-        : build-request.expand-no-defaults ;
-
-    assert.result
-        <toolset>gcc/<toolset-gcc:version>3.0.1/<stdlib>stlport/<variant>debug
-        <toolset>msvc/<stdlib>stlport/<variant>debug
-        <toolset>msvc/<variant>debug
-        : build-request.expand-no-defaults gcc-3.0.1/stlport msvc/stlport msvc debug ;
-
-    assert.result
-        <toolset>gcc/<toolset-gcc:version>3.0.1/<stdlib>stlport/<variant>debug
-        <toolset>msvc/<variant>debug
-        <variant>debug/<toolset>msvc/<stdlib>stlport
-        : build-request.expand-no-defaults gcc-3.0.1/stlport msvc debug msvc/stlport ;
-
-    assert.result
-        <toolset>gcc/<toolset-gcc:version>3.0.1/<stdlib>stlport/<variant>debug/<inlining>off
-        <toolset>gcc/<toolset-gcc:version>3.0.1/<stdlib>stlport/<variant>release/<inlining>off
-        : build-request.expand-no-defaults gcc-3.0.1/stlport debug release <inlining>off ;
-
-    assert.result
-        <include>a/b/c/<toolset>gcc/<toolset-gcc:version>3.0.1/<stdlib>stlport/<variant>debug/<include>x/y/z
-        <include>a/b/c/<toolset>msvc/<stdlib>stlport/<variant>debug/<include>x/y/z
-        <include>a/b/c/<toolset>msvc/<variant>debug/<include>x/y/z
-        : build-request.expand-no-defaults <include>a/b/c gcc-3.0.1/stlport msvc/stlport msvc debug  <include>x/y/z ;
-
-    local r ;
-
-    r = [ build-request.from-command-line bjam debug runtime-link=dynamic ] ;
-    assert.equal [ $(r).get-at 1 ] : ;
-    assert.equal [ $(r).get-at 2 ] : debug <runtime-link>dynamic ;
-
-    try ;
-    {
-        build-request.from-command-line bjam gcc/debug runtime-link=dynamic/static ;
-    }
-    catch \"static\" is not a value of an implicit feature ;
-
-    r = [ build-request.from-command-line bjam -d2 --debug debug target runtime-link=dynamic ] ;
-    assert.equal [ $(r).get-at 1 ] : target ;
-    assert.equal [ $(r).get-at 2 ] : debug <runtime-link>dynamic ;
-
-    r = [ build-request.from-command-line bjam debug runtime-link=dynamic,static ] ;
-    assert.equal [ $(r).get-at 1 ] : ;
-    assert.equal [ $(r).get-at 2 ] : debug <runtime-link>dynamic <runtime-link>static ;
-
-    r = [ build-request.from-command-line bjam debug gcc/runtime-link=dynamic,static ] ;
-    assert.equal [ $(r).get-at 1 ] : ;
-    assert.equal [ $(r).get-at 2 ] : debug gcc/<runtime-link>dynamic
-        gcc/<runtime-link>static ;
-
-    r = [ build-request.from-command-line bjam msvc gcc,borland/runtime-link=static ] ;
-    assert.equal [ $(r).get-at 1 ] : ;
-    assert.equal [ $(r).get-at 2 ] : msvc gcc/<runtime-link>static
-        borland/<runtime-link>static ;
-
-    r = [ build-request.from-command-line bjam gcc-3.0 ] ;
-    assert.equal [ $(r).get-at 1 ] : ;
-    assert.equal [ $(r).get-at 2 ] : gcc-3.0 ;
-
-    feature.finish-test build-request-test-temp ;
-}
diff --git a/jam-files/boost-build/build/build_request.py b/jam-files/boost-build/build/build_request.py
deleted file mode 100644
index cc9f2400..00000000
--- a/jam-files/boost-build/build/build_request.py
+++ /dev/null
@@ -1,216 +0,0 @@
-# Status: being ported by Vladimir Prus
-# TODO: need to re-compare with mainline of .jam
-# Base revision: 40480
-#
-#  (C) Copyright David Abrahams 2002. Permission to copy, use, modify, sell and
-#  distribute this software is granted provided this copyright notice appears in
-#  all copies. This software is provided "as is" without express or implied
-#  warranty, and with no claim as to its suitability for any purpose.
-
-import b2.build.feature
-feature = b2.build.feature
-
-from b2.util.utility import *
-import b2.build.property_set as property_set
-
-def expand_no_defaults (property_sets):
-    """ Expand the given build request by combining all property_sets which don't
-        specify conflicting non-free features.
-    """
-    # First make all features and subfeatures explicit
-    expanded_property_sets = [ps.expand_subfeatures() for ps in property_sets]
-    
-    # Now combine all of the expanded property_sets
-    product = __x_product (expanded_property_sets)
-    
-    return [property_set.create(p) for p in product]
-
-
-def __x_product (property_sets):
-    """ Return the cross-product of all elements of property_sets, less any
-        that would contain conflicting values for single-valued features.
-    """
-    x_product_seen = set()
-    return __x_product_aux (property_sets, x_product_seen)[0]
-
-def __x_product_aux (property_sets, seen_features):
-    """Returns non-conflicting combinations of property sets.
-
-    property_sets is a list of PropertySet instances. seen_features is a set of Property
-    instances.
-
-    Returns a tuple of:
-    - list of lists of Property instances, such that within each list, no two Property instance
-    have the same feature, and no Property is for feature in seen_features.
-    - set of features we saw in property_sets      
-    """
-    if not property_sets:
-        return ([], set())
-
-    properties = property_sets[0].all()
-
-    these_features = set()
-    for p in property_sets[0].non_free():
-        these_features.add(p.feature())
-
-    # Note: the algorithm as implemented here, as in original Jam code, appears to
-    # detect conflicts based on features, not properties. For example, if command
-    # line build request say:
-    #
-    # <a>1/<b>1 c<1>/<b>1
-    #
-    # It will decide that those two property sets conflict, because they both specify
-    # a value for 'b' and will not try building "<a>1 <c1> <b1>", but rather two
-    # different property sets. This is a topic for future fixing, maybe.
-    if these_features & seen_features:
-
-        (inner_result, inner_seen) = __x_product_aux(property_sets[1:], seen_features)
-        return (inner_result, inner_seen | these_features)
-
-    else:
-
-        result = []
-        (inner_result, inner_seen) = __x_product_aux(property_sets[1:], seen_features | these_features)
-        if inner_result:
-            for inner in inner_result:
-                result.append(properties + inner)
-        else:
-            result.append(properties)
-        
-        if inner_seen & these_features:
-            # Some of elements in property_sets[1:] conflict with elements of property_sets[0],
-            # Try again, this time omitting elements of property_sets[0]
-            (inner_result2, inner_seen2) = __x_product_aux(property_sets[1:], seen_features)
-            result.extend(inner_result2)
-
-        return (result, inner_seen | these_features)
-
-    
-
-def looks_like_implicit_value(v):
-    """Returns true if 'v' is either implicit value, or
-    the part before the first '-' symbol is implicit value."""
-    if feature.is_implicit_value(v):
-        return 1
-    else:
-        split = v.split("-")
-        if feature.is_implicit_value(split[0]):
-            return 1
-
-    return 0
-
-def from_command_line(command_line):
-    """Takes the command line tokens (such as taken from ARGV rule)
-    and constructs build request from it. Returns a list of two
-    lists. First is the set of targets specified in the command line,
-    and second is the set of requested build properties."""
-
-    targets = []
-    properties = []
-
-    for e in command_line:
-        if e[0] != "-":
-            # Build request spec either has "=" in it, or completely
-            # consists of implicit feature values.
-            if e.find("=") != -1 or looks_like_implicit_value(e.split("/")[0]):                
-                properties += convert_command_line_element(e)
-            else:
-                targets.append(e)
-
-    return [targets, properties]
- 
-# Converts one element of command line build request specification into
-# internal form.
-def convert_command_line_element(e):
-
-    result = None
-    parts = e.split("/")
-    for p in parts:
-        m = p.split("=")
-        if len(m) > 1:
-            feature = m[0]
-            values = m[1].split(",")
-            lresult = [("<%s>%s" % (feature, v)) for v in values]
-        else:
-            lresult = p.split(",")
-            
-        if p.find('-') == -1:
-            # FIXME: first port property.validate
-            # property.validate cannot handle subfeatures,
-            # so we avoid the check here.
-            #for p in lresult:
-            #    property.validate(p)
-            pass
-
-        if not result:
-            result = lresult
-        else:
-            result = [e1 + "/" + e2 for e1 in result for e2 in lresult]
-
-    return [property_set.create(b2.build.feature.split(r)) for r in result]
-
-### 
-### rule __test__ ( )
-### {
-###     import assert feature ;
-###     
-###     feature.prepare-test build-request-test-temp ;
-###     
-###     import build-request ;
-###     import build-request : expand_no_defaults : build-request.expand_no_defaults ;
-###     import errors : try catch ;
-###     import feature : feature subfeature ;
-### 
-###     feature toolset : gcc msvc borland : implicit ;
-###     subfeature toolset gcc : version : 2.95.2 2.95.3 2.95.4
-###       3.0 3.0.1 3.0.2 : optional ;
-### 
-###     feature variant : debug release : implicit composite ;
-###     feature inlining : on off ;
-###     feature "include" : : free ;
-### 
-###     feature stdlib : native stlport : implicit ;
-### 
-###     feature runtime-link : dynamic static : symmetric ;
-### 
-### 
-###     local r ;
-### 
-###     r = [ build-request.from-command-line bjam debug runtime-link=dynamic ] ;              
-###     assert.equal [ $(r).get-at 1 ] : ;
-###     assert.equal [ $(r).get-at 2 ] : debug <runtime-link>dynamic ;
-### 
-###     try ;
-###     {
-### 
-###         build-request.from-command-line bjam gcc/debug runtime-link=dynamic/static ;
-###     }
-###     catch \"static\" is not a value of an implicit feature ;
-### 
-### 
-###     r = [ build-request.from-command-line bjam -d2 --debug debug target runtime-link=dynamic ] ;
-###     assert.equal [ $(r).get-at 1 ] : target ;
-###     assert.equal [ $(r).get-at 2 ] : debug <runtime-link>dynamic ;
-### 
-###     r = [ build-request.from-command-line bjam debug runtime-link=dynamic,static ] ;
-###     assert.equal [ $(r).get-at 1 ] : ;
-###     assert.equal [ $(r).get-at 2 ] : debug <runtime-link>dynamic <runtime-link>static ;
-### 
-###     r = [ build-request.from-command-line bjam debug gcc/runtime-link=dynamic,static ] ;
-###     assert.equal [ $(r).get-at 1 ] : ;
-###     assert.equal [ $(r).get-at 2 ] : debug gcc/<runtime-link>dynamic 
-###                  gcc/<runtime-link>static ;
-### 
-###     r = [ build-request.from-command-line bjam msvc gcc,borland/runtime-link=static ] ;
-###     assert.equal [ $(r).get-at 1 ] : ;
-###     assert.equal [ $(r).get-at 2 ] : msvc gcc/<runtime-link>static 
-###                     borland/<runtime-link>static ;
-### 
-###     r = [ build-request.from-command-line bjam gcc-3.0 ] ;
-###     assert.equal [ $(r).get-at 1 ] : ;
-###     assert.equal [ $(r).get-at 2 ] : gcc-3.0 ;
-### 
-###     feature.finish-test build-request-test-temp ;
-### }
-### 
-### 
diff --git a/jam-files/boost-build/build/configure.jam b/jam-files/boost-build/build/configure.jam
deleted file mode 100644
index 14c1328a..00000000
--- a/jam-files/boost-build/build/configure.jam
+++ /dev/null
@@ -1,237 +0,0 @@
-# Copyright (c) 2010 Vladimir Prus.
-#
-# Use, modification and distribution is subject to the Boost Software
-# License Version 1.0. (See accompanying file LICENSE_1_0.txt or
-# http://www.boost.org/LICENSE_1_0.txt)
-
-# This module defines function to help with two main tasks:
-#
-# - Discovering build-time configuration for the purposes of adjusting
-#   build process.  
-# - Reporting what is built, and how it is configured.
-
-import targets ; 
-import errors ;
-import targets ;
-import sequence ;
-import property ;
-import property-set ;
-import "class" : new ;
-import common ;
-import path ;
-
-rule log-summary ( )
-{
-    
-}
-
-.width = 30 ;
-
-rule set-width ( width )
-{
-    .width = $(width) ;
-}
-
-# Declare that the components specified by the parameter exist.
-rule register-components ( components * )
-{
-    .components += $(components) ;
-}
-
-# Declare that the components specified by the parameters will
-# be build.
-rule components-building ( components * )
-{
-    .built-components += $(components) ;
-}
-
-# Report something about component configuration that the
-# user should better know.
-rule log-component-configuration ( component : message )
-{
-    # FIXME: implement per-property-set logs
-    .component-logs.$(component) += $(message) ;
-}
-
-
-
-rule log-check-result ( result )
-{
-    if ! $(.announced-checks)
-    {
-        ECHO "Performing configuration checks\n" ;
-        .announced-checks = 1 ;
-    }
-    
-    ECHO $(result) ;    
-    #.check-results += $(result) ;
-}
-
-rule log-library-search-result ( library : result )
-{
-    local x = [ PAD "    - $(library) : $(result)" : $(.width) ] ;
-    log-check-result "$(x)" ;
-}
-
-rule print-component-configuration ( )
-{
-    local c = [ sequence.unique $(.components) ] ;
-    
-    ECHO "\nComponent configuration:\n" ;
-    for c in $(.components)
-    {
-        local s ;
-        if $(c) in $(.built-components)
-        {
-            s = "building" ;
-        }
-        else
-        {
-            s = "not building" ;
-        }
-        ECHO [ PAD "    - $(c)" : $(.width) ] ": $(s)" ;
-        for local m in $(.component-logs.$(c))
-        {
-            ECHO "        -" $(m) ;
-        }        
-    }
-    ECHO ;
-}
-
-rule print-configure-checks-summary ( )
-{
-    # FIXME: the problem with that approach is tha
-    # the user sees checks summary when all checks are
-    # done, and has no progress reporting while the
-    # checks are being executed.    
-    if $(.check-results)
-    {        
-        ECHO "Configuration checks summary\n" ;
-    
-        for local r in $(.check-results)
-        {
-            ECHO $(r) ;
-        }
-        ECHO ;
-    }    
-}
-
-# Attempt to build a metatarget named by 'metatarget-reference'
-# in context of 'project' with properties 'ps'.
-# Returns non-empty value if build is OK.
-rule builds-raw ( metatarget-reference : project : ps : what : retry ? )
-{   
-    local result ;
-           
-    if ! $(retry) && ! $(.$(what)-tested.$(ps))
-    {        
-        .$(what)-tested.$(ps) = true ;
-        
-        local targets = [ targets.generate-from-reference 
-            $(metatarget-reference) : $(project) : $(ps) ] ;
-        
-        local jam-targets ;
-        for local t in $(targets[2-])
-        {
-            jam-targets += [ $(t).actualize ] ;
-        }
-                    
-        if ! UPDATE_NOW in [ RULENAMES ]
-        {
-            # Cannot determine. Assume existance.
-        }
-        else 
-        {           
-            local x = [ PAD "    - $(what)" : $(.width) ] ;            
-            if [ UPDATE_NOW $(jam-targets) :
-                 $(.log-fd) : ignore-minus-n : ignore-minus-q ] 
-            {
-                .$(what)-supported.$(ps) = yes ;
-                result = true ;
-                log-check-result "$(x) : yes" ;
-            }        
-            else
-            {
-                log-check-result "$(x) : no" ;
-            }
-        }        
-        return $(result) ;
-    }    
-    else
-    {
-        return $(.$(what)-supported.$(ps)) ;
-    }
-}
-
-rule builds ( metatarget-reference : properties * : what ? : retry ? )
-{
-    what ?= "$(metatarget-reference) builds" ;
-    
-    # FIXME: this should not be hardcoded. Other checks might
-    # want to consider different set of features as relevant.
-    local toolset = [ property.select <toolset> : $(properties) ] ;
-    local toolset-version-property = "<toolset-$(toolset:G=):version>" ;
-    local relevant = [ property.select <target-os> <toolset> $(toolset-version-property)
-      <address-model> <architecture>
-      : $(properties) ] ;
-    local ps = [ property-set.create $(relevant) ] ;        
-    local t = [ targets.current ] ;
-    local p = [ $(t).project ] ;
-
-    return [ builds-raw $(metatarget-reference) : $(p) : $(ps) : $(what) : $(retry) ] ;
-}
-
-
-# Called by Boost.Build startup code to specify name of a file
-# that will receive results of configure checks.  This
-# should never be called by users.
-rule set-log-file ( log-file )
-{
-    path.makedirs [ path.parent $(log-file) ] ;
-    
-    .log-fd = [ FILE_OPEN $(log-file) : "w" ] ;
-}
-
-# Frontend rules
-
-class check-target-builds-worker
-{
-    import configure ;
-    import property-set ;
-    import targets ;
-    import property ; 
-    
-    rule __init__ ( target message ? : true-properties * : false-properties * )    
-    {
-        self.target = $(target) ;
-        self.message = $(message) ;     
-        self.true-properties = $(true-properties) ;
-        self.false-properties = $(false-properties) ;
-    }
-        
-    rule check ( properties * )
-    {
-        local choosen ;
-        if [ configure.builds $(self.target) : $(properties) : $(self.message) ]
-        {
-            choosen = $(self.true-properties) ;
-        }        
-        else
-        {
-            choosen = $(self.false-properties) ;
-        }        
-        return [ property.evaluate-conditionals-in-context $(choosen) : $(properties) ] ;
-    }    
-}
-
-
-rule check-target-builds ( target message ? : true-properties * : false-properties * )
-{
-    local instance = [ new check-target-builds-worker $(target) $(message) : $(true-properties)
-      : $(false-properties) ] ;
-    return <conditional>@$(instance).check ;
-}
-
-IMPORT $(__name__) : check-target-builds :  : check-target-builds ;
-
-
diff --git a/jam-files/boost-build/build/configure.py b/jam-files/boost-build/build/configure.py
deleted file mode 100644
index 0426832c..00000000
--- a/jam-files/boost-build/build/configure.py
+++ /dev/null
@@ -1,164 +0,0 @@
-# Status: ported.
-# Base revison: 64488
-#
-# Copyright (c) 2010 Vladimir Prus.
-#
-# Use, modification and distribution is subject to the Boost Software
-# License Version 1.0. (See accompanying file LICENSE_1_0.txt or
-# http://www.boost.org/LICENSE_1_0.txt)
-
-# This module defines function to help with two main tasks:
-#
-# - Discovering build-time configuration for the purposes of adjusting
-#   build process.  
-# - Reporting what is built, and how it is configured.
-
-import b2.build.property as property
-import b2.build.property_set as property_set
-
-import b2.build.targets
-
-from b2.manager import get_manager
-from b2.util.sequence import unique
-from b2.util import bjam_signature, value_to_jam
-
-import bjam
-import os
-
-__width = 30
-
-def set_width(width):
-    global __width
-    __width = 30
-
-__components = []
-__built_components = []
-__component_logs = {}
-__announced_checks = False
-
-__log_file = None
-__log_fd = -1
-
-def register_components(components):
-    """Declare that the components specified by the parameter exist."""
-    __components.extend(components)
-    
-def components_building(components):
-    """Declare that the components specified by the parameters will be build."""
-    __built_components.extend(components)
-
-def log_component_configuration(component, message):
-    """Report something about component configuration that the user should better know."""
-    __component_logs.setdefault(component, []).append(message)
-
-def log_check_result(result):
-    global __announced_checks
-    if not __announced_checks:
-        print "Performing configuration checks"
-        __announced_checks = True
-
-    print result
-
-def log_library_search_result(library, result):
-    log_check_result(("    - %(library)s : %(result)s" % locals()).rjust(width))
-
-
-def print_component_configuration():
-
-    print "\nComponent configuration:"
-    for c in __components:
-        if c in __built_components:
-            s = "building"
-        else:
-            s = "not building"
-        message = "    - %s)" % c
-        message = message.rjust(__width)
-        message += " : " + s
-        for m in __component_logs.get(c, []):
-            print "        -" + m
-    print ""
-
-__builds_cache = {}
-
-def builds(metatarget_reference, project, ps, what):
-    # Attempt to build a metatarget named by 'metatarget-reference'
-    # in context of 'project' with properties 'ps'.
-    # Returns non-empty value if build is OK.
-
-    result = []
-
-    existing = __builds_cache.get((what, ps), None)
-    if existing is None:
-
-        result = False
-        __builds_cache[(what, ps)] = False
-
-        targets = b2.build.targets.generate_from_reference(
-            metatarget_reference, project, ps).targets()
-        jam_targets = []
-        for t in targets:
-            jam_targets.append(t.actualize())
-        
-        x = ("    - %s" % what).rjust(__width)
-        if bjam.call("UPDATE_NOW", jam_targets, str(__log_fd), "ignore-minus-n"):
-            __builds_cache[(what, ps)] = True
-            result = True
-            log_check_result("%s: yes" % x)
-        else:
-            log_check_result("%s: no" % x)
-
-        return result
-    else:
-        return existing
-
-def set_log_file(log_file_name):
-    # Called by Boost.Build startup code to specify name of a file
-    # that will receive results of configure checks.  This
-    # should never be called by users.
-    global __log_file, __log_fd
-    dirname = os.path.dirname(log_file_name)
-    if not os.path.exists(dirname):
-        os.makedirs(dirname)
-    # Make sure to keep the file around, so that it's not
-    # garbage-collected and closed
-    __log_file = open(log_file_name, "w")
-    __log_fd = __log_file.fileno()
-
-# Frontend rules
-
-class CheckTargetBuildsWorker:
-
-    def __init__(self, target, true_properties, false_properties):
-        self.target = target
-        self.true_properties = property.create_from_strings(true_properties, True)
-        self.false_properties = property.create_from_strings(false_properties, True)
-
-    def check(self, ps):
-        
-        # FIXME: this should not be hardcoded. Other checks might
-        # want to consider different set of features as relevant.
-        toolset = ps.get('toolset')[0]
-        toolset_version_property = "<toolset-" + toolset + ":version>" ;
-        relevant = ps.get_properties('target-os') + \
-                   ps.get_properties("toolset") + \
-                   ps.get_properties(toolset_version_property) + \
-                   ps.get_properties("address-model") + \
-                   ps.get_properties("architecture")
-        rps = property_set.create(relevant)
-        t = get_manager().targets().current()
-        p = t.project()        
-        if builds(self.target, p, rps, "%s builds" % self.target):
-            choosen = self.true_properties
-        else:
-            choosen = self.false_properties
-        return property.evaluate_conditionals_in_context(choosen, ps)
-
-@bjam_signature((["target"], ["true_properties", "*"], ["false_properties", "*"]))
-def check_target_builds(target, true_properties, false_properties):
-    worker = CheckTargetBuildsWorker(target, true_properties, false_properties)
-    value = value_to_jam(worker.check)
-    return "<conditional>" + value
-
-get_manager().projects().add_rule("check-target-builds", check_target_builds)
-
-
diff --git a/jam-files/boost-build/build/engine.py b/jam-files/boost-build/build/engine.py
deleted file mode 100644
index be9736e0..00000000
--- a/jam-files/boost-build/build/engine.py
+++ /dev/null
@@ -1,172 +0,0 @@
-# Copyright Pedro Ferreira 2005.
-# Copyright Vladimir Prus 2007.
-# Distributed under the Boost
-# Software License, Version 1.0. (See accompanying
-# file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
-
-bjam_interface = __import__('bjam')
-
-import operator
-import re
-
-import b2.build.property_set as property_set
-import b2.util
-
-class BjamAction:
-    """Class representing bjam action defined from Python."""
-    
-    def __init__(self, action_name, function):
-        self.action_name = action_name
-        self.function = function
-            
-    def __call__(self, targets, sources, property_set):
-        if self.function:
-            self.function(targets, sources, property_set)
-
-        # Bjam actions defined from Python have only the command
-        # to execute, and no associated jam procedural code. So
-        # passing 'property_set' to it is not necessary.
-        bjam_interface.call("set-update-action", self.action_name,
-                            targets, sources, [])
-
-class BjamNativeAction:
-    """Class representing bjam action defined by Jam code.
-
-    We still allow to associate a Python callable that will
-    be called when this action is installed on any target.
-    """
-    
-    def __init__(self, action_name, function):
-        self.action_name = action_name
-        self.function = function
-        
-    def __call__(self, targets, sources, property_set):
-        if self.function:
-            self.function(targets, sources, property_set)
-        
-        p = []
-        if property_set:
-            p = property_set.raw()
-
-        b2.util.set_jam_action(self.action_name, targets, sources, p)
-        
-action_modifiers = {"updated": 0x01,
-                    "together": 0x02,
-                    "ignore": 0x04,
-                    "quietly": 0x08,
-                    "piecemeal": 0x10,
-                    "existing": 0x20}
-
-class Engine:
-    """ The abstract interface to a build engine.
-
-    For now, the naming of targets, and special handling of some
-    target variables like SEARCH and LOCATE make this class coupled
-    to bjam engine.
-    """
-    def __init__ (self):
-        self.actions = {}
-
-    def add_dependency (self, targets, sources):
-        """Adds a dependency from 'targets' to 'sources'
-
-        Both 'targets' and 'sources' can be either list
-        of target names, or a single target name.
-        """
-        if isinstance (targets, str):
-            targets = [targets]
-        if isinstance (sources, str):
-            sources = [sources]
-
-        for target in targets:
-            for source in sources:
-                self.do_add_dependency (target, source)
-    
-    def set_target_variable (self, targets, variable, value, append=0):
-        """ Sets a target variable.
-
-        The 'variable' will be available to bjam when it decides
-        where to generate targets, and will also be available to
-        updating rule for that 'taret'.
-        """
-        if isinstance (targets, str): 
-            targets = [targets]
-
-        for target in targets:
-            self.do_set_target_variable (target, variable, value, append)
-
-    def set_update_action (self, action_name, targets, sources, properties=property_set.empty()):
-        """ Binds a target to the corresponding update action.
-            If target needs to be updated, the action registered
-            with action_name will be used.
-            The 'action_name' must be previously registered by
-            either 'register_action' or 'register_bjam_action'
-            method.
-        """
-        assert(isinstance(properties, property_set.PropertySet))
-        if isinstance (targets, str): 
-            targets = [targets]
-        self.do_set_update_action (action_name, targets, sources, properties)
-
-    def register_action (self, action_name, command, bound_list = [], flags = [],
-                         function = None):
-        """Creates a new build engine action.
-
-        Creates on bjam side an action named 'action_name', with
-        'command' as the command to be executed, 'bound_variables'
-        naming the list of variables bound when the command is executed
-        and specified flag.
-        If 'function' is not None, it should be a callable taking three
-        parameters:
-            - targets
-            - sources
-            - instance of the property_set class
-        This function will be called by set_update_action, and can
-        set additional target variables.
-        """
-        if self.actions.has_key(action_name):
-            raise "Bjam action %s is already defined" % action_name
-
-        assert(isinstance(flags, list))
-
-        bjam_flags = reduce(operator.or_,
-                            (action_modifiers[flag] for flag in flags), 0)
-
-        bjam_interface.define_action(action_name, command, bound_list, bjam_flags)
-
-        self.actions[action_name] = BjamAction(action_name, function)
-
-    def register_bjam_action (self, action_name, function=None):
-        """Informs self that 'action_name' is declared in bjam.
-
-        From this point, 'action_name' is a valid argument to the
-        set_update_action method. The action_name should be callable
-        in the global module of bjam.
-        """
-
-        # We allow duplicate calls to this rule for the same
-        # action name.  This way, jamfile rules that take action names
-        # can just register them without specially checking if
-        # action is already registered.
-        if not self.actions.has_key(action_name):
-            self.actions[action_name] = BjamNativeAction(action_name, function)
-    
-    # Overridables
-
-
-    def do_set_update_action (self, action_name, targets, sources, property_set):
-        action = self.actions.get(action_name)
-        if not action:
-            raise Exception("No action %s was registered" % action_name)
-        action(targets, sources, property_set)
-
-    def do_set_target_variable (self, target, variable, value, append):
-        if append:
-            bjam_interface.call("set-target-variable", target, variable, value, "true")
-        else:
-            bjam_interface.call("set-target-variable", target, variable, value)
-        
-    def do_add_dependency (self, target, source):
-        bjam_interface.call("DEPENDS", target, source)
-         
-        
diff --git a/jam-files/boost-build/build/errors.py b/jam-files/boost-build/build/errors.py
deleted file mode 100644
index d9dceefe..00000000
--- a/jam-files/boost-build/build/errors.py
+++ /dev/null
@@ -1,127 +0,0 @@
-# Status: being written afresh by Vladimir Prus
-
-# Copyright 2007 Vladimir Prus 
-# Distributed under the Boost Software License, Version 1.0. 
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt) 
-
-# This file is supposed to implement error reporting for Boost.Build.
-# Experience with jam version has shown that printing full backtrace
-# on each error is buffling. Further, for errors printed after parsing --
-# during target building, the stacktrace does not even mention what
-# target is being built.
-
-# This module implements explicit contexts -- where other code can
-# communicate which projects/targets are being built, and error
-# messages will show those contexts. For programming errors,
-# Python assertions are to be used.
-
-import bjam
-import traceback
-import sys
-
-def format(message, prefix=""):
-    parts = str(message).split("\n")
-    return "\n".join(prefix+p for p in parts)
-    
-
-class Context:
-
-    def __init__(self, message, nested=None):
-        self.message_ = message
-        self.nested_ = nested
-
-    def report(self, indent=""):
-        print indent + "    -", self.message_
-        if self.nested_:
-            print indent + "        declared at:"
-            for n in self.nested_:
-                n.report(indent + "    ")
-
-class JamfileContext:
-
-    def __init__(self):
-        raw = bjam.backtrace()
-        self.raw_ = raw
-
-    def report(self, indent=""):
-        for r in self.raw_:
-            print indent + "    - %s:%s" % (r[0], r[1])
-
-class ExceptionWithUserContext(Exception):
-
-    def __init__(self, message, context,
-                 original_exception=None, original_tb=None, stack=None):
-        Exception.__init__(self, message)
-        self.context_ = context
-        self.original_exception_ = original_exception
-        self.original_tb_ = original_tb
-        self.stack_ = stack
-
-    def report(self):
-        print "error:", self.args[0]
-        if self.original_exception_:
-            print format(str(self.original_exception_), "    ")
-        print
-        print "    error context (most recent first):"
-        for c in self.context_[::-1]:
-            c.report()
-        print
-        if "--stacktrace" in bjam.variable("ARGV"):
-            if self.original_tb_:
-                traceback.print_tb(self.original_tb_)
-            elif self.stack_:
-                for l in traceback.format_list(self.stack_):
-                    print l,                
-        else:
-            print "    use the '--stacktrace' option to get Python stacktrace"
-        print
-
-def user_error_checkpoint(callable):
-    def wrapper(self, *args):
-        errors = self.manager().errors()
-        try:
-            return callable(self, *args)
-        except ExceptionWithUserContext, e:
-            raise
-        except Exception, e:
-            errors.handle_stray_exception(e)
-        finally:
-            errors.pop_user_context()
-            
-    return wrapper
-                            
-class Errors:
-
-    def __init__(self):
-        self.contexts_ = []
-        self._count = 0
-
-    def count(self):
-        return self._count
-
-    def push_user_context(self, message, nested=None):
-        self.contexts_.append(Context(message, nested))
-
-    def pop_user_context(self):
-        del self.contexts_[-1]
-
-    def push_jamfile_context(self):
-        self.contexts_.append(JamfileContext())
-
-    def pop_jamfile_context(self):
-        del self.contexts_[-1]
-
-    def capture_user_context(self):
-        return self.contexts_[:]
-
-    def handle_stray_exception(self, e):
-        raise ExceptionWithUserContext("unexpected exception", self.contexts_[:],
-                                       e, sys.exc_info()[2])    
-    def __call__(self, message):
-        self._count = self._count + 1
-        raise ExceptionWithUserContext(message, self.contexts_[:], 
-                                       stack=traceback.extract_stack())
-
-        
-
-    
diff --git a/jam-files/boost-build/build/feature.jam b/jam-files/boost-build/build/feature.jam
deleted file mode 100644
index 6f54adef..00000000
--- a/jam-files/boost-build/build/feature.jam
+++ /dev/null
@@ -1,1335 +0,0 @@
-# Copyright 2001, 2002, 2003 Dave Abrahams
-# Copyright 2002, 2006 Rene Rivera
-# Copyright 2002, 2003, 2004, 2005, 2006 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-import assert : * ;
-import "class" : * ;
-import errors : lol->list ;
-import indirect ;
-import modules ;
-import regex ;
-import sequence ;
-import set ;
-import utility ;
-
-
-local rule setup ( )
-{
-    .all-attributes =
-        implicit
-        composite
-        optional
-        symmetric
-        free
-        incidental
-        path
-        dependency
-        propagated
-        link-incompatible
-        subfeature
-        order-sensitive
-    ;
-
-    .all-features = ;
-    .all-subfeatures = ;
-    .all-top-features = ;  # non-subfeatures
-    .all-implicit-values = ;
-}
-setup ;
-
-
-# Prepare a fresh space to test in by moving all global variable settings into
-# the given temporary module and erasing them here.
-#
-rule prepare-test ( temp-module )
-{
-    DELETE_MODULE $(temp-module) ;
-
-    # Transfer globals to temp-module.
-    for local v in [ VARNAMES feature ]
-    {
-        if [ MATCH (\\.) : $(v) ]
-        {
-            modules.poke $(temp-module) : $(v) : $($(v)) ;
-            $(v) = ;
-        }
-    }
-    setup ;
-}
-
-
-# Clear out all global variables and recover all variables from the given
-# temporary module.
-#
-rule finish-test ( temp-module )
-{
-    # Clear globals.
-    for local v in [ VARNAMES feature ]
-    {
-        if [ MATCH (\\.) : $(v) ]
-        {
-            $(v) = ;
-        }
-    }
-
-    for local v in [ VARNAMES $(temp-module) ]
-    {
-        $(v) = [ modules.peek $(temp-module) : $(v) ] ;
-    }
-    DELETE_MODULE $(temp-module) ;
-}
-
-
-# Transform features by bracketing any elements which are not already bracketed
-# by "<>".
-#
-local rule grist ( features * )
-{
-    local empty = "" ;
-    return $(empty:G=$(features)) ;
-}
-
-
-# Declare a new feature with the given name, values, and attributes.
-#
-rule feature (
-      name          # Feature name.
-    : values *      # Allowable values - may be extended later using feature.extend.
-    : attributes *  # Feature attributes (e.g. implicit, free, propagated...).
-)
-{
-    name = [ grist $(name) ] ;
-
-    local error ;
-
-    # Check for any unknown attributes.
-    if ! ( $(attributes) in $(.all-attributes) )
-    {
-        error = unknown attributes:
-            [ set.difference $(attributes) : $(.all-attributes) ] ;
-    }
-    else if $(name) in $(.all-features)
-    {
-        error = feature already defined: ;
-    }
-    else if implicit in $(attributes) && free in $(attributes)
-    {
-        error = free features cannot also be implicit ;
-    }
-    else if free in $(attributes) && propagated in $(attributes)
-    {
-        error = free features cannot be propagated ;
-    }
-    else
-    {
-        local m = [ MATCH (.*=.*) : $(values) ] ;
-        if $(m[1])
-        {
-            error = "feature value may not contain '='" ;
-        }
-    }
-
-    if $(error)
-    {
-        errors.error $(error)
-              : "in" feature declaration:
-              : feature [ lol->list $(1) : $(2) : $(3) ] ;
-    }
-
-    $(name).values ?= ;
-    $(name).attributes = $(attributes) ;
-    $(name).subfeatures ?= ;
-    $(attributes).features += $(name) ;
-
-    .all-features += $(name) ;
-    if subfeature in $(attributes)
-    {
-        .all-subfeatures += $(name) ;
-    }
-    else
-    {
-        .all-top-features += $(name) ;
-    }
-    extend $(name) : $(values) ;
-}
-
-
-# Sets the default value of the given feature, overriding any previous default.
-#
-rule set-default ( feature : value )
-{
-    local f = [ grist $(feature) ] ;
-    local a = $($(f).attributes) ;
-    local bad-attribute = ;
-    if free in $(a)
-    {
-        bad-attribute = free ;
-    }
-    else if optional in $(a)
-    {
-        bad-attribute = optional ;
-    }
-    if $(bad-attribute)
-    {
-        errors.error "$(bad-attribute) property $(f) cannot have a default." ;
-    }
-    if ! $(value) in $($(f).values)
-    {
-        errors.error "The specified default value, '$(value)' is invalid"
-          : "allowed values are: " $($(f).values) ;
-    }
-    $(f).default = $(value) ;
-}
-
-
-# Returns the default property values for the given features.
-#
-rule defaults ( features * )
-{
-    local result ;
-    for local f in $(features)
-    {
-        local gf = $(:E=:G=$(f)) ;
-        local a = $($(gf).attributes) ;
-        if ( free in $(a) ) || ( optional in $(a) )
-        {
-        }
-        else
-        {
-            result += $(gf)$($(gf).default) ;
-        }
-    }
-    return $(result) ;
-}
-
-
-# Returns true iff all 'names' elements are valid features.
-#
-rule valid ( names + )
-{
-    if $(names) in $(.all-features)
-    {
-        return true ;
-    }
-}
-
-
-# Returns the attibutes of the given feature.
-#
-rule attributes ( feature )
-{
-    return $($(:E=:G=$(feature)).attributes) ;
-}
-
-
-# Returns the values of the given feature.
-#
-rule values ( feature )
-{
-    return $($(:E=:G=$(feature)).values) ;
-}
-
-
-# Returns true iff 'value-string' is a value-string of an implicit feature.
-#
-rule is-implicit-value ( value-string )
-{
-    local v = [ regex.split $(value-string) - ] ;
-    local failed ;
-    if ! $(v[1]) in $(.all-implicit-values)
-    {
-        failed = true ;
-    }
-    else
-    {
-        local feature = $($(v[1]).implicit-feature) ;
-        for local subvalue in $(v[2-])
-        {
-            if ! [ find-implied-subfeature $(feature) $(subvalue) : $(v[1]) ]
-            {
-                failed = true ;
-            }
-        }
-    }
-
-    if ! $(failed)
-    {
-        return true ;
-    }
-}
-
-
-# Returns the implicit feature associated with the given implicit value.
-#
-rule implied-feature ( implicit-value )
-{
-    local components = [ regex.split $(implicit-value) "-" ] ;
-
-    local feature = $($(components[1]).implicit-feature) ;
-    if ! $(feature)
-    {
-        errors.error \"$(implicit-value)\" is not a value of an implicit feature ;
-        feature = "" ;  # Keep testing happy; it expects a result.
-    }
-    return $(feature) ;
-}
-
-
-local rule find-implied-subfeature ( feature subvalue : value-string ? )
-{
-    # Feature should be of the form <feature-name>.
-    if $(feature) != $(feature:G)
-    {
-        errors.error invalid feature $(feature) ;
-    }
-
-    return $($(feature)$(value-string:E="")<>$(subvalue).subfeature) ;
-}
-
-
-# Given a feature and a value of one of its subfeatures, find the name of the
-# subfeature. If value-string is supplied, looks for implied subfeatures that
-# are specific to that value of feature
-#
-rule implied-subfeature (
-      feature         # The main feature name.
-      subvalue        # The value of one of its subfeatures.
-    : value-string ?  # The value of the main feature.
-)
-{
-    local subfeature = [ find-implied-subfeature $(feature) $(subvalue)
-        : $(value-string) ] ;
-    if ! $(subfeature)
-    {
-        value-string ?= "" ;
-        errors.error \"$(subvalue)\" is not a known subfeature value of
-            $(feature)$(value-string) ;
-    }
-    return $(subfeature) ;
-}
-
-
-# Generate an error if the feature is unknown.
-#
-local rule validate-feature ( feature )
-{
-    if ! $(feature) in $(.all-features)
-    {
-        errors.error unknown feature \"$(feature)\" ;
-    }
-}
-
-
-# Given a feature and its value or just a value corresponding to an implicit
-# feature, returns a property set consisting of all component subfeatures and
-# their values. For example all the following calls:
-#
-#   expand-subfeatures-aux <toolset>gcc-2.95.2-linux-x86
-#   expand-subfeatures-aux gcc-2.95.2-linux-x86
-#
-# return:
-#
-#   <toolset>gcc <toolset-version>2.95.2 <toolset-os>linux <toolset-cpu>x86
-#
-local rule expand-subfeatures-aux (
-      feature ?        # Feature name or empty if value corresponds to an
-                       # implicit property.
-    : value            # Feature value.
-    : dont-validate ?  # If set, no value string validation will be done.
-)
-{
-    if $(feature)
-    {
-        feature = $(feature) ;
-    }
-
-    if ! $(feature)
-    {
-        feature = [ implied-feature $(value) ] ;
-    }
-    else
-    {
-        validate-feature $(feature) ;
-    }
-    if ! $(dont-validate)
-    {
-        validate-value-string $(feature) $(value) ;
-    }
-
-    local components = [ regex.split $(value) "-" ] ;
-
-    # Get the top-level feature's value.
-    local value = $(components[1]:G=) ;
-
-    local result = $(components[1]:G=$(feature)) ;
-
-    local subvalues = $(components[2-]) ;
-    while $(subvalues)
-    {
-        local subvalue = $(subvalues[1]) ;  # Pop the head off of subvalues.
-        subvalues = $(subvalues[2-]) ;
-
-        local subfeature = [ find-implied-subfeature $(feature) $(subvalue) :
-            $(value) ] ;
-
-        # If no subfeature was found reconstitute the value string and use that.
-        if ! $(subfeature)
-        {
-            result = $(components:J=-) ;
-            result = $(result:G=$(feature)) ;
-            subvalues = ;  # Stop looping.
-        }
-        else
-        {
-            local f = [ MATCH ^<(.*)>$ : $(feature) ] ;
-            result += $(subvalue:G=$(f)-$(subfeature)) ;
-        }
-    }
-
-    return $(result) ;
-}
-
-
-# Make all elements of properties corresponding to implicit features explicit,
-# and express all subfeature values as separate properties in their own right.
-# For example, all of the following properties
-#
-#    gcc-2.95.2-linux-x86
-#    <toolset>gcc-2.95.2-linux-x86
-#
-# might expand to
-#
-#   <toolset>gcc <toolset-version>2.95.2 <toolset-os>linux <toolset-cpu>x86
-#
-rule expand-subfeatures (
-    properties *       # Property set with elements of the form
-                       # <feature>value-string or just value-string in the case
-                       # of implicit features.
-    : dont-validate ?
-)
-{
-    local result ;
-    for local p in $(properties)
-    {
-        # Don't expand subfeatures in subfeatures
-        if ! [ MATCH "(:)" : $(p:G) ]
-        {
-            result += [ expand-subfeatures-aux $(p:G) : $(p:G=) : $(dont-validate) ] ;
-        }
-        else
-        {
-            result += $(p) ;
-        }
-    }
-    return $(result) ;
-}
-
-
-# Helper for extend, below. Handles the feature case.
-#
-local rule extend-feature ( feature : values * )
-{
-    feature = [ grist $(feature) ] ;
-    validate-feature $(feature) ;
-    if implicit in $($(feature).attributes)
-    {
-        for local v in $(values)
-        {
-            if $($(v).implicit-feature)
-            {
-                errors.error $(v) is already associated with the \"$($(v).implicit-feature)\" feature ;
-            }
-            $(v).implicit-feature = $(feature) ;
-        }
-
-        .all-implicit-values += $(values) ;
-    }
-    if ! $($(feature).values)
-    {
-        # This is the first value specified for this feature so make it be the
-        # default.
-        $(feature).default = $(values[1]) ;
-    }
-    $(feature).values += $(values) ;
-}
-
-
-# Checks that value-string is a valid value-string for the given feature.
-#
-rule validate-value-string ( feature value-string )
-{
-    if ! (
-        free in $($(feature).attributes)
-        || ( $(value-string) in $(feature).values )
-    )
-    {
-        local values = $(value-string) ;
-
-        if $($(feature).subfeatures)
-        {
-            if ! ( $(value-string) in $($(feature).values) )
-               && ! ( $(value-string) in $($(feature).subfeatures) ) 
-            {
-                values = [ regex.split $(value-string) - ] ;
-            }
-        }
-
-        if ! ( $(values[1]) in $($(feature).values) ) &&
-
-            # An empty value is allowed for optional features.
-            ( $(values[1]) || ! ( optional in $($(feature).attributes) ) )
-        {
-            errors.error \"$(values[1])\" is not a known value of feature $(feature)
-                : legal values: \"$($(feature).values)\" ;
-        }
-
-        for local v in $(values[2-])
-        {
-            # This will validate any subfeature values in value-string.
-            implied-subfeature $(feature) $(v) : $(values[1]) ;
-        }
-    }
-}
-
-
-# A helper that computes:
-#  * name(s) of module-local variable(s) used to record the correspondence
-#    between subvalue(s) and a subfeature
-#  * value of that variable when such a subfeature/subvalue has been defined and
-# returns a list consisting of the latter followed by the former.
-#
-local rule subvalue-var (
-    feature         # Main feature name.
-    value-string ?  # If supplied, specifies a specific value of the main
-                    # feature for which the subfeature values are valid.
-    : subfeature    # Subfeature name.
-    : subvalues *   # Subfeature values.
-)
-{
-    feature = [ grist $(feature) ] ;
-    validate-feature $(feature) ;
-    if $(value-string)
-    {
-        validate-value-string $(feature) $(value-string) ;
-    }
-
-    local subfeature-name = [ get-subfeature-name $(subfeature) $(value-string) ] ;
-
-    return $(subfeature-name)
-    $(feature)$(value-string:E="")<>$(subvalues).subfeature ;
-}
-
-
-# Extends the given subfeature with the subvalues. If the optional value-string
-# is provided, the subvalues are only valid for the given value of the feature.
-# Thus, you could say that <target-platform>mingw is specific to
-# <toolset>gcc-2.95.2 as follows:
-#
-#       extend-subfeature toolset gcc-2.95.2 : target-platform : mingw ;
-#
-rule extend-subfeature (
-    feature         # The feature whose subfeature is being extended.
-
-    value-string ?  # If supplied, specifies a specific value of the main
-                    # feature for which the new subfeature values are valid.
-
-    : subfeature    # Subfeature name.
-    : subvalues *   # Additional subfeature values.
-)
-{
-    local subfeature-vars = [ subvalue-var $(feature) $(value-string)
-        : $(subfeature) : $(subvalues) ] ;
-
-    local f = [ utility.ungrist [ grist $(feature) ] ] ;
-    extend $(f)-$(subfeature-vars[1]) : $(subvalues) ;
-
-    # Provide a way to get from the given feature or property and subfeature
-    # value to the subfeature name.
-    $(subfeature-vars[2-]) = $(subfeature-vars[1]) ;
-}
-
-
-# Returns true iff the subvalues are valid for the feature. When the optional
-# value-string is provided, returns true iff the subvalues are valid for the
-# given value of the feature.
-#
-rule is-subvalue ( feature : value-string ? : subfeature : subvalue )
-{
-    local subfeature-vars = [ subvalue-var $(feature) $(value-string)
-        : $(subfeature) : $(subvalue) ] ;
-
-    if $($(subfeature-vars[2])) = $(subfeature-vars[1])
-    {
-        return true ;
-    }
-}
-
-
-# Can be called three ways:
-#
-#    1. extend feature : values *
-#    2. extend <feature> subfeature : values *
-#    3. extend <feature>value-string subfeature : values *
-#
-# * Form 1 adds the given values to the given feature.
-# * Forms 2 and 3 add subfeature values to the given feature.
-# * Form 3 adds the subfeature values as specific to the given property
-#   value-string.
-#
-rule extend ( feature-or-property subfeature ? : values * )
-{
-    local feature ;       # If a property was specified this is its feature.
-    local value-string ;  # E.g., the gcc-2.95-2 part of <toolset>gcc-2.95.2.
-
-    # If a property was specified.
-    if $(feature-or-property:G) && $(feature-or-property:G=)
-    {
-        # Extract the feature and value-string, if any.
-        feature = $(feature-or-property:G) ;
-        value-string = $(feature-or-property:G=) ;
-    }
-    else
-    {
-        feature = [ grist $(feature-or-property) ] ;
-    }
-
-    # Dispatch to the appropriate handler.
-    if $(subfeature)
-    {
-        extend-subfeature $(feature) $(value-string) : $(subfeature)
-            : $(values) ;
-    }
-    else
-    {
-        # If no subfeature was specified, we do not expect to see a
-        # value-string.
-        if $(value-string)
-        {
-            errors.error can only specify a property as the first argument when
-                extending a subfeature
-                : usage:
-                : "    extend" feature ":" values...
-                : "  | extend" <feature>value-string subfeature ":" values...
-                ;
-        }
-
-        extend-feature $(feature) : $(values) ;
-    }
-}
-
-
-local rule get-subfeature-name ( subfeature value-string ? )
-{
-    local prefix = $(value-string): ;
-    return $(prefix:E="")$(subfeature) ;
-}
-
-
-# Declares a subfeature.
-#
-rule subfeature (
-    feature         # Root feature that is not a subfeature.
-    value-string ?  # A value-string specifying which feature or subfeature
-                    # values this subfeature is specific to, if any.
-    : subfeature    # The name of the subfeature being declared.
-    : subvalues *   # The allowed values of this subfeature.
-    : attributes *  # The attributes of the subfeature.
-)
-{
-    feature = [ grist $(feature) ] ;
-    validate-feature $(feature) ;
-
-    # Add grist to the subfeature name if a value-string was supplied.
-    local subfeature-name = [ get-subfeature-name $(subfeature) $(value-string) ] ;
-
-    if $(subfeature-name) in $($(feature).subfeatures)
-    {
-        errors.error \"$(subfeature)\" already declared as a subfeature of \"$(feature)\"
-            "specific to "$(value-string) ;
-    }
-    $(feature).subfeatures += $(subfeature-name) ;
-
-    # First declare the subfeature as a feature in its own right.
-    local f = [ utility.ungrist $(feature) ] ;
-    feature $(f)-$(subfeature-name) : $(subvalues) : $(attributes) subfeature ;
-
-    # Now make sure the subfeature values are known.
-    extend-subfeature $(feature) $(value-string) : $(subfeature) : $(subvalues) ;
-}
-
-
-# Set components of the given composite property.
-#
-rule compose ( composite-property : component-properties * )
-{
-    local feature = $(composite-property:G) ;
-    if ! ( composite in [ attributes $(feature) ] )
-    {
-        errors.error "$(feature)" is not a composite feature ;
-    }
-
-    $(composite-property).components ?= ;
-    if $($(composite-property).components)
-    {
-        errors.error components of "$(composite-property)" already set:
-            $($(composite-property).components) ;
-    }
-
-    if $(composite-property) in $(component-properties)
-    {
-        errors.error composite property "$(composite-property)" cannot have itself as a component ;
-    }
-    $(composite-property).components = $(component-properties) ;
-}
-
-
-local rule expand-composite ( property )
-{
-    return $(property)
-        [ sequence.transform expand-composite : $($(property).components) ] ;
-}
-
-
-# Return all values of the given feature specified by the given property set.
-#
-rule get-values ( feature : properties * )
-{
-    local result ;
-
-    feature = $(:E=:G=$(feature)) ;  # Add <> if necessary.
-    for local p in $(properties)
-    {
-        if $(p:G) = $(feature)
-        {
-            # Use MATCH instead of :G= to get the value, in order to preserve
-            # the value intact instead of having bjam treat it as a decomposable
-            # path.
-            result += [ MATCH ">(.*)" : $(p) ] ;
-        }
-    }
-    return $(result) ;
-}
-
-
-rule free-features ( )
-{
-    return $(free.features) ;
-}
-
-
-# Expand all composite properties in the set so that all components are
-# explicitly expressed.
-#
-rule expand-composites ( properties * )
-{
-    local explicit-features = $(properties:G) ;
-    local result ;
-
-    # Now expand composite features.
-    for local p in $(properties)
-    {
-        local expanded = [ expand-composite $(p) ] ;
-
-        for local x in $(expanded)
-        {
-            if ! $(x) in $(result)
-            {
-                local f = $(x:G) ;
-
-                if $(f) in $(free.features)
-                {
-                    result += $(x) ;
-                }
-                else if ! $(x) in $(properties)  # x is the result of expansion
-                {
-                    if ! $(f) in $(explicit-features)  # not explicitly-specified
-                    {
-                        if $(f) in $(result:G)
-                        {
-                            errors.error expansions of composite features result
-                                in conflicting values for $(f)
-                                : values: [ get-values $(f) : $(result) ] $(x:G=)
-                                : one contributing composite property was $(p) ;
-                        }
-                        else
-                        {
-                            result += $(x) ;
-                        }
-                    }
-                }
-                else if $(f) in $(result:G)
-                {
-                    errors.error explicitly-specified values of non-free feature
-                        $(f) conflict :
-                        "existing values:" [ get-values $(f) : $(properties) ] :
-                        "value from expanding " $(p) ":" $(x:G=) ;
-                }
-                else
-                {
-                    result += $(x) ;
-                }
-            }
-        }
-    }
-    return $(result) ;
-}
-
-
-# Return true iff f is an ordinary subfeature of the parent-property's feature,
-# or if f is a subfeature of the parent-property's feature specific to the
-# parent-property's value.
-#
-local rule is-subfeature-of ( parent-property f )
-{
-    if subfeature in $($(f).attributes)
-    {
-        local specific-subfeature = [ MATCH <(.*):(.*)> : $(f) ] ;
-        if $(specific-subfeature)
-        {
-            # The feature has the form <topfeature-topvalue:subfeature>, e.g.
-            # <toolset-msvc:version>.
-            local feature-value = [ split-top-feature $(specific-subfeature[1])
-                ] ;
-            if <$(feature-value[1])>$(feature-value[2]) = $(parent-property)
-            {
-                return true ;
-            }
-        }
-        else
-        {
-            # The feature has the form <topfeature-subfeature>, e.g.
-            # <toolset-version>
-            local top-sub = [ split-top-feature [ utility.ungrist $(f) ] ] ;
-            if $(top-sub[2]) && <$(top-sub[1])> = $(parent-property:G)
-            {
-                return true ;
-            }
-        }
-    }
-}
-
-
-# As for is-subfeature-of but for subproperties.
-#
-local rule is-subproperty-of ( parent-property p )
-{
-    return [ is-subfeature-of $(parent-property) $(p:G) ] ;
-}
-
-
-# Given a property, return the subset of features consisting of all ordinary
-# subfeatures of the property's feature, and all specific subfeatures of the
-# property's feature which are conditional on the property's value.
-#
-local rule select-subfeatures ( parent-property : features * )
-{
-    return [ sequence.filter is-subfeature-of $(parent-property) : $(features) ] ;
-}
-
-
-# As for select-subfeatures but for subproperties.
-#
-local rule select-subproperties ( parent-property : properties * )
-{
-    return [ sequence.filter is-subproperty-of $(parent-property) : $(properties) ] ;
-}
-
-
-# Given a property set which may consist of composite and implicit properties
-# and combined subfeature values, returns an expanded, normalized property set
-# with all implicit features expressed explicitly, all subfeature values
-# individually expressed, and all components of composite properties expanded.
-# Non-free features directly expressed in the input properties cause any values
-# of those features due to composite feature expansion to be dropped. If two
-# values of a given non-free feature are directly expressed in the input, an
-# error is issued.
-#
-rule expand ( properties * )
-{
-    local expanded = [ expand-subfeatures $(properties) ] ;
-    return [ expand-composites $(expanded) ] ;
-}
-
-
-# Helper rule for minimize. Returns true iff property's feature is present in
-# the contents of the variable named by feature-set-var.
-#
-local rule in-features ( feature-set-var property )
-{
-    if $(property:G) in $($(feature-set-var))
-    {
-        return true ;
-    }
-}
-
-
-# Helper rule for minimize. Returns the list with the same properties, but with
-# all subfeatures moved to the end of the list.
-#
-local rule move-subfeatures-to-the-end ( properties * )
-{
-    local x1 ;
-    local x2 ;
-    for local p in $(properties)
-    {
-        if subfeature in $($(p:G).attributes)
-        {
-            x2 += $(p) ;
-        }
-        else
-        {
-            x1 += $(p) ;
-        }
-    }
-    return $(x1) $(x2) ;
-}
-
-
-# Given an expanded property set, eliminate all redundancy: properties that are
-# elements of other (composite) properties in the set will be eliminated.
-# Non-symmetric properties equal to default values will be eliminated unless
-# they override a value from some composite property. Implicit properties will
-# be expressed without feature grist, and sub-property values will be expressed
-# as elements joined to the corresponding main property.
-#
-rule minimize ( properties * )
-{
-    # Precondition checking
-    local implicits = [ set.intersection $(p:G=) : $(p:G) ] ;
-    if $(implicits)
-    {
-        errors.error minimize requires an expanded property set, but
-            \"$(implicits[1])\" appears to be the value of an un-expanded
-            implicit feature ;
-    }
-
-    # Remove properties implied by composite features.
-    local components = $($(properties).components) ;
-    local x = [ set.difference $(properties) : $(components) ] ;
-
-    # Handle subfeatures and implicit features.
-    x = [ move-subfeatures-to-the-end $(x) ] ;
-    local result ;
-    while $(x)
-    {
-        local p fullp = $(x[1]) ;
-        local f = $(p:G) ;
-        local v = $(p:G=) ;
-
-        # Eliminate features in implicit properties.
-        if implicit in [ attributes $(f) ]
-        {
-            p = $(v) ;
-        }
-
-        # Locate all subproperties of $(x[1]) in the property set.
-        local subproperties = [ select-subproperties $(fullp) : $(x) ] ;
-        if $(subproperties)
-        {
-            # Reconstitute the joined property name.
-            local sorted = [ sequence.insertion-sort $(subproperties) ] ;
-            result += $(p)-$(sorted:G="":J=-) ;
-
-            x = [ set.difference $(x[2-]) : $(subproperties) ] ;
-        }
-        else
-        {
-            # Eliminate properties whose value is equal to feature's default,
-            # which are not symmetric and which do not contradict values implied
-            # by composite properties.
-
-            # Since all component properties of composites in the set have been
-            # eliminated, any remaining property whose feature is the same as a
-            # component of a composite in the set must have a non-redundant
-            # value.
-            if $(fullp) != [ defaults $(f) ]
-                || symmetric in [ attributes $(f) ]
-                || $(fullp:G) in $(components:G)
-            {
-                result += $(p) ;
-            }
-
-            x = $(x[2-]) ;
-        }
-    }
-    return $(result) ;
-}
-
-
-# Combine all subproperties into their parent properties
-#
-# Requires: for every subproperty, there is a parent property. All features are
-# explicitly expressed.
-#
-# This rule probably should not be needed, but build-request.expand-no-defaults
-# is being abused for unintended purposes and it needs help.
-#
-rule compress-subproperties ( properties * )
-{
-    local all-subs ;
-    local matched-subs ;
-    local result ;
-
-    for local p in $(properties)
-    {
-        if ! $(p:G)
-        {
-            # Expecting fully-gristed properties.
-            assert.variable-not-empty p:G ;
-        }
-
-        if ! subfeature in $($(p:G).attributes)
-        {
-            local subs = [ sequence.insertion-sort
-                [ sequence.filter is-subproperty-of $(p) : $(properties) ] ] ;
-
-            matched-subs += $(subs) ;
-
-            local subvalues = -$(subs:G=:J=-) ;
-            subvalues ?= "" ;
-            result += $(p)$(subvalues) ;
-        }
-        else
-        {
-            all-subs += $(p) ;
-        }
-    }
-    assert.result true : set.equal $(all-subs) : $(matched-subs) ;
-    return $(result) ;
-}
-
-
-# Given an ungristed string, finds the longest prefix which is a top-level
-# feature name followed by a dash, and return a pair consisting of the parts
-# before and after that dash. More interesting than a simple split because
-# feature names may contain dashes.
-#
-local rule split-top-feature ( feature-plus )
-{
-    local e = [ regex.split $(feature-plus) - ] ;
-    local f = $(e[1]) ;
-    local v ;
-    while $(e)
-    {
-        if <$(f)> in $(.all-top-features)
-        {
-            v = $(f) $(e[2-]:J=-) ;
-        }
-        e = $(e[2-]) ;
-        f = $(f)-$(e[1]) ;
-    }
-    return $(v) ;
-}
-
-
-# Given a set of properties, add default values for features not represented in
-# the set.
-#
-# Note: if there's an ordinary feature F1 and a composite feature F2 which
-# includes some value for F1 and both feature have default values then the
-# default value of F1 will be added (as opposed to the value in F2). This might
-# not be the right idea, e.g. consider:
-#
-#   feature variant : debug ... ;
-#        <variant>debug : .... <runtime-debugging>on
-#   feature <runtime-debugging> : off on ;
-#
-#   Here, when adding default for an empty property set, we'll get
-#
-#     <variant>debug <runtime_debugging>off
-#
-#   and that's kind of strange.
-#
-rule add-defaults ( properties * )
-{
-    for local v in $(properties:G=)
-    {
-        if $(v) in $(properties)
-        {
-            errors.error add-defaults requires explicitly specified features,
-                but \"$(v)\" appears to be the value of an un-expanded implicit
-                feature ;
-        }
-    }
-    # We don't add default for elements with ":" inside. This catches:
-    # 1. Conditional properties --- we don't want <variant>debug:<define>DEBUG
-    #    to be takes as specified value for <variant>
-    # 2. Free properties with ":" in values. We don't care, since free
-    #    properties don't have defaults.
-    local xproperties = [ MATCH "^([^:]+)$" : $(properties) ] ;
-    local missing-top = [ set.difference $(.all-top-features) : $(xproperties:G) ] ;
-    local more =  [ defaults $(missing-top) ] ;
-    properties += $(more) ;
-    xproperties += $(more) ;
-
-    # Add defaults for subfeatures of features which are present.
-    for local p in $(xproperties)
-    {
-        local s = $($(p:G).subfeatures) ;
-        local f = [ utility.ungrist $(p:G) ] ;
-        local missing-subs = [ set.difference <$(f)-$(s)> : $(properties:G) ] ;
-        properties += [ defaults [ select-subfeatures $(p) : $(missing-subs) ] ] ;
-    }
-
-    return $(properties)  ;
-}
-
-
-# Given a property-set of the form
-#       v1/v2/...vN-1/<fN>vN/<fN+1>vN+1/...<fM>vM
-#
-# Returns
-#       v1 v2 ... vN-1 <fN>vN <fN+1>vN+1 ... <fM>vM
-#
-# Note that vN...vM may contain slashes. This needs to be resilient to the
-# substitution of backslashes for slashes, since Jam, unbidden, sometimes swaps
-# slash direction on NT.
-#
-rule split ( property-set )
-{
-    local pieces = [ regex.split $(property-set) [\\/] ] ;
-    local result ;
-
-    for local x in $(pieces)
-    {
-        if ( ! $(x:G) ) && $(result[-1]:G)
-        {
-            result = $(result[1--2]) $(result[-1])/$(x) ;
-        }
-        else
-        {
-            result += $(x) ;
-        }
-    }
-
-    return $(result) ;
-}
-
-
-# Tests of module feature.
-#
-rule __test__ ( )
-{
-    # Use a fresh copy of the feature module.
-    prepare-test feature-test-temp ;
-
-    import assert ;
-    import errors : try catch ;
-
-    # These are local rules and so must be explicitly reimported into the
-    # testing module.
-    import feature : extend-feature validate-feature select-subfeatures ;
-
-    feature toolset : gcc : implicit ;
-    feature define : : free ;
-    feature runtime-link : dynamic static : symmetric ;
-    feature optimization : on off ;
-    feature variant : debug release profile : implicit composite symmetric ;
-    feature stdlib : native stlport ;
-    feature magic : : free ;
-
-    compose <variant>debug : <define>_DEBUG <optimization>off ;
-    compose <variant>release : <define>NDEBUG <optimization>on ;
-
-    assert.result dynamic static : values <runtime-link> ;
-    assert.result dynamic static : values runtime-link ;
-
-    try ;
-    {
-        compose <variant>profile : <variant>profile ;
-    }
-    catch composite property <variant>profile cannot have itself as a component ;
-
-    extend-feature toolset : msvc metrowerks ;
-    subfeature toolset gcc : version : 2.95.2 2.95.3 2.95.4 3.0 3.0.1 3.0.2 ;
-
-    assert.true is-subvalue toolset : gcc : version : 2.95.3 ;
-    assert.false is-subvalue toolset : gcc : version : 1.1 ;
-
-    assert.false is-subvalue toolset : msvc : version : 2.95.3 ;
-    assert.false is-subvalue toolset : : version : yabba ;
-
-    feature yabba ;
-    subfeature yabba : version : dabba ;
-    assert.true is-subvalue yabba : : version : dabba ;
-
-    subfeature toolset gcc : platform : linux cygwin : optional ;
-
-    assert.result <toolset-gcc:version>
-        : select-subfeatures <toolset>gcc
-        : <toolset-gcc:version>
-          <toolset-msvc:version>
-          <toolset-version>
-          <stdlib> ;
-
-    subfeature stdlib : version : 3 4 : optional ;
-
-    assert.result <stdlib-version>
-        : select-subfeatures <stdlib>native
-        : <toolset-gcc:version>
-          <toolset-msvc:version>
-          <toolset-version>
-          <stdlib-version> ;
-
-    assert.result <toolset>gcc <toolset-gcc:version>3.0.1
-        : expand-subfeatures <toolset>gcc-3.0.1 ;
-
-    assert.result <toolset>gcc <toolset-gcc:version>3.0.1 <toolset-gcc:platform>linux
-        : expand-subfeatures <toolset>gcc-3.0.1-linux ;
-
-    assert.result <toolset>gcc <toolset-gcc:version>3.0.1
-        : expand <toolset>gcc <toolset-gcc:version>3.0.1  ;
-
-    assert.result <define>foo=x-y
-        : expand-subfeatures <define>foo=x-y ;
-
-    assert.result <toolset>gcc <toolset-gcc:version>3.0.1
-        : expand-subfeatures gcc-3.0.1 ;
-
-    assert.result a c e
-        : get-values <x> : <x>a <y>b <x>c <y>d <x>e ;
-
-    assert.result <toolset>gcc <toolset-gcc:version>3.0.1
-        <variant>debug <define>_DEBUG <optimization>on
-        : expand gcc-3.0.1 debug <optimization>on ;
-
-    assert.result <variant>debug <define>_DEBUG <optimization>on
-        : expand debug <optimization>on ;
-
-    assert.result <optimization>on <variant>debug <define>_DEBUG
-        : expand <optimization>on debug ;
-
-    assert.result <runtime-link>dynamic <optimization>on
-        : defaults <runtime-link> <define> <optimization> ;
-
-    # Make sure defaults is resilient to missing grist.
-    assert.result <runtime-link>dynamic <optimization>on
-        : defaults runtime-link define optimization ;
-
-    feature dummy : dummy1 dummy2 ;
-    subfeature dummy : subdummy : x y z : optional ;
-
-    feature fu : fu1 fu2 : optional ;
-    subfeature fu : subfu : x y z : optional ;
-    subfeature fu : subfu2 : q r s ;
-
-    assert.result optional : attributes <fu> ;
-    assert.result optional : attributes fu ;
-
-    assert.result <runtime-link>static <define>foobar <optimization>on
-        <toolset>gcc:<define>FOO <toolset>gcc <variant>debug <stdlib>native
-        <dummy>dummy1 <toolset-gcc:version>2.95.2
-        : add-defaults <runtime-link>static <define>foobar <optimization>on
-          <toolset>gcc:<define>FOO ;
-
-    assert.result <runtime-link>static <define>foobar <optimization>on
-        <toolset>gcc:<define>FOO <fu>fu1 <toolset>gcc <variant>debug
-        <stdlib>native <dummy>dummy1 <fu-subfu2>q <toolset-gcc:version>2.95.2
-        : add-defaults <runtime-link>static <define>foobar <optimization>on
-          <toolset>gcc:<define>FOO <fu>fu1 ;
-
-    set-default <runtime-link> : static ;
-    assert.result <runtime-link>static : defaults <runtime-link> ;
-
-    assert.result gcc-3.0.1 debug <optimization>on
-        : minimize [ expand gcc-3.0.1 debug <optimization>on <stdlib>native ] ;
-
-    assert.result gcc-3.0.1 debug <runtime-link>dynamic
-        : minimize
-          [ expand gcc-3.0.1 debug <optimization>off <runtime-link>dynamic ] ;
-
-    assert.result gcc-3.0.1 debug
-        : minimize [ expand gcc-3.0.1 debug <optimization>off ] ;
-
-    assert.result debug <optimization>on
-        : minimize [ expand debug <optimization>on ] ;
-
-    assert.result gcc-3.0
-        : minimize <toolset>gcc <toolset-gcc:version>3.0 ;
-
-    assert.result gcc-3.0
-        : minimize <toolset-gcc:version>3.0 <toolset>gcc ;
-
-    assert.result <x>y/z <a>b/c <d>e/f
-        : split <x>y/z/<a>b/c/<d>e/f ;
-
-    assert.result <x>y/z <a>b/c <d>e/f
-        : split <x>y\\z\\<a>b\\c\\<d>e\\f ;
-
-    assert.result a b c <d>e/f/g <h>i/j/k
-        : split a/b/c/<d>e/f/g/<h>i/j/k ;
-
-    assert.result a b c <d>e/f/g <h>i/j/k
-        : split a\\b\\c\\<d>e\\f\\g\\<h>i\\j\\k ;
-
-    # Test error checking.
-
-    try ;
-    {
-        expand release <optimization>off <optimization>on ;
-    }
-    catch explicitly-specified values of non-free feature <optimization> conflict ;
-
-    try ;
-    {
-        validate-feature <foobar> ;
-    }
-    catch unknown feature ;
-
-    validate-value-string <toolset> gcc ;
-    validate-value-string <toolset> gcc-3.0.1 ;
-
-    try ;
-    {
-        validate-value-string <toolset> digital_mars ;
-    }
-    catch \"digital_mars\" is not a known value of <toolset> ;
-
-    try ;
-    {
-        feature foobar : : baz ;
-    }
-    catch unknown attributes: baz ;
-
-    feature feature1 ;
-    try ;
-    {
-        feature feature1 ;
-    }
-    catch feature already defined: ;
-
-    try ;
-    {
-        feature feature2 : : free implicit ;
-    }
-    catch free features cannot also be implicit ;
-
-    try ;
-    {
-        feature feature3 : : free propagated ;
-    }
-    catch free features cannot be propagated ;
-
-    try ;
-    {
-        implied-feature lackluster ;
-    }
-    catch \"lackluster\" is not a value of an implicit feature ;
-
-    try ;
-    {
-        implied-subfeature <toolset> 3.0.1 ;
-    }
-    catch \"3.0.1\" is not a known subfeature value of <toolset> ;
-
-    try ;
-    {
-        implied-subfeature <toolset> not-a-version : gcc ;
-    }
-    catch \"not-a-version\" is not a known subfeature value of <toolset>gcc ;
-
-    # Leave a clean copy of the features module behind.
-    finish-test feature-test-temp ;
-}
diff --git a/jam-files/boost-build/build/feature.py b/jam-files/boost-build/build/feature.py
deleted file mode 100644
index 315a18e9..00000000
--- a/jam-files/boost-build/build/feature.py
+++ /dev/null
@@ -1,905 +0,0 @@
-# Status: ported, except for unit tests.
-# Base revision: 64488
-#
-# Copyright 2001, 2002, 2003 Dave Abrahams 
-# Copyright 2002, 2006 Rene Rivera 
-# Copyright 2002, 2003, 2004, 2005, 2006 Vladimir Prus 
-# Distributed under the Boost Software License, Version 1.0. 
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt) 
-
-import re
-
-from b2.util import utility, bjam_signature
-import b2.util.set
-from b2.util.utility import add_grist, get_grist, ungrist, replace_grist, to_seq
-from b2.exceptions import *
-
-__re_split_subfeatures = re.compile ('<(.*):(.*)>')
-__re_no_hyphen = re.compile ('^([^:]+)$')
-__re_slash_or_backslash = re.compile (r'[\\/]')
-
-class Feature(object):
-
-    # Map from string attribute names to integers bit flags.
-    # This will be initialized after declaration of the class.
-    _attribute_name_to_integer = {}
-
-    def __init__(self, name, values, attributes):
-        self._name = name
-        self._values = values
-        self._default = None
-        self._attributes = 0
-        for a in attributes:
-            self._attributes = self._attributes | Feature._attribute_name_to_integer[a]
-        self._attributes_string_list = attributes
-        self._subfeatures = []
-        self._parent = None
-
-    def name(self):
-        return self._name
-
-    def values(self):
-        return self._values
-
-    def add_values(self, values):
-        self._values.extend(values)
-
-    def attributes(self):
-        return self._attributes
-
-    def set_default(self, value):
-        self._default = value
-
-    def default(self):
-        return self._default
-
-    # FIXME: remove when we fully move to using classes for features/properties
-    def attributes_string_list(self):
-        return self._attributes_string_list
-
-    def subfeatures(self):
-        return self._subfeatures
-
-    def add_subfeature(self, name):
-        self._subfeatures.append(name)
-
-    def parent(self):
-        """For subfeatures, return pair of (parent_feature, value).
-
-        Value may be None if this subfeature is not specific to any
-        value of the parent feature.
-        """
-        return self._parent
-
-    def set_parent(self, feature, value):
-        self._parent = (feature, value)
-
-    def __str__(self):
-        return self._name
-
-    
-def reset ():
-    """ Clear the module state. This is mainly for testing purposes.
-    """
-    global __all_attributes, __all_features, __implicit_features, __composite_properties
-    global __features_with_attributes, __subfeature_from_value, __all_top_features, __free_features
-    global __all_subfeatures
-        
-    # The list with all attribute names.
-    __all_attributes = [ 'implicit',
-                        'composite',
-                        'optional',
-                        'symmetric',
-                        'free',
-                        'incidental',
-                        'path',
-                        'dependency',
-                        'propagated',
-                        'link-incompatible',
-                        'subfeature',
-                        'order-sensitive'
-                       ]
-    i = 1
-    for a in __all_attributes:
-        setattr(Feature, a.upper(), i)
-        Feature._attribute_name_to_integer[a] = i
-        def probe(self, flag=i):
-            return getattr(self, "_attributes") & flag
-        setattr(Feature, a.replace("-", "_"), probe)
-        i = i << 1
-    
-    # A map containing all features. The key is the feature name.
-    # The value is an instance of Feature class.
-    __all_features = {}
-    
-    # All non-subfeatures.
-    __all_top_features = []
-    
-    # Maps valus to the corresponding implicit feature
-    __implicit_features = {}
-    
-    # A map containing all composite properties. The key is a Property instance,
-    # and the value is a list of Property instances
-    __composite_properties = {}
-    
-    __features_with_attributes = {}
-    for attribute in __all_attributes:
-        __features_with_attributes [attribute] = []
-    
-    # Maps a value to the corresponding subfeature name.
-    __subfeature_from_value = {}
-    
-    # All free features
-    __free_features = []
-
-    __all_subfeatures = []
-
-reset ()
-
-def enumerate ():
-    """ Returns an iterator to the features map.
-    """
-    return __all_features.iteritems ()
-
-def get(name):
-    """Return the Feature instance for the specified name.
-
-    Throws if no feature by such name exists
-    """
-    return __all_features[name]
-
-# FIXME: prepare-test/finish-test?
-
-@bjam_signature((["name"], ["values", "*"], ["attributes", "*"]))
-def feature (name, values, attributes = []):
-    """ Declares a new feature with the given name, values, and attributes.
-        name: the feature name
-        values: a sequence of the allowable values - may be extended later with feature.extend
-        attributes: a sequence of the feature's attributes (e.g. implicit, free, propagated, ...)
-    """
-    __validate_feature_attributes (name, attributes)
-
-    feature = Feature(name, [], attributes)
-    __all_features[name] = feature
-    # Temporary measure while we have not fully moved from 'gristed strings'
-    __all_features["<" + name + ">"] = feature
-        
-    for attribute in attributes:
-        __features_with_attributes [attribute].append (name)
-
-    name = add_grist(name)
-        
-    if 'subfeature' in attributes:
-        __all_subfeatures.append(name)
-    else:
-        __all_top_features.append(feature)
-
-    extend (name, values)
-
-    # FIXME: why his is needed.
-    if 'free' in attributes:
-        __free_features.append (name)
-
-    return feature
-
-@bjam_signature((["feature"], ["value"]))
-def set_default (feature, value):
-    """ Sets the default value of the given feature, overriding any previous default.
-        feature: the name of the feature
-        value: the default value to assign
-    """
-    f = __all_features[feature]
-    attributes = f.attributes()
-    bad_attribute = None
-
-    if attributes & Feature.FREE:
-        bad_attribute = "free"
-    elif attributes & Feature.OPTIONAL:
-        bad_attribute = "optional"
-        
-    if bad_attribute:
-        raise InvalidValue ("%s property %s cannot have a default" % (bad_attribute, feature.name()))
-        
-    if not value in f.values():
-        raise InvalidValue ("The specified default value, '%s' is invalid.\n" % value + "allowed values are: %s" % values)
-
-    f.set_default(value)
-
-def defaults(features):
-    """ Returns the default property values for the given features.
-    """
-    # FIXME: should merge feature and property modules.
-    import property
-    
-    result = []
-    for f in features:
-        if not f.free() and not f.optional() and f.default():
-            result.append(property.Property(f, f.default()))
-
-    return result
-
-def valid (names):
-    """ Returns true iff all elements of names are valid features.
-    """
-    def valid_one (name): return __all_features.has_key (name)
-        
-    if isinstance (names, str):
-        return valid_one (names)
-    else:
-        return [ valid_one (name) for name in names ]
-
-def attributes (feature):
-    """ Returns the attributes of the given feature.
-    """
-    return __all_features[feature].attributes_string_list()
-        
-def values (feature):
-    """ Return the values of the given feature.
-    """
-    validate_feature (feature)
-    return __all_features[feature].values()
-
-def is_implicit_value (value_string):
-    """ Returns true iff 'value_string' is a value_string
-    of an implicit feature.
-    """
-
-    if __implicit_features.has_key(value_string):
-        return __implicit_features[value_string]
-    
-    v = value_string.split('-')
-
-    if not __implicit_features.has_key(v[0]):
-        return False
-
-    feature = __implicit_features[v[0]]
-    
-    for subvalue in (v[1:]):
-        if not __find_implied_subfeature(feature, subvalue, v[0]):
-            return False
-            
-    return True
-
-def implied_feature (implicit_value):
-    """ Returns the implicit feature associated with the given implicit value.
-    """
-    components = implicit_value.split('-')
-    
-    if not __implicit_features.has_key(components[0]):
-        raise InvalidValue ("'%s' is not a value of an implicit feature" % implicit_value)
-        
-    return __implicit_features[components[0]]
-
-def __find_implied_subfeature (feature, subvalue, value_string):
-    
-    #if value_string == None: value_string = ''
-
-    if not __subfeature_from_value.has_key(feature) \
-        or not __subfeature_from_value[feature].has_key(value_string) \
-        or not __subfeature_from_value[feature][value_string].has_key (subvalue):
-        return None
-        
-    return __subfeature_from_value[feature][value_string][subvalue]
-
-# Given a feature and a value of one of its subfeatures, find the name
-# of the subfeature. If value-string is supplied, looks for implied
-# subfeatures that are specific to that value of feature
-#  feature             # The main feature name
-#  subvalue            # The value of one of its subfeatures
-#  value-string        # The value of the main feature
-
-def implied_subfeature (feature, subvalue, value_string):
-    result = __find_implied_subfeature (feature, subvalue, value_string)
-    if not result:
-        raise InvalidValue ("'%s' is not a known subfeature value of '%s%s'" % (subvalue, feature, value_string))
-
-    return result
-
-def validate_feature (name):
-    """ Checks if all name is a valid feature. Otherwise, raises an exception.
-    """
-    if not __all_features.has_key(name):
-        raise InvalidFeature ("'%s' is not a valid feature name" % name)
-    else:
-        return __all_features[name]
-
-def valid (names):
-    """ Returns true iff all elements of names are valid features.
-    """
-    def valid_one (name): return __all_features.has_key (name)
-        
-    if isinstance (names, str):
-        return valid_one (names)
-    else:
-        return [ valid_one (name) for name in names ]
-
-# Uses Property
-def __expand_subfeatures_aux (property, dont_validate = False):
-    """ Helper for expand_subfeatures.
-        Given a feature and value, or just a value corresponding to an
-        implicit feature, returns a property set consisting of all component
-        subfeatures and their values. For example:
-        
-          expand_subfeatures <toolset>gcc-2.95.2-linux-x86
-              -> <toolset>gcc <toolset-version>2.95.2 <toolset-os>linux <toolset-cpu>x86
-          equivalent to:
-              expand_subfeatures gcc-2.95.2-linux-x86
-
-        feature:        The name of the feature, or empty if value corresponds to an implicit property
-        value:          The value of the feature.
-        dont_validate:  If True, no validation of value string will be done.
-    """
-    f = property.feature()
-    v = property.value()
-    if not dont_validate:
-        validate_value_string(f, v)
-
-    components = v.split ("-")
-    
-    v = components[0]
-
-    import property
-
-    result = [property.Property(f, components[0])] 
-    
-    subvalues = components[1:]
-
-    while len(subvalues) > 0:
-        subvalue = subvalues [0]    # pop the head off of subvalues
-        subvalues = subvalues [1:]
-        
-        subfeature = __find_implied_subfeature (f, subvalue, v)
-        
-        # If no subfeature was found, reconstitute the value string and use that
-        if not subfeature:
-            return [property.Property(f, '-'.join(components))]
-            
-        result.append(property.Property(subfeature, subvalue))
-    
-    return result
-
-def expand_subfeatures(properties, dont_validate = False):
-    """
-    Make all elements of properties corresponding to implicit features
-    explicit, and express all subfeature values as separate properties
-    in their own right. For example, the property
-    
-       gcc-2.95.2-linux-x86
-    
-    might expand to
-    
-      <toolset>gcc <toolset-version>2.95.2 <toolset-os>linux <toolset-cpu>x86
-
-    properties:     A sequence with elements of the form
-                    <feature>value-string or just value-string in the
-                    case of implicit features.
-  : dont_validate:  If True, no validation of value string will be done.
-    """
-    result = []
-    for p in properties:
-        # Don't expand subfeatures in subfeatures
-        if p.feature().subfeature():
-            result.append (p)
-        else:
-            result.extend(__expand_subfeatures_aux (p, dont_validate))
-
-    return result
-
-
-
-# rule extend was defined as below:
-    # Can be called three ways:
-    #
-    #    1. extend feature : values *
-    #    2. extend <feature> subfeature : values *
-    #    3. extend <feature>value-string subfeature : values *
-    #
-    # * Form 1 adds the given values to the given feature
-    # * Forms 2 and 3 add subfeature values to the given feature
-    # * Form 3 adds the subfeature values as specific to the given
-    #   property value-string.
-    #
-    #rule extend ( feature-or-property subfeature ? : values * )
-#
-# Now, the specific rule must be called, depending on the desired operation:
-#   extend_feature
-#   extend_subfeature
-
-def extend (name, values):
-    """ Adds the given values to the given feature.
-    """
-    name = add_grist (name)
-    __validate_feature (name)
-    feature = __all_features [name]
-
-    if feature.implicit():
-        for v in values:
-            if __implicit_features.has_key(v):
-                raise BaseException ("'%s' is already associated with the feature '%s'" % (v, __implicit_features [v]))
-
-            __implicit_features[v] = feature
-
-    if len (feature.values()) == 0 and len (values) > 0:
-        # This is the first value specified for this feature,
-        # take it as default value
-        feature.set_default(values[0])
-
-    feature.add_values(values)
-
-def validate_value_string (f, value_string):
-    """ Checks that value-string is a valid value-string for the given feature.
-    """
-    if f.free() or value_string in f.values():
-        return
-
-    values = [value_string]
-
-    if f.subfeatures():
-        if not value_string in f.values() and \
-               not value_string in f.subfeatures():
-            values = value_string.split('-')
-
-    # An empty value is allowed for optional features
-    if not values[0] in f.values() and \
-           (values[0] or not f.optional()):
-        raise InvalidValue ("'%s' is not a known value of feature '%s'\nlegal values: '%s'" % (values [0], feature, f.values()))
-
-    for v in values [1:]:
-        # this will validate any subfeature values in value-string
-        implied_subfeature(f, v, values[0])
-
-
-""" Extends the given subfeature with the subvalues.  If the optional
-    value-string is provided, the subvalues are only valid for the given
-    value of the feature. Thus, you could say that
-    <target-platform>mingw is specifc to <toolset>gcc-2.95.2 as follows:
-    
-          extend-subfeature toolset gcc-2.95.2 : target-platform : mingw ;
-
-    feature:        The feature whose subfeature is being extended.
-    
-    value-string:   If supplied, specifies a specific value of the
-                    main feature for which the new subfeature values
-                    are valid.
-    
-    subfeature:     The name of the subfeature.
-    
-    subvalues:      The additional values of the subfeature being defined.
-"""
-def extend_subfeature (feature_name, value_string, subfeature_name, subvalues):
-
-    feature = validate_feature(feature_name)
-    
-    if value_string:
-        validate_value_string(feature, value_string)
-
-    subfeature_name = feature_name + '-' + __get_subfeature_name (subfeature_name, value_string)
-    
-    extend(subfeature_name, subvalues) ;
-    subfeature = __all_features[subfeature_name]
-
-    if value_string == None: value_string = ''
-    
-    if not __subfeature_from_value.has_key(feature):
-        __subfeature_from_value [feature] = {}
-        
-    if not __subfeature_from_value[feature].has_key(value_string):
-        __subfeature_from_value [feature][value_string] = {}
-        
-    for subvalue in subvalues:
-        __subfeature_from_value [feature][value_string][subvalue] = subfeature
-
-@bjam_signature((["feature_name", "value_string", "?"], ["subfeature"],
-                 ["subvalues", "*"], ["attributes", "*"]))
-def subfeature (feature_name, value_string, subfeature, subvalues, attributes = []):
-    """ Declares a subfeature.
-        feature_name:   Root feature that is not a subfeature.
-        value_string:   An optional value-string specifying which feature or
-                        subfeature values this subfeature is specific to,
-                        if any.                
-        subfeature:     The name of the subfeature being declared.
-        subvalues:      The allowed values of this subfeature.
-        attributes:     The attributes of the subfeature.
-    """
-    parent_feature = validate_feature (feature_name)
-    
-    # Add grist to the subfeature name if a value-string was supplied
-    subfeature_name = __get_subfeature_name (subfeature, value_string)
-    
-    if subfeature_name in __all_features[feature_name].subfeatures():
-        message = "'%s' already declared as a subfeature of '%s'" % (subfeature, feature_name)
-        message += " specific to '%s'" % value_string
-        raise BaseException (message)
-
-    # First declare the subfeature as a feature in its own right
-    f = feature (feature_name + '-' + subfeature_name, subvalues, attributes + ['subfeature'])
-    f.set_parent(parent_feature, value_string)
-    
-    parent_feature.add_subfeature(f)
-
-    # Now make sure the subfeature values are known.
-    extend_subfeature (feature_name, value_string, subfeature, subvalues)
-
-
-@bjam_signature((["composite_property_s"], ["component_properties_s", "*"]))
-def compose (composite_property_s, component_properties_s):
-    """ Sets the components of the given composite property.
-
-    All paremeters are <feature>value strings
-    """
-    import property
-
-    component_properties_s = to_seq (component_properties_s)
-    composite_property = property.create_from_string(composite_property_s)
-    f = composite_property.feature()
-
-    if len(component_properties_s) > 0 and isinstance(component_properties_s[0], property.Property):
-        component_properties = component_properties_s
-    else:
-        component_properties = [property.create_from_string(p) for p in component_properties_s]
-                                       
-    if not f.composite():
-        raise BaseException ("'%s' is not a composite feature" % f)
-
-    if __composite_properties.has_key(property):
-        raise BaseException ('components of "%s" already set: %s' % (composite_property, str (__composite_properties[composite_property])))
-
-    if composite_property in component_properties:
-        raise BaseException ('composite property "%s" cannot have itself as a component' % composite_property)
-
-    __composite_properties[composite_property] = component_properties
-
-
-def expand_composite(property):
-    result = [ property ]
-    if __composite_properties.has_key(property):
-        for p in __composite_properties[property]:
-            result.extend(expand_composite(p))
-    return result
-
-
-def get_values (feature, properties):
-    """ Returns all values of the given feature specified by the given property set.
-    """
-    result = []
-    for p in properties:
-        if get_grist (p) == feature:
-            result.append (replace_grist (p, ''))
-    
-    return result
-
-def free_features ():
-    """ Returns all free features.
-    """
-    return __free_features
-
-def expand_composites (properties):
-    """ Expand all composite properties in the set so that all components
-        are explicitly expressed.
-    """
-    explicit_features = set(p.feature() for p in properties)
-
-    result = []
-
-    # now expand composite features
-    for p in properties:
-        expanded = expand_composite(p)
-
-        for x in expanded:
-            if not x in result:
-                f = x.feature()
-
-                if f.free():
-                    result.append (x)
-                elif not x in properties:  # x is the result of expansion
-                    if not f in explicit_features:  # not explicitly-specified
-                        if any(r.feature() == f for r in result):
-                            raise FeatureConflict(
-                                "expansions of composite features result in "
-                                "conflicting values for '%s'\nvalues: '%s'\none contributing composite property was '%s'" %
-                                (f.name(), [r.value() for r in result if r.feature() == f] + [x.value()], p))
-                        else:
-                            result.append (x)
-                elif any(r.feature() == f for r in result):
-                    raise FeatureConflict ("explicitly-specified values of non-free feature '%s' conflict\n"
-                    "existing values: '%s'\nvalue from expanding '%s': '%s'" % (f, 
-                    [r.value() for r in result if r.feature() == f], p, x.value()))
-                else:
-                    result.append (x)
-
-    return result
-
-# Uses Property
-def is_subfeature_of (parent_property, f):
-    """ Return true iff f is an ordinary subfeature of the parent_property's
-        feature, or if f is a subfeature of the parent_property's feature
-        specific to the parent_property's value.
-    """
-    if not f.subfeature():
-        return False
-
-    p = f.parent()
-    if not p:
-        return False
-
-    parent_feature = p[0]
-    parent_value = p[1]
-
-    if parent_feature != parent_property.feature():
-        return False
-
-    if parent_value and parent_value != parent_property.value():
-        return False
-
-    return True
-
-def __is_subproperty_of (parent_property, p):
-    """ As is_subfeature_of, for subproperties.
-    """
-    return is_subfeature_of (parent_property, p.feature())
-
-    
-# Returns true iff the subvalue is valid for the feature.  When the
-# optional value-string is provided, returns true iff the subvalues
-# are valid for the given value of the feature.
-def is_subvalue(feature, value_string, subfeature, subvalue):
-
-    if not value_string:
-        value_string = ''
-
-    if not __subfeature_from_value.has_key(feature):
-        return False
-        
-    if not __subfeature_from_value[feature].has_key(value_string):
-        return False
-        
-    if not __subfeature_from_value[feature][value_string].has_key(subvalue):
-        return False
-
-    if __subfeature_from_value[feature][value_string][subvalue]\
-           != subfeature:
-        return False
-
-    return True
-
-def implied_subfeature (feature, subvalue, value_string):
-    result = __find_implied_subfeature (feature, subvalue, value_string)
-    if not result:
-        raise InvalidValue ("'%s' is not a known subfeature value of '%s%s'" % (subvalue, feature, value_string))
-
-    return result
-
-
-# Uses Property
-def expand (properties):
-    """ Given a property set which may consist of composite and implicit
-        properties and combined subfeature values, returns an expanded,
-        normalized property set with all implicit features expressed
-        explicitly, all subfeature values individually expressed, and all
-        components of composite properties expanded. Non-free features
-        directly expressed in the input properties cause any values of
-        those features due to composite feature expansion to be dropped. If
-        two values of a given non-free feature are directly expressed in the
-        input, an error is issued.
-    """
-    expanded = expand_subfeatures(properties)
-    return expand_composites (expanded)
-    
-# Accepts list of Property objects
-def add_defaults (properties):
-    """ Given a set of properties, add default values for features not
-        represented in the set. 
-        Note: if there's there's ordinary feature F1 and composite feature
-        F2, which includes some value for F1, and both feature have default values,
-        then the default value of F1 will be added, not the value in F2. This might
-        not be right idea: consider
-        
-          feature variant : debug ... ;
-               <variant>debug : .... <runtime-debugging>on
-          feature <runtime-debugging> : off on ;
-          
-          Here, when adding default for an empty property set, we'll get
-        
-            <variant>debug <runtime_debugging>off
-         
-          and that's kind of strange.        
-    """
-    result = [x for x in properties]
-    
-    handled_features = set()
-    for p in properties:
-        # We don't add default for conditional properties.  We don't want
-        # <variant>debug:<define>DEBUG to be takes as specified value for <variant>
-        if not p.condition():
-            handled_features.add(p.feature())
-        
-    missing_top = [f for f in __all_top_features if not f in handled_features]    
-    more = defaults(missing_top)
-    result.extend(more)
-    for p in more:
-        handled_features.add(p.feature())
-       
-    # Add defaults for subfeatures of features which are present
-    for p in result[:]:
-        s = p.feature().subfeatures()
-        more = defaults([s for s in p.feature().subfeatures() if not s in handled_features])
-        for p in more:
-            handled_features.add(p.feature())
-        result.extend(more)
-    
-    return result
-
-def minimize (properties):
-    """ Given an expanded property set, eliminate all redundancy: properties
-        which are elements of other (composite) properties in the set will
-        be eliminated. Non-symmetric properties equal to default values will be
-        eliminated, unless the override a value from some composite property.
-        Implicit properties will be expressed without feature
-        grist, and sub-property values will be expressed as elements joined
-        to the corresponding main property.
-    """    
-    
-    # remove properties implied by composite features
-    components = []
-    for property in properties:
-        if __composite_properties.has_key (property):
-            components.extend(__composite_properties[property])
-    properties = b2.util.set.difference (properties, components)
-    
-    # handle subfeatures and implicit features
-
-    # move subfeatures to the end of the list
-    properties = [p for p in properties if not p.feature().subfeature()] +\
-        [p for p in properties if p.feature().subfeature()]
-    
-    result = []
-    while properties:
-        p = properties[0]
-        f = p.feature()
-        
-        # locate all subproperties of $(x[1]) in the property set
-        subproperties = __select_subproperties (p, properties)
-        
-        if subproperties:
-            # reconstitute the joined property name
-            subproperties.sort ()
-            joined = b2.build.property.Property(p.feature(), p.value() + '-' + '-'.join ([sp.value() for sp in subproperties]))
-            result.append(joined)
-
-            properties = b2.util.set.difference(properties[1:], subproperties)
-
-        else:
-            # eliminate properties whose value is equal to feature's
-            # default and which are not symmetric and which do not
-            # contradict values implied by composite properties.
-            
-            # since all component properties of composites in the set
-            # have been eliminated, any remaining property whose
-            # feature is the same as a component of a composite in the
-            # set must have a non-redundant value.
-            if p.value() != f.default() or f.symmetric():
-                result.append (p)
-                  #\
-                   #or get_grist (fullp) in get_grist (components):
-                   # FIXME: restore above
-                  
-
-            properties = properties[1:]
-
-    return result
-
-
-def split (properties):
-    """ Given a property-set of the form
-        v1/v2/...vN-1/<fN>vN/<fN+1>vN+1/...<fM>vM
-
-    Returns
-        v1 v2 ... vN-1 <fN>vN <fN+1>vN+1 ... <fM>vM
-
-    Note that vN...vM may contain slashes. This is resilient to the
-    substitution of backslashes for slashes, since Jam, unbidden,
-    sometimes swaps slash direction on NT.
-    """
-
-    def split_one (properties):
-        pieces = re.split (__re_slash_or_backslash, properties)
-        result = []
-        
-        for x in pieces:
-            if not get_grist (x) and len (result) > 0 and get_grist (result [-1]):
-                result = result [0:-1] + [ result [-1] + '/' + x ]
-            else:
-                result.append (x)
-        
-        return result
-
-    if isinstance (properties, str):
-        return split_one (properties)
-
-    result = []
-    for p in properties:
-        result += split_one (p)
-    return result
-    
-
-def compress_subproperties (properties):
-    """ Combine all subproperties into their parent properties
-
-        Requires: for every subproperty, there is a parent property.  All
-        features are explicitly expressed.
-        
-        This rule probably shouldn't be needed, but
-        build-request.expand-no-defaults is being abused for unintended
-        purposes and it needs help
-    """
-    result = []
-    matched_subs = set()
-    all_subs = set()
-    for p in properties:
-        f = p.feature()
-        
-        if not f.subfeature():
-            subs = __select_subproperties (p, properties)
-            if subs:
-            
-                matched_subs.update(subs)
-
-                subvalues = '-'.join (sub.value() for sub in subs)
-                result.append(b2.build.property.Property(
-                    p.feature(), p.value() + '-' + subvalues,
-                    p.condition()))
-            else:
-                result.append(p)
-
-        else:
-            all_subs.add(p)
-
-    # TODO: this variables are used just for debugging. What's the overhead?
-    assert all_subs == matched_subs
-
-    return result
-
-######################################################################################
-# Private methods
-
-def __select_subproperties (parent_property, properties):
-    return [ x for x in properties if __is_subproperty_of (parent_property, x) ]
-
-def __get_subfeature_name (subfeature, value_string):
-    if value_string == None: 
-        prefix = ''
-    else:
-        prefix = value_string + ':'
-
-    return prefix + subfeature
-
-
-def __validate_feature_attributes (name, attributes):
-    for attribute in attributes:
-        if not attribute in __all_attributes:
-            raise InvalidAttribute ("unknown attributes: '%s' in feature declaration: '%s'" % (str (b2.util.set.difference (attributes, __all_attributes)), name))
-    
-    if name in __all_features:
-            raise AlreadyDefined ("feature '%s' already defined" % name)
-    elif 'implicit' in attributes and 'free' in attributes:
-        raise InvalidAttribute ("free features cannot also be implicit (in declaration of feature '%s')" % name)
-    elif 'free' in attributes and 'propagated' in attributes:
-        raise InvalidAttribute ("free features cannot also be propagated (in declaration of feature '%s')" % name)
-
-    
-def __validate_feature (feature):
-    """ Generates an error if the feature is unknown.
-    """
-    if not __all_features.has_key (feature):
-        raise BaseException ('unknown feature "%s"' % feature)
-
-
-def __select_subfeatures (parent_property, features):
-    """ Given a property, return the subset of features consisting of all
-        ordinary subfeatures of the property's feature, and all specific
-        subfeatures of the property's feature which are conditional on the
-        property's value.
-    """
-    return [f for f in features if is_subfeature_of (parent_property, f)]
-  
-# FIXME: copy over tests.
diff --git a/jam-files/boost-build/build/generators.jam b/jam-files/boost-build/build/generators.jam
deleted file mode 100644
index 1515525f..00000000
--- a/jam-files/boost-build/build/generators.jam
+++ /dev/null
@@ -1,1408 +0,0 @@
-# Copyright Vladimir Prus 2002.
-# Copyright Rene Rivera 2006.
-#
-# Distributed under the Boost Software License, Version 1.0.
-#    (See accompanying file LICENSE_1_0.txt or copy at
-#          http://www.boost.org/LICENSE_1_0.txt)
-
-# Manages 'generators' --- objects which can do transformation between different
-# target types and contain algorithm for finding transformation from sources to
-# targets.
-#
-# The main entry point to this module is generators.construct rule. It is given
-# a list of source targets, desired target type and a set of properties. It
-# starts by selecting 'viable generators', which have any chances of producing
-# the desired target type with the required properties. Generators are ranked
-# and a set of the most specific ones is selected.
-#
-# The most specific generators have their 'run' methods called, with the
-# properties and list of sources. Each one selects a target which can be
-# directly consumed, and tries to convert the remaining ones to the types it can
-# consume. This is done by recursively calling 'construct' with all consumable
-# types.
-#
-# If the generator has collected all the targets it needs, it creates targets
-# corresponding to result, and returns it. When all generators have been run,
-# results of one of them are selected and returned as a result.
-#
-# It is quite possible for 'construct' to return more targets that it was asked
-# for. For example, if it were asked to generate a target of type EXE, but the
-# only found generator produces both EXE and TDS (file with debug) information.
-# The extra target will be returned.
-#
-# Likewise, when generator tries to convert sources to consumable types, it can
-# get more targets that it was asked for. The question is what to do with extra
-# targets. Boost.Build attempts to convert them to requested types, and attempts
-# that as early as possible. Specifically, this is done after invoking each
-# generator. TODO: An example is needed to document the rationale for trying
-# extra target conversion at that point.
-#
-# In order for the system to be able to use a specific generator instance 'when
-# needed', the instance needs to be registered with the system using
-# generators.register() or one of its related rules. Unregistered generators may
-# only be run explicitly and will not be considered by Boost.Build when when
-# converting between given target types.
-
-import "class" : new ;
-import errors ;
-import property-set ;
-import sequence ;
-import set ;
-import type ;
-import utility ;
-import virtual-target ;
-
-
-if "--debug-generators" in [ modules.peek : ARGV ]
-{
-    .debug = true ;
-}
-
-
-# Updated cached viable source target type information as needed after a new
-# target type gets defined. This is needed because if a target type is a viable
-# source target type for some generator then all of the target type's derived
-# target types should automatically be considered as viable source target types
-# for the same generator as well. Does nothing if a non-derived target type is
-# passed to it.
-#
-rule update-cached-information-with-a-new-type ( type )
-{
-    local base-type = [ type.base $(type) ] ;
-    if $(base-type)
-    {
-        for local g in $(.vstg-cached-generators)
-        {
-            if $(base-type) in $(.vstg.$(g))
-            {
-                .vstg.$(g) += $(type) ;
-            }
-        }
-
-        for local t in $(.vst-cached-types)
-        {
-            if $(base-type) in $(.vst.$(t))
-            {
-                .vst.$(t) += $(type) ;
-            }
-        }
-    }
-}
-
-
-# Clears cached viable source target type information except for target types
-# and generators with all source types listed as viable. Should be called when
-# something invalidates those cached values by possibly causing some new source
-# types to become viable.
-#
-local rule invalidate-extendable-viable-source-target-type-cache ( )
-{
-    local generators-with-cached-source-types = $(.vstg-cached-generators) ;
-    .vstg-cached-generators = ;
-    for local g in $(generators-with-cached-source-types)
-    {
-        if $(.vstg.$(g)) = *
-        {
-            .vstg-cached-generators += $(g) ;
-        }
-        else
-        {
-            .vstg.$(g) = ;
-        }
-    }
-
-    local types-with-cached-source-types = $(.vst-cached-types) ;
-    .vst-cached-types = ;
-    for local t in $(types-with-cached-source-types)
-    {
-        if $(.vst.$(t)) = *
-        {
-            .vst-cached-types += $(t) ;
-        }
-        else
-        {
-            .vst.$(t) = ;
-        }
-    }
-}
-
-
-# Outputs a debug message if generators debugging is on. Each element of
-# 'message' is checked to see if it is a class instance. If so, instead of the
-# value, the result of 'str' call is output.
-#
-local rule generators.dout ( message * )
-{
-    if $(.debug)
-    {
-        ECHO [ sequence.transform utility.str : $(message) ] ;
-    }
-}
-
-
-local rule indent ( )
-{
-    return $(.indent:J="") ;
-}
-
-
-local rule increase-indent ( )
-{
-    .indent += "    " ;
-}
-
-
-local rule decrease-indent ( )
-{
-    .indent = $(.indent[2-]) ;
-}
-
-
-# Models a generator.
-#
-class generator
-{
-    import generators : indent increase-indent decrease-indent generators.dout ;
-    import set ;
-    import utility ;
-    import feature ;
-    import errors ;
-    import sequence ;
-    import type ;
-    import virtual-target ;
-    import "class" : new ;
-    import property ;
-    import path ;
-
-    EXPORT class@generator : indent increase-indent decrease-indent
-        generators.dout ;
-
-    rule __init__ (
-        id                          # Identifies the generator - should be name
-                                    # of the rule which sets up the build
-                                    # actions.
-
-        composing ?                 # Whether generator processes each source
-                                    # target in turn, converting it to required
-                                    # types. Ordinary generators pass all
-                                    # sources together to the recursive
-                                    # generators.construct-types call.
-
-        : source-types *            # Types that this generator can handle. If
-                                    # empty, the generator can consume anything.
-
-        : target-types-and-names +  # Types the generator will create and,
-                                    # optionally, names for created targets.
-                                    # Each element should have the form
-                                    # type["(" name-pattern ")"], for example,
-                                    # obj(%_x). Generated target name will be
-                                    # found by replacing % with the name of
-                                    # source, provided an explicit name was not
-                                    # specified.
-
-        : requirements *
-    )
-    {
-        self.id = $(id) ;
-        self.rule-name = $(id) ;
-        self.composing = $(composing) ;
-        self.source-types = $(source-types) ;
-        self.target-types-and-names = $(target-types-and-names) ;
-        self.requirements = $(requirements) ;
-
-        for local e in $(target-types-and-names)
-        {
-            # Create three parallel lists: one with the list of target types,
-            # and two other with prefixes and postfixes to be added to target
-            # name. We use parallel lists for prefix and postfix (as opposed to
-            # mapping), because given target type might occur several times, for
-            # example "H H(%_symbols)".
-            local m = [ MATCH ([^\\(]*)(\\((.*)%(.*)\\))? : $(e) ] ;
-            self.target-types += $(m[1]) ;
-            self.name-prefix += $(m[3]:E="") ;
-            self.name-postfix += $(m[4]:E="") ;
-        }
-
-        # Note that 'transform' here, is the same as 'for_each'.
-        sequence.transform type.validate : $(self.source-types) ;
-        sequence.transform type.validate : $(self.target-types) ;
-    }
-
-    ################# End of constructor #################
-
-    rule id ( )
-    {
-        return $(self.id) ;
-    }
-
-    # Returns the list of target type the generator accepts.
-    #
-    rule source-types ( )
-    {
-        return $(self.source-types) ;
-    }
-
-    # Returns the list of target types that this generator produces. It is
-    # assumed to be always the same -- i.e. it can not change depending on some
-    # provided list of sources.
-    #
-    rule target-types ( )
-    {
-        return $(self.target-types) ;
-    }
-
-    # Returns the required properties for this generator. Properties in returned
-    # set must be present in build properties if this generator is to be used.
-    # If result has grist-only element, that build properties must include some
-    # value of that feature.
-    #
-    # XXX: remove this method?
-    #
-    rule requirements ( )
-    {
-        return $(self.requirements) ;
-    }
-    
-    rule set-rule-name ( rule-name )
-    {
-        self.rule-name = $(rule-name) ;
-    }
-    
-    rule rule-name ( )
-    {
-        return $(self.rule-name) ;
-    }
-        
-    # Returns a true value if the generator can be run with the specified
-    # properties.
-    #
-    rule match-rank ( property-set-to-match )
-    {
-        # See if generator requirements are satisfied by 'properties'. Treat a
-        # feature name in requirements (i.e. grist-only element), as matching
-        # any value of the feature.
-        local all-requirements = [ requirements ] ;
-
-        local property-requirements feature-requirements ;
-        for local r in $(all-requirements)
-        {
-            if $(r:G=)
-            {
-                property-requirements += $(r) ;
-            }
-            else
-            {
-                feature-requirements += $(r) ;
-            }
-        }
-
-        local properties-to-match = [ $(property-set-to-match).raw ] ;
-        if $(property-requirements) in $(properties-to-match) &&
-            $(feature-requirements) in $(properties-to-match:G)
-        {
-            return true ;
-        }
-        else
-        {
-            return ;
-        }
-    }
-
-    # Returns another generator which differs from $(self) in
-    #   - id
-    #   - value to <toolset> feature in properties
-    #
-    rule clone ( new-id : new-toolset-properties + )
-    {
-        local g = [ new $(__class__) $(new-id) $(self.composing) :
-            $(self.source-types) : $(self.target-types-and-names) :
-            # Note: this does not remove any subfeatures of <toolset> which
-            # might cause problems.
-            [ property.change $(self.requirements) : <toolset> ]
-            $(new-toolset-properties) ] ;       
-        return $(g) ;
-    }
-
-    # Creates another generator that is the same as $(self), except that if
-    # 'base' is in target types of $(self), 'type' will in target types of the
-    # new generator.
-    #
-    rule clone-and-change-target-type ( base : type )
-    {
-        local target-types ;
-        for local t in $(self.target-types-and-names)
-        {
-            local m = [ MATCH ([^\\(]*)(\\(.*\\))? : $(t) ] ;
-            if $(m) = $(base)
-            {
-                target-types += $(type)$(m[2]:E="") ;
-            }
-            else
-            {
-                target-types += $(t) ;
-            }
-        }
-
-        local g = [ new $(__class__) $(self.id) $(self.composing) :
-            $(self.source-types) : $(target-types) : $(self.requirements) ] ;
-        if $(self.rule-name)
-        {            
-            $(g).set-rule-name $(self.rule-name) ;
-        }        
-        return $(g) ;        
-    }
-
-    # Tries to invoke this generator on the given sources. Returns a list of
-    # generated targets (instances of 'virtual-target') and optionally a set of
-    # properties to be added to the usage-requirements for all the generated
-    # targets. Returning nothing from run indicates that the generator was
-    # unable to create the target.
-    #
-    rule run
-    (
-        project         # Project for which the targets are generated.
-        name ?          # Used when determining the 'name' attribute for all
-                        # generated targets. See the 'generated-targets' method.
-        : property-set  # Desired properties for generated targets.
-        : sources +     # Source targets.
-    )
-    {
-        generators.dout [ indent ] "  ** generator" $(self.id) ;
-        generators.dout [ indent ] "  composing:" $(self.composing) ;
-
-        if ! $(self.composing) && $(sources[2]) && $(self.source-types[2])
-        {
-            errors.error "Unsupported source/source-type combination" ;
-        }
-
-        # We do not run composing generators if no name is specified. The reason
-        # is that composing generator combines several targets, which can have
-        # different names, and it cannot decide which name to give for produced
-        # target. Therefore, the name must be passed.
-        #
-        # This in effect, means that composing generators are runnable only at
-        # the top-level of a transformation graph, or if their name is passed
-        # explicitly. Thus, we dissallow composing generators in the middle. For
-        # example, the transformation CPP -> OBJ -> STATIC_LIB -> RSP -> EXE
-        # will not be allowed as the OBJ -> STATIC_LIB generator is composing.
-        if ! $(self.composing) || $(name)
-        {
-            run-really $(project) $(name) : $(property-set) : $(sources) ;
-        }
-    }
-
-    rule run-really ( project name ? : property-set : sources + )
-    {
-        # Targets that this generator will consume directly.
-        local consumed = ;
-        # Targets that can not be consumed and will be returned as-is.
-        local bypassed = ;
-
-        if $(self.composing)
-        {
-            convert-multiple-sources-to-consumable-types $(project)
-                : $(property-set) : $(sources) : consumed bypassed ;
-        }
-        else
-        {
-            convert-to-consumable-types $(project) $(name) : $(property-set)
-                : $(sources) : : consumed bypassed ;
-        }
-
-        local result ;
-        if $(consumed)
-        {
-            result = [ construct-result $(consumed) : $(project) $(name) :
-                $(property-set) ] ;
-        }
-
-        if $(result)
-        {
-            generators.dout [ indent ] "  SUCCESS: " $(result) ;
-        }
-        else
-        {
-            generators.dout [ indent ] "  FAILURE" ;
-        }
-        generators.dout ;
-        return $(result) ;
-    }
-
-    # Constructs the dependency graph to be returned by this generator.
-    #
-    rule construct-result
-    (
-        consumed +        # Already prepared list of consumable targets.
-                          # Composing generators may receive multiple sources
-                          # all of which will have types matching those in
-                          # $(self.source-types). Non-composing generators with
-                          # multiple $(self.source-types) will receive exactly
-                          # len $(self.source-types) sources with types matching
-                          # those in $(self.source-types). And non-composing
-                          # generators with only a single source type may
-                          # receive multiple sources with all of them of the
-                          # type listed in $(self.source-types).
-        : project name ?
-        : property-set    # Properties to be used for all actions created here.
-    )
-    {
-        local result ;
-        # If this is 1->1 transformation, apply it to all consumed targets in
-        # order.
-        if ! $(self.source-types[2]) && ! $(self.composing)
-        {
-            for local r in $(consumed)
-            {
-                result += [ generated-targets $(r) : $(property-set) :
-                    $(project) $(name) ] ;
-            }
-        }
-        else if $(consumed)
-        {
-            result += [ generated-targets $(consumed) : $(property-set) :
-                $(project) $(name) ] ;
-        }
-        return $(result) ;
-    }
-
-    # Determine target name from fullname (maybe including path components)
-    # Place optional prefix and postfix around basename
-    #
-    rule determine-target-name ( fullname  : prefix ? : postfix ? )
-    {
-        # See if we need to add directory to the target name.
-        local dir  = $(fullname:D) ;            
-        local name = $(fullname:B) ; 
-        
-        name = $(prefix:E=)$(name) ;
-        name = $(name)$(postfix:E=) ;
-
-        if $(dir) && 
-          # Never append '..' to target path.
-          ! [ MATCH .*(\\.\\.).* : $(dir) ] 
-            && 
-          ! [ path.is-rooted $(dir) ]
-        {
-            # Relative path is always relative to the source
-            # directory. Retain it, so that users can have files
-            # with the same in two different subdirectories.
-            name = $(dir)/$(name) ;                
-        }            
-        return $(name) ;
-    }
-
-    # Determine the name of the produced target from the names of the sources.
-    #
-    rule determine-output-name ( sources + )
-    {
-        # The simple case if when a name of source has single dot. Then, we take
-        # the part before dot. Several dots can be caused by:
-        #   - using source file like a.host.cpp, or
-        #   - a type whose suffix has a dot. Say, we can type 'host_cpp' with
-        #     extension 'host.cpp'.
-        # In the first case, we want to take the part up to the last dot. In the
-        # second case -- not sure, but for now take the part up to the last dot
-        # too.
-        name = [ utility.basename [ $(sources[1]).name ] ] ;
-
-        for local s in $(sources[2])
-        {
-            local n2 = [ utility.basename [ $(s).name ] ] ;
-            if $(n2) != $(name)
-            {
-                errors.error "$(self.id): source targets have different names: cannot determine target name" ;
-            }
-        }
-        name = [ determine-target-name [ $(sources[1]).name ] ] ;
-        return $(name) ;
-    }
-
-    # Constructs targets that are created after consuming 'sources'. The result
-    # will be the list of virtual-target, which has the same length as the
-    # 'target-types' attribute and with corresponding types.
-    #
-    # When 'name' is empty, all source targets must have the same 'name'
-    # attribute value, which will be used instead of the 'name' argument.
-    #
-    # The 'name' attribute value for each generated target will be equal to
-    # the 'name' parameter if there is no name pattern for this type. Otherwise,
-    # the '%' symbol in the name pattern will be replaced with the 'name'
-    # parameter to obtain the 'name' attribute.
-    #
-    # For example, if targets types are T1 and T2 (with name pattern "%_x"),
-    # suffixes for T1 and T2 are .t1 and .t2, and source is foo.z, then created
-    # files would be "foo.t1" and "foo_x.t2". The 'name' attribute actually
-    # determines the basename of a file.
-    #
-    # Note that this pattern mechanism has nothing to do with implicit patterns
-    # in make. It is a way to produce a target whose name is different than the
-    # name of its source.
-    #
-    rule generated-targets ( sources + : property-set : project name ? )
-    {
-        if ! $(name)
-        {
-            name = [ determine-output-name $(sources) ] ;
-        }
-
-        # Assign an action for each target.
-        local action = [ action-class ] ;
-        local a = [ class.new $(action) $(sources) : $(self.rule-name) :
-                    $(property-set) ] ;
-
-        # Create generated target for each target type.
-        local targets ;
-        local pre = $(self.name-prefix) ;
-        local post = $(self.name-postfix) ;
-        for local t in $(self.target-types)
-        {
-            local generated-name = $(pre[1])$(name:BS)$(post[1]) ;
-            generated-name = $(generated-name:R=$(name:D)) ;
-            pre = $(pre[2-]) ;
-            post = $(post[2-]) ;
-
-            targets += [ class.new file-target $(generated-name) : $(t) :
-                $(project) : $(a) ] ;
-        }
-
-        return [ sequence.transform virtual-target.register : $(targets) ] ;
-    }
-
-    # Attempts to convert 'sources' to targets of types that this generator can
-    # handle. The intention is to produce the set of targets that can be used
-    # when the generator is run.
-    #
-    rule convert-to-consumable-types
-    (
-        project name ?
-        : property-set
-        : sources +
-        : only-one ?    # Convert 'source' to only one of the source types. If
-                        # there is more that one possibility, report an error.
-        : consumed-var  # Name of the variable which receives all targets which
-                        # can be consumed.
-          bypassed-var  # Name of the variable which receives all targets which
-                        # can not be consumed.
-    )
-    {
-        # We are likely to be passed 'consumed' and 'bypassed' var names. Use
-        # '_' to avoid name conflicts.
-        local _consumed ;
-        local _bypassed ;
-        local missing-types ;
-
-        if $(sources[2])
-        {
-            # Do not know how to handle several sources yet. Just try to pass
-            # the request to other generator.
-            missing-types = $(self.source-types) ;
-        }
-        else
-        {
-            consume-directly $(sources) : _consumed : missing-types ;
-        }
-
-        # No need to search for transformation if some source type has consumed
-        # source and no more source types are needed.
-        if $(only-one) && $(_consumed)
-        {
-            missing-types = ;
-        }
-
-        # TODO: we should check that only one source type if create of
-        # 'only-one' is true.
-        # TODO: consider if consumed/bypassed separation should be done by
-        # 'construct-types'.
-
-        if $(missing-types)
-        {
-            local transformed = [ generators.construct-types $(project) $(name)
-                : $(missing-types) : $(property-set) : $(sources) ] ;
-
-            # Add targets of right type to 'consumed'. Add others to 'bypassed'.
-            # The 'generators.construct' rule has done its best to convert
-            # everything to the required type. There is no need to rerun it on
-            # targets of different types.
-
-            # NOTE: ignoring usage requirements.
-            for local t in $(transformed[2-])
-            {
-                if [ $(t).type ] in $(missing-types)
-                {
-                    _consumed += $(t) ;
-                }
-                else
-                {
-                    _bypassed += $(t) ;
-                }
-            }
-        }
-
-        _consumed = [ sequence.unique $(_consumed) ] ;
-        _bypassed = [ sequence.unique $(_bypassed) ] ;
-
-        # Remove elements of '_bypassed' that are in '_consumed'.
-
-        # Suppose the target type of current generator, X is produced from X_1
-        # and X_2, which are produced from Y by one generator. When creating X_1
-        # from Y, X_2 will be added to 'bypassed'. Likewise, when creating X_2
-        # from Y, X_1 will be added to 'bypassed', but they are also in
-        # 'consumed'. We have to remove them from bypassed, so that generators
-        # up the call stack do not try to convert them.
-
-        # In this particular case, X_1 instance in 'consumed' and X_1 instance
-        # in 'bypassed' will be the same: because they have the same source and
-        # action name, and 'virtual-target.register' will not allow two
-        # different instances. Therefore, it is OK to use 'set.difference'.
-
-        _bypassed = [ set.difference $(_bypassed) : $(_consumed) ] ;
-
-        $(consumed-var) += $(_consumed) ;
-        $(bypassed-var) += $(_bypassed) ;
-    }
-
-    # Converts several files to consumable types. Called for composing
-    # generators only.
-    #
-    rule convert-multiple-sources-to-consumable-types ( project : property-set :
-        sources * : consumed-var bypassed-var )
-    {
-        # We process each source one-by-one, trying to convert it to a usable
-        # type.
-        for local source in $(sources)
-        {
-            local _c ;
-            local _b ;
-            # TODO: need to check for failure on each source.
-            convert-to-consumable-types $(project) : $(property-set) : $(source)
-                : true : _c _b ;
-            if ! $(_c)
-            {
-                generators.dout [ indent ] " failed to convert " $(source) ;
-            }
-            $(consumed-var) += $(_c) ;
-            $(bypassed-var) += $(_b) ;
-        }
-    }
-
-    rule consume-directly ( source : consumed-var : missing-types-var )
-    {
-        local real-source-type = [ $(source).type ] ;
-
-        # If there are no source types, we can consume anything.
-        local source-types = $(self.source-types) ;
-        source-types ?= $(real-source-type) ;
-
-        for local st in $(source-types)
-        {
-            # The 'source' if of the right type already.
-            if $(real-source-type) = $(st) || [ type.is-derived
-                $(real-source-type) $(st) ]
-            {
-                $(consumed-var) += $(source) ;
-            }
-            else
-            {
-                $(missing-types-var) += $(st) ;
-            }
-        }
-    }
-
-    # Returns the class to be used to actions. Default implementation returns
-    # "action".
-    #
-    rule action-class ( )
-    {
-        return "action" ;
-    }
-}
-
-
-# Registers a new generator instance 'g'.
-#
-rule register ( g )
-{
-    .all-generators += $(g) ;
-        
-    # A generator can produce several targets of the same type. We want unique
-    # occurrence of that generator in .generators.$(t) in that case, otherwise,
-    # it will be tried twice and we will get a false ambiguity.
-    for local t in [ sequence.unique [ $(g).target-types ] ]
-    {
-        .generators.$(t) += $(g) ;
-    }
-
-    # Update the set of generators for toolset.
-
-    # TODO: should we check that generator with this id is not already
-    # registered. For example, the fop.jam module intentionally declared two
-    # generators with the same id, so such check will break it.
-    local id = [ $(g).id ] ;
-
-    # Some generators have multiple periods in their name, so a simple $(id:S=)
-    # will not generate the right toolset name. E.g. if id = gcc.compile.c++,
-    # then .generators-for-toolset.$(id:S=) will append to
-    # .generators-for-toolset.gcc.compile, which is a separate value from
-    # .generators-for-toolset.gcc. Correcting this makes generator inheritance
-    # work properly. See also inherit-generators in the toolset module.
-    local base = $(id) ;
-    while $(base:S)
-    {
-        base = $(base:B) ;
-    }
-    .generators-for-toolset.$(base) += $(g) ;
-
-
-    # After adding a new generator that can construct new target types, we need
-    # to clear the related cached viable source target type information for
-    # constructing a specific target type or using a specific generator. Cached
-    # viable source target type lists affected by this are those containing any
-    # of the target types constructed by the new generator or any of their base
-    # target types.
-    #
-    # A more advanced alternative to clearing that cached viable source target
-    # type information would be to expand it with additional source types or
-    # even better - mark it as needing to be expanded on next use.
-    #
-    # Also see the http://thread.gmane.org/gmane.comp.lib.boost.build/19077
-    # mailing list thread for an even more advanced idea of how we could convert
-    # Boost Build's Jamfile processing, target selection and generator selection
-    # into separate steps which would prevent these caches from ever being
-    # invalidated.
-    #
-    # For now we just clear all the cached viable source target type information
-    # that does not simply state 'all types' and may implement a more detailed
-    # algorithm later on if it becomes needed.
-
-    invalidate-extendable-viable-source-target-type-cache ;
-}
-
-
-# Creates a new non-composing 'generator' class instance and registers it.
-# Returns the created instance. Rationale: the instance is returned so that it
-# is possible to first register a generator and then call its 'run' method,
-# bypassing the whole generator selection process.
-#
-rule register-standard ( id : source-types * : target-types + : requirements * )
-{
-    local g = [ new generator $(id) : $(source-types) : $(target-types) :
-        $(requirements) ] ;
-    register $(g) ;
-    return $(g) ;
-}
-
-
-# Creates a new composing 'generator' class instance and registers it.
-#
-rule register-composing ( id : source-types * : target-types + : requirements *
-    )
-{
-    local g = [ new generator $(id) true : $(source-types) : $(target-types) :
-        $(requirements) ] ;
-    register $(g) ;
-    return $(g) ;
-}
-
-
-# Returns all generators belonging to the given 'toolset', i.e. whose ids are
-# '$(toolset).<something>'.
-#
-rule generators-for-toolset ( toolset )
-{
-    return $(.generators-for-toolset.$(toolset)) ;
-}
-
-
-# Make generator 'overrider-id' be preferred to 'overridee-id'. If, when
-# searching for generators that could produce a target of a certain type, both
-# those generators are among viable generators, the overridden generator is
-# immediately discarded.
-#
-# The overridden generators are discarded immediately after computing the list
-# of viable generators but before running any of them.
-#
-rule override ( overrider-id : overridee-id )
-{
-    .override.$(overrider-id) += $(overridee-id) ;
-}
-
-
-# Returns a list of source type which can possibly be converted to 'target-type'
-# by some chain of generator invocation.
-#
-# More formally, takes all generators for 'target-type' and returns a union of
-# source types for those generators and result of calling itself recursively on
-# source types.
-#
-# Returns '*' in case any type should be considered a viable source type for the
-# given type.
-#
-local rule viable-source-types-real ( target-type )
-{
-    local result ;
-
-    # 't0' is the initial list of target types we need to process to get a list
-    # of their viable source target types. New target types will not be added to
-    # this list.
-    local t0 = [ type.all-bases $(target-type) ] ;
-
-    # 't' is the list of target types which have not yet been processed to get a
-    # list of their viable source target types. This list will get expanded as
-    # we locate more target types to process.
-    local t = $(t0) ;
-
-    while $(t)
-    {
-        # Find all generators for the current type. Unlike
-        # 'find-viable-generators' we do not care about the property-set.
-        local generators = $(.generators.$(t[1])) ;
-        t = $(t[2-]) ;
-
-        while $(generators)
-        {
-            local g = $(generators[1]) ;
-            generators = $(generators[2-]) ;
-
-            if ! [ $(g).source-types ]
-            {
-                # Empty source types -- everything can be accepted.
-                result = * ;
-                # This will terminate this loop.
-                generators = ;
-                # This will terminate the outer loop.
-                t = ;
-            }
-
-            for local source-type in [ $(g).source-types ]
-            {
-                if ! $(source-type) in $(result)
-                {
-                    # If a generator accepts a 'source-type' it will also
-                    # happily accept any type derived from it.
-                    for local n in [ type.all-derived $(source-type) ]
-                    {
-                        if ! $(n) in $(result)
-                        {
-                            # Here there is no point in adding target types to
-                            # the list of types to process in case they are or
-                            # have already been on that list. We optimize this
-                            # check by realizing that we only need to avoid the
-                            # original target type's base types. Other target
-                            # types that are or have been on the list of target
-                            # types to process have been added to the 'result'
-                            # list as well and have thus already been eliminated
-                            # by the previous if.
-                            if ! $(n) in $(t0)
-                            {
-                                t += $(n) ;
-                            }
-                            result += $(n) ;
-                        }
-                    }
-                }
-            }
-        }
-    }
-
-    return $(result) ;
-}
-
-
-# Helper rule, caches the result of 'viable-source-types-real'.
-#
-rule viable-source-types ( target-type )
-{
-    local key = .vst.$(target-type) ;
-    if ! $($(key))
-    {
-        .vst-cached-types += $(target-type) ;
-        local v = [ viable-source-types-real $(target-type) ] ;
-        if ! $(v)
-        {
-            v = none ;
-        }
-        $(key) = $(v) ;
-    }
-
-    if $($(key)) != none
-    {
-        return $($(key)) ;
-    }
-}
-
-
-# Returns the list of source types, which, when passed to 'run' method of
-# 'generator', has some change of being eventually used (probably after
-# conversion by other generators).
-#
-# Returns '*' in case any type should be considered a viable source type for the
-# given generator.
-#
-rule viable-source-types-for-generator-real ( generator )
-{
-    local source-types = [ $(generator).source-types ] ;
-    if ! $(source-types)
-    {
-        # If generator does not specify any source types, it might be a special
-        # generator like builtin.lib-generator which just relays to other
-        # generators. Return '*' to indicate that any source type is possibly
-        # OK, since we do not know for sure.
-        return * ;
-    }
-    else
-    {
-        local result ;
-        while $(source-types)
-        {
-            local s = $(source-types[1]) ;
-            source-types = $(source-types[2-]) ;
-            local viable-sources = [ generators.viable-source-types $(s) ] ;
-            if $(viable-sources) = *
-            {
-                result = * ;
-                source-types = ;  # Terminate the loop.
-            }
-            else
-            {
-                result += [ type.all-derived $(s) ] $(viable-sources) ;
-            }
-        }
-        return [ sequence.unique $(result) ] ;
-    }
-}
-
-
-# Helper rule, caches the result of 'viable-source-types-for-generator'.
-#
-local rule viable-source-types-for-generator ( generator )
-{
-    local key = .vstg.$(generator) ;
-    if ! $($(key))
-    {
-        .vstg-cached-generators += $(generator) ;
-        local v = [ viable-source-types-for-generator-real $(generator) ] ;
-        if ! $(v)
-        {
-            v = none ;
-        }
-        $(key) = $(v) ;
-    }
-
-    if $($(key)) != none
-    {
-        return $($(key)) ;
-    }
-}
-
-
-# Returns usage requirements + list of created targets.
-#
-local rule try-one-generator-really ( project name ? : generator : target-type
-    : property-set : sources * )
-{
-    local targets =
-        [ $(generator).run $(project) $(name) : $(property-set) : $(sources) ] ;
-
-    local usage-requirements ;
-    local success ;
-
-    generators.dout [ indent ] returned $(targets) ;
-
-    if $(targets)
-    {
-        success = true ;
-
-        if  [ class.is-a $(targets[1]) : property-set ]
-        {
-            usage-requirements = $(targets[1]) ;
-            targets = $(targets[2-]) ;
-        }
-        else
-        {
-            usage-requirements = [ property-set.empty ] ;
-        }
-    }
-
-    generators.dout [ indent ] "  generator" [ $(generator).id ] " spawned " ;
-    generators.dout [ indent ] " " $(targets) ;
-    if $(usage-requirements)
-    {
-        generators.dout [ indent ] "  with usage requirements:" $(x) ;
-    }
-
-    if $(success)
-    {
-        return $(usage-requirements) $(targets) ;
-    }
-}
-
-
-# Checks if generator invocation can be pruned, because it is guaranteed to
-# fail. If so, quickly returns an empty list. Otherwise, calls
-# try-one-generator-really.
-#
-local rule try-one-generator ( project name ? : generator : target-type
-    : property-set : sources * )
-{
-    local source-types ;
-    for local s in $(sources)
-    {
-        source-types += [ $(s).type ] ;
-    }
-    local viable-source-types = [ viable-source-types-for-generator $(generator)
-        ] ;
-
-    if  $(source-types) && $(viable-source-types) != * &&
-        ! [ set.intersection $(source-types) : $(viable-source-types) ]
-    {
-        local id = [ $(generator).id ] ;
-        generators.dout [ indent ] "  ** generator '$(id)' pruned" ;
-        #generators.dout [ indent ] "source-types" '$(source-types)' ;
-        #generators.dout [ indent ] "viable-source-types" '$(viable-source-types)' ;
-    }
-    else
-    {
-        return [ try-one-generator-really $(project) $(name) : $(generator) :
-            $(target-type) : $(property-set) : $(sources) ] ;
-    }
-}
-
-
-rule construct-types ( project name ? : target-types + : property-set
-    : sources + )
-{
-    local result ;
-    local matched-types ;
-    local usage-requirements = [ property-set.empty ] ;
-    for local t in $(target-types)
-    {
-        local r = [ construct $(project) $(name) : $(t) : $(property-set) :
-            $(sources) ] ;
-        if $(r)
-        {
-            usage-requirements = [ $(usage-requirements).add $(r[1]) ] ;
-            result += $(r[2-]) ;
-            matched-types += $(t) ;
-        }
-    }
-    # TODO: have to introduce parameter controlling if several types can be
-    # matched and add appropriate checks.
-
-    # TODO: need to review the documentation for 'construct' to see if it should
-    # return $(source) even if nothing can be done with it. Currents docs seem
-    # to imply that, contrary to the behaviour.
-    if $(result)
-    {
-        return $(usage-requirements) $(result) ;
-    }
-    else
-    {
-        return $(usage-requirements) $(sources) ;
-    }
-}
-
-
-# Ensures all 'targets' have their type. If this is not so, exists with error.
-#
-local rule ensure-type ( targets * )
-{
-    for local t in $(targets)
-    {
-        if ! [ $(t).type ]
-        {
-            errors.error "target" [ $(t).str ] "has no type" ;
-        }
-    }
-}
-
-
-# Returns generators which can be used to construct target of specified type
-# with specified properties. Uses the following algorithm:
-# - iterates over requested target-type and all its bases (in the order returned
-#   by type.all-bases).
-# - for each type find all generators that generate that type and whose
-#   requirements are satisfied by properties.
-# - if the set of generators is not empty, returns that set.
-#
-# Note: this algorithm explicitly ignores generators for base classes if there
-# is at least one generator for the requested target-type.
-#
-local rule find-viable-generators-aux ( target-type : property-set )
-{
-    # Select generators that can create the required target type.
-    local viable-generators = ;
-    local generator-rank = ;
-
-    import type ;
-    local t = [ type.all-bases $(target-type) ] ;
-
-    generators.dout [ indent ] find-viable-generators target-type= $(target-type)
-        property-set= [ $(property-set).as-path ] ;
-
-    # Get the list of generators for the requested type. If no generator is
-    # registered, try base type, and so on.
-    local generators ;
-    while $(t[1])
-    {
-        generators.dout [ indent ] "trying type" $(t[1]) ;
-        if $(.generators.$(t[1]))
-        {
-            generators.dout [ indent ] "there are generators for this type" ;
-            generators = $(.generators.$(t[1])) ;
-
-            if $(t[1]) != $(target-type)
-            {
-                # We are here because there were no generators found for
-                # target-type but there are some generators for its base type.
-                # We will try to use them, but they will produce targets of
-                # base type, not of 'target-type'. So, we clone the generators
-                # and modify the list of target types.
-                local generators2 ;
-                for local g in $(generators)
-                {
-                    # generators.register adds a generator to the list of
-                    # generators for toolsets, which is a bit strange, but
-                    # should work. That list is only used when inheriting a
-                    # toolset, which should have been done before running
-                    # generators.
-                    generators2 += [ $(g).clone-and-change-target-type $(t[1]) :
-                        $(target-type) ] ;
-                    generators.register $(generators2[-1]) ;
-                }
-                generators = $(generators2) ;
-            }
-            t = ;
-        }
-        t = $(t[2-]) ;
-    }
-
-    for local g in $(generators)
-    {
-        generators.dout [ indent ] "trying generator" [ $(g).id ] "(" [ $(g).source-types ] -> [ $(g).target-types ] ")" ;
-
-        local m = [ $(g).match-rank $(property-set) ] ;
-        if $(m)
-        {
-            generators.dout [ indent ] "  is viable" ;
-            viable-generators += $(g) ;
-        }
-    }
-
-    return $(viable-generators) ;
-}
-
-
-rule find-viable-generators ( target-type : property-set )
-{
-    local key = $(target-type).$(property-set) ;
-    local l = $(.fv.$(key)) ;
-    if ! $(l)
-    {
-        l = [ find-viable-generators-aux $(target-type) : $(property-set) ] ;
-        if ! $(l)
-        {
-            l = none ;
-        }
-        .fv.$(key) = $(l) ;
-    }
-
-    if $(l) = none
-    {
-        l = ;
-    }
-
-    local viable-generators ;
-    for local g in $(l)
-    {
-        # Avoid trying the same generator twice on different levels.
-        if ! $(g) in $(.active-generators)
-        {
-            viable-generators += $(g) ;
-        }
-        else
-        {
-            generators.dout [ indent ] "   generator " [ $(g).id ] "is active, discaring" ;
-        }        
-    }
-
-    # Generators which override 'all'.
-    local all-overrides ;
-    # Generators which are overriden.
-    local overriden-ids ;
-    for local g in $(viable-generators)
-    {
-        local id = [ $(g).id ] ;
-        local this-overrides = $(.override.$(id)) ;
-        overriden-ids += $(this-overrides) ;
-        if all in $(this-overrides)
-        {
-            all-overrides += $(g) ;
-        }
-    }
-    if $(all-overrides)
-    {
-        viable-generators = $(all-overrides) ;
-    }
-    local result ;
-    for local g in $(viable-generators)
-    {
-        if ! [ $(g).id ] in $(overriden-ids)
-        {
-            result += $(g) ;
-        }
-    }
-
-    return $(result) ;
-}
-
-
-.construct-stack = ;
-
-
-# Attempts to construct a target by finding viable generators, running them and
-# selecting the dependency graph.
-#
-local rule construct-really ( project name ? : target-type : property-set :
-    sources * )
-{
-    viable-generators = [ find-viable-generators $(target-type) :
-        $(property-set) ] ;
-
-    generators.dout [ indent ] "*** " [ sequence.length $(viable-generators) ]
-        " viable generators" ;
-
-    local result ;
-    local generators-that-succeeded ;
-    for local g in $(viable-generators)
-    {
-        # This variable will be restored on exit from this scope.
-        local .active-generators = $(g) $(.active-generators) ;
-
-        local r = [ try-one-generator $(project) $(name) : $(g) : $(target-type)
-            : $(property-set) : $(sources) ] ;
-
-        if $(r)
-        {
-            generators-that-succeeded += $(g) ;
-            if $(result)
-            {
-                ECHO "Error: ambiguity found when searching for best transformation" ;
-                ECHO "Trying to produce type '$(target-type)' from: " ;
-                for local s in $(sources)
-                {
-                    ECHO " - " [ $(s).str ] ;
-                }
-                ECHO "Generators that succeeded:" ;
-                for local g in $(generators-that-succeeded)
-                {
-                    ECHO " - " [ $(g).id ] ;
-                }
-                ECHO "First generator produced: " ;
-                for local t in $(result[2-])
-                {
-                    ECHO " - " [ $(t).str ] ;
-                }
-                ECHO "Second generator produced: " ;
-                for local t in $(r[2-])
-                {
-                    ECHO " - " [ $(t).str ] ;
-                }
-                EXIT ;
-            }
-            else
-            {
-                result = $(r) ;
-            }
-        }
-    }
-
-    return $(result) ;
-}
-
-
-# Attempts to create a target of 'target-type' with 'properties' from 'sources'.
-# The 'sources' are treated as a collection of *possible* ingridients, i.e.
-# there is no obligation to consume them all.
-#
-# Returns a list of targets. When this invocation is first instance of
-# 'construct' in stack, returns only targets of requested 'target-type',
-# otherwise, returns also unused sources and additionally generated targets.
-#
-# If 'top-level' is set, does not suppress generators that are already
-# used in the stack. This may be useful in cases where a generator
-# has to build a metatargets -- for example a target corresponding to
-# built tool.
-#
-rule construct ( project name ? : target-type : property-set * : sources * : top-level ? )
-{
-    local saved-stack ;
-    if $(top-level)
-    {
-        saved-active = $(.active-generators) ;
-        .active-generators = ;
-    }
-        
-    if (.construct-stack)
-    {
-        ensure-type $(sources) ;
-    }
-
-    .construct-stack += 1 ;
-
-    increase-indent ;
-
-    if $(.debug)
-    {
-        generators.dout [ indent ] "*** construct" $(target-type) ;
-
-        for local s in $(sources)
-        {
-            generators.dout [ indent ] "    from" $(s) ;
-        }
-        generators.dout [ indent ] "    properties:" [ $(property-set).raw ] ;
-    }
-
-    local result = [ construct-really $(project) $(name) : $(target-type) :
-        $(property-set) : $(sources) ] ;
-
-    decrease-indent ;
-
-    .construct-stack = $(.construct-stack[2-]) ;
-    
-    if $(top-level)
-    {
-        .active-generators = $(saved-active) ;
-    }
-
-    return $(result) ;
-}
-
-# Given 'result', obtained from some generator or generators.construct, adds
-# 'raw-properties' as usage requirements to it. If result already contains usage
-# requirements -- that is the first element of result of an instance of the
-# property-set class, the existing usage requirements and 'raw-properties' are
-# combined.
-#
-rule add-usage-requirements ( result * : raw-properties * )
-{
-    if $(result)
-    {
-        if [ class.is-a $(result[1]) : property-set ]
-        {
-            return [ $(result[1]).add-raw $(raw-properties) ] $(result[2-]) ;
-        }
-        else
-        {
-            return [ property-set.create $(raw-properties) ] $(result) ;
-        }
-    }
-}
-
-rule dump ( )
-{
-    for local g in $(.all-generators)
-    {
-        ECHO [ $(g).id ] ":" [ $(g).source-types ] -> [ $(g).target-types ] ;            
-    }    
-}
-
diff --git a/jam-files/boost-build/build/generators.py b/jam-files/boost-build/build/generators.py
deleted file mode 100644
index 2c59f7ca..00000000
--- a/jam-files/boost-build/build/generators.py
+++ /dev/null
@@ -1,1089 +0,0 @@
-# Status: being ported by Vladimir Prus
-# Base revision: 48649
-# TODO: replace the logging with dout
-
-# Copyright Vladimir Prus 2002.
-# Copyright Rene Rivera 2006.
-#
-# Distributed under the Boost Software License, Version 1.0.
-#    (See accompanying file LICENSE_1_0.txt or copy at
-#          http://www.boost.org/LICENSE_1_0.txt)
-
-#  Manages 'generators' --- objects which can do transformation between different
-#  target types and contain algorithm for finding transformation from sources
-#  to targets.
-#
-#  The main entry point to this module is generators.construct rule. It is given
-#  a list of source targets, desired target type and a set of properties.
-#  It starts by selecting 'viable generators', which have any chances of producing
-#  the desired target type with the required properties. Generators are ranked and
-#  a set of most specific ones is selected.
-# 
-#  The most specific generators have their 'run' methods called, with the properties
-#  and list of sources. Each one selects target which can be directly consumed, and
-#  tries to convert the remaining ones to the types it can consume. This is done
-#  by recursively calling 'construct' with all consumable types.
-#
-#  If the generator has collected all the targets it needs, it creates targets 
-#  corresponding to result, and returns it. When all generators have been run,
-#  results of one of them are selected and returned as result.
-#
-#  It's quite possible that 'construct' returns more targets that it was asked for.
-#  For example, it was asked to target type EXE, but the only found generators produces
-#  both EXE and TDS (file with debug) information. The extra target will be returned.
-#
-#  Likewise, when generator tries to convert sources to consumable types, it can get
-#  more targets that it was asked for. The question is what to do with extra targets.
-#  Boost.Build attempts to convert them to requested types, and attempts as early as
-#  possible. Specifically, this is done after invoking each generator. (Later I'll 
-#  document the rationale for trying extra target conversion at that point).
-#
-#  That early conversion is not always desirable. Suppose a generator got a source of
-#  type Y and must consume one target of type X_1 and one target of type X_2.
-#  When converting Y to X_1 extra target of type Y_2 is created. We should not try to
-#  convert it to type X_1, because if we do so, the generator will get two targets
-#  of type X_1, and will be at loss as to which one to use. Because of that, the
-#  'construct' rule has a parameter, telling if multiple targets can be returned. If
-#  the parameter is false, conversion of extra targets is not performed.
-
-
-import re
-import cStringIO
-import os.path
-
-from virtual_target import Subvariant
-import virtual_target, type, property_set, property
-from b2.util.logger import *
-from b2.util.utility import *
-from b2.util import set
-from b2.util.sequence import unique
-import b2.util.sequence as sequence
-from b2.manager import get_manager
-import b2.build.type
-
-def reset ():
-    """ Clear the module state. This is mainly for testing purposes.
-    """
-    global __generators, __type_to_generators, __generators_for_toolset, __construct_stack
-    global __overrides, __active_generators
-    global __viable_generators_cache, __viable_source_types_cache
-    global __vstg_cached_generators, __vst_cached_types
-
-    __generators = {}
-    __type_to_generators = {}
-    __generators_for_toolset = {}
-    __overrides = {}
-    
-    # TODO: can these be global? 
-    __construct_stack = []
-    __viable_generators_cache = {}
-    __viable_source_types_cache = {}
-    __active_generators = []
-
-    __vstg_cached_generators = []
-    __vst_cached_types = []
-
-reset ()
-
-_re_separate_types_prefix_and_postfix = re.compile ('([^\\(]*)(\\((.*)%(.*)\\))?')
-_re_match_type = re.compile('([^\\(]*)(\\(.*\\))?')
-
-
-__debug = None
-__indent = ""
-
-def debug():
-    global __debug
-    if __debug is None:
-        __debug = "--debug-generators" in bjam.variable("ARGV")        
-    return __debug
-
-def increase_indent():
-    global __indent
-    __indent += "    "
-
-def decrease_indent():
-    global __indent
-    __indent = __indent[0:-4]
-
-
-# Updated cached viable source target type information as needed after a new
-# derived target type gets added. This is needed because if a target type is a
-# viable source target type for some generator then all of the target type's
-# derived target types are automatically viable as source target types for the
-# same generator. Does nothing if a non-derived target type is passed to it.
-#
-def update_cached_information_with_a_new_type(type):
-
-    base_type = b2.build.type.base(type)
-
-    if base_type:
-        for g in __vstg_cached_generators:
-            if base_type in __viable_source_types_cache.get(g, []):
-                __viable_source_types_cache[g].append(type)
-
-        for t in __vst_cached_types:
-            if base_type in __viable_source_types_cache.get(t, []):
-                __viable_source_types_cache[t].append(type)
-
-# Clears cached viable source target type information except for target types
-# and generators with all source types listed as viable. Should be called when
-# something invalidates those cached values by possibly causing some new source
-# types to become viable.
-#
-def invalidate_extendable_viable_source_target_type_cache():
-
-    global __vstg_cached_generators
-    generators_with_cached_source_types = __vstg_cached_generators
-    __vstg_cached_generators = []
-
-    for g in generators_with_cached_source_types:
-        if __viable_source_types_cache.has_key(g):
-            if __viable_source_types_cache[g] == ["*"]:
-                __vstg_cached_generators.append(g)
-            else:
-                del __viable_source_types_cache[g]
-
-    global __vst_cached_types
-    types_with_cached_sources_types = __vst_cached_types
-    __vst_cached_types = []
-    for t in types_with_cached_sources_types:
-        if __viable_source_types_cache.has_key(t):
-            if __viable_source_types_cache[t] == ["*"]:
-                __vst_cached_types.append(t)
-            else:
-                del __viable_source_types_cache[t]
- 
-def dout(message):
-    if debug():
-        print __indent + message
-
-class Generator:
-    """ Creates a generator.
-            manager:                 the build manager.
-            id:                      identifies the generator
-            
-            rule:                    the rule which sets up build actions.
-
-            composing:               whether generator processes each source target in
-                                     turn, converting it to required types.
-                                     Ordinary generators pass all sources together to
-                                     recusrive generators.construct_types call.
-
-            source_types (optional): types that this generator can handle
-    
-            target_types_and_names:  types the generator will create and, optionally, names for
-                                     created targets. Each element should have the form
-                                         type["(" name-pattern ")"]
-                                     for example, obj(%_x). Name of generated target will be found
-                                     by replacing % with the name of source, provided explicit name
-                                     was not specified.
-    
-            requirements (optional)
-            
-            NOTE: all subclasses must have a similar signature for clone to work!
-    """
-    def __init__ (self, id, composing, source_types, target_types_and_names, requirements = []):
-        assert(not isinstance(source_types, str))
-        assert(not isinstance(target_types_and_names, str))
-        self.id_ = id
-        self.composing_ = composing
-        self.source_types_ = source_types
-        self.target_types_and_names_ = target_types_and_names
-        self.requirements_ = requirements
-        
-        self.target_types_ = []
-        self.name_prefix_ = []
-        self.name_postfix_ = []
-        
-        for e in target_types_and_names:
-            # Create three parallel lists: one with the list of target types,
-            # and two other with prefixes and postfixes to be added to target 
-            # name. We use parallel lists for prefix and postfix (as opposed
-            # to mapping), because given target type might occur several times,
-            # for example "H H(%_symbols)".
-            m = _re_separate_types_prefix_and_postfix.match (e)
-            
-            if not m:
-                raise BaseException ("Invalid type and name '%s' in declaration of type '%s'" % (e, id))
-            
-            target_type = m.group (1)
-            if not target_type: target_type = ''
-            prefix = m.group (3)
-            if not prefix: prefix = ''
-            postfix = m.group (4)
-            if not postfix: postfix = ''
-            
-            self.target_types_.append (target_type)
-            self.name_prefix_.append (prefix)
-            self.name_postfix_.append (postfix)
-
-        for x in self.source_types_:
-            type.validate (x)
-
-        for x in self.target_types_:
-            type.validate (x)
-
-    def clone (self, new_id, new_toolset_properties):
-        """ Returns another generator which differers from $(self) in
-              - id
-              - value to <toolset> feature in properties
-        """
-        return self.__class__ (new_id, 
-                               self.composing_, 
-                               self.source_types_, 
-                               self.target_types_and_names_,
-                               # Note: this does not remove any subfeatures of <toolset>
-                               # which might cause problems
-                               property.change (self.requirements_, '<toolset>') + new_toolset_properties)
-
-    def clone_and_change_target_type(self, base, type):
-        """Creates another generator that is the same as $(self), except that
-        if 'base' is in target types of $(self), 'type' will in target types
-        of the new generator."""
-        target_types = []
-        for t in self.target_types_and_names_:
-            m = _re_match_type.match(t)
-            assert m
-            
-            if m.group(1) == base:
-                if m.group(2):
-                    target_types.append(type + m.group(2))
-                else:
-                    target_types.append(type)
-            else:
-                target_types.append(t)
-
-        return self.__class__(self.id_, self.composing_,
-                              self.source_types_,
-                              target_types,
-                              self.requirements_)
-                              
-
-    def id(self):
-        return self.id_
-
-    def source_types (self):
-        """ Returns the list of target type the generator accepts.
-        """
-        return self.source_types_
-
-    def target_types (self):
-        """ Returns the list of target types that this generator produces.
-            It is assumed to be always the same -- i.e. it cannot change depending
-            list of sources.    
-        """
-        return self.target_types_
-
-    def requirements (self):
-        """ Returns the required properties for this generator. Properties
-            in returned set must be present in build properties if this 
-            generator is to be used. If result has grist-only element,
-            that build properties must include some value of that feature.
-        """
-        return self.requirements_
-
-    def match_rank (self, ps):
-        """ Returns true if the generator can be run with the specified 
-            properties.
-        """
-        # See if generator's requirements are satisfied by
-        # 'properties'.  Treat a feature name in requirements
-        # (i.e. grist-only element), as matching any value of the
-        # feature.
-        all_requirements = self.requirements ()
-        
-        property_requirements = []
-        feature_requirements = []
-        # This uses strings because genenator requirements allow
-        # the '<feature>' syntax without value and regular validation
-        # is not happy about that.
-        for r in all_requirements:
-            if get_value (r):
-                property_requirements.append (r)
-
-            else:
-                feature_requirements.append (r)
-                
-        return all(ps.get(get_grist(s)) == [get_value(s)] for s in property_requirements) \
-               and all(ps.get(get_grist(s)) for s in feature_requirements)
-        
-    def run (self, project, name, prop_set, sources):
-        """ Tries to invoke this generator on the given sources. Returns a
-            list of generated targets (instances of 'virtual-target').
-
-            project:        Project for which the targets are generated.
-            
-            name:           Determines the name of 'name' attribute for 
-                            all generated targets. See 'generated_targets' method.
-                            
-            prop_set:       Desired properties for generated targets.
-            
-            sources:        Source targets.
-        """
-        
-        if project.manager ().logger ().on ():
-            project.manager ().logger ().log (__name__, "  generator '%s'" % self.id_)
-            project.manager ().logger ().log (__name__, "  composing: '%s'" % self.composing_)
-        
-        if not self.composing_ and len (sources) > 1 and len (self.source_types_) > 1:
-            raise BaseException ("Unsupported source/source_type combination")
-                
-        # We don't run composing generators if no name is specified. The reason
-        # is that composing generator combines several targets, which can have
-        # different names, and it cannot decide which name to give for produced
-        # target. Therefore, the name must be passed.
-        #
-        # This in effect, means that composing generators are runnable only
-        # at top-level of transofrmation graph, or if name is passed explicitly.
-        # Thus, we dissallow composing generators in the middle. For example, the
-        # transofrmation CPP -> OBJ -> STATIC_LIB -> RSP -> EXE won't be allowed 
-        # (the OBJ -> STATIC_LIB generator is composing)
-        if not self.composing_ or name:
-            return self.run_really (project, name, prop_set, sources)
-        else:
-            return []
-
-    def run_really (self, project, name, prop_set, sources):
-
-        # consumed: Targets that this generator will consume directly.
-        # bypassed: Targets that can't be consumed and will be returned as-is.
-        
-        if self.composing_:
-            (consumed, bypassed) = self.convert_multiple_sources_to_consumable_types (project, prop_set, sources)
-        else:
-            (consumed, bypassed) = self.convert_to_consumable_types (project, name, prop_set, sources)
-                
-        result = []
-        if consumed:
-            result = self.construct_result (consumed, project, name, prop_set)
-            result.extend (bypassed)
-
-        if result:
-            if project.manager ().logger ().on ():
-                project.manager ().logger ().log (__name__, "  SUCCESS: ", result)
-
-        else:
-                project.manager ().logger ().log (__name__, "  FAILURE")
-
-        return result
-
-    def construct_result (self, consumed, project, name, prop_set):
-        """ Constructs the dependency graph that will be returned by this 
-            generator.
-                consumed:        Already prepared list of consumable targets
-                                 If generator requires several source files will contain 
-                                 exactly len $(self.source_types_) targets with matching types
-                                 Otherwise, might contain several targets with the type of 
-                                 self.source_types_ [0]
-                project:
-                name:
-                prop_set:        Properties to be used for all actions create here
-        """
-        result = []
-        # If this is 1->1 transformation, apply it to all consumed targets in order.
-        if len (self.source_types_) < 2 and not self.composing_:
-
-            for r in consumed:
-                result.extend (self.generated_targets ([r], prop_set, project, name))
-
-        else:
-
-            if consumed:
-                result.extend (self.generated_targets (consumed, prop_set, project, name))
-
-        return result
-
-    def determine_target_name(self, fullname):
-        # Determine target name from fullname (maybe including path components)
-        # Place optional prefix and postfix around basename
-
-        dir = os.path.dirname(fullname)
-        name = os.path.basename(fullname)
-
-        if dir and not ".." in dir and not os.path.isabs(dir):
-            # Relative path is always relative to the source
-            # directory. Retain it, so that users can have files
-            # with the same in two different subdirectories.
-            name = dir + "/" + name
-
-        return name
-
-    def determine_output_name(self, sources):
-        """Determine the name of the produced target from the
-        names of the sources."""
-        
-        # The simple case if when a name
-        # of source has single dot. Then, we take the part before
-        # dot. Several dots can be caused by:
-        # - Using source file like a.host.cpp
-        # - A type which suffix has a dot. Say, we can
-        #   type 'host_cpp' with extension 'host.cpp'.
-        # In the first case, we want to take the part till the last
-        # dot. In the second case -- no sure, but for now take
-        # the part till the last dot too.
-        name = os.path.splitext(sources[0].name())[0]
-                        
-        for s in sources[1:]:
-            n2 = os.path.splitext(s.name())
-            if n2 != name:
-                get_manager().errors()(
-                    "%s: source targets have different names: cannot determine target name"
-                    % (self.id_))
-                        
-        # Names of sources might include directory. We should strip it.
-        return self.determine_target_name(sources[0].name())
-        
-        
-    def generated_targets (self, sources, prop_set, project, name):
-        """ Constructs targets that are created after consuming 'sources'.
-            The result will be the list of virtual-target, which the same length
-            as 'target_types' attribute and with corresponding types.
-            
-            When 'name' is empty, all source targets must have the same value of 
-            the 'name' attribute, which will be used instead of the 'name' argument.
-            
-            The value of 'name' attribute for each generated target will be equal to
-            the 'name' parameter if there's no name pattern for this type. Otherwise,
-            the '%' symbol in the name pattern will be replaced with the 'name' parameter 
-            to obtain the 'name' attribute.
-            
-            For example, if targets types are T1 and T2(with name pattern "%_x"), suffixes
-            for T1 and T2 are .t1 and t2, and source if foo.z, then created files would
-            be "foo.t1" and "foo_x.t2". The 'name' attribute actually determined the
-            basename of a file.
-            
-            Note that this pattern mechanism has nothing to do with implicit patterns
-            in make. It's a way to produce target which name is different for name of 
-            source.
-        """
-        if not name:
-            name = self.determine_output_name(sources)
-        
-        # Assign an action for each target
-        action = self.action_class()
-        a = action(project.manager(), sources, self.id_, prop_set)
-                
-        # Create generated target for each target type.
-        targets = []
-        pre = self.name_prefix_
-        post = self.name_postfix_
-        for t in self.target_types_:
-            basename = os.path.basename(name)
-            idx = basename.find(".")
-            if idx != -1:
-                basename = basename[:idx]
-            generated_name = pre[0] + basename + post[0]
-            generated_name = os.path.join(os.path.dirname(name), generated_name)
-            pre = pre[1:]
-            post = post[1:]
-            
-            targets.append(virtual_target.FileTarget(generated_name, t, project, a))
-        
-        return [ project.manager().virtual_targets().register(t) for t in targets ]
-
-    def convert_to_consumable_types (self, project, name, prop_set, sources, only_one=False):
-        """ Attempts to convert 'source' to the types that this generator can
-            handle. The intention is to produce the set of targets can should be
-            used when generator is run.
-            only_one:   convert 'source' to only one of source types
-                        if there's more that one possibility, report an
-                        error.
-                        
-            Returns a pair:
-                consumed: all targets that can be consumed. 
-                bypassed: all targets that cannot be consumed.
-        """
-        consumed = []
-        bypassed = []
-        missing_types = [] 
-
-        if len (sources) > 1:
-            # Don't know how to handle several sources yet. Just try 
-            # to pass the request to other generator
-            missing_types = self.source_types_
-
-        else:
-            (c, m) = self.consume_directly (sources [0])
-            consumed += c
-            missing_types += m
-        
-        # No need to search for transformation if
-        # some source type has consumed source and
-        # no more source types are needed.
-        if only_one and consumed:
-            missing_types = []
-            
-        #TODO: we should check that only one source type
-        #if create of 'only_one' is true.
-        # TODO: consider if consuned/bypassed separation should
-        # be done by 'construct_types'.
-                    
-        if missing_types:
-            transformed = construct_types (project, name, missing_types, prop_set, sources)
-                                
-            # Add targets of right type to 'consumed'. Add others to
-            # 'bypassed'. The 'generators.construct' rule has done
-            # its best to convert everything to the required type.
-            # There's no need to rerun it on targets of different types.
-                
-            # NOTE: ignoring usage requirements
-            for t in transformed[1]:
-                if t.type() in missing_types:
-                    consumed.append(t)
-
-                else:
-                    bypassed.append(t)
-        
-        consumed = unique(consumed)
-        bypassed = unique(bypassed)
-        
-        # remove elements of 'bypassed' that are in 'consumed'
-        
-        # Suppose the target type of current generator, X is produced from 
-        # X_1 and X_2, which are produced from Y by one generator.
-        # When creating X_1 from Y, X_2 will be added to 'bypassed'
-        # Likewise, when creating X_2 from Y, X_1 will be added to 'bypassed'
-        # But they are also in 'consumed'. We have to remove them from
-        # bypassed, so that generators up the call stack don't try to convert
-        # them. 
-
-        # In this particular case, X_1 instance in 'consumed' and X_1 instance
-        # in 'bypassed' will be the same: because they have the same source and
-        # action name, and 'virtual-target.register' won't allow two different
-        # instances. Therefore, it's OK to use 'set.difference'.
-        
-        bypassed = set.difference(bypassed, consumed)
-
-        return (consumed, bypassed)
-    
-
-    def convert_multiple_sources_to_consumable_types (self, project, prop_set, sources):
-        """ Converts several files to consumable types.
-        """        
-        consumed = []
-        bypassed = []
-
-        # We process each source one-by-one, trying to convert it to
-        # a usable type.
-        for s in sources:
-            # TODO: need to check for failure on each source.
-            (c, b) = self.convert_to_consumable_types (project, None, prop_set, [s], True)
-            if not c:
-                project.manager ().logger ().log (__name__, " failed to convert ", s)
-
-            consumed.extend (c)
-            bypassed.extend (b)
-
-        return (consumed, bypassed)
-
-    def consume_directly (self, source):
-        real_source_type = source.type ()
-
-        # If there are no source types, we can consume anything
-        source_types = self.source_types()
-        if not source_types:
-            source_types = [real_source_type]            
-
-        consumed = []
-        missing_types = []
-        for st in source_types:
-            # The 'source' if of right type already)
-            if real_source_type == st or type.is_derived (real_source_type, st):
-                consumed.append (source)
-
-            else:
-               missing_types.append (st)
-
-        return (consumed, missing_types)
-    
-    def action_class (self):
-        """ Returns the class to be used to actions. Default implementation 
-            returns "action".
-        """
-        return virtual_target.Action
-
-
-def find (id):
-    """ Finds the generator with id. Returns None if not found.
-    """
-    return __generators.get (id, None)
-
-def register (g):
-    """ Registers new generator instance 'g'.
-    """
-    id = g.id()
-
-    __generators [id] = g
-
-    # A generator can produce several targets of the
-    # same type. We want unique occurence of that generator
-    # in .generators.$(t) in that case, otherwise, it will
-    # be tried twice and we'll get false ambiguity.
-    for t in sequence.unique(g.target_types()):
-        __type_to_generators.setdefault(t, []).append(g)
-
-    # Update the set of generators for toolset
-
-    # TODO: should we check that generator with this id
-    # is not already registered. For example, the fop.jam
-    # module intentionally declared two generators with the
-    # same id, so such check will break it.
-
-    # Some generators have multiple periods in their name, so the
-    # normal $(id:S=) won't generate the right toolset name.
-    # e.g. if id = gcc.compile.c++, then
-    # .generators-for-toolset.$(id:S=) will append to
-    # .generators-for-toolset.gcc.compile, which is a separate
-    # value from .generators-for-toolset.gcc. Correcting this
-    # makes generator inheritance work properly.
-    # See also inherit-generators in module toolset
-    base = id.split ('.', 100) [0]
-
-    __generators_for_toolset.setdefault(base, []).append(g)
-
-    # After adding a new generator that can construct new target types, we need
-    # to clear the related cached viable source target type information for
-    # constructing a specific target type or using a specific generator. Cached
-    # viable source target type lists affected by this are those containing any
-    # of the target types constructed by the new generator or any of their base
-    # target types.
-    #
-    # A more advanced alternative to clearing that cached viable source target
-    # type information would be to expand it with additional source types or
-    # even better - mark it as needing to be expanded on next use.
-    #
-    # For now we just clear all the cached viable source target type information
-    # that does not simply state 'all types' and may implement a more detailed
-    # algorithm later on if it becomes needed.
-
-    invalidate_extendable_viable_source_target_type_cache()
-
-
-def register_standard (id, source_types, target_types, requirements = []):
-    """ Creates new instance of the 'generator' class and registers it.
-        Returns the creates instance.
-        Rationale: the instance is returned so that it's possible to first register
-        a generator and then call 'run' method on that generator, bypassing all
-        generator selection.
-    """
-    g = Generator (id, False, source_types, target_types, requirements)
-    register (g)
-    return g
-
-def register_composing (id, source_types, target_types, requirements = []):
-    g = Generator (id, True, source_types, target_types, requirements)
-    register (g)
-    return g
-
-def generators_for_toolset (toolset):
-    """ Returns all generators which belong to 'toolset'.
-    """
-    return __generators_for_toolset.get(toolset, [])
-
-def override (overrider_id, overridee_id):
-    """Make generator 'overrider-id' be preferred to
-    'overridee-id'. If, when searching for generators
-    that could produce a target of certain type,
-    both those generators are amoung viable generators,
-    the overridden generator is immediately discarded.
-    
-    The overridden generators are discarded immediately
-    after computing the list of viable generators, before
-    running any of them."""
-    
-    __overrides.get(overrider_id, []).append(overridee_id)
-
-def __viable_source_types_real (target_type):
-    """ Returns a list of source type which can possibly be converted
-        to 'target_type' by some chain of generator invocation.
-        
-        More formally, takes all generators for 'target_type' and
-        returns union of source types for those generators and result
-        of calling itself recusrively on source types.
-    """
-    generators = []
-
-    # 't0' is the initial list of target types we need to process to get a list
-    # of their viable source target types. New target types will not be added to
-    # this list.         
-    t0 = type.all_bases (target_type)
-
-
-    # 't' is the list of target types which have not yet been processed to get a
-    # list of their viable source target types. This list will get expanded as
-    # we locate more target types to process.
-    t = t0
-    
-    result = []
-    while t:
-        # Find all generators for current type. 
-        # Unlike 'find_viable_generators' we don't care about prop_set.
-        generators = __type_to_generators.get (t [0], [])
-        t = t[1:]
-        
-        for g in generators:
-            if not g.source_types():
-                # Empty source types -- everything can be accepted
-                result = "*"
-                # This will terminate outer loop.
-                t = None
-                break
-            
-            for source_type in g.source_types ():
-                if not source_type in result:
-                    # If generator accepts 'source_type' it
-                    # will happily accept any type derived from it
-                    all = type.all_derived (source_type)
-                    for n in all:
-                        if not n in result:
-
-                            # Here there is no point in adding target types to
-                            # the list of types to process in case they are or
-                            # have already been on that list. We optimize this
-                            # check by realizing that we only need to avoid the
-                            # original target type's base types. Other target
-                            # types that are or have been on the list of target
-                            # types to process have been added to the 'result'
-                            # list as well and have thus already been eliminated
-                            # by the previous if.
-                            if not n in t0:
-                                t.append (n)
-                            result.append (n)
-           
-    return result
-
-
-def viable_source_types (target_type):
-    """ Helper rule, caches the result of '__viable_source_types_real'.
-    """
-    if not __viable_source_types_cache.has_key(target_type):
-        __vst_cached_types.append(target_type)
-        __viable_source_types_cache [target_type] = __viable_source_types_real (target_type)
-    return __viable_source_types_cache [target_type]
-
-def viable_source_types_for_generator_real (generator):
-    """ Returns the list of source types, which, when passed to 'run'
-        method of 'generator', has some change of being eventually used
-        (probably after conversion by other generators)
-    """
-    source_types = generator.source_types ()
-
-    if not source_types:
-        # If generator does not specify any source types,
-        # it might be special generator like builtin.lib-generator
-        # which just relays to other generators. Return '*' to
-        # indicate that any source type is possibly OK, since we don't
-        # know for sure.
-        return ['*']
-
-    else:
-        result = []
-        for s in source_types:
-            viable_sources = viable_source_types(s)
-            if viable_sources == "*":
-                result = ["*"]
-                break
-            else:
-                result.extend(type.all_derived(s) + viable_sources)
-        return unique(result)
-
-def viable_source_types_for_generator (generator):
-    """ Caches the result of 'viable_source_types_for_generator'.
-    """
-    if not __viable_source_types_cache.has_key(generator):
-        __vstg_cached_generators.append(generator)
-        __viable_source_types_cache[generator] = viable_source_types_for_generator_real (generator)
-    
-    return __viable_source_types_cache[generator]
-
-def try_one_generator_really (project, name, generator, target_type, properties, sources):
-    """ Returns usage requirements + list of created targets.
-    """
-    targets = generator.run (project, name, properties, sources)
-
-    usage_requirements = []
-    success = False
-
-    dout("returned " + str(targets))
-
-    if targets:
-        success = True;
-        
-        if isinstance (targets[0], property_set.PropertySet):
-            usage_requirements = targets [0]
-            targets = targets [1]
-
-        else:
-            usage_requirements = property_set.empty ()
-
-    dout(  "  generator" + generator.id() + " spawned ")
-    #    generators.dout [ indent ] " " $(targets) ; 
-#    if $(usage-requirements)
-#    {
-#        generators.dout [ indent ] "  with usage requirements:" $(x) ;
-#    }
-
-    if success:
-        return (usage_requirements, targets)
-    else:
-        return None
-
-def try_one_generator (project, name, generator, target_type, properties, sources):
-    """ Checks if generator invocation can be pruned, because it's guaranteed
-        to fail. If so, quickly returns empty list. Otherwise, calls
-        try_one_generator_really.
-    """
-    source_types = []
-
-    for s in sources:
-        source_types.append (s.type ())
-
-    viable_source_types = viable_source_types_for_generator (generator)
-    
-    if source_types and viable_source_types != ['*'] and\
-           not set.intersection (source_types, viable_source_types):
-        if project.manager ().logger ().on ():
-            id = generator.id ()            
-            project.manager ().logger ().log (__name__, "generator '%s' pruned" % id)
-            project.manager ().logger ().log (__name__, "source_types" '%s' % source_types)
-            project.manager ().logger ().log (__name__, "viable_source_types '%s'" % viable_source_types)
-        
-        return []
-
-    else:
-        return try_one_generator_really (project, name, generator, target_type, properties, sources)
-
-
-def construct_types (project, name, target_types, prop_set, sources):
-    
-    result = []
-    usage_requirements = property_set.empty()
-    
-    for t in target_types:
-        r = construct (project, name, t, prop_set, sources)
-
-        if r:
-            (ur, targets) = r
-            usage_requirements = usage_requirements.add(ur)
-            result.extend(targets)
-
-    # TODO: have to introduce parameter controlling if
-    # several types can be matched and add appropriate
-    # checks 
-
-    # TODO: need to review the documentation for
-    # 'construct' to see if it should return $(source) even
-    # if nothing can be done with it. Currents docs seem to
-    # imply that, contrary to the behaviour.
-    if result:
-        return (usage_requirements, result)
-
-    else:
-        return (usage_requirements, sources)
-
-def __ensure_type (targets):
-    """ Ensures all 'targets' have types. If this is not so, exists with 
-        error.
-    """
-    for t in targets:
-        if not t.type ():
-            get_manager().errors()("target '%s' has no type" % str (t))
-
-def find_viable_generators_aux (target_type, prop_set):
-    """ Returns generators which can be used to construct target of specified type
-        with specified properties. Uses the following algorithm:
-        - iterates over requested target_type and all it's bases (in the order returned bt
-          type.all-bases.
-        - for each type find all generators that generate that type and which requirements
-          are satisfied by properties.
-        - if the set of generators is not empty, returns that set.
-        
-        Note: this algorithm explicitly ignores generators for base classes if there's
-        at least one generator for requested target_type.
-    """
-    # Select generators that can create the required target type.
-    viable_generators = []
-    initial_generators = []
-
-    import type
-
-    # Try all-type generators first. Assume they have
-    # quite specific requirements.
-    all_bases = type.all_bases(target_type)
-        
-    for t in all_bases:
-        
-        initial_generators = __type_to_generators.get(t, [])
-        
-        if initial_generators:
-            dout("there are generators for this type")
-            if t != target_type:
-                # We're here, when no generators for target-type are found,
-                # but there are some generators for a base type.
-                # We'll try to use them, but they will produce targets of
-                # base type, not of 'target-type'. So, we clone the generators
-                # and modify the list of target types.
-                generators2 = []
-                for g in initial_generators[:]:
-                    # generators.register adds generator to the list of generators
-                    # for toolsets, which is a bit strange, but should work.
-                    # That list is only used when inheriting toolset, which
-                    # should have being done before generators are run.
-                    ng = g.clone_and_change_target_type(t, target_type)
-                    generators2.append(ng)
-                    register(ng)
-                    
-                initial_generators = generators2
-            break
-    
-    for g in initial_generators:
-        dout("trying generator " + g.id()
-             + "(" + str(g.source_types()) + "->" + str(g.target_types()) + ")")
-        
-        m = g.match_rank(prop_set)
-        if m:
-            dout("  is viable")
-            viable_generators.append(g)            
-                            
-    return viable_generators
-
-def find_viable_generators (target_type, prop_set):
-    key = target_type + '.' + str (prop_set)
-
-    l = __viable_generators_cache.get (key, None)
-    if not l:
-        l = []
-
-    if not l:
-        l = find_viable_generators_aux (target_type, prop_set)
-
-        __viable_generators_cache [key] = l
-
-    viable_generators = []
-    for g in l:
-        # Avoid trying the same generator twice on different levels.
-        # TODO: is this really used?
-        if not g in __active_generators:
-            viable_generators.append (g)
-        else:
-            dout("      generator %s is active, discarding" % g.id())
-
-    # Generators which override 'all'.
-    all_overrides = []
-    
-    # Generators which are overriden
-    overriden_ids = [] 
-       
-    for g in viable_generators:
-        id = g.id ()
-        
-        this_overrides = __overrides.get (id, [])
-        
-        if this_overrides:
-            overriden_ids.extend (this_overrides)
-            if 'all' in this_overrides:
-                all_overrides.append (g)
-
-    if all_overrides:
-        viable_generators = all_overrides
-
-    result = []
-    for g in viable_generators:
-        if not g.id () in overriden_ids:
-            result.append (g)
-
-        
-    return result
-    
-def __construct_really (project, name, target_type, prop_set, sources):
-    """ Attempts to construct target by finding viable generators, running them
-        and selecting the dependency graph.
-    """
-    viable_generators = find_viable_generators (target_type, prop_set)
-                    
-    result = []
-
-    project.manager ().logger ().log (__name__, "*** %d viable generators" % len (viable_generators))
-
-    generators_that_succeeded = []
-    
-    for g in viable_generators:
-        __active_generators.append(g)        
-        r = try_one_generator (project, name, g, target_type, prop_set, sources)
-        del __active_generators[-1]
-        
-        if r:
-            generators_that_succeeded.append(g)
-            if result:
-                output = cStringIO.StringIO()
-                print >>output, "ambiguity found when searching for best transformation"
-                print >>output, "Trying to produce type '%s' from: " % (target_type)
-                for s in sources:
-                    print >>output, " - " + s.str()
-                print >>output, "Generators that succeeded:"
-                for g in generators_that_succeeded:
-                    print >>output, " - " + g.id()
-                print >>output, "First generator produced: "
-                for t in result[1:]:
-                    print >>output, " - " + str(t)
-                print >>output, "Second generator produced:"
-                for t in r[1:]:
-                    print >>output, " - " + str(t)
-                get_manager().errors()(output.getvalue())
-            else:
-                result = r;
-            
-    return result;
-
-
-def construct (project, name, target_type, prop_set, sources, top_level=False):
-    """ Attempts to create target of 'target-type' with 'properties'
-        from 'sources'. The 'sources' are treated as a collection of
-        *possible* ingridients -- i.e. it is not required to consume
-        them all. If 'multiple' is true, the rule is allowed to return
-        several targets of 'target-type'.          
-        
-        Returns a list of target. When this invocation is first instance of
-        'construct' in stack, returns only targets of requested 'target-type',
-        otherwise, returns also unused sources and additionally generated
-        targets.
-        
-        If 'top-level' is set, does not suppress generators that are already
-        used in the stack. This may be useful in cases where a generator
-        has to build a metatarget -- for example a target corresponding to
-        built tool.        
-    """
-
-    global __active_generators
-    if top_level:
-        saved_active = __active_generators
-        __active_generators = []
-
-    global __construct_stack
-    if not __construct_stack:
-        __ensure_type (sources)
-        
-    __construct_stack.append (1)
-
-    if project.manager().logger().on():
-        increase_indent ()
-        
-        dout( "*** construct " + target_type)
-        
-        for s in sources:
-            dout("    from " + str(s))
-
-        project.manager().logger().log (__name__, "    properties: ", prop_set.raw ())
-             
-    result = __construct_really(project, name, target_type, prop_set, sources)
-
-    project.manager().logger().decrease_indent()
-        
-    __construct_stack = __construct_stack [1:]
-
-    if top_level:
-        __active_generators = saved_active
-
-    return result
-    
diff --git a/jam-files/boost-build/build/modifiers.jam b/jam-files/boost-build/build/modifiers.jam
deleted file mode 100644
index 6b009343..00000000
--- a/jam-files/boost-build/build/modifiers.jam
+++ /dev/null
@@ -1,232 +0,0 @@
-# Copyright 2003 Rene Rivera
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-# Modifiers are generalized generators that mutate targets in specific ways.
-# This structure allows for grouping a variety of functionality in an
-# orthogonal way to the functionality in toolsets, and without specifying
-# more target variations. In turn the modifiers can be used as building
-# blocks to implement simple requests, like the <version> feature.
-
-import modules ;
-import feature ;
-import errors ;
-import type ;
-import "class" : new ;
-import generators ;
-import property ;
-import virtual-target ;
-import numbers ;
-import sequence ;
-import symlink ;
-import property-set ;
-
-# Base generator for creating targets that are modifications of existing
-# targets.
-#
-class modifier : generator
-{
-    rule __init__ (
-        id
-        composing ?
-        : source-types *
-        : target-types-and-names +
-        : requirements *
-        )
-    {
-        generator.__init__ $(id) $(composing)
-            : $(source-types)
-            : $(target-types-and-names)
-            : $(requirements) ;
-
-        self.targets-in-progress = ;
-    }
-
-    # Wraps the generation of the target to call before and after rules to
-    # affect the real target.
-    #
-    rule run ( project name ? : property-set : sources + )
-    {
-        local result ;
-        local current-target = $(project)^$(name) ;
-        if ! $(current-target) in $(self.targets-in-progress)
-        {
-            # Before modifications...
-            local project_ =
-                [ modify-project-before
-                    $(project) $(name) : $(property-set) : $(sources) ] ;
-            local name_ =
-                [ modify-name-before
-                    $(project) $(name) : $(property-set) : $(sources) ] ;
-            local property-set_ =
-                [ modify-properties-before
-                    $(project) $(name) : $(property-set) : $(sources) ] ;
-            local sources_ =
-                [ modify-sources-before
-                    $(project) $(name) : $(property-set) : $(sources) ] ;
-            project = $(project_) ;
-            name = $(name_) ;
-            property-set = $(property-set_) ;
-            sources = $(sources_) ;
-
-            # Generate the real target...
-            local target-type-p =
-                [ property.select <main-target-type> : [ $(property-set).raw ] ] ;
-            self.targets-in-progress += $(current-target) ;
-            result =
-                [ generators.construct $(project) $(name)
-                    : $(target-type-p:G=)
-                    : $(property-set)
-                    : $(sources) ] ;
-            self.targets-in-progress = $(self.targets-in-progress[1--2]) ;
-
-            # After modifications...
-            result =
-                [ modify-target-after $(result)
-                    : $(project) $(name)
-                    : $(property-set)
-                    : $(sources) ] ;
-        }
-        return $(result) ;
-    }
-
-    rule modify-project-before ( project name ? : property-set : sources + )
-    {
-        return $(project) ;
-    }
-
-    rule modify-name-before ( project name ? : property-set : sources + )
-    {
-        return $(name) ;
-    }
-
-    rule modify-properties-before ( project name ? : property-set : sources + )
-    {
-        return $(property-set) ;
-    }
-
-    rule modify-sources-before ( project name ? : property-set : sources + )
-    {
-        return $(sources) ;
-    }
-
-    rule modify-target-after ( target : project name ? : property-set : sources + )
-    {
-        return $(target) ;
-    }
-
-    # Utility, clones a file-target with optional changes to the name, type and
-    # project of the target.
-    # NOTE: This functionality should be moved, and generalized, to
-    # virtual-targets.
-    #
-    rule clone-file-target ( target : new-name ? : new-type ? : new-project ? )
-    {
-        # Need a MUTCH better way to clone a target...
-        new-name ?= [ $(target).name ] ;
-        new-type ?= [ $(target).type ] ;
-        new-project ?= [ $(target).project ] ;
-        local result = [ new file-target $(new-name) : $(new-type) : $(new-project) ] ;
-
-        if [ $(target).dependencies ] { $(result).depends [ $(target).dependencies ] ; }
-        $(result).root [ $(target).root ] ;
-        $(result).set-usage-requirements [ $(target).usage-requirements ] ;
-
-        local action = [ $(target).action ] ;
-        local action-class = [ modules.peek $(action) : __class__ ] ;
-
-        local ps = [ $(action).properties ] ;
-        local cloned-action = [ new $(action-class) $(result) :
-          [ $(action).sources ] : [ $(action).action-name ] : $(ps) ] ;
-        $(result).action $(cloned-action) ;
-
-        return $(result) ;
-    }
-}
-
-
-# A modifier that changes the name of a target, after it's generated, given a
-# regular expression to split the name, and a set of token to insert between the
-# split tokens of the name. This also exposes the target for other uses with a
-# symlink to the original name (optionally).
-#
-class name-modifier : modifier
-{
-    rule __init__ ( )
-    {
-        # Apply ourselves to EXE targets, for now.
-        modifier.__init__ name.modifier : : EXE LIB : <name-modify>yes ;
-    }
-
-    # Modifies the name, by cloning the target with the new name.
-    #
-    rule modify-target-after ( target : project name ? : property-set : sources + )
-    {
-        local result = $(target) ;
-
-        local name-mod-p = [ property.select <name-modifier> : [ $(property-set).raw ] ] ;
-        if $(name-mod-p)
-        {
-            local new-name = [ modify-name [ $(target).name ] : $(name-mod-p:G=) ] ;
-            if $(new-name) != [ $(target).name ]
-            {
-                result = [ clone-file-target $(target) : $(new-name) ] ;
-            }
-            local expose-original-as-symlink = [ MATCH "<symlink>(.*)" : $(name-mod-p) ] ;
-            if $(expose-original-as-symlink)
-            {
-                local symlink-t = [ new symlink-targets $(project) : $(name) : [ $(result).name ] ] ;
-                result = [ $(symlink-t).construct $(result)
-                    : [ property-set.create [ $(property-set).raw ] <symlink-location>build-relative ] ] ;
-            }
-        }
-
-        return $(result) ;
-    }
-
-    # Do the transformation of the name.
-    #
-    rule modify-name ( name : modifier-spec + )
-    {
-        local match = [ MATCH "<match>(.*)" : $(modifier-spec) ] ;
-        local name-parts = [ MATCH $(match) : $(name) ] ;
-        local insertions = [ sequence.insertion-sort [ MATCH "(<[0123456789]+>.*)" : $(modifier-spec) ] ] ;
-        local new-name-parts ;
-        local insert-position = 1 ;
-        while $(insertions)
-        {
-            local insertion = [ MATCH "<$(insert-position)>(.*)" : $(insertions[1]) ] ;
-            if $(insertion)
-            {
-                new-name-parts += $(insertion) ;
-                insertions = $(insertions[2-]) ;
-            }
-            new-name-parts += $(name-parts[1]) ;
-            name-parts = $(name-parts[2-]) ;
-            insert-position = [ numbers.increment $(insert-position) ] ;
-        }
-        new-name-parts += $(name-parts) ;
-        return [ sequence.join $(new-name-parts) ] ;
-    }
-
-    rule optional-properties ( )
-    {
-        return <name-modify>yes ;
-    }
-}
-feature.feature name-modifier : : free ;
-feature.feature name-modify : no yes : incidental optional ;
-generators.register [ new name-modifier ] ;
-
-# Translates <version> property to a set of modification properties
-# that are applied by the name-modifier, and symlink-modifier.
-#
-rule version-to-modifier ( property : properties * )
-{
-    return
-        <name-modify>yes
-            <name-modifier><match>"^([^.]*)(.*)" <name-modifier><2>.$(property:G=)
-            <name-modifier><symlink>yes
-        ;
-}
-feature.action <version> : version-to-modifier ;
diff --git a/jam-files/boost-build/build/project.ann.py b/jam-files/boost-build/build/project.ann.py
deleted file mode 100644
index 349f5495..00000000
--- a/jam-files/boost-build/build/project.ann.py
+++ /dev/null
@@ -1,996 +0,0 @@
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000   1) # Status: being ported by Vladimir Prus
-ddc17f01 (vladimir_prus 2007-10-26 14:57:56 +0000   2) # Base revision: 40480
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000   3) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000   4) # Copyright 2002, 2003 Dave Abrahams 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000   5) # Copyright 2002, 2005, 2006 Rene Rivera 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000   6) # Copyright 2002, 2003, 2004, 2005, 2006 Vladimir Prus 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000   7) # Distributed under the Boost Software License, Version 1.0. 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000   8) # (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000   9) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  10) #  Implements project representation and loading.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  11) #   Each project is represented by 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  12) #   - a module where all the Jamfile content live. 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  13) #   - an instance of 'project-attributes' class.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  14) #     (given module name, can be obtained by 'attributes' rule)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  15) #   - an instance of 'project-target' class (from targets.jam)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  16) #     (given a module name, can be obtained by 'target' rule)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  17) #
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  18) #  Typically, projects are created as result of loading Jamfile, which is
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  19) #  do by rules 'load' and 'initialize', below. First, module for Jamfile
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  20) #  is loaded and new project-attributes instance is created. Some rules
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  21) #  necessary for project are added to the module (see 'project-rules' module)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  22) #  at the bottom of this file.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  23) #  Default project attributes are set (inheriting attributes of parent project, if
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  24) #  it exists). After that, Jamfile is read. It can declare its own attributes,
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  25) #  via 'project' rule, which will be combined with already set attributes.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  26) #
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  27) #
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  28) #  The 'project' rule can also declare project id, which will be associated with 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  29) #  the project module.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  30) #
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  31) #  There can also be 'standalone' projects. They are created by calling 'initialize'
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  32) #  on arbitrary module, and not specifying location. After the call, the module can
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  33) #  call 'project' rule, declare main target and behave as regular projects. However,
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  34) #  since it's not associated with any location, it's better declare only prebuilt 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  35) #  targets.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  36) #
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  37) #  The list of all loaded Jamfile is stored in variable .project-locations. It's possible
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  38) #  to obtain module name for a location using 'module-name' rule. The standalone projects
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  39) #  are not recorded, the only way to use them is by project id.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  40) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  41) import b2.util.path
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000  42) from b2.build import property_set, property
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000  43) from b2.build.errors import ExceptionWithUserContext
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  44) import b2.build.targets
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  45) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  46) import bjam
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  47) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  48) import re
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  49) import sys
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  50) import os
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  51) import string
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000  52) import imp
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000  53) import traceback
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  54) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  55) class ProjectRegistry:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  56) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  57)     def __init__(self, manager, global_build_dir):
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  58)         self.manager = manager
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  59)         self.global_build_dir = None
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000  60)         self.project_rules_ = ProjectRules(self)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  61) 
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000  62)         # The target corresponding to the project being loaded now
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  63)         self.current_project = None
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  64)         
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  65)         # The set of names of loaded project modules
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  66)         self.jamfile_modules = {}
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  67) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  68)         # Mapping from location to module name
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  69)         self.location2module = {}
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  70) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  71)         # Mapping from project id to project module
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  72)         self.id2module = {}
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  73) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  74)         # Map from Jamfile directory to parent Jamfile/Jamroot
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  75)         # location.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  76)         self.dir2parent_jamfile = {}
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  77) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  78)         # Map from directory to the name of Jamfile in
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  79)         # that directory (or None).
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  80)         self.dir2jamfile = {}
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  81) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  82)         # Map from project module to attributes object.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  83)         self.module2attributes = {}
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  84) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  85)         # Map from project module to target for the project
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  86)         self.module2target = {}
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  87) 
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000  88)         # Map from names to Python modules, for modules loaded
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000  89)         # via 'using' and 'import' rules in Jamfiles.
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000  90)         self.loaded_tool_modules_ = {}
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000  91) 
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000  92)         # Map from project target to the list of
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000  93)         # (id,location) pairs corresponding to all 'use-project'
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000  94)         # invocations.
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000  95)         # TODO: should not have a global map, keep this
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000  96)         # in ProjectTarget.
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000  97)         self.used_projects = {}
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000  98) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000  99)         self.saved_current_project = []
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 100) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 101)         self.JAMROOT = self.manager.getenv("JAMROOT");
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 102) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 103)         # Note the use of character groups, as opposed to listing
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 104)         # 'Jamroot' and 'jamroot'. With the latter, we'd get duplicate
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 105)         # matches on windows and would have to eliminate duplicates.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 106)         if not self.JAMROOT:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 107)             self.JAMROOT = ["project-root.jam", "[Jj]amroot", "[Jj]amroot.jam"]
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 108) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 109)         # Default patterns to search for the Jamfiles to use for build
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 110)         # declarations.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 111)         self.JAMFILE = self.manager.getenv("JAMFILE")
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 112) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 113)         if not self.JAMFILE:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 114)             self.JAMFILE = ["[Bb]uild.jam", "[Jj]amfile.v2", "[Jj]amfile",
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 115)                             "[Jj]amfile.jam"]
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 116) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 117) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 118)     def load (self, jamfile_location):
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 119)         """Loads jamfile at the given location. After loading, project global
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 120)         file and jamfile needed by the loaded one will be loaded recursively.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 121)         If the jamfile at that location is loaded already, does nothing.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 122)         Returns the project module for the Jamfile."""
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 123) 
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 124)         absolute = os.path.join(os.getcwd(), jamfile_location)
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 125)         absolute = os.path.normpath(absolute)
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 126)         jamfile_location = b2.util.path.relpath(os.getcwd(), absolute)
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 127) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 128)         if "--debug-loading" in self.manager.argv():
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 129)             print "Loading Jamfile at '%s'" % jamfile_location
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 130) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 131)             
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 132)         mname = self.module_name(jamfile_location)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 133)         # If Jamfile is already loaded, don't try again.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 134)         if not mname in self.jamfile_modules:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 135)         
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 136)             self.load_jamfile(jamfile_location)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 137)                 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 138)             # We want to make sure that child project are loaded only
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 139)             # after parent projects. In particular, because parent projects
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 140)             # define attributes whch are inherited by children, and we don't
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 141)             # want children to be loaded before parents has defined everything.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 142)             #
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 143)             # While "build-project" and "use-project" can potentially refer
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 144)             # to child projects from parent projects, we don't immediately
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 145)             # load child projects when seing those attributes. Instead,
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 146)             # we record the minimal information that will be used only later.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 147)             
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 148)             self.load_used_projects(mname)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 149)              
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 150)         return mname
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 151) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 152)     def load_used_projects(self, module_name):
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 153)         # local used = [ modules.peek $(module-name) : .used-projects ] ;
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 154)         used = self.used_projects[module_name]
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 155)     
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 156)         location = self.attribute(module_name, "location")
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 157)         for u in used:
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 158)             id = u[0]
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 159)             where = u[1]
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 160) 
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 161)             self.use(id, os.path.join(location, where))
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 162) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 163)     def load_parent(self, location):
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 164)         """Loads parent of Jamfile at 'location'.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 165)         Issues an error if nothing is found."""
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 166) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 167)         found = b2.util.path.glob_in_parents(
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 168)             location, self.JAMROOT + self.JAMFILE) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 169) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 170)         if not found:
-1674e2d9 (jhunold       2008-08-08 19:52:05 +0000 171)             print "error: Could not find parent for project at '%s'" % location
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 172)             print "error: Did not find Jamfile or project-root.jam in any parent directory."
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 173)             sys.exit(1)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 174)     
-49c03622 (jhunold       2008-07-23 09:57:41 +0000 175)         return self.load(os.path.dirname(found[0]))
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 176) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 177)     def act_as_jamfile(self, module, location):
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 178)         """Makes the specified 'module' act as if it were a regularly loaded Jamfile 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 179)         at 'location'. If Jamfile is already located for that location, it's an 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 180)         error."""
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 181) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 182)         if self.module_name(location) in self.jamfile_modules:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 183)             self.manager.errors()(
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 184)                 "Jamfile was already loaded for '%s'" % location)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 185)     
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 186)         # Set up non-default mapping from location to module.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 187)         self.location2module[location] = module
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 188)     
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 189)         # Add the location to the list of project locations
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 190)         # so that we don't try to load Jamfile in future
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 191)         self.jamfile_modules.append(location)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 192)     
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 193)         self.initialize(module, location)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 194) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 195)     def find(self, name, current_location):
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 196)         """Given 'name' which can be project-id or plain directory name,
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 197)         return project module corresponding to that id or directory.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 198)         Returns nothing of project is not found."""
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 199) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 200)         project_module = None
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 201) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 202)         # Try interpreting name as project id.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 203)         if name[0] == '/':
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 204)             project_module = self.id2module.get(name)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 205) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 206)         if not project_module:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 207)             location = os.path.join(current_location, name)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 208)             # If no project is registered for the given location, try to
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 209)             # load it. First see if we have Jamfile. If not we might have project
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 210)             # root, willing to act as Jamfile. In that case, project-root
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 211)             # must be placed in the directory referred by id.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 212)         
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 213)             project_module = self.module_name(location)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 214)             if not project_module in self.jamfile_modules and \
-49c03622 (jhunold       2008-07-23 09:57:41 +0000 215)                b2.util.path.glob([location], self.JAMROOT + self.JAMFILE):
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 216)                 project_module = self.load(location)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 217) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 218)         return project_module
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 219) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 220)     def module_name(self, jamfile_location):
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 221)         """Returns the name of module corresponding to 'jamfile-location'.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 222)         If no module corresponds to location yet, associates default
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 223)         module name with that location."""
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 224)         module = self.location2module.get(jamfile_location)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 225)         if not module:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 226)             # Root the path, so that locations are always umbiguious.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 227)             # Without this, we can't decide if '../../exe/program1' and '.'
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 228)             # are the same paths, or not.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 229)             jamfile_location = os.path.realpath(
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 230)                 os.path.join(os.getcwd(), jamfile_location))
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 231)             module = "Jamfile<%s>" % jamfile_location
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 232)             self.location2module[jamfile_location] = module
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 233)         return module
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 234) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 235)     def find_jamfile (self, dir, parent_root=0, no_errors=0):
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 236)         """Find the Jamfile at the given location. This returns the
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 237)         exact names of all the Jamfiles in the given directory. The optional
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 238)         parent-root argument causes this to search not the given directory
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 239)         but the ones above it up to the directory given in it."""
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 240)         
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 241)         # Glob for all the possible Jamfiles according to the match pattern.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 242)         #
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 243)         jamfile_glob = None
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 244)         if parent_root:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 245)             parent = self.dir2parent_jamfile.get(dir)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 246)             if not parent:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 247)                 parent = b2.util.path.glob_in_parents(dir,
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 248)                                                                self.JAMFILE)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 249)                 self.dir2parent_jamfile[dir] = parent
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 250)             jamfile_glob = parent
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 251)         else:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 252)             jamfile = self.dir2jamfile.get(dir)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 253)             if not jamfile:
-49c03622 (jhunold       2008-07-23 09:57:41 +0000 254)                 jamfile = b2.util.path.glob([dir], self.JAMFILE)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 255)                 self.dir2jamfile[dir] = jamfile
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 256)             jamfile_glob = jamfile
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 257) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 258)         if len(jamfile_glob):
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 259)             # Multiple Jamfiles found in the same place. Warn about this.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 260)             # And ensure we use only one of them.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 261)             # As a temporary convenience measure, if there's Jamfile.v2 amount
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 262)             # found files, suppress the warning and use it.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 263)             #
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 264)             pattern = "(.*[Jj]amfile\\.v2)|(.*[Bb]uild\\.jam)"
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 265)             v2_jamfiles = [x for x in jamfile_glob if re.match(pattern, x)]
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 266)             if len(v2_jamfiles) == 1:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 267)                 jamfile_glob = v2_jamfiles
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 268)             else:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 269)                 print """warning: Found multiple Jamfiles at '%s'!
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 270) Loading the first one: '%s'.""" % (dir, jamfile_glob[0])
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 271)     
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 272)         # Could not find it, error.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 273)         if not no_errors and not jamfile_glob:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 274)             self.manager.errors()(
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 275)                 """Unable to load Jamfile.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 276) Could not find a Jamfile in directory '%s'
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 277) Attempted to find it with pattern '%s'.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 278) Please consult the documentation at 'http://boost.org/b2.'."""
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 279)                 % (dir, string.join(self.JAMFILE)))
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 280) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 281)         return jamfile_glob[0]
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 282)     
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 283)     def load_jamfile(self, dir):
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 284)         """Load a Jamfile at the given directory. Returns nothing.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 285)         Will attempt to load the file as indicated by the JAMFILE patterns.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 286)         Effect of calling this rule twice with the same 'dir' is underfined."""
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 287)       
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 288)         # See if the Jamfile is where it should be.
-49c03622 (jhunold       2008-07-23 09:57:41 +0000 289)         jamfile_to_load = b2.util.path.glob([dir], self.JAMROOT)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 290)         if not jamfile_to_load:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 291)             jamfile_to_load = self.find_jamfile(dir)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 292)         else:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 293)             jamfile_to_load = jamfile_to_load[0]
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 294)             
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 295)         # The module of the jamfile.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 296)         dir = os.path.realpath(os.path.dirname(jamfile_to_load))
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 297)         
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 298)         jamfile_module = self.module_name (dir)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 299) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 300)         # Initialize the jamfile module before loading.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 301)         #    
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 302)         self.initialize(jamfile_module, dir, os.path.basename(jamfile_to_load))
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 303) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 304)         saved_project = self.current_project
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 305) 
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 306)         self.used_projects[jamfile_module] = []
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 307)         
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 308)         # Now load the Jamfile in it's own context.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 309)         # Initialization might have load parent Jamfiles, which might have
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 310)         # loaded the current Jamfile with use-project. Do a final check to make
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 311)         # sure it's not loaded already.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 312)         if not jamfile_module in self.jamfile_modules:
-49c03622 (jhunold       2008-07-23 09:57:41 +0000 313)             self.jamfile_modules[jamfile_module] = True
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 314) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 315)             # FIXME:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 316)             # mark-as-user $(jamfile-module) ;
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 317) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 318)             bjam.call("load", jamfile_module, jamfile_to_load)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 319)             basename = os.path.basename(jamfile_to_load)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 320)                         
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 321)         # Now do some checks
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 322)         if self.current_project != saved_project:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 323)             self.manager.errors()(
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 324) """The value of the .current-project variable
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 325) has magically changed after loading a Jamfile.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 326) This means some of the targets might be defined a the wrong project.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 327) after loading %s
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 328) expected value %s
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 329) actual value %s""" % (jamfile_module, saved_project, self.current_project))
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 330)           
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 331)         if self.global_build_dir:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 332)             id = self.attribute(jamfile_module, "id")
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 333)             project_root = self.attribute(jamfile_module, "project-root")
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 334)             location = self.attribute(jamfile_module, "location")
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 335) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 336)             if location and project_root == dir:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 337)                 # This is Jamroot
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 338)                 if not id:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 339)                     # FIXME: go via errors module, so that contexts are
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 340)                     # shown?
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 341)                     print "warning: the --build-dir option was specified"
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 342)                     print "warning: but Jamroot at '%s'" % dir
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 343)                     print "warning: specified no project id"
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 344)                     print "warning: the --build-dir option will be ignored"
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 345) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 346) 
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 347)     def load_standalone(self, jamfile_module, file):
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 348)         """Loads 'file' as standalone project that has no location
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 349)         associated with it.  This is mostly useful for user-config.jam,
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 350)         which should be able to define targets, but although it has
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 351)         some location in filesystem, we don't want any build to
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 352)         happen in user's HOME, for example.
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 353) 
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 354)         The caller is required to never call this method twice on
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 355)         the same file.
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 356)         """
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 357) 
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 358)         self.initialize(jamfile_module)
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 359)         self.used_projects[jamfile_module] = []
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 360)         bjam.call("load", jamfile_module, file)
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 361)         self.load_used_projects(jamfile_module)
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 362)         
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 363)     def is_jamroot(self, basename):
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 364)         match = [ pat for pat in self.JAMROOT if re.match(pat, basename)]
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 365)         if match:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 366)             return 1
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 367)         else:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 368)             return 0
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 369) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 370)     def initialize(self, module_name, location=None, basename=None):
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 371)         """Initialize the module for a project.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 372)         
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 373)         module-name is the name of the project module.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 374)         location is the location (directory) of the project to initialize.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 375)                  If not specified, stanalone project will be initialized
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 376)         """
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 377) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 378)         if "--debug-loading" in self.manager.argv():
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 379)             print "Initializing project '%s'" % module_name
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 380) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 381)         # TODO: need to consider if standalone projects can do anything but defining
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 382)         # prebuilt targets. If so, we need to give more sensible "location", so that
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 383)         # source paths are correct.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 384)         if not location:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 385)             location = ""
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 386)         else:
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 387)             location = b2.util.path.relpath(os.getcwd(), location)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 388) 
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 389)         attributes = ProjectAttributes(self.manager, location, module_name)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 390)         self.module2attributes[module_name] = attributes
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 391) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 392)         if location:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 393)             attributes.set("source-location", location, exact=1)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 394)         else:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 395)             attributes.set("source-location", "", exact=1)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 396) 
-49c03622 (jhunold       2008-07-23 09:57:41 +0000 397)         attributes.set("requirements", property_set.empty(), exact=True)
-49c03622 (jhunold       2008-07-23 09:57:41 +0000 398)         attributes.set("usage-requirements", property_set.empty(), exact=True)
-49c03622 (jhunold       2008-07-23 09:57:41 +0000 399)         attributes.set("default-build", [], exact=True)
-49c03622 (jhunold       2008-07-23 09:57:41 +0000 400)         attributes.set("projects-to-build", [], exact=True)
-49c03622 (jhunold       2008-07-23 09:57:41 +0000 401)         attributes.set("project-root", None, exact=True)
-49c03622 (jhunold       2008-07-23 09:57:41 +0000 402)         attributes.set("build-dir", None, exact=True)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 403)         
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 404)         self.project_rules_.init_project(module_name)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 405) 
-49c03622 (jhunold       2008-07-23 09:57:41 +0000 406)         jamroot = False
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 407) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 408)         parent_module = None;
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 409)         if module_name == "site-config":
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 410)             # No parent
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 411)             pass
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 412)         elif module_name == "user-config":
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 413)             parent_module = "site-config"
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 414)         elif location and not self.is_jamroot(basename):
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 415)             # We search for parent/project-root only if jamfile was specified 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 416)             # --- i.e
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 417)             # if the project is not standalone.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 418)             parent_module = self.load_parent(location)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 419)         else:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 420)             # It's either jamroot, or standalone project.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 421)             # If it's jamroot, inherit from user-config.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 422)             if location:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 423)                 parent_module = "user-config" ;                
-49c03622 (jhunold       2008-07-23 09:57:41 +0000 424)                 jamroot = True ;
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 425)                 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 426)         if parent_module:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 427)             self.inherit_attributes(module_name, parent_module)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 428)             attributes.set("parent-module", parent_module, exact=1)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 429) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 430)         if jamroot:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 431)             attributes.set("project-root", location, exact=1)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 432)                                 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 433)         parent = None
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 434)         if parent_module:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 435)             parent = self.target(parent_module)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 436) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 437)         if not self.module2target.has_key(module_name):
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 438)             target = b2.build.targets.ProjectTarget(self.manager,
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 439)                 module_name, module_name, parent,
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 440)                 self.attribute(module_name,"requirements"),
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 441)                 # FIXME: why we need to pass this? It's not
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 442)                 # passed in jam code.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 443)                 self.attribute(module_name, "default-build"))
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 444)             self.module2target[module_name] = target
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 445) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 446)         self.current_project = self.target(module_name)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 447) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 448)     def inherit_attributes(self, project_module, parent_module):
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 449)         """Make 'project-module' inherit attributes of project
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 450)         root and parent module."""
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 451) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 452)         attributes = self.module2attributes[project_module]
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 453)         pattributes = self.module2attributes[parent_module]
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 454)         
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 455)         # Parent module might be locationless user-config.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 456)         # FIXME:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 457)         #if [ modules.binding $(parent-module) ]
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 458)         #{        
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 459)         #    $(attributes).set parent : [ path.parent 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 460)         #                                 [ path.make [ modules.binding $(parent-module) ] ] ] ;
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 461)         #    }
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 462)         
-49c03622 (jhunold       2008-07-23 09:57:41 +0000 463)         attributes.set("project-root", pattributes.get("project-root"), exact=True)
-49c03622 (jhunold       2008-07-23 09:57:41 +0000 464)         attributes.set("default-build", pattributes.get("default-build"), exact=True)
-49c03622 (jhunold       2008-07-23 09:57:41 +0000 465)         attributes.set("requirements", pattributes.get("requirements"), exact=True)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 466)         attributes.set("usage-requirements",
-cde6f09a (vladimir_prus 2007-10-19 23:12:33 +0000 467)                        pattributes.get("usage-requirements"), exact=1)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 468) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 469)         parent_build_dir = pattributes.get("build-dir")
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 470)         
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 471)         if parent_build_dir:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 472)         # Have to compute relative path from parent dir to our dir
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 473)         # Convert both paths to absolute, since we cannot
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 474)         # find relative path from ".." to "."
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 475) 
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 476)              location = attributes.get("location")
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 477)              parent_location = pattributes.get("location")
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 478) 
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 479)              our_dir = os.path.join(os.getcwd(), location)
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 480)              parent_dir = os.path.join(os.getcwd(), parent_location)
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 481) 
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 482)              build_dir = os.path.join(parent_build_dir,
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 483)                                       b2.util.path.relpath(parent_dir,
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 484)                                                                     our_dir))
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 485) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 486)     def register_id(self, id, module):
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 487)         """Associate the given id with the given project module."""
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 488)         self.id2module[id] = module
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 489) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 490)     def current(self):
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 491)         """Returns the project which is currently being loaded."""
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 492)         return self.current_project
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 493) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 494)     def push_current(self, project):
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 495)         """Temporary changes the current project to 'project'. Should
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 496)         be followed by 'pop-current'."""
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 497)         self.saved_current_project.append(self.current_project)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 498)         self.current_project = project
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 499) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 500)     def pop_current(self):
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 501)         self.current_project = self.saved_current_project[-1]
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 502)         del self.saved_current_project[-1]
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 503) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 504)     def attributes(self, project):
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 505)         """Returns the project-attribute instance for the
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 506)         specified jamfile module."""
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 507)         return self.module2attributes[project]
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 508) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 509)     def attribute(self, project, attribute):
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 510)         """Returns the value of the specified attribute in the
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 511)         specified jamfile module."""
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 512)         return self.module2attributes[project].get(attribute)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 513) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 514)     def target(self, project_module):
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 515)         """Returns the project target corresponding to the 'project-module'."""
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 516)         if not self.module2target[project_module]:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 517)             self.module2target[project_module] = \
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 518)                 ProjectTarget(project_module, project_module,
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 519)                               self.attribute(project_module, "requirements"))
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 520)         
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 521)         return self.module2target[project_module]
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 522) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 523)     def use(self, id, location):
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 524)         # Use/load a project.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 525)         saved_project = self.current_project
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 526)         project_module = self.load(location)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 527)         declared_id = self.attribute(project_module, "id")
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 528) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 529)         if not declared_id or declared_id != id:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 530)             # The project at 'location' either have no id or
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 531)             # that id is not equal to the 'id' parameter.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 532)             if self.id2module[id] and self.id2module[id] != project_module:
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 533)                 self.manager.errors()(
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 534) """Attempt to redeclare already existing project id '%s'""" % id)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 535)             self.id2module[id] = project_module
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 536) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 537)         self.current_module = saved_project
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 538) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 539)     def add_rule(self, name, callable):
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 540)         """Makes rule 'name' available to all subsequently loaded Jamfiles.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 541) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 542)         Calling that rule wil relay to 'callable'."""
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 543)         self.project_rules_.add_rule(name, callable)
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 544) 
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 545)     def project_rules(self):
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 546)         return self.project_rules_
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 547) 
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 548)     def glob_internal(self, project, wildcards, excludes, rule_name):
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 549)         location = project.get("source-location")
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 550) 
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 551)         result = []
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 552)         callable = b2.util.path.__dict__[rule_name]
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 553)         
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 554)         paths = callable(location, wildcards, excludes)
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 555)         has_dir = 0
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 556)         for w in wildcards:
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 557)             if os.path.dirname(w):
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 558)                 has_dir = 1
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 559)                 break
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 560) 
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 561)         if has_dir or rule_name != "glob":
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 562)             # The paths we've found are relative to current directory,
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 563)             # but the names specified in sources list are assumed to
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 564)             # be relative to source directory of the corresponding
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 565)             # prject. So, just make the name absolute.
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 566)             result = [os.path.join(os.getcwd(), p) for p in paths]
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 567)         else:
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 568)             # There were not directory in wildcard, so the files are all
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 569)             # in the source directory of the project. Just drop the
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 570)             # directory, instead of making paths absolute.
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 571)             result = [os.path.basename(p) for p in paths]
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 572)             
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 573)         return result
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 574) 
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 575)     def load_module(self, name, extra_path=None):
-53b0faa2 (jhunold       2008-08-10 18:25:50 +0000 576)         """Classic Boost.Build 'modules' are in fact global variables.
-53b0faa2 (jhunold       2008-08-10 18:25:50 +0000 577)         Therefore, try to find an already loaded Python module called 'name' in sys.modules. 
-53b0faa2 (jhunold       2008-08-10 18:25:50 +0000 578)         If the module ist not loaded, find it Boost.Build search
-53b0faa2 (jhunold       2008-08-10 18:25:50 +0000 579)         path and load it.  The new module is not entered in sys.modules.
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 580)         The motivation here is to have disjoint namespace of modules
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 581)         loaded via 'import/using' in Jamfile, and ordinary Python
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 582)         modules. We don't want 'using foo' in Jamfile to load ordinary
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 583)         Python module 'foo' which is going to not work. And we
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 584)         also don't want 'import foo' in regular Python module to
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 585)         accidentally grab module named foo that is internal to
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 586)         Boost.Build and intended to provide interface to Jamfiles."""
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 587) 
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 588)         existing = self.loaded_tool_modules_.get(name)
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 589)         if existing:
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 590)             return existing
-53b0faa2 (jhunold       2008-08-10 18:25:50 +0000 591) 
-53b0faa2 (jhunold       2008-08-10 18:25:50 +0000 592)         modules = sys.modules
-53b0faa2 (jhunold       2008-08-10 18:25:50 +0000 593)         for class_name in modules:
-53b0faa2 (jhunold       2008-08-10 18:25:50 +0000 594)             if name in class_name:
-53b0faa2 (jhunold       2008-08-10 18:25:50 +0000 595)                 module = modules[class_name]
-53b0faa2 (jhunold       2008-08-10 18:25:50 +0000 596)                 self.loaded_tool_modules_[name] = module
-53b0faa2 (jhunold       2008-08-10 18:25:50 +0000 597)                 return module
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 598)         
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 599)         path = extra_path
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 600)         if not path:
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 601)             path = []
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 602)         path.extend(self.manager.b2.path())
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 603)         location = None
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 604)         for p in path:
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 605)             l = os.path.join(p, name + ".py")
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 606)             if os.path.exists(l):
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 607)                 location = l
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 608)                 break
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 609) 
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 610)         if not location:
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 611)             self.manager.errors()("Cannot find module '%s'" % name)
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 612) 
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 613)         mname = "__build_build_temporary__"
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 614)         file = open(location)
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 615)         try:
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 616)             # TODO: this means we'll never make use of .pyc module,
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 617)             # which might be a problem, or not.
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 618)             module = imp.load_module(mname, file, os.path.basename(location),
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 619)                                      (".py", "r", imp.PY_SOURCE))
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 620)             del sys.modules[mname]
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 621)             self.loaded_tool_modules_[name] = module
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 622)             return module
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 623)         finally:
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 624)             file.close()
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 625)         
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 626) 
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 627) 
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 628) # FIXME:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 629) # Defines a Boost.Build extension project. Such extensions usually
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 630) # contain library targets and features that can be used by many people.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 631) # Even though extensions are really projects, they can be initialize as
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 632) # a module would be with the "using" (project.project-rules.using)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 633) # mechanism.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 634) #rule extension ( id : options * : * )
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 635) #{
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 636) #    # The caller is a standalone module for the extension.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 637) #    local mod = [ CALLER_MODULE ] ;
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 638) #    
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 639) #    # We need to do the rest within the extension module.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 640) #    module $(mod)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 641) #    {
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 642) #        import path ;
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 643) #        
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 644) #        # Find the root project.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 645) #        local root-project = [ project.current ] ;
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 646) #        root-project = [ $(root-project).project-module ] ;
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 647) #        while
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 648) #            [ project.attribute $(root-project) parent-module ] &&
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 649) #            [ project.attribute $(root-project) parent-module ] != user-config
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 650) #        {
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 651) #            root-project = [ project.attribute $(root-project) parent-module ] ;
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 652) #        }
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 653) #        
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 654) #        # Create the project data, and bring in the project rules
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 655) #        # into the module.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 656) #        project.initialize $(__name__) :
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 657) #            [ path.join [ project.attribute $(root-project) location ] ext $(1:L) ] ;
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 658) #        
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 659) #        # Create the project itself, i.e. the attributes.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 660) #        # All extensions are created in the "/ext" project space.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 661) #        project /ext/$(1) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ;
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 662) #        local attributes = [ project.attributes $(__name__) ] ;
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 663) #        
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 664) #        # Inherit from the root project of whomever is defining us.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 665) #        project.inherit-attributes $(__name__) : $(root-project) ;
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 666) #        $(attributes).set parent-module : $(root-project) : exact ;
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 667) #    }
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 668) #}
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 669)         
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 670) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 671) class ProjectAttributes:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 672)     """Class keeping all the attributes of a project.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 673) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 674)     The standard attributes are 'id', "location", "project-root", "parent"
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 675)     "requirements", "default-build", "source-location" and "projects-to-build".
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 676)     """
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 677)         
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 678)     def __init__(self, manager, location, project_module):
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 679)         self.manager = manager
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 680)         self.location = location
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 681)         self.project_module = project_module
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 682)         self.attributes = {}
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 683)         self.usage_requirements = None
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 684)         
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 685)     def set(self, attribute, specification, exact):
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 686)         """Set the named attribute from the specification given by the user.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 687)         The value actually set may be different."""
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 688) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 689)         if exact:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 690)             self.__dict__[attribute] = specification
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 691)             
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 692)         elif attribute == "requirements":
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000 693)             self.requirements = property_set.refine_from_user_input(
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000 694)                 self.requirements, specification,
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000 695)                 self.project_module, self.location)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 696)             
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 697)         elif attribute == "usage-requirements":
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 698)             unconditional = []
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 699)             for p in specification:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 700)                 split = property.split_conditional(p)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 701)                 if split:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 702)                     unconditional.append(split[1])
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 703)                 else:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 704)                     unconditional.append(p)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 705) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 706)             non_free = property.remove("free", unconditional)
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000 707)             if non_free:                
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 708)                 pass
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 709)                 # FIXME:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 710)                 #errors.error "usage-requirements" $(specification) "have non-free properties" $(non-free) ;
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 711) 
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 712)             t = property.translate_paths(specification, self.location)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 713) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 714)             existing = self.__dict__.get("usage-requirements")
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 715)             if existing:
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 716)                 new = property_set.create(existing.raw() +  t)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 717)             else:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 718)                 new = property_set.create(t)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 719)             self.__dict__["usage-requirements"] = new
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 720) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 721)                 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 722)         elif attribute == "default-build":
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 723)             self.__dict__["default-build"] = property_set.create(specification)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 724)             
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 725)         elif attribute == "source-location":
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 726)             source_location = []
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 727)             for path in specification:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 728)                 source_location += os.path.join(self.location, path)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 729)             self.__dict__["source-location"] = source_location
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 730)                 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 731)         elif attribute == "build-dir":
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 732)             self.__dict__["build-dir"] = os.path.join(self.location, specification)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 733)                  
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 734)         elif not attribute in ["id", "default-build", "location",
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 735)                                "source-location", "parent",
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 736)                                "projects-to-build", "project-root"]:
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 737)             self.manager.errors()(
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 738) """Invalid project attribute '%s' specified
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 739) for project at '%s'""" % (attribute, self.location))
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 740)         else:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 741)             self.__dict__[attribute] = specification
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 742) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 743)     def get(self, attribute):
-cde6f09a (vladimir_prus 2007-10-19 23:12:33 +0000 744)         return self.__dict__[attribute]
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 745) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 746)     def dump(self):
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 747)         """Prints the project attributes."""
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 748)         id = self.get("id")
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 749)         if not id:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 750)             id = "(none)"
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 751)         else:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 752)             id = id[0]
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 753) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 754)         parent = self.get("parent")
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 755)         if not parent:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 756)             parent = "(none)"
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 757)         else:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 758)             parent = parent[0]
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 759) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 760)         print "'%s'" % id
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 761)         print "Parent project:%s", parent
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 762)         print "Requirements:%s", self.get("requirements")
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 763)         print "Default build:%s", string.join(self.get("debuild-build"))
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 764)         print "Source location:%s", string.join(self.get("source-location"))
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 765)         print "Projects to build:%s", string.join(self.get("projects-to-build").sort());
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 766) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 767) class ProjectRules:
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 768)     """Class keeping all rules that are made available to Jamfile."""
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 769) 
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 770)     def __init__(self, registry):
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 771)         self.registry = registry
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000 772)         self.manager_ = registry.manager
-38d984eb (vladimir_prus 2007-10-13 17:52:25 +0000 773)         self.rules = {}
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 774)         self.local_names = [x for x in self.__class__.__dict__
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000 775)                             if x not in ["__init__", "init_project", "add_rule",
-7da7f9c1 (vladimir_prus 2008-05-18 04:29:53 +0000 776)                                          "error_reporting_wrapper", "add_rule_for_type"]]
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 777)         self.all_names_ = [x for x in self.local_names]
-7da7f9c1 (vladimir_prus 2008-05-18 04:29:53 +0000 778) 
-7da7f9c1 (vladimir_prus 2008-05-18 04:29:53 +0000 779)     def add_rule_for_type(self, type):
-7da7f9c1 (vladimir_prus 2008-05-18 04:29:53 +0000 780)         rule_name = type.lower();
-7da7f9c1 (vladimir_prus 2008-05-18 04:29:53 +0000 781) 
-7da7f9c1 (vladimir_prus 2008-05-18 04:29:53 +0000 782)         def xpto (name, sources, requirements = [], default_build = None, usage_requirements = []):
-7da7f9c1 (vladimir_prus 2008-05-18 04:29:53 +0000 783)             return self.manager_.targets().create_typed_target(
-7da7f9c1 (vladimir_prus 2008-05-18 04:29:53 +0000 784)                 type, self.registry.current(), name[0], sources,
-7da7f9c1 (vladimir_prus 2008-05-18 04:29:53 +0000 785)                 requirements, default_build, usage_requirements) 
-7da7f9c1 (vladimir_prus 2008-05-18 04:29:53 +0000 786) 
-7da7f9c1 (vladimir_prus 2008-05-18 04:29:53 +0000 787)         self.add_rule(type.lower(), xpto)
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 788)     
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 789)     def add_rule(self, name, callable):
-38d984eb (vladimir_prus 2007-10-13 17:52:25 +0000 790)         self.rules[name] = callable
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 791)         self.all_names_.append(name)
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 792) 
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 793)     def all_names(self):
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 794)         return self.all_names_
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 795) 
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000 796)     def call_and_report_errors(self, callable, *args):
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000 797)         result = None
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000 798)         try:
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000 799)             self.manager_.errors().push_jamfile_context()
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000 800)             result = callable(*args)
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000 801)         except ExceptionWithUserContext, e:
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000 802)             e.report()
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000 803)         except Exception, e:
-7da7f9c1 (vladimir_prus 2008-05-18 04:29:53 +0000 804)             try:
-7da7f9c1 (vladimir_prus 2008-05-18 04:29:53 +0000 805)                 self.manager_.errors().handle_stray_exception (e)
-7da7f9c1 (vladimir_prus 2008-05-18 04:29:53 +0000 806)             except ExceptionWithUserContext, e:
-7da7f9c1 (vladimir_prus 2008-05-18 04:29:53 +0000 807)                 e.report()
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000 808)         finally:                
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000 809)             self.manager_.errors().pop_jamfile_context()
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000 810)                                         
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000 811)         return result
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000 812) 
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000 813)     def make_wrapper(self, callable):
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000 814)         """Given a free-standing function 'callable', return a new
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000 815)         callable that will call 'callable' and report all exceptins,
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000 816)         using 'call_and_report_errors'."""
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000 817)         def wrapper(*args):
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000 818)             self.call_and_report_errors(callable, *args)
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000 819)         return wrapper
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000 820) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 821)     def init_project(self, project_module):
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 822) 
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 823)         for n in self.local_names:            
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 824)             # Using 'getattr' here gives us a bound method,
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 825)             # while using self.__dict__[r] would give unbound one.
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 826)             v = getattr(self, n)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 827)             if callable(v):
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 828)                 if n == "import_":
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 829)                     n = "import"
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 830)                 else:
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 831)                     n = string.replace(n, "_", "-")
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000 832)                     
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000 833)                 bjam.import_rule(project_module, n,
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000 834)                                  self.make_wrapper(v))
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 835) 
-38d984eb (vladimir_prus 2007-10-13 17:52:25 +0000 836)         for n in self.rules:
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000 837)             bjam.import_rule(project_module, n,
-0317671e (vladimir_prus 2007-10-28 14:02:06 +0000 838)                              self.make_wrapper(self.rules[n]))
-38d984eb (vladimir_prus 2007-10-13 17:52:25 +0000 839) 
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 840)     def project(self, *args):
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 841) 
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 842)         jamfile_module = self.registry.current().project_module()
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 843)         attributes = self.registry.attributes(jamfile_module)
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 844)         
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 845)         id = None
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 846)         if args and args[0]:
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 847)             id = args[0][0]
-092119e3 (vladimir_prus 2007-10-16 05:45:31 +0000 848)             args = args[1:]
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 849) 
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 850)         if id:
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 851)             if id[0] != '/':
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 852)                 id = '/' + id
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 853)             self.registry.register_id (id, jamfile_module)
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 854) 
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 855)         explicit_build_dir = None
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 856)         for a in args:
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 857)             if a:
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 858)                 attributes.set(a[0], a[1:], exact=0)
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 859)                 if a[0] == "build-dir":
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 860)                     explicit_build_dir = a[1]
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 861)         
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 862)         # If '--build-dir' is specified, change the build dir for the project.
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 863)         if self.registry.global_build_dir:
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 864) 
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 865)             location = attributes.get("location")
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 866)             # Project with empty location is 'standalone' project, like
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 867)             # user-config, or qt.  It has no build dir.
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 868)             # If we try to set build dir for user-config, we'll then
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 869)             # try to inherit it, with either weird, or wrong consequences.
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 870)             if location and location == attributes.get("project-root"):
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 871)                 # This is Jamroot.
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 872)                 if id:
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 873)                     if explicit_build_dir and os.path.isabs(explicit_build_dir):
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 874)                         self.register.manager.errors()(
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 875) """Absolute directory specified via 'build-dir' project attribute
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 876) Don't know how to combine that with the --build-dir option.""")
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 877) 
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 878)                     rid = id
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 879)                     if rid[0] == '/':
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 880)                         rid = rid[1:]
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 881) 
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 882)                     p = os.path.join(self.registry.global_build_dir,
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 883)                                      rid, explicit_build_dir)
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 884)                     attributes.set("build-dir", p, exact=1)
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 885)             elif explicit_build_dir:
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 886)                 self.registry.manager.errors()(
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 887) """When --build-dir is specified, the 'build-project'
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 888) attribute is allowed only for top-level 'project' invocations""")
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 889) 
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 890)     def constant(self, name, value):
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 891)         """Declare and set a project global constant.
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 892)         Project global constants are normal variables but should
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 893)         not be changed. They are applied to every child Jamfile."""
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 894)         m = "Jamfile</home/ghost/Work/Boost/boost-svn/tools/build/v2_python/python/tests/bjam/make>"
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 895)         self.registry.current().add_constant(name[0], value)
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 896) 
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 897)     def path_constant(self, name, value):
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 898)         """Declare and set a project global constant, whose value is a path. The
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 899)         path is adjusted to be relative to the invocation directory. The given
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 900)         value path is taken to be either absolute, or relative to this project
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 901)         root."""
-0ed8e16d (vladimir_prus 2007-10-13 21:34:05 +0000 902)         self.registry.current().add_constant(name[0], value, path=1)
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 903) 
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 904)     def use_project(self, id, where):
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 905)         # See comment in 'load' for explanation why we record the
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 906)         # parameters as opposed to loading the project now.
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 907)         m = self.registry.current().project_module();
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 908)         self.registry.used_projects[m].append((id, where))
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 909)         
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 910)     def build_project(self, dir):
-1674e2d9 (jhunold       2008-08-08 19:52:05 +0000 911)         assert(isinstance(dir, list))
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 912)         jamfile_module = self.registry.current().project_module()
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 913)         attributes = self.registry.attributes(jamfile_module)
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 914)         now = attributes.get("projects-to-build")
-1674e2d9 (jhunold       2008-08-08 19:52:05 +0000 915)         attributes.set("projects-to-build", now + dir, exact=True)
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 916) 
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 917)     def explicit(self, target_names):
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 918)         t = self.registry.current()
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 919)         for n in target_names:
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 920)             t.mark_target_as_explicit(n)
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 921) 
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 922)     def glob(self, wildcards, excludes=None):
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 923)         return self.registry.glob_internal(self.registry.current(),
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 924)                                            wildcards, excludes, "glob")
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 925) 
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 926)     def glob_tree(self, wildcards, excludes=None):
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 927)         bad = 0
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 928)         for p in wildcards:
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 929)             if os.path.dirname(p):
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 930)                 bad = 1
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 931) 
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 932)         if excludes:
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 933)             for p in excludes:
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 934)                 if os.path.dirname(p):
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 935)                     bad = 1
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 936) 
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 937)         if bad:
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 938)             self.registry.manager().errors()(
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 939) "The patterns to 'glob-tree' may not include directory")
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 940)         return self.registry.glob_internal(self.registry.current(),
-2a36874b (vladimir_prus 2007-10-14 07:20:55 +0000 941)                                            wildcards, excludes, "glob_tree")
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 942)     
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 943) 
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 944)     def using(self, toolset, *args):
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 945)         # The module referred by 'using' can be placed in
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 946)         # the same directory as Jamfile, and the user
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 947)         # will expect the module to be found even though
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 948)         # the directory is not in BOOST_BUILD_PATH.
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 949)         # So temporary change the search path.
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 950)         jamfile_module = self.registry.current().project_module()
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 951)         attributes = self.registry.attributes(jamfile_module)
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 952)         location = attributes.get("location")
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 953) 
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 954)         m = self.registry.load_module(toolset[0], [location])
-7da7f9c1 (vladimir_prus 2008-05-18 04:29:53 +0000 955)         if not m.__dict__.has_key("init"):
-7da7f9c1 (vladimir_prus 2008-05-18 04:29:53 +0000 956)             self.registry.manager.errors()(
-7da7f9c1 (vladimir_prus 2008-05-18 04:29:53 +0000 957)                 "Tool module '%s' does not define the 'init' method" % toolset[0])
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 958)         m.init(*args)
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 959) 
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 960) 
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 961)     def import_(self, name, names_to_import=None, local_names=None):
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 962) 
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 963)         name = name[0]
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 964)         jamfile_module = self.registry.current().project_module()
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 965)         attributes = self.registry.attributes(jamfile_module)
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 966)         location = attributes.get("location")
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 967) 
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 968)         m = self.registry.load_module(name, [location])
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 969) 
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 970)         for f in m.__dict__:
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 971)             v = m.__dict__[f]
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 972)             if callable(v):
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 973)                 bjam.import_rule(jamfile_module, name + "." + f, v)
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 974) 
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 975)         if names_to_import:
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 976)             if not local_names:
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 977)                 local_names = names_to_import
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 978) 
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 979)             if len(names_to_import) != len(local_names):
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 980)                 self.registry.manager.errors()(
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 981) """The number of names to import and local names do not match.""")
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 982) 
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 983)             for n, l in zip(names_to_import, local_names):
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 984)                 bjam.import_rule(jamfile_module, l, m.__dict__[n])
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 985)         
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 986)     def conditional(self, condition, requirements):
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 987)         """Calculates conditional requirements for multiple requirements
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 988)         at once. This is a shorthand to be reduce duplication and to
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 989)         keep an inline declarative syntax. For example:
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 990) 
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 991)             lib x : x.cpp : [ conditional <toolset>gcc <variant>debug :
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 992)                 <define>DEBUG_EXCEPTION <define>DEBUG_TRACE ] ;
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 993)         """
-f049766b (vladimir_prus 2007-10-10 09:31:06 +0000 994) 
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 995)         c = string.join(condition, ",")
-f2aef897 (vladimir_prus 2007-10-14 09:19:52 +0000 996)         return [c + ":" + r for r in requirements]
diff --git a/jam-files/boost-build/build/project.jam b/jam-files/boost-build/build/project.jam
deleted file mode 100644
index c9967613..00000000
--- a/jam-files/boost-build/build/project.jam
+++ /dev/null
@@ -1,1110 +0,0 @@
-# Copyright 2002, 2003 Dave Abrahams
-# Copyright 2002, 2005, 2006 Rene Rivera
-# Copyright 2002, 2003, 2004, 2005, 2006 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-# Implements project representation and loading. Each project is represented by:
-#  - a module where all the Jamfile content live.
-#  - an instance of 'project-attributes' class.
-#    (given a module name, can be obtained using the 'attributes' rule)
-#  - an instance of 'project-target' class (from targets.jam)
-#    (given a module name, can be obtained using the 'target' rule)
-#
-# Typically, projects are created as result of loading a Jamfile, which is done
-# by rules 'load' and 'initialize', below. First, module for Jamfile is loaded
-# and new project-attributes instance is created. Some rules necessary for
-# project are added to the module (see 'project-rules' module) at the bottom of
-# this file. Default project attributes are set (inheriting attributes of parent
-# project, if it exists). After that the Jamfile is read. It can declare its own
-# attributes using the 'project' rule which will be combined with any already
-# set attributes.
-#
-# The 'project' rule can also declare a project id which will be associated with
-# the project module.
-#
-# There can also be 'standalone' projects. They are created by calling
-# 'initialize' on an arbitrary module and not specifying their location. After
-# the call, the module can call the 'project' rule, declare main targets and
-# behave as a regular project except that, since it is not associated with any
-# location, it should not declare targets that are not prebuilt.
-#
-# The list of all loaded Jamfile is stored in the .project-locations variable.
-# It is possible to obtain a module name for a location using the 'module-name'
-# rule. Standalone projects are not recorded and can only be referenced using
-# their project id.
-
-import "class" : new ;
-import errors ;
-import modules ;
-import path ;
-import print ;
-import property-set ;
-import sequence ;
-
-
-# Loads the Jamfile at the given location. After loading, project global file
-# and Jamfiles needed by the requested one will be loaded recursively. If the
-# Jamfile at that location is loaded already, does nothing. Returns the project
-# module for the Jamfile.
-#
-rule load ( jamfile-location )
-{
-    if --debug-loading in [ modules.peek : ARGV ]
-    {
-        ECHO "Loading Jamfile at" '$(jamfile-location)' ;
-    }
-
-    local module-name = [ module-name $(jamfile-location) ] ;
-    # If Jamfile is already loaded, don't try again.
-    if ! $(module-name) in $(.jamfile-modules)
-    {
-        load-jamfile $(jamfile-location) : $(module-name) ;
-
-        # We want to make sure that child project are loaded only after parent
-        # projects. In particular, because parent projects define attributes
-        # which are inherited by children, and we don't want children to be
-        # loaded before parent has defined everything.
-        #
-        # While "build-project" and "use-project" can potentially refer to child
-        # projects from parent projects, we don't immediately load child
-        # projects when seeing those attributes. Instead, we record the minimal
-        # information to be used only later.
-        load-used-projects $(module-name) ;
-    }
-    return $(module-name) ;
-}
-
-
-rule load-used-projects ( module-name )
-{
-    local used = [ modules.peek $(module-name) : .used-projects ] ;
-    local location = [ attribute $(module-name) location ] ;
-    import project ;
-    while $(used)
-    {
-        local id = $(used[1]) ;
-        local where = $(used[2]) ;
-
-        project.use $(id) : [ path.root [ path.make $(where) ] $(location) ] ;
-        used = $(used[3-]) ;
-    }
-}
-
-
-# Note the use of character groups, as opposed to listing 'Jamroot' and
-# 'jamroot'. With the latter, we would get duplicate matches on Windows and
-# would have to eliminate duplicates.
-JAMROOT ?= [ modules.peek : JAMROOT ] ;
-JAMROOT ?= project-root.jam [Jj]amroot [Jj]amroot.jam ;
-
-
-# Loads parent of Jamfile at 'location'. Issues an error if nothing is found.
-#
-rule load-parent ( location )
-{
-    local found = [ path.glob-in-parents $(location) : $(JAMROOT) $(JAMFILE) ] ;
-
-    if ! $(found)
-    {
-        ECHO error: Could not find parent for project at '$(location)' ;
-        EXIT error: Did not find Jamfile.jam or Jamroot.jam in any parent
-            directory. ;
-    }
-
-    return [ load $(found[1]:D) ] ;
-}
-
-
-# Makes the specified 'module' act as if it were a regularly loaded Jamfile at
-# 'location'. Reports an error if a Jamfile has already been loaded for that
-# location.
-#
-rule act-as-jamfile ( module : location )
-{
-    if [ module-name $(location) ] in $(.jamfile-modules)
-    {
-        errors.error "Jamfile was already loaded for '$(location)'" ;
-    }
-    # Set up non-default mapping from location to module.
-    .module.$(location) = $(module) ;
-
-    # Add the location to the list of project locations so that we don't try to
-    # reload the same Jamfile in the future.
-    .jamfile-modules += [ module-name $(location) ] ;
-
-    initialize $(module) : $(location) ;
-}
-
-
-# Returns the project module corresponding to the given project-id or plain
-# directory name. Returns nothing if such a project can not be found.
-#
-rule find ( name : current-location )
-{
-    local project-module ;
-
-    # Try interpreting name as project id.
-    if [ path.is-rooted $(name) ]
-    {
-        project-module = $($(name).jamfile-module) ;
-    }
-
-    if ! $(project-module)
-    {
-        local location = [ path.root [ path.make $(name) ] $(current-location) ]
-            ;
-
-        # If no project is registered for the given location, try to load it.
-        # First see if we have a Jamfile. If not, then see if we might have a
-        # project root willing to act as a Jamfile. In that case, project root
-        # must be placed in the directory referred by id.
-
-        project-module = [ module-name $(location) ] ;
-        if ! $(project-module) in $(.jamfile-modules)
-        {
-            if [ path.glob $(location) : $(JAMROOT) $(JAMFILE) ]
-            {
-                project-module = [ load $(location) ] ;
-            }
-            else
-            {
-                project-module = ;
-            }
-        }
-    }
-
-    return $(project-module) ;
-}
-
-
-# Returns the name of the module corresponding to 'jamfile-location'. If no
-# module corresponds to that location yet, associates the default module name
-# with that location.
-#
-rule module-name ( jamfile-location )
-{
-    if ! $(.module.$(jamfile-location))
-    {
-        # Root the path, so that locations are always unambiguous. Without this,
-        # we can't decide if '../../exe/program1' and '.' are the same paths.
-        jamfile-location = [ path.root $(jamfile-location) [ path.pwd ] ] ;
-        .module.$(jamfile-location) = Jamfile<$(jamfile-location)> ;
-    }
-    return $(.module.$(jamfile-location)) ;
-}
-
-
-# Default patterns to search for the Jamfiles to use for build declarations.
-#
-JAMFILE = [ modules.peek : JAMFILE ] ;
-JAMFILE ?= [Bb]uild.jam [Jj]amfile.v2 [Jj]amfile [Jj]amfile.jam ;
-
-
-# Find the Jamfile at the given location. This returns the exact names of all
-# the Jamfiles in the given directory. The optional parent-root argument causes
-# this to search not the given directory but the ones above it up to the
-# directory given in it.
-#
-rule find-jamfile (
-    dir # The directory(s) to look for a Jamfile.
-    parent-root ? # Optional flag indicating to search for the parent Jamfile.
-    : no-errors ?
-    )
-{
-    # Glob for all the possible Jamfiles according to the match pattern.
-    #
-    local jamfile-glob = ;
-    if $(parent-root)
-    {
-        if ! $(.parent-jamfile.$(dir))
-        {
-            .parent-jamfile.$(dir) = [ path.glob-in-parents $(dir) : $(JAMFILE)
-                ] ;
-        }
-        jamfile-glob = $(.parent-jamfile.$(dir)) ;
-    }
-    else
-    {
-        if ! $(.jamfile.$(dir))
-        {
-            .jamfile.$(dir) = [ path.glob $(dir) : $(JAMFILE) ] ;
-        }
-        jamfile-glob = $(.jamfile.$(dir)) ;
-
-    }
-
-    local jamfile-to-load = $(jamfile-glob) ;
-    # Multiple Jamfiles found in the same place. Warn about this and ensure we
-    # use only one of them. As a temporary convenience measure, if there is
-    # Jamfile.v2 among found files, suppress the warning and use it.
-    #
-    if $(jamfile-to-load[2-])
-    {
-        local v2-jamfiles = [ MATCH (.*[Jj]amfile\\.v2)|(.*[Bb]uild\\.jam) : $(jamfile-to-load) ] ;
-
-        if $(v2-jamfiles) && ! $(v2-jamfiles[2])
-        {
-            jamfile-to-load = $(v2-jamfiles) ;
-        }
-        else
-        {
-            local jamfile = [ path.basename $(jamfile-to-load[1]) ] ;
-            ECHO "warning: Found multiple Jamfiles at '"$(dir)"'!"
-                "Loading the first one: '$(jamfile)'." ;
-        }
-
-        jamfile-to-load = $(jamfile-to-load[1]) ;
-    }
-
-    # Could not find it, error.
-    #
-    if ! $(no-errors) && ! $(jamfile-to-load)
-    {
-        errors.error Unable to load Jamfile.
-            : Could not find a Jamfile in directory '$(dir)'.
-            : Attempted to find it with pattern '"$(JAMFILE:J=" ")"'.
-            : Please consult the documentation at 'http://www.boost.org'. ;
-    }
-
-    return $(jamfile-to-load) ;
-}
-
-
-# Load a Jamfile at the given directory. Returns nothing. Will attempt to load
-# the file as indicated by the JAMFILE patterns. Effect of calling this rule
-# twice with the same 'dir' is undefined.
-#
-local rule load-jamfile (
-    dir  # The directory of the project Jamfile.
-    : jamfile-module
-    )
-{
-    # See if the Jamfile is where it should be.
-    #
-    local jamfile-to-load = [ path.glob $(dir) : $(JAMROOT) ] ;
-    if ! $(jamfile-to-load)
-    {
-        jamfile-to-load = [ find-jamfile $(dir) ] ;
-    }
-    
-    if $(jamfile-to-load[2])
-    {
-        errors.error "Multiple Jamfiles found at '$(dir)'" 
-          :  "Filenames are: " $(jamfile-to-load:D=) ;
-    }
-    
-    # Now load the Jamfile in it's own context. 
-    # The call to 'initialize' may load parent Jamfile, which might have
-    # 'use-project' statement that causes a second attempt to load the
-    # same project we're loading now.  Checking inside .jamfile-modules
-    # prevents that second attempt from messing up.
-    if ! $(jamfile-module) in $(.jamfile-modules)
-    {
-        .jamfile-modules += $(jamfile-module) ;
-
-        # Initialize the Jamfile module before loading.
-        #
-        initialize $(jamfile-module) : [ path.parent $(jamfile-to-load) ]
-            : $(jamfile-to-load:BS) ;
-
-        local saved-project = $(.current-project) ;
-
-        mark-as-user $(jamfile-module) ;
-        modules.load $(jamfile-module) : [ path.native $(jamfile-to-load) ] : . ;
-        if [ MATCH ($(JAMROOT)) : $(jamfile-to-load:BS) ]
-        {
-            jamfile = [ find-jamfile $(dir) : no-errors ] ;
-            if $(jamfile)
-            {
-                load-aux $(jamfile-module) : [ path.native $(jamfile) ] ;
-            }
-        }
-
-    # Now do some checks.
-    if $(.current-project) != $(saved-project)
-    {
-        errors.error "The value of the .current-project variable has magically"
-            : "changed after loading a Jamfile. This means some of the targets"
-            : "might be defined in the wrong project."
-            : "after loading" $(jamfile-module)
-            : "expected value" $(saved-project)
-            : "actual value" $(.current-project) ;
-    }
-
-    if $(.global-build-dir)
-    {
-        local id           = [ attribute $(jamfile-module) id           ] ;
-        local project-root = [ attribute $(jamfile-module) project-root ] ;
-        local location     = [ attribute $(jamfile-module) location     ] ;
-
-        if $(location) && $(project-root) = $(dir)
-        {
-            # This is Jamroot.
-            if ! $(id)
-            {
-                ECHO "warning: the --build-dir option was specified" ;
-                ECHO "warning: but Jamroot at '$(dir)'" ;
-                ECHO "warning: specified no project id" ;
-                ECHO "warning: the --build-dir option will be ignored" ;
-            }
-        }
-    }
-    }
-}
-
-
-rule mark-as-user ( module-name )
-{
-    if USER_MODULE in [ RULENAMES ]
-    {
-        USER_MODULE $(module-name) ;
-    }
-}
-
-
-rule load-aux ( module-name : file )
-{
-    mark-as-user $(module-name) ;
-
-    module $(module-name)
-    {
-        include $(2) ;
-        local rules = [ RULENAMES $(1) ] ;
-        IMPORT $(1) : $(rules) : $(1) : $(1).$(rules) ;
-    }
-}
-
-
-.global-build-dir = [ MATCH --build-dir=(.*) : [ modules.peek : ARGV ] ] ;
-if $(.global-build-dir)
-{
-    # If the option is specified several times, take the last value.
-    .global-build-dir = [ path.make $(.global-build-dir[-1]) ] ;
-}
-
-
-# Initialize the module for a project.
-#
-rule initialize (
-    module-name   # The name of the project module.
-    : location ?  # The location (directory) of the project to initialize. If
-                  # not specified, a standalone project will be initialized.
-    : basename ?
-    )
-{
-    if --debug-loading in [ modules.peek : ARGV ]
-    {
-        ECHO "Initializing project '$(module-name)'" ;
-    }
-
-    # TODO: need to consider if standalone projects can do anything but define
-    # prebuilt targets. If so, we need to give it a more sensible "location", so
-    # that source paths are correct.
-    location ?= "" ;
-    # Create the module for the Jamfile first.
-    module $(module-name)
-    {
-    }
-    $(module-name).attributes = [ new project-attributes $(location)
-        $(module-name) ] ;
-    local attributes = $($(module-name).attributes) ;
-
-    if $(location)
-    {
-        $(attributes).set source-location : [ path.make $(location) ] : exact ;
-    }
-    else if ! $(module-name) in test-config site-config user-config project-config
-    {
-        # This is a standalone project with known location. Set source location
-        # so that it can declare targets. This is intended so that you can put
-        # a .jam file in your sources and use it via 'using'. Standard modules
-        # (in 'tools' subdir) may not assume source dir is set.
-        local s = [ modules.binding $(module-name) ] ;
-        if ! $(s)
-        {
-            errors.error "Could not determine project location $(module-name)" ;
-        }        
-        $(attributes).set source-location : $(s:D) : exact ;
-    }
-
-    $(attributes).set requirements       : [ property-set.empty ] : exact ;
-    $(attributes).set usage-requirements : [ property-set.empty ] : exact ;
-
-    # Import rules common to all project modules from project-rules module,
-    # defined at the end of this file.
-    local rules = [ RULENAMES project-rules ] ;
-    IMPORT project-rules : $(rules) : $(module-name) : $(rules) ;
-
-    local jamroot ;
-
-    local parent-module ;
-    if $(module-name) = test-config
-    {
-        # No parent.
-    }
-    else if $(module-name) = site-config
-    {
-        parent-module = test-config ;
-    }
-    else if $(module-name) = user-config
-    {
-        parent-module = site-config ;
-    }
-    else if $(module-name) = project-config
-    {
-        parent-module = user-config ;
-    }    
-    else
-    {
-        # We search for parent/project-root only if Jamfile was specified, i.e.
-        # if the project is not standalone.
-        if $(location) && ! [ MATCH ($(JAMROOT)) : $(basename) ]
-        {
-            parent-module = [ load-parent $(location) ] ;
-        }
-        else
-        {
-            # It's either jamroot or standalone project. If it's jamroot,
-            # inherit from user-config.
-            if $(location)
-            {
-                # If project-config module exist, inherit from it.
-                if $(project-config.attributes)
-                {   
-                    parent-module = project-config ;
-                }
-                else
-                {                    
-                    parent-module = user-config ;
-                }                
-                jamroot = true ;
-            }
-        }
-    }
-
-    if $(parent-module)
-    {
-        inherit-attributes $(module-name) : $(parent-module) ;
-        $(attributes).set parent-module : $(parent-module) : exact ;
-    }
-
-    if $(jamroot)
-    {
-        $(attributes).set project-root : $(location) : exact ;
-    }
-
-    local parent ;
-    if $(parent-module)
-    {
-        parent = [ target $(parent-module) ] ;
-    }
-
-    if ! $(.target.$(module-name))
-    {
-        .target.$(module-name) = [ new project-target $(module-name)
-            : $(module-name) $(parent)
-            : [ attribute $(module-name) requirements ] ] ;
-
-        if --debug-loading in [ modules.peek : ARGV ]
-        {
-            ECHO "Assigned project target" $(.target.$(module-name))
-                "to '$(module-name)'" ;
-        }
-    }
-
-    .current-project = [ target $(module-name) ] ;
-}
-
-
-# Make 'project-module' inherit attributes of project root and parent module.
-#
-rule inherit-attributes ( project-module : parent-module )
-{
-    local attributes = $($(project-module).attributes) ;
-    local pattributes = [ attributes $(parent-module) ] ;
-    # Parent module might be locationless configuration module.
-    if [ modules.binding $(parent-module) ]
-    {
-        $(attributes).set parent : [ path.parent
-            [ path.make [ modules.binding $(parent-module) ] ] ] ;
-    }
-    local v = [ $(pattributes).get project-root ] ;
-    $(attributes).set project-root : $(v) : exact ;
-    $(attributes).set default-build
-        : [ $(pattributes).get default-build ] ;
-    $(attributes).set requirements
-        : [ $(pattributes).get requirements ] : exact ;
-    $(attributes).set usage-requirements
-        : [ $(pattributes).get usage-requirements ] : exact ;
-
-    local parent-build-dir = [ $(pattributes).get build-dir ] ;
-    if $(parent-build-dir)
-    {
-        # Have to compute relative path from parent dir to our dir. Convert both
-        # paths to absolute, since we cannot find relative path from ".." to
-        # ".".
-
-        local location = [ attribute $(project-module) location ] ;
-        local parent-location = [ attribute $(parent-module) location ] ;
-
-        local pwd = [ path.pwd ] ;
-        local parent-dir = [ path.root $(parent-location) $(pwd) ] ;
-        local our-dir = [ path.root $(location) $(pwd) ] ;
-        $(attributes).set build-dir : [ path.join $(parent-build-dir)
-            [ path.relative $(our-dir) $(parent-dir) ] ] : exact ;
-    }
-}
-
-
-# Associate the given id with the given project module.
-#
-rule register-id ( id : module )
-{
-    $(id).jamfile-module = $(module) ;
-}
-
-
-# Class keeping all the attributes of a project.
-#
-# The standard attributes are "id", "location", "project-root", "parent"
-# "requirements", "default-build", "source-location" and "projects-to-build".
-#
-class project-attributes
-{
-    import property ;
-    import property-set ;
-    import errors ;
-    import path ;
-    import print ;
-    import sequence ;
-    import project ;
-
-    rule __init__ ( location project-module )
-    {
-        self.location = $(location) ;
-        self.project-module = $(project-module) ;
-    }
-
-    # Set the named attribute from the specification given by the user. The
-    # value actually set may be different.
-    #
-    rule set ( attribute : specification *
-        : exact ?  # Sets value from 'specification' without any processing.
-        )
-    {
-        if $(exact)
-        {
-            self.$(attribute) = $(specification) ;
-        }
-        else if $(attribute) = "requirements"
-        {
-            local result = [ property-set.refine-from-user-input
-                $(self.requirements) : $(specification)
-                : $(self.project-module) : $(self.location) ] ;
-
-            if $(result[1]) = "@error"
-            {
-                errors.error Requirements for project at '$(self.location)'
-                    conflict with parent's. : Explanation: $(result[2-]) ;
-            }
-            else
-            {
-                self.requirements = $(result) ;
-            }
-        }
-        else if $(attribute) = "usage-requirements"
-        {
-            local unconditional ;
-            for local p in $(specification)
-            {
-                local split = [ property.split-conditional $(p) ] ;
-                split ?= nothing $(p) ;
-                unconditional += $(split[2]) ;
-            }
-
-            local non-free = [ property.remove free : $(unconditional) ] ;
-            if $(non-free)
-            {
-                errors.error usage-requirements $(specification) have non-free
-                    properties $(non-free) ;
-            }
-            local t = [ property.translate-paths $(specification)
-                                      : $(self.location) ] ;
-            if $(self.usage-requirements)
-            {
-                self.usage-requirements = [ property-set.create
-                    [ $(self.usage-requirements).raw ] $(t) ] ;
-            }
-            else
-            {
-                self.usage-requirements = [ property-set.create $(t) ] ;
-            }
-        }
-        else if $(attribute) = "default-build"
-        {
-            self.default-build = [ property.make $(specification) ] ;
-        }
-        else if $(attribute) = "source-location"
-        {
-            self.source-location = ;
-            for local src-path in $(specification)
-            {
-                self.source-location += [ path.root [ path.make $(src-path) ]
-                    $(self.location) ] ;
-            }
-        }
-        else if $(attribute) = "build-dir"
-        {
-            self.build-dir = [ path.root
-                [ path.make $(specification) ] $(self.location) ] ;
-        }
-        else if $(attribute) = "id"
-        {
-            id = [ path.root $(specification) / ] ;
-            project.register-id $(id) : $(self.project-module) ;
-            self.id = $(id) ;
-        }
-        else if ! $(attribute) in "default-build" "location" "parent"
-            "projects-to-build" "project-root" "source-location"
-        {
-            errors.error Invalid project attribute '$(attribute)' specified for
-                project at '$(self.location)' ;
-        }
-        else
-        {
-            self.$(attribute) = $(specification) ;
-        }
-    }
-
-    # Returns the value of the given attribute.
-    #
-    rule get ( attribute )
-    {
-        return $(self.$(attribute)) ;
-    }
-
-    # Prints the project attributes.
-    #
-    rule print ( )
-    {
-        local id = $(self.id) ; id ?= (none) ;
-        local parent = $(self.parent) ; parent ?= (none) ;
-        print.section "'"$(id)"'" ;
-        print.list-start ;
-        print.list-item "Parent project:" $(parent) ;
-        print.list-item "Requirements:" [ $(self.requirements).raw ] ;
-        print.list-item "Default build:" $(self.default-build) ;
-        print.list-item "Source location:" $(self.source-location) ;
-        print.list-item "Projects to build:"
-                        [ sequence.insertion-sort $(self.projects-to-build) ] ;
-        print.list-end ;
-    }
-}
-
-
-# Returns the project which is currently being loaded.
-#
-rule current ( )
-{
-    return $(.current-project) ;
-}
-
-
-# Temporarily changes the current project to 'project'. Should be followed by
-# 'pop-current'.
-#
-rule push-current ( project )
-{
-    .saved-current-project += $(.current-project) ;
-    .current-project = $(project) ;
-}
-
-
-rule pop-current ( )
-{
-    .current-project = $(.saved-current-project[-1]) ;
-    .saved-current-project = $(.saved-current-project[1--2]) ;
-}
-
-
-# Returns the project-attribute instance for the specified Jamfile module.
-#
-rule attributes ( project )
-{
-    return $($(project).attributes) ;
-}
-
-
-# Returns the value of the specified attribute in the specified Jamfile module.
-#
-rule attribute ( project attribute )
-{
-    return [ $($(project).attributes).get $(attribute) ] ;
-}
-
-
-# Returns the project target corresponding to the 'project-module'.
-#
-rule target ( project-module )
-{
-    if ! $(.target.$(project-module))
-    {
-        .target.$(project-module) = [ new project-target $(project-module)
-            : $(project-module)
-            : [ attribute $(project-module) requirements ] ] ;
-    }
-    return $(.target.$(project-module)) ;
-}
-
-
-# Use/load a project.
-#
-rule use ( id : location )
-{
-    local saved-project = $(.current-project) ;
-    local project-module = [ project.load $(location) ] ;
-    local declared-id = [ project.attribute $(project-module) id ] ;
-
-    if ! $(declared-id) || $(declared-id) != $(id)
-    {
-        # The project at 'location' either has no id or that id is not equal to
-        # the 'id' parameter.
-        if $($(id).jamfile-module) && ( $($(id).jamfile-module) !=
-            $(project-module) )
-        {
-            errors.user-error Attempt to redeclare already existing project id
-                '$(id)' 
-                location '$(location)' ;
-        }
-        $(id).jamfile-module = $(project-module) ;
-    }
-    .current-project = $(saved-project) ;
-}
-
-
-# Defines a Boost.Build extension project. Such extensions usually contain
-# library targets and features that can be used by many people. Even though
-# extensions are really projects, they can be initialized as a module would be
-# with the "using" (project.project-rules.using) mechanism.
-#
-rule extension ( id : options * : * )
-{
-    # The caller is a standalone module for the extension.
-    local mod = [ CALLER_MODULE ] ;
-
-    # We need to do the rest within the extension module.
-    module $(mod)
-    {
-        import path ;
-
-        # Find the root project.
-        local root-project = [ project.current ] ;
-        root-project = [ $(root-project).project-module ] ;
-        while
-            [ project.attribute $(root-project) parent-module ] &&
-            [ project.attribute $(root-project) parent-module ] != user-config
-        {
-            root-project = [ project.attribute $(root-project) parent-module ] ;
-        }
-
-        # Create the project data, and bring in the project rules into the
-        # module.
-        project.initialize $(__name__) : [ path.join [ project.attribute
-            $(root-project) location ] ext $(1:L) ] ;
-
-        # Create the project itself, i.e. the attributes. All extensions are
-        # created in the "/ext" project space.
-        project /ext/$(1) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) :
-            $(9) ;
-        local attributes = [ project.attributes $(__name__) ] ;
-
-        # Inherit from the root project of whomever is defining us.
-        project.inherit-attributes $(__name__) : $(root-project) ;
-        $(attributes).set parent-module : $(root-project) : exact ;
-    }
-}
-
-
-rule glob-internal ( project : wildcards + : excludes * : rule-name )
-{
-    local location = [ $(project).get source-location ] ;
-
-    local result ;
-    local paths = [ path.$(rule-name) $(location) :
-        [ sequence.transform path.make : $(wildcards) ] :
-        [ sequence.transform path.make : $(excludes) ] ] ;
-    if $(wildcards:D) || $(rule-name) != glob
-    {
-        # The paths we have found are relative to the current directory, but the
-        # names specified in the sources list are assumed to be relative to the
-        # source directory of the corresponding project. So, just make the names
-        # absolute.
-        for local p in $(paths)
-        {
-            # If the path is below source location, use relative path.
-            # Otherwise, use full path just to avoid any ambiguities.
-            local rel = [ path.relative $(p) $(location) : no-error ] ;
-            if $(rel) = not-a-child
-            {                   
-                result += [ path.root $(p) [ path.pwd ] ] ;
-            }
-            else
-            {
-                result += $(rel) ;
-            }                
-        }
-    }
-    else
-    {
-        # There were no wildcards in the directory path, so the files are all in
-        # the source directory of the project. Just drop the directory, instead
-        # of making paths absolute.
-        result = $(paths:D="") ;
-    }
-
-    return $(result) ;
-}
-
-
-# This module defines rules common to all projects.
-#
-module project-rules
-{
-    rule using ( toolset-module : * )
-    {
-        import toolset ;
-        import modules ;
-        import project ;
-
-        # Temporarily change the search path so the module referred to by
-        # 'using' can be placed in the same directory as Jamfile. User will
-        # expect the module to be found even though the directory is not in
-        # BOOST_BUILD_PATH.
-        local x = [ modules.peek : BOOST_BUILD_PATH ] ;
-        local caller = [ CALLER_MODULE ] ;
-        local caller-location = [ modules.binding $(caller) ] ;
-        modules.poke : BOOST_BUILD_PATH : $(caller-location:D) $(x) ;
-        toolset.using $(1) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ;
-        modules.poke : BOOST_BUILD_PATH : $(x) ;
-
-        # The above might have clobbered .current-project. Restore the correct
-        # value.
-        modules.poke project : .current-project
-            : [ project.target $(caller) ] ;
-    }
-
-    import modules ;
-
-    rule import ( * : * : * )
-    {
-        modules.import project ;
-
-        local caller = [ CALLER_MODULE ] ;
-        local saved = [ modules.peek project : .current-project ] ;
-        module $(caller)
-        {
-            modules.import $(1) : $(2) : $(3) ;
-        }
-        modules.poke project : .current-project : $(saved) ;
-    }
-
-    rule project ( id ? : options * : * )
-    {
-        import errors ;
-        import path ;
-        import project ;
-
-        local caller = [ CALLER_MODULE ] ;
-        local attributes = [ project.attributes $(caller) ] ;
-        if $(id)
-        {
-           $(attributes).set id : $(id) ;
-        }
-
-        local explicit-build-dir ;
-
-        for n in 2 3 4 5 6 7 8 9
-        {
-            local option = $($(n)) ;
-            if $(option)
-            {
-                $(attributes).set $(option[1]) : $(option[2-]) ;
-            }
-            if $(option[1]) = "build-dir"
-            {
-                explicit-build-dir = [ path.make $(option[2-]) ] ;
-            }
-        }
-
-        # If '--build-dir' is specified, change the build dir for the project.
-        local global-build-dir =
-            [ modules.peek project : .global-build-dir ] ;
-
-        if $(global-build-dir)
-        {
-            local location = [ $(attributes).get location ] ;
-            # Project with an empty location is a 'standalone' project such as
-            # user-config or qt. It has no build dir. If we try to set build dir
-            # for user-config, we shall then try to inherit it, with either
-            # weird or wrong consequences.
-            if $(location) && $(location) = [ $(attributes).get project-root ]
-            {
-                # Re-read the project id, since it might have been changed in
-                # the project's attributes.
-                id = [ $(attributes).get id ] ;
-                # This is Jamroot.
-                if $(id)
-                {
-                    if $(explicit-build-dir) &&
-                        [ path.is-rooted $(explicit-build-dir) ]
-                    {
-                        errors.user-error Absolute directory specified via
-                            'build-dir' project attribute : Do not know how to
-                            combine that with the --build-dir option. ;
-                    }
-                    # Strip the leading slash from id.
-                    local rid = [ MATCH /(.*) : $(id) ] ;
-                    local p = [ path.join
-                        $(global-build-dir) $(rid) $(explicit-build-dir) ] ;
-
-                    $(attributes).set build-dir : $(p) : exact ;
-                }
-            }
-            else
-            {
-                # Not Jamroot.
-                if $(explicit-build-dir)
-                {
-                    errors.user-error When --build-dir is specified, the
-                        'build-dir' project : attribute is allowed only for
-                        top-level 'project' invocations ;
-                }
-            }
-        }
-    }
-
-    # Declare and set a project global constant. Project global constants are
-    # normal variables but should not be changed. They are applied to every
-    # child Jamfile.
-    #
-    rule constant (
-        name  # Variable name of the constant.
-        : value +  # Value of the constant.
-    )
-    {
-        import project ;
-        local caller = [ CALLER_MODULE ] ;
-        local p = [ project.target $(caller) ] ;
-        $(p).add-constant $(name) : $(value) ;
-    }
-
-    # Declare and set a project global constant, whose value is a path. The path
-    # is adjusted to be relative to the invocation directory. The given value
-    # path is taken to be either absolute, or relative to this project root.
-    #
-    rule path-constant (
-        name  # Variable name of the constant.
-        : value +  # Value of the constant.
-        )
-    {
-        import project ;
-        local caller = [ CALLER_MODULE ] ;
-        local p = [ project.target $(caller) ] ;
-        $(p).add-constant $(name) : $(value) : path ;
-    }
-
-    rule use-project ( id : where )
-    {
-        import modules ;
-        # See comment in 'load' for explanation.
-        local caller = [ CALLER_MODULE ] ;
-        modules.poke $(caller) : .used-projects :
-            [ modules.peek $(caller) : .used-projects ]
-            $(id) $(where) ;
-    }
-
-    rule build-project ( dir )
-    {
-        import project ;
-        local caller = [ CALLER_MODULE ] ;
-        local attributes = [ project.attributes $(caller) ] ;
-
-        local now = [ $(attributes).get projects-to-build ] ;
-        $(attributes).set projects-to-build : $(now) $(dir) ;
-    }
-
-    rule explicit ( target-names * )
-    {
-        import project ;
-        # If 'explicit' is used in a helper rule defined in Jamroot and
-        # inherited by children, then most of the time we want 'explicit' to
-        # operate on the Jamfile where the helper rule is invoked.
-        local t = [ project.current ] ;
-        for local n in $(target-names)
-        {
-            $(t).mark-target-as-explicit $(n) ;
-        }
-    }
-
-    rule always ( target-names * )
-    {
-        import project ;
-        local t = [ project.current ] ;
-        for local n in $(target-names)
-        {
-            $(t).mark-target-as-always $(n) ;
-        }        
-    }
-    
-    rule glob ( wildcards + : excludes * )
-    {
-        import project ;
-        return [ project.glob-internal [ project.current ] : $(wildcards) :
-            $(excludes) : glob ] ;
-    }
-
-    rule glob-tree ( wildcards + : excludes * )
-    {
-        import project ;
-
-        if $(wildcards:D) || $(excludes:D)
-        {
-            errors.user-error The patterns to 'glob-tree' may not include
-                directory ;
-        }
-        return [ project.glob-internal [ project.current ] : $(wildcards) :
-            $(excludes) : glob-tree ] ;
-    }
-
-    # Calculates conditional requirements for multiple requirements at once.
-    # This is a shorthand to reduce duplication and to keep an inline
-    # declarative syntax. For example:
-    #
-    #   lib x : x.cpp : [ conditional <toolset>gcc <variant>debug :
-    #       <define>DEBUG_EXCEPTION <define>DEBUG_TRACE ] ;
-    #
-    rule conditional ( condition + : requirements * )
-    {
-        local condition = $(condition:J=,) ;
-        if [ MATCH (:) : $(condition) ]
-        {
-            return $(condition)$(requirements) ;
-        }
-        else
-        {
-            return $(condition):$(requirements) ;
-        }
-    }
-    
-    rule option ( name : value )
-    {
-        if $(__name__) != site-config && $(__name__) != user-config && $(__name__) != project-config
-        {
-            import errors ;
-            errors.error "The 'option' rule may be used only in site-config or user-config" ;
-        }        
-        import option ;
-        option.set $(name) : $(value) ;
-    }    
-}
diff --git a/jam-files/boost-build/build/project.py b/jam-files/boost-build/build/project.py
deleted file mode 100644
index 1e1e16fa..00000000
--- a/jam-files/boost-build/build/project.py
+++ /dev/null
@@ -1,1120 +0,0 @@
-# Status: ported.
-# Base revision: 64488
-
-# Copyright 2002, 2003 Dave Abrahams 
-# Copyright 2002, 2005, 2006 Rene Rivera 
-# Copyright 2002, 2003, 2004, 2005, 2006 Vladimir Prus 
-# Distributed under the Boost Software License, Version 1.0. 
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt) 
-
-#  Implements project representation and loading.
-#   Each project is represented by 
-#   - a module where all the Jamfile content live. 
-#   - an instance of 'project-attributes' class.
-#     (given module name, can be obtained by 'attributes' rule)
-#   - an instance of 'project-target' class (from targets.jam)
-#     (given a module name, can be obtained by 'target' rule)
-#
-#  Typically, projects are created as result of loading Jamfile, which is
-#  do by rules 'load' and 'initialize', below. First, module for Jamfile
-#  is loaded and new project-attributes instance is created. Some rules
-#  necessary for project are added to the module (see 'project-rules' module)
-#  at the bottom of this file.
-#  Default project attributes are set (inheriting attributes of parent project, if
-#  it exists). After that, Jamfile is read. It can declare its own attributes,
-#  via 'project' rule, which will be combined with already set attributes.
-#
-#
-#  The 'project' rule can also declare project id, which will be associated with 
-#  the project module.
-#
-#  There can also be 'standalone' projects. They are created by calling 'initialize'
-#  on arbitrary module, and not specifying location. After the call, the module can
-#  call 'project' rule, declare main target and behave as regular projects. However,
-#  since it's not associated with any location, it's better declare only prebuilt 
-#  targets.
-#
-#  The list of all loaded Jamfile is stored in variable .project-locations. It's possible
-#  to obtain module name for a location using 'module-name' rule. The standalone projects
-#  are not recorded, the only way to use them is by project id.
-
-import b2.util.path
-from b2.build import property_set, property
-from b2.build.errors import ExceptionWithUserContext
-import b2.build.targets
-
-import bjam
-
-import re
-import sys
-import os
-import string
-import imp
-import traceback
-import b2.util.option as option
-
-from b2.util import record_jam_to_value_mapping, qualify_jam_action
-
-class ProjectRegistry:
-
-    def __init__(self, manager, global_build_dir):
-        self.manager = manager
-        self.global_build_dir = global_build_dir
-        self.project_rules_ = ProjectRules(self)
-
-        # The target corresponding to the project being loaded now
-        self.current_project = None
-        
-        # The set of names of loaded project modules
-        self.jamfile_modules = {}
-
-        # Mapping from location to module name
-        self.location2module = {}
-
-        # Mapping from project id to project module
-        self.id2module = {}
-
-        # Map from Jamfile directory to parent Jamfile/Jamroot
-        # location.
-        self.dir2parent_jamfile = {}
-
-        # Map from directory to the name of Jamfile in
-        # that directory (or None).
-        self.dir2jamfile = {}
-
-        # Map from project module to attributes object.
-        self.module2attributes = {}
-
-        # Map from project module to target for the project
-        self.module2target = {}
-
-        # Map from names to Python modules, for modules loaded
-        # via 'using' and 'import' rules in Jamfiles.
-        self.loaded_tool_modules_ = {}
-
-        self.loaded_tool_module_path_ = {}
-
-        # Map from project target to the list of
-        # (id,location) pairs corresponding to all 'use-project'
-        # invocations.
-        # TODO: should not have a global map, keep this
-        # in ProjectTarget.
-        self.used_projects = {}
-
-        self.saved_current_project = []
-
-        self.JAMROOT = self.manager.getenv("JAMROOT");
-
-        # Note the use of character groups, as opposed to listing
-        # 'Jamroot' and 'jamroot'. With the latter, we'd get duplicate
-        # matches on windows and would have to eliminate duplicates.
-        if not self.JAMROOT:
-            self.JAMROOT = ["project-root.jam", "[Jj]amroot", "[Jj]amroot.jam"]
-
-        # Default patterns to search for the Jamfiles to use for build
-        # declarations.
-        self.JAMFILE = self.manager.getenv("JAMFILE")
-
-        if not self.JAMFILE:
-            self.JAMFILE = ["[Bb]uild.jam", "[Jj]amfile.v2", "[Jj]amfile",
-                            "[Jj]amfile.jam"]
-
-
-    def load (self, jamfile_location):
-        """Loads jamfile at the given location. After loading, project global
-        file and jamfile needed by the loaded one will be loaded recursively.
-        If the jamfile at that location is loaded already, does nothing.
-        Returns the project module for the Jamfile."""
-
-        absolute = os.path.join(os.getcwd(), jamfile_location)
-        absolute = os.path.normpath(absolute)
-        jamfile_location = b2.util.path.relpath(os.getcwd(), absolute)
-
-        if "--debug-loading" in self.manager.argv():
-            print "Loading Jamfile at '%s'" % jamfile_location
-
-            
-        mname = self.module_name(jamfile_location)
-        # If Jamfile is already loaded, don't try again.
-        if not mname in self.jamfile_modules:
-        
-            self.load_jamfile(jamfile_location, mname)
-                
-            # We want to make sure that child project are loaded only
-            # after parent projects. In particular, because parent projects
-            # define attributes whch are inherited by children, and we don't
-            # want children to be loaded before parents has defined everything.
-            #
-            # While "build-project" and "use-project" can potentially refer
-            # to child projects from parent projects, we don't immediately
-            # load child projects when seing those attributes. Instead,
-            # we record the minimal information that will be used only later.
-            
-            self.load_used_projects(mname)
-             
-        return mname
-
-    def load_used_projects(self, module_name):
-        # local used = [ modules.peek $(module-name) : .used-projects ] ;
-        used = self.used_projects[module_name]
-    
-        location = self.attribute(module_name, "location")
-        for u in used:
-            id = u[0]
-            where = u[1]
-
-            self.use(id, os.path.join(location, where))
-
-    def load_parent(self, location):
-        """Loads parent of Jamfile at 'location'.
-        Issues an error if nothing is found."""
-
-        found = b2.util.path.glob_in_parents(
-            location, self.JAMROOT + self.JAMFILE) 
-
-        if not found:
-            print "error: Could not find parent for project at '%s'" % location
-            print "error: Did not find Jamfile or project-root.jam in any parent directory."
-            sys.exit(1)
-    
-        return self.load(os.path.dirname(found[0]))
-
-    def act_as_jamfile(self, module, location):
-        """Makes the specified 'module' act as if it were a regularly loaded Jamfile 
-        at 'location'. If Jamfile is already located for that location, it's an 
-        error."""
-
-        if self.module_name(location) in self.jamfile_modules:
-            self.manager.errors()(
-                "Jamfile was already loaded for '%s'" % location)
-    
-        # Set up non-default mapping from location to module.
-        self.location2module[location] = module
-    
-        # Add the location to the list of project locations
-        # so that we don't try to load Jamfile in future
-        self.jamfile_modules.append(location)
-    
-        self.initialize(module, location)
-
-    def find(self, name, current_location):
-        """Given 'name' which can be project-id or plain directory name,
-        return project module corresponding to that id or directory.
-        Returns nothing of project is not found."""
-
-        project_module = None
-
-        # Try interpreting name as project id.
-        if name[0] == '/':
-            project_module = self.id2module.get(name)
-
-        if not project_module:
-            location = os.path.join(current_location, name)
-            # If no project is registered for the given location, try to
-            # load it. First see if we have Jamfile. If not we might have project
-            # root, willing to act as Jamfile. In that case, project-root
-            # must be placed in the directory referred by id.
-        
-            project_module = self.module_name(location)
-            if not project_module in self.jamfile_modules:
-                if b2.util.path.glob([location], self.JAMROOT + self.JAMFILE):
-                    project_module = self.load(location)
-                else:
-                    project_module = None
-
-        return project_module
-
-    def module_name(self, jamfile_location):
-        """Returns the name of module corresponding to 'jamfile-location'.
-        If no module corresponds to location yet, associates default
-        module name with that location."""
-        module = self.location2module.get(jamfile_location)
-        if not module:
-            # Root the path, so that locations are always umbiguious.
-            # Without this, we can't decide if '../../exe/program1' and '.'
-            # are the same paths, or not.
-            jamfile_location = os.path.realpath(
-                os.path.join(os.getcwd(), jamfile_location))
-            module = "Jamfile<%s>" % jamfile_location
-            self.location2module[jamfile_location] = module
-        return module
-
-    def find_jamfile (self, dir, parent_root=0, no_errors=0):
-        """Find the Jamfile at the given location. This returns the
-        exact names of all the Jamfiles in the given directory. The optional
-        parent-root argument causes this to search not the given directory
-        but the ones above it up to the directory given in it."""
-        
-        # Glob for all the possible Jamfiles according to the match pattern.
-        #
-        jamfile_glob = None
-        if parent_root:
-            parent = self.dir2parent_jamfile.get(dir)
-            if not parent:
-                parent = b2.util.path.glob_in_parents(dir,
-                                                               self.JAMFILE)
-                self.dir2parent_jamfile[dir] = parent
-            jamfile_glob = parent
-        else:
-            jamfile = self.dir2jamfile.get(dir)
-            if not jamfile:
-                jamfile = b2.util.path.glob([dir], self.JAMFILE)
-                self.dir2jamfile[dir] = jamfile
-            jamfile_glob = jamfile
-
-        if len(jamfile_glob) > 1:
-            # Multiple Jamfiles found in the same place. Warn about this.
-            # And ensure we use only one of them.
-            # As a temporary convenience measure, if there's Jamfile.v2 amount
-            # found files, suppress the warning and use it.
-            #
-            pattern = "(.*[Jj]amfile\\.v2)|(.*[Bb]uild\\.jam)"
-            v2_jamfiles = [x for x in jamfile_glob if re.match(pattern, x)]
-            if len(v2_jamfiles) == 1:
-                jamfile_glob = v2_jamfiles
-            else:
-                print """warning: Found multiple Jamfiles at '%s'!""" % (dir)
-                for j in jamfile_glob:
-                    print "    -", j
-                print "Loading the first one"
-    
-        # Could not find it, error.
-        if not no_errors and not jamfile_glob:
-            self.manager.errors()(
-                """Unable to load Jamfile.
-Could not find a Jamfile in directory '%s'
-Attempted to find it with pattern '%s'.
-Please consult the documentation at 'http://boost.org/boost-build2'."""
-                % (dir, string.join(self.JAMFILE)))
-
-        if jamfile_glob:
-            return jamfile_glob[0]
-    
-    def load_jamfile(self, dir, jamfile_module):
-        """Load a Jamfile at the given directory. Returns nothing.
-        Will attempt to load the file as indicated by the JAMFILE patterns.
-        Effect of calling this rule twice with the same 'dir' is underfined."""
-      
-        # See if the Jamfile is where it should be.
-        is_jamroot = False
-        jamfile_to_load = b2.util.path.glob([dir], self.JAMROOT)
-        if not jamfile_to_load:
-            jamfile_to_load = self.find_jamfile(dir)
-        else:
-            if len(jamfile_to_load) > 1:
-                get_manager().errors()("Multiple Jamfiles found at '%s'\n" +\
-                                       "Filenames are: %s"
-                                       % (dir, [os.path.basename(j) for j in jamfile_to_load]))
-
-            is_jamroot = True
-            jamfile_to_load = jamfile_to_load[0]
-
-        dir = os.path.dirname(jamfile_to_load)
-        if not dir:
-            dir = "."
-
-        self.used_projects[jamfile_module] = []
-        
-        # Now load the Jamfile in it's own context. 
-        # The call to 'initialize' may load parent Jamfile, which might have
-        # 'use-project' statement that causes a second attempt to load the
-        # same project we're loading now.  Checking inside .jamfile-modules
-        # prevents that second attempt from messing up.
-        if not jamfile_module in self.jamfile_modules:
-            self.jamfile_modules[jamfile_module] = True
-
-            # Initialize the jamfile module before loading.
-            #    
-            self.initialize(jamfile_module, dir, os.path.basename(jamfile_to_load))
-
-            saved_project = self.current_project
-
-            bjam.call("load", jamfile_module, jamfile_to_load)
-            basename = os.path.basename(jamfile_to_load)
-
-            if is_jamroot:
-                jamfile = self.find_jamfile(dir, no_errors=True)
-                if jamfile:
-                    bjam.call("load", jamfile_module, jamfile)
-                                    
-        # Now do some checks
-        if self.current_project != saved_project:
-            self.manager.errors()(
-"""The value of the .current-project variable
-has magically changed after loading a Jamfile.
-This means some of the targets might be defined a the wrong project.
-after loading %s
-expected value %s
-actual value %s""" % (jamfile_module, saved_project, self.current_project))
-          
-        if self.global_build_dir:
-            id = self.attributeDefault(jamfile_module, "id", None)
-            project_root = self.attribute(jamfile_module, "project-root")
-            location = self.attribute(jamfile_module, "location")
-
-            if location and project_root == dir:
-                # This is Jamroot
-                if not id:
-                    # FIXME: go via errors module, so that contexts are
-                    # shown?
-                    print "warning: the --build-dir option was specified"
-                    print "warning: but Jamroot at '%s'" % dir
-                    print "warning: specified no project id"
-                    print "warning: the --build-dir option will be ignored"
-
-
-    def load_standalone(self, jamfile_module, file):
-        """Loads 'file' as standalone project that has no location
-        associated with it.  This is mostly useful for user-config.jam,
-        which should be able to define targets, but although it has
-        some location in filesystem, we don't want any build to
-        happen in user's HOME, for example.
-
-        The caller is required to never call this method twice on
-        the same file.
-        """
-
-        self.used_projects[jamfile_module] = []
-        bjam.call("load", jamfile_module, file)
-        self.load_used_projects(jamfile_module)
-        
-    def is_jamroot(self, basename):
-        match = [ pat for pat in self.JAMROOT if re.match(pat, basename)]
-        if match:
-            return 1
-        else:
-            return 0
-
-    def initialize(self, module_name, location=None, basename=None):
-        """Initialize the module for a project.
-        
-        module-name is the name of the project module.
-        location is the location (directory) of the project to initialize.
-                 If not specified, stanalone project will be initialized
-        """
-
-        if "--debug-loading" in self.manager.argv():
-            print "Initializing project '%s'" % module_name
-
-        # TODO: need to consider if standalone projects can do anything but defining
-        # prebuilt targets. If so, we need to give more sensible "location", so that
-        # source paths are correct.
-        if not location:
-            location = ""
-
-        attributes = ProjectAttributes(self.manager, location, module_name)
-        self.module2attributes[module_name] = attributes
-
-        python_standalone = False
-        if location:
-            attributes.set("source-location", [location], exact=1)
-        elif not module_name in ["test-config", "site-config", "user-config", "project-config"]:
-            # This is a standalone project with known location. Set source location
-            # so that it can declare targets. This is intended so that you can put
-            # a .jam file in your sources and use it via 'using'. Standard modules
-            # (in 'tools' subdir) may not assume source dir is set.
-            module = sys.modules[module_name]          
-            attributes.set("source-location", self.loaded_tool_module_path_[module_name], exact=1)
-            python_standalone = True
-
-        attributes.set("requirements", property_set.empty(), exact=True)
-        attributes.set("usage-requirements", property_set.empty(), exact=True)
-        attributes.set("default-build", property_set.empty(), exact=True)
-        attributes.set("projects-to-build", [], exact=True)
-        attributes.set("project-root", None, exact=True)
-        attributes.set("build-dir", None, exact=True)
-        
-        self.project_rules_.init_project(module_name, python_standalone)
-
-        jamroot = False
-
-        parent_module = None;
-        if module_name == "test-config":
-            # No parent
-            pass
-        elif module_name == "site-config":
-            parent_module = "test-config"
-        elif module_name == "user-config":
-            parent_module = "site-config"
-        elif module_name == "project-config":
-            parent_module = "user-config"
-        elif location and not self.is_jamroot(basename):
-            # We search for parent/project-root only if jamfile was specified 
-            # --- i.e
-            # if the project is not standalone.
-            parent_module = self.load_parent(location)
-        else:
-            # It's either jamroot, or standalone project.
-            # If it's jamroot, inherit from user-config.
-            if location:
-                # If project-config module exist, inherit from it.
-                if self.module2attributes.has_key("project-config"):
-                    parent_module = "project-config"
-                else:
-                    parent_module = "user-config" ;
-                
-                jamroot = True ;
-                
-        if parent_module:
-            self.inherit_attributes(module_name, parent_module)
-            attributes.set("parent-module", parent_module, exact=1)
-
-        if jamroot:
-            attributes.set("project-root", location, exact=1)
-                                
-        parent = None
-        if parent_module:
-            parent = self.target(parent_module)
-
-        if not self.module2target.has_key(module_name):
-            target = b2.build.targets.ProjectTarget(self.manager,
-                module_name, module_name, parent,
-                self.attribute(module_name,"requirements"),
-                # FIXME: why we need to pass this? It's not
-                # passed in jam code.
-                self.attribute(module_name, "default-build"))
-            self.module2target[module_name] = target
-
-        self.current_project = self.target(module_name)
-
-    def inherit_attributes(self, project_module, parent_module):
-        """Make 'project-module' inherit attributes of project
-        root and parent module."""
-
-        attributes = self.module2attributes[project_module]
-        pattributes = self.module2attributes[parent_module]
-        
-        # Parent module might be locationless user-config.
-        # FIXME:
-        #if [ modules.binding $(parent-module) ]
-        #{        
-        #    $(attributes).set parent : [ path.parent 
-        #                                 [ path.make [ modules.binding $(parent-module) ] ] ] ;
-        #    }
-        
-        attributes.set("project-root", pattributes.get("project-root"), exact=True)
-        attributes.set("default-build", pattributes.get("default-build"), exact=True)
-        attributes.set("requirements", pattributes.get("requirements"), exact=True)
-        attributes.set("usage-requirements",
-                       pattributes.get("usage-requirements"), exact=1)
-
-        parent_build_dir = pattributes.get("build-dir")
-        
-        if parent_build_dir:
-        # Have to compute relative path from parent dir to our dir
-        # Convert both paths to absolute, since we cannot
-        # find relative path from ".." to "."
-
-             location = attributes.get("location")
-             parent_location = pattributes.get("location")
-
-             our_dir = os.path.join(os.getcwd(), location)
-             parent_dir = os.path.join(os.getcwd(), parent_location)
-
-             build_dir = os.path.join(parent_build_dir,
-                                      os.path.relpath(our_dir, parent_dir))
-             attributes.set("build-dir", build_dir, exact=True)
-
-    def register_id(self, id, module):
-        """Associate the given id with the given project module."""
-        self.id2module[id] = module
-
-    def current(self):
-        """Returns the project which is currently being loaded."""
-        return self.current_project
-
-    def set_current(self, c):
-        self.current_project = c
-
-    def push_current(self, project):
-        """Temporary changes the current project to 'project'. Should
-        be followed by 'pop-current'."""
-        self.saved_current_project.append(self.current_project)
-        self.current_project = project
-
-    def pop_current(self):
-        self.current_project = self.saved_current_project[-1]
-        del self.saved_current_project[-1]
-
-    def attributes(self, project):
-        """Returns the project-attribute instance for the
-        specified jamfile module."""
-        return self.module2attributes[project]
-
-    def attribute(self, project, attribute):
-        """Returns the value of the specified attribute in the
-        specified jamfile module."""
-        return self.module2attributes[project].get(attribute)
-        try:    
-            return self.module2attributes[project].get(attribute)
-        except:
-            raise BaseException("No attribute '%s' for project" % (attribute, project))
-
-    def attributeDefault(self, project, attribute, default):
-        """Returns the value of the specified attribute in the
-        specified jamfile module."""
-        return self.module2attributes[project].getDefault(attribute, default)
-
-    def target(self, project_module):
-        """Returns the project target corresponding to the 'project-module'."""
-        if not self.module2target.has_key(project_module):
-            self.module2target[project_module] = \
-                b2.build.targets.ProjectTarget(project_module, project_module,
-                              self.attribute(project_module, "requirements"))
-        
-        return self.module2target[project_module]
-
-    def use(self, id, location):
-        # Use/load a project.
-        saved_project = self.current_project
-        project_module = self.load(location)
-        declared_id = self.attributeDefault(project_module, "id", "")
-
-        if not declared_id or declared_id != id:
-            # The project at 'location' either have no id or
-            # that id is not equal to the 'id' parameter.
-            if self.id2module.has_key(id) and self.id2module[id] != project_module:
-                self.manager.errors()(
-"""Attempt to redeclare already existing project id '%s' at location '%s'""" % (id, location))
-            self.id2module[id] = project_module
-
-        self.current_module = saved_project
-
-    def add_rule(self, name, callable):
-        """Makes rule 'name' available to all subsequently loaded Jamfiles.
-
-        Calling that rule wil relay to 'callable'."""
-        self.project_rules_.add_rule(name, callable)
-
-    def project_rules(self):
-        return self.project_rules_
-
-    def glob_internal(self, project, wildcards, excludes, rule_name):
-        location = project.get("source-location")[0]
-
-        result = []
-        callable = b2.util.path.__dict__[rule_name]
-        
-        paths = callable([location], wildcards, excludes)
-        has_dir = 0
-        for w in wildcards:
-            if os.path.dirname(w):
-                has_dir = 1
-                break
-
-        if has_dir or rule_name != "glob":
-            result = []
-            # The paths we've found are relative to current directory,
-            # but the names specified in sources list are assumed to
-            # be relative to source directory of the corresponding
-            # prject. Either translate them or make absolute.
-
-            for p in paths:
-                rel = os.path.relpath(p, location)
-                # If the path is below source location, use relative path.
-                if not ".." in rel:
-                    result.append(rel)
-                else:
-                    # Otherwise, use full path just to avoid any ambiguities.
-                    result.append(os.path.abspath(p))
-                    
-        else:
-            # There were not directory in wildcard, so the files are all
-            # in the source directory of the project. Just drop the
-            # directory, instead of making paths absolute.
-            result = [os.path.basename(p) for p in paths]
-            
-        return result
-
-    def load_module(self, name, extra_path=None):
-        """Load a Python module that should be useable from Jamfiles.
-
-        There are generally two types of modules Jamfiles might want to
-        use:
-        - Core Boost.Build. Those are imported using plain names, e.g.
-        'toolset', so this function checks if we have module named
-        b2.package.module already.
-        - Python modules in the same directory as Jamfile. We don't
-        want to even temporary add Jamfile's directory to sys.path,
-        since then we might get naming conflicts between standard
-        Python modules and those.
-        """
-
-        # See if we loaded module of this name already
-        existing = self.loaded_tool_modules_.get(name)
-        if existing:
-            return existing
-
-        # See if we have a module b2.whatever.<name>, where <name>
-        # is what is passed to this function
-        modules = sys.modules
-        for class_name in modules:
-            parts = class_name.split('.')
-            if name is class_name or parts[0] == "b2" \
-            and parts[-1] == name.replace("-", "_"):
-                module = modules[class_name]
-                self.loaded_tool_modules_[name] = module
-                return module
-
-        # Lookup a module in BOOST_BUILD_PATH
-        path = extra_path
-        if not path:
-            path = []
-        path.extend(self.manager.boost_build_path())
-        location = None
-        for p in path:
-            l = os.path.join(p, name + ".py")
-            if os.path.exists(l):
-                location = l
-                break
-
-        if not location:
-            self.manager.errors()("Cannot find module '%s'" % name)
-
-        mname = name + "__for_jamfile"
-        file = open(location)
-        try:            
-            # TODO: this means we'll never make use of .pyc module,
-            # which might be a problem, or not.
-            self.loaded_tool_module_path_[mname] = location
-            module = imp.load_module(mname, file, os.path.basename(location),
-                                     (".py", "r", imp.PY_SOURCE))
-            self.loaded_tool_modules_[name] = module
-            return module
-        finally:
-            file.close()
-        
-
-
-# FIXME:
-# Defines a Boost.Build extension project. Such extensions usually
-# contain library targets and features that can be used by many people.
-# Even though extensions are really projects, they can be initialize as
-# a module would be with the "using" (project.project-rules.using)
-# mechanism.
-#rule extension ( id : options * : * )
-#{
-#    # The caller is a standalone module for the extension.
-#    local mod = [ CALLER_MODULE ] ;
-#    
-#    # We need to do the rest within the extension module.
-#    module $(mod)
-#    {
-#        import path ;
-#        
-#        # Find the root project.
-#        local root-project = [ project.current ] ;
-#        root-project = [ $(root-project).project-module ] ;
-#        while
-#            [ project.attribute $(root-project) parent-module ] &&
-#            [ project.attribute $(root-project) parent-module ] != user-config
-#        {
-#            root-project = [ project.attribute $(root-project) parent-module ] ;
-#        }
-#        
-#        # Create the project data, and bring in the project rules
-#        # into the module.
-#        project.initialize $(__name__) :
-#            [ path.join [ project.attribute $(root-project) location ] ext $(1:L) ] ;
-#        
-#        # Create the project itself, i.e. the attributes.
-#        # All extensions are created in the "/ext" project space.
-#        project /ext/$(1) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ;
-#        local attributes = [ project.attributes $(__name__) ] ;
-#        
-#        # Inherit from the root project of whomever is defining us.
-#        project.inherit-attributes $(__name__) : $(root-project) ;
-#        $(attributes).set parent-module : $(root-project) : exact ;
-#    }
-#}
-        
-
-class ProjectAttributes:
-    """Class keeping all the attributes of a project.
-
-    The standard attributes are 'id', "location", "project-root", "parent"
-    "requirements", "default-build", "source-location" and "projects-to-build".
-    """
-        
-    def __init__(self, manager, location, project_module):
-        self.manager = manager
-        self.location = location
-        self.project_module = project_module
-        self.attributes = {}
-        self.usage_requirements = None
-        
-    def set(self, attribute, specification, exact=False):
-        """Set the named attribute from the specification given by the user.
-        The value actually set may be different."""
-
-        if exact:
-            self.__dict__[attribute] = specification
-            
-        elif attribute == "requirements":
-            self.requirements = property_set.refine_from_user_input(
-                self.requirements, specification,
-                self.project_module, self.location)
-            
-        elif attribute == "usage-requirements":
-            unconditional = []
-            for p in specification:
-                split = property.split_conditional(p)
-                if split:
-                    unconditional.append(split[1])
-                else:
-                    unconditional.append(p)
-
-            non_free = property.remove("free", unconditional)
-            if non_free:                
-                get_manager().errors()("usage-requirements %s have non-free properties %s" \
-                                       % (specification, non_free))
-
-            t = property.translate_paths(
-                    property.create_from_strings(specification, allow_condition=True),
-                    self.location)
-
-            existing = self.__dict__.get("usage-requirements")
-            if existing:
-                new = property_set.create(existing.all() +  t)
-            else:
-                new = property_set.create(t)
-            self.__dict__["usage-requirements"] = new
-
-                
-        elif attribute == "default-build":
-            self.__dict__["default-build"] = property_set.create(specification)
-            
-        elif attribute == "source-location":
-            source_location = []
-            for path in specification:
-                source_location.append(os.path.join(self.location, path))
-            self.__dict__["source-location"] = source_location
-                
-        elif attribute == "build-dir":
-            self.__dict__["build-dir"] = os.path.join(self.location, specification[0])
-
-        elif attribute == "id":
-            id = specification[0]
-            if id[0] != '/':
-                id = "/" + id
-            self.manager.projects().register_id(id, self.project_module)
-            self.__dict__["id"] = id
-                
-        elif not attribute in ["default-build", "location",
-                               "source-location", "parent",
-                               "projects-to-build", "project-root"]:
-            self.manager.errors()(
-"""Invalid project attribute '%s' specified
-for project at '%s'""" % (attribute, self.location))
-        else:
-            self.__dict__[attribute] = specification
-
-    def get(self, attribute):
-        return self.__dict__[attribute]
-
-    def getDefault(self, attribute, default):
-        return self.__dict__.get(attribute, default)
-
-    def dump(self):
-        """Prints the project attributes."""
-        id = self.get("id")
-        if not id:
-            id = "(none)"
-        else:
-            id = id[0]
-
-        parent = self.get("parent")
-        if not parent:
-            parent = "(none)"
-        else:
-            parent = parent[0]
-
-        print "'%s'" % id
-        print "Parent project:%s", parent
-        print "Requirements:%s", self.get("requirements")
-        print "Default build:%s", string.join(self.get("debuild-build"))
-        print "Source location:%s", string.join(self.get("source-location"))
-        print "Projects to build:%s", string.join(self.get("projects-to-build").sort());
-
-class ProjectRules:
-    """Class keeping all rules that are made available to Jamfile."""
-
-    def __init__(self, registry):
-        self.registry = registry
-        self.manager_ = registry.manager
-        self.rules = {}
-        self.local_names = [x for x in self.__class__.__dict__
-                            if x not in ["__init__", "init_project", "add_rule",
-                                         "error_reporting_wrapper", "add_rule_for_type", "reverse"]]
-        self.all_names_ = [x for x in self.local_names]
-
-    def _import_rule(self, bjam_module, name, callable):
-        if hasattr(callable, "bjam_signature"):
-            bjam.import_rule(bjam_module, name, self.make_wrapper(callable), callable.bjam_signature)
-        else:
-            bjam.import_rule(bjam_module, name, self.make_wrapper(callable))
-        
-
-    def add_rule_for_type(self, type):
-        rule_name = type.lower().replace("_", "-")
-
-        def xpto (name, sources = [], requirements = [], default_build = [], usage_requirements = []):
-            return self.manager_.targets().create_typed_target(
-                type, self.registry.current(), name[0], sources,
-                requirements, default_build, usage_requirements) 
-
-        self.add_rule(rule_name, xpto)
-    
-    def add_rule(self, name, callable):
-        self.rules[name] = callable
-        self.all_names_.append(name)
-
-        # Add new rule at global bjam scope. This might not be ideal,
-        # added because if a jamroot does 'import foo' where foo calls
-        # add_rule, we need to import new rule to jamroot scope, and
-        # I'm lazy to do this now.
-        self._import_rule("", name, callable)
-
-    def all_names(self):
-        return self.all_names_
-
-    def call_and_report_errors(self, callable, *args, **kw):
-        result = None
-        try:
-            self.manager_.errors().push_jamfile_context()
-            result = callable(*args, **kw)
-        except ExceptionWithUserContext, e:
-            e.report()
-        except Exception, e:
-            try:
-                self.manager_.errors().handle_stray_exception (e)
-            except ExceptionWithUserContext, e:
-                e.report()
-        finally:                
-            self.manager_.errors().pop_jamfile_context()
-
-        return result
-
-    def make_wrapper(self, callable):
-        """Given a free-standing function 'callable', return a new
-        callable that will call 'callable' and report all exceptins,
-        using 'call_and_report_errors'."""
-        def wrapper(*args, **kw):
-            return self.call_and_report_errors(callable, *args, **kw)
-        return wrapper
-
-    def init_project(self, project_module, python_standalone=False):
-
-        if python_standalone:
-            m = sys.modules[project_module]
-
-            for n in self.local_names:
-                if n != "import_":
-                    setattr(m, n, getattr(self, n))
-                            
-            for n in self.rules:
-                setattr(m, n, self.rules[n])
-
-            return
-                        
-        for n in self.local_names:            
-            # Using 'getattr' here gives us a bound method,
-            # while using self.__dict__[r] would give unbound one.
-            v = getattr(self, n)
-            if callable(v):
-                if n == "import_":
-                    n = "import"
-                else:
-                    n = string.replace(n, "_", "-")
-                    
-                self._import_rule(project_module, n, v)
-
-        for n in self.rules:
-            self._import_rule(project_module, n, self.rules[n])
-
-    def project(self, *args):
-
-        jamfile_module = self.registry.current().project_module()
-        attributes = self.registry.attributes(jamfile_module)
-        
-        id = None
-        if args and args[0]:
-            id = args[0][0]
-            args = args[1:]
-
-        if id:
-            attributes.set('id', [id])
-
-        explicit_build_dir = None
-        for a in args:
-            if a:
-                attributes.set(a[0], a[1:], exact=0)
-                if a[0] == "build-dir":
-                    explicit_build_dir = a[1]
-        
-        # If '--build-dir' is specified, change the build dir for the project.
-        if self.registry.global_build_dir:
-
-            location = attributes.get("location")
-            # Project with empty location is 'standalone' project, like
-            # user-config, or qt.  It has no build dir.
-            # If we try to set build dir for user-config, we'll then
-            # try to inherit it, with either weird, or wrong consequences.
-            if location and location == attributes.get("project-root"):
-                # Re-read the project id, since it might have been changed in
-                # the project's attributes.
-                id = attributes.get('id')
-
-                # This is Jamroot.
-                if id:
-                    if explicit_build_dir and os.path.isabs(explicit_build_dir):
-                        self.registry.manager.errors()(
-"""Absolute directory specified via 'build-dir' project attribute
-Don't know how to combine that with the --build-dir option.""")
-
-                    rid = id
-                    if rid[0] == '/':
-                        rid = rid[1:]
-                    
-                    p = os.path.join(self.registry.global_build_dir, rid)
-                    if explicit_build_dir:
-                        p = os.path.join(p, explicit_build_dir)
-                    attributes.set("build-dir", p, exact=1)
-            elif explicit_build_dir:
-                self.registry.manager.errors()(
-"""When --build-dir is specified, the 'build-dir'
-attribute is allowed only for top-level 'project' invocations""")
-
-    def constant(self, name, value):
-        """Declare and set a project global constant.
-        Project global constants are normal variables but should
-        not be changed. They are applied to every child Jamfile."""
-        m = "Jamfile</home/ghost/Work/Boost/boost-svn/tools/build/v2_python/python/tests/bjam/make>"
-        self.registry.current().add_constant(name[0], value)
-
-    def path_constant(self, name, value):
-        """Declare and set a project global constant, whose value is a path. The
-        path is adjusted to be relative to the invocation directory. The given
-        value path is taken to be either absolute, or relative to this project
-        root."""
-        if len(value) > 1:
-            self.registry.manager.error()("path constant should have one element")
-        self.registry.current().add_constant(name[0], value[0], path=1)
-
-    def use_project(self, id, where):
-        # See comment in 'load' for explanation why we record the
-        # parameters as opposed to loading the project now.
-        m = self.registry.current().project_module();
-        self.registry.used_projects[m].append((id[0], where[0]))
-        
-    def build_project(self, dir):
-        assert(isinstance(dir, list))
-        jamfile_module = self.registry.current().project_module()
-        attributes = self.registry.attributes(jamfile_module)
-        now = attributes.get("projects-to-build")
-        attributes.set("projects-to-build", now + dir, exact=True)
-
-    def explicit(self, target_names):
-        self.registry.current().mark_targets_as_explicit(target_names)
-
-    def always(self, target_names):
-        self.registry.current().mark_targets_as_alays(target_names)
-
-    def glob(self, wildcards, excludes=None):
-        return self.registry.glob_internal(self.registry.current(),
-                                           wildcards, excludes, "glob")
-
-    def glob_tree(self, wildcards, excludes=None):
-        bad = 0
-        for p in wildcards:
-            if os.path.dirname(p):
-                bad = 1
-
-        if excludes:
-            for p in excludes:
-                if os.path.dirname(p):
-                    bad = 1
-
-        if bad:
-            self.registry.manager.errors()(
-"The patterns to 'glob-tree' may not include directory")
-        return self.registry.glob_internal(self.registry.current(),
-                                           wildcards, excludes, "glob_tree")
-    
-
-    def using(self, toolset, *args):
-        # The module referred by 'using' can be placed in
-        # the same directory as Jamfile, and the user
-        # will expect the module to be found even though
-        # the directory is not in BOOST_BUILD_PATH.
-        # So temporary change the search path.
-        current = self.registry.current()
-        location = current.get('location')
-
-        m = self.registry.load_module(toolset[0], [location])
-        if not m.__dict__.has_key("init"):
-            self.registry.manager.errors()(
-                "Tool module '%s' does not define the 'init' method" % toolset[0])
-        m.init(*args)
-
-        # The above might have clobbered .current-project. Restore the correct
-        # value.
-        self.registry.set_current(current)
-
-    def import_(self, name, names_to_import=None, local_names=None):
-
-        name = name[0]
-        py_name = name
-        if py_name == "os":
-            py_name = "os_j"
-        jamfile_module = self.registry.current().project_module()
-        attributes = self.registry.attributes(jamfile_module)
-        location = attributes.get("location")
-
-        saved = self.registry.current()
-
-        m = self.registry.load_module(py_name, [location])
-
-        for f in m.__dict__:
-            v = m.__dict__[f]
-            f = f.replace("_", "-")
-            if callable(v):
-                qn = name + "." + f
-                self._import_rule(jamfile_module, qn, v)
-                record_jam_to_value_mapping(qualify_jam_action(qn, jamfile_module), v)
-
-
-        if names_to_import:
-            if not local_names:
-                local_names = names_to_import
-
-            if len(names_to_import) != len(local_names):
-                self.registry.manager.errors()(
-"""The number of names to import and local names do not match.""")
-
-            for n, l in zip(names_to_import, local_names):
-                self._import_rule(jamfile_module, l, m.__dict__[n])
-                
-        self.registry.set_current(saved)
-        
-    def conditional(self, condition, requirements):
-        """Calculates conditional requirements for multiple requirements
-        at once. This is a shorthand to be reduce duplication and to
-        keep an inline declarative syntax. For example:
-
-            lib x : x.cpp : [ conditional <toolset>gcc <variant>debug :
-                <define>DEBUG_EXCEPTION <define>DEBUG_TRACE ] ;
-        """
-
-        c = string.join(condition, ",")
-        if c.find(":") != -1:
-            return [c + r for r in requirements]
-        else:
-            return [c + ":" + r for r in requirements]
-
-    def option(self, name, value):
-        name = name[0]
-        if not name in ["site-config", "user-config", "project-config"]:
-            get_manager().errors()("The 'option' rule may be used only in site-config or user-config")
-
-        option.set(name, value[0])
diff --git a/jam-files/boost-build/build/property-set.jam b/jam-files/boost-build/build/property-set.jam
deleted file mode 100644
index 70fd90cd..00000000
--- a/jam-files/boost-build/build/property-set.jam
+++ /dev/null
@@ -1,481 +0,0 @@
-# Copyright 2003 Dave Abrahams
-# Copyright 2003, 2004, 2005, 2006 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-import "class" : new ;
-import feature ;
-import path ;
-import project ;
-import property ;
-import sequence ;
-import set ;
-import option ;
-
-# Class for storing a set of properties.
-#
-#   There is 1<->1 correspondence between identity and value. No two instances
-# of the class are equal. To maintain this property, the 'property-set.create'
-# rule should be used to create new instances. Instances are immutable.
-#
-#   Each property is classified with regard to its effect on build results.
-# Incidental properties have no effect on build results, from Boost.Build's
-# point of view. Others are either free, or non-free and we refer to non-free
-# ones as 'base'. Each property belongs to exactly one of those categories.
-#
-#   It is possible to get a list of properties belonging to each category as
-# well as a list of properties with a specific attribute.
-#
-#   Several operations, like and refine and as-path are provided. They all use
-# caching whenever possible.
-#
-class property-set
-{
-    import errors ;
-    import feature ;
-    import path ;
-    import property ;
-    import property-set ;
-    import set ;
-    
-    rule __init__ ( raw-properties * )
-    {
-        self.raw = $(raw-properties) ;
-
-        for local p in $(raw-properties)
-        {
-            if ! $(p:G)
-            {
-                errors.error "Invalid property: '$(p)'" ;
-            }
-
-            local att = [ feature.attributes $(p:G) ] ;
-            # A feature can be both incidental and free, in which case we add it
-            # to incidental.
-            if incidental in $(att)
-            {
-                self.incidental += $(p) ;
-            }
-            else if free in $(att)
-            {
-                self.free += $(p) ;
-            }
-            else
-            {
-                self.base += $(p) ;
-            }
-
-            if dependency in $(att)
-            {
-                self.dependency += $(p) ;
-            }
-            else
-            {
-                self.non-dependency += $(p) ;
-            }
-
-            if [ MATCH (:) : $(p:G=) ]
-            {
-                self.conditional += $(p) ;
-            }
-            else
-            {
-                self.non-conditional += $(p) ;
-            }
-
-            if propagated in $(att)
-            {
-                self.propagated += $(p) ;
-            }
-            if link-incompatible in $(att)
-            {
-                self.link-incompatible += $(p) ;
-            }
-        }
-    }
-
-    # Returns Jam list of stored properties.
-    #
-    rule raw ( )
-    {
-        return $(self.raw) ;
-    }
-
-    rule str ( )
-    {
-        return "[" $(self.raw) "]" ;
-    }
-
-    # Returns properties that are neither incidental nor free.
-    #
-    rule base ( )
-    {
-        return $(self.base) ;
-    }
-
-    # Returns free properties which are not incidental.
-    #
-    rule free ( )
-    {
-        return $(self.free) ;
-    }
-
-    # Returns dependency properties.
-    #
-    rule dependency ( )
-    {
-        return $(self.dependency) ;
-    }
-
-    rule non-dependency ( )
-    {
-        return $(self.non-dependency) ;
-    }
-
-    rule conditional ( )
-    {
-        return $(self.conditional) ;
-    }
-
-    rule non-conditional ( )
-    {
-        return $(self.non-conditional) ;
-    }
-
-    # Returns incidental properties.
-    #
-    rule incidental ( )
-    {
-        return $(self.incidental) ;
-    }
-
-    rule refine ( ps )
-    {
-        if ! $(self.refined.$(ps))
-        {
-            local r = [ property.refine $(self.raw) : [ $(ps).raw ] ] ;
-            if $(r[1]) != "@error"
-            {
-                self.refined.$(ps) = [ property-set.create $(r) ] ;
-            }
-            else
-            {
-                self.refined.$(ps) = $(r) ;
-            }
-        }
-        return $(self.refined.$(ps)) ;
-    }
-
-    rule expand ( )
-    {
-        if ! $(self.expanded)
-        {
-            self.expanded = [ property-set.create [ feature.expand $(self.raw) ] ] ;
-        }
-        return $(self.expanded) ;
-    }
-
-    rule expand-composites ( )
-    {
-        if ! $(self.composites)
-        {
-            self.composites = [ property-set.create
-                [ feature.expand-composites $(self.raw) ] ] ;
-        }
-        return $(self.composites) ;
-    }
-
-    rule evaluate-conditionals ( context ? )
-    {
-        context ?= $(__name__) ;
-        if ! $(self.evaluated.$(context))
-        {
-            self.evaluated.$(context) = [ property-set.create
-                [ property.evaluate-conditionals-in-context $(self.raw) : [ $(context).raw ] ] ] ;
-        }
-        return $(self.evaluated.$(context)) ;
-    }
-
-    rule propagated ( )
-    {
-        if ! $(self.propagated-ps)
-        {
-            self.propagated-ps = [ property-set.create $(self.propagated) ] ;
-        }
-        return $(self.propagated-ps) ;
-    }
-
-    rule link-incompatible ( )
-    {
-        if ! $(self.link-incompatible-ps)
-        {
-            self.link-incompatible-ps =
-              [ property-set.create $(self.link-incompatible) ] ;
-        }
-        return $(self.link-incompatible-ps) ;
-    }
-
-    rule run-actions ( )
-    {
-        if ! $(self.run)
-        {
-            self.run = [ property-set.create [ feature.run-actions $(self.raw) ] ] ;
-        }
-        return $(self.run) ;
-    }
-
-    rule add-defaults ( )
-    {
-        if ! $(self.defaults)
-        {
-            self.defaults = [ property-set.create
-                [ feature.add-defaults $(self.raw) ] ] ;
-        }
-        return $(self.defaults) ;
-    }
-
-    rule as-path ( )
-    {
-        if ! $(self.as-path)
-        {
-            self.as-path = [ property.as-path $(self.base) ] ;
-        }
-        return $(self.as-path) ;
-    }
-
-    # Computes the path to be used for a target with the given properties.
-    # Returns a list of
-    #   - the computed path
-    #   - if the path is relative to the build directory, a value of 'true'.
-    #
-    rule target-path ( )
-    {
-        if ! $(self.target-path)
-        {
-            # The <location> feature can be used to explicitly change the
-            # location of generated targets.
-            local l = [ get <location> ] ;
-            if $(l)
-            {
-                self.target-path = $(l) ;
-            }
-            else
-            {
-                local p = [ as-path ] ;
-                p = [ property-set.hash-maybe $(p) ] ;
-                
-                # A real ugly hack. Boost regression test system requires
-                # specific target paths, and it seems that changing it to handle
-                # other directory layout is really hard. For that reason, we
-                # teach V2 to do the things regression system requires. The
-                # value of '<location-prefix>' is prepended to the path.
-                local prefix = [ get <location-prefix> ] ;
-                if $(prefix)
-                {
-                    self.target-path = [ path.join $(prefix) $(p) ] ;
-                }
-                else
-                {
-                    self.target-path = $(p) ;
-                }
-                if ! $(self.target-path)
-                {
-                    self.target-path = . ;
-                }
-                # The path is relative to build dir.
-                self.target-path += true ;
-            }
-        }
-        return $(self.target-path) ;
-    }
-
-    rule add ( ps )
-    {
-        if ! $(self.added.$(ps))
-        {
-            self.added.$(ps) = [ property-set.create $(self.raw) [ $(ps).raw ] ] ;
-        }
-        return $(self.added.$(ps)) ;
-    }
-
-    rule add-raw ( properties * )
-    {
-        return [ add [ property-set.create $(properties) ] ] ;
-    }
-
-    rule link-incompatible-with ( ps )
-    {
-        if ! $(.li.$(ps))
-        {
-            local li1 = [ $(__name__).link-incompatible ] ;
-            local li2 = [ $(ps).link-incompatible ] ;
-            if [ set.equal $(li1) : $(li2) ]
-            {
-                .li.$(ps) = false ;
-            }
-            else
-            {
-                .li.$(ps) = true ;
-            }
-        }
-        if $(.li.$(ps)) = true
-        {
-            return true ;
-        }
-        else
-        {
-            return ;
-        }
-    }
-
-    # Returns all values of 'feature'.
-    #
-    rule get ( feature )
-    {
-        if ! $(self.map-built)
-        {
-            # For each feature, create a member var and assign all values to it.
-            # Since all regular member vars start with 'self', there will be no
-            # conflicts between names.
-            self.map-built = true ;
-            for local v in $(self.raw)
-            {
-                $(v:G) += $(v:G=) ;
-            }
-        }
-        return $($(feature)) ;
-    }
-}
-
-
-# Creates a new 'property-set' instance for the given raw properties or returns
-# an already existing ones.
-#
-rule create ( raw-properties * )
-{
-    raw-properties = [ sequence.unique
-        [ sequence.insertion-sort $(raw-properties) ] ] ;
-
-    local key = $(raw-properties:J=-:E=) ;
-
-    if ! $(.ps.$(key))
-    {
-        .ps.$(key) = [ new property-set $(raw-properties) ] ;
-    }
-    return $(.ps.$(key)) ;
-}
-NATIVE_RULE property-set : create ;
-
-
-# Creates a new 'property-set' instance after checking that all properties are
-# valid and converting incidental properties into gristed form.
-#
-rule create-with-validation ( raw-properties * )
-{
-    property.validate $(raw-properties) ;
-    return [ create [ property.make $(raw-properties) ] ] ;
-}
-
-
-# Creates a property-set from the input given by the user, in the context of
-# 'jamfile-module' at 'location'.
-#
-rule create-from-user-input ( raw-properties * : jamfile-module location )
-{
-    local specification = [ property.translate-paths $(raw-properties)
-        : $(location) ] ;
-    specification = [ property.translate-indirect $(specification)
-        : $(jamfile-module) ] ;
-    local project-id = [ project.attribute $(jamfile-module) id ] ;
-    project-id ?= [ path.root $(location) [ path.pwd ] ] ;
-    specification = [ property.translate-dependencies
-                      $(specification) : $(project-id) : $(location) ] ;
-    specification =
-        [ property.expand-subfeatures-in-conditions $(specification) ] ;
-    specification = [ property.make $(specification) ] ;
-    return [ property-set.create $(specification) ] ;
-}
-
-
-# Refines requirements with requirements provided by the user. Specially handles
-# "-<property>value" syntax in specification to remove given requirements.
-# - parent-requirements -- property-set object with requirements to refine.
-# - specification       -- string list of requirements provided by the user.
-# - project-module      -- module to which context indirect features will be
-#                          bound.
-# - location            -- path to which path features are relative.
-#
-rule refine-from-user-input ( parent-requirements : specification * :
-    project-module : location )
-{
-    if ! $(specification)
-    {
-        return $(parent-requirements) ;
-    }
-    else
-    {
-        local add-requirements ;
-        local remove-requirements ;
-
-        for local r in $(specification)
-        {
-            local m = [ MATCH "^-(.*)" : $(r) ] ;
-            if $(m)
-            {
-                remove-requirements += $(m) ;
-            }
-            else
-            {
-                add-requirements += $(r) ;
-            }
-        }
-
-        if $(remove-requirements)
-        {
-            # Need to create a property set, so that path features and indirect
-            # features are translated just like they are in project
-            # requirements.
-            local ps = [ property-set.create-from-user-input
-                $(remove-requirements) : $(project-module) $(location) ] ;
-
-            parent-requirements = [ property-set.create
-                [ set.difference [ $(parent-requirements).raw ]
-                : [ $(ps).raw ] ] ] ;
-            specification = $(add-requirements) ;
-        }
-
-        local requirements = [ property-set.create-from-user-input
-            $(specification) : $(project-module) $(location) ] ;
-
-        return [ $(parent-requirements).refine $(requirements) ] ;
-    }
-}
-
-
-# Returns a property-set with an empty set of properties.
-#
-rule empty ( )
-{
-    if ! $(.empty)
-    {
-        .empty = [ create ] ;
-    }
-    return $(.empty) ;
-}
-
-if [ option.get hash : : yes ] = yes
-{    
-    rule hash-maybe ( path ? )
-    {
-        path ?= "" ;
-        return [ MD5 $(path) ] ;
-    }
-}
-else
-{
-    rule hash-maybe ( path ? )
-    {
-        return $(path) ;
-    }    
-}
-
diff --git a/jam-files/boost-build/build/property.jam b/jam-files/boost-build/build/property.jam
deleted file mode 100644
index a2ad5226..00000000
--- a/jam-files/boost-build/build/property.jam
+++ /dev/null
@@ -1,788 +0,0 @@
-# Copyright 2001, 2002, 2003 Dave Abrahams
-# Copyright 2006 Rene Rivera
-# Copyright 2002, 2003, 2004, 2005, 2006 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-import errors ;
-import feature ;
-import indirect ;
-import path ;
-import regex ;
-import string ;
-import sequence ;
-import set ;
-import utility ;
-
-
-# Refines 'properties' by overriding any non-free and non-conditional properties
-# for which a different value is specified in 'requirements'. Returns the
-# resulting list of properties.
-#
-rule refine ( properties * : requirements * )
-{
-    local result ;
-    local error ;
-
-    # All the 'requirements' elements should be present in the result. Record
-    # them so that we can handle 'properties'.
-    for local r in $(requirements)
-    {
-        # Do not consider conditional requirements.
-        if ! [ MATCH (:) : $(r:G=) ]
-        {
-            # Note: cannot use a local variable here, so use an ugly name.
-            __require__$(r:G) = $(r:G=) ;
-        }
-    }
-
-    for local p in $(properties)
-    {
-        if [ MATCH (:) : $(p:G=) ]
-        {
-            # Do not modify conditional properties.
-            result += $(p) ;
-        }
-        else if free in [ feature.attributes $(p:G) ]
-        {
-            # Do not modify free properties.
-            result += $(p) ;
-        }
-        else
-        {
-            local required-value = $(__require__$(p:G)) ;
-            if $(required-value)
-            {
-                if $(p:G=) != $(required-value)
-                {
-                    result += $(p:G)$(required-value) ;
-                }
-                else
-                {
-                    result += $(p) ;
-                }
-            }
-            else
-            {
-                result += $(p) ;
-            }
-        }
-    }
-
-    # Unset our ugly map.
-    for local r in $(requirements)
-    {
-        __require__$(r:G) = ;
-    }
-
-    if $(error)
-    {
-        return $(error) ;
-    }
-    else
-    {
-        return [ sequence.unique $(result) $(requirements) ] ;
-    }
-}
-
-
-# Removes all conditional properties whose conditions are not met. For those
-# with met conditions, removes the condition. Properties in conditions are
-# looked up in 'context'.
-#
-rule evaluate-conditionals-in-context ( properties * : context * )
-{
-    local base ;
-    local conditionals ;
-    for local p in $(properties)
-    {
-        if [ MATCH (:<) : $(p) ]
-        {
-            conditionals += $(p) ;
-        }
-        else
-        {
-            base += $(p) ;
-        }
-    }
-
-    local result = $(base) ;
-    for local p in $(conditionals)
-    {
-        # Separate condition and property.
-        local s = [ MATCH (.*):(<.*) : $(p) ] ;
-        # Split condition into individual properties.
-        local condition = [ regex.split $(s[1]) "," ] ;
-        # Evaluate condition.
-        if ! [ MATCH (!).* : $(condition:G=) ]
-        {
-            # Only positive checks
-            if $(condition) in $(context)
-            {
-                result += $(s[2]) ;
-            }
-        }
-        else
-        {
-            # Have negative checks
-            local fail ;
-            while $(condition)
-            {
-                local c = $(condition[1]) ;
-                local m = [ MATCH !(.*) : $(c) ] ;
-                if $(m)
-                {
-                    local p = $(m:G=$(c:G)) ;
-                    if $(p) in $(context)
-                    {
-                        fail = true ;
-                        c = ;
-                    }                    
-                }    
-                else
-                {
-                    if ! $(c) in $(context)
-                    {
-                        fail = true ;
-                        c = ;
-                    }                    
-                }
-                condition = $(condition[2-]) ;
-            }
-            if ! $(fail)
-            {
-                result += $(s[2]) ;
-            }            
-        }                
-    }
-    return $(result) ;
-}
-
-
-rule expand-subfeatures-in-conditions ( properties * )
-{
-    local result ;
-    for local p in $(properties)
-    {
-        local s = [ MATCH (.*):(<.*) : $(p) ] ;
-        if ! $(s)
-        {
-            result += $(p) ;
-        }
-        else
-        {
-            local condition = $(s[1]) ;
-            local value     = $(s[2]) ;
-            # Condition might include several elements.
-            condition = [ regex.split $(condition) "," ] ;
-            local e ;
-            for local c in $(condition)
-            {
-                # It is common for a condition to include a toolset or
-                # subfeatures that have not been defined. In that case we want
-                # the condition to simply 'never be satisfied' and validation
-                # would only produce a spurious error so we prevent it by
-                # passing 'true' as the second parameter.
-                e += [ feature.expand-subfeatures $(c) : true ] ;
-            }
-            if $(e) = $(condition)
-            {
-                # (todo)
-                #   This is just an optimization and possibly a premature one at
-                # that.
-                #                             (todo) (12.07.2008.) (Jurko)
-                result += $(p) ;
-            }
-            else
-            {
-                result += $(e:J=,):$(value) ;
-            }
-        }
-    }
-    return $(result) ;
-}
-
-
-# Helper for as-path, below. Orders properties with the implicit ones first, and
-# within the two sections in alphabetical order of feature name.
-#
-local rule path-order ( x y )
-{
-    if $(y:G) && ! $(x:G)
-    {
-        return true ;
-    }
-    else if $(x:G) && ! $(y:G)
-    {
-        return ;
-    }
-    else
-    {
-        if ! $(x:G)
-        {
-            x = [ feature.expand-subfeatures $(x) ] ;
-            y = [ feature.expand-subfeatures $(y) ] ;
-        }
-
-        if $(x[1]) < $(y[1])
-        {
-            return true ;
-        }
-    }
-}
-
-
-local rule abbreviate-dashed ( string )
-{
-    local r ;
-    for local part in [ regex.split $(string) - ]
-    {
-        r += [ string.abbreviate $(part) ] ;
-    }
-    return $(r:J=-) ;
-}
-
-
-local rule identity ( string )
-{
-    return $(string) ;
-}
-
-
-if --abbreviate-paths in [ modules.peek : ARGV ]
-{
-    .abbrev = abbreviate-dashed ;
-}
-else
-{
-    .abbrev = identity ;
-}
-
-
-# Returns a path representing the given expanded property set.
-#
-rule as-path ( properties * )
-{
-    local entry = .result.$(properties:J=-) ;
-
-    if ! $($(entry))
-    {
-        # Trim redundancy.
-        properties = [ feature.minimize $(properties) ] ;
-
-        # Sort according to path-order.
-        properties = [ sequence.insertion-sort $(properties) : path-order ] ;
-
-        local components ;
-        for local p in $(properties)
-        {
-            if $(p:G)
-            {
-                local f = [ utility.ungrist $(p:G) ] ;
-                p = $(f)-$(p:G=) ;
-            }
-            components += [ $(.abbrev) $(p) ] ;
-        }
-
-        $(entry) = $(components:J=/) ;
-    }
-
-    return $($(entry)) ;
-}
-
-
-# Exit with error if property is not valid.
-#
-local rule validate1 ( property )
-{
-    local msg ;
-    if $(property:G)
-    {
-        local feature = $(property:G) ;
-        local value = $(property:G=) ;
-
-        if ! [ feature.valid $(feature) ]
-        {
-            # Ungrist for better error messages.
-            feature = [ utility.ungrist $(property:G) ] ;
-            msg = "unknown feature '$(feature)'" ;
-        }
-        else if $(value) && ! free in [ feature.attributes $(feature) ]
-        {
-            feature.validate-value-string $(feature) $(value) ;
-        }
-        else if ! ( $(value) || ( optional in [ feature.attributes $(feature) ] ) )
-        {
-            # Ungrist for better error messages.
-            feature = [ utility.ungrist $(property:G) ] ;
-            msg = "No value specified for feature '$(feature)'" ;
-        }
-    }
-    else
-    {
-        local feature = [ feature.implied-feature $(property) ] ;
-        feature.validate-value-string $(feature) $(property) ;
-    }
-    if $(msg)
-    {
-        errors.error "Invalid property "'$(property:J=" ")'": "$(msg:J=" "). ;
-    }
-}
-
-
-rule validate ( properties * )
-{
-    for local p in $(properties)
-    {
-        validate1 $(p) ;
-    }
-}
-
-
-rule validate-property-sets ( property-sets * )
-{
-    for local s in $(property-sets)
-    {
-        validate [ feature.split $(s) ] ;
-    }
-}
-
-
-# Expands any implicit property values in the given property 'specification' so
-# they explicitly state their feature.
-#
-rule make ( specification * )
-{
-    local result ;
-    for local e in $(specification)
-    {
-        if $(e:G)
-        {
-            result += $(e) ;
-        }
-        else if [ feature.is-implicit-value $(e) ]
-        {
-            local feature = [ feature.implied-feature $(e) ] ;
-            result += $(feature)$(e) ;
-        }
-        else
-        {
-            errors.error "'$(e)' is not a valid property specification" ;
-        }
-    }
-    return $(result) ;
-}
-
-
-# Returns a property set containing all the elements in 'properties' that do not
-# have their attributes listed in 'attributes'.
-#
-rule remove ( attributes + : properties * )
-{
-    local result ;
-    for local e in $(properties)
-    {
-        if ! [ set.intersection $(attributes) : [ feature.attributes $(e:G) ] ]
-        {
-            result += $(e) ;
-        }
-    }
-    return $(result) ;
-}
-
-
-# Returns a property set containing all the elements in 'properties' that have
-# their attributes listed in 'attributes'.
-#
-rule take ( attributes + : properties * )
-{
-    local result ;
-    for local e in $(properties)
-    {
-        if [ set.intersection $(attributes) : [ feature.attributes $(e:G) ] ]
-        {
-            result += $(e) ;
-        }
-    }
-    return $(result) ;
-}
-
-
-# Selects properties corresponding to any of the given features.
-#
-rule select ( features * : properties * )
-{
-    local result ;
-
-    # Add any missing angle brackets.
-    local empty = "" ;
-    features = $(empty:G=$(features)) ;
-
-    for local p in $(properties)
-    {
-        if $(p:G) in $(features)
-        {
-            result += $(p) ;
-        }
-    }
-    return $(result) ;
-}
-
-
-# Returns a modified version of properties with all values of the given feature
-# replaced by the given value. If 'value' is empty the feature will be removed.
-#
-rule change ( properties * : feature value ? )
-{
-    local result ;
-    for local p in $(properties)
-    {
-        if $(p:G) = $(feature)
-        {
-            result += $(value:G=$(feature)) ;
-        }
-        else
-        {
-            result += $(p) ;
-        }
-    }
-    return $(result) ;
-}
-
-
-# If 'property' is a conditional property, returns the condition and the
-# property. E.g. <variant>debug,<toolset>gcc:<inlining>full will become
-# <variant>debug,<toolset>gcc <inlining>full. Otherwise, returns an empty
-# string.
-#
-rule split-conditional ( property )
-{
-    local m = [ MATCH "(.+):<(.+)" : $(property) ] ;
-    if $(m)
-    {
-        return $(m[1]) <$(m[2]) ;
-    }
-}
-
-
-# Interpret all path properties in 'properties' as relative to 'path'. The
-# property values are assumed to be in system-specific form, and will be
-# translated into normalized form.
-#
-rule translate-paths ( properties * : path )
-{
-    local result ;
-    for local p in $(properties)
-    {
-        local split = [ split-conditional $(p) ] ;
-        local condition = "" ;
-        if $(split)
-        {
-            condition = $(split[1]): ;
-            p = $(split[2]) ;
-        }
-
-        if path in [ feature.attributes $(p:G) ]
-        {
-            local values = [ regex.split $(p:TG=) "&&" ] ;
-            local t ;
-            for local v in $(values)
-            {
-                t += [ path.root [ path.make $(v) ] $(path) ] ;
-            }
-            t = $(t:J="&&") ;
-            result += $(condition)$(t:TG=$(p:G)) ;
-        }
-        else
-        {
-            result += $(condition)$(p) ;
-        }
-    }
-    return $(result) ;
-}
-
-
-# Assumes that all feature values that start with '@' are names of rules, used
-# in 'context-module'. Such rules can be either local to the module or global.
-# Converts such values into 'indirect-rule' format (see indirect.jam), so they
-# can be called from other modules. Does nothing for such values that are
-# already in the 'indirect-rule' format.
-#
-rule translate-indirect ( specification * : context-module )
-{
-    local result ;
-    for local p in $(specification)
-    {
-        local m = [ MATCH ^@(.+) : $(p:G=) ] ;
-        if $(m)
-        {
-            local v ;
-            if [ MATCH "^([^%]*)%([^%]+)$" : $(m) ]
-            {
-                # Rule is already in the 'indirect-rule' format.
-                v = $(m) ;
-            }
-            else
-            {
-                if ! [ MATCH ".*([.]).*" : $(m) ]
-                {
-                    # This is an unqualified rule name. The user might want to
-                    # set flags on this rule name and toolset.flag
-                    # auto-qualifies it. Need to do the same here so flag
-                    # setting works. We can arrange for toolset.flag to *not*
-                    # auto-qualify the argument but then two rules defined in
-                    # two Jamfiles would conflict.
-                    m = $(context-module).$(m) ;
-                }
-                v = [ indirect.make $(m) : $(context-module) ] ;
-            }
-
-            v = @$(v) ;
-            result += $(v:G=$(p:G)) ;
-        }
-        else
-        {
-            result += $(p) ;
-        }
-    }
-    return $(result) ;
-}
-
-
-# Binds all dependency properties in a list relative to the given project.
-# Targets with absolute paths will be left unchanged and targets which have a
-# project specified will have the path to the project interpreted relative to
-# the specified location.
-#
-rule translate-dependencies ( specification * : project-id : location )
-{
-    local result ;
-    for local p in $(specification)
-    {
-        local split = [ split-conditional $(p) ] ;
-        local condition = "" ;
-        if $(split)
-        {
-            condition = $(split[1]): ;
-            p = $(split[2]) ;
-        }
-        if dependency in [ feature.attributes $(p:G) ]
-        {
-            local split-target = [ regex.match (.*)//(.*) : $(p:G=) ] ;
-            if $(split-target)
-            {
-                local rooted = [ path.root [ path.make $(split-target[1]) ]
-                     [ path.root $(location) [ path.pwd ] ] ] ;
-                result += $(condition)$(p:G)$(rooted)//$(split-target[2]) ;
-            }
-            else if [ path.is-rooted $(p:G=) ]
-            {
-                result += $(condition)$(p) ;
-            }
-            else
-            {
-                result += $(condition)$(p:G)$(project-id)//$(p:G=) ;
-            }
-        }
-        else
-        {
-            result += $(condition)$(p) ;
-        }
-    }
-    return $(result) ;
-}
-
-
-# Class maintaining a property set -> string mapping.
-#
-class property-map
-{
-    import errors ;
-    import numbers ;
-    import sequence ;
-
-    rule __init__ ( )
-    {
-        self.next-flag = 1 ;
-    }
-
-    # Associate 'value' with 'properties'.
-    #
-    rule insert ( properties + : value )
-    {
-        self.all-flags += $(self.next-flag) ;
-        self.properties.$(self.next-flag) = $(properties) ;
-        self.value.$(self.next-flag) = $(value) ;
-
-        self.next-flag = [ numbers.increment $(self.next-flag) ] ;
-    }
-
-    # Returns the value associated with 'properties' or any subset of it. If
-    # more than one subset has a value assigned to it, returns the value for the
-    # longest subset, if it is unique.
-    #
-    rule find ( properties + )
-    {
-        return [ find-replace $(properties) ] ;
-    }
-
-    # Returns the value associated with 'properties'. If 'value' parameter is
-    # given, replaces the found value.
-    #
-    rule find-replace ( properties + : value ? )
-    {
-        # First find all matches.
-        local matches ;
-        local match-ranks ;
-        for local i in $(self.all-flags)
-        {
-            if $(self.properties.$(i)) in $(properties)
-            {
-                matches += $(i) ;
-                match-ranks += [ sequence.length $(self.properties.$(i)) ] ;
-            }
-        }
-        local best = [ sequence.select-highest-ranked $(matches)
-            : $(match-ranks) ] ;
-        if $(best[2])
-        {            
-            errors.error "Ambiguous key $(properties:J= :E=)" ;
-        }
-        local original = $(self.value.$(best)) ;
-        if $(value)
-        {
-            self.value.$(best) = $(value) ;
-        }
-        return $(original) ;
-    }
-}
-
-
-rule __test__ ( )
-{
-    import assert ;
-    import "class" : new ;
-    import errors : try catch ;
-    import feature ;
-
-    # Local rules must be explicitly re-imported.
-    import property : path-order abbreviate-dashed ;
-
-    feature.prepare-test property-test-temp ;
-
-    feature.feature toolset : gcc : implicit symmetric ;
-    feature.subfeature toolset gcc : version : 2.95.2 2.95.3 2.95.4 3.0 3.0.1
-        3.0.2 : optional ;
-    feature.feature define : : free ;
-    feature.feature runtime-link : dynamic static : symmetric link-incompatible ;
-    feature.feature optimization : on off ;
-    feature.feature variant : debug release : implicit composite symmetric ;
-    feature.feature rtti : on off : link-incompatible ;
-
-    feature.compose <variant>debug : <define>_DEBUG <optimization>off ;
-    feature.compose <variant>release : <define>NDEBUG <optimization>on ;
-
-    validate <toolset>gcc <toolset>gcc-3.0.1 : $(test-space) ;
-
-    assert.true  path-order $(test-space) debug <define>foo ;
-    assert.false path-order $(test-space) <define>foo debug ;
-    assert.true  path-order $(test-space) gcc debug ;
-    assert.false path-order $(test-space) debug gcc ;
-    assert.true  path-order $(test-space) <optimization>on <rtti>on ;
-    assert.false path-order $(test-space) <rtti>on <optimization>on ;
-
-    assert.result-set-equal <toolset>gcc <rtti>off <define>FOO
-        : refine <toolset>gcc <rtti>off
-        : <define>FOO
-        : $(test-space) ;
-
-    assert.result-set-equal <toolset>gcc <optimization>on
-        : refine <toolset>gcc <optimization>off
-        : <optimization>on
-        : $(test-space) ;
-
-    assert.result-set-equal <toolset>gcc <rtti>off
-        : refine <toolset>gcc : <rtti>off : $(test-space) ;
-
-    assert.result-set-equal <toolset>gcc <rtti>off <rtti>off:<define>FOO
-        : refine <toolset>gcc : <rtti>off <rtti>off:<define>FOO
-        : $(test-space) ;
-
-    assert.result-set-equal <toolset>gcc:<define>foo <toolset>gcc:<define>bar
-        : refine <toolset>gcc:<define>foo : <toolset>gcc:<define>bar
-        : $(test-space) ;
-
-    assert.result <define>MY_RELEASE
-        : evaluate-conditionals-in-context
-          <variant>release,<rtti>off:<define>MY_RELEASE
-        : <toolset>gcc <variant>release <rtti>off ;
-
-    assert.result debug
-        : as-path <optimization>off <variant>debug
-        : $(test-space) ;
-
-    assert.result gcc/debug/rtti-off
-        : as-path <toolset>gcc <optimization>off <rtti>off <variant>debug
-        : $(test-space) ;
-
-    assert.result optmz-off : abbreviate-dashed optimization-off ;
-    assert.result rntm-lnk-sttc : abbreviate-dashed runtime-link-static ;
-
-    try ;
-        validate <feature>value : $(test-space) ;
-    catch "Invalid property '<feature>value': unknown feature 'feature'." ;
-
-    try ;
-        validate <rtti>default : $(test-space) ;
-    catch \"default\" is not a known value of feature <rtti> ;
-
-    validate <define>WHATEVER : $(test-space) ;
-
-    try ;
-        validate <rtti> : $(test-space) ;
-    catch "Invalid property '<rtti>': No value specified for feature 'rtti'." ;
-
-    try ;
-        validate value : $(test-space) ;
-    catch "value" is not a value of an implicit feature ;
-
-    assert.result-set-equal <rtti>on
-        : remove free implicit : <toolset>gcc <define>foo <rtti>on : $(test-space) ;
-
-    assert.result-set-equal <include>a
-        : select include : <include>a <toolset>gcc ;
-
-    assert.result-set-equal <include>a
-        : select include bar : <include>a <toolset>gcc ;
-
-    assert.result-set-equal <include>a <toolset>gcc
-        : select include <bar> <toolset> : <include>a <toolset>gcc ;
-
-    assert.result-set-equal <toolset>kylix <include>a
-        : change <toolset>gcc <include>a : <toolset> kylix ;
-
-    pm = [ new property-map ] ;
-    $(pm).insert <toolset>gcc : o ;
-    $(pm).insert <toolset>gcc <os>NT : obj ;
-    $(pm).insert <toolset>gcc <os>CYGWIN : obj ;
-
-    assert.equal o : [ $(pm).find <toolset>gcc ] ;
-
-    assert.equal obj : [ $(pm).find <toolset>gcc <os>NT ] ;
-
-    try ;
-        $(pm).find <toolset>gcc <os>NT <os>CYGWIN ;
-    catch "Ambiguous key <toolset>gcc <os>NT <os>CYGWIN" ;
-
-    # Test ordinary properties.
-    assert.result : split-conditional <toolset>gcc ;
-
-    # Test properties with ":".
-    assert.result : split-conditional <define>FOO=A::B ;
-
-    # Test conditional feature.
-    assert.result-set-equal <toolset>gcc,<toolset-gcc:version>3.0 <define>FOO
-        : split-conditional <toolset>gcc,<toolset-gcc:version>3.0:<define>FOO ;
-
-    feature.finish-test property-test-temp ;
-}
diff --git a/jam-files/boost-build/build/property.py b/jam-files/boost-build/build/property.py
deleted file mode 100644
index c4b13dbc..00000000
--- a/jam-files/boost-build/build/property.py
+++ /dev/null
@@ -1,593 +0,0 @@
-# Status: ported, except for tests and --abbreviate-paths.
-# Base revision: 64070
-#
-# Copyright 2001, 2002, 2003 Dave Abrahams 
-# Copyright 2006 Rene Rivera 
-# Copyright 2002, 2003, 2004, 2005, 2006 Vladimir Prus 
-# Distributed under the Boost Software License, Version 1.0. 
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt) 
-
-import re
-from b2.util.utility import *
-from b2.build import feature
-from b2.util import sequence, qualify_jam_action
-import b2.util.set
-from b2.manager import get_manager
-
-__re_two_ampersands = re.compile ('&&')
-__re_comma = re.compile (',')
-__re_split_condition = re.compile ('(.*):(<.*)')
-__re_split_conditional = re.compile (r'(.+):<(.+)')
-__re_colon = re.compile (':')
-__re_has_condition = re.compile (r':<')
-__re_separate_condition_and_property = re.compile (r'(.*):(<.*)')
-
-class Property(object):
-
-    __slots__ = ('_feature', '_value', '_condition')
-
-    def __init__(self, f, value, condition = []):
-        if type(f) == type(""):
-            f = feature.get(f)
-        # At present, single property has a single value.
-        assert type(value) != type([])
-        assert(f.free() or value.find(':') == -1)
-        self._feature = f
-        self._value = value
-        self._condition = condition
-        
-    def feature(self):
-        return self._feature
-
-    def value(self):
-        return self._value
-
-    def condition(self):
-        return self._condition
-
-    def to_raw(self):
-        result = "<" + self._feature.name() + ">" + str(self._value)
-        if self._condition:
-            result = ",".join(str(p) for p in self._condition) + ':' + result
-        return result
-
-    def __str__(self):
-        return self.to_raw()
-
-    def __hash__(self):
-        # FIXME: consider if this class should be value-is-identity one
-        return hash((self._feature, self._value, tuple(self._condition)))
-
-    def __cmp__(self, other):
-        return cmp((self._feature, self._value, self._condition),
-                   (other._feature, other._value, other._condition))
-                           
-
-def create_from_string(s, allow_condition=False):
-
-    condition = []
-    import types
-    if not isinstance(s, types.StringType):
-        print type(s)
-    if __re_has_condition.search(s):
-
-        if not allow_condition:
-            raise BaseException("Conditional property is not allowed in this context")
-
-        m = __re_separate_condition_and_property.match(s)
-        condition = m.group(1)
-        s = m.group(2)
-
-    # FIXME: break dependency cycle
-    from b2.manager import get_manager
-
-    feature_name = get_grist(s)
-    if not feature_name:
-        if feature.is_implicit_value(s):
-            f = feature.implied_feature(s)
-            value = s
-        else:        
-            raise get_manager().errors()("Invalid property '%s' -- unknown feature" % s)
-    else:
-        f = feature.get(feature_name)        
-
-        value = get_value(s)
-        if not value:
-            get_manager().errors()("Invalid property '%s' -- no value specified" % s)
-
-
-    if condition:
-        condition = [create_from_string(x) for x in condition.split(',')]
-                   
-    return Property(f, value, condition)
-
-def create_from_strings(string_list, allow_condition=False):
-
-    return [create_from_string(s, allow_condition) for s in string_list]
-
-def reset ():
-    """ Clear the module state. This is mainly for testing purposes.
-    """
-    global __results
-
-    # A cache of results from as_path
-    __results = {}
-    
-reset ()
-
-        
-def path_order (x, y):
-    """ Helper for as_path, below. Orders properties with the implicit ones
-        first, and within the two sections in alphabetical order of feature
-        name.
-    """
-    if x == y:
-        return 0
-        
-    xg = get_grist (x)
-    yg = get_grist (y)
-
-    if yg and not xg:
-        return -1
-
-    elif xg and not yg:
-        return 1
-
-    else:
-        if not xg:            
-            x = feature.expand_subfeatures([x])
-            y = feature.expand_subfeatures([y])
-        
-        if x < y:
-            return -1
-        elif x > y:
-            return 1
-        else:
-            return 0
-
-def identify(string):
-    return string 
-
-# Uses Property
-def refine (properties, requirements):
-    """ Refines 'properties' by overriding any non-free properties 
-        for which a different value is specified in 'requirements'. 
-        Conditional requirements are just added without modification.
-        Returns the resulting list of properties.
-    """
-    # The result has no duplicates, so we store it in a set
-    result = set()
-    
-    # Records all requirements.
-    required = {}
-    
-    # All the elements of requirements should be present in the result
-    # Record them so that we can handle 'properties'.
-    for r in requirements:
-        # Don't consider conditional requirements.
-        if not r.condition():
-            required[r.feature()] = r
-
-    for p in properties:
-        # Skip conditional properties
-        if p.condition():
-            result.add(p)
-        # No processing for free properties
-        elif p.feature().free():
-            result.add(p)
-        else:
-            if required.has_key(p.feature()):
-                result.add(required[p.feature()])
-            else:
-                result.add(p)
-
-    return sequence.unique(list(result) + requirements)
-
-def translate_paths (properties, path):
-    """ Interpret all path properties in 'properties' as relative to 'path'
-        The property values are assumed to be in system-specific form, and
-        will be translated into normalized form.
-        """
-    result = []
-
-    for p in properties:
-
-        if p.feature().path():
-            values = __re_two_ampersands.split(p.value())
-            
-            new_value = "&&".join(os.path.join(path, v) for v in values)
-
-            if new_value != p.value():
-                result.append(Property(p.feature(), new_value, p.condition()))
-            else:
-                result.append(p)
-            
-        else:
-            result.append (p)
-
-    return result
-
-def translate_indirect(properties, context_module):
-    """Assumes that all feature values that start with '@' are
-    names of rules, used in 'context-module'. Such rules can be
-    either local to the module or global. Qualified local rules
-    with the name of the module."""
-    result = []
-    for p in properties:
-        if p.value()[0] == '@':
-            q = qualify_jam_action(p.value()[1:], context_module)
-            get_manager().engine().register_bjam_action(q)
-            result.append(Property(p.feature(), '@' + q, p.condition()))
-        else:
-            result.append(p)
-
-    return result
-
-def validate (properties):
-    """ Exit with error if any of the properties is not valid.
-        properties may be a single property or a sequence of properties.
-    """
-    
-    if isinstance (properties, str):
-        __validate1 (properties)
-    else:
-        for p in properties:
-            __validate1 (p)
-
-def expand_subfeatures_in_conditions (properties):
-
-    result = []
-    for p in properties:
-
-        if not p.condition():
-            result.append(p)
-        else:
-            expanded = []
-            for c in p.condition():
-
-                if c.feature().name().startswith("toolset") or c.feature().name() == "os":
-                    # It common that condition includes a toolset which
-                    # was never defined, or mentiones subfeatures which
-                    # were never defined. In that case, validation will
-                    # only produce an spirious error, so don't validate.
-                    expanded.extend(feature.expand_subfeatures ([c], True))
-                else:
-                    expanded.extend(feature.expand_subfeatures([c]))
-
-            result.append(Property(p.feature(), p.value(), expanded))
-
-    return result
-
-# FIXME: this should go
-def split_conditional (property):
-    """ If 'property' is conditional property, returns
-        condition and the property, e.g
-        <variant>debug,<toolset>gcc:<inlining>full will become
-        <variant>debug,<toolset>gcc <inlining>full.
-        Otherwise, returns empty string.
-    """
-    m = __re_split_conditional.match (property)
-    
-    if m:
-        return (m.group (1), '<' + m.group (2))
-
-    return None
-
-
-def select (features, properties):
-    """ Selects properties which correspond to any of the given features.
-    """
-    result = []
-    
-    # add any missing angle brackets
-    features = add_grist (features)
-
-    return [p for p in properties if get_grist(p) in features]
-
-def validate_property_sets (sets):
-    for s in sets:
-        validate(s.all())
-
-def evaluate_conditionals_in_context (properties, context):
-    """ Removes all conditional properties which conditions are not met
-        For those with met conditions, removes the condition. Properies
-        in conditions are looked up in 'context'
-    """
-    base = []
-    conditional = []
-
-    for p in properties:
-        if p.condition():
-            conditional.append (p)
-        else:
-            base.append (p)
-
-    result = base[:]
-    for p in conditional:
-
-        # Evaluate condition
-        # FIXME: probably inefficient
-        if all(x in context for x in p.condition()):
-            result.append(Property(p.feature(), p.value()))
-
-    return result
-
-
-def change (properties, feature, value = None):
-    """ Returns a modified version of properties with all values of the
-        given feature replaced by the given value.
-        If 'value' is None the feature will be removed.
-    """
-    result = []
-    
-    feature = add_grist (feature)
-
-    for p in properties:
-        if get_grist (p) == feature:
-            if value:
-                result.append (replace_grist (value, feature))
-
-        else:
-            result.append (p)
-
-    return result
-
-
-################################################################
-# Private functions
-
-def __validate1 (property):
-    """ Exit with error if property is not valid.
-    """        
-    msg = None
-
-    if not property.feature().free():
-        feature.validate_value_string (property.feature(), property.value())
-
-
-###################################################################
-# Still to port.
-# Original lines are prefixed with "#   "
-#
-#   
-#   import utility : ungrist ;
-#   import sequence : unique ;
-#   import errors : error ;
-#   import feature ;
-#   import regex ;
-#   import sequence ;
-#   import set ;
-#   import path ;
-#   import assert ;
-#   
-#   
-
-
-#   rule validate-property-sets ( property-sets * )
-#   {
-#       for local s in $(property-sets)
-#       {
-#           validate [ feature.split $(s) ] ;
-#       }
-#   }
-#
-
-def remove(attributes, properties):
-    """Returns a property sets which include all the elements
-    in 'properties' that do not have attributes listed in 'attributes'."""
-    
-    result = []
-    for e in properties:
-        attributes_new = feature.attributes(get_grist(e))
-        has_common_features = 0
-        for a in attributes_new:
-            if a in attributes:
-                has_common_features = 1
-                break
-
-        if not has_common_features:
-            result += e
-
-    return result
-
-
-def take(attributes, properties):
-    """Returns a property set which include all
-    properties in 'properties' that have any of 'attributes'."""
-    result = []
-    for e in properties:
-        if b2.util.set.intersection(attributes, feature.attributes(get_grist(e))):
-            result.append(e)
-    return result
-
-def translate_dependencies(properties, project_id, location):
-
-    result = []
-    for p in properties:
-
-        if not p.feature().dependency():
-            result.append(p)
-        else:
-            v = p.value()
-            m = re.match("(.*)//(.*)", v)
-            if m:
-                rooted = m.group(1)
-                if rooted[0] == '/':
-                    # Either project id or absolute Linux path, do nothing.
-                    pass
-                else:
-                    rooted = os.path.join(os.getcwd(), location, rooted)
-                    
-                result.append(Property(p.feature(), rooted + "//" + m.group(2), p.condition()))
-                
-            elif os.path.isabs(v):                
-                result.append(p)
-            else:
-                result.append(Property(p.feature(), project_id + "//" + v, p.condition()))
-
-    return result
-
-
-class PropertyMap:
-    """ Class which maintains a property set -> string mapping.
-    """
-    def __init__ (self):
-        self.__properties = []
-        self.__values = []
-    
-    def insert (self, properties, value):
-        """ Associate value with properties.
-        """
-        self.__properties.append(properties)
-        self.__values.append(value)
-
-    def find (self, properties):
-        """ Return the value associated with properties
-        or any subset of it. If more than one
-        subset has value assigned to it, return the
-        value for the longest subset, if it's unique.
-        """
-        return self.find_replace (properties)
-
-    def find_replace(self, properties, value=None):
-        matches = []
-        match_ranks = []
-        
-        for i in range(0, len(self.__properties)):
-            p = self.__properties[i]
-                        
-            if b2.util.set.contains (p, properties):
-                matches.append (i)
-                match_ranks.append(len(p))
-
-        best = sequence.select_highest_ranked (matches, match_ranks)
-
-        if not best:
-            return None
-
-        if len (best) > 1:
-            raise NoBestMatchingAlternative ()
-
-        best = best [0]
-            
-        original = self.__values[best]
-
-        if value:
-            self.__values[best] = value
-
-        return original
-
-#   local rule __test__ ( )
-#   {
-#       import errors : try catch ;
-#       import feature ;
-#       import feature : feature subfeature compose ;
-#       
-#       # local rules must be explicitly re-imported
-#       import property : path-order ;
-#       
-#       feature.prepare-test property-test-temp ;
-#   
-#       feature toolset : gcc : implicit symmetric ;
-#       subfeature toolset gcc : version : 2.95.2 2.95.3 2.95.4
-#         3.0 3.0.1 3.0.2 : optional ;
-#       feature define : : free ;
-#       feature runtime-link : dynamic static : symmetric link-incompatible ;
-#       feature optimization : on off ;
-#       feature variant : debug release : implicit composite symmetric ;
-#       feature rtti : on off : link-incompatible ;
-#   
-#       compose <variant>debug : <define>_DEBUG <optimization>off ;
-#       compose <variant>release : <define>NDEBUG <optimization>on ;
-#   
-#       import assert ;
-#       import "class" : new ;
-#       
-#       validate <toolset>gcc  <toolset>gcc-3.0.1 : $(test-space) ;
-#       
-#       assert.result <toolset>gcc <rtti>off <define>FOO
-#           : refine <toolset>gcc <rtti>off
-#           : <define>FOO
-#           : $(test-space)
-#           ;
-#   
-#       assert.result <toolset>gcc <optimization>on
-#           : refine <toolset>gcc <optimization>off
-#           : <optimization>on
-#           : $(test-space)
-#           ;
-#   
-#       assert.result <toolset>gcc <rtti>off
-#           : refine <toolset>gcc : <rtti>off : $(test-space)
-#           ;
-#   
-#       assert.result <toolset>gcc <rtti>off <rtti>off:<define>FOO
-#           : refine <toolset>gcc : <rtti>off <rtti>off:<define>FOO 
-#           : $(test-space)
-#           ;
-#       
-#       assert.result <toolset>gcc:<define>foo <toolset>gcc:<define>bar 
-#           : refine <toolset>gcc:<define>foo : <toolset>gcc:<define>bar 
-#           : $(test-space)
-#           ;
-#   
-#       assert.result <define>MY_RELEASE
-#           : evaluate-conditionals-in-context 
-#             <variant>release,<rtti>off:<define>MY_RELEASE
-#             : <toolset>gcc <variant>release <rtti>off
-#                    
-#           ;
-#   
-#       try ;
-#           validate <feature>value : $(test-space) ;
-#       catch "Invalid property '<feature>value': unknown feature 'feature'." ;
-#   
-#       try ;
-#           validate <rtti>default : $(test-space) ;
-#       catch \"default\" is not a known value of feature <rtti> ;
-#       
-#       validate <define>WHATEVER : $(test-space) ;
-#   
-#       try ;
-#           validate <rtti> : $(test-space) ;
-#       catch "Invalid property '<rtti>': No value specified for feature 'rtti'." ;
-#   
-#       try ;
-#           validate value : $(test-space) ;
-#       catch "value" is not a value of an implicit feature ;
-#              
-#   
-#       assert.result <rtti>on 
-#           : remove free implicit : <toolset>gcc <define>foo <rtti>on : $(test-space) ;
-#   
-#       assert.result <include>a 
-#           : select include : <include>a <toolset>gcc ;
-#   
-#       assert.result <include>a 
-#           : select include bar : <include>a <toolset>gcc ;
-#   
-#       assert.result <include>a <toolset>gcc
-#           : select include <bar> <toolset> : <include>a <toolset>gcc ;
-#       
-#       assert.result <toolset>kylix <include>a 
-#           : change <toolset>gcc <include>a : <toolset> kylix ;
-#   
-#       # Test ordinary properties 
-#       assert.result 
-#         : split-conditional <toolset>gcc 
-#         ;
-#       
-#       # Test properties with ":"
-#       assert.result
-#         : split-conditional <define>FOO=A::B
-#         ;
-#       
-#       # Test conditional feature
-#       assert.result <toolset>gcc,<toolset-gcc:version>3.0 <define>FOO
-#         : split-conditional <toolset>gcc,<toolset-gcc:version>3.0:<define>FOO
-#         ;
-#       
-#       feature.finish-test property-test-temp ;
-#   }
-#   
-    
diff --git a/jam-files/boost-build/build/property_set.py b/jam-files/boost-build/build/property_set.py
deleted file mode 100644
index f12eb90c..00000000
--- a/jam-files/boost-build/build/property_set.py
+++ /dev/null
@@ -1,449 +0,0 @@
-# Status: ported.
-# Base revision: 40480
-
-#  Copyright (C) Vladimir Prus 2002. Permission to copy, use, modify, sell and
-#  distribute this software is granted provided this copyright notice appears in
-#  all copies. This software is provided "as is" without express or implied
-#  warranty, and with no claim as to its suitability for any purpose.
-
-from b2.util.utility import *
-import property, feature, string
-import b2.build.feature
-from b2.exceptions import *
-from b2.util.sequence import unique
-from b2.util.set import difference
-from b2.util import cached
-
-from b2.manager import get_manager
-
-
-def reset ():
-    """ Clear the module state. This is mainly for testing purposes.
-    """
-    global __cache
-
-    # A cache of property sets
-    # TODO: use a map of weak refs?
-    __cache = {}
-    
-reset ()
-
-
-def create (raw_properties = []):
-    """ Creates a new 'PropertySet' instance for the given raw properties,
-        or returns an already existing one.
-    """
-    # FIXME: propagate to callers.
-    if len(raw_properties) > 0 and isinstance(raw_properties[0], property.Property):
-        x = raw_properties
-    else:        
-        x = [property.create_from_string(ps) for ps in raw_properties]
-    x.sort()
-    x = unique (x)
-
-    # FIXME: can we do better, e.g. by directly computing
-    # has value of the list?
-    key = tuple(x)
-
-    if not __cache.has_key (key):
-        __cache [key] = PropertySet(x)
-
-    return __cache [key]
-
-def create_with_validation (raw_properties):
-    """ Creates new 'PropertySet' instances after checking
-        that all properties are valid and converting incidental
-        properties into gristed form.
-    """
-    properties = [property.create_from_string(s) for s in raw_properties]
-    property.validate(properties)
-    
-    return create(properties)
-
-def empty ():
-    """ Returns PropertySet with empty set of properties.
-    """
-    return create ()
-
-def create_from_user_input(raw_properties, jamfile_module, location):
-    """Creates a property-set from the input given by the user, in the
-    context of 'jamfile-module' at 'location'"""
-
-    properties = property.create_from_strings(raw_properties, True)
-    properties = property.translate_paths(properties, location)
-    properties = property.translate_indirect(properties, jamfile_module)
-
-    project_id = get_manager().projects().attributeDefault(jamfile_module, 'id', None)
-    if not project_id:
-        project_id = os.path.abspath(location)    
-    properties = property.translate_dependencies(properties, project_id, location)
-    properties = property.expand_subfeatures_in_conditions(properties)
-    return create(properties)
-
-
-def refine_from_user_input(parent_requirements, specification, jamfile_module,
-                           location):
-    """Refines requirements with requirements provided by the user.
-    Specially handles "-<property>value" syntax in specification
-     to remove given requirements.
-     - parent-requirements -- property-set object with requirements
-       to refine
-     - specification -- string list of requirements provided by the use
-     - project-module -- the module to which context indirect features
-       will be bound.
-     - location -- the path to which path features are relative."""
-
-
-    if not specification:
-        return parent_requirements
-
-    
-    add_requirements = []
-    remove_requirements = []
-
-    for r in specification:
-        if r[0] == '-':
-            remove_requirements.append(r[1:])
-        else:
-            add_requirements.append(r)
-        
-    if remove_requirements:
-        # Need to create property set, so that path features
-        # and indirect features are translated just like they
-        # are in project requirements.
-        ps = create_from_user_input(remove_requirements,
-                                    jamfile_module, location)
-        
-        parent_requirements = create(difference(parent_requirements.all(),
-                                                ps.all()))
-        specification = add_requirements
-
-    requirements = create_from_user_input(specification,
-                                          jamfile_module, location)
-        
-    return parent_requirements.refine(requirements)
-    
-class PropertySet:
-    """ Class for storing a set of properties.
-        - there's 1<->1 correspondence between identity and value. No
-          two instances of the class are equal. To maintain this property,
-          the 'PropertySet.create' rule should be used to create new instances.
-          Instances are immutable.
-
-        - each property is classified with regard to it's effect on build
-          results. Incidental properties have no effect on build results, from
-          Boost.Build point of view. Others are either free, or non-free, which we
-          call 'base'. Each property belong to exactly one of those categories and
-          it's possible to get list of properties in each category.
-
-          In addition, it's possible to get list of properties with specific
-          attribute.
-
-        - several operations, like and refine and as_path are provided. They all use
-          caching whenever possible.
-    """
-    def __init__ (self, properties = []):
-
-
-        raw_properties = []
-        for p in properties:
-            raw_properties.append(p.to_raw())
-
-        self.all_ = properties
-        self.all_raw_ = raw_properties
-        self.all_set_ = set(properties)
-        
-        self.incidental_ = []
-        self.free_ = []
-        self.base_ = []
-        self.dependency_ = []
-        self.non_dependency_ = []
-        self.conditional_ = []
-        self.non_conditional_ = []
-        self.propagated_ = []
-        self.link_incompatible = []
-        
-        # A cache of refined properties.
-        self.refined_ = {}
-        
-        # A cache of property sets created by adding properties to this one.
-        self.added_ = {}
-
-        # Cache for the default properties.
-        self.defaults_ = None
-
-        # Cache for the expanded properties.
-        self.expanded_ = None
-
-        # Cache for the expanded composite properties
-        self.composites_ = None
-
-        # Cache for property set with expanded subfeatures
-        self.subfeatures_ = None
-
-        # Cache for the property set containing propagated properties.
-        self.propagated_ps_ = None
-        
-        # A map of features to its values.
-        self.feature_map_ = None
-        
-        # A tuple (target path, is relative to build directory)
-        self.target_path_ = None
-        
-        self.as_path_ = None
-        
-        # A cache for already evaluated sets.
-        self.evaluated_ = {}
-        
-        for p in raw_properties:
-            if not get_grist (p):
-                raise BaseException ("Invalid property: '%s'" % p)
-            
-            att = feature.attributes (get_grist (p))
-                                                                   
-            if 'propagated' in att:
-                self.propagated_.append (p)
-
-            if 'link_incompatible' in att:
-                self.link_incompatible.append (p)
-
-        for p in properties:
-
-            # A feature can be both incidental and free,
-            # in which case we add it to incidental.
-            if p.feature().incidental():
-                self.incidental_.append(p)
-            elif p.feature().free():
-                self.free_.append(p)
-            else:
-                self.base_.append(p)
-
-            if p.condition():
-                self.conditional_.append(p)
-            else:
-                self.non_conditional_.append(p)
-
-            if p.feature().dependency():
-                self.dependency_.append (p)
-            else:
-                self.non_dependency_.append (p)
-                
-
-    def all(self):
-        return self.all_
-    
-    def raw (self):
-        """ Returns the list of stored properties.
-        """
-        return self.all_raw_
-
-    def __str__(self):
-        return ' '.join(str(p) for p in self.all_)
-    
-    def base (self):
-        """ Returns properties that are neither incidental nor free.
-        """
-        return self.base_
-    
-    def free (self):
-        """ Returns free properties which are not dependency properties.
-        """
-        return self.free_
-
-    def non_free(self):
-        return self.base_ + self.incidental_
-
-    def dependency (self):
-        """ Returns dependency properties.
-        """
-        return self.dependency_
-    
-    def non_dependency (self):
-        """ Returns properties that are not dependencies.
-        """
-        return self.non_dependency_
-    
-    def conditional (self):
-        """ Returns conditional properties.
-        """
-        return self.conditional_
-        
-    def non_conditional (self):
-        """ Returns properties that are not conditional.
-        """
-        return self.non_conditional_
-              
-    def incidental (self):
-        """ Returns incidental properties.
-        """
-        return self.incidental_
-    
-    def refine (self, requirements):
-        """ Refines this set's properties using the requirements passed as an argument.
-        """
-        assert isinstance(requirements, PropertySet)
-        if not self.refined_.has_key (requirements):
-            r = property.refine(self.all_, requirements.all_)
-
-            self.refined_[requirements] = create(r)
-
-        return self.refined_[requirements]
-
-    def expand (self):
-        if not self.expanded_:
-            expanded = feature.expand(self.all_)
-            self.expanded_ = create(expanded)
-        return self.expanded_
-
-    def expand_subfeatures(self):
-        if not self.subfeatures_:
-            self.subfeatures_ = create(feature.expand_subfeatures(self.all_))
-        return self.subfeatures_
-
-    def evaluate_conditionals(self, context=None):
-        if not context:
-            context = self
-
-        if not self.evaluated_.has_key(context):
-            # FIXME: figure why the call messes up first parameter
-            self.evaluated_[context] = create(
-                property.evaluate_conditionals_in_context(self.all(), context))
-
-        return self.evaluated_[context]
-
-    def propagated (self):
-        if not self.propagated_ps_:
-            self.propagated_ps_ = create (self.propagated_)
-        return self.propagated_ps_
-
-    def add_defaults (self):
-        # FIXME: this caching is invalidated when new features
-        # are declare inside non-root Jamfiles.
-        if not self.defaults_:
-            expanded = feature.add_defaults(self.all_)
-            self.defaults_ = create(expanded)
-        return self.defaults_
-
-    def as_path (self):
-        if not self.as_path_:
-
-            def path_order (p1, p2):
-
-                i1 = p1.feature().implicit()
-                i2 = p2.feature().implicit()
-
-                if i1 != i2:
-                    return i2 - i1
-                else:
-                    return cmp(p1.feature().name(), p2.feature().name())
-
-            # trim redundancy
-            properties = feature.minimize(self.base_)
-                
-            # sort according to path_order
-            properties.sort (path_order)
-                
-            components = []
-            for p in properties:
-                if p.feature().implicit():
-                    components.append(p.value())
-                else:
-                    components.append(p.feature().name() + "-" + p.value())
-
-            self.as_path_ = '/'.join (components)
-
-        return self.as_path_
-
-    def target_path (self):
-        """ Computes the target path that should be used for 
-            target with these properties.
-            Returns a tuple of
-              - the computed path
-              - if the path is relative to build directory, a value of
-                'true'. 
-        """
-        if not self.target_path_:
-            # The <location> feature can be used to explicitly
-            # change the location of generated targets
-            l = self.get ('<location>')
-            if l:
-                computed = l[0]
-                is_relative = False
-
-            else:
-                p = self.as_path ()
-                
-                # Really, an ugly hack. Boost regression test system requires
-                # specific target paths, and it seems that changing it to handle
-                # other directory layout is really hard. For that reason,
-                # we teach V2 to do the things regression system requires.
-                # The value o '<location-prefix>' is predended to the path.
-                prefix = self.get ('<location-prefix>')
-                
-                if prefix:
-                    if len (prefix) > 1:
-                        raise AlreadyDefined ("Two <location-prefix> properties specified: '%s'" % prefix)
-                        
-                    computed = os.path.join(prefix[0], p)
-
-                else:
-                    computed = p
-
-                if not computed:
-                    computed = "."
-
-                is_relative = True
-
-            self.target_path_ = (computed, is_relative)
-
-        return self.target_path_
-                    
-    def add (self, ps):
-        """ Creates a new property set containing the properties in this one,
-            plus the ones of the property set passed as argument.
-        """
-        if not self.added_.has_key(ps):
-            self.added_[ps] = create(self.all_ + ps.all())
-        return self.added_[ps]
-    
-    def add_raw (self, properties):
-        """ Creates a new property set containing the properties in this one,
-            plus the ones passed as argument.
-        """
-        return self.add (create (properties))
-
-    
-    def get (self, feature):
-        """ Returns all values of 'feature'.
-        """
-        if type(feature) == type([]):
-            feature = feature[0]
-        if not isinstance(feature, b2.build.feature.Feature):
-            feature = b2.build.feature.get(feature)
-        
-        if not self.feature_map_:
-            self.feature_map_ = {}
-
-            for v in self.all_:
-                if not self.feature_map_.has_key(v.feature()):
-                    self.feature_map_[v.feature()] = []
-                self.feature_map_[v.feature()].append(v.value())
-        
-        return self.feature_map_.get(feature, [])
-
-    @cached
-    def get_properties(self, feature):
-        """Returns all contained properties associated with 'feature'"""
-
-        if not isinstance(feature, b2.build.feature.Feature):
-            feature = b2.build.feature.get(feature)
-
-        result = []        
-        for p in self.all_:
-            if p.feature() == feature:
-                result.append(p)
-        return result
-    
-    def __contains__(self, item):
-        return item in self.all_set_
-    
diff --git a/jam-files/boost-build/build/readme.txt b/jam-files/boost-build/build/readme.txt
deleted file mode 100644
index c3dddd8d..00000000
--- a/jam-files/boost-build/build/readme.txt
+++ /dev/null
@@ -1,13 +0,0 @@
-Copyright 2001, 2002 Dave Abrahams 
-Copyright 2002 Vladimir Prus 
-Distributed under the Boost Software License, Version 1.0. 
-(See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt) 
-
-Development code for new build system. To run unit tests for jam code, execute:
-
-  bjam --debug --build-system=test
-
-Comprehensive tests require Python. See ../test/readme.txt
-
-
-
diff --git a/jam-files/boost-build/build/scanner.jam b/jam-files/boost-build/build/scanner.jam
deleted file mode 100644
index d6042ea2..00000000
--- a/jam-files/boost-build/build/scanner.jam
+++ /dev/null
@@ -1,153 +0,0 @@
-# Copyright 2003 Dave Abrahams 
-# Copyright 2002, 2003, 2004, 2005 Vladimir Prus 
-# Distributed under the Boost Software License, Version 1.0. 
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt) 
-
-#  Implements scanners: objects that compute implicit dependencies for
-#  files, such as includes in C++.
-#
-#  Scanner has a regular expression used to find dependencies, some
-#  data needed to interpret those dependencies (for example, include
-#  paths), and a code which actually established needed relationship
-#  between actual jam targets.
-#
-#  Scanner objects are created by actions, when they try to actualize
-#  virtual targets, passed to 'virtual-target.actualize' method and are
-#  then associated with actual targets. It is possible to use
-#  several scanners for a virtual-target. For example, a single source
-#  might be used by to compile actions, with different include paths.
-#  In this case, two different actual targets will be created, each 
-#  having scanner of its own.
-#
-#  Typically, scanners are created from target type and action's 
-#  properties, using the rule 'get' in this module. Directly creating
-#  scanners is not recommended, because it might create many equvivalent
-#  but different instances, and lead in unneeded duplication of
-#  actual targets. However, actions can also create scanners in a special
-#  way, instead of relying on just target type.
-
-import "class" : new ;
-import property virtual-target property-set ;
-import errors : error ;
-
-#  Base scanner class. 
-class scanner 
-{
-    rule __init__ ( )
-    {
-    }
-    
-    # Returns a pattern to use for scanning
-    rule pattern ( )
-    {
-        error "method must be overriden" ;
-    }
-
-    # Establish necessary relationship between targets,
-    # given actual target beeing scanned, and a list of
-    # pattern matches in that file.
-    rule process ( target : matches * )
-    {
-        error "method must be overriden" ;
-    }        
-}
-
-# Registers a new generator class, specifying a set of 
-# properties relevant to this scanner.  Ctor for that class
-# should have one parameter: list of properties.
-rule register ( scanner-class : relevant-properties * )
-{
-    .registered += $(scanner-class) ;
-    .relevant-properties.$(scanner-class) = $(relevant-properties) ;
-}
-
-# Common scanner class, which can be used when there's only one
-# kind of includes (unlike C, where "" and <> includes have different
-# search paths).
-class common-scanner : scanner 
-{
-    import scanner ;
-    rule __init__ ( includes * )
-    {
-        scanner.__init__ ;
-        self.includes = $(includes) ;
-    }
-            
-    rule process ( target : matches * : binding )
-    {
-        local target_path = [ NORMALIZE_PATH $(binding:D) ] ;
-
-        NOCARE $(matches) ;
-        INCLUDES $(target) : $(matches) ;
-        SEARCH on $(matches) = $(target_path) $(self.includes:G=) ;
-        ISFILE $(matches) ;
-    
-        scanner.propagate $(__name__) : $(matches) : $(target) ;     
-    }
-}
-
-
-# Returns an instance of previously registered scanner,
-# with the specified properties.
-rule get ( scanner-class : property-set ) 
-{
-    if ! $(scanner-class) in $(.registered)
-    {
-        error "attempt to get unregisted scanner" ;
-    }
-    
-    local r = $(.rv-cache.$(property-set)) ;
-    if ! $(r)
-    {
-        r = [ property-set.create 
-            [ property.select $(.relevant-properties.$(scanner-class)) :
-              [ $(property-set).raw ] ] ] ;        
-        .rv-cache.$(property-set) = $(r) ;
-    }
-        
-    if ! $(scanner.$(scanner-class).$(r:J=-))
-    {
-        scanner.$(scanner-class).$(r:J=-) = [ new $(scanner-class) [ $(r).raw ] ] ;
-    }
-    return $(scanner.$(scanner-class).$(r:J=-)) ;    
-}
-
-
-# Installs the specified scanner on actual target 'target'. 
-rule install ( scanner : target 
-    vtarget # virtual target from which 'target' was actualized
-)
-{
-    HDRSCAN on $(target) = [ $(scanner).pattern ] ;
-    SCANNER on $(target) = $(scanner) ;
-    HDRRULE on $(target) = scanner.hdrrule ;
-    
-    # scanner reflects difference in properties affecting    
-    # binding of 'target', which will be known when processing
-    # includes for it, will give information on how to
-    # interpret quoted includes.
-    HDRGRIST on $(target) = $(scanner) ;
-}
-
-# Propagate scanner setting from 'including-target' to 'targets'.
-rule propagate ( scanner : targets * : including-target )
-{
-    HDRSCAN on $(targets) = [ on $(including-target) return $(HDRSCAN) ] ;
-    SCANNER on $(targets) = $(scanner) ;
-    HDRRULE on $(targets) = scanner.hdrrule ;
-    HDRGRIST on $(targets) = [ on $(including-target) return $(HDRGRIST) ] ;
-}
-
-
-rule hdrrule ( target : matches * : binding )
-{
-    local scanner = [ on $(target) return $(SCANNER) ] ;
-    $(scanner).process $(target) : $(matches) : $(binding) ;
-}
-# hdrrule must be available at global scope so that it can be invoked
-# by header scanning
-IMPORT scanner : hdrrule : : scanner.hdrrule ;
-
-
-
-
diff --git a/jam-files/boost-build/build/scanner.py b/jam-files/boost-build/build/scanner.py
deleted file mode 100644
index 19f1431d..00000000
--- a/jam-files/boost-build/build/scanner.py
+++ /dev/null
@@ -1,158 +0,0 @@
-# Status: ported.
-# Base revision: 45462
-# 
-# Copyright 2003 Dave Abrahams 
-# Copyright 2002, 2003, 2004, 2005 Vladimir Prus 
-# Distributed under the Boost Software License, Version 1.0. 
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt) 
-
-#  Implements scanners: objects that compute implicit dependencies for
-#  files, such as includes in C++.
-#
-#  Scanner has a regular expression used to find dependencies, some
-#  data needed to interpret those dependencies (for example, include
-#  paths), and a code which actually established needed relationship
-#  between actual jam targets.
-#
-#  Scanner objects are created by actions, when they try to actualize
-#  virtual targets, passed to 'virtual-target.actualize' method and are
-#  then associated with actual targets. It is possible to use
-#  several scanners for a virtual-target. For example, a single source
-#  might be used by to compile actions, with different include paths.
-#  In this case, two different actual targets will be created, each 
-#  having scanner of its own.
-#
-#  Typically, scanners are created from target type and action's 
-#  properties, using the rule 'get' in this module. Directly creating
-#  scanners is not recommended, because it might create many equvivalent
-#  but different instances, and lead in unneeded duplication of
-#  actual targets. However, actions can also create scanners in a special
-#  way, instead of relying on just target type.
-
-import property
-import bjam
-import os
-from b2.exceptions import *
-from b2.manager import get_manager
-
-def reset ():
-    """ Clear the module state. This is mainly for testing purposes.
-    """
-    global __scanners, __rv_cache, __scanner_cache
-
-    # Maps registered scanner classes to relevant properties
-    __scanners = {}
-    
-    # A cache of scanners.
-    # The key is: class_name.properties_tag, where properties_tag is the concatenation 
-    # of all relevant properties, separated by '-'
-    __scanner_cache = {}
-    
-reset ()
-
-
-def register(scanner_class, relevant_properties):
-    """ Registers a new generator class, specifying a set of 
-        properties relevant to this scanner.  Ctor for that class
-        should have one parameter: list of properties.
-    """
-    __scanners[str(scanner_class)] = relevant_properties
-
-def registered(scanner_class):
-    """ Returns true iff a scanner of that class is registered
-    """
-    return __scanners.has_key(str(scanner_class))
-    
-def get(scanner_class, properties):
-    """ Returns an instance of previously registered scanner
-        with the specified properties.
-    """
-    scanner_name = str(scanner_class)
-    
-    if not registered(scanner_name):
-        raise BaseException ("attempt to get unregisted scanner: %s" % scanner_name)
-
-    relevant_properties = __scanners[scanner_name]
-    r = property.select(relevant_properties, properties)
-
-    scanner_id = scanner_name + '.' + '-'.join(r)
-    
-    if not __scanner_cache.has_key(scanner_name):
-        __scanner_cache[scanner_name] = scanner_class(r)
-
-    return __scanner_cache[scanner_name]
-
-class Scanner:
-    """ Base scanner class.
-    """
-    def __init__ (self):
-        pass
-    
-    def pattern (self):
-        """ Returns a pattern to use for scanning.
-        """
-        raise BaseException ("method must be overriden")
-
-    def process (self, target, matches):
-        """ Establish necessary relationship between targets,
-            given actual target beeing scanned, and a list of
-            pattern matches in that file.
-        """
-        raise BaseException ("method must be overriden")
-
-
-# Common scanner class, which can be used when there's only one
-# kind of includes (unlike C, where "" and <> includes have different
-# search paths).
-class CommonScanner(Scanner):
-
-    def __init__ (self, includes):
-        Scanner.__init__(self)
-        self.includes = includes
-
-    def process(self, target, matches, binding):
-
-        target_path = os.path.normpath(os.path.dirname(binding[0]))
-        bjam.call("mark-included", target, matches)
-
-        get_manager().engine().set_target_variable(matches, "SEARCH",
-                                                   [target_path] + self.includes)
-        get_manager().scanners().propagate(self, matches)
-
-class ScannerRegistry:
-    
-    def __init__ (self, manager):
-        self.manager_ = manager
-        self.count_ = 0
-        self.exported_scanners_ = {}
-
-    def install (self, scanner, target, vtarget):
-        """ Installs the specified scanner on actual target 'target'. 
-            vtarget: virtual target from which 'target' was actualized.
-        """
-        engine = self.manager_.engine()
-        engine.set_target_variable(target, "HDRSCAN", scanner.pattern())
-        if not self.exported_scanners_.has_key(scanner):
-            exported_name = "scanner_" + str(self.count_)
-            self.count_ = self.count_ + 1
-            self.exported_scanners_[scanner] = exported_name
-            bjam.import_rule("", exported_name, scanner.process)
-        else:
-            exported_name = self.exported_scanners_[scanner]
-
-        engine.set_target_variable(target, "HDRRULE", exported_name)
-        
-        # scanner reflects difference in properties affecting    
-        # binding of 'target', which will be known when processing
-        # includes for it, will give information on how to
-        # interpret quoted includes.
-        engine.set_target_variable(target, "HDRGRIST", str(id(scanner)))
-        pass
-
-    def propagate(self, scanner, targets):
-        engine = self.manager_.engine()
-        engine.set_target_variable(targets, "HDRSCAN", scanner.pattern())
-        engine.set_target_variable(targets, "HDRRULE",
-                                   self.exported_scanners_[scanner])
-        engine.set_target_variable(targets, "HDRGRIST", str(id(scanner)))
-
diff --git a/jam-files/boost-build/build/targets.jam b/jam-files/boost-build/build/targets.jam
deleted file mode 100644
index a70532ce..00000000
--- a/jam-files/boost-build/build/targets.jam
+++ /dev/null
@@ -1,1659 +0,0 @@
-# Copyright Vladimir Prus 2002.
-# Copyright Rene Rivera 2006.
-#
-# Distributed under the Boost Software License, Version 1.0.
-#    (See accompanying file LICENSE_1_0.txt or copy at
-#          http://www.boost.org/LICENSE_1_0.txt)
-
-# Supports 'abstract' targets, which are targets explicitly defined in a
-# Jamfile.
-#
-# Abstract targets are represented by classes derived from 'abstract-target'
-# class. The first abstract target is 'project-target', which is created for
-# each Jamfile, and can be obtained by the 'target' rule in the Jamfile's module
-# (see project.jam).
-#
-# Project targets keep a list of 'main-target' instances. A main target is what
-# the user explicitly defines in a Jamfile. It is possible to have several
-# definitions for a main target, for example to have different lists of sources
-# for different platforms. So, main targets keep a list of alternatives.
-#
-# Each alternative is an instance of 'abstract-target'. When a main target
-# subvariant is defined by some rule, that rule will decide what class to use,
-# create an instance of that class and add it to the list of alternatives for
-# the main target.
-#
-# Rules supplied by the build system will use only targets derived from
-# 'basic-target' class, which will provide some default behaviour. There will be
-# different classes derived from it such as 'make-target', created by the 'make'
-# rule, and 'typed-target', created by rules such as 'exe' and 'lib'.
-
-#
-#                         +------------------------+
-#                         |abstract-target         |
-#                         +========================+
-#                         |name                    |
-#                         |project                 |
-#                         |                        |
-#                         |generate(properties) = 0|
-#                         +-----------+------------+
-#                                     |
-#                                     ^
-#                                    / \
-#                                   +-+-+
-#                                     |
-#                                     |
-#            +------------------------+------+------------------------------+
-#            |                               |                              |
-#            |                               |                              |
-# +----------+-----------+            +------+------+                +------+-------+
-# | project-target       |            | main-target |                | basic-target |
-# +======================+ 1        * +=============+  alternatives  +==============+
-# | generate(properties) |o-----------+ generate    |<>------------->| generate     |
-# | main-target          |            +-------------+                | construct = 0|
-# +----------------------+                                           +--------------+
-#                                                                           |
-#                                                                           ^
-#                                                                          / \
-#                                                                         +-+-+
-#                                                                           |
-#                                                                           |
-#                 ...--+----------------+------------------+----------------+---+
-#                      |                |                  |                    |
-#                      |                |                  |                    |
-#               ... ---+-----+   +------+-------+   +------+------+    +--------+-----+
-#                            |   | typed-target |   | make-target |    | stage-target |
-#                            .   +==============+   +=============+    +==============+
-#                            .   | construct    |   | construct   |    | construct    |
-#                                +--------------+   +-------------+    +--------------+
-
-import assert ;
-import "class" : new ;
-import errors ;
-import feature ;
-import indirect ;
-import path ;
-import property ;
-import property-set ;
-import sequence ;
-import set ;
-import toolset ;
-import build-request ;
-
-
-# Base class for all abstract targets.
-#
-class abstract-target
-{
-    import project ;
-    import assert ;
-    import "class" ;
-    import errors ;
-
-    rule __init__ ( name  # Name of the target in Jamfile.
-        : project-target  # The project target to which this one belongs.
-    )
-    {
-        # Note: it might seem that we don't need either name or project at all.
-        # However, there are places where we really need it. One example is
-        # error messages which should name problematic targets. Another is
-        # setting correct paths for sources and generated files.
-
-        self.name = $(name) ;
-        self.project = $(project-target) ;
-        self.location = [ errors.nearest-user-location ] ;
-    }
-
-    # Returns the name of this target.
-    rule name ( )
-    {
-        return $(self.name) ;
-    }
-
-    # Returns the project for this target.
-    rule project ( )
-    {
-        return $(self.project) ;
-    }
-
-    # Return the location where the target was declared.
-    rule location ( )
-    {
-        return $(self.location) ;
-    }
-
-    # Returns a user-readable name for this target.
-    rule full-name ( )
-    {
-        local location = [ $(self.project).get location ] ;
-        return $(location)/$(self.name) ;
-    }
-
-    # Generates virtual targets for this abstract target using the specified
-    # properties, unless a different value of some feature is required by the
-    # target.
-    # On success, returns:
-    # - a property-set with the usage requirements to be applied to dependants
-    # - a list of produced virtual targets, which may be empty.
-    # If 'property-set' is empty, performs the default build of this target, in
-    # a way specific to the derived class.
-    #
-    rule generate ( property-set )
-    {
-        errors.error "method should be defined in derived classes" ;
-    }
-
-    rule rename ( new-name )
-    {
-        self.name = $(new-name) ;
-    }
-}
-
-
-if --debug-building in [ modules.peek : ARGV ]
-{
-    modules.poke : .debug-building : true ;
-}
-
-
-rule indent ( )
-{
-    return $(.indent:J="") ;
-}
-
-
-rule increase-indent ( )
-{
-    .indent += "    " ;
-}
-
-
-rule decrease-indent ( )
-{
-    .indent = $(.indent[2-]) ;
-}
-
-
-#  Project target class (derived from 'abstract-target').
-#
-#  This class has the following responsibilities:
-#  - Maintaining a list of main targets in this project and building them.
-#
-#  Main targets are constructed in two stages:
-#  - When Jamfile is read, a number of calls to 'add-alternative' is made. At
-#    that time, alternatives can also be renamed to account for inline targets.
-#  - The first time 'main-target' or 'has-main-target' rule is called, all
-#    alternatives are enumerated and main targets are created.
-#
-class project-target : abstract-target
-{
-    import project ;
-    import targets ;
-    import path ;
-    import print ;
-    import property-set ;
-    import set ;
-    import sequence ;
-    import "class" : new ;
-    import errors ;
-
-    rule __init__ ( name : project-module parent-project ?
-        : requirements * : default-build * )
-    {
-        abstract-target.__init__ $(name) : $(__name__) ;
-
-        self.project-module = $(project-module) ;
-        self.location = [ project.attribute $(project-module) location ] ;
-        self.requirements = $(requirements) ;
-        self.default-build = $(default-build) ;
-
-        if $(parent-project)
-        {
-            inherit $(parent-project) ;
-        }
-    }
-
-    # This is needed only by the 'make' rule. Need to find the way to make
-    # 'make' work without this method.
-    #
-    rule project-module ( )
-    {
-        return $(self.project-module) ;
-    }
-
-    rule get ( attribute )
-    {
-        return [ project.attribute $(self.project-module) $(attribute) ] ;
-    }
-
-    rule build-dir ( )
-    {
-        if ! $(self.build-dir)
-        {
-            self.build-dir = [ get build-dir ] ;
-            if ! $(self.build-dir)
-            {
-                self.build-dir = [ path.join [ $(self.project).get location ]
-                    bin ] ;
-            }
-        }
-        return $(self.build-dir) ;
-    }
-
-    # Generates all possible targets contained in this project.
-    #
-    rule generate ( property-set * )
-    {
-        if [ modules.peek : .debug-building ]
-        {
-            ECHO [ targets.indent ] "building project" [ name ] " ('$(__name__)') with" [ $(property-set).raw ] ;
-            targets.increase-indent ;
-        }
-
-        local usage-requirements = [ property-set.empty ] ;
-        local targets ;
-
-        for local t in [ targets-to-build ]
-        {
-            local g = [ $(t).generate $(property-set) ] ;
-            usage-requirements = [ $(usage-requirements).add $(g[1]) ] ;
-            targets += $(g[2-]) ;
-        }
-        targets.decrease-indent ;
-        return $(usage-requirements) [ sequence.unique $(targets) ] ;
-    }
-
-    # Computes and returns a list of abstract-target instances which must be
-    # built when this project is built.
-    #
-    rule targets-to-build ( )
-    {
-        local result ;
-
-        if ! $(self.built-main-targets)
-        {
-            build-main-targets ;
-        }
-
-        # Collect all main targets here, except for "explicit" ones.
-        for local t in $(self.main-targets)
-        {
-            if ! [ $(t).name ] in $(self.explicit-targets)
-            {
-                result += $(t) ;
-            }
-        }
-
-        # Collect all projects referenced via "projects-to-build" attribute.
-        local self-location = [ get location ] ;
-        for local pn in [ get projects-to-build ]
-        {
-            result += [ find $(pn)/ ] ;
-        }
-
-        return $(result) ;
-    }
-
-    # Add 'target' to the list of targets in this project that should be build
-    # only by explicit request
-    #
-    rule mark-target-as-explicit ( target-name * )
-    {
-        # Record the name of the target, not instance, since this rule is called
-        # before main target instances are created.
-        self.explicit-targets += $(target-name) ;
-    }
-    
-    rule mark-target-as-always ( target-name * )
-    {
-        # Record the name of the target, not instance, since this rule is called
-        # before main target instances are created.
-        self.always-targets += $(target-name) ;
-    }
-
-    # Add new target alternative
-    #
-    rule add-alternative ( target-instance )
-    {
-        if $(self.built-main-targets)
-        {
-            errors.error add-alternative called when main targets are already
-                created. : in project [ full-name ] ;
-        }
-        self.alternatives += $(target-instance) ;
-    }
-
-    # Returns a 'main-target' class instance corresponding to 'name'.
-    #
-    rule main-target ( name )
-    {
-        if ! $(self.built-main-targets)
-        {
-            build-main-targets ;
-        }
-        return $(self.main-target.$(name)) ;
-    }
-
-    # Returns whether a main target with the specified name exists.
-    #
-    rule has-main-target ( name )
-    {
-        if ! $(self.built-main-targets)
-        {
-            build-main-targets ;
-        }
-
-        if $(self.main-target.$(name))
-        {
-            return true ;
-        }
-    }
-
-    # Worker function for the find rule not implementing any caching and simply
-    # returning nothing in case the target can not be found.
-    #
-    rule find-really ( id )
-    {
-        local result ;
-        local current-location = [ get location ] ;
-
-        local split = [ MATCH (.*)//(.*) : $(id) ] ;
-        local project-part = $(split[1]) ;
-        local target-part = $(split[2]) ;
-
-        local extra-error-message ;
-        if $(project-part)
-        {
-            # There is an explicitly specified project part in id. Looks up the
-            # project and passes the request to it.
-            local pm = [ project.find $(project-part) : $(current-location) ] ;
-            if $(pm)
-            {
-                project-target = [ project.target $(pm) ] ;
-                result = [ $(project-target).find $(target-part) : no-error ] ;
-            }
-            else
-            {
-                # TODO: This extra error message will not get displayed most
-                # likely due to some buggy refactoring. Refactor the code so the
-                # message gets diplayed again.
-                extra-error-message = error: could not find project
-                    '$(project-part)' ;
-            }
-        }
-        else
-        {
-            # Interpret target-name as name of main target. Need to do this
-            # before checking for file. Consider the following scenario with a
-            # toolset not modifying its executable's names, e.g. gcc on
-            # Unix-like platforms:
-            #
-            #  exe test : test.cpp ;
-            #  install s : test : <location>. ;
-            #
-            # After the first build we would have a target named 'test' in the
-            # Jamfile and a file named 'test' on the disk. We need the target to
-            # override the file.
-            result = [ main-target $(id) ] ;
-            
-            # Interpret id as an existing file reference.
-            if ! $(result)
-            {
-                result = [ new file-reference [ path.make $(id) ] :
-                    $(self.project) ] ;
-                if ! [ $(result).exists ]
-                {
-                    result = ;
-                }
-            }
-
-            # Interpret id as project-id.
-            if ! $(result)
-            {
-                local project-module = [ project.find $(id) :
-                    $(current-location) ] ;
-                if $(project-module)
-                {
-                    result = [ project.target $(project-module) ] ;
-                }
-            }
-        }
-
-        return $(result) ;
-    }
-
-    # Find and return the target with the specified id, treated relative to
-    # self. Id may specify either a target or a file name with the target taking
-    # priority. May report an error or return nothing if the target is not found
-    # depending on the 'no-error' parameter.
-    #
-    rule find ( id : no-error ? )
-    {
-        local v = $(.id.$(id)) ;
-        if ! $(v)
-        {
-            v = [ find-really $(id) ] ;
-            if ! $(v)
-            {
-                v = none ;
-            }
-            .id.$(id) = $(v) ;
-        }
-
-        if $(v) != none
-        {
-            return $(v) ;
-        }
-        else
-        {
-            if ! $(no-error)
-            {
-                local current-location = [ get location ] ;
-                ECHO "error: Unable to find file or target named" ;
-                ECHO "error:     '$(id)'" ;
-                ECHO "error: referred from project at" ;
-                ECHO "error:     '$(current-location)'" ;
-                ECHO $(extra-error-message) ;
-                EXIT ;
-            }
-        }
-    }
-
-    rule build-main-targets ( )
-    {
-        self.built-main-targets = true ;
-        for local a in $(self.alternatives)
-        {
-            local name = [ $(a).name ] ;
-            local target = $(self.main-target.$(name)) ;
-            if ! $(target)
-            {
-                local t = [ new main-target $(name) : $(self.project) ] ;
-                self.main-target.$(name) = $(t) ;
-                self.main-targets += $(t) ;
-                target = $(self.main-target.$(name)) ;
-            }
-            
-            if $(name) in $(self.always-targets)
-            {
-                $(a).always ;
-            }                
-
-            $(target).add-alternative $(a) ;
-        }
-    }
-
-    # Accessor, add a constant.
-    #
-    rule add-constant (
-        name       # Variable name of the constant.
-        : value +  # Value of the constant.
-        : type ?   # Optional type of value.
-        )
-    {
-        switch $(type)
-        {
-            case path :
-              local r ;
-              for local v in $(value)
-              {
-                local l = $(self.location) ;
-                if ! $(l)
-                {
-                    # Project corresponding to config files do not have 
-                    # 'location' attribute, but do have source location.
-                    # It might be more reasonable to make every project have
-                    # a location and use some other approach to prevent buildable
-                    # targets in config files, but that's for later.
-                    l = [ get source-location ] ;
-                }                
-                v = [ path.root [ path.make $(v) ] $(l) ] ;
-                # Now make the value absolute path.
-                v = [ path.root $(v) [ path.pwd ] ] ;
-                # Constants should be in platform-native form.
-                v = [ path.native $(v) ] ;
-                r += $(v) ;
-              }
-              value = $(r) ;
-        }
-        if ! $(name) in $(self.constants)
-        {
-            self.constants += $(name) ;
-        }
-        self.constant.$(name) = $(value) ;
-        # Inject the constant in the scope of the Jamroot module.
-        modules.poke $(self.project-module) : $(name) : $(value) ;
-    }
-
-    rule inherit ( parent )
-    {
-        for local c in [ modules.peek $(parent) : self.constants ]
-        {
-            # No need to pass the type. Path constants were converted to
-            # absolute paths already by parent.
-            add-constant $(c)
-              : [ modules.peek $(parent) : self.constant.$(c) ] ;
-        }
-
-        # Import rules from parent.
-        local this-module = [ project-module ] ;
-        local parent-module = [ $(parent).project-module ] ;
-        # Do not import rules coming from 'project-rules' as they must be
-        # imported localized.
-        local user-rules = [ set.difference
-            [ RULENAMES $(parent-module) ] :
-            [ RULENAMES project-rules ] ] ;
-        IMPORT $(parent-module) : $(user-rules) : $(this-module) : $(user-rules) ;
-        EXPORT $(this-module) : $(user-rules) ;
-    }
-}
-
-
-# Helper rules to detect cycles in main target references.
-#
-local rule start-building ( main-target-instance )
-{
-    if $(main-target-instance) in $(.targets-being-built)
-    {
-        local names ;
-        for local t in $(.targets-being-built) $(main-target-instance)
-        {
-            names += [ $(t).full-name ] ;
-        }
-
-        errors.error "Recursion in main target references"
-          : "the following target are being built currently:"
-          : $(names) ;
-    }
-    .targets-being-built += $(main-target-instance) ;
-}
-
-
-local rule end-building ( main-target-instance )
-{
-    .targets-being-built = $(.targets-being-built[1--2]) ;
-}
-
-
-# A named top-level target in Jamfile.
-#
-class main-target : abstract-target
-{
-    import assert ;
-    import errors ;
-    import feature ;
-    import print ;
-    import property-set ;
-    import sequence ;
-    import targets : start-building end-building ;
-
-    rule __init__ ( name : project )
-    {
-        abstract-target.__init__ $(name) : $(project) ;
-    }
-
-    # Add a new alternative for this target
-    rule add-alternative ( target )
-    {
-        local d = [ $(target).default-build ] ;
-        if $(self.alternatives) && ( $(self.default-build) != $(d) )
-        {
-            errors.error "default build must be identical in all alternatives"
-              : "main target is" [ full-name ]
-              : "with" [ $(d).raw ]
-              : "differing from previous default build" [ $(self.default-build).raw ] ;
-        }
-        else
-        {
-            self.default-build = $(d) ;
-        }
-        self.alternatives += $(target) ;
-    }
-
-    # Returns the best viable alternative for this property-set. See the
-    # documentation for selection rules.
-    #
-    local rule select-alternatives ( property-set debug ? )
-    {
-        # When selecting alternatives we have to consider defaults, for example:
-        #    lib l : l.cpp : <variant>debug ;
-        #    lib l : l_opt.cpp : <variant>release ;
-        # won't work unless we add default value <variant>debug.
-        property-set = [ $(p).add-defaults ] ;
-
-        # The algorithm: we keep the current best viable alternative. When we've
-        # got a new best viable alternative, we compare it with the current one.
-
-        local best ;
-        local best-properties ;
-
-        if $(self.alternatives[2-])
-        {
-            local bad ;
-            local worklist = $(self.alternatives) ;
-            while $(worklist) && ! $(bad)
-            {
-                local v = $(worklist[1]) ;
-                local properties = [ $(v).match $(property-set) $(debug) ] ;
-
-                if $(properties) != no-match
-                {
-                    if ! $(best)
-                    {
-                        best = $(v) ;
-                        best-properties = $(properties) ;
-                    }
-                    else
-                    {
-                        if $(properties) = $(best-properties)
-                        {
-                            bad = true ;
-                        }
-                        else if $(properties) in $(best-properties)
-                        {
-                            # Do nothing, this alternative is worse
-                        }
-                        else if $(best-properties) in $(properties)
-                        {
-                            best = $(v) ;
-                            best-properties = $(properties) ;
-                        }
-                        else
-                        {
-                            bad = true ;
-                        }
-                    }
-                }
-                worklist = $(worklist[2-]) ;
-            }
-            if ! $(bad)
-            {
-                return $(best) ;
-            }
-        }
-        else
-        {
-            return $(self.alternatives) ;
-        }
-    }
-
-    rule apply-default-build ( property-set )
-    {
-        return [ targets.apply-default-build $(property-set) 
-          : $(self.default-build) ] ;
-    }
-
-    # Select an alternative for this main target, by finding all alternatives
-    # which requirements are satisfied by 'properties' and picking the one with
-    # the longest requirements set. Returns the result of calling 'generate' on
-    # that alternative.
-    #
-    rule generate ( property-set )
-    {
-        start-building $(__name__) ;
-
-        # We want composite properties in build request act as if all the
-        # properties it expands too are explicitly specified.
-        property-set = [ $(property-set).expand ] ;
-
-        local all-property-sets = [ apply-default-build $(property-set) ] ;
-        local usage-requirements = [ property-set.empty ] ;
-        local result ;
-        for local p in $(all-property-sets)
-        {
-            local r = [ generate-really $(p) ] ;
-            if $(r)
-            {
-                usage-requirements = [ $(usage-requirements).add $(r[1]) ] ;
-                result += $(r[2-]) ;
-            }
-        }
-        end-building $(__name__) ;
-        return $(usage-requirements) [ sequence.unique $(result) ] ;
-    }
-
-    # Generates the main target with the given property set and returns a list
-    # which first element is property-set object containing usage-requirements
-    # of generated target and with generated virtual target in other elements.
-    # It is possible that no targets are generated.
-    #
-    local rule generate-really ( property-set )
-    {
-        local best-alternatives = [ select-alternatives $(property-set) ] ;
-        if ! $(best-alternatives)
-        {
-            ECHO "error: No best alternative for" [ full-name ] ;
-            select-alternatives $(property-set) debug ;
-            return [ property-set.empty ] ;
-        }
-        else
-        {
-            # Now return virtual targets for the only alternative.
-            return [ $(best-alternatives).generate $(property-set) ] ;
-        }
-    }
-
-    rule rename ( new-name )
-    {
-        abstract-target.rename $(new-name) ;
-        for local a in $(self.alternatives)
-        {
-            $(a).rename $(new-name) ;
-        }
-    }
-}
-
-
-# Abstract target refering to a source file. This is an artificial entity
-# allowing sources to a target to be represented using a list of abstract target
-# instances.
-#
-class file-reference : abstract-target
-{
-    import virtual-target ;
-    import property-set ;
-    import path ;
-
-    rule __init__ ( file : project )
-    {
-        abstract-target.__init__ $(file) : $(project) ;
-    }
-
-    rule generate ( properties )
-    {
-        return [ property-set.empty ] [ virtual-target.from-file $(self.name) :
-            [ location ] : $(self.project) ] ;
-    }
-
-    # Returns true if the referred file really exists.
-    rule exists ( )
-    {
-        location ;
-        return $(self.file-path) ;
-    }
-
-    # Returns the location of target. Needed by 'testing.jam'.
-    rule location ( )
-    {
-        if ! $(self.file-location)
-        {
-            local source-location = [ $(self.project).get source-location ] ;
-            for local src-dir in $(source-location)
-            {
-                if ! $(self.file-location)
-                {
-                    local location = [ path.root $(self.name) $(src-dir) ] ;
-                    if [ CHECK_IF_FILE [ path.native $(location) ] ]
-                    {
-                         self.file-location = $(src-dir) ;
-                         self.file-path = $(location) ;
-                    }
-                }
-            }
-        }
-        return $(self.file-location) ;
-    }
-}
-
-
-# Given a target-reference, made in context of 'project', returns the
-# abstract-target instance that is referred to, as well as properties explicitly
-# specified for this reference.
-#
-rule resolve-reference ( target-reference : project )
-{
-    # Separate target name from properties override.
-    local split = [ MATCH "^([^<]*)(/(<.*))?$" : $(target-reference) ] ;
-    local id = $(split[1]) ;
-    local sproperties = ;
-    if $(split[3])
-    {
-        sproperties = [ property.make [ feature.split $(split[3]) ] ] ;
-        sproperties = [ feature.expand-composites $(sproperties) ] ;
-    }
-
-    # Find the target.
-    local target = [ $(project).find $(id) ] ;
-
-    return $(target) [ property-set.create $(sproperties) ] ;
-}
-
-
-# Attempts to generate the target given by target reference, which can refer
-# both to a main target or to a file. Returns a list consisting of
-# - usage requirements
-# - generated virtual targets, if any
-#
-rule generate-from-reference (
-    target-reference  # Target reference.
-    : project         # Project where the reference is made.
-    : property-set    # Properties of the main target that makes the reference.
-)
-{
-    local r = [ resolve-reference $(target-reference) : $(project) ] ;
-    local target = $(r[1]) ;
-    local sproperties = $(r[2]) ;
-
-    # Take properties which should be propagated and refine them with
-    # source-specific requirements.
-    local propagated = [ $(property-set).propagated ] ;
-    local rproperties = [ $(propagated).refine $(sproperties) ] ;
-    if $(rproperties[1]) = "@error"
-    {
-        errors.error
-            "When building" [ full-name ] " with properties " $(properties) :
-            "Invalid properties specified for " $(source) ":"
-            $(rproperties[2-]) ;
-    }
-    return [ $(target).generate $(rproperties) ] ;
-}
-
-rule apply-default-build ( property-set : default-build )
-{
-    # 1. First, see what properties from default-build are already present
-    # in property-set.
-
-    local raw = [ $(property-set).raw ] ;
-    local specified-features = $(raw:G) ;
-
-    local defaults-to-apply ;
-    for local d in [ $(default-build).raw ]
-    {
-        if ! $(d:G) in $(specified-features)
-        {
-            defaults-to-apply += $(d) ;
-        }
-    }
-
-    # 2. If there are any defaults to be applied, form a new build request.
-    # Pass it through to 'expand-no-defaults' since default-build might
-    # contain "release debug" resulting in two property-sets.
-    local result ;
-    if $(defaults-to-apply)
-    {
-        properties = [
-          build-request.expand-no-defaults
-
-            # We have to compress subproperties here to prevent property
-            # lists like:
-            #
-            #    <toolset>msvc <toolset-msvc:version>7.1 <threading>multi
-            #
-            # from being expanded into:
-            #
-            #    <toolset-msvc:version>7.1/<threading>multi
-            #    <toolset>msvc/<toolset-msvc:version>7.1/<threading>multi
-            #
-            # due to a cross-product property combination. That may be an
-            # indication that build-request.expand-no-defaults is the wrong
-            # rule to use here.
-            [ feature.compress-subproperties $(raw) ]
-              $(defaults-to-apply)
-        ] ;
-
-        if $(properties)
-        {
-            for local p in $(properties)
-            {
-                result += [ property-set.create
-                    [ feature.expand [ feature.split $(p) ] ] ] ;
-            }
-        }
-        else
-        {
-            result = [ property-set.empty ] ;
-        }
-    }
-    else
-    {
-        result = $(property-set) ;
-    }
-    return $(result) ;
-}
-
-
-# Given a build request and requirements, return properties common to dependency
-# build request and target requirements.
-#
-# TODO: Document exactly what 'common properties' are, whether they should
-# include default property values, whether they should contain any conditional
-# properties or should those be already processed, etc. See whether there are
-# any differences between use cases with empty and non-empty build-request as
-# well as with requirements containing and those not containing any non-free
-# features.
-#
-rule common-properties ( build-request requirements )
-{
-    # For optimization, we add free requirements directly, without using a
-    # complex algorithm. This gives the complex algorithm a better chance of
-    # caching results.
-    local free = [ $(requirements).free ] ;
-    local non-free = [ property-set.create [ $(requirements).base ]
-        [ $(requirements).incidental ] ] ;
-
-    local key = .rp.$(build-request)-$(non-free) ;
-    if ! $($(key))
-    {
-        $(key) = [ common-properties2 $(build-request) $(non-free) ] ;
-    }
-    result = [ $($(key)).add-raw $(free) ] ;
-}
-
-
-# Given a 'context' -- a set of already present properties, and 'requirements',
-# decide which extra properties should be applied to 'context'. For conditional
-# requirements, this means evaluating the condition. For indirect conditional
-# requirements, this means calling a rule. Ordinary requirements are always
-# applied.
-#
-# Handles the situation where evaluating one conditional requirement affects
-# conditions of another conditional requirements, such as:
-#     <toolset>gcc:<variant>release <variant>release:<define>RELEASE
-#
-# If 'what' is 'refined' returns context refined with new requirements. If
-# 'what' is 'added' returns just the requirements to be applied.
-#
-rule evaluate-requirements ( requirements : context : what )
-{
-    # Apply non-conditional requirements. It is possible that further
-    # conditional requirement change a value set by non-conditional
-    # requirements. For example:
-    #
-    #    exe a : a.cpp : <threading>single <toolset>foo:<threading>multi ;
-    #
-    # I am not sure if this should be an error, or not, especially given that
-    #
-    #    <threading>single
-    #
-    # might come from project's requirements.
-
-    local unconditional = [ feature.expand [ $(requirements).non-conditional ] ] ;
- 
-    local raw = [ $(context).raw ] ;
-    raw = [ property.refine $(raw) : $(unconditional) ] ;
-
-    # We have collected properties that surely must be present in common
-    # properties. We now try to figure out what other properties should be added
-    # in order to satisfy rules (4)-(6) from the docs.
-
-    local conditionals = [ $(requirements).conditional ] ;
-    # The 'count' variable has one element for each conditional feature and for
-    # each occurrence of '<indirect-conditional>' feature. It is used as a loop
-    # counter: for each iteration of the loop before we remove one element and
-    # the property set should stabilize before we are done. It is assumed that
-    # #conditionals iterations should be enough for properties to propagate
-    # along conditions in any direction.
-    local count = $(conditionals)
-                  [ $(requirements).get <conditional> ]
-                  and-once-more ;
-
-    local added-requirements ;
-
-    local current = $(raw) ;
-
-    # It is assumed that ordinary conditional requirements can not add
-    # <conditional> properties (a.k.a. indirect conditional properties), and
-    # that rules referred to by <conditional> properties can not add new
-    # <conditional> properties. So the list of indirect conditionals does not
-    # change.
-    local indirect = [ $(requirements).get <conditional> ] ;
-    indirect = [ MATCH ^@(.*) : $(indirect) ] ;
-
-    local ok ;
-    while $(count)
-    {
-        # Evaluate conditionals in context of current properties.
-        local e = [ property.evaluate-conditionals-in-context $(conditionals)
-            : $(current) ] ;
-
-        # Evaluate indirect conditionals.
-        for local i in $(indirect)
-        {
-            e += [ indirect.call $(i) $(current) ] ;
-        }
-
-        if $(e) = $(added-requirements)
-        {
-            # If we got the same result, we have found the final properties.
-            count = ;
-            ok = true ;
-        }
-        else
-        {
-            # Oops, conditional evaluation results have changed. Also 'current'
-            # contains leftovers from a previous evaluation. Recompute 'current'
-            # using initial properties and conditional requirements.
-            added-requirements = $(e) ;
-            current = [ property.refine $(raw) : [ feature.expand $(e) ] ] ;
-        }
-        count = $(count[2-]) ;
-    }
-    if ! $(ok)
-    {
-        errors.error "Can not evaluate conditional properties " $(conditionals) ;
-    }
-
-    if $(what) = added
-    {
-        return [ property-set.create $(unconditional) $(added-requirements) ] ;
-    }
-    else if $(what) = refined
-    {
-        return [ property-set.create $(current) ] ;
-    }
-    else
-    {
-        errors.error "Invalid value of the 'what' parameter." ;
-    }
-}
-
-
-rule common-properties2 ( build-request requirements )
-{
-    # This guarantees that default properties are present in the result, unless
-    # they are overriden by some requirement. FIXME: There is possibility that
-    # we have added <foo>bar, which is composite and expands to <foo2>bar2, but
-    # default value of <foo2> is not bar2, in which case it is not clear what to
-    # do.
-    #
-    build-request = [ $(build-request).add-defaults ] ;
-    # Features added by 'add-default' can be composite and expand to features
-    # without default values -- so they are not added yet. It could be clearer/
-    # /faster to expand only newly added properties but that is not critical.
-    build-request = [ $(build-request).expand ] ;
-
-    return [ evaluate-requirements $(requirements) : $(build-request) :
-        refined ] ;
-}
-
-rule push-target ( target )
-{
-    .targets = $(target) $(.targets) ;
-}
-
-rule pop-target ( )
-{
-    .targets = $(.targets[2-]) ;
-}
-
-# Return the metatarget that is currently being generated.
-rule current ( )
-{
-    return $(.targets[1]) ;
-}
-
-
-# Implements the most standard way of constructing main target alternative from
-# sources. Allows sources to be either file or other main target and handles
-# generation of those dependency targets.
-#
-class basic-target : abstract-target
-{
-    import build-request ;
-    import build-system ;
-    import "class" : new ;
-    import errors ;
-    import feature ;
-    import property ;
-    import property-set ;
-    import sequence ;
-    import set ;
-    import targets ;
-    import virtual-target ;
-
-    rule __init__ ( name : project : sources * : requirements *
-        : default-build * : usage-requirements * )
-    {
-        abstract-target.__init__ $(name) : $(project) ;
-
-        self.sources = $(sources) ;
-        if ! $(requirements) {
-            requirements = [ property-set.empty ] ;
-        }
-        self.requirements = $(requirements) ;
-        if ! $(default-build)
-        {
-            default-build = [ property-set.empty ] ;
-        }
-        self.default-build = $(default-build) ;
-        if ! $(usage-requirements)
-        {
-            usage-requirements = [ property-set.empty ] ;
-        }
-        self.usage-requirements = $(usage-requirements) ;
-
-        if $(sources:G)
-        {
-            errors.user-error properties found in the 'sources' parameter for
-                [ full-name ] ;
-        }
-    }
-    
-    rule always ( )
-    {
-        self.always = 1 ;
-    }
-    
-    # Returns the list of abstract-targets which are used as sources. The extra
-    # properties specified for sources are not represented. The only user for
-    # this rule at the moment is the "--dump-tests" feature of the test system.
-    #
-    rule sources ( )
-    {
-        if ! $(self.source-targets)
-        {
-            for local s in $(self.sources)
-            {
-                self.source-targets +=
-                  [ targets.resolve-reference $(s) : $(self.project) ] ;
-            }
-        }
-        return $(self.source-targets) ;
-    }
-
-    rule requirements ( )
-    {
-        return $(self.requirements) ;
-    }
-
-    rule default-build ( )
-    {
-        return $(self.default-build) ;
-    }
-
-    # Returns the alternative condition for this alternative, if the condition
-    # is satisfied by 'property-set'.
-    #
-    rule match ( property-set debug ? )
-    {
-        # The condition is composed of all base non-conditional properties. It
-        # is not clear if we should expand 'self.requirements' or not. For one
-        # thing, it would be nice to be able to put
-        #    <toolset>msvc-6.0
-        # in requirements. On the other hand, if we have <variant>release as a
-        # condition it does not make sense to require <optimization>full to be
-        # in the build request just to select this variant.
-        local bcondition = [ $(self.requirements).base ] ;
-        local ccondition = [ $(self.requirements).conditional ] ;
-        local condition = [ set.difference $(bcondition) : $(ccondition) ] ;
-        if $(debug)
-        {
-            ECHO "    next alternative: required properties:" $(condition:E=(empty)) ;
-        }
-
-        if $(condition) in [ $(property-set).raw ]
-        {
-            if $(debug)
-            {
-                ECHO "        matched" ;
-            }
-            return $(condition) ;
-        }
-        else
-        {
-            if $(debug)
-            {
-                ECHO "        not matched" ;
-            }
-            return no-match ;
-        }
-    }
-
-    # Takes a target reference, which might be either target id or a dependency
-    # property, and generates that target using 'property-set' as build request.
-    #
-    # The results are added to the variable called 'result-var'. Usage
-    # requirements are added to the variable called 'usage-requirements-var'.
-    #
-    rule generate-dependencies ( dependencies * : property-set
-        : result-var usage-requirements-var )
-    {
-        for local dependency in $(dependencies)
-        {
-            local grist = $(dependency:G) ;
-            local id = $(dependency:G=) ;
-
-            local result = [ targets.generate-from-reference $(id) :
-                $(self.project) : $(property-set) ] ;
-
-            $(result-var) += $(result[2-]:G=$(grist)) ;
-            $(usage-requirements-var) += [ $(result[1]).raw ] ;
-        }
-    }
-
-    # Determines final build properties, generates sources, and calls
-    # 'construct'. This method should not be overridden.
-    #
-    rule generate ( property-set )
-    {
-        if [ modules.peek : .debug-building ]
-        {
-            ECHO ;
-            local fn = [ full-name ] ;
-            ECHO [ targets.indent ] "Building target '$(fn)'" ;
-            targets.increase-indent ;
-            ECHO [ targets.indent ] "Build request: " $(property-set) [ $(property-set).raw ] ;
-            local cf = [ build-system.command-line-free-features ] ;
-            ECHO [ targets.indent ] "Command line free features: " [ $(cf).raw ] ;
-            ECHO [ targets.indent ] "Target requirements: " [ $(self.requirements).raw ] ;
-        }
-        targets.push-target $(__name__) ;
-
-        if ! $(self.generated.$(property-set))
-        {
-            # Apply free features from the command line. If user said
-            #   define=FOO
-            # he most likely wants this define to be set for all compiles.
-            property-set = [ $(property-set).refine
-                [ build-system.command-line-free-features ] ] ;
-            local rproperties = [ targets.common-properties $(property-set)
-                $(self.requirements) ] ;
-
-            if [ modules.peek : .debug-building ]
-            {
-                ECHO ;
-                ECHO [ targets.indent ] "Common properties: " [ $(rproperties).raw ] ;
-            }
-
-            if ( $(rproperties[1]) != "@error" ) && ( [ $(rproperties).get
-                <build> ] != no )
-            {
-                local source-targets ;
-                local properties = [ $(rproperties).non-dependency ] ;
-                local usage-requirements ;
-
-                generate-dependencies [ $(rproperties).dependency ] :
-                    $(rproperties) : properties usage-requirements ;
-
-                generate-dependencies $(self.sources) : $(rproperties) :
-                    source-targets usage-requirements ;
-
-                if [ modules.peek : .debug-building ]
-                {
-                    ECHO ;
-                    ECHO [ targets.indent ] "Usage requirements for"
-                        $(self.name)": " $(usage-requirements) ;
-                }
-
-                rproperties = [ property-set.create $(properties)
-                    $(usage-requirements) ] ;
-                usage-requirements = [ property-set.create $(usage-requirements) ] ;
-
-                if [ modules.peek : .debug-building ]
-                {
-                    ECHO [ targets.indent ] "Build properties: "
-                        [ $(rproperties).raw ] ;
-                }
-
-                local extra = [ $(rproperties).get <source> ] ;
-                source-targets += $(extra:G=) ;
-                # We might get duplicate sources, for example if we link to two
-                # libraries having the same <library> usage requirement.
-                # Use stable sort, since for some targets the order is
-                # important. E.g. RUN_PY target need python source to come
-                # first.
-                source-targets = [ sequence.unique $(source-targets) : stable ] ;
-
-                local result = [ construct $(self.name) : $(source-targets) :
-                    $(rproperties) ] ;
-
-                if $(result)
-                {
-                    local gur = $(result[1]) ;
-                    result = $(result[2-]) ;
-                    
-                    if $(self.always)
-                    {
-                        for local t in $(result)
-                        {
-                            $(t).always ;
-                        }                        
-                    }
-                    
-                    local s = [ create-subvariant $(result)
-                        : [ virtual-target.recent-targets ]
-                        : $(property-set) : $(source-targets)
-                        : $(rproperties) : $(usage-requirements) ] ;
-                    virtual-target.clear-recent-targets ;
-
-                    local ur = [ compute-usage-requirements $(s) ] ;
-                    ur = [ $(ur).add $(gur) ] ;
-                    $(s).set-usage-requirements $(ur) ;
-                    if [ modules.peek : .debug-building ]
-                    {
-                        ECHO [ targets.indent ] "Usage requirements from"
-                            $(self.name)": " [ $(ur).raw ] ;
-                    }
-
-                    self.generated.$(property-set) = $(ur) $(result) ;
-                }
-            }
-            else
-            {
-                if $(rproperties[1]) = "@error"
-                {
-                    ECHO [ targets.indent ] "Skipping build of:" [ full-name ]
-                        "cannot compute common properties" ;
-                }
-                else if [ $(rproperties).get <build> ] = no
-                {
-                    # If we just see <build>no, we cannot produce any reasonable
-                    # diagnostics. The code that adds this property is expected
-                    # to explain why a target is not built, for example using
-                    # the configure.log-component-configuration function.
-                }
-                else
-                {
-                    ECHO [ targets.indent ] "Skipping build of: " [ full-name ]
-                        " unknown reason" ;
-                }
-
-                # We are here either because there has been an error computing
-                # properties or there is <build>no in properties. In the latter
-                # case we do not want any diagnostic. In the former case, we
-                # need diagnostics. FIXME
-
-                # If this target fails to build, add <build>no to properties to
-                # cause any parent target to fail to build. Except that it
-                # - does not work now, since we check for <build>no only in
-                #   common properties, but not in properties that came from
-                #   dependencies
-                # - it is not clear if that is a good idea anyway. The alias
-                #   target, for example, should not fail to build if a
-                #   dependency fails.
-                self.generated.$(property-set) = [ property-set.create <build>no ] ;
-            }
-        }
-        else
-        {
-            if [ modules.peek : .debug-building ]
-            {
-                ECHO [ targets.indent ] "Already built" ;
-                local ur = $(self.generated.$(property-set)) ;
-                ur = $(ur[0]) ;
-                targets.increase-indent ;
-                ECHO [ targets.indent ] "Usage requirements from"
-                    $(self.name)": " [ $(ur).raw ] ;
-                targets.decrease-indent ;
-            }
-        }
-
-        targets.pop-target ;
-        targets.decrease-indent ;
-        return $(self.generated.$(property-set)) ;
-    }
-
-    # Given the set of generated targets, and refined build properties,
-    # determines and sets appropriate usage requirements on those targets.
-    #
-    rule compute-usage-requirements ( subvariant )
-    {
-        local rproperties = [ $(subvariant).build-properties ] ;
-        xusage-requirements = [ targets.evaluate-requirements
-            $(self.usage-requirements) : $(rproperties) : added ] ;
-
-        # We generate all dependency properties and add them, as well as their
-        # usage requirements, to the result.
-        local extra ;
-        generate-dependencies [ $(xusage-requirements).dependency ] :
-            $(rproperties) : extra extra ;
-
-        local result = [ property-set.create
-            [ $(xusage-requirements).non-dependency ] $(extra) ] ;
-
-        # Propagate usage requirements we got from sources, except for the
-        # <pch-header> and <pch-file> features.
-        #
-        # That feature specifies which pch file to use, and should apply only to
-        # direct dependents. Consider:
-        #
-        #   pch pch1 : ...
-        #   lib lib1 : ..... pch1 ;
-        #   pch pch2 :
-        #   lib lib2 : pch2 lib1 ;
-        #
-        # Here, lib2 should not get <pch-header> property from pch1.
-        #
-        # Essentially, when those two features are in usage requirements, they
-        # are propagated only to direct dependents. We might need a more general
-        # mechanism, but for now, only those two features are special.
-        #
-        # TODO - Actually there are more possible candidates like for instance
-        # when listing static library X as a source for another static library.
-        # Then static library X will be added as a <source> property to the
-        # second library's usage requirements but those requirements should last
-        # only up to the first executable or shared library that actually links
-        # to it.
-        local raw = [ $(subvariant).sources-usage-requirements ] ;
-        raw = [ $(raw).raw ] ;
-        raw = [ property.change $(raw) : <pch-header> ] ;
-        raw = [ property.change $(raw) : <pch-file> ] ;
-        return [ $(result).add [ property-set.create $(raw) ] ] ;
-    }
-
-    # Creates new subvariant instances for 'targets'.
-    # 'root-targets'  - virtual targets to be returned to dependants
-    # 'all-targets'   - virtual targets created while building this main target
-    # 'build-request' - property-set instance with requested build properties
-    #
-    local rule create-subvariant ( root-targets * : all-targets * :
-        build-request : sources * : rproperties : usage-requirements )
-    {
-        for local e in $(root-targets)
-        {
-            $(e).root true ;
-        }
-
-        # Process all virtual targets that will be created if this main target
-        # is created.
-        local s = [ new subvariant $(__name__) : $(build-request) : $(sources) :
-            $(rproperties) : $(usage-requirements) : $(all-targets) ] ;
-        for local v in $(all-targets)
-        {
-            if ! [ $(v).creating-subvariant ]
-            {
-                $(v).creating-subvariant $(s) ;
-            }
-        }
-        return $(s) ;
-    }
-
-    # Constructs virtual targets for this abstract target and the dependency
-    # graph. Returns a usage-requirements property-set and a list of virtual
-    # targets. Should be overriden in derived classes.
-    #
-    rule construct ( name : source-targets * : properties * )
-    {
-        errors.error "method should be defined in derived classes" ;
-    }
-}
-
-
-class typed-target : basic-target
-{
-    import generators ;
-
-    rule __init__ ( name : project : type : sources * : requirements * :
-         default-build * : usage-requirements * )
-    {
-        basic-target.__init__ $(name) : $(project) : $(sources) :
-            $(requirements) : $(default-build) : $(usage-requirements) ;
-
-        self.type = $(type) ;
-    }
-
-    rule type ( )
-    {
-        return $(self.type) ;
-    }
-
-    rule construct ( name : source-targets * : property-set )
-    {
-        local r = [ generators.construct $(self.project) $(name:S=) : $(self.type)
-            : [ property-set.create [ $(property-set).raw ]
-                <main-target-type>$(self.type) ]
-            : $(source-targets) : true ] ;
-        if ! $(r)
-        {
-            ECHO "warn: Unable to construct" [ full-name ] ;
-
-            # Are there any top-level generators for this type/property set.
-            if ! [ generators.find-viable-generators $(self.type)
-                : $(property-set) ]
-            {
-                ECHO "error: no generators were found for type '$(self.type)'" ;
-                ECHO "error: and the requested properties" ;
-                ECHO "error: make sure you've configured the needed tools" ;
-                ECHO "See http://boost.org/boost-build2/doc/html/bbv2/advanced/configuration.html" ;
-                ECHO "To debug this problem, try the --debug-generators option." ;
-                EXIT ;
-            }
-        }
-        return $(r) ;
-    }
-}
-
-
-# Return the list of sources to use, if main target rule is invoked with
-# 'sources'. If there are any objects in 'sources', they are treated as main
-# target instances, and the name of such targets are adjusted to be
-# '<name_of_this_target>__<name_of_source_target>'. Such renaming is disabled if
-# a non-empty value is passed as the 'no-renaming' parameter.
-#
-rule main-target-sources ( sources * : main-target-name : no-renaming ? )
-{
-    local result ;
-    for local t in $(sources)
-    {
-        if [ class.is-instance $(t) ]
-        {
-            local name = [ $(t).name ] ;
-            if ! $(no-renaming)
-            {
-                name = $(main-target-name)__$(name) ;
-                $(t).rename $(name) ;
-            }
-            # Inline targets are not built by default.
-            local p = [ $(t).project ] ;
-            $(p).mark-target-as-explicit $(name) ;
-            result += $(name) ;
-        }
-        else
-        {
-            result += $(t) ;
-        }
-    }
-    return $(result) ;
-}
-
-
-# Returns the requirements to use when declaring a main target, obtained by
-# translating all specified property paths and refining project requirements
-# with the ones specified for the target.
-#
-rule main-target-requirements (
-    specification *  # Properties explicitly specified for the main target.
-    : project        # Project where the main target is to be declared.
-)
-{
-    specification += [ toolset.requirements ] ;
-
-    local requirements = [ property-set.refine-from-user-input
-        [ $(project).get requirements ] : $(specification) :
-        [ $(project).project-module ] : [ $(project).get location ] ] ;
-    if $(requirements[1]) = "@error"
-    {
-        errors.error "Conflicting requirements for target:" $(requirements) ;
-    }
-    return $(requirements) ;
-}
-
-
-# Returns the usage requirements to use when declaring a main target, which are
-# obtained by translating all specified property paths and adding project's
-# usage requirements.
-#
-rule main-target-usage-requirements (
-    specification *  # Use-properties explicitly specified for a main target.
-    : project        # Project where the main target is to be declared.
-)
-{
-    local project-usage-requirements = [ $(project).get usage-requirements ] ;
-
-    # We do not use 'refine-from-user-input' because:
-    # - I am not sure if removing parent's usage requirements makes sense
-    # - refining usage requirements is not needed, since usage requirements are
-    #   always free.
-    local usage-requirements = [ property-set.create-from-user-input
-        $(specification)
-        : [ $(project).project-module ] [ $(project).get location ] ] ;
-
-    return [ $(project-usage-requirements).add $(usage-requirements) ] ;
-}
-
-
-# Return the default build value to use when declaring a main target, which is
-# obtained by using the specified value if not empty and parent's default build
-# attribute otherwise.
-#
-rule main-target-default-build (
-    specification *  # Default build explicitly specified for a main target.
-    : project        # Project where the main target is to be declared.
-)
-{
-    local result ;
-    if $(specification)
-    {
-        result = $(specification) ;
-    }
-    else
-    {
-        result = [ $(project).get default-build ] ;
-    }
-    return [ property-set.create-with-validation $(result) ] ;
-}
-
-
-# Registers the specified target as a main target alternative and returns it.
-#
-rule main-target-alternative ( target )
-{
-    local ptarget = [ $(target).project ] ;
-    $(ptarget).add-alternative $(target) ;
-    return $(target) ;
-}
-
-# Creates a new metargets with the specified properties, using 'klass' as
-# the class. The 'name', 'sources',
-# 'requirements', 'default-build' and 'usage-requirements' are assumed to be in
-# the form specified by the user in Jamfile corresponding to 'project'.
-#
-rule create-metatarget ( klass : project : name : sources * : requirements * :
-    default-build * : usage-requirements * )
-{
-    return [
-        targets.main-target-alternative
-        [ new $(klass) $(name) : $(project)
-            : [ targets.main-target-sources $(sources) : $(name) ]
-            : [ targets.main-target-requirements $(requirements) : $(project) ]
-            : [ targets.main-target-default-build $(default-build) : $(project) ]
-            : [ targets.main-target-usage-requirements $(usage-requirements) : $(project) ]
-        ] ] ;
-}
-
-# Creates a typed-target with the specified properties. The 'name', 'sources',
-# 'requirements', 'default-build' and 'usage-requirements' are assumed to be in
-# the form specified by the user in Jamfile corresponding to 'project'.
-#
-rule create-typed-target ( type : project : name : sources * : requirements * :
-    default-build * : usage-requirements * )
-{
-    return [
-        targets.main-target-alternative
-        [ new typed-target $(name) : $(project) : $(type)
-            : [ targets.main-target-sources $(sources) : $(name) ]
-            : [ targets.main-target-requirements $(requirements) : $(project) ]
-            : [ targets.main-target-default-build $(default-build) : $(project) ]
-            : [ targets.main-target-usage-requirements $(usage-requirements) : $(project) ]
-        ] ] ;
-}
diff --git a/jam-files/boost-build/build/targets.py b/jam-files/boost-build/build/targets.py
deleted file mode 100644
index a35612ce..00000000
--- a/jam-files/boost-build/build/targets.py
+++ /dev/null
@@ -1,1401 +0,0 @@
-# Status: ported.
-# Base revision: 64488
-
-# Copyright Vladimir Prus 2002-2007.
-# Copyright Rene Rivera 2006.
-#
-# Distributed under the Boost Software License, Version 1.0.
-#    (See accompanying file LICENSE_1_0.txt or copy at
-#          http://www.boost.org/LICENSE_1_0.txt)
-
-#   Supports 'abstract' targets, which are targets explicitly defined in Jamfile.
-#
-#   Abstract targets are represented by classes derived from 'AbstractTarget' class. 
-#   The first abstract target is 'project_target', which is created for each
-#   Jamfile, and can be obtained by the 'target' rule in the Jamfile's module.
-#   (see project.jam). 
-#
-#   Project targets keep a list of 'MainTarget' instances.
-#   A main target is what the user explicitly defines in a Jamfile. It is
-#   possible to have several definitions for a main target, for example to have
-#   different lists of sources for different platforms. So, main targets
-#   keep a list of alternatives.
-#
-#   Each alternative is an instance of 'AbstractTarget'. When a main target
-#   subvariant is defined by some rule, that rule will decide what class to
-#   use, create an instance of that class and add it to the list of alternatives
-#   for the main target.
-#
-#   Rules supplied by the build system will use only targets derived
-#   from 'BasicTarget' class, which will provide some default behaviour.
-#   There will be two classes derived from it, 'make-target', created by the
-#   'make' rule, and 'TypedTarget', created by rules such as 'exe' and 'dll'.
-
-#
-#                         +------------------------+
-#                         |AbstractTarget          |
-#                         +========================+
-#                         |name                    |
-#                         |project                 |                                   
-#                         |                        |                                   
-#                         |generate(properties) = 0|                                   
-#                         +-----------+------------+                                   
-#                                     |                                                
-#                                     ^                                                
-#                                    / \                                               
-#                                   +-+-+                                              
-#                                     |                                                
-#                                     |                                                
-#            +------------------------+------+------------------------------+          
-#            |                               |                              |          
-#            |                               |                              |          
-# +----------+-----------+            +------+------+                +------+-------+  
-# | project_target       |            | MainTarget  |                | BasicTarget  |  
-# +======================+ 1        * +=============+  alternatives  +==============+  
-# | generate(properties) |o-----------+ generate    |<>------------->| generate     |  
-# | main-target          |            +-------------+                | construct = 0|
-# +----------------------+                                           +--------------+  
-#                                                                           |          
-#                                                                           ^          
-#                                                                          / \         
-#                                                                         +-+-+        
-#                                                                           |          
-#                                                                           |          
-#                 ...--+----------------+------------------+----------------+---+      
-#                      |                |                  |                    |      
-#                      |                |                  |                    |      
-#               ... ---+-----+   +------+-------+   +------+------+    +--------+-----+
-#                            |   | TypedTarget  |   | make-target |    | stage-target |
-#                            .   +==============+   +=============+    +==============+
-#                            .   | construct    |   | construct   |    | construct    |
-#                                +--------------+   +-------------+    +--------------+
-
-import re
-import os.path
-import sys
-
-from b2.manager import get_manager
-
-from b2.util.utility import *
-import property, project, virtual_target, property_set, feature, generators, toolset
-from virtual_target import Subvariant
-from b2.exceptions import *
-from b2.util.sequence import unique
-from b2.util import path, bjam_signature
-from b2.build.errors import user_error_checkpoint
-
-import b2.build.build_request as build_request
-
-import b2.util.set
-_re_separate_target_from_properties = re.compile (r'^([^<]*)(/(<.*))?$')
-
-class TargetRegistry:
-    
-    def __init__ (self):
-        # All targets that are currently being built.
-        # Only the key is id (target), the value is the actual object.
-        self.targets_being_built_ = {}
-
-        # Current indent for debugging messages
-        self.indent_ = ""
-
-        self.debug_building_ = "--debug-building" in bjam.variable("ARGV")
-
-        self.targets_ = []
-
-    def main_target_alternative (self, target):
-        """ Registers the specified target as a main target alternatives.
-            Returns 'target'.
-        """
-        target.project ().add_alternative (target)
-        return target
-
-    def main_target_sources (self, sources, main_target_name, no_renaming=0):
-        """Return the list of sources to use, if main target rule is invoked
-        with 'sources'. If there are any objects in 'sources', they are treated
-        as main target instances, and the name of such targets are adjusted to
-        be '<name_of_this_target>__<name_of_source_target>'. Such renaming
-        is disabled is non-empty value is passed for 'no-renaming' parameter."""
-        result = []
-
-        for t in sources:
-
-            t = b2.util.jam_to_value_maybe(t)
-            
-            if isinstance (t, AbstractTarget):
-                name = t.name ()
-
-                if not no_renaming:
-                    name = main_target_name + '__' + name
-                    t.rename (name)
-
-                # Inline targets are not built by default.
-                p = t.project()
-                p.mark_targets_as_explicit([name])                    
-                result.append(name)
-
-            else:
-                result.append (t)
-
-        return result
-
-
-    def main_target_requirements(self, specification, project):
-        """Returns the requirement to use when declaring a main target,
-         which are obtained by
-         - translating all specified property paths, and
-         - refining project requirements with the one specified for the target
-        
-         'specification' are the properties xplicitly specified for a
-          main target
-         'project' is the project where the main taret is to be declared."""
-
-        specification.extend(toolset.requirements())
-
-        requirements = property_set.refine_from_user_input(
-            project.get("requirements"), specification,
-            project.project_module(), project.get("location"))
-
-        return requirements
-
-    def main_target_usage_requirements (self, specification, project):
-        """ Returns the use requirement to use when declaraing a main target,
-            which are obtained by
-            - translating all specified property paths, and
-            - adding project's usage requirements
-            specification:  Use-properties explicitly specified for a main target
-            project:        Project where the main target is to be declared
-        """
-        project_usage_requirements = project.get ('usage-requirements')
-
-        # We don't use 'refine-from-user-input' because I'm not sure if:
-        # - removing of parent's usage requirements makes sense
-        # - refining of usage requirements is not needed, since usage requirements
-        #   are always free.
-        usage_requirements = property_set.create_from_user_input(
-            specification, project.project_module(), project.get("location"))
-        
-        return project_usage_requirements.add (usage_requirements)
-
-    def main_target_default_build (self, specification, project):
-        """ Return the default build value to use when declaring a main target,
-            which is obtained by using specified value if not empty and parent's
-            default build attribute otherwise.
-            specification:  Default build explicitly specified for a main target
-            project:        Project where the main target is to be declared
-        """
-        if specification:
-            return property_set.create_with_validation(specification)
-        else:
-            return project.get ('default-build')
-
-    def start_building (self, main_target_instance):
-        """ Helper rules to detect cycles in main target references.
-        """
-        if self.targets_being_built_.has_key(id(main_target_instance)):
-            names = []
-            for t in self.targets_being_built_.values() + [main_target_instance]:
-                names.append (t.full_name())
-            
-            get_manager().errors()("Recursion in main target references\n")
-        
-        self.targets_being_built_[id(main_target_instance)] = main_target_instance
-
-    def end_building (self, main_target_instance):
-        assert (self.targets_being_built_.has_key (id (main_target_instance)))
-        del self.targets_being_built_ [id (main_target_instance)]
-
-    def create_typed_target (self, type, project, name, sources, requirements, default_build, usage_requirements):
-        """ Creates a TypedTarget with the specified properties.
-            The 'name', 'sources', 'requirements', 'default_build' and
-            'usage_requirements' are assumed to be in the form specified
-            by the user in Jamfile corresponding to 'project'.
-        """
-        return self.main_target_alternative (TypedTarget (name, project, type,
-            self.main_target_sources (sources, name),
-            self.main_target_requirements (requirements, project),
-            self.main_target_default_build (default_build, project),
-            self.main_target_usage_requirements (usage_requirements, project)))
-
-    def increase_indent(self):
-        self.indent_ += "    "
-
-    def decrease_indent(self):
-        self.indent_ = self.indent_[0:-4]
-
-    def logging(self):
-        return self.debug_building_
-
-    def log(self, message):
-        if self.debug_building_:
-            print self.indent_ + message
-
-    def push_target(self, target):
-        self.targets_.append(target)
-
-    def pop_target(self):
-        self.targets_ = self.targets_[:-1]
-
-    def current(self):
-        return self.targets_[0]
-
-
-class GenerateResult:
-    
-    def __init__ (self, ur=None, targets=None):
-        if not targets:
-            targets = []
-        
-        self.__usage_requirements = ur
-        self.__targets = targets
-        assert all(isinstance(t, virtual_target.VirtualTarget) for t in targets)
-
-        if not self.__usage_requirements:
-            self.__usage_requirements = property_set.empty ()
-
-    def usage_requirements (self):
-        return self.__usage_requirements
-
-    def targets (self):
-        return self.__targets
-    
-    def extend (self, other):
-        assert (isinstance (other, GenerateResult))
-        
-        self.__usage_requirements = self.__usage_requirements.add (other.usage_requirements ())
-        self.__targets.extend (other.targets ())
-
-class AbstractTarget:
-    """ Base class for all abstract targets.
-    """
-    def __init__ (self, name, project, manager = None):
-        """ manager:     the Manager object
-            name:        name of the target
-            project:     the project target to which this one belongs
-            manager:the manager object. If none, uses project.manager ()
-        """
-        assert (isinstance (project, ProjectTarget))
-        # Note: it might seem that we don't need either name or project at all.
-        # However, there are places where we really need it. One example is error
-        # messages which should name problematic targets. Another is setting correct
-        # paths for sources and generated files.
-        
-        # Why allow manager to be specified? Because otherwise project target could not derive
-        # from this class.
-        if manager:
-            self.manager_ = manager
-        else:
-            self.manager_ = project.manager ()
-
-        self.name_ = name
-        self.project_ = project        
-    
-    def manager (self):
-        return self.manager_
-    
-    def name (self):
-        """ Returns the name of this target.
-        """
-        return self.name_
-    
-    def project (self):
-        """ Returns the project for this target.
-        """
-        return self.project_
-    
-    def location (self):
-        """ Return the location where the target was declared.
-        """
-        return self.location_
-            
-    def full_name (self):
-        """ Returns a user-readable name for this target.
-        """
-        location = self.project ().get ('location')
-        return location + '/' + self.name_
-        
-    def generate (self, property_set):
-        """ Takes a property set.  Generates virtual targets for this abstract
-            target, using the specified properties, unless a different value of some
-            feature is required by the target. 
-            On success, returns a GenerateResult instance with:
-                - a property_set with the usage requirements to be
-                  applied to dependents 
-                - a list of produced virtual targets, which may be
-                   empty.  
-            If 'property_set' is empty, performs default build of this
-            target, in a way specific to derived class.
-        """
-        raise BaseException ("method should be defined in derived classes")
-    
-    def rename (self, new_name):
-        self.name_ = new_name
-
-class ProjectTarget (AbstractTarget):
-    """ Project target class (derived from 'AbstractTarget')
-
-        This class these responsibilities:
-        - maintaining a list of main target in this project and
-          building it
-
-        Main targets are constructed in two stages:
-        - When Jamfile is read, a number of calls to 'add_alternative' is made.
-          At that time, alternatives can also be renamed to account for inline
-          targets.
-        - The first time 'main-target' or 'has-main-target' rule is called,
-          all alternatives are enumerated an main targets are created.
-    """
-    def __init__ (self, manager, name, project_module, parent_project, requirements, default_build):
-        AbstractTarget.__init__ (self, name, self, manager)
-        
-        self.project_module_ = project_module
-        self.location_ = manager.projects().attribute (project_module, 'location')
-        self.requirements_ = requirements
-        self.default_build_ = default_build
-       
-        self.build_dir_ = None
-        
-        # A cache of IDs
-        self.ids_cache_ = {}
-        
-        # True is main targets have already been built.
-        self.built_main_targets_ = False
-        
-        # A list of the registered alternatives for this project.
-        self.alternatives_ = []
-
-        # A map from main target name to the target corresponding
-        # to it.
-        self.main_target_ = {}
-        
-        # Targets marked as explicit.
-        self.explicit_targets_ = set()
-
-        # Targets marked as always
-        self.always_targets_ = set()
-
-        # The constants defined for this project.
-        self.constants_ = {}
-
-        # Whether targets for all main target are already created.
-        self.built_main_targets_ = 0
-
-        if parent_project:
-            self.inherit (parent_project)
-
-
-    # TODO: This is needed only by the 'make' rule. Need to find the
-    # way to make 'make' work without this method.
-    def project_module (self):
-        return self.project_module_
-    
-    def get (self, attribute):
-        return self.manager().projects().attribute(
-            self.project_module_, attribute)
-
-    def build_dir (self):
-        if not self.build_dir_:
-            self.build_dir_ = self.get ('build-dir')
-            if not self.build_dir_:
-                self.build_dir_ = os.path.join(self.project_.get ('location'), 'bin')
-
-        return self.build_dir_
-
-    def generate (self, ps):
-        """ Generates all possible targets contained in this project.
-        """
-        self.manager_.targets().log(
-            "Building project '%s' with '%s'" % (self.name (), str(ps)))
-        self.manager_.targets().increase_indent ()
-        
-        result = GenerateResult ()
-                
-        for t in self.targets_to_build ():
-            g = t.generate (ps)
-            result.extend (g)
-            
-        self.manager_.targets().decrease_indent ()
-        return result
-
-    def targets_to_build (self):
-        """ Computes and returns a list of AbstractTarget instances which
-            must be built when this project is built.
-        """
-        result = []
-        
-        if not self.built_main_targets_:
-            self.build_main_targets ()
-        
-        # Collect all main targets here, except for "explicit" ones.
-        for n, t  in self.main_target_.iteritems ():
-            if not t.name () in self.explicit_targets_:
-                result.append (t)
-
-        # Collect all projects referenced via "projects-to-build" attribute.
-        self_location = self.get ('location')
-        for pn in self.get ('projects-to-build'):
-            result.append (self.find(pn + "/"))
-                        
-        return result
-
-    def mark_targets_as_explicit (self, target_names):
-        """Add 'target' to the list of targets in this project
-        that should be build only by explicit request."""
-        
-        # Record the name of the target, not instance, since this
-        # rule is called before main target instaces are created.
-        self.explicit_targets_.update(target_names)
-
-    def mark_targets_as_always(self, target_names):
-        self.always_targets_.update(target_names)
-    
-    def add_alternative (self, target_instance):
-        """ Add new target alternative.
-        """
-        if self.built_main_targets_:
-            raise IllegalOperation ("add-alternative called when main targets are already created for project '%s'" % self.full_name ())
-
-        self.alternatives_.append (target_instance)
-
-    def main_target (self, name):
-        if not self.built_main_targets_:
-            self.build_main_targets()
-
-        return self.main_target_[name]
-
-    def has_main_target (self, name):
-        """Tells if a main target with the specified name exists."""
-        if not self.built_main_targets_:
-            self.build_main_targets()
-
-        return self.main_target_.has_key(name)
-            
-    def create_main_target (self, name):
-        """ Returns a 'MainTarget' class instance corresponding to the 'name'.
-        """
-        if not self.built_main_targets_:
-            self.build_main_targets ()
-                        
-        return self.main_targets_.get (name, None)
-
-
-    def find_really(self, id):
-        """ Find and return the target with the specified id, treated
-            relative to self.
-        """
-        result = None        
-        current_location = self.get ('location')
-
-        __re_split_project_target = re.compile (r'(.*)//(.*)')
-        split = __re_split_project_target.match (id)
-
-        project_part = None
-        target_part = None
-
-        if split:
-            project_part = split.group (1)
-            target_part = split.group (2)
-
-        project_registry = self.project_.manager ().projects ()
-        
-        extra_error_message = ''
-        if project_part:
-            # There's explicit project part in id. Looks up the
-            # project and pass the request to it.
-            pm = project_registry.find (project_part, current_location)
-            
-            if pm:
-                project_target = project_registry.target (pm)
-                result = project_target.find (target_part, no_error=1)
-
-            else:
-                extra_error_message = "error: could not find project '$(project_part)'"
-
-        else:
-            # Interpret target-name as name of main target
-            # Need to do this before checking for file. Consider this:
-            #
-            #  exe test : test.cpp ;
-            #  install s : test : <location>. ;
-            #
-            # After first build we'll have target 'test' in Jamfile and file
-            # 'test' on the disk. We need target to override the file.
-            
-            result = None
-            if self.has_main_target(id):
-                result = self.main_target(id)
-
-            if not result:
-                result = FileReference (self.manager_, id, self.project_)
-                if not result.exists ():
-                    # File actually does not exist.
-                    # Reset 'target' so that an error is issued.
-                    result = None
-                    
-
-            if not result:
-                # Interpret id as project-id
-                project_module = project_registry.find (id, current_location)
-                if project_module:
-                    result = project_registry.target (project_module)
-                                    
-        return result
-
-    def find (self, id, no_error = False):
-        v = self.ids_cache_.get (id, None)
-        
-        if not v:
-            v = self.find_really (id)
-            self.ids_cache_ [id] = v
-
-        if v or no_error:
-            return v
-
-        raise BaseException ("Unable to find file or target named '%s'\nreferred from project at '%s'" % (id, self.get ('location')))
-
-    
-    def build_main_targets (self):
-        self.built_main_targets_ = True
-        
-        for a in self.alternatives_:
-            name = a.name ()
-            if not self.main_target_.has_key (name):
-                t = MainTarget (name, self.project_)
-                self.main_target_ [name] = t
-
-            if name in self.always_targets_:
-                a.always()
-            
-            self.main_target_ [name].add_alternative (a)
-
-    def add_constant(self, name, value, path=0):
-        """Adds a new constant for this project.
-
-        The constant will be available for use in Jamfile
-        module for this project. If 'path' is true,
-        the constant will be interpreted relatively
-        to the location of project.
-        """
-
-        if path:
-            l = self.location_
-            if not l:
-                # Project corresponding to config files do not have 
-                # 'location' attribute, but do have source location.
-                # It might be more reasonable to make every project have
-                # a location and use some other approach to prevent buildable
-                # targets in config files, but that's for later.
-                l = get('source-location')
-                
-            value = os.path.join(l, value)
-            # Now make the value absolute path
-            value = os.path.join(os.getcwd(), value)
-
-        self.constants_[name] = value
-        bjam.call("set-variable", self.project_module(), name, value)
-
-    def inherit(self, parent_project):
-        for c in parent_project.constants_:
-            # No need to pass the type. Path constants were converted to
-            # absolute paths already by parent.
-            self.add_constant(c, parent_project.constants_[c])
-        
-        # Import rules from parent 
-        this_module = self.project_module()
-        parent_module = parent_project.project_module()
-
-        rules = bjam.call("RULENAMES", parent_module)
-        if not rules:
-            rules = []
-        user_rules = [x for x in rules
-                      if x not in self.manager().projects().project_rules().all_names()]
-        if user_rules:
-            bjam.call("import-rules-from-parent", parent_module, this_module, user_rules)
-        
-class MainTarget (AbstractTarget):
-    """ A named top-level target in Jamfile.
-    """
-    def __init__ (self, name, project):
-        AbstractTarget.__init__ (self, name, project)    
-        self.alternatives_ = []
-        self.default_build_ = property_set.empty ()
-        
-    def add_alternative (self, target):
-        """ Add a new alternative for this target.
-        """
-        d = target.default_build ()
-        
-        if self.alternatives_ and self.default_build_ != d:
-            get_manager().errors()("default build must be identical in all alternatives\n"
-              "main target is '%s'\n"
-              "with '%s'\n"
-              "differing from previous default build: '%s'" % (self.full_name (), d.raw (), self.default_build_.raw ()))
-
-        else:
-            self.default_build_ = d
-
-        self.alternatives_.append (target)
-
-    def __select_alternatives (self, property_set, debug):
-        """ Returns the best viable alternative for this property_set
-            See the documentation for selection rules.
-            # TODO: shouldn't this be 'alternative' (singular)?
-        """
-        # When selecting alternatives we have to consider defaults,
-        # for example:
-        #    lib l : l.cpp : <variant>debug ;
-        #    lib l : l_opt.cpp : <variant>release ;
-        # won't work unless we add default value <variant>debug.
-        property_set = property_set.add_defaults ()
-        
-        # The algorithm: we keep the current best viable alternative.
-        # When we've got new best viable alternative, we compare it
-        # with the current one. 
-        best = None
-        best_properties = None
-                        
-        if len (self.alternatives_) == 0:
-            return None
-
-        if len (self.alternatives_) == 1:
-            return self.alternatives_ [0]
-
-        if debug:
-            print "Property set for selection:", property_set
-
-        for v in self.alternatives_:
-            properties = v.match (property_set, debug)
-                       
-            if properties is not None:
-                if not best:
-                    best = v
-                    best_properties = properties
-
-                else:
-                    if b2.util.set.equal (properties, best_properties):
-                        return None
-
-                    elif b2.util.set.contains (properties, best_properties):
-                        # Do nothing, this alternative is worse
-                        pass
-
-                    elif b2.util.set.contains (best_properties, properties):
-                        best = v
-                        best_properties = properties
-
-                    else:
-                        return None
-
-        return best
-
-    def apply_default_build (self, property_set):
-        return apply_default_build(property_set, self.default_build_)
-
-    def generate (self, ps):
-        """ Select an alternative for this main target, by finding all alternatives
-            which requirements are satisfied by 'properties' and picking the one with
-            longest requirements set.
-            Returns the result of calling 'generate' on that alternative.
-        """
-        self.manager_.targets ().start_building (self)
-
-        # We want composite properties in build request act as if
-        # all the properties it expands too are explicitly specified.
-        ps = ps.expand ()
-        
-        all_property_sets = self.apply_default_build (ps)
-
-        result = GenerateResult ()
-        
-        for p in all_property_sets:
-            result.extend (self.__generate_really (p))
-
-        self.manager_.targets ().end_building (self)
-
-        return result
-        
-    def __generate_really (self, prop_set):
-        """ Generates the main target with the given property set
-            and returns a list which first element is property_set object
-            containing usage_requirements of generated target and with
-            generated virtual target in other elements. It's possible
-            that no targets are generated.
-        """
-        best_alternative = self.__select_alternatives (prop_set, debug=0)
-
-        if not best_alternative:
-            # FIXME: revive.
-            # self.__select_alternatives(prop_set, debug=1)
-            self.manager_.errors()(
-                "No best alternative for '%s'.\n"
-                  % (self.full_name(),))
-
-        result = best_alternative.generate (prop_set)
-                    
-        # Now return virtual targets for the only alternative
-        return result
-    
-    def rename(self, new_name):
-        AbstractTarget.rename(self, new_name)
-        for a in self.alternatives_:
-            a.rename(new_name)
-
-class FileReference (AbstractTarget):
-    """ Abstract target which refers to a source file.
-        This is artificial creature; it's usefull so that sources to 
-        a target can be represented as list of abstract target instances.
-    """
-    def __init__ (self, manager, file, project):
-        AbstractTarget.__init__ (self, file, project)
-        self.file_location_ = None
-    
-    def generate (self, properties):
-         return GenerateResult (None, [
-             self.manager_.virtual_targets ().from_file (
-             self.name_, self.location(), self.project_) ])
-
-    def exists (self):
-        """ Returns true if the referred file really exists.
-        """
-        if self.location ():
-            return True
-        else:
-            return False
-
-    def location (self):
-        # Returns the location of target. Needed by 'testing.jam'
-        if not self.file_location_:
-            source_location = self.project_.get('source-location')
-            
-            for src_dir in source_location:
-                location = os.path.join(src_dir, self.name())
-                if os.path.isfile(location):
-                    self.file_location_ = src_dir
-                    self.file_path = location
-                    break
-
-        return self.file_location_
-
-def resolve_reference(target_reference, project):
-    """ Given a target_reference, made in context of 'project',
-    returns the AbstractTarget instance that is referred to, as well
-    as properties explicitly specified for this reference.
-    """
-    # Separate target name from properties override
-    split = _re_separate_target_from_properties.match (target_reference)
-    if not split:
-        raise BaseException ("Invalid reference: '%s'" % target_reference)
-    
-    id = split.group (1)
-    
-    sproperties = []
-    
-    if split.group (3):
-        sproperties = property.create_from_strings(feature.split(split.group(3)))
-        sproperties = feature.expand_composites(sproperties)
-        
-    # Find the target
-    target = project.find (id)
-    
-    return (target, property_set.create(sproperties))
-
-def generate_from_reference(target_reference, project, property_set):
-    """ Attempts to generate the target given by target reference, which
-    can refer both to a main target or to a file.
-    Returns a list consisting of
-    - usage requirements
-    - generated virtual targets, if any
-    target_reference:  Target reference
-    project:           Project where the reference is made
-    property_set:      Properties of the main target that makes the reference
-    """
-    target, sproperties = resolve_reference(target_reference, project)
-    
-    # Take properties which should be propagated and refine them
-    # with source-specific requirements.
-    propagated = property_set.propagated()
-    rproperties = propagated.refine(sproperties)
-    
-    return target.generate(rproperties)
-
-
-
-class BasicTarget (AbstractTarget):
-    """ Implements the most standard way of constructing main target
-        alternative from sources. Allows sources to be either file or
-        other main target and handles generation of those dependency
-        targets.
-    """
-    def __init__ (self, name, project, sources, requirements = None, default_build = None, usage_requirements = None):
-        AbstractTarget.__init__ (self, name, project)
-    
-        for s in sources:
-            if get_grist (s):
-                raise InvalidSource ("property '%s' found in the 'sources' parameter for '%s'" % (s, name))
-    
-        self.sources_ = sources
-        
-        if not requirements: requirements = property_set.empty ()
-        self.requirements_ = requirements
-
-        if not default_build: default_build = property_set.empty ()
-        self.default_build_ = default_build
-
-        if not usage_requirements: usage_requirements = property_set.empty ()
-        self.usage_requirements_ = usage_requirements
-        
-        # A cache for resolved references
-        self.source_targets_ = None
-        
-        # A cache for generated targets
-        self.generated_ = {}
-        
-        # A cache for build requests
-        self.request_cache = {}
-
-        # Result of 'capture_user_context' has everything. For example, if this
-        # target is declare as result of loading Jamfile which was loaded when
-        # building target B which was requested from A, then we'll have A, B and
-        # Jamroot location in context. We only care about Jamroot location, most
-        # of the times.
-        self.user_context_ = self.manager_.errors().capture_user_context()[-1:]
-
-        self.always_ = False
-
-    def always(self):
-        self.always_ = True
-        
-    def sources (self):
-        """ Returns the list of AbstractTargets which are used as sources.
-            The extra properties specified for sources are not represented.
-            The only used of this rule at the moment is the '--dump-tests'
-            feature of the test system.            
-        """
-        if self.source_targets_ == None:
-            self.source_targets_ = []
-            for s in self.sources_:
-                self.source_targets_.append(resolve_reference(s, self.project_)[0])
-
-        return self.source_targets_
-
-    def requirements (self):
-        return self.requirements_
-                        
-    def default_build (self):
-        return self.default_build_
-
-    def common_properties (self, build_request, requirements):
-        """ Given build request and requirements, return properties
-            common to dependency build request and target build
-            properties.
-        """
-        # For optimization, we add free unconditional requirements directly,
-        # without using complex algorithsm.
-        # This gives the complex algorithm better chance of caching results.        
-        # The exact effect of this "optimization" is no longer clear
-        free_unconditional = []
-        other = []
-        for p in requirements.all():
-            if p.feature().free() and not p.condition() and p.feature().name() != 'conditional':
-                free_unconditional.append(p)
-            else:
-                other.append(p)
-        other = property_set.create(other)
-                
-        key = (build_request, other)
-        if not self.request_cache.has_key(key):
-            self.request_cache[key] = self.__common_properties2 (build_request, other)
-
-        return self.request_cache[key].add_raw(free_unconditional)
-
-    # Given 'context' -- a set of already present properties, and 'requirements',
-    # decide which extra properties should be applied to 'context'. 
-    # For conditional requirements, this means evaluating condition. For 
-    # indirect conditional requirements, this means calling a rule. Ordinary
-    # requirements are always applied.
-    #
-    # Handles situation where evaluating one conditional requirements affects
-    # condition of another conditional requirements, for example:
-    #
-    #     <toolset>gcc:<variant>release <variant>release:<define>RELEASE
-    #
-    # If 'what' is 'refined' returns context refined with new requirements. 
-    # If 'what' is 'added' returns just the requirements that must be applied.
-    def evaluate_requirements(self, requirements, context, what):
-        # Apply non-conditional requirements. 
-        # It's possible that that further conditional requirement change 
-        # a value set by non-conditional requirements. For example:
-        #
-        #    exe a : a.cpp : <threading>single <toolset>foo:<threading>multi ;
-        # 
-        # I'm not sure if this should be an error, or not, especially given that
-        #
-        #    <threading>single 
-        #
-        # might come from project's requirements.
-        unconditional = feature.expand(requirements.non_conditional())
-
-        context = context.refine(property_set.create(unconditional))
-
-        # We've collected properties that surely must be present in common
-        # properties. We now try to figure out what other properties
-        # should be added in order to satisfy rules (4)-(6) from the docs.
-    
-        conditionals = property_set.create(requirements.conditional())
-
-        # It's supposed that #conditionals iterations
-        # should be enough for properties to propagate along conditions in any
-        # direction.
-        max_iterations = len(conditionals.all()) +\
-                         len(requirements.get("<conditional>")) + 1
-    
-        added_requirements = []
-        current = context
-    
-        # It's assumed that ordinary conditional requirements can't add
-        # <indirect-conditional> properties, and that rules referred
-        # by <indirect-conditional> properties can't add new 
-        # <indirect-conditional> properties. So the list of indirect conditionals
-        # does not change.
-        indirect = requirements.get("<conditional>")
-    
-        ok = 0
-        for i in range(0, max_iterations):
-
-            e = conditionals.evaluate_conditionals(current).all()[:]
-        
-            # Evaluate indirect conditionals.
-            for i in indirect:
-                i = b2.util.jam_to_value_maybe(i)
-                if callable(i):
-                    # This is Python callable, yeah.
-                    e.extend(i(current))
-                else:
-                    # Name of bjam function. Because bjam is unable to handle
-                    # list of Property, pass list of strings.
-                    br = b2.util.call_jam_function(i[1:], [str(p) for p in current.all()])
-                    if br:
-                        e.extend(property.create_from_strings(br))
-
-            if e == added_requirements:
-                # If we got the same result, we've found final properties.
-                ok = 1
-                break
-            else:
-                # Oops, results of evaluation of conditionals has changed.
-                # Also 'current' contains leftover from previous evaluation.
-                # Recompute 'current' using initial properties and conditional
-                # requirements.
-                added_requirements = e
-                current = context.refine(property_set.create(feature.expand(e)))
-
-        if not ok:
-            self.manager().errors()("Can't evaluate conditional properties "
-                                    + str(conditionals))
-
-    
-        if what == "added":
-            return property_set.create(unconditional + added_requirements)
-        elif what == "refined":
-            return current
-        else:
-            self.manager().errors("Invalid value of the 'what' parameter")
-
-    def __common_properties2(self, build_request, requirements):
-        # This guarantees that default properties are present
-        # in result, unless they are overrided by some requirement.
-        # TODO: There is possibility that we've added <foo>bar, which is composite
-        # and expands to <foo2>bar2, but default value of <foo2> is not bar2,
-        # in which case it's not clear what to do.
-        #
-        build_request = build_request.add_defaults()
-        # Featured added by 'add-default' can be composite and expand
-        # to features without default values -- so they are not added yet.
-        # It could be clearer/faster to expand only newly added properties
-        # but that's not critical.
-        build_request = build_request.expand()
-      
-        return self.evaluate_requirements(requirements, build_request,
-                                          "refined")
-    
-    def match (self, property_set, debug):
-        """ Returns the alternative condition for this alternative, if
-            the condition is satisfied by 'property_set'.
-        """
-        # The condition is composed of all base non-conditional properties.
-        # It's not clear if we should expand 'self.requirements_' or not.
-        # For one thing, it would be nice to be able to put
-        #    <toolset>msvc-6.0 
-        # in requirements.
-        # On the other hand, if we have <variant>release in condition it 
-        # does not make sense to require <optimization>full to be in
-        # build request just to select this variant.
-        bcondition = self.requirements_.base ()
-        ccondition = self.requirements_.conditional ()
-        condition = b2.util.set.difference (bcondition, ccondition)
-
-        if debug:
-            print "    next alternative: required properties:", [str(p) for p in condition]
-        
-        if b2.util.set.contains (condition, property_set.all()):
-
-            if debug:
-                print "        matched"
-            
-            return condition
-
-        else:
-            return None
-
-
-    def generate_dependency_targets (self, target_ids, property_set):
-        targets = []
-        usage_requirements = []
-        for id in target_ids:
-                    
-            result = generate_from_reference(id, self.project_, property_set)
-            targets += result.targets()
-            usage_requirements += result.usage_requirements().all()
-
-        return (targets, usage_requirements)        
-    
-    def generate_dependency_properties(self, properties, ps):
-        """ Takes a target reference, which might be either target id
-            or a dependency property, and generates that target using
-            'property_set' as build request.
-
-            Returns a tuple (result, usage_requirements).
-        """
-        result_properties = []
-        usage_requirements = []
-        for p in properties:
-                   
-            result = generate_from_reference(p.value(), self.project_, ps)
-
-            for t in result.targets():
-                result_properties.append(property.Property(p.feature(), t))
-            
-            usage_requirements += result.usage_requirements().all()
-
-        return (result_properties, usage_requirements)        
-
-        
-
-
-    @user_error_checkpoint
-    def generate (self, ps):
-        """ Determines final build properties, generates sources,
-        and calls 'construct'. This method should not be
-        overridden.
-        """
-        self.manager_.errors().push_user_context(
-            "Generating target " + self.full_name(), self.user_context_)
-        
-        if self.manager().targets().logging():
-            self.manager().targets().log(
-                "Building target '%s'" % self.name_)
-            self.manager().targets().increase_indent ()
-            self.manager().targets().log(
-                "Build request: '%s'" % str (ps.raw ()))
-            cf = self.manager().command_line_free_features()
-            self.manager().targets().log(
-                "Command line free features: '%s'" % str (cf.raw ()))            
-            self.manager().targets().log(
-                "Target requirements: %s'" % str (self.requirements().raw ()))
-            
-        self.manager().targets().push_target(self)
-
-        if not self.generated_.has_key(ps):
-
-            # Apply free features form the command line.  If user
-            # said 
-            #   define=FOO
-            # he most likely want this define to be set for all compiles.
-            ps = ps.refine(self.manager().command_line_free_features())            
-            rproperties = self.common_properties (ps, self.requirements_)
-
-            self.manager().targets().log(
-                "Common properties are '%s'" % str (rproperties))
-          
-            if rproperties.get("<build>") != ["no"]:
-                
-                result = GenerateResult ()
-
-                properties = rproperties.non_dependency ()
-
-                (p, u) = self.generate_dependency_properties (rproperties.dependency (), rproperties)
-                properties += p
-                assert all(isinstance(p, property.Property) for p in properties)
-                usage_requirements = u
-
-                (source_targets, u) = self.generate_dependency_targets (self.sources_, rproperties)
-                usage_requirements += u
-
-                self.manager_.targets().log(
-                    "Usage requirements for '%s' are '%s'" % (self.name_, usage_requirements))
-
-                # FIXME:
-
-                rproperties = property_set.create(properties + usage_requirements)
-                usage_requirements = property_set.create (usage_requirements)
-
-                self.manager_.targets().log(
-                    "Build properties: '%s'" % str(rproperties))
-                
-                source_targets += rproperties.get('<source>')
-                
-                # We might get duplicate sources, for example if
-                # we link to two library which have the same <library> in
-                # usage requirements.
-                # Use stable sort, since for some targets the order is
-                # important. E.g. RUN_PY target need python source to come
-                # first.
-                source_targets = unique(source_targets, stable=True)
-
-                # FIXME: figure why this call messes up source_targets in-place
-                result = self.construct (self.name_, source_targets[:], rproperties)
-
-                if result:
-                    assert len(result) == 2
-                    gur = result [0]
-                    result = result [1]
-
-                    if self.always_:
-                        for t in result:
-                            t.always()
-
-                    s = self.create_subvariant (
-                        result,
-                        self.manager().virtual_targets().recent_targets(), ps,
-                        source_targets, rproperties, usage_requirements)
-                    self.manager().virtual_targets().clear_recent_targets()
-                    
-                    ur = self.compute_usage_requirements (s)
-                    ur = ur.add (gur)
-                    s.set_usage_requirements (ur)
-
-                    self.manager_.targets().log (
-                        "Usage requirements from '%s' are '%s'" %
-                        (self.name(), str(rproperties)))
-                    
-                    self.generated_[ps] = GenerateResult (ur, result)
-                else:
-                    self.generated_[ps] = GenerateResult (property_set.empty(), [])
-            else:
-                # If we just see <build>no, we cannot produce any reasonable
-                # diagnostics. The code that adds this property is expected
-                # to explain why a target is not built, for example using
-                # the configure.log-component-configuration function.
-
-                # If this target fails to build, add <build>no to properties
-                # to cause any parent target to fail to build.  Except that it
-                # - does not work now, since we check for <build>no only in
-                #   common properties, but not in properties that came from
-                #   dependencies
-                # - it's not clear if that's a good idea anyway.  The alias
-                #   target, for example, should not fail to build if a dependency
-                #   fails.                
-                self.generated_[ps] = GenerateResult(
-                    property_set.create(["<build>no"]), [])
-        else:
-            self.manager().targets().log ("Already built")
-
-        self.manager().targets().pop_target()
-        self.manager().targets().decrease_indent()
-
-        return self.generated_[ps]
-    
-    def compute_usage_requirements (self, subvariant):
-        """ Given the set of generated targets, and refined build 
-            properties, determines and sets appripriate usage requirements
-            on those targets.
-        """
-        rproperties = subvariant.build_properties ()
-        xusage_requirements =self.evaluate_requirements(
-            self.usage_requirements_, rproperties, "added")
-        
-        # We generate all dependency properties and add them,
-        # as well as their usage requirements, to result.
-        (r1, r2) = self.generate_dependency_properties(xusage_requirements.dependency (), rproperties)
-        extra = r1 + r2
-                
-        result = property_set.create (xusage_requirements.non_dependency () + extra)
-
-        # Propagate usage requirements we've got from sources, except
-        # for the <pch-header> and <pch-file> features.
-        #
-        # That feature specifies which pch file to use, and should apply
-        # only to direct dependents. Consider:
-        #
-        #   pch pch1 : ...
-        #   lib lib1 : ..... pch1 ;
-        #   pch pch2 : 
-        #   lib lib2 : pch2 lib1 ;
-        #
-        # Here, lib2 should not get <pch-header> property from pch1.
-        #
-        # Essentially, when those two features are in usage requirements,
-        # they are propagated only to direct dependents. We might need
-        # a more general mechanism, but for now, only those two
-        # features are special.
-        raw = subvariant.sources_usage_requirements().raw()
-        raw = property.change(raw, "<pch-header>", None);
-        raw = property.change(raw, "<pch-file>", None);              
-        result = result.add(property_set.create(raw))
-        
-        return result
-
-    def create_subvariant (self, root_targets, all_targets,
-                           build_request, sources,
-                           rproperties, usage_requirements):
-        """Creates a new subvariant-dg instances for 'targets'
-         - 'root-targets' the virtual targets will be returned to dependents
-         - 'all-targets' all virtual 
-              targets created while building this main target
-         - 'build-request' is property-set instance with
-         requested build properties"""
-         
-        for e in root_targets:
-            e.root (True)
-
-        s = Subvariant (self, build_request, sources,
-                        rproperties, usage_requirements, all_targets)
-        
-        for v in all_targets:
-            if not v.creating_subvariant():
-                v.creating_subvariant(s)
-                
-        return s
-        
-    def construct (self, name, source_targets, properties):
-        """ Constructs the virtual targets for this abstract targets and
-            the dependecy graph. Returns a tuple consisting of the properties and the list of virtual targets.
-            Should be overrided in derived classes.
-        """
-        raise BaseException ("method should be defined in derived classes")
-
-
-class TypedTarget (BasicTarget):
-    import generators
-    
-    def __init__ (self, name, project, type, sources, requirements, default_build, usage_requirements):
-        BasicTarget.__init__ (self, name, project, sources, requirements, default_build, usage_requirements)
-        self.type_ = type
-
-    def __jam_repr__(self):
-        return b2.util.value_to_jam(self)
-    
-    def type (self):
-        return self.type_
-            
-    def construct (self, name, source_targets, prop_set):
-
-        r = generators.construct (self.project_, name, self.type_, 
-                                  prop_set.add_raw(['<main-target-type>' + self.type_]),
-                                  source_targets, True)
-
-        if not r:
-            print "warning: Unable to construct '%s'" % self.full_name ()
-
-            # Are there any top-level generators for this type/property set.
-            if not generators.find_viable_generators (self.type_, prop_set):
-                print "error: no generators were found for type '" + self.type_ + "'"
-                print "error: and the requested properties"
-                print "error: make sure you've configured the needed tools"
-                print "See http://boost.org/boost-build2/doc/html/bbv2/advanced/configuration.html"
-                
-                print "To debug this problem, try the --debug-generators option."
-                sys.exit(1)
-        
-        return r
-
-def apply_default_build(property_set, default_build):
-    # 1. First, see what properties from default_build
-    # are already present in property_set. 
-
-    specified_features = set(p.feature() for p in property_set.all())
-
-    defaults_to_apply = []
-    for d in default_build.all():
-        if not d.feature() in specified_features:
-            defaults_to_apply.append(d)
-
-    # 2. If there's any defaults to be applied, form the new
-    # build request. Pass it throw 'expand-no-defaults', since
-    # default_build might contain "release debug", which will
-    # result in two property_sets.
-    result = []
-    if defaults_to_apply:
-
-        # We have to compress subproperties here to prevent
-        # property lists like:
-        #
-        #    <toolset>msvc <toolset-msvc:version>7.1 <threading>multi
-        #
-        # from being expanded into:
-        #
-        #    <toolset-msvc:version>7.1/<threading>multi
-        #    <toolset>msvc/<toolset-msvc:version>7.1/<threading>multi
-        #
-        # due to cross-product property combination.  That may
-        # be an indication that
-        # build_request.expand-no-defaults is the wrong rule
-        # to use here.
-        compressed = feature.compress_subproperties(property_set.all())
-
-        result = build_request.expand_no_defaults(
-            b2.build.property_set.create([p]) for p in (compressed + defaults_to_apply))
-
-    else:
-        result.append (property_set)
-
-    return result
-
-
-def create_typed_metatarget(name, type, sources, requirements, default_build, usage_requirements):
-    
-    from b2.manager import get_manager
-    t = get_manager().targets()
-    
-    project = get_manager().projects().current()
-        
-    return t.main_target_alternative(
-        TypedTarget(name, project, type,
-                    t.main_target_sources(sources, name),
-                    t.main_target_requirements(requirements, project),
-                    t.main_target_default_build(default_build, project),
-                    t.main_target_usage_requirements(usage_requirements, project)))
-
-
-def create_metatarget(klass, name, sources, requirements=[], default_build=[], usage_requirements=[]):
-    from b2.manager import get_manager
-    t = get_manager().targets()
-    
-    project = get_manager().projects().current()
-        
-    return t.main_target_alternative(
-        klass(name, project,
-              t.main_target_sources(sources, name),
-              t.main_target_requirements(requirements, project),
-              t.main_target_default_build(default_build, project),
-              t.main_target_usage_requirements(usage_requirements, project)))    
-
-def metatarget_function_for_class(class_):
-
-    @bjam_signature((["name"], ["sources", "*"], ["requirements", "*"],
-                     ["default_build", "*"], ["usage_requirements", "*"]))
-    def create_metatarget(name, sources, requirements = [], default_build = None, usage_requirements = []):
-
-        from b2.manager import get_manager
-        t = get_manager().targets()
-
-        project = get_manager().projects().current()
-        
-        return t.main_target_alternative(
-            class_(name, project,
-                   t.main_target_sources(sources, name),
-                   t.main_target_requirements(requirements, project),
-                   t.main_target_default_build(default_build, project),
-                   t.main_target_usage_requirements(usage_requirements, project)))
-
-    return create_metatarget
diff --git a/jam-files/boost-build/build/toolset.jam b/jam-files/boost-build/build/toolset.jam
deleted file mode 100644
index f2036d99..00000000
--- a/jam-files/boost-build/build/toolset.jam
+++ /dev/null
@@ -1,502 +0,0 @@
-# Copyright 2003 Dave Abrahams
-# Copyright 2005 Rene Rivera
-# Copyright 2002, 2003, 2004, 2005, 2006 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-#  Support for toolset definition.
-
-import errors ;
-import feature ;
-import generators ;
-import numbers ;
-import path ;
-import property ;
-import regex ;
-import sequence ;
-import set ;
-
-
-.flag-no = 1 ;
-
-.ignore-requirements = ;
-
-# This is used only for testing, to make sure we do not get random extra
-# elements in paths.
-if --ignore-toolset-requirements in [ modules.peek : ARGV ]
-{
-    .ignore-requirements = 1 ;
-}
-
-
-# Initializes an additional toolset-like module. First load the 'toolset-module'
-# and then calls its 'init' rule with trailing arguments.
-#
-rule using ( toolset-module : * )
-{
-    import $(toolset-module) ;
-    $(toolset-module).init $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ;
-}
-
-
-# Expands subfeatures in each property sets, e.g. '<toolset>gcc-3.2' will be
-# converted to '<toolset>gcc/<toolset-version>3.2'.
-#
-local rule normalize-condition ( property-sets * )
-{
-    local result ;
-    for local p in $(property-sets)
-    {
-        local split = [ feature.split $(p) ] ;
-        local expanded = [ feature.expand-subfeatures [ feature.split $(p) ] ] ;
-        result += $(expanded:J=/) ;
-    }
-    return $(result) ;
-}
-
-
-# Specifies if the 'flags' rule should check that the invoking module is the
-# same as the module we are setting the flag for. 'v' can be either 'checked' or
-# 'unchecked'. Subsequent call to 'pop-checking-for-flags-module' will restore
-# the setting that was in effect before calling this rule.
-#
-rule push-checking-for-flags-module ( v )
-{
-    .flags-module-checking = $(v) $(.flags-module-checking) ;
-}
-
-rule pop-checking-for-flags-module ( )
-{
-    .flags-module-checking = $(.flags-module-checking[2-]) ;
-}
-
-
-# Specifies the flags (variables) that must be set on targets under certain
-# conditions, described by arguments.
-#
-rule flags (
-    rule-or-module   # If contains a dot, should be a rule name. The flags will
-                     # be applied when that rule is used to set up build
-                     # actions.
-                     #
-                     # If does not contain dot, should be a module name. The
-                     # flag will be applied for all rules in that module. If
-                     # module for rule is different from the calling module, an
-                     # error is issued.
-
-    variable-name    # Variable that should be set on target.
-    condition * :    # A condition when this flag should be applied. Should be a
-                     # set of property sets. If one of those property sets is
-                     # contained in the build properties, the flag will be used.
-                     # Implied values are not allowed: "<toolset>gcc" should be
-                     # used, not just "gcc". Subfeatures, like in
-                     # "<toolset>gcc-3.2" are allowed. If left empty, the flag
-                     # will be used unconditionally.
-                     #
-                     # Propery sets may use value-less properties ('<a>'  vs.
-                     # '<a>value') to match absent properties. This allows to
-                     # separately match:
-                     #
-                     #   <architecture>/<address-model>64
-                     #   <architecture>ia64/<address-model>
-                     #
-                     # Where both features are optional. Without this syntax
-                     # we would be forced to define "default" values.
-
-    values * :       # The value to add to variable. If <feature> is specified,
-                     # then the value of 'feature' will be added.
-    unchecked ?      # If value 'unchecked' is passed, will not test that flags
-                     # are set for the calling module.
-    : hack-hack ?    # For
-                     #   flags rule OPTIONS <cxx-abi> : -model ansi
-                     # Treat <cxx-abi> as condition
-                     # FIXME: ugly hack.
-)
-{
-    local caller = [ CALLER_MODULE ] ;
-    if ! [ MATCH ".*([.]).*" : $(rule-or-module) ]
-       && [ MATCH "(Jamfile<.*)" : $(caller) ]
-    {
-        # Unqualified rule name, used inside Jamfile. Most likely used with
-        # 'make' or 'notfile' rules. This prevents setting flags on the entire
-        # Jamfile module (this will be considered as rule), but who cares?
-        # Probably, 'flags' rule should be split into 'flags' and
-        # 'flags-on-module'.
-        rule-or-module = $(caller).$(rule-or-module) ;
-    }
-    else
-    {
-        local module_ = [ MATCH "([^.]*).*" : $(rule-or-module) ] ;
-        if $(unchecked) != unchecked
-            && $(.flags-module-checking[1]) != unchecked
-            && $(module_) != $(caller)
-        {
-            errors.error "Module $(caller) attempted to set flags for module $(module_)" ;
-        }
-    }
-
-    if $(condition) && ! $(condition:G=) && ! $(hack-hack)
-    {
-        # We have condition in the form '<feature>', that is, without value.
-        # That is an older syntax:
-        #   flags gcc.link RPATH <dll-path> ;
-        # for compatibility, convert it to
-        #   flags gcc.link RPATH : <dll-path> ;
-        values = $(condition) ;
-        condition = ;
-    }
-
-    if $(condition)
-    {
-        property.validate-property-sets $(condition) ;
-        condition = [ normalize-condition $(condition) ] ;
-    }
-
-    add-flag $(rule-or-module) : $(variable-name) : $(condition) : $(values) ;
-}
-
-
-# Adds a new flag setting with the specified values. Does no checking.
-#
-local rule add-flag ( rule-or-module : variable-name : condition * : values * )
-{
-    .$(rule-or-module).flags += $(.flag-no) ;
-
-    # Store all flags for a module.
-    local module_ = [ MATCH "([^.]*).*" : $(rule-or-module) ] ;
-    .module-flags.$(module_) += $(.flag-no) ;
-    # Store flag-no -> rule-or-module mapping.
-    .rule-or-module.$(.flag-no) = $(rule-or-module) ;
-
-    .$(rule-or-module).variable.$(.flag-no) += $(variable-name) ;
-    .$(rule-or-module).values.$(.flag-no) += $(values) ;
-    .$(rule-or-module).condition.$(.flag-no) += $(condition) ;
-
-    .flag-no = [ numbers.increment $(.flag-no) ] ;
-}
-
-
-# Returns the first element of 'property-sets' which is a subset of
-# 'properties' or an empty list if no such element exists.
-#
-rule find-property-subset ( property-sets * : properties * )
-{
-    # Cut property values off.
-    local prop-keys = $(properties:G) ;
-
-    local result ;
-    for local s in $(property-sets)
-    {
-        if ! $(result)
-        {
-            # Handle value-less properties like '<architecture>' (compare with
-            # '<architecture>x86').
-
-            local set = [ feature.split $(s) ] ;
-
-            # Find the set of features that
-            # - have no property specified in required property set
-            # - are omitted in the build property set.
-            local default-props ;
-            for local i in $(set)
-            {
-                # If $(i) is a value-less property it should match default value
-                # of an optional property. See the first line in the example
-                # below:
-                #
-                #  property set     properties     result
-                # <a> <b>foo      <b>foo           match
-                # <a> <b>foo      <a>foo <b>foo    no match
-                # <a>foo <b>foo   <b>foo           no match
-                # <a>foo <b>foo   <a>foo <b>foo    match
-                if ! ( $(i:G=) || ( $(i:G) in $(prop-keys) ) )
-                {
-                    default-props += $(i) ;
-                }
-            }
-
-            if $(set) in $(properties) $(default-props)
-            {
-                result = $(s) ;
-            }
-        }
-    }
-    return $(result) ;
-}
-
-
-# Returns a value to be added to some flag for some target based on the flag's
-# value definition and the given target's property set.
-#
-rule handle-flag-value ( value * : properties * )
-{
-    local result ;
-    if $(value:G)
-    {
-        local matches = [ property.select $(value) : $(properties) ] ;
-        for local p in $(matches)
-        {
-            local att = [ feature.attributes $(p:G) ] ;
-            if dependency in $(att)
-            {
-                # The value of a dependency feature is a target and needs to be
-                # actualized.
-                result += [ $(p:G=).actualize ] ;
-            }
-            else if path in $(att) || free in $(att)
-            {
-                local values ;
-                # Treat features with && in the value specially -- each
-                # &&-separated element is considered a separate value. This is
-                # needed to handle searched libraries or include paths, which
-                # may need to be in a specific order.
-                if ! [ MATCH (&&) : $(p:G=) ]
-                {
-                    values = $(p:G=) ;
-                }
-                else
-                {
-                    values = [ regex.split $(p:G=) "&&" ] ;
-                }
-                if path in $(att)
-                {
-                    result += [ sequence.transform path.native : $(values) ] ;
-                }
-                else
-                {
-                    result += $(values) ;
-                }
-            }
-            else
-            {
-                result += $(p:G=) ;
-            }
-        }
-    }
-    else
-    {
-        result += $(value) ;
-    }
-    return $(result) ;
-}
-
-
-# Given a rule name and a property set, returns a list of interleaved variables
-# names and values which must be set on targets for that rule/property-set
-# combination.
-#
-rule set-target-variables-aux ( rule-or-module : property-set )
-{
-    local result ;
-    properties = [ $(property-set).raw ] ;
-    for local f in $(.$(rule-or-module).flags)
-    {
-        local variable = $(.$(rule-or-module).variable.$(f)) ;
-        local condition = $(.$(rule-or-module).condition.$(f)) ;
-        local values = $(.$(rule-or-module).values.$(f)) ;
-
-        if ! $(condition) ||
-            [ find-property-subset $(condition) : $(properties) ]
-        {
-            local processed ;
-            for local v in $(values)
-            {
-                # The value might be <feature-name> so needs special treatment.
-                processed += [ handle-flag-value $(v) : $(properties) ] ;
-            }
-            for local r in $(processed)
-            {
-                result += $(variable) $(r) ;
-            }
-        }
-    }
-
-    # Strip away last dot separated part and recurse.
-    local next = [ MATCH ^(.+)\\.([^\\.])* : $(rule-or-module) ] ;
-    if $(next)
-    {
-        result += [ set-target-variables-aux $(next[1]) : $(property-set) ] ;
-    }
-    return $(result) ;
-}
-
-
-rule set-target-variables ( rule-or-module targets + : property-set )
-{
-    properties = [ $(property-set).raw ] ;
-    local key = $(rule-or-module).$(property-set) ;
-    local settings = $(.stv.$(key)) ;
-    if ! $(settings)
-    {
-        settings = [ set-target-variables-aux $(rule-or-module) :
-            $(property-set) ] ;
-
-        if ! $(settings)
-        {
-            settings = none ;
-        }
-        .stv.$(key) = $(settings) ;
-    }
-
-    if $(settings) != none
-    {
-        local var-name = ;
-        for local name-or-value in $(settings)
-        {
-            if $(var-name)
-            {
-                $(var-name) on $(targets) += $(name-or-value) ;
-                var-name = ;
-            }
-            else
-            {
-                var-name = $(name-or-value) ;
-            }
-        }
-    }
-}
-
-
-# Make toolset 'toolset', defined in a module of the same name, inherit from
-# 'base'.
-# 1. The 'init' rule from 'base' is imported into 'toolset' with full name.
-#    Another 'init' is called, which forwards to the base one.
-# 2. All generators from 'base' are cloned. The ids are adjusted and <toolset>
-#    property in requires is adjusted too.
-# 3. All flags are inherited.
-# 4. All rules are imported.
-#
-rule inherit ( toolset : base )
-{
-    import $(base) ;
-    inherit-generators $(toolset) : $(base) ;
-    inherit-flags      $(toolset) : $(base) ;
-    inherit-rules      $(toolset) : $(base) ;
-}
-
-
-rule inherit-generators ( toolset properties * : base : generators-to-ignore * )
-{
-    properties ?= <toolset>$(toolset) ;
-    local base-generators = [ generators.generators-for-toolset $(base) ] ;
-    for local g in $(base-generators)
-    {
-        local id = [ $(g).id ] ;
-
-        if ! $(id) in $(generators-to-ignore)
-        {
-            # Some generator names have multiple periods in their name, so
-            # $(id:B=$(toolset)) does not generate the right new-id name. E.g.
-            # if id = gcc.compile.c++ then $(id:B=darwin) = darwin.c++, which is
-            # not what we want. Manually parse the base and suffix. If there is
-            # a better way to do this, I would love to see it. See also the
-            # register() rule in the generators module.
-            local base = $(id) ;
-            local suffix = "" ;
-            while $(base:S)
-            {
-                suffix = $(base:S)$(suffix) ;
-                base = $(base:B) ;
-            }
-            local new-id = $(toolset)$(suffix) ;
-
-            generators.register [ $(g).clone $(new-id) : $(properties) ] ;
-        }
-    }
-}
-
-
-# Brings all flag definitions from the 'base' toolset into the 'toolset'
-# toolset. Flag definitions whose conditions make use of properties in
-# 'prohibited-properties' are ignored. Do not confuse property and feature, for
-# example <debug-symbols>on and <debug-symbols>off, so blocking one of them does
-# not block the other one.
-#
-# The flag conditions are not altered at all, so if a condition includes a name,
-# or version of a base toolset, it will not ever match the inheriting toolset.
-# When such flag settings must be inherited, define a rule in base toolset
-# module and call it as needed.
-#
-rule inherit-flags ( toolset : base : prohibited-properties * : prohibited-vars * )
-{
-    for local f in $(.module-flags.$(base))
-    {
-        local rule-or-module = $(.rule-or-module.$(f)) ;
-        if ( [ set.difference
-            $(.$(rule-or-module).condition.$(f)) :
-                  $(prohibited-properties) ] 
-                  || ! $(.$(rule-or-module).condition.$(f)) 
-        ) && ( ! $(.$(rule-or-module).variable.$(f)) in $(prohibited-vars) )
-        {
-            local rule_ = [ MATCH "[^.]*\.(.*)" : $(rule-or-module) ] ;
-            local new-rule-or-module ;
-            if $(rule_)
-            {
-                new-rule-or-module = $(toolset).$(rule_) ;
-            }
-            else
-            {
-                new-rule-or-module = $(toolset) ;
-            }
-
-            add-flag
-                $(new-rule-or-module)
-                : $(.$(rule-or-module).variable.$(f))
-                : $(.$(rule-or-module).condition.$(f))
-                : $(.$(rule-or-module).values.$(f)) ;
-        }
-    }
-}
-
-
-rule inherit-rules ( toolset : base : localize ? )
-{
-    # It appears that "action" creates a local rule.
-    local base-generators = [ generators.generators-for-toolset $(base) ] ;
-    local rules ;
-    for local g in $(base-generators)
-    {
-        rules += [ MATCH "[^.]*\.(.*)" : [ $(g).rule-name ] ] ;
-    }
-    rules = [ sequence.unique $(rules) ] ;
-    IMPORT $(base) : $(rules) : $(toolset) : $(rules) : $(localize) ;
-    IMPORT $(toolset) : $(rules) : : $(toolset).$(rules) ;
-}
-
-
-# Return the list of global 'toolset requirements'. Those requirements will be
-# automatically added to the requirements of any main target.
-#
-rule requirements ( )
-{
-    return $(.requirements) ;
-}
-
-
-# Adds elements to the list of global 'toolset requirements'. The requirements
-# will be automatically added to the requirements for all main targets, as if
-# they were specified literally. For best results, all requirements added should
-# be conditional or indirect conditional.
-#
-rule add-requirements ( requirements * )
-{
-    if ! $(.ignore-requirements)
-    {
-        .requirements += $(requirements) ;
-    }
-}
-
-
-rule __test__ ( )
-{
-    import assert ;
-    local p = <b>0 <c>1 <d>2 <e>3 <f>4 ;
-    assert.result <c>1/<d>2/<e>3 : find-property-subset <c>1/<d>2/<e>3 <a>0/<b>0/<c>1 <d>2/<e>5 <a>9 : $(p) ;
-    assert.result : find-property-subset <a>0/<b>0/<c>9/<d>9/<e>5 <a>9 : $(p) ;
-
-    local p-set = <a>/<b> <a>0/<b> <a>/<b>1 <a>0/<b>1 ;
-    assert.result <a>/<b>   : find-property-subset $(p-set) :                ;
-    assert.result <a>0/<b>  : find-property-subset $(p-set) : <a>0      <c>2 ;
-    assert.result <a>/<b>1  : find-property-subset $(p-set) : <b>1      <c>2 ;
-    assert.result <a>0/<b>1 : find-property-subset $(p-set) : <a>0 <b>1      ;
-}
diff --git a/jam-files/boost-build/build/toolset.py b/jam-files/boost-build/build/toolset.py
deleted file mode 100644
index b4267987..00000000
--- a/jam-files/boost-build/build/toolset.py
+++ /dev/null
@@ -1,398 +0,0 @@
-# Status: being ported by Vladimir Prus
-# Base revision:  40958
-#
-# Copyright 2003 Dave Abrahams 
-# Copyright 2005 Rene Rivera 
-# Copyright 2002, 2003, 2004, 2005, 2006 Vladimir Prus 
-# Distributed under the Boost Software License, Version 1.0. 
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt) 
-
-""" Support for toolset definition.
-"""
-
-import feature, property, generators, property_set
-import b2.util.set
-from b2.util import cached, qualify_jam_action
-from b2.util.utility import *
-from b2.util import bjam_signature
-from b2.manager import get_manager
-
-__re_split_last_segment = re.compile (r'^(.+)\.([^\.])*')
-__re_two_ampersands = re.compile ('(&&)')
-__re_first_segment = re.compile ('([^.]*).*')
-__re_first_group = re.compile (r'[^.]*\.(.*)')
-
-# Flag is a mechanism to set a value 
-# A single toolset flag. Specifies that when certain
-# properties are in build property set, certain values
-# should be appended to some variable.
-#
-# A flag applies to a specific action in specific module.
-# The list of all flags for a module is stored, and each
-# flag further contains the name of the rule it applies
-# for, 
-class Flag:
-
-    def __init__(self, variable_name, values, condition, rule = None):
-        self.variable_name = variable_name
-        self.values = values
-        self.condition = condition        
-        self.rule = rule
-
-    def __str__(self):
-        return("Flag(" + str(self.variable_name) + ", " + str(self.values) +\
-               ", " + str(self.condition) + ", " + str(self.rule) + ")")
-
-def reset ():
-    """ Clear the module state. This is mainly for testing purposes.
-    """
-    global __module_flags, __flags, __stv
-    
-    # Mapping from module name to a list of all flags that apply
-    # to either that module directly, or to any rule in that module.
-    # Each element of the list is Flag instance.
-    # So, for module named xxx this might contain flags for 'xxx',
-    # for 'xxx.compile', for 'xxx.compile.c++', etc.
-    __module_flags = {}
-
-    # Mapping from specific rule or module name to a list of Flag instances
-    # that apply to that name.
-    # Say, it might contain flags for 'xxx.compile.c++'. If there are
-    # entries for module name 'xxx', they are flags for 'xxx' itself,
-    # not including any rules in that module.
-    __flags = {}
-    
-    # A cache for varaible settings. The key is generated from the rule name and the properties.
-    __stv = {}
-    
-reset ()
-
-# FIXME: --ignore-toolset-requirements
-# FIXME: using
-    
-# FIXME push-checking-for-flags-module ....
-# FIXME: investigate existing uses of 'hack-hack' parameter
-# in jam code.
-    
-@bjam_signature((["rule_or_module", "variable_name", "condition", "*"],
-                 ["values", "*"]))
-def flags(rule_or_module, variable_name, condition, values = []):
-    """ Specifies the flags (variables) that must be set on targets under certain
-        conditions, described by arguments.
-        rule_or_module:   If contains dot, should be a rule name.
-                          The flags will be applied when that rule is
-                          used to set up build actions.
-                          
-                          If does not contain dot, should be a module name.
-                          The flags will be applied for all rules in that
-                          module.
-                          If module for rule is different from the calling
-                          module, an error is issued.
-
-         variable_name:   Variable that should be set on target
-         
-         condition        A condition when this flag should be applied.
-                          Should be set of property sets. If one of
-                          those property sets is contained in build
-                          properties, the flag will be used.
-                          Implied values are not allowed:
-                          "<toolset>gcc" should be used, not just
-                          "gcc". Subfeatures, like in "<toolset>gcc-3.2"
-                          are allowed. If left empty, the flag will
-                          always used.
-                          
-                          Propery sets may use value-less properties 
-                          ('<a>'  vs. '<a>value') to match absent 
-                          properties. This allows to separately match
-                          
-                             <architecture>/<address-model>64
-                             <architecture>ia64/<address-model>
-                          
-                          Where both features are optional. Without this
-                          syntax we'd be forced to define "default" value.
-
-         values:          The value to add to variable. If <feature>
-                          is specified, then the value of 'feature' 
-                          will be added.
-    """
-    caller = bjam.caller()[:-1]
-    if not '.' in rule_or_module and caller.startswith("Jamfile"):
-        # Unqualified rule name, used inside Jamfile. Most likely used with
-        # 'make' or 'notfile' rules. This prevents setting flags on the entire
-        # Jamfile module (this will be considered as rule), but who cares?
-        # Probably, 'flags' rule should be split into 'flags' and
-        # 'flags-on-module'.
-        rule_or_module = qualify_jam_action(rule_or_module, caller)
-    else:
-        # FIXME: revive checking that we don't set flags for a different
-        # module unintentionally
-        pass
-                          
-    if condition and not replace_grist (condition, ''):
-        # We have condition in the form '<feature>', that is, without
-        # value. That's a previous syntax:
-        #
-        #   flags gcc.link RPATH <dll-path> ;
-        # for compatibility, convert it to
-        #   flags gcc.link RPATH : <dll-path> ;                
-        values = [ condition ]
-        condition = None
-    
-    if condition:
-        transformed = []
-        for c in condition:
-            # FIXME: 'split' might be a too raw tool here.
-            pl = [property.create_from_string(s) for s in c.split('/')]
-            pl = feature.expand_subfeatures(pl);
-            transformed.append(property_set.create(pl))
-        condition = transformed
-
-        property.validate_property_sets(condition)
-    
-    __add_flag (rule_or_module, variable_name, condition, values)
-
-def set_target_variables (manager, rule_or_module, targets, ps):
-    """
-    """
-    settings = __set_target_variables_aux(manager, rule_or_module, ps)
-        
-    if settings:
-        for s in settings:
-            for target in targets:
-                manager.engine ().set_target_variable (target, s [0], s[1], True)
-
-def find_satisfied_condition(conditions, ps):
-    """Returns the first element of 'property-sets' which is a subset of
-    'properties', or an empty list if no such element exists."""
-
-    features = set(p.feature() for p in ps.all())
-
-    for condition in conditions:
-
-        found_all = True
-        for i in condition.all():
-
-            found = False
-            if i.value():
-                found = i.value() in ps.get(i.feature())
-            else:            
-                # Handle value-less properties like '<architecture>' (compare with 
-                # '<architecture>x86').
-                # If $(i) is a value-less property it should match default 
-                # value of an optional property. See the first line in the 
-                # example below:
-                #
-                #  property set     properties     result
-                # <a> <b>foo      <b>foo           match
-                # <a> <b>foo      <a>foo <b>foo    no match
-                # <a>foo <b>foo   <b>foo           no match
-                # <a>foo <b>foo   <a>foo <b>foo    match
-                found = not i.feature() in features
-
-            found_all = found_all and found
-
-        if found_all:
-            return condition
-
-    return None
-    
-
-def register (toolset):
-    """ Registers a new toolset.
-    """
-    feature.extend('toolset', [toolset])
-
-def inherit_generators (toolset, properties, base, generators_to_ignore = []):
-    if not properties:
-        properties = [replace_grist (toolset, '<toolset>')]
-        
-    base_generators = generators.generators_for_toolset(base)
-    
-    for g in base_generators:
-        id = g.id()
-        
-        if not id in generators_to_ignore:
-            # Some generator names have multiple periods in their name, so
-            # $(id:B=$(toolset)) doesn't generate the right new_id name.
-            # e.g. if id = gcc.compile.c++, $(id:B=darwin) = darwin.c++,
-            # which is not what we want. Manually parse the base and suffix
-            # (if there's a better way to do this, I'd love to see it.)
-            # See also register in module generators.
-            (base, suffix) = split_action_id(id)
-
-            new_id = toolset + '.' + suffix
-
-            generators.register(g.clone(new_id, properties))
-
-def inherit_flags(toolset, base, prohibited_properties = []):
-    """Brings all flag definitions from the 'base' toolset into the 'toolset'
-    toolset. Flag definitions whose conditions make use of properties in
-    'prohibited-properties' are ignored. Don't confuse property and feature, for
-    example <debug-symbols>on and <debug-symbols>off, so blocking one of them does
-    not block the other one.
-    
-    The flag conditions are not altered at all, so if a condition includes a name,
-    or version of a base toolset, it won't ever match the inheriting toolset. When
-    such flag settings must be inherited, define a rule in base toolset module and
-    call it as needed."""
-    for f in __module_flags.get(base, []):
-        
-        if not f.condition or b2.util.set.difference(f.condition, prohibited_properties):
-            match = __re_first_group.match(f.rule)
-            rule_ = None
-            if match:
-                rule_ = match.group(1)
-
-            new_rule_or_module = ''
-
-            if rule_:
-                new_rule_or_module = toolset + '.' + rule_
-            else:
-                new_rule_or_module = toolset
-
-            __add_flag (new_rule_or_module, f.variable_name, f.condition, f.values)
-
-def inherit_rules (toolset, base):
-    pass
-    # FIXME: do something about this.
-#    base_generators = generators.generators_for_toolset (base)
-
-#    import action
-
-#    ids = []
-#    for g in base_generators:
-#        (old_toolset, id) = split_action_id (g.id ())
-#        ids.append (id) ;
-
-#    new_actions = []
-
-#    engine = get_manager().engine()
-    # FIXME: do this!
-#    for action in engine.action.values():
-#        pass
-#        (old_toolset, id) = split_action_id(action.action_name)
-#    
-#        if old_toolset == base:
-#            new_actions.append ((id, value [0], value [1]))
-#
-#    for a in new_actions:
-#        action.register (toolset + '.' + a [0], a [1], a [2])
-        
-    # TODO: how to deal with this?
-#       IMPORT $(base) : $(rules) : $(toolset) : $(rules) : localized ;
-#       # Import the rules to the global scope
-#       IMPORT $(toolset) : $(rules) : : $(toolset).$(rules) ;
-#   }
-#   
-
-######################################################################################
-# Private functions
-
-@cached
-def __set_target_variables_aux (manager, rule_or_module, ps):
-    """ Given a rule name and a property set, returns a list of tuples of
-        variables names and values, which must be set on targets for that
-        rule/properties combination. 
-    """
-    result = []
-
-    for f in __flags.get(rule_or_module, []):
-           
-        if not f.condition or find_satisfied_condition (f.condition, ps):
-            processed = []
-            for v in f.values:
-                # The value might be <feature-name> so needs special
-                # treatment.
-                processed += __handle_flag_value (manager, v, ps)
-
-            for r in processed:
-                result.append ((f.variable_name, r))
-    
-    # strip away last dot separated part and recurse.
-    next = __re_split_last_segment.match(rule_or_module)
-    
-    if next:
-        result.extend(__set_target_variables_aux(
-            manager, next.group(1), ps))
-
-    return result
-
-def __handle_flag_value (manager, value, ps):
-    result = []
-    
-    if get_grist (value):
-        f = feature.get(value)
-        values = ps.get(f)
-        
-        for value in values:
-
-            if f.dependency():
-                # the value of a dependency feature is a target
-                # and must be actualized
-                result.append(value.actualize())
-
-            elif f.path() or f.free():
-                
-                # Treat features with && in the value
-                # specially -- each &&-separated element is considered
-                # separate value. This is needed to handle searched
-                # libraries, which must be in specific order.
-                if not __re_two_ampersands.search(value):
-                    result.append(value)
-
-                else:
-                    result.extend(value.split ('&&'))
-            else:
-                result.append (ungristed)
-    else:
-        result.append (value)
-
-    return result
-
-def __add_flag (rule_or_module, variable_name, condition, values):
-    """ Adds a new flag setting with the specified values.
-        Does no checking.
-    """
-    f = Flag(variable_name, values, condition, rule_or_module)
-    
-    # Grab the name of the module
-    m = __re_first_segment.match (rule_or_module)
-    assert m
-    module = m.group(1)
-
-    __module_flags.setdefault(m, []).append(f)
-    __flags.setdefault(rule_or_module, []).append(f)
-
-__requirements = []
-
-def requirements():
-    """Return the list of global 'toolset requirements'.
-    Those requirements will be automatically added to the requirements of any main target."""
-    return __requirements
-
-def add_requirements(requirements):
-    """Adds elements to the list of global 'toolset requirements'. The requirements
-    will be automatically added to the requirements for all main targets, as if
-    they were specified literally. For best results, all requirements added should
-    be conditional or indirect conditional."""
-    
-    #if ! $(.ignore-requirements)
-    #{
-    print "XXXX", requirements
-    __requirements.extend(requirements)
-    #}
-         
-# Make toolset 'toolset', defined in a module of the same name,
-# inherit from 'base'
-# 1. The 'init' rule from 'base' is imported into 'toolset' with full
-#    name. Another 'init' is called, which forwards to the base one.
-# 2. All generators from 'base' are cloned. The ids are adjusted and 
-#    <toolset> property in requires is adjusted too
-# 3. All flags are inherited
-# 4. All rules are imported.
-def inherit(toolset, base):
-    get_manager().projects().load_module(base, []);
-
-    inherit_generators(toolset, [], base)
-    inherit_flags(toolset, base)
-    inherit_rules(toolset, base)
diff --git a/jam-files/boost-build/build/type.jam b/jam-files/boost-build/build/type.jam
deleted file mode 100644
index 1a7a5782..00000000
--- a/jam-files/boost-build/build/type.jam
+++ /dev/null
@@ -1,425 +0,0 @@
-# Copyright 2002, 2003 Dave Abrahams
-# Copyright 2002, 2003, 2004, 2005, 2006 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-#  Deals with target type declaration and defines target class which supports
-#  typed targets.
-
-import "class" : new ;
-import errors ;
-import feature ;
-import generators : * ;
-import project ;
-import property ;
-import scanner ;
-import os ;
-
-# The following import would create a circular dependency:
-# project -> project-root -> builtin -> type -> targets -> project
-# import targets ;
-
-# The feature is optional so it would never get added implicitly. It is used
-# only for internal purposes and in all cases we want to use it explicitly.
-feature.feature target-type : : composite optional ;
-
-feature.feature main-target-type : : optional incidental ;
-feature.feature base-target-type : : composite optional free ;
-
-
-# Registers a target type, possible derived from a 'base-type'. Providing a list
-# of 'suffixes' here is a shortcut for separately calling the register-suffixes
-# rule with the given suffixes and the set-generated-target-suffix rule with the
-# first given suffix.
-#
-rule register ( type : suffixes * : base-type ? )
-{
-    # Type names cannot contain hyphens, because when used as feature-values
-    # they would be interpreted as composite features which need to be
-    # decomposed.
-    switch $(type)
-    {
-        case *-* : errors.error "type name \"$(type)\" contains a hyphen" ;
-    }
-
-    if $(type) in $(.types)
-    {
-        errors.error "Type $(type) is already registered." ;
-    }
-    else
-    {
-        .types += $(type) ;
-        .base.$(type) = $(base-type) ;
-        .derived.$(base-type) += $(type) ;
-
-        if $(suffixes)-is-not-empty
-        {
-            # Specify mapping from suffixes to type.
-            register-suffixes $(suffixes) : $(type) ;
-            # By default generated targets of 'type' will use the first of
-            #'suffixes'. This may be overriden.
-            set-generated-target-suffix $(type) : : $(suffixes[1]) ;
-        }
-
-        feature.extend target-type      : $(type) ;
-        feature.extend main-target-type : $(type) ;
-        feature.extend base-target-type : $(type) ;
-
-        feature.compose <target-type>$(type) : $(base-type:G=<base-target-type>) ;
-        feature.compose <base-target-type>$(type) : <base-target-type>$(base-type) ;
-
-        # We used to declare the main target rule only when a 'main' parameter
-        # has been specified. However, it is hard to decide that a type will
-        # *never* need a main target rule and so from time to time we needed to
-        # make yet another type 'main'. So now a main target rule is defined for
-        # each type.
-        main-rule-name = [ type-to-rule-name $(type) ] ;
-        .main-target-type.$(main-rule-name) = $(type) ;
-        IMPORT $(__name__) : main-target-rule : : $(main-rule-name) ;
-
-        # Adding a new derived type affects generator selection so we need to
-        # make the generator selection module update any of its cached
-        # information related to a new derived type being defined.
-        generators.update-cached-information-with-a-new-type $(type) ;
-    }
-}
-
-
-# Given a type, returns the name of the main target rule which creates targets
-# of that type.
-#
-rule type-to-rule-name ( type )
-{
-    # Lowercase everything. Convert underscores to dashes.
-    import regex ;
-    local n = [ regex.split $(type:L) "_" ] ;
-    return $(n:J=-) ;
-}
-
-
-# Given a main target rule name, returns the type for which it creates targets.
-#
-rule type-from-rule-name ( rule-name )
-{
-    return $(.main-target-type.$(rule-name)) ;
-}
-
-
-# Specifies that files with suffix from 'suffixes' be recognized as targets of
-# type 'type'. Issues an error if a different type is already specified for any
-# of the suffixes.
-#
-rule register-suffixes ( suffixes + : type )
-{
-    for local s in $(suffixes)
-    {
-        if ! $(.type.$(s))
-        {
-            .type.$(s) = $(type) ;
-        }
-        else if $(.type.$(s)) != $(type)
-        {
-            errors.error Attempting to specify multiple types for suffix
-                \"$(s)\" : "Old type $(.type.$(s)), New type $(type)" ;
-        }
-    }
-}
-
-
-# Returns true iff type has been registered.
-#
-rule registered ( type )
-{
-    if $(type) in $(.types)
-    {
-        return true ;
-    }
-}
-
-
-# Issues an error if 'type' is unknown.
-#
-rule validate ( type )
-{
-    if ! [ registered $(type) ]
-    {
-        errors.error "Unknown target type $(type)" ;
-    }
-}
-
-
-# Sets a scanner class that will be used for this 'type'.
-#
-rule set-scanner ( type : scanner )
-{
-    validate $(type) ;
-    .scanner.$(type) = $(scanner) ;
-}
-
-
-# Returns a scanner instance appropriate to 'type' and 'properties'.
-#
-rule get-scanner ( type : property-set )
-{
-    if $(.scanner.$(type))
-    {
-        return [ scanner.get $(.scanner.$(type)) : $(property-set) ] ;
-    }
-}
-
-
-# Returns a base type for the given type or nothing in case the given type is
-# not derived.
-#
-rule base ( type )
-{
-    return $(.base.$(type)) ;
-}
-
-
-# Returns the given type and all of its base types in order of their distance
-# from type.
-#
-rule all-bases ( type )
-{
-    local result = $(type) ;
-    while $(type)
-    {
-        type = [ base $(type) ] ;
-        result += $(type) ;
-    }
-    return $(result) ;
-}
-
-
-# Returns the given type and all of its derived types in order of their distance
-# from type.
-#
-rule all-derived ( type )
-{
-    local result = $(type) ;
-    for local d in $(.derived.$(type))
-    {
-        result += [ all-derived $(d) ] ;
-    }
-    return $(result) ;
-}
-
-
-# Returns true if 'type' is equal to 'base' or has 'base' as its direct or
-# indirect base.
-#
-rule is-derived ( type base )
-{
-    if $(base) in [ all-bases $(type) ]
-    {
-        return true ;
-    }
-}
-
-# Returns true if 'type' is either derived from or is equal to 'base'.
-#
-# TODO: It might be that is-derived and is-subtype were meant to be different
-# rules - one returning true for type = base and one not, but as currently
-# implemented they are actually the same. Clean this up.
-#
-rule is-subtype ( type base )
-{
-    return [ is-derived $(type) $(base) ] ;
-}
-
-
-# Store suffixes for generated targets.
-.suffixes = [ new property-map ] ;
-
-# Store prefixes for generated targets (e.g. "lib" for library).
-.prefixes = [ new property-map ] ;
-
-
-# Sets a file suffix to be used when generating a target of 'type' with the
-# specified properties. Can be called with no properties if no suffix has
-# already been specified for the 'type'. The 'suffix' parameter can be an empty
-# string ("") to indicate that no suffix should be used.
-#
-# Note that this does not cause files with 'suffix' to be automatically
-# recognized as being of 'type'. Two different types can use the same suffix for
-# their generated files but only one type can be auto-detected for a file with
-# that suffix. User should explicitly specify which one using the
-# register-suffixes rule.
-#
-rule set-generated-target-suffix ( type : properties * : suffix )
-{
-    set-generated-target-ps suffix : $(type) : $(properties) : $(suffix) ;
-}
-
-
-# Change the suffix previously registered for this type/properties combination.
-# If suffix is not yet specified, sets it.
-#
-rule change-generated-target-suffix ( type : properties * : suffix )
-{
-    change-generated-target-ps suffix : $(type) : $(properties) : $(suffix) ;
-}
-
-
-# Returns the suffix used when generating a file of 'type' with the given
-# properties.
-#
-rule generated-target-suffix ( type : property-set )
-{
-    return [ generated-target-ps suffix : $(type) : $(property-set) ] ;
-}
-
-
-# Sets a target prefix that should be used when generating targets of 'type'
-# with the specified properties. Can be called with empty properties if no
-# prefix for 'type' has been specified yet.
-#
-# The 'prefix' parameter can be empty string ("") to indicate that no prefix
-# should be used.
-#
-# Usage example: library names use the "lib" prefix on unix.
-#
-rule set-generated-target-prefix ( type : properties * : prefix )
-{
-    set-generated-target-ps prefix : $(type) : $(properties) : $(prefix) ;
-}
-
-
-# Change the prefix previously registered for this type/properties combination.
-# If prefix is not yet specified, sets it.
-#
-rule change-generated-target-prefix ( type : properties * : prefix )
-{
-    change-generated-target-ps prefix : $(type) : $(properties) : $(prefix) ;
-}
-
-
-rule generated-target-prefix ( type : property-set )
-{
-    return [ generated-target-ps prefix : $(type) : $(property-set) ] ;
-}
-
-
-# Common rules for prefix/suffix provisioning follow.
-
-local rule set-generated-target-ps ( ps : type : properties * : psval )
-{
-    properties = <target-type>$(type) $(properties) ;
-    $(.$(ps)es).insert $(properties) : $(psval) ;
-}
-
-
-local rule change-generated-target-ps ( ps : type : properties * : psval )
-{
-    properties = <target-type>$(type) $(properties) ;
-    local prev = [ $(.$(ps)es).find-replace $(properties) : $(psval) ] ;
-    if ! $(prev)
-    {
-        set-generated-target-ps $(ps) : $(type) : $(properties) : $(psval) ;
-    }
-}
-
-
-# Returns either prefix or suffix (as indicated by 'ps') that should be used
-# when generating a target of 'type' with the specified properties. Parameter
-# 'ps' can be either "prefix" or "suffix".  If no prefix/suffix is specified for
-# 'type', returns prefix/suffix for base type, if any.
-#
-local rule generated-target-ps-real ( ps : type : properties * )
-{
-    local result ;
-    local found ;
-    while $(type) && ! $(found)
-    {
-        result = [ $(.$(ps)es).find <target-type>$(type) $(properties) ] ;
-        # If the prefix/suffix is explicitly set to an empty string, we consider
-        # prefix/suffix to be found. If we were not to compare with "", there
-        # would be no way to specify an empty prefix/suffix.
-        if $(result)-is-not-empty
-        {
-            found = true ;
-        }
-        type = $(.base.$(type)) ;
-    }
-    if $(result) = ""
-    {
-        result = ;
-    }
-    return $(result) ;
-}
-
-
-local rule generated-target-ps ( ps : type : property-set )
-{
-    local key = .$(ps).$(type).$(property-set) ;
-    local v = $($(key)) ;
-    if ! $(v)
-    {
-        v = [ generated-target-ps-real $(ps) : $(type) : [ $(property-set).raw ]
-            ] ;
-        if ! $(v)
-        {
-            v = none ;
-        }
-        $(key) = $(v) ;
-    }
-
-    if $(v) != none
-    {
-        return $(v) ;
-    }
-}
-
-
-# Returns file type given its name. If there are several dots in filename, tries
-# each suffix. E.g. for name of "file.so.1.2" suffixes "2", "1", and "so" will
-# be tried.
-#
-rule type ( filename )
-{
-    if [ os.name ] in NT CYGWIN
-    {
-        filename = $(filename:L) ;
-    }    
-    local type ;
-    while ! $(type) && $(filename:S)
-    {
-        local suffix = $(filename:S) ;
-        type = $(.type$(suffix)) ;
-        filename = $(filename:S=) ;
-    }
-    return $(type) ;
-}
-
-
-# Rule used to construct all main targets. Note that this rule gets imported
-# into the global namespace under different alias names and the exact target
-# type to construct is selected based on the alias used to actually invoke this
-# rule.
-#
-rule main-target-rule ( name : sources * : requirements * : default-build * :
-    usage-requirements * )
-{
-    # First discover the required target type based on the exact alias used to
-    # invoke this rule.
-    local bt = [ BACKTRACE 1 ] ;
-    local rulename = $(bt[4]) ;
-    local target-type = [ type-from-rule-name $(rulename) ] ;
-
-    # This is a circular module dependency and so must be imported here.
-    import targets ;
-
-    return [ targets.create-typed-target $(target-type) : [ project.current ] :
-        $(name) : $(sources) : $(requirements) : $(default-build) :
-        $(usage-requirements) ] ;
-}
-
-
-rule __test__ ( )
-{
-    import assert ;
-
-    # TODO: Add tests for all the is-derived, is-base & related type relation
-    # checking rules.
-}
diff --git a/jam-files/boost-build/build/type.py b/jam-files/boost-build/build/type.py
deleted file mode 100644
index ddb7ba09..00000000
--- a/jam-files/boost-build/build/type.py
+++ /dev/null
@@ -1,313 +0,0 @@
-# Status: ported.
-# Base revision: 45462.
-
-#  Copyright (C) Vladimir Prus 2002. Permission to copy, use, modify, sell and
-#  distribute this software is granted provided this copyright notice appears in
-#  all copies. This software is provided "as is" without express or implied
-#  warranty, and with no claim as to its suitability for any purpose.
-
-
-
-import re
-import os
-import os.path
-from b2.util.utility import replace_grist, os_name
-from b2.exceptions import *
-from b2.build import feature, property, scanner
-from b2.util import bjam_signature
-
-
-__re_hyphen = re.compile ('-')
-
-def __register_features ():
-    """ Register features need by this module.
-    """
-    # The feature is optional so that it is never implicitly added.
-    # It's used only for internal purposes, and in all cases we
-    # want to explicitly use it.
-    feature.feature ('target-type', [], ['composite', 'optional'])
-    feature.feature ('main-target-type', [], ['optional', 'incidental'])
-    feature.feature ('base-target-type', [], ['composite', 'optional', 'free'])
-
-def reset ():
-    """ Clear the module state. This is mainly for testing purposes.
-        Note that this must be called _after_ resetting the module 'feature'.
-    """    
-    global __prefixes_suffixes, __suffixes_to_types, __types, __rule_names_to_types, __target_suffixes_cache
-    
-    __register_features ()
-
-    # Stores suffixes for generated targets.
-    __prefixes_suffixes = [property.PropertyMap(), property.PropertyMap()]
-    
-    # Maps suffixes to types
-    __suffixes_to_types = {}
-    
-    # A map with all the registered types, indexed by the type name
-    # Each entry is a dictionary with following values:
-    # 'base': the name of base type or None if type has no base
-    # 'derived': a list of names of type which derive from this one
-    # 'scanner': the scanner class registered for this type, if any
-    __types = {}
-
-    # Caches suffixes for targets with certain properties.
-    __target_suffixes_cache = {}
-    
-reset ()
-
-@bjam_signature((["type"], ["suffixes", "*"], ["base_type", "?"]))
-def register (type, suffixes = [], base_type = None):
-    """ Registers a target type, possibly derived from a 'base-type'. 
-        If 'suffixes' are provided, they list all the suffixes that mean a file is of 'type'.
-        Also, the first element gives the suffix to be used when constructing and object of
-        'type'.
-        type: a string
-        suffixes: None or a sequence of strings
-        base_type: None or a string
-    """
-    # Type names cannot contain hyphens, because when used as
-    # feature-values they will be interpreted as composite features
-    # which need to be decomposed.
-    if __re_hyphen.search (type):
-        raise BaseException ('type name "%s" contains a hyphen' % type)
-    
-    if __types.has_key (type):
-        raise BaseException ('Type "%s" is already registered.' % type)
-
-    entry = {}
-    entry ['base'] = base_type
-    entry ['derived'] = []
-    entry ['scanner'] = None
-    __types [type] = entry
-    
-    if base_type:
-        __types [base_type]['derived'].append (type)
-
-    if len (suffixes) > 0:
-        # Generated targets of 'type' will use the first of 'suffixes'
-        # (this may be overriden)
-        set_generated_target_suffix (type, [], suffixes [0])
-        
-        # Specify mapping from suffixes to type
-        register_suffixes (suffixes, type)
-    
-    feature.extend('target-type', [type])
-    feature.extend('main-target-type', [type])
-    feature.extend('base-target-type', [type])
-
-    if base_type:
-        feature.compose ('<target-type>' + type, replace_grist (base_type, '<base-target-type>'))
-        feature.compose ('<base-target-type>' + type, '<base-target-type>' + base_type)
-
-    import b2.build.generators as generators
-    # Adding a new derived type affects generator selection so we need to
-    # make the generator selection module update any of its cached
-    # information related to a new derived type being defined.
-    generators.update_cached_information_with_a_new_type(type)
-
-    # FIXME: resolving recursive dependency.
-    from b2.manager import get_manager
-    get_manager().projects().project_rules().add_rule_for_type(type)
-
-# FIXME: quick hack.
-def type_from_rule_name(rule_name):
-    return rule_name.upper().replace("-", "_")
-
-
-def register_suffixes (suffixes, type):
-    """ Specifies that targets with suffix from 'suffixes' have the type 'type'. 
-        If a different type is already specified for any of syffixes, issues an error.
-    """
-    for s in suffixes:
-        if __suffixes_to_types.has_key (s):
-            old_type = __suffixes_to_types [s]
-            if old_type != type:
-                raise BaseException ('Attempting to specify type for suffix "%s"\nOld type: "%s", New type "%s"' % (s, old_type, type))
-        else:
-            __suffixes_to_types [s] = type
-
-def registered (type):
-    """ Returns true iff type has been registered.
-    """
-    return __types.has_key (type)
-
-def validate (type):
-    """ Issues an error if 'type' is unknown.
-    """
-    if not registered (type):
-        raise BaseException ("Unknown target type '%s'" % type)
-
-def set_scanner (type, scanner):
-    """ Sets a scanner class that will be used for this 'type'.
-    """
-    validate (type)
-    __types [type]['scanner'] = scanner
-
-def get_scanner (type, prop_set):
-    """ Returns a scanner instance appropriate to 'type' and 'property_set'.
-    """
-    if registered (type):
-        scanner_type = __types [type]['scanner']
-        if scanner_type:
-            return scanner.get (scanner_type, prop_set.raw ())
-            pass
-            
-    return None
-
-def base(type):
-    """Returns a base type for the given type or nothing in case the given type is
-    not derived."""
-
-    return __types[type]['base']
-
-def all_bases (type):
-    """ Returns type and all of its bases, in the order of their distance from type.
-    """
-    result = []
-    while type:
-        result.append (type)
-        type = __types [type]['base']
-
-    return result
-
-def all_derived (type):
-    """ Returns type and all classes that derive from it, in the order of their distance from type.
-    """
-    result = [type]
-    for d in __types [type]['derived']:
-        result.extend (all_derived (d))
-
-    return result
-
-def is_derived (type, base):
-    """ Returns true if 'type' is 'base' or has 'base' as its direct or indirect base.
-    """
-    # TODO: this isn't very efficient, especially for bases close to type
-    if base in all_bases (type):
-        return True
-    else: 
-        return False
-
-def is_subtype (type, base):
-    """ Same as is_derived. Should be removed.
-    """
-    # TODO: remove this method
-    return is_derived (type, base)
-
-@bjam_signature((["type"], ["properties", "*"], ["suffix"]))
-def set_generated_target_suffix (type, properties, suffix):
-    """ Sets a target suffix that should be used when generating target 
-        of 'type' with the specified properties. Can be called with
-        empty properties if no suffix for 'type' was specified yet.
-        This does not automatically specify that files 'suffix' have
-        'type' --- two different types can use the same suffix for
-        generating, but only one type should be auto-detected for
-        a file with that suffix. User should explicitly specify which
-        one.
-
-        The 'suffix' parameter can be empty string ("") to indicate that
-        no suffix should be used.
-    """
-    set_generated_target_ps(1, type, properties, suffix)
-
-
-    
-def change_generated_target_suffix (type, properties, suffix):
-    """ Change the suffix previously registered for this type/properties 
-        combination. If suffix is not yet specified, sets it.
-    """
-    change_generated_target_ps(1, type, properties, suffix)
-
-def generated_target_suffix(type, properties):
-    return generated_target_ps(1, type, properties)
-
-# Sets a target prefix that should be used when generating targets of 'type'
-# with the specified properties. Can be called with empty properties if no
-# prefix for 'type' has been specified yet.
-#
-# The 'prefix' parameter can be empty string ("") to indicate that no prefix
-# should be used.
-#
-# Usage example: library names use the "lib" prefix on unix.
-@bjam_signature((["type"], ["properties", "*"], ["suffix"]))
-def set_generated_target_prefix(type, properties, prefix):
-    set_generated_target_ps(0, type, properties, prefix)
-
-# Change the prefix previously registered for this type/properties combination.
-# If prefix is not yet specified, sets it.
-def change_generated_target_prefix(type, properties, prefix):
-    change_generated_target_ps(0, type, properties, prefix)
-
-def generated_target_prefix(type, properties):
-    return generated_target_ps(0, type, properties)
-
-def set_generated_target_ps(is_suffix, type, properties, val):
-    properties.append ('<target-type>' + type)
-    __prefixes_suffixes[is_suffix].insert (properties, val)
-
-def change_generated_target_ps(is_suffix, type, properties, val):
-    properties.append ('<target-type>' + type)
-    prev = __prefixes_suffixes[is_suffix].find_replace(properties, val)
-    if not prev:
-        set_generated_target_ps(is_suffix, type, properties, val)
-
-# Returns either prefix or suffix (as indicated by 'is_suffix') that should be used
-# when generating a target of 'type' with the specified properties.
-# If no prefix/suffix is specified for 'type', returns prefix/suffix for
-# base type, if any.
-def generated_target_ps_real(is_suffix, type, properties):
-
-    result = ''
-    found = False
-    while type and not found:
-        result = __prefixes_suffixes[is_suffix].find (['<target-type>' + type] + properties)
-
-        # Note that if the string is empty (""), but not null, we consider
-        # suffix found.  Setting prefix or suffix to empty string is fine.
-        if result is not None:
-            found = True
-
-        type = __types [type]['base']
-
-    if not result:
-        result = ''
-    return result
-
-def generated_target_ps(is_suffix, type, prop_set):
-    """ Returns suffix that should be used when generating target of 'type',
-        with the specified properties. If not suffix were specified for
-        'type', returns suffix for base type, if any.
-    """
-    key = (is_suffix, type, prop_set)
-    v = __target_suffixes_cache.get(key, None)
-
-    if not v:
-        v = generated_target_ps_real(is_suffix, type, prop_set.raw())
-        __target_suffixes_cache [key] = v
-
-    return v
-
-def type(filename):
-    """ Returns file type given it's name. If there are several dots in filename,
-        tries each suffix. E.g. for name of "file.so.1.2" suffixes "2", "1", and 
-        "so"  will be tried.
-    """
-    while 1:
-        filename, suffix = os.path.splitext (filename)
-        if not suffix: return None
-        suffix = suffix[1:]
-        
-        if __suffixes_to_types.has_key(suffix):
-            return __suffixes_to_types[suffix]
-
-# NOTE: moved from tools/types/register
-def register_type (type, suffixes, base_type = None, os = []):
-    """ Register the given type on the specified OSes, or on remaining OSes
-        if os is not specified.  This rule is injected into each of the type
-        modules for the sake of convenience.
-    """
-    if registered (type):
-        return
-
-    if not os or os_name () in os:
-        register (type, suffixes, base_type)
diff --git a/jam-files/boost-build/build/version.jam b/jam-files/boost-build/build/version.jam
deleted file mode 100644
index 7626ddda..00000000
--- a/jam-files/boost-build/build/version.jam
+++ /dev/null
@@ -1,161 +0,0 @@
-# Copyright 2002, 2003, 2004, 2006 Vladimir Prus
-# Copyright 2008 Jurko Gospodnetic
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-import errors ;
-import numbers ;
-
-major = "2011" ;
-minor = "04" ;
-
-rule boost-build ( )
-{
-    return "$(major).$(minor)-svn" ;
-}
-
-rule print ( )
-{
-    if [ verify-engine-version ]
-    {        
-        ECHO "Boost.Build" [ boost-build ] ;
-    }    
-}
-
-rule verify-engine-version ( )
-{
-    local v = [ modules.peek : JAM_VERSION ] ;
-    
-    if $(v[1]) != $(major) || $(v[2]) != $(minor)
-    {
-        local argv = [ modules.peek : ARGV ] ;
-        local e = $(argv[1]) ;
-        local l = [ modules.binding version ] ;
-        l = $(l:D) ;
-        l = $(l:D) ;
-        ECHO "warning: mismatched versions of Boost.Build engine and core" ;
-        ECHO "warning: Boost.Build engine ($(e)) is $(v:J=.)" ;
-        ECHO "warning: Boost.Build core (at $(l)) is" [ boost-build ] ;
-    }
-    else
-    {
-        return true ;
-    }    
-}
-
-
-
-# Utility rule for testing whether all elements in a sequence are equal to 0.
-#
-local rule is-all-zeroes ( sequence * )
-{
-    local result = "true" ;
-    for local e in $(sequence)
-    {
-        if $(e) != "0"
-        {
-            result = "" ;
-        }
-    }
-    return $(result) ;
-}
-
-
-# Returns "true" if the first version is less than the second one.
-#
-rule version-less ( lhs + : rhs + )
-{
-    numbers.check $(lhs) ;
-    numbers.check $(rhs) ;
-
-    local done ;
-    local result ;
-
-    while ! $(done) && $(lhs) && $(rhs)
-    {
-        if [ numbers.less $(lhs[1]) $(rhs[1]) ]
-        {
-            done = "true" ;
-            result = "true" ;
-        }
-        else if [ numbers.less $(rhs[1]) $(lhs[1])  ]
-        {
-            done = "true" ;
-        }
-        else
-        {
-            lhs = $(lhs[2-]) ;
-            rhs = $(rhs[2-]) ;
-        }
-    }
-    if ( ! $(done) && ! $(lhs) && ! [ is-all-zeroes $(rhs) ] )
-    {
-        result = "true" ;
-    }
-    
-    return $(result) ;
-}
-
-
-# Returns "true" if the current JAM version version is at least the given
-# version.
-#
-rule check-jam-version ( version + )
-{
-    local version-tag = $(version:J=.) ;
-    if ! $(version-tag)
-    {
-        errors.error Invalid version specifier: : $(version:E="(undefined)") ;
-    }
-
-    if ! $(.jam-version-check.$(version-tag))-is-not-empty
-    {
-        local jam-version = [ modules.peek : JAM_VERSION ] ;
-        if ! $(jam-version)
-        {
-            errors.error "Unable to deduce Boost Jam version. Your Boost Jam"
-                "installation is most likely terribly outdated." ;
-        }
-        .jam-version-check.$(version-tag) = "true" ;
-        if [ version-less [ modules.peek : JAM_VERSION ] : $(version) ]
-        {
-            .jam-version-check.$(version-tag) = "" ;
-        }
-    }
-    return $(.jam-version-check.$(version-tag)) ;
-}
-
-
-rule __test__ ( )
-{
-    import assert ;
-    
-    local jam-version = [ modules.peek : JAM_VERSION ] ;
-    local future-version = $(jam-version) ;
-    future-version += "1" ;
-
-    assert.true  check-jam-version $(jam-version)    ;
-    assert.false check-jam-version $(future-version) ;
-
-    assert.true  version-less  0          :  1          ;
-    assert.false version-less  0          :  0          ;
-    assert.true  version-less  1          :  2          ;
-    assert.false version-less  1          :  1          ;
-    assert.false version-less  2          :  1          ;
-    assert.true  version-less  3 1 20     :  3 4 10     ;
-    assert.false version-less  3 1 10     :  3 1 10     ;
-    assert.false version-less  3 4 10     :  3 1 20     ;
-    assert.true  version-less  3 1 20 5 1 :  3 4 10     ;
-    assert.false version-less  3 1 10 5 1 :  3 1 10     ;
-    assert.false version-less  3 4 10 5 1 :  3 1 20     ;
-    assert.true  version-less  3 1 20     :  3 4 10 5 1 ;
-    assert.true  version-less  3 1 10     :  3 1 10 5 1 ;
-    assert.false version-less  3 4 10     :  3 1 20 5 1 ;
-    assert.false version-less  3 1 10     :  3 1 10 0 0 ;
-    assert.false version-less  3 1 10 0 0 :  3 1 10     ;
-    assert.false version-less  3 1 10 0   :  3 1 10 0 0 ;
-    assert.false version-less  3 1 10 0   : 03 1 10 0 0 ;
-    assert.false version-less 03 1 10 0   :  3 1 10 0 0 ;
-
-    # TODO: Add tests for invalid input data being sent to version-less.
-}
diff --git a/jam-files/boost-build/build/virtual-target.jam b/jam-files/boost-build/build/virtual-target.jam
deleted file mode 100644
index 2e8446bc..00000000
--- a/jam-files/boost-build/build/virtual-target.jam
+++ /dev/null
@@ -1,1317 +0,0 @@
-# Copyright 2003 Dave Abrahams
-# Copyright 2005, 2006 Rene Rivera
-# Copyright 2002, 2003, 2004, 2005, 2006 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-# Implements virtual targets, which correspond to actual files created during a
-# build, but are not yet targets in Jam sense. They are needed, for example,
-# when searching for possible transformation sequences, when it is not yet known
-# whether a particular target should be created at all.
-
-import "class" : new ;
-import errors ;
-import path ;
-import sequence ;
-import set ;
-import type ;
-import utility ;
-
-
-#                       +--------------------------+
-#                       | virtual-target           |
-#                       +==========================+
-#                       | actualize                |
-#                       +--------------------------+
-#                       | actualize-action() = 0   |
-#                       | actualize-location() = 0 |
-#                       +----------------+---------+
-#                                        |
-#                                        ^
-#                                       / \
-#                                      +-+-+
-#                                        |
-#    +---------------------+     +-------+--------------+
-#    | action              |     | abstract-file-target |
-#    +=====================|   * +======================+
-#    | action-name         |  +--+ action               |
-#    | properties          |  |  +----------------------+
-#    +---------------------+--+  | actualize-action()   |
-#    | actualize()         |0..1 +-----------+----------+
-#    | path()              |                 |
-#    | adjust-properties() | sources         |
-#    | actualize-sources() | targets         |
-#    +------+--------------+                 ^
-#           |                               / \
-#           ^                              +-+-+
-#          / \                               |
-#         +-+-+                +-------------+-------------+
-#           |                  |                           |
-#           |           +------+---------------+  +--------+-------------+
-#           |           | file-target          |  | searched-lib-target  |
-#           |           +======================+  +======================+
-#           |           | actualize-location() |  | actualize-location() |
-#           |           +----------------------+  +----------------------+
-#           |
-#         +-+------------------------------+
-#         |                                |
-#    +----+----------------+     +---------+-----------+
-#    | compile-action      |     | link-action         |
-#    +=====================+     +=====================+
-#    | adjust-properties() |     | adjust-properties() |
-#    +---------------------+     | actualize-sources() |
-#                                +---------------------+
-#
-# The 'compile-action' and 'link-action' classes are not defined here but in
-# builtin.jam modules. They are shown in the diagram to give the big picture.
-
-
-# Models a potential target. It can be converted into a Jam target and used in
-# building, if needed. However, it can be also dropped, which allows us to
-# search for different transformations and select only one.
-#
-class virtual-target
-{
-    import scanner ;
-    import sequence ;
-    import utility ;
-    import virtual-target ;
-
-    rule __init__ (
-          name     # Target/project name.
-        : project  # Project to which this target belongs.
-    )
-    {
-        self.name = $(name) ;
-        self.project = $(project) ;
-        self.dependencies = ;
-    }
-
-    # Name of this target.
-    #
-    rule name ( )
-    {
-        return $(self.name) ;
-    }
-
-    # Project of this target.
-    #
-    rule project ( )
-    {
-        return $(self.project) ;
-    }
-
-    # Adds additional 'virtual-target' instances this one depends on.
-    #
-    rule depends ( d + )
-    {
-        self.dependencies = [ sequence.merge $(self.dependencies) :
-            [ sequence.insertion-sort $(d) ] ] ;
-    }
-
-    rule dependencies ( )
-    {
-        return $(self.dependencies) ;
-    }
-    
-    rule always ( )
-    {
-        .always = 1 ;
-    }
-    
-    # Generates all the actual targets and sets up build actions for this
-    # target.
-    #
-    # If 'scanner' is specified, creates an additional target with the same
-    # location as the actual target, which will depend on the actual target and
-    # be associated with a 'scanner'. That additional target is returned. See
-    # the docs (#dependency_scanning) for rationale. Target must correspond to a
-    # file if 'scanner' is specified.
-    #
-    # If scanner is not specified then the actual target is returned.
-    #
-    rule actualize ( scanner ? )
-    {
-        local actual-name = [ actualize-no-scanner ] ;
-        
-        if $(.always)
-        {
-            ALWAYS $(actual-name) ;
-        }
-        
-        if ! $(scanner)
-        {
-            return $(actual-name) ;
-        }
-        else
-        {
-            # Add the scanner instance to the grist for name.
-            local g = [ sequence.join
-                [ utility.ungrist $(actual-name:G) ] $(scanner) : - ] ;
-            local name = $(actual-name:G=$(g)) ;
-
-            if ! $(self.made.$(name))
-            {
-                self.made.$(name) = true ;
-
-                DEPENDS $(name) : $(actual-name) ;
-
-                actualize-location $(name) ;
-
-                scanner.install $(scanner) : $(name) $(__name__) ;
-            }
-            return $(name) ;
-        }
-    }
-
-# private: (overridables)
-
-    # Sets up build actions for 'target'. Should call appropriate rules and set
-    # target variables.
-    #
-    rule actualize-action ( target )
-    {
-        errors.error "method should be defined in derived classes" ;
-    }
-
-    # Sets up variables on 'target' which specify its location.
-    #
-    rule actualize-location ( target )
-    {
-        errors.error "method should be defined in derived classes" ;
-    }
-
-    # If the target is a generated one, returns the path where it will be
-    # generated. Otherwise, returns an empty list.
-    #
-    rule path ( )
-    {
-        errors.error "method should be defined in derived classes" ;
-    }
-
-    # Returns the actual target name to be used in case when no scanner is
-    # involved.
-    #
-    rule actual-name ( )
-    {
-        errors.error "method should be defined in derived classes" ;
-    }
-
-# implementation
-    rule actualize-no-scanner ( )
-    {
-        # In fact, we just need to merge virtual-target with
-        # abstract-file-target as the latter is the only class derived from the
-        # former. But that has been left for later.
-	
-        errors.error "method should be defined in derived classes" ;
-    }
-}
-
-
-# Target corresponding to a file. The exact mapping for file is not yet
-# specified in this class. (TODO: Actually, the class name could be better...)
-#
-# May be a source file (when no action is specified) or a derived file
-# (otherwise).
-#
-# The target's grist is a concatenation of its project's location, action
-# properties (for derived targets) and, optionally, value identifying the main
-# target.
-#
-class abstract-file-target : virtual-target
-{
-    import project ;
-    import regex ;
-    import sequence ;
-    import path ;
-    import type ;
-    import property-set ;
-    import indirect ;
-
-    rule __init__ (
-         name     # Target's name.
-         exact ?  # If non-empty, the name is exactly the name created file
-                  # should have. Otherwise, the '__init__' method will add a
-                  # suffix obtained from 'type' by calling
-                  # 'type.generated-target-suffix'.
-        : type ?  # Target's type.
-        : project
-        : action ?
-    )
-    {
-        virtual-target.__init__ $(name) : $(project) ;
-
-        self.type = $(type) ;
-        self.action = $(action) ;
-        if $(action)
-        {
-            $(action).add-targets $(__name__) ;
-
-            if $(self.type) && ! $(exact)
-            {
-                _adjust-name $(name) ;
-            }
-        }
-    }
-
-    rule type ( )
-    {
-        return $(self.type) ;
-    }
-
-    # Sets the path. When generating target name, it will override any path
-    # computation from properties.
-    #
-    rule set-path ( path )
-    {
-        self.path = [ path.native $(path) ] ;
-    }
-
-    # Returns the currently set action.
-    #
-    rule action ( )
-    {
-        return $(self.action) ;
-    }
-
-    # Sets/gets the 'root' flag. Target is root if it directly corresponds to
-    # some variant of a main target.
-    #
-    rule root ( set ? )
-    {
-        if $(set)
-        {
-            self.root = true ;
-        }
-        return $(self.root) ;
-    }
-
-    # Gets or sets the subvariant which created this target. Subvariant is set
-    # when target is brought into existance and is never changed after that. In
-    # particular, if a target is shared by a subvariant, only the first is
-    # stored.
-    #
-    rule creating-subvariant ( s ?  # If specified, specifies the value to set,
-                                    # which should be a 'subvariant' class
-                                    # instance.
-                             )
-    {
-        if $(s) && ! $(self.creating-subvariant)
-        {
-            self.creating-subvariant = $(s) ;
-        }
-        return $(self.creating-subvariant) ;
-    }
-
-    rule actualize-action ( target )
-    {
-        if $(self.action)
-        {
-            $(self.action).actualize ;
-        }
-    }
-
-    # Return a human-readable representation of this target. If this target has
-    # an action, that is:
-    #
-    #    { <action-name>-<self.name>.<self.type> <action-sources>... }
-    #
-    # otherwise, it is:
-    #
-    #    { <self.name>.<self.type> }
-    #
-    rule str ( )
-    {
-        local action = [ action ] ;
-        local name-dot-type = [ sequence.join $(self.name) "." $(self.type) ] ;
-
-        if $(action)
-        {
-            local sources     = [ $(action).sources     ] ;
-            local action-name = [ $(action).action-name ] ;
-
-            local ss ;
-            for local s in $(sources)
-            {
-                ss += [ $(s).str ] ;
-            }
-
-            return "{" $(action-name)-$(name-dot-type) $(ss) "}" ;
-        }
-        else
-        {
-            return "{" $(name-dot-type) "}" ;
-        }
-    }
-
-    rule less ( a )
-    {
-        if [ str ] < [ $(a).str ]
-        {
-            return true ;
-        }
-    }
-
-    rule equal ( a )
-    {
-        if [ str ] = [ $(a).str ]
-        {
-            return true ;
-        }
-    }
-
-# private:
-    rule actual-name ( )
-    {
-        if ! $(self.actual-name)
-        {
-            local grist = [ grist ] ;
-            local basename = [ path.native $(self.name) ] ;
-            self.actual-name = <$(grist)>$(basename) ;
-        }
-        return $(self.actual-name) ;
-    }
-
-    # Helper to 'actual-name', above. Computes a unique prefix used to
-    # distinguish this target from other targets with the same name creating
-    # different files.
-    #
-    rule grist ( )
-    {
-        # Depending on target, there may be different approaches to generating
-        # unique prefixes. We generate prefixes in the form:
-        # <one letter approach code> <the actual prefix>
-        local path = [ path ] ;
-        if $(path)
-        {
-            # The target will be generated to a known path. Just use the path
-            # for identification, since path is as unique as it can get.
-            return p$(path) ;
-        }
-        else
-        {
-            # File is either source, which will be searched for, or is not a
-            # file at all. Use the location of project for distinguishing.
-            local project-location = [ $(self.project).get location ] ;
-            local location-grist = [ sequence.join [ regex.split
-                $(project-location) "/" ] : "!" ] ;
-
-            if $(self.action)
-            {
-                local ps = [ $(self.action).properties ] ;
-                local property-grist = [ $(ps).as-path ] ;
-                # 'property-grist' can be empty when 'ps' is an empty property
-                # set.
-                if $(property-grist)
-                {
-                    location-grist = $(location-grist)/$(property-grist) ;
-                }
-            }
-
-            return l$(location-grist) ;
-        }
-    }
-
-    # Given the target name specified in constructor, returns the name which
-    # should be really used, by looking at the <tag> properties. Tag properties
-    # need to be specified as <tag>@rule-name. This makes Boost Build call the
-    # specified rule with the target name, type and properties to get the new
-    # name. If no <tag> property is specified or the rule specified by <tag>
-    # returns nothing, returns the result of calling
-    # virtual-target.add-prefix-and-suffix.
-    #
-    rule _adjust-name ( specified-name )
-    {
-        local ps ;
-        if $(self.action)
-        {
-            ps = [ $(self.action).properties ] ;
-        }
-        else
-        {
-            ps = [ property-set.empty ] ;
-        }
-
-        # We add ourselves to the properties so that any tag rule can get more
-        # direct information about the target than just that available through
-        # the properties. This is useful in implementing name changes based on
-        # the sources of the target. For example to make unique names of object
-        # files based on the source file.  --grafik
-        ps = [ property-set.create [ $(ps).raw ] <target>$(__name__) ] ;
-
-        local tag = [ $(ps).get <tag> ] ;
-
-        if $(tag)
-        {
-            local rule-name = [ MATCH ^@(.*) : $(tag) ] ;
-            if $(rule-name)
-            {
-                if $(tag[2])
-                {
-                    errors.error "<tag>@rulename is present but is not the only"
-                        "<tag> feature" ;
-                }
-
-                self.name = [ indirect.call $(rule-name) $(specified-name)
-                    : $(self.type) : $(ps) ] ;
-            }
-            else
-            {
-                errors.error
-                    "The value of the <tag> feature must be '@rule-name'" ;
-            }
-        }
-
-        # If there is no tag or the tag rule returned nothing.
-        if ! $(tag) || ! $(self.name)
-        {
-            self.name = [ virtual-target.add-prefix-and-suffix $(specified-name)
-                : $(self.type) : $(ps) ] ;
-        }
-    }
-
-    rule actualize-no-scanner ( )
-    {
-        local name = [ actual-name ] ;
-
-        # Do anything only on the first invocation.
-        if ! $(self.made.$(name))
-        {
-            self.made.$(name) = true ;
-
-            if $(self.action)
-            {
-                # For non-derived target, we do not care if there are several
-                # virtual targets that refer to the same name. One case when
-                # this is unavoidable is when the file name is main.cpp and two
-                # targets have types CPP (for compiling) and MOCCABLE_CPP (for
-                # conversion to H via Qt tools).
-                virtual-target.register-actual-name $(name) : $(__name__) ;
-            }
-
-            for local i in $(self.dependencies)
-            {
-                DEPENDS $(name) : [ $(i).actualize ] ;
-            }
-
-            actualize-location $(name) ;
-            actualize-action $(name) ;
-        }
-        return $(name) ;
-    }
-}
-
-
-# Appends the suffix appropriate to 'type/property-set' combination to the
-# specified name and returns the result.
-#
-rule add-prefix-and-suffix ( specified-name : type ? : property-set )
-{
-    local suffix = [ type.generated-target-suffix $(type) : $(property-set) ] ;
-
-    # Handle suffixes for which no leading dot is desired. Those are specified
-    # by enclosing them in <...>.  Needed by python so it can create "_d.so"
-    # extensions, for example.
-    if $(suffix:G)
-    {
-        suffix = [ utility.ungrist $(suffix) ] ;
-    }
-    else
-    {
-        suffix = .$(suffix) ;
-    }
-
-    local prefix = [ type.generated-target-prefix $(type) : $(property-set) ] ;
-
-    if  [ MATCH ^($(prefix)) : $(specified-name) ]
-    {
-        prefix = ;
-    }
-    return $(prefix:E="")$(specified-name)$(suffix:E="") ;
-}
-
-
-# File targets with explicitly known location.
-#
-# The file path is determined as
-#    * Value passed to the 'set-path' method, if any.
-#    * For derived files, project's build dir, joined with components that
-#      describe action properties. If free properties are not equal to the
-#      project's reference properties an element with the name of the main
-#      target is added.
-#    * For source files, project's source dir.
-#
-# The file suffix is determined as:
-#     * The value passed to the 'suffix' method, if any.
-#     * The suffix corresponding to the target's type.
-#
-class file-target : abstract-file-target
-{
-    import "class" : new ;
-    import common ;
-    import errors ;
-
-    rule __init__ (
-        name exact ?
-        : type ?  # Optional type for this target.
-        : project
-        : action ?
-        : path ?
-    )
-    {
-        abstract-file-target.__init__ $(name) $(exact) : $(type) : $(project) :
-            $(action) ;
-
-        self.path = $(path) ;
-    }
-
-    rule clone-with-different-type ( new-type )
-    {
-        return [ new file-target $(self.name) exact : $(new-type) :
-            $(self.project) : $(self.action) : $(self.path) ] ;
-    }
-
-    rule actualize-location ( target )
-    {
-        if $(self.action)
-        {
-            # This is a derived file.
-            local path = [ path ] ;
-            LOCATE on $(target) = $(path) ;
-
-            # Make sure the path exists.
-            DEPENDS $(target) : $(path) ;
-            common.MkDir $(path) ;
-
-            # It is possible that the target name includes a directory too, for
-            # example when installing headers. Create that directory.
-            if $(target:D)
-            {
-                local d = $(target:D) ;
-                d = $(d:R=$(path)) ;
-                DEPENDS $(target) : $(d) ;
-                common.MkDir $(d) ;
-            }
-
-            # For a real file target, we create a fake target depending on the
-            # real target. This allows us to run
-            #
-            #    bjam hello.o
-            #
-            # without trying to guess the name of the real target. Note that the
-            # target has no directory name and uses a special <e> grist.
-            #
-            # First, that means that "bjam hello.o" will build all known hello.o
-            # targets. Second, the <e> grist makes sure this target will not be
-            # confused with other targets, for example, if we have subdir 'test'
-            # with target 'test' in it that includes a 'test.o' file, then the
-            # target for directory will be just 'test' the target for test.o
-            # will be <ptest/bin/gcc/debug>test.o and the target we create below
-            # will be <e>test.o
-            DEPENDS $(target:G=e) : $(target) ;
-            # Allow bjam <path-to-file>/<file> to work. This will not catch all
-            # possible ways to refer to the path (relative/absolute, extra ".",
-            # various "..", but should help in obvious cases.
-            DEPENDS $(target:G=e:R=$(path)) : $(target) ;
-        }
-        else
-        {
-            SEARCH on $(target) = [ path.native $(self.path) ] ;
-        }
-    }
-
-    # Returns the directory for this target.
-    #
-    rule path ( )
-    {
-        if ! $(self.path)
-        {
-            if $(self.action)
-            {
-                local p = [ $(self.action).properties ] ;
-                local path,relative-to-build-dir = [ $(p).target-path ] ;
-                local path = $(path,relative-to-build-dir[1]) ;
-                local relative-to-build-dir = $(path,relative-to-build-dir[2]) ;
-
-                if $(relative-to-build-dir)
-                {
-                    path = [ path.join [ $(self.project).build-dir ] $(path) ] ;
-                }
-
-                self.path = [ path.native $(path) ] ;
-            }
-        }
-        return $(self.path) ;
-     }
-}
-
-
-class notfile-target : abstract-file-target
-{
-    rule __init__ ( name : project : action ? )
-    {
-        abstract-file-target.__init__ $(name) : : $(project) : $(action) ;
-    }
-
-    # Returns nothing to indicate that the target's path is not known.
-    #
-    rule path ( )
-    {
-        return ;
-    }
-
-    rule actualize-location ( target )
-    {
-        NOTFILE $(target) ;
-        ALWAYS $(target) ;
-        # TEMPORARY $(target) ;
-        NOUPDATE $(target) ;
-    }
-}
-
-
-# Class representing an action. Both 'targets' and 'sources' should list
-# instances of 'virtual-target'. Action name should name a rule with this
-# prototype:
-#     rule action-name ( targets + : sources * : properties * )
-# Targets and sources are passed as actual Jam targets. The rule may not
-# establish additional dependency relationships.
-#
-class action
-{
-    import "class" ;
-    import errors ;
-    import type ;
-    import toolset ;
-    import property-set ;
-    import indirect ;
-    import path ;
-    import set : difference ;
-
-    rule __init__ ( sources * : action-name + : property-set ? )
-    {
-        self.sources = $(sources) ;
-
-        self.action-name = [ indirect.make-qualified $(action-name) ] ;
-
-        if ! $(property-set)
-        {
-            property-set = [ property-set.empty ] ;
-        }
-
-        if ! [ class.is-instance $(property-set) ]
-        {
-            errors.error "Property set instance required" ;
-        }
-
-        self.properties = $(property-set) ;
-    }
-
-    rule add-targets ( targets * )
-    {
-        self.targets += $(targets) ;
-    }
-
-    rule replace-targets ( old-targets * : new-targets * )
-    {
-        self.targets = [ set.difference $(self.targets) : $(old-targets) ] ;
-        self.targets += $(new-targets) ;
-    }
-
-    rule targets ( )
-    {
-        return $(self.targets) ;
-    }
-
-    rule sources ( )
-    {
-        return $(self.sources) ;
-    }
-
-    rule action-name ( )
-    {
-        return $(self.action-name) ;
-    }
-
-    rule properties ( )
-    {
-        return $(self.properties) ;
-    }
-
-    # Generates actual build instructions.
-    #
-    rule actualize ( )
-    {
-        if ! $(self.actualized)
-        {
-            self.actualized = true ;
-
-            local ps = [ properties ] ;
-            local properties = [ adjust-properties $(ps) ] ;
-
-            local actual-targets ;
-            for local i in [ targets ]
-            {
-                actual-targets += [ $(i).actualize ] ;
-            }
-
-            actualize-sources [ sources ] : $(properties) ;
-
-            DEPENDS $(actual-targets) : $(self.actual-sources)
-                $(self.dependency-only-sources) ;
-            
-            # This works around a bug with -j and actions that
-            # produce multiple target, where:
-            # - dependency on the first output is found, and
-            #   the action is started
-            # - dependency on the second output is found, and
-            #   bjam noticed that command is already running
-            # - instead of waiting for the command, dependents
-            #   of the second targets are immediately updated.
-            if $(actual-targets[2])
-            {                
-                INCLUDES $(actual-targets) : $(actual-targets) ;
-            }
-            
-            # Action name can include additional argument to rule, which should
-            # not be passed to 'set-target-variables'
-            toolset.set-target-variables
-                [ indirect.get-rule $(self.action-name[1]) ] $(actual-targets)
-                : $(properties) ;
-
-            # Reflect ourselves in a variable for the target. This allows
-            # looking up additional info for the action given the raw target.
-            # For example to debug or output action information from action
-            # rules.
-            .action on $(actual-targets) = $(__name__) ;
-
-            indirect.call $(self.action-name) $(actual-targets)
-                : $(self.actual-sources) : [ $(properties).raw ] ;
-
-            # Since we set up the creating action here, we set up the action for
-            # cleaning up as well.
-            common.Clean clean-all : $(actual-targets) ;
-        }
-    }
-
-    # Helper for 'actualize-sources'. For each passed source, actualizes it with
-    # the appropriate scanner. Returns the actualized virtual targets.
-    #
-    rule actualize-source-type ( sources * : property-set )
-    {
-        local result = ;
-        for local i in $(sources)
-        {
-            local scanner ;
-            if [ $(i).type ]
-            {
-                scanner = [ type.get-scanner [ $(i).type ] : $(property-set) ] ;
-            }
-            result += [ $(i).actualize $(scanner) ] ;
-        }
-        return $(result) ;
-    }
-
-    # Creates actual Jam targets for sources. Initializes the following member
-    # variables:
-    #   'self.actual-sources'          -- sources passed to the updating action.
-    #   'self.dependency-only-sources' -- sources marked as dependencies, but
-    #                                     are not used otherwise.
-    #
-    # New values will be *appended* to the variables. They may be non-empty if
-    # caller wants it.
-    #
-    rule actualize-sources ( sources * : property-set )
-    {
-        local dependencies = [ $(self.properties).get <dependency> ] ;
-
-        self.dependency-only-sources +=
-            [ actualize-source-type $(dependencies) : $(property-set) ] ;
-        self.actual-sources +=
-            [ actualize-source-type $(sources) : $(property-set) ] ;
-
-        # This is used to help bjam find dependencies in generated headers and
-        # other main targets, e.g. in:
-        #
-        #   make a.h : ....... ;
-        #   exe hello : hello.cpp : <implicit-dependency>a.h ;
-        #
-        # For bjam to find the dependency the generated target must be
-        # actualized (i.e. have its Jam target constructed). In the above case,
-        # if we are building just hello ("bjam hello"), 'a.h' will not be
-        # actualized unless we do it here.
-        local implicit = [ $(self.properties).get <implicit-dependency> ] ;
-        for local i in $(implicit)
-        {
-            $(i:G=).actualize ;
-        }
-    }
-
-    # Determines real properties when trying to build with 'properties'. This is
-    # the last chance to fix properties, for example to adjust includes to get
-    # generated headers correctly. Default implementation simply returns its
-    # argument.
-    #
-    rule adjust-properties ( property-set )
-    {
-        return $(property-set) ;
-    }
-}
-
-
-# Action class which does nothing --- it produces the targets with specific
-# properties out of nowhere. It is needed to distinguish virtual targets with
-# different properties that are known to exist and have no actions which create
-# them.
-#
-class null-action : action
-{
-    rule __init__ ( property-set ? )
-    {
-        action.__init__ : .no-action : $(property-set) ;
-    }
-
-    rule actualize ( )
-    {
-        if ! $(self.actualized)
-        {
-            self.actualized = true ;
-            for local i in [ targets ]
-            {
-                $(i).actualize ;
-            }
-        }
-    }
-}
-
-
-# Class which acts exactly like 'action', except that its sources are not
-# scanned for dependencies.
-#
-class non-scanning-action : action
-{
-    rule __init__ ( sources * : action-name + : property-set ? )
-    {
-        action.__init__ $(sources) : $(action-name) : $(property-set) ;
-    }
-
-    rule actualize-source-type ( sources * : property-set )
-    {
-        local result ;
-        for local i in $(sources)
-        {
-            result += [ $(i).actualize ] ;
-        }
-        return $(result) ;
-    }
-}
-
-
-# Creates a virtual target with an appropriate name and type from 'file'. If a
-# target with that name in that project already exists, returns that already
-# created target.
-#
-# FIXME: a more correct way would be to compute the path to the file, based on
-# name and source location for the project, and use that path to determine if
-# the target has already been created. This logic should be shared with how we
-# usually find targets identified by a specific target id. It should also be
-# updated to work correctly when the file is specified using both relative and
-# absolute paths.
-#
-# TODO: passing a project with all virtual targets is starting to be annoying.
-#
-rule from-file ( file : file-loc : project )
-{
-    import type ;  # Had to do this here to break a circular dependency.
-
-    # Check whether we already created a target corresponding to this file.
-    local path = [ path.root [ path.root $(file) $(file-loc) ] [ path.pwd ] ] ;
-
-    if $(.files.$(path))
-    {
-        return $(.files.$(path)) ;
-    }
-    else
-    {
-        local name = [ path.make $(file) ] ;
-        local type = [ type.type $(file) ] ;
-        local result ;
-
-        result = [ new file-target $(file) : $(type) : $(project) : :
-            $(file-loc) ] ;
-
-        .files.$(path) = $(result) ;
-        return $(result) ;
-    }
-}
-
-
-# Registers a new virtual target. Checks if there is already a registered target
-# with the same name, type, project and subvariant properties as well as the
-# same sources and equal action. If such target is found it is returned and a
-# new 'target' is not registered. Otherwise, 'target' is registered and
-# returned.
-#
-rule register ( target )
-{
-    local signature = [ sequence.join
-        [ $(target).path ] [ $(target).name ] : - ] ;
-
-    local result ;
-    for local t in $(.cache.$(signature))
-    {
-        local a1 = [ $(t).action ] ;
-        local a2 = [ $(target).action ] ;
-
-        if ! $(result)
-        {
-            if ! $(a1) && ! $(a2)
-            {
-                result = $(t) ;
-            }
-            else
-            {
-                if $(a1) && $(a2) &&
-                    ( [ $(a1).action-name ] = [ $(a2).action-name ] ) &&
-                    ( [ $(a1).sources     ] = [ $(a2).sources     ] )
-                {
-                    local ps1 = [ $(a1).properties ] ;
-                    local ps2 = [ $(a2).properties ] ;
-                    local p1 = [ $(ps1).base ] [ $(ps1).free ] [ set.difference
-                        [ $(ps1).dependency ] : [ $(ps1).incidental ] ] ;
-                    local p2 = [ $(ps2).base ] [ $(ps2).free ] [ set.difference
-                        [ $(ps2).dependency ] : [ $(ps2).incidental ] ] ;
-                    if $(p1) = $(p2)
-                    {
-                        result = $(t) ;
-                    }
-                }
-            }
-        }
-    }
-
-    if ! $(result)
-    {
-        .cache.$(signature) += $(target) ;
-        result = $(target) ;
-    }
-
-    .recent-targets += $(result) ;
-    .all-targets += $(result) ;
-
-    return $(result) ;
-}
-
-
-# Each target returned by 'register' is added to the .recent-targets list,
-# returned by this function. This allows us to find all virtual targets created
-# when building a specific main target, even those constructed only as
-# intermediate targets.
-#
-rule recent-targets ( )
-{
-    return $(.recent-targets) ;
-}
-
-
-rule clear-recent-targets ( )
-{
-    .recent-targets = ;
-}
-
-
-# Returns all virtual targets ever created.
-#
-rule all-targets ( )
-{
-    return $(.all-targets) ;
-}
-
-
-# Returns all targets from 'targets' with types equal to 'type' or derived from
-# it.
-#
-rule select-by-type ( type : targets * )
-{
-    local result ;
-    for local t in $(targets)
-    {
-        if [ type.is-subtype [ $(t).type ] $(type) ]
-        {
-            result += $(t) ;
-        }
-    }
-    return $(result) ;
-}
-
-
-rule register-actual-name ( actual-name : virtual-target )
-{
-    if $(.actual.$(actual-name))
-    {
-        local cs1 = [ $(.actual.$(actual-name)).creating-subvariant ] ;
-        local cs2 = [ $(virtual-target).creating-subvariant ] ;
-        local cmt1 = [ $(cs1).main-target ] ;
-        local cmt2 = [ $(cs2).main-target ] ;
-
-        local action1 = [ $(.actual.$(actual-name)).action ] ;
-        local action2 = [ $(virtual-target).action ] ;
-        local properties-added ;
-        local properties-removed ;
-        if $(action1) && $(action2)
-        {
-            local p1 = [ $(action1).properties ] ;
-            p1 = [ $(p1).raw ] ;
-            local p2 = [ $(action2).properties ] ;
-            p2 = [ $(p2).raw ] ;
-            properties-removed = [ set.difference $(p1) : $(p2) ] ;
-            properties-removed ?= "none" ;
-            properties-added = [ set.difference $(p2) : $(p1) ] ;
-            properties-added ?= "none" ;
-        }
-        errors.error "Duplicate name of actual target:" $(actual-name)
-            : "previous virtual target" [ $(.actual.$(actual-name)).str ]
-            : "created from"            [ $(cmt1).full-name ]
-            : "another virtual target"  [ $(virtual-target).str ]
-            : "created from"            [ $(cmt2).full-name ]
-            : "added properties:"       $(properties-added)
-            : "removed properties:"     $(properties-removed) ;
-    }
-    else
-    {
-        .actual.$(actual-name) = $(virtual-target) ;
-    }
-}
-
-
-# Traverses the dependency graph of 'target' and return all targets that will be
-# created before this one is created. If the root of some dependency graph is
-# found during traversal, it is either included or not, depending on the
-# 'include-roots' value. In either case traversal stops at root targets, i.e.
-# root target sources are not traversed.
-#
-rule traverse ( target : include-roots ? : include-sources ? )
-{
-    local result ;
-    if [ $(target).action ]
-    {
-        local action = [ $(target).action ] ;
-        # This includes the 'target' as well.
-        result += [ $(action).targets ] ;
-
-        for local t in [ $(action).sources ]
-        {
-            if ! [ $(t).root ]
-            {
-                result += [ traverse $(t) : $(include-roots) : $(include-sources) ] ;
-            }
-            else if $(include-roots)
-            {
-                result += $(t) ;
-            }
-        }
-    }
-    else if $(include-sources)
-    {
-        result = $(target) ;
-    }
-    return $(result) ;
-}
-
-
-# Takes an 'action' instance and creates a new instance of it and all targets
-# produced by the action. The rule-name and properties are set to
-# 'new-rule-name' and 'new-properties', if those are specified. Returns the
-# cloned action.
-#
-rule clone-action ( action : new-project : new-action-name ? : new-properties ? )
-{
-    if ! $(new-action-name)
-    {
-        new-action-name = [ $(action).action-name ] ;
-    }
-    if ! $(new-properties)
-    {
-        new-properties = [ $(action).properties ] ;
-    }
-
-    local action-class = [ modules.peek $(action) : __class__ ] ;
-    local cloned-action = [ class.new $(action-class)
-        [ $(action).sources ] : $(new-action-name) : $(new-properties) ] ;
-
-    local cloned-targets ;
-    for local target in [ $(action).targets ]
-    {
-        local n = [ $(target).name ] ;
-        # Do not modify produced target names.
-        local cloned-target = [ class.new file-target $(n) exact :
-            [ $(target).type ] : $(new-project) : $(cloned-action) ] ;
-        local d = [ $(target).dependencies ] ;
-        if $(d)
-        {
-            $(cloned-target).depends $(d) ;
-        }
-        $(cloned-target).root [ $(target).root ] ;
-        $(cloned-target).creating-subvariant [ $(target).creating-subvariant ] ;
-
-        cloned-targets += $(cloned-target) ;
-    }
-
-    return $(cloned-action) ;
-}
-
-
-class subvariant
-{
-    import sequence ;
-    import type ;
-
-    rule __init__ ( main-target       # The instance of main-target class.
-        : property-set                # Properties requested for this target.
-        : sources *
-        : build-properties            # Actually used properties.
-        : sources-usage-requirements  # Properties propagated from sources.
-        : created-targets * )         # Top-level created targets.
-    {
-        self.main-target = $(main-target) ;
-        self.properties = $(property-set) ;
-        self.sources = $(sources) ;
-        self.build-properties = $(build-properties) ;
-        self.sources-usage-requirements = $(sources-usage-requirements) ;
-        self.created-targets = $(created-targets) ;
-
-        # Pre-compose a list of other dependency graphs this one depends on.
-        local deps = [ $(build-properties).get <implicit-dependency> ] ;
-        for local d in $(deps)
-        {
-            self.other-dg += [ $(d:G=).creating-subvariant ] ;
-        }
-
-        self.other-dg = [ sequence.unique $(self.other-dg) ] ;
-    }
-
-    rule main-target ( )
-    {
-        return $(self.main-target) ;
-    }
-
-    rule created-targets ( )
-    {
-        return $(self.created-targets) ;
-    }
-
-    rule requested-properties ( )
-    {
-        return $(self.properties) ;
-    }
-
-    rule build-properties ( )
-    {
-        return $(self.build-properties) ;
-    }
-
-    rule sources-usage-requirements ( )
-    {
-        return $(self.sources-usage-requirements) ;
-    }
-
-    rule set-usage-requirements ( usage-requirements )
-    {
-        self.usage-requirements = $(usage-requirements) ;
-    }
-
-    rule usage-requirements ( )
-    {
-        return $(self.usage-requirements) ;
-    }
-
-    # Returns all targets referenced by this subvariant, either directly or
-    # indirectly, and either as sources, or as dependency properties. Targets
-    # referred to using the dependency property are returned as properties, not
-    # targets.
-    #
-    rule all-referenced-targets ( theset )
-    {
-        # Find directly referenced targets.
-        local deps = [ $(self.build-properties).dependency ] ;
-        local all-targets = $(self.sources) $(deps) ;
-
-        # Find other subvariants.
-        local r ;
-        for local t in $(all-targets)
-        {
-            if ! [ $(theset).contains $(t) ]
-            {
-                $(theset).add $(t) ;
-                r += [ $(t:G=).creating-subvariant ] ;
-            }            
-        }
-        r = [ sequence.unique $(r) ] ;
-        for local s in $(r)
-        {
-            if $(s) != $(__name__)
-            {
-                $(s).all-referenced-targets $(theset) ;
-            }
-        }
-    }
-
-    # Returns the properties specifying implicit include paths to generated
-    # headers. This traverses all targets in this subvariant and subvariants
-    # referred by <implcit-dependecy> properties. For all targets of type
-    # 'target-type' (or for all targets, if 'target-type' is not specified), the
-    # result will contain <$(feature)>path-to-that-target.
-    #
-    rule implicit-includes ( feature : target-type ? )
-    {
-        local key = ii$(feature)-$(target-type:E="") ;
-        if ! $($(key))-is-not-empty
-        {
-            local target-paths = [ all-target-directories $(target-type) ] ;
-            target-paths = [ sequence.unique $(target-paths) ] ;
-            local result = $(target-paths:G=$(feature)) ;
-            if ! $(result)
-            {
-                result = "" ;
-            }
-            $(key) = $(result) ;
-        }
-        if $($(key)) = ""
-        {
-            return ;
-        }
-        else
-        {
-            return $($(key)) ;
-        }
-    }
-
-    rule all-target-directories ( target-type ? )
-    {
-        if ! $(self.target-directories)
-        {
-            compute-target-directories $(target-type) ;
-        }
-        return $(self.target-directories) ;
-    }
-
-    rule compute-target-directories ( target-type ? )
-    {
-        local result ;
-        for local t in $(self.created-targets)
-        {
-            # Skip targets of the wrong type.
-            if ! $(target-type) ||
-                [ type.is-derived [ $(t).type ] $(target-type) ]
-            {
-                result = [ sequence.merge $(result) : [ $(t).path ] ] ;
-            }
-        }
-        for local d in $(self.other-dg)
-        {
-            result += [ $(d).all-target-directories $(target-type) ] ;
-        }
-        self.target-directories = $(result) ;
-    }
-}
diff --git a/jam-files/boost-build/build/virtual_target.py b/jam-files/boost-build/build/virtual_target.py
deleted file mode 100644
index 51dff037..00000000
--- a/jam-files/boost-build/build/virtual_target.py
+++ /dev/null
@@ -1,1118 +0,0 @@
-# Status: ported.
-# Base revision: 64488.
-# 
-#  Copyright (C) Vladimir Prus 2002. Permission to copy, use, modify, sell and
-#  distribute this software is granted provided this copyright notice appears in
-#  all copies. This software is provided "as is" without express or implied
-#  warranty, and with no claim as to its suitability for any purpose.
-
-#  Implements virtual targets, which correspond to actual files created during
-#  build, but are not yet targets in Jam sense. They are needed, for example,
-#  when searching for possible transormation sequences, when it's not known
-#  if particular target should be created at all.
-#
-#
-#                       +--------------------------+
-#                       | VirtualTarget           |
-#                       +==========================+
-#                       | actualize                |
-#                       +--------------------------+
-#                       | actualize_action() = 0   |
-#                       | actualize_location() = 0 |
-#                       +----------------+---------+
-#                                        |
-#                                        ^
-#                                       / \
-#                                      +-+-+
-#                                        |
-#    +---------------------+     +-------+--------------+
-#    | Action              |     | AbstractFileTarget   |
-#    +=====================|   * +======================+
-#    | action_name         |  +--+ action               |
-#    | properties          |  |  +----------------------+
-#    +---------------------+--+  | actualize_action()   |
-#    | actualize()         |0..1 +-----------+----------+
-#    | path()              |                 |
-#    | adjust_properties() | sources         |
-#    | actualize_sources() | targets         |
-#    +------+--------------+                 ^
-#           |                               / \
-#           ^                              +-+-+
-#          / \                               |
-#         +-+-+                +-------------+-------------+
-#           |                  |                           |
-#           |           +------+---------------+  +--------+-------------+
-#           |           | FileTarget           |  | SearchedLibTarget    |
-#           |           +======================+  +======================+
-#           |           | actualize-location() |  | actualize-location() |
-#           |           +----------------------+  +----------------------+
-#           |
-#         +-+------------------------------+
-#         |                                |
-#    +----+----------------+     +---------+-----------+
-#    | CompileAction       |     | LinkAction          |
-#    +=====================+     +=====================+
-#    | adjust_properties() |     | adjust_properties() |
-#    +---------------------+     | actualize_sources() |
-#                                +---------------------+
-#
-# The 'CompileAction' and 'LinkAction' classes are defined not here,
-# but in builtin.jam modules. They are shown in the diagram to give
-# the big picture.
-
-import bjam
-
-import re
-import os.path
-import string
-import types
-
-from b2.util import path, utility, set
-from b2.util.utility import add_grist, get_grist, ungrist, replace_grist, get_value
-from b2.util.sequence import unique
-from b2.tools import common
-from b2.exceptions import *
-import b2.build.type
-import b2.build.property_set as property_set
-
-import b2.build.property as property
-
-from b2.manager import get_manager
-from b2.util import bjam_signature
-
-__re_starts_with_at = re.compile ('^@(.*)')
-
-class VirtualTargetRegistry:
-    def __init__ (self, manager):
-        self.manager_ = manager
-        
-        # A cache for FileTargets
-        self.files_ = {}
-
-        # A cache for targets.
-        self.cache_ = {}
-
-        # A map of actual names to virtual targets.
-        # Used to make sure we don't associate same
-        # actual target to two virtual targets.
-        self.actual_ = {}
-
-        self.recent_targets_ = []
-        
-        # All targets ever registed
-        self.all_targets_ = []
-
-        self.next_id_ = 0
-        
-    def register (self, target):
-        """ Registers a new virtual target. Checks if there's already registered target, with the same
-            name, type, project and subvariant properties, and also with the same sources
-            and equal action. If such target is found it is retured and 'target' is not registered.
-            Otherwise, 'target' is registered and returned.
-        """
-        if target.path():
-            signature = target.path() + "-" + target.name()
-        else:
-            signature = "-" + target.name()
-
-        result = None
-        if not self.cache_.has_key (signature):
-            self.cache_ [signature] = []
-
-        for t in self.cache_ [signature]:
-            a1 = t.action ()
-            a2 = target.action ()
-
-            # TODO: why are we checking for not result?
-            if not result:
-                if not a1 and not a2:
-                    result = t
-                else:
-                    if a1 and a2 and a1.action_name () == a2.action_name () and a1.sources () == a2.sources ():
-                        ps1 = a1.properties ()
-                        ps2 = a2.properties ()
-                        p1 = ps1.base () + ps1.free () +\
-                            b2.util.set.difference(ps1.dependency(), ps1.incidental())
-                        p2 = ps2.base () + ps2.free () +\
-                            b2.util.set.difference(ps2.dependency(), ps2.incidental())
-                        if p1 == p2:
-                            result = t
-        
-        if not result:
-            self.cache_ [signature].append (target)
-            result = target
-
-        # TODO: Don't append if we found pre-existing target?
-        self.recent_targets_.append(result)
-        self.all_targets_.append(result)
-    
-        return result
-
-    def from_file (self, file, file_location, project):
-        """ Creates a virtual target with appropriate name and type from 'file'.
-            If a target with that name in that project was already created, returns that already
-            created target.
-            TODO: more correct way would be to compute path to the file, based on name and source location
-            for the project, and use that path to determine if the target was already created.
-            TODO: passing project with all virtual targets starts to be annoying.
-        """
-        # Check if we've created a target corresponding to this file.
-        path = os.path.join(os.getcwd(), file_location, file)
-        path = os.path.normpath(path)
-
-        if self.files_.has_key (path):
-            return self.files_ [path]
-
-        file_type = b2.build.type.type (file)
-
-        result = FileTarget (file, file_type, project,
-                             None, file_location)       
-        self.files_ [path] = result
-                
-        return result
-
-    def recent_targets(self):
-        """Each target returned by 'register' is added to a list of
-        'recent-target', returned by this function. So, this allows
-        us to find all targets created when building a given main
-        target, even if the target."""
-
-        return self.recent_targets_
-
-    def clear_recent_targets(self):
-        self.recent_targets_ = []
-
-    def all_targets(self):
-        # Returns all virtual targets ever created
-        return self.all_targets_
-
-    # Returns all targets from 'targets' with types
-    # equal to 'type' or derived from it.
-    def select_by_type(self, type, targets):
-        return [t for t in targets if b2.build.type.is_sybtype(t.type(), type)]
-
-    def register_actual_name (self, actual_name, virtual_target):
-        if self.actual_.has_key (actual_name):
-            cs1 = self.actual_ [actual_name].creating_subvariant ()
-            cs2 = virtual_target.creating_subvariant ()
-            cmt1 = cs1.main_target ()
-            cmt2 = cs2.main_target ()            
-            
-            action1 = self.actual_ [actual_name].action ()
-            action2 = virtual_target.action ()
-            
-            properties_added = []
-            properties_removed = []
-            if action1 and action2:
-                p1 = action1.properties ()
-                p1 = p1.raw ()
-                p2 = action2.properties ()
-                p2 = p2.raw ()
-                
-                properties_removed = set.difference (p1, p2)
-                if not properties_removed: properties_removed = "none"
-
-                properties_added = set.difference (p2, p1)
-                if not properties_added: properties_added = "none"
-
-            # FIXME: Revive printing of real location.
-            get_manager().errors()(
-                "Duplicate name of actual target: '%s'\n" 
-                "previous virtual target '%s'\n"
-                "created from '%s'\n"
-                "another virtual target '%s'\n"
-                "created from '%s'\n"
-                "added properties: '%s'\n"
-                "removed properties: '%s'\n"
-                % (actual_name,
-                   self.actual_ [actual_name], "loc", #cmt1.location (),
-                   virtual_target, 
-                   "loc", #cmt2.location (),
-                   properties_added, properties_removed))
-
-        else:
-            self.actual_ [actual_name] = virtual_target
-    
-
-    def add_suffix (self, specified_name, file_type, prop_set):
-        """ Appends the suffix appropriate to 'type/property_set' combination
-            to the specified name and returns the result.
-        """
-        suffix = b2.build.type.generated_target_suffix (file_type, prop_set)
-
-        if suffix:
-            return specified_name + '.' + suffix
-
-        else:
-            return specified_name
-    
-class VirtualTarget:
-    """ Potential target. It can be converted into jam target and used in
-        building, if needed. However, it can be also dropped, which allows
-        to search for different transformation and select only one.
-        name:    name of this target.
-        project: project to which this target belongs.
-    """
-    def __init__ (self, name, project):
-        self.name_ = name
-        self.project_ = project
-        self.dependencies_ = []
-        self.always_ = False
-        
-        # Caches if dapendencies for scanners have already been set.
-        self.made_ = {}
-
-    def manager(self):
-        return self.project_.manager()
-
-    def virtual_targets(self):
-        return self.manager().virtual_targets()
-
-    def name (self):
-        """ Name of this target.
-        """
-        return self.name_
-
-    def project (self):
-        """ Project of this target.
-        """
-        return self.project_
-
-    def depends (self, d):
-        """ Adds additional instances of 'VirtualTarget' that this
-            one depends on.
-        """
-        self.dependencies_ = unique (self.dependencies_ + d).sort ()
-
-    def dependencies (self):
-        return self.dependencies_
-
-    def always(self):
-        self.always_ = True
-
-    def actualize (self, scanner = None):
-        """ Generates all the actual targets and sets up build actions for
-            this target.
-            
-            If 'scanner' is specified, creates an additional target
-            with the same location as actual target, which will depend on the
-            actual target and be associated with 'scanner'. That additional
-            target is returned. See the docs (#dependency_scanning) for rationale.
-            Target must correspond to a file if 'scanner' is specified.
-            
-            If scanner is not specified, then actual target is returned.
-        """
-        actual_name = self.actualize_no_scanner ()
-
-        if self.always_:
-            bjam.call("ALWAYS", actual_name)
-
-        if not scanner:
-            return actual_name
-
-        else:
-            # Add the scanner instance to the grist for name.
-            g = '-'.join ([ungrist(get_grist(actual_name)), str(id(scanner))])
-
-            name = replace_grist (actual_name, '<' + g + '>')
-
-            if not self.made_.has_key (name):
-                self.made_ [name] = True
-
-                self.project_.manager ().engine ().add_dependency (name, actual_name)
-
-                self.actualize_location (name)
-
-                self.project_.manager ().scanners ().install (scanner, name, str (self))
-
-            return name
-
-# private: (overridables)
-
-    def actualize_action (self, target):
-        """ Sets up build actions for 'target'. Should call appropriate rules
-            and set target variables.
-        """
-        raise BaseException ("method should be defined in derived classes")
-
-    def actualize_location (self, target):
-        """ Sets up variables on 'target' which specify its location.
-        """
-        raise BaseException ("method should be defined in derived classes")
-    
-    def path (self):
-        """ If the target is generated one, returns the path where it will be
-            generated. Otherwise, returns empty list.
-        """
-        raise BaseException ("method should be defined in derived classes")
-    
-    def actual_name (self):
-        """ Return that actual target name that should be used
-            (for the case where no scanner is involved)
-        """
-        raise BaseException ("method should be defined in derived classes")
-
-
-class AbstractFileTarget (VirtualTarget):
-    """ Target which correspond to a file. The exact mapping for file
-        is not yet specified in this class. (TODO: Actually, the class name
-        could be better...)
-        
-        May be a source file (when no action is specified), or
-        derived file (otherwise).
-        
-        The target's grist is concatenation of project's location,
-        properties of action (for derived files), and, optionally,
-        value identifying the main target.
-        
-        exact:  If non-empty, the name is exactly the name
-                created file should have. Otherwise, the '__init__'
-                method will add suffix obtained from 'type' by
-                calling 'type.generated-target-suffix'.
-                  
-        type:   optional type of this target.
-    """
-    def __init__ (self, name, type, project, action = None, exact=False):
-        VirtualTarget.__init__ (self, name, project)
-            
-        self.type_ = type
-
-        self.action_ = action
-        self.exact_ = exact
-        
-        if action:
-            action.add_targets ([self])
- 
-            if self.type and not exact:
-                self.__adjust_name (name)
-
-        
-        self.actual_name_ = None
-        self.path_ = None
-        self.intermediate_ = False
-        self.creating_subvariant_ = None
-        
-        # True if this is a root target.
-        self.root_ = False
-
-    def type (self):
-        return self.type_
-
-    def set_path (self, path):
-        """ Sets the path. When generating target name, it will override any path
-            computation from properties.
-        """
-        self.path_ = path
-
-    def action (self):
-        """ Returns the action.
-        """
-        return self.action_
-
-    def root (self, set = None):
-        """ Sets/gets the 'root' flag. Target is root is it directly correspods to some
-            variant of a main target.
-        """
-        if set:
-            self.root_ = True
-        return self.root_
-
-    def creating_subvariant (self, s = None):
-        """ Gets or sets the subvariant which created this target. Subvariant
-        is set when target is brought into existance, and is never changed
-        after that. In particual, if target is shared by subvariant, only 
-        the first is stored.
-        s:  If specified, specified the value to set,
-                which should be instance of 'subvariant' class.
-        """
-        if s and not self.creating_subvariant ():
-            if self.creating_subvariant ():
-                raise BaseException ("Attempt to change 'dg'")
-
-            else:
-                self.creating_subvariant_ = s
-
-        return self.creating_subvariant_
-
-    def actualize_action (self, target):
-        if self.action_:
-            self.action_.actualize ()
-
-    # Return a human-readable representation of this target
-    #
-    # If this target has an action, that's:
-    #
-    #    { <action-name>-<self.name>.<self.type> <action-sources>... }
-    #
-    # otherwise, it's:
-    #
-    #    { <self.name>.<self.type> }
-    #
-    def str(self):
-        a = self.action()
-
-        name_dot_type = self.name_ + "." + self.type_
-
-        if a:
-            action_name = a.action_name()
-            ss = [ s.str() for s in a.sources()]
-                       
-            return "{ %s-%s %s}" % (action_name, name_dot_type, str(ss))
-        else:
-            return "{ " + name_dot_type + " }"
-        
-# private:
-
-    def actual_name (self):
-        if not self.actual_name_:
-            self.actual_name_ = '<' + self.grist() + '>' + self.name_
-
-        return self.actual_name_
-
-    def grist (self):
-        """Helper to 'actual_name', above. Compute unique prefix used to distinguish
-            this target from other targets with the same name which create different
-            file.
-        """
-        # Depending on target, there may be different approaches to generating
-        # unique prefixes. We'll generate prefixes in the form 
-        # <one letter approach code> <the actual prefix>
-        path = self.path ()
-        
-        if path:
-            # The target will be generated to a known path. Just use the path
-            # for identification, since path is as unique as it can get.
-            return 'p' + path
-
-        else:
-            # File is either source, which will be searched for, or is not a file at
-            # all. Use the location of project for distinguishing.
-            project_location = self.project_.get ('location')
-            path_components = b2.util.path.split(project_location)
-            location_grist = '!'.join (path_components)
-            
-            if self.action_:
-                ps = self.action_.properties ()
-                property_grist = ps.as_path ()
-                # 'property_grist' can be empty when 'ps' is an empty
-                # property set.
-                if property_grist:
-                    location_grist = location_grist + '/' + property_grist
-                        
-            return 'l' + location_grist
-
-    def __adjust_name(self, specified_name):
-        """Given the target name specified in constructor, returns the
-        name which should be really used, by looking at the <tag> properties.
-        The tag properties come in two flavour:
-          - <tag>value, 
-          - <tag>@rule-name
-        In the first case, value is just added to name
-        In the second case, the specified rule is called with specified name,
-        target type and properties and should return the new name.
-        If not <tag> property is specified, or the rule specified by
-        <tag> returns nothing, returns the result of calling 
-        virtual-target.add-suffix"""
-
-        if self.action_:
-            ps = self.action_.properties()
-        else:
-            ps = property_set.empty()
-
-        # FIXME: I'm not sure how this is used, need to check with
-        # Rene to figure out how to implement
-        #~ We add ourselves to the properties so that any tag rule can get
-        #~ more direct information about the target than just that available
-        #~ through the properties. This is useful in implementing
-        #~ name changes based on the sources of the target. For example to
-        #~ make unique names of object files based on the source file.
-        #~ --grafik
-        #ps = property_set.create(ps.raw() + ["<target>%s" % "XXXX"])
-        #ps = [ property-set.create [ $(ps).raw ] <target>$(__name__) ] ;
-        
-        tag = ps.get("<tag>")
-        
-        if tag:
-
-            if len(tag) > 1:
-                get_manager().errors()(
-                    """<tag>@rulename is present but is not the only <tag> feature""")
-
-            tag = tag[0]
-            if callable(tag):
-                self.name_ = tag(specified_name, self.type_, ps)
-            else:
-                if not tag[0] == '@':
-                    self.manager_.errors()("""The value of the <tag> feature must be '@rule-nane'""")
-
-                exported_ps = b2.util.value_to_jam(ps, methods=True)
-                self.name_ = b2.util.call_jam_function(
-                    tag[1:], specified_name, self.type_, exported_ps)
-                if self.name_:
-                    self.name_ = self.name_[0]
-        
-        # If there's no tag or the tag rule returned nothing.
-        if not tag or not self.name_:
-            self.name_ = add_prefix_and_suffix(specified_name, self.type_, ps)
-
-    def actualize_no_scanner(self):
-        name = self.actual_name()
-
-        # Do anything only on the first invocation
-        if not self.made_:
-            self.made_[name] = True
-
-            if self.action_:  
-                # For non-derived target, we don't care if there
-                # are several virtual targets that refer to the same name.
-                # One case when this is unavoidable is when file name is
-                # main.cpp and two targets have types CPP (for compiling)
-                # and MOCCABLE_CPP (for convertion to H via Qt tools).
-                self.virtual_targets().register_actual_name(name, self)
-
-            for i in self.dependencies_:
-                self.manager_.engine().add_dependency(name, i.actualize())
-
-            self.actualize_location(name)
-            self.actualize_action(name)
-            
-        return name
-
-@bjam_signature((["specified_name"], ["type"], ["property_set"]))
-def add_prefix_and_suffix(specified_name, type, property_set):
-    """Appends the suffix appropriate to 'type/property-set' combination
-    to the specified name and returns the result."""
-
-    property_set = b2.util.jam_to_value_maybe(property_set)
-
-    suffix = ""
-    if type:
-        suffix = b2.build.type.generated_target_suffix(type, property_set)
-    
-    # Handle suffixes for which no leading dot is desired.  Those are
-    # specified by enclosing them in <...>.  Needed by python so it
-    # can create "_d.so" extensions, for example.
-    if get_grist(suffix):
-        suffix = ungrist(suffix)
-    elif suffix:
-        suffix = "." + suffix
-
-    prefix = ""
-    if type:
-        prefix = b2.build.type.generated_target_prefix(type, property_set)
-
-    if specified_name.startswith(prefix):
-        prefix = ""
-
-    if not prefix:
-        prefix = ""
-    if not suffix:
-        suffix = ""
-    return prefix + specified_name + suffix
-
-
-class FileTarget (AbstractFileTarget):
-    """ File target with explicitly known location.
-
-        The file path is determined as
-           - value passed to the 'set_path' method, if any
-           - for derived files, project's build dir, joined with components
-             that describe action's properties. If the free properties
-             are not equal to the project's reference properties
-             an element with name of main target is added.
-           - for source files, project's source dir
-        
-        The file suffix is
-            - the value passed to the 'suffix' method, if any, or
-            - the suffix which correspond to the target's type.
-    """
-    def __init__ (self, name, type, project, action = None, path=None, exact=False):
-        AbstractFileTarget.__init__ (self, name, type, project, action, exact)
-
-        self.path_ = path
-
-    def __str__(self):
-        if self.type_:
-            return self.name_ + "." + self.type_
-        else:
-            return self.name_
-
-    def clone_with_different_type(self, new_type):
-        return FileTarget(self.name_, new_type, self.project_,
-                          self.action_, self.path_, exact=True)
-        
-    def actualize_location (self, target):
-        engine = self.project_.manager_.engine ()
-
-        if self.action_:
-            # This is a derived file.
-            path = self.path ()
-            engine.set_target_variable (target, 'LOCATE', path)
-
-            # Make sure the path exists.
-            engine.add_dependency (target, path)
-            common.mkdir(engine, path)
-
-            # It's possible that the target name includes a directory
-            # too, for example when installing headers. Create that
-            # directory.
-            d = os.path.dirname(get_value(target))
-            if d:
-                d = os.path.join(path, d)
-                engine.add_dependency(target, d)
-                common.mkdir(engine, d)
-
-            # For real file target, we create a fake target that
-            # depends on the real target. This allows to run
-            #
-            #    bjam hello.o
-            #
-            # without trying to guess the name of the real target.            
-            # Note the that target has no directory name, and a special
-            # grist <e>.
-            #
-            # First, that means that "bjam hello.o" will build all
-            # known hello.o targets.
-            # Second, the <e> grist makes sure this target won't be confused
-            # with other targets, for example, if we have subdir 'test'
-            # with target 'test' in it that includes 'test.o' file,
-            # then the target for directory will be just 'test' the target
-            # for test.o will be <ptest/bin/gcc/debug>test.o and the target
-            # we create below will be <e>test.o
-            engine.add_dependency("<e>%s" % get_value(target), target)
-
-            # Allow bjam <path-to-file>/<file> to work.  This won't catch all
-            # possible ways to refer to the path (relative/absolute, extra ".",
-            # various "..", but should help in obvious cases.
-            engine.add_dependency("<e>%s" % (os.path.join(path, get_value(target))), target)
-            
-        else:
-            # This is a source file.
-            engine.set_target_variable (target, 'SEARCH', self.project_.get ('source-location'))
-    
-
-    def path (self):
-        """ Returns the directory for this target.
-        """
-        if not self.path_:
-            if self.action_:
-                p = self.action_.properties ()            
-                (target_path, relative_to_build_dir) = p.target_path ()
-                
-                if relative_to_build_dir:
-                    # Indicates that the path is relative to
-                    # build dir.
-                    target_path = os.path.join (self.project_.build_dir (), target_path)
-                                
-                # Store the computed path, so that it's not recomputed
-                # any more
-                self.path_ = target_path
-
-        return self.path_
-
-
-class NotFileTarget(AbstractFileTarget):
-
-    def __init__(self, name, project, action):
-        AbstractFileTarget.__init__(self, name, None, project, action)
-
-    def path(self):
-        """Returns nothing, to indicate that target path is not known."""
-        return None
-
-    def actualize_location(self, target):
-        bjam.call("NOTFILE", target)
-        bjam.call("ALWAYS", target)
-        bjam.call("NOUPDATE", target)
-
-
-class Action:
-    """ Class which represents an action.
-        Both 'targets' and 'sources' should list instances of 'VirtualTarget'.
-        Action name should name a rule with this prototype
-            rule action_name ( targets + : sources * : properties * )
-        Targets and sources are passed as actual jam targets. The rule may
-        not establish dependency relationship, but should do everything else.
-    """
-    def __init__ (self, manager, sources, action_name, prop_set):
-        assert(isinstance(prop_set, property_set.PropertySet))
-        assert type(sources) == types.ListType
-        self.sources_ = sources
-        self.action_name_ = action_name
-        if not prop_set:
-            prop_set = property_set.empty()
-        self.properties_ = prop_set
-        if not all(isinstance(v, VirtualTarget) for v in prop_set.get('implicit-dependency')):
-            import pdb
-            pdb.set_trace()
-
-        self.manager_ = manager
-        self.engine_ = self.manager_.engine ()
-        self.targets_ = []
-
-        # Indicates whether this has been actualized or not.
-        self.actualized_ = False
-        
-        self.dependency_only_sources_ = []
-        self.actual_sources_ = []
-        
-        
-    def add_targets (self, targets):
-        self.targets_ += targets
-
-
-    def replace_targets (old_targets, new_targets):
-        self.targets_ = [t for t in targets if not t in old_targets] + new_targets
-
-    def targets (self):
-        return self.targets_
-
-    def sources (self):
-        return self.sources_
-
-    def action_name (self):
-        return self.action_name_
-
-    def properties (self):
-        return self.properties_
-
-    def actualize (self):
-        """ Generates actual build instructions.
-        """
-        if self.actualized_:
-            return
-            
-        self.actualized_ = True
-
-        ps = self.properties ()
-        properties = self.adjust_properties (ps)
-
-
-        actual_targets = []
-        
-        for i in self.targets ():
-            actual_targets.append (i.actualize ())
-
-        self.actualize_sources (self.sources (), properties)
-
-        self.engine_.add_dependency (actual_targets, self.actual_sources_ + self.dependency_only_sources_)
-
-        # This works around a bug with -j and actions that
-        # produce multiple target, where:
-        # - dependency on the first output is found, and
-        #   the action is started
-        # - dependency on the second output is found, and
-        #   bjam noticed that command is already running
-        # - instead of waiting for the command, dependents
-        #   of the second targets are immediately updated.
-        if len(actual_targets) > 1:
-            bjam.call("INCLUDES", actual_targets, actual_targets)
-
-        # FIXME: check the comment below. Was self.action_name_ [1]
-        # Action name can include additional argument to rule, which should not
-        # be passed to 'set-target-variables'
-        # FIXME: breaking circular dependency
-        import toolset
-        toolset.set_target_variables (self.manager_, self.action_name_, actual_targets, properties)
-             
-        engine = self.manager_.engine ()
-
-        # FIXME: this is supposed to help --out-xml option, but we don't
-        # implement that now, and anyway, we should handle it in Python,
-        # not but putting variables on bjam-level targets.
-        bjam.call("set-target-variable", actual_targets, ".action", repr(self))
-        
-        self.manager_.engine ().set_update_action (self.action_name_, actual_targets, self.actual_sources_,
-                                                   properties)
-        
-        # Since we set up creating action here, we also set up
-        # action for cleaning up
-        self.manager_.engine ().set_update_action ('common.Clean', 'clean-all',
-                                                   actual_targets)
-
-        return actual_targets
-
-    def actualize_source_type (self, sources, prop_set):
-        """ Helper for 'actualize_sources'.
-            For each passed source, actualizes it with the appropriate scanner.
-            Returns the actualized virtual targets.
-        """
-        result = []
-        for i in sources:
-            scanner = None
-
-# FIXME: what's this?
-#            if isinstance (i, str):
-#                i = self.manager_.get_object (i)
-                
-            if i.type ():
-                scanner = b2.build.type.get_scanner (i.type (), prop_set)
-
-            r = i.actualize (scanner)
-            result.append (r)
-        
-        return result
-    
-    def actualize_sources (self, sources, prop_set):
-        """ Creates actual jam targets for sources. Initializes two member
-            variables:
-            'self.actual_sources_' -- sources which are passed to updating action
-            'self.dependency_only_sources_' -- sources which are made dependencies, but
-            are not used otherwise.
-            
-            New values will be *appended* to the variables. They may be non-empty,
-            if caller wants it.
-        """
-        dependencies = self.properties_.get ('<dependency>')
-                
-        self.dependency_only_sources_ += self.actualize_source_type (dependencies, prop_set)
-        self.actual_sources_ += self.actualize_source_type (sources, prop_set)
-
-        # This is used to help bjam find dependencies in generated headers
-        # in other main targets.
-        # Say:
-        #
-        #   make a.h : ....... ;
-        #   exe hello : hello.cpp : <implicit-dependency>a.h ;
-        #
-        # However, for bjam to find the dependency the generated target must
-        # be actualized (i.e. have the jam target). In the above case,
-        # if we're building just hello ("bjam hello"), 'a.h' won't be
-        # actualized unless we do it here.
-        implicit = self.properties_.get("<implicit-dependency>")
-
-        for i in implicit:
-            i.actualize()
-
-    def adjust_properties (self, prop_set):
-        """ Determines real properties when trying building with 'properties'.
-            This is last chance to fix properties, for example to adjust includes
-            to get generated headers correctly. Default implementation returns
-            its argument.
-        """
-        return prop_set
-
-
-class NullAction (Action):
-    """ Action class which does nothing --- it produces the targets with
-        specific properties out of nowhere. It's needed to distinguish virtual
-        targets with different properties that are known to exist, and have no 
-        actions which create them.
-    """
-    def __init__ (self, manager, prop_set):
-        Action.__init__ (self, manager, [], None, prop_set)
-        
-    def actualize (self):
-        if not self.actualized_:
-            self.actualized_ = True
-
-            for i in self.targets ():
-                i.actualize ()
-
-class NonScanningAction(Action):
-    """Class which acts exactly like 'action', except that the sources
-    are not scanned for dependencies."""
-
-    def __init__(self, sources, action_name, property_set):
-        #FIXME: should the manager parameter of Action.__init__
-        #be removed? -- Steven Watanabe
-        Action.__init__(self, b2.manager.get_manager(), sources, action_name, property_set)
-
-    def actualize_source_type(self, sources, property_set):
-
-        result = []
-        for s in sources:
-            result.append(s.actualize())
-        return result
-
-def traverse (target, include_roots = False, include_sources = False):
-    """ Traverses the dependency graph of 'target' and return all targets that will
-        be created before this one is created. If root of some dependency graph is
-        found during traversal, it's either included or not, dependencing of the
-        value of 'include_roots'. In either case, sources of root are not traversed.
-    """
-    result = []
-    
-    if target.action ():
-        action = target.action ()
-        
-        # This includes 'target' as well
-        result += action.targets ()
-
-        for t in action.sources ():
-
-            # FIXME:
-            # TODO: see comment in Manager.register_object ()
-            #if not isinstance (t, VirtualTarget):
-            #    t = target.project_.manager_.get_object (t)
-                
-            if not t.root ():
-                result += traverse (t, include_roots, include_sources)
-
-            elif include_roots:
-                result.append (t)
-
-    elif include_sources:
-        result.append (target)
-
-    return result
-
-def clone_action (action, new_project, new_action_name, new_properties):
-    """Takes an 'action' instances and creates new instance of it
-    and all produced target. The rule-name and properties are set
-    to 'new-rule-name' and 'new-properties', if those are specified.
-    Returns the cloned action."""
-
-    if not new_action_name:
-        new_action_name = action.action_name()
-
-    if not new_properties:
-        new_properties = action.properties()
-
-    cloned_action = action.__class__(action.manager_, action.sources(), new_action_name,
-                                     new_properties)
-                          
-    cloned_targets = []
-    for target in action.targets():
-
-        n = target.name()
-        # Don't modify the name of the produced targets. Strip the directory f
-        cloned_target = FileTarget(n, target.type(), new_project,
-                                   cloned_action, exact=True)
-
-        d = target.dependencies()
-        if d:
-            cloned_target.depends(d)
-        cloned_target.root(target.root())
-        cloned_target.creating_subvariant(target.creating_subvariant())
-
-        cloned_targets.append(cloned_target)
-
-    return cloned_action
-
-class Subvariant:
-    
-    def __init__ (self, main_target, prop_set, sources, build_properties, sources_usage_requirements, created_targets):
-        """ 
-        main_target:                 The instance of MainTarget class
-        prop_set:                    Properties requested for this target
-        sources:
-        build_properties:            Actually used properties
-        sources_usage_requirements:  Properties propagated from sources
-        created_targets:             Top-level created targets
-        """
-        self.main_target_ = main_target
-        self.properties_ = prop_set
-        self.sources_ = sources
-        self.build_properties_ = build_properties
-        self.sources_usage_requirements_ = sources_usage_requirements
-        self.created_targets_ = created_targets
-
-        self.usage_requirements_ = None
-        
-        # Pre-compose the list of other dependency graphs, on which this one
-        # depends
-        deps = build_properties.get('<implicit-dependency>')
-        
-        self.other_dg_ = []
-        for d in deps:
-            self.other_dg_.append(d.creating_subvariant ())
-
-        self.other_dg_ = unique (self.other_dg_)
-
-        self.implicit_includes_cache_ = {}
-        self.target_directories_ = None
-               
-    def main_target (self):
-        return self.main_target_
-    
-    def created_targets (self):
-        return self.created_targets_
-    
-    def requested_properties (self):
-        return self.properties_
-    
-    def build_properties (self):
-        return self.build_properties_
-    
-    def sources_usage_requirements (self):
-        return self.sources_usage_requirements_
-    
-    def set_usage_requirements (self, usage_requirements):
-        self.usage_requirements_ = usage_requirements
-    
-    def usage_requirements (self):
-        return self.usage_requirements_
-
-    def all_referenced_targets(self, result):
-        """Returns all targets referenced by this subvariant,
-        either directly or indirectly, and either as sources,
-        or as dependency properties. Targets referred with
-        dependency property are returned a properties, not targets."""
-
-        # Find directly referenced targets.
-        deps = self.build_properties().dependency()
-        all_targets = self.sources_ + deps
-        
-        # Find other subvariants.
-        r = []
-        for e in all_targets:
-            if not e in result:
-                result.add(e)
-                if isinstance(e, property.Property):
-                    t = e.value()
-                else:
-                    t = e
-                                    
-                # FIXME: how can this be?
-                cs = t.creating_subvariant()
-                if cs:
-                    r.append(cs)
-        r = unique(r)
-        for s in r:
-            if s != self:
-                s.all_referenced_targets(result)
-
-
-    def implicit_includes (self, feature, target_type):
-        """ Returns the properties which specify implicit include paths to
-            generated headers. This traverses all targets in this subvariant,
-            and subvariants referred by <implcit-dependecy>properties.
-            For all targets which are of type 'target-type' (or for all targets,
-            if 'target_type' is not specified), the result will contain
-            <$(feature)>path-to-that-target.
-        """
-
-        if not target_type:
-            key = feature
-        else:
-            key = feature + "-" + target_type
-
-            
-        result = self.implicit_includes_cache_.get(key)
-        if not result:
-            target_paths = self.all_target_directories(target_type)
-            target_paths = unique(target_paths)
-            result = ["<%s>%s" % (feature, p) for p in target_paths]
-            self.implicit_includes_cache_[key] = result
-
-        return result
-
-    def all_target_directories(self, target_type = None):
-        # TODO: does not appear to use target_type in deciding
-        # if we've computed this already.
-        if not self.target_directories_:
-            self.target_directories_ = self.compute_target_directories(target_type)
-        return self.target_directories_
-
-    def compute_target_directories(self, target_type=None):
-        result = []
-        for t in self.created_targets():
-            if not target_type or b2.build.type.is_derived(t.type(), target_type):
-                result.append(t.path())
-
-        for d in self.other_dg_:
-            result.extend(d.all_target_directories(target_type))
-
-        result = unique(result)
-        return result
diff --git a/jam-files/boost-build/kernel/boost-build.jam b/jam-files/boost-build/kernel/boost-build.jam
deleted file mode 100644
index 377f6ec0..00000000
--- a/jam-files/boost-build/kernel/boost-build.jam
+++ /dev/null
@@ -1,5 +0,0 @@
-# Copyright 2003 Dave Abrahams 
-# Distributed under the Boost Software License, Version 1.0. 
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt) 
-
-boost-build . ;
diff --git a/jam-files/boost-build/kernel/bootstrap.jam b/jam-files/boost-build/kernel/bootstrap.jam
deleted file mode 100644
index 89048af9..00000000
--- a/jam-files/boost-build/kernel/bootstrap.jam
+++ /dev/null
@@ -1,263 +0,0 @@
-# Copyright 2003 Dave Abrahams 
-# Copyright 2003, 2005, 2006 Rene Rivera 
-# Copyright 2003, 2005, 2006 Vladimir Prus 
-# Distributed under the Boost Software License, Version 1.0. 
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt) 
-
-# First of all, check the jam version
-
-if $(JAM_VERSION:J="") < 030112
-{
-    ECHO "error: Boost.Jam version 3.1.12 or later required" ;
-    EXIT ;
-}
-
-local required-rules = GLOB-RECURSIVELY HAS_NATIVE_RULE ;
-
-for local r in $(required-rules)
-{
-    if ! $(r) in [ RULENAMES ]
-    {
-        ECHO "error: builtin rule '$(r)' is not present" ;
-        ECHO "error: your version of bjam is likely out of date" ;
-        ECHO "error: please get a fresh version from SVN." ;
-        EXIT ;
-    }
-}
-
-local native =
-    regex transform 2
-    ;
-while $(native)
-{
-    if ! [ HAS_NATIVE_RULE $(native[1]) :
-                           $(native[2]) :
-               $(native[3]) ]
-    {
-        ECHO "error: missing native rule '$(native[1]).$(native[2])'" ;
-        ECHO "error: or interface version of that rule is too low" ;
-        ECHO "error: your version of bjam is likely out of date" ;
-        ECHO "error: please get a fresh version from SVN." ;
-        EXIT ;
-    }
-    native = $(native[4-]) ;
-}
-
-# Check that the builtin .ENVIRON module is present. We don't have a
-# builtin to check that a module is present, so we assume that the PATH
-# environment variable is always set and verify that the .ENVIRON module
-# has non-empty value of that variable.
-module .ENVIRON
-{
-    local p = $(PATH) $(Path) $(path) ;
-    if ! $(p)
-    {
-        ECHO "error: no builtin module .ENVIRON is found" ;
-        ECHO "error: your version of bjam is likely out of date" ;
-        ECHO "error: please get a fresh version from SVN." ;
-        EXIT ;
-    }
-}
-
-# Check that @() functionality is present. Similarly to modules,
-# we don't have a way to test that directly. Instead we check that
-# $(TMPNAME) functionality is present which was added at roughly
-# the same time (more precisely it was added just before).
-{
-    if ! $(TMPNAME)
-    {
-        ECHO "error: no @() functionality found" ;
-        ECHO "error: your version of bjam is likely out of date" ;
-        ECHO "error: please get a fresh version from SVN." ;
-        EXIT ;
-    }
-}
-
-# Make sure that \n escape is avaiable.
-if "\n" = "n"
-{
-    if $(OS) = CYGWIN 
-    {        
-        ECHO "warning: escape sequences are not supported" ;
-        ECHO "warning: this will cause major misbehaviour on cygwin" ;
-        ECHO "warning: your version of bjam is likely out of date" ;
-        ECHO "warning: please get a fresh version from SVN." ;
-    }    
-}
-
-# Bootstrap the module system. Then bring the import rule into the global module.
-#
-SEARCH on <module@>modules.jam = $(.bootstrap-file:D) ;
-module modules { include <module@>modules.jam ; }
-IMPORT modules : import : : import ;
-
-{
-    # Add module subdirectories to the BOOST_BUILD_PATH, which allows
-    # us to make an incremental refactoring step by moving modules to
-    # the appropriate subdirectories, thereby achieving some physical
-    # separation of different layers without changing all of our code
-    # to specify subdirectories in import statements or use an extra
-    # level of qualification on imported names.
-
-    local subdirs =
-      kernel        # only the most-intrinsic modules: modules, errors
-      util          # low-level substrate: string/number handling, etc.
-      build         # essential elements of the build system architecture
-      tools         # toolsets for handling specific build jobs and targets.
-      contrib       # user contributed (unreviewed) modules
-      .             # build-system.jam lives here
-      ;
-    local whereami = [ NORMALIZE_PATH $(.bootstrap-file:DT) ] ;
-    BOOST_BUILD_PATH += $(whereami:D)/$(subdirs) ;
-
-    modules.poke .ENVIRON : BOOST_BUILD_PATH : $(BOOST_BUILD_PATH) ;
-    
-    modules.poke : EXTRA_PYTHONPATH : $(whereami) ;
-}
-
-# Reload the modules, to clean up things. The modules module can tolerate
-# being included twice.
-#
-import modules ;
-
-# Process option plugins first to alow them to prevent loading
-# the rest of the build system.
-#
-import option ;
-local dont-build = [ option.process ] ;
-
-# Should we skip building, i.e. loading the build system, according
-# to the options processed?
-#
-if ! $(dont-build)
-{
-    if ! --python in $(ARGV)
-    {
-        # Allow users to override the build system file from the
-        # command-line (mostly for testing)
-        local build-system = [ MATCH --build-system=(.*) : $(ARGV) ] ;
-        build-system ?= build-system ;
-
-        # Use last element in case of multiple command-line options
-        import $(build-system[-1]) ;
-    }
-    else
-    {
-        ECHO "Boost.Build V2 Python port (experimental)" ;
-                
-        # Define additional interface that is exposed to Python code. Python code will
-        # also have access to select bjam builtins in the 'bjam' module, but some
-        # things are easier to define outside C.
-        module python_interface
-        {
-            rule load ( module-name : location )
-            {        
-                USER_MODULE $(module-name) ;
-	        # Make all rules in the loaded module available in
-	        # the global namespace, so that we don't have
-	        # to bother specifying "right" module when calling
-	        # from Python.
-                module $(module-name)
-                {
-                    __name__ = $(1) ;
-                    include $(2) ;
-                    local rules = [ RULENAMES $(1) ] ;
-                    IMPORT $(1) : $(rules) : $(1) : $(1).$(rules) ;
-                }
-            }    
-            
-            rule peek ( module-name ? : variables + )
-            {
-                module $(<)
-                {
-                    return $($(>)) ;
-                }
-            }
-            
-            rule set-variable ( module-name : name : value * )
-            {
-                module $(<)
-                {
-                    $(>) = $(3) ;
-                }        
-            }
-            
-            rule set-top-level-targets ( targets * )
-            {
-                DEPENDS all : $(targets) ;
-            }
-            
-            rule call-in-module ( m : rulename : * )
-            {
-                module $(m)
-                {
-                    return [ $(2) $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ] ;
-                }                
-            }
-
-            
-            rule set-update-action ( action : targets * : sources * : properties * )
-            {
-                $(action) $(targets) : $(sources) : $(properties) ;
-            }
-            
-            rule set-update-action-in-module ( m : action : targets * : sources * : properties * )
-            {
-                module $(m)
-                {
-                    $(2) $(3) : $(4) : $(5) ;
-                }                
-            }
-                        
-            rule set-target-variable ( targets + : variable : value * : append ? )
-            {
-                if $(append)
-                {            
-	            $(variable) on $(targets) += $(value) ;
-                }
-                else
-                {
-	            $(variable) on $(targets) = $(value) ;            
-                }        
-            }        
-
-            rule get-target-variable ( targets + : variable )
-            {
-                return [ on $(targets) return $($(variable)) ] ;
-            }
-
-            rule import-rules-from-parent ( parent-module : this-module : user-rules * )
-            {
-                IMPORT $(parent-module) : $(user-rules) : $(this-module) : $(user-rules) ;
-                EXPORT $(this-module) : $(user-rules) ;
-            }
-
-            rule mark-included ( targets * : includes * ) {
-                NOCARE $(includes) ;
-                INCLUDES $(targets) : $(includes) ;
-                ISFILE $(includes) ;
-            }
-        }
-
-        PYTHON_IMPORT_RULE bootstrap : bootstrap : PyBB : bootstrap ;
-        modules.poke PyBB : root : [ NORMALIZE_PATH $(.bootstrap-file:DT)/.. ] ;
-        
-        module PyBB
-        {
-            local ok = [ bootstrap $(root) ] ;
-            if ! $(ok)
-            {
-                EXIT ;
-            }            
-        }
-        
-        
-        #PYTHON_IMPORT_RULE boost.build.build_system : main : PyBB : main ;
-
-        #module PyBB
-        #{    
-        #    main ;
-        #}
-
-    }
-}
diff --git a/jam-files/boost-build/kernel/bootstrap.py b/jam-files/boost-build/kernel/bootstrap.py
deleted file mode 100644
index 2e8dd37b..00000000
--- a/jam-files/boost-build/kernel/bootstrap.py
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 2009 Vladimir Prus 
-#
-# Distributed under the Boost Software License, Version 1.0. 
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-import imp
-import sys
-
-def bootstrap(root_path):
-    """Performs python-side bootstrapping of Boost.Build/Python.
-
-    This function arranges for 'b2.whatever' package names to work, while also
-    allowing to put python files alongside corresponding jam modules.
-    """
-
-    m = imp.new_module("b2")
-    # Note that:
-    # 1. If __path__ is not list of strings, nothing will work
-    # 2. root_path is already list of strings.
-    m.__path__ = root_path
-    sys.modules["b2"] = m
-
-    import b2.build_system
-    return b2.build_system.main()
-
diff --git a/jam-files/boost-build/kernel/class.jam b/jam-files/boost-build/kernel/class.jam
deleted file mode 100644
index b8e55af3..00000000
--- a/jam-files/boost-build/kernel/class.jam
+++ /dev/null
@@ -1,420 +0,0 @@
-# Copyright 2001, 2002, 2003 Dave Abrahams
-# Copyright 2002, 2005 Rene Rivera
-# Copyright 2002, 2003 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-# Polymorphic class system built on top of core Jam facilities.
-#
-# Classes are defined by 'class' keywords::
-#
-#     class myclass
-#     {
-#         rule __init__ ( arg1 )     # constructor
-#         {
-#             self.attribute = $(arg1) ;
-#         }
-#
-#         rule method1 ( )           # method
-#         {
-#             return [ method2 ] ;
-#         }
-#
-#         rule method2 ( )           # method
-#         {
-#             return $(self.attribute) ;
-#         }
-#     }
-#
-# The __init__ rule is the constructor, and sets member variables.
-#
-# New instances are created by invoking [ new <class> <args...> ]:
-#
-#     local x = [ new myclass foo ] ;        # x is a new myclass object
-#     assert.result foo : [ $(x).method1 ] ; # $(x).method1 returns "foo"
-#
-# Derived class are created by mentioning base classes in the declaration::
-#
-#     class derived : myclass
-#     {
-#          rule __init__ ( arg )
-#          {
-#              myclass.__init__ $(arg) ;  # call base __init__
-#
-#          }
-#
-#          rule method2 ( )           # method override
-#          {
-#              return $(self.attribute)XXX ;
-#          }
-#     }
-#
-# All methods operate virtually, replacing behavior in the base classes. For
-# example::
-#
-#     local y = [ new derived foo ] ;            # y is a new derived object
-#     assert.result fooXXX : [ $(y).method1 ] ;  # $(y).method1 returns "foo"
-#
-# Each class instance is its own core Jam module. All instance attributes and
-# methods are accessible without additional qualification from within the class
-# instance. All rules imported in class declaration, or visible in base classses
-# are also visible. Base methods are available in qualified form:
-# base-name.method-name. By convention, attribute names are prefixed with
-# "self.".
-
-import modules ;
-import numbers ;
-
-
-rule xinit ( instance : class )
-{
-    module $(instance)
-    {
-        __class__ = $(2) ;
-        __name__ = $(1) ;
-    }
-}
-
-
-rule new ( class args * : * )
-{
-    .next-instance ?= 1 ;
-    local id = object($(class))@$(.next-instance) ;
-
-    xinit $(id) : $(class) ;
-
-    INSTANCE $(id) : class@$(class) ;
-    IMPORT_MODULE $(id) ;
-    $(id).__init__ $(args) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ;
-
-    # Bump the next unique object name.
-    .next-instance = [ numbers.increment $(.next-instance) ] ;
-
-    # Return the name of the new instance.
-    return $(id) ;
-}
-
-
-rule bases ( class )
-{
-    module class@$(class)
-    {
-        return $(__bases__) ;
-    }
-}
-
-
-rule is-derived ( class : bases + )
-{
-    local stack = $(class) ;
-    local visited found ;
-    while ! $(found) && $(stack)
-    {
-        local top = $(stack[1]) ;
-        stack = $(stack[2-]) ;
-        if ! ( $(top) in $(visited) )
-        {
-            visited += $(top) ;
-            stack += [ bases $(top) ] ;
-
-            if $(bases) in $(visited)
-            {
-                found = true ;
-            }
-        }
-    }
-    return $(found) ;
-}
-
-
-# Returns true if the 'value' is a class instance.
-#
-rule is-instance ( value )
-{
-    return [ MATCH "^(object\\()[^@]+\\)@.*" : $(value) ] ;
-}
-
-
-# Check if the given value is of the given type.
-#
-rule is-a (
-    instance  # The value to check.
-    : type  # The type to test for.
-)
-{
-    if [ is-instance $(instance) ]
-    {
-        return [ class.is-derived [ modules.peek $(instance) : __class__ ] : $(type) ] ;
-    }
-}
-
-
-local rule typecheck ( x )
-{
-    local class-name = [ MATCH "^\\[(.*)\\]$" : [ BACKTRACE 1 ] ] ;
-    if ! [ is-a $(x) : $(class-name) ]
-    {
-        return "Expected an instance of "$(class-name)" but got \""$(x)"\" for argument" ;
-    }
-}
-
-
-rule __test__ ( )
-{
-    import assert ;
-    import "class" : new ;
-
-    # This will be the construction function for a class called 'myclass'.
-    #
-    class myclass
-    {
-        import assert ;
-
-        rule __init__ ( x_ * : y_ * )
-        {
-            # Set some instance variables.
-            x = $(x_) ;
-            y = $(y_) ;
-            foo += 10 ;
-        }
-
-        rule set-x ( newx * )
-        {
-            x = $(newx) ;
-        }
-
-        rule get-x ( )
-        {
-            return $(x) ;
-        }
-
-        rule set-y ( newy * )
-        {
-            y = $(newy) ;
-        }
-
-        rule get-y ( )
-        {
-            return $(y) ;
-        }
-
-        rule f ( )
-        {
-            return [ g $(x) ] ;
-        }
-
-        rule g ( args * )
-        {
-            if $(x) in $(y)
-            {
-                return $(x) ;
-            }
-            else if $(y) in $(x)
-            {
-                return $(y) ;
-            }
-            else
-            {
-                return ;
-            }
-        }
-
-        rule get-class ( )
-        {
-            return $(__class__) ;
-        }
-
-        rule get-instance ( )
-        {
-            return $(__name__) ;
-        }
-
-        rule invariant ( )
-        {
-            assert.equal 1 : 1 ;
-        }
-
-        rule get-foo ( )
-        {
-            return $(foo) ;
-        }
-    }
-#    class myclass ;
-
-    class derived1 : myclass
-    {
-        rule __init__ ( z_ )
-        {
-            myclass.__init__ $(z_) : X ;
-            z = $(z_) ;
-        }
-
-        # Override g.
-        #
-        rule g ( args * )
-        {
-            return derived1.g ;
-        }
-
-        rule h ( )
-        {
-            return derived1.h ;
-        }
-
-        rule get-z ( )
-        {
-            return $(z) ;
-        }
-
-        # Check that 'assert.equal' visible in base class is visible here.
-        #
-        rule invariant2 ( )
-        {
-            assert.equal 2 : 2 ;
-        }
-
-        # Check that 'assert.variable-not-empty' visible in base class is
-        # visible here.
-        #
-        rule invariant3 ( )
-        {
-            local v = 10 ;
-            assert.variable-not-empty v ;
-        }
-    }
-#    class derived1 : myclass ;
-
-    class derived2 : myclass
-    {
-        rule __init__ ( )
-        {
-            myclass.__init__ 1 : 2 ;
-        }
-
-        # Override g.
-        #
-        rule g ( args * )
-        {
-            return derived2.g ;
-        }
-
-        # Test the ability to call base class functions with qualification.
-        #
-        rule get-x ( )
-        {
-            return [ myclass.get-x ] ;
-        }
-    }
-#    class derived2 : myclass ;
-
-    class derived2a : derived2
-    {
-        rule __init__
-        {
-            derived2.__init__ ;
-        }
-    }
-#    class derived2a : derived2 ;
-
-    local rule expect_derived2 ( [derived2] x ) { }
-
-    local a = [ new myclass 3 4 5 : 4 5 ] ;
-    local b = [ new derived1 4 ] ;
-    local b2 = [ new derived1 4 ] ;
-    local c = [ new derived2 ] ;
-    local d = [ new derived2 ] ;
-    local e = [ new derived2a ] ;
-
-    expect_derived2 $(d) ;
-    expect_derived2 $(e) ;
-
-    # Argument checking is set up to call exit(1) directly on failure, and we
-    # can not hijack that with try, so we should better not do this test by
-    # default. We could fix this by having errors look up and invoke the EXIT
-    # rule instead; EXIT can be hijacked (;-)
-    if --fail-typecheck in [ modules.peek : ARGV ]
-    {
-        try ;
-        {
-            expect_derived2 $(a) ;
-        }
-        catch
-            "Expected an instance of derived2 but got" instead
-            ;
-    }
-
-    #try ;
-    #{
-    #    new bad_subclass ;
-    #}
-    #catch
-    #  bad_subclass.bad_subclass failed to call base class constructor myclass.__init__
-    #  ;
-
-    #try ;
-    #{
-    #    class bad_subclass ;
-    #}
-    #catch bad_subclass has already been declared ;
-
-    assert.result 3 4 5 : $(a).get-x ;
-    assert.result 4 5 : $(a).get-y ;
-    assert.result 4 : $(b).get-x ;
-    assert.result X : $(b).get-y ;
-    assert.result 4 : $(b).get-z ;
-    assert.result 1 : $(c).get-x ;
-    assert.result 2 : $(c).get-y ;
-    assert.result 4 5 : $(a).f ;
-    assert.result derived1.g : $(b).f ;
-    assert.result derived2.g : $(c).f ;
-    assert.result derived2.g : $(d).f ;
-
-    assert.result 10 : $(b).get-foo ;
-
-    $(a).invariant ;
-    $(b).invariant2 ;
-    $(b).invariant3 ;
-
-    # Check that the __class__ attribute is getting properly set.
-    assert.result myclass : $(a).get-class ;
-    assert.result derived1 : $(b).get-class ;
-    assert.result $(a) : $(a).get-instance ;
-
-    $(a).set-x a.x ;
-    $(b).set-x b.x ;
-    $(c).set-x c.x ;
-    $(d).set-x d.x ;
-    assert.result a.x : $(a).get-x ;
-    assert.result b.x : $(b).get-x ;
-    assert.result c.x : $(c).get-x ;
-    assert.result d.x : $(d).get-x ;
-
-    class derived3 : derived1 derived2
-    {
-        rule __init__ ( )
-        {
-        }
-    }
-
-    assert.result : bases myclass ;
-    assert.result myclass : bases derived1 ;
-    assert.result myclass : bases derived2 ;
-    assert.result derived1 derived2 : bases derived3 ;
-
-    assert.true is-derived derived1 : myclass ;
-    assert.true is-derived derived2 : myclass ;
-    assert.true is-derived derived3 : derived1 ;
-    assert.true is-derived derived3 : derived2 ;
-    assert.true is-derived derived3 : derived1 derived2 myclass ;
-    assert.true is-derived derived3 : myclass ;
-
-    assert.false is-derived myclass : derived1 ;
-
-    assert.true is-instance $(a) ;
-    assert.false is-instance bar ;
-
-    assert.true is-a $(a) : myclass ;
-    assert.true is-a $(c) : derived2 ;
-    assert.true is-a $(d) : myclass ;
-    assert.false is-a literal : myclass ;
-}
diff --git a/jam-files/boost-build/kernel/errors.jam b/jam-files/boost-build/kernel/errors.jam
deleted file mode 100644
index 63b11e86..00000000
--- a/jam-files/boost-build/kernel/errors.jam
+++ /dev/null
@@ -1,274 +0,0 @@
-# Copyright 2003 Dave Abrahams
-# Copyright 2004 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-# Print a stack backtrace leading to this rule's caller. Each argument
-# represents a line of output to be printed after the first line of the
-# backtrace.
-#
-rule backtrace ( skip-frames prefix messages * : * )
-{
-    local frame-skips = 5 9 13 17 21 25 29 33 37 41 45 49 53 57 61 65 69 73 77 81 ;
-    local drop-elements = $(frame-skips[$(skip-frames)]) ;
-    if ! ( $(skip-frames) in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 )
-    {
-        ECHO "warning: backtrace doesn't support skipping $(skip-frames) frames;"
-            "using 1 instead." ;
-        drop-elements = 5 ;
-    }
-
-    local args = $(.args) ;
-    if $(.user-modules-only)
-    {
-        local bt = [ nearest-user-location ] ;
-        ECHO "$(prefix) at $(bt) " ;
-        for local n in $(args)
-        {
-            if $($(n))-is-not-empty
-            {
-                ECHO $(prefix) $($(n)) ;
-            }
-        }
-    }
-    else
-    {
-        # Get the whole backtrace, then drop the initial quadruples
-        # corresponding to the frames that must be skipped.
-        local bt = [ BACKTRACE ] ;
-        bt = $(bt[$(drop-elements)-]) ;
-
-        while $(bt)
-        {
-            local m = [ MATCH ^(.+)\\.$ : $(bt[3]) ] ;
-            ECHO $(bt[1]):$(bt[2]): "in" $(bt[4]) "from module" $(m) ;
-
-            # The first time through, print each argument on a separate line.
-            for local n in $(args)
-            {
-                if $($(n))-is-not-empty
-                {
-                    ECHO $(prefix) $($(n)) ;
-                }
-            }
-            args = ;  # Kill args so that this never happens again.
-
-            # Move on to the next quadruple.
-            bt = $(bt[5-]) ;
-        }
-    }
-}
-
-.args ?= messages 2 3 4 5 6 7 8 9 ;
-.disabled ?= ;
-.last-error-$(.args) ?= ;
-
-
-# try-catch --
-#
-# This is not really an exception-handling mechanism, but it does allow us to
-# perform some error-checking on our error-checking. Errors are suppressed after
-# a try, and the first one is recorded. Use catch to check that the error
-# message matched expectations.
-
-# Begin looking for error messages.
-#
-rule try ( )
-{
-    .disabled += true ;
-    .last-error-$(.args) = ;
-}
-
-
-# Stop looking for error messages; generate an error if an argument of messages
-# is not found in the corresponding argument in the error call.
-#
-rule catch ( messages * : * )
-{
-    .disabled = $(.disabled[2-]) ;  # Pop the stack.
-
-    import sequence ;
-
-    if ! $(.last-error-$(.args))-is-not-empty
-    {
-        error-skip-frames 3 expected an error, but none occurred ;
-    }
-    else
-    {
-        for local n in $(.args)
-        {
-            if ! $($(n)) in $(.last-error-$(n))
-            {
-                local v = [ sequence.join $($(n)) : " " ] ;
-                v ?= "" ;
-                local joined = [ sequence.join $(.last-error-$(n)) : " " ] ;
-
-                .last-error-$(.args) = ;
-                error-skip-frames 3 expected \"$(v)\" in argument $(n) of error
-                    : got \"$(joined)\" instead ;
-            }
-        }
-    }
-}
-
-
-rule error-skip-frames ( skip-frames messages * : * )
-{
-    if ! $(.disabled)
-    {
-        backtrace $(skip-frames) error: $(messages) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ;
-        EXIT ;
-    }
-    else if ! $(.last-error-$(.args))
-    {
-        for local n in $(.args)
-        {
-            # Add an extra empty string so that we always have
-            # something in the event of an error
-            .last-error-$(n) = $($(n)) "" ;
-        }
-    }
-}
-
-if --no-error-backtrace in [ modules.peek : ARGV ]
-{
-    .no-error-backtrace = true ;
-}
-
-
-# Print an error message with a stack backtrace and exit.
-#
-rule error ( messages * : * )
-{
-    if $(.no-error-backtrace)
-    {
-        # Print each argument on a separate line.
-        for local n in $(.args)
-        {
-            if $($(n))-is-not-empty
-            {
-                if ! $(first-printed)
-                {
-                    ECHO error: $($(n)) ;
-                    first-printed = true ;
-                }
-                else
-                {
-                    ECHO $($(n)) ;
-                }
-            }
-        }
-        EXIT ;
-    }
-    else
-    {
-        error-skip-frames 3 $(1) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ;
-    }
-}
-
-
-# Same as 'error', but the generated backtrace will include only user files.
-#
-rule user-error ( messages * : * )
-{
-    .user-modules-only = 1 ;
-    error-skip-frames 3 $(1) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ;
-}
-
-
-# Print a warning message with a stack backtrace and exit.
-#
-rule warning
-{
-    backtrace 2 warning: $(1) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ;
-}
-
-
-# Convert an arbitrary argument list into a list with ":" separators and quoted
-# elements representing the same information. This is mostly useful for
-# formatting descriptions of arguments with which a rule was called when
-# reporting an error.
-#
-rule lol->list ( * )
-{
-    local result ;
-    local remaining = 1 2 3 4 5 6 7 8 9 ;
-    while $($(remaining))
-    {
-        local n = $(remaining[1]) ;
-        remaining = $(remaining[2-]) ;
-
-        if $(n) != 1
-        {
-            result += ":" ;
-        }
-        result += \"$($(n))\" ;
-    }
-    return $(result) ;
-}
-
-
-# Return the file:line for the nearest entry in backtrace which correspond to a
-# user module.
-#
-rule nearest-user-location ( )
-{
-    local bt = [ BACKTRACE ] ;
-
-    local result ;
-    while $(bt) && ! $(result)
-    {
-        local m = [ MATCH ^(.+)\\.$ : $(bt[3]) ] ;
-        local user-modules = ([Jj]amroot(.jam|.v2|)|([Jj]amfile(.jam|.v2|)|user-config.jam|site-config.jam|project-root.jam) ;
-
-        if [ MATCH $(user-modules) : $(bt[1]:D=) ]
-        {
-            result = $(bt[1]):$(bt[2]) ;
-        }
-        bt = $(bt[5-]) ;
-    }
-    return $(result) ;
-}
-
-
-# If optimized rule is available in Jam, use it.
-if NEAREST_USER_LOCATION in [ RULENAMES ]
-{
-    rule nearest-user-location ( )
-    {
-        local r = [ NEAREST_USER_LOCATION ] ;
-        return $(r[1]):$(r[2]) ;
-    }
-}
-
-
-rule __test__ ( )
-{
-    # Show that we can correctly catch an expected error.
-    try ;
-    {
-        error an error occurred : somewhere ;
-    }
-    catch an error occurred : somewhere ;
-
-    # Show that unexpected errors generate real errors.
-    try ;
-    {
-        try ;
-        {
-            error an error occurred : somewhere ;
-        }
-        catch an error occurred : nowhere ;
-    }
-    catch expected \"nowhere\" in argument 2 ;
-
-    # Show that not catching an error where one was expected is an error.
-    try ;
-    {
-        try ;
-        {
-        }
-        catch ;
-    }
-    catch expected an error, but none occurred ;
-}
diff --git a/jam-files/boost-build/kernel/modules.jam b/jam-files/boost-build/kernel/modules.jam
deleted file mode 100644
index 1f75354f..00000000
--- a/jam-files/boost-build/kernel/modules.jam
+++ /dev/null
@@ -1,354 +0,0 @@
-# Copyright 2003 Dave Abrahams
-# Copyright 2003, 2005 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-# Essentially an include guard; ensures that no module is loaded multiple times.
-.loaded ?= ;
-
-# A list of modules currently being loaded for error reporting of circular
-# dependencies.
-.loading ?= ;
-
-# A list of modules needing to be tested using their __test__ rule.
-.untested ?= ;
-
-# A list of modules which have been tested using their __test__ rule.
-.tested ?= ;
-
-
-# Runs internal Boost Build unit tests for the specified module. The module's
-# __test__ rule is executed in its own module to eliminate any inadvertent
-# effects of testing module dependencies (such as assert) on the module itself.
-#
-local rule run-module-test ( m )
-{
-    local tested-modules = [ modules.peek modules : .tested ] ;
-
-    if ( ! $(m) in $(tested-modules) )  # Avoid recursive test invocations.
-        && ( ( --debug in $(argv) ) || ( --debug-module=$(m) in $(argv) ) )
-    {
-        modules.poke modules : .tested : $(tested-modules) $(m) ;
-
-        if ! ( __test__ in [ RULENAMES $(m) ] )
-        {
-            local argv = [ peek : ARGV ] ;
-            if ! ( --quiet in $(argv) ) && ( --debug-tests in $(argv) )
-            {
-                ECHO warning: no __test__ rule defined in module $(m) ;
-            }
-        }
-        else
-        {
-            if ! ( --quiet in $(argv) )
-            {
-                ECHO testing module $(m)... ;
-            }
-
-            local test-module = __test-$(m)__ ;
-            IMPORT $(m) : [ RULENAMES $(m) ] : $(test-module) : [ RULENAMES $(m) ] ;
-            IMPORT $(m) : __test__ : $(test-module) : __test__ : LOCALIZE ;
-            module $(test-module)
-            {
-                __test__ ;
-            }
-        }
-    }
-}
-
-
-# Return the binding of the given module.
-#
-rule binding ( module )
-{
-    return $($(module).__binding__) ;
-}
-
-
-# Sets the module-local value of a variable. This is the most reliable way to
-# set a module-local variable in a different module; it eliminates issues of
-# name shadowing due to dynamic scoping.
-#
-rule poke ( module-name ? : variables + : value * )
-{
-    module $(<)
-    {
-        $(>) = $(3) ;
-    }
-}
-
-
-# Returns the module-local value of a variable. This is the most reliable way to
-# examine a module-local variable in a different module; it eliminates issues of
-# name shadowing due to dynamic scoping.
-#
-rule peek ( module-name ? : variables + )
-{
-    module $(<)
-    {
-        return $($(>)) ;
-    }
-}
-
-
-# Call the given rule locally in the given module. Use this for rules accepting
-# rule names as arguments, so that the passed rule may be invoked in the context
-# of the rule's caller (for example, if the rule accesses module globals or is a
-# local rule). Note that rules called this way may accept at most 8 parameters.
-#
-rule call-in ( module-name ? : rule-name args * : * )
-{
-    module $(module-name)
-    {
-        return [ $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ] ;
-    }
-}
-
-
-# Given a possibly qualified rule name and arguments, remove any initial module
-# qualification from the rule and invoke it in that module. If there is no
-# module qualification, the rule is invoked in the global module. Note that
-# rules called this way may accept at most 8 parameters.
-#
-rule call-locally ( qualified-rule-name args * : * )
-{
-    local module-rule = [ MATCH (.*)\\.(.*) : $(qualified-rule-name) ] ;
-    local rule-name = $(module-rule[2]) ;
-    rule-name ?= $(qualified-rule-name) ;
-    #   We pass only 8 parameters here since Boost Jam allows at most 9 rule
-    # parameter positions and the call-in rule already uses up the initial
-    # position for the module name.
-    return [ call-in $(module-rule[1]) : $(rule-name) $(args) : $(2) : $(3) :
-        $(4) : $(5) : $(6) : $(7) : $(8) ] ;
-}
-
-
-# Load the indicated module if it is not already loaded.
-#
-rule load (
-      module-name  # Name of module to load. Rules will be defined in this
-                   # module.
-    : filename ?   # (partial) path to file; Defaults to $(module-name).jam.
-    : search *     # Directories in which to search for filename. Defaults to
-                   # $(BOOST_BUILD_PATH).
-)
-{
-    # Avoid loading modules twice.
-    if ! ( $(module-name) in $(.loaded) )
-    {
-        filename ?= $(module-name).jam ;
-
-        # Mark the module loaded so we do not try to load it recursively.
-        .loaded += $(module-name) ;
-
-        # Suppress tests if any module loads are already in progress.
-        local suppress-test = $(.loading[1]) ;
-
-        # Push this module on the loading stack.
-        .loading += $(module-name) ;
-
-        # Remember that it is untested.
-        .untested += $(module-name) ;
-
-        # Insert the new module's __name__ and __file__ globals.
-        poke $(module-name) : __name__ : $(module-name) ;
-        poke $(module-name) : __file__ : $(filename) ;
-
-        module $(module-name)
-        {
-            # Add some grist so that the module will have a unique target name.
-            local module-target = $(__file__:G=module@) ;
-
-            local search = $(3) ;
-            search ?= [ modules.peek : BOOST_BUILD_PATH ] ;
-            SEARCH on $(module-target) = $(search) ;
-            BINDRULE on $(module-target) = modules.record-binding ;
-
-            include $(module-target) ;
-
-            # Allow the module to see its own names with full qualification.
-            local rules = [ RULENAMES $(__name__) ] ;
-            IMPORT $(__name__) : $(rules) : $(__name__) : $(__name__).$(rules) ;
-        }
-
-        if $(module-name) != modules && ! [ binding $(module-name) ]
-        {
-            import errors ;
-            errors.error "Could not find module" $(module-name) in $(search) ;
-        }
-
-        # Pop the loading stack. Must happen before testing or we will run into
-        # a circular loading dependency.
-        .loading = $(.loading[1--2]) ;
-
-        # Run any pending tests if this is an outer load.
-        if ! $(suppress-test)
-        {
-            local argv = [ peek : ARGV ] ;
-            for local m in $(.untested)
-            {
-                run-module-test $(m) ;
-            }
-            .untested = ;
-        }
-    }
-    else if $(module-name) in $(.loading)
-    {
-        import errors ;
-        errors.error loading \"$(module-name)\"
-            : circular module loading dependency:
-            : $(.loading)" ->" $(module-name) ;
-    }
-}
-
-
-# This helper is used by load (above) to record the binding (path) of each
-# loaded module.
-#
-rule record-binding ( module-target : binding )
-{
-    $(.loading[-1]).__binding__ = $(binding) ;
-}
-
-
-# Transform each path in the list, with all backslashes converted to forward
-# slashes and all detectable redundancy removed. Something like this is probably
-# needed in path.jam, but I am not sure of that, I do not understand it, and I
-# am not ready to move all of path.jam into the kernel.
-#
-local rule normalize-raw-paths ( paths * )
-{
-    local result ;
-    for p in $(paths:T)
-    {
-        result += [ NORMALIZE_PATH $(p) ] ;
-    }
-    return $(result) ;
-}
-
-
-.cwd = [ PWD ] ;
-
-
-# Load the indicated module and import rule names into the current module. Any
-# members of rules-opt will be available without qualification in the caller's
-# module. Any members of rename-opt will be taken as the names of the rules in
-# the caller's module, in place of the names they have in the imported module.
-# If rules-opt = '*', all rules from the indicated module are imported into the
-# caller's module. If rename-opt is supplied, it must have the same number of
-# elements as rules-opt.
-#
-rule import ( module-names + : rules-opt * : rename-opt * )
-{
-    if ( $(rules-opt) = * || ! $(rules-opt) ) && $(rename-opt)
-    {
-        import errors ;
-        errors.error "Rule aliasing is only available for explicit imports." ;
-    }
-
-    if $(module-names[2]) && ( $(rules-opt) || $(rename-opt) )
-    {
-        import errors ;
-        errors.error "When loading multiple modules, no specific rules or"
-            "renaming is allowed" ;
-    }
-
-    local caller = [ CALLER_MODULE ] ;
-
-    # Import each specified module
-    for local m in $(module-names)
-    {
-        if ! $(m) in $(.loaded)
-        {
-            # If the importing module isn't already in the BOOST_BUILD_PATH,
-            # prepend it to the path.  We don't want to invert the search order
-            # of modules that are already there.
-
-            local caller-location ;
-            if $(caller)
-            {
-                caller-location = [ binding $(caller) ] ;
-                caller-location = $(caller-location:D) ;
-                caller-location = [ normalize-raw-paths $(caller-location:R=$(.cwd)) ] ;
-            }
-
-            local search = [ peek : BOOST_BUILD_PATH ] ;
-            search = [ normalize-raw-paths $(search:R=$(.cwd)) ] ;
-
-            if $(caller-location) && ! $(caller-location) in $(search)
-            {
-                search = $(caller-location) $(search) ;
-            }
-
-            load $(m) : : $(search) ;
-        }
-
-        IMPORT_MODULE $(m) : $(caller) ;
-
-        if $(rules-opt)
-        {
-            local source-names ;
-            if $(rules-opt) = *
-            {
-                local all-rules = [ RULENAMES $(m) ] ;
-                source-names = $(all-rules) ;
-            }
-            else
-            {
-                source-names = $(rules-opt) ;
-            }
-            local target-names = $(rename-opt) ;
-            target-names ?= $(source-names) ;
-            IMPORT $(m) : $(source-names) : $(caller) : $(target-names) ;
-        }
-    }
-}
-
-
-# Define exported copies in $(target-module) of all rules exported from
-# $(source-module). Also make them available in the global module with
-# qualification, so that it is just as though the rules were defined originally
-# in $(target-module).
-#
-rule clone-rules ( source-module target-module )
-{
-    local rules = [ RULENAMES $(source-module) ] ;
-
-    IMPORT $(source-module) : $(rules) : $(target-module) : $(rules) : LOCALIZE ;
-    EXPORT $(target-module) : $(rules) ;
-    IMPORT $(target-module) : $(rules) : : $(target-module).$(rules) ;
-}
-
-
-# These rules need to be available in all modules to implement module loading
-# itself and other fundamental operations.
-local globalize = peek poke record-binding ;
-IMPORT modules : $(globalize) : : modules.$(globalize) ;
-
-
-rule __test__ ( )
-{
-    import assert ;
-    import modules : normalize-raw-paths ;
-
-    module modules.__test__
-    {
-        foo = bar ;
-    }
-
-    assert.result bar : peek modules.__test__ : foo ;
-
-    poke modules.__test__ : foo : bar baz ;
-    assert.result bar baz : peek modules.__test__ : foo ;
-
-    assert.result c:/foo/bar : normalize-raw-paths c:/x/../foo/./xx/yy/../../bar ;
-    assert.result .          : normalize-raw-paths .                             ;
-    assert.result ..         : normalize-raw-paths ..                            ;
-    assert.result ../..      : normalize-raw-paths ../..                         ;
-    assert.result ..         : normalize-raw-paths ./..                          ;
-    assert.result / /        : normalize-raw-paths / \\                          ;
-    assert.result a          : normalize-raw-paths a                             ;
-    assert.result a          : normalize-raw-paths a/                            ;
-    assert.result /a         : normalize-raw-paths /a/                           ;
-    assert.result /          : normalize-raw-paths /a/..                         ;
-}
diff --git a/jam-files/boost-build/options/help.jam b/jam-files/boost-build/options/help.jam
deleted file mode 100644
index b507e1ed..00000000
--- a/jam-files/boost-build/options/help.jam
+++ /dev/null
@@ -1,212 +0,0 @@
-# Copyright 2003 Dave Abrahams 
-# Copyright 2003, 2006 Rene Rivera 
-# Copyright 2003, 2006 Vladimir Prus 
-# Distributed under the Boost Software License, Version 1.0. 
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt) 
-
-# This module is the plug-in handler for the --help and --help-.*
-# command-line options
-import modules ;
-import assert ;
-import doc : do-scan set-option set-output set-output-file print-help-usage print-help-top ;
-import sequence ;
-import set ;
-import project ;
-import print ;
-import os ;
-import version ;
-import path ;
-
-# List of possible modules, but which really aren't.
-#
-.not-modules =
-    boost-build bootstrap site-config test user-config
-    -tools allyourbase boost-base features python stlport testing unit-tests ;
-
-# The help system options are parsed here and handed off to the doc
-# module to translate into documentation requests and actions. The
-# understood options are:
-#
-#    --help-disable-<option>
-#    --help-doc-options
-#    --help-enable-<option>
-#    --help-internal
-#    --help-options
-#    --help-usage
-#    --help-output <type>
-#    --help-output-file <file>
-#    --help [<module-or-class>]
-#
-rule process (
-    command # The option.
-    : values * # The values, starting after the "=".
-    )
-{
-    assert.result --help : MATCH ^(--help).* : $(command) ;
-    local did-help = ;
-    switch $(command)
-    {
-        case --help-internal :
-        local path-to-modules = [ modules.peek : BOOST_BUILD_PATH ] ;
-        path-to-modules ?= . ;
-        local possible-modules = [ GLOB $(path-to-modules) : *\\.jam ] ;
-        local not-modules = [ GLOB $(path-to-modules) : *$(.not-modules)\\.jam ] ;
-        local modules-to-list =
-            [ sequence.insertion-sort
-                [ set.difference $(possible-modules:D=:S=) : $(not-modules:D=:S=) ] ] ;
-        local modules-to-scan ;
-        for local m in $(modules-to-list)
-        {
-            local module-files = [ GLOB $(path-to-modules) : $(m)\\.jam ] ;
-            modules-to-scan += $(module-files[1]) ;
-        }
-        do-scan $(modules-to-scan) : print-help-all ;
-        did-help = true ;
-
-        case --help-enable-* :
-        local option = [ MATCH --help-enable-(.*) : $(command) ] ; option = $(option:L) ;
-        set-option $(option) : enabled ;
-        did-help = true ;
-
-        case --help-disable-* :
-        local option = [ MATCH --help-disable-(.*) : $(command) ] ; option = $(option:L) ;
-        set-option $(option) ;
-        did-help = true ;
-
-        case --help-output :
-        set-output $(values[1]) ;
-        did-help = true ;
-
-        case --help-output-file :
-        set-output-file $(values[1]) ;
-        did-help = true ;
-
-        case --help-doc-options :
-        local doc-module-spec = [ split-symbol doc ] ;
-        do-scan $(doc-module-spec[1]) : print-help-options ;
-        did-help = true ;
-
-        case --help-options :
-        print-help-usage ;
-        did-help = true ;
-
-        case --help :
-        local spec = $(values[1]) ;
-        if $(spec)
-        {
-            local spec-parts = [ split-symbol $(spec) ] ;
-            if $(spec-parts)
-            {
-                if $(spec-parts[2])
-                {
-                    do-scan $(spec-parts[1]) : print-help-classes $(spec-parts[2]) ;
-                    do-scan $(spec-parts[1]) : print-help-rules $(spec-parts[2]) ;
-                    do-scan $(spec-parts[1]) : print-help-variables $(spec-parts[2]) ;
-                }
-                else
-                {
-                    do-scan $(spec-parts[1]) : print-help-module ;
-                }
-            }
-            else
-            {
-                EXIT "Unrecognized help option '"$(command)" "$(spec)"'." ;
-            }
-        }
-        else
-        {
-            version.print ;
-            ECHO ;
-            # First print documentation from the current Jamfile, if any.            
-            # FIXME: Generally, this duplication of project.jam logic is bad.
-            local names = [ modules.peek project : JAMROOT ]
-              [ modules.peek project : JAMFILE ] ;
-            local project-file = [ path.glob . : $(names) ] ;
-            if ! $(project-file)
-            {
-                project-file = [ path.glob-in-parents . : $(names) ] ;
-            }
-            
-            for local p in $(project-file)
-            {
-                do-scan $(p) : print-help-project $(p) ;
-            }
-            
-            # Next any user-config help.
-            local user-path = [ os.home-directories ] [ os.environ BOOST_BUILD_PATH ] ;
-            local user-config = [ GLOB $(user-path) : user-config.jam ] ;
-            if $(user-config)
-            {
-                do-scan $(user-config[1]) : print-help-config user $(user-config[1]) ;
-            }
-            
-            # Next any site-config help.
-            local site-config = [ GLOB $(user-path) : site-config.jam ] ;
-            if $(site-config)
-            {
-                do-scan $(site-config[1]) : print-help-config site $(site-config[1]) ;
-            }
-
-            # Then the overall help.
-            print-help-top ;
-        }
-        did-help = true ;
-    }
-    if $(did-help)
-    {
-        UPDATE all ;
-        NOCARE all ;
-    }
-    return $(did-help) ;
-}
-
-# Split a reference to a symbol into module and symbol parts.
-#
-local rule split-symbol (
-    symbol # The symbol to split.
-    )
-{
-    local path-to-modules = [ modules.peek : BOOST_BUILD_PATH ] ;
-    path-to-modules ?= . ;
-    local module-name = $(symbol) ;
-    local symbol-name = ;
-    local result = ;
-    while ! $(result)
-    {
-        local module-path = [ GLOB $(path-to-modules) : $(module-name)\\.jam ] ;
-        if $(module-path)
-        {
-            # The 'module-name' in fact refers to module. Return the full
-            # module path and a symbol within it. If 'symbol' passed to this
-            # rule is already module, 'symbol-name' will be empty. Otherwise,
-            # it's initialized on the previous loop iteration.
-            # In case there are several modules by this name,
-            # use the first one.
-            result = $(module-path[1]) $(symbol-name) ;
-        }
-        else
-        {
-            if ! $(module-name:S)
-            {
-                result = - ;
-            }
-            else
-            {
-                local next-symbol-part = [ MATCH ^.(.*) : $(module-name:S) ] ;
-                if $(symbol-name)
-                {
-                    symbol-name = $(next-symbol-part).$(symbol-name) ;
-                }
-                else
-                {
-                    symbol-name = $(next-symbol-part) ;
-                }
-                module-name = $(module-name:B) ;
-            }
-        }
-    }
-    if $(result) != -
-    {
-        return $(result) ;
-    }
-}
diff --git a/jam-files/boost-build/site-config.jam b/jam-files/boost-build/site-config.jam
deleted file mode 100644
index ad22d674..00000000
--- a/jam-files/boost-build/site-config.jam
+++ /dev/null
@@ -1,4 +0,0 @@
-# Copyright 2002, 2003 Vladimir Prus 
-# Distributed under the Boost Software License, Version 1.0. 
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt) 
-
diff --git a/jam-files/boost-build/tools/__init__.py b/jam-files/boost-build/tools/__init__.py
deleted file mode 100644
index e69de29b..00000000
--- a/jam-files/boost-build/tools/__init__.py
+++ /dev/null
diff --git a/jam-files/boost-build/tools/acc.jam b/jam-files/boost-build/tools/acc.jam
deleted file mode 100644
index f04c9dc8..00000000
--- a/jam-files/boost-build/tools/acc.jam
+++ /dev/null
@@ -1,118 +0,0 @@
-# Copyright Vladimir Prus 2004.
-# Copyright Toon Knapen 2004.
-# Copyright Boris Gubenko 2007.
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt
-# or copy at http://www.boost.org/LICENSE_1_0.txt)
-
-#
-# Boost.Build V2 toolset for the HP aC++ compiler.
-#
-
-import toolset : flags ;
-import feature ;
-import generators ;
-import common ;
-
-feature.extend toolset : acc ;
-toolset.inherit acc : unix ;
-generators.override builtin.lib-generator : acc.prebuilt ;
-generators.override acc.searched-lib-generator : searched-lib-generator ;
-
-# Configures the acc toolset.
-rule init ( version ? : user-provided-command * : options * )
-{
-    local condition = [ common.check-init-parameters acc
-        : version $(version) ] ;
-
-    local command = [ common.get-invocation-command acc : aCC
-        : $(user-provided-command) ] ;
-
-    common.handle-options acc : $(condition) : $(command) : $(options) ;
-}
-
-
-# Declare generators
-generators.register-c-compiler acc.compile.c : C : OBJ : <toolset>acc ;
-generators.register-c-compiler acc.compile.c++ : CPP : OBJ : <toolset>acc ;
-
-# Declare flags.
-flags acc CFLAGS <optimization>off : ;
-flags acc CFLAGS <optimization>speed : -O3 ;
-flags acc CFLAGS <optimization>space : -O2 ;
-
-flags acc CFLAGS <inlining>off : +d ;
-flags acc CFLAGS <inlining>on : ;
-flags acc CFLAGS <inlining>full : ;
-
-flags acc C++FLAGS <exception-handling>off : ;
-flags acc C++FLAGS <exception-handling>on : ;
-
-flags acc C++FLAGS <rtti>off : ;
-flags acc C++FLAGS <rtti>on : ;
-
-# We want the full path to the sources in the debug symbols because otherwise
-# the debugger won't find the sources when we use boost.build.
-flags acc CFLAGS <debug-symbols>on : -g ;
-flags acc LINKFLAGS <debug-symbols>on : -g ;
-flags acc LINKFLAGS <debug-symbols>off : -s ;
-
-# V2 does not have <shared-linkable>, not sure what this meant in V1.
-# flags acc CFLAGS <shared-linkable>true : +Z ;
-
-flags acc CFLAGS <profiling>on : -pg ;
-flags acc LINKFLAGS <profiling>on : -pg ;
-
-flags acc CFLAGS <address-model>64 : +DD64 ;
-flags acc LINKFLAGS <address-model>64 : +DD64 ;
-
-# It is unknown if there's separate option for rpath used only
-# at link time, similar to -rpath-link in GNU. We'll use -L.
-flags acc RPATH_LINK : <xdll-path> ;
-
-flags acc CFLAGS <cflags> ;
-flags acc C++FLAGS <cxxflags> ;
-flags acc DEFINES <define> ;
-flags acc UNDEFS <undef> ;
-flags acc HDRS <include> ;
-flags acc STDHDRS <sysinclude> ;
-flags acc LINKFLAGS <linkflags> ;
-flags acc ARFLAGS <arflags> ;
-
-flags acc LIBPATH <library-path> ;
-flags acc NEEDLIBS <library-file> ;
-flags acc FINDLIBS <find-shared-library> ;
-flags acc FINDLIBS <find-static-library> ;
-
-# Select the compiler name according to the threading model.
-flags acc CFLAGS <threading>multi : -mt   ;
-flags acc LINKFLAGS <threading>multi : -mt ;
-
-flags acc.compile.c++ TEMPLATE_DEPTH <c++-template-depth> ;
-
-
-actions acc.link bind NEEDLIBS
-{
-    $(CONFIG_COMMAND) -AA $(LINKFLAGS) -o "$(<[1])" -L"$(RPATH_LINK)" -L$(LIBPATH) -L$(STDLIBPATH) "$(>)" "$(NEEDLIBS)" "$(NEEDLIBS)" -l$(FINDLIBS) $(OPTIONS)
-}
-
-SPACE = " " ;
-actions acc.link.dll bind NEEDLIBS
-{
-    $(CONFIG_COMMAND) -AA -b $(LINKFLAGS) -o "$(<[1])" -L"$(RPATH_LINK)" -Wl,+h$(<[-1]:D=) -L$(LIBPATH) -L$(STDLIBPATH) "$(>)" "$(NEEDLIBS)" "$(NEEDLIBS)" -l$(FINDLIBS) $(OPTIONS)
-}
-
-actions acc.compile.c
-{
-    cc -c -I$(BOOST_ROOT) -U$(UNDEFS) -D$(DEFINES) $(CFLAGS) -I"$(HDRS)" -I"$(STDHDRS)" -o "$(<)" "$(>)" $(OPTIONS)
-}
-
-actions acc.compile.c++
-{
-    $(CONFIG_COMMAND) -AA -c -Wc,--pending_instantiations=$(TEMPLATE_DEPTH) -I$(BOOST_ROOT) -U$(UNDEFS) -D$(DEFINES) $(CFLAGS) $(C++FLAGS) -I"$(HDRS)" -I"$(STDHDRS)" -o "$(<)" "$(>)" $(OPTIONS)
-}
-
-actions updated together piecemeal acc.archive
-{
-    ar ru$(ARFLAGS:E="") "$(<)" "$(>)"
-}
diff --git a/jam-files/boost-build/tools/auto-index.jam b/jam-files/boost-build/tools/auto-index.jam
deleted file mode 100644
index ebbf344e..00000000
--- a/jam-files/boost-build/tools/auto-index.jam
+++ /dev/null
@@ -1,212 +0,0 @@
-
-import feature ;
-import generators ;
-import "class" ;
-import toolset ;
-import targets ;
-import "class" : new ;
-import project ;
-
-feature.feature auto-index : off "on" ;
-feature.feature auto-index-internal : off "on" ;
-feature.feature auto-index-verbose : off "on" ;
-feature.feature auto-index-no-duplicates : off "on" ;
-feature.feature auto-index-script : : free ;
-feature.feature auto-index-prefix : : free ;
-feature.feature auto-index-type : : free ;
-feature.feature auto-index-section-names : "on" off ;
-
-toolset.flags auto-index.auto-index FLAGS <auto-index-internal>on : --internal-index ;
-toolset.flags auto-index.auto-index SCRIPT <auto-index-script> ;
-toolset.flags auto-index.auto-index PREFIX <auto-index-prefix> ;
-toolset.flags auto-index.auto-index INDEX_TYPE <auto-index-type> ;
-toolset.flags auto-index.auto-index FLAGS <auto-index-verbose>on : --verbose ;
-toolset.flags auto-index.auto-index FLAGS <auto-index-no-duplicates>on : --no-duplicates ;
-toolset.flags auto-index.auto-index FLAGS <auto-index-section-names>off : --no-section-names ;
-
-# <auto-index-binary> shell command to run AutoIndex
-# <auto-index-binary-dependencies> targets to build AutoIndex from sources.
-feature.feature <auto-index-binary> : : free ;
-feature.feature <auto-index-binary-dependencies> : : free dependency ;
-
-class auto-index-generator : generator
-{
-    import common modules path targets build-system ;
-    rule run ( project name ? : property-set : sources * )
-    {
-        # AutoIndex invocation command and dependencies.
-        local auto-index-binary = [ modules.peek auto-index : .command ] ;
-        local auto-index-binary-dependencies ;
-
-        if $(auto-index-binary)
-        {
-            # Use user-supplied command.
-            auto-index-binary = [ common.get-invocation-command auto-index : auto-index : $(auto-index-binary) ] ;
-        }
-        else
-        {
-            # Search for AutoIndex sources in sensible places, like
-            #   $(BOOST_ROOT)/tools/auto_index
-            #   $(BOOST_BUILD_PATH)/../../auto_index
-
-            # And build auto-index executable from sources.
-
-            local boost-root = [ modules.peek : BOOST_ROOT ] ;
-            local boost-build-path = [ build-system.location ] ;
-            local boost-build-path2 = [ modules.peek : BOOST_BUILD_PATH ] ;
-
-            local auto-index-dir ;
-
-            if $(boost-root)
-            {
-                auto-index-dir += [ path.join $(boost-root) tools ] ;
-            }
-
-            if $(boost-build-path)
-            {
-                auto-index-dir += $(boost-build-path)/../.. ;
-            }
-            if $(boost-build-path2)
-            {
-                auto-index-dir += $(boost-build-path2)/.. ;
-            }
-
-            #ECHO $(auto-index-dir) ;
-            auto-index-dir = [ path.glob $(auto-index-dir) : auto_index ] ;
-            #ECHO $(auto-index-dir) ;
-
-            # If the AutoIndex source directory was found, mark its main target
-            # as a dependency for the current project. Otherwise, try to find
-            # 'auto-index' in user's PATH
-            if $(auto-index-dir)
-            {
-                auto-index-dir = [ path.make $(auto-index-dir[1]) ] ;
-                auto-index-dir = $(auto-index-dir)/build ;
-                
-                #ECHO $(auto-index-dir) ;
-
-                # Get the main-target in AutoIndex directory.
-                local auto-index-main-target = [ targets.resolve-reference $(auto-index-dir) : $(project) ] ;
-                
-                #ECHO $(auto-index-main-target) ;
-
-                # The first element are actual targets, the second are
-                # properties found in target-id. We do not care about these
-                # since we have passed the id ourselves.
-                auto-index-main-target =
-                    [ $(auto-index-main-target[1]).main-target auto_index ] ;
-
-                #ECHO $(auto-index-main-target) ;
-
-                auto-index-binary-dependencies =
-                    [ $(auto-index-main-target).generate [ $(property-set).propagated ] ] ;
-
-                # Ignore usage-requirements returned as first element.
-                auto-index-binary-dependencies = $(auto-index-binary-dependencies[2-]) ;
-
-                # Some toolsets generate extra targets (e.g. RSP). We must mark
-                # all targets as dependencies for the project, but we will only
-                # use the EXE target for auto-index-to-boostbook translation.
-                for local target in $(auto-index-binary-dependencies)
-                {
-                    if [ $(target).type ] = EXE
-                    {
-                        auto-index-binary = 
-                            [ path.native 
-                                [ path.join
-                                    [ $(target).path ]
-                                    [ $(target).name ]
-                                ]
-                            ] ;
-                    }
-                }
-            }
-            else
-            {
-                ECHO "AutoIndex warning: The path to the auto-index executable was" ;
-                ECHO "  not provided. Additionally, couldn't find AutoIndex" ;
-                ECHO "  sources searching in" ;
-                ECHO "    * BOOST_ROOT/tools/auto-index" ;
-                ECHO "    * BOOST_BUILD_PATH/../../auto-index" ;
-                ECHO "  Will now try to find a precompiled executable by searching" ;
-                ECHO "  the PATH for 'auto-index'." ;
-                ECHO "  To disable this warning in the future, or to completely" ;
-                ECHO "  avoid compilation of auto-index, you can explicitly set the" ;
-                ECHO "  path to a auto-index executable command in user-config.jam" ;
-                ECHO "  or site-config.jam with the call" ;
-                ECHO "    using auto-index : /path/to/auto-index ;" ;
-
-                # As a last resort, search for 'auto-index' command in path. Note
-                # that even if the 'auto-index' command is not found,
-                # get-invocation-command will still return 'auto-index' and might
-                # generate an error while generating the virtual-target.
-
-                auto-index-binary = [ common.get-invocation-command auto-index : auto-index ] ;
-            }
-        }
-
-        # Add $(auto-index-binary-dependencies) as a dependency of the current
-        # project and set it as the <auto-index-binary> feature for the
-        # auto-index-to-boostbook rule, below.
-        property-set = [ $(property-set).add-raw
-            <dependency>$(auto-index-binary-dependencies)
-            <auto-index-binary>$(auto-index-binary)
-            <auto-index-binary-dependencies>$(auto-index-binary-dependencies)
-        ] ;
-        
-        #ECHO "binary = " $(auto-index-binary) ;
-        #ECHO "dependencies = " $(auto-index-binary-dependencies) ;
-
-        if [ $(property-set).get <auto-index> ] = "on"
-        {
-            return [ generator.run $(project) $(name) : $(property-set) : $(sources) ] ;
-        }
-        else
-        {
-            return [ generators.construct $(project) $(name) : DOCBOOK : $(property-set)
-              : $(sources) ] ;
-        }        
-    }
-}
-
-# Initialization of toolset.
-#
-# Parameters:
-#   command ?    -> path to AutoIndex executable.
-#
-# When command is not supplied toolset will search for AutoIndex directory and
-# compile the executable from source. If that fails we still search the path for
-# 'auto_index'.
-#
-rule init (
-        command ?   # path to the AutoIndex executable.
-    )
-{
-    if ! $(.initialized)
-    {
-        .initialized = true ;
-        .command = $(command) ;
-    }
-}
-
-toolset.flags auto-index.auto-index AI-COMMAND      <auto-index-binary> ;
-toolset.flags auto-index.auto-index AI-DEPENDENCIES <auto-index-binary-dependencies> ;
-
-generators.register [ class.new auto-index-generator auto-index.auto-index : DOCBOOK : DOCBOOK(%.auto_index) ] ;
-generators.override auto-index.auto-index : boostbook.boostbook-to-docbook ;
-
-rule auto-index ( target : source : properties * )
-{
-    # Signal dependency of auto-index sources on <auto-index-binary-dependencies>
-    # upon invocation of auto-index-to-boostbook.
-    #ECHO "AI-COMMAND= " $(AI-COMMAND) ;
-    DEPENDS $(target) : [ on $(target) return $(AI-DEPENDENCIES) ] ;
-    #DEPENDS $(target) : [ on $(target) return $(SCRIPT) ] ;
-}
-
-actions auto-index
-{
-    $(AI-COMMAND) $(FLAGS) "--prefix="$(PREFIX) "--script="$(SCRIPT) "--index-type="$(INDEX_TYPE) "--in="$(>) "--out="$(<)
-}
-
-
diff --git a/jam-files/boost-build/tools/bison.jam b/jam-files/boost-build/tools/bison.jam
deleted file mode 100644
index 0689d4bd..00000000
--- a/jam-files/boost-build/tools/bison.jam
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 2003 Vladimir Prus 
-# Distributed under the Boost Software License, Version 1.0. 
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt) 
-
-import generators ;
-import feature ;
-import type ;
-import property ;
-
-feature.feature bison.prefix : : free ;
-type.register Y : y ;
-type.register YY : yy ;
-generators.register-standard bison.bison : Y : C H ;
-generators.register-standard bison.bison : YY : CPP HPP ;
-
-rule init ( )
-{
-}
-
-rule bison ( dst dst_header : src : properties * )
-{
-    local r = [ property.select bison.prefix : $(properties) ] ;
-    if $(r)
-    {
-        PREFIX_OPT on $(<) = -p $(r:G=) ;
-    }
-}
-
-actions bison 
-{
-    bison $(PREFIX_OPT) -d -o $(<[1]) $(>)
-}
diff --git a/jam-files/boost-build/tools/boostbook-config.jam b/jam-files/boost-build/tools/boostbook-config.jam
deleted file mode 100644
index 6e3f3ddc..00000000
--- a/jam-files/boost-build/tools/boostbook-config.jam
+++ /dev/null
@@ -1,13 +0,0 @@
-#~ Copyright 2005 Rene Rivera.
-#~ Distributed under the Boost Software License, Version 1.0.
-#~ (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-# Automatic configuration for BoostBook tools. To use, just import this module.
-#
-# This module is deprecated.
-#   using boostbook ;
-# with no arguments now suffices.
-
-import toolset : using ;
-
-using boostbook ;
diff --git a/jam-files/boost-build/tools/boostbook.jam b/jam-files/boost-build/tools/boostbook.jam
deleted file mode 100644
index 3a5964c6..00000000
--- a/jam-files/boost-build/tools/boostbook.jam
+++ /dev/null
@@ -1,727 +0,0 @@
-# Copyright 2003, 2004, 2005 Dave Abrahams 
-# Copyright 2003, 2004, 2005 Douglas Gregor 
-# Copyright 2005, 2006, 2007 Rene Rivera 
-# Copyright 2003, 2004, 2005 Vladimir Prus 
-# Distributed under the Boost Software License, Version 1.0. 
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt) 
-
-#  This module defines rules to handle generation of documentation
-#  from BoostBook sources.
-#
-#  The type of output is controlled by the <format> feature which can
-#  have the following values::
-#
-#   * html: Generates html documention.  This is the default.
-#   * xhtml: Generates xhtml documentation
-#   * htmlhelp: Generates html help output.
-#   * onehtml: Generates a single html page.
-#   * man: Generates man pages.
-#   * pdf: Generates pdf documentation.
-#   * ps: Generates postscript output.
-#   * docbook: Generates docbook XML.
-#   * fo: Generates XSL formating objects.
-#   * tests: Extracts test cases from the boostbook XML.
-#
-#  format is an implicit feature, so typing pdf on the command
-#  line (for example) is a short-cut for format=pdf.
-
-import "class" : new ;
-import common ;
-import errors ;
-import targets ;
-import feature ;
-import generators ;
-import print ;
-import property ;
-import project ;
-import property-set ;
-import regex ;
-import scanner ;
-import sequence ;
-import make ;
-import os ;
-import type ;
-import modules path project ;
-import build-system ;
-
-import xsltproc : xslt xslt-dir ;
-
-# Make this module into a project.
-project.initialize $(__name__) ;
-project boostbook ;
-
-
-feature.feature format : html xhtml htmlhelp onehtml man pdf ps docbook fo tests
-  : incidental implicit composite propagated ;
-
-type.register DTDXML : dtdxml ;
-type.register XML : xml ;
-type.register BOOSTBOOK : boostbook : XML ;
-type.register DOCBOOK : docbook : XML ; 
-type.register FO : fo : XML ;
-type.register PDF : pdf ;
-type.register PS : ps ;
-type.register XSLT : xsl : XML ;
-type.register HTMLDIR ;
-type.register XHTMLDIR ;
-type.register HTMLHELP ;
-type.register MANPAGES ;
-type.register TESTS : tests ;
-# Artificial target type, used to require invocation of top-level
-# BoostBook generator.
-type.register BOOSTBOOK_MAIN ;
-
-
-# Initialize BoostBook support.
-rule init (
-      docbook-xsl-dir ? # The DocBook XSL stylesheet directory. If not
-                        # provided, we use DOCBOOK_XSL_DIR from the environment
-                        # (if available) or look in standard locations.
-                        # Otherwise, we let the XML processor load the
-                        # stylesheets remotely.
-            
-    : docbook-dtd-dir ? # The DocBook DTD directory. If not provided, we use
-                        # DOCBOOK_DTD_DIR From the environment (if available) or
-                        # look in standard locations.  Otherwise, we let the XML
-                        # processor load the DTD remotely.
-
-    : boostbook-dir ?   # The BoostBook directory with the DTD and XSL subdirs.
-)
-{
-
-  if ! $(.initialized) 
-  {
-    .initialized = true ;
-    
-    check-boostbook-dir $(boostbook-dir) ;
-    find-tools $(docbook-xsl-dir) : $(docbook-dtd-dir) : $(boostbook-dir) ;
-
-    # Register generators only if we've were called via "using boostbook ; "
-    generators.register-standard boostbook.dtdxml-to-boostbook : DTDXML : XML ;
-    generators.register-standard boostbook.boostbook-to-docbook : XML : DOCBOOK ;
-    generators.register-standard boostbook.boostbook-to-tests : XML : TESTS ;
-    generators.register-standard boostbook.docbook-to-onehtml : DOCBOOK : HTML ;
-    generators.register-standard boostbook.docbook-to-htmldir : DOCBOOK : HTMLDIR ;
-    generators.register-standard boostbook.docbook-to-xhtmldir : DOCBOOK : XHTMLDIR ;
-    generators.register-standard boostbook.docbook-to-htmlhelp : DOCBOOK : HTMLHELP ;
-    generators.register-standard boostbook.docbook-to-manpages : DOCBOOK : MANPAGES ;
-    generators.register-standard boostbook.docbook-to-fo : DOCBOOK : FO ;
-    
-    # The same about Jamfile main target rules.
-    IMPORT $(__name__) : boostbook : : boostbook ;
-  }
-  else
-  {
-    if $(docbook-xsl-dir) 
-    {
-      modify-config ;
-      .docbook-xsl-dir = [ path.make $(docbook-xsl-dir) ] ;
-      check-docbook-xsl-dir ;
-    }
-    if $(docbook-dtd-dir) 
-    {
-      modify-config ;
-      .docbook-dtd-dir = [ path.make $(docbook-dtd-dir) ] ;
-      check-docbook-dtd-dir ;
-    }
-    if $(boostbook-dir)
-    {
-      modify-config ;
-      check-boostbook-dir $(boostbook-dir) ;
-      local boostbook-xsl-dir = [ path.glob $(boostbook-dir) : xsl ] ;
-      local boostbook-dtd-dir = [ path.glob $(boostbook-dir) : dtd ] ;
-      .boostbook-xsl-dir = $(boostbook-xsl-dir[1]) ;
-      .boostbook-dtd-dir = $(boostbook-dtd-dir[1]) ;
-      check-boostbook-xsl-dir ;
-      check-boostbook-dtd-dir ;
-    }
-  }
-}
-
-rule lock-config ( )
-{
-  if ! $(.initialized)
-  {
-    errors.user-error "BoostBook has not been configured." ;
-  }
-  if ! $(.config-locked)
-  {
-    .config-locked = true ;
-  }
-}
-
-rule modify-config ( )
-{
-  if $(.config-locked)
-  {
-    errors.user-error "BoostBook configuration cannot be changed after it has been used." ;
-  }
-}
-
-rule find-boost-in-registry ( keys * )
-{
-  local boost-root = ;
-  for local R in $(keys) 
-  {
-    local installed-boost = [ W32_GETREG
-      "HKEY_LOCAL_MACHINE\\SOFTWARE\\$(R)"
-      : "InstallRoot" ] ;
-    if $(installed-boost)
-    {
-      boost-root += [ path.make $(installed-boost) ] ;
-    }
-  }
-  return $(boost-root) ;
-}
-
-rule check-docbook-xsl-dir ( )
-{
-  if $(.docbook-xsl-dir)
-  {
-    if ! [ path.glob $(.docbook-xsl-dir) : common/common.xsl ]
-    {
-      errors.user-error "BoostBook: could not find docbook XSL stylesheets in:" [ path.native $(.docbook-xsl-dir) ] ;
-    }
-    else
-    {
-      if --debug-configuration in [ modules.peek : ARGV ]
-      {
-        ECHO "notice: BoostBook: found docbook XSL stylesheets in:" [ path.native $(.docbook-xsl-dir) ] ;
-      }
-    }
-  }
-}
-
-rule check-docbook-dtd-dir ( )
-{
-  if $(.docbook-dtd-dir)
-  {
-    if ! [ path.glob $(.docbook-dtd-dir) : docbookx.dtd ]
-    {
-      errors.user-error "error: BoostBook: could not find docbook DTD in:" [ path.native $(.docbook-dtd-dir) ] ;
-    }
-    else
-    {
-      if --debug-configuration in [ modules.peek : ARGV ]
-      {
-        ECHO "notice: BoostBook: found docbook DTD in:" [ path.native $(.docbook-dtd-dir) ] ;
-      }
-    }
-  }
-}
-
-rule check-boostbook-xsl-dir ( )
-{
-  if ! $(.boostbook-xsl-dir)
-  {
-    errors.user-error "error: BoostBook: could not find boostbook XSL stylesheets." ;
-  }
-  else if ! [ path.glob $(.boostbook-xsl-dir) : docbook.xsl ]
-  {
-    errors.user-error "error: BoostBook: could not find docbook XSL stylesheets in:" [ path.native $(.boostbook-xsl-dir) ] ;
-  }
-  else
-  {
-    if --debug-configuration in [ modules.peek : ARGV ]
-    {
-      ECHO "notice: BoostBook: found boostbook XSL stylesheets in:" [ path.native $(.boostbook-xsl-dir) ] ;
-    }
-  }
-}
-
-rule check-boostbook-dtd-dir ( )
-{
-  if ! $(.boostbook-dtd-dir)
-  {
-    errors.user-error "error: BoostBook: could not find boostbook DTD." ;
-  }
-  else if ! [ path.glob $(.boostbook-dtd-dir) : boostbook.dtd ]
-  {
-    errors.user-error "error: BoostBook: could not find boostbook DTD in:" [ path.native $(.boostbook-dtd-dir) ] ;
-  }
-  else
-  {
-    if --debug-configuration in [ modules.peek : ARGV ]
-    {
-      ECHO "notice: BoostBook: found boostbook DTD in:" [ path.native $(.boostbook-dtd-dir) ] ;
-    }
-  }
-}
-
-rule check-boostbook-dir ( boostbook-dir ? )
-{
-  if $(boostbook-dir) && ! [ path.glob $(boostbook-dir) : xsl ]
-  {
-    errors.user-error "error: BoostBook: could not find boostbook in:" [ path.native $(boostbook-dir) ] ;
-  }
-}
-
-rule find-tools ( docbook-xsl-dir ? : docbook-dtd-dir ? : boostbook-dir ? )
-{
-  docbook-xsl-dir ?= [ modules.peek : DOCBOOK_XSL_DIR ] ;
-  docbook-dtd-dir ?= [ modules.peek : DOCBOOK_DTD_DIR ] ;
-  boostbook-dir ?= [ modules.peek : BOOSTBOOK_DIR ] ;
-
-  # Look for the boostbook stylesheets relative to BOOST_ROOT
-  # and Boost.Build.
-  local boost-build-root = [ path.make [ build-system.location ] ] ;
-  local boostbook-search-dirs = [ path.join $(boost-build-root) .. .. ] ;
-
-  local boost-root =  [ modules.peek : BOOST_ROOT ] ;
-  if $(boost-root)
-  {
-    boostbook-search-dirs += [ path.join [ path.make $(boost-root) ] tools ] ;
-  }
-  boostbook-dir ?= [ path.glob $(boostbook-search-dirs) : boostbook* ] ; 
-
-  # Try to find the tools in platform specific locations
-  if [ os.name ] = NT
-  {
-    # If installed by the Boost installer.
-    local boost-root = ;
-
-    local boost-installer-versions = snapshot cvs 1.33.0 ;
-    local boost-consulting-installer-versions = 1.33.1 1.34.0 1.34.1 ;
-    local boostpro-installer-versions =
-        1.35.0 1.36.0 1.37.0 1.38.0 1.39.0 1.40.0 1.41.0 1.42.0
-        1.43.0 1.44.0 1.45.0 1.46.0 1.47.0 1.48.0 1.49.0 1.50.0 ;
-
-    local old-installer-root = [ find-boost-in-registry Boost.org\\$(boost-installer-versions) ] ;
-
-    # Make sure that the most recent version is searched for first
-    boost-root += [ sequence.reverse
-      [ find-boost-in-registry
-        Boost-Consulting.com\\$(boost-consulting-installer-versions)
-        boostpro.com\\$(boostpro-installer-versions) ] ] ;
-
-    # Plausible locations.
-    local root = [ PWD ] ;
-    while $(root) != $(root:D) { root = $(root:D) ; }
-    root = [ path.make $(root) ] ;
-    local search-dirs = ;
-    local docbook-search-dirs = ;
-    for local p in $(boost-root) {
-      search-dirs += [ path.join $(p) tools ] ;
-    }
-    for local p in $(old-installer-root)
-    {
-      search-dirs += [ path.join $(p) share ] ;
-      docbook-search-dirs += [ path.join $(p) share ] ;
-    }
-    search-dirs += [ path.join $(root) Boost tools ] ;
-    search-dirs += [ path.join $(root) Boost share ] ;
-    docbook-search-dirs += [ path.join $(root) Boost share ] ;
-
-    docbook-xsl-dir ?= [ path.glob $(docbook-search-dirs) : docbook-xsl* ] ;
-    docbook-dtd-dir ?= [ path.glob $(docbook-search-dirs) : docbook-xml* ] ;
-    boostbook-dir ?= [ path.glob $(search-dirs) : boostbook* ] ;
-  }
-  else
-  {
-    # Plausible locations.
-
-    local share = /usr/local/share /usr/share /opt/share /opt/local/share ;
-    local dtd-versions = 4.2 ;
-
-    docbook-xsl-dir ?= [ path.glob $(share) : docbook-xsl* ] ;
-    docbook-xsl-dir ?= [ path.glob $(share)/sgml/docbook : xsl-stylesheets ] ;
-    docbook-xsl-dir ?= [ path.glob $(share)/xsl : docbook* ] ;
-
-    docbook-dtd-dir ?= [ path.glob $(share) : docbook-xml* ] ;
-    docbook-dtd-dir ?= [ path.glob $(share)/sgml/docbook : xml-dtd-$(dtd-versions)* ] ;
-    docbook-dtd-dir ?= [ path.glob $(share)/xml/docbook : $(dtd-versions) ] ;
-
-    boostbook-dir ?= [ path.glob $(share) : boostbook* ] ;
-
-    # Ubuntu Linux
-    docbook-xsl-dir ?= [ path.glob /usr/share/xml/docbook/stylesheet : nwalsh ] ;
-    docbook-dtd-dir ?= [ path.glob /usr/share/xml/docbook/schema/dtd : $(dtd-versions) ] ;
-  }
-
-  if $(docbook-xsl-dir) 
-  {
-    .docbook-xsl-dir = [ path.make $(docbook-xsl-dir[1]) ] ;
-  }
-  if $(docbook-dtd-dir) 
-  {
-    .docbook-dtd-dir = [ path.make $(docbook-dtd-dir[1]) ] ;
-  }
-
-  if --debug-configuration in [ modules.peek : ARGV ] 
-  {
-    ECHO "notice: Boost.Book: searching XSL/DTD in" ;
-    ECHO "notice:" [ sequence.transform path.native : $(boostbook-dir) ] ;
-  }    
-  local boostbook-xsl-dir ;
-  for local dir in $(boostbook-dir) {
-    boostbook-xsl-dir += [ path.glob $(dir) : xsl ] ;
-  }
-  local boostbook-dtd-dir ; 
-  for local dir in $(boostbook-dir) {
-    boostbook-dtd-dir += [ path.glob $(dir) : dtd ] ;
-  }
-  .boostbook-xsl-dir = $(boostbook-xsl-dir[1]) ;
-  .boostbook-dtd-dir = $(boostbook-dtd-dir[1]) ;
-
-  check-docbook-xsl-dir ;
-  check-docbook-dtd-dir ;
-  check-boostbook-xsl-dir ;
-  check-boostbook-dtd-dir ; 
-}
-
-rule xsl-dir
-{
-  lock-config ;
-  return $(.boostbook-xsl-dir) ;
-}
-
-rule dtd-dir
-{
-  lock-config ;
-  return $(.boostbook-dtd-dir) ;
-}
-
-rule docbook-xsl-dir
-{
-  lock-config ;
-  return $(.docbook-xsl-dir) ;
-}
-
-rule docbook-dtd-dir
-{
-  lock-config ;
-  return $(.docbook-dtd-dir) ;
-}
-
-rule dtdxml-to-boostbook ( target : source : properties * )
-{
-  lock-config ;
-  xslt $(target) : $(source) "$(.boostbook-xsl-dir)/dtd/dtd2boostbook.xsl" 
-                 : $(properties) ;
-}
-
-rule boostbook-to-docbook ( target : source : properties * )
-{
-  lock-config ;
-  local stylesheet = [ path.native $(.boostbook-xsl-dir)/docbook.xsl ] ;
-  xslt $(target) : $(source) $(stylesheet) : $(properties) ;
-}
-
-rule docbook-to-onehtml ( target : source : properties * )
-{
-  lock-config ;
-  local stylesheet = [ path.native $(.boostbook-xsl-dir)/html-single.xsl ] ;
-  xslt $(target) : $(source) $(stylesheet) : $(properties) ;
-}
-
-rule docbook-to-htmldir ( target : source : properties * )
-{
-  lock-config ;
-  local stylesheet = [ path.native $(.boostbook-xsl-dir)/html.xsl ] ;
-  xslt-dir $(target) : $(source) $(stylesheet) : $(properties) : html ;
-}
-
-rule docbook-to-xhtmldir ( target : source : properties * )
-{
-  lock-config ;
-  local stylesheet = [ path.native $(.boostbook-xsl-dir)/xhtml.xsl ] ;
-  xslt-dir $(target) : $(source) $(stylesheet) : $(properties) : xhtml ;
-}
-
-rule docbook-to-htmlhelp ( target : source : properties * )
-{
-  lock-config ;
-  local stylesheet = [ path.native $(.boostbook-xsl-dir)/html-help.xsl ] ;
-  xslt-dir $(target) : $(source) $(stylesheet) : $(properties) : htmlhelp ;
-}
-
-rule docbook-to-manpages ( target : source : properties * )
-{
-  lock-config ;
-  local stylesheet = [ path.native $(.boostbook-xsl-dir)/manpages.xsl ] ;
-  xslt-dir $(target) : $(source) $(stylesheet) : $(properties) : man ;
-}
-
-rule docbook-to-fo ( target : source : properties * )
-{
-  lock-config ;
-  local stylesheet = [ path.native $(.boostbook-xsl-dir)/fo.xsl ] ;
-  xslt $(target) : $(source) $(stylesheet) : $(properties) ;
-}
-
-rule format-catalog-path ( path )
-{
-    local result = $(path) ;
-    if [ xsltproc.is-cygwin ]
-    {
-        if [ os.name ] = NT
-        {
-            drive = [ MATCH ^/(.):(.*)$ : $(path) ] ;
-            result = /cygdrive/$(drive[1])$(drive[2]) ;
-        }
-    }
-    else
-    {
-        if [ os.name ] = CYGWIN
-        {
-            local native-path = [ path.native $(path) ] ;
-            result = [ path.make $(native-path:W) ] ;
-        }
-    }
-    return [ regex.replace $(result) " " "%20" ] ;
-}
-
-rule generate-xml-catalog ( target : sources * : properties * )
-{
-  print.output $(target) ;
-
-  # BoostBook DTD catalog entry
-  local boostbook-dtd-dir = [ boostbook.dtd-dir ] ;
-  if $(boostbook-dtd-dir)
-  {      
-    boostbook-dtd-dir = [ format-catalog-path $(boostbook-dtd-dir) ] ;
-  }
-    
-  print.text
-    "<?xml version=\"1.0\"?>"
-    "<!DOCTYPE catalog "
-    "  PUBLIC \"-//OASIS/DTD Entity Resolution XML Catalog V1.0//EN\""
-    "  \"http://www.oasis-open.org/committees/entity/release/1.0/catalog.dtd\">"
-    "<catalog xmlns=\"urn:oasis:names:tc:entity:xmlns:xml:catalog\">"
-    "  <rewriteURI uriStartString=\"http://www.boost.org/tools/boostbook/dtd/\" rewritePrefix=\"file://$(boostbook-dtd-dir)/\"/>"
-    : true ;
-
-  local docbook-xsl-dir = [ boostbook.docbook-xsl-dir ] ;    
-  if ! $(docbook-xsl-dir) 
-  {
-    ECHO "BoostBook warning: no DocBook XSL directory specified." ;
-    ECHO "  If you have the DocBook XSL stylesheets installed, please " ;
-    ECHO "  set DOCBOOK_XSL_DIR to the stylesheet directory on either " ;
-    ECHO "  the command line (via -sDOCBOOK_XSL_DIR=...) or in a " ;
-    ECHO "  Boost.Jam configuration file. The DocBook XSL stylesheets " ;
-    ECHO "  are available here: http://docbook.sourceforge.net/ " ;
-    ECHO "  Stylesheets will be downloaded on-the-fly (very slow!) " ;
-  }
-  else 
-  {
-    docbook-xsl-dir = [ format-catalog-path $(docbook-xsl-dir) ] ;      
-    print.text "  <rewriteURI uriStartString=\"http://docbook.sourceforge.net/release/xsl/current/\" rewritePrefix=\"file://$(docbook-xsl-dir)/\"/>" ;
-  }
-
-  local docbook-dtd-dir = [ boostbook.docbook-dtd-dir ] ;  
-  if ! $(docbook-dtd-dir)
-  {
-    ECHO "BoostBook warning: no DocBook DTD directory specified." ;
-    ECHO "  If you have the DocBook DTD installed, please set " ;
-    ECHO "  DOCBOOK_DTD_DIR to the DTD directory on either " ;
-    ECHO "  the command line (via -sDOCBOOK_DTD_DIR=...) or in a " ;
-    ECHO "  Boost.Jam configuration file. The DocBook DTD is available " ;
-    ECHO "  here: http://www.oasis-open.org/docbook/xml/4.2/index.shtml" ;
-    ECHO "  The DTD will be downloaded on-the-fly (very slow!) " ;
-  }
-  else 
-  {
-    docbook-dtd-dir = [ format-catalog-path $(docbook-dtd-dir) ] ;      
-    print.text "  <rewriteURI uriStartString=\"http://www.oasis-open.org/docbook/xml/4.2/\" rewritePrefix=\"file://$(docbook-dtd-dir)/\"/>" ;
-  }
-
-  print.text "</catalog>" ;
-}
-
-rule xml-catalog ( )
-{
-    if ! $(.xml-catalog)
-    {
-        # The target is created as part of the root project. But ideally
-        # it would be created as part of the boostbook project. This is not
-        # current possible as such global projects don't inherit things like
-        # the build directory.
-        
-        # Find the root project.
-        local root-project = [ project.current ] ;
-        root-project = [ $(root-project).project-module ] ;
-        while
-            [ project.attribute $(root-project) parent-module ] &&
-            [ project.attribute $(root-project) parent-module ] != user-config &&
-            [ project.attribute $(root-project) parent-module ] != project-config
-        {
-            root-project = [ project.attribute $(root-project) parent-module ] ;
-        }
-        .xml-catalog = [ new file-target boostbook_catalog
-            : XML
-            : [ project.target $(root-project) ]
-            : [ new action : boostbook.generate-xml-catalog ]
-            :
-            ] ;
-        .xml-catalog-file = [ $(.xml-catalog).path ] [ $(.xml-catalog).name ] ;
-        .xml-catalog-file = $(.xml-catalog-file:J=/) ;
-    }
-    return $(.xml-catalog) $(.xml-catalog-file) ;
-}
-
-class boostbook-generator : generator
-{
-    import feature ;
-    import virtual-target ;
-    import generators ;
-    import boostbook ;
-      
-    
-    rule __init__ ( * : * )
-    {
-        generator.__init__ $(1) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ;
-    }
-    
-    rule run ( project name ? : property-set : sources * )
-    {
-        # Generate the catalog, but only once...
-        local global-catalog = [ boostbook.xml-catalog ] ;
-        local catalog = $(global-catalog[1]) ;
-        local catalog-file = $(global-catalog[2]) ;
-        local targets ;
-       
-        # Add the catalog to the property set
-        property-set = [ $(property-set).add-raw <catalog>$(catalog-file) ] ;
-
-        local type = none ;
-        local manifest ; 
-        local format = [ $(property-set).get <format> ] ;
-        switch $(format) 
-        {
-            case html    : 
-            {
-                type = HTMLDIR ;
-                manifest = HTML.manifest ;
-            }
-            case xhtml    : 
-            {
-                type = XHTMLDIR ;
-                manifest = HTML.manifest ;
-            }
-            case htmlhelp    : 
-            {
-                type = HTMLHELP ;
-                manifest = HTML.manifest ;
-            }
-            
-            case onehtml : type = HTML ;
-            
-            case man : 
-            {
-                type = MANPAGES ;
-                manifest = man.manifest ;
-            }
-            
-            case docbook : type = DOCBOOK ;
-            case fo      : type = FO ;
-            case pdf     : type = PDF ;
-            case ps      : type = PS ;
-            case tests   : type = TESTS ;
-        }
-        
-        if $(manifest)
-        {
-            # Create DOCBOOK file from BOOSTBOOK sources.
-            local base-target = [ generators.construct $(project) 
-              : DOCBOOK : $(property-set) : $(sources) ] ;
-            base-target = $(base-target[2]) ;
-            $(base-target).depends $(catalog) ;
-            
-            # Generate HTML/PDF/PS from DOCBOOK.
-            local target = [ generators.construct $(project) $(name)_$(manifest)
-                : $(type)
-                : [ $(property-set).add-raw
-                    <xsl:param>manifest=$(name)_$(manifest) ]
-                : $(base-target) ] ;
-            local name = [ $(property-set).get <name> ] ;
-            name ?= $(format) ;
-            $(target[2]).set-path $(name) ;
-            $(target[2]).depends $(catalog) ;            
-
-            targets += $(target[2]) ;
-        }
-        else {
-            local target = [ generators.construct $(project)
-              : $(type) : $(property-set) : $(sources) ] ;
-            
-            if ! $(target)
-            {
-                errors.error "Cannot build documentation type '$(format)'" ;
-            }
-            else 
-            {
-                $(target[2]).depends $(catalog) ;
-                targets += $(target[2]) ;
-            }
-        }
-        
-        return $(targets) ;
-    }
-}
-
-generators.register [ new boostbook-generator boostbook.main : : BOOSTBOOK_MAIN ] ;
-
-# Creates a boostbook target.
-rule boostbook ( target-name : sources * : requirements * : default-build * )
-{ 
-  local project = [ project.current ] ;
-    
-  targets.main-target-alternative 
-    [ new typed-target $(target-name) : $(project) : BOOSTBOOK_MAIN
-        : [ targets.main-target-sources $(sources) : $(target-name) ] 
-        : [ targets.main-target-requirements $(requirements) : $(project) ]
-        : [ targets.main-target-default-build $(default-build) : $(project) ] 
-    ] ;
-}
-
-#############################################################################
-# Dependency scanners
-#############################################################################
-# XInclude scanner. Mostly stolen from c-scanner :)
-# Note that this assumes an "xi" prefix for XIncludes. This isn't always the
-# case for XML documents, but we'll assume it's true for anything we encounter.
-class xinclude-scanner : scanner 
-{
-    import virtual-target ;
-    import path ;
-    import scanner ;
-        
-    rule __init__ ( includes * )
-    {
-        scanner.__init__ ;
-        self.includes = $(includes) ;
-    }
-    
-  rule pattern ( )
-  {
-    return "xi:include[ ]*href=\"([^\"]*)\"" ;
-  }
-
-  rule process ( target : matches * : binding )
-  {
-    local target_path = [ NORMALIZE_PATH $(binding:D) ] ;
-
-    NOCARE $(matches) ;
-    INCLUDES $(target) : $(matches) ;
-    SEARCH on $(matches) = $(target_path) $(self.includes:G=) ;
-    
-    scanner.propagate $(__name__) : $(matches) : $(target) ;     
-  }
-}
-
-scanner.register xinclude-scanner : xsl:path ;
-type.set-scanner XML : xinclude-scanner ;
-
-rule boostbook-to-tests ( target : source : properties * )
-{
-  lock-config ;
-  local boost_root = [ modules.peek : BOOST_ROOT ] ;
-  local native-path =
-    [ path.native [ path.join $(.boostbook-xsl-dir) testing Jamfile ] ] ;
-  local stylesheet = $(native-path:S=.xsl) ;
-  xslt $(target) : $(source) $(stylesheet) 
-                 : $(properties) <xsl:param>boost.root=$(boost_root) 
-                 ;
-}
-
-
diff --git a/jam-files/boost-build/tools/borland.jam b/jam-files/boost-build/tools/borland.jam
deleted file mode 100644
index 6e43ca93..00000000
--- a/jam-files/boost-build/tools/borland.jam
+++ /dev/null
@@ -1,220 +0,0 @@
-# Copyright 2005 Dave Abrahams 
-# Copyright 2003 Rene Rivera 
-# Copyright 2003, 2004, 2005 Vladimir Prus 
-# Distributed under the Boost Software License, Version 1.0. 
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt) 
-
-#  Support for the Borland's command line compiler
-
-import property ;
-import generators ;
-import os ;
-import toolset : flags ;
-import feature : get-values ;
-import type ;
-import common ;
-
-feature.extend toolset : borland ;
-
-rule init ( version ? : command * : options * )
-{
-    local condition = [ common.check-init-parameters borland :
-        version $(version) ] ;
-    
-    local command = [ common.get-invocation-command borland : bcc32.exe 
-        : $(command) ] ;
-     
-    common.handle-options borland : $(condition) : $(command) : $(options) ;    
-    
-    if $(command)
-    {
-        command = [ common.get-absolute-tool-path $(command[-1]) ] ;
-    }   
-    root = $(command:D) ;    
-    
-    flags borland.compile STDHDRS $(condition) : $(root)/include/ ;
-    flags borland.link STDLIBPATH $(condition) : $(root)/lib ;
-    flags borland.link RUN_PATH $(condition) : $(root)/bin ;
-    flags borland .root $(condition) : $(root)/bin/ ;    
-}
-
-
-# A borland-specific target type
-type.register BORLAND.TDS : tds ;
-
-# Declare generators
-
-generators.register-linker borland.link : OBJ SEARCHED_LIB STATIC_LIB IMPORT_LIB : EXE : <toolset>borland ;
-generators.register-linker borland.link.dll : OBJ SEARCHED_LIB STATIC_LIB IMPORT_LIB : SHARED_LIB IMPORT_LIB : <toolset>borland ;
-
-generators.register-archiver borland.archive : OBJ : STATIC_LIB : <toolset>borland ;
-generators.register-c-compiler borland.compile.c++ : CPP : OBJ : <toolset>borland ;
-generators.register-c-compiler borland.compile.c : C : OBJ : <toolset>borland ;
-generators.register-standard borland.asm : ASM : OBJ : <toolset>borland ;
-
-# Declare flags 
-
-flags borland.compile OPTIONS <debug-symbols>on : -v ;
-flags borland.link OPTIONS <debug-symbols>on : -v ;
-
-flags borland.compile OPTIONS <optimization>off : -Od ;
-flags borland.compile OPTIONS <optimization>speed : -O2 ;
-flags borland.compile OPTIONS <optimization>space : -O1 ;
-
-if $(.BORLAND_HAS_FIXED_INLINING_BUGS)
-{
-    flags borland CFLAGS <inlining>off : -vi- ;
-    flags borland CFLAGS <inlining>on : -vi -w-inl ;
-    flags borland CFLAGS <inlining>full : -vi -w-inl ;
-}
-else
-{
-    flags borland CFLAGS : -vi- ;
-}
-
-flags borland.compile OPTIONS <warnings>off : -w- ;
-flags borland.compile OPTIONS <warnings>all : -w ;
-flags borland.compile OPTIONS <warnings-as-errors>on : -w! ;
-
-
-# Deal with various runtime configs...
-
-# This should be not for DLL
-flags borland OPTIONS <user-interface>console : -tWC ;
-
-# -tWR sets -tW as well, so we turn it off here and then turn it 
-# on again later if we need it:
-flags borland OPTIONS <runtime-link>shared : -tWR -tWC ;
-flags borland OPTIONS <user-interface>gui : -tW ;
-
-flags borland OPTIONS <main-target-type>LIB/<link>shared : -tWD ;
-# Hmm.. not sure what's going on here.
-flags borland OPTIONS : -WM- ;
-flags borland OPTIONS <threading>multi : -tWM ;
-
-
-
-flags borland.compile OPTIONS <cxxflags> ;
-flags borland.compile DEFINES <define> ;
-flags borland.compile INCLUDES <include> ;
-
-flags borland NEED_IMPLIB <main-target-type>LIB/<link>shared : "" ;
-
-#
-# for C++ compiles the following options are turned on by default:
-#
-# -j5    stops after 5 errors
-# -g255  allow an unlimited number of warnings
-# -q     no banner
-# -c     compile to object
-# -P     C++ code regardless of file extention
-# -a8    8 byte alignment, this option is on in the IDE by default 
-#        and effects binary compatibility.
-#
-
-# -U$(UNDEFS) -D$(DEFINES) $(CFLAGS) $(C++FLAGS) -I"$(HDRS)"  -I"$(STDHDRS)" -o"$(<)" "$(>)"
-
-
-actions compile.c++
-{
-    "$(CONFIG_COMMAND)" -j5 -g255 -q -c -P -a8 -Vx- -Ve- -b- $(OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -I"$(STDHDRS)" -o"$(<)" "$(>)"
-}
-
-# For C, we don't pass -P flag
-actions compile.c
-{
-    "$(CONFIG_COMMAND)" -j5 -g255 -q -c -a8 -Vx- -Ve- -b- $(OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -I"$(STDHDRS)" -o"$(<)" "$(>)"
-}
-
-
-# Declare flags and action for linking
-toolset.flags borland.link OPTIONS <debug-symbols>on : -v ;
-toolset.flags borland.link LIBRARY_PATH <library-path> ;
-toolset.flags borland.link FINDLIBS_ST <find-static-library> ;
-toolset.flags borland.link FINDLIBS_SA <find-shared-library> ;
-toolset.flags borland.link LIBRARIES <library-file> ;
-
-flags borland.link OPTIONS <linkflags> ;
-flags borland.link OPTIONS <link>shared : -tWD ;
-
-flags borland.link LIBRARY_PATH_OPTION <toolset>borland : -L : unchecked ;
-flags borland.link LIBRARY_OPTION <toolset>borland : "" : unchecked ;
-
-
-
-# bcc32 needs to have ilink32 in the path in order to invoke it, so explicitly
-# specifying $(BCC_TOOL_PATH)bcc32 doesn't help. You need to add
-# $(BCC_TOOL_PATH) to the path
-# The NEED_IMPLIB variable controls whether we need to invoke implib.
-
-flags borland.archive AROPTIONS <archiveflags> ;
-
-# Declare action for archives. We don't use response file
-# since it's hard to get "+-" there.
-# The /P256 increases 'page' size -- with too low
-# values tlib fails when building large applications.
-# CONSIDER: don't know what 'together' is for...
-actions updated together piecemeal archive
-{ 
-    $(.set-path)$(.root:W)$(.old-path)
-    tlib $(AROPTIONS) /P256 /u /a /C "$(<:W)" +-"$(>:W)"
-}
-
-
-if [ os.name ] = CYGWIN
-{
-    .set-path = "cmd /S /C set \"PATH=" ;
-    .old-path = ";%PATH%\" \"&&\"" ;
-    
-
-    # Couldn't get TLIB to stop being confused about pathnames
-    # containing dashes (it seemed to treat them as option separators
-    # when passed through from bash), so we explicitly write the
-    # command into a .bat file and execute that.  TLIB is also finicky
-    # about pathname style! Forward slashes, too, are treated as
-    # options.
-    actions updated together piecemeal archive
-    { 
-       chdir $(<:D)
-       echo +-$(>:BS) > $(<:BS).rsp
-       $(.set-path)$(.root)$(.old-path) "tlib.exe" $(AROPTIONS) /P256 /C $(<:BS) @$(<:BS).rsp && $(RM) $(<:BS).rsp
-    }    
-}
-else if [ os.name ] = NT
-{
-    .set-path = "set \"PATH=" ;
-    .old-path = ";%PATH%\"
-      " ;
-}
-else
-{
-    .set-path = "PATH=\"" ;
-    .old-path = "\":$PATH
-      export PATH
-      " ;
-}
-
-RM = [ common.rm-command ] ;
-
-nl = "
-" ;
-
-actions link
-{
-    $(.set-path)$(.root:W)$(.old-path) "$(CONFIG_COMMAND)" -v -q $(OPTIONS) -L"$(LIBRARY_PATH:W)" -L"$(STDLIBPATH:W)" -e"$(<[1]:W)" @"@($(<[1]:W).rsp:E=$(nl)"$(>)" $(nl)$(LIBRARIES) $(nl)"$(LIBRARY_OPTION)$(FINDLIBS_ST:S=.lib)" $(nl)"$(LIBRARY_OPTION)$(FINDLIBS_SA:S=.lib)")"
-}
-
-
-actions link.dll bind LIBRARIES RSP
-{
-    $(.set-path)$(.root:W)$(.old-path) "$(CONFIG_COMMAND)" -v -q $(OPTIONS) -L"$(LIBRARY_PATH:W)" -L"$(STDLIBPATH:W)" -e"$(<[1]:W)" @"@($(<[1]:W).rsp:E=$(nl)"$(>)" $(nl)$(LIBRARIES) $(nl)"$(LIBRARY_OPTION)$(FINDLIBS_ST:S=.lib)" $(nl)"$(LIBRARY_OPTION)$(FINDLIBS_SA:S=.lib)")"  && "$(.root)implib" "$(<[2]:W)" "$(<[1]:W)"
-}
-
-# It seems impossible to specify output file with directory when compiling
-# asm files using bcc32, so use tasm32 directly.
-# /ml makes all symbol names case-sensitive
-actions asm
-{
-    $(.set-path)$(.root:W)$(.old-path) tasm32.exe /ml "$(>)" "$(<)"
-}
-
diff --git a/jam-files/boost-build/tools/builtin.jam b/jam-files/boost-build/tools/builtin.jam
deleted file mode 100644
index 148e7308..00000000
--- a/jam-files/boost-build/tools/builtin.jam
+++ /dev/null
@@ -1,960 +0,0 @@
-# Copyright 2002, 2003, 2004, 2005 Dave Abrahams
-# Copyright 2002, 2005, 2006, 2007, 2010 Rene Rivera
-# Copyright 2006 Juergen Hunold
-# Copyright 2005 Toon Knapen
-# Copyright 2002, 2003, 2004, 2005, 2006 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-# Defines standard features and rules.
-
-import alias ;
-import "class" : new ;
-import errors ;
-import feature ;
-import generators ;
-import numbers ;
-import os ;
-import path ;
-import print ;
-import project ;
-import property ;
-import regex ;
-import scanner ;
-import sequence ;
-import stage ;
-import symlink ;
-import toolset ;
-import type ;
-import targets ;
-import types/register ;
-import utility ;
-import virtual-target ;
-import message ;
-import convert ;
-
-# FIXME: the following generate module import is not needed here but removing it
-# too hastly will break using code (e.g. the main Boost library Jamroot file)
-# that forgot to import the generate module before calling the generate rule.
-import generate ;
-
-
-.os-names = aix bsd cygwin darwin freebsd hpux iphone linux netbsd
-    openbsd osf qnx qnxnto sgi solaris unix unixware windows 
-    elf # Not actually an OS -- used for targeting bare metal where
-        # object format is ELF.  This catches both -elf and -eabi gcc
-        # targets and well as other compilers targeting ELF. It is not
-        # clear how often do we need to key of ELF specifically as opposed
-        # to other bare metal targets, but let's stick with gcc naming.
-    ;
-
-# Feature used to determine which OS we're on. New <target-os> and <host-os>
-# features should be used instead.
-local os = [ modules.peek : OS ] ;
-feature.feature os : $(os) : propagated link-incompatible ;
-
-
-# Translates from bjam current OS to the os tags used in host-os and target-os,
-# i.e. returns the running host-os.
-#
-local rule default-host-os ( )
-{
-    local host-os ;
-    if [ os.name ] in $(.os-names:U)
-    {
-        host-os = [ os.name ] ;
-    }
-    else
-    {
-        switch [ os.name ]
-        {
-            case NT           : host-os = windows ;
-            case AS400        : host-os = unix    ;
-            case MINGW        : host-os = windows ;
-            case BSDI         : host-os = bsd     ;
-            case COHERENT     : host-os = unix    ;
-            case DRAGONFLYBSD : host-os = bsd     ;
-            case IRIX         : host-os = sgi     ;
-            case MACOSX       : host-os = darwin  ;
-            case KFREEBSD     : host-os = freebsd ;
-            case LINUX        : host-os = linux   ;
-            case SUNOS        : 
-              ECHO "SunOS is not a supported operating system." ;
-              ECHO "We believe last version of SunOS was released in 1992, " ;
-              ECHO "so if you get this message, something is very wrong with configuration logic. " ;
-              ECHO "Please report this as a bug. " ;
-              EXIT ;
-            case *            : host-os = unix    ;
-        }
-    }
-    return $(host-os:L) ;
-}
-
-
-# The two OS features define a known set of abstract OS names. The host-os is
-# the OS under which bjam is running. Even though this should really be a fixed
-# property we need to list all the values to prevent unknown value errors. Both
-# set the default value to the current OS to account for the default use case of
-# building on the target OS.
-feature.feature host-os : $(.os-names) ;
-feature.set-default host-os : [ default-host-os ] ;
-
-feature.feature target-os : $(.os-names) : propagated link-incompatible ;
-feature.set-default target-os : [ default-host-os ] ;
-
-
-feature.feature toolset            :                 : implicit propagated symmetric ;
-feature.feature stdlib             : native          : propagated composite ;
-feature.feature link               : shared static   : propagated ;
-feature.feature runtime-link       : shared static   : propagated ;
-feature.feature runtime-debugging  : on off          : propagated ;
-feature.feature optimization       : off speed space none : propagated ;
-feature.feature profiling          : off on          : propagated ;
-feature.feature inlining           : off on full     : propagated ;
-feature.feature threading          : single multi    : propagated ;
-feature.feature rtti               : on off          : propagated ;
-feature.feature exception-handling : on off          : propagated ;
-
-# Whether there is support for asynchronous EH (e.g. catching SEGVs).
-feature.feature asynch-exceptions  : off on          : propagated ;
-
-# Whether all extern "C" functions are considered nothrow by default.
-feature.feature extern-c-nothrow   : off on          : propagated ;
-
-feature.feature debug-symbols      : on off none          : propagated ;
-# Controls whether the binary should be stripped -- that is have
-# everything not necessary to running removed. This option should
-# not be very often needed. Also, this feature will show up in
-# target paths of everything, not just binaries. Should fix that
-# when impelementing feature relevance.
-feature.feature strip              : off on          : propagated ;
-feature.feature define             :                 : free ;
-feature.feature undef              :                 : free ;
-feature.feature "include"          :                 : free path ; #order-sensitive ;
-feature.feature cflags             :                 : free ;
-feature.feature cxxflags           :                 : free ;
-feature.feature fflags             :                 : free ;
-feature.feature asmflags           :                 : free ;
-feature.feature linkflags          :                 : free ;
-feature.feature archiveflags       :                 : free ;
-feature.feature version            :                 : free ;
-
-# Generic, i.e. non-language specific, flags for tools.
-feature.feature flags           : : free ;
-feature.feature location-prefix : : free ;
-
-
-# The following features are incidental since they have no effect on built
-# products. Not making them incidental will result in problems in corner cases,
-# e.g.:
-#
-#    unit-test a : a.cpp : <use>b ;
-#    lib b : a.cpp b ;
-#
-# Here, if <use> is not incidental, we would decide we have two targets for
-# a.obj with different properties and complain about it.
-#
-# Note that making a feature incidental does not mean it is ignored. It may be
-# ignored when creating a virtual target, but the rest of build process will use
-# them.
-feature.feature use                 : : free dependency incidental ;
-feature.feature dependency          : : free dependency incidental ;
-feature.feature implicit-dependency : : free dependency incidental ;
-
-feature.feature warnings :
-    on         # Enable default/"reasonable" warning level for the tool.
-    all        # Enable all possible warnings issued by the tool.
-    off        # Disable all warnings issued by the tool.
-  : incidental propagated ;
-
-feature.feature warnings-as-errors :
-    off        # Do not fail the compilation if there are warnings.
-    on         # Fail the compilation if there are warnings.
-  : incidental propagated ;
-
-# Feature that allows us to configure the maximal template instantiation depth
-# level allowed by a C++ compiler. Applies only to C++ toolsets whose compilers
-# actually support this configuration setting.
-#
-# Note that Boost Build currently does not allow defining features that take any
-# positive integral value as a parameter, which is what we need here, so we just
-# define some of the values here and leave it up to the user to extend this set
-# as he needs using the feature.extend rule.
-#
-# TODO: This should be upgraded as soon as Boost Build adds support for custom
-# validated feature values or at least features allowing any positive integral
-# value. See related Boost Build related trac ticket #194.
-#
-feature.feature c++-template-depth
-    :
-        [ numbers.range 64 1024 : 64 ]
-        [ numbers.range 20 1000 : 10 ]
-        #   Maximum template instantiation depth guaranteed for ANSI/ISO C++
-        # conforming programs.
-        17
-    :
-        incidental optional propagated ;
-
-feature.feature source              :            : free dependency incidental ;
-feature.feature library             :            : free dependency incidental ;
-feature.feature file                :            : free dependency incidental ;
-feature.feature find-shared-library :            : free ; #order-sensitive ;
-feature.feature find-static-library :            : free ; #order-sensitive ;
-feature.feature library-path        :            : free path ; #order-sensitive ;
-
-# Internal feature.
-feature.feature library-file        :            : free dependency ;
-
-feature.feature name                :            : free ;
-feature.feature tag                 :            : free ;
-feature.feature search              :            : free path ; #order-sensitive ;
-feature.feature location            :            : free path ;
-feature.feature dll-path            :            : free path ;
-feature.feature hardcode-dll-paths  : true false : incidental ;
-
-
-# An internal feature that holds the paths of all dependency shared libraries.
-# On Windows, it is needed so that we can add all those paths to PATH when
-# running applications. On Linux, it is needed to add proper -rpath-link command
-# line options.
-feature.feature xdll-path : : free path ;
-
-# Provides means to specify def-file for windows DLLs.
-feature.feature def-file : : free dependency ;
-
-feature.feature suppress-import-lib : false true : incidental ;
-
-# Internal feature used to store the name of a bjam action to call when building
-# a target.
-feature.feature action : : free ;
-
-# This feature is used to allow specific generators to run. For example, QT
-# tools can only be invoked when QT library is used. In that case, <allow>qt
-# will be in usage requirement of the library.
-feature.feature allow : : free ;
-
-# The addressing model to generate code for. Currently a limited set only
-# specifying the bit size of pointers.
-feature.feature address-model : 16 32 64 32_64 : propagated optional ;
-
-# Type of CPU architecture to compile for.
-feature.feature architecture :
-    # x86 and x86-64
-    x86
-
-    # ia64
-    ia64
-
-    # Sparc
-    sparc
-
-    # RS/6000 & PowerPC
-    power
-
-    # MIPS/SGI
-    mips1 mips2 mips3 mips4 mips32 mips32r2 mips64
-
-    # HP/PA-RISC
-    parisc
-
-    # Advanced RISC Machines
-    arm
-
-    # Combined architectures for platforms/toolsets that support building for
-    # multiple architectures at once. "combined" would be the default multi-arch
-    # for the toolset.
-    combined
-    combined-x86-power
-
-    : propagated optional ;
-
-# The specific instruction set in an architecture to compile.
-feature.feature instruction-set :
-    # x86 and x86-64
-    native i386 i486 i586 i686 pentium pentium-mmx pentiumpro pentium2 pentium3
-    pentium3m pentium-m pentium4 pentium4m prescott nocona core2 conroe conroe-xe
-    conroe-l allendale mermon mermon-xe kentsfield kentsfield-xe penryn wolfdale
-    yorksfield nehalem k6 k6-2 k6-3 athlon athlon-tbird athlon-4 athlon-xp
-    athlon-mp k8 opteron athlon64 athlon-fx winchip-c6 winchip2 c3 c3-2
-
-    # ia64
-    itanium itanium1 merced itanium2 mckinley
-
-    # Sparc
-    v7 cypress v8 supersparc sparclite hypersparc sparclite86x f930 f934
-    sparclet tsc701 v9 ultrasparc ultrasparc3
-
-    # RS/6000 & PowerPC
-    401 403 405 405fp 440 440fp 505 601 602 603 603e 604 604e 620 630 740 7400
-    7450 750 801 821 823 860 970 8540 power-common ec603e g3 g4 g5 power power2
-    power3 power4 power5 powerpc powerpc64 rios rios1 rsc rios2 rs64a
-
-    # MIPS
-    4kc 4kp 5kc 20kc m4k r2000 r3000 r3900 r4000 r4100 r4300 r4400 r4600 r4650
-    r6000 r8000 rm7000 rm9000 orion sb1 vr4100 vr4111 vr4120 vr4130 vr4300
-    vr5000 vr5400 vr5500
-
-    # HP/PA-RISC
-    700 7100 7100lc 7200 7300 8000
-
-    # Advanced RISC Machines
-    armv2 armv2a armv3 armv3m armv4 armv4t armv5 armv5t armv5te armv6 armv6j iwmmxt ep9312
-
-    : propagated optional ;
-
-# Used to select a specific variant of C++ ABI if the compiler supports several.
-feature.feature c++abi : : propagated optional ;
-
-feature.feature conditional : : incidental free ;
-
-# The value of 'no' prevents building of a target.
-feature.feature build : yes no : optional ;
-
-# Windows-specific features
-
-feature.feature user-interface : console gui wince native auto ;
-
-feature.feature variant : : implicit composite propagated symmetric ;
-
-
-# Declares a new variant.
-#
-# First determines explicit properties for this variant, by refining parents'
-# explicit properties with the passed explicit properties. The result is
-# remembered and will be used if this variant is used as parent.
-#
-# Second, determines the full property set for this variant by adding to the
-# explicit properties default values for all missing non-symmetric properties.
-#
-# Lastly, makes appropriate value of 'variant' property expand to the full
-# property set.
-#
-rule variant ( name            # Name of the variant
-    : parents-or-properties *  # Specifies parent variants, if
-                               # 'explicit-properties' are given, and
-                               # explicit-properties or parents otherwise.
-    : explicit-properties *    # Explicit properties.
-    )
-{
-    local parents ;
-    if ! $(explicit-properties)
-    {
-        if $(parents-or-properties[1]:G)
-        {
-            explicit-properties = $(parents-or-properties) ;
-        }
-        else
-        {
-            parents = $(parents-or-properties) ;
-        }
-    }
-    else
-    {
-        parents = $(parents-or-properties) ;
-    }
-
-    # The problem is that we have to check for conflicts between base variants.
-    if $(parents[2])
-    {
-        errors.error "multiple base variants are not yet supported" ;
-    }
-
-    local inherited ;
-    # Add explicitly specified properties for parents.
-    for local p in $(parents)
-    {
-        # TODO: This check may be made stricter.
-        if ! [ feature.is-implicit-value $(p) ]
-        {
-            errors.error "Invalid base variant" $(p)  ;
-        }
-
-        inherited += $(.explicit-properties.$(p)) ;
-    }
-    property.validate $(explicit-properties) ;
-    explicit-properties = [ property.refine $(inherited)
-        : $(explicit-properties) ] ;
-
-    # Record explicitly specified properties for this variant. We do this after
-    # inheriting parents' properties so they affect other variants derived from
-    # this one.
-    .explicit-properties.$(name) = $(explicit-properties) ;
-
-    feature.extend variant : $(name) ;
-    feature.compose <variant>$(name) : $(explicit-properties) ;
-}
-IMPORT $(__name__) : variant : : variant ;
-
-
-variant debug   : <optimization>off <debug-symbols>on <inlining>off
-                  <runtime-debugging>on ;
-variant release : <optimization>speed <debug-symbols>off <inlining>full
-                  <runtime-debugging>off <define>NDEBUG ;
-variant profile : release : <profiling>on <debug-symbols>on ;
-
-
-class searched-lib-target : abstract-file-target
-{
-    rule __init__ ( name
-        : project
-        : shared ?
-        : search *
-        : action
-    )
-    {
-        abstract-file-target.__init__ $(name) : SEARCHED_LIB : $(project)
-          : $(action) : ;
-
-        self.shared = $(shared) ;
-        self.search = $(search) ;
-    }
-
-    rule shared ( )
-    {
-        return $(self.shared) ;
-    }
-
-    rule search ( )
-    {
-        return $(self.search) ;
-    }
-
-    rule actualize-location ( target )
-    {
-        NOTFILE $(target) ;
-    }
-
-    rule path ( )
-    {
-    }
-}
-
-
-# The generator class for libraries (target type LIB). Depending on properties
-# it will request building of the appropriate specific library type --
-# -- SHARED_LIB, STATIC_LIB or SHARED_LIB.
-#
-class lib-generator : generator
-{
-    rule __init__ ( * : * )
-    {
-        generator.__init__ $(1) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ;
-    }
-
-    rule run ( project name ? : property-set : sources * )
-    {
-        # The lib generator is composing, and can be only invoked with an
-        # explicit name. This check is present in generator.run (and so in
-        # builtin.linking-generator) but duplicated here to avoid doing extra
-        # work.
-        if $(name)
-        {
-            local properties = [ $(property-set).raw ] ;
-            # Determine the needed target type.
-            local actual-type ;
-                # <source>files can be generated by <conditional>@rule feature
-                # in which case we do not consider it a SEARCHED_LIB type.
-            if ! <source> in $(properties:G) &&
-               ( <search> in $(properties:G) || <name> in $(properties:G) )
-            {
-                actual-type = SEARCHED_LIB ;
-            }
-            else if <file> in $(properties:G)
-            {
-                actual-type = LIB ;
-            }
-            else if <link>shared in $(properties)
-            {
-                actual-type = SHARED_LIB ;
-            }
-            else
-            {
-                actual-type = STATIC_LIB ;
-            }
-            property-set = [ $(property-set).add-raw <main-target-type>LIB ] ;
-            # Construct the target.
-            return [ generators.construct $(project) $(name) : $(actual-type)
-                : $(property-set) : $(sources) ] ;
-        }
-    }
-
-    rule viable-source-types ( )
-    {
-        return * ;
-    }
-}
-
-
-generators.register [ new lib-generator builtin.lib-generator :  : LIB ] ;
-
-
-# The implementation of the 'lib' rule. Beyond standard syntax that rule allows
-# simplified: "lib a b c ;".
-#
-rule lib ( names + : sources * : requirements * : default-build * :
-    usage-requirements * )
-{
-    if $(names[2])
-    {
-        if <name> in $(requirements:G)
-        {
-            errors.user-error "When several names are given to the 'lib' rule" :
-                "it is not allowed to specify the <name> feature." ;
-        }
-        if $(sources)
-        {
-            errors.user-error "When several names are given to the 'lib' rule" :
-                "it is not allowed to specify sources." ;
-        }
-    }
-
-    # This is a circular module dependency so it must be imported here.
-    import targets ;
-
-    local project = [ project.current ] ;
-    local result ;
-
-    for local name in $(names)
-    {
-        local r = $(requirements) ;
-        # Support " lib a ; " and " lib a b c ; " syntax.
-        if ! $(sources) && ! <name> in $(requirements:G)
-                        && ! <file> in $(requirements:G)
-        {
-            r += <name>$(name) ;
-        }
-        result += [ targets.main-target-alternative
-            [ new typed-target $(name) : $(project) : LIB
-                : [ targets.main-target-sources $(sources) : $(name) ]
-                : [ targets.main-target-requirements $(r) : $(project) ]
-                : [ targets.main-target-default-build $(default-build) : $(project) ]
-                : [ targets.main-target-usage-requirements $(usage-requirements) : $(project) ]
-            ] ] ;
-    }
-    return $(result) ;
-}
-IMPORT $(__name__) : lib : : lib ;
-
-
-class searched-lib-generator : generator
-{
-    import property-set ;
-
-    rule __init__ ( )
-    {
-        # The requirements cause the generators to be tried *only* when we're
-        # building a lib target with a 'search' feature. This seems ugly --- all
-        # we want is to make sure searched-lib-generator is not invoked deep
-        # inside transformation search to produce intermediate targets.
-        generator.__init__ searched-lib-generator : : SEARCHED_LIB ;
-    }
-
-    rule run ( project name ? : property-set : sources * )
-    {
-        if $(name)
-        {
-            # If 'name' is empty, it means we have not been called to build a
-            # top-level target. In this case, we just fail immediately, because
-            # searched-lib-generator cannot be used to produce intermediate
-            # targets.
-
-            local properties = [ $(property-set).raw ] ;
-            local shared ;
-            if <link>shared in $(properties)
-            {
-                shared = true ;
-            }
-
-            local search = [ feature.get-values <search> : $(properties) ] ;
-
-            local a = [ new null-action $(property-set) ] ;
-            local lib-name = [ feature.get-values <name> : $(properties) ] ;
-            lib-name ?= $(name) ;
-            local t = [ new searched-lib-target $(lib-name) : $(project)
-                : $(shared) : $(search) : $(a) ] ;
-            # We return sources for a simple reason. If there is
-            #    lib png : z : <name>png ;
-            # the 'z' target should be returned, so that apps linking to 'png'
-            # will link to 'z', too.
-            return [ property-set.create <xdll-path>$(search) ]
-                   [ virtual-target.register $(t) ] $(sources) ;
-        }
-    }
-}
-
-generators.register [ new searched-lib-generator ] ;
-
-
-class prebuilt-lib-generator : generator
-{
-    rule __init__ ( * : * )
-    {
-        generator.__init__ $(1) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ;
-    }
-
-    rule run ( project name ? : property-set : sources * )
-    {
-        local f = [ $(property-set).get <file> ] ;
-        return $(f) $(sources) ;
-    }
-}
-
-generators.register
-  [ new prebuilt-lib-generator builtin.prebuilt : : LIB : <file> ] ;
-
-generators.override builtin.prebuilt : builtin.lib-generator ;
-
-class preprocessed-target-class : basic-target
-{
-    import generators ;
-    rule construct ( name : sources * : property-set )
-    {
-        local result = [ generators.construct [ project ]
-            $(name) : PREPROCESSED_CPP : $(property-set) : $(sources) ] ;
-        if ! $(result)
-        {
-            result = [ generators.construct [ project ]
-                $(name) : PREPROCESSED_C : $(property-set) : $(sources) ] ;
-        }
-        if ! $(result)
-        {
-            local s ;
-            for x in $(sources)
-            {
-                s += [ $(x).name ] ;
-            }
-            local p = [ project ] ;
-            errors.user-error
-                "In project" [ $(p).name ] :
-                "Could not construct preprocessed file \"$(name)\" from $(s:J=, )." ;
-        }
-        return $(result) ;
-    }
-}
-
-rule preprocessed ( name : sources * : requirements * : default-build * :
-    usage-requirements * )
-{
-    local project = [ project.current ] ;
-    return [ targets.main-target-alternative
-        [ new preprocessed-target-class $(name) : $(project)
-            : [ targets.main-target-sources $(sources) : $(name) ]
-            : [ targets.main-target-requirements $(r) : $(project) ]
-            : [ targets.main-target-default-build $(default-build) : $(project) ]
-            : [ targets.main-target-usage-requirements $(usage-requirements) : $(project) ]
-        ] ] ;
-}
-
-IMPORT $(__name__) : preprocessed : : preprocessed ;
-
-class compile-action : action
-{
-    import sequence ;
-
-    rule __init__ ( targets * : sources * : action-name : properties * )
-    {
-        action.__init__ $(targets) : $(sources) : $(action-name) : $(properties) ;
-    }
-
-    # For all virtual targets for the same dependency graph as self, i.e. which
-    # belong to the same main target, add their directories to the include path.
-    #
-    rule adjust-properties ( property-set )
-    {
-        local s = [ $(self.targets[1]).creating-subvariant ] ;
-        return [ $(property-set).add-raw
-          [ $(s).implicit-includes "include" : H ] ] ;
-    }
-}
-
-
-# Declare a special compiler generator. The only thing it does is changing the
-# type used to represent 'action' in the constructed dependency graph to
-# 'compile-action'. That class in turn adds additional include paths to handle
-# cases when a source file includes headers which are generated themselves.
-#
-class C-compiling-generator : generator
-{
-    rule __init__ ( id : source-types + : target-types + : requirements *
-        : optional-properties * )
-    {
-        generator.__init__ $(id) : $(source-types) : $(target-types) :
-            $(requirements) : $(optional-properties) ;
-    }
-
-    rule action-class ( )
-    {
-        return compile-action ;
-    }
-}
-
-
-rule register-c-compiler ( id : source-types + : target-types + : requirements *
-    : optional-properties * )
-{
-    generators.register [ new C-compiling-generator $(id) : $(source-types) :
-        $(target-types) : $(requirements) : $(optional-properties) ] ;
-}
-
-# FIXME: this is ugly, should find a better way (we would like client code to
-# register all generators as "generators.some-rule" instead of
-# "some-module.some-rule".)
-#
-IMPORT $(__name__) : register-c-compiler : : generators.register-c-compiler ;
-
-
-# The generator class for handling EXE and SHARED_LIB creation.
-#
-class linking-generator : generator
-{
-    import path ;
-    import project ;
-    import property-set ;
-    import type ;
-
-    rule __init__ ( id
-        composing ?    :  # The generator will be composing if a non-empty
-                          # string is passed or the parameter is not given. To
-                          # make the generator non-composing, pass an empty
-                          # string ("").
-        source-types + :
-        target-types + :
-        requirements * )
-    {
-        composing ?= true ;
-        generator.__init__ $(id) $(composing) : $(source-types)
-            : $(target-types) : $(requirements) ;
-    }
-
-    rule run ( project name ? : property-set : sources + )
-    {
-        sources += [ $(property-set).get <library>  ] ;
-
-        # Add <library-path> properties for all searched libraries.
-        local extra ;
-        for local s in $(sources)
-        {
-            if [ $(s).type ] = SEARCHED_LIB
-            {
-                local search = [ $(s).search ] ;
-                extra += <library-path>$(search) ;
-            }
-        }
-
-        # It is possible that sources include shared libraries that did not came
-        # from 'lib' targets, e.g. .so files specified as sources. In this case
-        # we have to add extra dll-path properties and propagate extra xdll-path
-        # properties so that application linking to us will get xdll-path to
-        # those libraries.
-        local extra-xdll-paths ;
-        for local s in $(sources)
-        {
-            if [ type.is-derived [ $(s).type ] SHARED_LIB ] && ! [ $(s).action ]
-            {
-                # Unfortunately, we do not have a good way to find the path to a
-                # file, so use this nasty approach.
-                #
-                # TODO: This needs to be done better. One thing that is really
-                # broken with this is that it does not work correctly with
-                # projects having multiple source locations.
-                local p = [ $(s).project ] ;
-                local location = [ path.root [ $(s).name ]
-                    [ $(p).get source-location ] ] ;
-                extra-xdll-paths += [ path.parent $(location) ] ;
-            }
-        }
-
-        # Hardcode DLL paths only when linking executables.
-        # Pros: do not need to relink libraries when installing.
-        # Cons: "standalone" libraries (plugins, python extensions) can not
-        # hardcode paths to dependent libraries.
-        if [ $(property-set).get <hardcode-dll-paths> ] = true
-            && [ type.is-derived $(self.target-types[1]) EXE ]
-        {
-            local xdll-path = [ $(property-set).get <xdll-path> ] ;
-            extra += <dll-path>$(xdll-path) <dll-path>$(extra-xdll-paths) ;
-        }
-
-        if $(extra)
-        {
-            property-set = [ $(property-set).add-raw $(extra) ] ;
-        }
-
-        local result = [ generator.run $(project) $(name) : $(property-set)
-            : $(sources) ] ;
-
-        local ur ;
-        if $(result)
-        {
-            ur = [ extra-usage-requirements $(result) : $(property-set) ] ;
-            ur = [ $(ur).add
-              [ property-set.create <xdll-path>$(extra-xdll-paths) ] ] ;
-        }
-        return $(ur) $(result) ;
-    }
-
-    rule extra-usage-requirements ( created-targets * : property-set )
-    {
-        local result = [ property-set.empty ] ;
-        local extra ;
-
-        # Add appropricate <xdll-path> usage requirements.
-        local raw = [ $(property-set).raw ] ;
-        if <link>shared in $(raw)
-        {
-            local paths ;
-            local pwd = [ path.pwd ] ;
-            for local t in $(created-targets)
-            {
-                if [ type.is-derived [ $(t).type ] SHARED_LIB ]
-                {
-                    paths += [ path.root [ path.make [ $(t).path ] ] $(pwd) ] ;
-                }
-            }
-            extra += $(paths:G=<xdll-path>) ;
-        }
-
-        # We need to pass <xdll-path> features that we've got from sources,
-        # because if a shared library is built, exe using it needs to know paths
-        # to other shared libraries this one depends on in order to be able to
-        # find them all at runtime.
-
-        # Just pass all features in property-set, it is theorically possible
-        # that we will propagate <xdll-path> features explicitly specified by
-        # the user, but then the user is to blaim for using an internal feature.
-        local values = [ $(property-set).get <xdll-path> ] ;
-        extra += $(values:G=<xdll-path>) ;
-
-        if $(extra)
-        {
-            result = [ property-set.create $(extra) ] ;
-        }
-        return $(result) ;
-    }
-
-    rule generated-targets ( sources + : property-set : project name ? )
-    {
-        local sources2 ;     # Sources to pass to inherited rule.
-        local properties2 ;  # Properties to pass to inherited rule.
-        local libraries ;    # Library sources.
-
-        # Searched libraries are not passed as arguments to the linker but via
-        # some option. So, we pass them to the action using a property.
-        properties2 = [ $(property-set).raw ] ;
-        local fsa ;
-        local fst ;
-        for local s in $(sources)
-        {
-            if [ type.is-derived [ $(s).type ] SEARCHED_LIB ]
-            {
-                local name = [ $(s).name ] ;
-                if [ $(s).shared ]
-                {
-                    fsa += $(name) ;
-                }
-                else
-                {
-                    fst += $(name) ;
-                }
-            }
-            else
-            {
-                sources2 += $(s) ;
-            }
-        }
-        properties2 += <find-shared-library>$(fsa:J=&&)
-                       <find-static-library>$(fst:J=&&) ;
-
-        return [ generator.generated-targets $(sources2)
-            : [ property-set.create $(properties2) ] : $(project) $(name) ] ;
-    }
-}
-
-
-rule register-linker ( id composing ? : source-types + : target-types +
-    : requirements * )
-{
-    generators.register [ new linking-generator $(id) $(composing)
-        : $(source-types) : $(target-types) : $(requirements) ] ;
-}
-
-
-# The generator class for handling STATIC_LIB creation.
-#
-class archive-generator : generator
-{
-    import property-set ;
-
-    rule __init__ ( id composing ? : source-types + : target-types +
-        : requirements * )
-    {
-        composing ?= true ;
-        generator.__init__ $(id) $(composing) : $(source-types)
-            : $(target-types) : $(requirements) ;
-    }
-
-    rule run ( project name ? : property-set : sources + )
-    {
-        sources += [ $(property-set).get <library>  ] ;
-
-        local result = [ generator.run $(project) $(name) : $(property-set)
-            : $(sources) ] ;
-
-        # For static linking, if we get a library in source, we can not directly
-        # link to it so we need to cause our dependencies to link to that
-        # library. There are two approaches:
-        # - adding the library to the list of returned targets.
-        # - using the <library> usage requirements.
-        # The problem with the first is:
-        #
-        #     lib a1 : : <file>liba1.a ;
-        #     lib a2 : a2.cpp a1 : <link>static ;
-        #     install dist : a2 ;
-        #
-        # here we will try to install 'a1', even though it is not necessary in
-        # the general case. With the second approach, even indirect dependants
-        # will link to the library, but it should not cause any harm. So, return
-        # all LIB sources together with created targets, so that dependants link
-        # to them.
-        local usage-requirements ;
-        if [ $(property-set).get <link> ] = static
-        {
-            for local t in $(sources)
-            {
-                if [ type.is-derived [ $(t).type ] LIB ]
-                {
-                    usage-requirements += <library>$(t) ;
-                }
-            }
-        }
-
-        usage-requirements = [ property-set.create $(usage-requirements) ] ;
-
-        return $(usage-requirements) $(result) ;
-    }
-}
-
-
-rule register-archiver ( id composing ? : source-types + : target-types +
-    : requirements * )
-{
-    generators.register [ new archive-generator $(id) $(composing)
-        : $(source-types) : $(target-types) : $(requirements) ] ;
-}
-
-
-# Generator that accepts everything and produces nothing. Useful as a general
-# fallback for toolset-specific actions like PCH generation.
-#
-class dummy-generator : generator
-{
-    import property-set ;
-
-    rule run ( project name ? : property-set : sources + )
-    {
-        return [ property-set.empty ] ;
-    }
-}
-
-IMPORT $(__name__) : register-linker register-archiver
-    : : generators.register-linker generators.register-archiver ;
diff --git a/jam-files/boost-build/tools/builtin.py b/jam-files/boost-build/tools/builtin.py
deleted file mode 100644
index 31a7bffe..00000000
--- a/jam-files/boost-build/tools/builtin.py
+++ /dev/null
@@ -1,718 +0,0 @@
-# Status: minor updates by Steven Watanabe to make gcc work
-#
-#  Copyright (C) Vladimir Prus 2002. Permission to copy, use, modify, sell and
-#  distribute this software is granted provided this copyright notice appears in
-#  all copies. This software is provided "as is" without express or implied
-#  warranty, and with no claim as to its suitability for any purpose.
-
-""" Defines standard features and rules.
-"""
-
-import b2.build.targets as targets
-
-import sys
-from b2.build import feature, property, virtual_target, generators, type, property_set, scanner
-from b2.util.utility import *
-from b2.util import path, regex, bjam_signature
-import b2.tools.types
-from b2.manager import get_manager
-
-
-# Records explicit properties for a variant.
-# The key is the variant name.
-__variant_explicit_properties = {}
-
-def reset ():
-    """ Clear the module state. This is mainly for testing purposes.
-    """
-    global __variant_explicit_properties
-
-    __variant_explicit_properties = {}
-
-@bjam_signature((["name"], ["parents_or_properties", "*"], ["explicit_properties", "*"]))
-def variant (name, parents_or_properties, explicit_properties = []):
-    """ Declares a new variant.
-        First determines explicit properties for this variant, by
-        refining parents' explicit properties with the passed explicit
-        properties. The result is remembered and will be used if
-        this variant is used as parent.
-        
-        Second, determines the full property set for this variant by
-        adding to the explicit properties default values for all properties 
-        which neither present nor are symmetric.
-        
-        Lastly, makes appropriate value of 'variant' property expand
-        to the full property set.
-        name:                   Name of the variant
-        parents_or_properties:  Specifies parent variants, if 
-                                'explicit_properties' are given,
-                                and explicit_properties otherwise.
-        explicit_properties:    Explicit properties.
-    """
-    parents = []
-    if not explicit_properties:
-        explicit_properties = parents_or_properties
-    else:
-        parents = parents_or_properties
-    
-    inherited = property_set.empty()
-    if parents:
-
-        # If we allow multiple parents, we'd have to to check for conflicts
-        # between base variants, and there was no demand for so to bother.
-        if len (parents) > 1:
-            raise BaseException ("Multiple base variants are not yet supported")
-        
-        p = parents[0]
-        # TODO: the check may be stricter
-        if not feature.is_implicit_value (p):
-            raise BaseException ("Invalid base varaint '%s'" % p)
-        
-        inherited = __variant_explicit_properties[p]
-
-    explicit_properties = property_set.create_with_validation(explicit_properties)
-    explicit_properties = inherited.refine(explicit_properties)
-    
-    # Record explicitly specified properties for this variant
-    # We do this after inheriting parents' properties, so that
-    # they affect other variants, derived from this one.
-    __variant_explicit_properties[name] = explicit_properties
-           
-    feature.extend('variant', [name])
-    feature.compose ("<variant>" + name, explicit_properties.all())
-
-__os_names = """
-    amiga aix bsd cygwin darwin dos emx freebsd hpux iphone linux netbsd
-    openbsd osf qnx qnxnto sgi solaris sun sunos svr4 sysv ultrix unix unixware
-    vms windows
-""".split()
-
-# Translates from bjam current OS to the os tags used in host-os and target-os,
-# i.e. returns the running host-os.
-#
-def default_host_os():
-    host_os = os_name()
-    if host_os not in (x.upper() for x in __os_names):
-        if host_os == 'NT': host_os = 'windows'
-        elif host_os == 'AS400': host_os = 'unix'
-        elif host_os == 'MINGW': host_os = 'windows'
-        elif host_os == 'BSDI': host_os = 'bsd'
-        elif host_os == 'COHERENT': host_os = 'unix'
-        elif host_os == 'DRAGONFLYBSD': host_os = 'bsd'
-        elif host_os == 'IRIX': host_os = 'sgi'
-        elif host_os == 'MACOSX': host_os = 'darwin'
-        elif host_os == 'KFREEBSD': host_os = 'freebsd'
-        elif host_os == 'LINUX': host_os = 'linux'
-        else: host_os = 'unix'
-    return host_os.lower()
-
-def register_globals ():
-    """ Registers all features and variants declared by this module.
-    """
-
-    # This feature is used to determine which OS we're on.
-    # In future, this may become <target-os> and <host-os>
-    # TODO: check this. Compatibility with bjam names? Subfeature for version?
-    os = sys.platform
-    feature.feature ('os', [os], ['propagated', 'link-incompatible'])
-
-
-    # The two OS features define a known set of abstract OS names. The host-os is
-    # the OS under which bjam is running. Even though this should really be a fixed
-    # property we need to list all the values to prevent unknown value errors. Both
-    # set the default value to the current OS to account for the default use case of
-    # building on the target OS.
-    feature.feature('host-os', __os_names)
-    feature.set_default('host-os', default_host_os())
-
-    feature.feature('target-os', __os_names, ['propagated', 'link-incompatible'])
-    feature.set_default('target-os', default_host_os())
-    
-    feature.feature ('toolset', [], ['implicit', 'propagated' ,'symmetric'])
-    
-    feature.feature ('stdlib', ['native'], ['propagated', 'composite'])
-    
-    feature.feature ('link', ['shared', 'static'], ['propagated'])
-    feature.feature ('runtime-link', ['shared', 'static'], ['propagated'])
-    feature.feature ('runtime-debugging', ['on', 'off'], ['propagated'])
-    
-    
-    feature.feature ('optimization',  ['off', 'speed', 'space'], ['propagated'])
-    feature.feature ('profiling', ['off', 'on'], ['propagated'])
-    feature.feature ('inlining', ['off', 'on', 'full'], ['propagated'])
-    
-    feature.feature ('threading', ['single', 'multi'], ['propagated'])
-    feature.feature ('rtti', ['on', 'off'], ['propagated'])
-    feature.feature ('exception-handling', ['on', 'off'], ['propagated'])
-    feature.feature ('debug-symbols', ['on', 'off'], ['propagated'])
-    feature.feature ('define', [], ['free'])
-    feature.feature ('include', [], ['free', 'path']) #order-sensitive
-    feature.feature ('cflags', [], ['free'])
-    feature.feature ('cxxflags', [], ['free'])
-    feature.feature ('linkflags', [], ['free'])
-    feature.feature ('archiveflags', [], ['free'])
-    feature.feature ('version', [], ['free'])
-    
-    feature.feature ('location-prefix', [], ['free'])
-
-    feature.feature ('action', [], ['free'])
-
-    
-    # The following features are incidental, since
-    # in themself they have no effect on build products.
-    # Not making them incidental will result in problems in corner
-    # cases, for example:
-    # 
-    #    unit-test a : a.cpp : <use>b ;
-    #    lib b : a.cpp b ;
-    # 
-    # Here, if <use> is not incidental, we'll decide we have two 
-    # targets for a.obj with different properties, and will complain.
-    #
-    # Note that making feature incidental does not mean it's ignored. It may
-    # be ignored when creating the virtual target, but the rest of build process
-    # will use them.
-    feature.feature ('use', [], ['free', 'dependency', 'incidental'])
-    feature.feature ('dependency', [], ['free', 'dependency', 'incidental'])
-    feature.feature ('implicit-dependency', [], ['free', 'dependency', 'incidental'])
-
-    feature.feature('warnings', [
-        'on',         # Enable default/"reasonable" warning level for the tool.
-        'all',        # Enable all possible warnings issued by the tool.
-        'off'],       # Disable all warnings issued by the tool.
-        ['incidental', 'propagated'])
-
-    feature.feature('warnings-as-errors', [
-        'off',        # Do not fail the compilation if there are warnings.
-        'on'],        # Fail the compilation if there are warnings.
-        ['incidental', 'propagated'])
-    
-    feature.feature ('source', [], ['free', 'dependency', 'incidental'])
-    feature.feature ('library', [], ['free', 'dependency', 'incidental'])
-    feature.feature ('file', [], ['free', 'dependency', 'incidental'])
-    feature.feature ('find-shared-library', [], ['free']) #order-sensitive ;
-    feature.feature ('find-static-library', [], ['free']) #order-sensitive ;
-    feature.feature ('library-path', [], ['free', 'path']) #order-sensitive ;
-    # Internal feature.
-    feature.feature ('library-file', [], ['free', 'dependency'])
-    
-    feature.feature ('name', [], ['free'])
-    feature.feature ('tag', [], ['free'])
-    feature.feature ('search', [], ['free', 'path']) #order-sensitive ;
-    feature.feature ('location', [], ['free', 'path'])
-    
-    feature.feature ('dll-path', [], ['free', 'path'])
-    feature.feature ('hardcode-dll-paths', ['true', 'false'], ['incidental'])
-    
-    
-    # This is internal feature which holds the paths of all dependency
-    # dynamic libraries. On Windows, it's needed so that we can all
-    # those paths to PATH, when running applications.
-    # On Linux, it's needed to add proper -rpath-link command line options.
-    feature.feature ('xdll-path', [], ['free', 'path'])
-    
-    #provides means to specify def-file for windows dlls.
-    feature.feature ('def-file', [], ['free', 'dependency'])
-    
-    # This feature is used to allow specific generators to run.
-    # For example, QT tools can only be invoked when QT library
-    # is used. In that case, <allow>qt will be in usage requirement
-    # of the library.
-    feature.feature ('allow', [], ['free'])
-    
-    # The addressing model to generate code for. Currently a limited set only
-    # specifying the bit size of pointers.
-    feature.feature('address-model', ['16', '32', '64'], ['propagated', 'optional'])
-
-    # Type of CPU architecture to compile for.
-    feature.feature('architecture', [
-        # x86 and x86-64
-        'x86',
-
-        # ia64
-        'ia64',
-
-        # Sparc
-        'sparc',
-
-        # RS/6000 & PowerPC
-        'power',
-
-        # MIPS/SGI
-        'mips1', 'mips2', 'mips3', 'mips4', 'mips32', 'mips32r2', 'mips64',
-
-        # HP/PA-RISC
-        'parisc',
-        
-        # Advanced RISC Machines
-        'arm',
-
-        # Combined architectures for platforms/toolsets that support building for
-        # multiple architectures at once. "combined" would be the default multi-arch
-        # for the toolset.
-        'combined',
-        'combined-x86-power'],
-
-        ['propagated', 'optional'])
-
-    # The specific instruction set in an architecture to compile.
-    feature.feature('instruction-set', [
-        # x86 and x86-64
-        'i386', 'i486', 'i586', 'i686', 'pentium', 'pentium-mmx', 'pentiumpro', 'pentium2', 'pentium3',
-        'pentium3m', 'pentium-m', 'pentium4', 'pentium4m', 'prescott', 'nocona', 'conroe', 'conroe-xe',
-        'conroe-l', 'allendale', 'mermon', 'mermon-xe', 'kentsfield', 'kentsfield-xe', 'penryn', 'wolfdale',
-        'yorksfield', 'nehalem', 'k6', 'k6-2', 'k6-3', 'athlon', 'athlon-tbird', 'athlon-4', 'athlon-xp',
-        'athlon-mp', 'k8', 'opteron', 'athlon64', 'athlon-fx', 'winchip-c6', 'winchip2', 'c3', 'c3-2',
-
-        # ia64
-        'itanium', 'itanium1', 'merced', 'itanium2', 'mckinley',
-
-        # Sparc
-        'v7', 'cypress', 'v8', 'supersparc', 'sparclite', 'hypersparc', 'sparclite86x', 'f930', 'f934',
-        'sparclet', 'tsc701', 'v9', 'ultrasparc', 'ultrasparc3',
-
-        # RS/6000 & PowerPC
-        '401', '403', '405', '405fp', '440', '440fp', '505', '601', '602',
-        '603', '603e', '604', '604e', '620', '630', '740', '7400',
-        '7450', '750', '801', '821', '823', '860', '970', '8540',
-        'power-common', 'ec603e', 'g3', 'g4', 'g5', 'power', 'power2',
-        'power3', 'power4', 'power5', 'powerpc', 'powerpc64', 'rios',
-        'rios1', 'rsc', 'rios2', 'rs64a',
-
-        # MIPS
-        '4kc', '4kp', '5kc', '20kc', 'm4k', 'r2000', 'r3000', 'r3900', 'r4000',
-        'r4100', 'r4300', 'r4400', 'r4600', 'r4650',
-        'r6000', 'r8000', 'rm7000', 'rm9000', 'orion', 'sb1', 'vr4100',
-        'vr4111', 'vr4120', 'vr4130', 'vr4300',
-        'vr5000', 'vr5400', 'vr5500',
-
-        # HP/PA-RISC
-        '700', '7100', '7100lc', '7200', '7300', '8000',
-        
-        # Advanced RISC Machines
-        'armv2', 'armv2a', 'armv3', 'armv3m', 'armv4', 'armv4t', 'armv5',
-        'armv5t', 'armv5te', 'armv6', 'armv6j', 'iwmmxt', 'ep9312'],
-
-        ['propagated', 'optional'])
-
-    feature.feature('conditional', [], ['incidental', 'free'])
-
-    # The value of 'no' prevents building of a target.
-    feature.feature('build', ['yes', 'no'], ['optional'])
-    
-    # Windows-specific features
-    feature.feature ('user-interface', ['console', 'gui', 'wince', 'native', 'auto'], [])
-    feature.feature ('variant', [], ['implicit', 'composite', 'propagated', 'symmetric'])
-
-
-    variant ('debug', ['<optimization>off', '<debug-symbols>on', '<inlining>off', '<runtime-debugging>on'])
-    variant ('release', ['<optimization>speed', '<debug-symbols>off', '<inlining>full', 
-                         '<runtime-debugging>off', '<define>NDEBUG'])
-    variant ('profile', ['release'], ['<profiling>on', '<debug-symbols>on'])
-
-    type.register ('H', ['h'])
-    type.register ('HPP', ['hpp'], 'H')
-    type.register ('C', ['c'])
-    
-
-reset ()
-register_globals ()
-
-class SearchedLibTarget (virtual_target.AbstractFileTarget):
-    def __init__ (self, name, project, shared, real_name, search, action):
-        virtual_target.AbstractFileTarget.__init__ (self, name, 'SEARCHED_LIB', project, action)
-        
-        self.shared_ = shared
-        self.real_name_ = real_name
-        if not self.real_name_:
-            self.real_name_ = name
-        self.search_ = search
-
-    def shared (self):
-        return self.shared_
-    
-    def real_name (self):
-        return self.real_name_
-    
-    def search (self):
-        return self.search_
-        
-    def actualize_location (self, target):
-        bjam.call("NOTFILE", target)
-    
-    def path (self):
-        #FIXME: several functions rely on this not being None
-        return ""
-
-
-class CScanner (scanner.Scanner):
-    def __init__ (self, includes):
-        scanner.Scanner.__init__ (self)
-    
-        self.includes_ = includes
-
-    def pattern (self):
-        return r'#[ \t]*include[ ]*(<(.*)>|"(.*)")'
-
-    def process (self, target, matches, binding):
-       
-        angle = regex.transform (matches, "<(.*)>")
-        quoted = regex.transform (matches, '"(.*)"')
-
-        g = str(id(self))
-        b = os.path.normpath(os.path.dirname(binding[0]))
-        
-        # Attach binding of including file to included targets.
-        # When target is directly created from virtual target
-        # this extra information is unnecessary. But in other
-        # cases, it allows to distinguish between two headers of the 
-        # same name included from different places.      
-        # We don't need this extra information for angle includes,
-        # since they should not depend on including file (we can't
-        # get literal "." in include path).
-        g2 = g + "#" + b
-
-        g = "<" + g + ">"
-        g2 = "<" + g2 + ">"
-        angle = [g + x for x in angle]
-        quoted = [g2 + x for x in quoted]
-
-        all = angle + quoted
-        bjam.call("mark-included", target, all)
-
-        engine = get_manager().engine()
-        engine.set_target_variable(angle, "SEARCH", get_value(self.includes_))
-        engine.set_target_variable(quoted, "SEARCH", [b] + get_value(self.includes_))
-        
-        # Just propagate current scanner to includes, in a hope
-        # that includes do not change scanners. 
-        get_manager().scanners().propagate(self, angle + quoted)
-        
-scanner.register (CScanner, 'include')
-type.set_scanner ('CPP', CScanner)
-type.set_scanner ('C', CScanner)
-
-# Ported to trunk@47077
-class LibGenerator (generators.Generator):
-    """ The generator class for libraries (target type LIB). Depending on properties it will
-        request building of the approapriate specific type -- SHARED_LIB, STATIC_LIB or 
-        SHARED_LIB.
-    """
-
-    def __init__(self, id = 'LibGenerator', composing = True, source_types = [], target_types_and_names = ['LIB'], requirements = []):
-        generators.Generator.__init__(self, id, composing, source_types, target_types_and_names, requirements)
-    
-    def run(self, project, name, prop_set, sources):
-
-        # The lib generator is composing, and can be only invoked with
-        # explicit name. This check is present in generator.run (and so in
-        # builtin.LinkingGenerator), but duplicate it here to avoid doing
-        # extra work.
-        if name:
-            properties = prop_set.raw()
-            # Determine the needed target type
-            actual_type = None
-            properties_grist = get_grist(properties)
-            if '<source>' not in properties_grist  and \
-               ('<search>' in properties_grist or '<name>' in properties_grist):
-                actual_type = 'SEARCHED_LIB'
-            elif '<file>' in properties_grist:
-                # The generator for 
-                actual_type = 'LIB'
-            elif '<link>shared' in properties:
-                actual_type = 'SHARED_LIB'
-            else:
-                actual_type = 'STATIC_LIB'
-
-            prop_set = prop_set.add_raw(['<main-target-type>LIB'])
-
-            # Construct the target.
-            return generators.construct(project, name, actual_type, prop_set, sources)
-
-    def viable_source_types(self):
-        return ['*']
-
-generators.register(LibGenerator())
-
-def lib(names, sources=[], requirements=[], default_build=[], usage_requirements=[]):
-    """The implementation of the 'lib' rule. Beyond standard syntax that rule allows
-    simplified: 'lib a b c ;'."""
-
-    if len(names) > 1:
-        if any(r.startswith('<name>') for r in requirements):
-            get_manager().errors()("When several names are given to the 'lib' rule\n" +
-                                   "it is not allowed to specify the <name> feature.")
-
-        if sources:
-            get_manager().errors()("When several names are given to the 'lib' rule\n" +
-                                   "it is not allowed to specify sources.")
-
-    project = get_manager().projects().current()
-    result = []
-
-    for name in names:
-        r = requirements[:]
-
-        # Support " lib a ; " and " lib a b c ; " syntax.
-        if not sources and not any(r.startswith("<name>") for r in requirements) \
-           and not any(r.startswith("<file") for r in requirements):
-            r.append("<name>" + name)
-
-        result.append(targets.create_typed_metatarget(name, "LIB", sources,
-                                                      r,
-                                                      default_build,
-                                                      usage_requirements))
-    return result
-
-get_manager().projects().add_rule("lib", lib)
-
-
-# Updated to trunk@47077
-class SearchedLibGenerator (generators.Generator):
-    def __init__ (self, id = 'SearchedLibGenerator', composing = False, source_types = [], target_types_and_names = ['SEARCHED_LIB'], requirements = []):
-        # TODO: the comment below looks strange. There are no requirements!
-        # The requirements cause the generators to be tried *only* when we're building
-        # lib target and there's 'search' feature. This seems ugly --- all we want
-        # is make sure SearchedLibGenerator is not invoked deep in transformation
-        # search.
-        generators.Generator.__init__ (self, id, composing, source_types, target_types_and_names, requirements)
-    
-    def run(self, project, name, prop_set, sources):
-
-        if not name:
-            return None
-
-        # If name is empty, it means we're called not from top-level.
-        # In this case, we just fail immediately, because SearchedLibGenerator
-        # cannot be used to produce intermediate targets.
-        
-        properties = prop_set.raw ()
-        shared = '<link>shared' in properties
-
-        a = virtual_target.NullAction (project.manager(), prop_set)
-        
-        real_name = feature.get_values ('<name>', properties)
-        if real_name:
-            real_name = real_name[0]
-        else:
-            real_nake = name
-        search = feature.get_values('<search>', properties)
-        usage_requirements = property_set.create(['<xdll-path>' + p for p in search])
-        t = SearchedLibTarget(name, project, shared, real_name, search, a)
-
-        # We return sources for a simple reason. If there's
-        #    lib png : z : <name>png ; 
-        # the 'z' target should be returned, so that apps linking to
-        # 'png' will link to 'z', too.
-        return(usage_requirements, [b2.manager.get_manager().virtual_targets().register(t)] + sources)
-
-generators.register (SearchedLibGenerator ())
-
-### class prebuilt-lib-generator : generator
-### {
-###     rule __init__ ( * : * )
-###     {
-###         generator.__init__ $(1) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ;
-###     }
-### 
-###     rule run ( project name ? : prop_set : sources * : multiple ? )
-###     {
-###         local f = [ $(prop_set).get <file> ] ;
-###         return $(f) $(sources) ;
-###     }    
-### }
-### 
-### generators.register 
-###   [ new prebuilt-lib-generator builtin.prebuilt : : LIB : <file> ] ;
-
-
-class CompileAction (virtual_target.Action):
-    def __init__ (self, manager, sources, action_name, prop_set):
-        virtual_target.Action.__init__ (self, manager, sources, action_name, prop_set)
-
-    def adjust_properties (self, prop_set):
-        """ For all virtual targets for the same dependency graph as self, 
-            i.e. which belong to the same main target, add their directories
-            to include path.
-        """
-        s = self.targets () [0].creating_subvariant ()
-
-        return prop_set.add_raw (s.implicit_includes ('include', 'H'))
-
-class CCompilingGenerator (generators.Generator):
-    """ Declare a special compiler generator.
-        The only thing it does is changing the type used to represent
-        'action' in the constructed dependency graph to 'CompileAction'.
-        That class in turn adds additional include paths to handle a case
-        when a source file includes headers which are generated themselfs.
-    """
-    def __init__ (self, id, composing, source_types, target_types_and_names, requirements):
-        # TODO: (PF) What to do with optional_properties? It seemed that, in the bjam version, the arguments are wrong.
-        generators.Generator.__init__ (self, id, composing, source_types, target_types_and_names, requirements)
-            
-    def action_class (self):
-        return CompileAction
-
-def register_c_compiler (id, source_types, target_types, requirements, optional_properties = []):
-    g = CCompilingGenerator (id, False, source_types, target_types, requirements + optional_properties)
-    return generators.register (g)
-
-
-class LinkingGenerator (generators.Generator):
-    """ The generator class for handling EXE and SHARED_LIB creation.
-    """
-    def __init__ (self, id, composing, source_types, target_types_and_names, requirements):
-        generators.Generator.__init__ (self, id, composing, source_types, target_types_and_names, requirements)
-        
-    def run (self, project, name, prop_set, sources):
-       
-        lib_sources = prop_set.get('<library>')
-        sources.extend(lib_sources)
-        
-        # Add <library-path> properties for all searched libraries
-        extra = []
-        for s in sources:
-            if s.type () == 'SEARCHED_LIB':
-                search = s.search()
-                extra.extend(property.Property('<library-path>', sp) for sp in search)
-
-        orig_xdll_path = []
-                   
-        if prop_set.get('<hardcode-dll-paths>') == ['true'] \
-               and type.is_derived(self.target_types_ [0], 'EXE'):
-            xdll_path = prop_set.get('<xdll-path>')
-            orig_xdll_path = [ replace_grist(x, '<dll-path>') for x in xdll_path ]
-            # It's possible that we have libraries in sources which did not came
-            # from 'lib' target. For example, libraries which are specified
-            # just as filenames as sources. We don't have xdll-path properties
-            # for such target, but still need to add proper dll-path properties.
-            for s in sources:
-                if type.is_derived (s.type (), 'SHARED_LIB') and not s.action ():
-                    # Unfortunately, we don't have a good way to find the path
-                    # to a file, so use this nasty approach.
-                    p = s.project()
-                    location = path.root(s.name(), p.get('source-location'))
-                    xdll_path.append(path.parent(location))
-                          
-            extra.extend(property.Property('<dll-path>', sp) for sp in xdll_path)
-        
-        if extra:
-            prop_set = prop_set.add_raw (extra)
-                        
-        result = generators.Generator.run(self, project, name, prop_set, sources)
-
-        if result:
-            ur = self.extra_usage_requirements(result, prop_set)
-            ur = ur.add(property_set.create(orig_xdll_path))
-        else:
-            return None
-        
-        return(ur, result)
-    
-    def extra_usage_requirements (self, created_targets, prop_set):
-        
-        result = property_set.empty ()
-        extra = []
-                        
-        # Add appropriate <xdll-path> usage requirements.
-        raw = prop_set.raw ()
-        if '<link>shared' in raw:
-            paths = []
-            
-            # TODO: is it safe to use the current directory? I think we should use 
-            # another mechanism to allow this to be run from anywhere.
-            pwd = os.getcwd()
-            
-            for t in created_targets:
-                if type.is_derived(t.type(), 'SHARED_LIB'):
-                    paths.append(path.root(path.make(t.path()), pwd))
-
-            extra += replace_grist(paths, '<xdll-path>')
-        
-        # We need to pass <xdll-path> features that we've got from sources,
-        # because if shared library is built, exe which uses it must know paths
-        # to other shared libraries this one depends on, to be able to find them
-        # all at runtime.
-                        
-        # Just pass all features in property_set, it's theorically possible
-        # that we'll propagate <xdll-path> features explicitly specified by
-        # the user, but then the user's to blaim for using internal feature.                
-        values = prop_set.get('<xdll-path>')
-        extra += replace_grist(values, '<xdll-path>')
-        
-        if extra:
-            result = property_set.create(extra)
-
-        return result
-
-    def generated_targets (self, sources, prop_set, project, name):
-
-        # sources to pass to inherited rule
-        sources2 = []
-        # sources which are libraries
-        libraries  = []
-        
-        # Searched libraries are not passed as argument to linker
-        # but via some option. So, we pass them to the action
-        # via property. 
-        fsa = []
-        fst = []
-        for s in sources:
-            if type.is_derived(s.type(), 'SEARCHED_LIB'):
-                n = s.real_name()
-                if s.shared():
-                    fsa.append(n)
-
-                else:
-                    fst.append(n)
-
-            else:
-                sources2.append(s)
-
-        add = []
-        if fsa:
-            add.append("<find-shared-library>" + '&&'.join(fsa))
-        if fst:
-            add.append("<find-static-library>" + '&&'.join(fst))
-
-        spawn = generators.Generator.generated_targets(self, sources2, prop_set.add_raw(add), project, name)       
-        return spawn
-
-
-def register_linker(id, source_types, target_types, requirements):
-    g = LinkingGenerator(id, True, source_types, target_types, requirements)
-    generators.register(g)
-
-class ArchiveGenerator (generators.Generator):
-    """ The generator class for handling STATIC_LIB creation.
-    """
-    def __init__ (self, id, composing, source_types, target_types_and_names, requirements):
-        generators.Generator.__init__ (self, id, composing, source_types, target_types_and_names, requirements)
-        
-    def run (self, project, name, prop_set, sources):
-        sources += prop_set.get ('<library>')
-        
-        result = generators.Generator.run (self, project, name, prop_set, sources)
-             
-        return result
-
-### rule register-archiver ( id composing ? : source_types + : target_types + :
-###                             requirements * )
-### {
-###     local g = [ new ArchiveGenerator $(id) $(composing) : $(source_types) 
-###                 : $(target_types) : $(requirements) ] ;
-###     generators.register $(g) ;
-### }
-### 
-### 
-### IMPORT $(__name__) : register-linker register-archiver 
-###   : : generators.register-linker generators.register-archiver ;
-### 
-### 
-### 
-
-get_manager().projects().add_rule("variant", variant)
-
-import stage
-import symlink
-import message
diff --git a/jam-files/boost-build/tools/cast.jam b/jam-files/boost-build/tools/cast.jam
deleted file mode 100644
index 6c84922f..00000000
--- a/jam-files/boost-build/tools/cast.jam
+++ /dev/null
@@ -1,91 +0,0 @@
-# Copyright 2005 Vladimir Prus.
-# Distributed under the Boost Software License, Version 1.0. (See
-# accompanying file LICENSE_1_0.txt or copy at
-# http://www.boost.org/LICENSE_1_0.txt)
-
-# Defines main target 'cast', used to change type for target. For example, in Qt
-# library one wants two kinds of CPP files -- those that just compiled and those
-# that are passed via the MOC tool.
-#
-# This is done with:
-#
-#    exe main : main.cpp [ cast _ moccable-cpp : widget.cpp ] ;
-#
-# Boost.Build will assing target type CPP to both main.cpp and widget.cpp. Then,
-# the cast rule will change target type of widget.cpp to MOCCABLE-CPP, and Qt
-# support will run the MOC tool as part of the build process.
-#
-# At the moment, the 'cast' rule only works for non-derived (source) targets.
-#
-# TODO: The following comment is unclear or incorrect. Clean it up.
-# > Another solution would be to add a separate main target 'moc-them' that
-# > would moc all the passed sources, no matter what their type is, but I prefer
-# > cast, as defining a new target type + generator for that type is somewhat
-# > simpler than defining a main target rule.
-
-import "class" : new ;
-import errors ;
-import project ;
-import property-set ;
-import targets ;
-import type ;
-
-
-class cast-target-class : typed-target
-{
-    import type ;
-
-    rule __init__ ( name : project : type : sources * : requirements * :
-        default-build * : usage-requirements * )
-    {
-        typed-target.__init__ $(name) : $(project) : $(type) : $(sources) :
-            $(requirements) : $(default-build) : $(usage-requirements) ;
-    }
-
-    rule construct ( name : source-targets * : property-set )
-    {
-        local result ;
-        for local s in $(source-targets)
-        {
-            if ! [ class.is-a $(s) : file-target ]
-            {
-                import errors ;
-                errors.user-error Source to the 'cast' rule is not a file! ;
-            }
-            if [ $(s).action ]
-            {
-                import errors ;
-                errors.user-error Only non-derived target are allowed for
-                    'cast'. : when building [ full-name ] ;
-            }
-            local r = [ $(s).clone-with-different-type $(self.type) ] ;
-            result += [ virtual-target.register $(r) ] ;
-        }
-        return [ property-set.empty ] $(result) ;
-    }
-}
-
-
-rule cast ( name type : sources * : requirements * : default-build * :
-    usage-requirements * )
-{
-    local project = [ project.current ] ;
-
-    local real-type = [ type.type-from-rule-name $(type) ] ;
-    if ! $(real-type)
-    {
-        errors.user-error No type corresponds to the main target rule name
-            '$(type)' : "Hint: try a lowercase name" ;
-    }
-
-    targets.main-target-alternative [ new cast-target-class $(name) : $(project)
-        : $(real-type)
-        : [ targets.main-target-sources $(sources) : $(name) ]
-        : [ targets.main-target-requirements $(requirements) : $(project) ]
-        : [ targets.main-target-default-build $(default-build) : $(project) ]
-        : [ targets.main-target-usage-requirements $(usage-requirements) :
-            $(project) ] ] ;
-}
-
-
-IMPORT $(__name__) : cast : : cast ;
diff --git a/jam-files/boost-build/tools/cast.py b/jam-files/boost-build/tools/cast.py
deleted file mode 100644
index 8f053f11..00000000
--- a/jam-files/boost-build/tools/cast.py
+++ /dev/null
@@ -1,69 +0,0 @@
-# Status: ported
-# Base revision: 64432.
-# Copyright 2005-2010 Vladimir Prus.
-# Distributed under the Boost Software License, Version 1.0. (See
-# accompanying file LICENSE_1_0.txt or copy at
-# http://www.boost.org/LICENSE_1_0.txt)
-
-# Defines main target 'cast', used to change type for target. For example, in Qt
-# library one wants two kinds of CPP files -- those that just compiled and those
-# that are passed via the MOC tool.
-#
-# This is done with:
-#
-#    exe main : main.cpp [ cast _ moccable-cpp : widget.cpp ] ;
-#
-# Boost.Build will assing target type CPP to both main.cpp and widget.cpp. Then,
-# the cast rule will change target type of widget.cpp to MOCCABLE-CPP, and Qt
-# support will run the MOC tool as part of the build process.
-#
-# At the moment, the 'cast' rule only works for non-derived (source) targets.
-#
-# TODO: The following comment is unclear or incorrect. Clean it up.
-# > Another solution would be to add a separate main target 'moc-them' that
-# > would moc all the passed sources, no matter what their type is, but I prefer
-# > cast, as defining a new target type + generator for that type is somewhat
-# > simpler than defining a main target rule.
-
-import b2.build.targets as targets
-import b2.build.virtual_target as virtual_target
-
-from b2.manager import get_manager
-from b2.util import bjam_signature
-
-class CastTargetClass(targets.TypedTarget):
-
-    def construct(name, source_targets, ps):
-        result = []
-        for s in source_targets:
-            if not isinstance(s, virtual_targets.FileTarget):
-                get_manager().errors()("Source to the 'cast' metatager is not a file")
-
-            if s.action():
-                get_manager().errors()("Only non-derived targets allowed as sources for 'cast'.")
-
-
-            r = s.clone_with_different_type(self.type())
-            result.append(get_manager().virtual_targets().register(r))
-
-        return result
-    
-
-@bjam_signature((["name", "type"], ["sources", "*"], ["requirements", "*"],
-                 ["default_build", "*"], ["usage_requirements", "*"]))
-def cast(name, type, sources, requirements, default_build, usage_requirements):
-   
-    from b2.manager import get_manager
-    t = get_manager().targets()
-    
-    project = get_manager().projects().current()
-        
-    return t.main_target_alternative(
-        CastTargetClass(name, project, type,
-                        t.main_target_sources(sources, name),
-                        t.main_target_requirements(requirements, project),
-                        t.main_target_default_build(default_build, project),
-                        t.main_target_usage_requirements(usage_requirements, project)))
-
-
-get_manager().projects().add_rule("cast", cast)
diff --git a/jam-files/boost-build/tools/clang-darwin.jam b/jam-files/boost-build/tools/clang-darwin.jam
deleted file mode 100644
index a8abc7d6..00000000
--- a/jam-files/boost-build/tools/clang-darwin.jam
+++ /dev/null
@@ -1,170 +0,0 @@
-# Copyright Vladimir Prus 2004.
-# Copyright Noel Belcourt 2007.
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt
-# or copy at http://www.boost.org/LICENSE_1_0.txt)
-
-import clang ;
-import feature : feature ;
-import os ;
-import toolset ;
-import toolset : flags ;
-import gcc ;
-import common ;
-import errors ;
-import generators ;
-
-feature.extend-subfeature toolset clang : platform : darwin ;
-
-toolset.inherit-generators clang-darwin 
-  <toolset>clang <toolset-clang:platform>darwin 
-  : gcc 
-  # Don't inherit PCH generators. They were not tested, and probably
-  # don't work for this compiler.
-  : gcc.mingw.link gcc.mingw.link.dll gcc.compile.c.pch gcc.compile.c++.pch
-  ;
-
-generators.override clang-darwin.prebuilt : builtin.lib-generator ;
-generators.override clang-darwin.prebuilt : builtin.prebuilt ;
-generators.override clang-darwin.searched-lib-generator : searched-lib-generator ;
-
-toolset.inherit-rules clang-darwin : gcc ;
-toolset.inherit-flags clang-darwin : gcc 
-        : <inlining>off <inlining>on <inlining>full <optimization>space 
-          <warnings>off <warnings>all <warnings>on
-          <architecture>x86/<address-model>32
-          <architecture>x86/<address-model>64
-        ;
-        
-if [ MATCH (--debug-configuration) : [ modules.peek : ARGV ] ]
-{
-    .debug-configuration = true ;
-}
-                       
-# vectorization diagnostics
-feature vectorize : off on full ;
-
-# Initializes the clang-darwin toolset
-#   version in optional
-#   name (default clang++) is used to invoke the specified clang complier
-#   compile and link options allow you to specify addition command line options for each version
-rule init ( version ? :  command * : options * )
-{
-    command = [ common.get-invocation-command clang-darwin : clang++ 
-        : $(command) ] ;
-
-    # Determine the version
-    local command-string = $(command:J=" ") ;
-    if $(command)
-    {    
-        version ?= [ MATCH "^([0-9.]+)"
-            : [ SHELL "$(command-string) -dumpversion" ] ] ;
-    }
-
-    local condition = [ common.check-init-parameters clang-darwin
-        : version $(version) ] ;    
-
-    common.handle-options clang-darwin : $(condition) : $(command) : $(options) ;
-
-    gcc.init-link-flags clang-darwin darwin $(condition) ;
-
-}
-
-SPACE = " " ;
-
-flags clang-darwin.compile OPTIONS <cflags> ;
-flags clang-darwin.compile OPTIONS <cxxflags> ;
-# flags clang-darwin.compile INCLUDES <include> ;
-
-# Declare flags and action for compilation.
-toolset.flags clang-darwin.compile OPTIONS <optimization>off   : -O0 ;
-toolset.flags clang-darwin.compile OPTIONS <optimization>speed : -O3 ;
-toolset.flags clang-darwin.compile OPTIONS <optimization>space : -Os ;
-
-toolset.flags clang-darwin.compile OPTIONS <inlining>off  : -fno-inline ;
-toolset.flags clang-darwin.compile OPTIONS <inlining>on   : -Wno-inline ;
-toolset.flags clang-darwin.compile OPTIONS <inlining>full : -finline-functions -Wno-inline ;
-
-toolset.flags clang-darwin.compile OPTIONS <warnings>off : -w ;
-toolset.flags clang-darwin.compile OPTIONS <warnings>on  : -Wall ;
-toolset.flags clang-darwin.compile OPTIONS <warnings>all : -Wall -pedantic ;
-toolset.flags clang-darwin.compile OPTIONS <warnings-as-errors>on : -Werror ;
-
-toolset.flags clang-darwin.compile OPTIONS <debug-symbols>on : -g ;
-toolset.flags clang-darwin.compile OPTIONS <profiling>on : -pg ;
-toolset.flags clang-darwin.compile OPTIONS <rtti>off : -fno-rtti ;
-
-actions compile.c
-{
-    "$(CONFIG_COMMAND)" -x c $(OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -c -o "$(<)" "$(>)"
-}
-
-actions compile.c++
-{
-    "$(CONFIG_COMMAND)" -x c++ $(OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -c -o "$(<)" "$(>)"
-}
-
-flags clang-darwin ARFLAGS <archiveflags> ;
-
-# Default value. Mostly for the sake of clang-linux
-# that inherits from gcc, but does not has the same
-# logic to set the .AR variable. We can put the same
-# logic in clang-linux, but that's hardly worth the trouble
-# as on Linux, 'ar' is always available.
-.AR = ar ;
-
-rule archive ( targets * : sources * : properties * )
-{
-  # Always remove archive and start again. Here's rationale from
-  # Andre Hentz:
-  #
-  # I had a file, say a1.c, that was included into liba.a. 
-  # I moved a1.c to a2.c, updated my Jamfiles and rebuilt. 
-  # My program was crashing with absurd errors. 
-  # After some debugging I traced it back to the fact that a1.o was *still* 
-  # in liba.a 
-  #
-  # Rene Rivera:
-  #
-  # Originally removing the archive was done by splicing an RM
-  # onto the archive action. That makes archives fail to build on NT
-  # when they have many files because it will no longer execute the
-  # action directly and blow the line length limit. Instead we
-  # remove the file in a different action, just before the building
-  # of the archive.
-  #
-  local clean.a = $(targets[1])(clean) ;
-  TEMPORARY $(clean.a) ;
-  NOCARE $(clean.a) ;
-  LOCATE on $(clean.a) = [ on $(targets[1]) return $(LOCATE) ] ;
-  DEPENDS $(clean.a) : $(sources) ;
-  DEPENDS $(targets) : $(clean.a) ;
-  common.RmTemps $(clean.a) : $(targets) ;
-}
-
-actions piecemeal archive
-{
-  "$(.AR)" $(AROPTIONS) rc "$(<)" "$(>)"
-  "ranlib" -cs "$(<)"
-}
-
-flags clang-darwin.link USER_OPTIONS <linkflags> ;
-
-# Declare actions for linking
-rule link ( targets * : sources * : properties * )
-{
-  SPACE on $(targets) = " " ;
-  # Serialize execution of the 'link' action, since
-  # running N links in parallel is just slower.
-  JAM_SEMAPHORE on $(targets) = <s>clang-darwin-link-semaphore ;
-}
-
-actions link bind LIBRARIES
-{
-    "$(CONFIG_COMMAND)" $(USER_OPTIONS) -L"$(LINKPATH)" -o "$(<)" "$(>)" "$(LIBRARIES)" -l$(FINDLIBS-SA) -l$(FINDLIBS-ST) $(OPTIONS)
-}
-
-actions link.dll bind LIBRARIES
-{
-    "$(CONFIG_COMMAND)" $(USER_OPTIONS) -L"$(LINKPATH)" -o "$(<)" -single_module -dynamiclib -install_name "$(<[1]:D=)" "$(>)"  "$(LIBRARIES)" -l$(FINDLIBS-SA) -l$(FINDLIBS-ST) $(OPTIONS)
-}
diff --git a/jam-files/boost-build/tools/clang-linux.jam b/jam-files/boost-build/tools/clang-linux.jam
deleted file mode 100644
index 036d749e..00000000
--- a/jam-files/boost-build/tools/clang-linux.jam
+++ /dev/null
@@ -1,196 +0,0 @@
-#  Copyright (c) 2003      Michael Stevens
-#  Copyright (c) 2010-2011 Bryce Lelbach (blelbach@cct.lsu.edu, maintainer)
-#
-#  Use, modification and distribution is subject to the Boost Software
-#  License Version 1.0. (See accompanying file LICENSE_1_0.txt or
-#  http://www.boost.org/LICENSE_1_0.txt)
-
-import toolset ;
-import feature ;
-import toolset : flags ;
-
-import clang ;
-import gcc ;
-import common ;
-import errors ;
-import generators ;
-import type ;
-import numbers ;
-
-feature.extend-subfeature toolset clang : platform : linux ;
-
-toolset.inherit-generators clang-linux 
-    <toolset>clang <toolset-clang:platform>linux : gcc
-  : gcc.mingw.link gcc.mingw.link.dll gcc.cygwin.link gcc.cygwin.link.dll ;
-generators.override clang-linux.prebuilt : builtin.lib-generator ;
-generators.override clang-linux.prebuilt : builtin.prebuilt ;
-generators.override clang-linux.searched-lib-generator : searched-lib-generator ;
-
-# Override default do-nothing generators.
-generators.override clang-linux.compile.c.pch   : pch.default-c-pch-generator   ;
-generators.override clang-linux.compile.c++.pch : pch.default-cpp-pch-generator ;
- 
-type.set-generated-target-suffix PCH
-  : <toolset>clang <toolset-clang:platform>linux : pth ;
-
-toolset.inherit-rules clang-linux : gcc ;
-toolset.inherit-flags clang-linux : gcc 
-  : <inlining>off <inlining>on <inlining>full
-    <optimization>space <optimization>speed
-    <warnings>off <warnings>all <warnings>on ;
-        
-if [ MATCH (--debug-configuration) : [ modules.peek : ARGV ] ] {
-  .debug-configuration = true ;
-}
-                       
-rule init ( version ? :  command * : options * ) {
-  command = [ common.get-invocation-command clang-linux : clang++ 
-    : $(command) ] ;
-                
-  # Determine the version
-  local command-string = $(command:J=" ") ;
-
-  if $(command) {    
-    version ?= [ MATCH "version ([0-9.]+)"
-      : [ SHELL "$(command-string) --version" ] ] ;
-  }
-
-  local condition = [ common.check-init-parameters clang-linux
-    : version $(version) ] ;
-    
-  common.handle-options clang-linux : $(condition) : $(command) : $(options) ;
-
-  gcc.init-link-flags clang-linux gnu $(condition) ;
-}
-
-###############################################################################
-# Flags
-
-toolset.flags clang-linux.compile OPTIONS <cflags> ;
-toolset.flags clang-linux.compile OPTIONS <cxxflags> ;
-
-toolset.flags clang-linux.compile OPTIONS <optimization>off   : ;
-toolset.flags clang-linux.compile OPTIONS <optimization>speed : -O3 ;
-toolset.flags clang-linux.compile OPTIONS <optimization>space : -Os ;
-
-# note: clang silently ignores some of these inlining options
-toolset.flags clang-linux.compile OPTIONS <inlining>off  : -fno-inline ;
-toolset.flags clang-linux.compile OPTIONS <inlining>on   : -Wno-inline ;
-toolset.flags clang-linux.compile OPTIONS <inlining>full : -finline-functions -Wno-inline ;
-
-toolset.flags clang-linux.compile OPTIONS <warnings>off : -w ;
-toolset.flags clang-linux.compile OPTIONS <warnings>on  : -Wall ;
-toolset.flags clang-linux.compile OPTIONS <warnings>all : -Wall -pedantic ;
-toolset.flags clang-linux.compile OPTIONS <warnings-as-errors>on : -Werror ;
-
-toolset.flags clang-linux.compile OPTIONS <debug-symbols>on : -g ;
-toolset.flags clang-linux.compile OPTIONS <profiling>on : -pg ;
-toolset.flags clang-linux.compile OPTIONS <rtti>off : -fno-rtti ;
-
-###############################################################################
-# C and C++ compilation
-
-rule compile.c++ ( targets * : sources * : properties * ) {
-  gcc.setup-threading $(targets) : $(sources) : $(properties) ;
-  gcc.setup-fpic $(targets) : $(sources) : $(properties) ;
-  gcc.setup-address-model $(targets) : $(sources) : $(properties) ;
-
-  local pth-file = [ on $(<) return $(PCH_FILE) ] ;
-
-  if $(pth-file) {
-    DEPENDS $(<) : $(pth-file) ;
-    compile.c++.with-pch $(targets) : $(sources) ;
-  }
-  else {
-    compile.c++.without-pth $(targets) : $(sources) ;
-  }
-}
-
-actions compile.c++.without-pth {
-  "$(CONFIG_COMMAND)" -c -x c++ $(OPTIONS) $(USER_OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -o "$(<)" "$(>)"
-}
-
-actions compile.c++.with-pch bind PCH_FILE
-{
-  "$(CONFIG_COMMAND)" -c -x c++ $(OPTIONS) $(USER_OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -Xclang -include-pth -Xclang "$(PCH_FILE)" -o "$(<)" "$(>)"
-}
-
-rule compile.c ( targets * : sources * : properties * )
-{
-  gcc.setup-threading $(targets) : $(sources) : $(properties) ;
-  gcc.setup-fpic $(targets) : $(sources) : $(properties) ;
-  gcc.setup-address-model $(targets) : $(sources) : $(properties) ;    
-
-  local pth-file = [ on $(<) return $(PCH_FILE) ] ;
-
-  if $(pth-file) {
-    DEPENDS $(<) : $(pth-file) ;
-    compile.c.with-pch $(targets) : $(sources) ;
-  }
-  else {
-    compile.c.without-pth $(targets) : $(sources) ;
-  }
-}
-
-actions compile.c.without-pth
-{
-  "$(CONFIG_COMMAND)" -c -x c $(OPTIONS) $(USER_OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -c -o "$(<)" "$(>)"
-}
-
-actions compile.c.with-pch bind PCH_FILE
-{
-  "$(CONFIG_COMMAND)" -c -x c $(OPTIONS) $(USER_OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -Xclang -include-pth -Xclang "$(PCH_FILE)" -c -o "$(<)" "$(>)"
-}
-
-###############################################################################
-# PCH emission
-
-rule compile.c++.pch ( targets * : sources * : properties * ) {
-  gcc.setup-threading $(targets) : $(sources) : $(properties) ;
-  gcc.setup-fpic $(targets) : $(sources) : $(properties) ;
-  gcc.setup-address-model $(targets) : $(sources) : $(properties) ;    
-}
-
-actions compile.c++.pch {
-  rm -f "$(<)" && "$(CONFIG_COMMAND)" -x c++-header $(OPTIONS) $(USER_OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -Xclang -emit-pth -o "$(<)" "$(>)"
-}
-
-rule compile.c.pch ( targets * : sources * : properties * ) {
-  gcc.setup-threading $(targets) : $(sources) : $(properties) ;
-  gcc.setup-fpic $(targets) : $(sources) : $(properties) ;
-  gcc.setup-address-model $(targets) : $(sources) : $(properties) ;    
-}
-
-actions compile.c.pch
-{
-  rm -f "$(<)" && "$(CONFIG_COMMAND)" -x c-header $(OPTIONS) $(USER_OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -Xclang -emit-pth -o "$(<)" "$(>)"
-}
-
-###############################################################################
-# Linking
-
-SPACE = " " ;
-
-rule link ( targets * : sources * : properties * ) {
-  gcc.setup-threading $(targets) : $(sources) : $(properties) ;
-  gcc.setup-address-model $(targets) : $(sources) : $(properties) ;    
-  SPACE on $(targets) = " " ;
-  JAM_SEMAPHORE on $(targets) = <s>clang-linux-link-semaphore ;
-}
-
-actions link bind LIBRARIES {
-  "$(CONFIG_COMMAND)" -L"$(LINKPATH)" -Wl,-R$(SPACE)-Wl,"$(RPATH)" -Wl,-rpath-link$(SPACE)-Wl,"$(RPATH_LINK)" -o "$(<)" "$(>)" "$(LIBRARIES)" -l$(FINDLIBS-SA) -l$(FINDLIBS-ST) $(OPTIONS) $(USER_OPTIONS)
-}
-
-rule link.dll ( targets * : sources * : properties * ) {
-  gcc.setup-threading $(targets) : $(sources) : $(properties) ;
-  gcc.setup-address-model $(targets) : $(sources) : $(properties) ;    
-  SPACE on $(targets) = " " ;
-  JAM_SEMAPHORE on $(targets) = <s>clang-linux-link-semaphore ;
-}
-
-# Differ from 'link' above only by -shared.
-actions link.dll bind LIBRARIES {
-  "$(CONFIG_COMMAND)" -L"$(LINKPATH)" -Wl,-R$(SPACE)-Wl,"$(RPATH)" -o "$(<)" -Wl,-soname$(SPACE)-Wl,$(<[1]:D=) -shared "$(>)"  "$(LIBRARIES)" -l$(FINDLIBS-SA) -l$(FINDLIBS-ST) $(OPTIONS) $(USER_OPTIONS)
-}
-
diff --git a/jam-files/boost-build/tools/clang.jam b/jam-files/boost-build/tools/clang.jam
deleted file mode 100644
index e0ac9a55..00000000
--- a/jam-files/boost-build/tools/clang.jam
+++ /dev/null
@@ -1,27 +0,0 @@
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt
-# or copy at http://www.boost.org/LICENSE_1_0.txt)
-
-# This is a generic 'clang' toolset. Depending on the current system, it
-# forwards either to 'clang-unix' or 'clang-darwin' modules.
-
-import feature ;
-import os ;
-import toolset ;
-
-feature.extend toolset : clang ;
-feature.subfeature toolset clang : platform : : propagated link-incompatible ;
-
-rule init ( * : * )
-{
-    if [ os.name ] = MACOSX
-    {
-        toolset.using clang-darwin : 
-          $(1) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ;
-    }
-    else
-    {
-        toolset.using clang-linux : 
-          $(1) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ;
-    }
-}
diff --git a/jam-files/boost-build/tools/common.jam b/jam-files/boost-build/tools/common.jam
deleted file mode 100644
index ed835a36..00000000
--- a/jam-files/boost-build/tools/common.jam
+++ /dev/null
@@ -1,994 +0,0 @@
-# Copyright 2003, 2005 Dave Abrahams
-# Copyright 2005, 2006 Rene Rivera
-# Copyright 2005 Toon Knapen
-# Copyright 2002, 2003, 2004, 2005, 2006 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-#   Provides actions common to all toolsets, such as creating directories and
-# removing files.
-
-import os ;
-import modules ;
-import utility ;
-import print ;
-import type ;
-import feature ;
-import errors ;
-import path ;
-import sequence ;
-import toolset ;
-import virtual-target ;
-
-if [ MATCH (--debug-configuration) : [ modules.peek : ARGV ] ]
-{
-    .debug-configuration = true ;
-}
-if [ MATCH (--show-configuration) : [ modules.peek : ARGV ] ]
-{
-    .show-configuration = true ;
-}
-
-# Configurations
-#
-# The following class helps to manage toolset configurations. Each configuration
-# has a unique ID and one or more parameters. A typical example of a unique ID
-# is a condition generated by 'common.check-init-parameters' rule. Other kinds
-# of IDs can be used. Parameters may include any details about the configuration
-# like 'command', 'path', etc.
-#
-# A toolset configuration may be in one of the following states:
-#
-#   - registered
-#       Configuration has been registered (e.g. explicitly or by auto-detection
-#       code) but has not yet been marked as used, i.e. 'toolset.using' rule has
-#       not yet been called for it.
-#   - used
-#       Once called 'toolset.using' rule marks the configuration as 'used'.
-#
-# The main difference between the states above is that while a configuration is
-# 'registered' its options can be freely changed. This is useful in particular
-# for autodetection code - all detected configurations may be safely overwritten
-# by user code.
-
-class configurations
-{
-    import errors ;
-
-    rule __init__ ( )
-    {
-    }
-
-    # Registers a configuration.
-    #
-    # Returns 'true' if the configuration has been added and an empty value if
-    # it already exists. Reports an error if the configuration is 'used'.
-    #
-    rule register ( id )
-    {
-        if $(id) in $(self.used)
-        {
-            errors.error "common: the configuration '$(id)' is in use" ;
-        }
-
-        local retval ;
-
-        if ! $(id) in $(self.all)
-        {
-            self.all += $(id) ;
-
-            # Indicate that a new configuration has been added.
-            retval = true ;
-        }
-
-        return $(retval) ;
-    }
-
-    # Mark a configuration as 'used'.
-    #
-    # Returns 'true' if the state of the configuration has been changed to
-    # 'used' and an empty value if it the state has not been changed. Reports an
-    # error if the configuration is not known.
-    #
-    rule use ( id )
-    {
-        if ! $(id) in $(self.all)
-        {
-            errors.error "common: the configuration '$(id)' is not known" ;
-        }
-
-        local retval ;
-
-        if ! $(id) in $(self.used)
-        {
-            self.used += $(id) ;
-
-            # Indicate that the configuration has been marked as 'used'.
-            retval = true ;
-        }
-
-        return $(retval) ;
-    }
-
-    # Return all registered configurations.
-    #
-    rule all ( )
-    {
-        return $(self.all) ;
-    }
-
-    # Return all used configurations.
-    #
-    rule used ( )
-    {
-        return $(self.used) ;
-    }
-
-    # Returns the value of a configuration parameter.
-    #
-    rule get ( id : param )
-    {
-        return $(self.$(param).$(id)) ;
-    }
-
-    # Sets the value of a configuration parameter.
-    #
-    rule set ( id : param : value * )
-    {
-        self.$(param).$(id) = $(value) ;
-    }
-}
-
-
-# The rule for checking toolset parameters. Trailing parameters should all be
-# parameter name/value pairs. The rule will check that each parameter either has
-# a value in each invocation or has no value in each invocation. Also, the rule
-# will check that the combination of all parameter values is unique in all
-# invocations.
-#
-# Each parameter name corresponds to a subfeature. This rule will declare a
-# subfeature the first time a non-empty parameter value is passed and will
-# extend it with all the values.
-#
-# The return value from this rule is a condition to be used for flags settings.
-#
-rule check-init-parameters ( toolset requirement * : * )
-{
-    local sig = $(toolset) ;
-    local condition = <toolset>$(toolset) ;
-    local subcondition ;
-    for local index in 2 3 4 5 6 7 8 9
-    {
-        local name = $($(index)[1]) ;
-        local value = $($(index)[2]) ;
-
-        if $(value)-is-not-empty
-        {
-            condition = $(condition)-$(value) ;
-            if $(.had-unspecified-value.$(toolset).$(name))
-            {
-                errors.user-error
-                    "$(toolset) initialization: parameter '$(name)'"
-                    "inconsistent" : "no value was specified in earlier"
-                    "initialization" : "an explicit value is specified now" ;
-            }
-            # The below logic is for intel compiler. It calls this rule with
-            # 'intel-linux' and 'intel-win' as toolset, so we need to get the
-            # base part of toolset name. We can not pass 'intel' as toolset
-            # because in that case it will be impossible to register versionless
-            # intel-linux and intel-win toolsets of a specific version.
-            local t = $(toolset) ;
-            local m = [ MATCH ([^-]*)- : $(toolset) ] ;
-            if $(m)
-            {
-                t = $(m[1]) ;
-            }
-            if ! $(.had-value.$(toolset).$(name))
-            {
-                if ! $(.declared-subfeature.$(t).$(name))
-                {
-                    feature.subfeature toolset $(t) : $(name) : : propagated ;
-                    .declared-subfeature.$(t).$(name) = true ;
-                }
-                .had-value.$(toolset).$(name) = true ;
-            }
-            feature.extend-subfeature toolset $(t) : $(name) : $(value) ;
-            subcondition += <toolset-$(t):$(name)>$(value) ;
-        }
-        else
-        {
-            if $(.had-value.$(toolset).$(name))
-            {
-                errors.user-error
-                    "$(toolset) initialization: parameter '$(name)'"
-                    "inconsistent" : "an explicit value was specified in an"
-                    "earlier initialization" : "no value is specified now" ;
-            }
-            .had-unspecified-value.$(toolset).$(name) = true ;
-        }
-        sig = $(sig)$(value:E="")- ;
-    }
-    if $(sig) in $(.all-signatures)
-    {
-        local message =
-            "duplicate initialization of $(toolset) with the following parameters: " ;
-        for local index in 2 3 4 5 6 7 8 9
-        {
-            local p = $($(index)) ;
-            if $(p)
-            {
-                message += "$(p[1]) = $(p[2]:E=<unspecified>)" ;
-            }
-        }
-        message += "previous initialization at $(.init-loc.$(sig))" ;
-        errors.user-error
-            $(message[1]) : $(message[2]) : $(message[3]) : $(message[4]) :
-            $(message[5]) : $(message[6]) : $(message[7]) : $(message[8]) ;
-    }
-    .all-signatures += $(sig) ;
-    .init-loc.$(sig) = [ errors.nearest-user-location ] ;
-
-    # If we have a requirement, this version should only be applied under that
-    # condition. To accomplish this we add a toolset requirement that imposes
-    # the toolset subcondition, which encodes the version.
-    if $(requirement)
-    {
-        local r = <toolset>$(toolset) $(requirement) ;
-        r = $(r:J=,) ;
-        toolset.add-requirements $(r):$(subcondition) ;
-    }
-
-    # We add the requirements, if any, to the condition to scope the toolset
-    # variables and options to this specific version.
-    condition += $(requirement) ;
-
-    if $(.show-configuration)
-    {
-        ECHO notice: $(condition) ;
-    }
-    return $(condition:J=/) ;
-}
-
-
-# A helper rule to get the command to invoke some tool. If
-# 'user-provided-command' is not given, tries to find binary named 'tool' in
-# PATH and in the passed 'additional-path'. Otherwise, verifies that the first
-# element of 'user-provided-command' is an existing program.
-#
-# This rule returns the command to be used when invoking the tool. If we can not
-# find the tool, a warning is issued. If 'path-last' is specified, PATH is
-# checked after 'additional-paths' when searching for 'tool'.
-#
-rule get-invocation-command-nodefault ( toolset : tool :
-    user-provided-command * : additional-paths * : path-last ? )
-{
-    local command ;
-    if ! $(user-provided-command)
-    {
-        command = [ find-tool $(tool) : $(additional-paths) : $(path-last) ] ;
-        if ! $(command) && $(.debug-configuration)
-        {
-            ECHO "warning: toolset $(toolset) initialization: can not find tool $(tool)" ;
-            ECHO "warning: initialized from" [ errors.nearest-user-location ] ;
-        }
-    }
-    else
-    {
-        command = [ check-tool $(user-provided-command) ] ;
-        if ! $(command) && $(.debug-configuration)
-        {
-            ECHO "warning: toolset $(toolset) initialization: " ;
-            ECHO "warning: can not find user-provided command " '$(user-provided-command)' ;
-            ECHO "warning: initialized from" [ errors.nearest-user-location ] ;
-        }
-    }
-
-    return $(command) ;
-}
-
-
-# Same as get-invocation-command-nodefault, except that if no tool is found,
-# returns either the user-provided-command, if present, or the 'tool' parameter.
-#
-rule get-invocation-command ( toolset : tool : user-provided-command * :
-    additional-paths * : path-last ? )
-{
-    local result = [ get-invocation-command-nodefault $(toolset) : $(tool) :
-        $(user-provided-command) : $(additional-paths) : $(path-last) ] ;
-
-    if ! $(result)
-    {
-        if $(user-provided-command)
-        {
-            result = $(user-provided-command) ;
-        }
-        else
-        {
-            result = $(tool) ;
-        }
-    }
-    return $(result) ;
-}
-
-
-# Given an invocation command return the absolute path to the command. This
-# works even if command has no path element and was found on the PATH.
-#
-rule get-absolute-tool-path ( command )
-{
-    if $(command:D)
-    {
-        return $(command:D) ;
-    }
-    else
-    {
-        local m = [ GLOB [ modules.peek : PATH Path path ] : $(command) $(command).exe ] ;
-        return $(m[1]:D) ;
-    }
-}
-
-
-# Attempts to find tool (binary) named 'name' in PATH and in 'additional-paths'.
-# If found in PATH, returns 'name' and if found in additional paths, returns
-# absolute name. If the tool is found in several directories, returns the
-# first path found. Otherwise, returns an empty string. If 'path-last' is
-# specified, PATH is searched after 'additional-paths'.
-#
-local rule find-tool ( name : additional-paths * : path-last ? )
-{
-    local path = [ path.programs-path ] ;
-    local match = [ path.glob $(path) : $(name) $(name).exe ] ;
-    local additional-match = [ path.glob $(additional-paths) : $(name) $(name).exe ] ;
-
-    local result ;
-    if $(path-last)
-    {
-        result = $(additional-match) ;
-        if ! $(result) && $(match)
-        {
-            result = $(name) ;
-        }
-    }
-    else
-    {
-        if $(match)
-        {
-            result = $(name) ;
-        }
-        else
-        {
-            result = $(additional-match) ;
-        }
-    }
-    if $(result)
-    {
-        return [ path.native $(result[1]) ] ;
-    }
-}
-
-
-# Checks if 'command' can be found either in path or is a full name to an
-# existing file.
-#
-local rule check-tool-aux ( command )
-{
-    if $(command:D)
-    {
-        if [ path.exists $(command) ]
-            # Both NT and Cygwin will run .exe files by their unqualified names.
-            || ( [ os.on-windows ] && [ path.exists $(command).exe ] )
-            # Only NT will run .bat & .cmd files by their unqualified names.
-            || ( ( [ os.name ] = NT ) && ( [ path.exists $(command).bat ] ||
-                [ path.exists $(command).cmd ] ) )
-        {
-            return $(command) ;
-        }
-    }
-    else
-    {
-        if [ GLOB [ modules.peek : PATH Path path ] : $(command) ]
-        {
-            return $(command) ;
-        }
-    }
-}
-
-
-# Checks that a tool can be invoked by 'command'. If command is not an absolute
-# path, checks if it can be found in 'path'. If comand is an absolute path,
-# check that it exists. Returns 'command' if ok or empty string otherwise.
-#
-local rule check-tool ( xcommand + )
-{
-    if [ check-tool-aux $(xcommand[1]) ] ||
-       [ check-tool-aux $(xcommand[-1]) ]
-    {
-        return $(xcommand) ;
-    }
-}
-
-
-# Handle common options for toolset, specifically sets the following flag
-# variables:
-# - CONFIG_COMMAND to $(command)
-# - OPTIONS for compile         to the value of <compileflags> in $(options)
-# - OPTIONS for compile.c       to the value of <cflags>       in $(options)
-# - OPTIONS for compile.c++     to the value of <cxxflags>     in $(options)
-# - OPTIONS for compile.fortran to the value of <fflags>       in $(options)
-# - OPTIONS for link            to the value of <linkflags>    in $(options)
-#
-rule handle-options ( toolset : condition * : command * : options * )
-{
-    if $(.debug-configuration)
-    {
-        ECHO "notice: will use '$(command)' for $(toolset), condition $(condition:E=(empty))" ;
-    }
-
-    #   The last parameter ('unchecked') says it is OK to set flags for another
-    # module.
-    toolset.flags $(toolset) CONFIG_COMMAND $(condition) : $(command)
-        : unchecked ;
-
-    toolset.flags $(toolset).compile         OPTIONS $(condition) :
-        [ feature.get-values <compileflags> : $(options) ] : unchecked ;
-
-    toolset.flags $(toolset).compile.c       OPTIONS $(condition) :
-        [ feature.get-values <cflags>       : $(options) ] : unchecked ;
-
-    toolset.flags $(toolset).compile.c++     OPTIONS $(condition) :
-        [ feature.get-values <cxxflags>     : $(options) ] : unchecked ;
-
-    toolset.flags $(toolset).compile.fortran OPTIONS $(condition) :
-        [ feature.get-values <fflags>       : $(options) ] : unchecked ;
-
-    toolset.flags $(toolset).link            OPTIONS $(condition) :
-        [ feature.get-values <linkflags>    : $(options) ] : unchecked ;
-}
-
-
-# Returns the location of the "program files" directory on a Windows platform.
-#
-rule get-program-files-dir ( )
-{
-    local ProgramFiles = [ modules.peek : ProgramFiles ] ;
-    if $(ProgramFiles)
-    {
-        ProgramFiles = "$(ProgramFiles:J= )" ;
-    }
-    else
-    {
-        ProgramFiles = "c:\\Program Files" ;
-    }
-    return $(ProgramFiles) ;
-}
-
-
-if [ os.name ] = NT
-{
-    RM = del /f /q ;
-    CP = copy /b ;
-    IGNORE = "2>nul >nul & setlocal" ;
-    LN ?= $(CP) ;
-    # Ugly hack to convince copy to set the timestamp of the
-    # destination to the current time by concatenating the
-    # source with a nonexistent file.  Note that this requires
-    # /b (binary) as the default when concatenating files is /a (ascii).
-    WINDOWS-CP-HACK = "+ this-file-does-not-exist-A698EE7806899E69" ;
-}
-else
-{
-    RM = rm -f ;
-    CP = cp ;
-    LN = ln ;
-}
-
-
-rule rm-command ( )
-{
-    return $(RM) ;
-}
-
-
-rule copy-command ( )
-{
-    return $(CP) ;
-}
-
-
-if "\n" = "n" 
-{    
-    # Escape characters are not supported. Use ugly hacks that won't work,
-    # see below.
-    nl = "
-" ;
-    q = "" ;
-}
-else
-{
-    nl = "\n" ; 
-    q = "\"" ;
-}
-
-# Returns the command needed to set an environment variable on the current
-# platform. The variable setting persists through all following commands and is
-# visible in the environment seen by subsequently executed commands. In other
-# words, on Unix systems, the variable is exported, which is consistent with the
-# only possible behavior on Windows systems.
-#
-rule variable-setting-command ( variable : value )
-{
-    if [ os.name ] = NT
-    {
-        return "set $(variable)=$(value)$(nl)" ;
-    }
-    else
-    {
-        # If we don't have escape characters support in bjam, the below blows
-        # up on CYGWIN, since the $(nl) variable holds a Windows new-line \r\n 
-        # sequence that messes up the executed export command which then reports
-        # that the passed variable name is incorrect.
-        # But we have a check for cygwin in kernel/bootstrap.jam already.
-        return "$(variable)=$(q)$(value)$(q)$(nl)export $(variable)$(nl)" ;
-    }
-}
-
-
-# Returns a command to sets a named shell path variable to the given NATIVE
-# paths on the current platform.
-#
-rule path-variable-setting-command ( variable : paths * )
-{
-    local sep = [ os.path-separator ] ;
-    return [ variable-setting-command $(variable) : $(paths:J=$(sep)) ] ;
-}
-
-
-# Returns a command that prepends the given paths to the named path variable on
-# the current platform.
-#
-rule prepend-path-variable-command ( variable : paths * )
-{
-    return [ path-variable-setting-command $(variable)
-        : $(paths) [ os.expand-variable $(variable) ] ] ;
-}
-
-
-# Return a command which can create a file. If 'r' is result of invocation, then
-# 'r foobar' will create foobar with unspecified content. What happens if file
-# already exists is unspecified.
-#
-rule file-creation-command ( )
-{
-    if [ os.name ] = NT
-    {
-        # A few alternative implementations on Windows:
-        #
-        #   'type NUL >> '
-        #        That would construct an empty file instead of a file containing
-        #      a space and an end-of-line marker but it would also not change
-        #      the target's timestamp in case the file already exists.
-        #
-        #   'type NUL > '
-        #        That would construct an empty file instead of a file containing
-        #      a space and an end-of-line marker but it would also destroy an
-        #      already existing file by overwriting it with an empty one.
-        #
-        #   I guess the best solution would be to allow Boost Jam to define
-        # built-in functions such as 'create a file', 'touch a file' or 'copy a
-        # file' which could be used from inside action code. That would allow
-        # completely portable operations without this kind of kludge.
-        #                                            (22.02.2009.) (Jurko)
-        return "echo. > " ;
-    }
-    else
-    {
-        return "touch " ;
-    }
-}
-
-
-# Returns a command that may be used for 'touching' files. It is not a real
-# 'touch' command on NT because it adds an empty line at the end of file but it
-# works with source files.
-#
-rule file-touch-command ( )
-{
-    if [ os.name ] = NT
-    {
-        return "echo. >> " ;
-    }
-    else
-    {
-        return "touch " ;
-    }
-}
-
-
-rule MkDir
-{
-    # If dir exists, do not update it. Do this even for $(DOT).
-    NOUPDATE $(<) ;
-
-    if $(<) != $(DOT) && ! $($(<)-mkdir)
-    {
-        # Cheesy gate to prevent multiple invocations on same dir.
-        $(<)-mkdir = true ;
-
-        # Schedule the mkdir build action.
-        common.mkdir $(<) ;
-
-        # Prepare a Jam 'dirs' target that can be used to make the build only
-        # construct all the target directories.
-        DEPENDS dirs : $(<) ;
-
-        # Recursively create parent directories. $(<:P) = $(<)'s parent & we
-        # recurse until root.
-
-        local s = $(<:P) ;
-        if [ os.name ] = NT
-        {
-            switch $(s)
-            {
-                case *:   : s = ;
-                case *:\\ : s = ;
-            }
-        }
-
-        if $(s)
-        {
-            if $(s) != $(<)
-            {
-                DEPENDS $(<) : $(s) ;
-                MkDir $(s) ;
-            }
-            else
-            {
-                NOTFILE $(s) ;
-            }
-        }
-    }
-}
-
-
-#actions MkDir1
-#{
-#    mkdir "$(<)"
-#}
-
-#   The following quick-fix actions should be replaced using the original MkDir1
-# action once Boost Jam gets updated to correctly detect different paths leading
-# up to the same filesystem target and triggers their build action only once.
-#                                             (todo) (04.07.2008.) (Jurko)
-
-if [ os.name ] = NT
-{
-    actions mkdir
-    {
-        if not exist "$(<)\\" mkdir "$(<)"
-    }
-}
-else
-{
-    actions mkdir
-    {
-        mkdir -p "$(<)"
-    }
-}
-
-actions piecemeal together existing Clean
-{
-    $(RM) "$(>)"
-}
-
-
-rule copy
-{
-}
-
-
-actions copy
-{
-    $(CP) "$(>)" $(WINDOWS-CP-HACK) "$(<)"
-}
-
-
-rule RmTemps
-{
-}
-
-
-actions quietly updated piecemeal together RmTemps
-{
-    $(RM) "$(>)" $(IGNORE)
-}
-
-
-actions hard-link
-{
-    $(RM) "$(<)" 2$(NULL_OUT) $(NULL_OUT)
-    $(LN) "$(>)" "$(<)" $(NULL_OUT)
-}
-
-
-# Given a target, as given to a custom tag rule, returns a string formatted
-# according to the passed format. Format is a list of properties that is
-# represented in the result. For each element of format the corresponding target
-# information is obtained and added to the result string. For all, but the
-# literal, the format value is taken as the as string to prepend to the output
-# to join the item to the rest of the result. If not given "-" is used as a
-# joiner.
-#
-# The format options can be:
-#
-#   <base>[joiner]
-#       ::  The basename of the target name.
-#   <toolset>[joiner]
-#       ::  The abbreviated toolset tag being used to build the target.
-#   <threading>[joiner]
-#       ::  Indication of a multi-threaded build.
-#   <runtime>[joiner]
-#       ::  Collective tag of the build runtime.
-#   <version:/version-feature | X.Y[.Z]/>[joiner]
-#       ::  Short version tag taken from the given "version-feature" in the
-#           build properties. Or if not present, the literal value as the
-#           version number.
-#   <property:/property-name/>[joiner]
-#       ::  Direct lookup of the given property-name value in the build
-#           properties. /property-name/ is a regular expression. E.g.
-#           <property:toolset-.*:flavor> will match every toolset.
-#   /otherwise/
-#       ::  The literal value of the format argument.
-#
-# For example this format:
-#
-#   boost_ <base> <toolset> <threading> <runtime> <version:boost-version>
-#
-# Might return:
-#
-#   boost_thread-vc80-mt-gd-1_33.dll, or
-#   boost_regex-vc80-gd-1_33.dll
-#
-# The returned name also has the target type specific prefix and suffix which
-# puts it in a ready form to use as the value from a custom tag rule.
-#
-rule format-name ( format * : name : type ? : property-set )
-{
-    local result = "" ;
-    for local f in $(format)
-    {
-        switch $(f:G)
-        {
-            case <base> :
-                local matched = [ MATCH "^(boost.*python)-.*" : $(name) ] ;
-                if $(matched) = boost_python || $(matched) = boost_mpi_python
-                {
-                    result += $(name) ;
-                }
-                else
-                {
-                    result += $(name:B) ;
-                }
-            
-            case <toolset> :
-                result += [ join-tag $(f:G=) : [ toolset-tag $(name) : $(type) :
-                $(property-set) ] ] ;
-            
-            case <threading> :
-                result += [ join-tag $(f:G=) : [ threading-tag $(name) : $(type)
-                : $(property-set) ] ] ;
-            
-            case <runtime> :
-                result += [ join-tag $(f:G=) : [ runtime-tag $(name) : $(type) :
-                $(property-set) ] ] ;
-            
-            case <qt> :
-            result += [ join-tag $(f:G=) : [ qt-tag $(name) : $(type) :
-                $(property-set) ] ] ;
-
-            case <address-model> :
-            result += [ join-tag $(f:G=) : [ address-model-tag $(name) : $(type) :
-                $(property-set) ] ] ;
-
-            case <version:*> :
-                local key = [ MATCH <version:(.*)> : $(f:G) ] ;
-                local version = [ $(property-set).get <$(key)> ] ;
-                version ?= $(key) ;
-                version = [ MATCH "^([^.]+)[.]([^.]+)[.]?([^.]*)" : $(version) ] ;
-                result += [ join-tag $(f:G=) : $(version[1])_$(version[2]) ] ;
-
-            case <property:*> :
-                local key = [ MATCH <property:(.*)> : $(f:G) ] ;
-                local p0 = [ MATCH <($(key))> : [ $(property-set).raw ] ] ;
-                if $(p0)
-                {
-                    local p = [ $(property-set).get <$(p0)> ] ;
-                    if $(p)
-                    {
-                        result += [ join-tag $(f:G=) : $(p) ] ;
-                    }
-                }
-
-            case * :
-                result += $(f:G=) ;
-        }
-    }
-    result = [ virtual-target.add-prefix-and-suffix $(result:J=) : $(type) :
-      $(property-set) ] ;
-    return $(result) ;
-}
-
-
-local rule join-tag ( joiner ? : tag ? )
-{
-    if ! $(joiner) { joiner = - ; }
-    return $(joiner)$(tag) ;
-}
-
-
-local rule toolset-tag ( name : type ? : property-set )
-{
-    local tag = ;
-
-    local properties = [ $(property-set).raw ] ;
-    switch [ $(property-set).get <toolset> ]
-    {
-        case borland* : tag += bcb ;
-        case clang* :
-        {
-            switch [ $(property-set).get <toolset-clang:platform> ]
-            {
-               case darwin : tag += clang-darwin ;
-               case linux  : tag += clang ;
-            }
-        }
-        case como* : tag += como ;
-        case cw : tag += cw ;
-        case darwin* : tag += xgcc ;
-        case edg* : tag += edg ;
-        case gcc* :
-        {
-            switch [ $(property-set).get <toolset-gcc:flavor> ]
-            {
-                case *mingw* : tag += mgw ;
-                case * : tag += gcc ;
-            }
-        }
-        case intel :
-        if [ $(property-set).get <toolset-intel:platform> ] = win
-        {
-            tag += iw ;
-        }
-        else
-        {
-            tag += il ;
-        }
-        case kcc* : tag += kcc ;
-        case kylix* : tag += bck ;
-        #case metrowerks* : tag += cw ;
-        #case mingw* : tag += mgw ;
-        case mipspro* : tag += mp ;
-        case msvc* : tag += vc ;
-        case qcc* : tag += qcc ;
-        case sun* : tag += sw ;
-        case tru64cxx* : tag += tru ;
-        case vacpp* : tag += xlc ;
-    }
-    local version = [ MATCH "<toolset.*version>([0123456789]+)[.]([0123456789]*)"
-        : $(properties) ] ;
-    # For historical reasons, vc6.0 and vc7.0 use different naming.
-    if $(tag) = vc
-    {
-        if $(version[1]) = 6
-        {
-            # Cancel minor version.
-            version = 6 ;
-        }
-        else if $(version[1]) = 7 && $(version[2]) = 0
-        {
-            version = 7 ;
-        }
-    }
-    # On intel, version is not added, because it does not matter and it is the
-    # version of vc used as backend that matters. Ideally, we should encode the
-    # backend version but that would break compatibility with V1.
-    if $(tag) = iw
-    {
-        version = ;
-    }
-
-    # On borland, version is not added for compatibility with V1.
-    if $(tag) = bcb
-    {
-        version = ;
-    }
-
-    tag += $(version) ;
-
-    return $(tag:J=) ;
-}
-
-
-local rule threading-tag ( name : type ? : property-set )
-{
-    local tag = ;
-    local properties = [ $(property-set).raw ] ;
-    if <threading>multi in $(properties) { tag = mt ; }
-
-    return $(tag:J=) ;
-}
-
-
-local rule runtime-tag ( name : type ? : property-set )
-{
-    local tag = ;
-
-    local properties = [ $(property-set).raw ] ;
-    if <runtime-link>static in $(properties) { tag += s ; }
-
-    # This is an ugly thing. In V1, there is code to automatically detect which
-    # properties affect a target. So, if <runtime-debugging> does not affect gcc
-    # toolset, the tag rules will not even see <runtime-debugging>. Similar
-    # functionality in V2 is not implemented yet, so we just check for toolsets
-    # known to care about runtime debugging.
-    if ( <toolset>msvc in $(properties) ) ||
-        ( <stdlib>stlport in $(properties) ) ||
-        ( <toolset-intel:platform>win in $(properties) )
-    {
-        if <runtime-debugging>on in $(properties) { tag += g ; }
-    }
-
-    if <python-debugging>on in $(properties) { tag += y ; }
-    if <variant>debug in $(properties) { tag += d ; }
-    if <stdlib>stlport in $(properties) { tag += p ; }
-    if <stdlib-stlport:iostream>hostios in $(properties) { tag += n ; }
-
-    return $(tag:J=) ;
-}
-
-# Create a tag for the Qt library version
-# "<qt>4.6.0" will result in tag "qt460"
-local rule qt-tag ( name : type ? : property-set )
-{
-    local properties = [ $(property-set).get <qt> ] ;
-    local version = [ MATCH "([0123456789]+)[.]?([0123456789]*)[.]?([0123456789]*)"
-        : $(properties) ] ;
-    local tag = "qt"$(version:J=) ;
-    return $(tag) ;
-}
-
-# Create a tag for the address-model
-# <address-model>64 will simply generate "64"
-local rule address-model-tag ( name : type ? : property-set )
-{
-    local tag = ;
-    local version = [ $(property-set).get <address-model> ] ;
-    return $(version) ;
-}
-
-rule __test__ ( )
-{
-    import assert ;
-
-    local nl = "
-" ;
-
-    local save-os = [ modules.peek os : .name ] ;
-
-    modules.poke os : .name : LINUX ;
-
-    assert.result "PATH=\"foo:bar:baz\"$(nl)export PATH$(nl)"
-        : path-variable-setting-command PATH : foo bar baz ;
-
-    assert.result "PATH=\"foo:bar:$PATH\"$(nl)export PATH$(nl)"
-        : prepend-path-variable-command PATH : foo bar ;
-
-    modules.poke os : .name : NT ;
-
-    assert.result "set PATH=foo;bar;baz$(nl)"
-        : path-variable-setting-command PATH : foo bar baz ;
-
-    assert.result "set PATH=foo;bar;%PATH%$(nl)"
-        : prepend-path-variable-command PATH : foo bar ;
-
-    modules.poke os : .name : $(save-os) ;
-}
diff --git a/jam-files/boost-build/tools/common.py b/jam-files/boost-build/tools/common.py
deleted file mode 100644
index 612745b8..00000000
--- a/jam-files/boost-build/tools/common.py
+++ /dev/null
@@ -1,840 +0,0 @@
-#  Status: being ported by Steven Watanabe
-#  Base revision: 47174
-#
-#  Copyright (C) Vladimir Prus 2002. Permission to copy, use, modify, sell and
-#  distribute this software is granted provided this copyright notice appears in
-#  all copies. This software is provided "as is" without express or implied
-#  warranty, and with no claim as to its suitability for any purpose.
-
-""" Provides actions common to all toolsets, such as creating directories and
-    removing files.
-"""
-
-import re
-import bjam
-import os
-import os.path
-import sys
-
-from b2.build import feature
-from b2.util.utility import *
-from b2.util import path
-
-__re__before_first_dash = re.compile ('([^-]*)-')
-
-def reset ():
-    """ Clear the module state. This is mainly for testing purposes.
-        Note that this must be called _after_ resetting the module 'feature'.
-    """    
-    global __had_unspecified_value, __had_value, __declared_subfeature
-    global __init_loc
-    global __all_signatures, __debug_configuration, __show_configuration
-    
-    # Stores toolsets without specified initialization values.
-    __had_unspecified_value = {}
-
-    # Stores toolsets with specified initialization values.
-    __had_value = {}
-    
-    # Stores toolsets with declared subfeatures.
-    __declared_subfeature = {}
-    
-    # Stores all signatures of the toolsets.
-    __all_signatures = {}
-
-    # Stores the initialization locations of each toolset
-    __init_loc = {}
-
-    __debug_configuration = '--debug-configuration' in bjam.variable('ARGV')
-    __show_configuration = '--show-configuration' in bjam.variable('ARGV')
-
-    global __executable_path_variable
-    OS = bjam.call("peek", [], "OS")[0]
-    if OS == "NT":
-        # On Windows the case and capitalization of PATH is not always predictable, so
-        # let's find out what variable name was really set.
-        for n in sys.environ:
-            if n.lower() == "path":
-                __executable_path_variable = n
-                break
-    else:
-        __executable_path_variable = "PATH"
-
-    m = {"NT": __executable_path_variable,
-         "CYGWIN": "PATH",
-         "MACOSX": "DYLD_LIBRARY_PATH",
-         "AIX": "LIBPATH"}
-    global __shared_library_path_variable
-    __shared_library_path_variable = m.get(OS, "LD_LIBRARY_PATH")
-                            
-reset()
-
-def shared_library_path_variable():
-    return __shared_library_path_variable
-
-# ported from trunk@47174
-class Configurations(object):
-    """
-        This class helps to manage toolset configurations. Each configuration
-        has a unique ID and one or more parameters. A typical example of a unique ID
-        is a condition generated by 'common.check-init-parameters' rule. Other kinds
-        of IDs can be used. Parameters may include any details about the configuration
-        like 'command', 'path', etc.
-
-        A toolset configuration may be in one of the following states:
-
-        - registered
-              Configuration has been registered (e.g. by autodetection code) but has
-              not yet been marked as used, i.e. 'toolset.using' rule has not yet been
-              called for it.
-          - used
-              Once called 'toolset.using' rule marks the configuration as 'used'.
-
-        The main difference between the states above is that while a configuration is
-        'registered' its options can be freely changed. This is useful in particular
-        for autodetection code - all detected configurations may be safely overwritten
-        by user code.
-    """
-
-    def __init__(self):
-        self.used_ = set()
-        self.all_ = set()
-        self.params = {}
-
-    def register(self, id):
-        """
-            Registers a configuration.
-
-            Returns True if the configuration has been added and False if
-            it already exists. Reports an error if the configuration is 'used'.
-        """
-        if id in self.used_:
-            #FIXME
-            errors.error("common: the configuration '$(id)' is in use")
-
-        if id not in self.all_:
-            self.all_ += [id]
-
-            # Indicate that a new configuration has been added.
-            return True
-        else:
-            return False
-
-    def use(self, id):
-        """
-            Mark a configuration as 'used'.
-
-            Returns True if the state of the configuration has been changed to
-            'used' and False if it the state wasn't changed. Reports an error
-            if the configuration isn't known.
-        """
-        if id not in self.all_:
-            #FIXME:
-            errors.error("common: the configuration '$(id)' is not known")
-
-        if id not in self.used_:
-            self.used_ += [id]
-
-            # indicate that the configuration has been marked as 'used'
-            return True
-        else:
-            return False
-
-    def all(self):
-        """ Return all registered configurations. """
-        return self.all_
-
-    def used(self):
-        """ Return all used configurations. """
-        return self.used_
-
-    def get(self, id, param):
-        """ Returns the value of a configuration parameter. """
-        self.params_.getdefault(param, {}).getdefault(id, None)
-
-    def set (self, id, param, value):
-        """ Sets the value of a configuration parameter. """
-        self.params_.setdefault(param, {})[id] = value
-
-# Ported from trunk@47174
-def check_init_parameters(toolset, requirement, *args):
-    """ The rule for checking toolset parameters. Trailing parameters should all be
-        parameter name/value pairs. The rule will check that each parameter either has
-        a value in each invocation or has no value in each invocation. Also, the rule
-        will check that the combination of all parameter values is unique in all
-        invocations.
-
-        Each parameter name corresponds to a subfeature. This rule will declare a
-        subfeature the first time a non-empty parameter value is passed and will
-        extend it with all the values.
-
-        The return value from this rule is a condition to be used for flags settings.
-    """
-    # The type checking here is my best guess about
-    # what the types should be.
-    assert(isinstance(toolset, str))
-    assert(isinstance(requirement, str) or requirement is None)
-    sig = toolset
-    condition = replace_grist(toolset, '<toolset>')
-    subcondition = []
-    
-    for arg in args:
-        assert(isinstance(arg, tuple))
-        assert(len(arg) == 2)
-        name = arg[0]
-        value = arg[1]
-        assert(isinstance(name, str))
-        assert(isinstance(value, str) or value is None)
-        
-        str_toolset_name = str((toolset, name))
-
-        # FIXME: is this the correct translation?
-        ### if $(value)-is-not-empty
-        if value is not None:
-            condition = condition + '-' + value
-            if __had_unspecified_value.has_key(str_toolset_name):
-                raise BaseException("'%s' initialization: parameter '%s' inconsistent\n" \
-                "no value was specified in earlier initialization\n" \
-                "an explicit value is specified now" % (toolset, name))
-
-            # The logic below is for intel compiler. It calls this rule
-            # with 'intel-linux' and 'intel-win' as toolset, so we need to
-            # get the base part of toolset name.
-            # We can't pass 'intel' as toolset, because it that case it will
-            # be impossible to register versionles intel-linux and
-            # intel-win of specific version.
-            t = toolset
-            m = __re__before_first_dash.match(toolset)
-            if m:
-                t = m.group(1)
-
-            if not __had_value.has_key(str_toolset_name):
-                if not __declared_subfeature.has_key(str((t, name))):
-                    feature.subfeature('toolset', t, name, [], ['propagated'])
-                    __declared_subfeature[str((t, name))] = True
-
-                __had_value[str_toolset_name] = True
-
-            feature.extend_subfeature('toolset', t, name, [value])
-            subcondition += ['<toolset-' + t + ':' + name + '>' + value ]
-
-        else:
-            if __had_value.has_key(str_toolset_name):
-                raise BaseException ("'%s' initialization: parameter '%s' inconsistent\n" \
-                "an explicit value was specified in an earlier initialization\n" \
-                "no value is specified now" % (toolset, name))
-
-            __had_unspecified_value[str_toolset_name] = True
-
-        if value == None: value = ''
-        
-        sig = sig + value + '-'
-
-    if __all_signatures.has_key(sig):
-        message = "duplicate initialization of '%s' with the following parameters: " % toolset
-        
-        for arg in args:
-            name = arg[0]
-            value = arg[1]
-            if value == None: value = '<unspecified>'
-            
-            message += "'%s' = '%s'\n" % (name, value)
-
-        raise BaseException(message)
-
-    __all_signatures[sig] = True
-    # FIXME
-    __init_loc[sig] = "User location unknown" #[ errors.nearest-user-location ] ;
-
-    # If we have a requirement, this version should only be applied under that
-    # condition. To accomplish this we add a toolset requirement that imposes
-    # the toolset subcondition, which encodes the version.
-    if requirement:
-        r = ['<toolset>' + toolset, requirement]
-        r = ','.join(r)
-        toolset.add_requirements([r + ':' + c for c in subcondition])
-
-    # We add the requirements, if any, to the condition to scope the toolset
-    # variables and options to this specific version.
-    condition = [condition]
-    if requirement:
-        condition += [requirement]
-
-    if __show_configuration:
-        print "notice:", condition
-    return ['/'.join(condition)]
-
-# Ported from trunk@47077
-def get_invocation_command_nodefault(
-    toolset, tool, user_provided_command=[], additional_paths=[], path_last=False):
-    """
-        A helper rule to get the command to invoke some tool. If
-        'user-provided-command' is not given, tries to find binary named 'tool' in
-        PATH and in the passed 'additional-path'. Otherwise, verifies that the first
-        element of 'user-provided-command' is an existing program.
-        
-        This rule returns the command to be used when invoking the tool. If we can't
-        find the tool, a warning is issued. If 'path-last' is specified, PATH is
-        checked after 'additional-paths' when searching for 'tool'.
-    """
-    assert(isinstance(toolset, str))
-    assert(isinstance(tool, str))
-    assert(isinstance(user_provided_command, list))
-    if additional_paths is not None:
-        assert(isinstance(additional_paths, list))
-        assert(all([isinstance(path, str) for path in additional_paths]))
-    assert(all(isinstance(path, str) for path in additional_paths))
-    assert(isinstance(path_last, bool))
-    
-    if not user_provided_command:
-        command = find_tool(tool, additional_paths, path_last) 
-        if not command and __debug_configuration:
-            print "warning: toolset", toolset, "initialization: can't find tool, tool"
-            #FIXME
-            #print "warning: initialized from" [ errors.nearest-user-location ] ;
-    else:
-        command = check_tool(user_provided_command)
-        if not command and __debug_configuration:
-            print "warning: toolset", toolset, "initialization:"
-            print "warning: can't find user-provided command", user_provided_command
-            #FIXME
-            #ECHO "warning: initialized from" [ errors.nearest-user-location ]
-
-    assert(isinstance(command, str))
-    
-    return command
-
-# ported from trunk@47174
-def get_invocation_command(toolset, tool, user_provided_command = [],
-                           additional_paths = [], path_last = False):
-    """ Same as get_invocation_command_nodefault, except that if no tool is found,
-        returns either the user-provided-command, if present, or the 'tool' parameter.
-    """
-
-    assert(isinstance(toolset, str))
-    assert(isinstance(tool, str))
-    assert(isinstance(user_provided_command, list))
-    if additional_paths is not None:
-        assert(isinstance(additional_paths, list))
-        assert(all([isinstance(path, str) for path in additional_paths]))
-    assert(isinstance(path_last, bool))
-
-    result = get_invocation_command_nodefault(toolset, tool,
-                                              user_provided_command,
-                                              additional_paths,
-                                              path_last)
-
-    if not result:
-        if user_provided_command:
-            result = user_provided_command[0]
-        else:
-            result = tool
-
-    assert(isinstance(result, str))
-    
-    return result
-
-# ported from trunk@47281
-def get_absolute_tool_path(command):
-    """
-        Given an invocation command,
-        return the absolute path to the command. This works even if commnad
-        has not path element and is present in PATH.
-    """
-    if os.path.dirname(command):
-        return os.path.dirname(command)
-    else:
-        programs = path.programs_path()
-        m = path.glob(programs, [command, command + '.exe' ])
-        if not len(m):
-            print "Could not find:", command, "in", programs
-        return os.path.dirname(m[0])
-
-# ported from trunk@47174
-def find_tool(name, additional_paths = [], path_last = False):
-    """ Attempts to find tool (binary) named 'name' in PATH and in
-        'additional-paths'.  If found in path, returns 'name'.  If
-        found in additional paths, returns full name.  If the tool
-        is found in several directories, returns the first path found.
-        Otherwise, returns the empty string.  If 'path_last' is specified,
-        path is checked after 'additional_paths'.
-    """
-    assert(isinstance(name, str))
-    assert(isinstance(additional_paths, list))
-    assert(isinstance(path_last, bool))
-
-    programs = path.programs_path()
-    match = path.glob(programs, [name, name + '.exe'])
-    additional_match = path.glob(additional_paths, [name, name + '.exe'])
-
-    result = []
-    if path_last:
-        result = additional_match
-        if not result and match:
-            result = match
-
-    else:
-        if match:
-            result = match
-
-        elif additional_match:
-            result = additional_match
-
-    if result:
-        return path.native(result[0])
-    else:
-        return ''
-
-#ported from trunk@47281
-def check_tool_aux(command):
-    """ Checks if 'command' can be found either in path
-        or is a full name to an existing file.
-    """
-    assert(isinstance(command, str))
-    dirname = os.path.dirname(command)
-    if dirname:
-        if os.path.exists(command):
-            return command
-        # Both NT and Cygwin will run .exe files by their unqualified names.
-        elif on_windows() and os.path.exists(command + '.exe'):
-            return command
-        # Only NT will run .bat files by their unqualified names.
-        elif os_name() == 'NT' and os.path.exists(command + '.bat'):
-            return command
-    else:
-        paths = path.programs_path()
-        if path.glob(paths, [command]):
-            return command
-
-# ported from trunk@47281
-def check_tool(command):
-    """ Checks that a tool can be invoked by 'command'. 
-        If command is not an absolute path, checks if it can be found in 'path'.
-        If comand is absolute path, check that it exists. Returns 'command'
-        if ok and empty string otherwise.
-    """
-    assert(isinstance(command, list))
-    assert(all(isinstance(c, str) for c in command))
-    #FIXME: why do we check the first and last elements????
-    if check_tool_aux(command[0]) or check_tool_aux(command[-1]):
-        return command
-
-# ported from trunk@47281
-def handle_options(tool, condition, command, options):
-    """ Handle common options for toolset, specifically sets the following
-        flag variables:
-        - CONFIG_COMMAND to 'command'
-        - OPTIOns for compile to the value of <compileflags> in options
-        - OPTIONS for compile.c to the value of <cflags> in options
-        - OPTIONS for compile.c++ to the value of <cxxflags> in options
-        - OPTIONS for compile.fortran to the value of <fflags> in options
-        - OPTIONs for link to the value of <linkflags> in options
-    """
-    from b2.build import toolset
-
-    assert(isinstance(tool, str))
-    assert(isinstance(condition, list))
-    assert(isinstance(command, str))
-    assert(isinstance(options, list))
-    assert(command)
-    toolset.flags(tool, 'CONFIG_COMMAND', condition, [command])
-    toolset.flags(tool + '.compile', 'OPTIONS', condition, feature.get_values('<compileflags>', options))
-    toolset.flags(tool + '.compile.c', 'OPTIONS', condition, feature.get_values('<cflags>', options))
-    toolset.flags(tool + '.compile.c++', 'OPTIONS', condition, feature.get_values('<cxxflags>', options))
-    toolset.flags(tool + '.compile.fortran', 'OPTIONS', condition, feature.get_values('<fflags>', options))
-    toolset.flags(tool + '.link', 'OPTIONS', condition, feature.get_values('<linkflags>', options))
-
-# ported from trunk@47281
-def get_program_files_dir():
-    """ returns the location of the "program files" directory on a windows
-        platform
-    """
-    ProgramFiles = bjam.variable("ProgramFiles")
-    if ProgramFiles:
-        ProgramFiles = ' '.join(ProgramFiles)
-    else:
-        ProgramFiles = "c:\\Program Files"
-    return ProgramFiles
-
-# ported from trunk@47281
-def rm_command():
-    return __RM
-
-# ported from trunk@47281
-def copy_command():
-    return __CP
-
-# ported from trunk@47281
-def variable_setting_command(variable, value):
-    """
-        Returns the command needed to set an environment variable on the current
-        platform. The variable setting persists through all following commands and is
-        visible in the environment seen by subsequently executed commands. In other
-        words, on Unix systems, the variable is exported, which is consistent with the
-        only possible behavior on Windows systems.
-    """
-    assert(isinstance(variable, str))
-    assert(isinstance(value, str))
-
-    if os_name() == 'NT':
-        return "set " + variable + "=" + value + os.linesep
-    else:
-        # (todo)
-        #   The following does not work on CYGWIN and needs to be fixed. On
-        # CYGWIN the $(nl) variable holds a Windows new-line \r\n sequence that
-        # messes up the executed export command which then reports that the
-        # passed variable name is incorrect. This is most likely due to the
-        # extra \r character getting interpreted as a part of the variable name.
-        #
-        #   Several ideas pop to mind on how to fix this:
-        #     * One way would be to separate the commands using the ; shell
-        #       command separator. This seems like the quickest possible
-        #       solution but I do not know whether this would break code on any
-        #       platforms I I have no access to.
-        #     * Another would be to not use the terminating $(nl) but that would
-        #       require updating all the using code so it does not simply
-        #       prepend this variable to its own commands.
-        #     * I guess the cleanest solution would be to update Boost Jam to
-        #       allow explicitly specifying \n & \r characters in its scripts
-        #       instead of always relying only on the 'current OS native newline
-        #       sequence'.
-        #
-        #   Some code found to depend on this behaviour:
-        #     * This Boost Build module.
-        #         * __test__ rule.
-        #         * path-variable-setting-command rule.
-        #     * python.jam toolset.
-        #     * xsltproc.jam toolset.
-        #     * fop.jam toolset.
-        #                                     (todo) (07.07.2008.) (Jurko)
-        #
-        # I think that this works correctly in python -- Steven Watanabe
-        return variable + "=" + value + os.linesep + "export " + variable + os.linesep
-
-def path_variable_setting_command(variable, paths):
-    """
-        Returns a command to sets a named shell path variable to the given NATIVE
-        paths on the current platform.
-    """
-    assert(isinstance(variable, str))
-    assert(isinstance(paths, list))
-    sep = os.path.pathsep
-    return variable_setting_command(variable, sep.join(paths))
-
-def prepend_path_variable_command(variable, paths):
-    """
-        Returns a command that prepends the given paths to the named path variable on
-        the current platform.
-    """    
-    return path_variable_setting_command(variable,
-        paths + os.environ.get(variable, "").split(os.pathsep))
-
-def file_creation_command():
-    """
-        Return a command which can create a file. If 'r' is result of invocation, then
-        'r foobar' will create foobar with unspecified content. What happens if file
-        already exists is unspecified.
-    """
-    if os_name() == 'NT':
-        return "echo. > "
-    else:
-        return "touch "
-
-#FIXME: global variable
-__mkdir_set = set()
-__re_windows_drive = re.compile(r'^.*:\$')
-
-def mkdir(engine, target):
-    # If dir exists, do not update it. Do this even for $(DOT).
-    bjam.call('NOUPDATE', target)
-
-    global __mkdir_set
-
-    # FIXME: Where is DOT defined?
-    #if $(<) != $(DOT) && ! $($(<)-mkdir):
-    if target != '.' and target not in __mkdir_set:
-        # Cheesy gate to prevent multiple invocations on same dir.
-        __mkdir_set.add(target)
-
-        # Schedule the mkdir build action.
-        if os_name() == 'NT':
-            engine.set_update_action("common.MkDir1-quick-fix-for-windows", target, [])
-        else:
-            engine.set_update_action("common.MkDir1-quick-fix-for-unix", target, [])
-
-        # Prepare a Jam 'dirs' target that can be used to make the build only
-        # construct all the target directories.
-        engine.add_dependency('dirs', target)
-
-        # Recursively create parent directories. $(<:P) = $(<)'s parent & we
-        # recurse until root.
-
-        s = os.path.dirname(target)
-        if os_name() == 'NT':
-            if(__re_windows_drive.match(s)):
-                s = ''
-                
-        if s:
-            if s != target:
-                engine.add_dependency(target, s)
-                mkdir(engine, s)
-            else:
-                bjam.call('NOTFILE', s)
-
-__re_version = re.compile(r'^([^.]+)[.]([^.]+)[.]?([^.]*)')
-
-def format_name(format, name, target_type, prop_set):
-    """ Given a target, as given to a custom tag rule, returns a string formatted
-        according to the passed format. Format is a list of properties that is
-        represented in the result. For each element of format the corresponding target
-        information is obtained and added to the result string. For all, but the
-        literal, the format value is taken as the as string to prepend to the output
-        to join the item to the rest of the result. If not given "-" is used as a
-        joiner.
-
-        The format options can be:
-
-          <base>[joiner]
-              ::  The basename of the target name.
-          <toolset>[joiner]
-              ::  The abbreviated toolset tag being used to build the target.
-          <threading>[joiner]
-              ::  Indication of a multi-threaded build.
-          <runtime>[joiner]
-              ::  Collective tag of the build runtime.
-          <version:/version-feature | X.Y[.Z]/>[joiner]
-              ::  Short version tag taken from the given "version-feature"
-                  in the build properties. Or if not present, the literal
-                  value as the version number.
-          <property:/property-name/>[joiner]
-              ::  Direct lookup of the given property-name value in the
-                  build properties. /property-name/ is a regular expression.
-                  e.g. <property:toolset-.*:flavor> will match every toolset.
-          /otherwise/
-              ::  The literal value of the format argument.
-
-        For example this format:
-
-          boost_ <base> <toolset> <threading> <runtime> <version:boost-version>
-
-        Might return:
-
-          boost_thread-vc80-mt-gd-1_33.dll, or
-          boost_regex-vc80-gd-1_33.dll
-
-        The returned name also has the target type specific prefix and suffix which
-        puts it in a ready form to use as the value from a custom tag rule.
-    """
-    assert(isinstance(format, list))
-    assert(isinstance(name, str))
-    assert(isinstance(target_type, str) or not type)
-    # assert(isinstance(prop_set, property_set.PropertySet))
-    if type.is_derived(target_type, 'LIB'):
-        result = "" ;
-        for f in format:
-            grist = get_grist(f)
-            if grist == '<base>':
-                result += os.path.basename(name)
-            elif grist == '<toolset>':
-                result += join_tag(ungrist(f), 
-                    toolset_tag(name, target_type, prop_set))
-            elif grist == '<threading>':
-                result += join_tag(ungrist(f),
-                    threading_tag(name, target_type, prop_set))
-            elif grist == '<runtime>':
-                result += join_tag(ungrist(f),
-                    runtime_tag(name, target_type, prop_set))
-            elif grist.startswith('<version:'):
-                key = grist[len('<version:'):-1]
-                version = prop_set.get('<' + key + '>')
-                if not version:
-                    version = key
-                version = __re_version.match(version)
-                result += join_tag(ungrist(f), version[1] + '_' + version[2])
-            elif grist.startswith('<property:'):
-                key = grist[len('<property:'):-1]
-                property_re = re.compile('<(' + key + ')>')
-                p0 = None
-                for prop in prop_set.raw():
-                    match = property_re.match(prop)
-                    if match:
-                        p0 = match[1]
-                        break
-                if p0:
-                    p = prop_set.get('<' + p0 + '>')
-                    if p:
-                        assert(len(p) == 1)
-                        result += join_tag(ungrist(f), p)
-            else:
-                result += ungrist(f)
-
-        result = virtual_target.add_prefix_and_suffix(
-            ''.join(result), target_type, prop_set)
-        return result
-
-def join_tag(joiner, tag):
-    if not joiner: joiner = '-'
-    return joiner + tag
-
-__re_toolset_version = re.compile(r"<toolset.*version>(\d+)[.](\d*)")
-
-def toolset_tag(name, target_type, prop_set):
-    tag = ''
-
-    properties = prop_set.raw()
-    tools = prop_set.get('<toolset>')
-    assert(len(tools) == 0)
-    tools = tools[0]
-    if tools.startswith('borland'): tag += 'bcb'
-    elif tools.startswith('como'): tag += 'como'
-    elif tools.startswith('cw'): tag += 'cw'
-    elif tools.startswith('darwin'): tag += 'xgcc'
-    elif tools.startswith('edg'): tag += edg
-    elif tools.startswith('gcc'):
-        flavor = prop_set.get('<toolset-gcc:flavor>')
-        ''.find
-        if flavor.find('mingw') != -1:
-            tag += 'mgw'
-        else:
-            tag += 'gcc'
-    elif tools == 'intel':
-        if prop_set.get('<toolset-intel:platform>') == ['win']:
-            tag += 'iw'
-        else:
-            tag += 'il'
-    elif tools.startswith('kcc'): tag += 'kcc'
-    elif tools.startswith('kylix'): tag += 'bck'
-    #case metrowerks* : tag += cw ;
-    #case mingw* : tag += mgw ;
-    elif tools.startswith('mipspro'): tag += 'mp'
-    elif tools.startswith('msvc'): tag += 'vc'
-    elif tools.startswith('sun'): tag += 'sw'
-    elif tools.startswith('tru64cxx'): tag += 'tru'
-    elif tools.startswith('vacpp'): tag += 'xlc'
-
-    for prop in properties:
-        match = __re_toolset_version.match(prop)
-        if(match):
-            version = match
-            break
-    version_string = None
-    # For historical reasons, vc6.0 and vc7.0 use different naming.
-    if tag == 'vc':
-        if version.group(1) == '6':
-            # Cancel minor version.
-            version_string = '6'
-        elif version.group(1) == '7' and version.group(2) == '0':
-            version_string = '7'
-
-    # On intel, version is not added, because it does not matter and it's the
-    # version of vc used as backend that matters. Ideally, we'd encode the
-    # backend version but that would break compatibility with V1.
-    elif tag == 'iw':
-        version_string = ''
-
-    # On borland, version is not added for compatibility with V1.
-    elif tag == 'bcb':
-        version_string = ''
-
-    if version_string is None:
-        version = version.group(1) + version.group(2)
-
-    tag += version
-
-    return tag
-
-
-def threading_tag(name, target_type, prop_set):
-    tag = ''
-    properties = prop_set.raw()
-    if '<threading>multi' in properties: tag = 'mt'
-
-    return tag
-
-
-def runtime_tag(name, target_type, prop_set ):
-    tag = ''
-
-    properties = prop_set.raw()
-    if '<runtime-link>static' in properties: tag += 's'
-
-    # This is an ugly thing. In V1, there's a code to automatically detect which
-    # properties affect a target. So, if <runtime-debugging> does not affect gcc
-    # toolset, the tag rules won't even see <runtime-debugging>. Similar
-    # functionality in V2 is not implemented yet, so we just check for toolsets
-    # which are known to care about runtime debug.
-    if '<toolset>msvc' in properties \
-       or '<stdlib>stlport' in properties \
-       or '<toolset-intel:platform>win' in properties:
-        if '<runtime-debugging>on' in properties: tag += 'g'
-
-    if '<python-debugging>on' in properties: tag += 'y'
-    if '<variant>debug' in properties: tag += 'd'
-    if '<stdlib>stlport' in properties: tag += 'p'
-    if '<stdlib-stlport:iostream>hostios' in properties: tag += 'n'
-
-    return tag
-
-
-## TODO:
-##rule __test__ ( )
-##{
-##    import assert ;
-##
-##    local nl = "
-##" ;
-##
-##    local save-os = [ modules.peek os : .name ] ;
-##
-##    modules.poke os : .name : LINUX ;
-##
-##    assert.result "PATH=foo:bar:baz$(nl)export PATH$(nl)"
-##        : path-variable-setting-command PATH : foo bar baz ;
-##
-##    assert.result "PATH=foo:bar:$PATH$(nl)export PATH$(nl)"
-##        : prepend-path-variable-command PATH : foo bar ;
-##
-##    modules.poke os : .name : NT ;
-##
-##    assert.result "set PATH=foo;bar;baz$(nl)"
-##        : path-variable-setting-command PATH : foo bar baz ;
-##
-##    assert.result "set PATH=foo;bar;%PATH%$(nl)"
-##        : prepend-path-variable-command PATH : foo bar ;
-##
-##    modules.poke os : .name : $(save-os) ;
-##}
-
-def init(manager):
-    engine = manager.engine()
-
-    engine.register_action("common.MkDir1-quick-fix-for-unix", 'mkdir -p "$(<)"')
-    engine.register_action("common.MkDir1-quick-fix-for-windows", 'if not exist "$(<)\\" mkdir "$(<)"')
-
-    import b2.tools.make
-    import b2.build.alias
-
-    global __RM, __CP, __IGNORE, __LN
-    # ported from trunk@47281
-    if os_name() == 'NT':
-        __RM = 'del /f /q'
-        __CP = 'copy'
-        __IGNORE = '2>nul >nul & setlocal'
-        __LN = __CP
-        #if not __LN:
-        #    __LN = CP
-    else:
-        __RM = 'rm -f'
-        __CP = 'cp'
-        __IGNORE = ''
-        __LN = 'ln'
-        
-    engine.register_action("common.Clean", __RM + ' "$(>)"',
-                           flags=['piecemeal', 'together', 'existing'])
-    engine.register_action("common.copy", __CP + ' "$(>)" "$(<)"')
-    engine.register_action("common.RmTemps", __RM + ' "$(>)" ' + __IGNORE,
-                           flags=['quietly', 'updated', 'piecemeal', 'together'])
-
-    engine.register_action("common.hard-link", 
-        __RM + ' "$(<)" 2$(NULL_OUT) $(NULL_OUT)' + os.linesep +
-        __LN + ' "$(>)" "$(<)" $(NULL_OUT)')
diff --git a/jam-files/boost-build/tools/como-linux.jam b/jam-files/boost-build/tools/como-linux.jam
deleted file mode 100644
index 5c554c8f..00000000
--- a/jam-files/boost-build/tools/como-linux.jam
+++ /dev/null
@@ -1,103 +0,0 @@
-# Copyright 2004, 2005, 2006 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-# The following #// line will be used by the regression test table generation
-# program as the column heading for HTML tables. Must not include a version
-# number.
-#//<a href="http://www.comeaucomputing.com/">Comeau<br>C++</a>
-
-import toolset ;
-import feature ;
-import toolset : flags ;
-import common ;
-import generators ;
-
-import unix ;
-import como ;
-
-feature.extend-subfeature toolset como : platform : linux ;
-
-toolset.inherit-generators como-linux
-     <toolset>como <toolset-como:platform>linux : unix ;
-generators.override como-linux.prebuilt : builtin.lib-generator ;
-generators.override como-linux.searched-lib-generator : searched-lib-generator ;
-toolset.inherit-flags como-linux : unix ;
-toolset.inherit-rules como-linux : gcc ;
-
-generators.register-c-compiler como-linux.compile.c++ : CPP : OBJ
-    : <toolset>como <toolset-como:platform>linux ;
-generators.register-c-compiler como-linux.compile.c : C : OBJ
-    : <toolset>como <toolset-como:platform>linux ;
-
-
-rule init ( version ? : command * : options * )
-{
-    local condition = [ common.check-init-parameters como-linux
-        : version $(version) ] ;
-
-    command = [ common.get-invocation-command como-linux : como
-        : $(command) ] ;
-
-    common.handle-options como-linux : $(condition) : $(command) : $(options) ;
-}
-
-
-flags como-linux C++FLAGS <exception-handling>off : --no_exceptions ;
-flags como-linux C++FLAGS <exception-handling>on : --exceptions ;
-
-flags como-linux CFLAGS <inlining>off : --no_inlining ;
-flags como-linux CFLAGS <inlining>on <inlining>full : --inlining ;
-
-flags como-linux CFLAGS <optimization>off : -O0 ;
-flags como-linux CFLAGS <optimization>speed : -O3 ;
-flags como-linux CFLAGS <optimization>space : -Os ;
-
-flags como-linux CFLAGS <debug-symbols>on : -g ;
-flags como-linux LINKFLAGS <debug-symbols>on : -g ;
-
-flags como-linux FINDLIBS : m ;
-flags como-linux FINDLIBS : rt ;
-
-flags como-linux CFLAGS <cflags> ;
-flags como-linux C++FLAGS <cxxflags> ;
-flags como-linux DEFINES <define> ;
-flags como-linux UNDEFS <undef> ;
-flags como-linux HDRS <include> ;
-flags como-linux STDHDRS <sysinclude> ;
-flags como-linux LINKFLAGS <linkflags> ;
-flags como-linux ARFLAGS <arflags> ;
-
-flags como-linux.link LIBRARIES <library-file> ;
-flags como-linux.link LINKPATH <library-path> ;
-flags como-linux.link FINDLIBS-ST <find-static-library> ;
-flags como-linux.link FINDLIBS-SA <find-shared-library> ;
-
-flags como-linux.link RPATH <dll-path> ;
-flags como-linux.link RPATH_LINK <xdll-path> ;
-
-
-actions link bind LIBRARIES
-{
-    $(CONFIG_COMMAND) $(LINKFLAGS) -o "$(<[1])" "$(>)" -L"$(LINKPATH)" -Wl,-R$(SPACE)-Wl,"$(RPATH)" -Wl,-rpath-link$(SPACE)-Wl,"$(RPATH_LINK)"  "$(LIBRARIES)"  "$(LIBRARIES)" -l$(FINDLIBS-SA) -l$(FINDLIBS-ST) 2>&1
-}
-
-actions link.dll bind LIBRARIES
-{
-    $(CONFIG_COMMAND) $(LINKFLAGS) -shared -o "$(<[1])" "$(>)" -L"$(LINKPATH)" -Wl,-R$(SPACE)-Wl,"$(RPATH)" -Wl,-rpath-link$(SPACE)-Wl,"$(RPATH_LINK)" "$(LIBRARIES)"  "$(LIBRARIES)" -l$(FINDLIBS-SA) -l$(FINDLIBS-ST) 2>&1
-}
-
-actions compile.c
-{
-    $(CONFIG_COMMAND) -c --c99 --long_long -U$(UNDEFS) -D$(DEFINES) $(CFLAGS) -I"$(HDRS)" -I"$(STDHDRS)" -o "$(<)" "$(>)" 2>&1
-}
-
-actions compile.c++
-{
-    $(CONFIG_COMMAND) -tused -c --long_long -U$(UNDEFS) -D$(DEFINES) $(CFLAGS) $(C++FLAGS) -I"$(HDRS)" -I"$(STDHDRS)"  -o "$(<)" "$(>)" 2>&1
-}
-
-actions archive
-{
-    ar rcu $(<) $(>)
-}
diff --git a/jam-files/boost-build/tools/como-win.jam b/jam-files/boost-build/tools/como-win.jam
deleted file mode 100644
index d21a70d6..00000000
--- a/jam-files/boost-build/tools/como-win.jam
+++ /dev/null
@@ -1,117 +0,0 @@
-# (C) Copyright David Abrahams 2001.
-# (C) Copyright MetaCommunications, Inc. 2004.
-
-# Distributed under the Boost Software License, Version 1.0. (See
-# accompanying file LICENSE_1_0.txt or copy at
-# http://www.boost.org/LICENSE_1_0.txt)
-
-# The following #// line will be used by the regression test table generation
-# program as the column heading for HTML tables. Must not include a version
-# number.
-#//<a href="http://www.comeaucomputing.com/">Comeau<br>C++</a>
-
-import common ;
-import como ;
-import feature ;
-import generators ;
-import toolset : flags ;
-
-feature.extend-subfeature toolset como : platform : win ;
-
-
-# Initializes the Comeau toolset for windows. The command is the command which
-# invokes the compiler. You should either set environment variable
-# COMO_XXX_INCLUDE where XXX is the used backend (as described in the
-# documentation), or pass that as part of command, e.g:
-#
-#   using como-win : 4.3 : "set COMO_BCC_INCLUDE=C:/include &&" como.exe ;
-#
-rule init ( version ? : command * : options * )
-{
-    local condition = [  common.check-init-parameters como-win
-        : version $(version) ] ;
-
-    command = [ common.get-invocation-command como-win : como.exe :
-        $(command) ] ;
-
-    common.handle-options como-win : $(condition) : $(command) : $(options) ;
-}
-
-generators.register-c-compiler como-win.compile.c++ : CPP : OBJ
-    : <toolset>como <toolset-como:platform>win ;
-generators.register-c-compiler como-win.compile.c : C : OBJ
-    : <toolset>como <toolset-como:platform>win ;
-
-
-generators.register-linker como-win.link
-    : OBJ SEARCHED_LIB STATIC_LIB IMPORT_LIB
-    : EXE
-    : <toolset>como <toolset-como:platform>win ;
-
-# Note that status of shared libraries support is not clear, so we do not define
-# the link.dll generator.
-generators.register-archiver como-win.archive
-    : OBJ : STATIC_LIB
-    : <toolset>como <toolset-como:platform>win ;
-
-
-flags como-win C++FLAGS <exception-handling>off : --no_exceptions ;
-flags como-win C++FLAGS <exception-handling>on : --exceptions ;
-
-flags como-win CFLAGS <inlining>off : --no_inlining ;
-flags como-win CFLAGS <inlining>on <inlining>full : --inlining ;
-
-
-# The following seems to be VC-specific options. At least, when I uncomment
-# then, Comeau with bcc as backend reports that bcc32 invocation failed.
-#
-#flags como-win CFLAGS <debug-symbols>on : /Zi ;
-#flags como-win CFLAGS <optimization>off : /Od ;
-
-
-flags como-win CFLAGS <cflags> ;
-flags como-win CFLAGS : -D_WIN32 ;  # Make sure that we get the Boost Win32 platform config header.
-flags como-win CFLAGS <threading>multi : -D_MT ;  # Make sure that our config knows that threading is on.
-flags como-win C++FLAGS <cxxflags> ;
-flags como-win DEFINES <define> ;
-flags como-win UNDEFS <undef> ;
-flags como-win HDRS <include> ;
-flags como-win SYSHDRS <sysinclude> ;
-flags como-win LINKFLAGS <linkflags> ;
-flags como-win ARFLAGS <arflags> ;
-flags como-win NO_WARN <no-warn> ;
-
-#flags como-win STDHDRS : $(COMO_INCLUDE_PATH) ;
-#flags como-win STDLIB_PATH : $(COMO_STDLIB_PATH)$(SLASH) ;
-
-flags como-win LIBPATH <library-path> ;
-flags como-win LIBRARIES <library-file> ;
-flags como-win FINDLIBS <find-shared-library> ;
-flags como-win FINDLIBS <find-static-library> ;
-
-nl = "
-" ;
-
-
-# For como, we repeat all libraries so that dependencies are always resolved.
-#
-actions link bind LIBRARIES
-{
-    $(CONFIG_COMMAND) --no_version --no_prelink_verbose $(LINKFLAGS) -o "$(<[1]:S=)" @"@($(<[1]:W).rsp:E=$(nl)"$(>)")" "$(LIBRARIES)" "$(FINDLIBS:S=.lib)"
-}
-
-actions compile.c
-{
-    $(CONFIG_COMMAND) -c --c99 -e5 --no_version --display_error_number --diag_suppress=9,21,161,748,940,962 -U$(UNDEFS) -D$(DEFINES) $(WARN) $(CFLAGS) -I"$(HDRS)" -I"$(STDHDRS)" -I"$(SYSHDRS)" -o "$(<:D=)" "$(>)"
-}
-
-actions compile.c++
-{
-    $(CONFIG_COMMAND) -c -e5 --no_version --no_prelink_verbose --display_error_number --long_long --diag_suppress=9,21,161,748,940,962 --diag_error=461 -D__STL_LONG_LONG -U$(UNDEFS) -D$(DEFINES) $(WARN) $(CFLAGS) $(C++FLAGS) -I"$(HDRS)" -I"$(STDHDRS)" -I"$(SYSHDRS)" -o "$(<)" "$(>)"
-}
-
-actions archive
-{
-    $(CONFIG_COMMAND) --no_version --no_prelink_verbose --prelink_object @"@($(<[1]:W).rsp:E=$(nl)"$(>)")"
-    lib $(ARFLAGS) /nologo /out:"$(<:S=.lib)" @"@($(<[1]:W).rsp:E=$(nl)"$(>)")"
-}
diff --git a/jam-files/boost-build/tools/como.jam b/jam-files/boost-build/tools/como.jam
deleted file mode 100644
index 04a05a94..00000000
--- a/jam-files/boost-build/tools/como.jam
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright Vladimir Prus 2004.
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt
-# or copy at http://www.boost.org/LICENSE_1_0.txt)
-
-# This is a generic 'como' toolset. Depending on the current system, it
-# forwards either to 'como-linux' or 'como-win' modules.
-
-import feature ;
-import os ;
-import toolset ;
-
-feature.extend toolset : como ;
-feature.subfeature toolset como : platform : : propagated link-incompatible ;
-
-rule init ( * : * )
-{
-    if [ os.name ] = LINUX
-    {
-        toolset.using como-linux : 
-          $(1) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ;
-    }
-    else
-    {
-        toolset.using como-win :
-          $(1) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ;
-
-    }        
-}
diff --git a/jam-files/boost-build/tools/convert.jam b/jam-files/boost-build/tools/convert.jam
deleted file mode 100644
index ac1d7010..00000000
--- a/jam-files/boost-build/tools/convert.jam
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright (c) 2009 Vladimir Prus
-#
-# Use, modification and distribution is subject to the Boost Software
-# License Version 1.0. (See accompanying file LICENSE_1_0.txt or
-# http://www.boost.org/LICENSE_1_0.txt)
-
-# Implements 'convert' target that takes a bunch of source and
-# tries to convert each one to the specified type.
-#
-# For example:
-#
-#   convert objects obj : a.cpp b.cpp ;
-#
-
-import targets ;
-import generators ;
-import project ;
-import type ;
-import "class" : new ;
-
-class convert-target-class : typed-target
-{
-    rule __init__ ( name : project : type
-    : sources * : requirements * : default-build * : usage-requirements * )
-    {
-        typed-target.__init__ $(name) : $(project) : $(type)
-          : $(sources) : $(requirements) : $(default-build) : $(usage-requirements) ;
-    }
-
-    rule construct ( name : source-targets * : property-set )
-    {
-        local r = [ generators.construct $(self.project) : $(self.type)
-          : [ property-set.create [ $(property-set).raw ] # [ feature.expand
-              <main-target-type>$(self.type) ]
-          # ]
-            : $(source-targets) ] ;
-        if ! $(r)
-        {
-            errors.error "unable to construct" [ full-name ] ;
-        }
-
-        return $(r) ;
-    }
-
-}
-
-rule convert ( name type : sources * : requirements * : default-build *
-    : usage-requirements * )
-{
-    local project = [ project.current ] ;
-
-    # This is a circular module dependency, so it must be imported here
-    modules.import targets ;
-    targets.main-target-alternative
-      [ new convert-target-class $(name) : $(project) : [ type.type-from-rule-name $(type) ]
-        : [ targets.main-target-sources $(sources) : $(name) ]
-        : [ targets.main-target-requirements $(requirements) : $(project) ]
-        : [ targets.main-target-default-build $(default-build) : $(project) ]
-        : [ targets.main-target-usage-requirements $(usage-requirements) : $(project) ]
-      ] ;
-}
-IMPORT $(__name__) : convert : : convert ;
diff --git a/jam-files/boost-build/tools/cw-config.jam b/jam-files/boost-build/tools/cw-config.jam
deleted file mode 100644
index 1211b7c0..00000000
--- a/jam-files/boost-build/tools/cw-config.jam
+++ /dev/null
@@ -1,34 +0,0 @@
-#~ Copyright 2005 Rene Rivera.
-#~ Distributed under the Boost Software License, Version 1.0.
-#~ (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-# Automatic configuration for CodeWarrior toolset. To use, just import this module.
-
-import os ;
-import toolset : using ;
-
-if [ os.name ] = NT
-{
-    for local R in 9 8 7
-    {
-        local cw-path = [ W32_GETREG
-            "HKEY_LOCAL_MACHINE\\SOFTWARE\\Metrowerks\\CodeWarrior\\Product Versions\\CodeWarrior for Windows R$(R)"
-            : "PATH" ] ;
-        local cw-version = [ W32_GETREG
-            "HKEY_LOCAL_MACHINE\\SOFTWARE\\Metrowerks\\CodeWarrior\\Product Versions\\CodeWarrior for Windows R$(R)"
-            : "VERSION" ] ;
-        cw-path ?= [ W32_GETREG
-            "HKEY_LOCAL_MACHINE\\SOFTWARE\\Metrowerks\\CodeWarrior for Windows\\$(R).0"
-            : "PATH" ] ;
-        cw-version ?= $(R).0 ;
-        
-        if $(cw-path)
-        {
-            if --debug-configuration in [ modules.peek : ARGV ]
-            {
-                ECHO "notice:" using cw ":" $(cw-version) ":" "$(cw-path)\\Other Metrowerks Tools\\Command Line Tools\\mwcc.exe" ;
-            }
-            using cw : $(cw-version) : "$(cw-path)\\Other Metrowerks Tools\\Command Line Tools\\mwcc.exe" ;
-        }
-    }
-}
diff --git a/jam-files/boost-build/tools/cw.jam b/jam-files/boost-build/tools/cw.jam
deleted file mode 100644
index ddcbfeb2..00000000
--- a/jam-files/boost-build/tools/cw.jam
+++ /dev/null
@@ -1,246 +0,0 @@
-# Copyright (C) Reece H Dunn 2004
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or copy at
-# http://www.boost.org/LICENSE_1_0.txt)
-
-# based on the msvc.jam toolset
-
-import property ;
-import generators ;
-import os ;
-import type ;
-import toolset : flags ;
-import errors : error ;
-import feature : feature get-values ;
-import path ;
-import sequence : unique ;
-import common ;
-
-if [ MATCH (--debug-configuration) : [ modules.peek : ARGV ] ]
-{
-   .debug-configuration = true ;
-}
-
-feature.extend toolset : cw ;
-
-toolset.add-requirements <toolset>cw,<runtime-link>shared:<threading>multi ;
-
-nl = "
-" ;
-
-rule init ( version ? : command * : options * )
-{
-   # TODO: fix the $(command[1]) = $(compiler) issue
-    
-    setup = [ get-values <setup> : $(options) ] ;
-    setup    ?= cwenv.bat ;
-    compiler = [ get-values <compiler> : $(options) ] ;
-    compiler ?= mwcc ;
-    linker = [ get-values <linker> : $(options) ] ;
-    linker   ?= mwld ;
-
-    local condition = [ common.check-init-parameters cw :
-        version $(version) ] ;
-
-    command = [ common.get-invocation-command cw : mwcc.exe : $(command) :
-        [ default-paths $(version) ] ] ;
-    
-    common.handle-options cw : $(condition) : $(command) : $(options) ;
-
-    local root = [ feature.get-values <root> : $(options) ] ;    
-    if $(command)
-    {
-        command = [ common.get-absolute-tool-path $(command[-1]) ] ;
-    }
-    local tool-root = $(command) ;
-
-    setup = $(tool-root)\\$(setup) ;
-
-   # map the batch file in setup so it can be executed
-
-    other-tools = $(tool-root:D) ;
-    root ?= $(other-tools:D) ;
-    
-    flags cw.link RUN_PATH $(condition) : 
-        "$(root)\\Win32-x86 Support\\Libraries\\Runtime"
-        "$(root)\\Win32-x86 Support\\Libraries\\Runtime\\Libs\\MSL_All-DLLs" ;      
-    
-    setup = "set \"CWFOLDER="$(root)"\" && call \""$(setup)"\" > nul " ;
-
-   if [ os.name ] = NT
-   {
-      setup = $(setup)"
-" ;
-   }
-   else
-   {
-      setup = "cmd /S /C "$(setup)" \"&&\" " ;
-   }
-
-   # bind the setup command to the tool so it can be executed before the
-   # command
-
-   local prefix = $(setup) ;
-
-   flags cw.compile .CC $(condition) : $(prefix)$(compiler) ;
-   flags cw.link .LD $(condition) : $(prefix)$(linker) ;
-   flags cw.archive .LD $(condition) : $(prefix)$(linker) ;
-
-    if [ MATCH ^([89]\\.) : $(version) ]   
-    {
-        if [ os.name ] = NT
-        {
-        # The runtime libraries
-        flags cw.compile CFLAGS <runtime-link>static/<threading>single/<runtime-debugging>off : -runtime ss ;
-        flags cw.compile CFLAGS <runtime-link>static/<threading>single/<runtime-debugging>on : -runtime ssd ;
-        
-        flags cw.compile CFLAGS <runtime-link>static/<threading>multi/<runtime-debugging>off : -runtime sm ;
-        flags cw.compile CFLAGS <runtime-link>static/<threading>multi/<runtime-debugging>on : -runtime smd ;
-        
-        flags cw.compile CFLAGS <runtime-link>shared/<runtime-debugging>off : -runtime dm ;
-        flags cw.compile CFLAGS <runtime-link>shared/<runtime-debugging>on : -runtime dmd ;
-        }        
-    }    
-}
-
-
-local rule default-paths ( version ? )  # FIXME
-{
-   local possible-paths ;
-   local ProgramFiles = [ common.get-program-files-dir ] ;
-
-   # TODO: add support for cw8 and cw9 detection
-
-   local version-6-path = $(ProgramFiles)"\\Metrowerks\\CodeWarrior" ;
-   possible-paths += $(version-6-path) ;
-
-   # perform post-processing
-
-   possible-paths
-      = $(possible-paths)"\\Other Metrowerks Tools\\Command Line Tools" ;
-
-   possible-paths += [ modules.peek : PATH Path path ] ;
-
-   return $(possible-paths) ;
-}
-
-
-
-
-## declare generators
-
-generators.register-c-compiler cw.compile.c++ : CPP : OBJ : <toolset>cw ;
-generators.register-c-compiler cw.compile.c : C : OBJ : <toolset>cw ;
-
-generators.register-linker cw.link
-   : OBJ SEARCHED_LIB STATIC_LIB IMPORT_LIB
-   : EXE
-   : <toolset>cw
-   ;
-generators.register-linker cw.link.dll
-   : OBJ SEARCHED_LIB STATIC_LIB IMPORT_LIB
-   : SHARED_LIB IMPORT_LIB
-   : <toolset>cw
-   ;
-
-generators.register-archiver cw.archive
-   : OBJ
-   : STATIC_LIB
-   : <toolset>cw
-   ;
-
-## compilation phase
-
-flags cw WHATEVER <toolset-cw:version> ;
-
-flags cw.compile CFLAGS <debug-symbols>on : -g ;
-flags cw.compile CFLAGS <optimization>off : -O0 ;
-flags cw.compile CFLAGS <optimization>speed : -O4,p ;
-flags cw.compile CFLAGS <optimization>space : -O4,s ;
-flags cw.compile CFLAGS <inlining>off : -inline off ;
-flags cw.compile CFLAGS <inlining>on : -inline on ;
-flags cw.compile CFLAGS <inlining>full : -inline all ;
-flags cw.compile CFLAGS <exception-handling>off : -Cpp_exceptions off ;
-
-
-flags cw.compile CFLAGS <rtti>on : -RTTI on ;
-flags cw.compile CFLAGS <rtti>off : -RTTI off ;
-
-flags cw.compile CFLAGS <warnings>on : -w on ;
-flags cw.compile CFLAGS <warnings>off : -w off ;
-flags cw.compile CFLAGS <warnings>all : -w all ;
-flags cw.compile CFLAGS <warnings-as-errors>on : -w error ;
-
-flags cw.compile USER_CFLAGS <cflags> : ;
-flags cw.compile.c++ USER_CFLAGS <cxxflags> : ;
-
-flags cw.compile DEFINES <define> ;
-flags cw.compile UNDEFS <undef> ;
-flags cw.compile INCLUDES <include> ;
-
-actions compile.c
-{
-   $(.CC) -c -cwd include -lang c -U$(UNDEFS) $(CFLAGS) $(USER_CFLAGS) -I- -o "$(<)" @"@($(<[1]:W).rsp:E=$(nl)"$(>)" $(nl)-D$(DEFINES) $(nl)"-I$(INCLUDES)")"
-}
-actions compile.c++
-{
-   $(.CC) -c -cwd include -lang c++ -U$(UNDEFS) $(CFLAGS) $(USER_CFLAGS) -I- -o "$(<)" @"@($(<[1]:W).rsp:E=$(nl)"$(>)" $(nl)-D$(DEFINES) $(nl)"-I$(INCLUDES)")"
-}
-
-## linking phase
-
-flags cw.link DEF_FILE <def-file> ;
-
-flags cw LINKFLAGS : -search ;
-flags cw LINKFLAGS <debug-symbols>on : -g ;
-flags cw LINKFLAGS <user-interface>console : -subsystem console ;
-flags cw LINKFLAGS <user-interface>gui : -subsystem windows ;
-flags cw LINKFLAGS <user-interface>wince : -subsystem wince ;
-flags cw LINKFLAGS <user-interface>native : -subsystem native ;
-flags cw LINKFLAGS <user-interface>auto : -subsystem auto ;
-
-flags cw LINKFLAGS <main-target-type>LIB/<link>static : -library ;
-
-flags cw.link USER_LINKFLAGS <linkflags> ;
-flags cw.link LINKPATH <library-path> ;
-
-flags cw.link FINDLIBS_ST <find-static-library> ;
-flags cw.link FINDLIBS_SA <find-shared-library> ;
-flags cw.link LIBRARY_OPTION <toolset>cw : "" : unchecked ;
-flags cw.link LIBRARIES_MENTIONED_BY_FILE : <library-file> ;
-
-rule link.dll ( targets + : sources * : properties * )
-{
-    DEPENDS $(<) : [ on $(<) return $(DEF_FILE) ] ;
-}
-
-if [ os.name ] in NT
-{
-   actions archive
-   {
-      if exist "$(<[1])" DEL "$(<[1])"
-      $(.LD) -library -o "$(<[1])" @"@($(<[1]:W).rsp:E=$(nl)"$(>)" $(nl)$(LIBRARIES_MENTIONED_BY_FILE) $(nl)"$(LIBRARY_OPTION)$(FINDLIBS_ST:S=.lib)" $(nl)"$(LIBRARY_OPTION)$(FINDLIBS_SA:S=.lib)")"
-   }
-}
-else # cygwin
-{
-   actions archive
-   {
-      _bbv2_out_="$(<)"
-      if test -f "$_bbv2_out_" ; then
-         _bbv2_existing_="$(<:W)"
-      fi
-      $(.LD) -library -o "$(<:W)" $_bbv2_existing_ @"@($(<[1]:W).rsp:E=$(nl)"$(>)" $(nl)$(LIBRARIES_MENTIONED_BY_FILE) $(nl)"$(LIBRARY_OPTION)$(FINDLIBS_ST:S=.lib)" $(nl)"$(LIBRARY_OPTION)$(FINDLIBS_SA:S=.lib)")"
-   }
-}
-
-actions link bind DEF_FILE
-{
-   $(.LD) -o "$(<[1]:W)" -L"$(LINKPATH)" $(LINKFLAGS) $(USER_LINKFLAGS) @"@($(<[1]:W).rsp:E=$(nl)"$(>)" $(nl)$(LIBRARIES_MENTIONED_BY_FILE) $(nl)"$(LIBRARY_OPTION)$(FINDLIBS_ST:S=.lib)" $(nl)"$(LIBRARY_OPTION)$(FINDLIBS_SA:S=.lib)")"
-}
-
-actions link.dll bind DEF_FILE
-{
-   $(.LD) -shared -o "$(<[1]:W)" -implib "$(<[2]:W)" -L"$(LINKPATH)" $(LINKFLAGS) -f"$(DEF_FILE)" $(USER_LINKFLAGS) @"@($(<[1]:W).rsp:E=$(nl)"$(>)" $(nl)$(LIBRARIES_MENTIONED_BY_FILE) $(nl)"$(LIBRARY_OPTION)$(FINDLIBS_ST:S=.lib)" $(nl)"$(LIBRARY_OPTION)$(FINDLIBS_SA:S=.lib)")"
-}
-
diff --git a/jam-files/boost-build/tools/darwin.jam b/jam-files/boost-build/tools/darwin.jam
deleted file mode 100644
index bb6dd45e..00000000
--- a/jam-files/boost-build/tools/darwin.jam
+++ /dev/null
@@ -1,568 +0,0 @@
-# Copyright 2003 Christopher Currie
-# Copyright 2006 Dave Abrahams 
-# Copyright 2003, 2004, 2005, 2006 Vladimir Prus 
-# Copyright 2005-2007 Mat Marcus
-# Copyright 2005-2007 Adobe Systems Incorporated
-# Copyright 2007-2010 Rene Rivera
-# Distributed under the Boost Software License, Version 1.0. 
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt) 
-
-#  Please see http://article.gmane.org/gmane.comp.lib.boost.build/3389/
-#  for explanation why it's a separate toolset.
-
-import feature : feature ;
-import toolset : flags ;
-import type ;
-import common ;
-import generators ;
-import path : basename ;
-import version ;
-import property-set ;
-import regex ;
-import errors ;
-
-## Use a framework.
-feature framework : : free ;
-
-## The MacOSX version to compile for, which maps to the SDK to use (sysroot).
-feature macosx-version : : propagated link-incompatible symmetric optional ;
-
-## The minimal MacOSX version to target.
-feature macosx-version-min : : propagated optional ;
-
-## A dependency, that is forced to be included in the link.
-feature force-load : : free dependency incidental ;
-
-#############################################################################
-
-if [ MATCH (--debug-configuration) : [ modules.peek : ARGV ] ]
-{
-    .debug-configuration = true ;
-}
-
-feature.extend toolset : darwin ;
-import gcc ;
-toolset.inherit-generators darwin : gcc : gcc.mingw.link gcc.mingw.link.dll ;
-
-generators.override darwin.prebuilt : builtin.prebuilt ;
-generators.override darwin.searched-lib-generator : searched-lib-generator ;
-
-# Override default do-nothing generators.
-generators.override darwin.compile.c.pch   : pch.default-c-pch-generator   ;
-generators.override darwin.compile.c++.pch : pch.default-cpp-pch-generator ;
-
-type.set-generated-target-suffix PCH : <toolset>darwin : gch ;
-
-toolset.inherit-rules darwin : gcc : localize ;
-toolset.inherit-flags darwin : gcc     
-  :  <runtime-link>static
-     <architecture>arm/<address-model>32
-     <architecture>arm/<address-model>64
-     <architecture>arm/<instruction-set>
-     <architecture>x86/<address-model>32
-     <architecture>x86/<address-model>64
-     <architecture>x86/<instruction-set>
-     <architecture>power/<address-model>32
-     <architecture>power/<address-model>64
-     <architecture>power/<instruction-set>  ;
-
-# Options:
-#
-#   <root>PATH
-#       Platform root path. The common autodetection will set this to
-#       "/Developer". And when a command is given it will be set to
-#       the corresponding "*.platform/Developer" directory.
-#
-rule init ( version ? : command * : options * : requirement * )
-{
-    # First time around, figure what is host OSX version
-    if ! $(.host-osx-version)  
-    {
-        .host-osx-version = [ MATCH "^([0-9.]+)"
-          : [ SHELL "/usr/bin/sw_vers -productVersion" ] ] ;
-        if $(.debug-configuration)
-        {
-            ECHO notice: OSX version on this machine is $(.host-osx-version) ;
-        }
-    }
-                      
-    # - The root directory of the tool install.
-    local root = [ feature.get-values <root> : $(options) ] ;
-    
-    # - The bin directory where to find the commands to execute.
-    local bin ;
-    
-    # - The configured compile driver command.
-    local command = [ common.get-invocation-command darwin : g++ : $(command) ] ;
-    
-    # The version as reported by the compiler
-    local real-version ;
-    
-    # - Autodetect the root and bin dir if not given.
-    if $(command)
-    {
-        bin ?= [ common.get-absolute-tool-path $(command[1]) ] ;
-        if $(bin) = "/usr/bin"
-        {
-            root ?= /Developer ;
-        }
-        else
-        {
-            local r = $(bin:D) ;
-            r = $(r:D) ;
-            root ?= $(r) ;
-        }
-    }
-    
-    # - Autodetect the version if not given.
-    if $(command)
-    {
-        # - The 'command' variable can have multiple elements. When calling
-        #   the SHELL builtin we need a single string.
-        local command-string = $(command:J=" ") ;
-        real-version = [ MATCH "^([0-9.]+)"
-            : [ SHELL "$(command-string) -dumpversion" ] ] ;
-        version ?= $(real-version) ;
-    }
-    
-    .real-version.$(version) = $(real-version) ;
-    
-    # - Define the condition for this toolset instance.
-    local condition =
-        [ common.check-init-parameters darwin $(requirement) : version $(version) ] ;
-    
-    # - Set the toolset generic common options.
-    common.handle-options darwin : $(condition) : $(command) : $(options) ;
-    
-    # - GCC 4.0 and higher in Darwin does not have -fcoalesce-templates.
-    if $(real-version) < "4.0.0"
-    {
-        flags darwin.compile.c++ OPTIONS $(condition) : -fcoalesce-templates ;
-    }
-    # - GCC 4.2 and higher in Darwin does not have -Wno-long-double.
-    if $(real-version) < "4.2.0"
-    {
-        flags darwin.compile OPTIONS $(condition) : -Wno-long-double ;
-    }
-
-    # - Set the link flags common with the GCC toolset.
-    gcc.init-link-flags darwin darwin $(condition) ;
-
-    # - The symbol strip program.
-    local strip ;
-    if <striper> in $(options)
-    {
-        # We can turn off strip by specifying it as empty. In which
-        # case we switch to using the linker to do the strip.
-        flags darwin.link.dll OPTIONS
-            $(condition)/<main-target-type>LIB/<link>shared/<address-model>32/<strip>on : -Wl,-x ;
-        flags darwin.link.dll OPTIONS
-            $(condition)/<main-target-type>LIB/<link>shared/<address-model>/<strip>on : -Wl,-x ;
-        flags darwin.link OPTIONS
-            $(condition)/<main-target-type>EXE/<address-model>32/<strip>on : -s ;
-        flags darwin.link OPTIONS
-            $(condition)/<main-target-type>EXE/<address-model>/<strip>on : -s ;
-    }
-    else
-    {
-        # Otherwise we need to find a strip program to use. And hence
-        # also tell the link action that we need to use a strip
-        # post-process.
-        flags darwin.link NEED_STRIP $(condition)/<strip>on : "" ;
-        strip =
-            [ common.get-invocation-command darwin
-                : strip : [ feature.get-values <striper> : $(options) ] : $(bin) : search-path ] ;
-        flags darwin.link .STRIP $(condition) : $(strip[1]) ;
-        if $(.debug-configuration)
-        {
-            ECHO notice: using strip for $(condition) at $(strip[1]) ;
-        }
-    }
-
-    # - The archive builder (libtool is the default as creating
-    #   archives in darwin is complicated.
-    local archiver =
-        [ common.get-invocation-command darwin
-            : libtool : [ feature.get-values <archiver> : $(options) ] : $(bin) : search-path ] ;
-    flags darwin.archive .LIBTOOL $(condition) : $(archiver[1]) ;
-    if $(.debug-configuration)
-    {
-        ECHO notice: using archiver for $(condition) at $(archiver[1]) ;
-    }
-    
-    # - Initialize the SDKs available in the root for this tool.
-    local sdks = [ init-available-sdk-versions $(condition) : $(root) ] ;
-    
-    #~ ECHO --- ;
-    #~ ECHO --- bin :: $(bin) ;
-    #~ ECHO --- root :: $(root) ;
-    #~ ECHO --- version :: $(version) ;
-    #~ ECHO --- condition :: $(condition) ;
-    #~ ECHO --- strip :: $(strip) ;
-    #~ ECHO --- archiver :: $(archiver) ;
-    #~ ECHO --- sdks :: $(sdks) ;
-    #~ ECHO --- ;
-    #~ EXIT ;
-}
-
-# Add and set options for a discovered SDK version.
-local rule init-sdk ( condition * : root ? : version + : version-feature ? )
-{
-    local rule version-to-feature ( version + )
-    {
-        switch $(version[1])
-        {
-            case iphone* :
-            {
-                return $(version[1])-$(version[2-]:J=.) ;
-            }
-            case mac* :
-            {
-                return $(version[2-]:J=.) ;
-            }
-            case * :
-            {
-                return $(version:J=.) ;
-            }
-        }
-    }
-    
-    if $(version-feature)
-    {
-        if $(.debug-configuration)
-        {
-            ECHO notice: available sdk for $(condition)/<macosx-version>$(version-feature) at $(sdk) ;
-        }
-        
-        # Add the version to the features for specifying them.
-        if ! $(version-feature) in [ feature.values macosx-version ]
-        {
-            feature.extend macosx-version : $(version-feature) ;
-        }
-        if ! $(version-feature) in [ feature.values macosx-version-min ]
-        {
-            feature.extend macosx-version-min : $(version-feature) ;
-        }
-        
-        # Set the flags the version needs to compile with, first
-        # generic options.
-        flags darwin.compile OPTIONS $(condition)/<macosx-version>$(version-feature)
-            : -isysroot $(sdk) ;
-        flags darwin.link OPTIONS $(condition)/<macosx-version>$(version-feature)
-            : -isysroot $(sdk) ;
-        
-        # Then device variation options.
-        switch $(version[1])
-        {
-            case iphonesim* :
-            {
-                local N = $(version[2]) ;
-                if ! $(version[3]) { N += 00 ; }
-                else if [ regex.match (..) : $(version[3]) ] { N += $(version[3]) ; }
-                else { N += 0$(version[3]) ; }
-                if ! $(version[4]) { N += 00 ; }
-                else if [ regex.match (..) : $(version[4]) ] { N += $(version[4]) ; }
-                else { N += 0$(version[4]) ; }
-                N = $(N:J=) ;
-                flags darwin.compile OPTIONS <macosx-version-min>$(version-feature)
-                    : -D__IPHONE_OS_VERSION_MIN_REQUIRED=$(N) ;
-                flags darwin.link OPTIONS <macosx-version-min>$(version-feature)
-                    : -D__IPHONE_OS_VERSION_MIN_REQUIRED=$(N) ;
-            }
-            
-            case iphone* :
-            {
-                flags darwin.compile OPTIONS <macosx-version-min>$(version-feature)
-                    : -miphoneos-version-min=$(version[2-]:J=.) ;
-                flags darwin.link OPTIONS <macosx-version-min>$(version-feature)
-                    : -miphoneos-version-min=$(version[2-]:J=.) ;
-            }
-            
-            case mac* :
-            {
-                flags darwin.compile OPTIONS <macosx-version-min>$(version-feature)
-                    : -mmacosx-version-min=$(version[2-]:J=.) ;
-                flags darwin.link OPTIONS <macosx-version-min>$(version-feature)
-                    : -mmacosx-version-min=$(version[2-]:J=.) ;
-            }
-        }
-        
-        return $(version-feature) ;
-    }
-    else if $(version[4])
-    {
-        # We have a patch version of an SDK. We want to set up
-        # both the specific patch version, and the minor version.
-        # So we recurse to set up the minor version. Plus the minor version.
-        return
-            [ init-sdk $(condition) : $(root)
-                : $(version[1-3]) : [ version-to-feature $(version[1-3]) ] ]
-            [ init-sdk $(condition) : $(root)
-                : $(version) : [ version-to-feature $(version) ] ] ;
-    }
-    else
-    {
-        # Yes, this is intentionally recursive.
-        return
-            [ init-sdk $(condition) : $(root)
-                : $(version) : [ version-to-feature $(version) ] ] ;
-    }
-}
-
-# Determine the MacOSX SDK versions installed and their locations.
-local rule init-available-sdk-versions ( condition * : root ? )
-{
-    root ?= /Developer ;
-    local sdks-root = $(root)/SDKs ;
-    local sdks = [ GLOB $(sdks-root) : MacOSX*.sdk iPhoneOS*.sdk iPhoneSimulator*.sdk ] ;
-    local result ;
-    for local sdk in $(sdks)
-    {
-        local sdk-match = [ MATCH ([^0-9]+)([0-9]+)[.]([0-9x]+)[.]?([0-9x]+)? : $(sdk:D=) ] ;
-        local sdk-platform = $(sdk-match[1]:L) ;
-        local sdk-version = $(sdk-match[2-]) ;
-        if $(sdk-version)
-        {
-            switch $(sdk-platform)
-            {
-                case macosx :
-                {
-                    sdk-version = mac $(sdk-version) ;
-                }
-                case iphoneos :
-                {
-                    sdk-version = iphone $(sdk-version) ;
-                }
-                case iphonesimulator :
-                {
-                    sdk-version = iphonesim $(sdk-version) ;
-                }
-                case * :
-                {
-                    sdk-version = $(sdk-version:J=-) ;
-                }
-            }
-            result += [ init-sdk $(condition) : $(sdk) : $(sdk-version) ] ;
-        }
-    }
-    return $(result) ;
-}
-
-# Generic options.
-flags darwin.compile OPTIONS <flags> ;
-
-# The following adds objective-c support to darwin.
-# Thanks to http://thread.gmane.org/gmane.comp.lib.boost.build/13759
-
-generators.register-c-compiler darwin.compile.m : OBJECTIVE_C : OBJ : <toolset>darwin ;
-generators.register-c-compiler darwin.compile.mm : OBJECTIVE_CPP : OBJ : <toolset>darwin ;
-
-rule setup-address-model ( targets * : sources * : properties * )
-{
-    local ps = [ property-set.create $(properties) ] ;
-    local arch = [ $(ps).get <architecture> ] ;
-    local address-model = [ $(ps).get <address-model> ] ;
-    local osx-version = [ $(ps).get <macosx-version> ] ;
-    local gcc-version = [ $(ps).get <toolset-darwin:version> ] ;
-    gcc-version = $(.real-version.$(gcc-version)) ;
-    local options ;
-    
-    local support-ppc64 = 1 ;
-    
-    osx-version ?= $(.host-osx-version) ;
-
-    switch $(osx-version)
-    {
-        case iphone* :
-        {
-            support-ppc64 = ;
-        }
-        
-        case * :
-        if $(osx-version) && ! [ version.version-less [ regex.split $(osx-version) \\. ] : 10 6 ]
-        {
-            # When targeting 10.6:
-            # - gcc 4.2 will give a compiler errir if ppc64 compilation is requested
-            # - gcc 4.0 will compile fine, somehow, but then fail at link time
-            support-ppc64 = ;
-        }
-    }
-    switch $(arch)
-    {
-        case combined : 
-        {
-            if $(address-model) = 32_64 {
-                if $(support-ppc64) {
-                    options = -arch i386 -arch ppc -arch x86_64 -arch ppc64 ;                    
-                } else {
-                    # Build 3-way binary
-                    options = -arch i386 -arch ppc -arch x86_64 ;
-                }                                
-            } else if $(address-model) = 64 {
-                if $(support-ppc64) {
-                    options = -arch x86_64 -arch ppc64 ;
-                } else {
-                    errors.user-error "64-bit PPC compilation is not supported when targeting OSX 10.6 or later" ;
-                }                
-            } else {
-                options = -arch i386 -arch ppc ;
-            }
-        }
-        
-        case x86 : 
-        {
-            if $(address-model) = 32_64 {
-                options = -arch i386 -arch x86_64 ;
-            } else if $(address-model) = 64 {
-                options = -arch x86_64 ;
-            } else {
-                options = -arch i386 ;
-            }
-        }        
-        
-        case power :
-        {
-            if ! $(support-ppc64) 
-              && (  $(address-model) = 32_64 || $(address-model) = 64 )
-            {
-                errors.user-error "64-bit PPC compilation is not supported when targeting OSX 10.6 or later" ;
-            }
-            
-            if $(address-model) = 32_64 {
-                options = -arch ppc -arch ppc64 ;
-            } else if $(address-model) = 64 {
-                options = -arch ppc64 ;
-            } else {
-                options = -arch ppc ;
-            }
-        }
-        
-        case arm :
-        {
-            options = -arch armv6 ;
-        }        
-    }
-    
-    if $(options)
-    {
-        OPTIONS on $(targets) += $(options) ;
-    }            
-}
-
-rule setup-threading ( targets * : sources * : properties * )
-{
-    gcc.setup-threading $(targets) : $(sources) : $(properties) ;
-}
-
-rule setup-fpic ( targets * : sources * : properties * )
-{
-    gcc.setup-fpic $(targets) : $(sources) : $(properties) ;
-}
-
-rule compile.m ( targets * : sources * : properties * )
-{
-    LANG on $(<) = "-x objective-c" ;
-    gcc.setup-fpic $(targets) : $(sources) : $(properties) ;
-    setup-address-model $(targets) : $(sources) : $(properties) ;
-}
-
-actions compile.m
-{
-    "$(CONFIG_COMMAND)" $(LANG) $(OPTIONS) $(USER_OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -c -o "$(<)" "$(>)"
-}
-
-rule compile.mm  ( targets * : sources * : properties * )
-{
-    LANG on $(<) = "-x objective-c++" ;
-    gcc.setup-fpic $(targets) : $(sources) : $(properties) ;
-    setup-address-model $(targets) : $(sources) : $(properties) ;
-}
-
-actions compile.mm
-{
-    "$(CONFIG_COMMAND)" $(LANG) $(OPTIONS) $(USER_OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -c -o "$(<)" "$(>)"
-}
-
-# Set the max header padding to allow renaming of libs for installation.
-flags darwin.link.dll OPTIONS : -headerpad_max_install_names ;
-
-# To link the static runtime we need to link to all the core runtime libraries.
-flags darwin.link OPTIONS <runtime-link>static
-    : -nodefaultlibs -shared-libgcc -lstdc++-static -lgcc_eh -lgcc -lSystem ;
-
-# Strip as much as possible when optimizing.
-flags darwin.link OPTIONS <optimization>speed : -Wl,-dead_strip -no_dead_strip_inits_and_terms ;
-flags darwin.link OPTIONS <optimization>space : -Wl,-dead_strip -no_dead_strip_inits_and_terms ;
-
-# Dynamic/shared linking.
-flags darwin.compile OPTIONS <link>shared : -dynamic ;
-
-# Misc options.
-flags darwin.compile OPTIONS : -gdwarf-2 -fexceptions ;
-#~ flags darwin.link OPTIONS : -fexceptions ;
-
-# Add the framework names to use.
-flags darwin.link FRAMEWORK <framework> ;
-
-#
-flags darwin.link FORCE_LOAD <force-load> ;
-
-# This is flag is useful for debugging the link step
-# uncomment to see what libtool is doing under the hood
-#~ flags darwin.link.dll OPTIONS : -Wl,-v ;
-
-_ = " " ;
-
-# set up the -F option to include the paths to any frameworks used.
-local rule prepare-framework-path ( target + )
-{
-    # The -framework option only takes basename of the framework.
-    # The -F option specifies the directories where a framework
-    # is searched for.  So, if we find <framework> feature
-    # with some path, we need to generate property -F option.
-    local framework-paths = [ on $(target) return $(FRAMEWORK:D) ] ;
-
-    # Be sure to generate no -F if there's no path.
-    for local framework-path in $(framework-paths)
-    {
-        if $(framework-path) != ""
-        {
-            FRAMEWORK_PATH on $(target) += -F$(framework-path) ;
-        }
-    }
-}
-
-rule link ( targets * : sources * : properties * )
-{
-    DEPENDS $(targets) : [ on $(targets) return $(FORCE_LOAD) ] ;
-    setup-address-model $(targets) : $(sources) : $(properties) ;
-    prepare-framework-path $(<) ;
-}
-
-# Note that using strip without any options was reported to result in broken
-# binaries, at least on OS X 10.5.5, see:
-#    http://svn.boost.org/trac/boost/ticket/2347
-# So we pass -S -x.
-actions link bind LIBRARIES FORCE_LOAD
-{
-    "$(CONFIG_COMMAND)" -L"$(LINKPATH)" -o "$(<)" "$(>)" -Wl,-force_load$(_)"$(FORCE_LOAD)" "$(LIBRARIES)" -l$(FINDLIBS-SA) -l$(FINDLIBS-ST) $(FRAMEWORK_PATH) -framework$(_)$(FRAMEWORK:D=:S=) $(OPTIONS) $(USER_OPTIONS)
-    $(NEED_STRIP)"$(.STRIP)" $(NEED_STRIP)-S $(NEED_STRIP)-x $(NEED_STRIP)"$(<)"
-}
-
-rule link.dll ( targets * : sources * : properties * )
-{
-    setup-address-model $(targets) : $(sources) : $(properties) ;
-    prepare-framework-path $(<) ;
-}
-
-actions link.dll bind LIBRARIES
-{
-    "$(CONFIG_COMMAND)" -dynamiclib -Wl,-single_module -install_name "$(<:B)$(<:S)" -L"$(LINKPATH)" -o "$(<)" "$(>)" "$(LIBRARIES)" -l$(FINDLIBS-SA) -l$(FINDLIBS-ST) $(FRAMEWORK_PATH) -framework$(_)$(FRAMEWORK:D=:S=) $(OPTIONS) $(USER_OPTIONS)
-}
-
-# We use libtool instead of ar to support universal binary linking
-# TODO: Find a way to use the underlying tools, i.e. lipo, to do this.
-actions piecemeal archive
-{
-    "$(.LIBTOOL)" -static -o "$(<:T)"  $(ARFLAGS)  "$(>:T)"
-}
diff --git a/jam-files/boost-build/tools/darwin.py b/jam-files/boost-build/tools/darwin.py
deleted file mode 100644
index c2919606..00000000
--- a/jam-files/boost-build/tools/darwin.py
+++ /dev/null
@@ -1,57 +0,0 @@
-#  Copyright (C) Christopher Currie 2003. Permission to copy, use,
-#  modify, sell and distribute this software is granted provided this
-#  copyright notice appears in all copies. This software is provided
-# "as is" without express or implied warranty, and with no claim as to
-#  its suitability for any purpose.
-
-#  Please see http://article.gmane.org/gmane.comp.lib.boost.build/3389/
-#  for explanation why it's a separate toolset.
-
-import common, gcc, builtin
-from b2.build import feature, toolset, type, action, generators
-from b2.util.utility import *
-
-toolset.register ('darwin')
-
-toolset.inherit_generators ('darwin', [], 'gcc')
-toolset.inherit_flags ('darwin', 'gcc')
-toolset.inherit_rules ('darwin', 'gcc')
-
-def init (version = None, command = None, options = None):
-    options = to_seq (options)
-
-    condition = common.check_init_parameters ('darwin', None, ('version', version))
-    
-    command = common.get_invocation_command ('darwin', 'g++', command)
-
-    common.handle_options ('darwin', condition, command, options)
-    
-    gcc.init_link_flags ('darwin', 'darwin', condition)
-
-# Darwin has a different shared library suffix
-type.set_generated_target_suffix ('SHARED_LIB', ['<toolset>darwin'], 'dylib')
-
-# we need to be able to tell the type of .dylib files
-type.register_suffixes ('dylib', 'SHARED_LIB')
-
-feature.feature ('framework', [], ['free'])
-
-toolset.flags ('darwin.compile', 'OPTIONS', '<link>shared', ['-dynamic'])
-toolset.flags ('darwin.compile', 'OPTIONS', None, ['-Wno-long-double', '-no-cpp-precomp'])
-toolset.flags ('darwin.compile.c++', 'OPTIONS', None, ['-fcoalesce-templates'])
-
-toolset.flags ('darwin.link', 'FRAMEWORK', '<framework>')
-
-# This is flag is useful for debugging the link step
-# uncomment to see what libtool is doing under the hood
-# toolset.flags ('darwin.link.dll', 'OPTIONS', None, '[-Wl,-v'])
-
-action.register ('darwin.compile.cpp', None, ['$(CONFIG_COMMAND) $(ST_OPTIONS) -L"$(LINKPATH)" -o "$(<)" "$(>)" "$(LIBRARIES)" -l$(FINDLIBS-SA) -l$(FINDLIBS-ST) -framework$(_)$(FRAMEWORK) $(OPTIONS)'])
-
-# TODO: how to set 'bind LIBRARIES'?
-action.register ('darwin.link.dll', None, ['$(CONFIG_COMMAND) -dynamiclib -L"$(LINKPATH)" -o "$(<)" "$(>)" "$(LIBRARIES)" -l$(FINDLIBS-SA) -l$(FINDLIBS-ST) -framework$(_)$(FRAMEWORK) $(OPTIONS)'])
-
-def darwin_archive (manager, targets, sources, properties):
-    pass
-
-action.register ('darwin.archive', darwin_archive, ['ar -c -r -s $(ARFLAGS) "$(<:T)" "$(>:T)"'])
diff --git a/jam-files/boost-build/tools/dmc.jam b/jam-files/boost-build/tools/dmc.jam
deleted file mode 100644
index 8af8725a..00000000
--- a/jam-files/boost-build/tools/dmc.jam
+++ /dev/null
@@ -1,134 +0,0 @@
-# Digital Mars C++
-
-# (C) Copyright Christof Meerwald 2003.
-# (C) Copyright Aleksey Gurtovoy 2004.
-# (C) Copyright Arjan Knepper 2006.
-#
-# Distributed under the Boost Software License, Version 1.0. (See
-# accompanying file LICENSE_1_0.txt or copy at
-# http://www.boost.org/LICENSE_1_0.txt)
-
-# The following #// line will be used by the regression test table generation
-# program as the column heading for HTML tables. Must not include version number.
-#//<a href="http://www.digitalmars.com/">Digital<br>Mars C++</a>
-
-import feature generators common ;
-import toolset : flags ;
-import sequence regex ;
-
-feature.extend toolset : dmc ;
-
-rule init ( version ? : command * : options * )
-{
-    local condition = [ common.check-init-parameters dmc : version $(version) ] ;
-    
-    local command = [ common.get-invocation-command dmc : dmc : $(command) ] ;
-    command ?= dmc ;
-
-    common.handle-options dmc : $(condition) : $(command) : $(options) ;   
-    
-    if $(command)
-    {
-        command = [ common.get-absolute-tool-path $(command[-1]) ] ;
-    }   
-    root = $(command:D) ;    
-    
-    if $(root)
-    {        
-        # DMC linker is sensitive the the direction of slashes, and
-        # won't link if forward slashes are used in command.
-        root = [ sequence.join [ regex.split $(root) "/" ] : "\\" ] ;
-        flags dmc .root $(condition) : $(root)\\bin\\ ;
-    }
-    else
-    {
-        flags dmc .root $(condition) : "" ;
-    }    
-}
-
-
-# Declare generators
-generators.register-linker dmc.link : OBJ SEARCHED_LIB STATIC_LIB IMPORT_LIB : EXE : <toolset>dmc ;
-generators.register-linker dmc.link.dll : OBJ SEARCHED_LIB STATIC_LIB IMPORT_LIB : SHARED_LIB IMPORT_LIB : <toolset>dmc ;
-
-generators.register-archiver dmc.archive : OBJ : STATIC_LIB : <toolset>dmc ;
-generators.register-c-compiler dmc.compile.c++ : CPP : OBJ : <toolset>dmc ;
-generators.register-c-compiler dmc.compile.c : C : OBJ : <toolset>dmc ;
-
-
-# Declare flags
-# dmc optlink has some limitation on the amount of debug-info included. Therefore only linenumbers are enabled in debug builds.
-# flags dmc.compile OPTIONS <debug-symbols>on : -g ;
-flags dmc.compile OPTIONS <debug-symbols>on : -gl ;
-flags dmc.link OPTIONS <debug-symbols>on : /CO /NOPACKF /DEBUGLI ;
-flags dmc.link OPTIONS <debug-symbols>off : /PACKF ;
-
-flags dmc.compile OPTIONS <optimization>off : -S -o+none ;
-flags dmc.compile OPTIONS <optimization>speed : -o+time ;
-flags dmc.compile OPTIONS <optimization>space : -o+space ;
-flags dmc.compile OPTIONS <exception-handling>on : -Ae ;
-flags dmc.compile OPTIONS <rtti>on : -Ar ;
-# FIXME:
-# Compiling sources to be linked into a shared lib (dll) the -WD cflag should be used
-# Compiling sources to be linked into a static lib (lib) or executable the -WA cflag should be used
-# But for some reason the -WD cflag is always in use.
-# flags dmc.compile OPTIONS <link>shared : -WD ;
-# flags dmc.compile OPTIONS <link>static : -WA ;
-
-# Note that these two options actually imply multithreading support on DMC
-# because there is no single-threaded dynamic runtime library. Specifying
-# <threading>multi would be a bad idea, though, because no option would be
-# matched when the build uses the default settings of <runtime-link>dynamic
-# and <threading>single.
-flags dmc.compile OPTIONS <runtime-debugging>off/<runtime-link>shared : -ND ;
-flags dmc.compile OPTIONS <runtime-debugging>on/<runtime-link>shared : -ND ;
-
-flags dmc.compile OPTIONS <runtime-debugging>off/<runtime-link>static/<threading>single : ;
-flags dmc.compile OPTIONS <runtime-debugging>on/<runtime-link>static/<threading>single : ;
-flags dmc.compile OPTIONS <runtime-debugging>off/<runtime-link>static/<threading>multi : -D_MT ;
-flags dmc.compile OPTIONS <runtime-debugging>on/<runtime-link>static/<threading>multi : -D_MT ;
-
-flags dmc.compile OPTIONS : <cflags> ;
-flags dmc.compile.c++ OPTIONS : <cxxflags> ;
-
-flags dmc.compile DEFINES : <define> ;
-flags dmc.compile INCLUDES : <include> ;
-
-flags dmc.link <linkflags> ;
-flags dmc.archive OPTIONS <arflags> ;
-
-flags dmc LIBPATH <library-path> ;
-flags dmc LIBRARIES <library-file> ;
-flags dmc FINDLIBS <find-library-sa> ;
-flags dmc FINDLIBS <find-library-st> ;
-
-actions together link bind LIBRARIES
-{
-    "$(.root)link" $(OPTIONS) /NOI /DE /XN "$(>)" , "$(<[1])" ,, $(LIBRARIES) user32.lib kernel32.lib "$(FINDLIBS:S=.lib)" , "$(<[2]:B).def"
-}
-
-actions together link.dll bind LIBRARIES
-{
-    echo LIBRARY "$(<[1])" > $(<[2]:B).def
-    echo DESCRIPTION 'A Library' >> $(<[2]:B).def
-    echo EXETYPE NT >> $(<[2]:B).def
-    echo SUBSYSTEM WINDOWS >> $(<[2]:B).def
-    echo CODE	EXECUTE READ >> $(<[2]:B).def
-    echo DATA	READ WRITE >> $(<[2]:B).def
-    "$(.root)link" $(OPTIONS) /NOI /DE /XN /ENTRY:_DllMainCRTStartup /IMPLIB:"$(<[2])" "$(>)" $(LIBRARIES) , "$(<[1])" ,, user32.lib kernel32.lib "$(FINDLIBS:S=.lib)" , "$(<[2]:B).def"
-}
-
-actions compile.c
-{
-    "$(.root)dmc"  -c $(OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -o"$(<)" "$(>)"
-}
-
-actions compile.c++
-{
-    "$(.root)dmc" -cpp -c -Ab $(OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -o"$(<)" "$(>)"
-}
-
-actions together piecemeal archive
-{
-    "$(.root)lib" $(OPTIONS) -c -n -p256 "$(<)" "$(>)"
-}
diff --git a/jam-files/boost-build/tools/docutils.jam b/jam-files/boost-build/tools/docutils.jam
deleted file mode 100644
index bf061617..00000000
--- a/jam-files/boost-build/tools/docutils.jam
+++ /dev/null
@@ -1,84 +0,0 @@
-# Copyright David Abrahams 2004. Distributed under the Boost
-# Software License, Version 1.0. (See accompanying
-# file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
-
-# Support for docutils ReStructuredText processing.
-
-import type ;
-import scanner ;
-import generators ;
-import os ;
-import common ;
-import toolset ;
-import path ;
-import feature : feature ;
-import property ;
-
-.initialized = ;
-
-type.register ReST : rst ;
-
-class rst-scanner : common-scanner
-{
-    rule __init__ ( paths * )
-    {
-        common-scanner.__init__ . $(paths) ;
-    }
-    
-    rule pattern ( )
-    {
-         return "^[ 	]*\\.\\.[ 	]+include::[ 	]+([^
-]+)"
-        "^[ 	]*\\.\\.[ 	]+image::[ 	]+([^
-]+)"
-        "^[ 	]*\\.\\.[ 	]+figure::[ 	]+([^
-]+)"
-        ;
-    }
-}
-
-scanner.register rst-scanner : include ;
-type.set-scanner ReST : rst-scanner ;
-
-generators.register-standard docutils.html : ReST : HTML ;
-
-rule init ( docutils-dir ? : tools-dir ? )
-{
-    docutils-dir ?= [ modules.peek : DOCUTILS_DIR ] ;
-    tools-dir ?= $(docutils-dir)/tools ;
-
-    if ! $(.initialized)
-    {
-        .initialized = true ;
-        .docutils-dir = $(docutils-dir) ;
-        .tools-dir = $(tools-dir:R="") ;
-       
-        .setup = [ 
-          common.prepend-path-variable-command PYTHONPATH 
-            : $(.docutils-dir) $(.docutils-dir)/extras ] ;
-    }
-}
-
-rule html ( target : source : properties *  )
-{
-    if ! [ on $(target) return $(RST2XXX) ]
-    {
-        local python-cmd = [ property.select <python.interpreter> : $(properties) ] ;
-        RST2XXX on $(target) = $(python-cmd:G=:E="python") $(.tools-dir)/rst2html.py ;
-    }
-}
-
-
-feature docutils : : free ;
-feature docutils-html : : free ;
-feature docutils-cmd : : free ;
-toolset.flags docutils COMMON-FLAGS : <docutils> ;
-toolset.flags docutils HTML-FLAGS : <docutils-html> ;
-toolset.flags docutils RST2XXX : <docutils-cmd> ;
-  
-actions html
-{
-    $(.setup)
-    "$(RST2XXX)" $(COMMON-FLAGS) $(HTML-FLAGS) $(>) $(<)
-}
-
diff --git a/jam-files/boost-build/tools/doxproc.py b/jam-files/boost-build/tools/doxproc.py
deleted file mode 100644
index 4cbd5edd..00000000
--- a/jam-files/boost-build/tools/doxproc.py
+++ /dev/null
@@ -1,859 +0,0 @@
-#!/usr/bin/python
-# Copyright 2006 Rene Rivera
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-'''
-Processing of Doxygen generated XML.
-'''
-
-import os
-import os.path
-import sys
-import time
-import string
-import getopt
-import glob
-import re
-import xml.dom.minidom
-
-    
-def usage():
-    print '''
-Usage:
-    %s options
-
-Options:
-    --xmldir        Directory with the Doxygen xml result files.
-    --output        Write the output BoostBook to the given location.
-    --id            The ID of the top level BoostBook section.
-    --title         The title of the top level BoostBook section.
-    --enable-index  Generate additional index sections for classes and
-                    types.
-''' % ( sys.argv[0] )
-
-
-def get_args( argv = sys.argv[1:] ):
-    spec = [
-        'xmldir=',
-        'output=',
-        'id=',
-        'title=',
-        'enable-index',
-        'help' ]
-    options = {
-        '--xmldir' : 'xml',
-        '--output' : None,
-        '--id' : 'dox',
-        '--title' : 'Doxygen'
-        }
-    ( option_pairs, other ) = getopt.getopt( argv, '', spec )
-    map( lambda x: options.__setitem__( x[0], x[1] ), option_pairs )
-    
-    if options.has_key( '--help' ):
-        usage()
-        sys.exit(1)
-    
-    return {
-        'xmldir' : options['--xmldir'],
-        'output' : options['--output'],
-        'id' : options['--id'],
-        'title' : options['--title'],
-        'index' : options.has_key('--enable-index')
-        }
-
-def if_attribute(node, attribute, true_value, false_value=None):
-    if node.getAttribute(attribute) == 'yes':
-        return true_value
-    else:
-        return false_value
-
-class Doxygen2BoostBook:
-    
-    def __init__( self, **kwargs ):
-        ##
-        self.args = kwargs
-        self.args.setdefault('id','')
-        self.args.setdefault('title','')
-        self.args.setdefault('last_revision', time.asctime())
-        self.args.setdefault('index', False)
-        self.id = '%(id)s.reference' % self.args
-        self.args['id'] = self.id
-        #~ This is our template BoostBook document we insert the generated content into.
-        self.boostbook = xml.dom.minidom.parseString('''<?xml version="1.0" encoding="UTF-8"?>
-<section id="%(id)s" name="%(title)s" last-revision="%(last_revision)s">
-    <title>%(title)s</title>
-    <library-reference id="%(id)s.headers">
-        <title>Headers</title>
-    </library-reference>
-    <index id="%(id)s.classes">
-        <title>Classes</title>
-    </index>
-    <index id="%(id)s.index">
-        <title>Index</title>
-    </index>
-</section>
-''' % self.args )
-        self.section = {
-            'headers' : self._getChild('library-reference',id='%(id)s.headers' % self.args),
-            'classes' : self._getChild('index',id='%(id)s.classes' % self.args),
-            'index' : self._getChild('index',id='%(id)s.index' % self.args)
-            }
-        #~ Remove the index sections if we aren't generating it.
-        if not self.args['index']:
-            self.section['classes'].parentNode.removeChild(self.section['classes'])
-            self.section['classes'].unlink()
-            del self.section['classes']
-            self.section['index'].parentNode.removeChild(self.section['index'])
-            self.section['index'].unlink()
-            del self.section['index']
-        #~ The symbols, per Doxygen notion, that we translated.
-        self.symbols = {}
-        #~ Map of Doxygen IDs and BoostBook IDs, so we can translate as needed.
-        self.idmap = {}
-        #~ Marks generation, to prevent redoing it.
-        self.generated = False
-    
-    #~ Add an Doxygen generated XML document to the content we are translating.
-    def addDox( self, document ):
-        self._translateNode(document.documentElement)
-    
-    #~ Turns the internal XML tree into an output UTF-8 string.
-    def tostring( self ):
-        self._generate()
-        #~ return self.boostbook.toprettyxml('  ')
-        return self.boostbook.toxml('utf-8')
-    
-    #~ Does post-processing on the partial generated content to generate additional info
-    #~ now that we have the complete source documents.
-    def _generate( self ):
-        if not self.generated:
-            self.generated = True
-            symbols = self.symbols.keys()
-            symbols.sort()
-            #~ Populate the header section.
-            for symbol in symbols:
-                if self.symbols[symbol]['kind'] in ('header'):
-                    self.section['headers'].appendChild(self.symbols[symbol]['dom'])
-            for symbol in symbols:
-                if self.symbols[symbol]['kind'] not in ('namespace', 'header'):
-                    container = self._resolveContainer(self.symbols[symbol],
-                        self.symbols[self.symbols[symbol]['header']]['dom'])
-                    if container.nodeName != 'namespace':
-                        ## The current BoostBook to Docbook translation doesn't
-                        ## respect, nor assign, IDs to inner types of any kind.
-                        ## So nuke the ID entry so as not create bogus links.
-                        del self.idmap[self.symbols[symbol]['id']]
-                    container.appendChild(self.symbols[symbol]['dom'])
-            self._rewriteIDs(self.boostbook.documentElement)
-    
-    #~ Rewrite the various IDs from Doxygen references to the newly created
-    #~ BoostBook references.
-    def _rewriteIDs( self, node ):
-        if node.nodeName in ('link'):
-            if (self.idmap.has_key(node.getAttribute('linkend'))):
-                #~ A link, and we have someplace to repoint it at.
-                node.setAttribute('linkend',self.idmap[node.getAttribute('linkend')])
-            else:
-                #~ A link, but we don't have a generated target for it.
-                node.removeAttribute('linkend')
-        elif hasattr(node,'hasAttribute') and node.hasAttribute('id') and self.idmap.has_key(node.getAttribute('id')):
-            #~ Simple ID, and we have a translation.
-            node.setAttribute('id',self.idmap[node.getAttribute('id')])
-        #~ Recurse, and iterate, depth-first traversal which turns out to be
-        #~ left-to-right and top-to-bottom for the document.
-        if node.firstChild:
-            self._rewriteIDs(node.firstChild)
-        if node.nextSibling:
-            self._rewriteIDs(node.nextSibling)
-    
-    def _resolveContainer( self, cpp, root ):
-        container = root
-        for ns in cpp['namespace']:
-            node = self._getChild('namespace',name=ns,root=container)
-            if not node:
-                node = container.appendChild(
-                    self._createNode('namespace',name=ns))
-            container = node
-        for inner in cpp['name'].split('::'):
-            node = self._getChild(name=inner,root=container)
-            if not node:
-                break
-            container = node
-        return container
-    
-    def _setID( self, id, name ):
-        self.idmap[id] = name.replace('::','.').replace('/','.')
-        #~ print '--| setID:',id,'::',self.idmap[id]
-    
-    #~ Translate a given node within a given context.
-    #~ The translation dispatches to a local method of the form
-    #~ "_translate[_context0,...,_contextN]", and the keyword args are
-    #~ passed along. If there is no translation handling method we
-    #~ return None.
-    def _translateNode( self, *context, **kwargs ):
-        node = None
-        names = [ ]
-        for c in context:
-            if c:
-                if not isinstance(c,xml.dom.Node):
-                    suffix = '_'+c.replace('-','_')
-                else:
-                    suffix = '_'+c.nodeName.replace('-','_')
-                    node = c
-                names.append('_translate')
-                names = map(lambda x: x+suffix,names)
-        if node:
-            for name in names:
-                if hasattr(self,name):
-                    return getattr(self,name)(node,**kwargs)
-        return None
-    
-    #~ Translates the children of the given parent node, appending the results
-    #~ to the indicated target. For nodes not translated by the translation method
-    #~ it copies the child over and recurses on that child to translate any
-    #~ possible interior nodes. Hence this will translate the entire subtree.
-    def _translateChildren( self, parent, **kwargs ):
-        target = kwargs['target']
-        for n in parent.childNodes:
-            child = self._translateNode(n,target=target)
-            if child:
-                target.appendChild(child)
-            else:
-                child = n.cloneNode(False)
-                if hasattr(child,'data'):
-                    child.data = re.sub(r'\s+',' ',child.data)
-                target.appendChild(child)
-                self._translateChildren(n,target=child)
-    
-    #~ Translate the given node as a description, into the description subnode
-    #~ of the target. If no description subnode is present in the target it
-    #~ is created.
-    def _translateDescription( self, node, target=None, tag='description', **kwargs ):
-        description = self._getChild(tag,root=target)
-        if not description:
-            description = target.appendChild(self._createNode(tag))
-        self._translateChildren(node,target=description)
-        return description
-    
-    #~ Top level translation of: <doxygen ...>...</doxygen>,
-    #~ translates the children.
-    def _translate_doxygen( self, node ):
-        #~ print '_translate_doxygen:', node.nodeName
-        result = []
-        for n in node.childNodes:
-            newNode = self._translateNode(n)
-            if newNode:
-                result.append(newNode)
-        return result
-    
-    #~ Top level translation of:
-    #~ <doxygenindex ...>
-    #~   <compound ...>
-    #~     <member ...>
-    #~       <name>...</name>
-    #~     </member>
-    #~     ...
-    #~   </compound>
-    #~   ...
-    #~ </doxygenindex>
-    #~ builds the class and symbol sections, if requested.
-    def _translate_doxygenindex( self, node ):
-        #~ print '_translate_doxygenindex:', node.nodeName
-        if self.args['index']:
-            entries = []
-            classes = []
-            #~ Accumulate all the index entries we care about.
-            for n in node.childNodes:
-                if n.nodeName == 'compound':
-                    if n.getAttribute('kind') not in ('file','dir','define'):
-                        cpp = self._cppName(self._getChildData('name',root=n))
-                        entry = {
-                            'name' : cpp['name'],
-                            'compoundname' : cpp['compoundname'],
-                            'id' : n.getAttribute('refid')
-                            }
-                        if n.getAttribute('kind') in ('class','struct'):
-                            classes.append(entry)
-                        entries.append(entry)
-                        for m in n.childNodes:
-                            if m.nodeName == 'member':
-                                cpp = self._cppName(self._getChildData('name',root=m))
-                                entry = {
-                                    'name' : cpp['name'],
-                                    'compoundname' : cpp['compoundname'],
-                                    'id' : n.getAttribute('refid')
-                                    }
-                                if hasattr(m,'getAttribute') and m.getAttribute('kind') in ('class','struct'):
-                                    classes.append(entry)
-                                entries.append(entry)
-            #~ Put them in a sensible order.
-            entries.sort(lambda x,y: cmp(x['name'].lower(),y['name'].lower()))
-            classes.sort(lambda x,y: cmp(x['name'].lower(),y['name'].lower()))
-            #~ And generate the BoostBook for them.
-            self._translate_index_(entries,target=self.section['index'])
-            self._translate_index_(classes,target=self.section['classes'])
-        return None
-    
-    #~ Translate a set of index entries in the BoostBook output. The output
-    #~ is grouped into groups of the first letter of the entry names.
-    def _translate_index_(self, entries, target=None, **kwargs ):
-        i = 0
-        targetID = target.getAttribute('id')
-        while i < len(entries):
-            dividerKey = entries[i]['name'][0].upper()
-            divider = target.appendChild(self._createNode('indexdiv',id=targetID+'.'+dividerKey))
-            divider.appendChild(self._createText('title',dividerKey))
-            while i < len(entries) and dividerKey == entries[i]['name'][0].upper():
-                iename = entries[i]['name']
-                ie = divider.appendChild(self._createNode('indexentry'))
-                ie = ie.appendChild(self._createText('primaryie',iename))
-                while i < len(entries) and entries[i]['name'] == iename:
-                    ie.appendChild(self.boostbook.createTextNode(' ('))
-                    ie.appendChild(self._createText(
-                        'link',entries[i]['compoundname'],linkend=entries[i]['id']))
-                    ie.appendChild(self.boostbook.createTextNode(')'))
-                    i += 1
-    
-    #~ Translate a <compounddef ...>...</compounddef>,
-    #~ by retranslating with the "kind" of compounddef.
-    def _translate_compounddef( self, node, target=None, **kwargs ):
-        return self._translateNode(node,node.getAttribute('kind'))
-    
-    #~ Translate a <compounddef kind="namespace"...>...</compounddef>. For
-    #~ namespaces we just collect the information for later use as there is no
-    #~ currently namespaces are not included in the BoostBook format. In the future
-    #~ it might be good to generate a namespace index.
-    def _translate_compounddef_namespace( self, node, target=None, **kwargs ):
-        namespace = {
-            'id' : node.getAttribute('id'),
-            'kind' : 'namespace',
-            'name' : self._getChildData('compoundname',root=node),
-            'brief' : self._getChildData('briefdescription',root=node),
-            'detailed' : self._getChildData('detaileddescription',root=node),
-            'parsed' : False
-            }
-        if self.symbols.has_key(namespace['name']):
-            if not self.symbols[namespace['name']]['parsed']:
-                self.symbols[namespace['name']]['parsed'] = True
-                #~ for n in node.childNodes:
-                    #~ if hasattr(n,'getAttribute'):
-                        #~ self._translateNode(n,n.getAttribute('kind'),target=target,**kwargs)
-        else:
-            self.symbols[namespace['name']] = namespace
-            #~ self._setID(namespace['id'],namespace['name'])
-        return None
-    
-    #~ Translate a <compounddef kind="class"...>...</compounddef>, which
-    #~ forwards to the kind=struct as they are the same.
-    def _translate_compounddef_class( self, node, target=None, **kwargs ):
-        return self._translate_compounddef_struct(node,tag='class',target=target,**kwargs)
-    
-    #~ Translate a <compounddef kind="struct"...>...</compounddef> into:
-    #~ <header id="?" name="?">
-    #~   <struct name="?">
-    #~     ...
-    #~   </struct>
-    #~ </header>
-    def _translate_compounddef_struct( self, node, tag='struct', target=None, **kwargs ):
-        result = None
-        includes = self._getChild('includes',root=node)
-        if includes:
-            ## Add the header into the output table.
-            self._translate_compounddef_includes_(includes,includes,**kwargs)
-            ## Compounds are the declared symbols, classes, types, etc.
-            ## We add them to the symbol table, along with the partial DOM for them
-            ## so that they can be organized into the output later.
-            compoundname = self._getChildData('compoundname',root=node)
-            compoundname = self._cppName(compoundname)
-            self._setID(node.getAttribute('id'),compoundname['compoundname'])
-            struct = self._createNode(tag,name=compoundname['name'].split('::')[-1])
-            self.symbols[compoundname['compoundname']] = {
-                'header' : includes.firstChild.data,
-                'namespace' : compoundname['namespace'],
-                'id' : node.getAttribute('id'),
-                'kind' : tag,
-                'name' : compoundname['name'],
-                'dom' : struct
-                }
-            ## Add the children which will be the members of the struct.
-            for n in node.childNodes:
-                self._translateNode(n,target=struct,scope=compoundname['compoundname'])
-            result = struct
-        return result
-    
-    #~ Translate a <compounddef ...><includes ...>...</includes></compounddef>,
-    def _translate_compounddef_includes_( self, node, target=None, **kwargs ):
-        name = node.firstChild.data
-        if not self.symbols.has_key(name):
-            self._setID(node.getAttribute('refid'),name)
-            self.symbols[name] = {
-                'kind' : 'header',
-                'id' : node.getAttribute('refid'),
-                'dom' : self._createNode('header',
-                    id=node.getAttribute('refid'),
-                    name=name)
-                }
-        return None
-    
-    #~ Translate a <basecompoundref...>...</basecompoundref> into:
-    #~ <inherit access="?">
-    #~   ...
-    #~ </inherit>
-    def _translate_basecompoundref( self, ref, target=None, **kwargs ):
-        inherit = target.appendChild(self._createNode('inherit',
-            access=ref.getAttribute('prot')))
-        self._translateChildren(ref,target=inherit)
-        return
-    
-    #~ Translate:
-    #~   <templateparamlist>
-    #~     <param>
-    #~       <type>...</type>
-    #~       <declname>...</declname>
-    #~       <defname>...</defname>
-    #~       <defval>...</defval>
-    #~     </param>
-    #~     ...
-    #~   </templateparamlist>
-    #~ Into:
-    #~   <template>
-    #~     <template-type-parameter name="?" />
-    #~     <template-nontype-parameter name="?">
-    #~       <type>?</type>
-    #~       <default>?</default>
-    #~     </template-nontype-parameter>
-    #~   </template>
-    def _translate_templateparamlist( self, templateparamlist, target=None, **kwargs ):
-        template = target.appendChild(self._createNode('template'))
-        for param in templateparamlist.childNodes:
-            if param.nodeName == 'param':
-                type = self._getChildData('type',root=param)
-                defval = self._getChild('defval',root=param)
-                paramKind = None
-                if type in ('class','typename'):
-                    paramKind = 'template-type-parameter'
-                else:
-                    paramKind = 'template-nontype-parameter'
-                templateParam = template.appendChild(
-                    self._createNode(paramKind,
-                        name=self._getChildData('declname',root=param)))
-                if paramKind == 'template-nontype-parameter':
-                    template_type = templateParam.appendChild(self._createNode('type'))
-                    self._translate_type(
-                        self._getChild('type',root=param),target=template_type)
-                if defval:
-                    value = self._getChildData('ref',root=defval.firstChild)
-                    if not value:
-                        value = self._getData(defval)
-                    templateParam.appendChild(self._createText('default',value))
-        return template
-    
-    #~ Translate:
-    #~   <briefdescription>...</briefdescription>
-    #~ Into:
-    #~   <purpose>...</purpose>
-    def _translate_briefdescription( self, brief, target=None, **kwargs ):
-        self._translateDescription(brief,target=target,**kwargs)
-        return self._translateDescription(brief,target=target,tag='purpose',**kwargs)
-    
-    #~ Translate:
-    #~   <detaileddescription>...</detaileddescription>
-    #~ Into:
-    #~   <description>...</description>
-    def _translate_detaileddescription( self, detailed, target=None, **kwargs ):
-        return self._translateDescription(detailed,target=target,**kwargs)
-    
-    #~ Translate:
-    #~   <sectiondef kind="?">...</sectiondef>
-    #~ With kind specific translation.
-    def _translate_sectiondef( self, sectiondef, target=None, **kwargs ):
-        self._translateNode(sectiondef,sectiondef.getAttribute('kind'),target=target,**kwargs)
-    
-    #~ Translate non-function sections.
-    def _translate_sectiondef_x_( self, sectiondef, target=None, **kwargs ):
-        for n in sectiondef.childNodes:
-            if hasattr(n,'getAttribute'):
-                self._translateNode(n,n.getAttribute('kind'),target=target,**kwargs)
-        return None
-    
-    #~ Translate:
-    #~   <sectiondef kind="public-type">...</sectiondef>
-    def _translate_sectiondef_public_type( self, sectiondef, target=None, **kwargs ):
-        return self._translate_sectiondef_x_(sectiondef,target=target,**kwargs)
-    
-    #~ Translate:
-    #~   <sectiondef kind="public-sttrib">...</sectiondef>
-    def _translate_sectiondef_public_attrib( self, sectiondef, target=None, **kwargs):
-        return self._translate_sectiondef_x_(sectiondef,target=target,**kwargs)
-    
-    #~ Translate:
-    #~   <sectiondef kind="?-func">...</sectiondef>
-    #~ All the various function group translations end up here for which
-    #~ they are translated into:
-    #~   <method-group name="?">
-    #~   ...
-    #~   </method-group>
-    def _translate_sectiondef_func_( self, sectiondef, name='functions', target=None, **kwargs ):
-        members = target.appendChild(self._createNode('method-group',name=name))
-        for n in sectiondef.childNodes:
-            if hasattr(n,'getAttribute'):
-                self._translateNode(n,n.getAttribute('kind'),target=members,**kwargs)
-        return members
-    
-    #~ Translate:
-    #~   <sectiondef kind="public-func">...</sectiondef>
-    def _translate_sectiondef_public_func( self, sectiondef, target=None, **kwargs ):
-        return self._translate_sectiondef_func_(sectiondef,
-            name='public member functions',target=target,**kwargs)
-    
-    #~ Translate:
-    #~   <sectiondef kind="public-static-func">...</sectiondef>
-    def _translate_sectiondef_public_static_func( self, sectiondef, target=None, **kwargs):
-        return self._translate_sectiondef_func_(sectiondef,
-            name='public static functions',target=target,**kwargs)
-    
-    #~ Translate:
-    #~   <sectiondef kind="protected-func">...</sectiondef>
-    def _translate_sectiondef_protected_func( self, sectiondef, target=None, **kwargs ):
-        return self._translate_sectiondef_func_(sectiondef,
-            name='protected member functions',target=target,**kwargs)
-    
-    #~ Translate:
-    #~   <sectiondef kind="private-static-func">...</sectiondef>
-    def _translate_sectiondef_private_static_func( self, sectiondef, target=None, **kwargs):
-        return self._translate_sectiondef_func_(sectiondef,
-            name='private static functions',target=target,**kwargs)
-    
-    #~ Translate:
-    #~   <sectiondef kind="public-func">...</sectiondef>
-    def _translate_sectiondef_private_func( self, sectiondef, target=None, **kwargs ):
-        return self._translate_sectiondef_func_(sectiondef,
-            name='private member functions',target=target,**kwargs)
-
-    #~ Translate:
-    #~   <sectiondef kind="user-defined"><header>...</header>...</sectiondef>
-    def _translate_sectiondef_user_defined( self, sectiondef, target=None, **kwargs ):
-        return self._translate_sectiondef_func_(sectiondef,
-            name=self._getChildData('header', root=sectiondef),target=target,**kwargs)
-    
-    #~ Translate:
-    #~   <memberdef kind="typedef" id="?">
-    #~     <name>...</name>
-    #~   </memberdef>
-    #~ To:
-    #~   <typedef id="?" name="?">
-    #~     <type>...</type>
-    #~   </typedef>
-    def _translate_memberdef_typedef( self, memberdef, target=None, scope=None, **kwargs ):
-        self._setID(memberdef.getAttribute('id'),
-            scope+'::'+self._getChildData('name',root=memberdef))
-        typedef = target.appendChild(self._createNode('typedef',
-            id=memberdef.getAttribute('id'),
-            name=self._getChildData('name',root=memberdef)))
-        typedef_type = typedef.appendChild(self._createNode('type'))
-        self._translate_type(self._getChild('type',root=memberdef),target=typedef_type)
-        return typedef
-    
-    #~ Translate:
-    #~   <memberdef kind="function" id="?" const="?" static="?" explicit="?" inline="?">
-    #~     <name>...</name>
-    #~   </memberdef>
-    #~ To:
-    #~   <method name="?" cv="?" specifiers="?">
-    #~     ...
-    #~   </method>
-    def _translate_memberdef_function( self, memberdef, target=None, scope=None, **kwargs ):
-        name = self._getChildData('name',root=memberdef)
-        self._setID(memberdef.getAttribute('id'),scope+'::'+name)
-        ## Check if we have some specific kind of method.
-        if name == scope.split('::')[-1]:
-            kind = 'constructor'
-            target = target.parentNode
-        elif name == '~'+scope.split('::')[-1]:
-            kind = 'destructor'
-            target = target.parentNode
-        elif name == 'operator=':
-            kind = 'copy-assignment'
-            target = target.parentNode
-        else:
-            kind = 'method'
-        method = target.appendChild(self._createNode(kind,
-            # id=memberdef.getAttribute('id'),
-            name=name,
-            cv=' '.join([
-                if_attribute(memberdef,'const','const','').strip()
-                ]),
-            specifiers=' '.join([
-                if_attribute(memberdef,'static','static',''),
-                if_attribute(memberdef,'explicit','explicit',''),
-                if_attribute(memberdef,'inline','inline','')
-                ]).strip()
-            ))
-        ## We iterate the children to translate each part of the function.
-        for n in memberdef.childNodes:
-            self._translateNode(memberdef,'function',n,target=method)
-        return method
-    
-    #~ Translate:
-    #~   <memberdef kind="function"...><templateparamlist>...</templateparamlist></memberdef>
-    def _translate_memberdef_function_templateparamlist(
-        self, templateparamlist, target=None, **kwargs ):
-        return self._translate_templateparamlist(templateparamlist,target=target,**kwargs)
-    
-    #~ Translate:
-    #~   <memberdef kind="function"...><type>...</type></memberdef>
-    #~ To:
-    #~   ...<type>?</type>
-    def _translate_memberdef_function_type( self, resultType, target=None, **kwargs ):
-        methodType = self._createNode('type')
-        self._translate_type(resultType,target=methodType)
-        if methodType.hasChildNodes():
-            target.appendChild(methodType)
-        return methodType
-    
-    #~ Translate:
-    #~   <memberdef kind="function"...><briefdescription>...</briefdescription></memberdef>
-    def _translate_memberdef_function_briefdescription( self, description, target=None, **kwargs ):
-        result = self._translateDescription(description,target=target,**kwargs)
-        ## For functions if we translate the brief docs to the purpose they end up
-        ## right above the regular description. And since we just added the brief to that
-        ## on the previous line, don't bother with the repetition.
-        # result = self._translateDescription(description,target=target,tag='purpose',**kwargs)
-        return result
-    
-    #~ Translate:
-    #~   <memberdef kind="function"...><detaileddescription>...</detaileddescription></memberdef>
-    def _translate_memberdef_function_detaileddescription( self, description, target=None, **kwargs ):
-        return self._translateDescription(description,target=target,**kwargs)
-    
-    #~ Translate:
-    #~   <memberdef kind="function"...><inbodydescription>...</inbodydescription></memberdef>
-    def _translate_memberdef_function_inbodydescription( self, description, target=None, **kwargs ):
-        return self._translateDescription(description,target=target,**kwargs)
-    
-    #~ Translate:
-    #~   <memberdef kind="function"...><param>...</param></memberdef>
-    def _translate_memberdef_function_param( self, param, target=None, **kwargs ):
-        return self._translate_param(param,target=target,**kwargs)
-    
-    #~ Translate:
-    #~   <memberdef kind="variable" id="?">
-    #~     <name>...</name>
-    #~     <type>...</type>
-    #~   </memberdef>
-    #~ To:
-    #~   <data-member id="?" name="?">
-    #~     <type>...</type>
-    #~   </data-member>
-    def _translate_memberdef_variable( self, memberdef, target=None, scope=None, **kwargs ):
-        self._setID(memberdef.getAttribute('id'),
-            scope+'::'+self._getChildData('name',root=memberdef))
-        data_member = target.appendChild(self._createNode('data-member',
-            id=memberdef.getAttribute('id'),
-            name=self._getChildData('name',root=memberdef)))
-        data_member_type = data_member.appendChild(self._createNode('type'))
-        self._translate_type(self._getChild('type',root=memberdef),target=data_member_type)
-    
-    #~ Translate:
-    #~   <memberdef kind="enum" id="?">
-    #~     <name>...</name>
-    #~     ...
-    #~   </memberdef>
-    #~ To:
-    #~   <enum id="?" name="?">
-    #~     ...
-    #~   </enum>
-    def _translate_memberdef_enum( self, memberdef, target=None, scope=None, **kwargs ):
-        self._setID(memberdef.getAttribute('id'),
-            scope+'::'+self._getChildData('name',root=memberdef))
-        enum = target.appendChild(self._createNode('enum',
-            id=memberdef.getAttribute('id'),
-            name=self._getChildData('name',root=memberdef)))
-        for n in memberdef.childNodes:
-            self._translateNode(memberdef,'enum',n,target=enum,scope=scope,**kwargs)
-        return enum
-    
-    #~ Translate:
-    #~   <memberdef kind="enum"...>
-    #~     <enumvalue id="?">
-    #~       <name>...</name>
-    #~       <initializer>...</initializer>
-    #~     </enumvalue>
-    #~   </memberdef>
-    #~ To:
-    #~   <enumvalue id="?" name="?">
-    #~     <default>...</default>
-    #~   </enumvalue>
-    def _translate_memberdef_enum_enumvalue( self, enumvalue, target=None, scope=None, **kwargs ):
-        self._setID(enumvalue.getAttribute('id'),
-            scope+'::'+self._getChildData('name',root=enumvalue))
-        value = target.appendChild(self._createNode('enumvalue',
-            id=enumvalue.getAttribute('id'),
-            name=self._getChildData('name',root=enumvalue)))
-        initializer = self._getChild('initializer',root=enumvalue)
-        if initializer:
-            self._translateChildren(initializer,
-                target=target.appendChild(self._createNode('default')))
-        return value
-    
-    #~ Translate:
-    #~   <param>
-    #~     <type>...</type>
-    #~     <declname>...</declname>
-    #~     <defval>...</defval>
-    #~   </param>
-    #~ To:
-    #~   <parameter name="?">
-    #~     <paramtype>...</paramtype>
-    #~     ...
-    #~   </parameter>
-    def _translate_param( self, param, target=None, **kwargs):
-        parameter = target.appendChild(self._createNode('parameter',
-            name=self._getChildData('declname',root=param)))
-        paramtype = parameter.appendChild(self._createNode('paramtype'))
-        self._translate_type(self._getChild('type',root=param),target=paramtype)
-        defval = self._getChild('defval',root=param)
-        if defval:
-            self._translateChildren(self._getChild('defval',root=param),target=parameter)
-        return parameter
-    
-    #~ Translate:
-    #~   <ref kindref="?" ...>...</ref>
-    def _translate_ref( self, ref, **kwargs ):
-        return self._translateNode(ref,ref.getAttribute('kindref'))
-    
-    #~ Translate:
-    #~   <ref refid="?" kindref="compound">...</ref>
-    #~ To:
-    #~   <link linkend="?"><classname>...</classname></link>
-    def _translate_ref_compound( self, ref, **kwargs ):
-        result = self._createNode('link',linkend=ref.getAttribute('refid'))
-        classname = result.appendChild(self._createNode('classname'))
-        self._translateChildren(ref,target=classname)
-        return result
-    
-    #~ Translate:
-    #~   <ref refid="?" kindref="member">...</ref>
-    #~ To:
-    #~   <link linkend="?">...</link>
-    def _translate_ref_member( self, ref, **kwargs ):
-        result = self._createNode('link',linkend=ref.getAttribute('refid'))
-        self._translateChildren(ref,target=result)
-        return result
-    
-    #~ Translate:
-    #~   <type>...</type>
-    def _translate_type( self, type, target=None, **kwargs ):
-        result = self._translateChildren(type,target=target,**kwargs)
-        #~ Filter types to clean up various readability problems, most notably
-        #~ with really long types.
-        xml = target.toxml('utf-8');
-        if (
-            xml.startswith('<type>boost::mpl::') or
-            xml.startswith('<type>BOOST_PP_') or
-            re.match('<type>boost::(lazy_)?(enable|disable)_if',xml)
-            ):
-            while target.firstChild:
-                target.removeChild(target.firstChild)
-            target.appendChild(self._createText('emphasis','unspecified'))
-        return result
-    
-    def _getChild( self, tag = None, id = None, name = None, root = None ):
-        if not root:
-            root = self.boostbook.documentElement
-        for n in root.childNodes:
-            found = True
-            if tag and found:
-                found = found and tag == n.nodeName
-            if id and found:
-                if n.hasAttribute('id'):
-                    found = found and n.getAttribute('id') == id
-                else:
-                    found = found and n.hasAttribute('id') and n.getAttribute('id') == id
-            if name and found:
-                found = found and n.hasAttribute('name') and n.getAttribute('name') == name
-            if found:
-                #~ print '--|', n
-                return n
-        return None
-    
-    def _getChildData( self, tag, **kwargs ):
-        return self._getData(self._getChild(tag,**kwargs),**kwargs)
-    
-    def _getData( self, node, **kwargs ):
-        if node:
-            text = self._getChild('#text',root=node)
-            if text:
-                return text.data.strip()
-        return ''
-    
-    def _cppName( self, type ):
-        parts = re.search('^([^<]+)[<]?(.*)[>]?$',type.strip().strip(':'))
-        result = {
-            'compoundname' : parts.group(1),
-            'namespace' : parts.group(1).split('::')[0:-1],
-            'name' : parts.group(1).split('::')[-1],
-            'specialization' : parts.group(2)
-            }
-        if result['namespace'] and len(result['namespace']) > 0:
-            namespace = '::'.join(result['namespace'])
-            while (
-                len(result['namespace']) > 0 and (
-                    not self.symbols.has_key(namespace) or
-                    self.symbols[namespace]['kind'] != 'namespace')
-                ):
-                result['name'] = result['namespace'].pop()+'::'+result['name']
-                namespace = '::'.join(result['namespace'])
-        return result
-    
-    def _createNode( self, tag, **kwargs ):
-        result = self.boostbook.createElement(tag)
-        for k in kwargs.keys():
-            if kwargs[k] != '':
-                if k == 'id':
-                    result.setAttribute('id',kwargs[k])
-                else:
-                    result.setAttribute(k,kwargs[k])
-        return result
-    
-    def _createText( self, tag, data, **kwargs ):
-        result = self._createNode(tag,**kwargs)
-        data = data.strip()
-        if len(data) > 0:
-            result.appendChild(self.boostbook.createTextNode(data))
-        return result
-
-
-def main( xmldir=None, output=None, id=None, title=None, index=False ):
-    #~ print '--- main: xmldir = %s, output = %s' % (xmldir,output)
-    
-    input = glob.glob( os.path.abspath( os.path.join( xmldir, "*.xml" ) ) )
-    input.sort
-    translator = Doxygen2BoostBook(id=id, title=title, index=index)
-    #~ Feed in the namespaces first to build up the set of namespaces
-    #~ and definitions so that lookup is unambiguous when reading in the definitions.
-    namespace_files = filter(
-        lambda x:
-            os.path.basename(x).startswith('namespace'),
-        input)
-    decl_files = filter(
-        lambda x:
-            not os.path.basename(x).startswith('namespace') and not os.path.basename(x).startswith('_'),
-        input)
-    for dox in namespace_files:
-        #~ print '--|',os.path.basename(dox)
-        translator.addDox(xml.dom.minidom.parse(dox))
-    for dox in decl_files:
-        #~ print '--|',os.path.basename(dox)
-        translator.addDox(xml.dom.minidom.parse(dox))
-    
-    if output:
-        output = open(output,'w')
-    else:
-        output = sys.stdout
-    if output:
-        output.write(translator.tostring())
-
-
-main( **get_args() )
diff --git a/jam-files/boost-build/tools/doxygen-config.jam b/jam-files/boost-build/tools/doxygen-config.jam
deleted file mode 100644
index 2cd2ccae..00000000
--- a/jam-files/boost-build/tools/doxygen-config.jam
+++ /dev/null
@@ -1,11 +0,0 @@
-#~ Copyright 2005, 2006 Rene Rivera.
-#~ Distributed under the Boost Software License, Version 1.0.
-#~ (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-# Automatic configuration for Doxygen tools. To use, just import this module.
-
-import toolset : using ;
-
-ECHO "warning: doxygen-config.jam is deprecated. Use 'using doxygen ;' instead." ;
-
-using doxygen ;
diff --git a/jam-files/boost-build/tools/doxygen.jam b/jam-files/boost-build/tools/doxygen.jam
deleted file mode 100644
index 8394848d..00000000
--- a/jam-files/boost-build/tools/doxygen.jam
+++ /dev/null
@@ -1,776 +0,0 @@
-# Copyright 2003, 2004 Douglas Gregor
-# Copyright 2003, 2004, 2005 Vladimir Prus
-# Copyright 2006 Rene Rivera
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-# This module defines rules to handle generation of various outputs from source
-# files documented with doxygen comments. The supported transformations are:
-#
-# * Source -> Doxygen XML -> BoostBook XML
-# * Source -> Doxygen HTML
-#
-# The type of transformation is selected based on the target requested. For
-# BoostBook XML, the default, specifying a target with an ".xml" suffix, or an
-# empty suffix, will produce a <target>.xml and <target>.boostbook. For Doxygen
-# HTML specifying a target with an ".html" suffix will produce a directory
-# <target> with the Doxygen html files, and a <target>.html file redirecting to
-# that directory.
-
-import "class" : new ;
-import targets ;
-import feature ;
-import property ;
-import generators ;
-import boostbook ;
-import type ;
-import path ;
-import print ;
-import regex ;
-import stage ;
-import project ;
-import xsltproc ;
-import make ;
-import os ;
-import toolset : flags ;
-import alias ;
-import common ;
-import modules ;
-import project ;
-import utility ;
-import errors ;
-
-
-# Use to specify extra configuration paramters. These get translated
-# into a doxyfile which configures the building of the docs.
-feature.feature doxygen:param : : free ;
-
-# Specify the "<xsl:param>boost.doxygen.header.prefix" XSLT option.
-feature.feature prefix : : free ;
-
-# Specify the "<xsl:param>boost.doxygen.reftitle" XSLT option.
-feature.feature reftitle : : free ;
-
-# Which processor to use for various translations from Doxygen.
-feature.feature doxygen.processor : xsltproc doxproc : propagated implicit ;
-
-# To generate, or not, index sections.
-feature.feature doxygen.doxproc.index : no yes : propagated incidental ;
-
-# The ID for the resulting BoostBook reference section.
-feature.feature doxygen.doxproc.id : : free ;
-
-# The title for the resulting BoostBook reference section.
-feature.feature doxygen.doxproc.title : : free ;
-
-# Location for images when generating XML
-feature.feature doxygen:xml-imagedir : : free ;
-
-# Indicates whether the entire directory should be deleted
-feature.feature doxygen.rmdir : off on : optional incidental ;
-
-# Doxygen configuration input file.
-type.register DOXYFILE : doxyfile ;
-
-# Doxygen XML multi-file output.
-type.register DOXYGEN_XML_MULTIFILE : xml-dir : XML ;
-
-# Doxygen XML coallesed output.
-type.register DOXYGEN_XML : doxygen : XML ;
-
-# Doxygen HTML multifile directory.
-type.register DOXYGEN_HTML_MULTIFILE : html-dir : HTML ;
-
-# Redirection HTML file to HTML multifile directory.
-type.register DOXYGEN_HTML : : HTML ;
-
-type.register DOXYGEN_XML_IMAGES : doxygen-xml-images ;
-
-# Initialize the Doxygen module. Parameters are:
-#   name: the name of the 'doxygen' executable. If not specified, the name
-#         'doxygen' will be used
-#
-rule init ( name ? )
-{
-    if ! $(.initialized)
-    {
-        .initialized = true ;
-
-        .doxproc = [ modules.binding $(__name__) ] ;
-        .doxproc = $(.doxproc:D)/doxproc.py ;
-
-        generators.register-composing doxygen.headers-to-doxyfile
-            : H HPP CPP : DOXYFILE ;
-        generators.register-standard doxygen.run
-            : DOXYFILE : DOXYGEN_XML_MULTIFILE ;
-        generators.register-standard doxygen.xml-dir-to-boostbook
-            : DOXYGEN_XML_MULTIFILE : BOOSTBOOK : <doxygen.processor>doxproc ;
-        generators.register-standard doxygen.xml-to-boostbook
-            : DOXYGEN_XML : BOOSTBOOK : <doxygen.processor>xsltproc ;
-        generators.register-standard doxygen.collect
-            : DOXYGEN_XML_MULTIFILE : DOXYGEN_XML ;
-        generators.register-standard doxygen.run
-            : DOXYFILE : DOXYGEN_HTML_MULTIFILE ;
-        generators.register-standard doxygen.html-redirect
-            : DOXYGEN_HTML_MULTIFILE : DOXYGEN_HTML ;
-        generators.register-standard doxygen.copy-latex-pngs
-            : DOXYGEN_HTML : DOXYGEN_XML_IMAGES ;
-
-        IMPORT $(__name__) : doxygen : : doxygen ;
-    }
-
-    if $(name)
-    {
-        modify-config ;
-        .doxygen = $(name) ;
-        check-doxygen ;
-    }
-
-    if ! $(.doxygen)
-    {
-        check-doxygen ;
-    }
-}
-
-rule freeze-config ( )
-{
-    if ! $(.initialized)
-    {
-        errors.user-error "doxygen must be initialized before it can be used." ;
-    }
-    if ! $(.config-frozen)
-    {
-        .config-frozen = true ;
-
-        if [ .is-cygwin ]
-        {
-            .is-cygwin = true ;
-        }
-    }
-}
-
-rule modify-config ( )
-{
-    if $(.config-frozen)
-    {
-        errors.user-error "Cannot change doxygen after it has been used." ;
-    }
-}
-
-rule check-doxygen ( )
-{
-    if --debug-configuration in [ modules.peek : ARGV ]
-    {
-        ECHO "notice:" using doxygen ":" $(.doxygen) ;
-    }
-    local extra-paths ;
-    if [ os.name ] = NT
-    {
-        local ProgramFiles = [ modules.peek : ProgramFiles ] ;
-        if $(ProgramFiles)
-        {
-            extra-paths = "$(ProgramFiles:J= )" ;
-        }
-        else
-        {
-            extra-paths = "C:\\Program Files" ;
-        }
-    }
-    .doxygen = [ common.get-invocation-command doxygen :
-                 doxygen : $(.doxygen) : $(extra-paths) ] ;
-}
-
-rule name ( )
-{
-    freeze-config ;
-    return $(.doxygen) ;
-}
-
-rule .is-cygwin ( )
-{
-    if [ os.on-windows ]
-    {
-        local file = [ path.make [ modules.binding $(__name__) ] ] ;
-        local dir = [ path.native
-                      [ path.join [ path.parent $(file) ] doxygen ] ] ;
-        local command =
-         "cd \"$(dir)\" && \"$(.doxygen)\" windows-paths-check.doxyfile 2>&1" ;
-        result = [ SHELL $(command) ] ;
-        if [ MATCH "(Parsing file /)" : $(result) ]
-        {
-            return true ;
-        }
-    }
-}
-
-# Runs Doxygen on the given Doxygen configuration file (the source) to generate
-# the Doxygen files. The output is dumped according to the settings in the
-# Doxygen configuration file, not according to the target! Because of this, we
-# essentially "touch" the target file, in effect making it look like we have
-# really written something useful to it. Anyone that uses this action must deal
-# with this behavior.
-#
-actions doxygen-action
-{
-    $(RM) "$(*.XML)" & "$(NAME:E=doxygen)" "$(>)" && echo "Stamped" > "$(<)"
-}
-
-
-# Runs the Python doxproc XML processor.
-#
-actions doxproc
-{
-    python "$(DOXPROC)" "--xmldir=$(>)" "--output=$(<)" "$(OPTIONS)" "--id=$(ID)" "--title=$(TITLE)"
-}
-
-
-rule translate-path ( path )
-{
-    freeze-config ;
-    if [ os.on-windows ]
-    {
-        if [ os.name ] = CYGWIN
-        {
-            if $(.is-cygwin)
-            {
-                return $(path) ;
-            }
-            else
-            {
-                return $(path:W) ;
-            }
-        }
-        else
-        {
-            if $(.is-cygwin)
-            {
-                match = [ MATCH ^(.):(.*) : $(path) ] ;
-                if $(match)
-                {
-                    return /cygdrive/$(match[1])$(match[2]:T) ;
-                }
-                else
-                {
-                    return $(path:T) ;
-                }
-            }
-            else
-            {
-                return $(path) ;
-            }
-        }
-    }
-    else
-    {
-        return $(path) ;
-    }
-}
-
-
-# Generates a doxygen configuration file (doxyfile) given a set of C++ sources
-# and a property list that may contain <doxygen:param> features.
-#
-rule headers-to-doxyfile ( target : sources * : properties * )
-{
-    local text "# Generated by Boost.Build version 2" ;
-
-    local output-dir ;
-
-    # Translate <doxygen:param> into command line flags.
-    for local param in [ feature.get-values <doxygen:param> : $(properties) ]
-    {
-        local namevalue = [ regex.match ([^=]*)=(.*) : $(param) ] ;
-        if $(namevalue[1]) = OUTPUT_DIRECTORY
-        {
-            output-dir = [ translate-path
-                           [ utility.unquote $(namevalue[2]) ] ] ;
-            text += "OUTPUT_DIRECTORY = \"$(output-dir)\"" ;
-        }
-        else
-        {
-            text += "$(namevalue[1]) = $(namevalue[2])" ;
-        }
-    }
-
-    if ! $(output-dir)
-    {
-        output-dir = [ translate-path [ on $(target) return $(LOCATE) ] ] ;
-        text += "OUTPUT_DIRECTORY = \"$(output-dir)\"" ;
-    }
-
-    local headers = ;
-    for local header in $(sources:G=)
-    {
-        header = [ translate-path $(header) ] ;
-        headers += \"$(header)\" ;
-    }
-
-    # Doxygen generates LaTex by default. So disable it unconditionally, or at
-    # least until someone needs, and hence writes support for, LaTex output.
-    text += "GENERATE_LATEX = NO" ;
-    text += "INPUT = $(headers:J= )" ;
-    print.output $(target) plain ;
-    print.text $(text) : true ;
-}
-
-
-# Run Doxygen. See doxygen-action for a description of the strange properties of
-# this rule.
-#
-rule run ( target : source : properties * )
-{
-    freeze-config ;
-    if <doxygen.rmdir>on in $(properties)
-    {
-        local output-dir =
-            [ path.make
-                [ MATCH <doxygen:param>OUTPUT_DIRECTORY=\"?([^\"]*) :
-                  $(properties) ] ] ;
-        local html-dir =
-            [ path.make
-                [ MATCH <doxygen:param>HTML_OUTPUT=(.*) :
-                  $(properties) ] ] ;
-        if $(output-dir) && $(html-dir) &&
-            [ path.glob $(output-dir) : $(html-dir) ]
-        {
-            HTMLDIR on $(target) =
-                [ path.native [ path.join $(output-dir) $(html-dir) ] ] ;
-            rm-htmldir $(target) ;
-        }
-    }
-    doxygen-action $(target) : $(source) ;
-    NAME on $(target) = $(.doxygen) ;
-    RM on $(target) = [ modules.peek common : RM ] ;
-    *.XML on $(target) =
-        [ path.native
-            [ path.join
-                [ path.make [ on $(target) return $(LOCATE) ] ]
-                $(target:B:S=)
-                *.xml ] ] ;
-}
-
-if [ os.name ] = NT
-{
-    RMDIR = rmdir /s /q ;
-}
-else
-{
-    RMDIR = rm -rf ;
-}
-
-actions quietly rm-htmldir
-{
-    $(RMDIR) $(HTMLDIR)
-}
-
-# The rules below require Boost.Book stylesheets, so we need some code to check
-# that the boostbook module has actualy been initialized.
-#
-rule check-boostbook ( )
-{
-    if ! [ modules.peek boostbook : .initialized ]
-    {
-        ECHO "error: the boostbook module is not initialized" ;
-        ECHO "error: you've attempted to use the 'doxygen' toolset, " ;
-        ECHO "error: which requires Boost.Book," ;
-        ECHO "error: but never initialized Boost.Book." ;
-        EXIT "error: Hint: add 'using boostbook ;' to your user-config.jam" ;
-    }
-}
-
-
-# Collect the set of Doxygen XML files into a single XML source file that can be
-# handled by an XSLT processor. The source is completely ignored (see
-# doxygen-action), because this action picks up the Doxygen XML index file
-# xml/index.xml. This is because we can not teach Doxygen to act like a NORMAL
-# program and take a "-o output.xml" argument (grrrr). The target of the
-# collection will be a single Doxygen XML file.
-#
-rule collect ( target : source : properties * )
-{
-    check-boostbook ;
-    local collect-xsl-dir
-        = [ path.native [ path.join [ boostbook.xsl-dir ] doxygen collect ] ] ;
-    local source-path
-        = [ path.make [ on $(source) return $(LOCATE) ] ] ;
-    local collect-path
-        = [ path.root [ path.join $(source-path) $(source:B) ] [ path.pwd ] ] ;
-    local native-path
-        = [ path.native $(collect-path) ] ;
-    local real-source
-        = [ path.native [ path.join $(collect-path) index.xml ] ] ;
-    xsltproc.xslt $(target) : $(real-source) $(collect-xsl-dir:S=.xsl)
-        : <xsl:param>doxygen.xml.path=$(native-path) ;
-}
-
-
-# Translate Doxygen XML into BoostBook.
-#
-rule xml-to-boostbook ( target : source : properties * )
-{
-    check-boostbook ;
-    local xsl-dir = [ boostbook.xsl-dir ] ;
-    local d2b-xsl = [ path.native [ path.join [ boostbook.xsl-dir ] doxygen
-        doxygen2boostbook.xsl ] ] ;
-
-    local xslt-properties = $(properties) ;
-    for local prefix in [ feature.get-values <prefix> : $(properties) ]
-    {
-        xslt-properties += "<xsl:param>boost.doxygen.header.prefix=$(prefix)" ;
-    }
-    for local title in [ feature.get-values <reftitle> : $(properties) ]
-    {
-        xslt-properties += "<xsl:param>boost.doxygen.reftitle=$(title)" ;
-    }
-
-    xsltproc.xslt $(target) : $(source) $(d2b-xsl) : $(xslt-properties) ;
-}
-
-
-flags doxygen.xml-dir-to-boostbook OPTIONS <doxygen.doxproc.index>yes : --enable-index ;
-flags doxygen.xml-dir-to-boostbook ID <doxygen.doxproc.id> ;
-flags doxygen.xml-dir-to-boostbook TITLE <doxygen.doxproc.title> ;
-
-
-rule xml-dir-to-boostbook ( target : source : properties * )
-{
-    DOXPROC on $(target) = $(.doxproc) ;
-
-    LOCATE on $(source:S=) = [ on $(source) return $(LOCATE) ] ;
-
-    doxygen.doxproc $(target) : $(source:S=) ;
-}
-
-
-# Generate the HTML redirect to HTML dir index.html file.
-#
-rule html-redirect ( target : source : properties * )
-{
-    local uri = "$(target:B)/index.html" ;
-    print.output $(target) plain ;
-    print.text
-"<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Strict//EN\"
-    \"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd\">
-<html xmlns=\"http://www.w3.org/1999/xhtml\">
-<head>
-  <meta http-equiv=\"refresh\" content=\"0; URL=$(uri)\" />
-
-  <title></title>
-</head>
-
-<body>
-  Automatic redirection failed, please go to <a href=
-  \"$(uri)\">$(uri)</a>.
-</body>
-</html>
-"
-        : true ;
-}
-
-rule copy-latex-pngs ( target : source : requirements * )
-{
-    local directory = [ path.native
-                        [ feature.get-values <doxygen:xml-imagedir> :
-                          $(requirements) ] ] ;
-
-    local location = [ on $(target) return $(LOCATE) ] ;
-
-    local pdf-location =
-        [ path.native
-            [ path.join
-                [ path.make $(location) ]
-                [ path.make $(directory) ] ] ] ;
-    local html-location =
-        [ path.native
-            [ path.join
-                .
-                html
-                [ path.make $(directory) ] ] ] ;
-
-    common.MkDir $(pdf-location) ;
-    common.MkDir $(html-location) ;
-
-    DEPENDS $(target) : $(pdf-location) $(html-location) ;
-
-    if [ os.name ] = NT
-    {
-        CP on $(target) = copy /y ;
-        FROM on $(target) = \\*.png ;
-        TOHTML on $(target) = .\\html\\$(directory) ;
-        TOPDF on $(target) = \\$(directory) ;
-    }
-    else
-    {
-        CP on $(target) = cp ;
-        FROM on $(target) = /*.png ;
-        TOHTML on $(target) = ./html/$(directory) ;
-        TOPDF on $(target) = $(target:D)/$(directory) ;
-    }
-}
-
-actions copy-latex-pngs
-{
-    $(CP) $(>:S=)$(FROM) $(TOHTML)
-    $(CP) $(>:S=)$(FROM) $(<:D)$(TOPDF)
-    echo "Stamped" > "$(<)"
-}
-
-# building latex images for doxygen XML depends
-# on latex, dvips, and ps being in your PATH.
-# This is true for most Unix installs, but
-# not on Win32, where you will need to install
-# MkTex and Ghostscript and add these tools
-# to your path.
-
-actions check-latex
-{
-    latex -version >$(<)
-}
-
-actions check-dvips
-{
-    dvips -version >$(<)
-}
-
-if [ os.name ] = "NT"
-{
-   actions check-gs
-   {
-       gswin32c -version >$(<)
-   }
-}
-else
-{
-   actions check-gs
-   {
-       gs -version >$(<)
-   }
-}
-
-rule check-tools ( )
-{
-    if ! $(.check-tools-targets)
-    {
-        # Find the root project.
-        local root-project = [ project.current ] ;
-        root-project = [ $(root-project).project-module ] ;
-        while
-            [ project.attribute $(root-project) parent-module ] &&
-            [ project.attribute $(root-project) parent-module ] != user-config
-        {
-            root-project =
-                [ project.attribute $(root-project) parent-module ] ;
-        }
-
-        .latex.check = [ new file-target latex.check
-            :
-            : [ project.target $(root-project) ]
-            : [ new action : doxygen.check-latex ]
-            :
-            ] ;
-        .dvips.check = [ new file-target dvips.check
-            :
-            : [ project.target $(root-project) ]
-            : [ new action : doxygen.check-dvips ]
-            :
-            ] ;
-        .gs.check = [ new file-target gs.check
-            :
-            : [ project.target $(root-project) ]
-            : [ new action : doxygen.check-gs ]
-            :
-            ] ;
-        .check-tools-targets = $(.latex.check) $(.dvips.check) $(.gs.check) ;
-    }
-    return $(.check-tools-targets) ;
-}
-
-project.initialize $(__name__) ;
-project doxygen ;
-
-class doxygen-check-tools-target-class : basic-target
-{
-    import doxygen ;
-    rule construct ( name : sources * : property-set )
-    {
-        return [ property-set.empty ] [ doxygen.check-tools ] ;
-    }
-}
-
-local project = [ project.current ] ;
-
-targets.main-target-alternative
-    [ new doxygen-check-tools-target-class check-tools : $(project)
-        : [ targets.main-target-sources : check-tools : no-renaming ]
-        : [ targets.main-target-requirements : $(project) ]
-        : [ targets.main-target-default-build : $(project) ]
-        : [ targets.main-target-usage-requirements : $(project) ]
-    ] ;
-
-# User-level rule to generate BoostBook XML from a set of headers via Doxygen.
-#
-rule doxygen ( target : sources * : requirements * : default-build * : usage-requirements * )
-{
-    freeze-config ;
-    local project = [ project.current ] ;
-
-    if $(target:S) = .html
-    {
-        # Build an HTML directory from the sources.
-        local html-location = [ feature.get-values <location> : $(requirements) ] ;
-        local output-dir ;
-        if [ $(project).get build-dir ] 
-        {
-            # Explicitly specified build dir. Add html at the end.
-            output-dir = [ path.join [ $(project).build-dir ] $(html-location:E=html) ] ;
-        }
-        else
-        {
-            # Trim 'bin' from implicit build dir, for no other reason that backward
-            # compatibility.
-            output-dir = [ path.join [ path.parent [ $(project).build-dir ] ] 
-              $(html-location:E=html) ] ;
-        }
-        output-dir = [ path.root $(output-dir) [ path.pwd ] ] ;        
-        local output-dir-native = [ path.native $(output-dir) ] ;
-        requirements = [ property.change $(requirements) : <location> ] ;
-
-        ## The doxygen configuration file.
-        targets.main-target-alternative
-            [ new typed-target $(target:S=.tag) : $(project) : DOXYFILE
-                : [ targets.main-target-sources $(sources) : $(target:S=.tag) ]
-                : [ targets.main-target-requirements $(requirements)
-                    <doxygen:param>GENERATE_HTML=YES
-                    <doxygen:param>GENERATE_XML=NO
-                    <doxygen:param>"OUTPUT_DIRECTORY=\"$(output-dir-native)\""
-                    <doxygen:param>HTML_OUTPUT=$(target:B)
-                    : $(project) ]
-                : [ targets.main-target-default-build $(default-build) : $(project) ]
-            ] ;
-        $(project).mark-target-as-explicit $(target:S=.tag) ;
-
-        ## The html directory to generate by running doxygen.
-        targets.main-target-alternative
-            [ new typed-target $(target:S=.dir) : $(project) : DOXYGEN_HTML_MULTIFILE
-                : $(target:S=.tag)
-                : [ targets.main-target-requirements $(requirements)
-                    <doxygen:param>"OUTPUT_DIRECTORY=\"$(output-dir-native)\""
-                    <doxygen:param>HTML_OUTPUT=$(target:B)
-                    : $(project) ]
-                : [ targets.main-target-default-build $(default-build) : $(project) ]
-                ] ;
-        $(project).mark-target-as-explicit $(target:S=.dir) ;
-
-        ## The redirect html file into the generated html.
-        targets.main-target-alternative
-            [ new typed-target $(target) : $(project) : DOXYGEN_HTML
-                : $(target:S=.dir)
-                : [ targets.main-target-requirements $(requirements)
-                    <location>$(output-dir)
-                    : $(project) ]
-                : [ targets.main-target-default-build $(default-build) : $(project) ]
-                ] ;
-    }
-    else
-    {
-        # Build a BoostBook XML file from the sources.
-        local location-xml = [ feature.get-values <location> : $(requirements) ] ;
-        requirements = [ property.change $(requirements) : <location> ] ;
-        local target-xml = $(target:B=$(target:B)-xml) ;
-
-        # Check whether we need to build images
-        local images-location =
-            [ feature.get-values <doxygen:xml-imagedir> : $(requirements) ] ;
-        if $(images-location)
-        {
-            doxygen $(target).doxygen-xml-images.html : $(sources)
-                : $(requirements)
-                  <doxygen.rmdir>on
-                  <doxygen:param>QUIET=YES
-                  <doxygen:param>WARNINGS=NO
-                  <doxygen:param>WARN_IF_UNDOCUMENTED=NO
-                  <dependency>/doxygen//check-tools ;
-            $(project).mark-target-as-explicit
-                $(target).doxygen-xml-images.html ;
-
-            targets.main-target-alternative
-                [ new typed-target $(target).doxygen-xml-images
-                    : $(project) : DOXYGEN_XML_IMAGES
-                    : $(target).doxygen-xml-images.html
-                    : [ targets.main-target-requirements $(requirements)
-                        : $(project) ]
-                    : [ targets.main-target-default-build $(default-build)
-                        : $(project) ]
-                ] ;
-
-            $(project).mark-target-as-explicit
-                $(target).doxygen-xml-images ;
-
-            if ! [ regex.match "^(.*/)$" : $(images-location) ]
-            {
-                images-location = $(images-location)/ ;
-            }
-
-            requirements +=
-                <dependency>$(target).doxygen-xml-images
-                <xsl:param>boost.doxygen.formuladir=$(images-location) ;
-        }
-
-        ## The doxygen configuration file.
-        targets.main-target-alternative
-            [ new typed-target $(target-xml:S=.tag) : $(project) : DOXYFILE
-                : [ targets.main-target-sources $(sources) : $(target-xml:S=.tag) ]
-                : [ targets.main-target-requirements $(requirements)
-                    <doxygen:param>GENERATE_HTML=NO
-                    <doxygen:param>GENERATE_XML=YES
-                    <doxygen:param>XML_OUTPUT=$(target-xml)
-                    : $(project) ]
-                : [ targets.main-target-default-build $(default-build) : $(project) ]
-            ] ;
-        $(project).mark-target-as-explicit $(target-xml:S=.tag) ;
-
-        ## The Doxygen XML directory of the processed source files.
-        targets.main-target-alternative
-            [ new typed-target $(target-xml:S=.dir) : $(project) : DOXYGEN_XML_MULTIFILE
-                : $(target-xml:S=.tag)
-                : [ targets.main-target-requirements $(requirements)
-                    : $(project) ]
-                : [ targets.main-target-default-build $(default-build) : $(project) ]
-            ] ;
-        $(project).mark-target-as-explicit $(target-xml:S=.dir) ;
-
-        ## The resulting BoostBook file is generated by the processor tool. The
-        ## tool can be either the xsltproc plus accompanying XSL scripts. Or it
-        ## can be the python doxproc.py script.
-        targets.main-target-alternative
-            [ new typed-target $(target-xml) : $(project) : BOOSTBOOK
-                :  $(target-xml:S=.dir)
-                : [ targets.main-target-requirements $(requirements)
-                    : $(project) ]
-                : [ targets.main-target-default-build $(default-build) : $(project) ]
-            ] ;
-        $(project).mark-target-as-explicit $(target-xml) ;
-
-        targets.main-target-alternative
-            [ new install-target-class $(target:S=.xml) : $(project)
-                : $(target-xml)
-                : [ targets.main-target-requirements $(requirements)
-                    <location>$(location-xml:E=.)
-                    <name>$(target:S=.xml)
-                    : $(project) ]
-                : [ targets.main-target-default-build $(default-build) : $(project) ]
-            ] ;
-        $(project).mark-target-as-explicit $(target:S=.xml) ;
-
-        targets.main-target-alternative
-            [ new alias-target-class $(target) : $(project)
-                :
-                : [ targets.main-target-requirements $(requirements)
-                    : $(project) ]
-                : [ targets.main-target-default-build $(default-build) : $(project) ]
-                : [ targets.main-target-usage-requirements $(usage-requirements)
-                    <dependency>$(target:S=.xml)
-                    : $(project) ]
-            ] ;
-    }
-}
diff --git a/jam-files/boost-build/tools/doxygen/windows-paths-check.doxyfile b/jam-files/boost-build/tools/doxygen/windows-paths-check.doxyfile
deleted file mode 100644
index 9b969df9..00000000
--- a/jam-files/boost-build/tools/doxygen/windows-paths-check.doxyfile
+++ /dev/null
@@ -1,3 +0,0 @@
-INPUT = windows-paths-check.hpp
-GENERATE_HTML = NO
-GENERATE_LATEX = NO
diff --git a/jam-files/boost-build/tools/doxygen/windows-paths-check.hpp b/jam-files/boost-build/tools/doxygen/windows-paths-check.hpp
deleted file mode 100644
index e69de29b..00000000
--- a/jam-files/boost-build/tools/doxygen/windows-paths-check.hpp
+++ /dev/null
diff --git a/jam-files/boost-build/tools/fop.jam b/jam-files/boost-build/tools/fop.jam
deleted file mode 100644
index c24b8725..00000000
--- a/jam-files/boost-build/tools/fop.jam
+++ /dev/null
@@ -1,69 +0,0 @@
-#  Copyright (C) 2003-2004 Doug Gregor and Dave Abrahams. Distributed
-# under the Boost Software License, Version 1.0. (See accompanying
-# file LICENSE_1_0.txt or copy at
-# http://www.boost.org/LICENSE_1_0.txt)
-#
-#  This module defines rules to handle generation of PDF and
-#  PostScript files from XSL Formatting Objects via Apache FOP
-
-import generators ;
-import common ;
-import boostbook ;
-
-generators.register-standard fop.render.pdf : FO : PDF ;
-generators.register-standard fop.render.ps : FO : PS ;
-
-# Initializes the fop toolset.
-#
-rule init ( fop-command ? : java-home ? : java ? )
-{
-    local has-command = $(.has-command) ;
-
-    if $(fop-command)
-    {
-        .has-command = true ;
-    }
-
-    if $(fop-command) || ! $(has-command)
-    {
-        fop-command = [ common.get-invocation-command fop : fop : $(fop-command) 
-          : [ modules.peek : FOP_DIR ] ] ;
-    }
-    
-    if $(fop-command)
-    {
-        .FOP_COMMAND = $(fop-command) ;
-    }
-
-    if $(java-home) || $(java)
-    {
-        .FOP_SETUP = ;
-
-    
-        # JAVA_HOME is the location that java was installed to.
-    
-        if $(java-home)
-        {
-            .FOP_SETUP += [ common.variable-setting-command JAVA_HOME : $(java-home) ] ;
-        }
-
-        # JAVACMD is the location that of the java executable, useful for a
-        # non-standard java installation, where the executable isn't at
-        # $JAVA_HOME/bin/java.
-    
-        if $(java)
-        {
-            .FOP_SETUP += [ common.variable-setting-command JAVACMD : $(java) ] ;
-        }
-    }
-}
-
-actions render.pdf
-{
-    $(.FOP_SETUP) $(.FOP_COMMAND:E=fop) $(>) $(<)
-}
-
-actions render.ps
-{
-    $(.FOP_SETUP) $(.FOP_COMMAND:E=fop) $(>) -ps $(<)
-}
diff --git a/jam-files/boost-build/tools/fortran.jam b/jam-files/boost-build/tools/fortran.jam
deleted file mode 100644
index 37665825..00000000
--- a/jam-files/boost-build/tools/fortran.jam
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright (C) 2004 Toon Knapen
-#
-#  Use, modification and distribution is subject to the Boost Software
-#  License Version 1.0. (See accompanying file LICENSE_1_0.txt or
-#  http://www.boost.org/LICENSE_1_0.txt)
-
-#
-# This file contains common settings for all fortran tools
-#
-
-import "class" : new ;
-import feature : feature ;
-
-import type ;
-import generators ;
-import common ;
-
-type.register FORTRAN : f F for f77 ;
-type.register FORTRAN90 : f90 F90 ;
-
-feature fortran : : free ;
-feature fortran90 : : free ;
-
-class fortran-compiling-generator : generator
-{
-    rule __init__ ( id : source-types + : target-types + : requirements * : optional-properties * )
-    {
-        generator.__init__ $(id) : $(source-types) : $(target-types) : $(requirements) : $(optional-properties) ;
-    }
-}
-
-rule register-fortran-compiler ( id : source-types + : target-types + : requirements * : optional-properties * )
-{
-    local g = [ new fortran-compiling-generator $(id) : $(source-types) : $(target-types) : $(requirements) : $(optional-properties) ] ;
-    generators.register $(g) ;
-}
-
-class fortran90-compiling-generator : generator
-{
-    rule __init__ ( id : source-types + : target-types + : requirements * : optional-properties * )
-    {
-        generator.__init__ $(id) : $(source-types) : $(target-types) : $(requirements) : $(optional-properties) ;
-    }
-}
-
-rule register-fortran90-compiler ( id : source-types + : target-types + : requirements * : optional-properties * )
-{
-    local g = [ new fortran90-compiling-generator $(id) : $(source-types) : $(target-types) : $(requirements) : $(optional-properties) ] ;
-    generators.register $(g) ;
-}
-
-# FIXME: this is ugly, should find a better way (we'd want client code to
-# register all generators as "generator.some-rule", not with "some-module.some-rule".)
-IMPORT $(__name__) : register-fortran-compiler : : generators.register-fortran-compiler ;
-IMPORT $(__name__) : register-fortran90-compiler : : generators.register-fortran90-compiler ;
diff --git a/jam-files/boost-build/tools/gcc.jam b/jam-files/boost-build/tools/gcc.jam
deleted file mode 100644
index f7b0da54..00000000
--- a/jam-files/boost-build/tools/gcc.jam
+++ /dev/null
@@ -1,1185 +0,0 @@
-# Copyright 2001 David Abrahams.
-# Copyright 2002-2006 Rene Rivera.
-# Copyright 2002-2003 Vladimir Prus.
-#  Copyright (c) 2005 Reece H. Dunn.
-# Copyright 2006 Ilya Sokolov.
-# Copyright 2007 Roland Schwarz
-# Copyright 2007 Boris Gubenko.
-#
-# Distributed under the Boost Software License, Version 1.0.
-#    (See accompanying file LICENSE_1_0.txt or copy at
-#          http://www.boost.org/LICENSE_1_0.txt)
-
-import "class" : new ;
-import common ;
-import errors ;
-import feature ;
-import generators ;
-import os ;
-import pch ;
-import property ;
-import property-set ;
-import toolset ;
-import type ;
-import rc ;
-import regex ;
-import set ;
-import unix ;
-import fortran ;
-
-
-if [ MATCH (--debug-configuration) : [ modules.peek : ARGV ] ]
-{
-    .debug-configuration = true ;
-}
-
-
-feature.extend toolset : gcc ;
-# feature.subfeature toolset gcc : flavor : : optional ;
-
-toolset.inherit-generators gcc : unix : unix.link unix.link.dll ;
-toolset.inherit-flags gcc : unix ;
-toolset.inherit-rules gcc : unix ;
-
-generators.override gcc.prebuilt : builtin.prebuilt ;
-generators.override gcc.searched-lib-generator : searched-lib-generator ;
-
-# Make gcc toolset object files use the "o" suffix on all platforms.
-type.set-generated-target-suffix OBJ : <toolset>gcc : o ;
-type.set-generated-target-suffix OBJ : <toolset>gcc <target-os>windows : o ;
-type.set-generated-target-suffix OBJ : <toolset>gcc <target-os>cygwin : o ;
-
-# Initializes the gcc toolset for the given version. If necessary, command may
-# be used to specify where the compiler is located. The parameter 'options' is a
-# space-delimited list of options, each one specified as
-# <option-name>option-value. Valid option names are: cxxflags, linkflags and
-# linker-type. Accepted linker-type values are aix, darwin, gnu, hpux, osf or
-# sun and the default value will be selected based on the current OS.
-# Example:
-#   using gcc : 3.4 : : <cxxflags>foo <linkflags>bar <linker-type>sun ;
-#
-# The compiler command to use is detected in a three step manner:
-# 1) If an explicit command is specified by the user, it will be used and must available.
-# 2) If only a certain version is specified, it is enforced:
-#    - either a command 'g++-VERSION' must be available
-#    - or the default command 'g++' must be available and match the exact version.
-# 3) Without user-provided restrictions use default 'g++'
-rule init ( version ? : command * : options * )
-{
-    #1): use user-provided command
-    local tool-command = ;
-    if $(command)
-    {
-       tool-command  =  [ common.get-invocation-command-nodefault gcc : g++ : $(command) ] ;
-       if ! $(tool-command)
-       {
-           errors.error "toolset gcc initialization:" :
-                        "provided command '$(command)' not found" :
-                        "initialized from" [ errors.nearest-user-location ] ;
-       }
-    }
-    #2): enforce user-provided version
-    else if $(version)
-    {
-        tool-command  =  [ common.get-invocation-command-nodefault gcc : "g++-$(version[1])" ] ;
-        
-        #2.1) fallback: check whether "g++" reports the requested version
-        if ! $(tool-command)
-        {
-            tool-command = [ common.get-invocation-command-nodefault gcc : g++ ] ;
-            if $(tool-command)
-            {
-                local tool-command-string = $(tool-command:J=" ") ;
-                local tool-version = [ MATCH "^([0-9.]+)" : [ SHELL "$(tool-command-string) -dumpversion" ] ] ;
-                if $(tool-version) != $(version)
-                {
-                    # Permit a match betwen two-digit version specified by the user
-                    # (e.g. 4.4) and 3-digit version reported by gcc.
-                    # Since only two digits are present in binary name anyway,
-                    # insisting that user specify 3-digit version when
-                    # configuring Boost.Build while it's not required on 
-                    # command like would be strange.
-                    local stripped = [ MATCH "^([0-9]+\.[0-9]+).*" : $(tool-version) ] ;
-                    if $(stripped) != $(version)
-                    {                                            
-                        errors.error "toolset gcc initialization:" :
-                          "version '$(version)' requested but 'g++-$(version)' not found and version '$(tool-version)' of default '$(tool-command)' does not match" :
-                            "initialized from" [ errors.nearest-user-location ] ;
-                        tool-command = ;
-                    }
-                    # Use full 3-digit version to be compatible with the 'using gcc ;' case
-                    version = $(tool-version) ;
-                }
-            }
-            else
-            {
-                errors.error "toolset gcc initialization:" :
-                             "version '$(version)' requested but neither 'g++-$(version)' nor default 'g++' found" :
-                             "initialized from" [ errors.nearest-user-location ] ;
-            }
-        }
-    }
-    #3) default: no command and no version specified, try using default command "g++"
-    else
-    {
-        tool-command = [ common.get-invocation-command-nodefault gcc : g++ ] ;
-        if ! $(tool-command)
-        {
-            errors.error "toolset gcc initialization:" :
-                         "no command provided, default command 'g++' not found" :
-                         "initialized from" [ errors.nearest-user-location ] ;
-        }
-    }
-    
-    
-    # Information about the gcc command...
-    #   The command.
-    local command = $(tool-command) ;
-    #   The root directory of the tool install.
-    local root = [ feature.get-values <root> : $(options) ] ;
-    #   The bin directory where to find the command to execute.
-    local bin ;
-    #   The flavor of compiler.
-    local flavor = [ feature.get-values <flavor> : $(options) ] ;
-    #   Autodetect the root and bin dir if not given.
-    if $(command)
-    {
-        bin ?= [ common.get-absolute-tool-path $(command[-1]) ] ;
-        root ?= $(bin:D) ;
-    }
-    # The 'command' variable can have multiple elements. When calling
-    # the SHELL builtin we need a single string.
-    local command-string = $(command:J=" ") ;
-    #   Autodetect the version and flavor if not given.
-    if $(command)
-    {    
-        local machine = [ MATCH "^([^ ]+)"
-            : [ SHELL "$(command-string) -dumpmachine" ] ] ;
-        version ?= [ MATCH "^([0-9.]+)"
-            : [ SHELL "$(command-string) -dumpversion" ] ] ;
-        switch $(machine:L)
-        {
-            case *mingw* : flavor ?= mingw ;
-        }
-    }
-
-    local condition ;
-    if $(flavor)
-    {
-        condition = [ common.check-init-parameters gcc
-            : version $(version)
-            : flavor $(flavor)
-            ] ;
-    }
-    else
-    {
-        condition = [ common.check-init-parameters gcc
-            : version $(version)
-            ] ;
-        condition = $(condition) ;  #/<toolset-gcc:flavor> ;
-    }
-
-    common.handle-options gcc : $(condition) : $(command) : $(options) ;
-
-    local linker = [ feature.get-values <linker-type> : $(options) ] ;
-    # The logic below should actually be keyed on <target-os>
-    if ! $(linker)
-    {
-        if [ os.name ] = OSF
-        {
-            linker = osf ;
-        }
-        else if [ os.name ] = HPUX
-        {
-            linker = hpux ;
-        }
-        else if [ os.name ] = AIX
-        {
-            linker = aix ;
-        }
-        else if [ os.name ] = SOLARIS
-        {
-            linker = sun ;
-        }        
-        else
-        {
-            linker = gnu ;
-        }
-    }
-    init-link-flags gcc $(linker) $(condition) ;
-
-
-    # If gcc is installed in non-standard location, we'd need to add
-    # LD_LIBRARY_PATH when running programs created with it (for unit-test/run
-    # rules).
-    if $(command)
-    {
-        # On multilib 64-bit boxes, there are both 32-bit and 64-bit libraries
-        # and all must be added to LD_LIBRARY_PATH. The linker will pick the
-        # right onces. Note that we don't provide a clean way to build 32-bit
-        # binary with 64-bit compiler, but user can always pass -m32 manually.
-        local lib_path = $(root)/bin $(root)/lib $(root)/lib32 $(root)/lib64 ;
-        if $(.debug-configuration)
-        {
-            ECHO notice: using gcc libraries :: $(condition) :: $(lib_path) ;
-        }
-        toolset.flags gcc.link RUN_PATH $(condition) : $(lib_path) ;
-    }
-
-    # If it's not a system gcc install we should adjust the various programs as
-    # needed to prefer using the install specific versions. This is essential
-    # for correct use of MinGW and for cross-compiling.
-    
-    local nl = "
-" ;
-
-    # - The archive builder.
-    local archiver = [ common.get-invocation-command gcc
-            : [ NORMALIZE_PATH [ MATCH "(.*)[$(nl)]+" : [ SHELL "$(command-string) -print-prog-name=ar" ] ] ]
-            : [ feature.get-values <archiver> : $(options) ] 
-            : $(bin) 
-            : search-path ] ;
-    toolset.flags gcc.archive .AR $(condition) : $(archiver[1]) ;
-    if $(.debug-configuration)
-    {
-        ECHO notice: using gcc archiver :: $(condition) :: $(archiver[1]) ;
-    }
-
-    # - Ranlib
-    local ranlib = [ common.get-invocation-command gcc
-            : [ NORMALIZE_PATH [ MATCH "(.*)[$(nl)]+" : [ SHELL "$(command-string) -print-prog-name=ranlib" ] ] ]
-            : [ feature.get-values <ranlib> : $(options) ] 
-            : $(bin) 
-            : search-path ] ;
-    toolset.flags gcc.archive .RANLIB $(condition) : $(ranlib[1]) ;
-    if $(.debug-configuration)
-    {
-        ECHO notice: using gcc ranlib :: $(condition) :: $(ranlib[1]) ;
-    }
-
-
-    # - The resource compiler.
-    local rc =
-        [ common.get-invocation-command-nodefault gcc
-            : windres : [ feature.get-values <rc> : $(options) ] : $(bin) : search-path ] ;
-    local rc-type =
-        [ feature.get-values <rc-type> : $(options) ] ;
-    rc-type ?= windres ;
-    if ! $(rc)
-    {
-        # If we can't find an RC compiler we fallback to a null RC compiler that
-        # creates empty object files. This allows the same Jamfiles to work
-        # across the board. The null RC uses the assembler to create the empty
-        # objects, so configure that.
-        rc = [ common.get-invocation-command gcc : as : : $(bin) : search-path ] ;
-        rc-type = null ;
-    }
-    rc.configure $(rc) : $(condition) : <rc-type>$(rc-type) ;
-}
-
-if [ os.name ] = NT
-{
-    # This causes single-line command invocation to not go through .bat files,
-    # thus avoiding command-line length limitations.
-    JAMSHELL = % ;
-}
-
-generators.register-c-compiler gcc.compile.c++.preprocess : CPP : PREPROCESSED_CPP : <toolset>gcc ;
-generators.register-c-compiler gcc.compile.c.preprocess   : C   : PREPROCESSED_C   : <toolset>gcc ;
-generators.register-c-compiler gcc.compile.c++ : CPP : OBJ : <toolset>gcc ;
-generators.register-c-compiler gcc.compile.c   : C   : OBJ : <toolset>gcc ;
-generators.register-c-compiler gcc.compile.asm : ASM : OBJ : <toolset>gcc ;
-generators.register-fortran-compiler gcc.compile.fortran : FORTRAN FORTRAN90 : OBJ : <toolset>gcc ;
-
-# pch support
-
-# The compiler looks for a precompiled header in each directory just before it
-# looks for the include file in that directory. The name searched for is the
-# name specified in the #include directive with ".gch" suffix appended. The
-# logic in gcc-pch-generator will make sure that BASE_PCH suffix is appended to
-# full name of the header.
-
-type.set-generated-target-suffix PCH : <toolset>gcc : gch ;
-
-# GCC-specific pch generator.
-class gcc-pch-generator : pch-generator
-{
-    import project ;
-    import property-set ;
-    import type ;
-
-    rule run-pch ( project name ? : property-set : sources + )
-    {
-        # Find the header in sources. Ignore any CPP sources.
-        local header ;
-        for local s in $(sources)
-        {
-            if [ type.is-derived [ $(s).type ] H ]
-            {
-                header = $(s) ;
-            }
-        }
-
-        # Error handling: Base header file name should be the same as the base
-        # precompiled header name.
-        local header-name = [ $(header).name ] ;
-        local header-basename = $(header-name:B) ;
-        if $(header-basename) != $(name)
-        {
-            local location = [ $(project).project-module ] ;
-            errors.user-error "in" $(location)": pch target name `"$(name)"' should be the same as the base name of header file `"$(header-name)"'" ;
-        }
-
-        local pch-file = [ generator.run $(project) $(name) : $(property-set)
-            : $(header) ] ;
-
-        # return result of base class and pch-file property as usage-requirements
-        return
-            [ property-set.create <pch-file>$(pch-file) <cflags>-Winvalid-pch ]
-            $(pch-file)
-          ;
-    }
-
-    # Calls the base version specifying source's name as the name of the created
-    # target. As result, the PCH will be named whatever.hpp.gch, and not
-    # whatever.gch.
-    rule generated-targets ( sources + : property-set : project name ? )
-    {
-        name = [ $(sources[1]).name ] ;
-        return [ generator.generated-targets $(sources)
-          : $(property-set) : $(project) $(name) ] ;
-    }
-}
-
-# Note: the 'H' source type will catch both '.h' header and '.hpp' header. The
-# latter have HPP type, but HPP type is derived from H. The type of compilation
-# is determined entirely by the destination type.
-generators.register [ new gcc-pch-generator gcc.compile.c.pch   : H :   C_PCH : <pch>on <toolset>gcc ] ;
-generators.register [ new gcc-pch-generator gcc.compile.c++.pch : H : CPP_PCH : <pch>on <toolset>gcc ] ;
-
-# Override default do-nothing generators.
-generators.override gcc.compile.c.pch   : pch.default-c-pch-generator   ;
-generators.override gcc.compile.c++.pch : pch.default-cpp-pch-generator ;
-
-toolset.flags gcc.compile PCH_FILE <pch>on : <pch-file> ;
-
-# Declare flags and action for compilation.
-toolset.flags gcc.compile OPTIONS <optimization>off   : -O0 ;
-toolset.flags gcc.compile OPTIONS <optimization>speed : -O3 ;
-toolset.flags gcc.compile OPTIONS <optimization>space : -Os ;
-
-toolset.flags gcc.compile OPTIONS <inlining>off  : -fno-inline ;
-toolset.flags gcc.compile OPTIONS <inlining>on   : -Wno-inline ;
-toolset.flags gcc.compile OPTIONS <inlining>full : -finline-functions -Wno-inline ;
-
-toolset.flags gcc.compile OPTIONS <warnings>off : -w ;
-toolset.flags gcc.compile OPTIONS <warnings>on  : -Wall ;
-toolset.flags gcc.compile OPTIONS <warnings>all : -Wall -pedantic ;
-toolset.flags gcc.compile OPTIONS <warnings-as-errors>on : -Werror ;
-
-toolset.flags gcc.compile OPTIONS <debug-symbols>on : -g ;
-toolset.flags gcc.compile OPTIONS <profiling>on : -pg ;
-toolset.flags gcc.compile OPTIONS <rtti>off : -fno-rtti ;
-
-rule setup-fpic ( targets * : sources * : properties * )
-{
-    local link = [ feature.get-values link : $(properties) ] ;
-    if $(link) = shared
-    {        
-        local target = [ feature.get-values target-os : $(properties) ] ;
-        
-        # This logic will add -fPIC for all compilations:
-        #
-        # lib a : a.cpp b ;
-        # obj b : b.cpp ;
-        # exe c : c.cpp a d ;
-        # obj d : d.cpp ;
-        #
-        # This all is fine, except that 'd' will be compiled with -fPIC even though
-        # it is not needed, as 'd' is used only in exe. However, it is hard to
-        # detect where a target is going to be used. Alternatively, we can set -fPIC
-        # only when main target type is LIB but than 'b' would be compiled without
-        # -fPIC which would lead to link errors on x86-64. So, compile everything
-        # with -fPIC.
-        #
-        # Yet another alternative would be to create a propagated <sharedable>
-        # feature and set it when building shared libraries, but that would be hard
-        # to implement and would increase the target path length even more.
-        
-        # On Windows, fPIC is default, specifying -fPIC explicitly leads to
-        # a warning.
-        if $(target) != cygwin && $(target) != windows
-        {
-            OPTIONS on $(targets) += -fPIC ;
-        }        
-    }
-}
-
-rule setup-address-model ( targets * : sources * : properties * )
-{
-    local model = [ feature.get-values address-model : $(properties) ] ;
-    if $(model)
-    {
-        local option ;
-        local os = [ feature.get-values target-os : $(properties) ] ;
-        if $(os) = aix
-        {
-            if $(model) = 32
-            {
-                option = -maix32 ;
-            }
-            else
-            {
-                option = -maix64 ;
-            }
-        }
-        else if $(os) = hpux
-        {
-            if $(model) = 32
-            {
-                option = -milp32 ;
-            }
-            else
-            {
-                option = -mlp64 ;
-            }
-        }
-        else
-        {
-            if $(model) = 32
-            {
-                option = -m32 ;
-            }
-            else if $(model) = 64
-            {
-                option = -m64 ;
-            }
-            # For darwin, the model can be 32_64. darwin.jam will handle that
-            # on its own.
-        }
-        OPTIONS on $(targets) += $(option) ;
-    }    
-}
-
-
-# FIXME: this should not use os.name.
-if [ os.name ] != NT && [ os.name ] != OSF && [ os.name ] != HPUX && [ os.name ] != AIX
-{
-    # OSF does have an option called -soname but it does not seem to work as
-    # expected, therefore it has been disabled.
-    HAVE_SONAME   = "" ;
-    SONAME_OPTION = -h ;
-}
-
-# HPUX, for some reason, seem to use '+h', not '-h'.
-if [ os.name ] = HPUX
-{
-    HAVE_SONAME   = "" ;
-    SONAME_OPTION = +h ;
-}
-
-toolset.flags gcc.compile USER_OPTIONS <cflags> ;
-toolset.flags gcc.compile.c++ USER_OPTIONS <cxxflags> ;
-toolset.flags gcc.compile DEFINES <define> ;
-toolset.flags gcc.compile INCLUDES <include> ;
-toolset.flags gcc.compile.c++ TEMPLATE_DEPTH <c++-template-depth> ;
-toolset.flags gcc.compile.fortran USER_OPTIONS <fflags> ;
-
-rule compile.c++.pch ( targets * : sources * : properties * )
-{
-    setup-threading $(targets) : $(sources) : $(properties) ;
-    setup-fpic $(targets) : $(sources) : $(properties) ;
-    setup-address-model $(targets) : $(sources) : $(properties) ;
-}
-
-actions compile.c++.pch
-{
-    "$(CONFIG_COMMAND)" -x c++-header $(OPTIONS) $(USER_OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -c -o "$(<)" "$(>)"
-}
-
-rule compile.c.pch ( targets * : sources * : properties * )
-{
-    setup-threading $(targets) : $(sources) : $(properties) ;
-    setup-fpic $(targets) : $(sources) : $(properties) ;
-    setup-address-model $(targets) : $(sources) : $(properties) ;    
-}
-
-actions compile.c.pch
-{
-    "$(CONFIG_COMMAND)" -x c-header $(OPTIONS) $(USER_OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -c -o "$(<)" "$(>)"
-}
-
-rule compile.c++.preprocess ( targets * : sources * : properties * )
-{
-    setup-threading $(targets) : $(sources) : $(properties) ;
-    setup-fpic $(targets) : $(sources) : $(properties) ;
-    setup-address-model $(targets) : $(sources) : $(properties) ;
-    
-    # Some extensions are compiled as C++ by default. For others, we need to
-    # pass -x c++. We could always pass -x c++ but distcc does not work with it.
-    if ! $(>:S) in .cc .cp .cxx .cpp .c++ .C
-    {
-        LANG on $(<) = "-x c++" ;
-    }
-    DEPENDS $(<) : [ on $(<) return $(PCH_FILE) ] ;
-}
-
-rule compile.c.preprocess ( targets * : sources * : properties * )
-{
-    setup-threading $(targets) : $(sources) : $(properties) ;
-    setup-fpic $(targets) : $(sources) : $(properties) ;
-    setup-address-model $(targets) : $(sources) : $(properties) ;
-    
-    # If we use the name g++ then default file suffix -> language mapping does
-    # not work. So have to pass -x option. Maybe, we can work around this by
-    # allowing the user to specify both C and C++ compiler names.
-    #if $(>:S) != .c
-    #{
-        LANG on $(<) = "-x c" ;
-    #}
-    DEPENDS $(<) : [ on $(<) return $(PCH_FILE) ] ;
-}
-
-rule compile.c++ ( targets * : sources * : properties * )
-{
-    setup-threading $(targets) : $(sources) : $(properties) ;
-    setup-fpic $(targets) : $(sources) : $(properties) ;
-    setup-address-model $(targets) : $(sources) : $(properties) ;
-    
-    # Some extensions are compiled as C++ by default. For others, we need to
-    # pass -x c++. We could always pass -x c++ but distcc does not work with it.
-    if ! $(>:S) in .cc .cp .cxx .cpp .c++ .C
-    {
-        LANG on $(<) = "-x c++" ;
-    }
-    DEPENDS $(<) : [ on $(<) return $(PCH_FILE) ] ;
-    
-    # Here we want to raise the template-depth parameter value to something
-    # higher than the default value of 17. Note that we could do this using the
-    # feature.set-default rule but we do not want to set the default value for
-    # all toolsets as well.
-    #
-    # TODO: This 'modified default' has been inherited from some 'older Boost
-    # Build implementation' and has most likely been added to make some Boost
-    # library parts compile correctly. We should see what exactly prompted this
-    # and whether we can get around the problem more locally.
-    local template-depth = [ on $(<) return $(TEMPLATE_DEPTH) ] ;
-    if ! $(template-depth)
-    {
-        TEMPLATE_DEPTH on $(<) = 128 ;
-    }
-}
-
-rule compile.c ( targets * : sources * : properties * )
-{
-    setup-threading $(targets) : $(sources) : $(properties) ;
-    setup-fpic $(targets) : $(sources) : $(properties) ;
-    setup-address-model $(targets) : $(sources) : $(properties) ;
-    
-    # If we use the name g++ then default file suffix -> language mapping does
-    # not work. So have to pass -x option. Maybe, we can work around this by
-    # allowing the user to specify both C and C++ compiler names.
-    #if $(>:S) != .c
-    #{
-        LANG on $(<) = "-x c" ;
-    #}
-    DEPENDS $(<) : [ on $(<) return $(PCH_FILE) ] ;
-}
-
-rule compile.fortran ( targets * : sources * : properties * )
-{
-    setup-threading $(targets) : $(sources) : $(properties) ;
-    setup-fpic $(targets) : $(sources) : $(properties) ;
-    setup-address-model $(targets) : $(sources) : $(properties) ;
-}
-
-actions compile.c++ bind PCH_FILE
-{
-    "$(CONFIG_COMMAND)" $(LANG) -ftemplate-depth-$(TEMPLATE_DEPTH) $(OPTIONS) $(USER_OPTIONS) -D$(DEFINES) -I"$(PCH_FILE:D)" -I"$(INCLUDES)" -c -o "$(<:W)" "$(>:W)"
-}
-
-actions compile.c bind PCH_FILE
-{
-    "$(CONFIG_COMMAND)" $(LANG) $(OPTIONS) $(USER_OPTIONS) -D$(DEFINES) -I"$(PCH_FILE:D)" -I"$(INCLUDES)" -c -o "$(<)" "$(>)"
-}
-
-actions compile.c++.preprocess bind PCH_FILE
-{
-    "$(CONFIG_COMMAND)" $(LANG) -ftemplate-depth-$(TEMPLATE_DEPTH) $(OPTIONS) $(USER_OPTIONS) -D$(DEFINES) -I"$(PCH_FILE:D)" -I"$(INCLUDES)" "$(>:W)" -E >"$(<:W)"
-}
-
-actions compile.c.preprocess bind PCH_FILE
-{
-    "$(CONFIG_COMMAND)" $(LANG) $(OPTIONS) $(USER_OPTIONS) -D$(DEFINES) -I"$(PCH_FILE:D)" -I"$(INCLUDES)" "$(>)" -E >$(<)
-}
-
-actions compile.fortran
-{
-  "$(CONFIG_COMMAND)" $(LANG) $(OPTIONS) $(USER_OPTIONS) -D$(DEFINES) -I"$(PCH_FILE:D)" -I"$(INCLUDES)" -c -o "$(<)" "$(>)" 
-}
-
-rule compile.asm ( targets * : sources * : properties * )
-{
-    setup-fpic $(targets) : $(sources) : $(properties) ;    
-    setup-address-model $(targets) : $(sources) : $(properties) ;
-    LANG on $(<) = "-x assembler-with-cpp" ;
-}
-
-actions compile.asm
-{
-    "$(CONFIG_COMMAND)" $(LANG) $(OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -c -o "$(<)" "$(>)"
-}
-
-# The class which check that we don't try to use the <runtime-link>static
-# property while creating or using shared library, since it's not supported by
-# gcc/libc.
-class gcc-linking-generator : unix-linking-generator
-{
-    rule run ( project name ? : property-set : sources + )
-    {
-        # TODO: Replace this with the use of a target-os property.
-        local no-static-link = ;
-        if [ modules.peek : UNIX ]
-        {
-            switch [ modules.peek : JAMUNAME ]
-            {
-                case * : no-static-link = true ;
-            }
-        }
-
-        local properties = [ $(property-set).raw ] ;
-        local reason ;
-        if $(no-static-link) && <runtime-link>static in $(properties)
-        {
-            if <link>shared in $(properties)
-            {
-                reason =
-                    "On gcc, DLL can't be build with '<runtime-link>static'." ;
-            }
-            else if [ type.is-derived $(self.target-types[1]) EXE ]
-            {
-                for local s in $(sources)
-                {
-                    local type = [ $(s).type ] ;
-                    if $(type) &&  [ type.is-derived $(type) SHARED_LIB ]
-                    {
-                        reason =
-                            "On gcc, using DLLS together with the"
-                            "<runtime-link>static options is not possible " ;
-                    }
-                }
-            }
-        }
-        if $(reason)
-        {
-            ECHO warning:
-                $(reason) ;
-            ECHO warning:
-                "It is suggested to use '<runtime-link>static' together"
-                "with '<link>static'." ;
-            return ;
-        }
-        else
-        {
-            local generated-targets = [ unix-linking-generator.run $(project)
-                $(name) : $(property-set) : $(sources) ] ;
-            return $(generated-targets) ;
-        }
-    }
-}
-
-# The set of permissible input types is different on mingw.
-# So, define two sets of generators, with mingw generators
-# selected when target-os=windows.
-
-local g ;
-g = [ new gcc-linking-generator gcc.mingw.link
-      : OBJ SEARCHED_LIB STATIC_LIB IMPORT_LIB
-      : EXE
-      : <toolset>gcc <target-os>windows ] ;
-$(g).set-rule-name gcc.link ;
-generators.register $(g) ;
-
-g = [ new gcc-linking-generator gcc.mingw.link.dll
-      : OBJ SEARCHED_LIB STATIC_LIB IMPORT_LIB
-      : IMPORT_LIB SHARED_LIB
-      : <toolset>gcc <target-os>windows ] ;
-$(g).set-rule-name gcc.link.dll ;
-generators.register $(g) ;
-
-generators.register
-  [ new gcc-linking-generator gcc.link
-      : LIB OBJ
-      : EXE
-      : <toolset>gcc ] ;
-generators.register
-  [ new gcc-linking-generator gcc.link.dll
-      : LIB OBJ
-      : SHARED_LIB
-      : <toolset>gcc ] ;
-
-generators.override gcc.mingw.link : gcc.link ;
-generators.override gcc.mingw.link.dll : gcc.link.dll ;
-
-# Cygwin is similar to msvc and mingw in that it uses import libraries.
-# While in simple cases, it can directly link to a shared library,
-# it is believed to be slower, and not always possible. Define cygwin-specific
-# generators here.
-
-g = [ new gcc-linking-generator gcc.cygwin.link
-      : OBJ SEARCHED_LIB STATIC_LIB IMPORT_LIB
-      : EXE
-      : <toolset>gcc <target-os>cygwin ] ;
-$(g).set-rule-name gcc.link ;
-generators.register $(g) ;
-
-g = [ new gcc-linking-generator gcc.cygwin.link.dll
-      : OBJ SEARCHED_LIB STATIC_LIB IMPORT_LIB
-      : IMPORT_LIB SHARED_LIB
-      : <toolset>gcc <target-os>cygwin ] ;
-$(g).set-rule-name gcc.link.dll ;
-generators.register $(g) ;
-
-generators.override gcc.cygwin.link : gcc.link ;
-generators.override gcc.cygwin.link.dll : gcc.link.dll ;
-
-# Declare flags for linking.
-# First, the common flags.
-toolset.flags gcc.link OPTIONS <debug-symbols>on : -g ;
-toolset.flags gcc.link OPTIONS <profiling>on : -pg ;
-toolset.flags gcc.link USER_OPTIONS <linkflags> ;
-toolset.flags gcc.link LINKPATH <library-path> ;
-toolset.flags gcc.link FINDLIBS-ST <find-static-library> ;
-toolset.flags gcc.link FINDLIBS-SA <find-shared-library> ;
-toolset.flags gcc.link LIBRARIES <library-file> ;
-
-toolset.flags gcc.link.dll .IMPLIB-COMMAND <target-os>windows : "-Wl,--out-implib," ;
-toolset.flags gcc.link.dll .IMPLIB-COMMAND <target-os>cygwin : "-Wl,--out-implib," ;
-
-# For <runtime-link>static we made sure there are no dynamic libraries in the
-# link. On HP-UX not all system libraries exist as archived libraries (for
-# example, there is no libunwind.a), so, on this platform, the -static option
-# cannot be specified.
-if [ os.name ] != HPUX
-{
-    toolset.flags gcc.link OPTIONS <runtime-link>static : -static ;
-}
-
-# Now, the vendor specific flags.
-# The parameter linker can be either aix, darwin, gnu, hpux, osf or sun.
-rule init-link-flags ( toolset linker condition )
-{
-    switch $(linker)
-    {
-    case aix :
-        {
-        #
-        # On AIX we *have* to use the native linker.
-        #
-        # Using -brtl, the AIX linker will look for libraries with both the .a
-        # and .so extensions, such as libfoo.a and libfoo.so. Without -brtl, the
-        # AIX linker looks only for libfoo.a. Note that libfoo.a is an archived
-        # file that may contain shared objects and is different from static libs
-        # as on Linux.
-        #
-        # The -bnoipath strips the prepending (relative) path of libraries from
-        # the loader section in the target library or executable. Hence, during
-        # load-time LIBPATH (identical to LD_LIBRARY_PATH) or a hard-coded
-        # -blibpath (*similar* to -lrpath/-lrpath-link) is searched. Without
-        # this option, the prepending (relative) path + library name is
-        # hard-coded in the loader section, causing *only* this path to be
-        # searched during load-time. Note that the AIX linker does not have an
-        # -soname equivalent, this is as close as it gets.
-        #
-        # The above options are definately for AIX 5.x, and most likely also for
-        # AIX 4.x and AIX 6.x. For details about the AIX linker see:
-        # http://download.boulder.ibm.com/ibmdl/pub/software/dw/aix/es-aix_ll.pdf
-        #
-
-        toolset.flags $(toolset).link OPTIONS : -Wl,-brtl -Wl,-bnoipath
-            : unchecked ;
-        }
-
-    case darwin :
-        {
-        # On Darwin, the -s option to ld does not work unless we pass -static,
-        # and passing -static unconditionally is a bad idea. So, don't pass -s.
-        # at all, darwin.jam will use separate 'strip' invocation.
-        toolset.flags $(toolset).link RPATH $(condition) : <dll-path> : unchecked ;
-        toolset.flags $(toolset).link RPATH_LINK $(condition) : <xdll-path> : unchecked ;
-        }
-
-    case gnu :
-        {
-        # Strip the binary when no debugging is needed. We use --strip-all flag
-        # as opposed to -s since icc (intel's compiler) is generally
-        # option-compatible with and inherits from the gcc toolset, but does not
-        # support -s.
-        toolset.flags $(toolset).link OPTIONS     $(condition)/<strip>on          : -Wl,--strip-all   : unchecked ;
-        toolset.flags $(toolset).link RPATH       $(condition)                    : <dll-path>        : unchecked ;
-        toolset.flags $(toolset).link RPATH_LINK  $(condition)                    : <xdll-path>       : unchecked ;
-        toolset.flags $(toolset).link START-GROUP $(condition)                    : -Wl,--start-group : unchecked ;
-        toolset.flags $(toolset).link END-GROUP   $(condition)                    : -Wl,--end-group   : unchecked ;
-
-        # gnu ld has the ability to change the search behaviour for libraries
-        # referenced by -l switch. These modifiers are -Bstatic and -Bdynamic
-        # and change search for -l switches that follow them. The following list
-        # shows the tried variants.
-        # The search stops at the first variant that has a match.
-        # *nix: -Bstatic -lxxx
-        #    libxxx.a
-        #
-        # *nix: -Bdynamic -lxxx
-        #    libxxx.so
-        #    libxxx.a
-        #
-        # windows (mingw,cygwin) -Bstatic -lxxx
-        #    libxxx.a
-        #    xxx.lib
-        #
-        # windows (mingw,cygwin) -Bdynamic -lxxx
-        #    libxxx.dll.a
-        #    xxx.dll.a
-        #    libxxx.a
-        #    xxx.lib
-        #    cygxxx.dll (*)
-        #    libxxx.dll
-        #    xxx.dll
-        #    libxxx.a
-        #
-        # (*) This is for cygwin
-        # Please note that -Bstatic and -Bdynamic are not a guarantee that a
-        # static or dynamic lib indeed gets linked in. The switches only change
-        # search patterns!
-
-        # On *nix mixing shared libs with static runtime is not a good idea.
-        toolset.flags $(toolset).link FINDLIBS-ST-PFX $(condition)/<runtime-link>shared
-            : -Wl,-Bstatic : unchecked ;
-        toolset.flags $(toolset).link FINDLIBS-SA-PFX $(condition)/<runtime-link>shared
-            : -Wl,-Bdynamic : unchecked ;
-
-        # On windows allow mixing of static and dynamic libs with static
-        # runtime.
-        toolset.flags $(toolset).link FINDLIBS-ST-PFX $(condition)/<runtime-link>static/<target-os>windows
-            : -Wl,-Bstatic : unchecked ;
-        toolset.flags $(toolset).link FINDLIBS-SA-PFX $(condition)/<runtime-link>static/<target-os>windows
-            : -Wl,-Bdynamic : unchecked ;
-        toolset.flags $(toolset).link OPTIONS $(condition)/<runtime-link>static/<target-os>windows
-            : -Wl,-Bstatic : unchecked ;
-        }
-
-    case hpux :
-        {
-        toolset.flags $(toolset).link OPTIONS $(condition)/<strip>on
-            : -Wl,-s : unchecked ;
-        toolset.flags $(toolset).link OPTIONS $(condition)/<link>shared
-            : -fPIC : unchecked ;
-        }
-
-    case osf :
-        {
-        # No --strip-all, just -s.
-        toolset.flags $(toolset).link OPTIONS $(condition)/<strip>on
-            : -Wl,-s : unchecked ;
-        toolset.flags $(toolset).link RPATH $(condition) : <dll-path>
-            : unchecked ;
-        # This does not supports -R.
-        toolset.flags $(toolset).link RPATH_OPTION $(condition) : -rpath
-            : unchecked ;
-        # -rpath-link is not supported at all.
-        }
-
-    case sun :
-        {
-        toolset.flags $(toolset).link OPTIONS $(condition)/<strip>on
-            : -Wl,-s : unchecked ;
-        toolset.flags $(toolset).link RPATH $(condition) : <dll-path>
-            : unchecked ;
-        # Solaris linker does not have a separate -rpath-link, but allows to use
-        # -L for the same purpose.
-        toolset.flags $(toolset).link LINKPATH $(condition) : <xdll-path>
-            : unchecked ;
-
-        # This permits shared libraries with non-PIC code on Solaris.
-        # VP, 2004/09/07: Now that we have -fPIC hardcode in link.dll, the
-        # following is not needed. Whether -fPIC should be hardcoded, is a
-        # separate question.
-        # AH, 2004/10/16: it is still necessary because some tests link against
-        # static libraries that were compiled without PIC.
-        toolset.flags $(toolset).link OPTIONS $(condition)/<link>shared
-            : -mimpure-text : unchecked ;
-        }
-
-    case * :
-        {
-        errors.user-error
-            "$(toolset) initialization: invalid linker '$(linker)'" :
-            "The value '$(linker)' specified for <linker> is not recognized." :
-            "Possible values are 'aix', 'darwin', 'gnu', 'hpux', 'osf' or 'sun'" ;
-        }
-    }
-}
-
-# Enclose the RPATH variable on 'targets' in (double) quotes,
-# unless it's already enclosed in single quotes.
-# This special casing is done because it's common to pass
-# '$ORIGIN' to linker -- and it has to have single quotes
-# to prevent expansion by shell -- and if we add double
-# quotes then preventing properties of single quotes disappear.
-rule quote-rpath ( targets * )
-{
-    local r = [ on $(targets[1]) return $(RPATH) ] ;
-    if ! [ MATCH "('.*')" : $(r) ] 
-    {
-        r = "\"$(r)\"" ;
-    }
-    RPATH on $(targets) = $(r) ;
-}
-
-# Declare actions for linking.
-rule link ( targets * : sources * : properties * )
-{
-    setup-threading $(targets) : $(sources) : $(properties) ;
-    setup-address-model $(targets) : $(sources) : $(properties) ;
-    SPACE on $(targets) = " " ;
-    # Serialize execution of the 'link' action, since running N links in
-    # parallel is just slower. For now, serialize only gcc links, it might be a
-    # good idea to serialize all links.
-    JAM_SEMAPHORE on $(targets) = <s>gcc-link-semaphore ;
-    quote-rpath $(targets) ;
-}
-
-actions link bind LIBRARIES
-{
-    "$(CONFIG_COMMAND)" -L"$(LINKPATH)" -Wl,$(RPATH_OPTION:E=-R)$(SPACE)-Wl,$(RPATH) -Wl,-rpath-link$(SPACE)-Wl,"$(RPATH_LINK)" -o "$(<)" $(START-GROUP) "$(>)" "$(LIBRARIES)" $(FINDLIBS-ST-PFX) -l$(FINDLIBS-ST) $(FINDLIBS-SA-PFX) -l$(FINDLIBS-SA) $(END-GROUP) $(OPTIONS) $(USER_OPTIONS)
-
-}
-
-# Default value. Mostly for the sake of intel-linux that inherits from gcc, but
-# does not have the same logic to set the .AR variable. We can put the same
-# logic in intel-linux, but that's hardly worth the trouble as on Linux, 'ar' is
-# always available.
-.AR = ar ;
-.RANLIB = ranlib ;
-
-toolset.flags gcc.archive AROPTIONS <archiveflags> ;
-
-rule archive ( targets * : sources * : properties * )
-{
-    # Always remove archive and start again. Here is the rationale from
-    #
-    # Andre Hentz:
-    #
-    # I had a file, say a1.c, that was included into liba.a. I moved a1.c to
-    # a2.c, updated my Jamfiles and rebuilt. My program was crashing with absurd
-    # errors. After some debugging I traced it back to the fact that a1.o was
-    # *still* in liba.a
-    #
-    # Rene Rivera:
-    #
-    # Originally removing the archive was done by splicing an RM onto the
-    # archive action. That makes archives fail to build on NT when they have
-    # many files because it will no longer execute the action directly and blow
-    # the line length limit. Instead we remove the file in a different action,
-    # just before building the archive.
-    #
-    local clean.a = $(targets[1])(clean) ;
-    TEMPORARY $(clean.a) ;
-    NOCARE $(clean.a) ;
-    LOCATE on $(clean.a) = [ on $(targets[1]) return $(LOCATE) ] ;
-    DEPENDS $(clean.a) : $(sources) ;
-    DEPENDS $(targets) : $(clean.a) ;
-    common.RmTemps $(clean.a) : $(targets) ;
-}
-
-# Declare action for creating static libraries.
-# The letter 'r' means to add files to the archive with replacement. Since we
-# remove archive, we don't care about replacement, but there's no option "add
-# without replacement".
-# The letter 'c' suppresses the warning in case the archive does not exists yet.
-# That warning is produced only on some platforms, for whatever reasons.
-actions piecemeal archive
-{
-    "$(.AR)" $(AROPTIONS) rc "$(<)" "$(>)"
-    "$(.RANLIB)" "$(<)"
-}
-
-rule link.dll ( targets * : sources * : properties * )
-{
-    setup-threading $(targets) : $(sources) : $(properties) ;
-    setup-address-model $(targets) : $(sources) : $(properties) ;
-    SPACE on $(targets) = " " ;
-    JAM_SEMAPHORE on $(targets) = <s>gcc-link-semaphore ;
-    quote-rpath $(targets) ;
-}
-
-# Differs from 'link' above only by -shared.
-actions link.dll bind LIBRARIES
-{
-    "$(CONFIG_COMMAND)" -L"$(LINKPATH)" -Wl,$(RPATH_OPTION:E=-R)$(SPACE)-Wl,$(RPATH) "$(.IMPLIB-COMMAND)$(<[1])" -o "$(<[-1])" $(HAVE_SONAME)-Wl,$(SONAME_OPTION)$(SPACE)-Wl,$(<[-1]:D=) -shared $(START-GROUP) "$(>)" "$(LIBRARIES)" $(FINDLIBS-ST-PFX) -l$(FINDLIBS-ST) $(FINDLIBS-SA-PFX) -l$(FINDLIBS-SA) $(END-GROUP) $(OPTIONS) $(USER_OPTIONS)
-}
-
-rule setup-threading ( targets * : sources * : properties * )
-{
-    local threading = [ feature.get-values threading : $(properties) ] ;
-    if $(threading) = multi
-    {        
-        local target = [ feature.get-values target-os : $(properties) ] ;
-        local option ;
-        local libs ;
-        
-        switch $(target)
-        {
-            case windows :
-            {
-                option = -mthreads ;
-            }
-            case cygwin :
-            {
-                option = -mthreads ;
-            }
-            case solaris :
-            {
-                option = -pthreads ;
-                libs = rt ;
-            }
-            case beos :
-            {            
-                # BeOS has no threading options, so do not set anything here.
-            }        
-            case *bsd :
-            {
-                option = -pthread ;
-                # There is no -lrt on BSD.
-            }
-            case sgi :
-            {
-                # gcc on IRIX does not support multi-threading so do not set anything
-                # here.
-            }
-            case darwin :
-            {
-                # Darwin has no threading options so do not set anything here.
-            }
-            case * :
-            {
-                option = -pthread ;
-                libs = rt ;
-            }
-        }
-    
-        if $(option)
-        {
-            OPTIONS on $(targets) += $(option) ;
-        }
-        if $(libs)
-        {
-            FINDLIBS-SA on $(targets) += $(libs) ;
-        }
-    }    
-}
-
-local rule cpu-flags ( toolset variable : architecture : instruction-set + : values + : default ? )
-{
-    if $(default)
-    {
-        toolset.flags $(toolset) $(variable)
-            <architecture>$(architecture)/<instruction-set>
-            : $(values) ;
-    }
-    toolset.flags $(toolset) $(variable)
-        <architecture>/<instruction-set>$(instruction-set)
-        <architecture>$(architecture)/<instruction-set>$(instruction-set)
-        : $(values) ;
-}
-
-# Set architecture/instruction-set options.
-#
-# x86 and compatible
-# The 'native' option appeared in gcc 4.2 so we cannot safely use it
-# as default. Use conservative i386 instead.
-cpu-flags gcc OPTIONS : x86 : native : -march=native ;
-cpu-flags gcc OPTIONS : x86 : i386 : -march=i386 : default ;
-cpu-flags gcc OPTIONS : x86 : i486 : -march=i486 ;
-cpu-flags gcc OPTIONS : x86 : i586 : -march=i586 ;
-cpu-flags gcc OPTIONS : x86 : i686 : -march=i686 ;
-cpu-flags gcc OPTIONS : x86 : pentium : -march=pentium ;
-cpu-flags gcc OPTIONS : x86 : pentium-mmx : -march=pentium-mmx ;
-cpu-flags gcc OPTIONS : x86 : pentiumpro : -march=pentiumpro ;
-cpu-flags gcc OPTIONS : x86 : pentium2 : -march=pentium2 ;
-cpu-flags gcc OPTIONS : x86 : pentium3 : -march=pentium3 ;
-cpu-flags gcc OPTIONS : x86 : pentium3m : -march=pentium3m ;
-cpu-flags gcc OPTIONS : x86 : pentium-m : -march=pentium-m ;
-cpu-flags gcc OPTIONS : x86 : pentium4 : -march=pentium4 ;
-cpu-flags gcc OPTIONS : x86 : pentium4m : -march=pentium4m ;
-cpu-flags gcc OPTIONS : x86 : prescott : -march=prescott ;
-cpu-flags gcc OPTIONS : x86 : nocona : -march=nocona ;
-cpu-flags gcc OPTIONS : x86 : core2 : -march=core2 ;
-cpu-flags gcc OPTIONS : x86 : k6 : -march=k6 ;
-cpu-flags gcc OPTIONS : x86 : k6-2 : -march=k6-2 ;
-cpu-flags gcc OPTIONS : x86 : k6-3 : -march=k6-3 ;
-cpu-flags gcc OPTIONS : x86 : athlon : -march=athlon ;
-cpu-flags gcc OPTIONS : x86 : athlon-tbird : -march=athlon-tbird ;
-cpu-flags gcc OPTIONS : x86 : athlon-4 : -march=athlon-4 ;
-cpu-flags gcc OPTIONS : x86 : athlon-xp : -march=athlon-xp ;
-cpu-flags gcc OPTIONS : x86 : athlon-mp : -march=athlon-mp ;
-##
-cpu-flags gcc OPTIONS : x86 : k8 : -march=k8 ;
-cpu-flags gcc OPTIONS : x86 : opteron : -march=opteron ;
-cpu-flags gcc OPTIONS : x86 : athlon64 : -march=athlon64 ;
-cpu-flags gcc OPTIONS : x86 : athlon-fx : -march=athlon-fx ;
-cpu-flags gcc OPTIONS : x86 : winchip-c6 : -march=winchip-c6 ;
-cpu-flags gcc OPTIONS : x86 : winchip2 : -march=winchip2 ;
-cpu-flags gcc OPTIONS : x86 : c3 : -march=c3 ;
-cpu-flags gcc OPTIONS : x86 : c3-2 : -march=c3-2 ;
-# Sparc
-cpu-flags gcc OPTIONS : sparc : c3 : -mcpu=c3 : default ;
-cpu-flags gcc OPTIONS : sparc : v7 : -mcpu=v7 ;
-cpu-flags gcc OPTIONS : sparc : cypress : -mcpu=cypress ;
-cpu-flags gcc OPTIONS : sparc : v8 : -mcpu=v8 ;
-cpu-flags gcc OPTIONS : sparc : supersparc : -mcpu=supersparc ;
-cpu-flags gcc OPTIONS : sparc : sparclite : -mcpu=sparclite ;
-cpu-flags gcc OPTIONS : sparc : hypersparc : -mcpu=hypersparc ;
-cpu-flags gcc OPTIONS : sparc : sparclite86x : -mcpu=sparclite86x ;
-cpu-flags gcc OPTIONS : sparc : f930 : -mcpu=f930 ;
-cpu-flags gcc OPTIONS : sparc : f934 : -mcpu=f934 ;
-cpu-flags gcc OPTIONS : sparc : sparclet : -mcpu=sparclet ;
-cpu-flags gcc OPTIONS : sparc : tsc701 : -mcpu=tsc701 ;
-cpu-flags gcc OPTIONS : sparc : v9 : -mcpu=v9 ;
-cpu-flags gcc OPTIONS : sparc : ultrasparc : -mcpu=ultrasparc ;
-cpu-flags gcc OPTIONS : sparc : ultrasparc3 : -mcpu=ultrasparc3 ;
-# RS/6000 & PowerPC
-cpu-flags gcc OPTIONS : power : 403 : -mcpu=403 ;
-cpu-flags gcc OPTIONS : power : 505 : -mcpu=505 ;
-cpu-flags gcc OPTIONS : power : 601 : -mcpu=601 ;
-cpu-flags gcc OPTIONS : power : 602 : -mcpu=602 ;
-cpu-flags gcc OPTIONS : power : 603 : -mcpu=603 ;
-cpu-flags gcc OPTIONS : power : 603e : -mcpu=603e ;
-cpu-flags gcc OPTIONS : power : 604 : -mcpu=604 ;
-cpu-flags gcc OPTIONS : power : 604e : -mcpu=604e ;
-cpu-flags gcc OPTIONS : power : 620 : -mcpu=620 ;
-cpu-flags gcc OPTIONS : power : 630 : -mcpu=630 ;
-cpu-flags gcc OPTIONS : power : 740 : -mcpu=740 ;
-cpu-flags gcc OPTIONS : power : 7400 : -mcpu=7400 ;
-cpu-flags gcc OPTIONS : power : 7450 : -mcpu=7450 ;
-cpu-flags gcc OPTIONS : power : 750 : -mcpu=750 ;
-cpu-flags gcc OPTIONS : power : 801 : -mcpu=801 ;
-cpu-flags gcc OPTIONS : power : 821 : -mcpu=821 ;
-cpu-flags gcc OPTIONS : power : 823 : -mcpu=823 ;
-cpu-flags gcc OPTIONS : power : 860 : -mcpu=860 ;
-cpu-flags gcc OPTIONS : power : 970 : -mcpu=970 ;
-cpu-flags gcc OPTIONS : power : 8540 : -mcpu=8540 ;
-cpu-flags gcc OPTIONS : power : power : -mcpu=power ;
-cpu-flags gcc OPTIONS : power : power2 : -mcpu=power2 ;
-cpu-flags gcc OPTIONS : power : power3 : -mcpu=power3 ;
-cpu-flags gcc OPTIONS : power : power4 : -mcpu=power4 ;
-cpu-flags gcc OPTIONS : power : power5 : -mcpu=power5 ;
-cpu-flags gcc OPTIONS : power : powerpc : -mcpu=powerpc ;
-cpu-flags gcc OPTIONS : power : powerpc64 : -mcpu=powerpc64 ;
-cpu-flags gcc OPTIONS : power : rios : -mcpu=rios ;
-cpu-flags gcc OPTIONS : power : rios1 : -mcpu=rios1 ;
-cpu-flags gcc OPTIONS : power : rios2 : -mcpu=rios2 ;
-cpu-flags gcc OPTIONS : power : rsc : -mcpu=rsc ;
-cpu-flags gcc OPTIONS : power : rs64a : -mcpu=rs64 ;
-# AIX variant of RS/6000 & PowerPC
-toolset.flags gcc AROPTIONS <address-model>64/<target-os>aix : "-X 64" ;
diff --git a/jam-files/boost-build/tools/gcc.py b/jam-files/boost-build/tools/gcc.py
deleted file mode 100644
index 2a3e675e..00000000
--- a/jam-files/boost-build/tools/gcc.py
+++ /dev/null
@@ -1,796 +0,0 @@
-# Status: being ported by Steven Watanabe
-# Base revision: 47077
-# TODO: common.jam needs to be ported
-# TODO: generators.jam needs to have register_c_compiler.
-#
-# Copyright 2001 David Abrahams.
-# Copyright 2002-2006 Rene Rivera.
-# Copyright 2002-2003 Vladimir Prus.
-#  Copyright (c) 2005 Reece H. Dunn.
-# Copyright 2006 Ilya Sokolov.
-# Copyright 2007 Roland Schwarz
-# Copyright 2007 Boris Gubenko.
-# Copyright 2008 Steven Watanabe
-#
-# Distributed under the Boost Software License, Version 1.0.
-#    (See accompanying file LICENSE_1_0.txt or copy at
-#          http://www.boost.org/LICENSE_1_0.txt)
-
-import os
-import subprocess
-import re
-
-import bjam
-
-from b2.tools import unix, common, rc, pch, builtin
-from b2.build import feature, type, toolset, generators
-from b2.util.utility import os_name, on_windows
-from b2.manager import get_manager
-from b2.build.generators import Generator
-from b2.build.toolset import flags
-from b2.util.utility import to_seq
-
-__debug = None
-
-def debug():
-    global __debug
-    if __debug is None:
-        __debug = "--debug-configuration" in bjam.variable("ARGV")        
-    return __debug
-
-feature.extend('toolset', ['gcc'])
-
-
-toolset.inherit_generators('gcc', [], 'unix', ['unix.link', 'unix.link.dll'])
-toolset.inherit_flags('gcc', 'unix')
-toolset.inherit_rules('gcc', 'unix')
-
-generators.override('gcc.prebuilt', 'builtin.prebuilt')
-generators.override('gcc.searched-lib-generator', 'searched-lib-generator')
-
-# Target naming is determined by types/lib.jam and the settings below this
-# comment.
-#
-# On *nix:
-#     libxxx.a     static library
-#     libxxx.so    shared library
-#
-# On windows (mingw):
-#     libxxx.lib   static library
-#     xxx.dll      DLL
-#     xxx.lib      import library
-#
-# On windows (cygwin) i.e. <target-os>cygwin
-#     libxxx.a     static library
-#     xxx.dll      DLL
-#     libxxx.dll.a import library
-#
-# Note: user can always override by using the <tag>@rule
-#       This settings have been choosen, so that mingw
-#       is in line with msvc naming conventions. For
-#       cygwin the cygwin naming convention has been choosen.
-
-# Make the "o" suffix used for gcc toolset on all
-# platforms
-type.set_generated_target_suffix('OBJ', ['<toolset>gcc'], 'o')
-type.set_generated_target_suffix('STATIC_LIB', ['<toolset>gcc', '<target-os>cygwin'], 'a')
-
-type.set_generated_target_suffix('IMPORT_LIB', ['<toolset>gcc', '<target-os>cygwin'], 'dll.a')
-type.set_generated_target_prefix('IMPORT_LIB', ['<toolset>gcc', '<target-os>cygwin'], 'lib')
-
-__machine_match = re.compile('^([^ ]+)')
-__version_match = re.compile('^([0-9.]+)')
-
-def init(version = None, command = None, options = None):
-    """
-        Initializes the gcc toolset for the given version. If necessary, command may
-        be used to specify where the compiler is located. The parameter 'options' is a
-        space-delimited list of options, each one specified as
-        <option-name>option-value. Valid option names are: cxxflags, linkflags and
-        linker-type. Accepted linker-type values are gnu, darwin, osf, hpux or sun
-        and the default value will be selected based on the current OS.
-        Example:
-          using gcc : 3.4 : : <cxxflags>foo <linkflags>bar <linker-type>sun ;
-    """
-
-    options = to_seq(options)
-    command = to_seq(command)
-
-    # Information about the gcc command...
-    #   The command.
-    command = to_seq(common.get_invocation_command('gcc', 'g++', command))
-    #   The root directory of the tool install.
-    root = feature.get_values('<root>', options) ;
-    #   The bin directory where to find the command to execute.
-    bin = None
-    #   The flavor of compiler.
-    flavor = feature.get_values('<flavor>', options)
-    #   Autodetect the root and bin dir if not given.
-    if command:
-        if not bin:
-            bin = common.get_absolute_tool_path(command[-1])
-        if not root:
-            root = os.path.dirname(bin)
-    #   Autodetect the version and flavor if not given.
-    if command:
-        machine_info = subprocess.Popen(command + ['-dumpmachine'], stdout=subprocess.PIPE).communicate()[0]
-        machine = __machine_match.search(machine_info).group(1)
-
-        version_info = subprocess.Popen(command + ['-dumpversion'], stdout=subprocess.PIPE).communicate()[0]
-        version = __version_match.search(version_info).group(1)
-        if not flavor and machine.find('mingw') != -1:
-            flavor = 'mingw'
-
-    condition = None
-    if flavor:
-        condition = common.check_init_parameters('gcc', None,
-            ('version', version),
-            ('flavor', flavor))
-    else:
-        condition = common.check_init_parameters('gcc', None,
-            ('version', version))
-
-    if command:
-        command = command[0]
-
-    common.handle_options('gcc', condition, command, options)
-
-    linker = feature.get_values('<linker-type>', options)
-    if not linker:
-        if os_name() == 'OSF':
-            linker = 'osf'
-        elif os_name() == 'HPUX':
-            linker = 'hpux' ;
-        else:
-            linker = 'gnu'
-
-    init_link_flags('gcc', linker, condition)
-
-    # If gcc is installed in non-standard location, we'd need to add
-    # LD_LIBRARY_PATH when running programs created with it (for unit-test/run
-    # rules).
-    if command:
-        # On multilib 64-bit boxes, there are both 32-bit and 64-bit libraries
-        # and all must be added to LD_LIBRARY_PATH. The linker will pick the
-        # right onces. Note that we don't provide a clean way to build 32-bit
-        # binary with 64-bit compiler, but user can always pass -m32 manually.
-        lib_path = [os.path.join(root, 'bin'),
-                    os.path.join(root, 'lib'),
-                    os.path.join(root, 'lib32'),
-                    os.path.join(root, 'lib64')]
-        if debug():
-            print 'notice: using gcc libraries ::', condition, '::', lib_path
-        toolset.flags('gcc.link', 'RUN_PATH', condition, lib_path)
-
-    # If it's not a system gcc install we should adjust the various programs as
-    # needed to prefer using the install specific versions. This is essential
-    # for correct use of MinGW and for cross-compiling.
-
-    # - The archive builder.
-    archiver = common.get_invocation_command('gcc',
-            'ar', feature.get_values('<archiver>', options), [bin], path_last=True)
-    toolset.flags('gcc.archive', '.AR', condition, [archiver])
-    if debug():
-        print 'notice: using gcc archiver ::', condition, '::', archiver
-
-    # - The resource compiler.
-    rc_command = common.get_invocation_command_nodefault('gcc',
-            'windres', feature.get_values('<rc>', options), [bin], path_last=True)
-    rc_type = feature.get_values('<rc-type>', options)
-
-    if not rc_type:
-        rc_type = 'windres'
-
-    if not rc_command:
-        # If we can't find an RC compiler we fallback to a null RC compiler that
-        # creates empty object files. This allows the same Jamfiles to work
-        # across the board. The null RC uses the assembler to create the empty
-        # objects, so configure that.
-        rc_command = common.get_invocation_command('gcc', 'as', [], [bin], path_last=True)
-        rc_type = 'null'
-    rc.configure(rc_command, condition, '<rc-type>' + rc_type)
-
-###if [ os.name ] = NT
-###{
-###    # This causes single-line command invocation to not go through .bat files,
-###    # thus avoiding command-line length limitations.
-###    JAMSHELL = % ;
-###}
-
-#FIXME: when register_c_compiler is moved to
-# generators, these should be updated
-builtin.register_c_compiler('gcc.compile.c++', ['CPP'], ['OBJ'], ['<toolset>gcc'])
-builtin.register_c_compiler('gcc.compile.c', ['C'], ['OBJ'], ['<toolset>gcc'])
-builtin.register_c_compiler('gcc.compile.asm', ['ASM'], ['OBJ'], ['<toolset>gcc'])
-
-# pch support
-
-# The compiler looks for a precompiled header in each directory just before it
-# looks for the include file in that directory. The name searched for is the
-# name specified in the #include directive with ".gch" suffix appended. The
-# logic in gcc-pch-generator will make sure that BASE_PCH suffix is appended to
-# full name of the header.
-
-type.set_generated_target_suffix('PCH', ['<toolset>gcc'], 'gch')
-
-# GCC-specific pch generator.
-class GccPchGenerator(pch.PchGenerator):
-
-    # Inherit the __init__ method
-
-    def run_pch(self, project, name, prop_set, sources):
-        # Find the header in sources. Ignore any CPP sources.
-        header = None
-        for s in sources:
-            if type.is_derived(s.type, 'H'):
-                header = s
-
-        # Error handling: Base header file name should be the same as the base
-        # precompiled header name.
-        header_name = header.name
-        header_basename = os.path.basename(header_name).rsplit('.', 1)[0]
-        if header_basename != name:
-            location = project.project_module
-            ###FIXME:
-            raise Exception()
-            ### errors.user-error "in" $(location)": pch target name `"$(name)"' should be the same as the base name of header file `"$(header-name)"'" ;
-
-        pch_file = Generator.run(self, project, name, prop_set, [header])
-
-        # return result of base class and pch-file property as usage-requirements
-        # FIXME: what about multiple results from generator.run?
-        return (property_set.create('<pch-file>' + pch_file[0], '<cflags>-Winvalid-pch'),
-                pch_file)
-
-    # Calls the base version specifying source's name as the name of the created
-    # target. As result, the PCH will be named whatever.hpp.gch, and not
-    # whatever.gch.
-    def generated_targets(self, sources, prop_set, project, name = None):
-        name = sources[0].name
-        return Generator.generated_targets(self, sources,
-            prop_set, project, name)
-
-# Note: the 'H' source type will catch both '.h' header and '.hpp' header. The
-# latter have HPP type, but HPP type is derived from H. The type of compilation
-# is determined entirely by the destination type.
-generators.register(GccPchGenerator('gcc.compile.c.pch', False, ['H'], ['C_PCH'], ['<pch>on', '<toolset>gcc' ]))
-generators.register(GccPchGenerator('gcc.compile.c++.pch', False, ['H'], ['CPP_PCH'], ['<pch>on', '<toolset>gcc' ]))
-
-# Override default do-nothing generators.
-generators.override('gcc.compile.c.pch', 'pch.default-c-pch-generator')
-generators.override('gcc.compile.c++.pch', 'pch.default-cpp-pch-generator')
-
-flags('gcc.compile', 'PCH_FILE', ['<pch>on'], ['<pch-file>'])
-
-# Declare flags and action for compilation
-flags('gcc.compile', 'OPTIONS', ['<optimization>off'], ['-O0'])
-flags('gcc.compile', 'OPTIONS', ['<optimization>speed'], ['-O3'])
-flags('gcc.compile', 'OPTIONS', ['<optimization>space'], ['-Os'])
-
-flags('gcc.compile', 'OPTIONS', ['<inlining>off'], ['-fno-inline'])
-flags('gcc.compile', 'OPTIONS', ['<inlining>on'], ['-Wno-inline'])
-flags('gcc.compile', 'OPTIONS', ['<inlining>full'], ['-finline-functions', '-Wno-inline'])
-
-flags('gcc.compile', 'OPTIONS', ['<warnings>off'], ['-w'])
-flags('gcc.compile', 'OPTIONS', ['<warnings>on'], ['-Wall'])
-flags('gcc.compile', 'OPTIONS', ['<warnings>all'], ['-Wall', '-pedantic'])
-flags('gcc.compile', 'OPTIONS', ['<warnings-as-errors>on'], ['-Werror'])
-
-flags('gcc.compile', 'OPTIONS', ['<debug-symbols>on'], ['-g'])
-flags('gcc.compile', 'OPTIONS', ['<profiling>on'], ['-pg'])
-flags('gcc.compile', 'OPTIONS', ['<rtti>off'], ['-fno-rtti'])
-
-# On cygwin and mingw, gcc generates position independent code by default, and
-# warns if -fPIC is specified. This might not be the right way of checking if
-# we're using cygwin. For example, it's possible to run cygwin gcc from NT
-# shell, or using crosscompiling. But we'll solve that problem when it's time.
-# In that case we'll just add another parameter to 'init' and move this login
-# inside 'init'.
-if not os_name () in ['CYGWIN', 'NT']:
-    # This logic will add -fPIC for all compilations:
-    #
-    # lib a : a.cpp b ;
-    # obj b : b.cpp ;
-    # exe c : c.cpp a d ;
-    # obj d : d.cpp ;
-    #
-    # This all is fine, except that 'd' will be compiled with -fPIC even though
-    # it's not needed, as 'd' is used only in exe. However, it's hard to detect
-    # where a target is going to be used. Alternative, we can set -fPIC only
-    # when main target type is LIB but than 'b' will be compiled without -fPIC.
-    # In x86-64 that will lead to link errors. So, compile everything with
-    # -fPIC.
-    #
-    # Yet another alternative would be to create propagated <sharedable>
-    # feature, and set it when building shared libraries, but that's hard to
-    # implement and will increase target path length even more.
-    flags('gcc.compile', 'OPTIONS', ['<link>shared'], ['-fPIC'])
-
-if os_name() != 'NT' and os_name() != 'OSF' and os_name() != 'HPUX':
-    # OSF does have an option called -soname but it doesn't seem to work as
-    # expected, therefore it has been disabled.
-    HAVE_SONAME   = ''
-    SONAME_OPTION = '-h'
-
-
-flags('gcc.compile', 'USER_OPTIONS', [], ['<cflags>'])
-flags('gcc.compile.c++', 'USER_OPTIONS',[], ['<cxxflags>'])
-flags('gcc.compile', 'DEFINES', [], ['<define>'])
-flags('gcc.compile', 'INCLUDES', [], ['<include>'])
-
-engine = get_manager().engine()
-
-engine.register_action('gcc.compile.c++.pch', 
-    '"$(CONFIG_COMMAND)" -x c++-header $(OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -c -o "$(<)" "$(>)"')
-
-engine.register_action('gcc.compile.c.pch',
-    '"$(CONFIG_COMMAND)" -x c-header $(OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -c -o "$(<)" "$(>)"')
-
-
-def gcc_compile_cpp(targets, sources, properties):
-    # Some extensions are compiled as C++ by default. For others, we need to
-    # pass -x c++. We could always pass -x c++ but distcc does not work with it.
-    extension = os.path.splitext (sources [0]) [1]
-    lang = ''
-    if not extension in ['.cc', '.cp', '.cxx', '.cpp', '.c++', '.C']:
-        lang = '-x c++'
-    get_manager().engine().set_target_variable (targets, 'LANG', lang)
-    engine.add_dependency(targets, bjam.call('get-target-variable', targets, 'PCH_FILE'))
-
-def gcc_compile_c(targets, sources, properties):
-    engine = get_manager().engine()
-    # If we use the name g++ then default file suffix -> language mapping does
-    # not work. So have to pass -x option. Maybe, we can work around this by
-    # allowing the user to specify both C and C++ compiler names.
-    #if $(>:S) != .c
-    #{
-    engine.set_target_variable (targets, 'LANG', '-x c')
-    #}
-    engine.add_dependency(targets, bjam.call('get-target-variable', targets, 'PCH_FILE'))
-    
-engine.register_action(
-    'gcc.compile.c++',
-    '"$(CONFIG_COMMAND)" $(LANG) -ftemplate-depth-128 $(OPTIONS) ' +
-        '$(USER_OPTIONS) -D$(DEFINES) -I"$(PCH_FILE:D)" -I"$(INCLUDES)" ' +
-        '-c -o "$(<:W)" "$(>:W)"',
-    function=gcc_compile_cpp,
-    bound_list=['PCH_FILE'])
-
-engine.register_action(
-    'gcc.compile.c',
-    '"$(CONFIG_COMMAND)" $(LANG) $(OPTIONS) $(USER_OPTIONS) -D$(DEFINES) ' +
-        '-I"$(PCH_FILE:D)" -I"$(INCLUDES)" -c -o "$(<)" "$(>)"',
-    function=gcc_compile_c,
-    bound_list=['PCH_FILE'])
-
-def gcc_compile_asm(targets, sources, properties):
-    get_manager().engine().set_target_variable(targets, 'LANG', '-x assembler-with-cpp')
-
-engine.register_action(
-    'gcc.compile.asm',
-    '"$(CONFIG_COMMAND)" $(LANG) $(OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -c -o "$(<)" "$(>)"',
-    function=gcc_compile_asm)
-
-
-class GccLinkingGenerator(unix.UnixLinkingGenerator):
-    """
-        The class which check that we don't try to use the <runtime-link>static
-        property while creating or using shared library, since it's not supported by
-        gcc/libc.
-    """
-    def run(self, project, name, ps, sources):
-        # TODO: Replace this with the use of a target-os property.
-
-        no_static_link = False
-        if bjam.variable('UNIX'):
-            no_static_link = True;
-        ##FIXME: what does this mean?
-##        {
-##            switch [ modules.peek : JAMUNAME ]
-##            {
-##                case * : no-static-link = true ;
-##            }
-##        }
-
-        reason = None
-        if no_static_link and ps.get('runtime-link') == 'static':
-            if ps.get('link') == 'shared':
-                reason = "On gcc, DLL can't be build with '<runtime-link>static'."
-            elif type.is_derived(self.target_types[0], 'EXE'):
-                for s in sources:
-                    source_type = s.type()
-                    if source_type and type.is_derived(source_type, 'SHARED_LIB'):
-                        reason = "On gcc, using DLLS together with the " +\
-                                 "<runtime-link>static options is not possible "
-        if reason:
-            print 'warning:', reason
-            print 'warning:',\
-                "It is suggested to use '<runtime-link>static' together",\
-                "with '<link>static'." ;
-            return
-        else:
-            generated_targets = unix.UnixLinkingGenerator.run(self, project,
-                name, ps, sources)
-            return generated_targets
-
-if on_windows():
-    flags('gcc.link.dll', '.IMPLIB-COMMAND', [], ['-Wl,--out-implib,'])
-    generators.register(
-        GccLinkingGenerator('gcc.link', True,
-            ['OBJ', 'SEARCHED_LIB', 'STATIC_LIB', 'IMPORT_LIB'],
-            [ 'EXE' ],
-            [ '<toolset>gcc' ]))
-    generators.register(
-        GccLinkingGenerator('gcc.link.dll', True,
-            ['OBJ', 'SEARCHED_LIB', 'STATIC_LIB', 'IMPORT_LIB'],
-            ['IMPORT_LIB', 'SHARED_LIB'],
-            ['<toolset>gcc']))
-else:
-    generators.register(
-        GccLinkingGenerator('gcc.link', True,
-            ['LIB', 'OBJ'],
-            ['EXE'],
-            ['<toolset>gcc']))
-    generators.register(
-        GccLinkingGenerator('gcc.link.dll', True,
-            ['LIB', 'OBJ'],
-            ['SHARED_LIB'],
-            ['<toolset>gcc']))
-
-# Declare flags for linking.
-# First, the common flags.
-flags('gcc.link', 'OPTIONS', ['<debug-symbols>on'], ['-g'])
-flags('gcc.link', 'OPTIONS', ['<profiling>on'], ['-pg'])
-flags('gcc.link', 'USER_OPTIONS', [], ['<linkflags>'])
-flags('gcc.link', 'LINKPATH', [], ['<library-path>'])
-flags('gcc.link', 'FINDLIBS-ST', [], ['<find-static-library>'])
-flags('gcc.link', 'FINDLIBS-SA', [], ['<find-shared-library>'])
-flags('gcc.link', 'LIBRARIES', [], ['<library-file>'])
-
-# For <runtime-link>static we made sure there are no dynamic libraries in the
-# link. On HP-UX not all system libraries exist as archived libraries (for
-# example, there is no libunwind.a), so, on this platform, the -static option
-# cannot be specified.
-if os_name() != 'HPUX':
-    flags('gcc.link', 'OPTIONS', ['<runtime-link>static'], ['-static'])
-
-# Now, the vendor specific flags.
-# The parameter linker can be either gnu, darwin, osf, hpux or sun.
-def init_link_flags(toolset, linker, condition):
-    """
-        Now, the vendor specific flags.
-        The parameter linker can be either gnu, darwin, osf, hpux or sun.
-    """
-    toolset_link = toolset + '.link'
-    if linker == 'gnu':
-        # Strip the binary when no debugging is needed. We use --strip-all flag
-        # as opposed to -s since icc (intel's compiler) is generally
-        # option-compatible with and inherits from the gcc toolset, but does not
-        # support -s.
-
-        # FIXME: what does unchecked translate to?
-        flags(toolset_link, 'OPTIONS', map(lambda x: x + '/<debug-symbols>off', condition), ['-Wl,--strip-all'])  # : unchecked ;
-        flags(toolset_link, 'RPATH',       condition,                      ['<dll-path>'])       # : unchecked ;
-        flags(toolset_link, 'RPATH_LINK',  condition,                      ['<xdll-path>'])      # : unchecked ;
-        flags(toolset_link, 'START-GROUP', condition,                      ['-Wl,--start-group'])# : unchecked ;
-        flags(toolset_link, 'END-GROUP',   condition,                      ['-Wl,--end-group'])  # : unchecked ;
-
-        # gnu ld has the ability to change the search behaviour for libraries
-        # referenced by -l switch. These modifiers are -Bstatic and -Bdynamic
-        # and change search for -l switches that follow them. The following list
-        # shows the tried variants.
-        # The search stops at the first variant that has a match.
-        # *nix: -Bstatic -lxxx
-        #    libxxx.a
-        #
-        # *nix: -Bdynamic -lxxx
-        #    libxxx.so
-        #    libxxx.a
-        #
-        # windows (mingw,cygwin) -Bstatic -lxxx
-        #    libxxx.a
-        #    xxx.lib
-        #
-        # windows (mingw,cygwin) -Bdynamic -lxxx
-        #    libxxx.dll.a
-        #    xxx.dll.a
-        #    libxxx.a
-        #    xxx.lib
-        #    cygxxx.dll (*)
-        #    libxxx.dll
-        #    xxx.dll
-        #    libxxx.a
-        #
-        # (*) This is for cygwin
-        # Please note that -Bstatic and -Bdynamic are not a guarantee that a
-        # static or dynamic lib indeed gets linked in. The switches only change
-        # search patterns!
-
-        # On *nix mixing shared libs with static runtime is not a good idea.
-        flags(toolset_link, 'FINDLIBS-ST-PFX',
-              map(lambda x: x + '/<runtime-link>shared', condition),
-            ['-Wl,-Bstatic']) # : unchecked ;
-        flags(toolset_link, 'FINDLIBS-SA-PFX',
-              map(lambda x: x + '/<runtime-link>shared', condition),
-            ['-Wl,-Bdynamic']) # : unchecked ;
-
-        # On windows allow mixing of static and dynamic libs with static
-        # runtime.
-        flags(toolset_link, 'FINDLIBS-ST-PFX',
-              map(lambda x: x + '/<runtime-link>static/<target-os>windows', condition),
-              ['-Wl,-Bstatic']) # : unchecked ;
-        flags(toolset_link, 'FINDLIBS-SA-PFX',
-              map(lambda x: x + '/<runtime-link>static/<target-os>windows', condition),
-              ['-Wl,-Bdynamic']) # : unchecked ;
-        flags(toolset_link, 'OPTIONS',
-              map(lambda x: x + '/<runtime-link>static/<target-os>windows', condition),
-              ['-Wl,-Bstatic']) # : unchecked ;
-
-    elif linker == 'darwin':
-        # On Darwin, the -s option to ld does not work unless we pass -static,
-        # and passing -static unconditionally is a bad idea. So, don't pass -s.
-        # at all, darwin.jam will use separate 'strip' invocation.
-        flags(toolset_link, 'RPATH', condition, ['<dll-path>']) # : unchecked ;
-        flags(toolset_link, 'RPATH_LINK', condition, ['<xdll-path>']) # : unchecked ;
-
-    elif linker == 'osf':
-        # No --strip-all, just -s.
-        flags(toolset_link, 'OPTIONS', map(lambda x: x + '/<debug-symbols>off', condition), ['-Wl,-s'])
-            # : unchecked ;
-        flags(toolset_link, 'RPATH', condition, ['<dll-path>']) # : unchecked ;
-        # This does not supports -R.
-        flags(toolset_link, 'RPATH_OPTION', condition, ['-rpath']) # : unchecked ;
-        # -rpath-link is not supported at all.
-
-    elif linker == 'sun':
-        flags(toolset_link, 'OPTIONS', map(lambda x: x + '/<debug-symbols>off', condition), ['-Wl,-s'])
-            # : unchecked ;
-        flags(toolset_link, 'RPATH', condition, ['<dll-path>']) # : unchecked ;
-        # Solaris linker does not have a separate -rpath-link, but allows to use
-        # -L for the same purpose.
-        flags(toolset_link, 'LINKPATH', condition, ['<xdll-path>']) # : unchecked ;
-
-        # This permits shared libraries with non-PIC code on Solaris.
-        # VP, 2004/09/07: Now that we have -fPIC hardcode in link.dll, the
-        # following is not needed. Whether -fPIC should be hardcoded, is a
-        # separate question.
-        # AH, 2004/10/16: it is still necessary because some tests link against
-        # static libraries that were compiled without PIC.
-        flags(toolset_link, 'OPTIONS', map(lambda x: x + '/<link>shared', condition), ['-mimpure-text'])
-            # : unchecked ;
-
-    elif linker == 'hpux':
-        flags(toolset_link, 'OPTIONS', map(lambda x: x + '/<debug-symbols>off', condition),
-            ['-Wl,-s']) # : unchecked ;
-        flags(toolset_link, 'OPTIONS', map(lambda x: x + '/<link>shared', condition),
-            ['-fPIC']) # : unchecked ;
-
-    else:
-        # FIXME:
-        errors.user_error(
-        "$(toolset) initialization: invalid linker '$(linker)' " +
-        "The value '$(linker)' specified for <linker> is not recognized. " +
-        "Possible values are 'gnu', 'darwin', 'osf', 'hpux' or 'sun'")
-
-# Declare actions for linking.
-def gcc_link(targets, sources, properties):
-    engine = get_manager().engine()
-    engine.set_target_variable(targets, 'SPACE', ' ')
-    # Serialize execution of the 'link' action, since running N links in
-    # parallel is just slower. For now, serialize only gcc links, it might be a
-    # good idea to serialize all links.
-    engine.set_target_variable(targets, 'JAM_SEMAPHORE', '<s>gcc-link-semaphore')
-
-engine.register_action(
-    'gcc.link',
-    '"$(CONFIG_COMMAND)" -L"$(LINKPATH)" ' +
-        '-Wl,$(RPATH_OPTION:E=-R)$(SPACE)-Wl,"$(RPATH)" ' +
-        '-Wl,-rpath-link$(SPACE)-Wl,"$(RPATH_LINK)" -o "$(<)" ' +
-        '$(START-GROUP) "$(>)" "$(LIBRARIES)" $(FINDLIBS-ST-PFX) ' +
-        '-l$(FINDLIBS-ST) $(FINDLIBS-SA-PFX) -l$(FINDLIBS-SA) $(END-GROUP) ' +
-        '$(OPTIONS) $(USER_OPTIONS)',
-    function=gcc_link,
-    bound_list=['LIBRARIES'])
-
-# Default value. Mostly for the sake of intel-linux that inherits from gcc, but
-# does not have the same logic to set the .AR variable. We can put the same
-# logic in intel-linux, but that's hardly worth the trouble as on Linux, 'ar' is
-# always available.
-__AR = 'ar'
-
-flags('gcc.archive', 'AROPTIONS', [], ['<archiveflags>'])
-
-def gcc_archive(targets, sources, properties):
-    # Always remove archive and start again. Here's rationale from
-    #
-    # Andre Hentz:
-    #
-    # I had a file, say a1.c, that was included into liba.a. I moved a1.c to
-    # a2.c, updated my Jamfiles and rebuilt. My program was crashing with absurd
-    # errors. After some debugging I traced it back to the fact that a1.o was
-    # *still* in liba.a
-    #
-    # Rene Rivera:
-    #
-    # Originally removing the archive was done by splicing an RM onto the
-    # archive action. That makes archives fail to build on NT when they have
-    # many files because it will no longer execute the action directly and blow
-    # the line length limit. Instead we remove the file in a different action,
-    # just before building the archive.
-    clean = targets[0] + '(clean)'
-    bjam.call('TEMPORARY', clean)
-    bjam.call('NOCARE', clean)
-    engine = get_manager().engine()
-    engine.set_target_variable('LOCATE', clean, bjam.call('get-target-variable', targets, 'LOCATE'))
-    engine.add_dependency(clean, sources)
-    engine.add_dependency(targets, clean)
-    engine.set_update_action('common.RmTemps', clean, targets)
-
-# Declare action for creating static libraries.
-# The letter 'r' means to add files to the archive with replacement. Since we
-# remove archive, we don't care about replacement, but there's no option "add
-# without replacement".
-# The letter 'c' suppresses the warning in case the archive does not exists yet.
-# That warning is produced only on some platforms, for whatever reasons.
-engine.register_action('gcc.archive',
-                       '"$(.AR)" $(AROPTIONS) rc "$(<)" "$(>)"',
-                       function=gcc_archive,
-                       flags=['piecemeal'])
-
-def gcc_link_dll(targets, sources, properties):
-    engine = get_manager().engine()
-    engine.set_target_variable(targets, 'SPACE', ' ')
-    engine.set_target_variable(targets, 'JAM_SEMAPHORE', '<s>gcc-link-semaphore')
-    engine.set_target_variable(targets, "HAVE_SONAME", HAVE_SONAME)
-    engine.set_target_variable(targets, "SONAME_OPTION", SONAME_OPTION)
-
-engine.register_action(
-    'gcc.link.dll',
-    # Differ from 'link' above only by -shared.
-    '"$(CONFIG_COMMAND)" -L"$(LINKPATH)" ' +
-        '-Wl,$(RPATH_OPTION:E=-R)$(SPACE)-Wl,"$(RPATH)" ' +
-        '"$(.IMPLIB-COMMAND)$(<[1])" -o "$(<[-1])" ' +
-        '$(HAVE_SONAME)-Wl,$(SONAME_OPTION)$(SPACE)-Wl,$(<[-1]:D=) ' +
-        '-shared $(START-GROUP) "$(>)" "$(LIBRARIES)" $(FINDLIBS-ST-PFX) ' +
-        '-l$(FINDLIBS-ST) $(FINDLIBS-SA-PFX) -l$(FINDLIBS-SA) $(END-GROUP) ' +
-        '$(OPTIONS) $(USER_OPTIONS)',
-    function = gcc_link_dll,
-    bound_list=['LIBRARIES'])
-
-# Set up threading support. It's somewhat contrived, so perform it at the end,
-# to avoid cluttering other code.
-
-if on_windows():
-    flags('gcc', 'OPTIONS', ['<threading>multi'], ['-mthreads'])
-elif bjam.variable('UNIX'):
-    jamuname = bjam.variable('JAMUNAME')
-    host_os_name = jamuname[0]
-    if host_os_name.startswith('SunOS'):
-        flags('gcc', 'OPTIONS', ['<threading>multi'], ['-pthreads'])
-        flags('gcc', 'FINDLIBS-SA', [], ['rt'])
-    elif host_os_name == 'BeOS':
-        # BeOS has no threading options, don't set anything here.
-        pass
-    elif host_os_name.endswith('BSD'):
-        flags('gcc', 'OPTIONS', ['<threading>multi'], ['-pthread'])
-        # there is no -lrt on BSD
-    elif host_os_name == 'DragonFly':
-        flags('gcc', 'OPTIONS', ['<threading>multi'], ['-pthread'])
-        # there is no -lrt on BSD - DragonFly is a FreeBSD variant,
-        # which anoyingly doesn't say it's a *BSD.
-    elif host_os_name == 'IRIX':
-        # gcc on IRIX does not support multi-threading, don't set anything here.
-        pass
-    elif host_os_name == 'Darwin':
-        # Darwin has no threading options, don't set anything here.
-        pass
-    else:
-        flags('gcc', 'OPTIONS', ['<threading>multi'], ['-pthread'])
-        flags('gcc', 'FINDLIBS-SA', [], ['rt'])
-
-def cpu_flags(toolset, variable, architecture, instruction_set, values, default=None):
-    #FIXME: for some reason this fails.  Probably out of date feature code
-##    if default:
-##        flags(toolset, variable,
-##              ['<architecture>' + architecture + '/<instruction-set>'],
-##              values)
-    flags(toolset, variable,
-          #FIXME: same as above
-          [##'<architecture>/<instruction-set>' + instruction_set,
-           '<architecture>' + architecture + '/<instruction-set>' + instruction_set],
-          values)
-
-# Set architecture/instruction-set options.
-#
-# x86 and compatible
-flags('gcc', 'OPTIONS', ['<architecture>x86/<address-model>32'], ['-m32'])
-flags('gcc', 'OPTIONS', ['<architecture>x86/<address-model>64'], ['-m64'])
-cpu_flags('gcc', 'OPTIONS', 'x86', 'i386', ['-march=i386'], default=True)
-cpu_flags('gcc', 'OPTIONS', 'x86', 'i486', ['-march=i486'])
-cpu_flags('gcc', 'OPTIONS', 'x86', 'i586', ['-march=i586'])
-cpu_flags('gcc', 'OPTIONS', 'x86', 'i686', ['-march=i686'])
-cpu_flags('gcc', 'OPTIONS', 'x86', 'pentium', ['-march=pentium'])
-cpu_flags('gcc', 'OPTIONS', 'x86', 'pentium-mmx', ['-march=pentium-mmx'])
-cpu_flags('gcc', 'OPTIONS', 'x86', 'pentiumpro', ['-march=pentiumpro'])
-cpu_flags('gcc', 'OPTIONS', 'x86', 'pentium2', ['-march=pentium2'])
-cpu_flags('gcc', 'OPTIONS', 'x86', 'pentium3', ['-march=pentium3'])
-cpu_flags('gcc', 'OPTIONS', 'x86', 'pentium3m', ['-march=pentium3m'])
-cpu_flags('gcc', 'OPTIONS', 'x86', 'pentium-m', ['-march=pentium-m'])
-cpu_flags('gcc', 'OPTIONS', 'x86', 'pentium4', ['-march=pentium4'])
-cpu_flags('gcc', 'OPTIONS', 'x86', 'pentium4m', ['-march=pentium4m'])
-cpu_flags('gcc', 'OPTIONS', 'x86', 'prescott', ['-march=prescott'])
-cpu_flags('gcc', 'OPTIONS', 'x86', 'nocona', ['-march=nocona'])
-cpu_flags('gcc', 'OPTIONS', 'x86', 'k6', ['-march=k6'])
-cpu_flags('gcc', 'OPTIONS', 'x86', 'k6-2', ['-march=k6-2'])
-cpu_flags('gcc', 'OPTIONS', 'x86', 'k6-3', ['-march=k6-3'])
-cpu_flags('gcc', 'OPTIONS', 'x86', 'athlon', ['-march=athlon'])
-cpu_flags('gcc', 'OPTIONS', 'x86', 'athlon-tbird', ['-march=athlon-tbird'])
-cpu_flags('gcc', 'OPTIONS', 'x86', 'athlon-4', ['-march=athlon-4'])
-cpu_flags('gcc', 'OPTIONS', 'x86', 'athlon-xp', ['-march=athlon-xp'])
-cpu_flags('gcc', 'OPTIONS', 'x86', 'athlon-mp', ['-march=athlon-mp'])
-##
-cpu_flags('gcc', 'OPTIONS', 'x86', 'k8', ['-march=k8'])
-cpu_flags('gcc', 'OPTIONS', 'x86', 'opteron', ['-march=opteron'])
-cpu_flags('gcc', 'OPTIONS', 'x86', 'athlon64', ['-march=athlon64'])
-cpu_flags('gcc', 'OPTIONS', 'x86', 'athlon-fx', ['-march=athlon-fx'])
-cpu_flags('gcc', 'OPTIONS', 'x86', 'winchip-c6', ['-march=winchip-c6'])
-cpu_flags('gcc', 'OPTIONS', 'x86', 'winchip2', ['-march=winchip2'])
-cpu_flags('gcc', 'OPTIONS', 'x86', 'c3', ['-march=c3'])
-cpu_flags('gcc', 'OPTIONS', 'x86', 'c3-2', ['-march=c3-2'])
-# Sparc
-flags('gcc', 'OPTIONS', ['<architecture>sparc/<address-model>32'], ['-m32'])
-flags('gcc', 'OPTIONS', ['<architecture>sparc/<address-model>64'], ['-m64'])
-cpu_flags('gcc', 'OPTIONS', 'sparc', 'c3', ['-mcpu=c3'], default=True)
-cpu_flags('gcc', 'OPTIONS', 'sparc', 'v7', ['-mcpu=v7'])
-cpu_flags('gcc', 'OPTIONS', 'sparc', 'cypress', ['-mcpu=cypress'])
-cpu_flags('gcc', 'OPTIONS', 'sparc', 'v8', ['-mcpu=v8'])
-cpu_flags('gcc', 'OPTIONS', 'sparc', 'supersparc', ['-mcpu=supersparc'])
-cpu_flags('gcc', 'OPTIONS', 'sparc', 'sparclite', ['-mcpu=sparclite'])
-cpu_flags('gcc', 'OPTIONS', 'sparc', 'hypersparc', ['-mcpu=hypersparc'])
-cpu_flags('gcc', 'OPTIONS', 'sparc', 'sparclite86x', ['-mcpu=sparclite86x'])
-cpu_flags('gcc', 'OPTIONS', 'sparc', 'f930', ['-mcpu=f930'])
-cpu_flags('gcc', 'OPTIONS', 'sparc', 'f934', ['-mcpu=f934'])
-cpu_flags('gcc', 'OPTIONS', 'sparc', 'sparclet', ['-mcpu=sparclet'])
-cpu_flags('gcc', 'OPTIONS', 'sparc', 'tsc701', ['-mcpu=tsc701'])
-cpu_flags('gcc', 'OPTIONS', 'sparc', 'v9', ['-mcpu=v9'])
-cpu_flags('gcc', 'OPTIONS', 'sparc', 'ultrasparc', ['-mcpu=ultrasparc'])
-cpu_flags('gcc', 'OPTIONS', 'sparc', 'ultrasparc3', ['-mcpu=ultrasparc3'])
-# RS/6000 & PowerPC
-flags('gcc', 'OPTIONS', ['<architecture>power/<address-model>32'], ['-m32'])
-flags('gcc', 'OPTIONS', ['<architecture>power/<address-model>64'], ['-m64'])
-cpu_flags('gcc', 'OPTIONS', 'power', '403', ['-mcpu=403'])
-cpu_flags('gcc', 'OPTIONS', 'power', '505', ['-mcpu=505'])
-cpu_flags('gcc', 'OPTIONS', 'power', '601', ['-mcpu=601'])
-cpu_flags('gcc', 'OPTIONS', 'power', '602', ['-mcpu=602'])
-cpu_flags('gcc', 'OPTIONS', 'power', '603', ['-mcpu=603'])
-cpu_flags('gcc', 'OPTIONS', 'power', '603e', ['-mcpu=603e'])
-cpu_flags('gcc', 'OPTIONS', 'power', '604', ['-mcpu=604'])
-cpu_flags('gcc', 'OPTIONS', 'power', '604e', ['-mcpu=604e'])
-cpu_flags('gcc', 'OPTIONS', 'power', '620', ['-mcpu=620'])
-cpu_flags('gcc', 'OPTIONS', 'power', '630', ['-mcpu=630'])
-cpu_flags('gcc', 'OPTIONS', 'power', '740', ['-mcpu=740'])
-cpu_flags('gcc', 'OPTIONS', 'power', '7400', ['-mcpu=7400'])
-cpu_flags('gcc', 'OPTIONS', 'power', '7450', ['-mcpu=7450'])
-cpu_flags('gcc', 'OPTIONS', 'power', '750', ['-mcpu=750'])
-cpu_flags('gcc', 'OPTIONS', 'power', '801', ['-mcpu=801'])
-cpu_flags('gcc', 'OPTIONS', 'power', '821', ['-mcpu=821'])
-cpu_flags('gcc', 'OPTIONS', 'power', '823', ['-mcpu=823'])
-cpu_flags('gcc', 'OPTIONS', 'power', '860', ['-mcpu=860'])
-cpu_flags('gcc', 'OPTIONS', 'power', '970', ['-mcpu=970'])
-cpu_flags('gcc', 'OPTIONS', 'power', '8540', ['-mcpu=8540'])
-cpu_flags('gcc', 'OPTIONS', 'power', 'power', ['-mcpu=power'])
-cpu_flags('gcc', 'OPTIONS', 'power', 'power2', ['-mcpu=power2'])
-cpu_flags('gcc', 'OPTIONS', 'power', 'power3', ['-mcpu=power3'])
-cpu_flags('gcc', 'OPTIONS', 'power', 'power4', ['-mcpu=power4'])
-cpu_flags('gcc', 'OPTIONS', 'power', 'power5', ['-mcpu=power5'])
-cpu_flags('gcc', 'OPTIONS', 'power', 'powerpc', ['-mcpu=powerpc'])
-cpu_flags('gcc', 'OPTIONS', 'power', 'powerpc64', ['-mcpu=powerpc64'])
-cpu_flags('gcc', 'OPTIONS', 'power', 'rios', ['-mcpu=rios'])
-cpu_flags('gcc', 'OPTIONS', 'power', 'rios1', ['-mcpu=rios1'])
-cpu_flags('gcc', 'OPTIONS', 'power', 'rios2', ['-mcpu=rios2'])
-cpu_flags('gcc', 'OPTIONS', 'power', 'rsc', ['-mcpu=rsc'])
-cpu_flags('gcc', 'OPTIONS', 'power', 'rs64a', ['-mcpu=rs64'])
-# AIX variant of RS/6000 & PowerPC
-flags('gcc', 'OPTIONS', ['<architecture>power/<address-model>32/<target-os>aix'], ['-maix32'])
-flags('gcc', 'OPTIONS', ['<architecture>power/<address-model>64/<target-os>aix'], ['-maix64'])
-flags('gcc', 'AROPTIONS', ['<architecture>power/<address-model>64/<target-os>aix'], ['-X 64'])
diff --git a/jam-files/boost-build/tools/generate.jam b/jam-files/boost-build/tools/generate.jam
deleted file mode 100644
index 6732fa35..00000000
--- a/jam-files/boost-build/tools/generate.jam
+++ /dev/null
@@ -1,108 +0,0 @@
-# Copyright 2006 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-# Declares main target 'generate' used to produce targets by calling a
-# user-provided rule that takes and produces virtual targets.
-
-import "class" : new ;
-import errors ;
-import feature ;
-import project ;
-import property ;
-import property-set ;
-import targets ;
-import regex ;
-
-
-feature.feature generating-rule : : free ;
-
-
-class generated-target-class : basic-target
-{
-    import errors ;
-    import indirect ;
-    import virtual-target ;
-
-    rule __init__ ( name : project : sources * : requirements *
-        : default-build * : usage-requirements * )
-    {
-        basic-target.__init__ $(name) : $(project) : $(sources)
-            : $(requirements) : $(default-build) : $(usage-requirements) ;
-
-        if ! [ $(self.requirements).get <generating-rule> ]
-        {
-            errors.user-error "The generate rule requires the <generating-rule>"
-                "property to be set" ;
-        }
-    }
-
-    rule construct ( name : sources * : property-set )
-    {
-        local result ;
-        local gr = [ $(property-set).get <generating-rule> ] ;
-
-        # FIXME: this is a copy-paste from virtual-target.jam. We should add a
-        # utility rule to call a rule like this.
-        local rule-name = [ MATCH ^@(.*) : $(gr) ] ;
-        if $(rule-name)
-        {
-            if $(gr[2])
-            {
-                local target-name = [ full-name ] ;
-                errors.user-error "Multiple <generating-rule> properties"
-                    "encountered for target $(target-name)." ;
-            }
-
-            result = [ indirect.call $(rule-name) $(self.project) $(name)
-                : $(property-set) : $(sources) ] ;
-
-            if ! $(result)
-            {
-                ECHO "warning: Unable to construct" [ full-name ] ;
-            }
-        }
-
-        local ur ;
-        local targets ;
-
-        if $(result)
-        {
-            if  [ class.is-a $(result[1]) : property-set ]
-            {
-                ur = $(result[1]) ;
-                targets = $(result[2-]) ;
-            }
-            else
-            {
-                ur = [ property-set.empty ] ;
-                targets = $(result) ;
-            }
-        }
-        # FIXME: the following loop should be doable using sequence.transform or
-        # some similar utility rule.
-        local rt ;
-        for local t in $(targets)
-        {
-            rt += [ virtual-target.register $(t) ] ;
-        }
-        return $(ur) $(rt) ;
-    }
-}
-
-
-rule generate ( name : sources * : requirements * : default-build *
-    : usage-requirements * )
-{
-    local project = [ project.current ] ;
-
-    targets.main-target-alternative
-        [ new generated-target-class $(name) : $(project)
-            : [ targets.main-target-sources $(sources) : $(name) ]
-            : [ targets.main-target-requirements $(requirements) : $(project) ]
-            : [ targets.main-target-default-build $(default-build) : $(project) ]
-            : [ targets.main-target-usage-requirements $(usage-requirements) : $(project) ]
-        ] ;
-}
-
-IMPORT $(__name__) : generate : : generate ;
diff --git a/jam-files/boost-build/tools/gettext.jam b/jam-files/boost-build/tools/gettext.jam
deleted file mode 100644
index 99a43ffe..00000000
--- a/jam-files/boost-build/tools/gettext.jam
+++ /dev/null
@@ -1,230 +0,0 @@
-# Copyright 2003, 2004, 2005, 2006 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-#  This module support GNU gettext internationalization utilities.
-#
-#  It provides two main target rules: 'gettext.catalog', used for
-#  creating machine-readable catalogs from translations files, and
-#  'gettext.update', used for update translation files from modified
-#  sources.
-#
-#  To add i18n support to your application you should follow these
-#  steps.
-#
-#  - Decide on a file name which will contain translations and
-#  what main target name will be used to update it. For example::
-#
-#    gettext.update update-russian : russian.po a.cpp my_app ;
-#
-#  - Create the initial translation file by running::
-#
-#    bjam update-russian
-#
-#  - Edit russian.po. For example, you might change fields like LastTranslator.
-#
-#  - Create a main target for final message catalog::
-#
-#    gettext.catalog russian : russian.po ;
-#
-#  The machine-readable catalog will be updated whenever you update
-#  "russian.po". The "russian.po" file will be updated only on explicit
-#  request. When you're ready to update translations, you should
-#
-#  - Run::
-#
-#    bjam update-russian
-#
-#  - Edit "russian.po" in appropriate editor.
-#
-#  The next bjam run will convert "russian.po" into machine-readable form.
-#
-#  By default, translations are marked by 'i18n' call. The 'gettext.keyword'
-#  feature can be used to alter this.
-
-
-import targets ;
-import property-set ;
-import virtual-target ;
-import "class" : new ;
-import project ;
-import type ;
-import generators ;
-import errors ;
-import feature : feature ;
-import toolset : flags ;
-import regex ;
-
-.path = "" ;
-
-# Initializes the gettext module.
-rule init ( path ? # Path where all tools are located. If not specified,
-                   # they should be in PATH.
-          )
-{
-    if $(.initialized) && $(.path) != $(path)
-    {
-        errors.error "Attempt to reconfigure with different path" ;
-    }
-    .initialized = true ;
-    if $(path)
-    {
-        .path = $(path)/ ;
-    }
-}
-
-# Creates a main target 'name', which, when updated, will cause
-# file 'existing-translation' to be updated with translations
-# extracted from 'sources'. It's possible to specify main target
-# in sources --- it which case all target from dependency graph
-# of those main targets will be scanned, provided they are of
-# appropricate type. The 'gettext.types' feature can be used to
-# control the types.
-#
-# The target will be updated only if explicitly requested on the
-# command line.
-rule update ( name : existing-translation sources + : requirements * )
-{
-    local project = [ project.current ] ;
-
-    targets.main-target-alternative
-      [ new typed-target $(name) : $(project) : gettext.UPDATE :
-        $(existing-translation) $(sources)
-        : [ targets.main-target-requirements $(requirements) : $(project) ]
-      ] ;
-    $(project).mark-target-as-explicit $(name) ;
-}
-
-
-# The human editable source, containing translation.
-type.register gettext.PO : po ;
-# The machine readable message catalog.
-type.register gettext.catalog : mo ;
-# Intermediate type produce by extracting translations from
-# sources.
-type.register gettext.POT : pot ;
-# Pseudo type used to invoke update-translations generator
-type.register gettext.UPDATE ;
-
-# Identifies the keyword that should be used when scanning sources.
-# Default: i18n
-feature gettext.keyword : : free ;
-# Contains space-separated list of sources types which should be scanned.
-# Default: "C CPP"
-feature gettext.types : : free ;
-
-generators.register-standard gettext.compile : gettext.PO : gettext.catalog ;
-
-class update-translations-generator : generator
-{
-    import regex : split ;
-    import property-set ;
-
-    rule __init__ ( * : * )
-    {
-        generator.__init__ $(1) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ;
-    }
-
-    # The rule should be called with at least two sources. The first source
-    # is the translation (.po) file to update. The remaining sources are targets
-    # which should be scanned for new messages. All sources files for those targets
-    # will be found and passed to the 'xgettext' utility, which extracts the
-    # messages for localization. Those messages will be merged to the .po file.
-    rule run ( project name ? : property-set : sources * : multiple ? )
-    {
-        local types = [ $(property-set).get <gettext.types> ] ;
-        types ?= "C CPP" ;
-        types = [ regex.split $(types) " " ] ;
-
-        local keywords = [ $(property-set).get <gettext.keyword> ] ;
-        property-set = [ property-set.create $(keywords:G=<gettext.keyword>) ] ;
-
-        # First deterime the list of sources that must be scanned for
-        # messages.
-        local all-sources ;
-        # CONSIDER: I'm not sure if the logic should be the same as for 'stage':
-        # i.e. following dependency properties as well.
-        for local s in $(sources[2-])
-        {
-            all-sources += [ virtual-target.traverse $(s) : : include-sources ] ;
-        }
-        local right-sources ;
-        for local s in $(all-sources)
-        {
-            if [ $(s).type ] in $(types)
-            {
-                right-sources += $(s) ;
-            }
-        }
-
-        local .constructed ;
-        if $(right-sources)
-        {
-            # Create the POT file, which will contain list of messages extracted
-            # from the sources.
-            local extract =
-              [ new action $(right-sources) : gettext.extract : $(property-set) ] ;
-            local new-messages = [ new file-target $(name) : gettext.POT
-              : $(project) : $(extract) ] ;
-
-            # Create a notfile target which will update the existing translation file
-            # with new messages.
-            local a = [ new action $(sources[1]) $(new-messages)
-              : gettext.update-po-dispatch ] ;
-            local r = [ new notfile-target $(name) : $(project) : $(a) ] ;
-            .constructed = [ virtual-target.register $(r) ] ;
-        }
-        else
-        {
-            errors.error "No source could be scanned by gettext tools" ;
-        }
-        return $(.constructed) ;
-    }
-}
-generators.register [ new update-translations-generator gettext.update : : gettext.UPDATE ] ;
-
-flags gettext.extract KEYWORD <gettext.keyword> ;
-actions extract
-{
-    $(.path)xgettext -k$(KEYWORD:E=i18n) -o $(<) $(>)
-}
-
-# Does realy updating of po file. The tricky part is that
-# we're actually updating one of the sources:
-# $(<) is the NOTFILE target we're updating
-# $(>[1]) is the PO file to be really updated.
-# $(>[2]) is the PO file created from sources.
-#
-# When file to be updated does not exist (during the
-# first run), we need to copy the file created from sources.
-# In all other cases, we need to update the file.
-rule update-po-dispatch
-{
-    NOCARE $(>[1]) ;
-    gettext.create-po $(<) : $(>) ;
-    gettext.update-po $(<) : $(>) ;
-    _ on $(<) = " " ;
-    ok on $(<) = "" ;
-    EXISTING_PO on $(<) = $(>[1]) ;
-}
-
-# Due to fancy interaction of existing and updated, this rule can be called with
-# one source, in which case we copy the lonely source into EXISTING_PO, or with
-# two sources, in which case the action body expands to nothing. I'd really like
-# to have "missing" action modifier.
-actions quietly existing updated create-po bind EXISTING_PO
-{
-    cp$(_)"$(>[1])"$(_)"$(EXISTING_PO)"$($(>[2]:E=ok))
-}
-
-actions updated update-po bind EXISTING_PO
-{
-    $(.path)msgmerge$(_)-U$(_)"$(EXISTING_PO)"$(_)"$(>[1])"
-}
-
-actions gettext.compile
-{
-    $(.path)msgfmt -o $(<) $(>)
-}
-
-IMPORT $(__name__) : update : : gettext.update ;
diff --git a/jam-files/boost-build/tools/gfortran.jam b/jam-files/boost-build/tools/gfortran.jam
deleted file mode 100644
index 0aa69b85..00000000
--- a/jam-files/boost-build/tools/gfortran.jam
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright (C) 2004 Toon Knapen
-#
-#  Use, modification and distribution is subject to the Boost Software
-#  License Version 1.0. (See accompanying file LICENSE_1_0.txt or
-#  http://www.boost.org/LICENSE_1_0.txt)
-
-import toolset : flags ;
-import feature ;
-import fortran ;
-
-rule init ( version ? : command * : options * )
-{
-}
-
-# Declare flags and action for compilation
-flags gfortran OPTIONS <fflags> ;
-
-flags gfortran OPTIONS <optimization>off : -O0 ;
-flags gfortran OPTIONS <optimization>speed : -O3 ;
-flags gfortran OPTIONS <optimization>space : -Os ;
-
-flags gfortran OPTIONS <debug-symbols>on : -g ;
-flags gfortran OPTIONS <profiling>on : -pg ;
-
-flags gfortran OPTIONS <link>shared/<main-target-type>LIB : -fPIC ;
-
-flags gfortran DEFINES <define> ;
-flags gfortran INCLUDES <include> ;
-
-rule compile.fortran
-{
-}
-
-actions compile.fortran
-{
-  gcc -Wall $(OPTIONS) -D$(DEFINES) -I$(INCLUDES) -c -o "$(<)" "$(>)" 
-}
-
-generators.register-fortran-compiler gfortran.compile.fortran : FORTRAN FORTRAN90 : OBJ ; 
diff --git a/jam-files/boost-build/tools/hp_cxx.jam b/jam-files/boost-build/tools/hp_cxx.jam
deleted file mode 100644
index 86cd783e..00000000
--- a/jam-files/boost-build/tools/hp_cxx.jam
+++ /dev/null
@@ -1,181 +0,0 @@
-# Copyright 2001 David Abrahams.
-# Copyright 2004, 2005 Markus Schoepflin.
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-#
-# HP CXX compiler
-# See http://h30097.www3.hp.com/cplus/?jumpid=reg_R1002_USEN
-#
-#
-# Notes on this toolset:
-#
-# - Because of very subtle issues with the default ansi mode, strict_ansi mode
-#   is used for compilation. One example of things that don't work correctly in
-#   the default ansi mode is overload resolution of function templates when
-#   mixed with non-template functions.
-#
-# - For template instantiation "-timplicit_local" is used. Previously,
-#   "-tlocal" has been tried to avoid the need for a template repository
-#   but this doesn't work with manually instantiated templates. "-tweak"
-#   has not been used to avoid the stream of warning messages issued by
-#   ar or ld when creating a library or linking an application.
-#
-# - Debug symbols are generated with "-g3", as this works both in debug and
-#   release mode. When compiling C++ code without optimization, we additionally
-#   use "-gall", which generates full symbol table information for all classes,
-#   structs, and unions. As this turns off optimization, it can't be used when
-#   optimization is needed.
-#
-
-import feature generators common ;
-import toolset : flags ;
-
-feature.extend toolset : hp_cxx ;
-feature.extend c++abi : cxxarm ;
-
-# Inherit from Unix toolset to get library ordering magic.
-toolset.inherit  hp_cxx : unix ;
-
-generators.override hp_cxx.prebuilt : builtin.lib-generator ;
-generators.override hp_cxx.prebuilt : builtin.prebuilt ;
-generators.override hp_cxx.searched-lib-generator : searched-lib-generator ;
-
-
-rule init ( version ? : command * : options * )
-{
-    local condition = [ common.check-init-parameters hp_cxx : version $(version) ] ;
-    
-    local command = [ common.get-invocation-command hp_cxx : cxx : $(command) ] ;
-    
-    if $(command)
-    {
-        local root = [ common.get-absolute-tool-path $(command[-1]) ] ;
-
-        if $(root)
-        {
-            flags hp_cxx .root $(condition) : "\"$(root)\"/" ;
-        }        
-    }      
-    # If we can't find 'cxx' anyway, at least show 'cxx' in the commands
-    command ?= cxx ;
-        
-    common.handle-options hp_cxx : $(condition) : $(command) : $(options) ;               
-}
-
-generators.register-c-compiler hp_cxx.compile.c++ : CPP : OBJ : <toolset>hp_cxx ;
-generators.register-c-compiler hp_cxx.compile.c : C : OBJ : <toolset>hp_cxx ;
-
-
-
-# No static linking as far as I can tell.
-# flags cxx LINKFLAGS <runtime-link>static : -bstatic ;
-flags hp_cxx.compile OPTIONS <debug-symbols>on : -g3 ;
-flags hp_cxx.compile OPTIONS <optimization>off/<debug-symbols>on : -gall ;
-flags hp_cxx.link OPTIONS <debug-symbols>on : -g ;
-flags hp_cxx.link OPTIONS <debug-symbols>off : -s ;
-
-flags hp_cxx.compile OPTIONS <optimization>off : -O0 ;
-flags hp_cxx.compile OPTIONS <optimization>speed/<inlining>on : -O2 ;
-flags hp_cxx.compile OPTIONS <optimization>speed : -O2 ;
-
-# This (undocumented) macro needs to be defined to get all C function
-# overloads required by the C++ standard.
-flags hp_cxx.compile.c++ OPTIONS : -D__CNAME_OVERLOADS ;
-
-# Added for threading support
-flags hp_cxx.compile OPTIONS <threading>multi : -pthread ;
-flags hp_cxx.link OPTIONS <threading>multi : -pthread ;
-
-flags hp_cxx.compile OPTIONS <optimization>space/<inlining>on : <inlining>size ;
-flags hp_cxx.compile OPTIONS <optimization>space : -O1 ;
-flags hp_cxx.compile OPTIONS <inlining>off : -inline none ;
-
-# The compiler versions tried (up to V6.5-040) hang when compiling Boost code
-# with full inlining enabled. So leave it at the default level for now.
-#
-# flags hp_cxx.compile OPTIONS <inlining>full : -inline all ;
-
-flags hp_cxx.compile OPTIONS <profiling>on : -pg ;
-flags hp_cxx.link OPTIONS <profiling>on : -pg ;
-
-# Selection of the object model. This flag is needed on both the C++ compiler
-# and linker command line.
-
-# Unspecified ABI translates to '-model ansi' as most
-# standard-conforming.
-flags hp_cxx.compile.c++ OPTIONS <c++abi> : -model ansi : : hack-hack ;
-flags hp_cxx.compile.c++ OPTIONS <c++abi>cxxarm : -model arm ;
-flags hp_cxx.link OPTIONS <c++abi> : -model ansi : : hack-hack ;
-flags hp_cxx.link OPTIONS <c++abi>cxxarm : -model arm ;
-
-# Display a descriptive tag together with each compiler message. This tag can
-# be used by the user to explicitely suppress the compiler message.
-flags hp_cxx.compile OPTIONS : -msg_display_tag ;
-
-flags hp_cxx.compile OPTIONS <cflags> ;
-flags hp_cxx.compile.c++ OPTIONS <cxxflags> ;
-flags hp_cxx.compile DEFINES <define> ;
-flags hp_cxx.compile INCLUDES <include> ;
-flags hp_cxx.link OPTIONS <linkflags> ;
-
-flags hp_cxx.link LIBPATH <library-path> ;
-flags hp_cxx.link LIBRARIES <library-file> ;
-flags hp_cxx.link FINDLIBS-ST <find-static-library> ;
-flags hp_cxx.link FINDLIBS-SA <find-shared-library> ;
-
-flags hp_cxx.compile.c++ TEMPLATE_DEPTH <c++-template-depth> ;
-
-actions link bind LIBRARIES
-{
-    $(CONFIG_COMMAND) -noimplicit_include $(OPTIONS) -o "$(<)" -L$(LIBPATH) "$(>)" "$(LIBRARIES)" -l$(FINDLIBS-ST) -l$(FINDLIBS-SA) -lrt -lm
-}
-
-# When creating dynamic libraries, we don't want to be warned about unresolved
-# symbols, therefore all unresolved symbols are marked as expected by
-# '-expect_unresolved *'. This also mirrors the behaviour of the GNU tool
-# chain.
-
-actions link.dll bind LIBRARIES
-{
-    $(CONFIG_COMMAND) -shared -expect_unresolved \* -noimplicit_include $(OPTIONS) -o "$(<[1])" -L$(LIBPATH)  "$(>)" "$(LIBRARIES)" -l$(FINDLIBS-ST) -l$(FINDLIBS-SA) -lm
-}
-
-
-# Note: Relaxed ANSI mode (-std) is used for compilation because in strict ANSI
-# C89 mode (-std1) the compiler doesn't accept C++ comments in C files. As -std
-# is the default, no special flag is needed.
-actions compile.c
-{
-    $(.root:E=)cc -c $(OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -o "$(<)" "$(>)"
-}
-
-# Note: The compiler is forced to compile the files as C++ (-x cxx) because
-# otherwise it will silently ignore files with no file extension.
-#
-# Note: We deliberately don't suppress any warnings on the compiler command
-# line, the user can always do this in a customized toolset later on.
-
-rule compile.c++
-{
-    # We preprocess the TEMPLATE_DEPTH command line option here because we found
-    # no way to do it correctly in the actual action code. There we either get
-    # the -pending_instantiations parameter when no c++-template-depth property
-    # has been specified or we get additional quotes around
-    # "-pending_instantiations ".
-    local template-depth = [ on $(1) return $(TEMPLATE_DEPTH) ] ;
-    TEMPLATE_DEPTH on $(1) = "-pending_instantiations "$(template-depth) ;
-}
-
-actions compile.c++
-{
-    $(CONFIG_COMMAND) -x cxx -c -std strict_ansi -nopure_cname -noimplicit_include -timplicit_local -ptr "$(<[1]:D)/cxx_repository" $(OPTIONS) $(TEMPLATE_DEPTH) -D$(DEFINES) -I"$(INCLUDES)" -o "$(<)" "$(>)"
-}
-
-# Always create archive from scratch. See the gcc toolet for rationale.
-RM = [ common.rm-command ] ;
-actions together piecemeal archive
-{
-  $(RM) "$(<)"
-  ar rc $(<) $(>)
-}
diff --git a/jam-files/boost-build/tools/hpfortran.jam b/jam-files/boost-build/tools/hpfortran.jam
deleted file mode 100644
index 96e8d18b..00000000
--- a/jam-files/boost-build/tools/hpfortran.jam
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright (C) 2004 Toon Knapen
-#
-#  Use, modification and distribution is subject to the Boost Software
-#  License Version 1.0. (See accompanying file LICENSE_1_0.txt or
-#  http://www.boost.org/LICENSE_1_0.txt)
-
-import toolset : flags ;
-import feature ;
-import fortran ;
-
-rule init ( version ? : command * : options * )
-{
-}
-
-# Declare flags and action for compilation
-flags hpfortran OPTIONS <optimization>off : -O0 ;
-flags hpfortran OPTIONS <optimization>speed : -O3 ;
-flags hpfortran OPTIONS <optimization>space : -O1 ;
-
-flags hpfortran OPTIONS <debug-symbols>on : -g ;
-flags hpfortran OPTIONS <profiling>on : -pg ;
-
-flags hpfortran DEFINES <define> ;
-flags hpfortran INCLUDES <include> ;
-
-rule compile.fortran
-{
-}
-
-actions compile.fortran
-{
-  f77 +DD64 $(OPTIONS) -D$(DEFINES) -I$(INCLUDES) -c -o "$(<)" "$(>)" 
-}
-
-generators.register-fortran-compiler hpfortran.compile.fortran : FORTRAN : OBJ ; 
diff --git a/jam-files/boost-build/tools/ifort.jam b/jam-files/boost-build/tools/ifort.jam
deleted file mode 100644
index eb7c1988..00000000
--- a/jam-files/boost-build/tools/ifort.jam
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright (C) 2004 Toon Knapen
-#
-#  Use, modification and distribution is subject to the Boost Software
-#  License Version 1.0. (See accompanying file LICENSE_1_0.txt or
-#  http://www.boost.org/LICENSE_1_0.txt)
-
-import toolset : flags ;
-import feature ;
-import fortran ;
-
-rule init ( version ? : command * : options * )
-{
-}
-
-# Declare flags and action for compilation
-flags ifort OPTIONS <fflags> ;
-
-flags ifort OPTIONS <optimization>off : /Od ;
-flags ifort OPTIONS <optimization>speed : /O3 ;
-flags ifort OPTIONS <optimization>space : /O1 ;
-
-flags ifort OPTIONS <debug-symbols>on : /debug:full ;
-flags ifort OPTIONS <profiling>on : /Qprof_gen ;
-
-flags ifort.compile FFLAGS <runtime-debugging>off/<runtime-link>shared : /MD ;
-flags ifort.compile FFLAGS <runtime-debugging>on/<runtime-link>shared : /MDd ;
-flags ifort.compile FFLAGS <runtime-debugging>off/<runtime-link>static/<threading>single : /ML ;
-flags ifort.compile FFLAGS <runtime-debugging>on/<runtime-link>static/<threading>single : /MLd ;
-flags ifort.compile FFLAGS <runtime-debugging>off/<runtime-link>static/<threading>multi : /MT ;
-flags ifort.compile FFLAGS <runtime-debugging>on/<runtime-link>static/<threading>multi : /MTd ;
-
-flags ifort DEFINES <define> ;
-flags ifort INCLUDES <include> ;
-
-rule compile.fortran
-{
-}
-
-actions compile.fortran
-{
-  ifort $(FFLAGS) $(OPTIONS) /names:lowercase /D$(DEFINES) /I"$(INCLUDES)" /c /object:"$(<)" "$(>)" 
-}
-
-generators.register-fortran-compiler ifort.compile.fortran : FORTRAN : OBJ ; 
diff --git a/jam-files/boost-build/tools/intel-darwin.jam b/jam-files/boost-build/tools/intel-darwin.jam
deleted file mode 100644
index aa0fd8fb..00000000
--- a/jam-files/boost-build/tools/intel-darwin.jam
+++ /dev/null
@@ -1,220 +0,0 @@
-# Copyright Vladimir Prus 2004.
-# Copyright Noel Belcourt 2007.
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt
-# or copy at http://www.boost.org/LICENSE_1_0.txt)
-
-import intel ;
-import feature : feature ;
-import os ;
-import toolset ;
-import toolset : flags ;
-import gcc ;
-import common ;
-import errors ;
-import generators ;
-
-feature.extend-subfeature toolset intel : platform : darwin ;
-
-toolset.inherit-generators intel-darwin 
-  <toolset>intel <toolset-intel:platform>darwin 
-  : gcc 
-  # Don't inherit PCH generators. They were not tested, and probably
-  # don't work for this compiler.
-  : gcc.mingw.link gcc.mingw.link.dll gcc.compile.c.pch gcc.compile.c++.pch
-  ;
-
-generators.override intel-darwin.prebuilt : builtin.lib-generator ;
-generators.override intel-darwin.prebuilt : builtin.prebuilt ;
-generators.override intel-darwin.searched-lib-generator : searched-lib-generator ;
-
-toolset.inherit-rules intel-darwin : gcc ;
-toolset.inherit-flags intel-darwin : gcc 
-        : <inlining>off <inlining>on <inlining>full <optimization>space 
-          <warnings>off <warnings>all <warnings>on
-          <architecture>x86/<address-model>32
-          <architecture>x86/<address-model>64
-        ;
-        
-if [ MATCH (--debug-configuration) : [ modules.peek : ARGV ] ]
-{
-    .debug-configuration = true ;
-}
-                       
-# vectorization diagnostics
-feature vectorize : off on full ;
-
-# Initializes the intel-darwin toolset
-#   version in mandatory
-#   name (default icc) is used to invoke the specified intel complier
-#   compile and link options allow you to specify addition command line options for each version
-rule init ( version ? :  command * : options * )
-{
-    local condition = [ common.check-init-parameters intel-darwin
-        : version $(version) ] ;
-    
-    command = [ common.get-invocation-command intel-darwin : icc 
-        : $(command) : /opt/intel_cc_80/bin ] ;
-
-    common.handle-options intel-darwin : $(condition) : $(command) : $(options) ;
-
-    gcc.init-link-flags intel-darwin darwin $(condition) ;
-
-    # handle <library-path>
-    # local library-path = [ feature.get-values <library-path> : $(options) ] ;
-    # flags intel-darwin.link USER_OPTIONS $(condition) : [ feature.get-values <dll-path> : $(options) ] ;
-
-    local root = [ feature.get-values <root> : $(options) ] ;
-    local bin ;
-    if $(command) || $(root)
-    {
-        bin ?= [ common.get-absolute-tool-path $(command[-1]) ] ;
-        root ?= $(bin:D) ;
-    
-        if $(root)
-        {
-            # Libraries required to run the executable may be in either
-            # $(root)/lib (10.1 and earlier) 
-            #     or 
-            # $(root)/lib/architecture-name (11.0 and later:
-            local lib_path = $(root)/lib $(root:P)/lib/$(bin:B) ;
-            if $(.debug-configuration)
-            {
-                ECHO notice: using intel libraries :: $(condition) :: $(lib_path) ;
-            }
-            flags intel-darwin.link RUN_PATH $(condition) : $(lib_path) ;
-        }   
-    }
-
-    local m = [ MATCH (..).* : $(version) ] ;
-    local n = [ MATCH (.)\\. : $(m) ] ;
-    if $(n) {
-      m = $(n) ;
-    }
-
-    local major = $(m) ;
-    
-    if $(major) = "9" {
-      flags intel-darwin.compile OPTIONS $(condition)/<inlining>off : -Ob0 ;
-      flags intel-darwin.compile OPTIONS $(condition)/<inlining>on : -Ob1  ;
-      flags intel-darwin.compile OPTIONS $(condition)/<inlining>full : -Ob2  ;
-      flags intel-darwin.compile OPTIONS $(condition)/<vectorize>off : -vec-report0 ;
-      flags intel-darwin.compile OPTIONS $(condition)/<vectorize>on : -vec-report1 ;
-      flags intel-darwin.compile OPTIONS $(condition)/<vectorize>full : -vec-report5 ;
-      flags intel-darwin.link OPTIONS $(condition)/<runtime-link>static : -static -static-libcxa -lstdc++ -lpthread ;
-      flags intel-darwin.link OPTIONS $(condition)/<runtime-link>shared : -shared-libcxa -lstdc++ -lpthread ;
-    }
-    else {
-      flags intel-darwin.compile OPTIONS $(condition)/<inlining>off : -inline-level=0 ;
-      flags intel-darwin.compile OPTIONS $(condition)/<inlining>on : -inline-level=1  ;
-      flags intel-darwin.compile OPTIONS $(condition)/<inlining>full : -inline-level=2  ;
-      flags intel-darwin.compile OPTIONS $(condition)/<vectorize>off : -vec-report0 ;
-      flags intel-darwin.compile OPTIONS $(condition)/<vectorize>on : -vec-report1 ;
-      flags intel-darwin.compile OPTIONS $(condition)/<vectorize>full : -vec-report5 ;
-      flags intel-darwin.link OPTIONS $(condition)/<runtime-link>static : -static -static-intel -lstdc++ -lpthread ;
-      flags intel-darwin.link OPTIONS $(condition)/<runtime-link>shared : -shared-intel -lstdc++ -lpthread ;
-    }
-
-    local minor = [ MATCH ".*\\.(.).*" : $(version) ] ;
-
-    # wchar_t char_traits workaround for compilers older than 10.2
-    if $(major) = "9" || ( $(major) = "10" && ( $(minor) = "0" || $(minor) = "1" ) ) {
-        flags intel-darwin.compile DEFINES $(condition) : __WINT_TYPE__=int : unchecked ;
-    }
-}
-
-SPACE = " " ;
-
-flags intel-darwin.compile OPTIONS <cflags> ;
-flags intel-darwin.compile OPTIONS <cxxflags> ;
-# flags intel-darwin.compile INCLUDES <include> ;
-
-flags intel-darwin.compile OPTIONS <optimization>space : -O1 ; # no specific space optimization flag in icc
-
-# 
-cpu-type-em64t = prescott nocona ;
-flags intel-darwin.compile OPTIONS <instruction-set>$(cpu-type-em64t)/<address-model>32 : -m32 ; # -mcmodel=small ;
-flags intel-darwin.compile OPTIONS <instruction-set>$(cpu-type-em64t)/<address-model>64 : -m64 ; # -mcmodel=large ;
-
-flags intel-darwin.compile.c OPTIONS <warnings>off : -w0 ;
-flags intel-darwin.compile.c OPTIONS <warnings>on : -w1 ;
-flags intel-darwin.compile.c OPTIONS <warnings>all : -w2 ;
-
-flags intel-darwin.compile.c++ OPTIONS <warnings>off : -w0 ;
-flags intel-darwin.compile.c++ OPTIONS <warnings>on : -w1 ;
-flags intel-darwin.compile.c++ OPTIONS <warnings>all : -w2 ;
-
-actions compile.c
-{
-    "$(CONFIG_COMMAND)" -xc $(OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -c -o "$(<)" "$(>)"
-}
-
-actions compile.c++
-{
-    "$(CONFIG_COMMAND)" -xc++ $(OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -c -o "$(<)" "$(>)"
-}
-
-flags intel-darwin ARFLAGS <archiveflags> ;
-
-# Default value. Mostly for the sake of intel-linux
-# that inherits from gcc, but does not has the same
-# logic to set the .AR variable. We can put the same
-# logic in intel-linux, but that's hardly worth the trouble
-# as on Linux, 'ar' is always available.
-.AR = ar ;
-
-rule archive ( targets * : sources * : properties * )
-{
-  # Always remove archive and start again. Here's rationale from
-  # Andre Hentz:
-  #
-  # I had a file, say a1.c, that was included into liba.a. 
-  # I moved a1.c to a2.c, updated my Jamfiles and rebuilt. 
-  # My program was crashing with absurd errors. 
-  # After some debugging I traced it back to the fact that a1.o was *still* 
-  # in liba.a 
-  #
-  # Rene Rivera:
-  #
-  # Originally removing the archive was done by splicing an RM
-  # onto the archive action. That makes archives fail to build on NT
-  # when they have many files because it will no longer execute the
-  # action directly and blow the line length limit. Instead we
-  # remove the file in a different action, just before the building
-  # of the archive.
-  #
-  local clean.a = $(targets[1])(clean) ;
-  TEMPORARY $(clean.a) ;
-  NOCARE $(clean.a) ;
-  LOCATE on $(clean.a) = [ on $(targets[1]) return $(LOCATE) ] ;
-  DEPENDS $(clean.a) : $(sources) ;
-  DEPENDS $(targets) : $(clean.a) ;
-  common.RmTemps $(clean.a) : $(targets) ;
-}
-
-actions piecemeal archive
-{
-  "$(.AR)" $(AROPTIONS) rc "$(<)" "$(>)"
-  "ranlib" -cs "$(<)"
-}
-
-flags intel-darwin.link USER_OPTIONS <linkflags> ;
-
-# Declare actions for linking
-rule link ( targets * : sources * : properties * )
-{
-  SPACE on $(targets) = " " ;
-  # Serialize execution of the 'link' action, since
-  # running N links in parallel is just slower.
-  JAM_SEMAPHORE on $(targets) = <s>intel-darwin-link-semaphore ;
-}
-
-actions link bind LIBRARIES
-{
-    "$(CONFIG_COMMAND)" $(USER_OPTIONS) -L"$(LINKPATH)" -o "$(<)" "$(>)" "$(LIBRARIES)" -l$(FINDLIBS-SA) -l$(FINDLIBS-ST) $(OPTIONS)
-}
-
-actions link.dll bind LIBRARIES
-{
-    "$(CONFIG_COMMAND)" $(USER_OPTIONS) -L"$(LINKPATH)" -o "$(<)" -single_module -dynamiclib -install_name "$(<[1]:D=)" "$(>)"  "$(LIBRARIES)" -l$(FINDLIBS-SA) -l$(FINDLIBS-ST) $(OPTIONS)
-}
diff --git a/jam-files/boost-build/tools/intel-linux.jam b/jam-files/boost-build/tools/intel-linux.jam
deleted file mode 100644
index d9164add..00000000
--- a/jam-files/boost-build/tools/intel-linux.jam
+++ /dev/null
@@ -1,250 +0,0 @@
-#  Copyright (c) 2003 Michael Stevens
-#  Copyright (c) 2011 Bryce Lelbach
-#
-#  Use, modification and distribution is subject to the Boost Software
-#  License Version 1.0. (See accompanying file LICENSE_1_0.txt or
-#  http://www.boost.org/LICENSE_1_0.txt)
-
-import toolset ;
-import feature ;
-import toolset : flags ;
-
-import intel ;
-import gcc ;
-import common ;
-import errors ;
-import generators ;
-import type ;
-import numbers ;
-
-feature.extend-subfeature toolset intel : platform : linux ;
-
-toolset.inherit-generators intel-linux 
-     <toolset>intel <toolset-intel:platform>linux : gcc : gcc.mingw.link gcc.mingw.link.dll ;
-generators.override intel-linux.prebuilt : builtin.lib-generator ;
-generators.override intel-linux.prebuilt : builtin.prebuilt ;
-generators.override intel-linux.searched-lib-generator : searched-lib-generator ;
-
-# Override default do-nothing generators.
-generators.override intel-linux.compile.c.pch   : pch.default-c-pch-generator   ;
-generators.override intel-linux.compile.c++.pch : pch.default-cpp-pch-generator ;
- 
-type.set-generated-target-suffix PCH : <toolset>intel <toolset-intel:platform>linux : pchi ;
-
-toolset.inherit-rules intel-linux : gcc ;
-toolset.inherit-flags intel-linux : gcc 
-        : <inlining>off <inlining>on <inlining>full
-          <optimization>space <optimization>speed
-          <warnings>off <warnings>all <warnings>on
-        ;
-        
-if [ MATCH (--debug-configuration) : [ modules.peek : ARGV ] ]
-{
-    .debug-configuration = true ;
-}
-                       
-# Initializes the intel-linux toolset
-#   version in mandatory
-#   name (default icpc) is used to invoke the specified intel-linux complier
-#   compile and link options allow you to specify addition command line options for each version
-rule init ( version ? :  command * : options * )
-{
-    local condition = [ common.check-init-parameters intel-linux
-        : version $(version) ] ;
-    
-    if $(.debug-configuration)
-    {
-        ECHO "notice: intel-linux version is" $(version) ;
-    }
-
-    local default_path ;
-
-    # Intel C++ Composer XE 2011 for Linux, aka Intel C++ Compiler XE 12.0,
-    # aka intel-linux-12.0. In this version, Intel thankfully decides to install
-    # to a sane 'intel' folder in /opt.
-    if [ MATCH "(12[.]0|12)" : $(version) ]
-        { default_path = /opt/intel/bin ; }
-    # Intel C++ Compiler 11.1. 
-    else if [ MATCH "(11[.]1)" : $(version) ]
-        { default_path = /opt/intel_cce_11.1.064.x86_64/bin ; }
-    # Intel C++ Compiler 11.0. 
-    else if [ MATCH "(11[.]0|11)" : $(version) ]
-        { default_path = /opt/intel_cce_11.0.074.x86_64/bin ; }
-    # Intel C++ Compiler 10.1. 
-    else if [ MATCH "(10[.]1)" : $(version) ]
-        { default_path = /opt/intel_cce_10.1.013_x64/bin ; }
-    # Intel C++ Compiler 9.1. 
-    else if [ MATCH "(9[.]1)" : $(version) ]
-        { default_path = /opt/intel_cc_91/bin ; }
-    # Intel C++ Compiler 9.0. 
-    else if [ MATCH "(9[.]0|9)" : $(version) ]
-        { default_path = /opt/intel_cc_90/bin ; }
-    # Intel C++ Compiler 8.1. 
-    else if [ MATCH "(8[.]1)" : $(version) ]
-        { default_path = /opt/intel_cc_81/bin ; }
-    # Intel C++ Compiler 8.0 - this used to be the default, so now it's the
-    # fallback. 
-    else 
-        { default_path = /opt/intel_cc_80/bin ; }
-            
-    if $(.debug-configuration)
-    {
-        ECHO "notice: default search path for intel-linux is" $(default_path) ;
-    }
-
-    command = [ common.get-invocation-command intel-linux : icpc 
-        : $(command) : $(default_path) ] ;
-                
-    common.handle-options intel-linux : $(condition) : $(command) : $(options) ;
-
-    gcc.init-link-flags intel-linux gnu $(condition) ;
-    
-    local root = [ feature.get-values <root> : $(options) ] ;
-    local bin ;
-    if $(command) || $(root)
-    {
-        bin ?= [ common.get-absolute-tool-path $(command[-1]) ] ;
-        root ?= $(bin:D) ;
-        
-        local command-string = $(command:J=" ") ;
-        local version-output = [ SHELL "$(command-string) --version" ] ;
-        local real-version = [ MATCH "([0-9.]+)" : $(version-output) ] ;
-        local major = [ MATCH "([0-9]+).*" : $(real-version) ] ;
-        
-        # If we failed to determine major version, use the behaviour for
-        # the current compiler.
-        if $(major) && [ numbers.less $(major) 10 ]
-        {
-            flags intel-linux.compile OPTIONS $(condition)/<inlining>off : "-Ob0" ;
-            flags intel-linux.compile OPTIONS $(condition)/<inlining>on : "-Ob1" ;
-            flags intel-linux.compile OPTIONS $(condition)/<inlining>full : "-Ob2" ;            
-            flags intel-linux.compile OPTIONS $(condition)/<optimization>space : "-O1" ;
-            flags intel-linux.compile OPTIONS $(condition)/<optimization>speed : "-O3 -ip" ;
-        }
-        else if $(major) && [ numbers.less $(major) 11 ]
-        {
-            flags intel-linux.compile OPTIONS $(condition)/<inlining>off : "-inline-level=0" ; 
-            flags intel-linux.compile OPTIONS $(condition)/<inlining>on : "-inline-level=1" ; 
-            flags intel-linux.compile OPTIONS $(condition)/<inlining>full : "-inline-level=2" ;                
-            flags intel-linux.compile OPTIONS $(condition)/<optimization>space : "-O1" ;
-            flags intel-linux.compile OPTIONS $(condition)/<optimization>speed : "-O3 -ip" ;
-        }
-        else # newer version of intel do have -Os (at least 11+, don't know about 10)
-        {                        
-            flags intel-linux.compile OPTIONS $(condition)/<inlining>off : "-inline-level=0" ; 
-            flags intel-linux.compile OPTIONS $(condition)/<inlining>on : "-inline-level=1" ; 
-            flags intel-linux.compile OPTIONS $(condition)/<inlining>full : "-inline-level=2" ;                
-            flags intel-linux.compile OPTIONS $(condition)/<optimization>space : "-Os" ;
-            flags intel-linux.compile OPTIONS $(condition)/<optimization>speed : "-O3 -ip" ;
-        }        
-           
-        if $(root)
-        {
-            # Libraries required to run the executable may be in either
-            # $(root)/lib (10.1 and earlier) 
-            #     or 
-            # $(root)/lib/architecture-name (11.0 and later:
-            local lib_path = $(root)/lib $(root:P)/lib/$(bin:B) ;
-            if $(.debug-configuration)
-            {
-                ECHO notice: using intel libraries :: $(condition) :: $(lib_path) ;
-            }
-            flags intel-linux.link RUN_PATH $(condition) : $(lib_path) ;
-        }   
-    }
-}
-
-SPACE = " " ;
-
-flags intel-linux.compile OPTIONS <warnings>off : -w0 ;
-flags intel-linux.compile OPTIONS <warnings>on : -w1 ;
-flags intel-linux.compile OPTIONS <warnings>all : -w2 ;
-
-rule compile.c++ ( targets * : sources * : properties * )
-{
-    gcc.setup-threading $(targets) : $(sources) : $(properties) ;
-    gcc.setup-fpic $(targets) : $(sources) : $(properties) ;
-    gcc.setup-address-model $(targets) : $(sources) : $(properties) ;
-    DEPENDS $(<) : [ on $(<) return $(PCH_FILE) ] ;
-}
-
-actions compile.c++ bind PCH_FILE
-{
-    "$(CONFIG_COMMAND)" -c -xc++ $(OPTIONS) $(USER_OPTIONS) -D$(DEFINES) -I"$(INCLUDES)"  -use-pch"$(PCH_FILE)" -c -o "$(<)" "$(>)"
-}
-
-rule compile.c ( targets * : sources * : properties * )
-{
-    gcc.setup-threading $(targets) : $(sources) : $(properties) ;
-    gcc.setup-fpic $(targets) : $(sources) : $(properties) ;
-    gcc.setup-address-model $(targets) : $(sources) : $(properties) ;    
-    DEPENDS $(<) : [ on $(<) return $(PCH_FILE) ] ;
-}
-
-actions compile.c bind PCH_FILE
-{
-    "$(CONFIG_COMMAND)" -c -xc $(OPTIONS) $(USER_OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -use-pch"$(PCH_FILE)" -c -o "$(<)" "$(>)"
-}
-
-rule compile.c++.pch ( targets * : sources * : properties * )
-{
-    gcc.setup-threading $(targets) : $(sources) : $(properties) ;
-    gcc.setup-fpic $(targets) : $(sources) : $(properties) ;
-    gcc.setup-address-model $(targets) : $(sources) : $(properties) ;    
-}
-#
-# Compiling a pch first deletes any existing *.pchi file, as Intel's compiler
-# won't over-write an existing pch: instead it creates filename$1.pchi, filename$2.pchi
-# etc - which appear not to do anything except take up disk space :-(
-#
-actions compile.c++.pch
-{
-    rm -f "$(<)" && "$(CONFIG_COMMAND)" -x c++-header $(OPTIONS) $(USER_OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -c -pch-create "$(<)" "$(>)"
-}
-
-actions compile.fortran
-{
-    "ifort" -c $(OPTIONS) $(USER_OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -c -o "$(<)" "$(>)"
-}
-
-rule compile.c.pch ( targets * : sources * : properties * )
-{
-    gcc.setup-threading $(targets) : $(sources) : $(properties) ;
-    gcc.setup-fpic $(targets) : $(sources) : $(properties) ;
-    gcc.setup-address-model $(targets) : $(sources) : $(properties) ;    
-}
-
-actions compile.c.pch
-{
-    rm -f "$(<)" && "$(CONFIG_COMMAND)" -x c-header $(OPTIONS) $(USER_OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -c -pch-create "$(<)" "$(>)"
-}
-
-rule link ( targets * : sources * : properties * )
-{
-    gcc.setup-threading $(targets) : $(sources) : $(properties) ;
-    gcc.setup-address-model $(targets) : $(sources) : $(properties) ;    
-    SPACE on $(targets) = " " ;
-    JAM_SEMAPHORE on $(targets) = <s>intel-linux-link-semaphore ;
-}
-
-actions link bind LIBRARIES
-{
-    "$(CONFIG_COMMAND)" -L"$(LINKPATH)" -Wl,-R$(SPACE)-Wl,"$(RPATH)" -Wl,-rpath-link$(SPACE)-Wl,"$(RPATH_LINK)" -o "$(<)" "$(>)" "$(LIBRARIES)" -l$(FINDLIBS-SA) -l$(FINDLIBS-ST) $(OPTIONS) $(USER_OPTIONS)
-}
-
-rule link.dll ( targets * : sources * : properties * )
-{
-    gcc.setup-threading $(targets) : $(sources) : $(properties) ;
-    gcc.setup-address-model $(targets) : $(sources) : $(properties) ;    
-    SPACE on $(targets) = " " ;
-    JAM_SEMAPHORE on $(targets) = <s>intel-linux-link-semaphore ;
-}
-
-# Differ from 'link' above only by -shared.
-actions link.dll bind LIBRARIES
-{
-    "$(CONFIG_COMMAND)" -L"$(LINKPATH)" -Wl,-R$(SPACE)-Wl,"$(RPATH)" -o "$(<)" -Wl,-soname$(SPACE)-Wl,$(<[1]:D=) -shared "$(>)"  "$(LIBRARIES)" -l$(FINDLIBS-SA) -l$(FINDLIBS-ST) $(OPTIONS) $(USER_OPTIONS)
-}
-
-
-
diff --git a/jam-files/boost-build/tools/intel-win.jam b/jam-files/boost-build/tools/intel-win.jam
deleted file mode 100644
index 691b5dce..00000000
--- a/jam-files/boost-build/tools/intel-win.jam
+++ /dev/null
@@ -1,184 +0,0 @@
-# Copyright Vladimir Prus 2004.
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt
-# or copy at http://www.boost.org/LICENSE_1_0.txt)
-
-# Importing common is needed because the rules we inherit here depend on it.
-# That is nasty.
-import common ;
-import errors ;
-import feature ;
-import intel ;
-import msvc ;
-import os ;
-import toolset ;
-import generators ;
-import type ;
-
-feature.extend-subfeature toolset intel : platform : win ;
-
-toolset.inherit-generators intel-win <toolset>intel <toolset-intel:platform>win : msvc ;
-toolset.inherit-flags intel-win : msvc : : YLOPTION ;
-toolset.inherit-rules intel-win : msvc ;
-
-# Override default do-nothing generators.
-generators.override intel-win.compile.c.pch   : pch.default-c-pch-generator   ;
-generators.override intel-win.compile.c++.pch : pch.default-cpp-pch-generator ;
-generators.override intel-win.compile.rc : rc.compile.resource ;
-generators.override intel-win.compile.mc : mc.compile ;
-
-toolset.flags intel-win.compile PCH_SOURCE <pch>on : <pch-source> ;
-
-toolset.add-requirements <toolset>intel-win,<runtime-link>shared:<threading>multi ;
-
-# Initializes the intel toolset for windows
-rule init ( version ? :     # the compiler version
-            command * :     # the command to invoke the compiler itself
-            options *       # Additional option: <compatibility>
-                            # either 'vc6', 'vc7', 'vc7.1'
-                            # or 'native'(default).
-          )
-{
-    local compatibility =
-      [ feature.get-values <compatibility> : $(options) ] ;
-    local condition = [  common.check-init-parameters intel-win
-        : version $(version) : compatibility $(compatibility) ] ;
-
-    command = [ common.get-invocation-command intel-win : icl.exe :
-        $(command) ] ;
-
-    common.handle-options intel-win : $(condition) : $(command) : $(options) ;
-
-    local root ;
-    if $(command)
-    {
-        root = [ common.get-absolute-tool-path $(command[-1]) ] ;
-        root = $(root)/ ;
-    }
-
-    local setup ;
-    setup = [ GLOB $(root) : iclvars_*.bat ] ;
-    if ! $(setup)
-    {
-       setup = $(root)/iclvars.bat ;
-    }
-    setup = "call \""$(setup)"\" > nul " ;
-
-    if [ os.name ] = NT
-    {
-        setup = $(setup)"
-" ;
-    }
-    else
-    {
-        setup = "cmd /S /C "$(setup)" \"&&\" " ;
-    }
-
-    toolset.flags intel-win.compile .CC $(condition) : $(setup)icl ;
-    toolset.flags intel-win.link .LD $(condition) : $(setup)xilink ;
-    toolset.flags intel-win.archive .LD $(condition) : $(setup)xilink /lib ;
-    toolset.flags intel-win.link .MT $(condition) : $(setup)mt -nologo ;
-    toolset.flags intel-win.compile .MC $(condition) : $(setup)mc ;
-    toolset.flags intel-win.compile .RC $(condition) : $(setup)rc ;
-
-    local m = [ MATCH (.).* : $(version) ] ;
-    local major = $(m[1]) ;
-
-    local C++FLAGS ;
-
-    C++FLAGS += /nologo ;
-
-    # Reduce the number of spurious error messages
-    C++FLAGS += /Qwn5 /Qwd985 ;
-
-    # Enable ADL
-    C++FLAGS += -Qoption,c,--arg_dep_lookup ; #"c" works for C++, too
-
-    # Disable Microsoft "secure" overloads in Dinkumware libraries since they
-    # cause compile errors with Intel versions 9 and 10.
-    C++FLAGS += -D_SECURE_SCL=0 ;
-
-    if $(major) > 5
-    {
-        C++FLAGS += /Zc:forScope ;  # Add support for correct for loop scoping.
-    }
-
-    # Add options recognized only by intel7 and above.
-    if $(major) >= 7
-    {
-        C++FLAGS += /Qansi_alias ;
-    }
-
-    if $(compatibility) = vc6
-    {
-        C++FLAGS +=
-          # Emulate VC6
-          /Qvc6
-
-          # No wchar_t support in vc6 dinkum library.  Furthermore, in vc6
-          # compatibility-mode, wchar_t is not a distinct type from unsigned
-          # short.
-          -DBOOST_NO_INTRINSIC_WCHAR_T
-          ;
-    }
-    else
-    {
-        if $(major) > 5
-        {
-            # Add support for wchar_t
-            C++FLAGS += /Zc:wchar_t
-              # Tell the dinkumware library about it.
-              -D_NATIVE_WCHAR_T_DEFINED
-              ;
-        }
-    }
-
-    if $(compatibility) && $(compatibility) != native
-    {
-        C++FLAGS += /Q$(base-vc) ;
-    }
-    else
-    {
-        C++FLAGS +=
-          -Qoption,cpp,--arg_dep_lookup
-          # The following options were intended to disable the Intel compiler's
-          # 'bug-emulation' mode, but were later reported to be causing ICE with
-          # Intel-Win 9.0. It is not yet clear which options can be safely used.
-          # -Qoption,cpp,--const_string_literals
-          # -Qoption,cpp,--new_for_init
-          # -Qoption,cpp,--no_implicit_typename
-          # -Qoption,cpp,--no_friend_injection
-          # -Qoption,cpp,--no_microsoft_bugs
-          ;
-    }
-
-    toolset.flags intel-win CFLAGS $(condition) : $(C++FLAGS) ;
-    # By default, when creating PCH, intel adds 'i' to the explicitly
-    # specified name of the PCH file. Of course, Boost.Build is not
-    # happy when compiler produces not the file it was asked for.
-    # The option below stops this behaviour.
-    toolset.flags intel-win CFLAGS : -Qpchi- ;
-
-    if ! $(compatibility)
-    {
-        # If there's no backend version, assume 7.1.
-        compatibility = vc7.1 ;
-    }
-
-    local extract-version = [ MATCH ^vc(.*) : $(compatibility) ] ;
-    if ! $(extract-version)
-    {
-        errors.user-error "Invalid value for compatibility option:"
-            $(compatibility) ;
-    }
-
-    # Depending on the settings, running of tests require some runtime DLLs.
-    toolset.flags intel-win RUN_PATH $(condition) : $(root) ;
-
-    msvc.configure-version-specific intel-win : $(extract-version[1]) : $(condition) ;
-}
-
-toolset.flags intel-win.link LIBRARY_OPTION <toolset>intel : "" ;
-
-toolset.flags intel-win YLOPTION ;
-
diff --git a/jam-files/boost-build/tools/intel.jam b/jam-files/boost-build/tools/intel.jam
deleted file mode 100644
index 67038aa2..00000000
--- a/jam-files/boost-build/tools/intel.jam
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright Vladimir Prus 2004.
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt
-# or copy at http://www.boost.org/LICENSE_1_0.txt)
-
-# This is a generic 'intel' toolset. Depending on the current
-# system, it forwards either to 'intel-linux' or 'intel-win'
-# modules.
-
-import feature ;
-import os ;
-import toolset ;
-
-feature.extend toolset : intel ;
-feature.subfeature toolset intel : platform : : propagated link-incompatible ;
-
-rule init ( * : * )
-{
-    if [ os.name ] = LINUX
-    {
-        toolset.using intel-linux : 
-          $(1) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ;
-    }
-    else if [ os.name ] = MACOSX
-    {
-        toolset.using intel-darwin : 
-          $(1) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ;
-    }
-    else
-    {
-        toolset.using intel-win :
-          $(1) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ;
-    }        
-}
diff --git a/jam-files/boost-build/tools/lex.jam b/jam-files/boost-build/tools/lex.jam
deleted file mode 100644
index 75d64131..00000000
--- a/jam-files/boost-build/tools/lex.jam
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 2003 Vladimir Prus 
-# Distributed under the Boost Software License, Version 1.0. 
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt) 
-
-import type ;
-import generators ;
-import feature ;
-import property ;
-
-
-feature.feature flex.prefix : : free ;
-type.register LEX : l ;
-type.register LEX++ : ll ;
-generators.register-standard lex.lex : LEX : C ;
-generators.register-standard lex.lex : LEX++ : CPP ;
-
-rule init ( )
-{
-}
-
-rule lex ( target : source : properties * )
-{   
-    local r = [ property.select flex.prefix : $(properties) ] ;
-    if $(r)
-    {
-        PREFIX on $(<) = $(r:G=) ;
-    }
-}
-
-actions lex 
-{
-    flex -P$(PREFIX) -o$(<) $(>)    
-}
diff --git a/jam-files/boost-build/tools/make.jam b/jam-files/boost-build/tools/make.jam
deleted file mode 100644
index 08567285..00000000
--- a/jam-files/boost-build/tools/make.jam
+++ /dev/null
@@ -1,72 +0,0 @@
-# Copyright 2003 Dave Abrahams
-# Copyright 2003 Douglas Gregor
-# Copyright 2006 Rene Rivera
-# Copyright 2002, 2003, 2004, 2005, 2006 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-#  This module defines the 'make' main target rule.
-
-import "class" : new ;
-import errors : error ;
-import project ;
-import property ;
-import property-set ;
-import regex ;
-import targets ;
-
-
-class make-target-class : basic-target
-{
-    import type regex virtual-target ;
-    import "class" : new ;
-
-    rule __init__ ( name : project : sources * : requirements *
-        : default-build * : usage-requirements * )
-    {
-        basic-target.__init__ $(name) : $(project) : $(sources) :
-            $(requirements) : $(default-build) : $(usage-requirements) ;
-    }
-
-    rule construct ( name : source-targets * : property-set )
-    {
-        local action-name = [ $(property-set).get <action> ] ;
-        # 'm' will always be set -- we add '@' ourselves in the 'make' rule
-        # below.
-        local m = [ MATCH ^@(.*) : $(action-name) ] ;
-
-        local a = [ new action $(source-targets) : $(m[1]) : $(property-set) ] ;
-        local t = [ new file-target $(self.name) exact : [ type.type
-            $(self.name) ] : $(self.project) : $(a) ] ;
-        return [ property-set.empty ] [ virtual-target.register $(t) ] ;
-    }
-}
-
-
-# Declares the 'make' main target.
-#
-rule make ( target-name : sources * : generating-rule + : requirements * :
-    usage-requirements * )
-{
-    local project = [ project.current ] ;
-
-    # The '@' sign causes the feature.jam module to qualify rule name with the
-    # module name of current project, if needed.
-    local m = [ MATCH ^(@).* : $(generating-rule) ] ;
-    if ! $(m)
-    {
-        generating-rule = @$(generating-rule) ;
-    }
-    requirements += <action>$(generating-rule) ;
-
-    targets.main-target-alternative
-        [ new make-target-class $(target-name) : $(project)
-            : [ targets.main-target-sources $(sources) : $(target-name) ]
-            : [ targets.main-target-requirements $(requirements) : $(project) ]
-            : [ targets.main-target-default-build : $(project) ]
-            : [ targets.main-target-usage-requirements $(usage-requirements) :
-                $(project) ] ] ;
-}
-
-
-IMPORT $(__name__) : make : : make ;
diff --git a/jam-files/boost-build/tools/make.py b/jam-files/boost-build/tools/make.py
deleted file mode 100644
index 10baa1cb..00000000
--- a/jam-files/boost-build/tools/make.py
+++ /dev/null
@@ -1,59 +0,0 @@
-# Status: ported.
-# Base revision: 64068
-
-# Copyright 2003 Dave Abrahams 
-# Copyright 2003 Douglas Gregor 
-# Copyright 2006 Rene Rivera 
-# Copyright 2002, 2003, 2004, 2005, 2006 Vladimir Prus 
-# Distributed under the Boost Software License, Version 1.0. 
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt) 
-
-#  This module defines the 'make' main target rule.
-
-from b2.build.targets import BasicTarget
-from b2.build.virtual_target import Action, FileTarget
-from b2.build import type
-from b2.manager import get_manager
-import b2.build.property_set
-
-
-class MakeTarget(BasicTarget):
-  
-    def construct(self, name, source_targets, property_set):
-
-        action_name = property_set.get("<action>")[0]            
-        action = Action(get_manager(), source_targets, action_name[1:], property_set)
-        target = FileTarget(self.name(), type.type(self.name()),
-                            self.project(), action, exact=True)    
-        return [ b2.build.property_set.empty(),
-                 [self.project().manager().virtual_targets().register(target)]]
-
-def make (target_name, sources, generating_rule,
-          requirements=None, usage_requirements=None):
-
-    target_name = target_name[0]
-    generating_rule = generating_rule[0]
-    if generating_rule[0] != '@':
-        generating_rule = '@' + generating_rule
-
-    if not requirements:
-        requirements = []
-
-        
-    requirements.append("<action>%s" % generating_rule)
-    
-    m = get_manager()
-    targets = m.targets()
-    project = m.projects().current()
-    engine = m.engine()
-    engine.register_bjam_action(generating_rule)
-
-    targets.main_target_alternative(MakeTarget(
-        target_name, project,
-        targets.main_target_sources(sources, target_name),
-        targets.main_target_requirements(requirements, project),
-        targets.main_target_default_build([], project),
-        targets.main_target_usage_requirements(usage_requirements or [], project)))
-
-get_manager().projects().add_rule("make", make)
-
diff --git a/jam-files/boost-build/tools/mc.jam b/jam-files/boost-build/tools/mc.jam
deleted file mode 100644
index 57837773..00000000
--- a/jam-files/boost-build/tools/mc.jam
+++ /dev/null
@@ -1,44 +0,0 @@
-#~ Copyright 2005 Alexey Pakhunov.
-#~ Distributed under the Boost Software License, Version 1.0.
-#~ (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-#  Support for Microsoft message compiler tool.
-#  Notes:
-#  - there's just message compiler tool, there's no tool for 
-#    extracting message strings from sources
-#  - This file allows to use Microsoft message compiler
-#    with any toolset. In msvc.jam, there's more specific
-#    message compiling action.
-
-import common ;
-import generators ;
-import feature : feature get-values ;
-import toolset : flags ;
-import type ;
-import rc ;
-
-rule init ( )
-{
-}
-
-type.register MC : mc ;
-
-
-# Command line options
-feature mc-input-encoding : ansi unicode : free ;
-feature mc-output-encoding : unicode ansi : free ;
-feature mc-set-customer-bit : no yes : free ;
-
-flags mc.compile MCFLAGS <mc-input-encoding>ansi : -a ;
-flags mc.compile MCFLAGS <mc-input-encoding>unicode : -u ;
-flags mc.compile MCFLAGS <mc-output-encoding>ansi : -A ;
-flags mc.compile MCFLAGS <mc-output-encoding>unicode : -U ;
-flags mc.compile MCFLAGS <mc-set-customer-bit>no : ;
-flags mc.compile MCFLAGS <mc-set-customer-bit>yes : -c ;
-
-generators.register-standard mc.compile : MC : H RC ;
-
-actions compile
-{
-    mc $(MCFLAGS) -h "$(<[1]:DW)" -r "$(<[2]:DW)" "$(>:W)"
-}
diff --git a/jam-files/boost-build/tools/message.jam b/jam-files/boost-build/tools/message.jam
deleted file mode 100644
index 212d8542..00000000
--- a/jam-files/boost-build/tools/message.jam
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 2008 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-# Defines main target type 'message', that prints a message when built for the
-# first time.
-
-import project ;
-import "class" : new ;
-import targets ;
-import property-set ;
-
-class message-target-class : basic-target
-{
-    rule __init__ ( name-and-dir : project : * )
-    {
-        basic-target.__init__ $(name-and-dir) : $(project) ;
-        self.3 = $(3) ;
-        self.4 = $(4) ;
-        self.5 = $(5) ;
-        self.6 = $(6) ;
-        self.7 = $(7) ;
-        self.8 = $(8) ;        
-        self.9 = $(9) ;        
-        self.built = ;
-    }
-    
-    rule construct ( name : source-targets * : property-set )
-    {
-        if ! $(self.built)
-        {
-            for i in 3 4 5 6 7 8 9
-            {
-                if $(self.$(i))
-                {
-                    ECHO $(self.$(i)) ;
-                }
-            }
-            self.built = 1 ;
-        }
-        
-        return [ property-set.empty ] ;
-    }
-}
-
-
-rule message ( name : * )
-{
-    local project = [ project.current ] ;
-
-    targets.main-target-alternative
-      [ new message-target-class $(name) : $(project) 
-        : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) ] ;
-}
-IMPORT $(__name__) : message : : message ;
\ No newline at end of file
diff --git a/jam-files/boost-build/tools/message.py b/jam-files/boost-build/tools/message.py
deleted file mode 100644
index cc0b946f..00000000
--- a/jam-files/boost-build/tools/message.py
+++ /dev/null
@@ -1,46 +0,0 @@
-# Status: ported.
-# Base revision: 64488.
-#
-# Copyright 2008, 2010 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-# Defines main target type 'message', that prints a message when built for the
-# first time.
-
-import b2.build.targets as targets
-import b2.build.property_set as property_set
-
-from b2.manager import get_manager
-
-class MessageTargetClass(targets.BasicTarget):
-
-    def __init__(self, name, project, *args):
-
-        targets.BasicTarget.__init__(self, name, project, [])
-        self.args = args
-        self.built = False
-
-    def construct(self, name, sources, ps):
-
-        if not self.built:
-            for arg in self.args:
-                if type(arg) == type([]):
-                    arg = " ".join(arg)                
-                print arg
-            self.built = True
-
-        return (property_set.empty(), [])
-
-def message(name, *args):
-
-    if type(name) == type([]):
-        name = name[0]
-
-    t = get_manager().targets()
-    
-    project = get_manager().projects().current()
-        
-    return t.main_target_alternative(MessageTargetClass(*((name, project) + args)))
-
-get_manager().projects().add_rule("message", message)
diff --git a/jam-files/boost-build/tools/midl.jam b/jam-files/boost-build/tools/midl.jam
deleted file mode 100644
index 0aa5dda3..00000000
--- a/jam-files/boost-build/tools/midl.jam
+++ /dev/null
@@ -1,142 +0,0 @@
-# Copyright (c) 2005 Alexey Pakhunov.
-#
-# Use, modification and distribution is subject to the Boost Software
-# License Version 1.0. (See accompanying file LICENSE_1_0.txt or
-# http://www.boost.org/LICENSE_1_0.txt)
-
-# Microsoft Interface Definition Language (MIDL) related routines
-
-import common ;
-import generators ;
-import feature : feature get-values ;
-import os ;
-import scanner ;
-import toolset : flags ;
-import type ;
-
-rule init ( )
-{
-}
-
-type.register IDL : idl ;
-
-# A type library (.tlb) is generated by MIDL compiler and can be included
-# to resources of an application (.rc). In order to be found by a resource 
-# compiler its target type should be derived from 'H' - otherwise
-# the property '<implicit-dependency>' will be ignored.
-type.register MSTYPELIB : tlb : H ;
-
-
-# Register scanner for MIDL files
-class midl-scanner : scanner 
-{
-    import path property-set regex scanner type virtual-target ;
-    
-    rule __init__ ( includes * )
-    {
-        scanner.__init__ ;
-    
-        self.includes = $(includes) ;
-
-        # List of quoted strings 
-        self.re-strings = "[ \t]*\"([^\"]*)\"([ \t]*,[ \t]*\"([^\"]*)\")*[ \t]*" ;
-
-        # 'import' and 'importlib' directives 
-        self.re-import    = "import"$(self.re-strings)"[ \t]*;" ;
-        self.re-importlib = "importlib[ \t]*[(]"$(self.re-strings)"[)][ \t]*;" ;
-
-        # C preprocessor 'include' directive
-        self.re-include-angle  = "#[ \t]*include[ \t]*<(.*)>" ;
-        self.re-include-quoted = "#[ \t]*include[ \t]*\"(.*)\"" ;
-    }    
-
-    rule pattern ( )
-    {
-        # Match '#include', 'import' and 'importlib' directives
-        return "((#[ \t]*include|import(lib)?).+(<(.*)>|\"(.*)\").+)" ;
-    }
-
-    rule process ( target : matches * : binding )
-    {
-        local included-angle  = [ regex.transform $(matches) : $(self.re-include-angle)  : 1 ] ;
-        local included-quoted = [ regex.transform $(matches) : $(self.re-include-quoted) : 1 ] ;
-        local imported        = [ regex.transform $(matches) : $(self.re-import)         : 1 3 ] ;
-        local imported_tlbs   = [ regex.transform $(matches) : $(self.re-importlib)      : 1 3 ] ;
-
-        # CONSIDER: the new scoping rule seem to defeat "on target" variables.
-        local g = [ on $(target) return $(HDRGRIST) ] ;  
-        local b = [ NORMALIZE_PATH $(binding:D) ] ;
-
-        # Attach binding of including file to included targets.
-        # When target is directly created from virtual target
-        # this extra information is unnecessary. But in other
-        # cases, it allows to distinguish between two headers of the 
-        # same name included from different places.      
-        local g2 = $(g)"#"$(b) ;
-
-        included-angle = $(included-angle:G=$(g)) ;
-        included-quoted = $(included-quoted:G=$(g2)) ;
-        imported = $(imported:G=$(g2)) ;
-        imported_tlbs = $(imported_tlbs:G=$(g2)) ;
-
-        local all = $(included-angle) $(included-quoted) $(imported) ;
-
-        INCLUDES $(target) : $(all) ;
-        DEPENDS $(target) : $(imported_tlbs) ;
-        NOCARE $(all) $(imported_tlbs) ;
-        SEARCH on $(included-angle)  = $(self.includes:G=) ;
-        SEARCH on $(included-quoted) = $(b) $(self.includes:G=) ;
-        SEARCH on $(imported)        = $(b) $(self.includes:G=) ;
-        SEARCH on $(imported_tlbs)   = $(b) $(self.includes:G=) ;
-        
-        scanner.propagate 
-            [ type.get-scanner CPP : [ property-set.create $(self.includes) ] ] : 
-            $(included-angle) $(included-quoted) : $(target) ;
-
-        scanner.propagate $(__name__) : $(imported) : $(target) ;
-    }        
-}
-
-scanner.register midl-scanner : include ;
-type.set-scanner IDL : midl-scanner ;
-
-
-# Command line options
-feature midl-stubless-proxy : yes no : propagated ;
-feature midl-robust : yes no : propagated ;
-
-flags midl.compile.idl MIDLFLAGS <midl-stubless-proxy>yes : /Oicf ;
-flags midl.compile.idl MIDLFLAGS <midl-stubless-proxy>no : /Oic ;
-flags midl.compile.idl MIDLFLAGS <midl-robust>yes : /robust ;
-flags midl.compile.idl MIDLFLAGS <midl-robust>no : /no_robust ;
-
-# Architecture-specific options
-architecture-x86 = <architecture> <architecture>x86 ;
-address-model-32 = <address-model> <address-model>32 ;
-address-model-64 = <address-model> <address-model>64 ;
-
-flags midl.compile.idl MIDLFLAGS $(architecture-x86)/$(address-model-32) : /win32 ;
-flags midl.compile.idl MIDLFLAGS $(architecture-x86)/<address-model>64 : /x64 ;
-flags midl.compile.idl MIDLFLAGS <architecture>ia64/$(address-model-64) : /ia64 ;
-
-
-flags midl.compile.idl DEFINES <define> ;
-flags midl.compile.idl UNDEFS <undef> ;
-flags midl.compile.idl INCLUDES <include> ;
-
-
-generators.register-c-compiler midl.compile.idl : IDL : MSTYPELIB H C(%_i) C(%_proxy) C(%_dlldata) ;
-
-
-# MIDL does not always generate '%_proxy.c' and '%_dlldata.c'. This behavior 
-# depends on contents of the source IDL file. Calling TOUCH_FILE below ensures
-# that both files will be created so bjam will not try to recreate them 
-# constantly.
-TOUCH_FILE = [ common.file-touch-command ] ;
-
-actions compile.idl
-{
-    midl /nologo @"@($(<[1]:W).rsp:E=$(nl)"$(>:W)" $(nl)-D$(DEFINES) $(nl)"-I$(INCLUDES)" $(nl)-U$(UNDEFS) $(nl)$(MIDLFLAGS) $(nl)/tlb "$(<[1]:W)" $(nl)/h "$(<[2]:W)" $(nl)/iid "$(<[3]:W)" $(nl)/proxy "$(<[4]:W)" $(nl)/dlldata "$(<[5]:W)")"
-    $(TOUCH_FILE) "$(<[4]:W)"  
-    $(TOUCH_FILE) "$(<[5]:W)"  
-}
diff --git a/jam-files/boost-build/tools/mipspro.jam b/jam-files/boost-build/tools/mipspro.jam
deleted file mode 100644
index 417eaefc..00000000
--- a/jam-files/boost-build/tools/mipspro.jam
+++ /dev/null
@@ -1,145 +0,0 @@
-#  Copyright Noel Belcourt 2007.
-#  Distributed under the Boost Software License, Version 1.0.
-#    (See accompanying file LICENSE_1_0.txt or copy at
-#          http://www.boost.org/LICENSE_1_0.txt)
-
-import property ;
-import generators ;
-import os ;
-import toolset : flags ;
-import feature ;
-import fortran ;
-import type ;
-import common ;
-
-feature.extend toolset : mipspro ;
-toolset.inherit mipspro : unix ;
-generators.override mipspro.prebuilt : builtin.lib-generator ;
-generators.override mipspro.searched-lib-generator : searched-lib-generator ;
-
-#  Documentation and toolchain description located
-#  http://www.sgi.com/products/software/irix/tools/
-
-rule init ( version ? : command * : options * ) 
-{
-  local condition = [ 
-    common.check-init-parameters mipspro : version $(version) ] ;
-
-  command = [ common.get-invocation-command mipspro : CC : $(command) ] ;
-
-  common.handle-options mipspro : $(condition) : $(command) : $(options) ;
-    
-  command_c = $(command_c[1--2]) $(command[-1]:B=cc) ;
-
-  toolset.flags mipspro CONFIG_C_COMMAND $(condition) : $(command_c) ;
-
-  # fortran support
-  local command = [ 
-    common.get-invocation-command mipspro : f77 : $(command) : $(install_dir) ] ;
-
-  command_f = $(command_f[1--2]) $(command[-1]:B=f77) ;
-  toolset.flags mipspro CONFIG_F_COMMAND $(condition) : $(command_f) ;
-
-  # set link flags
-  flags mipspro.link FINDLIBS-ST : [ 
-    feature.get-values <find-static-library> : $(options) ] : unchecked ;
-
-  flags mipspro.link FINDLIBS-SA : [ 
-    feature.get-values <find-shared-library> : $(options) ] : unchecked ;
-}
-
-# Declare generators
-generators.register-c-compiler mipspro.compile.c : C : OBJ : <toolset>mipspro ;
-generators.register-c-compiler mipspro.compile.c++ : CPP : OBJ : <toolset>mipspro ;
-generators.register-fortran-compiler mipspro.compile.fortran : FORTRAN : OBJ : <toolset>mipspro ;
-
-cpu-arch-32 =
-  <architecture>/<address-model>
-  <architecture>/<address-model>32 ;
-
-cpu-arch-64 =
-  <architecture>/<address-model>64 ;
-
-flags mipspro.compile OPTIONS $(cpu-arch-32) : -n32 ;
-flags mipspro.compile OPTIONS $(cpu-arch-64) : -64 ;
-
-# Declare flags and actions for compilation
-flags mipspro.compile OPTIONS <debug-symbols>on : -g ; 
-# flags mipspro.compile OPTIONS <profiling>on : -xprofile=tcov ;
-flags mipspro.compile OPTIONS <warnings>off : -w ;
-flags mipspro.compile OPTIONS <warnings>on : -ansiW -diag_suppress 1429 ; # suppress long long is nonstandard warning
-flags mipspro.compile OPTIONS <warnings>all : -fullwarn ;
-flags mipspro.compile OPTIONS <optimization>speed : -Ofast ;
-flags mipspro.compile OPTIONS <optimization>space : -O2 ;
-flags mipspro.compile OPTIONS <cflags> : -LANG:std ;
-flags mipspro.compile.c++ OPTIONS <inlining>off : -INLINE:none ;
-flags mipspro.compile.c++ OPTIONS <cxxflags> ;
-flags mipspro.compile DEFINES <define> ;
-flags mipspro.compile INCLUDES <include> ;
-
-
-flags mipspro.compile.fortran OPTIONS <fflags> ;
-
-actions compile.c
-{
-    "$(CONFIG_C_COMMAND)" $(OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -c -o "$(<)" "$(>)"
-}
-
-actions compile.c++
-{
-    "$(CONFIG_COMMAND)" -FE:template_in_elf_section -ptused $(OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -c -o "$(<)" "$(>)"
-}
-
-actions compile.fortran
-{
-    "$(CONFIG_F_COMMAND)" $(OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -c -o "$(<)" "$(>)"
-}
-
-# Declare flags and actions for linking
-flags mipspro.link OPTIONS <debug-symbols>on : -g ;
-# Strip the binary when no debugging is needed
-# flags mipspro.link OPTIONS <debug-symbols>off : -s ;
-# flags mipspro.link OPTIONS <profiling>on : -xprofile=tcov ;
-# flags mipspro.link OPTIONS <threading>multi : -mt ;
-
-flags mipspro.link OPTIONS $(cpu-arch-32) : -n32 ;
-flags mipspro.link OPTIONS $(cpu-arch-64) : -64 ;
-
-flags mipspro.link OPTIONS <optimization>speed : -Ofast ;
-flags mipspro.link OPTIONS <optimization>space : -O2 ;
-flags mipspro.link OPTIONS <linkflags> ;
-flags mipspro.link LINKPATH <library-path> ;
-flags mipspro.link FINDLIBS-ST <find-static-library> ;
-flags mipspro.link FINDLIBS-SA <find-shared-library> ;
-flags mipspro.link FINDLIBS-SA <threading>multi : pthread ;
-flags mipspro.link LIBRARIES <library-file> ;
-flags mipspro.link LINK-RUNTIME <runtime-link>static : static ;
-flags mipspro.link LINK-RUNTIME <runtime-link>shared : dynamic ;
-flags mipspro.link RPATH <dll-path> ;
-
-rule link ( targets * : sources * : properties * )
-{
-    SPACE on $(targets) = " " ;
-}
-
-actions link bind LIBRARIES
-{
-    "$(CONFIG_COMMAND)" -FE:template_in_elf_section -ptused $(OPTIONS) -L"$(LINKPATH)" -R"$(RPATH)" -o "$(<)" "$(>)" "$(LIBRARIES)" -Bdynamic -l$(FINDLIBS-SA) -Bstatic -l$(FINDLIBS-ST) -B$(LINK-RUNTIME) -lm
-}
-
-# Slight mods for dlls
-rule link.dll ( targets * : sources * : properties * )
-{
-    SPACE on $(targets) = " " ;
-}
-
-actions link.dll bind LIBRARIES
-{
-    "$(CONFIG_COMMAND)" $(OPTIONS) -L"$(LINKPATH)" -R"$(RPATH)" -o "$(<)" "$(>)" "$(LIBRARIES)" -Bdynamic -l$(FINDLIBS-SA) -Bstatic -l$(FINDLIBS-ST) -B$(LINK-RUNTIME)
-}
-
-# Declare action for creating static libraries
-actions piecemeal archive
-{
-    ar -cr "$(<)" "$(>)"
-}
diff --git a/jam-files/boost-build/tools/mpi.jam b/jam-files/boost-build/tools/mpi.jam
deleted file mode 100644
index 0fe490be..00000000
--- a/jam-files/boost-build/tools/mpi.jam
+++ /dev/null
@@ -1,583 +0,0 @@
-# Support for the Message Passing Interface (MPI)
-#
-# (C) Copyright 2005, 2006 Trustees of Indiana University
-# (C) Copyright 2005 Douglas Gregor
-#
-# Distributed under the Boost Software License, Version 1.0. (See accompanying 
-# file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt.)
-#
-# Authors: Douglas Gregor
-#          Andrew Lumsdaine
-#
-# ==== MPI Configuration ====
-# 
-# For many users, MPI support can be enabled simply by adding the following 
-# line to your user-config.jam file:
-#
-#   using mpi ;
-#
-# This should auto-detect MPI settings based on the MPI wrapper compiler in 
-# your path, e.g., "mpic++". If the wrapper compiler is not in your path, or
-# has a different name, you can pass the name of the wrapper compiler as the
-# first argument to the mpi module:
-#
-#   using mpi : /opt/mpich2-1.0.4/bin/mpiCC ;
-#
-# If your MPI implementation does not have a wrapper compiler, or the MPI 
-# auto-detection code does not work with your MPI's wrapper compiler,
-# you can pass MPI-related options explicitly via the second parameter to the 
-# mpi module:
-#
-#    using mpi : : <find-shared-library>lammpio <find-shared-library>lammpi++
-#                  <find-shared-library>mpi <find-shared-library>lam 
-#                  <find-shared-library>dl ;
-#
-# To see the results of MPI auto-detection, pass "--debug-configuration" on
-# the bjam command line.
-#
-# The (optional) fourth argument configures Boost.MPI for running
-# regression tests. These parameters specify the executable used to
-# launch jobs (default: "mpirun") followed by any necessary arguments
-# to this to run tests and tell the program to expect the number of
-# processors to follow (default: "-np").  With the default parameters,
-# for instance, the test harness will execute, e.g.,
-#  
-#    mpirun -np 4 all_gather_test
-#
-# ==== Linking Against the MPI Libraries ===
-#
-# To link against the MPI libraries, import the "mpi" module and add the 
-# following requirement to your target:
-# 
-#   <library>/mpi//mpi 
-#
-# Since MPI support is not always available, you should check 
-# "mpi.configured" before trying to link against the MPI libraries.
-
-import "class" : new ;
-import common ;
-import feature : feature ;
-import generators ;
-import os ;
-import project ;
-import property ;
-import testing ;
-import toolset ;
-import type ;
-import path ;
-
-# Make this module a project
-project.initialize $(__name__) ;
-project mpi ;
-
-if [ MATCH (--debug-configuration) : [ modules.peek : ARGV ] ]
-{
-  .debug-configuration = true ;
-}
-
-# Assuming the first part of the command line is the given prefix
-# followed by some non-empty value, remove the first argument. Returns
-# either nothing (if there was no prefix or no value) or a pair
-#
-#   <name>value rest-of-cmdline
-#
-# This is a subroutine of cmdline_to_features
-rule add_feature ( prefix name cmdline ) 
-{
-    local match = [ MATCH "^$(prefix)([^\" ]+|\"[^\"]+\") *(.*)$" : $(cmdline) ] ;
-
-    # If there was no value associated with the prefix, abort
-    if ! $(match) {
-      return ;
-    }
-
-    local value = $(match[1]) ;
-
-    if [ MATCH " +" : $(value) ] {
-      value = "\"$(value)\"" ;
-    }
-
-    return "<$(name)>$(value)" $(match[2]) ;
-}
-
-# Strip any end-of-line characters off the given string and return the
-# result.
-rule strip-eol ( string )
-{
-  local match = [ MATCH "^(([A-Za-z0-9~`\.!@#$%^&*()_+={};:'\",.<>/?\\| -]|[|])*).*$" : $(string) ] ;
-
-  if $(match)
-  {
-    return $(match[1]) ;
-  }
-  else
-  {
-    return $(string) ;
-  }
-}
-
-# Split a command-line into a set of features. Certain kinds of
-# compiler flags are recognized (e.g., -I, -D, -L, -l) and replaced
-# with their Boost.Build equivalents (e.g., <include>, <define>,
-# <library-path>, <find-library>). All other arguments are introduced
-# using the features in the unknown-features parameter, because we
-# don't know how to deal with them. For instance, if your compile and
-# correct. The incoming command line should be a string starting with
-# an executable (e.g., g++ -I/include/path") and may contain any
-# number of command-line arguments thereafter. The result is a list of
-# features corresponding to the given command line, ignoring the
-# executable.
-rule cmdline_to_features ( cmdline : unknown-features ? )
-{
-    local executable ;
-    local features ;
-    local otherflags ;
-    local result ;
-
-    unknown-features ?= <cxxflags> <linkflags> ;
-
-    # Pull the executable out of the command line. At this point, the
-    # executable is just thrown away.
-    local match = [ MATCH "^([^\" ]+|\"[^\"]+\") *(.*)$" : $(cmdline) ] ;
-    executable = $(match[1]) ;
-    cmdline = $(match[2]) ;
-
-    # List the prefix/feature pairs that we will be able to transform. 
-    # Every kind of parameter not mentioned here will be placed in both
-    # cxxflags and linkflags, because we don't know where they should go.
-    local feature_kinds-D = "define" ;
-    local feature_kinds-I = "include" ;
-    local feature_kinds-L = "library-path" ;
-    local feature_kinds-l = "find-shared-library" ;
-
-    while $(cmdline) {
-
-        # Check for one of the feature prefixes we know about. If we
-        # find one (and the associated value is nonempty), convert it
-        # into a feature.
-        local match = [ MATCH "^(-.)(.*)" : $(cmdline) ] ;
-        local matched ;
-        if $(match) && $(match[2]) {
-           local prefix = $(match[1]) ;
-           if $(feature_kinds$(prefix)) {
-               local name = $(feature_kinds$(prefix)) ;
-               local add = [ add_feature $(prefix) $(name) $(cmdline) ] ;
-
-               if $(add) {
-
-                  if $(add[1]) = <find-shared-library>pthread
-                  {
-                      # Uhm. It's not really nice that this MPI implementation
-                      # uses -lpthread as opposed to -pthread. We do want to
-                      # set <threading>multi, instead of -lpthread.
-                      result += "<threading>multi" ;
-                      MPI_EXTRA_REQUIREMENTS += "<threading>multi" ;                      
-                  }
-                  else
-                  {                      
-                      result += $(add[1]) ;                  
-                  }
-                                     
-                  cmdline = $(add[2]) ;
-                  matched = yes ;
-               }
-           }
-        }
-
-        # If we haven't matched a feature prefix, just grab the command-line
-        # argument itself. If we can map this argument to a feature
-        # (e.g., -pthread -> <threading>multi), then do so; otherwise,
-        # and add it to the list of "other" flags that we don't
-        # understand.
-        if ! $(matched) {
-           match = [ MATCH "^([^\" ]+|\"[^\"]+\") *(.*)$" : $(cmdline) ] ;
-           local value = $(match[1]) ;
-           cmdline = $(match[2]) ;
-
-           # Check for multithreading support
-           if $(value) = "-pthread" || $(value) = "-pthreads"
-           {
-             result += "<threading>multi" ;
-
-             # DPG: This is a hack intended to work around a BBv2 bug where
-             # requirements propagated from libraries are not checked for
-             # conflicts when BBv2 determines which "common" properties to
-             # apply to a target. In our case, the <threading>single property
-             # gets propagated from the common properties to Boost.MPI
-             # targets, even though <threading>multi is in the usage 
-             # requirements of <library>/mpi//mpi.
-             MPI_EXTRA_REQUIREMENTS += "<threading>multi" ;
-           }
-           else if [ MATCH "(.*[a-zA-Z0-9<>?-].*)" : $(value) ] {
-              otherflags += $(value) ;
-           }
-        }
-    }
-
-    # If there are other flags that we don't understand, add them to the
-    # result as both <cxxflags> and <linkflags>
-    if $(otherflags) {
-       for unknown in $(unknown-features)
-       {
-         result += "$(unknown)$(otherflags:J= )" ;
-       }
-    }
-
-    return $(result) ;
-}
-
-# Determine if it is safe to execute the given shell command by trying
-# to execute it and determining whether the exit code is zero or
-# not. Returns true for an exit code of zero, false otherwise.
-local rule safe-shell-command ( cmdline )
-{
-  local result = [ SHELL "$(cmdline) > /dev/null 2>/dev/null; if [ "$?" -eq "0" ]; then echo SSCOK; fi" ] ;
-  return [ MATCH ".*(SSCOK).*" : $(result) ] ;
-}
-
-# Initialize the MPI module.  
-rule init ( mpicxx ? : options * : mpirun-with-options * )
-{
-  if ! $(options) && $(.debug-configuration)
-  {
-    ECHO "===============MPI Auto-configuration===============" ;
-  }
-    
-  if ! $(mpicxx) && [ os.on-windows ]
-  {  
-    # Try to auto-configure to the Microsoft Compute Cluster Pack
-    local cluster_pack_path_native = "C:\\Program Files\\Microsoft Compute Cluster Pack" ;
-    local cluster_pack_path = [ path.make $(cluster_pack_path_native) ] ;
-    if [ GLOB $(cluster_pack_path_native)\\Include : mpi.h ]
-    {
-      if $(.debug-configuration)
-      {
-        ECHO "Found Microsoft Compute Cluster Pack: $(cluster_pack_path_native)" ;
-      }
-      
-      # Pick up either the 32-bit or 64-bit library, depending on which address
-      # model the user has selected. Default to 32-bit.
-      options = <include>$(cluster_pack_path)/Include 
-                <address-model>64:<library-path>$(cluster_pack_path)/Lib/amd64
-                <library-path>$(cluster_pack_path)/Lib/i386
-                <find-static-library>msmpi
-                <toolset>msvc:<define>_SECURE_SCL=0
-              ;
-              
-      # Setup the "mpirun" equivalent (mpiexec)
-      .mpirun = "\"$(cluster_pack_path_native)\\Bin\\mpiexec.exe"\" ;
-      .mpirun_flags = -n ;
-    }
-    else if $(.debug-configuration)
-    {
-      ECHO "Did not find Microsoft Compute Cluster Pack in $(cluster_pack_path_native)." ;
-    }
-  } 
-   
-  if ! $(options)
-  { 
-    # Try to auto-detect options based on the wrapper compiler
-    local command = [ common.get-invocation-command mpi : mpic++ : $(mpicxx) ] ;
-
-    if ! $(mpicxx) && ! $(command) 
-    {
-      # Try "mpiCC", which is used by MPICH 
-      command = [ common.get-invocation-command mpi : mpiCC ] ;
-    }
-
-    if ! $(mpicxx) && ! $(command) 
-    {
-      # Try "mpicxx", which is used by OpenMPI and MPICH2
-      command = [ common.get-invocation-command mpi : mpicxx ] ;
-    }
-
-    local result ;
-    local compile_flags ;
-    local link_flags ;
-
-    if ! $(command)
-    { 
-      # Do nothing: we'll complain later
-    }
-    # OpenMPI and newer versions of LAM-MPI have -showme:compile and 
-    # -showme:link.
-    else if [ safe-shell-command "$(command) -showme:compile" ] &&
-              [ safe-shell-command "$(command) -showme:link" ]
-    {
-      if $(.debug-configuration)
-      {
-        ECHO "Found recent LAM-MPI or Open MPI wrapper compiler: $(command)" ;
-      }
-
-      compile_flags = [ SHELL "$(command) -showme:compile" ] ;
-      link_flags = [ SHELL "$(command) -showme:link" ] ;
-   
-      # Prepend COMPILER as the executable name, to match the format of 
-      # other compilation commands.
-      compile_flags = "COMPILER $(compile_flags)" ;
-      link_flags = "COMPILER $(link_flags)" ;
-    }
-    # Look for LAM-MPI's -showme
-    else if [ safe-shell-command "$(command) -showme" ]
-    {
-      if $(.debug-configuration)
-      {
-        ECHO "Found older LAM-MPI wrapper compiler: $(command)" ;
-      }
-
-      result = [ SHELL "$(command) -showme" ] ;
-    }
-    # Look for MPICH
-    else if [ safe-shell-command "$(command) -show" ]
-    {
-      if $(.debug-configuration)
-      {
-        ECHO "Found MPICH wrapper compiler: $(command)" ;
-      }
-      compile_flags = [ SHELL "$(command) -compile_info" ] ;
-      link_flags = [ SHELL "$(command) -link_info" ] ;
-    }
-    # Sun HPC and Ibm POE
-    else if [ SHELL "$(command) -v 2>/dev/null" ]
-    {
-      compile_flags = [ SHELL "$(command) -c -v -xtarget=native64 2>/dev/null" ] ;
-
-      local back = [ MATCH "--------------------(.*)" : $(compile_flags) ] ;
-      if $(back)
-      {
-        # Sun HPC
-        if $(.debug-configuration)
-        {
-          ECHO "Found Sun MPI wrapper compiler: $(command)" ;
-        }
-
-        compile_flags = [ MATCH "(.*)--------------------" : $(back) ] ;
-        compile_flags = [ MATCH "(.*)-v" :  $(compile_flags) ] ;
-        link_flags = [ SHELL "$(command) -v -xtarget=native64 2>/dev/null" ] ;
-        link_flags = [ MATCH "--------------------(.*)" : $(link_flags) ] ;
-        link_flags = [ MATCH "(.*)--------------------" : $(link_flags) ] ;
-
-        # strip out -v from compile options
-        local front = [ MATCH "(.*)-v" :  $(link_flags) ] ;
-        local back = [ MATCH "-v(.*)" :  $(link_flags) ] ;
-        link_flags = "$(front) $(back)" ;
-        front = [ MATCH "(.*)-xtarget=native64" :  $(link_flags) ] ;
-        back = [ MATCH "-xtarget=native64(.*)" :  $(link_flags) ] ;
-        link_flags = "$(front) $(back)" ;
-      }
-      else
-      {
-        # Ibm POE
-        if $(.debug-configuration)
-        {
-          ECHO "Found IBM MPI wrapper compiler: $(command)" ;
-        }
-
-        # 
-        compile_flags = [ SHELL "$(command) -c -v 2>/dev/null" ] ;
-        compile_flags = [ MATCH "(.*)exec: export.*" : $(compile_flags) ] ;
-        local front = [ MATCH "(.*)-v" :  $(compile_flags) ] ;
-        local back = [ MATCH "-v(.*)" :  $(compile_flags) ] ;
-        compile_flags = "$(front) $(back)" ;
-        front = [ MATCH "(.*)-c" :  $(compile_flags) ] ;
-        back = [ MATCH "-c(.*)" :  $(compile_flags) ] ;
-        compile_flags = "$(front) $(back)" ;
-        link_flags = $(compile_flags) ;
-
-        # get location of mpif.h from mpxlf
-        local f_flags = [ SHELL "mpxlf -v 2>/dev/null" ] ;
-        f_flags = [ MATCH "(.*)exec: export.*" : $(f_flags) ] ;
-        front = [ MATCH "(.*)-v" :  $(f_flags) ] ;
-        back = [ MATCH "-v(.*)" :  $(f_flags) ] ;
-        f_flags = "$(front) $(back)" ;
-        f_flags = [ MATCH "xlf_r(.*)" : $(f_flags) ] ;
-        f_flags = [ MATCH "-F:mpxlf_r(.*)" : $(f_flags) ] ;
-        compile_flags = [ strip-eol $(compile_flags) ] ;
-        compile_flags = "$(compile_flags) $(f_flags)" ;
-      }
-    }
-
-    if $(result) || $(compile_flags) && $(link_flags)
-    {
-      if $(result)
-      {
-         result = [ strip-eol $(result) ] ;
-         options = [ cmdline_to_features $(result) ] ;
-      }
-      else 
-      { 
-         compile_flags = [ strip-eol $(compile_flags) ] ;
-         link_flags = [ strip-eol $(link_flags) ] ;
-
-         # Separately process compilation and link features, then combine
-         # them at the end.
-         local compile_features = [ cmdline_to_features $(compile_flags) 
-                                                        : "<cxxflags>" ] ; 
-         local link_features = [ cmdline_to_features $(link_flags) 
-                                                     : "<linkflags>" ] ; 
-         options = $(compile_features) $(link_features) ;
-      }
-
-      # If requested, display MPI configuration information.
-      if $(.debug-configuration)
-      {
-        if $(result)
-        {
-          ECHO "  Wrapper compiler command line: $(result)" ;
-        }
-        else
-        {
-	  local match = [ MATCH "^([^\" ]+|\"[^\"]+\") *(.*)$" 
-                                : $(compile_flags) ] ;
-          ECHO "MPI compilation flags: $(match[2])" ;
-	  local match = [ MATCH "^([^\" ]+|\"[^\"]+\") *(.*)$" 
-                                : $(link_flags) ] ;
-          ECHO "MPI link flags: $(match[2])" ;
-        }
-      }
-    } 
-    else 
-    {
-      if $(command)
-      {
-        ECHO "MPI auto-detection failed: unknown wrapper compiler $(command)" ;
-        ECHO "Please report this error to the Boost mailing list: http://www.boost.org" ;
-      }     
-      else if $(mpicxx)
-      {
-        ECHO "MPI auto-detection failed: unable to find wrapper compiler $(mpicxx)" ;
-      } 
-      else
-      {
-        ECHO "MPI auto-detection failed: unable to find wrapper compiler `mpic++' or `mpiCC'" ;
-      }
-      ECHO "You will need to manually configure MPI support." ;
-    }
- 
-  }
-
-  # Find mpirun (or its equivalent) and its flags
-  if ! $(.mpirun)
-  {
-    .mpirun = 
-        [ common.get-invocation-command mpi : mpirun : $(mpirun-with-options[1]) ] ;
-    .mpirun_flags = $(mpirun-with-options[2-]) ;
-    .mpirun_flags ?= -np ;
-  }
-  
-  if $(.debug-configuration)
-  {
-    if $(options)
-    {
-      echo "MPI build features: " ;
-      ECHO $(options) ;
-    }
-
-    if $(.mpirun)
-    {
-      echo "MPI launcher: $(.mpirun) $(.mpirun_flags)" ;
-    }
-        
-    ECHO "====================================================" ;
-  }
-
-  if $(options)  
-  {
-    .configured = true ;
-
-    # Set up the "mpi" alias 
-    alias mpi : : : : $(options) ;
-  }
-}
-
-# States whether MPI has bee configured
-rule configured ( )
-{
-  return $(.configured) ;
-}
-
-# Returs the "extra" requirements needed to build MPI. These requirements are
-# part of the /mpi//mpi library target, but they need to be added to anything
-# that uses MPI directly to work around bugs in BBv2's propagation of
-# requirements.
-rule extra-requirements ( )
-{
-  return $(MPI_EXTRA_REQUIREMENTS) ;
-}
-
-# Support for testing; borrowed from Python
-type.register RUN_MPI_OUTPUT ;
-type.register RUN_MPI : : TEST ;
-
-class mpi-test-generator : generator
-{
-    import property-set ;
-
-    rule __init__ ( * : * )
-    {
-        generator.__init__ $(1) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ;
-        self.composing = true ;
-    }
-
-    rule run ( project name ? : property-set : sources * : multiple ? )
-    {  
-      # Generate an executable from the sources. This is the executable we will run.
-      local executable = 
-        [ generators.construct $(project) $(name) : EXE : $(property-set) : $(sources) ] ;
-
-      result = 
-        [ construct-result $(executable[2-]) : $(project) $(name)-run : $(property-set) ] ;
-    }
-}
-
-# Use mpi-test-generator to generate MPI tests from sources
-generators.register 
-  [ new mpi-test-generator mpi.capture-output : : RUN_MPI_OUTPUT ] ;
-
-generators.register-standard testing.expect-success 
-  : RUN_MPI_OUTPUT : RUN_MPI ;
-
-# The number of processes to spawn when executing an MPI test.
-feature mpi:processes : : free incidental ;
-
-# The flag settings on testing.capture-output do not
-# apply to mpi.capture output at the moment.
-# Redo this explicitly.
-toolset.flags mpi.capture-output ARGS <testing.arg> ;
-rule capture-output ( target : sources * : properties * )
-{
-    # Use the standard capture-output rule to run the tests
-    testing.capture-output $(target) : $(sources[1]) : $(properties) ;
-
-    # Determine the number of processes we should run on.
-    local num_processes = [ property.select <mpi:processes> : $(properties) ] ;
-    num_processes = $(num_processes:G=) ;
-
-    # serialize the MPI tests to avoid overloading systems
-    JAM_SEMAPHORE on $(target) = <s>mpi-run-semaphore ;
-
-    # We launch MPI processes using the "mpirun" equivalent specified by the user.
-    LAUNCHER on $(target) =  
-      [ on $(target) return $(.mpirun) $(.mpirun_flags) $(num_processes) ] ;
-}
-
-# Creates a set of test cases to be run through the MPI launcher. The name, sources, 
-# and requirements are the same as for any other test generator. However, schedule is 
-# a list of numbers, which indicates how many processes each test run will use. For 
-# example, passing 1 2 7 will run the test with 1 process, then 2 processes, then 7
-# 7 processes. The name provided is just the base name: the actual tests will be 
-# the name followed by a hypen, then the number of processes. 
-rule mpi-test ( name : sources * : requirements * : schedule * )
-{        
-    sources ?= $(name).cpp ;
-    schedule ?= 1 2 3 4 7 8 13 17 ;
-
-    local result ;
-    for processes in $(schedule)
-    {  
-      result += [ testing.make-test 
-        run-mpi : $(sources) /boost/mpi//boost_mpi
-          : $(requirements) <toolset>msvc:<link>static <mpi:processes>$(processes) : $(name)-$(processes) ] ;
-    }
-    return $(result) ;
-}
diff --git a/jam-files/boost-build/tools/msvc-config.jam b/jam-files/boost-build/tools/msvc-config.jam
deleted file mode 100644
index 6c71e3b0..00000000
--- a/jam-files/boost-build/tools/msvc-config.jam
+++ /dev/null
@@ -1,12 +0,0 @@
-#~ Copyright 2005 Rene Rivera.
-#~ Distributed under the Boost Software License, Version 1.0.
-#~ (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-# Automatic configuration for VisualStudio toolset. To use, just import this module.
-
-import toolset : using ;
-
-ECHO "warning: msvc-config.jam is deprecated. Use 'using msvc : all ;' instead." ;
-
-using msvc : all ;
-
diff --git a/jam-files/boost-build/tools/msvc.jam b/jam-files/boost-build/tools/msvc.jam
deleted file mode 100644
index e33a66d2..00000000
--- a/jam-files/boost-build/tools/msvc.jam
+++ /dev/null
@@ -1,1392 +0,0 @@
-# Copyright (c) 2003 David Abrahams.
-# Copyright (c) 2005 Vladimir Prus.
-# Copyright (c) 2005 Alexey Pakhunov.
-# Copyright (c) 2006 Bojan Resnik.
-# Copyright (c) 2006 Ilya Sokolov.
-# Copyright (c) 2007 Rene Rivera
-# Copyright (c) 2008 Jurko Gospodnetic
-#
-# Use, modification and distribution is subject to the Boost Software
-# License Version 1.0. (See accompanying file LICENSE_1_0.txt or
-# http://www.boost.org/LICENSE_1_0.txt)
-
-################################################################################
-#
-# MSVC Boost Build toolset module.
-# --------------------------------
-#
-# All toolset versions need to have their location either auto-detected or
-# explicitly specified except for the special 'default' version that expects the
-# environment to find the needed tools or report an error.
-#
-################################################################################
-
-import "class" : new ;
-import common ;
-import errors ;
-import feature ;
-import generators ;
-import mc ;
-import midl ;
-import os ;
-import path ;
-import pch ;
-import property ;
-import rc ;
-import toolset ;
-import type ;
-
-
-type.register MANIFEST : manifest ;
-feature.feature embed-manifest : on off : incidental propagated ;
-
-type.register PDB : pdb ;
-
-################################################################################
-#
-# Public rules.
-#
-################################################################################
-
-# Initialize a specific toolset version configuration. As the result, path to
-# compiler and, possible, program names are set up, and will be used when that
-# version of compiler is requested. For example, you might have:
-#
-#    using msvc : 6.5 : cl.exe ;
-#    using msvc : 7.0 : Y:/foo/bar/cl.exe ;
-#
-# The version parameter may be ommited:
-#
-#    using msvc : : Z:/foo/bar/cl.exe ;
-#
-# The following keywords have special meanings when specified as versions:
-#   - all     - all detected but not yet used versions will be marked as used
-#               with their default options.
-#   - default - this is an equivalent to an empty version.
-#
-# Depending on a supplied version, detected configurations and presence 'cl.exe'
-# in the path different results may be achieved. The following table describes
-# the possible scenarios:
-#
-#                                      Nothing            "x.y"
-# Passed   Nothing       "x.y"         detected,          detected,
-# version  detected      detected      cl.exe in path     cl.exe in path
-#
-# default  Error         Use "x.y"     Create "default"   Use "x.y"
-# all      None          Use all       None               Use all
-# x.y      -             Use "x.y"     -                  Use "x.y"
-# a.b      Error         Error         Create "a.b"       Create "a.b"
-#
-# "x.y" - refers to a detected version;
-# "a.b" - refers to an undetected version.
-#
-# FIXME: Currently the command parameter and the <compiler> property parameter
-# seem to overlap in duties. Remove this duplication. This seems to be related
-# to why someone started preparing to replace init with configure rules.
-#
-rule init (
-    # The msvc version being configured. When omitted the tools invoked when no
-    # explicit version is given will be configured.
-    version ?
-
-    # The command used to invoke the compiler. If not specified:
-    #   - if version is given, default location for that version will be
-    #     searched
-    #
-    #   - if version is not given, default locations for MSVC 9.0, 8.0, 7.1, 7.0
-    #     and 6.* will be searched
-    #
-    #   - if compiler is not found in the default locations, PATH will be
-    #     searched.
-    : command *
-
-    # Options may include:
-    #
-    #     All options shared by multiple toolset types as handled by the
-    #   common.handle-options() rule, e.g. <cflags>, <compileflags>, <cxxflags>,
-    #   <fflags> & <linkflags>.
-    #
-    #   <assembler>
-    #   <compiler>
-    #   <idl-compiler>
-    #   <linker>
-    #   <mc-compiler>
-    #   <resource-compiler>
-    #       Exact tool names to be used by this msvc toolset configuration.
-    #
-    #   <compiler-filter>
-    #       Command through which to pipe the output of running the compiler.
-    #     For example to pass the output to STLfilt.
-    #
-    #   <setup>
-    #       Global setup command to invoke before running any of the msvc tools.
-    #     It will be passed additional option parameters depending on the actual
-    #     target platform.
-    #
-    #   <setup-amd64>
-    #   <setup-i386>
-    #   <setup-ia64>
-    #       Platform specific setup command to invoke before running any of the
-    #     msvc tools used when builing a target for a specific platform, e.g.
-    #     when building a 32 or 64 bit executable.
-    : options *
-)
-{
-    if $(command)
-    {
-        options += <command>$(command) ;
-    }
-    configure $(version) : $(options) ;
-}
-
-
-# 'configure' is a newer version of 'init'. The parameter 'command' is passed as
-# a part of the 'options' list. See the 'init' rule comment for more detailed
-# information.
-#
-rule configure ( version ? : options * )
-{
-    switch $(version)
-    {
-        case "all" :
-            if $(options)
-            {
-                errors.error "MSVC toolset configuration: options should be"
-                    "empty when '$(version)' is specified." ;
-            }
-
-            # Configure (i.e. mark as used) all registered versions.
-            local all-versions = [ $(.versions).all ] ;
-            if ! $(all-versions)
-            {
-                if $(.debug-configuration)
-                {
-                    ECHO "notice: [msvc-cfg] Asked to configure all registered"
-                        "msvc toolset versions when there are none currently"
-                        "registered." ;
-                }
-            }
-            else
-            {
-                for local v in $(all-versions)
-                {
-                    # Note that there is no need to skip already configured
-                    # versions here as this will request configure-really rule
-                    # to configure the version using default options which will
-                    # in turn cause it to simply do nothing in case the version
-                    # has already been configured.
-                    configure-really $(v) ;
-                }
-            }
-
-        case "default" :
-            configure-really : $(options) ;
-
-        case * :
-            configure-really $(version) : $(options) ;
-    }
-}
-
-
-# Sets up flag definitions dependent on the compiler version used.
-# - 'version' is the version of compiler in N.M format.
-# - 'conditions' is the property set to be used as flag conditions.
-# - 'toolset' is the toolset for which flag settings are to be defined.
-#   This makes the rule reusable for other msvc-option-compatible compilers.
-#
-rule configure-version-specific ( toolset : version : conditions )
-{
-    toolset.push-checking-for-flags-module unchecked ;
-    # Starting with versions 7.0, the msvc compiler have the /Zc:forScope and
-    # /Zc:wchar_t options that improve C++ standard conformance, but those
-    # options are off by default. If we are sure that the msvc version is at
-    # 7.*, add those options explicitly. We can be sure either if user specified
-    # version 7.* explicitly or if we auto-detected the version ourselves.
-    if ! [ MATCH ^(6\\.) : $(version) ]
-    {
-        toolset.flags $(toolset).compile CFLAGS $(conditions) : /Zc:forScope /Zc:wchar_t ;
-        toolset.flags $(toolset).compile.c++ C++FLAGS $(conditions) : /wd4675 ;
-
-        # Explicitly disable the 'function is deprecated' warning. Some msvc
-        # versions have a bug, causing them to emit the deprecation warning even
-        # with /W0.
-        toolset.flags $(toolset).compile CFLAGS $(conditions)/<warnings>off : /wd4996 ;
-
-        if [ MATCH ^([78]\\.) : $(version) ]
-        {
-            # 64-bit compatibility warning deprecated since 9.0, see
-            # http://msdn.microsoft.com/en-us/library/yt4xw8fh.aspx
-            toolset.flags $(toolset).compile CFLAGS $(conditions)/<warnings>all : /Wp64 ;
-        }
-    }
-
-    #
-    # Processor-specific optimization.
-    #
-
-    if [ MATCH ^([67]) : $(version) ]
-    {
-        # 8.0 deprecates some of the options.
-        toolset.flags $(toolset).compile CFLAGS $(conditions)/<optimization>speed $(conditions)/<optimization>space : /Ogiy /Gs ;
-        toolset.flags $(toolset).compile CFLAGS $(conditions)/<optimization>speed : /Ot ;
-        toolset.flags $(toolset).compile CFLAGS $(conditions)/<optimization>space : /Os ;
-
-        toolset.flags $(toolset).compile CFLAGS $(conditions)/$(.cpu-arch-i386)/<instruction-set> : /GB ;
-        toolset.flags $(toolset).compile CFLAGS $(conditions)/$(.cpu-arch-i386)/<instruction-set>i386 : /G3 ;
-        toolset.flags $(toolset).compile CFLAGS $(conditions)/$(.cpu-arch-i386)/<instruction-set>i486 : /G4 ;
-        toolset.flags $(toolset).compile CFLAGS $(conditions)/$(.cpu-arch-i386)/<instruction-set>$(.cpu-type-g5) : /G5 ;
-        toolset.flags $(toolset).compile CFLAGS $(conditions)/$(.cpu-arch-i386)/<instruction-set>$(.cpu-type-g6) : /G6 ;
-        toolset.flags $(toolset).compile CFLAGS $(conditions)/$(.cpu-arch-i386)/<instruction-set>$(.cpu-type-g7) : /G7 ;
-
-        # Improve floating-point accuracy. Otherwise, some of C++ Boost's "math"
-        # tests will fail.
-        toolset.flags $(toolset).compile CFLAGS $(conditions) : /Op ;
-
-        # 7.1 and below have single-threaded static RTL.
-        toolset.flags $(toolset).compile CFLAGS $(conditions)/<runtime-debugging>off/<runtime-link>static/<threading>single : /ML ;
-        toolset.flags $(toolset).compile CFLAGS $(conditions)/<runtime-debugging>on/<runtime-link>static/<threading>single : /MLd ;
-    }
-    else
-    {
-        # 8.0 and above adds some more options.
-        toolset.flags $(toolset).compile CFLAGS $(conditions)/$(.cpu-arch-amd64)/<instruction-set> : /favor:blend ;
-        toolset.flags $(toolset).compile CFLAGS $(conditions)/$(.cpu-arch-amd64)/<instruction-set>$(.cpu-type-em64t) : /favor:EM64T ;
-        toolset.flags $(toolset).compile CFLAGS $(conditions)/$(.cpu-arch-amd64)/<instruction-set>$(.cpu-type-amd64) : /favor:AMD64 ;
-
-        # 8.0 and above only has multi-threaded static RTL.
-        toolset.flags $(toolset).compile CFLAGS $(conditions)/<runtime-debugging>off/<runtime-link>static/<threading>single : /MT ;
-        toolset.flags $(toolset).compile CFLAGS $(conditions)/<runtime-debugging>on/<runtime-link>static/<threading>single : /MTd ;
-
-        # Specify target machine type so the linker will not need to guess.
-        toolset.flags $(toolset).link LINKFLAGS $(conditions)/$(.cpu-arch-amd64) : /MACHINE:X64 ;
-        toolset.flags $(toolset).link LINKFLAGS $(conditions)/$(.cpu-arch-i386)  : /MACHINE:X86 ;
-        toolset.flags $(toolset).link LINKFLAGS $(conditions)/$(.cpu-arch-ia64)  : /MACHINE:IA64 ;
-        
-        # Make sure that manifest will be generated even if there is no
-        # dependencies to put there.
-        toolset.flags $(toolset).link LINKFLAGS $(conditions)/<embed-manifest>off : /MANIFEST ;
-    }
-    toolset.pop-checking-for-flags-module ;
-}
-
-
-# Registers this toolset including all of its flags, features & generators. Does
-# nothing on repeated calls.
-#
-rule register-toolset ( )
-{
-    if ! msvc in [ feature.values toolset ]
-    {
-        register-toolset-really ;
-    }
-}
-
-
-# Declare action for creating static libraries. If library exists, remove it
-# before adding files. See
-# http://article.gmane.org/gmane.comp.lib.boost.build/4241 for rationale.
-if [ os.name ] in NT
-{
-    # The 'DEL' command would issue a message to stdout if the file does not
-    # exist, so need a check.
-    actions archive
-    {
-        if exist "$(<[1])" DEL "$(<[1])"
-        $(.LD) $(AROPTIONS) /out:"$(<[1])" @"@($(<[1]:W).rsp:E=$(.nl)"$(>)" $(.nl)$(LIBRARIES_MENTIONED_BY_FILE) $(.nl)"$(LIBRARY_OPTION)$(FINDLIBS_ST).lib" $(.nl)"$(LIBRARY_OPTION)$(FINDLIBS_SA).lib")"
-    }
-}
-else
-{
-    actions archive
-    {
-        $(.RM) "$(<[1])"
-        $(.LD) $(AROPTIONS) /out:"$(<[1])" @"@($(<[1]:W).rsp:E=$(.nl)"$(>)" $(.nl)$(LIBRARIES_MENTIONED_BY_FILE) $(.nl)"$(LIBRARY_OPTION)$(FINDLIBS_ST).lib" $(.nl)"$(LIBRARY_OPTION)$(FINDLIBS_SA).lib")"
-    }
-}
-
-
-# For the assembler the following options are turned on by default:
-#
-#   -Zp4   align structures to 4 bytes
-#   -Cp    preserve case of user identifiers
-#   -Cx    preserve case in publics, externs
-#
-actions compile.asm
-{
-    $(.ASM) -c -Zp4 -Cp -Cx -D$(DEFINES) $(ASMFLAGS) $(USER_ASMFLAGS) -Fo "$(<:W)" "$(>:W)"
-}
-
-
-rule compile.c ( targets + : sources * : properties * )
-{
-    C++FLAGS on $(targets[1]) = ;
-    get-rspline $(targets) : -TC ;
-    compile-c-c++ $(<) : $(>) [ on $(<) return $(PCH_FILE) ] [ on $(<) return $(PCH_HEADER) ] ;
-}
-
-
-rule compile.c.preprocess ( targets + : sources * : properties * )
-{
-    C++FLAGS on $(targets[1]) = ;
-    get-rspline $(targets) : -TC ;
-    preprocess-c-c++ $(<) : $(>) [ on $(<) return $(PCH_FILE) ] [ on $(<) return $(PCH_HEADER) ] ;
-}
-
-
-rule compile.c.pch ( targets + : sources * : properties * )
-{
-    C++FLAGS on $(targets[1]) = ;
-    get-rspline $(targets[1]) : -TC ;
-    get-rspline $(targets[2]) : -TC ;
-    local pch-source = [ on $(<) return $(PCH_SOURCE) ] ;
-    if $(pch-source)
-    {
-        DEPENDS $(<) : $(pch-source) ;
-        compile-c-c++-pch-s $(targets) : $(sources) $(pch-source) ;
-    }
-    else
-    {
-        compile-c-c++-pch $(targets) : $(sources) ;
-    }
-}
-
-toolset.flags msvc YLOPTION : "-Yl" ;
-
-# Action for running the C/C++ compiler without using precompiled headers.
-#
-# WARNING: Synchronize any changes this in action with intel-win
-#
-# Notes regarding PDB generation, for when we use <debug-symbols>on/<debug-store>database
-#
-# 1. PDB_CFLAG is only set for <debug-symbols>on/<debug-store>database, ensuring that the /Fd flag is dropped if PDB_CFLAG is empty
-#
-# 2. When compiling executables's source files, PDB_NAME is set on a per-source file basis by rule compile-c-c++. 
-#    The linker will pull these into the executable's PDB
-#
-# 3. When compiling library's source files, PDB_NAME is updated to <libname>.pdb for each source file by rule archive, 
-#    as in this case the compiler must be used to create a single PDB for our library.
-#
-actions compile-c-c++ bind PDB_NAME
-{
-    $(.CC) @"@($(<[1]:W).rsp:E="$(>[1]:W)" -Fo"$(<[1]:W)" $(PDB_CFLAG)"$(PDB_NAME)" -Yu"$(>[3]:D=)" -Fp"$(>[2]:W)" $(CC_RSPLINE))" $(.CC.FILTER)
-}
-
-actions preprocess-c-c++ bind PDB_NAME
-{
-    $(.CC) @"@($(<[1]:W).rsp:E="$(>[1]:W)" -E $(PDB_CFLAG)"$(PDB_NAME)" -Yu"$(>[3]:D=)" -Fp"$(>[2]:W)" $(CC_RSPLINE))" >"$(<[1]:W)"
-}
-
-rule compile-c-c++ ( targets + : sources * )
-{
-    DEPENDS $(<[1]) : [ on $(<[1]) return $(PCH_HEADER) ] ;
-    DEPENDS $(<[1]) : [ on $(<[1]) return $(PCH_FILE) ] ;
-    PDB_NAME on $(<) = $(<:S=.pdb) ;
-}
-
-rule preprocess-c-c++ ( targets + : sources * )
-{
-    DEPENDS $(<[1]) : [ on $(<[1]) return $(PCH_HEADER) ] ;
-    DEPENDS $(<[1]) : [ on $(<[1]) return $(PCH_FILE) ] ;
-    PDB_NAME on $(<) = $(<:S=.pdb) ;
-}
-
-# Action for running the C/C++ compiler using precompiled headers. In addition
-# to whatever else it needs to compile, this action also adds a temporary source
-# .cpp file used to compile the precompiled headers themselves.
-#
-# The global .escaped-double-quote variable is used to avoid messing up Emacs
-# syntax highlighting in the messy N-quoted code below.
-actions compile-c-c++-pch
-{
-    $(.CC) @"@($(<[1]:W).rsp:E="$(>[2]:W)" -Fo"$(<[2]:W)" -Yc"$(>[1]:D=)" $(YLOPTION)"__bjam_pch_symbol_$(>[1]:D=)" -Fp"$(<[1]:W)" $(CC_RSPLINE))" "@($(<[1]:W).cpp:E=#include $(.escaped-double-quote)$(>[1]:D=)$(.escaped-double-quote)$(.nl))" $(.CC.FILTER)
-}
-
-
-# Action for running the C/C++ compiler using precompiled headers. An already
-# built source file for compiling the precompiled headers is expected to be
-# given as one of the source parameters.
-actions compile-c-c++-pch-s
-{
-    $(.CC) @"@($(<[1]:W).rsp:E="$(>[2]:W)" -Fo"$(<[2]:W)" -Yc"$(>[1]:D=)" $(YLOPTION)"__bjam_pch_symbol_$(>[1]:D=)" -Fp"$(<[1]:W)" $(CC_RSPLINE))" $(.CC.FILTER)
-}
-
-
-rule compile.c++ ( targets + : sources * : properties * )
-{
-    get-rspline $(targets) : -TP ;
-    compile-c-c++ $(<) : $(>) [ on $(<) return $(PCH_FILE) ] [ on $(<) return $(PCH_HEADER) ] ;
-}
-
-rule compile.c++.preprocess ( targets + : sources * : properties * )
-{
-    get-rspline $(targets) : -TP ;
-    preprocess-c-c++ $(<) : $(>) [ on $(<) return $(PCH_FILE) ] [ on $(<) return $(PCH_HEADER) ] ;
-}
-
-
-rule compile.c++.pch ( targets + : sources * : properties * )
-{
-    get-rspline $(targets[1]) : -TP ;
-    get-rspline $(targets[2]) : -TP ;
-    local pch-source = [ on $(<) return $(PCH_SOURCE) ] ;
-    if $(pch-source)
-    {
-        DEPENDS $(<) : $(pch-source) ;
-        compile-c-c++-pch-s $(targets) : $(sources) $(pch-source) ;
-    }
-    else
-    {
-        compile-c-c++-pch $(targets) : $(sources) ;
-    }
-}
-
-
-# See midl.jam for details.
-#
-actions compile.idl
-{
-    $(.IDL) /nologo @"@($(<[1]:W).rsp:E=$(.nl)"$(>:W)" $(.nl)-D$(DEFINES) $(.nl)"-I$(INCLUDES:W)" $(.nl)-U$(UNDEFS) $(.nl)$(MIDLFLAGS) $(.nl)/tlb "$(<[1]:W)" $(.nl)/h "$(<[2]:W)" $(.nl)/iid "$(<[3]:W)" $(.nl)/proxy "$(<[4]:W)" $(.nl)/dlldata "$(<[5]:W)")"
-    $(.TOUCH_FILE) "$(<[4]:W)"
-    $(.TOUCH_FILE) "$(<[5]:W)"
-}
-
-
-actions compile.mc
-{
-    $(.MC) $(MCFLAGS) -h "$(<[1]:DW)" -r "$(<[2]:DW)" "$(>:W)"
-}
-
-
-actions compile.rc
-{
-    $(.RC) -l 0x409 -U$(UNDEFS) -D$(DEFINES) -I"$(INCLUDES:W)" -fo "$(<:W)" "$(>:W)"
-}
-
-
-rule link ( targets + : sources * : properties * )
-{
-    if <embed-manifest>on in $(properties)
-    {        
-        msvc.manifest $(targets) : $(sources) : $(properties) ;
-    }    
-}
-
-rule link.dll ( targets + : sources * : properties * )
-{
-    DEPENDS $(<) : [ on $(<) return $(DEF_FILE) ] ;
-    if <embed-manifest>on in $(properties)
-    {        
-        msvc.manifest.dll $(targets) : $(sources) : $(properties) ;
-    }    
-}
-
-# Incremental linking a DLL causes no end of problems: if the actual exports do
-# not change, the import .lib file is never updated. Therefore, the .lib is
-# always out-of-date and gets rebuilt every time. I am not sure that incremental
-# linking is such a great idea in general, but in this case I am sure we do not
-# want it.
-
-# Windows manifest is a new way to specify dependencies on managed DotNet
-# assemblies and Windows native DLLs. The manifests are embedded as resources
-# and are useful in any PE target (both DLL and EXE).
-
-if [ os.name ] in NT
-{
-    actions link bind DEF_FILE LIBRARIES_MENTIONED_BY_FILE
-    {
-        $(.LD) $(LINKFLAGS) /out:"$(<[1]:W)" /LIBPATH:"$(LINKPATH:W)" $(OPTIONS) @"@($(<[1]:W).rsp:E=$(.nl)"$(>)" $(.nl)$(LIBRARIES_MENTIONED_BY_FILE) $(.nl)$(LIBRARIES) $(.nl)"$(LIBRARY_OPTION)$(FINDLIBS_ST).lib" $(.nl)"$(LIBRARY_OPTION)$(FINDLIBS_SA).lib")"
-        if %ERRORLEVEL% NEQ 0 EXIT %ERRORLEVEL%
-    }
-    
-    actions manifest
-    {        
-        if exist "$(<[1]).manifest" (
-            $(.MT) -manifest "$(<[1]).manifest" "-outputresource:$(<[1]);1"
-        )
-    }
-    
-    actions link.dll bind DEF_FILE LIBRARIES_MENTIONED_BY_FILE
-    {
-        $(.LD) /DLL $(LINKFLAGS) /out:"$(<[1]:W)" /IMPLIB:"$(<[2]:W)" /LIBPATH:"$(LINKPATH:W)" /def:"$(DEF_FILE)" $(OPTIONS) @"@($(<[1]:W).rsp:E=$(.nl)"$(>)" $(.nl)$(LIBRARIES_MENTIONED_BY_FILE) $(.nl)$(LIBRARIES) $(.nl)"$(LIBRARY_OPTION)$(FINDLIBS_ST).lib" $(.nl)"$(LIBRARY_OPTION)$(FINDLIBS_SA).lib")"
-        if %ERRORLEVEL% NEQ 0 EXIT %ERRORLEVEL%
-    }
-
-    actions manifest.dll
-    {        
-        if exist "$(<[1]).manifest" (
-            $(.MT) -manifest "$(<[1]).manifest" "-outputresource:$(<[1]);2"
-        )
-    }    
-}
-else
-{        
-    actions link bind DEF_FILE LIBRARIES_MENTIONED_BY_FILE
-    {
-        $(.LD) $(LINKFLAGS) /out:"$(<[1]:W)" /LIBPATH:"$(LINKPATH:W)" $(OPTIONS) @"@($(<[1]:W).rsp:E=$(.nl)"$(>)" $(.nl)$(LIBRARIES_MENTIONED_BY_FILE) $(.nl)$(LIBRARIES) $(.nl)"$(LIBRARY_OPTION)$(FINDLIBS_ST).lib" $(.nl)"$(LIBRARY_OPTION)$(FINDLIBS_SA).lib")"
-    }
-
-    actions manifest
-    {        
-        if test -e "$(<[1]).manifest"; then
-            $(.MT) -manifest "$(<[1]:W).manifest" "-outputresource:$(<[1]:W);1"
-        fi
-    }
-    
-    actions link.dll bind DEF_FILE LIBRARIES_MENTIONED_BY_FILE
-    {
-        $(.LD) /DLL $(LINKFLAGS) /out:"$(<[1]:W)" /IMPLIB:"$(<[2]:W)" /LIBPATH:"$(LINKPATH:W)" /def:"$(DEF_FILE)" $(OPTIONS) @"@($(<[1]:W).rsp:E=$(.nl)"$(>)" $(.nl)$(LIBRARIES_MENTIONED_BY_FILE) $(.nl)$(LIBRARIES) $(.nl)"$(LIBRARY_OPTION)$(FINDLIBS_ST).lib" $(.nl)"$(LIBRARY_OPTION)$(FINDLIBS_SA).lib")"
-    }
-    
-    actions manifest.dll
-    {
-        if test -e "$(<[1]).manifest"; then
-          $(.MT) -manifest "$(<[1]:W).manifest" "-outputresource:$(<[1]:W);2"
-        fi
-    }    
-}
-
-# this rule sets up the pdb file that will be used when generating static 
-# libraries and the debug-store option is database, so that the compiler 
-# puts all debug info into a single .pdb file named after the library
-#
-# Poking at source targets this way is probably not clean, but it's the
-# easiest approach.
-rule archive ( targets + : sources * : properties * )
-{
-    PDB_NAME on $(>) = $(<:S=.pdb) ;
-}
-
-################################################################################
-#
-# Classes.
-#
-################################################################################
-
-class msvc-pch-generator : pch-generator
-{
-    import property-set ;
-
-    rule run-pch ( project name ? : property-set : sources * )
-    {
-        # Searching for the header and source file in the sources.
-        local pch-header ;
-        local pch-source ;
-        for local s in $(sources)
-        {
-            if [ type.is-derived [ $(s).type ] H ]
-            {
-                pch-header = $(s) ;
-            }
-            else if
-                [ type.is-derived [ $(s).type ] CPP ] ||
-                [ type.is-derived [ $(s).type ] C ]
-            {
-                pch-source = $(s) ;
-            }
-        }
-
-        if ! $(pch-header)
-        {
-            errors.user-error "can not build pch without pch-header" ;
-        }
-
-        # If we do not have the PCH source - that is fine. We will just create a
-        # temporary .cpp file in the action.
-
-        local generated = [ generator.run $(project) $(name)
-            : [ property-set.create
-                # Passing of <pch-source> is a dirty trick, needed because
-                # non-composing generators with multiple inputs are subtly
-                # broken. For more detailed information see:
-                # https://zigzag.cs.msu.su:7813/boost.build/ticket/111
-                <pch-source>$(pch-source)
-                [ $(property-set).raw ] ]
-            : $(pch-header) ] ;
-
-        local pch-file ;
-        for local g in $(generated)
-        {
-            if [ type.is-derived [ $(g).type ] PCH ]
-            {
-                pch-file = $(g) ;
-            }
-        }
-
-        return [ property-set.create <pch-header>$(pch-header)
-            <pch-file>$(pch-file) ] $(generated) ;
-    }
-}
-
-
-################################################################################
-#
-# Local rules.
-#
-################################################################################
-
-# Detects versions listed as '.known-versions' by checking registry information,
-# environment variables & default paths. Supports both native Windows and
-# Cygwin.
-#
-local rule auto-detect-toolset-versions ( )
-{
-    if [ os.name ] in NT CYGWIN
-    {
-        # Get installation paths from the registry.
-        for local i in $(.known-versions)
-        {
-            if $(.version-$(i)-reg)
-            {
-                local vc-path ;
-                for local x in "" "Wow6432Node\\"
-                {
-                    vc-path += [ W32_GETREG
-                        "HKEY_LOCAL_MACHINE\\SOFTWARE\\"$(x)"\\Microsoft\\"$(.version-$(i)-reg)
-                        : "ProductDir" ] ;
-                }
-
-                if $(vc-path)
-                {
-                    vc-path = [ path.join [ path.make-NT $(vc-path[1]) ] "bin" ] ;
-                    register-configuration $(i) : [ path.native $(vc-path[1]) ] ;
-                }
-            }
-        }
-    }
-
-    # Check environment and default installation paths.
-    for local i in $(.known-versions)
-    {
-        if ! $(i) in [ $(.versions).all ]
-        {
-            register-configuration $(i) : [ default-path $(i) ] ;
-        }
-    }
-}
-
-
-# Worker rule for toolset version configuration. Takes an explicit version id or
-# nothing in case it should configure the default toolset version (the first
-# registered one or a new 'default' one in case no toolset versions have been
-# registered yet).
-#
-local rule configure-really ( version ? : options * )
-{
-    local v = $(version) ;
-
-    # Decide what the 'default' version is.
-    if ! $(v)
-    {
-        # Take the first registered (i.e. auto-detected) version.
-        version = [ $(.versions).all ] ;
-        version = $(version[1]) ;
-        v = $(version) ;
-
-        # Note: 'version' can still be empty at this point if no versions have
-        # been auto-detected.
-        version ?= "default" ;
-    }
-
-    # Version alias -> real version number.
-    if $(.version-alias-$(version))
-    {
-        version = $(.version-alias-$(version)) ;
-    }
-
-    # Check whether the selected configuration is already in use.
-    if $(version) in [ $(.versions).used ]
-    {
-        # Allow multiple 'toolset.using' calls for the same configuration if the
-        # identical sets of options are used.
-        if $(options) && ( $(options) != [ $(.versions).get $(version) : options ] )
-        {
-            errors.error "MSVC toolset configuration: Toolset version"
-                "'$(version)' already configured." ;
-        }
-    }
-    else
-    {
-        # Register a new configuration.
-        $(.versions).register $(version) ;
-
-        # Add user-supplied to auto-detected options.
-        options = [ $(.versions).get $(version) : options ] $(options) ;
-
-        # Mark the configuration as 'used'.
-        $(.versions).use $(version) ;
-
-        # Generate conditions and save them.
-        local conditions = [ common.check-init-parameters msvc : version $(v) ]
-            ;
-
-        $(.versions).set $(version) : conditions : $(conditions) ;
-
-        local command = [ feature.get-values <command> : $(options) ] ;
-
-        # If version is specified, we try to search first in default paths, and
-        # only then in PATH.
-        command = [ common.get-invocation-command msvc : cl.exe : $(command) :
-            [ default-paths $(version) ] : $(version) ] ;
-
-        common.handle-options msvc : $(conditions) : $(command) : $(options) ;
-
-        if ! $(version)
-        {
-            # Even if version is not explicitly specified, try to detect the
-            # version from the path.
-            # FIXME: We currently detect both Microsoft Visual Studio 9.0 and
-            # 9.0express as 9.0 here.
-            if [ MATCH "(Microsoft Visual Studio 10)" : $(command) ]
-            {
-                version = 10.0 ;
-            }
-            else if [ MATCH "(Microsoft Visual Studio 9)" : $(command) ]
-            {
-                version = 9.0 ;
-            }
-            else if [ MATCH "(Microsoft Visual Studio 8)" : $(command) ]
-            {
-                version = 8.0 ;
-            }
-            else if [ MATCH "(NET 2003[\/\\]VC7)" : $(command) ]
-            {
-                version = 7.1 ;
-            }
-            else if [ MATCH "(Microsoft Visual C\\+\\+ Toolkit 2003)" :
-                $(command) ]
-            {
-                version = 7.1toolkit ;
-            }
-            else if [ MATCH "(.NET[\/\\]VC7)" : $(command) ]
-            {
-                version = 7.0 ;
-            }
-            else
-            {
-                version = 6.0 ;
-            }
-        }
-
-        # Generate and register setup command.
-
-        local below-8.0 = [ MATCH ^([67]\\.) : $(version) ] ;
-
-        local cpu = i386 amd64 ia64 ;
-        if $(below-8.0)
-        {
-            cpu = i386 ;
-        }
-
-        local setup-amd64 ;
-        local setup-i386 ;
-        local setup-ia64 ;
-
-        if $(command)
-        {
-            # TODO: Note that if we specify a non-existant toolset version then
-            # this rule may find and use a corresponding compiler executable
-            # belonging to an incorrect toolset version. For example, if you
-            # have only MSVC 7.1 installed, have its executable on the path and
-            # specify you want Boost Build to use MSVC 9.0, then you want Boost
-            # Build to report an error but this may cause it to silently use the
-            # MSVC 7.1 compiler even though it thinks it is using the msvc-9.0
-            # toolset version.
-            command = [ common.get-absolute-tool-path $(command[-1]) ] ;
-        }
-        
-        if $(command)
-        {            
-            local parent = [ path.make $(command) ] ;
-            parent = [ path.parent $(parent) ] ;
-            parent = [ path.native $(parent) ] ;
-
-            # Setup will be used if the command name has been specified. If
-            # setup is not specified explicitly then a default setup script will
-            # be used instead. Setup scripts may be global or arhitecture/
-            # /platform/cpu specific. Setup options are used only in case of
-            # global setup scripts.
-
-            # Default setup scripts provided with different VC distributions:
-            #
-            #   VC 7.1 had only the vcvars32.bat script specific to 32 bit i386
-            # builds. It was located in the bin folder for the regular version
-            # and in the root folder for the free VC 7.1 tools.
-            #
-            #   Later 8.0 & 9.0 versions introduce separate platform specific
-            # vcvars*.bat scripts (e.g. 32 bit, 64 bit AMD or 64 bit Itanium)
-            # located in or under the bin folder. Most also include a global
-            # vcvarsall.bat helper script located in the root folder which runs
-            # one of the aforementioned vcvars*.bat scripts based on the options
-            # passed to it. So far only the version coming with some PlatformSDK
-            # distributions does not include this top level script but to
-            # support those we need to fall back to using the worker scripts
-            # directly in case the top level script can not be found.
-
-            local global-setup = [ feature.get-values <setup> : $(options) ] ;
-            global-setup = $(global-setup[1]) ;
-            if ! $(below-8.0)
-            {
-                global-setup ?= [ locate-default-setup $(command) : $(parent) :
-                    vcvarsall.bat ] ;
-            }
-
-            local default-setup-amd64 = vcvarsx86_amd64.bat ;
-            local default-setup-i386  = vcvars32.bat ;
-            local default-setup-ia64  = vcvarsx86_ia64.bat ;
-
-            # http://msdn2.microsoft.com/en-us/library/x4d2c09s(VS.80).aspx and
-            # http://msdn2.microsoft.com/en-us/library/x4d2c09s(vs.90).aspx
-            # mention an x86_IPF option, that seems to be a documentation bug
-            # and x86_ia64 is the correct option.
-            local default-global-setup-options-amd64 = x86_amd64 ;
-            local default-global-setup-options-i386  = x86 ;
-            local default-global-setup-options-ia64  = x86_ia64 ;
-
-            # When using 64-bit Windows, and targeting 64-bit, it is possible to
-            # use a native 64-bit compiler, selected by the "amd64" & "ia64"
-            # parameters to vcvarsall.bat. There are two variables we can use --
-            # PROCESSOR_ARCHITECTURE and PROCESSOR_IDENTIFIER. The first is
-            # 'x86' when running 32-bit Windows, no matter which processor is
-            # used, and 'AMD64' on 64-bit windows on x86 (either AMD64 or EM64T)
-            # Windows.
-            #
-            if [ MATCH ^(AMD64) : [ os.environ PROCESSOR_ARCHITECTURE ] ]
-            {
-                default-global-setup-options-amd64 = amd64 ;
-            }
-            # TODO: The same 'native compiler usage' should be implemented for
-            # the Itanium platform by using the "ia64" parameter. For this
-            # though we need someone with access to this platform who can find
-            # out how to correctly detect this case.
-            else if $(somehow-detect-the-itanium-platform)
-            {
-                default-global-setup-options-ia64 = ia64 ;
-            }
-
-            local setup-prefix = "call " ;
-            local setup-suffix = " >nul"$(.nl) ;
-            if ! [ os.name ] in NT
-            {
-                setup-prefix = "cmd.exe /S /C call " ;
-                setup-suffix = " \">nul\" \"&&\" " ;
-            }
-
-            for local c in $(cpu)
-            {
-                local setup-options ;
-
-                setup-$(c) = [ feature.get-values <setup-$(c)> : $(options) ] ;
-
-                if ! $(setup-$(c))-is-not-empty
-                {
-                    if $(global-setup)-is-not-empty
-                    {
-                        setup-$(c) = $(global-setup) ;
-
-                        # If needed we can easily add using configuration flags
-                        # here for overriding which options get passed to the
-                        # global setup command for which target platform:
-                        # setup-options = [ feature.get-values <setup-options-$(c)> : $(options) ] ;
-
-                        setup-options ?= $(default-global-setup-options-$(c)) ;
-                    }
-                    else
-                    {
-                        setup-$(c) = [ locate-default-setup $(command) : $(parent) : $(default-setup-$(c)) ] ;
-                    }
-                }
-
-                # Cygwin to Windows path translation.
-                setup-$(c) = "\""$(setup-$(c):W)"\"" ;
-
-                # Append setup options to the setup name and add the final setup
-                # prefix & suffix.
-                setup-options ?= "" ;
-                setup-$(c) = $(setup-prefix)$(setup-$(c):J=" ")" "$(setup-options:J=" ")$(setup-suffix) ;
-            }
-        }
-
-        # Get tool names (if any) and finish setup.
-
-        compiler = [ feature.get-values <compiler> : $(options) ] ;
-        compiler ?= cl ;
-
-        linker = [ feature.get-values <linker> : $(options) ] ;
-        linker ?= link ;
-
-        resource-compiler = [ feature.get-values <resource-compiler> : $(options) ] ;
-        resource-compiler ?= rc ;
-
-        # Turn on some options for i386 assembler
-        #  -coff  generate COFF format object file (compatible with cl.exe output)
-        local default-assembler-amd64 = ml64 ;
-        local default-assembler-i386  = "ml -coff" ;
-        local default-assembler-ia64  = ias ;
-
-        assembler = [ feature.get-values <assembler> : $(options) ] ;
-
-        idl-compiler = [ feature.get-values <idl-compiler> : $(options) ] ;
-        idl-compiler ?= midl ;
-
-        mc-compiler = [ feature.get-values <mc-compiler> : $(options) ] ;
-        mc-compiler ?= mc ;
-
-        manifest-tool = [ feature.get-values <manifest-tool> : $(options) ] ;
-        manifest-tool ?= mt ;
-        
-        local cc-filter = [ feature.get-values <compiler-filter> : $(options) ] ;
-
-        for local c in $(cpu)
-        {
-            # Setup script is not required in some configurations.
-            setup-$(c) ?= "" ;
-
-            local cpu-conditions = $(conditions)/$(.cpu-arch-$(c)) ;
-
-            if $(.debug-configuration)
-            {
-                for local cpu-condition in $(cpu-conditions)
-                {
-                    ECHO "notice: [msvc-cfg] condition: '$(cpu-condition)', setup: '$(setup-$(c))'" ;
-                }
-            }
-
-            local cpu-assembler = $(assembler) ;
-            cpu-assembler ?= $(default-assembler-$(c)) ;
-
-            toolset.flags msvc.compile .CC  $(cpu-conditions) : $(setup-$(c))$(compiler) /Zm800 -nologo ;
-            toolset.flags msvc.compile .RC  $(cpu-conditions) : $(setup-$(c))$(resource-compiler) ;
-            toolset.flags msvc.compile .ASM $(cpu-conditions) : $(setup-$(c))$(cpu-assembler) -nologo ;
-            toolset.flags msvc.link    .LD  $(cpu-conditions) : $(setup-$(c))$(linker) /NOLOGO /INCREMENTAL:NO ;
-            toolset.flags msvc.archive .LD  $(cpu-conditions) : $(setup-$(c))$(linker) /lib /NOLOGO  ;
-            toolset.flags msvc.compile .IDL $(cpu-conditions) : $(setup-$(c))$(idl-compiler) ;
-            toolset.flags msvc.compile .MC  $(cpu-conditions) : $(setup-$(c))$(mc-compiler) ;
-
-            toolset.flags msvc.link .MT $(cpu-conditions) : $(setup-$(c))$(manifest-tool) -nologo ;
-
-            if $(cc-filter)
-            {
-                toolset.flags msvc .CC.FILTER $(cpu-conditions) : "|" $(cc-filter) ;
-            }
-        }
-
-        # Set version-specific flags.
-        configure-version-specific msvc : $(version) : $(conditions) ;
-    }
-}
-
-
-# Returns the default installation path for the given version.
-#
-local rule default-path ( version )
-{
-    # Use auto-detected path if possible.
-    local path = [ feature.get-values <command> : [ $(.versions).get $(version)
-        : options ] ] ;
-
-    if $(path)
-    {
-        path = $(path:D) ;
-    }
-    else
-    {
-        # Check environment.
-        if $(.version-$(version)-env)
-        {
-            local vc-path = [ os.environ $(.version-$(version)-env) ] ;
-            if $(vc-path)
-            {
-                vc-path = [ path.make $(vc-path) ] ;
-                vc-path = [ path.join $(vc-path) $(.version-$(version)-envpath) ] ;
-                vc-path = [ path.native $(vc-path) ] ;
-
-                path = $(vc-path) ;
-            }
-        }
-
-        # Check default path.
-        if ! $(path) && $(.version-$(version)-path)
-        {
-            path = [ path.native [ path.join $(.ProgramFiles) $(.version-$(version)-path) ] ] ;
-        }
-    }
-
-    return $(path) ;
-}
-
-
-# Returns either the default installation path (if 'version' is not empty) or
-# list of all known default paths (if no version is given)
-#
-local rule default-paths ( version ? )
-{
-    local possible-paths ;
-
-    if $(version)
-    {
-        possible-paths += [ default-path $(version) ] ;
-    }
-    else
-    {
-        for local i in $(.known-versions)
-        {
-            possible-paths += [ default-path $(i) ] ;
-        }
-    }
-
-    return $(possible-paths) ;
-}
-
-
-rule get-rspline ( target : lang-opt )
-{
-    CC_RSPLINE on $(target) = [ on $(target) return $(lang-opt) -U$(UNDEFS)
-        $(CFLAGS) $(C++FLAGS) $(OPTIONS) -c $(.nl)-D$(DEFINES)
-        $(.nl)\"-I$(INCLUDES:W)\" ] ;
-}
-
-class msvc-linking-generator : linking-generator
-{
-    # Calls the base version.  If necessary, also create a target for the
-    # manifest file.specifying source's name as the name of the created
-    # target. As result, the PCH will be named whatever.hpp.gch, and not
-    # whatever.gch.
-    rule generated-targets ( sources + : property-set : project name ? )
-    {
-        local result = [ linking-generator.generated-targets $(sources)
-          : $(property-set) : $(project) $(name) ] ;
-
-        if $(result)
-        {
-            local name-main = [ $(result[0]).name ] ;
-            local action = [ $(result[0]).action ] ;
-            
-            if [ $(property-set).get <debug-symbols> ] = "on"
-            {		 
-                # We force exact name on PDB. The reason is tagging -- the tag rule may
-                # reasonably special case some target types, like SHARED_LIB. The tag rule
-                # will not catch PDB, and it cannot even easily figure if PDB is paired with
-                # SHARED_LIB or EXE or something else. Because PDB always get the
-                # same name as the main target, with .pdb as extension, just force it.
-                local target = [ class.new file-target $(name-main:S=.pdb) exact : PDB : $(project) : $(action) ] ;
-                local registered-target = [ virtual-target.register $(target) ] ;
-                if $(target) != $(registered-target)
-                {
-                    $(action).replace-targets $(target) : $(registered-target) ;
-                }
-                result += $(registered-target) ;
-            }
-
-            if [ $(property-set).get <embed-manifest> ] = "off"
-            {
-                # Manifest is evil target. It has .manifest appened to the name of 
-                # main target, including extension. E.g. a.exe.manifest. We use 'exact'
-                # name because to achieve this effect.
-                local target = [ class.new file-target $(name-main).manifest exact : MANIFEST : $(project) : $(action) ] ;
-                local registered-target = [ virtual-target.register $(target) ] ;
-                if $(target) != $(registered-target)
-                {
-                    $(action).replace-targets $(target) : $(registered-target) ;
-                }
-                result += $(registered-target) ;
-            }
-        }
-        return $(result) ;
-    }
-}
-
-
-
-# Unsafe worker rule for the register-toolset() rule. Must not be called
-# multiple times.
-#
-local rule register-toolset-really ( )
-{
-    feature.extend toolset : msvc ;
-
-    # Intel and msvc supposedly have link-compatible objects.
-    feature.subfeature toolset msvc : vendor : intel : propagated optional ;
-
-    # Inherit MIDL flags.
-    toolset.inherit-flags msvc : midl ;
-
-    # Inherit MC flags.
-    toolset.inherit-flags msvc : mc ;
-
-    # Dynamic runtime comes only in MT flavour.
-    toolset.add-requirements
-        <toolset>msvc,<runtime-link>shared:<threading>multi ;
-
-    # Declare msvc toolset specific features.
-    {
-        feature.feature debug-store : object database : propagated ;
-        feature.feature pch-source  :                 : dependency free ;
-    }
-
-    # Declare generators.
-    {
-        # TODO: Is it possible to combine these? Make the generators
-        # non-composing so that they do not convert each source into a separate
-        # .rsp file.
-        generators.register [ new msvc-linking-generator 
-            msvc.link : OBJ SEARCHED_LIB STATIC_LIB IMPORT_LIB : EXE : <toolset>msvc ] ;
-        generators.register [ new msvc-linking-generator 
-            msvc.link.dll : OBJ SEARCHED_LIB STATIC_LIB IMPORT_LIB : SHARED_LIB IMPORT_LIB : <toolset>msvc ] ;
-
-        generators.register-archiver msvc.archive : OBJ : STATIC_LIB : <toolset>msvc ;
-        generators.register-c-compiler msvc.compile.c++ : CPP : OBJ : <toolset>msvc ;
-        generators.register-c-compiler msvc.compile.c : C : OBJ : <toolset>msvc ;
-        generators.register-c-compiler msvc.compile.c++.preprocess : CPP : PREPROCESSED_CPP : <toolset>msvc ;
-        generators.register-c-compiler msvc.compile.c.preprocess : C : PREPROCESSED_C : <toolset>msvc ;
-
-        # Using 'register-c-compiler' adds the build directory to INCLUDES.
-        generators.register-c-compiler msvc.compile.rc : RC : OBJ(%_res) : <toolset>msvc ;
-        generators.override msvc.compile.rc : rc.compile.resource ;
-        generators.register-standard msvc.compile.asm : ASM : OBJ : <toolset>msvc ;
-
-        generators.register-c-compiler msvc.compile.idl : IDL : MSTYPELIB H C(%_i) C(%_proxy) C(%_dlldata) : <toolset>msvc ;
-        generators.override msvc.compile.idl : midl.compile.idl ;
-
-        generators.register-standard msvc.compile.mc : MC : H RC : <toolset>msvc ;
-        generators.override msvc.compile.mc : mc.compile ;
-
-        # Note: the 'H' source type will catch both '.h' and '.hpp' headers as
-        # the latter have their HPP type derived from H. The type of compilation
-        # is determined entirely by the destination type.
-        generators.register [ new msvc-pch-generator msvc.compile.c.pch   : H :   C_PCH OBJ : <pch>on <toolset>msvc ] ;
-        generators.register [ new msvc-pch-generator msvc.compile.c++.pch : H : CPP_PCH OBJ : <pch>on <toolset>msvc ] ;
-
-        generators.override msvc.compile.c.pch   : pch.default-c-pch-generator ;
-        generators.override msvc.compile.c++.pch : pch.default-cpp-pch-generator ;
-    }
-
-    toolset.flags msvc.compile PCH_FILE   <pch>on : <pch-file>   ;
-    toolset.flags msvc.compile PCH_SOURCE <pch>on : <pch-source> ;
-    toolset.flags msvc.compile PCH_HEADER <pch>on : <pch-header> ;
-
-    #
-    # Declare flags for compilation.
-    #
-
-    toolset.flags msvc.compile CFLAGS <optimization>speed : /O2 ;
-    toolset.flags msvc.compile CFLAGS <optimization>space : /O1 ;
-
-    toolset.flags msvc.compile CFLAGS $(.cpu-arch-ia64)/<instruction-set>$(.cpu-type-itanium) : /G1 ;
-    toolset.flags msvc.compile CFLAGS $(.cpu-arch-ia64)/<instruction-set>$(.cpu-type-itanium2) : /G2 ;
-
-    toolset.flags msvc.compile CFLAGS <debug-symbols>on/<debug-store>object : /Z7 ;
-    toolset.flags msvc.compile CFLAGS <debug-symbols>on/<debug-store>database : /Zi ;
-    toolset.flags msvc.compile CFLAGS <optimization>off : /Od ;
-    toolset.flags msvc.compile CFLAGS <inlining>off : /Ob0 ;
-    toolset.flags msvc.compile CFLAGS <inlining>on : /Ob1 ;
-    toolset.flags msvc.compile CFLAGS <inlining>full : /Ob2 ;
-
-    toolset.flags msvc.compile CFLAGS <warnings>on : /W3 ;
-    toolset.flags msvc.compile CFLAGS <warnings>off : /W0 ;
-    toolset.flags msvc.compile CFLAGS <warnings>all : /W4 ;
-    toolset.flags msvc.compile CFLAGS <warnings-as-errors>on : /WX ;
-
-    toolset.flags msvc.compile C++FLAGS  <exception-handling>on/<asynch-exceptions>off/<extern-c-nothrow>off : /EHs ;
-    toolset.flags msvc.compile C++FLAGS  <exception-handling>on/<asynch-exceptions>off/<extern-c-nothrow>on : /EHsc ;
-    toolset.flags msvc.compile C++FLAGS  <exception-handling>on/<asynch-exceptions>on/<extern-c-nothrow>off : /EHa ;
-    toolset.flags msvc.compile C++FLAGS  <exception-handling>on/<asynch-exceptions>on/<extern-c-nothrow>on : /EHac ;
-
-    # By default 8.0 enables rtti support while prior versions disabled it. We
-    # simply enable or disable it explicitly so we do not have to depend on this
-    # default behaviour.
-    toolset.flags msvc.compile CFLAGS <rtti>on : /GR ;
-    toolset.flags msvc.compile CFLAGS <rtti>off : /GR- ;
-    toolset.flags msvc.compile CFLAGS <runtime-debugging>off/<runtime-link>shared : /MD ;
-    toolset.flags msvc.compile CFLAGS <runtime-debugging>on/<runtime-link>shared : /MDd ;
-
-    toolset.flags msvc.compile CFLAGS <runtime-debugging>off/<runtime-link>static/<threading>multi : /MT ;
-    toolset.flags msvc.compile CFLAGS <runtime-debugging>on/<runtime-link>static/<threading>multi : /MTd ;
-
-    toolset.flags msvc.compile OPTIONS <cflags> : ;
-    toolset.flags msvc.compile.c++ OPTIONS <cxxflags> : ;
-
-    toolset.flags msvc.compile PDB_CFLAG <debug-symbols>on/<debug-store>database : /Fd ;
-
-    toolset.flags msvc.compile DEFINES <define> ;
-    toolset.flags msvc.compile UNDEFS <undef> ;
-    toolset.flags msvc.compile INCLUDES <include> ;
-
-    # Declare flags for the assembler.
-    toolset.flags msvc.compile.asm USER_ASMFLAGS <asmflags> ;
-
-    toolset.flags msvc.compile.asm ASMFLAGS <debug-symbols>on : "/Zi /Zd" ;
-
-    toolset.flags msvc.compile.asm ASMFLAGS <warnings>on : /W3 ;
-    toolset.flags msvc.compile.asm ASMFLAGS <warnings>off : /W0 ;
-    toolset.flags msvc.compile.asm ASMFLAGS <warnings>all : /W4 ;
-    toolset.flags msvc.compile.asm ASMFLAGS <warnings-as-errors>on : /WX ;
-
-    toolset.flags msvc.compile.asm DEFINES <define> ;
-
-    # Declare flags for linking.
-    {
-        toolset.flags msvc.link PDB_LINKFLAG <debug-symbols>on/<debug-store>database : /PDB: ;  # not used yet
-        toolset.flags msvc.link LINKFLAGS <debug-symbols>on : /DEBUG ;
-        toolset.flags msvc.link DEF_FILE <def-file> ;
-
-        # The linker disables the default optimizations when using /DEBUG so we
-        # have to enable them manually for release builds with debug symbols.
-        toolset.flags msvc LINKFLAGS <debug-symbols>on/<runtime-debugging>off : /OPT:REF,ICF ;
-
-        toolset.flags msvc LINKFLAGS <user-interface>console : /subsystem:console ;
-        toolset.flags msvc LINKFLAGS <user-interface>gui : /subsystem:windows ;
-        toolset.flags msvc LINKFLAGS <user-interface>wince : /subsystem:windowsce ;
-        toolset.flags msvc LINKFLAGS <user-interface>native : /subsystem:native ;
-        toolset.flags msvc LINKFLAGS <user-interface>auto : /subsystem:posix ;
-
-        toolset.flags msvc.link OPTIONS <linkflags> ;
-        toolset.flags msvc.link LINKPATH <library-path> ;
-
-        toolset.flags msvc.link FINDLIBS_ST <find-static-library> ;
-        toolset.flags msvc.link FINDLIBS_SA <find-shared-library> ;
-        toolset.flags msvc.link LIBRARY_OPTION <toolset>msvc : "" : unchecked ;
-        toolset.flags msvc.link LIBRARIES_MENTIONED_BY_FILE : <library-file> ;
-    }
-
-    toolset.flags msvc.archive AROPTIONS <archiveflags> ;
-}
-
-
-# Locates the requested setup script under the given folder and returns its full
-# path or nothing in case the script can not be found. In case multiple scripts
-# are found only the first one is returned.
-#
-# TODO: There used to exist a code comment for the msvc.init rule stating that
-# we do not correctly detect the location of the vcvars32.bat setup script for
-# the free VC7.1 tools in case user explicitly provides a path. This should be
-# tested or simply remove this whole comment in case this toolset version is no
-# longer important.
-#
-local rule locate-default-setup ( command : parent : setup-name )
-{
-    local result = [ GLOB $(command) $(parent) : $(setup-name) ] ;
-    if $(result[1])
-    {
-        return $(result[1]) ;
-    }
-}
-
-
-# Validates given path, registers found configuration and prints debug
-# information about it.
-#
-local rule register-configuration ( version : path ? )
-{
-    if $(path)
-    {
-        local command = [ GLOB $(path) : cl.exe ] ;
-
-        if $(command)
-        {
-            if $(.debug-configuration)
-            {
-                ECHO "notice: [msvc-cfg] msvc-$(version) detected, command: '$(command)'" ;
-            }
-
-            $(.versions).register $(version) ;
-            $(.versions).set $(version) : options : <command>$(command) ;
-        }
-    }
-}
-
-
-################################################################################
-#
-#   Startup code executed when loading this module.
-#
-################################################################################
-
-if [ MATCH (--debug-configuration) : [ modules.peek : ARGV ] ]
-{
-    .debug-configuration = true ;
-}
-
-# Miscellaneous constants.
-.RM = [ common.rm-command ] ;
-.nl = "
-" ;
-.ProgramFiles = [ path.make [ common.get-program-files-dir ] ] ;
-.escaped-double-quote = "\"" ;
-.TOUCH_FILE = [ common.file-touch-command ] ;
-
-# List of all registered configurations.
-.versions = [ new configurations ] ;
-
-# Supported CPU architectures.
-.cpu-arch-i386 =
-    <architecture>/<address-model>
-    <architecture>/<address-model>32
-    <architecture>x86/<address-model>
-    <architecture>x86/<address-model>32 ;
-
-.cpu-arch-amd64 =
-    <architecture>/<address-model>64
-    <architecture>x86/<address-model>64 ;
-
-.cpu-arch-ia64 =
-    <architecture>ia64/<address-model>
-    <architecture>ia64/<address-model>64 ;
-
-
-# Supported CPU types (only Itanium optimization options are supported from
-# VC++ 2005 on). See
-# http://msdn2.microsoft.com/en-us/library/h66s5s0e(vs.90).aspx for more
-# detailed information.
-.cpu-type-g5       = i586 pentium pentium-mmx ;
-.cpu-type-g6       = i686 pentiumpro pentium2 pentium3 pentium3m pentium-m k6
-                     k6-2 k6-3 winchip-c6 winchip2 c3 c3-2 ;
-.cpu-type-em64t    = prescott nocona conroe conroe-xe conroe-l allendale mermon
-                     mermon-xe kentsfield kentsfield-xe penryn wolfdale
-                     yorksfield nehalem ;
-.cpu-type-amd64    = k8 opteron athlon64 athlon-fx ;
-.cpu-type-g7       = pentium4 pentium4m athlon athlon-tbird athlon-4 athlon-xp
-                     athlon-mp $(.cpu-type-em64t) $(.cpu-type-amd64) ;
-.cpu-type-itanium  = itanium itanium1 merced ;
-.cpu-type-itanium2 = itanium2 mckinley ;
-
-
-# Known toolset versions, in order of preference.
-.known-versions = 10.0 10.0express 9.0 9.0express 8.0 8.0express 7.1 7.1toolkit 7.0 6.0 ;
-
-# Version aliases.
-.version-alias-6 = 6.0 ;
-.version-alias-6.5 = 6.0 ;
-.version-alias-7 = 7.0 ;
-.version-alias-8 = 8.0 ;
-.version-alias-9 = 9.0 ;
-.version-alias-10 = 10.0 ;
-
-# Names of registry keys containing the Visual C++ installation path (relative
-# to "HKEY_LOCAL_MACHINE\SOFTWARE\\Microsoft").
-.version-6.0-reg = "VisualStudio\\6.0\\Setup\\Microsoft Visual C++" ;
-.version-7.0-reg = "VisualStudio\\7.0\\Setup\\VC" ;
-.version-7.1-reg = "VisualStudio\\7.1\\Setup\\VC" ;
-.version-8.0-reg = "VisualStudio\\8.0\\Setup\\VC" ;
-.version-8.0express-reg = "VCExpress\\8.0\\Setup\\VC" ;
-.version-9.0-reg = "VisualStudio\\9.0\\Setup\\VC" ;
-.version-9.0express-reg = "VCExpress\\9.0\\Setup\\VC" ;
-.version-10.0-reg = "VisualStudio\\10.0\\Setup\\VC" ;
-.version-10.0express-reg = "VCExpress\\10.0\\Setup\\VC" ;
-
-# Visual C++ Toolkit 2003 does not store its installation path in the registry.
-# The environment variable 'VCToolkitInstallDir' and the default installation
-# path will be checked instead.
-.version-7.1toolkit-path    = "Microsoft Visual C++ Toolkit 2003" "bin" ;
-.version-7.1toolkit-env     = VCToolkitInstallDir ;
-
-# Path to the folder containing "cl.exe" relative to the value of the
-# corresponding environment variable.
-.version-7.1toolkit-envpath = "bin" ;
-
-
-# Auto-detect all the available msvc installations on the system.
-auto-detect-toolset-versions ;
-
-
-# And finally trigger the actual Boost Build toolset registration.
-register-toolset ;
diff --git a/jam-files/boost-build/tools/notfile.jam b/jam-files/boost-build/tools/notfile.jam
deleted file mode 100644
index 97a5b0e8..00000000
--- a/jam-files/boost-build/tools/notfile.jam
+++ /dev/null
@@ -1,74 +0,0 @@
-#  Copyright (c) 2005 Vladimir Prus.
-#
-#  Use, modification and distribution is subject to the Boost Software
-#  License Version 1.0. (See accompanying file LICENSE_1_0.txt or
-#  http://www.boost.org/LICENSE_1_0.txt)
-
-import "class" : new ;
-import generators ;
-import project ;
-import targets ;
-import toolset ;
-import type ;
-
-
-type.register NOTFILE_MAIN ;
-
-
-class notfile-generator : generator
-{
-    rule __init__ ( * : * )
-    {
-        generator.__init__ $(1) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ;
-    }
-
-    rule run ( project name ? : property-set : sources * : multiple ? )
-    {
-        local action ;
-        local action-name = [ $(property-set).get <action> ] ;
-
-        local m = [ MATCH ^@(.*) : $(action-name) ] ;
-
-        if $(m)
-        {
-            action = [ new action $(sources) : $(m[1])
-              : $(property-set) ] ;
-        }
-        else
-        {
-            action = [ new action $(sources) : notfile.run
-              : $(property-set) ] ;
-        }
-        return [ virtual-target.register 
-            [ new notfile-target $(name) : $(project) : $(action) ] ] ;
-    }
-}
-
-
-generators.register [ new notfile-generator notfile.main : : NOTFILE_MAIN ] ;
-
-
-toolset.flags notfile.run ACTION : <action> ;
-
-
-actions run
-{
-    $(ACTION)
-}
-
-
-rule notfile ( target-name : action + : sources * : requirements * : default-build * )
-{
-    local project = [ project.current ] ;
-
-    requirements += <action>$(action) ;
-
-    targets.main-target-alternative
-        [ new typed-target $(target-name) : $(project) : NOTFILE_MAIN
-            : [ targets.main-target-sources $(sources) : $(target-name) ]
-            : [ targets.main-target-requirements $(requirements) : $(project) ]
-            : [ targets.main-target-default-build $(default-build) : $(project) ]
-        ] ;
-}
-
-IMPORT $(__name__) : notfile : : notfile ;
diff --git a/jam-files/boost-build/tools/notfile.py b/jam-files/boost-build/tools/notfile.py
deleted file mode 100644
index afbf68fb..00000000
--- a/jam-files/boost-build/tools/notfile.py
+++ /dev/null
@@ -1,51 +0,0 @@
-# Status: ported.
-# Base revision: 64429.
-#
-#  Copyright (c) 2005-2010 Vladimir Prus.
-#
-#  Use, modification and distribution is subject to the Boost Software
-#  License Version 1.0. (See accompanying file LICENSE_1_0.txt or
-#  http://www.boost.org/LICENSE_1_0.txt)
-
-
-import b2.build.type as type
-import b2.build.generators as generators
-import b2.build.virtual_target as virtual_target
-import b2.build.toolset as toolset
-import b2.build.targets as targets
-
-from b2.manager import get_manager
-from b2.util import bjam_signature
-
-type.register("NOTFILE_MAIN")
-
-class NotfileGenerator(generators.Generator):
-
-    def run(self, project, name, ps, sources):
-        pass
-        action_name = ps.get('action')[0]
-        if action_name[0] == '@':
-            action = virtual_target.Action(get_manager(), sources, action_name[1:], ps)
-        else:
-            action = virtual_target.Action(get_manager(), sources, "notfile.run", ps)
-
-        return [get_manager().virtual_targets().register(
-            virtual_target.NotFileTarget(name, project, action))]
-
-generators.register(NotfileGenerator("notfile.main", False, [], ["NOTFILE_MAIN"]))
-
-toolset.flags("notfile.run", "ACTION", [], ["<action>"])
-
-get_manager().engine().register_action("notfile.run", "$(ACTION)")
-
-@bjam_signature((["target_name"], ["action"], ["sources", "*"], ["requirements", "*"],
-                 ["default_build", "*"]))
-def notfile(target_name, action, sources, requirements, default_build):
-
-    requirements.append("<action>" + action)
-
-    return targets.create_typed_metatarget(target_name, "NOTFILE_MAIN", sources, requirements,
-                                           default_build, [])
-
-
-get_manager().projects().add_rule("notfile", notfile)
diff --git a/jam-files/boost-build/tools/package.jam b/jam-files/boost-build/tools/package.jam
deleted file mode 100644
index 198c2231..00000000
--- a/jam-files/boost-build/tools/package.jam
+++ /dev/null
@@ -1,165 +0,0 @@
-# Copyright (c) 2005 Vladimir Prus.
-# Copyright 2006 Rene Rivera.
-#
-# Use, modification and distribution is subject to the Boost Software
-# License Version 1.0. (See accompanying file LICENSE_1_0.txt or
-# http://www.boost.org/LICENSE_1_0.txt)
-
-# Provides mechanism for installing whole packages into a specific directory
-# structure. This is opposed to the 'install' rule, that installs a number of
-# targets to a single directory, and does not care about directory structure at
-# all.
-
-# Example usage:
-#
-#   package.install boost : <properties>
-#                         : <binaries>
-#                         : <libraries>
-#                         : <headers>
-#                         ;
-#
-# This will install binaries, libraries and headers to the 'proper' location,
-# given by command line options --prefix, --exec-prefix, --bindir, --libdir and
-# --includedir.
-#
-# The rule is just a convenient wrapper, avoiding the need to define several
-# 'install' targets.
-#
-# The only install-related feature is <install-source-root>. It will apply to
-# headers only and if present, paths of headers relatively to source root will
-# be retained after installing. If it is not specified, then "." is assumed, so
-# relative paths in headers are always preserved.
-
-import "class" : new ;
-import option ;
-import project ;
-import feature ;
-import property ;
-import stage ;
-import targets ;
-import modules ;
-
-feature.feature install-default-prefix : : free incidental ;
-
-rule install ( name package-name ? : requirements * : binaries * : libraries * : headers * )
-{
-    package-name ?= $(name) ;
-    if [ MATCH --prefix=(.*) : [ modules.peek : ARGV ] ]
-    {
-        # If --prefix is explicitly specified on the command line,
-        # then we need wipe away any settings of libdir/includir that
-        # is specified via options in config files.
-        option.set bindir : ;
-        option.set libdir : ;
-        option.set includedir : ;
-    }
-            
-    # If <install-source-root> is not specified, all headers are installed to
-    # prefix/include, no matter what their relative path is. Sometimes that is
-    # what is needed.
-    local install-source-root = [ property.select <install-source-root> :
-        $(requirements) ] ;
-    install-source-root = $(install-source-root:G=) ;
-    requirements = [ property.change $(requirements) : <install-source-root> ] ;
-
-    local install-header-subdir = [ property.select <install-header-subdir> :
-        $(requirements) ] ;
-    install-header-subdir = /$(install-header-subdir:G=) ;
-    install-header-subdir ?= "" ;
-    requirements = [ property.change $(requirements) : <install-header-subdir> ]
-        ;
-
-    # First, figure out all locations. Use the default if no prefix option
-    # given.
-    local prefix = [ get-prefix $(name) : $(requirements) ] ;
-
-    # Architecture dependent files.
-    local exec-locate = [ option.get exec-prefix : $(prefix) ] ;
-
-    # Binaries.
-    local bin-locate = [ option.get bindir : $(prefix)/bin ] ;
-
-    # Object code libraries.
-    local lib-locate = [ option.get libdir : $(prefix)/lib ] ;
-
-    # Source header files.
-    local include-locate = [ option.get includedir : $(prefix)/include ] ;
-
-    stage.install $(name)-bin : $(binaries) : $(requirements)
-        <location>$(bin-locate) ;
-    alias $(name)-lib : $(name)-lib-shared $(name)-lib-static ;
-    
-    # Since the install location of shared libraries differs on universe
-    # and cygwin, use target alternatives to make different targets.
-    # We should have used indirection conditioanl requirements, but it's
-    # awkward to pass bin-locate and lib-locate from there to another rule.
-    alias $(name)-lib-shared : $(name)-lib-shared-universe ;
-    alias $(name)-lib-shared : $(name)-lib-shared-cygwin : <target-os>cygwin ;
-    
-    # For shared libraries, we install both explicitly specified one and the
-    # shared libraries that the installed executables depend on.
-    stage.install $(name)-lib-shared-universe : $(binaries) $(libraries) : $(requirements)
-      <location>$(lib-locate) <install-dependencies>on <install-type>SHARED_LIB ;
-    stage.install $(name)-lib-shared-cygwin : $(binaries) $(libraries) : $(requirements)
-      <location>$(bin-locate) <install-dependencies>on <install-type>SHARED_LIB ;
-
-    # For static libraries, we do not care about executable dependencies, since
-    # static libraries are already incorporated into them.
-    stage.install $(name)-lib-static : $(libraries) : $(requirements)
-        <location>$(lib-locate) <install-dependencies>on <install-type>STATIC_LIB ;
-    stage.install $(name)-headers : $(headers) : $(requirements)
-        <location>$(include-locate)$(install-header-subdir)
-        <install-source-root>$(install-source-root) ;
-    alias $(name) : $(name)-bin $(name)-lib $(name)-headers ;
-
-    local c = [ project.current ] ;
-    local project-module = [ $(c).project-module ] ;
-    module $(project-module)
-    {
-        explicit $(1)-bin $(1)-lib $(1)-headers $(1) $(1)-lib-shared $(1)-lib-static 
-          $(1)-lib-shared-universe $(1)-lib-shared-cygwin ;
-    }
-}
-
-rule install-data ( target-name : package-name : data * : requirements * )
-{
-    package-name ?= target-name ;
-    if [ MATCH --prefix=(.*) : [ modules.peek : ARGV ] ]
-    {
-        # If --prefix is explicitly specified on the command line,
-        # then we need wipe away any settings of datarootdir
-        option.set datarootdir : ;
-    }   
-    
-    local prefix = [ get-prefix $(package-name) : $(requirements) ] ;
-    local datadir = [ option.get datarootdir : $(prefix)/share ] ;
-
-    stage.install $(target-name) 
-        : $(data)
-        : $(requirements) <location>$(datadir)/$(package-name)
-        ;
-    
-    local c = [ project.current ] ;
-    local project-module = [ $(c).project-module ] ;
-    module $(project-module)
-    {
-        explicit $(1) ;
-    }
-}
-
-local rule get-prefix ( package-name : requirements * )
-{
-    local prefix = [ option.get prefix : [ property.select
-        <install-default-prefix> : $(requirements) ] ] ;
-    prefix = $(prefix:G=) ;
-    requirements = [ property.change $(requirements) : <install-default-prefix>
-        ] ;
-    # Or some likely defaults if neither is given.
-    if ! $(prefix)
-    {
-        if [ modules.peek : NT ] { prefix = C:\\$(package-name) ; }
-        else if [ modules.peek : UNIX ] { prefix = /usr/local ; }        
-    }
-    return $(prefix) ;
-}           
-
diff --git a/jam-files/boost-build/tools/package.py b/jam-files/boost-build/tools/package.py
deleted file mode 100644
index aa081b4f..00000000
--- a/jam-files/boost-build/tools/package.py
+++ /dev/null
@@ -1,168 +0,0 @@
-# Status: ported
-# Base revision: 64488
-#
-# Copyright (c) 2005, 2010 Vladimir Prus.
-# Copyright 2006 Rene Rivera.
-#
-# Use, modification and distribution is subject to the Boost Software
-# License Version 1.0. (See accompanying file LICENSE_1_0.txt or
-# http://www.boost.org/LICENSE_1_0.txt)
-
-# Provides mechanism for installing whole packages into a specific directory
-# structure. This is opposed to the 'install' rule, that installs a number of
-# targets to a single directory, and does not care about directory structure at
-# all.
-
-# Example usage:
-#
-#   package.install boost : <properties>
-#                         : <binaries>
-#                         : <libraries>
-#                         : <headers>
-#                         ;
-#
-# This will install binaries, libraries and headers to the 'proper' location,
-# given by command line options --prefix, --exec-prefix, --bindir, --libdir and
-# --includedir.
-#
-# The rule is just a convenient wrapper, avoiding the need to define several
-# 'install' targets.
-#
-# The only install-related feature is <install-source-root>. It will apply to
-# headers only and if present, paths of headers relatively to source root will
-# be retained after installing. If it is not specified, then "." is assumed, so
-# relative paths in headers are always preserved.
-
-import b2.build.feature as feature
-import b2.build.property as property
-import b2.util.option as option
-import b2.tools.stage as stage
-
-from b2.build.alias import alias
-
-from b2.manager import get_manager
-
-from b2.util import bjam_signature
-from b2.util.utility import ungrist
-
-
-import os
-
-feature.feature("install-default-prefix", [], ["free", "incidental"])
-
-@bjam_signature((["name", "package_name", "?"], ["requirements", "*"],
-                 ["binaries", "*"], ["libraries", "*"], ["headers", "*"]))
-def install(name, package_name=None, requirements=[], binaries=[], libraries=[], headers=[]):
-
-    requirements = requirements[:]
-    binaries = binaries[:]
-    libraries
-
-    if not package_name:
-        package_name = name
-
-    if option.get("prefix"):
-        # If --prefix is explicitly specified on the command line,
-        # then we need wipe away any settings of libdir/includir that
-        # is specified via options in config files.
-        option.set("bindir", None)
-        option.set("libdir", None)
-        option.set("includedir", None)
-            
-    # If <install-source-root> is not specified, all headers are installed to
-    # prefix/include, no matter what their relative path is. Sometimes that is
-    # what is needed.
-    install_source_root = property.select('install-source-root', requirements)
-    if install_source_root:
-        requirements = property.change(requirements, 'install-source-root', None)
-            
-    install_header_subdir = property.select('install-header-subdir', requirements)
-    if install_header_subdir:
-        install_header_subdir = ungrist(install_header_subdir[0])
-        requirements = property.change(requirements, 'install-header-subdir', None)
-
-    # First, figure out all locations. Use the default if no prefix option
-    # given.
-    prefix = get_prefix(name, requirements)
-
-    # Architecture dependent files.
-    exec_locate = option.get("exec-prefix", prefix)
-
-    # Binaries.
-    bin_locate = option.get("bindir", os.path.join(prefix, "bin"))
-
-    # Object code libraries.
-    lib_locate = option.get("libdir", os.path.join(prefix, "lib"))
-
-    # Source header files.
-    include_locate = option.get("includedir", os.path.join(prefix, "include"))
-
-    stage.install(name + "-bin", binaries, requirements + ["<location>" + bin_locate])
-    
-    alias(name + "-lib", [name + "-lib-shared", name + "-lib-static"])
-    
-    # Since the install location of shared libraries differs on universe
-    # and cygwin, use target alternatives to make different targets.
-    # We should have used indirection conditioanl requirements, but it's
-    # awkward to pass bin-locate and lib-locate from there to another rule.
-    alias(name + "-lib-shared", [name + "-lib-shared-universe"])
-    alias(name + "-lib-shared", [name + "-lib-shared-cygwin"], ["<target-os>cygwin"])
-    
-    # For shared libraries, we install both explicitly specified one and the
-    # shared libraries that the installed executables depend on.
-    stage.install(name + "-lib-shared-universe", binaries + libraries,
-                  requirements + ["<location>" + lib_locate, "<install-dependencies>on",
-                                  "<install-type>SHARED_LIB"])
-    stage.install(name + "-lib-shared-cygwin", binaries + libraries,
-                  requirements + ["<location>" + bin_locate, "<install-dependencies>on",
-                                  "<install-type>SHARED_LIB"])
-
-    # For static libraries, we do not care about executable dependencies, since
-    # static libraries are already incorporated into them.
-    stage.install(name + "-lib-static", libraries, requirements +
-                  ["<location>" + lib_locate, "<install-dependencies>on", "<install-type>STATIC_LIB"])
-    stage.install(name + "-headers", headers, requirements \
-                  + ["<location>" + os.path.join(include_locate, s) for s in install_header_subdir]
-                  + install_source_root)
-
-    alias(name, [name + "-bin", name + "-lib", name + "-headers"])
-
-    pt = get_manager().projects().current()
-
-    for subname in ["bin", "lib", "headers", "lib-shared", "lib-static", "lib-shared-universe", "lib-shared-cygwin"]:
-        pt.mark_targets_as_explicit([name + "-" + subname])
-
-@bjam_signature((["target_name"], ["package_name"], ["data", "*"], ["requirements", "*"]))
-def install_data(target_name, package_name, data, requirements):
-    if not package_name:
-        package_name = target_name
-
-    if option.get("prefix"):
-        # If --prefix is explicitly specified on the command line,
-        # then we need wipe away any settings of datarootdir
-        option.set("datarootdir", None)
-    
-    prefix = get_prefix(package_name, requirements)
-    datadir = option.get("datarootdir", os.path.join(prefix, "share"))
-
-    stage.install(target_name, data,
-                  requirements + ["<location>" + os.path.join(datadir, package_name)])
-
-    get_manager().projects().current().mark_targets_as_explicit([target_name])
-
-def get_prefix(package_name, requirements):
-
-    specified = property.select("install-default-prefix", requirements)
-    if specified:
-        specified = ungrist(specified[0])
-    prefix = option.get("prefix", specified)
-    requirements = property.change(requirements, "install-default-prefix", None)    
-    # Or some likely defaults if neither is given.
-    if not prefix:
-        if os.name == "nt":
-            prefix = "C:\\" + package_name
-        elif os.name == "posix":
-            prefix = "/usr/local"
-
-    return prefix
-
diff --git a/jam-files/boost-build/tools/pathscale.jam b/jam-files/boost-build/tools/pathscale.jam
deleted file mode 100644
index 454e3454..00000000
--- a/jam-files/boost-build/tools/pathscale.jam
+++ /dev/null
@@ -1,168 +0,0 @@
-#  Copyright 2006 Noel Belcourt
-#  Distributed under the Boost Software License, Version 1.0.
-#    (See accompanying file LICENSE_1_0.txt or copy at
-#          http://www.boost.org/LICENSE_1_0.txt)
-
-import property ;
-import generators ;
-import toolset : flags ;
-import feature ;
-import type ;
-import common ;
-import fortran ;
-
-feature.extend toolset : pathscale ;
-toolset.inherit pathscale : unix ;
-generators.override pathscale.prebuilt : builtin.prebuilt ;
-generators.override pathscale.searched-lib-generator : searched-lib-generator ;
-
-# Documentation and toolchain description located
-# http://www.pathscale.com/docs.html
-
-rule init ( version ? : command * : options * ) 
-{
-  command = [ common.get-invocation-command pathscale : pathCC : $(command) 
-    : /opt/ekopath/bin ] ;
-  
-  # Determine the version
-  local command-string = $(command:J=" ") ;
-  if $(command)
-  {    
-      version ?= [ MATCH "^([0-9.]+)"
-          : [ SHELL "$(command-string) -dumpversion" ] ] ;
-  }
-  
-  local condition = [ common.check-init-parameters pathscale
-    : version $(version) ] ;
-
-  common.handle-options pathscale : $(condition) : $(command) : $(options) ;
-    
-  toolset.flags pathscale.compile.fortran90 OPTIONS $(condition) :
-    [ feature.get-values <fflags> : $(options) ] : unchecked ;
-
-  command_c = $(command_c[1--2]) $(command[-1]:B=pathcc) ;
-
-  toolset.flags pathscale CONFIG_C_COMMAND $(condition) : $(command_c) ;
-
-  # fortran support
-  local f-command = [ common.get-invocation-command pathscale : pathf90 : $(command) ] ;
-  local command_f = $(command_f[1--2]) $(f-command[-1]:B=pathf90) ;
-  local command_f90 = $(command_f[1--2]) $(f-command[-1]:B=pathf90) ;
-
-  toolset.flags pathscale CONFIG_F_COMMAND $(condition) : $(command_f) ;
-  toolset.flags pathscale CONFIG_F90_COMMAND $(condition) : $(command_f90) ;
-
-  # always link lib rt to resolve clock_gettime()
-  flags pathscale.link FINDLIBS-SA : rt : unchecked ;
-}
-
-# Declare generators
-generators.register-c-compiler pathscale.compile.c : C : OBJ : <toolset>pathscale ;
-generators.register-c-compiler pathscale.compile.c++ : CPP : OBJ : <toolset>pathscale ;
-generators.register-fortran-compiler pathscale.compile.fortran : FORTRAN : OBJ : <toolset>pathscale ;
-generators.register-fortran90-compiler pathscale.compile.fortran90 : FORTRAN90 : OBJ : <toolset>pathscale ;
-
-# Declare flags and actions for compilation
-flags pathscale.compile OPTIONS <optimization>off   : -O0 ;
-flags pathscale.compile OPTIONS <optimization>speed : -O3 ;
-flags pathscale.compile OPTIONS <optimization>space : -Os ;
-
-flags pathscale.compile OPTIONS <inlining>off  : -noinline ;
-flags pathscale.compile OPTIONS <inlining>on   : -inline ;
-flags pathscale.compile OPTIONS <inlining>full : -inline ;
-
-flags pathscale.compile OPTIONS <warnings>off           : -woffall ;
-flags pathscale.compile OPTIONS <warnings>on            : -Wall ;
-flags pathscale.compile OPTIONS <warnings>all           : -Wall -pedantic ;
-flags pathscale.compile OPTIONS <warnings-as-errors>on  : -Werror ;
-
-flags pathscale.compile OPTIONS <debug-symbols>on : -ggdb ;
-flags pathscale.compile OPTIONS <profiling>on     : -pg ;
-flags pathscale.compile OPTIONS <link>shared      : -fPIC ;
-flags pathscale.compile OPTIONS <address-model>32 : -m32 ;
-flags pathscale.compile OPTIONS <address-model>64 : -m64 ;
-
-flags pathscale.compile USER_OPTIONS <cflags> ;
-flags pathscale.compile.c++ USER_OPTIONS <cxxflags> ;
-flags pathscale.compile DEFINES <define> ;
-flags pathscale.compile INCLUDES <include> ;
-
-flags pathscale.compile.fortran USER_OPTIONS <fflags> ;
-flags pathscale.compile.fortran90 USER_OPTIONS <fflags> ;
-
-actions compile.c
-{
-    "$(CONFIG_C_COMMAND)" $(OPTIONS) $(USER_OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -c -o "$(<)" "$(>)"
-}
-
-actions compile.c++
-{
-    "$(CONFIG_COMMAND)" $(OPTIONS) $(USER_OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -c -o "$(<)" "$(>)"
-}
-
-actions compile.fortran
-{
-    "$(CONFIG_F_COMMAND)" $(OPTIONS) $(USER_OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -c -o "$(<)" "$(>)"
-}
-
-rule compile.fortran90 ( targets * : sources * : properties * )
-{
-  # the space rule inserts spaces between targets and it's necessary
-  SPACE on $(targets) = " " ;
-  # Serialize execution of the compile.fortran90 action
-  # F90 source must be compiled in a particular order so we
-  # serialize the build as a parallel F90 compile might fail
-  JAM_SEMAPHORE on $(targets) = <s>pathscale-f90-semaphore ;
-}
-
-actions compile.fortran90
-{
-    "$(CONFIG_F90_COMMAND)" $(OPTIONS) $(USER_OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -module $(<[1]:D) -c -o "$(<)" "$(>)"
-}
-
-# Declare flags and actions for linking
-flags pathscale.link OPTIONS <debug-symbols>on : -ggdb -rdynamic ;
-# Strip the binary when no debugging is needed
-flags pathscale.link OPTIONS <debug-symbols>off : -g0 ;
-flags pathscale.link OPTIONS <profiling>on : -pg ;
-flags pathscale.link USER_OPTIONS <linkflags> ;
-flags pathscale.link LINKPATH <library-path> ;
-flags pathscale.link FINDLIBS-ST <find-static-library> ;
-flags pathscale.link FINDLIBS-SA <find-shared-library> ;
-flags pathscale.link FINDLIBS-SA <threading>multi : pthread ;
-flags pathscale.link LIBRARIES <library-file> ;
-flags pathscale.link LINK-RUNTIME <runtime-link>static : static ;
-flags pathscale.link LINK-RUNTIME <runtime-link>shared : dynamic ;
-flags pathscale.link RPATH <dll-path> ;
-# On gcc, there are separate options for dll path at runtime and
-# link time. On Solaris, there's only one: -R, so we have to use
-# it, even though it's bad idea.
-flags pathscale.link RPATH <xdll-path> ;
-
-rule link ( targets * : sources * : properties * )
-{
-    SPACE on $(targets) = " " ;
-}
-
-actions link bind LIBRARIES
-{
-    "$(CONFIG_COMMAND)" $(OPTIONS) $(USER_OPTIONS) -L"$(LINKPATH)" -Wl,$(RPATH_OPTION:E=-R)$(SPACE)-Wl,"$(RPATH)" -o "$(<)" "$(>)" "$(LIBRARIES)" -l$(FINDLIBS-SA) -l$(FINDLIBS-ST)
-}
-
-# Slight mods for dlls
-rule link.dll ( targets * : sources * : properties * )
-{
-    SPACE on $(targets) = " " ;
-}
-
-actions link.dll bind LIBRARIES
-{
-    "$(CONFIG_COMMAND)" $(OPTIONS) $(USER_OPTIONS) -L"$(LINKPATH)" -Wl,$(RPATH_OPTION:E=-R)$(SPACE)-Wl,"$(RPATH)" -o "$(<)" -Wl,-soname$(SPACE)-Wl,$(<[1]:D=) -shared "$(>)" "$(LIBRARIES)" -l$(FINDLIBS-SA) -l$(FINDLIBS-ST)
-}
-
-# Declare action for creating static libraries
-# "$(CONFIG_COMMAND)" -ar -o "$(<)" "$(>)"
-actions piecemeal archive
-{
-    ar $(ARFLAGS) ru "$(<)" "$(>)"
-}
diff --git a/jam-files/boost-build/tools/pch.jam b/jam-files/boost-build/tools/pch.jam
deleted file mode 100644
index 0c6e98fa..00000000
--- a/jam-files/boost-build/tools/pch.jam
+++ /dev/null
@@ -1,95 +0,0 @@
-# Copyright (c) 2005 Reece H. Dunn.
-# Copyright 2006 Ilya Sokolov
-#
-# Use, modification and distribution is subject to the Boost Software
-# License Version 1.0. (See accompanying file LICENSE_1_0.txt or
-# http://www.boost.org/LICENSE_1_0.txt)
-
-##### Using Precompiled Headers (Quick Guide) #####
-#
-# Make precompiled mypch.hpp:
-#
-#    import pch ;
-#
-#    cpp-pch mypch
-#      : # sources
-#        mypch.hpp
-#      : # requiremnts
-#        <toolset>msvc:<source>mypch.cpp
-#      ;
-#
-# Add cpp-pch to sources:
-#
-#    exe hello
-#      : main.cpp hello.cpp mypch
-#      ;
-
-import "class" : new ;
-import type ;
-import feature ;
-import generators ;
-
-type.register     PCH : pch ;
-
-type.register   C_PCH : : PCH ;
-type.register CPP_PCH : : PCH ;
-
-# Control precompiled header (PCH) generation.
-feature.feature pch :
-      on
-      off
-    : propagated ;
-
-
-feature.feature pch-header : : free dependency ;
-feature.feature pch-file   : : free dependency ;
-
-# Base PCH generator. The 'run' method has the logic to prevent this generator
-# from being run unless it's being used for a top-level PCH target.
-class pch-generator : generator
-{
-    import property-set ;
-
-    rule action-class ( )
-    {
-        return compile-action ;
-    }
-
-    rule run ( project name ? : property-set : sources + )
-    {
-        if ! $(name)
-        {
-            # Unless this generator is invoked as the top-most generator for a
-            # main target, fail. This allows using 'H' type as input type for
-            # this generator, while preventing Boost.Build to try this generator
-            # when not explicitly asked for.
-            #
-            # One bad example is msvc, where pch generator produces both PCH
-            # target and OBJ target, so if there's any header generated (like by
-            # bison, or by msidl), we'd try to use pch generator to get OBJ from
-            # that H, which is completely wrong. By restricting this generator
-            # only to pch main target, such problem is solved.
-        }
-        else
-        {
-            local r = [ run-pch $(project) $(name)
-              : [ $(property-set).add-raw <define>BOOST_BUILD_PCH_ENABLED ]
-              : $(sources) ] ;
-            return [ generators.add-usage-requirements $(r)
-              : <define>BOOST_BUILD_PCH_ENABLED ] ;
-        }
-    }
-
-    # This rule must be overridden by the derived classes.
-    rule run-pch ( project name ? : property-set : sources + )
-    {
-    }
-}
-
-
-# NOTE: requirements are empty, default pch generator can be applied when
-# pch=off.
-generators.register
-    [ new dummy-generator pch.default-c-pch-generator   : :   C_PCH ] ;
-generators.register
-    [ new dummy-generator pch.default-cpp-pch-generator : : CPP_PCH ] ;
diff --git a/jam-files/boost-build/tools/pch.py b/jam-files/boost-build/tools/pch.py
deleted file mode 100644
index 21d3db09..00000000
--- a/jam-files/boost-build/tools/pch.py
+++ /dev/null
@@ -1,83 +0,0 @@
-# Status: Being ported by Steven Watanabe
-# Base revision: 47077
-#
-# Copyright (c) 2005 Reece H. Dunn.
-# Copyright 2006 Ilya Sokolov
-# Copyright (c) 2008 Steven Watanabe
-#
-# Use, modification and distribution is subject to the Boost Software
-# License Version 1.0. (See accompanying file LICENSE_1_0.txt or
-# http://www.boost.org/LICENSE_1_0.txt)
-
-##### Using Precompiled Headers (Quick Guide) #####
-#
-# Make precompiled mypch.hpp:
-#
-#    import pch ;
-#
-#    cpp-pch mypch
-#      : # sources
-#        mypch.hpp
-#      : # requiremnts
-#        <toolset>msvc:<source>mypch.cpp
-#      ;
-#
-# Add cpp-pch to sources:
-#
-#    exe hello
-#      : main.cpp hello.cpp mypch
-#      ;
-
-from b2.build import type, feature, generators
-
-type.register('PCH', ['pch'])
-type.register('C_PCH', [], 'PCH')
-type.register('CPP_PCH', [], 'PCH')
-
-# Control precompiled header (PCH) generation.
-feature.feature('pch',
-                ['on', 'off'],
-                ['propagated'])
-
-feature.feature('pch-header', [], ['free', 'dependency'])
-feature.feature('pch-file', [], ['free', 'dependency'])
-
-class PchGenerator(generators.Generator):
-    """
-        Base PCH generator. The 'run' method has the logic to prevent this generator
-        from being run unless it's being used for a top-level PCH target.
-    """
-    def action_class(self):
-        return 'compile-action'
-
-    def run(self, project, name, prop_set, sources):
-        if not name:
-            # Unless this generator is invoked as the top-most generator for a
-            # main target, fail. This allows using 'H' type as input type for
-            # this generator, while preventing Boost.Build to try this generator
-            # when not explicitly asked for.
-            #
-            # One bad example is msvc, where pch generator produces both PCH
-            # target and OBJ target, so if there's any header generated (like by
-            # bison, or by msidl), we'd try to use pch generator to get OBJ from
-            # that H, which is completely wrong. By restricting this generator
-            # only to pch main target, such problem is solved.
-            pass
-        else:
-            r = self.run_pch(project, name,
-                 prop_set.add_raw('<define>BOOST_BUILD_PCH_ENABLED'),
-                 sources)
-            return generators.add_usage_requirements(
-                r, ['<define>BOOST_BUILD_PCH_ENABLED'])
-
-    # This rule must be overridden by the derived classes.
-    def run_pch(self, project, name, prop_set, sources):
-        pass
-
-#FIXME: dummy-generator in builtins.jam needs to be ported.
-# NOTE: requirements are empty, default pch generator can be applied when
-# pch=off.
-###generators.register(
-###    [ new dummy-generator pch.default-c-pch-generator   : :   C_PCH ] ;
-###generators.register
-###    [ new dummy-generator pch.default-cpp-pch-generator : : CPP_PCH ] ;
diff --git a/jam-files/boost-build/tools/pgi.jam b/jam-files/boost-build/tools/pgi.jam
deleted file mode 100644
index 3a35c644..00000000
--- a/jam-files/boost-build/tools/pgi.jam
+++ /dev/null
@@ -1,147 +0,0 @@
-#  Copyright Noel Belcourt 2007.
-#  Distributed under the Boost Software License, Version 1.0.
-#    (See accompanying file LICENSE_1_0.txt or copy at
-#          http://www.boost.org/LICENSE_1_0.txt)
-
-import property ;
-import generators ;
-import os ;
-import toolset : flags ;
-import feature ;
-import fortran ;
-import type ;
-import common ;
-import gcc ;
-
-feature.extend toolset : pgi ;
-toolset.inherit pgi : unix ;
-generators.override pgi.prebuilt : builtin.lib-generator ;
-generators.override pgi.searched-lib-generator : searched-lib-generator ;
-
-# Documentation and toolchain description located
-# http://www.pgroup.com/resources/docs.htm
-
-rule init ( version ? : command * : options * ) 
-{
-  local condition = [ common.check-init-parameters pgi : version $(version) ] ;
-
-  local l_command = [ common.get-invocation-command pgi : pgCC : $(command) ] ;
-
-  common.handle-options pgi : $(condition) : $(l_command) : $(options) ;
-    
-  command_c = $(command_c[1--2]) $(l_command[-1]:B=cc) ;
-
-  toolset.flags pgi CONFIG_C_COMMAND $(condition) : $(command_c) ;
-
-  flags pgi.compile DEFINES $(condition) :
-    [ feature.get-values <define> : $(options) ] : unchecked ;
-
-  # IOV_MAX support
-  flags pgi.compile DEFINES $(condition) : __need_IOV_MAX : unchecked ;
-
-  # set link flags
-  flags pgi.link FINDLIBS-ST : [
-    feature.get-values <find-static-library> : $(options) ] : unchecked ;
-
-  # always link lib rt to resolve clock_gettime()
-  flags pgi.link FINDLIBS-SA : rt [
-    feature.get-values <find-shared-library> : $(options) ] : unchecked ;
-
-  gcc.init-link-flags pgi gnu $(condition) ;
-}
-
-# Declare generators
-generators.register-c-compiler pgi.compile.c : C : OBJ : <toolset>pgi ;
-generators.register-c-compiler pgi.compile.c++ : CPP : OBJ : <toolset>pgi ;
-generators.register-fortran-compiler pgi.compile.fortran : FORTRAN : OBJ : <toolset>pgi ;
-
-# Declare flags and actions for compilation
-flags pgi.compile OPTIONS : -Kieee ;
-flags pgi.compile OPTIONS <link>shared : -fpic -fPIC ;
-flags pgi.compile OPTIONS <debug-symbols>on : -gopt ;
-flags pgi.compile OPTIONS <profiling>on : -xprofile=tcov ;
-flags pgi.compile OPTIONS <optimization>speed : -fast -Mx,8,0x10000000 ;
-flags pgi.compile OPTIONS <optimization>space : -xO2 -xspace ;
-# flags pgi.compile OPTIONS <threading>multi : -mt ;
-
-flags pgi.compile OPTIONS <warnings>off : -Minform=severe ;
-flags pgi.compile OPTIONS <warnings>on : -Minform=warn ;
-
-flags pgi.compile.c++ OPTIONS <inlining>off : -INLINE:none ;
-
-flags pgi.compile OPTIONS <cflags> ;
-flags pgi.compile.c++ OPTIONS <cxxflags> ;
-flags pgi.compile DEFINES <define> ;
-flags pgi.compile INCLUDES <include> ;
-
-flags pgi.compile.fortran OPTIONS <fflags> ;
-
-actions compile.c
-{
-    "$(CONFIG_C_COMMAND)" $(OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -c -o "$(<)" "$(>)"
-}
-
-actions compile.c++
-{
-    "$(CONFIG_COMMAND)" $(OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -c -o "$(<)" "$(>)"
-}
-
-actions compile.fortran
-{
-    "$(CONFIG_F_COMMAND)" $(OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -c -o "$(<)" "$(>)"
-}
-
-# Declare flags and actions for linking
-flags pgi.link OPTIONS <debug-symbols>on : -gopt ;
-# Strip the binary when no debugging is needed
-flags pgi.link OPTIONS <debug-symbols>off : -s ;
-flags pgi.link OPTIONS <profiling>on : -xprofile=tcov ;
-flags pgi.link OPTIONS <linkflags> ;
-flags pgi.link OPTIONS <link>shared : -fpic -fPIC ;
-flags pgi.link LINKPATH <library-path> ;
-flags pgi.link FINDLIBS-ST <find-static-library> ;
-flags pgi.link FINDLIBS-SA <find-shared-library> ;
-flags pgi.link FINDLIBS-SA <threading>multi : pthread rt ;
-flags pgi.link LIBRARIES <library-file> ;
-flags pgi.link LINK-RUNTIME <runtime-link>static : static ;
-flags pgi.link LINK-RUNTIME <runtime-link>shared : dynamic ;
-flags pgi.link RPATH <dll-path> ;
-
-# On gcc, there are separate options for dll path at runtime and
-# link time. On Solaris, there's only one: -R, so we have to use
-# it, even though it's bad idea.
-flags pgi.link RPATH <xdll-path> ;
-
-rule link ( targets * : sources * : properties * )
-{
-    SPACE on $(targets) = " " ;
-}
-
-# reddish can only link statically and, somehow, the presence of -Bdynamic on the link line 
-# marks the executable as a dynamically linked exec even though no dynamic libraries are supplied.
-# Yod on redstorm refuses to load an executable that is dynamically linked.
-# removing the dynamic link options should get us where we need to be on redstorm.
-# "$(CONFIG_COMMAND)" $(OPTIONS) -L"$(LINKPATH)" -R"$(RPATH)" -o "$(<)" "$(>)" "$(LIBRARIES)" -Bdynamic -l$(FINDLIBS-SA) -Bstatic -l$(FINDLIBS-ST) -B$(LINK-RUNTIME)
-actions link bind LIBRARIES
-{
-    "$(CONFIG_COMMAND)" $(OPTIONS) -L"$(LINKPATH)" -R"$(RPATH)" -o "$(<)" "$(>)" "$(LIBRARIES)" -Bstatic -l$(FINDLIBS-ST) -Bdynamic -l$(FINDLIBS-SA) -B$(LINK-RUNTIME)
-}
-
-# Slight mods for dlls
-rule link.dll ( targets * : sources * : properties * )
-{
-    SPACE on $(targets) = " " ;
-}
-
-# "$(CONFIG_COMMAND)" $(OPTIONS) -L"$(LINKPATH)" -R"$(RPATH)" -o "$(<)" -h$(<[1]:D=) -G "$(>)" "$(LIBRARIES)" -Bdynamic -l$(FINDLIBS-SA) -Bstatic -l$(FINDLIBS-ST) -B$(LINK-RUNTIME)
-
-actions link.dll bind LIBRARIES
-{
-    "$(CONFIG_COMMAND)" $(OPTIONS) -shared -L"$(LINKPATH)" -R"$(RPATH)" -o "$(<)" "$(>)" -Wl,-h -Wl,$(<[1]:D=) "$(LIBRARIES)" -Bdynamic -l$(FINDLIBS-SA) -Bstatic -l$(FINDLIBS-ST) -B$(LINK-RUNTIME)
-}
-
-actions updated together piecemeal pgi.archive
-{
-    ar -rc$(ARFLAGS:E=) "$(<)" "$(>)"
-}
-
diff --git a/jam-files/boost-build/tools/python-config.jam b/jam-files/boost-build/tools/python-config.jam
deleted file mode 100644
index 40aa825b..00000000
--- a/jam-files/boost-build/tools/python-config.jam
+++ /dev/null
@@ -1,27 +0,0 @@
-#~ Copyright 2005 Rene Rivera.
-#~ Distributed under the Boost Software License, Version 1.0.
-#~ (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-# Automatic configuration for Python tools and librries. To use, just import this module.
-
-import os ;
-import toolset : using ;
-
-if [ os.name ] = NT
-{
-    for local R in 2.4 2.3 2.2
-    {
-        local python-path = [ W32_GETREG
-            "HKEY_LOCAL_MACHINE\\SOFTWARE\\Python\\PythonCore\\$(R)\\InstallPath" ] ;
-        local python-version = $(R) ;
-        
-        if $(python-path)
-        {
-            if --debug-configuration in [ modules.peek : ARGV ]
-            {
-                ECHO "notice:" using python ":" $(python-version) ":" $(python-path) ;
-            }
-            using python : $(python-version) : $(python-path) ;
-        }
-    }
-}
diff --git a/jam-files/boost-build/tools/python.jam b/jam-files/boost-build/tools/python.jam
deleted file mode 100644
index 97a9f9a5..00000000
--- a/jam-files/boost-build/tools/python.jam
+++ /dev/null
@@ -1,1267 +0,0 @@
-# Copyright 2004 Vladimir Prus.
-# Distributed under the Boost Software License, Version 1.0. (See
-# accompanying file LICENSE_1_0.txt or copy at
-# http://www.boost.org/LICENSE_1_0.txt)
-
-# Support for Python and the the Boost.Python library.
-#
-# This module defines
-#
-# - a project 'python' with a target 'python' in it, that corresponds to the
-#   python library
-#
-# - a main target rule 'python-extension' which can be used to build a python
-#   extension.
-#
-# Extensions that use Boost.Python must explicitly link to it.
-
-import type ;
-import testing ;
-import generators ;
-import project ;
-import errors ;
-import targets ;
-import "class" : new ;
-import os ;
-import common ;
-import toolset ;
-import regex ;
-import numbers ;
-import string ;
-import property ;
-import sequence ;
-import path ;
-import feature ;
-import set ;
-import builtin ;
-import version ;
-
-
-# Make this module a project.
-project.initialize $(__name__) ;
-project python ;
-
-# Save the project so that if 'init' is called several times we define new
-# targets in the python project, not in whatever project we were called by.
-.project = [ project.current ] ;
-
-# Dynamic linker lib. Necessary to specify it explicitly on some platforms.
-lib dl ;
-# This contains 'openpty' function need by python. Again, on some system need to
-# pass this to linker explicitly.
-lib util ;
-# Python uses pthread symbols.
-lib pthread ;
-# Extra library needed by phtread on some platforms.
-lib rt ;
-
-# The pythonpath feature specifies additional elements for the PYTHONPATH
-# environment variable, set by run-pyd. For example, pythonpath can be used to
-# access Python modules that are part of the product being built, but are not
-# installed in the development system's default paths.
-feature.feature pythonpath : : free optional path ;
-
-# Initializes the Python toolset. Note that all parameters are optional.
-#
-# - version -- the version of Python to use. Should be in Major.Minor format,
-#   for example 2.3.  Do not include the subminor version.
-#
-# - cmd-or-prefix: Preferably, a command that invokes a Python interpreter.
-#   Alternatively, the installation prefix for Python libraries and includes. If
-#   empty, will be guessed from the version, the platform's installation
-#   patterns, and the python executables that can be found in PATH.
-#
-# - includes: the include path to Python headers. If empty, will be guessed.
-#
-# - libraries: the path to Python library binaries. If empty, will be guessed.
-#   On MacOS/Darwin, you can also pass the path of the Python framework.
-#
-# - condition: if specified, should be a set of properties that are matched
-#   against the build configuration when Boost.Build selects a Python
-#   configuration to use.
-#
-# - extension-suffix: A string to append to the name of extension modules before
-#   the true filename extension.  Ordinarily we would just compute this based on
-#   the value of the <python-debugging> feature. However ubuntu's python-dbg
-#   package uses the windows convention of appending _d to debug-build extension
-#   modules. We have no way of detecting ubuntu, or of probing python for the
-#   "_d" requirement, and if you configure and build python using
-#   --with-pydebug, you'll be using the standard *nix convention. Defaults to ""
-#   (or "_d" when targeting windows and <python-debugging> is set).
-#
-# Example usage:
-#
-#   using python : 2.3 ;
-#   using python : 2.3 : /usr/local/bin/python ;
-#
-rule init ( version ? : cmd-or-prefix ? : includes * : libraries ?
-    : condition * : extension-suffix ? )
-{
-    project.push-current $(.project) ;
-
-    debug-message Configuring python... ;
-    for local v in version cmd-or-prefix includes libraries condition
-    {
-        if $($(v))
-        {
-            debug-message "  user-specified "$(v): \"$($(v))\" ;
-        }
-    }
-
-    configure $(version) : $(cmd-or-prefix) : $(includes) : $(libraries) : $(condition) : $(extension-suffix) ;
-
-    project.pop-current ;
-}
-
-# A simpler version of SHELL that grabs stderr as well as stdout, but returns
-# nothing if there was an error.
-#
-local rule shell-cmd ( cmd )
-{
-    debug-message running command '$(cmd)" 2>&1"' ;
-    x = [ SHELL $(cmd)" 2>&1" : exit-status ] ;
-    if $(x[2]) = 0
-    {
-        return $(x[1]) ;
-    }
-    else
-    {
-        return ;
-    }
-}
-
-
-# Try to identify Cygwin symlinks. Invoking such a file directly as an NT
-# executable from a native Windows build of bjam would be fatal to the bjam
-# process. One /can/ invoke them through sh.exe or bash.exe, if you can prove
-# that those are not also symlinks. ;-)
-#
-# If a symlink is found returns non-empty; we try to extract the target of the
-# symlink from the file and return that.
-#
-# Note: 1. only works on NT  2. path is a native path.
-local rule is-cygwin-symlink ( path )
-{
-    local is-symlink = ;
-
-    # Look for a file with the given path having the S attribute set, as cygwin
-    # symlinks do. /-C means "do not use thousands separators in file sizes."
-    local dir-listing = [ shell-cmd "DIR /-C /A:S \""$(path)"\"" ] ;
-
-    if $(dir-listing)
-    {
-        # Escape any special regex characters in the base part of the path.
-        local base-pat = [ regex.escape $(path:D=) : ].[()*+?|\\$^ : \\ ] ;
-
-        # Extract the file's size from the directory listing.
-        local size-of-system-file = [ MATCH "([0-9]+) "$(base-pat) : $(dir-listing) : 1 ] ;
-
-        # If the file has a reasonably small size, look for the special symlink
-        # identification text.
-        if $(size-of-system-file) && [ numbers.less $(size-of-system-file) 1000 ]
-        {
-            local link = [ SHELL "FIND /OFF \"!<symlink>\" \""$(path)"\" 2>&1" ] ;
-            if $(link[2]) != 0
-            {
-                local nl = "
-
-" ;
-                is-symlink = [ MATCH ".*!<symlink>([^"$(nl)"]*)" : $(link[1]) : 1 ] ;
-                if $(is-symlink)
-                {
-                    is-symlink = [ *nix-path-to-native $(is-symlink) ] ;
-                    is-symlink = $(is-symlink:R=$(path:D)) ;
-                }
-
-            }
-        }
-    }
-    return $(is-symlink) ;
-}
-
-
-# Append ext to each member of names that does not contain '.'.
-#
-local rule default-extension ( names * : ext * )
-{
-    local result ;
-    for local n in $(names)
-    {
-        switch $(n)
-        {
-            case *.* : result += $(n) ;
-            case * : result += $(n)$(ext) ;
-        }
-    }
-    return $(result) ;
-}
-
-
-# Tries to determine whether invoking "cmd" would actually attempt to launch a
-# cygwin symlink.
-#
-# Note: only works on NT.
-#
-local rule invokes-cygwin-symlink ( cmd )
-{
-    local dirs = $(cmd:D) ;
-    if ! $(dirs)
-    {
-        dirs = . [ os.executable-path ] ;
-    }
-    local base = [ default-extension $(cmd:D=) : .exe .cmd .bat ] ;
-    local paths = [ GLOB $(dirs) : $(base) ] ;
-    if $(paths)
-    {
-        # Make sure we have not run into a Cygwin symlink. Invoking such a file
-        # as an NT executable would be fatal for the bjam process.
-        return [ is-cygwin-symlink $(paths[1]) ] ;
-    }
-}
-
-
-local rule debug-message ( message * )
-{
-    if --debug-configuration in [ modules.peek : ARGV ]
-    {
-        ECHO notice: [python-cfg] $(message) ;
-    }
-}
-
-
-# Like W32_GETREG, except prepend HKEY_CURRENT_USER\SOFTWARE and
-# HKEY_LOCAL_MACHINE\SOFTWARE to the first argument, returning the first result
-# found. Also accounts for the fact that on 64-bit machines, 32-bit software has
-# its own area, under SOFTWARE\Wow6432node.
-#
-local rule software-registry-value ( path : data ? )
-{
-    local result ;
-    for local root in HKEY_CURRENT_USER HKEY_LOCAL_MACHINE
-    {
-        for local x64elt in "" Wow6432node\\ # Account for 64-bit windows
-        {
-            if ! $(result)
-            {
-                result = [ W32_GETREG $(root)\\SOFTWARE\\$(x64elt)$(path) : $(data) ] ;
-            }
-        }
-
-    }
-    return $(result) ;
-}
-
-
-.windows-drive-letter-re = ^([A-Za-z]):[\\/](.*) ;
-.cygwin-drive-letter-re = ^/cygdrive/([a-z])/(.*) ;
-
-.working-directory = [ PWD ] ;
-.working-drive-letter = [ SUBST $(.working-directory) $(.windows-drive-letter-re) $1 ] ;
-.working-drive-letter ?= [ SUBST $(.working-directory) $(.cygwin-drive-letter-re) $1 ] ;
-
-
-local rule windows-to-cygwin-path ( path )
-{
-    # If path is rooted with a drive letter, rewrite it using the /cygdrive
-    # mountpoint.
-    local p = [ SUBST $(path:T) $(.windows-drive-letter-re) /cygdrive/$1/$2 ] ;
-
-    # Else if path is rooted without a drive letter, use the working directory.
-    p ?= [ SUBST $(path:T) ^/(.*) /cygdrive/$(.working-drive-letter:L)/$2 ] ;
-
-    # Else return the path unchanged.
-    return $(p:E=$(path:T)) ;
-}
-
-
-# :W only works in Cygwin builds of bjam.  This one works on NT builds as well.
-#
-local rule cygwin-to-windows-path ( path )
-{
-    path = $(path:R="") ; # strip any trailing slash
-
-    local drive-letter = [ SUBST $(path) $(.cygwin-drive-letter-re) $1:/$2 ] ;
-    if $(drive-letter)
-    {
-        path = $(drive-letter) ;
-    }
-    else if $(path:R=/x) = $(path) # already rooted?
-    {
-        # Look for a cygwin mount that includes each head sequence in $(path).
-        local head = $(path) ;
-        local tail = "" ;
-
-        while $(head)
-        {
-            local root = [ software-registry-value
-                "Cygnus Solutions\\Cygwin\\mounts v2\\"$(head) : native ] ;
-
-            if $(root)
-            {
-                path = $(tail:R=$(root)) ;
-                head = ;
-            }
-            tail = $(tail:R=$(head:D=)) ;
-
-            if $(head) = /
-            {
-                head = ;
-            }
-            else
-            {
-                head = $(head:D) ;
-            }
-        }
-    }
-    return [ regex.replace $(path:R="") / \\ ] ;
-}
-
-
-# Convert a *nix path to native.
-#
-local rule *nix-path-to-native ( path )
-{
-    if [ os.name ] = NT
-    {
-        path = [ cygwin-to-windows-path $(path) ] ;
-    }
-    return $(path) ;
-}
-
-
-# Convert an NT path to native.
-#
-local rule windows-path-to-native ( path )
-{
-    if [ os.name ] = NT
-    {
-        return $(path) ;
-    }
-    else
-    {
-        return [ windows-to-cygwin-path $(path) ] ;
-    }
-}
-
-
-# Return nonempty if path looks like a windows path, i.e. it starts with a drive
-# letter or contains backslashes.
-#
-local rule guess-windows-path ( path )
-{
-    return [ SUBST $(path) ($(.windows-drive-letter-re)|.*([\\]).*) $1 ] ;
-}
-
-
-local rule path-to-native ( paths * )
-{
-    local result ;
-
-    for local p in $(paths)
-    {
-        if [ guess-windows-path $(p) ]
-        {
-            result += [ windows-path-to-native $(p) ] ;
-        }
-        else
-        {
-            result += [ *nix-path-to-native $(p:T) ] ;
-        }
-    }
-    return $(result) ;
-}
-
-
-# Validate the version string and extract the major/minor part we care about.
-#
-local rule split-version ( version )
-{
-    local major-minor = [ MATCH ^([0-9]+)\.([0-9]+)(.*)$ : $(version) : 1 2 3 ] ;
-    if ! $(major-minor[2]) || $(major-minor[3])
-    {
-        ECHO "Warning: \"using python\" expects a two part (major, minor) version number; got" $(version) instead ;
-
-        # Add a zero to account for the missing digit if necessary.
-        major-minor += 0 ;
-    }
-
-    return $(major-minor[1]) $(major-minor[2]) ;
-}
-
-
-# Build a list of versions from 3.0 down to 1.5. Because bjam can not enumerate
-# registry sub-keys, we have no way of finding a version with a 2-digit minor
-# version, e.g. 2.10 -- let us hope that never happens.
-#
-.version-countdown = ;
-for local v in [ numbers.range 15 30 ]
-{
-    .version-countdown = [ SUBST $(v) (.)(.*) $1.$2 ] $(.version-countdown) ;
-}
-
-
-local rule windows-installed-pythons ( version ? )
-{
-    version ?= $(.version-countdown) ;
-    local interpreters ;
-
-    for local v in $(version)
-    {
-        local install-path = [
-          software-registry-value "Python\\PythonCore\\"$(v)"\\InstallPath" ] ;
-
-        if $(install-path)
-        {
-            install-path = [ windows-path-to-native $(install-path) ] ;
-            debug-message Registry indicates Python $(v) installed at \"$(install-path)\" ;
-        }
-
-        interpreters += $(:E=python:R=$(install-path)) ;
-    }
-    return $(interpreters) ;
-}
-
-
-local rule darwin-installed-pythons ( version ? )
-{
-    version ?= $(.version-countdown) ;
-
-    local prefix
-      = [ GLOB /System/Library/Frameworks /Library/Frameworks
-          : Python.framework ] ;
-
-    return $(prefix)/Versions/$(version)/bin/python ;
-}
-
-
-# Assume "python-cmd" invokes a python interpreter and invoke it to extract all
-# the information we care about from its "sys" module. Returns void if
-# unsuccessful.
-#
-local rule probe ( python-cmd )
-{
-    # Avoid invoking a Cygwin symlink on NT.
-    local skip-symlink ;
-    if [ os.name ] = NT
-    {
-        skip-symlink = [ invokes-cygwin-symlink $(python-cmd) ] ;
-    }
-
-    if $(skip-symlink)
-    {
-        debug-message -------------------------------------------------------------------- ;
-        debug-message \"$(python-cmd)\" would attempt to invoke a Cygwin symlink, ;
-        debug-message causing a bjam built for Windows to hang. ;
-        debug-message ;
-        debug-message If you intend to target a Cygwin build of Python, please ;
-        debug-message replace the path to the link with the path to a real executable ;
-        debug-message (guessing: \"$(skip-symlink)\") "in" your 'using python' line ;
-        debug-message "in" user-config.jam or site-config.jam. Do not forget to escape ;
-        debug-message backslashes ;
-        debug-message -------------------------------------------------------------------- ;
-    }
-    else
-    {
-        # Prepare a List of Python format strings and expressions that can be
-        # used to print the constants we want from the sys module.
-
-        # We do not really want sys.version since that is a complicated string,
-        # so get the information from sys.version_info instead.
-        local format = "version=%d.%d" ;
-        local exprs = "version_info[0]" "version_info[1]" ;
-
-        for local s in $(sys-elements[2-])
-        {
-            format += $(s)=%s ;
-            exprs += $(s) ;
-        }
-
-        # Invoke Python and ask it for all those values.
-        if [ version.check-jam-version 3 1 17 ] || ( [ os.name ] != NT )
-        {
-            # Prior to version 3.1.17 Boost Jam's SHELL command did not support
-            # quoted commands correctly on Windows. This means that on that
-            # platform we do not support using a Python command interpreter
-            # executable whose path contains a space character.
-            python-cmd = \"$(python-cmd)\" ;
-        }
-        local full-cmd =
-            $(python-cmd)" -c \"from sys import *; print('"$(format:J=\\n)"' % ("$(exprs:J=,)"))\"" ;
-
-        local output = [ shell-cmd $(full-cmd) ] ;
-        if $(output)
-        {
-            # Parse the output to get all the results.
-            local nl = "
-
-" ;
-            for s in $(sys-elements)
-            {
-                # These variables are expected to be declared local in the
-                # caller, so Jam's dynamic scoping will set their values there.
-                sys.$(s) = [ SUBST $(output) \\<$(s)=([^$(nl)]+) $1 ] ;
-            }
-        }
-        return $(output) ;
-    }
-}
-
-
-# Make sure the "libraries" and "includes" variables (in an enclosing scope)
-# have a value based on the information given.
-#
-local rule compute-default-paths ( target-os : version ? : prefix ? :
-    exec-prefix ? )
-{
-    exec-prefix ?= $(prefix) ;
-
-    if $(target-os) = windows
-    {
-        # The exec_prefix is where you're supposed to look for machine-specific
-        # libraries.
-        local default-library-path = $(exec-prefix)\\libs ;
-        local default-include-path = $(:E=Include:R=$(prefix)) ;
-
-        # If the interpreter was found in a directory called "PCBuild" or
-        # "PCBuild8," assume we're looking at a Python built from the source
-        # distro, and go up one additional level to the default root. Otherwise,
-        # the default root is the directory where the interpreter was found.
-
-        # We ask Python itself what the executable path is in case of
-        # intermediate symlinks or shell scripts.
-        local executable-dir = $(sys.executable:D) ;
-
-        if [ MATCH ^(PCBuild) : $(executable-dir:D=) ]
-        {
-            debug-message "This Python appears to reside in a source distribution;" ;
-            debug-message "prepending \""$(executable-dir)"\" to default library search path" ;
-
-            default-library-path = $(executable-dir) $(default-library-path) ;
-
-            default-include-path = $(:E=PC:R=$(executable-dir:D)) $(default-include-path) ;
-
-            debug-message "and \""$(default-include-path[1])"\" to default #include path" ;
-        }
-
-        libraries ?= $(default-library-path) ;
-        includes ?= $(default-include-path) ;
-    }
-    else
-    {
-        includes ?= $(prefix)/include/python$(version) ;
-
-        local lib = $(exec-prefix)/lib ;
-        libraries ?= $(lib)/python$(version)/config $(lib) ;
-    }
-}
-
-# The version of the python interpreter to use.
-feature.feature python : : propagated ;
-feature.feature python.interpreter : : free ;
-
-toolset.flags python.capture-output PYTHON : <python.interpreter> ;
-
-#
-# Support for Python configured --with-pydebug
-#
-feature.feature python-debugging : off on : propagated ;
-builtin.variant debug-python : debug : <python-debugging>on ;
-
-
-# Return a list of candidate commands to try when looking for a Python
-# interpreter. prefix is expected to be a native path.
-#
-local rule candidate-interpreters ( version ? : prefix ? : target-os )
-{
-    local bin-path = bin ;
-    if $(target-os) = windows
-    {
-        # On Windows, look in the root directory itself and, to work with the
-        # result of a build-from-source, the PCBuild directory.
-        bin-path = PCBuild8 PCBuild "" ;
-    }
-
-    bin-path = $(bin-path:R=$(prefix)) ;
-
-    if $(target-os) in windows darwin
-    {
-        return                                            # Search:
-            $(:E=python:R=$(bin-path))                    #   Relative to the prefix, if any
-            python                                        #   In the PATH
-            [ $(target-os)-installed-pythons $(version) ] #   Standard install locations
-        ;
-    }
-    else
-    {
-        # Search relative to the prefix, or if none supplied, in PATH.
-        local unversioned = $(:E=python:R=$(bin-path:E=)) ;
-
-        # If a version was specified, look for a python with that specific
-        # version appended before looking for one called, simply, "python"
-        return $(unversioned)$(version) $(unversioned) ;
-    }
-}
-
-
-# Compute system library dependencies for targets linking with static Python
-# libraries.
-#
-# On many systems, Python uses libraries such as pthreads or libdl. Since static
-# libraries carry no library dependency information of their own that the linker
-# can extract, these extra dependencies have to be given explicitly on the link
-# line of the client.  The information about these dependencies is packaged into
-# the "python" target below.
-#
-# Even where Python itself uses pthreads, it never allows extension modules to
-# be entered concurrently (unless they explicitly give up the interpreter lock).
-# Therefore, extension modules do not need the efficiency overhead of threadsafe
-# code as produced by <threading>multi, and we handle libpthread along with
-# other libraries here. Note: this optimization is based on an assumption that
-# the compiler generates link-compatible code in both the single- and
-# multi-threaded cases, and that system libraries do not change their ABIs
-# either.
-#
-# Returns a list of usage-requirements that link to the necessary system
-# libraries.
-#
-local rule system-library-dependencies ( target-os )
-{
-    switch $(target-os)
-    {
-        case s[uo][nl]* : # solaris, sun, sunos
-            # Add a librt dependency for the gcc toolset on SunOS (the sun
-            # toolset adds -lrt unconditionally). While this appears to
-            # duplicate the logic already in gcc.jam, it does not as long as
-            # we are not forcing <threading>multi.
-
-            # On solaris 10, distutils.sysconfig.get_config_var('LIBS') yields
-            # '-lresolv -lsocket -lnsl -lrt -ldl'. However, that does not seem
-            # to be the right list for extension modules. For example, on my
-            # installation, adding -ldl causes at least one test to fail because
-            # the library can not be found and removing it causes no failures.
-
-            # Apparently, though, we need to add -lrt for gcc.
-            return <toolset>gcc:<library>rt ;
-
-        case osf : return  <library>pthread <toolset>gcc:<library>rt ;
-
-        case qnx* : return ;
-        case darwin : return ;
-        case windows : return ;
-
-        case hpux : return  <library>rt ;
-        case *bsd : return  <library>pthread <toolset>gcc:<library>util ;
-
-        case aix : return  <library>pthread <library>dl ;
-
-        case * : return  <library>pthread <library>dl 
-            <toolset>gcc:<library>util <toolset-intel:platform>linux:<library>util ;
-    }
-}
-
-
-# Declare a target to represent Python's library.
-#
-local rule declare-libpython-target ( version ? : requirements * )
-{
-    # Compute the representation of Python version in the name of Python's
-    # library file.
-    local lib-version = $(version) ;
-    if <target-os>windows in $(requirements)
-    {
-        local major-minor = [ split-version $(version) ] ;
-        lib-version = $(major-minor:J="") ;
-        if <python-debugging>on in $(requirements)
-        {
-            lib-version = $(lib-version)_d ;
-        }
-    }
-
-    if ! $(lib-version)
-    {
-        ECHO *** warning: could not determine Python version, which will ;
-        ECHO *** warning: probably prevent us from linking with the python ;
-        ECHO *** warning: library.  Consider explicitly passing the version ;
-        ECHO *** warning: to 'using python'. ;
-    }
-
-    # Declare it.
-    lib python.lib : : <name>python$(lib-version) $(requirements) ;
-}
-
-
-# Implementation of init.
-local rule configure ( version ? : cmd-or-prefix ? : includes * : libraries ? :
-    condition * : extension-suffix ? )
-{
-    local prefix ;
-    local exec-prefix ;
-    local cmds-to-try ;
-    local interpreter-cmd ;
-
-    local target-os = [ feature.get-values target-os : $(condition) ] ;
-    target-os ?= [ feature.defaults target-os ] ;
-    target-os = $(target-os:G=) ;
-
-    if $(target-os) = windows && <python-debugging>on in $(condition)
-    {
-        extension-suffix ?= _d ;
-    }
-    extension-suffix ?= "" ;
-
-    # Normalize and dissect any version number.
-    local major-minor ;
-    if $(version)
-    {
-        major-minor = [ split-version $(version) ] ;
-        version = $(major-minor:J=.) ;
-    }
-
-    local cmds-to-try ;
-
-    if ! $(cmd-or-prefix) || [ GLOB $(cmd-or-prefix) : * ]
-    {
-        # If the user did not pass a command, whatever we got was a prefix.
-        prefix = $(cmd-or-prefix) ;
-        cmds-to-try = [ candidate-interpreters $(version) : $(prefix) : $(target-os) ] ;
-    }
-    else
-    {
-        # Work with the command the user gave us.
-        cmds-to-try = $(cmd-or-prefix) ;
-
-        # On Windows, do not nail down the interpreter command just yet in case
-        # the user specified something that turns out to be a cygwin symlink,
-        # which could bring down bjam if we invoke it.
-        if $(target-os) != windows
-        {
-            interpreter-cmd = $(cmd-or-prefix) ;
-        }
-    }
-
-    # Values to use in case we can not really find anything in the system.
-    local fallback-cmd = $(cmds-to-try[1]) ;
-    local fallback-version ;
-
-    # Anything left to find or check?
-    if ! ( $(interpreter-cmd) && $(includes) && $(libraries) )
-    {
-        # Values to be extracted from python's sys module. These will be set by
-        # the probe rule, above, using Jam's dynamic scoping.
-        local sys-elements = version platform prefix exec_prefix executable ;
-        local sys.$(sys-elements) ;
-
-        # Compute the string Python's sys.platform needs to match. If not
-        # targeting Windows or cygwin we will assume only native builds can
-        # possibly run, so we will not require a match and we leave sys.platform
-        # blank.
-        local platform ;
-        switch $(target-os)
-        {
-            case windows : platform = win32 ;
-            case cygwin : platform = cygwin ;
-        }
-
-        while $(cmds-to-try)
-        {
-            # Pop top command.
-            local cmd = $(cmds-to-try[1]) ;
-            cmds-to-try = $(cmds-to-try[2-]) ;
-
-            debug-message Checking interpreter command \"$(cmd)\"... ;
-            if [ probe $(cmd) ]
-            {
-                fallback-version ?= $(sys.version) ;
-
-                # Check for version/platform validity.
-                for local x in version platform
-                {
-                    if $($(x)) && $($(x)) != $(sys.$(x))
-                    {
-                        debug-message ...$(x) "mismatch (looking for"
-                            $($(x)) but found $(sys.$(x))")" ;
-                        cmd = ;
-                    }
-                }
-
-                if $(cmd)
-                {
-                    debug-message ...requested configuration matched! ;
-
-                    exec-prefix = $(sys.exec_prefix) ;
-
-                    compute-default-paths $(target-os) : $(sys.version) :
-                        $(sys.prefix) : $(sys.exec_prefix) ;
-
-                    version = $(sys.version) ;
-                    interpreter-cmd ?= $(cmd) ;
-                    cmds-to-try = ;  # All done.
-                }
-            }
-            else
-            {
-                debug-message ...does not invoke a working interpreter ;
-            }
-        }
-    }
-
-    # Anything left to compute?
-    if $(includes) && $(libraries)
-    {
-        .configured = true ;
-    }
-    else
-    {
-        version ?= $(fallback-version) ;
-        version ?= 2.5 ;
-        exec-prefix ?= $(prefix) ;
-        compute-default-paths $(target-os) : $(version) : $(prefix:E=) ;
-    }
-
-    if ! $(interpreter-cmd)
-    {
-        fallback-cmd ?= python ;
-        debug-message No working Python interpreter found. ;
-        if [ os.name ] != NT || ! [ invokes-cygwin-symlink $(fallback-cmd) ]
-        {
-            interpreter-cmd = $(fallback-cmd) ;
-            debug-message falling back to \"$(interpreter-cmd)\" ;
-        }
-    }
-
-    includes = [ path-to-native $(includes) ] ;
-    libraries = [ path-to-native $(libraries) ] ;
-
-    debug-message "Details of this Python configuration:" ;
-    debug-message "  interpreter command:" \"$(interpreter-cmd:E=<empty>)\" ;
-    debug-message "  include path:" \"$(includes:E=<empty>)\" ;
-    debug-message "  library path:" \"$(libraries:E=<empty>)\" ;
-    if $(target-os) = windows
-    {
-        debug-message "  DLL search path:" \"$(exec-prefix:E=<empty>)\" ;
-    }
-
-    #
-    # End autoconfiguration sequence.
-    #
-    local target-requirements = $(condition) ;
-
-    # Add the version, if any, to the target requirements.
-    if $(version)
-    {
-        if ! $(version) in [ feature.values python ]
-        {
-            feature.extend python : $(version) ;
-        }
-        target-requirements += <python>$(version:E=default) ;
-    }
- 
-    target-requirements += <target-os>$(target-os) ;
-
-    # See if we can find a framework directory on darwin.
-    local framework-directory ;
-    if $(target-os) = darwin
-    {
-        # Search upward for the framework directory.
-        local framework-directory = $(libraries[-1]) ;
-        while $(framework-directory:D=) && $(framework-directory:D=) != Python.framework
-        {
-            framework-directory = $(framework-directory:D) ;
-        }
-
-        if $(framework-directory:D=) = Python.framework
-        {
-            debug-message framework directory is \"$(framework-directory)\" ;
-        }
-        else
-        {
-            debug-message "no framework directory found; using library path" ;
-            framework-directory = ;
-        }
-    }
-
-    local dll-path = $(libraries) ;
-
-    # Make sure that we can find the Python DLL on Windows.
-    if ( $(target-os) = windows ) && $(exec-prefix)
-    {
-        dll-path += $(exec-prefix) ;
-    }
-
-    #
-    # Prepare usage requirements.
-    #
-    local usage-requirements = [ system-library-dependencies $(target-os) ] ;
-    usage-requirements += <include>$(includes) <python.interpreter>$(interpreter-cmd) ;
-    if <python-debugging>on in $(condition)
-    {
-        if $(target-os) = windows
-        {
-            # In pyconfig.h, Py_DEBUG is set if _DEBUG is set. If we define
-            # Py_DEBUG we will get multiple definition warnings.
-            usage-requirements += <define>_DEBUG ;
-        }
-        else
-        {
-            usage-requirements += <define>Py_DEBUG ;
-        }
-    }
-
-    # Global, but conditional, requirements to give access to the interpreter
-    # for general utilities, like other toolsets, that run Python scripts.
-    toolset.add-requirements
-        $(target-requirements:J=,):<python.interpreter>$(interpreter-cmd) ;
-
-    # Register the right suffix for extensions.
-    register-extension-suffix $(extension-suffix) : $(target-requirements) ;
-
-    #
-    # Declare the "python" target. This should really be called
-    # python_for_embedding.
-    #
-
-    if $(framework-directory)
-    {
-        alias python
-          :
-          : $(target-requirements)
-          :
-          : $(usage-requirements) <framework>$(framework-directory)
-          ;
-    }
-    else
-    {
-        declare-libpython-target $(version) : $(target-requirements) ;
-
-        # This is an evil hack.  On, Windows, when Python is embedded, nothing
-        # seems to set up sys.path to include Python's standard library
-        # (http://article.gmane.org/gmane.comp.python.general/544986). The evil
-        # here, aside from the workaround necessitated by Python's bug, is that:
-        #
-        # a. we're guessing the location of the python standard library from the
-        #    location of pythonXX.lib
-        #
-        # b. we're hijacking the <testing.launcher> property to get the
-        #    environment variable set up, and the user may want to use it for
-        #    something else (e.g. launch the debugger).
-        local set-PYTHONPATH ;
-        if $(target-os) = windows
-        {
-            set-PYTHONPATH = [ common.prepend-path-variable-command PYTHONPATH :
-                $(libraries:D)/Lib ] ;
-        }
-
-        alias python
-          :
-          : $(target-requirements)
-          :
-            # Why python.lib must be listed here instead of along with the
-            # system libs is a mystery, but if we do not do it, on cygwin,
-            # -lpythonX.Y never appears in the command line (although it does on
-            # linux).
-          : $(usage-requirements)
-            <testing.launcher>$(set-PYTHONPATH)
-              <library-path>$(libraries) <library>python.lib
-          ;
-    }
-
-    # On *nix, we do not want to link either Boost.Python or Python extensions
-    # to libpython, because the Python interpreter itself provides all those
-    # symbols. If we linked to libpython, we would get duplicate symbols. So
-    # declare two targets -- one for building extensions and another for
-    # embedding.
-    #
-    # Unlike most *nix systems, Mac OS X's linker does not permit undefined
-    # symbols when linking a shared library. So, we still need to link against
-    # the Python framework, even when building extensions. Note that framework
-    # builds of Python always use shared libraries, so we do not need to worry
-    # about duplicate Python symbols.
-    if $(target-os) in windows cygwin darwin
-    {
-        alias python_for_extensions : python : $(target-requirements) ;
-    }
-    # On AIX we need Python extensions and Boost.Python to import symbols from
-    # the Python interpreter. Dynamic libraries opened with dlopen() do not
-    # inherit the symbols from the Python interpreter.
-    else if $(target-os) = aix
-    {
-        alias python_for_extensions
-            :
-            : $(target-requirements)
-            :
-            : $(usage-requirements) <linkflags>-Wl,-bI:$(libraries[1])/python.exp
-            ;
-    }
-    else
-    {
-        alias python_for_extensions
-            :
-            : $(target-requirements)
-            :
-            : $(usage-requirements)
-            ;
-    }
-}
-
-
-rule configured ( )
-{
-     return $(.configured) ;
-}
-
-
-type.register PYTHON_EXTENSION : : SHARED_LIB ;
-
-
-local rule register-extension-suffix ( root : condition * )
-{
-    local suffix ;
-
-    switch [ feature.get-values target-os : $(condition) ]
-    {
-        case windows : suffix = pyd ;
-        case cygwin : suffix = dll ;
-        case hpux :
-        {
-            if [ feature.get-values python : $(condition) ] in 1.5 1.6 2.0 2.1 2.2 2.3 2.4
-            {
-                suffix = sl ;
-            }
-            else
-            {
-                suffix = so ;
-            }
-        }
-        case * : suffix = so ;
-    }
-
-    type.set-generated-target-suffix PYTHON_EXTENSION : $(condition) : <$(root).$(suffix)> ;
-}
-
-
-# Unset 'lib' prefix for PYTHON_EXTENSION
-type.set-generated-target-prefix PYTHON_EXTENSION : : "" ;
-
-
-rule python-extension ( name : sources * : requirements * : default-build * :
-                        usage-requirements * )
-{
-    if [ configured ]
-    {
-        requirements += <use>/python//python_for_extensions ;
-    }
-    requirements += <suppress-import-lib>true ;
-
-    local project = [ project.current ] ;
-
-    targets.main-target-alternative
-        [ new typed-target $(name) : $(project) : PYTHON_EXTENSION
-            : [ targets.main-target-sources $(sources) : $(name) ]
-            : [ targets.main-target-requirements $(requirements) : $(project) ]
-            : [ targets.main-target-default-build $(default-build) : $(project) ]
-        ] ;
-}
-
-IMPORT python : python-extension : : python-extension ;
-
-rule py2to3
-{
-    common.copy $(>) $(<) ;
-    2to3 $(<) ;
-}
-
-actions 2to3
-{
-    2to3 -wn "$(<)"
-    2to3 -dwn "$(<)"
-}
-
-
-# Support for testing.
-type.register PY : py ;
-type.register RUN_PYD_OUTPUT ;
-type.register RUN_PYD : : TEST ;
-
-
-class python-test-generator : generator
-{
-    import set ;
-
-    rule __init__ ( * : * )
-    {
-        generator.__init__ $(1) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ;
-        self.composing = true ;
-    }
-
-    rule run ( project name ? : property-set : sources * : multiple ? )
-    {
-        local pyversion = [ $(property-set).get <python> ] ;
-        local python ;
-        local other-pythons ;
-    
-        # Make new target that converting Python source by 2to3 when running with Python 3.
-        local rule make-2to3-source ( source )
-        {
-            if $(pyversion) >= 3.0
-            {
-                local a = [ new action $(source) : python.py2to3 : $(property-set) ] ;
-                local t =  [ utility.basename [ $(s).name ] ] ;
-                local p = [ new file-target $(t) : PY : $(project) : $(a) ] ;
-                return $(p) ;
-            }
-            else
-            {
-                return $(source) ;
-            }
-        }
-
-        for local s in $(sources)
-        {
-            if [ $(s).type ] = PY
-            {
-                if ! $(python)
-                {
-                    # First Python source ends up on command line.
-                    python = [ make-2to3-source $(s) ] ;
-
-                }
-                else
-                {
-                    # Other Python sources become dependencies.
-                    other-pythons += [ make-2to3-source $(s) ] ;
-                }
-            }
-        }
-
-        local extensions ;
-        for local s in $(sources)
-        {
-            if [ $(s).type ] = PYTHON_EXTENSION
-            {
-                extensions += $(s) ;
-            }
-        }
-
-        local libs ;
-        for local s in $(sources)
-        {
-            if [ type.is-derived [ $(s).type ] LIB ]
-              && ! $(s) in $(extensions)
-            {
-                libs += $(s) ;
-            }
-        }
-
-        local new-sources ;
-        for local s in $(sources)
-        {
-            if [ type.is-derived [ $(s).type ] CPP ]
-            {
-                local name = [ utility.basename [ $(s).name ] ] ;
-                if $(name) = [ utility.basename [ $(python).name ] ]
-                {
-                    name = $(name)_ext ;
-                }
-                local extension = [ generators.construct $(project) $(name) :
-                  PYTHON_EXTENSION : $(property-set) : $(s) $(libs) ] ;
-
-                # The important part of usage requirements returned from
-                # PYTHON_EXTENSION generator are xdll-path properties that will
-                # allow us to find the python extension at runtime.
-                property-set = [ $(property-set).add $(extension[1]) ] ;
-
-                # Ignore usage requirements. We're a top-level generator and
-                # nobody is going to use what we generate.
-                new-sources += $(extension[2-]) ;
-            }
-        }
-
-        property-set = [ $(property-set).add-raw <dependency>$(other-pythons) ] ;
-
-        result = [ construct-result $(python) $(extensions) $(new-sources) :
-            $(project) $(name) : $(property-set) ] ;
-    }
-}
-
-
-generators.register
-  [ new python-test-generator python.capture-output : : RUN_PYD_OUTPUT ] ;
-
-generators.register-standard testing.expect-success
-  : RUN_PYD_OUTPUT : RUN_PYD ;
-
-
-# There are two different ways of spelling OS names. One is used for [ os.name ]
-# and the other is used for the <host-os> and <target-os> properties. Until that
-# is remedied, this sets up a crude mapping from the latter to the former, that
-# will work *for the purposes of cygwin/NT cross-builds only*. Could not think
-# of a better name than "translate".
-#
-.translate-os-windows = NT ;
-.translate-os-cygwin = CYGWIN ;
-local rule translate-os ( src-os )
-{
-    local x = $(.translate-os-$(src-os)) [ os.name ] ;
-    return $(x[1]) ;
-}
-
-
-# Extract the path to a single ".pyd" source. This is used to build the
-# PYTHONPATH for running bpl tests.
-#
-local rule pyd-pythonpath ( source )
-{
-    return [ on $(source) return $(LOCATE) $(SEARCH) ] ;
-}
-
-
-# The flag settings on testing.capture-output do not apply to python.capture
-# output at the moment. Redo this explicitly.
-toolset.flags python.capture-output ARGS <testing.arg> ;
-
-
-rule capture-output ( target : sources * : properties * )
-{
-    # Setup up a proper DLL search path. Here, $(sources[1]) is a python module
-    # and $(sources[2]) is a DLL. Only $(sources[1]) is passed to
-    # testing.capture-output, so RUN_PATH variable on $(sources[2]) is not
-    # consulted. Move it over explicitly.
-    RUN_PATH on $(sources[1]) = [ on $(sources[2-]) return $(RUN_PATH) ] ;
-
-    PYTHONPATH  = [ sequence.transform pyd-pythonpath : $(sources[2-]) ] ;
-    PYTHONPATH += [ feature.get-values pythonpath : $(properties) ] ;
-
-    # After test is run, we remove the Python module, but not the Python script.
-    testing.capture-output $(target) : $(sources[1]) : $(properties) :
-        $(sources[2-]) ;
-
-    # PYTHONPATH is different; it will be interpreted by whichever Python is
-    # invoked and so must follow path rules for the target os. The only OSes
-    # where we can run python for other OSes currently are NT and CYGWIN so we
-    # only need to handle those cases.
-    local target-os = [ feature.get-values target-os : $(properties) ] ;
-    # Oddly, host-os is not in properties, so grab the default value.
-    local host-os = [ feature.defaults host-os ] ;
-    host-os = $(host-os:G=) ;
-    if $(target-os) != $(host-os)
-    {
-        PYTHONPATH = [ sequence.transform $(host-os)-to-$(target-os)-path :
-            $(PYTHONPATH) ] ;
-    }
-    local path-separator = [ os.path-separator [ translate-os $(target-os) ] ] ;
-    local set-PYTHONPATH = [ common.variable-setting-command PYTHONPATH :
-        $(PYTHONPATH:J=$(path-separator)) ] ;
-    LAUNCHER on $(target) = $(set-PYTHONPATH) [ on $(target) return \"$(PYTHON)\" ] ;
-}
-
-
-rule bpl-test ( name : sources * : requirements * )
-{
-    local s ;
-    sources ?= $(name).py $(name).cpp ;
-    return [ testing.make-test run-pyd : $(sources) /boost/python//boost_python
-        : $(requirements) : $(name) ] ;
-}
-
-
-IMPORT $(__name__) : bpl-test : : bpl-test ;
diff --git a/jam-files/boost-build/tools/qcc.jam b/jam-files/boost-build/tools/qcc.jam
deleted file mode 100644
index 4f2a4fc1..00000000
--- a/jam-files/boost-build/tools/qcc.jam
+++ /dev/null
@@ -1,236 +0,0 @@
-#  Copyright (c) 2001 David Abrahams.
-#  Copyright (c) 2002-2003 Rene Rivera.
-#  Copyright (c) 2002-2003 Vladimir Prus.
-#
-#  Use, modification and distribution is subject to the Boost Software
-#  License Version 1.0. (See accompanying file LICENSE_1_0.txt or
-#  http://www.boost.org/LICENSE_1_0.txt)
-
-import "class" : new ;
-import common ;
-import errors ;
-import feature ;
-import generators ;
-import os ;
-import property ;
-import set ;
-import toolset ;
-import type ;
-import unix ;
-
-feature.extend toolset : qcc ;
-
-toolset.inherit-generators qcc : unix : unix.link unix.link.dll ;
-generators.override builtin.lib-generator : qcc.prebuilt ;
-toolset.inherit-flags qcc : unix ;
-toolset.inherit-rules qcc : unix ;
-
-# Initializes the qcc toolset for the given version. If necessary, command may
-# be used to specify where the compiler is located. The parameter 'options' is a
-# space-delimited list of options, each one being specified as
-# <option-name>option-value. Valid option names are: cxxflags, linkflags and
-# linker-type. Accepted values for linker-type are gnu and sun, gnu being the
-# default.
-#
-# Example:
-#   using qcc : 3.4 : : <cxxflags>foo <linkflags>bar <linker-type>sun ;
-#
-rule init ( version ? : command * : options * )
-{
-    local condition = [ common.check-init-parameters qcc : version $(version) ] ;
-    local command = [ common.get-invocation-command qcc : QCC : $(command) ] ;
-    common.handle-options qcc : $(condition) : $(command) : $(options) ;
-}
-
-
-generators.register-c-compiler qcc.compile.c++ : CPP : OBJ : <toolset>qcc ;
-generators.register-c-compiler qcc.compile.c   : C   : OBJ : <toolset>qcc ;
-generators.register-c-compiler qcc.compile.asm : ASM : OBJ : <toolset>qcc ;
-
-
-# Declare flags for compilation.
-toolset.flags qcc.compile OPTIONS <debug-symbols>on : -gstabs+ ;
-
-# Declare flags and action for compilation.
-toolset.flags qcc.compile OPTIONS <optimization>off : -O0 ;
-toolset.flags qcc.compile OPTIONS <optimization>speed : -O3 ;
-toolset.flags qcc.compile OPTIONS <optimization>space : -Os ;
-
-toolset.flags qcc.compile OPTIONS <inlining>off : -Wc,-fno-inline ;
-toolset.flags qcc.compile OPTIONS <inlining>on : -Wc,-Wno-inline ;
-toolset.flags qcc.compile OPTIONS <inlining>full : -Wc,-finline-functions -Wc,-Wno-inline ;
-
-toolset.flags qcc.compile OPTIONS <warnings>off : -w ;
-toolset.flags qcc.compile OPTIONS <warnings>all : -Wc,-Wall ;
-toolset.flags qcc.compile OPTIONS <warnings-as-errors>on : -Wc,-Werror ;
-
-toolset.flags qcc.compile OPTIONS <profiling>on : -p ;
-
-toolset.flags qcc.compile OPTIONS <cflags> ;
-toolset.flags qcc.compile.c++ OPTIONS <cxxflags> ;
-toolset.flags qcc.compile DEFINES <define> ;
-toolset.flags qcc.compile INCLUDES <include> ;
-
-toolset.flags qcc.compile OPTIONS <link>shared : -shared ;
-
-toolset.flags qcc.compile.c++ TEMPLATE_DEPTH <c++-template-depth> ;
-
-
-rule compile.c++
-{
-    # Here we want to raise the template-depth parameter value to something
-    # higher than the default value of 17. Note that we could do this using the
-    # feature.set-default rule but we do not want to set the default value for
-    # all toolsets as well.
-    #
-    # TODO: This 'modified default' has been inherited from some 'older Boost
-    # Build implementation' and has most likely been added to make some Boost
-    # library parts compile correctly. We should see what exactly prompted this
-    # and whether we can get around the problem more locally.
-    local template-depth = [ on $(1) return $(TEMPLATE_DEPTH) ] ;
-    if ! $(template-depth)
-    {
-        TEMPLATE_DEPTH on $(1) = 128 ;
-    }
-}
-
-actions compile.c++
-{
-    "$(CONFIG_COMMAND)" -Wc,-ftemplate-depth-$(TEMPLATE_DEPTH) $(OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -c -o "$(<)" "$(>)"
-}
-
-actions compile.c
-{
-    "$(CONFIG_COMMAND)" $(OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -c -o "$(<)" "$(>)"
-}
-
-actions compile.asm
-{
-    "$(CONFIG_COMMAND)" $(OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -c -o "$(<)" "$(>)"
-}
-
-
-# The class checking that we do not try to use the <runtime-link>static property
-# while creating or using a shared library, since it is not supported by qcc/
-# /libc.
-#
-class qcc-linking-generator : unix-linking-generator
-{
-    rule generated-targets ( sources + : property-set : project name ? )
-    {
-        if <runtime-link>static in [ $(property-set).raw ]
-        {
-            local m ;
-            if [ id ] = "qcc.link.dll"
-            {
-                m = "on qcc, DLL can't be build with <runtime-link>static" ;
-            }
-            if ! $(m)
-            {
-                for local s in $(sources)
-                {
-                    local type = [ $(s).type ] ;
-                    if $(type) && [ type.is-derived $(type) SHARED_LIB ]
-                    {
-                        m = "on qcc, using DLLS together with the <runtime-link>static options is not possible " ;
-                    }
-                }
-            }
-            if $(m)
-            {
-                errors.user-error $(m) : "It is suggested to use"
-                    "<runtime-link>static together with <link>static." ;
-            }
-        }
-
-        return [ unix-linking-generator.generated-targets
-            $(sources) : $(property-set) : $(project) $(name) ] ;
-    }
-}
-
-generators.register [ new qcc-linking-generator qcc.link : LIB OBJ : EXE
-    : <toolset>qcc ] ;
-
-generators.register [ new qcc-linking-generator qcc.link.dll : LIB OBJ
-    : SHARED_LIB : <toolset>qcc ] ;
-
-generators.override qcc.prebuilt : builtin.prebuilt ;
-generators.override qcc.searched-lib-generator : searched-lib-generator ;
-
-
-# Declare flags for linking.
-# First, the common flags.
-toolset.flags qcc.link OPTIONS <debug-symbols>on : -gstabs+ ;
-toolset.flags qcc.link OPTIONS <profiling>on : -p ;
-toolset.flags qcc.link OPTIONS <linkflags> ;
-toolset.flags qcc.link LINKPATH <library-path> ;
-toolset.flags qcc.link FINDLIBS-ST <find-static-library> ;
-toolset.flags qcc.link FINDLIBS-SA <find-shared-library> ;
-toolset.flags qcc.link LIBRARIES <library-file> ;
-
-toolset.flags qcc.link FINDLIBS-SA : m ;
-
-# For <runtime-link>static we made sure there are no dynamic libraries in the
-# link.
-toolset.flags qcc.link OPTIONS <runtime-link>static : -static ;
-
-# Assuming this is just like with gcc.
-toolset.flags qcc.link RPATH : <dll-path> : unchecked ;
-toolset.flags qcc.link RPATH_LINK : <xdll-path> : unchecked ;
-
-
-# Declare actions for linking.
-#
-rule link ( targets * : sources * : properties * )
-{
-    SPACE on $(targets) = " " ;
-    # Serialize execution of the 'link' action, since running N links in
-    # parallel is just slower. For now, serialize only qcc links while it might
-    # be a good idea to serialize all links.
-    JAM_SEMAPHORE on $(targets) = <s>qcc-link-semaphore ;
-}
-
-actions link bind LIBRARIES
-{
-    "$(CONFIG_COMMAND)" -L"$(LINKPATH)" -Wl,-R$(SPACE)-Wl,"$(RPATH)" -Wl,-rpath-link$(SPACE)-Wl,"$(RPATH_LINK)" -o "$(<)" "$(>)" "$(LIBRARIES)" -l$(FINDLIBS-ST) -l$(FINDLIBS-SA) $(OPTIONS)
-}
-
-
-# Always remove archive and start again. Here is the rationale from Andre Hentz:
-# I had a file, say a1.c, that was included into liba.a. I moved a1.c to a2.c,
-# updated my Jamfiles and rebuilt. My program was crashing with absurd errors.
-# After some debugging I traced it back to the fact that a1.o was *still* in
-# liba.a
-RM = [ common.rm-command ] ;
-if [ os.name ] = NT
-{
-    RM = "if exist \"$(<[1])\" DEL \"$(<[1])\""  ;
-}
-
-
-# Declare action for creating static libraries. The 'r' letter means to add
-# files to the archive with replacement. Since we remove the archive, we do not
-# care about replacement, but there is no option to "add without replacement".
-# The 'c' letter suppresses warnings in case the archive does not exists yet.
-# That warning is produced only on some platforms, for whatever reasons.
-#
-actions piecemeal archive
-{
-    $(RM) "$(<)"
-    ar rc "$(<)" "$(>)"
-}
-
-
-rule link.dll ( targets * : sources * : properties * )
-{
-    SPACE on $(targets) = " " ;
-    JAM_SEMAPHORE on $(targets) = <s>qcc-link-semaphore ;
-}
-
-
-# Differ from 'link' above only by -shared.
-#
-actions link.dll bind LIBRARIES
-{
-    "$(CONFIG_COMMAND)" -L"$(LINKPATH)" -Wl,-R$(SPACE)-Wl,"$(RPATH)" -o "$(<)" $(HAVE_SONAME)-Wl,-h$(SPACE)-Wl,$(<[1]:D=) -shared "$(>)"  "$(LIBRARIES)" -l$(FINDLIBS-ST) -l$(FINDLIBS-SA) $(OPTIONS)
-}
diff --git a/jam-files/boost-build/tools/qt.jam b/jam-files/boost-build/tools/qt.jam
deleted file mode 100644
index 8aa7ca26..00000000
--- a/jam-files/boost-build/tools/qt.jam
+++ /dev/null
@@ -1,17 +0,0 @@
-#  Copyright (c) 2006 Vladimir Prus.
-#
-#  Use, modification and distribution is subject to the Boost Software
-#  License Version 1.0. (See accompanying file LICENSE_1_0.txt or
-#  http://www.boost.org/LICENSE_1_0.txt)
-
-#  Forwarning toolset file to Qt GUI library. Forwards to the toolset file
-#  for the current version of Qt.
-
-import qt4 ;
-
-rule init ( prefix : full_bin ? : full_inc ? : full_lib ? : version ? : condition * )
-{
-    qt4.init $(prefix) : $(full_bin)  : $(full_inc) : $(full_lib) : $(version) : $(condition) ;
-}
-
-
diff --git a/jam-files/boost-build/tools/qt3.jam b/jam-files/boost-build/tools/qt3.jam
deleted file mode 100644
index f82cf0ac..00000000
--- a/jam-files/boost-build/tools/qt3.jam
+++ /dev/null
@@ -1,209 +0,0 @@
-# Copyright 2006 Vladimir Prus 
-# Distributed under the Boost Software License, Version 1.0. 
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt) 
-
-# Support for the Qt GUI library version 3
-# (http://www.trolltech.com/products/qt3/index.html).
-# For new developments, it is recommended to use Qt4 via the qt4 Boost.Build
-# module.
-
-import modules ;
-import feature ;
-import errors ;
-import type ;
-import "class" : new ;
-import generators ;
-import project ;
-import toolset : flags ;
-
-# Convert this module into a project, so that we can declare targets here.
-project.initialize $(__name__) ;
-project qt3 ;
-
-
-# Initialized the QT support module. The 'prefix' parameter tells where QT is
-# installed. When not given, environmental variable QTDIR should be set.
-#
-rule init ( prefix ? )
-{
-    if ! $(prefix)
-    {
-        prefix = [ modules.peek : QTDIR ] ;
-        if ! $(prefix) 
-        {
-            errors.error 
-              "QT installation prefix not given and QTDIR variable is empty" ;
-        }        
-    }
- 
-    if $(.initialized)
-    {
-        if $(prefix) != $(.prefix)
-        {
-            errors.error 
-              "Attempt the reinitialize QT with different installation prefix" ;
-        }        
-    } 
-    else
-    {            
-        .initialized = true ;
-        .prefix = $(prefix) ;
-        
-        generators.register-standard qt3.moc : H : CPP(moc_%) : <allow>qt3 ;
-        # Note: the OBJ target type here is fake, take a look at
-        # qt4.jam/uic-h-generator for explanations that apply in this case as
-        # well.
-        generators.register [ new moc-h-generator-qt3 
-            qt3.moc.cpp : MOCCABLE_CPP : OBJ : <allow>qt3 ] ;
-        
-        # The UI type is defined in types/qt.jam, and UIC_H is only used in
-        # qt.jam, but not in qt4.jam, so define it here.
-        type.register UIC_H : : H ;
-        
-        generators.register-standard qt3.uic-h : UI : UIC_H : <allow>qt3 ;
-        
-        # The following generator is used to convert UI files to CPP. It creates
-        # UIC_H from UI, and constructs CPP from UI/UIC_H. In addition, it also
-        # returns UIC_H target, so that it can be mocced.
-        class qt::uic-cpp-generator : generator
-        {
-            rule __init__ ( )
-            {
-                generator.__init__ qt3.uic-cpp : UI UIC_H : CPP : <allow>qt3 ;
-            }
-                        
-            rule run ( project name ? : properties * : sources + )
-            {
-                # Consider this:
-                #    obj test : test_a.cpp : <optimization>off ;
-                #
-                # This generator will somehow be called in this case, and,
-                # will fail -- which is okay. However, if there are <library>
-                # properties they will be converted to sources, so the size of 
-                # 'sources' will be more than 1. In this case, the base generator
-                # will just crash -- and that's not good. Just use a quick test
-                # here.
-                                
-                local result ;
-                if ! $(sources[2])
-                {    
-                    # Construct CPP as usual
-                    result = [ generator.run $(project) $(name) 
-                      : $(properties) : $(sources) ] ;
-                    
-                    # If OK, process UIC_H with moc. It's pretty clear that
-                    # the object generated with UIC will have Q_OBJECT macro.
-                    if $(result)
-                    {
-                        local action = [ $(result[1]).action ] ;
-                        local sources = [ $(action).sources ] ;
-                        local mocced = [ generators.construct $(project) $(name)
-                          : CPP : $(properties) : $(sources[2]) ] ;
-                        result += $(mocced[2-]) ;
-                    }
-                }
-                            
-                return $(result) ;
-            }               
-        }
-    
-        generators.register [ new qt::uic-cpp-generator ] ;
-        
-        # Finally, declare prebuilt target for QT library.
-        local usage-requirements = 
-             <include>$(.prefix)/include 
-             <dll-path>$(.prefix)/lib
-             <library-path>$(.prefix)/lib     
-             <allow>qt3
-             ;  
-        lib qt : : <name>qt-mt <threading>multi : : $(usage-requirements) ;
-        lib qt : : <name>qt <threading>single : : $(usage-requirements) ;        
-    }
-}
-
-class moc-h-generator-qt3 : generator
-{
-    rule __init__ ( * : * )
-    {
-        generator.__init__ $(1) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ;
-    }
-
-    rule run ( project name ? : property-set : sources * )
-    {       
-        if ! $(sources[2]) && [ $(sources[1]).type ] = MOCCABLE_CPP
-        {                              
-            name = [ $(sources[1]).name ] ;
-            name = $(name:B) ;
-            
-            local a = [ new action $(sources[1]) : qt3.moc.cpp :
-              $(property-set) ] ;
-            
-            local target = [ 
-              new file-target $(name) : MOC : $(project) : $(a) ] ;
-            
-            local r = [ virtual-target.register $(target) ] ; 
-                                  
-            # Since this generator will return a H target, the linking generator
-            # won't use it at all, and won't set any dependency on it. However, 
-            # we need the target to be seen by bjam, so that the dependency from
-            # sources to this generated header is detected -- if Jam does not
-            # know about this target, it won't do anything.
-            DEPENDS all : [ $(r).actualize ] ;
-            
-            return $(r) ;            
-        }        
-    }    
-}
-
-
-# Query the installation directory. This is needed in at least two scenarios.
-# First, when re-using sources from the Qt-Tree. Second, to "install" custom Qt
-# plugins to the Qt-Tree.
-#
-rule directory 
-{ 
-    return $(.prefix) ; 
-} 
-
-# -f forces moc to include the processed source file. Without it, it would think
-# that .qpp is not a header and would not include it from the generated file.
-#
-actions moc 
-{
-    $(.prefix)/bin/moc -f $(>) -o $(<)
-}
-
-# When moccing .cpp files, we don't need -f, otherwise generated code will
-# include .cpp and we'll get duplicated symbols.
-#
-actions moc.cpp
-{
-    $(.prefix)/bin/moc $(>) -o $(<)
-}
-
-
-space = " " ;
-
-# Sometimes it's required to make 'plugins' available during uic invocation. To
-# help with this we add paths to all dependency libraries to uic commane line.
-# The intention is that it's possible to write
-#    
-#     exe a : ... a.ui ... : <uses>some_plugin ; 
-# 
-# and have everything work. We'd add quite a bunch of unrelated paths but it
-# won't hurt.
-#
-flags qt3.uic-h LIBRARY_PATH <xdll-path> ;
-actions uic-h
-{
-    $(.prefix)/bin/uic $(>) -o $(<) -L$(space)$(LIBRARY_PATH)
-}
-
-
-flags qt3.uic-cpp LIBRARY_PATH <xdll-path> ;
-# The second target is uic-generated header name. It's placed in build dir, but
-# we want to include it using only basename.
-actions uic-cpp
-{
-    $(.prefix)/bin/uic $(>[1]) -i $(>[2]:D=) -o $(<) -L$(space)$(LIBRARY_PATH)
-}
diff --git a/jam-files/boost-build/tools/qt4.jam b/jam-files/boost-build/tools/qt4.jam
deleted file mode 100644
index 71d1b762..00000000
--- a/jam-files/boost-build/tools/qt4.jam
+++ /dev/null
@@ -1,724 +0,0 @@
-# Copyright 2002-2006 Vladimir Prus
-# Copyright 2005 Alo Sarv
-# Copyright 2005-2009 Juergen Hunold
-#
-# Distributed under the Boost Software License, Version 1.0. (See
-# accompanying file LICENSE_1_0.txt or copy at
-# http://www.boost.org/LICENSE_1_0.txt)
-
-# Qt4 library support module
-#
-# The module attempts to auto-detect QT installation location from QTDIR
-# environment variable; failing that, installation location can be passed as
-# argument:
-#
-# toolset.using qt4 : /usr/local/Trolltech/Qt-4.0.0 ;
-#
-# The module supports code generation from .ui and .qrc files, as well as
-# running the moc preprocessor on headers. Note that you must list all your
-# moc-able headers in sources.
-#
-# Example:
-#
-#     exe myapp : myapp.cpp myapp.h myapp.ui myapp.qrc
-#                 /qt4//QtGui /qt4//QtNetwork ;
-#
-# It's also possible to run moc on cpp sources:
-#
-#   import cast ;
-#
-#   exe myapp : myapp.cpp [ cast _ moccable-cpp : myapp.cpp ] /qt4//QtGui ;
-#
-# When moccing source file myapp.cpp you need to include "myapp.moc" from
-# myapp.cpp. When moccing .h files, the output of moc will be automatically
-# compiled and linked in, you don't need any includes.
-#
-# This is consistent with Qt guidelines:
-# http://doc.trolltech.com/4.0/moc.html
-
-import modules ;
-import feature ;
-import errors ;
-import type ;
-import "class" : new ;
-import generators ;
-import project ;
-import toolset : flags ;
-import os ;
-import virtual-target ;
-import scanner ;
-
-# Qt3Support control feature
-#
-# Qt4 configure defaults to build Qt4 libraries with Qt3Support.
-# The autodetection is missing, so we default to disable Qt3Support.
-# This prevents the user from inadvertedly using a deprecated API.
-#
-# The Qt3Support library can be activated by adding
-# "<qt3support>on" to requirements
-#
-# Use "<qt3support>on:<define>QT3_SUPPORT_WARNINGS"
-# to get warnings about deprecated Qt3 support funtions and classes.
-# Files ported by the "qt3to4" conversion tool contain _tons_ of
-# warnings, so this define is not set as default.
-#
-# Todo: Detect Qt3Support from Qt's configure data.
-#       Or add more auto-configuration (like python).
-feature.feature qt3support : off on : propagated link-incompatible ;
-
-# The Qt version used for requirements
-# Valid are <qt>4.4 or <qt>4.5.0
-# Auto-detection via qmake sets '<qt>major.minor.patch'
-feature.feature qt : : propagated ;
-
-project.initialize $(__name__) ;
-project qt ;
-
-# Save the project so that we tolerate 'import + using' combo.
-.project = [ project.current ] ;
-
-# Helper utils for easy debug output
-if [ MATCH (--debug-configuration) : [ modules.peek : ARGV ] ]
-{
-    .debug-configuration = TRUE ;
-}
-
-local rule debug-message ( message * )
-{
-    if $(.debug-configuration) = TRUE
-    {
-        ECHO notice: [qt4-cfg] $(message) ;
-    }
-}
-
-# Capture qmake output line by line
-local rule read-output ( content )
-{
-    local lines ;
-    local nl = "
-" ;
-    local << = "([^$(nl)]*)[$(nl)](.*)" ;
-    local line+ = [ MATCH "$(<<)" : "$(content)" ] ;
-    while $(line+)
-    {
-        lines += $(line+[1]) ;
-        line+ = [ MATCH "$(<<)" : "$(line+[2])" ] ;
-    }
-    return $(lines) ;
-}
-
-# Capture Qt version from qmake
-local rule check-version ( bin_prefix )
-{
-    full-cmd = $(bin_prefix)"/qmake -v" ;
-    debug-message Running '$(full-cmd)' ;
-    local output = [ SHELL $(full-cmd) ] ;
-    for line in [ read-output $(output) ]
-    {
-        # Parse the output to get all the results.
-        if [ MATCH "QMake" : $(line) ]
-        {
-            # Skip first line of output
-        }
-        else
-        {
-            temp = [ MATCH "([0-9]*)\\.([0-9]*)\\.([0-9]*)" : $(line) ] ;
-        }
-    }
-    return $(temp) ;
-}
-
-# Validate the version string and extract the major/minor part we care about.
-#
-local rule split-version ( version )
-{
-    local major-minor = [ MATCH ^([0-9]+)\.([0-9]+)(.*)$ : $(version) : 1 2 3 ] ;
-    if ! $(major-minor[2]) || $(major-minor[3])
-    {
-        ECHO "Warning: 'using qt' expects a two part (major, minor) version number; got" $(version) instead ;
-
-        # Add a zero to account for the missing digit if necessary.
-        major-minor += 0 ;
-    }
-
-    return $(major-minor[1]) $(major-minor[2]) ;
-}
-
-# Initialize the QT support module.
-# Parameters:
-# - 'prefix'    parameter tells where Qt is installed.
-# - 'full_bin'  optional full path to Qt binaries (qmake,moc,uic,rcc)
-# - 'full_inc'  optional full path to Qt top-level include directory
-# - 'full_lib'  optional full path to Qt library directory
-# - 'version'   optional version of Qt, else autodetected via 'qmake -v'
-# - 'condition' optional requirements
-rule init ( prefix : full_bin ? : full_inc ? : full_lib ? : version ? : condition * )
-{
-    project.push-current $(.project) ;
-
-    debug-message "==== Configuring Qt ... ====" ;
-    for local v in version cmd-or-prefix includes libraries condition
-    {
-        if $($(v))
-        {
-            debug-message "  user-specified "$(v): '$($(v))' ;
-        }
-    }
-
-    # Needed as default value
-    .prefix = $(prefix) ;
-
-    # pre-build paths to detect reinitializations changes
-    local inc_prefix lib_prefix bin_prefix ;
-    if $(full_inc)
-    {
-        inc_prefix = $(full_inc) ;
-    }
-    else
-    {
-        inc_prefix = $(prefix)/include ;
-    }
-    if $(full_lib)
-    {
-        lib_prefix = $(full_lib) ;
-    }
-    else
-    {
-        lib_prefix = $(prefix)/lib ;
-    }
-    if $(full_bin)
-    {
-        bin_prefix = $(full_bin) ;
-    }
-    else
-    {
-        bin_prefix = $(prefix)/bin ;
-    }
-
-    # Globally needed variables
-    .incprefix = $(inc_prefix) ;
-    .libprefix = $(lib_prefix) ;
-    .binprefix = $(bin_prefix) ;
-
-    if ! $(.initialized)
-    {
-        # Make sure this is initialised only once
-        .initialized = true ;
-
-        # Generates cpp files from header files using "moc" tool
-        generators.register-standard qt4.moc : H : CPP(moc_%) : <allow>qt4 ;
-
-        # The OBJ result type is a fake, 'H' will be really produced. See
-        # comments on the generator class, defined below the 'init' function.
-        generators.register [ new uic-generator qt4.uic : UI : OBJ :
-            <allow>qt4  ] ;
-
-        # The OBJ result type is a fake here too.
-        generators.register [ new moc-h-generator
-            qt4.moc.inc : MOCCABLE_CPP : OBJ : <allow>qt4 ] ;
-
-        generators.register [ new moc-inc-generator
-            qt4.moc.inc : MOCCABLE_H : OBJ : <allow>qt4 ] ;
-
-        # Generates .cpp files from .qrc files.
-        generators.register-standard qt4.rcc : QRC : CPP(qrc_%) ;
-
-        # dependency scanner for wrapped files.
-        type.set-scanner QRC : qrc-scanner ;
-
-        # Save value of first occuring prefix
-        .PREFIX = $(prefix) ;
-    }
-
-    if $(version)
-    {
-        major-minor = [ split-version $(version) ] ;
-        version = $(major-minor:J=.) ;
-    }
-    else
-    {
-        version = [ check-version $(bin_prefix) ] ;
-        if $(version)
-        {
-            version = $(version:J=.) ;
-        }
-        debug-message Detected version '$(version)' ;
-    }
-
-    local target-requirements = $(condition) ;
-
-    # Add the version, if any, to the target requirements.
-    if $(version)
-    {
-        if ! $(version) in [ feature.values qt ]
-        {
-            feature.extend qt : $(version) ;
-        }
-        target-requirements += <qt>$(version:E=default) ;
-    }
-
-    local target-os = [ feature.get-values target-os : $(condition) ] ;
-    if ! $(target-os)
-    {
-        target-os ?= [ feature.defaults target-os ] ;
-        target-os = $(target-os:G=) ;
-        target-requirements += <target-os>$(target-os) ;
-    }
-
-    # Build exact requirements for the tools
-    local tools-requirements = $(target-requirements:J=/) ;
-
-    debug-message "Details of this Qt configuration:" ;
-    debug-message "  prefix:      " '$(prefix:E=<empty>)' ;
-    debug-message "  binary path: " '$(bin_prefix:E=<empty>)' ;
-    debug-message "  include path:" '$(inc_prefix:E=<empty>)' ;
-    debug-message "  library path:" '$(lib_prefix:E=<empty>)' ;
-    debug-message "  target requirements:" '$(target-requirements)' ;
-    debug-message "  tool requirements:  " '$(tools-requirements)' ;
-
-    # setup the paths for the tools
-    toolset.flags qt4.moc .BINPREFIX $(tools-requirements) : $(bin_prefix) ;
-    toolset.flags qt4.rcc .BINPREFIX $(tools-requirements) : $(bin_prefix) ;
-    toolset.flags qt4.uic .BINPREFIX $(tools-requirements) : $(bin_prefix) ;
-
-    # TODO: 2009-02-12: Better support for directories
-    # Most likely needed are separate getters for: include,libraries,binaries and sources.
-    toolset.flags qt4.directory .PREFIX $(tools-requirements) : $(prefix) ;
-
-    # Test for a buildable Qt.
-    if [ glob $(.prefix)/Jamroot ]
-    {
-       .bjam-qt = true
-
-       # this will declare QtCore (and qtmain on <target-os>windows)
-       add-shared-library QtCore ;
-   }
-   else
-   # Setup common pre-built Qt.
-   # Special setup for QtCore on which everything depends
-   {
-       local usage-requirements =
-           <include>$(.incprefix)
-           <library-path>$(.libprefix)
-           <dll-path>$(.libprefix)
-           <threading>multi
-           <allow>qt4 ;
-
-       local suffix ;
-
-       # Since Qt-4.2, debug versions on unix have to be built
-       # separately and therefore have no suffix.
-       .suffix_version = "" ;
-       .suffix_debug = "" ;
-
-       # Control flag for auto-configuration of the debug libraries.
-       # This setup requires Qt 'configure -debug-and-release'.
-       # Only available on some platforms.
-       # ToDo: 2009-02-12: Maybe throw this away and
-       # require separate setup with <variant>debug as condition.
-       .have_separate_debug = FALSE ;
-
-       # Setup other platforms
-       if $(target-os) in windows cygwin
-       {
-           .have_separate_debug = TRUE ;
-
-           # On NT, the libs have "4" suffix, and "d" suffix in debug builds.
-           .suffix_version = "4" ;
-           .suffix_debug = "d" ;
-
-           # On Windows we must link against the qtmain library
-           lib qtmain
-               : # sources
-               : # requirements
-                  <name>qtmain$(.suffix_debug)
-                  <variant>debug
-                  $(target-requirements)
-               ;
-
-           lib qtmain
-               : # sources
-               : # requirements
-                   <name>qtmain
-                   $(target-requirements)
-               ;
-       }
-       else if $(target-os) = darwin
-       {
-           # On MacOS X, both debug and release libraries are available.
-           .suffix_debug = "_debug" ;
-
-           .have_separate_debug = TRUE ;
-
-           alias qtmain ;
-       }
-       else
-       {
-           alias qtmain : : $(target-requirements) ;
-       }
-
-       lib QtCore : qtmain
-           : # requirements
-             <name>QtCore$(.suffix_version)
-             $(target-requirements)
-           : # default-build
-           : # usage-requirements
-             <define>QT_CORE_LIB
-             <define>QT_NO_DEBUG
-             <include>$(.incprefix)/QtCore
-             $(usage-requirements)
-           ;
-
-       if $(.have_separate_debug) = TRUE
-       {
-           debug-message Configure debug libraries with suffix '$(.suffix_debug)' ;
-
-           lib QtCore : $(main)
-               : # requirements
-                 <name>QtCore$(.suffix_debug)$(.suffix_version)
-                 <variant>debug
-                 $(target-requirements)
-               : # default-build
-               : # usage-requirements
-                 <define>QT_CORE_LIB
-                 <include>$(.incprefix)/QtCore
-                 $(usage-requirements)
-               ;
-        }
-    }
-
-    # Initialising the remaining libraries is canonical
-    # parameters 'module' : 'depends-on' : 'usage-define' : 'requirements' : 'include'
-    # 'include' only for non-canonical include paths.
-    add-shared-library QtGui     : QtCore : QT_GUI_LIB     : $(target-requirements) ;
-    add-shared-library QtNetwork : QtCore : QT_NETWORK_LIB : $(target-requirements) ;
-    add-shared-library QtSql     : QtCore : QT_SQL_LIB     : $(target-requirements) ;
-    add-shared-library QtXml     : QtCore : QT_XML_LIB     : $(target-requirements) ;
-
-    add-shared-library Qt3Support : QtGui QtNetwork QtXml QtSql
-                                  : QT_QT3SUPPORT_LIB QT3_SUPPORT
-                                  : <qt3support>on $(target-requirements) ;
-
-    # Dummy target to enable "<qt3support>off" and
-    # "<library>/qt//Qt3Support" at the same time. This enables quick
-    # switching from one to the other for test/porting purposes.
-    alias Qt3Support : : <qt3support>off $(target-requirements) ;
-
-    # OpenGl Support
-    add-shared-library QtOpenGL : QtGui : QT_OPENGL_LIB : $(target-requirements) ;
-
-    # SVG-Support (Qt 4.1)
-    add-shared-library QtSvg : QtXml QtOpenGL : QT_SVG_LIB : $(target-requirements) ;
-
-    # Test-Support (Qt 4.1)
-    add-shared-library QtTest : QtCore : : $(target-requirements) ;
-
-    # Qt designer library
-    add-shared-library QtDesigner : QtGui QtXml : : $(target-requirements) ;
-    add-shared-library QtDesignerComponents : QtGui QtXml : : $(target-requirements) ;
-
-    # Support for dynamic Widgets (Qt 4.1)
-    add-static-library  QtUiTools : QtGui QtXml : $(target-requirements) ;
-
-    # DBus-Support (Qt 4.2)
-    add-shared-library QtDBus : QtXml : : $(target-requirements) ;
-
-    # Script-Engine (Qt 4.3)
-    add-shared-library QtScript : QtGui QtXml : QT_SCRIPT_LIB : $(target-requirements) ;
-
-    # Tools for the Script-Engine (Qt 4.5)
-    add-shared-library QtScriptTools : QtScript : QT_SCRIPTTOOLS_LIB : $(target-requirements) ;
-
-    # WebKit (Qt 4.4)
-    add-shared-library QtWebKit : QtGui : QT_WEBKIT_LIB : $(target-requirements) ;
-
-    # Phonon Multimedia (Qt 4.4)
-    add-shared-library phonon : QtGui QtXml : QT_PHONON_LIB : $(target-requirements) ;
-
-    # Multimedia engine (Qt 4.6)
-    add-shared-library QtMultimedia : QtGui : QT_MULTIMEDIA_LIB : $(target-requirements) ;
-
-    # XmlPatterns-Engine (Qt 4.4)
-    add-shared-library QtXmlPatterns : QtNetwork : QT_XMLPATTERNS_LIB : $(target-requirements) ;
-
-    # Help-Engine (Qt 4.4)
-    add-shared-library QtHelp    : QtGui QtSql QtXml : : $(target-requirements) ;
-    add-shared-library QtCLucene : QCore QtSql QtXml : : $(target-requirements) ;
-
-    # QML-Engine (Qt 4.7)
-    add-shared-library QtDeclarative : QtGui QtXml : : $(target-requirements) ;
-
-    # AssistantClient Support
-    # Compat library removed in 4.7.0
-    # Pre-4.4 help system, use QtHelp for new programs
-    if $(version) < "4.7"
-    {
-       add-shared-library QtAssistantClient : QtGui : : $(target-requirements) : QtAssistant ;
-    }
-    debug-message "==== Configured Qt-$(version) ====" ;
-
-    project.pop-current ;
-}
-
-rule initialized ( )
-{
-    return $(.initialized) ;
-}
-
-
-
-# This custom generator is needed because in QT4, UI files are translated only
-# into H files, and no C++ files are created. Further, the H files need not be
-# passed via MOC. The header is used only via inclusion. If we define a standard
-# UI -> H generator, Boost.Build will run MOC on H, and then compile the
-# resulting cpp. It will give a warning, since output from moc will be empty.
-#
-# This generator is declared with a UI -> OBJ signature, so it gets invoked when
-# linking generator tries to convert sources to OBJ, but it produces target of
-# type H. This is non-standard, but allowed. That header won't be mocced.
-#
-class uic-generator : generator
-{
-    rule __init__ ( * : * )
-    {
-        generator.__init__ $(1) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ;
-    }
-
-    rule run ( project name ? : property-set : sources * )
-    {
-        if ! $(name)
-        {
-            name = [ $(sources[0]).name ] ;
-            name = $(name:B) ;
-        }
-
-        local a = [ new action $(sources[1]) : qt4.uic : $(property-set) ] ;
-
-        # The 'ui_' prefix is to match qmake's default behavior.
-        local target = [ new file-target ui_$(name) : H : $(project) : $(a) ] ;
-
-        local r = [ virtual-target.register $(target) ] ;
-
-        # Since this generator will return a H target, the linking generator
-        # won't use it at all, and won't set any dependency on it. However, we
-        # need the target to be seen by bjam, so that dependency from sources to
-        # this generated header is detected -- if jam does not know about this
-        # target, it won't do anything.
-        DEPENDS all : [ $(r).actualize ] ;
-
-        return $(r) ;
-    }
-}
-
-
-class moc-h-generator : generator
-{
-    rule __init__ ( * : * )
-    {
-        generator.__init__ $(1) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ;
-    }
-
-    rule run ( project name ? : property-set : sources * )
-    {
-        if ! $(sources[2]) && [ $(sources[1]).type ] = MOCCABLE_CPP
-        {
-            name = [ $(sources[0]).name ] ;
-            name = $(name:B) ;
-
-            local a = [ new action $(sources[1]) : qt4.moc.inc :
-                $(property-set) ] ;
-
-            local target = [ new file-target $(name) : MOC : $(project) : $(a)
-                ] ;
-
-            local r = [ virtual-target.register $(target) ] ;
-
-            # Since this generator will return a H target, the linking generator
-            # won't use it at all, and won't set any dependency on it. However,
-            # we need the target to be seen by bjam, so that dependency from
-            # sources to this generated header is detected -- if jam does not
-            # know about this target, it won't do anything.
-            DEPENDS all : [ $(r).actualize ] ;
-
-            return $(r) ;
-        }
-    }
-}
-
-
-class moc-inc-generator : generator
-{
-    rule __init__ ( * : * )
-    {
-        generator.__init__ $(1) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ;
-    }
-
-    rule run ( project name ? : property-set : sources * )
-    {
-        if ! $(sources[2]) && [ $(sources[1]).type ] = MOCCABLE_H
-        {
-            name = [ $(sources[0]).name ] ;
-            name = $(name:B) ;
-
-            local a = [ new action $(sources[1]) : qt4.moc.inc :
-                $(property-set) ] ;
-
-            local target = [ new file-target moc_$(name) : CPP : $(project) :
-                $(a) ] ;
-
-            # Since this generator will return a H target, the linking generator
-            # won't use it at all, and won't set any dependency on it. However,
-            # we need the target to be seen by bjam, so that dependency from
-            # sources to this generated header is detected -- if jam does not
-            # know about this target, it won't do anything.
-            DEPENDS all : [ $(target).actualize ] ;
-
-            return [ virtual-target.register $(target) ] ;
-        }
-    }
-}
-
-
-# Query the installation directory. This is needed in at least two scenarios.
-# First, when re-using sources from the Qt-Tree. Second, to "install" custom Qt
-# plugins to the Qt-Tree.
-#
-rule directory
-{
-    return $(.PREFIX) ;
-}
-
-# Add a shared Qt library.
-rule add-shared-library ( lib-name : depends-on * : usage-defines * : requirements * :  include ? )
-{
-     add-library $(lib-name) : $(.suffix_version) : $(depends-on) : $(usage-defines) : $(requirements) : $(include) ;
-}
-
-# Add a static Qt library.
-rule add-static-library ( lib-name : depends-on * : usage-defines * : requirements * : include ? )
-{
-     add-library $(lib-name) : : $(depends-on) : $(usage-defines) : $(requirements) : $(include) ;
-}
-
-# Add a Qt library.
-# Static libs are unversioned, whereas shared libs have the major number as suffix.
-# Creates both release and debug versions on platforms where both are enabled by Qt configure.
-# Flags:
-# - lib-name Qt library Name
-# - version  Qt major number used as shared library suffix (QtCore4.so)
-# - depends-on other Qt libraries
-# - usage-defines those are set by qmake, so set them when using this library
-# - requirements addional requirements
-# - include non-canonical include path. The canonical path is $(.incprefix)/$(lib-name).
-rule add-library ( lib-name : version ? : depends-on * : usage-defines * : requirements * : include ? )
-{
-    if $(.bjam-qt)
-    {
-        # Import Qt module
-        # Eveything will be setup there
-        alias $(lib-name)
-           : $(.prefix)//$(lib-name)
-           :
-           :
-           : <allow>qt4 ;
-    }
-    else
-    {
-        local real_include ;
-        real_include ?= $(include) ;
-        real_include ?= $(lib-name) ;
-
-        lib $(lib-name)
-           : # sources
-             $(depends-on)
-           : # requirements
-             <name>$(lib-name)$(version)
-             $(requirements)
-           : # default-build
-           : # usage-requirements
-             <define>$(usage-defines)
-             <include>$(.incprefix)/$(real_include)
-           ;
-
-        if $(.have_separate_debug) = TRUE
-        {
-            lib $(lib-name)
-               : # sources
-                 $(depends-on)
-               : # requirements
-                 <name>$(lib-name)$(.suffix_debug)$(version)
-                 $(requirements)
-                 <variant>debug
-               : # default-build
-               : # usage-requirements
-                 <define>$(usage-defines)
-                 <include>$(.incprefix)/$(real_include)
-               ;
-        }
-    }
-
-    # Make library explicit so that a simple <use>qt4 will not bring in everything.
-    # And some components like QtDBus/Phonon may not be available on all platforms.
-    explicit $(lib-name) ;
-}
-
-# Use $(.BINPREFIX[-1]) for the paths as several tools-requirements can match.
-# The exact match is the last one.
-
-# Get <include> and <defines> from current toolset.
-flags qt4.moc INCLUDES <include> ;
-flags qt4.moc DEFINES <define> ;
-
-# need a newline for expansion of DEFINES and INCLUDES in the response file.
-.nl  = "
-" ;
-
-# Processes headers to create Qt MetaObject information. Qt4-moc has its
-# c++-parser, so pass INCLUDES and DEFINES.
-# We use response file with one INCLUDE/DEFINE per line
-#
-actions moc
-{
-    $(.BINPREFIX[-1])/moc -f $(>) -o $(<) @"@($(<).rsp:E=-D$(DEFINES)$(.nl) -I$(INCLUDES:T)$(.nl))"
-}
-
-# When moccing files for include only, we don't need -f, otherwise the generated
-# code will include the .cpp and we'll get duplicated symbols.
-#
-actions moc.inc
-{
-    $(.BINPREFIX[-1])/moc $(>) -o $(<) @"@($(<).rsp:E=-D$(DEFINES)$(.nl) -I$(INCLUDES:T)$(.nl))"
-}
-
-
-# Generates source files from resource files.
-#
-actions rcc
-{
-    $(.BINPREFIX[-1])/rcc $(>) -name $(>:B) -o $(<)
-}
-
-
-# Generates user-interface source from .ui files.
-#
-actions uic
-{
-    $(.BINPREFIX[-1])/uic $(>) -o $(<)
-}
-
-
-# Scanner for .qrc files. Look for the CDATA section of the <file> tag. Ignore
-# the "alias" attribute. See http://doc.trolltech.com/qt/resources.html for
-# detailed documentation of the Qt Resource System.
-#
-class qrc-scanner : common-scanner
-{
-    rule pattern ( )
-    {
-        return "<file.*>(.*)</file>" ;
-    }
-}
-
-
-# Wrapped files are "included".
-scanner.register qrc-scanner : include ;
diff --git a/jam-files/boost-build/tools/quickbook-config.jam b/jam-files/boost-build/tools/quickbook-config.jam
deleted file mode 100644
index e983a78a..00000000
--- a/jam-files/boost-build/tools/quickbook-config.jam
+++ /dev/null
@@ -1,44 +0,0 @@
-#~ Copyright 2005 Rene Rivera.
-#~ Distributed under the Boost Software License, Version 1.0.
-#~ (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-# Automatic configuration for BoostBook tools. To use, just import this module.
-
-import os ;
-import toolset : using ;
-
-if [ os.name ] = NT
-{
-    local boost-dir = ;
-    for local R in snapshot cvs 1.33.0
-    {
-        boost-dir += [ W32_GETREG
-            "HKEY_LOCAL_MACHINE\\SOFTWARE\\Boost.org\\$(R)"
-            : "InstallRoot" ] ;
-    }
-    local quickbook-path = [ GLOB "$(boost-dir)\\bin" "\\Boost\\bin" : quickbook.exe ] ;
-    quickbook-path = $(quickbook-path[1]) ;
-    
-    if $(quickbook-path)
-    {
-        if --debug-configuration in [ modules.peek : ARGV ]
-        {
-            ECHO "notice:" using quickbook ":" $(quickbook-path) ;
-        }
-        using quickbook : $(quickbook-path) ;
-    }
-}
-else
-{
-    local quickbook-path = [ GLOB "/usr/local/bin" "/usr/bin" "/opt/bin" : quickbook ] ;
-    quickbook-path = $(quickbook-path[1]) ;
-    
-    if $(quickbook-path)
-    {
-        if --debug-configuration in [ modules.peek : ARGV ]
-        {
-            ECHO "notice:" using quickbook ":" $(quickbook-path) ;
-        }
-        using quickbook : $(quickbook-path) ;
-    }
-}
diff --git a/jam-files/boost-build/tools/quickbook.jam b/jam-files/boost-build/tools/quickbook.jam
deleted file mode 100644
index 6de2d42f..00000000
--- a/jam-files/boost-build/tools/quickbook.jam
+++ /dev/null
@@ -1,361 +0,0 @@
-#
-#   Copyright (c) 2005 João Abecasis
-#   Copyright (c) 2005 Vladimir Prus
-#   Copyright (c) 2006 Rene Rivera
-#
-#   Distributed under the Boost Software License, Version 1.0. (See
-#   accompanying file LICENSE_1_0.txt or copy at
-#   http://www.boost.org/LICENSE_1_0.txt)
-#
-
-# This toolset defines a generator to translate QuickBook to BoostBook. It can
-# be used to generate nice (!) user documentation in different formats
-# (pdf/html/...), from a single text file with simple markup.
-#
-# The toolset defines the QUICKBOOK type (file extension 'qbk') and
-# a QUICKBOOK to XML (BOOSTBOOK) generator.
-#
-#
-#   ===========================================================================
-#   Q & A
-#   ===========================================================================
-#
-#   If you don't know what this is all about, some Q & A will hopefully get you
-#   up to speed with QuickBook and this toolset.
-#
-#
-#   What is QuickBook ?
-#
-#       QuickBook is a WikiWiki style documentation tool geared towards C++
-#       documentation using simple rules and markup for simple formatting tasks.
-#       QuickBook extends the WikiWiki concept. Like the WikiWiki, QuickBook
-#       documents are simple text files. A single QuickBook document can
-#       generate a fully linked set of nice HTML and PostScript/PDF documents
-#       complete with images and syntax-colorized source code.
-#
-#
-#   Where can I get QuickBook ?
-#
-#       Quickbook can be found in Boost's repository, under the tools/quickbook
-#       directory it was added there on Jan 2005, some time after the release of
-#       Boost v1.32.0 and has been an integral part of the Boost distribution
-#       since v1.33.
-#
-#       Here's a link to the SVN repository:
-#           https://svn.boost.org/svn/boost/trunk/tools/quickbook
-#
-#       And to QuickBook's QuickBook-generated docs:
-#           http://www.boost.org/doc/libs/release/tools/quickbook/index.html
-#
-#
-#   How do I use QuickBook and this toolset in my projects ?
-#
-#       The minimal example is:
-#
-#           using boostbook ;
-#           import quickbook ;
-#
-#           boostbook my_docs : my_docs_source.qbk ;
-#
-#       where my_docs is a target name and my_docs_source.qbk is a QuickBook
-#       file. The documentation format to be generated is determined by the
-#       boostbook toolset. By default html documentation should be generated,
-#       but you should check BoostBook's docs to be sure.
-#
-#
-#   What do I need ?
-#
-#       You should start by setting up the BoostBook toolset. Please refer to
-#       boostbook.jam and the BoostBook documentation for information on how to
-#       do this.
-#
-#       A QuickBook executable is also needed. The toolset will generate this
-#       executable if it can find the QuickBook sources. The following
-#       directories will be searched:
-#
-#           BOOST_ROOT/tools/quickbook/
-#           BOOST_BUILD_PATH/../../quickbook/
-#
-#       (BOOST_ROOT and BOOST_BUILD_PATH are environment variables)
-#
-#       If QuickBook sources are not found the toolset will then try to use
-#       the shell command 'quickbook'.
-#
-#
-#   How do I provide a custom QuickBook executable ?
-#
-#       You may put the following in your user-config.jam or site-config.jam:
-#
-#           using quickbook : /path/to/quickbook ;
-#
-#       or, if 'quickbook' can be found in your PATH,
-#
-#           using quickbook : quickbook ;
-#
-#
-#   For convenience three alternatives are tried to get a QuickBook executable:
-#
-#       1.  If the user points us to the a QuickBook executable, that is used.
-#
-#       2.  Otherwise, we search for the QuickBook sources and compile QuickBook
-#           using the default toolset.
-#
-#       3.  As a last resort, we rely on the shell for finding 'quickbook'.
-#
-
-import boostbook ;
-import "class" : new ;
-import feature ;
-import generators ;
-import toolset ;
-import type ;
-import scanner ;
-import project ;
-import targets ;
-import build-system ;
-import path ;
-import common ;
-import errors ;
-
-# The one and only QUICKBOOK type!
-type.register QUICKBOOK : qbk ;
-
-# <quickbook-binary> shell command to run QuickBook
-# <quickbook-binary-dependencies> targets to build QuickBook from sources.
-feature.feature <quickbook-binary> : : free ;
-feature.feature <quickbook-binary-dependencies> : : free dependency ;
-feature.feature <quickbook-define> : : free ;
-feature.feature <quickbook-indent> : : free ;
-feature.feature <quickbook-line-width> : : free ;
-
-
-# quickbook-binary-generator handles generation of the QuickBook executable, by
-# marking it as a dependency for QuickBook docs.
-#
-# If the user supplied the QuickBook command that will be used.
-#
-# Otherwise we search some sensible places for the QuickBook sources and compile
-# from scratch using the default toolset.
-#
-# As a last resort we rely on the shell to find 'quickbook'.
-#
-class quickbook-binary-generator : generator
-{
-    import modules path targets quickbook ;
-
-    rule run ( project name ? : property-set : sources * : multiple ? )
-    {
-        quickbook.freeze-config ;
-        # QuickBook invocation command and dependencies.
-        local quickbook-binary = [ modules.peek quickbook : .quickbook-binary ] ;
-        local quickbook-binary-dependencies ;
-
-        if ! $(quickbook-binary)
-        {
-            # If the QuickBook source directory was found, mark its main target
-            # as a dependency for the current project. Otherwise, try to find
-            # 'quickbook' in user's PATH
-            local quickbook-dir = [ modules.peek quickbook : .quickbook-dir ] ;
-            if $(quickbook-dir)
-            {
-                # Get the main-target in QuickBook directory.
-                local quickbook-main-target = [ targets.resolve-reference $(quickbook-dir) : $(project) ] ;
-
-                # The first element are actual targets, the second are
-                # properties found in target-id. We do not care about these
-                # since we have passed the id ourselves.
-                quickbook-main-target =
-                    [ $(quickbook-main-target[1]).main-target quickbook ] ;
-
-                quickbook-binary-dependencies =
-                    [ $(quickbook-main-target).generate [ $(property-set).propagated ] ] ;
-
-                # Ignore usage-requirements returned as first element.
-                quickbook-binary-dependencies = $(quickbook-binary-dependencies[2-]) ;
-
-                # Some toolsets generate extra targets (e.g. RSP). We must mark
-                # all targets as dependencies for the project, but we will only
-                # use the EXE target for quickbook-to-boostbook translation.
-                for local target in $(quickbook-binary-dependencies)
-                {
-                    if [ $(target).type ] = EXE
-                    {
-                        quickbook-binary = 
-                            [ path.native 
-                                [ path.join
-                                    [ $(target).path ]
-                                    [ $(target).name ]
-                                ]
-                            ] ;
-                    }
-                }
-            }
-        }
-
-        # Add $(quickbook-binary-dependencies) as a dependency of the current
-        # project and set it as the <quickbook-binary> feature for the
-        # quickbook-to-boostbook rule, below.
-        property-set = [ $(property-set).add-raw
-            <dependency>$(quickbook-binary-dependencies)
-            <quickbook-binary>$(quickbook-binary)
-            <quickbook-binary-dependencies>$(quickbook-binary-dependencies)
-        ] ;
-
-        return [ generator.run $(project) $(name) : $(property-set) : $(sources) : $(multiple) ] ;
-    }
-}
-
-
-# Define a scanner for tracking QBK include dependencies.
-#
-class qbk-scanner : common-scanner
-{
-    rule pattern ( )
-    {
-        return "\\[[ ]*include[ ]+([^]]+)\\]" 
-        "\\[[ ]*include:[a-zA-Z0-9_]+[ ]+([^]]+)\\]" 
-        "\\[[ ]*import[ ]+([^]]+)\\]" ;
-    }
-}
-
-
-scanner.register qbk-scanner : include ;
-
-type.set-scanner QUICKBOOK : qbk-scanner ;
-
-
-# Initialization of toolset.
-#
-# Parameters:
-#   command ?    -> path to QuickBook executable.
-#
-# When command is not supplied toolset will search for QuickBook directory and
-# compile the executable from source. If that fails we still search the path for
-# 'quickbook'.
-#
-rule init (
-        command ?   # path to the QuickBook executable.
-    )
-{
-    if $(command)
-    {
-        if $(.config-frozen)
-        {
-            errors.user-error "quickbook: configuration cannot be changed after it has been used." ;
-        }
-        .command = $(command) ;
-    }
-}
-
-rule freeze-config ( )
-{
-    if ! $(.config-frozen)
-    {
-        .config-frozen = true ;
-
-        # QuickBook invocation command and dependencies.
-
-        .quickbook-binary = $(.command) ;
-
-        if $(.quickbook-binary)
-        {
-            # Use user-supplied command.
-            .quickbook-binary = [ common.get-invocation-command quickbook : quickbook : $(.quickbook-binary) ] ;
-        }
-        else
-        {
-            # Search for QuickBook sources in sensible places, like
-            #   $(BOOST_ROOT)/tools/quickbook
-            #   $(BOOST_BUILD_PATH)/../../quickbook
-
-            # And build quickbook executable from sources.
-
-            local boost-root = [ modules.peek : BOOST_ROOT ] ;
-            local boost-build-path = [ build-system.location ] ;
-
-            if $(boost-root)
-            {
-                .quickbook-dir += [ path.join $(boost-root) tools ] ;
-            }
-
-            if $(boost-build-path)
-            {
-                .quickbook-dir += $(boost-build-path)/../.. ;
-            }
-
-            .quickbook-dir = [ path.glob $(.quickbook-dir) : quickbook ] ;
-
-            # If the QuickBook source directory was found, mark its main target
-            # as a dependency for the current project. Otherwise, try to find
-            # 'quickbook' in user's PATH
-            if $(.quickbook-dir)
-            {
-                .quickbook-dir = [ path.make $(.quickbook-dir[1]) ] ;
-            }
-            else
-            {
-                ECHO "QuickBook warning: The path to the quickbook executable was" ;
-                ECHO "  not provided. Additionally, couldn't find QuickBook" ;
-                ECHO "  sources searching in" ;
-                ECHO "    * BOOST_ROOT/tools/quickbook" ;
-                ECHO "    * BOOST_BUILD_PATH/../../quickbook" ;
-                ECHO "  Will now try to find a precompiled executable by searching" ;
-                ECHO "  the PATH for 'quickbook'." ;
-                ECHO "  To disable this warning in the future, or to completely" ;
-                ECHO "  avoid compilation of quickbook, you can explicitly set the" ;
-                ECHO "  path to a quickbook executable command in user-config.jam" ;
-                ECHO "  or site-config.jam with the call" ;
-                ECHO "    using quickbook : /path/to/quickbook ;" ;
-
-                # As a last resort, search for 'quickbook' command in path. Note
-                # that even if the 'quickbook' command is not found,
-                # get-invocation-command will still return 'quickbook' and might
-                # generate an error while generating the virtual-target.
-
-                .quickbook-binary = [ common.get-invocation-command quickbook : quickbook ] ;
-            }
-        }
-    }
-}
-
-
-generators.register [ new quickbook-binary-generator quickbook.quickbook-to-boostbook : QUICKBOOK : XML ] ;
-
-
-# <quickbook-binary> shell command to run QuickBook
-# <quickbook-binary-dependencies> targets to build QuickBook from sources.
-toolset.flags quickbook.quickbook-to-boostbook QB-COMMAND      <quickbook-binary> ;
-toolset.flags quickbook.quickbook-to-boostbook QB-DEPENDENCIES <quickbook-binary-dependencies> ;
-toolset.flags quickbook.quickbook-to-boostbook INCLUDES        <include> ;
-toolset.flags quickbook.quickbook-to-boostbook QB-DEFINES      <quickbook-define> ;
-toolset.flags quickbook.quickbook-to-boostbook QB-INDENT       <quickbook-indent> ;
-toolset.flags quickbook.quickbook-to-boostbook QB-LINE-WIDTH   <quickbook-line-width> ;
-
-
-rule quickbook-to-boostbook ( target : source : properties * )
-{
-    # Signal dependency of quickbook sources on <quickbook-binary-dependencies>
-    # upon invocation of quickbook-to-boostbook.
-    DEPENDS $(target) : [ on $(target) return $(QB-DEPENDENCIES) ] ;
-}
-
-
-actions quickbook-to-boostbook
-{
-    "$(QB-COMMAND)" -I"$(INCLUDES)" -D"$(QB-DEFINES)" --indent="$(QB-INDENT)" --linewidth="$(QB-LINE-WIDTH)" --output-file="$(1)" "$(2)"
-}
-
-
-# Declare a main target to convert a quickbook source into a boostbook XML file.
-#
-rule to-boostbook ( target-name : sources * : requirements * : default-build * )
-{ 
-  local project = [ project.current ] ;
-    
-  targets.main-target-alternative 
-    [ new typed-target $(target-name) : $(project) : XML
-        : [ targets.main-target-sources $(sources) : $(target-name) ] 
-        : [ targets.main-target-requirements $(requirements) : $(project) ]
-        : [ targets.main-target-default-build $(default-build) : $(project) ] 
-    ] ;
-}
diff --git a/jam-files/boost-build/tools/rc.jam b/jam-files/boost-build/tools/rc.jam
deleted file mode 100644
index 9964d339..00000000
--- a/jam-files/boost-build/tools/rc.jam
+++ /dev/null
@@ -1,156 +0,0 @@
-#  Copyright (C) Andre Hentz 2003. Permission to copy, use, modify, sell and
-#  distribute this software is granted provided this copyright notice appears in
-#  all copies. This software is provided "as is" without express or implied
-#  warranty, and with no claim as to its suitability for any purpose.
-#  
-#  Copyright (c) 2006 Rene Rivera.
-#
-#  Use, modification and distribution is subject to the Boost Software
-#  License Version 1.0. (See accompanying file LICENSE_1_0.txt or
-#  http://www.boost.org/LICENSE_1_0.txt)
-
-import type ;
-import generators ;
-import feature ;
-import errors ;
-import scanner ;
-import toolset : flags ;
-
-if [ MATCH (--debug-configuration) : [ modules.peek : ARGV ] ]
-{
-    .debug-configuration = true ;
-}
-
-type.register RC : rc ;
-
-rule init ( )
-{
-}
-
-# Configures a new resource compilation command specific to a condition,
-# usually a toolset selection condition. The possible options are:
-#
-#     * <rc-type>(rc|windres) - Indicates the type of options the command
-#       accepts.
-#
-# Even though the arguments are all optional, only when a command, condition,
-# and at minimum the rc-type option are given will the command be configured.
-# This is so that callers don't have to check auto-configuration values
-# before calling this. And still get the functionality of build failures when
-# the resource compiler can't be found.
-#
-rule configure ( command ? : condition ? : options * )
-{
-    local rc-type = [ feature.get-values <rc-type> : $(options) ] ;
-
-    if $(command) && $(condition) && $(rc-type)
-    {
-        flags rc.compile.resource .RC $(condition) : $(command) ;
-        flags rc.compile.resource .RC_TYPE $(condition) : $(rc-type:L) ;
-        flags rc.compile.resource DEFINES <define> ;
-        flags rc.compile.resource INCLUDES <include> ;
-        if $(.debug-configuration)
-        {
-            ECHO notice: using rc compiler :: $(condition) :: $(command) ;
-        }
-    }
-}
-
-rule compile.resource ( target : sources * : properties * )
-{
-    local rc-type = [ on $(target) return $(.RC_TYPE) ] ;
-    rc-type ?= null ;
-    compile.resource.$(rc-type) $(target) : $(sources[1]) ;
-}
-
-actions compile.resource.rc
-{
-    "$(.RC)" -l 0x409 "-U$(UNDEFS)" "-D$(DEFINES)" -I"$(>:D)" -I"$(<:D)" -I"$(INCLUDES)" -fo "$(<)" "$(>)"
-}
-
-actions compile.resource.windres
-{
-    "$(.RC)" "-U$(UNDEFS)" "-D$(DEFINES)" -I"$(>:D)" -I"$(<:D)" -I"$(INCLUDES)" -o "$(<)" -i "$(>)"
-}
-
-actions quietly compile.resource.null
-{
-    as /dev/null -o "$(<)"
-}
-
-# Since it's a common practice to write
-# exe hello : hello.cpp hello.rc
-# we change the name of object created from RC file, to
-# avoid conflict with hello.cpp.
-# The reason we generate OBJ and not RES, is that gcc does not
-# seem to like RES files, but works OK with OBJ.
-# See http://article.gmane.org/gmane.comp.lib.boost.build/5643/
-#
-# Using 'register-c-compiler' adds the build directory to INCLUDES
-generators.register-c-compiler rc.compile.resource : RC : OBJ(%_res) ;
-
-# Register scanner for resources
-class res-scanner : scanner 
-{
-    import regex virtual-target path scanner ;    
-    
-    rule __init__ ( includes * )
-    {
-        scanner.__init__ ;
-    
-        self.includes = $(includes) ;
-    }    
-
-    rule pattern ( )
-    {
-        return "(([^ ]+[ ]+(BITMAP|CURSOR|FONT|ICON|MESSAGETABLE|RT_MANIFEST)[ ]+([^ \"]+|\"[^\"]+\"))|(#include[ ]*(<[^<]+>|\"[^\"]+\")))" ;
-    }
-
-    rule process ( target : matches * : binding )
-    {
-        local angle = [ regex.transform $(matches) : "#include[ ]*<([^<]+)>" ] ;
-        local quoted = [ regex.transform $(matches) : "#include[ ]*\"([^\"]+)\"" ] ;
-        local res = [ regex.transform $(matches) : "[^ ]+[ ]+(BITMAP|CURSOR|FONT|ICON|MESSAGETABLE|RT_MANIFEST)[ ]+(([^ \"]+)|\"([^\"]+)\")" : 3 4 ] ;
-
-        # Icons and other includes may referenced as 
-        #
-        # IDR_MAINFRAME ICON "res\\icon.ico"
-        #
-        # so we have to replace double backslashes to single ones.
-        res = [ regex.replace-list $(res) : "\\\\\\\\" : "/" ] ;
-
-        # CONSIDER: the new scoping rule seem to defeat "on target" variables.
-        local g = [ on $(target) return $(HDRGRIST) ] ;  
-        local b = [ NORMALIZE_PATH $(binding:D) ] ;
-
-        # Attach binding of including file to included targets.
-        # When target is directly created from virtual target
-        # this extra information is unnecessary. But in other
-        # cases, it allows to distinguish between two headers of the 
-        # same name included from different places.      
-        # We don't need this extra information for angle includes,
-        # since they should not depend on including file (we can't
-        # get literal "." in include path).
-        local g2 = $(g)"#"$(b) ;
-       
-        angle = $(angle:G=$(g)) ;
-        quoted = $(quoted:G=$(g2)) ;
-        res = $(res:G=$(g2)) ;
-        
-        local all = $(angle) $(quoted) ;
-
-        INCLUDES $(target) : $(all) ;
-        DEPENDS $(target) : $(res) ;
-        NOCARE $(all) $(res) ;
-        SEARCH on $(angle) = $(self.includes:G=) ;
-        SEARCH on $(quoted) = $(b) $(self.includes:G=) ;
-        SEARCH on $(res) = $(b) $(self.includes:G=) ;
-        
-        # Just propagate current scanner to includes, in a hope
-        # that includes do not change scanners. 
-        scanner.propagate $(__name__) : $(angle) $(quoted) : $(target) ;
-    }        
-}
-
-scanner.register res-scanner : include ;
-type.set-scanner RC : res-scanner ;
diff --git a/jam-files/boost-build/tools/rc.py b/jam-files/boost-build/tools/rc.py
deleted file mode 100644
index 0b82d231..00000000
--- a/jam-files/boost-build/tools/rc.py
+++ /dev/null
@@ -1,189 +0,0 @@
-# Status: being ported by Steven Watanabe
-# Base revision: 47077
-#
-#  Copyright (C) Andre Hentz 2003. Permission to copy, use, modify, sell and
-#  distribute this software is granted provided this copyright notice appears in
-#  all copies. This software is provided "as is" without express or implied
-#  warranty, and with no claim as to its suitability for any purpose.
-#  
-#  Copyright (c) 2006 Rene Rivera.
-#
-#  Copyright (c) 2008 Steven Watanabe
-#
-#  Use, modification and distribution is subject to the Boost Software
-#  License Version 1.0. (See accompanying file LICENSE_1_0.txt or
-#  http://www.boost.org/LICENSE_1_0.txt)
-
-##import type ;
-##import generators ;
-##import feature ;
-##import errors ;
-##import scanner ;
-##import toolset : flags ;
-
-from b2.build import type, toolset, generators, scanner, feature
-from b2.tools import builtin
-from b2.util import regex
-from b2.build.toolset import flags
-from b2.manager import get_manager
-
-__debug = None
-
-def debug():
-    global __debug
-    if __debug is None:
-        __debug = "--debug-configuration" in bjam.variable("ARGV")        
-    return __debug
-
-type.register('RC', ['rc'])
-
-def init():
-    pass
-
-def configure (command = None, condition = None, options = None):
-    """
-        Configures a new resource compilation command specific to a condition,
-        usually a toolset selection condition. The possible options are:
-        
-            * <rc-type>(rc|windres) - Indicates the type of options the command
-              accepts.
-        
-        Even though the arguments are all optional, only when a command, condition,
-        and at minimum the rc-type option are given will the command be configured.
-        This is so that callers don't have to check auto-configuration values
-        before calling this. And still get the functionality of build failures when
-        the resource compiler can't be found.
-    """
-    rc_type = feature.get_values('<rc-type>', options)
-    if rc_type:
-        assert(len(rc_type) == 1)
-        rc_type = rc_type[0]
-
-    if command and condition and rc_type:
-        flags('rc.compile.resource', '.RC', condition, command)
-        flags('rc.compile.resource', '.RC_TYPE', condition, rc_type.lower())
-        flags('rc.compile.resource', 'DEFINES', [], ['<define>'])
-        flags('rc.compile.resource', 'INCLUDES', [], ['<include>'])
-        if debug():
-            print 'notice: using rc compiler ::', condition, '::', command
-
-engine = get_manager().engine()
-
-class RCAction:
-    """Class representing bjam action defined from Python.
-    The function must register the action to execute."""
-    
-    def __init__(self, action_name, function):
-        self.action_name = action_name
-        self.function = function
-            
-    def __call__(self, targets, sources, property_set):
-        if self.function:
-            self.function(targets, sources, property_set)
-
-# FIXME: What is the proper way to dispatch actions?
-def rc_register_action(action_name, function = None):
-    global engine
-    if engine.actions.has_key(action_name):
-        raise "Bjam action %s is already defined" % action_name
-    engine.actions[action_name] = RCAction(action_name, function)
-
-def rc_compile_resource(targets, sources, properties):
-    rc_type = bjam.call('get-target-variable', targets, '.RC_TYPE')
-    global engine
-    engine.set_update_action('rc.compile.resource.' + rc_type, targets, sources, properties)
-
-rc_register_action('rc.compile.resource', rc_compile_resource)
-
-
-engine.register_action(
-    'rc.compile.resource.rc',
-    '"$(.RC)" -l 0x409 "-U$(UNDEFS)" "-D$(DEFINES)" -I"$(>:D)" -I"$(<:D)" -I"$(INCLUDES)" -fo "$(<)" "$(>)"')
-
-engine.register_action(
-    'rc.compile.resource.windres',
-    '"$(.RC)" "-U$(UNDEFS)" "-D$(DEFINES)" -I"$(>:D)" -I"$(<:D)" -I"$(INCLUDES)" -o "$(<)" -i "$(>)"')
-
-# FIXME: this was originally declared quietly
-engine.register_action(
-    'compile.resource.null',
-    'as /dev/null -o "$(<)"')
-
-# Since it's a common practice to write
-# exe hello : hello.cpp hello.rc
-# we change the name of object created from RC file, to
-# avoid conflict with hello.cpp.
-# The reason we generate OBJ and not RES, is that gcc does not
-# seem to like RES files, but works OK with OBJ.
-# See http://article.gmane.org/gmane.comp.lib.boost.build/5643/
-#
-# Using 'register-c-compiler' adds the build directory to INCLUDES
-# FIXME: switch to generators
-builtin.register_c_compiler('rc.compile.resource', ['RC'], ['OBJ(%_res)'], [])
-
-__angle_include_re = "#include[ ]*<([^<]+)>"
-
-# Register scanner for resources
-class ResScanner(scanner.Scanner):
-    
-    def __init__(self, includes):
-        scanner.__init__ ;
-        self.includes = includes
-
-    def pattern(self):
-        return "(([^ ]+[ ]+(BITMAP|CURSOR|FONT|ICON|MESSAGETABLE|RT_MANIFEST)" +\
-               "[ ]+([^ \"]+|\"[^\"]+\"))|(#include[ ]*(<[^<]+>|\"[^\"]+\")))" ;
-
-    def process(self, target, matches, binding):
-
-        angle = regex.transform(matches, "#include[ ]*<([^<]+)>")
-        quoted = regex.transform(matches, "#include[ ]*\"([^\"]+)\"")
-        res = regex.transform(matches,
-                              "[^ ]+[ ]+(BITMAP|CURSOR|FONT|ICON|MESSAGETABLE|RT_MANIFEST)" +\
-                              "[ ]+(([^ \"]+)|\"([^\"]+)\")", [3, 4])
-
-        # Icons and other includes may referenced as 
-        #
-        # IDR_MAINFRAME ICON "res\\icon.ico"
-        #
-        # so we have to replace double backslashes to single ones.
-        res = [ re.sub(r'\\\\', '/', match) for match in res ]
-
-        # CONSIDER: the new scoping rule seem to defeat "on target" variables.
-        g = bjam.call('get-target-variable', target, 'HDRGRIST')
-        b = os.path.normalize_path(os.path.dirname(binding))
-
-        # Attach binding of including file to included targets.
-        # When target is directly created from virtual target
-        # this extra information is unnecessary. But in other
-        # cases, it allows to distinguish between two headers of the 
-        # same name included from different places.      
-        # We don't need this extra information for angle includes,
-        # since they should not depend on including file (we can't
-        # get literal "." in include path).
-        g2 = g + "#" + b
-       
-        g = "<" + g + ">"
-        g2 = "<" + g2 + ">"
-        angle = [g + x for x in angle]
-        quoted = [g2 + x for x in quoted]
-        res = [g2 + x for x in res]
-        
-        all = angle + quoted
-
-        bjam.call('mark-included', target, all)
-
-        engine = get_manager().engine()
-
-        engine.add_dependency(target, res)
-        bjam.call('NOCARE', all + res)
-        engine.set_target_variable(angle, 'SEARCH', ungrist(self.includes))
-        engine.set_target_variable(quoted, 'SEARCH', b + ungrist(self.includes))
-        engine.set_target_variable(res, 'SEARCH', b + ungrist(self.includes)) ;
-        
-        # Just propagate current scanner to includes, in a hope
-        # that includes do not change scanners.
-        get_manager().scanners().propagate(self, angle + quoted)
-
-scanner.register(ResScanner, 'include')
-type.set_scanner('RC', ResScanner)
diff --git a/jam-files/boost-build/tools/stage.jam b/jam-files/boost-build/tools/stage.jam
deleted file mode 100644
index 296e7558..00000000
--- a/jam-files/boost-build/tools/stage.jam
+++ /dev/null
@@ -1,524 +0,0 @@
-# Copyright 2003 Dave Abrahams
-# Copyright 2005, 2006 Rene Rivera
-# Copyright 2002, 2003, 2004, 2005, 2006 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-# This module defines the 'install' rule, used to copy a set of targets to a
-# single location.
-
-import targets ;
-import "class" : new ;
-import errors ;
-import type ;
-import generators ;
-import feature ;
-import project ;
-import virtual-target ;
-import path ;
-import types/register ;
-
-
-feature.feature <install-dependencies> : off on : incidental      ;
-feature.feature <install-type>         :        : free incidental ;
-feature.feature <install-source-root>  :        : free path       ;
-feature.feature <so-version>           :        : free incidental ;
-
-# If 'on', version symlinks for shared libraries will not be created. Affects
-# Unix builds only.
-feature.feature <install-no-version-symlinks> : on : optional incidental ;
-
-
-class install-target-class : basic-target
-{
-    import feature ;
-    import project ;
-    import type ;
-    import errors ;
-    import generators ;
-    import path ;
-    import stage ;
-    import "class" : new ;
-    import property ;
-    import property-set ;
-
-    rule __init__ ( name-and-dir : project : sources * : requirements * : default-build * )
-    {
-        basic-target.__init__ $(name-and-dir) : $(project) : $(sources) :
-            $(requirements) : $(default-build) ;
-    }
-
-    # If <location> is not set, sets it based on the project data.
-    #
-    rule update-location ( property-set )
-    {
-        local loc = [ $(property-set).get <location> ] ;
-        if ! $(loc)
-        {
-            loc = [ path.root $(self.name) [ $(self.project).get location ] ] ;
-            property-set = [ $(property-set).add-raw $(loc:G=<location>) ] ;
-        }
-
-        return $(property-set) ;
-    }
-
-    # Takes a target that is installed and a property set which is used when
-    # installing.
-    #
-    rule adjust-properties ( target : build-property-set )
-    {
-        local ps-raw ;
-        local a = [ $(target).action ] ;
-        if $(a)
-        {
-            local ps = [ $(a).properties ] ;
-            ps-raw = [ $(ps).raw ] ;
-
-            # Unless <hardcode-dll-paths>true is in properties, which can happen
-            # only if the user has explicitly requested it, nuke all <dll-path>
-            # properties.
-            if [ $(build-property-set).get <hardcode-dll-paths> ] != true
-            {
-                ps-raw = [ property.change $(ps-raw) : <dll-path> ] ;
-            }
-
-            # If any <dll-path> properties were specified for installing, add
-            # them.
-            local l = [ $(build-property-set).get <dll-path> ] ;
-            ps-raw += $(l:G=<dll-path>) ;
-
-            # Also copy <linkflags> feature from current build set, to be used
-            # for relinking.
-            local l = [ $(build-property-set).get <linkflags> ] ;
-            ps-raw += $(l:G=<linkflags>) ;
-
-            # Remove the <tag> feature on original targets.
-            ps-raw = [ property.change $(ps-raw) : <tag> ] ;
-
-            # And <location>. If stage target has another stage target in
-            # sources, then we shall get virtual targets with the <location>
-            # property set.
-            ps-raw = [ property.change $(ps-raw) : <location> ] ;
-        }
-
-        local d = [ $(build-property-set).get <dependency> ] ;
-        ps-raw += $(d:G=<dependency>) ;
-
-        local d = [ $(build-property-set).get <location> ] ;
-        ps-raw += $(d:G=<location>) ;
-
-        local ns = [ $(build-property-set).get <install-no-version-symlinks> ] ;
-        ps-raw += $(ns:G=<install-no-version-symlinks>) ;
-
-        local d = [ $(build-property-set).get <install-source-root> ] ;
-        # Make the path absolute: we shall use it to compute relative paths and
-        # making the path absolute will help.
-        if $(d)
-        {
-            d = [ path.root $(d) [ path.pwd ] ] ;
-            ps-raw += $(d:G=<install-source-root>) ;
-        }
-
-        if $(ps-raw)
-        {
-            return [ property-set.create $(ps-raw) ]  ;
-        }
-        else
-        {
-            return [ property-set.empty ] ;
-        }
-    }
-
-    rule construct ( name : source-targets * : property-set )
-    {
-        source-targets = [ targets-to-stage $(source-targets) :
-            $(property-set) ] ;
-
-        property-set = [ update-location $(property-set) ] ;
-
-        local ename = [ $(property-set).get <name> ] ;
-
-        if $(ename) && $(source-targets[2])
-        {
-            errors.error "When <name> property is used in 'install', only one"
-                "source is allowed" ;
-        }
-
-        local result ;
-        for local i in $(source-targets)
-        {
-            local staged-targets ;
-
-            local new-properties = [ adjust-properties $(i) :
-                $(property-set) ] ;
-
-            # See if something special should be done when staging this type. It
-            # is indicated by the presence of a special "INSTALLED_" type.
-            local t = [ $(i).type ] ;
-            if $(t) && [ type.registered INSTALLED_$(t) ]
-            {
-                if $(ename)
-                {
-                    errors.error "In 'install': <name> property specified with target that requires relinking." ;
-                }
-                else
-                {
-                    local targets = [ generators.construct $(self.project)
-                        $(name) : INSTALLED_$(t) : $(new-properties) : $(i) ] ;
-                    staged-targets += $(targets[2-]) ;
-                }
-            }
-            else
-            {
-                staged-targets = [ stage.copy-file $(self.project) $(ename) :
-                    $(i) : $(new-properties) ] ;
-            }
-
-            if ! $(staged-targets)
-            {
-                errors.error "Unable to generate staged version of " [ $(source).str ] ;
-            }
-
-            for t in $(staged-targets)
-            {
-                result += [ virtual-target.register $(t) ] ;
-            }
-        }
-
-        return [ property-set.empty ] $(result) ;
-    }
-
-    # Given the list of source targets explicitly passed to 'stage', returns the
-    # list of targets which must be staged.
-    #
-    rule targets-to-stage ( source-targets * : property-set )
-    {
-        local result ;
-
-        # Traverse the dependencies, if needed.
-        if [ $(property-set).get <install-dependencies> ] = "on"
-        {
-            source-targets = [ collect-targets $(source-targets) ] ;
-        }
-
-        # Filter the target types, if needed.
-        local included-types = [ $(property-set).get <install-type> ] ;
-        for local r in $(source-targets)
-        {
-            local ty = [ $(r).type ] ;
-            if $(ty)
-            {
-                # Do not stage searched libs.
-                if $(ty) != SEARCHED_LIB
-                {
-                    if $(included-types)
-                    {
-                        if [ include-type $(ty) : $(included-types) ]
-                        {
-                            result += $(r) ;
-                        }
-                    }
-                    else
-                    {
-                        result += $(r) ;
-                    }
-                }
-            }
-            else if ! $(included-types)
-            {
-                # Don't install typeless target if there is an explicit list of
-                # allowed types.
-                result += $(r) ;
-            }
-        }
-
-        return $(result) ;
-    }
-
-    # CONSIDER: figure out why we can not use virtual-target.traverse here.
-    #
-    rule collect-targets ( targets * )
-    {
-        # Find subvariants
-        local s ;
-        for local t in $(targets)
-        {
-            s += [ $(t).creating-subvariant ] ;
-        }
-        s = [ sequence.unique $(s) ] ;
-        
-        local result = [ new set ] ;
-        $(result).add $(targets) ;
-        
-        for local i in $(s)
-        {
-            $(i).all-referenced-targets $(result) ;
-        }
-        local result2 ;
-        for local r in [ $(result).list ]
-        {
-            if $(r:G) != <use>
-            {
-                result2 += $(r:G=) ;
-            }
-        }
-        DELETE_MODULE $(result) ;
-        result = [ sequence.unique $(result2) ] ;
-    }
-
-    # Returns true iff 'type' is subtype of some element of 'types-to-include'.
-    #
-    local rule include-type ( type : types-to-include * )
-    {
-        local found ;
-        while $(types-to-include) && ! $(found)
-        {
-            if [ type.is-subtype $(type) $(types-to-include[1]) ]
-            {
-                found = true ;
-            }
-            types-to-include = $(types-to-include[2-]) ;
-        }
-
-        return $(found) ;
-    }
-}
-
-
-# Creates a copy of target 'source'. The 'properties' object should have a
-# <location> property which specifies where the target must be placed.
-#
-rule copy-file ( project name ? : source : properties )
-{
-    name ?= [ $(source).name ] ;
-    local relative ;
-
-    local new-a = [ new non-scanning-action $(source) : common.copy :
-        $(properties) ] ;
-    local source-root = [ $(properties).get <install-source-root> ] ;
-    if $(source-root)
-    {
-        # Get the real path of the target. We probably need to strip relative
-        # path from the target name at construction.
-        local path = [ $(source).path ] ;
-        path = [ path.root $(name:D) $(path) ] ;
-        # Make the path absolute. Otherwise, it would be hard to compute the
-        # relative path. The 'source-root' is already absolute, see the
-        # 'adjust-properties' method above.
-        path = [ path.root $(path) [ path.pwd ] ] ;
-
-        relative = [ path.relative-to $(source-root) $(path) ] ;
-    }
-
-    # Note: Using $(name:D=$(relative)) might be faster here, but then we would
-    # need to explicitly check that relative is not ".", otherwise we might get
-    # paths like '<prefix>/boost/.', try to create it and mkdir would obviously
-    # fail.
-    name = [ path.join $(relative) $(name:D=) ] ;
-
-    return [ new file-target $(name) exact : [ $(source).type ] : $(project) :
-        $(new-a) ] ;
-}
-
-
-rule symlink ( name : project : source : properties )
-{
-    local a = [ new action $(source) : symlink.ln : $(properties) ] ;
-    return [ new file-target $(name) exact : [ $(source).type ] : $(project) :
-        $(a) ] ;
-}
-
-
-rule relink-file ( project : source : property-set  )
-{
-    local action = [ $(source).action ] ;
-    local cloned-action = [ virtual-target.clone-action $(action) : $(project) :
-        "" : $(property-set) ] ;
-    return [ $(cloned-action).targets ] ;
-}
-
-
-# Declare installed version of the EXE type. Generator for this type will cause
-# relinking to the new location.
-type.register INSTALLED_EXE : : EXE ;
-
-
-class installed-exe-generator : generator
-{
-    import type ;
-    import property-set ;
-    import modules ;
-    import stage ;
-
-    rule __init__ ( )
-    {
-        generator.__init__ install-exe : EXE : INSTALLED_EXE ;
-    }
-
-    rule run ( project name ? : property-set : source : multiple ? )
-    {
-        local need-relink ;
-        
-        if [ $(property-set).get <os> ] in NT CYGWIN ||
-            [ $(property-set).get <target-os> ] in windows cygwin
-        {
-        }
-        else
-        {
-            # See if the dll-path properties are not changed during
-            # install. If so, copy, don't relink.
-            local a = [ $(source).action ] ;
-            local p = [ $(a).properties ] ;
-            local original = [ $(p).get <dll-path> ] ;
-            local current = [ $(property-set).get <dll-path> ] ;
-            
-            if $(current) != $(original)
-            {
-                need-relink = true ;
-            }            
-        }
-        
-            
-        if $(need-relink)
-        {
-            return [ stage.relink-file $(project)
-              : $(source) : $(property-set) ] ;
-        }
-        else
-        {
-            return [ stage.copy-file $(project)
-              : $(source) : $(property-set) ] ;
-        }
-    }
-}
-
-
-generators.register [ new installed-exe-generator ] ;
-
-
-# Installing a shared link on Unix might cause a creation of versioned symbolic
-# links.
-type.register INSTALLED_SHARED_LIB : : SHARED_LIB ;
-
-
-class installed-shared-lib-generator : generator
-{
-    import type ;
-    import property-set ;
-    import modules ;
-    import stage ;
-
-    rule __init__ ( )
-    {
-        generator.__init__ install-shared-lib : SHARED_LIB
-          : INSTALLED_SHARED_LIB ;
-    }
-
-    rule run ( project name ? : property-set : source : multiple ? )
-    {
-        if [ $(property-set).get <os> ] in NT CYGWIN ||
-            [ $(property-set).get <target-os> ] in windows cygwin
-        {
-            local copied = [ stage.copy-file $(project) : $(source) :
-                $(property-set) ] ;
-            return [ virtual-target.register $(copied) ] ;
-        }
-        else
-        {
-            local a = [ $(source).action ] ;
-            local copied ;
-            if ! $(a)
-            {
-                # Non-derived file, just copy.
-                copied = [ stage.copy-file $(project) : $(source) :
-                    $(property-set) ] ;
-            }
-            else
-            {
-                local cp = [ $(a).properties ] ;
-                local current-dll-path = [ $(cp).get <dll-path> ] ;
-                local new-dll-path = [ $(property-set).get <dll-path> ] ;
-
-                if $(current-dll-path) != $(new-dll-path)
-                {
-                    # Rpath changed, need to relink.
-                    copied = [ stage.relink-file $(project) : $(source) :
-                        $(property-set) ] ;
-                }
-                else
-                {
-                    copied = [ stage.copy-file $(project) : $(source) :
-                        $(property-set) ] ;
-                }
-            }
-
-            copied = [ virtual-target.register $(copied) ] ;
-
-            local result = $(copied) ;
-            # If the name is in the form NNN.XXX.YYY.ZZZ, where all 'X', 'Y' and
-            # 'Z' are numbers, we need to create NNN.XXX and NNN.XXX.YYY
-            # symbolic links.
-            local m = [ MATCH (.*)\\.([0123456789]+)\\.([0123456789]+)\\.([0123456789]+)$
-                : [ $(copied).name ] ] ;
-            if $(m)
-            {
-                # Symlink without version at all is used to make
-                # -lsome_library work.
-                result += [ stage.symlink $(m[1]) : $(project) : $(copied) :
-                    $(property-set) ] ;
-
-                # Symlinks of some libfoo.N and libfoo.N.M are used so that
-                # library can found at runtime, if libfoo.N.M.X has soname of
-                # libfoo.N. That happens when the library makes some binary
-                # compatibility guarantees. If not, it is possible to skip those
-                # symlinks.
-                local suppress =
-                    [ $(property-set).get <install-no-version-symlinks> ] ;
-
-                if $(suppress) != "on"
-                {
-                    result += [ stage.symlink $(m[1]).$(m[2]) : $(project)
-                      : $(copied) : $(property-set) ] ;
-                    result += [ stage.symlink $(m[1]).$(m[2]).$(m[3])  : $(project)
-                      : $(copied) : $(property-set) ] ;
-                }
-            }
-
-            return $(result) ;
-        }
-    }
-}
-
-generators.register [ new installed-shared-lib-generator ] ;
-
-
-# Main target rule for 'install'.
-#
-rule install ( name : sources * : requirements * : default-build * )
-{
-    local project = [ project.current ] ;
-
-    # Unless the user has explicitly asked us to hardcode dll paths, add
-    # <hardcode-dll-paths>false in requirements, to override default value.
-    if ! <hardcode-dll-paths>true in $(requirements)
-    {
-        requirements += <hardcode-dll-paths>false ;
-    }
-
-    if <tag> in $(requirements:G)
-    {
-        errors.user-error
-            "The <tag> property is not allowed for the 'install' rule" ;
-    }
-
-    targets.main-target-alternative
-      [ new install-target-class $(name) : $(project)
-        : [ targets.main-target-sources $(sources) : $(name) ]
-        : [ targets.main-target-requirements $(requirements) : $(project) ]
-        : [ targets.main-target-default-build $(default-build) : $(project) ]
-      ] ;
-}
-
-
-IMPORT $(__name__) : install : : install ;
-IMPORT $(__name__) : install : : stage ;
diff --git a/jam-files/boost-build/tools/stage.py b/jam-files/boost-build/tools/stage.py
deleted file mode 100644
index 25eccbe5..00000000
--- a/jam-files/boost-build/tools/stage.py
+++ /dev/null
@@ -1,350 +0,0 @@
-# Status: ported.
-# Base revision 64444.
-#
-# Copyright 2003 Dave Abrahams
-# Copyright 2005, 2006 Rene Rivera
-# Copyright 2002, 2003, 2004, 2005, 2006, 2010 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-# This module defines the 'install' rule, used to copy a set of targets to a
-# single location.
-
-import b2.build.feature as feature
-import b2.build.targets as targets
-import b2.build.property as property
-import b2.build.property_set as property_set
-import b2.build.generators as generators
-import b2.build.virtual_target as virtual_target
-
-from b2.manager import get_manager
-from b2.util.sequence import unique
-from b2.util import bjam_signature
-
-import b2.build.type
-
-import os.path
-import re
-import types
-
-feature.feature('install-dependencies', ['off', 'on'], ['incidental'])
-feature.feature('install-type', [], ['free', 'incidental'])
-feature.feature('install-source-root', [], ['free', 'path'])
-feature.feature('so-version', [], ['free', 'incidental'])
-
-# If 'on', version symlinks for shared libraries will not be created. Affects
-# Unix builds only.
-feature.feature('install-no-version-symlinks', ['on'], ['optional', 'incidental'])
-
-class InstallTargetClass(targets.BasicTarget):
-
-    def update_location(self, ps):
-        """If <location> is not set, sets it based on the project data."""
-
-        loc = ps.get('location')
-        if not loc:
-            loc = os.path.join(self.project().get('location'), self.name())
-            ps = ps.add_raw(["<location>" + loc])
-
-        return ps
-
-    def adjust_properties(self, target, build_ps):
-        a = target.action()
-        properties = []
-        if a:
-            ps = a.properties()
-            properties = ps.all()
-            
-            # Unless <hardcode-dll-paths>true is in properties, which can happen
-            # only if the user has explicitly requested it, nuke all <dll-path>
-            # properties.
-
-            if build_ps.get('hardcode-dll-paths') != ['true']:
-                properties = [p for p in properties if p.feature().name() != 'dll-path']
-
-            # If any <dll-path> properties were specified for installing, add
-            # them.
-            properties.extend(build_ps.get_properties('dll-path'))
-
-            # Also copy <linkflags> feature from current build set, to be used
-            # for relinking.
-            properties.extend(build_ps.get_properties('linkflags'))
-
-            # Remove the <tag> feature on original targets.
-            # And <location>. If stage target has another stage target in
-            # sources, then we shall get virtual targets with the <location>
-            # property set.
-            properties = [p for p in properties
-                          if not p.feature().name() in ['tag', 'location']]
-
-        properties.extend(build_ps.get_properties('dependency'))
-
-        properties.extend(build_ps.get_properties('location'))
-        
-
-        properties.extend(build_ps.get_properties('install-no-version-symlinks'))
-
-        d = build_ps.get_properties('install-source-root')
-
-        # Make the path absolute: we shall use it to compute relative paths and
-        # making the path absolute will help.
-        if d:
-            p = d[0]
-            properties.append(property.Property(p.feature(), os.path.abspath(p.value())))
-
-        return property_set.create(properties)
-    
-
-    def construct(self, name, source_targets, ps):
-
-        source_targets = self.targets_to_stage(source_targets, ps)
-        ps = self.update_location(ps)
-
-        ename = ps.get('name')
-        if ename:
-            ename = ename[0]
-        if ename and len(source_targets) > 1:
-            get_manager().errors()("When <name> property is used in 'install', only one source is allowed")
-
-        result = []
-
-        for i in source_targets:
-
-            staged_targets = []
-            new_ps = self.adjust_properties(i, ps)
-
-            # See if something special should be done when staging this type. It
-            # is indicated by the presence of a special "INSTALLED_" type.
-            t = i.type()
-            if t and b2.build.type.registered("INSTALLED_" + t):
-
-                if ename:
-                    get_manager().errors()("In 'install': <name> property specified with target that requires relinking.")
-                else:
-                    (r, targets) = generators.construct(self.project(), name, "INSTALLED_" + t,
-                                                        new_ps, [i])
-                    assert isinstance(r, property_set.PropertySet)
-                    staged_targets.extend(targets)
-                    
-            else:
-                staged_targets.append(copy_file(self.project(), ename, i, new_ps))
-
-            if not staged_targets:
-                get_manager().errors()("Unable to generate staged version of " + i)
-
-            result.extend(get_manager().virtual_targets().register(t) for t in staged_targets)
-
-        return (property_set.empty(), result)
-
-    def targets_to_stage(self, source_targets, ps):
-        """Given the list of source targets explicitly passed to 'stage', returns the
-        list of targets which must be staged."""
-
-        result = []
-
-        # Traverse the dependencies, if needed.
-        if ps.get('install-dependencies') == ['on']:
-            source_targets = self.collect_targets(source_targets)
-
-        # Filter the target types, if needed.
-        included_types = ps.get('install-type')
-        for r in source_targets:
-            ty = r.type()
-            if ty:
-                # Do not stage searched libs.
-                if ty != "SEARCHED_LIB":
-                    if included_types:
-                        if self.include_type(ty, included_types):
-                            result.append(r)
-                    else:
-                        result.append(r)
-            elif not included_types:
-                # Don't install typeless target if there is an explicit list of
-                # allowed types.
-                result.append(r)
-
-        return result
-
-    # CONSIDER: figure out why we can not use virtual-target.traverse here.
-    #
-    def collect_targets(self, targets):
-        
-        s = [t.creating_subvariant() for t in targets]
-        s = unique(s)
-        
-        result = set(targets)
-        for i in s:
-            i.all_referenced_targets(result)
-           
-        result2 = []
-        for r in result:
-            if isinstance(r, property.Property):
-                
-                if r.feature().name() != 'use':
-                    result2.append(r.value())
-            else:
-                result2.append(r)
-        result2 = unique(result2)
-        return result2
-
-    # Returns true iff 'type' is subtype of some element of 'types-to-include'.
-    #
-    def include_type(self, type, types_to_include):
-        return any(b2.build.type.is_subtype(type, ti) for ti in types_to_include)
-
-# Creates a copy of target 'source'. The 'properties' object should have a
-# <location> property which specifies where the target must be placed.
-#
-def copy_file(project, name, source, ps):
-
-    if not name:
-        name = source.name()
-
-    relative = ""
-
-    new_a = virtual_target.NonScanningAction([source], "common.copy", ps)
-    source_root = ps.get('install-source-root')
-    if source_root:
-        source_root = source_root[0]
-        # Get the real path of the target. We probably need to strip relative
-        # path from the target name at construction.
-        path = os.path.join(source.path(), os.path.dirname(name))
-        # Make the path absolute. Otherwise, it would be hard to compute the
-        # relative path. The 'source-root' is already absolute, see the
-        # 'adjust-properties' method above.
-        path = os.path.abspath(path)
-
-        relative = os.path.relpath(path, source_root)
-
-    name = os.path.join(relative, os.path.basename(name))
-    return virtual_target.FileTarget(name, source.type(), project, new_a, exact=True)
-
-def symlink(name, project, source, ps):
-    a = virtual_target.Action([source], "symlink.ln", ps)
-    return virtual_target.FileTarget(name, source.type(), project, a, exact=True)
-
-def relink_file(project, source, ps):
-    action = source.action()
-    cloned_action = virtual_target.clone_action(action, project, "", ps)
-    targets = cloned_action.targets()
-    # We relink only on Unix, where exe or shared lib is always a single file.
-    assert len(targets) == 1
-    return targets[0]
-
-
-# Declare installed version of the EXE type. Generator for this type will cause
-# relinking to the new location.
-b2.build.type.register('INSTALLED_EXE', [], 'EXE')
-
-class InstalledExeGenerator(generators.Generator):
-
-    def __init__(self):
-        generators.Generator.__init__(self, "install-exe", False, ['EXE'], ['INSTALLED_EXE'])
-
-    def run(self, project, name, ps, source):
-
-        need_relink = False;
-
-        if ps.get('os') in ['NT', 'CYGWIN'] or ps.get('target-os') in ['windows', 'cygwin']:
-            # Never relink
-            pass
-        else:
-            # See if the dll-path properties are not changed during
-            # install. If so, copy, don't relink.
-            need_relink = ps.get('dll-path') != source[0].action().properties().get('dll-path')
-
-        if need_relink:
-            return [relink_file(project, source, ps)]
-        else:
-            return [copy_file(project, None, source[0], ps)]
-
-generators.register(InstalledExeGenerator())
-
-
-# Installing a shared link on Unix might cause a creation of versioned symbolic
-# links.
-b2.build.type.register('INSTALLED_SHARED_LIB', [], 'SHARED_LIB')
-
-class InstalledSharedLibGenerator(generators.Generator):
-
-    def __init__(self):
-        generators.Generator.__init__(self, 'install-shared-lib', False, ['SHARED_LIB'], ['INSTALLED_SHARED_LIB'])
-
-    def run(self, project, name, ps, source):
-
-        source = source[0]
-        if ps.get('os') in ['NT', 'CYGWIN'] or ps.get('target-os') in ['windows', 'cygwin']:
-            copied = copy_file(project, None, source, ps)
-            return [get_manager().virtual_targets().register(copied)]
-        else:
-            a = source.action()
-            if not a:
-                # Non-derived file, just copy.
-                copied = copy_file(project, source, ps)
-            else:
-
-                need_relink = ps.get('dll-path') != source.action().properties().get('dll-path')
-                
-                if need_relink:
-                    # Rpath changed, need to relink.
-                    copied = relink_file(project, source, ps)
-                else:
-                    copied = copy_file(project, None, source, ps)
-
-            result = [get_manager().virtual_targets().register(copied)]
-            # If the name is in the form NNN.XXX.YYY.ZZZ, where all 'X', 'Y' and
-            # 'Z' are numbers, we need to create NNN.XXX and NNN.XXX.YYY
-            # symbolic links.
-            m = re.match("(.*)\\.([0123456789]+)\\.([0123456789]+)\\.([0123456789]+)$",
-                         copied.name());
-            if m:
-                # Symlink without version at all is used to make
-                # -lsome_library work.
-                result.append(symlink(m.group(1), project, copied, ps))
-
-                # Symlinks of some libfoo.N and libfoo.N.M are used so that
-                # library can found at runtime, if libfoo.N.M.X has soname of
-                # libfoo.N. That happens when the library makes some binary
-                # compatibility guarantees. If not, it is possible to skip those
-                # symlinks.
-                if ps.get('install-no-version-symlinks') != ['on']:
-                
-                    result.append(symlink(m.group(1) + '.' + m.group(2), project, copied, ps))
-                    result.append(symlink(m.group(1) + '.' + m.group(2) + '.' + m.group(3),
-                                          project, copied, ps))
-
-            return result
-            
-generators.register(InstalledSharedLibGenerator())
-
-
-# Main target rule for 'install'.
-#
-@bjam_signature((["name"], ["sources", "*"], ["requirements", "*"],
-                 ["default_build", "*"], ["usage_requirements", "*"]))
-def install(name, sources, requirements=[], default_build=[], usage_requirements=[]):
-
-    requirements = requirements[:]
-    # Unless the user has explicitly asked us to hardcode dll paths, add
-    # <hardcode-dll-paths>false in requirements, to override default value.
-    if not '<hardcode-dll-paths>true' in requirements:
-        requirements.append('<hardcode-dll-paths>false')
-
-    if any(r.startswith('<tag>') for r in requirements):
-        get_manager().errors()("The <tag> property is not allowed for the 'install' rule")
-
-    from b2.manager import get_manager
-    t = get_manager().targets()
-    
-    project = get_manager().projects().current()
-        
-    return t.main_target_alternative(
-        InstallTargetClass(name, project,
-                           t.main_target_sources(sources, name),
-                           t.main_target_requirements(requirements, project),
-                           t.main_target_default_build(default_build, project),
-                           t.main_target_usage_requirements(usage_requirements, project)))
-
-get_manager().projects().add_rule("install", install)
-get_manager().projects().add_rule("stage", install)
-
diff --git a/jam-files/boost-build/tools/stlport.jam b/jam-files/boost-build/tools/stlport.jam
deleted file mode 100644
index 62eebda5..00000000
--- a/jam-files/boost-build/tools/stlport.jam
+++ /dev/null
@@ -1,303 +0,0 @@
-# Copyright Gennadiy Rozental
-# Copyright 2006 Rene Rivera 
-# Copyright 2003, 2004, 2006 Vladimir Prus 
-# Distributed under the Boost Software License, Version 1.0. 
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt) 
-
-# The STLPort is usable by means of 'stdlib' feature. When
-# stdlib=stlport is specified, default version of STLPort will be used,
-# while stdlib=stlport-4.5 will use specific version.
-# The subfeature value 'hostios' means to use host compiler's iostreams.
-#
-# The specific version of stlport is selected by features:
-# The <runtime-link> feature selects between static and shared library
-# The <runtime-debugging>on selects STLPort with debug symbols
-# and stl debugging.
-# There's no way to use STLPort with debug symbols but without
-# stl debugging.
-
-# TODO: must implement selection of different STLPort installations based
-# on used toolset.
-# Also, finish various flags:
-#
-# This is copied from V1 toolset, "+" means "implemented"
-#+flags $(CURR_TOOLSET) DEFINES <stlport-iostream>off : _STLP_NO_OWN_IOSTREAMS=1 _STLP_HAS_NO_NEW_IOSTREAMS=1 ;
-#+flags $(CURR_TOOLSET) DEFINES <stlport-extensions>off : _STLP_NO_EXTENSIONS=1 ;
-# flags $(CURR_TOOLSET) DEFINES <stlport-anachronisms>off : _STLP_NO_ANACHRONISMS=1 ;
-# flags $(CURR_TOOLSET) DEFINES <stlport-cstd-namespace>global : _STLP_VENDOR_GLOBAL_CSTD=1 ;
-# flags $(CURR_TOOLSET) DEFINES <exception-handling>off : _STLP_NO_EXCEPTIONS=1 ;
-# flags $(CURR_TOOLSET) DEFINES <stlport-debug-alloc>on : _STLP_DEBUG_ALLOC=1 ;
-#+flags $(CURR_TOOLSET) DEFINES <runtime-build>debug : _STLP_DEBUG=1 _STLP_DEBUG_UNINITIALIZED=1 ;
-#+flags $(CURR_TOOLSET) DEFINES <runtime-link>dynamic : _STLP_USE_DYNAMIC_LIB=1 ;
-
-
-import feature : feature subfeature ;
-import project ;
-import "class" : new ;
-import targets ;
-import property-set ;
-import common ;
-import type ;
-
-# Make this module into a project.
-project.initialize $(__name__) ;
-project stlport ;
-
-# The problem: how to request to use host compiler's iostreams?
-#
-# Solution 1: Global 'stlport-iostream' feature.
-#    That's ugly. Subfeature make more sense for stlport-specific thing.
-# Solution 2: Use subfeature with two values, one of which ("use STLPort iostream")
-#     is default.
-#    The problem is that such subfeature will appear in target paths, and that's ugly
-# Solution 3: Use optional subfeature with only one value.
-
-feature.extend stdlib : stlport ;
-feature.compose <stdlib>stlport : <library>/stlport//stlport ;
-
-# STLport iostreams or native iostreams
-subfeature stdlib stlport : iostream : hostios : optional propagated  ;
-
-# STLport extensions
-subfeature stdlib stlport : extensions : noext : optional propagated ;
-
-# STLport anachronisms -- NOT YET SUPPORTED
-# subfeature stdlib stlport : anachronisms : on off ;
-
-# STLport debug allocation -- NOT YET SUPPORTED
-#subfeature stdlib stlport : debug-alloc : off on ;
-
-# Declare a special target class to handle the creation of search-lib-target
-# instances for STLport. We need a special class, because otherwise we'll have
-# - declare prebuilt targets for all possible toolsets. And by the time 'init'
-#   is called we don't even know the list of toolsets that are registered
-# - when host iostreams are used, we really should produce nothing. It would
-#   be hard/impossible to achieve this using prebuilt targets.
-
-class stlport-target-class : basic-target
-{
-    import feature project type errors generators ;
-    import set : difference ;
-
-    rule __init__ ( project : headers ? : libraries * :  version ? )
-    {
-        basic-target.__init__ stlport : $(project) ;
-        self.headers = $(headers) ;
-        self.libraries = $(libraries) ;
-        self.version = $(version) ;
-        self.version.5 = [ MATCH "^(5[.][0123456789]+).*" : $(version) ] ;
-        
-        local requirements ;
-        requirements += <stdlib-stlport:version>$(self.version) ;
-        self.requirements = [ property-set.create $(requirements) ] ;
-    }
-
-    rule generate ( property-set )
-    {
-        # Since this target is built with <stdlib>stlport, it will also
-        # have <library>/stlport//stlport in requirements, which will
-        # cause a loop in main target references. Remove that property
-        # manually.
-
-        property-set = [ property-set.create
-            [ difference
-                [ $(property-set).raw ] :
-                <library>/stlport//stlport
-                <stdlib>stlport
-                ]
-            ] ;
-        return [ basic-target.generate $(property-set) ] ;
-    }
-
-    rule construct ( name : source-targets * : property-set )
-    {
-        # Deduce the name of stlport library, based on toolset and
-        # debug setting.
-        local raw = [ $(property-set).raw ] ;
-        local hostios = [ feature.get-values <stdlib-stlport:iostream> : $(raw) ] ;
-        local toolset = [ feature.get-values <toolset> : $(raw) ] ;
-
-        if $(self.version.5)
-        {
-            # Version 5.x
-            
-            # STLport host IO streams no longer supported. So we always 
-            # need libraries.
-            
-            # name: stlport(stl)?[dg]?(_static)?.M.R
-            local name = stlport ;
-            if [ feature.get-values <runtime-debugging> : $(raw) ] = "on"
-            {
-                name += stl ;
-                switch $(toolset)
-                {
-                    case gcc* : name += g ;
-                    case darwin* : name += g ;
-                    case * : name += d ;
-                }
-            }
-
-            if [ feature.get-values <runtime-link> : $(raw) ] = "static"
-            {
-                name += _static ;
-            }
-
-            # Starting with version 5.2.0, the STLport static libraries no longer
-            #  include a version number in their name
-            local version.pre.5.2 = [ MATCH "^(5[.][01]+).*" : $(version) ] ;
-            if $(version.pre.5.2) || [ feature.get-values <runtime-link> : $(raw) ] != "static" 
-            {
-                name += .$(self.version.5) ;
-            }
-			
-            name = $(name:J=) ;
-            
-            if [ feature.get-values <install-dependencies> : $(raw) ] = "on"
-            {
-                #~ Allow explicitly asking to install the STLport lib by
-                #~ refering to it directly: /stlport//stlport/<install-dependencies>on
-                #~ This allows for install packaging of all libs one might need for
-                #~ a standalone distribution.
-                import path : make : path-make ;
-                local runtime-link
-                    = [ feature.get-values <runtime-link> : $(raw) ] ;
-                local lib-file.props
-                    = [ property-set.create $(raw) <link>$(runtime-link) ] ;
-                local lib-file.prefix
-                    = [ type.generated-target-prefix $(runtime-link:U)_LIB : $(lib-file.props) ] ;
-                local lib-file.suffix
-                    = [ type.generated-target-suffix $(runtime-link:U)_LIB : $(lib-file.props) ] ;
-                lib-file.prefix
-                    ?= "" "lib" ;
-                lib-file.suffix
-                    ?= "" ;
-                local lib-file
-                    = [ GLOB $(self.libraries) [ modules.peek : PATH ] :
-                        $(lib-file.prefix)$(name).$(lib-file.suffix) ] ;
-                lib-file
-                    = [ new file-reference [ path-make $(lib-file[1]) ] : $(self.project) ] ;
-                lib-file
-                    = [ $(lib-file).generate "" ] ;
-                local lib-file.requirements
-                    = [ targets.main-target-requirements
-                        [ $(lib-file.props).raw ] <file>$(lib-file[-1])
-                        : $(self.project) ] ;
-                return [ generators.construct $(self.project) $(name) : LIB : $(lib-file.requirements) ] ;
-            }
-            else
-            {
-                #~ Otherwise, it's just a regular usage of the library.
-                return [ generators.construct
-                    $(self.project) $(name) : SEARCHED_LIB : $(property-set) ] ;
-            }
-        }
-        else if ! $(hostios) && $(toolset) != msvc
-        {
-            # We don't need libraries if host istreams are used. For
-            # msvc, automatic library selection will be used.
-            
-            # name: stlport_<toolset>(_stldebug)?
-            local name = stlport ;
-            name = $(name)_$(toolset) ;
-            if [ feature.get-values <runtime-debugging> : $(raw) ] = "on"
-            {
-                name = $(name)_stldebug ;
-            }
-
-            return [ generators.construct
-                $(self.project) $(name) : SEARCHED_LIB : $(property-set) ] ;
-        }
-        else
-        {
-            return [ property-set.empty ] ;
-        }
-    }
-
-    rule compute-usage-requirements ( subvariant )
-    {
-        local usage-requirements =
-            <include>$(self.headers)
-            <dll-path>$(self.libraries)
-            <library-path>$(self.libraries)
-            ;
-
-        local rproperties = [ $(subvariant).build-properties ] ;
-        # CONSIDER: should this "if" sequence be replaced with
-        # some use of 'property-map' class?
-        if [ $(rproperties).get <runtime-debugging> ] = "on"
-        {
-            usage-requirements +=
-                <define>_STLP_DEBUG=1
-                <define>_STLP_DEBUG_UNINITIALIZED=1 ;
-        }
-        if [ $(rproperties).get <runtime-link> ] = "shared"
-        {
-            usage-requirements +=
-                <define>_STLP_USE_DYNAMIC_LIB=1 ;
-        }
-        if [ $(rproperties).get <stdlib-stlport:extensions> ] = noext
-        {
-            usage-requirements +=
-                <define>_STLP_NO_EXTENSIONS=1 ;
-        }
-        if [ $(rproperties).get <stdlib-stlport:iostream> ] = hostios
-        {
-            usage-requirements +=
-                <define>_STLP_NO_OWN_IOSTREAMS=1
-                <define>_STLP_HAS_NO_NEW_IOSTREAMS=1 ;
-        }
-        if $(self.version.5)
-        {
-            # Version 5.x
-            if [ $(rproperties).get <threading> ] = "single"
-            {
-                # Since STLport5 doesn't normally support single-thread
-                # we force STLport5 into the multi-thread mode. Hence
-                # getting what other libs provide of single-thread code
-                # linking against a multi-thread lib.
-                usage-requirements +=
-                    <define>_STLP_THREADS=1 ;
-            }
-        }
-        
-        return [ property-set.create $(usage-requirements) ] ;
-    }
-}
-
-rule stlport-target ( headers ? : libraries * : version ? )
-{
-    local project = [ project.current ] ;
-
-    targets.main-target-alternative
-      [ new stlport-target-class  $(project) : $(headers) : $(libraries)
-        : $(version)
-      ] ;
-}
-
-local .version-subfeature-defined ;
-
-# Initialize stlport support.
-rule init (
-    version ? :
-    headers   :     # Location of header files
-    libraries *     # Location of libraries, lib and bin subdirs of STLport.
-    )
-{
-    # FIXME: need to use common.check-init-parameters here.
-    # At the moment, that rule always tries to define subfeature
-    # of the 'toolset' feature, while we need to define subfeature
-    # of <stdlib>stlport, so tweaks to check-init-parameters are needed.
-    if $(version)
-    {
-        if ! $(.version-subfeature-defined)
-        {
-            feature.subfeature stdlib stlport : version : : propagated ;
-            .version-subfeature-defined = true ;
-        }
-        feature.extend-subfeature stdlib stlport : version : $(version) ;
-    }
-
-    # Declare the main target for this STLPort version.
-    stlport-target $(headers) : $(libraries) : $(version) ;
-}
-
diff --git a/jam-files/boost-build/tools/sun.jam b/jam-files/boost-build/tools/sun.jam
deleted file mode 100644
index 0ca927d3..00000000
--- a/jam-files/boost-build/tools/sun.jam
+++ /dev/null
@@ -1,142 +0,0 @@
-#  Copyright (C) Christopher Currie 2003. Permission to copy, use,
-#  modify, sell and distribute this software is granted provided this
-#  copyright notice appears in all copies. This software is provided
-#  "as is" without express or implied warranty, and with no claim as
-#  to its suitability for any purpose.
-
-import property ;
-import generators ;
-import os ;
-import toolset : flags ;
-import feature ;
-import type ;
-import common ;
-
-feature.extend toolset : sun ;
-toolset.inherit  sun : unix ;
-generators.override sun.prebuilt : builtin.lib-generator ;
-generators.override sun.prebuilt : builtin.prebuilt ;
-generators.override sun.searched-lib-generator : searched-lib-generator ;
-
-feature.extend stdlib : sun-stlport ;
-feature.compose <stdlib>sun-stlport
-    : <cxxflags>-library=stlport4 <linkflags>-library=stlport4
-    ;
-
-rule init ( version ? : command * : options * ) 
-{
-    local condition = [ 
-      common.check-init-parameters sun : version $(version) ] ;
-    
-    command = [ common.get-invocation-command sun : CC 
-        : $(command) : "/opt/SUNWspro/bin" ] ;
-
-    # Even if the real compiler is not found, put CC to
-    # command line so that user see command line that would have being executed.
-    command ?= CC ;
-
-    common.handle-options sun : $(condition) : $(command) : $(options) ;
-    
-    command_c = $(command[1--2]) $(command[-1]:B=cc) ;
-
-    toolset.flags sun CONFIG_C_COMMAND $(condition) : $(command_c) ;
-}
-
-# Declare generators
-generators.register-c-compiler sun.compile.c : C : OBJ : <toolset>sun ;
-generators.register-c-compiler sun.compile.c++ : CPP : OBJ : <toolset>sun ;
-
-# Declare flags and actions for compilation
-flags sun.compile OPTIONS <debug-symbols>on : -g ;
-flags sun.compile OPTIONS <profiling>on : -xprofile=tcov ;
-flags sun.compile OPTIONS <optimization>speed : -xO4  ;
-flags sun.compile OPTIONS <optimization>space : -xO2 -xspace ;
-flags sun.compile OPTIONS <threading>multi : -mt ;
-flags sun.compile OPTIONS <warnings>off : -erroff ;
-flags sun.compile OPTIONS <warnings>on : -erroff=%none ;
-flags sun.compile OPTIONS <warnings>all  : -erroff=%none ;
-flags sun.compile OPTIONS <warnings-as-errors>on : -errwarn ;
-
-flags sun.compile.c++ OPTIONS <inlining>off : +d ;
-
-# The -m32 and -m64 options are supported starting
-# with Sun Studio 12.  On earlier compilers, the
-# 'address-model' feature is not supported and should not
-# be used. Instead, use -xarch=generic64 command line
-# option.
-# See http://svn.boost.org/trac/boost/ticket/1186
-# for details.
-flags sun OPTIONS <address-model>32 : -m32 ;
-flags sun OPTIONS <address-model>64 : -m64 ;
-# On sparc, there's a difference between -Kpic
-# and -KPIC. The first is slightly more efficient,
-# but has the limits on the size of GOT table.
-# For minimal fuss on user side, we use -KPIC here.
-# See http://svn.boost.org/trac/boost/ticket/1186#comment:6
-# for detailed explanation.
-flags sun OPTIONS <link>shared : -KPIC ;
-
-flags sun.compile OPTIONS <cflags> ;
-flags sun.compile.c++ OPTIONS <cxxflags> ;
-flags sun.compile DEFINES <define> ;
-flags sun.compile INCLUDES <include> ;
-
-actions compile.c
-{
-    "$(CONFIG_C_COMMAND)" $(OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -c -o "$(<)" "$(>)"
-}
-
-actions compile.c++
-{
-    "$(CONFIG_COMMAND)" $(OPTIONS) -D$(DEFINES) -I"$(INCLUDES)" -c -o "$(<)" "$(>)"
-}
-
-# Declare flags and actions for linking
-flags sun.link OPTIONS <debug-symbols>on : -g ;
-# Strip the binary when no debugging is needed
-flags sun.link OPTIONS <debug-symbols>off : -s ;
-flags sun.link OPTIONS <profiling>on : -xprofile=tcov ;
-flags sun.link OPTIONS <threading>multi : -mt ;
-flags sun.link OPTIONS <linkflags> ;
-flags sun.link LINKPATH <library-path> ;
-flags sun.link FINDLIBS-ST <find-static-library> ;
-flags sun.link FINDLIBS-SA <find-shared-library> ;
-flags sun.link LIBRARIES <library-file> ;
-flags sun.link LINK-RUNTIME <runtime-link>static : static ;
-flags sun.link LINK-RUNTIME <runtime-link>shared : dynamic ;
-flags sun.link RPATH <dll-path> ;
-# On gcc, there are separate options for dll path at runtime and
-# link time. On Solaris, there's only one: -R, so we have to use
-# it, even though it's bad idea.
-flags sun.link RPATH <xdll-path> ;
-
-# The POSIX real-time library is always needed (nanosleep, clock_gettime etc.)
-flags sun.link FINDLIBS-SA : rt ;
-
-rule link ( targets * : sources * : properties * )
-{
-    SPACE on $(targets) = " " ;
-}
-
-actions link bind LIBRARIES
-{
-    "$(CONFIG_COMMAND)" $(OPTIONS) -L"$(LINKPATH)" -R"$(RPATH)" -o "$(<)" "$(>)" "$(LIBRARIES)" -Bdynamic -l$(FINDLIBS-SA) -Bstatic -l$(FINDLIBS-ST) -B$(LINK-RUNTIME)
-}
-
-# Slight mods for dlls
-rule link.dll ( targets * : sources * : properties * )
-{
-    SPACE on $(targets) = " " ;
-}
-
-actions link.dll bind LIBRARIES
-{
-    "$(CONFIG_COMMAND)" $(OPTIONS) -L"$(LINKPATH)" -R"$(RPATH)" -o "$(<)" -h$(<[1]:D=) -G "$(>)" "$(LIBRARIES)" -Bdynamic -l$(FINDLIBS-SA) -Bstatic -l$(FINDLIBS-ST) -B$(LINK-RUNTIME)
-}
-
-# Declare action for creating static libraries
-actions piecemeal archive
-{
-    "$(CONFIG_COMMAND)" -xar -o "$(<)" "$(>)"
-}
-
diff --git a/jam-files/boost-build/tools/symlink.jam b/jam-files/boost-build/tools/symlink.jam
deleted file mode 100644
index b33e8260..00000000
--- a/jam-files/boost-build/tools/symlink.jam
+++ /dev/null
@@ -1,140 +0,0 @@
-# Copyright 2003 Dave Abrahams 
-# Copyright 2002, 2003 Rene Rivera 
-# Copyright 2002, 2003, 2004, 2005 Vladimir Prus 
-# Distributed under the Boost Software License, Version 1.0. 
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt) 
-
-# Defines the "symlink" special target. 'symlink' targets make symbolic links
-# to the sources.
-
-import targets modules path class os feature project property-set ;
-
-.count = 0 ;
-
-feature.feature symlink-location : project-relative build-relative : incidental ;
-
-# The class representing "symlink" targets.
-#
-class symlink-targets : basic-target
-{
-    import numbers modules class property project path ;
-    
-    rule __init__ (
-      project
-        : targets *
-        : sources *
-    )
-    {    
-        # Generate a fake name for now. Need unnamed targets eventually.
-        local c = [ modules.peek symlink : .count ] ;
-        modules.poke symlink : .count : [ numbers.increment $(c) ] ;
-        local fake-name = symlink#$(c) ;
-    
-          basic-target.__init__ $(fake-name) : $(project) : $(sources) ;
-    
-        # Remember the targets to map the sources onto. Pad or truncate
-        # to fit the sources given.
-        self.targets = ;
-        for local source in $(sources)
-        {
-            if $(targets)
-            {
-                self.targets += $(targets[1]) ;
-                targets = $(targets[2-]) ;
-            }
-            else
-            {
-                self.targets += $(source) ;
-            }
-        }
-    
-        # The virtual targets corresponding to the given targets.
-        self.virtual-targets = ;
-    }    
-    
-    rule construct ( name : source-targets * : property-set )
-    {
-        local i = 1 ;
-        for local t in $(source-targets)
-        {
-            local s = $(self.targets[$(i)]) ;
-            local a = [ class.new action  $(t) : symlink.ln : $(property-set) ] ;
-            local vt = [ class.new file-target $(s:D=) 
-              : [ $(t).type ] : $(self.project) : $(a) ] ;
-            
-            # Place the symlink in the directory relative to the project
-            # location, instead of placing it in the build directory.
-            if [ property.select <symlink-location> : [ $(property-set).raw ] ] = <symlink-location>project-relative
-            {
-                $(vt).set-path [ path.root $(s:D) [ $(self.project).get location ] ] ;
-            }
-            
-            self.virtual-targets += $(vt) ;
-            i = [ numbers.increment $(i) ] ;
-        }
-        return [ property-set.empty ] $(self.virtual-targets) ;
-    }
-}
-
-# Creates a symbolic link from a set of targets to a set of sources.
-# The targets and sources map one to one. The symlinks generated are
-# limited to be the ones given as the sources. That is, the targets
-# are either padded or trimmed to equate to the sources. The padding
-# is done with the name of the corresponding source. For example::
-#
-#     symlink : one two ;
-#
-# Is equal to::
-#
-#     symlink one two : one two ;
-#
-# Names for symlink are relative to the project location. They cannot
-# include ".." path components.
-rule symlink (
-    targets *
-    : sources *
-    )
-{
-    local project = [ project.current ] ;
-    
-    return [ targets.main-target-alternative
-        [ class.new symlink-targets $(project) : $(targets) : 
-          # Note: inline targets are not supported for symlink, intentionally,
-          # since it's used to linking existing non-local targets.
-          $(sources) ] ] ;
-}
-
-rule ln
-{
-    local os ;
-    if [ modules.peek : UNIX ] { os = UNIX ; }
-    else { os ?= [ os.name ] ; }
-    # Remember the path to make the link relative to where the symlink is located.
-    local path-to-source = [ path.relative-to
-        [ path.make [ on $(<) return $(LOCATE) ] ]
-        [ path.make [ on $(>) return $(LOCATE) ] ] ] ;
-    if $(path-to-source) = .
-    {
-        PATH_TO_SOURCE on $(<) = "" ;
-    }
-    else
-    {
-        PATH_TO_SOURCE on $(<) = [ path.native $(path-to-source) ] ;
-    }
-    ln-$(os) $(<) : $(>) ;
-}
-
-actions ln-UNIX
-{
-    ln -f -s '$(>:D=:R=$(PATH_TO_SOURCE))' '$(<)'
-}
-
-# there is a way to do this; we fall back to a copy for now
-actions ln-NT
-{
-    echo "NT symlinks not supported yet, making copy"
-    del /f /q "$(<)" 2>nul >nul
-    copy "$(>)" "$(<)" $(NULL_OUT)
-}
-
-IMPORT $(__name__) : symlink : : symlink ;
diff --git a/jam-files/boost-build/tools/symlink.py b/jam-files/boost-build/tools/symlink.py
deleted file mode 100644
index 6345ded6..00000000
--- a/jam-files/boost-build/tools/symlink.py
+++ /dev/null
@@ -1,112 +0,0 @@
-# Status: ported.
-# Base revision: 64488.
-
-# Copyright 2003 Dave Abrahams 
-# Copyright 2002, 2003 Rene Rivera 
-# Copyright 2002, 2003, 2004, 2005 Vladimir Prus 
-# Distributed under the Boost Software License, Version 1.0. 
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt) 
-
-# Defines the "symlink" special target. 'symlink' targets make symbolic links
-# to the sources.
-
-import b2.build.feature as feature
-import b2.build.targets as targets
-import b2.build.property_set as property_set
-import b2.build.virtual_target as virtual_target
-import b2.build.targets
-
-from b2.manager import get_manager
-
-import bjam
-
-import os
-
-
-feature.feature("symlink-location", ["project-relative", "build-relative"], ["incidental"])
-
-class SymlinkTarget(targets.BasicTarget):
-
-    _count = 0
-
-    def __init__(self, project, targets, sources):
-         
-        # Generate a fake name for now. Need unnamed targets eventually.
-        fake_name = "symlink#%s" % SymlinkTarget._count
-        SymlinkTarget._count = SymlinkTarget._count + 1
-
-        b2.build.targets.BasicTarget.__init__(self, fake_name, project, sources)
-    
-        # Remember the targets to map the sources onto. Pad or truncate
-        # to fit the sources given.
-        assert len(targets) <= len(sources)
-        self.targets = targets[:] + sources[len(targets):]
-            
-        # The virtual targets corresponding to the given targets.
-        self.virtual_targets = []
-
-    def construct(self, name, source_targets, ps):
-        i = 0
-        for t in source_targets:
-            s = self.targets[i]
-            a = virtual_target.Action(self.manager(), [t], "symlink.ln", ps)
-            vt = virtual_target.FileTarget(os.path.basename(s), t.type(), self.project(), a)
-                        
-            # Place the symlink in the directory relative to the project
-            # location, instead of placing it in the build directory.
-            if not ps.get('symlink-location') == "project-relative":
-                vt.set_path(os.path.join(self.project().get('location'), os.path.dirname(s)))
-
-            vt = get_manager().virtual_targets().register(vt)
-            self.virtual_targets.append(vt)
-            i = i + 1
-
-        return (property_set.empty(), self.virtual_targets)
-
-# Creates a symbolic link from a set of targets to a set of sources.
-# The targets and sources map one to one. The symlinks generated are
-# limited to be the ones given as the sources. That is, the targets
-# are either padded or trimmed to equate to the sources. The padding
-# is done with the name of the corresponding source. For example::
-#
-#     symlink : one two ;
-#
-# Is equal to::
-#
-#     symlink one two : one two ;
-#
-# Names for symlink are relative to the project location. They cannot
-# include ".." path components.
-def symlink(targets, sources):
-
-    from b2.manager import get_manager
-    t = get_manager().targets()   
-    p = get_manager().projects().current()
-
-    return t.main_target_alternative(
-        SymlinkTarget(p, targets, 
-                      # Note: inline targets are not supported for symlink, intentionally,
-                      # since it's used to linking existing non-local targets.
-                      sources))
-
-
-def setup_ln(targets, sources, ps):
-
-    source_path = bjam.call("get-target-variable", sources[0], "LOCATE")[0]
-    target_path = bjam.call("get-target-variable", targets[0], "LOCATE")[0]
-    rel = os.path.relpath(source_path, target_path)
-    if rel == ".":
-        bjam.call("set-target-variable", targets, "PATH_TO_SOURCE", "")
-    else:
-        bjam.call("set-target-variable", targets, "PATH_TO_SOURCE", rel)
-
-if os.name == 'nt':
-    ln_action = """echo "NT symlinks not supported yet, making copy"
-del /f /q "$(<)" 2>nul >nul
-copy "$(>)" "$(<)" $(NULL_OUT)"""
-else:
-    ln_action = "ln -f -s '$(>:D=:R=$(PATH_TO_SOURCE))' '$(<)'"
-
-get_manager().engine().register_action("symlink.ln", ln_action, function=setup_ln)
-
-get_manager().projects().add_rule("symlink", symlink)
diff --git a/jam-files/boost-build/tools/testing-aux.jam b/jam-files/boost-build/tools/testing-aux.jam
deleted file mode 100644
index 525dafd0..00000000
--- a/jam-files/boost-build/tools/testing-aux.jam
+++ /dev/null
@@ -1,210 +0,0 @@
-# This module is imported by testing.py. The definitions here are
-# too tricky to do in Python
-
-# Causes the 'target' to exist after bjam invocation if and only if all the
-# dependencies were successfully built.
-#
-rule expect-success ( target : dependency + : requirements * )
-{
-    **passed** $(target) : $(sources) ;
-}
-IMPORT testing : expect-success : : testing.expect-success ;
-
-# Causes the 'target' to exist after bjam invocation if and only if all some of
-# the dependencies were not successfully built.
-#
-rule expect-failure ( target : dependency + : properties * )
-{
-    local grist = [ MATCH ^<(.*)> : $(dependency:G) ] ;
-    local marker = $(dependency:G=$(grist)*fail) ;
-    (failed-as-expected) $(marker) ;
-    FAIL_EXPECTED $(dependency) ;
-    LOCATE on $(marker) = [ on $(dependency) return $(LOCATE) ] ;
-    RMOLD $(marker) ;
-    DEPENDS $(marker) : $(dependency) ;
-    DEPENDS $(target) : $(marker) ;
-    **passed** $(target) : $(marker) ;
-}
-IMPORT testing : expect-failure : : testing.expect-failure ;
-
-# The rule/action combination used to report successful passing of a test.
-#
-rule **passed**
-{
-    # Force deletion of the target, in case any dependencies failed to build.
-    RMOLD $(<) ;
-}
-
-
-# Used to create test files signifying passed tests.
-#
-actions **passed**
-{
-    echo passed > "$(<)"
-}
-
-
-# Used to create replacement object files that do not get created during tests
-# that are expected to fail.
-#
-actions (failed-as-expected)
-{
-    echo failed as expected > "$(<)"
-}
-
-# Runs executable 'sources' and stores stdout in file 'target'. Unless
-# --preserve-test-targets command line option has been specified, removes the
-# executable. The 'target-to-remove' parameter controls what should be removed:
-#   - if 'none', does not remove anything, ever
-#   - if empty, removes 'source'
-#   - if non-empty and not 'none', contains a list of sources to remove.
-#
-rule capture-output ( target : source : properties * : targets-to-remove * )
-{
-    output-file on $(target) = $(target:S=.output) ;
-    LOCATE on $(target:S=.output) = [ on $(target) return $(LOCATE) ] ;
-
-    # The INCLUDES kill a warning about independent target...
-    INCLUDES $(target) : $(target:S=.output) ;
-    # but it also puts .output into dependency graph, so we must tell jam it is
-    # OK if it cannot find the target or updating rule.
-    NOCARE $(target:S=.output) ;
-
-    # This has two-fold effect. First it adds input files to the dependendency
-    # graph, preventing a warning. Second, it causes input files to be bound
-    # before target is created. Therefore, they are bound using SEARCH setting
-    # on them and not LOCATE setting of $(target), as in other case (due to jam
-    # bug).
-    DEPENDS $(target) : [ on $(target) return $(INPUT_FILES) ] ;
-
-    if $(targets-to-remove) = none
-    {
-        targets-to-remove = ;
-    }
-    else if ! $(targets-to-remove)
-    {
-        targets-to-remove = $(source) ;
-    }
-
-    if [ on $(target) return $(REMOVE_TEST_TARGETS) ]
-    {
-        TEMPORARY $(targets-to-remove) ;
-        # Set a second action on target that will be executed after capture
-        # output action. The 'RmTemps' rule has the 'ignore' modifier so it is
-        # always considered succeeded. This is needed for 'run-fail' test. For
-        # that test the target will be marked with FAIL_EXPECTED, and without
-        # 'ignore' successful execution will be negated and be reported as
-        # failure. With 'ignore' we do not detect a case where removing files
-        # fails, but it is not likely to happen.
-        RmTemps $(target) : $(targets-to-remove) ;
-    }
-}
-
-
-if [ os.name ] = NT
-{
-    .STATUS        = %status% ;
-    .SET_STATUS    = "set status=%ERRORLEVEL%" ;
-    .RUN_OUTPUT_NL = "echo." ;
-    .STATUS_0      = "%status% EQU 0 (" ;
-    .STATUS_NOT_0  = "%status% NEQ 0 (" ;
-    .VERBOSE       = "%verbose% EQU 1 (" ;
-    .ENDIF         = ")" ;
-    .SHELL_SET     = "set " ;
-    .CATENATE      = type ;
-    .CP            = copy ;
-}
-else
-{
-    .STATUS        = "$status" ;
-    .SET_STATUS    = "status=$?" ;
-    .RUN_OUTPUT_NL = "echo" ;
-    .STATUS_0      = "test $status -eq 0 ; then" ;
-    .STATUS_NOT_0  = "test $status -ne 0 ; then" ;
-    .VERBOSE       = "test $verbose -eq 1 ; then" ;
-    .ENDIF         = "fi" ;
-    .SHELL_SET     = "" ;
-    .CATENATE      = cat ;
-    .CP            = cp ;
-}
-
-
-.VERBOSE_TEST = 0 ;
-if --verbose-test in [ modules.peek : ARGV ]
-{
-    .VERBOSE_TEST = 1 ;
-}
-
-
-.RM = [ common.rm-command ] ;
-
-
-actions capture-output bind INPUT_FILES output-file
-{
-    $(PATH_SETUP)
-    $(LAUNCHER) "$(>)" $(ARGS) "$(INPUT_FILES)" > "$(output-file)" 2>&1
-    $(.SET_STATUS)
-    $(.RUN_OUTPUT_NL) >> "$(output-file)"
-    echo EXIT STATUS: $(.STATUS) >> "$(output-file)"
-    if $(.STATUS_0)
-        $(.CP) "$(output-file)" "$(<)"
-    $(.ENDIF)
-    $(.SHELL_SET)verbose=$(.VERBOSE_TEST)
-    if $(.STATUS_NOT_0)
-        $(.SHELL_SET)verbose=1
-    $(.ENDIF)
-    if $(.VERBOSE)
-        echo ====== BEGIN OUTPUT ======
-        $(.CATENATE) "$(output-file)"
-        echo ====== END OUTPUT ======
-    $(.ENDIF)
-    exit $(.STATUS)
-}
-
-IMPORT testing : capture-output : : testing.capture-output ;
-
-
-actions quietly updated ignore piecemeal together RmTemps
-{
-    $(.RM) "$(>)"
-}
-
-
-.MAKE_FILE = [ common.file-creation-command ] ;
-
-actions unit-test
-{
-    $(PATH_SETUP)
-    $(LAUNCHER) $(>) $(ARGS) && $(.MAKE_FILE) $(<)
-}
-
-rule record-time ( target : source : start end user system )
-{
-    local src-string = [$(source:G=:J=",")"] " ;
-    USER_TIME on $(target) += $(src-string)$(user) ;
-    SYSTEM_TIME on $(target) += $(src-string)$(system) ;
-}
-
-# Calling this rule requests that Boost Build time how long it taks to build the
-# 'source' target and display the results both on the standard output and in the
-# 'target' file.
-#
-rule time ( target : source : properties *  )
-{
-    # Set up rule for recording timing information.
-    __TIMING_RULE__ on $(source) = testing.record-time $(target) ;
-
-    # Make sure that the source is rebuilt any time we need to retrieve that
-    # information.
-    REBUILDS $(target) : $(source) ;
-}
-
-
-actions time
-{
-    echo user: $(USER_TIME)
-    echo system: $(SYSTEM_TIME)
-
-    echo user: $(USER_TIME)" seconds" > "$(<)"
-    echo system: $(SYSTEM_TIME)" seconds" >> "$(<)"
-}
diff --git a/jam-files/boost-build/tools/testing.jam b/jam-files/boost-build/tools/testing.jam
deleted file mode 100644
index c42075b7..00000000
--- a/jam-files/boost-build/tools/testing.jam
+++ /dev/null
@@ -1,581 +0,0 @@
-# Copyright 2005 Dave Abrahams
-# Copyright 2002, 2003, 2004, 2005, 2006 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-# This module implements regression testing framework. It declares a number of
-# main target rules which perform some action and, if the results are OK,
-# creates an output file.
-#
-# The exact list of rules is:
-# 'compile'       -- creates .test file if compilation of sources was
-#                    successful.
-# 'compile-fail'  -- creates .test file if compilation of sources failed.
-# 'run'           -- creates .test file is running of executable produced from
-#                    sources was successful. Also leaves behind .output file
-#                    with the output from program run.
-# 'run-fail'      -- same as above, but .test file is created if running fails.
-#
-# In all cases, presence of .test file is an indication that the test passed.
-# For more convenient reporting, you might want to use C++ Boost regression
-# testing utilities (see http://www.boost.org/more/regression.html).
-#
-# For historical reason, a 'unit-test' rule is available which has the same
-# syntax as 'exe' and behaves just like 'run'.
-
-# Things to do:
-#  - Teach compiler_status handle Jamfile.v2.
-# Notes:
-#  - <no-warn> is not implemented, since it is Como-specific, and it is not
-#    clear how to implement it
-#  - std::locale-support is not implemented (it is used in one test).
-
-
-import alias ;
-import "class" ;
-import common ;
-import errors ;
-import feature ;
-import generators ;
-import os ;
-import path ;
-import project ;
-import property ;
-import property-set ;
-import regex ;
-import sequence ;
-import targets ;
-import toolset ;
-import type ;
-import virtual-target ;
-
-
-rule init ( )
-{
-}
-
-
-# Feature controling the command used to lanch test programs.
-feature.feature testing.launcher   : : free optional ;
-
-feature.feature test-info          : : free incidental ;
-feature.feature testing.arg        : : free incidental ;
-feature.feature testing.input-file : : free dependency ;
-
-feature.feature preserve-test-targets : on off : incidental propagated ;
-
-# Register target types.
-type.register TEST         : test          ;
-type.register COMPILE      :        : TEST ;
-type.register COMPILE_FAIL :        : TEST ;
-type.register RUN_OUTPUT   : run           ;
-type.register RUN          :        : TEST ;
-type.register RUN_FAIL     :        : TEST ;
-type.register LINK_FAIL    :        : TEST ;
-type.register LINK         :        : TEST ;
-type.register UNIT_TEST    : passed : TEST ;
-
-
-# Declare the rules which create main targets. While the 'type' module already
-# creates rules with the same names for us, we need extra convenience: default
-# name of main target, so write our own versions.
-
-# Helper rule. Create a test target, using basename of first source if no target
-# name is explicitly passed. Remembers the created target in a global variable.
-#
-rule make-test ( target-type : sources + : requirements * : target-name ? )
-{
-    target-name ?= $(sources[1]:D=:S=) ;
-
-    # Having periods (".") in the target name is problematic because the typed
-    # generator will strip the suffix and use the bare name for the file
-    # targets. Even though the location-prefix averts problems most times it
-    # does not prevent ambiguity issues when referring to the test targets. For
-    # example when using the XML log output. So we rename the target to remove
-    # the periods, and provide an alias for users.
-    local real-name = [ regex.replace $(target-name) "[.]" "~" ] ;
-
-    local project = [ project.current ] ;
-    # The <location-prefix> forces the build system for generate paths in the
-    # form '$build_dir/array1.test/gcc/debug'. This is necessary to allow
-    # post-processing tools to work.
-    local t = [ targets.create-typed-target [ type.type-from-rule-name
-        $(target-type) ] : $(project) : $(real-name) : $(sources) :
-        $(requirements) <location-prefix>$(real-name).test ] ;
-
-    # The alias to the real target, per period replacement above.
-    if $(real-name) != $(target-name)
-    {
-        alias $(target-name) : $(t) ;
-    }
-
-    # Remember the test (for --dump-tests). A good way would be to collect all
-    # given a project. This has some technical problems: e.g. we can not call
-    # this dump from a Jamfile since projects referred by 'build-project' are
-    # not available until the whole Jamfile has been loaded.
-    .all-tests += $(t) ;
-    return $(t) ;
-}
-
-
-# Note: passing more that one cpp file here is known to fail. Passing a cpp file
-# and a library target works.
-#
-rule compile ( sources + : requirements * : target-name ? )
-{
-    return [ make-test compile : $(sources) : $(requirements) : $(target-name) ]
-        ;
-}
-
-
-rule compile-fail ( sources + : requirements * : target-name ? )
-{
-    return [ make-test compile-fail : $(sources) : $(requirements) :
-        $(target-name) ] ;
-}
-
-
-rule link ( sources + : requirements * : target-name ? )
-{
-    return [ make-test link : $(sources) : $(requirements) : $(target-name) ] ;
-}
-
-
-rule link-fail ( sources + : requirements * : target-name ? )
-{
-    return [ make-test link-fail : $(sources) : $(requirements) : $(target-name)
-        ] ;
-}
-
-
-rule handle-input-files ( input-files * )
-{
-    if $(input-files[2])
-    {
-        # Check that sorting made when creating property-set instance will not
-        # change the ordering.
-        if [ sequence.insertion-sort $(input-files) ] != $(input-files)
-        {
-            errors.user-error "Names of input files must be sorted alphabetically"
-                : "due to internal limitations" ;
-        }
-    }
-    return <testing.input-file>$(input-files) ;
-}
-
-
-rule run ( sources + : args * : input-files * : requirements * : target-name ? :
-    default-build * )
-{
-    requirements += <testing.arg>$(args:J=" ") ;
-    requirements += [ handle-input-files $(input-files) ] ;
-    return [ make-test run : $(sources) : $(requirements) : $(target-name) ] ;
-}
-
-
-rule run-fail ( sources + : args * : input-files * : requirements * :
-    target-name ? : default-build * )
-{
-    requirements += <testing.arg>$(args:J=" ") ;
-    requirements += [ handle-input-files $(input-files) ] ;
-    return [ make-test run-fail : $(sources) : $(requirements) : $(target-name)
-        ] ;
-}
-
-
-# Use 'test-suite' as a synonym for 'alias', for backward compatibility.
-IMPORT : alias : : test-suite ;
-
-
-# For all main targets in 'project-module', which are typed targets with type
-# derived from 'TEST', produce some interesting information.
-#
-rule dump-tests
-{
-    for local t in $(.all-tests)
-    {
-        dump-test $(t) ;
-    }
-}
-
-
-# Given a project location in normalized form (slashes are forward), compute the
-# name of the Boost library.
-#
-local rule get-library-name ( path )
-{
-    # Path is in normalized form, so all slashes are forward.
-    local match1 = [ MATCH /(tools|libs)/(.*)/(test|example) : $(path) ] ;
-    local match2 = [ MATCH /(tools|libs)/(.*)$ : $(path) ] ;
-    local match3 = [ MATCH (/status$) : $(path) ] ;
-
-    if $(match1) { return $(match1[2]) ; }
-    else if $(match2) { return $(match2[2]) ; }
-    else if $(match3) { return "" ; }
-    else if --dump-tests in [ modules.peek : ARGV ]
-    {
-        # The 'run' rule and others might be used outside boost. In that case,
-        # just return the path, since the 'library name' makes no sense.
-        return $(path) ;
-    }
-}
-
-
-# Was an XML dump requested?
-.out-xml = [ MATCH --out-xml=(.*) : [ modules.peek : ARGV ] ] ;
-
-
-# Takes a target (instance of 'basic-target') and prints
-#   - its type
-#   - its name
-#   - comments specified via the <test-info> property
-#   - relative location of all source from the project root.
-#
-rule dump-test ( target )
-{
-    local type = [ $(target).type ] ;
-    local name = [ $(target).name ] ;
-    local project = [ $(target).project ] ;
-
-    local project-root = [ $(project).get project-root ] ;
-    local library = [ get-library-name [ path.root [ $(project).get location ]
-        [ path.pwd ] ] ] ;
-    if $(library)
-    {
-        name = $(library)/$(name) ;
-    }
-
-    local sources = [ $(target).sources ] ;
-    local source-files ;
-    for local s in $(sources)
-    {
-        if [ class.is-a $(s) : file-reference ]
-        {
-            local location = [ path.root [ path.root [ $(s).name ]
-                [ $(s).location ] ] [ path.pwd ] ] ;
-
-            source-files += [ path.relative-to [ path.root $(project-root)
-                [ path.pwd ] ] $(location) ] ;
-        }
-    }
-
-    local target-name = [ $(project).get location ] // [ $(target).name ] .test
-        ;
-    target-name = $(target-name:J=) ;
-
-    local r = [ $(target).requirements ] ;
-    # Extract values of the <test-info> feature.
-    local test-info = [ $(r).get <test-info> ] ;
-
-    # If the user requested XML output on the command-line, add the test info to
-    # that XML file rather than dumping them to stdout.
-    if $(.out-xml)
-    {
-        local nl = "
-" ;
-        .contents on $(.out-xml) +=
-            "$(nl)  <test type=\"$(type)\" name=\"$(name)\">"
-            "$(nl)    <target><![CDATA[$(target-name)]]></target>"
-            "$(nl)    <info><![CDATA[$(test-info)]]></info>"
-            "$(nl)    <source><![CDATA[$(source-files)]]></source>"
-            "$(nl)  </test>"
-            ;
-    }
-    else
-    {
-        # Format them into a single string of quoted strings.
-        test-info = \"$(test-info:J=\"\ \")\" ;
-
-        ECHO boost-test($(type)) \"$(name)\" [$(test-info)] ":"
-            \"$(source-files)\" ;
-    }
-}
-
-
-# Register generators. Depending on target type, either 'expect-success' or
-# 'expect-failure' rule will be used.
-generators.register-standard testing.expect-success : OBJ        : COMPILE      ;
-generators.register-standard testing.expect-failure : OBJ        : COMPILE_FAIL ;
-generators.register-standard testing.expect-success : RUN_OUTPUT : RUN          ;
-generators.register-standard testing.expect-failure : RUN_OUTPUT : RUN_FAIL     ;
-generators.register-standard testing.expect-failure : EXE        : LINK_FAIL    ;
-generators.register-standard testing.expect-success : EXE        : LINK         ;
-
-# Generator which runs an EXE and captures output.
-generators.register-standard testing.capture-output : EXE : RUN_OUTPUT ;
-
-# Generator which creates a target if sources run successfully. Differs from RUN
-# in that run output is not captured. The reason why it exists is that the 'run'
-# rule is much better for automated testing, but is not user-friendly (see
-# http://article.gmane.org/gmane.comp.lib.boost.build/6353).
-generators.register-standard testing.unit-test : EXE : UNIT_TEST ;
-
-
-# The action rules called by generators.
-
-# Causes the 'target' to exist after bjam invocation if and only if all the
-# dependencies were successfully built.
-#
-rule expect-success ( target : dependency + : requirements * )
-{
-    **passed** $(target) : $(sources) ;
-}
-
-
-# Causes the 'target' to exist after bjam invocation if and only if all some of
-# the dependencies were not successfully built.
-#
-rule expect-failure ( target : dependency + : properties * )
-{
-    local grist = [ MATCH ^<(.*)> : $(dependency:G) ] ;
-    local marker = $(dependency:G=$(grist)*fail) ;
-    (failed-as-expected) $(marker) ;
-    FAIL_EXPECTED $(dependency) ;
-    LOCATE on $(marker) = [ on $(dependency) return $(LOCATE) ] ;
-    RMOLD $(marker) ;
-    DEPENDS $(marker) : $(dependency) ;
-    DEPENDS $(target) : $(marker) ;
-    **passed** $(target) : $(marker) ;
-}
-
-
-# The rule/action combination used to report successful passing of a test.
-#
-rule **passed**
-{
-    # Dump all the tests, if needed. We do it here, since dump should happen
-    # only after all Jamfiles have been read, and there is no such place
-    # currently defined (but there should be).
-    if ! $(.dumped-tests) && ( --dump-tests in [ modules.peek : ARGV ] )
-    {
-        .dumped-tests = true ;
-        dump-tests ;
-    }
-
-    # Force deletion of the target, in case any dependencies failed to build.
-    RMOLD $(<) ;
-}
-
-
-# Used to create test files signifying passed tests.
-#
-actions **passed**
-{
-    echo passed > "$(<)"
-}
-
-
-# Used to create replacement object files that do not get created during tests
-# that are expected to fail.
-#
-actions (failed-as-expected)
-{
-    echo failed as expected > "$(<)"
-}
-
-
-rule run-path-setup ( target : source : properties * )
-{
-    # For testing, we need to make sure that all dynamic libraries needed by the
-    # test are found. So, we collect all paths from dependency libraries (via
-    # xdll-path property) and add whatever explicit dll-path user has specified.
-    # The resulting paths are added to the environment on each test invocation.
-    local dll-paths = [ feature.get-values <dll-path> : $(properties) ] ;
-    dll-paths += [ feature.get-values <xdll-path> : $(properties) ] ;
-    dll-paths += [ on $(source) return $(RUN_PATH) ] ;
-    dll-paths = [ sequence.unique $(dll-paths) ] ;
-    if $(dll-paths)
-    {
-        dll-paths = [ sequence.transform path.native : $(dll-paths) ] ;
-        PATH_SETUP on $(target) = [ common.prepend-path-variable-command
-            [ os.shared-library-path-variable ] : $(dll-paths) ] ;
-    }
-}
-
-
-local argv = [ modules.peek : ARGV ] ;
-
-toolset.flags testing.capture-output ARGS <testing.arg> ;
-toolset.flags testing.capture-output INPUT_FILES <testing.input-file> ;
-toolset.flags testing.capture-output LAUNCHER <testing.launcher> ;
-
-
-# Runs executable 'sources' and stores stdout in file 'target'. Unless
-# --preserve-test-targets command line option has been specified, removes the
-# executable. The 'target-to-remove' parameter controls what should be removed:
-#   - if 'none', does not remove anything, ever
-#   - if empty, removes 'source'
-#   - if non-empty and not 'none', contains a list of sources to remove.
-#
-rule capture-output ( target : source : properties * : targets-to-remove * )
-{
-    output-file on $(target) = $(target:S=.output) ;
-    LOCATE on $(target:S=.output) = [ on $(target) return $(LOCATE) ] ;
-
-    # The INCLUDES kill a warning about independent target...
-    INCLUDES $(target) : $(target:S=.output) ;
-    # but it also puts .output into dependency graph, so we must tell jam it is
-    # OK if it cannot find the target or updating rule.
-    NOCARE $(target:S=.output) ;
-
-    # This has two-fold effect. First it adds input files to the dependendency
-    # graph, preventing a warning. Second, it causes input files to be bound
-    # before target is created. Therefore, they are bound using SEARCH setting
-    # on them and not LOCATE setting of $(target), as in other case (due to jam
-    # bug).
-    DEPENDS $(target) : [ on $(target) return $(INPUT_FILES) ] ;
-
-    if $(targets-to-remove) = none
-    {
-        targets-to-remove = ;
-    }
-    else if ! $(targets-to-remove)
-    {
-        targets-to-remove = $(source) ;
-    }
-
-    run-path-setup $(target) : $(source) : $(properties) ;
-
-    if [ feature.get-values preserve-test-targets : $(properties) ] = off
-    {
-        TEMPORARY $(targets-to-remove) ;
-        # Set a second action on target that will be executed after capture
-        # output action. The 'RmTemps' rule has the 'ignore' modifier so it is
-        # always considered succeeded. This is needed for 'run-fail' test. For
-        # that test the target will be marked with FAIL_EXPECTED, and without
-        # 'ignore' successful execution will be negated and be reported as
-        # failure. With 'ignore' we do not detect a case where removing files
-        # fails, but it is not likely to happen.
-        RmTemps $(target) : $(targets-to-remove) ;
-    }
-}
-
-
-if [ os.name ] = NT
-{
-    .STATUS        = %status% ;
-    .SET_STATUS    = "set status=%ERRORLEVEL%" ;
-    .RUN_OUTPUT_NL = "echo." ;
-    .STATUS_0      = "%status% EQU 0 (" ;
-    .STATUS_NOT_0  = "%status% NEQ 0 (" ;
-    .VERBOSE       = "%verbose% EQU 1 (" ;
-    .ENDIF         = ")" ;
-    .SHELL_SET     = "set " ;
-    .CATENATE      = type ;
-    .CP            = copy ;
-}
-else
-{
-    .STATUS        = "$status" ;
-    .SET_STATUS    = "status=$?" ;
-    .RUN_OUTPUT_NL = "echo" ;
-    .STATUS_0      = "test $status -eq 0 ; then" ;
-    .STATUS_NOT_0  = "test $status -ne 0 ; then" ;
-    .VERBOSE       = "test $verbose -eq 1 ; then" ;
-    .ENDIF         = "fi" ;
-    .SHELL_SET     = "" ;
-    .CATENATE      = cat ;
-    .CP            = cp ;
-}
-
-
-.VERBOSE_TEST = 0 ;
-if --verbose-test in [ modules.peek : ARGV ]
-{
-    .VERBOSE_TEST = 1 ;
-}
-
-
-.RM = [ common.rm-command ] ;
-
-
-actions capture-output bind INPUT_FILES output-file
-{
-    $(PATH_SETUP)
-    $(LAUNCHER) "$(>)" $(ARGS) "$(INPUT_FILES)" > "$(output-file)" 2>&1
-    $(.SET_STATUS)
-    $(.RUN_OUTPUT_NL) >> "$(output-file)"
-    echo EXIT STATUS: $(.STATUS) >> "$(output-file)"
-    if $(.STATUS_0)
-        $(.CP) "$(output-file)" "$(<)"
-    $(.ENDIF)
-    $(.SHELL_SET)verbose=$(.VERBOSE_TEST)
-    if $(.STATUS_NOT_0)
-        $(.SHELL_SET)verbose=1
-    $(.ENDIF)
-    if $(.VERBOSE)
-        echo ====== BEGIN OUTPUT ======
-        $(.CATENATE) "$(output-file)"
-        echo ====== END OUTPUT ======
-    $(.ENDIF)
-    exit $(.STATUS)
-}
-
-
-actions quietly updated ignore piecemeal together RmTemps
-{
-    $(.RM) "$(>)"
-}
-
-
-.MAKE_FILE = [ common.file-creation-command ] ;
-
-toolset.flags testing.unit-test LAUNCHER <testing.launcher> ;
-toolset.flags testing.unit-test ARGS <testing.arg> ;
-
-
-rule unit-test ( target : source : properties * )
-{
-    run-path-setup $(target) : $(source) : $(properties) ;
-}
-
-
-actions unit-test
-{
-    $(PATH_SETUP)
-    $(LAUNCHER) $(>) $(ARGS) && $(.MAKE_FILE) $(<)
-}
-
-
-IMPORT $(__name__) : compile compile-fail run run-fail link link-fail
-    : : compile compile-fail run run-fail link link-fail ;
-
-
-type.register TIME : time ;
-generators.register-standard testing.time : : TIME ;
-
-
-rule record-time ( target : source : start end user system )
-{
-    local src-string = [$(source:G=:J=",")"] " ;
-    USER_TIME on $(target) += $(src-string)$(user) ;
-    SYSTEM_TIME on $(target) += $(src-string)$(system) ;
-}
-
-
-IMPORT testing : record-time : : testing.record-time ;
-
-
-# Calling this rule requests that Boost Build time how long it taks to build the
-# 'source' target and display the results both on the standard output and in the
-# 'target' file.
-#
-rule time ( target : source : properties *  )
-{
-    # Set up rule for recording timing information.
-    __TIMING_RULE__ on $(source) = testing.record-time $(target) ;
-
-    # Make sure that the source is rebuilt any time we need to retrieve that
-    # information.
-    REBUILDS $(target) : $(source) ;
-}
-
-
-actions time
-{
-    echo user: $(USER_TIME)
-    echo system: $(SYSTEM_TIME)
-
-    echo user: $(USER_TIME)" seconds" > "$(<)"
-    echo system: $(SYSTEM_TIME)" seconds" >> "$(<)"
-}
diff --git a/jam-files/boost-build/tools/testing.py b/jam-files/boost-build/tools/testing.py
deleted file mode 100644
index 3b53500c..00000000
--- a/jam-files/boost-build/tools/testing.py
+++ /dev/null
@@ -1,342 +0,0 @@
-# Status: ported, except for --out-xml
-# Base revision: 64488
-#
-# Copyright 2005 Dave Abrahams
-# Copyright 2002, 2003, 2004, 2005, 2010 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-# This module implements regression testing framework. It declares a number of
-# main target rules which perform some action and, if the results are OK,
-# creates an output file.
-#
-# The exact list of rules is:
-# 'compile'       -- creates .test file if compilation of sources was
-#                    successful.
-# 'compile-fail'  -- creates .test file if compilation of sources failed.
-# 'run'           -- creates .test file is running of executable produced from
-#                    sources was successful. Also leaves behind .output file
-#                    with the output from program run.
-# 'run-fail'      -- same as above, but .test file is created if running fails.
-#
-# In all cases, presence of .test file is an indication that the test passed.
-# For more convenient reporting, you might want to use C++ Boost regression
-# testing utilities (see http://www.boost.org/more/regression.html).
-#
-# For historical reason, a 'unit-test' rule is available which has the same
-# syntax as 'exe' and behaves just like 'run'.
-
-# Things to do:
-#  - Teach compiler_status handle Jamfile.v2.
-# Notes:
-#  - <no-warn> is not implemented, since it is Como-specific, and it is not
-#    clear how to implement it
-#  - std::locale-support is not implemented (it is used in one test).
-
-import b2.build.feature as feature
-import b2.build.type as type
-import b2.build.targets as targets
-import b2.build.generators as generators
-import b2.build.toolset as toolset
-import b2.tools.common as common
-import b2.util.option as option
-import b2.build_system as build_system
-
-
-
-from b2.manager import get_manager
-from b2.util import stem, bjam_signature
-from b2.util.sequence import unique
-
-import bjam
-
-import re
-import os.path
-import sys
-
-def init():
-    pass
-
-# Feature controling the command used to lanch test programs.
-feature.feature("testing.launcher", [], ["free", "optional"])
-
-feature.feature("test-info", [], ["free", "incidental"])
-feature.feature("testing.arg", [], ["free", "incidental"])
-feature.feature("testing.input-file", [], ["free", "dependency"])
-
-feature.feature("preserve-test-targets", ["on", "off"], ["incidental", "propagated"])
-
-# Register target types.
-type.register("TEST", ["test"])
-type.register("COMPILE", [], "TEST")
-type.register("COMPILE_FAIL", [], "TEST")
-
-type.register("RUN_OUTPUT", ["run"])
-type.register("RUN", [], "TEST")
-type.register("RUN_FAIL", [], "TEST")
-
-type.register("LINK", [], "TEST")
-type.register("LINK_FAIL", [], "TEST")
-type.register("UNIT_TEST", ["passed"], "TEST")
-
-__all_tests = []
-
-# Declare the rules which create main targets. While the 'type' module already
-# creates rules with the same names for us, we need extra convenience: default
-# name of main target, so write our own versions.
-
-# Helper rule. Create a test target, using basename of first source if no target
-# name is explicitly passed. Remembers the created target in a global variable.
-def make_test(target_type, sources, requirements, target_name=None):
-
-    if not target_name:
-        target_name = stem(os.path.basename(sources[0]))
-
-    # Having periods (".") in the target name is problematic because the typed
-    # generator will strip the suffix and use the bare name for the file
-    # targets. Even though the location-prefix averts problems most times it
-    # does not prevent ambiguity issues when referring to the test targets. For
-    # example when using the XML log output. So we rename the target to remove
-    # the periods, and provide an alias for users.
-    real_name = target_name.replace(".", "~")
-
-    project = get_manager().projects().current()
-    # The <location-prefix> forces the build system for generate paths in the
-    # form '$build_dir/array1.test/gcc/debug'. This is necessary to allow
-    # post-processing tools to work.
-    t = get_manager().targets().create_typed_target(
-        type.type_from_rule_name(target_type), project, real_name, sources,
-        requirements + ["<location-prefix>" + real_name + ".test"], [], [])
-
-    # The alias to the real target, per period replacement above.
-    if real_name != target_name:
-        get_manager().projects().project_rules().all_names_["alias"](
-            target_name, [t])
-
-    # Remember the test (for --dump-tests). A good way would be to collect all
-    # given a project. This has some technical problems: e.g. we can not call
-    # this dump from a Jamfile since projects referred by 'build-project' are
-    # not available until the whole Jamfile has been loaded.
-    __all_tests.append(t)
-    return t
-
-
-# Note: passing more that one cpp file here is known to fail. Passing a cpp file
-# and a library target works.
-#
-@bjam_signature((["sources", "*"], ["requirements", "*"], ["target_name", "?"]))
-def compile(sources, requirements, target_name=None):
-    return make_test("compile", sources, requirements, target_name)
-
-@bjam_signature((["sources", "*"], ["requirements", "*"], ["target_name", "?"]))
-def compile_fail(sources, requirements, target_name=None):
-    return make_test("compile-fail", sources, requirements, target_name)
-
-@bjam_signature((["sources", "*"], ["requirements", "*"], ["target_name", "?"]))
-def link(sources, requirements, target_name=None):
-    return make_test("link", sources, requirements, target_name)
-
-@bjam_signature((["sources", "*"], ["requirements", "*"], ["target_name", "?"]))
-def link_fail(sources, requirements, target_name=None):
-    return make_test("link-fail", sources, requirements, target_name)
-
-def handle_input_files(input_files):
-    if len(input_files) > 1:
-        # Check that sorting made when creating property-set instance will not
-        # change the ordering.
-        if sorted(input_files) != input_files:
-            get_manager().errors()("Names of input files must be sorted alphabetically\n" +
-                                   "due to internal limitations")
-    return ["<testing.input-file>" + f for f in input_files]
-
-@bjam_signature((["sources", "*"], ["args", "*"], ["input_files", "*"],
-                 ["requirements", "*"], ["target_name", "?"],
-                 ["default_build", "*"]))                 
-def run(sources, args, input_files, requirements, target_name=None, default_build=[]):
-    if args:
-        requirements.append("<testing.arg>" + " ".join(args))
-    requirements.extend(handle_input_files(input_files))
-    return make_test("run", sources, requirements, target_name)
-
-@bjam_signature((["sources", "*"], ["args", "*"], ["input_files", "*"],
-                 ["requirements", "*"], ["target_name", "?"],
-                 ["default_build", "*"]))                 
-def run_fail(sources, args, input_files, requirements, target_name=None, default_build=[]):
-    if args:
-        requirements.append("<testing.arg>" + " ".join(args))
-    requirements.extend(handle_input_files(input_files))
-    return make_test("run-fail", sources, requirements, target_name)
-
-# Register all the rules
-for name in ["compile", "compile-fail", "link", "link-fail", "run", "run-fail"]:
-    get_manager().projects().add_rule(name, getattr(sys.modules[__name__], name.replace("-", "_")))
-
-# Use 'test-suite' as a synonym for 'alias', for backward compatibility.
-from b2.build.alias import alias
-get_manager().projects().add_rule("test-suite", alias)
-
-# For all main targets in 'project-module', which are typed targets with type
-# derived from 'TEST', produce some interesting information.
-#
-def dump_tests():
-    for t in __all_tests:
-        dump_test(t)
-
-# Given a project location in normalized form (slashes are forward), compute the
-# name of the Boost library.
-#
-__ln1 = re.compile("/(tools|libs)/(.*)/(test|example)")
-__ln2 = re.compile("/(tools|libs)/(.*)$")
-__ln3 = re.compile("(/status$)")
-def get_library_name(path):
-    
-    path = path.replace("\\", "/")
-    match1 = __ln1.match(path)
-    match2 = __ln2.match(path)
-    match3 = __ln3.match(path)
-
-    if match1:
-        return match1.group(2)
-    elif match2:
-        return match2.group(2)
-    elif match3:
-        return ""
-    elif option.get("dump-tests", False, True):
-        # The 'run' rule and others might be used outside boost. In that case,
-        # just return the path, since the 'library name' makes no sense.
-        return path
-
-# Was an XML dump requested?
-__out_xml = option.get("out-xml", False, True)
-
-# Takes a target (instance of 'basic-target') and prints
-#   - its type
-#   - its name
-#   - comments specified via the <test-info> property
-#   - relative location of all source from the project root.
-#
-def dump_test(target):
-    type = target.type()
-    name = target.name()
-    project = target.project()
-
-    project_root = project.get('project-root')
-    library = get_library_name(os.path.abspath(project.get('location')))
-    if library:
-        name = library + "/" + name
-
-    sources = target.sources()
-    source_files = []
-    for s in sources:
-        if isinstance(s, targets.FileReference):
-            location = os.path.abspath(os.path.join(s.location(), s.name()))
-            source_files.append(os.path.relpath(location, os.path.abspath(project_root)))
-
-    target_name = project.get('location') + "//" + target.name() + ".test"
-
-    test_info = target.requirements().get('test-info')
-    test_info = " ".join('"' + ti + '"' for ti in test_info)
-
-    # If the user requested XML output on the command-line, add the test info to
-    # that XML file rather than dumping them to stdout.
-    #if $(.out-xml)
-    #{
-#        local nl = "
-#" ;
-#        .contents on $(.out-xml) +=
-#            "$(nl)  <test type=\"$(type)\" name=\"$(name)\">"
-#            "$(nl)    <target><![CDATA[$(target-name)]]></target>"
-#            "$(nl)    <info><![CDATA[$(test-info)]]></info>"
-#            "$(nl)    <source><![CDATA[$(source-files)]]></source>"
-#            "$(nl)  </test>"
-#            ;
-#    }
-#    else
-
-    source_files = " ".join('"' + s + '"' for s in source_files)
-    if test_info:
-        print 'boost-test(%s) "%s" [%s] : %s' % (type, name, test_info, source_files)
-    else:
-        print 'boost-test(%s) "%s" : %s' % (type, name, source_files)
-
-# Register generators. Depending on target type, either 'expect-success' or
-# 'expect-failure' rule will be used.
-generators.register_standard("testing.expect-success", ["OBJ"], ["COMPILE"])
-generators.register_standard("testing.expect-failure", ["OBJ"], ["COMPILE_FAIL"])
-generators.register_standard("testing.expect-success", ["RUN_OUTPUT"], ["RUN"])
-generators.register_standard("testing.expect-failure", ["RUN_OUTPUT"], ["RUN_FAIL"])
-generators.register_standard("testing.expect-success", ["EXE"], ["LINK"])
-generators.register_standard("testing.expect-failure", ["EXE"], ["LINK_FAIL"])
-
-# Generator which runs an EXE and captures output.
-generators.register_standard("testing.capture-output", ["EXE"], ["RUN_OUTPUT"])
-
-# Generator which creates a target if sources run successfully. Differs from RUN
-# in that run output is not captured. The reason why it exists is that the 'run'
-# rule is much better for automated testing, but is not user-friendly (see
-# http://article.gmane.org/gmane.comp.lib.boost.build/6353).
-generators.register_standard("testing.unit-test", ["EXE"], ["UNIT_TEST"])
-
-# FIXME: if those calls are after bjam.call, then bjam will crash
-# when toolset.flags calls bjam.caller.
-toolset.flags("testing.capture-output", "ARGS", [], ["<testing.arg>"])
-toolset.flags("testing.capture-output", "INPUT_FILES", [], ["<testing.input-file>"])
-toolset.flags("testing.capture-output", "LAUNCHER", [], ["<testing.launcher>"])
-
-toolset.flags("testing.unit-test", "LAUNCHER", [], ["<testing.launcher>"])
-toolset.flags("testing.unit-test", "ARGS", [], ["<testing.arg>"])
-
-type.register("TIME", ["time"])
-generators.register_standard("testing.time", [], ["TIME"])
-
-
-# The following code sets up actions for this module. It's pretty convoluted,
-# but the basic points is that we most of actions are defined by Jam code
-# contained in testing-aux.jam, which we load into Jam module named 'testing'
-
-def run_path_setup(target, sources, ps):
-
-    # For testing, we need to make sure that all dynamic libraries needed by the
-    # test are found. So, we collect all paths from dependency libraries (via
-    # xdll-path property) and add whatever explicit dll-path user has specified.
-    # The resulting paths are added to the environment on each test invocation.
-    dll_paths = ps.get('dll-path')
-    dll_paths.extend(ps.get('xdll-path'))
-    dll_paths.extend(bjam.call("get-target-variable", sources, "RUN_PATH"))
-    dll_paths = unique(dll_paths)
-    if dll_paths:
-        bjam.call("set-target-variable", target, "PATH_SETUP",
-                  common.prepend_path_variable_command(
-                     common.shared_library_path_variable(), dll_paths))
-
-def capture_output_setup(target, sources, ps):
-    run_path_setup(target, sources, ps)
-
-    if ps.get('preserve-test-targets') == ['off']:
-        bjam.call("set-target-variable", target, "REMOVE_TEST_TARGETS", "1")
-
-get_manager().engine().register_bjam_action("testing.capture-output",
-                                            capture_output_setup)
-
-
-path = os.path.dirname(get_manager().projects().loaded_tool_module_path_[__name__])
-import b2.util.os_j
-get_manager().projects().project_rules()._import_rule("testing", "os.name",
-                                                      b2.util.os_j.name)
-import b2.tools.common
-get_manager().projects().project_rules()._import_rule("testing", "common.rm-command",
-                                                      b2.tools.common.rm_command)
-get_manager().projects().project_rules()._import_rule("testing", "common.file-creation-command",
-                                                      b2.tools.common.file_creation_command)
-
-bjam.call("load", "testing", os.path.join(path, "testing-aux.jam"))
-
-
-for name in ["expect-success", "expect-failure", "time"]:
-    get_manager().engine().register_bjam_action("testing." + name)
-
-get_manager().engine().register_bjam_action("testing.unit-test",
-                                            run_path_setup)
-
-if option.get("dump-tests", False, True):
-    build_system.add_pre_build_hook(dump_tests)
diff --git a/jam-files/boost-build/tools/types/__init__.py b/jam-files/boost-build/tools/types/__init__.py
deleted file mode 100644
index f972b714..00000000
--- a/jam-files/boost-build/tools/types/__init__.py
+++ /dev/null
@@ -1,18 +0,0 @@
-__all__ = [
-    'asm',
-    'cpp',
-    'exe',
-    'html',
-    'lib',
-    'obj',
-    'rsp',
-]
-
-def register_all ():
-    for i in __all__:
-        m = __import__ (__name__ + '.' + i)
-        reg = i + '.register ()'
-        #exec (reg)
-
-# TODO: (PF) I thought these would be imported automatically. Anyone knows why they aren't?
-register_all ()
diff --git a/jam-files/boost-build/tools/types/asm.jam b/jam-files/boost-build/tools/types/asm.jam
deleted file mode 100644
index a340db36..00000000
--- a/jam-files/boost-build/tools/types/asm.jam
+++ /dev/null
@@ -1,4 +0,0 @@
-# Copyright Craig Rodrigues 2005. Distributed under the Boost
-# Software License, Version 1.0. (See accompanying
-# file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
-type ASM : s S asm ;
diff --git a/jam-files/boost-build/tools/types/asm.py b/jam-files/boost-build/tools/types/asm.py
deleted file mode 100644
index b4e1c30e..00000000
--- a/jam-files/boost-build/tools/types/asm.py
+++ /dev/null
@@ -1,13 +0,0 @@
-# Copyright Craig Rodrigues 2005.
-# Copyright (c) 2008 Steven Watanabe
-#
-# Distributed under the Boost
-# Software License, Version 1.0. (See accompanying
-# file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
-
-from b2.build import type
-
-def register():
-    type.register_type('ASM', ['s', 'S', 'asm'])
-
-register()
diff --git a/jam-files/boost-build/tools/types/cpp.jam b/jam-files/boost-build/tools/types/cpp.jam
deleted file mode 100644
index 3159cdd7..00000000
--- a/jam-files/boost-build/tools/types/cpp.jam
+++ /dev/null
@@ -1,86 +0,0 @@
-# Copyright David Abrahams 2004.
-# Copyright 2002, 2003, 2004, 2005, 2006 Vladimir Prus
-# Copyright 2010 Rene Rivera
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-import type ;
-import scanner ;
-
-class c-scanner : scanner
-{
-    import path ;
-    import regex ;
-    import scanner ;
-    import sequence ;
-    import virtual-target ;
-
-    rule __init__ ( includes * )
-    {
-        scanner.__init__ ;
-
-        for local i in $(includes)
-        {
-            self.includes += [ sequence.transform path.native
-                                : [ regex.split $(i:G=) "&&" ] ] ;
-        }
-    }
-
-    rule pattern ( )
-    {
-        return "#[ \t]*include[ ]*(<(.*)>|\"(.*)\")" ;
-    }
-
-    rule process ( target : matches * : binding )
-    {
-        local angle  = [ regex.transform $(matches) : "<(.*)>"   ] ;
-        angle = [ sequence.transform path.native : $(angle) ] ;
-        local quoted = [ regex.transform $(matches) : "\"(.*)\"" ] ;
-        quoted = [ sequence.transform path.native : $(quoted) ] ;
-
-        # CONSIDER: the new scoping rule seem to defeat "on target" variables.
-        local g = [ on $(target) return $(HDRGRIST) ] ;
-        local b = [ NORMALIZE_PATH $(binding:D) ] ;
-
-        # Attach binding of including file to included targets. When a target is
-        # directly created from virtual target this extra information is
-        # unnecessary. But in other cases, it allows us to distinguish between
-        # two headers of the same name included from different places. We do not
-        # need this extra information for angle includes, since they should not
-        # depend on including file (we can not get literal "." in include path).
-        local g2 = $(g)"#"$(b) ;
-
-        angle = $(angle:G=$(g)) ;
-        quoted = $(quoted:G=$(g2)) ;
-
-        local all = $(angle) $(quoted) ;
-
-        INCLUDES $(target) : $(all) ;
-        NOCARE $(all) ;
-        SEARCH on $(angle) = $(self.includes:G=) ;
-        SEARCH on $(quoted) = $(b) $(self.includes:G=) ;
-
-        # Just propagate the current scanner to includes in hope that includes
-        # do not change scanners.
-        scanner.propagate $(__name__) : $(angle) $(quoted) : $(target) ;
-
-        ISFILE $(angle) $(quoted) ;
-    }
-}
-
-scanner.register c-scanner : include ;
-
-type.register CPP : cpp cxx cc ;
-type.register H   : h ;
-type.register HPP : hpp : H ;
-type.register C   : c ;
-
-# It most cases where a CPP file or a H file is a source of some action, we
-# should rebuild the result if any of files included by CPP/H are changed. One
-# case when this is not needed is installation, which is handled specifically.
-type.set-scanner CPP : c-scanner ;
-type.set-scanner C   : c-scanner ;
-# One case where scanning of H/HPP files is necessary is PCH generation -- if
-# any header included by HPP being precompiled changes, we need to recompile the
-# header.
-type.set-scanner H   : c-scanner ;
-type.set-scanner HPP : c-scanner ;
diff --git a/jam-files/boost-build/tools/types/cpp.py b/jam-files/boost-build/tools/types/cpp.py
deleted file mode 100644
index 7b56111c..00000000
--- a/jam-files/boost-build/tools/types/cpp.py
+++ /dev/null
@@ -1,10 +0,0 @@
-# Copyright David Abrahams 2004. Distributed under the Boost
-# Software License, Version 1.0. (See accompanying
-# file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
-
-from b2.build import type
-
-def register ():
-    type.register_type ('CPP', ['cpp', 'cxx', 'cc'])
-
-register ()
diff --git a/jam-files/boost-build/tools/types/exe.jam b/jam-files/boost-build/tools/types/exe.jam
deleted file mode 100644
index 47109513..00000000
--- a/jam-files/boost-build/tools/types/exe.jam
+++ /dev/null
@@ -1,9 +0,0 @@
-# Copyright David Abrahams 2004. Distributed under the Boost
-# Software License, Version 1.0. (See accompanying
-# file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
-
-import type ;
-
-type.register EXE ;
-type.set-generated-target-suffix EXE : <target-os>windows : "exe" ;
-type.set-generated-target-suffix EXE : <target-os>cygwin : "exe" ;
diff --git a/jam-files/boost-build/tools/types/exe.py b/jam-files/boost-build/tools/types/exe.py
deleted file mode 100644
index a4935e24..00000000
--- a/jam-files/boost-build/tools/types/exe.py
+++ /dev/null
@@ -1,11 +0,0 @@
-# Copyright David Abrahams 2004. Distributed under the Boost
-# Software License, Version 1.0. (See accompanying
-# file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
-
-from b2.build import type
-
-def register ():
-    type.register_type ('EXE', ['exe'], None, ['NT', 'CYGWIN'])
-    type.register_type ('EXE', [], None, [])
-
-register ()
diff --git a/jam-files/boost-build/tools/types/html.jam b/jam-files/boost-build/tools/types/html.jam
deleted file mode 100644
index 5cd337d0..00000000
--- a/jam-files/boost-build/tools/types/html.jam
+++ /dev/null
@@ -1,4 +0,0 @@
-# Copyright David Abrahams 2004. Distributed under the Boost
-# Software License, Version 1.0. (See accompanying
-# file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
-type HTML : html ;
diff --git a/jam-files/boost-build/tools/types/html.py b/jam-files/boost-build/tools/types/html.py
deleted file mode 100644
index 63af4d90..00000000
--- a/jam-files/boost-build/tools/types/html.py
+++ /dev/null
@@ -1,10 +0,0 @@
-# Copyright David Abrahams 2004. Distributed under the Boost
-# Software License, Version 1.0. (See accompanying
-# file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
-
-from b2.build import type
-
-def register ():
-    type.register_type ('HTML', ['html'])
-
-register ()
diff --git a/jam-files/boost-build/tools/types/lib.jam b/jam-files/boost-build/tools/types/lib.jam
deleted file mode 100644
index 854ab8fd..00000000
--- a/jam-files/boost-build/tools/types/lib.jam
+++ /dev/null
@@ -1,74 +0,0 @@
-# Copyright David Abrahams 2004. Distributed under the Boost
-# Software License, Version 1.0. (See accompanying
-# file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
-
-import type ; # for set-generated-target-suffix
-import os ;
-
-# The following naming scheme is used for libraries.
-#
-# On *nix:
-#     libxxx.a       static library
-#     libxxx.so      shared library
-#
-# On windows (msvc)
-#     libxxx.lib     static library
-#     xxx.dll        DLL
-#     xxx.lib        import library
-#
-# On windows (mingw):
-#     libxxx.a       static library
-#     libxxx.dll     DLL
-#     libxxx.dll.a   import library
-#
-# On cygwin i.e. <target-os>cygwin
-#     libxxx.a       static library
-#     cygxxx.dll     DLL
-#     libxxx.dll.a   import library
-#
-
-type.register LIB ;
-
-# FIXME: should not register both extensions on both platforms.
-type.register STATIC_LIB : a lib : LIB ;
-
-# The 'lib' prefix is used everywhere
-type.set-generated-target-prefix STATIC_LIB : : lib ;
-
-# Use '.lib' suffix for windows
-type.set-generated-target-suffix STATIC_LIB : <target-os>windows : lib ;
-
-# Except with gcc.
-type.set-generated-target-suffix STATIC_LIB : <toolset>gcc <target-os>windows : a ;
-
-# Use xxx.lib for import libs
-type IMPORT_LIB : : STATIC_LIB ;
-type.set-generated-target-prefix IMPORT_LIB : : "" ;
-type.set-generated-target-suffix IMPORT_LIB : : lib ;
-
-# Except with gcc (mingw or cygwin), where use libxxx.dll.a
-type.set-generated-target-prefix IMPORT_LIB : <toolset>gcc : lib ;
-type.set-generated-target-suffix IMPORT_LIB : <toolset>gcc : dll.a ;
-
-type.register SHARED_LIB : so dll dylib : LIB ;
-
-# Both mingw and cygwin use libxxx.dll naming scheme.
-# On Linux, use "lib" prefix
-type.set-generated-target-prefix SHARED_LIB : : lib ;
-# But don't use it on windows
-type.set-generated-target-prefix SHARED_LIB : <target-os>windows : "" ;
-# But use it again on mingw
-type.set-generated-target-prefix SHARED_LIB : <toolset>gcc <target-os>windows : lib ;
-# And use 'cyg' on cygwin
-type.set-generated-target-prefix SHARED_LIB : <target-os>cygwin : cyg ;
-
-
-type.set-generated-target-suffix SHARED_LIB : <target-os>windows : dll ;
-type.set-generated-target-suffix SHARED_LIB : <target-os>cygwin : dll ;
-type.set-generated-target-suffix SHARED_LIB : <target-os>darwin : dylib ;
-
-type SEARCHED_LIB : : LIB ;
-# This is needed so that when we create a target of SEARCHED_LIB
-# type, there's no prefix or suffix automatically added.
-type.set-generated-target-prefix SEARCHED_LIB : : "" ;
-type.set-generated-target-suffix SEARCHED_LIB : : "" ;
diff --git a/jam-files/boost-build/tools/types/lib.py b/jam-files/boost-build/tools/types/lib.py
deleted file mode 100644
index d0ec1fb5..00000000
--- a/jam-files/boost-build/tools/types/lib.py
+++ /dev/null
@@ -1,77 +0,0 @@
-# Status: ported
-# Base revision: 64456.
-# Copyright David Abrahams 2004.
-# Copyright Vladimir Prus 2010.
-# Distributed under the Boost
-# Software License, Version 1.0. (See accompanying
-# file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
-
-import b2.build.type as type
-
-# The following naming scheme is used for libraries.
-#
-# On *nix:
-#     libxxx.a       static library
-#     libxxx.so      shared library
-#
-# On windows (msvc)
-#     libxxx.lib     static library
-#     xxx.dll        DLL
-#     xxx.lib        import library
-#
-# On windows (mingw):
-#     libxxx.a       static library
-#     libxxx.dll     DLL
-#     libxxx.dll.a   import library
-#
-# On cygwin i.e. <target-os>cygwin
-#     libxxx.a       static library
-#     cygxxx.dll     DLL
-#     libxxx.dll.a   import library
-#
-
-type.register('LIB')
-
-# FIXME: should not register both extensions on both platforms.
-type.register('STATIC_LIB', ['a', 'lib'], 'LIB')
-
-# The 'lib' prefix is used everywhere
-type.set_generated_target_prefix('STATIC_LIB', [], 'lib')
-
-# Use '.lib' suffix for windows
-type.set_generated_target_suffix('STATIC_LIB', ['<target-os>windows'], 'lib')
-
-# Except with gcc.
-type.set_generated_target_suffix('STATIC_LIB', ['<toolset>gcc', '<target-os>windows'], 'a')
-
-# Use xxx.lib for import libs
-type.register('IMPORT_LIB', [], 'STATIC_LIB')
-type.set_generated_target_prefix('IMPORT_LIB', [], '')
-type.set_generated_target_suffix('IMPORT_LIB', [], 'lib')
-
-# Except with gcc (mingw or cygwin), where use libxxx.dll.a
-type.set_generated_target_prefix('IMPORT_LIB', ['<toolset>gcc'], 'lib')
-type.set_generated_target_suffix('IMPORT_LIB', ['<toolset>gcc'], 'dll.a')
-
-type.register('SHARED_LIB', ['so', 'dll', 'dylib'], 'LIB')
-
-# Both mingw and cygwin use libxxx.dll naming scheme.
-# On Linux, use "lib" prefix
-type.set_generated_target_prefix('SHARED_LIB', [], 'lib')
-# But don't use it on windows
-type.set_generated_target_prefix('SHARED_LIB', ['<target-os>windows'], '')
-# But use it again on mingw
-type.set_generated_target_prefix('SHARED_LIB', ['<toolset>gcc', '<target-os>windows'], 'lib')
-# And use 'cyg' on cygwin
-type.set_generated_target_prefix('SHARED_LIB', ['<target-os>cygwin'], 'cyg')
-
-
-type.set_generated_target_suffix('SHARED_LIB', ['<target-os>windows'], 'dll')
-type.set_generated_target_suffix('SHARED_LIB', ['<target-os>cygwin'], 'dll')
-type.set_generated_target_suffix('SHARED_LIB', ['<target-os>darwin'], 'dylib')
-
-type.register('SEARCHED_LIB', [], 'LIB')
-# This is needed so that when we create a target of SEARCHED_LIB
-# type, there's no prefix or suffix automatically added.
-type.set_generated_target_prefix('SEARCHED_LIB', [], '')
-type.set_generated_target_suffix('SEARCHED_LIB', [], '')
diff --git a/jam-files/boost-build/tools/types/obj.jam b/jam-files/boost-build/tools/types/obj.jam
deleted file mode 100644
index 6afbcaa6..00000000
--- a/jam-files/boost-build/tools/types/obj.jam
+++ /dev/null
@@ -1,9 +0,0 @@
-# Copyright David Abrahams 2004. Distributed under the Boost
-# Software License, Version 1.0. (See accompanying
-# file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
-
-import type ;
-
-type.register OBJ : o obj ;
-type.set-generated-target-suffix OBJ : <target-os>windows : obj ;
-type.set-generated-target-suffix OBJ : <target-os>cygwin : obj ;
diff --git a/jam-files/boost-build/tools/types/obj.py b/jam-files/boost-build/tools/types/obj.py
deleted file mode 100644
index e61e99a8..00000000
--- a/jam-files/boost-build/tools/types/obj.py
+++ /dev/null
@@ -1,11 +0,0 @@
-# Copyright David Abrahams 2004. Distributed under the Boost
-# Software License, Version 1.0. (See accompanying
-# file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
-
-from b2.build import type
-
-def register ():
-    type.register_type ('OBJ', ['obj'], None, ['NT', 'CYGWIN'])
-    type.register_type ('OBJ', ['o'])
-
-register ()
diff --git a/jam-files/boost-build/tools/types/objc.jam b/jam-files/boost-build/tools/types/objc.jam
deleted file mode 100644
index 709cbd0c..00000000
--- a/jam-files/boost-build/tools/types/objc.jam
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright Rene Rivera 2008, 2010.
-# Distributed under the Boost Software License, Version 1.0. (See accompanying
-# file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
-import type ;
-import scanner ;
-import types/cpp ;
-
-class objc-scanner : c-scanner
-{
-    rule __init__ ( includes * )
-    {
-        c-scanner.__init__ $(includes) ;
-    }
-
-    rule pattern ( )
-    {
-        return "#[ \t]*include|import[ ]*(<(.*)>|\"(.*)\")" ;
-    }
-}
-
-scanner.register objc-scanner : include ;
-
-type.register OBJECTIVE_C : m ;
-type.register OBJECTIVE_CPP : mm ;
-type.set-scanner OBJECTIVE_C : objc-scanner ;
-type.set-scanner OBJECTIVE_CPP : objc-scanner ;
diff --git a/jam-files/boost-build/tools/types/preprocessed.jam b/jam-files/boost-build/tools/types/preprocessed.jam
deleted file mode 100644
index c9187ba6..00000000
--- a/jam-files/boost-build/tools/types/preprocessed.jam
+++ /dev/null
@@ -1,9 +0,0 @@
-# Copyright Steven Watanabe 2011
-# Distributed under the Boost Software License Version 1.0. (See
-# accompanying file LICENSE_1_0.txt or copy at
-# http://www.boost.org/LICENSE_1_0.txt)
-
-import type ;
-
-type.register PREPROCESSED_C : i : C ;
-type.register PREPROCESSED_CPP : ii : CPP ;
diff --git a/jam-files/boost-build/tools/types/qt.jam b/jam-files/boost-build/tools/types/qt.jam
deleted file mode 100644
index 6d1dfbd4..00000000
--- a/jam-files/boost-build/tools/types/qt.jam
+++ /dev/null
@@ -1,10 +0,0 @@
-# Copyright Vladimir Prus 2005. Distributed under the Boost
-# Software License, Version 1.0. (See accompanying
-# file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
-
-type UI : ui ;
-type QRC : qrc ;
-type MOCCABLE_CPP ;
-type MOCCABLE_H ;
-# Result of running moc.
-type MOC : moc : H ;
diff --git a/jam-files/boost-build/tools/types/register.jam b/jam-files/boost-build/tools/types/register.jam
deleted file mode 100644
index 203992ca..00000000
--- a/jam-files/boost-build/tools/types/register.jam
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright David Abrahams 2004. Distributed under the Boost
-# Software License, Version 1.0. (See accompanying
-# file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
-
-# This module's job is to automatically import all the type
-# registration modules in its directory.
-import type os path modules ;
-
-# Register the given type on the specified OSes, or on remaining OSes
-# if os is not specified.  This rule is injected into each of the type
-# modules for the sake of convenience.
-local rule type ( type : suffixes * : base-type ? : os * )
-{
-    if ! [ type.registered $(type) ]
-    {
-        if ( ! $(os) ) || [ os.name ] in $(os)
-        {
-            type.register $(type) : $(suffixes) : $(base-type) ;
-        }
-    }
-}
-
-.this-module's-file = [ modules.binding $(__name__) ] ;
-.this-module's-dir = [ path.parent $(.this-module's-file) ] ;
-.sibling-jamfiles =  [ path.glob $(.this-module's-dir) : *.jam ] ;
-.sibling-modules = [ MATCH ^(.*)\.jam$ : $(.sibling-jamfiles) ] ;
-
-# A loop over all modules in this directory
-for m in $(.sibling-modules)
-{
-    m = [ path.basename $(m) ] ;
-    m = types/$(m) ;
-    
-    # Inject the type rule into the new module
-    IMPORT $(__name__) : type : $(m) : type ;
-    import $(m) ;
-}
-
-
diff --git a/jam-files/boost-build/tools/types/rsp.jam b/jam-files/boost-build/tools/types/rsp.jam
deleted file mode 100644
index bdf8a7c9..00000000
--- a/jam-files/boost-build/tools/types/rsp.jam
+++ /dev/null
@@ -1,4 +0,0 @@
-# Copyright David Abrahams 2004. Distributed under the Boost
-# Software License, Version 1.0. (See accompanying
-# file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
-type RSP : rsp ;
diff --git a/jam-files/boost-build/tools/types/rsp.py b/jam-files/boost-build/tools/types/rsp.py
deleted file mode 100644
index ccb379e9..00000000
--- a/jam-files/boost-build/tools/types/rsp.py
+++ /dev/null
@@ -1,10 +0,0 @@
-# Copyright David Abrahams 2004. Distributed under the Boost
-# Software License, Version 1.0. (See accompanying
-# file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
-
-from b2.build import type
-
-def register ():
-    type.register_type ('RSP', ['rsp'])
-
-register ()
diff --git a/jam-files/boost-build/tools/unix.jam b/jam-files/boost-build/tools/unix.jam
deleted file mode 100644
index 75949851..00000000
--- a/jam-files/boost-build/tools/unix.jam
+++ /dev/null
@@ -1,224 +0,0 @@
-#  Copyright (c) 2004 Vladimir Prus.
-#
-#  Use, modification and distribution is subject to the Boost Software
-#  License Version 1.0. (See accompanying file LICENSE_1_0.txt or
-#  http://www.boost.org/LICENSE_1_0.txt)
-
-#  This file implements linking semantic common to all unixes. On unix, static
-#  libraries must be specified in a fixed order on the linker command line. Generators
-#  declared there store information about the order and use it property.
-
-import feature ;
-import "class" : new ;
-import generators ;
-import type ;
-import set ;
-import order ;
-import builtin ;
-
-class unix-linking-generator : linking-generator
-{
-    import property-set ;
-    import type ;
-    import unix ;
-    
-    rule __init__ ( id 
-        composing ? : # Specify if generator is composing. The generator will be
-        # composing if non-empty string is passed, or parameter is
-        # not given. To make generator non-composing, pass empty
-        # string ("")
-        source-types + : target-types + : 
-        requirements * )
-    {
-        composing ?= true ;
-        generator.__init__ $(id) $(composing) : $(source-types) : $(target-types) :
-          $(requirements) ;
-    }
-    
-    rule run ( project name ? : property-set : sources + )
-    {   
-        local result = [ linking-generator.run $(project) $(name) : $(property-set)
-          : $(sources) ] ;
-        
-        unix.set-library-order $(sources) : $(property-set) : $(result[2-]) ;
-                                
-        return $(result) ;
-    }
-    
-    rule generated-targets ( sources + : property-set : project name ? )
-    {
-        local sources2 ;
-        local libraries ;
-        for local l in $(sources)
-        {
-            if [ type.is-derived [ $(l).type ] LIB ]
-            {
-                libraries += $(l) ;
-            }
-            else
-            {
-                sources2 += $(l) ;
-            }            
-        }
-        
-        sources = $(sources2) [ unix.order-libraries $(libraries) ] ;
-        
-        return [ linking-generator.generated-targets $(sources) : $(property-set)
-          : $(project) $(name) ] ;
-    }
-    
-} 
-
-class unix-archive-generator : archive-generator
-{
-    import unix ; 
-
-    rule __init__ ( id composing ? : source-types + : target-types + : 
-        requirements * )
-    {
-        composing ?= true ;
-        archive-generator.__init__ $(id) $(composing) : $(source-types) : $(target-types) :
-          $(requirements) ;
-    }
-        
-    rule run ( project name ? : property-set : sources + )
-    {                                
-        local result = [ archive-generator.run $(project) $(name) : $(property-set)
-          : $(sources) ] ;
-        
-        unix.set-library-order $(sources) : $(property-set) : $(result[2-]) ;
-        
-        return $(result) ;
-
-    }    
-}
-
-class unix-searched-lib-generator : searched-lib-generator
-{
-    import unix ;
-    rule __init__ ( * : * )
-    { 
-        generator.__init__ 
-          $(1) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ;
-    }
-    
-    rule optional-properties ( )
-    {
-        return $(self.requirements) ;
-    }
-              
-    rule run ( project name ? : property-set : sources * )
-    {
-        local result = [ searched-lib-generator.run $(project) $(name) 
-          : $(property-set) : $(sources) ] ;
-        
-        unix.set-library-order $(sources) : $(property-set) : $(result[2-]) ;
-        
-        return $(result) ;
-    }    
-}
-
-class unix-prebuilt-lib-generator : generator
-{
-    import unix ;
-    rule __init__ ( * : * )
-    {
-        generator.__init__ $(1) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ;
-    }
-
-    rule run ( project name ? : property-set : sources * )
-    {
-        local f = [ $(property-set).get <file> ] ;
-        unix.set-library-order-aux $(f) : $(sources) ;
-        return $(f) $(sources) ;
-    }    
-}
-
-generators.register 
-  [ new unix-prebuilt-lib-generator unix.prebuilt : : LIB 
-      : <file> <toolset>unix ] ;
-
-generators.override unix.prebuilt : builtin.lib-generator ;
-
-
-# Declare generators
-generators.register [ new unix-linking-generator unix.link : LIB OBJ : EXE 
-    : <toolset>unix ] ;
-
-generators.register [ new unix-archive-generator unix.archive : OBJ : STATIC_LIB 
-    : <toolset>unix ] ;
-
-generators.register [ new unix-linking-generator unix.link.dll : LIB OBJ : SHARED_LIB 
-    : <toolset>unix ] ;
-
-generators.register [ new unix-searched-lib-generator 
-   unix.searched-lib-generator : : SEARCHED_LIB : <toolset>unix ] ;
-
-
-# The derived toolset must specify their own actions.
-actions link {
-}
-
-actions link.dll {
-}
-
-actions archive {    
-}
-
-actions searched-lib-generator {    
-}
-
-actions prebuilt {
-}
-
-    
-
-
-
-.order = [ new order ] ;
-
-rule set-library-order-aux ( from * : to * )
-{        
-    for local f in $(from)
-    {
-        for local t in $(to)
-        {            
-            if $(f) != $(t)
-            {                
-                $(.order).add-pair $(f) $(t) ;
-            }            
-        }        
-    }    
-}
-
-rule set-library-order ( sources * : property-set : result * )
-{
-    local used-libraries ;
-    local deps = [ $(property-set).dependency ] ;        
-    for local l in $(sources) $(deps:G=)        
-    {
-        if [ $(l).type ] && [ type.is-derived [ $(l).type ] LIB ]
-        {
-            used-libraries += $(l) ;
-        }
-    }
-
-    local created-libraries ;
-    for local l in $(result)
-    {
-        if [ $(l).type ] && [ type.is-derived [ $(l).type ] LIB ] 
-        {
-            created-libraries += $(l) ;
-        }            
-    }
-    
-    created-libraries = [ set.difference $(created-libraries) : $(used-libraries) ] ;
-    set-library-order-aux $(created-libraries) : $(used-libraries) ;
-}
-
-rule order-libraries ( libraries * )
-{
-    local r = [ $(.order).order $(libraries) ] ;
-    return $(r) ;
-}
-     
\ No newline at end of file
diff --git a/jam-files/boost-build/tools/unix.py b/jam-files/boost-build/tools/unix.py
deleted file mode 100644
index d409c2e4..00000000
--- a/jam-files/boost-build/tools/unix.py
+++ /dev/null
@@ -1,150 +0,0 @@
-#  Copyright (c) 2004 Vladimir Prus.
-#
-#  Use, modification and distribution is subject to the Boost Software
-#  License Version 1.0. (See accompanying file LICENSE_1_0.txt or
-#  http://www.boost.org/LICENSE_1_0.txt)
-
-""" This file implements linking semantics common to all unixes. On unix, static
-    libraries must be specified in a fixed order on the linker command line. Generators
-    declared there store information about the order and use it properly.
-"""
-
-import builtin
-from b2.build import generators, type
-from b2.util.utility import *
-from b2.util import set, sequence
-
-class UnixLinkingGenerator (builtin.LinkingGenerator):
-    
-    def __init__ (self, id, composing, source_types, target_types, requirements):
-        builtin.LinkingGenerator.__init__ (self, id, composing, source_types, target_types, requirements)
-    
-    def run (self, project, name, prop_set, sources):
-        result = builtin.LinkingGenerator.run (self, project, name, prop_set, sources)
-        if result:
-            set_library_order (project.manager (), sources, prop_set, result [1])
-                                
-        return result
-    
-    def generated_targets (self, sources, prop_set, project, name):
-        sources2 = []
-        libraries = []
-        for l in sources:
-            if type.is_derived (l.type (), 'LIB'):
-                libraries.append (l)
-
-            else:
-                sources2.append (l)
-        
-        sources = sources2 + order_libraries (libraries)
-        
-        return builtin.LinkingGenerator.generated_targets (self, sources, prop_set, project, name)
-
-
-class UnixArchiveGenerator (builtin.ArchiveGenerator):
-    def __init__ (self, id, composing, source_types, target_types_and_names, requirements):
-        builtin.ArchiveGenerator.__init__ (self, id, composing, source_types, target_types_and_names, requirements)
-        
-    def run (self, project, name, prop_set, sources):
-        result = builtin.ArchiveGenerator.run(self, project, name, prop_set, sources)
-        set_library_order(project.manager(), sources, prop_set, result)
-        return result
-
-class UnixSearchedLibGenerator (builtin.SearchedLibGenerator):
-    
-    def __init__ (self):
-        builtin.SearchedLibGenerator.__init__ (self)
-    
-    def optional_properties (self):
-        return self.requirements ()
-              
-    def run (self, project, name, prop_set, sources, multiple):
-        result = SearchedLibGenerator.run (project, name, prop_set, sources, multiple)
-        
-        set_library_order (sources, prop_set, result)
-        
-        return result
-
-class UnixPrebuiltLibGenerator (generators.Generator):
-    def __init__ (self, id, composing, source_types, target_types_and_names, requirements):
-        generators.Generator.__init__ (self, id, composing, source_types, target_types_and_names, requirements)
-
-    def run (self, project, name, prop_set, sources, multiple):
-        f = prop_set.get ('<file>')
-        set_library_order_aux (f, sources)
-        return (f, sources)
-
-### # The derived toolset must specify their own rules and actions.
-# FIXME: restore?
-# action.register ('unix.prebuilt', None, None)
-
-
-generators.register (UnixPrebuiltLibGenerator ('unix.prebuilt', False, [], ['LIB'], ['<file>', '<toolset>unix']))
-
-
-
-
-
-### # Declare generators
-### generators.register [ new UnixLinkingGenerator unix.link : LIB OBJ : EXE 
-###     : <toolset>unix ] ;
-generators.register (UnixArchiveGenerator ('unix.archive', True, ['OBJ'], ['STATIC_LIB'], ['<toolset>unix']))
-
-### generators.register [ new UnixLinkingGenerator unix.link.dll : LIB OBJ : SHARED_LIB 
-###     : <toolset>unix ] ;
-### 
-### generators.register [ new UnixSearchedLibGenerator 
-###    unix.SearchedLibGenerator : : SEARCHED_LIB : <toolset>unix ] ;
-### 
-### 
-### # The derived toolset must specify their own actions.
-### actions link {
-### }
-### 
-### actions link.dll {
-### }
-
-def unix_archive (manager, targets, sources, properties):
-    pass
-
-# FIXME: restore?
-#action.register ('unix.archive', unix_archive, [''])
-
-### actions searched-lib-generator {    
-### }
-### 
-### actions prebuilt {
-### }
-
-
-from b2.util.order import Order
-__order = Order ()
-
-def set_library_order_aux (from_libs, to_libs):
-    for f in from_libs:
-        for t in to_libs:
-            if f != t:
-                __order.add_pair (f, t)
-
-def set_library_order (manager, sources, prop_set, result):
-    used_libraries = []
-    deps = prop_set.dependency ()
-
-    sources.extend(d.value() for d in deps)
-    sources = sequence.unique(sources)
-
-    for l in sources:
-        if l.type () and type.is_derived (l.type (), 'LIB'):
-            used_libraries.append (l)
-
-    created_libraries = []
-    for l in result:
-        if l.type () and type.is_derived (l.type (), 'LIB'):
-            created_libraries.append (l)
-    
-    created_libraries = set.difference (created_libraries, used_libraries)
-    set_library_order_aux (created_libraries, used_libraries)
-
-def order_libraries (libraries):
-    return __order.order (libraries)
-     
diff --git a/jam-files/boost-build/tools/vacpp.jam b/jam-files/boost-build/tools/vacpp.jam
deleted file mode 100644
index f4080fc0..00000000
--- a/jam-files/boost-build/tools/vacpp.jam
+++ /dev/null
@@ -1,150 +0,0 @@
-# Copyright Vladimir Prus 2004.
-# Copyright Toon Knapen 2004.
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt
-# or copy at http://www.boost.org/LICENSE_1_0.txt)
-
-#
-# Boost.Build V2 toolset for the IBM XL C++ compiler
-#
-
-import toolset : flags ;
-import feature ;
-import common ;
-import generators ;
-import os ;
-
-feature.extend toolset : vacpp ;
-toolset.inherit vacpp : unix ;
-generators.override vacpp.prebuilt : builtin.prebuilt ;
-generators.override vacpp.searched-lib-generator : searched-lib-generator ;
-
-# Configure the vacpp toolset
-rule init ( version ? : command * : options * )
-{
-    local condition = [ 
-        common.check-init-parameters vacpp : version $(version) ] ;
-              
-    command = [ common.get-invocation-command vacpp : xlC
-        : $(command) : "/usr/vacpp/bin/xlC" ] ;
-        
-    common.handle-options vacpp : $(condition) : $(command) : $(options) ;
-}
-
-# Declare generators
-generators.register-c-compiler vacpp.compile.c : C : OBJ : <toolset>vacpp ;
-generators.register-c-compiler vacpp.compile.c++ : CPP : OBJ : <toolset>vacpp ;
-
-# Allow C++ style comments in C files
-flags vacpp CFLAGS : -qcpluscmt ;
-
-# Declare flags
-flags vacpp CFLAGS <optimization>off : -qNOOPTimize ;
-flags vacpp CFLAGS <optimization>speed : -O3 -qstrict ;
-flags vacpp CFLAGS <optimization>space : -O2 -qcompact ;
-
-# Discretionary inlining (not recommended)
-flags vacpp CFLAGS <inlining>off : -qnoinline ;
-flags vacpp CFLAGS <inlining>on : -qinline ;
-#flags vacpp CFLAGS <inlining>full : -qinline ;
-flags vacpp CFLAGS <inlining>full : ;
-
-# Exception handling
-flags vacpp C++FLAGS <exception-handling>off : -qnoeh ;
-flags vacpp C++FLAGS <exception-handling>on : -qeh ;
-
-# Run-time Type Identification
-flags vacpp C++FLAGS <rtti>off : -qnortti ;
-flags vacpp C++FLAGS <rtti>on : -qrtti ;
-
-# Enable 64-bit memory addressing model
-flags vacpp CFLAGS <address-model>64 : -q64 ;
-flags vacpp LINKFLAGS <address-model>64 : -q64 ;
-flags vacpp ARFLAGS <target-os>aix/<address-model>64 : -X 64 ;
-
-# Use absolute path when generating debug information
-flags vacpp CFLAGS <debug-symbols>on : -g -qfullpath ;
-flags vacpp LINKFLAGS <debug-symbols>on : -g -qfullpath ;
-flags vacpp LINKFLAGS <debug-symbols>off : -s ;
-
-if [ os.name ] = AIX
-{
-    flags vacpp.compile C++FLAGS : -qfuncsect ;
-
-    # The -bnoipath strips the prepending (relative) path of libraries from
-    # the loader section in the target library or executable. Hence, during
-    # load-time LIBPATH (identical to LD_LIBRARY_PATH) or a hard-coded
-    # -blibpath (*similar* to -lrpath/-lrpath-link) is searched. Without
-    # this option, the prepending (relative) path + library name is
-    # hard-coded in the loader section, causing *only* this path to be
-    # searched during load-time. Note that the AIX linker does not have an
-    # -soname equivalent, this is as close as it gets.
-    #
-    # The above options are definately for AIX 5.x, and most likely also for
-    # AIX 4.x and AIX 6.x. For details about the AIX linker see:
-    # http://download.boulder.ibm.com/ibmdl/pub/software/dw/aix/es-aix_ll.pdf
-    #
-    flags vacpp.link LINKFLAGS <link>shared : -bnoipath ;
-
-    # Run-time linking
-    flags vacpp.link EXE-LINKFLAGS <link>shared : -brtl ;
-}
-else
-{
-    # Linux PPC
-    flags vacpp.compile CFLAGS <link>shared : -qpic=large ;
-    flags vacpp FINDLIBS : rt ;
-}
-
-# Profiling
-flags vacpp CFLAGS <profiling>on : -pg ;
-flags vacpp LINKFLAGS <profiling>on : -pg ;
-
-flags vacpp.compile OPTIONS <cflags> ;
-flags vacpp.compile.c++ OPTIONS <cxxflags> ;
-flags vacpp DEFINES <define> ;
-flags vacpp UNDEFS <undef> ;
-flags vacpp HDRS <include> ;
-flags vacpp STDHDRS <sysinclude> ;
-flags vacpp.link OPTIONS <linkflags> ;
-flags vacpp ARFLAGS <arflags> ;
-
-flags vacpp LIBPATH <library-path> ;
-flags vacpp NEEDLIBS <library-file> ;
-flags vacpp FINDLIBS <find-shared-library> ;
-flags vacpp FINDLIBS <find-static-library> ;
-
-# Select the compiler name according to the threading model.
-flags vacpp VA_C_COMPILER  <threading>single : xlc   ;
-flags vacpp VA_C_COMPILER  <threading>multi : xlc_r ;
-flags vacpp VA_CXX_COMPILER <threading>single : xlC   ;
-flags vacpp VA_CXX_COMPILER <threading>multi : xlC_r ;
-
-SPACE = " " ;
-
-flags vacpp.link.dll HAVE_SONAME <target-os>linux : "" ;
-
-actions vacpp.link bind NEEDLIBS
-{
-    $(VA_CXX_COMPILER) $(EXE-LINKFLAGS) $(LINKFLAGS) -o "$(<[1])" -L$(LIBPATH) -L$(STDLIBPATH) "$(>)" "$(NEEDLIBS)" "$(NEEDLIBS)" -l$(FINDLIBS) $(OPTIONS) $(USER_OPTIONS)
-}
-
-actions vacpp.link.dll bind NEEDLIBS
-{
-    xlC_r -G $(LINKFLAGS) -o "$(<[1])" $(HAVE_SONAME)-Wl,-soname$(SPACE)-Wl,$(<[-1]:D=) -L$(LIBPATH) -L$(STDLIBPATH) "$(>)" "$(NEEDLIBS)" "$(NEEDLIBS)" -l$(FINDLIBS) $(OPTIONS) $(USER_OPTIONS) 
-}
-
-actions vacpp.compile.c
-{
-    $(VA_C_COMPILER) -c $(OPTIONS) $(USER_OPTIONS) -I$(BOOST_ROOT) -U$(UNDEFS) -D$(DEFINES) $(CFLAGS) -I"$(HDRS)" -I"$(STDHDRS)" -o "$(<)" "$(>)"
-}
-
-actions vacpp.compile.c++
-{
-    $(VA_CXX_COMPILER) -c $(OPTIONS) $(USER_OPTIONS) -I$(BOOST_ROOT) -U$(UNDEFS) -D$(DEFINES) $(CFLAGS) $(C++FLAGS) -I"$(HDRS)" -I"$(STDHDRS)" -o "$(<)" "$(>)"
-}
-
-actions updated together piecemeal vacpp.archive
-{
-    ar $(ARFLAGS) ru "$(<)" "$(>)"
-}
diff --git a/jam-files/boost-build/tools/whale.jam b/jam-files/boost-build/tools/whale.jam
deleted file mode 100644
index 9335ff0c..00000000
--- a/jam-files/boost-build/tools/whale.jam
+++ /dev/null
@@ -1,116 +0,0 @@
-#  Copyright (C) Vladimir Prus 2002-2005. 
-
-#  Use, modification and distribution is subject to the Boost Software
-#  License Version 1.0. (See accompanying file LICENSE_1_0.txt or
-#  http://www.boost.org/LICENSE_1_0.txt)
-
-#  This module implements support for Whale/Dolphin/WD parser/lexer tools. 
-#  See http://www.cs.queensu.ca/home/okhotin/whale/ for details.
-#
-#  There are three interesting target types:
-#  - WHL (the parser sources), that are converted to CPP and H
-#  - DLP (the lexer sources), that are converted to CPP and H
-#  - WD (combined parser/lexer sources), that are converted to WHL + DLP
-
-import type ;
-import generators ;
-import path ;
-import "class" : new ;
-import errors ;
-
-rule init ( path # path the Whale/Dolphin/WD binaries 
-          )
-{
-    if $(.configured) && $(.path) != $(path)
-    {
-        errors.user-error "Attempt to reconfigure Whale support" :
-          "Previously configured with path \"$(.path:E=<empty>)\"" :
-          "Now configuring with path \"$(path:E=<empty>)\"" ;
-
-    }
-    .configured = true ;
-    .path = $(path) ;
-
-    .whale = [ path.join $(path) whale ] ;
-    .dolphin = [ path.join $(path) dolphin ] ;
-    .wd = [ path.join $(path) wd ] ;
-}     
-
-
-# Declare the types.
-type.register WHL : whl ;
-type.register DLP : dlp ;
-type.register WHL_LR0 : lr0 ;
-type.register WD : wd ;
-
-# Declare standard generators.
-generators.register-standard whale.whale : WHL : CPP H H(%_symbols) ;
-generators.register-standard whale.dolphin : DLP : CPP H ;
-generators.register-standard whale.wd : WD : WHL(%_parser) DLP(%_lexer) ;
-
-# The conversions defines above a ambiguious when we generated CPP from WD.
-# We can either go via WHL type, or via DLP type.
-# The following custom generator handles this by running both conversions.
-
-class wd-to-cpp : generator
-{
-    rule __init__ ( * : * : * )
-    {
-        generator.__init__ $(1) : $(2) : $(3) ;
-    }
-    
-    rule run ( project name ? : property-set : source * )
-    {
-        if ! $(source[2])
-        {                
-            local new-sources ;
-            if ! [ $(source).type ] in WHL DLP
-            {            
-                local r1 = [ generators.construct $(project) $(name) 
-                  : WHL : $(property-set) : $(source) ] ;
-                local r2 = [ generators.construct $(project) $(name) 
-                  : DLP : $(property-set) : $(source) ] ;
-                
-                new-sources = [ sequence.unique $(r1[2-]) $(r2[2-]) ] ;
-            }
-            else
-            {
-                new-sources = $(source) ;
-            }
-            
-            local result ;
-            for local i in $(new-sources) 
-            {
-                local t = [ generators.construct $(project) $(name) : CPP 
-                  : $(property-set) : $(i) ] ;          
-                result += $(t[2-]) ;
-            }
-            return $(result) ;
-        }        
-    }
-    
-}
-
-
-generators.override whale.wd-to-cpp : whale.whale ;
-generators.override whale.wd-to-cpp : whale.dolphin ;
-
-
-generators.register [ new wd-to-cpp whale.wd-to-cpp : : CPP ] ;
-
-
-actions whale 
-{
-    $(.whale) -d $(<[1]:D) $(>)      
-}
-
-actions dolphin
-{    
-    $(.dolphin) -d $(<[1]:D) $(>)
-}
-
-actions wd
-{    
-    $(.wd) -d $(<[1]:D) -g $(>)
-}
-
diff --git a/jam-files/boost-build/tools/xlf.jam b/jam-files/boost-build/tools/xlf.jam
deleted file mode 100644
index e7fcc608..00000000
--- a/jam-files/boost-build/tools/xlf.jam
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright (C) 2004 Toon Knapen
-#
-#  Use, modification and distribution is subject to the Boost Software
-#  License Version 1.0. (See accompanying file LICENSE_1_0.txt or
-#  http://www.boost.org/LICENSE_1_0.txt)
-
-#
-# toolset configuration for the IBM Fortran compiler (xlf)
-# 
-
-import toolset : flags ;
-import feature ;
-import fortran ;
-
-rule init ( version ? : command * : options * )
-{
-}
-
-# Declare flags and action for compilation
-flags xlf OPTIONS <optimization>off : -O0 ;
-flags xlf OPTIONS <optimization>speed : -O3 ;
-flags xlf OPTIONS <optimization>space : -Os ;
-
-flags xlf OPTIONS <debug-symbols>on : -g ;
-flags xlf OPTIONS <profiling>on : -pg ;
-
-flags xlf DEFINES <define> ;
-flags xlf INCLUDES <include> ;
-
-rule compile-fortran
-{
-}
-
-actions compile-fortran
-{
-  xlf $(OPTIONS) -I$(INCLUDES) -c -o "$(<)" "$(>)" 
-}
-
-generators.register-fortran-compiler xlf.compile-fortran : FORTRAN : OBJ ; 
diff --git a/jam-files/boost-build/tools/xsltproc-config.jam b/jam-files/boost-build/tools/xsltproc-config.jam
deleted file mode 100644
index de54a2eb..00000000
--- a/jam-files/boost-build/tools/xsltproc-config.jam
+++ /dev/null
@@ -1,37 +0,0 @@
-#~ Copyright 2005 Rene Rivera.
-#~ Distributed under the Boost Software License, Version 1.0.
-#~ (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-# Automatic configuration for Python tools and librries. To use, just import this module.
-
-import os ;
-import toolset : using ;
-
-if [ os.name ] = NT
-{
-    local xsltproc-path = [ GLOB [ modules.peek : PATH ] "C:\\Boost\\bin" : xsltproc\.exe ] ;
-    xsltproc-path = $(xsltproc-path[1]) ;
-    
-    if $(xsltproc-path)
-    {
-        if --debug-configuration in [ modules.peek : ARGV ]
-        {
-            ECHO "notice:" using xsltproc ":" $(xsltproc-path) ;
-        }
-        using xsltproc : $(xsltproc-path) ;
-    }
-}
-else
-{
-    local xsltproc-path = [ GLOB [ modules.peek : PATH ] : xsltproc ] ;
-    xsltproc-path = $(xsltproc-path[1]) ;
-    
-    if $(xsltproc-path)
-    {
-        if --debug-configuration in [ modules.peek : ARGV ]
-        {
-            ECHO "notice:" using xsltproc ":" $(xsltproc-path) ;
-        }
-        using xsltproc : $(xsltproc-path) ;
-    }
-}
diff --git a/jam-files/boost-build/tools/xsltproc.jam b/jam-files/boost-build/tools/xsltproc.jam
deleted file mode 100644
index 96f5170b..00000000
--- a/jam-files/boost-build/tools/xsltproc.jam
+++ /dev/null
@@ -1,194 +0,0 @@
-# Copyright (C) 2003 Doug Gregor. Permission to copy, use, modify, sell and
-# distribute this software is granted provided this copyright notice appears in
-# all copies. This software is provided "as is" without express or implied
-# warranty, and with no claim as to its suitability for any purpose.
-
-# This module defines rules to apply an XSLT stylesheet to an XML file using the
-# xsltproc driver, part of libxslt.
-#
-# Note: except for 'init', this modules does not provide any rules for end
-# users.
-
-import feature ;
-import regex ;
-import sequence ;
-import common ;
-import os ;
-import modules ;
-import path ;
-import errors ;
-
-feature.feature xsl:param : : free ;
-feature.feature xsl:path : : free ;
-feature.feature catalog : : free ;
-
-
-# Initialize xsltproc support. The parameters are:
-#   xsltproc: The xsltproc executable
-#
-rule init ( xsltproc ? )
-{
-    if $(xsltproc)
-    {
-        modify-config ;
-        .xsltproc = $(xsltproc) ;
-        check-xsltproc ;
-    }
-}
-
-rule freeze-config ( )
-{
-    if ! $(.config-frozen)
-    {
-        .config-frozen = true ;
-        .xsltproc ?= [ modules.peek : XSLTPROC ] ;
-        .xsltproc ?= xsltproc ;
-        check-xsltproc ;
-        .is-cygwin = [ .is-cygwin $(.xsltproc) ] ;
-    }
-}
-
-rule modify-config
-{
-    if $(.config-frozen)
-    {
-        errors.user-error "xsltproc: Cannot change xsltproc command after it has been used." ;
-    }
-}
-
-rule check-xsltproc ( )
-{
-    if $(.xsltproc)
-    {
-        local status = [ SHELL "\"$(.xsltproc)\" -V" : no-output : exit-status ] ;
-        if $(status[2]) != "0"
-        {
-            errors.user-error "xsltproc: Could not run \"$(.xsltproc)\" -V." ;
-        }
-    }
-}
-
-# Returns a non-empty string if a cygwin xsltproc binary was specified.
-rule is-cygwin ( )
-{
-    freeze-config ;
-    return $(.is-cygwin) ;
-}
-
-rule .is-cygwin ( xsltproc )
-{
-    if [ os.on-windows ]
-    {
-        local file = [ path.make [ modules.binding $(__name__) ] ] ;
-        local dir = [ path.native
-                      [ path.join [ path.parent $(file) ] xsltproc ] ] ;
-        if [ os.name ] = CYGWIN
-        {
-            dir = $(dir:W) ;
-        }
-        local command =
-            "\"$(xsltproc)\" \"$(dir)\\test.xsl\" \"$(dir)\\test.xml\" 2>&1" ;
-        local status = [ SHELL $(command) : no-output : exit-status ] ;
-        if $(status[2]) != "0"
-        {
-            return true ;
-        }
-    }
-}
-
-rule compute-xslt-flags ( target : properties * )
-{
-    local flags ;
-
-    # Raw flags.
-    flags += [ feature.get-values <flags> : $(properties) ] ;
-
-    # Translate <xsl:param> into command line flags.
-    for local param in [ feature.get-values <xsl:param> : $(properties) ]
-    {
-        local namevalue = [ regex.split $(param) "=" ] ;
-        flags += --stringparam $(namevalue[1]) \"$(namevalue[2])\" ;
-    }
-
-    # Translate <xsl:path>.
-    for local path in [ feature.get-values <xsl:path> : $(properties) ]
-    {
-        flags += --path \"$(path:G=)\" ;
-    }
-
-    # Take care of implicit dependencies.
-    local other-deps ;
-    for local dep in [ feature.get-values <implicit-dependency> : $(properties) ]
-    {
-        other-deps += [ $(dep:G=).creating-subvariant ] ;
-    }
-
-    local implicit-target-directories ;
-    for local dep in [ sequence.unique $(other-deps) ]
-    {
-        implicit-target-directories += [ $(dep).all-target-directories ] ;
-    }
-
-    for local dir in $(implicit-target-directories)
-    {
-        flags += --path \"$(dir:T)\" ;
-    }
-
-    return $(flags) ;
-}
-
-
-local rule .xsltproc ( target : source stylesheet : properties * : dirname ? : action )
-{
-    freeze-config ;
-    STYLESHEET on $(target) = $(stylesheet) ;
-    FLAGS on $(target) += [ compute-xslt-flags $(target) : $(properties) ] ;
-    NAME on $(target) = $(.xsltproc) ;
-
-    for local catalog in [ feature.get-values <catalog> : $(properties) ]
-    {
-        CATALOG = [ common.variable-setting-command XML_CATALOG_FILES : $(catalog:T) ] ;
-    }
-
-    if [ os.on-windows ] && ! [ is-cygwin ]
-    {
-        action = $(action).windows ;
-    }
-
-    $(action) $(target) : $(source) ;
-}
-
-
-rule xslt ( target : source stylesheet : properties * )
-{
-    return [ .xsltproc $(target) : $(source) $(stylesheet) : $(properties) : : xslt-xsltproc ] ;
-}
-
-
-rule xslt-dir ( target : source stylesheet : properties * : dirname )
-{
-    return [ .xsltproc $(target) : $(source) $(stylesheet) : $(properties) : $(dirname) : xslt-xsltproc-dir ] ;
-}
-
-actions xslt-xsltproc.windows
-{
-    $(CATALOG) "$(NAME:E=xsltproc)" $(FLAGS) --xinclude -o "$(<)" "$(STYLESHEET:W)" "$(>:W)"
-}
-
-
-actions xslt-xsltproc bind STYLESHEET
-{
-    $(CATALOG) "$(NAME:E=xsltproc)" $(FLAGS) --xinclude -o "$(<)" "$(STYLESHEET:T)" "$(>:T)"
-}
-
-
-actions xslt-xsltproc-dir.windows bind STYLESHEET
-{
-    $(CATALOG) "$(NAME:E=xsltproc)" $(FLAGS) --xinclude -o "$(<:D)/" "$(STYLESHEET:W)" "$(>:W)"
-}
-
-
-actions xslt-xsltproc-dir bind STYLESHEET
-{
-    $(CATALOG) "$(NAME:E=xsltproc)" $(FLAGS) --xinclude -o "$(<:D)/" "$(STYLESHEET:T)" "$(>:T)"
-}
diff --git a/jam-files/boost-build/tools/xsltproc/included.xsl b/jam-files/boost-build/tools/xsltproc/included.xsl
deleted file mode 100644
index ef86394a..00000000
--- a/jam-files/boost-build/tools/xsltproc/included.xsl
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<!--
-   Copyright (c) 2010 Steven Watanabe
-  
-   Distributed under the Boost Software License, Version 1.0.
-   (See accompanying file LICENSE_1_0.txt or copy at
-   http://www.boost.org/LICENSE_1_0.txt)
-  -->
-<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
-                version="1.0">
-</xsl:stylesheet>
diff --git a/jam-files/boost-build/tools/xsltproc/test.xml b/jam-files/boost-build/tools/xsltproc/test.xml
deleted file mode 100644
index 57c8ba18..00000000
--- a/jam-files/boost-build/tools/xsltproc/test.xml
+++ /dev/null
@@ -1,2 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<root/>
diff --git a/jam-files/boost-build/tools/xsltproc/test.xsl b/jam-files/boost-build/tools/xsltproc/test.xsl
deleted file mode 100644
index a142c91d..00000000
--- a/jam-files/boost-build/tools/xsltproc/test.xsl
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<!--
-   Copyright (c) 2010 Steven Watanabe
-  
-   Distributed under the Boost Software License, Version 1.0.
-   (See accompanying file LICENSE_1_0.txt or copy at
-   http://www.boost.org/LICENSE_1_0.txt)
-  -->
-<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
-                version="1.0">
-  <xsl:include href="included.xsl"/>
-</xsl:stylesheet>
diff --git a/jam-files/boost-build/tools/zlib.jam b/jam-files/boost-build/tools/zlib.jam
deleted file mode 100644
index f9138fd5..00000000
--- a/jam-files/boost-build/tools/zlib.jam
+++ /dev/null
@@ -1,92 +0,0 @@
-# Copyright (c) 2010 Vladimir Prus.
-#
-# Use, modification and distribution is subject to the Boost Software
-# License Version 1.0. (See accompanying file LICENSE_1_0.txt or
-# http://www.boost.org/LICENSE_1_0.txt)
-
-# Supports the zlib library
-#
-# After 'using zlib', the following targets are available:
-#
-# /zlib//zlib -- The zlib library
-
-
-# In addition to direct purpose of supporting zlib, this module also
-# serves as canonical example of how third-party condiguration works
-# in Boost.Build. The operation is as follows
-#
-# - For each 'using zlib : condition ... : ...' we create a target alternative
-#   for zlib, with the specified condition.
-# - There's one target alternative for 'zlib' with no specific condition
-#   properties. 
-#
-# Two invocations of 'using zlib' with the same condition but different
-# properties are not permitted, e.g.:
-#
-#   using zlib : condition <target-os>windows : include foo ;
-#   using zlib : condition <target-os>windows : include bar ;
-#
-# is in error. One exception is for empty condition, 'using' without any
-# parameters is overridable. That is:
-#
-#   using zlib ;
-#   using zlib : include foo ;
-# 
-# Is OK then the first 'using' is ignored. Likewise if the order of the statements
-# is reversed.
-#
-# When 'zlib' target is built, a target alternative is selected as usual for
-# Boost.Build. The selected alternative is a custom target class, which:
-#
-# - calls ac.find-include-path to find header path. If explicit path is provided
-#   in 'using', only that path is checked, and if no header is found there, error
-#   is emitted. Otherwise, we check a directory specified using ZLIB_INCLUDE
-#   environment variable, and failing that, in standard directories.
-#   [TODO: document sysroot handling]
-# - calls ac.find-library to find the library, in an identical fashion.
-#
-
-import project ;
-import ac ;
-import errors ;
-import "class" : new ;
-import targets ; 
-
-project.initialize $(__name__) ;
-project = [ project.current ] ;
-project zlib ;
-
-header = zlib.h ;
-names = z zlib zll zdll ;
-
-.default-alternative = [ new ac-library zlib : $(project) ] ;
-$(.default-alternative).set-header $(header) ;
-$(.default-alternative).set-default-names $(names) ;
-targets.main-target-alternative $(.default-alternative) ;
-
-rule init ( * : * )
-{
-    if ! $(condition)
-    {
-        # Special case the no-condition case so that 'using' without parameters
-        # can mix with more specific 'using'.
-        $(.default-alternative).reconfigure $(1) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ;
-    }
-    else                    
-    {
-        # FIXME: consider if we should allow overriding definitions for a given
-        # condition -- e.g. project-config.jam might want to override whatever is
-        # in user-config.jam. 
-        local mt = [ new ac-library zlib : $(project)
-          : $(1) : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ] ;
-        $(mt).set-header $(header) ;
-        $(mt).set-default-names $(names) ;
-        targets.main-target-alternative $(mt) ;
-    }    
-}
-
-
-
-
-
-
diff --git a/jam-files/boost-build/user-config.jam b/jam-files/boost-build/user-config.jam
deleted file mode 100644
index fbbf13fd..00000000
--- a/jam-files/boost-build/user-config.jam
+++ /dev/null
@@ -1,92 +0,0 @@
-# Copyright 2003, 2005 Douglas Gregor
-# Copyright 2004 John Maddock
-# Copyright 2002, 2003, 2004, 2007 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-#   This file is used to configure your Boost.Build installation. You can modify
-# this file in place, or you can place it in a permanent location so that it
-# does not get overwritten should you get a new version of Boost.Build. See:
-#
-#   http://www.boost.org/boost-build2/doc/html/bbv2/overview/configuration.html
-#
-# for documentation about possible permanent locations.
-
-#   This file specifies which toolsets (C++ compilers), libraries, and other
-# tools are available. Often, you should be able to just uncomment existing
-# example lines and adjust them to taste. The complete list of supported tools,
-# and configuration instructions can be found at:
-#
-#   http://boost.org/boost-build2/doc/html/bbv2/reference/tools.html
-#
-
-#   This file uses Jam language syntax to describe available tools. Mostly,
-# there are 'using' lines, that contain the name of the used tools, and
-# parameters to pass to those tools -- where paremeters are separated by
-# semicolons. Important syntax notes:
-#
-#   - Both ':' and ';' must be separated from other tokens by whitespace
-#   - The '\' symbol is a quote character, so when specifying Windows paths you
-#     should use '/' or '\\' instead.
-#
-# More details about the syntax can be found at:
-#
-#   http://boost.org/boost-build2/doc/html/bbv2/advanced.html#bbv2.advanced.jam_language
-#
-
-# ------------------
-# GCC configuration.
-# ------------------
-
-# Configure gcc (default version).
-# using gcc ;
-
-# Configure specific gcc version, giving alternative name to use.
-# using gcc : 3.2 : g++-3.2 ;
-
-
-# -------------------
-# MSVC configuration.
-# -------------------
-
-# Configure msvc (default version, searched for in standard locations and PATH).
-# using msvc ;
-
-# Configure specific msvc version (searched for in standard locations and PATH).
-# using msvc : 8.0 ;
-
-
-# ----------------------
-# Borland configuration.
-# ----------------------
-# using borland ;
-
-
-# ----------------------
-# STLPort configuration.
-# ----------------------
-
-#   Configure specifying location of STLPort headers. Libraries must be either
-# not needed or available to the compiler by default.
-# using stlport : : /usr/include/stlport ;
-
-# Configure specifying location of both headers and libraries explicitly.
-# using stlport : : /usr/include/stlport /usr/lib ;
-
-
-# -----------------
-# QT configuration.
-# -----------------
-
-# Configure assuming QTDIR gives the installation prefix.
-# using qt ;
-
-# Configure with an explicit installation prefix.
-# using qt : /usr/opt/qt ;
-
-# ---------------------
-# Python configuration.
-# ---------------------
-
-# Configure specific Python version.
-# using python : 3.1 : /usr/bin/python3 : /usr/include/python3.1 : /usr/lib ;
diff --git a/jam-files/boost-build/util/__init__.py b/jam-files/boost-build/util/__init__.py
deleted file mode 100644
index f80fe70e..00000000
--- a/jam-files/boost-build/util/__init__.py
+++ /dev/null
@@ -1,136 +0,0 @@
-
-import bjam
-import re
-import types
-
-# Decorator the specifies bjam-side prototype for a Python function
-def bjam_signature(s):
-
-    def wrap(f):       
-        f.bjam_signature = s
-        return f
-
-    return wrap
-
-def metatarget(f):
-
-    f.bjam_signature = (["name"], ["sources", "*"], ["requirements", "*"],
-                        ["default_build", "*"], ["usage_requirements", "*"])
-    return f
-
-class cached(object):
-
-    def __init__(self, function):
-        self.function = function
-        self.cache = {}
-
-    def __call__(self, *args):
-        try:
-            return self.cache[args]
-        except KeyError:
-            v = self.function(*args)
-            self.cache[args] = v
-            return v
-
-    def __get__(self, instance, type):
-        return types.MethodType(self, instance, type)
-
-def unquote(s):
-    if s and s[0] == '"' and s[-1] == '"':
-        return s[1:-1]
-    else:
-        return s
-
-_extract_jamfile_and_rule = re.compile("(Jamfile<.*>)%(.*)")
-
-def qualify_jam_action(action_name, context_module):
-
-    if action_name.startswith("###"):
-        # Callable exported from Python. Don't touch
-        return action_name
-    elif _extract_jamfile_and_rule.match(action_name):
-        # Rule is already in indirect format
-        return action_name
-    else:
-        ix = action_name.find('.')
-        if ix != -1 and action_name[:ix] == context_module:
-            return context_module + '%' + action_name[ix+1:]
-        
-        return context_module + '%' + action_name        
-    
-
-def set_jam_action(name, *args):
-
-    m = _extract_jamfile_and_rule.match(name)
-    if m:
-        args = ("set-update-action-in-module", m.group(1), m.group(2)) + args
-    else:
-        args = ("set-update-action", name) + args
-
-    return bjam.call(*args)
-
-
-def call_jam_function(name, *args):
-
-    m = _extract_jamfile_and_rule.match(name)
-    if m:
-        args = ("call-in-module", m.group(1), m.group(2)) + args
-        return bjam.call(*args)
-    else:
-        return bjam.call(*((name,) + args))
-
-__value_id = 0
-__python_to_jam = {}
-__jam_to_python = {}
-
-def value_to_jam(value, methods=False):
-    """Makes a token to refer to a Python value inside Jam language code.
-
-    The token is merely a string that can be passed around in Jam code and
-    eventually passed back. For example, we might want to pass PropertySet
-    instance to a tag function and it might eventually call back
-    to virtual_target.add_suffix_and_prefix, passing the same instance.
-
-    For values that are classes, we'll also make class methods callable
-    from Jam.
-
-    Note that this is necessary to make a bit more of existing Jamfiles work.
-    This trick should not be used to much, or else the performance benefits of
-    Python port will be eaten.
-    """
-
-    global __value_id
-
-    r = __python_to_jam.get(value, None)
-    if r:
-        return r
-
-    exported_name = '###_' + str(__value_id)
-    __value_id = __value_id + 1
-    __python_to_jam[value] = exported_name
-    __jam_to_python[exported_name] = value
-
-    if methods and type(value) == types.InstanceType:
-        for field_name in dir(value):
-            field = getattr(value, field_name)
-            if callable(field) and not field_name.startswith("__"):
-                bjam.import_rule("", exported_name + "." + field_name, field)
-
-    return exported_name
-
-def record_jam_to_value_mapping(jam_value, python_value):
-    __jam_to_python[jam_value] = python_value
-
-def jam_to_value_maybe(jam_value):
-
-    if type(jam_value) == type(""):
-        return __jam_to_python.get(jam_value, jam_value)
-    else:
-        return jam_value
-
-def stem(filename):
-    i = filename.find('.')
-    if i != -1:
-        return filename[0:i]
-    else:
-        return filename
diff --git a/jam-files/boost-build/util/assert.jam b/jam-files/boost-build/util/assert.jam
deleted file mode 100644
index abedad52..00000000
--- a/jam-files/boost-build/util/assert.jam
+++ /dev/null
@@ -1,336 +0,0 @@
-# Copyright 2001, 2002, 2003 Dave Abrahams
-# Copyright 2006 Rene Rivera
-# Copyright 2002, 2003 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-import errors ;
-import modules ;
-
-
-################################################################################
-#
-# Private implementation details.
-#
-################################################################################
-
-# Rule added as a replacement for the regular Jam = operator but which does not
-# ignore trailing empty string elements.
-#
-local rule exact-equal-test ( lhs * : rhs * )
-{
-    local lhs_extended = $(lhs) xxx ;
-    local rhs_extended = $(rhs) xxx ;
-    if $(lhs_extended) = $(rhs_extended)
-    {
-        return true ;
-    }
-}
-
-
-# Two lists are considered set-equal if they contain the same elements, ignoring
-# duplicates and ordering.
-#
-local rule set-equal-test ( set1 * : set2 * )
-{
-    if ( $(set1) in $(set2) ) && ( $(set2) in $(set1) )
-    {
-        return true ;
-    }
-}
-
-
-################################################################################
-#
-# Public interface.
-#
-################################################################################
-
-# Assert the equality of A and B, ignoring trailing empty string elements.
-#
-rule equal ( a * : b * )
-{
-    if $(a) != $(b)
-    {
-        errors.error-skip-frames 3 assertion failure: \"$(a)\" "==" \"$(b)\"
-            (ignoring trailing empty strings) ;
-    }
-}
-
-
-# Assert that the result of calling RULE-NAME on the given arguments has a false
-# logical value (is either an empty list or all empty strings).
-#
-rule false ( rule-name args * : * )
-{
-    local result ;
-    module [ CALLER_MODULE ]
-    {
-        modules.poke assert : result : [ $(1) : $(2) : $(3) : $(4) : $(5) : $(6)
-            : $(7) : $(8) : $(9) ] ;
-    }
-
-    if $(result)
-    {
-        errors.error-skip-frames 3 assertion failure: Expected false result from
-            "[" $(rule-name) [ errors.lol->list $(args) : $(2) : $(3) : $(4) :
-            $(5) : $(6) : $(7) : $(8) : $(9) ] "]" : Got: "[" \"$(result)\" "]" ;
-    }
-}
-
-
-# Assert that ELEMENT is present in LIST.
-#
-rule "in" ( element : list * )
-{
-    if ! $(element) in $(list)
-    {
-        errors.error-skip-frames 3 assertion failure: Expected \"$(element)\" in
-            "[" \"$(list)\" "]" ;
-    }
-}
-
-
-# Assert the inequality of A and B, ignoring trailing empty string elements.
-#
-rule not-equal ( a * : b * )
-{
-    if $(a) = $(b)
-    {
-        errors.error-skip-frames 3 assertion failure: \"$(a)\" "!=" \"$(b)\"
-            (ignoring trailing empty strings) ;
-    }
-}
-
-
-# Assert that ELEMENT is not present in LIST.
-#
-rule not-in ( element : list * )
-{
-    if $(element) in $(list)
-    {
-        errors.error-skip-frames 3 assertion failure: Did not expect
-            \"$(element)\" in "[" \"$(list)\" "]" ;
-    }
-}
-
-
-# Assert the inequality of A and B as sets.
-#
-rule not-set-equal ( a * : b * )
-{
-    if [ set-equal-test $(a) : $(b) ]
-    {
-        errors.error-skip-frames 3 assertion failure: Expected "[" \"$(a)\" "]"
-            and "[" \"$(b)\" "]" to not be equal as sets ;
-    }
-}
-
-
-# Assert that A and B are not exactly equal, not ignoring trailing empty string
-# elements.
-#
-rule not-exact-equal ( a * : b * )
-{
-    if [ exact-equal-test $(a) : $(b) ]
-    {
-        errors.error-skip-frames 3 assertion failure: \"$(a)\" "!=" \"$(b)\" ;
-    }
-}
-
-
-# Assert that EXPECTED is the result of calling RULE-NAME with the given
-# arguments.
-#
-rule result ( expected * : rule-name args * : * )
-{
-    local result ;
-    module [ CALLER_MODULE ]
-    {
-        modules.poke assert : result : [ $(2) : $(3) : $(4) : $(5) : $(6) : $(7)
-            : $(8) : $(9) ] ;
-    }
-
-    if ! [ exact-equal-test $(result) : $(expected) ]
-    {
-        errors.error-skip-frames 3 assertion failure: "[" $(rule-name) [
-            errors.lol->list $(args) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) :
-            $(9) ] "]" : Expected: "[" \"$(expected)\" "]" : Got: "["
-            \"$(result)\" "]" ;
-    }
-}
-
-
-# Assert that EXPECTED is set-equal (i.e. duplicates and ordering are ignored)
-# to the result of calling RULE-NAME with the given arguments. Note that rules
-# called this way may accept at most 8 parameters.
-#
-rule result-set-equal ( expected * : rule-name args * : * )
-{
-    local result ;
-    module [ CALLER_MODULE ]
-    {
-        modules.poke assert : result : [ $(2) : $(3) : $(4) : $(5) : $(6) : $(7)
-            : $(8) : $(9) ] ;
-    }
-
-    if ! [ set-equal-test $(result) : $(expected) ]
-    {
-        errors.error-skip-frames 3 assertion failure: "[" $(rule-name) [
-            errors.lol->list $(args) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) :
-            $(9) ] "]" : Expected: "[" \"$(expected)\" "]" : Got: "["
-            \"$(result)\" "]" ;
-    }
-}
-
-
-# Assert the equality of A and B as sets.
-#
-rule set-equal ( a * : b * )
-{
-    if ! [ set-equal-test $(a) : $(b) ]
-    {
-        errors.error-skip-frames 3 assertion failure: Expected "[" \"$(a)\" "]"
-            and "[" \"$(b)\" "]" to be equal as sets ;
-    }
-}
-
-
-# Assert that the result of calling RULE-NAME on the given arguments has a true
-# logical value (is neither an empty list nor all empty strings).
-#
-rule true ( rule-name args * : * )
-{
-    local result ;
-    module [ CALLER_MODULE ]
-    {
-        modules.poke assert : result : [ $(1) : $(2) : $(3) : $(4) : $(5) : $(6)
-            : $(7) : $(8) : $(9) ] ;
-    }
-
-    if ! $(result)
-    {
-        errors.error-skip-frames 3 assertion failure: Expected true result from
-            "[" $(rule-name) [ errors.lol->list $(args) : $(2) : $(3) : $(4) :
-            $(5) : $(6) : $(7) : $(8) : $(9) ] "]" ;
-    }
-}
-
-
-# Assert the exact equality of A and B, not ignoring trailing empty string
-# elements.
-#
-rule exact-equal ( a * : b * )
-{
-    if ! [ exact-equal-test $(a) : $(b) ]
-    {
-        errors.error-skip-frames 3 assertion failure: \"$(a)\" "==" \"$(b)\" ;
-    }
-}
-
-
-# Assert that the given variable is not an empty list.
-#
-rule variable-not-empty ( name )
-{
-    local value = [ modules.peek [ CALLER_MODULE ] : $(name) ] ;
-    if ! $(value)-is-not-empty
-    {
-        errors.error-skip-frames 3 assertion failure: Expected variable
-            \"$(name)\" not to be an empty list ;
-    }
-}
-
-
-rule __test__ ( )
-{
-    # Helper rule used to avoid test duplication related to different list
-    # equality test rules.
-    #
-    local rule run-equality-test ( equality-assert : ignore-trailing-empty-strings ? )
-    {
-        local not-equality-assert = not-$(equality-assert) ;
-
-        # When the given equality test is expected to ignore trailing empty
-        # strings some of the test results should be inverted.
-        local not-equality-assert-i = not-$(equality-assert) ;
-        if $(ignore-trailing-empty-strings)
-        {
-            not-equality-assert-i = $(equality-assert) ;
-        }
-
-            $(equality-assert)         :       ;
-            $(equality-assert)   "" "" : "" "" ;
-        $(not-equality-assert-i)       : "" "" ;
-            $(equality-assert)   x     : x     ;
-        $(not-equality-assert)         : x     ;
-        $(not-equality-assert)   ""    : x     ;
-        $(not-equality-assert)   "" "" : x     ;
-        $(not-equality-assert-i) x     : x ""  ;
-            $(equality-assert)   x ""  : x ""  ;
-        $(not-equality-assert)   x     : "" x  ;
-            $(equality-assert)   "" x  : "" x  ;
-
-            $(equality-assert) 1 2 3 : 1 2 3   ;
-        $(not-equality-assert) 1 2 3 : 3 2 1   ;
-        $(not-equality-assert) 1 2 3 : 1 5 3   ;
-        $(not-equality-assert) 1 2 3 : 1 "" 3  ;
-        $(not-equality-assert) 1 2 3 : 1 1 2 3 ;
-        $(not-equality-assert) 1 2 3 : 1 2 2 3 ;
-        $(not-equality-assert) 1 2 3 : 5 6 7   ;
-
-        # Extra variables used here just to make sure Boost Jam or Boost Build
-        # do not handle lists with empty strings differently depending on
-        # whether they are literals or stored in variables.
-
-        local empty           =         ;
-        local empty-strings   = "" ""   ;
-        local x-empty-strings = x "" "" ;
-        local empty-strings-x = "" "" x ;
-
-            $(equality-assert)                      : $(empty)           ;
-        $(not-equality-assert-i) ""                 : $(empty)           ;
-        $(not-equality-assert-i) "" ""              : $(empty)           ;
-        $(not-equality-assert-i)                    : $(empty-strings)   ;
-        $(not-equality-assert-i) ""                 : $(empty-strings)   ;
-            $(equality-assert)   "" ""              : $(empty-strings)   ;
-            $(equality-assert)   $(empty)           : $(empty)           ;
-            $(equality-assert)   $(empty-strings)   : $(empty-strings)   ;
-        $(not-equality-assert-i) $(empty)           : $(empty-strings)   ;
-            $(equality-assert)   $(x-empty-strings) : $(x-empty-strings) ;
-            $(equality-assert)   $(empty-strings-x) : $(empty-strings-x) ;
-        $(not-equality-assert)   $(empty-strings-x) : $(x-empty-strings) ;
-        $(not-equality-assert-i) x                  : $(x-empty-strings) ;
-        $(not-equality-assert)   x                  : $(empty-strings-x) ;
-        $(not-equality-assert-i) x                  : $(x-empty-strings) ;
-        $(not-equality-assert-i) x ""               : $(x-empty-strings) ;
-            $(equality-assert)   x "" ""            : $(x-empty-strings) ;
-        $(not-equality-assert)   x                  : $(empty-strings-x) ;
-        $(not-equality-assert)   "" x               : $(empty-strings-x) ;
-            $(equality-assert)   "" "" x            : $(empty-strings-x) ;
-    }                                    
-
-
-    # ---------------
-    # Equality tests.
-    # ---------------
-
-    run-equality-test equal : ignore-trailing-empty-strings ;
-    run-equality-test exact-equal ;
-
-
-    # -------------------------
-    # assert.set-equal() tests.
-    # -------------------------
-
-        set-equal         :         ;
-    not-set-equal "" ""   :         ;
-        set-equal "" ""   : ""      ;
-        set-equal "" ""   : "" ""   ;
-        set-equal a b c   : a b c   ;
-        set-equal a b c   : b c a   ;
-        set-equal a b c a : a b c   ;
-        set-equal a b c   : a b c a ;
-    not-set-equal a b c   : a b c d ;
-    not-set-equal a b c d : a b c   ;
-}
diff --git a/jam-files/boost-build/util/container.jam b/jam-files/boost-build/util/container.jam
deleted file mode 100644
index dd496393..00000000
--- a/jam-files/boost-build/util/container.jam
+++ /dev/null
@@ -1,339 +0,0 @@
-# Copyright 2003 Dave Abrahams
-# Copyright 2002, 2003 Rene Rivera
-# Copyright 2002, 2003, 2004 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-# Various container classes.
-
-# Base for container objects. This lets us construct recursive structures. That
-# is containers with containers in them, specifically so we can tell literal
-# values from node values.
-#
-class node
-{
-    rule __init__ (
-        value ?  # Optional value to set node to initially.
-    )
-    {
-        self.value = $(value) ;
-    }
-
-    # Set the value of this node, passing nothing will clear it.
-    #
-    rule set ( value * )
-    {
-        self.value = $(value) ;
-    }
-
-    # Get the value of this node.
-    #
-    rule get ( )
-    {
-        return $(self.value) ;
-    }
-}
-
-
-# A simple vector. Interface mimics the C++ std::vector and std::list, with the
-# exception that indices are one (1) based to follow Jam standard.
-#
-# TODO: Possibly add assertion checks.
-#
-class vector : node
-{
-    import numbers ;
-    import utility ;
-    import sequence ;
-
-    rule __init__ (
-        values *  # Initial contents of vector.
-    )
-    {
-        node.__init__ ;
-        self.value = $(values) ;
-    }
-
-    # Get the value of the first element.
-    #
-    rule front ( )
-    {
-        return $(self.value[1]) ;
-    }
-
-    # Get the value of the last element.
-    #
-    rule back ( )
-    {
-        return $(self.value[-1]) ;
-    }
-
-    # Get the value of the element at the given index, one based. Access to
-    # elements of recursive structures is supported directly. Specifying
-    # additional index values recursively accesses the elements as containers.
-    # For example: [ $(v).at 1 : 2 ] would retrieve the second element of our
-    # first element, assuming the first element is a container.
-    #
-    rule at (
-        index  # The element index, one based.
-        : *  # Additional indices to access recursively.
-    )
-    {
-        local r = $(self.value[$(index)]) ;
-        if $(2)
-        {
-            r = [ $(r).at $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ] ;
-        }
-        return $(r) ;
-    }
-
-    # Get the value contained in the given element. This has the same
-    # functionality and interface as "at" but in addition gets the value of the
-    # referenced element, assuming it is a "node".
-    #
-    rule get-at (
-        index  # The element index, one based.
-        : *  # Additional indices to access recursively.
-    )
-    {
-        local r = $(self.value[$(index)]) ;
-        if $(2)
-        {
-            r = [ $(r).at $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ] ;
-        }
-        return [ $(r).get ] ;
-    }
-
-    # Insert the given value into the front of the vector pushing the rest of
-    # the elements back.
-    #
-    rule push-front (
-        value  # Value to become first element.
-    )
-    {
-        self.value = $(value) $(self.value) ;
-    }
-
-    # Remove the front element from the vector. Does not return the value. No
-    # effect if vector is empty.
-    #
-    rule pop-front ( )
-    {
-        self.value = $(self.value[2-]) ;
-    }
-
-    # Add the given value at the end of the vector.
-    #
-    rule push-back (
-        value  # Value to become back element.
-    )
-    {
-        self.value += $(value) ;
-    }
-
-    # Remove the back element from the vector. Does not return the value. No
-    # effect if vector is empty.
-    #
-    rule pop-back ( )
-    {
-        self.value = $(self.value[1--2]) ;
-    }
-
-    # Insert the given value at the given index, one based. The values at and to
-    # the right of the index are pushed back to make room for the new value.
-    # If the index is passed the end of the vector the element is added to the
-    # end.
-    #
-    rule insert (
-        index  # The index to insert at, one based.
-        : value  # The value to insert.
-    )
-    {
-        local left = $(self.value[1-$(index)]) ;
-        local right = $(self.value[$(index)-]) ;
-        if $(right)-is-not-empty
-        {
-            left = $(left[1--2]) ;
-        }
-        self.value = $(left) $(value) $(right) ;
-    }
-
-    # Remove one or more elements from the vector. The range is inclusive, and
-    # not specifying an end is equivalent to the [start, start] range.
-    #
-    rule erase (
-        start  # Index of first element to remove.
-        end ?  # Optional, index of last element to remove.
-    )
-    {
-        end ?= $(start) ;
-        local left = $(self.value[1-$(start)]) ;
-        left = $(left[1--2]) ;
-        local right = $(self.value[$(end)-]) ;
-        right = $(right[2-]) ;
-        self.value = $(left) $(right) ;
-    }
-
-    # Remove all elements from the vector.
-    #
-    rule clear ( )
-    {
-        self.value = ;
-    }
-
-    # The number of elements in the vector.
-    #
-    rule size ( )
-    {
-        return [ sequence.length $(self.value) ] ;
-    }
-
-    # Returns "true" if there are NO elements in the vector, empty otherwise.
-    #
-    rule empty ( )
-    {
-        if ! $(self.value)-is-not-empty
-        {
-            return true ;
-        }
-    }
-
-    # Returns the textual representation of content.
-    #
-    rule str ( )
-    {
-        return "[" [ sequence.transform utility.str : $(self.value) ] "]" ;
-    }
-
-    # Sorts the vector inplace, calling 'utility.less' for comparisons.
-    #
-    rule sort ( )
-    {
-        self.value = [ sequence.insertion-sort $(self.value) : utility.less ] ;
-    }
-
-    # Returns true if content is equal to the content of other vector. Uses
-    # 'utility.equal' for comparison.
-    #
-    rule equal ( another )
-    {
-        local mismatch ;
-        local size = [ size ] ;
-        if $(size) = [ $(another).size ]
-        {
-            for local i in [ numbers.range 1 $(size) ]
-            {
-                if ! [ utility.equal [ at $(i) ] [ $(another).at $(i) ] ]
-                {
-                    mismatch = true ;
-                }
-            }
-        }
-        else
-        {
-            mismatch = true ;
-        }
-
-        if ! $(mismatch)
-        {
-            return true ;
-        }
-    }
-}
-
-
-rule __test__ ( )
-{
-    import assert ;
-    import "class" : new ;
-
-    local v1 = [ new vector ] ;
-    assert.true $(v1).equal $(v1) ;
-    assert.true $(v1).empty ;
-    assert.result 0 : $(v1).size ;
-    assert.result "[" "]" : $(v1).str ;
-    $(v1).push-back b ;
-    $(v1).push-front a ;
-    assert.result "[" a b "]" : $(v1).str ;
-    assert.result a : $(v1).front ;
-    assert.result b : $(v1).back ;
-    $(v1).insert 2 : d ;
-    $(v1).insert 2 : c ;
-    $(v1).insert 4 : f ;
-    $(v1).insert 4 : e ;
-    $(v1).pop-back ;
-    assert.result 5 : $(v1).size ;
-    assert.result d : $(v1).at 3 ;
-    $(v1).pop-front ;
-    assert.result c : $(v1).front ;
-    assert.false $(v1).empty ;
-    $(v1).erase 3 4 ;
-    assert.result 2 : $(v1).size ;
-
-    local v2 = [ new vector q w e r t y ] ;
-    assert.result 6 : $(v2).size ;
-    $(v1).push-back $(v2) ;
-    assert.result 3 : $(v1).size ;
-    local v2-alias = [ $(v1).back ] ;
-    assert.result e : $(v2-alias).at 3 ;
-    $(v1).clear ;
-    assert.true $(v1).empty ;
-    assert.false $(v2-alias).empty ;
-    $(v2).pop-back ;
-    assert.result t : $(v2-alias).back ;
-
-    local v3 = [ new vector ] ;
-    $(v3).push-back [ new vector 1 2 3 4 5 ] ;
-    $(v3).push-back [ new vector a b c ] ;
-    assert.result "[" "[" 1 2 3 4 5 "]" "[" a b c "]" "]" : $(v3).str ;
-    $(v3).push-back [ new vector [ new vector x y z ] [ new vector 7 8 9 ] ] ;
-    assert.result 1 : $(v3).at 1 : 1 ;
-    assert.result b : $(v3).at 2 : 2 ;
-    assert.result a b c : $(v3).get-at 2 ;
-    assert.result 7 8 9 : $(v3).get-at 3 : 2 ;
-
-    local v4 = [ new vector 4 3 6 ] ;
-    $(v4).sort ;
-    assert.result 3 4 6 : $(v4).get ;
-    assert.false $(v4).equal $(v3) ;
-
-    local v5 = [ new vector 3 4 6 ] ;
-    assert.true $(v4).equal $(v5) ;
-    # Check that vectors of different sizes are considered non-equal.
-    $(v5).pop-back ;
-    assert.false $(v4).equal $(v5) ;
-
-    local v6 = [ new vector [ new vector 1 2 3 ] ] ;
-    assert.true $(v6).equal [ new vector [ new vector 1 2 3 ] ] ;
-
-    local v7 = [ new vector 111 222 333 ] ;
-    assert.true $(v7).equal $(v7) ;
-    $(v7).insert 4 : 444 ;
-    assert.result 111 222 333 444 : $(v7).get ;
-    $(v7).insert 999 : xxx ;
-    assert.result 111 222 333 444 xxx : $(v7).get ;
-
-    local v8 = [ new vector "" "" "" ] ;
-    assert.true $(v8).equal $(v8) ;
-    assert.false $(v8).empty ;
-    assert.result 3  : $(v8).size ;
-    assert.result "" : $(v8).at 1 ;
-    assert.result "" : $(v8).at 2 ;
-    assert.result "" : $(v8).at 3 ;
-    assert.result    : $(v8).at 4 ;
-    $(v8).insert 2 : 222 ;
-    assert.result 4 : $(v8).size ;
-    assert.result "" 222 "" "" : $(v8).get ;
-    $(v8).insert 999 : "" ;
-    assert.result 5 : $(v8).size ;
-    assert.result "" 222 "" "" "" : $(v8).get ;
-    $(v8).insert 999 : xxx ;
-    assert.result 6 : $(v8).size ;
-    assert.result "" 222 "" "" "" xxx : $(v8).get ;
-
-    # Regression test for a bug causing vector.equal to compare only the first
-    # and the last element in the given vectors.
-    local v9 = [ new vector 111 xxx 222 ] ;
-    local v10 = [ new vector 111 yyy 222 ] ;
-    assert.false $(v9).equal $(v10) ;
-}
diff --git a/jam-files/boost-build/util/doc.jam b/jam-files/boost-build/util/doc.jam
deleted file mode 100644
index a7515588..00000000
--- a/jam-files/boost-build/util/doc.jam
+++ /dev/null
@@ -1,997 +0,0 @@
-# Copyright 2002, 2005 Dave Abrahams
-# Copyright 2002, 2003, 2006 Rene Rivera
-# Copyright 2003 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-# Documentation system, handles --help requests.
-# It defines rules that attach documentation to modules, rules, and variables.
-# Collects and generates documentation for the various parts of the build
-# system. The documentation is collected from comments integrated into the code.
-
-import modules ;
-import print ;
-import set ;
-import container ;
-import "class" ;
-import sequence ;
-import path ;
-
-
-# The type of output to generate.
-# "console" is formated text echoed to the console (the default);
-# "text" is formated text appended to the output file;
-# "html" is HTML output to the file.
-#
-help-output = console ;
-
-
-# The file to output documentation to when generating "text" or "html" help.
-# This is without extension as the extension is determined by the type of
-# output.
-#
-help-output-file = help ;
-
-# Whether to include local rules in help output.
-#
-.option.show-locals ?= ;
-
-# When showing documentation for a module, whether to also generate
-# automatically the detailed docs for each item in the module.
-#
-.option.detailed ?= ;
-
-# Generate debug output as the help is generated and modules are parsed.
-#
-.option.debug ?= ;
-
-# Enable or disable a documentation option.
-#
-local rule set-option (
-    option  # The option name.
-    : value ?  # Enabled (non-empty), or disabled (empty)
-)
-{
-    .option.$(option) = $(value) ;
-}
-
-
-# Set the type of output.
-#
-local rule set-output ( type )
-{
-    help-output = $(type) ;
-}
-
-
-# Set the output to a file.
-#
-local rule set-output-file ( file )
-{
-    help-output-file = $(file) ;
-}
-
-
-# Extracts the brief comment from a complete comment. The brief comment is the
-# first sentence.
-#
-local rule brief-comment (
-    docs *  # The comment documentation.
-)
-{
-    local d = $(docs:J=" ") ;
-    local p = [ MATCH ".*([.])$" : $(d) ] ;
-    if ! $(p) { d = $(d)"." ; }
-    d = $(d)" " ;
-    local m = [ MATCH "^([^.]+[.])(.*)" : $(d) ] ;
-    local brief = $(m[1]) ;
-    while $(m[2]) && [ MATCH "^([^ ])" : $(m[2]) ]
-    {
-        m = [ MATCH "^([^.]+[.])(.*)" : $(m[2]) ] ;
-        brief += $(m[1]) ;
-    }
-    return $(brief:J="") ;
-}
-
-
-# Specifies the documentation for the current module.
-#
-local rule set-module-doc (
-    module-name ?  # The name of the module to document.
-    : docs *  # The documentation for the module.
-)
-{
-    module-name ?= * ;
-
-    $(module-name).brief = [ brief-comment $(docs) ] ;
-    $(module-name).docs = $(docs) ;
-
-    if ! $(module-name) in $(documented-modules)
-    {
-        documented-modules += $(module-name) ;
-    }
-}
-
-
-# Specifies the documentation for the current module.
-#
-local rule set-module-copyright (
-    module-name ?  # The name of the module to document.
-    : copyright *  # The copyright for the module.
-)
-{
-    module-name ?= * ;
-
-    $(module-name).copy-brief = [ brief-comment $(copyright) ] ;
-    $(module-name).copy-docs = $(docs) ;
-
-    if ! $(module-name) in $(documented-modules)
-    {
-        documented-modules += $(module-name) ;
-    }
-}
-
-
-# Specifies the documentation for a rule in the current module. If called in the
-# global module, this documents a global rule.
-#
-local rule set-rule-doc (
-    name  # The name of the rule.
-    module-name ?  # The name of the module to document.
-    is-local ?  # Whether the rule is local to the module.
-    : docs *  # The documentation for the rule.
-)
-{
-    module-name ?= * ;
-
-    $(module-name).$(name).brief = [ brief-comment $(docs) ] ;
-    $(module-name).$(name).docs = $(docs) ;
-    $(module-name).$(name).is-local = $(is-local) ;
-
-    if ! $(name) in $($(module-name).rules)
-    {
-        $(module-name).rules += $(name) ;
-    }
-}
-
-
-# Specify a class, will turn a rule into a class.
-#
-local rule set-class-doc (
-    name  # The name of the class.
-    module-name ?  # The name of the module to document.
-    : super-name ?  # The super class name.
-)
-{
-    module-name ?= * ;
-
-    $(module-name).$(name).is-class = true ;
-    $(module-name).$(name).super-name = $(super-name) ;
-    $(module-name).$(name).class-rules =
-        [ MATCH "^($(name)[.].*)" : $($(module-name).rules) ] ;
-    $(module-name).$($(module-name).$(name).class-rules).is-class-rule = true ;
-
-    $(module-name).classes += $(name) ;
-    $(module-name).class-rules += $($(module-name).$(name).class-rules) ;
-    $(module-name).rules =
-        [ set.difference $($(module-name).rules) :
-            $(name) $($(module-name).$(name).class-rules) ] ;
-}
-
-
-# Set the argument call signature of a rule.
-#
-local rule set-rule-arguments-signature (
-    name  # The name of the rule.
-    module-name ?  # The name of the module to document.
-    : signature *  # The arguments signature.
-)
-{
-    module-name ?= * ;
-
-    $(module-name).$(name).signature = $(signature) ;
-}
-
-
-# Specifies the documentation for an argument of a rule.
-#
-local rule set-argument-doc (
-    name  # The name of the argument.
-    qualifier  # Argument syntax qualifier, "*", "+", etc.
-    rule-name  # The name of the rule.
-    module-name ?  # THe optional name of the module.
-    : docs *  # The documentation.
-)
-{
-    module-name ?= * ;
-
-    $(module-name).$(rule-name).args.$(name).qualifier = $(qualifier) ;
-    $(module-name).$(rule-name).args.$(name).docs = $(docs) ;
-
-    if ! $(name) in $($(module-name).$(rule-name).args)
-    {
-        $(module-name).$(rule-name).args += $(name) ;
-    }
-}
-
-
-# Specifies the documentation for a variable in the current module. If called in
-# the global module, the global variable is documented.
-#
-local rule set-variable-doc (
-    name  # The name of the variable.
-    default  # The default value.
-    initial  # The initial value.
-    module-name ?  # The name of the module to document.
-    : docs *  # The documentation for the variable.
-)
-{
-    module-name ?= * ;
-
-    $(module-name).$(name).brief = [ brief-comment $(docs) ] ;
-    $(module-name).$(name).default = $(default) ;
-    $(module-name).$(name).initial = $(initial) ;
-    $(module-name).$(name).docs = $(docs) ;
-
-    if ! $(name) in $($(module-name).variables)
-    {
-        $(module-name).variables += $(name) ;
-    }
-}
-
-
-# Generates a general description of the documentation and help system.
-#
-local rule print-help-top ( )
-{
-    print.section "General command line usage" ;
-
-    print.text "    bjam [options] [properties] [targets]
-
-  Options, properties and targets can be specified in any order.
-      " ;
-
-    print.section "Important Options" ;
-
-    print.list-start ;
-    print.list-item "--clean Remove targets instead of building" ;
-    print.list-item "-a Rebuild everything" ;
-    print.list-item "-n Don't execute the commands, only print them" ;
-    print.list-item "-d+2 Show commands as they are executed" ;
-    print.list-item "-d0 Supress all informational messages" ;
-    print.list-item "-q Stop at first error" ;
-    print.list-item "--debug-configuration Diagnose configuration" ;
-    print.list-item "--debug-building Report which targets are built with what properties" ;
-    print.list-item "--debug-generator Diagnose generator search/execution" ;
-    print.list-end ;
-
-    print.section "Further Help"
-        The following options can be used to obtain additional documentation.
-      ;
-
-    print.list-start ;
-    print.list-item "--help-options Print more obscure command line options." ;
-    print.list-item "--help-internal Boost.Build implementation details." ;
-    print.list-item "--help-doc-options Implementation details doc formatting." ;
-    print.list-end ;
-}
-
-
-# Generate Jam/Boost.Jam command usage information.
-#
-local rule print-help-usage ( )
-{
-    print.section "Boost.Jam Usage"
-        "bjam [ options... ] targets..."
-        ;
-    print.list-start ;
-    print.list-item -a;
-        Build all targets, even if they are current. ;
-    print.list-item -fx;
-        Read '"x"' as the Jamfile for building instead of searching for the
-        Boost.Build system. ;
-    print.list-item -jx;
-        Run up to '"x"' commands concurrently. ;
-    print.list-item -n;
-        Do not execute build commands. Instead print out the commands as they
-        would be executed if building. ;
-    print.list-item -ox;
-        Output the used build commands to file '"x"'. ;
-    print.list-item -q;
-        Quit as soon as a build failure is encountered. Without this option
-        Boost.Jam will continue building as many targets as it can.
-    print.list-item -sx=y;
-        Sets a Jam variable '"x"' to the value '"y"', overriding any value that
-        variable would have from the environment. ;
-    print.list-item -tx;
-        Rebuild the target '"x"', even if it is up-to-date. ;
-    print.list-item -v;
-        Display the version of bjam. ;
-    print.list-item --x;
-        Any option not explicitly handled by Boost.Jam remains available to
-        build scripts using the '"ARGV"' variable. ;
-    print.list-item -dn;
-        Enables output of diagnostic messages. The debug level '"n"' and all
-        below it are enabled by this option. ;
-    print.list-item -d+n;
-        Enables output of diagnostic messages. Only the output for debug level
-        '"n"' is enabled. ;
-    print.list-end ;
-    print.section "Debug Levels"
-        Each debug level shows a different set of information. Usually with
-        higher levels producing more verbose information. The following levels
-        are supported: ;
-    print.list-start ;
-    print.list-item 0;
-        Turn off all diagnostic output. Only errors are reported. ;
-    print.list-item 1;
-        Show the actions taken for building targets, as they are executed. ;
-    print.list-item 2;
-        Show "quiet" actions and display all action text, as they are executed. ;
-    print.list-item 3;
-        Show dependency analysis, and target/source timestamps/paths. ;
-    print.list-item 4;
-        Show arguments of shell invocations. ;
-    print.list-item 5;
-        Show rule invocations and variable expansions. ;
-    print.list-item 6;
-        Show directory/header file/archive scans, and attempts at binding to targets. ;
-    print.list-item 7;
-        Show variable settings. ;
-    print.list-item 8;
-        Show variable fetches, variable expansions, and evaluation of '"if"' expressions. ;
-    print.list-item 9;
-        Show variable manipulation, scanner tokens, and memory usage. ;
-    print.list-item 10;
-        Show execution times for rules. ;
-    print.list-item 11;
-        Show parsing progress of Jamfiles. ;
-    print.list-item 12;
-        Show graph for target dependencies. ;
-    print.list-item 13;
-        Show changes in target status (fate). ;
-    print.list-end ;
-}
-
-
-# Generates description of options controlling the help system. This
-# automatically reads the options as all variables in the doc module of the form
-# ".option.*".
-#
-local rule print-help-options (
-    module-name  # The doc module.
-)
-{
-    print.section "Help Options"
-        These are all the options available for enabling or disabling to control
-        the help system in various ways. Options can be enabled or disabled with
-        '"--help-enable-<option>"', and "'--help-disable-<option>'"
-        respectively.
-        ;
-    local options-to-list = [ MATCH ^[.]option[.](.*) : $($(module-name).variables) ] ;
-    if $(options-to-list)
-    {
-        print.list-start ;
-        for local option in [ sequence.insertion-sort $(options-to-list) ]
-        {
-            local def = disabled ;
-            if $($(module-name)..option.$(option).default) != "(empty)"
-            {
-                def = enabled ;
-            }
-            print.list-item $(option): $($(module-name)..option.$(option).docs)
-                Default is $(def). ;
-        }
-        print.list-end ;
-    }
-}
-
-
-# Generate brief documentation for all the known items in the section for a
-# module. Possible sections are: "rules", and "variables".
-#
-local rule print-help-module-section (
-    module  # The module name.
-    section  # rules or variables.
-    : section-head  # The title of the section.
-    section-description *  # The detailed description of the section.
-)
-{
-    if $($(module).$(section))
-    {
-        print.section $(section-head) $(section-description) ;
-        print.list-start ;
-        for local item in [ sequence.insertion-sort $($(module).$(section)) ]
-        {
-            local show = ;
-            if ! $($(module).$(item).is-local)
-            {
-                show = yes ;
-            }
-            if $(.option.show-locals)
-            {
-                show = yes ;
-            }
-            if $(show)
-            {
-                print.list-item $(item): $($(module).$(item).brief) ;
-            }
-        }
-        print.list-end ;
-    }
-}
-
-
-# Generate documentation for all possible modules. We attempt to list all known
-# modules together with a brief description of each.
-#
-local rule print-help-all (
-    ignored  # Usually the module name, but is ignored here.
-)
-{
-    print.section "Modules"
-        "These are all the known modules. Use --help <module> to get more"
-        "detailed information."
-        ;
-    if $(documented-modules)
-    {
-        print.list-start ;
-        for local module-name in [ sequence.insertion-sort $(documented-modules) ]
-        {
-            # The brief docs for each module.
-            print.list-item $(module-name): $($(module-name).brief) ;
-        }
-        print.list-end ;
-    }
-    # The documentation for each module when details are requested.
-    if $(documented-modules) && $(.option.detailed)
-    {
-        for local module-name in [ sequence.insertion-sort $(documented-modules) ]
-        {
-            # The brief docs for each module.
-            print-help-module $(module-name) ;
-        }
-    }
-}
-
-
-# Generate documentation for a module. Basic information about the module is
-# generated.
-#
-local rule print-help-module (
-    module-name  # The module to generate docs for.
-)
-{
-    # Print the docs.
-    print.section "Module '$(module-name)'" $($(module-name).docs) ;
-
-    # Print out the documented classes.
-    print-help-module-section $(module-name) classes : "Module '$(module-name)' classes"
-        Use --help $(module-name).<class-name> to get more information. ;
-
-    # Print out the documented rules.
-    print-help-module-section $(module-name) rules : "Module '$(module-name)' rules"
-        Use --help $(module-name).<rule-name> to get more information. ;
-
-    # Print out the documented variables.
-    print-help-module-section $(module-name) variables : "Module '$(module-name)' variables"
-        Use --help $(module-name).<variable-name> to get more information. ;
-
-    # Print out all the same information but indetailed form.
-    if $(.option.detailed)
-    {
-        print-help-classes $(module-name) ;
-        print-help-rules $(module-name) ;
-        print-help-variables $(module-name) ;
-    }
-}
-
-
-# Generate documentation for a set of rules in a module.
-#
-local rule print-help-rules (
-    module-name  # Module of the rules.
-    : name *  # Optional list of rules to describe.
-)
-{
-    name ?= $($(module-name).rules) ;
-    if [ set.intersection $(name) : $($(module-name).rules) $($(module-name).class-rules) ]
-    {
-        # Print out the given rules.
-        for local rule-name in [ sequence.insertion-sort $(name) ]
-        {
-            if $(.option.show-locals) || ! $($(module-name).$(rule-name).is-local)
-            {
-                local signature = $($(module-name).$(rule-name).signature:J=" ") ;
-                signature ?= "" ;
-                print.section "Rule '$(module-name).$(rule-name) ( $(signature) )'"
-                    $($(module-name).$(rule-name).docs) ;
-                if $($(module-name).$(rule-name).args)
-                {
-                    print.list-start ;
-                    for local arg-name in $($(module-name).$(rule-name).args)
-                    {
-                        print.list-item $(arg-name): $($(module-name).$(rule-name).args.$(arg-name).docs) ;
-                    }
-                    print.list-end ;
-                }
-            }
-        }
-    }
-}
-
-
-# Generate documentation for a set of classes in a module.
-#
-local rule print-help-classes (
-    module-name  # Module of the classes.
-    : name *  # Optional list of classes to describe.
-)
-{
-    name ?= $($(module-name).classes) ;
-    if [ set.intersection $(name) : $($(module-name).classes) ]
-    {
-        # Print out the given classes.
-        for local class-name in [ sequence.insertion-sort $(name) ]
-        {
-            if $(.option.show-locals) || ! $($(module-name).$(class-name).is-local)
-            {
-                local signature = $($(module-name).$(class-name).signature:J=" ") ;
-                signature ?= "" ;
-                print.section "Class '$(module-name).$(class-name) ( $(signature) )'"
-                    $($(module-name).$(class-name).docs)
-                   "Inherits from '"$($(module-name).$(class-name).super-name)"'." ;
-                if $($(module-name).$(class-name).args)
-                {
-                    print.list-start ;
-                    for local arg-name in $($(module-name).$(class-name).args)
-                    {
-                        print.list-item $(arg-name): $($(module-name).$(class-name).args.$(arg-name).docs) ;
-                    }
-                    print.list-end ;
-                }
-            }
-
-            # Print out the documented rules of the class.
-            print-help-module-section $(module-name) $(class-name).class-rules : "Class '$(module-name).$(class-name)' rules"
-                Use --help $(module-name).<rule-name> to get more information. ;
-
-            # Print out all the rules if details are requested.
-            if $(.option.detailed)
-            {
-                print-help-rules $(module-name) : $($(module-name).$(class-name).class-rules) ;
-            }
-        }
-    }
-}
-
-
-# Generate documentation for a set of variables in a module.
-#
-local rule print-help-variables (
-    module-name ?  # Module of the variables.
-    : name *  # Optional list of variables to describe.
-)
-{
-    name ?= $($(module-name).variables) ;
-    if [ set.intersection $(name) : $($(module-name).variables) ]
-    {
-        # Print out the given variables.
-        for local variable-name in [ sequence.insertion-sort $(name) ]
-        {
-            print.section "Variable '$(module-name).$(variable-name)'" $($(module-name).$(variable-name).docs) ;
-            if $($(module-name).$(variable-name).default) ||
-                $($(module-name).$(variable-name).initial)
-            {
-                print.list-start ;
-                if $($(module-name).$(variable-name).default)
-                {
-                    print.list-item "default value:" '$($(module-name).$(variable-name).default:J=" ")' ;
-                }
-                if $($(module-name).$(variable-name).initial)
-                {
-                    print.list-item "initial value:" '$($(module-name).$(variable-name).initial:J=" ")' ;
-                }
-                print.list-end ;
-            }
-        }
-    }
-}
-
-
-# Generate documentation for a project.
-#
-local rule print-help-project (
-    unused ?
-    : jamfile *  # The project Jamfile.
-)
-{
-    if $(jamfile<$(jamfile)>.docs)
-    {
-        # Print the docs.
-        print.section "Project-specific help"
-            Project has jamfile at $(jamfile) ;
-
-        print.lines $(jamfile<$(jamfile)>.docs) "" ;
-    }
-}
-
-
-# Generate documentation for a config file.
-#
-local rule print-help-config (
-    unused ?
-    : type  # The type of configuration file user or site.
-    config-file  # The configuration Jamfile.
-)
-{
-    if $(jamfile<$(config-file)>.docs)
-    {
-        # Print the docs.
-        print.section "Configuration help"
-            Configuration file at $(config-file) ;
-
-        print.lines $(jamfile<$(config-file)>.docs) "" ;
-    }
-}
-
-
-ws = "	 " ;
-
-# Extract the text from a block of comments.
-#
-local rule extract-comment (
-    var  # The name of the variable to extract from.
-)
-{
-    local comment = ;
-    local line = $($(var)[1]) ;
-    local l = [ MATCH "^[$(ws)]*(#)(.*)$" : $(line) ] ;
-    while $(l[1]) && $($(var))
-    {
-        if $(l[2]) { comment += [ MATCH "^[$(ws)]?(.*)$" : $(l[2]) ] ; }
-        else { comment += "" ; }
-        $(var) = $($(var)[2-]) ;
-        line = $($(var)[1]) ;
-        l = [ MATCH "^[$(ws)]*(#)(.*)$" : $(line) ] ;
-    }
-    return $(comment) ;
-}
-
-
-# Extract s single line of Jam syntax, ignoring any comments.
-#
-local rule extract-syntax (
-    var  # The name of the variable to extract from.
-)
-{
-    local syntax = ;
-    local line = $($(var)[1]) ;
-    while ! $(syntax) && ! [ MATCH "^[$(ws)]*(#)" : $(line) ] && $($(var))
-    {
-        local m = [ MATCH "^[$(ws)]*(.*)$" : $(line) ] ;
-        if $(m) && ! $(m) = ""
-        {
-            syntax = $(m) ;
-        }
-        $(var) = $($(var)[2-]) ;
-        line = $($(var)[1]) ;
-    }
-    return $(syntax) ;
-}
-
-
-# Extract the next token, this is either a single Jam construct or a comment as
-# a single token.
-#
-local rule extract-token (
-    var  # The name of the variable to extract from.
-)
-{
-    local parts = ;
-    while ! $(parts)
-    {
-        parts = [ MATCH "^[$(ws)]*([^$(ws)]+)[$(ws)]*(.*)" : $($(var)[1]) ] ;
-        if ! $(parts)
-        {
-            $(var) = $($(var)[2-]) ;
-        }
-    }
-    local token = ;
-    if [ MATCH "^(#)" : $(parts[1]) ]
-    {
-        token = $(parts:J=" ") ;
-        $(var) = $($(var)[2-]) ;
-    }
-    else
-    {
-        token = $(parts[1]) ;
-        $(var) = $(parts[2-]:J=" ") $($(var)[2-]) ;
-    }
-    return $(token) ;
-}
-
-
-# Scan for a rule declaration as the next item in the variable.
-#
-local rule scan-rule (
-    syntax ?  # The first part of the text which contains the rule declaration.
-    : var  # The name of the variable to extract from.
-)
-{
-    local rule-parts =
-        [ MATCH "^[$(ws)]*(rule|local[$(ws)]*rule)[$(ws)]+([^$(ws)]+)[$(ws)]*(.*)" : $(syntax:J=" ") ] ;
-    if $(rule-parts[1])
-    {
-        # Mark as doc for rule.
-        local rule-name = $(rule-parts[2]) ;
-        if $(scope-name)
-        {
-            rule-name = $(scope-name).$(rule-name) ;
-        }
-        local is-local = [ MATCH "^(local).*" : $(rule-parts[1]) ] ;
-        if $(comment-block)
-        {
-            set-rule-doc $(rule-name) $(module-name) $(is-local) : $(comment-block) ;
-        }
-        # Parse args of rule.
-        $(var) = $(rule-parts[3-]) $($(var)) ;
-        set-rule-arguments-signature $(rule-name) $(module-name) : [ scan-rule-arguments $(var) ] ;
-        # Scan within this rules scope.
-        local scope-level = [ extract-token $(var) ] ;
-        local scope-name = $(rule-name) ;
-        while $(scope-level)
-        {
-            local comment-block = [ extract-comment $(var) ] ;
-            local syntax-block = [ extract-syntax $(var) ] ;
-            if [ scan-rule $(syntax-block) : $(var) ]
-            {
-            }
-            else if [ MATCH "^(\\{)" : $(syntax-block) ]
-            {
-                scope-level += "{" ;
-            }
-            else if [ MATCH "^[^\\}]*([\\}])[$(ws)]*$"  : $(syntax-block) ]
-            {
-                scope-level = $(scope-level[2-]) ;
-            }
-        }
-
-        return true ;
-    }
-}
-
-
-# Scan the arguments of a rule.
-#
-local rule scan-rule-arguments (
-    var  # The name of the variable to extract from.
-)
-{
-    local arg-syntax = ;
-    local token = [ extract-token $(var) ] ;
-    while $(token) != "(" && $(token) != "{"
-    {
-        token = [ extract-token $(var) ] ;
-    }
-    if $(token) != "{"
-    {
-        token = [ extract-token $(var) ] ;
-    }
-    local arg-signature = ;
-    while $(token) != ")" && $(token) != "{"
-    {
-        local arg-name = ;
-        local arg-qualifier = " " ;
-        local arg-doc = ;
-        if $(token) = ":"
-        {
-            arg-signature += $(token) ;
-            token = [ extract-token $(var) ] ;
-        }
-        arg-name = $(token) ;
-        arg-signature += $(token) ;
-        token = [ extract-token $(var) ] ;
-        if [ MATCH "^([\\*\\+\\?])" : $(token) ]
-        {
-            arg-qualifier = $(token) ;
-            arg-signature += $(token) ;
-            token = [ extract-token $(var) ] ;
-        }
-        if $(token) = ":"
-        {
-            arg-signature += $(token) ;
-            token = [ extract-token $(var) ] ;
-        }
-        if [ MATCH "^(#)" : $(token) ]
-        {
-            $(var) = $(token) $($(var)) ;
-            arg-doc = [ extract-comment $(var) ] ;
-            token = [ extract-token $(var) ] ;
-        }
-        set-argument-doc $(arg-name) $(arg-qualifier) $(rule-name) $(module-name) : $(arg-doc) ;
-    }
-    while $(token) != "{"
-    {
-        token = [ extract-token $(var) ] ;
-    }
-    $(var) = "{" $($(var)) ;
-    arg-signature ?= "" ;
-    return $(arg-signature) ;
-}
-
-
-# Scan for a variable declaration.
-#
-local rule scan-variable (
-    syntax ?  # The first part of the text which contains the variable declaration.
-    : var  # The name of the variable to extract from.
-)
-{
-    # [1] = name, [2] = value(s)
-    local var-parts =
-        [ MATCH "^[$(ws)]*([^$(ws)]+)[$(ws)]+([\\?\\=]*)[$(ws)]+([^\\;]*)\\;" : $(syntax) ] ;
-    if $(var-parts)
-    {
-        local value = [ MATCH "^(.*)[ ]$" : $(var-parts[3-]:J=" ") ] ;
-        local default-value = "" ;
-        local initial-valie = "" ;
-        if $(var-parts[2]) = "?="
-        {
-            default-value = $(value) ;
-            default-value ?= "(empty)" ;
-        }
-        else
-        {
-            initial-value = $(value) ;
-            initial-value ?= "(empty)" ;
-        }
-        if $(comment-block)
-        {
-            set-variable-doc $(var-parts[1]) $(default-value) $(initial-value) $(module-name) : $(comment-block) ;
-        }
-        return true ;
-    }
-}
-
-
-# Scan a class declaration.
-#
-local rule scan-class (
-    syntax ?  # The syntax text for the class declaration.
-)
-{
-    # [1] = class?, [2] = name, [3] = superclass
-    local class-parts =
-        [ MATCH "^[$(ws)]*([^$(ws)]+)[$(ws)]+([^$(ws)]+)[$(ws)]+:*[$(ws)]*([^$(ws);]*)" : $(syntax) ] ;
-    if $(class-parts[1]) = "class" || $(class-parts[1]) = "class.class"
-    {
-        set-class-doc $(class-parts[2]) $(module-name) : $(class-parts[3]) ;
-    }
-}
-
-
-# Scan a module file for documentation comments. This also invokes any actions
-# assigned to the module. The actions are the rules that do the actual output of
-# the documentation. This rule is invoked as the header scan rule for the module
-# file.
-#
-rule scan-module (
-    target  # The module file.
-    : text *  # The text in the file, one item per line.
-    : action *  # Rule to call to output docs for the module.
-)
-{
-    if $(.option.debug) { ECHO "HELP:" scanning module target '$(target)' ; }
-    local module-name = $(target:B) ;
-    local module-documented = ;
-    local comment-block = ;
-    local syntax-block = ;
-    # This is a hack because we can not get the line of a file if it happens to
-    # not have a new-line termination.
-    text += "}" ;
-    while $(text)
-    {
-        comment-block = [ extract-comment text ] ;
-        syntax-block = [ extract-syntax text ] ;
-        if $(.option.debug)
-        {
-            ECHO "HELP:" comment block; '$(comment-block)' ;
-            ECHO "HELP:" syntax block; '$(syntax-block)' ;
-        }
-        if [ scan-rule $(syntax-block) : text ] { }
-        else if [ scan-variable $(syntax-block) : text ] { }
-        else if [ scan-class $(syntax-block) ] { }
-        else if [ MATCH .*([cC]opyright).* : $(comment-block:J=" ") ]
-        {
-            # mark as the copy for the module.
-            set-module-copyright $(module-name) : $(comment-block) ;
-        }
-        else if $(action[1]) in "print-help-project" "print-help-config"
-            && ! $(jamfile<$(target)>.docs)
-        {
-            # special module docs for the project jamfile.
-            jamfile<$(target)>.docs = $(comment-block) ;
-        }
-        else if ! $(module-documented)
-        {
-            # document the module.
-            set-module-doc $(module-name) : $(comment-block) ;
-            module-documented = true ;
-        }
-    }
-    if $(action)
-    {
-        $(action[1]) $(module-name) : $(action[2-]) ;
-    }
-}
-
-
-# Import scan-module to global scope, so that it is available during header
-# scanning phase.
-#
-IMPORT $(__name__) : scan-module : : doc.scan-module ;
-
-
-# Read in a file using the SHELL builtin and return the individual lines as
-# would be done for header scanning.
-#
-local rule read-file (
-    file  # The file to read in.
-)
-{
-    file = [ path.native [ path.root [ path.make $(file) ] [ path.pwd ] ] ] ;
-    if ! $(.file<$(file)>.lines)
-    {
-        local content ;
-        switch [ modules.peek : OS ]
-        {
-            case NT :
-            content = [ SHELL "TYPE \"$(file)\"" ] ;
-
-            case * :
-            content = [ SHELL "cat \"$(file)\"" ] ;
-        }
-        local lines ;
-        local nl = "
-" ;
-        local << = "([^$(nl)]*)[$(nl)](.*)" ;
-        local line+ = [ MATCH "$(<<)" : "$(content)" ] ;
-        while $(line+)
-        {
-            lines += $(line+[1]) ;
-            line+ = [ MATCH "$(<<)" : "$(line+[2])" ] ;
-        }
-        .file<$(file)>.lines = $(lines) ;
-    }
-    return $(.file<$(file)>.lines) ;
-}
-
-
-# Add a scan action to perform to generate the help documentation. The action
-# rule is passed the name of the module as the first argument. The second
-# argument(s) are optional and passed directly as specified here.
-#
-local rule do-scan (
-    modules +  # The modules to scan and perform the action on.
-    : action *  # The action rule, plus the secondary arguments to pass to the action rule.
-)
-{
-    if $(help-output) = text
-    {
-        print.output $(help-output-file).txt plain ;
-        ALWAYS $(help-output-file).txt ;
-        DEPENDS all : $(help-output-file).txt ;
-    }
-    if $(help-output) = html
-    {
-        print.output $(help-output-file).html html ;
-        ALWAYS $(help-output-file).html ;
-        DEPENDS all : $(help-output-file).html ;
-    }
-    for local module-file in $(modules[1--2])
-    {
-        scan-module $(module-file) : [ read-file $(module-file) ] ;
-    }
-    scan-module $(modules[-1]) : [ read-file $(modules[-1]) ] : $(action) ;
-}
diff --git a/jam-files/boost-build/util/indirect.jam b/jam-files/boost-build/util/indirect.jam
deleted file mode 100644
index ec63f192..00000000
--- a/jam-files/boost-build/util/indirect.jam
+++ /dev/null
@@ -1,115 +0,0 @@
-# Copyright 2003 Dave Abrahams
-# Copyright 2003 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-import modules ;
-import numbers ;
-
-
-# The pattern that indirect rules must match: module%rule
-.pattern = ^([^%]*)%([^%]+)$ ;
-
-
-#
-# Type checking rules.
-#
-local rule indirect-rule ( x )
-{
-    if ! [ MATCH $(.pattern) : $(x) ]
-    {
-        return "expected a string of the form module%rule, but got \""$(x)"\" for argument" ;
-    }
-}
-
-
-# Make an indirect rule which calls the given rule. If context is supplied it is
-# expected to be the module in which to invoke the rule by the 'call' rule
-# below. Otherwise, the rule will be invoked in the module of this rule's
-# caller.
-#
-rule make ( rulename bound-args * : context ? )
-{
-    context ?= [ CALLER_MODULE ] ;
-    context ?= "" ;
-    return $(context)%$(rulename) $(bound-args) ;
-}
-
-
-# Make an indirect rule which calls the given rule. 'rulename' may be a
-# qualified rule; if so it is returned unchanged. Otherwise, if frames is not
-# supplied, the result will be invoked (by 'call', below) in the module of the
-# caller. Otherwise, frames > 1 specifies additional call frames to back up in
-# order to find the module context.
-#
-rule make-qualified ( rulename bound-args * : frames ? )
-{
-    if [ MATCH $(.pattern) : $(rulename) ]
-    {
-        return $(rulename) $(bound-args) ;
-    }
-    else
-    {
-        frames ?= 1 ;
-        # If the rule name includes a Jamfile module, grab it.
-        local module-context = [ MATCH ^(Jamfile<[^>]*>)\\..* : $(rulename) ] ;
-        
-        if ! $(module-context)
-        {                    
-            # Take the first dot-separated element as module name. This disallows
-            # module names with dots, but allows rule names with dots.
-            module-context = [ MATCH ^([^.]*)\\..* : $(rulename) ] ;
-        }        
-        module-context ?= [ CALLER_MODULE $(frames) ] ;
-        return [ make $(rulename) $(bound-args) : $(module-context) ] ;
-    }
-}
-
-
-# Returns the module name in which the given indirect rule will be invoked.
-#
-rule get-module ( [indirect-rule] x )
-{
-    local m = [ MATCH $(.pattern) : $(x) ] ;
-    if ! $(m[1])
-    {
-        m = ;
-    }
-    return $(m[1]) ;
-}
-
-
-# Returns the rulename that will be called when x is invoked.
-#
-rule get-rule ( [indirect-rule] x )
-{
-    local m = [ MATCH $(.pattern) : $(x) ] ;
-    return $(m[2]) ;
-}
-
-
-# Invoke the given indirect-rule.
-#
-rule call ( [indirect-rule] r args * : * )
-{
-    return [ modules.call-in [ get-module $(r) ] : [ get-rule $(r) ] $(args)
-        : $(2) : $(3) : $(4) : $(5) : $(6) : $(7) : $(8) : $(9) ] ;
-}
-
-
-rule __test__
-{
-    import assert ;
-
-    rule foo-barr! ( x )
-    {
-        assert.equal $(x) : x ;
-    }
-
-    assert.equal [ get-rule [ make foo-barr! ] ] : foo-barr! ;
-    assert.equal [ get-module [ make foo-barr! ] ] : [ CALLER_MODULE ] ;
-
-    call [ make foo-barr! ] x ;
-    call [ make foo-barr! x ] ;
-    call [ make foo-barr! : [ CALLER_MODULE ] ] x ;
-}
diff --git a/jam-files/boost-build/util/indirect.py b/jam-files/boost-build/util/indirect.py
deleted file mode 100644
index 78fa8994..00000000
--- a/jam-files/boost-build/util/indirect.py
+++ /dev/null
@@ -1,15 +0,0 @@
-# Status: minimally ported. This module is not supposed to be used much
-# with Boost.Build/Python.
-# 
-# Copyright 2003 Dave Abrahams
-# Copyright 2003 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-from b2.util import call_jam_function, bjam_signature
-
-def call(*args):
-    a1 = args[0]
-    name = a1[0]
-    a1tail = a1[1:]
-    call_jam_function(name, *((a1tail,) + args[1:]))
diff --git a/jam-files/boost-build/util/logger.py b/jam-files/boost-build/util/logger.py
deleted file mode 100644
index de652129..00000000
--- a/jam-files/boost-build/util/logger.py
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright Pedro Ferreira 2005. Distributed under the Boost
-# Software License, Version 1.0. (See accompanying
-# file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
-
-import sys
-
-class NullLogger:
-    def __init__ (self):
-        self.indent_ = ''
-    
-    def log (self, source_name, *args):
-        if self.on () and self.interesting (source_name):
-            self.do_log (self.indent_)
-            for i in args:
-                self.do_log (i)
-            self.do_log ('\n')
-    
-    def increase_indent (self):
-        if self.on ():
-            self.indent_ += '    '
-        
-    def decrease_indent (self):
-        if self.on () and len (self.indent_) > 4:
-            self.indent_ = self.indent_ [-4:]
-
-    def do_log (self, *args):
-        pass
-    
-    def interesting (self, source_name):
-        return False
-
-    def on (self):
-        return True
-
-class TextLogger (NullLogger):
-    def __init__ (self):
-        NullLogger.__init__ (self)
-    
-    def do_log (self, arg):
-            sys.stdout.write (str (arg))
-    
-    def interesting (self, source_name):
-        return True
-
-    def on (self):
-        return True
diff --git a/jam-files/boost-build/util/numbers.jam b/jam-files/boost-build/util/numbers.jam
deleted file mode 100644
index 665347d3..00000000
--- a/jam-files/boost-build/util/numbers.jam
+++ /dev/null
@@ -1,218 +0,0 @@
-# Copyright 2001, 2002 Dave Abrahams
-# Copyright 2002, 2003 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-import errors ;
-
-
-rule trim-leading-zeroes ( value )
-{
-    return [ CALC $(value) + 0 ] ;
-}
-
-
-rule check ( numbers * )
-{
-    for local n in $(numbers)
-    {
-        switch $(n)
-        {
-            case *[^0-9]* :
-                errors.error $(n) "in" $(numbers) : is not a number ;
-        }
-    }
-}
-
-
-rule increment ( number )
-{
-    return [ CALC $(number) + 1 ] ;
-}
-
-
-rule decrement ( number )
-{
-    return [ CALC $(number) - 1 ] ;
-}
-
-
-rule range ( start finish ? : step ? )
-{
-    if ! $(finish)
-    {
-        finish = $(start) ;
-        start = 1 ;
-    }
-    step ?= 1 ;
-
-    check $(start) $(finish) $(step) ;
-
-    if $(finish) != 0
-    {
-        local result ;
-        while [ less $(start) $(finish) ] || $(start) = $(finish)
-        {
-            result += $(start) ;
-            start = [ CALC $(start) + $(step) ] ;
-        }
-        return $(result) ;
-    }
-}
-
-
-rule less ( n1 n2 )
-{
-    switch [ CALC $(n2) - $(n1) ]
-    {
-        case [1-9]* : return true ;
-    }
-}
-
-
-rule log10 ( number )
-{
-    switch $(number)
-    {
-        case *[^0-9]* : errors.error $(number) is not a number ;
-        case 0 : errors.error can't take log of zero ;
-        case [1-9] : return 0 ;
-        case [1-9]? : return 1 ;
-        case [1-9]?? : return 2 ;
-        case [1-9]??? : return 3 ;
-        case [1-9]???? : return 4 ;
-        case [1-9]????? : return 5 ;
-        case [1-9]?????? : return 6 ;
-        case [1-9]??????? : return 7 ;
-        case [1-9]???????? : return 8 ;
-        case [1-9]????????? : return 9 ;
-        case * :
-        {
-            import sequence ;
-            import string ;
-            local chars = [ string.chars $(number) ] ;
-            while $(chars[1]) = 0
-            {
-                chars = $(chars[2-]) ;
-            }
-            if ! $(chars)
-            {
-                errors.error can't take log of zero ;
-            }
-            else
-            {
-                return [ decrement [ sequence.length $(chars) ] ] ;
-            }
-        }
-    }
-}
-
-
-rule __test__ ( )
-{
-    import assert ;
-
-    assert.result 1 : increment 0 ;
-    assert.result 2 : increment 1 ;
-    assert.result 1 : decrement 2 ;
-    assert.result 0 : decrement 1 ;
-    assert.result 50 : increment 49 ;
-    assert.result 49 : decrement 50 ;
-    assert.result 99 : increment 98 ;
-    assert.result 99 : decrement 100 ;
-    assert.result 100 : increment 99 ;
-    assert.result 999 : decrement 1000 ;
-    assert.result 1000 : increment 999 ;
-
-    assert.result 1 2 3 : range 3 ;
-    assert.result 1 2 3 4 5 6 7 8 9 10 11 12 : range 12 ;
-    assert.result 3 4 5 6 7 8 9 10 11 : range 3 11 ;
-    assert.result : range 0 ;
-    assert.result 1 4 7 10 : range 10 : 3 ;
-    assert.result 2 4 6 8 10 : range 2 10 : 2 ;
-    assert.result 25 50 75 100 : range 25 100 : 25 ;
-
-    assert.result 0           : trim-leading-zeroes 0           ;
-    assert.result 1234        : trim-leading-zeroes 1234        ;
-    assert.result 123456      : trim-leading-zeroes 0000123456  ;
-    assert.result 1000123456  : trim-leading-zeroes 1000123456  ;
-    assert.result 10000       : trim-leading-zeroes 10000       ;
-    assert.result 10000       : trim-leading-zeroes 00010000    ;
-
-    assert.true  less 1 2 ;
-    assert.true  less 1 12 ;
-    assert.true  less 1 21 ;
-    assert.true  less 005 217 ;
-    assert.false less 0 0 ;
-    assert.false less 03 3 ;
-    assert.false less 3 03 ;
-    assert.true  less 005 217 ;
-    assert.true  less 0005 217 ;
-    assert.true  less 5 00217 ;
-
-    # TEMPORARY disabled, because nested "try"/"catch" do not work and I do no
-    # have the time to fix that right now.
-    if $(0)
-    {
-    try ;
-    {
-        decrement 0 ;
-    }
-    catch can't decrement zero! ;
-
-    try ;
-    {
-        check foo ;
-    }
-    catch : not a number ;
-
-    try ;
-    {
-        increment foo ;
-    }
-    catch : not a number ;
-
-    try ;
-    {
-        log10 0 ;
-    }
-    catch can't take log of zero ;
-
-    try ;
-    {
-        log10 000 ;
-    }
-    catch can't take log of zero ;
-
-    }
-
-    assert.result 0 : log10 1 ;
-    assert.result 0 : log10 9 ;
-    assert.result 1 : log10 10 ;
-    assert.result 1 : log10 99 ;
-    assert.result 2 : log10 100 ;
-    assert.result 2 : log10 101 ;
-    assert.result 2 : log10 125 ;
-    assert.result 2 : log10 999 ;
-    assert.result 3 : log10 1000 ;
-    assert.result 10 : log10 12345678901 ;
-
-    for local x in [ range 75 110 : 5 ]
-    {
-        for local y in [ range $(x) 111 : 3 ]
-        {
-            if $(x) != $(y)
-            {
-                assert.true less $(x) $(y) ;
-            }
-        }
-    }
-
-    for local x in [ range 90 110 : 2 ]
-    {
-        for local y in [ range 80 $(x) : 4 ]
-        {
-            assert.false less $(x) $(y) ;
-        }
-    }
-}
diff --git a/jam-files/boost-build/util/option.jam b/jam-files/boost-build/util/option.jam
deleted file mode 100644
index f6dc3752..00000000
--- a/jam-files/boost-build/util/option.jam
+++ /dev/null
@@ -1,109 +0,0 @@
-#  Copyright (c) 2005 Vladimir Prus.
-#
-#  Use, modification and distribution is subject to the Boost Software
-#  License Version 1.0. (See accompanying file LICENSE_1_0.txt or
-#  http://www.boost.org/LICENSE_1_0.txt)
-
-import modules ;
-
-# Set a value for a named option, to be used when not overridden on the command
-# line.
-rule set ( name : value ? )
-{
-    .option.$(name) = $(value) ;
-}
-
-rule get ( name : default-value ? : implied-value ? )
-{
-    local m = [ MATCH --$(name)=(.*) : [ modules.peek : ARGV ] ] ;
-    if $(m)
-    {
-        return $(m[1]) ;
-    }
-    else  
-    {        
-        m = [ MATCH (--$(name)) : [ modules.peek : ARGV ] ] ;
-        if $(m) && $(implied-value)
-        {
-            return $(implied-value) ;
-        }
-        else if $(.option.$(name))
-        {
-            return $(.option.$(name)) ;
-        }    
-        else
-        {
-            return $(default-value) ;
-        }    
-    }              
-}
-
-
-# Check command-line args as soon as possible. For each option try to load
-# module named after option. Is that succeeds, invoke 'process' rule in the
-# module. The rule may return "true" to indicate that the regular build process
-# should not be attempted.
-#
-# Options take the general form of: --<name>[=<value>] [<value>]
-#
-rule process ( )
-{
-    local ARGV = [ modules.peek : ARGV ] ;
-    local BOOST_BUILD_PATH = [ modules.peek : BOOST_BUILD_PATH ] ;
-
-    local dont-build ;
-    local args = $(ARGV) ;
-    while $(args)
-    {
-        local arg = [ MATCH ^--(.*) : $(args[1]) ] ;
-        while $(args[2-]) && ! $(arg)
-        {
-            args = $(args[2-]) ;
-            arg = [ MATCH ^--(.*) : $(args[1]) ] ;
-        }
-        args = $(args[2-]) ;
-
-        if $(arg)
-        {
-            local split = [ MATCH ^(([^-=]+)[^=]*)(=?)(.*)$ : $(arg) ] ;
-            local full-name = $(split[1]) ;
-            local prefix = $(split[2]) ;
-            local values ;
-
-            if $(split[3])
-            {
-                values = $(split[4]) ;
-            }
-            if $(args) && ! [ MATCH ^(--).* : $(args[1]) ]
-            {
-                values += $(args[1]) ;
-                args = $(args[2-]) ;
-            }
-
-            # Jook in options subdirectories of BOOST_BUILD_PATH for modules
-            # matching the full option name and then its prefix.
-            local plugin-dir = options ;
-            local option-files = [ GLOB $(plugin-dir:D=$(BOOST_BUILD_PATH)) :
-                $(full-name).jam $(prefix).jam ] ;
-
-            if $(option-files)
-            {
-                # Load the file into a module named for the option.
-                local f = $(option-files[1]) ;
-                local module-name = --$(f:D=:S=) ;
-                modules.load $(module-name) : $(f:D=) : $(f:D) ;
-
-                # If there is a process rule, call it with the full option name
-                # and its value (if any). If there was no "=" in the option, the
-                # value will be empty.
-                if process in [ RULENAMES $(module-name) ]
-                {
-                    dont-build += [ modules.call-in $(module-name) : process
-                        --$(full-name) : $(values) ] ;
-                }
-            }
-        }
-    }
-
-    return $(dont-build) ;
-}
diff --git a/jam-files/boost-build/util/option.py b/jam-files/boost-build/util/option.py
deleted file mode 100644
index 47d6abdf..00000000
--- a/jam-files/boost-build/util/option.py
+++ /dev/null
@@ -1,35 +0,0 @@
-#  Copyright (c) 2005-2010 Vladimir Prus.
-#
-#  Use, modification and distribution is subject to the Boost Software
-#  License Version 1.0. (See accompanying file LICENSE_1_0.txt or
-#  http://www.boost.org/LICENSE_1_0.txt)
-
-import sys
-import re
-import b2.util.regex
-
-options = {}
-
-# Set a value for a named option, to be used when not overridden on the command
-# line.
-def set(name, value=None):
-    
-    global options
-    
-    options[name] = value
-
-def get(name, default_value=None, implied_value=None):
-
-    global options
-
-    matches = b2.util.regex.transform(sys.argv, "--" + re.escape(name) + "=(.*)")
-    if matches:
-        return matches[-1]
-    else:
-        m = b2.util.regex.transform(sys.argv, "--(" + re.escape(name) + ")")
-        if m and implied_value:
-            return implied_value
-        elif options.has_key(name) and options[name] != None:
-            return options[name]
-        else:
-            return default_value
diff --git a/jam-files/boost-build/util/order.jam b/jam-files/boost-build/util/order.jam
deleted file mode 100644
index a74fc8c8..00000000
--- a/jam-files/boost-build/util/order.jam
+++ /dev/null
@@ -1,169 +0,0 @@
-#  Copyright (C) 2003 Vladimir Prus
-#  Use, modification, and distribution is subject to the Boost Software
-#  License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy
-#  at http://www.boost.org/LICENSE_1_0.txt)
-
-#  This module defines a class which allows to order arbitrary object with
-# regard to arbitrary binary relation.
-#
-#  The primary use case is the gcc toolset, which is sensitive to library order:
-#  if library 'a' uses symbols from library 'b', then 'a' must be present before
-#  'b' on the linker's command line.
-#
-#  This requirement can be lifted for gcc with GNU ld, but for gcc with Solaris
-#  LD (and for Solaris toolset as well), the order always matters.
-#
-#  So, we need to store order requirements and then order libraries according to
-#  them. It is not possible to use the dependency graph as order requirements.
-#  What we need is a "use symbols" relationship while dependency graph provides
-#  the "needs to be updated" relationship.
-#
-#  For example::
-#    lib a : a.cpp b;
-#    lib b ;
-#
-#  For static linking, library 'a' need not depend on 'b'. However, it should
-#  still come before 'b' on the command line.
-
-class order
-{
-    rule __init__ ( )
-    {
-    }
-
-    # Adds the constraint that 'first' should preceede 'second'.
-    rule add-pair ( first second )
-    {
-        .constraits += $(first)--$(second) ;
-    }
-    NATIVE_RULE class@order : add-pair ;
-
-    # Given a list of objects, reorder them so that the constraints specified by
-    # 'add-pair' are satisfied.
-    #
-    # The algorithm was adopted from an awk script by Nikita Youshchenko
-    # (yoush at cs dot msu dot su)
-    rule order ( objects * )
-    {
-        # The algorithm used is the same is standard transitive closure, except
-        # that we're not keeping in-degree for all vertices, but rather removing
-        # edges.
-        local result ;
-        if $(objects)
-        {
-            local constraints = [ eliminate-unused-constraits $(objects) ] ;
-
-            # Find some library that nobody depends upon and add it to the
-            # 'result' array.
-            local obj ;
-            while $(objects)
-            {
-                local new_objects ;
-                while $(objects)
-                {
-                    obj = $(objects[1]) ;
-                    if [ has-no-dependents $(obj) : $(constraints) ]
-                    {
-                        # Emulate break ;
-                        new_objects += $(objects[2-]) ;
-                        objects = ;
-                    }
-                    else
-                    {
-                        new_objects += $(obj) ;
-                        obj = ;
-                        objects = $(objects[2-]) ;
-                    }
-                }
-
-                if ! $(obj)
-                {
-                    errors.error "Circular order dependencies" ;
-                }
-                # No problem with placing first.
-                result += $(obj) ;
-                # Remove all contraints where 'obj' comes first, since they are
-                # already satisfied.
-                constraints = [ remove-satisfied $(constraints) : $(obj) ] ;
-
-                # Add the remaining objects for further processing on the next
-                # iteration
-                objects = $(new_objects) ;
-            }
-
-        }
-        return $(result) ;
-    }
-    NATIVE_RULE class@order : order ;
-
-    # Eliminate constraints which mention objects not in 'objects'. In
-    # graph-theory terms, this is finding a subgraph induced by ordered
-    # vertices.
-    rule eliminate-unused-constraits ( objects * )
-    {
-        local result ;
-        for local c in $(.constraints)
-        {
-            local m = [ MATCH (.*)--(.*) : $(c) ] ;
-            if $(m[1]) in $(objects) && $(m[2]) in $(objects)
-            {
-                result += $(c) ;
-            }
-        }
-        return $(result) ;
-    }
-
-    # Returns true if there's no constraint in 'constaraints' where 'obj' comes
-    # second.
-    rule has-no-dependents ( obj : constraints * )
-    {
-        local failed ;
-        while $(constraints) && ! $(failed)
-        {
-            local c = $(constraints[1]) ;
-            local m = [ MATCH (.*)--(.*) : $(c) ] ;
-            if $(m[2]) = $(obj)
-            {
-                failed = true ;
-            }
-            constraints = $(constraints[2-]) ;
-        }
-        if ! $(failed)
-        {
-            return true ;
-        }
-    }
-
-    rule remove-satisfied ( constraints * : obj )
-    {
-        local result ;
-        for local c in $(constraints)
-        {
-            local m = [ MATCH (.*)--(.*) : $(c) ] ;
-            if $(m[1]) != $(obj)
-            {
-                result += $(c) ;
-            }
-        }
-        return $(result) ;
-    }
-}
-
-
-rule __test__ ( )
-{
-    import "class" : new ;
-    import assert ;
-
-    c1 = [ new order ] ;
-    $(c1).add-pair l1 l2 ;
-
-    assert.result l1 l2 : $(c1).order l1 l2 ;
-    assert.result l1 l2 : $(c1).order l2 l1 ;
-
-    $(c1).add-pair l2 l3 ;
-    assert.result l1 l2 : $(c1).order l2 l1 ;
-    $(c1).add-pair x l2 ;
-    assert.result l1 l2 : $(c1).order l2 l1 ;
-    assert.result l1 l2 l3 : $(c1).order l2 l3 l1 ;
-}
diff --git a/jam-files/boost-build/util/order.py b/jam-files/boost-build/util/order.py
deleted file mode 100644
index 4e67b3f1..00000000
--- a/jam-files/boost-build/util/order.py
+++ /dev/null
@@ -1,121 +0,0 @@
-#  Copyright (C) 2003 Vladimir Prus
-#  Use, modification, and distribution is subject to the Boost Software
-#  License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy
-#  at http://www.boost.org/LICENSE_1_0.txt)
-
-class Order:
-    """Allows ordering arbitrary objects with regard to arbitrary binary relation.
-
-        The primary use case is the gcc toolset, which is sensitive to
-        library order: if library 'a' uses symbols from library 'b',
-        then 'a' must be present before 'b' on the linker's command line.
-        
-        This requirement can be lifted for gcc with GNU ld, but for gcc with
-        Solaris LD (and for Solaris toolset as well), the order always matters.
-        
-        So, we need to store order requirements and then order libraries
-        according to them. It it not possible to use dependency graph as
-        order requirements. What we need is "use symbols" relationship
-        while dependency graph provides "needs to be updated" relationship.
-        
-        For example::
-          lib a : a.cpp b;
-          lib b ;
-        
-        For static linking, the 'a' library need not depend on 'b'. However, it
-        still should come before 'b' on the command line.
-    """
-
-    def __init__ (self):
-        self.constraints_ = []
-        
-    def add_pair (self, first, second):
-        """ Adds the constraint that 'first' should precede 'second'.
-        """
-        self.constraints_.append ((first, second))
-
-    def order (self, objects):
-        """ Given a list of objects, reorder them so that the constains specified
-            by 'add_pair' are satisfied.
-            
-            The algorithm was adopted from an awk script by Nikita Youshchenko
-            (yoush at cs dot msu dot su)
-        """
-        # The algorithm used is the same is standard transitive closure,
-        # except that we're not keeping in-degree for all vertices, but
-        # rather removing edges.
-        result = []
-
-        if not objects: 
-            return result
-
-        constraints = self.__eliminate_unused_constraits (objects)
-        
-        # Find some library that nobody depends upon and add it to
-        # the 'result' array.
-        obj = None
-        while objects:
-            new_objects = []
-            while objects:
-                obj = objects [0]
-
-                if self.__has_no_dependents (obj, constraints):
-                    # Emulate break ;
-                    new_objects.extend (objects [1:])
-                    objects = []
-
-                else:
-                    new_objects.append (obj)
-                    obj = None
-                    objects = objects [1:]
-            
-            if not obj:
-                raise BaseException ("Circular order dependencies")
-
-            # No problem with placing first.
-            result.append (obj)
-
-            # Remove all containts where 'obj' comes first,
-            # since they are already satisfied.
-            constraints = self.__remove_satisfied (constraints, obj)
-
-            # Add the remaining objects for further processing
-            # on the next iteration
-            objects = new_objects
-            
-        return result
-
-    def __eliminate_unused_constraits (self, objects):
-        """ Eliminate constraints which mention objects not in 'objects'.
-            In graph-theory terms, this is finding subgraph induced by
-            ordered vertices.
-        """
-        result = []
-        for c in self.constraints_:
-            if c [0] in objects and c [1] in objects:
-                result.append (c)
-
-        return result
-    
-    def __has_no_dependents (self, obj, constraints):
-        """ Returns true if there's no constraint in 'constraints' where 
-            'obj' comes second.
-        """
-        failed = False
-        while constraints and not failed:
-            c = constraints [0]
-
-            if c [1] == obj:
-                failed = True
-
-            constraints = constraints [1:]
-
-        return not failed
-    
-    def __remove_satisfied (self, constraints, obj):
-        result = []
-        for c in constraints:
-            if c [0] != obj:
-                result.append (c)
-
-        return result
diff --git a/jam-files/boost-build/util/os.jam b/jam-files/boost-build/util/os.jam
deleted file mode 100644
index daef27f7..00000000
--- a/jam-files/boost-build/util/os.jam
+++ /dev/null
@@ -1,171 +0,0 @@
-# Copyright 2001, 2002, 2003, 2005 Dave Abrahams
-# Copyright 2006 Rene Rivera
-# Copyright 2003, 2005 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-import modules ;
-import string ;
-
-
-# Return the value(s) of the given environment variable(s) at the time bjam was
-# invoked.
-rule environ ( variable-names + )
-{
-    return [ modules.peek .ENVIRON : $(variable-names) ] ;
-}
-
-.name = [ modules.peek : OS ] ;
-.platform = [ modules.peek : OSPLAT ] ;
-.version = [ modules.peek : OSVER ] ;
-
-
-local rule constant ( c : os ? )
-{
-    os ?= $(.name) ;
-    # First look for a platform-specific name, then the general value.
-    local variables = .$(c)-$(os) .$(c) ;
-    local result = $($(variables)) ;
-    return $(result[1]) ;
-}
-
-rule get-constant ( os ? )
-{
-    # Find the name of the constant being accessed, which is equal to the name
-    # used to invoke us.
-    local bt = [ BACKTRACE 1 ] ;
-    local rulename = [ MATCH ([^.]*)$ : $(bt[4]) ] ;
-    return [ constant $(rulename) : $(os) ] ;
-}
-
-
-# export all the common constants
-.constants = name platform version shared-library-path-variable path-separator executable-path-variable executable-suffix ;
-for local constant in $(.constants)
-{
-    IMPORT $(__name__) : get-constant : $(__name__) : $(constant) ;
-}
-EXPORT $(__name__) : $(.constants) ;
-
-.executable-path-variable-NT = PATH ;
-# On Windows the case and capitalization of PATH is not always predictable, so
-# let's find out what variable name was really set.
-if $(.name) = NT
-{
-    for local n in [ VARNAMES .ENVIRON ]
-    {
-        if $(n:L) = path
-        {
-            .executable-path-variable-NT = $(n) ;
-        }
-    }
-}
-
-# Specific constants for various platforms.  There's no need to define any
-# constant whose value would be the same as the default, below.
-.shared-library-path-variable-NT = $(.executable-path-variable-NT) ;
-.path-separator-NT = ";" ;
-.expand-variable-prefix-NT = % ;
-.expand-variable-suffix-NT = % ;
-.executable-suffix-NT = .exe ;
-
-.shared-library-path-variable-CYGWIN = PATH ;
-
-.shared-library-path-variable-MACOSX = DYLD_LIBRARY_PATH ;
-
-.shared-library-path-variable-AIX = LIBPATH ;
-
-# Default constants
-.shared-library-path-variable = LD_LIBRARY_PATH ;
-.path-separator = ":" ;
-.expand-variable-prefix = $ ;
-.expand-variable-suffix = "" ;
-.executable-path-variable = PATH ;
-.executable-suffix = "" ;
-
-
-# Return a list of the directories in the PATH. Yes, that information is (sort
-# of) available in the global module, but jam code can change those values, and
-# it isn't always clear what case/capitalization to use when looking. This rule
-# is a more reliable way to get there.
-rule executable-path ( )
-{
-    return [ string.words [ environ [ constant executable-path-variable ] ]
-        : [ constant path-separator ] ] ;
-}
-
-
-# Initialize the list of home directories for the current user depending on the
-# OS.
-if $(.name) = NT
-{
-    local home = [ environ HOMEDRIVE HOMEPATH ] ;
-    .home-directories = $(home[1])$(home[2]) [ environ HOME ] [ environ USERPROFILE ] ;
-}
-else
-{
-    .home-directories = [ environ HOME ] ;
-}
-
-
-# Can't use 'constant' mechanism because it only returns 1-element values.
-rule home-directories ( )
-{
-    return $(.home-directories) ;
-}
-
-
-# Return the string needed to represent the expansion of the named shell
-# variable.
-rule expand-variable ( variable )
-{
-    local prefix = [ constant expand-variable-prefix ] ;
-    local suffix = [ constant expand-variable-suffix ] ;
-    return $(prefix)$(variable)$(suffix) ;
-}
-
-
-# Returns true if running on windows, whether in cygwin or not.
-rule on-windows ( )
-{
-    local result ;
-    if [ modules.peek : NT ]
-    {
-        result = true ;
-    }
-    else if [ modules.peek : UNIX ]
-    {
-        switch [ modules.peek : JAMUNAME ]
-        {
-            case CYGWIN* :
-            {
-                result = true ;
-            }
-        }
-    }
-    return $(result) ;
-}
-
-
-if ! [ on-windows ]
-{
-    .on-unix = 1 ;
-}
-
-
-rule on-unix
-{
-    return $(.on-unix) ;
-}
-
-
-rule __test__
-{
-    import assert ;
-    if ! ( --quiet in [ modules.peek : ARGV ] )
-    {
-        ECHO os: name= [ name ] ;
-        ECHO os: version= [ version ] ;
-    }
-    assert.true name ;
-}
diff --git a/jam-files/boost-build/util/os_j.py b/jam-files/boost-build/util/os_j.py
deleted file mode 100644
index f44cca62..00000000
--- a/jam-files/boost-build/util/os_j.py
+++ /dev/null
@@ -1,19 +0,0 @@
-# Status: stub, just enough to make tests work.
-#
-# Named os_j to avoid conflicts with standard 'os'. See
-# project.py:import for special-casing.
-#
-# Copyright 2001, 2002, 2003, 2005 Dave Abrahams
-# Copyright 2006 Rene Rivera
-# Copyright 2003, 2005 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-import bjam
-
-__OS = bjam.call("peek", [], "OS")[0]
-
-# Return Jam's name of OS to prevent existing code from burning
-# when faced with Python naming
-def name():
-    return __OS
diff --git a/jam-files/boost-build/util/path.jam b/jam-files/boost-build/util/path.jam
deleted file mode 100644
index ea26b816..00000000
--- a/jam-files/boost-build/util/path.jam
+++ /dev/null
@@ -1,934 +0,0 @@
-# Copyright Vladimir Prus 2002-2006.
-# Copyright Dave Abrahams 2003-2004.
-# Copyright Rene Rivera 2003-2006.
-#
-# Distributed under the Boost Software License, Version 1.0.
-#    (See accompanying file LICENSE_1_0.txt or copy at
-#          http://www.boost.org/LICENSE_1_0.txt)
-
-# Performs various path manipulations. Paths are always in a 'normalized'
-# representation. In it, a path may be either:
-#
-#     - '.', or
-#
-#     - ['/'] [ ( '..' '/' )* (token '/')* token ]
-#
-# In plain english, path can be rooted, '..' elements are allowed only at the
-# beginning, and it never ends in slash, except for path consisting of slash
-# only.
-
-import errors ;
-import modules ;
-import regex ;
-import sequence ;
-import set ;
-import version ;
-
-
-os = [ modules.peek : OS ] ;
-if [ modules.peek : UNIX ]
-{
-    local uname = [ modules.peek : JAMUNAME ] ;
-    switch $(uname)
-    {
-        case CYGWIN* : os = CYGWIN ;
-        case *       : os = UNIX ;
-    }
-}
-
-
-# Converts the native path into normalized form.
-#
-rule make ( native )
-{
-    return [ make-$(os) $(native) ] ;
-}
-
-
-# Builds native representation of the path.
-#
-rule native ( path )
-{
-    return [ native-$(os) $(path) ] ;
-}
-
-
-# Tests if a path is rooted.
-#
-rule is-rooted ( path )
-{
-    return [ MATCH "^(/)" : $(path) ] ;
-}
-
-
-# Tests if a path has a parent.
-#
-rule has-parent ( path )
-{
-    if $(path) != /
-    {
-        return 1 ;
-    }
-    else
-    {
-        return ;
-    }
-}
-
-
-# Returns the path without any directory components.
-#
-rule basename ( path )
-{
-    return [ MATCH "([^/]+)$" : $(path) ] ;
-}
-
-
-# Returns parent directory of the path. If no parent exists, error is issued.
-#
-rule parent ( path )
-{
-    if [ has-parent $(path) ]
-    {
-        if $(path) = .
-        {
-            return .. ;
-        }
-        else
-        {
-            # Strip everything at the end of path up to and including the last
-            # slash.
-            local result = [ regex.match "((.*)/)?([^/]+)" : $(path) : 2 3 ] ;
-
-            # Did we strip what we shouldn't?
-            if $(result[2]) = ".."
-            {
-                return $(path)/.. ;
-            }
-            else
-            {
-                if ! $(result[1])
-                {
-                    if [ is-rooted $(path) ]
-                    {
-                        result = / ;
-                    }
-                    else
-                    {
-                        result = . ;
-                    }
-                }
-                return $(result[1]) ;
-            }
-        }
-    }
-    else
-    {
-        errors.error "Path '$(path)' has no parent" ;
-    }
-}
-
-
-# Returns path2 such that "[ join path path2 ] = .". The path may not contain
-# ".." element or be rooted.
-#
-rule reverse ( path )
-{
-    if $(path) = .
-    {
-        return $(path) ;
-    }
-    else
-    {
-        local tokens = [ regex.split $(path) "/" ] ;
-        local tokens2 ;
-        for local i in $(tokens)
-        {
-            tokens2 += .. ;
-        }
-        return [ sequence.join $(tokens2) : "/" ] ;
-    }
-}
-
-
-# Concatenates the passed path elements. Generates an error if any element other
-# than the first one is rooted. Skips any empty or undefined path elements.
-#
-rule join ( elements + )
-{
-    if ! $(elements[2-])
-    {
-        return $(elements[1]) ;
-    }
-    else
-    {
-        for local e in $(elements[2-])
-        {
-            if [ is-rooted $(e) ]
-            {
-                errors.error only the first element may be rooted ;
-            }
-        }
-        if [ version.check-jam-version 3 1 17 ]
-        {
-            return [ NORMALIZE_PATH "$(elements)" ] ;
-        }
-        else
-        {
-            # Boost Jam prior to version 3.1.17 had problems with its
-            # NORMALIZE_PATH rule in case you passed it a leading backslash
-            # instead of a slash, in some cases when you sent it an empty
-            # initial path element and possibly some others. At least some of
-            # those cases were being hit and relied upon when calling this rule
-            # from the path.make-NT rule.
-            if ! $(elements[1]) && $(elements[2])
-            {
-                return [ NORMALIZE_PATH "/" "$(elements[2-])" ] ;
-            }
-            else
-            {
-                return [ NORMALIZE_PATH "$(elements)" ] ;
-            }
-        }
-    }
-}
-
-
-# If 'path' is relative, it is rooted at 'root'. Otherwise, it is unchanged.
-#
-rule root ( path root )
-{
-    if [ is-rooted $(path) ]
-    {
-        return $(path) ;
-    }
-    else
-    {
-        return [ join $(root) $(path) ] ;
-    }
-}
-
-
-# Returns the current working directory.
-#
-rule pwd ( )
-{
-    if ! $(.pwd)
-    {
-        .pwd = [ make [ PWD ] ] ;
-    }
-    return $(.pwd) ;
-}
-
-
-# Returns the list of files matching the given pattern in the specified
-# directory. Both directories and patterns are supplied as portable paths. Each
-# pattern should be non-absolute path, and can't contain "." or ".." elements.
-# Each slash separated element of pattern can contain the following special
-# characters:
-#   - '?', which match any character
-#   - '*', which matches arbitrary number of characters.
-# A file $(d)/e1/e2/e3 (where 'd' is in $(dirs)) matches pattern p1/p2/p3 if and
-# only if e1 matches p1, e2 matches p2 and so on.
-#
-# For example:
-#   [ glob . : *.cpp ]
-#   [ glob . : */build/Jamfile ]
-#
-rule glob ( dirs * : patterns + : exclude-patterns * )
-{
-    local result ;
-    local real-patterns ;
-    local real-exclude-patterns ;
-    for local d in $(dirs)
-    {
-        for local p in $(patterns)
-        {
-            local pattern = [ path.root $(p) $(d) ] ;
-            real-patterns += [ path.native $(pattern) ] ;
-        }
-
-        for local p in $(exclude-patterns)
-        {
-            local pattern = [ path.root $(p) $(d) ] ;
-            real-exclude-patterns += [ path.native $(pattern) ] ;
-        }
-    }
-
-    local inc = [ GLOB-RECURSIVELY $(real-patterns) ] ;
-    inc = [ sequence.transform NORMALIZE_PATH : $(inc) ] ;
-    local exc = [ GLOB-RECURSIVELY $(real-exclude-patterns) ] ;
-    exc = [ sequence.transform NORMALIZE_PATH : $(exc) ] ;
-
-    return [ sequence.transform path.make : [ set.difference $(inc) : $(exc) ] ]
-        ;
-}
-
-
-# Recursive version of GLOB. Builds the glob of files while also searching in
-# the subdirectories of the given roots. An optional set of exclusion patterns
-# will filter out the matching entries from the result. The exclusions also
-# apply to the subdirectory scanning, such that directories that match the
-# exclusion patterns will not be searched.
-#
-rule glob-tree ( roots * : patterns + : exclude-patterns * )
-{
-    return [ sequence.transform path.make : [ .glob-tree [ sequence.transform
-        path.native : $(roots) ] : $(patterns) : $(exclude-patterns) ] ] ;
-}
-
-
-local rule .glob-tree ( roots * : patterns * : exclude-patterns * )
-{
-    local excluded ;
-    if $(exclude-patterns)
-    {
-        excluded = [ GLOB $(roots) : $(exclude-patterns) ] ;
-    }
-    local result = [ set.difference [ GLOB $(roots) : $(patterns) ] :
-        $(excluded) ] ;
-    local subdirs ;
-    for local d in [ set.difference [ GLOB $(roots) : * ] : $(excluded) ]
-    {
-        if ! ( $(d:D=) in . .. ) && ! [ CHECK_IF_FILE $(d) ]
-        {
-            subdirs += $(d) ;
-        }
-    }
-    if $(subdirs)
-    {
-        result += [ .glob-tree $(subdirs) : $(patterns) : $(exclude-patterns) ]
-            ;
-    }
-    return $(result) ;
-}
-
-
-# Returns true is the specified file exists.
-#
-rule exists ( file )
-{
-    return [ path.glob $(file:D) : $(file:D=) ] ;
-}
-NATIVE_RULE path : exists ;
-
-
-# Find out the absolute name of path and returns the list of all the parents,
-# starting with the immediate one. Parents are returned as relative names. If
-# 'upper_limit' is specified, directories above it will be pruned.
-#
-rule all-parents ( path : upper_limit ? : cwd ? )
-{
-    cwd ?= [ pwd ] ;
-    local path_ele = [ regex.split [ root $(path) $(cwd) ] "/" ] ;
-
-    if ! $(upper_limit)
-    {
-        upper_limit = / ;
-    }
-    local upper_ele = [ regex.split [ root $(upper_limit) $(cwd) ] "/" ] ;
-
-    # Leave only elements in 'path_ele' below 'upper_ele'.
-    while $(path_ele) && ( $(upper_ele[1]) = $(path_ele[1]) )
-    {
-        upper_ele = $(upper_ele[2-]) ;
-        path_ele = $(path_ele[2-]) ;
-    }
-
-    # Have all upper elements been removed ?
-    if $(upper_ele)
-    {
-        errors.error "$(upper_limit) is not prefix of $(path)" ;
-    }
-    
-    # Create the relative paths to parents, number of elements in 'path_ele'.
-    local result ;
-    for local i in $(path_ele)
-    {
-        path = [ parent $(path) ] ;
-        result += $(path) ;
-    }
-    return $(result) ;
-}
-
-
-# Search for 'pattern' in parent directories of 'dir', up till and including
-# 'upper_limit', if it is specified, or till the filesystem root otherwise.
-#
-rule glob-in-parents ( dir : patterns + : upper-limit ? )
-{
-    local result ;
-    local parent-dirs = [ all-parents $(dir) : $(upper-limit) ] ;
-
-    while $(parent-dirs) && ! $(result)
-    {
-        result = [ glob $(parent-dirs[1]) : $(patterns) ] ;
-        parent-dirs = $(parent-dirs[2-]) ;
-    }
-    return $(result) ;
-}
-
-
-# Assuming 'child' is a subdirectory of 'parent', return the relative path from
-# 'parent' to 'child'.
-#
-rule relative ( child parent : no-error ? )
-{
-    local not-a-child ;
-    if $(parent) = "."
-    {
-        return $(child) ;
-    }
-    else
-    {
-        local split1 = [ regex.split $(parent) / ] ;
-        local split2 = [ regex.split $(child) / ] ;
-
-        while $(split1)
-        {
-            if $(split1[1]) = $(split2[1])
-            {
-                split1 = $(split1[2-]) ;
-                split2 = $(split2[2-]) ;
-            }
-            else
-            {
-                not-a-child = true ;
-                split1 = ;
-            }
-        }
-        if $(split2)
-        {
-            if $(not-a-child)
-            {
-                if $(no-error)
-                {
-                    return not-a-child ;
-                }
-                else
-                {
-                    errors.error $(child) is not a subdir of $(parent) ;
-                }                        
-            }
-            else
-            {
-                return [ join $(split2) ] ;    
-            }        
-        }
-        else
-        {
-            return "." ;
-        }
-    }
-}
-
-
-# Returns the minimal path to path2 that is relative path1.
-#
-rule relative-to ( path1 path2 )
-{
-    local root_1 = [ regex.split [ reverse $(path1) ] / ] ;
-    local split1 = [ regex.split $(path1) / ] ;
-    local split2 = [ regex.split $(path2) / ] ;
-
-    while $(split1) && $(root_1)
-    {
-        if $(split1[1]) = $(split2[1])
-        {
-            root_1 = $(root_1[2-]) ;
-            split1 = $(split1[2-]) ;
-            split2 = $(split2[2-]) ;
-        }
-        else
-        {
-            split1 = ;
-        }
-    }
-    return [ join . $(root_1) $(split2) ] ;
-}
-
-
-# Returns the list of paths which are used by the operating system for looking
-# up programs.
-#
-rule programs-path ( )
-{
-    local result ;
-    local raw = [ modules.peek : PATH Path path ] ;
-    for local p in $(raw)
-    {
-        if $(p)
-        {
-            result += [ path.make $(p) ] ;
-        }
-    }
-    return $(result) ;
-}
-
-rule makedirs ( path )
-{
-    local result = true ;
-    local native = [ native $(path) ] ;
-    if ! [ exists $(native) ]
-    {
-        if [ makedirs [ parent $(path) ] ]
-        {            
-            if ! [ MAKEDIR $(native) ]
-            {
-                errors.error "Could not create directory '$(path)'" ;
-                result = ;
-            }
-        }        
-    }    
-    return $(result) ;
-}
-
-# Converts native Windows paths into our internal canonic path representation.
-# Supports 'invalid' paths containing multiple successive path separator
-# characters.
-#
-# TODO: Check and if needed add support for Windows 'X:file' path format where
-# the file is located in the current folder on drive X.
-#
-rule make-NT ( native )
-{
-    local result ;
-
-    if [ version.check-jam-version 3 1 17 ]
-    {
-        result = [ NORMALIZE_PATH $(native) ] ;
-    }
-    else
-    {
-        # This old implementation is really fragile due to a not so clear way
-        # NORMALIZE_PATH rule worked in Boost.Jam versions prior to 3.1.17. E.g.
-        # path.join would mostly ignore empty path elements but would root the
-        # joined path in case the initial two path elements were empty or some
-        # similar accidental wierdness.
-        result = [ path.join [ regex.split $(native) "[/\\]" ] ] ;
-    }
-
-    # We need to add an extra '/' in front in case this is a rooted Windows path
-    # starting with a drive letter and not a path separator character since the
-    # builtin NORMALIZE_PATH rule has no knowledge of this leading drive letter
-    # and treats it as a regular folder name.
-    if [ regex.match "(^.:)" : $(native) ]
-    {
-        result = /$(result) ;
-    }
-
-    return $(result) ;
-}
-
-
-rule native-NT ( path )
-{
-    local result ;
-    if [ is-rooted $(path) ] && ! [ regex.match "^/(.:)" : $(path) ]
-    {
-        result = $(path) ;
-    }
-    else
-    {
-        result = [ MATCH "^/?(.*)" : $(path) ] ;
-    }
-    result = [ sequence.join [ regex.split $(result) "/" ] : "\\" ] ;
-    return $(result) ;
-}
-
-
-rule make-UNIX ( native )
-{
-    # VP: I have no idea now 'native' can be empty here! But it can!
-    if ! $(native)
-    {
-        errors.error "Empty path passed to 'make-UNIX'" ;
-    }
-    else
-    {
-        return [ NORMALIZE_PATH $(native:T) ] ;
-    }
-}
-
-
-rule native-UNIX ( path )
-{
-    return $(path) ;
-}
-
-
-rule make-CYGWIN ( path )
-{
-    return [ make-NT $(path) ] ;
-}
-
-
-rule native-CYGWIN ( path )
-{
-    local result = $(path) ;
-    if [ regex.match "(^/.:)" : $(path)  ]  # Windows absolute path.
-    {
-        result = [ MATCH "^/?(.*)" : $(path) ] ;  # Remove leading '/'.
-    }
-    return [ native-UNIX $(result) ] ;
-}
-
-
-# split-path-VMS: splits input native path into device dir file (each part is
-# optional).
-#
-# example:
-#
-# dev:[dir]file.c => dev: [dir] file.c
-#
-rule split-path-VMS ( native )
-{
-    local matches = [ MATCH ([a-zA-Z0-9_-]+:)?(\\[[^\]]*\\])?(.*)?$   : $(native) ] ;
-    local device = $(matches[1]) ;
-    local dir = $(matches[2]) ;
-    local file = $(matches[3]) ;
-
-    return $(device) $(dir) $(file) ;
-}
-
-
-# Converts a native VMS path into a portable path spec.
-#
-# Does not handle current-device absolute paths such as "[dir]File.c" as it is
-# not clear how to represent them in the portable path notation.
-#
-# Adds a trailing dot (".") to the file part if no extension is present (helps
-# when converting it back into native path).
-#
-rule make-VMS ( native )
-{
-    if [ MATCH ^(\\[[a-zA-Z0-9]) : $(native) ]
-    {
-        errors.error "Can't handle default-device absolute paths: " $(native) ;
-    }
-
-    local parts = [ split-path-VMS $(native) ] ;
-    local device = $(parts[1]) ;
-    local dir = $(parts[2]) ;
-    local file = $(parts[3]) ;
-    local elems ;
-
-    if $(device)
-    {
-        #
-        # rooted
-        #
-        elems = /$(device) ;
-    }
-
-    if $(dir) = "[]"
-    {
-        #
-        # Special case: current directory
-        #
-        elems = $(elems) "." ;
-    }
-    else if $(dir)
-    {
-        dir = [ regex.replace $(dir) "\\[|\\]" "" ] ;
-        local dir_parts = [ regex.split $(dir) \\. ]  ;
-
-        if $(dir_parts[1]) = ""
-        {
-            #
-            # Relative path
-            #
-            dir_parts = $(dir_parts[2--1]) ;
-        }
-
-        #
-        # replace "parent-directory" parts (- => ..)
-        #
-        dir_parts = [ regex.replace-list $(dir_parts) : - : .. ] ;
-
-        elems = $(elems) $(dir_parts) ;
-    }
-
-    if $(file)
-    {
-        if ! [ MATCH (\\.) : $(file) ]
-        {
-            #
-            # Always add "." to end of non-extension file.
-            #
-            file = $(file). ;
-        }
-        elems = $(elems) $(file) ;
-    }
-
-    local portable = [ path.join $(elems) ] ;
-
-    return $(portable) ;
-}
-
-
-# Converts a portable path spec into a native VMS path.
-#
-# Relies on having at least one dot (".") included in the file name to be able
-# to differentiate it from the directory part.
-#
-rule native-VMS ( path )
-{
-    local device = "" ;
-    local dir = $(path) ;
-    local file = "" ;
-    local native ;
-    local split ;
-
-    #
-    # Has device ?
-    #
-    if [ is-rooted $(dir) ]
-    {
-        split = [ MATCH ^/([^:]+:)/?(.*) : $(dir) ] ;
-        device = $(split[1]) ;
-        dir = $(split[2]) ;
-    }
-
-    #
-    # Has file ?
-    #
-    # This is no exact science, just guess work:
-    #
-    # If the last part of the current path spec
-    # includes some chars, followed by a dot,
-    # optionally followed by more chars -
-    # then it is a file (keep your fingers crossed).
-    #
-    split = [ regex.split $(dir) / ] ;
-    local maybe_file = $(split[-1]) ;
-
-    if [ MATCH ^([^.]+\\..*) : $(maybe_file) ]
-    {
-        file = $(maybe_file) ;
-        dir = [ sequence.join $(split[1--2]) : / ] ;
-    }
-
-    #
-    # Has dir spec ?
-    #
-    if $(dir) = "."
-    {
-        dir = "[]" ;
-    }
-    else if $(dir)
-    {
-        dir = [ regex.replace $(dir) \\.\\. - ] ;
-        dir = [ regex.replace $(dir) / . ] ;
-
-        if $(device) = ""
-        {
-            #
-            # Relative directory
-            #
-            dir = "."$(dir) ;
-        }
-        dir = "["$(dir)"]" ;
-    }
-
-    native = [ sequence.join $(device) $(dir) $(file) ] ;
-
-    return $(native) ;
-}
-
-
-rule __test__ ( )
-{
-    import assert ;
-    import errors : try catch ;
-
-    assert.true is-rooted "/" ;
-    assert.true is-rooted "/foo" ;
-    assert.true is-rooted "/foo/bar" ;
-    assert.result : is-rooted "." ;
-    assert.result : is-rooted "foo" ;
-    assert.result : is-rooted "foo/bar" ;
-
-    assert.true has-parent "foo" ;
-    assert.true has-parent "foo/bar" ;
-    assert.true has-parent "." ;
-    assert.result : has-parent "/" ;
-
-    assert.result "." : basename "." ;
-    assert.result ".." : basename ".." ;
-    assert.result "foo" : basename "foo" ;
-    assert.result "foo" : basename "bar/foo" ;
-    assert.result "foo" : basename "gaz/bar/foo" ;
-    assert.result "foo" : basename "/gaz/bar/foo" ;
-
-    assert.result "." : parent "foo" ;
-    assert.result "/" : parent "/foo" ;
-    assert.result "foo/bar" : parent "foo/bar/giz" ;
-    assert.result ".." : parent "." ;
-    assert.result ".." : parent "../foo" ;
-    assert.result "../../foo" : parent "../../foo/bar" ;
-
-    assert.result "." : reverse "." ;
-    assert.result ".." : reverse "foo" ;
-    assert.result "../../.." : reverse "foo/bar/giz" ;
-
-    assert.result "foo" : join "foo" ;
-    assert.result "/foo" : join "/" "foo" ;
-    assert.result "foo/bar" : join "foo" "bar" ;
-    assert.result "foo/bar" : join "foo/giz" "../bar" ;
-    assert.result "foo/giz" : join "foo/bar/baz" "../../giz" ;
-    assert.result ".." : join "." ".." ;
-    assert.result ".." : join "foo" "../.." ;
-    assert.result "../.." : join "../foo" "../.." ;
-    assert.result "/foo" : join "/bar" "../foo" ;
-    assert.result "foo/giz" : join "foo/giz" "." ;
-    assert.result "." : join lib2 ".." ;
-    assert.result "/" : join "/a" ".." ;
-
-    assert.result /a/b : join /a/b/c .. ;
-
-    assert.result "foo/bar/giz" : join "foo" "bar" "giz" ;
-    assert.result "giz" : join "foo" ".." "giz" ;
-    assert.result "foo/giz" : join "foo" "." "giz" ;
-
-    try ;
-    {
-        join "a" "/b" ;
-    }
-    catch only first element may be rooted ;
-
-    local CWD = "/home/ghost/build" ;
-    assert.result : all-parents . : . : $(CWD) ;
-    assert.result . .. ../.. ../../..  : all-parents "Jamfile" : "" : $(CWD) ;
-    assert.result foo . .. ../.. ../../.. : all-parents "foo/Jamfile" : "" : $(CWD) ;
-    assert.result ../Work .. ../.. ../../.. : all-parents "../Work/Jamfile" : "" : $(CWD) ;
-
-    local CWD = "/home/ghost" ;
-    assert.result . .. : all-parents "Jamfile" : "/home" : $(CWD) ;
-    assert.result . : all-parents "Jamfile" : "/home/ghost" : $(CWD) ;
-
-    assert.result "c/d" : relative "a/b/c/d" "a/b" ;
-    assert.result "foo" : relative "foo" "." ;
-
-    local save-os = [ modules.peek path : os ] ;
-    modules.poke path : os : NT ;
-
-    assert.result "foo/bar/giz" : make "foo/bar/giz" ;
-    assert.result "foo/bar/giz" : make "foo\\bar\\giz" ;
-    assert.result "foo" : make "foo/" ;
-    assert.result "foo" : make "foo\\" ;
-    assert.result "foo" : make "foo/." ;
-    assert.result "foo" : make "foo/bar/.." ;
-    assert.result "foo" : make "foo/bar/../" ;
-    assert.result "foo" : make "foo/bar/..\\" ;
-    assert.result "foo/bar" : make "foo/././././bar" ;
-    assert.result "/foo" : make "\\foo" ;
-    assert.result "/D:/My Documents" : make "D:\\My Documents" ;
-    assert.result "/c:/boost/tools/build/new/project.jam" : make "c:\\boost\\tools\\build\\test\\..\\new\\project.jam" ;
-    
-    #   Test processing 'invalid' paths containing multiple successive path
-    # separators.
-    assert.result "foo" : make "foo//" ;
-    assert.result "foo" : make "foo///" ;
-    assert.result "foo" : make "foo\\\\" ;
-    assert.result "foo" : make "foo\\\\\\" ;
-    assert.result "/foo" : make "//foo" ;
-    assert.result "/foo" : make "///foo" ;
-    assert.result "/foo" : make "\\\\foo" ;
-    assert.result "/foo" : make "\\\\\\foo" ;
-    assert.result "/foo" : make "\\/\\/foo" ;
-    assert.result "foo/bar" : make "foo//\\//\\\\bar//\\//\\\\\\//\\//\\\\" ;
-    assert.result "foo" : make "foo/bar//.." ;
-    assert.result "foo/bar" : make "foo/bar/giz//.." ;
-    assert.result "foo/giz" : make "foo//\\//\\\\bar///\\\\//\\\\////\\/..///giz\\//\\\\\\//\\//\\\\" ;
-    assert.result "../../../foo" : make "..///.//..///.//..////foo///" ;
-
-    #   Test processing 'invalid' rooted paths with too many '..' path elements
-    # that would place them before the root.
-    assert.result : make "/.." ;
-    assert.result : make "/../" ;
-    assert.result : make "/../." ;
-    assert.result : make "/.././" ;
-    assert.result : make "/foo/../bar/giz/.././././../../." ;
-    assert.result : make "/foo/../bar/giz/.././././../.././" ;
-    assert.result : make "//foo/../bar/giz/.././././../../." ;
-    assert.result : make "//foo/../bar/giz/.././././../.././" ;
-    assert.result : make "\\\\foo/../bar/giz/.././././../../." ;
-    assert.result : make "\\\\foo/../bar/giz/.././././../.././" ;
-    assert.result : make "/..///.//..///.//..////foo///" ;
-
-    assert.result "foo\\bar\\giz" : native "foo/bar/giz" ;
-    assert.result "foo" : native "foo" ;
-    assert.result "\\foo" : native "/foo" ;
-    assert.result "D:\\My Documents\\Work" : native "/D:/My Documents/Work" ;
-
-    modules.poke path : os : UNIX ;
-
-    assert.result "foo/bar/giz" : make "foo/bar/giz" ;
-    assert.result "/sub1" : make "/sub1/." ;
-    assert.result "/sub1" : make "/sub1/sub2/.." ;
-    assert.result "sub1" : make "sub1/." ;
-    assert.result "sub1" : make "sub1/sub2/.." ;
-    assert.result "/foo/bar" : native "/foo/bar" ;
-
-    modules.poke path : os : VMS ;
-
-    #
-    # Don't really need to poke os before these
-    #
-    assert.result "disk:" "[dir]"  "file" : split-path-VMS "disk:[dir]file" ;
-    assert.result "disk:" "[dir]"  ""     : split-path-VMS "disk:[dir]" ;
-    assert.result "disk:" ""       ""     : split-path-VMS "disk:" ;
-    assert.result "disk:" ""       "file" : split-path-VMS "disk:file" ;
-    assert.result ""      "[dir]"  "file" : split-path-VMS "[dir]file" ;
-    assert.result ""      "[dir]"  ""     : split-path-VMS "[dir]" ;
-    assert.result ""      ""       "file" : split-path-VMS "file" ;
-    assert.result ""      ""       ""     : split-path-VMS "" ;
-
-    #
-    # Special case: current directory
-    #
-    assert.result ""      "[]"     ""     : split-path-VMS "[]" ;
-    assert.result "disk:" "[]"     ""     : split-path-VMS "disk:[]" ;
-    assert.result ""      "[]"     "file" : split-path-VMS "[]file" ;
-    assert.result "disk:" "[]"     "file" : split-path-VMS "disk:[]file" ;
-
-    #
-    # Make portable paths
-    #
-    assert.result "/disk:" : make "disk:" ;
-    assert.result "foo/bar/giz" : make "[.foo.bar.giz]" ;
-    assert.result "foo" : make "[.foo]" ;
-    assert.result "foo" : make "[.foo.bar.-]" ;
-    assert.result ".." : make "[.-]" ;
-    assert.result ".." : make "[-]" ;
-    assert.result "." : make "[]" ;
-    assert.result "giz.h" : make "giz.h" ;
-    assert.result "foo/bar/giz.h" : make "[.foo.bar]giz.h" ;
-    assert.result "/disk:/my_docs" : make "disk:[my_docs]" ;
-    assert.result "/disk:/boost/tools/build/new/project.jam" : make "disk:[boost.tools.build.test.-.new]project.jam" ;
-
-    #
-    # Special case (adds '.' to end of file w/o extension to
-    # disambiguate from directory in portable path spec).
-    #
-    assert.result "Jamfile." : make "Jamfile" ;
-    assert.result "dir/Jamfile." : make "[.dir]Jamfile" ;
-    assert.result "/disk:/dir/Jamfile." : make "disk:[dir]Jamfile" ;
-
-    #
-    # Make native paths
-    #
-    assert.result "disk:" : native "/disk:" ;
-    assert.result "[.foo.bar.giz]" : native "foo/bar/giz" ;
-    assert.result "[.foo]" : native "foo" ;
-    assert.result "[.-]" : native ".." ;
-    assert.result "[.foo.-]" : native "foo/.." ;
-    assert.result "[]" : native "." ;
-    assert.result "disk:[my_docs.work]" : native "/disk:/my_docs/work" ;
-    assert.result "giz.h" : native "giz.h" ;
-    assert.result "disk:Jamfile." : native "/disk:Jamfile." ;
-    assert.result "disk:[my_docs.work]Jamfile." : native "/disk:/my_docs/work/Jamfile." ;
-
-    modules.poke path : os : $(save-os) ;
-}
diff --git a/jam-files/boost-build/util/path.py b/jam-files/boost-build/util/path.py
deleted file mode 100644
index 222b96bf..00000000
--- a/jam-files/boost-build/util/path.py
+++ /dev/null
@@ -1,904 +0,0 @@
-# Status: this module is ported on demand by however needs something
-# from it.  Functionality that is not needed by Python port will
-# be dropped.
-
-#  Copyright (C) Vladimir Prus 2002. Permission to copy, use, modify, sell and
-#  distribute this software is granted provided this copyright notice appears in
-#  all copies. This software is provided "as is" without express or implied
-#  warranty, and with no claim as to its suitability for any purpose.
-
-#  Performs various path manipulations. Path are always in a 'normilized' 
-#  representation. In it, a path may be either:
-#
-#     - '.', or
-#
-#     - ['/'] [ ( '..' '/' )*  (token '/')* token ]
-# 
-#   In plain english, path can be rooted, '..' elements are allowed only
-#   at the beginning, and it never ends in slash, except for path consisting
-#   of slash only.
-
-import os.path
-from utility import to_seq
-from glob import glob as builtin_glob
-
-from b2.util import bjam_signature
-
-@bjam_signature((["path", "root"],))
-def root (path, root):
-    """ If 'path' is relative, it is rooted at 'root'. Otherwise, it's unchanged.
-    """
-    if os.path.isabs (path):
-        return path
-    else:
-        return os.path.join (root, path)
-
-@bjam_signature((["native"],))
-def make (native):
-    """ Converts the native path into normalized form.
-    """
-    # TODO: make os selection here.
-    return make_UNIX (native)
-
-def make_UNIX (native):
-
-    # VP: I have no idea now 'native' can be empty here! But it can!
-    assert (native)
-
-    return os.path.normpath (native)
-
-@bjam_signature((["path"],))
-def native (path):
-    """ Builds a native representation of the path.
-    """
-    # TODO: make os selection here.
-    return native_UNIX (path)
-
-def native_UNIX (path):
-    return path
-
-
-def pwd ():
-    """ Returns the current working directory.
-        # TODO: is it a good idea to use the current dir? Some use-cases 
-                may not allow us to depend on the current dir.
-    """
-    return make (os.getcwd ())
-
-def is_rooted (path):
-    """ Tests if a path is rooted.
-    """
-    return path and path [0] == '/'
-
-
-###################################################################
-# Still to port.
-# Original lines are prefixed with "#   "
-#
-#   #  Copyright (C) Vladimir Prus 2002. Permission to copy, use, modify, sell and
-#   #  distribute this software is granted provided this copyright notice appears in
-#   #  all copies. This software is provided "as is" without express or implied
-#   #  warranty, and with no claim as to its suitability for any purpose.
-#   
-#   #  Performs various path manipulations. Path are always in a 'normilized' 
-#   #  representation. In it, a path may be either:
-#   #
-#   #     - '.', or
-#   #
-#   #     - ['/'] [ ( '..' '/' )*  (token '/')* token ]
-#   # 
-#   #   In plain english, path can be rooted, '..' elements are allowed only
-#   #   at the beginning, and it never ends in slash, except for path consisting
-#   #   of slash only.
-#   
-#   import modules ;
-#   import sequence ;
-#   import regex ;
-#   import errors : error ;
-#   
-#   
-#   os = [ modules.peek : OS ] ;
-#   if [ modules.peek : UNIX ] 
-#   {    
-#       local uname = [ modules.peek : JAMUNAME ] ;
-#       switch $(uname)
-#       {
-#           case CYGWIN* :
-#             os = CYGWIN ;
-#           
-#           case * :
-#             os = UNIX ;
-#       }        
-#   }
-#   
-#   #
-#   #    Tests if a path is rooted.
-#   #
-#   rule is-rooted ( path )
-#   {
-#       return [ MATCH "^(/)" : $(path) ] ;
-#   }
-#   
-#   #
-#   #    Tests if a path has a parent.
-#   #
-#   rule has-parent ( path )
-#   {
-#       if $(path) != / {
-#           return 1 ;
-#       } else {
-#           return ;
-#       }
-#   }
-#   
-#   #
-#   #    Returns the path without any directory components.
-#   #
-#   rule basename ( path )
-#   {
-#       return [ MATCH "([^/]+)$" : $(path) ] ;
-#   }
-#   
-#   #
-#   #    Returns parent directory of the path. If no parent exists, error is issued.
-#   #
-#   rule parent ( path )
-#   {
-#       if [ has-parent $(path) ] {
-#   
-#           if $(path) = . {
-#               return .. ;
-#           } else {
-#   
-#               # Strip everything at the end of path up to and including
-#               # the last slash
-#               local result = [ regex.match "((.*)/)?([^/]+)" : $(path) : 2 3 ] ;
-#   
-#               # Did we strip what we shouldn't?
-#               if $(result[2]) = ".." {
-#                   return $(path)/.. ;
-#               } else {
-#                   if ! $(result[1]) {
-#                       if [ is-rooted $(path) ] {
-#                           result = / ;
-#                       } else {
-#                           result = . ;
-#                       }
-#                   }
-#                   return $(result[1]) ;
-#               }
-#           }
-#       } else {
-#           error "Path '$(path)' has no parent" ;
-#       }
-#   }
-#   
-#   #
-#   #    Returns path2 such that "[ join path path2 ] = .".
-#   #    The path may not contain ".." element or be rooted.
-#   #
-#   rule reverse ( path )
-#   {
-#       if $(path) = .
-#       {
-#           return $(path) ;
-#       }
-#       else
-#       {
-#           local tokens = [ regex.split $(path) "/" ] ;
-#           local tokens2 ;
-#           for local i in $(tokens) {
-#               tokens2 += .. ;
-#           }
-#           return [ sequence.join $(tokens2) : "/" ] ;
-#       }
-#   }
-#   
-#   #
-#   # Auxillary rule: does all the semantic of 'join', except for error cheching.
-#   # The error checking is separated because this rule is recursive, and I don't
-#   # like the idea of checking the same input over and over.
-#   #
-#   local rule join-imp ( elements + )
-#   {
-#       return [ NORMALIZE_PATH $(elements:J="/") ] ;
-#   }
-#   
-#   #
-#   #    Contanenates the passed path elements. Generates an error if
-#   #    any element other than the first one is rooted.
-#   #
-#   rule join ( elements + )
-#   {
-#       if ! $(elements[2]) 
-#       {
-#           return $(elements[1]) ;
-#       }
-#       else
-#       {        
-#           for local e in $(elements[2-])
-#           {
-#               if [ is-rooted $(e) ]
-#               {
-#                   error only first element may be rooted ;
-#               }
-#           }
-#           return [ join-imp $(elements) ] ;
-#       }    
-#   }
-
-
-def glob (dirs, patterns):
-    """ Returns the list of files matching the given pattern in the
-    specified directory.  Both directories and patterns are 
-    supplied as portable paths. Each pattern should be non-absolute
-    path, and can't contain "." or ".." elements. Each slash separated
-    element of pattern can contain the following special characters:
-    -  '?', which match any character
-    -  '*', which matches arbitrary number of characters.
-    A file $(d)/e1/e2/e3 (where 'd' is in $(dirs)) matches pattern p1/p2/p3
-    if and only if e1 matches p1, e2 matches p2 and so on.
-    
-    For example: 
-        [ glob . : *.cpp ] 
-        [ glob . : */build/Jamfile ] 
-    """
-#   {
-#       local result ;
-#       if $(patterns:D)
-#       {
-#           # When a pattern has a directory element, we first glob for
-#           # directory, and then glob for file name is the found directories.
-#           for local p in $(patterns)
-#           {
-#               # First glob for directory part.
-#               local globbed-dirs = [ glob $(dirs) : $(p:D) ] ;
-#               result += [ glob $(globbed-dirs) : $(p:D="") ] ;
-#           }        
-#       }
-#       else
-#       {        
-#           # When a pattern has not directory, we glob directly.
-#           # Take care of special ".." value. The "GLOB" rule simply ignores
-#           # the ".." element (and ".") element in directory listings. This is
-#           # needed so that 
-#           #
-#           #    [ glob libs/*/Jamfile ]
-#           #
-#           # don't return 
-#           #
-#           #    libs/../Jamfile (which is the same as ./Jamfile)
-#           #
-#           # On the other hand, when ".." is explicitly present in the pattern
-#           # we need to return it.
-#           # 
-#           for local dir in $(dirs)
-#           {
-#               for local p in $(patterns)
-#               {                
-#                   if $(p) != ".."
-#                   {                
-#                       result += [ sequence.transform make 
-#                           : [ GLOB [ native $(dir) ] : $(p) ] ] ;
-#                   }            
-#                   else
-#                   {
-#                       result += [ path.join $(dir) .. ] ;
-#                   }            
-#               }            
-#           }
-#       }    
-#       return $(result) ;
-#   }
-#   
-
-# TODO: (PF) I replaced the code above by this. I think it should work but needs to be tested.
-    result = []
-    dirs = to_seq (dirs)
-    patterns = to_seq (patterns)
-
-    splitdirs = []
-    for dir in dirs:
-        splitdirs += dir.split (os.pathsep)
-
-    for dir in splitdirs:
-        for pattern in patterns:
-            p = os.path.join (dir, pattern)
-            import glob
-            result.extend (glob.glob (p))
-    return result
-    
-#
-#   Find out the absolute name of path and returns the list of all the parents,
-#   starting with the immediate one. Parents are returned as relative names.
-#   If 'upper_limit' is specified, directories above it will be pruned.
-#
-def all_parents(path, upper_limit=None, cwd=None):
-
-    if not cwd:
-        cwd = os.getcwd()
-
-    path_abs = os.path.join(cwd, path)
-
-    if upper_limit:
-        upper_limit = os.path.join(cwd, upper_limit)
-
-    result = []
-    while path_abs and path_abs != upper_limit:
-        (head, tail) = os.path.split(path)
-        path = os.path.join(path, "..")        
-        result.append(path)
-        path_abs = head
-
-    if upper_limit and path_abs != upper_limit:
-        raise BaseException("'%s' is not a prefix of '%s'" % (upper_limit, path))
-
-    return result
-    
-#  Search for 'pattern' in parent directories of 'dir', up till and including
-#  'upper_limit', if it is specified, or till the filesystem root otherwise.
-#
-def glob_in_parents(dir, patterns, upper_limit=None):
-
-    result = []
-    parent_dirs = all_parents(dir, upper_limit)
-
-    for p in parent_dirs:
-        result = glob(p, patterns)
-        if result: break
-
-    return result
-
-#   
-#   #
-#   # Assuming 'child' is a subdirectory of 'parent', return the relative
-#   # path from 'parent' to 'child'
-#   #
-#   rule relative ( child parent )
-#   {
-#       if $(parent) = "." 
-#       {
-#           return $(child) ;
-#       }
-#       else 
-#       {       
-#           local split1 = [ regex.split $(parent) / ] ;
-#           local split2 = [ regex.split $(child) / ] ;
-#       
-#           while $(split1)
-#           {
-#               if $(split1[1]) = $(split2[1])
-#               {
-#                   split1 = $(split1[2-]) ;
-#                   split2 = $(split2[2-]) ;
-#               }
-#               else
-#               {
-#                   errors.error $(child) is not a subdir of $(parent) ;
-#               }                
-#           }    
-#           return [ join $(split2) ] ;    
-#       }    
-#   }
-#   
-#   # Returns the minimal path to path2 that is relative path1.
-#   #
-#   rule relative-to ( path1 path2 )
-#   {
-#       local root_1 = [ regex.split [ reverse $(path1) ] / ] ;
-#       local split1 = [ regex.split $(path1) / ] ;
-#       local split2 = [ regex.split $(path2) / ] ;
-#   
-#       while $(split1) && $(root_1)
-#       {
-#           if $(split1[1]) = $(split2[1])
-#           {
-#               root_1 = $(root_1[2-]) ;
-#               split1 = $(split1[2-]) ;
-#               split2 = $(split2[2-]) ;
-#           }
-#           else
-#           {
-#               split1 = ;
-#           }
-#       }
-#       return [ join . $(root_1) $(split2) ] ;
-#   }
-
-# Returns the list of paths which are used by the operating system
-# for looking up programs
-def programs_path ():
-    raw = []
-    names = ['PATH', 'Path', 'path']
-    
-    for name in names:
-        raw.append(os.environ.get (name, ''))
-    
-    result = []
-    for elem in raw:
-        if elem:
-            for p in elem.split(os.path.pathsep):
-                result.append(make(p))
-
-    return result
-
-#   rule make-NT ( native )
-#   {
-#       local tokens = [ regex.split $(native) "[/\\]" ] ;
-#       local result ;
-#   
-#       # Handle paths ending with slashes
-#       if $(tokens[-1]) = ""
-#       {
-#           tokens = $(tokens[1--2]) ; # discard the empty element
-#       }
-#   
-#       result = [ path.join $(tokens) ] ;
-#   
-#       if [ regex.match "(^.:)" : $(native)  ]
-#       {
-#           result = /$(result) ;
-#       }
-#       
-#       if $(native) = ""
-#       {
-#           result = "." ;
-#       }
-#           
-#       return $(result) ;
-#   }
-#   
-#   rule native-NT ( path )
-#   {
-#       local result = [ MATCH "^/?(.*)" : $(path) ] ;
-#       result = [ sequence.join [ regex.split $(result) "/" ] : "\\" ] ;
-#       return $(result) ;
-#   }
-#   
-#   rule make-CYGWIN ( path )
-#   {
-#       return [ make-NT $(path) ] ;
-#   }
-#   
-#   rule native-CYGWIN ( path )
-#   {
-#       local result = $(path) ;
-#       if [ regex.match "(^/.:)" : $(path)  ] # win absolute
-#       {
-#           result = [ MATCH "^/?(.*)" : $(path) ] ; # remove leading '/'
-#       }
-#       return [ native-UNIX $(result) ] ;
-#   }
-#   
-#   #
-#   # split-VMS: splits input native path into
-#   # device dir file (each part is optional),
-#   # example:
-#   #
-#   # dev:[dir]file.c => dev: [dir] file.c
-#   #
-#   rule split-path-VMS ( native )
-#   {
-#       local matches = [ MATCH ([a-zA-Z0-9_-]+:)?(\\[[^\]]*\\])?(.*)?$   : $(native) ] ;
-#       local device = $(matches[1]) ;
-#       local dir = $(matches[2]) ;
-#       local file = $(matches[3]) ;
-#   
-#       return $(device) $(dir) $(file) ;
-#   }
-#   
-#   #
-#   # Converts a native VMS path into a portable path spec.
-#   #
-#   # Does not handle current-device absolute paths such
-#   # as "[dir]File.c" as it is not clear how to represent
-#   # them in the portable path notation.
-#   #
-#   # Adds a trailing dot (".") to the file part if no extension
-#   # is present (helps when converting it back into native path).
-#   #
-#   rule make-VMS ( native )
-#   {
-#       if [ MATCH ^(\\[[a-zA-Z0-9]) : $(native) ]
-#       {
-#           errors.error "Can't handle default-device absolute paths: " $(native) ;
-#       }
-#           
-#       local parts = [ split-path-VMS $(native) ] ;
-#       local device = $(parts[1]) ;
-#       local dir = $(parts[2]) ;
-#       local file = $(parts[3]) ;
-#       local elems ;
-#       
-#       if $(device)
-#       {
-#           #
-#           # rooted
-#           #
-#           elems = /$(device) ;
-#       }
-#       
-#       if $(dir) = "[]"
-#       {
-#           #
-#           # Special case: current directory
-#           #
-#           elems = $(elems) "." ;
-#       }
-#       else if $(dir)
-#       {
-#           dir = [ regex.replace $(dir) "\\[|\\]" "" ] ;
-#           local dir_parts = [ regex.split $(dir) \\. ]  ;
-#       
-#           if $(dir_parts[1]) = ""
-#           {
-#               #
-#               # Relative path
-#               #
-#               dir_parts = $(dir_parts[2--1]) ;
-#           }
-#           
-#           #
-#           # replace "parent-directory" parts (- => ..)
-#           #
-#           dir_parts = [ regex.replace-list $(dir_parts) : - : .. ] ;
-#           
-#           elems = $(elems) $(dir_parts) ;
-#       }
-#       
-#       if $(file)
-#       {
-#           if ! [ MATCH (\\.) : $(file) ]
-#           {
-#               #
-#               # Always add "." to end of non-extension file
-#               #
-#               file = $(file). ;
-#           }
-#           elems = $(elems) $(file) ;
-#       }
-#   
-#       local portable = [ path.join $(elems) ] ;
-#   
-#       return $(portable) ;
-#   }
-#   
-#   #
-#   # Converts a portable path spec into a native VMS path.
-#   #
-#   # Relies on having at least one dot (".") included in the file
-#   # name to be able to differentiate it ftom the directory part.
-#   #
-#   rule native-VMS ( path )
-#   {
-#       local device = "" ;
-#       local dir = $(path) ;
-#       local file = "" ;
-#       local native ;
-#       local split ;
-#   
-#       #
-#       # Has device ?
-#       #
-#       if [ is-rooted $(dir) ]
-#       {
-#           split = [ MATCH ^/([^:]+:)/?(.*) : $(dir) ] ;
-#           device = $(split[1]) ;
-#           dir = $(split[2]) ;
-#       }
-#   
-#       #
-#       # Has file ?
-#       #
-#       # This is no exact science, just guess work:
-#       #
-#       # If the last part of the current path spec
-#       # includes some chars, followed by a dot,
-#       # optionally followed by more chars -
-#       # then it is a file (keep your fingers crossed).
-#       #
-#       split = [ regex.split $(dir) / ] ;
-#       local maybe_file = $(split[-1]) ;
-#   
-#       if [ MATCH ^([^.]+\\..*) : $(maybe_file) ]
-#       {
-#           file = $(maybe_file) ;
-#           dir = [ sequence.join $(split[1--2]) : / ] ;
-#       }
-#       
-#       #
-#       # Has dir spec ?
-#       #
-#       if $(dir) = "."
-#       {
-#           dir = "[]" ;
-#       }
-#       else if $(dir)
-#       {
-#           dir = [ regex.replace $(dir) \\.\\. - ] ;
-#           dir = [ regex.replace $(dir) / . ] ;
-#   
-#           if $(device) = ""
-#           {
-#               #
-#               # Relative directory
-#               # 
-#               dir = "."$(dir) ;
-#           }
-#           dir = "["$(dir)"]" ;
-#       }
-#       
-#       native = [ sequence.join $(device) $(dir) $(file) ] ;
-#   
-#       return $(native) ;
-#   }
-#   
-#   
-#   rule __test__ ( ) {
-#   
-#       import assert ;
-#       import errors : try catch ;
-#   
-#       assert.true is-rooted "/" ;
-#       assert.true is-rooted "/foo" ;
-#       assert.true is-rooted "/foo/bar" ;
-#       assert.result : is-rooted "." ;
-#       assert.result : is-rooted "foo" ;
-#       assert.result : is-rooted "foo/bar" ;
-#   
-#       assert.true has-parent "foo" ;
-#       assert.true has-parent "foo/bar" ;
-#       assert.true has-parent "." ;
-#       assert.result : has-parent "/" ;
-#   
-#       assert.result "." : basename "." ;
-#       assert.result ".." : basename ".." ;
-#       assert.result "foo" : basename "foo" ;
-#       assert.result "foo" : basename "bar/foo" ;
-#       assert.result "foo" : basename "gaz/bar/foo" ;
-#       assert.result "foo" : basename "/gaz/bar/foo" ;
-#   
-#       assert.result "." : parent "foo" ;
-#       assert.result "/" : parent "/foo" ;
-#       assert.result "foo/bar" : parent "foo/bar/giz" ;
-#       assert.result ".." : parent "." ;
-#       assert.result ".." : parent "../foo" ;
-#       assert.result "../../foo" : parent "../../foo/bar" ;
-#   
-#   
-#       assert.result "." : reverse "." ;
-#       assert.result ".." : reverse "foo" ;
-#       assert.result "../../.." : reverse "foo/bar/giz" ;
-#   
-#       assert.result "foo" : join "foo" ;
-#       assert.result "/foo" : join "/" "foo" ;
-#       assert.result "foo/bar" : join "foo" "bar" ;
-#       assert.result "foo/bar" : join "foo/giz" "../bar" ;
-#       assert.result "foo/giz" : join "foo/bar/baz" "../../giz" ;
-#       assert.result ".." : join "." ".." ;
-#       assert.result ".." : join "foo" "../.." ;
-#       assert.result "../.." : join "../foo" "../.." ;
-#       assert.result "/foo" : join "/bar" "../foo" ;
-#       assert.result "foo/giz" : join "foo/giz" "." ;
-#       assert.result "." : join lib2 ".." ;
-#       assert.result "/" : join "/a" ".." ;
-#   
-#       assert.result /a/b : join /a/b/c .. ;
-#   
-#       assert.result "foo/bar/giz" : join "foo" "bar" "giz" ;
-#       assert.result "giz" : join "foo" ".." "giz" ;
-#       assert.result "foo/giz" : join "foo" "." "giz" ;
-#   
-#       try ;
-#       {
-#           join "a" "/b" ;
-#       }
-#       catch only first element may be rooted ;
-#   
-#       local CWD = "/home/ghost/build" ;
-#       assert.result : all-parents . : . : $(CWD) ;
-#       assert.result . .. ../.. ../../..  : all-parents "Jamfile" : "" : $(CWD) ;
-#       assert.result foo . .. ../.. ../../.. : all-parents "foo/Jamfile" : "" : $(CWD) ;
-#       assert.result ../Work .. ../.. ../../.. : all-parents "../Work/Jamfile" : "" : $(CWD) ;
-#   
-#       local CWD = "/home/ghost" ;
-#       assert.result . .. : all-parents "Jamfile" : "/home" : $(CWD) ;
-#       assert.result . : all-parents "Jamfile" : "/home/ghost" : $(CWD) ;
-#       
-#       assert.result "c/d" : relative "a/b/c/d" "a/b" ;
-#       assert.result "foo" : relative "foo" "." ;
-#   
-#       local save-os = [ modules.peek path : os ] ;
-#       modules.poke path : os : NT ;
-#   
-#       assert.result "foo/bar/giz" : make "foo/bar/giz" ;
-#       assert.result "foo/bar/giz" : make "foo\\bar\\giz" ;
-#       assert.result "foo" : make "foo/." ;
-#       assert.result "foo" : make "foo/bar/.." ;
-#       assert.result "/D:/My Documents" : make "D:\\My Documents" ;
-#       assert.result "/c:/boost/tools/build/new/project.jam" : make "c:\\boost\\tools\\build\\test\\..\\new\\project.jam" ;
-#   
-#       assert.result "foo\\bar\\giz" : native "foo/bar/giz" ;
-#       assert.result "foo" : native "foo" ;
-#       assert.result "D:\\My Documents\\Work" : native "/D:/My Documents/Work" ;
-#   
-#       modules.poke path : os : UNIX ;
-#   
-#       assert.result "foo/bar/giz" : make "foo/bar/giz" ;
-#       assert.result "/sub1" : make "/sub1/." ;
-#       assert.result "/sub1" : make "/sub1/sub2/.." ;    
-#       assert.result "sub1" : make "sub1/." ;
-#       assert.result "sub1" : make "sub1/sub2/.." ;
-#       assert.result "/foo/bar" : native "/foo/bar" ;
-#   
-#       modules.poke path : os : VMS ;
-#   
-#       #
-#       # Don't really need to poke os before these
-#       #
-#       assert.result "disk:" "[dir]"  "file" : split-path-VMS "disk:[dir]file" ;
-#       assert.result "disk:" "[dir]"  ""     : split-path-VMS "disk:[dir]" ;
-#       assert.result "disk:" ""     ""       : split-path-VMS "disk:" ;
-#       assert.result "disk:" ""     "file"   : split-path-VMS "disk:file" ;
-#       assert.result ""      "[dir]"  "file" : split-path-VMS "[dir]file" ;
-#       assert.result ""      "[dir]"  ""     : split-path-VMS "[dir]" ;
-#       assert.result ""      ""     "file"   : split-path-VMS "file" ;
-#       assert.result ""      ""     ""       : split-path-VMS "" ;
-#   
-#       #
-#       # Special case: current directory
-#       #
-#       assert.result ""      "[]"     ""     : split-path-VMS "[]" ;
-#       assert.result "disk:" "[]"     ""     : split-path-VMS "disk:[]" ;
-#       assert.result ""      "[]"     "file" : split-path-VMS "[]file" ;
-#       assert.result "disk:" "[]"     "file" : split-path-VMS "disk:[]file" ;
-#   
-#       #
-#       # Make portable paths
-#       #
-#       assert.result "/disk:" : make "disk:" ;
-#       assert.result "foo/bar/giz" : make "[.foo.bar.giz]" ;
-#       assert.result "foo" : make "[.foo]" ;
-#       assert.result "foo" : make "[.foo.bar.-]" ;
-#       assert.result ".." : make "[.-]" ;
-#       assert.result ".." : make "[-]" ;
-#       assert.result "." : make "[]" ;
-#       assert.result "giz.h" : make "giz.h" ;
-#       assert.result "foo/bar/giz.h" : make "[.foo.bar]giz.h" ;
-#       assert.result "/disk:/my_docs" : make "disk:[my_docs]" ;
-#       assert.result "/disk:/boost/tools/build/new/project.jam" : make "disk:[boost.tools.build.test.-.new]project.jam" ;
-#   
-#       #
-#       # Special case (adds '.' to end of file w/o extension to
-#       # disambiguate from directory in portable path spec).
-#       #
-#       assert.result "Jamfile." : make "Jamfile" ;
-#       assert.result "dir/Jamfile." : make "[.dir]Jamfile" ;
-#       assert.result "/disk:/dir/Jamfile." : make "disk:[dir]Jamfile" ;
-#   
-#       #
-#       # Make native paths
-#       #
-#       assert.result "disk:" : native "/disk:" ;
-#       assert.result "[.foo.bar.giz]" : native "foo/bar/giz" ;
-#       assert.result "[.foo]" : native "foo" ;
-#       assert.result "[.-]" : native ".." ;
-#       assert.result "[.foo.-]" : native "foo/.." ;
-#       assert.result "[]" : native "." ;
-#       assert.result "disk:[my_docs.work]" : native "/disk:/my_docs/work" ;
-#       assert.result "giz.h" : native "giz.h" ;
-#       assert.result "disk:Jamfile." : native "/disk:Jamfile." ;
-#       assert.result "disk:[my_docs.work]Jamfile." : native "/disk:/my_docs/work/Jamfile." ;
-#   
-#       modules.poke path : os : $(save-os) ;
-#   
-#   }
-
-#
-
-
-#def glob(dir, patterns):
-#    result = []
-#    for pattern in patterns:
-#        result.extend(builtin_glob(os.path.join(dir, pattern)))
-#    return result
-
-def glob(dirs, patterns, exclude_patterns=None):
-    """Returns the list of files matching the given pattern in the
-    specified directory.  Both directories and patterns are 
-    supplied as portable paths. Each pattern should be non-absolute
-    path, and can't contain '.' or '..' elements. Each slash separated
-    element of pattern can contain the following special characters:
-    -  '?', which match any character
-    -  '*', which matches arbitrary number of characters.
-    A file $(d)/e1/e2/e3 (where 'd' is in $(dirs)) matches pattern p1/p2/p3
-    if and only if e1 matches p1, e2 matches p2 and so on.
-    For example: 
-        [ glob . : *.cpp ] 
-        [ glob . : */build/Jamfile ]
-    """
-
-    assert(isinstance(patterns, list))
-    assert(isinstance(dirs, list))
-
-    if not exclude_patterns:
-        exclude_patterns = []
-    else:
-       assert(isinstance(exclude_patterns, list))
-
-    real_patterns = [os.path.join(d, p) for p in patterns for d in dirs]    
-    real_exclude_patterns = [os.path.join(d, p) for p in exclude_patterns
-                             for d in dirs]
-
-    inc = [os.path.normpath(name) for p in real_patterns
-           for name in builtin_glob(p)]
-    exc = [os.path.normpath(name) for p in real_exclude_patterns
-           for name in builtin_glob(p)]
-    return [x for x in inc if x not in exc]
-
-def glob_tree(roots, patterns, exclude_patterns=None):
-    """Recursive version of GLOB. Builds the glob of files while
-    also searching in the subdirectories of the given roots. An
-    optional set of exclusion patterns will filter out the
-    matching entries from the result. The exclusions also apply
-    to the subdirectory scanning, such that directories that
-    match the exclusion patterns will not be searched."""
-
-    if not exclude_patterns:
-        exclude_patterns = []
-
-    result = glob(roots, patterns, exclude_patterns)
-    subdirs = [s for s in glob(roots, ["*"]) if s != "." and s != ".." and os.path.isdir(s)]
-    if subdirs:
-        result.extend(glob_tree(subdirs, patterns, exclude_patterns))
-        
-    return result
-
-def glob_in_parents(dir, patterns, upper_limit=None):
-    """Recursive version of GLOB which glob sall parent directories
-    of dir until the first match is found. Returns an empty result if no match
-    is found"""    
-    
-    assert(isinstance(dir, str))
-    assert(isinstance(patterns, list))
-
-    result = []
-
-    absolute_dir = os.path.join(os.getcwd(), dir)
-    absolute_dir = os.path.normpath(absolute_dir)
-    while absolute_dir:
-        new_dir = os.path.split(absolute_dir)[0]
-        if new_dir == absolute_dir:
-            break
-        result = glob([new_dir], patterns)
-        if result:
-            break
-        absolute_dir = new_dir
-
-    return result
-
-
-# The relpath functionality is written by
-# Cimarron Taylor
-def split(p, rest=[]):
-    (h,t) = os.path.split(p)
-    if len(h) < 1: return [t]+rest
-    if len(t) < 1: return [h]+rest
-    return split(h,[t]+rest)
-
-def commonpath(l1, l2, common=[]):
-    if len(l1) < 1: return (common, l1, l2)
-    if len(l2) < 1: return (common, l1, l2)
-    if l1[0] != l2[0]: return (common, l1, l2)
-    return commonpath(l1[1:], l2[1:], common+[l1[0]])
-
-def relpath(p1, p2):
-    (common,l1,l2) = commonpath(split(p1), split(p2))
-    p = []
-    if len(l1) > 0:
-        p = [ '../' * len(l1) ]
-    p = p + l2
-    if p:
-        return os.path.join( *p )
-    else:
-        return "."
diff --git a/jam-files/boost-build/util/print.jam b/jam-files/boost-build/util/print.jam
deleted file mode 100644
index 708d21ab..00000000
--- a/jam-files/boost-build/util/print.jam
+++ /dev/null
@@ -1,488 +0,0 @@
-# Copyright 2003 Douglas Gregor 
-# Copyright 2002, 2003, 2005 Rene Rivera 
-# Copyright 2002, 2003, 2004, 2005 Vladimir Prus 
-# Distributed under the Boost Software License, Version 1.0. 
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt) 
-
-# Utilities for generating format independent output. Using these
-# will help in generation of documentation in at minimum plain/console
-# and html.
-
-import modules ;
-import numbers ;
-import string ;
-import regex ;
-import "class" ;
-import scanner ;
-import path ;
-
-# The current output target. Defaults to console.
-output-target = console ;
-
-# The current output type. Defaults to plain. Other possible values are "html".
-output-type = plain ;
-
-# Whitespace.
-.whitespace = [ string.whitespace ] ;
-
-
-# Set the target and type of output to generate. This sets both the destination
-# output and the type of docs to generate to that output. The target can be
-# either a file or "console" for echoing to the console. If the type of output
-# is not specified it defaults to plain text.
-#
-rule output (
-    target  # The target file or device; file or "console".
-    type ?  # The type of output; "plain" or "html".
-)
-{
-    type ?= plain ;
-    if $(output-target) != $(target)
-    {
-        output-target = $(target) ;
-        output-type = $(type) ;
-        if $(output-type) = html
-        {
-            text
-                "<!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.01 Transitional//EN\">"
-                "<html>"
-                "<head>"
-                "</head>"
-                "<body link=\"#0000ff\" vlink=\"#800080\">"
-                : true
-                : prefix ;
-            text
-                "</body>"
-                "</html>"
-                :
-                : suffix ;
-        }
-    }
-}
-
-
-# Generate a section with a description. The type of output can be controlled by
-# the value of the 'output-type' variable.
-#
-rule section (
-    name  # The name of the section.
-    description *  # A number of description lines.
-)
-{
-    if $(output-type) = plain
-    {
-        lines [ split-at-words $(name): ] ;
-        lines ;
-    }
-    else if $(output-type) = html
-    {
-        name = [ escape-html $(name) ] ;
-        text <h3>$(name)</h3> <p> ;
-    }
-    local pre = ;
-    while $(description)
-    {
-        local paragraph = ;
-        while $(description) && [ string.is-whitespace $(description[1]) ] { description = $(description[2-]) ; }
-        if $(pre)
-        {
-            while $(description) && (
-                $(pre) = " $(description[1])" ||
-                ( $(pre) < [ string.chars [ MATCH "^([$(.whitespace)]*)" : " $(description[1])" ] ] )
-                )
-                { paragraph += $(description[1]) ; description = $(description[2-]) ; }
-            while [ string.is-whitespace $(paragraph[-1]) ] { paragraph = $(paragraph[1--2]) ; }
-            pre = ;
-            if $(output-type) = plain
-            {
-                lines $(paragraph) "" : "  " "  " ;
-            }
-            else if $(output-type) = html
-            {
-                text <blockquote> ;
-                lines $(paragraph) ;
-                text </blockquote> ;
-            }
-        }
-        else
-        {
-            while $(description) && ! [ string.is-whitespace $(description[1]) ]
-                { paragraph += $(description[1]) ; description = $(description[2-]) ; }
-            if $(paragraph[1]) = :: && ! $(paragraph[2])
-            {
-                pre = " " ;
-            }
-            if $(paragraph[1]) = ::
-            {
-                if $(output-type) = plain
-                {
-                    lines $(paragraph[2-]) "" : "  " "  " ;
-                    lines ;
-                }
-                else if $(output-type) = html
-                {
-                    text <blockquote> ;
-                    lines $(paragraph[2-]) ;
-                    text </blockquote> ;
-                }
-            }
-            else
-            {
-                local p = [ MATCH "(.*)(::)$" : $(paragraph[-1]) ] ;
-                local pws = [ MATCH "([ 	]*)$" : $(p[1]) ] ;
-                p = [ MATCH "(.*)($(pws))($(p[2]))$" :  $(paragraph[-1]) ] ;
-                if $(p[3]) = ::
-                {
-                    pre = [ string.chars [ MATCH "^([$(.whitespace)]*)" : " $(p[1])" ] ] ;
-                    if ! $(p[2]) || $(p[2]) = "" { paragraph = $(paragraph[1--2]) $(p[1]): ; }
-                    else { paragraph = $(paragraph[1--2]) $(p[1]) ; }
-                    if $(output-type) = plain
-                    {
-                        lines [ split-at-words " " $(paragraph) ] : "  " "  " ;
-                        lines ;
-                    }
-                    else if $(output-type) = html
-                    {
-                        text </p> <p> [ escape-html $(paragraph) ] ;
-                    }
-                }
-                else
-                {
-                    if $(output-type) = plain
-                    {
-                        lines [ split-at-words " " $(paragraph) ] : "  " "  " ;
-                        lines ;
-                    }
-                    else if $(output-type) = html
-                    {
-                        text </p> <p> [ escape-html $(paragraph) ] ;
-                    }
-                }
-            }
-        }
-    }
-    if $(output-type) = html
-    {
-        text </p> ;
-    }
-}
-
-
-# Generate the start of a list of items. The type of output can be controlled by
-# the value of the 'output-type' variable.
-#
-rule list-start ( )
-{
-    if $(output-type) = plain
-    {
-    }
-    else if $(output-type) = html
-    {
-        text <ul> ;
-    }
-}
-
-
-# Generate an item in a list. The type of output can be controlled by the value
-# of the 'output-type' variable.
-#
-rule list-item (
-    item +  # The item to list.
-)
-{
-    if $(output-type) = plain
-    {
-        lines [ split-at-words "*" $(item) ] : "    " "  " ;
-    }
-    else if $(output-type) = html
-    {
-        text <li> [ escape-html $(item) ] </li> ;
-    }
-}
-
-
-# Generate the end of a list of items. The type of output can be controlled by
-# the value of the 'output-type' variable.
-#
-rule list-end ( )
-{
-    if $(output-type) = plain
-    {
-        lines ;
-    }
-    else if $(output-type) = html
-    {
-        text </ul> ;
-    }
-}
-
-
-# Split the given text into separate lines, word-wrapping to a margin. The
-# default margin is 78 characters.
-#
-rule split-at-words (
-    text +  # The text to split.
-    : margin ?  # An optional margin, default is 78.
-)
-{
-    local lines = ;
-    text = [ string.words $(text:J=" ") ] ;
-    text = $(text:J=" ") ;
-    margin ?= 78 ;
-    local char-match-1 = ".?" ;
-    local char-match = "" ;
-    while $(margin) != 0
-    {
-        char-match = $(char-match)$(char-match-1) ;
-        margin = [ numbers.decrement $(margin) ] ;
-    }
-    while $(text)
-    {
-        local s = "" ;
-        local t = "" ;
-        # divide s into the first X characters and the rest
-        s = [ MATCH "^($(char-match))(.*)" : $(text) ] ;
-        
-        if $(s[2])
-        {
-            # split the first half at a space
-            t = [ MATCH "^(.*)[\\ ]([^\\ ]*)$" : $(s[1]) ] ;
-        }
-        else
-        {
-            t = $(s) ;
-        }
-        
-        if ! $(t[2])
-        {
-            t += "" ;
-        }
-        
-        text = $(t[2])$(s[2]) ;
-        lines += $(t[1]) ;
-    }
-    return $(lines) ;
-}
-
-
-# Generate a set of fixed lines. Each single item passed in is output on a
-# separate line. For console this just echos each line, but for html this will
-# split them with <br>.
-#
-rule lines (
-    text *  # The lines of text.
-    : indent ?  # Optional indentation prepended to each line after the first one.
-    outdent ?  # Optional indentation to prepend to the first line.
-)
-{
-    text ?= "" ;
-    indent ?= "" ;
-    outdent ?= "" ;
-    if $(output-type) = plain
-    {
-        text $(outdent)$(text[1]) $(indent)$(text[2-]) ;
-    }
-    else if $(output-type) = html
-    {
-        local indent-chars = [ string.chars $(indent) ] ;
-        indent = "" ;
-        for local c in $(indent-chars)
-        {
-            if $(c) = " " { c = "&nbsp;" ; }
-            else if $(c) = "	" { c = "&nbsp;&nbsp;&nbsp;&nbsp;" ; }
-            indent = $(indent)$(c) ;
-        }
-        local html-text = [ escape-html $(text) : "&nbsp;" ] ;
-        text $(html-text[1])<br> $(indent)$(html-text[2-])<br> ;
-    }
-}
-
-
-# Output text directly to the current target. When doing output to a file, one
-# can indicate if the text should be output to "prefix" it, as the "body"
-# (default), or "suffix" of the file. This is independant of the actual
-# execution order of the text rule. This rule invokes a singular action, one
-# action only once, which does the build of the file. Therefore actions on the
-# target outside of this rule will happen entirely before and/or after all
-# output using this rule.
-#
-rule text (
-    strings *  # The strings of text to output.
-    : overwrite ?  # true to overwrite the output (if it is a file)
-    : prefix-body-suffix ?  # Indication to output prefix, body, or suffix (for a file).
-)
-{
-    prefix-body-suffix ?= body ;
-    if $(output-target) = console
-    {
-        if ! $(strings)
-        {
-            ECHO ;
-        }
-        else
-        {
-            for local s in $(strings)
-            {
-                ECHO $(s) ;
-            }
-        }
-    }
-    if ! $($(output-target).did-action)
-    {
-        $(output-target).did-action = yes ;
-        $(output-target).text-prefix = ;
-        $(output-target).text-body = ;
-        $(output-target).text-suffix = ;
-        
-        nl on $(output-target) = "
-" ;
-        text-redirect on $(output-target) = ">>" ;
-        if $(overwrite)
-        {
-            text-redirect on $(output-target) = ">" ;
-        }
-        text-content on $(output-target) = ;
-        
-        text-action $(output-target) ;
-
-        if $(overwrite) && $(output-target) != console
-        {
-            check-for-update $(output-target) ;
-        }
-    }
-    $(output-target).text-$(prefix-body-suffix) += $(strings) ;
-    text-content on $(output-target) =
-        $($(output-target).text-prefix)
-        $($(output-target).text-body)
-        $($(output-target).text-suffix) ;
-}
-
-
-# Outputs the text to the current targets, after word-wrapping it.
-#
-rule wrapped-text ( text + )
-{
-    local lines = [ split-at-words $(text) ] ;
-    text $(lines) ;
-}
-
-
-# Escapes text into html/xml printable equivalents. Does not know about tags and
-# therefore tags fed into this will also be escaped. Currently escapes space,
-# "<", ">", and "&".
-#
-rule escape-html (
-    text +  # The text to escape.
-    : space ?  # What to replace spaces with, defaults to " ".
-)
-{
-    local html-text = ;
-    while $(text)
-    {
-        local html = $(text[1]) ;
-        text = $(text[2-]) ;
-        html = [ regex.replace $(html) "&" "&amp;" ] ;
-        html = [ regex.replace $(html) "<" "&lt;" ] ;
-        html = [ regex.replace $(html) ">" "&gt;" ] ;
-        if $(space)
-        {
-            html = [ regex.replace $(html) " " "$(space)" ] ;
-        }
-        html-text += $(html) ;
-    }
-    return $(html-text) ;
-}
-
-
-# Outputs the text strings collected by the text rule to the output file.
-#
-actions quietly text-action
-{
-    @($(STDOUT):E=$(text-content:J=$(nl))) $(text-redirect) "$(<)"
-}
-
-
-rule get-scanner ( )
-{
-    if ! $(.scanner)
-    {
-        .scanner = [ class.new print-scanner ] ;
-    }
-    return $(.scanner) ;
-}
-
-
-# The following code to update print targets when their contents
-# change is a horrible hack.  It basically creates a target which
-# binds to this file (print.jam) and installs a scanner on it
-# which reads the target and compares its contents to the new
-# contents that we're writing.
-#
-rule check-for-update ( target )
-{
-    local scanner = [ get-scanner ] ;
-    local file = [ path.native [ modules.binding $(__name__) ] ] ;
-    local g = [ MATCH <(.*)> : $(target:G) ] ;
-    local dependency-target = $(__file__:G=$(g:E=)-$(target:G=)-$(scanner)) ;
-    DEPENDS $(target) : $(dependency-target) ;
-    SEARCH on $(dependency-target) = $(file:D) ;
-    ISFILE $(dependency-target) ;
-    NOUPDATE $(dependency-target) ;
-    base on $(dependency-target) = $(target) ;
-    scanner.install $(scanner) : $(dependency-target) none ;
-    return $(dependency-target) ;
-}
-
-
-class print-scanner : scanner
-{
-    import path ;
-    import os ;
-
-    rule pattern ( )
-    {
-        return "(One match...)" ;
-    }
-
-    rule process ( target : matches * : binding )
-    {
-        local base = [ on $(target) return $(base) ] ;
-        local nl = [ on $(base) return $(nl) ] ;
-        local text-content = [ on $(base) return $(text-content) ] ;
-        local dir = [ on $(base) return $(LOCATE) ] ;
-        if $(dir)
-        {
-            dir = [ path.make $(dir) ] ;
-        }
-        local file = [ path.native [ path.join $(dir) $(base:G=) ] ] ;
-        local actual-content ;
-        if [ os.name ] = NT
-        {
-            actual-content = [ SHELL "type \"$(file)\" 2>nul" ] ;
-        }
-        else
-        {
-            actual-content = [ SHELL "cat \"$(file)\" 2>/dev/null" ] ;
-        }
-        if $(text-content:J=$(nl)) != $(actual-content)
-        {
-            ALWAYS $(base) ;
-        }
-    }
-}
-
-
-rule __test__ ( )
-{
-    import assert ;
-    
-    assert.result one two three   : split-at-words one two three : 5 ;
-    assert.result "one two" three : split-at-words one two three : 8 ;
-    assert.result "one two" three : split-at-words one two three : 9 ;
-    assert.result "one two three" : split-at-words one two three ;
-
-    # VP, 2004-12-03 The following test fails for some reason, so commenting it
-    # out.
-    #assert.result "one&nbsp;two&nbsp;three" "&amp;&lt;&gt;" :
-    #    escape-html "one two three" "&<>" ;
-}
diff --git a/jam-files/boost-build/util/regex.jam b/jam-files/boost-build/util/regex.jam
deleted file mode 100644
index 234c36f6..00000000
--- a/jam-files/boost-build/util/regex.jam
+++ /dev/null
@@ -1,193 +0,0 @@
-# Copyright 2001, 2002 Dave Abrahams
-# Copyright 2003 Douglas Gregor
-# Copyright 2003 Rene Rivera
-# Copyright 2002, 2003, 2004, 2005 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-#
-#   Returns a list of the following substrings:
-#   1) from beginning till the first occurrence of 'separator' or till the end,
-#   2) between each occurrence of 'separator' and the next occurrence,
-#   3) from the last occurrence of 'separator' till the end.
-#   If no separator is present, the result will contain only one element.
-#
-
-rule split ( string separator )
-{
-    local result ;
-    local s = $(string) ;
-
-    # Break pieaces off 's' until it has no separators left.
-    local match = 1 ;
-    while $(match)
-    {
-        match = [ MATCH ^(.*)($(separator))(.*) : $(s) ] ;
-        if $(match)
-        {
-            match += "" ;  # in case 3rd item was empty - works around MATCH bug
-            result = $(match[3]) $(result) ;
-            s = $(match[1]) ;
-        }
-    }
-    # Combine the remaining part at the beginning, which does not have
-    # separators, with the pieces broken off. Note that the rule's signature
-    # does not allow the initial s to be empty.
-    return $(s) $(result) ;
-}
-
-
-# Returns the concatenated results of Applying regex.split to every element of
-# the list using the separator pattern.
-#
-rule split-list ( list * : separator )
-{
-    local result ;
-    for s in $(list)
-    {
-        result += [ split $(s) $(separator) ] ;
-    }
-    return $(result) ;
-}
-
-
-# Match string against pattern, and return the elements indicated by indices.
-#
-rule match ( pattern : string : indices * )
-{
-    indices ?= 1 2 3 4 5 6 7 8 9 ;
-    local x = [ MATCH $(pattern) : $(string) ] ;
-    return $(x[$(indices)]) ;
-}
-
-
-# Matches all elements of 'list' agains the 'pattern' and returns a list of
-# elements indicated by indices of all successful matches. If 'indices' is
-# omitted returns a list of first paranthethised groups of all successful
-# matches.
-#
-rule transform ( list * : pattern : indices * )
-{
-    indices ?= 1 ;
-    local result ;
-    for local e in $(list)
-    {
-        local m = [ MATCH $(pattern) : $(e) ] ;
-        if $(m)
-        {
-            result += $(m[$(indices)]) ;
-        }
-    }
-    return $(result) ;
-}
-
-NATIVE_RULE regex : transform ;
-
-
-# Escapes all of the characters in symbols using the escape symbol escape-symbol
-# for the given string, and returns the escaped string.
-#
-rule escape ( string : symbols : escape-symbol )
-{
-    local result = "" ;
-    local m = 1 ;
-    while $(m)
-    {
-        m = [ MATCH ^([^$(symbols)]*)([$(symbols)])(.*) : $(string) ] ;
-        if $(m)
-        {
-            m += "" ;  # Supposedly a bug fix; borrowed from regex.split
-            result = "$(result)$(m[1])$(escape-symbol)$(m[2])" ;
-            string = $(m[3]) ;
-        }
-    }
-    string ?= "" ;
-    result = "$(result)$(string)" ;
-    return $(result) ;
-}
-
-
-# Replaces occurrences of a match string in a given string and returns the new
-# string. The match string can be a regex expression.
-#
-rule replace (
-    string  # The string to modify.
-    match  # The characters to replace.
-    replacement  # The string to replace with.
-    )
-{
-    local result = "" ;
-    local parts = 1 ;
-    while $(parts)
-    {
-        parts = [ MATCH ^(.*)($(match))(.*) : $(string) ] ;
-        if $(parts)
-        {
-            parts += "" ;
-            result = "$(replacement)$(parts[3])$(result)" ;
-            string = $(parts[1]) ;
-        }
-    }
-    string ?= "" ;
-    result = "$(string)$(result)" ;
-    return $(result) ;
-}
-
-
-# Replaces occurrences of a match string in a given list of strings and returns
-# a list of new strings. The match string can be a regex expression.
-#
-# list        - the list of strings to modify.
-# match       - the search expression.
-# replacement - the string to replace with.
-#
-rule replace-list ( list * : match : replacement )
-{
-    local result ;
-    for local e in $(list)
-    {
-        result += [ replace $(e) $(match) $(replacement) ] ;
-    }
-    return $(result) ;
-}
-
-
-rule __test__ ( )
-{
-    import assert ;
-
-    assert.result a b c : split "a/b/c" / ;
-    assert.result "" a b c : split "/a/b/c" / ;
-    assert.result "" "" a b c : split "//a/b/c" / ;
-    assert.result "" a "" b c : split "/a//b/c" / ;
-    assert.result "" a "" b c "" : split "/a//b/c/" / ;
-    assert.result "" a "" b c "" "" : split "/a//b/c//" / ;
-
-    assert.result a c b d
-        : match (.)(.)(.)(.) : abcd : 1 3 2 4 ;
-
-    assert.result a b c d
-        : match (.)(.)(.)(.) : abcd ;
-
-    assert.result ababab cddc
-        : match ((ab)*)([cd]+) : abababcddc : 1 3 ;
-
-    assert.result a.h c.h
-        : transform <a.h> \"b.h\" <c.h> : <(.*)> ;
-
-    assert.result a.h b.h c.h
-        : transform <a.h> \"b.h\" <c.h> : <([^>]*)>|\"([^\"]*)\" : 1 2 ;
-
-    assert.result "^<?xml version=\"1.0\"^>"
-        : escape "<?xml version=\"1.0\">" : "&|()<>^" : "^" ;
-
-    assert.result "<?xml version=\\\"1.0\\\">"
-        : escape "<?xml version=\"1.0\">" : "\\\"" : "\\" ;
-
-    assert.result "string&nbsp;string&nbsp;" : replace "string string " " " "&nbsp;" ;
-    assert.result "&nbsp;string&nbsp;string" : replace " string string" " " "&nbsp;" ;
-    assert.result "string&nbsp;&nbsp;string" : replace "string  string" " " "&nbsp;" ;
-    assert.result "-" : replace "&" "&" "-" ;
-
-    assert.result "-" "a-b" : replace-list "&" "a&b" : "&" : "-" ;
-}
diff --git a/jam-files/boost-build/util/regex.py b/jam-files/boost-build/util/regex.py
deleted file mode 100644
index 29e26ecf..00000000
--- a/jam-files/boost-build/util/regex.py
+++ /dev/null
@@ -1,25 +0,0 @@
-#  (C) Copyright David Abrahams 2001. Permission to copy, use, modify, sell and
-#  distribute this software is granted provided this copyright notice appears in
-#  all copies. This software is provided "as is" without express or implied
-#  warranty, and with no claim as to its suitability for any purpose.
-
-import re
-
-def transform (list, pattern, indices = [1]):
-    """ Matches all elements of 'list' agains the 'pattern' 
-        and returns a list of the elements indicated by indices of 
-        all successfull matches. If 'indices' is omitted returns
-        a list of first paranthethised groups of all successfull
-        matches.
-    """
-    result = []
-
-    for e in list:
-        m = re.match (pattern, e)
-
-        if m:
-            for i in indices:
-                result.append (m.group (i))
-
-    return result
-
diff --git a/jam-files/boost-build/util/sequence.jam b/jam-files/boost-build/util/sequence.jam
deleted file mode 100644
index 73919a65..00000000
--- a/jam-files/boost-build/util/sequence.jam
+++ /dev/null
@@ -1,335 +0,0 @@
-# Copyright 2001, 2002, 2003 Dave Abrahams 
-# Copyright 2006 Rene Rivera 
-# Copyright 2002, 2003 Vladimir Prus 
-# Distributed under the Boost Software License, Version 1.0. 
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt) 
-
-import assert ;
-import numbers ; 
-import modules ;
-
-
-# Note that algorithms in this module execute largely in the caller's module
-# namespace, so that local rules can be used as function objects. Also note that
-# most predicates can be multi-element lists. In that case, all but the first
-# element are prepended to the first argument which is passed to the rule named
-# by the first element.
-
-
-# Return the elements e of $(sequence) for which [ $(predicate) e ] has a
-# non-null value.
-#
-rule filter ( predicate + : sequence * )
-{
-    local caller = [ CALLER_MODULE ] ;
-    local result ;
-
-    for local e in $(sequence)
-    {
-        if [ modules.call-in $(caller) : $(predicate) $(e) ]
-        {
-            result += $(e) ;
-        }
-    }
-    return $(result) ;
-}
-
-
-# Return a new sequence consisting of [ $(function) $(e) ] for each element e of
-# $(sequence).
-#
-rule transform ( function + : sequence * )
-{
-    local caller = [ CALLER_MODULE ] ;
-    local result ;
-
-    for local e in $(sequence)
-    {
-        result += [ modules.call-in $(caller) : $(function) $(e) ] ;
-    }
-    return $(result) ;
-}
-
-
-rule reverse ( s * )
-{
-    local r ;
-    for local x in $(s)
-    {
-        r = $(x) $(r) ;
-    }
-    return $(r) ;
-}
-
-
-rule less ( a b )
-{
-    if $(a) < $(b)
-    {
-        return true ;
-    }
-}
-
-
-# Insertion-sort s using the BinaryPredicate ordered.
-#
-rule insertion-sort ( s * : ordered * )
-{
-    if ! $(ordered)
-    {
-        return [ SORT $(s) ] ;
-    }
-    else 
-    {           
-        local caller = [ CALLER_MODULE ] ;
-        ordered ?= sequence.less ;
-        local result = $(s[1]) ;
-        if $(ordered) = sequence.less
-        {
-            local head tail ;
-            for local x in $(s[2-])
-            {
-                head = ;
-                tail = $(result) ;
-                while $(tail) && ( $(tail[1]) < $(x) )
-                {
-                    head += $(tail[1]) ;
-                    tail = $(tail[2-]) ;
-                }
-                result = $(head) $(x) $(tail) ;
-            }
-        }
-        else
-        {
-            for local x in $(s[2-])
-            {
-                local head tail ;
-                tail = $(result) ;
-                while $(tail) && [ modules.call-in $(caller) : $(ordered) $(tail[1]) $(x) ]
-                {
-                    head += $(tail[1]) ;
-                    tail = $(tail[2-]) ;
-                }
-                result = $(head) $(x) $(tail) ;
-            }
-        }
-        
-        return $(result) ;
-    }    
-}
-
-
-# Merge two ordered sequences using the BinaryPredicate ordered.
-#
-rule merge ( s1 * : s2 * : ordered * )
-{
-    ordered ?= sequence.less ;
-    local result__ ;
-    local caller = [ CALLER_MODULE ] ;
-
-    while $(s1) && $(s2)
-    {
-        if [ modules.call-in $(caller) : $(ordered) $(s1[1]) $(s2[1]) ]
-        {
-            result__ += $(s1[1]) ;
-            s1 = $(s1[2-]) ;
-        }
-        else if [ modules.call-in $(caller) : $(ordered) $(s2[1]) $(s1[1]) ]
-        {
-            result__ += $(s2[1]) ;
-            s2 = $(s2[2-]) ;
-        }
-        else 
-        {           
-            s2 = $(s2[2-]) ;
-        }
-        
-    }
-    result__ += $(s1) ;
-    result__ += $(s2) ;
-
-    return $(result__) ;
-}
-
-
-# Join the elements of s into one long string. If joint is supplied, it is used
-# as a separator.
-#
-rule join ( s * : joint ? )
-{
-    joint ?= "" ;
-    return $(s:J=$(joint)) ;
-}
-
-
-# Find the length of any sequence.
-#
-rule length ( s * )
-{
-    local result = 0 ;
-    for local i in $(s)
-    {
-        result = [ CALC $(result) + 1 ] ;
-    }
-    return $(result) ;
-}
-
-
-rule unique ( list * : stable ? )
-{
-    local result ;
-    local prev ;
-    if $(stable)
-    {
-        for local f in $(list)
-        {
-            if ! $(f) in $(result)
-            {
-                result += $(f) ;
-            }
-        }
-    }
-    else
-    {
-        for local i in [ SORT $(list) ]
-        {
-            if $(i) != $(prev)
-            {
-                result += $(i) ;
-            }
-            prev = $(i) ;
-        }
-    }
-    return $(result) ;
-}
-
-
-# Returns the maximum number in 'elements'. Uses 'ordered' for comparisons or
-# 'numbers.less' if none is provided.
-#
-rule max-element ( elements + : ordered ? )
-{
-    ordered ?= numbers.less ;
-
-    local max = $(elements[1]) ;
-    for local e in $(elements[2-]) 
-    {
-        if [ $(ordered) $(max) $(e) ] 
-        {
-            max = $(e) ;
-        }
-    }
-    return $(max) ;           
-}
-
-
-# Returns all of 'elements' for which corresponding element in parallel list
-# 'rank' is equal to the maximum value in 'rank'.
-#
-rule select-highest-ranked ( elements * : ranks * )
-{
-    if $(elements)
-    {        
-        local max-rank = [ max-element $(ranks) ] ;
-        local result ;
-        while $(elements) 
-        {
-            if $(ranks[1]) = $(max-rank)
-            {
-                result += $(elements[1]) ;
-            }
-            elements = $(elements[2-]) ;
-            ranks = $(ranks[2-]) ;
-        }
-        return $(result) ;
-    }    
-}
-NATIVE_RULE sequence : select-highest-ranked ;
-
-
-rule __test__ ( )
-{
-    # Use a unique module so we can test the use of local rules.
-    module sequence.__test__
-    {
-        import assert ;
-        import sequence ;
-        
-        local rule is-even ( n )
-        {
-            if $(n) in 0 2 4 6 8
-            {
-                return true ;
-            }
-        }
-
-        assert.result 4 6 4 2 8 : sequence.filter is-even : 1 4 6 3 4 7 2 3 8 ;
-
-        # Test that argument binding works.
-        local rule is-equal-test ( x y )
-        {
-            if $(x) = $(y)
-            {
-                return true ;
-            }
-        }
-
-        assert.result 3 3 3 : sequence.filter is-equal-test 3 : 1 2 3 4 3 5 3 5 7 ;
-
-        local rule append-x ( n )
-        {
-            return $(n)x ;
-        }
-
-        assert.result 1x 2x 3x : sequence.transform append-x : 1 2 3 ;
-
-        local rule repeat2 ( x )
-        {
-            return $(x) $(x) ;
-        }
-
-        assert.result 1 1 2 2 3 3 : sequence.transform repeat2 : 1 2 3 ;
-
-        local rule test-greater ( a b )
-        {
-            if $(a) > $(b)
-            {
-                return true ;
-            }
-        }
-        assert.result 1 2 3 4 5 6 7 8 9 : sequence.insertion-sort 9 6 5 3 8 7 1 2 4 ;
-        assert.result 9 8 7 6 5 4 3 2 1 : sequence.insertion-sort 9 6 5 3 8 7 1 2 4 : test-greater ;
-        assert.result 1 2 3 4 5 6 :  sequence.merge 1 3 5 : 2 4 6 ;
-        assert.result 6 5 4 3 2 1 :  sequence.merge 5 3 1 : 6 4 2 : test-greater ;
-        assert.result 1 2 3 : sequence.merge 1 2 3 : ;
-        assert.result 1 : sequence.merge 1 : 1 ;
-
-        assert.result foo-bar-baz : sequence.join foo bar baz : - ;
-        assert.result substandard : sequence.join sub stan dard ;
-        assert.result 3.0.1 : sequence.join 3.0.1 : - ;
-
-        assert.result 0 : sequence.length ;
-        assert.result 3 : sequence.length a b c ;
-        assert.result 17 : sequence.length 17 16 15 14 13 12 11 10 9 8 7 6 5 4 3 2 1 ;
-
-        assert.result 1 : sequence.length a ;
-        assert.result 10 : sequence.length a b c d e f g h i j ;
-        assert.result 11 : sequence.length a b c d e f g h i j k ;
-        assert.result 12 : sequence.length a b c d e f g h i j k l ;
-
-        local p2 = x ;
-        for local i in 1 2 3 4 5 6 7 8
-        {
-            p2 = $(p2) $(p2) ;
-        }
-        assert.result 256 : sequence.length $(p2) ;
-
-        assert.result 1 2 3 4 5 : sequence.unique 1 2 3 2 4 3 3 5 5 5 ;
-                
-        assert.result 5 : sequence.max-element 1 3 5 0 4 ;
-        
-        assert.result e-3 h-3 : sequence.select-highest-ranked e-1 e-3 h-3 m-2 : 1 3 3 2 ;
-        
-        assert.result 7 6 5 4 3 2 1 : sequence.reverse 1 2 3 4 5 6 7 ;
-    }
-}
diff --git a/jam-files/boost-build/util/sequence.py b/jam-files/boost-build/util/sequence.py
deleted file mode 100644
index 1d32efd2..00000000
--- a/jam-files/boost-build/util/sequence.py
+++ /dev/null
@@ -1,50 +0,0 @@
-#  (C) Copyright David Abrahams 2002. Permission to copy, use, modify, sell and
-#  distribute this software is granted provided this copyright notice appears in
-#  all copies. This software is provided "as is" without express or implied
-#  warranty, and with no claim as to its suitability for any purpose.
-
-import operator
-
-def unique (values, stable=False):
-    if stable:
-        s = set()
-        r = []
-        for v in values:
-            if not v in s:
-                r.append(v)
-                s.add(v)
-        return r
-    else:
-        return list(set(values))
-
-def max_element (elements, ordered = None):
-    """ Returns the maximum number in 'elements'. Uses 'ordered' for comparisons,
-        or '<' is none is provided.
-    """
-    if not ordered: ordered = operator.lt
-
-    max = elements [0]
-    for e in elements [1:]:
-        if ordered (max, e):
-            max = e
-
-    return max
-
-def select_highest_ranked (elements, ranks):
-    """ Returns all of 'elements' for which corresponding element in parallel
-        list 'rank' is equal to the maximum value in 'rank'.
-    """
-    if not elements:
-        return []
-
-    max_rank = max_element (ranks)
-
-    result = []
-    while elements:
-        if ranks [0] == max_rank:
-            result.append (elements [0])
-
-        elements = elements [1:]
-        ranks = ranks [1:]
-
-    return result
diff --git a/jam-files/boost-build/util/set.jam b/jam-files/boost-build/util/set.jam
deleted file mode 100644
index fc179134..00000000
--- a/jam-files/boost-build/util/set.jam
+++ /dev/null
@@ -1,93 +0,0 @@
-# Copyright 2001, 2002 Dave Abrahams
-# Copyright 2003 Vladimir Prus
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-class set
-{
-    rule __init__ ( )
-    {
-    }  
-    
-    rule add ( elements * )
-    {
-        for local e in $(elements)
-        {
-            if ! $($(e))
-            {
-                $(e) = 1 ;
-                self.result += $(e) ;
-            }            
-        }        
-    }    
-    
-    rule contains ( element )
-    {
-        return $($(element)) ;
-    }
-    
-    rule list ( )
-    {
-        return $(self.result) ;
-    }            
-}
-
-
-
-# Returns the elements of set1 that are not in set2.
-#
-rule difference ( set1 * : set2 * )
-{
-    local result = ;
-    for local element in $(set1)
-    {
-        if ! ( $(element) in $(set2) )
-        {
-            result += $(element) ;
-        }
-    }
-    return $(result) ;
-}
-
-NATIVE_RULE set : difference ;
-
-
-# Removes all the items appearing in both set1 & set2.
-#
-rule intersection ( set1 * : set2 * )
-{
-    local result ;
-    for local v in $(set1)
-    {
-        if $(v) in $(set2)
-        {
-            result += $(v) ;
-        }
-    }
-    return $(result) ;
-}
-
-
-# Returns whether set1 & set2 contain the same elements. Note that this ignores
-# any element ordering differences as well as any element duplication.
-#
-rule equal ( set1 * : set2 * )
-{
-    if $(set1) in $(set2) && ( $(set2) in $(set1) )
-    {
-        return true ;
-    }
-}
-
-
-rule __test__ ( )
-{
-    import assert ;
-
-    assert.result 0 1 4 6 8 9 : difference   0 1 2 3 4 5 6 7 8 9 : 2 3 5 7 ;
-    assert.result 2 5 7       : intersection 0 1 2   4 5 6 7 8 9 : 2 3 5 7 ;
-
-    assert.true  equal         :         ;
-    assert.true  equal 1 1 2 3 : 3 2 2 1 ;
-    assert.false equal 2 3     : 3 2 2 1 ;
-}
diff --git a/jam-files/boost-build/util/set.py b/jam-files/boost-build/util/set.py
deleted file mode 100644
index dc7cf328..00000000
--- a/jam-files/boost-build/util/set.py
+++ /dev/null
@@ -1,42 +0,0 @@
-#  (C) Copyright David Abrahams 2001. Permission to copy, use, modify, sell and
-#  distribute this software is granted provided this copyright notice appears in
-#  all copies. This software is provided "as is" without express or implied
-#  warranty, and with no claim as to its suitability for any purpose.
-
-from utility import to_seq
-
-def difference (b, a):
-    """ Returns the elements of B that are not in A.
-    """
-    result = []
-    for element in b:
-        if not element in a:
-            result.append (element)
-
-    return result
-
-def intersection (set1, set2):
-    """ Removes from set1 any items which don't appear in set2 and returns the result.
-    """
-    result = []
-    for v in set1:
-        if v in set2:
-            result.append (v)
-    return result
-
-def contains (small, large):
-    """ Returns true iff all elements of 'small' exist in 'large'.
-    """
-    small = to_seq (small)
-    large = to_seq (large)
-
-    for s in small:
-        if not s in large:
-            return False
-    return True
-
-def equal (a, b):
-    """ Returns True iff 'a' contains the same elements as 'b', irrespective of their order.
-        # TODO: Python 2.4 has a proper set class.
-    """
-    return contains (a, b) and contains (b, a)
diff --git a/jam-files/boost-build/util/string.jam b/jam-files/boost-build/util/string.jam
deleted file mode 100644
index a39ed119..00000000
--- a/jam-files/boost-build/util/string.jam
+++ /dev/null
@@ -1,189 +0,0 @@
-# Copyright 2002 Dave Abrahams
-# Copyright 2002, 2003 Rene Rivera
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-import regex ;
-
-
-# Characters considered whitespace, as a list.
-.whitespace-chars = " " "	" "
-" ;
-
-# Characters considered whitespace, as a single string.
-.whitespace = $(.whitespace-chars:J="") ;
-
-
-# Returns the canonical set of whitespace characters, as a list.
-#
-rule whitespace-chars ( )
-{
-    return $(.whitespace-chars) ;
-}
-
-
-# Returns the canonical set of whitespace characters, as a single string.
-#
-rule whitespace ( )
-{
-    return $(.whitespace) ;
-}
-
-
-# Splits the given string into a list of strings composed of each character of
-# the string in sequence.
-#
-rule chars (
-    string  # The string to split.
-    )
-{
-    local result ;
-    while $(string)
-    {
-        local s = [ MATCH (.?)(.?)(.?)(.?)(.?)(.?)(.?)(.?)(.*) : $(string) ] ;
-        string = $(s[9]) ;
-        result += $(s[1-8]) ;
-    }
-
-    # Trim off empty strings.
-    while $(result[1]) && ! $(result[-1])
-    {
-        result = $(result[1--2]) ;
-    }
-
-    return $(result) ;
-}
-
-
-# Apply a set of standard transformations to string to produce an abbreviation
-# no more than 5 characters long.
-#
-rule abbreviate ( string )
-{
-    local r = $(.abbreviated-$(string)) ;
-    if $(r)
-    {
-        return $(r) ;
-    }
-    # Anything less than 4 characters gets no abbreviation.
-    else if ! [ MATCH (....) : $(string) ]
-    {
-        .abbreviated-$(string) = $(string) ;
-        return $(string) ;
-    }
-    else
-    {
-        # Separate the initial letter in case it's a vowel.
-        local s1 = [ MATCH ^(.)(.*) : $(string) ] ;
-
-        # Drop trailing "ing".
-        local s2 = [ MATCH ^(.*)ing$ : $(s1[2]) ] ;
-        s2 ?= $(s1[2]) ;
-
-        # Reduce all doubled characters to one.
-        local last = "" ;
-        for local c in [ chars $(s2) ]
-        {
-            if $(c) != $(last)
-            {
-                r += $(c) ;
-                last = $(c) ;
-            }
-        }
-        s2 = $(r:J="") ;
-
-        # Chop all vowels out of the remainder.
-        s2 = [ regex.replace $(s2) [AEIOUaeiou] "" ] ;
-
-        # Shorten remaining consonants to 4 characters.
-        s2 = [ MATCH ^(.?.?.?.?) : $(s2) ] ;
-
-        # Glue the initial character back on to the front.
-        s2 = $(s1[1])$(s2) ;
-
-        .abbreviated-$(string) = $(s2) ;
-        return $(s2) ;
-    }
-}
-
-
-# Concatenates the given strings, inserting the given separator between each
-# string.
-#
-rule join (
-    strings *  # The strings to join.
-    : separator ?  # The optional separator.
-    )
-{
-    separator ?= "" ;
-    return $(strings:J=$(separator)) ;
-}
-
-
-# Split a string into whitespace separated words.
-#
-rule words (
-    string  # The string to split.
-    : whitespace *  # Optional, characters to consider as whitespace.
-    )
-{
-    whitespace = $(whitespace:J="") ;
-    whitespace ?= $(.whitespace) ;
-    local w = ;
-    while $(string)
-    {
-        string = [ MATCH "^[$(whitespace)]*([^$(whitespace)]*)(.*)" : $(string) ] ;
-        if $(string[1]) && $(string[1]) != ""
-        {
-            w += $(string[1]) ;
-        }
-        string = $(string[2]) ;
-    }
-    return $(w) ;
-}
-
-
-# Check that the given string is composed entirely of whitespace.
-#
-rule is-whitespace (
-    string ?  # The string to test.
-    )
-{
-    if ! $(string) { return true ; }
-    else if $(string) = "" { return true ; }
-    else if [ MATCH "^([$(.whitespace)]+)$" : $(string) ] { return true ; }
-    else { return ; }
-}
-
-rule __test__ ( )
-{
-    import assert ;
-    assert.result a b c : chars abc ;
-
-    assert.result rntm : abbreviate runtime ;
-    assert.result ovrld : abbreviate overload ;
-    assert.result dbg : abbreviate debugging ;
-    assert.result async : abbreviate asynchronous ;
-    assert.result pop : abbreviate pop ;
-    assert.result aaa : abbreviate aaa ;
-    assert.result qck : abbreviate quack ;
-    assert.result sttc : abbreviate static ;
-
-    # Check boundary cases.
-    assert.result a : chars a ;
-    assert.result : chars "" ;
-    assert.result a b c d e f g h : chars abcdefgh ;
-    assert.result a b c d e f g h i : chars abcdefghi ;
-    assert.result a b c d e f g h i j : chars abcdefghij ;
-    assert.result a b c d e f g h i j k : chars abcdefghijk ;
-
-    assert.result a//b/c/d : join a "" b c d : / ;
-    assert.result abcd : join  a "" b c d ;
-
-    assert.result a b c : words "a b	c" ;
-
-    assert.true is-whitespace "     	" ;
-    assert.false is-whitespace "  a b c	" ;
-    assert.true is-whitespace "" ;
-    assert.true is-whitespace ;
-}
diff --git a/jam-files/boost-build/util/utility.jam b/jam-files/boost-build/util/utility.jam
deleted file mode 100644
index c46747f5..00000000
--- a/jam-files/boost-build/util/utility.jam
+++ /dev/null
@@ -1,235 +0,0 @@
-# Copyright 2001, 2002 Dave Abrahams
-# Copyright 2002, 2003, 2004, 2005 Vladimir Prus
-# Copyright 2008 Jurko Gospodnetic
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-import "class" : is-instance ;
-import errors ;
-
-
-# For all elements of 'list' which do not already have 'suffix', add 'suffix'.
-#
-rule apply-default-suffix ( suffix : list * )
-{
-    local result ;
-    for local i in $(list)
-    {
-        if $(i:S) = $(suffix)
-        {
-            result += $(i) ;
-        }
-        else
-        {
-            result += $(i)$(suffix) ;
-        }
-    }
-    return $(result) ;
-}
-
-
-# If 'name' contains a dot, returns the part before the last dot. If 'name'
-# contains no dot, returns it unmodified.
-#
-rule basename ( name )
-{
-    if $(name:S)
-    {
-        name = $(name:B) ;
-    }
-    return $(name) ;
-}
-
-
-# Return the file of the caller of the rule that called caller-file.
-#
-rule caller-file ( )
-{
-    local bt = [ BACKTRACE ] ;
-    return $(bt[9]) ;
-}
-
-
-# Tests if 'a' is equal to 'b'. If 'a' is a class instance, calls its 'equal'
-# method. Uses ordinary jam's comparison otherwise.
-#
-rule equal ( a b )
-{
-    if [ is-instance $(a) ]
-    {
-        return [ $(a).equal $(b) ] ;
-    }
-    else
-    {
-        if $(a) = $(b)
-        {
-            return true ;
-        }
-    }
-}
-
-
-# Tests if 'a' is less than 'b'. If 'a' is a class instance, calls its 'less'
-# method. Uses ordinary jam's comparison otherwise.
-#
-rule less ( a b )
-{
-    if [ is-instance $(a) ]
-    {
-        return [ $(a).less $(b) ] ;
-    }
-    else
-    {
-        if $(a) < $(b)
-        {
-            return true ;
-        }
-    }
-}
-
-
-# Returns the textual representation of argument. If it is a class instance,
-# class its 'str' method. Otherwise, returns the argument.
-#
-rule str ( value )
-{
-    if [ is-instance $(value) ]
-    {
-        return [ $(value).str ] ;
-    }
-    else
-    {
-        return $(value) ;
-    }
-}
-
-
-# Accepts a list of gristed values and returns them ungristed. Reports an error
-# in case any of the passed parameters is not gristed, i.e. surrounded in angle
-# brackets < and >.
-#
-rule ungrist ( names * )
-{
-    local result ;
-    for local name in $(names)
-    {
-        local stripped = [ MATCH ^<(.*)>$ : $(name) ] ;
-        if ! $(stripped)
-        {
-            errors.error "in ungrist $(names) : $(name) is not of the form <.*>" ;
-        }
-        result += $(stripped) ;
-    }
-    return $(result) ;
-}
-
-
-# If the passed value is quoted, unquotes it. Otherwise returns the value
-# unchanged.
-#
-rule unquote ( value ? )
-{
-    local match-result = [ MATCH ^(\")(.*)(\")$ : $(value) ] ;
-    if $(match-result)
-    {
-        return $(match-result[2]) ;
-    }
-    else
-    {
-        return $(value) ;
-    }
-}
-
-
-rule __test__ ( )
-{
-    import assert ;
-    import "class" : new ;
-    import errors : try catch ;
-
-    assert.result 123 : str 123 ;
-
-    class test-class__
-    {
-        rule __init__ (   ) {                            }
-        rule str      (   ) { return "str-test-class"  ; }
-        rule less     ( a ) { return "yes, of course!" ; }
-        rule equal    ( a ) { return "not sure"        ; }
-    }
-
-    assert.result "str-test-class" : str [ new test-class__ ] ;
-    assert.true less 1 2 ;
-    assert.false less 2 1 ;
-    assert.result "yes, of course!" : less [ new test-class__ ] 1 ;
-    assert.true equal 1 1 ;
-    assert.false equal 1 2 ;
-    assert.result "not sure" : equal [ new test-class__ ] 1 ;
-
-    assert.result foo.lib foo.lib : apply-default-suffix .lib : foo.lib foo.lib
-        ;
-
-    assert.result foo : basename foo ;
-    assert.result foo : basename foo.so ;
-    assert.result foo.so : basename foo.so.1 ;
-
-    assert.result         : unquote ;
-    assert.result ""      : unquote "" ;
-    assert.result foo     : unquote foo ;
-    assert.result \"foo   : unquote \"foo ;
-    assert.result foo\"   : unquote foo\" ;
-    assert.result foo     : unquote \"foo\" ;
-    assert.result \"foo\" : unquote \"\"foo\"\" ;
-
-    assert.result         : ungrist ;
-    assert.result foo     : ungrist <foo> ;
-    assert.result <foo>   : ungrist <<foo>> ;
-    assert.result foo bar : ungrist <foo> <bar> ;
-
-    try ;
-    {
-        ungrist "" ;
-    }
-    catch "in ungrist  :  is not of the form <.*>" ;
-
-    try ;
-    {
-        ungrist <> ;
-    }
-    catch "in ungrist <> : <> is not of the form <.*>" ;
-
-    try ;
-    {
-        ungrist foo ;
-    }
-    catch "in ungrist foo : foo is not of the form <.*>" ;
-
-    try ;
-    {
-        ungrist <foo ;
-    }
-    catch "in ungrist <foo : <foo is not of the form <.*>" ;
-
-    try ;
-    {
-        ungrist foo> ;
-    }
-    catch "in ungrist foo> : foo> is not of the form <.*>" ;
-
-    try ;
-    {
-        ungrist foo bar ;
-    }
-    catch "in ungrist foo : foo is not of the form <.*>" ;
-
-    try ;
-    {
-        ungrist foo <bar> ;
-    }
-    catch "in ungrist foo : foo is not of the form <.*>" ;
-
-    try ;
-    {
-        ungrist <foo> bar ;
-    }
-    catch "in ungrist bar : bar is not of the form <.*>" ;
-}
diff --git a/jam-files/boost-build/util/utility.py b/jam-files/boost-build/util/utility.py
deleted file mode 100644
index afea765b..00000000
--- a/jam-files/boost-build/util/utility.py
+++ /dev/null
@@ -1,155 +0,0 @@
-#  (C) Copyright David Abrahams 2001. Permission to copy, use, modify, sell and
-#  distribute this software is granted provided this copyright notice appears in
-#  all copies. This software is provided "as is" without express or implied
-#  warranty, and with no claim as to its suitability for any purpose.
-
-""" Utility functions to add/remove/get grists.
-    Grists are string enclosed in angle brackets (<>) that are used as prefixes. See Jam for more information.
-"""
-
-import re
-import os
-import bjam
-from b2.exceptions import *
-
-__re_grist_and_value = re.compile (r'(<[^>]*>)(.*)')
-__re_grist_content = re.compile ('^<(.*)>$')
-__re_backslash = re.compile (r'\\')
-
-def to_seq (value):
-    """ If value is a sequence, returns it.
-        If it is a string, returns a sequence with value as its sole element.
-        """
-    if not value:
-        return []
-
-    if isinstance (value, str):
-        return [value]
-
-    else:
-        return value
-
-def replace_references_by_objects (manager, refs):
-    objs = []
-    for r in refs:
-        objs.append (manager.get_object (r))
-    return objs
-
-def add_grist (features):
-    """ Transform a string by bracketing it with "<>". If already bracketed, does nothing.
-        features: one string or a sequence of strings
-        return: the gristed string, if features is a string, or a sequence of gristed strings, if features is a sequence
-    """
-
-    def grist_one (feature):
-        if feature [0] != '<' and feature [len (feature) - 1] != '>':
-            return '<' + feature + '>'
-        else:
-            return feature
-    
-    if isinstance (features, str):
-        return grist_one (features)
-    else:
-        return [ grist_one (feature) for feature in features ]
-
-def replace_grist (features, new_grist):
-    """ Replaces the grist of a string by a new one.
-        Returns the string with the new grist.
-    """
-    def replace_grist_one (name, new_grist):
-        split = __re_grist_and_value.match (name)
-        if not split:
-            return new_grist + name
-        else:
-            return new_grist + split.group (2)
-
-    if isinstance (features, str):
-        return replace_grist_one (features, new_grist)
-    else:
-        return [ replace_grist_one (feature, new_grist) for feature in features ]
-
-def get_value (property):
-    """ Gets the value of a property, that is, the part following the grist, if any.
-    """
-    return replace_grist (property, '')
-    
-def get_grist (value):
-    """ Returns the grist of a string.
-        If value is a sequence, does it for every value and returns the result as a sequence.
-    """
-    def get_grist_one (name):
-        split = __re_grist_and_value.match (name)
-        if not split:
-            return ''
-        else:
-            return split.group (1)
-
-    if isinstance (value, str):
-        return get_grist_one (value)
-    else:
-        return [ get_grist_one (v) for v in value ]
-
-def ungrist (value):
-    """ Returns the value without grist. 
-        If value is a sequence, does it for every value and returns the result as a sequence.
-    """
-    def ungrist_one (value):
-        stripped = __re_grist_content.match (value)
-        if not stripped:
-            raise BaseException ("in ungrist: '%s' is not of the form <.*>" % value)
-
-        return stripped.group (1)
-
-    if isinstance (value, str):
-        return ungrist_one (value)
-    else:
-        return [ ungrist_one (v) for v in value ]
-
-def replace_suffix (name, new_suffix):
-    """ Replaces the suffix of name by new_suffix.
-        If no suffix exists, the new one is added.
-    """
-    split = os.path.splitext (name)
-    return split [0] + new_suffix
-
-def forward_slashes (s):
-    """ Converts all backslashes to forward slashes.
-    """
-    return __re_backslash.sub ('/', s)
-
-
-def split_action_id (id):
-    """ Splits an id in the toolset and specific rule parts. E.g.
-        'gcc.compile.c++' returns ('gcc', 'compile.c++')
-    """
-    split = id.split ('.', 1)
-    toolset = split [0]
-    name = ''
-    if len (split) > 1:
-        name = split [1]
-    return (toolset, name)
-
-def os_name ():
-    result = bjam.variable("OS")
-    assert(len(result) == 1)
-    return result[0]
-
-def platform ():
-    return bjam.variable("OSPLAT")
-    
-def os_version ():
-    return bjam.variable("OSVER")
-
-def on_windows ():
-    """ Returns true if running on windows, whether in cygwin or not.
-    """
-    if bjam.variable("NT"):
-        return True
-
-    elif bjam.variable("UNIX"):
-
-        uname = bjam.variable("JAMUNAME")
-        if uname and uname[0].startswith("CYGWIN"):
-            return True
-
-    return False
diff --git a/jam-files/engine/Jambase b/jam-files/engine/Jambase
deleted file mode 100644
index 94f8fbde..00000000
--- a/jam-files/engine/Jambase
+++ /dev/null
@@ -1,2473 +0,0 @@
-#
-# /+\
-# +\    Copyright 1993, 2000 Christopher Seiwald.
-# \+/
-#
-# This file is part of Jam - see jam.c for Copyright information.
-#
-
-# This file is ALSO:
-# Copyright 2001-2004 David Abrahams.
-# Copyright 2002-2004 Rene Rivera.
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-if $(NT)
-{
-    SLASH ?= \\ ;
-}
-SLASH ?= / ;
-
-
-# Glob for patterns in the directories starting from the given start directory,
-# up to and including the root of the file-system. We stop globbing as soon as
-# we find at least one match.
-#
-rule find-to-root ( dir : patterns + )
-{
-    local globs = [ GLOB $(dir) : $(patterns) ] ;
-    while ! $(globs) && $(dir:P) != $(dir)
-    {
-        dir = $(dir:P) ;
-        globs = [ GLOB $(dir) : $(patterns) ] ;
-    }
-    return $(globs) ;
-}
-
-
-# This global will hold the location of the user's boost-build.jam file.
-.boost-build-file = ;
-
-# This global will hold the location of the build system bootstrap file.
-.bootstrap-file = ;
-
-# Remember the value of $(BOOST_BUILD_PATH) supplied to us by the user.
-BOOST_BUILD_PATH.user-value = $(BOOST_BUILD_PATH) ;
-
-# On Unix only, when BOOST_BUILD_PATH is not supplied by the user, set it to a
-# sensible default value. This allows Boost.Build to work without any
-# environment variables, which is good in itself and also required by the Debian
-# Policy.
-if ! $(BOOST_BUILD_PATH) && $(UNIX)
-{
-    BOOST_BUILD_PATH = /usr/share/boost-build ;
-}
-
-
-rule _poke ( module-name ? : variables + : value * )
-{
-    module $(<)
-    {
-        $(>) = $(3) ;
-    }
-}
-
-
-# This rule can be invoked from an optional user's boost-build.jam file to both
-# indicate where to find the build system files, and to load them. The path
-# indicated is relative to the location of the boost-build.jam file.
-#
-rule boost-build ( dir ? )
-{
-    if $(.bootstrap-file)
-    {
-        ECHO "Error: Illegal attempt to re-bootstrap the build system by invoking" ;
-        ECHO ;
-        ECHO "   'boost-build" $(dir) ";'" ;
-        ECHO ;
-        EXIT "Please consult the documentation at 'http://www.boost.org'." ;
-    }
-
-    # Add the given directory to the path so we can find the build system. If
-    # dir is empty, has no effect.
-    BOOST_BUILD_PATH = $(dir:R=$(.boost-build-file:D)) $(BOOST_BUILD_PATH) ;
-
-    # We might have just modified the *global* value of BOOST_BUILD_PATH. The
-    # code that loads the rest of Boost.Build, in particular the site-config.jam
-    # and user-config.jam configuration files uses os.environ, so we need to
-    # update the value there.
-    _poke .ENVIRON : BOOST_BUILD_PATH : $(BOOST_BUILD_PATH) ;
-
-    # Try to find the build system bootstrap file 'bootstrap.jam'.
-    local bootstrap-file = [ GLOB $(BOOST_BUILD_PATH) : bootstrap.jam ] ;
-    .bootstrap-file = $(bootstrap-file[1]) ;
-
-    # There is no bootstrap.jam we can find, exit with an error.
-    if ! $(.bootstrap-file)
-    {
-        ECHO "Unable to load Boost.Build: could not find build system." ;
-        ECHO --------------------------------------------------------- ;
-        ECHO "$(.boost-build-file) attempted to load the build system by invoking" ;
-        ECHO ;
-        ECHO "   'boost-build" $(dir) ";'" ;
-        ECHO ;
-        ECHO "but we were unable to find \"bootstrap.jam\" in the specified directory" ;
-        ECHO "or in BOOST_BUILD_PATH (searching "$(BOOST_BUILD_PATH:J=", ")")." ;
-        ECHO ;
-        EXIT "Please consult the documentation at 'http://www.boost.org'." ;
-    }
-
-    if [ MATCH .*(--debug-configuration).* : $(ARGV) ]
-    {
-        ECHO "notice: loading Boost.Build from"
-            [ NORMALIZE_PATH $(.bootstrap-file:D) ] ;
-    }
-
-    # Load the build system, now that we know where to start from.
-    include $(.bootstrap-file) ;
-}
-
-
-if [ MATCH .*(b2).* : $(ARGV[1]:BL) ] 
-  || [ MATCH .*(bjam).* : $(ARGV[1]:BL) ]
-  || $(BOOST_ROOT)    # A temporary measure so Jam works with Boost.Build v1.
-{
-    # We attempt to load "boost-build.jam" by searching from the current
-    # invocation directory up to the root of the file-system.
-    #
-    # boost-build.jam is expected to invoke the "boost-build" rule to load the
-    # Boost.Build files.
-
-    local search-path = $(BOOST_BUILD_PATH) $(BOOST_ROOT) ;
-    local self = [ SELF_PATH ] ;
-    local boost-build-relative = ../../share/boost-build ;
-    local self-based-path = [ NORMALIZE_PATH $(boost-build-relative:R=$(self)) ] ;
-
-    local boost-build-files =
-        [ find-to-root [ PWD ] : boost-build.jam ]
-        [ GLOB $(self-based-path) : boost-build.jam ]
-        # Another temporary measure so Jam works with Boost.Build v1.
-        [ GLOB $(search-path) : boost-build.jam ] ;
-
-    .boost-build-file = $(boost-build-files[1]) ;
-
-    # There is no boost-build.jam we can find, exit with an error, and
-    # information.
-    if ! $(.boost-build-file)
-    {
-        ECHO "Unable to load Boost.Build: could not find \"boost-build.jam\"" ;
-        ECHO --------------------------------------------------------------- ;
-
-        if ! [ MATCH .*(bjam).* : $(ARGV[1]:BL) ]
-        {
-            ECHO "BOOST_ROOT must be set, either in the environment, or " ;
-            ECHO "on the command-line with -sBOOST_ROOT=..., to the root" ;
-            ECHO "of the boost installation." ;
-            ECHO ;
-        }
-
-        ECHO "Attempted search from" [ PWD ] "up to the root" ;
-        ECHO "at" $(self-based-path) ;
-        ECHO "and in these directories from BOOST_BUILD_PATH and BOOST_ROOT: "$(search-path:J=", ")"." ;
-        EXIT "Please consult the documentation at 'http://www.boost.org'." ;
-    }
-
-    if [ MATCH .*(--debug-configuration).* : $(ARGV) ]
-    {
-        ECHO "notice: found boost-build.jam at"
-            [ NORMALIZE_PATH $(.boost-build-file) ] ;
-    }
-
-    # Now load the boost-build.jam to get the build system loaded. This
-    # incidentaly loads the users jamfile and attempts to build targets.
-    #
-    # We also set it up so we can tell whether we are loading the new V2 system
-    # or the the old V1 system.
-    include $(.boost-build-file) ;
-
-    # Check that, at minimum, the bootstrap file was found.
-    if ! $(.bootstrap-file)
-    {
-        ECHO "Unable to load Boost.Build" ;
-        ECHO -------------------------- ;
-        ECHO "\"$(.boost-build-file)\" was found by searching from" [ PWD ] "up to the root" ;
-        ECHO "and in these directories from BOOST_BUILD_PATH and BOOST_ROOT: "$(search-path:J=", ")"." ;
-        ECHO ;
-        ECHO "However, it failed to call the \"boost-build\" rule to indicate" ;
-        ECHO "the location of the build system." ;
-        ECHO ;
-        EXIT "Please consult the documentation at 'http://www.boost.org'." ;
-    }
-}
-else
-{
-
-#
-# JAMBASE - jam 2.3 ruleset providing make(1)-like functionality
-#
-# Supports UNIX, NT, and VMS.
-#
-# 12/27/93 (seiwald) - purturb library sources with SOURCE_GRIST
-# 04/18/94 (seiwald) - use '?=' when setting OS specific vars
-# 04/21/94 (seiwald) - do RmTemps together
-# 05/05/94 (seiwald) - all supported C compilers support -o: relegate
-#              RELOCATE as an option; set Ranlib to "" to disable it
-# 06/01/94 (seiwald) - new 'actions existing' to do existing sources
-# 08/25/94 (seiwald) - new ObjectCcFlags rule to append to per-target CCFLAGS
-# 08/29/94 (seiwald) - new ObjectHdrs rule to append to per-target HDRS
-# 09/19/94 (seiwald) - LinkLibraries and Undefs now append
-#            - Rule names downshifted.
-# 10/06/94 (seiwald) - Dumb yyacc stuff moved into Jamfile.
-# 10/14/94 (seiwald) - (Crude) support for .s, .C, .cc, .cpp, and .f files.
-# 01/08/95 (seiwald) - Shell now handled with awk, not sed
-# 01/09/95 (seiwald) - Install* now take dest directory as target
-# 01/10/95 (seiwald) - All entries sorted.
-# 01/10/95 (seiwald) - NT support moved in, with LauraW's help.
-# 01/10/95 (seiwald) - VMS support moved in.
-# 02/06/95 (seiwald) - ObjectC++Flags and SubDirC++Flags added.
-# 02/07/95 (seiwald) - Iron out when HDRSEARCH uses "" or SEARCH_SOURCE.
-# 02/08/95 (seiwald) - SubDir works on VMS.
-# 02/14/95 (seiwald) - MkDir and entourage.
-# 04/30/95 (seiwald) - Use install -c flag so that it copies, not moves.
-# 07/10/95 (taylor) - Support for Microsoft C++.
-# 11/21/96 (peterk) - Support for BeOS
-# 07/19/99 (sickel) - Support for Mac OS X Server (and maybe client)
-# 02/18/00 (belmonte)- Support for Cygwin.
-
-# Special targets defined in this file:
-#
-# all       - parent of first, shell, files, lib, exe
-# first     - first dependency of 'all', for potential initialization
-# shell     - parent of all Shell targets
-# files     - parent of all File targets
-# lib       - parent of all Library targets
-# exe       - parent of all Main targets
-# dirs      - parent of all MkDir targets
-# clean     - removes all Shell, File, Library, and Main targets
-# uninstall - removes all Install targets
-#
-
-# Rules defined by this file:
-#
-# as obj.o : source.s ;         .s -> .o
-# Bulk dir : files ;            populate directory with many files
-# Cc obj.o : source.c ;         .c -> .o
-# C++ obj.o : source.cc ;       .cc -> .o
-# Clean clean : sources ;       remove sources with 'jam clean'
-# File dest : source ;          copy file
-# Fortran obj.o : source.f ;        .f -> .o
-# GenFile source.c : program args ; make custom file
-# Hardlink target : source ;        make link from source to target
-# HdrRule source : headers ;        handle #includes
-# InstallInto dir : sources ;       install any files
-# InstallBin dir : sources ;        install binaries
-# InstallLib dir : sources ;        install files
-# InstallFile dir : sources ;       install files
-# InstallMan dir : sources ;        install man pages
-# InstallShell dir : sources ;      install shell scripts
-# Lex source.c : source.l ;     .l -> .c
-# Library lib : source ;        archive library from compiled sources
-# LibraryFromObjects lib : objects ;    archive library from objects
-# LinkLibraries images : libraries ;    bag libraries onto Mains
-# Main image : source ;         link executable from compiled sources
-# MainFromObjects image : objects ; link executable from objects
-# MkDir dir ;               make a directory, if not there
-# Object object : source ;      compile object from source
-# ObjectCcFlags source : flags ;    add compiler flags for object
-# ObjectC++Flags source : flags ;   add compiler flags for object
-# ObjectHdrs source : dirs ;        add include directories for object
-# Objects sources ;         compile sources
-# RmTemps target : sources ;        remove temp sources after target made
-# Setuid images ;           mark executables Setuid
-# SubDir TOP d1 d2 ... ;        start a subdirectory Jamfile
-# SubDirCcFlags flags ;         add compiler flags until next SubDir
-# SubDirC++Flags flags ;        add compiler flags until next SubDir
-# SubDirHdrs dirs ;         add include dirs until next SubDir
-# SubInclude TOP d1 d2 ... ;        include a subdirectory Jamfile
-# Shell exe : source ;          make a shell executable
-# Undefines images : symbols ;      save undef's for linking
-# UserObject object : source ;      handle unknown suffixes for Object
-# Yacc source.c : source.y ;        .y -> .c
-#
-# Utility rules that have no side effects (not supported):
-#
-# FAppendSuffix f1 f2 ... : $(SUF) ;    return $(<) with suffixes
-# FConcat value ... ;               return contatenated values
-# FDirName d1 d2 ... ;          return path from root to dir
-# FGrist d1 d2 ... ;            return d1!d2!...
-# FGristFiles value ;           return $(value:G=$(SOURCE_GRIST))
-# FGristSourceFiles value ;     return $(value:G=$(SOURCE_GRIST))
-# FRelPath d1 : d2 ;            return rel path from d1 to d2
-# FSubDir d1 d2 ... ;           return path to root
-#
-
-
-# Brief review of the jam language:
-#
-# Statements:
-#   rule RULE - statements to process a rule
-#   actions RULE - system commands to carry out target update
-#
-# Modifiers on actions:
-#   together - multiple instances of same rule on target get executed
-#          once with their sources ($(>)) concatenated
-#   updated - refers to updated sources ($(>)) only
-#   ignore - ignore return status of command
-#   quietly - don't trace its execution unless verbose
-#   piecemeal - iterate command each time with a small subset of $(>)
-#   existing - refers to currently existing sources ($(>)) only
-#   bind vars - subject to binding before expanding in actions
-#
-# Special rules:
-#   ALWAYS - always build a target
-#   DEPENDS - builds the dependency graph
-#   ECHO - blurt out targets on stdout
-#   EXIT - blurt out targets and exit
-#   INCLUDES - marks sources as headers for target (a codependency)
-#   NOCARE - don't panic if the target can't be built
-#   NOUPDATE - create the target if needed but never update it
-#   NOTFILE - ignore the timestamp of the target (it's not a file)
-#   TEMPORARY - target need not be present if sources haven't changed
-#
-# Special variables set by jam:
-#   $(<) - targets of a rule (to the left of the :)
-#   $(>) - sources of a rule (to the right of the :)
-#   $(xxx) - true on xxx (UNIX, VMS, NT, OS2, MAC)
-#   $(OS) - name of OS - varies wildly
-#   $(JAMVERSION) - version number (2.3)
-#
-# Special variables used by jam:
-#   SEARCH - where to find something (used during binding and actions)
-#   LOCATE - where to plop something not found with SEARCH
-#   HDRRULE - rule to call to handle include files
-#   HDRSCAN - egrep regex to extract include files
-#
-# Special targets:
-#   all - default if none given on command line
-#
-
-# Initialize variables
-#
-
-#
-# OS specific variable settings
-#
-if $(NT)
-{
-    # the list of supported toolsets on Windows NT and Windows 95/98
-    #
-    local SUPPORTED_TOOLSETS = "BORLANDC" "VC7" "VISUALC" "VISUALC16" "INTELC" "WATCOM"
-                               "MINGW" "LCC" ;
-
-    # this variable holds the current toolset
-    #
-    TOOLSET = "" ;
-
-    # if the JAM_TOOLSET environment variable is defined, check that it is
-    # one of our supported values
-    #
-    if $(JAM_TOOLSET)
-    {
-      local t ;
-
-      for t in $(SUPPORTED_TOOLSETS)
-      {
-        $(t) = $($(t):J=" ") ; # reconstitute paths with spaces in them
-        if $(t) = $(JAM_TOOLSET) { TOOLSET = $(t) ; }
-      }
-
-      if ! $(TOOLSET)
-      {
-        ECHO  "The JAM_TOOLSET environment variable is defined but its value" ;
-        ECHO  "is invalid, please use one of the following:" ;
-        ECHO  ;
-
-        for t in $(SUPPORTED_TOOLSETS) { ECHO "  " $(t) ; }
-        EXIT ;
-      }
-    }
-
-    # if TOOLSET is empty, we'll try to detect the toolset from other
-    # environment variables to remain backwards compatible with Jam 2.3
-    #
-    if ! $(TOOLSET)
-    {
-      if $(BCCROOT)
-      {
-        TOOLSET  = BORLANDC ;
-        BORLANDC = $(BCCROOT:J=" ") ;
-      }
-      else if $(MSVC)
-      {
-        TOOLSET   = VISUALC16 ;
-        VISUALC16 = $(MSVC:J=" ") ;
-      }
-      else if $(MSVCNT)
-      {
-        TOOLSET = VISUALC ;
-        VISUALC = $(MSVCNT:J=" ") ;
-      }
-      else if $(MSVCDir)
-      {
-        TOOLSET = VISUALC ;
-        VISUALC = $(MSVCDir:J=" ") ;
-      }
-      else if $(MINGW)
-      {
-        TOOLSET = MINGW ;
-      }
-      else
-      {
-        ECHO  "Jam cannot be run because, either:" ;
-        ECHO  "   a. You didn't set BOOST_ROOT to indicate the root of your" ;
-        ECHO  "      Boost installation." ;
-        ECHO  "   b. You are trying to use stock Jam but didn't indicate which" ;
-        ECHO  "      compilation toolset to use. To do so, follow these simple" ;
-        ECHO  "      instructions:" ;
-        ECHO  ;
-        ECHO  "  - define one of the following environment variable, with the" ;
-        ECHO  "    appropriate value according to this list:" ;
-        ECHO  ;
-        ECHO  "   Variable    Toolset                      Description" ;
-        ECHO  ;
-        ECHO  "   BORLANDC    Borland C++                  BC++ install path" ;
-        ECHO  "   VISUALC     Microsoft Visual C++         VC++ install path" ;
-        ECHO  "   VISUALC16   Microsoft Visual C++ 16 bit  VC++ 16 bit install" ;
-        ECHO  "   INTELC      Intel C/C++                  IC++ install path" ;
-        ECHO  "   WATCOM      Watcom C/C++                 Watcom install path" ;
-        ECHO  "   MINGW       MinGW (gcc)                  MinGW install path" ;
-        ECHO  "   LCC         Win32-LCC                    LCC-Win32 install path" ;
-        ECHO  ;
-        ECHO  "  - define the JAM_TOOLSET environment variable with the *name*" ;
-        ECHO  "    of the toolset variable you want to use." ;
-        ECHO  ;
-        ECHO  "  e.g.:  set VISUALC=C:\\Visual6" ;
-        ECHO  "         set JAM_TOOLSET=VISUALC" ;
-        EXIT  ;
-      }
-    }
-
-    CP          ?= copy ;
-    RM          ?= del /f/q ;
-    SLASH       ?= \\ ;
-    SUFLIB      ?= .lib ;
-    SUFOBJ      ?= .obj ;
-    SUFEXE      ?= .exe ;
-
-    if $(TOOLSET) = BORLANDC
-    {
-    ECHO "Compiler is Borland C++" ;
-
-    AR          ?= tlib /C /P64 ;
-    CC          ?= bcc32 ;
-    CCFLAGS     ?= -q -y -d -v -w-par -w-ccc -w-rch -w-pro -w-aus ;
-    C++         ?= bcc32 ;
-    C++FLAGS    ?= -q -y -d -v -w-par -w-ccc -w-rch -w-pro -w-aus -P ;
-    LINK        ?= $(CC) ;
-    LINKFLAGS   ?= $(CCFLAGS) ;
-    STDLIBPATH  ?= $(BORLANDC)\\lib ;
-    STDHDRS     ?= $(BORLANDC)\\include ;
-    NOARSCAN    ?= true ;
-    }
-    else if $(TOOLSET) = VISUALC16
-    {
-    ECHO "Compiler is Microsoft Visual C++ 16 bit" ;
-
-    AR          ?= lib /nologo ;
-    CC          ?= cl /nologo ;
-    CCFLAGS     ?= /D \"WIN\" ;
-    C++         ?= $(CC) ;
-    C++FLAGS    ?= $(CCFLAGS) ;
-    LINK        ?= $(CC) ;
-    LINKFLAGS   ?= $(CCFLAGS) ;
-    LINKLIBS    ?=
-                \"$(VISUALC16)\\lib\\mlibce.lib\"
-                \"$(VISUALC16)\\lib\\oldnames.lib\"
-                ;
-    LINKLIBS    ?= ;
-    NOARSCAN    ?= true ;
-    OPTIM       ?= "" ;
-    STDHDRS     ?= $(VISUALC16)\\include ;
-    UNDEFFLAG   ?= "/u _" ;
-    }
-    else if $(TOOLSET) = VISUALC
-    {
-    ECHO "Compiler is Microsoft Visual C++" ;
-
-    AR          ?= lib ;
-    AS          ?= masm386 ;
-    CC          ?= cl /nologo ;
-    CCFLAGS     ?= "" ;
-    C++         ?= $(CC) ;
-    C++FLAGS    ?= $(CCFLAGS) ;
-    LINK        ?= link /nologo ;
-    LINKFLAGS   ?= "" ;
-    LINKLIBS    ?= \"$(VISUALC)\\lib\\advapi32.lib\"
-                   # $(VISUALC)\\lib\\libc.lib
-                   # $(VISUALC)\\lib\\oldnames.lib
-                   \"$(VISUALC)\\lib\\gdi32.lib\"
-                   \"$(VISUALC)\\lib\\user32.lib\"
-                   \"$(VISUALC)\\lib\\kernel32.lib\" ;
-    OPTIM       ?= "" ;
-    STDHDRS     ?= $(VISUALC)\\include ;
-    UNDEFFLAG   ?= "/u _" ;
-    }
-    else if $(TOOLSET) = VC7
-    {
-    ECHO "Compiler is Microsoft Visual C++ .NET" ;
-
-    AR          ?= lib ;
-    AS          ?= masm386 ;
-    CC          ?= cl /nologo ;
-    CCFLAGS     ?= "" ;
-    C++         ?= $(CC) ;
-    C++FLAGS    ?= $(CCFLAGS) ;
-    LINK        ?= link /nologo ;
-    LINKFLAGS   ?= "" ;
-    LINKLIBS    ?= \"$(VISUALC)\\PlatformSDK\\lib\\advapi32.lib\"
-                   # $(VISUALC)\\lib\\libc.lib
-                   # $(VISUALC)\\lib\\oldnames.lib
-                   \"$(VISUALC)\\PlatformSDK\\lib\\gdi32.lib\"
-                   \"$(VISUALC)\\PlatformSDK\\lib\\user32.lib\"
-                   \"$(VISUALC)\\PlatformSDK\\lib\\kernel32.lib\" ;
-    OPTIM       ?= "" ;
-    STDHDRS     ?= \"$(VISUALC)\\include\"
-									 \"$(VISUALC)\\PlatformSDK\\include\" ;
-    UNDEFFLAG   ?= "/u _" ;
-    }
-    else if $(TOOLSET) = INTELC
-    {
-    ECHO "Compiler is Intel C/C++" ;
-
-        if ! $(VISUALC)
-        {
-          ECHO "As a special exception, when using the Intel C++ compiler, you need" ;
-          ECHO "to define the VISUALC environment variable to indicate the location" ;
-          ECHO "of your Visual C++ installation. Aborting.." ;
-          EXIT ;
-        }
-
-    AR          ?= lib ;
-    AS          ?= masm386 ;
-    CC          ?= icl /nologo ;
-    CCFLAGS     ?= "" ;
-    C++         ?= $(CC) ;
-    C++FLAGS    ?= $(CCFLAGS) ;
-    LINK        ?= link /nologo ;
-    LINKFLAGS   ?= "" ;
-    LINKLIBS    ?= $(VISUALC)\\lib\\advapi32.lib
-                   # $(VISUALC)\\lib\\libc.lib
-                   # $(VISUALC)\\lib\\oldnames.lib
-                   $(VISUALC)\\lib\\kernel32.lib
-                   ;
-    OPTIM       ?= "" ;
-    STDHDRS     ?= $(INTELC)\include $(VISUALC)\\include ;
-    UNDEFFLAG   ?= "/u _" ;
-    }
-    else if $(TOOLSET) = WATCOM
-    {
-        ECHO "Compiler is Watcom C/C++" ;
-
-    AR          ?= wlib ;
-    CC          ?= wcc386 ;
-    CCFLAGS     ?= /zq /DWIN32 /I$(WATCOM)\\h ; # zq=quiet
-    C++         ?= wpp386 ;
-    C++FLAGS    ?= $(CCFLAGS) ;
-    CP          ?= copy ;
-    DOT         ?= . ;
-    DOTDOT      ?= .. ;
-    LINK        ?= wcl386 ;
-    LINKFLAGS   ?= /zq ; # zq=quiet
-    LINKLIBS    ?= ;
-    MV          ?= move ;
-    NOARSCAN    ?= true ;
-    OPTIM       ?= ;
-    RM          ?= del /f ;
-    SLASH       ?= \\ ;
-    STDHDRS     ?= $(WATCOM)\\h $(WATCOM)\\h\\nt ;
-    SUFEXE      ?= .exe ;
-    SUFLIB      ?= .lib ;
-    SUFOBJ      ?= .obj ;
-    UNDEFFLAG   ?= "/u _" ;
-    }
-    else if $(TOOLSET) = MINGW
-    {
-        ECHO "Compiler is GCC with Mingw" ;
-
-        AR              ?= ar -ru ;
-        CC              ?= gcc ;
-        CCFLAGS         ?= "" ;
-        C++             ?= $(CC) ;
-        C++FLAGS        ?= $(CCFLAGS) ;
-        LINK            ?= $(CC) ;
-        LINKFLAGS       ?= "" ;
-        LINKLIBS        ?= "" ;
-        OPTIM           ?= ;
-        SUFOBJ           = .o ;
-        SUFLIB           = .a ;
-        SLASH            = / ;
-#       NOARSCAN        ?= true ;
-    }
-    else if $(TOOLSET) = LCC
-    {
-        ECHO "Compiler is Win32-LCC" ;
-
-        AR              ?= lcclib ;
-        CC              ?= lcc ;
-        CCFLAGS         ?= "" ;
-        C++             ?= $(CC) ;
-        C++FLAGS        ?= $(CCFLAGS) ;
-        LINK            ?= lcclnk ;
-        LINKFLAGS       ?= "" ;
-        LINKLIBS        ?= "" ;
-        OPTIM           ?= ;
-        NOARSCAN         = true ;
-    }
-    else
-    {
-#
-# XXX: We need better comments here !!
-#
-    EXIT On NT, set BCCROOT, MSVCNT, MINGW or MSVC to the root of the
-        Borland or Microsoft directories. ;
-    }
-
-}
-else if $(OS2)
-{
-    # the list of supported toolsets on Windows NT and Windows 95/98
-    #
-    local SUPPORTED_TOOLSETS = "EMX" "WATCOM" ;
-
-    # this variable holds the current toolset
-    #
-    TOOLSET = "" ;
-
-    # if the JAM_TOOLSET environment variable is defined, check that it is
-    # one of our supported values
-    #
-    if $(JAM_TOOLSET)
-    {
-      local t ;
-
-      for t in $(SUPPORTED_TOOLSETS)
-      {
-        $(t) = $($(t):J=" ") ; # reconstitute paths with spaces in them
-        if $(t) = $(JAM_TOOLSET) { TOOLSET = $(t) ; }
-      }
-
-      if ! $(TOOLSET)
-      {
-        ECHO  "The JAM_TOOLSET environment variable is defined but its value" ;
-        ECHO  "is invalid, please use one of the following:" ;
-        ECHO  ;
-
-        for t in $(SUPPORTED_TOOLSETS) { ECHO "  " $(t) ; }
-        EXIT ;
-      }
-    }
-
-    # if TOOLSET is empty, we'll try to detect the toolset from other
-    # environment variables to remain backwards compatible with Jam 2.3
-    #
-    if ! $(TOOLSET)
-    {
-      if $(watcom)
-      {
-        WATCOM   = $(watcom:J=" ") ;
-        TOOLSET  = WATCOM ;
-      }
-      else
-      {
-        ECHO  "Jam cannot be run because you didn't indicate which compilation toolset" ;
-        ECHO  "to use. To do so, follow these simple instructions:" ;
-        ECHO  ;
-        ECHO  "  - define one of the following environment variable, with the" ;
-        ECHO  "    appropriate value according to this list:" ;
-        ECHO  ;
-        ECHO  "   Variable    Toolset                      Description" ;
-        ECHO  ;
-        ECHO  "   WATCOM      Watcom C/C++                 Watcom install path" ;
-        ECHO  "   EMX         EMX (gcc)                    EMX install path" ;
-        ECHO  "   VISUALAGE   IBM Visual Age C/C++         VisualAge install path" ;
-        ECHO  ;
-        ECHO  "  - define the JAM_TOOLSET environment variable with the *name*" ;
-        ECHO  "    of the toolset variable you want to use." ;
-        ECHO  ;
-        ECHO  "  e.g.:  set WATCOM=C:\WATCOM" ;
-        ECHO  "         set JAM_TOOLSET=WATCOM" ;
-        ECHO  ;
-        EXIT  ;
-      }
-    }
-
-    RM       = del /f ;
-    CP       = copy ;
-    MV      ?= move ;
-    DOT     ?= . ;
-    DOTDOT  ?= .. ;
-    SUFLIB  ?= .lib ;
-    SUFOBJ  ?= .obj ;
-    SUFEXE  ?= .exe ;
-
-    if $(TOOLSET) = WATCOM
-    {
-       AR           ?= wlib ;
-       BINDIR       ?= \\os2\\apps ;
-       CC           ?= wcc386 ;
-       CCFLAGS      ?= /zq /DOS2 /I$(WATCOM)\\h ; # zq=quiet
-       C++          ?= wpp386 ;
-       C++FLAGS     ?= $(CCFLAGS) ;
-       LINK         ?= wcl386 ;
-       LINKFLAGS    ?= /zq ; # zq=quiet
-       LINKLIBS     ?= ;
-       NOARSCAN     ?= true ;
-       OPTIM        ?= ;
-       SLASH        ?= \\ ;
-       STDHDRS      ?= $(WATCOM)\\h ;
-       UNDEFFLAG    ?= "/u _" ;
-    }
-    else if $(TOOLSET) = EMX
-    {
-      ECHO "Compiler is GCC-EMX" ;
-      AR            ?= ar -ru ;
-      CC            ?= gcc ;
-      CCFLAGS       ?= "" ;
-      C++           ?= $(CC) ;
-      C++FLAGS      ?= $(CCFLAGS) ;
-      LINK          ?= $(CC) ;
-      LINKFLAGS     ?= "" ;
-      LINKLIBS      ?= "" ;
-      OPTIM         ?= ;
-      SUFOBJ         = .o ;
-      SUFLIB         = .a ;
-      UNDEFFLAG     ?= "-U" ;
-      SLASH          = / ;
-#     NOARSCAN      ?= true ;
-    }
-    else
-    {
-      # should never happen
-      EXIT  "Sorry, but the $(JAM_TOOLSET) toolset isn't supported for now" ;
-    }
-}
-else if $(VMS)
-{
-    C++         ?= cxx ;
-    C++FLAGS    ?= ;
-    CC          ?= cc ;
-    CCFLAGS     ?= ;
-    CHMOD       ?= set file/prot= ;
-    CP          ?= copy/replace ;
-    CRELIB      ?= true ;
-    DOT         ?= [] ;
-    DOTDOT      ?= [-] ;
-    EXEMODE     ?= (w:e) ;
-    FILEMODE    ?= (w:r) ;
-    HDRS        ?= ;
-    LINK        ?= link ;
-    LINKFLAGS   ?= "" ;
-    LINKLIBS    ?= ;
-    MKDIR       ?= create/dir ;
-    MV          ?= rename ;
-    OPTIM       ?= "" ;
-    RM          ?= delete ;
-    RUNVMS      ?= mcr ;
-    SHELLMODE   ?= (w:er) ;
-    SLASH       ?= . ;
-    STDHDRS     ?= decc$library_include ;
-    SUFEXE      ?= .exe ;
-    SUFLIB      ?= .olb ;
-    SUFOBJ      ?= .obj ;
-
-    switch $(OS)
-    {
-    case OPENVMS : CCFLAGS  ?= /stand=vaxc ;
-    case VMS     : LINKLIBS ?= sys$library:vaxcrtl.olb/lib ;
-    }
-}
-else if $(MAC)
-{
-    local OPT ;
-
-    CW  ?= "{CW}" ;
-
-    MACHDRS ?=
-        "$(UMACHDRS):Universal:Interfaces:CIncludes"
-        "$(CW):MSL:MSL_C:MSL_Common:Include"
-        "$(CW):MSL:MSL_C:MSL_MacOS:Include" ;
-
-    MACLIBS ?=
-        "$(CW):MacOS Support:Universal:Libraries:StubLibraries:Interfacelib"
-        "$(CW):MacOS Support:Universal:Libraries:StubLibraries:Mathlib" ;
-
-    MPWLIBS ?=
-        "$(CW):MacOS Support:Libraries:Runtime:Runtime PPC:MSL MPWCRuntime.lib"
-        "$(CW):MSL:MSL_C:MSL_MacOS:Lib:PPC:MSL C.PPC MPW.Lib" ;
-
-    MPWNLLIBS ?=
-        "$(CW):MacOS Support:Libraries:Runtime:Runtime PPC:MSL MPWCRuntime.lib"
-        "$(CW):MSL:MSL_C:MSL_MacOS:Lib:PPC:MSL C.PPC MPW(NL).Lib" ;
-
-    SIOUXHDRS ?= ;
-
-    SIOUXLIBS ?=
-        "$(CW):MacOS Support:Libraries:Runtime:Runtime PPC:MSL RuntimePPC.lib"
-        "$(CW):MSL:MSL_C:MSL_MacOS:Lib:PPC:MSL SIOUX.PPC.Lib"
-        "$(CW):MSL:MSL_C:MSL_MacOS:Lib:PPC:MSL C.PPC.Lib" ;
-
-    C++         ?= mwcppc ;
-    C++FLAGS    ?= -w off -nomapcr ;
-    CC          ?= mwcppc ;
-    CCFLAGS     ?= -w off -nomapcr ;
-    CP          ?= duplicate -y ;
-    DOT         ?= ":" ;
-    DOTDOT      ?= "::" ;
-    HDRS        ?= $(MACHDRS) $(MPWHDRS) ;
-    LINK        ?= mwlinkppc ;
-    LINKFLAGS   ?= -mpwtool -warn ;
-    LINKLIBS    ?= $(MACLIBS) $(MPWLIBS) ;
-    MKDIR       ?= newfolder ;
-    MV          ?= rename -y ;
-    NOARSCAN    ?= true ;
-    OPTIM       ?= ;
-    RM          ?= delete -y ;
-    SLASH       ?= ":" ;
-    STDHDRS     ?= ;
-    SUFLIB      ?= .lib ;
-    SUFOBJ      ?= .o ;
-}
-else if $(OS) = BEOS && $(METROWERKS)
-{
-    AR          ?= mwld -xml -o ;
-    BINDIR      ?= /boot/apps ;
-    CC          ?= mwcc ;
-    CCFLAGS     ?= -nosyspath ;
-    C++         ?= $(CC) ;
-    C++FLAGS    ?= -nosyspath ;
-    FORTRAN     ?= "" ;
-    LIBDIR      ?= /boot/develop/libraries ;
-    LINK        ?= mwld ;
-    LINKFLAGS   ?= "" ;
-    MANDIR      ?= /boot/documentation/"Shell Tools"/HTML ;
-    NOARSCAN    ?= true ;
-    STDHDRS     ?= /boot/develop/headers/posix ;
-}
-else if $(OS) = BEOS
-{
-    BINDIR      ?= /boot/apps ;
-    CC          ?= gcc ;
-    C++         ?= $(CC) ;
-    FORTRAN     ?= "" ;
-    LIBDIR      ?= /boot/develop/libraries ;
-    LINK        ?= gcc ;
-    LINKLIBS    ?= -lnet ;
-    NOARSCAN    ?= true ;
-    STDHDRS     ?= /boot/develop/headers/posix ;
-}
-else if $(UNIX)
-{
-    switch $(OS)
-    {
-    case AIX :
-    LINKLIBS    ?= -lbsd ;
-
-    case AMIGA :
-    CC          ?= gcc ;
-    YACC        ?= "bison -y" ;
-
-    case CYGWIN :
-    CC          ?= gcc ;
-    CCFLAGS     += -D__cygwin__ ;
-    LEX         ?= flex ;
-    RANLIB      ?= "" ;
-    SUFEXE      ?= .exe ;
-    YACC        ?= "bison -y" ;
-
-    case DGUX :
-    RANLIB      ?= "" ;
-    RELOCATE    ?= true ;
-
-    case HPUX :
-    YACC        = ;
-    CFLAGS      += -Ae ;
-    CCFLAGS     += -Ae ;
-    RANLIB      ?= "" ;
-
-    case INTERIX :
-    CC          ?= gcc ;
-    RANLIB      ?= "" ;
-
-    case IRIX :
-    RANLIB      ?= "" ;
-
-    case MPEIX :
-    CC          ?= gcc ;
-    C++         ?= gcc ;
-    CCFLAGS     += -D_POSIX_SOURCE ;
-    HDRS        += /usr/include ;
-    RANLIB      ?= "" ;
-    NOARSCAN    ?= true ;
-    NOARUPDATE  ?= true ;
-
-    case MVS :
-    RANLIB      ?= "" ;
-
-    case NEXT :
-    AR          ?= libtool -o ;
-    RANLIB      ?= "" ;
-
-    case MACOSX :
-    AR          ?= libtool -o ;
-    C++         ?= c++ ;
-    MANDIR      ?= /usr/local/share/man ;
-    RANLIB      ?= "" ;
-
-    case NCR :
-    RANLIB      ?= "" ;
-
-    case PTX :
-    RANLIB      ?= "" ;
-
-    case QNX :
-    AR          ?= wlib ;
-    CC          ?= cc ;
-    CCFLAGS     ?= -Q ; # quiet
-    C++         ?= $(CC) ;
-    C++FLAGS    ?= -Q ; # quiet
-    LINK        ?= $(CC) ;
-    LINKFLAGS   ?= -Q ; # quiet
-    NOARSCAN    ?= true ;
-    RANLIB      ?= "" ;
-
-    case SCO :
-    RANLIB      ?= "" ;
-    RELOCATE    ?= true ;
-
-    case SINIX :
-    RANLIB      ?= "" ;
-
-    case SOLARIS :
-    RANLIB      ?= "" ;
-    AR          ?= "/usr/ccs/bin/ar ru" ;
-
-    case UNICOS :
-    NOARSCAN    ?= true ;
-    OPTIM       ?= -O0 ;
-
-    case UNIXWARE :
-    RANLIB      ?= "" ;
-    RELOCATE    ?= true ;
-    }
-
-    # UNIX defaults
-
-    CCFLAGS     ?= ;
-    C++FLAGS    ?= $(CCFLAGS) ;
-    CHMOD       ?= chmod ;
-    CHGRP       ?= chgrp ;
-    CHOWN       ?= chown ;
-    LEX         ?= lex ;
-    LINKFLAGS   ?= $(CCFLAGS) ;
-    LINKLIBS    ?= ;
-    OPTIM       ?= -O ;
-    RANLIB      ?= ranlib ;
-    YACC        ?= yacc ;
-    YACCFILES   ?= y.tab ;
-    YACCFLAGS   ?= -d ;
-}
-
-#
-# General defaults; a lot like UNIX
-#
-
-    AR          ?= ar ru ;
-    AS          ?= as ;
-    ASFLAGS     ?= ;
-    AWK         ?= awk ;
-    BINDIR      ?= /usr/local/bin ;
-    C++         ?= cc ;
-    C++FLAGS    ?= ;
-    CC          ?= cc ;
-    CCFLAGS     ?= ;
-    CP          ?= cp -f ;
-    CRELIB      ?= ;
-    DOT         ?= . ;
-    DOTDOT      ?= .. ;
-    EXEMODE     ?= 711 ;
-    FILEMODE    ?= 644 ;
-    FORTRAN     ?= f77 ;
-    FORTRANFLAGS ?= ;
-    HDRS        ?= ;
-    INSTALLGRIST ?= installed ;
-    JAMFILE     ?= Jamfile ;
-    JAMRULES    ?= Jamrules ;
-    LEX         ?= ;
-    LIBDIR      ?= /usr/local/lib ;
-    LINK        ?= $(CC) ;
-    LINKFLAGS   ?= ;
-    LINKLIBS    ?= ;
-    LN          ?= ln ;
-    MANDIR      ?= /usr/local/man ;
-    MKDIR       ?= mkdir ;
-    MV          ?= mv -f ;
-    OPTIM       ?= ;
-    RCP         ?= rcp ;
-    RM          ?= rm -f ;
-    RSH         ?= rsh ;
-    SED         ?= sed ;
-    SHELLHEADER ?= "#!/bin/sh" ;
-    SHELLMODE   ?= 755 ;
-    SLASH       ?= / ;
-    STDHDRS     ?= /usr/include ;
-    SUFEXE      ?= "" ;
-    SUFLIB      ?= .a ;
-    SUFOBJ      ?= .o ;
-    UNDEFFLAG   ?= "-u _" ;
-    YACC        ?= ;
-    YACCFILES   ?= ;
-    YACCFLAGS   ?= ;
-
-    HDRPATTERN =
-            "^[     ]*#[    ]*include[  ]*[<\"]([^\">]*)[\">].*$" ;
-
-    OSFULL = $(OS)$(OSVER)$(OSPLAT) $(OS)$(OSPLAT) $(OS)$(OSVER) $(OS) ;
-
-
-#
-# Base dependencies - first for "bootstrap" kinds of rules
-#
-
-DEPENDS all : shell files lib exe obj ;
-DEPENDS all shell files lib exe obj : first ;
-NOTFILE all first shell files lib exe obj dirs clean uninstall ;
-ALWAYS clean uninstall ;
-
-#
-# Rules
-#
-
-rule As
-{
-    DEPENDS $(<) : $(>) ;
-    ASFLAGS on $(<) += $(ASFLAGS) $(SUBDIRASFLAGS) ;
-}
-
-rule Bulk
-{
-    local i ;
-
-    for i in $(>)
-    {
-        File $(i:D=$(<)) : $(i) ;
-    }
-}
-
-rule Cc
-{
-    local _h ;
-
-    DEPENDS $(<) : $(>) ;
-
-    # Just to clarify here: this sets the per-target CCFLAGS to
-    # be the current value of (global) CCFLAGS and SUBDIRCCFLAGS.
-
-    CCFLAGS on $(<) += $(CCFLAGS) $(SUBDIRCCFLAGS) ;
-
-    # If the compiler's -o flag doesn't work, relocate the .o
-
-    if $(RELOCATE)
-    {
-        CcMv $(<) : $(>) ;
-    }
-
-    _h = $(SEARCH_SOURCE) $(HDRS) $(SUBDIRHDRS) ;
-
-    if $(VMS) && $(_h)
-    {
-        SLASHINC on $(<) = "/inc=(" $(_h[1]) ,$(_h[2-]) ")" ;
-    }
-    else if $(MAC) && $(_h)
-    {
-        local _i _j ;
-        _j = $(_h[1]) ;
-        for _i in $(_h[2-])
-        {
-            _j = $(_j),$(_i) ;
-        }
-        MACINC on $(<) = \"$(_j)\" ;
-    }
-}
-
-rule C++
-{
-    local _h ;
-
-    DEPENDS $(<) : $(>) ;
-    C++FLAGS on $(<) += $(C++FLAGS) $(SUBDIRC++FLAGS) ;
-
-    if $(RELOCATE)
-    {
-        CcMv $(<) : $(>) ;
-    }
-
-    _h = $(SEARCH_SOURCE) $(HDRS) $(SUBDIRHDRS) ;
-
-    if $(VMS) && $(_h)
-    {
-        SLASHINC on $(<) = "/inc=(" $(_h[1]) ,$(_h[2-]) ")" ;
-    }
-    else if $(MAC) && $(_h)
-    {
-        local _i _j ;
-        _j = $(_h[1]) ;
-        for _i in $(_h[2-])
-        {
-            _j = $(_j),$(_i) ;
-        }
-        MACINC on $(<) = \"$(_j)\" ;
-    }
-}
-
-rule Chmod
-{
-    if $(CHMOD) { Chmod1 $(<) ; }
-}
-
-rule File
-{
-    DEPENDS files : $(<) ;
-    DEPENDS $(<) : $(>) ;
-    SEARCH on $(>) = $(SEARCH_SOURCE) ;
-    MODE on $(<) = $(FILEMODE) ;
-    Chmod $(<) ;
-}
-
-rule Fortran
-{
-    DEPENDS $(<) : $(>) ;
-}
-
-rule GenFile
-{
-    local _t = [ FGristSourceFiles $(<) ] ;
-    local _s = [ FAppendSuffix $(>[1]) : $(SUFEXE) ] ;
-    Depends $(_t) : $(_s) $(>[2-]) ;
-    GenFile1 $(_t) : $(_s) $(>[2-]) ;
-    Clean clean : $(_t) ;
-}
-
-rule GenFile1
-{
-    MakeLocate $(<) : $(LOCATE_SOURCE) ;
-    SEARCH on $(>) = $(SEARCH_SOURCE) ;
-}
-
-rule HardLink
-{
-    DEPENDS files : $(<) ;
-    DEPENDS $(<) : $(>) ;
-    SEARCH on $(>) = $(SEARCH_SOURCE) ;
-}
-
-rule HdrMacroFile
-{
-  # HdrMacroFile file ;
-  #
-  # this rule is used to indicate that a given file contains definitions
-  # for filename macros (e.g. "#define  MYFILE_H <myfile.h>") that can
-  # later be used in #include statements in the rest of the source
-  #
-  # theses files must be parsed before any make is tried..
-  #
-  HDRMACRO $(<) ;
-}
-
-rule HdrRule
-{
-    # HdrRule source : headers ;
-
-    # N.B.  This rule is called during binding, potentially after
-    # the fate of many targets has been determined, and must be
-    # used with caution: don't add dependencies to unrelated
-    # targets, and don't set variables on $(<).
-
-    # Tell Jam that anything depending on $(<) also depends on $(>),
-    # set SEARCH so Jam can find the headers, but then say we don't
-    # care if we can't actually find the headers (they may have been
-    # within ifdefs),
-
-    local s ;
-
-    if $(HDRGRIST)
-    {
-        s = $(>:G=$(HDRGRIST)) ;
-    } else {
-        s = $(>) ;
-    }
-
-    INCLUDES $(<) : $(s) ;
-    SEARCH on $(s) = $(HDRSEARCH) ;
-    NOCARE $(s) ;
-
-    # Propagate on $(<) to $(>)
-
-    HDRSEARCH on $(s) = $(HDRSEARCH) ;
-    HDRSCAN on $(s) = $(HDRSCAN) ;
-    HDRRULE on $(s) = $(HDRRULE) ;
-    HDRGRIST on $(s) = $(HDRGRIST) ;
-}
-
-rule InstallInto
-{
-    # InstallInto dir : sources ;
-
-    local i t ;
-
-    t = $(>:G=$(INSTALLGRIST)) ;
-
-    # Arrange for jam install
-    # Arrange for jam uninstall
-    # sources are in SEARCH_SOURCE
-    # targets are in dir
-
-    Depends install : $(t) ;
-    Clean uninstall : $(t) ;
-    SEARCH on $(>) = $(SEARCH_SOURCE) ;
-    MakeLocate $(t) : $(<) ;
-
-    # For each source, make gristed target name
-    # and Install, Chmod, Chown, and Chgrp
-
-    for i in $(>)
-    {
-        local tt = $(i:G=$(INSTALLGRIST)) ;
-
-        Depends $(tt) : $(i) ;
-        Install $(tt) : $(i) ;
-        Chmod $(tt) ;
-
-        if $(OWNER) && $(CHOWN)
-        {
-        Chown $(tt) ;
-        OWNER on $(tt) = $(OWNER) ;
-        }
-
-        if $(GROUP) && $(CHGRP)
-        {
-        Chgrp $(tt) ;
-        GROUP on $(tt) = $(GROUP) ;
-        }
-    }
-}
-
-rule InstallBin
-{
-    local _t = [ FAppendSuffix $(>) : $(SUFEXE) ] ;
-
-    InstallInto $(<) : $(_t) ;
-    MODE on $(_t:G=installed) = $(EXEMODE) ;
-}
-
-rule InstallFile
-{
-    InstallInto $(<) : $(>) ;
-    MODE on $(>:G=installed) = $(FILEMODE) ;
-}
-
-rule InstallLib
-{
-    InstallInto $(<) : $(>) ;
-    MODE on $(>:G=installed) = $(FILEMODE) ;
-}
-
-rule InstallMan
-{
-    # Really this just strips the . from the suffix
-
-    local i s d ;
-
-    for i in $(>)
-    {
-        switch $(i:S)
-        {
-        case .1 : s = 1 ; case .2 : s = 2 ; case .3 : s = 3 ;
-        case .4 : s = 4 ; case .5 : s = 5 ; case .6 : s = 6 ;
-        case .7 : s = 7 ; case .8 : s = 8 ; case .l : s = l ;
-        case .n : s = n ; case .man : s = 1 ;
-        }
-
-        d = man$(s) ;
-
-        InstallInto $(d:R=$(<)) : $(i) ;
-    }
-
-    MODE on $(>:G=installed) = $(FILEMODE) ;
-}
-
-rule InstallShell
-{
-    InstallInto $(<) : $(>) ;
-    MODE on $(>:G=installed) = $(SHELLMODE) ;
-}
-
-rule Lex
-{
-    LexMv $(<) : $(>) ;
-    DEPENDS $(<) : $(>) ;
-    MakeLocate $(<) : $(LOCATE_SOURCE) ;
-    Clean clean : $(<) ;
-}
-
-rule Library
-{
-    LibraryFromObjects $(<) : $(>:S=$(SUFOBJ)) ;
-    Objects $(>) ;
-}
-
-rule LibraryFromObjects
-{
-    local _i _l _s ;
-
-    # Add grist to file names
-
-    _s = [ FGristFiles $(>) ] ;
-    _l = $(<:S=$(SUFLIB)) ;
-
-    # library depends on its member objects
-
-    if $(KEEPOBJS)
-    {
-        DEPENDS obj : $(_s) ;
-    }
-    else
-    {
-        DEPENDS lib : $(_l) ;
-    }
-
-    # Set LOCATE for the library and its contents.  The bound
-    # value shows up as $(NEEDLIBS) on the Link actions.
-    # For compatibility, we only do this if the library doesn't
-    # already have a path.
-
-    if ! $(_l:D)
-    {
-        MakeLocate $(_l) $(_l)($(_s:BS)) : $(LOCATE_TARGET) ;
-    }
-
-    if $(NOARSCAN)
-    {
-        # If we can't scan the library to timestamp its contents,
-        # we have to just make the library depend directly on the
-        # on-disk object files.
-
-        DEPENDS $(_l) : $(_s) ;
-    }
-    else
-    {
-        # If we can scan the library, we make the library depend
-        # on its members and each member depend on the on-disk
-        # object file.
-
-        DEPENDS $(_l) : $(_l)($(_s:BS)) ;
-
-        for _i in $(_s)
-        {
-        DEPENDS $(_l)($(_i:BS)) : $(_i) ;
-        }
-    }
-
-    Clean clean : $(_l) ;
-
-    if $(CRELIB) { CreLib $(_l) : $(_s[1]) ; }
-
-    Archive $(_l) : $(_s) ;
-
-    if $(RANLIB) { Ranlib $(_l) ; }
-
-    # If we can't scan the library, we have to leave the .o's around.
-
-    if ! ( $(NOARSCAN) || $(KEEPOBJS) ) { RmTemps $(_l) : $(_s) ; }
-}
-
-rule Link
-{
-    MODE on $(<) = $(EXEMODE) ;
-    Chmod $(<) ;
-}
-
-rule LinkLibraries
-{
-    # make library dependencies of target
-    # set NEEDLIBS variable used by 'actions Main'
-
-    local _t = [ FAppendSuffix $(<) : $(SUFEXE) ] ;
-
-    DEPENDS $(_t) : $(>:S=$(SUFLIB)) ;
-    NEEDLIBS on $(_t) += $(>:S=$(SUFLIB)) ;
-}
-
-rule Main
-{
-    MainFromObjects $(<) : $(>:S=$(SUFOBJ)) ;
-    Objects $(>) ;
-}
-
-rule MainFromObjects
-{
-    local _s _t ;
-
-    # Add grist to file names
-    # Add suffix to exe
-
-    _s = [ FGristFiles $(>) ] ;
-    _t = [ FAppendSuffix $(<) : $(SUFEXE) ] ;
-
-    if $(_t) != $(<)
-    {
-        DEPENDS $(<) : $(_t) ;
-        NOTFILE $(<) ;
-    }
-
-    # make compiled sources a dependency of target
-
-    DEPENDS exe : $(_t) ;
-    DEPENDS $(_t) : $(_s) ;
-    MakeLocate $(_t) : $(LOCATE_TARGET) ;
-
-    Clean clean : $(_t) ;
-
-    Link $(_t) : $(_s) ;
-}
-
-rule MakeLocate
-{
-    if $(>)
-    {
-        LOCATE on $(<) = $(>) ;
-        Depends $(<) : $(>[1]) ;
-        MkDir $(>[1]) ;
-    }
-}
-
-rule MkDir
-{
-    # If dir exists, don't update it
-    # Do this even for $(DOT).
-
-    NOUPDATE $(<) ;
-
-    if $(<) != $(DOT) && ! $($(<)-mkdir)
-    {
-        local s ;
-
-        # Cheesy gate to prevent multiple invocations on same dir
-        # MkDir1 has the actions
-        # Arrange for jam dirs
-
-        $(<)-mkdir = true ;
-        MkDir1 $(<) ;
-        Depends dirs : $(<) ;
-
-        # Recursively make parent directories.
-        # $(<:P) = $(<)'s parent, & we recurse until root
-
-        s = $(<:P) ;
-
-        if $(NT)
-        {
-            switch $(s)
-        {
-        case *:   : s = ;
-        case *:\\ : s = ;
-        }
-        }
-
-        if $(s) && $(s) != $(<)
-        {
-        Depends $(<) : $(s) ;
-        MkDir $(s) ;
-        }
-        else if $(s)
-        {
-            NOTFILE $(s) ;
-        }
-
-    }
-}
-
-rule Object
-{
-    local h ;
-
-    # locate object and search for source, if wanted
-
-    Clean clean : $(<) ;
-
-    MakeLocate $(<) : $(LOCATE_TARGET) ;
-    SEARCH on $(>) = $(SEARCH_SOURCE) ;
-
-    # Save HDRS for -I$(HDRS) on compile.
-    # We shouldn't need -I$(SEARCH_SOURCE) as cc can find headers
-    # in the .c file's directory, but generated .c files (from
-    # yacc, lex, etc) are located in $(LOCATE_TARGET), possibly
-    # different from $(SEARCH_SOURCE).
-
-    HDRS on $(<) = $(SEARCH_SOURCE) $(HDRS) $(SUBDIRHDRS) ;
-
-    # handle #includes for source: Jam scans for headers with
-    # the regexp pattern $(HDRSCAN) and then invokes $(HDRRULE)
-    # with the scanned file as the target and the found headers
-    # as the sources.  HDRSEARCH is the value of SEARCH used for
-    # the found header files.  Finally, if jam must deal with
-    # header files of the same name in different directories,
-    # they can be distinguished with HDRGRIST.
-
-    # $(h) is where cc first looks for #include "foo.h" files.
-    # If the source file is in a distant directory, look there.
-    # Else, look in "" (the current directory).
-
-    if $(SEARCH_SOURCE)
-    {
-        h = $(SEARCH_SOURCE) ;
-    }
-    else
-    {
-        h = "" ;
-    }
-
-    HDRRULE on $(>) = HdrRule ;
-    HDRSCAN on $(>) = $(HDRPATTERN) ;
-    HDRSEARCH on $(>) = $(HDRS) $(SUBDIRHDRS) $(h) $(STDHDRS) ;
-    HDRGRIST on $(>) = $(HDRGRIST) ;
-
-    # if source is not .c, generate .c with specific rule
-
-    switch $(>:S)
-    {
-        case .asm : As $(<) : $(>) ;
-        case .c :   Cc $(<) : $(>) ;
-        case .C :   C++ $(<) : $(>) ;
-        case .cc :  C++ $(<) : $(>) ;
-        case .cpp : C++ $(<) : $(>) ;
-        case .f :   Fortran $(<) : $(>) ;
-        case .l :   Cc $(<) : $(<:S=.c) ;
-                    Lex $(<:S=.c) : $(>) ;
-        case .s :   As $(<) : $(>) ;
-        case .y :   Cc $(<) : $(<:S=.c) ;
-                    Yacc $(<:S=.c) : $(>) ;
-        case * :    UserObject $(<) : $(>) ;
-    }
-}
-
-
-rule ObjectCcFlags
-{
-    CCFLAGS on [ FGristFiles $(<:S=$(SUFOBJ)) ] += $(>) ;
-}
-
-rule ObjectC++Flags
-{
-    C++FLAGS on [ FGristFiles $(<:S=$(SUFOBJ)) ] += $(>) ;
-}
-
-rule ObjectHdrs
-{
-    HDRS on [ FGristFiles $(<:S=$(SUFOBJ)) ] += $(>) ;
-}
-
-rule Objects
-{
-    local _i ;
-
-    for _i in [ FGristFiles $(<) ]
-    {
-        Object $(_i:S=$(SUFOBJ)) : $(_i) ;
-        DEPENDS obj : $(_i:S=$(SUFOBJ)) ;
-    }
-}
-
-rule RmTemps
-{
-    TEMPORARY $(>) ;
-}
-
-rule Setuid
-{
-    MODE on [ FAppendSuffix $(<) : $(SUFEXE) ] = 4711 ;
-}
-
-rule Shell
-{
-    DEPENDS shell : $(<) ;
-    DEPENDS $(<) : $(>) ;
-    SEARCH on $(>) = $(SEARCH_SOURCE) ;
-    MODE on $(<) = $(SHELLMODE) ;
-    Clean clean : $(<) ;
-    Chmod $(<) ;
-}
-
-rule SubDir
-{
-    local _r _s ;
-
-    #
-    # SubDir TOP d1 [ ... ]
-    #
-    # This introduces a Jamfile that is part of a project tree
-    # rooted at $(TOP).  It (only once) includes the project-specific
-    # rules file $(TOP)/Jamrules and then sets search & locate stuff.
-    #
-    # If the variable $(TOPRULES) is set (where TOP is the first arg
-    # to SubDir), that file is included instead of $(TOP)/Jamrules.
-    #
-    # d1 ... are the directory elements that lead to this directory
-    # from $(TOP).  We construct the system dependent path from these
-    # directory elements in order to set search & locate stuff.
-    #
-
-    if ! $($(<[1]))
-    {
-        if ! $(<[1])
-        {
-            EXIT SubDir syntax error ;
-        }
-
-        $(<[1]) = [ FSubDir $(<[2-]) ] ;
-    }
-
-    #
-    # If $(TOP)/Jamrules hasn't been included, do so.
-    #
-
-    if ! $($(<[1])-included)
-    {
-        # Gated entry.
-
-        $(<[1])-included = TRUE ;
-
-        # File is $(TOPRULES) or $(TOP)/Jamrules.
-
-        _r = $($(<[1])RULES) ;
-
-        if ! $(_r)
-        {
-        _r = $(JAMRULES:R=$($(<[1]))) ;
-        }
-
-        # Include it.
-
-        include $(_r) ;
-    }
-
-    # Get path to current directory from root using SubDir.
-    # Save dir tokens for other potential uses.
-
-    _s = [ FDirName $(<[2-]) ] ;
-    SUBDIR = $(_s:R=$($(<[1]))) ;
-        SUBDIR_TOKENS = $(<[2-]) ;
-
-    # Now set up SEARCH_SOURCE, LOCATE_TARGET, SOURCE_GRIST
-    # These can be reset if needed.  For example, if the source
-    # directory should not hold object files, LOCATE_TARGET can
-    # subsequently be redefined.
-
-    SEARCH_SOURCE = $(SUBDIR) ;
-    LOCATE_SOURCE = $(ALL_LOCATE_TARGET) $(SUBDIR) ;
-    LOCATE_TARGET = $(ALL_LOCATE_TARGET) $(SUBDIR) ;
-    SOURCE_GRIST = [ FGrist $(<[2-]) ] ;
-
-    # Reset per-directory ccflags, hdrs
-
-    SUBDIRCCFLAGS = ;
-    SUBDIRC++FLAGS = ;
-    SUBDIRHDRS = ;
-}
-
-rule SubDirCcFlags
-{
-    SUBDIRCCFLAGS += $(<) ;
-}
-
-rule SubDirC++Flags
-{
-    SUBDIRC++FLAGS += $(<) ;
-}
-
-rule SubDirHdrs
-{
-    SUBDIRHDRS += $(<) ;
-}
-
-rule SubInclude
-{
-    local _s ;
-
-    # That's
-    #   SubInclude TOP d1 [ d2 [ d3 [ d4 ] ] ]
-    #
-    # to include a subdirectory's Jamfile.
-
-    if ! $($(<[1]))
-    {
-        EXIT Top level of source tree has not been set with $(<[1]) ;
-    }
-
-    _s = [ FDirName $(<[2-]) ] ;
-
-    include $(JAMFILE:D=$(_s):R=$($(<[1]))) ;
-}
-
-rule Undefines
-{
-    UNDEFS on [ FAppendSuffix $(<) : $(SUFEXE) ] += $(UNDEFFLAG)$(>) ;
-}
-
-rule UserObject
-{
-    EXIT "Unknown suffix on" $(>) "- see UserObject rule in Jamfile(5)." ;
-}
-
-rule Yacc
-{
-    local _h ;
-
-    _h = $(<:BS=.h) ;
-
-    # Some places don't have a yacc.
-
-    MakeLocate $(<) $(_h) : $(LOCATE_SOURCE) ;
-
-    if $(YACC)
-    {
-        DEPENDS $(<) $(_h) : $(>) ;
-        Yacc1 $(<) $(_h) : $(>) ;
-        YaccMv $(<) $(_h) : $(>) ;
-        Clean clean : $(<) $(_h) ;
-    }
-
-    # Make sure someone includes $(_h) else it will be a deadly independent
-    # target.
-    INCLUDES $(<) : $(_h) ;
-}
-
-#
-# Utility rules; no side effects on these.
-#
-
-rule FGrist
-{
-    # Turn individual elements in $(<) into grist.
-
-    local _g _i ;
-
-    _g = $(<[1]) ;
-
-    for _i in $(<[2-])
-    {
-        _g = $(_g)!$(_i) ;
-    }
-
-    return $(_g) ;
-}
-
-rule FGristFiles
-{
-    if ! $(SOURCE_GRIST)
-    {
-        return $(<) ;
-    }
-    else
-    {
-        return $(<:G=$(SOURCE_GRIST)) ;
-    }
-}
-
-rule FGristSourceFiles
-{
-    # Produce source file name name with grist in it,
-    # if SOURCE_GRIST is set.
-
-    # Leave header files alone, because they have a global
-    # visibility.
-
-    if ! $(SOURCE_GRIST)
-    {
-        return $(<) ;
-    }
-    else
-    {
-        local _i _o ;
-
-        for _i in $(<)
-        {
-        switch $(_i)
-        {
-        case *.h :  _o += $(_i) ;
-        case * :    _o += $(_i:G=$(SOURCE_GRIST)) ;
-        }
-        }
-
-        return $(_o) ;
-    }
-}
-
-rule FConcat
-{
-    # Puts the variables together, removing spaces.
-
-    local _t _r ;
-
-    $(_r) = $(<[1]) ;
-
-    for _t in $(<[2-])
-    {
-        $(_r) = $(_r)$(_t) ;
-    }
-
-    return $(_r) ;
-}
-
-rule FSubDir
-{
-    local _i _d ;
-
-    # If $(>) is the path to the current directory, compute the
-    # path (using ../../ etc) back to that root directory.
-    # Sets result in $(<)
-
-    if ! $(<[1])
-    {
-        _d = $(DOT) ;
-    }
-    else
-    {
-        _d = $(DOTDOT) ;
-
-        for _i in $(<[2-])
-        {
-        _d = $(_d:R=$(DOTDOT)) ;
-        }
-    }
-
-    return $(_d) ;
-}
-
-rule FDirName
-{
-    local _s _i ;
-
-    # Turn individual elements in $(<) into a usable path.
-
-    if ! $(<)
-    {
-        _s = $(DOT) ;
-    }
-    else if $(VMS)
-    {
-        # This handles the following cases:
-        #   a -> [.a]
-        #   a b c -> [.a.b.c]
-        #   x: -> x:
-        #   x: a -> x:[a]
-        #   x:[a] b -> x:[a.b]
-
-        switch $(<[1])
-        {
-        case *:* : _s = $(<[1]) ;
-        case \\[*\\] : _s = $(<[1]) ;
-        case * : _s = [.$(<[1])] ;
-        }
-
-        for _i in [.$(<[2-])]
-        {
-        _s = $(_i:R=$(_s)) ;
-        }
-    }
-    else if $(MAC)
-    {
-        _s = $(DOT) ;
-
-        for _i in $(<)
-        {
-            _s = $(_i:R=$(_s)) ;
-        }
-    }
-    else
-    {
-        _s = $(<[1]) ;
-
-        for _i in $(<[2-])
-        {
-        _s = $(_i:R=$(_s)) ;
-        }
-    }
-
-    return $(_s) ;
-}
-
-
-rule _makeCommon
-{
-    # strip common initial elements
-
-    if $($(<)[1]) && $($(<)[1]) = $($(>)[1])
-    {
-        $(<) = $($(<)[2-]) ;
-        $(>) = $($(>)[2-]) ;
-        _makeCommon $(<) : $(>) ;
-    }
-}
-
-
-rule FRelPath
-{
-    local _l _r ;
-
-    # first strip off common parts
-
-    _l = $(<) ;
-    _r = $(>) ;
-
-    _makeCommon _l : _r ;
-
-    # now make path to root and path down
-
-    _l = [ FSubDir $(_l) ] ;
-    _r = [ FDirName $(_r) ] ;
-
-    # Concatenate and save
-
-    # XXX This should be better
-
-    if $(_r) = $(DOT) {
-        return $(_l) ;
-    } else {
-        return $(_r:R=$(_l)) ;
-    }
-}
-
-rule FAppendSuffix
-{
-       # E.g., "FAppendSuffix yacc lex foo.bat : $(SUFEXE) ;"
-       # returns (yacc,lex,foo.bat) on Unix and
-       # (yacc.exe,lex.exe,foo.bat) on NT.
-
-    if $(>)
-    {
-        local _i _o ;
-
-        for _i in $(<)
-        {
-        if $(_i:S)
-        {
-            _o += $(_i) ;
-        }
-        else
-        {
-            _o += $(_i:S=$(>)) ;
-        }
-        }
-        return $(_o) ;
-    }
-    else
-    {
-        return $(<) ;
-    }
-}
-
-rule unmakeDir
-{
-    if $(>[1]:D) && $(>[1]:D) != $(>[1]) && $(>[1]:D) != \\\\
-    {
-        unmakeDir $(<) : $(>[1]:D) $(>[1]:BS) $(>[2-]) ;
-    }
-    else
-    {
-        $(<) = $(>) ;
-    }
-}
-
-
-rule FConvertToSlashes
-{
-  local _d, _s, _i ;
-
-  unmakeDir _d : $(<) ;
-
-  _s = $(_d[1]) ;
-  for _i in $(_d[2-])
-  {
-    _s = $(_s)/$(_i) ;
-  }
-  return $(_s) ;
-}
-
-
-#
-# Actions
-#
-
-#
-# First the defaults
-#
-
-actions updated together piecemeal Archive
-{
-    $(AR) $(<) $(>)
-}
-
-actions As
-{
-    $(AS) $(ASFLAGS) -I$(HDRS) -o $(<) $(>)
-}
-
-actions C++
-{
-    $(C++) -c $(C++FLAGS) $(OPTIM) -I$(HDRS) -o $(<) $(>)
-}
-
-actions Cc
-{
-    $(CC) -c $(CCFLAGS) $(OPTIM) -I$(HDRS) -o $(<) $(>)
-}
-
-actions Chgrp
-{
-    $(CHGRP) $(GROUP) $(<)
-}
-
-actions Chmod1
-{
-    $(CHMOD) $(MODE) $(<)
-}
-
-actions Chown
-{
-    $(CHOWN) $(OWNER) $(<)
-}
-
-actions piecemeal together existing Clean
-{
-    $(RM) $(>)
-}
-
-actions File
-{
-    $(CP) $(>) $(<)
-}
-
-actions GenFile1
-{
-    $(>[1]) $(<) $(>[2-])
-}
-
-actions Fortran
-{
-    $(FORTRAN) $(FORTRANFLAGS) -o $(<) $(>)
-}
-
-actions HardLink
-{
-    $(RM) $(<) && $(LN) $(>) $(<)
-}
-
-actions Install
-{
-    $(CP) $(>) $(<)
-}
-
-actions Lex
-{
-    $(LEX) $(>)
-}
-
-actions LexMv
-{
-    $(MV) lex.yy.c $(<)
-}
-
-actions Link bind NEEDLIBS
-{
-    $(LINK) $(LINKFLAGS) -o $(<) $(UNDEFS) $(>) $(NEEDLIBS) $(LINKLIBS)
-}
-
-actions MkDir1
-{
-    $(MKDIR) $(<)
-}
-
-actions together Ranlib
-{
-    $(RANLIB) $(<)
-}
-
-actions quietly updated piecemeal together RmTemps
-{
-    $(RM) $(>)
-}
-
-actions Shell
-{
-    $(AWK) '
-        NR == 1 { print "$(SHELLHEADER)" }
-        NR == 1 && /^[#:]/ { next }
-        /^##/ { next }
-        { print }
-    ' < $(>) > $(<)
-}
-
-actions Yacc1
-{
-    $(YACC) $(YACCFLAGS) $(>)
-}
-
-actions YaccMv
-{
-    $(MV) $(YACCFILES).c $(<[1])
-    $(MV) $(YACCFILES).h $(<[2])
-}
-
-#
-# RELOCATE - for compilers with broken -o flags
-#
-
-if $(RELOCATE)
-{
-    actions C++
-    {
-    $(C++) -c $(C++FLAGS) $(OPTIM) -I$(HDRS) $(>)
-    }
-
-    actions Cc
-    {
-    $(CC) -c $(CCFLAGS) $(OPTIM) -I$(HDRS) $(>)
-    }
-
-    actions ignore CcMv
-    {
-    [ $(<) != $(>:BS=$(SUFOBJ)) ] && $(MV) $(>:BS=$(SUFOBJ)) $(<)
-    }
-}
-
-#
-# NOARUPDATE - can't update an archive
-#
-
-if $(NOARUPDATE)
-{
-    actions Archive
-    {
-    $(AR) $(<) $(>)
-    }
-}
-
-#
-# NT specific actions
-#
-
-if $(NT)
-{
-  if $(TOOLSET) = VISUALC || $(TOOLSET) = VC7 || $(TOOLSET) = INTELC
-  {
-    actions updated together piecemeal Archive
-    {
-    if exist $(<) set _$(<:B)_=$(<)
-    $(AR) /out:$(<) %_$(<:B)_% $(>)
-    }
-
-    actions As
-    {
-    $(AS) /Ml /p /v /w2 $(>) $(<) ,nul,nul;
-    }
-
-    actions Cc
-    {
-    $(CC) /c $(CCFLAGS) $(OPTIM) /Fo$(<) /I$(HDRS) /I$(STDHDRS) $(>)
-    }
-
-    actions C++
-    {
-    $(C++) /c $(C++FLAGS) $(OPTIM) /Fo$(<) /I$(HDRS) /I$(STDHDRS) /Tp$(>)
-    }
-
-    actions Link bind NEEDLIBS
-    {
-    $(LINK) $(LINKFLAGS) /out:$(<) $(UNDEFS) $(>) $(NEEDLIBS) $(LINKLIBS)
-    }
-  }
-  else if $(TOOLSET) = VISUALC16
-  {
-    actions updated together piecemeal Archive
-    {
-    $(AR) $(<) -+$(>)
-    }
-
-    actions Cc
-    {
-    $(CC) /c $(CCFLAGS) $(OPTIM) /Fo$(<) /I$(HDRS) $(>)
-    }
-
-    actions C++
-    {
-    $(C++) /c $(C++FLAGS) $(OPTIM) /Fo$(<) /I$(HDRS) /Tp$(>)
-    }
-
-    actions Link bind NEEDLIBS
-    {
-    $(LINK) $(LINKFLAGS) /out:$(<) $(UNDEFS) $(>) $(NEEDLIBS) $(LINKLIBS)
-    }
-  }
-  else if $(TOOLSET) = BORLANDC
-  {
-    actions updated together piecemeal Archive
-    {
-    $(AR) $(<) -+$(>)
-    }
-
-    actions Link bind NEEDLIBS
-    {
-    $(LINK) -e$(<) $(LINKFLAGS) $(UNDEFS) -L$(LINKLIBS) $(NEEDLIBS) $(>)
-    }
-
-    actions C++
-    {
-    $(C++) -c $(C++FLAGS) $(OPTIM) -I$(HDRS) -o$(<) $(>)
-    }
-
-    actions Cc
-    {
-    $(CC) -c $(CCFLAGS) $(OPTIM) -I$(HDRS) -o$(<) $(>)
-    }
-
-  }
-  else if $(TOOLSET) = MINGW
-  {
-    actions together piecemeal Archive
-    {
-      $(AR) $(<) $(>:T)
-    }
-
-    actions Cc
-    {
-    $(CC) -c $(CCFLAGS) $(OPTIM) -I$(HDRS) -o$(<) $(>)
-    }
-
-    actions C++
-    {
-    $(C++) -c $(C++FLAGS) $(OPTIM) -I$(HDRS) -o$(<) $(>)
-    }
-  }
-  else if $(TOOLSET) = WATCOM
-  {
-    actions together piecemeal Archive
-    {
-    $(AR) $(<) +-$(>)
-    }
-
-    actions Cc
-    {
-    $(CC) $(CCFLAGS) $(OPTIM) /Fo=$(<) /I$(HDRS) $(>)
-    }
-
-    actions C++
-    {
-    $(C++) $(C++FLAGS) $(OPTIM) /Fo=$(<) /I$(HDRS) $(>)
-    }
-
-    actions Link bind NEEDLIBS
-    {
-    $(LINK) $(LINKFLAGS) /Fe=$(<) $(UNDEFS) $(>) $(NEEDLIBS) $(LINKLIBS)
-    }
-
-    actions Shell
-    {
-    $(CP) $(>) $(<)
-    }
-  }
-  else if $(TOOLSET) = LCC
-  {
-    actions together piecemeal Archive
-    {
-    $(AR) /out:$(<) $(>)
-    }
-
-    actions Cc
-    {
-    $(CC) $(CCFLAGS) $(OPTIM) -Fo$(<) -I$(HDRS) $(>)
-    }
-
-    actions Link bind NEEDLIBS
-    {
-    $(LINK) $(LINKFLAGS) -o $(<) $(UNDEFS) $(>) $(NEEDLIBS) $(LINKLIBS)
-    }
-
-    actions Shell
-    {
-    $(CP) $(>) $(<)
-    }
-  }
-}
-
-#
-# OS2 specific actions
-#
-
-else if $(OS2)
-{
-  if $(TOOLSET) = WATCOM
-  {
-    actions together piecemeal Archive
-    {
-    $(AR) $(<) +-$(>)
-    }
-
-    actions Cc
-    {
-    $(CC) $(CCFLAGS) $(OPTIM) /Fo=$(<) /I$(HDRS) $(>)
-    }
-
-    actions C++
-    {
-    $(C++) $(C++FLAGS) $(OPTIM) /Fo=$(<) /I$(HDRS) $(>)
-    }
-
-    actions Link bind NEEDLIBS
-    {
-    $(LINK) $(LINKFLAGS) /Fe=$(<) $(UNDEFS) $(>) $(NEEDLIBS) $(LINKLIBS)
-    }
-
-    actions Shell
-    {
-    $(CP) $(>) $(<)
-    }
-  }
-  else if $(TOOLSET) = EMX
-  {
-    actions together piecemeal Archive
-    {
-      $(AR) $(<) $(>:T)
-    }
-
-    actions Cc
-    {
-    $(CC) -c $(CCFLAGS) $(OPTIM) -I$(HDRS) -o$(<) $(>)
-    }
-
-    actions C++
-    {
-    $(C++) -c $(C++FLAGS) $(OPTIM) -I$(HDRS) -o$(<) $(>)
-    }
-  }
-}
-
-#
-# VMS specific actions
-#
-
-else if $(VMS)
-{
-    actions updated together piecemeal Archive
-    {
-    lib/replace $(<) $(>[1]) ,$(>[2-])
-    }
-
-    actions Cc
-    {
-    $(CC)/obj=$(<) $(CCFLAGS) $(OPTIM) $(SLASHINC) $(>)
-    }
-
-    actions C++
-    {
-    $(C++)/obj=$(<) $(C++FLAGS) $(OPTIM) $(SLASHINC) $(>)
-    }
-
-    actions piecemeal together existing Clean
-    {
-    $(RM) $(>[1]);* ,$(>[2-]);*
-    }
-
-    actions together quietly CreLib
-    {
-    if f$search("$(<)") .eqs. "" then lib/create $(<)
-    }
-
-    actions GenFile1
-    {
-    mcr $(>[1]) $(<) $(>[2-])
-    }
-
-    actions Link bind NEEDLIBS
-    {
-    $(LINK)/exe=$(<) $(LINKFLAGS) $(>[1]) ,$(>[2-]) ,$(NEEDLIBS)/lib ,$(LINKLIBS)
-    }
-
-    actions quietly updated piecemeal together RmTemps
-    {
-    $(RM) $(>[1]);* ,$(>[2-]);*
-    }
-
-    actions Shell
-    {
-    $(CP) $(>) $(<)
-    }
-}
-
-#
-# Mac specifc actions
-#
-
-else if $(MAC)
-{
-    actions together Archive
-    {
-    $(LINK) -library -o $(<) $(>)
-    }
-
-    actions Cc
-    {
-    set -e MWCincludes $(MACINC)
-    $(CC) -o $(<) $(CCFLAGS) $(OPTIM) $(>)
-    }
-
-    actions C++
-    {
-    set -e MWCincludes $(MACINC)
-    $(CC) -o $(<) $(C++FLAGS) $(OPTIM) $(>)
-    }
-
-    actions Link bind NEEDLIBS
-    {
-    $(LINK) -o $(<) $(LINKFLAGS) $(>) $(NEEDLIBS) "$(LINKLIBS)"
-    }
-}
-
-#
-# Backwards compatibility with jam 1, where rules were uppercased.
-#
-
-rule BULK { Bulk $(<) : $(>) ; }
-rule FILE { File $(<) : $(>) ; }
-rule HDRRULE { HdrRule $(<) : $(>) ; }
-rule INSTALL { Install $(<) : $(>) ; }
-rule LIBRARY { Library $(<) : $(>) ; }
-rule LIBS { LinkLibraries $(<) : $(>) ; }
-rule LINK { Link $(<) : $(>) ; }
-rule MAIN { Main $(<) : $(>) ; }
-rule SETUID { Setuid $(<) ; }
-rule SHELL { Shell $(<) : $(>) ; }
-rule UNDEFINES { Undefines $(<) : $(>) ; }
-
-# Old INSTALL* didn't take dest directory.
-
-rule INSTALLBIN { InstallBin $(BINDIR) : $(<) ; }
-rule INSTALLLIB { InstallLib $(LIBDIR) : $(<) ; }
-rule INSTALLMAN { InstallMan $(MANDIR) : $(<) ; }
-
-# Compatibility with jam 2.2.
-
-rule addDirName { $(<) += [ FDirName $(>) ] ; }
-rule makeDirName { $(<) = [ FDirName $(>) ] ; }
-rule makeGristedName { $(<) = [ FGristSourceFiles $(>) ] ; }
-rule makeRelPath { $(<[1]) = [ FRelPath $(<[2-]) : $(>) ] ; }
-rule makeSuffixed { $(<[1]) = [ FAppendSuffix $(>) : $(<[2]) ] ; }
-
-#
-# Now include the user's Jamfile.
-#
-
-{
-    if $(JAMFILE) { include $(JAMFILE) ; }
-}
-
-}
diff --git a/jam-files/engine/boost-jam.spec b/jam-files/engine/boost-jam.spec
deleted file mode 100644
index bc572fc9..00000000
--- a/jam-files/engine/boost-jam.spec
+++ /dev/null
@@ -1,64 +0,0 @@
-Name: boost-jam
-Version: 3.1.19
-Summary: Build tool
-Release: 1
-Source: %{name}-%{version}.tgz
-
-License: Boost Software License, Version 1.0
-Group: Development/Tools
-URL: http://www.boost.org
-Packager: Rene Rivera <grafik@redshift-software.com>
-BuildRoot: /var/tmp/%{name}-%{version}.root
-
-%description
-Boost Jam is a build tool based on FTJam, which in turn is based on
-Perforce Jam. It contains significant improvements made to facilitate
-its use in the Boost Build System, but should be backward compatible
-with Perforce Jam.
-
-Authors:
-    Perforce Jam : Cristopher Seiwald
-    FT Jam : David Turner
-    Boost Jam : David Abrahams
-
-Copyright:
-    /+\
-    +\  Copyright 1993-2002 Christopher Seiwald and Perforce Software, Inc.
-    \+/
-    License is hereby granted to use this software and distribute it
-    freely, as long as this copyright notice is retained and modifications
-    are clearly marked.
-    ALL WARRANTIES ARE HEREBY DISCLAIMED.
-
-Also:
-    Copyright 2001-2006 David Abrahams.
-    Copyright 2002-2006 Rene Rivera.
-    Copyright 2003-2006 Vladimir Prus.
-
-    Distributed under the Boost Software License, Version 1.0.
-    (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-%prep
-%setup -n %{name}-%{version}
-
-%build
-LOCATE_TARGET=bin ./build.sh $BOOST_JAM_TOOLSET
-
-%install
-rm -rf $RPM_BUILD_ROOT
-mkdir -p $RPM_BUILD_ROOT%{_bindir}
-mkdir -p $RPM_BUILD_ROOT%{_docdir}/%{name}-%{version}
-install -m 755 bin/bjam $RPM_BUILD_ROOT%{_bindir}/bjam-%{version}
-ln -sf bjam-%{version} $RPM_BUILD_ROOT%{_bindir}/bjam
-cp -R *.html *.png *.css LICENSE*.txt images jam $RPM_BUILD_ROOT%{_docdir}/%{name}-%{version}
-
-find $RPM_BUILD_ROOT -name CVS -type d -exec rm -r {} \;
-
-%files
-%defattr(-,root,root)
-%attr(755,root,root) /usr/bin/*
-%doc %{_docdir}/%{name}-%{version}
-
-
-%clean
-rm -rf $RPM_BUILD_ROOT
diff --git a/jam-files/engine/boost-no-inspect b/jam-files/engine/boost-no-inspect
deleted file mode 100644
index 8a06f3a7..00000000
--- a/jam-files/engine/boost-no-inspect
+++ /dev/null
@@ -1 +0,0 @@
-this really out of our hands, so tell inspect to ignore directory
\ No newline at end of file
diff --git a/jam-files/engine/build.bat b/jam-files/engine/build.bat
deleted file mode 100644
index f927b769..00000000
--- a/jam-files/engine/build.bat
+++ /dev/null
@@ -1,532 +0,0 @@
-@ECHO OFF
-
-REM ~ Copyright 2002-2007 Rene Rivera.
-REM ~ Distributed under the Boost Software License, Version 1.0.
-REM ~ (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-setlocal
-goto Start
-
-
-:Set_Error
-color 00
-goto :eof
-
-
-:Clear_Error
-ver >nul
-goto :eof
-
-
-:Error_Print
-REM Output an error message and set the errorlevel to indicate failure.
-setlocal
-ECHO ###
-ECHO ### %1
-ECHO ###
-ECHO ### You can specify the toolset as the argument, i.e.:
-ECHO ###     .\build.bat msvc
-ECHO ###
-ECHO ### Toolsets supported by this script are: borland, como, gcc, gcc-nocygwin,
-ECHO ###     intel-win32, metrowerks, mingw, msvc, vc7, vc8, vc9, vc10
-ECHO ###
-call :Set_Error
-endlocal
-goto :eof
-
-
-:Test_Path
-REM Tests for the given file(executable) presence in the directories in the PATH
-REM environment variable. Additionaly sets FOUND_PATH to the path of the
-REM found file.
-call :Clear_Error
-setlocal
-set test=%~$PATH:1
-endlocal
-if not errorlevel 1 set FOUND_PATH=%~dp$PATH:1
-goto :eof
-
-
-:Test_Option
-REM Tests whether the given string is in the form of an option: "--*"
-call :Clear_Error
-setlocal
-set test=%1
-if not defined test (
-    call :Set_Error
-    goto Test_Option_End
-)
-set test=###%test%###
-set test=%test:"###=%
-set test=%test:###"=%
-set test=%test:###=%
-if not "-" == "%test:~1,1%" call :Set_Error
-:Test_Option_End
-endlocal
-goto :eof
-
-
-:Test_Empty
-REM Tests whether the given string is not empty
-call :Clear_Error
-setlocal
-set test=%1
-if not defined test (
-    call :Clear_Error
-    goto Test_Empty_End
-)
-set test=###%test%###
-set test=%test:"###=%
-set test=%test:###"=%
-set test=%test:###=%
-if not "" == "%test%" call :Set_Error
-:Test_Empty_End
-endlocal
-goto :eof
-
-
-:Call_If_Exists
-if EXIST %1 call %*
-goto :eof
-
-
-:Guess_Toolset
-REM Try and guess the toolset to bootstrap the build with...
-REM Sets BOOST_JAM_TOOLSET to the first found toolset.
-REM May also set BOOST_JAM_TOOLSET_ROOT to the
-REM location of the found toolset.
-
-call :Clear_Error
-call :Test_Empty %ProgramFiles%
-if not errorlevel 1 set ProgramFiles=C:\Program Files
-
-call :Clear_Error
-if NOT "_%VS100COMNTOOLS%_" == "__" (
-    set "BOOST_JAM_TOOLSET=vc10"
-    set "BOOST_JAM_TOOLSET_ROOT=%VS100COMNTOOLS%..\..\VC\"
-    goto :eof)
-call :Clear_Error
-if EXIST "%ProgramFiles%\Microsoft Visual Studio 10.0\VC\VCVARSALL.BAT" (
-    set "BOOST_JAM_TOOLSET=vc10"
-    set "BOOST_JAM_TOOLSET_ROOT=%ProgramFiles%\Microsoft Visual Studio 10.0\VC\"
-    goto :eof)
-call :Clear_Error
-if NOT "_%VS90COMNTOOLS%_" == "__" (
-    set "BOOST_JAM_TOOLSET=vc9"
-    set "BOOST_JAM_TOOLSET_ROOT=%VS90COMNTOOLS%..\..\VC\"
-    goto :eof)
-call :Clear_Error
-if EXIST "%ProgramFiles%\Microsoft Visual Studio 9.0\VC\VCVARSALL.BAT" (
-    set "BOOST_JAM_TOOLSET=vc9"
-    set "BOOST_JAM_TOOLSET_ROOT=%ProgramFiles%\Microsoft Visual Studio 9.0\VC\"
-    goto :eof)
-call :Clear_Error
-if NOT "_%VS80COMNTOOLS%_" == "__" (
-    set "BOOST_JAM_TOOLSET=vc8"
-    set "BOOST_JAM_TOOLSET_ROOT=%VS80COMNTOOLS%..\..\VC\"
-    goto :eof)
-call :Clear_Error
-if EXIST "%ProgramFiles%\Microsoft Visual Studio 8\VC\VCVARSALL.BAT" (
-    set "BOOST_JAM_TOOLSET=vc8"
-    set "BOOST_JAM_TOOLSET_ROOT=%ProgramFiles%\Microsoft Visual Studio 8\VC\"
-    goto :eof)
-call :Clear_Error
-if NOT "_%VS71COMNTOOLS%_" == "__" (
-    set "BOOST_JAM_TOOLSET=vc7"
-    set "BOOST_JAM_TOOLSET_ROOT=%VS71COMNTOOLS%\..\..\VC7\"
-    goto :eof)
-call :Clear_Error
-if NOT "_%VCINSTALLDIR%_" == "__" (
-    REM %VCINSTALLDIR% is also set for VC9 (and probably VC8)
-    set "BOOST_JAM_TOOLSET=vc7"
-    set "BOOST_JAM_TOOLSET_ROOT=%VCINSTALLDIR%\VC7\"
-    goto :eof)
-call :Clear_Error
-if EXIST "%ProgramFiles%\Microsoft Visual Studio .NET 2003\VC7\bin\VCVARS32.BAT" (
-    set "BOOST_JAM_TOOLSET=vc7"
-    set "BOOST_JAM_TOOLSET_ROOT=%ProgramFiles%\Microsoft Visual Studio .NET 2003\VC7\"
-    goto :eof)
-call :Clear_Error
-if EXIST "%ProgramFiles%\Microsoft Visual Studio .NET\VC7\bin\VCVARS32.BAT" (
-    set "BOOST_JAM_TOOLSET=vc7"
-    set "BOOST_JAM_TOOLSET_ROOT=%ProgramFiles%\Microsoft Visual Studio .NET\VC7\"
-    goto :eof)
-call :Clear_Error
-if NOT "_%MSVCDir%_" == "__" (
-    set "BOOST_JAM_TOOLSET=msvc"
-    set "BOOST_JAM_TOOLSET_ROOT=%MSVCDir%\"
-    goto :eof)
-call :Clear_Error
-if EXIST "%ProgramFiles%\Microsoft Visual Studio\VC98\bin\VCVARS32.BAT" (
-    set "BOOST_JAM_TOOLSET=msvc"
-    set "BOOST_JAM_TOOLSET_ROOT=%ProgramFiles%\Microsoft Visual Studio\VC98\"
-    goto :eof)
-call :Clear_Error
-if EXIST "%ProgramFiles%\Microsoft Visual C++\VC98\bin\VCVARS32.BAT" (
-    set "BOOST_JAM_TOOLSET=msvc"
-    set "BOOST_JAM_TOOLSET_ROOT=%ProgramFiles%\Microsoft Visual C++\VC98\"
-    goto :eof)
-call :Clear_Error
-call :Test_Path cl.exe
-if not errorlevel 1 (
-    set "BOOST_JAM_TOOLSET=msvc"
-    set "BOOST_JAM_TOOLSET_ROOT=%FOUND_PATH%..\"
-    goto :eof)
-call :Clear_Error
-call :Test_Path vcvars32.bat
-if not errorlevel 1 (
-    set "BOOST_JAM_TOOLSET=msvc"
-    call "%FOUND_PATH%VCVARS32.BAT"
-    set "BOOST_JAM_TOOLSET_ROOT=%MSVCDir%\"
-    goto :eof)
-call :Clear_Error
-if EXIST "C:\Borland\BCC55\Bin\bcc32.exe" (
-    set "BOOST_JAM_TOOLSET=borland"
-    set "BOOST_JAM_TOOLSET_ROOT=C:\Borland\BCC55\"
-    goto :eof)
-call :Clear_Error
-call :Test_Path bcc32.exe
-if not errorlevel 1 (
-    set "BOOST_JAM_TOOLSET=borland"
-    set "BOOST_JAM_TOOLSET_ROOT=%FOUND_PATH%..\"
-    goto :eof)
-call :Clear_Error
-call :Test_Path icl.exe
-if not errorlevel 1 (
-    set "BOOST_JAM_TOOLSET=intel-win32"
-    set "BOOST_JAM_TOOLSET_ROOT=%FOUND_PATH%..\"
-    goto :eof)
-call :Clear_Error
-if EXIST "C:\MinGW\bin\gcc.exe" (
-    set "BOOST_JAM_TOOLSET=mingw"
-    set "BOOST_JAM_TOOLSET_ROOT=C:\MinGW\"
-    goto :eof)
-call :Clear_Error
-if NOT "_%CWFolder%_" == "__" (
-    set "BOOST_JAM_TOOLSET=metrowerks"
-    set "BOOST_JAM_TOOLSET_ROOT=%CWFolder%\"
-    goto :eof )
-call :Clear_Error
-call :Test_Path mwcc.exe
-if not errorlevel 1 (
-    set "BOOST_JAM_TOOLSET=metrowerks"
-    set "BOOST_JAM_TOOLSET_ROOT=%FOUND_PATH%..\..\"
-    goto :eof)
-call :Clear_Error
-call :Error_Print "Could not find a suitable toolset."
-goto :eof
-
-
-:Guess_Yacc
-REM Tries to find bison or yacc in common places so we can build the grammar.
-call :Clear_Error
-call :Test_Path yacc.exe
-if not errorlevel 1 (
-    set "YACC=yacc -d"
-    goto :eof)
-call :Clear_Error
-call :Test_Path bison.exe
-if not errorlevel 1 (
-    set "YACC=bison -d --yacc"
-    goto :eof)
-call :Clear_Error
-if EXIST "C:\Program Files\GnuWin32\bin\bison.exe" (
-    set "YACC=C:\Program Files\GnuWin32\bin\bison.exe" -d --yacc
-    goto :eof)
-call :Clear_Error
-call :Error_Print "Could not find Yacc to build the Jam grammar."
-goto :eof
-
-
-:Start
-set BOOST_JAM_TOOLSET=
-set BOOST_JAM_ARGS=
-
-REM If no arguments guess the toolset;
-REM or if first argument is an option guess the toolset;
-REM otherwise the argument is the toolset to use.
-call :Clear_Error
-call :Test_Empty %1
-if not errorlevel 1 (
-    call :Guess_Toolset
-    if not errorlevel 1 ( goto Setup_Toolset ) else ( goto Finish )
-)
-
-call :Clear_Error
-call :Test_Option %1
-if not errorlevel 1 (
-    call :Guess_Toolset
-    if not errorlevel 1 ( goto Setup_Toolset ) else ( goto Finish )
-)
-
-call :Clear_Error
-set BOOST_JAM_TOOLSET=%1
-shift
-goto Setup_Toolset
-
-
-:Setup_Toolset
-REM Setup the toolset command and options. This bit of code
-REM needs to be flexible enough to handle both when
-REM the toolset was guessed at and found, or when the toolset
-REM was indicated in the command arguments.
-REM NOTE: The strange multiple "if ?? == _toolset_" tests are that way
-REM because in BAT variables are subsituted only once during a single
-REM command. A complete "if ... ( commands ) else ( commands )"
-REM is a single command, even though it's in multiple lines here.
-:Setup_Args
-call :Clear_Error
-call :Test_Empty %1
-if not errorlevel 1 goto Config_Toolset
-call :Clear_Error
-call :Test_Option %1
-if errorlevel 1 (
-    set BOOST_JAM_ARGS=%BOOST_JAM_ARGS% %1
-    shift
-    goto Setup_Args
-)
-:Config_Toolset
-if NOT "_%BOOST_JAM_TOOLSET%_" == "_metrowerks_" goto Skip_METROWERKS
-if NOT "_%CWFolder%_" == "__" (
-    set "BOOST_JAM_TOOLSET_ROOT=%CWFolder%\"
-    )
-set "PATH=%BOOST_JAM_TOOLSET_ROOT%Other Metrowerks Tools\Command Line Tools;%PATH%"
-set "BOOST_JAM_CC=mwcc -runtime ss -cwd include -DNT -lkernel32.lib -ladvapi32.lib -luser32.lib"
-set "BOOST_JAM_OPT_JAM=-o bootstrap\jam0.exe"
-set "BOOST_JAM_OPT_MKJAMBASE=-o bootstrap\mkjambase0.exe"
-set "BOOST_JAM_OPT_YYACC=-o bootstrap\yyacc0.exe"
-set "_known_=1"
-:Skip_METROWERKS
-if NOT "_%BOOST_JAM_TOOLSET%_" == "_msvc_" goto Skip_MSVC
-if NOT "_%MSVCDir%_" == "__" (
-    set "BOOST_JAM_TOOLSET_ROOT=%MSVCDir%\"
-    )
-call :Call_If_Exists "%BOOST_JAM_TOOLSET_ROOT%bin\VCVARS32.BAT"
-if not "_%BOOST_JAM_TOOLSET_ROOT%_" == "__" (
-    set "PATH=%BOOST_JAM_TOOLSET_ROOT%bin;%PATH%"
-    )
-set "BOOST_JAM_CC=cl /nologo /GZ /Zi /MLd /Fobootstrap/ /Fdbootstrap/ -DNT -DYYDEBUG kernel32.lib advapi32.lib user32.lib"
-set "BOOST_JAM_OPT_JAM=/Febootstrap\jam0"
-set "BOOST_JAM_OPT_MKJAMBASE=/Febootstrap\mkjambase0"
-set "BOOST_JAM_OPT_YYACC=/Febootstrap\yyacc0"
-set "_known_=1"
-:Skip_MSVC
-if NOT "_%BOOST_JAM_TOOLSET%_" == "_vc7_" goto Skip_VC7
-if NOT "_%VS71COMNTOOLS%_" == "__" (
-    set "BOOST_JAM_TOOLSET_ROOT=%VS71COMNTOOLS%..\..\VC7\"
-    )
-if "_%VCINSTALLDIR%_" == "__" call :Call_If_Exists "%BOOST_JAM_TOOLSET_ROOT%bin\VCVARS32.BAT"
-if NOT "_%BOOST_JAM_TOOLSET_ROOT%_" == "__" (
-    if "_%VCINSTALLDIR%_" == "__" (
-        set "PATH=%BOOST_JAM_TOOLSET_ROOT%bin;%PATH%"
-        ) )
-set "BOOST_JAM_CC=cl /nologo /GZ /Zi /MLd /Fobootstrap/ /Fdbootstrap/ -DNT -DYYDEBUG kernel32.lib advapi32.lib user32.lib"
-set "BOOST_JAM_OPT_JAM=/Febootstrap\jam0"
-set "BOOST_JAM_OPT_MKJAMBASE=/Febootstrap\mkjambase0"
-set "BOOST_JAM_OPT_YYACC=/Febootstrap\yyacc0"
-set "_known_=1"
-:Skip_VC7
-if NOT "_%BOOST_JAM_TOOLSET%_" == "_vc8_" goto Skip_VC8
-if NOT "_%VS80COMNTOOLS%_" == "__" (
-    set "BOOST_JAM_TOOLSET_ROOT=%VS80COMNTOOLS%..\..\VC\"
-    )
-if "_%VCINSTALLDIR%_" == "__" call :Call_If_Exists "%BOOST_JAM_TOOLSET_ROOT%VCVARSALL.BAT" %BOOST_JAM_ARGS%
-if NOT "_%BOOST_JAM_TOOLSET_ROOT%_" == "__" (
-    if "_%VCINSTALLDIR%_" == "__" (
-        set "PATH=%BOOST_JAM_TOOLSET_ROOT%bin;%PATH%"
-        ) )
-set "BOOST_JAM_CC=cl /nologo /RTC1 /Zi /MTd /Fobootstrap/ /Fdbootstrap/ -DNT -DYYDEBUG -wd4996 kernel32.lib advapi32.lib user32.lib"
-set "BOOST_JAM_OPT_JAM=/Febootstrap\jam0"
-set "BOOST_JAM_OPT_MKJAMBASE=/Febootstrap\mkjambase0"
-set "BOOST_JAM_OPT_YYACC=/Febootstrap\yyacc0"
-set "_known_=1"
-:Skip_VC8
-if NOT "_%BOOST_JAM_TOOLSET%_" == "_vc9_" goto Skip_VC9
-if NOT "_%VS90COMNTOOLS%_" == "__" (
-    set "BOOST_JAM_TOOLSET_ROOT=%VS90COMNTOOLS%..\..\VC\"
-    )
-if "_%VCINSTALLDIR%_" == "__" call :Call_If_Exists "%BOOST_JAM_TOOLSET_ROOT%VCVARSALL.BAT" %BOOST_JAM_ARGS%
-if NOT "_%BOOST_JAM_TOOLSET_ROOT%_" == "__" (
-    if "_%VCINSTALLDIR%_" == "__" (
-        set "PATH=%BOOST_JAM_TOOLSET_ROOT%bin;%PATH%"
-        ) )
-set "BOOST_JAM_CC=cl /nologo /RTC1 /Zi /MTd /Fobootstrap/ /Fdbootstrap/ -DNT -DYYDEBUG -wd4996 kernel32.lib advapi32.lib user32.lib"
-set "BOOST_JAM_OPT_JAM=/Febootstrap\jam0"
-set "BOOST_JAM_OPT_MKJAMBASE=/Febootstrap\mkjambase0"
-set "BOOST_JAM_OPT_YYACC=/Febootstrap\yyacc0"
-set "_known_=1"
-:Skip_VC9
-if NOT "_%BOOST_JAM_TOOLSET%_" == "_vc10_" goto Skip_VC10
-if NOT "_%VS100COMNTOOLS%_" == "__" (
-    set "BOOST_JAM_TOOLSET_ROOT=%VS100COMNTOOLS%..\..\VC\"
-    )
-if "_%VCINSTALLDIR%_" == "__" call :Call_If_Exists "%BOOST_JAM_TOOLSET_ROOT%VCVARSALL.BAT" %BOOST_JAM_ARGS%
-if NOT "_%BOOST_JAM_TOOLSET_ROOT%_" == "__" (
-    if "_%VCINSTALLDIR%_" == "__" (
-        set "PATH=%BOOST_JAM_TOOLSET_ROOT%bin;%PATH%"
-        ) )
-set "BOOST_JAM_CC=cl /nologo /RTC1 /Zi /MTd /Fobootstrap/ /Fdbootstrap/ -DNT -DYYDEBUG -wd4996 kernel32.lib advapi32.lib user32.lib"
-set "BOOST_JAM_OPT_JAM=/Febootstrap\jam0"
-set "BOOST_JAM_OPT_MKJAMBASE=/Febootstrap\mkjambase0"
-set "BOOST_JAM_OPT_YYACC=/Febootstrap\yyacc0"
-set "_known_=1"
-:Skip_VC10
-if NOT "_%BOOST_JAM_TOOLSET%_" == "_borland_" goto Skip_BORLAND
-if "_%BOOST_JAM_TOOLSET_ROOT%_" == "__" (
-    call :Test_Path bcc32.exe )
-if "_%BOOST_JAM_TOOLSET_ROOT%_" == "__" (
-    if not errorlevel 1 (
-        set "BOOST_JAM_TOOLSET_ROOT=%FOUND_PATH%..\"
-        ) )
-if not "_%BOOST_JAM_TOOLSET_ROOT%_" == "__" (
-    set "PATH=%BOOST_JAM_TOOLSET_ROOT%Bin;%PATH%"
-    )
-set "BOOST_JAM_CC=bcc32 -WC -w- -q -I%BOOST_JAM_TOOLSET_ROOT%Include -L%BOOST_JAM_TOOLSET_ROOT%Lib /DNT -nbootstrap"
-set "BOOST_JAM_OPT_JAM=-ejam0"
-set "BOOST_JAM_OPT_MKJAMBASE=-emkjambasejam0"
-set "BOOST_JAM_OPT_YYACC=-eyyacc0"
-set "_known_=1"
-:Skip_BORLAND
-if NOT "_%BOOST_JAM_TOOLSET%_" == "_como_" goto Skip_COMO
-set "BOOST_JAM_CC=como -DNT"
-set "BOOST_JAM_OPT_JAM=-o bootstrap\jam0.exe"
-set "BOOST_JAM_OPT_MKJAMBASE=-o bootstrap\mkjambase0.exe"
-set "BOOST_JAM_OPT_YYACC=-o bootstrap\yyacc0.exe"
-set "_known_=1"
-:Skip_COMO
-if NOT "_%BOOST_JAM_TOOLSET%_" == "_gcc_" goto Skip_GCC
-set "BOOST_JAM_CC=gcc -DNT"
-set "BOOST_JAM_OPT_JAM=-o bootstrap\jam0.exe"
-set "BOOST_JAM_OPT_MKJAMBASE=-o bootstrap\mkjambase0.exe"
-set "BOOST_JAM_OPT_YYACC=-o bootstrap\yyacc0.exe"
-set "_known_=1"
-:Skip_GCC
-if NOT "_%BOOST_JAM_TOOLSET%_" == "_gcc-nocygwin_" goto Skip_GCC_NOCYGWIN
-set "BOOST_JAM_CC=gcc -DNT -mno-cygwin"
-set "BOOST_JAM_OPT_JAM=-o bootstrap\jam0.exe"
-set "BOOST_JAM_OPT_MKJAMBASE=-o bootstrap\mkjambase0.exe"
-set "BOOST_JAM_OPT_YYACC=-o bootstrap\yyacc0.exe"
-set "_known_=1"
-:Skip_GCC_NOCYGWIN
-if NOT "_%BOOST_JAM_TOOLSET%_" == "_intel-win32_" goto Skip_INTEL_WIN32
-set "BOOST_JAM_CC=icl -DNT /nologo kernel32.lib advapi32.lib user32.lib"
-set "BOOST_JAM_OPT_JAM=/Febootstrap\jam0"
-set "BOOST_JAM_OPT_MKJAMBASE=/Febootstrap\mkjambase0"
-set "BOOST_JAM_OPT_YYACC=/Febootstrap\yyacc0"
-set "_known_=1"
-:Skip_INTEL_WIN32
-if NOT "_%BOOST_JAM_TOOLSET%_" == "_mingw_" goto Skip_MINGW
-if not "_%BOOST_JAM_TOOLSET_ROOT%_" == "__" (
-    set "PATH=%BOOST_JAM_TOOLSET_ROOT%bin;%PATH%"
-    )
-set "BOOST_JAM_CC=gcc -DNT"
-set "BOOST_JAM_OPT_JAM=-o bootstrap\jam0.exe"
-set "BOOST_JAM_OPT_MKJAMBASE=-o bootstrap\mkjambase0.exe"
-set "BOOST_JAM_OPT_YYACC=-o bootstrap\yyacc0.exe"
-set "_known_=1"
-:Skip_MINGW
-call :Clear_Error
-if "_%_known_%_" == "__" (
-    call :Error_Print "Unknown toolset: %BOOST_JAM_TOOLSET%"
-)
-if errorlevel 1 goto Finish
-
-echo ###
-echo ### Using '%BOOST_JAM_TOOLSET%' toolset.
-echo ###
-
-set YYACC_SOURCES=yyacc.c
-set MKJAMBASE_SOURCES=mkjambase.c
-set BJAM_SOURCES=
-set BJAM_SOURCES=%BJAM_SOURCES% command.c compile.c debug.c execnt.c expand.c filent.c glob.c hash.c
-set BJAM_SOURCES=%BJAM_SOURCES% hdrmacro.c headers.c jam.c jambase.c jamgram.c lists.c make.c make1.c
-set BJAM_SOURCES=%BJAM_SOURCES% newstr.c option.c output.c parse.c pathunix.c regexp.c
-set BJAM_SOURCES=%BJAM_SOURCES% rules.c scan.c search.c subst.c timestamp.c variable.c modules.c
-set BJAM_SOURCES=%BJAM_SOURCES% strings.c filesys.c builtins.c md5.c pwd.c class.c w32_getreg.c native.c
-set BJAM_SOURCES=%BJAM_SOURCES% modules/set.c modules/path.c modules/regex.c
-set BJAM_SOURCES=%BJAM_SOURCES% modules/property-set.c modules/sequence.c modules/order.c
-
-set BJAM_UPDATE=
-:Check_Update
-call :Test_Empty %1
-if not errorlevel 1 goto Check_Update_End
-call :Clear_Error
-setlocal
-set test=%1
-set test=###%test%###
-set test=%test:"###=%
-set test=%test:###"=%
-set test=%test:###=%
-if "%test%" == "--update" set BJAM_UPDATE=update
-endlocal
-shift
-if not "_%BJAM_UPDATE%_" == "_update_" goto Check_Update
-:Check_Update_End
-if "_%BJAM_UPDATE%_" == "_update_" (
-    if not exist ".\bootstrap\jam0.exe" (
-        set BJAM_UPDATE=
-    )
-)
-
-@echo ON
-@if "_%BJAM_UPDATE%_" == "_update_" goto Skip_Bootstrap
-if exist bootstrap rd /S /Q bootstrap
-md bootstrap
-@if not exist jamgram.y goto Bootstrap_GrammarPrep
-@if not exist jamgramtab.h goto Bootstrap_GrammarPrep
-@goto Skip_GrammarPrep
-:Bootstrap_GrammarPrep
-%BOOST_JAM_CC% %BOOST_JAM_OPT_YYACC% %YYACC_SOURCES%
-@if not exist ".\bootstrap\yyacc0.exe" goto Skip_GrammarPrep
-.\bootstrap\yyacc0 jamgram.y jamgramtab.h jamgram.yy
-:Skip_GrammarPrep
-@if not exist jamgram.c goto Bootstrap_GrammarBuild
-@if not exist jamgram.h goto Bootstrap_GrammarBuild
-@goto Skip_GrammarBuild
-:Bootstrap_GrammarBuild
-@echo OFF
-if "_%YACC%_" == "__" (
-    call :Guess_Yacc
-)
-if errorlevel 1 goto Finish
-@echo ON
-%YACC% jamgram.y
-@if errorlevel 1 goto Finish
-del /f jamgram.c
-rename y.tab.c jamgram.c
-del /f jamgram.h
-rename y.tab.h jamgram.h
-:Skip_GrammarBuild
-@echo ON
-@if exist jambase.c goto Skip_Jambase
-%BOOST_JAM_CC% %BOOST_JAM_OPT_MKJAMBASE% %MKJAMBASE_SOURCES%
-@if not exist ".\bootstrap\mkjambase0.exe" goto Skip_Jambase
-.\bootstrap\mkjambase0 jambase.c Jambase
-:Skip_Jambase
-%BOOST_JAM_CC% %BOOST_JAM_OPT_JAM% %BJAM_SOURCES%
-:Skip_Bootstrap
-@if not exist ".\bootstrap\jam0.exe" goto Skip_Jam
-@if "_%BJAM_UPDATE%_" == "_update_" goto Skip_Clean
-.\bootstrap\jam0 -f build.jam --toolset=%BOOST_JAM_TOOLSET% "--toolset-root=%BOOST_JAM_TOOLSET_ROOT% " clean
-:Skip_Clean
-@set args=%*
-@echo OFF
-:Set_Args
-setlocal
-call :Test_Empty %args%
-if not errorlevel 1 goto Set_Args_End
-set test=###%args:~0,2%###
-set test=%test:"###=%
-set test=%test:###"=%
-set test=%test:###=%
-set test=%test:~0,1%
-if "-" == "%test%" goto Set_Args_End
-endlocal
-set args=%args:~1%
-goto Set_Args
-:Set_Args_End
-@echo ON
-.\bootstrap\jam0 -f build.jam --toolset=%BOOST_JAM_TOOLSET% "--toolset-root=%BOOST_JAM_TOOLSET_ROOT% " %args%
-:Skip_Jam
-
-:Finish
diff --git a/jam-files/engine/build.jam b/jam-files/engine/build.jam
deleted file mode 100644
index 266b07a1..00000000
--- a/jam-files/engine/build.jam
+++ /dev/null
@@ -1,1070 +0,0 @@
-#~ Copyright 2002-2007 Rene Rivera.
-#~ Distributed under the Boost Software License, Version 1.0.
-#~ (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-# Clean env vars of any "extra" empty values.
-for local v in ARGV CC CFLAGS LIBS
-{
-	local values ;
-	for local x in $($(v))
-	{
-		if $(x) != ""
-		{
-			values += $(x) ;
-		}
-	}
-	$(v) = $(values) ;
-}
-
-# Platform related specifics.
-if $(OS) = NT { rule .path { return "$(<:J=\\)" ; } ./ = "/" ; }
-else if $(OS) = OS2 { rule .path { return "$(<:J=\\)" ; } ./ = "/" ; }
-else if $(OS) = VMS { rule .path { return "[.$(<:J=/)]" ; } }
-else if $(OS) = MAC { rule .path { return ":$(<:J=\:)" ; } }
-else { rule .path { return "$(<:J=/)" ; } }
-if $(OS) = VMS { . = "_" ; }
-else { . = "." ; }
-./ ?= "" ;
-
-# Info about what we are building.
-_VERSION_ = 3 1 19 ;
-NAME = boost-jam ;
-VERSION = $(_VERSION_:J=$(.)) ;
-RELEASE = 1 ;
-LICENSE = LICENSE_1_0 ;
-
-# Generate development debug binaries?
-if --debug in $(ARGV)
-{
-    debug = true ;
-}
-
-if --profile in $(ARGV)
-{
-    profile = true ;
-}
-
-# Attempt to generate and/or build the grammar?
-if --grammar in $(ARGV)
-{
-    grammar = true ;
-}
-
-# Do we need to add a default build type argument?
-if ! ( --release in $(ARGV) ) &&
-   ! ( --debug in $(ARGV) ) &&
-   ! ( --profile in $(ARGV) )
-{
-    ARGV += --release ;
-}
-
-# Enable, and configure, Python hooks.
-with-python = ;
-python-location = [ MATCH --with-python=(.*) : $(ARGV) ] ;
-if $(python-location)
-{
-    with-python = true ;
-}
-if $(with-python)
-{
-    if $(OS) = NT
-    {
-        --python-include = [ .path $(python-location) include ] ;
-        --python-lib = ;
-        for local v in 26 25 24 23 22
-        {
-            --python-lib ?=
-                [ GLOB [ .path $(python-location) libs ] : "python$(v).lib" ]
-                [ GLOB $(python-location) [ .path $(python-location) libs ]
-                    $(Path) $(PATH) $(path) : "python$(v).dll" ]
-                ;
-            if ! $(--python-lib[2])
-            {
-                --python-lib = ;
-            }
-        }
-        --python-lib = $(--python-lib[1]) ;
-    }
-    else if $(OS) = MACOSX
-    {
-        --python-include = [ .path $(python-location) Headers ] ;
-        --python-lib = $(python-location) Python ;
-    }
-    else
-    {
-        --python-include = ;
-        --python-lib = ;
-        for local v in 2.6 2.5 2.4 2.3 2.2
-        {
-            local inc = [ GLOB [ .path $(python-location) include ] : python$(v) ] ;
-            local lib = [ GLOB [ .path $(python-location) lib ] : libpython$(v)* ] ;
-            if $(inc) && $(lib)
-            {
-                --python-include ?= $(inc) ;
-                --python-lib ?= $(lib[1]:D) python$(v) ;
-            }
-        }
-    }
-}
-
-# Boehm GC?
-if --gc in $(ARGV)
-{
-    --boehm-gc = true ;
-}
-if $(--boehm-gc)
-{
-    --extra-include += [ .path [ PWD ] "boehm_gc" "include" ] ;
-}
-
-# Duma?
-if --duma in $(ARGV)
-{
-    --duma = true ;
-}
-if $(--duma)
-{
-    --extra-include += [ .path [ PWD ] "duma" ] ;
-}
-
-# An explicit root for the toolset? (trim spaces)
-toolset-root = [ MATCH --toolset-root=(.*) : $(ARGV) ] ;
-{
-    local t = [ MATCH "[ ]*(.*)" : $(toolset-root:J=" ") ] ;
-    toolset-root = ;
-    while $(t)
-    {
-        t = [ MATCH "([^ ]+)([ ]*)(.*)" : $(t) ] ;
-        toolset-root += $(t[1]) ;
-        if $(t[3]) { toolset-root += $(t[2]) ; }
-        t = $(t[3]) ;
-    }
-    toolset-root = $(toolset-root:J="") ;
-}
-
-# Configure the implemented toolsets. These are minimal
-# commands and options to compile the full Jam. When
-# adding new toolsets make sure to add them to the
-# "known" list also.
-
-rule toolset ( name command .type ? : opt.out + : opt.define * : flags * : linklibs * )
-{
-    .type ?= "" ;
-    tool.$(name)$(.type).cc ?= $(command) ;
-    tool.$(name)$(.type).opt.out ?= $(opt.out) ;
-    tool.$(name)$(.type).opt.define ?= $(opt.define) ;
-    tool.$(name)$(.type).flags ?= $(flags) ;
-    tool.$(name)$(.type).linklibs ?= $(linklibs) ;
-    if ! $(name) in $(toolsets) { toolsets += $(name) ; }
-}
-
-rule if-os ( os + : yes-opt * : no-opt * )
-    { if $(os) in $(OS) { return $(yes-opt) ; } else { return $(no-opt) ; } }
-
-rule opt ( type : yes-opt * : no-opt * )
-    { if $(type) in $(ARGV) { return $(yes-opt) ; } else { return $(no-opt) ; } }
-
-## HP-UX aCC compiler
-toolset acc cc : "-o " : -D
-    : -Ae
-    [ opt --release : -s -O3 ]
-    [ opt --debug : -g -pg ]
-    -I$(--python-include) -I$(--extra-include)
-    : -L$(--python-lib[1]) -l$(--python-lib[2]) ;
-## Borland C++ 5.5.x
-toolset borland bcc32 : -e -n : /D
-    : -WC -w- -q "-I$(toolset-root)Include" "-L$(toolset-root)Lib"
-    [ opt --release : -O2 -vi -w-inl ]
-    [ opt --debug : -v -Od -vi- ]
-    -I$(--python-include) -I$(--extra-include)
-    : $(--python-lib[1]) ;
-## Generic Unix cc
-if ! $(CC) { CC = cc ; }
-toolset cc $(CC) : "-o " : -D
-    : $(CFLAGS)
-    [ opt --release : -s -O ]
-    [ opt --debug : -g ]
-    -I$(--python-include) -I$(--extra-include)
-    : $(LIBS) -L$(--python-lib[1]) -l$(--python-lib[2]) ;
-## Comeau C/C++ 4.x
-toolset como como : "-o " : -D
-    : --c
-    [ opt --release : --inlining ]
-    [ opt --debug : --no_inlining ]
-    -I$(--python-include) -I$(--extra-include)
-    : -L$(--python-lib[1]) -l$(--python-lib[2]) ;
-## Clang Linux 2.8+
-toolset clang clang :  "-o " : -D
-    : -Wno-unused -Wno-format
-    [ opt --release : -Os ]
-    [ opt --debug : -g -O0 -fno-inline ]
-    [ opt --profile : -finline-functions -g ]
-    -I$(--python-include) -I$(--extra-include)
-    : -L$(--python-lib[1]) -l$(--python-lib[2]) ;
-## MacOSX Darwin, using GCC 2.9.x, 3.x
-toolset darwin cc :  "-o " : -D
-    :
-    [ opt --release : -Wl,-x -O3 -finline-functions ]
-    [ opt --debug : -g -O0 -fno-inline -pg ]
-    [ opt --profile : -Wl,-x -O3 -finline-functions -g -pg ]
-    -I$(--python-include) -I$(--extra-include)
-    : -L$(--python-lib[1]) -l$(--python-lib[2]) ;
-## GCC 2.x, 3.x, 4.x
-toolset gcc gcc : "-o " : -D
-    : -pedantic -fno-strict-aliasing
-    [ opt --release : [ opt --symbols : -g : -s ] -O3 ]
-    [ opt --debug : -g -O0 -fno-inline ]
-    -I$(--python-include) -I$(--extra-include) -Wno-long-long
-    : -L$(--python-lib[1]) -l$(--python-lib[2]) ;
-## GCC 2.x, 3.x on CYGWIN but without cygwin1.dll
-toolset gcc-nocygwin gcc : "-o " : -D
-    : -s -O3 -mno-cygwin
-    [ opt --release : -finline-functions ]
-    [ opt --debug : -s -O3 -fno-inline -pg ]
-    -I$(--python-include) -I$(--extra-include)
-    : -L$(--python-lib[1]) -l$(--python-lib[2]) ;
-## Intel C/C++ for Darwin
-toolset intel-darwin icc : "-o " : -D
-    :
-    [ opt --release : -O3 ]
-    [ opt --debug : -g -O0 -p ]
-    -I$(--python-include) -I$(--extra-include)
-    : -L$(--python-lib[1]) -l$(--python-lib[2]) ;
-## Intel C/C++ for Linux
-toolset intel-linux icc : "-o " : -D
-    :
-    [ opt --release : -Xlinker -s -O3 ]
-    [ opt --debug : -g -O0 -p ]
-    -I$(--python-include) -I$(--extra-include)
-    : -L$(--python-lib[1]) -l$(--python-lib[2]) ;
-## Intel C/C++ for Win32
-toolset intel-win32 icl : /Fe : -D
-    : /nologo
-    [ opt --release : /MT /O2 /Ob2 /Gy /GF /GA /GB ]
-    [ opt --debug : /MTd /DEBUG /Z7 /Od /Ob0 ]
-    -I$(--python-include) -I$(--extra-include)
-    : kernel32.lib advapi32.lib user32.lib $(--python-lib[1]) ;
-## KCC ?
-toolset kcc KCC : "-o " : -D
-    :
-    [ opt --release : -s +K2 ]
-    [ opt --debug : -g +K0 ]
-    -I$(--python-include) -I$(--extra-include)
-    : -L$(--python-lib[1]) -l$(--python-lib[2]) ;
-## Borland Kylix
-toolset kylix bc++ : -o : -D
-    : -tC -q
-    [ opt --release : -O2 -vi -w-inl ]
-    [ opt --debug : -v -Od -vi- ]
-    -I$(--python-include) -I$(--extra-include)
-    : -L$(--python-lib[1]) -l$(--python-lib[2]) ;
-## Metrowerks CodeWarrior 8.x
-{
-    # Even though CW can compile all files at once, it crashes if it tries in the bjam case.
-    local mwcc = ; if $(OS) = NT { mwcc = mwcc ; } else { mwcc = mwc$(OSPLAT:L) ; }
-    mwcc ?= mwcc ;
-    toolset metrowerks $(mwcc) : "-o " : -D
-        : -c -lang c -subsystem console -cwd include
-        [ opt --release : -runtime ss -opt full -inline all ]
-        [ opt --debug : -runtime ssd -opt none -inline off ]
-        -I$(--python-include) -I$(--extra-include) ;
-    toolset metrowerks $(mwcc) .link : "-o " :
-        : -subsystem console -lkernel32.lib -ladvapi32.lib -luser32.lib
-        [ opt --release : -runtime ss ]
-        [ opt --debug : -runtime ssd ]
-        : $(--python-lib[1]) ;
-}
-## MINGW GCC
-toolset mingw gcc : "-o " : -D
-    :
-    [ opt --release : -s -O3 -finline-functions ]
-    [ opt --debug : -g -O0 -fno-inline -pg ]
-    -I$(--python-include) -I$(--extra-include)
-    : $(--python-lib[2]) ;
-## MIPS Pro
-toolset mipspro cc : "-o " : -D
-    :
-    [ opt --release : -s -O3 -g0 -INLINE:none ]
-    [ opt --debug : -g -O0 -INLINE ]
-    -I$(--python-include) -I$(--extra-include)
-    : -L$(--python-lib[1]) -l$(--python-lib[2]) ;
-## Microsoft Visual Studio C++ 6.x
-toolset msvc cl : /Fe /Fe /Fd /Fo : -D
-    : /nologo
-    [ opt --release : /ML /O2 /Ob2 /Gy /GF /GA /GB ]
-    [ opt --debug : /MLd /DEBUG /Z7 /Od /Ob0 ]
-    -I$(--python-include) -I$(--extra-include)
-    : kernel32.lib advapi32.lib user32.lib $(--python-lib[1]) ;
-## QNX 6.x GCC 3.x/2.95.3
-toolset qcc qcc : "-o " : -D
-    : -Wc,-pedantic -Wc,-fno-strict-aliasing
-    [ opt --release : [ opt --symbols : -g ] -O3 -Wc,-finline-functions ]
-    [ opt --debug : -g -O0 -Wc,-fno-inline ]
-    -I$(--python-include) -I$(--extra-include)
-    : -L$(--python-lib[1]) -l$(--python-lib[2]) ;
-## Qlogic Pathscale 2.4
-toolset pathscale pathcc : "-o " : -D
-    :
-    [ opt --release : -s -Ofast -O3 ]
-    [ opt --debug : -g ]
-    -I$(--python-include) -I$(--extra-include)
-    : -L$(--python-lib[1]) -l$(--python-lib[2]) ;
-## Portland Group Pgi 6.2
-toolset pgi pgcc : "-o " : -D
-    :
-    [ opt --release : -s -O3 ]
-    [ opt --debug : -g ]
-    -I$(--python-include) -I$(--extra-include)
-    : -L$(--python-lib[1]) -l$(--python-lib[2]) ;
-## Sun Workshop 6 C++
-toolset sun cc : "-o " : -D
-    :
-    [ opt --release : -s -fast -xO4 ]
-    [ opt --debug : -g ]
-    -I$(--python-include) -I$(--extra-include)
-    : -L$(--python-lib[1]) -l$(--python-lib[2]) ;
-## Sun Workshop 6 C++ (old alias)
-toolset sunpro cc : "-o " : -D
-    :
-    [ opt --release : -s -fast -xO4 ]
-    [ opt --debug : -g ]
-    -I$(--python-include) -I$(--extra-include)
-    : -L$(--python-lib[1]) -l$(--python-lib[2]) ;
-## Compaq Alpha CXX
-toolset tru64cxx cc : "-o " : -D
-    :
-    [ opt --release : -s -O5 -inline speed ]
-    [ opt --debug : -g -O0 -pg ]
-    -I$(--python-include) -I$(--extra-include)
-    : -L$(--python-lib[1]) -l$(--python-lib[2]) ;
-## IBM VisualAge C++
-toolset vacpp xlc : "-o " : -D
-    :
-    [ opt --release : -s -O3 -qstrict -qinline ]
-    [ opt --debug : -g -qNOOPTimize -qnoinline -pg ]
-    -I$(--python-include) -I$(--extra-include)
-    : -L$(--python-lib[1]) -l$(--python-lib[2]) [ if-os AIX : -bmaxdata:0x40000000 ] ;
-## Microsoft Visual C++ .NET 7.x
-toolset vc7 cl : /Fe /Fe /Fd /Fo : -D
-    : /nologo
-    [ opt --release : /ML /O2 /Ob2 /Gy /GF /GA /GB ]
-    [ opt --debug : /MLd /DEBUG /Z7 /Od /Ob0 ]
-    -I$(--python-include) -I$(--extra-include)
-    : kernel32.lib advapi32.lib user32.lib $(--python-lib[1]) ;
-## Microsoft Visual C++ 2005
-toolset vc8 cl : /Fe /Fe /Fd /Fo : -D
-    : /nologo
-    [ opt --release : /MT /O2 /Ob2 /Gy /GF /GA /wd4996 ]
-    [ opt --debug : /MTd /DEBUG /Z7 /Od /Ob0 /wd4996 ]
-    -I$(--python-include) -I$(--extra-include)
-    : kernel32.lib advapi32.lib user32.lib $(--python-lib[1]) ;
-## Microsoft Visual C++ 2008
-toolset vc9 cl : /Fe /Fe /Fd /Fo : -D
-    : /nologo
-    [ opt --release : /MT /O2 /Ob2 /Gy /GF /GA /wd4996 ]
-    [ opt --debug : /MTd /DEBUG /Z7 /Od /Ob0 /wd4996 ]
-    -I$(--python-include) -I$(--extra-include)
-    : kernel32.lib advapi32.lib user32.lib $(--python-lib[1]) ;
-## Microsoft Visual C++ 2010
-toolset vc10 cl : /Fe /Fe /Fd /Fo : -D
-    : /nologo
-    [ opt --release : /MT /O2 /Ob2 /Gy /GF /GA /wd4996 ]
-    [ opt --debug : /MTd /DEBUG /Z7 /Od /Ob0 /wd4996 ]
-    -I$(--python-include) -I$(--extra-include)
-    : kernel32.lib advapi32.lib user32.lib $(--python-lib[1]) ;
-## VMS/OpenVMS DEC C
-toolset vmsdecc cc : /OBJECT= : "/DEFINES=(" "," ")"
-    : /STANDARD=VAXC /PREFIX_LIBRARY_ENTRIES=ALL_ENTRIES
-    [ opt --release : /OPTIMIZE /NODEBUG ]
-    [ opt --debug : /NOOPTIMIZE /DEBUG ]
-    ;
-toolset vmsdecc link .link : /EXECUTABLE= :
-    : /NOMAP
-    [ opt --release : /NODEBUG ]
-    [ opt --debug : /DEBUG ]
-    ;
-
-# First set the build commands and options according to the
-# preset toolset.
-toolset = [ MATCH --toolset=(.*) : $(ARGV) ] ;
-if ! $(toolset)
-{
-    # For some reason, the following test does not catch empty toolset.
-    ECHO "###" ;
-    ECHO "###" No toolset specified. Please use --toolset option. ;
-    ECHO "###" ;
-    ECHO "###" Known toolsets are: $(toolsets:J=", ") ;
-    EXIT "###" ;
-}
-if ! $(toolset) in $(toolsets)
-{
-    ECHO "###" ;
-    ECHO "###" Unknown toolset: $(toolset) ;
-    ECHO "###" ;
-    ECHO "###" Known toolsets are: $(toolsets:J=", ") ;
-    EXIT "###" ;
-}
---cc = $(tool.$(toolset).cc) ;
-if $(tool.$(toolset).opt.out[2])
-{
-    if $(tool.$(toolset).opt.out[1]) = $(tool.$(toolset).opt.out[2])
-    {
-        --out = $(tool.$(toolset).opt.out[1]) ;
-        --dir = $(tool.$(toolset).opt.out[3-]) ;
-    }
-    else
-    {
-        --bin = $(tool.$(toolset).opt.out[1]) ;
-        --dir = $(tool.$(toolset).opt.out[2-]) ;
-    }
-}
-else
-{
-    --out = $(tool.$(toolset).opt.out) ;
-}
---def = $(tool.$(toolset).opt.define) ;
---flags = $(tool.$(toolset).flags) ;
---defs = $(tool.$(toolset).defines) ;
---libs = $(tool.$(toolset).linklibs) ;
-if $(tool.$(toolset).link.cc)
-{
-    --link = $(tool.$(toolset).link.cc) ;
-    if $(tool.$(toolset).link.opt.out[2])
-    {
-        if $(tool.$(toolset).link.opt.out[1]) = $(tool.$(toolset).link.opt.out[2])
-        {
-            --link-out = $(tool.$(toolset).link.opt.out[1]) ;
-            --link-dir = $(tool.$(toolset).link.opt.out[3-]) ;
-        }
-        else
-        {
-            --link-bin = $(tool.$(toolset).link.opt.out[1]) ;
-            --link-dir = $(tool.$(toolset).link.opt.out[2-]) ;
-        }
-    }
-    else
-    {
-        --link-out = $(tool.$(toolset).link.opt.out) ;
-    }
-    --link-def = $(tool.$(toolset).link.opt.define) ;
-    --link-flags = $(tool.$(toolset).link.flags) ;
-    --link-defs = $(tool.$(toolset).link.defines) ;
-    --link-libs = $(tool.$(toolset).link.linklibs) ;
-}
-
-# Put executables in platform-specific subdirectory.
-locate-target = $(LOCATE_TARGET) ;
-if $(OS) = VMS
-{
-    locate-target ?= bin$(.)vms ;
-    platform = vms ;
-}
-else if $(OS) = MAC
-{
-    locate-target ?= bin$(.)$(OS:L)$(OSPLAT:L) ;
-    platform = $(OS:L)$(OSPLAT:L) ;
-}
-else if $(OSPLAT)
-{
-    locate-target ?= bin$(.)$(OS:L)$(OSPLAT:L) ;
-    platform = $(OS:L)$(OSPLAT:L) ;
-}
-else
-{
-    locate-target ?= bin$(.)$(OS:L) ;
-    platform = $(OS:L) ;
-}
-if $(debug)
-{
-    locate-target = [ .path $(locate-target)$(.)debug ] ;
-}
-if $(profile)
-{
-    locate-target = [ .path $(locate-target)$(.)profile ] ;
-}
-else
-{
-    locate-target = [ .path $(locate-target) ] ;
-}
-
-if --show-locate-target in $(ARGV)
-{
-  ECHO $(locate-target) ;
-}
-
-# We have some different files for UNIX, VMS, and NT.
-jam.source =
-    command.c compile.c debug.c expand.c glob.c
-    hash.c hcache.c headers.c hdrmacro.c
-    jam.c jambase.c jamgram.c
-    lists.c make.c make1.c mem.c newstr.c
-    option.c output.c parse.c regexp.c rules.c
-    scan.c search.c subst.c w32_getreg.c
-    timestamp.c variable.c modules.c strings.c filesys.c
-    builtins.c pwd.c class.c native.c md5.c modules/set.c
-    modules/path.c modules/regex.c modules/property-set.c
-    modules/sequence.c modules/order.c
-    ;
-if $(OS) = NT
-{
-    jam.source += execnt.c filent.c pathunix.c ;
-}
-else if $(OS) = OS2
-{
-    jam.source += execunix.c fileos2.c pathunix.c ;
-}
-else if $(OS) = VMS
-{
-    jam.source += execvms.c filevms.c pathvms.c ;
-}
-else if $(OS) = MAC
-{
-    jam.source += execmac.c filemac.c pathmac.c ;
-}
-else
-{
-    jam.source += execunix.c fileunix.c pathunix.c ;
-}
-
-# Debug assertions, or not.
-if ! $(debug) || --noassert in $(ARGV)
-{
-    --defs += NDEBUG ;
-}
-
-# Enable some optional features.
---defs += OPT_HEADER_CACHE_EXT ;
---defs += OPT_GRAPH_DEBUG_EXT ;
---defs += OPT_SEMAPHORE ;
---defs += OPT_AT_FILES ;
---defs += OPT_DEBUG_PROFILE ;
-
-# Bug fixes
---defs += OPT_FIX_TARGET_VARIABLES_EXT ;
-#~ --defs += OPT_NO_EXTERNAL_VARIABLE_SPLIT ;
-
-# Improvements
---defs += OPT_IMPROVED_PATIENCE_EXT ;
-
-# Use Boehm GC memory allocator?
-if $(--boehm-gc)
-{
-    --defs += OPT_BOEHM_GC ;
-    if $(debug)
-    {
-        --defs += GC_DEBUG ;
-    }
-}
-
-if $(--duma)
-{
-    --defs += OPT_DUMA ;
-}
-
-if ( $(OS) = NT ) && ! NT in $(--defs)
-{
-    --defs += NT ;
-}
-if $(OS) = VMS
-{
-    --defs += VMS ;
-}
---defs += YYSTACKSIZE=5000 ;
-
-if $(with-python)
-{
-    --defs += HAVE_PYTHON ;
-}
-
-if $(debug)
-{
-    --defs += BJAM_NEWSTR_NO_ALLOCATE ;
-}
-
-
-# The basic symbolic targets...
-NOTFILE all clean dist ;
-ALWAYS clean ;
-
-# Utility rules and actions...
-rule .clean
-{
-    [DELETE] clean : $(<) ;
-}
-if $(OS) = NT { actions piecemeal together existing [DELETE] {
-    del /F /Q "$(>)"
-} }
-if $(UNIX) = true { actions piecemeal together existing [DELETE] {
-    rm -f "$(>)"
-} }
-if $(OS) = VMS { actions piecemeal together existing [DELETE] {
-    DELETE $(>[--2]:J=";*, ") $(>[-1]);*
-} }
-if $(OS) = NT {
-    --chmod+w = "attrib -r " ;
-}
-if $(UNIX) = true {
-    --chmod+w = "chmod +w " ;
-}
-if $(OS) = VMS {
-    --chmod+w = "SET FILE/PROT=(S:RWED) " ;
-}
-
-rule .mkdir
-{
-    NOUPDATE $(<) ;
-    if $(<:P) { DEPENDS $(<) : $(<:P) ; .mkdir $(<:P) ; }
-    if ! $(md<$(<)>) { [MKDIR] $(<) ; md<$(<)> = - ; }
-}
-if $(OS) = NT { actions [MKDIR] {
-    md "$(<)"
-} }
-if $(UNIX) = true { actions [MKDIR] {
-    mkdir "$(<)"
-} }
-if $(OS) = VMS { actions [MKDIR] {
-    CREATE/DIR $(<J=", ")
-} }
-
-rule .exe
-{
-    local exe = $(<) ;
-    if $(OS) = NT || ( $(UNIX) = true && $(OS) = CYGWIN ) || $(OS) = VMS { exe = $(exe:S=.exe) ; }
-    LOCATE on $(exe) = $(locate-target) ;
-    DEPENDS all : $(exe) ;
-    .mkdir $(locate-target) ;
-    if $(--link)
-    {
-        local objs = ;
-        for local s in $(>)
-        {
-            # Translate any subdir elements into a simple file name.
-            local o = [ MATCH "([^/]+)[/]?(.+)" : $(s) ] ;
-            o = $(o:J=_) ;
-            o = $(o:S=.o) ;
-            objs += $(o) ;
-            LOCATE on $(o) = $(locate-target) ;
-            DEPENDS $(exe) : $(o) ;
-            DEPENDS $(o) : $(s) ;
-            DEPENDS $(o) : $(locate-target) ;
-            [COMPILE] $(o) : $(s) ;
-            .clean $(o) ;
-        }
-        DEPENDS $(exe) : $(objs) ;
-        DEPENDS $(exe) : $(locate-target) ;
-        [COMPILE.LINK] $(exe) : $(objs) ;
-        .clean $(exe) ;
-    }
-    else
-    {
-        DEPENDS $(exe) : $(>) ;
-        DEPENDS $(exe) : $(locate-target) ;
-        [COMPILE] $(exe) : $(>) ;
-        .clean $(exe) ;
-    }
-    return $(exe) ;
-}
-if ! $(--def[2]) { actions [COMPILE] {
-    "$(--cc)" "$(--bin)$(<:D=)" "$(--dir)$(<:D)$(./)" $(--out)$(<) "$(--def)$(--defs)" "$(--flags)" "$(--libs)" "$(>)"
-} }
-else { actions [COMPILE] {
-    "$(--cc)" "$(--bin)$(<:D=)" "$(--dir)$(<:D)$(./)" $(--out)$(<) "$(--def[1])$(--defs:J=$(--def[2]))$(--def[3])" "$(--flags)" "$(--libs)" "$(>)"
-} }
-if $(OS) = VMS { actions [COMPILE.LINK] {
-    "$(--link)" $(--link-bin)$(<:D=) $(--link-dir)$(<:D)$(./) $(--link-out)$(<) $(--link-def)$(--link-defs) $(--link-flags) "$(--link-libs)" $(>J=", ")
-} }
-else { actions [COMPILE.LINK] {
-    "$(--link)" "$(--link-bin)$(<:D=)" "$(--link-dir)$(<:D)$(./)" "$(--link-out)$(<)" "$(--link-def)$(--link-defs)" "$(--link-flags)" "$(--link-libs)" "$(>)"
-} }
-
-rule .link
-{
-    DEPENDS all : $(<) ;
-    DEPENDS $(<) : $(>) ;
-    [LINK] $(<) : $(>) ;
-    .clean $(<) ;
-}
-if $(OS) = NT { actions [LINK] {
-    copy "$(>)" "$(<)"
-} }
-if $(UNIX) = true { actions [LINK] {
-    ln -fs "$(>)" "$(<)"
-} }
-if $(OS) = VMS { actions [LINK] {
-    COPY/REPLACE $(>) $(<)
-} }
-
-rule .copy
-{
-    DEPENDS all : $(<) ;
-    DEPENDS $(<) : $(>) ;
-    [COPY] $(<) : $(>) ;
-    .clean $(<) ;
-}
-
-# Will be redefined later.
-actions [COPY]
-{
-}
-
-
-rule .move
-{
-    DEPENDS $(<) : $(>) ;
-    [MOVE] $(<) : $(>) ;
-}
-if $(OS) = NT { actions [MOVE] {
-    del /f "$(<)"
-    rename "$(>)" "$(<)"
-} }
-if $(UNIX) = true { actions [MOVE] {
-    mv -f "$(>)" "$(<)"
-} }
-if $(OS) = VMS { actions [MOVE] {
-    RENAME "$(>)" "$(<)"
-} }
-
-# Generate the grammar tokens table, and the real yacc grammar.
-rule .yyacc
-{
-    local exe = [ .exe yyacc : yyacc.c ] ;
-    NOUPDATE $(exe) ;
-    DEPENDS $(<) : $(exe) $(>) ;
-    LEAVES $(<) ;
-    yyacc.exe on $(<) = $(exe:R=$(locate-target)) ;
-    [YYACC] $(<) : $(>) ;
-}
-actions [YYACC] {
-    $(--chmod+w)$(<[1])
-    $(--chmod+w)$(<[2])
-    "$(yyacc.exe)" "$(<)" "$(>)"
-}
-if $(grammar)
-{
-    .yyacc jamgram.y jamgramtab.h : jamgram.yy ;
-}
-else if $(debug)
-{
-    .exe yyacc : yyacc.c ;
-}
-
-# How to build the grammar.
-if $(OS) = NT
-{
-    SUFEXE = .exe ;
-    # try some other likely spellings...
-    PATH ?= $(Path) ;
-    PATH ?= $(path) ;
-}
-SUFEXE ?= "" ;
-
-yacc ?= [ GLOB $(PATH) : yacc$(SUFEXE) ] ;
-yacc ?= [ GLOB $(PATH) : bison$(SUFEXE) ] ;
-yacc ?= [ GLOB "$(ProgramFiles:J= )\\GnuWin32\\bin" "C:\\Program Files\\GnuWin32\\bin" : bison$(SUFEXE) ] ;
-yacc = $(yacc[1]) ;
-switch $(yacc:D=:S=)
-{
-    case bison : yacc += -d --yacc ;
-    case yacc  : yacc += -d ;
-}
-if $(debug) && $(yacc)
-{
-    yacc += -t -v ;
-}
-yacc += $(YACCFLAGS) ;
-
-rule .yacc
-{
-    DEPENDS $(<) : $(>) ;
-    LEAVES $(<) ;
-    [YACC] $(<) : $(>) ;
-}
-if $(OS) = NT { actions [YACC] {
-    "$(yacc)" "$(>)"
-    if not errorlevel 1 (
-        del /f "$(<[1])"
-        rename y.tab$(<[1]:S) "$(<[1])"
-        del /f $(<[2])
-        rename y.tab$(<[2]:S) "$(<[2])"
-    ) else set _error_ =
-} }
-if $(UNIX) = true { actions [YACC] {
-    if ` "$(yacc)" "$(>)" ` ; then
-        mv -f y.tab$(<[1]:S) "$(<[1])"
-        mv -f y.tab$(<[2]:S) "$(<[2])"
-    else
-        exit 1
-    fi
-} }
-if $(OS) = VMS { actions [YACC] {
-    IF "$(yacc)" $(>)
-    THEN
-        RENAME y_tab$(<[1]:S) $(<[1])
-        RENAME y_tab$(<[2]:S) $(<[2])
-    ENDIF
-} }
-if $(grammar) && ! $(yacc)
-{
-    EXIT "Could not find the 'yacc' tool, and therefore can not build the grammar." ;
-}
-if $(grammar) && $(yacc)
-{
-    .yacc jamgram.c jamgram.h : jamgram.y ;
-}
-
-# How to build the compiled in jambase.
-rule .mkjambase
-{
-    local exe = [ .exe mkjambase : mkjambase.c ] ;
-    DEPENDS $(<) : $(exe) $(>) ;
-    LEAVES $(<) ;
-    mkjambase.exe on $(<) = $(exe:R=$(locate-target)) ;
-    [MKJAMBASE] $(<) : $(>) ;
-}
-actions [MKJAMBASE] {
-    $(--chmod+w)$(<)
-    $(mkjambase.exe) "$(<)" "$(>)"
-}
-if $(debug)
-{
-    .mkjambase jambase.c : Jambase ;
-}
-
-# How to build Jam.
-rule .jam
-{
-    $(>).exe = [ .exe $(>) : $(jam.source) ] ;
-    DEPENDS all : $($(>).exe) ;
-    
-    # Make a copy under the old name.
-    $(<).exe = $(<:S=$($(>).exe:S)) ;
-    LOCATE on $($(<).exe) = $(locate-target) ;
-    .copy $($(<).exe) : $($(>).exe) ;
-    DEPENDS all : $($(<).exe) ;
-}
-.jam bjam : b2 ;
-
-
-# Scan sources for header dependencies.
-#	WARNING: Yes those are *REAL TABS* below. DO NOT CHANGE,
-#	under any circumstances, to spaces!! And the tabs
-#	indenting this are so that if someone is in the mood to
-#	replace tabs they hit this comment, and hopefully notice
-#	their error.
-rule .scan
-{
-    HDRRULE on $(<:D=) = .hdr.scan ;
-    HDRSCAN on $(<:D=) = "^[ 	]*#[ 	]*include[ 	]*([<\"][^\">]*[\">]).*$" ;
-}
-rule .hdr.scan
-{
-    local hdrs = [ GLOB . : $(>:D=) ] ;
-    INCLUDES $(<:D=) : $(hdrs:D=) ;
-    HDRRULE on $(>:D=) = .hdr.scan ;
-    HDRSCAN on $(>:D=) = "^[ 	]*#[ 	]*include[ 	]*([<\"][^\">]*[\">]).*$" ;
-}
-.scan [ GLOB . : *.c ] ;
-
-# Distribution making from here on out. Assumes that
-# the docs are already built as html at ../doc/html. If
-# they aren't, then the docs are not included in the dist
-# archive.
-dist.license =
-    [ GLOB . : $(LICENSE).txt ]
-    ;
-dist.license = $(dist.license:D=)
-    [ GLOB [ .path .. .. .. ] : $(LICENSE).txt ]
-    [ GLOB [ .path .. boost ] : $(LICENSE).txt ] ;
-dist.docs =
-    [ GLOB . : *.png *.css *.html ]
-    ;
-dist.docs = $(dist.docs:D=)
-    [ GLOB [ .path images ] : *.png ]
-    [ GLOB [ .path jam ] : *.html ]
-    ;
-dist.source =
-    [ GLOB . : *.c *.h ]
-    ;
-dist.source = $(dist.source:D=)
-    $(dist.license[1])
-    $(dist.docs)
-    build.jam build.bat build.sh build_vms.com
-    Jambase
-    jamgram.y jamgram.yy
-    [ .path modules set.c ]
-    [ .path modules path.c ]
-    [ .path modules regex.c ]
-    [ .path modules property-set.c ]
-    [ .path modules sequence.c ]
-    [ .path modules order.c ]
-    [ GLOB [ .path boehm_gc ] : * ]
-    [ GLOB [ .path boehm_gc include ] : * ]
-    [ GLOB [ .path boehm_gc include private ] : * ]
-    [ GLOB [ .path boehm_gc cord ] : * ]
-    [ GLOB [ .path boehm_gc Mac_files ] : * ]
-    [ GLOB [ .path boehm_gc tests ] : * ]
-    [ GLOB [ .path boehm_gc doc ] : * ]
-    ;
-dist.bin =
-    bjam
-    ;
-dist.bin =
-    $(dist.license[1])
-    $(dist.bin:S=$(bjam.exe:S))
-    ;
-
-if $(OS) = NT
-{
-    zip ?= [ GLOB "$(ProgramFiles:J= )\\7-ZIP" "C:\\Program Files\\7-ZIP" : "7z.exe" ] ;
-    zip ?= [ GLOB "$(ProgramFiles:J= )\\7-ZIP" "C:\\Program Files\\7-ZIP" : "7zn.exe" ] ;
-    zip ?= [ GLOB $(PATH) : zip.exe ] ;
-    zip ?= zip ;
-    zip = $(zip[1]) ;
-    switch $(zip:D=:S=)
-    {
-        case 7z* : zip += a -r -tzip -mx=9 ;
-        case zip  : zip += -9r ;
-    }
-    actions piecemeal [PACK] {
-    "$(zip)" "$(<)" "$(>)"
-    }
-    actions piecemeal [ZIP] {
-    "$(zip)" "$(<)" "$(>)"
-    }
-    actions piecemeal [COPY] {
-    copy /Y "$(>)" "$(<)" >NUL:
-    }
-}
-if $(UNIX) = true
-{
-    tar ?= [ GLOB $(PATH) : star bsdtar tar ] ;
-    tar = $(tar[1]) ;
-    switch $(tar:D=:S=)
-    {
-        case star : tar += -c artype=pax -D -d -to-stdout ;
-        case * : tar += -c -f - ;
-    }
-    actions [PACK] {
-    "$(tar)" "$(>)" | gzip -c9 > "$(<)"
-    }
-    #~ actions [PACK] {
-    #~ tar cf "$(<:S=.tar)" "$(>)"
-    #~ }
-    actions [ZIP] {
-    gzip -c9 "$(>)" > "$(<)"
-    }
-    actions [COPY] {
-    cp -Rpf "$(>)" "$(<)"
-    }
-}
-
-# The single binary, compressed.
-rule .binary
-{
-    local zip = ;
-    if $(OS) = NT { zip = $($(<).exe:S=.zip) ; }
-    if $(UNIX) = true { zip = $($(<).exe:S=.tgz) ; }
-    zip = $(zip:S=)-$(VERSION)-$(RELEASE)-$(platform)$(zip:S) ;
-    DEPENDS $(zip) : $($(<).exe) ;
-    DEPENDS dist : $(zip) ;
-    #~ LOCATE on $(zip) = $(locate-target) ;
-    if $(OS) = NT { [ZIP] $(zip) : $($(<).exe) ; }
-    if $(UNIX) = true { [PACK] $(zip) : $($(<).exe) ; }
-    .clean $(zip) ;
-}
-
-# Package some file.
-rule .package ( dst-dir : src-files + )
-{
-    local dst-files ;
-    local src-files-actual ;
-    for local src-path in $(src-files)
-    {
-        if ! [ GLOB $(src-path:P) : $(src-path:B) ] || [ CHECK_IF_FILE $(src-path) ]
-        {
-            local src-subdir = $(src-path:D) ;
-            local src-file = $(src-path) ;
-            while $(src-subdir:D) { src-subdir = $(src-subdir:D) ; }
-            if $(src-subdir) = ".."
-            {
-                src-file = $(src-file:D=) ;
-            }
-            dst-files += $(src-file:R=$(dst-dir)) ;
-            src-files-actual += $(src-path) ;
-        }
-    }
-
-    local pack = ;
-    if $(OS) = NT { pack = $(dst-dir).zip ; }
-    if $(UNIX) = true { pack = $(dst-dir).tgz ; }
-
-    DEPENDS dist : $(pack) ;
-    DEPENDS $(pack) : $(dst-files) ;
-
-    local dst-files-queue = $(dst-files) ;
-    for local src-path in $(src-files-actual)
-    {
-        local dst-file = $(dst-files-queue[1]) ;
-        dst-files-queue = $(dst-files-queue[2-]) ;
-        DEPENDS $(dst-file) : $(src-path) $(dst-file:D) ;
-        .mkdir $(dst-file:D) ;
-
-        [COPY] $(dst-file) : $(src-path) ;
-        .clean $(dst-file) ;
-    }
-
-    [PACK] $(pack) : $(dst-files) ;
-    .clean $(pack) ;
-}
-
-# RPM distro file.
-rpm-tool = [ GLOB $(PATH) : "rpmbuild" ] ;
-rpm-tool ?= [ GLOB $(PATH) : "rpm" ] ;
-rpm-tool = $(rpm-tool[1]) ;
-rule .rpm ( name : source )
-{
-    local rpm-arch = ;
-    switch $(OSPLAT)
-    {
-        case X86       : rpm-arch ?= i386 ;
-        case PPC       : rpm-arch ?= ppc ;
-        case AXP       : rpm-arch ?= alpha ;
-        # no guaranty for these:
-        case IA64      : rpm-arch ?= ia64 ;
-        case ARM       : rpm-arch ?= arm ;
-        case SPARC     : rpm-arch ?= sparc ;
-        case *         : rpm-arch ?= other ;
-    }
-    local target = $(name)-rpm ;
-    NOTFILE $(target) ;
-    DEPENDS dist : $(target) ;
-    DEPENDS $(target) : $(name).$(rpm-arch).rpm $(name).src.rpm ;
-    DEPENDS $(name).$(rpm-arch).rpm : $(source) ;
-    DEPENDS $(name).src.rpm : $(name).$(rpm-arch).rpm ;
-    docs on $(target) = $(dist.docs:J=" ") ;
-    arch on $(target) = $(rpm-arch) ;
-    if $(rpm-arch) = ppc { target-opt on $(target) = --target= ; }
-    else { target-opt on $(target) = "--target " ; }
-    [RPM] $(target) : $(source) ;
-    .clean $(name).$(rpm-arch).rpm $(name).src.rpm ;
-}
-actions [RPM] {
-    set -e
-    export BOOST_JAM_TOOLSET="$(toolset)"
-    $(rpm-tool) -ta $(target-opt)$(arch) $(>) | tee rpm.out
-    cp `grep -e '^Wrote:' rpm.out | sed 's/^Wrote: //'` .
-    rm -f rpm.out
-}
-
-# The distribution targets. Don't bother with the targets if
-# distribution build not requested.
-if dist in $(ARGV)
-{
-    #~ .binary bjam ;
-    .package $(NAME)-$(VERSION) : $(dist.source) ;
-    .package $(NAME)-$(VERSION)-$(RELEASE)-$(platform) : $(dist.bin) ;
-    if $(rpm-tool)
-    {
-        #~ .rpm $(NAME)-$(VERSION)-$(RELEASE) : $(NAME)-$(VERSION).tgz ;
-    }
-}
diff --git a/jam-files/engine/build.sh b/jam-files/engine/build.sh
deleted file mode 100755
index f1fb806d..00000000
--- a/jam-files/engine/build.sh
+++ /dev/null
@@ -1,303 +0,0 @@
-#!/bin/sh
-
-#~ Copyright 2002-2005 Rene Rivera.
-#~ Distributed under the Boost Software License, Version 1.0.
-#~ (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-
-# Reset the toolset.
-BOOST_JAM_TOOLSET=
-
-# Run a command, and echo before doing so. Also checks the exit
-# status and quits if there was an error.
-echo_run ()
-{
-    echo "$@"
-    $@
-    r=$?
-    if test $r -ne 0 ; then
-        exit $r
-    fi
-}
-
-# Print an error message, and exit with a status of 1.
-error_exit ()
-{
-    echo "###"
-    echo "###" "$@"
-    echo "###"
-    echo "### You can specify the toolset as the argument, i.e.:"
-    echo "###     ./build.sh gcc"
-    echo "###"
-    echo "### Toolsets supported by this script are:"
-    echo "###     acc, como, darwin, gcc, intel-darwin, intel-linux, kcc, kylix,"
-    echo "###     mipspro, mingw(msys), pathscale, pgi, qcc, sun, sunpro, tru64cxx, vacpp"
-    echo "###"
-    echo "### A special toolset; cc, is available which is used as a fallback"
-    echo "### when a more specific toolset is not found and the cc command is"
-    echo "### detected. The 'cc' toolset will use the CC, CFLAGS, and LIBS"
-    echo "### envrironment variables, if present."
-    echo "###"
-    exit 1
-}
-
-# Check that a command is in the PATH.
-test_path ()
-{
-    if `command -v command 1>/dev/null 2>/dev/null`; then
-        command -v $1 1>/dev/null 2>/dev/null
-    else
-        hash $1 1>/dev/null 2>/dev/null
-    fi
-}
-
-# Check that the OS name, as returned by "uname", is as given.
-test_uname ()
-{
-    if test_path uname; then
-        test `uname` = $*
-    fi
-}
-
-# Try and guess the toolset to bootstrap the build with...
-Guess_Toolset ()
-{
-    if test -r /mingw/bin/gcc ; then
-        BOOST_JAM_TOOLSET=mingw
-        BOOST_JAM_TOOLSET_ROOT=/mingw/
-    elif test_uname Darwin ; then BOOST_JAM_TOOLSET=darwin
-    elif test_uname IRIX ; then BOOST_JAM_TOOLSET=mipspro
-    elif test_uname IRIX64 ; then BOOST_JAM_TOOLSET=mipspro
-    elif test_uname OSF1 ; then BOOST_JAM_TOOLSET=tru64cxx
-    elif test_uname QNX && test_path qcc ; then BOOST_JAM_TOOLSET=qcc
-    elif test_path gcc ; then BOOST_JAM_TOOLSET=gcc
-    elif test_path icc ; then BOOST_JAM_TOOLSET=intel-linux
-    elif test -r /opt/intel/cc/9.0/bin/iccvars.sh ; then
-        BOOST_JAM_TOOLSET=intel-linux
-        BOOST_JAM_TOOLSET_ROOT=/opt/intel/cc/9.0
-    elif test -r /opt/intel_cc_80/bin/iccvars.sh ; then
-        BOOST_JAM_TOOLSET=intel-linux
-        BOOST_JAM_TOOLSET_ROOT=/opt/intel_cc_80
-    elif test -r /opt/intel/compiler70/ia32/bin/iccvars.sh ; then
-        BOOST_JAM_TOOLSET=intel-linux
-        BOOST_JAM_TOOLSET_ROOT=/opt/intel/compiler70/ia32/
-    elif test -r /opt/intel/compiler60/ia32/bin/iccvars.sh ; then
-        BOOST_JAM_TOOLSET=intel-linux
-        BOOST_JAM_TOOLSET_ROOT=/opt/intel/compiler60/ia32/
-    elif test -r /opt/intel/compiler50/ia32/bin/iccvars.sh ; then
-        BOOST_JAM_TOOLSET=intel-linux
-        BOOST_JAM_TOOLSET_ROOT=/opt/intel/compiler50/ia32/
-    elif test_path pgcc ; then BOOST_JAM_TOOLSET=pgi
-    elif test_path pathcc ; then BOOST_JAM_TOOLSET=pathscale
-    elif test_path xlc ; then BOOST_JAM_TOOLSET=vacpp
-    elif test_path como ; then BOOST_JAM_TOOLSET=como
-    elif test_path KCC ; then BOOST_JAM_TOOLSET=kcc
-    elif test_path bc++ ; then BOOST_JAM_TOOLSET=kylix
-    elif test_path aCC ; then BOOST_JAM_TOOLSET=acc
-    elif test_uname HP-UX ; then BOOST_JAM_TOOLSET=acc
-    elif test -r /opt/SUNWspro/bin/cc ; then
-        BOOST_JAM_TOOLSET=sunpro
-        BOOST_JAM_TOOLSET_ROOT=/opt/SUNWspro/
-    # Test for "cc" as the default fallback.
-    elif test_path $CC ; then BOOST_JAM_TOOLSET=cc
-    elif test_path cc ; then
-        BOOST_JAM_TOOLSET=cc
-        CC=cc
-    fi
-    if test "$BOOST_JAM_TOOLSET" = "" ; then
-        error_exit "Could not find a suitable toolset."
-    fi
-}
-
-# The one option we support in the invocation
-# is the name of the toolset to force building
-# with.
-case "$1" in
-    --guess-toolset) Guess_Toolset ; echo "$BOOST_JAM_TOOLSET" ; exit 1 ;;
-    -*) Guess_Toolset ;;
-    ?*) BOOST_JAM_TOOLSET=$1 ; shift ;;
-    *) Guess_Toolset ;;
-esac
-BOOST_JAM_OPT_JAM="-o bootstrap/jam0"
-BOOST_JAM_OPT_MKJAMBASE="-o bootstrap/mkjambase0"
-BOOST_JAM_OPT_YYACC="-o bootstrap/yyacc0"
-case $BOOST_JAM_TOOLSET in
-    mingw)
-    if test -r ${BOOST_JAM_TOOLSET_ROOT}bin/gcc ; then
-        export PATH=${BOOST_JAM_TOOLSET_ROOT}bin:$PATH
-    fi
-    BOOST_JAM_CC="gcc -DNT"
-    ;;
-
-    gcc)
-    BOOST_JAM_CC=gcc
-    ;;
-
-    darwin)
-    BOOST_JAM_CC=cc
-    ;;
-
-    intel-darwin)
-    BOOST_JAM_CC=icc
-    ;;
-
-    intel-linux)
-    if test -r /opt/intel/cc/9.0/bin/iccvars.sh ; then
-        BOOST_JAM_TOOLSET_ROOT=/opt/intel/cc/9.0/
-    elif test -r /opt/intel_cc_80/bin/iccvars.sh ; then
-        BOOST_JAM_TOOLSET_ROOT=/opt/intel_cc_80/
-    elif test -r /opt/intel/compiler70/ia32/bin/iccvars.sh ; then
-        BOOST_JAM_TOOLSET_ROOT=/opt/intel/compiler70/ia32/
-    elif test -r /opt/intel/compiler60/ia32/bin/iccvars.sh ; then
-        BOOST_JAM_TOOLSET_ROOT=/opt/intel/compiler60/ia32/
-    elif test -r /opt/intel/compiler50/ia32/bin/iccvars.sh ; then
-        BOOST_JAM_TOOLSET_ROOT=/opt/intel/compiler50/ia32/
-    fi
-    if test -r ${BOOST_JAM_TOOLSET_ROOT}bin/iccvars.sh ; then
-        # iccvars doesn't change LD_RUN_PATH. We adjust LD_RUN_PATH
-        # here in order not to have to rely on ld.so.conf knowing the
-        # icc library directory. We do this before running iccvars.sh
-        # in order to allow a user to add modifications to LD_RUN_PATH
-        # in iccvars.sh.
-        if test -z "${LD_RUN_PATH}"; then
-            LD_RUN_PATH="${BOOST_JAM_TOOLSET_ROOT}lib"
-        else
-            LD_RUN_PATH="${BOOST_JAM_TOOLSET_ROOT}lib:${LD_RUN_PATH}"
-        fi
-        export LD_RUN_PATH
-        . ${BOOST_JAM_TOOLSET_ROOT}bin/iccvars.sh
-    fi
-    BOOST_JAM_CC=icc
-    ;;
-
-    vacpp)
-    BOOST_JAM_CC=xlc
-    ;;
-
-    como)
-    BOOST_JAM_CC="como --c"
-    ;;
-
-    kcc)
-    BOOST_JAM_CC=KCC
-    ;;
-
-    kylix)
-    BOOST_JAM_CC=bc++
-    ;;
-
-    mipspro)
-    BOOST_JAM_CC=cc
-    ;;
-
-    pathscale)
-    BOOST_JAM_CC=pathcc
-    ;;
-
-    pgi)
-    BOOST_JAM_CC=pgcc
-    ;;
-
-    sun*)
-    if test -z "${BOOST_JAM_TOOLSET_ROOT}" -a -r /opt/SUNWspro/bin/cc ; then
-        BOOST_JAM_TOOLSET_ROOT=/opt/SUNWspro/
-    fi
-    if test -r "${BOOST_JAM_TOOLSET_ROOT}bin/cc" ; then
-        PATH=${BOOST_JAM_TOOLSET_ROOT}bin:${PATH}
-        export PATH
-    fi
-    BOOST_JAM_CC=cc
-    ;;
-
-    clang*)
-    BOOST_JAM_CC="clang -Wno-unused -Wno-format"
-    BOOST_JAM_TOOLSET=clang
-    ;;
-
-    tru64cxx)
-    BOOST_JAM_CC=cc
-    ;;
-
-    acc)
-    BOOST_JAM_CC="cc -Ae"
-    ;;
-
-    cc)
-    if test -z "$CC" ; then CC=cc ; fi
-    BOOST_JAM_CC=$CC
-    BOOST_JAM_OPT_JAM="$BOOST_JAM_OPT_JAM $CFLAGS $LIBS"
-    BOOST_JAM_OPT_MKJAMBASE="$BOOST_JAM_OPT_MKJAMBASE $CFLAGS $LIBS"
-    BOOST_JAM_OPT_YYACC="$BOOST_JAM_OPT_YYACC $CFLAGS $LIBS"
-    ;;
-
-    qcc)
-    BOOST_JAM_CC=qcc
-    ;;
-
-    *)
-    error_exit "Unknown toolset: $BOOST_JAM_TOOLSET"
-    ;;
-esac
-
-echo "###"
-echo "### Using '$BOOST_JAM_TOOLSET' toolset."
-echo "###"
-
-YYACC_SOURCES="yyacc.c"
-MKJAMBASE_SOURCES="mkjambase.c"
-BJAM_SOURCES="\
- command.c compile.c debug.c expand.c glob.c hash.c\
- hdrmacro.c headers.c jam.c jambase.c jamgram.c lists.c make.c make1.c\
- newstr.c option.c output.c parse.c pathunix.c pathvms.c regexp.c\
- rules.c scan.c search.c subst.c timestamp.c variable.c modules.c\
- strings.c filesys.c builtins.c pwd.c class.c native.c md5.c w32_getreg.c\
- modules/set.c modules/path.c modules/regex.c modules/property-set.c\
- modules/sequence.c modules/order.c"
-case $BOOST_JAM_TOOLSET in
-    mingw)
-    BJAM_SOURCES="${BJAM_SOURCES} execnt.c filent.c"
-    ;;
-
-    *)
-    BJAM_SOURCES="${BJAM_SOURCES} execunix.c fileunix.c"
-    ;;
-esac
-
-BJAM_UPDATE=
-if test "$1" = "--update" -o "$2" = "--update" -o "$3" = "--update" -o "$4" = "--update"  ; then
-    BJAM_UPDATE="update"
-fi
-if test "${BJAM_UPDATE}" = "update" -a ! -x "./bootstrap/jam0" ; then
-    BJAM_UPDATE=
-fi
-
-if test "${BJAM_UPDATE}" != "update" ; then
-    echo_run rm -rf bootstrap
-    echo_run mkdir bootstrap
-    if test ! -r jamgram.y -o ! -r jamgramtab.h ; then
-        echo_run ${BOOST_JAM_CC} ${BOOST_JAM_OPT_YYACC} ${YYACC_SOURCES}
-        if test -x "./bootstrap/yyacc0" ; then
-            echo_run ./bootstrap/yyacc0 jamgram.y jamgramtab.h jamgram.yy
-        fi
-    fi
-    if test ! -r jamgram.c -o ! -r jamgram.h ; then
-        if test_path yacc ; then YACC="yacc -d"
-        elif test_path bison ; then YACC="bison -y -d --yacc"
-        fi
-        echo_run $YACC jamgram.y
-        mv -f y.tab.c jamgram.c
-        mv -f y.tab.h jamgram.h
-    fi
-    if test ! -r jambase.c ; then
-        echo_run ${BOOST_JAM_CC} ${BOOST_JAM_OPT_MKJAMBASE} ${MKJAMBASE_SOURCES}
-        if test -x "./bootstrap/mkjambase0" ; then
-            echo_run ./bootstrap/mkjambase0 jambase.c Jambase
-        fi
-    fi
-    echo_run ${BOOST_JAM_CC} ${BOOST_JAM_OPT_JAM} ${BJAM_SOURCES}
-fi
-if test -x "./bootstrap/jam0" ; then
-    if test "${BJAM_UPDATE}" != "update" ; then
-        echo_run ./bootstrap/jam0 -f build.jam --toolset=$BOOST_JAM_TOOLSET "--toolset-root=$BOOST_JAM_TOOLSET_ROOT" clean
-    fi
-    echo_run ./bootstrap/jam0 -f build.jam --toolset=$BOOST_JAM_TOOLSET "--toolset-root=$BOOST_JAM_TOOLSET_ROOT" "$@"
-fi
diff --git a/jam-files/engine/build_vms.com b/jam-files/engine/build_vms.com
deleted file mode 100644
index 965b6342..00000000
--- a/jam-files/engine/build_vms.com
+++ /dev/null
@@ -1,105 +0,0 @@
-$ ! Copyright 2002-2003 Rene Rivera, Johan Nilsson.
-$ ! Distributed under the Boost Software License, Version 1.0.
-$ ! (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-$ !
-$ ! bootstrap build script for Jam
-$ !
-$ SAY :== WRITE SYS$OUTPUT
-$ !
-$ ON WARNING THEN CONTINUE
-$ !
-$ IF "" .NES. F$SEARCH("[.bootstrap_vms]*.*")
-$ THEN
-$   SAY "Cleaning previous boostrap files..."
-$ !
-$   SET FILE/PROTECTION=(S:RWED) [.bootstrap_vms]*.*;*
-$   DELETE [.bootstrap_vms]*.*;*
-$ ENDIF
-$ !
-$ IF "" .NES. F$SEARCH("bootstrap_vms.dir")
-$ THEN
-$   SAY "Removing previous boostrap directory..."
-$ !
-$   SET FILE/PROT=(S:RWED) bootstrap_vms.dir
-$   DELETE bootstrap_vms.dir;
-$ ENDIF
-$ !
-$ SAY "Creating boostrap directory..."
-$ !
-$ CREATE/DIR [.bootstrap_vms]
-$ !
-$ SAY "Building bootstrap jam..."
-$ !
-$ CC_FLAGS = "/DEFINE=VMS /STANDARD=VAXC /PREFIX_LIBRARY_ENTRIES=ALL_ENTRIES "
-$ cc 'CC_FLAGS /OBJECT=[.bootstrap_vms]builtins.obj builtins.c
-$ cc 'CC_FLAGS /OBJECT=[.bootstrap_vms]command.obj command.c
-$ cc 'CC_FLAGS /OBJECT=[.bootstrap_vms]compile.obj compile.c
-$ cc 'CC_FLAGS /OBJECT=[.bootstrap_vms]execvms.obj execvms.c
-$ cc 'CC_FLAGS /OBJECT=[.bootstrap_vms]expand.obj expand.c
-$ cc 'CC_FLAGS /OBJECT=[.bootstrap_vms]filesys.obj filesys.c
-$ cc 'CC_FLAGS /OBJECT=[.bootstrap_vms]filevms.obj filevms.c
-$ cc 'CC_FLAGS /OBJECT=[.bootstrap_vms]glob.obj glob.c
-$ cc 'CC_FLAGS /OBJECT=[.bootstrap_vms]hash.obj hash.c
-$ cc 'CC_FLAGS /OBJECT=[.bootstrap_vms]hdrmacro.obj hdrmacro.c
-$ cc 'CC_FLAGS /OBJECT=[.bootstrap_vms]headers.obj headers.c
-$ cc 'CC_FLAGS /OBJECT=[.bootstrap_vms]jam.obj jam.c
-$ cc 'CC_FLAGS /OBJECT=[.bootstrap_vms]jambase.obj jambase.c
-$ cc 'CC_FLAGS /OBJECT=[.bootstrap_vms]jamgram.obj jamgram.c
-$ cc 'CC_FLAGS /OBJECT=[.bootstrap_vms]lists.obj lists.c
-$ cc 'CC_FLAGS /OBJECT=[.bootstrap_vms]make.obj make.c
-$ cc 'CC_FLAGS /OBJECT=[.bootstrap_vms]make1.obj make1.c
-$ cc 'CC_FLAGS /OBJECT=[.bootstrap_vms]modules.obj modules.c
-$ cc 'CC_FLAGS /OBJECT=[.bootstrap_vms]newstr.obj newstr.c
-$ cc 'CC_FLAGS /OBJECT=[.bootstrap_vms]option.obj option.c
-$ cc 'CC_FLAGS /OBJECT=[.bootstrap_vms]parse.obj parse.c
-$ cc 'CC_FLAGS /OBJECT=[.bootstrap_vms]pathvms.obj pathvms.c
-$ cc 'CC_FLAGS /OBJECT=[.bootstrap_vms]pwd.obj pwd.c
-$ cc 'CC_FLAGS /OBJECT=[.bootstrap_vms]regexp.obj regexp.c
-$ cc 'CC_FLAGS /OBJECT=[.bootstrap_vms]rules.obj rules.c
-$ cc 'CC_FLAGS /OBJECT=[.bootstrap_vms]scan.obj scan.c
-$ cc 'CC_FLAGS /OBJECT=[.bootstrap_vms]search.obj search.c
-$ cc 'CC_FLAGS /OBJECT=[.bootstrap_vms]strings.obj strings.c
-$ cc 'CC_FLAGS /OBJECT=[.bootstrap_vms]subst.obj subst.c
-$ cc 'CC_FLAGS /OBJECT=[.bootstrap_vms]timestamp.obj timestamp.c
-$ cc 'CC_FLAGS /OBJECT=[.bootstrap_vms]variable.obj variable.c
-$ link -
- /EXECUTABLE=[.bootstrap_vms]jam0.exe -
- [.bootstrap_vms]builtins.obj, -
- [.bootstrap_vms]command.obj, -
- [.bootstrap_vms]compile.obj, -
- [.bootstrap_vms]execvms.obj, -
- [.bootstrap_vms]expand.obj, -
- [.bootstrap_vms]filesys.obj, -
- [.bootstrap_vms]filevms.obj, -
- [.bootstrap_vms]glob.obj, -
- [.bootstrap_vms]hash.obj, -
- [.bootstrap_vms]hdrmacro.obj, -
- [.bootstrap_vms]headers.obj, -
- [.bootstrap_vms]jam.obj, -
- [.bootstrap_vms]jambase.obj, -
- [.bootstrap_vms]jamgram.obj, -
- [.bootstrap_vms]lists.obj, -
- [.bootstrap_vms]make.obj, -
- [.bootstrap_vms]make1.obj, -
- [.bootstrap_vms]modules.obj, -
- [.bootstrap_vms]newstr.obj, -
- [.bootstrap_vms]option.obj, -
- [.bootstrap_vms]parse.obj, -
- [.bootstrap_vms]pathvms.obj, -
- [.bootstrap_vms]pwd.obj, -
- [.bootstrap_vms]regexp.obj, -
- [.bootstrap_vms]rules.obj, -
- [.bootstrap_vms]scan.obj, -
- [.bootstrap_vms]search.obj, -
- [.bootstrap_vms]strings.obj, -
- [.bootstrap_vms]subst.obj, -
- [.bootstrap_vms]timestamp.obj, -
- [.bootstrap_vms]variable.obj
-$ !
-$ SAY "Cleaning any previous build..."
-$ !
-$ MCR [.bootstrap_vms]jam0.exe -f build.jam --toolset=vmsdecc clean
-$ !
-$ SAY "Building Boost.Jam..."
-$ !
-$ MCR [.bootstrap_vms]jam0.exe -f build.jam --toolset=vmsdecc
diff --git a/jam-files/engine/builtins.c b/jam-files/engine/builtins.c
deleted file mode 100644
index b28a484e..00000000
--- a/jam-files/engine/builtins.c
+++ /dev/null
@@ -1,2310 +0,0 @@
-/*
- * Copyright 1993-2002 Christopher Seiwald and Perforce Software, Inc.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-#include "jam.h"
-
-#include "lists.h"
-#include "parse.h"
-#include "builtins.h"
-#include "rules.h"
-#include "filesys.h"
-#include "newstr.h"
-#include "regexp.h"
-#include "frames.h"
-#include "hash.h"
-#include "strings.h"
-#include "pwd.h"
-#include "pathsys.h"
-#include "make.h"
-#include "hdrmacro.h"
-#include "compile.h"
-#include "native.h"
-#include "variable.h"
-#include "timestamp.h"
-#include "md5.h"
-#include <ctype.h>
-
-#if defined(USE_EXECUNIX)
-# include <sys/types.h>
-# include <sys/wait.h>
-#else
-/*
-  NT does not have wait() and associated macros, it uses the return value
-  of system() instead. Status code group are documented at
-  http://msdn.microsoft.com/en-gb/library/ff565436.aspx
-*/
-# define WIFEXITED(w)  (((w) & 0XFFFFFF00) == 0)
-# define WEXITSTATUS(w)(w)
-#endif
-
-/*
- * builtins.c - builtin jam rules
- *
- * External routines:
- *
- *  load_builtin() - define builtin rules
- *
- * Internal routines:
- *
- *  builtin_depends() - DEPENDS/INCLUDES rule.
- *  builtin_echo() - ECHO rule.
- *  builtin_exit() - EXIT rule.
- *  builtin_flags() - NOCARE, NOTFILE, TEMPORARY rule.
- *  builtin_glob() - GLOB rule.
- *  builtin_match() - MATCH rule.
- *
- * 01/10/01 (seiwald) - split from compile.c
- */
-
-
-/*
- * compile_builtin() - define builtin rules
- */
-
-#define P0 (PARSE *)0
-#define C0 (char *)0
-
-#if defined( OS_NT ) || defined( OS_CYGWIN )
-    LIST * builtin_system_registry      ( PARSE *, FRAME * );
-    LIST * builtin_system_registry_names( PARSE *, FRAME * );
-#endif
-
-int glob( char * s, char * c );
-
-void backtrace        ( FRAME * );
-void backtrace_line   ( FRAME * );
-void print_source_line( PARSE * );
-
-
-RULE * bind_builtin( char * name, LIST * (* f)( PARSE *, FRAME * ), int flags, char * * args )
-{
-    argument_list* arg_list = 0;
-
-    if ( args )
-    {
-        arg_list = args_new();
-        lol_build( arg_list->data, args );
-    }
-
-    return new_rule_body( root_module(), name, arg_list,
-                          parse_make( f, P0, P0, P0, C0, C0, flags ), 1 );
-}
-
-
-RULE * duplicate_rule( char * name, RULE * other )
-{
-    return import_rule( other, root_module(), name );
-}
-
-
-void load_builtins()
-{
-    duplicate_rule( "Always",
-      bind_builtin( "ALWAYS",
-                    builtin_flags, T_FLAG_TOUCHED, 0 ) );
-
-    duplicate_rule( "Depends",
-      bind_builtin( "DEPENDS",
-                    builtin_depends, 0, 0 ) );
-
-    duplicate_rule( "echo",
-    duplicate_rule( "Echo",
-      bind_builtin( "ECHO",
-                    builtin_echo, 0, 0 ) ) );
-
-    {
-        char * args[] = { "message", "*", ":", "result-value", "?", 0 };
-        duplicate_rule( "exit",
-        duplicate_rule( "Exit",
-          bind_builtin( "EXIT",
-                        builtin_exit, 0, args ) ) );
-    }
-
-    {
-        char * args[] = { "directories", "*", ":", "patterns", "*", ":", "case-insensitive", "?", 0 };
-        duplicate_rule( "Glob",
-                        bind_builtin( "GLOB", builtin_glob, 0, args ) );
-    }
-
-    {
-        char * args[] = { "patterns", "*", 0 };
-        bind_builtin( "GLOB-RECURSIVELY",
-                      builtin_glob_recursive, 0, args );
-    }
-
-    duplicate_rule( "Includes",
-      bind_builtin( "INCLUDES",
-                    builtin_depends, 1, 0 ) );
-
-    {
-        char * args[] = { "targets", "*", ":", "targets-to-rebuild", "*", 0 };
-        bind_builtin( "REBUILDS",
-                      builtin_rebuilds, 0, args );
-    }
-
-    duplicate_rule( "Leaves",
-      bind_builtin( "LEAVES",
-                    builtin_flags, T_FLAG_LEAVES, 0 ) );
-
-    duplicate_rule( "Match",
-      bind_builtin( "MATCH",
-                    builtin_match, 0, 0 ) );
-
-    {
-        char * args[] = { "string", ":", "delimiters" };
-        bind_builtin( "SPLIT_BY_CHARACTERS", 
-                      builtin_split_by_characters, 0, 0 );
-    }
-
-    duplicate_rule( "NoCare",
-      bind_builtin( "NOCARE",
-                    builtin_flags, T_FLAG_NOCARE, 0 ) );
-
-    duplicate_rule( "NOTIME",
-    duplicate_rule( "NotFile",
-      bind_builtin( "NOTFILE",
-                    builtin_flags, T_FLAG_NOTFILE, 0 ) ) );
-
-    duplicate_rule( "NoUpdate",
-      bind_builtin( "NOUPDATE",
-                    builtin_flags, T_FLAG_NOUPDATE, 0 ) );
-
-    duplicate_rule( "Temporary",
-      bind_builtin( "TEMPORARY",
-                    builtin_flags, T_FLAG_TEMP, 0 ) );
-
-      bind_builtin( "ISFILE",
-                    builtin_flags, T_FLAG_ISFILE, 0 );
-
-    duplicate_rule( "HdrMacro",
-      bind_builtin( "HDRMACRO",
-                    builtin_hdrmacro, 0, 0 ) );
-
-    /* FAIL_EXPECTED is used to indicate that the result of a target build
-     * action should be inverted (ok <=> fail) this can be useful when
-     * performing test runs from Jamfiles.
-     */
-      bind_builtin( "FAIL_EXPECTED",
-                    builtin_flags, T_FLAG_FAIL_EXPECTED, 0 );
-
-      bind_builtin( "RMOLD",
-                    builtin_flags, T_FLAG_RMOLD, 0 );
-
-      {
-          char * args[] = { "targets", "*", 0 };
-          bind_builtin( "UPDATE",
-                        builtin_update, 0, args );
-      }
-
-      {
-          char * args[] = { "targets", "*", 
-                            ":", "log", "?",
-                            ":", "ignore-minus-n", "?", 
-                            ":", "ignore-minus-q", "?", 0 };
-          bind_builtin( "UPDATE_NOW",
-                        builtin_update_now, 0, args );
-      }
-
-      {
-          char * args[] = { "string", "pattern", "replacements", "+", 0 };
-          duplicate_rule( "subst",
-            bind_builtin( "SUBST",
-                          builtin_subst, 0, args ) );
-      }
-
-      {
-          char * args[] = { "module", "?", 0 };
-          bind_builtin( "RULENAMES",
-                         builtin_rulenames, 0, args );
-      }
-
-
-      {
-          char * args[] = { "module", "?", 0 };
-          bind_builtin( "VARNAMES",
-                         builtin_varnames, 0, args );
-      }
-
-      {
-          char * args[] = { "module", "?", 0 };
-          bind_builtin( "DELETE_MODULE",
-                         builtin_delete_module, 0, args );
-      }
-
-      {
-          char * args[] = { "source_module", "?",
-                            ":", "source_rules", "*",
-                            ":", "target_module", "?",
-                            ":", "target_rules", "*",
-                            ":", "localize", "?", 0 };
-          bind_builtin( "IMPORT",
-                        builtin_import, 0, args );
-      }
-
-      {
-          char * args[] = { "module", "?", ":", "rules", "*", 0 };
-          bind_builtin( "EXPORT",
-                        builtin_export, 0, args );
-      }
-
-      {
-          char * args[] = { "levels", "?", 0 };
-          bind_builtin( "CALLER_MODULE",
-                         builtin_caller_module, 0, args );
-      }
-
-      {
-          char * args[] = { "levels", "?", 0 };
-          bind_builtin( "BACKTRACE",
-                        builtin_backtrace, 0, args );
-      }
-
-      {
-          char * args[] = { 0 };
-          bind_builtin( "PWD",
-                        builtin_pwd, 0, args );
-      }
-
-      {
-          char * args[] = { "target", "*", ":", "path", "*", 0 };
-          bind_builtin( "SEARCH_FOR_TARGET",
-                        builtin_search_for_target, 0, args );
-      }
-
-      {
-          char * args[] = { "modules_to_import", "+", ":", "target_module", "?", 0 };
-          bind_builtin( "IMPORT_MODULE",
-                        builtin_import_module, 0, args );
-      }
-
-      {
-          char * args[] = { "module", "?", 0 };
-          bind_builtin( "IMPORTED_MODULES",
-                        builtin_imported_modules, 0, args );
-      }
-
-      {
-          char * args[] = { "instance_module", ":", "class_module", 0 };
-          bind_builtin( "INSTANCE",
-                        builtin_instance, 0, args );
-      }
-
-      {
-          char * args[] = { "sequence", "*", 0 };
-          bind_builtin( "SORT",
-                        builtin_sort, 0, args );
-      }
-
-      {
-          char * args[] = { "path_parts", "*", 0 };
-          bind_builtin( "NORMALIZE_PATH",
-                        builtin_normalize_path, 0, args );
-      }
-
-      {
-          char * args[] = { "args", "*", 0 };
-          bind_builtin( "CALC",
-                        builtin_calc, 0, args );
-      }
-
-      {
-          char * args[] = { "module", ":", "rule", 0 };
-          bind_builtin( "NATIVE_RULE",
-                        builtin_native_rule, 0, args );
-      }
-
-      {
-          char * args[] = { "module", ":", "rule", ":", "version", 0 };
-          bind_builtin( "HAS_NATIVE_RULE",
-                        builtin_has_native_rule, 0, args );
-      }
-
-      {
-          char * args[] = { "module", "*", 0 };
-          bind_builtin( "USER_MODULE",
-                        builtin_user_module, 0, args );
-      }
-
-      {
-          char * args[] = { 0 };
-          bind_builtin( "NEAREST_USER_LOCATION",
-                        builtin_nearest_user_location, 0, args );
-      }
-
-      {
-          char * args[] = { "file", 0 };
-          bind_builtin( "CHECK_IF_FILE",
-                        builtin_check_if_file, 0, args );
-      }
-
-#ifdef HAVE_PYTHON
-      {
-          char * args[] = { "python-module", ":", "function", ":",
-                            "jam-module", ":", "rule-name", 0 };
-          bind_builtin( "PYTHON_IMPORT_RULE",
-                        builtin_python_import_rule, 0, args );
-      }
-#endif
-
-# if defined( OS_NT ) || defined( OS_CYGWIN )
-      {
-          char * args[] = { "key_path", ":", "data", "?", 0 };
-          bind_builtin( "W32_GETREG",
-                        builtin_system_registry, 0, args );
-      }
-
-      {
-          char * args[] = { "key_path", ":", "result-type", 0 };
-          bind_builtin( "W32_GETREGNAMES",
-                        builtin_system_registry_names, 0, args );
-      }
-# endif
-
-      {
-          char * args[] = { "command", ":", "*", 0 };
-          duplicate_rule( "SHELL",
-            bind_builtin( "COMMAND",
-                          builtin_shell, 0, args ) );
-      }
-
-      {
-          char * args[] = { "string", 0 };
-          bind_builtin( "MD5",
-                        builtin_md5, 0, args ) ;
-      }
-
-      {
-          char * args[] = { "name", ":", "mode", 0 };
-          bind_builtin( "FILE_OPEN",
-                        builtin_file_open, 0, args );
-      }
-
-      {
-          char * args[] = { "string", ":", "width", 0 };
-          bind_builtin( "PAD",
-                        builtin_pad, 0, args );
-      }
-
-      {
-          char * args[] = { "targets", "*", 0 };
-          bind_builtin( "PRECIOUS",
-                        builtin_precious, 0, args );
-      }
-
-      {
-          char * args [] = { 0 };
-          bind_builtin( "SELF_PATH", builtin_self_path, 0, args );
-      }
-
-      {
-          char * args [] = { "path", 0 };
-          bind_builtin( "MAKEDIR", builtin_makedir, 0, args );
-      }
-
-      /* Initialize builtin modules. */
-      init_set();
-      init_path();
-      init_regex();
-      init_property_set();
-      init_sequence();
-      init_order();
-}
-
-
-/*
- * builtin_calc() - CALC rule.
- *
- * The CALC rule performs simple mathematical operations on two arguments.
- */
-
-LIST * builtin_calc( PARSE * parse, FRAME * frame )
-{
-    LIST * arg = lol_get( frame->args, 0 );
-
-    LIST * result = 0;
-    long lhs_value;
-    long rhs_value;
-    long result_value;
-    char buffer [ 16 ];
-    char const * lhs;
-    char const * op;
-    char const * rhs;
-
-    if ( arg == 0 ) return L0;
-    lhs = arg->string;
-
-    arg = list_next( arg );
-    if ( arg == 0 ) return L0;
-    op = arg->string;
-
-    arg = list_next( arg );
-    if ( arg == 0 ) return L0;
-    rhs = arg->string;
-
-    lhs_value = atoi( lhs );
-    rhs_value = atoi( rhs );
-
-    if ( strcmp( "+", op ) == 0 )
-    {
-        result_value = lhs_value + rhs_value;
-    }
-    else if ( strcmp( "-", op ) == 0 )
-    {
-        result_value = lhs_value - rhs_value;
-    }
-    else
-    {
-        return L0;
-    }
-
-    sprintf( buffer, "%ld", result_value );
-    result = list_new( result, newstr( buffer ) );
-    return result;
-}
-
-
-/*
- * builtin_depends() - DEPENDS/INCLUDES rule.
- *
- * The DEPENDS/INCLUDES builtin rule appends each of the listed sources on the
- * dependency/includes list of each of the listed targets. It binds both the
- * targets and sources as TARGETs.
- */
-
-LIST * builtin_depends( PARSE * parse, FRAME * frame )
-{
-    LIST * targets = lol_get( frame->args, 0 );
-    LIST * sources = lol_get( frame->args, 1 );
-    LIST * l;
-
-    for ( l = targets; l; l = list_next( l ) )
-    {
-        TARGET * t = bindtarget( l->string );
-
-        /* If doing INCLUDES, switch to the TARGET's include */
-        /* TARGET, creating it if needed.  The internal include */
-        /* TARGET shares the name of its parent. */
-
-        if ( parse->num )
-        {
-            if ( !t->includes )
-            {
-                t->includes = copytarget( t );
-                t->includes->original_target = t;
-            }
-            t = t->includes;
-        }
-
-        t->depends = targetlist( t->depends, sources );
-    }
-
-    /* Enter reverse links */
-    for ( l = sources; l; l = list_next( l ) )
-    {
-        TARGET * s = bindtarget( l->string );
-        s->dependants = targetlist( s->dependants, targets );
-    }
-
-    return L0;
-}
-
-
-/*
- * builtin_rebuilds() - REBUILDS rule.
- *
- * The REBUILDS builtin rule appends each of the listed rebuild-targets in its
- * 2nd argument on the rebuilds list of each of the listed targets in its first
- * argument.
- */
-
-LIST * builtin_rebuilds( PARSE * parse, FRAME * frame )
-{
-    LIST * targets = lol_get( frame->args, 0 );
-    LIST * rebuilds = lol_get( frame->args, 1 );
-    LIST * l;
-
-    for ( l = targets; l; l = list_next( l ) )
-    {
-        TARGET * t = bindtarget( l->string );
-        t->rebuilds = targetlist( t->rebuilds, rebuilds );
-    }
-
-    return L0;
-}
-
-
-/*
- * builtin_echo() - ECHO rule.
- *
- * The ECHO builtin rule echoes the targets to the user. No other actions are
- * taken.
- */
-
-LIST * builtin_echo( PARSE * parse, FRAME * frame )
-{
-    list_print( lol_get( frame->args, 0 ) );
-    printf( "\n" );
-    fflush( stdout );
-    return L0;
-}
-
-
-/*
- * builtin_exit() - EXIT rule.
- *
- * The EXIT builtin rule echoes the targets to the user and exits the program
- * with a failure status.
- */
-
-LIST * builtin_exit( PARSE * parse, FRAME * frame )
-{
-    list_print( lol_get( frame->args, 0 ) );
-    printf( "\n" );
-    if ( lol_get( frame->args, 1 ) )
-    {
-        exit( atoi( lol_get( frame->args, 1 )->string ) );
-    }
-    else
-    {
-        exit( EXITBAD );  /* yeech */
-    }
-    return L0;
-}
-
-
-/*
- * builtin_flags() - NOCARE, NOTFILE, TEMPORARY rule.
- *
- * Builtin_flags() marks the target with the appropriate flag, for use by make0().
- * It binds each target as a TARGET.
- */
-
-LIST * builtin_flags( PARSE * parse, FRAME * frame )
-{
-    LIST * l = lol_get( frame->args, 0 );
-    for ( ; l; l = list_next( l ) )
-        bindtarget( l->string )->flags |= parse->num;
-    return L0;
-}
-
-
-/*
- * builtin_globbing() - GLOB rule.
- */
-
-struct globbing
-{
-    LIST * patterns;
-    LIST * results;
-    LIST * case_insensitive;
-};
-
-
-static void downcase_inplace( char * p )
-{
-    for ( ; *p; ++p )
-        *p = tolower( *p );
-}
-
-
-static void builtin_glob_back
-(
-    void * closure,
-    char * file,
-    int    status,
-    time_t time
-)
-{
-    PROFILE_ENTER( BUILTIN_GLOB_BACK );
-
-    struct globbing * globbing = (struct globbing *)closure;
-    LIST            * l;
-    PATHNAME          f;
-    string            buf[ 1 ];
-
-    /* Null out directory for matching. We wish we had file_dirscan() pass up a
-     * PATHNAME.
-     */
-    path_parse( file, &f );
-    f.f_dir.len = 0;
-
-    /* For globbing, we unconditionally ignore current and parent directory
-     * items. Since they items always exist, there is no reason why caller of
-     * GLOB would want to see them. We could also change file_dirscan(), but
-     * then paths with embedded "." and ".." would not work anywhere.
-    */
-    if ( !strcmp( f.f_base.ptr, "." ) || !strcmp( f.f_base.ptr, ".." ) )
-    {
-        PROFILE_EXIT( BUILTIN_GLOB_BACK );
-        return;
-    }
-
-    string_new( buf );
-    path_build( &f, buf, 0 );
-
-    if ( globbing->case_insensitive )
-        downcase_inplace( buf->value );
-
-    for ( l = globbing->patterns; l; l = l->next )
-    {
-        if ( !glob( l->string, buf->value ) )
-        {
-            globbing->results = list_new( globbing->results, newstr( file ) );
-            break;
-        }
-    }
-
-    string_free( buf );
-
-    PROFILE_EXIT( BUILTIN_GLOB_BACK );
-}
-
-
-static LIST * downcase_list( LIST * in )
-{
-    LIST * result = 0;
-
-    string s[ 1 ];
-    string_new( s );
-
-    while ( in )
-    {
-        string_copy( s, in->string );
-        downcase_inplace( s->value );
-        result = list_append( result, list_new( 0, newstr( s->value ) ) );
-        in = in->next;
-    }
-
-    string_free( s );
-    return result;
-}
-
-
-LIST * builtin_glob( PARSE * parse, FRAME * frame )
-{
-    LIST * l = lol_get( frame->args, 0 );
-    LIST * r = lol_get( frame->args, 1 );
-
-    struct globbing globbing;
-
-    globbing.results = L0;
-    globbing.patterns = r;
-
-    globbing.case_insensitive
-# if defined( OS_NT ) || defined( OS_CYGWIN )
-       = l;  /* Always case-insensitive if any files can be found. */
-# else
-       = lol_get( frame->args, 2 );
-# endif
-
-    if ( globbing.case_insensitive )
-        globbing.patterns = downcase_list( r );
-
-    for ( ; l; l = list_next( l ) )
-        file_dirscan( l->string, builtin_glob_back, &globbing );
-
-    if ( globbing.case_insensitive )
-        list_free( globbing.patterns );
-
-    return globbing.results;
-}
-
-
-static int has_wildcards( char const * str )
-{
-    size_t const index = strcspn( str, "[]*?" );
-    return str[ index ] == '\0' ? 0 : 1;
-}
-
-
-/*
- * If 'file' exists, append 'file' to 'list'. Returns 'list'.
- */
-
-static LIST * append_if_exists( LIST * list, char * file )
-{
-    time_t time;
-    timestamp( file, &time );
-    return time > 0
-        ? list_new( list, newstr( file ) )
-        : list;
-}
-
-
-LIST * glob1( char * dirname, char * pattern )
-{
-    LIST * plist = list_new( L0, pattern );
-    struct globbing globbing;
-
-    globbing.results = L0;
-    globbing.patterns = plist;
-
-    globbing.case_insensitive
-# if defined( OS_NT ) || defined( OS_CYGWIN )
-       = plist;  /* always case-insensitive if any files can be found */
-# else
-       = L0;
-# endif
-
-    if ( globbing.case_insensitive )
-        globbing.patterns = downcase_list( plist );
-
-    file_dirscan( dirname, builtin_glob_back, &globbing );
-
-    if ( globbing.case_insensitive )
-        list_free( globbing.patterns );
-
-    list_free( plist );
-
-    return globbing.results;
-}
-
-
-LIST * glob_recursive( char * pattern )
-{
-    LIST * result = L0;
-
-    /* Check if there's metacharacters in pattern */
-    if ( !has_wildcards( pattern ) )
-    {
-        /* No metacharacters. Check if the path exists. */
-        result = append_if_exists(result, pattern);
-    }
-    else
-    {
-        /* Have metacharacters in the pattern. Split into dir/name. */
-        PATHNAME path[ 1 ];
-        path_parse( pattern, path );
-
-        if ( path->f_dir.ptr )
-        {
-            LIST * dirs = L0;
-            string dirname[ 1 ];
-            string basename[ 1 ];
-            string_new( dirname );
-            string_new( basename );
-
-            string_append_range( dirname, path->f_dir.ptr,
-                                path->f_dir.ptr + path->f_dir.len );
-
-            path->f_grist.ptr = 0;
-            path->f_grist.len = 0;
-            path->f_dir.ptr = 0;
-            path->f_dir.len = 0;
-            path_build( path, basename, 0 );
-
-            dirs =  has_wildcards( dirname->value )
-                ? glob_recursive( dirname->value )
-                : list_new( dirs, dirname->value );
-
-            if ( has_wildcards( basename->value ) )
-            {
-                for ( ; dirs; dirs = dirs->next )
-                    result = list_append( result, glob1( dirs->string,
-                        basename->value ) );
-            }
-            else
-            {
-                string file_string[ 1 ];
-                string_new( file_string );
-
-                /* No wildcard in basename. */
-                for ( ; dirs; dirs = dirs->next )
-                {
-                    path->f_dir.ptr = dirs->string;
-                    path->f_dir.len = strlen( dirs->string );
-                    path_build( path, file_string, 0 );
-
-                    result = append_if_exists( result, file_string->value );
-
-                    string_truncate( file_string, 0 );
-                }
-
-                string_free( file_string );
-            }
-
-            string_free( dirname );
-            string_free( basename );
-        }
-        else
-        {
-            /** No directory, just a pattern. */
-            result = list_append( result, glob1( ".", pattern ) );
-        }
-    }
-
-    return result;
-}
-
-
-LIST * builtin_glob_recursive( PARSE * parse, FRAME * frame )
-{
-    LIST * result = L0;
-    LIST * l = lol_get( frame->args, 0 );
-    for ( ; l; l = l->next )
-        result = list_append( result, glob_recursive( l->string ) );
-    return result;
-}
-
-
-/*
- * builtin_match() - MATCH rule, regexp matching.
- */
-
-LIST * builtin_match( PARSE * parse, FRAME * frame )
-{
-    LIST * l;
-    LIST * r;
-    LIST * result = 0;
-
-    string buf[ 1 ];
-    string_new( buf );
-
-    /* For each pattern */
-
-    for ( l = lol_get( frame->args, 0 ); l; l = l->next )
-    {
-        /* Result is cached and intentionally never freed. */
-        regexp * re = regex_compile( l->string );
-
-        /* For each string to match against. */
-        for ( r = lol_get( frame->args, 1 ); r; r = r->next )
-        {
-            if ( regexec( re, r->string ) )
-            {
-                int i;
-                int top;
-
-                /* Find highest parameter */
-
-                for ( top = NSUBEXP; top-- > 1; )
-                    if ( re->startp[ top ] )
-                        break;
-
-                /* And add all parameters up to highest onto list. */
-                /* Must have parameters to have results! */
-                for ( i = 1; i <= top; ++i )
-                {
-                    string_append_range( buf, re->startp[ i ], re->endp[ i ] );
-                    result = list_new( result, newstr( buf->value ) );
-                    string_truncate( buf, 0 );
-                }
-            }
-        }
-    }
-
-    string_free( buf );
-    return result;
-}
-
-LIST * builtin_split_by_characters( PARSE * parse, FRAME * frame )
-{
-    LIST * l1 = lol_get( frame->args, 0 );
-    LIST * l2 = lol_get( frame->args, 1 );
-
-    LIST * result = 0;
-
-    char* s = strdup (l1->string);
-    char* delimiters = l2->string;
-    char* t;
-
-    t = strtok (s, delimiters);
-    while (t)
-    {
-        result = list_new(result, newstr(t));
-        t = strtok (NULL, delimiters);
-    }
-
-    free (s);
-
-    return result;
-}
-
-LIST * builtin_hdrmacro( PARSE * parse, FRAME * frame )
-{
-  LIST * l = lol_get( frame->args, 0 );
-
-  for ( ; l; l = list_next( l ) )
-  {
-    TARGET * t = bindtarget( l->string );
-
-    /* Scan file for header filename macro definitions. */
-    if ( DEBUG_HEADER )
-        printf( "scanning '%s' for header file macro definitions\n",
-            l->string );
-
-    macro_headers( t );
-  }
-
-  return L0;
-}
-
-
-/*
- * builtin_rulenames() - RULENAMES ( MODULE ? ).
- *
- * Returns a list of the non-local rule names in the given MODULE. If MODULE is
- * not supplied, returns the list of rule names in the global module.
- */
-
-static void add_rule_name( void * r_, void * result_ )
-{
-    RULE * r = (RULE *)r_;
-    LIST * * result = (LIST * *)result_;
-    if ( r->exported )
-        *result = list_new( *result, copystr( r->name ) );
-}
-
-
-LIST * builtin_rulenames( PARSE * parse, FRAME * frame )
-{
-    LIST * arg0 = lol_get( frame->args, 0 );
-    LIST * result = L0;
-    module_t * source_module = bindmodule( arg0 ? arg0->string : 0 );
-
-    if ( source_module->rules )
-        hashenumerate( source_module->rules, add_rule_name, &result );
-    return result;
-}
-
-
-/*
- * builtin_varnames() - VARNAMES ( MODULE ? ).
- *
- * Returns a list of the variable names in the given MODULE. If MODULE is not
- * supplied, returns the list of variable names in the global module.
- */
-
-/* helper function for builtin_varnames(), below. Used with hashenumerate, will
- * prepend the key of each element to the list
- */
-static void add_hash_key( void * np, void * result_ )
-{
-    LIST * * result = (LIST * *)result_;
-    *result = list_new( *result, copystr( *(char * *)np ) );
-}
-
-
-static struct hash * get_running_module_vars()
-{
-    struct hash * dummy;
-    struct hash * vars = NULL;
-    /* Get the global variables pointer (that of the currently running module).
-     */
-    var_hash_swap( &vars );
-    dummy = vars;
-    /* Put the global variables pointer in its right place. */
-    var_hash_swap( &dummy );
-    return vars;
-}
-
-
-LIST * builtin_varnames( PARSE * parse, FRAME * frame )
-{
-    LIST * arg0 = lol_get( frame->args, 0 );
-    LIST * result = L0;
-    module_t * source_module = bindmodule( arg0 ? arg0->string : 0 );
-
-    /* The running module _always_ has its 'variables' member set to NULL due to
-     * the way enter_module() and var_hash_swap() work.
-     */
-    struct hash * vars = source_module == frame->module
-        ? get_running_module_vars()
-        : source_module->variables;
-
-    if ( vars )
-        hashenumerate( vars, add_hash_key, &result );
-    return result;
-}
-
-
-/*
- * builtin_delete_module() - MODULE ?.
- *
- * Clears all rules and variables from the given module.
- */
-
-LIST * builtin_delete_module( PARSE * parse, FRAME * frame )
-{
-    LIST     * arg0 = lol_get( frame->args, 0 );
-    LIST     * result = L0;
-    module_t * source_module = bindmodule( arg0 ? arg0->string : 0 );
-    delete_module( source_module );
-    return result;
-}
-
-
-static void unknown_rule( FRAME * frame, char * key, char * module_name, char * rule_name )
-{
-    backtrace_line( frame->prev );
-    printf( "%s error: rule \"%s\" unknown in module \"%s\"\n", key, rule_name, module_name );
-    backtrace( frame->prev );
-    exit( 1 );
-}
-
-
-/*
- * builtin_import() - IMPORT
- * (
- *     SOURCE_MODULE ? :
- *     SOURCE_RULES  * :
- *     TARGET_MODULE ? :
- *     TARGET_RULES  * :
- *     LOCALIZE      ?
- * )
- *
- * The IMPORT rule imports rules from the SOURCE_MODULE into the TARGET_MODULE
- * as local rules. If either SOURCE_MODULE or TARGET_MODULE is not supplied, it
- * refers to the global module. SOURCE_RULES specifies which rules from the
- * SOURCE_MODULE to import; TARGET_RULES specifies the names to give those rules
- * in TARGET_MODULE. If SOURCE_RULES contains a name which doesn't correspond to
- * a rule in SOURCE_MODULE, or if it contains a different number of items than
- * TARGET_RULES, an error is issued. If LOCALIZE is specified, the rules will be
- * executed in TARGET_MODULE, with corresponding access to its module local
- * variables.
- */
-
-LIST * builtin_import( PARSE * parse, FRAME * frame )
-{
-    LIST * source_module_list = lol_get( frame->args, 0 );
-    LIST * source_rules       = lol_get( frame->args, 1 );
-    LIST * target_module_list = lol_get( frame->args, 2 );
-    LIST * target_rules       = lol_get( frame->args, 3 );
-    LIST * localize           = lol_get( frame->args, 4 );
-
-    module_t * target_module =
-        bindmodule( target_module_list ? target_module_list->string : 0 );
-    module_t * source_module =
-        bindmodule( source_module_list ? source_module_list->string : 0 );
-
-    LIST * source_name;
-    LIST * target_name;
-
-    for ( source_name = source_rules, target_name = target_rules;
-          source_name && target_name;
-          source_name = list_next( source_name ),
-          target_name = list_next( target_name ) )
-    {
-        RULE   r_;
-        RULE * r = &r_;
-        RULE * imported;
-        r_.name = source_name->string;
-
-        if ( !source_module->rules ||
-            !hashcheck( source_module->rules, (HASHDATA * *)&r ) )
-            unknown_rule( frame, "IMPORT", source_module->name, r_.name );
-
-        imported = import_rule( r, target_module, target_name->string );
-        if ( localize )
-            imported->module = target_module;
-        /* This rule is really part of some other module. Just refer to it here,
-         * but do not let it out.
-         */
-        imported->exported = 0;
-    }
-
-    if ( source_name || target_name )
-    {
-        backtrace_line( frame->prev );
-        printf( "import error: length of source and target rule name lists don't match!\n" );
-        printf( "    source: " );
-        list_print( source_rules );
-        printf( "\n    target: " );
-        list_print( target_rules );
-        printf( "\n" );
-        backtrace( frame->prev );
-        exit( 1 );
-    }
-
-    return L0;
-}
-
-
-/*
- * builtin_export() - EXPORT ( MODULE ? : RULES * ).
- *
- * The EXPORT rule marks RULES from the SOURCE_MODULE as non-local (and thus
- * exportable). If an element of RULES does not name a rule in MODULE, an error
- * is issued.
- */
-
-LIST * builtin_export( PARSE * parse, FRAME * frame )
-{
-    LIST     * module_list = lol_get( frame->args, 0 );
-    LIST     * rules       = lol_get( frame->args, 1 );
-    module_t * m           = bindmodule( module_list ? module_list->string : 0 );
-
-    for ( ; rules; rules = list_next( rules ) )
-    {
-        RULE   r_;
-        RULE * r = &r_;
-        r_.name = rules->string;
-
-        if ( !m->rules || !hashcheck( m->rules, (HASHDATA * *)&r ) )
-            unknown_rule( frame, "EXPORT", m->name, r_.name );
-
-        r->exported = 1;
-    }
-    return L0;
-}
-
-
-/*
- * get_source_line() - Retrieve the file and line number that should be
- * indicated for a given procedure in debug output or an error backtrace.
- */
-
-static void get_source_line( PARSE * procedure, char * * file, int * line )
-{
-    if ( procedure )
-    {
-        char * f = procedure->file;
-        int    l = procedure->line;
-        if ( !strcmp( f, "+" ) )
-        {
-            f = "jambase.c";
-            l += 3;
-        }
-        *file = f;
-        *line = l;
-    }
-    else
-    {
-        *file = "(builtin)";
-        *line = -1;
-    }
-}
-
-
-void print_source_line( PARSE * p )
-{
-    char * file;
-    int    line;
-
-    get_source_line( p, &file, &line );
-    if ( line < 0 )
-        printf( "(builtin):" );
-    else
-        printf( "%s:%d:", file, line );
-}
-
-
-/*
- * backtrace_line() - print a single line of error backtrace for the given
- * frame.
- */
-
-void backtrace_line( FRAME * frame )
-{
-    if ( frame == 0 )
-    {
-        printf( "(no frame):" );
-    }
-    else
-    {
-        print_source_line( frame->procedure );
-        printf( " in %s\n", frame->rulename );
-    }
-}
-
-
-/*
- * backtrace() - Print the entire backtrace from the given frame to the Jambase
- * which invoked it.
- */
-
-void backtrace( FRAME * frame )
-{
-    if ( !frame ) return;
-    while ( ( frame = frame->prev ) )
-        backtrace_line( frame );
-}
-
-
-/*
- * builtin_backtrace() - A Jam version of the backtrace function, taking no
- * arguments and returning a list of quadruples: FILENAME LINE MODULE. RULENAME
- * describing each frame. Note that the module-name is always followed by a
- * period.
- */
-
-LIST * builtin_backtrace( PARSE * parse, FRAME * frame )
-{
-    LIST * levels_arg = lol_get( frame->args, 0 );
-    int levels = levels_arg ? atoi( levels_arg->string ) : ( (unsigned int)(-1) >> 1 ) ;
-
-    LIST * result = L0;
-    for ( ; ( frame = frame->prev ) && levels ; --levels )
-    {
-        char * file;
-        int    line;
-        char   buf[32];
-        get_source_line( frame->procedure, &file, &line );
-        sprintf( buf, "%d", line );
-        result = list_new( result, newstr( file ) );
-        result = list_new( result, newstr( buf ) );
-        result = list_new( result, newstr( frame->module->name ) );
-        result = list_new( result, newstr( frame->rulename ) );
-    }
-    return result;
-}
-
-
-/*
- * builtin_caller_module() - CALLER_MODULE ( levels ? )
- *
- * If levels is not supplied, returns the name of the module of the rule which
- * called the one calling this one. If levels is supplied, it is interpreted as
- * an integer specifying a number of additional levels of call stack to traverse
- * in order to locate the module in question. If no such module exists, returns
- * the empty list. Also returns the empty list when the module in question is
- * the global module. This rule is needed for implementing module import
- * behavior.
- */
-
-LIST * builtin_caller_module( PARSE * parse, FRAME * frame )
-{
-    LIST * levels_arg = lol_get( frame->args, 0 );
-    int levels = levels_arg ? atoi( levels_arg->string ) : 0 ;
-
-    int i;
-    for ( i = 0; ( i < levels + 2 ) && frame->prev; ++i )
-        frame = frame->prev;
-
-    if ( frame->module == root_module() )
-        return L0;
-
-    {
-        LIST * result;
-        string name;
-        string_copy( &name, frame->module->name );
-        string_pop_back( &name );
-        result = list_new( L0, newstr(name.value) );
-        string_free( &name );
-        return result;
-    }
-}
-
-
-/*
- * Return the current working directory.
- *
- * Usage: pwd = [ PWD ] ;
- */
-
-LIST * builtin_pwd( PARSE * parse, FRAME * frame )
-{
-    return pwd();
-}
-
-
-/*
- * Adds targets to the list of target that jam will attempt to update.
- */
-
-LIST * builtin_update( PARSE * parse, FRAME * frame )
-{
-    LIST * result = list_copy( L0, targets_to_update() );
-    LIST * arg1 = lol_get( frame->args, 0 );
-    clear_targets_to_update();
-    for ( ; arg1; arg1 = list_next( arg1 ) )
-        mark_target_for_updating( newstr( arg1->string ) );
-    return result;
-}
-
-extern int anyhow;
-int last_update_now_status;
-
-/* Takes a list of target names as first argument, and immediately
-   updates them.
-   Second parameter, if specified, if the descriptor (converted to a string)
-   of a log file where all build output is redirected.
-   Third parameter, if non-empty, specifies that the -n option should have
-   no effect -- that is, all out-of-date targets should be rebuild.
-*/
-LIST * builtin_update_now( PARSE * parse, FRAME * frame )
-{
-    LIST * targets = lol_get( frame->args, 0 );
-    LIST * log = lol_get( frame->args, 1 );
-    LIST * force = lol_get (frame->args, 2);
-    LIST * continue_ = lol_get(frame->args, 3);
-    int status = 0;
-    int original_stdout;
-    int original_stderr;
-    int n;
-    int targets_count;
-    const char** targets2;
-    int i;
-    int original_noexec;
-    int original_quitquick;
-	
-
-    if (log)
-    {
-        int fd = atoi(log->string);
-        /* Redirect stdout and stderr, temporary, to the log file.  */
-        original_stdout = dup (0);
-        original_stderr = dup (1);
-        dup2 (fd, 0);
-        dup2 (fd, 1);
-    }
-
-    if (force)
-    {
-        original_noexec = globs.noexec;
-        globs.noexec = 0;
-        original_quitquick = globs.quitquick;
-        globs.quitquick = 0;
-    }
-
-    if (continue_)
-    {
-        original_quitquick = globs.quitquick;
-        globs.quitquick = 0;
-    }
-
-    targets_count = list_length( targets );
-    targets2 = (const char * *)BJAM_MALLOC( targets_count * sizeof( char * ) );    
-    for (i = 0 ; targets; targets = list_next( targets ) )
-        targets2[ i++ ] = targets->string;
-    status |= make( targets_count, targets2, anyhow);
-    free( targets );
-
-    if (force)
-    {
-        globs.noexec = original_noexec;
-        globs.quitquick = original_quitquick;
-    }
-
-    if (continue_)
-    {
-        globs.quitquick = original_quitquick;
-    }
-
-    if (log)
-    {
-        /* Flush whatever stdio might have buffered, while descriptions
-           0 and 1 still refer to the log file.  */
-        fflush (stdout);
-        fflush (stderr);
-        dup2 (original_stdout, 0);
-        dup2 (original_stderr, 1);
-        close (original_stdout);
-        close (original_stderr);
-    }
-
-    last_update_now_status = status;
-	
-    if (status == 0)
-        return list_new (L0, newstr ("ok"));
-    else
-        return L0;
-}
-
-LIST * builtin_search_for_target( PARSE * parse, FRAME * frame )
-{
-    LIST * arg1 = lol_get( frame->args, 0 );
-    LIST * arg2 = lol_get( frame->args, 1 );
-    TARGET * t = search_for_target( arg1->string, arg2 );
-    return list_new( L0, t->name );
-}
-
-
-LIST * builtin_import_module( PARSE * parse, FRAME * frame )
-{
-    LIST * arg1 = lol_get( frame->args, 0 );
-    LIST * arg2 = lol_get( frame->args, 1 );
-    module_t * m = arg2 ? bindmodule( arg2->string ) : root_module();
-    import_module( arg1, m );
-    return L0;
-}
-
-
-LIST * builtin_imported_modules( PARSE * parse, FRAME * frame )
-{
-    LIST * arg0 = lol_get( frame->args, 0 );
-    return imported_modules( bindmodule( arg0 ? arg0->string : 0 ) );
-}
-
-
-LIST * builtin_instance( PARSE * parse, FRAME * frame )
-{
-    LIST * arg1 = lol_get( frame->args, 0 );
-    LIST * arg2 = lol_get( frame->args, 1 );
-    module_t * const instance     = bindmodule( arg1->string );
-    module_t * const class_module = bindmodule( arg2->string );
-    instance->class_module = class_module;
-    return L0;
-}
-
-
-LIST * builtin_sort( PARSE * parse, FRAME * frame )
-{
-    LIST * arg1 = lol_get( frame->args, 0 );
-    return list_sort( arg1 );
-}
-
-
-LIST * builtin_normalize_path( PARSE * parse, FRAME * frame )
-{
-    LIST * arg = lol_get( frame->args, 0 );
-
-    /* First, we iterate over all '/'-separated elements, starting from the end
-     * of string. If we see a '..', we remove a previous path elements. If we
-     * see '.', we remove it. The removal is done by overwriting data using '\1'
-     * in the string. After the whole string has been processed, we do a second
-     * pass, removing all the entered '\1' characters.
-     */
-
-    string   in[ 1 ];
-    string   out[ 1 ];
-	/* Last character of the part of string still to be processed. */
-    char   * end;
-	/* Working pointer. */
-    char   * current;
-	/* Number of '..' elements seen and not processed yet. */
-    int      dotdots = 0;
-    int      rooted  = 0;
-    char   * result  = 0;
-
-    /* Make a copy of input: we should not change it. Prepend a '/' before it as
-     * a guard for the algorithm later on and remember whether it was originally
-     * rooted or not.
-     */
-    string_new( in );
-    string_push_back( in, '/' );
-    for ( ; arg; arg = list_next( arg ) )
-    {
-        if ( arg->string[ 0 ] != '\0' )
-        {
-            if ( in->size == 1 )
-                rooted = ( ( arg->string[ 0 ] == '/'  ) ||
-                           ( arg->string[ 0 ] == '\\' ) );
-            else
-                string_append( in, "/" );
-            string_append( in, arg->string );
-        }
-    }
-
-    /* Convert \ into /. On Windows, paths using / and \ are equivalent, and we
-     * want this function to obtain a canonic representation.
-     */
-    for ( current = in->value, end = in->value + in->size;
-        current < end; ++current )
-        if ( *current == '\\' )
-            *current = '/';
-
-    /* Now we remove any extra path elements by overwriting them with '\1'
-     * characters and cound how many more unused '..' path elements there are
-     * remaining. Note that each remaining path element with always starts with
-     * a '/' character.
-     */
-    for ( end = in->value + in->size - 1; end >= in->value; )
-    {
-        /* Set 'current' to the next occurence of '/', which always exists. */
-        for ( current = end; *current != '/'; --current );
-
-        if ( current == end )
-        {
-            /* Found a trailing or duplicate '/'. Remove it. */
-            *current = '\1';
-        }
-        else if ( ( end - current == 1 ) && ( *(current + 1) == '.' ) )
-        {
-            /* Found '/.'. Remove them all. */
-            *current = '\1';
-            *(current + 1) = '\1';
-        }
-        else if ( ( end - current == 2 ) && ( *(current + 1) == '.' ) && ( *(current + 2) == '.' ) )
-        {
-            /* Found '/..'. Remove them all. */
-            *current = '\1';
-            *(current + 1) = '\1';
-            *(current + 2) = '\1';
-            ++dotdots;
-        }
-        else if ( dotdots )
-        {
-            memset( current, '\1', end - current + 1 );
-            --dotdots;
-        }
-        end = current - 1;
-    }
-
-    string_new( out );
-
-    /* Now we know that we need to add exactly dotdots '..' path elements to the
-     * front and that our string is either empty or has a '/' as its first
-     * significant character. If we have any dotdots remaining then the passed
-     * path must not have been rooted or else it is invalid we return an empty
-     * list.
-     */
-    if ( dotdots )
-    {
-        if ( rooted ) return L0;
-        do
-            string_append( out, "/.." );
-        while ( --dotdots );
-    }
-
-    /* Now we actually remove all the path characters marked for removal. */
-    for ( current = in->value; *current; ++current )
-        if ( *current != '\1' )
-            string_push_back( out, *current );
-
-    /* Here we know that our string contains no '\1' characters and is either
-     * empty or has a '/' as its initial character. If the original path was not
-     * rooted and we have a non-empty path we need to drop the initial '/'. If
-     * the original path was rooted and we have an empty path we need to add
-     * back the '/'.
-     */
-    result = newstr( out->size ? out->value + !rooted : ( rooted ? "/" : "." ) );
-
-    string_free( out );
-    string_free( in );
-
-    return list_new( 0, result );
-}
-
-
-LIST * builtin_native_rule( PARSE * parse, FRAME * frame )
-{
-    LIST * module_name = lol_get( frame->args, 0 );
-    LIST * rule_name = lol_get( frame->args, 1 );
-
-    module_t * module = bindmodule( module_name->string );
-
-    native_rule_t n;
-    native_rule_t * np = &n;
-    n.name = rule_name->string;
-    if ( module->native_rules && hashcheck( module->native_rules, (HASHDATA * *)&np ) )
-    {
-        new_rule_body( module, np->name, np->arguments, np->procedure, 1 );
-    }
-    else
-    {
-        backtrace_line( frame->prev );
-        printf( "error: no native rule \"%s\" defined in module \"%s\"\n",
-                n.name, module->name );
-        backtrace( frame->prev );
-        exit( 1 );
-    }
-    return L0;
-}
-
-
-LIST * builtin_has_native_rule( PARSE * parse, FRAME * frame )
-{
-    LIST * module_name = lol_get( frame->args, 0 );
-    LIST * rule_name   = lol_get( frame->args, 1 );
-    LIST * version     = lol_get( frame->args, 2 );
-
-    module_t * module = bindmodule( module_name->string );
-
-    native_rule_t n;
-    native_rule_t * np = &n;
-    n.name = rule_name->string;
-    if ( module->native_rules && hashcheck( module->native_rules, (HASHDATA * *)&np ) )
-    {
-        int expected_version = atoi( version->string );
-        if ( np->version == expected_version )
-            return list_new( 0, newstr( "true" ) );
-    }
-    return L0;
-}
-
-
-LIST * builtin_user_module( PARSE * parse, FRAME * frame )
-{
-    LIST * module_name = lol_get( frame->args, 0 );
-    for ( ; module_name; module_name = module_name->next )
-    {
-        module_t * m = bindmodule( module_name->string );
-        m->user_module = 1;
-    }
-    return L0;
-}
-
-
-LIST * builtin_nearest_user_location( PARSE * parse, FRAME * frame )
-{
-    FRAME * nearest_user_frame =
-        frame->module->user_module ? frame : frame->prev_user;
-    if ( !nearest_user_frame )
-        return L0;
-
-    {
-        LIST * result = 0;
-        char * file;
-        int    line;
-        char   buf[32];
-
-        get_source_line( nearest_user_frame->procedure, &file, &line );
-        sprintf( buf, "%d", line );
-        result = list_new( result, newstr( file ) );
-        result = list_new( result, newstr( buf ) );
-        return result;
-    }
-}
-
-
-LIST * builtin_check_if_file( PARSE * parse, FRAME * frame )
-{
-    LIST * name = lol_get( frame->args, 0 );
-    return file_is_file( name->string ) == 1
-        ? list_new( 0, newstr( "true" ) )
-        : L0 ;
-}
-
-
-LIST * builtin_md5( PARSE * parse, FRAME * frame )
-{
-    LIST * l = lol_get( frame->args, 0 );
-    char* s = l->string;
-
-    md5_state_t state;
-    md5_byte_t digest[16];
-    char hex_output[16*2 + 1];
-
-    int di;
-
-    md5_init(&state);
-    md5_append(&state, (const md5_byte_t *)s, strlen(s));
-    md5_finish(&state, digest);
-
-    for (di = 0; di < 16; ++di)
-        sprintf(hex_output + di * 2, "%02x", digest[di]);
-
-    return list_new (0, newstr(hex_output));
-}
-
-LIST *builtin_file_open( PARSE *parse, FRAME *frame )
-{
-    char* name = lol_get(frame->args, 0)->string;
-    char* mode = lol_get(frame->args, 1)->string;
-    int fd;
-    char buffer[sizeof("4294967295")];
-
-    if (strcmp(mode, "w") == 0)
-    {
-        fd = open(name, O_WRONLY|O_CREAT|O_TRUNC, 0666);
-    }
-    else
-    {
-        fd = open(name, O_RDONLY);
-    }
-
-    if (fd != -1)
-    {
-        sprintf(buffer, "%d", fd);
-        return list_new(L0, newstr(buffer));
-    }
-    else
-    {
-        return L0;
-    }
-}
-
-LIST *builtin_pad( PARSE *parse, FRAME *frame )
-{
-    char *string = lol_get(frame->args, 0)->string;
-    char *width_s = lol_get(frame->args, 1)->string;
-
-    int current = strlen (string);
-    int desired = atoi(width_s);
-    if (current >= desired)
-        return list_new (L0, string);
-    else
-    {
-        char *buffer = malloc (desired + 1);
-        int i;
-        LIST *result;
-
-        strcpy (buffer, string);
-        for (i = current; i < desired; ++i)
-            buffer[i] = ' ';
-        buffer[desired] = '\0';
-        result = list_new (L0, newstr (buffer));
-        free (buffer);
-        return result;
-    }
-}
-
-LIST *builtin_precious( PARSE *parse, FRAME *frame )
-{
-    LIST* targets = lol_get(frame->args, 0);
-
-    for ( ; targets; targets = list_next( targets ) )    
-    {
-        TARGET* t = bindtarget (targets->string);
-        t->flags |= T_FLAG_PRECIOUS;
-    }
-
-    return L0;
-}
-
-LIST *builtin_self_path( PARSE *parse, FRAME *frame )
-{
-    extern char *saved_argv0;
-    char *p = executable_path (saved_argv0);
-    if (p)
-    {
-        LIST* result = list_new (0, newstr (p));
-        free(p);
-        return result;
-    }
-    else
-    {
-        return L0;
-    }
-}
-
-LIST *builtin_makedir( PARSE *parse, FRAME *frame )
-{
-    LIST *path = lol_get(frame->args, 0);
-
-    if (file_mkdir(path->string) == 0)
-    {
-        LIST *result = list_new (0, newstr(path->string));
-        return result;
-    }
-    else
-    {
-        return L0;
-    }    
-}
-
-#ifdef HAVE_PYTHON
-
-LIST * builtin_python_import_rule( PARSE * parse, FRAME * frame )
-{
-    static int first_time = 1;
-    char * python_module   = lol_get( frame->args, 0 )->string;
-    char * python_function = lol_get( frame->args, 1 )->string;
-    char * jam_module      = lol_get( frame->args, 2 )->string;
-    char * jam_rule        = lol_get( frame->args, 3 )->string;
-
-    PyObject * pName;
-    PyObject * pModule;
-    PyObject * pDict;
-    PyObject * pFunc;
-
-    if ( first_time )
-    {
-        /* At the first invocation, we add the value of the global
-         * EXTRA_PYTHONPATH to the sys.path Python variable.
-         */
-        LIST * extra = 0;
-        module_t * outer_module = frame->module;
-
-        first_time = 0;
-
-        if ( outer_module != root_module() )
-        {
-            exit_module( outer_module );
-            enter_module( root_module() );
-        }
-
-        extra = var_get( "EXTRA_PYTHONPATH" );
-
-        if ( outer_module != root_module() )
-        {
-             exit_module( root_module() );
-             enter_module( outer_module );
-        }
-
-        for ( ; extra; extra = extra->next )
-        {
-            string buf[ 1 ];
-            string_new( buf );
-            string_append( buf, "import sys\nsys.path.append(\"" );
-            string_append( buf, extra->string );
-            string_append( buf, "\")\n" );
-            PyRun_SimpleString( buf->value );
-            string_free( buf );
-        }
-    }
-
-    pName   = PyString_FromString( python_module );
-    pModule = PyImport_Import( pName );
-    Py_DECREF( pName );
-
-    if ( pModule != NULL )
-    {
-        pDict = PyModule_GetDict( pModule );
-        pFunc = PyDict_GetItemString( pDict, python_function );
-
-        if ( pFunc && PyCallable_Check( pFunc ) )
-        {
-            module_t * m = bindmodule( jam_module );
-            RULE * r = bindrule( jam_rule, m );
-
-            /* Make pFunc owned. */
-            Py_INCREF( pFunc );
-
-            r->python_function = pFunc;
-        }
-        else
-        {
-            if ( PyErr_Occurred() )
-                PyErr_Print();
-            fprintf( stderr, "Cannot find function \"%s\"\n", python_function );
-        }
-        Py_DECREF( pModule );
-    }
-    else
-    {
-        PyErr_Print();
-        fprintf( stderr, "Failed to load \"%s\"\n", python_module );
-    }
-    return L0;
-
-}
-
-#endif
-
-void lol_build( LOL * lol, char * * elements )
-{
-    LIST * l = L0;
-    lol_init( lol );
-
-    while ( elements && *elements )
-    {
-        if ( !strcmp( *elements, ":" ) )
-        {
-            lol_add( lol, l );
-            l = L0 ;
-        }
-        else
-        {
-            l = list_new( l, newstr( *elements ) );
-        }
-        ++elements;
-    }
-
-    if ( l != L0 )
-        lol_add( lol, l );
-}
-
-
-#ifdef HAVE_PYTHON
-
-/*
- * Calls the bjam rule specified by name passed in 'args'. The name is looked up
- * in the context of bjam's 'python_interface' module. Returns the list of
- * string retured by the rule.
- */
-
-PyObject* bjam_call( PyObject * self, PyObject * args )
-{
-    FRAME   inner[ 1 ];
-    LIST  * result;
-    PARSE * p;
-    char  * rulename;
-
-    /* Build up the list of arg lists. */
-    frame_init( inner );
-    inner->prev = 0;
-    inner->prev_user = 0;
-    inner->module = bindmodule( "python_interface" );
-    inner->procedure = 0;
-
-    /* Extract the rule name and arguments from 'args'. */
-
-    /* PyTuple_GetItem returns borrowed reference. */
-    rulename = PyString_AsString( PyTuple_GetItem( args, 0 ) );
-    {
-        int i = 1;
-        int size = PyTuple_Size( args );
-        for ( ; i < size; ++i )
-        {
-            PyObject * a = PyTuple_GetItem( args, i );
-            if ( PyString_Check( a ) )
-            {
-                lol_add( inner->args, list_new( 0, newstr(
-                    PyString_AsString( a ) ) ) );
-            }
-            else if ( PySequence_Check( a ) )
-            {
-                LIST * l = 0;
-                int s = PySequence_Size( a );
-                int i = 0;
-                for ( ; i < s; ++i )
-                {
-                    /* PySequence_GetItem returns new reference. */
-                    PyObject * e = PySequence_GetItem( a, i );
-                    char * s = PyString_AsString( e );
-                    if ( !s )
-                    {
-                        printf( "Invalid parameter type passed from Python\n" );
-                        exit( 1 );
-                    }
-                    l = list_new( l, newstr( s ) );
-                    Py_DECREF( e );
-                }
-                lol_add( inner->args, l );
-            }
-        }
-    }
-
-    result = evaluate_rule( rulename, inner );
-
-    frame_free( inner );
-
-    /* Convert the bjam list into a Python list result. */
-    {
-        PyObject * pyResult = PyList_New( list_length( result ) );
-        int i = 0;
-        while ( result )
-        {
-            PyList_SetItem( pyResult, i, PyString_FromString( result->string ) );
-            result = list_next( result );
-            i += 1;
-        }
-        list_free( result );
-        return pyResult;
-    }
-}
-
-
-/*
- * Accepts four arguments: 
- * - module name
- * - rule name,
- * - Python callable. 
- * - (optional) bjam language function signature.
- * Creates a bjam rule with the specified name in the specified module, which will
- * invoke the Python callable.
- */
-
-PyObject * bjam_import_rule( PyObject * self, PyObject * args )
-{
-    char     * module;
-    char     * rule;
-    PyObject * func;
-    PyObject * bjam_signature = NULL;
-    module_t * m;
-    RULE     * r;
-
-    if ( !PyArg_ParseTuple( args, "ssO|O:import_rule", 
-                            &module, &rule, &func, &bjam_signature ) )
-        return NULL;
-
-    if ( !PyCallable_Check( func ) )
-    {
-        PyErr_SetString( PyExc_RuntimeError,
-                        "Non-callable object passed to bjam.import_rule" );
-        return NULL;
-    }
-
-    m = bindmodule( *module ? module : 0 );
-    r = bindrule( rule, m );
-
-    /* Make pFunc owned. */
-    Py_INCREF( func );
-
-    r->python_function = func;
-    r->arguments = 0;
-
-    if (bjam_signature)
-    {
-        argument_list * arg_list = args_new();
-        Py_ssize_t i;
-
-        Py_ssize_t s = PySequence_Size (bjam_signature);
-        for (i = 0; i < s; ++i)
-        {
-            PyObject* v = PySequence_GetItem (bjam_signature, i);
-            lol_add(arg_list->data, list_from_python (v));
-            Py_DECREF(v);
-        }
-        r->arguments = arg_list;
-    }
-
-    Py_INCREF( Py_None );
-    return Py_None;
-}
-
-
-/*
- * Accepts four arguments:
- *  - an action name
- *  - an action body
- *  - a list of variable that will be bound inside the action
- *  - integer flags.
- *  Defines an action on bjam side.
- */
-
-PyObject * bjam_define_action( PyObject * self, PyObject * args )
-{
-    char     * name;
-    char     * body;
-    module_t * m;
-    PyObject * bindlist_python;
-    int        flags;
-    LIST     * bindlist = L0;
-    int        n;
-    int        i;
-
-    if ( !PyArg_ParseTuple( args, "ssO!i:define_action", &name, &body,
-                          &PyList_Type, &bindlist_python, &flags ) )
-        return NULL;
-
-    n = PyList_Size( bindlist_python );
-    for ( i = 0; i < n; ++i )
-    {
-        PyObject * next = PyList_GetItem( bindlist_python, i );
-        if ( !PyString_Check( next ) )
-        {
-            PyErr_SetString( PyExc_RuntimeError,
-                            "bind list has non-string type" );
-            return NULL;
-        }
-        bindlist = list_new( bindlist, PyString_AsString( next ) );
-    }
-
-    new_rule_actions( root_module(), name, newstr( body ), bindlist, flags );
-
-    Py_INCREF( Py_None );
-    return Py_None;
-}
-
-
-/*
- * Returns the value of a variable in root Jam module.
- */
-
-PyObject * bjam_variable( PyObject * self, PyObject * args )
-{
-    char     * name;
-    LIST     * value;
-    PyObject * result;
-    int        i;
-
-    if ( !PyArg_ParseTuple( args, "s", &name ) )
-        return NULL;
-
-    enter_module( root_module() );
-    value = var_get( name );
-    exit_module( root_module() );
-
-    result = PyList_New( list_length( value ) );
-    for ( i = 0; value; value = list_next( value ), ++i )
-        PyList_SetItem( result, i, PyString_FromString( value->string ) );
-
-    return result;
-}
-
-
-PyObject * bjam_backtrace( PyObject * self, PyObject * args )
-{
-    PyObject     * result = PyList_New( 0 );
-    struct frame * f = frame_before_python_call;
-
-    for ( ; f = f->prev; )
-    {
-        PyObject * tuple = PyTuple_New( 4 );
-        char     * file;
-        int        line;
-        char       buf[ 32 ];
-
-        get_source_line( f->procedure, &file, &line );
-        sprintf( buf, "%d", line );
-
-        /* PyTuple_SetItem steals reference. */
-        PyTuple_SetItem( tuple, 0, PyString_FromString( file            ) );
-        PyTuple_SetItem( tuple, 1, PyString_FromString( buf             ) );
-        PyTuple_SetItem( tuple, 2, PyString_FromString( f->module->name ) );
-        PyTuple_SetItem( tuple, 3, PyString_FromString( f->rulename     ) );
-
-        PyList_Append( result, tuple );
-        Py_DECREF( tuple );
-    }
-    return result;
-}
-
-PyObject * bjam_caller( PyObject * self, PyObject * args )
-{
-    PyObject *result = PyString_FromString(
-        frame_before_python_call->prev->module->name);
-    return result;
-}
-
-#endif  /* #ifdef HAVE_PYTHON */
-
-
-#ifdef HAVE_POPEN
-
-#if defined(_MSC_VER) || defined(__BORLANDC__)
-    #define popen windows_popen_wrapper
-    #define pclose _pclose
-
-    /*
-     * This wrapper is a workaround for a funny _popen() feature on Windows
-     * where it eats external quotes in some cases. The bug seems to be related
-     * to the quote stripping functionality used by the Windows cmd.exe
-     * interpreter when its /S is not specified.
-     *
-     * Cleaned up quote from the cmd.exe help screen as displayed on Windows XP
-     * SP3:
-     *
-     *   1. If all of the following conditions are met, then quote characters on
-     *      the command line are preserved:
-     *
-     *       - no /S switch
-     *       - exactly two quote characters
-     *       - no special characters between the two quote characters, where
-     *         special is one of: &<>()@^|
-     *       - there are one or more whitespace characters between the two quote
-     *         characters
-     *       - the string between the two quote characters is the name of an
-     *         executable file.
-     *
-     *   2. Otherwise, old behavior is to see if the first character is a quote
-     *      character and if so, strip the leading character and remove the last
-     *      quote character on the command line, preserving any text after the
-     *      last quote character.
-     *
-     * This causes some commands containing quotes not to be executed correctly.
-     * For example:
-     *
-     *   "\Long folder name\aaa.exe" --name="Jurko" --no-surname
-     *
-     * would get its outermost quotes stripped and would be executed as:
-     *
-     *   \Long folder name\aaa.exe" --name="Jurko --no-surname
-     *
-     * which would report an error about '\Long' not being a valid command.
-     *
-     * cmd.exe help seems to indicate it would be enough to add an extra space
-     * character in front of the command to avoid this but this does not work,
-     * most likely due to the shell first stripping all leading whitespace
-     * characters from the command.
-     *
-     * Solution implemented here is to quote the whole command in case it
-     * contains any quote characters. Note thought this will not work correctly
-     * should Windows ever 'fix' this feature.
-     *                                               (03.06.2008.) (Jurko)
-     */
-    static FILE * windows_popen_wrapper( char * command, char * mode )
-    {
-        int extra_command_quotes_needed = ( strchr( command, '"' ) != 0 );
-        string quoted_command;
-        FILE * result;
-
-        if ( extra_command_quotes_needed )
-        {
-            string_new( &quoted_command );
-            string_append( &quoted_command, "\"" );
-            string_append( &quoted_command, command );
-            string_append( &quoted_command, "\"" );
-            command = quoted_command.value;
-        }
-
-        result = _popen( command, "r" );
-
-        if ( extra_command_quotes_needed )
-            string_free( &quoted_command );
-
-        return result;
-    }
-#endif
-
-
-static char * rtrim(char *s)
-{
-    char *p = s;
-    while(*p) ++p;
-    for(--p; p >= s && isspace(*p); *p-- = 0);
-    return s;
-}
-
-LIST * builtin_shell( PARSE * parse, FRAME * frame )
-{
-    LIST   * command = lol_get( frame->args, 0 );
-    LIST   * result = 0;
-    string   s;
-    int      ret;
-    char     buffer[ 1024 ];
-    FILE   * p = NULL;
-    int      exit_status = -1;
-    int      exit_status_opt = 0;
-    int      no_output_opt = 0;
-    int      strip_eol_opt = 0;
-
-    /* Process the variable args options. */
-    {
-        int a = 1;
-        LIST * arg = lol_get( frame->args, a );
-        while ( arg )
-        {
-            if ( strcmp( "exit-status", arg->string ) == 0 )
-            {
-                exit_status_opt = 1;
-            }
-            else if ( strcmp( "no-output", arg->string ) == 0 )
-            {
-                no_output_opt = 1;
-            }
-            else if ( strcmp("strip-eol", arg->string) == 0 )
-            {
-                strip_eol_opt = 1;
-            }
-            arg = lol_get( frame->args, ++a );
-        }
-    }
-
-    /* The following fflush() call seems to be indicated as a workaround for a
-     * popen() bug on POSIX implementations related to synhronizing input
-     * stream positions for the called and the calling process.
-     */
-    fflush( NULL );
-
-    p = popen( command->string, "r" );
-    if ( p == NULL )
-        return L0;
-
-    string_new( &s );
-
-    while ( ( ret = fread( buffer, sizeof( char ), sizeof( buffer ) - 1, p ) ) > 0 )
-    {
-        buffer[ret] = 0;
-        if ( !no_output_opt )
-        {
-            if ( strip_eol_opt )
-                rtrim(buffer);
-            string_append( &s, buffer );
-        }
-    }
-
-    exit_status = pclose( p );
-
-    /* The command output is returned first. */
-    result = list_new( L0, newstr( s.value ) );
-    string_free( &s );
-
-    /* The command exit result next. */
-    if ( exit_status_opt )
-    {
-        if ( WIFEXITED(exit_status) )
-            exit_status = WEXITSTATUS(exit_status);
-        else
-            exit_status = -1;
-        sprintf( buffer, "%d", exit_status );
-        result = list_new( result, newstr( buffer ) );
-    }
-
-    return result;
-}
-
-#else  /* #ifdef HAVE_POPEN */
-
-LIST * builtin_shell( PARSE * parse, FRAME * frame )
-{
-    return L0;
-}
-
-#endif /* #ifdef HAVE_POPEN */
diff --git a/jam-files/engine/builtins.h b/jam-files/engine/builtins.h
deleted file mode 100644
index 5fed07c9..00000000
--- a/jam-files/engine/builtins.h
+++ /dev/null
@@ -1,69 +0,0 @@
-/*
- * Copyright 1993-2002 Christopher Seiwald and Perforce Software, Inc.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-#ifndef JAM_BUILTINS_H
-# define JAM_BUILTINS_H
-
-# include "frames.h"
-
-/*
- * builtins.h - compile parsed jam statements
- */
-
-void load_builtins();
-void init_set();
-void init_path();
-void init_regex();
-void init_property_set();
-void init_sequence();
-void init_order();
-
-LIST *builtin_calc( PARSE *parse, FRAME *args );
-LIST *builtin_depends( PARSE *parse, FRAME *args );
-LIST *builtin_rebuilds( PARSE *parse, FRAME *args );
-LIST *builtin_echo( PARSE *parse, FRAME *args );
-LIST *builtin_exit( PARSE *parse, FRAME *args );
-LIST *builtin_flags( PARSE *parse, FRAME *args );
-LIST *builtin_glob( PARSE *parse, FRAME *args );
-LIST *builtin_glob_recursive( PARSE   *parse, FRAME *frame );
-LIST *builtin_subst( PARSE  *parse, FRAME *args );
-LIST *builtin_match( PARSE *parse, FRAME *args );
-LIST *builtin_split_by_characters( PARSE *parse, FRAME *args );
-LIST *builtin_hdrmacro( PARSE *parse, FRAME *args );
-LIST *builtin_rulenames( PARSE *parse, FRAME *args );
-LIST *builtin_varnames( PARSE *parse, FRAME *args );
-LIST *builtin_delete_module( PARSE *parse, FRAME *args );
-LIST *builtin_import( PARSE *parse, FRAME *args );
-LIST *builtin_export( PARSE *parse, FRAME *args );
-LIST *builtin_caller_module( PARSE *parse, FRAME *args );
-LIST *builtin_backtrace( PARSE *parse, FRAME *args );
-LIST *builtin_pwd( PARSE *parse, FRAME *args );
-LIST *builtin_update( PARSE *parse, FRAME *args );
-LIST *builtin_update_now( PARSE *parse, FRAME *args );
-LIST *builtin_search_for_target( PARSE *parse, FRAME *args );
-LIST *builtin_import_module( PARSE *parse, FRAME *args );
-LIST *builtin_imported_modules( PARSE *parse, FRAME *frame );
-LIST *builtin_instance( PARSE *parse, FRAME *frame );
-LIST *builtin_sort( PARSE *parse, FRAME *frame );
-LIST *builtin_normalize_path( PARSE *parse, FRAME *frame );
-LIST *builtin_native_rule( PARSE *parse, FRAME *frame );
-LIST *builtin_has_native_rule( PARSE *parse, FRAME *frame );
-LIST *builtin_user_module( PARSE *parse, FRAME *frame );
-LIST *builtin_nearest_user_location( PARSE *parse, FRAME *frame );
-LIST *builtin_check_if_file( PARSE *parse, FRAME *frame );
-LIST *builtin_python_import_rule( PARSE *parse, FRAME *frame );
-LIST *builtin_shell( PARSE *parse, FRAME *frame );
-LIST *builtin_md5( PARSE *parse, FRAME *frame );
-LIST *builtin_file_open( PARSE *parse, FRAME *frame );
-LIST *builtin_pad( PARSE *parse, FRAME *frame );
-LIST *builtin_precious( PARSE *parse, FRAME *frame );
-LIST *builtin_self_path( PARSE *parse, FRAME *frame );
-LIST *builtin_makedir( PARSE *parse, FRAME *frame );
-
-void backtrace( FRAME *frame );
-extern int last_update_now_status;
-
-#endif
diff --git a/jam-files/engine/bump_version.py b/jam-files/engine/bump_version.py
deleted file mode 100644
index 9423c4c7..00000000
--- a/jam-files/engine/bump_version.py
+++ /dev/null
@@ -1,80 +0,0 @@
-#!/usr/bin/python
-
-# This script is used to bump version of bjam. It takes a single argument, e.g
-#
-#    ./bump_version.py 3.1.9
-#
-# and updates all necessary files. For the time being, it's assumes presense
-# of 'perl' executable and Debian-specific 'dch' executable.
-#
-
-
-import os
-import os.path
-import re
-import string
-import sys
-
-srcdir = os.path.abspath(os.path.dirname(__file__ ))
-docdir = os.path.abspath(os.path.join(srcdir,"..","doc"))
-
-def edit(file,replacements):
-    print "  '%s'..." %(file)
-    text = open(file,'r').read()
-    while len(replacements) > 0:
-        #~ print  "  '%s' ==> '%s'" % (replacements[0],replacements[1])
-        text = re.compile(replacements[0],re.M).subn(replacements[1],text)[0]
-        replacements = replacements[2:]
-    #~ print text
-    open(file,'w').write(text)
-
-def make_edits(version):
-    edit(os.path.join(srcdir,"boost-jam.spec"), [
-        '^Version:.*$','Version: %s' % string.join(version, "."),
-        ])
-
-    edit(os.path.join(srcdir,"build.jam"), [
-        '^_VERSION_ = .* ;$','_VERSION_ = %s %s %s ;' % (version[0], version[1], version[2]),
-        ])
-
-    edit(os.path.join(docdir,"bjam.qbk"), [
-        '\[version.*\]','[version: %s]' % string.join(version, '.'),
-        '\[def :version:.*\]','[def :version: %s]' % string.join(version, '.'),
-        ])
-
-    edit(os.path.join(srcdir,"patchlevel.h"), [
-        '^#define VERSION_MAJOR .*$',
-            '#define VERSION_MAJOR %s' % (version[0]),
-        '^#define VERSION_MINOR .*$',
-            '#define VERSION_MINOR %s' % (version[1]),
-        '^#define VERSION_PATCH .*$',
-            '#define VERSION_PATCH %s' % (version[2]),
-        '^#define VERSION_MAJOR_SYM .*$',
-            '#define VERSION_MAJOR_SYM "0%s"' % (version[0]),
-        '^#define VERSION_MINOR_SYM .*$',
-            '#define VERSION_MINOR_SYM "%s"' % (version[1]),
-        '^#define VERSION_PATCH_SYM .*$',
-            '#define VERSION_PATCH_SYM "%s"' % (version[2]),
-        '^#define VERSION .*$',
-            '#define VERSION "%s"' % string.join(version, '.'),
-        '^#define JAMVERSYM .*$',
-            '#define JAMVERSYM "JAMVERSION=%s.%s"' % (version[0],version[1]),
-        ])
-
-def main():
-
-    if len(sys.argv) < 2:
-        print "Expect new version as argument"
-        sys.exit(1)
-
-    version = string.split(sys.argv[1], ".")
-    print "Setting version to", version
-    make_edits(version)
-
-if __name__ == '__main__':
-    main()
-
-#~ Copyright 2006 Rene Rivera.
-#~ Copyright 2005-2006 Vladimir Prus.
-#~ Distributed under the Boost Software License, Version 1.0.
-#~ (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
diff --git a/jam-files/engine/class.c b/jam-files/engine/class.c
deleted file mode 100644
index ff4ec568..00000000
--- a/jam-files/engine/class.c
+++ /dev/null
@@ -1,141 +0,0 @@
-/* Copyright Vladimir Prus 2003. Distributed under the Boost */
-/* Software License, Version 1.0. (See accompanying */
-/* file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */
-
-#include "class.h"
-#include "strings.h"
-#include "variable.h"
-#include "frames.h"
-#include "rules.h"
-#include "newstr.h"
-
-#include "hash.h"
-
-
-static struct hash * classes = 0;
-
-
-static void check_defined( LIST * class_names )
-{
-    for ( ; class_names; class_names = class_names->next )
-    {
-        char * * p = &class_names->string;
-        if ( !hashcheck( classes, (HASHDATA * *)&p ) )
-        {
-            printf( "Class %s is not defined\n", class_names->string );
-            abort();
-        }
-    }
-}
-
-
-static char * class_module_name( char * declared_name )
-{
-    string name[ 1 ];
-    char * result;
-
-    string_new( name );
-    string_append( name, "class@" );
-    string_append( name, declared_name );
-
-    result = newstr( name->value );
-    string_free( name );
-
-    return result;
-}
-
-
-struct import_base_data
-{
-    char     * base_name;
-    module_t * base_module;
-    module_t * class_module;
-};
-
-
-static void import_base_rule( void * r_, void * d_ )
-{
-    RULE * r = (RULE *)r_;
-    RULE * ir1;
-    RULE * ir2;
-    struct import_base_data * d = (struct import_base_data *)d_;
-    string qualified_name[ 1 ];
-
-    string_new      ( qualified_name               );
-    string_append   ( qualified_name, d->base_name );
-    string_push_back( qualified_name, '.'          );
-    string_append   ( qualified_name, r->name      );
-
-    ir1 = import_rule( r, d->class_module, r->name );
-    ir2 = import_rule( r, d->class_module, qualified_name->value );
-
-    /* Copy 'exported' flag. */
-    ir1->exported = ir2->exported = r->exported;
-
-    /* If we are importing a class method, localize it. */
-    if ( ( r->module == d->base_module ) || ( r->module->class_module &&
-        ( r->module->class_module == d->base_module ) ) )
-        ir1->module = ir2->module = d->class_module;
-
-    string_free( qualified_name );
-}
-
-
-/*
- * For each exported rule 'n', declared in class module for base, imports that
- * rule in 'class' as 'n' and as 'base.n'. Imported rules are localized and
- * marked as exported.
- */
-
-static void import_base_rules( module_t * class, char * base )
-{
-    module_t * base_module = bindmodule( class_module_name( base ) );
-    struct import_base_data d;
-    d.base_name = base;
-    d.base_module = base_module;
-    d.class_module = class;
-
-    if ( base_module->rules )
-        hashenumerate( base_module->rules, import_base_rule, &d );
-
-    import_module( imported_modules( base_module ), class );
-}
-
-
-char * make_class_module( LIST * xname, LIST * bases, FRAME * frame )
-{
-    char       * name = class_module_name( xname->string );
-    char     * * pp = &xname->string;
-    module_t   * class_module = 0;
-    module_t   * outer_module = frame->module;
-
-    if ( !classes )
-        classes = hashinit( sizeof( char * ), "classes" );
-
-    if ( hashcheck( classes, (HASHDATA * *)&pp ) )
-    {
-        printf( "Class %s already defined\n", xname->string );
-        abort();
-    }
-    else
-    {
-        hashenter( classes, (HASHDATA * *)&pp );
-    }
-    check_defined( bases );
-
-    class_module = bindmodule( name );
-
-    exit_module( outer_module );
-    enter_module( class_module );
-
-    var_set( "__name__", xname, VAR_SET );
-    var_set( "__bases__", bases, VAR_SET );
-
-    exit_module( class_module );
-    enter_module( outer_module );
-
-    for ( ; bases; bases = bases->next )
-        import_base_rules( class_module, bases->string );
-
-    return name;
-}
diff --git a/jam-files/engine/class.h b/jam-files/engine/class.h
deleted file mode 100644
index f7faeff6..00000000
--- a/jam-files/engine/class.h
+++ /dev/null
@@ -1,13 +0,0 @@
-/* Copyright Vladimir Prus 2003. Distributed under the Boost */
-/* Software License, Version 1.0. (See accompanying */
-/* file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */
-
-#ifndef CLASS_H_VP_2003_08_01
-#define CLASS_H_VP_2003_08_01
-
-#include "lists.h"
-#include "frames.h"
-
-char* make_class_module(LIST* xname, LIST* bases, FRAME* frame);
-
-#endif
diff --git a/jam-files/engine/command.c b/jam-files/engine/command.c
deleted file mode 100644
index d2ea0681..00000000
--- a/jam-files/engine/command.c
+++ /dev/null
@@ -1,100 +0,0 @@
-/*
- * Copyright 1993, 1995 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*  This file is ALSO:
- *  Copyright 2001-2004 David Abrahams.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-
-/*
- * command.c - maintain lists of commands
- */
-
-#include "jam.h"
-
-#include "lists.h"
-#include "parse.h"
-#include "variable.h"
-#include "rules.h"
-
-#include "command.h"
-#include <limits.h>
-#include <string.h>
-
-
-/*
- * cmd_new() - return a new CMD or 0 if too many args
- */
-
-CMD * cmd_new( RULE * rule, LIST * targets, LIST * sources, LIST * shell )
-{
-    CMD * cmd = (CMD *)BJAM_MALLOC( sizeof( CMD ) );
-    /* Lift line-length limitation entirely when JAMSHELL is just "%". */
-    int no_limit = ( shell && !strcmp(shell->string,"%") && !list_next(shell) );
-    int max_line = MAXLINE;
-    int allocated = -1;
-
-    cmd->rule = rule;
-    cmd->shell = shell;
-    cmd->next = 0;
-
-    lol_init( &cmd->args );
-    lol_add( &cmd->args, targets );
-    lol_add( &cmd->args, sources );
-    cmd->buf = 0;
-
-    do
-    {
-        BJAM_FREE( cmd->buf );  /* free any buffer from previous iteration */
-
-        cmd->buf = (char*)BJAM_MALLOC_ATOMIC( max_line + 1 );
-
-        if ( cmd->buf == 0 )
-            break;
-
-        allocated = var_string( rule->actions->command, cmd->buf, max_line, &cmd->args );
-
-        max_line = max_line * 2;
-    }
-    while ( ( allocated < 0 ) && ( max_line < INT_MAX / 2 ) );
-
-    if ( !no_limit )
-    {
-        /* Bail if the result will not fit in MAXLINE. */
-        char * s = cmd->buf;
-        while ( *s )
-        {
-            size_t l = strcspn( s, "\n" );
-
-            if ( l > MAXLINE )
-            {
-                /* We do not free targets/sources/shell if bailing. */
-                cmd_free( cmd );
-                return 0;
-            }
-
-            s += l;
-            if ( *s )
-                ++s;
-        }
-    }
-
-    return cmd;
-}
-
-
-/*
- * cmd_free() - free a CMD
- */
-
-void cmd_free( CMD * cmd )
-{
-    lol_free( &cmd->args );
-    list_free( cmd->shell );
-    BJAM_FREE( cmd->buf );
-    BJAM_FREE( (char *)cmd );
-}
diff --git a/jam-files/engine/command.h b/jam-files/engine/command.h
deleted file mode 100644
index ddd38e68..00000000
--- a/jam-files/engine/command.h
+++ /dev/null
@@ -1,61 +0,0 @@
-/*
- * Copyright 1994 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*
- * command.h - the CMD structure and routines to manipulate them
- *
- * Both ACTION and CMD contain a rule, targets, and sources.  An
- * ACTION describes a rule to be applied to the given targets and
- * sources; a CMD is what actually gets executed by the shell.  The
- * differences are due to:
- *
- *  ACTIONS must be combined if 'actions together' is given.
- *  ACTIONS must be split if 'actions piecemeal' is given.
- *  ACTIONS must have current sources omitted for 'actions updated'.
- *
- * The CMD datatype holds a single command that is to be executed
- * against a target, and they can chain together to represent the
- * full collection of commands used to update a target.
- *
- * Structures:
- *
- *  CMD - an action, ready to be formatted into a buffer and executed.
- *
- * External routines:
- *
- *  cmd_new() - return a new CMD or 0 if too many args.
- *  cmd_free() - delete CMD and its parts.
- *  cmd_next() - walk the CMD chain.
- */
-
-
-/*
- * CMD - an action, ready to be formatted into a buffer and executed.
- */
-
-typedef struct _cmd CMD;
-
-struct _cmd
-{
-    CMD  * next;
-    CMD  * tail;   /* valid on in head */
-    RULE * rule;   /* rule->actions contains shell script */
-    LIST * shell;  /* $(SHELL) value */
-    LOL    args;   /* LISTs for $(<), $(>) */
-    char * buf;    /* actual commands */
-};
-
-CMD * cmd_new
-(
-    RULE * rule,     /* rule (referenced) */
-    LIST * targets,  /* $(<) (freed) */
-    LIST * sources,  /* $(>) (freed) */
-    LIST * shell     /* $(SHELL) (freed) */
-);
-
-void cmd_free( CMD * );
-
-#define cmd_next( c ) ( ( c )->next )
diff --git a/jam-files/engine/compile.c b/jam-files/engine/compile.c
deleted file mode 100644
index 2c049aae..00000000
--- a/jam-files/engine/compile.c
+++ /dev/null
@@ -1,1424 +0,0 @@
-/*
- * Copyright 1993, 2000 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*  This file is ALSO:
- *  Copyright 2001-2004 David Abrahams.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-
-# include "jam.h"
-
-# include "lists.h"
-# include "parse.h"
-# include "compile.h"
-# include "variable.h"
-# include "expand.h"
-# include "rules.h"
-# include "newstr.h"
-# include "make.h"
-# include "search.h"
-# include "hdrmacro.h"
-# include "hash.h"
-# include "modules.h"
-# include "strings.h"
-# include "builtins.h"
-# include "class.h"
-
-# include <assert.h>
-# include <string.h>
-# include <stdarg.h>
-
-/*
- * compile.c - compile parsed jam statements
- *
- * External routines:
- *
- *  compile_append() - append list results of two statements
- *  compile_eval() - evaluate if to determine which leg to compile
- *  compile_foreach() - compile the "for x in y" statement
- *  compile_if() - compile 'if' rule
- *  compile_while() - compile 'while' rule
- *  compile_include() - support for 'include' - call include() on file
- *  compile_list() - expand and return a list
- *  compile_local() - declare (and set) local variables
- *  compile_null() - do nothing -- a stub for parsing
- *  compile_on() - run rule under influence of on-target variables
- *  compile_rule() - compile a single user defined rule
- *  compile_rules() - compile a chain of rules
- *  compile_set() - compile the "set variable" statement
- *  compile_setcomp() - support for `rule` - save parse tree
- *  compile_setexec() - support for `actions` - save execution string
- *  compile_settings() - compile the "on =" (set variable on exec) statement
- *  compile_switch() - compile 'switch' rule
- *
- * Internal routines:
- *
- *  debug_compile() - printf with indent to show rule expansion.
- *  evaluate_rule() - execute a rule invocation
- *
- *  builtin_depends() - DEPENDS/INCLUDES rule
- *  builtin_echo() - ECHO rule
- *  builtin_exit() - EXIT rule
- *  builtin_flags() - NOCARE, NOTFILE, TEMPORARY rule
- *
- * 02/03/94 (seiwald) - Changed trace output to read "setting" instead of
- *          the awkward sounding "settings".
- * 04/12/94 (seiwald) - Combined build_depends() with build_includes().
- * 04/12/94 (seiwald) - actionlist() now just appends a single action.
- * 04/13/94 (seiwald) - added shorthand L0 for null list pointer
- * 05/13/94 (seiwald) - include files are now bound as targets, and thus
- *          can make use of $(SEARCH)
- * 06/01/94 (seiwald) - new 'actions existing' does existing sources
- * 08/23/94 (seiwald) - Support for '+=' (append to variable)
- * 12/20/94 (seiwald) - NOTIME renamed NOTFILE.
- * 01/22/95 (seiwald) - Exit rule.
- * 02/02/95 (seiwald) - Always rule; LEAVES rule.
- * 02/14/95 (seiwald) - NoUpdate rule.
- * 09/11/00 (seiwald) - new evaluate_rule() for headers().
- * 09/11/00 (seiwald) - compile_xxx() now return LIST *.
- *          New compile_append() and compile_list() in
- *          support of building lists here, rather than
- *          in jamgram.yy.
- * 01/10/00 (seiwald) - built-ins split out to builtin.c.
- */
-
-static void debug_compile( int which, char *s, FRAME* frame );
-int glob( char *s, char *c );
-/* Internal functions from builtins.c */
-void backtrace( FRAME *frame );
-void backtrace_line( FRAME *frame );
-void print_source_line( PARSE* p );
-
-struct frame * frame_before_python_call;
-
-void frame_init( FRAME* frame )
-{
-    frame->prev = 0;
-    frame->prev_user = 0;
-    lol_init(frame->args);
-    frame->module = root_module();
-    frame->rulename = "module scope";
-    frame->procedure = 0;
-}
-
-
-void frame_free( FRAME* frame )
-{
-    lol_free( frame->args );
-}
-
-
-/*
- * compile_append() - append list results of two statements
- *
- *  parse->left more compile_append() by left-recursion
- *  parse->right    single rule
- */
-
-LIST * compile_append( PARSE * parse, FRAME * frame )
-{
-    /* Append right to left. */
-    return list_append(
-        parse_evaluate( parse->left, frame ),
-        parse_evaluate( parse->right, frame ) );
-}
-
-
-/*
- * compile_eval() - evaluate if to determine which leg to compile
- *
- * Returns:
- *  list    if expression true - compile 'then' clause
- *  L0  if expression false - compile 'else' clause
- */
-
-static int lcmp( LIST * t, LIST * s )
-{
-    int status = 0;
-
-    while ( !status && ( t || s ) )
-    {
-        char *st = t ? t->string : "";
-        char *ss = s ? s->string : "";
-
-        status = strcmp( st, ss );
-
-        t = t ? list_next( t ) : t;
-        s = s ? list_next( s ) : s;
-    }
-
-    return status;
-}
-
-LIST * compile_eval( PARSE * parse, FRAME * frame )
-{
-    LIST * ll;
-    LIST * lr;
-    LIST * s;
-    LIST * t;
-    int status = 0;
-
-    /* Short circuit lr eval for &&, ||, and 'in'. */
-
-    ll = parse_evaluate( parse->left, frame );
-    lr = 0;
-
-    switch ( parse->num )
-    {
-        case EXPR_AND:
-        case EXPR_IN : if ( ll ) goto eval; break;
-        case EXPR_OR : if ( !ll ) goto eval; break;
-        default: eval: lr = parse_evaluate( parse->right, frame );
-    }
-
-    /* Now eval. */
-    switch ( parse->num )
-    {
-    case EXPR_NOT: if ( !ll      ) status = 1; break;
-    case EXPR_AND: if ( ll && lr ) status = 1; break;
-    case EXPR_OR : if ( ll || lr ) status = 1; break;
-
-    case EXPR_IN:
-        /* "a in b": make sure each of ll is equal to something in lr. */
-        for ( t = ll; t; t = list_next( t ) )
-        {
-            for ( s = lr; s; s = list_next( s ) )
-            if ( !strcmp( t->string, s->string ) )
-                break;
-            if ( !s ) break;
-        }
-        /* No more ll? Success. */
-        if ( !t ) status = 1;
-        break;
-
-    case EXPR_EXISTS: if ( lcmp( ll, L0 ) != 0 ) status = 1; break;
-    case EXPR_EQUALS: if ( lcmp( ll, lr ) == 0 ) status = 1; break;
-    case EXPR_NOTEQ : if ( lcmp( ll, lr ) != 0 ) status = 1; break;
-    case EXPR_LESS  : if ( lcmp( ll, lr ) < 0  ) status = 1; break;
-    case EXPR_LESSEQ: if ( lcmp( ll, lr ) <= 0 ) status = 1; break;
-    case EXPR_MORE  : if ( lcmp( ll, lr ) > 0  ) status = 1; break;
-    case EXPR_MOREEQ: if ( lcmp( ll, lr ) >= 0 ) status = 1; break;
-    }
-
-    if ( DEBUG_IF )
-    {
-        debug_compile( 0, "if", frame );
-        list_print( ll );
-        printf( "(%d) ", status );
-        list_print( lr );
-        printf( "\n" );
-    }
-
-    /* Find something to return. */
-    /* In odd circumstances (like "" = "") */
-    /* we'll have to return a new string. */
-
-    if ( !status ) t = 0;
-    else if ( ll ) t = ll, ll = 0;
-    else if ( lr ) t = lr, lr = 0;
-    else t = list_new( L0, newstr( "1" ) );
-
-    if ( ll ) list_free( ll );
-    if ( lr ) list_free( lr );
-    return t;
-}
-
-
-/*
- * compile_foreach() - compile the "for x in y" statement
- *
- * Compile_foreach() resets the given variable name to each specified
- * value, executing the commands enclosed in braces for each iteration.
- *
- *  parse->string   index variable
- *  parse->left variable values
- *  parse->right    rule to compile
- */
-
-LIST * compile_foreach( PARSE * parse, FRAME * frame )
-{
-    LIST     * nv = parse_evaluate( parse->left, frame );
-    LIST     * l;
-    SETTINGS * s = 0;
-
-    if ( parse->num )
-    {
-        s = addsettings( s, VAR_SET, parse->string, L0 );
-        pushsettings( s );
-    }
-
-    /* Call var_set to reset $(parse->string) for each val. */
-
-    for ( l = nv; l; l = list_next( l ) )
-    {
-        LIST * val = list_new( L0, copystr( l->string ) );
-        var_set( parse->string, val, VAR_SET );
-        list_free( parse_evaluate( parse->right, frame ) );
-    }
-
-    if ( parse->num )
-    {
-        popsettings( s );
-        freesettings( s );
-    }
-
-    list_free( nv );
-
-    return L0;
-}
-
-/*
- * compile_if() - compile 'if' rule
- *
- *  parse->left     condition tree
- *  parse->right        then tree
- *  parse->third        else tree
- */
-
-LIST * compile_if( PARSE * p, FRAME * frame )
-{
-    LIST * l = parse_evaluate( p->left, frame );
-    if ( l )
-    {
-        list_free( l );
-        return parse_evaluate( p->right, frame );
-    }
-    return parse_evaluate( p->third, frame );
-}
-
-
-LIST * compile_while( PARSE * p, FRAME * frame )
-{
-    LIST * r = 0;
-    LIST * l;
-    while ( ( l = parse_evaluate( p->left, frame ) ) )
-    {
-        list_free( l );
-        if ( r ) list_free( r );
-        r = parse_evaluate( p->right, frame );
-    }
-    return r;
-}
-
-
-/*
- * compile_include() - support for 'include' - call include() on file
- *
- *  parse->left list of files to include (can only do 1)
- */
-
-LIST * compile_include( PARSE * parse, FRAME * frame )
-{
-    LIST * nt = parse_evaluate( parse->left, frame );
-
-    if ( DEBUG_COMPILE )
-    {
-        debug_compile( 0, "include", frame);
-        list_print( nt );
-        printf( "\n" );
-    }
-
-    if ( nt )
-    {
-        TARGET * t = bindtarget( nt->string );
-
-        /* DWA 2001/10/22 - Perforce Jam cleared the arguments here, which
-         * prevents an included file from being treated as part of the body of a
-         * rule. I did not see any reason to do that, so I lifted the
-         * restriction.
-         */
-
-        /* Bind the include file under the influence of */
-        /* "on-target" variables.  Though they are targets, */
-        /* include files are not built with make(). */
-
-        pushsettings( t->settings );
-        /* We don't expect that file to be included is generated by some
-           action. Therefore, pass 0 as third argument.
-           If the name resolves to directory, let it error out.  */
-        t->boundname = search( t->name, &t->time, 0, 0 );
-        popsettings( t->settings );
-
-        parse_file( t->boundname, frame );
-    }
-
-    list_free( nt );
-
-    return L0;
-}
-
-static LIST* evaluate_in_module ( char* module_name, PARSE * p, FRAME* frame)
-{
-    LIST* result;
-
-    module_t* outer_module = frame->module;
-    frame->module = module_name ? bindmodule( module_name ) : root_module();
-
-    if ( outer_module != frame->module )
-    {
-        exit_module( outer_module );
-        enter_module( frame->module );
-    }
-
-    result = parse_evaluate( p, frame );
-
-    if ( outer_module != frame->module )
-    {
-        exit_module( frame->module );
-        enter_module( outer_module );
-        frame->module = outer_module;
-    }
-
-    return result;
-}
-
-
-LIST * compile_module( PARSE * p, FRAME * frame )
-{
-    /* Here we are entering a module declaration block. */
-    LIST * module_name = parse_evaluate( p->left, frame );
-    LIST * result = evaluate_in_module( module_name ? module_name->string : 0,
-                                       p->right, frame );
-    list_free( module_name );
-    return result;
-}
-
-
-LIST * compile_class( PARSE * p, FRAME * frame )
-{
-    /** Todo: check for empty class name.
-        Check for class redeclaration. */
-
-    char * class_module = 0;
-
-    LIST * name = parse_evaluate( p->left->right, frame );
-    LIST * bases = 0;
-
-    if ( p->left->left )
-        bases = parse_evaluate( p->left->left->right, frame );
-
-    class_module = make_class_module( name, bases, frame );
-    evaluate_in_module( class_module, p->right, frame );
-
-    return L0;
-}
-
-
-/*
- * compile_list() - expand and return a list.
- *
- *  parse->string - character string to expand.
- */
-
-LIST * compile_list( PARSE * parse, FRAME * frame )
-{
-    /* s is a copyable string */
-    char * s = parse->string;
-    return var_expand( L0, s, s + strlen( s ), frame->args, 1 );
-}
-
-
-/*
- * compile_local() - declare (and set) local variables.
- *
- *  parse->left    list of variables
- *  parse->right   list of values
- *  parse->third   rules to execute
- */
-
-LIST * compile_local( PARSE * parse, FRAME * frame )
-{
-    LIST * l;
-    SETTINGS * s = 0;
-    LIST     * nt = parse_evaluate( parse->left, frame );
-    LIST     * ns = parse_evaluate( parse->right, frame );
-    LIST     * result;
-
-    if ( DEBUG_COMPILE )
-    {
-        debug_compile( 0, "local", frame );
-        list_print( nt );
-        printf( " = " );
-        list_print( ns );
-        printf( "\n" );
-    }
-
-    /* Initial value is ns. */
-    for ( l = nt; l; l = list_next( l ) )
-        s = addsettings( s, VAR_SET, l->string, list_copy( (LIST *)0, ns ) );
-
-    list_free( ns );
-    list_free( nt );
-
-    /* Note that callees of the current context get this "local" variable,
-     * making it not so much local as layered.
-     */
-
-    pushsettings( s );
-    result = parse_evaluate( parse->third, frame );
-    popsettings( s );
-
-    freesettings( s );
-
-    return result;
-}
-
-
-/*
- * compile_null() - do nothing -- a stub for parsing.
- */
-
-LIST * compile_null( PARSE * parse, FRAME * frame )
-{
-    return L0;
-}
-
-
-/*
- * compile_on() - run rule under influence of on-target variables
- *
- *  parse->left    list of files to include (can only do 1).
- *  parse->right   rule to run.
- *
- * EXPERIMENTAL!
- */
-
-LIST * compile_on( PARSE * parse, FRAME * frame )
-{
-    LIST * nt = parse_evaluate( parse->left, frame );
-    LIST * result = 0;
-
-    if ( DEBUG_COMPILE )
-    {
-        debug_compile( 0, "on", frame );
-        list_print( nt );
-        printf( "\n" );
-    }
-
-    if ( nt )
-    {
-        TARGET * t = bindtarget( nt->string );
-        pushsettings( t->settings );
-        result = parse_evaluate( parse->right, frame );
-        popsettings( t->settings );
-    }
-
-    list_free( nt );
-
-    return result;
-}
-
-
-/*
- * compile_rule() - compile a single user defined rule.
- *
- *  parse->string   name of user defined rule.
- *  parse->left     parameters (list of lists) to rule, recursing left.
- *
- * Wrapped around evaluate_rule() so that headers() can share it.
- */
-
-LIST * compile_rule( PARSE * parse, FRAME * frame )
-{
-    FRAME   inner[ 1 ];
-    LIST  * result;
-    PARSE * p;
-
-    /* Build up the list of arg lists. */
-    frame_init( inner );
-    inner->prev = frame;
-    inner->prev_user = frame->module->user_module ? frame : frame->prev_user;
-    inner->module = frame->module;  /* This gets fixed up in evaluate_rule(), below. */
-    inner->procedure = parse;
-    /* Special-case LOL of length 1 where the first list is totally empty.
-       This is created when calling functions with no parameters, due to
-       the way jam grammar is written. This is OK when one jam function
-       calls another, but really not good when Jam function calls Python.  */
-    if ( parse->left->left == NULL && parse->left->right->func == compile_null)
-        ;
-    else
-        for ( p = parse->left; p; p = p->left )
-            lol_add( inner->args, parse_evaluate( p->right, frame ) );
-
-    /* And invoke the rule. */
-    result = evaluate_rule( parse->string, inner );
-    frame_free( inner );
-    return result;
-}
-
-
-static void argument_error( char * message, RULE * rule, FRAME * frame, LIST* arg )
-{
-    LOL * actual = frame->args;
-    assert( frame->procedure != 0 );
-    backtrace_line( frame->prev );
-    printf( "*** argument error\n* rule %s ( ", frame->rulename );
-    lol_print( rule->arguments->data );
-    printf( " )\n* called with: ( " );
-    lol_print( actual );
-    printf( " )\n* %s %s\n", message, arg ? arg->string : "" );
-    print_source_line( rule->procedure );
-    printf( "see definition of rule '%s' being called\n", rule->name );
-    backtrace( frame->prev );
-    exit( 1 );
-}
-
-
-/* Define delimiters for type check elements in argument lists (and return type
- * specifications, eventually).
- */
-# define TYPE_OPEN_DELIM '['
-# define TYPE_CLOSE_DELIM ']'
-
-/*
- * is_type_name() - true iff the given string represents a type check
- * specification.
- */
-
-static int is_type_name( char * s )
-{
-    return ( s[ 0 ] == TYPE_OPEN_DELIM ) &&
-        ( s[ strlen( s ) - 1 ] == TYPE_CLOSE_DELIM );
-}
-
-
-/*
- * arg_modifier - if the next element of formal is a single character, return
- * that; return 0 otherwise. Used to extract "*+?" modifiers * from argument
- * lists.
- */
-
-static char arg_modifier( LIST * formal )
-{
-    if ( formal->next )
-    {
-        char * next = formal->next->string;
-        if ( next && ( next[ 0 ] != 0 ) && ( next[ 1 ] == 0 ) )
-            return next[ 0 ];
-    }
-    return 0;
-}
-
-
-/*
- * type_check() - checks that each element of values satisfies the requirements
- * of type_name.
- *
- *      caller   - the frame of the rule calling the rule whose arguments are
- *                 being checked
- *
- *      called   - the rule being called
- *
- *      arg_name - a list element containing the name of the argument being
- *                 checked
- */
-
-static void type_check
-(
-    char  * type_name,
-    LIST  * values,
-    FRAME * caller,
-    RULE  * called,
-    LIST  * arg_name
-)
-{
-    static module_t * typecheck = 0;
-
-    /* If nothing to check, bail now. */
-    if ( !values || !type_name )
-        return;
-
-    if ( !typecheck )
-        typecheck = bindmodule( ".typecheck" );
-
-    /* If the checking rule can not be found, also bail. */
-    {
-        RULE checker_, *checker = &checker_;
-
-        checker->name = type_name;
-        if ( !typecheck->rules || !hashcheck( typecheck->rules, (HASHDATA * *)&checker ) )
-            return;
-    }
-
-    exit_module( caller->module );
-
-    while ( values != 0 )
-    {
-        LIST *error;
-        FRAME frame[1];
-        frame_init( frame );
-        frame->module = typecheck;
-        frame->prev = caller;
-        frame->prev_user = caller->module->user_module ? caller : caller->prev_user;
-
-        enter_module( typecheck );
-        /* Prepare the argument list */
-        lol_add( frame->args, list_new( L0, values->string ) );
-        error = evaluate_rule( type_name, frame );
-
-        exit_module( typecheck );
-
-        if ( error )
-            argument_error( error->string, called, caller, arg_name );
-
-        frame_free( frame );
-        values = values->next;
-    }
-
-    enter_module( caller->module );
-}
-
-/*
- * collect_arguments() - local argument checking and collection
- */
-static SETTINGS *
-collect_arguments( RULE* rule, FRAME* frame )
-{
-    SETTINGS *locals = 0;
-
-    LOL * all_actual = frame->args;
-    LOL * all_formal = rule->arguments ? rule->arguments->data : 0;
-    if ( all_formal ) /* Nothing to set; nothing to check */
-    {
-        int max = all_formal->count > all_actual->count
-            ? all_formal->count
-            : all_actual->count;
-
-        int n;
-        for ( n = 0; n < max ; ++n )
-        {
-            LIST *actual = lol_get( all_actual, n );
-            char *type_name = 0;
-
-            LIST *formal;
-            for ( formal = lol_get( all_formal, n ); formal; formal = formal->next )
-            {
-                char* name = formal->string;
-
-                if ( is_type_name(name) )
-                {
-                    if ( type_name )
-                        argument_error( "missing argument name before type name:", rule, frame, formal );
-
-                    if ( !formal->next )
-                        argument_error( "missing argument name after type name:", rule, frame, formal );
-
-                    type_name = formal->string;
-                }
-                else
-                {
-                    LIST* value = 0;
-                    char modifier;
-                    LIST* arg_name = formal; /* hold the argument name for type checking */
-                    int multiple = 0;
-
-                    /* Stop now if a variable number of arguments are specified */
-                    if ( name[0] == '*' && name[1] == 0 )
-                        return locals;
-
-                    modifier = arg_modifier( formal );
-
-                    if ( !actual && modifier != '?' && modifier != '*' )
-                        argument_error( "missing argument", rule, frame, formal );
-
-                    switch ( modifier )
-                    {
-                    case '+':
-                    case '*':
-                        value = list_copy( 0, actual );
-                        multiple = 1;
-                        actual = 0;
-                        /* skip an extra element for the modifier */
-                        formal = formal->next;
-                        break;
-                    case '?':
-                        /* skip an extra element for the modifier */
-                        formal = formal->next;
-                        /* fall through */
-                    default:
-                        if ( actual ) /* in case actual is missing */
-                        {
-                            value = list_new( 0, actual->string );
-                            actual = actual->next;
-                        }
-                    }
-
-                    locals = addsettings(locals, VAR_SET, name, value);
-                    locals->multiple = multiple;
-                    type_check( type_name, value, frame, rule, arg_name );
-                    type_name = 0;
-                }
-            }
-
-            if ( actual )
-            {
-                argument_error( "extra argument", rule, frame, actual );
-            }
-        }
-    }
-    return locals;
-}
-
-RULE *
-enter_rule( char *rulename, module_t *target_module );
-
-#ifdef HAVE_PYTHON
-
-static int python_instance_number = 0;
-
-
-/* Given a Python object, return a string to use in Jam
-   code instead of said object.
-   If the object is string, use the string value
-   If the object implemenets __jam_repr__ method, use that.
-   Otherwise return 0.
-
-   The result value is newstr-ed.  */
-char *python_to_string(PyObject* value)
-{
-    if (PyString_Check(value))
-    {
-        return newstr(PyString_AsString(value));
-    }
-    else
-    {
-        /* See if this is an instance that defines special __jam_repr__
-           method. */
-        if (PyInstance_Check(value)
-            && PyObject_HasAttrString(value, "__jam_repr__"))
-        {
-            PyObject* repr = PyObject_GetAttrString(value, "__jam_repr__");
-            if (repr)
-            {
-                PyObject* arguments2 = PyTuple_New(0);
-                PyObject* value2 = PyObject_Call(repr, arguments2, 0);
-                Py_DECREF(repr);
-                Py_DECREF(arguments2);
-                if (PyString_Check(value2))
-                {
-                    return newstr(PyString_AsString(value2));
-                }
-                Py_DECREF(value2);
-            }
-        }
-        return 0;
-    }
-}
-
-static LIST*
-call_python_function(RULE* r, FRAME* frame)
-{
-    LIST * result = 0;
-    PyObject * arguments = 0;
-    PyObject * kw = NULL;
-    int i ;
-    PyObject * py_result;
-
-    if (r->arguments)
-    {
-        SETTINGS * args;
-
-        arguments = PyTuple_New(0);
-        kw = PyDict_New();
-
-        for (args = collect_arguments(r, frame); args; args = args->next)
-        {
-            PyObject *key = PyString_FromString(args->symbol);
-            PyObject *value = 0;
-            if (args->multiple)
-                value = list_to_python(args->value);
-            else {
-                if (args->value)
-                    value = PyString_FromString(args->value->string);
-            }
-
-            if (value)
-                PyDict_SetItem(kw, key, value);
-            Py_DECREF(key);
-            Py_XDECREF(value);
-        }
-    }
-    else
-    {
-        arguments = PyTuple_New( frame->args->count );
-        for ( i = 0; i < frame->args->count; ++i )
-        {
-            PyObject * arg = PyList_New(0);
-            LIST* l = lol_get( frame->args, i);
-            
-            for ( ; l; l = l->next )
-            {
-                PyObject * v = PyString_FromString(l->string);
-                PyList_Append( arg, v );
-                Py_DECREF(v);
-            }
-            /* Steals reference to 'arg' */
-            PyTuple_SetItem( arguments, i, arg );
-        }
-    }
-
-    frame_before_python_call = frame;
-    py_result = PyObject_Call( r->python_function, arguments, kw );
-    Py_DECREF(arguments);
-    Py_XDECREF(kw);
-    if ( py_result != NULL )
-    {
-        if ( PyList_Check( py_result ) )
-        {
-            int size = PyList_Size( py_result );
-            int i;
-            for ( i = 0; i < size; ++i )
-            {
-                PyObject * item = PyList_GetItem( py_result, i );
-                char *s = python_to_string (item);
-                if (!s) {
-                    fprintf( stderr, "Non-string object returned by Python call.\n" );
-                } else {
-                    result = list_new (result, s);
-                }
-            }
-        }
-        else if ( py_result == Py_None )
-        {
-            result = L0;
-        }
-        else 
-        {
-            char *s = python_to_string(py_result);
-            if (s)
-                result = list_new(0, s);
-            else 
-                /* We have tried all we could.  Return empty list. There are
-                   cases, e.g.  feature.feature function that should return
-                   value for the benefit of Python code and which also can be
-                   called by Jam code, where no sensible value can be
-                   returned. We cannot even emit a warning, since there will
-                   be a pile of them.  */                
-                result = L0;                    
-        }
-
-        Py_DECREF( py_result );
-    }
-    else
-    {
-        PyErr_Print();
-        fprintf(stderr,"Call failed\n");
-    }
-
-    return result;
-}
-
-
-module_t * python_module()
-{
-    static module_t * python = 0;
-    if ( !python )
-        python = bindmodule("__python__");
-    return python;
-}
-
-#endif
-
-
-/*
- * evaluate_rule() - execute a rule invocation.
- */
-
-LIST *
-evaluate_rule(
-    char  * rulename,
-    FRAME * frame )
-{
-    LIST          * result = L0;
-    RULE          * rule;
-    profile_frame   prof[1];
-    module_t      * prev_module = frame->module;
-
-    LIST * l;
-    {
-        LOL arg_context_, * arg_context = &arg_context_;
-        if ( !frame->prev )
-            lol_init(arg_context);
-        else
-            arg_context = frame->prev->args;
-        l = var_expand( L0, rulename, rulename+strlen(rulename), arg_context, 0 );
-    }
-
-    if ( !l )
-    {
-        backtrace_line( frame->prev );
-        printf( "warning: rulename %s expands to empty string\n", rulename );
-        backtrace( frame->prev );
-        return result;
-    }
-
-    rulename = l->string;
-    rule = bindrule( l->string, frame->module );
-
-#ifdef HAVE_PYTHON
-    if ( rule->python_function )
-    {
-        /* The below messing with modules is due to the way modules are
-         * implemented in Jam. Suppose we are in module M1 now. The global
-         * variable map actually holds 'M1' variables, and M1->variables hold
-         * global variables.
-         *
-         * If we call Python right away, Python calls back Jam and then Jam
-         * does 'module M1 { }' then Jam will try to swap the current global
-         * variables with M1->variables. The result will be that global
-         * variables map will hold global variables, and any variable settings
-         * we do will go to the global module, not M1.
-         *
-         * By restoring basic state, where the global variable map holds global
-         * variable, we make sure any future 'module M1' entry will work OK.
-         */
-
-        LIST * result;
-        module_t * m = python_module();
-
-        frame->module = m;
-
-        exit_module( prev_module );
-        enter_module( m );
-
-        result = call_python_function( rule, frame );
-
-        exit_module( m );
-        enter_module ( prev_module );
-
-        return result;
-    }
-#endif
-
-    /* Drop the rule name. */
-    l = list_pop_front( l );
-
-    /* Tack the rest of the expansion onto the front of the first argument. */
-    frame->args->list[0] = list_append( l, lol_get( frame->args, 0 ) );
-
-    if ( DEBUG_COMPILE )
-    {
-        /* Try hard to indicate in which module the rule is going to execute. */
-        if ( rule->module != frame->module
-             && rule->procedure != 0 && strcmp( rulename, rule->procedure->rulename ) )
-        {
-            char buf[256] = "";
-            strncat( buf, rule->module->name, sizeof( buf ) - 1 );
-            strncat( buf, rule->name, sizeof( buf ) - 1 );
-            debug_compile( 1, buf, frame );
-        }
-        else
-        {
-            debug_compile( 1, rulename, frame );
-        }
-
-        lol_print( frame->args );
-        printf( "\n" );
-    }
-
-    if ( rule->procedure && rule->module != prev_module )
-    {
-        /* Propagate current module to nested rule invocations. */
-        frame->module = rule->module;
-
-        /* Swap variables. */
-        exit_module( prev_module );
-        enter_module( rule->module );
-    }
-
-    /* Record current rule name in frame. */
-    if ( rule->procedure )
-    {
-        frame->rulename = rulename;
-        /* And enter record profile info. */
-        if ( DEBUG_PROFILE )
-            profile_enter( rule->procedure->rulename, prof );
-    }
-
-    /* Check traditional targets $(<) and sources $(>). */
-    if ( !rule->actions && !rule->procedure )
-    {
-        backtrace_line( frame->prev );
-        printf( "rule %s unknown in module %s\n", rule->name, frame->module->name );
-        backtrace( frame->prev );
-        exit( 1 );
-    }
-
-    /* If this rule will be executed for updating the targets then construct the
-     * action for make().
-     */
-    if ( rule->actions )
-    {
-        TARGETS * t;
-        ACTION  * action;
-
-        /* The action is associated with this instance of this rule. */
-        action = (ACTION *)BJAM_MALLOC( sizeof( ACTION ) );
-        memset( (char *)action, '\0', sizeof( *action ) );
-
-        action->rule = rule;
-        action->targets = targetlist( (TARGETS *)0, lol_get( frame->args, 0 ) );
-        action->sources = targetlist( (TARGETS *)0, lol_get( frame->args, 1 ) );
-
-        /* If we have a group of targets all being built using the same action
-         * then we must not allow any of them to be used as sources unless they
-         * had all already been built in the first place or their joined action
-         * has had a chance to finish its work and build all of them anew.
-         *
-         * Without this it might be possible, in case of a multi-process build,
-         * for their action, triggered by buiding one of the targets, to still
-         * be running when another target in the group reports as done in order
-         * to avoid triggering the same action again and gets used prematurely.
-         *
-         * As a quick-fix to achieve this effect we make all the targets list
-         * each other as 'included targets'. More precisely, we mark the first
-         * listed target as including all the other targets in the list and vice
-         * versa. This makes anyone depending on any of those targets implicitly
-         * depend on all of them, thus making sure none of those targets can be
-         * used as sources until all of them have been built. Note that direct
-         * dependencies could not have been used due to the 'circular
-         * dependency' issue.
-         *
-         * TODO: Although the current implementation solves the problem of one
-         * of the targets getting used before its action completes its work it
-         * also forces the action to run whenever any of the targets in the
-         * group is not up to date even though some of them might not actually
-         * be used by the targets being built. We should see how we can
-         * correctly recognize such cases and use that to avoid running the
-         * action if possible and not rebuild targets not actually depending on
-         * targets that are not up to date.
-         *
-         * TODO: Using the 'include' feature might have side-effects due to
-         * interaction with the actual 'inclusion scanning' system. This should
-         * be checked.
-         */
-        if ( action->targets )
-        {
-            TARGET * t0 = action->targets->target;
-            for ( t = action->targets->next; t; t = t->next )
-            {
-                target_include( t->target, t0 );
-                target_include( t0, t->target );
-            }
-        }
-
-        /* Append this action to the actions of each target. */
-        for ( t = action->targets; t; t = t->next )
-            t->target->actions = actionlist( t->target->actions, action );
-    }
-
-    /* Now recursively compile any parse tree associated with this rule.
-     * parse_refer()/parse_free() call pair added to ensure rule not freed
-     * during use.
-     */
-    if ( rule->procedure )
-    {
-        SETTINGS * local_args = collect_arguments( rule, frame );
-        PARSE * parse = rule->procedure;
-        parse_refer( parse );
-
-        pushsettings( local_args );
-        result = parse_evaluate( parse, frame );
-        popsettings( local_args );
-        freesettings( local_args );
-
-        parse_free( parse );
-    }
-
-    if ( frame->module != prev_module )
-    {
-        exit_module( frame->module );
-        enter_module( prev_module );
-    }
-
-    if ( DEBUG_PROFILE && rule->procedure )
-        profile_exit( prof );
-
-    if ( DEBUG_COMPILE )
-        debug_compile( -1, 0, frame);
-
-    return result;
-}
-
-
-/*
- * Call the given rule with the specified parameters. The parameters should be
- * of type LIST* and end with a NULL pointer. This differs from 'evaluate_rule'
- * in that frame for the called rule is prepared inside 'call_rule'.
- *
- * This function is useful when a builtin rule (in C) wants to call another rule
- * which might be implemented in Jam.
- */
-
-LIST * call_rule( char * rulename, FRAME * caller_frame, ... )
-{
-    va_list va;
-    LIST * result;
-
-    FRAME       inner[1];
-    frame_init( inner );
-    inner->prev = caller_frame;
-    inner->prev_user = caller_frame->module->user_module ?
-        caller_frame : caller_frame->prev_user;
-    inner->module = caller_frame->module;
-    inner->procedure = 0;
-
-    va_start( va, caller_frame );
-    for ( ; ; )
-    {
-        LIST * l = va_arg( va, LIST* );
-        if ( !l )
-            break;
-        lol_add( inner->args, l );
-    }
-    va_end( va );
-
-    result = evaluate_rule( rulename, inner );
-
-    frame_free( inner );
-
-    return result;
-}
-
-
-/*
- * compile_rules() - compile a chain of rules
- *
- *  parse->left single rule
- *  parse->right    more compile_rules() by right-recursion
- */
-
-LIST * compile_rules( PARSE * parse, FRAME * frame )
-{
-    /* Ignore result from first statement; return the 2nd. */
-    /* Optimize recursion on the right by looping. */
-    do list_free( parse_evaluate( parse->left, frame ) );
-    while ( ( parse = parse->right )->func == compile_rules );
-    return parse_evaluate( parse, frame );
-}
-
-
-/*
- * assign_var_mode() - convert ASSIGN_XXX compilation flag into corresponding
- *                     VAR_XXX variable set flag.
- */
-
-static int assign_var_mode( int parsenum, char const * * tracetext )
-{
-    char const * trace;
-    int          setflag;
-    switch ( parsenum )
-    {
-        case ASSIGN_SET    : setflag = VAR_SET    ; trace = "=" ; break;
-        case ASSIGN_APPEND : setflag = VAR_APPEND ; trace = "+="; break;
-        case ASSIGN_DEFAULT: setflag = VAR_DEFAULT; trace = "?="; break;
-        default:             setflag = VAR_SET    ; trace = ""  ; break;
-    }
-    if ( tracetext )
-        *tracetext = trace ;
-    return setflag;
-}
-
-/*
- * compile_set() - compile the "set variable" statement
- *
- *  parse->left variable names
- *  parse->right    variable values
- *  parse->num  ASSIGN_SET/APPEND/DEFAULT
- */
-
-LIST * compile_set( PARSE * parse, FRAME * frame )
-{
-    LIST       * nt = parse_evaluate( parse->left, frame );
-    LIST       * ns = parse_evaluate( parse->right, frame );
-    LIST       * l;
-    char const * trace;
-    int          setflag = assign_var_mode( parse->num, &trace );
-
-    if ( DEBUG_COMPILE )
-    {
-        debug_compile( 0, "set", frame );
-        list_print( nt );
-        printf( " %s ", trace );
-        list_print( ns );
-        printf( "\n" );
-    }
-
-    /* Call var_set to set variable. var_set keeps ns, so need to copy it. */
-    for ( l = nt; l; l = list_next( l ) )
-        var_set( l->string, list_copy( L0, ns ), setflag );
-    list_free( nt );
-    return ns;
-}
-
-
-/*
- * compile_setcomp() - support for `rule` - save parse tree.
- *
- *  parse->string  rule name
- *  parse->left    rules for rule
- *  parse->right   optional list-of-lists describing arguments
- */
-
-LIST * compile_setcomp( PARSE * parse, FRAME * frame )
-{
-    argument_list * arg_list = 0;
-
-    /* Create new LOL describing argument requirements if supplied. */
-    if ( parse->right )
-    {
-        PARSE * p;
-        arg_list = args_new();
-        for ( p = parse->right; p; p = p->left )
-            lol_add( arg_list->data, parse_evaluate( p->right, frame ) );
-    }
-
-    new_rule_body( frame->module, parse->string, arg_list, parse->left, !parse->num );
-    return L0;
-}
-
-
-/*
- * compile_setexec() - support for `actions` - save execution string.
- *
- *  parse->string   rule name
- *  parse->string1  OS command string
- *  parse->num      flags
- *  parse->left     `bind` variables
- *
- * Note that the parse flags (as defined in compile.h) are transferred directly
- * to the rule flags (as defined in rules.h).
- */
-
-LIST * compile_setexec( PARSE * parse, FRAME * frame )
-{
-    LIST * bindlist = parse_evaluate( parse->left, frame );
-    new_rule_actions( frame->module, parse->string, parse->string1, bindlist, parse->num );
-    return L0;
-}
-
-
-/*
- * compile_settings() - compile the "on =" (set variable on exec) statement.
- *
- *  parse->left   variable names
- *  parse->right  target name
- *  parse->third  variable value
- *  parse->num    ASSIGN_SET/APPEND
- */
-
-LIST * compile_settings( PARSE * parse, FRAME * frame )
-{
-    LIST       * nt = parse_evaluate( parse->left, frame );
-    LIST       * ns = parse_evaluate( parse->third, frame );
-    LIST       * targets = parse_evaluate( parse->right, frame );
-    LIST       * ts;
-    char const * trace;
-    int          setflag = assign_var_mode( parse->num, &trace );
-
-    if ( DEBUG_COMPILE )
-    {
-        debug_compile( 0, "set", frame );
-        list_print( nt );
-        printf( " on " );
-        list_print( targets );
-        printf( " %s ", trace );
-        list_print( ns );
-        printf( "\n" );
-    }
-
-    /* Call addsettings() to save variable setting. addsettings() keeps ns, so
-     * need to copy it. Pass append flag to addsettings().
-     */
-    for ( ts = targets; ts; ts = list_next( ts ) )
-    {
-        TARGET * t = bindtarget( ts->string );
-        LIST   * l;
-
-        for ( l = nt; l; l = list_next( l ) )
-        t->settings = addsettings( t->settings, setflag, l->string,
-            list_copy( (LIST *)0, ns ) );
-    }
-
-    list_free( nt );
-    list_free( targets );
-    return ns;
-}
-
-
-/*
- * compile_switch() - compile 'switch' rule.
- *
- *  parse->left   switch value (only 1st used)
- *  parse->right  cases
- *
- *  cases->left   1st case
- *  cases->right  next cases
- *
- *  case->string  argument to match
- *  case->left    parse tree to execute
- */
-
-LIST * compile_switch( PARSE * parse, FRAME * frame )
-{
-    LIST * nt = parse_evaluate( parse->left, frame );
-    LIST * result = 0;
-
-    if ( DEBUG_COMPILE )
-    {
-        debug_compile( 0, "switch", frame );
-        list_print( nt );
-        printf( "\n" );
-    }
-
-    /* Step through cases. */
-    for ( parse = parse->right; parse; parse = parse->right )
-    {
-        if ( !glob( parse->left->string, nt ? nt->string : "" ) )
-        {
-            /* Get & exec parse tree for this case. */
-            parse = parse->left->left;
-            result = parse_evaluate( parse, frame );
-            break;
-        }
-    }
-
-    list_free( nt );
-    return result;
-}
-
-
-/*
- * debug_compile() - printf with indent to show rule expansion.
- */
-
-static void debug_compile( int which, char * s, FRAME * frame )
-{
-    static int level = 0;
-    static char indent[36] = ">>>>|>>>>|>>>>|>>>>|>>>>|>>>>|>>>>|";
-
-    if ( which >= 0 )
-    {
-        int i;
-
-        print_source_line( frame->procedure );
-
-        i = ( level + 1 ) * 2;
-        while ( i > 35 )
-        {
-            fputs( indent, stdout );
-            i -= 35;
-        }
-
-        printf( "%*.*s ", i, i, indent );
-    }
-
-    if ( s )
-        printf( "%s ", s );
-
-    level += which;
-}
diff --git a/jam-files/engine/compile.h b/jam-files/engine/compile.h
deleted file mode 100644
index 7d5191f0..00000000
--- a/jam-files/engine/compile.h
+++ /dev/null
@@ -1,82 +0,0 @@
-/*
- * Copyright 1993, 2000 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*  This file is ALSO:
- *  Copyright 2001-2004 David Abrahams.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-
-#ifndef COMPILE_DWA20011022_H
-# define COMPILE_DWA20011022_H
-
-# include "frames.h"
-# include "parse.h"
-# include "regexp.h"
-
-/*
- * compile.h - compile parsed jam statements
- */
-
-void compile_builtins();
-
-LIST *compile_append( PARSE *parse, FRAME *frame );
-LIST *compile_foreach( PARSE *parse, FRAME *frame );
-LIST *compile_if( PARSE *parse, FRAME *frame );
-LIST *compile_eval( PARSE *parse, FRAME *args );
-LIST *compile_include( PARSE *parse, FRAME *frame );
-LIST *compile_list( PARSE *parse, FRAME *frame );
-LIST *compile_local( PARSE *parse, FRAME *frame );
-LIST *compile_module( PARSE *parse, FRAME *frame );
-LIST *compile_class( PARSE *parse, FRAME *frame );
-LIST *compile_null( PARSE *parse, FRAME *frame );
-LIST *compile_on( PARSE *parse, FRAME *frame );
-LIST *compile_rule( PARSE *parse, FRAME *frame );
-LIST *compile_rules( PARSE *parse, FRAME *frame );
-LIST *compile_set( PARSE *parse, FRAME *frame );
-LIST *compile_setcomp( PARSE *parse, FRAME *frame );
-LIST *compile_setexec( PARSE *parse, FRAME *frame );
-LIST *compile_settings( PARSE *parse, FRAME *frame );
-LIST *compile_switch( PARSE *parse, FRAME *frame );
-LIST *compile_while( PARSE *parse, FRAME *frame );
-
-LIST *evaluate_rule( char *rulename, FRAME *frame );
-LIST *call_rule( char *rulename, FRAME* caller_frame, ...);
-
-regexp* regex_compile( const char* pattern );
-
-/* Flags for compile_set(), etc */
-
-# define ASSIGN_SET 0x00    /* = assign variable */
-# define ASSIGN_APPEND  0x01    /* += append variable */
-# define ASSIGN_DEFAULT 0x02    /* set only if unset */
-
-/* Flags for compile_setexec() */
-
-# define EXEC_UPDATED   0x01    /* executes updated */
-# define EXEC_TOGETHER  0x02    /* executes together */
-# define EXEC_IGNORE    0x04    /* executes ignore */
-# define EXEC_QUIETLY   0x08    /* executes quietly */
-# define EXEC_PIECEMEAL 0x10    /* executes piecemeal */
-# define EXEC_EXISTING  0x20    /* executes existing */
-
-/* Conditions for compile_if() */
-
-# define EXPR_NOT   0   /* ! cond */
-# define EXPR_AND   1   /* cond && cond */
-# define EXPR_OR    2   /* cond || cond */
-
-# define EXPR_EXISTS    3   /* arg */
-# define EXPR_EQUALS    4   /* arg = arg */
-# define EXPR_NOTEQ 5   /* arg != arg */
-# define EXPR_LESS  6   /* arg < arg  */
-# define EXPR_LESSEQ    7   /* arg <= arg */
-# define EXPR_MORE  8   /* arg > arg  */
-# define EXPR_MOREEQ    9   /* arg >= arg */
-# define EXPR_IN    10  /* arg in arg */
-
-#endif
-
diff --git a/jam-files/engine/debian/changelog b/jam-files/engine/debian/changelog
deleted file mode 100644
index 29084289..00000000
--- a/jam-files/engine/debian/changelog
+++ /dev/null
@@ -1,72 +0,0 @@
-bjam (3.1.12-1) unstable; urgency=low
-
-  * New upstream release.
-
- -- Rene Rivera <grafik@redshift-software.com>  Sat, 01 Oct 2005 00:00:00 +0000
-
-bjam (3.1.11-1) unstable; urgency=low
-
-  * New upstream release.
-
- -- Rene Rivera <grafik@redshift-software.com>  Sat, 30 Apr 2005 00:00:00 +0000
-
-bjam (3.1.10-1) unstable; urgency=low
-
-  * New upstream release.
-
- -- Rene Rivera <grafik@redshift-software.com>  Tue, 1 Jun 2004 05:42:35 +0000
-
-bjam (3.1.9-2) unstable; urgency=low
-
-  * Use default value of BOOST_BUILD_PATH is not is set in environment.
-
- -- Vladimir Prus <ghost@zigzag.lvk.cs.msu.su>  Wed, 17 Dec 2003 16:44:35 +0300
-
-bjam (3.1.9-1) unstable; urgency=low
-
-  * Implement NATIVE_FILE builtin and several native rules.
-
- -- Vladimir Prus <ghost@zigzag.lvk.cs.msu.su>  Thu, 11 Dec 2003 13:15:26 +0300
-
-bjam (3.1.8-1) unstable; urgency=low
-
-  * New upstream release.
-
- -- Vladimir Prus <ghost@zigzag.lvk.cs.msu.su>  Tue,  4 Nov 2003 20:50:43 +0300
-
-bjam (3.1.7-1) unstable; urgency=low
-
-  * New upstream release.
-
- -- Vladimir Prus <ghost@zigzag.lvk.cs.msu.su>  Thu, 11 Sep 2003 10:45:44 +0400
-
-bjam (3.1.6-1) unstable; urgency=low
-
-  * New upstream release.
-
- -- Vladimir Prus <ghost@zigzag.lvk.cs.msu.su>  Tue,  1 Jul 2003 09:12:18 +0400
-
-bjam (3.1.5-1) unstable; urgency=low
-
-  * New upstream release.
-
- -- Vladimir Prus <ghost@zigzag.lvk.cs.msu.su>  Mon, 19 May 2003 14:05:13 +0400
-
-bjam (3.1.3-2) unstable; urgency=low
-
-  * Changed Debian package to be similar to Jam's package.
-
- -- Vladimir Prus <ghost@cs.msu.su>  Thu, 10 Oct 2002 18:43:26 +0400
-
-bjam (3.1.3-1) unstable; urgency=low
-
-  * New upstream release.
-
- -- Vladimir Prus <ghost@zigzag.lvk.cs.msu.su>  Fri,  4 Oct 2002 18:16:54 +0400
-
-bjam (3.1.2-1) unstable; urgency=low
-
-  * Initial Release.
-
- -- Vladimir Prus <ghost@cs.msu.su>  Wed, 14 Aug 2002 14:08:00 +0400
-
diff --git a/jam-files/engine/debian/control b/jam-files/engine/debian/control
deleted file mode 100644
index c7f15193..00000000
--- a/jam-files/engine/debian/control
+++ /dev/null
@@ -1,16 +0,0 @@
-Source: bjam
-Section: devel
-Priority: optional
-Maintainer: Vladimir Prus <ghost@cs.msu.su>
-Build-Depends: debhelper (>> 3.0.0), docbook-to-man, bison
-Standards-Version: 3.5.2
-
-Package: bjam
-Architecture: any
-Depends: ${shlibs:Depends}
-Description: Build tool 
- Boost.Jam is a portable build tool with its own interpreted language, which 
- allows to implement rather complex logic in a readable way and without 
- resorting to external programs. It is a descendant of Jam/MR tool modified to 
- suit the needs of Boost.Build. In particular, modules and rule parameters
- were added, as well as several new builtins.
diff --git a/jam-files/engine/debian/copyright b/jam-files/engine/debian/copyright
deleted file mode 100644
index f72e4e3a..00000000
--- a/jam-files/engine/debian/copyright
+++ /dev/null
@@ -1,25 +0,0 @@
-This package was debianized by Vladimir Prus <ghost@cs.msu.su> on
-Wed, 17 July 2002, 19:27:00 +0400.
-
-Copyright:
-
-    /+\
-    +\	Copyright 1993-2002 Christopher Seiwald and Perforce Software, Inc.
-    \+/
-
-    This is Release 2.4 of Jam/MR, a make-like program.
-
-    License is hereby granted to use this software and distribute it
-    freely, as long as this copyright notice is retained and modifications 
-    are clearly marked.
-
-    ALL WARRANTIES ARE HEREBY DISCLAIMED.
-
-Some portions are also:
-
-    Copyright 2001-2006 David Abrahams.
-    Copyright 2002-2006 Rene Rivera.
-    Copyright 2003-2006 Vladimir Prus.
-    
-    Distributed under the Boost Software License, Version 1.0.
-    (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
diff --git a/jam-files/engine/debian/jam.man.sgml b/jam-files/engine/debian/jam.man.sgml
deleted file mode 100644
index ee21d4d8..00000000
--- a/jam-files/engine/debian/jam.man.sgml
+++ /dev/null
@@ -1,236 +0,0 @@
-<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
-
-<!-- Process this file with docbook-to-man to generate an nroff manual
-     page: `docbook-to-man manpage.sgml > manpage.1'.  You may view
-     the manual page with: `docbook-to-man manpage.sgml | nroff -man |
-     less'.  A typical entry in a Makefile or Makefile.am is:
-
-manpage.1: manpage.sgml
-	docbook-to-man $< > $@
-  -->
-
-  <!ENTITY dhfirstname "<firstname>Yann</firstname>">
-  <!ENTITY dhsurname   "<surname>Dirson</surname>">
-  <!-- Please adjust the date whenever revising the manpage. -->
-  <!ENTITY dhdate      "<date>mai 23, 2001</date>">
-  <!ENTITY dhemail     "<email>dirson@debian.org</email>">
-  <!ENTITY dhusername  "Yann Dirson">
-  <!ENTITY dhpackage   "jam">
-
-  <!ENTITY debian      "<productname>Debian GNU/Linux</productname>">
-  <!ENTITY gnu         "<acronym>GNU</acronym>">
-]>
-
-<refentry>
-  <refentryinfo>
-    <address>
-      &dhemail;
-    </address>
-    <author>
-      &dhfirstname;
-      &dhsurname;
-    </author>
-    <copyright>
-      <year>2001</year>
-      <holder>&dhusername;</holder>
-    </copyright>
-    &dhdate;
-  </refentryinfo>
-
-  <refmeta>
-    <refentrytitle>JAM</refentrytitle>
-    <manvolnum>1</manvolnum>
-  </refmeta>
-
-  <refnamediv>
-    <refname>Jam/MR</refname>
-    <refpurpose>Make(1) Redux</refpurpose>
-  </refnamediv>
-
-  <refsynopsisdiv>
-    <cmdsynopsis>
-      <command>jam</command>
-
-      <arg><option>-a</option></arg>
-      <arg><option>-n</option></arg>
-      <arg><option>-v</option></arg>
-
-      <arg><option>-d <replaceable/debug/</option></arg>
-      <arg><option>-f <replaceable/jambase/</option></arg>
-      <arg><option>-j <replaceable/jobs/</option></arg>
-      <arg><option>-o <replaceable/actionsfile/</option></arg>
-      <arg><option>-s <replaceable/var/=<replaceable/value/</option></arg>
-      <arg><option>-t <replaceable/target/</option></arg>
-
-      <arg repeat><option><replaceable/target/</option></arg>
-    </cmdsynopsis>
-  </refsynopsisdiv>
-
-  <refsect1>
-    <title>DESCRIPTION</title>
-
-    <para>Jam is a program construction tool, like make(1).</para>
-
-    <para>Jam recursively builds target files from source files, using
-    dependency information and updating actions expressed in the
-    Jambase file, which is written in jam's own interpreted language.
-    The default Jambase is compiled into jam and provides a
-    boilerplate for common use, relying on a user-provide file
-    "Jamfile" to enumerate actual targets and sources.</para>
-  </refsect1>
-
-  <refsect1>
-    <title>OPTIONS</title>
-
-    <variablelist>
-      <varlistentry>
-        <term><option/-a/</term>
-        <listitem>
-          <para>Build all targets anyway, even if they are up-to-date.</para>
-        </listitem>
-      </varlistentry>
-
-      <varlistentry>
-        <term><option>-d <replaceable/n/</option></term>
-        <listitem>
-          <para>Enable cummulative debugging levels from 1 to
-	    <replaceable/n/. Interesting values are:
-
-	    <glosslist>
-	      <glossentry><glossterm/1/ <glossdef><simpara/Show
-	      actions (the default)/</glossdef></glossentry>
-
-	      <glossentry><glossterm/2/ <glossdef><simpara/Show
-	      "quiet" actions and display all action
-	      text/</glossdef></glossentry>
-
-	      <glossentry><glossterm/3/ <glossdef><simpara>Show
-	      dependency analysis, and target/source
-	      timestamps/paths</simpara></glossdef></glossentry>
-
-	      <glossentry><glossterm/4/ <glossdef><simpara/Show shell
-	      arguments/</glossdef></glossentry>
-
-	      <glossentry><glossterm/5/ <glossdef><simpara/Show rule
-	      invocations and variable
-	      expansions/</glossdef></glossentry>
-
-	      <glossentry><glossterm/6/ <glossdef><simpara>Show
-	      directory/header file/archive
-	      scans</simpara></glossdef></glossentry>
-
-	      <glossentry><glossterm/7/ <glossdef><simpara/Show
-	      variable settings/</glossdef></glossentry>
-
-	      <glossentry><glossterm/8/ <glossdef><simpara/Show
-	      variable fetches/</glossdef></glossentry>
-
-	      <glossentry><glossterm/9/ <glossdef><simpara/Show
-	      variable manipulation, scanner
-	      tokens/</glossdef></glossentry>
-	    </glosslist>
-	  </para>
-        </listitem>
-      </varlistentry>
-
-      <varlistentry>
-        <term><option>-d +<replaceable/n/</option></term>
-        <listitem>
-          <para>Enable debugging level <replaceable/n/.</para>
-        </listitem>
-      </varlistentry>
-
-      <varlistentry>
-        <term><option/-d 0/</term>
-        <listitem>
-          <para>Turn off all debugging levels. Only errors are not
-          suppressed.</para>
-        </listitem>
-      </varlistentry>
-
-      <varlistentry>
-        <term><option>-f <replaceable/jambase/</option></term>
-        <listitem>
-          <para>Read <replaceable/jambase/ instead of using the
-          built-in Jambase. Only one <option/-f/ flag is permitted,
-          but the <replaceable/jambase/ may explicitly include other
-          files.</para>
-        </listitem>
-      </varlistentry>
-
-      <varlistentry>
-        <term><option>-j <replaceable/n/</option></term>
-        <listitem>
-          <para>Run up to <replaceable/n/ shell commands concurrently
-          (UNIX and NT only). The default is 1.</para>
-        </listitem>
-      </varlistentry>
-
-      <varlistentry>
-        <term><option/-n/</term>
-        <listitem>
-          <para>Don't actually execute the updating actions, but do
-          everything else. This changes the debug level default to
-          <option/-d2/.</para>
-        </listitem>
-      </varlistentry>
-
-      <varlistentry>
-        <term><option>-o <replaceable/file/</option></term>
-        <listitem>
-          <para>Write the updating actions to the specified file
-          instead of running them (or outputting them, as on the
-          Mac).</para>
-        </listitem>
-      </varlistentry>
-
-      <varlistentry>
-        <term><option>-s <replaceable/var/=<replaceable/value/</option></term>
-        <listitem>
-          <para>Set the variable <replaceable/var/ to
-          <replaceable/value/, overriding both internal variables and
-          variables imported from the environment. </para>
-        </listitem>
-      </varlistentry>
-
-      <varlistentry>
-        <term><option>-t <replaceable/target/</option></term>
-        <listitem>
-          <para>Rebuild <replaceable/target/ and everything that
-          depends on it, even if it is up-to-date.</para>
-        </listitem>
-      </varlistentry>
-
-      <varlistentry>
-        <term><option/-v/</term>
-        <listitem>
-          <para>Print the version of jam and exit.</para>
-        </listitem>
-      </varlistentry>
-
-    </variablelist>
-  </refsect1>
-
-  <refsect1>
-    <title>SEE ALSO</title>
-
-    <para>Jam is documented fully in HTML pages available on Debian
-    systems from
-    <filename>/usr/share/doc/jam/Jam.html</filename>.</para>
-  </refsect1>
-
-  <refsect1>
-    <title>AUTHOR</title>
-
-    <para>This manual page was created by &dhusername; &dhemail; from
-    the <filename/Jam.html/ documentation, for the &debian; system
-    (but may be used by others).</para>
-  </refsect1>
-</refentry>
-
-<!-- Keep this comment at the end of the file
-Local variables:
-sgml-omittag:t
-sgml-shorttag:t
-End:
--->
diff --git a/jam-files/engine/debian/rules b/jam-files/engine/debian/rules
deleted file mode 100755
index 756052a3..00000000
--- a/jam-files/engine/debian/rules
+++ /dev/null
@@ -1,73 +0,0 @@
-#!/usr/bin/make -f
-# Sample debian/rules that uses debhelper.
-# GNU copyright 1997 to 1999 by Joey Hess.
-# GNU copyright 2001 by Yann Dirson.
-
-# This is the debian/rules file for packages jam and ftjam
-# It should be usable with both packages without any change
-
-# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
-
-# This is the debhelper compatability version to use.
-export DH_COMPAT=3
-
-topdir=$(shell pwd)
-
-jam=bjam
-binname=bjam
-
-build: build-stamp
-build-stamp: debian/jam.1
-	dh_testdir
-
-	./build.sh
-
-	touch build-stamp
-
-%.1: %.man.sgml
-	/usr/bin/docbook-to-man $< > $@
-
-clean:
-	dh_testdir
-	dh_testroot
-	rm -f build-stamp
-	rm -rf bin.*
-	rm -f jam0 debian/jam.1
-	dh_clean
-
-install: build
-	dh_testdir
-	dh_testroot
-	dh_clean -k
-	dh_installdirs
-
-	install -d ${topdir}/debian/${jam}/usr/bin
-	install -m755 bin.linuxx86/bjam ${topdir}/debian/${jam}/usr/bin/
-	install -d ${topdir}/debian/${jam}/usr/share/man/man1/
-	install -m644 debian/jam.1 ${topdir}/debian/${jam}/usr/share/man/man1/${binname}.1
-
-
-# Build architecture-independent files here.
-binary-indep: build install
-# We have nothing to do by default.
-
-# Build architecture-dependent files here.
-binary-arch: build install
-	dh_testdir
-	dh_testroot
-	dh_installdocs README RELNOTES Jambase *.html
-#	dh_installemacsen
-#	dh_undocumented
-	dh_installchangelogs 
-	dh_strip
-	dh_compress
-	dh_fixperms
-	dh_installdeb
-	dh_shlibdeps
-	dh_gencontrol
-	dh_md5sums
-	dh_builddeb
-
-binary: binary-indep binary-arch
-.PHONY: build clean binary-indep binary-arch binary install configure
diff --git a/jam-files/engine/debug.c b/jam-files/engine/debug.c
deleted file mode 100644
index 7290555a..00000000
--- a/jam-files/engine/debug.c
+++ /dev/null
@@ -1,132 +0,0 @@
-/*
-    Copyright Rene Rivera 2005.
-    Distributed under the Boost Software License, Version 1.0.
-    (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-#include "jam.h"
-
-#include "hash.h"
-
-#include <time.h>
-#include <assert.h>
-
-
-static profile_frame * profile_stack = 0;
-static struct hash   * profile_hash  = 0;
-static profile_info    profile_other = { "[OTHER]", 0, 0, 0, 0, 0 };
-static profile_info    profile_total = { "[TOTAL]", 0, 0, 0, 0, 0 };
-
-
-profile_frame * profile_init( char * rulename, profile_frame * frame )
-{
-    if ( DEBUG_PROFILE ) profile_enter( rulename, frame );
-    return frame;
-}
-
-
-void profile_enter( char * rulename, profile_frame * frame )
-{
-    if ( DEBUG_PROFILE )
-    {
-        clock_t start = clock();
-        profile_info info;
-        profile_info * p = &info;
-
-        if ( !rulename ) p = &profile_other;
-
-        if ( !profile_hash && rulename )
-            profile_hash = hashinit( sizeof( profile_info ), "profile" );
-
-        info.name = rulename;
-
-        if ( rulename && hashenter( profile_hash, (HASHDATA * *)&p ) )
-            p->cumulative = p->net = p->num_entries = p->stack_count = p->memory = 0;
-
-        ++p->num_entries;
-        ++p->stack_count;
-
-        frame->info = p;
-
-        frame->caller = profile_stack;
-        profile_stack = frame;
-
-        frame->entry_time = clock();
-        frame->overhead = 0;
-        frame->subrules = 0;
-
-        /* caller pays for the time it takes to play with the hash table */
-        if ( frame->caller )
-            frame->caller->overhead += frame->entry_time - start;
-    }
-}
-
-
-void profile_memory( long mem )
-{
-    if ( DEBUG_PROFILE )
-        if ( profile_stack && profile_stack->info )
-            profile_stack->info->memory += mem;
-}
-
-
-void profile_exit( profile_frame * frame )
-{
-    if ( DEBUG_PROFILE )
-    {
-        /* Cumulative time for this call. */
-        clock_t t = clock() - frame->entry_time - frame->overhead;
-        /* If this rule is already present on the stack, don't add the time for
-         * this instance.
-         */
-        if ( frame->info->stack_count == 1 )
-            frame->info->cumulative += t;
-        /* Net time does not depend on presense of the same rule in call stack.
-         */
-        frame->info->net += t - frame->subrules;
-
-        if ( frame->caller )
-        {
-            /* Caller's cumulative time must account for this overhead. */
-            frame->caller->overhead += frame->overhead;
-            frame->caller->subrules += t;
-        }
-        /* Pop this stack frame. */
-        --frame->info->stack_count;
-        profile_stack = frame->caller;
-    }
-}
-
-
-static void dump_profile_entry( void * p_, void * ignored )
-{
-    profile_info * p = (profile_info *)p_;
-    unsigned long mem_each = ( p->memory / ( p->num_entries ? p->num_entries : 1 ) );
-    double cumulative = p->cumulative;
-    double net = p->net;
-    double q = p->net;
-    q /= ( p->num_entries ? p->num_entries : 1 );
-    cumulative /= CLOCKS_PER_SEC;
-    net /= CLOCKS_PER_SEC;
-    q /= CLOCKS_PER_SEC;
-    if ( !ignored )
-    {
-        profile_total.cumulative += p->net;
-        profile_total.memory += p->memory;
-    }
-    printf( "%10ld %12.6f %12.6f %12.8f %10ld %10ld %s\n", p->num_entries,
-        cumulative, net, q, p->memory, mem_each, p->name );
-}
-
-
-void profile_dump()
-{
-    if ( profile_hash )
-    {
-        printf( "%10s %12s %12s %12s %10s %10s %s\n", "--count--", "--gross--",
-            "--net--", "--each--", "--mem--", "--each--", "--name--" );
-        hashenumerate( profile_hash, dump_profile_entry, 0 );
-        dump_profile_entry( &profile_other, 0 );
-        dump_profile_entry( &profile_total, (void *)1 );
-    }
-}
diff --git a/jam-files/engine/debug.h b/jam-files/engine/debug.h
deleted file mode 100644
index 115a8873..00000000
--- a/jam-files/engine/debug.h
+++ /dev/null
@@ -1,54 +0,0 @@
-/*
-    Copyright Rene Rivera 2005.
-    Distributed under the Boost Software License, Version 1.0.
-    (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-*/
-#ifndef BJAM_DEBUG_H
-#define BJAM_DEBUG_H
-
-#include "jam.h"
-#include <time.h>
-
-
-struct profile_info
-{
-    /* name of rule being called */
-    char* name;
-    /* cumulative time spent in rule */
-    clock_t cumulative;
-    /* time spent in rule proper */
-    clock_t net;
-    /* number of time rule was entered */
-    unsigned long num_entries;
-    /* number of the times this function is present in stack */
-    unsigned long stack_count;
-    /* bytes of memory allocated by the call */
-    unsigned long memory;
-};
-typedef struct profile_info profile_info;
-
-struct profile_frame
-{
-    /* permanent storage where data accumulates */
-    profile_info* info;
-    /* overhead for profiling in this call */
-    clock_t overhead;
-    /* time of last entry to rule */
-    clock_t entry_time;
-    /* stack frame of caller */
-    struct profile_frame* caller;
-    /* time spent in subrules */
-    clock_t subrules;
-};
-typedef struct profile_frame profile_frame;
-
-profile_frame * profile_init( char * rulename, profile_frame * frame );
-void profile_enter( char* rulename, profile_frame * frame );
-void profile_memory( long mem );
-void profile_exit( profile_frame * frame );
-void profile_dump();
-
-#define PROFILE_ENTER( scope ) profile_frame PROF_ ## scope, *PROF_ ## scope ## _p = profile_init( #scope, &PROF_ ## scope )
-#define PROFILE_EXIT( scope ) profile_exit( PROF_ ## scope ## _p )
-
-#endif
diff --git a/jam-files/engine/execcmd.h b/jam-files/engine/execcmd.h
deleted file mode 100644
index 67f2b839..00000000
--- a/jam-files/engine/execcmd.h
+++ /dev/null
@@ -1,45 +0,0 @@
-/*
- * Copyright 1993, 1995 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*
- * execcmd.h - execute a shell script.
- *
- * Defines the interface to be implemented in platform specific implementation
- * modules.
- *
- * 05/04/94 (seiwald) - async multiprocess interface
- */
-
-#ifndef EXECCMD_H
-#define EXECCMD_H
-
-#include <time.h>
-
-typedef struct timing_info
-{
-    double system;
-    double user;
-    time_t start;
-    time_t end;
-} timing_info;
-
-void exec_cmd
-(
-    char * string,
-    void (* func)( void * closure, int status, timing_info *, char *, char * ),
-    void * closure,
-    LIST * shell,
-    char * action,
-    char * target
-);
-
-int exec_wait();
-
-#define EXEC_CMD_OK    0
-#define EXEC_CMD_FAIL  1
-#define EXEC_CMD_INTR  2
-
-#endif
diff --git a/jam-files/engine/execmac.c b/jam-files/engine/execmac.c
deleted file mode 100644
index 2ddddedd..00000000
--- a/jam-files/engine/execmac.c
+++ /dev/null
@@ -1,69 +0,0 @@
-/*
- * Copyright 1993, 1995 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-#include "jam.h"
-#include "lists.h"
-#include "execcmd.h"
-#include <errno.h>
-
-#ifdef OS_MAC
-
-/*
- * execunix.c - execute a shell script on UNIX
- *
- * If $(JAMSHELL) is defined, uses that to formulate execvp().
- * The default is:
- *
- *  /bin/sh -c %
- *
- * Each word must be an individual element in a jam variable value.
- *
- * In $(JAMSHELL), % expands to the command string and ! expands to
- * the slot number (starting at 1) for multiprocess (-j) invocations.
- * If $(JAMSHELL) doesn't include a %, it is tacked on as the last
- * argument.
- *
- * Don't just set JAMSHELL to /bin/sh - it won't work!
- *
- * External routines:
- *  exec_cmd()  - launch an async command execution.
- *  exec_wait() - wait and drive at most one execution completion.
- *
- * Internal routines:
- *  onintr() - bump intr to note command interruption.
- *
- * 04/08/94 (seiwald) - Coherent/386 support added.
- * 05/04/94 (seiwald) - async multiprocess interface
- * 01/22/95 (seiwald) - $(JAMSHELL) support
- */
-
-
-/*
- * exec_cmd() - launch an async command execution.
- */
-
-void exec_cmd
-(
-    char * string,
-    void (* func)( void * closure, int status, timing_info *, char *, char * ),
-    void * closure,
-    LIST * shell
-)
-{
-    printf( "%s", string );
-    (*func)( closure, EXEC_CMD_OK );
-}
-
-/*
- * exec_wait() - wait and drive at most one execution completion.
- */
-
-int exec_wait()
-{
-    return 0;
-}
-
-#endif /* OS_MAC */
diff --git a/jam-files/engine/execnt.c b/jam-files/engine/execnt.c
deleted file mode 100644
index 76420451..00000000
--- a/jam-files/engine/execnt.c
+++ /dev/null
@@ -1,1296 +0,0 @@
-/*
- * Copyright 1993, 1995 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*  This file is ALSO:
- *  Copyright 2001-2004 David Abrahams.
- *  Copyright 2007 Rene Rivera.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-
-#include "jam.h"
-#include "lists.h"
-#include "execcmd.h"
-#include "pathsys.h"
-#include "string.h"
-#include "output.h"
-#include <errno.h>
-#include <assert.h>
-#include <ctype.h>
-#include <time.h>
-#include <math.h>
-
-#ifdef USE_EXECNT
-
-#define WIN32_LEAN_AND_MEAN
-#include <windows.h>
-#include <process.h>
-#include <tlhelp32.h>
-
-/*
- * execnt.c - execute a shell command on Windows NT
- *
- * If $(JAMSHELL) is defined, uses that to formulate execvp()/spawnvp().
- * The default is:
- *
- *  /bin/sh -c %        [ on UNIX/AmigaOS ]
- *  cmd.exe /c %        [ on Windows NT ]
- *
- * Each word must be an individual element in a jam variable value.
- *
- * In $(JAMSHELL), % expands to the command string and ! expands to
- * the slot number (starting at 1) for multiprocess (-j) invocations.
- * If $(JAMSHELL) doesn't include a %, it is tacked on as the last
- * argument.
- *
- * Don't just set JAMSHELL to /bin/sh or cmd.exe - it won't work!
- *
- * External routines:
- *  exec_cmd() - launch an async command execution.
- *  exec_wait() - wait and drive at most one execution completion.
- *
- * Internal routines:
- *  onintr() - bump intr to note command interruption.
- *
- * 04/08/94 (seiwald) - Coherent/386 support added.
- * 05/04/94 (seiwald) - async multiprocess interface
- * 01/22/95 (seiwald) - $(JAMSHELL) support
- * 06/02/97 (gsar)    - full async multiprocess support for Win32
- */
-
-/* get the maximum command line length according to the OS */
-int maxline();
-
-/* delete and argv list */
-static void free_argv(char**);
-/* Convert a command string into arguments for spawnvp. */
-static char** string_to_args(const char*);
-/* bump intr to note command interruption */
-static void onintr(int);
-/* If the command is suitable for execution via spawnvp */
-long can_spawn(char*);
-/* Add two 64-bit unsigned numbers, h1l1 and h2l2 */
-static FILETIME add_64(
-    unsigned long h1, unsigned long l1,
-    unsigned long h2, unsigned long l2);
-static FILETIME add_FILETIME(FILETIME t1, FILETIME t2);
-static FILETIME negate_FILETIME(FILETIME t);
-/* Convert a FILETIME to a number of seconds */
-static double filetime_seconds(FILETIME t);
-/* record the timing info for the process */
-static void record_times(HANDLE, timing_info*);
-/* calc the current running time of an *active* process */
-static double running_time(HANDLE);
-/* */
-DWORD get_process_id(HANDLE);
-/* terminate the given process, after terminating all its children */
-static void kill_process_tree(DWORD, HANDLE);
-/* waits for a command to complete or for the given timeout, whichever is first */
-static int try_wait(int timeoutMillis);
-/* reads any pending output for running commands */
-static void read_output();
-/* checks if a command ran out of time, and kills it */
-static int try_kill_one();
-/* */
-static double creation_time(HANDLE);
-/* Recursive check if first process is parent (directly or indirectly) of
-the second one. */
-static int is_parent_child(DWORD, DWORD);
-/* */
-static void close_alert(HANDLE);
-/* close any alerts hanging around */
-static void close_alerts();
-
-/* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */
-
-static int intr = 0;
-static int cmdsrunning = 0;
-static void (* istat)( int );
-
-
-/* The list of commands we run. */
-static struct
-{
-    string action;   /* buffer to hold action */
-    string target;   /* buffer to hold target */
-    string command;  /* buffer to hold command being invoked */
-
-    /* Temporary batch file used to execute the action when needed. */
-    char * tempfile_bat;
-
-    /* Pipes for communicating with the child process. Parent reads from (0),
-     * child writes to (1).
-     */
-    HANDLE pipe_out[ 2 ];
-    HANDLE pipe_err[ 2 ];
-
-    string              buffer_out;   /* buffer to hold stdout, if any */
-    string              buffer_err;   /* buffer to hold stderr, if any */
-
-    PROCESS_INFORMATION pi;           /* running process information */
-    DWORD               exit_code;    /* executed command's exit code */
-    int                 exit_reason;  /* reason why a command completed */
-
-    /* Function called when the command completes. */
-    void (* func)( void * closure, int status, timing_info *, char *, char * );
-
-    /* Opaque data passed back to the 'func' callback called when the command
-     * completes.
-     */
-    void * closure;
-}
-cmdtab[ MAXJOBS ] = { { 0 } };
-
-
-/*
- * Execution unit tests.
- */
-
-void execnt_unit_test()
-{
-#if !defined( NDEBUG )
-    /* vc6 preprocessor is broken, so assert with these strings gets confused.
-     * Use a table instead.
-     */
-    typedef struct test { char * command; int result; } test;
-    test tests[] = {
-        { "x", 0 },
-        { "x\n ", 0 },
-        { "x\ny", 1 },
-        { "x\n\n y", 1 },
-        { "echo x > foo.bar", 1 },
-        { "echo x < foo.bar", 1 },
-        { "echo x \">\" foo.bar", 0 },
-        { "echo x \"<\" foo.bar", 0 },
-        { "echo x \\\">\\\" foo.bar", 1 },
-        { "echo x \\\"<\\\" foo.bar", 1 } };
-    int i;
-    for ( i = 0; i < sizeof( tests ) / sizeof( *tests ); ++i )
-        assert( !can_spawn( tests[ i ].command ) == tests[ i ].result );
-
-    {
-        char * long_command = BJAM_MALLOC_ATOMIC( MAXLINE + 10 );
-        assert( long_command != 0 );
-        memset( long_command, 'x', MAXLINE + 9 );
-        long_command[ MAXLINE + 9 ] = 0;
-        assert( can_spawn( long_command ) == MAXLINE + 9 );
-        BJAM_FREE( long_command );
-    }
-
-    {
-        /* Work around vc6 bug; it doesn't like escaped string
-         * literals inside assert
-         */
-        char * * argv = string_to_args(" \"g++\" -c -I\"Foobar\"" );
-        char const expected[] = "-c -I\"Foobar\"";
-
-        assert( !strcmp( argv[ 0 ], "g++" ) );
-        assert( !strcmp( argv[ 1 ], expected ) );
-        free_argv( argv );
-    }
-#endif
-}
-
-
-/*
- * exec_cmd() - launch an async command execution.
- */
-
-void exec_cmd
-(
-    char * command,
-    void (* func)( void * closure, int status, timing_info *, char * invoked_command, char * command_output ),
-    void * closure,
-    LIST * shell,
-    char * action,
-    char * target
-)
-{
-    int      slot;
-    int      raw_cmd = 0 ;
-    char   * argv_static[ MAXARGC + 1 ];  /* +1 for NULL */
-    char * * argv = argv_static;
-    char   * p;
-    char   * command_orig = command;
-
-    /* Check to see if we need to hack around the line-length limitation. Look
-     * for a JAMSHELL setting of "%", indicating that the command should be
-     * invoked directly.
-     */
-    if ( shell && !strcmp( shell->string, "%" ) && !list_next( shell ) )
-    {
-        raw_cmd = 1;
-        shell = 0;
-    }
-
-    /* Find a slot in the running commands table for this one. */
-    for ( slot = 0; slot < MAXJOBS; ++slot )
-        if ( !cmdtab[ slot ].pi.hProcess )
-            break;
-    if ( slot == MAXJOBS )
-    {
-        printf( "no slots for child!\n" );
-        exit( EXITBAD );
-    }
-
-    /* Compute the name of a temp batch file, for possible use. */
-    if ( !cmdtab[ slot ].tempfile_bat )
-    {
-        char const * tempdir = path_tmpdir();
-        DWORD procID = GetCurrentProcessId();
-
-        /* SVA - allocate 64 bytes extra just to be safe. */
-        cmdtab[ slot ].tempfile_bat = BJAM_MALLOC_ATOMIC( strlen( tempdir ) + 64 );
-
-        sprintf( cmdtab[ slot ].tempfile_bat, "%s\\jam%d-%02d.bat",
-            tempdir, procID, slot );
-    }
-
-    /* Trim leading, -ending- white space */
-    while ( *( command + 1 ) && isspace( *command ) )
-        ++command;
-
-    /* Write to .BAT file unless the line would be too long and it meets the
-     * other spawnability criteria.
-     */
-    if ( raw_cmd && ( can_spawn( command ) >= MAXLINE ) )
-    {
-        if ( DEBUG_EXECCMD )
-            printf("Executing raw command directly\n");
-    }
-    else
-    {
-        FILE * f = 0;
-        int tries = 0;
-        raw_cmd = 0;
-
-        /* Write command to bat file. For some reason this open can fail
-         * intermitently. But doing some retries works. Most likely this is due
-         * to a previously existing file of the same name that happens to be
-         * opened by an active virus scanner. Pointed out and fixed by Bronek
-         * Kozicki.
-         */
-        for ( ; !f && ( tries < 4 ); ++tries )
-        {
-            f = fopen( cmdtab[ slot ].tempfile_bat, "w" );
-            if ( !f && ( tries < 4 ) ) Sleep( 250 );
-        }
-        if ( !f )
-        {
-            printf( "failed to write command file!\n" );
-            exit( EXITBAD );
-        }
-        fputs( command, f );
-        fclose( f );
-
-        command = cmdtab[ slot ].tempfile_bat;
-
-        if ( DEBUG_EXECCMD )
-        {
-            if ( shell )
-                printf( "using user-specified shell: %s", shell->string );
-            else
-                printf( "Executing through .bat file\n" );
-        }
-    }
-
-    /* Formulate argv; If shell was defined, be prepared for % and ! subs.
-     * Otherwise, use stock cmd.exe.
-     */
-    if ( shell )
-    {
-        int i;
-        char jobno[ 4 ];
-        int gotpercent = 0;
-
-        sprintf( jobno, "%d", slot + 1 );
-
-        for ( i = 0; shell && ( i < MAXARGC ); ++i, shell = list_next( shell ) )
-        {
-            switch ( shell->string[ 0 ] )
-            {
-                case '%': argv[ i ] = command; ++gotpercent; break;
-                case '!': argv[ i ] = jobno; break;
-                default : argv[ i ] = shell->string;
-            }
-            if ( DEBUG_EXECCMD )
-                printf( "argv[%d] = '%s'\n", i, argv[ i ] );
-        }
-
-        if ( !gotpercent )
-            argv[ i++ ] = command;
-
-        argv[ i ] = 0;
-    }
-    else if ( raw_cmd )
-    {
-        argv = string_to_args( command );
-    }
-    else
-    {
-        argv[ 0 ] = "cmd.exe";
-        argv[ 1 ] = "/Q/C";  /* anything more is non-portable */
-        argv[ 2 ] = command;
-        argv[ 3 ] = 0;
-    }
-
-    /* Catch interrupts whenever commands are running. */
-    if ( !cmdsrunning++ )
-        istat = signal( SIGINT, onintr );
-
-    /* Start the command. */
-    {
-        SECURITY_ATTRIBUTES sa
-            = { sizeof( SECURITY_ATTRIBUTES ), 0, 0 };
-        SECURITY_DESCRIPTOR sd;
-        STARTUPINFO si
-            = { sizeof( STARTUPINFO ), 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 };
-        string cmd;
-
-        /* Init the security data. */
-        InitializeSecurityDescriptor( &sd, SECURITY_DESCRIPTOR_REVISION );
-        SetSecurityDescriptorDacl( &sd, TRUE, NULL, FALSE );
-        sa.lpSecurityDescriptor = &sd;
-        sa.bInheritHandle = TRUE;
-
-        /* Create the stdout, which is also the merged out + err, pipe. */
-        if ( !CreatePipe( &cmdtab[ slot ].pipe_out[ 0 ],
-            &cmdtab[ slot ].pipe_out[ 1 ], &sa, 0 ) )
-        {
-            perror( "CreatePipe" );
-            exit( EXITBAD );
-        }
-
-        /* Create the stdout, which is also the merged out+err, pipe. */
-        if ( globs.pipe_action == 2 )
-        {
-            if ( !CreatePipe( &cmdtab[ slot ].pipe_err[ 0 ],
-                &cmdtab[ slot ].pipe_err[ 1 ], &sa, 0 ) )
-            {
-                perror( "CreatePipe" );
-                exit( EXITBAD );
-            }
-        }
-
-        /* Set handle inheritance off for the pipe ends the parent reads from. */
-        SetHandleInformation( cmdtab[ slot ].pipe_out[ 0 ], HANDLE_FLAG_INHERIT, 0 );
-        if ( globs.pipe_action == 2 )
-            SetHandleInformation( cmdtab[ slot ].pipe_err[ 0 ], HANDLE_FLAG_INHERIT, 0 );
-
-        /* Hide the child window, if any. */
-        si.dwFlags |= STARTF_USESHOWWINDOW;
-        si.wShowWindow = SW_HIDE;
-
-        /* Set the child outputs to the pipes. */
-        si.dwFlags |= STARTF_USESTDHANDLES;
-        si.hStdOutput = cmdtab[ slot ].pipe_out[ 1 ];
-        if ( globs.pipe_action == 2 )
-        {
-            /* Pipe stderr to the action error output. */
-            si.hStdError = cmdtab[ slot ].pipe_err[ 1 ];
-        }
-        else if ( globs.pipe_action == 1 )
-        {
-            /* Pipe stderr to the console error output. */
-            si.hStdError = GetStdHandle( STD_ERROR_HANDLE );
-        }
-        else
-        {
-            /* Pipe stderr to the action merged output. */
-            si.hStdError = cmdtab[ slot ].pipe_out[ 1 ];
-        }
-
-        /* Let the child inherit stdin, as some commands assume it's available. */
-        si.hStdInput = GetStdHandle(STD_INPUT_HANDLE);
-
-        /* Save the operation for exec_wait() to find. */
-        cmdtab[ slot ].func = func;
-        cmdtab[ slot ].closure = closure;
-        if ( action && target )
-        {
-            string_copy( &cmdtab[ slot ].action, action );
-            string_copy( &cmdtab[ slot ].target, target );
-        }
-        else
-        {
-            string_free( &cmdtab[ slot ].action );
-            string_new ( &cmdtab[ slot ].action );
-            string_free( &cmdtab[ slot ].target );
-            string_new ( &cmdtab[ slot ].target );
-        }
-        string_copy( &cmdtab[ slot ].command, command_orig );
-
-        /* Put together the command we run. */
-        {
-            char * * argp = argv;
-            string_new( &cmd );
-            string_copy( &cmd, *(argp++) );
-            while ( *argp )
-            {
-                string_push_back( &cmd, ' ' );
-                string_append( &cmd, *(argp++) );
-            }
-        }
-
-        /* Create output buffers. */
-        string_new( &cmdtab[ slot ].buffer_out );
-        string_new( &cmdtab[ slot ].buffer_err );
-
-        /* Run the command by creating a sub-process for it. */
-        if (
-            ! CreateProcess(
-                NULL                    ,  /* application name               */
-                cmd.value               ,  /* command line                   */
-                NULL                    ,  /* process attributes             */
-                NULL                    ,  /* thread attributes              */
-                TRUE                    ,  /* inherit handles                */
-                CREATE_NEW_PROCESS_GROUP,  /* create flags                   */
-                NULL                    ,  /* env vars, null inherits env    */
-                NULL                    ,  /* current dir, null is our       */
-                                           /* current dir                    */
-                &si                     ,  /* startup info                   */
-                &cmdtab[ slot ].pi         /* child process info, if created */
-                )
-            )
-        {
-            perror( "CreateProcess" );
-            exit( EXITBAD );
-        }
-
-        /* Clean up temporary stuff. */
-        string_free( &cmd );
-    }
-
-    /* Wait until we are under the limit of concurrent commands. Do not trust
-     * globs.jobs alone.
-     */
-    while ( ( cmdsrunning >= MAXJOBS ) || ( cmdsrunning >= globs.jobs ) )
-        if ( !exec_wait() )
-            break;
-
-    if ( argv != argv_static )
-        free_argv( argv );
-}
-
-
-/*
- * exec_wait()
- *  * wait and drive at most one execution completion.
- *  * waits for one command to complete, while processing the i/o for all
- *    ongoing commands.
- *
- *   Returns 0 if called when there were no more commands being executed or 1
- * otherwise.
- */
-
-int exec_wait()
-{
-    int i = -1;
-
-    /* Handle naive make1() which does not know if cmds are running. */
-    if ( !cmdsrunning )
-        return 0;
-
-    /* Wait for a command to complete, while snarfing up any output. */
-    do
-    {
-        /* Check for a complete command, briefly. */
-        i = try_wait(500);
-        /* Read in the output of all running commands. */
-        read_output();
-        /* Close out pending debug style dialogs. */
-        close_alerts();
-        /* Check if a command ran out of time. */
-        if ( i < 0 ) i = try_kill_one();
-    }
-    while ( i < 0 );
-
-    /* We have a command... process it. */
-    --cmdsrunning;
-    {
-        timing_info time;
-        int rstat;
-
-        /* The time data for the command. */
-        record_times( cmdtab[ i ].pi.hProcess, &time );
-
-        /* Clear the temp file. */
-        if ( cmdtab[ i ].tempfile_bat )
-        {
-            unlink( cmdtab[ i ].tempfile_bat );
-            BJAM_FREE( cmdtab[ i ].tempfile_bat );
-            cmdtab[ i ].tempfile_bat = NULL;
-        }
-
-        /* Find out the process exit code. */
-        GetExitCodeProcess( cmdtab[ i ].pi.hProcess, &cmdtab[ i ].exit_code );
-
-        /* The dispossition of the command. */
-        if ( intr )
-            rstat = EXEC_CMD_INTR;
-        else if ( cmdtab[ i ].exit_code != 0 )
-            rstat = EXEC_CMD_FAIL;
-        else
-            rstat = EXEC_CMD_OK;
-
-        /* Output the action block. */
-        out_action(
-            cmdtab[ i ].action.size     > 0 ? cmdtab[ i ].action.value     : 0,
-            cmdtab[ i ].target.size     > 0 ? cmdtab[ i ].target.value     : 0,
-            cmdtab[ i ].command.size    > 0 ? cmdtab[ i ].command.value    : 0,
-            cmdtab[ i ].buffer_out.size > 0 ? cmdtab[ i ].buffer_out.value : 0,
-            cmdtab[ i ].buffer_err.size > 0 ? cmdtab[ i ].buffer_err.value : 0,
-            cmdtab[ i ].exit_reason );
-
-        /* Call the callback, may call back to jam rule land. Assume -p0 in
-         * effect so only pass buffer containing merged output.
-         */
-        (*cmdtab[ i ].func)(
-            cmdtab[ i ].closure,
-            rstat,
-            &time,
-            cmdtab[ i ].command.value,
-            cmdtab[ i ].buffer_out.value );
-
-        /* Clean up the command data, process, etc. */
-        string_free( &cmdtab[ i ].action  ); string_new( &cmdtab[ i ].action  );
-        string_free( &cmdtab[ i ].target  ); string_new( &cmdtab[ i ].target  );
-        string_free( &cmdtab[ i ].command ); string_new( &cmdtab[ i ].command );
-        if ( cmdtab[ i ].pi.hProcess   ) { CloseHandle( cmdtab[ i ].pi.hProcess   ); cmdtab[ i ].pi.hProcess   = 0; }
-        if ( cmdtab[ i ].pi.hThread    ) { CloseHandle( cmdtab[ i ].pi.hThread    ); cmdtab[ i ].pi.hThread    = 0; }
-        if ( cmdtab[ i ].pipe_out[ 0 ] ) { CloseHandle( cmdtab[ i ].pipe_out[ 0 ] ); cmdtab[ i ].pipe_out[ 0 ] = 0; }
-        if ( cmdtab[ i ].pipe_out[ 1 ] ) { CloseHandle( cmdtab[ i ].pipe_out[ 1 ] ); cmdtab[ i ].pipe_out[ 1 ] = 0; }
-        if ( cmdtab[ i ].pipe_err[ 0 ] ) { CloseHandle( cmdtab[ i ].pipe_err[ 0 ] ); cmdtab[ i ].pipe_err[ 0 ] = 0; }
-        if ( cmdtab[ i ].pipe_err[ 1 ] ) { CloseHandle( cmdtab[ i ].pipe_err[ 1 ] ); cmdtab[ i ].pipe_err[ 1 ] = 0; }
-        string_free( &cmdtab[ i ].buffer_out ); string_new( &cmdtab[ i ].buffer_out );
-        string_free( &cmdtab[ i ].buffer_err ); string_new( &cmdtab[ i ].buffer_err );
-        cmdtab[ i ].exit_code = 0;
-        cmdtab[ i ].exit_reason = EXIT_OK;
-    }
-
-    return 1;
-}
-
-
-/* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */
-
-static void free_argv( char * * args )
-{
-    BJAM_FREE( args[ 0 ] );
-    BJAM_FREE( args );
-}
-
-
-/*
- * For more details on Windows cmd.exe shell command-line length limitations see
- * the following MSDN article:
- *     http://support.microsoft.com/default.aspx?scid=kb;en-us;830473
- */
-
-int maxline()
-{
-    OSVERSIONINFO os_info;
-    os_info.dwOSVersionInfoSize = sizeof( os_info );
-    GetVersionEx( &os_info );
-
-    if ( os_info.dwMajorVersion >= 5 ) return 8191; /* XP >     */
-    if ( os_info.dwMajorVersion == 4 ) return 2047; /* NT 4.x   */
-    return 996;                                     /* NT 3.5.1 */
-}
-
-
-/*
- * Convert a command string into arguments for spawnvp(). The original code,
- * inherited from ftjam, tried to break up every argument on the command-line,
- * dealing with quotes, but that is really a waste of time on Win32, at least.
- * It turns out that all you need to do is get the raw path to the executable in
- * the first argument to spawnvp(), and you can pass all the rest of the
- * command-line arguments to spawnvp() in one, un-processed string.
- *
- * New strategy: break the string in at most one place.
- */
-
-static char * * string_to_args( char const * string )
-{
-    int            src_len;
-    int            in_quote;
-    char         * line;
-    char   const * src;
-    char         * dst;
-    char *       * argv;
-
-    /* Drop leading and trailing whitespace if any. */
-    while ( isspace( *string ) )
-        ++string;
-
-    src_len = strlen( string );
-    while ( ( src_len > 0 ) && isspace( string[ src_len - 1 ] ) )
-        --src_len;
-
-    /* Copy the input string into a buffer we can modify. */
-    line = (char *)BJAM_MALLOC_ATOMIC( src_len + 1 );
-    if ( !line )
-        return 0;
-
-    /* Allocate the argv array.
-     *   element 0: stores the path to the executable
-     *   element 1: stores the command-line arguments to the executable
-     *   element 2: NULL terminator
-     */
-    argv = (char * *)BJAM_MALLOC( 3 * sizeof( char * ) );
-    if ( !argv )
-    {
-        BJAM_FREE( line );
-        return 0;
-    }
-
-    /* Strip quotes from the first command-line argument and find where it ends.
-     * Quotes are illegal in Win32 pathnames, so we do not need to worry about
-     * preserving escaped quotes here. Spaces can not be escaped in Win32, only
-     * enclosed in quotes, so removing backslash escapes is also a non-issue.
-     */
-    in_quote = 0;
-    for ( src = string, dst = line ; *src; ++src )
-    {
-        if ( *src == '"' )
-            in_quote = !in_quote;
-        else if ( !in_quote && isspace( *src ) )
-            break;
-        else
-            *dst++ = *src;
-    }
-    *dst++ = 0;
-    argv[ 0 ] = line;
-
-    /* Skip whitespace in src. */
-    while ( isspace( *src ) )
-        ++src;
-
-    argv[ 1 ] = dst;
-
-    /* Copy the rest of the arguments verbatim. */
-    src_len -= src - string;
-
-    /* Use strncat() because it appends a trailing nul. */
-    *dst = 0;
-    strncat( dst, src, src_len );
-
-    argv[ 2 ] = 0;
-
-    return argv;
-}
-
-
-static void onintr( int disp )
-{
-    ++intr;
-    printf( "...interrupted\n" );
-}
-
-
-/*
- * can_spawn() - If the command is suitable for execution via spawnvp(), return
- * a number >= the number of characters it would occupy on the command-line.
- * Otherwise, return zero.
- */
-
-long can_spawn( char * command )
-{
-    char * p;
-    char inquote = 0;
-
-    /* Move to the first non-whitespace. */
-    command += strspn( command, " \t" );
-
-    p = command;
-
-    /* Look for newlines and unquoted i/o redirection. */
-    do
-    {
-        p += strcspn( p, "'\n\"<>|" );
-
-        switch ( *p )
-        {
-        case '\n':
-            /* Skip over any following spaces. */
-            while ( isspace( *p ) )
-                ++p;
-            /* Must use a .bat file if there is anything significant following
-             * the newline.
-             */
-            if ( *p )
-                return 0;
-            break;
-
-        case '"':
-        case '\'':
-            if ( ( p > command ) && ( p[ -1 ] != '\\' ) )
-            {
-                if ( inquote == *p )
-                    inquote = 0;
-                else if ( inquote == 0 )
-                    inquote = *p;
-            }
-            ++p;
-            break;
-
-        case '<':
-        case '>':
-        case '|':
-            if ( !inquote )
-                return 0;
-            ++p;
-            break;
-        }
-    }
-    while ( *p );
-
-    /* Return the number of characters the command will occupy. */
-    return p - command;
-}
-
-
-/* 64-bit arithmetic helpers. */
-
-/* Compute the carry bit from the addition of two 32-bit unsigned numbers. */
-#define add_carry_bit( a, b ) ( (((a) | (b)) >> 31) & (~((a) + (b)) >> 31) & 0x1 )
-
-/* Compute the high 32 bits of the addition of two 64-bit unsigned numbers, h1l1 and h2l2. */
-#define add_64_hi( h1, l1, h2, l2 ) ((h1) + (h2) + add_carry_bit(l1, l2))
-
-
-/*
- * Add two 64-bit unsigned numbers, h1l1 and h2l2.
- */
-
-static FILETIME add_64
-(
-    unsigned long h1, unsigned long l1,
-    unsigned long h2, unsigned long l2
-)
-{
-    FILETIME result;
-    result.dwLowDateTime = l1 + l2;
-    result.dwHighDateTime = add_64_hi( h1, l1, h2, l2 );
-    return result;
-}
-
-
-static FILETIME add_FILETIME( FILETIME t1, FILETIME t2 )
-{
-    return add_64( t1.dwHighDateTime, t1.dwLowDateTime, t2.dwHighDateTime,
-        t2.dwLowDateTime );
-}
-
-
-static FILETIME negate_FILETIME( FILETIME t )
-{
-    /* 2s complement negation */
-    return add_64( ~t.dwHighDateTime, ~t.dwLowDateTime, 0, 1 );
-}
-
-
-/*
- * Convert a FILETIME to a number of seconds.
- */
-
-static double filetime_seconds( FILETIME t )
-{
-    return t.dwHighDateTime * ( (double)( 1UL << 31 ) * 2.0 * 1.0e-7 ) + t.dwLowDateTime * 1.0e-7;
-}
-
-
-/*
- * What should be a simple conversion, turns out to be horribly complicated by
- * the defficiencies of MSVC and the Win32 API.
- */
-
-static time_t filetime_dt( FILETIME t_utc )
-{
-    static int calc_time_diff = 1;
-    static double time_diff;
-    if ( calc_time_diff )
-    {
-        struct tm t0_;
-        FILETIME f0_local;
-        FILETIME f0_;
-        SYSTEMTIME s0_;
-        GetSystemTime( &s0_ );
-        t0_.tm_year = s0_.wYear-1900;
-        t0_.tm_mon = s0_.wMonth-1;
-        t0_.tm_wday = s0_.wDayOfWeek;
-        t0_.tm_mday = s0_.wDay;
-        t0_.tm_hour = s0_.wHour;
-        t0_.tm_min = s0_.wMinute;
-        t0_.tm_sec = s0_.wSecond;
-        t0_.tm_isdst = 0;
-        SystemTimeToFileTime( &s0_, &f0_local );
-        LocalFileTimeToFileTime( &f0_local, &f0_ );
-        time_diff = filetime_seconds( f0_ ) - (double)mktime( &t0_ );
-        calc_time_diff = 0;
-    }
-    return ceil( filetime_seconds( t_utc ) - time_diff );
-}
-
-
-static void record_times( HANDLE process, timing_info * time )
-{
-    FILETIME creation;
-    FILETIME exit;
-    FILETIME kernel;
-    FILETIME user;
-    if ( GetProcessTimes( process, &creation, &exit, &kernel, &user ) )
-    {
-        time->system = filetime_seconds( kernel   );
-        time->user   = filetime_seconds( user     );
-        time->start  = filetime_dt     ( creation );
-        time->end    = filetime_dt     ( exit     );
-    }
-}
-
-
-#define IO_BUFFER_SIZE ( 16 * 1024 )
-
-static char ioBuffer[ IO_BUFFER_SIZE + 1 ];
-
-
-static void read_pipe
-(
-    HANDLE   in,  /* the pipe to read from */
-    string * out
-)
-{
-    DWORD bytesInBuffer = 0;
-    DWORD bytesAvailable = 0;
-
-    do
-    {
-        /* check if we have any data to read */
-        if ( !PeekNamedPipe( in, ioBuffer, IO_BUFFER_SIZE, &bytesInBuffer, &bytesAvailable, NULL ) )
-            bytesAvailable = 0;
-
-        /* read in the available data */
-        if ( bytesAvailable > 0 )
-        {
-            /* we only read in the available bytes, to avoid blocking */
-            if ( ReadFile( in, ioBuffer,
-                bytesAvailable <= IO_BUFFER_SIZE ? bytesAvailable : IO_BUFFER_SIZE,
-                &bytesInBuffer, NULL ) )
-            {
-                if ( bytesInBuffer > 0 )
-                {
-                    /* Clean up some illegal chars. */
-                    int i;
-                    for ( i = 0; i < bytesInBuffer; ++i )
-                    {
-                        if ( ( (unsigned char)ioBuffer[ i ] < 1 ) )
-                            ioBuffer[ i ] = '?';
-                    }
-                    /* Null, terminate. */
-                    ioBuffer[ bytesInBuffer ] = '\0';
-                    /* Append to the output. */
-                    string_append( out, ioBuffer );
-                    /* Subtract what we read in. */
-                    bytesAvailable -= bytesInBuffer;
-                }
-                else
-                {
-                    /* Likely read a error, bail out. */
-                    bytesAvailable = 0;
-                }
-            }
-            else
-            {
-                /* Definitely read a error, bail out. */
-                bytesAvailable = 0;
-            }
-        }
-    }
-    while ( bytesAvailable > 0 );
-}
-
-
-static void read_output()
-{
-    int i;
-    for ( i = 0; i < globs.jobs && i < MAXJOBS; ++i )
-    {
-        /* Read stdout data. */
-        if ( cmdtab[ i ].pipe_out[ 0 ] )
-            read_pipe( cmdtab[ i ].pipe_out[ 0 ], & cmdtab[ i ].buffer_out );
-        /* Read stderr data. */
-        if ( cmdtab[ i ].pipe_err[ 0 ] )
-            read_pipe( cmdtab[ i ].pipe_err[ 0 ], & cmdtab[ i ].buffer_err );
-    }
-}
-
-
-/*
- * Waits for a single child process command to complete, or the timeout,
- * whichever comes first. Returns the index of the completed command in the
- * cmdtab array, or -1.
- */
-
-static int try_wait( int timeoutMillis )
-{
-    int i;
-    int num_active;
-    int wait_api_result;
-    HANDLE active_handles[ MAXJOBS ];
-    int active_procs[ MAXJOBS ];
-
-    /* Prepare a list of all active processes to wait for. */
-    for ( num_active = 0, i = 0; i < globs.jobs; ++i )
-    {
-        if ( cmdtab[ i ].pi.hProcess )
-        {
-            active_handles[ num_active ] = cmdtab[ i ].pi.hProcess;
-            active_procs[ num_active ] = i;
-            ++num_active;
-        }
-    }
-
-    /* Wait for a child to complete, or for our timeout window to expire. */
-    wait_api_result = WaitForMultipleObjects( num_active, active_handles,
-        FALSE, timeoutMillis );
-    if ( ( WAIT_OBJECT_0 <= wait_api_result ) &&
-        ( wait_api_result < WAIT_OBJECT_0 + num_active ) )
-    {
-        /* Rerminated process detected - return its index. */
-        return active_procs[ wait_api_result - WAIT_OBJECT_0 ];
-    }
-
-    /* Timeout. */
-    return -1;
-}
-
-
-static int try_kill_one()
-{
-    /* Only need to check if a timeout was specified with the -l option. */
-    if ( globs.timeout > 0 )
-    {
-        int i;
-        for ( i = 0; i < globs.jobs; ++i )
-        {
-            double t = running_time( cmdtab[ i ].pi.hProcess );
-            if ( t > (double)globs.timeout )
-            {
-                /* The job may have left an alert dialog around, try and get rid
-                 * of it before killing
-                 */
-                close_alert( cmdtab[ i ].pi.hProcess );
-                /* We have a "runaway" job, kill it. */
-                kill_process_tree( 0, cmdtab[ i ].pi.hProcess );
-                /* And return it marked as a timeout. */
-                cmdtab[ i ].exit_reason = EXIT_TIMEOUT;
-                return i;
-            }
-        }
-    }
-    return -1;
-}
-
-
-static void close_alerts()
-{
-    /* We only attempt this every 5 seconds, or so, because it is not a cheap
-     * operation, and we will catch the alerts eventually. This check uses
-     * floats as some compilers define CLOCKS_PER_SEC as a float or double.
-     */
-    if ( ( (float)clock() / (float)( CLOCKS_PER_SEC * 5 ) ) < ( 1.0 / 5.0 ) )
-    {
-        int i;
-        for ( i = 0; i < globs.jobs; ++i )
-            close_alert( cmdtab[ i ].pi.hProcess );
-    }
-}
-
-
-/*
- * Calc the current running time of an *active* process.
- */
-
-static double running_time( HANDLE process )
-{
-    FILETIME creation;
-    FILETIME exit;
-    FILETIME kernel;
-    FILETIME user;
-    FILETIME current;
-    if ( GetProcessTimes( process, &creation, &exit, &kernel, &user ) )
-    {
-        /* Compute the elapsed time. */
-        GetSystemTimeAsFileTime( &current );
-        return filetime_seconds( add_FILETIME( current,
-            negate_FILETIME( creation ) ) );
-    }
-    return 0.0;
-}
-
-
-/* It is just stupidly silly that one has to do this. */
-typedef struct PROCESS_BASIC_INFORMATION__
-{
-    LONG  ExitStatus;
-    PVOID PebBaseAddress;
-    ULONG AffinityMask;
-    LONG  BasePriority;
-    ULONG UniqueProcessId;
-    ULONG InheritedFromUniqueProcessId;
-} PROCESS_BASIC_INFORMATION_;
-typedef LONG (__stdcall * NtQueryInformationProcess__)(
-    HANDLE ProcessHandle,
-    LONG ProcessInformationClass,
-    PVOID ProcessInformation,
-    ULONG ProcessInformationLength,
-    PULONG ReturnLength);
-static NtQueryInformationProcess__ NtQueryInformationProcess_ = NULL;
-static HMODULE NTDLL_ = NULL;
-DWORD get_process_id( HANDLE process )
-{
-    PROCESS_BASIC_INFORMATION_ pinfo;
-    if ( !NtQueryInformationProcess_ )
-    {
-        if ( ! NTDLL_ )
-            NTDLL_ = GetModuleHandleA( "ntdll" );
-        if ( NTDLL_ )
-            NtQueryInformationProcess_
-                = (NtQueryInformationProcess__)GetProcAddress( NTDLL_, "NtQueryInformationProcess" );
-    }
-    if ( NtQueryInformationProcess_ )
-    {
-        LONG r = (*NtQueryInformationProcess_)( process,
-            /* ProcessBasicInformation == */ 0, &pinfo,
-            sizeof( PROCESS_BASIC_INFORMATION_ ), NULL );
-        return pinfo.UniqueProcessId;
-    }
-    return 0;
-}
-
-
-/*
- * Not really optimal, or efficient, but it is easier this way, and it is not
- * like we are going to be killing thousands, or even tens of processes.
- */
-
-static void kill_process_tree( DWORD pid, HANDLE process )
-{
-    HANDLE process_snapshot_h = INVALID_HANDLE_VALUE;
-    if ( !pid )
-        pid = get_process_id( process );
-    process_snapshot_h = CreateToolhelp32Snapshot( TH32CS_SNAPPROCESS, 0 );
-
-    if ( INVALID_HANDLE_VALUE != process_snapshot_h )
-    {
-        BOOL ok = TRUE;
-        PROCESSENTRY32 pinfo;
-        pinfo.dwSize = sizeof( PROCESSENTRY32 );
-        for (
-            ok = Process32First( process_snapshot_h, &pinfo );
-            ok == TRUE;
-            ok = Process32Next( process_snapshot_h, &pinfo ) )
-        {
-            if ( pinfo.th32ParentProcessID == pid )
-            {
-                /* Found a child, recurse to kill it and anything else below it.
-                 */
-                HANDLE ph = OpenProcess( PROCESS_ALL_ACCESS, FALSE,
-                    pinfo.th32ProcessID );
-                if ( NULL != ph )
-                {
-                    kill_process_tree( pinfo.th32ProcessID, ph );
-                    CloseHandle( ph );
-                }
-            }
-        }
-        CloseHandle( process_snapshot_h );
-    }
-    /* Now that the children are all dead, kill the root. */
-    TerminateProcess( process, -2 );
-}
-
-
-static double creation_time( HANDLE process )
-{
-    FILETIME creation;
-    FILETIME exit;
-    FILETIME kernel;
-    FILETIME user;
-    FILETIME current;
-    return GetProcessTimes( process, &creation, &exit, &kernel, &user )
-        ? filetime_seconds( creation )
-        : 0.0;
-}
-
-
-/*
- * Recursive check if first process is parent (directly or indirectly) of the
- * second one. Both processes are passed as process ids, not handles. Special
- * return value 2 means that the second process is smss.exe and its parent
- * process is System (first argument is ignored).
- */
-
-static int is_parent_child( DWORD parent, DWORD child )
-{
-    HANDLE process_snapshot_h = INVALID_HANDLE_VALUE;
-
-    if ( !child )
-        return 0;
-    if ( parent == child )
-        return 1;
-
-    process_snapshot_h = CreateToolhelp32Snapshot( TH32CS_SNAPPROCESS, 0 );
-    if ( INVALID_HANDLE_VALUE != process_snapshot_h )
-    {
-        BOOL ok = TRUE;
-        PROCESSENTRY32 pinfo;
-        pinfo.dwSize = sizeof( PROCESSENTRY32 );
-        for (
-            ok = Process32First( process_snapshot_h, &pinfo );
-            ok == TRUE;
-            ok = Process32Next( process_snapshot_h, &pinfo ) )
-        {
-            if ( pinfo.th32ProcessID == child )
-            {
-                /* Unfortunately, process ids are not really unique. There might
-                 * be spurious "parent and child" relationship match between two
-                 * non-related processes if real parent process of a given
-                 * process has exited (while child process kept running as an
-                 * "orphan") and the process id of such parent process has been
-                 * reused by internals of the operating system when creating
-                 * another process.
-                 *
-                 * Thus additional check is needed - process creation time. This
-                 * check may fail (i.e. return 0) for system processes due to
-                 * insufficient privileges, and that is OK.
-                 */
-                double tchild = 0.0;
-                double tparent = 0.0;
-                HANDLE hchild = OpenProcess( PROCESS_QUERY_INFORMATION, FALSE, pinfo.th32ProcessID );
-                CloseHandle( process_snapshot_h );
-
-                /* csrss.exe may display message box like following:
-                 *   xyz.exe - Unable To Locate Component
-                 *   This application has failed to start because
-                 *   boost_foo-bar.dll was not found. Re-installing the
-                 *   application may fix the problem
-                 * This actually happens when starting test process that depends
-                 * on a dynamic library which failed to build. We want to
-                 * automatically close these message boxes even though csrss.exe
-                 * is not our child process. We may depend on the fact that (in
-                 * all current versions of Windows) csrss.exe is directly child
-                 * of the smss.exe process, which in turn is directly child of
-                 * the System process, which always has process id == 4. This
-                 * check must be performed before comparison of process creation
-                 * times.
-                 */
-                if ( !stricmp( pinfo.szExeFile, "csrss.exe" ) &&
-                    ( is_parent_child( parent, pinfo.th32ParentProcessID ) == 2 ) )
-                    return 1;
-                if ( !stricmp( pinfo.szExeFile, "smss.exe" ) &&
-                    ( pinfo.th32ParentProcessID == 4 ) )
-                    return 2;
-
-                if ( hchild )
-                {
-                    HANDLE hparent = OpenProcess( PROCESS_QUERY_INFORMATION,
-                        FALSE, pinfo.th32ParentProcessID );
-                    if ( hparent )
-                    {
-                        tchild = creation_time( hchild );
-                        tparent = creation_time( hparent );
-                        CloseHandle( hparent );
-                    }
-                    CloseHandle( hchild );
-                }
-
-                /* Return 0 if one of the following is true:
-                 *  1. we failed to read process creation time
-                 *  2. child was created before alleged parent
-                 */
-                if ( ( tchild == 0.0 ) || ( tparent == 0.0 ) ||
-                    ( tchild < tparent ) )
-                    return 0;
-
-                return is_parent_child( parent, pinfo.th32ParentProcessID ) & 1;
-            }
-        }
-
-        CloseHandle( process_snapshot_h );
-    }
-
-    return 0;
-}
-
-typedef struct PROCESS_HANDLE_ID { HANDLE h; DWORD pid; } PROCESS_HANDLE_ID;
-
-
-/*
- * This function is called by the operating system for each topmost window.
- */
-
-BOOL CALLBACK close_alert_window_enum( HWND hwnd, LPARAM lParam )
-{
-    char buf[ 7 ] = { 0 };
-    PROCESS_HANDLE_ID p = *( (PROCESS_HANDLE_ID *)lParam );
-    DWORD pid = 0;
-    DWORD tid = 0;
-
-    /* We want to find and close any window that:
-     *  1. is visible and
-     *  2. is a dialog and
-     *  3. is displayed by any of our child processes
-     */
-    if ( !IsWindowVisible( hwnd ) )
-        return TRUE;
-
-    if ( !GetClassNameA( hwnd, buf, sizeof( buf ) ) )
-        return TRUE;  /* Failed to read class name; presume it is not a dialog. */
-
-    if ( strcmp( buf, "#32770" ) )
-        return TRUE;  /* Not a dialog */
-
-    /* GetWindowThreadProcessId() returns 0 on error, otherwise thread id of
-     * window message pump thread.
-     */
-    tid = GetWindowThreadProcessId( hwnd, &pid );
-
-    if ( tid && is_parent_child( p.pid, pid ) )
-    {
-        /* Ask really nice. */
-        PostMessageA( hwnd, WM_CLOSE, 0, 0 );
-        /* Now wait and see if it worked. If not, insist. */
-        if ( WaitForSingleObject( p.h, 200 ) == WAIT_TIMEOUT )
-        {
-            PostThreadMessageA( tid, WM_QUIT, 0, 0 );
-            WaitForSingleObject( p.h, 300 );
-        }
-
-        /* Done, we do not want to check any other window now. */
-        return FALSE;
-    }
-
-    return TRUE;
-}
-
-
-static void close_alert( HANDLE process )
-{
-    DWORD pid = get_process_id( process );
-    /* If process already exited or we just can not get its process id, do not
-     * go any further.
-     */
-    if ( pid )
-    {
-        PROCESS_HANDLE_ID p;
-        p.h = process;
-        p.pid = pid;
-        EnumWindows( &close_alert_window_enum, (LPARAM)&p );
-    }
-}
-
-#endif /* USE_EXECNT */
diff --git a/jam-files/engine/execunix.c b/jam-files/engine/execunix.c
deleted file mode 100644
index ef9dba00..00000000
--- a/jam-files/engine/execunix.c
+++ /dev/null
@@ -1,569 +0,0 @@
-/*
- * Copyright 1993, 1995 Christopher Seiwald.
- * Copyright 2007 Noel Belcourt.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-#include "jam.h"
-#include "lists.h"
-#include "execcmd.h"
-#include "output.h"
-#include <errno.h>
-#include <signal.h>
-#include <stdio.h>
-#include <time.h>
-#include <unistd.h>  /* needed for vfork(), _exit() prototypes */
-#include <sys/resource.h>
-#include <sys/times.h>
-#include <sys/wait.h>
-
-#if defined(sun) || defined(__sun) || defined(linux)
-    #include <wait.h>
-#endif
-
-#ifdef USE_EXECUNIX
-
-#include <sys/times.h>
-
-#if defined(__APPLE__)
-    #define NO_VFORK
-#endif
-
-#ifdef NO_VFORK
-    #define vfork() fork()
-#endif
-
-
-/*
- * execunix.c - execute a shell script on UNIX/WinNT/OS2/AmigaOS
- *
- * If $(JAMSHELL) is defined, uses that to formulate execvp()/spawnvp().
- * The default is:
- *
- *  /bin/sh -c %        [ on UNIX/AmigaOS ]
- *  cmd.exe /c %        [ on OS2/WinNT ]
- *
- * Each word must be an individual element in a jam variable value.
- *
- * In $(JAMSHELL), % expands to the command string and ! expands to the slot
- * number (starting at 1) for multiprocess (-j) invocations. If $(JAMSHELL) does
- * not include a %, it is tacked on as the last argument.
- *
- * Do not just set JAMSHELL to /bin/sh or cmd.exe - it will not work!
- *
- * External routines:
- *  exec_cmd() - launch an async command execution.
- *  exec_wait() - wait and drive at most one execution completion.
- *
- * Internal routines:
- *  onintr() - bump intr to note command interruption.
- *
- * 04/08/94 (seiwald) - Coherent/386 support added.
- * 05/04/94 (seiwald) - async multiprocess interface
- * 01/22/95 (seiwald) - $(JAMSHELL) support
- * 06/02/97 (gsar)    - full async multiprocess support for Win32
- */
-
-static clock_t tps = 0;
-static struct timeval tv;
-static int select_timeout = 0;
-static int intr = 0;
-static int cmdsrunning = 0;
-static struct tms old_time;
-
-#define OUT 0
-#define ERR 1
-
-static struct
-{
-    int     pid;              /* on win32, a real process handle */
-    int     fd[2];            /* file descriptors for stdout and stderr */
-    FILE   *stream[2];        /* child's stdout (0) and stderr (1) file stream */
-    clock_t start_time;       /* start time of child process */
-    int     exit_reason;      /* termination status */
-    int     action_length;    /* length of action string */
-    int     target_length;    /* length of target string */
-    char   *action;           /* buffer to hold action and target invoked */
-    char   *target;           /* buffer to hold action and target invoked */
-    char   *command;          /* buffer to hold command being invoked */
-    char   *buffer[2];        /* buffer to hold stdout and stderr, if any */
-    void    (*func)( void *closure, int status, timing_info*, char *, char * );
-    void   *closure;
-    time_t  start_dt;         /* start of command timestamp */
-} cmdtab[ MAXJOBS ] = {{0}};
-
-/*
- * onintr() - bump intr to note command interruption
- */
-
-void onintr( int disp )
-{
-    ++intr;
-    printf( "...interrupted\n" );
-}
-
-
-/*
- * exec_cmd() - launch an async command execution.
- */
-
-void exec_cmd
-(
-    char * string,
-    void (*func)( void *closure, int status, timing_info*, char *, char * ),
-    void * closure,
-    LIST * shell,
-    char * action,
-    char * target
-)
-{
-    static int initialized = 0;
-    int    out[2];
-    int    err[2];
-    int    slot;
-    int    len;
-    char * argv[ MAXARGC + 1 ];  /* +1 for NULL */
-
-    /* Find a slot in the running commands table for this one. */
-    for ( slot = 0; slot < MAXJOBS; ++slot )
-        if ( !cmdtab[ slot ].pid )
-            break;
-
-    if ( slot == MAXJOBS )
-    {
-        printf( "no slots for child!\n" );
-        exit( EXITBAD );
-    }
-
-    /* Forumulate argv. If shell was defined, be prepared for % and ! subs.
-     * Otherwise, use stock /bin/sh on unix or cmd.exe on NT.
-     */
-    if ( shell )
-    {
-        int  i;
-        char jobno[4];
-        int  gotpercent = 0;
-
-        sprintf( jobno, "%d", slot + 1 );
-
-        for ( i = 0; shell && i < MAXARGC; ++i, shell = list_next( shell ) )
-        {
-            switch ( shell->string[0] )
-            {
-                case '%': argv[ i ] = string; ++gotpercent; break;
-                case '!': argv[ i ] = jobno;                break;
-                default : argv[ i ] = shell->string;
-            }
-            if ( DEBUG_EXECCMD )
-                printf( "argv[%d] = '%s'\n", i, argv[ i ] );
-        }
-
-        if ( !gotpercent )
-        argv[ i++ ] = string;
-
-        argv[ i ] = 0;
-    }
-    else
-    {
-        argv[ 0 ] = "/bin/sh";
-        argv[ 1 ] = "-c";
-        argv[ 2 ] = string;
-        argv[ 3 ] = 0;
-    }
-
-    /* Increment jobs running. */
-    ++cmdsrunning;
-
-    /* Save off actual command string. */
-    cmdtab[ slot ].command = BJAM_MALLOC_ATOMIC( strlen( string ) + 1 );
-    strcpy( cmdtab[ slot ].command, string );
-
-    /* Initialize only once. */
-    if ( !initialized )
-    {
-        times( &old_time );
-        initialized = 1;
-    }
-
-    /* Create pipes from child to parent. */
-    {
-        if ( pipe( out ) < 0 )
-            exit( EXITBAD );
-
-        if ( pipe( err ) < 0 )
-            exit( EXITBAD );
-    }
-
-    /* Start the command */
-
-    cmdtab[ slot ].start_dt = time(0);
-
-    if ( 0 < globs.timeout )
-    {
-        /*
-         * Handle hung processes by manually tracking elapsed time and signal
-         * process when time limit expires.
-         */
-        struct tms buf;
-        cmdtab[ slot ].start_time = times( &buf );
-
-        /* Make a global, only do this once. */
-        if ( tps == 0 ) tps = sysconf( _SC_CLK_TCK );
-    }
-
-    if ( ( cmdtab[ slot ].pid = vfork() ) == 0 )
-    {
-        int pid = getpid();
-
-        close( out[0] );
-        close( err[0] );
-
-        dup2( out[1], STDOUT_FILENO );
-
-        if ( globs.pipe_action == 0 )
-            dup2( out[1], STDERR_FILENO );
-        else
-            dup2( err[1], STDERR_FILENO );
-
-        close( out[1] );
-        close( err[1] );
-
-        /* Make this process a process group leader so that when we kill it, all
-         * child processes of this process are terminated as well. We use
-         * killpg(pid, SIGKILL) to kill the process group leader and all its
-         * children.
-         */
-        if ( 0 < globs.timeout )
-        {
-            struct rlimit r_limit;
-            r_limit.rlim_cur = globs.timeout;
-            r_limit.rlim_max = globs.timeout;
-            setrlimit( RLIMIT_CPU, &r_limit );
-        }
-        setpgid( pid,pid );
-        execvp( argv[0], argv );
-        perror( "execvp" );
-        _exit( 127 );
-    }
-    else if ( cmdtab[ slot ].pid == -1 )
-    {
-        perror( "vfork" );
-        exit( EXITBAD );
-    }
-
-    setpgid( cmdtab[ slot ].pid, cmdtab[ slot ].pid );
-
-    /* close write end of pipes */
-    close( out[1] );
-    close( err[1] );
-
-    /* set both file descriptors to non-blocking */
-    fcntl(out[0], F_SETFL, O_NONBLOCK);
-    fcntl(err[0], F_SETFL, O_NONBLOCK);
-
-    /* child writes stdout to out[1], parent reads from out[0] */
-    cmdtab[ slot ].fd[ OUT ] = out[0];
-    cmdtab[ slot ].stream[ OUT ] = fdopen( cmdtab[ slot ].fd[ OUT ], "rb" );
-    if ( cmdtab[ slot ].stream[ OUT ] == NULL )
-    {
-        perror( "fdopen" );
-        exit( EXITBAD );
-    }
-
-    /* child writes stderr to err[1], parent reads from err[0] */
-    if (globs.pipe_action == 0)
-    {
-      close(err[0]);
-    }
-    else
-    {
-        cmdtab[ slot ].fd[ ERR ] = err[0];
-        cmdtab[ slot ].stream[ ERR ] = fdopen( cmdtab[ slot ].fd[ ERR ], "rb" );
-        if ( cmdtab[ slot ].stream[ ERR ] == NULL )
-        {
-            perror( "fdopen" );
-            exit( EXITBAD );
-        }
-    }
-
-    /* Ensure enough room for rule and target name. */
-    if ( action && target )
-    {
-        len = strlen( action ) + 1;
-        if ( cmdtab[ slot ].action_length < len )
-        {
-            BJAM_FREE( cmdtab[ slot ].action );
-            cmdtab[ slot ].action = BJAM_MALLOC_ATOMIC( len );
-            cmdtab[ slot ].action_length = len;
-        }
-        strcpy( cmdtab[ slot ].action, action );
-        len = strlen( target ) + 1;
-        if ( cmdtab[ slot ].target_length < len )
-        {
-            BJAM_FREE( cmdtab[ slot ].target );
-            cmdtab[ slot ].target = BJAM_MALLOC_ATOMIC( len );
-            cmdtab[ slot ].target_length = len;
-        }
-        strcpy( cmdtab[ slot ].target, target );
-    }
-    else
-    {
-        BJAM_FREE( cmdtab[ slot ].action );
-        BJAM_FREE( cmdtab[ slot ].target );
-        cmdtab[ slot ].action = 0;
-        cmdtab[ slot ].target = 0;
-        cmdtab[ slot ].action_length = 0;
-        cmdtab[ slot ].target_length = 0;
-    }
-
-    /* Save the operation for exec_wait() to find. */
-    cmdtab[ slot ].func = func;
-    cmdtab[ slot ].closure = closure;
-
-    /* Wait until we are under the limit of concurrent commands. Do not trust
-     * globs.jobs alone.
-     */
-    while ( ( cmdsrunning >= MAXJOBS ) || ( cmdsrunning >= globs.jobs ) )
-        if ( !exec_wait() )
-            break;
-}
-
-
-/* Returns 1 if file is closed, 0 if descriptor is still live.
- *
- * i is index into cmdtab
- *
- * s (stream) indexes:
- *  - cmdtab[ i ].stream[ s ]
- *  - cmdtab[ i ].buffer[ s ]
- *  - cmdtab[ i ].fd    [ s ]
- */
-
-int read_descriptor( int i, int s )
-{
-    int  ret;
-    int  len;
-    char buffer[BUFSIZ];
-
-    while ( 0 < ( ret = fread( buffer, sizeof(char),  BUFSIZ-1, cmdtab[ i ].stream[ s ] ) ) )
-    {
-        buffer[ret] = 0;
-        if  ( !cmdtab[ i ].buffer[ s ] )
-        {
-            /* Never been allocated. */
-            cmdtab[ i ].buffer[ s ] = (char*)BJAM_MALLOC_ATOMIC( ret + 1 );
-            memcpy( cmdtab[ i ].buffer[ s ], buffer, ret + 1 );
-        }
-        else
-        {
-            /* Previously allocated. */
-            char * tmp = cmdtab[ i ].buffer[ s ];
-            len = strlen( tmp );
-            cmdtab[ i ].buffer[ s ] = (char*)BJAM_MALLOC_ATOMIC( len + ret + 1 );
-            memcpy( cmdtab[ i ].buffer[ s ], tmp, len );
-            memcpy( cmdtab[ i ].buffer[ s ] + len, buffer, ret + 1 );
-            BJAM_FREE( tmp );
-        }
-    }
-
-    return feof(cmdtab[ i ].stream[ s ]);
-}
-
-
-void close_streams( int i, int s )
-{
-    /* Close the stream and pipe descriptor. */
-    fclose(cmdtab[ i ].stream[ s ]);
-    cmdtab[ i ].stream[ s ] = 0;
-
-    close(cmdtab[ i ].fd[ s ]);
-    cmdtab[ i ].fd[ s ] = 0;
-}
-
-
-void populate_file_descriptors( int * fmax, fd_set * fds)
-{
-    int i, fd_max = 0;
-    struct tms buf;
-    clock_t current = times( &buf );
-    select_timeout = globs.timeout;
-
-    /* Compute max read file descriptor for use in select. */
-    FD_ZERO(fds);
-    for ( i = 0; i < globs.jobs; ++i )
-    {
-        if ( 0 < cmdtab[ i ].fd[ OUT ] )
-        {
-            fd_max = fd_max < cmdtab[ i ].fd[ OUT ] ? cmdtab[ i ].fd[ OUT ] : fd_max;
-            FD_SET(cmdtab[ i ].fd[ OUT ], fds);
-        }
-        if ( globs.pipe_action != 0 )
-        {
-            if (0 < cmdtab[ i ].fd[ ERR ])
-            {
-                fd_max = fd_max < cmdtab[ i ].fd[ ERR ] ? cmdtab[ i ].fd[ ERR ] : fd_max;
-                FD_SET(cmdtab[ i ].fd[ ERR ], fds);
-            }
-        }
-
-        if (globs.timeout && cmdtab[ i ].pid) {
-            clock_t consumed = (current - cmdtab[ i ].start_time) / tps;
-            clock_t process_timesout = globs.timeout - consumed;
-            if (0 < process_timesout && process_timesout < select_timeout) {
-                select_timeout = process_timesout;
-            }
-            if ( globs.timeout <= consumed )
-            {
-                killpg( cmdtab[ i ].pid, SIGKILL );
-                cmdtab[ i ].exit_reason = EXIT_TIMEOUT;
-            }
-        }
-    }
-    *fmax = fd_max;
-}
-
-
-/*
- * exec_wait() - wait and drive at most one execution completion.
- */
-
-int exec_wait()
-{
-    int         i;
-    int         ret;
-    int         fd_max;
-    int         pid;
-    int         status;
-    int         finished;
-    int         rstat;
-    timing_info time_info;
-    fd_set      fds;
-    struct tms  new_time;
-
-    /* Handle naive make1() which does not know if commands are running. */
-    if ( !cmdsrunning )
-        return 0;
-
-    /* Process children that signaled. */
-    finished = 0;
-    while ( !finished && cmdsrunning )
-    {
-        /* Compute max read file descriptor for use in select(). */
-        populate_file_descriptors( &fd_max, &fds );
-
-        if ( 0 < globs.timeout )
-        {
-            /* Force select() to timeout so we can terminate expired processes.
-             */
-            tv.tv_sec = select_timeout;
-            tv.tv_usec = 0;
-
-            /* select() will wait until: i/o on a descriptor, a signal, or we
-             * time out.
-             */
-            ret = select( fd_max + 1, &fds, 0, 0, &tv );
-        }
-        else
-        {
-            /* select() will wait until i/o on a descriptor or a signal. */
-            ret = select( fd_max + 1, &fds, 0, 0, 0 );
-        }
-
-        if ( 0 < ret )
-        {
-            for ( i = 0; i < globs.jobs; ++i )
-            {
-                int out = 0;
-                int err = 0;
-                if ( FD_ISSET( cmdtab[ i ].fd[ OUT ], &fds ) )
-                    out = read_descriptor( i, OUT );
-
-                if ( ( globs.pipe_action != 0 ) &&
-                    ( FD_ISSET( cmdtab[ i ].fd[ ERR ], &fds ) ) )
-                    err = read_descriptor( i, ERR );
-
-                /* If feof on either descriptor, then we are done. */
-                if ( out || err )
-                {
-                    /* Close the stream and pipe descriptors. */
-                    close_streams( i, OUT );
-                    if ( globs.pipe_action != 0 )
-                        close_streams( i, ERR );
-
-                    /* Reap the child and release resources. */
-                    pid = waitpid( cmdtab[ i ].pid, &status, 0 );
-
-                    if ( pid == cmdtab[ i ].pid )
-                    {
-                        finished = 1;
-                        pid = 0;
-                        cmdtab[ i ].pid = 0;
-
-                        /* Set reason for exit if not timed out. */
-                        if ( WIFEXITED( status ) )
-                        {
-                            cmdtab[ i ].exit_reason = 0 == WEXITSTATUS( status )
-                                ? EXIT_OK
-                                : EXIT_FAIL;
-                        }
-
-                        /* Print out the rule and target name. */
-                        out_action( cmdtab[ i ].action, cmdtab[ i ].target,
-                            cmdtab[ i ].command, cmdtab[ i ].buffer[ OUT ],
-                            cmdtab[ i ].buffer[ ERR ], cmdtab[ i ].exit_reason
-                        );
-
-                        times( &new_time );
-
-                        time_info.system = (double)( new_time.tms_cstime - old_time.tms_cstime ) / CLOCKS_PER_SEC;
-                        time_info.user   = (double)( new_time.tms_cutime - old_time.tms_cutime ) / CLOCKS_PER_SEC;
-                        time_info.start  = cmdtab[ i ].start_dt;
-                        time_info.end    = time( 0 );
-
-                        old_time = new_time;
-
-                        /* Drive the completion. */
-                        --cmdsrunning;
-
-                        if ( intr )
-                            rstat = EXEC_CMD_INTR;
-                        else if ( status != 0 )
-                            rstat = EXEC_CMD_FAIL;
-                        else
-                            rstat = EXEC_CMD_OK;
-
-                        /* Assume -p0 in effect so only pass buffer[ 0 ]
-                         * containing merged output.
-                         */
-                        (*cmdtab[ i ].func)( cmdtab[ i ].closure, rstat,
-                            &time_info, cmdtab[ i ].command,
-                            cmdtab[ i ].buffer[ 0 ] );
-
-                        BJAM_FREE( cmdtab[ i ].buffer[ OUT ] );
-                        cmdtab[ i ].buffer[ OUT ] = 0;
-
-                        BJAM_FREE( cmdtab[ i ].buffer[ ERR ] );
-                        cmdtab[ i ].buffer[ ERR ] = 0;
-
-                        BJAM_FREE( cmdtab[ i ].command );
-                        cmdtab[ i ].command = 0;
-
-                        cmdtab[ i ].func = 0;
-                        cmdtab[ i ].closure = 0;
-                        cmdtab[ i ].start_time = 0;
-                    }
-                    else
-                    {
-                        printf( "unknown pid %d with errno = %d\n", pid, errno );
-                        exit( EXITBAD );
-                    }
-                }
-            }
-        }
-    }
-
-    return 1;
-}
-
-# endif /* USE_EXECUNIX */
diff --git a/jam-files/engine/execvms.c b/jam-files/engine/execvms.c
deleted file mode 100644
index 729917d3..00000000
--- a/jam-files/engine/execvms.c
+++ /dev/null
@@ -1,161 +0,0 @@
-/*
- * Copyright 1993, 1995 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-#include "jam.h"
-#include "lists.h"
-#include "execcmd.h"
-
-#ifdef OS_VMS
-
-#include <stdio.h>
-#include <string.h>
-#include <stdlib.h>
-#include <iodef.h>
-#include <ssdef.h>
-#include <descrip.h>
-#include <dvidef.h>
-#include <clidef.h>
-
-/*
- * execvms.c - execute a shell script, ala VMS.
- *
- * The approach is this:
- *
- * If the command is a single line, and shorter than WRTLEN (what we believe to
- * be the maximum line length), we just system() it.
- *
- * If the command is multi-line, or longer than WRTLEN, we write the command
- * block to a temp file, splitting long lines (using "-" at the end of the line
- * to indicate contiuation), and then source that temp file. We use special
- * logic to make sure we do not continue in the middle of a quoted string.
- *
- * 05/04/94 (seiwald) - async multiprocess interface; noop on VMS
- * 12/20/96 (seiwald) - rewritten to handle multi-line commands well
- * 01/14/96 (seiwald) - do not put -'s between "'s
- */
-
-#define WRTLEN 240
-
-#define MIN( a, b ) ((a) < (b) ? (a) : (b))
-
-/* 1 for the @ and 4 for the .com */
-
-char tempnambuf[ L_tmpnam + 1 + 4 ] = { 0 };
-
-
-void exec_cmd
-(
-    char * string,
-    void (* func)( void * closure, int status, timing_info *, char *, char * ),
-    void * closure,
-    LIST * shell,
-    char * rule_name,
-    char * target
-)
-{
-    char * s;
-    char * e;
-    cahr * p;
-    int rstat = EXEC_CMD_OK;
-    int status;
-
-    /* See if string is more than one line discounting leading/trailing white
-     * space.
-     */
-    for ( s = string; *s && isspace( *s ); ++s );
-
-    e = p = strchr( s, '\n' );
-
-    while ( p && isspace( *p ) )
-        ++p;
-
-    /* If multi line or long, write to com file. Otherwise, exec directly. */
-    if ( ( p && *p ) || ( e - s > WRTLEN ) )
-    {
-        FILE * f;
-
-        /* Create temp file invocation "@sys$scratch:tempfile.com". */
-        if ( !*tempnambuf )
-        {
-            tempnambuf[0] = '@';
-            (void)tmpnam( tempnambuf + 1 );
-            strcat( tempnambuf, ".com" );
-        }
-
-        /* Open tempfile. */
-        if ( !( f = fopen( tempnambuf + 1, "w" ) ) )
-        {
-            printf( "can't open command file\n" );
-            (*func)( closure, EXEC_CMD_FAIL );
-            return;
-        }
-
-        /* For each line of the string. */
-        while ( *string )
-        {
-            char * s = strchr( string, '\n' );
-            int len = s ? s + 1 - string : strlen( string );
-
-            fputc( '$', f );
-
-            /* For each chunk of a line that needs to be split. */
-            while ( len > 0 )
-            {
-                char * q = string;
-                char * qe = string + MIN( len, WRTLEN );
-                char * qq = q;
-                int quote = 0;
-
-                /* Look for matching "s. */
-                for ( ; q < qe; ++q )
-                    if ( ( *q == '"' ) && ( quote = !quote ) )
-                        qq = q;
-
-                /* Back up to opening quote, if in one. */
-                if ( quote )
-                    q = qq;
-
-                fwrite( string, ( q - string ), 1, f );
-
-                len -= ( q - string );
-                string = q;
-
-                if ( len )
-                {
-                    fputc( '-', f );
-                    fputc( '\n', f );
-                }
-            }
-        }
-
-        fclose( f );
-
-        status = system( tempnambuf ) & 0x07;
-
-        unlink( tempnambuf + 1 );
-    }
-    else
-    {
-        /* Execute single line command. Strip trailing newline before execing.
-         */
-        if ( e ) *e = 0;
-        status = system( s ) & 0x07;
-    }
-
-    /* Fail for error or fatal error. OK on OK, warning or info exit. */
-    if ( ( status == 2 ) || ( status == 4 ) )
-        rstat = EXEC_CMD_FAIL;
-
-    (*func)( closure, rstat );
-}
-
-
-int exec_wait()
-{
-    return 0;
-}
-
-# endif /* VMS */
diff --git a/jam-files/engine/expand.c b/jam-files/engine/expand.c
deleted file mode 100644
index d8e58827..00000000
--- a/jam-files/engine/expand.c
+++ /dev/null
@@ -1,733 +0,0 @@
-/*
- * Copyright 1993-2002 Christopher Seiwald and Perforce Software, Inc.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-# include "jam.h"
-# include "lists.h"
-# include "variable.h"
-# include "expand.h"
-# include "pathsys.h"
-# include "newstr.h"
-# include <assert.h>
-# include <stdlib.h>
-# include <limits.h>
-
-# ifdef OS_CYGWIN
-#  include <sys/cygwin.h>
-#  include <windows.h>
-# endif
-
-/*
- * expand.c - expand a buffer, given variable values
- *
- * External routines:
- *
- *  var_expand() - variable-expand input string into list of strings
- *
- * Internal routines:
- *
- *  var_edit_parse() - parse : modifiers into PATHNAME structure.
- *  var_edit_file() - copy input target name to output, modifying filename.
- *  var_edit_shift() - do upshift/downshift mods.
- *
- * 01/25/94 (seiwald) - $(X)$(UNDEF) was expanding like plain $(X)
- * 04/13/94 (seiwald) - added shorthand L0 for null list pointer
- * 01/11/01 (seiwald) - added support for :E=emptyvalue, :J=joinval
- */
-
-typedef struct
-{
-    PATHNAME f;           /* :GDBSMR -- pieces */
-    char     parent;      /* :P -- go to parent directory */
-    char     filemods;    /* one of the above applied */
-    char     downshift;   /* :L -- downshift result */
-    char     upshift;     /* :U -- upshift result */
-    char     to_slashes;  /* :T -- convert "\" to "/" */
-    char     to_windows;  /* :W -- convert cygwin to native paths */
-    PATHPART empty;       /* :E -- default for empties */
-    PATHPART join;        /* :J -- join list with char */
-} VAR_EDITS ;
-
-static void var_edit_parse( char * mods, VAR_EDITS * edits );
-static void var_edit_file ( char * in, string * out, VAR_EDITS * edits );
-static void var_edit_shift( string * out, VAR_EDITS * edits );
-
-#define MAGIC_COLON '\001'
-#define MAGIC_LEFT  '\002'
-#define MAGIC_RIGHT '\003'
-
-
-/*
- * var_expand() - variable-expand input string into list of strings.
- *
- * Would just copy input to output, performing variable expansion, except that
- * since variables can contain multiple values the result of variable expansion
- * may contain multiple values (a list). Properly performs "product" operations
- * that occur in "$(var1)xxx$(var2)" or even "$($(var2))".
- *
- * Returns a newly created list.
- */
-
-LIST * var_expand( LIST * l, char * in, char * end, LOL * lol, int cancopyin )
-{
-    char out_buf[ MAXSYM ];
-    string buf[ 1 ];
-    string out1[ 1 ];  /* temporary buffer */
-    size_t prefix_length;
-    char * out;
-    char * inp = in;
-    char * ov;  /* for temp copy of variable in outbuf */
-    int depth;
-
-    if ( DEBUG_VAREXP )
-        printf( "expand '%.*s'\n", end - in, in );
-
-    /* This gets a lot of cases: $(<) and $(>). */
-    if
-    (
-        ( in[ 0 ] == '$'  ) &&
-        ( in[ 1 ] == '('  ) &&
-        ( in[ 3 ] == ')'  ) &&
-        ( in[ 4 ] == '\0' )
-    )
-    {
-        switch ( in[ 2 ] )
-        {
-            case '<': return list_copy( l, lol_get( lol, 0 ) );
-            case '>': return list_copy( l, lol_get( lol, 1 ) );
-
-            case '1':
-            case '2':
-            case '3':
-            case '4':
-            case '5':
-            case '6':
-            case '7':
-            case '8':
-            case '9':
-                return list_copy( l, lol_get( lol, in[ 2 ] - '1' ) );
-        }
-    }
-    else if ( in[0] == '$' && in[1] == '(' && in[2] == '1' && in[4] == ')' &&
-              in[5] == '\0') {
-
-        switch( in[3] )
-        {
-        case '0':
-        case '1':
-        case '2':
-        case '3':
-        case '4':
-        case '5':
-        case '6':
-        case '7':
-        case '8':
-        case '9':
-            return list_copy( l, lol_get( lol, in[3]-'0'+10-1 ) );
-        }
-    }
-
-    /* Expand @() files, to single item plus accompanying file. */
-    if ( ( in[ 0 ] == '@' ) && ( in[ 1 ] == '(' ) && ( *( end - 1 ) == ')' ) )
-    {
-        /* We try the expansion until it fits within the propective output
-         * buffer.
-         */
-        char * at_buf = 0;
-        int at_size = MAXJPATH;
-        int at_len = 0;
-        do
-        {
-            BJAM_FREE( at_buf );
-            at_buf = (char *)BJAM_MALLOC_ATOMIC( at_size + 1 );
-            at_len = var_string( in, at_buf, at_size, lol );
-            at_size *= 2;
-        }
-        while ( ( at_len < 0 ) && ( at_size < INT_MAX / 2 ) );
-        /* Return the result as a single item list. */
-        if ( at_len > 0 )
-        {
-            LIST * r;
-            string_copy( buf, at_buf );
-            r = list_new( l, newstr( buf->value ) );
-            string_free( buf );
-            BJAM_FREE( at_buf );
-            return r;
-        }
-        BJAM_FREE( at_buf );
-    }
-
-    /* Just try simple copy of in to out. */
-    while ( in < end )
-        if ( ( *in++ == '$' ) && ( *in == '(' ) )
-            goto expand;
-
-    /* No variables expanded - just add copy of input string to list. */
-
-    /* 'cancopyin' is an optimization: if the input was already a list item, we
-     * can use copystr() to put it on the new list. Otherwise, we use the slower
-     * newstr().
-     */
-    if ( cancopyin )
-        return list_new( l, copystr( inp ) );
-
-    {
-        LIST * r;
-        string_new( buf );
-        string_append_range( buf, inp, end );
-        r = list_new( l, newstr( buf->value ) );
-        string_free( buf );
-        return r;
-    }
-
-expand:
-    string_new( buf );
-    string_append_range( buf, inp, in - 1 );  /* Copy the part before '$'. */
-    /*
-     * Input so far (ignore blanks):
-     *
-     *  stuff-in-outbuf $(variable) remainder
-     *                   ^                   ^
-     *                   in                  end
-     * Output so far:
-     *
-     *  stuff-in-outbuf $
-     *  ^                ^
-     *  out_buf          out
-     *
-     *
-     * We just copied the $ of $(...), so back up one on the output. We now find
-     * the matching close paren, copying the variable and modifiers between the
-     * $( and ) temporarily into out_buf, so that we can replace :'s with
-     * MAGIC_COLON. This is necessary to avoid being confused by modifier values
-     * that are variables containing :'s. Ugly.
-     */
-
-    depth = 1;
-    inp = ++in;  /* Skip over the '('. */
-
-    while ( ( in < end ) && depth )
-    {
-        switch ( *in++ )
-        {
-            case '(': ++depth; break;
-            case ')': --depth; break;
-        }
-    }
-
-    /*
-     * Input so far (ignore blanks):
-     *
-     *  stuff-in-outbuf $(variable) remainder
-     *                    ^        ^         ^
-     *                    inp      in        end
-     */
-    prefix_length = buf->size;
-    string_append_range( buf, inp, in - 1 );
-
-    out = buf->value + prefix_length;
-    for ( ov = out; ov < buf->value + buf->size; ++ov )
-    {
-        switch ( *ov )
-        {
-            case ':': *ov = MAGIC_COLON; break;
-            case '[': *ov = MAGIC_LEFT ; break;
-            case ']': *ov = MAGIC_RIGHT; break;
-        }
-    }
-
-    /*
-     * Input so far (ignore blanks):
-     *
-     *  stuff-in-outbuf $(variable) remainder
-     *                              ^        ^
-     *                              in       end
-     * Output so far:
-     *
-     *  stuff-in-outbuf variable
-     *  ^               ^       ^
-     *  out_buf         out     ov
-     *
-     * Later we will overwrite 'variable' in out_buf, but we will be done with
-     * it by then. 'variable' may be a multi-element list, so may each value for
-     * '$(variable element)', and so may 'remainder'. Thus we produce a product
-     * of three lists.
-     */
-    {
-        LIST * variables = 0;
-        LIST * remainder = 0;
-        LIST * vars;
-
-        /* Recursively expand variable name & rest of input. */
-        if ( out < ov ) variables = var_expand( L0, out, ov, lol, 0 );
-        if ( in < end ) remainder = var_expand( L0, in, end, lol, 0 );
-
-        /* Now produce the result chain. */
-
-        /* For each variable name. */
-        for ( vars = variables; vars; vars = list_next( vars ) )
-        {
-            LIST * value = 0;
-            LIST * evalue = 0;
-            char * colon;
-            char * bracket;
-            string variable[1];
-            char * varname;
-            int sub1 = 0;
-            int sub2 = -1;
-            VAR_EDITS edits;
-
-            /* Look for a : modifier in the variable name. Must copy into
-             * varname so we can modify it.
-             */
-            string_copy( variable, vars->string );
-            varname = variable->value;
-
-            if ( ( colon = strchr( varname, MAGIC_COLON ) ) )
-            {
-                string_truncate( variable, colon - varname );
-                var_edit_parse( colon + 1, &edits );
-            }
-
-            /* Look for [x-y] subscripting. sub1 and sub2 are x and y. */
-            if ( ( bracket = strchr( varname, MAGIC_LEFT ) ) )
-            {
-                /* Make all syntax errors in [] subscripting result in the same
-                 * behavior: silenty return an empty expansion (by setting sub2
-                 * = 0). Brute force parsing; May get moved into yacc someday.
-                 */
-
-                char * s = bracket + 1;
-
-                string_truncate( variable, bracket - varname );
-
-                do  /* so we can use "break" */
-                {
-                    /* Allow negative indexes. */
-                    if ( !isdigit( *s ) && ( *s != '-' ) )
-                    {
-                        sub2 = 0;
-                        break;
-                    }
-                    sub1 = atoi( s );
-
-                    /* Skip over the first symbol, which is either a digit or dash. */
-                    ++s;
-                    while ( isdigit( *s ) ) ++s;
-
-                    if ( *s == MAGIC_RIGHT )
-                    {
-                        sub2 = sub1;
-                        break;
-                    }
-
-                    if ( *s != '-' )
-                    {
-                        sub2 = 0;
-                        break;
-                    }
-
-                    ++s;
-
-                    if ( *s == MAGIC_RIGHT )
-                    {
-                        sub2 = -1;
-                        break;
-                    }
-
-                    if ( !isdigit( *s ) && ( *s != '-' ) )
-                    {
-                        sub2 = 0;
-                        break;
-                    }
-
-                    /* First, compute the index of the last element. */
-                    sub2 = atoi( s );
-                    while ( isdigit( *++s ) );
-
-                    if ( *s != MAGIC_RIGHT )
-                        sub2 = 0;
-
-                } while ( 0 );
-
-                /* Anything but the end of the string, or the colon introducing
-                 * a modifier is a syntax error.
-                 */
-                ++s;
-                if ( *s && ( *s != MAGIC_COLON ) )
-                    sub2 = 0;
-
-                *bracket = '\0';
-            }
-
-            /* Get variable value, with special handling for $(<), $(>), $(n).
-             */
-            if ( !varname[1] )
-            {
-                if ( varname[0] == '<' )
-                    value = lol_get( lol, 0 );
-                else if ( varname[0] == '>' )
-                    value = lol_get( lol, 1 );
-                else if ( ( varname[0] >= '1' ) && ( varname[0] <= '9' ) )
-                    value = lol_get( lol, varname[0] - '1' );
-                else if( varname[0] == '1' && varname[1] >= '0' &&
-                     varname[1] <= '9' && !varname[2] )
-                value = lol_get( lol, varname[1] - '0' + 10 - 1 );
-            }
-
-            if ( !value )
-                value = var_get( varname );
-
-            /* Handle negitive indexes: part two. */
-            {
-                int length = list_length( value );
-
-                if ( sub1 < 0 )
-                    sub1 = length + sub1;
-                else
-                    sub1 -= 1;
-
-                if ( sub2 < 0 )
-                    sub2 = length + 1 + sub2 - sub1;
-                else
-                    sub2 -= sub1;
-                /* The "sub2 < 0" test handles the semantic error of sub2 <
-                 * sub1.
-                 */
-                if ( sub2 < 0 )
-                    sub2 = 0;
-            }
-
-            /* The fast path: $(x) - just copy the variable value. This is only
-             * an optimization.
-             */
-            if ( ( out == out_buf ) && !bracket && !colon && ( in == end ) )
-            {
-                string_free( variable );
-                l = list_copy( l, value );
-                continue;
-            }
-
-            /* Handle start subscript. */
-            while ( ( sub1 > 0 ) && value )
-                --sub1, value = list_next( value );
-
-            /* Empty w/ :E=default?. */
-            if ( !value && colon && edits.empty.ptr )
-                evalue = value = list_new( L0, newstr( edits.empty.ptr ) );
-
-            /* For each variable value. */
-            string_new( out1 );
-            for ( ; value; value = list_next( value ) )
-            {
-                LIST * rem;
-                size_t postfix_start;
-
-                /* Handle end subscript (length actually). */
-
-                if ( sub2 >= 0 && --sub2 < 0 )
-                    break;
-
-                string_truncate( buf, prefix_length );
-
-                /* Apply : mods, if present */
-
-                if ( colon && edits.filemods )
-                    var_edit_file( value->string, out1, &edits );
-                else
-                    string_append( out1, value->string );
-
-                if ( colon && ( edits.upshift || edits.downshift || edits.to_slashes || edits.to_windows ) )
-                    var_edit_shift( out1, &edits );
-
-                /* Handle :J=joinval */
-                /* If we have more values for this var, just keep appending them
-                 * (using the join value) rather than creating separate LIST
-                 * elements.
-                 */
-                if ( colon && edits.join.ptr &&
-                    ( list_next( value ) || list_next( vars ) ) )
-                {
-                    string_append( out1, edits.join.ptr );
-                    continue;
-                }
-
-                string_append( buf, out1->value );
-                string_free( out1 );
-                string_new( out1 );
-
-                /* If no remainder, append result to output chain. */
-                if ( in == end )
-                {
-                    l = list_new( l, newstr( buf->value ) );
-                    continue;
-                }
-
-                /* For each remainder, append the complete string to the output
-                 * chain. Remember the end of the variable expansion so we can
-                 * just tack on each instance of 'remainder'.
-                 */
-                postfix_start = buf->size;
-                for ( rem = remainder; rem; rem = list_next( rem ) )
-                {
-                    string_truncate( buf, postfix_start );
-                    string_append( buf, rem->string );
-                    l = list_new( l, newstr( buf->value ) );
-                }
-            }
-            string_free( out1 );
-
-            /* Toss used empty. */
-            if ( evalue )
-                list_free( evalue );
-
-            string_free( variable );
-        }
-
-        /* variables & remainder were gifts from var_expand and must be freed. */
-        if ( variables ) list_free( variables );
-        if ( remainder ) list_free( remainder );
-
-        if ( DEBUG_VAREXP )
-        {
-            printf( "expanded to " );
-            list_print( l );
-            printf( "\n" );
-        }
-
-        string_free( buf );
-        return l;
-    }
-}
-
-
-/*
- * var_edit_parse() - parse : modifiers into PATHNAME structure
- *
- * The : modifiers in a $(varname:modifier) currently support replacing or
- * omitting elements of a filename, and so they are parsed into a PATHNAME
- * structure (which contains pointers into the original string).
- *
- * Modifiers of the form "X=value" replace the component X with the given value.
- * Modifiers without the "=value" cause everything but the component X to be
- * omitted. X is one of:
- *
- *  G <grist>
- *  D directory name
- *  B base name
- *  S .suffix
- *  M (member)
- *  R root directory - prepended to whole path
- *
- * This routine sets:
- *
- *  f->f_xxx.ptr = 0
- *  f->f_xxx.len = 0
- *      -> leave the original component xxx
- *
- *  f->f_xxx.ptr = string
- *  f->f_xxx.len = strlen( string )
- *      -> replace component xxx with string
- *
- *  f->f_xxx.ptr = ""
- *  f->f_xxx.len = 0
- *      -> omit component xxx
- *
- * var_edit_file() below and path_build() obligingly follow this convention.
- */
-
-static void var_edit_parse( char * mods, VAR_EDITS * edits )
-{
-    int havezeroed = 0;
-    memset( (char *)edits, 0, sizeof( *edits ) );
-
-    while ( *mods )
-    {
-        char * p;
-        PATHPART * fp;
-
-        switch ( *mods++ )
-        {
-            case 'L': edits->downshift = 1; continue;
-            case 'U': edits->upshift = 1; continue;
-            case 'P': edits->parent = edits->filemods = 1; continue;
-            case 'E': fp = &edits->empty; goto strval;
-            case 'J': fp = &edits->join; goto strval;
-            case 'G': fp = &edits->f.f_grist; goto fileval;
-            case 'R': fp = &edits->f.f_root; goto fileval;
-            case 'D': fp = &edits->f.f_dir; goto fileval;
-            case 'B': fp = &edits->f.f_base; goto fileval;
-            case 'S': fp = &edits->f.f_suffix; goto fileval;
-            case 'M': fp = &edits->f.f_member; goto fileval;
-            case 'T': edits->to_slashes = 1; continue;
-            case 'W': edits->to_windows = 1; continue;
-            default:
-                return;  /* Should complain, but so what... */
-        }
-
-    fileval:
-        /* Handle :CHARS, where each char (without a following =) selects a
-         * particular file path element. On the first such char, we deselect all
-         * others (by setting ptr = "", len = 0) and for each char we select
-         * that element (by setting ptr = 0).
-         */
-        edits->filemods = 1;
-
-        if ( *mods != '=' )
-        {
-            if ( !havezeroed++ )
-            {
-                int i;
-                for ( i = 0; i < 6; ++i )
-                {
-                    edits->f.part[ i ].len = 0;
-                    edits->f.part[ i ].ptr = "";
-                }
-            }
-
-            fp->ptr = 0;
-            continue;
-        }
-
-    strval:
-        /* Handle :X=value, or :X */
-        if ( *mods != '=' )
-        {
-            fp->ptr = "";
-            fp->len = 0;
-        }
-        else if ( ( p = strchr( mods, MAGIC_COLON ) ) )
-        {
-            *p = 0;
-            fp->ptr = ++mods;
-            fp->len = p - mods;
-            mods = p + 1;
-        }
-        else
-        {
-            fp->ptr = ++mods;
-            fp->len = strlen( mods );
-            mods += fp->len;
-        }
-    }
-}
-
-
-/*
- * var_edit_file() - copy input target name to output, modifying filename.
- */
-
-static void var_edit_file( char * in, string * out, VAR_EDITS * edits )
-{
-    PATHNAME pathname;
-
-    /* Parse apart original filename, putting parts into "pathname". */
-    path_parse( in, &pathname );
-
-    /* Replace any pathname with edits->f */
-    if ( edits->f.f_grist .ptr ) pathname.f_grist  = edits->f.f_grist;
-    if ( edits->f.f_root  .ptr ) pathname.f_root   = edits->f.f_root;
-    if ( edits->f.f_dir   .ptr ) pathname.f_dir    = edits->f.f_dir;
-    if ( edits->f.f_base  .ptr ) pathname.f_base   = edits->f.f_base;
-    if ( edits->f.f_suffix.ptr ) pathname.f_suffix = edits->f.f_suffix;
-    if ( edits->f.f_member.ptr ) pathname.f_member = edits->f.f_member;
-
-    /* If requested, modify pathname to point to parent. */
-    if ( edits->parent )
-        path_parent( &pathname );
-
-    /* Put filename back together. */
-    path_build( &pathname, out, 0 );
-}
-
-
-/*
- * var_edit_shift() - do upshift/downshift mods.
- */
-
-static void var_edit_shift( string * out, VAR_EDITS * edits )
-{
-    /* Handle upshifting, downshifting and slash translation now. */
-    char * p;
-    for ( p = out->value; *p; ++p)
-    {
-        if ( edits->upshift )
-            *p = toupper( *p );
-        else if ( edits->downshift )
-            *p = tolower( *p );
-        if ( edits->to_slashes && ( *p == '\\' ) )
-            *p = '/';
-# ifdef OS_CYGWIN
-        if ( edits->to_windows )
-        {
-            char result[ MAX_PATH + 1 ];
-            cygwin_conv_to_win32_path( out->value, result );
-            assert( strlen( result ) <= MAX_PATH );
-            string_free( out );
-            string_copy( out, result );
-        }
-# endif
-    }
-    out->size = p - out->value;
-}
-
-
-#ifndef NDEBUG
-void var_expand_unit_test()
-{
-    LOL lol[ 1 ];
-    LIST * l;
-    LIST * l2;
-    LIST * expected = list_new( list_new( L0, newstr( "axb" ) ), newstr( "ayb" ) );
-    LIST * e2;
-    char axyb[] = "a$(xy)b";
-    char azb[] = "a$($(z))b";
-    char path[] = "$(p:W)";
-
-# ifdef OS_CYGWIN
-    char cygpath[ 256 ];
-    cygwin_conv_to_posix_path( "c:\\foo\\bar", cygpath );
-# else
-    char cygpath[] = "/cygdrive/c/foo/bar";
-# endif
-
-    lol_init(lol);
-    var_set( "xy", list_new( list_new( L0, newstr( "x" ) ), newstr( "y" ) ), VAR_SET );
-    var_set( "z", list_new( L0, newstr( "xy" ) ), VAR_SET );
-    var_set( "p", list_new( L0, newstr( cygpath ) ), VAR_SET );
-
-    l = var_expand( 0, axyb, axyb + sizeof( axyb ) - 1, lol, 0 );
-    for ( l2 = l, e2 = expected; l2 && e2; l2 = list_next( l2 ), e2 = list_next( e2 ) )
-        assert( !strcmp( e2->string, l2->string ) );
-    assert( l2 == 0 );
-    assert( e2 == 0 );
-    list_free( l );
-
-    l = var_expand( 0, azb, azb + sizeof( azb ) - 1, lol, 0 );
-    for ( l2 = l, e2 = expected; l2 && e2; l2 = list_next( l2 ), e2 = list_next( e2 ) )
-        assert( !strcmp( e2->string, l2->string ) );
-    assert( l2 == 0 );
-    assert( e2 == 0 );
-    list_free( l );
-
-    l = var_expand( 0, path, path + sizeof( path ) - 1, lol, 0 );
-    assert( l != 0 );
-    assert( list_next( l ) == 0 );
-# ifdef OS_CYGWIN
-    /* On some installations of cygwin the drive letter is expanded to other
-     * case. This has been reported to be the case if cygwin has been installed
-     * to C:\ as opposed to C:\cygwin. Since case of the drive letter will not
-     * matter, we allow for both.
-     */
-    assert( !strcmp( l->string, "c:\\foo\\bar" ) ||
-            !strcmp( l->string, "C:\\foo\\bar" ) );
-# else
-    assert( !strcmp( l->string, cygpath ) );
-# endif
-    list_free( l );
-    list_free( expected );
-    lol_free( lol );
-}
-#endif
diff --git a/jam-files/engine/expand.h b/jam-files/engine/expand.h
deleted file mode 100644
index cc25d190..00000000
--- a/jam-files/engine/expand.h
+++ /dev/null
@@ -1,14 +0,0 @@
-/*
- * Copyright 1993, 1995 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*
- * expand.h - expand a buffer, given variable values
- */
-
-#include "lists.h"
-
-LIST *var_expand( LIST  *l, char *in, char *end, LOL *lol, int cancopyin );
-void var_expand_unit_test();
diff --git a/jam-files/engine/filemac.c b/jam-files/engine/filemac.c
deleted file mode 100644
index e69aa648..00000000
--- a/jam-files/engine/filemac.c
+++ /dev/null
@@ -1,175 +0,0 @@
-/*
- * Copyright 1993-2002 Christopher Seiwald and Perforce Software, Inc.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*  This file is ALSO:
- *  Copyright 2001-2004 David Abrahams.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-
-# include "jam.h"
-# include "filesys.h"
-# include "pathsys.h"
-
-# ifdef OS_MAC
-
-#include <Files.h>
-#include <Folders.h>
-
-# include <:sys:stat.h>
-
-/*
- * filemac.c - manipulate file names and scan directories on macintosh
- *
- * External routines:
- *
- *  file_dirscan() - scan a directory for files
- *  file_time() - get timestamp of file, if not done by file_dirscan()
- *  file_archscan() - scan an archive for files
- *
- * File_dirscan() and file_archscan() call back a caller provided function
- * for each file found.  A flag to this callback function lets file_dirscan()
- * and file_archscan() indicate that a timestamp is being provided with the
- * file.   If file_dirscan() or file_archscan() do not provide the file's
- * timestamp, interested parties may later call file_time().
- *
- * 04/08/94 (seiwald) - Coherent/386 support added.
- * 12/19/94 (mikem) - solaris string table insanity support
- * 02/14/95 (seiwald) - parse and build /xxx properly
- * 05/03/96 (seiwald) - split into pathunix.c
- * 11/21/96 (peterk) - BEOS does not have Unix-style archives
- */
-
-
-void CopyC2PStr( char const * cstr, StringPtr pstr )
-{
-    int len;
-    for ( len = 0; *cstr && ( len < 255 ); pstr[ ++len ] = *cstr++ );
-    pstr[ 0 ] = len;
-}
-
-
-/*
- * file_dirscan() - scan a directory for files.
- */
-
-void file_dirscan( char * dir, scanback func, void * closure )
-{
-    PATHNAME f;
-    string filename[ 1 ];
-    unsigned char fullPath[ 512 ];
-
-    FSSpec spec;
-    WDPBRec vol;
-    Str63 volName;
-    CInfoPBRec lastInfo;
-    int index = 1;
-
-    /* First enter directory itself. */
-
-    memset( (char *)&f, '\0', sizeof( f ) );
-
-    f.f_dir.ptr = dir;
-    f.f_dir.len = strlen(dir);
-
-    if ( DEBUG_BINDSCAN )
-        printf( "scan directory %s\n", dir );
-
-    /* Special case ":" - enter it */
-
-    if ( ( f.f_dir.len == 1 ) && ( f.f_dir.ptr[0] == ':' ) )
-        (*func)( closure, dir, 0 /* not stat()'ed */, (time_t)0 );
-
-    /* Now enter contents of directory */
-
-    vol.ioNamePtr = volName;
-
-    if ( PBHGetVolSync( &vol ) )
-        return;
-
-    CopyC2PStr( dir, fullPath );
-
-    if ( FSMakeFSSpec( vol.ioWDVRefNum, vol.ioWDDirID, fullPath, &spec ) )
-        return;
-
-    lastInfo.dirInfo.ioVRefNum   = spec.vRefNum;
-    lastInfo.dirInfo.ioDrDirID   = spec.parID;
-    lastInfo.dirInfo.ioNamePtr   = spec.name;
-    lastInfo.dirInfo.ioFDirIndex = 0;
-    lastInfo.dirInfo.ioACUser    = 0;
-
-    if ( PBGetCatInfoSync( &lastInfo ) )
-        return;
-
-    if ( !( lastInfo.dirInfo.ioFlAttrib & 0x10 ) )
-        return;
-
-    /* ioDrDirID must be reset each time. */
-    spec.parID = lastInfo.dirInfo.ioDrDirID;
-
-    string_new( filename );
-    for ( ; ; )
-    {
-        lastInfo.dirInfo.ioVRefNum  = spec.vRefNum;
-        lastInfo.dirInfo.ioDrDirID  = spec.parID;
-        lastInfo.dirInfo.ioNamePtr  = fullPath;
-        lastInfo.dirInfo.ioFDirIndex = index++;
-
-        if ( PBGetCatInfoSync( &lastInfo ) )
-            return;
-
-        f.f_base.ptr = (char *)fullPath + 1;
-        f.f_base.len = *fullPath;
-
-        string_truncate( filename, 0 );
-        path_build( &f, filename, 0 );
-        (*func)( closure, filename->value, 0 /* not stat()'ed */, (time_t)0 );
-    }
-    string_free( filename );
-}
-
-
-/*
- * file_time() - get timestamp of file, if not done by file_dirscan().
- */
-
-int file_time( char * filename, time_t * time )
-{
-    struct stat statbuf;
-
-    if ( stat( filename, &statbuf ) < 0 )
-        return -1;
-
-    *time = statbuf.st_mtime;
-
-    return 0;
-}
-
-
-int file_is_file( char * filename )
-{
-    struct stat statbuf;
-    if ( stat( filename, &statbuf ) < 0 )
-        return -1;
-    return S_ISREG( statbuf.st_mode ) ? 1 : 0;
-}
-
-int file_mkdir(char *pathname)
-{
-    return mkdir(pathname, 0766);
-}
-
-
-/*
- * file_archscan() - scan an archive for files.
- */
-
-void file_archscan( char * archive, scanback func, void * closure )
-{
-}
-
-
-# endif /* macintosh */
diff --git a/jam-files/engine/filent.c b/jam-files/engine/filent.c
deleted file mode 100644
index ab189576..00000000
--- a/jam-files/engine/filent.c
+++ /dev/null
@@ -1,387 +0,0 @@
-/*
- * Copyright 1993, 1995 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*  This file is ALSO:
- *  Copyright 2001-2004 David Abrahams.
- *  Copyright 2005 Rene Rivera.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-
-# include "jam.h"
-
-# include "filesys.h"
-# include "pathsys.h"
-# include "strings.h"
-# include "newstr.h"
-
-# ifdef OS_NT
-
-# ifdef __BORLANDC__
-# if __BORLANDC__ < 0x550
-# include <dir.h>
-# include <dos.h>
-# endif
-# undef FILENAME    /* cpp namespace collision */
-# define _finddata_t ffblk
-# endif
-
-# include <io.h>
-# include <sys/stat.h>
-# include <ctype.h>
-# include <direct.h>
-
-/*
- * filent.c - scan directories and archives on NT
- *
- * External routines:
- *
- *  file_dirscan() - scan a directory for files
- *  file_time() - get timestamp of file, if not done by file_dirscan()
- *  file_archscan() - scan an archive for files
- *
- * File_dirscan() and file_archscan() call back a caller provided function
- * for each file found.  A flag to this callback function lets file_dirscan()
- * and file_archscan() indicate that a timestamp is being provided with the
- * file.   If file_dirscan() or file_archscan() do not provide the file's
- * timestamp, interested parties may later call file_time().
- *
- * 07/10/95 (taylor)  Findfirst() returns the first file on NT.
- * 05/03/96 (seiwald) split apart into pathnt.c
- */
-
-/*
- * file_dirscan() - scan a directory for files
- */
-
-void file_dirscan( char * dir, scanback func, void * closure )
-{
-    PROFILE_ENTER( FILE_DIRSCAN );
-
-    file_info_t * d = 0;
-
-    dir = short_path_to_long_path( dir );
-
-    /* First enter directory itself */
-
-    d = file_query( dir );
-
-    if ( !d || !d->is_dir )
-    {
-        PROFILE_EXIT( FILE_DIRSCAN );
-        return;
-    }
-
-    if ( !d->files )
-    {
-        PATHNAME f;
-        string filespec[ 1 ];
-        string filename[ 1 ];
-        long handle;
-        int ret;
-        struct _finddata_t finfo[ 1 ];
-        LIST * files = L0;
-        int d_length = strlen( d->name );
-
-        memset( (char *)&f, '\0', sizeof( f ) );
-
-        f.f_dir.ptr = d->name;
-        f.f_dir.len = d_length;
-
-        /* Now enter contents of directory */
-
-        /* Prepare file search specification for the findfirst() API. */
-        if ( d_length == 0 )
-            string_copy( filespec, ".\\*" );
-        else
-        {
-            /*
-             * We can not simply assume the given folder name will never include
-             * its trailing path separator or otherwise we would not support the
-             * Windows root folder specified without its drive letter, i.e. '\'.
-             */
-            char trailingChar = d->name[ d_length - 1 ] ;
-            string_copy( filespec, d->name );
-            if ( ( trailingChar != '\\' ) && ( trailingChar != '/' ) )
-                string_append( filespec, "\\" );
-            string_append( filespec, "*" );
-        }
-
-        if ( DEBUG_BINDSCAN )
-            printf( "scan directory %s\n", dir );
-
-        #if defined(__BORLANDC__) && __BORLANDC__ < 0x550
-        if ( ret = findfirst( filespec->value, finfo, FA_NORMAL | FA_DIREC ) )
-        {
-            string_free( filespec );
-            PROFILE_EXIT( FILE_DIRSCAN );
-            return;
-        }
-
-        string_new ( filename );
-        while ( !ret )
-        {
-            file_info_t * ff = 0;
-
-            f.f_base.ptr = finfo->ff_name;
-            f.f_base.len = strlen( finfo->ff_name );
-
-            string_truncate( filename, 0 );
-            path_build( &f, filename );
-
-            files = list_new( files, newstr(filename->value) );
-            ff = file_info( filename->value );
-            ff->is_file = finfo->ff_attrib & FA_DIREC ? 0 : 1;
-            ff->is_dir = finfo->ff_attrib & FA_DIREC ? 1 : 0;
-            ff->size = finfo->ff_fsize;
-            ff->time = (finfo->ff_ftime << 16) | finfo->ff_ftime;
-
-            ret = findnext( finfo );
-        }
-        # else
-        handle = _findfirst( filespec->value, finfo );
-
-        if ( ret = ( handle < 0L ) )
-        {
-            string_free( filespec );
-            PROFILE_EXIT( FILE_DIRSCAN );
-            return;
-        }
-
-        string_new( filename );
-        while ( !ret )
-        {
-            file_info_t * ff = 0;
-
-            f.f_base.ptr = finfo->name;
-            f.f_base.len = strlen( finfo->name );
-
-            string_truncate( filename, 0 );
-            path_build( &f, filename, 0 );
-
-            files = list_new( files, newstr( filename->value ) );
-            ff = file_info( filename->value );
-            ff->is_file = finfo->attrib & _A_SUBDIR ? 0 : 1;
-            ff->is_dir = finfo->attrib & _A_SUBDIR ? 1 : 0;
-            ff->size = finfo->size;
-            ff->time = finfo->time_write;
-
-            ret = _findnext( handle, finfo );
-        }
-
-        _findclose( handle );
-        # endif
-        string_free( filename );
-        string_free( filespec );
-
-        d->files = files;
-    }
-
-    /* Special case \ or d:\ : enter it */
-    {
-        unsigned long len = strlen(d->name);
-        if ( len == 1 && d->name[0] == '\\' )
-            (*func)( closure, d->name, 1 /* stat()'ed */, d->time );
-        else if ( len == 3 && d->name[1] == ':' ) {
-            (*func)( closure, d->name, 1 /* stat()'ed */, d->time );
-            /* We've just entered 3-letter drive name spelling (with trailing
-               slash), into the hash table. Now enter two-letter variant,
-               without trailing slash, so that if we try to check whether
-               "c:" exists, we hit it.
-
-               Jam core has workarounds for that. Given:
-                  x = c:\whatever\foo ;
-                  p = $(x:D) ;
-                  p2 = $(p:D) ;
-               There will be no trailing slash in $(p), but there will be one
-               in $(p2). But, that seems rather fragile.                
-            */
-            d->name[2] = 0;
-            (*func)( closure, d->name, 1 /* stat()'ed */, d->time );
-        }
-    }
-
-    /* Now enter contents of directory */
-    if ( d->files )
-    {
-        LIST * files = d->files;
-        while ( files )
-        {
-            file_info_t * ff = file_info( files->string );
-            (*func)( closure, ff->name, 1 /* stat()'ed */, ff->time );
-            files = list_next( files );
-        }
-    }
-
-    PROFILE_EXIT( FILE_DIRSCAN );
-}
-
-file_info_t * file_query( char * filename )
-{
-    file_info_t * ff = file_info( filename );
-    if ( ! ff->time )
-    {
-        struct stat statbuf;
-
-        if ( stat( *filename ? filename : ".", &statbuf ) < 0 )
-            return 0;
-
-        ff->is_file = statbuf.st_mode & S_IFREG ? 1 : 0;
-        ff->is_dir = statbuf.st_mode & S_IFDIR ? 1 : 0;
-        ff->size = statbuf.st_size;
-        ff->time = statbuf.st_mtime ? statbuf.st_mtime : 1;
-    }
-    return ff;
-}
-
-/*
- * file_time() - get timestamp of file, if not done by file_dirscan()
- */
-
-int
-file_time(
-    char    *filename,
-    time_t  *time )
-{
-    file_info_t * ff = file_query( filename );
-    if ( !ff ) return -1;
-    *time = ff->time;
-    return 0;
-}
-
-int file_is_file(char* filename)
-{
-    file_info_t * ff = file_query( filename );
-    if ( !ff ) return -1;
-    return ff->is_file;
-}
-
-int file_mkdir(char *pathname)
-{
-    return _mkdir(pathname);
-}
-
-/*
- * file_archscan() - scan an archive for files
- */
-
-/* Straight from SunOS */
-
-#define ARMAG   "!<arch>\n"
-#define SARMAG  8
-
-#define ARFMAG  "`\n"
-
-struct ar_hdr {
-    char    ar_name[16];
-    char    ar_date[12];
-    char    ar_uid[6];
-    char    ar_gid[6];
-    char    ar_mode[8];
-    char    ar_size[10];
-    char    ar_fmag[2];
-};
-
-# define SARFMAG 2
-# define SARHDR sizeof( struct ar_hdr )
-
-void
-file_archscan(
-    char *archive,
-    scanback func,
-    void *closure )
-{
-    struct ar_hdr ar_hdr;
-    char *string_table = 0;
-    char buf[ MAXJPATH ];
-    long offset;
-    int fd;
-
-    if ( ( fd = open( archive, O_RDONLY | O_BINARY, 0 ) ) < 0 )
-        return;
-
-    if ( read( fd, buf, SARMAG ) != SARMAG ||
-        strncmp( ARMAG, buf, SARMAG ) )
-    {
-        close( fd );
-        return;
-    }
-
-    offset = SARMAG;
-
-    if ( DEBUG_BINDSCAN )
-        printf( "scan archive %s\n", archive );
-
-    while ( ( read( fd, &ar_hdr, SARHDR ) == SARHDR ) &&
-           !memcmp( ar_hdr.ar_fmag, ARFMAG, SARFMAG ) )
-    {
-        long    lar_date;
-        long    lar_size;
-        char    *name = 0;
-        char    *endname;
-        char    *c;
-
-        sscanf( ar_hdr.ar_date, "%ld", &lar_date );
-        sscanf( ar_hdr.ar_size, "%ld", &lar_size );
-
-        lar_size = ( lar_size + 1 ) & ~1;
-
-        if (ar_hdr.ar_name[0] == '/' && ar_hdr.ar_name[1] == '/' )
-        {
-        /* this is the "string table" entry of the symbol table,
-        ** which holds strings of filenames that are longer than
-        ** 15 characters (ie. don't fit into a ar_name
-        */
-
-        string_table = BJAM_MALLOC_ATOMIC(lar_size+1);
-        if (read(fd, string_table, lar_size) != lar_size)
-            printf("error reading string table\n");
-        string_table[lar_size] = '\0';
-        offset += SARHDR + lar_size;
-        continue;
-        }
-        else if (ar_hdr.ar_name[0] == '/' && ar_hdr.ar_name[1] != ' ')
-        {
-            /* Long filenames are recognized by "/nnnn" where nnnn is
-            ** the offset of the string in the string table represented
-            ** in ASCII decimals.
-            */
-
-            name = string_table + atoi( ar_hdr.ar_name + 1 );
-            for ( endname = name; *endname && *endname != '\n'; ++endname) {}
-        }
-        else
-        {
-            /* normal name */
-            name = ar_hdr.ar_name;
-            endname = name + sizeof( ar_hdr.ar_name );
-        }
-
-        /* strip trailing white-space, slashes, and backslashes */
-
-        while ( endname-- > name )
-            if ( !isspace(*endname) && ( *endname != '\\' ) && ( *endname != '/' ) )
-                break;
-        *++endname = 0;
-
-        /* strip leading directory names, an NT specialty */
-
-        if ( c = strrchr( name, '/' ) )
-        name = c + 1;
-        if ( c = strrchr( name, '\\' ) )
-        name = c + 1;
-
-        sprintf( buf, "%s(%.*s)", archive, endname - name, name );
-        (*func)( closure, buf, 1 /* time valid */, (time_t)lar_date );
-
-        offset += SARHDR + lar_size;
-        lseek( fd, offset, 0 );
-    }
-
-    close( fd );
-}
-
-# endif /* NT */
diff --git a/jam-files/engine/fileos2.c b/jam-files/engine/fileos2.c
deleted file mode 100644
index af2373ea..00000000
--- a/jam-files/engine/fileos2.c
+++ /dev/null
@@ -1,138 +0,0 @@
-/*
- * Copyright 1993-2002 Christopher Seiwald and Perforce Software, Inc.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*  This file is ALSO:
- *  Copyright 2001-2004 David Abrahams.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-
-# include "jam.h"
-# include "filesys.h"
-# include "pathsys.h"
-
-/* note that we use "fileunix.c" when compiling with EMX on OS/2 */
-# if defined(OS_OS2) && !defined(__EMX__)
-
-# include <io.h>
-# include <dos.h>
-
-/*
- * fileos2.c - scan directories and archives on NT
- *
- * External routines:
- *
- *  file_dirscan() - scan a directory for files
- *  file_time() - get timestamp of file, if not done by file_dirscan()
- *  file_archscan() - scan an archive for files
- *
- * File_dirscan() and file_archscan() call back a caller provided function
- * for each file found.  A flag to this callback function lets file_dirscan()
- * and file_archscan() indicate that a timestamp is being provided with the
- * file.   If file_dirscan() or file_archscan() do not provide the file's
- * timestamp, interested parties may later call file_time().
- *
- * 07/10/95 (taylor)  Findfirst() returns the first file on NT.
- * 05/03/96 (seiwald) split apart into pathnt.c
- * 09/22/00 (seiwald) handle \ and c:\ specially: don't add extra /
- */
-
-/*
- * file_dirscan() - scan a directory for files
- */
-
-void
-file_dirscan(
-    char *dir,
-    scanback func,
-    void    *closure )
-{
-    PATHNAME f;
-    string filespec[1];
-    long handle;
-    int ret;
-    struct _find_t finfo[1];
-
-    /* First enter directory itself */
-
-    memset( (char *)&f, '\0', sizeof( f ) );
-
-    f.f_dir.ptr = dir;
-    f.f_dir.len = strlen(dir);
-
-    dir = *dir ? dir : ".";
-
-    /* Special case \ or d:\ : enter it */
-    string_copy( filespec, dir );
-
-    if ( f.f_dir.len == 1 && f.f_dir.ptr[0] == '\\' )
-        (*func)( closure, dir, 0 /* not stat()'ed */, (time_t)0 );
-    else if ( f.f_dir.len == 3 && f.f_dir.ptr[1] == ':' )
-        (*func)( closure, dir, 0 /* not stat()'ed */, (time_t)0 );
-    else
-        string_push_back( filespec, '/' );
-
-    string_push_back( filespec, '*' );
-
-    /* Now enter contents of directory */
-
-    if ( DEBUG_BINDSCAN )
-        printf( "scan directory %s\n", filespec->value );
-
-    /* Time info in dos find_t is not very useful.  It consists */
-    /* of a separate date and time, and putting them together is */
-    /* not easy.  So we leave that to a later stat() call. */
-
-    if ( !_dos_findfirst( filespec->value, _A_NORMAL|_A_RDONLY|_A_SUBDIR, finfo ) )
-    {
-        string filename[1];
-        string_new( filename );
-        do
-        {
-            f.f_base.ptr = finfo->name;
-            f.f_base.len = strlen( finfo->name );
-
-            string_truncate( filename, 0 );
-            path_build( &f, filename, 0 );
-            (*func)( closure, filename->value, 0 /* not stat()'ed */, (time_t)0 );
-        }
-        while ( !_dos_findnext( finfo ) );
-        string_free( filename );
-    }
-}
-
-/*
- * file_time() - get timestamp of file, if not done by file_dirscan()
- */
-
-int
-file_time(
-    char    *filename,
-    time_t  *time )
-{
-    /* This is called on OS2, not NT.  */
-    /* NT fills in the time in the dirscan. */
-
-    struct stat statbuf;
-
-    if ( stat( filename, &statbuf ) < 0 )
-        return -1;
-
-    *time = statbuf.st_mtime;
-
-    return 0;
-}
-
-void
-file_archscan(
-    char *archive,
-    scanback func,
-    void    *closure )
-{
-}
-
-# endif /* OS2 && !__EMX__ */
-
diff --git a/jam-files/engine/filesys.c b/jam-files/engine/filesys.c
deleted file mode 100644
index eb62ed40..00000000
--- a/jam-files/engine/filesys.c
+++ /dev/null
@@ -1,83 +0,0 @@
-# include "jam.h"
-# include "pathsys.h"
-# include "strings.h"
-# include "newstr.h"
-# include "filesys.h"
-# include "lists.h"
-
-void file_build1( PATHNAME * f, string * file )
-{
-    if ( DEBUG_SEARCH )
-    {
-        printf("build file: ");
-        if ( f->f_root.len )
-            printf( "root = '%.*s' ", f->f_root.len, f->f_root.ptr );
-        if ( f->f_dir.len )
-            printf( "dir = '%.*s' ", f->f_dir.len, f->f_dir.ptr );
-        if ( f->f_base.len )
-            printf( "base = '%.*s' ", f->f_base.len, f->f_base.ptr );
-        printf( "\n" );
-    }
-
-    /* Start with the grist.  If the current grist isn't */
-    /* surrounded by <>'s, add them. */
-
-    if ( f->f_grist.len )
-    {
-        if ( f->f_grist.ptr[0] != '<' )
-            string_push_back( file, '<' );
-        string_append_range(
-            file, f->f_grist.ptr, f->f_grist.ptr + f->f_grist.len );
-        if ( file->value[file->size - 1] != '>' )
-            string_push_back( file, '>' );
-    }
-}
-
-static struct hash * filecache_hash = 0;
-static file_info_t filecache_finfo;
-
-file_info_t * file_info(char * filename)
-{
-    file_info_t *finfo = &filecache_finfo;
-
-    if ( !filecache_hash )
-        filecache_hash = hashinit( sizeof( file_info_t ), "file_info" );
-
-    finfo->name = filename;
-    finfo->is_file = 0;
-    finfo->is_dir = 0;
-    finfo->size = 0;
-    finfo->time = 0;
-    finfo->files = 0;
-    if ( hashenter( filecache_hash, (HASHDATA**)&finfo ) )
-    {
-        /* printf( "file_info: %s\n", filename ); */
-        finfo->name = newstr( finfo->name );
-    }
-
-    return finfo;
-}
-
-static LIST * files_to_remove = L0;
-
-static void remove_files_atexit(void)
-{
-    /* we do pop front in case this exit function is called
-       more than once */
-    while ( files_to_remove )
-    {
-        remove( files_to_remove->string );
-        files_to_remove = list_pop_front( files_to_remove );
-    }
-}
-
-void file_done()
-{
-    remove_files_atexit();
-    hashdone( filecache_hash );
-}
-
-void file_remove_atexit( const char * path )
-{
-    files_to_remove = list_new( files_to_remove, newstr((char*)path) );
-}
diff --git a/jam-files/engine/filesys.h b/jam-files/engine/filesys.h
deleted file mode 100644
index efc081d1..00000000
--- a/jam-files/engine/filesys.h
+++ /dev/null
@@ -1,60 +0,0 @@
-/*
- * Copyright 1993-2002 Christopher Seiwald and Perforce Software, Inc.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*  This file is ALSO:
- *  Copyright 2001-2004 David Abrahams.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-
-/*
- * filesys.h - OS specific file routines
- */
-
-#ifndef FILESYS_DWA20011025_H
-# define FILESYS_DWA20011025_H
-
-# include "pathsys.h"
-#include "hash.h"
-#include "lists.h"
-
-typedef void (*scanback)( void *closure, char *file, int found, time_t t );
-
-void file_dirscan( char *dir, scanback func, void *closure );
-void file_archscan( char *arch, scanback func, void *closure );
-
-int file_time( char *filename, time_t *time );
-
-void file_build1(PATHNAME *f, string* file) ;
-int file_is_file(char* filename);
-int file_mkdir(char *pathname);
-
-typedef struct file_info_t file_info_t ;
-struct file_info_t
-{
-    char          * name;
-    short           is_file;
-    short           is_dir;
-    unsigned long   size;
-    time_t          time;
-    LIST          * files;
-};
-
-
-/* Creates a pointer to information about file 'filename', creating it as
- * necessary. If created, the structure will be default initialized.
- */
-file_info_t * file_info( char * filename );
-
-/* Returns information about a file, queries the OS if needed. */
-file_info_t * file_query( char * filename );
-
-void file_done();
-
-/* Marks a path/file to be removed when jam exits. */
-void file_remove_atexit( const char * path );
-
-#endif
diff --git a/jam-files/engine/fileunix.c b/jam-files/engine/fileunix.c
deleted file mode 100644
index 680c3f53..00000000
--- a/jam-files/engine/fileunix.c
+++ /dev/null
@@ -1,501 +0,0 @@
-/*
- * Copyright 1993-2002 Christopher Seiwald and Perforce Software, Inc.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*  This file is ALSO:
- *  Copyright 2001-2004 David Abrahams.
- *  Copyright 2005 Rene Rivera.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-
-# include "jam.h"
-# include "filesys.h"
-# include "strings.h"
-# include "pathsys.h"
-# include "newstr.h"
-# include <stdio.h>
-# include <sys/stat.h>
-
-#if defined(sun) || defined(__sun) || defined(linux)
-# include <unistd.h> /* needed for read and close prototype */
-#endif
-
-# ifdef USE_FILEUNIX
-
-#if defined(sun) || defined(__sun)
-# include <unistd.h> /* needed for read and close prototype */
-#endif
-
-# if defined( OS_SEQUENT ) || \
-     defined( OS_DGUX ) || \
-     defined( OS_SCO ) || \
-     defined( OS_ISC )
-# define PORTAR 1
-# endif
-
-# ifdef __EMX__
-# include <sys/types.h>
-# include <sys/stat.h>
-# endif
-
-# if defined( OS_RHAPSODY ) || \
-     defined( OS_MACOSX ) || \
-     defined( OS_NEXT )
-/* need unistd for rhapsody's proper lseek */
-# include <sys/dir.h>
-# include <unistd.h>
-# define STRUCT_DIRENT struct direct
-# else
-# include <dirent.h>
-# define STRUCT_DIRENT struct dirent
-# endif
-
-# ifdef OS_COHERENT
-# include <arcoff.h>
-# define HAVE_AR
-# endif
-
-# if defined( OS_MVS ) || \
-         defined( OS_INTERIX )
-
-#define ARMAG   "!<arch>\n"
-#define SARMAG  8
-#define ARFMAG  "`\n"
-
-struct ar_hdr       /* archive file member header - printable ascii */
-{
-    char    ar_name[16];    /* file member name - `/' terminated */
-    char    ar_date[12];    /* file member date - decimal */
-    char    ar_uid[6];  /* file member user id - decimal */
-    char    ar_gid[6];  /* file member group id - decimal */
-    char    ar_mode[8]; /* file member mode - octal */
-    char    ar_size[10];    /* file member size - decimal */
-    char    ar_fmag[2]; /* ARFMAG - string to end header */
-};
-
-# define HAVE_AR
-# endif
-
-# if defined( OS_QNX ) || \
-     defined( OS_BEOS ) || \
-     defined( OS_MPEIX )
-# define NO_AR
-# define HAVE_AR
-# endif
-
-# ifndef HAVE_AR
-
-# ifdef OS_AIX
-/* Define those for AIX to get the definitions for both the small and the
- * big variant of the archive file format. */
-#    define __AR_SMALL__
-#    define __AR_BIG__
-# endif
-
-# include <ar.h>
-# endif
-
-/*
- * fileunix.c - manipulate file names and scan directories on UNIX/AmigaOS
- *
- * External routines:
- *
- *  file_dirscan() - scan a directory for files
- *  file_time() - get timestamp of file, if not done by file_dirscan()
- *  file_archscan() - scan an archive for files
- *
- * File_dirscan() and file_archscan() call back a caller provided function
- * for each file found.  A flag to this callback function lets file_dirscan()
- * and file_archscan() indicate that a timestamp is being provided with the
- * file.   If file_dirscan() or file_archscan() do not provide the file's
- * timestamp, interested parties may later call file_time().
- *
- * 04/08/94 (seiwald) - Coherent/386 support added.
- * 12/19/94 (mikem) - solaris string table insanity support
- * 02/14/95 (seiwald) - parse and build /xxx properly
- * 05/03/96 (seiwald) - split into pathunix.c
- * 11/21/96 (peterk) - BEOS does not have Unix-style archives
- */
-
-
-/*
- * file_dirscan() - scan a directory for files.
- */
-
-void file_dirscan( char * dir, scanback func, void * closure )
-{
-    PROFILE_ENTER( FILE_DIRSCAN );
-
-    file_info_t * d = 0;
-
-    d = file_query( dir );
-
-    if ( !d || !d->is_dir )
-    {
-        PROFILE_EXIT( FILE_DIRSCAN );
-        return;
-    }
-
-    if ( ! d->files )
-    {
-        LIST* files = L0;
-        PATHNAME f;
-        DIR *dd;
-        STRUCT_DIRENT *dirent;
-        string filename[1];
-
-        /* First enter directory itself */
-
-        memset( (char *)&f, '\0', sizeof( f ) );
-
-        f.f_dir.ptr = dir;
-        f.f_dir.len = strlen(dir);
-
-        dir = *dir ? dir : ".";
-
-        /* Now enter contents of directory. */
-
-        if ( !( dd = opendir( dir ) ) )
-        {
-            PROFILE_EXIT( FILE_DIRSCAN );
-            return;
-        }
-
-        if ( DEBUG_BINDSCAN )
-            printf( "scan directory %s\n", dir );
-
-        string_new( filename );
-        while ( ( dirent = readdir( dd ) ) )
-        {
-            # ifdef old_sinix
-            /* Broken structure definition on sinix. */
-            f.f_base.ptr = dirent->d_name - 2;
-            # else
-            f.f_base.ptr = dirent->d_name;
-            # endif
-            f.f_base.len = strlen( f.f_base.ptr );
-
-            string_truncate( filename, 0 );
-            path_build( &f, filename, 0 );
-
-            files = list_new( files, newstr(filename->value) );
-            file_query( filename->value );
-        }
-        string_free( filename );
-
-        closedir( dd );
-
-        d->files = files;
-    }
-
-    /* Special case / : enter it */
-    {
-        unsigned long len = strlen(d->name);
-        if ( ( len == 1 ) && ( d->name[0] == '/' ) )
-            (*func)( closure, d->name, 1 /* stat()'ed */, d->time );
-    }
-
-    /* Now enter contents of directory */
-    if ( d->files )
-    {
-        LIST * files = d->files;
-        while ( files )
-        {
-            file_info_t * ff = file_info( files->string );
-            (*func)( closure, ff->name, 1 /* stat()'ed */, ff->time );
-            files = list_next( files );
-        }
-    }
-
-    PROFILE_EXIT( FILE_DIRSCAN );
-}
-
-
-file_info_t * file_query( char * filename )
-{
-    file_info_t * ff = file_info( filename );
-    if ( ! ff->time )
-    {
-        struct stat statbuf;
-
-        if ( stat( *filename ? filename : ".", &statbuf ) < 0 )
-            return 0;
-
-        ff->is_file = statbuf.st_mode & S_IFREG ? 1 : 0;
-        ff->is_dir = statbuf.st_mode & S_IFDIR ? 1 : 0;
-        ff->size = statbuf.st_size;
-        ff->time = statbuf.st_mtime ? statbuf.st_mtime : 1;
-    }
-    return ff;
-}
-
-/*
- * file_time() - get timestamp of file, if not done by file_dirscan()
- */
-
-int
-file_time(
-    char    *filename,
-    time_t  *time )
-{
-    file_info_t * ff = file_query( filename );
-    if ( !ff ) return -1;
-    *time = ff->time;
-    return 0;
-}
-
-int file_is_file(char* filename)
-{
-    file_info_t * ff = file_query( filename );
-    if ( !ff ) return -1;
-    return ff->is_file;
-}
-
-int file_mkdir(char* pathname)
-{
-    return mkdir(pathname, 0766);
-}
-
-/*
- * file_archscan() - scan an archive for files
- */
-
-# ifndef AIAMAG /* God-fearing UNIX */
-
-# define SARFMAG 2
-# define SARHDR sizeof( struct ar_hdr )
-
-void
-file_archscan(
-    char *archive,
-    scanback func,
-    void *closure )
-{
-# ifndef NO_AR
-    struct ar_hdr ar_hdr;
-    char buf[ MAXJPATH ];
-    long offset;
-    char    *string_table = 0;
-    int fd;
-
-    if ( ( fd = open( archive, O_RDONLY, 0 ) ) < 0 )
-        return;
-
-    if ( read( fd, buf, SARMAG ) != SARMAG ||
-        strncmp( ARMAG, buf, SARMAG ) )
-    {
-        close( fd );
-        return;
-    }
-
-    offset = SARMAG;
-
-    if ( DEBUG_BINDSCAN )
-        printf( "scan archive %s\n", archive );
-
-    while ( ( read( fd, &ar_hdr, SARHDR ) == SARHDR )
-           && !( memcmp( ar_hdr.ar_fmag, ARFMAG, SARFMAG )
-#ifdef ARFZMAG
-              /* OSF also has a compressed format */
-              && memcmp( ar_hdr.ar_fmag, ARFZMAG, SARFMAG )
-#endif
-          ) )
-    {
-        char   lar_name_[257];
-        char * lar_name = lar_name_ + 1;
-        long   lar_date;
-        long   lar_size;
-        long   lar_offset;
-        char * c;
-        char * src;
-        char * dest;
-
-        strncpy( lar_name, ar_hdr.ar_name, sizeof(ar_hdr.ar_name) );
-
-        sscanf( ar_hdr.ar_date, "%ld", &lar_date );
-        sscanf( ar_hdr.ar_size, "%ld", &lar_size );
-
-        if (ar_hdr.ar_name[0] == '/')
-        {
-        if (ar_hdr.ar_name[1] == '/')
-        {
-            /* this is the "string table" entry of the symbol table,
-            ** which holds strings of filenames that are longer than
-            ** 15 characters (ie. don't fit into a ar_name
-            */
-
-            string_table = (char *)BJAM_MALLOC_ATOMIC(lar_size);
-            lseek(fd, offset + SARHDR, 0);
-            if (read(fd, string_table, lar_size) != lar_size)
-            printf("error reading string table\n");
-        }
-        else if (string_table && ar_hdr.ar_name[1] != ' ')
-        {
-            /* Long filenames are recognized by "/nnnn" where nnnn is
-            ** the offset of the string in the string table represented
-            ** in ASCII decimals.
-            */
-            dest = lar_name;
-            lar_offset = atoi(lar_name + 1);
-            src = &string_table[lar_offset];
-            while (*src != '/')
-            *dest++ = *src++;
-            *dest = '/';
-        }
-        }
-
-        c = lar_name - 1;
-        while ( ( *++c != ' ' ) && ( *c != '/' ) ) ;
-        *c = '\0';
-
-        if ( DEBUG_BINDSCAN )
-        printf( "archive name %s found\n", lar_name );
-
-        sprintf( buf, "%s(%s)", archive, lar_name );
-
-        (*func)( closure, buf, 1 /* time valid */, (time_t)lar_date );
-
-        offset += SARHDR + ( ( lar_size + 1 ) & ~1 );
-        lseek( fd, offset, 0 );
-    }
-
-    if (string_table)
-        BJAM_FREE(string_table);
-
-    close( fd );
-
-# endif /* NO_AR */
-
-}
-
-# else /* AIAMAG - RS6000 AIX */
-
-static void file_archscan_small(
-    int fd, char const *archive, scanback func, void *closure)
-{
-    struct fl_hdr fl_hdr;
-
-    struct {
-        struct ar_hdr hdr;
-        char pad[ 256 ];
-    } ar_hdr ;
-
-    char buf[ MAXJPATH ];
-    long offset;
-
-    if ( read( fd, (char *)&fl_hdr, FL_HSZ ) != FL_HSZ)
-        return;
-
-    sscanf( fl_hdr.fl_fstmoff, "%ld", &offset );
-
-    if ( DEBUG_BINDSCAN )
-        printf( "scan archive %s\n", archive );
-
-    while ( ( offset > 0 )
-           && ( lseek( fd, offset, 0 ) >= 0 )
-           && ( read( fd, &ar_hdr, sizeof( ar_hdr ) ) >= sizeof( ar_hdr.hdr ) ) )
-    {
-        long lar_date;
-        int  lar_namlen;
-
-        sscanf( ar_hdr.hdr.ar_namlen, "%d" , &lar_namlen );
-        sscanf( ar_hdr.hdr.ar_date  , "%ld", &lar_date   );
-        sscanf( ar_hdr.hdr.ar_nxtmem, "%ld", &offset     );
-
-        if ( !lar_namlen )
-            continue;
-
-        ar_hdr.hdr._ar_name.ar_name[ lar_namlen ] = '\0';
-
-        sprintf( buf, "%s(%s)", archive, ar_hdr.hdr._ar_name.ar_name );
-
-        (*func)( closure, buf, 1 /* time valid */, (time_t)lar_date );
-    }
-}
-
-/* Check for OS version which supports the big variant. */
-#ifdef AR_HSZ_BIG
-
-static void file_archscan_big(
-    int fd, char const *archive, scanback func, void *closure)
-{
-    struct fl_hdr_big fl_hdr;
-
-    struct {
-        struct ar_hdr_big hdr;
-        char pad[ 256 ];
-    } ar_hdr ;
-
-    char buf[ MAXJPATH ];
-    long long offset;
-
-    if ( read( fd, (char *)&fl_hdr, FL_HSZ_BIG) != FL_HSZ_BIG)
-        return;
-
-    sscanf( fl_hdr.fl_fstmoff, "%lld", &offset );
-
-    if ( DEBUG_BINDSCAN )
-        printf( "scan archive %s\n", archive );
-
-    while ( ( offset > 0 )
-           && ( lseek( fd, offset, 0 ) >= 0 )
-           && ( read( fd, &ar_hdr, sizeof( ar_hdr ) ) >= sizeof( ar_hdr.hdr ) ) )
-    {
-        long lar_date;
-        int  lar_namlen;
-
-        sscanf( ar_hdr.hdr.ar_namlen, "%d"  , &lar_namlen );
-        sscanf( ar_hdr.hdr.ar_date  , "%ld" , &lar_date   );
-        sscanf( ar_hdr.hdr.ar_nxtmem, "%lld", &offset     );
-
-        if ( !lar_namlen )
-            continue;
-
-        ar_hdr.hdr._ar_name.ar_name[ lar_namlen ] = '\0';
-
-        sprintf( buf, "%s(%s)", archive, ar_hdr.hdr._ar_name.ar_name );
-
-        (*func)( closure, buf, 1 /* time valid */, (time_t)lar_date );
-    }
-
-}
-
-#endif /* AR_HSZ_BIG */
-
-void file_archscan(char *archive, scanback func, void *closure)
-{
-    int fd;
-    char fl_magic[SAIAMAG];
-
-    if (( fd = open(archive, O_RDONLY, 0)) < 0)
-        return;
-
-    if (read( fd, fl_magic, SAIAMAG) != SAIAMAG
-       || lseek(fd, 0, SEEK_SET) == -1)
-    {
-        close(fd);
-        return;
-    }
-
-    if (strncmp(AIAMAG, fl_magic, SAIAMAG) == 0)
-    {
-        /* read small variant */
-        file_archscan_small(fd, archive, func, closure);
-    }
-#ifdef AR_HSZ_BIG
-    else if (strncmp(AIAMAGBIG, fl_magic, SAIAMAG) == 0)
-    {
-        /* read big variant */
-        file_archscan_big(fd, archive, func, closure);
-    }
-#endif
-
-    close( fd );
-}
-
-# endif /* AIAMAG - RS6000 AIX */
-
-# endif /* USE_FILEUNIX */
diff --git a/jam-files/engine/filevms.c b/jam-files/engine/filevms.c
deleted file mode 100644
index d2ab2047..00000000
--- a/jam-files/engine/filevms.c
+++ /dev/null
@@ -1,327 +0,0 @@
-/*
- * Copyright 1993-2002 Christopher Seiwald and Perforce Software, Inc.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*  This file is ALSO:
- *  Copyright 2001-2004 David Abrahams.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-
-# include "jam.h"
-# include "filesys.h"
-# include "pathsys.h"
-
-# ifdef OS_VMS
-
-/*
- * filevms.c - scan directories and libaries on VMS
- *
- * External routines:
- *
- *  file_dirscan() - scan a directory for files
- *  file_time() - get timestamp of file, if not done by file_dirscan()
- *  file_archscan() - scan an archive for files
- *
- * File_dirscan() and file_archscan() call back a caller provided function
- * for each file found.  A flag to this callback function lets file_dirscan()
- * and file_archscan() indicate that a timestamp is being provided with the
- * file.   If file_dirscan() or file_archscan() do not provide the file's
- * timestamp, interested parties may later call file_time().
- *
- * 02/09/95 (seiwald) - bungled R=[xxx] - was using directory length!
- * 05/03/96 (seiwald) - split into pathvms.c
- */
-
-# include <rms.h>
-# include <iodef.h>
-# include <ssdef.h>
-# include <string.h>
-# include <stdlib.h>
-# include <stdio.h>
-# include <descrip.h>
-
-#include <lbrdef.h>
-#include <credef.h>
-#include <mhddef.h>
-#include <lhidef.h>
-#include <lib$routines.h>
-#include <starlet.h>
-
-/* Supply missing prototypes for lbr$-routines*/
-
-#ifdef __cplusplus
-extern "C" {
-#endif /* __cplusplus */
-
-int lbr$set_module(
-    void **,
-    unsigned long *,
-    struct dsc$descriptor_s *,
-    unsigned short *,
-    void * );
-
-int lbr$open( void **,
-    struct dsc$descriptor_s *,
-    void *,
-    void *,
-    void *,
-    void *,
-    void * );
-
-int lbr$ini_control(
-    void **,
-    unsigned long *,
-    unsigned long *,
-    void * );
-
-int lbr$get_index(
-    void **,
-    unsigned long *,
-    int (*func)( struct dsc$descriptor_s *, unsigned long *),
-    void * );
-
-int lbr$close(
-    void ** );
-
-#ifdef __cplusplus
-}
-#endif /* __cplusplus */
-
-static void
-file_cvttime(
-    unsigned int *curtime,
-    time_t *unixtime )
-{
-    static const size_t divisor = 10000000;
-    static unsigned int bastim[2] = { 0x4BEB4000, 0x007C9567 }; /* 1/1/1970 */
-    int delta[2], remainder;
-
-    lib$subx( curtime, bastim, delta );
-    lib$ediv( &divisor, delta, unixtime, &remainder );
-}
-
-# define DEFAULT_FILE_SPECIFICATION "[]*.*;0"
-
-# define min( a,b ) ((a)<(b)?(a):(b))
-
-void
-file_dirscan(
-    char *dir,
-    scanback func,
-    void    *closure )
-{
-
-    struct FAB xfab;
-    struct NAM xnam;
-    struct XABDAT xab;
-    char esa[256];
-    char filename[256];
-    string filename2[1];
-    char dirname[256];
-    register int status;
-    PATHNAME f;
-
-    memset( (char *)&f, '\0', sizeof( f ) );
-
-    f.f_root.ptr = dir;
-    f.f_root.len = strlen( dir );
-
-    /* get the input file specification
-     */
-    xnam = cc$rms_nam;
-    xnam.nam$l_esa = esa;
-    xnam.nam$b_ess = sizeof( esa ) - 1;
-    xnam.nam$l_rsa = filename;
-    xnam.nam$b_rss = min( sizeof( filename ) - 1, NAM$C_MAXRSS );
-
-    xab = cc$rms_xabdat;                /* initialize extended attributes */
-    xab.xab$b_cod = XAB$C_DAT;      /* ask for date */
-    xab.xab$l_nxt = NULL;               /* terminate XAB chain      */
-
-    xfab = cc$rms_fab;
-    xfab.fab$l_dna = DEFAULT_FILE_SPECIFICATION;
-    xfab.fab$b_dns = sizeof( DEFAULT_FILE_SPECIFICATION ) - 1;
-    xfab.fab$l_fop = FAB$M_NAM;
-    xfab.fab$l_fna = dir;           /* address of file name     */
-    xfab.fab$b_fns = strlen( dir );     /* length of file name      */
-    xfab.fab$l_nam = &xnam;         /* address of NAB block     */
-    xfab.fab$l_xab = (char *)&xab;       /* address of XAB block     */
-
-
-    status = sys$parse( &xfab );
-
-    if ( DEBUG_BINDSCAN )
-    printf( "scan directory %s\n", dir );
-
-    if ( !( status & 1 ) )
-    return;
-
-
-
-    /* Add bogus directory for [000000] */
-
-    if ( !strcmp( dir, "[000000]" ) )
-    {
-    (*func)( closure, "[000000]", 1 /* time valid */, 1 /* old but true */ );
-    }
-
-    /* Add bogus directory for [] */
-
-    if ( !strcmp( dir, "[]" ) )
-    {
-        (*func)( closure, "[]", 1 /* time valid */, 1 /* old but true */ );
-        (*func)( closure, "[-]", 1 /* time valid */, 1 /* old but true */ );
-    }
-
-    string_new( filename2 );
-    while ( (status = sys$search( &xfab )) & 1 )
-    {
-    char *s;
-    time_t time;
-
-    /* "I think that might work" - eml */
-
-    sys$open( &xfab );
-    sys$close( &xfab );
-
-    file_cvttime( (unsigned int *)&xab.xab$q_rdt, &time );
-
-    filename[xnam.nam$b_rsl] = '\0';
-
-    /* What we do with the name depends on the suffix: */
-    /* .dir is a directory */
-    /* .xxx is a file with a suffix */
-    /* . is no suffix at all */
-
-    if ( xnam.nam$b_type == 4 && !strncmp( xnam.nam$l_type, ".DIR", 4 ) )
-    {
-        /* directory */
-        sprintf( dirname, "[.%.*s]", xnam.nam$b_name, xnam.nam$l_name );
-        f.f_dir.ptr = dirname;
-        f.f_dir.len = strlen( dirname );
-        f.f_base.ptr = 0;
-        f.f_base.len = 0;
-        f.f_suffix.ptr = 0;
-        f.f_suffix.len = 0;
-    }
-    else
-    {
-        /* normal file with a suffix */
-        f.f_dir.ptr = 0;
-        f.f_dir.len = 0;
-        f.f_base.ptr = xnam.nam$l_name;
-        f.f_base.len = xnam.nam$b_name;
-        f.f_suffix.ptr = xnam.nam$l_type;
-        f.f_suffix.len = xnam.nam$b_type;
-    }
-
-        string_truncate( filename2, 0 );
-    path_build( &f, filename2, 0 );
-
-    /*
-    if ( DEBUG_SEARCH )
-        printf("root '%s' base %.*s suf %.*s = %s\n",
-            dir,
-            xnam.nam$b_name, xnam.nam$l_name,
-            xnam.nam$b_type, xnam.nam$l_type,
-            filename2 );
-    */
-
-    (*func)( closure, filename2->value, 1 /* time valid */, time );
-    }
-    string_free( filename2 );
-}
-
-int
-file_time(
-    char    *filename,
-    time_t  *time )
-{
-    /* This should never be called, as all files are */
-    /* timestampped in file_dirscan() and file_archscan() */
-    return -1;
-}
-
-static char *VMS_archive = 0;
-static scanback VMS_func;
-static void *VMS_closure;
-static void *context;
-
-static int
-file_archmember(
-    struct dsc$descriptor_s *module,
-    unsigned long *rfa )
-{
-    static struct dsc$descriptor_s bufdsc =
-          {0, DSC$K_DTYPE_T, DSC$K_CLASS_S, NULL};
-
-    struct mhddef *mhd;
-    char filename[128];
-    char buf[ MAXJPATH ];
-
-    int status;
-    time_t library_date;
-
-    register int i;
-    register char *p;
-
-    bufdsc.dsc$a_pointer = filename;
-    bufdsc.dsc$w_length = sizeof( filename );
-    status = lbr$set_module( &context, rfa, &bufdsc,
-                 &bufdsc.dsc$w_length, NULL );
-
-    if ( !(status & 1) )
-    return ( 1 );
-
-    mhd = (struct mhddef *)filename;
-
-    file_cvttime( &mhd->mhd$l_datim, &library_date );
-
-    for ( i = 0, p = module->dsc$a_pointer; i < module->dsc$w_length; ++i, ++p )
-    filename[ i ] = *p;
-
-    filename[ i ] = '\0';
-
-    sprintf( buf, "%s(%s.obj)", VMS_archive, filename );
-
-    (*VMS_func)( VMS_closure, buf, 1 /* time valid */, (time_t)library_date );
-
-    return ( 1 );
-}
-
-
-void file_archscan( char * archive, scanback func, void * closure )
-{
-    static struct dsc$descriptor_s library =
-          {0, DSC$K_DTYPE_T, DSC$K_CLASS_S, NULL};
-
-    unsigned long lfunc = LBR$C_READ;
-    unsigned long typ = LBR$C_TYP_UNK;
-    unsigned long index = 1;
-
-    register int status;
-
-    VMS_archive = archive;
-    VMS_func = func;
-    VMS_closure = closure;
-
-    status = lbr$ini_control( &context, &lfunc, &typ, NULL );
-    if ( !( status & 1 ) )
-        return;
-
-    library.dsc$a_pointer = archive;
-    library.dsc$w_length = strlen( archive );
-
-    status = lbr$open( &context, &library, NULL, NULL, NULL, NULL, NULL );
-    if ( !( status & 1 ) )
-        return;
-
-    (void) lbr$get_index( &context, &index, file_archmember, NULL );
-
-    (void) lbr$close( &context );
-}
-
-# endif /* VMS */
diff --git a/jam-files/engine/frames.c b/jam-files/engine/frames.c
deleted file mode 100644
index 84889f09..00000000
--- a/jam-files/engine/frames.c
+++ /dev/null
@@ -1,22 +0,0 @@
-/*
- *  Copyright 2001-2004 David Abrahams.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-
-# include "frames.h"
-# include "lists.h"
-
-void frame_init( FRAME* frame )
-{
-    frame->prev = 0;
-    lol_init(frame->args);
-    frame->module = root_module();
-    frame->rulename = "module scope";
-    frame->procedure = 0;
-}
-
-void frame_free( FRAME* frame )
-{
-    lol_free( frame->args );
-}
diff --git a/jam-files/engine/frames.h b/jam-files/engine/frames.h
deleted file mode 100644
index 693d77fa..00000000
--- a/jam-files/engine/frames.h
+++ /dev/null
@@ -1,37 +0,0 @@
-/*
- *  Copyright 2001-2004 David Abrahams.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-#ifndef FRAMES_DWA20011021_H
-#define FRAMES_DWA20011021_H
-
-#include "lists.h"
-#include "modules.h"
-
-typedef struct _PARSE PARSE;
-typedef struct frame FRAME;
-
-struct frame
-{
-    FRAME    * prev;
-    /* The nearest enclosing frame for which module->user_module is true. */
-    FRAME    * prev_user;
-    LOL        args[ 1 ];
-    module_t * module;
-    PARSE    * procedure;
-    char     * rulename;
-};
-
-
-/* When call into Python is in progress, this variable points to the bjam frame
- * that was current at the moment of call. When the call completes, the variable
- * is not defined. Further, if Jam calls Python which calls Jam and so on, this
- * variable only keeps the most recent Jam frame.
- */
-extern struct frame * frame_before_python_call;
-
-void frame_init( FRAME * );  /* implemented in compile.c */
-void frame_free( FRAME * );  /* implemented in compile.c */
-
-#endif
diff --git a/jam-files/engine/glob.c b/jam-files/engine/glob.c
deleted file mode 100644
index 527d6c80..00000000
--- a/jam-files/engine/glob.c
+++ /dev/null
@@ -1,152 +0,0 @@
-/*
- * Copyright 1994 Christopher Seiwald.  All rights reserved.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*
- * glob.c - match a string against a simple pattern
- *
- * Understands the following patterns:
- *
- *  *   any number of characters
- *  ?   any single character
- *  [a-z]   any single character in the range a-z
- *  [^a-z]  any single character not in the range a-z
- *  \x  match x
- *
- * External functions:
- *
- *  glob() - match a string against a simple pattern
- *
- * Internal functions:
- *
- *  globchars() - build a bitlist to check for character group match
- */
-
-# include "jam.h"
-
-# define CHECK_BIT( tab, bit ) ( tab[ (bit)/8 ] & (1<<( (bit)%8 )) )
-# define BITLISTSIZE 16 /* bytes used for [chars] in compiled expr */
-
-static void globchars( char * s, char * e, char * b );
-
-
-/*
- * glob() - match a string against a simple pattern.
- */
-
-int glob( char * c, char * s )
-{
-    char   bitlist[ BITLISTSIZE ];
-    char * here;
-
-    for ( ; ; )
-    switch ( *c++ )
-    {
-    case '\0':
-        return *s ? -1 : 0;
-
-    case '?':
-        if ( !*s++ )
-            return 1;
-        break;
-
-    case '[':
-        /* Scan for matching ]. */
-
-        here = c;
-        do if ( !*c++ ) return 1;
-        while ( ( here == c ) || ( *c != ']' ) );
-        ++c;
-
-        /* Build character class bitlist. */
-
-        globchars( here, c, bitlist );
-
-        if ( !CHECK_BIT( bitlist, *(unsigned char *)s ) )
-            return 1;
-        ++s;
-        break;
-
-    case '*':
-        here = s;
-
-        while ( *s )
-            ++s;
-
-        /* Try to match the rest of the pattern in a recursive */
-        /* call.  If the match fails we'll back up chars, retrying. */
-
-        while ( s != here )
-        {
-            int r;
-
-            /* A fast path for the last token in a pattern. */
-            r = *c ? glob( c, s ) : *s ? -1 : 0;
-
-            if ( !r )
-                return 0;
-            if ( r < 0 )
-                return 1;
-            --s;
-        }
-        break;
-
-    case '\\':
-        /* Force literal match of next char. */
-        if ( !*c || ( *s++ != *c++ ) )
-            return 1;
-        break;
-
-    default:
-        if ( *s++ != c[ -1 ] )
-            return 1;
-        break;
-    }
-}
-
-
-/*
- * globchars() - build a bitlist to check for character group match.
- */
-
-static void globchars( char * s,  char * e, char * b )
-{
-    int neg = 0;
-
-    memset( b, '\0', BITLISTSIZE  );
-
-    if ( *s == '^' )
-    {
-        ++neg;
-        ++s;
-    }
-
-    while ( s < e )
-    {
-        int c;
-
-        if ( ( s + 2 < e ) && ( s[1] == '-' ) )
-        {
-            for ( c = s[0]; c <= s[2]; ++c )
-                b[ c/8 ] |= ( 1 << ( c % 8 ) );
-            s += 3;
-        }
-        else
-        {
-            c = *s++;
-            b[ c/8 ] |= ( 1 << ( c % 8 ) );
-        }
-    }
-
-    if ( neg )
-    {
-        int i;
-        for ( i = 0; i < BITLISTSIZE; ++i )
-            b[ i ] ^= 0377;
-    }
-
-    /* Do not include \0 in either $[chars] or $[^chars]. */
-    b[0] &= 0376;
-}
diff --git a/jam-files/engine/hash.c b/jam-files/engine/hash.c
deleted file mode 100644
index fbd1a899..00000000
--- a/jam-files/engine/hash.c
+++ /dev/null
@@ -1,459 +0,0 @@
-/*
- * Copyright 1993, 1995 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-# include "jam.h"
-# include "hash.h"
-# include "compile.h"
-# include <assert.h>
-
-/*
- * hash.c - simple in-memory hashing routines
- *
- * External routines:
- *
- *     hashinit() - initialize a hash table, returning a handle
- *     hashitem() - find a record in the table, and optionally enter a new one
- *     hashdone() - free a hash table, given its handle
- *
- * Internal routines:
- *
- *     hashrehash() - resize and rebuild hp->tab, the hash table
- *
- * 4/29/93 - ensure ITEM's are aligned
- */
-
-/* */
-#define HASH_DEBUG_PROFILE 1
-/* */
-
-char    *hashsccssid="@(#)hash.c    1.14  ()  6/20/88";
-
-/* Header attached to all data items entered into a hash table. */
-
-struct hashhdr
-{
-    struct item  * next;
-    unsigned int   keyval;  /* for quick comparisons */
-};
-
-/* This structure overlays the one handed to hashenter(). Its actual size is
- * given to hashinit().
- */
-
-struct hashdata
-{
-    char * key;
-    /* rest of user data */
-};
-
-typedef struct item
-{
-    struct hashhdr  hdr;
-    struct hashdata data;
-} ITEM ;
-
-# define MAX_LISTS 32
-
-struct hash
-{
-    /*
-     * the hash table, just an array of item pointers
-     */
-    struct {
-        int nel;
-        ITEM **base;
-    } tab;
-
-    int bloat;  /* tab.nel / items.nel */
-    int inel;   /* initial number of elements */
-
-    /*
-     * the array of records, maintained by these routines
-     * essentially a microallocator
-     */
-    struct {
-        int more;   /* how many more ITEMs fit in lists[ list ] */
-        ITEM *free; /* free list of items */
-        char *next; /* where to put more ITEMs in lists[ list ] */
-        int datalen;    /* length of records in this hash table */
-        int size;   /* sizeof( ITEM ) + aligned datalen */
-        int nel;    /* total ITEMs held by all lists[] */
-        int list;   /* index into lists[] */
-
-        struct {
-            int nel;    /* total ITEMs held by this list */
-            char *base; /* base of ITEMs array */
-        } lists[ MAX_LISTS ];
-    } items;
-
-    char * name; /* just for hashstats() */
-};
-
-static void hashrehash( struct hash *hp );
-static void hashstat( struct hash *hp );
-static void * hash_mem_alloc(size_t datalen, size_t size);
-static void hash_mem_free(size_t datalen, void * data);
-#ifdef OPT_BOEHM_GC
-static void hash_mem_finalizer(char * key, struct hash * hp);
-#endif
-
-static unsigned int jenkins_one_at_a_time_hash(const unsigned char *key)
-{
-    unsigned int hash = 0;
-
-    while ( *key )
-    {
-        hash += *key++;
-        hash += (hash << 10);
-        hash ^= (hash >> 6);
-    }
-    hash += (hash << 3);
-    hash ^= (hash >> 11);
-    hash += (hash << 15);
-	
-    return hash;
-}
-
-/*
-static unsigned int knuth_hash(const unsigned char *key)
-{
-    unsigned int keyval = *key;
-    while ( *key )
-        keyval = keyval * 2147059363 + *key++;
-    return keyval;
-}
-*/
-
-static unsigned int hash_keyval( const char * key_ )
-{
-    /*
-	return knuth_hash((const unsigned char *)key_);
-	*/
-    return jenkins_one_at_a_time_hash((const unsigned char *)key_);
-}
-
-#define hash_bucket(hp,keyval) ((hp)->tab.base + ( (keyval) % (hp)->tab.nel ))
-
-/*  Find the hash item for the given data. Returns pointer to the
-    item and if given a pointer to the item before the found item.
-    If it's the first item in a bucket, there is no previous item,
-    and zero is returned for the previous item instead.
-*/
-static ITEM * hash_search(
-    struct hash *hp,
-    unsigned int keyval,
-    const char * keydata,
-    ITEM * * previous )
-{
-    ITEM * i = *hash_bucket(hp,keyval);
-    ITEM * p = 0;
-
-    for ( ; i; i = i->hdr.next )
-    {
-        if ( ( keyval == i->hdr.keyval ) &&
-            !strcmp( i->data.key, keydata ) )
-        {
-            if (previous)
-            {
-                *previous = p;
-            }
-            return i;
-        }
-        p = i;
-    }
-
-    return 0;
-}
-
-/*
- * hash_free() - remove the given item from the table if it's there.
- * Returns 1 if found, 0 otherwise.
- *
- * NOTE: 2nd argument is HASHDATA*, not HASHDATA** as elsewhere.
- */
-int
-hash_free(
-    register struct hash *hp,
-    HASHDATA *data)
-{
-    ITEM * i = 0;
-    ITEM * prev = 0;
-    unsigned int keyval = hash_keyval(data->key);
-
-    i = hash_search( hp, keyval, data->key, &prev );
-    if (i)
-    {
-        /* mark it free so we skip it during enumeration */
-        i->data.key = 0;
-        /* unlink the record from the hash chain */
-        if (prev) prev->hdr.next = i->hdr.next;
-        else *hash_bucket(hp,keyval) = i->hdr.next;
-        /* link it into the freelist */
-        i->hdr.next = hp->items.free;
-        hp->items.free = i;
-        /* we have another item */
-        hp->items.more++;
-
-        return 1;
-    }
-    return 0;
-}
-
-/*
- * hashitem() - find a record in the table, and optionally enter a new one
- */
-
-int
-hashitem(
-    register struct hash *hp,
-    HASHDATA **data,
-    int enter )
-{
-    register ITEM *i;
-    char *b = (*data)->key;
-    unsigned int keyval = hash_keyval(b);
-
-    #ifdef HASH_DEBUG_PROFILE
-    profile_frame prof[1];
-    if ( DEBUG_PROFILE )
-        profile_enter( 0, prof );
-    #endif
-
-    if ( enter && !hp->items.more )
-        hashrehash( hp );
-
-    if ( !enter && !hp->items.nel )
-    {
-        #ifdef HASH_DEBUG_PROFILE
-        if ( DEBUG_PROFILE )
-            profile_exit( prof );
-        #endif
-        return 0;
-    }
-
-    i = hash_search( hp, keyval, (*data)->key, 0 );
-    if (i)
-    {
-        *data = &i->data;
-        #ifdef HASH_DEBUG_PROFILE
-        if ( DEBUG_PROFILE ) profile_exit( prof );
-        #endif
-        return !0;
-    }
-
-    if ( enter )
-    {
-        ITEM * * base = hash_bucket(hp,keyval);
-
-        /* try to grab one from the free list */
-        if ( hp->items.free )
-        {
-            i = hp->items.free;
-            hp->items.free = i->hdr.next;
-            assert( i->data.key == 0 );
-        }
-        else
-        {
-            i = (ITEM *)hp->items.next;
-            hp->items.next += hp->items.size;
-        }
-        hp->items.more--;
-        memcpy( (char *)&i->data, (char *)*data, hp->items.datalen );
-        i->hdr.keyval = keyval;
-        i->hdr.next = *base;
-        *base = i;
-        *data = &i->data;
-        #ifdef OPT_BOEHM_GC
-        if (sizeof(HASHDATA) == hp->items.datalen)
-        {
-            GC_REGISTER_FINALIZER(i->data.key,&hash_mem_finalizer,hp,0,0);
-        }
-        #endif
-    }
-
-    #ifdef HASH_DEBUG_PROFILE
-    if ( DEBUG_PROFILE )
-        profile_exit( prof );
-    #endif
-    return 0;
-}
-
-/*
- * hashrehash() - resize and rebuild hp->tab, the hash table
- */
-
-static void hashrehash( register struct hash *hp )
-{
-    int i = ++hp->items.list;
-    hp->items.more = i ? 2 * hp->items.nel : hp->inel;
-    hp->items.next = (char *)hash_mem_alloc( hp->items.datalen, hp->items.more * hp->items.size );
-    hp->items.free = 0;
-
-    hp->items.lists[i].nel = hp->items.more;
-    hp->items.lists[i].base = hp->items.next;
-    hp->items.nel += hp->items.more;
-
-    if ( hp->tab.base )
-        hash_mem_free( hp->items.datalen, (char *)hp->tab.base );
-
-    hp->tab.nel = hp->items.nel * hp->bloat;
-    hp->tab.base = (ITEM **)hash_mem_alloc( hp->items.datalen, hp->tab.nel * sizeof(ITEM **) );
-
-    memset( (char *)hp->tab.base, '\0', hp->tab.nel * sizeof( ITEM * ) );
-
-    for ( i = 0; i < hp->items.list; ++i )
-    {
-        int nel = hp->items.lists[i].nel;
-        char *next = hp->items.lists[i].base;
-
-        for ( ; nel--; next += hp->items.size )
-        {
-            register ITEM *i = (ITEM *)next;
-            ITEM **ip = hp->tab.base + i->hdr.keyval % hp->tab.nel;
-            /* code currently assumes rehashing only when there are no free items */
-            assert( i->data.key != 0 );
-
-            i->hdr.next = *ip;
-            *ip = i;
-        }
-    }
-}
-
-void hashenumerate( struct hash * hp, void (* f)( void *, void * ), void * data )
-{
-    int i;
-    for ( i = 0; i <= hp->items.list; ++i )
-    {
-        char * next = hp->items.lists[i].base;
-        int nel = hp->items.lists[i].nel;
-        if ( i == hp->items.list )
-            nel -= hp->items.more;
-
-        for ( ; nel--; next += hp->items.size )
-        {
-            ITEM * i = (ITEM *)next;
-            if ( i->data.key != 0 )  /* DO not enumerate freed items. */
-                f( &i->data, data );
-        }
-    }
-}
-
-/* --- */
-
-# define ALIGNED(x) ( ( x + sizeof( ITEM ) - 1 ) & ~( sizeof( ITEM ) - 1 ) )
-
-/*
- * hashinit() - initialize a hash table, returning a handle
- */
-
-struct hash *
-hashinit(
-    int datalen,
-    char *name )
-{
-    struct hash *hp = (struct hash *)hash_mem_alloc( datalen, sizeof( *hp ) );
-
-    hp->bloat = 3;
-    hp->tab.nel = 0;
-    hp->tab.base = (ITEM **)0;
-    hp->items.more = 0;
-    hp->items.free = 0;
-    hp->items.datalen = datalen;
-    hp->items.size = sizeof( struct hashhdr ) + ALIGNED( datalen );
-    hp->items.list = -1;
-    hp->items.nel = 0;
-    hp->inel = 11 /* 47 */;
-    hp->name = name;
-
-    return hp;
-}
-
-/*
- * hashdone() - free a hash table, given its handle
- */
-
-void
-hashdone( struct hash *hp )
-{
-    int i;
-
-    if ( !hp )
-        return;
-
-    if ( DEBUG_MEM || DEBUG_PROFILE )
-        hashstat( hp );
-
-    if ( hp->tab.base )
-        hash_mem_free( hp->items.datalen, (char *)hp->tab.base );
-    for ( i = 0; i <= hp->items.list; ++i )
-        hash_mem_free( hp->items.datalen, hp->items.lists[i].base );
-    hash_mem_free( hp->items.datalen, (char *)hp );
-}
-
-static void * hash_mem_alloc(size_t datalen, size_t size)
-{
-    if (sizeof(HASHDATA) == datalen)
-    {
-        return BJAM_MALLOC_RAW(size);
-    }
-    else
-    {
-        return BJAM_MALLOC(size);
-    }
-}
-
-static void hash_mem_free(size_t datalen, void * data)
-{
-    if (sizeof(HASHDATA) == datalen)
-    {
-        BJAM_FREE_RAW(data);
-    }
-    else
-    {
-        BJAM_FREE(data);
-    }
-}
-
-#ifdef OPT_BOEHM_GC
-static void hash_mem_finalizer(char * key, struct hash * hp)
-{
-    HASHDATA d;
-    d.key = key;
-    hash_free(hp,&d);
-}
-#endif
-
-
-/* ---- */
-
-static void hashstat( struct hash * hp )
-{
-    ITEM * * tab = hp->tab.base;
-    int nel = hp->tab.nel;
-    int count = 0;
-    int sets = 0;
-    int run = ( tab[ nel - 1 ] != (ITEM *)0 );
-    int i;
-    int here;
-
-    for ( i = nel; i > 0; --i )
-    {
-        if ( ( here = ( *tab++ != (ITEM *)0 ) ) )
-            count++;
-        if ( here && !run )
-            sets++;
-        run = here;
-    }
-
-    printf( "%s table: %d+%d+%d (%dK+%luK) items+table+hash, %f density\n",
-        hp->name,
-        count,
-        hp->items.nel,
-        hp->tab.nel,
-        hp->items.nel * hp->items.size / 1024,
-        (long unsigned)hp->tab.nel * sizeof( ITEM ** ) / 1024,
-        (float)count / (float)sets );
-}
diff --git a/jam-files/engine/hash.h b/jam-files/engine/hash.h
deleted file mode 100644
index 7195b414..00000000
--- a/jam-files/engine/hash.h
+++ /dev/null
@@ -1,25 +0,0 @@
-/*
- * Copyright 1993, 1995 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*
- * hash.h - simple in-memory hashing routines
- */
-
-#ifndef BOOST_JAM_HASH_H
-#define BOOST_JAM_HASH_H
-
-typedef struct hashdata HASHDATA;
-
-struct hash * hashinit     ( int datalen, char * name );
-int           hashitem     ( struct hash * hp, HASHDATA * * data, int enter );
-void          hashdone     ( struct hash * hp );
-void          hashenumerate( struct hash * hp, void (* f)( void *, void * ), void * data );
-int           hash_free    ( struct hash * hp, HASHDATA * data);
-
-#define hashenter( hp, data ) ( !hashitem( hp, data, !0 ) )
-#define hashcheck( hp, data ) hashitem( hp, data, 0 )
-
-#endif
diff --git a/jam-files/engine/hcache.c b/jam-files/engine/hcache.c
deleted file mode 100644
index 70bb798c..00000000
--- a/jam-files/engine/hcache.c
+++ /dev/null
@@ -1,434 +0,0 @@
-/*
- * This file has been donated to Jam.
- */
-
-# include "jam.h"
-# include "lists.h"
-# include "parse.h"
-# include "rules.h"
-# include "regexp.h"
-# include "headers.h"
-# include "newstr.h"
-# include "hash.h"
-# include "hcache.h"
-# include "variable.h"
-# include "search.h"
-
-#ifdef OPT_HEADER_CACHE_EXT
-
-/*
- * Craig W. McPheeters, Alias|Wavefront.
- *
- * hcache.c hcache.h - handle cacheing of #includes in source files.
- *
- * Create a cache of files scanned for headers. When starting jam, look for the
- * cache file and load it if present. When finished the binding phase, create a
- * new header cache. The cache contains files, their timestamps and the header
- * files found in their scan. During the binding phase of jam, look in the
- * header cache first for the headers contained in a file. If the cache is
- * present and valid, use its contents. This results in dramatic speedups with
- * large projects (eg. 3min -> 1min startup for one project.)
- *
- * External routines:
- *    hcache_init() - read and parse the local .jamdeps file.
- *    hcache_done() - write a new .jamdeps file.
- *    hcache()      - return list of headers on target. Use cache or do a scan.
- *
- * The dependency file format is an ASCII file with 1 line per target. Each line
- * has the following fields:
- * @boundname@ timestamp @file@ @file@ @file@ ... \n
- */
-
-typedef struct hcachedata HCACHEDATA ;
-
-struct hcachedata
-{
-    char       * boundname;
-    time_t       time;
-    LIST       * includes;
-    LIST       * hdrscan;    /* the HDRSCAN value for this target */
-    int          age;        /* if too old, we'll remove it from cache */
-    HCACHEDATA * next;
-};
-
-
-static struct hash * hcachehash = 0;
-static HCACHEDATA  * hcachelist = 0;
-
-static int queries = 0;
-static int hits = 0;
-
-#define CACHE_FILE_VERSION "version 4"
-#define CACHE_RECORD_HEADER "header"
-#define CACHE_RECORD_END "end"
-
-
-/*
- * Return the name of the header cache file. May return NULL.
- *
- * The user sets this by setting the HCACHEFILE variable in a Jamfile. We cache
- * the result so the user can not change the cache file during header scanning.
- */
-
-static char * cache_name( void )
-{
-    static char * name = 0;
-    if ( !name )
-    {
-        LIST * hcachevar = var_get( "HCACHEFILE" );
-
-        if ( hcachevar )
-        {
-            TARGET * t = bindtarget( hcachevar->string );
-
-            pushsettings( t->settings );
-            /* Do not expect the cache file to be generated, so pass 0 as the
-             * third argument to search. Expect the location to be specified via
-             * LOCATE, so pass 0 as the fourth arugment.
-             */
-            t->boundname = search( t->name, &t->time, 0, 0 );
-            popsettings( t->settings );
-
-            if ( hcachevar )
-                name = copystr( t->boundname );
-        }
-    }
-    return name;
-}
-
-
-/*
- * Return the maximum age a cache entry can have before it is purged ftom the
- * cache.
- */
-
-static int cache_maxage( void )
-{
-    int age = 100;
-    LIST * var = var_get( "HCACHEMAXAGE" );
-    if ( var )
-    {
-        age = atoi( var->string );
-        if ( age < 0 )
-            age = 0;
-    }
-    return age;
-}
-
-
-/*
- * Read a netstring. The caveat is that the string can not contain ASCII 0. The
- * returned value is as returned by newstr(), so it need not be freed.
- */
-
-char * read_netstring( FILE * f )
-{
-    unsigned long len;
-    static char * buf = NULL;
-    static unsigned long buf_len = 0;
-
-    if ( fscanf( f, " %9lu", &len ) != 1 )
-        return NULL;
-    if ( fgetc( f ) != (int)'\t' )
-        return NULL;
-
-    if ( len > 1024 * 64 )
-        return NULL;  /* sanity check */
-
-    if ( len > buf_len )
-    {
-        unsigned long new_len = buf_len * 2;
-        if ( new_len < len )
-            new_len = len;
-        buf = (char *)BJAM_REALLOC( buf, new_len + 1 );
-        if ( buf )
-            buf_len = new_len;
-    }
-
-    if ( !buf )
-        return NULL;
-
-    if ( fread( buf, 1, len, f ) != len )
-        return NULL;
-    if ( fgetc( f ) != (int)'\n' )
-        return NULL;
-
-    buf[ len ] = 0;
-    return newstr( buf );
-}
-
-
-/*
- * Write a netstring.
- */
-
-void write_netstring( FILE * f, char const * s )
-{
-    if ( !s )
-        s = "";
-    fprintf( f, "%lu\t%s\n", (long unsigned)strlen( s ), s );
-}
-
-
-void hcache_init()
-{
-    HCACHEDATA   cachedata;
-    HCACHEDATA * c;
-    FILE       * f;
-    char       * version;
-    int          header_count = 0;
-    char       * hcachename;
-
-    hcachehash = hashinit( sizeof( HCACHEDATA ), "hcache" );
-
-    if ( !( hcachename = cache_name() ) )
-        return;
-
-    if ( !( f = fopen( hcachename, "rb" ) ) )
-        return;
-
-    version = read_netstring( f );
-    if ( !version || strcmp( version, CACHE_FILE_VERSION ) )
-    {
-        fclose( f );
-        return;
-    }
-
-    while ( 1 )
-    {
-        char * record_type;
-        char * time_str;
-        char * age_str;
-        char * includes_count_str;
-        char * hdrscan_count_str;
-        int    i;
-        int    count;
-        LIST * l;
-
-        record_type = read_netstring( f );
-        if ( !record_type )
-        {
-            fprintf( stderr, "invalid %s\n", hcachename );
-            goto bail;
-        }
-        if ( !strcmp( record_type, CACHE_RECORD_END ) )
-            break;
-        if ( strcmp( record_type, CACHE_RECORD_HEADER ) )
-        {
-            fprintf( stderr, "invalid %s with record separator <%s>\n",
-                hcachename, record_type ? record_type : "<null>" );
-            goto bail;
-        }
-
-        c = &cachedata;
-
-        c->boundname       = read_netstring( f );
-        time_str           = read_netstring( f );
-        age_str            = read_netstring( f );
-        includes_count_str = read_netstring( f );
-
-        if ( !c->boundname || !time_str || !age_str || !includes_count_str )
-        {
-            fprintf( stderr, "invalid %s\n", hcachename );
-            goto bail;
-        }
-
-        c->time = atoi( time_str );
-        c->age = atoi( age_str ) + 1;
-
-        count = atoi( includes_count_str );
-        for ( l = 0, i = 0; i < count; ++i )
-        {
-            char * s = read_netstring( f );
-            if ( !s )
-            {
-                fprintf( stderr, "invalid %s\n", hcachename );
-                goto bail;
-            }
-            l = list_new( l, s );
-        }
-        c->includes = l;
-
-        hdrscan_count_str = read_netstring( f );
-        if ( !includes_count_str )
-        {
-            list_free( c->includes );
-            fprintf( stderr, "invalid %s\n", hcachename );
-            goto bail;
-        }
-
-        count = atoi( hdrscan_count_str );
-        for ( l = 0, i = 0; i < count; ++i )
-        {
-            char * s = read_netstring( f );
-            if ( !s )
-            {
-                fprintf( stderr, "invalid %s\n", hcachename );
-                goto bail;
-            }
-            l = list_new( l, s );
-        }
-        c->hdrscan = l;
-
-        if ( !hashenter( hcachehash, (HASHDATA * *)&c ) )
-        {
-            fprintf( stderr, "can't insert header cache item, bailing on %s\n",
-                hcachename );
-            goto bail;
-        }
-
-        c->next = hcachelist;
-        hcachelist = c;
-
-        ++header_count;
-    }
-
-    if ( DEBUG_HEADER )
-        printf( "hcache read from file %s\n", hcachename );
-
- bail:
-    fclose( f );
-}
-
-
-void hcache_done()
-{
-    FILE       * f;
-    HCACHEDATA * c;
-    int          header_count = 0;
-    char       * hcachename;
-    int          maxage;
-
-    if ( !hcachehash )
-        return;
-
-    if ( !( hcachename = cache_name() ) )
-        return;
-
-    if ( !( f = fopen( hcachename, "wb" ) ) )
-        return;
-
-    maxage = cache_maxage();
-
-    /* Print out the version. */
-    write_netstring( f, CACHE_FILE_VERSION );
-
-    c = hcachelist;
-    for ( c = hcachelist; c; c = c->next )
-    {
-        LIST * l;
-        char   time_str[ 30 ];
-        char   age_str[ 30 ];
-        char   includes_count_str[ 30 ];
-        char   hdrscan_count_str[ 30 ];
-
-        if ( maxage == 0 )
-            c->age = 0;
-        else if ( c->age > maxage )
-            continue;
-
-        sprintf( includes_count_str, "%lu", (long unsigned) list_length( c->includes ) );
-        sprintf( hdrscan_count_str, "%lu", (long unsigned) list_length( c->hdrscan ) );
-        sprintf( time_str, "%lu", (long unsigned) c->time );
-        sprintf( age_str, "%lu", (long unsigned) c->age );
-
-        write_netstring( f, CACHE_RECORD_HEADER );
-        write_netstring( f, c->boundname );
-        write_netstring( f, time_str );
-        write_netstring( f, age_str );
-        write_netstring( f, includes_count_str );
-        for ( l = c->includes; l; l = list_next( l ) )
-            write_netstring( f, l->string );
-        write_netstring( f, hdrscan_count_str );
-        for ( l = c->hdrscan; l; l = list_next( l ) )
-            write_netstring( f, l->string );
-        fputs( "\n", f );
-        ++header_count;
-    }
-    write_netstring( f, CACHE_RECORD_END );
-
-    if ( DEBUG_HEADER )
-        printf( "hcache written to %s.   %d dependencies, %.0f%% hit rate\n",
-            hcachename, header_count, queries ? 100.0 * hits / queries : 0 );
-
-    fclose ( f );
-}
-
-
-LIST * hcache( TARGET * t, int rec, regexp * re[], LIST * hdrscan )
-{
-    HCACHEDATA cachedata;
-    HCACHEDATA * c = &cachedata;
-
-    LIST * l = 0;
-
-    ++queries;
-
-    c->boundname = t->boundname;
-
-    if (hashcheck (hcachehash, (HASHDATA **) &c))
-    {
-    if (c->time == t->time)
-    {
-        LIST *l1 = hdrscan, *l2 = c->hdrscan;
-        while (l1 && l2) {
-        if (l1->string != l2->string) {
-            l1 = NULL;
-        } else {
-            l1 = list_next(l1);
-            l2 = list_next(l2);
-        }
-        }
-        if (l1 || l2) {
-        if (DEBUG_HEADER)
-            printf("HDRSCAN out of date in cache for %s\n",
-               t->boundname);
-
-        printf("HDRSCAN out of date for %s\n", t->boundname);
-        printf(" real  : ");
-        list_print(hdrscan);
-        printf("\n cached: ");
-        list_print(c->hdrscan);
-        printf("\n");
-
-        list_free(c->includes);
-        list_free(c->hdrscan);
-        c->includes = 0;
-        c->hdrscan = 0;
-        } else {
-        if (DEBUG_HEADER)
-            printf ("using header cache for %s\n", t->boundname);
-        c->age = 0;
-        ++hits;
-        l = list_copy (0, c->includes);
-        return l;
-        }
-    } else {
-        if (DEBUG_HEADER)
-            printf ("header cache out of date for %s\n", t->boundname);
-        list_free (c->includes);
-        list_free(c->hdrscan);
-        c->includes = 0;
-        c->hdrscan = 0;
-    }
-    } else {
-    if (hashenter (hcachehash, (HASHDATA **)&c)) {
-        c->boundname = newstr (c->boundname);
-        c->next = hcachelist;
-        hcachelist = c;
-    }
-    }
-
-    /* 'c' points at the cache entry. Its out of date. */
-
-    l = headers1 (0, t->boundname, rec, re);
-
-    c->time = t->time;
-    c->age = 0;
-    c->includes = list_copy (0, l);
-    c->hdrscan = list_copy(0, hdrscan);
-
-    return l;
-}
-
-#endif
diff --git a/jam-files/engine/hcache.h b/jam-files/engine/hcache.h
deleted file mode 100644
index c316e3bc..00000000
--- a/jam-files/engine/hcache.h
+++ /dev/null
@@ -1,18 +0,0 @@
-/*
- * This file is not part of Jam
- */
-
-/*
- * hcache.h - handle #includes in source files
- */
-#ifndef HCACHE_H
-# define HCACHE_H
-
-# include "regexp.h"
-# include "lists.h"
-
-void hcache_init(void);
-void hcache_done(void);
-LIST *hcache(TARGET *t, int rec, regexp *re[], LIST *hdrscan);
-
-#endif
diff --git a/jam-files/engine/hdrmacro.c b/jam-files/engine/hdrmacro.c
deleted file mode 100644
index 43031d48..00000000
--- a/jam-files/engine/hdrmacro.c
+++ /dev/null
@@ -1,137 +0,0 @@
-/*
- * Copyright 1993, 2000 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*  This file is ALSO:
- *  Copyright 2001-2004 David Abrahams.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-
-# include "jam.h"
-# include "lists.h"
-# include "parse.h"
-# include "compile.h"
-# include "rules.h"
-# include "variable.h"
-# include "regexp.h"
-# include "hdrmacro.h"
-# include "hash.h"
-# include "newstr.h"
-# include "strings.h"
-
-/*
- * hdrmacro.c - handle header files that define macros used in
- *              #include statements.
- *
- *  we look for lines like "#define MACRO  <....>" or '#define MACRO  "    "'
- *  in the target file. When found, we
- *
- *  we then phony up a rule invocation like:
- *
- *  $(HDRRULE) <target> : <resolved included files> ;
- *
- * External routines:
- *    headers1() - scan a target for "#include MACRO" lines and try
- *                 to resolve them when needed
- *
- * Internal routines:
- *    headers1() - using regexp, scan a file and build include LIST
- *
- * 04/13/94 (seiwald) - added shorthand L0 for null list pointer
- * 09/10/00 (seiwald) - replaced call to compile_rule with evaluate_rule,
- *      so that headers() doesn't have to mock up a parse structure
- *      just to invoke a rule.
- */
-
-/* this type is used to store a dictionary of file header macros */
-typedef struct header_macro
-{
-  char * symbol;
-  char * filename;  /* we could maybe use a LIST here ?? */
-} HEADER_MACRO;
-
-static struct hash * header_macros_hash = 0;
-
-
-/*
- * headers() - scan a target for include files and call HDRRULE
- */
-
-# define MAXINC 10
-
-void
-macro_headers( TARGET *t )
-{
-    static regexp *re = 0;
-    FILE    *f;
-    char    buf[ 1024 ];
-
-    if ( DEBUG_HEADER )
-        printf( "macro header scan for %s\n", t->name );
-
-    /* this regexp is used to detect lines of the form       */
-    /* "#define  MACRO  <....>" or "#define  MACRO  "....."  */
-    /* in the header macro files..                           */
-    if ( re == 0 )
-    {
-        re = regex_compile(
-            "^[     ]*#[    ]*define[   ]*([A-Za-z][A-Za-z0-9_]*)[  ]*"
-            "[<\"]([^\">]*)[\">].*$" );
-    }
-
-    if ( !( f = fopen( t->boundname, "r" ) ) )
-        return;
-
-    while ( fgets( buf, sizeof( buf ), f ) )
-    {
-        HEADER_MACRO var;
-        HEADER_MACRO *v = &var;
-
-        if ( regexec( re, buf ) && re->startp[1] )
-        {
-            /* we detected a line that looks like "#define  MACRO  filename */
-            re->endp[1][0] = '\0';
-            re->endp[2][0] = '\0';
-
-            if ( DEBUG_HEADER )
-                printf( "macro '%s' used to define filename '%s' in '%s'\n",
-                        re->startp[1], re->startp[2], t->boundname );
-
-            /* add macro definition to hash table */
-            if ( !header_macros_hash )
-                header_macros_hash = hashinit( sizeof( HEADER_MACRO ), "hdrmacros" );
-
-            v->symbol   = re->startp[1];
-            v->filename = 0;
-            if ( hashenter( header_macros_hash, (HASHDATA **)&v ) )
-            {
-                v->symbol   = newstr( re->startp[1] );  /* never freed */
-                v->filename = newstr( re->startp[2] );  /* never freed */
-            }
-            /* XXXX: FOR NOW, WE IGNORE MULTIPLE MACRO DEFINITIONS !! */
-            /*       WE MIGHT AS WELL USE A LIST TO STORE THEM..      */
-        }
-    }
-
-    fclose( f );
-}
-
-
-char * macro_header_get( const char * macro_name )
-{
-    HEADER_MACRO var;
-    HEADER_MACRO * v = &var;
-
-    v->symbol = (char* )macro_name;
-
-    if ( header_macros_hash && hashcheck( header_macros_hash, (HASHDATA **)&v ) )
-    {
-        if ( DEBUG_HEADER )
-            printf( "### macro '%s' evaluated to '%s'\n", macro_name, v->filename );
-        return v->filename;
-    }
-    return 0;
-}
diff --git a/jam-files/engine/hdrmacro.h b/jam-files/engine/hdrmacro.h
deleted file mode 100644
index 08cc1116..00000000
--- a/jam-files/engine/hdrmacro.h
+++ /dev/null
@@ -1,14 +0,0 @@
-/*
- * Copyright 1993, 1995 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*
- * hdrmacro.h - parses header files for #define MACRO  <filename> or
- *              #define MACRO  "filename" definitions
- */
-
-void   macro_headers( TARGET *t );
-
-char*  macro_header_get( const char*  macro_name );
diff --git a/jam-files/engine/headers.c b/jam-files/engine/headers.c
deleted file mode 100644
index b9d8f637..00000000
--- a/jam-files/engine/headers.c
+++ /dev/null
@@ -1,203 +0,0 @@
-/*
- * Copyright 1993, 2000 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-/*  This file is ALSO:
- *  Copyright 2001-2004 David Abrahams.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-
-# include "jam.h"
-# include "lists.h"
-# include "parse.h"
-# include "compile.h"
-# include "rules.h"
-# include "variable.h"
-# include "regexp.h"
-# include "headers.h"
-# include "hdrmacro.h"
-# include "newstr.h"
-
-#ifdef OPT_HEADER_CACHE_EXT
-# include "hcache.h"
-#endif
-
-/*
- * headers.c - handle #includes in source files
- *
- * Using regular expressions provided as the variable $(HDRSCAN),
- * headers() searches a file for #include files and phonies up a
- * rule invocation:
- *
- *  $(HDRRULE) <target> : <include files> ;
- *
- * External routines:
- *    headers() - scan a target for include files and call HDRRULE
- *
- * Internal routines:
- *    headers1() - using regexp, scan a file and build include LIST
- *
- * 04/13/94 (seiwald) - added shorthand L0 for null list pointer
- * 09/10/00 (seiwald) - replaced call to compile_rule with evaluate_rule,
- *      so that headers() doesn't have to mock up a parse structure
- *      just to invoke a rule.
- */
-
-#ifndef OPT_HEADER_CACHE_EXT
-static LIST *headers1( LIST *l, char *file, int rec, regexp *re[]);
-#endif
-
-/*
- * headers() - scan a target for include files and call HDRRULE
- */
-
-# define MAXINC 10
-
-void
-headers( TARGET *t )
-{
-    LIST   * hdrscan;
-    LIST   * hdrrule;
-	#ifndef OPT_HEADER_CACHE_EXT
-    LIST   * headlist = 0;
-	#endif
-    regexp * re[ MAXINC ];
-    int rec = 0;
-
-    if ( !( hdrscan = var_get( "HDRSCAN" ) ) ||
-        !( hdrrule = var_get( "HDRRULE" ) ) )
-        return;
-
-    if ( DEBUG_HEADER )
-        printf( "header scan %s\n", t->name );
-
-    /* Compile all regular expressions in HDRSCAN */
-    while ( ( rec < MAXINC ) && hdrscan )
-    {
-        re[ rec++ ] = regex_compile( hdrscan->string );
-        hdrscan = list_next( hdrscan );
-    }
-
-    /* Doctor up call to HDRRULE rule */
-    /* Call headers1() to get LIST of included files. */
-    {
-        FRAME   frame[1];
-        frame_init( frame );
-        lol_add( frame->args, list_new( L0, t->name ) );
-#ifdef OPT_HEADER_CACHE_EXT
-        lol_add( frame->args, hcache( t, rec, re, hdrscan ) );
-#else
-        lol_add( frame->args, headers1( headlist, t->boundname, rec, re ) );
-#endif
-
-        if ( lol_get( frame->args, 1 ) )
-        {
-            /* The third argument to HDRRULE is the bound name of
-             * $(<) */
-            lol_add( frame->args, list_new( L0, t->boundname ) );
-
-            list_free( evaluate_rule( hdrrule->string, frame ) );
-        }
-
-        /* Clean up. */
-        frame_free( frame );
-    }
-}
-
-
-/*
- * headers1() - using regexp, scan a file and build include LIST.
- */
-
-#ifdef OPT_HEADER_CACHE_EXT
-LIST *
-#else
-static LIST *
-#endif
-headers1(
-    LIST    * l,
-    char    * file,
-    int rec,
-    regexp  * re[] )
-{
-    FILE * f;
-    char buf[ 1024 ];
-    int  i;
-    static regexp * re_macros = 0;
-
-#ifdef OPT_IMPROVED_PATIENCE_EXT
-    static int count = 0;
-    ++count;
-    if ( ((count == 100) || !( count % 1000 )) && DEBUG_MAKE )
-        printf("...patience...\n");
-#endif
-
-    /* the following regexp is used to detect cases where a  */
-    /* file is included through a line line "#include MACRO" */
-    if ( re_macros == 0 )
-        re_macros = regex_compile(
-            "^[     ]*#[    ]*include[  ]*([A-Za-z][A-Za-z0-9_]*).*$" );
-
-    if ( !( f = fopen( file, "r" ) ) )
-        return l;
-
-    while ( fgets( buf, sizeof( buf ), f ) )
-    {
-        int size = strlen( buf );
-        /* Remove trailing \r and \n, if any. */
-        while ( ( size > 0 ) &&
-            ( buf[ size - 1 ] == '\n' ) &&
-            ( buf[ size - 1 ] == '\r' ) )
-        {
-            buf[ size - 1 ] = '\0';
-            --size;
-        }
-
-        for ( i = 0; i < rec; ++i )
-            if ( regexec( re[i], buf ) && re[i]->startp[1] )
-            {
-                re[i]->endp[1][0] = '\0';
-
-                if ( DEBUG_HEADER )
-                    printf( "header found: %s\n", re[i]->startp[1] );
-
-                l = list_new( l, newstr( re[i]->startp[1] ) );
-            }
-
-        /* special treatment for #include MACRO */
-        if ( regexec( re_macros, buf ) && re_macros->startp[1] )
-        {
-            char*  header_filename;
-
-            re_macros->endp[1][0] = '\0';
-
-            if ( DEBUG_HEADER )
-                printf( "macro header found: %s", re_macros->startp[1] );
-
-            header_filename = macro_header_get( re_macros->startp[1] );
-            if ( header_filename )
-            {
-                if ( DEBUG_HEADER )
-                    printf( " resolved to '%s'\n", header_filename );
-                l = list_new( l, newstr( header_filename ) );
-            }
-            else
-            {
-                if ( DEBUG_HEADER )
-                    printf( " ignored !!\n" );
-            }
-        }
-    }
-
-    fclose( f );
-
-    return l;
-}
-
-
-void regerror( char * s )
-{
-    printf( "re error %s\n", s );
-}
diff --git a/jam-files/engine/headers.h b/jam-files/engine/headers.h
deleted file mode 100644
index 624475fe..00000000
--- a/jam-files/engine/headers.h
+++ /dev/null
@@ -1,16 +0,0 @@
-/*
- * Copyright 1993, 1995 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*
- * headers.h - handle #includes in source files
- */
-
-void headers( TARGET *t );
-
-#ifdef OPT_HEADER_CACHE_EXT
-struct regexp;
-LIST *headers1( LIST *l, char *file, int rec, struct regexp *re[] );
-#endif
diff --git a/jam-files/engine/jam.c b/jam-files/engine/jam.c
deleted file mode 100644
index e11d082b..00000000
--- a/jam-files/engine/jam.c
+++ /dev/null
@@ -1,632 +0,0 @@
-/*
- * /+\
- * +\   Copyright 1993-2002 Christopher Seiwald and Perforce Software, Inc.
- * \+/
- *
- * This file is part of jam.
- *
- * License is hereby granted to use this software and distribute it
- * freely, as long as this copyright notice is retained and modifications
- * are clearly marked.
- *
- * ALL WARRANTIES ARE HEREBY DISCLAIMED.
- */
-
-/*  This file is ALSO:
- *  Copyright 2001-2004 David Abrahams.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-
-/*
- * jam.c - make redux
- *
- * See Jam.html for usage information.
- *
- * These comments document the code.
- *
- * The top half of the code is structured such:
- *
- *                       jam
- *                      / | \
- *                 +---+  |  \
- *                /       |   \
- *         jamgram     option  \
- *        /  |   \              \
- *       /   |    \              \
- *      /    |     \             |
- *  scan     |     compile      make
- *   |       |    /  | \       / |  \
- *   |       |   /   |  \     /  |   \
- *   |       |  /    |   \   /   |    \
- * jambase parse     |   rules  search make1
- *                   |           |      |   \
- *                   |           |      |    \
- *                   |           |      |     \
- *               builtins    timestamp command execute
- *                               |
- *                               |
- *                               |
- *                             filesys
- *
- *
- * The support routines are called by all of the above, but themselves
- * are layered thus:
- *
- *                     variable|expand
- *                      /  |   |   |
- *                     /   |   |   |
- *                    /    |   |   |
- *                 lists   |   |   pathsys
- *                    \    |   |
- *                     \   |   |
- *                      \  |   |
- *                     newstr  |
- *                        \    |
- *                         \   |
- *                          \  |
- *                          hash
- *
- * Roughly, the modules are:
- *
- *  builtins.c - jam's built-in rules
- *  command.c - maintain lists of commands
- *  compile.c - compile parsed jam statements
- *  execunix.c - execute a shell script on UNIX
- *  execvms.c - execute a shell script, ala VMS
- *  expand.c - expand a buffer, given variable values
- *  file*.c - scan directories and archives on *
- *  hash.c - simple in-memory hashing routines
- *  hdrmacro.c - handle header file parsing for filename macro definitions
- *  headers.c - handle #includes in source files
- *  jambase.c - compilable copy of Jambase
- *  jamgram.y - jam grammar
- *  lists.c - maintain lists of strings
- *  make.c - bring a target up to date, once rules are in place
- *  make1.c - execute command to bring targets up to date
- *  newstr.c - string manipulation routines
- *  option.c - command line option processing
- *  parse.c - make and destroy parse trees as driven by the parser
- *  path*.c - manipulate file names on *
- *  hash.c - simple in-memory hashing routines
- *  regexp.c - Henry Spencer's regexp
- *  rules.c - access to RULEs, TARGETs, and ACTIONs
- *  scan.c - the jam yacc scanner
- *  search.c - find a target along $(SEARCH) or $(LOCATE)
- *  timestamp.c - get the timestamp of a file or archive member
- *  variable.c - handle jam multi-element variables
- *
- * 05/04/94 (seiwald) - async multiprocess (-j) support
- * 02/08/95 (seiwald) - -n implies -d2.
- * 02/22/95 (seiwald) - -v for version info.
- * 09/11/00 (seiwald) - PATCHLEVEL folded into VERSION.
- * 01/10/01 (seiwald) - pathsys.h split from filesys.h
- */
-
-
-#include "jam.h"
-#include "option.h"
-#include "patchlevel.h"
-
-/* These get various function declarations. */
-#include "lists.h"
-#include "parse.h"
-#include "variable.h"
-#include "compile.h"
-#include "builtins.h"
-#include "rules.h"
-#include "newstr.h"
-#include "scan.h"
-#include "timestamp.h"
-#include "make.h"
-#include "strings.h"
-#include "expand.h"
-#include "filesys.h"
-#include "output.h"
-
-/* Macintosh is "special" */
-#ifdef OS_MAC
-    #include <QuickDraw.h>
-#endif
-
-/* And UNIX for this. */
-#ifdef unix
-    #include <sys/utsname.h>
-    #include <signal.h>
-#endif
-
-struct globs globs =
-{
-    0,          /* noexec */
-    1,          /* jobs */
-    0,          /* quitquick */
-    0,          /* newestfirst */
-    0,          /* pipes action stdout and stderr merged to action output */
-#ifdef OS_MAC
-    { 0, 0 },   /* debug - suppress tracing output */
-#else
-    { 0, 1 },   /* debug ... */
-#endif
-    0,          /* output commands, not run them */
-    0           /* action timeout */
-};
-
-/* Symbols to be defined as true for use in Jambase. */
-static char * othersyms[] = { OSMAJOR, OSMINOR, OSPLAT, JAMVERSYM, 0 };
-
-
-/* Known for sure:
- *  mac needs arg_enviro
- *  OS2 needs extern environ
- */
-
-#ifdef OS_MAC
-    #define use_environ arg_environ
-    #ifdef MPW
-        QDGlobals qd;
-    #endif
-#endif
-
-/* on Win32-LCC */
-#if defined( OS_NT ) && defined( __LCC__ )
-    #define use_environ _environ
-#endif
-
-# if defined( __MWERKS__)
-    #define use_environ _environ
-    extern char * * _environ;
-#endif
-
-#ifndef use_environ
-    #define use_environ environ
-    #if !defined( __WATCOM__ ) && !defined( OS_OS2 ) && !defined( OS_NT )
-        extern char **environ;
-    #endif
-#endif
-
-#if YYDEBUG != 0
-    extern int yydebug;
-#endif
-
-#ifndef NDEBUG
-static void run_unit_tests()
-{
-#if defined( USE_EXECNT )
-    extern void execnt_unit_test();
-    execnt_unit_test();
-#endif
-    string_unit_test();
-    var_expand_unit_test();
-}
-#endif
-
-int anyhow = 0;
-
-#ifdef HAVE_PYTHON
-    extern PyObject * bjam_call         ( PyObject * self, PyObject * args );
-    extern PyObject * bjam_import_rule  ( PyObject * self, PyObject * args );
-    extern PyObject * bjam_define_action( PyObject * self, PyObject * args );
-    extern PyObject * bjam_variable     ( PyObject * self, PyObject * args );
-    extern PyObject * bjam_backtrace    ( PyObject * self, PyObject * args );
-    extern PyObject * bjam_caller       ( PyObject * self, PyObject * args );
-#endif
-
-char *saved_argv0;
-
-int main( int argc, char * * argv, char * * arg_environ )
-{
-    int                     n;
-    char                  * s;
-    struct bjam_option      optv[N_OPTS];
-    char            const * all = "all";
-    int                     status;
-    int                     arg_c = argc;
-    char          *       * arg_v = argv;
-    char            const * progname = argv[0];
-
-    saved_argv0 = argv[0];
-
-    BJAM_MEM_INIT();
-
-# ifdef OS_MAC
-    InitGraf(&qd.thePort);
-# endif
-
-    --argc;
-    ++argv;
-
-    if ( getoptions( argc, argv, "-:l:d:j:p:f:gs:t:ano:qv", optv ) < 0 )
-    {
-        printf( "\nusage: %s [ options ] targets...\n\n", progname );
-
-        printf( "-a      Build all targets, even if they are current.\n" );
-        printf( "-dx     Set the debug level to x (0-9).\n" );
-        printf( "-fx     Read x instead of Jambase.\n" );
-        /* printf( "-g      Build from newest sources first.\n" ); */
-        printf( "-jx     Run up to x shell commands concurrently.\n" );
-        printf( "-lx     Limit actions to x number of seconds after which they are stopped.\n" );
-        printf( "-n      Don't actually execute the updating actions.\n" );
-        printf( "-ox     Write the updating actions to file x.\n" );
-        printf( "-px     x=0, pipes action stdout and stderr merged into action output.\n" );
-        printf( "-q      Quit quickly as soon as a target fails.\n" );
-        printf( "-sx=y   Set variable x=y, overriding environment.\n" );
-        printf( "-tx     Rebuild x, even if it is up-to-date.\n" );
-        printf( "-v      Print the version of jam and exit.\n" );
-        printf( "--x     Option is ignored.\n\n" );
-
-        exit( EXITBAD );
-    }
-
-    /* Version info. */
-    if ( ( s = getoptval( optv, 'v', 0 ) ) )
-    {
-        printf( "Boost.Jam  " );
-        printf( "Version %s. %s.\n", VERSION, OSMINOR );
-        printf( "   Copyright 1993-2002 Christopher Seiwald and Perforce Software, Inc.  \n" );
-        printf( "   Copyright 2001 David Turner.\n" );
-        printf( "   Copyright 2001-2004 David Abrahams.\n" );
-        printf( "   Copyright 2002-2008 Rene Rivera.\n" );
-        printf( "   Copyright 2003-2008 Vladimir Prus.\n" );
-
-        return EXITOK;
-    }
-
-    /* Pick up interesting options. */
-    if ( ( s = getoptval( optv, 'n', 0 ) ) )
-        globs.noexec++, globs.debug[2] = 1;
-
-    if ( ( s = getoptval( optv, 'p', 0 ) ) )
-    {
-        /* Undocumented -p3 (acts like both -p1 -p2) means separate pipe action
-         * stdout and stderr.
-         */
-        globs.pipe_action = atoi( s );
-        if ( ( 3 < globs.pipe_action ) || ( globs.pipe_action < 0 ) )
-        {
-            printf(
-                "Invalid pipe descriptor '%d', valid values are -p[0..3].\n",
-                globs.pipe_action );
-            exit( EXITBAD );
-        }
-    }
-
-    if ( ( s = getoptval( optv, 'q', 0 ) ) )
-        globs.quitquick = 1;
-
-    if ( ( s = getoptval( optv, 'a', 0 ) ) )
-        anyhow++;
-
-    if ( ( s = getoptval( optv, 'j', 0 ) ) )
-    {
-        globs.jobs = atoi( s );
-        if (globs.jobs == 0)
-        {
-            printf("Invalid value for the '-j' option.\n");
-            exit(EXITBAD);
-        }
-    }
-
-    if ( ( s = getoptval( optv, 'g', 0 ) ) )
-        globs.newestfirst = 1;
-
-    if ( ( s = getoptval( optv, 'l', 0 ) ) )
-        globs.timeout = atoi( s );
-
-    /* Turn on/off debugging */
-    for ( n = 0; ( s = getoptval( optv, 'd', n ) ); ++n )
-    {
-        int i;
-
-        /* First -d, turn off defaults. */
-        if ( !n )
-            for ( i = 0; i < DEBUG_MAX; ++i )
-                globs.debug[i] = 0;
-
-        i = atoi( s );
-
-        if ( ( i < 0 ) || ( i >= DEBUG_MAX ) )
-        {
-            printf( "Invalid debug level '%s'.\n", s );
-            continue;
-        }
-
-        /* n turns on levels 1-n. */
-        /* +n turns on level n. */
-        if ( *s == '+' )
-            globs.debug[i] = 1;
-        else while ( i )
-            globs.debug[i--] = 1;
-    }
-
-    {
-        PROFILE_ENTER( MAIN );
-
-#ifdef HAVE_PYTHON
-        {
-            PROFILE_ENTER( MAIN_PYTHON );
-            Py_Initialize();
-            {
-                static PyMethodDef BjamMethods[] = {
-                    {"call", bjam_call, METH_VARARGS,
-                     "Call the specified bjam rule."},
-                    {"import_rule", bjam_import_rule, METH_VARARGS,
-                     "Imports Python callable to bjam."},
-                    {"define_action", bjam_define_action, METH_VARARGS,
-                     "Defines a command line action."},
-                    {"variable", bjam_variable, METH_VARARGS,
-                     "Obtains a variable from bjam's global module."},
-                    {"backtrace", bjam_backtrace, METH_VARARGS,
-                     "Returns bjam backtrace from the last call into Python."},
-                    {"caller", bjam_caller, METH_VARARGS,
-                     "Returns the module from which the last call into Python is made."},
-                    {NULL, NULL, 0, NULL}
-                };
-
-                Py_InitModule( "bjam", BjamMethods );
-            }
-            PROFILE_EXIT( MAIN_PYTHON );
-        }
-#endif
-
-#ifndef NDEBUG
-        run_unit_tests();
-#endif
-#if YYDEBUG != 0
-        if ( DEBUG_PARSE )
-            yydebug = 1;
-#endif
-
-        /* Set JAMDATE. */
-        var_set( "JAMDATE", list_new( L0, outf_time(time(0)) ), VAR_SET );
-
-        /* Set JAM_VERSION. */
-        var_set( "JAM_VERSION",
-                 list_new( list_new( list_new( L0,
-                   newstr( VERSION_MAJOR_SYM ) ),
-                   newstr( VERSION_MINOR_SYM ) ),
-                   newstr( VERSION_PATCH_SYM ) ),
-                   VAR_SET );
-
-        /* Set JAMUNAME. */
-#ifdef unix
-        {
-            struct utsname u;
-
-            if ( uname( &u ) >= 0 )
-            {
-                var_set( "JAMUNAME",
-                         list_new(
-                             list_new(
-                                 list_new(
-                                     list_new(
-                                         list_new( L0,
-                                            newstr( u.sysname ) ),
-                                         newstr( u.nodename ) ),
-                                     newstr( u.release ) ),
-                                 newstr( u.version ) ),
-                             newstr( u.machine ) ), VAR_SET );
-            }
-        }
-#endif /* unix */
-
-        /* Load up environment variables. */
-
-        /* First into the global module, with splitting, for backward
-         * compatibility.
-         */
-        var_defines( use_environ, 1 );
-
-        /* Then into .ENVIRON, without splitting. */
-        enter_module( bindmodule(".ENVIRON") );
-        var_defines( use_environ, 0 );
-        exit_module( bindmodule(".ENVIRON") );
-
-        /*
-         * Jam defined variables OS & OSPLAT. We load them after environment, so
-         * that setting OS in environment does not change Jam's notion of the
-         * current platform.
-         */
-        var_defines( othersyms, 1 );
-
-        /* Load up variables set on command line. */
-        for ( n = 0; ( s = getoptval( optv, 's', n ) ); ++n )
-        {
-            char *symv[2];
-            symv[ 0 ] = s;
-            symv[ 1 ] = 0;
-            var_defines( symv, 1 );
-            enter_module( bindmodule(".ENVIRON") );
-            var_defines( symv, 0 );
-            exit_module( bindmodule(".ENVIRON") );
-        }
-
-        /* Set the ARGV to reflect the complete list of arguments of invocation.
-         */
-        for ( n = 0; n < arg_c; ++n )
-            var_set( "ARGV", list_new( L0, newstr( arg_v[n] ) ), VAR_APPEND );
-
-        /* Initialize built-in rules. */
-        load_builtins();
-
-        /* Add the targets in the command line to the update list. */
-        for ( n = 1; n < arg_c; ++n )
-        {
-            if ( arg_v[ n ][ 0 ] == '-' )
-            {
-                char * f = "-:l:d:j:f:gs:t:ano:qv";
-                for ( ; *f; ++f ) if ( *f == arg_v[ n ][ 1 ] ) break;
-                if ( ( f[ 1 ] == ':' ) && ( arg_v[ n ][ 2 ] == '\0' ) ) ++n;
-            }
-            else
-            {
-                mark_target_for_updating( arg_v[ n ] );
-            }
-        }
-
-        if (!targets_to_update())
-            mark_target_for_updating("all");
-
-        /* Parse ruleset. */
-        {
-            FRAME frame[ 1 ];
-            frame_init( frame );
-            for ( n = 0; ( s = getoptval( optv, 'f', n ) ); ++n )
-                parse_file( s, frame );
-
-            if ( !n )
-                parse_file( "+", frame );
-        }
-
-        status = yyanyerrors();
-
-        /* Manually touch -t targets. */
-        for ( n = 0; ( s = getoptval( optv, 't', n ) ); ++n )
-            touch_target( s );
-
-        /* If an output file is specified, set globs.cmdout to that. */
-        if ( ( s = getoptval( optv, 'o', 0 ) ) )
-        {
-            if ( !( globs.cmdout = fopen( s, "w" ) ) )
-            {
-                printf( "Failed to write to '%s'\n", s );
-                exit( EXITBAD );
-            }
-            ++globs.noexec;
-        }
-
-        /* The build system may set the PARALLELISM variable to override -j
-           options.  */
-        {
-            LIST *p = L0;
-            p = var_get ("PARALLELISM");
-            if (p)
-            {
-                int j = atoi (p->string);
-                if (j == -1)
-                {
-                    printf( "Invalid value of PARALLELISM: %s\n", p->string);
-                }
-                else
-                {
-                    globs.jobs = j;
-                }
-            }
-        }
-
-        /* KEEP_GOING overrides -q option. */
-        {
-            LIST *p = L0;
-            p = var_get ("KEEP_GOING");
-            if (p)
-            {
-                int v = atoi (p->string);
-                if (v == 0)
-                    globs.quitquick = 1;
-                else
-                    globs.quitquick = 0;
-            }
-        }
-
-        /* Now make target. */
-        {
-            PROFILE_ENTER( MAIN_MAKE );
-
-            LIST * targets = targets_to_update();
-            if (targets)
-            {
-                int targets_count = list_length( targets );
-                const char * * targets2 = (const char * *)
-                    BJAM_MALLOC( targets_count * sizeof( char * ) );
-                int n = 0;
-                for ( ; targets; targets = list_next( targets ) )
-                    targets2[ n++ ] = targets->string;
-                status |= make( targets_count, targets2, anyhow );
-                free( targets );
-            }
-            else
-            {
-                status = last_update_now_status;
-            }
-
-            PROFILE_EXIT( MAIN_MAKE );
-        }
-
-        PROFILE_EXIT( MAIN );
-    }
-
-    if ( DEBUG_PROFILE )
-        profile_dump();
-
-    /* Widely scattered cleanup. */
-    var_done();
-    file_done();
-    rules_done();
-    stamps_done();
-    str_done();
-
-    /* Close cmdout. */
-    if ( globs.cmdout )
-        fclose( globs.cmdout );
-
-#ifdef HAVE_PYTHON
-    Py_Finalize();
-#endif
-
-    BJAM_MEM_CLOSE();
-
-    return status ? EXITBAD : EXITOK;
-}
-
-#if defined(_WIN32)
-#include <windows.h>
-char *executable_path(char *argv0) {
-    char buf[1024];
-    DWORD ret = GetModuleFileName(NULL, buf, sizeof(buf));
-    if (ret == 0 || ret == sizeof(buf)) return NULL;
-    return strdup (buf);
-}
-#elif defined(__APPLE__)  /* Not tested */
-#include <mach-o/dyld.h>
-char *executable_path(char *argv0) {
-    char buf[1024];
-    uint32_t size = sizeof(buf);
-    int ret = _NSGetExecutablePath(buf, &size);
-    if (ret != 0) return NULL;
-    return strdup(buf);
-}
-#elif defined(sun) || defined(__sun) /* Not tested */
-#include <stdlib.h>
-
-char *executable_path(char *argv0) {
-    return strdup(getexecname());
-}
-#elif defined(__FreeBSD__)
-#include <sys/sysctl.h>
-char *executable_path(char *argv0) {
-    int mib[4];
-    mib[0] = CTL_KERN;
-    mib[1] = KERN_PROC;
-    mib[2] = KERN_PROC_PATHNAME;
-    mib[3] = -1;
-    char buf[1024];
-    size_t size = sizeof(buf);
-    sysctl(mib, 4, buf, &size, NULL, 0);
-    if (size == 0 || size == sizeof(buf)) return NULL;
-    return strndup(buf, size);
-}
-#elif defined(__linux__)
-#include <unistd.h>
-char *executable_path(char *argv0) {
-    char buf[1024];
-    ssize_t ret = readlink("/proc/self/exe", buf, sizeof(buf));
-    if (ret == 0 || ret == sizeof(buf)) return NULL;
-    return strndup(buf, ret);
-}
-#else
-char *executable_path(char *argv0) {
-    /* If argv0 is absolute path, assume it's the right absolute path. */
-    if (argv0[0] == "/")
-        return strdup(argv0);
-    return NULL;
-}
-#endif
diff --git a/jam-files/engine/jam.h b/jam-files/engine/jam.h
deleted file mode 100644
index 73a7a04c..00000000
--- a/jam-files/engine/jam.h
+++ /dev/null
@@ -1,579 +0,0 @@
-/*
- * Copyright 1993, 1995 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*  This file is ALSO:
- *  Copyright 2001-2004 David Abrahams.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-
-/*
- * jam.h - includes and globals for jam
- *
- * 04/08/94 (seiwald) - Coherent/386 support added.
- * 04/21/94 (seiwald) - DGUX is __DGUX__, not just __DGUX.
- * 05/04/94 (seiwald) - new globs.jobs (-j jobs)
- * 11/01/94 (wingerd) - let us define path of Jambase at compile time.
- * 12/30/94 (wingerd) - changed command buffer size for NT (MS-DOS shell).
- * 02/22/95 (seiwald) - Jambase now in /usr/local/lib.
- * 04/30/95 (seiwald) - FreeBSD added.  Live Free or Die.
- * 05/10/95 (seiwald) - SPLITPATH character set up here.
- * 08/20/95 (seiwald) - added LINUX.
- * 08/21/95 (seiwald) - added NCR.
- * 10/23/95 (seiwald) - added SCO.
- * 01/03/96 (seiwald) - SINIX (nixdorf) added.
- * 03/13/96 (seiwald) - Jambase now compiled in; remove JAMBASE variable.
- * 04/29/96 (seiwald) - AIX now has 31 and 42 OSVERs.
- * 11/21/96 (peterk)  - added BeOS with MW CW mwcc
- * 12/21/96 (seiwald) - OSPLAT now defined for NT.
- * 07/19/99 (sickel)  - Mac OS X Server and Client support added
- * 02/18/00 (belmonte)- Support for Cygwin.
- * 09/12/00 (seiwald) - OSSYMS split to OSMAJOR/OSMINOR/OSPLAT
- * 12/29/00 (seiwald) - OSVER dropped.
- */
-
-#ifndef JAM_H_VP_2003_08_01
-#define JAM_H_VP_2003_08_01
-
-#ifdef HAVE_PYTHON
-#include <Python.h>
-#endif
-
-/* Assume popen support is available unless known otherwise. */
-#define HAVE_POPEN 1
-
-/*
- * VMS, OPENVMS
- */
-
-#ifdef VMS
-
-#include <types.h>
-#include <file.h>
-#include <stat.h>
-#include <stdio.h>
-#include <ctype.h>
-#include <stdlib.h>
-#include <signal.h>
-#include <string.h>
-#include <time.h>
-#include <unistd.h>
-#include <unixlib.h>
-
-#define OSMINOR "OS=VMS"
-#define OSMAJOR "VMS=true"
-#define OS_VMS
-#define MAXLINE 1024 /* longest 'together' actions */
-#define SPLITPATH ','
-#define EXITOK 1
-#define EXITBAD 0
-#define DOWNSHIFT_PATHS
-
-/* This may be inaccurate. */
-#ifndef __DECC
-#define OSPLAT "OSPLAT=VAX"
-#endif
-
-#endif
-
-/*
- * Windows NT
- */
-
-#ifdef NT
-
-#include <fcntl.h>
-#include <stdlib.h>
-#include <stdio.h>
-#include <ctype.h>
-#include <malloc.h>
-#ifndef __MWERKS__
-    #include <memory.h>
-#endif
-#include <signal.h>
-#include <string.h>
-#include <time.h>
-
-#define OSMAJOR "NT=true"
-#define OSMINOR "OS=NT"
-#define OS_NT
-#define SPLITPATH ';'
-/* Windows NT 3.51 only allows 996 chars per line, but we deal with the problem
- * in "execnt.c".
- */
-#define MAXLINE (maxline())    /* longest 'together' actions */
-#define USE_EXECNT
-#define USE_PATHUNIX
-#define PATH_DELIM '\\'
-#define DOWNSHIFT_PATHS
-
-/* AS400 cross-compile from NT. */
-
-#ifdef AS400
-    #undef OSMINOR
-    #undef OSMAJOR
-    #define OSMAJOR "AS400=true"
-    #define OSMINOR "OS=AS400"
-    #define OS_AS400
-#endif
-
-/* Metrowerks Standard Library on Windows. */
-
-#ifdef __MSL__
-    #undef HAVE_POPEN
-#endif
-
-# endif
-
-/*
- * Windows MingW32
- */
-
-#ifdef MINGW
-
-#include <fcntl.h>
-#include <stdlib.h>
-#include <stdio.h>
-#include <ctype.h>
-#include <malloc.h>
-#include <memory.h>
-#include <signal.h>
-#include <string.h>
-#include <time.h>
-
-#define OSMAJOR "MINGW=true"
-#define OSMINOR "OS=MINGW"
-#define OS_NT
-#define SPLITPATH ';'
-#define MAXLINE 996    /* longest 'together' actions */
-#define USE_EXECUNIX
-#define USE_PATHUNIX
-#define PATH_DELIM '\\'
-#define DOWNSHIFT_PATHS
-
-#endif
-
-/*
- * OS2
- */
-
-#ifdef __OS2__
-
-#include <fcntl.h>
-#include <stdlib.h>
-#include <stdio.h>
-#include <ctype.h>
-#include <malloc.h>
-#include <signal.h>
-#include <string.h>
-#include <time.h>
-
-#define OSMAJOR "OS2=true"
-#define OSMINOR "OS=OS2"
-#define OS_OS2
-#define SPLITPATH ';'
-#define MAXLINE 996    /* longest 'together' actions */
-#define USE_EXECUNIX
-#define USE_PATHUNIX
-#define PATH_DELIM '\\'
-#define DOWNSHIFT_PATHS
-
-#ifdef __EMX__
-    #define USE_FILEUNIX
-#endif
-
-#endif
-
-/*
- * Macintosh MPW
- */
-
-#ifdef macintosh
-
-#include <time.h>
-#include <stdlib.h>
-#include <string.h>
-#include <stdio.h>
-
-#define OSMAJOR "MAC=true"
-#define OSMINOR "OS=MAC"
-#define OS_MAC
-#define SPLITPATH ','
-
-#endif
-
-/*
- * God fearing UNIX.
- */
-
-#ifndef OSMINOR
-
-#define OSMAJOR "UNIX=true"
-#define USE_EXECUNIX
-#define USE_FILEUNIX
-#define USE_PATHUNIX
-#define PATH_DELIM '/'
-
-#ifdef _AIX
-    #define unix
-    #define MAXLINE 23552  /* 24k - 1k, longest 'together' actions */
-    #define OSMINOR "OS=AIX"
-    #define OS_AIX
-    #define NO_VFORK
-#endif
-#ifdef AMIGA
-    #define OSMINOR "OS=AMIGA"
-    #define OS_AMIGA
-#endif
-#ifdef __BEOS__
-    #define unix
-    #define OSMINOR "OS=BEOS"
-    #define OS_BEOS
-    #define NO_VFORK
-#endif
-#ifdef __bsdi__
-    #define OSMINOR "OS=BSDI"
-    #define OS_BSDI
-#endif
-#if defined (COHERENT) && defined (_I386)
-    #define OSMINOR "OS=COHERENT"
-    #define OS_COHERENT
-    #define NO_VFORK
-#endif
-#if defined(__cygwin__) || defined(__CYGWIN__)
-    #define OSMINOR "OS=CYGWIN"
-    #define OS_CYGWIN
-#endif
-#if defined(__FreeBSD__) && !defined(__DragonFly__)
-    #define OSMINOR "OS=FREEBSD"
-    #define OS_FREEBSD
-#endif
-#ifdef __DragonFly__
-    #define OSMINOR "OS=DRAGONFLYBSD"
-    #define OS_DRAGONFLYBSD
-#endif
-#ifdef __DGUX__
-    #define OSMINOR "OS=DGUX"
-    #define OS_DGUX
-#endif
-#ifdef __hpux
-    #define OSMINOR "OS=HPUX"
-    #define OS_HPUX
-#endif
-#ifdef __OPENNT
-    #define unix
-    #define OSMINOR "OS=INTERIX"
-    #define OS_INTERIX
-    #define NO_VFORK
-#endif
-#ifdef __sgi
-    #define OSMINOR "OS=IRIX"
-    #define OS_IRIX
-    #define NO_VFORK
-#endif
-#ifdef __ISC
-    #define OSMINOR "OS=ISC"
-    #define OS_ISC
-    #define NO_VFORK
-#endif
-#ifdef linux
-    #define OSMINOR "OS=LINUX"
-    #define OS_LINUX
-#endif
-#ifdef __Lynx__
-    #define OSMINOR "OS=LYNX"
-    #define OS_LYNX
-    #define NO_VFORK
-    #define unix
-#endif
-#ifdef __MACHTEN__
-    #define OSMINOR "OS=MACHTEN"
-    #define OS_MACHTEN
-#endif
-#ifdef mpeix
-    #define unix
-    #define OSMINOR "OS=MPEIX"
-    #define OS_MPEIX
-    #define NO_VFORK
-#endif
-#ifdef __MVS__
-    #define unix
-    #define OSMINOR "OS=MVS"
-    #define OS_MVS
-#endif
-#ifdef _ATT4
-    #define OSMINOR "OS=NCR"
-    #define OS_NCR
-#endif
-#ifdef __NetBSD__
-    #define unix
-    #define OSMINOR "OS=NETBSD"
-    #define OS_NETBSD
-    #define NO_VFORK
-#endif
-#ifdef __QNX__
-    #define unix
-    #ifdef __QNXNTO__
-        #define OSMINOR "OS=QNXNTO"
-        #define OS_QNXNTO
-    #else
-        #define OSMINOR "OS=QNX"
-        #define OS_QNX
-        #define NO_VFORK
-        #define MAXLINE 996
-    #endif
-#endif
-#ifdef NeXT
-    #ifdef __APPLE__
-        #define OSMINOR "OS=RHAPSODY"
-        #define OS_RHAPSODY
-    #else
-        #define OSMINOR "OS=NEXT"
-        #define OS_NEXT
-    #endif
-#endif
-#ifdef __APPLE__
-    #define unix
-    #define OSMINOR "OS=MACOSX"
-    #define OS_MACOSX
-#endif
-#ifdef __osf__
-    #ifndef unix
-        #define unix
-    #endif
-    #define OSMINOR "OS=OSF"
-    #define OS_OSF
-#endif
-#ifdef _SEQUENT_
-    #define OSMINOR "OS=PTX"
-    #define OS_PTX
-#endif
-#ifdef M_XENIX
-    #define OSMINOR "OS=SCO"
-    #define OS_SCO
-    #define NO_VFORK
-#endif
-#ifdef sinix
-    #define unix
-    #define OSMINOR "OS=SINIX"
-    #define OS_SINIX
-#endif
-#ifdef sun
-    #if defined(__svr4__) || defined(__SVR4)
-        #define OSMINOR "OS=SOLARIS"
-        #define OS_SOLARIS
-    #else
-        #define OSMINOR "OS=SUNOS"
-        #define OS_SUNOS
-    #endif
-#endif
-#ifdef ultrix
-    #define OSMINOR "OS=ULTRIX"
-    #define OS_ULTRIX
-#endif
-#ifdef _UNICOS
-    #define OSMINOR "OS=UNICOS"
-    #define OS_UNICOS
-#endif
-#if defined(__USLC__) && !defined(M_XENIX)
-    #define OSMINOR "OS=UNIXWARE"
-    #define OS_UNIXWARE
-#endif
-#ifdef __OpenBSD__
-    #define OSMINOR "OS=OPENBSD"
-    #define OS_OPENBSD
-    #define unix
-#endif
-#if defined (__FreeBSD_kernel__) && !defined(__FreeBSD__)
-    #define OSMINOR "OS=KFREEBSD"
-    #define OS_KFREEBSD
-#endif
-#ifndef OSMINOR
-    #define OSMINOR "OS=UNKNOWN"
-#endif
-
-/* All the UNIX includes */
-
-#include <sys/types.h>
-#include <sys/stat.h>
-
-#ifndef OS_MPEIX
-    #include <sys/file.h>
-#endif
-
-#include <fcntl.h>
-#include <stdio.h>
-#include <ctype.h>
-#include <signal.h>
-#include <string.h>
-#include <time.h>
-#include <unistd.h>
-
-#ifndef OS_QNX
-    #include <memory.h>
-#endif
-
-#ifndef OS_ULTRIX
-    #include <stdlib.h>
-#endif
-
-#if !defined( OS_BSDI         ) && \
-    !defined( OS_FREEBSD      ) && \
-    !defined( OS_DRAGONFLYBSD ) && \
-    !defined( OS_NEXT         ) && \
-    !defined( OS_MACHTEN      ) && \
-    !defined( OS_MACOSX       ) && \
-    !defined( OS_RHAPSODY     ) && \
-    !defined( OS_MVS          ) && \
-    !defined( OS_OPENBSD      )
-    #include <malloc.h>
-#endif
-
-#endif
-
-/*
- * OSPLAT definitions - suppressed when it is a one-of-a-kind.
- */
-
-#if defined( _M_PPC      ) || \
-    defined( PPC         ) || \
-    defined( ppc         ) || \
-    defined( __powerpc__ ) || \
-    defined( __ppc__     )
-    #define OSPLAT "OSPLAT=PPC"
-#endif
-
-#if defined( _ALPHA_   ) || \
-    defined( __alpha__ )
-    #define OSPLAT "OSPLAT=AXP"
-#endif
-
-#if defined( _i386_   ) || \
-    defined( __i386__ ) || \
-    defined( __i386   ) || \
-    defined( _M_IX86  )
-    #define OSPLAT "OSPLAT=X86"
-#endif
-
-#if defined( __ia64__ ) || \
-    defined( __IA64__ ) || \
-    defined( __ia64   )
-    #define OSPLAT "OSPLAT=IA64"
-#endif
-
-#if defined( __x86_64__ ) || \
-    defined( __amd64__  ) || \
-    defined( _M_AMD64   )
-    #define OSPLAT "OSPLAT=X86_64"
-#endif
-
-
-#if defined( __sparc__ ) || \
-    defined( __sparc   )
-    #define OSPLAT "OSPLAT=SPARC"
-#endif
-
-#ifdef __mips__
-    #define OSPLAT "OSPLAT=MIPS"
-#endif
-
-#ifdef __arm__
-    #define OSPLAT "OSPLAT=ARM"
-#endif
-
-#ifdef __s390__
-    #define OSPLAT "OSPLAT=390"
-#endif
-
-#ifdef __hppa
-    #define OSPLAT "OSPLAT=PARISC"
-#endif
-
-#ifndef OSPLAT
-    #define OSPLAT ""
-#endif
-
-/*
- * Jam implementation misc.
- */
-
-#ifndef MAXLINE
-    #define MAXLINE 102400 /* longest 'together' actions' */
-#endif
-
-#ifndef EXITOK
-    #define EXITOK 0
-    #define EXITBAD 1
-#endif
-
-#ifndef SPLITPATH
-    #define SPLITPATH ':'
-#endif
-
-/* You probably do not need to muck with these. */
-
-#define MAXSYM   1024  /* longest symbol in the environment */
-#define MAXJPATH 1024  /* longest filename */
-
-#define MAXJOBS  64    /* silently enforced -j limit */
-#define MAXARGC  32    /* words in $(JAMSHELL) */
-
-/* Jam private definitions below. */
-
-#define DEBUG_MAX  14
-
-
-struct globs
-{
-    int    noexec;
-    int    jobs;
-    int    quitquick;
-    int    newestfirst;         /* build newest sources first */
-    int    pipe_action;
-    char   debug[ DEBUG_MAX ];
-    FILE * cmdout;              /* print cmds, not run them */
-    long   timeout;             /* number of seconds to limit actions to,
-                                 * default 0 for no limit.
-                                 */
-    int    dart;                /* output build and test results formatted for Dart */
-};
-
-extern struct globs globs;
-
-#define DEBUG_MAKE     ( globs.debug[ 1 ] )   /* show actions when executed */
-#define DEBUG_MAKEQ    ( globs.debug[ 2 ] )   /* show even quiet actions */
-#define DEBUG_EXEC     ( globs.debug[ 2 ] )   /* show text of actons */
-#define DEBUG_MAKEPROG ( globs.debug[ 3 ] )   /* show progress of make0 */
-#define DEBUG_BIND     ( globs.debug[ 3 ] )   /* show when files bound */
-
-#define DEBUG_EXECCMD  ( globs.debug[ 4 ] )   /* show execcmds()'s work */
-
-#define DEBUG_COMPILE  ( globs.debug[ 5 ] )   /* show rule invocations */
-
-#define DEBUG_HEADER   ( globs.debug[ 6 ] )   /* show result of header scan */
-#define DEBUG_BINDSCAN ( globs.debug[ 6 ] )   /* show result of dir scan */
-#define DEBUG_SEARCH   ( globs.debug[ 6 ] )   /* show attempts at binding */
-
-#define DEBUG_VARSET   ( globs.debug[ 7 ] )   /* show variable settings */
-#define DEBUG_VARGET   ( globs.debug[ 8 ] )   /* show variable fetches */
-#define DEBUG_VAREXP   ( globs.debug[ 8 ] )   /* show variable expansions */
-#define DEBUG_IF       ( globs.debug[ 8 ] )   /* show 'if' calculations */
-#define DEBUG_LISTS    ( globs.debug[ 9 ] )   /* show list manipulation */
-#define DEBUG_SCAN     ( globs.debug[ 9 ] )   /* show scanner tokens */
-#define DEBUG_MEM      ( globs.debug[ 9 ] )   /* show memory use */
-
-#define DEBUG_PROFILE  ( globs.debug[ 10 ] )  /* dump rule execution times */
-#define DEBUG_PARSE    ( globs.debug[ 11 ] )  /* debug parsing */
-#define DEBUG_GRAPH    ( globs.debug[ 12 ] )  /* debug dependencies */
-#define DEBUG_FATE     ( globs.debug[ 13 ] )  /* show changes to fate in make0() */
-
-/* Everyone gets the memory definitions. */
-#include "mem.h"
-
-/* They also get the profile functions. */
-#include "debug.h"
-
-#endif
diff --git a/jam-files/engine/jambase.c b/jam-files/engine/jambase.c
deleted file mode 100644
index b15282bc..00000000
--- a/jam-files/engine/jambase.c
+++ /dev/null
@@ -1,1691 +0,0 @@
-/* Generated by mkjambase from Jambase */
-char *jambase[] = {
-/* Jambase */
-"if $(NT)\n",
-"{\n",
-"SLASH ?= \\\\ ;\n",
-"}\n",
-"SLASH ?= / ;\n",
-"rule find-to-root ( dir : patterns + )\n",
-"{\n",
-"local globs = [ GLOB $(dir) : $(patterns) ] ;\n",
-"while ! $(globs) && $(dir:P) != $(dir)\n",
-"{\n",
-"dir = $(dir:P) ;\n",
-"globs = [ GLOB $(dir) : $(patterns) ] ;\n",
-"}\n",
-"return $(globs) ;\n",
-"}\n",
-".boost-build-file = ;\n",
-".bootstrap-file = ;\n",
-"BOOST_BUILD_PATH.user-value = $(BOOST_BUILD_PATH) ;\n",
-"if ! $(BOOST_BUILD_PATH) && $(UNIX)\n",
-"{\n",
-"BOOST_BUILD_PATH = /usr/share/boost-build ;\n",
-"}\n",
-"rule _poke ( module-name ? : variables + : value * )\n",
-"{\n",
-"module $(<)\n",
-"{\n",
-"$(>) = $(3) ;\n",
-"}\n",
-"}\n",
-"rule boost-build ( dir ? )\n",
-"{\n",
-"if $(.bootstrap-file)\n",
-"{\n",
-"ECHO \"Error: Illegal attempt to re-bootstrap the build system by invoking\" ;\n",
-"ECHO ;\n",
-"ECHO \"   'boost-build\" $(dir) \";'\" ;\n",
-"ECHO ;\n",
-"EXIT \"Please consult the documentation at 'http://www.boost.org'.\" ;\n",
-"}\n",
-"BOOST_BUILD_PATH = $(dir:R=$(.boost-build-file:D)) $(BOOST_BUILD_PATH) ;\n",
-"_poke .ENVIRON : BOOST_BUILD_PATH : $(BOOST_BUILD_PATH) ;\n",
-"local bootstrap-file = [ GLOB $(BOOST_BUILD_PATH) : bootstrap.jam ] ;\n",
-".bootstrap-file = $(bootstrap-file[1]) ;\n",
-"if ! $(.bootstrap-file)\n",
-"{\n",
-"ECHO \"Unable to load Boost.Build: could not find build system.\" ;\n",
-"ECHO --------------------------------------------------------- ;\n",
-"ECHO \"$(.boost-build-file) attempted to load the build system by invoking\" ;\n",
-"ECHO ;\n",
-"ECHO \"   'boost-build\" $(dir) \";'\" ;\n",
-"ECHO ;\n",
-"ECHO \"but we were unable to find \\\"bootstrap.jam\\\" in the specified directory\" ;\n",
-"ECHO \"or in BOOST_BUILD_PATH (searching \"$(BOOST_BUILD_PATH:J=\", \")\").\" ;\n",
-"ECHO ;\n",
-"EXIT \"Please consult the documentation at 'http://www.boost.org'.\" ;\n",
-"}\n",
-"if [ MATCH .*(--debug-configuration).* : $(ARGV) ]\n",
-"{\n",
-"ECHO \"notice: loading Boost.Build from\"\n",
-"[ NORMALIZE_PATH $(.bootstrap-file:D) ] ;\n",
-"}\n",
-"include $(.bootstrap-file) ;\n",
-"}\n",
-"if [ MATCH .*(b2).* : $(ARGV[1]:BL) ] \n",
-"|| [ MATCH .*(bjam).* : $(ARGV[1]:BL) ]\n",
-"|| $(BOOST_ROOT)    # A temporary measure so Jam works with Boost.Build v1.\n",
-"{\n",
-"local search-path = $(BOOST_BUILD_PATH) $(BOOST_ROOT) ;\n",
-"local self = [ SELF_PATH ] ;\n",
-"local boost-build-relative = ../../share/boost-build ;\n",
-"local self-based-path = [ NORMALIZE_PATH $(boost-build-relative:R=$(self)) ] ;\n",
-"local boost-build-files =\n",
-"[ find-to-root [ PWD ] : boost-build.jam ]\n",
-"[ GLOB $(self-based-path) : boost-build.jam ]\n",
-"[ GLOB $(search-path) : boost-build.jam ] ;\n",
-".boost-build-file = $(boost-build-files[1]) ;\n",
-"if ! $(.boost-build-file)\n",
-"{\n",
-"ECHO \"Unable to load Boost.Build: could not find \\\"boost-build.jam\\\"\" ;\n",
-"ECHO --------------------------------------------------------------- ;\n",
-"if ! [ MATCH .*(bjam).* : $(ARGV[1]:BL) ]\n",
-"{\n",
-"ECHO \"BOOST_ROOT must be set, either in the environment, or \" ;\n",
-"ECHO \"on the command-line with -sBOOST_ROOT=..., to the root\" ;\n",
-"ECHO \"of the boost installation.\" ;\n",
-"ECHO ;\n",
-"}\n",
-"ECHO \"Attempted search from\" [ PWD ] \"up to the root\" ;\n",
-"ECHO \"at\" $(self-based-path) ;\n",
-"ECHO \"and in these directories from BOOST_BUILD_PATH and BOOST_ROOT: \"$(search-path:J=\", \")\".\" ;\n",
-"EXIT \"Please consult the documentation at 'http://www.boost.org'.\" ;\n",
-"}\n",
-"if [ MATCH .*(--debug-configuration).* : $(ARGV) ]\n",
-"{\n",
-"ECHO \"notice: found boost-build.jam at\"\n",
-"[ NORMALIZE_PATH $(.boost-build-file) ] ;\n",
-"}\n",
-"include $(.boost-build-file) ;\n",
-"if ! $(.bootstrap-file)\n",
-"{\n",
-"ECHO \"Unable to load Boost.Build\" ;\n",
-"ECHO -------------------------- ;\n",
-"ECHO \"\\\"$(.boost-build-file)\\\" was found by searching from\" [ PWD ] \"up to the root\" ;\n",
-"ECHO \"and in these directories from BOOST_BUILD_PATH and BOOST_ROOT: \"$(search-path:J=\", \")\".\" ;\n",
-"ECHO ;\n",
-"ECHO \"However, it failed to call the \\\"boost-build\\\" rule to indicate\" ;\n",
-"ECHO \"the location of the build system.\" ;\n",
-"ECHO ;\n",
-"EXIT \"Please consult the documentation at 'http://www.boost.org'.\" ;\n",
-"}\n",
-"}\n",
-"else\n",
-"{\n",
-"if $(NT)\n",
-"{\n",
-"local SUPPORTED_TOOLSETS = \"BORLANDC\" \"VC7\" \"VISUALC\" \"VISUALC16\" \"INTELC\" \"WATCOM\"\n",
-"\"MINGW\" \"LCC\" ;\n",
-"TOOLSET = \"\" ;\n",
-"if $(JAM_TOOLSET)\n",
-"{\n",
-"local t ;\n",
-"for t in $(SUPPORTED_TOOLSETS)\n",
-"{\n",
-"$(t) = $($(t):J=\" \") ; # reconstitute paths with spaces in them\n",
-"if $(t) = $(JAM_TOOLSET) { TOOLSET = $(t) ; }\n",
-"}\n",
-"if ! $(TOOLSET)\n",
-"{\n",
-"ECHO  \"The JAM_TOOLSET environment variable is defined but its value\" ;\n",
-"ECHO  \"is invalid, please use one of the following:\" ;\n",
-"ECHO  ;\n",
-"for t in $(SUPPORTED_TOOLSETS) { ECHO \"  \" $(t) ; }\n",
-"EXIT ;\n",
-"}\n",
-"}\n",
-"if ! $(TOOLSET)\n",
-"{\n",
-"if $(BCCROOT)\n",
-"{\n",
-"TOOLSET  = BORLANDC ;\n",
-"BORLANDC = $(BCCROOT:J=\" \") ;\n",
-"}\n",
-"else if $(MSVC)\n",
-"{\n",
-"TOOLSET   = VISUALC16 ;\n",
-"VISUALC16 = $(MSVC:J=\" \") ;\n",
-"}\n",
-"else if $(MSVCNT)\n",
-"{\n",
-"TOOLSET = VISUALC ;\n",
-"VISUALC = $(MSVCNT:J=\" \") ;\n",
-"}\n",
-"else if $(MSVCDir)\n",
-"{\n",
-"TOOLSET = VISUALC ;\n",
-"VISUALC = $(MSVCDir:J=\" \") ;\n",
-"}\n",
-"else if $(MINGW)\n",
-"{\n",
-"TOOLSET = MINGW ;\n",
-"}\n",
-"else\n",
-"{\n",
-"ECHO  \"Jam cannot be run because, either:\" ;\n",
-"ECHO  \"   a. You didn't set BOOST_ROOT to indicate the root of your\" ;\n",
-"ECHO  \"      Boost installation.\" ;\n",
-"ECHO  \"   b. You are trying to use stock Jam but didn't indicate which\" ;\n",
-"ECHO  \"      compilation toolset to use. To do so, follow these simple\" ;\n",
-"ECHO  \"      instructions:\" ;\n",
-"ECHO  ;\n",
-"ECHO  \"  - define one of the following environment variable, with the\" ;\n",
-"ECHO  \"    appropriate value according to this list:\" ;\n",
-"ECHO  ;\n",
-"ECHO  \"   Variable    Toolset                      Description\" ;\n",
-"ECHO  ;\n",
-"ECHO  \"   BORLANDC    Borland C++                  BC++ install path\" ;\n",
-"ECHO  \"   VISUALC     Microsoft Visual C++         VC++ install path\" ;\n",
-"ECHO  \"   VISUALC16   Microsoft Visual C++ 16 bit  VC++ 16 bit install\" ;\n",
-"ECHO  \"   INTELC      Intel C/C++                  IC++ install path\" ;\n",
-"ECHO  \"   WATCOM      Watcom C/C++                 Watcom install path\" ;\n",
-"ECHO  \"   MINGW       MinGW (gcc)                  MinGW install path\" ;\n",
-"ECHO  \"   LCC         Win32-LCC                    LCC-Win32 install path\" ;\n",
-"ECHO  ;\n",
-"ECHO  \"  - define the JAM_TOOLSET environment variable with the *name*\" ;\n",
-"ECHO  \"    of the toolset variable you want to use.\" ;\n",
-"ECHO  ;\n",
-"ECHO  \"  e.g.:  set VISUALC=C:\\\\Visual6\" ;\n",
-"ECHO  \"         set JAM_TOOLSET=VISUALC\" ;\n",
-"EXIT  ;\n",
-"}\n",
-"}\n",
-"CP          ?= copy ;\n",
-"RM          ?= del /f/q ;\n",
-"SLASH       ?= \\\\ ;\n",
-"SUFLIB      ?= .lib ;\n",
-"SUFOBJ      ?= .obj ;\n",
-"SUFEXE      ?= .exe ;\n",
-"if $(TOOLSET) = BORLANDC\n",
-"{\n",
-"ECHO \"Compiler is Borland C++\" ;\n",
-"AR          ?= tlib /C /P64 ;\n",
-"CC          ?= bcc32 ;\n",
-"CCFLAGS     ?= -q -y -d -v -w-par -w-ccc -w-rch -w-pro -w-aus ;\n",
-"C++         ?= bcc32 ;\n",
-"C++FLAGS    ?= -q -y -d -v -w-par -w-ccc -w-rch -w-pro -w-aus -P ;\n",
-"LINK        ?= $(CC) ;\n",
-"LINKFLAGS   ?= $(CCFLAGS) ;\n",
-"STDLIBPATH  ?= $(BORLANDC)\\\\lib ;\n",
-"STDHDRS     ?= $(BORLANDC)\\\\include ;\n",
-"NOARSCAN    ?= true ;\n",
-"}\n",
-"else if $(TOOLSET) = VISUALC16\n",
-"{\n",
-"ECHO \"Compiler is Microsoft Visual C++ 16 bit\" ;\n",
-"AR          ?= lib /nologo ;\n",
-"CC          ?= cl /nologo ;\n",
-"CCFLAGS     ?= /D \\\"WIN\\\" ;\n",
-"C++         ?= $(CC) ;\n",
-"C++FLAGS    ?= $(CCFLAGS) ;\n",
-"LINK        ?= $(CC) ;\n",
-"LINKFLAGS   ?= $(CCFLAGS) ;\n",
-"LINKLIBS    ?=\n",
-"\\\"$(VISUALC16)\\\\lib\\\\mlibce.lib\\\"\n",
-"\\\"$(VISUALC16)\\\\lib\\\\oldnames.lib\\\"\n",
-";\n",
-"LINKLIBS    ?= ;\n",
-"NOARSCAN    ?= true ;\n",
-"OPTIM       ?= \"\" ;\n",
-"STDHDRS     ?= $(VISUALC16)\\\\include ;\n",
-"UNDEFFLAG   ?= \"/u _\" ;\n",
-"}\n",
-"else if $(TOOLSET) = VISUALC\n",
-"{\n",
-"ECHO \"Compiler is Microsoft Visual C++\" ;\n",
-"AR          ?= lib ;\n",
-"AS          ?= masm386 ;\n",
-"CC          ?= cl /nologo ;\n",
-"CCFLAGS     ?= \"\" ;\n",
-"C++         ?= $(CC) ;\n",
-"C++FLAGS    ?= $(CCFLAGS) ;\n",
-"LINK        ?= link /nologo ;\n",
-"LINKFLAGS   ?= \"\" ;\n",
-"LINKLIBS    ?= \\\"$(VISUALC)\\\\lib\\\\advapi32.lib\\\"\n",
-"\\\"$(VISUALC)\\\\lib\\\\gdi32.lib\\\"\n",
-"\\\"$(VISUALC)\\\\lib\\\\user32.lib\\\"\n",
-"\\\"$(VISUALC)\\\\lib\\\\kernel32.lib\\\" ;\n",
-"OPTIM       ?= \"\" ;\n",
-"STDHDRS     ?= $(VISUALC)\\\\include ;\n",
-"UNDEFFLAG   ?= \"/u _\" ;\n",
-"}\n",
-"else if $(TOOLSET) = VC7\n",
-"{\n",
-"ECHO \"Compiler is Microsoft Visual C++ .NET\" ;\n",
-"AR          ?= lib ;\n",
-"AS          ?= masm386 ;\n",
-"CC          ?= cl /nologo ;\n",
-"CCFLAGS     ?= \"\" ;\n",
-"C++         ?= $(CC) ;\n",
-"C++FLAGS    ?= $(CCFLAGS) ;\n",
-"LINK        ?= link /nologo ;\n",
-"LINKFLAGS   ?= \"\" ;\n",
-"LINKLIBS    ?= \\\"$(VISUALC)\\\\PlatformSDK\\\\lib\\\\advapi32.lib\\\"\n",
-"\\\"$(VISUALC)\\\\PlatformSDK\\\\lib\\\\gdi32.lib\\\"\n",
-"\\\"$(VISUALC)\\\\PlatformSDK\\\\lib\\\\user32.lib\\\"\n",
-"\\\"$(VISUALC)\\\\PlatformSDK\\\\lib\\\\kernel32.lib\\\" ;\n",
-"OPTIM       ?= \"\" ;\n",
-"STDHDRS     ?= \\\"$(VISUALC)\\\\include\\\"\n",
-"\\\"$(VISUALC)\\\\PlatformSDK\\\\include\\\" ;\n",
-"UNDEFFLAG   ?= \"/u _\" ;\n",
-"}\n",
-"else if $(TOOLSET) = INTELC\n",
-"{\n",
-"ECHO \"Compiler is Intel C/C++\" ;\n",
-"if ! $(VISUALC)\n",
-"{\n",
-"ECHO \"As a special exception, when using the Intel C++ compiler, you need\" ;\n",
-"ECHO \"to define the VISUALC environment variable to indicate the location\" ;\n",
-"ECHO \"of your Visual C++ installation. Aborting..\" ;\n",
-"EXIT ;\n",
-"}\n",
-"AR          ?= lib ;\n",
-"AS          ?= masm386 ;\n",
-"CC          ?= icl /nologo ;\n",
-"CCFLAGS     ?= \"\" ;\n",
-"C++         ?= $(CC) ;\n",
-"C++FLAGS    ?= $(CCFLAGS) ;\n",
-"LINK        ?= link /nologo ;\n",
-"LINKFLAGS   ?= \"\" ;\n",
-"LINKLIBS    ?= $(VISUALC)\\\\lib\\\\advapi32.lib\n",
-"$(VISUALC)\\\\lib\\\\kernel32.lib\n",
-";\n",
-"OPTIM       ?= \"\" ;\n",
-"STDHDRS     ?= $(INTELC)\\include $(VISUALC)\\\\include ;\n",
-"UNDEFFLAG   ?= \"/u _\" ;\n",
-"}\n",
-"else if $(TOOLSET) = WATCOM\n",
-"{\n",
-"ECHO \"Compiler is Watcom C/C++\" ;\n",
-"AR          ?= wlib ;\n",
-"CC          ?= wcc386 ;\n",
-"CCFLAGS     ?= /zq /DWIN32 /I$(WATCOM)\\\\h ; # zq=quiet\n",
-"C++         ?= wpp386 ;\n",
-"C++FLAGS    ?= $(CCFLAGS) ;\n",
-"CP          ?= copy ;\n",
-"DOT         ?= . ;\n",
-"DOTDOT      ?= .. ;\n",
-"LINK        ?= wcl386 ;\n",
-"LINKFLAGS   ?= /zq ; # zq=quiet\n",
-"LINKLIBS    ?= ;\n",
-"MV          ?= move ;\n",
-"NOARSCAN    ?= true ;\n",
-"OPTIM       ?= ;\n",
-"RM          ?= del /f ;\n",
-"SLASH       ?= \\\\ ;\n",
-"STDHDRS     ?= $(WATCOM)\\\\h $(WATCOM)\\\\h\\\\nt ;\n",
-"SUFEXE      ?= .exe ;\n",
-"SUFLIB      ?= .lib ;\n",
-"SUFOBJ      ?= .obj ;\n",
-"UNDEFFLAG   ?= \"/u _\" ;\n",
-"}\n",
-"else if $(TOOLSET) = MINGW\n",
-"{\n",
-"ECHO \"Compiler is GCC with Mingw\" ;\n",
-"AR              ?= ar -ru ;\n",
-"CC              ?= gcc ;\n",
-"CCFLAGS         ?= \"\" ;\n",
-"C++             ?= $(CC) ;\n",
-"C++FLAGS        ?= $(CCFLAGS) ;\n",
-"LINK            ?= $(CC) ;\n",
-"LINKFLAGS       ?= \"\" ;\n",
-"LINKLIBS        ?= \"\" ;\n",
-"OPTIM           ?= ;\n",
-"SUFOBJ           = .o ;\n",
-"SUFLIB           = .a ;\n",
-"SLASH            = / ;\n",
-"}\n",
-"else if $(TOOLSET) = LCC\n",
-"{\n",
-"ECHO \"Compiler is Win32-LCC\" ;\n",
-"AR              ?= lcclib ;\n",
-"CC              ?= lcc ;\n",
-"CCFLAGS         ?= \"\" ;\n",
-"C++             ?= $(CC) ;\n",
-"C++FLAGS        ?= $(CCFLAGS) ;\n",
-"LINK            ?= lcclnk ;\n",
-"LINKFLAGS       ?= \"\" ;\n",
-"LINKLIBS        ?= \"\" ;\n",
-"OPTIM           ?= ;\n",
-"NOARSCAN         = true ;\n",
-"}\n",
-"else\n",
-"{\n",
-"EXIT On NT, set BCCROOT, MSVCNT, MINGW or MSVC to the root of the\n",
-"Borland or Microsoft directories. ;\n",
-"}\n",
-"}\n",
-"else if $(OS2)\n",
-"{\n",
-"local SUPPORTED_TOOLSETS = \"EMX\" \"WATCOM\" ;\n",
-"TOOLSET = \"\" ;\n",
-"if $(JAM_TOOLSET)\n",
-"{\n",
-"local t ;\n",
-"for t in $(SUPPORTED_TOOLSETS)\n",
-"{\n",
-"$(t) = $($(t):J=\" \") ; # reconstitute paths with spaces in them\n",
-"if $(t) = $(JAM_TOOLSET) { TOOLSET = $(t) ; }\n",
-"}\n",
-"if ! $(TOOLSET)\n",
-"{\n",
-"ECHO  \"The JAM_TOOLSET environment variable is defined but its value\" ;\n",
-"ECHO  \"is invalid, please use one of the following:\" ;\n",
-"ECHO  ;\n",
-"for t in $(SUPPORTED_TOOLSETS) { ECHO \"  \" $(t) ; }\n",
-"EXIT ;\n",
-"}\n",
-"}\n",
-"if ! $(TOOLSET)\n",
-"{\n",
-"if $(watcom)\n",
-"{\n",
-"WATCOM   = $(watcom:J=\" \") ;\n",
-"TOOLSET  = WATCOM ;\n",
-"}\n",
-"else\n",
-"{\n",
-"ECHO  \"Jam cannot be run because you didn't indicate which compilation toolset\" ;\n",
-"ECHO  \"to use. To do so, follow these simple instructions:\" ;\n",
-"ECHO  ;\n",
-"ECHO  \"  - define one of the following environment variable, with the\" ;\n",
-"ECHO  \"    appropriate value according to this list:\" ;\n",
-"ECHO  ;\n",
-"ECHO  \"   Variable    Toolset                      Description\" ;\n",
-"ECHO  ;\n",
-"ECHO  \"   WATCOM      Watcom C/C++                 Watcom install path\" ;\n",
-"ECHO  \"   EMX         EMX (gcc)                    EMX install path\" ;\n",
-"ECHO  \"   VISUALAGE   IBM Visual Age C/C++         VisualAge install path\" ;\n",
-"ECHO  ;\n",
-"ECHO  \"  - define the JAM_TOOLSET environment variable with the *name*\" ;\n",
-"ECHO  \"    of the toolset variable you want to use.\" ;\n",
-"ECHO  ;\n",
-"ECHO  \"  e.g.:  set WATCOM=C:\\WATCOM\" ;\n",
-"ECHO  \"         set JAM_TOOLSET=WATCOM\" ;\n",
-"ECHO  ;\n",
-"EXIT  ;\n",
-"}\n",
-"}\n",
-"RM       = del /f ;\n",
-"CP       = copy ;\n",
-"MV      ?= move ;\n",
-"DOT     ?= . ;\n",
-"DOTDOT  ?= .. ;\n",
-"SUFLIB  ?= .lib ;\n",
-"SUFOBJ  ?= .obj ;\n",
-"SUFEXE  ?= .exe ;\n",
-"if $(TOOLSET) = WATCOM\n",
-"{\n",
-"AR           ?= wlib ;\n",
-"BINDIR       ?= \\\\os2\\\\apps ;\n",
-"CC           ?= wcc386 ;\n",
-"CCFLAGS      ?= /zq /DOS2 /I$(WATCOM)\\\\h ; # zq=quiet\n",
-"C++          ?= wpp386 ;\n",
-"C++FLAGS     ?= $(CCFLAGS) ;\n",
-"LINK         ?= wcl386 ;\n",
-"LINKFLAGS    ?= /zq ; # zq=quiet\n",
-"LINKLIBS     ?= ;\n",
-"NOARSCAN     ?= true ;\n",
-"OPTIM        ?= ;\n",
-"SLASH        ?= \\\\ ;\n",
-"STDHDRS      ?= $(WATCOM)\\\\h ;\n",
-"UNDEFFLAG    ?= \"/u _\" ;\n",
-"}\n",
-"else if $(TOOLSET) = EMX\n",
-"{\n",
-"ECHO \"Compiler is GCC-EMX\" ;\n",
-"AR            ?= ar -ru ;\n",
-"CC            ?= gcc ;\n",
-"CCFLAGS       ?= \"\" ;\n",
-"C++           ?= $(CC) ;\n",
-"C++FLAGS      ?= $(CCFLAGS) ;\n",
-"LINK          ?= $(CC) ;\n",
-"LINKFLAGS     ?= \"\" ;\n",
-"LINKLIBS      ?= \"\" ;\n",
-"OPTIM         ?= ;\n",
-"SUFOBJ         = .o ;\n",
-"SUFLIB         = .a ;\n",
-"UNDEFFLAG     ?= \"-U\" ;\n",
-"SLASH          = / ;\n",
-"}\n",
-"else\n",
-"{\n",
-"EXIT  \"Sorry, but the $(JAM_TOOLSET) toolset isn't supported for now\" ;\n",
-"}\n",
-"}\n",
-"else if $(VMS)\n",
-"{\n",
-"C++         ?= cxx ;\n",
-"C++FLAGS    ?= ;\n",
-"CC          ?= cc ;\n",
-"CCFLAGS     ?= ;\n",
-"CHMOD       ?= set file/prot= ;\n",
-"CP          ?= copy/replace ;\n",
-"CRELIB      ?= true ;\n",
-"DOT         ?= [] ;\n",
-"DOTDOT      ?= [-] ;\n",
-"EXEMODE     ?= (w:e) ;\n",
-"FILEMODE    ?= (w:r) ;\n",
-"HDRS        ?= ;\n",
-"LINK        ?= link ;\n",
-"LINKFLAGS   ?= \"\" ;\n",
-"LINKLIBS    ?= ;\n",
-"MKDIR       ?= create/dir ;\n",
-"MV          ?= rename ;\n",
-"OPTIM       ?= \"\" ;\n",
-"RM          ?= delete ;\n",
-"RUNVMS      ?= mcr ;\n",
-"SHELLMODE   ?= (w:er) ;\n",
-"SLASH       ?= . ;\n",
-"STDHDRS     ?= decc$library_include ;\n",
-"SUFEXE      ?= .exe ;\n",
-"SUFLIB      ?= .olb ;\n",
-"SUFOBJ      ?= .obj ;\n",
-"switch $(OS)\n",
-"{\n",
-"case OPENVMS : CCFLAGS  ?= /stand=vaxc ;\n",
-"case VMS     : LINKLIBS ?= sys$library:vaxcrtl.olb/lib ;\n",
-"}\n",
-"}\n",
-"else if $(MAC)\n",
-"{\n",
-"local OPT ;\n",
-"CW  ?= \"{CW}\" ;\n",
-"MACHDRS ?=\n",
-"\"$(UMACHDRS):Universal:Interfaces:CIncludes\"\n",
-"\"$(CW):MSL:MSL_C:MSL_Common:Include\"\n",
-"\"$(CW):MSL:MSL_C:MSL_MacOS:Include\" ;\n",
-"MACLIBS ?=\n",
-"\"$(CW):MacOS Support:Universal:Libraries:StubLibraries:Interfacelib\"\n",
-"\"$(CW):MacOS Support:Universal:Libraries:StubLibraries:Mathlib\" ;\n",
-"MPWLIBS ?=\n",
-"\"$(CW):MacOS Support:Libraries:Runtime:Runtime PPC:MSL MPWCRuntime.lib\"\n",
-"\"$(CW):MSL:MSL_C:MSL_MacOS:Lib:PPC:MSL C.PPC MPW.Lib\" ;\n",
-"MPWNLLIBS ?=\n",
-"\"$(CW):MacOS Support:Libraries:Runtime:Runtime PPC:MSL MPWCRuntime.lib\"\n",
-"\"$(CW):MSL:MSL_C:MSL_MacOS:Lib:PPC:MSL C.PPC MPW(NL).Lib\" ;\n",
-"SIOUXHDRS ?= ;\n",
-"SIOUXLIBS ?=\n",
-"\"$(CW):MacOS Support:Libraries:Runtime:Runtime PPC:MSL RuntimePPC.lib\"\n",
-"\"$(CW):MSL:MSL_C:MSL_MacOS:Lib:PPC:MSL SIOUX.PPC.Lib\"\n",
-"\"$(CW):MSL:MSL_C:MSL_MacOS:Lib:PPC:MSL C.PPC.Lib\" ;\n",
-"C++         ?= mwcppc ;\n",
-"C++FLAGS    ?= -w off -nomapcr ;\n",
-"CC          ?= mwcppc ;\n",
-"CCFLAGS     ?= -w off -nomapcr ;\n",
-"CP          ?= duplicate -y ;\n",
-"DOT         ?= \":\" ;\n",
-"DOTDOT      ?= \"::\" ;\n",
-"HDRS        ?= $(MACHDRS) $(MPWHDRS) ;\n",
-"LINK        ?= mwlinkppc ;\n",
-"LINKFLAGS   ?= -mpwtool -warn ;\n",
-"LINKLIBS    ?= $(MACLIBS) $(MPWLIBS) ;\n",
-"MKDIR       ?= newfolder ;\n",
-"MV          ?= rename -y ;\n",
-"NOARSCAN    ?= true ;\n",
-"OPTIM       ?= ;\n",
-"RM          ?= delete -y ;\n",
-"SLASH       ?= \":\" ;\n",
-"STDHDRS     ?= ;\n",
-"SUFLIB      ?= .lib ;\n",
-"SUFOBJ      ?= .o ;\n",
-"}\n",
-"else if $(OS) = BEOS && $(METROWERKS)\n",
-"{\n",
-"AR          ?= mwld -xml -o ;\n",
-"BINDIR      ?= /boot/apps ;\n",
-"CC          ?= mwcc ;\n",
-"CCFLAGS     ?= -nosyspath ;\n",
-"C++         ?= $(CC) ;\n",
-"C++FLAGS    ?= -nosyspath ;\n",
-"FORTRAN     ?= \"\" ;\n",
-"LIBDIR      ?= /boot/develop/libraries ;\n",
-"LINK        ?= mwld ;\n",
-"LINKFLAGS   ?= \"\" ;\n",
-"MANDIR      ?= /boot/documentation/\"Shell Tools\"/HTML ;\n",
-"NOARSCAN    ?= true ;\n",
-"STDHDRS     ?= /boot/develop/headers/posix ;\n",
-"}\n",
-"else if $(OS) = BEOS\n",
-"{\n",
-"BINDIR      ?= /boot/apps ;\n",
-"CC          ?= gcc ;\n",
-"C++         ?= $(CC) ;\n",
-"FORTRAN     ?= \"\" ;\n",
-"LIBDIR      ?= /boot/develop/libraries ;\n",
-"LINK        ?= gcc ;\n",
-"LINKLIBS    ?= -lnet ;\n",
-"NOARSCAN    ?= true ;\n",
-"STDHDRS     ?= /boot/develop/headers/posix ;\n",
-"}\n",
-"else if $(UNIX)\n",
-"{\n",
-"switch $(OS)\n",
-"{\n",
-"case AIX :\n",
-"LINKLIBS    ?= -lbsd ;\n",
-"case AMIGA :\n",
-"CC          ?= gcc ;\n",
-"YACC        ?= \"bison -y\" ;\n",
-"case CYGWIN :\n",
-"CC          ?= gcc ;\n",
-"CCFLAGS     += -D__cygwin__ ;\n",
-"LEX         ?= flex ;\n",
-"RANLIB      ?= \"\" ;\n",
-"SUFEXE      ?= .exe ;\n",
-"YACC        ?= \"bison -y\" ;\n",
-"case DGUX :\n",
-"RANLIB      ?= \"\" ;\n",
-"RELOCATE    ?= true ;\n",
-"case HPUX :\n",
-"YACC        = ;\n",
-"CFLAGS      += -Ae ;\n",
-"CCFLAGS     += -Ae ;\n",
-"RANLIB      ?= \"\" ;\n",
-"case INTERIX :\n",
-"CC          ?= gcc ;\n",
-"RANLIB      ?= \"\" ;\n",
-"case IRIX :\n",
-"RANLIB      ?= \"\" ;\n",
-"case MPEIX :\n",
-"CC          ?= gcc ;\n",
-"C++         ?= gcc ;\n",
-"CCFLAGS     += -D_POSIX_SOURCE ;\n",
-"HDRS        += /usr/include ;\n",
-"RANLIB      ?= \"\" ;\n",
-"NOARSCAN    ?= true ;\n",
-"NOARUPDATE  ?= true ;\n",
-"case MVS :\n",
-"RANLIB      ?= \"\" ;\n",
-"case NEXT :\n",
-"AR          ?= libtool -o ;\n",
-"RANLIB      ?= \"\" ;\n",
-"case MACOSX :\n",
-"AR          ?= libtool -o ;\n",
-"C++         ?= c++ ;\n",
-"MANDIR      ?= /usr/local/share/man ;\n",
-"RANLIB      ?= \"\" ;\n",
-"case NCR :\n",
-"RANLIB      ?= \"\" ;\n",
-"case PTX :\n",
-"RANLIB      ?= \"\" ;\n",
-"case QNX :\n",
-"AR          ?= wlib ;\n",
-"CC          ?= cc ;\n",
-"CCFLAGS     ?= -Q ; # quiet\n",
-"C++         ?= $(CC) ;\n",
-"C++FLAGS    ?= -Q ; # quiet\n",
-"LINK        ?= $(CC) ;\n",
-"LINKFLAGS   ?= -Q ; # quiet\n",
-"NOARSCAN    ?= true ;\n",
-"RANLIB      ?= \"\" ;\n",
-"case SCO :\n",
-"RANLIB      ?= \"\" ;\n",
-"RELOCATE    ?= true ;\n",
-"case SINIX :\n",
-"RANLIB      ?= \"\" ;\n",
-"case SOLARIS :\n",
-"RANLIB      ?= \"\" ;\n",
-"AR          ?= \"/usr/ccs/bin/ar ru\" ;\n",
-"case UNICOS :\n",
-"NOARSCAN    ?= true ;\n",
-"OPTIM       ?= -O0 ;\n",
-"case UNIXWARE :\n",
-"RANLIB      ?= \"\" ;\n",
-"RELOCATE    ?= true ;\n",
-"}\n",
-"CCFLAGS     ?= ;\n",
-"C++FLAGS    ?= $(CCFLAGS) ;\n",
-"CHMOD       ?= chmod ;\n",
-"CHGRP       ?= chgrp ;\n",
-"CHOWN       ?= chown ;\n",
-"LEX         ?= lex ;\n",
-"LINKFLAGS   ?= $(CCFLAGS) ;\n",
-"LINKLIBS    ?= ;\n",
-"OPTIM       ?= -O ;\n",
-"RANLIB      ?= ranlib ;\n",
-"YACC        ?= yacc ;\n",
-"YACCFILES   ?= y.tab ;\n",
-"YACCFLAGS   ?= -d ;\n",
-"}\n",
-"AR          ?= ar ru ;\n",
-"AS          ?= as ;\n",
-"ASFLAGS     ?= ;\n",
-"AWK         ?= awk ;\n",
-"BINDIR      ?= /usr/local/bin ;\n",
-"C++         ?= cc ;\n",
-"C++FLAGS    ?= ;\n",
-"CC          ?= cc ;\n",
-"CCFLAGS     ?= ;\n",
-"CP          ?= cp -f ;\n",
-"CRELIB      ?= ;\n",
-"DOT         ?= . ;\n",
-"DOTDOT      ?= .. ;\n",
-"EXEMODE     ?= 711 ;\n",
-"FILEMODE    ?= 644 ;\n",
-"FORTRAN     ?= f77 ;\n",
-"FORTRANFLAGS ?= ;\n",
-"HDRS        ?= ;\n",
-"INSTALLGRIST ?= installed ;\n",
-"JAMFILE     ?= Jamfile ;\n",
-"JAMRULES    ?= Jamrules ;\n",
-"LEX         ?= ;\n",
-"LIBDIR      ?= /usr/local/lib ;\n",
-"LINK        ?= $(CC) ;\n",
-"LINKFLAGS   ?= ;\n",
-"LINKLIBS    ?= ;\n",
-"LN          ?= ln ;\n",
-"MANDIR      ?= /usr/local/man ;\n",
-"MKDIR       ?= mkdir ;\n",
-"MV          ?= mv -f ;\n",
-"OPTIM       ?= ;\n",
-"RCP         ?= rcp ;\n",
-"RM          ?= rm -f ;\n",
-"RSH         ?= rsh ;\n",
-"SED         ?= sed ;\n",
-"SHELLHEADER ?= \"#!/bin/sh\" ;\n",
-"SHELLMODE   ?= 755 ;\n",
-"SLASH       ?= / ;\n",
-"STDHDRS     ?= /usr/include ;\n",
-"SUFEXE      ?= \"\" ;\n",
-"SUFLIB      ?= .a ;\n",
-"SUFOBJ      ?= .o ;\n",
-"UNDEFFLAG   ?= \"-u _\" ;\n",
-"YACC        ?= ;\n",
-"YACCFILES   ?= ;\n",
-"YACCFLAGS   ?= ;\n",
-"HDRPATTERN =\n",
-"\"^[     ]*#[    ]*include[  ]*[<\\\"]([^\\\">]*)[\\\">].*$\" ;\n",
-"OSFULL = $(OS)$(OSVER)$(OSPLAT) $(OS)$(OSPLAT) $(OS)$(OSVER) $(OS) ;\n",
-"DEPENDS all : shell files lib exe obj ;\n",
-"DEPENDS all shell files lib exe obj : first ;\n",
-"NOTFILE all first shell files lib exe obj dirs clean uninstall ;\n",
-"ALWAYS clean uninstall ;\n",
-"rule As\n",
-"{\n",
-"DEPENDS $(<) : $(>) ;\n",
-"ASFLAGS on $(<) += $(ASFLAGS) $(SUBDIRASFLAGS) ;\n",
-"}\n",
-"rule Bulk\n",
-"{\n",
-"local i ;\n",
-"for i in $(>)\n",
-"{\n",
-"File $(i:D=$(<)) : $(i) ;\n",
-"}\n",
-"}\n",
-"rule Cc\n",
-"{\n",
-"local _h ;\n",
-"DEPENDS $(<) : $(>) ;\n",
-"CCFLAGS on $(<) += $(CCFLAGS) $(SUBDIRCCFLAGS) ;\n",
-"if $(RELOCATE)\n",
-"{\n",
-"CcMv $(<) : $(>) ;\n",
-"}\n",
-"_h = $(SEARCH_SOURCE) $(HDRS) $(SUBDIRHDRS) ;\n",
-"if $(VMS) && $(_h)\n",
-"{\n",
-"SLASHINC on $(<) = \"/inc=(\" $(_h[1]) ,$(_h[2-]) \")\" ;\n",
-"}\n",
-"else if $(MAC) && $(_h)\n",
-"{\n",
-"local _i _j ;\n",
-"_j = $(_h[1]) ;\n",
-"for _i in $(_h[2-])\n",
-"{\n",
-"_j = $(_j),$(_i) ;\n",
-"}\n",
-"MACINC on $(<) = \\\"$(_j)\\\" ;\n",
-"}\n",
-"}\n",
-"rule C++\n",
-"{\n",
-"local _h ;\n",
-"DEPENDS $(<) : $(>) ;\n",
-"C++FLAGS on $(<) += $(C++FLAGS) $(SUBDIRC++FLAGS) ;\n",
-"if $(RELOCATE)\n",
-"{\n",
-"CcMv $(<) : $(>) ;\n",
-"}\n",
-"_h = $(SEARCH_SOURCE) $(HDRS) $(SUBDIRHDRS) ;\n",
-"if $(VMS) && $(_h)\n",
-"{\n",
-"SLASHINC on $(<) = \"/inc=(\" $(_h[1]) ,$(_h[2-]) \")\" ;\n",
-"}\n",
-"else if $(MAC) && $(_h)\n",
-"{\n",
-"local _i _j ;\n",
-"_j = $(_h[1]) ;\n",
-"for _i in $(_h[2-])\n",
-"{\n",
-"_j = $(_j),$(_i) ;\n",
-"}\n",
-"MACINC on $(<) = \\\"$(_j)\\\" ;\n",
-"}\n",
-"}\n",
-"rule Chmod\n",
-"{\n",
-"if $(CHMOD) { Chmod1 $(<) ; }\n",
-"}\n",
-"rule File\n",
-"{\n",
-"DEPENDS files : $(<) ;\n",
-"DEPENDS $(<) : $(>) ;\n",
-"SEARCH on $(>) = $(SEARCH_SOURCE) ;\n",
-"MODE on $(<) = $(FILEMODE) ;\n",
-"Chmod $(<) ;\n",
-"}\n",
-"rule Fortran\n",
-"{\n",
-"DEPENDS $(<) : $(>) ;\n",
-"}\n",
-"rule GenFile\n",
-"{\n",
-"local _t = [ FGristSourceFiles $(<) ] ;\n",
-"local _s = [ FAppendSuffix $(>[1]) : $(SUFEXE) ] ;\n",
-"Depends $(_t) : $(_s) $(>[2-]) ;\n",
-"GenFile1 $(_t) : $(_s) $(>[2-]) ;\n",
-"Clean clean : $(_t) ;\n",
-"}\n",
-"rule GenFile1\n",
-"{\n",
-"MakeLocate $(<) : $(LOCATE_SOURCE) ;\n",
-"SEARCH on $(>) = $(SEARCH_SOURCE) ;\n",
-"}\n",
-"rule HardLink\n",
-"{\n",
-"DEPENDS files : $(<) ;\n",
-"DEPENDS $(<) : $(>) ;\n",
-"SEARCH on $(>) = $(SEARCH_SOURCE) ;\n",
-"}\n",
-"rule HdrMacroFile\n",
-"{\n",
-"HDRMACRO $(<) ;\n",
-"}\n",
-"rule HdrRule\n",
-"{\n",
-"local s ;\n",
-"if $(HDRGRIST)\n",
-"{\n",
-"s = $(>:G=$(HDRGRIST)) ;\n",
-"} else {\n",
-"s = $(>) ;\n",
-"}\n",
-"INCLUDES $(<) : $(s) ;\n",
-"SEARCH on $(s) = $(HDRSEARCH) ;\n",
-"NOCARE $(s) ;\n",
-"HDRSEARCH on $(s) = $(HDRSEARCH) ;\n",
-"HDRSCAN on $(s) = $(HDRSCAN) ;\n",
-"HDRRULE on $(s) = $(HDRRULE) ;\n",
-"HDRGRIST on $(s) = $(HDRGRIST) ;\n",
-"}\n",
-"rule InstallInto\n",
-"{\n",
-"local i t ;\n",
-"t = $(>:G=$(INSTALLGRIST)) ;\n",
-"Depends install : $(t) ;\n",
-"Clean uninstall : $(t) ;\n",
-"SEARCH on $(>) = $(SEARCH_SOURCE) ;\n",
-"MakeLocate $(t) : $(<) ;\n",
-"for i in $(>)\n",
-"{\n",
-"local tt = $(i:G=$(INSTALLGRIST)) ;\n",
-"Depends $(tt) : $(i) ;\n",
-"Install $(tt) : $(i) ;\n",
-"Chmod $(tt) ;\n",
-"if $(OWNER) && $(CHOWN)\n",
-"{\n",
-"Chown $(tt) ;\n",
-"OWNER on $(tt) = $(OWNER) ;\n",
-"}\n",
-"if $(GROUP) && $(CHGRP)\n",
-"{\n",
-"Chgrp $(tt) ;\n",
-"GROUP on $(tt) = $(GROUP) ;\n",
-"}\n",
-"}\n",
-"}\n",
-"rule InstallBin\n",
-"{\n",
-"local _t = [ FAppendSuffix $(>) : $(SUFEXE) ] ;\n",
-"InstallInto $(<) : $(_t) ;\n",
-"MODE on $(_t:G=installed) = $(EXEMODE) ;\n",
-"}\n",
-"rule InstallFile\n",
-"{\n",
-"InstallInto $(<) : $(>) ;\n",
-"MODE on $(>:G=installed) = $(FILEMODE) ;\n",
-"}\n",
-"rule InstallLib\n",
-"{\n",
-"InstallInto $(<) : $(>) ;\n",
-"MODE on $(>:G=installed) = $(FILEMODE) ;\n",
-"}\n",
-"rule InstallMan\n",
-"{\n",
-"local i s d ;\n",
-"for i in $(>)\n",
-"{\n",
-"switch $(i:S)\n",
-"{\n",
-"case .1 : s = 1 ; case .2 : s = 2 ; case .3 : s = 3 ;\n",
-"case .4 : s = 4 ; case .5 : s = 5 ; case .6 : s = 6 ;\n",
-"case .7 : s = 7 ; case .8 : s = 8 ; case .l : s = l ;\n",
-"case .n : s = n ; case .man : s = 1 ;\n",
-"}\n",
-"d = man$(s) ;\n",
-"InstallInto $(d:R=$(<)) : $(i) ;\n",
-"}\n",
-"MODE on $(>:G=installed) = $(FILEMODE) ;\n",
-"}\n",
-"rule InstallShell\n",
-"{\n",
-"InstallInto $(<) : $(>) ;\n",
-"MODE on $(>:G=installed) = $(SHELLMODE) ;\n",
-"}\n",
-"rule Lex\n",
-"{\n",
-"LexMv $(<) : $(>) ;\n",
-"DEPENDS $(<) : $(>) ;\n",
-"MakeLocate $(<) : $(LOCATE_SOURCE) ;\n",
-"Clean clean : $(<) ;\n",
-"}\n",
-"rule Library\n",
-"{\n",
-"LibraryFromObjects $(<) : $(>:S=$(SUFOBJ)) ;\n",
-"Objects $(>) ;\n",
-"}\n",
-"rule LibraryFromObjects\n",
-"{\n",
-"local _i _l _s ;\n",
-"_s = [ FGristFiles $(>) ] ;\n",
-"_l = $(<:S=$(SUFLIB)) ;\n",
-"if $(KEEPOBJS)\n",
-"{\n",
-"DEPENDS obj : $(_s) ;\n",
-"}\n",
-"else\n",
-"{\n",
-"DEPENDS lib : $(_l) ;\n",
-"}\n",
-"if ! $(_l:D)\n",
-"{\n",
-"MakeLocate $(_l) $(_l)($(_s:BS)) : $(LOCATE_TARGET) ;\n",
-"}\n",
-"if $(NOARSCAN)\n",
-"{\n",
-"DEPENDS $(_l) : $(_s) ;\n",
-"}\n",
-"else\n",
-"{\n",
-"DEPENDS $(_l) : $(_l)($(_s:BS)) ;\n",
-"for _i in $(_s)\n",
-"{\n",
-"DEPENDS $(_l)($(_i:BS)) : $(_i) ;\n",
-"}\n",
-"}\n",
-"Clean clean : $(_l) ;\n",
-"if $(CRELIB) { CreLib $(_l) : $(_s[1]) ; }\n",
-"Archive $(_l) : $(_s) ;\n",
-"if $(RANLIB) { Ranlib $(_l) ; }\n",
-"if ! ( $(NOARSCAN) || $(KEEPOBJS) ) { RmTemps $(_l) : $(_s) ; }\n",
-"}\n",
-"rule Link\n",
-"{\n",
-"MODE on $(<) = $(EXEMODE) ;\n",
-"Chmod $(<) ;\n",
-"}\n",
-"rule LinkLibraries\n",
-"{\n",
-"local _t = [ FAppendSuffix $(<) : $(SUFEXE) ] ;\n",
-"DEPENDS $(_t) : $(>:S=$(SUFLIB)) ;\n",
-"NEEDLIBS on $(_t) += $(>:S=$(SUFLIB)) ;\n",
-"}\n",
-"rule Main\n",
-"{\n",
-"MainFromObjects $(<) : $(>:S=$(SUFOBJ)) ;\n",
-"Objects $(>) ;\n",
-"}\n",
-"rule MainFromObjects\n",
-"{\n",
-"local _s _t ;\n",
-"_s = [ FGristFiles $(>) ] ;\n",
-"_t = [ FAppendSuffix $(<) : $(SUFEXE) ] ;\n",
-"if $(_t) != $(<)\n",
-"{\n",
-"DEPENDS $(<) : $(_t) ;\n",
-"NOTFILE $(<) ;\n",
-"}\n",
-"DEPENDS exe : $(_t) ;\n",
-"DEPENDS $(_t) : $(_s) ;\n",
-"MakeLocate $(_t) : $(LOCATE_TARGET) ;\n",
-"Clean clean : $(_t) ;\n",
-"Link $(_t) : $(_s) ;\n",
-"}\n",
-"rule MakeLocate\n",
-"{\n",
-"if $(>)\n",
-"{\n",
-"LOCATE on $(<) = $(>) ;\n",
-"Depends $(<) : $(>[1]) ;\n",
-"MkDir $(>[1]) ;\n",
-"}\n",
-"}\n",
-"rule MkDir\n",
-"{\n",
-"NOUPDATE $(<) ;\n",
-"if $(<) != $(DOT) && ! $($(<)-mkdir)\n",
-"{\n",
-"local s ;\n",
-"$(<)-mkdir = true ;\n",
-"MkDir1 $(<) ;\n",
-"Depends dirs : $(<) ;\n",
-"s = $(<:P) ;\n",
-"if $(NT)\n",
-"{\n",
-"switch $(s)\n",
-"{\n",
-"case *:   : s = ;\n",
-"case *:\\\\ : s = ;\n",
-"}\n",
-"}\n",
-"if $(s) && $(s) != $(<)\n",
-"{\n",
-"Depends $(<) : $(s) ;\n",
-"MkDir $(s) ;\n",
-"}\n",
-"else if $(s)\n",
-"{\n",
-"NOTFILE $(s) ;\n",
-"}\n",
-"}\n",
-"}\n",
-"rule Object\n",
-"{\n",
-"local h ;\n",
-"Clean clean : $(<) ;\n",
-"MakeLocate $(<) : $(LOCATE_TARGET) ;\n",
-"SEARCH on $(>) = $(SEARCH_SOURCE) ;\n",
-"HDRS on $(<) = $(SEARCH_SOURCE) $(HDRS) $(SUBDIRHDRS) ;\n",
-"if $(SEARCH_SOURCE)\n",
-"{\n",
-"h = $(SEARCH_SOURCE) ;\n",
-"}\n",
-"else\n",
-"{\n",
-"h = \"\" ;\n",
-"}\n",
-"HDRRULE on $(>) = HdrRule ;\n",
-"HDRSCAN on $(>) = $(HDRPATTERN) ;\n",
-"HDRSEARCH on $(>) = $(HDRS) $(SUBDIRHDRS) $(h) $(STDHDRS) ;\n",
-"HDRGRIST on $(>) = $(HDRGRIST) ;\n",
-"switch $(>:S)\n",
-"{\n",
-"case .asm : As $(<) : $(>) ;\n",
-"case .c :   Cc $(<) : $(>) ;\n",
-"case .C :   C++ $(<) : $(>) ;\n",
-"case .cc :  C++ $(<) : $(>) ;\n",
-"case .cpp : C++ $(<) : $(>) ;\n",
-"case .f :   Fortran $(<) : $(>) ;\n",
-"case .l :   Cc $(<) : $(<:S=.c) ;\n",
-"Lex $(<:S=.c) : $(>) ;\n",
-"case .s :   As $(<) : $(>) ;\n",
-"case .y :   Cc $(<) : $(<:S=.c) ;\n",
-"Yacc $(<:S=.c) : $(>) ;\n",
-"case * :    UserObject $(<) : $(>) ;\n",
-"}\n",
-"}\n",
-"rule ObjectCcFlags\n",
-"{\n",
-"CCFLAGS on [ FGristFiles $(<:S=$(SUFOBJ)) ] += $(>) ;\n",
-"}\n",
-"rule ObjectC++Flags\n",
-"{\n",
-"C++FLAGS on [ FGristFiles $(<:S=$(SUFOBJ)) ] += $(>) ;\n",
-"}\n",
-"rule ObjectHdrs\n",
-"{\n",
-"HDRS on [ FGristFiles $(<:S=$(SUFOBJ)) ] += $(>) ;\n",
-"}\n",
-"rule Objects\n",
-"{\n",
-"local _i ;\n",
-"for _i in [ FGristFiles $(<) ]\n",
-"{\n",
-"Object $(_i:S=$(SUFOBJ)) : $(_i) ;\n",
-"DEPENDS obj : $(_i:S=$(SUFOBJ)) ;\n",
-"}\n",
-"}\n",
-"rule RmTemps\n",
-"{\n",
-"TEMPORARY $(>) ;\n",
-"}\n",
-"rule Setuid\n",
-"{\n",
-"MODE on [ FAppendSuffix $(<) : $(SUFEXE) ] = 4711 ;\n",
-"}\n",
-"rule Shell\n",
-"{\n",
-"DEPENDS shell : $(<) ;\n",
-"DEPENDS $(<) : $(>) ;\n",
-"SEARCH on $(>) = $(SEARCH_SOURCE) ;\n",
-"MODE on $(<) = $(SHELLMODE) ;\n",
-"Clean clean : $(<) ;\n",
-"Chmod $(<) ;\n",
-"}\n",
-"rule SubDir\n",
-"{\n",
-"local _r _s ;\n",
-"if ! $($(<[1]))\n",
-"{\n",
-"if ! $(<[1])\n",
-"{\n",
-"EXIT SubDir syntax error ;\n",
-"}\n",
-"$(<[1]) = [ FSubDir $(<[2-]) ] ;\n",
-"}\n",
-"if ! $($(<[1])-included)\n",
-"{\n",
-"$(<[1])-included = TRUE ;\n",
-"_r = $($(<[1])RULES) ;\n",
-"if ! $(_r)\n",
-"{\n",
-"_r = $(JAMRULES:R=$($(<[1]))) ;\n",
-"}\n",
-"include $(_r) ;\n",
-"}\n",
-"_s = [ FDirName $(<[2-]) ] ;\n",
-"SUBDIR = $(_s:R=$($(<[1]))) ;\n",
-"SUBDIR_TOKENS = $(<[2-]) ;\n",
-"SEARCH_SOURCE = $(SUBDIR) ;\n",
-"LOCATE_SOURCE = $(ALL_LOCATE_TARGET) $(SUBDIR) ;\n",
-"LOCATE_TARGET = $(ALL_LOCATE_TARGET) $(SUBDIR) ;\n",
-"SOURCE_GRIST = [ FGrist $(<[2-]) ] ;\n",
-"SUBDIRCCFLAGS = ;\n",
-"SUBDIRC++FLAGS = ;\n",
-"SUBDIRHDRS = ;\n",
-"}\n",
-"rule SubDirCcFlags\n",
-"{\n",
-"SUBDIRCCFLAGS += $(<) ;\n",
-"}\n",
-"rule SubDirC++Flags\n",
-"{\n",
-"SUBDIRC++FLAGS += $(<) ;\n",
-"}\n",
-"rule SubDirHdrs\n",
-"{\n",
-"SUBDIRHDRS += $(<) ;\n",
-"}\n",
-"rule SubInclude\n",
-"{\n",
-"local _s ;\n",
-"if ! $($(<[1]))\n",
-"{\n",
-"EXIT Top level of source tree has not been set with $(<[1]) ;\n",
-"}\n",
-"_s = [ FDirName $(<[2-]) ] ;\n",
-"include $(JAMFILE:D=$(_s):R=$($(<[1]))) ;\n",
-"}\n",
-"rule Undefines\n",
-"{\n",
-"UNDEFS on [ FAppendSuffix $(<) : $(SUFEXE) ] += $(UNDEFFLAG)$(>) ;\n",
-"}\n",
-"rule UserObject\n",
-"{\n",
-"EXIT \"Unknown suffix on\" $(>) \"- see UserObject rule in Jamfile(5).\" ;\n",
-"}\n",
-"rule Yacc\n",
-"{\n",
-"local _h ;\n",
-"_h = $(<:BS=.h) ;\n",
-"MakeLocate $(<) $(_h) : $(LOCATE_SOURCE) ;\n",
-"if $(YACC)\n",
-"{\n",
-"DEPENDS $(<) $(_h) : $(>) ;\n",
-"Yacc1 $(<) $(_h) : $(>) ;\n",
-"YaccMv $(<) $(_h) : $(>) ;\n",
-"Clean clean : $(<) $(_h) ;\n",
-"}\n",
-"INCLUDES $(<) : $(_h) ;\n",
-"}\n",
-"rule FGrist\n",
-"{\n",
-"local _g _i ;\n",
-"_g = $(<[1]) ;\n",
-"for _i in $(<[2-])\n",
-"{\n",
-"_g = $(_g)!$(_i) ;\n",
-"}\n",
-"return $(_g) ;\n",
-"}\n",
-"rule FGristFiles\n",
-"{\n",
-"if ! $(SOURCE_GRIST)\n",
-"{\n",
-"return $(<) ;\n",
-"}\n",
-"else\n",
-"{\n",
-"return $(<:G=$(SOURCE_GRIST)) ;\n",
-"}\n",
-"}\n",
-"rule FGristSourceFiles\n",
-"{\n",
-"if ! $(SOURCE_GRIST)\n",
-"{\n",
-"return $(<) ;\n",
-"}\n",
-"else\n",
-"{\n",
-"local _i _o ;\n",
-"for _i in $(<)\n",
-"{\n",
-"switch $(_i)\n",
-"{\n",
-"case *.h :  _o += $(_i) ;\n",
-"case * :    _o += $(_i:G=$(SOURCE_GRIST)) ;\n",
-"}\n",
-"}\n",
-"return $(_o) ;\n",
-"}\n",
-"}\n",
-"rule FConcat\n",
-"{\n",
-"local _t _r ;\n",
-"$(_r) = $(<[1]) ;\n",
-"for _t in $(<[2-])\n",
-"{\n",
-"$(_r) = $(_r)$(_t) ;\n",
-"}\n",
-"return $(_r) ;\n",
-"}\n",
-"rule FSubDir\n",
-"{\n",
-"local _i _d ;\n",
-"if ! $(<[1])\n",
-"{\n",
-"_d = $(DOT) ;\n",
-"}\n",
-"else\n",
-"{\n",
-"_d = $(DOTDOT) ;\n",
-"for _i in $(<[2-])\n",
-"{\n",
-"_d = $(_d:R=$(DOTDOT)) ;\n",
-"}\n",
-"}\n",
-"return $(_d) ;\n",
-"}\n",
-"rule FDirName\n",
-"{\n",
-"local _s _i ;\n",
-"if ! $(<)\n",
-"{\n",
-"_s = $(DOT) ;\n",
-"}\n",
-"else if $(VMS)\n",
-"{\n",
-"switch $(<[1])\n",
-"{\n",
-"case *:* : _s = $(<[1]) ;\n",
-"case \\\\[*\\\\] : _s = $(<[1]) ;\n",
-"case * : _s = [.$(<[1])] ;\n",
-"}\n",
-"for _i in [.$(<[2-])]\n",
-"{\n",
-"_s = $(_i:R=$(_s)) ;\n",
-"}\n",
-"}\n",
-"else if $(MAC)\n",
-"{\n",
-"_s = $(DOT) ;\n",
-"for _i in $(<)\n",
-"{\n",
-"_s = $(_i:R=$(_s)) ;\n",
-"}\n",
-"}\n",
-"else\n",
-"{\n",
-"_s = $(<[1]) ;\n",
-"for _i in $(<[2-])\n",
-"{\n",
-"_s = $(_i:R=$(_s)) ;\n",
-"}\n",
-"}\n",
-"return $(_s) ;\n",
-"}\n",
-"rule _makeCommon\n",
-"{\n",
-"if $($(<)[1]) && $($(<)[1]) = $($(>)[1])\n",
-"{\n",
-"$(<) = $($(<)[2-]) ;\n",
-"$(>) = $($(>)[2-]) ;\n",
-"_makeCommon $(<) : $(>) ;\n",
-"}\n",
-"}\n",
-"rule FRelPath\n",
-"{\n",
-"local _l _r ;\n",
-"_l = $(<) ;\n",
-"_r = $(>) ;\n",
-"_makeCommon _l : _r ;\n",
-"_l = [ FSubDir $(_l) ] ;\n",
-"_r = [ FDirName $(_r) ] ;\n",
-"if $(_r) = $(DOT) {\n",
-"return $(_l) ;\n",
-"} else {\n",
-"return $(_r:R=$(_l)) ;\n",
-"}\n",
-"}\n",
-"rule FAppendSuffix\n",
-"{\n",
-"if $(>)\n",
-"{\n",
-"local _i _o ;\n",
-"for _i in $(<)\n",
-"{\n",
-"if $(_i:S)\n",
-"{\n",
-"_o += $(_i) ;\n",
-"}\n",
-"else\n",
-"{\n",
-"_o += $(_i:S=$(>)) ;\n",
-"}\n",
-"}\n",
-"return $(_o) ;\n",
-"}\n",
-"else\n",
-"{\n",
-"return $(<) ;\n",
-"}\n",
-"}\n",
-"rule unmakeDir\n",
-"{\n",
-"if $(>[1]:D) && $(>[1]:D) != $(>[1]) && $(>[1]:D) != \\\\\\\\\n",
-"{\n",
-"unmakeDir $(<) : $(>[1]:D) $(>[1]:BS) $(>[2-]) ;\n",
-"}\n",
-"else\n",
-"{\n",
-"$(<) = $(>) ;\n",
-"}\n",
-"}\n",
-"rule FConvertToSlashes\n",
-"{\n",
-"local _d, _s, _i ;\n",
-"unmakeDir _d : $(<) ;\n",
-"_s = $(_d[1]) ;\n",
-"for _i in $(_d[2-])\n",
-"{\n",
-"_s = $(_s)/$(_i) ;\n",
-"}\n",
-"return $(_s) ;\n",
-"}\n",
-"actions updated together piecemeal Archive\n",
-"{\n",
-"$(AR) $(<) $(>)\n",
-"}\n",
-"actions As\n",
-"{\n",
-"$(AS) $(ASFLAGS) -I$(HDRS) -o $(<) $(>)\n",
-"}\n",
-"actions C++\n",
-"{\n",
-"$(C++) -c $(C++FLAGS) $(OPTIM) -I$(HDRS) -o $(<) $(>)\n",
-"}\n",
-"actions Cc\n",
-"{\n",
-"$(CC) -c $(CCFLAGS) $(OPTIM) -I$(HDRS) -o $(<) $(>)\n",
-"}\n",
-"actions Chgrp\n",
-"{\n",
-"$(CHGRP) $(GROUP) $(<)\n",
-"}\n",
-"actions Chmod1\n",
-"{\n",
-"$(CHMOD) $(MODE) $(<)\n",
-"}\n",
-"actions Chown\n",
-"{\n",
-"$(CHOWN) $(OWNER) $(<)\n",
-"}\n",
-"actions piecemeal together existing Clean\n",
-"{\n",
-"$(RM) $(>)\n",
-"}\n",
-"actions File\n",
-"{\n",
-"$(CP) $(>) $(<)\n",
-"}\n",
-"actions GenFile1\n",
-"{\n",
-"$(>[1]) $(<) $(>[2-])\n",
-"}\n",
-"actions Fortran\n",
-"{\n",
-"$(FORTRAN) $(FORTRANFLAGS) -o $(<) $(>)\n",
-"}\n",
-"actions HardLink\n",
-"{\n",
-"$(RM) $(<) && $(LN) $(>) $(<)\n",
-"}\n",
-"actions Install\n",
-"{\n",
-"$(CP) $(>) $(<)\n",
-"}\n",
-"actions Lex\n",
-"{\n",
-"$(LEX) $(>)\n",
-"}\n",
-"actions LexMv\n",
-"{\n",
-"$(MV) lex.yy.c $(<)\n",
-"}\n",
-"actions Link bind NEEDLIBS\n",
-"{\n",
-"$(LINK) $(LINKFLAGS) -o $(<) $(UNDEFS) $(>) $(NEEDLIBS) $(LINKLIBS)\n",
-"}\n",
-"actions MkDir1\n",
-"{\n",
-"$(MKDIR) $(<)\n",
-"}\n",
-"actions together Ranlib\n",
-"{\n",
-"$(RANLIB) $(<)\n",
-"}\n",
-"actions quietly updated piecemeal together RmTemps\n",
-"{\n",
-"$(RM) $(>)\n",
-"}\n",
-"actions Shell\n",
-"{\n",
-"$(AWK) '\n",
-"NR == 1 { print \"$(SHELLHEADER)\" }\n",
-"NR == 1 && /^[#:]/ { next }\n",
-"/^##/ { next }\n",
-"{ print }\n",
-"' < $(>) > $(<)\n",
-"}\n",
-"actions Yacc1\n",
-"{\n",
-"$(YACC) $(YACCFLAGS) $(>)\n",
-"}\n",
-"actions YaccMv\n",
-"{\n",
-"$(MV) $(YACCFILES).c $(<[1])\n",
-"$(MV) $(YACCFILES).h $(<[2])\n",
-"}\n",
-"if $(RELOCATE)\n",
-"{\n",
-"actions C++\n",
-"{\n",
-"$(C++) -c $(C++FLAGS) $(OPTIM) -I$(HDRS) $(>)\n",
-"}\n",
-"actions Cc\n",
-"{\n",
-"$(CC) -c $(CCFLAGS) $(OPTIM) -I$(HDRS) $(>)\n",
-"}\n",
-"actions ignore CcMv\n",
-"{\n",
-"[ $(<) != $(>:BS=$(SUFOBJ)) ] && $(MV) $(>:BS=$(SUFOBJ)) $(<)\n",
-"}\n",
-"}\n",
-"if $(NOARUPDATE)\n",
-"{\n",
-"actions Archive\n",
-"{\n",
-"$(AR) $(<) $(>)\n",
-"}\n",
-"}\n",
-"if $(NT)\n",
-"{\n",
-"if $(TOOLSET) = VISUALC || $(TOOLSET) = VC7 || $(TOOLSET) = INTELC\n",
-"{\n",
-"actions updated together piecemeal Archive\n",
-"{\n",
-"if exist $(<) set _$(<:B)_=$(<)\n",
-"$(AR) /out:$(<) %_$(<:B)_% $(>)\n",
-"}\n",
-"actions As\n",
-"{\n",
-"$(AS) /Ml /p /v /w2 $(>) $(<) ,nul,nul;\n",
-"}\n",
-"actions Cc\n",
-"{\n",
-"$(CC) /c $(CCFLAGS) $(OPTIM) /Fo$(<) /I$(HDRS) /I$(STDHDRS) $(>)\n",
-"}\n",
-"actions C++\n",
-"{\n",
-"$(C++) /c $(C++FLAGS) $(OPTIM) /Fo$(<) /I$(HDRS) /I$(STDHDRS) /Tp$(>)\n",
-"}\n",
-"actions Link bind NEEDLIBS\n",
-"{\n",
-"$(LINK) $(LINKFLAGS) /out:$(<) $(UNDEFS) $(>) $(NEEDLIBS) $(LINKLIBS)\n",
-"}\n",
-"}\n",
-"else if $(TOOLSET) = VISUALC16\n",
-"{\n",
-"actions updated together piecemeal Archive\n",
-"{\n",
-"$(AR) $(<) -+$(>)\n",
-"}\n",
-"actions Cc\n",
-"{\n",
-"$(CC) /c $(CCFLAGS) $(OPTIM) /Fo$(<) /I$(HDRS) $(>)\n",
-"}\n",
-"actions C++\n",
-"{\n",
-"$(C++) /c $(C++FLAGS) $(OPTIM) /Fo$(<) /I$(HDRS) /Tp$(>)\n",
-"}\n",
-"actions Link bind NEEDLIBS\n",
-"{\n",
-"$(LINK) $(LINKFLAGS) /out:$(<) $(UNDEFS) $(>) $(NEEDLIBS) $(LINKLIBS)\n",
-"}\n",
-"}\n",
-"else if $(TOOLSET) = BORLANDC\n",
-"{\n",
-"actions updated together piecemeal Archive\n",
-"{\n",
-"$(AR) $(<) -+$(>)\n",
-"}\n",
-"actions Link bind NEEDLIBS\n",
-"{\n",
-"$(LINK) -e$(<) $(LINKFLAGS) $(UNDEFS) -L$(LINKLIBS) $(NEEDLIBS) $(>)\n",
-"}\n",
-"actions C++\n",
-"{\n",
-"$(C++) -c $(C++FLAGS) $(OPTIM) -I$(HDRS) -o$(<) $(>)\n",
-"}\n",
-"actions Cc\n",
-"{\n",
-"$(CC) -c $(CCFLAGS) $(OPTIM) -I$(HDRS) -o$(<) $(>)\n",
-"}\n",
-"}\n",
-"else if $(TOOLSET) = MINGW\n",
-"{\n",
-"actions together piecemeal Archive\n",
-"{\n",
-"$(AR) $(<) $(>:T)\n",
-"}\n",
-"actions Cc\n",
-"{\n",
-"$(CC) -c $(CCFLAGS) $(OPTIM) -I$(HDRS) -o$(<) $(>)\n",
-"}\n",
-"actions C++\n",
-"{\n",
-"$(C++) -c $(C++FLAGS) $(OPTIM) -I$(HDRS) -o$(<) $(>)\n",
-"}\n",
-"}\n",
-"else if $(TOOLSET) = WATCOM\n",
-"{\n",
-"actions together piecemeal Archive\n",
-"{\n",
-"$(AR) $(<) +-$(>)\n",
-"}\n",
-"actions Cc\n",
-"{\n",
-"$(CC) $(CCFLAGS) $(OPTIM) /Fo=$(<) /I$(HDRS) $(>)\n",
-"}\n",
-"actions C++\n",
-"{\n",
-"$(C++) $(C++FLAGS) $(OPTIM) /Fo=$(<) /I$(HDRS) $(>)\n",
-"}\n",
-"actions Link bind NEEDLIBS\n",
-"{\n",
-"$(LINK) $(LINKFLAGS) /Fe=$(<) $(UNDEFS) $(>) $(NEEDLIBS) $(LINKLIBS)\n",
-"}\n",
-"actions Shell\n",
-"{\n",
-"$(CP) $(>) $(<)\n",
-"}\n",
-"}\n",
-"else if $(TOOLSET) = LCC\n",
-"{\n",
-"actions together piecemeal Archive\n",
-"{\n",
-"$(AR) /out:$(<) $(>)\n",
-"}\n",
-"actions Cc\n",
-"{\n",
-"$(CC) $(CCFLAGS) $(OPTIM) -Fo$(<) -I$(HDRS) $(>)\n",
-"}\n",
-"actions Link bind NEEDLIBS\n",
-"{\n",
-"$(LINK) $(LINKFLAGS) -o $(<) $(UNDEFS) $(>) $(NEEDLIBS) $(LINKLIBS)\n",
-"}\n",
-"actions Shell\n",
-"{\n",
-"$(CP) $(>) $(<)\n",
-"}\n",
-"}\n",
-"}\n",
-"else if $(OS2)\n",
-"{\n",
-"if $(TOOLSET) = WATCOM\n",
-"{\n",
-"actions together piecemeal Archive\n",
-"{\n",
-"$(AR) $(<) +-$(>)\n",
-"}\n",
-"actions Cc\n",
-"{\n",
-"$(CC) $(CCFLAGS) $(OPTIM) /Fo=$(<) /I$(HDRS) $(>)\n",
-"}\n",
-"actions C++\n",
-"{\n",
-"$(C++) $(C++FLAGS) $(OPTIM) /Fo=$(<) /I$(HDRS) $(>)\n",
-"}\n",
-"actions Link bind NEEDLIBS\n",
-"{\n",
-"$(LINK) $(LINKFLAGS) /Fe=$(<) $(UNDEFS) $(>) $(NEEDLIBS) $(LINKLIBS)\n",
-"}\n",
-"actions Shell\n",
-"{\n",
-"$(CP) $(>) $(<)\n",
-"}\n",
-"}\n",
-"else if $(TOOLSET) = EMX\n",
-"{\n",
-"actions together piecemeal Archive\n",
-"{\n",
-"$(AR) $(<) $(>:T)\n",
-"}\n",
-"actions Cc\n",
-"{\n",
-"$(CC) -c $(CCFLAGS) $(OPTIM) -I$(HDRS) -o$(<) $(>)\n",
-"}\n",
-"actions C++\n",
-"{\n",
-"$(C++) -c $(C++FLAGS) $(OPTIM) -I$(HDRS) -o$(<) $(>)\n",
-"}\n",
-"}\n",
-"}\n",
-"else if $(VMS)\n",
-"{\n",
-"actions updated together piecemeal Archive\n",
-"{\n",
-"lib/replace $(<) $(>[1]) ,$(>[2-])\n",
-"}\n",
-"actions Cc\n",
-"{\n",
-"$(CC)/obj=$(<) $(CCFLAGS) $(OPTIM) $(SLASHINC) $(>)\n",
-"}\n",
-"actions C++\n",
-"{\n",
-"$(C++)/obj=$(<) $(C++FLAGS) $(OPTIM) $(SLASHINC) $(>)\n",
-"}\n",
-"actions piecemeal together existing Clean\n",
-"{\n",
-"$(RM) $(>[1]);* ,$(>[2-]);*\n",
-"}\n",
-"actions together quietly CreLib\n",
-"{\n",
-"if f$search(\"$(<)\") .eqs. \"\" then lib/create $(<)\n",
-"}\n",
-"actions GenFile1\n",
-"{\n",
-"mcr $(>[1]) $(<) $(>[2-])\n",
-"}\n",
-"actions Link bind NEEDLIBS\n",
-"{\n",
-"$(LINK)/exe=$(<) $(LINKFLAGS) $(>[1]) ,$(>[2-]) ,$(NEEDLIBS)/lib ,$(LINKLIBS)\n",
-"}\n",
-"actions quietly updated piecemeal together RmTemps\n",
-"{\n",
-"$(RM) $(>[1]);* ,$(>[2-]);*\n",
-"}\n",
-"actions Shell\n",
-"{\n",
-"$(CP) $(>) $(<)\n",
-"}\n",
-"}\n",
-"else if $(MAC)\n",
-"{\n",
-"actions together Archive\n",
-"{\n",
-"$(LINK) -library -o $(<) $(>)\n",
-"}\n",
-"actions Cc\n",
-"{\n",
-"set -e MWCincludes $(MACINC)\n",
-"$(CC) -o $(<) $(CCFLAGS) $(OPTIM) $(>)\n",
-"}\n",
-"actions C++\n",
-"{\n",
-"set -e MWCincludes $(MACINC)\n",
-"$(CC) -o $(<) $(C++FLAGS) $(OPTIM) $(>)\n",
-"}\n",
-"actions Link bind NEEDLIBS\n",
-"{\n",
-"$(LINK) -o $(<) $(LINKFLAGS) $(>) $(NEEDLIBS) \"$(LINKLIBS)\"\n",
-"}\n",
-"}\n",
-"rule BULK { Bulk $(<) : $(>) ; }\n",
-"rule FILE { File $(<) : $(>) ; }\n",
-"rule HDRRULE { HdrRule $(<) : $(>) ; }\n",
-"rule INSTALL { Install $(<) : $(>) ; }\n",
-"rule LIBRARY { Library $(<) : $(>) ; }\n",
-"rule LIBS { LinkLibraries $(<) : $(>) ; }\n",
-"rule LINK { Link $(<) : $(>) ; }\n",
-"rule MAIN { Main $(<) : $(>) ; }\n",
-"rule SETUID { Setuid $(<) ; }\n",
-"rule SHELL { Shell $(<) : $(>) ; }\n",
-"rule UNDEFINES { Undefines $(<) : $(>) ; }\n",
-"rule INSTALLBIN { InstallBin $(BINDIR) : $(<) ; }\n",
-"rule INSTALLLIB { InstallLib $(LIBDIR) : $(<) ; }\n",
-"rule INSTALLMAN { InstallMan $(MANDIR) : $(<) ; }\n",
-"rule addDirName { $(<) += [ FDirName $(>) ] ; }\n",
-"rule makeDirName { $(<) = [ FDirName $(>) ] ; }\n",
-"rule makeGristedName { $(<) = [ FGristSourceFiles $(>) ] ; }\n",
-"rule makeRelPath { $(<[1]) = [ FRelPath $(<[2-]) : $(>) ] ; }\n",
-"rule makeSuffixed { $(<[1]) = [ FAppendSuffix $(>) : $(<[2]) ] ; }\n",
-"{\n",
-"if $(JAMFILE) { include $(JAMFILE) ; }\n",
-"}\n",
-"}\n",
-0 };
diff --git a/jam-files/engine/jambase.h b/jam-files/engine/jambase.h
deleted file mode 100644
index c05ec792..00000000
--- a/jam-files/engine/jambase.h
+++ /dev/null
@@ -1,15 +0,0 @@
-/*
- * Copyright 1993, 1995 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*
- * jambase.h - declaration for the internal jambase
- *
- * The file Jambase is turned into a C array of strings in jambase.c
- * so that it can be built in to the executable.  This is the
- * declaration for that array.
- */
-
-extern char *jambase[];
diff --git a/jam-files/engine/jamgram.c b/jam-files/engine/jamgram.c
deleted file mode 100644
index b1fa0835..00000000
--- a/jam-files/engine/jamgram.c
+++ /dev/null
@@ -1,1830 +0,0 @@
-/* A Bison parser, made by GNU Bison 1.875.  */
-
-/* Skeleton parser for Yacc-like parsing with Bison,
-   Copyright (C) 1984, 1989, 1990, 2000, 2001, 2002 Free Software Foundation, Inc.
-
-   This program is free software; you can redistribute it and/or modify
-   it under the terms of the GNU General Public License as published by
-   the Free Software Foundation; either version 2, or (at your option)
-   any later version.
-
-   This program is distributed in the hope that it will be useful,
-   but WITHOUT ANY WARRANTY; without even the implied warranty of
-   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-   GNU General Public License for more details.
-
-   You should have received a copy of the GNU General Public License
-   along with this program; if not, write to the Free Software
-   Foundation, Inc., 59 Temple Place - Suite 330,
-   Boston, MA 02111-1307, USA.  */
-
-/* As a special exception, when this file is copied by Bison into a
-   Bison output file, you may use that output file without restriction.
-   This special exception was added by the Free Software Foundation
-   in version 1.24 of Bison.  */
-
-/* Written by Richard Stallman by simplifying the original so called
-   ``semantic'' parser.  */
-
-/* All symbols defined below should begin with yy or YY, to avoid
-   infringing on user name space.  This should be done even for local
-   variables, as they might otherwise be expanded by user macros.
-   There are some unavoidable exceptions within include files to
-   define necessary library symbols; they are noted "INFRINGES ON
-   USER NAME SPACE" below.  */
-
-/* Identify Bison output.  */
-#define YYBISON 1
-
-/* Skeleton name.  */
-#define YYSKELETON_NAME "yacc.c"
-
-/* Pure parsers.  */
-#define YYPURE 0
-
-/* Using locations.  */
-#define YYLSP_NEEDED 0
-
-
-
-/* Tokens.  */
-#ifndef YYTOKENTYPE
-# define YYTOKENTYPE
-   /* Put the tokens into the symbol table, so that GDB and other debuggers
-      know about them.  */
-   enum yytokentype {
-     _BANG_t = 258,
-     _BANG_EQUALS_t = 259,
-     _AMPER_t = 260,
-     _AMPERAMPER_t = 261,
-     _LPAREN_t = 262,
-     _RPAREN_t = 263,
-     _PLUS_EQUALS_t = 264,
-     _COLON_t = 265,
-     _SEMIC_t = 266,
-     _LANGLE_t = 267,
-     _LANGLE_EQUALS_t = 268,
-     _EQUALS_t = 269,
-     _RANGLE_t = 270,
-     _RANGLE_EQUALS_t = 271,
-     _QUESTION_EQUALS_t = 272,
-     _LBRACKET_t = 273,
-     _RBRACKET_t = 274,
-     ACTIONS_t = 275,
-     BIND_t = 276,
-     CASE_t = 277,
-     CLASS_t = 278,
-     DEFAULT_t = 279,
-     ELSE_t = 280,
-     EXISTING_t = 281,
-     FOR_t = 282,
-     IF_t = 283,
-     IGNORE_t = 284,
-     IN_t = 285,
-     INCLUDE_t = 286,
-     LOCAL_t = 287,
-     MODULE_t = 288,
-     ON_t = 289,
-     PIECEMEAL_t = 290,
-     QUIETLY_t = 291,
-     RETURN_t = 292,
-     RULE_t = 293,
-     SWITCH_t = 294,
-     TOGETHER_t = 295,
-     UPDATED_t = 296,
-     WHILE_t = 297,
-     _LBRACE_t = 298,
-     _BAR_t = 299,
-     _BARBAR_t = 300,
-     _RBRACE_t = 301,
-     ARG = 302,
-     STRING = 303
-   };
-#endif
-#define _BANG_t 258
-#define _BANG_EQUALS_t 259
-#define _AMPER_t 260
-#define _AMPERAMPER_t 261
-#define _LPAREN_t 262
-#define _RPAREN_t 263
-#define _PLUS_EQUALS_t 264
-#define _COLON_t 265
-#define _SEMIC_t 266
-#define _LANGLE_t 267
-#define _LANGLE_EQUALS_t 268
-#define _EQUALS_t 269
-#define _RANGLE_t 270
-#define _RANGLE_EQUALS_t 271
-#define _QUESTION_EQUALS_t 272
-#define _LBRACKET_t 273
-#define _RBRACKET_t 274
-#define ACTIONS_t 275
-#define BIND_t 276
-#define CASE_t 277
-#define CLASS_t 278
-#define DEFAULT_t 279
-#define ELSE_t 280
-#define EXISTING_t 281
-#define FOR_t 282
-#define IF_t 283
-#define IGNORE_t 284
-#define IN_t 285
-#define INCLUDE_t 286
-#define LOCAL_t 287
-#define MODULE_t 288
-#define ON_t 289
-#define PIECEMEAL_t 290
-#define QUIETLY_t 291
-#define RETURN_t 292
-#define RULE_t 293
-#define SWITCH_t 294
-#define TOGETHER_t 295
-#define UPDATED_t 296
-#define WHILE_t 297
-#define _LBRACE_t 298
-#define _BAR_t 299
-#define _BARBAR_t 300
-#define _RBRACE_t 301
-#define ARG 302
-#define STRING 303
-
-
-
-
-/* Copy the first part of user declarations.  */
-#line 96 "jamgram.y"
-
-#include "jam.h"
-
-#include "lists.h"
-#include "parse.h"
-#include "scan.h"
-#include "compile.h"
-#include "newstr.h"
-#include "rules.h"
-
-# define YYMAXDEPTH 10000	/* for OSF and other less endowed yaccs */
-
-# define F0 (LIST *(*)(PARSE *, FRAME *))0
-# define P0 (PARSE *)0
-# define S0 (char *)0
-
-# define pappend( l,r )    	parse_make( compile_append,l,r,P0,S0,S0,0 )
-# define peval( c,l,r )	parse_make( compile_eval,l,r,P0,S0,S0,c )
-# define pfor( s,l,r,x )    	parse_make( compile_foreach,l,r,P0,s,S0,x )
-# define pif( l,r,t )	  	parse_make( compile_if,l,r,t,S0,S0,0 )
-# define pincl( l )       	parse_make( compile_include,l,P0,P0,S0,S0,0 )
-# define plist( s )	  	parse_make( compile_list,P0,P0,P0,s,S0,0 )
-# define plocal( l,r,t )  	parse_make( compile_local,l,r,t,S0,S0,0 )
-# define pmodule( l,r )	  	parse_make( compile_module,l,r,P0,S0,S0,0 )
-# define pclass( l,r )	  	parse_make( compile_class,l,r,P0,S0,S0,0 )
-# define pnull()	  	parse_make( compile_null,P0,P0,P0,S0,S0,0 )
-# define pon( l,r )	  	parse_make( compile_on,l,r,P0,S0,S0,0 )
-# define prule( s,p )     	parse_make( compile_rule,p,P0,P0,s,S0,0 )
-# define prules( l,r )	  	parse_make( compile_rules,l,r,P0,S0,S0,0 )
-# define pset( l,r,a )          parse_make( compile_set,l,r,P0,S0,S0,a )
-# define pset1( l,r,t,a )	parse_make( compile_settings,l,r,t,S0,S0,a )
-# define psetc( s,p,a,l )     	parse_make( compile_setcomp,p,a,P0,s,S0,l )
-# define psete( s,l,s1,f ) 	parse_make( compile_setexec,l,P0,P0,s,s1,f )
-# define pswitch( l,r )   	parse_make( compile_switch,l,r,P0,S0,S0,0 )
-# define pwhile( l,r )   	parse_make( compile_while,l,r,P0,S0,S0,0 )
-
-# define pnode( l,r )    	parse_make( F0,l,r,P0,S0,S0,0 )
-# define psnode( s,l )     	parse_make( F0,l,P0,P0,s,S0,0 )
-
-
-
-/* Enabling traces.  */
-#ifndef YYDEBUG
-# define YYDEBUG 0
-#endif
-
-/* Enabling verbose error messages.  */
-#ifdef YYERROR_VERBOSE
-# undef YYERROR_VERBOSE
-# define YYERROR_VERBOSE 1
-#else
-# define YYERROR_VERBOSE 0
-#endif
-
-#if ! defined (YYSTYPE) && ! defined (YYSTYPE_IS_DECLARED)
-typedef int YYSTYPE;
-# define yystype YYSTYPE /* obsolescent; will be withdrawn */
-# define YYSTYPE_IS_DECLARED 1
-# define YYSTYPE_IS_TRIVIAL 1
-#endif
-
-
-
-/* Copy the second part of user declarations.  */
-
-
-/* Line 214 of yacc.c.  */
-#line 223 "y.tab.c"
-
-#if ! defined (yyoverflow) || YYERROR_VERBOSE
-
-/* The parser invokes alloca or malloc; define the necessary symbols.  */
-
-# if YYSTACK_USE_ALLOCA
-#  define YYSTACK_ALLOC alloca
-# else
-#  ifndef YYSTACK_USE_ALLOCA
-#   if defined (alloca) || defined (_ALLOCA_H)
-#    define YYSTACK_ALLOC alloca
-#   else
-#    ifdef __GNUC__
-#     define YYSTACK_ALLOC __builtin_alloca
-#    endif
-#   endif
-#  endif
-# endif
-
-# ifdef YYSTACK_ALLOC
-   /* Pacify GCC's `empty if-body' warning. */
-#  define YYSTACK_FREE(Ptr) do { /* empty */; } while (0)
-# else
-#  if defined (__STDC__) || defined (__cplusplus)
-#   include <stdlib.h> /* INFRINGES ON USER NAME SPACE */
-#   define YYSIZE_T size_t
-#  endif
-#  define YYSTACK_ALLOC malloc
-#  define YYSTACK_FREE free
-# endif
-#endif /* ! defined (yyoverflow) || YYERROR_VERBOSE */
-
-
-#if (! defined (yyoverflow) \
-     && (! defined (__cplusplus) \
-	 || (YYSTYPE_IS_TRIVIAL)))
-
-/* A type that is properly aligned for any stack member.  */
-union yyalloc
-{
-  short yyss;
-  YYSTYPE yyvs;
-  };
-
-/* The size of the maximum gap between one aligned stack and the next.  */
-# define YYSTACK_GAP_MAXIMUM (sizeof (union yyalloc) - 1)
-
-/* The size of an array large to enough to hold all stacks, each with
-   N elements.  */
-# define YYSTACK_BYTES(N) \
-     ((N) * (sizeof (short) + sizeof (YYSTYPE))				\
-      + YYSTACK_GAP_MAXIMUM)
-
-/* Copy COUNT objects from FROM to TO.  The source and destination do
-   not overlap.  */
-# ifndef YYCOPY
-#  if 1 < __GNUC__
-#   define YYCOPY(To, From, Count) \
-      __builtin_memcpy (To, From, (Count) * sizeof (*(From)))
-#  else
-#   define YYCOPY(To, From, Count)		\
-      do					\
-	{					\
-	  register YYSIZE_T yyi;		\
-	  for (yyi = 0; yyi < (Count); yyi++)	\
-	    (To)[yyi] = (From)[yyi];		\
-	}					\
-      while (0)
-#  endif
-# endif
-
-/* Relocate STACK from its old location to the new one.  The
-   local variables YYSIZE and YYSTACKSIZE give the old and new number of
-   elements in the stack, and YYPTR gives the new location of the
-   stack.  Advance YYPTR to a properly aligned location for the next
-   stack.  */
-# define YYSTACK_RELOCATE(Stack)					\
-    do									\
-      {									\
-	YYSIZE_T yynewbytes;						\
-	YYCOPY (&yyptr->Stack, Stack, yysize);				\
-	Stack = &yyptr->Stack;						\
-	yynewbytes = yystacksize * sizeof (*Stack) + YYSTACK_GAP_MAXIMUM; \
-	yyptr += yynewbytes / sizeof (*yyptr);				\
-      }									\
-    while (0)
-
-#endif
-
-#if defined (__STDC__) || defined (__cplusplus)
-   typedef signed char yysigned_char;
-#else
-   typedef short yysigned_char;
-#endif
-
-/* YYFINAL -- State number of the termination state. */
-#define YYFINAL  43
-/* YYLAST -- Last index in YYTABLE.  */
-#define YYLAST   261
-
-/* YYNTOKENS -- Number of terminals. */
-#define YYNTOKENS  49
-/* YYNNTS -- Number of nonterminals. */
-#define YYNNTS  24
-/* YYNRULES -- Number of rules. */
-#define YYNRULES  75
-/* YYNRULES -- Number of states. */
-#define YYNSTATES  159
-
-/* YYTRANSLATE(YYLEX) -- Bison symbol number corresponding to YYLEX.  */
-#define YYUNDEFTOK  2
-#define YYMAXUTOK   303
-
-#define YYTRANSLATE(YYX) 						\
-  ((unsigned int) (YYX) <= YYMAXUTOK ? yytranslate[YYX] : YYUNDEFTOK)
-
-/* YYTRANSLATE[YYLEX] -- Bison symbol number corresponding to YYLEX.  */
-static const unsigned char yytranslate[] =
-{
-       0,     2,     2,     2,     2,     2,     2,     2,     2,     2,
-       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
-       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
-       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
-       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
-       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
-       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
-       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
-       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
-       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
-       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
-       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
-       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
-       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
-       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
-       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
-       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
-       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
-       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
-       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
-       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
-       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
-       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
-       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
-       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
-       2,     2,     2,     2,     2,     2,     1,     2,     3,     4,
-       5,     6,     7,     8,     9,    10,    11,    12,    13,    14,
-      15,    16,    17,    18,    19,    20,    21,    22,    23,    24,
-      25,    26,    27,    28,    29,    30,    31,    32,    33,    34,
-      35,    36,    37,    38,    39,    40,    41,    42,    43,    44,
-      45,    46,    47,    48
-};
-
-#if YYDEBUG
-/* YYPRHS[YYN] -- Index of the first RHS symbol of rule number YYN in
-   YYRHS.  */
-static const unsigned char yyprhs[] =
-{
-       0,     0,     3,     4,     6,     8,    10,    12,    15,    21,
-      22,    25,    27,    31,    32,    34,    35,    39,    43,    47,
-      52,    59,    63,    72,    78,    84,    90,    96,   102,   110,
-     116,   120,   121,   122,   132,   134,   136,   138,   141,   143,
-     147,   151,   155,   159,   163,   167,   171,   175,   179,   183,
-     187,   190,   194,   195,   198,   203,   205,   209,   211,   212,
-     215,   217,   218,   223,   226,   231,   236,   237,   240,   242,
-     244,   246,   248,   250,   252,   253
-};
-
-/* YYRHS -- A `-1'-separated list of the rules' RHS. */
-static const yysigned_char yyrhs[] =
-{
-      50,     0,    -1,    -1,    52,    -1,    53,    -1,    52,    -1,
-      57,    -1,    57,    52,    -1,    32,    65,    54,    11,    51,
-      -1,    -1,    14,    65,    -1,    53,    -1,     7,    64,     8,
-      -1,    -1,    32,    -1,    -1,    43,    51,    46,    -1,    31,
-      65,    11,    -1,    47,    64,    11,    -1,    67,    60,    65,
-      11,    -1,    67,    34,    65,    60,    65,    11,    -1,    37,
-      65,    11,    -1,    27,    56,    47,    30,    65,    43,    51,
-      46,    -1,    39,    65,    43,    62,    46,    -1,    28,    61,
-      43,    51,    46,    -1,    33,    65,    43,    51,    46,    -1,
-      23,    64,    43,    51,    46,    -1,    42,    61,    43,    51,
-      46,    -1,    28,    61,    43,    51,    46,    25,    57,    -1,
-      56,    38,    47,    55,    57,    -1,    34,    67,    57,    -1,
-      -1,    -1,    20,    70,    47,    72,    43,    58,    48,    59,
-      46,    -1,    14,    -1,     9,    -1,    17,    -1,    24,    14,
-      -1,    67,    -1,    61,    14,    61,    -1,    61,     4,    61,
-      -1,    61,    12,    61,    -1,    61,    13,    61,    -1,    61,
-      15,    61,    -1,    61,    16,    61,    -1,    61,     5,    61,
-      -1,    61,     6,    61,    -1,    61,    44,    61,    -1,    61,
-      45,    61,    -1,    67,    30,    65,    -1,     3,    61,    -1,
-       7,    61,     8,    -1,    -1,    63,    62,    -1,    22,    47,
-      10,    51,    -1,    65,    -1,    65,    10,    64,    -1,    66,
-      -1,    -1,    66,    67,    -1,    47,    -1,    -1,    18,    68,
-      69,    19,    -1,    67,    64,    -1,    34,    67,    67,    64,
-      -1,    34,    67,    37,    65,    -1,    -1,    70,    71,    -1,
-      41,    -1,    40,    -1,    29,    -1,    36,    -1,    35,    -1,
-      26,    -1,    -1,    21,    65,    -1
-};
-
-/* YYRLINE[YYN] -- source line where rule number YYN was defined.  */
-static const unsigned short yyrline[] =
-{
-       0,   139,   139,   141,   152,   154,   158,   160,   162,   167,
-     170,   172,   176,   179,   182,   185,   188,   190,   192,   194,
-     196,   198,   200,   202,   204,   206,   208,   210,   212,   214,
-     216,   219,   221,   218,   230,   232,   234,   236,   243,   245,
-     247,   249,   251,   253,   255,   257,   259,   261,   263,   265,
-     267,   269,   281,   282,   286,   295,   297,   307,   312,   313,
-     317,   319,   319,   328,   330,   332,   343,   344,   348,   350,
-     352,   354,   356,   358,   368,   369
-};
-#endif
-
-#if YYDEBUG || YYERROR_VERBOSE
-/* YYTNME[SYMBOL-NUM] -- String name of the symbol SYMBOL-NUM.
-   First, the terminals, then, starting at YYNTOKENS, nonterminals. */
-static const char *const yytname[] =
-{
-  "$end", "error", "$undefined", "_BANG_t", "_BANG_EQUALS_t", "_AMPER_t",
-  "_AMPERAMPER_t", "_LPAREN_t", "_RPAREN_t", "_PLUS_EQUALS_t", "_COLON_t",
-  "_SEMIC_t", "_LANGLE_t", "_LANGLE_EQUALS_t", "_EQUALS_t", "_RANGLE_t",
-  "_RANGLE_EQUALS_t", "_QUESTION_EQUALS_t", "_LBRACKET_t", "_RBRACKET_t",
-  "ACTIONS_t", "BIND_t", "CASE_t", "CLASS_t", "DEFAULT_t", "ELSE_t",
-  "EXISTING_t", "FOR_t", "IF_t", "IGNORE_t", "IN_t", "INCLUDE_t",
-  "LOCAL_t", "MODULE_t", "ON_t", "PIECEMEAL_t", "QUIETLY_t", "RETURN_t",
-  "RULE_t", "SWITCH_t", "TOGETHER_t", "UPDATED_t", "WHILE_t", "_LBRACE_t",
-  "_BAR_t", "_BARBAR_t", "_RBRACE_t", "ARG", "STRING", "$accept", "run",
-  "block", "rules", "null", "assign_list_opt", "arglist_opt", "local_opt",
-  "rule", "@1", "@2", "assign", "expr", "cases", "case", "lol", "list",
-  "listp", "arg", "@3", "func", "eflags", "eflag", "bindlist", 0
-};
-#endif
-
-# ifdef YYPRINT
-/* YYTOKNUM[YYLEX-NUM] -- Internal token number corresponding to
-   token YYLEX-NUM.  */
-static const unsigned short yytoknum[] =
-{
-       0,   256,   257,   258,   259,   260,   261,   262,   263,   264,
-     265,   266,   267,   268,   269,   270,   271,   272,   273,   274,
-     275,   276,   277,   278,   279,   280,   281,   282,   283,   284,
-     285,   286,   287,   288,   289,   290,   291,   292,   293,   294,
-     295,   296,   297,   298,   299,   300,   301,   302,   303
-};
-# endif
-
-/* YYR1[YYN] -- Symbol number of symbol that rule YYN derives.  */
-static const unsigned char yyr1[] =
-{
-       0,    49,    50,    50,    51,    51,    52,    52,    52,    53,
-      54,    54,    55,    55,    56,    56,    57,    57,    57,    57,
-      57,    57,    57,    57,    57,    57,    57,    57,    57,    57,
-      57,    58,    59,    57,    60,    60,    60,    60,    61,    61,
-      61,    61,    61,    61,    61,    61,    61,    61,    61,    61,
-      61,    61,    62,    62,    63,    64,    64,    65,    66,    66,
-      67,    68,    67,    69,    69,    69,    70,    70,    71,    71,
-      71,    71,    71,    71,    72,    72
-};
-
-/* YYR2[YYN] -- Number of symbols composing right hand side of rule YYN.  */
-static const unsigned char yyr2[] =
-{
-       0,     2,     0,     1,     1,     1,     1,     2,     5,     0,
-       2,     1,     3,     0,     1,     0,     3,     3,     3,     4,
-       6,     3,     8,     5,     5,     5,     5,     5,     7,     5,
-       3,     0,     0,     9,     1,     1,     1,     2,     1,     3,
-       3,     3,     3,     3,     3,     3,     3,     3,     3,     3,
-       2,     3,     0,     2,     4,     1,     3,     1,     0,     2,
-       1,     0,     4,     2,     4,     4,     0,     2,     1,     1,
-       1,     1,     1,     1,     0,     2
-};
-
-/* YYDEFACT[STATE-NAME] -- Default rule to reduce with in state
-   STATE-NUM when YYTABLE doesn't specify something else to do.  Zero
-   means the default is an error.  */
-static const unsigned char yydefact[] =
-{
-       2,    61,    66,    58,    15,     0,    58,    58,    58,     0,
-      58,    58,     0,     9,    60,     0,     3,     0,     6,     0,
-       0,     0,     0,    55,    57,    14,     0,     0,     0,    60,
-       0,    38,     0,     9,     0,    15,     0,     0,     0,     0,
-       5,     4,     0,     1,     0,     7,    35,    34,    36,     0,
-      58,    58,     0,    58,     0,    73,    70,    72,    71,    69,
-      68,    74,    67,     9,    58,    59,     0,    50,     0,     0,
-       0,     0,     0,     0,     0,     0,     0,     9,     0,     0,
-      58,    17,    58,    11,     0,     9,    30,    21,    52,     9,
-      16,    18,    13,    37,     0,     0,     0,    63,    62,    58,
-       0,     0,    56,    58,    51,    40,    45,    46,    41,    42,
-      39,    43,    44,     0,    47,    48,    49,    10,     9,     0,
-       0,     0,    52,     0,    58,    15,    58,    19,    58,    58,
-      75,    31,    26,     0,    24,     8,    25,     0,    23,    53,
-      27,     0,    29,     0,    65,    64,     0,     9,    15,     9,
-      12,    20,    32,     0,    28,    54,     0,    22,    33
-};
-
-/* YYDEFGOTO[NTERM-NUM]. */
-static const short yydefgoto[] =
-{
-      -1,    15,    39,    40,    41,    84,   125,    17,    18,   146,
-     156,    51,    30,   121,   122,    22,    23,    24,    31,    20,
-      54,    21,    62,   100
-};
-
-/* YYPACT[STATE-NUM] -- Index in YYTABLE of the portion describing
-   STATE-NUM.  */
-#define YYPACT_NINF -48
-static const short yypact[] =
-{
-     179,   -48,   -48,   -48,   -15,     7,   -48,   -16,   -48,     3,
-     -48,   -48,     7,   179,     1,    27,   -48,    -9,   179,    19,
-      -3,    33,   -11,    24,     3,   -48,   -10,     7,     7,   -48,
-     138,     9,    30,    35,    13,   205,    53,    22,   151,    20,
-     -48,   -48,    56,   -48,    23,   -48,   -48,   -48,   -48,    61,
-     -48,   -48,     3,   -48,    62,   -48,   -48,   -48,   -48,   -48,
-     -48,    58,   -48,   179,   -48,   -48,    52,   -48,   164,     7,
-       7,     7,     7,     7,     7,     7,     7,   179,     7,     7,
-     -48,   -48,   -48,   -48,    72,   179,   -48,   -48,    68,   179,
-     -48,   -48,    85,   -48,    77,    73,     8,   -48,   -48,   -48,
-      50,    57,   -48,   -48,   -48,    45,    93,    93,   -48,   -48,
-      45,   -48,   -48,    64,   245,   245,   -48,   -48,   179,    66,
-      67,    69,    68,    71,   -48,   205,   -48,   -48,   -48,   -48,
-     -48,   -48,   -48,    70,    79,   -48,   -48,   109,   -48,   -48,
-     -48,   112,   -48,   115,   -48,   -48,    75,   179,   205,   179,
-     -48,   -48,   -48,    81,   -48,   -48,    82,   -48,   -48
-};
-
-/* YYPGOTO[NTERM-NUM].  */
-static const short yypgoto[] =
-{
-     -48,   -48,   -47,     5,   104,   -48,   -48,   136,   -27,   -48,
-     -48,    47,    60,    36,   -48,   -13,    -4,   -48,     0,   -48,
-     -48,   -48,   -48,   -48
-};
-
-/* YYTABLE[YYPACT[STATE-NUM]].  What to do in state STATE-NUM.  If
-   positive, shift that token.  If negative, reduce the rule which
-   number is the opposite.  If zero, do what YYDEFACT says.
-   If YYTABLE_NINF, syntax error.  */
-#define YYTABLE_NINF -59
-static const short yytable[] =
-{
-      19,    42,    32,    33,    34,    16,    36,    37,    86,    35,
-      27,   -58,   -58,    19,    28,     1,   101,    25,    19,   -58,
-      53,     1,   -14,    45,    65,     1,     1,    43,    46,    44,
-     113,    52,    63,    47,    64,    19,    48,    66,   119,    80,
-      97,    81,   123,    49,    29,   128,    94,    95,   -58,    82,
-      29,   102,    96,    50,    29,    29,    85,    72,    73,    55,
-      75,    76,    56,    19,    87,    88,    90,    91,    57,    58,
-      92,   135,    38,    59,    60,    93,   116,    19,   117,    99,
-      61,    98,   103,   118,   127,    19,    46,    67,    68,    19,
-     120,    47,   124,   131,    48,   130,   129,    69,   142,   133,
-     153,    49,   155,   132,   148,    72,    73,    74,    75,    76,
-     134,   141,   136,   147,   137,   138,   145,   140,    19,   149,
-     150,   154,   143,   152,   144,    19,   151,   157,   158,   105,
-     106,   107,   108,   109,   110,   111,   112,    83,   114,   115,
-      26,   126,    69,    70,    71,     0,     0,    19,    19,    19,
-      72,    73,    74,    75,    76,    69,    70,    71,   139,     0,
-       0,     0,     0,    72,    73,    74,    75,    76,    69,    70,
-      71,     0,   104,     0,     0,     0,    72,    73,    74,    75,
-      76,    77,    78,    79,     0,     0,     0,     0,     0,     0,
-       0,     0,     0,     0,    89,    78,    79,     1,     0,     2,
-       0,     0,     3,     0,     0,     0,     4,     5,    78,    79,
-       6,     7,     8,     9,     0,     0,    10,   -15,    11,     0,
-       0,    12,    13,     1,     0,     2,    14,     0,     3,     0,
-       0,     0,     4,     5,     0,     0,     6,    25,     8,     9,
-       0,     0,    10,     0,    11,     0,     0,    12,    13,    69,
-      70,    71,    14,     0,     0,     0,     0,    72,    73,    74,
-      75,    76
-};
-
-static const short yycheck[] =
-{
-       0,    14,     6,     7,     8,     0,    10,    11,    35,     9,
-       3,    10,    11,    13,     7,    18,    63,    32,    18,    18,
-      20,    18,    38,    18,    24,    18,    18,     0,     9,    38,
-      77,    34,    43,    14,    10,    35,    17,    47,    85,    30,
-      53,    11,    89,    24,    47,    37,    50,    51,    47,    14,
-      47,    64,    52,    34,    47,    47,    43,    12,    13,    26,
-      15,    16,    29,    63,    11,    43,    46,    11,    35,    36,
-      47,   118,    12,    40,    41,    14,    80,    77,    82,    21,
-      47,    19,    30,    11,    11,    85,     9,    27,    28,    89,
-      22,    14,     7,    43,    17,    99,    96,     4,   125,   103,
-     147,    24,   149,    46,    25,    12,    13,    14,    15,    16,
-      46,   124,    46,    43,    47,    46,   129,    46,   118,    10,
-       8,   148,   126,    48,   128,   125,    11,    46,    46,    69,
-      70,    71,    72,    73,    74,    75,    76,    33,    78,    79,
-       4,    94,     4,     5,     6,    -1,    -1,   147,   148,   149,
-      12,    13,    14,    15,    16,     4,     5,     6,   122,    -1,
-      -1,    -1,    -1,    12,    13,    14,    15,    16,     4,     5,
-       6,    -1,     8,    -1,    -1,    -1,    12,    13,    14,    15,
-      16,    43,    44,    45,    -1,    -1,    -1,    -1,    -1,    -1,
-      -1,    -1,    -1,    -1,    43,    44,    45,    18,    -1,    20,
-      -1,    -1,    23,    -1,    -1,    -1,    27,    28,    44,    45,
-      31,    32,    33,    34,    -1,    -1,    37,    38,    39,    -1,
-      -1,    42,    43,    18,    -1,    20,    47,    -1,    23,    -1,
-      -1,    -1,    27,    28,    -1,    -1,    31,    32,    33,    34,
-      -1,    -1,    37,    -1,    39,    -1,    -1,    42,    43,     4,
-       5,     6,    47,    -1,    -1,    -1,    -1,    12,    13,    14,
-      15,    16
-};
-
-/* YYSTOS[STATE-NUM] -- The (internal number of the) accessing
-   symbol of state STATE-NUM.  */
-static const unsigned char yystos[] =
-{
-       0,    18,    20,    23,    27,    28,    31,    32,    33,    34,
-      37,    39,    42,    43,    47,    50,    52,    56,    57,    67,
-      68,    70,    64,    65,    66,    32,    56,     3,     7,    47,
-      61,    67,    65,    65,    65,    67,    65,    65,    61,    51,
-      52,    53,    64,     0,    38,    52,     9,    14,    17,    24,
-      34,    60,    34,    67,    69,    26,    29,    35,    36,    40,
-      41,    47,    71,    43,    10,    67,    47,    61,    61,     4,
-       5,     6,    12,    13,    14,    15,    16,    43,    44,    45,
-      30,    11,    14,    53,    54,    43,    57,    11,    43,    43,
-      46,    11,    47,    14,    65,    65,    67,    64,    19,    21,
-      72,    51,    64,    30,     8,    61,    61,    61,    61,    61,
-      61,    61,    61,    51,    61,    61,    65,    65,    11,    51,
-      22,    62,    63,    51,     7,    55,    60,    11,    37,    67,
-      65,    43,    46,    65,    46,    51,    46,    47,    46,    62,
-      46,    64,    57,    65,    65,    64,    58,    43,    25,    10,
-       8,    11,    48,    51,    57,    51,    59,    46,    46
-};
-
-#if ! defined (YYSIZE_T) && defined (__SIZE_TYPE__)
-# define YYSIZE_T __SIZE_TYPE__
-#endif
-#if ! defined (YYSIZE_T) && defined (size_t)
-# define YYSIZE_T size_t
-#endif
-#if ! defined (YYSIZE_T)
-# if defined (__STDC__) || defined (__cplusplus)
-#  include <stddef.h> /* INFRINGES ON USER NAME SPACE */
-#  define YYSIZE_T size_t
-# endif
-#endif
-#if ! defined (YYSIZE_T)
-# define YYSIZE_T unsigned int
-#endif
-
-#define yyerrok		(yyerrstatus = 0)
-#define yyclearin	(yychar = YYEMPTY)
-#define YYEMPTY		(-2)
-#define YYEOF		0
-
-#define YYACCEPT	goto yyacceptlab
-#define YYABORT		goto yyabortlab
-#define YYERROR		goto yyerrlab1
-
-/* Like YYERROR except do call yyerror.  This remains here temporarily
-   to ease the transition to the new meaning of YYERROR, for GCC.
-   Once GCC version 2 has supplanted version 1, this can go.  */
-
-#define YYFAIL		goto yyerrlab
-
-#define YYRECOVERING()  (!!yyerrstatus)
-
-#define YYBACKUP(Token, Value)					\
-do								\
-  if (yychar == YYEMPTY && yylen == 1)				\
-    {								\
-      yychar = (Token);						\
-      yylval = (Value);						\
-      yytoken = YYTRANSLATE (yychar);				\
-      YYPOPSTACK;						\
-      goto yybackup;						\
-    }								\
-  else								\
-    { 								\
-      yyerror ("syntax error: cannot back up");\
-      YYERROR;							\
-    }								\
-while (0)
-
-#define YYTERROR	1
-#define YYERRCODE	256
-
-/* YYLLOC_DEFAULT -- Compute the default location (before the actions
-   are run).  */
-
-#ifndef YYLLOC_DEFAULT
-# define YYLLOC_DEFAULT(Current, Rhs, N)         \
-  Current.first_line   = Rhs[1].first_line;      \
-  Current.first_column = Rhs[1].first_column;    \
-  Current.last_line    = Rhs[N].last_line;       \
-  Current.last_column  = Rhs[N].last_column;
-#endif
-
-/* YYLEX -- calling `yylex' with the right arguments.  */
-
-#ifdef YYLEX_PARAM
-# define YYLEX yylex (YYLEX_PARAM)
-#else
-# define YYLEX yylex ()
-#endif
-
-/* Enable debugging if requested.  */
-#if YYDEBUG
-
-# ifndef YYFPRINTF
-#  include <stdio.h> /* INFRINGES ON USER NAME SPACE */
-#  define YYFPRINTF fprintf
-# endif
-
-# define YYDPRINTF(Args)			\
-do {						\
-  if (yydebug)					\
-    YYFPRINTF Args;				\
-} while (0)
-
-# define YYDSYMPRINT(Args)			\
-do {						\
-  if (yydebug)					\
-    yysymprint Args;				\
-} while (0)
-
-# define YYDSYMPRINTF(Title, Token, Value, Location)		\
-do {								\
-  if (yydebug)							\
-    {								\
-      YYFPRINTF (stderr, "%s ", Title);				\
-      yysymprint (stderr, 					\
-                  Token, Value);	\
-      YYFPRINTF (stderr, "\n");					\
-    }								\
-} while (0)
-
-/*------------------------------------------------------------------.
-| yy_stack_print -- Print the state stack from its BOTTOM up to its |
-| TOP (cinluded).                                                   |
-`------------------------------------------------------------------*/
-
-#if defined (__STDC__) || defined (__cplusplus)
-static void
-yy_stack_print (short *bottom, short *top)
-#else
-static void
-yy_stack_print (bottom, top)
-    short *bottom;
-    short *top;
-#endif
-{
-  YYFPRINTF (stderr, "Stack now");
-  for (/* Nothing. */; bottom <= top; ++bottom)
-    YYFPRINTF (stderr, " %d", *bottom);
-  YYFPRINTF (stderr, "\n");
-}
-
-# define YY_STACK_PRINT(Bottom, Top)				\
-do {								\
-  if (yydebug)							\
-    yy_stack_print ((Bottom), (Top));				\
-} while (0)
-
-
-/*------------------------------------------------.
-| Report that the YYRULE is going to be reduced.  |
-`------------------------------------------------*/
-
-#if defined (__STDC__) || defined (__cplusplus)
-static void
-yy_reduce_print (int yyrule)
-#else
-static void
-yy_reduce_print (yyrule)
-    int yyrule;
-#endif
-{
-  int yyi;
-  unsigned int yylineno = yyrline[yyrule];
-  YYFPRINTF (stderr, "Reducing stack by rule %d (line %u), ",
-             yyrule - 1, yylineno);
-  /* Print the symbols being reduced, and their result.  */
-  for (yyi = yyprhs[yyrule]; 0 <= yyrhs[yyi]; yyi++)
-    YYFPRINTF (stderr, "%s ", yytname [yyrhs[yyi]]);
-  YYFPRINTF (stderr, "-> %s\n", yytname [yyr1[yyrule]]);
-}
-
-# define YY_REDUCE_PRINT(Rule)		\
-do {					\
-  if (yydebug)				\
-    yy_reduce_print (Rule);		\
-} while (0)
-
-/* Nonzero means print parse trace.  It is left uninitialized so that
-   multiple parsers can coexist.  */
-int yydebug;
-#else /* !YYDEBUG */
-# define YYDPRINTF(Args)
-# define YYDSYMPRINT(Args)
-# define YYDSYMPRINTF(Title, Token, Value, Location)
-# define YY_STACK_PRINT(Bottom, Top)
-# define YY_REDUCE_PRINT(Rule)
-#endif /* !YYDEBUG */
-
-
-/* YYINITDEPTH -- initial size of the parser's stacks.  */
-#ifndef	YYINITDEPTH
-# define YYINITDEPTH 200
-#endif
-
-/* YYMAXDEPTH -- maximum size the stacks can grow to (effective only
-   if the built-in stack extension method is used).
-
-   Do not make this value too large; the results are undefined if
-   SIZE_MAX < YYSTACK_BYTES (YYMAXDEPTH)
-   evaluated with infinite-precision integer arithmetic.  */
-
-#if YYMAXDEPTH == 0
-# undef YYMAXDEPTH
-#endif
-
-#ifndef YYMAXDEPTH
-# define YYMAXDEPTH 10000
-#endif
-
-
-
-#if YYERROR_VERBOSE
-
-# ifndef yystrlen
-#  if defined (__GLIBC__) && defined (_STRING_H)
-#   define yystrlen strlen
-#  else
-/* Return the length of YYSTR.  */
-static YYSIZE_T
-#   if defined (__STDC__) || defined (__cplusplus)
-yystrlen (const char *yystr)
-#   else
-yystrlen (yystr)
-     const char *yystr;
-#   endif
-{
-  register const char *yys = yystr;
-
-  while (*yys++ != '\0')
-    continue;
-
-  return yys - yystr - 1;
-}
-#  endif
-# endif
-
-# ifndef yystpcpy
-#  if defined (__GLIBC__) && defined (_STRING_H) && defined (_GNU_SOURCE)
-#   define yystpcpy stpcpy
-#  else
-/* Copy YYSRC to YYDEST, returning the address of the terminating '\0' in
-   YYDEST.  */
-static char *
-#   if defined (__STDC__) || defined (__cplusplus)
-yystpcpy (char *yydest, const char *yysrc)
-#   else
-yystpcpy (yydest, yysrc)
-     char *yydest;
-     const char *yysrc;
-#   endif
-{
-  register char *yyd = yydest;
-  register const char *yys = yysrc;
-
-  while ((*yyd++ = *yys++) != '\0')
-    continue;
-
-  return yyd - 1;
-}
-#  endif
-# endif
-
-#endif /* !YYERROR_VERBOSE */
-
-
-
-#if YYDEBUG
-/*--------------------------------.
-| Print this symbol on YYOUTPUT.  |
-`--------------------------------*/
-
-#if defined (__STDC__) || defined (__cplusplus)
-static void
-yysymprint (FILE *yyoutput, int yytype, YYSTYPE *yyvaluep)
-#else
-static void
-yysymprint (yyoutput, yytype, yyvaluep)
-    FILE *yyoutput;
-    int yytype;
-    YYSTYPE *yyvaluep;
-#endif
-{
-  /* Pacify ``unused variable'' warnings.  */
-  (void) yyvaluep;
-
-  if (yytype < YYNTOKENS)
-    {
-      YYFPRINTF (yyoutput, "token %s (", yytname[yytype]);
-# ifdef YYPRINT
-      YYPRINT (yyoutput, yytoknum[yytype], *yyvaluep);
-# endif
-    }
-  else
-    YYFPRINTF (yyoutput, "nterm %s (", yytname[yytype]);
-
-  switch (yytype)
-    {
-      default:
-        break;
-    }
-  YYFPRINTF (yyoutput, ")");
-}
-
-#endif /* ! YYDEBUG */
-/*-----------------------------------------------.
-| Release the memory associated to this symbol.  |
-`-----------------------------------------------*/
-
-#if defined (__STDC__) || defined (__cplusplus)
-static void
-yydestruct (int yytype, YYSTYPE *yyvaluep)
-#else
-static void
-yydestruct (yytype, yyvaluep)
-    int yytype;
-    YYSTYPE *yyvaluep;
-#endif
-{
-  /* Pacify ``unused variable'' warnings.  */
-  (void) yyvaluep;
-
-  switch (yytype)
-    {
-
-      default:
-        break;
-    }
-}
-
-
-/* Prevent warnings from -Wmissing-prototypes.  */
-
-#ifdef YYPARSE_PARAM
-# if defined (__STDC__) || defined (__cplusplus)
-int yyparse (void *YYPARSE_PARAM);
-# else
-int yyparse ();
-# endif
-#else /* ! YYPARSE_PARAM */
-#if defined (__STDC__) || defined (__cplusplus)
-int yyparse (void);
-#else
-int yyparse ();
-#endif
-#endif /* ! YYPARSE_PARAM */
-
-
-
-/* The lookahead symbol.  */
-int yychar;
-
-/* The semantic value of the lookahead symbol.  */
-YYSTYPE yylval;
-
-/* Number of syntax errors so far.  */
-int yynerrs;
-
-
-
-/*----------.
-| yyparse.  |
-`----------*/
-
-#ifdef YYPARSE_PARAM
-# if defined (__STDC__) || defined (__cplusplus)
-int yyparse (void *YYPARSE_PARAM)
-# else
-int yyparse (YYPARSE_PARAM)
-  void *YYPARSE_PARAM;
-# endif
-#else /* ! YYPARSE_PARAM */
-#if defined (__STDC__) || defined (__cplusplus)
-int
-yyparse (void)
-#else
-int
-yyparse ()
-
-#endif
-#endif
-{
-
-  register int yystate;
-  register int yyn;
-  int yyresult;
-  /* Number of tokens to shift before error messages enabled.  */
-  int yyerrstatus;
-  /* Lookahead token as an internal (translated) token number.  */
-  int yytoken = 0;
-
-  /* Three stacks and their tools:
-     `yyss': related to states,
-     `yyvs': related to semantic values,
-     `yyls': related to locations.
-
-     Refer to the stacks thru separate pointers, to allow yyoverflow
-     to reallocate them elsewhere.  */
-
-  /* The state stack.  */
-  short	yyssa[YYINITDEPTH];
-  short *yyss = yyssa;
-  register short *yyssp;
-
-  /* The semantic value stack.  */
-  YYSTYPE yyvsa[YYINITDEPTH];
-  YYSTYPE *yyvs = yyvsa;
-  register YYSTYPE *yyvsp;
-
-
-
-#define YYPOPSTACK   (yyvsp--, yyssp--)
-
-  YYSIZE_T yystacksize = YYINITDEPTH;
-
-  /* The variables used to return semantic value and location from the
-     action routines.  */
-  YYSTYPE yyval;
-
-
-  /* When reducing, the number of symbols on the RHS of the reduced
-     rule.  */
-  int yylen;
-
-  YYDPRINTF ((stderr, "Starting parse\n"));
-
-  yystate = 0;
-  yyerrstatus = 0;
-  yynerrs = 0;
-  yychar = YYEMPTY;		/* Cause a token to be read.  */
-
-  /* Initialize stack pointers.
-     Waste one element of value and location stack
-     so that they stay on the same level as the state stack.
-     The wasted elements are never initialized.  */
-
-  yyssp = yyss;
-  yyvsp = yyvs;
-
-  goto yysetstate;
-
-/*------------------------------------------------------------.
-| yynewstate -- Push a new state, which is found in yystate.  |
-`------------------------------------------------------------*/
- yynewstate:
-  /* In all cases, when you get here, the value and location stacks
-     have just been pushed. so pushing a state here evens the stacks.
-     */
-  yyssp++;
-
- yysetstate:
-  *yyssp = yystate;
-
-  if (yyss + yystacksize - 1 <= yyssp)
-    {
-      /* Get the current used size of the three stacks, in elements.  */
-      YYSIZE_T yysize = yyssp - yyss + 1;
-
-#ifdef yyoverflow
-      {
-	/* Give user a chance to reallocate the stack. Use copies of
-	   these so that the &'s don't force the real ones into
-	   memory.  */
-	YYSTYPE *yyvs1 = yyvs;
-	short *yyss1 = yyss;
-
-
-	/* Each stack pointer address is followed by the size of the
-	   data in use in that stack, in bytes.  This used to be a
-	   conditional around just the two extra args, but that might
-	   be undefined if yyoverflow is a macro.  */
-	yyoverflow ("parser stack overflow",
-		    &yyss1, yysize * sizeof (*yyssp),
-		    &yyvs1, yysize * sizeof (*yyvsp),
-
-		    &yystacksize);
-
-	yyss = yyss1;
-	yyvs = yyvs1;
-      }
-#else /* no yyoverflow */
-# ifndef YYSTACK_RELOCATE
-      goto yyoverflowlab;
-# else
-      /* Extend the stack our own way.  */
-      if (YYMAXDEPTH <= yystacksize)
-	goto yyoverflowlab;
-      yystacksize *= 2;
-      if (YYMAXDEPTH < yystacksize)
-	yystacksize = YYMAXDEPTH;
-
-      {
-	short *yyss1 = yyss;
-	union yyalloc *yyptr =
-	  (union yyalloc *) YYSTACK_ALLOC (YYSTACK_BYTES (yystacksize));
-	if (! yyptr)
-	  goto yyoverflowlab;
-	YYSTACK_RELOCATE (yyss);
-	YYSTACK_RELOCATE (yyvs);
-
-#  undef YYSTACK_RELOCATE
-	if (yyss1 != yyssa)
-	  YYSTACK_FREE (yyss1);
-      }
-# endif
-#endif /* no yyoverflow */
-
-      yyssp = yyss + yysize - 1;
-      yyvsp = yyvs + yysize - 1;
-
-
-      YYDPRINTF ((stderr, "Stack size increased to %lu\n",
-		  (unsigned long int) yystacksize));
-
-      if (yyss + yystacksize - 1 <= yyssp)
-	YYABORT;
-    }
-
-  YYDPRINTF ((stderr, "Entering state %d\n", yystate));
-
-  goto yybackup;
-
-/*-----------.
-| yybackup.  |
-`-----------*/
-yybackup:
-
-/* Do appropriate processing given the current state.  */
-/* Read a lookahead token if we need one and don't already have one.  */
-/* yyresume: */
-
-  /* First try to decide what to do without reference to lookahead token.  */
-
-  yyn = yypact[yystate];
-  if (yyn == YYPACT_NINF)
-    goto yydefault;
-
-  /* Not known => get a lookahead token if don't already have one.  */
-
-  /* YYCHAR is either YYEMPTY or YYEOF or a valid lookahead symbol.  */
-  if (yychar == YYEMPTY)
-    {
-      YYDPRINTF ((stderr, "Reading a token: "));
-      yychar = YYLEX;
-    }
-
-  if (yychar <= YYEOF)
-    {
-      yychar = yytoken = YYEOF;
-      YYDPRINTF ((stderr, "Now at end of input.\n"));
-    }
-  else
-    {
-      yytoken = YYTRANSLATE (yychar);
-      YYDSYMPRINTF ("Next token is", yytoken, &yylval, &yylloc);
-    }
-
-  /* If the proper action on seeing token YYTOKEN is to reduce or to
-     detect an error, take that action.  */
-  yyn += yytoken;
-  if (yyn < 0 || YYLAST < yyn || yycheck[yyn] != yytoken)
-    goto yydefault;
-  yyn = yytable[yyn];
-  if (yyn <= 0)
-    {
-      if (yyn == 0 || yyn == YYTABLE_NINF)
-	goto yyerrlab;
-      yyn = -yyn;
-      goto yyreduce;
-    }
-
-  if (yyn == YYFINAL)
-    YYACCEPT;
-
-  /* Shift the lookahead token.  */
-  YYDPRINTF ((stderr, "Shifting token %s, ", yytname[yytoken]));
-
-  /* Discard the token being shifted unless it is eof.  */
-  if (yychar != YYEOF)
-    yychar = YYEMPTY;
-
-  *++yyvsp = yylval;
-
-
-  /* Count tokens shifted since error; after three, turn off error
-     status.  */
-  if (yyerrstatus)
-    yyerrstatus--;
-
-  yystate = yyn;
-  goto yynewstate;
-
-
-/*-----------------------------------------------------------.
-| yydefault -- do the default action for the current state.  |
-`-----------------------------------------------------------*/
-yydefault:
-  yyn = yydefact[yystate];
-  if (yyn == 0)
-    goto yyerrlab;
-  goto yyreduce;
-
-
-/*-----------------------------.
-| yyreduce -- Do a reduction.  |
-`-----------------------------*/
-yyreduce:
-  /* yyn is the number of a rule to reduce with.  */
-  yylen = yyr2[yyn];
-
-  /* If YYLEN is nonzero, implement the default value of the action:
-     `$$ = $1'.
-
-     Otherwise, the following line sets YYVAL to garbage.
-     This behavior is undocumented and Bison
-     users should not rely upon it.  Assigning to YYVAL
-     unconditionally makes the parser a bit smaller, and it avoids a
-     GCC warning that YYVAL may be used uninitialized.  */
-  yyval = yyvsp[1-yylen];
-
-
-  YY_REDUCE_PRINT (yyn);
-  switch (yyn)
-    {
-        case 3:
-#line 142 "jamgram.y"
-    { parse_save( yyvsp[0].parse ); }
-    break;
-
-  case 4:
-#line 153 "jamgram.y"
-    { yyval.parse = yyvsp[0].parse; }
-    break;
-
-  case 5:
-#line 155 "jamgram.y"
-    { yyval.parse = yyvsp[0].parse; }
-    break;
-
-  case 6:
-#line 159 "jamgram.y"
-    { yyval.parse = yyvsp[0].parse; }
-    break;
-
-  case 7:
-#line 161 "jamgram.y"
-    { yyval.parse = prules( yyvsp[-1].parse, yyvsp[0].parse ); }
-    break;
-
-  case 8:
-#line 163 "jamgram.y"
-    { yyval.parse = plocal( yyvsp[-3].parse, yyvsp[-2].parse, yyvsp[0].parse ); }
-    break;
-
-  case 9:
-#line 167 "jamgram.y"
-    { yyval.parse = pnull(); }
-    break;
-
-  case 10:
-#line 171 "jamgram.y"
-    { yyval.parse = yyvsp[0].parse; yyval.number = ASSIGN_SET; }
-    break;
-
-  case 11:
-#line 173 "jamgram.y"
-    { yyval.parse = yyvsp[0].parse; yyval.number = ASSIGN_APPEND; }
-    break;
-
-  case 12:
-#line 177 "jamgram.y"
-    { yyval.parse = yyvsp[-1].parse; }
-    break;
-
-  case 13:
-#line 179 "jamgram.y"
-    { yyval.parse = P0; }
-    break;
-
-  case 14:
-#line 183 "jamgram.y"
-    { yyval.number = 1; }
-    break;
-
-  case 15:
-#line 185 "jamgram.y"
-    { yyval.number = 0; }
-    break;
-
-  case 16:
-#line 189 "jamgram.y"
-    { yyval.parse = yyvsp[-1].parse; }
-    break;
-
-  case 17:
-#line 191 "jamgram.y"
-    { yyval.parse = pincl( yyvsp[-1].parse ); }
-    break;
-
-  case 18:
-#line 193 "jamgram.y"
-    { yyval.parse = prule( yyvsp[-2].string, yyvsp[-1].parse ); }
-    break;
-
-  case 19:
-#line 195 "jamgram.y"
-    { yyval.parse = pset( yyvsp[-3].parse, yyvsp[-1].parse, yyvsp[-2].number ); }
-    break;
-
-  case 20:
-#line 197 "jamgram.y"
-    { yyval.parse = pset1( yyvsp[-5].parse, yyvsp[-3].parse, yyvsp[-1].parse, yyvsp[-2].number ); }
-    break;
-
-  case 21:
-#line 199 "jamgram.y"
-    { yyval.parse = yyvsp[-1].parse; }
-    break;
-
-  case 22:
-#line 201 "jamgram.y"
-    { yyval.parse = pfor( yyvsp[-5].string, yyvsp[-3].parse, yyvsp[-1].parse, yyvsp[-6].number ); }
-    break;
-
-  case 23:
-#line 203 "jamgram.y"
-    { yyval.parse = pswitch( yyvsp[-3].parse, yyvsp[-1].parse ); }
-    break;
-
-  case 24:
-#line 205 "jamgram.y"
-    { yyval.parse = pif( yyvsp[-3].parse, yyvsp[-1].parse, pnull() ); }
-    break;
-
-  case 25:
-#line 207 "jamgram.y"
-    { yyval.parse = pmodule( yyvsp[-3].parse, yyvsp[-1].parse ); }
-    break;
-
-  case 26:
-#line 209 "jamgram.y"
-    { yyval.parse = pclass( yyvsp[-3].parse, yyvsp[-1].parse ); }
-    break;
-
-  case 27:
-#line 211 "jamgram.y"
-    { yyval.parse = pwhile( yyvsp[-3].parse, yyvsp[-1].parse ); }
-    break;
-
-  case 28:
-#line 213 "jamgram.y"
-    { yyval.parse = pif( yyvsp[-5].parse, yyvsp[-3].parse, yyvsp[0].parse ); }
-    break;
-
-  case 29:
-#line 215 "jamgram.y"
-    { yyval.parse = psetc( yyvsp[-2].string, yyvsp[0].parse, yyvsp[-1].parse, yyvsp[-4].number ); }
-    break;
-
-  case 30:
-#line 217 "jamgram.y"
-    { yyval.parse = pon( yyvsp[-1].parse, yyvsp[0].parse ); }
-    break;
-
-  case 31:
-#line 219 "jamgram.y"
-    { yymode( SCAN_STRING ); }
-    break;
-
-  case 32:
-#line 221 "jamgram.y"
-    { yymode( SCAN_NORMAL ); }
-    break;
-
-  case 33:
-#line 223 "jamgram.y"
-    { yyval.parse = psete( yyvsp[-6].string,yyvsp[-5].parse,yyvsp[-2].string,yyvsp[-7].number ); }
-    break;
-
-  case 34:
-#line 231 "jamgram.y"
-    { yyval.number = ASSIGN_SET; }
-    break;
-
-  case 35:
-#line 233 "jamgram.y"
-    { yyval.number = ASSIGN_APPEND; }
-    break;
-
-  case 36:
-#line 235 "jamgram.y"
-    { yyval.number = ASSIGN_DEFAULT; }
-    break;
-
-  case 37:
-#line 237 "jamgram.y"
-    { yyval.number = ASSIGN_DEFAULT; }
-    break;
-
-  case 38:
-#line 244 "jamgram.y"
-    { yyval.parse = peval( EXPR_EXISTS, yyvsp[0].parse, pnull() ); }
-    break;
-
-  case 39:
-#line 246 "jamgram.y"
-    { yyval.parse = peval( EXPR_EQUALS, yyvsp[-2].parse, yyvsp[0].parse ); }
-    break;
-
-  case 40:
-#line 248 "jamgram.y"
-    { yyval.parse = peval( EXPR_NOTEQ, yyvsp[-2].parse, yyvsp[0].parse ); }
-    break;
-
-  case 41:
-#line 250 "jamgram.y"
-    { yyval.parse = peval( EXPR_LESS, yyvsp[-2].parse, yyvsp[0].parse ); }
-    break;
-
-  case 42:
-#line 252 "jamgram.y"
-    { yyval.parse = peval( EXPR_LESSEQ, yyvsp[-2].parse, yyvsp[0].parse ); }
-    break;
-
-  case 43:
-#line 254 "jamgram.y"
-    { yyval.parse = peval( EXPR_MORE, yyvsp[-2].parse, yyvsp[0].parse ); }
-    break;
-
-  case 44:
-#line 256 "jamgram.y"
-    { yyval.parse = peval( EXPR_MOREEQ, yyvsp[-2].parse, yyvsp[0].parse ); }
-    break;
-
-  case 45:
-#line 258 "jamgram.y"
-    { yyval.parse = peval( EXPR_AND, yyvsp[-2].parse, yyvsp[0].parse ); }
-    break;
-
-  case 46:
-#line 260 "jamgram.y"
-    { yyval.parse = peval( EXPR_AND, yyvsp[-2].parse, yyvsp[0].parse ); }
-    break;
-
-  case 47:
-#line 262 "jamgram.y"
-    { yyval.parse = peval( EXPR_OR, yyvsp[-2].parse, yyvsp[0].parse ); }
-    break;
-
-  case 48:
-#line 264 "jamgram.y"
-    { yyval.parse = peval( EXPR_OR, yyvsp[-2].parse, yyvsp[0].parse ); }
-    break;
-
-  case 49:
-#line 266 "jamgram.y"
-    { yyval.parse = peval( EXPR_IN, yyvsp[-2].parse, yyvsp[0].parse ); }
-    break;
-
-  case 50:
-#line 268 "jamgram.y"
-    { yyval.parse = peval( EXPR_NOT, yyvsp[0].parse, pnull() ); }
-    break;
-
-  case 51:
-#line 270 "jamgram.y"
-    { yyval.parse = yyvsp[-1].parse; }
-    break;
-
-  case 52:
-#line 281 "jamgram.y"
-    { yyval.parse = P0; }
-    break;
-
-  case 53:
-#line 283 "jamgram.y"
-    { yyval.parse = pnode( yyvsp[-1].parse, yyvsp[0].parse ); }
-    break;
-
-  case 54:
-#line 287 "jamgram.y"
-    { yyval.parse = psnode( yyvsp[-2].string, yyvsp[0].parse ); }
-    break;
-
-  case 55:
-#line 296 "jamgram.y"
-    { yyval.parse = pnode( P0, yyvsp[0].parse ); }
-    break;
-
-  case 56:
-#line 298 "jamgram.y"
-    { yyval.parse = pnode( yyvsp[0].parse, yyvsp[-2].parse ); }
-    break;
-
-  case 57:
-#line 308 "jamgram.y"
-    { yyval.parse = yyvsp[0].parse; yymode( SCAN_NORMAL ); }
-    break;
-
-  case 58:
-#line 312 "jamgram.y"
-    { yyval.parse = pnull(); yymode( SCAN_PUNCT ); }
-    break;
-
-  case 59:
-#line 314 "jamgram.y"
-    { yyval.parse = pappend( yyvsp[-1].parse, yyvsp[0].parse ); }
-    break;
-
-  case 60:
-#line 318 "jamgram.y"
-    { yyval.parse = plist( yyvsp[0].string ); }
-    break;
-
-  case 61:
-#line 319 "jamgram.y"
-    { yymode( SCAN_NORMAL ); }
-    break;
-
-  case 62:
-#line 320 "jamgram.y"
-    { yyval.parse = yyvsp[-1].parse; }
-    break;
-
-  case 63:
-#line 329 "jamgram.y"
-    { yyval.parse = prule( yyvsp[-1].string, yyvsp[0].parse ); }
-    break;
-
-  case 64:
-#line 331 "jamgram.y"
-    { yyval.parse = pon( yyvsp[-2].parse, prule( yyvsp[-1].string, yyvsp[0].parse ) ); }
-    break;
-
-  case 65:
-#line 333 "jamgram.y"
-    { yyval.parse = pon( yyvsp[-2].parse, yyvsp[0].parse ); }
-    break;
-
-  case 66:
-#line 343 "jamgram.y"
-    { yyval.number = 0; }
-    break;
-
-  case 67:
-#line 345 "jamgram.y"
-    { yyval.number = yyvsp[-1].number | yyvsp[0].number; }
-    break;
-
-  case 68:
-#line 349 "jamgram.y"
-    { yyval.number = EXEC_UPDATED; }
-    break;
-
-  case 69:
-#line 351 "jamgram.y"
-    { yyval.number = EXEC_TOGETHER; }
-    break;
-
-  case 70:
-#line 353 "jamgram.y"
-    { yyval.number = EXEC_IGNORE; }
-    break;
-
-  case 71:
-#line 355 "jamgram.y"
-    { yyval.number = EXEC_QUIETLY; }
-    break;
-
-  case 72:
-#line 357 "jamgram.y"
-    { yyval.number = EXEC_PIECEMEAL; }
-    break;
-
-  case 73:
-#line 359 "jamgram.y"
-    { yyval.number = EXEC_EXISTING; }
-    break;
-
-  case 74:
-#line 368 "jamgram.y"
-    { yyval.parse = pnull(); }
-    break;
-
-  case 75:
-#line 370 "jamgram.y"
-    { yyval.parse = yyvsp[0].parse; }
-    break;
-
-
-    }
-
-/* Line 991 of yacc.c.  */
-#line 1621 "y.tab.c"
-
-  yyvsp -= yylen;
-  yyssp -= yylen;
-
-
-  YY_STACK_PRINT (yyss, yyssp);
-
-  *++yyvsp = yyval;
-
-
-  /* Now `shift' the result of the reduction.  Determine what state
-     that goes to, based on the state we popped back to and the rule
-     number reduced by.  */
-
-  yyn = yyr1[yyn];
-
-  yystate = yypgoto[yyn - YYNTOKENS] + *yyssp;
-  if (0 <= yystate && yystate <= YYLAST && yycheck[yystate] == *yyssp)
-    yystate = yytable[yystate];
-  else
-    yystate = yydefgoto[yyn - YYNTOKENS];
-
-  goto yynewstate;
-
-
-/*------------------------------------.
-| yyerrlab -- here on detecting error |
-`------------------------------------*/
-yyerrlab:
-  /* If not already recovering from an error, report this error.  */
-  if (!yyerrstatus)
-    {
-      ++yynerrs;
-#if YYERROR_VERBOSE
-      yyn = yypact[yystate];
-
-      if (YYPACT_NINF < yyn && yyn < YYLAST)
-	{
-	  YYSIZE_T yysize = 0;
-	  int yytype = YYTRANSLATE (yychar);
-	  char *yymsg;
-	  int yyx, yycount;
-
-	  yycount = 0;
-	  /* Start YYX at -YYN if negative to avoid negative indexes in
-	     YYCHECK.  */
-	  for (yyx = yyn < 0 ? -yyn : 0;
-	       yyx < (int) (sizeof (yytname) / sizeof (char *)); yyx++)
-	    if (yycheck[yyx + yyn] == yyx && yyx != YYTERROR)
-	      yysize += yystrlen (yytname[yyx]) + 15, yycount++;
-	  yysize += yystrlen ("syntax error, unexpected ") + 1;
-	  yysize += yystrlen (yytname[yytype]);
-	  yymsg = (char *) YYSTACK_ALLOC (yysize);
-	  if (yymsg != 0)
-	    {
-	      char *yyp = yystpcpy (yymsg, "syntax error, unexpected ");
-	      yyp = yystpcpy (yyp, yytname[yytype]);
-
-	      if (yycount < 5)
-		{
-		  yycount = 0;
-		  for (yyx = yyn < 0 ? -yyn : 0;
-		       yyx < (int) (sizeof (yytname) / sizeof (char *));
-		       yyx++)
-		    if (yycheck[yyx + yyn] == yyx && yyx != YYTERROR)
-		      {
-			const char *yyq = ! yycount ? ", expecting " : " or ";
-			yyp = yystpcpy (yyp, yyq);
-			yyp = yystpcpy (yyp, yytname[yyx]);
-			yycount++;
-		      }
-		}
-	      yyerror (yymsg);
-	      YYSTACK_FREE (yymsg);
-	    }
-	  else
-	    yyerror ("syntax error; also virtual memory exhausted");
-	}
-      else
-#endif /* YYERROR_VERBOSE */
-	yyerror ("syntax error");
-    }
-
-
-
-  if (yyerrstatus == 3)
-    {
-      /* If just tried and failed to reuse lookahead token after an
-	 error, discard it.  */
-
-      /* Return failure if at end of input.  */
-      if (yychar == YYEOF)
-        {
-	  /* Pop the error token.  */
-          YYPOPSTACK;
-	  /* Pop the rest of the stack.  */
-	  while (yyss < yyssp)
-	    {
-	      YYDSYMPRINTF ("Error: popping", yystos[*yyssp], yyvsp, yylsp);
-	      yydestruct (yystos[*yyssp], yyvsp);
-	      YYPOPSTACK;
-	    }
-	  YYABORT;
-        }
-
-      YYDSYMPRINTF ("Error: discarding", yytoken, &yylval, &yylloc);
-      yydestruct (yytoken, &yylval);
-      yychar = YYEMPTY;
-
-    }
-
-  /* Else will try to reuse lookahead token after shifting the error
-     token.  */
-  goto yyerrlab2;
-
-
-/*----------------------------------------------------.
-| yyerrlab1 -- error raised explicitly by an action.  |
-`----------------------------------------------------*/
-yyerrlab1:
-
-  /* Suppress GCC warning that yyerrlab1 is unused when no action
-     invokes YYERROR.  */
-#if defined (__GNUC_MINOR__) && 2093 <= (__GNUC__ * 1000 + __GNUC_MINOR__)
-  __attribute__ ((__unused__))
-#endif
-
-
-  goto yyerrlab2;
-
-
-/*---------------------------------------------------------------.
-| yyerrlab2 -- pop states until the error token can be shifted.  |
-`---------------------------------------------------------------*/
-yyerrlab2:
-  yyerrstatus = 3;	/* Each real token shifted decrements this.  */
-
-  for (;;)
-    {
-      yyn = yypact[yystate];
-      if (yyn != YYPACT_NINF)
-	{
-	  yyn += YYTERROR;
-	  if (0 <= yyn && yyn <= YYLAST && yycheck[yyn] == YYTERROR)
-	    {
-	      yyn = yytable[yyn];
-	      if (0 < yyn)
-		break;
-	    }
-	}
-
-      /* Pop the current state because it cannot handle the error token.  */
-      if (yyssp == yyss)
-	YYABORT;
-
-      YYDSYMPRINTF ("Error: popping", yystos[*yyssp], yyvsp, yylsp);
-      yydestruct (yystos[yystate], yyvsp);
-      yyvsp--;
-      yystate = *--yyssp;
-
-      YY_STACK_PRINT (yyss, yyssp);
-    }
-
-  if (yyn == YYFINAL)
-    YYACCEPT;
-
-  YYDPRINTF ((stderr, "Shifting error token, "));
-
-  *++yyvsp = yylval;
-
-
-  yystate = yyn;
-  goto yynewstate;
-
-
-/*-------------------------------------.
-| yyacceptlab -- YYACCEPT comes here.  |
-`-------------------------------------*/
-yyacceptlab:
-  yyresult = 0;
-  goto yyreturn;
-
-/*-----------------------------------.
-| yyabortlab -- YYABORT comes here.  |
-`-----------------------------------*/
-yyabortlab:
-  yyresult = 1;
-  goto yyreturn;
-
-#ifndef yyoverflow
-/*----------------------------------------------.
-| yyoverflowlab -- parser overflow comes here.  |
-`----------------------------------------------*/
-yyoverflowlab:
-  yyerror ("parser stack overflow");
-  yyresult = 2;
-  /* Fall through.  */
-#endif
-
-yyreturn:
-#ifndef yyoverflow
-  if (yyss != yyssa)
-    YYSTACK_FREE (yyss);
-#endif
-  return yyresult;
-}
-
-
-
diff --git a/jam-files/engine/jamgram.h b/jam-files/engine/jamgram.h
deleted file mode 100644
index 3cb76564..00000000
--- a/jam-files/engine/jamgram.h
+++ /dev/null
@@ -1,140 +0,0 @@
-/* A Bison parser, made by GNU Bison 1.875.  */
-
-/* Skeleton parser for Yacc-like parsing with Bison,
-   Copyright (C) 1984, 1989, 1990, 2000, 2001, 2002 Free Software Foundation, Inc.
-
-   This program is free software; you can redistribute it and/or modify
-   it under the terms of the GNU General Public License as published by
-   the Free Software Foundation; either version 2, or (at your option)
-   any later version.
-
-   This program is distributed in the hope that it will be useful,
-   but WITHOUT ANY WARRANTY; without even the implied warranty of
-   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-   GNU General Public License for more details.
-
-   You should have received a copy of the GNU General Public License
-   along with this program; if not, write to the Free Software
-   Foundation, Inc., 59 Temple Place - Suite 330,
-   Boston, MA 02111-1307, USA.  */
-
-/* As a special exception, when this file is copied by Bison into a
-   Bison output file, you may use that output file without restriction.
-   This special exception was added by the Free Software Foundation
-   in version 1.24 of Bison.  */
-
-/* Tokens.  */
-#ifndef YYTOKENTYPE
-# define YYTOKENTYPE
-   /* Put the tokens into the symbol table, so that GDB and other debuggers
-      know about them.  */
-   enum yytokentype {
-     _BANG_t = 258,
-     _BANG_EQUALS_t = 259,
-     _AMPER_t = 260,
-     _AMPERAMPER_t = 261,
-     _LPAREN_t = 262,
-     _RPAREN_t = 263,
-     _PLUS_EQUALS_t = 264,
-     _COLON_t = 265,
-     _SEMIC_t = 266,
-     _LANGLE_t = 267,
-     _LANGLE_EQUALS_t = 268,
-     _EQUALS_t = 269,
-     _RANGLE_t = 270,
-     _RANGLE_EQUALS_t = 271,
-     _QUESTION_EQUALS_t = 272,
-     _LBRACKET_t = 273,
-     _RBRACKET_t = 274,
-     ACTIONS_t = 275,
-     BIND_t = 276,
-     CASE_t = 277,
-     CLASS_t = 278,
-     DEFAULT_t = 279,
-     ELSE_t = 280,
-     EXISTING_t = 281,
-     FOR_t = 282,
-     IF_t = 283,
-     IGNORE_t = 284,
-     IN_t = 285,
-     INCLUDE_t = 286,
-     LOCAL_t = 287,
-     MODULE_t = 288,
-     ON_t = 289,
-     PIECEMEAL_t = 290,
-     QUIETLY_t = 291,
-     RETURN_t = 292,
-     RULE_t = 293,
-     SWITCH_t = 294,
-     TOGETHER_t = 295,
-     UPDATED_t = 296,
-     WHILE_t = 297,
-     _LBRACE_t = 298,
-     _BAR_t = 299,
-     _BARBAR_t = 300,
-     _RBRACE_t = 301,
-     ARG = 302,
-     STRING = 303
-   };
-#endif
-#define _BANG_t 258
-#define _BANG_EQUALS_t 259
-#define _AMPER_t 260
-#define _AMPERAMPER_t 261
-#define _LPAREN_t 262
-#define _RPAREN_t 263
-#define _PLUS_EQUALS_t 264
-#define _COLON_t 265
-#define _SEMIC_t 266
-#define _LANGLE_t 267
-#define _LANGLE_EQUALS_t 268
-#define _EQUALS_t 269
-#define _RANGLE_t 270
-#define _RANGLE_EQUALS_t 271
-#define _QUESTION_EQUALS_t 272
-#define _LBRACKET_t 273
-#define _RBRACKET_t 274
-#define ACTIONS_t 275
-#define BIND_t 276
-#define CASE_t 277
-#define CLASS_t 278
-#define DEFAULT_t 279
-#define ELSE_t 280
-#define EXISTING_t 281
-#define FOR_t 282
-#define IF_t 283
-#define IGNORE_t 284
-#define IN_t 285
-#define INCLUDE_t 286
-#define LOCAL_t 287
-#define MODULE_t 288
-#define ON_t 289
-#define PIECEMEAL_t 290
-#define QUIETLY_t 291
-#define RETURN_t 292
-#define RULE_t 293
-#define SWITCH_t 294
-#define TOGETHER_t 295
-#define UPDATED_t 296
-#define WHILE_t 297
-#define _LBRACE_t 298
-#define _BAR_t 299
-#define _BARBAR_t 300
-#define _RBRACE_t 301
-#define ARG 302
-#define STRING 303
-
-
-
-
-#if ! defined (YYSTYPE) && ! defined (YYSTYPE_IS_DECLARED)
-typedef int YYSTYPE;
-# define yystype YYSTYPE /* obsolescent; will be withdrawn */
-# define YYSTYPE_IS_DECLARED 1
-# define YYSTYPE_IS_TRIVIAL 1
-#endif
-
-extern YYSTYPE yylval;
-
-
-
diff --git a/jam-files/engine/jamgram.y b/jam-files/engine/jamgram.y
deleted file mode 100644
index c26b1e1b..00000000
--- a/jam-files/engine/jamgram.y
+++ /dev/null
@@ -1,371 +0,0 @@
-%token _BANG_t
-%token _BANG_EQUALS_t
-%token _AMPER_t
-%token _AMPERAMPER_t
-%token _LPAREN_t
-%token _RPAREN_t
-%token _PLUS_EQUALS_t
-%token _COLON_t
-%token _SEMIC_t
-%token _LANGLE_t
-%token _LANGLE_EQUALS_t
-%token _EQUALS_t
-%token _RANGLE_t
-%token _RANGLE_EQUALS_t
-%token _QUESTION_EQUALS_t
-%token _LBRACKET_t
-%token _RBRACKET_t
-%token ACTIONS_t
-%token BIND_t
-%token CASE_t
-%token CLASS_t
-%token DEFAULT_t
-%token ELSE_t
-%token EXISTING_t
-%token FOR_t
-%token IF_t
-%token IGNORE_t
-%token IN_t
-%token INCLUDE_t
-%token LOCAL_t
-%token MODULE_t
-%token ON_t
-%token PIECEMEAL_t
-%token QUIETLY_t
-%token RETURN_t
-%token RULE_t
-%token SWITCH_t
-%token TOGETHER_t
-%token UPDATED_t
-%token WHILE_t
-%token _LBRACE_t
-%token _BAR_t
-%token _BARBAR_t
-%token _RBRACE_t
-/*
- * Copyright 1993, 2000 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*  This file is ALSO:
- *  Copyright 2001-2004 David Abrahams.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-
-/*
- * jamgram.yy - jam grammar
- *
- * 04/13/94 (seiwald) - added shorthand L0 for null list pointer
- * 06/01/94 (seiwald) - new 'actions existing' does existing sources
- * 08/23/94 (seiwald) - Support for '+=' (append to variable)
- * 08/31/94 (seiwald) - Allow ?= as alias for "default =".
- * 09/15/94 (seiwald) - if conditionals take only single arguments, so
- *			that 'if foo == bar' gives syntax error (use =).
- * 02/11/95 (seiwald) - when scanning arguments to rules, only treat
- *			punctuation keywords as keywords.  All arg lists
- *			are terminated with punctuation keywords.
- *
- * 09/11/00 (seiwald) - Support for function calls:
- *
- *		Rules now return lists (LIST *), rather than void.
- *
- *		New "[ rule ]" syntax evals rule into a LIST.
- *
- *		Lists are now generated by compile_list() and
- *		compile_append(), and any other rule that indirectly
- *		makes a list, rather than being built directly here,
- *		so that lists values can contain rule evaluations.
- *
- *		New 'return' rule sets the return value, though
- *		other statements also may have return values.
- *
- *		'run' production split from 'block' production so
- *		that empty blocks can be handled separately.
- */
-
-%token ARG STRING
-
-%left _BARBAR_t _BAR_t
-%left _AMPERAMPER_t _AMPER_t
-%left _EQUALS_t _BANG_EQUALS_t IN_t
-%left _LANGLE_t _LANGLE_EQUALS_t _RANGLE_t _RANGLE_EQUALS_t
-%left _BANG_t
-
-%{
-#include "jam.h"
-
-#include "lists.h"
-#include "parse.h"
-#include "scan.h"
-#include "compile.h"
-#include "newstr.h"
-#include "rules.h"
-
-# define YYMAXDEPTH 10000	/* for OSF and other less endowed yaccs */
-
-# define F0 (LIST *(*)(PARSE *, FRAME *))0
-# define P0 (PARSE *)0
-# define S0 (char *)0
-
-# define pappend( l,r )    	parse_make( compile_append,l,r,P0,S0,S0,0 )
-# define peval( c,l,r )	parse_make( compile_eval,l,r,P0,S0,S0,c )
-# define pfor( s,l,r,x )    	parse_make( compile_foreach,l,r,P0,s,S0,x )
-# define pif( l,r,t )	  	parse_make( compile_if,l,r,t,S0,S0,0 )
-# define pincl( l )       	parse_make( compile_include,l,P0,P0,S0,S0,0 )
-# define plist( s )	  	parse_make( compile_list,P0,P0,P0,s,S0,0 )
-# define plocal( l,r,t )  	parse_make( compile_local,l,r,t,S0,S0,0 )
-# define pmodule( l,r )	  	parse_make( compile_module,l,r,P0,S0,S0,0 )
-# define pclass( l,r )	  	parse_make( compile_class,l,r,P0,S0,S0,0 )
-# define pnull()	  	parse_make( compile_null,P0,P0,P0,S0,S0,0 )
-# define pon( l,r )	  	parse_make( compile_on,l,r,P0,S0,S0,0 )
-# define prule( s,p )     	parse_make( compile_rule,p,P0,P0,s,S0,0 )
-# define prules( l,r )	  	parse_make( compile_rules,l,r,P0,S0,S0,0 )
-# define pset( l,r,a )          parse_make( compile_set,l,r,P0,S0,S0,a )
-# define pset1( l,r,t,a )	parse_make( compile_settings,l,r,t,S0,S0,a )
-# define psetc( s,p,a,l )     	parse_make( compile_setcomp,p,a,P0,s,S0,l )
-# define psete( s,l,s1,f ) 	parse_make( compile_setexec,l,P0,P0,s,s1,f )
-# define pswitch( l,r )   	parse_make( compile_switch,l,r,P0,S0,S0,0 )
-# define pwhile( l,r )   	parse_make( compile_while,l,r,P0,S0,S0,0 )
-
-# define pnode( l,r )    	parse_make( F0,l,r,P0,S0,S0,0 )
-# define psnode( s,l )     	parse_make( F0,l,P0,P0,s,S0,0 )
-
-%}
-
-%%
-
-run	: /* empty */
-		/* do nothing */
-	| rules
-		{ parse_save( $1.parse ); }
-	;
-
-/*
- * block - zero or more rules
- * rules - one or more rules
- * rule - any one of jam's rules
- * right-recursive so rules execute in order.
- */
-
-block	: null
-                { $$.parse = $1.parse; }
-	| rules
-		{ $$.parse = $1.parse; }
-	;
-
-rules	: rule
-		{ $$.parse = $1.parse; }
-	| rule rules
-		{ $$.parse = prules( $1.parse, $2.parse ); }
-	| LOCAL_t list assign_list_opt _SEMIC_t block
-		{ $$.parse = plocal( $2.parse, $3.parse, $5.parse ); }
-	;
-
-null    : /* empty */
-        { $$.parse = pnull(); }
-        ;
-
-assign_list_opt : _EQUALS_t list
-                { $$.parse = $2.parse; $$.number = ASSIGN_SET; }
-        | null
-		{ $$.parse = $1.parse; $$.number = ASSIGN_APPEND; }
-        ;
-
-arglist_opt : _LPAREN_t lol _RPAREN_t
-                { $$.parse = $2.parse; }
-        |
-                { $$.parse = P0; }
-        ;
-
-local_opt : LOCAL_t
-                { $$.number = 1; }
-          | /* empty */
-                { $$.number = 0; }
-          ;
-
-rule	: _LBRACE_t block _RBRACE_t
-		{ $$.parse = $2.parse; }
-	| INCLUDE_t list _SEMIC_t
-		{ $$.parse = pincl( $2.parse ); }
-	| ARG lol _SEMIC_t
-		{ $$.parse = prule( $1.string, $2.parse ); }
-	| arg assign list _SEMIC_t
-		{ $$.parse = pset( $1.parse, $3.parse, $2.number ); }
-	| arg ON_t list assign list _SEMIC_t
-		{ $$.parse = pset1( $1.parse, $3.parse, $5.parse, $4.number ); }
-	| RETURN_t list _SEMIC_t
-		{ $$.parse = $2.parse; }
-	| FOR_t local_opt ARG IN_t list _LBRACE_t block _RBRACE_t
-		{ $$.parse = pfor( $3.string, $5.parse, $7.parse, $2.number ); }
-	| SWITCH_t list _LBRACE_t cases _RBRACE_t
-		{ $$.parse = pswitch( $2.parse, $4.parse ); }
-	| IF_t expr _LBRACE_t block _RBRACE_t
-		{ $$.parse = pif( $2.parse, $4.parse, pnull() ); }
-	| MODULE_t list _LBRACE_t block _RBRACE_t
-		{ $$.parse = pmodule( $2.parse, $4.parse ); }
-	| CLASS_t lol _LBRACE_t block _RBRACE_t
-		{ $$.parse = pclass( $2.parse, $4.parse ); }
-	| WHILE_t expr _LBRACE_t block _RBRACE_t
-		{ $$.parse = pwhile( $2.parse, $4.parse ); }
-	| IF_t expr _LBRACE_t block _RBRACE_t ELSE_t rule
-		{ $$.parse = pif( $2.parse, $4.parse, $7.parse ); }
-     | local_opt RULE_t ARG arglist_opt rule
-		{ $$.parse = psetc( $3.string, $5.parse, $4.parse, $1.number ); }
-	| ON_t arg rule
-		{ $$.parse = pon( $2.parse, $3.parse ); }
-	| ACTIONS_t eflags ARG bindlist _LBRACE_t
-		{ yymode( SCAN_STRING ); }
-	  STRING
-		{ yymode( SCAN_NORMAL ); }
-	  _RBRACE_t
-		{ $$.parse = psete( $3.string,$4.parse,$7.string,$2.number ); }
-	;
-
-/*
- * assign - = or +=
- */
-
-assign	: _EQUALS_t
-		{ $$.number = ASSIGN_SET; }
-	| _PLUS_EQUALS_t
-		{ $$.number = ASSIGN_APPEND; }
-	| _QUESTION_EQUALS_t
-		{ $$.number = ASSIGN_DEFAULT; }
-	| DEFAULT_t _EQUALS_t
-		{ $$.number = ASSIGN_DEFAULT; }
-	;
-
-/*
- * expr - an expression for if
- */
-expr	: arg
-		{ $$.parse = peval( EXPR_EXISTS, $1.parse, pnull() ); }
-	| expr _EQUALS_t expr
-		{ $$.parse = peval( EXPR_EQUALS, $1.parse, $3.parse ); }
-	| expr _BANG_EQUALS_t expr
-		{ $$.parse = peval( EXPR_NOTEQ, $1.parse, $3.parse ); }
-	| expr _LANGLE_t expr
-		{ $$.parse = peval( EXPR_LESS, $1.parse, $3.parse ); }
-	| expr _LANGLE_EQUALS_t expr
-		{ $$.parse = peval( EXPR_LESSEQ, $1.parse, $3.parse ); }
-	| expr _RANGLE_t expr
-		{ $$.parse = peval( EXPR_MORE, $1.parse, $3.parse ); }
-	| expr _RANGLE_EQUALS_t expr
-		{ $$.parse = peval( EXPR_MOREEQ, $1.parse, $3.parse ); }
-	| expr _AMPER_t expr
-		{ $$.parse = peval( EXPR_AND, $1.parse, $3.parse ); }
-	| expr _AMPERAMPER_t expr
-		{ $$.parse = peval( EXPR_AND, $1.parse, $3.parse ); }
-	| expr _BAR_t expr
-		{ $$.parse = peval( EXPR_OR, $1.parse, $3.parse ); }
-	| expr _BARBAR_t expr
-		{ $$.parse = peval( EXPR_OR, $1.parse, $3.parse ); }
-	| arg IN_t list
-		{ $$.parse = peval( EXPR_IN, $1.parse, $3.parse ); }
-	| _BANG_t expr
-		{ $$.parse = peval( EXPR_NOT, $2.parse, pnull() ); }
-	| _LPAREN_t expr _RPAREN_t
-		{ $$.parse = $2.parse; }
-	;
-
-
-/*
- * cases - action elements inside a 'switch'
- * case - a single action element inside a 'switch'
- * right-recursive rule so cases can be examined in order.
- */
-
-cases	: /* empty */
-		{ $$.parse = P0; }
-	| case cases
-		{ $$.parse = pnode( $1.parse, $2.parse ); }
-	;
-
-case	: CASE_t ARG _COLON_t block
-		{ $$.parse = psnode( $2.string, $4.parse ); }
-	;
-
-/*
- * lol - list of lists
- * right-recursive rule so that lists can be added in order.
- */
-
-lol	: list
-		{ $$.parse = pnode( P0, $1.parse ); }
-	| list _COLON_t lol
-		{ $$.parse = pnode( $3.parse, $1.parse ); }
-	;
-
-/*
- * list - zero or more args in a LIST
- * listp - list (in puncutation only mode)
- * arg - one ARG or function call
- */
-
-list	: listp
-		{ $$.parse = $1.parse; yymode( SCAN_NORMAL ); }
-	;
-
-listp	: /* empty */
-		{ $$.parse = pnull(); yymode( SCAN_PUNCT ); }
-	| listp arg
-        	{ $$.parse = pappend( $1.parse, $2.parse ); }
-	;
-
-arg	: ARG
-		{ $$.parse = plist( $1.string ); }
-	| _LBRACKET_t { yymode( SCAN_NORMAL ); } func _RBRACKET_t
-		{ $$.parse = $3.parse; }
-	;
-
-/*
- * func - a function call (inside [])
- * This needs to be split cleanly out of 'rule'
- */
-
-func	: arg lol
-		{ $$.parse = prule( $1.string, $2.parse ); }
-	| ON_t arg arg lol
-		{ $$.parse = pon( $2.parse, prule( $3.string, $4.parse ) ); }
-	| ON_t arg RETURN_t list
-		{ $$.parse = pon( $2.parse, $4.parse ); }
-	;
-
-
-/*
- * eflags - zero or more modifiers to 'executes'
- * eflag - a single modifier to 'executes'
- */
-
-eflags	: /* empty */
-		{ $$.number = 0; }
-	| eflags eflag
-		{ $$.number = $1.number | $2.number; }
-	;
-
-eflag	: UPDATED_t
-		{ $$.number = EXEC_UPDATED; }
-	| TOGETHER_t
-		{ $$.number = EXEC_TOGETHER; }
-	| IGNORE_t
-		{ $$.number = EXEC_IGNORE; }
-	| QUIETLY_t
-		{ $$.number = EXEC_QUIETLY; }
-	| PIECEMEAL_t
-		{ $$.number = EXEC_PIECEMEAL; }
-	| EXISTING_t
-		{ $$.number = EXEC_EXISTING; }
-	;
-
-
-/*
- * bindlist - list of variable to bind for an action
- */
-
-bindlist : /* empty */
-		{ $$.parse = pnull(); }
-	| BIND_t list
-		{ $$.parse = $2.parse; }
-	;
diff --git a/jam-files/engine/jamgram.yy b/jam-files/engine/jamgram.yy
deleted file mode 100644
index 15243487..00000000
--- a/jam-files/engine/jamgram.yy
+++ /dev/null
@@ -1,329 +0,0 @@
-/*
- * Copyright 1993, 2000 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*  This file is ALSO:
- *  Copyright 2001-2004 David Abrahams.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-
-/*
- * jamgram.yy - jam grammar
- *
- * 04/13/94 (seiwald) - added shorthand L0 for null list pointer
- * 06/01/94 (seiwald) - new 'actions existing' does existing sources
- * 08/23/94 (seiwald) - Support for '+=' (append to variable)
- * 08/31/94 (seiwald) - Allow ?= as alias for "default =".
- * 09/15/94 (seiwald) - if conditionals take only single arguments, so
- *			that 'if foo == bar' gives syntax error (use =).
- * 02/11/95 (seiwald) - when scanning arguments to rules, only treat
- *			punctuation keywords as keywords.  All arg lists
- *			are terminated with punctuation keywords.
- *
- * 09/11/00 (seiwald) - Support for function calls:
- *
- *		Rules now return lists (LIST *), rather than void.
- *
- *		New "[ rule ]" syntax evals rule into a LIST.
- *
- *		Lists are now generated by compile_list() and
- *		compile_append(), and any other rule that indirectly
- *		makes a list, rather than being built directly here,
- *		so that lists values can contain rule evaluations.
- *
- *		New 'return' rule sets the return value, though
- *		other statements also may have return values.
- *
- *		'run' production split from 'block' production so
- *		that empty blocks can be handled separately.
- */
-
-%token ARG STRING
-
-%left `||` `|`
-%left `&&` `&`
-%left `=` `!=` `in`
-%left `<` `<=` `>` `>=`
-%left `!`
-
-%{
-#include "jam.h"
-
-#include "lists.h"
-#include "parse.h"
-#include "scan.h"
-#include "compile.h"
-#include "newstr.h"
-#include "rules.h"
-
-# define YYMAXDEPTH 10000	/* for OSF and other less endowed yaccs */
-
-# define F0 (LIST *(*)(PARSE *, FRAME *))0
-# define P0 (PARSE *)0
-# define S0 (char *)0
-
-# define pappend( l,r )    	parse_make( compile_append,l,r,P0,S0,S0,0 )
-# define peval( c,l,r )	parse_make( compile_eval,l,r,P0,S0,S0,c )
-# define pfor( s,l,r,x )    	parse_make( compile_foreach,l,r,P0,s,S0,x )
-# define pif( l,r,t )	  	parse_make( compile_if,l,r,t,S0,S0,0 )
-# define pincl( l )       	parse_make( compile_include,l,P0,P0,S0,S0,0 )
-# define plist( s )	  	parse_make( compile_list,P0,P0,P0,s,S0,0 )
-# define plocal( l,r,t )  	parse_make( compile_local,l,r,t,S0,S0,0 )
-# define pmodule( l,r )	  	parse_make( compile_module,l,r,P0,S0,S0,0 )
-# define pclass( l,r )	  	parse_make( compile_class,l,r,P0,S0,S0,0 )
-# define pnull()	  	parse_make( compile_null,P0,P0,P0,S0,S0,0 )
-# define pon( l,r )	  	parse_make( compile_on,l,r,P0,S0,S0,0 )
-# define prule( s,p )     	parse_make( compile_rule,p,P0,P0,s,S0,0 )
-# define prules( l,r )	  	parse_make( compile_rules,l,r,P0,S0,S0,0 )
-# define pset( l,r,a )          parse_make( compile_set,l,r,P0,S0,S0,a )
-# define pset1( l,r,t,a )	parse_make( compile_settings,l,r,t,S0,S0,a )
-# define psetc( s,p,a,l )     	parse_make( compile_setcomp,p,a,P0,s,S0,l )
-# define psete( s,l,s1,f ) 	parse_make( compile_setexec,l,P0,P0,s,s1,f )
-# define pswitch( l,r )   	parse_make( compile_switch,l,r,P0,S0,S0,0 )
-# define pwhile( l,r )   	parse_make( compile_while,l,r,P0,S0,S0,0 )
-
-# define pnode( l,r )    	parse_make( F0,l,r,P0,S0,S0,0 )
-# define psnode( s,l )     	parse_make( F0,l,P0,P0,s,S0,0 )
-
-%}
-
-%%
-
-run	: /* empty */
-		/* do nothing */
-	| rules
-		{ parse_save( $1.parse ); }
-	;
-
-/*
- * block - zero or more rules
- * rules - one or more rules
- * rule - any one of jam's rules
- * right-recursive so rules execute in order.
- */
-
-block	: null
-                { $$.parse = $1.parse; }
-	| rules
-		{ $$.parse = $1.parse; }
-	;
-
-rules	: rule
-		{ $$.parse = $1.parse; }
-	| rule rules
-		{ $$.parse = prules( $1.parse, $2.parse ); }
-	| `local` list assign_list_opt `;` block
-		{ $$.parse = plocal( $2.parse, $3.parse, $5.parse ); }
-	;
-
-null    : /* empty */
-        { $$.parse = pnull(); }
-        ;
-
-assign_list_opt : `=` list
-                { $$.parse = $2.parse; $$.number = ASSIGN_SET; }
-        | null
-		{ $$.parse = $1.parse; $$.number = ASSIGN_APPEND; }
-        ;
-
-arglist_opt : `(` lol `)`
-                { $$.parse = $2.parse; }
-        |
-                { $$.parse = P0; }
-        ;
-
-local_opt : `local`
-                { $$.number = 1; }
-          | /* empty */
-                { $$.number = 0; }
-          ;
-
-rule	: `{` block `}`
-		{ $$.parse = $2.parse; }
-	| `include` list `;`
-		{ $$.parse = pincl( $2.parse ); }
-	| ARG lol `;`
-		{ $$.parse = prule( $1.string, $2.parse ); }
-	| arg assign list `;`
-		{ $$.parse = pset( $1.parse, $3.parse, $2.number ); }
-	| arg `on` list assign list `;`
-		{ $$.parse = pset1( $1.parse, $3.parse, $5.parse, $4.number ); }
-	| `return` list `;`
-		{ $$.parse = $2.parse; }
-	| `for` local_opt ARG `in` list `{` block `}`
-		{ $$.parse = pfor( $3.string, $5.parse, $7.parse, $2.number ); }
-	| `switch` list `{` cases `}`
-		{ $$.parse = pswitch( $2.parse, $4.parse ); }
-	| `if` expr `{` block `}`
-		{ $$.parse = pif( $2.parse, $4.parse, pnull() ); }
-	| `module` list `{` block `}`
-		{ $$.parse = pmodule( $2.parse, $4.parse ); }
-	| `class` lol `{` block `}`
-		{ $$.parse = pclass( $2.parse, $4.parse ); }
-	| `while` expr `{` block `}`
-		{ $$.parse = pwhile( $2.parse, $4.parse ); }
-	| `if` expr `{` block `}` `else` rule
-		{ $$.parse = pif( $2.parse, $4.parse, $7.parse ); }
-     | local_opt `rule` ARG arglist_opt rule
-		{ $$.parse = psetc( $3.string, $5.parse, $4.parse, $1.number ); }
-	| `on` arg rule
-		{ $$.parse = pon( $2.parse, $3.parse ); }
-	| `actions` eflags ARG bindlist `{`
-		{ yymode( SCAN_STRING ); }
-	  STRING
-		{ yymode( SCAN_NORMAL ); }
-	  `}`
-		{ $$.parse = psete( $3.string,$4.parse,$7.string,$2.number ); }
-	;
-
-/*
- * assign - = or +=
- */
-
-assign	: `=`
-		{ $$.number = ASSIGN_SET; }
-	| `+=`
-		{ $$.number = ASSIGN_APPEND; }
-	| `?=`
-		{ $$.number = ASSIGN_DEFAULT; }
-	| `default` `=`
-		{ $$.number = ASSIGN_DEFAULT; }
-	;
-
-/*
- * expr - an expression for if
- */
-expr	: arg
-		{ $$.parse = peval( EXPR_EXISTS, $1.parse, pnull() ); }
-	| expr `=` expr
-		{ $$.parse = peval( EXPR_EQUALS, $1.parse, $3.parse ); }
-	| expr `!=` expr
-		{ $$.parse = peval( EXPR_NOTEQ, $1.parse, $3.parse ); }
-	| expr `<` expr
-		{ $$.parse = peval( EXPR_LESS, $1.parse, $3.parse ); }
-	| expr `<=` expr
-		{ $$.parse = peval( EXPR_LESSEQ, $1.parse, $3.parse ); }
-	| expr `>` expr
-		{ $$.parse = peval( EXPR_MORE, $1.parse, $3.parse ); }
-	| expr `>=` expr
-		{ $$.parse = peval( EXPR_MOREEQ, $1.parse, $3.parse ); }
-	| expr `&` expr
-		{ $$.parse = peval( EXPR_AND, $1.parse, $3.parse ); }
-	| expr `&&` expr
-		{ $$.parse = peval( EXPR_AND, $1.parse, $3.parse ); }
-	| expr `|` expr
-		{ $$.parse = peval( EXPR_OR, $1.parse, $3.parse ); }
-	| expr `||` expr
-		{ $$.parse = peval( EXPR_OR, $1.parse, $3.parse ); }
-	| arg `in` list
-		{ $$.parse = peval( EXPR_IN, $1.parse, $3.parse ); }
-	| `!` expr
-		{ $$.parse = peval( EXPR_NOT, $2.parse, pnull() ); }
-	| `(` expr `)`
-		{ $$.parse = $2.parse; }
-	;
-
-
-/*
- * cases - action elements inside a 'switch'
- * case - a single action element inside a 'switch'
- * right-recursive rule so cases can be examined in order.
- */
-
-cases	: /* empty */
-		{ $$.parse = P0; }
-	| case cases
-		{ $$.parse = pnode( $1.parse, $2.parse ); }
-	;
-
-case	: `case` ARG `:` block
-		{ $$.parse = psnode( $2.string, $4.parse ); }
-	;
-
-/*
- * lol - list of lists
- * right-recursive rule so that lists can be added in order.
- */
-
-lol	: list
-		{ $$.parse = pnode( P0, $1.parse ); }
-	| list `:` lol
-		{ $$.parse = pnode( $3.parse, $1.parse ); }
-	;
-
-/*
- * list - zero or more args in a LIST
- * listp - list (in puncutation only mode)
- * arg - one ARG or function call
- */
-
-list	: listp
-		{ $$.parse = $1.parse; yymode( SCAN_NORMAL ); }
-	;
-
-listp	: /* empty */
-		{ $$.parse = pnull(); yymode( SCAN_PUNCT ); }
-	| listp arg
-        	{ $$.parse = pappend( $1.parse, $2.parse ); }
-	;
-
-arg	: ARG
-		{ $$.parse = plist( $1.string ); }
-	| `[` { yymode( SCAN_NORMAL ); } func `]`
-		{ $$.parse = $3.parse; }
-	;
-
-/*
- * func - a function call (inside [])
- * This needs to be split cleanly out of 'rule'
- */
-
-func	: arg lol
-		{ $$.parse = prule( $1.string, $2.parse ); }
-	| `on` arg arg lol
-		{ $$.parse = pon( $2.parse, prule( $3.string, $4.parse ) ); }
-	| `on` arg `return` list
-		{ $$.parse = pon( $2.parse, $4.parse ); }
-	;
-
-
-/*
- * eflags - zero or more modifiers to 'executes'
- * eflag - a single modifier to 'executes'
- */
-
-eflags	: /* empty */
-		{ $$.number = 0; }
-	| eflags eflag
-		{ $$.number = $1.number | $2.number; }
-	;
-
-eflag	: `updated`
-		{ $$.number = EXEC_UPDATED; }
-	| `together`
-		{ $$.number = EXEC_TOGETHER; }
-	| `ignore`
-		{ $$.number = EXEC_IGNORE; }
-	| `quietly`
-		{ $$.number = EXEC_QUIETLY; }
-	| `piecemeal`
-		{ $$.number = EXEC_PIECEMEAL; }
-	| `existing`
-		{ $$.number = EXEC_EXISTING; }
-	;
-
-
-/*
- * bindlist - list of variable to bind for an action
- */
-
-bindlist : /* empty */
-		{ $$.parse = pnull(); }
-	| `bind` list
-		{ $$.parse = $2.parse; }
-	;
-
-
diff --git a/jam-files/engine/jamgramtab.h b/jam-files/engine/jamgramtab.h
deleted file mode 100644
index a0fd43f6..00000000
--- a/jam-files/engine/jamgramtab.h
+++ /dev/null
@@ -1,44 +0,0 @@
-    { "!", _BANG_t },
-    { "!=", _BANG_EQUALS_t },
-    { "&", _AMPER_t },
-    { "&&", _AMPERAMPER_t },
-    { "(", _LPAREN_t },
-    { ")", _RPAREN_t },
-    { "+=", _PLUS_EQUALS_t },
-    { ":", _COLON_t },
-    { ";", _SEMIC_t },
-    { "<", _LANGLE_t },
-    { "<=", _LANGLE_EQUALS_t },
-    { "=", _EQUALS_t },
-    { ">", _RANGLE_t },
-    { ">=", _RANGLE_EQUALS_t },
-    { "?=", _QUESTION_EQUALS_t },
-    { "[", _LBRACKET_t },
-    { "]", _RBRACKET_t },
-    { "actions", ACTIONS_t },
-    { "bind", BIND_t },
-    { "case", CASE_t },
-    { "class", CLASS_t },
-    { "default", DEFAULT_t },
-    { "else", ELSE_t },
-    { "existing", EXISTING_t },
-    { "for", FOR_t },
-    { "if", IF_t },
-    { "ignore", IGNORE_t },
-    { "in", IN_t },
-    { "include", INCLUDE_t },
-    { "local", LOCAL_t },
-    { "module", MODULE_t },
-    { "on", ON_t },
-    { "piecemeal", PIECEMEAL_t },
-    { "quietly", QUIETLY_t },
-    { "return", RETURN_t },
-    { "rule", RULE_t },
-    { "switch", SWITCH_t },
-    { "together", TOGETHER_t },
-    { "updated", UPDATED_t },
-    { "while", WHILE_t },
-    { "{", _LBRACE_t },
-    { "|", _BAR_t },
-    { "||", _BARBAR_t },
-    { "}", _RBRACE_t },
diff --git a/jam-files/engine/lists.c b/jam-files/engine/lists.c
deleted file mode 100644
index ebabb63e..00000000
--- a/jam-files/engine/lists.c
+++ /dev/null
@@ -1,339 +0,0 @@
-/*
- * Copyright 1993, 1995 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-# include "jam.h"
-# include "newstr.h"
-# include "lists.h"
-
-/*
- * lists.c - maintain lists of strings
- *
- * This implementation essentially uses a singly linked list, but
- * guarantees that the head element of every list has a valid pointer
- * to the tail of the list, so the new elements can efficiently and
- * properly be appended to the end of a list.
- *
- * To avoid massive allocation, list_free() just tacks the whole freed
- * chain onto freelist and list_new() looks on freelist first for an
- * available list struct.  list_free() does not free the strings in the
- * chain: it lazily lets list_new() do so.
- *
- * 08/23/94 (seiwald) - new list_append()
- * 09/07/00 (seiwald) - documented lol_*() functions
- */
-
-static LIST *freelist = 0;  /* junkpile for list_free() */
-
-/*
- * list_append() - append a list onto another one, returning total
- */
-
-LIST * list_append( LIST * l, LIST * nl )
-{
-    if ( !nl )
-    {
-        /* Just return l */
-    }
-    else if ( !l )
-    {
-        l = nl;
-    }
-    else
-    {
-        /* Graft two non-empty lists. */
-        l->tail->next = nl;
-        l->tail = nl->tail;
-    }
-
-    return l;
-}
-
-/*
- * list_new() - tack a string onto the end of a list of strings
- */
-
-LIST * list_new( LIST * head, char * string )
-{
-    LIST * l;
-
-    if ( DEBUG_LISTS )
-        printf( "list > %s <\n", string );
-
-    /* Get list struct from freelist, if one available.  */
-    /* Otherwise allocate. */
-    /* If from freelist, must free string first */
-
-    if ( freelist )
-    {
-        l = freelist;
-        freestr( l->string );
-        freelist = freelist->next;
-    }
-    else
-    {
-        l = (LIST *)BJAM_MALLOC( sizeof( LIST ) );
-    }
-
-    /* If first on chain, head points here. */
-    /* If adding to chain, tack us on. */
-    /* Tail must point to this new, last element. */
-
-    if ( !head ) head = l;
-    else head->tail->next = l;
-    head->tail = l;
-    l->next = 0;
-
-    l->string = string;
-
-    return head;
-}
-
-
-/*
- * list_copy() - copy a whole list of strings (nl) onto end of another (l).
- */
-
-LIST * list_copy( LIST * l, LIST * nl )
-{
-    for ( ; nl; nl = list_next( nl ) )
-        l = list_new( l, copystr( nl->string ) );
-    return l;
-}
-
-
-/*
- * list_sublist() - copy a subset of a list of strings.
- */
-
-LIST * list_sublist( LIST * l, int start, int count )
-{
-    LIST * nl = 0;
-    for ( ; l && start--; l = list_next( l ) );
-    for ( ; l && count--; l = list_next( l ) )
-        nl = list_new( nl, copystr( l->string ) );
-    return nl;
-}
-
-
-static int str_ptr_compare( void const * va, void const * vb )
-{
-    char * a = *( (char * *)va );
-    char * b = *( (char * *)vb );
-    return strcmp(a, b);
-}
-
-
-LIST * list_sort( LIST * l )
-{
-    int len;
-    int ii;
-    char * * strings;
-    LIST * listp;
-    LIST * result = 0;
-
-    if ( !l )
-        return L0;
-
-    len = list_length( l );
-    strings = (char * *)BJAM_MALLOC( len * sizeof(char*) );
-
-    listp = l;
-    for ( ii = 0; ii < len; ++ii )
-    {
-        strings[ ii ] = listp->string;
-        listp = listp->next;
-    }
-
-    qsort( strings, len, sizeof( char * ), str_ptr_compare );
-
-    for ( ii = 0; ii < len; ++ii )
-        result = list_append( result, list_new( 0, strings[ ii ] ) );
-
-    BJAM_FREE( strings );
-
-    return result;
-}
-
-
-/*
- * list_free() - free a list of strings
- */
-
-void list_free( LIST * head )
-{
-    /* Just tack onto freelist. */
-    if ( head )
-    {
-        head->tail->next = freelist;
-        freelist = head;
-    }
-}
-
-
-/*
- * list_pop_front() - remove the front element from a list of strings
- */
-
-LIST * list_pop_front( LIST * l )
-{
-    LIST * result = l->next;
-    if ( result )
-    {
-        result->tail = l->tail;
-        l->next = L0;
-        l->tail = l;
-    }
-    list_free( l );
-    return result;
-}
-
-
-/*
- * list_print() - print a list of strings to stdout
- */
-
-void list_print( LIST * l )
-{
-    LIST * p = 0;
-    for ( ; l; p = l, l = list_next( l ) )
-        if ( p )
-            printf( "%s ", p->string );
-    if ( p )
-        printf( "%s", p->string );
-}
-
-
-/*
- * list_length() - return the number of items in the list
- */
-
-int list_length( LIST * l )
-{
-    int n = 0;
-    for ( ; l; l = list_next( l ), ++n );
-    return n;
-}
-
-
-int list_in( LIST * l, char * value )
-{
-    for ( ; l; l = l->next )
-        if ( strcmp( l->string, value ) == 0 )
-            return 1;
-    return 0;
-}
-
-
-LIST * list_unique( LIST * sorted_list )
-{
-    LIST * result = 0;
-    LIST * last_added = 0;
-
-    for ( ; sorted_list; sorted_list = sorted_list->next )
-    {
-        if ( !last_added || strcmp( sorted_list->string, last_added->string ) != 0 )
-        {
-            result = list_new( result, sorted_list->string );
-            last_added = sorted_list;
-        }
-    }
-    return result;
-}
-
-
-/*
- * lol_init() - initialize a LOL (list of lists).
- */
-
-void lol_init( LOL * lol )
-{
-    lol->count = 0;
-}
-
-
-/*
- * lol_add() - append a LIST onto an LOL.
- */
-
-void lol_add( LOL * lol, LIST * l )
-{
-    if ( lol->count < LOL_MAX )
-        lol->list[ lol->count++ ] = l;
-}
-
-
-/*
- * lol_free() - free the LOL and its LISTs.
- */
-
-void lol_free( LOL * lol )
-{
-    int i;
-    for ( i = 0; i < lol->count; ++i )
-        list_free( lol->list[ i ] );
-    lol->count = 0;
-}
-
-
-/*
- * lol_get() - return one of the LISTs in the LOL.
- */
-
-LIST * lol_get( LOL * lol, int i )
-{
-    return i < lol->count ? lol->list[ i ] : 0;
-}
-
-
-/*
- * lol_print() - debug print LISTS separated by ":".
- */
-
-void lol_print( LOL * lol )
-{
-    int i;
-
-    for ( i = 0; i < lol->count; ++i )
-    {
-        if ( i )
-            printf( " : " );
-        list_print( lol->list[ i ] );
-    }
-}
-
-#ifdef HAVE_PYTHON
-
-PyObject *list_to_python(LIST *l)
-{
-    PyObject *result = PyList_New(0);
-
-    for (; l; l = l->next)
-    {
-        PyObject* s = PyString_FromString(l->string);
-        PyList_Append(result, s);
-        Py_DECREF(s);
-    }
-
-    return result;
-}
-
-LIST *list_from_python(PyObject *l)
-{
-    LIST * result = 0;
-
-    Py_ssize_t i, n;
-    n = PySequence_Size(l);
-    for (i = 0; i < n; ++i)
-    {
-        PyObject *v = PySequence_GetItem(l, i);        
-        result = list_new (result, newstr (PyString_AsString(v)));
-        Py_DECREF(v);
-    }
-
-    return result;
-}
-
-#endif
diff --git a/jam-files/engine/lists.h b/jam-files/engine/lists.h
deleted file mode 100644
index 1dc59827..00000000
--- a/jam-files/engine/lists.h
+++ /dev/null
@@ -1,108 +0,0 @@
-/*
- * Copyright 1993, 1995 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*  This file is ALSO:
- *  Copyright 2001-2004 David Abrahams.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-
-/*
- * lists.h - the LIST structure and routines to manipulate them
- *
- * The whole of jam relies on lists of strings as a datatype.  This
- * module, in conjunction with newstr.c, handles these relatively
- * efficiently.
- *
- * Structures defined:
- *
- *  LIST - list of strings
- *  LOL - list of LISTs
- *
- * External routines:
- *
- *  list_append() - append a list onto another one, returning total
- *  list_new() - tack a string onto the end of a list of strings
- *  list_copy() - copy a whole list of strings
- *  list_sublist() - copy a subset of a list of strings
- *  list_free() - free a list of strings
- *  list_print() - print a list of strings to stdout
- *  list_length() - return the number of items in the list
- *
- *  lol_init() - initialize a LOL (list of lists)
- *  lol_add() - append a LIST onto an LOL
- *  lol_free() - free the LOL and its LISTs
- *  lol_get() - return one of the LISTs in the LOL
- *  lol_print() - debug print LISTS separated by ":"
- *
- * 04/13/94 (seiwald) - added shorthand L0 for null list pointer
- * 08/23/94 (seiwald) - new list_append()
- */
-
-#ifndef LISTS_DWA20011022_H
-# define LISTS_DWA20011022_H
-
-#ifdef HAVE_PYTHON
-#include <Python.h>
-#endif
-
-/*
- * LIST - list of strings
- */
-
-typedef struct _list LIST;
-
-struct _list {
-    LIST    *next;
-    LIST    *tail;      /* only valid in head node */
-    char    *string;    /* private copy */
-};
-
-/*
- * LOL - list of LISTs
- */
-
-typedef struct _lol LOL;
-
-# define LOL_MAX 19
-
-struct _lol {
-    int count;
-    LIST    *list[ LOL_MAX ];
-};
-
-LIST *  list_append( LIST *l, LIST *nl );
-LIST *  list_copy( LIST *l, LIST  *nl );
-void    list_free( LIST *head );
-LIST *  list_new( LIST *head, char *string );
-void    list_print( LIST *l );
-int list_length( LIST *l );
-LIST *  list_sublist( LIST *l, int start, int count );
-LIST *  list_pop_front( LIST *l );
-LIST *  list_sort( LIST *l);
-LIST *  list_unique( LIST *sorted_list);
-int     list_in(LIST* l, char* value);
-
-# define list_next( l ) ((l)->next)
-
-# define L0 ((LIST *)0)
-
-void    lol_add( LOL *lol, LIST *l );
-void    lol_init( LOL *lol );
-void    lol_free( LOL *lol );
-LIST *  lol_get( LOL *lol, int i );
-void    lol_print( LOL *lol );
-void    lol_build( LOL* lol, char** elements );
-
-#ifdef HAVE_PYTHON
-
-PyObject *list_to_python(LIST *l);
-LIST *list_from_python(PyObject *l);
-
-#endif
-
-#endif
-
diff --git a/jam-files/engine/make.c b/jam-files/engine/make.c
deleted file mode 100644
index c871f0be..00000000
--- a/jam-files/engine/make.c
+++ /dev/null
@@ -1,814 +0,0 @@
-/*
- * Copyright 1993, 1995 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*  This file is ALSO:
- *  Copyright 2001-2004 David Abrahams.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-
-/*
- * make.c - bring a target up to date, once rules are in place.
- *
- * This modules controls the execution of rules to bring a target and its
- * dependencies up to date. It is invoked after the targets, rules, et. al.
- * described in rules.h are created by the interpreting jam files.
- *
- * This file contains the main make() entry point and the first pass make0().
- * The second pass, make1(), which actually does the command execution, is in
- * make1.c.
- *
- * External routines:
- *  make() - make a target, given its name
- *
- * Internal routines:
- *  make0() - bind and scan everything to make a TARGET
- *  make0sort() - reorder TARGETS chain by their time (newest to oldest)
- *
- * 12/26/93 (seiwald) - allow NOTIME targets to be expanded via $(<), $(>).
- * 01/04/94 (seiwald) - print all targets, bounded, when tracing commands.
- * 04/08/94 (seiwald) - progress report now reflects only targets with actions.
- * 04/11/94 (seiwald) - Combined deps & headers into deps[2] in TARGET.
- * 12/20/94 (seiwald) - NOTIME renamed NOTFILE.
- * 12/20/94 (seiwald) - make0() headers after determining fate of target, so
- *                      that headers are not seen as being dependent on
- *                      themselves.
- * 01/19/95 (seiwald) - distinguish between CANTFIND/CANTMAKE targets.
- * 02/02/95 (seiwald) - propagate leaf source time for new LEAVES rule.
- * 02/14/95 (seiwald) - NOUPDATE rule means don't update existing target.
- * 08/22/95 (seiwald) - NOUPDATE targets immune to anyhow (-a) flag.
- * 09/06/00 (seiwald) - NOCARE affects targets with sources/actions.
- * 03/02/01 (seiwald) - reverse NOCARE change.
- * 03/14/02 (seiwald) - TEMPORARY targets no longer take on parents age.
- * 03/16/02 (seiwald) - support for -g (reorder builds by source time).
- */
-
-#include "jam.h"
-
-#include "lists.h"
-#include "parse.h"
-#include "variable.h"
-#include "rules.h"
-
-#ifdef OPT_HEADER_CACHE_EXT
-    #include "hcache.h"
-#endif
-
-#include "search.h"
-#include "newstr.h"
-#include "make.h"
-#include "headers.h"
-#include "command.h"
-#include <assert.h>
-
-#ifndef max
-    #define max( a,b ) ((a)>(b)?(a):(b))
-#endif
-
-static TARGETS * make0sort( TARGETS * c );
-
-#ifdef OPT_GRAPH_DEBUG_EXT
-    static void dependGraphOutput( TARGET * t, int depth );
-#endif
-
-static const char * target_fate[] =
-{
-    "init",     /* T_FATE_INIT     */
-    "making",   /* T_FATE_MAKING   */
-    "stable",   /* T_FATE_STABLE   */
-    "newer",    /* T_FATE_NEWER    */
-    "temp",     /* T_FATE_ISTMP    */
-    "touched",  /* T_FATE_TOUCHED  */
-    "rebuild",  /* T_FATE_REBUILD  */
-    "missing",  /* T_FATE_MISSING  */
-    "needtmp",  /* T_FATE_NEEDTMP  */
-    "old",      /* T_FATE_OUTDATED */
-    "update",   /* T_FATE_UPDATE   */
-    "nofind",   /* T_FATE_CANTFIND */
-    "nomake"    /* T_FATE_CANTMAKE */
-};
-
-static const char * target_bind[] =
-{
-    "unbound",
-    "missing",
-    "parents",
-    "exists",
-};
-
-# define spaces(x) ( "                    " + ( x > 20 ? 0 : 20-x ) )
-
-
-/*
- * make() - make a target, given its name.
- */
-
-int make( int n_targets, char const * * targets, int anyhow )
-{
-    int    i;
-    COUNTS counts[ 1 ];
-    int    status = 0;     /* 1 if anything fails */
-
-#ifdef OPT_HEADER_CACHE_EXT
-    hcache_init();
-#endif
-
-    memset( (char *)counts, 0, sizeof( *counts ) );
-
-    /* First bind all targets with LOCATE_TARGET setting. This is needed to
-     * correctly handle dependencies to generated headers.
-     */
-    bind_explicitly_located_targets();
-
-    {
-        PROFILE_ENTER( MAKE_MAKE0 );
-        for ( i = 0; i < n_targets; ++i )
-            make0( bindtarget( targets[ i ] ), 0, 0, counts, anyhow );
-        PROFILE_EXIT( MAKE_MAKE0 );
-    }
-
-#ifdef OPT_GRAPH_DEBUG_EXT
-    if ( DEBUG_GRAPH )
-        for ( i = 0; i < n_targets; ++i )
-            dependGraphOutput( bindtarget( targets[ i ] ), 0 );
-#endif
-
-    if ( DEBUG_MAKE )
-    {
-        if ( counts->targets )
-            printf( "...found %d target%s...\n", counts->targets,
-                counts->targets > 1 ? "s" : "" );
-        if ( counts->temp )
-            printf( "...using %d temp target%s...\n", counts->temp,
-                counts->temp > 1 ? "s" : "" );
-        if ( counts->updating )
-            printf( "...updating %d target%s...\n", counts->updating,
-                counts->updating > 1 ? "s" : "" );
-        if ( counts->cantfind )
-            printf( "...can't find %d target%s...\n", counts->cantfind,
-                counts->cantfind > 1 ? "s" : "" );
-        if ( counts->cantmake )
-            printf( "...can't make %d target%s...\n", counts->cantmake,
-                counts->cantmake > 1 ? "s" : "" );
-    }
-
-#ifdef OPT_HEADER_CACHE_EXT
-    hcache_done();
-#endif
-
-    status = counts->cantfind || counts->cantmake;
-
-    {
-        PROFILE_ENTER( MAKE_MAKE1 );
-        for ( i = 0; i < n_targets; ++i )
-            status |= make1( bindtarget( targets[ i ] ) );
-        PROFILE_EXIT( MAKE_MAKE1 );
-    }
-
-    return status;
-}
-
-
-/* Force any dependants of t that have already at least begun being visited by
- * make0() to be updated.
- */
-
-static void update_dependants( TARGET * t )
-{
-    TARGETS * q;
-
-    for ( q = t->dependants; q; q = q->next )
-    {
-        TARGET * p = q->target;
-        char fate0 = p->fate;
-
-        /* If we have already at least begun visiting it and we are not already
-         * rebuilding it for other reasons.
-         */
-        if ( ( fate0 != T_FATE_INIT ) && ( fate0 < T_FATE_BUILD ) )
-        {
-            p->fate = T_FATE_UPDATE;
-
-            if ( DEBUG_FATE )
-            {
-                printf( "fate change  %s from %s to %s (as dependant of %s)\n",
-                        p->name, target_fate[ (int) fate0 ], target_fate[ (int) p->fate ], t->name );
-            }
-
-            /* If we are done visiting it, go back and make sure its dependants
-             * get rebuilt.
-             */
-            if ( fate0 > T_FATE_MAKING )
-                update_dependants( p );
-        }
-    }
-}
-
-
-/*
- * Make sure that all of t's rebuilds get rebuilt.
- */
-
-static void force_rebuilds( TARGET * t )
-{
-    TARGETS * d;
-    for ( d = t->rebuilds; d; d = d->next )
-    {
-        TARGET * r = d->target;
-
-        /* If it is not already being rebuilt for other reasons. */
-        if ( r->fate < T_FATE_BUILD )
-        {
-            if ( DEBUG_FATE )
-                printf( "fate change  %s from %s to %s (by rebuild)\n",
-                        r->name, target_fate[ (int) r->fate ], target_fate[ T_FATE_REBUILD ] );
-
-            /* Force rebuild it. */
-            r->fate = T_FATE_REBUILD;
-
-            /* And make sure its dependants are updated too. */
-            update_dependants( r );
-        }
-    }
-}
-
-
-/*
- * make0() - bind and scan everything to make a TARGET.
- *
- * Recursively binds a target, searches for #included headers, calls itself on
- * those headers and any dependencies.
- */
-
-void make0
-(
-    TARGET * t,
-    TARGET * p,       /* parent */
-    int      depth,   /* for display purposes */
-    COUNTS * counts,  /* for reporting */
-    int      anyhow
-)  /* forcibly touch all (real) targets */
-{
-    TARGETS    * c;
-    TARGET     * ptime = t;
-    time_t       last;
-    time_t       leaf;
-    time_t       hlast;
-    int          fate;
-    char const * flag = "";
-    SETTINGS   * s;
-
-#ifdef OPT_GRAPH_DEBUG_EXT
-    int savedFate, oldTimeStamp;
-#endif
-
-    if ( DEBUG_MAKEPROG )
-        printf( "make\t--\t%s%s\n", spaces( depth ), t->name );
-
-    /*
-     * Step 1: initialize
-     */
-
-    if ( DEBUG_MAKEPROG )
-        printf( "make\t--\t%s%s\n", spaces( depth ), t->name );
-
-    t->fate = T_FATE_MAKING;
-
-    /*
-     * Step 2: under the influence of "on target" variables,
-     * bind the target and search for headers.
-     */
-
-    /* Step 2a: set "on target" variables. */
-    s = copysettings( t->settings );
-    pushsettings( s );
-
-    /* Step 2b: find and timestamp the target file (if it is a file). */
-    if ( ( t->binding == T_BIND_UNBOUND ) && !( t->flags & T_FLAG_NOTFILE ) )
-    {
-        char * another_target;
-        t->boundname = search( t->name, &t->time, &another_target,
-                               t->flags & T_FLAG_ISFILE );
-        /* If it was detected that this target refers to an already existing and
-         * bound one, we add an include dependency, so that every target
-         * depending on us will depend on that other target as well.
-         */
-        if ( another_target )
-            target_include( t, bindtarget( another_target ) );
-
-        t->binding = t->time ? T_BIND_EXISTS : T_BIND_MISSING;
-    }
-
-    /* INTERNAL, NOTFILE header nodes have the time of their parents. */
-    if ( p && ( t->flags & T_FLAG_INTERNAL ) )
-        ptime = p;
-
-    /* If temp file does not exist but parent does, use parent. */
-    if ( p && ( t->flags & T_FLAG_TEMP ) &&
-        ( t->binding == T_BIND_MISSING ) &&
-        ( p->binding != T_BIND_MISSING ) )
-    {
-        t->binding = T_BIND_PARENTS;
-        ptime = p;
-    }
-
-#ifdef OPT_SEMAPHORE
-    {
-        LIST * var = var_get( "JAM_SEMAPHORE" );
-        if ( var )
-        {
-            TARGET * semaphore = bindtarget( var->string );
-            semaphore->progress = T_MAKE_SEMAPHORE;
-            t->semaphore = semaphore;
-        }
-    }
-#endif
-
-    /* Step 2c: If its a file, search for headers. */
-    if ( t->binding == T_BIND_EXISTS )
-        headers( t );
-
-    /* Step 2d: reset "on target" variables. */
-    popsettings( s );
-    freesettings( s );
-
-    /*
-     * Pause for a little progress reporting .
-     */
-
-    if ( DEBUG_BIND )
-    {
-        if ( strcmp( t->name, t->boundname ) )
-            printf( "bind\t--\t%s%s: %s\n",
-                spaces( depth ), t->name, t->boundname );
-
-        switch ( t->binding )
-        {
-        case T_BIND_UNBOUND:
-        case T_BIND_MISSING:
-        case T_BIND_PARENTS:
-            printf( "time\t--\t%s%s: %s\n",
-                spaces( depth ), t->name, target_bind[ (int) t->binding ] );
-            break;
-
-        case T_BIND_EXISTS:
-            printf( "time\t--\t%s%s: %s",
-                spaces( depth ), t->name, ctime( &t->time ) );
-            break;
-        }
-    }
-
-    /*
-     * Step 3: recursively make0() dependencies & headers.
-     */
-
-    /* Step 3a: recursively make0() dependencies. */
-    for ( c = t->depends; c; c = c->next )
-    {
-        int internal = t->flags & T_FLAG_INTERNAL;
-
-        /* Warn about circular deps, except for includes, which include each
-         * other alot.
-         */
-        if ( c->target->fate == T_FATE_INIT )
-            make0( c->target, ptime, depth + 1, counts, anyhow );
-        else if ( c->target->fate == T_FATE_MAKING && !internal )
-            printf( "warning: %s depends on itself\n", c->target->name );
-    }
-
-    /* Step 3b: recursively make0() internal includes node. */
-    if ( t->includes )
-        make0( t->includes, p, depth + 1, counts, anyhow );
-
-    /* Step 3c: add dependencies' includes to our direct dependencies. */
-    {
-        TARGETS * incs = 0;
-        for ( c = t->depends; c; c = c->next )
-            if ( c->target->includes )
-                incs = targetentry( incs, c->target->includes );
-        t->depends = targetchain( t->depends, incs );
-    }
-
-    /*
-     * Step 4: compute time & fate
-     */
-
-    /* Step 4a: pick up dependencies' time and fate */
-    last = 0;
-    leaf = 0;
-    fate = T_FATE_STABLE;
-    for ( c = t->depends; c; c = c->next )
-    {
-        /* If LEAVES has been applied, we only heed the timestamps of the leaf
-         * source nodes.
-         */
-        leaf = max( leaf, c->target->leaf );
-
-        if ( t->flags & T_FLAG_LEAVES )
-        {
-            last = leaf;
-            continue;
-        }
-
-        last = max( last, c->target->time );
-        fate = max( fate, c->target->fate );
-
-#ifdef OPT_GRAPH_DEBUG_EXT
-        if ( DEBUG_FATE )
-            if ( fate < c->target->fate )
-                printf( "fate change %s from %s to %s by dependency %s\n",
-                    t->name, target_fate[(int) fate], target_fate[(int) c->target->fate],
-                    c->target->name );
-#endif
-    }
-
-    /* Step 4b: pick up included headers time */
-
-    /*
-     * If a header is newer than a temp source that includes it,
-     * the temp source will need building.
-     */
-
-    hlast = t->includes ? t->includes->time : 0;
-
-    /* Step 4c: handle NOUPDATE oddity.
-     *
-     * If a NOUPDATE file exists, mark it as having eternally old dependencies.
-     * Do not inherit our fate from our dependencies. Decide fate based only on
-     * other flags and our binding (done later).
-     */
-    if ( t->flags & T_FLAG_NOUPDATE )
-    {
-#ifdef OPT_GRAPH_DEBUG_EXT
-        if ( DEBUG_FATE )
-            if ( fate != T_FATE_STABLE )
-                printf( "fate change  %s back to stable, NOUPDATE.\n", t->name
-                    );
-#endif
-
-        last = 0;
-        t->time = 0;
-
-        /* Do not inherit our fate from our dependencies. Decide fate based only
-         * upon other flags and our binding (done later).
-         */
-        fate = T_FATE_STABLE;
-    }
-
-    /* Step 4d: determine fate: rebuild target or what? */
-
-    /*
-        In English:
-        If can not find or make child, can not make target.
-        If children changed, make target.
-        If target missing, make it.
-        If children newer, make target.
-        If temp's children newer than parent, make temp.
-        If temp's headers newer than parent, make temp.
-        If deliberately touched, make it.
-        If up-to-date temp file present, use it.
-        If target newer than non-notfile parent, mark target newer.
-        Otherwise, stable!
-
-        Note this block runs from least to most stable:
-        as we make it further down the list, the target's
-        fate is getting stabler.
-    */
-
-#ifdef OPT_GRAPH_DEBUG_EXT
-    savedFate = fate;
-    oldTimeStamp = 0;
-#endif
-
-    if ( fate >= T_FATE_BROKEN )
-    {
-        fate = T_FATE_CANTMAKE;
-    }
-    else if ( fate >= T_FATE_SPOIL )
-    {
-        fate = T_FATE_UPDATE;
-    }
-    else if ( t->binding == T_BIND_MISSING )
-    {
-        fate = T_FATE_MISSING;
-    }
-    else if ( ( t->binding == T_BIND_EXISTS ) && ( last > t->time ) )
-    {
-#ifdef OPT_GRAPH_DEBUG_EXT
-        oldTimeStamp = 1;
-#endif
-        fate = T_FATE_OUTDATED;
-    }
-    else if ( ( t->binding == T_BIND_PARENTS ) && ( last > p->time ) )
-    {
-#ifdef OPT_GRAPH_DEBUG_EXT
-        oldTimeStamp = 1;
-#endif
-        fate = T_FATE_NEEDTMP;
-    }
-    else if ( ( t->binding == T_BIND_PARENTS ) && ( hlast > p->time ) )
-    {
-        fate = T_FATE_NEEDTMP;
-    }
-    else if ( t->flags & T_FLAG_TOUCHED )
-    {
-        fate = T_FATE_TOUCHED;
-    }
-    else if ( anyhow && !( t->flags & T_FLAG_NOUPDATE ) )
-    {
-        fate = T_FATE_TOUCHED;
-    }
-    else if ( ( t->binding == T_BIND_EXISTS ) && ( t->flags & T_FLAG_TEMP ) )
-    {
-        fate = T_FATE_ISTMP;
-    }
-    else if ( ( t->binding == T_BIND_EXISTS ) && p &&
-         ( p->binding != T_BIND_UNBOUND ) && ( t->time > p->time ) )
-    {
-#ifdef OPT_GRAPH_DEBUG_EXT
-        oldTimeStamp = 1;
-#endif
-        fate = T_FATE_NEWER;
-    }
-    else
-    {
-        fate = T_FATE_STABLE;
-    }
-#ifdef OPT_GRAPH_DEBUG_EXT
-    if ( DEBUG_FATE && ( fate != savedFate ) )
-	{
-        if ( savedFate == T_FATE_STABLE )
-            printf( "fate change  %s set to %s%s\n", t->name,
-                target_fate[ fate ], oldTimeStamp ? " (by timestamp)" : "" );
-        else
-            printf( "fate change  %s from %s to %s%s\n", t->name,
-                target_fate[ savedFate ], target_fate[ fate ],
-                oldTimeStamp ? " (by timestamp)" : "" );
-	}
-#endif
-
-    /* Step 4e: handle missing files */
-    /* If it is missing and there are no actions to create it, boom. */
-    /* If we can not make a target we do not care about it, okay. */
-    /* We could insist that there are updating actions for all missing */
-    /* files, but if they have dependencies we just pretend it is a NOTFILE. */
-
-    if ( ( fate == T_FATE_MISSING ) && !t->actions && !t->depends )
-    {
-        if ( t->flags & T_FLAG_NOCARE )
-        {
-#ifdef OPT_GRAPH_DEBUG_EXT
-            if ( DEBUG_FATE )
-                printf( "fate change %s to STABLE from %s, "
-                    "no actions, no dependencies and do not care\n",
-                    t->name, target_fate[ fate ] );
-#endif
-            fate = T_FATE_STABLE;
-        }
-        else
-        {
-            printf( "don't know how to make %s\n", t->name );
-            fate = T_FATE_CANTFIND;
-        }
-    }
-
-    /* Step 4f: propagate dependencies' time & fate. */
-    /* Set leaf time to be our time only if this is a leaf. */
-
-    t->time = max( t->time, last );
-    t->leaf = leaf ? leaf : t->time ;
-    /* This target's fate may have been updated by virtue of following some
-     * target's rebuilds list, so only allow it to be increased to the fate we
-     * have calculated. Otherwise, grab its new fate.
-     */
-    if ( fate > t->fate )
-        t->fate = fate;
-    else
-        fate = t->fate;
-
-    /* Step 4g: if this target needs to be built, force rebuild everything in
-     * this target's rebuilds list.
-     */
-    if ( ( fate >= T_FATE_BUILD ) && ( fate < T_FATE_BROKEN ) )
-        force_rebuilds( t );
-
-    /*
-     * Step 5: sort dependencies by their update time.
-     */
-
-    if ( globs.newestfirst )
-        t->depends = make0sort( t->depends );
-
-    /*
-     * Step 6: a little harmless tabulating for tracing purposes
-     */
-
-    /* Do not count or report interal includes nodes. */
-    if ( t->flags & T_FLAG_INTERNAL )
-        return;
-
-    if ( counts )
-    {
-#ifdef OPT_IMPROVED_PATIENCE_EXT
-        ++counts->targets;
-#else
-        if ( !( ++counts->targets % 1000 ) && DEBUG_MAKE )
-            printf( "...patience...\n" );
-#endif
-
-        if ( fate == T_FATE_ISTMP )
-            ++counts->temp;
-        else if ( fate == T_FATE_CANTFIND )
-            ++counts->cantfind;
-        else if ( ( fate == T_FATE_CANTMAKE ) && t->actions )
-            ++counts->cantmake;
-        else if ( ( fate >= T_FATE_BUILD ) && ( fate < T_FATE_BROKEN ) &&
-            t->actions )
-            ++counts->updating;
-    }
-
-    if ( !( t->flags & T_FLAG_NOTFILE ) && ( fate >= T_FATE_SPOIL ) )
-        flag = "+";
-    else if ( ( t->binding == T_BIND_EXISTS ) && p && ( t->time > p->time ) )
-        flag = "*";
-
-    if ( DEBUG_MAKEPROG )
-        printf( "made%s\t%s\t%s%s\n", flag, target_fate[ (int) t->fate ],
-            spaces( depth ), t->name );
-}
-
-
-#ifdef OPT_GRAPH_DEBUG_EXT
-
-static const char * target_name( TARGET * t )
-{
-    static char buf[ 1000 ];
-    if ( t->flags & T_FLAG_INTERNAL )
-    {
-        sprintf( buf, "%s (internal node)", t->name );
-        return buf;
-    }
-    return t->name;
-}
-
-
-/*
- * dependGraphOutput() - output the DG after make0 has run.
- */
-
-static void dependGraphOutput( TARGET * t, int depth )
-{
-    TARGETS * c;
-
-    if ( ( t->flags & T_FLAG_VISITED ) || !t->name || !t->boundname )
-        return;
-
-    t->flags |= T_FLAG_VISITED;
-
-    switch ( t->fate )
-    {
-    case T_FATE_TOUCHED:
-    case T_FATE_MISSING:
-    case T_FATE_OUTDATED:
-    case T_FATE_UPDATE:
-        printf( "->%s%2d Name: %s\n", spaces( depth ), depth, target_name( t ) );
-        break;
-    default:
-        printf( "  %s%2d Name: %s\n", spaces( depth ), depth, target_name( t ) );
-        break;
-    }
-
-    if ( strcmp( t->name, t->boundname ) )
-        printf( "  %s    Loc: %s\n", spaces( depth ), t->boundname );
-
-    switch ( t->fate )
-    {
-    case T_FATE_STABLE:
-        printf( "  %s       : Stable\n", spaces( depth ) );
-        break;
-    case T_FATE_NEWER:
-        printf( "  %s       : Newer\n", spaces( depth ) );
-        break;
-    case T_FATE_ISTMP:
-        printf( "  %s       : Up to date temp file\n", spaces( depth ) );
-        break;
-    case T_FATE_NEEDTMP:
-        printf( "  %s       : Temporary file, to be updated\n", spaces( depth ) );
-        break;
-    case T_FATE_TOUCHED:
-        printf( "  %s       : Been touched, updating it\n", spaces( depth ) );
-        break;
-    case T_FATE_MISSING:
-        printf( "  %s       : Missing, creating it\n", spaces( depth ) );
-        break;
-    case T_FATE_OUTDATED:
-        printf( "  %s       : Outdated, updating it\n", spaces( depth ) );
-        break;
-    case T_FATE_REBUILD:
-        printf( "  %s       : Rebuild, updating it\n", spaces( depth ) );
-        break;
-    case T_FATE_UPDATE:
-        printf( "  %s       : Updating it\n", spaces( depth ) );
-        break;
-    case T_FATE_CANTFIND:
-        printf( "  %s       : Can not find it\n", spaces( depth ) );
-        break;
-    case T_FATE_CANTMAKE:
-        printf( "  %s       : Can make it\n", spaces( depth ) );
-        break;
-    }
-
-    if ( t->flags & ~T_FLAG_VISITED )
-    {
-        printf( "  %s       : ", spaces( depth ) );
-        if ( t->flags & T_FLAG_TEMP     ) printf( "TEMPORARY " );
-        if ( t->flags & T_FLAG_NOCARE   ) printf( "NOCARE "    );
-        if ( t->flags & T_FLAG_NOTFILE  ) printf( "NOTFILE "   );
-        if ( t->flags & T_FLAG_TOUCHED  ) printf( "TOUCHED "   );
-        if ( t->flags & T_FLAG_LEAVES   ) printf( "LEAVES "    );
-        if ( t->flags & T_FLAG_NOUPDATE ) printf( "NOUPDATE "  );
-        printf( "\n" );
-    }
-
-    for ( c = t->depends; c; c = c->next )
-    {
-        printf( "  %s       : Depends on %s (%s)", spaces( depth ),
-               target_name( c->target ), target_fate[ (int) c->target->fate ] );
-        if ( c->target->time == t->time )
-            printf( " (max time)");
-        printf( "\n" );
-    }
-
-    for ( c = t->depends; c; c = c->next )
-        dependGraphOutput( c->target, depth + 1 );
-}
-#endif
-
-
-/*
- * make0sort() - reorder TARGETS chain by their time (newest to oldest).
- *
- * We walk chain, taking each item and inserting it on the sorted result, with
- * newest items at the front. This involves updating each of the TARGETS'
- * c->next and c->tail. Note that we make c->tail a valid prev pointer for every
- * entry. Normally, it is only valid at the head, where prev == tail. Note also
- * that while tail is a loop, next ends at the end of the chain.
- */
-
-static TARGETS * make0sort( TARGETS * chain )
-{
-    PROFILE_ENTER( MAKE_MAKE0SORT );
-
-    TARGETS * result = 0;
-
-    /* Walk the current target list. */
-    while ( chain )
-    {
-        TARGETS * c = chain;
-        TARGETS * s = result;
-
-        chain = chain->next;
-
-        /* Find point s in result for c. */
-        while ( s && ( s->target->time > c->target->time ) )
-            s = s->next;
-
-        /* Insert c in front of s (might be 0). Do not even think of deciphering
-         * this.
-         */
-        c->next = s;                           /* good even if s = 0       */
-        if ( result == s ) result = c;         /* new head of chain?       */
-        if ( !s ) s = result;                  /* wrap to ensure a next    */
-        if ( result != c ) s->tail->next = c;  /* not head? be prev's next */
-        c->tail = s->tail;                     /* take on next's prev      */
-        s->tail = c;                           /* make next's prev us      */
-    }
-
-    PROFILE_EXIT( MAKE_MAKE0SORT );
-    return result;
-}
-
-
-static LIST * targets_to_update_ = 0;
-
-
-void mark_target_for_updating( char * target )
-{
-    targets_to_update_ = list_new( targets_to_update_, target );
-}
-
-
-LIST * targets_to_update()
-{
-    return targets_to_update_;
-}
-
-
-void clear_targets_to_update()
-{
-    list_free( targets_to_update_ );
-    targets_to_update_ = 0;
-}
diff --git a/jam-files/engine/make.h b/jam-files/engine/make.h
deleted file mode 100644
index b372263e..00000000
--- a/jam-files/engine/make.h
+++ /dev/null
@@ -1,41 +0,0 @@
-/*
- * Copyright 1993, 1995 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*
- * make.h - bring a target up to date, once rules are in place
- */
-
-#include "lists.h"
-
-int make( int n_targets, const char **targets, int anyhow );
-int make1( TARGET *t );
-
-typedef struct {
-    int temp;
-    int updating;
-    int cantfind;
-    int cantmake;
-    int targets;
-    int made;
-} COUNTS ;
-
-
-void make0( TARGET *t, TARGET  *p, int depth,
-            COUNTS *counts, int anyhow );
-
-
-/*
- * Specifies that the target should be updated.
- */
-void mark_target_for_updating(char *target);
-/*
- * Returns the list of all the target previously passed to 'mark_target_for_updating'.
- */
-LIST *targets_to_update();
-/*
- * Cleasr/unmarks all targets that are currently marked for update.
- */
-void clear_targets_to_update();
diff --git a/jam-files/engine/make1.c b/jam-files/engine/make1.c
deleted file mode 100644
index 8001f333..00000000
--- a/jam-files/engine/make1.c
+++ /dev/null
@@ -1,1145 +0,0 @@
-/*
- * Copyright 1993-2002 Christopher Seiwald and Perforce Software, Inc.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*  This file is ALSO:
- *  Copyright 2001-2004 David Abrahams.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-
-/*
- * make1.c - execute command to bring targets up to date
- *
- * This module contains make1(), the entry point called by make() to
- * recursively decend the dependency graph executing update actions as
- * marked by make0().
- *
- * External routines:
- *
- *  make1() - execute commands to update a TARGET and all of its dependencies.
- *
- * Internal routines, the recursive/asynchronous command executors:
- *
- *  make1a()     - recursively traverse dependency target tree, calling make1b().
- *  make1atail() - started processing all dependencies so go on to make1b().
- *  make1b()     - when dependencies are up to date, build target with make1c().
- *  make1c()     - launch target's next command, call parents' make1b() if none.
- *  make1d()     - handle command execution completion and call back make1c().
- *
- * Internal support routines:
- *
- *  make1cmds()     - turn ACTIONS into CMDs, grouping, splitting, etc.
- *  make1list()     - turn a list of targets into a LIST, for $(<) and $(>).
- *  make1settings() - for vars that get bound values, build up replacement lists.
- *  make1bind()     - bind targets that weren't bound in dependency analysis.
- *
- * 04/16/94 (seiwald) - Split from make.c.
- * 04/21/94 (seiwald) - Handle empty "updated" actions.
- * 05/04/94 (seiwald) - async multiprocess (-j) support.
- * 06/01/94 (seiwald) - new 'actions existing' does existing sources.
- * 12/20/94 (seiwald) - NOTIME renamed NOTFILE.
- * 01/19/95 (seiwald) - distinguish between CANTFIND/CANTMAKE targets.
- * 01/22/94 (seiwald) - pass per-target JAMSHELL down to exec_cmd().
- * 02/28/95 (seiwald) - Handle empty "existing" actions.
- * 03/10/95 (seiwald) - Fancy counts.
- */
-
-#include "jam.h"
-
-#include "lists.h"
-#include "parse.h"
-#include "assert.h"
-#include "variable.h"
-#include "rules.h"
-#include "headers.h"
-
-#include "search.h"
-#include "newstr.h"
-#include "make.h"
-#include "command.h"
-#include "execcmd.h"
-#include "compile.h"
-#include "output.h"
-
-#include <stdlib.h>
-
-#if ! defined(NT) || defined(__GNUC__)
-    #include <unistd.h>  /* for unlink */
-#endif
-
-static CMD      * make1cmds    ( TARGET * );
-static LIST     * make1list    ( LIST *, TARGETS *, int flags );
-static SETTINGS * make1settings( LIST * vars );
-static void       make1bind    ( TARGET * );
-
-/* Ugly static - it is too hard to carry it through the callbacks. */
-
-static struct
-{
-    int failed;
-    int skipped;
-    int total;
-    int made;
-} counts[ 1 ] ;
-
-/* Target state - remove recursive calls by just keeping track of state target
- * is in.
- */
-typedef struct _state
-{
-    struct _state * prev;      /* previous state on stack */
-    TARGET        * t;         /* current target */
-    TARGET        * parent;    /* parent argument necessary for make1a() */
-#define T_STATE_MAKE1A     0   /* make1a() should be called */
-#define T_STATE_MAKE1ATAIL 1   /* make1atail() should be called */
-#define T_STATE_MAKE1B     2   /* make1b() should be called */
-#define T_STATE_MAKE1C     3   /* make1c() should be called */
-#define T_STATE_MAKE1D     4   /* make1d() should be called */
-    int             curstate;  /* current state */
-    int             status;
-} state;
-
-static void make1a      ( state * );
-static void make1atail  ( state * );
-static void make1b      ( state * );
-static void make1c      ( state * );
-static void make1d      ( state * );
-static void make_closure( void * closure, int status, timing_info *, char *, char * );
-
-typedef struct _stack
-{
-    state * stack;
-} stack;
-
-static stack state_stack = { NULL };
-
-static state * state_freelist = NULL;
-
-
-static state * alloc_state()
-{
-    if ( state_freelist != NULL )
-    {
-        state * pState = state_freelist;
-        state_freelist = pState->prev;
-        memset( pState, 0, sizeof( state ) );
-        return pState;
-    }
-
-    return (state *)BJAM_MALLOC( sizeof( state ) );
-}
-
-
-static void free_state( state * pState )
-{
-    pState->prev = state_freelist;
-    state_freelist = pState;
-}
-
-
-static void clear_state_freelist()
-{
-    while ( state_freelist != NULL )
-    {
-        state * pState = state_freelist;
-        state_freelist = state_freelist->prev;
-        BJAM_FREE( pState );
-    }
-}
-
-
-static state * current_state( stack * pStack )
-{
-    return pStack->stack;
-}
-
-
-static void pop_state( stack * pStack )
-{
-    if ( pStack->stack != NULL )
-    {
-        state * pState = pStack->stack->prev;
-        free_state( pStack->stack );
-        pStack->stack = pState;
-    }
-}
-
-
-static state * push_state( stack * pStack, TARGET * t, TARGET * parent, int curstate )
-{
-    state * pState = alloc_state();
-
-    pState->t = t;
-    pState->parent = parent;
-    pState->prev = pStack->stack;
-    pState->curstate = curstate;
-
-    pStack->stack = pState;
-
-    return pStack->stack;
-}
-
-
-/*
- * Pushes a stack onto another stack, effectively reversing the order.
- */
-
-static void push_stack_on_stack( stack * pDest, stack * pSrc )
-{
-    while ( pSrc->stack != NULL )
-    {
-        state * pState = pSrc->stack;
-        pSrc->stack = pSrc->stack->prev;
-        pState->prev = pDest->stack;
-        pDest->stack = pState;
-    }
-}
-
-
-/*
- * make1() - execute commands to update a TARGET and all of its dependencies.
- */
-
-static int intr = 0;
-
-int make1( TARGET * t )
-{
-    state * pState;
-
-    memset( (char *)counts, 0, sizeof( *counts ) );
-
-    /* Recursively make the target and its dependencies. */
-    push_state( &state_stack, t, NULL, T_STATE_MAKE1A );
-
-    do
-    {
-        while ( ( pState = current_state( &state_stack ) ) != NULL )
-        {
-            if ( intr )
-                pop_state( &state_stack );
-
-            switch ( pState->curstate )
-            {
-                case T_STATE_MAKE1A    : make1a    ( pState ); break;
-                case T_STATE_MAKE1ATAIL: make1atail( pState ); break;
-                case T_STATE_MAKE1B    : make1b    ( pState ); break;
-                case T_STATE_MAKE1C    : make1c    ( pState ); break;
-                case T_STATE_MAKE1D    : make1d    ( pState ); break;
-            }
-        }
-    }
-    /* Wait for any outstanding commands to finish running. */
-    while ( exec_wait() );
-
-    clear_state_freelist();
-
-    /* Talk about it. */
-    if ( counts->failed )
-        printf( "...failed updating %d target%s...\n", counts->failed,
-                counts->failed > 1 ? "s" : "" );
-    if ( DEBUG_MAKE && counts->skipped )
-        printf( "...skipped %d target%s...\n", counts->skipped,
-                counts->skipped > 1 ? "s" : "" );
-    if ( DEBUG_MAKE && counts->made )
-        printf( "...updated %d target%s...\n", counts->made,
-                counts->made > 1 ? "s" : "" );
-
-    return counts->total != counts->made;
-}
-
-
-/*
- * make1a() - recursively traverse target tree, calling make1b().
- *
- * Called to start processing a specified target. Does nothing if the target is
- * already being processed or otherwise starts processing all of its
- * dependencies. Once all of its dependencies have started being processed goes
- * on and calls make1b() (actually does that indirectly via a helper
- * make1atail() state).
- */
-
-static void make1a( state * pState )
-{
-    TARGET * t = pState->t;
-    TARGETS * c;
-
-    /* If the parent is the first to try to build this target or this target is
-     * in the make1c() quagmire, arrange for the parent to be notified when this
-     * target is built.
-     */
-    if ( pState->parent )
-        switch ( pState->t->progress )
-        {
-            case T_MAKE_INIT:
-            case T_MAKE_ACTIVE:
-            case T_MAKE_RUNNING:
-                pState->t->parents = targetentry( pState->t->parents,
-                    pState->parent );
-                ++pState->parent->asynccnt;
-        }
-
-    /* If this target is already being processed then do nothing. There is no
-     * need to start processing the same target all over again.
-     */
-    if ( pState->t->progress != T_MAKE_INIT )
-    {
-        pop_state( &state_stack );
-        return;
-    }
-
-    /* Asynccnt counts the dependencies preventing this target from proceeding
-     * to make1b() for actual building. We start off with a count of 1 to
-     * prevent anything from happening until we can notify all dependencies that
-     * they are needed. This 1 is accounted for when we call make1b() ourselves,
-     * below. Without this if a a dependency gets built before we finish
-     * processing all of our other dependencies our build might be triggerred
-     * prematurely.
-     */
-    pState->t->asynccnt = 1;
-
-    /* Add header nodes created during the building process. */
-    {
-        TARGETS * inc = 0;
-        for ( c = t->depends; c; c = c->next )
-            if ( c->target->rescanned && c->target->includes )
-                inc = targetentry( inc, c->target->includes );
-        t->depends = targetchain( t->depends, inc );
-    }
-
-    /* Guard against circular dependencies. */
-    pState->t->progress = T_MAKE_ONSTACK;
-
-    {
-        stack temp_stack = { NULL };
-        for ( c = t->depends; c && !intr; c = c->next )
-            push_state( &temp_stack, c->target, pState->t, T_STATE_MAKE1A );
-
-        /* Using stacks reverses the order of execution. Reverse it back. */
-        push_stack_on_stack( &state_stack, &temp_stack );
-    }
-
-    pState->curstate = T_STATE_MAKE1ATAIL;
-}
-
-
-/*
- * make1atail() - started processing all dependencies so go on to make1b().
- */
-
-static void make1atail( state * pState )
-{
-    pState->t->progress = T_MAKE_ACTIVE;
-    /* Now that all of our dependencies have bumped up our asynccnt we can
-     * remove our own internal bump added to prevent this target from being
-     * built before all of its dependencies start getting processed.
-     */
-    pState->curstate = T_STATE_MAKE1B;
-}
-
-
-/*
- * make1b() - when dependencies are up to date, build target with make1c().
- *
- * Called after all dependencies have started being processed and after each of
- * them finishes its processing. The target actually goes on to getting built in
- * make1c() only after all of its dependencies have finished their processing.
- */
-
-static void make1b( state * pState )
-{
-    TARGET  * t = pState->t;
-    TARGETS * c;
-    TARGET  * failed = 0;
-    char    * failed_name = "dependencies";
-
-    /* If any dependencies are still outstanding, wait until they call make1b()
-     * to signal their completion.
-     */
-    if ( --pState->t->asynccnt )
-    {
-        pop_state( &state_stack );
-        return;
-    }
-
-    /* Try to aquire a semaphore. If it is locked, wait until the target that
-     * locked it is built and signal completition.
-     */
-#ifdef OPT_SEMAPHORE
-    if ( t->semaphore && t->semaphore->asynccnt )
-    {
-        /* Append 't' to the list of targets waiting on semaphore. */
-        t->semaphore->parents = targetentry( t->semaphore->parents, t );
-        t->asynccnt++;
-
-        if ( DEBUG_EXECCMD )
-            printf( "SEM: %s is busy, delaying launch of %s\n",
-                t->semaphore->name, t->name );
-        pop_state( &state_stack );
-        return;
-    }
-#endif
-
-    /* Now ready to build target 't', if dependencies built OK. */
-
-    /* Collect status from dependencies. */
-    for ( c = t->depends; c; c = c->next )
-        if ( c->target->status > t->status && !( c->target->flags & T_FLAG_NOCARE ) )
-        {
-            failed = c->target;
-            pState->t->status = c->target->status;
-        }
-    /* If an internal header node failed to build, we want to output the target
-     * that it failed on.
-     */
-    if ( failed )
-    {
-        failed_name = failed->flags & T_FLAG_INTERNAL
-            ? failed->failed
-            : failed->name;
-    }
-    t->failed = failed_name;
-
-    /* If actions for building any of the dependencies have failed, bail.
-     * Otherwise, execute all actions to make the current target.
-     */
-    if ( ( pState->t->status == EXEC_CMD_FAIL ) && pState->t->actions )
-    {
-        ++counts->skipped;
-        if ( ( pState->t->flags & ( T_FLAG_RMOLD | T_FLAG_NOTFILE ) ) == T_FLAG_RMOLD )
-        {
-            if ( !unlink( pState->t->boundname ) )
-                printf( "...removing outdated %s\n", pState->t->boundname );
-        }
-        else
-            printf( "...skipped %s for lack of %s...\n", pState->t->name, failed_name );
-    }
-
-    if ( pState->t->status == EXEC_CMD_OK )
-        switch ( pState->t->fate )
-        {
-            /* These are handled by the default case below now
-        case T_FATE_INIT:
-        case T_FATE_MAKING:
-            */
-
-        case T_FATE_STABLE:
-        case T_FATE_NEWER:
-            break;
-
-        case T_FATE_CANTFIND:
-        case T_FATE_CANTMAKE:
-            pState->t->status = EXEC_CMD_FAIL;
-            break;
-
-        case T_FATE_ISTMP:
-            if ( DEBUG_MAKE )
-                printf( "...using %s...\n", pState->t->name );
-            break;
-
-        case T_FATE_TOUCHED:
-        case T_FATE_MISSING:
-        case T_FATE_NEEDTMP:
-        case T_FATE_OUTDATED:
-        case T_FATE_UPDATE:
-        case T_FATE_REBUILD:
-            /* Prepare commands for executing actions scheduled for this target
-             * and then schedule transfer to make1c() state to proceed with
-             * executing the prepared commands. Commands have their embedded
-             * variables automatically expanded, including making use of any "on
-             * target" variables.
-             */
-            if ( pState->t->actions )
-            {
-                ++counts->total;
-                if ( DEBUG_MAKE && !( counts->total % 100 ) )
-                    printf( "...on %dth target...\n", counts->total );
-
-                pState->t->cmds = (char *)make1cmds( pState->t );
-                /* Set the target's "progress" so that make1c() counts it among
-                 * its successes/failures.
-                 */
-                pState->t->progress = T_MAKE_RUNNING;
-            }
-            break;
-
-            /* All possible fates should have been accounted for by now. */
-        default:
-            printf( "ERROR: %s has bad fate %d", pState->t->name,
-                pState->t->fate );
-            abort();
-        }
-
-    /* Call make1c() to begin the execution of the chain of commands needed to
-     * build the target. If we are not going to build the target (due of
-     * dependency failures or no commands needing to be run) the chain will be
-     * empty and make1c() will directly signal the target's completion.
-     */
-
-#ifdef OPT_SEMAPHORE
-    /* If there is a semaphore, indicate that it is in use. */
-    if ( pState->t->semaphore )
-    {
-        ++pState->t->semaphore->asynccnt;
-        if ( DEBUG_EXECCMD )
-            printf( "SEM: %s now used by %s\n", pState->t->semaphore->name,
-                pState->t->name );
-    }
-#endif
-
-    pState->curstate = T_STATE_MAKE1C;
-}
-
-
-/*
- * make1c() - launch target's next command, call parents' make1b() if none.
- *
- * If there are (more) commands to run to build this target (and we have not hit
- * an error running earlier comands) we launch the command using exec_cmd(). If
- * there are no more commands to run, we collect the status from all the actions
- * and report our completion to all the parents.
- */
-
-static void make1c( state * pState )
-{
-    CMD * cmd = (CMD *)pState->t->cmds;
-
-    if ( cmd && ( pState->t->status == EXEC_CMD_OK ) )
-    {
-        char * rule_name = 0;
-        char * target = 0;
-
-        if ( DEBUG_MAKEQ ||
-            ( !( cmd->rule->actions->flags & RULE_QUIETLY ) && DEBUG_MAKE ) )
-        {
-            rule_name = cmd->rule->name;
-            target = lol_get( &cmd->args, 0 )->string;
-            if ( globs.noexec )
-                out_action( rule_name, target, cmd->buf, "", "", EXIT_OK );
-        }
-
-        if ( globs.noexec )
-        {
-            pState->curstate = T_STATE_MAKE1D;
-            pState->status = EXEC_CMD_OK;
-        }
-        else
-        {
-            /* Pop state first because exec_cmd() could push state. */
-            pop_state( &state_stack );
-            exec_cmd( cmd->buf, make_closure, pState->t, cmd->shell, rule_name,
-                target );
-        }
-    }
-    else
-    {
-        TARGETS * c;
-        ACTIONS * actions;
-
-        /* Collect status from actions, and distribute it as well. */
-        for ( actions = pState->t->actions; actions; actions = actions->next )
-            if ( actions->action->status > pState->t->status )
-                pState->t->status = actions->action->status;
-        for ( actions = pState->t->actions; actions; actions = actions->next )
-            if ( pState->t->status > actions->action->status )
-                actions->action->status = pState->t->status;
-
-        /* Tally success/failure for those we tried to update. */
-        if ( pState->t->progress == T_MAKE_RUNNING )
-            switch ( pState->t->status )
-            {
-                case EXEC_CMD_OK  : ++counts->made  ; break;
-                case EXEC_CMD_FAIL: ++counts->failed; break;
-            }
-
-        /* Tell parents their dependency has been built. */
-        {
-            stack temp_stack = { NULL };
-            TARGET * t = pState->t;
-            TARGET * additional_includes = NULL;
-
-            t->progress = T_MAKE_DONE;
-
-            /* Target has been updated so rescan it for dependencies. */
-            if ( ( t->fate >= T_FATE_MISSING ) &&
-                ( t->status == EXEC_CMD_OK ) &&
-                !t->rescanned )
-            {
-                TARGET * target_to_rescan = t;
-                SETTINGS * s;
-
-                target_to_rescan->rescanned = 1;
-
-                if ( target_to_rescan->flags & T_FLAG_INTERNAL )
-                    target_to_rescan = t->original_target;
-
-                /* Clean current includes. */
-                target_to_rescan->includes = 0;
-
-                s = copysettings( target_to_rescan->settings );
-                pushsettings( s );
-                headers( target_to_rescan );
-                popsettings( s );
-                freesettings( s );
-
-                if ( target_to_rescan->includes )
-                {
-                    target_to_rescan->includes->rescanned = 1;
-                    /* Tricky. The parents have already been processed, but they
-                     * have not seen the internal node, because it was just
-                     * created. We need to make the calls to make1a() that would
-                     * have been made by the parents here, and also make sure
-                     * all unprocessed parents will pick up the includes. We
-                     * must make sure processing of the additional make1a()
-                     * invocations is done before make1b() which means this
-                     * target is built, otherwise the parent would be considered
-                     * built before this make1a() processing has even started.
-                     */
-                    make0( target_to_rescan->includes, target_to_rescan->parents->target, 0, 0, 0 );
-                    for ( c = target_to_rescan->parents; c; c = c->next )
-                        c->target->depends = targetentry( c->target->depends,
-                                                          target_to_rescan->includes );
-                    /* Will be processed below. */
-                    additional_includes = target_to_rescan->includes;
-                }
-            }
-
-            if ( additional_includes )
-                for ( c = t->parents; c; c = c->next )
-                    push_state( &temp_stack, additional_includes, c->target, T_STATE_MAKE1A );
-
-            for ( c = t->parents; c; c = c->next )
-                push_state( &temp_stack, c->target, NULL, T_STATE_MAKE1B );
-
-#ifdef OPT_SEMAPHORE
-            /* If there is a semaphore, it is now free. */
-            if ( t->semaphore )
-            {
-                assert( t->semaphore->asynccnt == 1 );
-                --t->semaphore->asynccnt;
-
-                if ( DEBUG_EXECCMD )
-                    printf( "SEM: %s is now free\n", t->semaphore->name );
-
-                /* If anything is waiting, notify the next target. There is no
-                 * point in notifying waiting targets, since they will be
-                 * notified again.
-                 */
-                if ( t->semaphore->parents )
-                {
-                    TARGETS * first = t->semaphore->parents;
-                    if ( first->next )
-                        first->next->tail = first->tail;
-                    t->semaphore->parents = first->next;
-
-                    if ( DEBUG_EXECCMD )
-                        printf( "SEM: placing %s on stack\n", first->target->name );
-                    push_state( &temp_stack, first->target, NULL, T_STATE_MAKE1B );
-                    BJAM_FREE( first );
-                }
-            }
-#endif
-
-            /* Must pop state before pushing any more. */
-            pop_state( &state_stack );
-
-            /* Using stacks reverses the order of execution. Reverse it back. */
-            push_stack_on_stack( &state_stack, &temp_stack );
-        }
-    }
-}
-
-
-/*
- * call_timing_rule() - Look up the __TIMING_RULE__ variable on the given
- * target, and if non-empty, invoke the rule it names, passing the given
- * timing_info.
- */
-
-static void call_timing_rule( TARGET * target, timing_info * time )
-{
-    LIST * timing_rule;
-
-    pushsettings( target->settings );
-    timing_rule = var_get( "__TIMING_RULE__" );
-    popsettings( target->settings );
-
-    if ( timing_rule )
-    {
-        /* rule timing-rule ( args * : target : start end user system ) */
-
-        /* Prepare the argument list. */
-        FRAME frame[ 1 ];
-        frame_init( frame );
-
-        /* args * :: $(__TIMING_RULE__[2-]) */
-        lol_add( frame->args, list_copy( L0, timing_rule->next ) );
-
-        /* target :: the name of the target */
-        lol_add( frame->args, list_new( L0, target->name ) );
-
-        /* start end user system :: info about the action command */
-        lol_add( frame->args, list_new( list_new( list_new( list_new( L0,
-            outf_time  ( time->start  ) ),
-            outf_time  ( time->end    ) ),
-            outf_double( time->user   ) ),
-            outf_double( time->system ) ) );
-
-        /* Call the rule. */
-        evaluate_rule( timing_rule->string, frame );
-
-        /* Clean up. */
-        frame_free( frame );
-    }
-}
-
-
-/*
- * call_action_rule() - Look up the __ACTION_RULE__ variable on the given
- * target, and if non-empty, invoke the rule it names, passing the given info,
- * timing_info, executed command and command output.
- */
-
-static void call_action_rule
-(
-    TARGET      * target,
-    int           status,
-    timing_info * time,
-    char        * executed_command,
-    char        * command_output
-)
-{
-    LIST * action_rule;
-
-    pushsettings( target->settings );
-    action_rule = var_get( "__ACTION_RULE__" );
-    popsettings( target->settings );
-
-    if ( action_rule )
-    {
-        /* rule action-rule (
-            args * :
-            target :
-            command status start end user system :
-            output ? ) */
-
-        /* Prepare the argument list. */
-        FRAME frame[ 1 ];
-        frame_init( frame );
-
-        /* args * :: $(__ACTION_RULE__[2-]) */
-        lol_add( frame->args, list_copy( L0, action_rule->next ) );
-
-        /* target :: the name of the target */
-        lol_add( frame->args, list_new( L0, target->name ) );
-
-        /* command status start end user system :: info about the action command */
-        lol_add( frame->args,
-            list_new( list_new( list_new( list_new( list_new( list_new( L0,
-                newstr( executed_command ) ),
-                outf_int( status ) ),
-                outf_time( time->start ) ),
-                outf_time( time->end ) ),
-                outf_double( time->user ) ),
-                outf_double( time->system ) ) );
-
-        /* output ? :: the output of the action command */
-        if ( command_output )
-            lol_add( frame->args, list_new( L0, newstr( command_output ) ) );
-        else
-            lol_add( frame->args, L0 );
-
-        /* Call the rule. */
-        evaluate_rule( action_rule->string, frame );
-
-        /* Clean up. */
-        frame_free( frame );
-    }
-}
-
-
-/*
- * make_closure() - internal function passed as a notification callback for when
- * commands finish getting executed by the OS.
- */
-
-static void make_closure
-(
-    void        * closure,
-    int           status,
-    timing_info * time,
-    char        * executed_command,
-    char        * command_output
-)
-{
-    TARGET * built = (TARGET *)closure;
-
-    call_timing_rule( built, time );
-    if ( DEBUG_EXECCMD )
-        printf( "%f sec system; %f sec user\n", time->system, time->user );
-
-    call_action_rule( built, status, time, executed_command, command_output );
-
-    push_state( &state_stack, built, NULL, T_STATE_MAKE1D )->status = status;
-}
-
-
-/*
- * make1d() - handle command execution completion and call back make1c().
- *
- * exec_cmd() has completed and now all we need to do is fiddle with the status
- * and call back to make1c() so it can run the next command scheduled for
- * building this target or close up the target's build process in case there are
- * no more commands scheduled for it. On interrupts, we bail heavily.
- */
-
-static void make1d( state * pState )
-{
-    TARGET * t      = pState->t;
-    CMD    * cmd    = (CMD *)t->cmds;
-    int      status = pState->status;
-
-    if ( t->flags & T_FLAG_FAIL_EXPECTED )
-    {
-        /* Invert execution result when FAIL_EXPECTED has been applied. */
-        switch ( status )
-        {
-            case EXEC_CMD_FAIL: status = EXEC_CMD_OK  ; break;
-            case EXEC_CMD_OK:   status = EXEC_CMD_FAIL; break;
-        }
-    }
-
-    if ( ( status == EXEC_CMD_FAIL ) &&
-         ( cmd->rule->actions->flags & RULE_IGNORE ) )
-        status = EXEC_CMD_OK;
-
-    /* On interrupt, set intr so _everything_ fails. */
-    if ( status == EXEC_CMD_INTR )
-        ++intr;
-
-    /* Print command text on failure. */
-    if ( ( status == EXEC_CMD_FAIL ) && DEBUG_MAKE )
-    {
-        if ( !DEBUG_EXEC )
-            printf( "%s\n", cmd->buf );
-
-        printf( "...failed %s ", cmd->rule->name );
-        list_print( lol_get( &cmd->args, 0 ) );
-        printf( "...\n" );
-    }
-
-    /* Treat failed commands as interrupts in case we were asked to stop the
-     * build in case of any errors.
-     */
-    if ( ( status == EXEC_CMD_FAIL ) && globs.quitquick )
-        ++intr;
-
-    /* If the command was interrupted or failed and the target is not
-     * "precious", remove the targets.
-     */
-    if (status != EXEC_CMD_OK) 
-    {
-        LIST * targets = lol_get( &cmd->args, 0 );
-        for ( ; targets; targets = list_next( targets ) )
-        {
-            int need_unlink = 1;
-            TARGET* t = bindtarget ( targets->string );
-            if (t->flags & T_FLAG_PRECIOUS)
-            {                
-                need_unlink = 0;
-            }
-            if (need_unlink && !unlink( targets->string ) )
-                printf( "...removing %s\n", targets->string );
-        }
-    }
-
-    /* Free this command and call make1c() to move onto the next one scheduled
-     * for building this same target.
-     */
-    t->status = status;
-    t->cmds = (char *)cmd_next( cmd );
-    cmd_free( cmd );
-    pState->curstate = T_STATE_MAKE1C;
-}
-
-
-/*
- * swap_settings() - replace the settings from the current module and target
- *                   with those from the new module and target
- */
-
-static void swap_settings
-(
-    module_t * * current_module,
-    TARGET   * * current_target,
-    module_t   * new_module,
-    TARGET     * new_target
-)
-{
-    if ( new_module == root_module() )
-        new_module = 0;
-
-    if ( ( new_target == *current_target ) && ( new_module == *current_module ) )
-        return;
-
-    if ( *current_target )
-        popsettings( (*current_target)->settings );
-
-    if ( new_module != *current_module )
-    {
-        if ( *current_module )
-            exit_module( *current_module );
-
-        *current_module = new_module;
-
-        if ( new_module )
-            enter_module( new_module );
-    }
-
-    *current_target = new_target;
-    if ( new_target )
-        pushsettings( new_target->settings );
-}
-
-
-/*
- * make1cmds() - turn ACTIONS into CMDs, grouping, splitting, etc.
- *
- * Essentially copies a chain of ACTIONs to a chain of CMDs, grouping
- * RULE_TOGETHER actions, splitting RULE_PIECEMEAL actions, and handling
- * RULE_NEWSRCS actions. The result is a chain of CMDs which can be expanded by
- * var_string() and executed using exec_cmd().
- */
-
-static CMD * make1cmds( TARGET * t )
-{
-    CMD      * cmds = 0;
-    LIST     * shell = 0;
-    module_t * settings_module = 0;
-    TARGET   * settings_target = 0;
-    ACTIONS  * a0;
-
-    /* Step through actions. Actions may be shared with other targets or grouped
-     * using RULE_TOGETHER, so actions already seen are skipped.
-     */
-    for ( a0 = t->actions ; a0; a0 = a0->next )
-    {
-        RULE         * rule = a0->action->rule;
-        rule_actions * actions = rule->actions;
-        SETTINGS     * boundvars;
-        LIST         * nt;
-        LIST         * ns;
-        ACTIONS      * a1;
-        int            start;
-        int            chunk;
-        int            length;
-
-        /* Only do rules with commands to execute. If this action has already
-         * been executed, use saved status.
-         */
-        if ( !actions || a0->action->running )
-            continue;
-
-        a0->action->running = 1;
-
-        /* Make LISTS of targets and sources. If `execute together` has been
-         * specified for this rule, tack on sources from each instance of this
-         * rule for this target.
-         */
-        nt = make1list( L0, a0->action->targets, 0 );
-        ns = make1list( L0, a0->action->sources, actions->flags );
-        if ( actions->flags & RULE_TOGETHER )
-            for ( a1 = a0->next; a1; a1 = a1->next )
-                if ( a1->action->rule == rule && !a1->action->running )
-                {
-                    ns = make1list( ns, a1->action->sources, actions->flags );
-                    a1->action->running = 1;
-                }
-
-        /* If doing only updated (or existing) sources, but none have been
-         * updated (or exist), skip this action.
-         */
-        if ( !ns && ( actions->flags & ( RULE_NEWSRCS | RULE_EXISTING ) ) )
-        {
-            list_free( nt );
-            continue;
-        }
-
-        swap_settings( &settings_module, &settings_target, rule->module, t );
-        if ( !shell )
-            shell = var_get( "JAMSHELL" );  /* shell is per-target */
-
-        /* If we had 'actions xxx bind vars' we bind the vars now. */
-        boundvars = make1settings( actions->bindlist );
-        pushsettings( boundvars );
-
-        /*
-         * Build command, starting with all source args.
-         *
-         * If cmd_new returns 0, it is because the resulting command length is
-         * > MAXLINE. In this case, we will slowly reduce the number of source
-         * arguments presented until it does fit. This only applies to actions
-         * that allow PIECEMEAL commands.
-         *
-         * While reducing slowly takes a bit of compute time to get things just
-         * right, it is worth it to get as close to MAXLINE as possible, because
-         * launching the commands we are executing is likely to be much more
-         * compute intensive.
-         *
-         * Note we loop through at least once, for sourceless actions.
-         */
-
-        start = 0;
-        chunk = length = list_length( ns );
-
-        do
-        {
-            /* Build cmd: cmd_new consumes its lists. */
-            CMD * cmd = cmd_new( rule,
-                list_copy( L0, nt ),
-                list_sublist( ns, start, chunk ),
-                list_copy( L0, shell ) );
-
-            if ( cmd )
-            {
-                /* It fit: chain it up. */
-                if ( !cmds ) cmds = cmd;
-                else cmds->tail->next = cmd;
-                cmds->tail = cmd;
-                start += chunk;
-            }
-            else if ( ( actions->flags & RULE_PIECEMEAL ) && ( chunk > 1 ) )
-            {
-                /* Reduce chunk size slowly. */
-                chunk = chunk * 9 / 10;
-            }
-            else
-            {
-                /* Too long and not splittable. */
-                printf( "%s actions too long (max %d):\n", rule->name, MAXLINE
-                    );
-
-                /* Tell the user what didn't fit. */
-                cmd = cmd_new( rule, list_copy( L0, nt ),
-                    list_sublist( ns, start, chunk ),
-                    list_new( L0, newstr( "%" ) ) );
-                fputs( cmd->buf, stdout );
-                exit( EXITBAD );
-            }
-        }
-        while ( start < length );
-
-        /* These were always copied when used. */
-        list_free( nt );
-        list_free( ns );
-
-        /* Free the variables whose values were bound by 'actions xxx bind
-         * vars'.
-         */
-        popsettings( boundvars );
-        freesettings( boundvars );
-    }
-
-    swap_settings( &settings_module, &settings_target, 0, 0 );
-    return cmds;
-}
-
-
-/*
- * make1list() - turn a list of targets into a LIST, for $(<) and $(>).
- */
-
-static LIST * make1list( LIST * l, TARGETS * targets, int flags )
-{
-    for ( ; targets; targets = targets->next )
-    {
-        TARGET * t = targets->target;
-
-        if ( t->binding == T_BIND_UNBOUND )
-            make1bind( t );
-
-        if ( ( flags & RULE_EXISTING ) && ( flags & RULE_NEWSRCS ) )
-        {
-            if ( ( t->binding != T_BIND_EXISTS ) && ( t->fate <= T_FATE_STABLE ) )
-                continue;
-        }
-        else
-        {
-            if ( ( flags & RULE_EXISTING ) && ( t->binding != T_BIND_EXISTS ) )
-                continue;
-
-            if ( ( flags & RULE_NEWSRCS ) && ( t->fate <= T_FATE_STABLE ) )
-                continue;
-        }
-
-        /* Prohibit duplicates for RULE_TOGETHER. */
-        if ( flags & RULE_TOGETHER )
-        {
-            LIST * m;
-            for ( m = l; m; m = m->next )
-                if ( !strcmp( m->string, t->boundname ) )
-                    break;
-            if ( m )
-                continue;
-        }
-
-        /* Build new list. */
-        l = list_new( l, copystr( t->boundname ) );
-    }
-
-    return l;
-}
-
-
-/*
- * make1settings() - for vars that get bound values, build up replacement lists.
- */
-
-static SETTINGS * make1settings( LIST * vars )
-{
-    SETTINGS * settings = 0;
-
-    for ( ; vars; vars = list_next( vars ) )
-    {
-        LIST * l = var_get( vars->string );
-        LIST * nl = 0;
-
-        for ( ; l; l = list_next( l ) )
-        {
-            TARGET * t = bindtarget( l->string );
-
-            /* Make sure the target is bound. */
-            if ( t->binding == T_BIND_UNBOUND )
-                make1bind( t );
-
-            /* Build a new list. */
-            nl = list_new( nl, copystr( t->boundname ) );
-        }
-
-        /* Add to settings chain. */
-        settings = addsettings( settings, VAR_SET, vars->string, nl );
-    }
-
-    return settings;
-}
-
-
-/*
- * make1bind() - bind targets that were not bound during dependency analysis
- *
- * Spot the kludge! If a target is not in the dependency tree, it did not get
- * bound by make0(), so we have to do it here. Ugly.
- */
-
-static void make1bind( TARGET * t )
-{
-    if ( t->flags & T_FLAG_NOTFILE )
-        return;
-
-    pushsettings( t->settings );
-    t->boundname = search( t->name, &t->time, 0, ( t->flags & T_FLAG_ISFILE ) );
-    t->binding = t->time ? T_BIND_EXISTS : T_BIND_MISSING;
-    popsettings( t->settings );
-}
diff --git a/jam-files/engine/md5.c b/jam-files/engine/md5.c
deleted file mode 100644
index c35d96c5..00000000
--- a/jam-files/engine/md5.c
+++ /dev/null
@@ -1,381 +0,0 @@
-/*
-  Copyright (C) 1999, 2000, 2002 Aladdin Enterprises.  All rights reserved.
-
-  This software is provided 'as-is', without any express or implied
-  warranty.  In no event will the authors be held liable for any damages
-  arising from the use of this software.
-
-  Permission is granted to anyone to use this software for any purpose,
-  including commercial applications, and to alter it and redistribute it
-  freely, subject to the following restrictions:
-
-  1. The origin of this software must not be misrepresented; you must not
-     claim that you wrote the original software. If you use this software
-     in a product, an acknowledgment in the product documentation would be
-     appreciated but is not required.
-  2. Altered source versions must be plainly marked as such, and must not be
-     misrepresented as being the original software.
-  3. This notice may not be removed or altered from any source distribution.
-
-  L. Peter Deutsch
-  ghost@aladdin.com
-
- */
-/* $Id: md5.c,v 1.6 2002/04/13 19:20:28 lpd Exp $ */
-/*
-  Independent implementation of MD5 (RFC 1321).
-
-  This code implements the MD5 Algorithm defined in RFC 1321, whose
-  text is available at
-	http://www.ietf.org/rfc/rfc1321.txt
-  The code is derived from the text of the RFC, including the test suite
-  (section A.5) but excluding the rest of Appendix A.  It does not include
-  any code or documentation that is identified in the RFC as being
-  copyrighted.
-
-  The original and principal author of md5.c is L. Peter Deutsch
-  <ghost@aladdin.com>.  Other authors are noted in the change history
-  that follows (in reverse chronological order):
-
-  2002-04-13 lpd Clarified derivation from RFC 1321; now handles byte order
-	either statically or dynamically; added missing #include <string.h>
-	in library.
-  2002-03-11 lpd Corrected argument list for main(), and added int return
-	type, in test program and T value program.
-  2002-02-21 lpd Added missing #include <stdio.h> in test program.
-  2000-07-03 lpd Patched to eliminate warnings about "constant is
-	unsigned in ANSI C, signed in traditional"; made test program
-	self-checking.
-  1999-11-04 lpd Edited comments slightly for automatic TOC extraction.
-  1999-10-18 lpd Fixed typo in header comment (ansi2knr rather than md5).
-  1999-05-03 lpd Original version.
- */
-
-#include "md5.h"
-#include <string.h>
-
-#undef BYTE_ORDER	/* 1 = big-endian, -1 = little-endian, 0 = unknown */
-#ifdef ARCH_IS_BIG_ENDIAN
-#  define BYTE_ORDER (ARCH_IS_BIG_ENDIAN ? 1 : -1)
-#else
-#  define BYTE_ORDER 0
-#endif
-
-#define T_MASK ((md5_word_t)~0)
-#define T1 /* 0xd76aa478 */ (T_MASK ^ 0x28955b87)
-#define T2 /* 0xe8c7b756 */ (T_MASK ^ 0x173848a9)
-#define T3    0x242070db
-#define T4 /* 0xc1bdceee */ (T_MASK ^ 0x3e423111)
-#define T5 /* 0xf57c0faf */ (T_MASK ^ 0x0a83f050)
-#define T6    0x4787c62a
-#define T7 /* 0xa8304613 */ (T_MASK ^ 0x57cfb9ec)
-#define T8 /* 0xfd469501 */ (T_MASK ^ 0x02b96afe)
-#define T9    0x698098d8
-#define T10 /* 0x8b44f7af */ (T_MASK ^ 0x74bb0850)
-#define T11 /* 0xffff5bb1 */ (T_MASK ^ 0x0000a44e)
-#define T12 /* 0x895cd7be */ (T_MASK ^ 0x76a32841)
-#define T13    0x6b901122
-#define T14 /* 0xfd987193 */ (T_MASK ^ 0x02678e6c)
-#define T15 /* 0xa679438e */ (T_MASK ^ 0x5986bc71)
-#define T16    0x49b40821
-#define T17 /* 0xf61e2562 */ (T_MASK ^ 0x09e1da9d)
-#define T18 /* 0xc040b340 */ (T_MASK ^ 0x3fbf4cbf)
-#define T19    0x265e5a51
-#define T20 /* 0xe9b6c7aa */ (T_MASK ^ 0x16493855)
-#define T21 /* 0xd62f105d */ (T_MASK ^ 0x29d0efa2)
-#define T22    0x02441453
-#define T23 /* 0xd8a1e681 */ (T_MASK ^ 0x275e197e)
-#define T24 /* 0xe7d3fbc8 */ (T_MASK ^ 0x182c0437)
-#define T25    0x21e1cde6
-#define T26 /* 0xc33707d6 */ (T_MASK ^ 0x3cc8f829)
-#define T27 /* 0xf4d50d87 */ (T_MASK ^ 0x0b2af278)
-#define T28    0x455a14ed
-#define T29 /* 0xa9e3e905 */ (T_MASK ^ 0x561c16fa)
-#define T30 /* 0xfcefa3f8 */ (T_MASK ^ 0x03105c07)
-#define T31    0x676f02d9
-#define T32 /* 0x8d2a4c8a */ (T_MASK ^ 0x72d5b375)
-#define T33 /* 0xfffa3942 */ (T_MASK ^ 0x0005c6bd)
-#define T34 /* 0x8771f681 */ (T_MASK ^ 0x788e097e)
-#define T35    0x6d9d6122
-#define T36 /* 0xfde5380c */ (T_MASK ^ 0x021ac7f3)
-#define T37 /* 0xa4beea44 */ (T_MASK ^ 0x5b4115bb)
-#define T38    0x4bdecfa9
-#define T39 /* 0xf6bb4b60 */ (T_MASK ^ 0x0944b49f)
-#define T40 /* 0xbebfbc70 */ (T_MASK ^ 0x4140438f)
-#define T41    0x289b7ec6
-#define T42 /* 0xeaa127fa */ (T_MASK ^ 0x155ed805)
-#define T43 /* 0xd4ef3085 */ (T_MASK ^ 0x2b10cf7a)
-#define T44    0x04881d05
-#define T45 /* 0xd9d4d039 */ (T_MASK ^ 0x262b2fc6)
-#define T46 /* 0xe6db99e5 */ (T_MASK ^ 0x1924661a)
-#define T47    0x1fa27cf8
-#define T48 /* 0xc4ac5665 */ (T_MASK ^ 0x3b53a99a)
-#define T49 /* 0xf4292244 */ (T_MASK ^ 0x0bd6ddbb)
-#define T50    0x432aff97
-#define T51 /* 0xab9423a7 */ (T_MASK ^ 0x546bdc58)
-#define T52 /* 0xfc93a039 */ (T_MASK ^ 0x036c5fc6)
-#define T53    0x655b59c3
-#define T54 /* 0x8f0ccc92 */ (T_MASK ^ 0x70f3336d)
-#define T55 /* 0xffeff47d */ (T_MASK ^ 0x00100b82)
-#define T56 /* 0x85845dd1 */ (T_MASK ^ 0x7a7ba22e)
-#define T57    0x6fa87e4f
-#define T58 /* 0xfe2ce6e0 */ (T_MASK ^ 0x01d3191f)
-#define T59 /* 0xa3014314 */ (T_MASK ^ 0x5cfebceb)
-#define T60    0x4e0811a1
-#define T61 /* 0xf7537e82 */ (T_MASK ^ 0x08ac817d)
-#define T62 /* 0xbd3af235 */ (T_MASK ^ 0x42c50dca)
-#define T63    0x2ad7d2bb
-#define T64 /* 0xeb86d391 */ (T_MASK ^ 0x14792c6e)
-
-
-static void
-md5_process(md5_state_t *pms, const md5_byte_t *data /*[64]*/)
-{
-    md5_word_t
-	a = pms->abcd[0], b = pms->abcd[1],
-	c = pms->abcd[2], d = pms->abcd[3];
-    md5_word_t t;
-#if BYTE_ORDER > 0
-    /* Define storage only for big-endian CPUs. */
-    md5_word_t X[16];
-#else
-    /* Define storage for little-endian or both types of CPUs. */
-    md5_word_t xbuf[16];
-    const md5_word_t *X;
-#endif
-
-    {
-#if BYTE_ORDER == 0
-	/*
-	 * Determine dynamically whether this is a big-endian or
-	 * little-endian machine, since we can use a more efficient
-	 * algorithm on the latter.
-	 */
-	static const int w = 1;
-
-	if (*((const md5_byte_t *)&w)) /* dynamic little-endian */
-#endif
-#if BYTE_ORDER <= 0		/* little-endian */
-	{
-	    /*
-	     * On little-endian machines, we can process properly aligned
-	     * data without copying it.
-	     */
-	    if (!((data - (const md5_byte_t *)0) & 3)) {
-		/* data are properly aligned */
-		X = (const md5_word_t *)data;
-	    } else {
-		/* not aligned */
-		memcpy(xbuf, data, 64);
-		X = xbuf;
-	    }
-	}
-#endif
-#if BYTE_ORDER == 0
-	else			/* dynamic big-endian */
-#endif
-#if BYTE_ORDER >= 0		/* big-endian */
-	{
-	    /*
-	     * On big-endian machines, we must arrange the bytes in the
-	     * right order.
-	     */
-	    const md5_byte_t *xp = data;
-	    int i;
-
-#  if BYTE_ORDER == 0
-	    X = xbuf;		/* (dynamic only) */
-#  else
-#    define xbuf X		/* (static only) */
-#  endif
-	    for (i = 0; i < 16; ++i, xp += 4)
-		xbuf[i] = xp[0] + (xp[1] << 8) + (xp[2] << 16) + (xp[3] << 24);
-	}
-#endif
-    }
-
-#define ROTATE_LEFT(x, n) (((x) << (n)) | ((x) >> (32 - (n))))
-
-    /* Round 1. */
-    /* Let [abcd k s i] denote the operation
-       a = b + ((a + F(b,c,d) + X[k] + T[i]) <<< s). */
-#define F(x, y, z) (((x) & (y)) | (~(x) & (z)))
-#define SET(a, b, c, d, k, s, Ti)\
-  t = a + F(b,c,d) + X[k] + Ti;\
-  a = ROTATE_LEFT(t, s) + b
-    /* Do the following 16 operations. */
-    SET(a, b, c, d,  0,  7,  T1);
-    SET(d, a, b, c,  1, 12,  T2);
-    SET(c, d, a, b,  2, 17,  T3);
-    SET(b, c, d, a,  3, 22,  T4);
-    SET(a, b, c, d,  4,  7,  T5);
-    SET(d, a, b, c,  5, 12,  T6);
-    SET(c, d, a, b,  6, 17,  T7);
-    SET(b, c, d, a,  7, 22,  T8);
-    SET(a, b, c, d,  8,  7,  T9);
-    SET(d, a, b, c,  9, 12, T10);
-    SET(c, d, a, b, 10, 17, T11);
-    SET(b, c, d, a, 11, 22, T12);
-    SET(a, b, c, d, 12,  7, T13);
-    SET(d, a, b, c, 13, 12, T14);
-    SET(c, d, a, b, 14, 17, T15);
-    SET(b, c, d, a, 15, 22, T16);
-#undef SET
-
-     /* Round 2. */
-     /* Let [abcd k s i] denote the operation
-          a = b + ((a + G(b,c,d) + X[k] + T[i]) <<< s). */
-#define G(x, y, z) (((x) & (z)) | ((y) & ~(z)))
-#define SET(a, b, c, d, k, s, Ti)\
-  t = a + G(b,c,d) + X[k] + Ti;\
-  a = ROTATE_LEFT(t, s) + b
-     /* Do the following 16 operations. */
-    SET(a, b, c, d,  1,  5, T17);
-    SET(d, a, b, c,  6,  9, T18);
-    SET(c, d, a, b, 11, 14, T19);
-    SET(b, c, d, a,  0, 20, T20);
-    SET(a, b, c, d,  5,  5, T21);
-    SET(d, a, b, c, 10,  9, T22);
-    SET(c, d, a, b, 15, 14, T23);
-    SET(b, c, d, a,  4, 20, T24);
-    SET(a, b, c, d,  9,  5, T25);
-    SET(d, a, b, c, 14,  9, T26);
-    SET(c, d, a, b,  3, 14, T27);
-    SET(b, c, d, a,  8, 20, T28);
-    SET(a, b, c, d, 13,  5, T29);
-    SET(d, a, b, c,  2,  9, T30);
-    SET(c, d, a, b,  7, 14, T31);
-    SET(b, c, d, a, 12, 20, T32);
-#undef SET
-
-     /* Round 3. */
-     /* Let [abcd k s t] denote the operation
-          a = b + ((a + H(b,c,d) + X[k] + T[i]) <<< s). */
-#define H(x, y, z) ((x) ^ (y) ^ (z))
-#define SET(a, b, c, d, k, s, Ti)\
-  t = a + H(b,c,d) + X[k] + Ti;\
-  a = ROTATE_LEFT(t, s) + b
-     /* Do the following 16 operations. */
-    SET(a, b, c, d,  5,  4, T33);
-    SET(d, a, b, c,  8, 11, T34);
-    SET(c, d, a, b, 11, 16, T35);
-    SET(b, c, d, a, 14, 23, T36);
-    SET(a, b, c, d,  1,  4, T37);
-    SET(d, a, b, c,  4, 11, T38);
-    SET(c, d, a, b,  7, 16, T39);
-    SET(b, c, d, a, 10, 23, T40);
-    SET(a, b, c, d, 13,  4, T41);
-    SET(d, a, b, c,  0, 11, T42);
-    SET(c, d, a, b,  3, 16, T43);
-    SET(b, c, d, a,  6, 23, T44);
-    SET(a, b, c, d,  9,  4, T45);
-    SET(d, a, b, c, 12, 11, T46);
-    SET(c, d, a, b, 15, 16, T47);
-    SET(b, c, d, a,  2, 23, T48);
-#undef SET
-
-     /* Round 4. */
-     /* Let [abcd k s t] denote the operation
-          a = b + ((a + I(b,c,d) + X[k] + T[i]) <<< s). */
-#define I(x, y, z) ((y) ^ ((x) | ~(z)))
-#define SET(a, b, c, d, k, s, Ti)\
-  t = a + I(b,c,d) + X[k] + Ti;\
-  a = ROTATE_LEFT(t, s) + b
-     /* Do the following 16 operations. */
-    SET(a, b, c, d,  0,  6, T49);
-    SET(d, a, b, c,  7, 10, T50);
-    SET(c, d, a, b, 14, 15, T51);
-    SET(b, c, d, a,  5, 21, T52);
-    SET(a, b, c, d, 12,  6, T53);
-    SET(d, a, b, c,  3, 10, T54);
-    SET(c, d, a, b, 10, 15, T55);
-    SET(b, c, d, a,  1, 21, T56);
-    SET(a, b, c, d,  8,  6, T57);
-    SET(d, a, b, c, 15, 10, T58);
-    SET(c, d, a, b,  6, 15, T59);
-    SET(b, c, d, a, 13, 21, T60);
-    SET(a, b, c, d,  4,  6, T61);
-    SET(d, a, b, c, 11, 10, T62);
-    SET(c, d, a, b,  2, 15, T63);
-    SET(b, c, d, a,  9, 21, T64);
-#undef SET
-
-     /* Then perform the following additions. (That is increment each
-        of the four registers by the value it had before this block
-        was started.) */
-    pms->abcd[0] += a;
-    pms->abcd[1] += b;
-    pms->abcd[2] += c;
-    pms->abcd[3] += d;
-}
-
-void
-md5_init(md5_state_t *pms)
-{
-    pms->count[0] = pms->count[1] = 0;
-    pms->abcd[0] = 0x67452301;
-    pms->abcd[1] = /*0xefcdab89*/ T_MASK ^ 0x10325476;
-    pms->abcd[2] = /*0x98badcfe*/ T_MASK ^ 0x67452301;
-    pms->abcd[3] = 0x10325476;
-}
-
-void
-md5_append(md5_state_t *pms, const md5_byte_t *data, int nbytes)
-{
-    const md5_byte_t *p = data;
-    int left = nbytes;
-    int offset = (pms->count[0] >> 3) & 63;
-    md5_word_t nbits = (md5_word_t)(nbytes << 3);
-
-    if (nbytes <= 0)
-	return;
-
-    /* Update the message length. */
-    pms->count[1] += nbytes >> 29;
-    pms->count[0] += nbits;
-    if (pms->count[0] < nbits)
-	pms->count[1]++;
-
-    /* Process an initial partial block. */
-    if (offset) {
-	int copy = (offset + nbytes > 64 ? 64 - offset : nbytes);
-
-	memcpy(pms->buf + offset, p, copy);
-	if (offset + copy < 64)
-	    return;
-	p += copy;
-	left -= copy;
-	md5_process(pms, pms->buf);
-    }
-
-    /* Process full blocks. */
-    for (; left >= 64; p += 64, left -= 64)
-	md5_process(pms, p);
-
-    /* Process a final partial block. */
-    if (left)
-	memcpy(pms->buf, p, left);
-}
-
-void
-md5_finish(md5_state_t *pms, md5_byte_t digest[16])
-{
-    static const md5_byte_t pad[64] = {
-	0x80, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-	0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-	0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-	0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
-    };
-    md5_byte_t data[8];
-    int i;
-
-    /* Save the length before padding. */
-    for (i = 0; i < 8; ++i)
-	data[i] = (md5_byte_t)(pms->count[i >> 2] >> ((i & 3) << 3));
-    /* Pad to 56 bytes mod 64. */
-    md5_append(pms, pad, ((55 - (pms->count[0] >> 3)) & 63) + 1);
-    /* Append the length. */
-    md5_append(pms, data, 8);
-    for (i = 0; i < 16; ++i)
-	digest[i] = (md5_byte_t)(pms->abcd[i >> 2] >> ((i & 3) << 3));
-}
diff --git a/jam-files/engine/md5.h b/jam-files/engine/md5.h
deleted file mode 100644
index 698c995d..00000000
--- a/jam-files/engine/md5.h
+++ /dev/null
@@ -1,91 +0,0 @@
-/*
-  Copyright (C) 1999, 2002 Aladdin Enterprises.  All rights reserved.
-
-  This software is provided 'as-is', without any express or implied
-  warranty.  In no event will the authors be held liable for any damages
-  arising from the use of this software.
-
-  Permission is granted to anyone to use this software for any purpose,
-  including commercial applications, and to alter it and redistribute it
-  freely, subject to the following restrictions:
-
-  1. The origin of this software must not be misrepresented; you must not
-     claim that you wrote the original software. If you use this software
-     in a product, an acknowledgment in the product documentation would be
-     appreciated but is not required.
-  2. Altered source versions must be plainly marked as such, and must not be
-     misrepresented as being the original software.
-  3. This notice may not be removed or altered from any source distribution.
-
-  L. Peter Deutsch
-  ghost@aladdin.com
-
- */
-/* $Id: md5.h,v 1.4 2002/04/13 19:20:28 lpd Exp $ */
-/*
-  Independent implementation of MD5 (RFC 1321).
-
-  This code implements the MD5 Algorithm defined in RFC 1321, whose
-  text is available at
-	http://www.ietf.org/rfc/rfc1321.txt
-  The code is derived from the text of the RFC, including the test suite
-  (section A.5) but excluding the rest of Appendix A.  It does not include
-  any code or documentation that is identified in the RFC as being
-  copyrighted.
-
-  The original and principal author of md5.h is L. Peter Deutsch
-  <ghost@aladdin.com>.  Other authors are noted in the change history
-  that follows (in reverse chronological order):
-
-  2002-04-13 lpd Removed support for non-ANSI compilers; removed
-	references to Ghostscript; clarified derivation from RFC 1321;
-	now handles byte order either statically or dynamically.
-  1999-11-04 lpd Edited comments slightly for automatic TOC extraction.
-  1999-10-18 lpd Fixed typo in header comment (ansi2knr rather than md5);
-	added conditionalization for C++ compilation from Martin
-	Purschke <purschke@bnl.gov>.
-  1999-05-03 lpd Original version.
- */
-
-#ifndef md5_INCLUDED
-#  define md5_INCLUDED
-
-/*
- * This package supports both compile-time and run-time determination of CPU
- * byte order.  If ARCH_IS_BIG_ENDIAN is defined as 0, the code will be
- * compiled to run only on little-endian CPUs; if ARCH_IS_BIG_ENDIAN is
- * defined as non-zero, the code will be compiled to run only on big-endian
- * CPUs; if ARCH_IS_BIG_ENDIAN is not defined, the code will be compiled to
- * run on either big- or little-endian CPUs, but will run slightly less
- * efficiently on either one than if ARCH_IS_BIG_ENDIAN is defined.
- */
-
-typedef unsigned char md5_byte_t; /* 8-bit byte */
-typedef unsigned int md5_word_t; /* 32-bit word */
-
-/* Define the state of the MD5 Algorithm. */
-typedef struct md5_state_s {
-    md5_word_t count[2];	/* message length in bits, lsw first */
-    md5_word_t abcd[4];		/* digest buffer */
-    md5_byte_t buf[64];		/* accumulate block */
-} md5_state_t;
-
-#ifdef __cplusplus
-extern "C" 
-{
-#endif
-
-/* Initialize the algorithm. */
-void md5_init(md5_state_t *pms);
-
-/* Append a string to the message. */
-void md5_append(md5_state_t *pms, const md5_byte_t *data, int nbytes);
-
-/* Finish the message and return the digest. */
-void md5_finish(md5_state_t *pms, md5_byte_t digest[16]);
-
-#ifdef __cplusplus
-}  /* end extern "C" */
-#endif
-
-#endif /* md5_INCLUDED */
diff --git a/jam-files/engine/mem.c b/jam-files/engine/mem.c
deleted file mode 100644
index 6a11fb38..00000000
--- a/jam-files/engine/mem.c
+++ /dev/null
@@ -1,75 +0,0 @@
-/*
-Copyright Rene Rivera 2006.
-Distributed under the Boost Software License, Version 1.0.
-(See accompanying file LICENSE_1_0.txt or copy at
-http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-#include "jam.h"
-
-#ifdef OPT_BOEHM_GC
-
-    /* Compile the Boehm GC as one big chunk of code. It's much easier
-    this way, than trying to make radical changes to the bjam build
-    scripts. */
-
-    #define ATOMIC_UNCOLLECTABLE
-    #define NO_EXECUTE_PERMISSION
-    #define ALL_INTERIOR_POINTERS
-
-    #define LARGE_CONFIG
-    /*
-    #define NO_SIGNALS
-    #define SILENT
-    */
-    #ifndef GC_DEBUG
-    #define NO_DEBUGGING
-    #endif
-
-    #ifdef __GLIBC__
-    #define __USE_GNU
-    #endif
-
-    #include "boehm_gc/reclaim.c"
-    #include "boehm_gc/allchblk.c"
-    #include "boehm_gc/misc.c"
-    #include "boehm_gc/alloc.c"
-    #include "boehm_gc/mach_dep.c"
-    #include "boehm_gc/os_dep.c"
-    #include "boehm_gc/mark_rts.c"
-    #include "boehm_gc/headers.c"
-    #include "boehm_gc/mark.c"
-    #include "boehm_gc/obj_map.c"
-    #include "boehm_gc/pcr_interface.c"
-    #include "boehm_gc/blacklst.c"
-    #include "boehm_gc/new_hblk.c"
-    #include "boehm_gc/real_malloc.c"
-    #include "boehm_gc/dyn_load.c"
-    #include "boehm_gc/dbg_mlc.c"
-    #include "boehm_gc/malloc.c"
-    #include "boehm_gc/stubborn.c"
-    #include "boehm_gc/checksums.c"
-    #include "boehm_gc/pthread_support.c"
-    #include "boehm_gc/pthread_stop_world.c"
-    #include "boehm_gc/darwin_stop_world.c"
-    #include "boehm_gc/typd_mlc.c"
-    #include "boehm_gc/ptr_chck.c"
-    #include "boehm_gc/mallocx.c"
-    #include "boehm_gc/gcj_mlc.c"
-    #include "boehm_gc/specific.c"
-    #include "boehm_gc/gc_dlopen.c"
-    #include "boehm_gc/backgraph.c"
-    #include "boehm_gc/win32_threads.c"
-
-    /* Needs to be last. */
-    #include "boehm_gc/finalize.c"
-
-#elif defined(OPT_DUMA)
-
-    #ifdef OS_NT
-        #define WIN32
-    #endif
-    #include "duma/duma.c"
-    #include "duma/print.c"
-
-#endif
diff --git a/jam-files/engine/mem.h b/jam-files/engine/mem.h
deleted file mode 100644
index 71b2fb4b..00000000
--- a/jam-files/engine/mem.h
+++ /dev/null
@@ -1,134 +0,0 @@
-/*
-Copyright Rene Rivera 2006.
-Distributed under the Boost Software License, Version 1.0.
-(See accompanying file LICENSE_1_0.txt or copy at
-http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-#ifndef BJAM_MEM_H
-#define BJAM_MEM_H
-
-
-#ifdef OPT_BOEHM_GC
-
-    /* Use Boehm GC memory allocator. */
-    #include <gc.h>
-    #define bjam_malloc_x(s) memset(GC_malloc(s),0,s)
-    #define bjam_malloc_atomic_x(s) memset(GC_malloc_atomic(s),0,s)
-    #define bjam_calloc_x(n,s) memset(GC_malloc((n)*(s)),0,(n)*(s))
-    #define bjam_calloc_atomic_x(n,s) memset(GC_malloc_atomic((n)*(s)),0,(n)*(s))
-    #define bjam_realloc_x(p,s) GC_realloc(p,s)
-    #define bjam_free_x(p) GC_free(p)
-    #define bjam_mem_init_x() GC_init(); GC_enable_incremental()
-
-    #define bjam_malloc_raw_x(s) malloc(s)
-    #define bjam_calloc_raw_x(n,s) calloc(n,s)
-    #define bjam_realloc_raw_x(p,s) realloc(p,s)
-    #define bjam_free_raw_x(p) free(p)
-
-    #ifndef BJAM_NEWSTR_NO_ALLOCATE
-    #define BJAM_NEWSTR_NO_ALLOCATE
-    #endif
-
-#elif defined(OPT_DUMA)
-
-    /* Use Duma memory debugging library. */
-    #include <stdlib.h>
-    #define _DUMA_CONFIG_H_
-    #define DUMA_NO_GLOBAL_MALLOC_FREE
-    #define DUMA_EXPLICIT_INIT
-    #define DUMA_NO_THREAD_SAFETY
-    #define DUMA_NO_CPP_SUPPORT
-    /* #define DUMA_NO_LEAKDETECTION */
-    /* #define DUMA_USE_FRAMENO */
-    /* #define DUMA_PREFER_ATEXIT */
-    /* #define DUMA_OLD_DEL_MACRO */
-    /* #define DUMA_NO_HANG_MSG */
-    #define DUMA_PAGE_SIZE 4096
-    #define DUMA_MIN_ALIGNMENT 1
-    /* #define DUMA_GNU_INIT_ATTR 0 */
-    typedef unsigned int DUMA_ADDR;
-    typedef unsigned int DUMA_SIZE;
-    #include <duma.h>
-    #define bjam_malloc_x(s) malloc(s)
-    #define bjam_calloc_x(n,s) calloc(n,s)
-    #define bjam_realloc_x(p,s) realloc(p,s)
-    #define bjam_free_x(p) free(p)
-
-    #ifndef BJAM_NEWSTR_NO_ALLOCATE
-    #define BJAM_NEWSTR_NO_ALLOCATE
-    #endif
-
-#else
-
-    /* Standard C memory allocation. */
-    #define bjam_malloc_x(s) malloc(s)
-    #define bjam_calloc_x(n,s) calloc(n,s)
-    #define bjam_realloc_x(p,s) realloc(p,s)
-    #define bjam_free_x(p) free(p)
-
-#endif
-
-#ifndef bjam_malloc_atomic_x
-    #define bjam_malloc_atomic_x(s) bjam_malloc_x(s)
-#endif
-#ifndef bjam_calloc_atomic_x
-    #define bjam_calloc_atomic_x(n,s) bjam_calloc_x(n,s)
-#endif
-#ifndef bjam_mem_init_x
-    #define bjam_mem_init_x()
-#endif
-#ifndef bjam_mem_close_x
-    #define bjam_mem_close_x()
-#endif
-#ifndef bjam_malloc_raw_x
-    #define bjam_malloc_raw_x(s) bjam_malloc_x(s)
-#endif
-#ifndef bjam_calloc_raw_x
-    #define bjam_calloc_raw_x(n,s) bjam_calloc_x(n,s)
-#endif
-#ifndef bjam_realloc_raw_x
-    #define bjam_realloc_raw_x(p,s) bjam_realloc_x(p,s)
-#endif
-#ifndef bjam_free_raw_x
-    #define bjam_free_raw_x(p) bjam_free_x(p)
-#endif
-
-#ifdef OPT_DEBUG_PROFILE
-
-    /* Profile tracing of memory allocations. */
-    #define BJAM_MALLOC(s) (profile_memory(s), bjam_malloc_x(s))
-    #define BJAM_MALLOC_ATOMIC(s) (profile_memory(s), bjam_malloc_atomic_x(s))
-    #define BJAM_CALLOC(n,s) (profile_memory(n*s), bjam_calloc_x(n,s))
-    #define BJAM_CALLOC_ATOMIC(n,s) (profile_memory(n*s), bjam_calloc_atomic_x(n,s))
-    #define BJAM_REALLOC(p,s) (profile_memory(s), bjam_realloc_x(p,s))
-    #define BJAM_FREE(p) bjam_free_x(p)
-    #define BJAM_MEM_INIT() bjam_mem_init_x()
-    #define BJAM_MEM_CLOSE() bjam_mem_close_x()
-
-    #define BJAM_MALLOC_RAW(s) (profile_memory(s), bjam_malloc_raw_x(s))
-    #define BJAM_CALLOC_RAW(n,s) (profile_memory(n*s), bjam_calloc_raw_x(n,s))
-    #define BJAM_REALLOC_RAW(p,s) (profile_memory(s), bjam_realloc_raw_x(p,s))
-    #define BJAM_FREE_RAW(p) bjam_free_raw_x(p)
-
-#else
-
-    /* No mem tracing. */
-    #define BJAM_MALLOC(s) bjam_malloc_x(s)
-    #define BJAM_MALLOC_ATOMIC(s) bjam_malloc_atomic_x(s)
-    #define BJAM_CALLOC(n,s) bjam_calloc_x(n,s)
-    #define BJAM_CALLOC_ATOMIC(n,s) bjam_calloc_atomic_x(n,s)
-    #define BJAM_REALLOC(p,s) bjam_realloc_x(p,s)
-    #define BJAM_FREE(p) bjam_free_x(p)
-    #define BJAM_MEM_INIT() bjam_mem_init_x()
-    #define BJAM_MEM_CLOSE() bjam_mem_close_x()
-
-    #define BJAM_MALLOC_RAW(s) bjam_malloc_raw_x(s)
-    #define BJAM_CALLOC_RAW(n,s) bjam_calloc_raw_x(n,s)
-    #define BJAM_REALLOC_RAW(p,s) bjam_realloc_raw_x(p,s)
-    #define BJAM_FREE_RAW(p) bjam_free_raw_x(p)
-
-#endif
-
-
-#endif
diff --git a/jam-files/engine/mkjambase.c b/jam-files/engine/mkjambase.c
deleted file mode 100644
index cdf59982..00000000
--- a/jam-files/engine/mkjambase.c
+++ /dev/null
@@ -1,123 +0,0 @@
-/*
- * Copyright 1993, 1995 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*  This file is ALSO:
- *  Copyright 2001-2004 David Abrahams.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-
-/*
- * mkjambase.c - turn Jambase into a big C structure
- *
- * Usage: mkjambase jambase.c Jambase ...
- *
- * Results look like this:
- *
- *   char *jambase[] = {
- *   "...\n",
- *   ...
- *   0 };
- *
- * Handles \'s and "'s specially; knows to delete blank and comment lines.
- *
- */
-
-#include <stdio.h>
-#include <string.h>
-
-
-int main( int argc, char * * argv, char * * envp )
-{
-    char buf[ 1024 ];
-    FILE * fin;
-    FILE * fout;
-    char * p;
-    int doDotC = 0;
-
-    if ( argc < 3 )
-    {
-        fprintf( stderr, "usage: %s jambase.c Jambase ...\n", argv[ 0 ] );
-        return -1;
-    }
-
-    if ( !( fout = fopen( argv[1], "w" ) ) )
-    {
-        perror( argv[ 1 ] );
-        return -1;
-    }
-
-    /* If the file ends in .c generate a C source file. */
-    if ( ( p = strrchr( argv[1], '.' ) ) && !strcmp( p, ".c" ) )
-        doDotC++;
-
-    /* Now process the files. */
-
-    argc -= 2;
-    argv += 2;
-
-    if ( doDotC )
-    {
-        fprintf( fout, "/* Generated by mkjambase from Jambase */\n" );
-        fprintf( fout, "char *jambase[] = {\n" );
-    }
-
-    for ( ; argc--; ++argv )
-    {
-        if ( !( fin = fopen( *argv, "r" ) ) )
-        {
-            perror( *argv );
-            return -1;
-        }
-
-        if ( doDotC )
-            fprintf( fout, "/* %s */\n", *argv );
-        else
-            fprintf( fout, "### %s ###\n", *argv );
-
-        while ( fgets( buf, sizeof( buf ), fin ) )
-        {
-            if ( doDotC )
-            {
-                char * p = buf;
-
-                /* Strip leading whitespace. */
-                while ( ( *p == ' ' ) || ( *p == '\t' ) || ( *p == '\n' ) )
-                    ++p;
-
-                /* Drop comments and empty lines. */
-                if ( ( *p == '#' ) || !*p )
-                    continue;
-
-                /* Copy. */
-                putc( '"', fout );
-                for ( ; *p && ( *p != '\n' ); ++p )
-                    switch ( *p )
-                    {
-                        case '\\': putc( '\\', fout ); putc( '\\', fout ); break;
-                        case '"' : putc( '\\', fout ); putc( '"' , fout ); break;
-                        case '\r': break;
-                        default: putc( *p, fout ); break;
-                    }
-
-                fprintf( fout, "\\n\",\n" );
-            }
-            else
-            {
-                fprintf( fout, "%s", buf );
-            }
-        }
-
-        fclose( fin );
-    }
-
-    if ( doDotC )
-        fprintf( fout, "0 };\n" );
-
-    fclose( fout );
-
-    return 0;
-}
diff --git a/jam-files/engine/modules.c b/jam-files/engine/modules.c
deleted file mode 100644
index 72952594..00000000
--- a/jam-files/engine/modules.c
+++ /dev/null
@@ -1,168 +0,0 @@
-/*
- *  Copyright 2001-2004 David Abrahams.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-#include "jam.h"
-
-#include "modules.h"
-#include "string.h"
-#include "hash.h"
-#include "newstr.h"
-#include "lists.h"
-#include "parse.h"
-#include "rules.h"
-#include "variable.h"
-#include "strings.h"
-#include <assert.h>
-
-static struct hash * module_hash = 0;
-
-
-static char * new_module_str( module_t * m, char * suffix )
-{
-    char * result;
-    string s;
-    string_copy( &s, m->name );
-    string_append( &s, suffix );
-    result = newstr( s.value );
-    string_free( &s );
-    return result;
-}
-
-
-module_t * bindmodule( char * name )
-{
-    PROFILE_ENTER( BINDMODULE );
-
-    string s;
-    module_t m_;
-    module_t * m = &m_;
-
-    if ( !module_hash )
-        module_hash = hashinit( sizeof( module_t ), "modules" );
-
-    string_new( &s );
-    if ( name )
-    {
-        string_append( &s, name );
-        string_push_back( &s, '.' );
-    }
-
-    m->name = s.value;
-
-    if ( hashenter( module_hash, (HASHDATA * *)&m ) )
-    {
-        m->name = newstr( m->name );
-        m->variables = 0;
-        m->rules = 0;
-        m->imported_modules = 0;
-        m->class_module = 0;
-        m->native_rules = 0;
-        m->user_module = 0;
-    }
-    string_free( &s );
-
-    PROFILE_EXIT( BINDMODULE );
-
-    return m;
-}
-
-/*
- * demand_rules() - Get the module's "rules" hash on demand.
- */
-struct hash * demand_rules( module_t * m )
-{
-    if ( !m->rules )
-        m->rules = hashinit( sizeof( RULE ), new_module_str( m, "rules" ) );
-    return m->rules;
-}
-
-
-/*
- * delete_module() - wipe out the module's rules and variables.
- */
-
-static void delete_rule_( void * xrule, void * data )
-{
-    rule_free( (RULE *)xrule );
-}
-
-
-void delete_module( module_t * m )
-{
-    /* Clear out all the rules. */
-    if ( m->rules )
-    {
-        hashenumerate( m->rules, delete_rule_, (void *)0 );
-        hashdone( m->rules );
-        m->rules = 0;
-    }
-
-    if ( m->variables )
-    {
-        var_hash_swap( &m->variables );
-        var_done();
-        var_hash_swap( &m->variables );
-        m->variables = 0;
-    }
-}
-
-
-module_t * root_module()
-{
-    static module_t * root = 0;
-    if ( !root )
-        root = bindmodule( 0 );
-    return root;
-}
-
-void enter_module( module_t * m )
-{
-    var_hash_swap( &m->variables );
-}
-
-
-void exit_module( module_t * m )
-{
-    var_hash_swap( &m->variables );
-}
-
-
-void import_module( LIST * module_names, module_t * target_module )
-{
-    PROFILE_ENTER( IMPORT_MODULE );
-
-    struct hash * h;
-
-    if ( !target_module->imported_modules )
-        target_module->imported_modules = hashinit( sizeof( char * ), "imported" );
-    h = target_module->imported_modules;
-
-    for ( ; module_names; module_names = module_names->next )
-    {
-        char * s = module_names->string;
-        char * * ss = &s;
-        hashenter( h, (HASHDATA * *)&ss );
-    }
-
-    PROFILE_EXIT( IMPORT_MODULE );
-}
-
-
-static void add_module_name( void * r_, void * result_ )
-{
-    char * * r = (char * *)r_;
-    LIST * * result = (LIST * *)result_;
-
-    *result = list_new( *result, copystr( *r ) );
-}
-
-
-LIST * imported_modules( module_t * module )
-{
-    LIST * result = L0;
-    if ( module->imported_modules )
-        hashenumerate( module->imported_modules, add_module_name, &result );
-    return result;
-}
diff --git a/jam-files/engine/modules.h b/jam-files/engine/modules.h
deleted file mode 100644
index 60053a23..00000000
--- a/jam-files/engine/modules.h
+++ /dev/null
@@ -1,37 +0,0 @@
-/*
- *  Copyright 2001-2004 David Abrahams.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-#ifndef MODULES_DWA10182001_H
-# define MODULES_DWA10182001_H
-
-#include "lists.h"
-
-struct module_t
-{
-    char* name;
-    struct hash* rules;
-    struct hash* variables;
-    struct hash* imported_modules;
-    struct module_t* class_module;
-    struct hash* native_rules;
-    int user_module;
-};
-
-typedef struct module_t module_t ; /* MSVC debugger gets confused unless this is provided */
-
-module_t* bindmodule( char* name );
-module_t* root_module();
-void enter_module( module_t* );
-void exit_module( module_t* );
-void delete_module( module_t* );
-
-void import_module(LIST* module_names, module_t* target_module);
-LIST* imported_modules(module_t* module);
-
-struct hash* demand_rules( module_t* );
-
-
-#endif
-
diff --git a/jam-files/engine/modules/order.c b/jam-files/engine/modules/order.c
deleted file mode 100644
index d77943a7..00000000
--- a/jam-files/engine/modules/order.c
+++ /dev/null
@@ -1,144 +0,0 @@
-/* Copyright Vladimir Prus 2004. Distributed under the Boost */
-/* Software License, Version 1.0. (See accompanying */
-/* file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */
-
-#include "../native.h"
-#include "../lists.h"
-#include "../strings.h"
-#include "../newstr.h"
-#include "../variable.h"
-
-
-/* Use quite klugy approach: when we add order dependency from 'a' to 'b',
-   just append 'b' to of value of variable 'a'.
-*/
-LIST *add_pair( PARSE *parse, FRAME *frame )
-{
-    LIST* arg = lol_get( frame->args, 0 );    
-
-    var_set(arg->string, list_copy(0, arg->next), VAR_APPEND);
-
-    return L0;
-}
-
-/** Given a list and a value, returns position of that value in
-    the list, or -1 if not found.
-*/
-int list_index(LIST* list, const char* value)
-{
-    int result = 0;
-    for(; list; list = list->next, ++result) {
-        if (strcmp(list->string, value) == 0)
-            return result;
-    }
-    return -1;
-}
-
-enum colors { white, gray, black };
-
-/* Main routite of topological sort. Calls itself recursively on all
-   adjacent vertices which were not yet visited. After that, 'current_vertex'
-   is added to '*result_ptr'.
-*/
-void do_ts(int** graph, int current_vertex, int* colors, int** result_ptr)
-{
-    int i;
-
-    colors[current_vertex] = gray;
-    for(i = 0; graph[current_vertex][i] != -1; ++i) {
-        int adjacent_vertex = graph[current_vertex][i];
-
-        if (colors[adjacent_vertex] == white)
-            do_ts(graph, adjacent_vertex, colors, result_ptr);
-        /* The vertex is either black, in which case we don't have to do
-           anything, a gray, in which case we have a loop. If we have a loop,
-           it's not clear what useful diagnostic we can emit, so we emit
-           nothing.  */
-    }
-    colors[current_vertex] = black;
-    **result_ptr = current_vertex;    
-    (*result_ptr)++;
-}
-
-void topological_sort(int** graph, int num_vertices, int* result)
-{
-    int i;
-    int* colors = (int*)BJAM_CALLOC(num_vertices, sizeof(int));
-    for (i = 0; i < num_vertices; ++i)
-        colors[i] = white;
-
-    for(i = 0; i < num_vertices; ++i)
-        if (colors[i] == white)
-            do_ts(graph, i, colors, &result);
-
-    BJAM_FREE(colors);
-}
-
-LIST *order( PARSE *parse, FRAME *frame )
-{
-    LIST* arg = lol_get( frame->args, 0 );  
-    LIST* tmp;
-    LIST* result = 0;
-    int src;
-
-    /* We need to create a graph of order dependencies between
-       the passed objects. We assume that there are no duplicates
-       passed to 'add_pair'.
-    */
-    int length = list_length(arg);
-    int** graph = (int**)BJAM_CALLOC(length, sizeof(int*));
-    int* order = (int*)BJAM_MALLOC((length+1)*sizeof(int));
-   
-    for(tmp = arg, src = 0; tmp; tmp = tmp->next, ++src) {
-        /* For all object this one depend upon, add elements
-           to 'graph' */
-        LIST* dependencies = var_get(tmp->string);
-        int index = 0;
-
-        graph[src] = (int*)BJAM_CALLOC(list_length(dependencies)+1, sizeof(int));
-        for(; dependencies; dependencies = dependencies->next) {          
-            int dst = list_index(arg, dependencies->string);
-            if (dst != -1)
-                graph[src][index++] = dst;
-        }
-        graph[src][index] = -1;               
-    }
-
-    topological_sort(graph, length, order);
-
-    {
-        int index = length-1;
-        for(; index >= 0; --index) {
-            int i;
-            tmp = arg;
-            for (i = 0; i < order[index]; ++i, tmp = tmp->next);
-            result = list_new(result, tmp->string);
-        }
-    }
-
-    /* Clean up */
-    {
-        int i;
-        for(i = 0; i < length; ++i)
-            BJAM_FREE(graph[i]);
-        BJAM_FREE(graph);
-        BJAM_FREE(order);
-    }
-
-    return result;
-}
-
-void init_order()
-{
-    {
-        char* args[] = { "first", "second", 0 };
-        declare_native_rule("class@order", "add-pair", args, add_pair, 1);
-    }
-
-    {
-        char* args[] = { "objects", "*", 0 };
-        declare_native_rule("class@order", "order", args, order, 1);
-    }
-
-
-}
diff --git a/jam-files/engine/modules/path.c b/jam-files/engine/modules/path.c
deleted file mode 100644
index f5d09622..00000000
--- a/jam-files/engine/modules/path.c
+++ /dev/null
@@ -1,32 +0,0 @@
-/* Copyright Vladimir Prus 2003. Distributed under the Boost */
-/* Software License, Version 1.0. (See accompanying */
-/* file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */
-
-#include "../native.h"
-#include "../timestamp.h"
-#include "../newstr.h"
-
-LIST *path_exists( PARSE *parse, FRAME *frame )
-{
-    LIST* l = lol_get( frame->args, 0 );    
-
-    time_t time;
-    timestamp(l->string, &time);
-    if (time != 0)
-    {
-        return list_new(0, newstr("true"));
-    }
-    else
-    {
-        return L0;
-    }
-}
-
-void init_path()
-{
-    {
-        char* args[] = { "location", 0 };
-        declare_native_rule("path", "exists", args, path_exists, 1);
-    }
-
-}
diff --git a/jam-files/engine/modules/property-set.c b/jam-files/engine/modules/property-set.c
deleted file mode 100644
index 2b0fb5d9..00000000
--- a/jam-files/engine/modules/property-set.c
+++ /dev/null
@@ -1,110 +0,0 @@
-/* Copyright Vladimir Prus 2003. Distributed under the Boost */
-/* Software License, Version 1.0. (See accompanying */
-/* file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */
-
-#include "../native.h"
-#include "../timestamp.h"
-#include "../newstr.h"
-#include "../strings.h"
-#include "../lists.h"
-#include "../variable.h"
-#include "../compile.h"
-
-LIST* get_grist(char* f)
-{
-    char* end = strchr(f, '>');
-    string s[1];
-    LIST* result;
-
-    string_new(s);
-
-    string_append_range(s, f, end+1);
-    result = list_new(0, newstr(s->value));
-
-    string_free(s);
-    return result;
-}
-
-/*
-rule create ( raw-properties * )
-{
-    raw-properties = [ sequence.unique
-        [ sequence.insertion-sort $(raw-properties) ] ] ;
-
-    local key = $(raw-properties:J=-:E=) ;
-
-    if ! $(.ps.$(key))
-    {
-        .ps.$(key) = [ new property-set $(raw-properties) ] ;
-    }
-    return $(.ps.$(key)) ;
-}
-*/
-
-LIST *property_set_create( PARSE *parse, FRAME *frame )
-{
-    LIST* properties = lol_get( frame->args, 0 );
-    LIST* sorted = 0;
-#if 0
-    LIST* order_sensitive = 0;
-#endif
-    LIST* unique;
-    LIST* tmp;
-    LIST* val;
-    string var[1];
-
-#if 0
-    /* Sort all properties which are not order sensitive */
-    for(tmp = properties; tmp; tmp = tmp->next) {
-        LIST* g = get_grist(tmp->string);
-        LIST* att = call_rule("feature.attributes", frame, g, 0);
-        if (list_in(att, "order-sensitive")) {
-            order_sensitive = list_new( order_sensitive, tmp->string);
-        } else {
-            sorted = list_new( sorted, tmp->string);
-        }
-        list_free(att);
-    }
-
-    sorted = list_sort(sorted);
-    sorted = list_append(sorted, order_sensitive);
-    unique = list_unique(sorted);
-#endif
-    sorted = list_sort(properties);
-    unique = list_unique(sorted);
-
-    string_new(var);
-    string_append(var, ".ps.");
-
-    for(tmp = unique; tmp; tmp = tmp->next) {
-        string_append(var, tmp->string);
-        string_push_back(var, '-');
-    }
-    val = var_get(var->value);
-    if (val == 0)
-    {
-        val = call_rule("new", frame,
-                        list_append(list_new(0, "property-set"), unique), 0);
-
-        var_set(newstr(var->value), list_copy(0, val), VAR_SET);
-    }
-    else
-    {
-        val = list_copy(0, val);
-    }
-
-    string_free(var);
-    /* The 'unique' variable is freed in 'call_rule'. */
-    list_free(sorted);
-
-    return val;
-
-}
-
-void init_property_set()
-{
-    {
-        char* args[] = { "raw-properties", "*", 0 };
-        declare_native_rule("property-set", "create", args, property_set_create, 1);
-    }
-}
diff --git a/jam-files/engine/modules/readme.txt b/jam-files/engine/modules/readme.txt
deleted file mode 100644
index 2edf6e17..00000000
--- a/jam-files/engine/modules/readme.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-
-This directory constains sources which declare native
-rules for Boost.Build modules.
\ No newline at end of file
diff --git a/jam-files/engine/modules/regex.c b/jam-files/engine/modules/regex.c
deleted file mode 100644
index d048ba1d..00000000
--- a/jam-files/engine/modules/regex.c
+++ /dev/null
@@ -1,96 +0,0 @@
-/* Copyright Vladimir Prus 2003. Distributed under the Boost */
-/* Software License, Version 1.0. (See accompanying */
-/* file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */
-
-#include "../native.h"
-#include "../timestamp.h"
-#include "../newstr.h"
-#include "../strings.h"
-#include "../regexp.h"
-#include "../compile.h"
-
-/*
-rule transform ( list * : pattern : indices * )
-{
-    indices ?= 1 ;
-    local result ;
-    for local e in $(list)
-    {
-        local m = [ MATCH $(pattern) : $(e) ] ;
-        if $(m)
-        {
-            result += $(m[$(indices)]) ;
-        }        
-    }
-    return $(result) ;
-}
-*/
-LIST *regex_transform( PARSE *parse, FRAME *frame )
-{
-    LIST* l = lol_get( frame->args, 0 );    
-    LIST* pattern = lol_get( frame->args, 1 );    
-    LIST* indices_list = lol_get(frame->args, 2);
-    int* indices = 0;
-    int size;
-    int* p;
-    LIST* result = 0;
-
-    string buf[1];
-    string_new(buf);
-
-    if (indices_list)
-    {
-        size = list_length(indices_list);
-        indices = (int*)BJAM_MALLOC(size*sizeof(int));
-        for(p = indices; indices_list; indices_list = indices_list->next)
-        {
-            *p++ = atoi(indices_list->string);
-        }        
-    }
-    else 
-    {
-        size = 1;
-        indices = (int*)BJAM_MALLOC(sizeof(int));
-        *indices = 1;
-    }
-
-    {
-        /* Result is cached and intentionally never freed */
-        regexp *re = regex_compile( pattern->string );
-
-        for(; l; l = l->next)
-        {
-            if( regexec( re, l->string ) )
-            {
-                int i = 0;
-                for(; i < size; ++i)
-                {
-                    int index = indices[i];
-                    /* Skip empty submatches. Not sure it's right in all cases,
-                       but surely is right for the case for which this routine
-                       is optimized -- header scanning.
-                    */
-                    if (re->startp[index] != re->endp[index])
-                    {
-                        string_append_range( buf, re->startp[index], re->endp[index] );
-                        result = list_new( result, newstr( buf->value ) ); 
-                        string_truncate( buf, 0 );
-                    }
-                }
-            }
-        }
-        string_free( buf );
-    }
-
-    BJAM_FREE(indices);
-    
-    return result;
-}
-
-void init_regex()
-{
-    {
-        char* args[] = { "list", "*", ":", "pattern", ":", "indices", "*", 0 };
-        declare_native_rule("regex", "transform", args, regex_transform, 2);
-    }
-}
diff --git a/jam-files/engine/modules/sequence.c b/jam-files/engine/modules/sequence.c
deleted file mode 100644
index bda80d94..00000000
--- a/jam-files/engine/modules/sequence.c
+++ /dev/null
@@ -1,42 +0,0 @@
-/* Copyright Vladimir Prus 2003. Distributed under the Boost */
-/* Software License, Version 1.0. (See accompanying */
-/* file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */
-
-#include "../native.h"
-
-# ifndef max
-# define max( a,b ) ((a)>(b)?(a):(b))
-# endif
-
-
-LIST *sequence_select_highest_ranked( PARSE *parse, FRAME *frame )
-{
-   /* Returns all of 'elements' for which corresponding element in parallel */
-   /* list 'rank' is equal to the maximum value in 'rank'.                  */
-
-    LIST* elements = lol_get( frame->args, 0 );    
-    LIST* rank = lol_get( frame->args, 1 );    
-    
-    LIST* result = 0;
-    LIST* tmp;
-    int highest_rank = -1;
-
-    for (tmp = rank; tmp; tmp = tmp->next)
-        highest_rank = max(highest_rank, atoi(tmp->string));
-
-    for (; rank; rank = rank->next, elements = elements->next)
-        if (atoi(rank->string) == highest_rank)
-            result = list_new(result, elements->string);
-
-    return result;
-}
-
-void init_sequence()
-{
-    {
-        char* args[] = { "elements", "*", ":", "rank", "*", 0 };
-        declare_native_rule("sequence", "select-highest-ranked", args, 
-                            sequence_select_highest_ranked, 1);
-    }
-
-}
diff --git a/jam-files/engine/modules/set.c b/jam-files/engine/modules/set.c
deleted file mode 100644
index f8219403..00000000
--- a/jam-files/engine/modules/set.c
+++ /dev/null
@@ -1,41 +0,0 @@
-/* Copyright Vladimir Prus 2003. Distributed under the Boost */
-/* Software License, Version 1.0. (See accompanying */
-/* file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */
-
-#include "../native.h"
-
-/*
-    local result = ;
-    local element ;
-    for element in $(B)
-    {
-        if ! ( $(element) in $(A) )
-        {
-            result += $(element) ;
-        }
-    }
-    return $(result) ;
-*/
-LIST *set_difference( PARSE *parse, FRAME *frame )
-{
-
-    LIST* b = lol_get( frame->args, 0 );    
-    LIST* a = lol_get( frame->args, 1 );    
-
-    LIST* result = 0;
-    for(; b; b = b->next)
-    {
-        if (!list_in(a, b->string))
-            result = list_new(result, b->string);
-    }
-    return result;
-}
-
-void init_set()
-{
-    {
-        char* args[] = { "B", "*", ":", "A", "*", 0 };
-        declare_native_rule("set", "difference", args, set_difference, 1);
-    }
-
-}
diff --git a/jam-files/engine/native.c b/jam-files/engine/native.c
deleted file mode 100644
index 4c289959..00000000
--- a/jam-files/engine/native.c
+++ /dev/null
@@ -1,36 +0,0 @@
-/* Copyright Vladimir Prus 2003. Distributed under the Boost */
-/* Software License, Version 1.0. (See accompanying */
-/* file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */
-
-#include "native.h"
-#include "hash.h"
-
-# define P0 (PARSE *)0
-# define C0 (char *)0
-
-
-void declare_native_rule(char* module, char* rule, char** args,
-                         LIST*(*f)(PARSE*, FRAME*), int version)
-{
-    module_t* m = bindmodule(module);
-    if (m->native_rules == 0) {
-        m->native_rules = hashinit( sizeof( native_rule_t ), "native rules");
-    }
-
-    {
-        native_rule_t n, *np = &n;
-        n.name = rule;
-        if (args)
-        {
-            n.arguments = args_new();
-            lol_build( n.arguments->data, args );
-        }
-        else
-        {
-            n.arguments = 0;
-        }
-        n.procedure = parse_make( f, P0, P0, P0, C0, C0, 0 );
-        n.version = version;
-        hashenter(m->native_rules, (HASHDATA**)&np);
-    }
-}
diff --git a/jam-files/engine/native.h b/jam-files/engine/native.h
deleted file mode 100644
index 3fc710b9..00000000
--- a/jam-files/engine/native.h
+++ /dev/null
@@ -1,34 +0,0 @@
-/* Copyright David Abrahams 2003. Distributed under the Boost */
-/* Software License, Version 1.0. (See accompanying */
-/* file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */
-
-#ifndef NATIVE_H_VP_2003_12_09
-#define NATIVE_H_VP_2003_12_09
-
-#include "rules.h"
-
-struct native_rule_t
-{
-    char* name;
-    argument_list* arguments;
-    PARSE* procedure;
-    /* Version of the interface that the native rule provides.
-       It's possible that we want to change the set parameter
-       for existing native rule. In that case, version number
-       should be incremented so that Boost.Build can check for
-       version it relies on.
-
-       Versions are numbered from 1.
-    */
-    int version;
-};
-
-/* MSVC debugger gets confused unless this is provided */
-typedef struct native_rule_t native_rule_t ;
-
-void declare_native_rule(char* module, char* rule, char** args,
-                         LIST*(*f)(PARSE*, FRAME*), int version);
-
-
-
-#endif
diff --git a/jam-files/engine/newstr.c b/jam-files/engine/newstr.c
deleted file mode 100644
index 6a229eb2..00000000
--- a/jam-files/engine/newstr.c
+++ /dev/null
@@ -1,174 +0,0 @@
-/*
- * Copyright 1993, 1995 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-# include "jam.h"
-# include "newstr.h"
-# include "hash.h"
-# include "compile.h"
-# include <stddef.h>
-# include <stdlib.h>
-
-/*
- * newstr.c - string manipulation routines
- *
- * To minimize string copying, string creation, copying, and freeing
- * is done through newstr.
- *
- * External functions:
- *
- *    newstr() - return a dynamically allocated copy of a string
- *    copystr() - return a copy of a string previously returned by newstr()
- *    freestr() - free a string returned by newstr() or copystr()
- *    str_done() - free string tables
- *
- * Once a string is passed to newstr(), the returned string is readonly.
- *
- * This implementation builds a hash table of all strings, so that multiple
- * calls of newstr() on the same string allocate memory for the string once.
- * Strings are never actually freed.
- */
-
-typedef char * STRING;
-
-static struct hash * strhash      = 0;
-static int           strtotal     = 0;
-static int           strcount_in  = 0;
-static int           strcount_out = 0;
-
-
-/*
- * Immortal string allocator implementation speeds string allocation and cuts
- * down on internal fragmentation.
- */
-
-# define STRING_BLOCK 4096
-typedef struct strblock
-{
-    struct strblock * next;
-    char              data[STRING_BLOCK];
-} strblock;
-
-static strblock * strblock_chain = 0;
-
-/* Storage remaining in the current strblock */
-static char * storage_start = 0;
-static char * storage_finish = 0;
-
-
-/*
- * allocate() - Allocate n bytes of immortal string storage.
- */
-
-static char * allocate( size_t const n )
-{
-#ifdef BJAM_NEWSTR_NO_ALLOCATE
-    return (char*)BJAM_MALLOC_ATOMIC(n);
-#else
-    /* See if we can grab storage from an existing block. */
-    size_t remaining = storage_finish - storage_start;
-    if ( remaining >= n )
-    {
-        char * result = storage_start;
-        storage_start += n;
-        return result;
-    }
-    else /* Must allocate a new block. */
-    {
-        strblock * new_block;
-        size_t nalloc = n;
-        if ( nalloc < STRING_BLOCK )
-            nalloc = STRING_BLOCK;
-
-        /* Allocate a new block and link into the chain. */
-        new_block = (strblock *)BJAM_MALLOC( offsetof( strblock, data[0] ) + nalloc * sizeof( new_block->data[0] ) );
-        if ( new_block == 0 )
-            return 0;
-        new_block->next = strblock_chain;
-        strblock_chain = new_block;
-
-        /* Take future allocations out of the larger remaining space. */
-        if ( remaining < nalloc - n )
-        {
-            storage_start = new_block->data + n;
-            storage_finish = new_block->data + nalloc;
-        }
-        return new_block->data;
-    }
-#endif
-}
-
-
-/*
- * newstr() - return a dynamically allocated copy of a string.
- */
-
-char * newstr( char * string )
-{
-    STRING str;
-    STRING * s = &str;
-
-    if ( !strhash )
-        strhash = hashinit( sizeof( STRING ), "strings" );
-
-    *s = string;
-
-    if ( hashenter( strhash, (HASHDATA **)&s ) )
-    {
-        int l = strlen( string );
-        char * m = (char *)allocate( l + 1 );
-
-        strtotal += l + 1;
-        memcpy( m, string, l + 1 );
-        *s = m;
-    }
-
-    strcount_in += 1;
-    return *s;
-}
-
-
-/*
- * copystr() - return a copy of a string previously returned by newstr()
- */
-
-char * copystr( char * s )
-{
-    strcount_in += 1;
-    return s;
-}
-
-
-/*
- * freestr() - free a string returned by newstr() or copystr()
- */
-
-void freestr( char * s )
-{
-    strcount_out += 1;
-}
-
-
-/*
- * str_done() - free string tables.
- */
-
-void str_done()
-{
-    /* Reclaim string blocks. */
-    while ( strblock_chain != 0 )
-    {
-        strblock * n = strblock_chain->next;
-        BJAM_FREE(strblock_chain);
-        strblock_chain = n;
-    }
-
-    hashdone( strhash );
-
-    if ( DEBUG_MEM )
-        printf( "%dK in strings\n", strtotal / 1024 );
-
-    /* printf( "--- %d strings of %d dangling\n", strcount_in-strcount_out, strcount_in ); */
-}
diff --git a/jam-files/engine/newstr.h b/jam-files/engine/newstr.h
deleted file mode 100644
index 84a4d7b6..00000000
--- a/jam-files/engine/newstr.h
+++ /dev/null
@@ -1,14 +0,0 @@
-/*
- * Copyright 1993, 1995 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*
- * newstr.h - string manipulation routines
- */
-
-char * copystr ( char * );
-void   freestr ( char * );
-char * newstr  ( char * );
-void   str_done();
diff --git a/jam-files/engine/option.c b/jam-files/engine/option.c
deleted file mode 100644
index d25e5e8a..00000000
--- a/jam-files/engine/option.c
+++ /dev/null
@@ -1,94 +0,0 @@
-/*
- * Copyright 1993, 1995 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-# include "jam.h"
-# include "option.h"
-
-/*
- * option.c - command line option processing
- *
- * {o >o
- *  \<>) "Process command line options as defined in <option.h>.
- *        Return the number of argv[] elements used up by options,
- *        or -1 if an invalid option flag was given or an argument
- *        was supplied for an option that does not require one."
- */
-
-int getoptions( int argc, char * * argv, char * opts, bjam_option * optv )
-{
-    int i;
-    int optc = N_OPTS;
-
-    memset( (char *)optv, '\0', sizeof( *optv ) * N_OPTS );
-
-    for ( i = 0; i < argc; ++i )
-    {
-        char *arg;
-
-        if ( ( argv[ i ][ 0 ] != '-' ) ||
-            ( ( argv[ i ][ 1 ] != '-' ) && !isalpha( argv[ i ][ 1 ] ) ) )
-            continue;
-
-        if ( !optc-- )
-        {
-            printf( "too many options (%d max)\n", N_OPTS );
-            return -1;
-        }
-
-        for ( arg = &argv[ i ][ 1 ]; *arg; ++arg )
-        {
-            char * f;
-
-            for ( f = opts; *f; ++f )
-                if ( *f == *arg )
-                    break;
-
-            if ( !*f )
-            {
-                printf( "Invalid option: -%c\n", *arg );
-                return -1;
-            }
-
-            optv->flag = *f;
-
-            if ( f[ 1 ] != ':' )
-            {
-                optv++->val = "true";
-            }
-            else if ( arg[ 1 ] )
-            {
-                optv++->val = &arg[1];
-                break;
-            }
-            else if ( ++i < argc )
-            {
-                optv++->val = argv[ i ];
-                break;
-            }
-            else
-            {
-                printf( "option: -%c needs argument\n", *f );
-                return -1;
-            }
-        }
-    }
-
-    return i;
-}
-
-
-/*
- * Name: getoptval() - find an option given its character.
- */
-
-char * getoptval( bjam_option * optv, char opt, int subopt )
-{
-    int i;
-    for ( i = 0; i < N_OPTS; ++i, ++optv )
-        if ( ( optv->flag == opt ) && !subopt-- )
-            return optv->val;
-    return 0;
-}
diff --git a/jam-files/engine/option.h b/jam-files/engine/option.h
deleted file mode 100644
index 99ef620d..00000000
--- a/jam-files/engine/option.h
+++ /dev/null
@@ -1,23 +0,0 @@
-/*
- * Copyright 1993, 1995 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*
- * option.h - command line option processing
- *
- * {o >o
- *  \ -) "Command line option."
- */
-
-typedef struct bjam_option
-{
-    char    flag;       /* filled in by getoption() */
-    char    *val;       /* set to random address if true */
-} bjam_option;
-
-# define N_OPTS 256
-
-int     getoptions( int argc, char **argv, char *opts, bjam_option *optv );
-char *  getoptval( bjam_option *optv, char opt, int subopt );
diff --git a/jam-files/engine/output.c b/jam-files/engine/output.c
deleted file mode 100644
index 483c6ca9..00000000
--- a/jam-files/engine/output.c
+++ /dev/null
@@ -1,125 +0,0 @@
-/*
-    Copyright 2007 Rene Rivera
-    Distributed under the Boost Software License, Version 1.0.
-    (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-#include "jam.h"
-#include "output.h"
-#include "newstr.h"
-#include <stdio.h>
-
-#define bjam_out (stdout)
-#define bjam_err (stderr)
-
-static void out_
-(
-    char const * data,
-    FILE       * io
-)
-{
-    while ( *data )
-    {
-        size_t len = strcspn(data,"\r");
-        data += fwrite(data,1,len,io);
-        if ( *data == '\r' ) ++data;
-    }
-}
-
-
-void out_action
-(
-    char const * action,
-    char const * target,
-    char const * command,
-    char const * out_data,
-    char const * err_data,
-    int          exit_reason
-)
-{
-    /* Print out the action+target line, if the action is quite the action
-     * should be null.
-     */
-    if ( action )
-    {
-        fprintf( bjam_out, "%s %s\n", action, target );
-    }
-
-    /* Print out the command executed if given -d+2. */
-    if ( DEBUG_EXEC )
-    {
-        fputs( command, bjam_out );
-        fputc( '\n', bjam_out );
-    }
-
-    /* Print out the command executed to the command stream. */
-    if ( globs.cmdout )
-    {
-        fputs( command, globs.cmdout );
-    }
-
-    switch ( exit_reason )
-    {
-        case EXIT_OK:
-            break;
-        case EXIT_FAIL:
-            break;
-        case EXIT_TIMEOUT:
-        {
-            /* Process expired, make user aware with explicit message. */
-            if ( action )
-            {
-                /* But only output for non-quietly actions. */
-                fprintf( bjam_out, "%ld second time limit exceeded\n", globs.timeout );
-            }
-            break;
-        }
-        default:
-          break;
-    }
-
-    /* Print out the command output, if requested, or if the program failed. */
-    if ( action || exit_reason != EXIT_OK)
-    {
-        /* But only output for non-quietly actions. */
-        if ( ( 0 != out_data ) &&
-           ( ( globs.pipe_action & 1 /* STDOUT_FILENO */ ) ||
-             ( globs.pipe_action == 0 ) ) )
-        {
-            out_( out_data, bjam_out );
-        }
-        if ( ( 0 != err_data ) &&
-            ( globs.pipe_action & 2 /* STDERR_FILENO */ ) )
-        {
-            out_( err_data, bjam_err );
-        }
-    }
-
-    fflush( bjam_out );
-    fflush( bjam_err );
-    fflush( globs.cmdout );
-}
-
-
-char * outf_int( int value )
-{
-    char buffer[50];
-    sprintf( buffer, "%i", value );
-    return newstr( buffer );
-}
-
-
-char * outf_double( double value )
-{
-    char buffer[50];
-    sprintf( buffer, "%f", value );
-    return newstr( buffer );
-}
-
-
-char * outf_time( time_t value )
-{
-    char buffer[50];
-    strftime( buffer, 49, "%Y-%m-%d %H:%M:%SZ", gmtime( &value ) );
-    return newstr( buffer );
-}
diff --git a/jam-files/engine/output.h b/jam-files/engine/output.h
deleted file mode 100644
index 9e9876cf..00000000
--- a/jam-files/engine/output.h
+++ /dev/null
@@ -1,29 +0,0 @@
-/*
-    Copyright 2007 Rene Rivera
-    Distributed under the Boost Software License, Version 1.0.
-    (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-#ifndef BJAM_OUTPUT_H
-#define BJAM_OUTPUT_H
-
-#include <time.h>
-
-#define EXIT_OK 0
-#define EXIT_FAIL 1
-#define EXIT_TIMEOUT 2
-
-void out_action(
-    const char * action,
-    const char * target,
-    const char * command,
-    const char * out_data,
-    const char * err_data,
-    int exit_reason
-    );
-
-char * outf_int( int value );
-char * outf_double( double value );
-char * outf_time( time_t value );
-
-#endif
diff --git a/jam-files/engine/parse.c b/jam-files/engine/parse.c
deleted file mode 100644
index 9114fa05..00000000
--- a/jam-files/engine/parse.c
+++ /dev/null
@@ -1,132 +0,0 @@
-/*
- * Copyright 1993, 2000 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*  This file is ALSO:
- *  Copyright 2001-2004 David Abrahams.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-
-#include "jam.h"
-#include "lists.h"
-#include "parse.h"
-#include "scan.h"
-#include "newstr.h"
-#include "modules.h"
-#include "frames.h"
-
-/*
- * parse.c - make and destroy parse trees as driven by the parser
- *
- * 09/07/00 (seiwald) - ref count on PARSE to avoid freeing when used,
- *      as per Matt Armstrong.
- * 09/11/00 (seiwald) - structure reworked to reflect that (*func)()
- *      returns a LIST *.
- */
-
-static PARSE * yypsave;
-
-void parse_file( char * f, FRAME * frame )
-{
-    /* Suspend scan of current file and push this new file in the stream. */
-    yyfparse( f );
-
-    /* Now parse each block of rules and execute it. Execute it outside of the
-     * parser so that recursive calls to yyrun() work (no recursive yyparse's).
-     */
-
-    for ( ; ; )
-    {
-        PARSE * p;
-
-        /* Filled by yyparse() calling parse_save(). */
-        yypsave = 0;
-
-        /* If parse error or empty parse, outta here. */
-        if ( yyparse() || !( p = yypsave ) )
-            break;
-
-        /* Run the parse tree. */
-        parse_evaluate( p, frame );
-        parse_free( p );
-    }
-}
-
-
-void parse_save( PARSE * p )
-{
-    yypsave = p;
-}
-
-
-PARSE * parse_make(
-    LIST  * (* func)( PARSE *, FRAME * ),
-    PARSE * left,
-    PARSE * right,
-    PARSE * third,
-    char  * string,
-    char  * string1,
-    int     num )
-{
-    PARSE * p = (PARSE *)BJAM_MALLOC( sizeof( PARSE ) );
-
-    p->func = func;
-    p->left = left;
-    p->right = right;
-    p->third = third;
-    p->string = string;
-    p->string1 = string1;
-    p->num = num;
-    p->refs = 1;
-    p->rulename = 0;
-
-    if ( left )
-    {
-        p->file = left->file;
-        p->line = left->line;
-    }
-    else
-    {
-        yyinput_stream( &p->file, &p->line );
-    }
-
-    return p;
-}
-
-
-void parse_refer( PARSE * p )
-{
-    ++p->refs;
-}
-
-
-void parse_free( PARSE * p )
-{
-    if ( --p->refs )
-        return;
-
-    if ( p->string )
-        freestr( p->string );
-    if ( p->string1 )
-        freestr( p->string1 );
-    if ( p->left )
-        parse_free( p->left );
-    if ( p->right )
-        parse_free( p->right );
-    if ( p->third )
-        parse_free( p->third );
-    if ( p->rulename )
-        freestr( p->rulename );
-
-    BJAM_FREE( (char *)p );
-}
-
-
-LIST * parse_evaluate( PARSE * p, FRAME * frame )
-{
-    frame->procedure = p;
-    return (*p->func)( p, frame );
-}
diff --git a/jam-files/engine/parse.h b/jam-files/engine/parse.h
deleted file mode 100644
index e324972f..00000000
--- a/jam-files/engine/parse.h
+++ /dev/null
@@ -1,59 +0,0 @@
-/*
- * Copyright 1993, 2000 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/* This file is ALSO:
- * Copyright 2001-2004 David Abrahams.
- * Distributed under the Boost Software License, Version 1.0.
- * (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-
-#ifndef PARSE_DWA20011020_H
-#define PARSE_DWA20011020_H
-
-#include "frames.h"
-#include "modules.h"
-#include "lists.h"
-
-/*
- * parse.h - make and destroy parse trees as driven by the parser.
- */
-
-/*
- * Parse tree node.
- */
-
-struct _PARSE {
-    LIST   * (* func)( PARSE *, FRAME * );
-    PARSE  * left;
-    PARSE  * right;
-    PARSE  * third;
-    char   * string;
-    char   * string1;
-    int      num;
-    int      refs;
-/*  module * module; */
-    char   * rulename;
-    char   * file;
-    int      line;
-};
-
-void    parse_file( char *, FRAME * );
-void    parse_save( PARSE * );
-
-PARSE * parse_make(
-    LIST  * (* func)( PARSE *, FRAME * ),
-    PARSE * left,
-    PARSE * right,
-    PARSE * third,
-    char  * string,
-    char  * string1,
-    int     num );
-
-void   parse_refer   ( PARSE * );
-void   parse_free    ( PARSE * );
-LIST * parse_evaluate( PARSE *, FRAME * );
-
-#endif
diff --git a/jam-files/engine/patchlevel.h b/jam-files/engine/patchlevel.h
deleted file mode 100644
index 699efd84..00000000
--- a/jam-files/engine/patchlevel.h
+++ /dev/null
@@ -1,17 +0,0 @@
-/*
- * Copyright 1993-2002 Christopher Seiwald and Perforce Software, Inc.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/* Keep JAMVERSYM in sync with VERSION. */
-/* It can be accessed as $(JAMVERSION) in the Jamfile. */
-
-#define VERSION_MAJOR 2011
-#define VERSION_MINOR 04
-#define VERSION_PATCH 0
-#define VERSION_MAJOR_SYM "2011"
-#define VERSION_MINOR_SYM "04"
-#define VERSION_PATCH_SYM "00"
-#define VERSION "2011.4"
-#define JAMVERSYM "JAMVERSION=2011.4"
diff --git a/jam-files/engine/pathmac.c b/jam-files/engine/pathmac.c
deleted file mode 100644
index e2c250e3..00000000
--- a/jam-files/engine/pathmac.c
+++ /dev/null
@@ -1,252 +0,0 @@
-/*
- * Copyright 1993-2002 Christopher Seiwald and Perforce Software, Inc.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*  This file is ALSO:
- *  Copyright 2001-2004 David Abrahams.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-
-# include "jam.h"
-# include "pathsys.h"
-
-# ifdef OS_MAC
-
-# define DELIM ':'
-
-/*
- * pathunix.c - manipulate file names on UNIX, NT, OS2
- *
- * External routines:
- *
- *  path_parse() - split a file name into dir/base/suffix/member
- *  path_build() - build a filename given dir/base/suffix/member
- *  path_parent() - make a PATHNAME point to its parent dir
- *
- * File_parse() and path_build() just manipuate a string and a structure;
- * they do not make system calls.
- *
- * 04/08/94 (seiwald) - Coherent/386 support added.
- * 12/26/93 (seiwald) - handle dir/.suffix properly in path_build()
- * 12/19/94 (mikem) - solaris string table insanity support
- * 12/21/94 (wingerd) Use backslashes for pathnames - the NT way.
- * 02/14/95 (seiwald) - parse and build /xxx properly
- * 02/23/95 (wingerd) Compilers on NT can handle "/" in pathnames, so we
- *                    should expect hdr searches to come up with strings
- *                    like "thing/thing.h". So we need to test for "/" as
- *                    well as "\" when parsing pathnames.
- * 03/16/95 (seiwald) - fixed accursed typo on line 69.
- * 05/03/96 (seiwald) - split from filent.c, fileunix.c
- * 12/20/96 (seiwald) - when looking for the rightmost . in a file name,
- *            don't include the archive member name.
- * 01/10/01 (seiwald) - path_parse now strips the trailing : from the
- *          directory name, unless the directory name is all
- *          :'s, so that $(d:P) works.
- */
-
-/*
- * path_parse() - split a file name into dir/base/suffix/member
- */
-
-void
-path_parse(
-    char    *file,
-    PATHNAME *f )
-{
-    char *p, *q;
-    char *end;
-
-    memset( (char *)f, 0, sizeof( *f ) );
-
-    /* Look for <grist> */
-
-    if ( file[0] == '<' && ( p = strchr( file, '>' ) ) )
-    {
-        f->f_grist.ptr = file;
-        f->f_grist.len = p - file;
-        file = p + 1;
-    }
-
-    /* Look for dir: */
-
-    if ( p = strrchr( file, DELIM ) )
-    {
-        f->f_dir.ptr = file;
-        f->f_dir.len = p - file;
-        file = p + 1;
-
-        /* All :'s? Include last : as part of directory name */
-
-        while ( ( p > f->f_dir.ptr ) && ( *--p == DELIM ) );
-
-        if ( p == f->f_dir.ptr )
-            ++f->f_dir.len;
-    }
-
-    end = file + strlen( file );
-
-    /* Look for (member). */
-
-    if ( ( p = strchr( file, '(' ) ) && ( end[-1] == ')' ) )
-    {
-        f->f_member.ptr = p + 1;
-        f->f_member.len = end - p - 2;
-        end = p;
-    }
-
-    /* Look for .suffix */
-    /* This would be memrchr() */
-
-    p = 0;
-    q = file;
-
-    while ( q = memchr( q, '.', end - q ) )
-        p = q++;
-
-    if ( p )
-    {
-        f->f_suffix.ptr = p;
-        f->f_suffix.len = end - p;
-        end = p;
-    }
-
-    /* Leaves base */
-
-    f->f_base.ptr = file;
-    f->f_base.len = end - file;
-}
-
-/*
- * path_build() - build a filename given dir/base/suffix/member.
- */
-
-# define DIR_EMPTY  0   /* "" */
-# define DIR_DOT    1   /* : */
-# define DIR_DOTDOT 2   /* :: */
-# define DIR_ABS    3   /* dira:dirb: */
-# define DIR_REL    4   /* :dira:dirb: */
-
-# define G_DIR      0   /* take dir */
-# define G_ROOT     1   /* take root */
-# define G_CAT      2   /* prepend root to dir */
-# define G_DTDR     3   /* :: of rel dir */
-# define G_DDDD     4   /* make it ::: (../..) */
-# define G_MT       5   /* leave it empty */
-
-char grid[5][5] = {
-/*      EMPTY   DOT DOTDOT  ABS REL */
-/* EMPTY */   { G_MT,   G_DIR,  G_DIR,  G_DIR,  G_DIR },
-/* DOT */     { G_ROOT, G_DIR,  G_DIR,  G_DIR,  G_DIR },
-/* DOTDOT */  { G_ROOT, G_ROOT, G_DDDD, G_DIR,  G_DTDR },
-/* ABS */     { G_ROOT, G_ROOT, G_ROOT, G_DIR,  G_CAT },
-/* REL */     { G_ROOT, G_ROOT, G_ROOT, G_DIR,  G_CAT }
-};
-
-static int file_flags( char * ptr, int len )
-{
-    if ( !len )
-        return DIR_EMPTY;
-    if ( ( len == 1 ) && ( ptr[0] == DELIM ) )
-        return DIR_DOT;
-    if ( ( len == 2 ) && ( ptr[0] == DELIM ) && ( ptr[1] == DELIM ) )
-        return DIR_DOTDOT;
-    if ( ptr[0] == DELIM )
-        return DIR_REL;
-    return DIR_ABS;
-}
-
-
-void path_build( PATHNAME * f, string * file, int binding )
-{
-    int dflag;
-    int rflag;
-    int act;
-
-    file_build1( f, file );
-
-    /* Combine root & directory, according to the grid. */
-
-    dflag = file_flags( f->f_dir.ptr, f->f_dir.len );
-    rflag = file_flags( f->f_root.ptr, f->f_root.len );
-
-    switch ( act = grid[ rflag ][ dflag ] )
-    {
-    case G_DTDR:
-        {
-            /* :: of rel dir */
-            string_push_back( file, DELIM );
-        }
-        /* fall through */
-
-    case G_DIR:
-        /* take dir */
-        string_append_range( file, f->f_dir.ptr, f->f_dir.ptr + f->f_dir.len  );
-        break;
-
-    case G_ROOT:
-        /* take root */
-        string_append_range( file, f->f_root.ptr, f->f_root.ptr + f->f_root.len  );
-        break;
-
-    case G_CAT:
-        /* prepend root to dir */
-        string_append_range( file, f->f_root.ptr, f->f_root.ptr + f->f_root.len  );
-        if ( file->value[ file->size - 1 ] == DELIM )
-            string_pop_back( file );
-        string_append_range( file, f->f_dir.ptr, f->f_dir.ptr + f->f_dir.len  );
-        break;
-
-    case G_DDDD:
-        /* make it ::: (../..) */
-        string_append( file, ":::" );
-        break;
-    }
-
-    /* Put : between dir and file (if none already). */
-
-    if ( ( act != G_MT ) &&
-        ( file->value[ file->size - 1 ] != DELIM ) &&
-        ( f->f_base.len || f->f_suffix.len ) )
-    {
-        string_push_back( file, DELIM );
-    }
-
-    if ( f->f_base.len )
-        string_append_range( file, f->f_base.ptr, f->f_base.ptr + f->f_base.len  );
-
-    if ( f->f_suffix.len )
-        string_append_range( file, f->f_suffix.ptr, f->f_suffix.ptr + f->f_suffix.len  );
-
-    if ( f->f_member.len )
-    {
-        string_push_back( file, '(' );
-        string_append_range( file, f->f_member.ptr, f->f_member.ptr + f->f_member.len  );
-        string_push_back( file, ')' );
-    }
-
-    if ( DEBUG_SEARCH )
-        printf( " -> '%s'\n", file->value );
-}
-
-
-/*
- *  path_parent() - make a PATHNAME point to its parent dir
- */
-
-void path_parent( PATHNAME * f )
-{
-    /* Just set everything else to nothing. */
-
-    f->f_base.ptr =
-    f->f_suffix.ptr =
-    f->f_member.ptr = "";
-
-    f->f_base.len =
-    f->f_suffix.len =
-    f->f_member.len = 0;
-}
-
-# endif /* OS_MAC */
diff --git a/jam-files/engine/pathsys.h b/jam-files/engine/pathsys.h
deleted file mode 100644
index 73775810..00000000
--- a/jam-files/engine/pathsys.h
+++ /dev/null
@@ -1,91 +0,0 @@
-/*
- * Copyright 1993-2002 Christopher Seiwald and Perforce Software, Inc.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*
- * pathsys.h - PATHNAME struct
- */
-
-/*
- * PATHNAME - a name of a file, broken into <grist>dir/base/suffix(member)
- *
- * <grist> is salt to distinguish between targets that otherwise would
- * have the same name:  it never appears in the bound name of a target.
- * (member) is an archive member name: the syntax is arbitrary, but must
- * agree in path_parse(), path_build() and the Jambase.
- *
- * On VMS, we keep track of whether the original path was a directory
- * (without a file), so that $(VAR:D) can climb to the parent.
- */
-
-#ifndef PATHSYS_VP_20020211_H
-# define PATHSYS_VP_20020211_H
-
-#include "strings.h"
-
-typedef struct _pathname PATHNAME;
-typedef struct _pathpart PATHPART;
-
-struct _pathpart
-{
-    char * ptr;
-    int    len;
-};
-
-struct _pathname
-{
-    PATHPART    part[6];
-#ifdef OS_VMS
-    int     parent;
-#endif
-
-#define f_grist    part[0]
-#define f_root     part[1]
-#define f_dir      part[2]
-#define f_base     part[3]
-#define f_suffix   part[4]
-#define f_member   part[5]
-};
-
-void path_build( PATHNAME * f, string * file, int binding );
-void path_build1( PATHNAME * f, string * file );
-
-void path_parse( char * file, PATHNAME * f );
-void path_parent( PATHNAME * f );
-
-#ifdef NT
-
-/** Returns newstr-allocated string with long equivivalent of 'short_name'.
-    If none exists -- i.e. 'short_path' is already long path, it's returned
-    unaltered. */
-char * short_path_to_long_path( char * short_path );
-
-#endif
-
-#ifdef USE_PATHUNIX
-/** Returns a static pointer to the system dependent path to the temporary
-    directory. NOTE: *without* a trailing path separator.
-*/
-const char * path_tmpdir( void );
-
-/** Returns a new temporary name.
-*/
-const char * path_tmpnam( void );
-
-/** Returns a new temporary path.
-*/
-const char * path_tmpfile( void );
-#endif
-
-/** Give the first argument to 'main', return a full path to
-    our executable.  Returns null in the unlikely case it
-    cannot be determined. Caller is responsible for freeing
-    the string.
-
-    Implemented in jam.c
-*/
-char * executable_path (char *argv0);
-
-#endif
diff --git a/jam-files/engine/pathunix.c b/jam-files/engine/pathunix.c
deleted file mode 100644
index 2daad14b..00000000
--- a/jam-files/engine/pathunix.c
+++ /dev/null
@@ -1,457 +0,0 @@
-/*
- * Copyright 1993-2002 Christopher Seiwald and Perforce Software, Inc.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*  This file is ALSO:
- *  Copyright 2001-2004 David Abrahams.
- *  Copyright 2005 Rene Rivera.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-
-# include "jam.h"
-# include "pathsys.h"
-# include "strings.h"
-# include "newstr.h"
-# include "filesys.h"
-# include <time.h>
-# include <stdlib.h>
-# ifndef OS_NT
-# include <unistd.h>
-# endif
-
-# ifdef USE_PATHUNIX
-
-/*
- * pathunix.c - manipulate file names on UNIX, NT, OS2, AmigaOS
- *
- * External routines:
- *
- *  path_parse() - split a file name into dir/base/suffix/member
- *  path_build() - build a filename given dir/base/suffix/member
- *  path_parent() - make a PATHNAME point to its parent dir
- *
- * File_parse() and path_build() just manipuate a string and a structure;
- * they do not make system calls.
- *
- * 04/08/94 (seiwald) - Coherent/386 support added.
- * 12/26/93 (seiwald) - handle dir/.suffix properly in path_build()
- * 12/19/94 (mikem) - solaris string table insanity support
- * 12/21/94 (wingerd) Use backslashes for pathnames - the NT way.
- * 02/14/95 (seiwald) - parse and build /xxx properly
- * 02/23/95 (wingerd) Compilers on NT can handle "/" in pathnames, so we
- *                    should expect hdr searches to come up with strings
- *                    like "thing/thing.h". So we need to test for "/" as
- *                    well as "\" when parsing pathnames.
- * 03/16/95 (seiwald) - fixed accursed typo on line 69.
- * 05/03/96 (seiwald) - split from filent.c, fileunix.c
- * 12/20/96 (seiwald) - when looking for the rightmost . in a file name,
- *            don't include the archive member name.
- * 01/13/01 (seiwald) - turn on \ handling on UNIX, on by accident
- */
-
-/*
- * path_parse() - split a file name into dir/base/suffix/member
- */
-
-void path_parse( char * file, PATHNAME * f )
-{
-    char * p;
-    char * q;
-    char * end;
-
-    memset( (char *)f, 0, sizeof( *f ) );
-
-    /* Look for <grist> */
-
-    if ( ( file[0] == '<' ) && ( p = strchr( file, '>' ) ) )
-    {
-        f->f_grist.ptr = file;
-        f->f_grist.len = p - file;
-        file = p + 1;
-    }
-
-    /* Look for dir/ */
-
-    p = strrchr( file, '/' );
-
-# if PATH_DELIM == '\\'
-    /* On NT, look for dir\ as well */
-    {
-        char *p1 = strrchr( file, '\\' );
-        p = p1 > p ? p1 : p;
-    }
-# endif
-
-    if ( p )
-    {
-        f->f_dir.ptr = file;
-        f->f_dir.len = p - file;
-
-        /* Special case for / - dirname is /, not "" */
-
-        if ( !f->f_dir.len )
-        f->f_dir.len = 1;
-
-# if PATH_DELIM == '\\'
-        /* Special case for D:/ - dirname is D:/, not "D:" */
-
-        if ( f->f_dir.len == 2 && file[1] == ':' )
-            f->f_dir.len = 3;
-# endif
-
-        file = p + 1;
-    }
-
-    end = file + strlen( file );
-
-    /* Look for (member) */
-
-    if ( ( p = strchr( file, '(' ) ) && ( end[ -1 ] == ')' ) )
-    {
-        f->f_member.ptr = p + 1;
-        f->f_member.len = end - p - 2;
-        end = p;
-    }
-
-    /* Look for .suffix */
-    /* This would be memrchr() */
-
-    p = 0;
-    q = file;
-
-    while ( ( q = (char *)memchr( q, '.', end - q ) ) )
-        p = q++;
-
-    if ( p )
-    {
-        f->f_suffix.ptr = p;
-        f->f_suffix.len = end - p;
-        end = p;
-    }
-
-    /* Leaves base */
-
-    f->f_base.ptr = file;
-    f->f_base.len = end - file;
-}
-
-/*
- * path_delims - the string of legal path delimiters
- */
-static char path_delims[] = {
-    PATH_DELIM,
-#  if PATH_DELIM == '\\'
-    '/',
-#  endif
-    0
-};
-
-/*
- * is_path_delim() - true iff c is a path delimiter
- */
-static int is_path_delim( char c )
-{
-    char* p = strchr( path_delims, c );
-    return p && *p;
-}
-
-/*
- * as_path_delim() - convert c to a path delimiter if it isn't one
- * already
- */
-static char as_path_delim( char c )
-{
-    return is_path_delim( c ) ? c : PATH_DELIM;
-}
-
-/*
- * path_build() - build a filename given dir/base/suffix/member
- *
- * To avoid changing slash direction on NT when reconstituting paths,
- * instead of unconditionally appending PATH_DELIM we check the
- * past-the-end character of the previous path element.  If it is in
- * path_delims, we append that, and only append PATH_DELIM as a last
- * resort.  This heuristic is based on the fact that PATHNAME objects
- * are usually the result of calling path_parse, which leaves the
- * original slashes in the past-the-end position. Correctness depends
- * on the assumption that all strings are zero terminated, so a
- * past-the-end character will always be available.
- *
- * As an attendant patch, we had to ensure that backslashes are used
- * explicitly in timestamp.c
- */
-
-void
-path_build(
-    PATHNAME *f,
-    string  *file,
-    int binding )
-{
-    file_build1( f, file );
-
-    /* Don't prepend root if it's . or directory is rooted */
-# if PATH_DELIM == '/'
-
-    if ( f->f_root.len
-        && !( f->f_root.len == 1 && f->f_root.ptr[0] == '.' )
-        && !( f->f_dir.len && f->f_dir.ptr[0] == '/' ) )
-
-# else /* unix */
-
-    if ( f->f_root.len
-        && !( f->f_root.len == 1 && f->f_root.ptr[0] == '.' )
-        && !( f->f_dir.len && f->f_dir.ptr[0] == '/' )
-        && !( f->f_dir.len && f->f_dir.ptr[0] == '\\' )
-        && !( f->f_dir.len && f->f_dir.ptr[1] == ':' ) )
-
-# endif /* unix */
-
-    {
-        string_append_range( file, f->f_root.ptr, f->f_root.ptr + f->f_root.len  );
-        /* If 'root' already ends with path delimeter,
-           don't add yet another one. */
-        if ( ! is_path_delim( f->f_root.ptr[f->f_root.len-1] ) )
-            string_push_back( file, as_path_delim( f->f_root.ptr[f->f_root.len] ) );
-    }
-
-    if ( f->f_dir.len )
-        string_append_range( file, f->f_dir.ptr, f->f_dir.ptr + f->f_dir.len  );
-
-    /* UNIX: Put / between dir and file */
-    /* NT:   Put \ between dir and file */
-
-    if ( f->f_dir.len && ( f->f_base.len || f->f_suffix.len ) )
-    {
-        /* UNIX: Special case for dir \ : don't add another \ */
-        /* NT:   Special case for dir / : don't add another / */
-
-# if PATH_DELIM == '\\'
-        if ( !( f->f_dir.len == 3 && f->f_dir.ptr[1] == ':' ) )
-# endif
-            if ( !( f->f_dir.len == 1 && is_path_delim( f->f_dir.ptr[0] ) ) )
-                string_push_back( file, as_path_delim( f->f_dir.ptr[f->f_dir.len] ) );
-    }
-
-    if ( f->f_base.len )
-    {
-        string_append_range( file, f->f_base.ptr, f->f_base.ptr + f->f_base.len  );
-    }
-
-    if ( f->f_suffix.len )
-    {
-        string_append_range( file, f->f_suffix.ptr, f->f_suffix.ptr + f->f_suffix.len  );
-    }
-
-    if ( f->f_member.len )
-    {
-        string_push_back( file, '(' );
-        string_append_range( file, f->f_member.ptr, f->f_member.ptr + f->f_member.len  );
-        string_push_back( file, ')' );
-    }
-}
-
-/*
- *  path_parent() - make a PATHNAME point to its parent dir
- */
-
-void
-path_parent( PATHNAME *f )
-{
-    /* just set everything else to nothing */
-
-    f->f_base.ptr =
-    f->f_suffix.ptr =
-    f->f_member.ptr = "";
-
-    f->f_base.len =
-    f->f_suffix.len =
-    f->f_member.len = 0;
-}
-
-#ifdef NT
-#include <windows.h>
-#include <tchar.h>
-
-/* The definition of this in winnt.h is not ANSI-C compatible. */
-#undef INVALID_FILE_ATTRIBUTES
-#define INVALID_FILE_ATTRIBUTES ((DWORD)-1)
-
-
-DWORD ShortPathToLongPath(LPCTSTR lpszShortPath,LPTSTR lpszLongPath,DWORD
-                          cchBuffer)
-{
-    LONG i=0;
-    TCHAR path[_MAX_PATH]={0};
-    TCHAR ret[_MAX_PATH]={0};
-    LONG pos=0, prev_pos=0;
-    LONG len=_tcslen(lpszShortPath);
-
-    /* Is the string valid? */
-    if (!lpszShortPath) {
-        SetLastError(ERROR_INVALID_PARAMETER);
-        return 0;
-    }
-
-    /* Is the path valid? */
-    if (GetFileAttributes(lpszShortPath)==INVALID_FILE_ATTRIBUTES)
-        return 0;
-
-    /* Convert "/" to "\" */
-    for (i=0;i<len;++i) {
-        if (lpszShortPath[i]==_T('/'))
-            path[i]=_T('\\');
-        else
-            path[i]=lpszShortPath[i];
-    }
-
-    /* UNC path? */
-    if (path[0]==_T('\\') && path[1]==_T('\\')) {
-        pos=2;
-        for (i=0;i<2;++i) {
-            while (path[pos]!=_T('\\') && path[pos]!=_T('\0'))
-                ++pos;
-            ++pos;
-        }
-        _tcsncpy(ret,path,pos-1);
-    } /* Drive letter? */
-    else if (path[1]==_T(':')) {
-        if (path[2]==_T('\\'))
-            pos=3;
-        if (len==3) {
-            if (cchBuffer>3)
-                _tcscpy(lpszLongPath,lpszShortPath);
-            return len;
-        }
-        _tcsncpy(ret,path,2);
-    }
-
-    /* Expand the path for each subpath, and strip trailing backslashes */
-    for (prev_pos = pos-1;pos<=len;++pos) {
-        if (path[pos]==_T('\\') || (path[pos]==_T('\0') &&
-                                    path[pos-1]!=_T('\\'))) {
-            WIN32_FIND_DATA fd;
-            HANDLE hf=0;
-            TCHAR c=path[pos];
-            char* new_element;
-            path[pos]=_T('\0');
-
-            /* the path[prev_pos+1]... path[pos] range is the part of
-               path we're handling right now. We need to find long
-               name for that element and add it. */
-            new_element = path + prev_pos + 1;
-
-            /* First add separator, but only if there's something in result already. */
-            if (ret[0] != _T('\0'))
-            {
-                _tcscat(ret,_T("\\"));
-            }
-
-            /* If it's ".." element, we need to append it, not
-               the name in parent that FindFirstFile will return.
-               Same goes for "." */
-
-            if (new_element[0] == _T('.') && new_element[1] == _T('\0') ||
-                new_element[0] == _T('.') && new_element[1] == _T('.')
-                && new_element[2] == _T('\0'))
-            {
-                _tcscat(ret, new_element);
-            }
-            else
-            {
-                hf=FindFirstFile(path, &fd);
-                if (hf==INVALID_HANDLE_VALUE)
-                    return 0;
-
-                _tcscat(ret,fd.cFileName);
-                FindClose(hf);
-            }
-
-            path[pos]=c;
-
-            prev_pos = pos;
-        }
-    }
-
-    len=_tcslen(ret)+1;
-    if (cchBuffer>=len)
-        _tcscpy(lpszLongPath,ret);
-
-    return len;
-}
-
-char* short_path_to_long_path(char* short_path)
-{
-    char buffer2[_MAX_PATH];
-    int ret = ShortPathToLongPath(short_path, buffer2, _MAX_PATH);
-
-    if (ret)
-    return newstr(buffer2);
-    else
-      return newstr(short_path);
-}
-
-#endif
-
-static string path_tmpdir_buffer[1];
-static const char * path_tmpdir_result = 0;
-
-const char * path_tmpdir()
-{
-    if (!path_tmpdir_result)
-    {
-        # ifdef OS_NT
-        DWORD pathLength = 0;
-        pathLength = GetTempPath(pathLength,NULL);
-        string_new(path_tmpdir_buffer);
-        string_reserve(path_tmpdir_buffer,pathLength);
-        pathLength = GetTempPathA(pathLength,path_tmpdir_buffer[0].value);
-        path_tmpdir_buffer[0].value[pathLength-1] = '\0';
-        path_tmpdir_buffer[0].size = pathLength-1;
-        # else
-        const char * t = getenv("TMPDIR");
-        if (!t)
-        {
-            t = "/tmp";
-        }
-        string_new(path_tmpdir_buffer);
-        string_append(path_tmpdir_buffer,t);
-        # endif
-        path_tmpdir_result = path_tmpdir_buffer[0].value;
-    }
-    return path_tmpdir_result;
-}
-
-const char * path_tmpnam(void)
-{
-    char name_buffer[64];
-    # ifdef OS_NT
-    unsigned long c0 = GetCurrentProcessId();
-    # else
-    unsigned long c0 = getpid();
-    # endif
-    static unsigned long c1 = 0;
-    if (0 == c1) c1 = time(0)&0xffff;
-    c1 += 1;
-    sprintf(name_buffer,"jam%lx%lx.000",c0,c1);
-    return newstr(name_buffer);
-}
-
-const char * path_tmpfile(void)
-{
-    const char * result = 0;
-
-    string file_path;
-    string_copy(&file_path,path_tmpdir());
-    string_push_back(&file_path,PATH_DELIM);
-    string_append(&file_path,path_tmpnam());
-    result = newstr(file_path.value);
-    string_free(&file_path);
-
-    return result;
-}
-
-
-# endif /* unix, NT, OS/2, AmigaOS */
diff --git a/jam-files/engine/pathvms.c b/jam-files/engine/pathvms.c
deleted file mode 100644
index 975fe5a5..00000000
--- a/jam-files/engine/pathvms.c
+++ /dev/null
@@ -1,406 +0,0 @@
-/*
- * Copyright 1993-2002 Christopher Seiwald and Perforce Software, Inc.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*  This file is ALSO:
- *  Copyright 2001-2004 David Abrahams.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-
-# include "jam.h"
-# include "pathsys.h"
-
-# ifdef OS_VMS
-
-# define DEBUG
-
-/*
- * pathvms.c - manipulate file names on VMS
- *
- * External routines:
- *
- *  path_parse() - split a file name into dir/base/suffix/member
- *  path_build() - build a filename given dir/base/suffix/member
- *  path_parent() - make a PATHNAME point to its parent dir
- *
- * File_parse() and path_build() just manipuate a string and a structure;
- * they do not make system calls.
- *
- * WARNING!  This file contains voodoo logic, as black magic is
- * necessary for wrangling with VMS file name.  Woe be to people
- * who mess with this code.
- *
- * 02/09/95 (seiwald) - bungled R=[xxx] - was using directory length!
- * 05/03/96 (seiwald) - split from filevms.c
- */
-
-/*
- * path_parse() - split a file name into dir/base/suffix/member.
- */
-
-void path_parse( char * file, PATHNAME * f )
-{
-    char * p;
-    char * q;
-    char * end;
-
-    memset( (char *)f, 0, sizeof( *f ) );
-
-    /* Look for <grist> */
-
-    if ( ( file[0] == '<' ) && ( p = strchr( file, '>' ) ) )
-    {
-        f->f_grist.ptr = file;
-        f->f_grist.len = p - file;
-        file = p + 1;
-    }
-
-    /* Look for dev:[dir] or dev: */
-
-    if ( ( p = strchr( file, ']' ) ) || ( p = strchr( file, ':' ) ) )
-    {
-        f->f_dir.ptr = file;
-        f->f_dir.len = p + 1 - file;
-        file = p + 1;
-    }
-
-    end = file + strlen( file );
-
-    /* Look for (member). */
-
-    if ( ( p = strchr( file, '(' ) ) && ( end[ -1 ] == ')' ) )
-    {
-        f->f_member.ptr = p + 1;
-        f->f_member.len = end - p - 2;
-        end = p;
-    }
-
-    /* Look for .suffix */
-    /* This would be memrchr(). */
-
-    p = 0;
-    q = file;
-
-    while ( q = (char *)memchr( q, '.', end - q ) )
-        p = q++;
-
-    if ( p )
-    {
-        f->f_suffix.ptr = p;
-        f->f_suffix.len = end - p;
-        end = p;
-    }
-
-    /* Leaves base. */
-    f->f_base.ptr = file;
-    f->f_base.len = end - file;
-
-    /* Is this a directory without a file spec? */
-    f->parent = 0;
-}
-
-/*
- *  dir     mods        result
- *  ---     ---     ------
- * Rerooting:
- *
- *  (none)      :R=dev:     dev:
- *  devd:       :R=dev:     devd:
- *  devd:[dir]  :R=dev:     devd:[dir]
- *  [.dir]      :R=dev:     dev:[dir]   questionable
- *  [dir]       :R=dev:     dev:[dir]
- *
- *  (none)      :R=[rdir]   [rdir]      questionable
- *  devd:       :R=[rdir]   devd:
- *  devd:[dir]  :R=[rdir]   devd:[dir]
- *  [.dir]      :R=[rdir]   [rdir.dir]  questionable
- *  [dir]       :R=[rdir]   [rdir]
- *
- *  (none)      :R=dev:[root]   dev:[root]
- *  devd:       :R=dev:[root]   devd:
- *  devd:[dir]  :R=dev:[root]   devd:[dir]
- *  [.dir]      :R=dev:[root]   dev:[root.dir]
- *  [dir]       :R=dev:[root]   [dir]
- *
- * Climbing to parent:
- *
- */
-
-# define DIR_EMPTY  0   /* empty string */
-# define DIR_DEV    1   /* dev: */
-# define DIR_DEVDIR 2   /* dev:[dir] */
-# define DIR_DOTDIR 3   /* [.dir] */
-# define DIR_DASHDIR    4   /* [-] or [-.dir] */
-# define DIR_ABSDIR 5   /* [dir] */
-# define DIR_ROOT   6   /* [000000] or dev:[000000] */
-
-# define G_DIR      0   /* take just dir */
-# define G_ROOT     1   /* take just root */
-# define G_VAD      2   /* root's dev: + [abs] */
-# define G_DRD      3   /* root's dev:[dir] + [.rel] */
-# define G_VRD      4   /* root's dev: + [.rel] made [abs] */
-# define G_DDD      5   /* root's dev:[dir] + . + [dir] */
-
-static int grid[7][7] = {
-
-/* root/dir EMPTY   DEV DEVDIR  DOTDIR  DASH,   ABSDIR  ROOT */
-/* EMPTY */ G_DIR,  G_DIR,  G_DIR,  G_DIR,  G_DIR,  G_DIR,  G_DIR,
-/* DEV */   G_ROOT, G_DIR,  G_DIR,  G_VRD,  G_VAD,  G_VAD,  G_VAD,
-/* DEVDIR */    G_ROOT, G_DIR,  G_DIR,  G_DRD,  G_VAD,  G_VAD,  G_VAD,
-/* DOTDIR */    G_ROOT, G_DIR,  G_DIR,  G_DRD,  G_DIR,  G_DIR,  G_DIR,
-/* DASHDIR */   G_ROOT, G_DIR,  G_DIR,  G_DRD,  G_DDD,  G_DIR,  G_DIR,
-/* ABSDIR */    G_ROOT, G_DIR,  G_DIR,  G_DRD,  G_DIR,  G_DIR,  G_DIR,
-/* ROOT */  G_ROOT, G_DIR,  G_DIR,  G_VRD,  G_DIR,  G_DIR,  G_DIR,
-
-};
-
-struct dirinf
-{
-    int flags;
-
-    struct
-    {
-        char * ptr;
-        int   len;
-    } dev, dir;
-};
-
-static char * strnchr( char * buf, int c, int len )
-{
-    while ( len-- )
-        if ( *buf && ( *buf++ == c ) )
-            return buf - 1;
-    return 0;
-}
-
-
-static void dir_flags( char * buf, int len, struct dirinf * i )
-{
-    char * p;
-
-    if ( !buf || !len )
-    {
-        i->flags = DIR_EMPTY;
-        i->dev.ptr =
-        i->dir.ptr = 0;
-        i->dev.len =
-        i->dir.len = 0;
-    }
-    else if ( p = strnchr( buf, ':', len ) )
-    {
-        i->dev.ptr = buf;
-        i->dev.len = p + 1 - buf;
-        i->dir.ptr = buf + i->dev.len;
-        i->dir.len = len - i->dev.len;
-        i->flags = i->dir.len && *i->dir.ptr == '[' ? DIR_DEVDIR : DIR_DEV;
-    }
-    else
-    {
-        i->dev.ptr = buf;
-        i->dev.len = 0;
-        i->dir.ptr = buf;
-        i->dir.len = len;
-
-        if ( ( *buf == '[' ) && ( buf[1] == ']' ) )
-            i->flags = DIR_EMPTY;
-        else if ( ( *buf == '[' ) && ( buf[1] == '.' ) )
-            i->flags = DIR_DOTDIR;
-        else if ( ( *buf == '[' ) && ( buf[1] == '-' ) )
-            i->flags = DIR_DASHDIR;
-        else
-            i->flags = DIR_ABSDIR;
-    }
-
-    /* But if its rooted in any way. */
-
-    if ( ( i->dir.len == 8 ) && !strncmp( i->dir.ptr, "[000000]", 8 ) )
-        i->flags = DIR_ROOT;
-}
-
-
-/*
- * path_build() - build a filename given dir/base/suffix/member
- */
-
-void path_build( PATHNAME * f, string * file, int binding )
-{
-    struct dirinf root;
-    struct dirinf dir;
-    int g;
-
-    file_build1( f, file );
-
-    /* Get info on root and dir for combining. */
-    dir_flags( f->f_root.ptr, f->f_root.len, &root );
-    dir_flags( f->f_dir.ptr, f->f_dir.len, &dir );
-
-    /* Combine. */
-    switch ( g = grid[ root.flags ][ dir.flags ] )
-    {
-    case G_DIR:
-        /* take dir */
-        string_append_range( file, f->f_dir.ptr, f->f_dir.ptr + f->f_dir.len  );
-        break;
-
-    case G_ROOT:
-        /* take root */
-        string_append_range( file, f->f_root.ptr, f->f_root.ptr + f->f_root.len  );
-        break;
-
-    case G_VAD:
-        /* root's dev + abs directory */
-        string_append_range( file, root.dev.ptr, root.dev.ptr + root.dev.len  );
-        string_append_range( file, dir.dir.ptr, dir.dir.ptr + dir.dir.len  );
-        break;
-
-    case G_DRD:
-    case G_DDD:
-        /* root's dev:[dir] + rel directory */
-        string_append_range( file, f->f_root.ptr, f->f_root.ptr + f->f_root.len  );
-
-        /* sanity checks: root ends with ] */
-
-        if ( file->value[file->size - 1] == ']' )
-            string_pop_back( file );
-
-        /* Add . if separating two -'s */
-
-        if ( g == G_DDD )
-            string_push_back( file, '.' );
-
-        /* skip [ of dir */
-        string_append_range( file, dir.dir.ptr + 1, dir.dir.ptr + 1 + dir.dir.len - 1  );
-        break;
-
-    case G_VRD:
-        /* root's dev + rel directory made abs */
-        string_append_range( file, root.dev.ptr, root.dev.ptr + root.dev.len  );
-        string_push_back( file, '[' );
-        /* skip [. of rel dir */
-        string_append_range( file, dir.dir.ptr + 2, dir.dir.ptr + 2 + dir.dir.len - 2  );
-        break;
-    }
-
-# ifdef DEBUG
-    if ( DEBUG_SEARCH && ( root.flags || dir.flags ) )
-        printf( "%d x %d = %d (%s)\n", root.flags, dir.flags,
-                grid[ root.flags ][ dir.flags ], file->value );
-# endif
-
-    /*
-     * Now do the special :P modifier when no file was present.
-     *  (none)      (none)
-     *  [dir1.dir2] [dir1]
-     *  [dir]       [000000]
-     *  [.dir]      (none)
-     *  []      []
-     */
-
-    if ( ( file->value[ file->size - 1 ] == ']' ) && f->parent )
-    {
-        char * p = file->value + file->size;
-        while ( p-- > file->value )
-        {
-            if ( *p == '.' )
-            {
-                /* If we've truncated everything and left with '[',
-                   return empty string. */
-                if ( p == file->value + 1 )
-                    string_truncate( file, 0 );
-                else
-                {
-                    string_truncate( file, p - file->value );
-                    string_push_back( file, ']' );
-                }
-                break;
-            }
-            
-            if ( *p == '-' )
-            {
-                /* handle .- or - */
-                if ( ( p > file->value ) && ( p[ -1 ] == '.' ) )
-                    --p;
-
-                *p++ = ']';
-                break;
-            }
-            
-            if ( *p == '[' )
-            {
-                if ( p[ 1 ] == ']' )
-                {
-                    /* CONSIDER: I don't see any use of this code. We immediately
-                       break, and 'p' is a local variable. */
-                    p += 2;
-                }
-                else
-                {
-                    string_truncate( file, p - file->value );
-                    string_append( file, "[000000]" );
-                }
-                break;
-            }
-        }
-    }
-
-    /* Now copy the file pieces. */
-    if ( f->f_base.len )
-    {
-        string_append_range( file, f->f_base.ptr, f->f_base.ptr + f->f_base.len  );
-    }
-
-    /* If there is no suffix, we append a "." onto all generated names. This
-     * keeps VMS from appending its own (wrong) idea of what the suffix should
-     * be.
-     */
-    if ( f->f_suffix.len )
-        string_append_range( file, f->f_suffix.ptr, f->f_suffix.ptr + f->f_suffix.len  );
-    else if ( binding && f->f_base.len )
-        string_push_back( file, '.' );
-
-    if ( f->f_member.len )
-    {
-        string_push_back( file, '(' );
-        string_append_range( file, f->f_member.ptr, f->f_member.ptr + f->f_member.len  );
-        string_push_back( file, ')' );
-    }
-
-# ifdef DEBUG
-    if ( DEBUG_SEARCH )
-        printf( "built %.*s + %.*s / %.*s suf %.*s mem %.*s -> %s\n",
-               f->f_root.len, f->f_root.ptr,
-               f->f_dir.len, f->f_dir.ptr,
-               f->f_base.len, f->f_base.ptr,
-               f->f_suffix.len, f->f_suffix.ptr,
-               f->f_member.len, f->f_member.ptr,
-               file->value );
-# endif
-}
-
-
-/*
- *  path_parent() - make a PATHNAME point to its parent dir
- */
-
-void path_parent( PATHNAME * f )
-{
-    if ( f->f_base.len )
-    {
-        f->f_base.ptr =
-        f->f_suffix.ptr =
-        f->f_member.ptr = "";
-
-        f->f_base.len =
-        f->f_suffix.len =
-        f->f_member.len = 0;
-    }
-    else
-    {
-        f->parent = 1;
-    }
-}
-
-# endif /* VMS */
diff --git a/jam-files/engine/pwd.c b/jam-files/engine/pwd.c
deleted file mode 100644
index 90c8eb17..00000000
--- a/jam-files/engine/pwd.c
+++ /dev/null
@@ -1,66 +0,0 @@
-/* Copyright Vladimir Prus 2002, Rene Rivera 2005. Distributed under the Boost */
-/* Software License, Version 1.0. (See accompanying */
-/* file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */
-
-#include "jam.h"
-#include "lists.h"
-#include "newstr.h"
-#include "pathsys.h"
-#include "mem.h"
-
-#include <limits.h>
-#include <errno.h>
-
-/* MinGW on windows declares PATH_MAX in limits.h */
-#if defined(NT) && ! defined(__GNUC__)
-#include <direct.h>
-#define PATH_MAX _MAX_PATH
-#else
-#include <unistd.h>
-#if defined(__COMO__)
-     #include <linux/limits.h>
-#endif
-#endif
-
-#ifndef PATH_MAX
-	#define PATH_MAX 1024
-#endif
-
-/* The current directory can't change in bjam, so optimize this to cache
-** the result.
-*/
-static char * pwd_result = NULL;
-
-
-LIST*
-pwd(void)
-{
-    if (!pwd_result)
-    {
-		int buffer_size = PATH_MAX;
-		char * result_buffer = 0;
-		do
-		{
-			char * buffer = BJAM_MALLOC_RAW(buffer_size);
-			result_buffer = getcwd(buffer,buffer_size);
-			if (result_buffer)
-			{
-				#ifdef NT
-				pwd_result = short_path_to_long_path(result_buffer);
-				#else
-				pwd_result = newstr(result_buffer);
-				#endif
-			}
-			buffer_size *= 2;
-			BJAM_FREE_RAW(buffer);
-		}
-		while (!pwd_result && errno == ERANGE);
-		
-		if (!pwd_result)
-		{
-            perror("can not get current directory");
-            return L0;
-        }
-    }
-    return list_new(L0, pwd_result);
-}
diff --git a/jam-files/engine/pwd.h b/jam-files/engine/pwd.h
deleted file mode 100644
index 37cb531e..00000000
--- a/jam-files/engine/pwd.h
+++ /dev/null
@@ -1,10 +0,0 @@
-/* Copyright Vladimir Prus 2002. Distributed under the Boost */
-/* Software License, Version 1.0. (See accompanying */
-/* file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */
-
-#ifndef PWD_H
-#define PWD_H
-
-LIST* pwd(void);
-
-#endif
diff --git a/jam-files/engine/regexp.c b/jam-files/engine/regexp.c
deleted file mode 100644
index 30197a2f..00000000
--- a/jam-files/engine/regexp.c
+++ /dev/null
@@ -1,1328 +0,0 @@
-/*
- * regcomp and regexec -- regsub and regerror are elsewhere
- *
- *  Copyright (c) 1986 by University of Toronto.
- *  Written by Henry Spencer.  Not derived from licensed software.
- *
- *  Permission is granted to anyone to use this software for any
- *  purpose on any computer system, and to redistribute it freely,
- *  subject to the following restrictions:
- *
- *  1. The author is not responsible for the consequences of use of
- *      this software, no matter how awful, even if they arise
- *      from defects in it.
- *
- *  2. The origin of this software must not be misrepresented, either
- *      by explicit claim or by omission.
- *
- *  3. Altered versions must be plainly marked as such, and must not
- *      be misrepresented as being the original software.
- *** THIS IS AN ALTERED VERSION.  It was altered by John Gilmore,
- *** hoptoad!gnu, on 27 Dec 1986, to add \n as an alternative to |
- *** to assist in implementing egrep.
- *** THIS IS AN ALTERED VERSION.  It was altered by John Gilmore,
- *** hoptoad!gnu, on 27 Dec 1986, to add \< and \> for word-matching
- *** as in BSD grep and ex.
- *** THIS IS AN ALTERED VERSION.  It was altered by John Gilmore,
- *** hoptoad!gnu, on 28 Dec 1986, to optimize characters quoted with \.
- *** THIS IS AN ALTERED VERSION.  It was altered by James A. Woods,
- *** ames!jaw, on 19 June 1987, to quash a regcomp() redundancy.
- *** THIS IS AN ALTERED VERSION.  It was altered by Christopher Seiwald
- *** seiwald@vix.com, on 28 August 1993, for use in jam.  Regmagic.h
- *** was moved into regexp.h, and the include of regexp.h now uses "'s
- *** to avoid conflicting with the system regexp.h.  Const, bless its
- *** soul, was removed so it can compile everywhere.  The declaration
- *** of strchr() was in conflict on AIX, so it was removed (as it is
- *** happily defined in string.h).
- *** THIS IS AN ALTERED VERSION.  It was altered by Christopher Seiwald
- *** seiwald@perforce.com, on 20 January 2000, to use function prototypes.
- *
- * Beware that some of this code is subtly aware of the way operator precedence
- * is structured in regular expressions. Serious changes in regular-expression
- * syntax might require a total rethink.
- */
-
-
-#include "jam.h"
-#include "regexp.h"
-#include <stdio.h>
-#include <ctype.h>
-#ifndef ultrix
-    #include <stdlib.h>
-#endif
-#include <string.h>
-
-
-/*
- * The "internal use only" fields in regexp.h are present to pass info from
- * compile to execute that permits the execute phase to run lots faster on
- * simple cases. They are:
- :
- *  regstart char that must begin a match; '\0' if none obvious.
- *  reganch  is the match anchored (at beginning-of-line only)?
- *  regmust  string (pointer into program) that match must include, or NULL.
- *  regmlen  length of regmust string.
- *
- * Regstart and reganch permit very fast decisions on suitable starting points
- * for a match, cutting down the work a lot.  Regmust permits fast rejection of
- * lines that cannot possibly match.  The regmust tests are costly enough that
- * regcomp() supplies a regmust only if the r.e. contains something potentially
- * expensive (at present, the only such thing detected is * or + at the start of
- * the r.e., which can involve a lot of backup). Regmlen is supplied because the
- * test in regexec() needs it and regcomp() is computing it anyway.
- */
-
-/*
- * Structure for regexp "program". This is essentially a linear encoding of a
- * nondeterministic finite-state machine (aka syntax charts or "railroad normal
- * form" in parsing technology). Each node is an opcode plus a "next" pointer,
- * possibly plus an operand. "Next" pointers of all nodes except BRANCH
- * implement concatenation; a "next" pointer with a BRANCH on both ends of it is
- * connecting two alternatives. [Here we have one of the subtle syntax
- * dependencies: an individual BRANCH, as opposed to a collection of them, is
- * never concatenated with anything because of operator precedence.] The operand
- * of some types of node is a literal string; for others, it is a node leading
- * into a sub-FSM. In particular, the operand of a BRANCH node is the first node
- * of the branch. [NB this is *not* a tree structure: the tail of the branch
- * connects to the thing following the set of BRANCHes.] The opcodes are:
- */
-
-/* definition   number  opnd?   meaning */
-#define END 0   /* no   End of program. */
-#define BOL 1   /* no   Match "" at beginning of line. */
-#define EOL 2   /* no   Match "" at end of line. */
-#define ANY 3   /* no   Match any one character. */
-#define ANYOF   4   /* str  Match any character in this string. */
-#define ANYBUT  5   /* str  Match any character not in this string. */
-#define BRANCH  6   /* node Match this alternative, or the next... */
-#define BACK    7   /* no   Match "", "next" ptr points backward. */
-#define EXACTLY 8   /* str  Match this string. */
-#define NOTHING 9   /* no   Match empty string. */
-#define STAR    10  /* node Match this (simple) thing 0 or more times. */
-#define PLUS    11  /* node Match this (simple) thing 1 or more times. */
-#define WORDA   12  /* no   Match "" at wordchar, where prev is nonword */
-#define WORDZ   13  /* no   Match "" at nonwordchar, where prev is word */
-#define OPEN    20  /* no   Mark this point in input as start of #n. */
-            /*  OPEN+1 is number 1, etc. */
-#define CLOSE   30  /* no   Analogous to OPEN. */
-
-
-/*
- * Opcode notes:
- *
- * BRANCH   The set of branches constituting a single choice are hooked
- *      together with their "next" pointers, since precedence prevents
- *      anything being concatenated to any individual branch.  The
- *      "next" pointer of the last BRANCH in a choice points to the
- *      thing following the whole choice.  This is also where the
- *      final "next" pointer of each individual branch points; each
- *      branch starts with the operand node of a BRANCH node.
- *
- * BACK     Normal "next" pointers all implicitly point forward; BACK
- *      exists to make loop structures possible.
- *
- * STAR,PLUS    '?', and complex '*' and '+', are implemented as circular
- *      BRANCH structures using BACK.  Simple cases (one character
- *      per match) are implemented with STAR and PLUS for speed
- *      and to minimize recursive plunges.
- *
- * OPEN,CLOSE   ...are numbered at compile time.
- */
-
-/*
- * A node is one char of opcode followed by two chars of "next" pointer.
- * "Next" pointers are stored as two 8-bit pieces, high order first.  The
- * value is a positive offset from the opcode of the node containing it.
- * An operand, if any, simply follows the node.  (Note that much of the
- * code generation knows about this implicit relationship.)
- *
- * Using two bytes for the "next" pointer is vast overkill for most things,
- * but allows patterns to get big without disasters.
- */
-#define OP(p)   (*(p))
-#define NEXT(p) (((*((p)+1)&0377)<<8) + (*((p)+2)&0377))
-#define OPERAND(p)  ((p) + 3)
-
-/*
- * See regmagic.h for one further detail of program structure.
- */
-
-
-/*
- * Utility definitions.
- */
-#ifndef CHARBITS
-#define UCHARAT(p)  ((int)*(unsigned char *)(p))
-#else
-#define UCHARAT(p)  ((int)*(p)&CHARBITS)
-#endif
-
-#define FAIL(m) { regerror(m); return(NULL); }
-#define ISMULT(c)   ((c) == '*' || (c) == '+' || (c) == '?')
-
-/*
- * Flags to be passed up and down.
- */
-#define HASWIDTH    01  /* Known never to match null string. */
-#define SIMPLE      02  /* Simple enough to be STAR/PLUS operand. */
-#define SPSTART     04  /* Starts with * or +. */
-#define WORST       0   /* Worst case. */
-
-/*
- * Global work variables for regcomp().
- */
-static char *regparse;      /* Input-scan pointer. */
-static int regnpar;     /* () count. */
-static char regdummy;
-static char *regcode;       /* Code-emit pointer; &regdummy = don't. */
-static long regsize;        /* Code size. */
-
-/*
- * Forward declarations for regcomp()'s friends.
- */
-#ifndef STATIC
-#define STATIC  static
-#endif
-STATIC char *reg( int paren, int *flagp );
-STATIC char *regbranch( int *flagp );
-STATIC char *regpiece( int *flagp );
-STATIC char *regatom( int *flagp );
-STATIC char *regnode( int op );
-STATIC char *regnext( register char *p );
-STATIC void regc( int b );
-STATIC void reginsert( char op, char *opnd );
-STATIC void regtail( char *p, char *val );
-STATIC void regoptail( char *p, char *val );
-#ifdef STRCSPN
-STATIC int strcspn();
-#endif
-
-/*
- - regcomp - compile a regular expression into internal code
- *
- * We can't allocate space until we know how big the compiled form will be,
- * but we can't compile it (and thus know how big it is) until we've got a
- * place to put the code.  So we cheat:  we compile it twice, once with code
- * generation turned off and size counting turned on, and once "for real".
- * This also means that we don't allocate space until we are sure that the
- * thing really will compile successfully, and we never have to move the
- * code and thus invalidate pointers into it.  (Note that it has to be in
- * one piece because free() must be able to free it all.)
- *
- * Beware that the optimization-preparation code in here knows about some
- * of the structure of the compiled regexp.
- */
-regexp *
-regcomp( char *exp )
-{
-    register regexp *r;
-    register char *scan;
-    register char *longest;
-    register unsigned len;
-    int flags;
-
-    if (exp == NULL)
-        FAIL("NULL argument");
-
-    /* First pass: determine size, legality. */
-#ifdef notdef
-    if (exp[0] == '.' && exp[1] == '*') exp += 2;  /* aid grep */
-#endif
-    regparse = (char *)exp;
-    regnpar = 1;
-    regsize = 0L;
-    regcode = &regdummy;
-    regc(MAGIC);
-    if (reg(0, &flags) == NULL)
-        return(NULL);
-
-    /* Small enough for pointer-storage convention? */
-    if (regsize >= 32767L)      /* Probably could be 65535L. */
-        FAIL("regexp too big");
-
-    /* Allocate space. */
-    r = (regexp *)BJAM_MALLOC(sizeof(regexp) + (unsigned)regsize);
-    if (r == NULL)
-        FAIL("out of space");
-
-    /* Second pass: emit code. */
-    regparse = (char *)exp;
-    regnpar = 1;
-    regcode = r->program;
-    regc(MAGIC);
-    if (reg(0, &flags) == NULL)
-        return(NULL);
-
-    /* Dig out information for optimizations. */
-    r->regstart = '\0'; /* Worst-case defaults. */
-    r->reganch = 0;
-    r->regmust = NULL;
-    r->regmlen = 0;
-    scan = r->program+1;            /* First BRANCH. */
-    if (OP(regnext(scan)) == END) {     /* Only one top-level choice. */
-        scan = OPERAND(scan);
-
-        /* Starting-point info. */
-        if (OP(scan) == EXACTLY)
-            r->regstart = *OPERAND(scan);
-        else if (OP(scan) == BOL)
-            r->reganch++;
-
-        /*
-         * If there's something expensive in the r.e., find the
-         * longest literal string that must appear and make it the
-         * regmust.  Resolve ties in favor of later strings, since
-         * the regstart check works with the beginning of the r.e.
-         * and avoiding duplication strengthens checking.  Not a
-         * strong reason, but sufficient in the absence of others.
-         */
-        if (flags&SPSTART) {
-            longest = NULL;
-            len = 0;
-            for (; scan != NULL; scan = regnext(scan))
-                if (OP(scan) == EXACTLY && strlen(OPERAND(scan)) >= len) {
-                    longest = OPERAND(scan);
-                    len = strlen(OPERAND(scan));
-                }
-            r->regmust = longest;
-            r->regmlen = len;
-        }
-    }
-
-    return(r);
-}
-
-/*
- - reg - regular expression, i.e. main body or parenthesized thing
- *
- * Caller must absorb opening parenthesis.
- *
- * Combining parenthesis handling with the base level of regular expression
- * is a trifle forced, but the need to tie the tails of the branches to what
- * follows makes it hard to avoid.
- */
-static char *
-reg(
-    int paren,          /* Parenthesized? */
-    int *flagp )
-{
-    register char *ret;
-    register char *br;
-    register char *ender;
-    register int parno = 0;
-    int flags;
-
-    *flagp = HASWIDTH;  /* Tentatively. */
-
-    /* Make an OPEN node, if parenthesized. */
-    if (paren) {
-        if (regnpar >= NSUBEXP)
-            FAIL("too many ()");
-        parno = regnpar;
-        regnpar++;
-        ret = regnode(OPEN+parno);
-    } else
-        ret = NULL;
-
-    /* Pick up the branches, linking them together. */
-    br = regbranch(&flags);
-    if (br == NULL)
-        return(NULL);
-    if (ret != NULL)
-        regtail(ret, br);   /* OPEN -> first. */
-    else
-        ret = br;
-    if (!(flags&HASWIDTH))
-        *flagp &= ~HASWIDTH;
-    *flagp |= flags&SPSTART;
-    while (*regparse == '|' || *regparse == '\n') {
-        regparse++;
-        br = regbranch(&flags);
-        if (br == NULL)
-            return(NULL);
-        regtail(ret, br);   /* BRANCH -> BRANCH. */
-        if (!(flags&HASWIDTH))
-            *flagp &= ~HASWIDTH;
-        *flagp |= flags&SPSTART;
-    }
-
-    /* Make a closing node, and hook it on the end. */
-    ender = regnode((paren) ? CLOSE+parno : END);
-    regtail(ret, ender);
-
-    /* Hook the tails of the branches to the closing node. */
-    for (br = ret; br != NULL; br = regnext(br))
-        regoptail(br, ender);
-
-    /* Check for proper termination. */
-    if (paren && *regparse++ != ')') {
-        FAIL("unmatched ()");
-    } else if (!paren && *regparse != '\0') {
-        if (*regparse == ')') {
-            FAIL("unmatched ()");
-        } else
-            FAIL("junk on end");    /* "Can't happen". */
-        /* NOTREACHED */
-    }
-
-    return(ret);
-}
-
-/*
- - regbranch - one alternative of an | operator
- *
- * Implements the concatenation operator.
- */
-static char *
-regbranch( int *flagp )
-{
-    register char *ret;
-    register char *chain;
-    register char *latest;
-    int flags;
-
-    *flagp = WORST;     /* Tentatively. */
-
-    ret = regnode(BRANCH);
-    chain = NULL;
-    while (*regparse != '\0' && *regparse != ')' &&
-           *regparse != '\n' && *regparse != '|') {
-        latest = regpiece(&flags);
-        if (latest == NULL)
-            return(NULL);
-        *flagp |= flags&HASWIDTH;
-        if (chain == NULL)  /* First piece. */
-            *flagp |= flags&SPSTART;
-        else
-            regtail(chain, latest);
-        chain = latest;
-    }
-    if (chain == NULL)  /* Loop ran zero times. */
-        (void) regnode(NOTHING);
-
-    return(ret);
-}
-
-/*
- - regpiece - something followed by possible [*+?]
- *
- * Note that the branching code sequences used for ? and the general cases
- * of * and + are somewhat optimized:  they use the same NOTHING node as
- * both the endmarker for their branch list and the body of the last branch.
- * It might seem that this node could be dispensed with entirely, but the
- * endmarker role is not redundant.
- */
-static char *
-regpiece( int *flagp )
-{
-    register char *ret;
-    register char op;
-    register char *next;
-    int flags;
-
-    ret = regatom(&flags);
-    if (ret == NULL)
-        return(NULL);
-
-    op = *regparse;
-    if (!ISMULT(op)) {
-        *flagp = flags;
-        return(ret);
-    }
-
-    if (!(flags&HASWIDTH) && op != '?')
-        FAIL("*+ operand could be empty");
-    *flagp = (op != '+') ? (WORST|SPSTART) : (WORST|HASWIDTH);
-
-    if (op == '*' && (flags&SIMPLE))
-        reginsert(STAR, ret);
-    else if (op == '*') {
-        /* Emit x* as (x&|), where & means "self". */
-        reginsert(BRANCH, ret);         /* Either x */
-        regoptail(ret, regnode(BACK));      /* and loop */
-        regoptail(ret, ret);            /* back */
-        regtail(ret, regnode(BRANCH));      /* or */
-        regtail(ret, regnode(NOTHING));     /* null. */
-    } else if (op == '+' && (flags&SIMPLE))
-        reginsert(PLUS, ret);
-    else if (op == '+') {
-        /* Emit x+ as x(&|), where & means "self". */
-        next = regnode(BRANCH);         /* Either */
-        regtail(ret, next);
-        regtail(regnode(BACK), ret);        /* loop back */
-        regtail(next, regnode(BRANCH));     /* or */
-        regtail(ret, regnode(NOTHING));     /* null. */
-    } else if (op == '?') {
-        /* Emit x? as (x|) */
-        reginsert(BRANCH, ret);         /* Either x */
-        regtail(ret, regnode(BRANCH));      /* or */
-        next = regnode(NOTHING);        /* null. */
-        regtail(ret, next);
-        regoptail(ret, next);
-    }
-    regparse++;
-    if (ISMULT(*regparse))
-        FAIL("nested *?+");
-
-    return(ret);
-}
-
-/*
- - regatom - the lowest level
- *
- * Optimization:  gobbles an entire sequence of ordinary characters so that
- * it can turn them into a single node, which is smaller to store and
- * faster to run.  Backslashed characters are exceptions, each becoming a
- * separate node; the code is simpler that way and it's not worth fixing.
- */
-static char *
-regatom( int *flagp )
-{
-    register char *ret;
-    int flags;
-
-    *flagp = WORST;     /* Tentatively. */
-
-    switch (*regparse++) {
-    /* FIXME: these chars only have meaning at beg/end of pat? */
-    case '^':
-        ret = regnode(BOL);
-        break;
-    case '$':
-        ret = regnode(EOL);
-        break;
-    case '.':
-        ret = regnode(ANY);
-        *flagp |= HASWIDTH|SIMPLE;
-        break;
-    case '[': {
-            register int classr;
-            register int classend;
-
-            if (*regparse == '^') { /* Complement of range. */
-                ret = regnode(ANYBUT);
-                regparse++;
-            } else
-                ret = regnode(ANYOF);
-            if (*regparse == ']' || *regparse == '-')
-                regc(*regparse++);
-            while (*regparse != '\0' && *regparse != ']') {
-                if (*regparse == '-') {
-                    regparse++;
-                    if (*regparse == ']' || *regparse == '\0')
-                        regc('-');
-                    else {
-                        classr = UCHARAT(regparse-2)+1;
-                        classend = UCHARAT(regparse);
-                        if (classr > classend+1)
-                            FAIL("invalid [] range");
-                        for (; classr <= classend; classr++)
-                            regc(classr);
-                        regparse++;
-                    }
-                } else
-                    regc(*regparse++);
-            }
-            regc('\0');
-            if (*regparse != ']')
-                FAIL("unmatched []");
-            regparse++;
-            *flagp |= HASWIDTH|SIMPLE;
-        }
-        break;
-    case '(':
-        ret = reg(1, &flags);
-        if (ret == NULL)
-            return(NULL);
-        *flagp |= flags&(HASWIDTH|SPSTART);
-        break;
-    case '\0':
-    case '|':
-    case '\n':
-    case ')':
-        FAIL("internal urp");   /* Supposed to be caught earlier. */
-        break;
-    case '?':
-    case '+':
-    case '*':
-        FAIL("?+* follows nothing");
-        break;
-    case '\\':
-        switch (*regparse++) {
-        case '\0':
-            FAIL("trailing \\");
-            break;
-        case '<':
-            ret = regnode(WORDA);
-            break;
-        case '>':
-            ret = regnode(WORDZ);
-            break;
-        /* FIXME: Someday handle \1, \2, ... */
-        default:
-            /* Handle general quoted chars in exact-match routine */
-            goto de_fault;
-        }
-        break;
-    de_fault:
-    default:
-        /*
-         * Encode a string of characters to be matched exactly.
-         *
-         * This is a bit tricky due to quoted chars and due to
-         * '*', '+', and '?' taking the SINGLE char previous
-         * as their operand.
-         *
-         * On entry, the char at regparse[-1] is going to go
-         * into the string, no matter what it is.  (It could be
-         * following a \ if we are entered from the '\' case.)
-         *
-         * Basic idea is to pick up a good char in  ch  and
-         * examine the next char.  If it's *+? then we twiddle.
-         * If it's \ then we frozzle.  If it's other magic char
-         * we push  ch  and terminate the string.  If none of the
-         * above, we push  ch  on the string and go around again.
-         *
-         *  regprev  is used to remember where "the current char"
-         * starts in the string, if due to a *+? we need to back
-         * up and put the current char in a separate, 1-char, string.
-         * When  regprev  is NULL,  ch  is the only char in the
-         * string; this is used in *+? handling, and in setting
-         * flags |= SIMPLE at the end.
-         */
-        {
-            char *regprev;
-            register char ch;
-
-            regparse--;         /* Look at cur char */
-            ret = regnode(EXACTLY);
-            for ( regprev = 0 ; ; ) {
-                ch = *regparse++;   /* Get current char */
-                switch (*regparse) {    /* look at next one */
-
-                default:
-                    regc(ch);   /* Add cur to string */
-                    break;
-
-                case '.': case '[': case '(':
-                case ')': case '|': case '\n':
-                case '$': case '^':
-                case '\0':
-                /* FIXME, $ and ^ should not always be magic */
-                magic:
-                    regc(ch);   /* dump cur char */
-                    goto done;  /* and we are done */
-
-                case '?': case '+': case '*':
-                    if (!regprev)   /* If just ch in str, */
-                        goto magic; /* use it */
-                    /* End mult-char string one early */
-                    regparse = regprev; /* Back up parse */
-                    goto done;
-
-                case '\\':
-                    regc(ch);   /* Cur char OK */
-                    switch (regparse[1]){ /* Look after \ */
-                    case '\0':
-                    case '<':
-                    case '>':
-                    /* FIXME: Someday handle \1, \2, ... */
-                        goto done; /* Not quoted */
-                    default:
-                        /* Backup point is \, scan                           * point is after it. */
-                        regprev = regparse;
-                        regparse++;
-                        continue;   /* NOT break; */
-                    }
-                }
-                regprev = regparse; /* Set backup point */
-            }
-        done:
-            regc('\0');
-            *flagp |= HASWIDTH;
-            if (!regprev)       /* One char? */
-                *flagp |= SIMPLE;
-        }
-        break;
-    }
-
-    return(ret);
-}
-
-/*
- - regnode - emit a node
- */
-static char *           /* Location. */
-regnode( int op )
-{
-    register char *ret;
-    register char *ptr;
-
-    ret = regcode;
-    if (ret == &regdummy) {
-        regsize += 3;
-        return(ret);
-    }
-
-    ptr = ret;
-    *ptr++ = op;
-    *ptr++ = '\0';      /* Null "next" pointer. */
-    *ptr++ = '\0';
-    regcode = ptr;
-
-    return(ret);
-}
-
-/*
- - regc - emit (if appropriate) a byte of code
- */
-static void
-regc( int b )
-{
-    if (regcode != &regdummy)
-        *regcode++ = b;
-    else
-        regsize++;
-}
-
-/*
- - reginsert - insert an operator in front of already-emitted operand
- *
- * Means relocating the operand.
- */
-static void
-reginsert(
-    char op,
-    char *opnd )
-{
-    register char *src;
-    register char *dst;
-    register char *place;
-
-    if (regcode == &regdummy) {
-        regsize += 3;
-        return;
-    }
-
-    src = regcode;
-    regcode += 3;
-    dst = regcode;
-    while (src > opnd)
-        *--dst = *--src;
-
-    place = opnd;       /* Op node, where operand used to be. */
-    *place++ = op;
-    *place++ = '\0';
-    *place++ = '\0';
-}
-
-/*
- - regtail - set the next-pointer at the end of a node chain
- */
-static void
-regtail(
-    char *p,
-    char *val )
-{
-    register char *scan;
-    register char *temp;
-    register int offset;
-
-    if (p == &regdummy)
-        return;
-
-    /* Find last node. */
-    scan = p;
-    for (;;) {
-        temp = regnext(scan);
-        if (temp == NULL)
-            break;
-        scan = temp;
-    }
-
-    if (OP(scan) == BACK)
-        offset = scan - val;
-    else
-        offset = val - scan;
-    *(scan+1) = (offset>>8)&0377;
-    *(scan+2) = offset&0377;
-}
-
-/*
- - regoptail - regtail on operand of first argument; nop if operandless
- */
-
-static void
-regoptail(
-    char *p,
-    char *val )
-{
-    /* "Operandless" and "op != BRANCH" are synonymous in practice. */
-    if (p == NULL || p == &regdummy || OP(p) != BRANCH)
-        return;
-    regtail(OPERAND(p), val);
-}
-
-/*
- * regexec and friends
- */
-
-/*
- * Global work variables for regexec().
- */
-static char *reginput;      /* String-input pointer. */
-static char *regbol;        /* Beginning of input, for ^ check. */
-static char **regstartp;    /* Pointer to startp array. */
-static char **regendp;      /* Ditto for endp. */
-
-/*
- * Forwards.
- */
-STATIC int regtry( regexp *prog, char *string );
-STATIC int regmatch( char *prog );
-STATIC int regrepeat( char *p );
-
-#ifdef DEBUG
-int regnarrate = 0;
-void regdump();
-STATIC char *regprop();
-#endif
-
-/*
- - regexec - match a regexp against a string
- */
-int
-regexec(
-    register regexp *prog,
-    register char *string )
-{
-    register char *s;
-
-    /* Be paranoid... */
-    if (prog == NULL || string == NULL) {
-        regerror("NULL parameter");
-        return(0);
-    }
-
-    /* Check validity of program. */
-    if (UCHARAT(prog->program) != MAGIC) {
-        regerror("corrupted program");
-        return(0);
-    }
-
-    /* If there is a "must appear" string, look for it. */
-    if ( prog->regmust != NULL )
-    {
-        s = (char *)string;
-        while ( ( s = strchr( s, prog->regmust[ 0 ] ) ) != NULL )
-        {
-            if ( !strncmp( s, prog->regmust, prog->regmlen ) )
-                break;  /* Found it. */
-            ++s;
-        }
-        if ( s == NULL )  /* Not present. */
-            return 0;
-    }
-
-    /* Mark beginning of line for ^ . */
-    regbol = (char *)string;
-
-    /* Simplest case:  anchored match need be tried only once. */
-    if ( prog->reganch )
-        return regtry( prog, string );
-
-    /* Messy cases:  unanchored match. */
-    s = (char *)string;
-    if (prog->regstart != '\0')
-        /* We know what char it must start with. */
-        while ((s = strchr(s, prog->regstart)) != NULL) {
-            if (regtry(prog, s))
-                return(1);
-            s++;
-        }
-    else
-        /* We do not -- general case. */
-        do {
-            if ( regtry( prog, s ) )
-                return( 1 );
-        } while ( *s++ != '\0' );
-
-    /* Failure. */
-    return 0;
-}
-
-
-/*
- * regtry() - try match at specific point.
- */
-
-static int          /* 0 failure, 1 success */
-regtry(
-    regexp *prog,
-    char *string )
-{
-    register int i;
-    register char * * sp;
-    register char * * ep;
-
-    reginput = string;
-    regstartp = prog->startp;
-    regendp = prog->endp;
-
-    sp = prog->startp;
-    ep = prog->endp;
-    for ( i = NSUBEXP; i > 0; --i )
-    {
-        *sp++ = NULL;
-        *ep++ = NULL;
-    }
-    if ( regmatch( prog->program + 1 ) )
-    {
-        prog->startp[ 0 ] = string;
-        prog->endp[ 0 ] = reginput;
-        return 1;
-    }
-    else
-        return 0;
-}
-
-
-/*
- * regmatch() - main matching routine.
- *
- * Conceptually the strategy is simple: check to see whether the current node
- * matches, call self recursively to see whether the rest matches, and then act
- * accordingly. In practice we make some effort to avoid recursion, in
- * particular by going through "ordinary" nodes (that do not need to know
- * whether the rest of the match failed) by a loop instead of by recursion.
- */
-
-static int          /* 0 failure, 1 success */
-regmatch( char * prog )
-{
-    char * scan;  /* Current node. */
-    char * next;  /* Next node. */
-
-    scan = prog;
-#ifdef DEBUG
-    if (scan != NULL && regnarrate)
-        fprintf(stderr, "%s(\n", regprop(scan));
-#endif
-    while (scan != NULL) {
-#ifdef DEBUG
-        if (regnarrate)
-            fprintf(stderr, "%s...\n", regprop(scan));
-#endif
-        next = regnext(scan);
-
-        switch (OP(scan)) {
-        case BOL:
-            if (reginput != regbol)
-                return(0);
-            break;
-        case EOL:
-            if (*reginput != '\0')
-                return(0);
-            break;
-        case WORDA:
-            /* Must be looking at a letter, digit, or _ */
-            if ((!isalnum(*reginput)) && *reginput != '_')
-                return(0);
-            /* Prev must be BOL or nonword */
-            if (reginput > regbol &&
-                (isalnum(reginput[-1]) || reginput[-1] == '_'))
-                return(0);
-            break;
-        case WORDZ:
-            /* Must be looking at non letter, digit, or _ */
-            if (isalnum(*reginput) || *reginput == '_')
-                return(0);
-            /* We don't care what the previous char was */
-            break;
-        case ANY:
-            if (*reginput == '\0')
-                return(0);
-            reginput++;
-            break;
-        case EXACTLY: {
-                register int len;
-                register char *opnd;
-
-                opnd = OPERAND(scan);
-                /* Inline the first character, for speed. */
-                if (*opnd != *reginput)
-                    return(0);
-                len = strlen(opnd);
-                if (len > 1 && strncmp(opnd, reginput, len) != 0)
-                    return(0);
-                reginput += len;
-            }
-            break;
-        case ANYOF:
-            if (*reginput == '\0' || strchr(OPERAND(scan), *reginput) == NULL)
-                return(0);
-            reginput++;
-            break;
-        case ANYBUT:
-            if (*reginput == '\0' || strchr(OPERAND(scan), *reginput) != NULL)
-                return(0);
-            reginput++;
-            break;
-        case NOTHING:
-            break;
-        case BACK:
-            break;
-        case OPEN+1:
-        case OPEN+2:
-        case OPEN+3:
-        case OPEN+4:
-        case OPEN+5:
-        case OPEN+6:
-        case OPEN+7:
-        case OPEN+8:
-        case OPEN+9: {
-                register int no;
-                register char *save;
-
-                no = OP(scan) - OPEN;
-                save = reginput;
-
-                if (regmatch(next)) {
-                    /*
-                     * Don't set startp if some later
-                     * invocation of the same parentheses
-                     * already has.
-                     */
-                    if (regstartp[no] == NULL)
-                        regstartp[no] = save;
-                    return(1);
-                } else
-                    return(0);
-            }
-            break;
-        case CLOSE+1:
-        case CLOSE+2:
-        case CLOSE+3:
-        case CLOSE+4:
-        case CLOSE+5:
-        case CLOSE+6:
-        case CLOSE+7:
-        case CLOSE+8:
-        case CLOSE+9: {
-                register int no;
-                register char *save;
-
-                no = OP(scan) - CLOSE;
-                save = reginput;
-
-                if (regmatch(next)) {
-                    /*
-                     * Don't set endp if some later
-                     * invocation of the same parentheses
-                     * already has.
-                     */
-                    if (regendp[no] == NULL)
-                        regendp[no] = save;
-                    return(1);
-                } else
-                    return(0);
-            }
-            break;
-        case BRANCH: {
-                register char *save;
-
-                if (OP(next) != BRANCH)     /* No choice. */
-                    next = OPERAND(scan);   /* Avoid recursion. */
-                else {
-                    do {
-                        save = reginput;
-                        if (regmatch(OPERAND(scan)))
-                            return(1);
-                        reginput = save;
-                        scan = regnext(scan);
-                    } while (scan != NULL && OP(scan) == BRANCH);
-                    return(0);
-                    /* NOTREACHED */
-                }
-            }
-            break;
-        case STAR:
-        case PLUS: {
-                register char nextch;
-                register int no;
-                register char *save;
-                register int min;
-
-                /*
-                 * Lookahead to avoid useless match attempts
-                 * when we know what character comes next.
-                 */
-                nextch = '\0';
-                if (OP(next) == EXACTLY)
-                    nextch = *OPERAND(next);
-                min = (OP(scan) == STAR) ? 0 : 1;
-                save = reginput;
-                no = regrepeat(OPERAND(scan));
-                while (no >= min) {
-                    /* If it could work, try it. */
-                    if (nextch == '\0' || *reginput == nextch)
-                        if (regmatch(next))
-                            return(1);
-                    /* Couldn't or didn't -- back up. */
-                    no--;
-                    reginput = save + no;
-                }
-                return(0);
-            }
-            break;
-        case END:
-            return(1);  /* Success! */
-            break;
-        default:
-            regerror("memory corruption");
-            return(0);
-            break;
-        }
-
-        scan = next;
-    }
-
-    /*
-     * We get here only if there's trouble -- normally "case END" is
-     * the terminating point.
-     */
-    regerror("corrupted pointers");
-    return(0);
-}
-
-/*
- - regrepeat - repeatedly match something simple, report how many
- */
-static int
-regrepeat( char *p )
-{
-    register int count = 0;
-    register char *scan;
-    register char *opnd;
-
-    scan = reginput;
-    opnd = OPERAND(p);
-    switch (OP(p)) {
-    case ANY:
-        count = strlen(scan);
-        scan += count;
-        break;
-    case EXACTLY:
-        while (*opnd == *scan) {
-            count++;
-            scan++;
-        }
-        break;
-    case ANYOF:
-        while (*scan != '\0' && strchr(opnd, *scan) != NULL) {
-            count++;
-            scan++;
-        }
-        break;
-    case ANYBUT:
-        while (*scan != '\0' && strchr(opnd, *scan) == NULL) {
-            count++;
-            scan++;
-        }
-        break;
-    default:        /* Oh dear.  Called inappropriately. */
-        regerror("internal foulup");
-        count = 0;  /* Best compromise. */
-        break;
-    }
-    reginput = scan;
-
-    return(count);
-}
-
-/*
- - regnext - dig the "next" pointer out of a node
- */
-static char *
-regnext( register char *p )
-{
-    register int offset;
-
-    if (p == &regdummy)
-        return(NULL);
-
-    offset = NEXT(p);
-    if (offset == 0)
-        return(NULL);
-
-    if (OP(p) == BACK)
-        return(p-offset);
-    else
-        return(p+offset);
-}
-
-#ifdef DEBUG
-
-STATIC char *regprop();
-
-/*
- - regdump - dump a regexp onto stdout in vaguely comprehensible form
- */
-void
-regdump( regexp *r )
-{
-    register char *s;
-    register char op = EXACTLY; /* Arbitrary non-END op. */
-    register char *next;
-
-
-    s = r->program + 1;
-    while (op != END) { /* While that wasn't END last time... */
-        op = OP(s);
-        printf("%2d%s", s-r->program, regprop(s));  /* Where, what. */
-        next = regnext(s);
-        if (next == NULL)       /* Next ptr. */
-            printf("(0)");
-        else
-            printf("(%d)", (s-r->program)+(next-s));
-        s += 3;
-        if (op == ANYOF || op == ANYBUT || op == EXACTLY) {
-            /* Literal string, where present. */
-            while (*s != '\0') {
-                putchar(*s);
-                s++;
-            }
-            s++;
-        }
-        putchar('\n');
-    }
-
-    /* Header fields of interest. */
-    if (r->regstart != '\0')
-        printf("start `%c' ", r->regstart);
-    if (r->reganch)
-        printf("anchored ");
-    if (r->regmust != NULL)
-        printf("must have \"%s\"", r->regmust);
-    printf("\n");
-}
-
-/*
- - regprop - printable representation of opcode
- */
-static char *
-regprop( char *op )
-{
-    register char *p;
-    static char buf[50];
-
-    (void) strcpy(buf, ":");
-
-    switch (OP(op)) {
-    case BOL:
-        p = "BOL";
-        break;
-    case EOL:
-        p = "EOL";
-        break;
-    case ANY:
-        p = "ANY";
-        break;
-    case ANYOF:
-        p = "ANYOF";
-        break;
-    case ANYBUT:
-        p = "ANYBUT";
-        break;
-    case BRANCH:
-        p = "BRANCH";
-        break;
-    case EXACTLY:
-        p = "EXACTLY";
-        break;
-    case NOTHING:
-        p = "NOTHING";
-        break;
-    case BACK:
-        p = "BACK";
-        break;
-    case END:
-        p = "END";
-        break;
-    case OPEN+1:
-    case OPEN+2:
-    case OPEN+3:
-    case OPEN+4:
-    case OPEN+5:
-    case OPEN+6:
-    case OPEN+7:
-    case OPEN+8:
-    case OPEN+9:
-        sprintf(buf+strlen(buf), "OPEN%d", OP(op)-OPEN);
-        p = NULL;
-        break;
-    case CLOSE+1:
-    case CLOSE+2:
-    case CLOSE+3:
-    case CLOSE+4:
-    case CLOSE+5:
-    case CLOSE+6:
-    case CLOSE+7:
-    case CLOSE+8:
-    case CLOSE+9:
-        sprintf(buf+strlen(buf), "CLOSE%d", OP(op)-CLOSE);
-        p = NULL;
-        break;
-    case STAR:
-        p = "STAR";
-        break;
-    case PLUS:
-        p = "PLUS";
-        break;
-    case WORDA:
-        p = "WORDA";
-        break;
-    case WORDZ:
-        p = "WORDZ";
-        break;
-    default:
-        regerror("corrupted opcode");
-        break;
-    }
-    if (p != NULL)
-        (void) strcat(buf, p);
-    return(buf);
-}
-#endif
-
-/*
- * The following is provided for those people who do not have strcspn() in
- * their C libraries.  They should get off their butts and do something
- * about it; at least one public-domain implementation of those (highly
- * useful) string routines has been published on Usenet.
- */
-#ifdef STRCSPN
-/*
- * strcspn - find length of initial segment of s1 consisting entirely
- * of characters not from s2
- */
-
-static int
-strcspn(
-    char *s1,
-    char *s2 )
-{
-    register char *scan1;
-    register char *scan2;
-    register int count;
-
-    count = 0;
-    for (scan1 = s1; *scan1 != '\0'; scan1++) {
-        for (scan2 = s2; *scan2 != '\0';)   /* ++ moved down. */
-            if (*scan1 == *scan2++)
-                return(count);
-        count++;
-    }
-    return(count);
-}
-#endif
diff --git a/jam-files/engine/regexp.h b/jam-files/engine/regexp.h
deleted file mode 100644
index 9d4604f6..00000000
--- a/jam-files/engine/regexp.h
+++ /dev/null
@@ -1,32 +0,0 @@
-/*
- * Definitions etc. for regexp(3) routines.
- *
- * Caveat:  this is V8 regexp(3) [actually, a reimplementation thereof],
- * not the System V one.
- */
-#ifndef REGEXP_DWA20011023_H
-# define REGEXP_DWA20011023_H
-
-#define NSUBEXP  10
-typedef struct regexp {
-    char *startp[NSUBEXP];
-    char *endp[NSUBEXP];
-    char regstart;      /* Internal use only. */
-    char reganch;       /* Internal use only. */
-    char *regmust;      /* Internal use only. */
-    int regmlen;        /* Internal use only. */
-    char program[1];    /* Unwarranted chumminess with compiler. */
-} regexp;
-
-regexp *regcomp( char *exp );
-int regexec( regexp *prog, char *string );
-void regerror( char *s );
-
-/*
- * The first byte of the regexp internal "program" is actually this magic
- * number; the start node begins in the second byte.
- */
-#define MAGIC   0234
-
-#endif
-
diff --git a/jam-files/engine/rules.c b/jam-files/engine/rules.c
deleted file mode 100644
index a0be1d34..00000000
--- a/jam-files/engine/rules.c
+++ /dev/null
@@ -1,810 +0,0 @@
-/*
- * Copyright 1993, 1995 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-# include "jam.h"
-# include "lists.h"
-# include "parse.h"
-# include "variable.h"
-# include "rules.h"
-# include "newstr.h"
-# include "hash.h"
-# include "modules.h"
-# include "search.h"
-# include "lists.h"
-# include "pathsys.h"
-# include "timestamp.h"
-
-/*  This file is ALSO:
- *  Copyright 2001-2004 David Abrahams.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-
-/*
- * rules.c - access to RULEs, TARGETs, and ACTIONs
- *
- * External routines:
- *
- *    bindrule()     - return pointer to RULE, creating it if necessary.
- *    bindtarget()   - return pointer to TARGET, creating it if necessary.
- *    touch_target() - mark a target to simulate being new.
- *    targetlist()   - turn list of target names into a TARGET chain.
- *    targetentry()  - add a TARGET to a chain of TARGETS.
- *    actionlist()   - append to an ACTION chain.
- *    addsettings()  - add a deferred "set" command to a target.
- *    pushsettings() - set all target specific variables.
- *    popsettings()  - reset target specific variables to their pre-push values.
- *    freesettings() - delete a settings list.
- *    rules_done()   - free RULE and TARGET tables.
- *
- * 04/12/94 (seiwald) - actionlist() now just appends a single action.
- * 08/23/94 (seiwald) - Support for '+=' (append to variable)
- */
-
-static void set_rule_actions( RULE *, rule_actions * );
-static void set_rule_body   ( RULE *, argument_list *, PARSE * procedure );
-
-static struct hash * targethash = 0;
-
-struct _located_target
-{
-    char   * file_name;
-    TARGET * target;
-};
-typedef struct _located_target LOCATED_TARGET ;
-
-static struct hash * located_targets = 0;
-
-
-/*
- * target_include() - adds the 'included' TARGET to the list of targets included
- * by the 'including' TARGET. Such targets are modeled as dependencies of the
- * internal include node belonging to the 'including' TARGET.
- */
-
-void target_include( TARGET * including, TARGET * included )
-{
-    TARGET * internal;
-    if ( !including->includes )
-    {
-        including->includes = copytarget( including );
-        including->includes->original_target = including;
-    }
-    internal = including->includes;
-    internal->depends = targetentry( internal->depends, included );
-}
-
-
-/*
- * enter_rule() - return pointer to RULE, creating it if necessary in
- * target_module.
- */
-
-static RULE * enter_rule( char * rulename, module_t * target_module )
-{
-    RULE rule;
-    RULE * r = &rule;
-
-    r->name = rulename;
-
-    if ( hashenter( demand_rules( target_module ), (HASHDATA * *)&r ) )
-    {
-        r->name = newstr( rulename );   /* never freed */
-        r->procedure = (PARSE *)0;
-        r->module = 0;
-        r->actions = 0;
-        r->arguments = 0;
-        r->exported = 0;
-        r->module = target_module;
-#ifdef HAVE_PYTHON
-        r->python_function = 0;
-#endif
-    }
-    return r;
-}
-
-
-/*
- * define_rule() - return pointer to RULE, creating it if necessary in
- * target_module. Prepare it to accept a body or action originating in
- * src_module.
- */
-
-static RULE * define_rule
-(
-    module_t * src_module,
-    char     * rulename,
-    module_t * target_module
-)
-{
-    RULE * r = enter_rule( rulename, target_module );
-    if ( r->module != src_module ) /* if the rule was imported from elsewhere, clear it now */
-    {
-        set_rule_body( r, 0, 0 );
-        set_rule_actions( r, 0 );
-        r->module = src_module; /* r will be executed in the source module */
-    }
-    return r;
-}
-
-
-void rule_free( RULE * r )
-{
-    freestr( r->name );
-    r->name = "";
-    parse_free( r->procedure );
-    r->procedure = 0;
-    if ( r->arguments )
-        args_free( r->arguments );
-    r->arguments = 0;
-    if ( r->actions )
-        actions_free( r->actions );
-    r->actions = 0;
-}
-
-
-/*
- * bindtarget() - return pointer to TARGET, creating it if necessary.
- */
-
-TARGET * bindtarget( char const * target_name )
-{
-    TARGET target;
-    TARGET * t = &target;
-
-    if ( !targethash )
-        targethash = hashinit( sizeof( TARGET ), "targets" );
-
-    /* Perforce added const everywhere. No time to merge that change. */
-#ifdef NT
-    target_name = short_path_to_long_path( (char *)target_name );
-#endif
-    t->name = (char *)target_name;
-
-    if ( hashenter( targethash, (HASHDATA * *)&t ) )
-    {
-        memset( (char *)t, '\0', sizeof( *t ) );
-        t->name = newstr( (char *)target_name );  /* never freed */
-        t->boundname = t->name;  /* default for T_FLAG_NOTFILE */
-    }
-
-    return t;
-}
-
-
-static void bind_explicitly_located_target( void * xtarget, void * data )
-{
-    TARGET * t = (TARGET *)xtarget;
-    if ( !( t->flags & T_FLAG_NOTFILE ) )
-    {
-        /* Check if there's a setting for LOCATE */
-        SETTINGS * s = t->settings;
-        for ( ; s ; s = s->next )
-        {
-            if ( strcmp( s->symbol, "LOCATE" ) == 0 )
-            {
-                pushsettings( t->settings );
-                /* We are binding a target with explicit LOCATE. So third
-                 * argument is of no use: nothing will be returned through it.
-                 */
-                t->boundname = search( t->name, &t->time, 0, 0 );
-                popsettings( t->settings );
-                break;
-            }
-        }
-    }
-}
-
-
-void bind_explicitly_located_targets()
-{
-    if ( targethash )
-        hashenumerate( targethash, bind_explicitly_located_target, (void *)0 );
-}
-
-
-/* TODO: It is probably not a good idea to use functions in other modules like
-  this. */
-void call_bind_rule( char * target, char * boundname );
-
-
-TARGET * search_for_target ( char * name, LIST * search_path )
-{
-    PATHNAME f[1];
-    string buf[1];
-    LOCATED_TARGET lt;
-    LOCATED_TARGET * lta = &lt;
-    time_t time;
-    int found = 0;
-    TARGET * result;
-
-    string_new( buf );
-
-    path_parse( name, f );
-
-    f->f_grist.ptr = 0;
-    f->f_grist.len = 0;
-
-    while ( search_path )
-    {
-        f->f_root.ptr = search_path->string;
-        f->f_root.len = strlen( search_path->string );
-
-        string_truncate( buf, 0 );
-        path_build( f, buf, 1 );
-
-        lt.file_name = buf->value ;
-
-        if ( !located_targets )
-            located_targets = hashinit( sizeof(LOCATED_TARGET),
-                                        "located targets" );
-
-        if ( hashcheck( located_targets, (HASHDATA * *)&lta ) )
-        {
-            return lta->target;
-        }
-
-        timestamp( buf->value, &time );
-        if ( time )
-        {
-            found = 1;
-            break;
-        }
-
-        search_path = list_next( search_path );
-    }
-
-    if ( !found )
-    {
-        f->f_root.ptr = 0;
-        f->f_root.len = 0;
-
-        string_truncate( buf, 0 );
-        path_build( f, buf, 1 );
-
-        timestamp( buf->value, &time );
-    }
-
-    result = bindtarget( name );
-    result->boundname = newstr( buf->value );
-    result->time = time;
-    result->binding = time ? T_BIND_EXISTS : T_BIND_MISSING;
-
-    call_bind_rule( result->name, result->boundname );
-
-    string_free( buf );
-
-    return result;
-}
-
-
-/*
- * copytarget() - make a new target with the old target's name.
- *
- * Not entered into hash table -- for internal nodes.
- */
-
-TARGET * copytarget( const TARGET * ot )
-{
-    TARGET * t = (TARGET *)BJAM_MALLOC( sizeof( *t ) );
-    memset( (char *)t, '\0', sizeof( *t ) );
-    t->name = copystr( ot->name );
-    t->boundname = t->name;
-
-    t->flags |= T_FLAG_NOTFILE | T_FLAG_INTERNAL;
-
-    return t;
-}
-
-
-/*
- * touch_target() - mark a target to simulate being new.
- */
-
-void touch_target( char * t )
-{
-    bindtarget( t )->flags |= T_FLAG_TOUCHED;
-}
-
-
-/*
- * targetlist() - turn list of target names into a TARGET chain.
- *
- * Inputs:
- *  chain   existing TARGETS to append to
- *  targets list of target names
- */
-
-TARGETS * targetlist( TARGETS * chain, LIST * target_names )
-{
-    for ( ; target_names; target_names = list_next( target_names ) )
-        chain = targetentry( chain, bindtarget( target_names->string ) );
-    return chain;
-}
-
-
-/*
- * targetentry() - add a TARGET to a chain of TARGETS.
- *
- * Inputs:
- *  chain   existing TARGETS to append to
- *  target  new target to append
- */
-
-TARGETS * targetentry( TARGETS * chain, TARGET * target )
-{
-    TARGETS * c = (TARGETS *)BJAM_MALLOC( sizeof( TARGETS ) );
-    c->target = target;
-
-    if ( !chain ) chain = c;
-    else chain->tail->next = c;
-    chain->tail = c;
-    c->next = 0;
-
-    return chain;
-}
-
-
-/*
- * targetchain() - append two TARGET chains.
- *
- * Inputs:
- *  chain   exisitng TARGETS to append to
- *  target  new target to append
- */
-
-TARGETS * targetchain( TARGETS * chain, TARGETS * targets )
-{
-    if ( !targets ) return chain;
-    if ( !chain   ) return targets;
-
-    chain->tail->next = targets;
-    chain->tail = targets->tail;
-
-    return chain;
-}
-
-/*
- * actionlist() - append to an ACTION chain.
- */
-
-ACTIONS * actionlist( ACTIONS * chain, ACTION * action )
-{
-    ACTIONS * actions = (ACTIONS *)BJAM_MALLOC( sizeof( ACTIONS ) );
-
-    actions->action = action;
-
-    if ( !chain ) chain = actions;
-    else chain->tail->next = actions;
-    chain->tail = actions;
-    actions->next = 0;
-
-    return chain;
-}
-
-static SETTINGS * settings_freelist;
-
-
-/*
- * addsettings() - add a deferred "set" command to a target.
- *
- * Adds a variable setting (varname=list) onto a chain of settings for a
- * particular target. 'flag' controls the relationship between new and old
- * values in the same way as in var_set() function (see variable.c). Returns
- * the head of the settings chain.
- */
-
-SETTINGS * addsettings( SETTINGS * head, int flag, char * symbol, LIST * value )
-{
-    SETTINGS * v;
-
-    /* Look for previous settings. */
-    for ( v = head; v; v = v->next )
-        if ( !strcmp( v->symbol, symbol ) )
-            break;
-
-    /* If not previously set, alloc a new. */
-    /* If appending, do so. */
-    /* Else free old and set new. */
-    if ( !v )
-    {
-        v = settings_freelist;
-
-        if ( v )
-            settings_freelist = v->next;
-        else
-            v = (SETTINGS *)BJAM_MALLOC( sizeof( *v ) );
-
-        v->symbol = newstr( symbol );
-        v->value = value;
-        v->next = head;
-        v->multiple = 0;
-        head = v;
-    }
-    else if ( flag == VAR_APPEND )
-    {
-        v->value = list_append( v->value, value );
-    }
-    else if ( flag != VAR_DEFAULT )
-    {
-        list_free( v->value );
-        v->value = value;
-    }
-    else
-        list_free( value );
-
-    /* Return (new) head of list. */
-    return head;
-}
-
-
-/*
- * pushsettings() - set all target specific variables.
- */
-
-void pushsettings( SETTINGS * v )
-{
-    for ( ; v; v = v->next )
-        v->value = var_swap( v->symbol, v->value );
-}
-
-
-/*
- * popsettings() - reset target specific variables to their pre-push values.
- */
-
-void popsettings( SETTINGS * v )
-{
-    pushsettings( v );  /* just swap again */
-}
-
-
-/*
- * copysettings() - duplicate a settings list, returning the new copy.
- */
-
-SETTINGS * copysettings( SETTINGS * head )
-{
-    SETTINGS * copy = 0;
-    SETTINGS * v;
-    for ( v = head; v; v = v->next )
-        copy = addsettings( copy, VAR_SET, v->symbol, list_copy( 0, v->value ) );
-    return copy;
-}
-
-
-/*
- * freetargets() - delete a targets list.
- */
-
-void freetargets( TARGETS * chain )
-{
-    while ( chain )
-    {
-        TARGETS * n = chain->next;
-        BJAM_FREE( chain );
-        chain = n;
-    }
-}
-
-
-/*
- * freeactions() - delete an action list.
- */
-
-void freeactions( ACTIONS * chain )
-{
-    while ( chain )
-    {
-        ACTIONS * n = chain->next;
-        BJAM_FREE( chain );
-        chain = n;
-    }
-}
-
-
-/*
- * freesettings() - delete a settings list.
- */
-
-void freesettings( SETTINGS * v )
-{
-    while ( v )
-    {
-        SETTINGS * n = v->next;
-        freestr( v->symbol );
-        list_free( v->value );
-        v->next = settings_freelist;
-        settings_freelist = v;
-        v = n;
-    }
-}
-
-
-static void freetarget( void * xt, void * data )
-{
-    TARGET * t = (TARGET *)xt;
-    if ( t->settings ) freesettings( t->settings            );
-    if ( t->depends  ) freetargets ( t->depends             );
-    if ( t->includes ) freetarget  ( t->includes, (void *)0 );
-    if ( t->actions  ) freeactions ( t->actions             );
-}
-
-
-/*
- * rules_done() - free RULE and TARGET tables.
- */
-
-void rules_done()
-{
-    hashenumerate( targethash, freetarget, 0 );
-    hashdone( targethash );
-    while ( settings_freelist )
-    {
-        SETTINGS * n = settings_freelist->next;
-        BJAM_FREE( settings_freelist );
-        settings_freelist = n;
-    }
-}
-
-
-/*
- * args_new() - make a new reference-counted argument list.
- */
-
-argument_list * args_new()
-{
-    argument_list * r = (argument_list *)BJAM_MALLOC( sizeof(argument_list) );
-    r->reference_count = 0;
-    lol_init( r->data );
-    return r;
-}
-
-
-/*
- * args_refer() - add a new reference to the given argument list.
- */
-
-void args_refer( argument_list * a )
-{
-    ++a->reference_count;
-}
-
-
-/*
- * args_free() - release a reference to the given argument list.
- */
-
-void args_free( argument_list * a )
-{
-    if ( --a->reference_count <= 0 )
-    {
-        lol_free( a->data );
-        BJAM_FREE( a );
-    }
-}
-
-
-/*
- * actions_refer() - add a new reference to the given actions.
- */
-
-void actions_refer( rule_actions * a )
-{
-    ++a->reference_count;
-}
-
-
-/*
- * actions_free() - release a reference to the given actions.
- */
-
-void actions_free( rule_actions * a )
-{
-    if ( --a->reference_count <= 0 )
-    {
-        freestr( a->command );
-        list_free( a->bindlist );
-        BJAM_FREE( a );
-    }
-}
-
-
-/*
- * set_rule_body() - set the argument list and procedure of the given rule.
- */
-
-static void set_rule_body( RULE * rule, argument_list * args, PARSE * procedure )
-{
-    if ( args )
-        args_refer( args );
-    if ( rule->arguments )
-        args_free( rule->arguments );
-    rule->arguments = args;
-
-    if ( procedure )
-        parse_refer( procedure );
-    if ( rule->procedure )
-        parse_free( rule->procedure );
-    rule->procedure = procedure;
-}
-
-
-/*
- * global_name() - given a rule, return the name for a corresponding rule in the
- * global module.
- */
-
-static char * global_rule_name( RULE * r )
-{
-    if ( r->module == root_module() )
-        return r->name;
-
-    {
-        char name[4096] = "";
-        strncat( name, r->module->name, sizeof( name ) - 1 );
-        strncat( name, r->name, sizeof( name ) - 1 );
-        return newstr( name);
-    }
-}
-
-
-/*
- * global_rule() - given a rule, produce the corresponding entry in the global
- * module.
- */
-
-static RULE * global_rule( RULE * r )
-{
-    if ( r->module == root_module() )
-        return r;
-
-    {
-        char * name = global_rule_name( r );
-        RULE * result = define_rule( r->module, name, root_module() );
-        freestr( name );
-        return result;
-    }
-}
-
-
-/*
- * new_rule_body() - make a new rule named rulename in the given module, with
- * the given argument list and procedure. If exported is true, the rule is
- * exported to the global module as modulename.rulename.
- */
-
-RULE * new_rule_body( module_t * m, char * rulename, argument_list * args, PARSE * procedure, int exported )
-{
-    RULE * local = define_rule( m, rulename, m );
-    local->exported = exported;
-    set_rule_body( local, args, procedure );
-
-    /* Mark the procedure with the global rule name, regardless of whether the
-     * rule is exported. That gives us something reasonably identifiable that we
-     * can use, e.g. in profiling output. Only do this once, since this could be
-     * called multiple times with the same procedure.
-     */
-    if ( procedure->rulename == 0 )
-        procedure->rulename = global_rule_name( local );
-
-    return local;
-}
-
-
-static void set_rule_actions( RULE * rule, rule_actions * actions )
-{
-    if ( actions )
-        actions_refer( actions );
-    if ( rule->actions )
-        actions_free( rule->actions );
-    rule->actions = actions;
-}
-
-
-static rule_actions * actions_new( char * command, LIST * bindlist, int flags )
-{
-    rule_actions * result = (rule_actions *)BJAM_MALLOC( sizeof( rule_actions ) );
-    result->command = copystr( command );
-    result->bindlist = bindlist;
-    result->flags = flags;
-    result->reference_count = 0;
-    return result;
-}
-
-
-RULE * new_rule_actions( module_t * m, char * rulename, char * command, LIST * bindlist, int flags )
-{
-    RULE * local = define_rule( m, rulename, m );
-    RULE * global = global_rule( local );
-    set_rule_actions( local, actions_new( command, bindlist, flags ) );
-    set_rule_actions( global, local->actions );
-    return local;
-}
-
-
-/*
- * Looks for a rule in the specified module, and returns it, if found. First
- * checks if the rule is present in the module's rule table. Second, if name of
- * the rule is in the form name1.name2 and name1 is in the list of imported
- * modules, look in module 'name1' for rule 'name2'.
- */
-
-RULE * lookup_rule( char * rulename, module_t * m, int local_only )
-{
-    RULE       rule;
-    RULE     * r = &rule;
-    RULE     * result = 0;
-    module_t * original_module = m;
-
-    r->name = rulename;
-
-    if ( m->class_module )
-        m = m->class_module;
-
-    if ( m->rules && hashcheck( m->rules, (HASHDATA * *)&r ) )
-        result = r;
-    else if ( !local_only && m->imported_modules )
-    {
-        /* Try splitting the name into module and rule. */
-        char *p = strchr( r->name, '.' ) ;
-        if ( p )
-        {
-            *p = '\0';
-            /* Now, r->name keeps the module name, and p+1 keeps the rule name.
-             */
-            if ( hashcheck( m->imported_modules, (HASHDATA * *)&r ) )
-                result = lookup_rule( p + 1, bindmodule( rulename ), 1 );
-            *p = '.';
-        }
-    }
-
-    if ( result )
-    {
-        if ( local_only && !result->exported )
-            result = 0;
-        else
-        {
-            /* Lookup started in class module. We have found a rule in class
-             * module, which is marked for execution in that module, or in some
-             * instances. Mark it for execution in the instance where we started
-             * the lookup.
-             */
-            int execute_in_class = ( result->module == m );
-            int execute_in_some_instance = ( result->module->class_module &&
-                ( result->module->class_module == m ) );
-            if ( ( original_module != m ) &&
-                ( execute_in_class || execute_in_some_instance ) )
-                result->module = original_module;
-        }
-    }
-
-    return result;
-}
-
-
-RULE * bindrule( char * rulename, module_t * m )
-{
-    RULE * result = lookup_rule( rulename, m, 0 );
-    if ( !result )
-        result = lookup_rule( rulename, root_module(), 0 );
-    /* We have only one caller, 'evaluate_rule', which will complain about
-     * calling an undefined rule. We could issue the error here, but we do not
-     * have the necessary information, such as frame.
-     */
-    if ( !result )
-        result = enter_rule( rulename, m );
-    return result;
-}
-
-
-RULE * import_rule( RULE * source, module_t * m, char * name )
-{
-    RULE * dest = define_rule( source->module, name, m );
-    set_rule_body( dest, source->arguments, source->procedure );
-    set_rule_actions( dest, source->actions );
-    return dest;
-}
diff --git a/jam-files/engine/rules.h b/jam-files/engine/rules.h
deleted file mode 100644
index 806a1469..00000000
--- a/jam-files/engine/rules.h
+++ /dev/null
@@ -1,280 +0,0 @@
-/*
- * Copyright 1993, 1995 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*  This file is ALSO:
- *  Copyright 2001-2004 David Abrahams.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-
-#ifndef RULES_DWA_20011020_H
-#define RULES_DWA_20011020_H
-
-#include "modules.h"
-#include "jam.h"
-#include "parse.h"
-
-
-/*
- * rules.h -  targets, rules, and related information
- *
- * This file describes the structures holding the targets, rules, and
- * related information accumulated by interpreting the statements
- * of the jam files.
- *
- * The following are defined:
- *
- *  RULE - a generic jam rule, the product of RULE and ACTIONS.
- *  ACTIONS - a chain of ACTIONs.
- *  ACTION - a RULE instance with targets and sources.
- *  SETTINGS - variables to set when executing a TARGET's ACTIONS.
- *  TARGETS - a chain of TARGETs.
- *  TARGET - an entity (e.g. a file) that can be built.
- *
- * 04/11/94 (seiwald) - Combined deps & headers into deps[2] in TARGET.
- * 04/12/94 (seiwald) - actionlist() now just appends a single action.
- * 06/01/94 (seiwald) - new 'actions existing' does existing sources
- * 12/20/94 (seiwald) - NOTIME renamed NOTFILE.
- * 01/19/95 (seiwald) - split DONTKNOW into CANTFIND/CANTMAKE.
- * 02/02/95 (seiwald) - new LEAVES modifier on targets.
- * 02/14/95 (seiwald) - new NOUPDATE modifier on targets.
- */
-
-typedef struct _rule RULE;
-typedef struct _target TARGET;
-typedef struct _targets TARGETS;
-typedef struct _action ACTION;
-typedef struct _actions ACTIONS;
-typedef struct _settings SETTINGS ;
-
-/* RULE - a generic jam rule, the product of RULE and ACTIONS. */
-
-/* A rule's argument list. */
-struct argument_list
-{
-    int reference_count;
-    LOL data[1];
-};
-
-/* Build actions corresponding to a rule. */
-struct rule_actions
-{
-    int    reference_count;
-    char * command;          /* command string from ACTIONS */
-    LIST * bindlist;
-    int    flags;            /* modifiers on ACTIONS */
-
-#define RULE_NEWSRCS   0x01  /* $(>) is updated sources only */
-#define RULE_TOGETHER  0x02  /* combine actions on single target */
-#define RULE_IGNORE    0x04  /* ignore return status of executes */
-#define RULE_QUIETLY   0x08  /* do not mention it unless verbose */
-#define RULE_PIECEMEAL 0x10  /* split exec so each $(>) is small */
-#define RULE_EXISTING  0x20  /* $(>) is pre-exisitng sources only */
-};
-
-typedef struct rule_actions rule_actions;
-typedef struct argument_list argument_list;
-
-struct _rule
-{
-    char          * name;
-    PARSE         * procedure;  /* parse tree from RULE */
-    argument_list * arguments;  /* argument checking info, or NULL for unchecked
-                                 */
-    rule_actions  * actions;    /* build actions, or NULL for no actions */
-    module_t      * module;     /* module in which this rule is executed */
-    int             exported;   /* nonzero if this rule is supposed to appear in
-                                 * the global module and be automatically
-                                 * imported into other modules
-                                 */
-#ifdef HAVE_PYTHON
-    PyObject * python_function;
-#endif
-};
-
-/* ACTIONS - a chain of ACTIONs. */
-struct _actions
-{
-    ACTIONS * next;
-    ACTIONS * tail;           /* valid only for head */
-    ACTION  * action;
-};
-
-/* ACTION - a RULE instance with targets and sources. */
-struct _action
-{
-    RULE    * rule;
-    TARGETS * targets;
-    TARGETS * sources;        /* aka $(>) */
-    char      running;        /* has been started */
-    char      status;         /* see TARGET status */
-};
-
-/* SETTINGS - variables to set when executing a TARGET's ACTIONS. */
-struct _settings
-{
-    SETTINGS * next;
-    char     * symbol;        /* symbol name for var_set() */
-    LIST     * value;         /* symbol value for var_set() */
-    int multiple;
-};
-
-/* TARGETS - a chain of TARGETs. */
-struct _targets
-{
-    TARGETS * next;
-    TARGETS * tail;           /* valid only for head */
-    TARGET  * target;
-};
-
-/* TARGET - an entity (e.g. a file) that can be built. */
-struct _target
-{
-    char     * name;
-    char     * boundname;             /* if search() relocates target */
-    ACTIONS  * actions;               /* rules to execute, if any */
-    SETTINGS * settings;              /* variables to define */
-
-    short      flags;                 /* status info */
-
-#define T_FLAG_TEMP           0x0001  /* TEMPORARY applied */
-#define T_FLAG_NOCARE         0x0002  /* NOCARE applied */
-#define T_FLAG_NOTFILE        0x0004  /* NOTFILE applied */
-#define T_FLAG_TOUCHED        0x0008  /* ALWAYS applied or -t target */
-#define T_FLAG_LEAVES         0x0010  /* LEAVES applied */
-#define T_FLAG_NOUPDATE       0x0020  /* NOUPDATE applied */
-#define T_FLAG_VISITED        0x0040  /* CWM: Used in debugging */
-
-/* This flag has been added to support a new built-in rule named "RMBAD". It is
- * used to force removal of outdated targets whose dependencies fail to build.
- */
-#define T_FLAG_RMOLD          0x0080  /* RMBAD applied */
-
-/* This flag was added to support a new built-in rule named "FAIL_EXPECTED" used
- * to indicate that the result of running a given action should be inverted,
- * i.e. ok <=> fail. This is useful for launching certain test runs from a
- * Jamfile.
- */
-#define T_FLAG_FAIL_EXPECTED  0x0100  /* FAIL_EXPECTED applied */
-
-#define T_FLAG_INTERNAL       0x0200  /* internal INCLUDES node */
-
-/* Indicates that the target must be a file. This prevents matching non-files,
- * like directories, when a target is searched.
- */
-#define T_FLAG_ISFILE         0x0400
-
-#define T_FLAG_PRECIOUS       0x0800 
-
-    char       binding;               /* how target relates to a real file or
-                                       * folder
-                                       */
-
-#define T_BIND_UNBOUND        0       /* a disembodied name */
-#define T_BIND_MISSING        1       /* could not find real file */
-#define T_BIND_PARENTS        2       /* using parent's timestamp */
-#define T_BIND_EXISTS         3       /* real file, timestamp valid */
-
-    TARGETS  * depends;               /* dependencies */
-    TARGETS  * dependants;            /* the inverse of dependencies */
-    TARGETS  * rebuilds;              /* targets that should be force-rebuilt
-                                       * whenever this one is
-                                       */
-    TARGET   * includes;              /* internal includes node */
-    TARGET   * original_target;       /* original_target->includes = this */
-    char       rescanned;
-
-    time_t     time;                  /* update time */
-    time_t     leaf;                  /* update time of leaf sources */
-
-    char       fate;                  /* make0()'s diagnosis */
-
-#define T_FATE_INIT           0       /* nothing done to target */
-#define T_FATE_MAKING         1       /* make0(target) on stack */
-
-#define T_FATE_STABLE         2       /* target did not need updating */
-#define T_FATE_NEWER          3       /* target newer than parent */
-                                  
-#define T_FATE_SPOIL          4       /* >= SPOIL rebuilds parents */
-#define T_FATE_ISTMP          4       /* unneeded temp target oddly present */
-
-#define T_FATE_BUILD          5       /* >= BUILD rebuilds target */
-#define T_FATE_TOUCHED        5       /* manually touched with -t */
-#define T_FATE_REBUILD        6       
-#define T_FATE_MISSING        7       /* is missing, needs updating */
-#define T_FATE_NEEDTMP        8       /* missing temp that must be rebuild */
-#define T_FATE_OUTDATED       9       /* is out of date, needs updating */
-#define T_FATE_UPDATE         10      /* deps updated, needs updating */
-
-#define T_FATE_BROKEN         11      /* >= BROKEN ruins parents */
-#define T_FATE_CANTFIND       11      /* no rules to make missing target */
-#define T_FATE_CANTMAKE       12      /* can not find dependencies */
-
-    char       progress;              /* tracks make1() progress */
-
-#define T_MAKE_INIT           0       /* make1(target) not yet called */
-#define T_MAKE_ONSTACK        1       /* make1(target) on stack */
-#define T_MAKE_ACTIVE         2       /* make1(target) in make1b() */
-#define T_MAKE_RUNNING        3       /* make1(target) running commands */
-#define T_MAKE_DONE           4       /* make1(target) done */
-
-#ifdef OPT_SEMAPHORE
-    #define T_MAKE_SEMAPHORE  5       /* Special target type for semaphores */
-#endif
-
-#ifdef OPT_SEMAPHORE
-    TARGET   * semaphore;             /* used in serialization */
-#endif
-
-    char       status;                /* exec_cmd() result */
-
-    int        asynccnt;              /* child deps outstanding */
-    TARGETS  * parents;               /* used by make1() for completion */
-    char     * cmds;                  /* type-punned command list */
-
-    char     * failed;
-};
-
-
-/* Action related functions. */
-ACTIONS  * actionlist   ( ACTIONS *, ACTION * );
-void       freeactions  ( ACTIONS * );
-SETTINGS * addsettings  ( SETTINGS *, int flag, char * symbol, LIST * value );
-void       pushsettings ( SETTINGS * );
-void       popsettings  ( SETTINGS * );
-SETTINGS * copysettings ( SETTINGS * );
-void       freesettings ( SETTINGS * );
-void       actions_refer( rule_actions * );
-void       actions_free ( rule_actions * );
-
-/* Argument list related functions. */
-void            args_free ( argument_list * );
-argument_list * args_new  ();
-void            args_refer( argument_list * );
-
-/* Rule related functions. */
-RULE * bindrule        ( char * rulename, module_t * );
-RULE * import_rule     ( RULE * source, module_t *, char * name );
-RULE * new_rule_body   ( module_t *, char * rulename, argument_list *, PARSE * procedure, int exprt );
-RULE * new_rule_actions( module_t *, char * rulename, char * command, LIST * bindlist, int flags );
-void   rule_free       ( RULE * );
-
-/* Target related functions. */
-void      bind_explicitly_located_targets();
-TARGET  * bindtarget                     ( char const * target_name );
-TARGET  * copytarget                     ( TARGET const * t );
-void      freetargets                    ( TARGETS * );
-TARGET  * search_for_target              ( char * name, LIST * search_path );
-TARGETS * targetchain                    ( TARGETS * chain, TARGETS * );
-TARGETS * targetentry                    ( TARGETS * chain, TARGET * );
-void      target_include                 ( TARGET * including, TARGET * included );
-TARGETS * targetlist                     ( TARGETS * chain, LIST * target_names );
-void      touch_target                   ( char * t );
-
-/* Final module cleanup. */
-void rules_done();
-
-#endif
diff --git a/jam-files/engine/scan.c b/jam-files/engine/scan.c
deleted file mode 100644
index 11c44c0e..00000000
--- a/jam-files/engine/scan.c
+++ /dev/null
@@ -1,418 +0,0 @@
-/*
- * Copyright 1993-2002 Christopher Seiwald and Perforce Software, Inc.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-#include "jam.h"
-#include "lists.h"
-#include "parse.h"
-#include "scan.h"
-#include "jamgram.h"
-#include "jambase.h"
-#include "newstr.h"
-
-/*
- * scan.c - the jam yacc scanner
- *
- * 12/26/93 (seiwald) - bump buf in yylex to 10240 - yuk.
- * 09/16/94 (seiwald) - check for overflows, unmatched {}'s, etc.
- *          Also handle tokens abutting EOF by remembering
- *          to return EOF now matter how many times yylex()
- *          reinvokes yyline().
- * 02/11/95 (seiwald) - honor only punctuation keywords if SCAN_PUNCT.
- * 07/27/95 (seiwald) - Include jamgram.h after scan.h, so that YYSTYPE is
- *          defined before Linux's yacc tries to redefine it.
- */
-
-struct keyword
-{
-    char * word;
-    int    type;
-} keywords[] =
-{
-#include "jamgramtab.h"
-    { 0, 0 }
-};
-
-struct include
-{
-    struct include   * next;       /* next serial include file */
-    char             * string;     /* pointer into current line */
-    char           * * strings;    /* for yyfparse() -- text to parse */
-    FILE             * file;       /* for yyfparse() -- file being read */
-    char             * fname;      /* for yyfparse() -- file name */
-    int                line;       /* line counter for error messages */
-    char               buf[ 512 ]; /* for yyfparse() -- line buffer */
-};
-
-static struct include * incp = 0; /* current file; head of chain */
-
-static int scanmode = SCAN_NORMAL;
-static int anyerrors = 0;
-
-
-static char * symdump( YYSTYPE * );
-
-#define BIGGEST_TOKEN 10240  /* no single token can be larger */
-
-
-/*
- * Set parser mode: normal, string, or keyword.
- */
-
-void yymode( int n )
-{
-    scanmode = n;
-}
-
-
-void yyerror( char * s )
-{
-    /* We use yylval instead of incp to access the error location information as
-     * the incp pointer will already be reset to 0 in case the error occurred at
-     * EOF.
-     *
-     * The two may differ only if we get an error while reading a lexical token
-     * spanning muliple lines, e.g. a multi-line string literal or action body,
-     * in which case yylval location information will hold the information about
-     * where this token started while incp will hold the information about where
-     * reading it broke.
-     *
-     * TODO: Test the theory about when yylval and incp location information are
-     * the same and when they differ.
-     */
-    printf( "%s:%d: %s at %s\n", yylval.file, yylval.line, s, symdump( &yylval ) );
-    ++anyerrors;
-}
-
-
-int yyanyerrors()
-{
-    return anyerrors != 0;
-}
-
-
-void yyfparse( char * s )
-{
-    struct include * i = (struct include *)BJAM_MALLOC( sizeof( *i ) );
-
-    /* Push this onto the incp chain. */
-    i->string = "";
-    i->strings = 0;
-    i->file = 0;
-    i->fname = copystr( s );
-    i->line = 0;
-    i->next = incp;
-    incp = i;
-
-    /* If the filename is "+", it means use the internal jambase. */
-    if ( !strcmp( s, "+" ) )
-        i->strings = jambase;
-}
-
-
-/*
- * yyline() - read new line and return first character.
- *
- * Fabricates a continuous stream of characters across include files, returning
- * EOF at the bitter end.
- */
-
-int yyline()
-{
-    struct include * i = incp;
-
-    if ( !incp )
-        return EOF;
-
-    /* Once we start reading from the input stream, we reset the include
-     * insertion point so that the next include file becomes the head of the
-     * list.
-     */
-
-    /* If there is more data in this line, return it. */
-    if ( *i->string )
-        return *i->string++;
-
-    /* If we are reading from an internal string list, go to the next string. */
-    if ( i->strings )
-    {
-        if ( *i->strings )
-        {
-            ++i->line;
-            i->string = *(i->strings++);
-            return *i->string++;
-        }
-    }
-    else
-    {
-        /* If necessary, open the file. */
-        if ( !i->file )
-        {
-            FILE * f = stdin;
-            if ( strcmp( i->fname, "-" ) && !( f = fopen( i->fname, "r" ) ) )
-                perror( i->fname );
-            i->file = f;
-        }
-
-        /* If there is another line in this file, start it. */
-        if ( i->file && fgets( i->buf, sizeof( i->buf ), i->file ) )
-        {
-            ++i->line;
-            i->string = i->buf;
-            return *i->string++;
-        }
-    }
-
-    /* This include is done. Free it up and return EOF so yyparse() returns to
-     * parse_file().
-     */
-
-    incp = i->next;
-
-    /* Close file, free name. */
-    if ( i->file && ( i->file != stdin ) )
-        fclose( i->file );
-    freestr( i->fname );
-    BJAM_FREE( (char *)i );
-
-    return EOF;
-}
-
-
-/*
- * yylex() - set yylval to current token; return its type.
- *
- * Macros to move things along:
- *
- *  yychar() - return and advance character; invalid after EOF.
- *  yyprev() - back up one character; invalid before yychar().
- *
- * yychar() returns a continuous stream of characters, until it hits the EOF of
- * the current include file.
- */
-
-#define yychar() ( *incp->string ? *incp->string++ : yyline() )
-#define yyprev() ( incp->string-- )
-
-int yylex()
-{
-    int c;
-    char buf[ BIGGEST_TOKEN ];
-    char * b = buf;
-
-    if ( !incp )
-        goto eof;
-
-    /* Get first character (whitespace or of token). */
-    c = yychar();
-
-    if ( scanmode == SCAN_STRING )
-    {
-        /* If scanning for a string (action's {}'s), look for the closing brace.
-         * We handle matching braces, if they match.
-         */
-
-        int nest = 1;
-
-        while ( ( c != EOF ) && ( b < buf + sizeof( buf ) ) )
-        {
-            if ( c == '{' )
-                ++nest;
-
-            if ( ( c == '}' ) && !--nest )
-                break;
-
-            *b++ = c;
-
-            c = yychar();
-
-            /* Turn trailing "\r\n" sequences into plain "\n" for Cygwin. */
-            if ( ( c == '\n' ) && ( b[ -1 ] == '\r' ) )
-                --b;
-        }
-
-        /* We ate the ending brace -- regurgitate it. */
-        if ( c != EOF )
-            yyprev();
-
-        /* Check for obvious errors. */
-        if ( b == buf + sizeof( buf ) )
-        {
-            yyerror( "action block too big" );
-            goto eof;
-        }
-
-        if ( nest )
-        {
-            yyerror( "unmatched {} in action block" );
-            goto eof;
-        }
-
-        *b = 0;
-        yylval.type = STRING;
-        yylval.string = newstr( buf );
-        yylval.file = incp->fname;
-        yylval.line = incp->line;
-    }
-    else
-    {
-        char * b = buf;
-        struct keyword * k;
-        int inquote = 0;
-        int notkeyword;
-
-        /* Eat white space. */
-        for ( ;; )
-        {
-            /* Skip past white space. */
-            while ( ( c != EOF ) && isspace( c ) )
-                c = yychar();
-
-            /* Not a comment? */
-            if ( c != '#' )
-                break;
-
-            /* Swallow up comment line. */
-            while ( ( ( c = yychar() ) != EOF ) && ( c != '\n' ) ) ;
-        }
-
-        /* c now points to the first character of a token. */
-        if ( c == EOF )
-            goto eof;
-
-        yylval.file = incp->fname;
-        yylval.line = incp->line;
-
-        /* While scanning the word, disqualify it for (expensive) keyword lookup
-         * when we can: $anything, "anything", \anything
-         */
-        notkeyword = c == '$';
-
-        /* Look for white space to delimit word. "'s get stripped but preserve
-         * white space. \ protects next character.
-         */
-        while
-        (
-            ( c != EOF ) &&
-            ( b < buf + sizeof( buf ) ) &&
-            ( inquote || !isspace( c ) )
-        )
-        {
-            if ( c == '"' )
-            {
-                /* begin or end " */
-                inquote = !inquote;
-                notkeyword = 1;
-            }
-            else if ( c != '\\' )
-            {
-                /* normal char */
-                *b++ = c;
-            }
-            else if ( ( c = yychar() ) != EOF )
-            {
-                /* \c */
-                if (c == 'n')
-                    c = '\n';
-                else if (c == 'r')
-                    c = '\r';
-                else if (c == 't')
-                    c = '\t';
-                *b++ = c;
-                notkeyword = 1;
-            }
-            else
-            {
-                /* \EOF */
-                break;
-            }
-
-            c = yychar();
-        }
-
-        /* Check obvious errors. */
-        if ( b == buf + sizeof( buf ) )
-        {
-            yyerror( "string too big" );
-            goto eof;
-        }
-
-        if ( inquote )
-        {
-            yyerror( "unmatched \" in string" );
-            goto eof;
-        }
-
-        /* We looked ahead a character - back up. */
-        if ( c != EOF )
-            yyprev();
-
-        /* Scan token table. Do not scan if it is obviously not a keyword or if
-         * it is an alphabetic when were looking for punctuation.
-         */
-
-        *b = 0;
-        yylval.type = ARG;
-
-        if ( !notkeyword && !( isalpha( *buf ) && ( scanmode == SCAN_PUNCT ) ) )
-            for ( k = keywords; k->word; ++k )
-                if ( ( *buf == *k->word ) && !strcmp( k->word, buf ) )
-                { 
-                    yylval.type = k->type;
-                    yylval.string = k->word;  /* used by symdump */
-                    break;
-                }
-
-        if ( yylval.type == ARG )
-            yylval.string = newstr( buf );
-    }
-
-    if ( DEBUG_SCAN )
-        printf( "scan %s\n", symdump( &yylval ) );
-
-    return yylval.type;
-
-eof:
-    /* We do not reset yylval.file & yylval.line here so unexpected EOF error
-     * messages would include correct error location information.
-     */
-    yylval.type = EOF;
-    return yylval.type;
-}
-
-
-static char * symdump( YYSTYPE * s )
-{
-    static char buf[ BIGGEST_TOKEN + 20 ];
-    switch ( s->type )
-    {
-        case EOF   : sprintf( buf, "EOF"                          ); break;
-        case 0     : sprintf( buf, "unknown symbol %s", s->string ); break;
-        case ARG   : sprintf( buf, "argument %s"      , s->string ); break;
-        case STRING: sprintf( buf, "string \"%s\""    , s->string ); break;
-        default    : sprintf( buf, "keyword %s"       , s->string ); break;
-    }
-    return buf;
-}
-
-
-/*
- * Get information about the current file and line, for those epsilon
- * transitions that produce a parse.
- */
-
-void yyinput_stream( char * * name, int * line )
-{
-    if ( incp )
-    {
-        *name = incp->fname;
-        *line = incp->line;
-    }
-    else
-    {
-        *name = "(builtin)";
-        *line = -1;
-    }
-}
diff --git a/jam-files/engine/scan.h b/jam-files/engine/scan.h
deleted file mode 100644
index 3fad1c24..00000000
--- a/jam-files/engine/scan.h
+++ /dev/null
@@ -1,56 +0,0 @@
-/*
- * Copyright 1993, 1995 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*
- * scan.h - the jam yacc scanner
- *
- * External functions:
- *
- *  yyerror( char *s ) - print a parsing error message.
- *  yyfparse( char *s ) - scan include file s.
- *  yylex() - parse the next token, returning its type.
- *  yymode() - adjust lexicon of scanner.
- *  yyparse() - declaration for yacc parser.
- *  yyanyerrors() - indicate if any parsing errors occured.
- *
- * The yymode() function is for the parser to adjust the lexicon of the scanner.
- * Aside from normal keyword scanning, there is a mode to handle action strings
- * (look only for the closing }) and a mode to ignore most keywords when looking
- * for a punctuation keyword. This allows non-punctuation keywords to be used in
- * lists without quoting.
- */
-
-/*
- * YYSTYPE - value of a lexical token
- */
-
-#define YYSTYPE YYSYMBOL
-
-typedef struct _YYSTYPE
-{
-    int     type;
-    char  * string;
-    PARSE * parse;
-    LIST  * list;
-    int     number;
-    char  * file;
-    int     line;
-} YYSTYPE;
-
-extern YYSTYPE yylval;
-
-void yymode( int n );
-void yyerror( char * s );
-int yyanyerrors();
-void yyfparse( char * s );
-int yyline();
-int yylex();
-int yyparse();
-void yyinput_stream( char * * name, int * line );
-
-# define SCAN_NORMAL  0   /* normal parsing */
-# define SCAN_STRING  1   /* look only for matching } */
-# define SCAN_PUNCT   2   /* only punctuation keywords */
diff --git a/jam-files/engine/search.c b/jam-files/engine/search.c
deleted file mode 100644
index 6c23d97a..00000000
--- a/jam-files/engine/search.c
+++ /dev/null
@@ -1,223 +0,0 @@
-/*
- * Copyright 1993-2002 Christopher Seiwald and Perforce Software, Inc.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*  This file is ALSO:
- *  Copyright 2001-2004 David Abrahams.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-
-#include "jam.h"
-#include "lists.h"
-#include "search.h"
-#include "timestamp.h"
-#include "pathsys.h"
-#include "variable.h"
-#include "newstr.h"
-#include "compile.h"
-#include "strings.h"
-#include "hash.h"
-#include "filesys.h"
-#include <string.h>
-
-
-typedef struct _binding
-{
-    char * binding;
-    char * target;
-} BINDING;
-
-static struct hash *explicit_bindings = 0;
-
-
-void call_bind_rule
-(
-    char * target_,
-    char * boundname_
-)
-{
-    LIST * bind_rule = var_get( "BINDRULE" );
-    if ( bind_rule )
-    {
-        /* No guarantee that the target is an allocated string, so be on the
-         * safe side.
-         */
-        char * target = copystr( target_ );
-
-        /* Likewise, do not rely on implementation details of newstr.c: allocate
-         * a copy of boundname.
-         */
-        char * boundname = copystr( boundname_ );
-        if ( boundname && target )
-        {
-            /* Prepare the argument list. */
-            FRAME frame[1];
-            frame_init( frame );
-
-            /* First argument is the target name. */
-            lol_add( frame->args, list_new( L0, target ) );
-
-            lol_add( frame->args, list_new( L0, boundname ) );
-            if ( lol_get( frame->args, 1 ) )
-                evaluate_rule( bind_rule->string, frame );
-
-            /* Clean up */
-            frame_free( frame );
-        }
-        else
-        {
-            if ( boundname )
-                freestr( boundname );
-            if ( target )
-                freestr( target );
-        }
-    }
-}
-
-/*
- * search.c - find a target along $(SEARCH) or $(LOCATE)
- * First, check if LOCATE is set. If so, use it to determine
- * the location of target and return, regardless of whether anything
- * exists on that location.
- *
- * Second, examine all directories in SEARCH. If there's file already
- * or there's another target with the same name which was placed
- * to this location via LOCATE setting, stop and return the location.
- * In case of previous target, return it's name via the third argument.
- *
- * This bevahiour allow to handle dependency on generated files. If
- * caller does not expect that target is generated, 0 can be passed as
- * the third argument.
- */
-
-char *
-search(
-    char *target,
-    time_t *time,
-    char **another_target,
-    int file
-)
-{
-    PATHNAME f[1];
-    LIST    *varlist;
-    string    buf[1];
-    int     found = 0;
-    /* Will be set to 1 if target location is specified via LOCATE. */
-    int     explicitly_located = 0;
-    char    *boundname = 0;
-
-    if ( another_target )
-        *another_target = 0;
-
-    if (! explicit_bindings )
-        explicit_bindings = hashinit( sizeof(BINDING),
-                                     "explicitly specified locations");
-
-    string_new( buf );
-    /* Parse the filename */
-
-    path_parse( target, f );
-
-    f->f_grist.ptr = 0;
-    f->f_grist.len = 0;
-
-    if ( ( varlist = var_get( "LOCATE" ) ) )
-      {
-        f->f_root.ptr = varlist->string;
-        f->f_root.len = strlen( varlist->string );
-
-        path_build( f, buf, 1 );
-
-        if ( DEBUG_SEARCH )
-            printf( "locate %s: %s\n", target, buf->value );
-
-        explicitly_located = 1;
-
-        timestamp( buf->value, time );
-        found = 1;
-    }
-    else if ( ( varlist = var_get( "SEARCH" ) ) )
-    {
-        while ( varlist )
-        {
-            BINDING b, *ba = &b;
-            file_info_t *ff;
-
-            f->f_root.ptr = varlist->string;
-            f->f_root.len = strlen( varlist->string );
-
-            string_truncate( buf, 0 );
-            path_build( f, buf, 1 );
-
-            if ( DEBUG_SEARCH )
-                printf( "search %s: %s\n", target, buf->value );
-
-            ff = file_query(buf->value);
-            timestamp( buf->value, time );
-
-            b.binding = buf->value;
-
-            if ( hashcheck( explicit_bindings, (HASHDATA**)&ba ) )
-            {
-                if ( DEBUG_SEARCH )
-                    printf(" search %s: found explicitly located target %s\n",
-                           target, ba->target);
-                if ( another_target )
-                    *another_target = ba->target;
-                found = 1;
-                break;
-            }
-            else if ( ff && ff->time )
-            {
-                if ( !file || ff->is_file )
-                {
-                    found = 1;
-                    break;
-                }
-            }
-
-            varlist = list_next( varlist );
-        }
-    }
-
-    if ( !found )
-    {
-        /* Look for the obvious */
-        /* This is a questionable move.  Should we look in the */
-        /* obvious place if SEARCH is set? */
-
-        f->f_root.ptr = 0;
-        f->f_root.len = 0;
-
-        string_truncate( buf, 0 );
-        path_build( f, buf, 1 );
-
-        if ( DEBUG_SEARCH )
-            printf( "search %s: %s\n", target, buf->value );
-
-        timestamp( buf->value, time );
-    }
-
-    boundname = newstr( buf->value );
-    string_free( buf );
-
-    if ( explicitly_located )
-    {
-        BINDING b;
-        BINDING * ba = &b;
-        b.binding = boundname;
-        b.target = target;
-        /* CONSIDER: we probably should issue a warning is another file
-           is explicitly bound to the same location. This might break
-           compatibility, though. */
-        hashenter( explicit_bindings, (HASHDATA * *)&ba );
-    }
-
-    /* prepare a call to BINDRULE if the variable is set */
-    call_bind_rule( target, boundname );
-
-    return boundname;
-}
diff --git a/jam-files/engine/search.h b/jam-files/engine/search.h
deleted file mode 100644
index c364cac0..00000000
--- a/jam-files/engine/search.h
+++ /dev/null
@@ -1,11 +0,0 @@
-/*
- * Copyright 1993, 1995 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*
- * search.h - find a target along $(SEARCH) or $(LOCATE)
- */
-
-char *search( char *target, time_t *time, char **another_target, int file );
diff --git a/jam-files/engine/strings.c b/jam-files/engine/strings.c
deleted file mode 100644
index 89561237..00000000
--- a/jam-files/engine/strings.c
+++ /dev/null
@@ -1,201 +0,0 @@
-/* Copyright David Abrahams 2004. Distributed under the Boost */
-/* Software License, Version 1.0. (See accompanying */
-/* file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */
-
-#include "jam.h"
-#include "strings.h"
-#include <stdlib.h>
-#include <string.h>
-#include <assert.h>
-#include <stdio.h>
-
-
-#ifndef NDEBUG
-# define JAM_STRING_MAGIC ((char)0xcf)
-# define JAM_STRING_MAGIC_SIZE 4
-static void assert_invariants( string* self )
-{
-    int i;
-
-    if ( self->value == 0 )
-    {
-        assert( self->size == 0 );
-        assert( self->capacity == 0 );
-        assert( self->opt[0] == 0 );
-        return;
-    }
-
-    assert( self->size < self->capacity );
-    assert( ( self->capacity <= sizeof(self->opt) ) == ( self->value == self->opt ) );
-    assert( strlen( self->value ) == self->size );
-
-    for (i = 0; i < 4; ++i)
-    {
-        assert( self->magic[i] == JAM_STRING_MAGIC );
-        assert( self->value[self->capacity + i] == JAM_STRING_MAGIC );
-    }
-}
-#else
-# define JAM_STRING_MAGIC_SIZE 0
-# define assert_invariants(x) do {} while (0)
-#endif
-
-void string_new( string* s )
-{
-    s->value = s->opt;
-    s->size = 0;
-    s->capacity = sizeof(s->opt);
-    s->opt[0] = 0;
-#ifndef NDEBUG
-    memset(s->magic, JAM_STRING_MAGIC, sizeof(s->magic));
-#endif
-    assert_invariants( s );
-}
-
-void string_free( string* s )
-{
-    assert_invariants( s );
-    if ( s->value != s->opt )
-        BJAM_FREE( s->value );
-    string_new( s );
-}
-
-static void string_reserve_internal( string* self, size_t capacity )
-{
-    if ( self->value == self->opt )
-    {
-        self->value = (char*)BJAM_MALLOC_ATOMIC( capacity + JAM_STRING_MAGIC_SIZE );
-        self->value[0] = 0;
-        strncat( self->value, self->opt, sizeof(self->opt) );
-        assert( strlen( self->value ) <= self->capacity ); /* This is a regression test */
-    }
-    else
-    {
-        self->value = (char*)BJAM_REALLOC( self->value, capacity + JAM_STRING_MAGIC_SIZE );
-    }
-#ifndef NDEBUG
-    memcpy( self->value + capacity, self->magic, JAM_STRING_MAGIC_SIZE );
-#endif
-    self->capacity = capacity;
-}
-
-void string_reserve( string* self, size_t capacity )
-{
-    assert_invariants( self );
-    if ( capacity <= self->capacity )
-        return;
-    string_reserve_internal( self, capacity );
-    assert_invariants( self );
-}
-
-static void extend_full( string* self, char const* start, char const* finish )
-{
-    size_t new_size = self->capacity + ( finish - start );
-    size_t new_capacity = self->capacity;
-    size_t old_size = self->capacity;
-    while ( new_capacity < new_size + 1)
-        new_capacity <<= 1;
-    string_reserve_internal( self, new_capacity );
-    memcpy( self->value + old_size, start, new_size - old_size );
-    self->value[new_size] = 0;
-    self->size = new_size;
-}
-
-void string_append( string* self, char const* rhs )
-{
-    char* p = self->value + self->size;
-    char* end = self->value + self->capacity;
-    assert_invariants( self );
-
-    while ( *rhs && p != end)
-        *p++ = *rhs++;
-
-    if ( p != end )
-    {
-        *p = 0;
-        self->size = p - self->value;
-    }
-    else
-    {
-        extend_full( self, rhs, rhs + strlen(rhs) );
-    }
-    assert_invariants( self );
-}
-
-void string_append_range( string* self, char const* start, char const* finish )
-{
-    char* p = self->value + self->size;
-    char* end = self->value + self->capacity;
-    assert_invariants( self );
-
-    while ( p != end && start != finish )
-        *p++ = *start++;
-
-    if ( p != end )
-    {
-        *p = 0;
-        self->size = p - self->value;
-    }
-    else
-    {
-        extend_full( self, start, finish );
-    }
-    assert_invariants( self );
-}
-
-void string_copy( string* s, char const* rhs )
-{
-    string_new( s );
-    string_append( s, rhs );
-}
-
-void string_truncate( string* self, size_t n )
-{
-    assert_invariants( self );
-    assert( n <= self->capacity );
-    self->value[self->size = n] = 0;
-    assert_invariants( self );
-}
-
-void string_pop_back( string* self )
-{
-    string_truncate( self, self->size - 1 );
-}
-
-void string_push_back( string* self, char x )
-{
-    string_append_range( self, &x, &x + 1 );
-}
-
-char string_back( string* self )
-{
-    assert_invariants( self );
-    return self->value[self->size - 1];
-}
-
-#ifndef NDEBUG
-void string_unit_test()
-{
-    string s[1];
-    int i;
-    char buffer[sizeof(s->opt) * 2 + 2];
-    int limit = sizeof(buffer) > 254 ? 254 : sizeof(buffer);
-
-    string_new(s);
-
-    for (i = 0; i < limit; ++i)
-    {
-        string_push_back( s, (char)(i + 1) );
-    };
-
-    for (i = 0; i < limit; ++i)
-    {
-        assert( i < s->size );
-        assert( s->value[i] == (char)(i + 1));
-    }
-
-    string_free(s);
-
-}
-#endif
-
diff --git a/jam-files/engine/strings.h b/jam-files/engine/strings.h
deleted file mode 100644
index 33c77bd7..00000000
--- a/jam-files/engine/strings.h
+++ /dev/null
@@ -1,34 +0,0 @@
-#ifndef STRINGS_DWA20011024_H
-# define STRINGS_DWA20011024_H
-
-/* Copyright David Abrahams 2004. Distributed under the Boost */
-/* Software License, Version 1.0. (See accompanying */
-/* file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */
-
-# include <stddef.h>
-
-typedef struct string
-{
-    char* value;
-    unsigned long size;
-    unsigned long capacity;
-    char opt[32];
-#ifndef NDEBUG
-    char magic[4];
-#endif
-} string;
-
-void string_new( string* );
-void string_copy( string*, char const* );
-void string_free( string* );
-void string_append( string*, char const* );
-void string_append_range( string*, char const*, char const* );
-void string_push_back( string* s, char x );
-void string_reserve( string*, size_t );
-void string_truncate( string*, size_t );
-void string_pop_back( string* );
-char string_back( string* );
-void string_unit_test();
-
-#endif
-
diff --git a/jam-files/engine/subst.c b/jam-files/engine/subst.c
deleted file mode 100644
index 75524ecc..00000000
--- a/jam-files/engine/subst.c
+++ /dev/null
@@ -1,94 +0,0 @@
-#include <stddef.h>
-#include "jam.h"
-#include "regexp.h"
-#include "hash.h"
-
-#include "newstr.h"
-#include "lists.h"
-#include "parse.h"
-#include "compile.h"
-#include "frames.h"
-
-struct regex_entry
-{
-    const char* pattern;
-    regexp* regex;
-};
-typedef struct regex_entry regex_entry;
-
-static struct hash* regex_hash;
-
-regexp* regex_compile( const char* pattern )
-{
-    regex_entry entry, *e = &entry;
-    entry.pattern = pattern;
-
-    if ( !regex_hash )
-        regex_hash = hashinit(sizeof(regex_entry), "regex");
-
-    if ( hashenter( regex_hash, (HASHDATA **)&e ) )
-        e->regex = regcomp( (char*)pattern );
-
-    return e->regex;
-}
-
-LIST*
-builtin_subst(
-    PARSE    *parse,
-    FRAME      *frame )
-{
-  LIST* result = L0;
-  LIST* arg1 = lol_get( frame->args, 0 );
-
-  if ( arg1 && list_next(arg1) && list_next(list_next(arg1)) )
-  {
-
-      const char* source = arg1->string;
-      const char* pattern = list_next(arg1)->string;
-      regexp* repat = regex_compile( pattern );
-
-      if ( regexec( repat, (char*)source) )
-      {
-          LIST* subst = list_next(arg1);
-
-          while ((subst = list_next(subst)) != L0)
-          {
-# define BUFLEN 4096
-              char buf[BUFLEN + 1];
-              const char* in = subst->string;
-              char* out = buf;
-
-              for ( in = subst->string; *in && out < buf + BUFLEN; ++in )
-              {
-                  if ( *in == '\\' || *in == '$' )
-                  {
-                      ++in;
-                      if ( *in == 0 )
-                      {
-                          break;
-                      }
-                      else if ( *in >= '0' && *in <= '9' )
-                      {
-                          unsigned n = *in - '0';
-                          const size_t srclen = repat->endp[n] - repat->startp[n];
-                          const size_t remaining = buf + BUFLEN - out;
-                          const size_t len = srclen < remaining ? srclen : remaining;
-                          memcpy( out, repat->startp[n], len );
-                          out += len;
-                          continue;
-                      }
-                      /* fall through and copy the next character */
-                  }
-                  *out++ = *in;
-              }
-              *out = 0;
-
-              result = list_new( result, newstr( buf ) );
-#undef BUFLEN
-          }
-      }
-  }
-
-  return result;
-}
-
diff --git a/jam-files/engine/timestamp.c b/jam-files/engine/timestamp.c
deleted file mode 100644
index 8a59c8c0..00000000
--- a/jam-files/engine/timestamp.c
+++ /dev/null
@@ -1,226 +0,0 @@
-/*
- * Copyright 1993-2002 Christopher Seiwald and Perforce Software, Inc.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*  This file is ALSO:
- *  Copyright 2001-2004 David Abrahams.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-
-# include "jam.h"
-
-# include "hash.h"
-# include "filesys.h"
-# include "pathsys.h"
-# include "timestamp.h"
-# include "newstr.h"
-# include "strings.h"
-
-/*
- * timestamp.c - get the timestamp of a file or archive member
- *
- * 09/22/00 (seiwald) - downshift names on OS2, too
- */
-
-/*
- * BINDING - all known files
- */
-
-typedef struct _binding BINDING;
-
-struct _binding {
-    char    *name;
-    short   flags;
-
-# define BIND_SCANNED   0x01    /* if directory or arch, has been scanned */
-
-    short   progress;
-
-# define BIND_INIT  0   /* never seen */
-# define BIND_NOENTRY   1   /* timestamp requested but file never found */
-# define BIND_SPOTTED   2   /* file found but not timed yet */
-# define BIND_MISSING   3   /* file found but can't get timestamp */
-# define BIND_FOUND 4   /* file found and time stamped */
-
-    time_t  time;       /* update time - 0 if not exist */
-};
-
-static struct hash * bindhash = 0;
-static void time_enter( void *, char *, int, time_t );
-
-static char * time_progress[] =
-{
-    "INIT",
-    "NOENTRY",
-    "SPOTTED",
-    "MISSING",
-    "FOUND"
-};
-
-
-/*
- * timestamp() - return timestamp on a file, if present.
- */
-
-void timestamp( char * target, time_t * time )
-{
-    PROFILE_ENTER( timestamp );
-
-    PATHNAME   f1;
-    PATHNAME   f2;
-    BINDING    binding;
-    BINDING  * b = &binding;
-    string     buf[ 1 ];
-#ifdef DOWNSHIFT_PATHS
-    string     path;
-    char     * p;
-#endif
-
-#ifdef DOWNSHIFT_PATHS
-    string_copy( &path, target );
-    p = path.value;
-
-    do
-    {
-        *p = tolower( *p );
-#ifdef NT
-        /* On NT, we must use backslashes or the file will not be found. */
-        if ( *p == '/' )
-            *p = PATH_DELIM;
-#endif
-    }
-    while ( *p++ );
-
-    target = path.value;
-#endif  /* #ifdef DOWNSHIFT_PATHS */
-    string_new( buf );
-
-    if ( !bindhash )
-        bindhash = hashinit( sizeof( BINDING ), "bindings" );
-
-    /* Quick path - is it there? */
-    b->name = target;
-    b->time = b->flags = 0;
-    b->progress = BIND_INIT;
-
-    if ( hashenter( bindhash, (HASHDATA * *)&b ) )
-        b->name = newstr( target );  /* never freed */
-
-    if ( b->progress != BIND_INIT )
-        goto afterscanning;
-
-    b->progress = BIND_NOENTRY;
-
-    /* Not found - have to scan for it. */
-    path_parse( target, &f1 );
-
-    /* Scan directory if not already done so. */
-    {
-        BINDING binding;
-        BINDING * b = &binding;
-
-        f2 = f1;
-        f2.f_grist.len = 0;
-        path_parent( &f2 );
-        path_build( &f2, buf, 0 );
-
-        b->name = buf->value;
-        b->time = b->flags = 0;
-        b->progress = BIND_INIT;
-
-        if ( hashenter( bindhash, (HASHDATA * *)&b ) )
-            b->name = newstr( buf->value );  /* never freed */
-
-        if ( !( b->flags & BIND_SCANNED ) )
-        {
-            file_dirscan( buf->value, time_enter, bindhash );
-            b->flags |= BIND_SCANNED;
-        }
-    }
-
-    /* Scan archive if not already done so. */
-    if ( f1.f_member.len )
-    {
-        BINDING binding;
-        BINDING * b = &binding;
-
-        f2 = f1;
-        f2.f_grist.len = 0;
-        f2.f_member.len = 0;
-        string_truncate( buf, 0 );
-        path_build( &f2, buf, 0 );
-
-        b->name = buf->value;
-        b->time = b->flags = 0;
-        b->progress = BIND_INIT;
-
-        if ( hashenter( bindhash, (HASHDATA * *)&b ) )
-            b->name = newstr( buf->value );  /* never freed */
-
-        if ( !( b->flags & BIND_SCANNED ) )
-        {
-            file_archscan( buf->value, time_enter, bindhash );
-            b->flags |= BIND_SCANNED;
-        }
-    }
-
-    afterscanning:
-
-    if ( b->progress == BIND_SPOTTED )
-    {
-         b->progress = file_time( b->name, &b->time ) < 0
-            ? BIND_MISSING
-            : BIND_FOUND;
-    }
-
-    *time = b->progress == BIND_FOUND ? b->time : 0;
-        string_free( buf );
-#ifdef DOWNSHIFT_PATHS
-    string_free( &path );
-#endif
-
-    PROFILE_EXIT( timestamp );
-}
-
-
-static void time_enter( void * closure, char * target, int found, time_t time )
-{
-    BINDING binding;
-    BINDING * b = &binding;
-    struct hash * bindhash = (struct hash *)closure;
-
-#ifdef DOWNSHIFT_PATHS
-    char path[ MAXJPATH ];
-    char * p = path;
-
-    do *p++ = tolower( *target );
-    while ( *target++ );
-
-    target = path;
-#endif
-
-    b->name = target;
-    b->flags = 0;
-
-    if ( hashenter( bindhash, (HASHDATA * *)&b ) )
-        b->name = newstr( target );  /* never freed */
-
-    b->time = time;
-    b->progress = found ? BIND_FOUND : BIND_SPOTTED;
-
-    if ( DEBUG_BINDSCAN )
-        printf( "time ( %s ) : %s\n", target, time_progress[ b->progress ] );
-}
-
-
-/*
- * stamps_done() - free timestamp tables.
- */
-
-void stamps_done()
-{
-    hashdone( bindhash );
-}
diff --git a/jam-files/engine/timestamp.h b/jam-files/engine/timestamp.h
deleted file mode 100644
index f5752763..00000000
--- a/jam-files/engine/timestamp.h
+++ /dev/null
@@ -1,12 +0,0 @@
-/*
- * Copyright 1993, 1995 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*
- * timestamp.h - get the timestamp of a file or archive member
- */
-
-void timestamp( char * target, time_t * time );
-void stamps_done();
diff --git a/jam-files/engine/variable.c b/jam-files/engine/variable.c
deleted file mode 100644
index 795f3458..00000000
--- a/jam-files/engine/variable.c
+++ /dev/null
@@ -1,631 +0,0 @@
-/*
- * Copyright 1993, 2000 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*  This file is ALSO:
- *  Copyright 2001-2004 David Abrahams.
- *  Copyright 2005 Reece H. Dunn.
- *  Copyright 2005 Rene Rivera.
- *  Distributed under the Boost Software License, Version 1.0.
- *  (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
- */
-
-#include "jam.h"
-#include "lists.h"
-#include "parse.h"
-#include "variable.h"
-#include "expand.h"
-#include "hash.h"
-#include "filesys.h"
-#include "newstr.h"
-#include "strings.h"
-#include "pathsys.h"
-#include <stdlib.h>
-#include <stdio.h>
-
-/*
- * variable.c - handle Jam multi-element variables.
- *
- * External routines:
- *
- *  var_defines() - load a bunch of variable=value settings.
- *  var_string()  - expand a string with variables in it.
- *  var_get()     - get value of a user defined symbol.
- *  var_set()     - set a variable in jam's user defined symbol table.
- *  var_swap()    - swap a variable's value with the given one.
- *  var_done()    - free variable tables.
- *
- * Internal routines:
- *
- *  var_enter() - make new var symbol table entry, returning var ptr.
- *  var_dump()  - dump a variable to stdout.
- *
- * 04/13/94 (seiwald) - added shorthand L0 for null list pointer
- * 08/23/94 (seiwald) - Support for '+=' (append to variable)
- * 01/22/95 (seiwald) - split environment variables at blanks or :'s
- * 05/10/95 (seiwald) - split path variables at SPLITPATH (not :)
- * 09/11/00 (seiwald) - defunct var_list() removed
- */
-
-static struct hash *varhash = 0;
-
-/*
- * VARIABLE - a user defined multi-value variable
- */
-
-typedef struct _variable VARIABLE ;
-
-struct _variable
-{
-    char * symbol;
-    LIST * value;
-};
-
-static VARIABLE * var_enter( char * symbol );
-static void var_dump( char * symbol, LIST * value, char * what );
-
-
-/*
- * var_hash_swap() - swap all variable settings with those passed
- *
- * Used to implement separate settings spaces for modules
- */
-
-void var_hash_swap( struct hash * * new_vars )
-{
-    struct hash * old = varhash;
-    varhash = *new_vars;
-    *new_vars = old;
-}
-
-
-/*
- * var_defines() - load a bunch of variable=value settings
- *
- * If preprocess is false, take the value verbatim.
- *
- * Otherwise, if the variable value is enclosed in quotes, strip the
- * quotes.
- *
- * Otherwise, if variable name ends in PATH, split value at :'s.
- *
- * Otherwise, split the value at blanks.
- */
-
-void var_defines( char * const * e, int preprocess )
-{
-    string buf[1];
-
-    string_new( buf );
-
-    for ( ; *e; ++e )
-    {
-        char * val;
-
-# ifdef OS_MAC
-        /* On the mac (MPW), the var=val is actually var\0val */
-        /* Think different. */
-
-        if ( ( val = strchr( *e, '=' ) ) || ( val = *e + strlen( *e ) ) )
-# else
-        if ( ( val = strchr( *e, '=' ) ) )
-# endif
-        {
-            LIST * l = L0;
-            char * pp;
-            char * p;
-# ifdef OPT_NO_EXTERNAL_VARIABLE_SPLIT
-            char split = '\0';
-# else
-    # ifdef OS_MAC
-            char split = ',';
-    # else
-            char split = ' ';
-    # endif
-# endif
-            size_t len = strlen( val + 1 );
-
-            int quoted = ( val[1] == '"' ) && ( val[len] == '"' ) &&
-                ( len > 1 );
-
-            if ( quoted && preprocess )
-            {
-                string_append_range( buf, val + 2, val + len );
-                l = list_new( l, newstr( buf->value ) );
-                string_truncate( buf, 0 );
-            }
-            else
-            {
-                /* Split *PATH at :'s, not spaces. */
-                if ( val - 4 >= *e )
-                {
-                    if ( !strncmp( val - 4, "PATH", 4 ) ||
-                        !strncmp( val - 4, "Path", 4 ) ||
-                        !strncmp( val - 4, "path", 4 ) )
-                        split = SPLITPATH;
-                }
-
-                /* Do the split. */
-                for
-                (
-                    pp = val + 1;
-                    preprocess && ( ( p = strchr( pp, split ) ) != 0 );
-                    pp = p + 1
-                )
-                {
-                    string_append_range( buf, pp, p );
-                    l = list_new( l, newstr( buf->value ) );
-                    string_truncate( buf, 0 );
-                }
-
-                l = list_new( l, newstr( pp ) );
-            }
-
-            /* Get name. */
-            string_append_range( buf, *e, val );
-            var_set( buf->value, l, VAR_SET );
-            string_truncate( buf, 0 );
-        }
-    }
-    string_free( buf );
-}
-
-
-/*
- * var_string() - expand a string with variables in it
- *
- * Copies in to out; doesn't modify targets & sources.
- */
-
-int var_string( char * in, char * out, int outsize, LOL * lol )
-{
-    char * out0 = out;
-    char * oute = out + outsize - 1;
-
-    while ( *in )
-    {
-        char * lastword;
-        int    dollar = 0;
-
-        /* Copy white space. */
-        while ( isspace( *in ) )
-        {
-            if ( out >= oute )
-                return -1;
-            *out++ = *in++;
-        }
-
-        lastword = out;
-
-        /* Copy non-white space, watching for variables. */
-        while ( *in && !isspace( *in ) )
-        {
-            if ( out >= oute )
-                return -1;
-
-            if ( ( in[ 0 ] == '$' ) && ( in[ 1 ] == '(' ) )
-            {
-                ++dollar;
-                *out++ = *in++;
-            }
-            #ifdef OPT_AT_FILES
-            else if ( ( in[ 0 ] == '@' ) && ( in[ 1 ] == '(' ) )
-            {
-                int depth = 1;
-                char * ine = in + 2;
-                char * split = 0;
-
-                /* Scan the content of the response file @() section. */
-                while ( *ine && ( depth > 0 ) )
-                {
-                    switch ( *ine )
-                    {
-                    case '(': ++depth; break;
-                    case ')': --depth; break;
-                    case ':':
-                        if ( ( depth == 1 ) && ( ine[ 1 ] == 'E' ) && ( ine[ 2 ] == '=' ) )
-                            split = ine;
-                        break;
-                    }
-                    ++ine;
-                }
-
-                if ( !split )
-                {
-                    /*  the @() reference doesn't match the @(foo:E=bar) format.
-                        hence we leave it alone by copying directly to output. */
-                    int l = 0;
-                    if ( out + 2 >= oute ) return -1;
-                    *( out++ ) = '@';
-                    *( out++ ) = '(';
-                    l = var_string( in + 2, out, oute - out, lol );
-                    if ( l < 0 ) return -1;
-                    out += l;
-                    if ( out + 1 >= oute ) return -1;
-                    *( out++ ) = ')';
-                }
-                else if ( depth == 0 )
-                {
-                    string file_name_v;
-                    int file_name_l = 0;
-                    const char * file_name_s = 0;
-
-                    /* Expand the temporary file name var inline. */
-                    #if 0
-                    string_copy( &file_name_v, "$(" );
-                    string_append_range( &file_name_v, in + 2, split );
-                    string_push_back( &file_name_v, ')' );
-                    #else
-                    string_new( &file_name_v );
-                    string_append_range( &file_name_v, in + 2, split );
-                    #endif
-                    file_name_l = var_string( file_name_v.value, out, oute - out + 1, lol );
-                    string_free( &file_name_v );
-                    if ( file_name_l < 0 ) return -1;
-                    file_name_s = out;
-
-                    /* For stdout/stderr we will create a temp file and generate
-                     * a command that outputs the content as needed.
-                     */
-                    if ( ( strcmp( "STDOUT", out ) == 0 ) ||
-                        ( strcmp( "STDERR", out ) == 0 ) )
-                    {
-                        int err_redir = strcmp( "STDERR", out ) == 0;
-                        out[ 0 ] = '\0';
-                        file_name_s = path_tmpfile();
-                        file_name_l = strlen(file_name_s);
-                        #ifdef OS_NT
-                        if ( ( out + 7 + file_name_l + ( err_redir ? 5 : 0 ) ) >= oute )
-                            return -1;
-                        sprintf( out,"type \"%s\"%s", file_name_s,
-                            err_redir ? " 1>&2" : "" );
-                        #else
-                        if ( ( out + 6 + file_name_l + ( err_redir ? 5 : 0 ) ) >= oute )
-                            return -1;
-                        sprintf( out,"cat \"%s\"%s", file_name_s,
-                            err_redir ? " 1>&2" : "" );
-                        #endif
-                        /* We also make sure that the temp files created by this
-                         * get nuked eventually.
-                         */
-                        file_remove_atexit( file_name_s );
-                    }
-
-                    /* Expand the file value into the file reference. */
-                    var_string_to_file( split + 3, ine - split - 4, file_name_s,
-                        lol );
-
-                    /* Continue on with the expansion. */
-                    out += strlen( out );
-                }
-
-                /* And continue with the parsing just past the @() reference. */
-                in = ine;
-            }
-            #endif
-            else
-            {
-                *out++ = *in++;
-            }
-        }
-
-        /* Add zero to 'out' so that 'lastword' is correctly zero-terminated. */
-        if ( out >= oute )
-            return -1;
-        /* Do not increment, intentionally. */
-        *out = '\0';
-
-        /* If a variable encountered, expand it and and embed the
-         * space-separated members of the list in the output.
-         */
-        if ( dollar )
-        {
-            LIST * l = var_expand( L0, lastword, out, lol, 0 );
-
-            out = lastword;
-
-            while ( l )
-            {
-                int so = strlen( l->string );
-
-                if ( out + so >= oute )
-                    return -1;
-
-                strcpy( out, l->string );
-                out += so;
-                l = list_next( l );
-                if ( l ) *out++ = ' ';
-            }
-
-            list_free( l );
-        }
-    }
-
-    if ( out >= oute )
-        return -1;
-
-    *out++ = '\0';
-
-    return out - out0;
-}
-
-
-void var_string_to_file( const char * in, int insize, const char * out, LOL * lol )
-{
-    char const * ine = in + insize;
-    FILE * out_file = 0;
-    int out_debug = DEBUG_EXEC ? 1 : 0;
-    if ( globs.noexec )
-    {
-        /* out_debug = 1; */
-    }
-    else if ( strcmp( out, "STDOUT" ) == 0 )
-    {
-        out_file = stdout;
-    }
-    else if ( strcmp( out, "STDERR" ) == 0 )
-    {
-        out_file = stderr;
-    }
-    else
-    {
-        /* Handle "path to file" filenames. */
-        string out_name;
-        if ( ( out[ 0 ] == '"' ) && ( out[ strlen( out ) - 1 ] == '"' ) )
-        {
-            string_copy( &out_name, out + 1 );
-            string_truncate( &out_name, out_name.size - 1 );
-        }
-        else
-        {
-            string_copy( &out_name,out );
-        }
-        out_file = fopen( out_name.value, "w" );
-        if ( !out_file )
-        {
-            printf( "failed to write output file '%s'!\n", out_name.value );
-            exit( EXITBAD );
-        }
-        string_free( &out_name );
-    }
-
-    if ( out_debug ) printf( "\nfile %s\n", out );
-
-    while ( *in && ( in < ine ) )
-    {
-        int dollar = 0;
-        const char * output_0 = in;
-        const char * output_1 = in;
-
-        /* Copy white space. */
-        while ( ( output_1 < ine ) && isspace( *output_1 ) )
-            ++output_1;
-
-        if ( output_0 < output_1 )
-        {
-            if ( out_file  ) fwrite( output_0, output_1 - output_0, 1, out_file );
-            if ( out_debug ) fwrite( output_0, output_1 - output_0, 1, stdout   );
-        }
-        output_0 = output_1;
-
-        /* Copy non-white space, watching for variables. */
-        while ( ( output_1 < ine ) && *output_1 && !isspace( *output_1 ) )
-        {
-            if ( ( output_1[ 0 ] == '$' ) && ( output_1[ 1 ] == '(' ) )
-                ++dollar;
-            ++output_1;
-        }
-
-        /* If a variable encountered, expand it and embed the space-separated
-         * members of the list in the output.
-         */
-        if ( dollar )
-        {
-            LIST * l = var_expand( L0, (char *)output_0, (char *)output_1, lol, 0 );
-
-            while ( l )
-            {
-                if ( out_file ) fputs( l->string, out_file );
-                if ( out_debug ) puts( l->string );
-                l = list_next( l );
-                if ( l )
-                {
-                    if ( out_file ) fputc( ' ', out_file );
-                    if ( out_debug ) fputc( ' ', stdout );
-                }
-            }
-
-            list_free( l );
-        }
-        else if ( output_0 < output_1 )
-        {
-            if ( out_file )
-            {
-                const char * output_n = output_0;
-                while ( output_n < output_1 )
-                {
-                    output_n += fwrite( output_n, 1, output_1-output_n, out_file );
-                }
-            }
-            if ( out_debug )
-            {
-                const char * output_n = output_0;
-                while ( output_n < output_1 )
-                {
-                    output_n += fwrite( output_n, 1, output_1-output_n, stdout );
-                }
-            }
-        }
-
-        in = output_1;
-    }
-
-    if ( out_file && ( out_file != stdout ) && ( out_file != stderr ) )
-    {
-        fflush( out_file );
-        fclose( out_file );
-    }
-
-    if ( out_debug ) fputc( '\n', stdout );
-}
-
-
-/*
- * var_get() - get value of a user defined symbol.
- *
- * Returns NULL if symbol unset.
- */
-
-LIST * var_get( char * symbol )
-{
-    LIST * result = 0;
-#ifdef OPT_AT_FILES
-    /* Some "fixed" variables... */
-    if ( strcmp( "TMPDIR", symbol ) == 0 )
-    {
-        result = list_new( L0, newstr( (char *)path_tmpdir() ) );
-    }
-    else if ( strcmp( "TMPNAME", symbol ) == 0 )
-    {
-        result = list_new( L0, newstr( (char *)path_tmpnam() ) );
-    }
-    else if ( strcmp( "TMPFILE", symbol ) == 0 )
-    {
-        result = list_new( L0, newstr( (char *)path_tmpfile() ) );
-    }
-    else if ( strcmp( "STDOUT", symbol ) == 0 )
-    {
-        result = list_new( L0, newstr( "STDOUT" ) );
-    }
-    else if ( strcmp( "STDERR", symbol ) == 0 )
-    {
-        result = list_new( L0, newstr( "STDERR" ) );
-    }
-    else
-#endif
-    {
-        VARIABLE var;
-        VARIABLE * v = &var;
-
-        v->symbol = symbol;
-
-        if ( varhash && hashcheck( varhash, (HASHDATA * *)&v ) )
-        {
-            if ( DEBUG_VARGET )
-                var_dump( v->symbol, v->value, "get" );
-            result = v->value;
-        }
-    }
-    return result;
-}
-
-
-/*
- * var_set() - set a variable in Jam's user defined symbol table.
- *
- * 'flag' controls the relationship between new and old values of the variable:
- * SET replaces the old with the new; APPEND appends the new to the old; DEFAULT
- * only uses the new if the variable was previously unset.
- *
- * Copies symbol. Takes ownership of value.
- */
-
-void var_set( char * symbol, LIST * value, int flag )
-{
-    VARIABLE * v = var_enter( symbol );
-
-    if ( DEBUG_VARSET )
-        var_dump( symbol, value, "set" );
-
-    switch ( flag )
-    {
-    case VAR_SET:
-        /* Replace value */
-        list_free( v->value );
-        v->value = value;
-        break;
-
-    case VAR_APPEND:
-        /* Append value */
-        v->value = list_append( v->value, value );
-        break;
-
-    case VAR_DEFAULT:
-        /* Set only if unset */
-        if ( !v->value )
-            v->value = value;
-        else
-            list_free( value );
-        break;
-    }
-}
-
-
-/*
- * var_swap() - swap a variable's value with the given one.
- */
-
-LIST * var_swap( char * symbol, LIST * value )
-{
-    VARIABLE * v = var_enter( symbol );
-    LIST     * oldvalue = v->value;
-    if ( DEBUG_VARSET )
-        var_dump( symbol, value, "set" );
-    v->value = value;
-    return oldvalue;
-}
-
-
-/*
- * var_enter() - make new var symbol table entry, returning var ptr.
- */
-
-static VARIABLE * var_enter( char * symbol )
-{
-    VARIABLE var;
-    VARIABLE * v = &var;
-
-    if ( !varhash )
-        varhash = hashinit( sizeof( VARIABLE ), "variables" );
-
-    v->symbol = symbol;
-    v->value = 0;
-
-    if ( hashenter( varhash, (HASHDATA * *)&v ) )
-        v->symbol = newstr( symbol );  /* never freed */
-
-    return v;
-}
-
-
-/*
- * var_dump() - dump a variable to stdout.
- */
-
-static void var_dump( char * symbol, LIST * value, char * what )
-{
-    printf( "%s %s = ", what, symbol );
-    list_print( value );
-    printf( "\n" );
-}
-
-
-/*
- * var_done() - free variable tables.
- */
-
-static void delete_var_( void * xvar, void * data )
-{
-    VARIABLE * v = (VARIABLE *)xvar;
-    freestr( v->symbol );
-    list_free( v-> value );
-}
-
-
-void var_done()
-{
-    hashenumerate( varhash, delete_var_, (void *)0 );
-    hashdone( varhash );
-}
diff --git a/jam-files/engine/variable.h b/jam-files/engine/variable.h
deleted file mode 100644
index 5c49e3ca..00000000
--- a/jam-files/engine/variable.h
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * Copyright 1993, 2000 Christopher Seiwald.
- *
- * This file is part of Jam - see jam.c for Copyright information.
- */
-
-/*
- * variable.h - handle jam multi-element variables
- */
-
-struct hash;
-
-void    var_defines( char* const *e, int preprocess );
-int     var_string( char *in, char *out, int outsize, LOL *lol );
-LIST *  var_get( char *symbol );
-void    var_set( char *symbol, LIST *value, int flag );
-LIST *  var_swap( char *symbol, LIST *value );
-void    var_done();
-void    var_hash_swap( struct hash** );
-
-/** Expands the "in" expression directly into the "out" file.
-    The file can be one of: a path, STDOUT, or STDERR to send
-    the output to a file overwriting previous content, to
-    the console, or to the error output respectively.
-*/
-void var_string_to_file( const char * in, int insize, const char * out, LOL * lol );
-
-/*
- * Defines for var_set().
- */
-
-# define VAR_SET    0   /* override previous value */
-# define VAR_APPEND 1   /* append to previous value */
-# define VAR_DEFAULT    2   /* set only if no previous value */
-
diff --git a/jam-files/engine/w32_getreg.c b/jam-files/engine/w32_getreg.c
deleted file mode 100644
index 5a06f43e..00000000
--- a/jam-files/engine/w32_getreg.c
+++ /dev/null
@@ -1,207 +0,0 @@
-/*
-Copyright Paul Lin 2003. Copyright 2006 Bojan Resnik.
-Distributed under the Boost Software License, Version 1.0. (See accompanying
-file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-# include "jam.h"
-
-# if defined( OS_NT ) || defined( OS_CYGWIN )
-
-# include "lists.h"
-# include "newstr.h"
-# include "parse.h"
-# include "frames.h"
-# include "strings.h"
-
-# define WIN32_LEAN_AND_MEAN
-# include <windows.h>
-
-# define  MAX_REGISTRY_DATA_LENGTH 4096
-# define  MAX_REGISTRY_KEYNAME_LENGTH 256
-# define  MAX_REGISTRY_VALUENAME_LENGTH 16384
-
-typedef struct
-{
-    LPCSTR  name;
-    HKEY    value;
-} KeyMap;
-
-static const KeyMap dlRootKeys[] = {
-    { "HKLM", HKEY_LOCAL_MACHINE },
-    { "HKCU", HKEY_CURRENT_USER },
-    { "HKCR", HKEY_CLASSES_ROOT },
-    { "HKEY_LOCAL_MACHINE", HKEY_LOCAL_MACHINE },
-    { "HKEY_CURRENT_USER", HKEY_CURRENT_USER },
-    { "HKEY_CLASSES_ROOT", HKEY_CLASSES_ROOT },
-    { 0, 0 }
-};
-
-static HKEY get_key(char const** path)
-{
-    const KeyMap *p;
-
-    for (p = dlRootKeys; p->name; ++p)
-    {
-        int n = strlen(p->name);
-        if (!strncmp(*path,p->name,n))
-        {
-            if ((*path)[n] == '\\' || (*path)[n] == 0)
-            {
-                *path += n + 1;
-                break;
-            }
-        }
-    }
-
-    return p->value;
-}
-
-LIST*
-builtin_system_registry(
-    PARSE    *parse,
-    FRAME    *frame )
-{
-    char const* path = lol_get(frame->args, 0)->string;
-    LIST* result = L0;
-    HKEY key = get_key(&path);
-
-    if (
-        key != 0
-        && ERROR_SUCCESS == RegOpenKeyEx(key, path, 0, KEY_QUERY_VALUE, &key)
-    )
-    {
-        DWORD  type;
-        BYTE   data[MAX_REGISTRY_DATA_LENGTH];
-        DWORD  len = sizeof(data);
-        LIST const* const field = lol_get(frame->args, 1);
-
-        if ( ERROR_SUCCESS ==
-             RegQueryValueEx(key, field ? field->string : 0, 0, &type, data, &len) )
-        {
-            switch (type)
-            {
-
-             case REG_EXPAND_SZ:
-                 {
-                     long len;
-                     string expanded[1];
-                     string_new(expanded);
-
-                     while (
-                         (len = ExpandEnvironmentStrings(
-                             (LPCSTR)data, expanded->value, expanded->capacity))
-                         > expanded->capacity
-                     )
-                         string_reserve(expanded, len);
-
-                     expanded->size = len - 1;
-
-                     result = list_new( result, newstr(expanded->value) );
-                     string_free( expanded );
-                 }
-                 break;
-
-             case REG_MULTI_SZ:
-                 {
-                     char* s;
-
-                     for (s = (char*)data; *s; s += strlen(s) + 1)
-                         result = list_new( result, newstr(s) );
-
-                 }
-                 break;
-
-             case REG_DWORD:
-                 {
-                     char buf[100];
-                     sprintf( buf, "%u", *(PDWORD)data );
-                     result = list_new( result, newstr(buf) );
-                 }
-                 break;
-
-             case REG_SZ:
-                 result = list_new( result, newstr((char*)data) );
-                 break;
-            }
-        }
-        RegCloseKey(key);
-    }
-    return  result;
-}
-
-static LIST* get_subkey_names(HKEY key, char const* path)
-{
-    LIST* result = 0;
-
-    if ( ERROR_SUCCESS ==
-         RegOpenKeyEx(key, path, 0, KEY_ENUMERATE_SUB_KEYS, &key)
-    )
-    {
-        char name[MAX_REGISTRY_KEYNAME_LENGTH];
-        DWORD name_size = sizeof(name);
-        DWORD index;
-        FILETIME last_write_time;
-
-        for ( index = 0;
-              ERROR_SUCCESS == RegEnumKeyEx(
-                  key, index, name, &name_size, 0, 0, 0, &last_write_time);
-              ++index,
-              name_size = sizeof(name)
-        )
-        {
-            name[name_size] = 0;
-            result = list_append(result, list_new(0, newstr(name)));
-        }
-
-        RegCloseKey(key);
-    }
-
-    return result;
-}
-
-static LIST* get_value_names(HKEY key, char const* path)
-{
-    LIST* result = 0;
-
-    if ( ERROR_SUCCESS == RegOpenKeyEx(key, path, 0, KEY_QUERY_VALUE, &key) )
-    {
-        char name[MAX_REGISTRY_VALUENAME_LENGTH];
-        DWORD name_size = sizeof(name);
-        DWORD index;
-
-        for ( index = 0;
-              ERROR_SUCCESS == RegEnumValue(
-                  key, index, name, &name_size, 0, 0, 0, 0);
-              ++index,
-              name_size = sizeof(name)
-        )
-        {
-            name[name_size] = 0;
-            result = list_append(result, list_new(0, newstr(name)));
-        }
-
-        RegCloseKey(key);
-    }
-
-    return result;
-}
-
-LIST*
-builtin_system_registry_names(
-    PARSE    *parse,
-    FRAME    *frame )
-{
-    char const* path        = lol_get(frame->args, 0)->string;
-    char const* result_type = lol_get(frame->args, 1)->string;
-
-    HKEY key = get_key(&path);
-
-    if ( !strcmp(result_type, "subkeys") )
-        return get_subkey_names(key, path);
-    if ( !strcmp(result_type, "values") )
-        return get_value_names(key, path);
-    return 0;
-}
-
-# endif
diff --git a/jam-files/engine/yyacc.c b/jam-files/engine/yyacc.c
deleted file mode 100644
index b5efc96b..00000000
--- a/jam-files/engine/yyacc.c
+++ /dev/null
@@ -1,268 +0,0 @@
-/* Copyright 2002 Rene Rivera.
-** Distributed under the Boost Software License, Version 1.0.
-** (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-#include <stdio.h>
-#include <string.h>
-#include <ctype.h>
-#include <stdlib.h>
-
-/*
-# yyacc - yacc wrapper
-#
-# Allows tokens to be written as `literal` and then automatically
-# substituted with #defined tokens.
-#
-# Usage:
-#    yyacc file.y filetab.h file.yy
-#
-# inputs:
-#    file.yy        yacc grammar with ` literals
-#
-# outputs:
-#    file.y        yacc grammar
-#    filetab.h    array of string <-> token mappings
-#
-# 3-13-93
-#    Documented and p moved in sed command (for some reason,
-#    s/x/y/p doesn't work).
-# 10-12-93
-#    Take basename as second argument.
-# 12-31-96
-#    reversed order of args to be compatible with GenFile rule
-# 11-20-2002
-#    Reimplemented as a C program for portability. (Rene Rivera)
-*/
-
-void print_usage();
-char * copy_string(char * s, int l);
-char * tokenize_string(char * s);
-int cmp_literal(const void * a, const void * b);
-
-typedef struct
-{
-    char * string;
-    char * token;
-} literal;
-
-int main(int argc, char ** argv)
-{
-    int result = 0;
-    if (argc != 4)
-    {
-        print_usage();
-        result = 1;
-    }
-    else
-    {
-        FILE * token_output_f = 0;
-        FILE * grammar_output_f = 0;
-        FILE * grammar_source_f = 0;
-
-        grammar_source_f = fopen(argv[3],"r");
-        if (grammar_source_f == 0) { result = 1; }
-        if (result == 0)
-        {
-            literal literals[1024];
-            int t = 0;
-            char l[2048];
-            while (1)
-            {
-                if (fgets(l,2048,grammar_source_f) != 0)
-                {
-                    char * c = l;
-                    while (1)
-                    {
-                        char * c1 = strchr(c,'`');
-                        if (c1 != 0)
-                        {
-                            char * c2 = strchr(c1+1,'`');
-                            if (c2 != 0)
-                            {
-                                literals[t].string = copy_string(c1+1,c2-c1-1);
-                                literals[t].token = tokenize_string(literals[t].string);
-                                t += 1;
-                                c = c2+1;
-                            }
-                            else
-                                break;
-                        }
-                        else
-                            break;
-                    }
-                }
-                else
-                {
-                    break;
-                }
-            }
-            literals[t].string = 0;
-            literals[t].token = 0;
-            qsort(literals,t,sizeof(literal),cmp_literal);
-            {
-                int p = 1;
-                int i = 1;
-                while (literals[i].string != 0)
-                {
-                    if (strcmp(literals[p-1].string,literals[i].string) != 0)
-                    {
-                        literals[p] = literals[i];
-                        p += 1;
-                    }
-                    i += 1;
-                }
-                literals[p].string = 0;
-                literals[p].token = 0;
-                t = p;
-            }
-            token_output_f = fopen(argv[2],"w");
-            if (token_output_f != 0)
-            {
-                int i = 0;
-                while (literals[i].string != 0)
-                {
-                    fprintf(token_output_f,"    { \"%s\", %s },\n",literals[i].string,literals[i].token);
-                    i += 1;
-                }
-                fclose(token_output_f);
-            }
-            else
-                result = 1;
-            if (result == 0)
-            {
-                grammar_output_f = fopen(argv[1],"w");
-                if (grammar_output_f != 0)
-                {
-                    int i = 0;
-                    while (literals[i].string != 0)
-                    {
-                        fprintf(grammar_output_f,"%%token %s\n",literals[i].token);
-                        i += 1;
-                    }
-                    rewind(grammar_source_f);
-                    while (1)
-                    {
-                        if (fgets(l,2048,grammar_source_f) != 0)
-                        {
-                            char * c = l;
-                            while (1)
-                            {
-                                char * c1 = strchr(c,'`');
-                                if (c1 != 0)
-                                {
-                                    char * c2 = strchr(c1+1,'`');
-                                    if (c2 != 0)
-                                    {
-                                        literal key;
-                                        literal * replacement = 0;
-                                        key.string = copy_string(c1+1,c2-c1-1);
-                                        key.token = 0;
-                                        replacement = (literal*)bsearch(
-                                            &key,literals,t,sizeof(literal),cmp_literal);
-                                        *c1 = 0;
-                                        fprintf(grammar_output_f,"%s%s",c,replacement->token);
-                                        c = c2+1;
-                                    }
-                                    else
-                                    {
-                                        fprintf(grammar_output_f,"%s",c);
-                                        break;
-                                    }
-                                }
-                                else
-                                {
-                                    fprintf(grammar_output_f,"%s",c);
-                                    break;
-                                }
-                            }
-                        }
-                        else
-                        {
-                            break;
-                        }
-                    }
-                    fclose(grammar_output_f);
-                }
-                else
-                    result = 1;
-            }
-        }
-        if (result != 0)
-        {
-            perror("yyacc");
-        }
-    }
-    return result;
-}
-
-static char * usage[] = {
-    "yyacc <grammar output.y> <token table output.h> <grammar source.yy>",
-    0 };
-
-void print_usage()
-{
-    char ** u;
-    for (u = usage; *u != 0; ++u)
-    {
-        fputs(*u,stderr); putc('\n',stderr);
-    }
-}
-
-char * copy_string(char * s, int l)
-{
-    char * result = (char*)malloc(l+1);
-    strncpy(result,s,l);
-    result[l] = 0;
-    return result;
-}
-
-char * tokenize_string(char * s)
-{
-    char * result;
-    char * literal = s;
-    int l;
-    int c;
-
-    if (strcmp(s,":") == 0) literal = "_colon";
-    else if (strcmp(s,"!") == 0) literal = "_bang";
-    else if (strcmp(s,"!=") == 0) literal = "_bang_equals";
-    else if (strcmp(s,"&&") == 0) literal = "_amperamper";
-    else if (strcmp(s,"&") == 0) literal = "_amper";
-    else if (strcmp(s,"+") == 0) literal = "_plus";
-    else if (strcmp(s,"+=") == 0) literal = "_plus_equals";
-    else if (strcmp(s,"||") == 0) literal = "_barbar";
-    else if (strcmp(s,"|") == 0) literal = "_bar";
-    else if (strcmp(s,";") == 0) literal = "_semic";
-    else if (strcmp(s,"-") == 0) literal = "_minus";
-    else if (strcmp(s,"<") == 0) literal = "_langle";
-    else if (strcmp(s,"<=") == 0) literal = "_langle_equals";
-    else if (strcmp(s,">") == 0) literal = "_rangle";
-    else if (strcmp(s,">=") == 0) literal = "_rangle_equals";
-    else if (strcmp(s,".") == 0) literal = "_period";
-    else if (strcmp(s,"?") == 0) literal = "_question";
-    else if (strcmp(s,"?=") == 0) literal = "_question_equals";
-    else if (strcmp(s,"=") == 0) literal = "_equals";
-    else if (strcmp(s,",") == 0) literal = "_comma";
-    else if (strcmp(s,"[") == 0) literal = "_lbracket";
-    else if (strcmp(s,"]") == 0) literal = "_rbracket";
-    else if (strcmp(s,"{") == 0) literal = "_lbrace";
-    else if (strcmp(s,"}") == 0) literal = "_rbrace";
-    else if (strcmp(s,"(") == 0) literal = "_lparen";
-    else if (strcmp(s,")") == 0) literal = "_rparen";
-    l = strlen(literal)+2;
-    result = (char*)malloc(l+1);
-    for (c = 0; literal[c] != 0; ++c)
-    {
-        result[c] = toupper(literal[c]);
-    }
-    result[l-2] = '_';
-    result[l-1] = 't';
-    result[l] = 0;
-    return result;
-}
-
-int cmp_literal(const void * a, const void * b)
-{
-    return strcmp(((const literal *)a)->string,((const literal *)b)->string);
-}
diff --git a/jam-files/sanity.jam b/jam-files/sanity.jam
deleted file mode 100644
index aefed9c0..00000000
--- a/jam-files/sanity.jam
+++ /dev/null
@@ -1,201 +0,0 @@
-import modules ;
-import option ;
-import os ;
-import path ;
-import project ;
-
-#Shell with trailing line removed http://lists.boost.org/boost-build/2007/08/17051.php
-rule trim-nl ( str extras * ) {
-return [ MATCH "([^
-]*)" : $(str) ] $(extras) ;
-}
-rule _shell ( cmd : extras * ) {
-  return [ trim-nl [ SHELL $(cmd) : $(extras) ] ] ;
-}
-
-cxxflags = [ os.environ "CXXFLAGS" ] ;
-cflags = [ os.environ "CFLAGS" ] ;
-ldflags = [ os.environ "LDFLAGS" ] ;
-
-#Run g++ with empty main and these arguments to see if it passes.  
-rule test_flags ( flags * ) {
-  flags = $(cxxflags) $(ldflags) $(flags) ;
-  local cmd = "bash -c \"g++ "$(flags:J=" ")" -x c++ - <<<'int main() {}' -o /dev/null >/dev/null 2>/dev/null\"" ;
-  local ret = [ SHELL $(cmd) : exit-status ] ;
-  if --debug-configuration in [ modules.peek : ARGV ] {
-    echo $(cmd) ;
-    echo $(ret) ;
-  }
-  if $(ret[2]) = 0 {
-    return true ;
-  } else {
-    return ;
-  }
-}
-
-rule test_header ( name ) {
-  return [ test_flags "-include $(name)" ] ;
-}
-
-rule test_library ( name ) {
-  return [ test_flags "-l$(name)" ] ;
-}
-
-{
-  local cleaning = [ option.get "clean" : : yes ] ;
-  cleaning ?= [ option.get "clean-all" : no : yes ] ;
-  if "clean" in [ modules.peek : ARGV ] {
-    cleaning = yes ;
-  }
-  constant CLEANING : $(cleaning) ;
-}
-
-#Determine if a library can be compiled statically.  
-rule auto-shared ( name : additional * ) {
-  additional ?= "" ;
-  if [ test_flags $(additional)" -static -l"$(name) ] {
-    return ;
-  } else {
-    return "<link>shared" ;
-  }
-}
-
-# MacPorts' default location is /opt/local -- use this if no path is given.
-with-macports = [ option.get "with-macports" : : "/opt/local" ] ;
-if $(with-macports) {
-  using darwin ;
-  ECHO "Using --with-macports=$(with-macports), implying use of darwin GCC" ;
-
-  L-boost-search = -L$(with-macports)/lib ;
-  boost-search = <search>$(with-macports)/lib ;
-  I-boost-include = -I$(with-macports)/include ;
-  boost-include = <include>$(with-macports)/include ;
-}
-else {
-  with-boost = [ option.get "with-boost" ] ;
-  with-boost ?= [ os.environ "BOOST_ROOT" ] ;
-  if $(with-boost) {
-    L-boost-search = -L$(with-boost)/lib" "-L$(with-boost)/lib64 ;
-    boost-search = <search>$(with-boost)/lib <search>$(with-boost)/lib64 ;
-    I-boost-include = -I$(with-boost)/include ;
-    boost-include = <include>$(with-boost)/include ;
-  } else {
-    L-boost-search = "" ;
-    boost-search = ;
-    I-boost-include = "" ;
-    boost-include = ;
-  }
-}
-
-requirements = ;
- 
-#Are we linking static binaries against shared boost?
-boost-auto-shared = [ auto-shared "boost_program_options" : $(L-boost-search) ] ;
-#Convenience rule for boost libraries.  Defines library boost_$(name).  
-rule boost-lib ( name macro ) {
-  #Link multi-threaded programs against the -mt version if available.  Old 
-  #versions of boost do not have -mt tagged versions of all libraries.   Sadly,
-  #boost.jam does not handle this correctly.  
-  if [ test_flags $(L-boost-search)" -lboost_"$(name)"-mt" ] {
-#    if [ test_flags $(L-boost-search)" -lboost_"$(name) ] {
-#      lib inner_boost_$(name) : : <threading>single $(boost-search) <name>boost_$(name) ;
-#      lib inner_boost_$(name) : : <threading>multi $(boost-search) <name>boost_$(name)-mt ;
-#    } else {
-      if ! <threading>multi in $(requirements) {
-        requirements += <threading>multi ;
-      }
-      lib inner_boost_$(name) : : <threading>multi $(boost-search) <name>boost_$(name)-mt ;
-#    }
-  } else {
-    lib inner_boost_$(name) : : $(boost-search) <name>boost_$(name) ;
-  }
-
-  alias boost_$(name) : inner_boost_$(name) : $(boost-auto-shared) : : <link>shared:<define>BOOST_$(macro) $(boost-include) ;
-}
-
-#Argument is e.g. 103600
-rule boost ( min-version ) {
-  local cmd = "bash -c \"g++ "$(I-boost-include)" -dM -x c++ -E /dev/null -include boost/version.hpp 2>/dev/null |grep '#define BOOST_VERSION '\"" ;
-  local boost-shell = [ SHELL "$(cmd)" : exit-status ] ;
-  if $(boost-shell[2]) != 0 && $(CLEANING) = no {
-    echo Failed to run "$(cmd)" ;
-    exit Boost does not seem to be installed or g++ is confused. : 1 ;
-  }
-  boost-version = [ MATCH "#define BOOST_VERSION ([0-9]*)" : $(boost-shell[1]) ] ;
-  if $(boost-version) < $(min-version) && $(CLEANING) = no {
-    exit You have Boost $(boost-version).  This package requires Boost at least $(min-version) (and preferably newer). : 1 ;
-  }
-  #See tools/build/v2/contrib/boost.jam in a boost distribution for a table of macros to define.   
-  boost-lib thread THREAD_DYN_DLL ;
-  boost-lib program_options PROGRAM_OPTIONS_DYN_LINK ;
-  boost-lib unit_test_framework TEST_DYN_LINK ;
-  boost-lib iostreams IOSTREAMS_DYN_LINK ;
-  boost-lib serialization SERIALIZATION_DYN_LINK ;
-  boost-lib mpi MPI_DYN_LINK ;
-}
- 
-#Link normally to a library, but sometimes static isn't installed so fall back to dynamic.
-rule external-lib ( name : search-path * ) {
-  lib $(name) : : [ auto-shared $(name) : "-L"$(search-path) ] <search>$(search-path) ;
-}
-
-#Write the current command line to previous.sh.  This does not do shell escaping.  
-{
-  local build-log = $(TOP)/previous.sh ;
-  if ! [ path.exists $(build-log) ] {
-    SHELL "touch $(build-log) && chmod +x $(build-log)" ;
-  }
-  local script = [ modules.peek : ARGV ] ;
-  if $(script[1]) = "./jam-files/bjam" {
-    #The ./bjam shell script calls ./jam-files/bjam so that appears in argv but
-    #we want ./bjam to appear so the environment variables are set correctly.  
-    script = "./bjam "$(script[2-]:J=" ") ;
-  } else {
-    script = $(script:J=" ") ;
-  }
-  script = "#!/bin/sh\n$(script)\n" ;
-  local ignored = @($(build-log):E=$(script)) ;
-}
-
-{
-  #Boost jam's static clang for Linux is buggy.
-  requirements += <cxxflags>$(cxxflags) <cflags>$(cflags) <linkflags>$(ldflags) <os>LINUX,<toolset>clang:<link>shared ;
-
-  #libSegFault prints a stack trace on segfault.  Link against it if available.  
-  if [ test_flags "-lSegFault" ] {
-    external-lib SegFault ;
-    requirements += <library>SegFault ;
-  }
-}
-
-if [ option.get "git" : : "yes" ] {
-  local revision = [ _shell "git rev-parse --verify HEAD |head -c 7" ] ;
-  constant GITTAG : "/"$(revision) ;
-} else {
-  constant GITTAG : "" ;
-}
-
-prefix = [ option.get "prefix" ] ;
-if $(prefix) {
-  prefix = [ path.root $(prefix) [ path.pwd ] ] ;
-} else {
-  prefix = $(TOP)/dist$(GITTAG) ;
-}
-
-bindir = [ option.get "bindir" : $(prefix)/bin ] ;
-libdir = [ option.get "libdir" : $(prefix)/lib ] ;
-rule install-bin-libs ( deps * ) {
-  install prefix-bin : $(deps) : <location>$(bindir) <install-dependencies>on <install-type>EXE <link>shared:<dll-path>$(libdir) ;
-  install prefix-lib : $(deps) : <location>$(libdir) <install-dependencies>on <install-type>LIB <link>shared:<dll-path>$(libdir) ;
-}
-rule install-headers ( name : list * : source-root ? ) {
-  local includedir = [ option.get "includedir" : $(prefix)/include ] ;
-  source-root ?= "." ;
-  install $(name) : $(list) : <location>$(includedir) <install-source-root>$(source-root) ;
-}
-
-rule build-projects ( projects * ) {
-  for p in $(projects) {
-    build-project $(p) ;
-  }
-}
diff --git a/klm/lm/Jamfile b/klm/lm/Jamfile
deleted file mode 100644
index b1971d88..00000000
--- a/klm/lm/Jamfile
+++ /dev/null
@@ -1,14 +0,0 @@
-lib kenlm : bhiksha.cc binary_format.cc config.cc lm_exception.cc model.cc quantize.cc read_arpa.cc search_hashed.cc search_trie.cc trie.cc trie_sort.cc value_build.cc virtual_interface.cc vocab.cc ../util//kenutil : <include>.. : : <include>.. <library>../util//kenutil ;
-
-import testing ;
-
-run left_test.cc ../util//kenutil kenlm ../..//boost_unit_test_framework : : test.arpa ;
-run model_test.cc ../util//kenutil kenlm ../..//boost_unit_test_framework : : test.arpa test_nounk.arpa ;
-
-exe query : ngram_query.cc kenlm ../util//kenutil ;
-exe build_binary : build_binary.cc kenlm ../util//kenutil ;
-
-install legacy : build_binary query 
-  : <location>$(TOP)/klm/lm <install-type>EXE <install-dependencies>on <link>shared:<dll-path>$(TOP)/klm/lm <link>shared:<install-type>LIB ;
-
-alias programs : build_binary query ;
diff --git a/klm/lm/bhiksha.cc b/klm/lm/bhiksha.cc
index cdeafb47..088ea98d 100644
--- a/klm/lm/bhiksha.cc
+++ b/klm/lm/bhiksha.cc
@@ -1,6 +1,7 @@
 #include "lm/bhiksha.hh"
 #include "lm/config.hh"
 #include "util/file.hh"
+#include "util/exception.hh"
 
 #include <limits>
 
@@ -49,7 +50,7 @@ std::size_t ArrayCount(uint64_t max_offset, uint64_t max_next, const Config &con
 }
 } // namespace
 
-std::size_t ArrayBhiksha::Size(uint64_t max_offset, uint64_t max_next, const Config &config) {
+uint64_t ArrayBhiksha::Size(uint64_t max_offset, uint64_t max_next, const Config &config) {
   return sizeof(uint64_t) * (1 /* header */ + ArrayCount(max_offset, max_next, config)) + 7 /* 8-byte alignment */;
 }
 
diff --git a/klm/lm/bhiksha.hh b/klm/lm/bhiksha.hh
index 5182ee2e..8ff88654 100644
--- a/klm/lm/bhiksha.hh
+++ b/klm/lm/bhiksha.hh
@@ -23,7 +23,7 @@
 
 namespace lm {
 namespace ngram {
-class Config;
+struct Config;
 
 namespace trie {
 
@@ -33,7 +33,7 @@ class DontBhiksha {
 
     static void UpdateConfigFromBinary(int /*fd*/, Config &/*config*/) {}
 
-    static std::size_t Size(uint64_t /*max_offset*/, uint64_t /*max_next*/, const Config &/*config*/) { return 0; }
+    static uint64_t Size(uint64_t /*max_offset*/, uint64_t /*max_next*/, const Config &/*config*/) { return 0; }
 
     static uint8_t InlineBits(uint64_t /*max_offset*/, uint64_t max_next, const Config &/*config*/) {
       return util::RequiredBits(max_next);
@@ -67,7 +67,7 @@ class ArrayBhiksha {
 
     static void UpdateConfigFromBinary(int fd, Config &config);
 
-    static std::size_t Size(uint64_t max_offset, uint64_t max_next, const Config &config);
+    static uint64_t Size(uint64_t max_offset, uint64_t max_next, const Config &config);
 
     static uint8_t InlineBits(uint64_t max_offset, uint64_t max_next, const Config &config);
 
diff --git a/klm/lm/binary_format.cc b/klm/lm/binary_format.cc
index a56e998e..efa67056 100644
--- a/klm/lm/binary_format.cc
+++ b/klm/lm/binary_format.cc
@@ -83,7 +83,13 @@ void WriteHeader(void *to, const Parameters &params) {
 uint8_t *SetupJustVocab(const Config &config, uint8_t order, std::size_t memory_size, Backing &backing) {
   if (config.write_mmap) {
     std::size_t total = TotalHeaderSize(order) + memory_size;
-    backing.vocab.reset(util::MapZeroedWrite(config.write_mmap, total, backing.file), total, util::scoped_memory::MMAP_ALLOCATED);
+    backing.file.reset(util::CreateOrThrow(config.write_mmap));
+    if (config.write_method == Config::WRITE_MMAP) {
+      backing.vocab.reset(util::MapZeroedWrite(backing.file.get(), total), total, util::scoped_memory::MMAP_ALLOCATED);
+    } else {
+      util::ResizeOrThrow(backing.file.get(), 0);
+      util::MapAnonymous(total, backing.vocab);
+    }
     strncpy(reinterpret_cast<char*>(backing.vocab.get()), kMagicIncomplete, TotalHeaderSize(order));
     return reinterpret_cast<uint8_t*>(backing.vocab.get()) + TotalHeaderSize(order);
   } else {
@@ -121,12 +127,14 @@ uint8_t *GrowForSearch(const Config &config, std::size_t vocab_pad, std::size_t
 
 void FinishFile(const Config &config, ModelType model_type, unsigned int search_version, const std::vector<uint64_t> &counts, std::size_t vocab_pad, Backing &backing) {
   if (!config.write_mmap) return;
-  util::SyncOrThrow(backing.vocab.get(), backing.vocab.size());
   switch (config.write_method) {
     case Config::WRITE_MMAP:
+      util::SyncOrThrow(backing.vocab.get(), backing.vocab.size());
       util::SyncOrThrow(backing.search.get(), backing.search.size());
       break;
     case Config::WRITE_AFTER:
+      util::SeekOrThrow(backing.file.get(), 0);
+      util::WriteOrThrow(backing.file.get(), backing.vocab.get(), backing.vocab.size());
       util::SeekOrThrow(backing.file.get(), backing.vocab.size() + vocab_pad);
       util::WriteOrThrow(backing.file.get(), backing.search.get(), backing.search.size());
       util::FSyncOrThrow(backing.file.get());
@@ -141,6 +149,10 @@ void FinishFile(const Config &config, ModelType model_type, unsigned int search_
   params.fixed.has_vocabulary = config.include_vocab;
   params.fixed.search_version = search_version;
   WriteHeader(backing.vocab.get(), params);
+  if (config.write_method == Config::WRITE_AFTER) {
+    util::SeekOrThrow(backing.file.get(), 0);
+    util::WriteOrThrow(backing.file.get(), backing.vocab.get(), TotalHeaderSize(counts.size()));
+  }
 }
 
 namespace detail {
@@ -200,10 +212,10 @@ void SeekPastHeader(int fd, const Parameters &params) {
   util::SeekOrThrow(fd, TotalHeaderSize(params.counts.size()));
 }
 
-uint8_t *SetupBinary(const Config &config, const Parameters &params, std::size_t memory_size, Backing &backing) {
+uint8_t *SetupBinary(const Config &config, const Parameters &params, uint64_t memory_size, Backing &backing) {
   const uint64_t file_size = util::SizeFile(backing.file.get());
   // The header is smaller than a page, so we have to map the whole header as well.  
-  std::size_t total_map = TotalHeaderSize(params.counts.size()) + memory_size;
+  std::size_t total_map = util::CheckOverflow(TotalHeaderSize(params.counts.size()) + memory_size);
   if (file_size != util::kBadSize && static_cast<uint64_t>(file_size) < total_map)
     UTIL_THROW(FormatLoadException, "Binary file has size " << file_size << " but the headers say it should be at least " << total_map);
 
diff --git a/klm/lm/binary_format.hh b/klm/lm/binary_format.hh
index dd795f62..bf699d5f 100644
--- a/klm/lm/binary_format.hh
+++ b/klm/lm/binary_format.hh
@@ -70,7 +70,7 @@ void MatchCheck(ModelType model_type, unsigned int search_version, const Paramet
 
 void SeekPastHeader(int fd, const Parameters &params);
 
-uint8_t *SetupBinary(const Config &config, const Parameters &params, std::size_t memory_size, Backing &backing);
+uint8_t *SetupBinary(const Config &config, const Parameters &params, uint64_t memory_size, Backing &backing);
 
 void ComplainAboutARPA(const Config &config, ModelType model_type);
 
@@ -90,7 +90,7 @@ template <class To> void LoadLM(const char *file, const Config &config, To &to)
       new_config.probing_multiplier = params.fixed.probing_multiplier;
       detail::SeekPastHeader(backing.file.get(), params);
       To::UpdateConfigFromBinary(backing.file.get(), params.counts, new_config);
-      std::size_t memory_size = To::Size(params.counts, new_config);
+      uint64_t memory_size = To::Size(params.counts, new_config);
       uint8_t *start = detail::SetupBinary(new_config, params, memory_size, backing);
       to.InitializeFromBinary(start, params, new_config, backing.file.get());
     } else {
diff --git a/klm/lm/build_binary.cc b/klm/lm/build_binary.cc
index c4a01cb4..2b8c9d5b 100644
--- a/klm/lm/build_binary.cc
+++ b/klm/lm/build_binary.cc
@@ -11,6 +11,8 @@
 
 #ifdef WIN32
 #include "util/getopt.hh"
+#else
+#include <unistd.h>
 #endif
 
 namespace lm {
@@ -25,7 +27,11 @@ void Usage(const char *name) {
 "-i allows buggy models from IRSTLM by mapping positive log probability to 0.\n"
 "-w mmap|after determines how writing is done.\n"
 "   mmap maps the binary file and writes to it.  Default for trie.\n"
-"   after allocates anonymous memory, builds, and writes.  Default for probing.\n\n"
+"   after allocates anonymous memory, builds, and writes.  Default for probing.\n"
+"-r \"order1.arpa order2 order3 order4\" adds lower-order rest costs from these\n"
+"   model files.  order1.arpa must be an ARPA file.  All others may be ARPA or\n"
+"   the same data structure as being built.  All files must have the same\n"
+"   vocabulary.  For probing, the unigrams must be in the same order.\n\n"
 "type is either probing or trie.  Default is probing.\n\n"
 "probing uses a probing hash table.  It is the fastest but uses the most memory.\n"
 "-p sets the space multiplier and must be >1.0.  The default is 1.5.\n\n"
@@ -81,16 +87,16 @@ void ShowSizes(const char *file, const lm::ngram::Config &config) {
   std::vector<uint64_t> counts;
   util::FilePiece f(file);
   lm::ReadARPACounts(f, counts);
-  std::size_t sizes[6];
+  uint64_t sizes[6];
   sizes[0] = ProbingModel::Size(counts, config);
   sizes[1] = RestProbingModel::Size(counts, config);
   sizes[2] = TrieModel::Size(counts, config);
   sizes[3] = QuantTrieModel::Size(counts, config);
   sizes[4] = ArrayTrieModel::Size(counts, config);
   sizes[5] = QuantArrayTrieModel::Size(counts, config);
-  std::size_t max_length = *std::max_element(sizes, sizes + sizeof(sizes) / sizeof(size_t));
-  std::size_t min_length = *std::min_element(sizes, sizes + sizeof(sizes) / sizeof(size_t));
-  std::size_t divide;
+  uint64_t max_length = *std::max_element(sizes, sizes + sizeof(sizes) / sizeof(uint64_t));
+  uint64_t min_length = *std::min_element(sizes, sizes + sizeof(sizes) / sizeof(uint64_t));
+  uint64_t divide;
   char prefix;
   if (min_length < (1 << 10) * 10) {
     prefix = ' ';
@@ -111,7 +117,7 @@ void ShowSizes(const char *file, const lm::ngram::Config &config) {
   for (long int i = 0; i < length - 2; ++i) std::cout << ' ';
   std::cout << prefix << "B\n"
     "probing " << std::setw(length) << (sizes[0] / divide) << " assuming -p " << config.probing_multiplier << "\n"
-    "probing " << std::setw(length) << (sizes[1] / divide) << " assuming -r -p " << config.probing_multiplier << "\n"
+    "probing " << std::setw(length) << (sizes[1] / divide) << " assuming -r models -p " << config.probing_multiplier << "\n"
     "trie    " << std::setw(length) << (sizes[2] / divide) << " without quantization\n"
     "trie    " << std::setw(length) << (sizes[3] / divide) << " assuming -q " << (unsigned)config.prob_bits << " -b " << (unsigned)config.backoff_bits << " quantization \n"
     "trie    " << std::setw(length) << (sizes[4] / divide) << " assuming -a " << (unsigned)config.pointer_bhiksha_bits << " array pointer compression\n"
diff --git a/klm/lm/fragment.cc b/klm/lm/fragment.cc
new file mode 100644
index 00000000..0267cd4e
--- /dev/null
+++ b/klm/lm/fragment.cc
@@ -0,0 +1,37 @@
+#include "lm/binary_format.hh"
+#include "lm/model.hh"
+#include "lm/left.hh"
+#include "util/tokenize_piece.hh"
+
+template <class Model> void Query(const char *name) {
+  Model model(name);
+  std::string line;
+  lm::ngram::ChartState ignored;
+  while (getline(std::cin, line)) {
+    lm::ngram::RuleScore<Model> scorer(model, ignored);
+    for (util::TokenIter<util::SingleCharacter, true> i(line, ' '); i; ++i) {
+      scorer.Terminal(model.GetVocabulary().Index(*i));
+    }
+    std::cout << scorer.Finish() << '\n';
+  }
+}
+
+int main(int argc, char *argv[]) {
+  if (argc != 2) {
+    std::cerr << "Expected model file name." << std::endl;
+    return 1;
+  }
+  const char *name = argv[1];
+  lm::ngram::ModelType model_type = lm::ngram::PROBING;
+  lm::ngram::RecognizeBinary(name, model_type);
+  switch (model_type) {
+    case lm::ngram::PROBING:
+      Query<lm::ngram::ProbingModel>(name);
+      break;
+    case lm::ngram::REST_PROBING:
+      Query<lm::ngram::RestProbingModel>(name);
+      break;
+    default:
+      std::cerr << "Model type not supported yet." << std::endl;
+  }
+}
diff --git a/klm/lm/left.hh b/klm/lm/left.hh
index c00af88a..8c27232e 100644
--- a/klm/lm/left.hh
+++ b/klm/lm/left.hh
@@ -111,7 +111,7 @@ template <class M> class RuleScore {
         return;
       }
 
-      float backoffs[kMaxOrder - 1], backoffs2[kMaxOrder - 1];
+      float backoffs[KENLM_MAX_ORDER - 1], backoffs2[KENLM_MAX_ORDER - 1];
       float *back = backoffs, *back2 = backoffs2;
       unsigned char next_use = out_.right.length;
 
diff --git a/klm/lm/max_order.cc b/klm/lm/max_order.cc
new file mode 100644
index 00000000..94221201
--- /dev/null
+++ b/klm/lm/max_order.cc
@@ -0,0 +1,6 @@
+#include "lm/max_order.hh"
+#include <iostream>
+
+int main(int argc, char *argv[]) {
+  std::cerr << "KenLM was compiled with a maximum supported n-gram order set to " << KENLM_MAX_ORDER << "." << std::endl;
+}
diff --git a/klm/lm/max_order.hh b/klm/lm/max_order.hh
index aff9de27..989f8324 100644
--- a/klm/lm/max_order.hh
+++ b/klm/lm/max_order.hh
@@ -1,14 +1,12 @@
-#ifndef LM_MAX_ORDER__
-#define LM_MAX_ORDER__
-namespace lm {
-namespace ngram {
-// If you need higher order, change this and recompile.  
-// Having this limit means that State can be
-// (kMaxOrder - 1) * sizeof(float) bytes instead of
-// sizeof(float*) + (kMaxOrder - 1) * sizeof(float) + malloc overhead
-const unsigned char kMaxOrder = 5;
-
-} // namespace ngram
-} // namespace lm
-
-#endif // LM_MAX_ORDER__
+/* IF YOUR BUILD SYSTEM PASSES -DKENLM_MAX_ORDER, THEN CHANGE THE BUILD SYSTEM.
+ * If not, this is the default maximum order.  
+ * Having this limit means that State can be
+ * (kMaxOrder - 1) * sizeof(float) bytes instead of
+ * sizeof(float*) + (kMaxOrder - 1) * sizeof(float) + malloc overhead
+ */
+#ifndef KENLM_MAX_ORDER
+#define KENLM_MAX_ORDER 6
+#endif
+#ifndef KENLM_ORDER_MESSAGE
+#define KENLM_ORDER_MESSAGE "If your build system supports changing KENLM_MAX_ORDER, change it there and recompile.  In the KenLM tarball or Moses, use e.g. `bjam --kenlm-max-order=6 -a'.  Otherwise, edit lm/max_order.hh."
+#endif
diff --git a/klm/lm/model.cc b/klm/lm/model.cc
index a2d31ce0..2fd20481 100644
--- a/klm/lm/model.cc
+++ b/klm/lm/model.cc
@@ -5,12 +5,14 @@
 #include "lm/search_hashed.hh"
 #include "lm/search_trie.hh"
 #include "lm/read_arpa.hh"
+#include "util/have.hh"
 #include "util/murmur_hash.hh"
 
 #include <algorithm>
 #include <functional>
 #include <numeric>
 #include <cmath>
+#include <limits>
 
 namespace lm {
 namespace ngram {
@@ -18,17 +20,18 @@ namespace detail {
 
 template <class Search, class VocabularyT> const ModelType GenericModel<Search, VocabularyT>::kModelType = Search::kModelType;
 
-template <class Search, class VocabularyT> size_t GenericModel<Search, VocabularyT>::Size(const std::vector<uint64_t> &counts, const Config &config) {
+template <class Search, class VocabularyT> uint64_t GenericModel<Search, VocabularyT>::Size(const std::vector<uint64_t> &counts, const Config &config) {
   return VocabularyT::Size(counts[0], config) + Search::Size(counts, config);
 }
 
 template <class Search, class VocabularyT> void GenericModel<Search, VocabularyT>::SetupMemory(void *base, const std::vector<uint64_t> &counts, const Config &config) {
+  size_t goal_size = util::CheckOverflow(Size(counts, config));
   uint8_t *start = static_cast<uint8_t*>(base);
   size_t allocated = VocabularyT::Size(counts[0], config);
   vocab_.SetupMemory(start, allocated, counts[0], config);
   start += allocated;
   start = search_.SetupMemory(start, counts, config);
-  if (static_cast<std::size_t>(start - static_cast<uint8_t*>(base)) != Size(counts, config)) UTIL_THROW(FormatLoadException, "The data structures took " << (start - static_cast<uint8_t*>(base)) << " but Size says they should take " << Size(counts, config));
+  if (static_cast<std::size_t>(start - static_cast<uint8_t*>(base)) != goal_size) UTIL_THROW(FormatLoadException, "The data structures took " << (start - static_cast<uint8_t*>(base)) << " but Size says they should take " << goal_size);
 }
 
 template <class Search, class VocabularyT> GenericModel<Search, VocabularyT>::GenericModel(const char *file, const Config &config) {
@@ -47,7 +50,19 @@ template <class Search, class VocabularyT> GenericModel<Search, VocabularyT>::Ge
   P::Init(begin_sentence, null_context, vocab_, search_.Order());
 }
 
+namespace {
+void CheckCounts(const std::vector<uint64_t> &counts) {
+  UTIL_THROW_IF(counts.size() > KENLM_MAX_ORDER, FormatLoadException, "This model has order " << counts.size() << " but KenLM was compiled to support up to " << KENLM_MAX_ORDER << ".  " << KENLM_ORDER_MESSAGE);
+  if (sizeof(uint64_t) > sizeof(std::size_t)) {
+    for (std::vector<uint64_t>::const_iterator i = counts.begin(); i != counts.end(); ++i) {
+      UTIL_THROW_IF(*i > static_cast<uint64_t>(std::numeric_limits<size_t>::max()), util::OverflowException, "This model has " << *i << " " << (i - counts.begin() + 1) << "-grams which is too many for 32-bit machines.");
+    }
+  }
+}
+} // namespace
+
 template <class Search, class VocabularyT> void GenericModel<Search, VocabularyT>::InitializeFromBinary(void *start, const Parameters &params, const Config &config, int fd) {
+  CheckCounts(params.counts);
   SetupMemory(start, params.counts, config);
   vocab_.LoadedBinary(params.fixed.has_vocabulary, fd, config.enumerate_vocab);
   search_.LoadedBinary();
@@ -60,12 +75,11 @@ template <class Search, class VocabularyT> void GenericModel<Search, VocabularyT
     std::vector<uint64_t> counts;
     // File counts do not include pruned trigrams that extend to quadgrams etc.   These will be fixed by search_.
     ReadARPACounts(f, counts);
-
-    if (counts.size() > kMaxOrder) UTIL_THROW(FormatLoadException, "This model has order " << counts.size() << ".  Edit lm/max_order.hh, set kMaxOrder to at least this value, and recompile.");
+    CheckCounts(counts);
     if (counts.size() < 2) UTIL_THROW(FormatLoadException, "This ngram implementation assumes at least a bigram model.");
     if (config.probing_multiplier <= 1.0) UTIL_THROW(ConfigException, "probing multiplier must be > 1.0");
 
-    std::size_t vocab_size = VocabularyT::Size(counts[0], config);
+    std::size_t vocab_size = util::CheckOverflow(VocabularyT::Size(counts[0], config));
     // Setup the binary file for writing the vocab lookup table.  The search_ is responsible for growing the binary file to its needs.  
     vocab_.SetupMemory(SetupJustVocab(config, counts.size(), vocab_size, backing_), vocab_size, counts[0], config);
 
@@ -73,7 +87,7 @@ template <class Search, class VocabularyT> void GenericModel<Search, VocabularyT
       WriteWordsWrapper wrap(config.enumerate_vocab);
       vocab_.ConfigureEnumerate(&wrap, counts[0]);
       search_.InitializeFromARPA(file, f, counts, config, vocab_, backing_);
-      wrap.Write(backing_.file.get());
+      wrap.Write(backing_.file.get(), backing_.vocab.size() + vocab_.UnkCountChangePadding() + backing_.search.size());
     } else {
       vocab_.ConfigureEnumerate(config.enumerate_vocab, counts[0]);
       search_.InitializeFromARPA(file, f, counts, config, vocab_, backing_);
diff --git a/klm/lm/model.hh b/klm/lm/model.hh
index be872178..13ff864e 100644
--- a/klm/lm/model.hh
+++ b/klm/lm/model.hh
@@ -5,7 +5,6 @@
 #include "lm/binary_format.hh"
 #include "lm/config.hh"
 #include "lm/facade.hh"
-#include "lm/max_order.hh"
 #include "lm/quantize.hh"
 #include "lm/search_hashed.hh"
 #include "lm/search_trie.hh"
@@ -42,7 +41,7 @@ template <class Search, class VocabularyT> class GenericModel : public base::Mod
      * does not include small non-mapped control structures, such as this class
      * itself.  
      */
-    static size_t Size(const std::vector<uint64_t> &counts, const Config &config = Config());
+    static uint64_t Size(const std::vector<uint64_t> &counts, const Config &config = Config());
 
     /* Load the model from a file.  It may be an ARPA or binary file.  Binary
      * files must have the format expected by this class or you'll get an
diff --git a/klm/lm/partial.hh b/klm/lm/partial.hh
new file mode 100644
index 00000000..1dede359
--- /dev/null
+++ b/klm/lm/partial.hh
@@ -0,0 +1,167 @@
+#ifndef LM_PARTIAL__
+#define LM_PARTIAL__
+
+#include "lm/return.hh"
+#include "lm/state.hh"
+
+#include <algorithm>
+
+#include <assert.h>
+
+namespace lm {
+namespace ngram {
+
+struct ExtendReturn {
+  float adjust;
+  bool make_full;
+  unsigned char next_use;
+};
+
+template <class Model> ExtendReturn ExtendLoop(
+    const Model &model,
+    unsigned char seen, const WordIndex *add_rbegin, const WordIndex *add_rend, const float *backoff_start,
+    const uint64_t *pointers, const uint64_t *pointers_end,
+    uint64_t *&pointers_write,
+    float *backoff_write) {
+  unsigned char add_length = add_rend - add_rbegin;
+
+  float backoff_buf[2][KENLM_MAX_ORDER - 1];
+  float *backoff_in = backoff_buf[0], *backoff_out = backoff_buf[1];
+  std::copy(backoff_start, backoff_start + add_length, backoff_in);
+
+  ExtendReturn value;
+  value.make_full = false;
+  value.adjust = 0.0;
+  value.next_use = add_length;
+
+  unsigned char i = 0;
+  unsigned char length = pointers_end - pointers;
+  // pointers_write is NULL means that the existing left state is full, so we should use completed probabilities.  
+  if (pointers_write) {
+    // Using full context, writing to new left state.   
+    for (; i < length; ++i) {
+      FullScoreReturn ret(model.ExtendLeft(
+          add_rbegin, add_rbegin + value.next_use,
+          backoff_in,
+          pointers[i], i + seen + 1,
+          backoff_out,
+          value.next_use));
+      std::swap(backoff_in, backoff_out);
+      if (ret.independent_left) {
+        value.adjust += ret.prob;
+        value.make_full = true;
+        ++i;
+        break;
+      }
+      value.adjust += ret.rest;
+      *pointers_write++ = ret.extend_left;
+      if (value.next_use != add_length) {
+        value.make_full = true;
+        ++i;
+        break;
+      }
+    }
+  }
+  // Using some of the new context.  
+  for (; i < length && value.next_use; ++i) {
+    FullScoreReturn ret(model.ExtendLeft(
+        add_rbegin, add_rbegin + value.next_use,
+        backoff_in,
+        pointers[i], i + seen + 1,
+        backoff_out,
+        value.next_use));
+    std::swap(backoff_in, backoff_out);
+    value.adjust += ret.prob;
+  }
+  float unrest = model.UnRest(pointers + i, pointers_end, i + seen + 1);
+  // Using none of the new context.  
+  value.adjust += unrest;
+
+  std::copy(backoff_in, backoff_in + value.next_use, backoff_write);
+  return value;
+}
+
+template <class Model> float RevealBefore(const Model &model, const Right &reveal, const unsigned char seen, bool reveal_full, Left &left, Right &right) {
+  assert(seen < reveal.length || reveal_full);
+  uint64_t *pointers_write = reveal_full ? NULL : left.pointers;
+  float backoff_buffer[KENLM_MAX_ORDER - 1];
+  ExtendReturn value(ExtendLoop(
+      model,
+      seen, reveal.words + seen, reveal.words + reveal.length, reveal.backoff + seen,
+      left.pointers, left.pointers + left.length,
+      pointers_write,
+      left.full ? backoff_buffer : (right.backoff + right.length)));
+  if (reveal_full) {
+    left.length = 0;
+    value.make_full = true;
+  } else {
+    left.length = pointers_write - left.pointers;
+    value.make_full |= (left.length == model.Order() - 1);
+  }
+  if (left.full) {
+    for (unsigned char i = 0; i < value.next_use; ++i) value.adjust += backoff_buffer[i];
+  } else {
+    // If left wasn't full when it came in, put words into right state.  
+    std::copy(reveal.words + seen, reveal.words + seen + value.next_use, right.words + right.length);
+    right.length += value.next_use;
+    left.full = value.make_full || (right.length == model.Order() - 1);
+  }
+  return value.adjust;
+}
+
+template <class Model> float RevealAfter(const Model &model, Left &left, Right &right, const Left &reveal, unsigned char seen) {
+  assert(seen < reveal.length || reveal.full);
+  uint64_t *pointers_write = left.full ? NULL : (left.pointers + left.length);
+  ExtendReturn value(ExtendLoop(
+      model,
+      seen, right.words, right.words + right.length, right.backoff,
+      reveal.pointers + seen, reveal.pointers + reveal.length,
+      pointers_write,
+      right.backoff));
+  if (reveal.full) {
+    for (unsigned char i = 0; i < value.next_use; ++i) value.adjust += right.backoff[i];
+    right.length = 0;
+    value.make_full = true;
+  } else {
+    right.length = value.next_use;
+    value.make_full |= (right.length == model.Order() - 1);
+  }
+  if (!left.full) {
+    left.length = pointers_write - left.pointers;
+    left.full = value.make_full || (left.length == model.Order() - 1);
+  }
+  return value.adjust;
+}
+
+template <class Model> float Subsume(const Model &model, Left &first_left, const Right &first_right, const Left &second_left, Right &second_right, const unsigned int between_length) {
+  assert(first_right.length < KENLM_MAX_ORDER);
+  assert(second_left.length < KENLM_MAX_ORDER);
+  assert(between_length < KENLM_MAX_ORDER - 1);
+  uint64_t *pointers_write = first_left.full ? NULL : (first_left.pointers + first_left.length);
+  float backoff_buffer[KENLM_MAX_ORDER - 1];
+  ExtendReturn value(ExtendLoop(
+        model,
+        between_length, first_right.words, first_right.words + first_right.length, first_right.backoff,
+        second_left.pointers, second_left.pointers + second_left.length,
+        pointers_write,
+        second_left.full ? backoff_buffer : (second_right.backoff + second_right.length)));
+  if (second_left.full) {
+    for (unsigned char i = 0; i < value.next_use; ++i) value.adjust += backoff_buffer[i];
+  } else {
+    std::copy(first_right.words, first_right.words + value.next_use, second_right.words + second_right.length);
+    second_right.length += value.next_use;
+    value.make_full |= (second_right.length == model.Order() - 1);
+  }
+  if (!first_left.full) {
+    first_left.length = pointers_write - first_left.pointers;
+    first_left.full = value.make_full || second_left.full || (first_left.length == model.Order() - 1);
+  }
+  assert(first_left.length < KENLM_MAX_ORDER);
+  assert(second_right.length < KENLM_MAX_ORDER);
+  return value.adjust;
+}
+
+} // namespace ngram
+} // namespace lm
+
+#endif // LM_PARTIAL__
diff --git a/klm/lm/partial_test.cc b/klm/lm/partial_test.cc
new file mode 100644
index 00000000..8d309c85
--- /dev/null
+++ b/klm/lm/partial_test.cc
@@ -0,0 +1,199 @@
+#include "lm/partial.hh"
+
+#include "lm/left.hh"
+#include "lm/model.hh"
+#include "util/tokenize_piece.hh"
+
+#define BOOST_TEST_MODULE PartialTest
+#include <boost/test/unit_test.hpp>
+#include <boost/test/floating_point_comparison.hpp>
+
+namespace lm {
+namespace ngram {
+namespace {
+
+const char *TestLocation() {
+  if (boost::unit_test::framework::master_test_suite().argc < 2) {
+    return "test.arpa";
+  }
+  return boost::unit_test::framework::master_test_suite().argv[1];
+}
+
+Config SilentConfig() {
+  Config config;
+  config.arpa_complain = Config::NONE;
+  config.messages = NULL;
+  return config;
+}
+
+struct ModelFixture {
+  ModelFixture() : m(TestLocation(), SilentConfig()) {}
+
+  RestProbingModel m;
+};
+
+BOOST_FIXTURE_TEST_SUITE(suite, ModelFixture)
+
+BOOST_AUTO_TEST_CASE(SimpleBefore) {
+  Left left;
+  left.full = false;
+  left.length = 0;
+  Right right;
+  right.length = 0;
+
+  Right reveal;
+  reveal.length = 1;
+  WordIndex period = m.GetVocabulary().Index(".");
+  reveal.words[0] = period;
+  reveal.backoff[0] = -0.845098;
+
+  BOOST_CHECK_CLOSE(0.0, RevealBefore(m, reveal, 0, false, left, right), 0.001);
+  BOOST_CHECK_EQUAL(0, left.length);
+  BOOST_CHECK(!left.full);
+  BOOST_CHECK_EQUAL(1, right.length);
+  BOOST_CHECK_EQUAL(period, right.words[0]);
+  BOOST_CHECK_CLOSE(-0.845098, right.backoff[0], 0.001);
+
+  WordIndex more = m.GetVocabulary().Index("more");
+  reveal.words[1] = more;
+  reveal.backoff[1] =  -0.4771212;
+  reveal.length = 2;
+  BOOST_CHECK_CLOSE(0.0, RevealBefore(m, reveal, 1, false, left, right), 0.001);
+  BOOST_CHECK_EQUAL(0, left.length);
+  BOOST_CHECK(!left.full);
+  BOOST_CHECK_EQUAL(2, right.length);
+  BOOST_CHECK_EQUAL(period, right.words[0]);
+  BOOST_CHECK_EQUAL(more, right.words[1]);
+  BOOST_CHECK_CLOSE(-0.845098, right.backoff[0], 0.001);
+  BOOST_CHECK_CLOSE(-0.4771212, right.backoff[1], 0.001);
+}
+
+BOOST_AUTO_TEST_CASE(AlsoWouldConsider) {
+  WordIndex would = m.GetVocabulary().Index("would");
+  WordIndex consider = m.GetVocabulary().Index("consider");
+
+  ChartState current;
+  current.left.length = 1;
+  current.left.pointers[0] = would;
+  current.left.full = false;
+  current.right.length = 1;
+  current.right.words[0] = would;
+  current.right.backoff[0] = -0.30103;
+
+  Left after;
+  after.full = false;
+  after.length = 1;
+  after.pointers[0] = consider;
+
+  // adjustment for would consider
+  BOOST_CHECK_CLOSE(-1.687872 - -0.2922095 - 0.30103, RevealAfter(m, current.left, current.right, after, 0), 0.001);
+
+  BOOST_CHECK_EQUAL(2, current.left.length);
+  BOOST_CHECK_EQUAL(would, current.left.pointers[0]);
+  BOOST_CHECK_EQUAL(false, current.left.full);
+
+  WordIndex also = m.GetVocabulary().Index("also");
+  Right before;
+  before.length = 1;
+  before.words[0] = also;
+  before.backoff[0] = -0.30103;
+  // r(would) = -0.2922095 [i would], r(would -> consider) = -1.988902 [b(would) + p(consider)]
+  // p(also -> would) = -2, p(also would -> consider) = -3
+  BOOST_CHECK_CLOSE(-2 + 0.2922095 -3 + 1.988902, RevealBefore(m, before, 0, false, current.left, current.right), 0.001);
+  BOOST_CHECK_EQUAL(0, current.left.length);
+  BOOST_CHECK(current.left.full);
+  BOOST_CHECK_EQUAL(2, current.right.length);
+  BOOST_CHECK_EQUAL(would, current.right.words[0]);
+  BOOST_CHECK_EQUAL(also, current.right.words[1]);
+}
+
+BOOST_AUTO_TEST_CASE(EndSentence) {
+  WordIndex loin = m.GetVocabulary().Index("loin");
+  WordIndex period = m.GetVocabulary().Index(".");
+  WordIndex eos = m.GetVocabulary().EndSentence();
+
+  ChartState between;
+  between.left.length = 1;
+  between.left.pointers[0] = eos;
+  between.left.full = true;
+  between.right.length = 0;
+
+  Right before;
+  before.words[0] = period;
+  before.words[1] = loin;
+  before.backoff[0] = -0.845098;
+  before.backoff[1] = 0.0;
+  
+  before.length = 1;
+  BOOST_CHECK_CLOSE(-0.0410707, RevealBefore(m, before, 0, true, between.left, between.right), 0.001);
+  BOOST_CHECK_EQUAL(0, between.left.length);
+}
+
+float ScoreFragment(const RestProbingModel &model, unsigned int *begin, unsigned int *end, ChartState &out) {
+  RuleScore<RestProbingModel> scorer(model, out);
+  for (unsigned int *i = begin; i < end; ++i) {
+    scorer.Terminal(*i);
+  }
+  return scorer.Finish();
+}
+
+void CheckAdjustment(const RestProbingModel &model, float expect, const Right &before_in, bool before_full, ChartState between, const Left &after_in) {
+  Right before(before_in);
+  Left after(after_in);
+  after.full = false;
+  float got = 0.0;
+  for (unsigned int i = 1; i < 5; ++i) {
+    if (before_in.length >= i) {
+      before.length = i;
+      got += RevealBefore(model, before, i - 1, false, between.left, between.right);
+    }
+    if (after_in.length >= i) {
+      after.length = i;
+      got += RevealAfter(model, between.left, between.right, after, i - 1);
+    }
+  }
+  if (after_in.full) {
+    after.full = true;
+    got += RevealAfter(model, between.left, between.right, after, after.length);
+  }
+  if (before_full) {
+    got += RevealBefore(model, before, before.length, true, between.left, between.right);
+  }
+  // Sometimes they're zero and BOOST_CHECK_CLOSE fails for this. 
+  BOOST_CHECK(fabs(expect - got) < 0.001);
+}
+
+void FullDivide(const RestProbingModel &model, StringPiece str) {
+  std::vector<WordIndex> indices;
+  for (util::TokenIter<util::SingleCharacter, true> i(str, ' '); i; ++i) {
+    indices.push_back(model.GetVocabulary().Index(*i));
+  }
+  ChartState full_state;
+  float full = ScoreFragment(model, &indices.front(), &indices.back() + 1, full_state);
+
+  ChartState before_state;
+  before_state.left.full = false;
+  RuleScore<RestProbingModel> before_scorer(model, before_state);
+  float before_score = 0.0;
+  for (unsigned int before = 0; before < indices.size(); ++before) {
+    for (unsigned int after = before; after <= indices.size(); ++after) {
+      ChartState after_state, between_state;
+      float after_score = ScoreFragment(model, &indices.front() + after, &indices.front() + indices.size(), after_state);
+      float between_score = ScoreFragment(model, &indices.front() + before, &indices.front() + after, between_state);
+      CheckAdjustment(model, full - before_score - after_score - between_score, before_state.right, before_state.left.full, between_state, after_state.left);
+    }
+    before_scorer.Terminal(indices[before]);
+    before_score = before_scorer.Finish();
+  }
+}
+
+BOOST_AUTO_TEST_CASE(Strings) {
+  FullDivide(m, "also would consider");
+  FullDivide(m, "looking on a little more loin . </s>");
+  FullDivide(m, "in biarritz watching considering looking . on a little more loin also would consider higher to look good unknown the screening foo bar , unknown however unknown </s>");
+}
+
+BOOST_AUTO_TEST_SUITE_END()
+} // namespace
+} // namespace ngram
+} // namespace lm
diff --git a/klm/lm/quantize.hh b/klm/lm/quantize.hh
index 3e9153e3..8ce2378a 100644
--- a/klm/lm/quantize.hh
+++ b/klm/lm/quantize.hh
@@ -17,14 +17,14 @@
 namespace lm {
 namespace ngram {
 
-class Config;
+struct Config;
 
 /* Store values directly and don't quantize. */
 class DontQuantize {
   public:
     static const ModelType kModelTypeAdd = static_cast<ModelType>(0);
     static void UpdateConfigFromBinary(int, const std::vector<uint64_t> &, Config &) {}
-    static std::size_t Size(uint8_t /*order*/, const Config &/*config*/) { return 0; }
+    static uint64_t Size(uint8_t /*order*/, const Config &/*config*/) { return 0; }
     static uint8_t MiddleBits(const Config &/*config*/) { return 63; }
     static uint8_t LongestBits(const Config &/*config*/) { return 31; }
 
@@ -138,9 +138,9 @@ class SeparatelyQuantize {
 
     static void UpdateConfigFromBinary(int fd, const std::vector<uint64_t> &counts, Config &config);
 
-    static std::size_t Size(uint8_t order, const Config &config) {
-      size_t longest_table = (static_cast<size_t>(1) << static_cast<size_t>(config.prob_bits)) * sizeof(float);
-      size_t middle_table = (static_cast<size_t>(1) << static_cast<size_t>(config.backoff_bits)) * sizeof(float) + longest_table;
+    static uint64_t Size(uint8_t order, const Config &config) {
+      uint64_t longest_table = (static_cast<uint64_t>(1) << static_cast<uint64_t>(config.prob_bits)) * sizeof(float);
+      uint64_t middle_table = (static_cast<uint64_t>(1) << static_cast<uint64_t>(config.backoff_bits)) * sizeof(float) + longest_table;
       // unigrams are currently not quantized so no need for a table.  
       return (order - 2) * middle_table + longest_table + /* for the bit counts and alignment padding) */ 8;
     }
@@ -217,7 +217,7 @@ class SeparatelyQuantize {
     const Bins &LongestTable() const { return longest_; }
 
   private:
-    Bins tables_[kMaxOrder - 1][2];
+    Bins tables_[KENLM_MAX_ORDER - 1][2];
 
     Bins longest_;
 
diff --git a/klm/lm/read_arpa.cc b/klm/lm/read_arpa.cc
index 2d9a337d..b709fef9 100644
--- a/klm/lm/read_arpa.cc
+++ b/klm/lm/read_arpa.cc
@@ -2,14 +2,20 @@
 
 #include "lm/blank.hh"
 
+#include <cmath>
 #include <cstdlib>
 #include <iostream>
+#include <sstream>
 #include <vector>
 
 #include <ctype.h>
 #include <string.h>
 #include <stdint.h>
 
+#ifdef WIN32
+#include <float.h>
+#endif
+
 namespace lm {
 
 // 1 for '\t', '\n', and ' '.  This is stricter than isspace.  
@@ -26,6 +32,15 @@ bool IsEntirelyWhiteSpace(const StringPiece &line) {
 
 const char kBinaryMagic[] = "mmap lm http://kheafield.com/code";
 
+// strtoull isn't portable enough :-(
+uint64_t ReadCount(const std::string &from) {
+  std::stringstream stream(from);
+  uint64_t ret;
+  stream >> ret;
+  UTIL_THROW_IF(!stream, FormatLoadException, "Bad count " << from);
+  return ret;
+}
+
 } // namespace
 
 void ReadARPACounts(util::FilePiece &in, std::vector<uint64_t> &number) {
@@ -47,15 +62,11 @@ void ReadARPACounts(util::FilePiece &in, std::vector<uint64_t> &number) {
     // So strtol doesn't go off the end of line.  
     std::string remaining(line.data() + 6, line.size() - 6);
     char *end_ptr;
-    unsigned long int length = std::strtol(remaining.c_str(), &end_ptr, 10);
+    unsigned int length = std::strtol(remaining.c_str(), &end_ptr, 10);
     if ((end_ptr == remaining.c_str()) || (length - 1 != number.size())) UTIL_THROW(FormatLoadException, "ngram count lengths should be consecutive starting with 1: " << line);
     if (*end_ptr != '=') UTIL_THROW(FormatLoadException, "Expected = immediately following the first number in the count line " << line);
     ++end_ptr;
-    const char *start = end_ptr;
-    long int count = std::strtol(start, &end_ptr, 10);
-    if (count < 0) UTIL_THROW(FormatLoadException, "Negative n-gram count " << count);
-    if (start == end_ptr) UTIL_THROW(FormatLoadException, "Couldn't parse n-gram count from " << line);
-    number.push_back(count);
+    number.push_back(ReadCount(end_ptr));
   }
 }
 
@@ -93,7 +104,16 @@ void ReadBackoff(util::FilePiece &in, float &backoff) {
     case '\t':
       backoff = in.ReadFloat();
       if (backoff == ngram::kExtensionBackoff) backoff = ngram::kNoExtensionBackoff;
-      if ((in.get() != '\n')) UTIL_THROW(FormatLoadException, "Expected newline after backoff");
+      {
+#ifdef WIN32
+		int float_class = _fpclass(backoff);
+        UTIL_THROW_IF(float_class == _FPCLASS_SNAN || float_class == _FPCLASS_QNAN || float_class == _FPCLASS_NINF || float_class == _FPCLASS_PINF, FormatLoadException, "Bad backoff " << backoff);
+#else
+        int float_class = std::fpclassify(backoff);
+        UTIL_THROW_IF(float_class == FP_NAN || float_class == FP_INFINITE, FormatLoadException, "Bad backoff " << backoff);
+#endif
+      }
+      UTIL_THROW_IF(in.get() != '\n', FormatLoadException, "Expected newline after backoff");
       break;
     case '\n':
       backoff = ngram::kNoExtensionBackoff;
diff --git a/klm/lm/search_hashed.cc b/klm/lm/search_hashed.cc
index 13942309..a1623834 100644
--- a/klm/lm/search_hashed.cc
+++ b/klm/lm/search_hashed.cc
@@ -234,7 +234,7 @@ template <> void HashedSearch<BackoffValue>::DispatchBuild(util::FilePiece &f, c
   ApplyBuild(f, counts, config, vocab, warn, build);
 }
 
-template <> void HashedSearch<RestValue>::DispatchBuild(util::FilePiece &f, const std::vector<uint64_t> &counts, const Config &config, const      ProbingVocabulary &vocab, PositiveProbWarn &warn) {
+template <> void HashedSearch<RestValue>::DispatchBuild(util::FilePiece &f, const std::vector<uint64_t> &counts, const Config &config, const ProbingVocabulary &vocab, PositiveProbWarn &warn) {
   switch (config.rest_function) {
     case Config::REST_MAX:
       {
diff --git a/klm/lm/search_hashed.hh b/klm/lm/search_hashed.hh
index 7e8c1220..a52f107b 100644
--- a/klm/lm/search_hashed.hh
+++ b/klm/lm/search_hashed.hh
@@ -74,8 +74,8 @@ template <class Value> class HashedSearch {
     // TODO: move probing_multiplier here with next binary file format update.  
     static void UpdateConfigFromBinary(int, const std::vector<uint64_t> &, Config &) {}
 
-    static std::size_t Size(const std::vector<uint64_t> &counts, const Config &config) {
-      std::size_t ret = Unigram::Size(counts[0]);
+    static uint64_t Size(const std::vector<uint64_t> &counts, const Config &config) {
+      uint64_t ret = Unigram::Size(counts[0]);
       for (unsigned char n = 1; n < counts.size() - 1; ++n) {
         ret += Middle::Size(counts[n], config.probing_multiplier);
       }
@@ -160,8 +160,8 @@ template <class Value> class HashedSearch {
 #endif
       {}
 
-        static std::size_t Size(uint64_t count) {
-          return (count + 1) * sizeof(ProbBackoff); // +1 for hallucinate <unk>
+        static uint64_t Size(uint64_t count) {
+          return (count + 1) * sizeof(typename Value::Weights); // +1 for hallucinate <unk>
         }
 
         const typename Value::Weights &Lookup(WordIndex index) const {
diff --git a/klm/lm/search_trie.cc b/klm/lm/search_trie.cc
index 18e80d5a..debcfd07 100644
--- a/klm/lm/search_trie.cc
+++ b/klm/lm/search_trie.cc
@@ -89,7 +89,7 @@ class BackoffMessages {
         if (!HasExtension(weights.backoff)) {
           weights.backoff = kExtensionBackoff;
           UTIL_THROW_IF(fseek(unigrams, -sizeof(weights), SEEK_CUR), util::ErrnoException, "Seeking backwards to denote unigram extension failed.");
-          WriteOrThrow(unigrams, &weights, sizeof(weights));
+          util::WriteOrThrow(unigrams, &weights, sizeof(weights));
         }
         const ProbPointer &write_to = *reinterpret_cast<const ProbPointer*>(current_ + sizeof(WordIndex));
         base[write_to.array][write_to.index] += weights.backoff;
@@ -180,7 +180,7 @@ const float kBadProb = std::numeric_limits<float>::infinity();
 class SRISucks {
   public:
     SRISucks() {
-      for (BackoffMessages *i = messages_; i != messages_ + kMaxOrder - 1; ++i)
+      for (BackoffMessages *i = messages_; i != messages_ + KENLM_MAX_ORDER - 1; ++i)
         i->Init(sizeof(ProbPointer) + sizeof(WordIndex) * (i - messages_ + 1));
     }
 
@@ -196,7 +196,7 @@ class SRISucks {
     }
 
     void ObtainBackoffs(unsigned char total_order, FILE *unigram_file, RecordReader *reader) {
-      for (unsigned char i = 0; i < kMaxOrder - 1; ++i) {
+      for (unsigned char i = 0; i < KENLM_MAX_ORDER - 1; ++i) {
         it_[i] = values_[i].empty() ? NULL : &*values_[i].begin();
       }
       messages_[0].Apply(it_, unigram_file);
@@ -221,10 +221,10 @@ class SRISucks {
 
   private:
     // This used to be one array.  Then I needed to separate it by order for quantization to work.  
-    std::vector<float> values_[kMaxOrder - 1];
-    BackoffMessages messages_[kMaxOrder - 1];
+    std::vector<float> values_[KENLM_MAX_ORDER - 1];
+    BackoffMessages messages_[KENLM_MAX_ORDER - 1];
 
-    float *it_[kMaxOrder - 1];
+    float *it_[KENLM_MAX_ORDER - 1];
 };
 
 class FindBlanks {
@@ -337,7 +337,7 @@ struct Gram {
 template <class Doing> class BlankManager {
   public:
     BlankManager(unsigned char total_order, Doing &doing) : total_order_(total_order), been_length_(0), doing_(doing) {
-      for (float *i = basis_; i != basis_ + kMaxOrder - 1; ++i) *i = kBadProb;
+      for (float *i = basis_; i != basis_ + KENLM_MAX_ORDER - 1; ++i) *i = kBadProb;
     }
 
     void Visit(const WordIndex *to, unsigned char length, float prob) {
@@ -373,10 +373,10 @@ template <class Doing> class BlankManager {
   private:
     const unsigned char total_order_;
 
-    WordIndex been_[kMaxOrder];
+    WordIndex been_[KENLM_MAX_ORDER];
     unsigned char been_length_;
 
-    float basis_[kMaxOrder];
+    float basis_[KENLM_MAX_ORDER];
     
     Doing &doing_;
 };
@@ -470,8 +470,8 @@ void PopulateUnigramWeights(FILE *file, WordIndex unigram_count, RecordReader &c
 } // namespace
 
 template <class Quant, class Bhiksha> void BuildTrie(SortedFiles &files, std::vector<uint64_t> &counts, const Config &config, TrieSearch<Quant, Bhiksha> &out, Quant &quant, const SortedVocabulary &vocab, Backing &backing) {
-  RecordReader inputs[kMaxOrder - 1];
-  RecordReader contexts[kMaxOrder - 1];
+  RecordReader inputs[KENLM_MAX_ORDER - 1];
+  RecordReader contexts[KENLM_MAX_ORDER - 1];
 
   for (unsigned char i = 2; i <= counts.size(); ++i) {
     inputs[i-2].Init(files.Full(i), i * sizeof(WordIndex) + (i == counts.size() ? sizeof(Prob) : sizeof(ProbBackoff)));
diff --git a/klm/lm/search_trie.hh b/klm/lm/search_trie.hh
index 10b22ab1..1264baf5 100644
--- a/klm/lm/search_trie.hh
+++ b/klm/lm/search_trie.hh
@@ -44,8 +44,8 @@ template <class Quant, class Bhiksha> class TrieSearch {
       Bhiksha::UpdateConfigFromBinary(fd, config);
     }
 
-    static std::size_t Size(const std::vector<uint64_t> &counts, const Config &config) {
-      std::size_t ret = Quant::Size(counts.size(), config) + Unigram::Size(counts[0]);
+    static uint64_t Size(const std::vector<uint64_t> &counts, const Config &config) {
+      uint64_t ret = Quant::Size(counts.size(), config) + Unigram::Size(counts[0]);
       for (unsigned char i = 1; i < counts.size() - 1; ++i) {
         ret += Middle::Size(Quant::MiddleBits(config), counts[i], counts[0], counts[i+1], config);
       }
diff --git a/klm/lm/sri_test.cc b/klm/lm/sri_test.cc
deleted file mode 100644
index e697d722..00000000
--- a/klm/lm/sri_test.cc
+++ /dev/null
@@ -1,65 +0,0 @@
-#include "lm/sri.hh"
-
-#include <stdlib.h>
-
-#define BOOST_TEST_MODULE SRITest
-#include <boost/test/unit_test.hpp>
-
-namespace lm {
-namespace sri {
-namespace {
-
-#define StartTest(word, ngram, score) \
-  ret = model.FullScore( \
-      state, \
-      model.GetVocabulary().Index(word), \
-      out);\
-  BOOST_CHECK_CLOSE(score, ret.prob, 0.001); \
-  BOOST_CHECK_EQUAL(static_cast<unsigned int>(ngram), ret.ngram_length); \
-  BOOST_CHECK_EQUAL(std::min<unsigned char>(ngram, 5 - 1), out.valid_length_);
-
-#define AppendTest(word, ngram, score) \
-  StartTest(word, ngram, score) \
-  state = out;
-
-template <class M> void Starters(M &model) {
-  FullScoreReturn ret;
-  Model::State state(model.BeginSentenceState());
-  Model::State out;
-
-  StartTest("looking", 2, -0.4846522);
-
-  // , probability plus <s> backoff
-  StartTest(",", 1, -1.383514 + -0.4149733);
-  // <unk> probability plus <s> backoff
-  StartTest("this_is_not_found", 0, -1.995635 + -0.4149733);
-}
-
-template <class M> void Continuation(M &model) {
-  FullScoreReturn ret;
-  Model::State state(model.BeginSentenceState());
-  Model::State out;
-
-  AppendTest("looking", 2, -0.484652);
-  AppendTest("on", 3, -0.348837);
-  AppendTest("a", 4, -0.0155266);
-  AppendTest("little", 5, -0.00306122);
-  State preserve = state;
-  AppendTest("the", 1, -4.04005);
-  AppendTest("biarritz", 1, -1.9889);
-  AppendTest("not_found", 0, -2.29666);
-  AppendTest("more", 1, -1.20632);
-  AppendTest(".", 2, -0.51363);
-  AppendTest("</s>", 3, -0.0191651);
-
-  state = preserve;
-  AppendTest("more", 5, -0.00181395);
-  AppendTest("loin", 5, -0.0432557);
-}
-
-BOOST_AUTO_TEST_CASE(starters) { Model m("test.arpa", 5); Starters(m); }
-BOOST_AUTO_TEST_CASE(continuation) { Model m("test.arpa", 5); Continuation(m); }
-
-} // namespace
-} // namespace sri
-} // namespace lm
diff --git a/klm/lm/state.hh b/klm/lm/state.hh
index c7438414..551510a8 100644
--- a/klm/lm/state.hh
+++ b/klm/lm/state.hh
@@ -32,7 +32,7 @@ class State {
 
     // Call this before using raw memcmp.  
     void ZeroRemaining() {
-      for (unsigned char i = length; i < kMaxOrder - 1; ++i) {
+      for (unsigned char i = length; i < KENLM_MAX_ORDER - 1; ++i) {
         words[i] = 0;
         backoff[i] = 0.0;
       }
@@ -42,11 +42,13 @@ class State {
 
     // You shouldn't need to touch anything below this line, but the members are public so FullState will qualify as a POD.  
     // This order minimizes total size of the struct if WordIndex is 64 bit, float is 32 bit, and alignment of 64 bit integers is 64 bit.  
-    WordIndex words[kMaxOrder - 1];
-    float backoff[kMaxOrder - 1];
+    WordIndex words[KENLM_MAX_ORDER - 1];
+    float backoff[KENLM_MAX_ORDER - 1];
     unsigned char length;
 };
 
+typedef State Right;
+
 inline uint64_t hash_value(const State &state, uint64_t seed = 0) {
   return util::MurmurHashNative(state.words, sizeof(WordIndex) * state.length, seed);
 }
@@ -72,11 +74,11 @@ struct Left {
   }
 
   void ZeroRemaining() {
-    for (uint64_t * i = pointers + length; i < pointers + kMaxOrder - 1; ++i)
+    for (uint64_t * i = pointers + length; i < pointers + KENLM_MAX_ORDER - 1; ++i)
       *i = 0;
   }
 
-  uint64_t pointers[kMaxOrder - 1];
+  uint64_t pointers[KENLM_MAX_ORDER - 1];
   unsigned char length;
   bool full;
 };
diff --git a/klm/lm/trie.cc b/klm/lm/trie.cc
index 0f1ca574..d9895f89 100644
--- a/klm/lm/trie.cc
+++ b/klm/lm/trie.cc
@@ -36,7 +36,7 @@ bool FindBitPacked(const void *base, uint64_t key_mask, uint8_t key_bits, uint8_
 }
 } // namespace
 
-std::size_t BitPacked::BaseSize(uint64_t entries, uint64_t max_vocab, uint8_t remaining_bits) {
+uint64_t BitPacked::BaseSize(uint64_t entries, uint64_t max_vocab, uint8_t remaining_bits) {
   uint8_t total_bits = util::RequiredBits(max_vocab) + remaining_bits;
   // Extra entry for next pointer at the end.  
   // +7 then / 8 to round up bits and convert to bytes
@@ -57,7 +57,7 @@ void BitPacked::BaseInit(void *base, uint64_t max_vocab, uint8_t remaining_bits)
   max_vocab_ = max_vocab;
 }
 
-template <class Bhiksha> std::size_t BitPackedMiddle<Bhiksha>::Size(uint8_t quant_bits, uint64_t entries, uint64_t max_vocab, uint64_t max_ptr, const Config &config) {
+template <class Bhiksha> uint64_t BitPackedMiddle<Bhiksha>::Size(uint8_t quant_bits, uint64_t entries, uint64_t max_vocab, uint64_t max_ptr, const Config &config) {
   return Bhiksha::Size(entries + 1, max_ptr, config) + BaseSize(entries, max_vocab, quant_bits + Bhiksha::InlineBits(entries + 1, max_ptr, config));
 }
 
diff --git a/klm/lm/trie.hh b/klm/lm/trie.hh
index eff93292..9ea3c546 100644
--- a/klm/lm/trie.hh
+++ b/klm/lm/trie.hh
@@ -11,7 +11,7 @@
 
 namespace lm {
 namespace ngram {
-class Config;
+struct Config;
 namespace trie {
 
 struct NodeRange {
@@ -49,7 +49,7 @@ class Unigram {
       unigram_ = static_cast<UnigramValue*>(start);
     }
     
-    static std::size_t Size(uint64_t count) {
+    static uint64_t Size(uint64_t count) {
       // +1 in case unknown doesn't appear.  +1 for the final next.  
       return (count + 2) * sizeof(UnigramValue);
     }
@@ -84,7 +84,7 @@ class BitPacked {
     }
 
   protected:
-    static std::size_t BaseSize(uint64_t entries, uint64_t max_vocab, uint8_t remaining_bits);
+    static uint64_t BaseSize(uint64_t entries, uint64_t max_vocab, uint8_t remaining_bits);
 
     void BaseInit(void *base, uint64_t max_vocab, uint8_t remaining_bits);
 
@@ -99,7 +99,7 @@ class BitPacked {
 
 template <class Bhiksha> class BitPackedMiddle : public BitPacked {
   public:
-    static std::size_t Size(uint8_t quant_bits, uint64_t entries, uint64_t max_vocab, uint64_t max_next, const Config &config);
+    static uint64_t Size(uint8_t quant_bits, uint64_t entries, uint64_t max_vocab, uint64_t max_next, const Config &config);
 
     // next_source need not be initialized.  
     BitPackedMiddle(void *base, uint8_t quant_bits, uint64_t entries, uint64_t max_vocab, uint64_t max_next, const BitPacked &next_source, const Config &config);
@@ -128,7 +128,7 @@ template <class Bhiksha> class BitPackedMiddle : public BitPacked {
 
 class BitPackedLongest : public BitPacked {
   public:
-    static std::size_t Size(uint8_t quant_bits, uint64_t entries, uint64_t max_vocab) {
+    static uint64_t Size(uint8_t quant_bits, uint64_t entries, uint64_t max_vocab) {
       return BaseSize(entries, max_vocab, quant_bits);
     }
 
diff --git a/klm/lm/trie_sort.cc b/klm/lm/trie_sort.cc
index b80fed02..8663e94e 100644
--- a/klm/lm/trie_sort.cc
+++ b/klm/lm/trie_sort.cc
@@ -22,12 +22,6 @@
 namespace lm {
 namespace ngram {
 namespace trie {
-
-void WriteOrThrow(FILE *to, const void *data, size_t size) {
-  assert(size);
-  if (1 != std::fwrite(data, size, 1, to)) UTIL_THROW(util::ErrnoException, "Short write; requested size " << size);
-}
-
 namespace {
 
 typedef util::SizedIterator NGramIter;
@@ -95,12 +89,12 @@ FILE *WriteContextFile(uint8_t *begin, uint8_t *end, const util::TempMaker &make
   // Write out to file and uniqueify at the same time.  Could have used unique_copy if there was an appropriate OutputIterator.  
   if (context_begin == context_end) return out.release();
   PartialIter i(context_begin);
-  WriteOrThrow(out.get(), i->Data(), context_size);
+  util::WriteOrThrow(out.get(), i->Data(), context_size);
   const void *previous = i->Data();
   ++i;
   for (; i != context_end; ++i) {
     if (memcmp(previous, i->Data(), context_size)) {
-      WriteOrThrow(out.get(), i->Data(), context_size);
+      util::WriteOrThrow(out.get(), i->Data(), context_size);
       previous = i->Data();
     }
   }
@@ -116,7 +110,7 @@ struct ThrowCombine {
 // Useful for context files that just contain records with no value.  
 struct FirstCombine {
   void operator()(std::size_t entry_size, const void *first, const void * /*second*/, FILE *out) const {
-    WriteOrThrow(out, first, entry_size);
+    util::WriteOrThrow(out, first, entry_size);
   }
 };
 
@@ -129,10 +123,10 @@ template <class Combine> FILE *MergeSortedFiles(FILE *first_file, FILE *second_f
   EntryCompare less(order);
   while (first && second) {
     if (less(first.Data(), second.Data())) {
-      WriteOrThrow(out_file.get(), first.Data(), entry_size);
+      util::WriteOrThrow(out_file.get(), first.Data(), entry_size);
       ++first;
     } else if (less(second.Data(), first.Data())) {
-      WriteOrThrow(out_file.get(), second.Data(), entry_size);
+      util::WriteOrThrow(out_file.get(), second.Data(), entry_size);
       ++second;
     } else {
       combine(entry_size, first.Data(), second.Data(), out_file.get());
@@ -140,7 +134,7 @@ template <class Combine> FILE *MergeSortedFiles(FILE *first_file, FILE *second_f
     }
   }
   for (RecordReader &remains = (first ? first : second); remains; ++remains) {
-    WriteOrThrow(out_file.get(), remains.Data(), entry_size);
+    util::WriteOrThrow(out_file.get(), remains.Data(), entry_size);
   }
   return out_file.release();
 }
@@ -148,19 +142,23 @@ template <class Combine> FILE *MergeSortedFiles(FILE *first_file, FILE *second_f
 } // namespace
 
 void RecordReader::Init(FILE *file, std::size_t entry_size) {
-  rewind(file);
-  file_ = file;
+  entry_size_ = entry_size;
   data_.reset(malloc(entry_size));
   UTIL_THROW_IF(!data_.get(), util::ErrnoException, "Failed to malloc read buffer");
-  remains_ = true;
-  entry_size_ = entry_size;
-  ++*this;
+  file_ = file;
+  if (file) {
+    rewind(file);
+    remains_ = true;
+    ++*this;
+  } else {
+    remains_ = false;
+  }
 }
 
 void RecordReader::Overwrite(const void *start, std::size_t amount) {
   long internal = (uint8_t*)start - (uint8_t*)data_.get();
   UTIL_THROW_IF(fseek(file_, internal - entry_size_, SEEK_CUR), util::ErrnoException, "Couldn't seek backwards for revision");
-  WriteOrThrow(file_, start, amount);
+  util::WriteOrThrow(file_, start, amount);
   long forward = entry_size_ - internal - amount;
 #if !defined(_WIN32) && !defined(_WIN64)
   if (forward) 
@@ -169,9 +167,13 @@ void RecordReader::Overwrite(const void *start, std::size_t amount) {
 }
 
 void RecordReader::Rewind() {
-  rewind(file_);
-  remains_ = true;
-  ++*this;
+  if (file_) {
+    rewind(file_);
+    remains_ = true;
+    ++*this;
+  } else {
+    remains_ = false;
+  }
 }
 
 SortedFiles::SortedFiles(const Config &config, util::FilePiece &f, std::vector<uint64_t> &counts, size_t buffer, const std::string &file_prefix, SortedVocabulary &vocab) {
diff --git a/klm/lm/trie_sort.hh b/klm/lm/trie_sort.hh
index 3036319d..2197b80c 100644
--- a/klm/lm/trie_sort.hh
+++ b/klm/lm/trie_sort.hh
@@ -25,12 +25,10 @@ namespace lm {
 class PositiveProbWarn;
 namespace ngram {
 class SortedVocabulary;
-class Config;
+struct Config;
 
 namespace trie {
 
-void WriteOrThrow(FILE *to, const void *data, size_t size);
-
 class EntryCompare : public std::binary_function<const void*, const void*, bool> {
   public:
     explicit EntryCompare(unsigned char order) : order_(order) {}
@@ -107,7 +105,7 @@ class SortedFiles {
     
     util::scoped_fd unigram_;
 
-    util::scoped_FILE full_[kMaxOrder - 1], context_[kMaxOrder - 1];
+    util::scoped_FILE full_[KENLM_MAX_ORDER - 1], context_[KENLM_MAX_ORDER - 1];
 };
 
 } // namespace trie
diff --git a/klm/lm/value.hh b/klm/lm/value.hh
index 85e53f14..ba716713 100644
--- a/klm/lm/value.hh
+++ b/klm/lm/value.hh
@@ -6,7 +6,7 @@
 #include "lm/weights.hh"
 #include "util/bit_packing.hh"
 
-#include <inttypes.h>
+#include <stdint.h>
 
 namespace lm {
 namespace ngram {
diff --git a/klm/lm/value_build.hh b/klm/lm/value_build.hh
index 687a41a0..461e6a5c 100644
--- a/klm/lm/value_build.hh
+++ b/klm/lm/value_build.hh
@@ -10,9 +10,9 @@
 namespace lm {
 namespace ngram {
 
-class Config;
-class BackoffValue;
-class RestValue;
+struct Config;
+struct BackoffValue;
+struct RestValue;
 
 class NoRestBuild {
   public:
diff --git a/klm/lm/vocab.cc b/klm/lm/vocab.cc
index 5de68f16..11c27518 100644
--- a/klm/lm/vocab.cc
+++ b/klm/lm/vocab.cc
@@ -80,14 +80,14 @@ void WriteWordsWrapper::Add(WordIndex index, const StringPiece &str) {
   buffer_.push_back(0);
 }
 
-void WriteWordsWrapper::Write(int fd) {
-  util::SeekEnd(fd);
+void WriteWordsWrapper::Write(int fd, uint64_t start) {
+  util::SeekOrThrow(fd, start);
   util::WriteOrThrow(fd, buffer_.data(), buffer_.size());
 }
 
 SortedVocabulary::SortedVocabulary() : begin_(NULL), end_(NULL), enumerate_(NULL) {}
 
-std::size_t SortedVocabulary::Size(std::size_t entries, const Config &/*config*/) {
+uint64_t SortedVocabulary::Size(uint64_t entries, const Config &/*config*/) {
   // Lead with the number of entries.  
   return sizeof(uint64_t) + sizeof(uint64_t) * entries;
 }
@@ -165,7 +165,7 @@ struct ProbingVocabularyHeader {
 
 ProbingVocabulary::ProbingVocabulary() : enumerate_(NULL) {}
 
-std::size_t ProbingVocabulary::Size(std::size_t entries, const Config &config) {
+uint64_t ProbingVocabulary::Size(uint64_t entries, const Config &config) {
   return ALIGN8(sizeof(detail::ProbingVocabularyHeader)) + Lookup::Size(entries, config.probing_multiplier);
 }
 
diff --git a/klm/lm/vocab.hh b/klm/lm/vocab.hh
index c3efcb4a..de54eb06 100644
--- a/klm/lm/vocab.hh
+++ b/klm/lm/vocab.hh
@@ -13,11 +13,11 @@
 #include <vector>
 
 namespace lm {
-class ProbBackoff;
+struct ProbBackoff;
 class EnumerateVocab;
 
 namespace ngram {
-class Config;
+struct Config;
 
 namespace detail {
 uint64_t HashForVocab(const char *str, std::size_t len);
@@ -35,7 +35,7 @@ class WriteWordsWrapper : public EnumerateVocab {
     
     void Add(WordIndex index, const StringPiece &str);
 
-    void Write(int fd);
+    void Write(int fd, uint64_t start);
 
   private:
     EnumerateVocab *inner_;
@@ -62,7 +62,7 @@ class SortedVocabulary : public base::Vocabulary {
     }
 
     // Size for purposes of file writing
-    static size_t Size(std::size_t entries, const Config &config);
+    static uint64_t Size(uint64_t entries, const Config &config);
 
     // Vocab words are [0, Bound())  Only valid after FinishedLoading/LoadedBinary.  
     WordIndex Bound() const { return bound_; }
@@ -129,7 +129,7 @@ class ProbingVocabulary : public base::Vocabulary {
       return lookup_.Find(detail::HashForVocab(str), i) ? i->value : 0;
     }
 
-    static size_t Size(std::size_t entries, const Config &config);
+    static uint64_t Size(uint64_t entries, const Config &config);
 
     // Vocab words are [0, Bound()).  
     WordIndex Bound() const { return bound_; }
diff --git a/klm/lm/word_index.hh b/klm/lm/word_index.hh
index 67841c30..e09557a7 100644
--- a/klm/lm/word_index.hh
+++ b/klm/lm/word_index.hh
@@ -2,8 +2,11 @@
 #ifndef LM_WORD_INDEX__
 #define LM_WORD_INDEX__
 
+#include <limits.h>
+
 namespace lm {
 typedef unsigned int WordIndex;
+const WordIndex kMaxWordIndex = UINT_MAX;
 } // namespace lm
 
 typedef lm::WordIndex LMWordIndex;
diff --git a/klm/search/Jamfile b/klm/search/Jamfile
new file mode 100644
index 00000000..bc95c53a
--- /dev/null
+++ b/klm/search/Jamfile
@@ -0,0 +1,5 @@
+lib search : weights.cc vertex.cc vertex_generator.cc edge_generator.cc rule.cc ../lm//kenlm ../util//kenutil /top//boost_system : : : <include>.. ;
+
+import testing ;
+
+unit-test weights_test : weights_test.cc search /top//boost_unit_test_framework ;
diff --git a/klm/search/Makefile.am b/klm/search/Makefile.am
new file mode 100644
index 00000000..ccc5b7f6
--- /dev/null
+++ b/klm/search/Makefile.am
@@ -0,0 +1,11 @@
+noinst_LIBRARIES = libksearch.a
+
+libksearch_a_SOURCES = \
+  edge_generator.cc \
+  rule.cc \
+  vertex.cc \
+  vertex_generator.cc \
+  weights.cc
+
+AM_CPPFLAGS = -W -Wall -Wno-sign-compare $(GTEST_CPPFLAGS) -I..
+
diff --git a/klm/search/config.hh b/klm/search/config.hh
new file mode 100644
index 00000000..ef8e2354
--- /dev/null
+++ b/klm/search/config.hh
@@ -0,0 +1,25 @@
+#ifndef SEARCH_CONFIG__
+#define SEARCH_CONFIG__
+
+#include "search/weights.hh"
+#include "util/string_piece.hh"
+
+namespace search {
+
+class Config {
+  public:
+    Config(const Weights &weights, unsigned int pop_limit) :
+      weights_(weights), pop_limit_(pop_limit) {}
+
+    const Weights &GetWeights() const { return weights_; }
+
+    unsigned int PopLimit() const { return pop_limit_; }
+
+  private:
+    Weights weights_;
+    unsigned int pop_limit_;
+};
+
+} // namespace search
+
+#endif // SEARCH_CONFIG__
diff --git a/klm/search/context.hh b/klm/search/context.hh
new file mode 100644
index 00000000..62163144
--- /dev/null
+++ b/klm/search/context.hh
@@ -0,0 +1,65 @@
+#ifndef SEARCH_CONTEXT__
+#define SEARCH_CONTEXT__
+
+#include "lm/model.hh"
+#include "search/config.hh"
+#include "search/final.hh"
+#include "search/types.hh"
+#include "search/vertex.hh"
+#include "util/exception.hh"
+#include "util/pool.hh"
+
+#include <boost/pool/object_pool.hpp>
+#include <boost/ptr_container/ptr_vector.hpp>
+
+#include <vector>
+
+namespace search {
+
+class Weights;
+
+class ContextBase {
+  public:
+    explicit ContextBase(const Config &config) : pop_limit_(config.PopLimit()), weights_(config.GetWeights()) {}
+
+    util::Pool &FinalPool() {
+      return final_pool_;
+    }
+
+    VertexNode *NewVertexNode() {
+      VertexNode *ret = vertex_node_pool_.construct();
+      assert(ret);
+      return ret;
+    }
+
+    void DeleteVertexNode(VertexNode *node) {
+      vertex_node_pool_.destroy(node);
+    }
+
+    unsigned int PopLimit() const { return pop_limit_; }
+
+    const Weights &GetWeights() const { return weights_; }
+
+  private:
+    util::Pool final_pool_;
+
+    boost::object_pool<VertexNode> vertex_node_pool_;
+
+    unsigned int pop_limit_;
+
+    const Weights &weights_;
+};
+
+template <class Model> class Context : public ContextBase {
+  public:
+    Context(const Config &config, const Model &model) : ContextBase(config), model_(model) {}
+
+    const Model &LanguageModel() const { return model_; }
+
+  private:
+    const Model &model_;
+};
+
+} // namespace search
+
+#endif // SEARCH_CONTEXT__
diff --git a/klm/search/edge.hh b/klm/search/edge.hh
new file mode 100644
index 00000000..187904bf
--- /dev/null
+++ b/klm/search/edge.hh
@@ -0,0 +1,54 @@
+#ifndef SEARCH_EDGE__
+#define SEARCH_EDGE__
+
+#include "lm/state.hh"
+#include "search/header.hh"
+#include "search/types.hh"
+#include "search/vertex.hh"
+#include "util/pool.hh"
+
+#include <functional>
+
+#include <stdint.h>
+
+namespace search {
+
+// Copyable, but the copy will be shallow.
+class PartialEdge : public Header {
+  public:
+    // Allow default construction for STL.  
+    PartialEdge() {}
+
+    PartialEdge(util::Pool &pool, Arity arity) 
+      : Header(pool.Allocate(Size(arity, arity + 1)), arity) {}
+    
+    PartialEdge(util::Pool &pool, Arity arity, Arity chart_states) 
+      : Header(pool.Allocate(Size(arity, chart_states)), arity) {}
+
+    // Non-terminals
+    const PartialVertex *NT() const {
+      return reinterpret_cast<const PartialVertex*>(After());
+    }
+    PartialVertex *NT() {
+      return reinterpret_cast<PartialVertex*>(After());
+    }
+
+    const lm::ngram::ChartState &CompletedState() const {
+      return *Between();
+    }
+    const lm::ngram::ChartState *Between() const {
+      return reinterpret_cast<const lm::ngram::ChartState*>(After() + GetArity() * sizeof(PartialVertex));
+    }
+    lm::ngram::ChartState *Between() {
+      return reinterpret_cast<lm::ngram::ChartState*>(After() + GetArity() * sizeof(PartialVertex));
+    }
+
+  private:
+    static std::size_t Size(Arity arity, Arity chart_states) {
+      return kHeaderSize + arity * sizeof(PartialVertex) + chart_states * sizeof(lm::ngram::ChartState);
+    }
+};
+
+
+} // namespace search
+#endif // SEARCH_EDGE__
diff --git a/klm/search/edge_generator.cc b/klm/search/edge_generator.cc
new file mode 100644
index 00000000..260159b1
--- /dev/null
+++ b/klm/search/edge_generator.cc
@@ -0,0 +1,110 @@
+#include "search/edge_generator.hh"
+
+#include "lm/left.hh"
+#include "lm/partial.hh"
+#include "search/context.hh"
+#include "search/vertex.hh"
+
+#include <numeric>
+
+namespace search {
+
+namespace {
+
+template <class Model> void FastScore(const Context<Model> &context, Arity victim, Arity before_idx, Arity incomplete, const PartialVertex &previous_vertex, PartialEdge update) {
+  lm::ngram::ChartState *between = update.Between();
+  lm::ngram::ChartState *before = &between[before_idx], *after = &between[before_idx + 1];
+
+  float adjustment = 0.0;
+  const lm::ngram::ChartState &previous_reveal = previous_vertex.State();
+  const PartialVertex &update_nt = update.NT()[victim];
+  const lm::ngram::ChartState &update_reveal = update_nt.State();
+  if ((update_reveal.left.length > previous_reveal.left.length) || (update_reveal.left.full && !previous_reveal.left.full)) {
+    adjustment += lm::ngram::RevealAfter(context.LanguageModel(), before->left, before->right, update_reveal.left, previous_reveal.left.length);
+  }
+  if ((update_reveal.right.length > previous_reveal.right.length) || (update_nt.RightFull() && !previous_vertex.RightFull())) {
+    adjustment += lm::ngram::RevealBefore(context.LanguageModel(), update_reveal.right, previous_reveal.right.length, update_nt.RightFull(), after->left, after->right);
+  }
+  if (update_nt.Complete()) {
+    if (update_reveal.left.full) {
+      before->left.full = true;
+    } else {
+      assert(update_reveal.left.length == update_reveal.right.length);
+      adjustment += lm::ngram::Subsume(context.LanguageModel(), before->left, before->right, after->left, after->right, update_reveal.left.length);
+    }
+    before->right = after->right;
+    // Shift the others shifted one down, covering after.  
+    for (lm::ngram::ChartState *cover = after; cover < between + incomplete; ++cover) {
+      *cover = *(cover + 1);
+    }
+  }
+  update.SetScore(update.GetScore() + adjustment * context.GetWeights().LM());
+}
+
+} // namespace
+
+template <class Model> PartialEdge EdgeGenerator::Pop(Context<Model> &context) {
+  assert(!generate_.empty());
+  PartialEdge top = generate_.top();
+  generate_.pop();
+  PartialVertex *const top_nt = top.NT();
+  const Arity arity = top.GetArity();
+
+  Arity victim = 0;
+  Arity victim_completed;
+  Arity incomplete;
+  // Select victim or return if complete.   
+  {
+    Arity completed = 0;
+    unsigned char lowest_length = 255;
+    for (Arity i = 0; i != arity; ++i) {
+      if (top_nt[i].Complete()) {
+        ++completed;
+      } else if (top_nt[i].Length() < lowest_length) {
+        lowest_length = top_nt[i].Length();
+        victim = i;
+        victim_completed = completed;
+      }
+    }
+    if (lowest_length == 255) {
+      return top;
+    }
+    incomplete = arity - completed;
+  }
+
+  PartialVertex old_value(top_nt[victim]);
+  PartialVertex alternate_changed;
+  if (top_nt[victim].Split(alternate_changed)) {
+    PartialEdge alternate(partial_edge_pool_, arity, incomplete + 1);
+    alternate.SetScore(top.GetScore() + alternate_changed.Bound() - old_value.Bound());
+
+    alternate.SetNote(top.GetNote());
+
+    PartialVertex *alternate_nt = alternate.NT();
+    for (Arity i = 0; i < victim; ++i) alternate_nt[i] = top_nt[i];
+    alternate_nt[victim] = alternate_changed;
+    for (Arity i = victim + 1; i < arity; ++i) alternate_nt[i] = top_nt[i];
+
+    memcpy(alternate.Between(), top.Between(), sizeof(lm::ngram::ChartState) * (incomplete + 1));
+
+    // TODO: dedupe?  
+    generate_.push(alternate);
+  }
+
+  // top is now the continuation.
+  FastScore(context, victim, victim - victim_completed, incomplete, old_value, top);
+  // TODO: dedupe?  
+  generate_.push(top);
+
+  // Invalid indicates no new hypothesis generated.  
+  return PartialEdge();
+}
+
+template PartialEdge EdgeGenerator::Pop(Context<lm::ngram::RestProbingModel> &context);
+template PartialEdge EdgeGenerator::Pop(Context<lm::ngram::ProbingModel> &context);
+template PartialEdge EdgeGenerator::Pop(Context<lm::ngram::TrieModel> &context);
+template PartialEdge EdgeGenerator::Pop(Context<lm::ngram::QuantTrieModel> &context);
+template PartialEdge EdgeGenerator::Pop(Context<lm::ngram::ArrayTrieModel> &context);
+template PartialEdge EdgeGenerator::Pop(Context<lm::ngram::QuantArrayTrieModel> &context);
+
+} // namespace search
diff --git a/klm/search/edge_generator.hh b/klm/search/edge_generator.hh
new file mode 100644
index 00000000..582c78b7
--- /dev/null
+++ b/klm/search/edge_generator.hh
@@ -0,0 +1,57 @@
+#ifndef SEARCH_EDGE_GENERATOR__
+#define SEARCH_EDGE_GENERATOR__
+
+#include "search/edge.hh"
+#include "search/note.hh"
+#include "search/types.hh"
+
+#include <queue>
+
+namespace lm {
+namespace ngram {
+class ChartState;
+} // namespace ngram
+} // namespace lm
+
+namespace search {
+
+template <class Model> class Context;
+
+class EdgeGenerator {
+  public:
+    EdgeGenerator() {}
+
+    PartialEdge AllocateEdge(Arity arity) {
+      return PartialEdge(partial_edge_pool_, arity);
+    }
+
+    void AddEdge(PartialEdge edge) {
+      generate_.push(edge);
+    }
+
+    bool Empty() const { return generate_.empty(); }
+
+    // Pop.  If there's a complete hypothesis, return it.  Otherwise return an invalid PartialEdge.
+    template <class Model> PartialEdge Pop(Context<Model> &context);
+
+    template <class Model, class Output> void Search(Context<Model> &context, Output &output) {
+      unsigned to_pop = context.PopLimit();
+      while (to_pop > 0 && !generate_.empty()) {
+        PartialEdge got(Pop(context));
+        if (got.Valid()) {
+          output.NewHypothesis(got);
+          --to_pop;
+        }
+      }
+      output.FinishedSearch();
+    }
+
+  private:
+    util::Pool partial_edge_pool_;
+
+    typedef std::priority_queue<PartialEdge> Generate;
+    Generate generate_;
+};
+
+} // namespace search
+#endif // SEARCH_EDGE_GENERATOR__
diff --git a/klm/search/final.hh b/klm/search/final.hh
new file mode 100644
index 00000000..50e62cf2
--- /dev/null
+++ b/klm/search/final.hh
@@ -0,0 +1,36 @@
+#ifndef SEARCH_FINAL__
+#define SEARCH_FINAL__
+
+#include "search/header.hh"
+#include "util/pool.hh"
+
+namespace search {
+
+// A full hypothesis with pointers to children.
+class Final : public Header {
+  public:
+    Final() {}
+
+    Final(util::Pool &pool, Score score, Arity arity, Note note) 
+      : Header(pool.Allocate(Size(arity)), arity) {
+      SetScore(score);
+      SetNote(note);
+    }
+
+    // These are arrays of length GetArity().
+    Final *Children() {
+      return reinterpret_cast<Final*>(After());
+    }
+    const Final *Children() const {
+      return reinterpret_cast<const Final*>(After());
+    }
+
+  private:
+    static std::size_t Size(Arity arity) {
+      return kHeaderSize + arity * sizeof(const Final);
+    }
+};
+
+} // namespace search
+
+#endif // SEARCH_FINAL__
diff --git a/klm/search/header.hh b/klm/search/header.hh
new file mode 100644
index 00000000..25550dbe
--- /dev/null
+++ b/klm/search/header.hh
@@ -0,0 +1,57 @@
+#ifndef SEARCH_HEADER__
+#define SEARCH_HEADER__
+
+// Header consisting of Score, Arity, and Note
+
+#include "search/note.hh"
+#include "search/types.hh"
+
+#include <stdint.h>
+
+namespace search {
+
+// Copying is shallow.  
+class Header {
+  public:
+    bool Valid() const { return base_; }
+
+    Score GetScore() const {
+      return *reinterpret_cast<const float*>(base_);
+    }
+    void SetScore(Score to) {
+      *reinterpret_cast<float*>(base_) = to;
+    }
+    bool operator<(const Header &other) const {
+      return GetScore() < other.GetScore();
+    }
+
+    Arity GetArity() const {
+      return *reinterpret_cast<const Arity*>(base_ + sizeof(Score));
+    }
+
+    Note GetNote() const {
+      return *reinterpret_cast<const Note*>(base_ + sizeof(Score) + sizeof(Arity));
+    }
+    void SetNote(Note to) {
+      *reinterpret_cast<Note*>(base_ + sizeof(Score) + sizeof(Arity)) = to;
+    }
+
+  protected:
+    Header() : base_(NULL) {}
+
+    Header(void *base, Arity arity) : base_(static_cast<uint8_t*>(base)) {
+      *reinterpret_cast<Arity*>(base_ + sizeof(Score)) = arity;
+    }
+
+    static const std::size_t kHeaderSize = sizeof(Score) + sizeof(Arity) + sizeof(Note);
+
+    uint8_t *After() { return base_ + kHeaderSize; }
+    const uint8_t *After() const { return base_ + kHeaderSize; }
+
+  private:
+    uint8_t *base_;
+};
+
+} // namespace search
+
+#endif // SEARCH_HEADER__
diff --git a/klm/search/note.hh b/klm/search/note.hh
new file mode 100644
index 00000000..50bed06e
--- /dev/null
+++ b/klm/search/note.hh
@@ -0,0 +1,12 @@
+#ifndef SEARCH_NOTE__
+#define SEARCH_NOTE__
+
+namespace search {
+
+union Note {
+  const void *vp;
+};
+
+} // namespace search
+
+#endif // SEARCH_NOTE__
diff --git a/klm/search/rule.cc b/klm/search/rule.cc
new file mode 100644
index 00000000..5b00207e
--- /dev/null
+++ b/klm/search/rule.cc
@@ -0,0 +1,43 @@
+#include "search/rule.hh"
+
+#include "search/context.hh"
+#include "search/final.hh"
+
+#include <ostream>
+
+#include <math.h>
+
+namespace search {
+
+template <class Model> float ScoreRule(const Context<Model> &context, const std::vector<lm::WordIndex> &words, bool prepend_bos, lm::ngram::ChartState *writing) {
+  unsigned int oov_count = 0;
+  float prob = 0.0;
+  const Model &model = context.LanguageModel();
+  const lm::WordIndex oov = model.GetVocabulary().NotFound();
+  for (std::vector<lm::WordIndex>::const_iterator word = words.begin(); ; ++word) {
+    lm::ngram::RuleScore<Model> scorer(model, *(writing++));
+    // TODO: optimize
+    if (prepend_bos && (word == words.begin())) {
+      scorer.BeginSentence();
+    }
+    for (; ; ++word) {
+      if (word == words.end()) {
+        prob += scorer.Finish();
+        return static_cast<float>(oov_count) * context.GetWeights().OOV() + prob * context.GetWeights().LM();
+      }
+      if (*word == kNonTerminal) break;
+      if (*word == oov) ++oov_count;
+      scorer.Terminal(*word);
+    }
+    prob += scorer.Finish();
+  }
+}
+
+template float ScoreRule(const Context<lm::ngram::RestProbingModel> &model, const std::vector<lm::WordIndex> &words, bool prepend_bos, lm::ngram::ChartState *writing);
+template float ScoreRule(const Context<lm::ngram::ProbingModel> &model, const std::vector<lm::WordIndex> &words, bool prepend_bos, lm::ngram::ChartState *writing);
+template float ScoreRule(const Context<lm::ngram::TrieModel> &model, const std::vector<lm::WordIndex> &words, bool prepend_bos, lm::ngram::ChartState *writing);
+template float ScoreRule(const Context<lm::ngram::QuantTrieModel> &model, const std::vector<lm::WordIndex> &words, bool prepend_bos, lm::ngram::ChartState *writing);
+template float ScoreRule(const Context<lm::ngram::ArrayTrieModel> &model, const std::vector<lm::WordIndex> &words, bool prepend_bos, lm::ngram::ChartState *writing);
+template float ScoreRule(const Context<lm::ngram::QuantArrayTrieModel> &model, const std::vector<lm::WordIndex> &words, bool prepend_bos, lm::ngram::ChartState *writing);
+
+} // namespace search
diff --git a/klm/search/rule.hh b/klm/search/rule.hh
new file mode 100644
index 00000000..0ce2794d
--- /dev/null
+++ b/klm/search/rule.hh
@@ -0,0 +1,20 @@
+#ifndef SEARCH_RULE__
+#define SEARCH_RULE__
+
+#include "lm/left.hh"
+#include "lm/word_index.hh"
+#include "search/types.hh"
+
+#include <vector>
+
+namespace search {
+
+template <class Model> class Context;
+
+const lm::WordIndex kNonTerminal = lm::kMaxWordIndex;
+
+template <class Model> float ScoreRule(const Context<Model> &context, const std::vector<lm::WordIndex> &words, bool prepend_bos, lm::ngram::ChartState *state_out);
+
+} // namespace search
+
+#endif // SEARCH_RULE__
diff --git a/klm/search/types.hh b/klm/search/types.hh
new file mode 100644
index 00000000..06eb5bfa
--- /dev/null
+++ b/klm/search/types.hh
@@ -0,0 +1,14 @@
+#ifndef SEARCH_TYPES__
+#define SEARCH_TYPES__
+
+#include <stdint.h>
+
+namespace search {
+
+typedef float Score;
+
+typedef uint32_t Arity;
+
+} // namespace search
+
+#endif // SEARCH_TYPES__
diff --git a/klm/search/vertex.cc b/klm/search/vertex.cc
new file mode 100644
index 00000000..11f4631f
--- /dev/null
+++ b/klm/search/vertex.cc
@@ -0,0 +1,42 @@
+#include "search/vertex.hh"
+
+#include "search/context.hh"
+
+#include <algorithm>
+#include <functional>
+
+#include <assert.h>
+
+namespace search {
+
+namespace {
+
+struct GreaterByBound : public std::binary_function<const VertexNode *, const VertexNode *, bool> {
+  bool operator()(const VertexNode *first, const VertexNode *second) const {
+    return first->Bound() > second->Bound();
+  }
+};
+
+} // namespace
+
+void VertexNode::SortAndSet(ContextBase &context, VertexNode **parent_ptr) {
+  if (Complete()) {
+    assert(end_.Valid());
+    assert(extend_.empty());
+    bound_ = end_.GetScore();
+    return;
+  }
+  if (extend_.size() == 1 && parent_ptr) {
+    *parent_ptr = extend_[0];
+    extend_[0]->SortAndSet(context, parent_ptr);
+    context.DeleteVertexNode(this);
+    return;
+  }
+  for (std::vector<VertexNode*>::iterator i = extend_.begin(); i != extend_.end(); ++i) {
+    (*i)->SortAndSet(context, &*i);
+  }
+  std::sort(extend_.begin(), extend_.end(), GreaterByBound());
+  bound_ = extend_.front()->Bound();
+}
+
+} // namespace search
diff --git a/klm/search/vertex.hh b/klm/search/vertex.hh
new file mode 100644
index 00000000..52bc1dfe
--- /dev/null
+++ b/klm/search/vertex.hh
@@ -0,0 +1,159 @@
+#ifndef SEARCH_VERTEX__
+#define SEARCH_VERTEX__
+
+#include "lm/left.hh"
+#include "search/final.hh"
+#include "search/types.hh"
+
+#include <boost/unordered_set.hpp>
+
+#include <queue>
+#include <vector>
+
+#include <stdint.h>
+
+namespace search {
+
+class ContextBase;
+
+class VertexNode {
+  public:
+    VertexNode() {}
+
+    void InitRoot() {
+      extend_.clear();
+      state_.left.full = false;
+      state_.left.length = 0;
+      state_.right.length = 0;
+      right_full_ = false;
+      end_ = Final();
+    }
+
+    lm::ngram::ChartState &MutableState() { return state_; }
+    bool &MutableRightFull() { return right_full_; }
+
+    void AddExtend(VertexNode *next) {
+      extend_.push_back(next);
+    }
+
+    void SetEnd(Final end) {
+      assert(!end_.Valid());
+      end_ = end;
+    }
+    
+    void SortAndSet(ContextBase &context, VertexNode **parent_pointer);
+
+    // Should only happen to a root node when the entire vertex is empty.   
+    bool Empty() const {
+      return !end_.Valid() && extend_.empty();
+    }
+
+    bool Complete() const {
+      return end_.Valid();
+    }
+
+    const lm::ngram::ChartState &State() const { return state_; }
+    bool RightFull() const { return right_full_; }
+
+    Score Bound() const {
+      return bound_;
+    }
+
+    unsigned char Length() const {
+      return state_.left.length + state_.right.length;
+    }
+
+    // Will be invalid unless this is a leaf.   
+    const Final End() const { return end_; }
+
+    const VertexNode &operator[](size_t index) const {
+      return *extend_[index];
+    }
+
+    size_t Size() const {
+      return extend_.size();
+    }
+
+  private:
+    std::vector<VertexNode*> extend_;
+
+    lm::ngram::ChartState state_;
+    bool right_full_;
+
+    Score bound_;
+    Final end_;
+};
+
+class PartialVertex {
+  public:
+    PartialVertex() {}
+
+    explicit PartialVertex(const VertexNode &back) : back_(&back), index_(0) {}
+
+    bool Empty() const { return back_->Empty(); }
+
+    bool Complete() const { return back_->Complete(); }
+
+    const lm::ngram::ChartState &State() const { return back_->State(); }
+    bool RightFull() const { return back_->RightFull(); }
+
+    Score Bound() const { return Complete() ? back_->End().GetScore() : (*back_)[index_].Bound(); }
+
+    unsigned char Length() const { return back_->Length(); }
+
+    bool HasAlternative() const {
+      return index_ + 1 < back_->Size();
+    }
+
+    // Split into continuation and alternative, rendering this the continuation.
+    bool Split(PartialVertex &alternative) {
+      assert(!Complete());
+      bool ret;
+      if (index_ + 1 < back_->Size()) {
+        alternative.index_ = index_ + 1;
+        alternative.back_ = back_;
+        ret = true;
+      } else {
+        ret = false;
+      }
+      back_ = &((*back_)[index_]);
+      index_ = 0;
+      return ret;
+    }
+
+    const Final End() const {
+      return back_->End();
+    }
+
+  private:
+    const VertexNode *back_;
+    unsigned int index_;
+};
+
+class Vertex {
+  public:
+    Vertex() {}
+
+    PartialVertex RootPartial() const { return PartialVertex(root_); }
+
+    const Final BestChild() const {
+      PartialVertex top(RootPartial());
+      if (top.Empty()) {
+        return Final();
+      } else {
+        PartialVertex continuation;
+        while (!top.Complete()) {
+          top.Split(continuation);
+        }
+        return top.End();
+      }
+    }
+
+  private:
+    friend class VertexGenerator;
+
+    VertexNode root_;
+};
+
+} // namespace search
+#endif // SEARCH_VERTEX__
diff --git a/klm/search/vertex_generator.cc b/klm/search/vertex_generator.cc
new file mode 100644
index 00000000..0945fe55
--- /dev/null
+++ b/klm/search/vertex_generator.cc
@@ -0,0 +1,94 @@
+#include "search/vertex_generator.hh"
+
+#include "lm/left.hh"
+#include "search/context.hh"
+#include "search/edge.hh"
+
+#include <stdint.h>
+
+namespace search {
+
+VertexGenerator::VertexGenerator(ContextBase &context, Vertex &gen) : context_(context), gen_(gen) {
+  gen.root_.InitRoot();
+}
+
+namespace {
+
+const uint64_t kCompleteAdd = static_cast<uint64_t>(-1);
+
+// Parallel structure to VertexNode.  
+struct Trie {
+  Trie() : under(NULL) {}
+
+  VertexNode *under;
+  boost::unordered_map<uint64_t, Trie> extend;
+};
+
+Trie &FindOrInsert(ContextBase &context, Trie &node, uint64_t added, const lm::ngram::ChartState &state, unsigned char left, bool left_full, unsigned char right, bool right_full) {
+  Trie &next = node.extend[added];
+  if (!next.under) {
+    next.under = context.NewVertexNode();
+    lm::ngram::ChartState &writing = next.under->MutableState();
+    writing = state;
+    writing.left.full &= left_full && state.left.full;
+    next.under->MutableRightFull() = right_full && state.left.full;
+    writing.left.length = left;
+    writing.right.length = right;
+    node.under->AddExtend(next.under);
+  }
+  return next;
+}
+
+void CompleteTransition(ContextBase &context, Trie &starter, PartialEdge partial) {
+  Final final(context.FinalPool(), partial.GetScore(), partial.GetArity(), partial.GetNote());
+  Final *child_out = final.Children();
+  const PartialVertex *part = partial.NT();
+  const PartialVertex *const part_end_loop = part + partial.GetArity();
+  for (; part != part_end_loop; ++part, ++child_out)
+    *child_out = part->End();
+
+  starter.under->SetEnd(final);
+}
+
+void AddHypothesis(ContextBase &context, Trie &root, PartialEdge partial) {
+  const lm::ngram::ChartState &state = partial.CompletedState();
+  
+  unsigned char left = 0, right = 0;
+  Trie *node = &root;
+  while (true) {
+    if (left == state.left.length) {
+      node = &FindOrInsert(context, *node, kCompleteAdd - state.left.full, state, left, true, right, false);
+      for (; right < state.right.length; ++right) {
+        node = &FindOrInsert(context, *node, state.right.words[right], state, left, true, right + 1, false);
+      }
+      break;
+    }
+    node = &FindOrInsert(context, *node, state.left.pointers[left], state, left + 1, false, right, false);
+    left++;
+    if (right == state.right.length) {
+      node = &FindOrInsert(context, *node, kCompleteAdd - state.left.full, state, left, false, right, true);
+      for (; left < state.left.length; ++left) {
+        node = &FindOrInsert(context, *node, state.left.pointers[left], state, left + 1, false, right, true);
+      }
+      break;
+    }
+    node = &FindOrInsert(context, *node, state.right.words[right], state, left, false, right + 1, false);
+    right++;
+  }
+
+  node = &FindOrInsert(context, *node, kCompleteAdd - state.left.full, state, state.left.length, true, state.right.length, true);
+  CompleteTransition(context, *node, partial);
+}
+
+} // namespace
+
+void VertexGenerator::FinishedSearch() {
+  Trie root;
+  root.under = &gen_.root_;
+  for (Existing::const_iterator i(existing_.begin()); i != existing_.end(); ++i) {
+    AddHypothesis(context_, root, i->second);
+  }
+  root.under->SortAndSet(context_, NULL);
+}
+
+} // namespace search
diff --git a/klm/search/vertex_generator.hh b/klm/search/vertex_generator.hh
new file mode 100644
index 00000000..60e86112
--- /dev/null
+++ b/klm/search/vertex_generator.hh
@@ -0,0 +1,46 @@
+#ifndef SEARCH_VERTEX_GENERATOR__
+#define SEARCH_VERTEX_GENERATOR__
+
+#include "search/edge.hh"
+#include "search/vertex.hh"
+
+#include <boost/unordered_map.hpp>
+
+namespace lm {
+namespace ngram {
+class ChartState;
+} // namespace ngram
+} // namespace lm
+
+namespace search {
+
+class ContextBase;
+class Final;
+
+class VertexGenerator {
+  public:
+    VertexGenerator(ContextBase &context, Vertex &gen);
+
+    void NewHypothesis(PartialEdge partial) {
+      const lm::ngram::ChartState &state = partial.CompletedState();
+      std::pair<Existing::iterator, bool> ret(existing_.insert(std::make_pair(hash_value(state), partial)));
+      if (!ret.second && ret.first->second < partial) {
+        ret.first->second = partial;
+      }
+    }
+
+    void FinishedSearch();
+
+    const Vertex &Generating() const { return gen_; }
+
+  private:
+    ContextBase &context_;
+
+    Vertex &gen_;
+
+    typedef boost::unordered_map<uint64_t, PartialEdge> Existing;
+    Existing existing_;
+};
+
+} // namespace search
+#endif // SEARCH_VERTEX_GENERATOR__
diff --git a/klm/search/weights.cc b/klm/search/weights.cc
new file mode 100644
index 00000000..d65471ad
--- /dev/null
+++ b/klm/search/weights.cc
@@ -0,0 +1,71 @@
+#include "search/weights.hh"
+#include "util/tokenize_piece.hh"
+
+#include <cstdlib>
+
+namespace search {
+
+namespace {
+struct Insert {
+  void operator()(boost::unordered_map<std::string, search::Score> &map, StringPiece name, search::Score score) const {
+    std::string copy(name.data(), name.size());
+    map[copy] = score;
+  }
+};
+
+struct DotProduct {
+  search::Score total;
+  DotProduct() : total(0.0) {}
+
+  void operator()(const boost::unordered_map<std::string, search::Score> &map, StringPiece name, search::Score score) {
+    boost::unordered_map<std::string, search::Score>::const_iterator i(FindStringPiece(map, name));
+    if (i != map.end()) 
+      total += score * i->second;
+  }
+};
+
+template <class Map, class Op> void Parse(StringPiece text, Map &map, Op &op) {
+  for (util::TokenIter<util::SingleCharacter, true> spaces(text, ' '); spaces; ++spaces) {
+    util::TokenIter<util::SingleCharacter> equals(*spaces, '=');
+    UTIL_THROW_IF(!equals, WeightParseException, "Bad weight token " << *spaces);
+    StringPiece name(*equals);
+    UTIL_THROW_IF(!++equals, WeightParseException, "Bad weight token " << *spaces);
+    char *end;
+    // Assumes proper termination.  
+    double value = std::strtod(equals->data(), &end);
+    UTIL_THROW_IF(end != equals->data() + equals->size(), WeightParseException, "Failed to parse weight" << *equals);
+    UTIL_THROW_IF(++equals, WeightParseException, "Too many equals in " << *spaces);
+    op(map, name, value);
+  }
+}
+
+} // namespace
+
+Weights::Weights(StringPiece text) {
+  Insert op;
+  Parse<Map, Insert>(text, map_, op);
+  lm_ = Steal("LanguageModel");
+  oov_ = Steal("OOV");
+  word_penalty_ = Steal("WordPenalty");
+}
+
+Weights::Weights(Score lm, Score oov, Score word_penalty) : lm_(lm), oov_(oov), word_penalty_(word_penalty) {}
+
+search::Score Weights::DotNoLM(StringPiece text) const {
+  DotProduct dot;
+  Parse<const Map, DotProduct>(text, map_, dot);
+  return dot.total;
+}
+
+float Weights::Steal(const std::string &str) {
+  Map::iterator i(map_.find(str));
+  if (i == map_.end()) {
+    return 0.0;
+  } else {
+    float ret = i->second;
+    map_.erase(i);
+    return ret;
+  }
+}
+
+} // namespace search
diff --git a/klm/search/weights.hh b/klm/search/weights.hh
new file mode 100644
index 00000000..df1c419f
--- /dev/null
+++ b/klm/search/weights.hh
@@ -0,0 +1,52 @@
+// For now, the individual features are not kept.  
+#ifndef SEARCH_WEIGHTS__
+#define SEARCH_WEIGHTS__
+
+#include "search/types.hh"
+#include "util/exception.hh"
+#include "util/string_piece.hh"
+
+#include <boost/unordered_map.hpp>
+
+#include <string>
+
+namespace search {
+
+class WeightParseException : public util::Exception {
+  public:
+    WeightParseException() {}
+    ~WeightParseException() throw() {}
+};
+
+class Weights {
+  public:
+    // Parses weights, sets lm_weight_, removes it from map_.
+    explicit Weights(StringPiece text);
+
+    // Just the three scores we care about adding.   
+    Weights(Score lm, Score oov, Score word_penalty);
+
+    Score DotNoLM(StringPiece text) const;
+
+    Score LM() const { return lm_; }
+
+    Score OOV() const { return oov_; }
+
+    Score WordPenalty() const { return word_penalty_; }
+
+    // Mostly for testing.  
+    const boost::unordered_map<std::string, Score> &GetMap() const { return map_; }
+
+  private:
+    float Steal(const std::string &str);
+
+    typedef boost::unordered_map<std::string, Score> Map;
+
+    Map map_;
+
+    Score lm_, oov_, word_penalty_;
+};
+
+} // namespace search
+
+#endif // SEARCH_WEIGHTS__
diff --git a/klm/search/weights_test.cc b/klm/search/weights_test.cc
new file mode 100644
index 00000000..4811ff06
--- /dev/null
+++ b/klm/search/weights_test.cc
@@ -0,0 +1,38 @@
+#include "search/weights.hh"
+
+#define BOOST_TEST_MODULE WeightTest
+#include <boost/test/unit_test.hpp>
+#include <boost/test/floating_point_comparison.hpp>
+
+namespace search {
+namespace {
+
+#define CHECK_WEIGHT(value, string) \
+  i = parsed.find(string); \
+  BOOST_REQUIRE(i != parsed.end()); \
+  BOOST_CHECK_CLOSE((value), i->second, 0.001);
+
+BOOST_AUTO_TEST_CASE(parse) {
+  // These are not real feature weights.  
+  Weights w("rarity=0 phrase-SGT=0 phrase-TGS=9.45117 lhsGrhs=0 lexical-SGT=2.33833 lexical-TGS=-28.3317 abstract?=0 LanguageModel=3 lexical?=1 glue?=5");
+  const boost::unordered_map<std::string, search::Score> &parsed = w.GetMap();
+  boost::unordered_map<std::string, search::Score>::const_iterator i;
+  CHECK_WEIGHT(0.0, "rarity");
+  CHECK_WEIGHT(0.0, "phrase-SGT");
+  CHECK_WEIGHT(9.45117, "phrase-TGS");
+  CHECK_WEIGHT(2.33833, "lexical-SGT");
+  BOOST_CHECK(parsed.end() == parsed.find("lm"));
+  BOOST_CHECK_CLOSE(3.0, w.LM(), 0.001);
+  CHECK_WEIGHT(-28.3317, "lexical-TGS");
+  CHECK_WEIGHT(5.0, "glue?");
+}
+
+BOOST_AUTO_TEST_CASE(dot) {
+  Weights w("rarity=0 phrase-SGT=0 phrase-TGS=9.45117 lhsGrhs=0 lexical-SGT=2.33833 lexical-TGS=-28.3317 abstract?=0 LanguageModel=3 lexical?=1 glue?=5");
+  BOOST_CHECK_CLOSE(9.45117 * 3.0, w.DotNoLM("phrase-TGS=3.0"), 0.001);
+  BOOST_CHECK_CLOSE(9.45117 * 3.0, w.DotNoLM("phrase-TGS=3.0 LanguageModel=10"), 0.001);
+  BOOST_CHECK_CLOSE(9.45117 * 3.0 + 28.3317 * 17.4, w.DotNoLM("rarity=5 phrase-TGS=3.0 LanguageModel=10 lexical-TGS=-17.4"), 0.001);
+}
+
+} // namespace
+} // namespace search
diff --git a/klm/util/Jamfile b/klm/util/Jamfile
deleted file mode 100644
index 3ee2c2c2..00000000
--- a/klm/util/Jamfile
+++ /dev/null
@@ -1,10 +0,0 @@
-lib kenutil : bit_packing.cc ersatz_progress.cc exception.cc file.cc file_piece.cc mmap.cc murmur_hash.cc usage.cc ../..//z : <include>.. : : <include>.. ;
-
-import testing ;
-
-unit-test bit_packing_test : bit_packing_test.cc kenutil ../..///boost_unit_test_framework ;
-run file_piece_test.cc kenutil ../..///boost_unit_test_framework : : file_piece.cc ;
-unit-test joint_sort_test : joint_sort_test.cc kenutil ../..///boost_unit_test_framework ;
-unit-test probing_hash_table_test : probing_hash_table_test.cc kenutil ../..///boost_unit_test_framework ;
-unit-test sorted_uniform_test : sorted_uniform_test.cc kenutil ../..///boost_unit_test_framework ;
-unit-test tokenize_piece_test : tokenize_piece_test.cc kenutil ../..///boost_unit_test_framework ;
diff --git a/klm/util/Makefile.am b/klm/util/Makefile.am
index 5ceccf2c..5306850f 100644
--- a/klm/util/Makefile.am
+++ b/klm/util/Makefile.am
@@ -26,6 +26,8 @@ libklm_util_a_SOURCES = \
   file_piece.cc \
   mmap.cc \
   murmur_hash.cc \
+  pool.cc \
+  string_piece.cc \
 	usage.cc
 
 AM_CPPFLAGS = -W -Wall -Wno-sign-compare $(GTEST_CPPFLAGS) -I..
diff --git a/klm/util/ersatz_progress.cc b/klm/util/ersatz_progress.cc
index 07b14e26..eb635ad8 100644
--- a/klm/util/ersatz_progress.cc
+++ b/klm/util/ersatz_progress.cc
@@ -9,16 +9,16 @@ namespace util {
 
 namespace { const unsigned char kWidth = 100; }
 
-ErsatzProgress::ErsatzProgress() : current_(0), next_(std::numeric_limits<std::size_t>::max()), complete_(next_), out_(NULL) {}
+ErsatzProgress::ErsatzProgress() : current_(0), next_(std::numeric_limits<uint64_t>::max()), complete_(next_), out_(NULL) {}
 
 ErsatzProgress::~ErsatzProgress() {
   if (out_) Finished();
 }
 
-ErsatzProgress::ErsatzProgress(std::size_t complete, std::ostream *to, const std::string &message) 
+ErsatzProgress::ErsatzProgress(uint64_t complete, std::ostream *to, const std::string &message) 
   : current_(0), next_(complete / kWidth), complete_(complete), stones_written_(0), out_(to) {
   if (!out_) {
-    next_ = std::numeric_limits<std::size_t>::max();
+    next_ = std::numeric_limits<uint64_t>::max();
     return;
   }
   if (!message.empty()) *out_ << message << '\n';
@@ -28,14 +28,14 @@ ErsatzProgress::ErsatzProgress(std::size_t complete, std::ostream *to, const std
 void ErsatzProgress::Milestone() {
   if (!out_) { current_ = 0; return; }
   if (!complete_) return;
-  unsigned char stone = std::min(static_cast<std::size_t>(kWidth), (current_ * kWidth) / complete_);
+  unsigned char stone = std::min(static_cast<uint64_t>(kWidth), (current_ * kWidth) / complete_);
 
   for (; stones_written_ < stone; ++stones_written_) {
     (*out_) << '*';
   }
   if (stone == kWidth) {
     (*out_) << std::endl;
-    next_ = std::numeric_limits<std::size_t>::max();
+    next_ = std::numeric_limits<uint64_t>::max();
     out_ = NULL;
   } else {
     next_ = std::max(next_, (stone * complete_) / kWidth);
diff --git a/klm/util/ersatz_progress.hh b/klm/util/ersatz_progress.hh
index f709dc51..9909736d 100644
--- a/klm/util/ersatz_progress.hh
+++ b/klm/util/ersatz_progress.hh
@@ -4,6 +4,8 @@
 #include <iostream>
 #include <string>
 
+#include <stdint.h>
+
 // Ersatz version of boost::progress so core language model doesn't depend on
 // boost.  Also adds option to print nothing.  
 
@@ -14,7 +16,7 @@ class ErsatzProgress {
     ErsatzProgress();
 
     // Null means no output.  The null value is useful for passing along the ostream pointer from another caller.   
-    explicit ErsatzProgress(std::size_t complete, std::ostream *to = &std::cerr, const std::string &message = "");
+    explicit ErsatzProgress(uint64_t complete, std::ostream *to = &std::cerr, const std::string &message = "");
 
     ~ErsatzProgress();
 
@@ -23,12 +25,12 @@ class ErsatzProgress {
       return *this;
     }
 
-    ErsatzProgress &operator+=(std::size_t amount) {
+    ErsatzProgress &operator+=(uint64_t amount) {
       if ((current_ += amount) >= next_) Milestone();
       return *this;
     }
 
-    void Set(std::size_t to) {
+    void Set(uint64_t to) {
       if ((current_ = to) >= next_) Milestone();
       Milestone();
     }
@@ -40,7 +42,7 @@ class ErsatzProgress {
   private:
     void Milestone();
 
-    std::size_t current_, next_, complete_;
+    uint64_t current_, next_, complete_;
     unsigned char stones_written_;
     std::ostream *out_;
 
diff --git a/klm/util/exception.cc b/klm/util/exception.cc
index c4f8c04c..3806e6de 100644
--- a/klm/util/exception.cc
+++ b/klm/util/exception.cc
@@ -84,4 +84,7 @@ EndOfFileException::EndOfFileException() throw() {
 }
 EndOfFileException::~EndOfFileException() throw() {}
 
+OverflowException::OverflowException() throw() {}
+OverflowException::~OverflowException() throw() {}
+
 } // namespace util
diff --git a/klm/util/exception.hh b/klm/util/exception.hh
index 6d6a37cb..053a850b 100644
--- a/klm/util/exception.hh
+++ b/klm/util/exception.hh
@@ -2,9 +2,12 @@
 #define UTIL_EXCEPTION__
 
 #include <exception>
+#include <limits>
 #include <sstream>
 #include <string>
 
+#include <stdint.h>
+
 namespace util {
 
 template <class Except, class Data> typename Except::template ExceptionTag<Except&>::Identity operator<<(Except &e, const Data &data);
@@ -111,6 +114,25 @@ class EndOfFileException : public Exception {
     ~EndOfFileException() throw();
 };
 
+class OverflowException : public Exception {
+  public:
+    OverflowException() throw();
+    ~OverflowException() throw();
+};
+
+template <unsigned len> inline std::size_t CheckOverflowInternal(uint64_t value) {
+  UTIL_THROW_IF(value > static_cast<uint64_t>(std::numeric_limits<std::size_t>::max()), OverflowException, "Integer overflow detected.  This model is too big for 32-bit code.");
+  return value;
+}
+
+template <> inline std::size_t CheckOverflowInternal<8>(uint64_t value) {
+  return value;
+}
+
+inline std::size_t CheckOverflow(uint64_t value) {
+  return CheckOverflowInternal<sizeof(std::size_t)>(value);
+}
+
 } // namespace util
 
 #endif // UTIL_EXCEPTION__
diff --git a/klm/util/file.cc b/klm/util/file.cc
index 6a3885a7..6bf879ac 100644
--- a/klm/util/file.cc
+++ b/klm/util/file.cc
@@ -6,6 +6,7 @@
 #include <cstdio>
 #include <iostream>
 
+#include <assert.h>
 #include <sys/types.h>
 #include <sys/stat.h>
 #include <fcntl.h>
@@ -44,6 +45,16 @@ int OpenReadOrThrow(const char *name) {
   return ret;
 }
 
+int CreateOrThrow(const char *name) {
+  int ret;
+#if defined(_WIN32) || defined(_WIN64)
+  UTIL_THROW_IF(-1 == (ret = _open(name, _O_CREAT | _O_TRUNC | _O_RDWR, _S_IREAD | _S_IWRITE)), ErrnoException, "while creating " << name);
+#else
+  UTIL_THROW_IF(-1 == (ret = open(name, O_CREAT | O_TRUNC | O_RDWR, S_IRUSR | S_IWUSR | S_IRGRP | S_IROTH)), ErrnoException, "while creating " << name);
+#endif
+  return ret;
+}
+
 uint64_t SizeFile(int fd) {
 #if defined(_WIN32) || defined(_WIN64)
   __int64 ret = _filelengthi64(fd);
@@ -101,6 +112,11 @@ void WriteOrThrow(int fd, const void *data_void, std::size_t size) {
   }
 }
 
+void WriteOrThrow(FILE *to, const void *data, std::size_t size) {
+  assert(size);
+  if (1 != std::fwrite(data, size, 1, to)) UTIL_THROW(util::ErrnoException, "Short write; requested size " << size);
+}
+
 void FSyncOrThrow(int fd) {
 // Apparently windows doesn't have fsync?  
 #if !defined(_WIN32) && !defined(_WIN64)
@@ -109,8 +125,13 @@ void FSyncOrThrow(int fd) {
 }
 
 namespace {
-void InternalSeek(int fd, off_t off, int whence) {
+void InternalSeek(int fd, int64_t off, int whence) {
+#if defined(_WIN32) || defined(_WIN64)
+  UTIL_THROW_IF((__int64)-1 == _lseeki64(fd, off, whence), ErrnoException, "Windows seek failed");
+
+#else
   UTIL_THROW_IF((off_t)-1 == lseek(fd, off, whence), ErrnoException, "Seek failed");
+#endif
 }
 } // namespace
 
@@ -133,6 +154,12 @@ std::FILE *FDOpenOrThrow(scoped_fd &file) {
   return ret;
 }
 
+std::FILE *FOpenOrThrow(const char *path, const char *mode) {
+  std::FILE *ret;
+  UTIL_THROW_IF(!(ret = fopen(path, mode)), util::ErrnoException, "Could not fopen " << path << " for " << mode);
+  return ret;
+}
+
 TempMaker::TempMaker(const std::string &prefix) : base_(prefix) {
   base_ += "XXXXXX";
 }
@@ -232,7 +259,9 @@ mkstemp_and_unlink(char *tmpl)
 
     /* Modified for windows and to unlink */
     //      fd = open (tmpl, O_RDWR | O_CREAT | O_EXCL, _S_IREAD | _S_IWRITE);
-    fd = _open (tmpl, _O_RDWR | _O_CREAT | _O_TEMPORARY | _O_EXCL | _O_BINARY, _S_IREAD | _S_IWRITE);
+    int flags = _O_RDWR | _O_CREAT | _O_EXCL | _O_BINARY;
+    flags |= _O_TEMPORARY;
+    fd = _open (tmpl, flags, _S_IREAD | _S_IWRITE);
     if (fd >= 0)
     {
       errno = save_errno;
@@ -250,17 +279,18 @@ mkstemp_and_unlink(char *tmpl)
 int
 mkstemp_and_unlink(char *tmpl) {
   int ret = mkstemp(tmpl);
-  if (ret == -1) return -1;
-  UTIL_THROW_IF(unlink(tmpl), util::ErrnoException, "Failed to delete " << tmpl);
+  if (ret != -1) {
+    UTIL_THROW_IF(unlink(tmpl), util::ErrnoException, "Failed to delete " << tmpl);
+  }
   return ret;
 }
 #endif
 
 int TempMaker::Make() const {
-  std::string copy(base_);
-  copy.push_back(0);
+  std::string name(base_);
+  name.push_back(0);
   int ret;
-  UTIL_THROW_IF(-1 == (ret = mkstemp_and_unlink(&copy[0])), util::ErrnoException, "Failed to make a temporary based on " << base_);
+  UTIL_THROW_IF(-1 == (ret = mkstemp_and_unlink(&name[0])), util::ErrnoException, "Failed to make a temporary based on " << base_);
   return ret;
 }
 
diff --git a/klm/util/file.hh b/klm/util/file.hh
index 5c57e2a9..185cb1f3 100644
--- a/klm/util/file.hh
+++ b/klm/util/file.hh
@@ -65,7 +65,10 @@ class scoped_FILE {
     std::FILE *file_;
 };
 
+// Open for read only.  
 int OpenReadOrThrow(const char *name);
+// Create file if it doesn't exist, truncate if it does.  Opened for write.   
+int CreateOrThrow(const char *name);
 
 // Return value for SizeFile when it can't size properly.  
 const uint64_t kBadSize = (uint64_t)-1;
@@ -77,6 +80,7 @@ void ReadOrThrow(int fd, void *to, std::size_t size);
 std::size_t ReadOrEOF(int fd, void *to_void, std::size_t amount);
 
 void WriteOrThrow(int fd, const void *data_void, std::size_t size);
+void WriteOrThrow(FILE *to, const void *data, std::size_t size);
 
 void FSyncOrThrow(int fd);
 
@@ -87,12 +91,14 @@ void SeekEnd(int fd);
 
 std::FILE *FDOpenOrThrow(scoped_fd &file);
 
+std::FILE *FOpenOrThrow(const char *path, const char *mode);
+
 class TempMaker {
   public:
     explicit TempMaker(const std::string &prefix);
 
+    // These will already be unlinked for you.  
     int Make() const;
-
     std::FILE *MakeFile() const;
 
   private:
diff --git a/klm/util/file_piece.cc b/klm/util/file_piece.cc
index a205995a..280f438c 100644
--- a/klm/util/file_piece.cc
+++ b/klm/util/file_piece.cc
@@ -5,6 +5,8 @@
 #include "util/mmap.hh"
 #ifdef WIN32
 #include <io.h>
+#else
+#include <unistd.h>
 #endif // WIN32
 
 #include <iostream>
@@ -27,7 +29,7 @@ ParseNumberException::ParseNumberException(StringPiece value) throw() {
 #ifdef HAVE_ZLIB
 GZException::GZException(gzFile file) {
   int num;
-  *this << gzerror( file, &num) << " from zlib";
+  *this << gzerror(file, &num) << " from zlib";
 }
 #endif // HAVE_ZLIB
 
diff --git a/klm/util/mmap.cc b/klm/util/mmap.cc
index 576fd4cc..bc9e3f81 100644
--- a/klm/util/mmap.cc
+++ b/klm/util/mmap.cc
@@ -19,8 +19,8 @@
 #include <windows.h>
 #include <io.h>
 #else
-#include <unistd.h>
 #include <sys/mman.h>
+#include <unistd.h>
 #endif
 
 namespace util {
@@ -171,20 +171,6 @@ void *MapZeroedWrite(int fd, std::size_t size) {
   return MapOrThrow(size, true, kFileFlags, false, fd, 0);
 }
 
-namespace {
-
-int CreateOrThrow(const char *name) {
-  int ret;
-#if defined(_WIN32) || defined(_WIN64)
-  UTIL_THROW_IF(-1 == (ret = _open(name, _O_CREAT | _O_TRUNC | _O_RDWR, _S_IREAD | _S_IWRITE)), ErrnoException, "while creating " << name);
-#else
-  UTIL_THROW_IF(-1 == (ret = open(name, O_CREAT | O_TRUNC | O_RDWR, S_IRUSR | S_IWUSR | S_IRGRP | S_IROTH)), ErrnoException, "while creating " << name);
-#endif
-  return ret;
-}
-
-} // namespace
-
 void *MapZeroedWrite(const char *name, std::size_t size, scoped_fd &file) {
   file.reset(CreateOrThrow(name));
   try {
diff --git a/klm/util/pool.cc b/klm/util/pool.cc
new file mode 100644
index 00000000..2dffd06f
--- /dev/null
+++ b/klm/util/pool.cc
@@ -0,0 +1,35 @@
+#include "util/pool.hh"
+
+#include <stdlib.h>
+
+namespace util {
+
+Pool::Pool() {
+  current_ = NULL;
+  current_end_ = NULL;
+}
+
+Pool::~Pool() {
+  FreeAll();
+}
+
+void Pool::FreeAll() {
+  for (std::vector<void *>::const_iterator i(free_list_.begin()); i != free_list_.end(); ++i) {
+    free(*i);
+  }
+  free_list_.clear();
+  current_ = NULL;
+  current_end_ = NULL;
+}
+
+void *Pool::More(std::size_t size) {
+  std::size_t amount = std::max(static_cast<size_t>(32) << free_list_.size(), size);
+  uint8_t *ret = static_cast<uint8_t*>(malloc(amount));
+  if (!ret) throw std::bad_alloc();
+  free_list_.push_back(ret);
+  current_ = ret + size;
+  current_end_ = ret + amount;
+  return ret;
+}
+
+} // namespace util
diff --git a/klm/util/pool.hh b/klm/util/pool.hh
new file mode 100644
index 00000000..72f8a0c8
--- /dev/null
+++ b/klm/util/pool.hh
@@ -0,0 +1,45 @@
+// Very simple pool.  It can only allocate memory.  And all of the memory it
+// allocates must be freed at the same time.  
+
+#ifndef UTIL_POOL__
+#define UTIL_POOL__
+
+#include <vector>
+
+#include <stdint.h>
+
+namespace util {
+
+class Pool {
+  public:
+    Pool();
+
+    ~Pool();
+
+    void *Allocate(std::size_t size) {
+      void *ret = current_;
+      current_ += size;
+      if (current_ < current_end_) {
+        return ret;
+      } else {
+        return More(size);
+      }
+    }
+
+    void FreeAll();
+
+  private:
+    void *More(std::size_t size);
+
+    std::vector<void *> free_list_;
+
+    uint8_t *current_, *current_end_;
+
+    // no copying
+    Pool(const Pool &);
+    Pool &operator=(const Pool &);
+}; 
+
+} // namespace util
+
+#endif // UTIL_POOL__
diff --git a/klm/util/probing_hash_table.hh b/klm/util/probing_hash_table.hh
index 3354b68e..4a8aff35 100644
--- a/klm/util/probing_hash_table.hh
+++ b/klm/util/probing_hash_table.hh
@@ -8,6 +8,7 @@
 #include <functional>
 
 #include <assert.h>
+#include <stdint.h>
 
 namespace util {
 
@@ -42,8 +43,8 @@ template <class EntryT, class HashT, class EqualT = std::equal_to<typename Entry
     typedef EqualT Equal;
 
   public:
-    static std::size_t Size(std::size_t entries, float multiplier) {
-      std::size_t buckets = std::max(entries + 1, static_cast<std::size_t>(multiplier * static_cast<float>(entries)));
+    static uint64_t Size(uint64_t entries, float multiplier) {
+      uint64_t buckets = std::max(entries + 1, static_cast<uint64_t>(multiplier * static_cast<float>(entries)));
       return buckets * sizeof(Entry);
     }
 
diff --git a/klm/util/string_piece.cc b/klm/util/string_piece.cc
new file mode 100644
index 00000000..b422cefc
--- /dev/null
+++ b/klm/util/string_piece.cc
@@ -0,0 +1,192 @@
+// Copyright 2004 The RE2 Authors.  All Rights Reserved.
+// Use of this source code is governed by a BSD-style
+// license that can be found in string_piece.hh.
+
+#include "util/string_piece.hh"
+
+#include <algorithm>
+
+#include <limits.h>
+
+#ifndef HAVE_ICU
+
+typedef StringPiece::size_type size_type;
+
+void StringPiece::CopyToString(std::string* target) const {
+  target->assign(ptr_, length_);
+}
+
+size_type StringPiece::find(const StringPiece& s, size_type pos) const {
+  if (length_ < 0 || pos > static_cast<size_type>(length_))
+    return npos;
+
+  const char* result = std::search(ptr_ + pos, ptr_ + length_,
+                                   s.ptr_, s.ptr_ + s.length_);
+  const size_type xpos = result - ptr_;
+  return xpos + s.length_ <= length_ ? xpos : npos;
+}
+
+size_type StringPiece::find(char c, size_type pos) const {
+  if (length_ <= 0 || pos >= static_cast<size_type>(length_)) {
+    return npos;
+  }
+  const char* result = std::find(ptr_ + pos, ptr_ + length_, c);
+  return result != ptr_ + length_ ? result - ptr_ : npos;
+}
+
+size_type StringPiece::rfind(const StringPiece& s, size_type pos) const {
+  if (length_ < s.length_) return npos;
+  const size_t ulen = length_;
+  if (s.length_ == 0) return std::min(ulen, pos);
+
+  const char* last = ptr_ + std::min(ulen - s.length_, pos) + s.length_;
+  const char* result = std::find_end(ptr_, last, s.ptr_, s.ptr_ + s.length_);
+  return result != last ? result - ptr_ : npos;
+}
+
+size_type StringPiece::rfind(char c, size_type pos) const {
+  if (length_ <= 0) return npos;
+  for (int i = std::min(pos, static_cast<size_type>(length_ - 1));
+       i >= 0; --i) {
+    if (ptr_[i] == c) {
+      return i;
+    }
+  }
+  return npos;
+}
+
+// For each character in characters_wanted, sets the index corresponding
+// to the ASCII code of that character to 1 in table.  This is used by
+// the find_.*_of methods below to tell whether or not a character is in
+// the lookup table in constant time.
+// The argument `table' must be an array that is large enough to hold all
+// the possible values of an unsigned char.  Thus it should be be declared
+// as follows:
+//   bool table[UCHAR_MAX + 1]
+static inline void BuildLookupTable(const StringPiece& characters_wanted,
+                                    bool* table) {
+  const size_type length = characters_wanted.length();
+  const char* const data = characters_wanted.data();
+  for (size_type i = 0; i < length; ++i) {
+    table[static_cast<unsigned char>(data[i])] = true;
+  }
+}
+
+size_type StringPiece::find_first_of(const StringPiece& s,
+                                     size_type pos) const {
+  if (length_ == 0 || s.length_ == 0)
+    return npos;
+
+  // Avoid the cost of BuildLookupTable() for a single-character search.
+  if (s.length_ == 1)
+    return find_first_of(s.ptr_[0], pos);
+
+  bool lookup[UCHAR_MAX + 1] = { false };
+  BuildLookupTable(s, lookup);
+  for (size_type i = pos; i < length_; ++i) {
+    if (lookup[static_cast<unsigned char>(ptr_[i])]) {
+      return i;
+    }
+  }
+  return npos;
+}
+
+size_type StringPiece::find_first_not_of(const StringPiece& s,
+                                         size_type pos) const {
+  if (length_ == 0)
+    return npos;
+
+  if (s.length_ == 0)
+    return 0;
+
+  // Avoid the cost of BuildLookupTable() for a single-character search.
+  if (s.length_ == 1)
+    return find_first_not_of(s.ptr_[0], pos);
+
+  bool lookup[UCHAR_MAX + 1] = { false };
+  BuildLookupTable(s, lookup);
+  for (size_type i = pos; i < length_; ++i) {
+    if (!lookup[static_cast<unsigned char>(ptr_[i])]) {
+      return i;
+    }
+  }
+  return npos;
+}
+
+size_type StringPiece::find_first_not_of(char c, size_type pos) const {
+  if (length_ == 0)
+    return npos;
+
+  for (; pos < length_; ++pos) {
+    if (ptr_[pos] != c) {
+      return pos;
+    }
+  }
+  return npos;
+}
+
+size_type StringPiece::find_last_of(const StringPiece& s, size_type pos) const {
+  if (length_ == 0 || s.length_ == 0)
+    return npos;
+
+  // Avoid the cost of BuildLookupTable() for a single-character search.
+  if (s.length_ == 1)
+    return find_last_of(s.ptr_[0], pos);
+
+  bool lookup[UCHAR_MAX + 1] = { false };
+  BuildLookupTable(s, lookup);
+  for (size_type i = std::min(pos, length_ - 1); ; --i) {
+    if (lookup[static_cast<unsigned char>(ptr_[i])])
+      return i;
+    if (i == 0)
+      break;
+  }
+  return npos;
+}
+
+size_type StringPiece::find_last_not_of(const StringPiece& s,
+                                        size_type pos) const {
+  if (length_ == 0)
+    return npos;
+
+  size_type i = std::min(pos, length_ - 1);
+  if (s.length_ == 0)
+    return i;
+
+  // Avoid the cost of BuildLookupTable() for a single-character search.
+  if (s.length_ == 1)
+    return find_last_not_of(s.ptr_[0], pos);
+
+  bool lookup[UCHAR_MAX + 1] = { false };
+  BuildLookupTable(s, lookup);
+  for (; ; --i) {
+    if (!lookup[static_cast<unsigned char>(ptr_[i])])
+      return i;
+    if (i == 0)
+      break;
+  }
+  return npos;
+}
+
+size_type StringPiece::find_last_not_of(char c, size_type pos) const {
+  if (length_ == 0)
+    return npos;
+
+  for (size_type i = std::min(pos, length_ - 1); ; --i) {
+    if (ptr_[i] != c)
+      return i;
+    if (i == 0)
+      break;
+  }
+  return npos;
+}
+
+StringPiece StringPiece::substr(size_type pos, size_type n) const {
+  if (pos > length_) pos = length_;
+  if (n > length_ - pos) n = length_ - pos;
+  return StringPiece(ptr_ + pos, n);
+}
+
+const size_type StringPiece::npos = size_type(-1);
+
+#endif // !HAVE_ICU
diff --git a/klm/util/string_piece.hh b/klm/util/string_piece.hh
index 5de053aa..be6a643d 100644
--- a/klm/util/string_piece.hh
+++ b/klm/util/string_piece.hh
@@ -85,6 +85,11 @@ U_NAMESPACE_BEGIN
 #include <string>
 #include <string.h>
 
+#ifdef WIN32
+#undef max
+#undef min
+#endif
+
 class StringPiece {
  public:
   typedef size_t size_type;
diff --git a/klm/util/tokenize_piece.hh b/klm/util/tokenize_piece.hh
index c7e1c863..4a7f5460 100644
--- a/klm/util/tokenize_piece.hh
+++ b/klm/util/tokenize_piece.hh
@@ -54,6 +54,18 @@ class AnyCharacter {
     StringPiece chars_;
 };
 
+class AnyCharacterLast {
+  public:
+    explicit AnyCharacterLast(const StringPiece &chars) : chars_(chars) {}
+
+    StringPiece Find(const StringPiece &in) const {
+      return StringPiece(std::find_end(in.data(), in.data() + in.size(), chars_.data(), chars_.data() + chars_.size()), 1);
+    }
+
+  private:
+    StringPiece chars_;
+};
+
 template <class Find, bool SkipEmpty = false> class TokenIter : public boost::iterator_facade<TokenIter<Find, SkipEmpty>, const StringPiece, boost::forward_traversal_tag> {
   public:
     TokenIter() {}
diff --git a/m4/cython.m4 b/m4/cython.m4
new file mode 100644
index 00000000..2d98eee7
--- /dev/null
+++ b/m4/cython.m4
@@ -0,0 +1,81 @@
+dnl Taken from the python bindings to the Enlightenment foundation libraries, 
+dnl and was part of a GPL package. I have included this file to fix the build.
+dnl
+dnl
+dnl AM_CHECK_CYTHON([VERSION [,ACTION-IF-FOUND [,ACTION-IF-NOT-FOUND]]])
+dnl Check if a Cython version is installed
+dnl Defines CYTHON_VERSION and CYTHON_FOUND
+AC_DEFUN([AM_CHECK_CYTHON],
+[
+AC_REQUIRE([AM_PATH_PYTHON])
+ifelse([$1], [], [_msg=""], [_msg=" >= $1"])
+AC_MSG_CHECKING(for Cython$_msg)
+AC_CACHE_VAL(py_cv_cython, [
+
+prog="import Cython.Compiler.Version; print Cython.Compiler.Version.version"
+CYTHON_VERSION=`$PYTHON -c "$prog" 2>&AC_FD_CC`
+
+py_cv_cython=no
+if test "x$CYTHON_VERSION" != "x"; then
+   py_cv_cython=yes
+fi
+
+if test "x$py_cv_cython" = "xyes"; then
+   ifelse([$1], [], [:],
+      AS_VERSION_COMPARE([$CYTHON_VERSION], [$1], [py_cv_cython=no]))
+fi
+])
+
+AC_MSG_RESULT([$py_cv_cython])
+
+if test "x$py_cv_cython" = "xyes"; then
+   CYTHON_FOUND=yes
+   ifelse([$2], [], [:], [$2])
+else
+   CYTHON_FOUND=no
+   ifelse([$3], [], [AC_MSG_ERROR([Could not find usable Cython$_msg])], [$3])
+fi
+])
+
+dnl AM_CHECK_CYTHON_PRECOMPILED(FILE-LIST [, ACTION-IF-ALL [, ACTION-IF-NOT-ALL]])
+dnl given a list of files ending in .pyx (FILE-LIST), check if their .c
+dnl counterpart exists and is not older than the source.
+dnl    ACTION-IF-ALL is called only if no files failed the check and thus
+dnl       all pre-generated files are usable.
+dnl    ACTION-IF-NOT-ALL is called if some or all failed. If not provided,
+dnl       an error will be issued.
+AC_DEFUN([AM_CHECK_CYTHON_PRECOMPILED],
+[
+_to_check_list="$1"
+_failed_list=""
+_exists_list=""
+
+for inf in $_to_check_list; do
+    outf=`echo "$inf" | sed -e 's/^\(.*\)[.]pyx$/\1.c/'`
+    if test "$outf" = "$inf"; then
+       AC_MSG_WARN([File to check must end in .pyx, but got: $inf -- Skip])
+       continue
+    fi
+
+    AC_MSG_CHECKING([for pre-generated $outf for $inf])
+    if ! test -f "$outf"; then
+       _res=no
+       _failed_list="${_failed_list} $outf"
+    elif ! test "$outf" -nt "$inf"; then
+       _res="no (older)"
+       _failed_list="${_failed_list} $outf"
+    else
+       _res=yes
+       _exists_list="${_exists_list} $outf"
+    fi
+    AC_MSG_RESULT($_res)
+done
+
+if test -z "$_failed_list" -a -n "$_exists_list"; then
+   ifelse([$2], [], [:], [$2])
+else
+   ifelse([$3], [],
+   [AC_MSG_ERROR([Missing pre-generated files: $_failed_list])],
+   [$3])
+fi
+])
diff --git a/mira/Jamfile b/mira/Jamfile
deleted file mode 100644
index 8825b887..00000000
--- a/mira/Jamfile
+++ /dev/null
@@ -1 +0,0 @@
-exe kbest_mira : kbest_mira.cc ..//decoder ;
diff --git a/mira/Makefile.am b/mira/Makefile.am
index 7b4a4e12..3f8f17cd 100644
--- a/mira/Makefile.am
+++ b/mira/Makefile.am
@@ -1,6 +1,6 @@
 bin_PROGRAMS = kbest_mira
 
 kbest_mira_SOURCES = kbest_mira.cc
-kbest_mira_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a ../klm/lm/libklm.a ../klm/util/libklm_util.a -lz
+kbest_mira_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/klm/search/libksearch.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a ../klm/lm/libklm.a ../klm/util/libklm_util.a -lz
 
 AM_CPPFLAGS = -W -Wall -Wno-sign-compare -I$(top_srcdir)/utils -I$(top_srcdir)/decoder -I$(top_srcdir)/mteval
diff --git a/mteval/Jamfile b/mteval/Jamfile
deleted file mode 100644
index 3ed2c2cc..00000000
--- a/mteval/Jamfile
+++ /dev/null
@@ -1,8 +0,0 @@
-import testing ;
-
-lib mteval : ter.cc comb_scorer.cc aer_scorer.cc scorer.cc external_scorer.cc ns.cc ns_ter.cc ns_ext.cc ns_comb.cc ns_docscorer.cc ns_cer.cc ..//utils : <include>. : : <include>. <library>..//z ;
-exe fast_score : fast_score.cc mteval ..//utils ..//boost_program_options ;
-exe mbr_kbest : mbr_kbest.cc mteval ..//utils ..//boost_program_options ;
-alias programs : fast_score mbr_kbest ;
-
-unit-test scorer_test : scorer_test.cc mteval ..//utils ..//z ..//boost_unit_test_framework : <testing.arg>$(TOP)/mteval/test_data ;
diff --git a/mteval/mbr_kbest.cc b/mteval/mbr_kbest.cc
index 2bd31566..2519bc01 100644
--- a/mteval/mbr_kbest.cc
+++ b/mteval/mbr_kbest.cc
@@ -1,7 +1,9 @@
 #include <iostream>
 #include <vector>
+#include <tr1/unordered_map>
 
 #include <boost/program_options.hpp>
+#include <boost/functional/hash.hpp>
 
 #include "prob.h"
 #include "tdict.h"
@@ -10,6 +12,7 @@
 #include "stringlib.h"
 
 using namespace std;
+using namespace std::tr1;
 
 namespace po = boost::program_options;
 
@@ -31,27 +34,33 @@ void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
   }
 }
 
+struct ScoreComparer {
+  bool operator()(const pair<vector<WordID>, prob_t>& a, const pair<vector<WordID>, prob_t>& b) const {
+    return a.second > b.second;
+  }
+};
+
 struct LossComparer {
   bool operator()(const pair<vector<WordID>, prob_t>& a, const pair<vector<WordID>, prob_t>& b) const {
     return a.second < b.second;
   }
 };
 
-bool ReadKBestList(istream* in, string* sent_id, vector<pair<vector<WordID>, prob_t> >* list) {
+bool ReadKBestList(const double mbr_scale, istream* in, string* sent_id, vector<pair<vector<WordID>, prob_t> >* list) {
   static string cache_id;
   static pair<vector<WordID>, prob_t> cache_pair;
   list->clear();
   string cur_id;
+  unordered_map<vector<WordID>, unsigned, boost::hash<vector<WordID> > > sent2id;
   if (cache_pair.first.size() > 0) {
     list->push_back(cache_pair);
+    sent2id[cache_pair.first] = 0;
     cur_id = cache_id;
     cache_pair.first.clear();
   }
   string line;
   string tstr;
-  while(*in) {
-    getline(*in, line);
-    if (line.empty()) continue;
+  while(getline(*in, line)) {
     size_t p1 = line.find(" ||| ");
     if (p1 == string::npos) { cerr << "Bad format: " << line << endl; abort(); }
     size_t p2 = line.find(" ||| ", p1 + 4);
@@ -59,16 +68,25 @@ bool ReadKBestList(istream* in, string* sent_id, vector<pair<vector<WordID>, pro
     size_t p3 = line.rfind(" ||| ");
     cache_id = line.substr(0, p1);
     tstr = line.substr(p1 + 5, p2 - p1 - 5);
-    double val = strtod(line.substr(p3 + 5).c_str(), NULL);
+    double val = strtod(line.substr(p3 + 5).c_str(), NULL) * mbr_scale;
     TD::ConvertSentence(tstr, &cache_pair.first);
     cache_pair.second.logeq(val);
     if (cur_id.empty()) cur_id = cache_id;
     if (cur_id == cache_id) {
-      list->push_back(cache_pair);
+      unordered_map<vector<WordID>, unsigned, boost::hash<vector<WordID> > >::iterator it =
+        sent2id.find(cache_pair.first);
+      if (it == sent2id.end()) {
+        sent2id.insert(make_pair(cache_pair.first, unsigned(list->size())));
+        list->push_back(cache_pair);
+      } else {
+        (*list)[it->second].second += cache_pair.second;
+        // cerr << "Cruch: " << line << "\n newp=" << (*list)[it->second].second << endl;
+      }
       *sent_id = cur_id;
       cache_pair.first.clear();
     } else { break; }
   }
+  sort(list->begin(), list->end(), ScoreComparer());
   return !list->empty();
 }
 
@@ -87,14 +105,14 @@ int main(int argc, char** argv) {
   vector<pair<vector<WordID>, prob_t> > list;
   ReadFile rf(file);
   string sent_id;
-  while(ReadKBestList(rf.stream(), &sent_id, &list)) {
+  while(ReadKBestList(mbr_scale, rf.stream(), &sent_id, &list)) {
     vector<prob_t> joints(list.size());
-    const prob_t max_score = pow(list.front().second, mbr_scale);
+    const prob_t max_score = list.front().second;
     prob_t marginal = prob_t::Zero();
     for (int i = 0 ; i < list.size(); ++i) {
-      const prob_t joint = pow(list[i].second, mbr_scale) / max_score;
+      const prob_t joint = list[i].second / max_score;
       joints[i] = joint;
-      // cerr << "list[" << i << "] joint=" << log(joint) << endl;
+      //cerr << "list[" << i << "] joint=" << log(joint) << endl;
       marginal += joint;
     }
     int mbr_idx = -1;
diff --git a/mteval/ns.cc b/mteval/ns.cc
index 33952da7..3af7cc63 100644
--- a/mteval/ns.cc
+++ b/mteval/ns.cc
@@ -252,7 +252,7 @@ EvaluationMetric* EvaluationMetric::Instance(const string& imetric_id) {
     } else if (metric_id == "TER") {
       m = new TERMetric;
     } else if (metric_id == "METEOR") {
-      m = new ExternalMetric("METEOR", "java -Xmx1536m -jar /Users/cdyer/software/meteor/meteor-1.3.jar - - -mira -lower -t tune -l en");
+      m = new ExternalMetric("METEOR", "java -Xmx1536m -jar /cab0/tools/meteor-1.3/meteor-1.3.jar - - -mira -lower -t tune -l en");
     } else if (metric_id.find("COMB:") == 0) {
       m = new CombinationMetric(metric_id);
     } else if (metric_id == "CER") {
diff --git a/mteval/ns_docscorer.cc b/mteval/ns_docscorer.cc
index 28a2fd09..f72ad115 100644
--- a/mteval/ns_docscorer.cc
+++ b/mteval/ns_docscorer.cc
@@ -16,7 +16,7 @@ void DocumentScorer::Init(const EvaluationMetric* metric,
             const string& src_file,
             bool verbose) {
   scorers_.clear();
-  cerr << "Loading references (" << ref_files.size() << " files)\n";
+  if (verbose) cerr << "Loading references (" << ref_files.size() << " files)\n";
   assert(src_file.empty());
   std::vector<ReadFile> ifs(ref_files.begin(),ref_files.end());
   for (int i=0; i < ref_files.size(); ++i) ifs[i].Init(ref_files[i]);
@@ -55,6 +55,6 @@ void DocumentScorer::Init(const EvaluationMetric* metric,
       ++line;
     }
   }
-  cerr << "Loaded reference translations for " << scorers_.size() << " sentences.\n";
+  if (verbose) cerr << "Loaded reference translations for " << scorers_.size() << " sentences.\n";
 }
 
diff --git a/mteval/ns_docscorer.h b/mteval/ns_docscorer.h
index 170ac627..a5757258 100644
--- a/mteval/ns_docscorer.h
+++ b/mteval/ns_docscorer.h
@@ -5,7 +5,7 @@
 #include <string>
 #include <boost/shared_ptr.hpp>
 
-struct EvaluationMetric;
+class EvaluationMetric;
 struct SegmentEvaluator;
 class DocumentScorer {
  public:
diff --git a/phrasinator/Jamfile b/phrasinator/Jamfile
deleted file mode 100644
index 1fc34f79..00000000
--- a/phrasinator/Jamfile
+++ /dev/null
@@ -1,4 +0,0 @@
-exe gibbs_train_plm : gibbs_train_plm.cc ..//utils ..//z ..//boost_program_options ;
-exe gibbs_train_plm_notables : gibbs_train_plm.notables.cc ..//utils ..//z ..//boost_program_options ;
-
-alias programs : gibbs_train_plm gibbs_train_plm_notables ;
diff --git a/phrasinator/Makefile.am b/phrasinator/Makefile.am
deleted file mode 100644
index 3ddd1934..00000000
--- a/phrasinator/Makefile.am
+++ /dev/null
@@ -1,14 +0,0 @@
-bin_PROGRAMS = gibbs_train_plm gibbs_train_plm_notables
-
-#head_bigram_model
-
-gibbs_train_plm_notables_SOURCES = gibbs_train_plm.notables.cc
-gibbs_train_plm_notables_LDADD = $(top_srcdir)/utils/libutils.a -lz
-
-gibbs_train_plm_SOURCES = gibbs_train_plm.cc
-gibbs_train_plm_LDADD = $(top_srcdir)/utils/libutils.a -lz
-
-#head_bigram_model_SOURCES = head_bigram_model.cc
-#head_bigram_model_LDADD = $(top_srcdir)/utils/libutils.a -lz
-
-AM_CPPFLAGS = -funroll-loops -ffast-math -W -Wall -I$(top_srcdir)/utils
diff --git a/phrasinator/README b/phrasinator/README
deleted file mode 100644
index fb5b93ef..00000000
--- a/phrasinator/README
+++ /dev/null
@@ -1,16 +0,0 @@
-The "phrasinator" uses a simple Bayesian nonparametric model to segment
-text into chunks. The inferred model is then saved so that it can rapidly
-predict segments in new (but related) texts.
-
-  Input will be a corpus of sentences, e.g.:
-
-    economists have argued that real interest rates have fallen .
-
-  The output will be a model that, when run with cdec, will produce
-  a segmentation into phrasal units, e.g.:
-
-    economists have argued that real_interest_rates have fallen .
-
-
-To train a model, run ./train-phrasinator.pl and follow instructions.
-
diff --git a/phrasinator/gibbs_train_plm.cc b/phrasinator/gibbs_train_plm.cc
deleted file mode 100644
index 7847a460..00000000
--- a/phrasinator/gibbs_train_plm.cc
+++ /dev/null
@@ -1,309 +0,0 @@
-#include <iostream>
-#include <tr1/memory>
-
-#include <boost/program_options.hpp>
-#include <boost/program_options/variables_map.hpp>
-
-#include "filelib.h"
-#include "dict.h"
-#include "sampler.h"
-#include "ccrp.h"
-#include "m.h"
-
-using namespace std;
-using namespace std::tr1;
-namespace po = boost::program_options;
-
-Dict d; // global dictionary
-
-string Join(char joiner, const vector<int>& phrase) {
-  ostringstream os;
-  for (unsigned i = 0; i < phrase.size(); ++i) {
-    if (i > 0) os << joiner;
-    os << d.Convert(phrase[i]);
-  }
-  return os.str();
-}
-
-ostream& operator<<(ostream& os, const vector<int>& phrase) {
-  for (unsigned i = 0; i < phrase.size(); ++i)
-    os << (i == 0 ? "" : " ") << d.Convert(phrase[i]);
-  return os;
-}
-
-struct UnigramLM {
-  explicit UnigramLM(const string& fname) {
-    ifstream in(fname.c_str());
-    assert(in);
-  }
-
-  double logprob(unsigned word) const {
-    assert(word < freqs_.size());
-    return freqs_[word];
-  }
-
-  vector<double> freqs_;
-};
-
-void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
-  po::options_description opts("Configuration options");
-  opts.add_options()
-        ("samples,s",po::value<unsigned>()->default_value(1000),"Number of samples")
-        ("input,i",po::value<string>(),"Read file from")
-        ("random_seed,S",po::value<uint32_t>(), "Random seed")
-        ("write_cdec_grammar,g", po::value<string>(), "Write cdec grammar to this file")
-        ("write_cdec_weights,w", po::value<string>(), "Write cdec weights to this file")
-        ("poisson_length,p", "Use a Poisson distribution as the length of a phrase in the base distribuion")
-        ("no_hyperparameter_inference,N", "Disable hyperparameter inference");
-  po::options_description clo("Command line options");
-  clo.add_options()
-        ("config", po::value<string>(), "Configuration file")
-        ("help,h", "Print this help message and exit");
-  po::options_description dconfig_options, dcmdline_options;
-  dconfig_options.add(opts);
-  dcmdline_options.add(opts).add(clo);
-  
-  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
-  if (conf->count("config")) {
-    ifstream config((*conf)["config"].as<string>().c_str());
-    po::store(po::parse_config_file(config, dconfig_options), *conf);
-  }
-  po::notify(*conf);
-
-  if (conf->count("help") || (conf->count("input") == 0)) {
-    cerr << dcmdline_options << endl;
-    exit(1);
-  }
-}
-
-void ReadCorpus(const string& filename, vector<vector<int> >* c, set<int>* vocab) {
-  c->clear();
-  istream* in;
-  if (filename == "-")
-    in = &cin;
-  else
-    in = new ifstream(filename.c_str());
-  assert(*in);
-  string line;
-  while(*in) {
-    getline(*in, line);
-    if (line.empty() && !*in) break;
-    c->push_back(vector<int>());
-    vector<int>& v = c->back();
-    d.ConvertWhitespaceDelimitedLine(line, &v);
-    for (unsigned i = 0; i < v.size(); ++i) vocab->insert(v[i]);
-  }
-  if (in != &cin) delete in;
-}
-
-struct UniphraseLM {
-  UniphraseLM(const vector<vector<int> >& corpus,
-              const set<int>& vocab,
-              const po::variables_map& conf) :
-    phrases_(1,1,1,1),
-    gen_(1,1,1,1),
-    corpus_(corpus),
-    uniform_word_(1.0 / vocab.size()),
-    gen_p0_(0.5),
-    p_end_(0.5),
-    use_poisson_(conf.count("poisson_length") > 0) {}
-
-  double p0(const vector<int>& phrase) const {
-    static vector<double> p0s(10000, 0.0);
-    assert(phrase.size() < 10000);
-    double& p = p0s[phrase.size()];
-    if (p) return p;
-    p = exp(log_p0(phrase));
-    if (!p) {
-      cerr << "0 prob phrase: " << phrase << "\nAssigning std::numeric_limits<double>::min()\n";
-      p = std::numeric_limits<double>::min();
-    }
-    return p;
-  }
-
-  double log_p0(const vector<int>& phrase) const {
-    double len_logprob;
-    if (use_poisson_)
-      len_logprob = Md::log_poisson(phrase.size(), 1.0);
-    else
-      len_logprob = log(1 - p_end_) * (phrase.size() -1) + log(p_end_);
-    return log(uniform_word_) * phrase.size() + len_logprob;
-  }
-
-  double llh() const {
-    double llh = gen_.log_crp_prob();
-    llh += gen_.num_tables(false) * log(gen_p0_) +
-           gen_.num_tables(true) * log(1 - gen_p0_);
-    double llhr = phrases_.log_crp_prob();
-    for (CCRP<vector<int> >::const_iterator it = phrases_.begin(); it != phrases_.end(); ++it) {
-      llhr += phrases_.num_tables(it->first) * log_p0(it->first);
-      //llhr += log_p0(it->first);
-      if (!isfinite(llh)) {
-        cerr << it->first << endl;
-        cerr << log_p0(it->first) << endl;
-        abort();
-      }
-    }
-    return llh + llhr;
-  }
-
-  void Sample(unsigned int samples, bool hyp_inf, MT19937* rng) {
-    cerr << "Initializing...\n";
-    z_.resize(corpus_.size());
-    int tc = 0;
-    for (unsigned i = 0; i < corpus_.size(); ++i) {
-      const vector<int>& line = corpus_[i];
-      const int ls = line.size();
-      const int last_pos = ls - 1;
-      vector<bool>& z = z_[i];
-      z.resize(ls);
-      int prev = 0;
-      for (int j = 0; j < ls; ++j) {
-        z[j] = rng->next() < 0.5;
-        if (j == last_pos) z[j] = true;  // break phrase at the end of the sentence
-        if (z[j]) {
-          const vector<int> p(line.begin() + prev, line.begin() + j + 1);
-          phrases_.increment(p, p0(p), rng);
-          //cerr << p << ": " << p0(p) << endl;
-          prev = j + 1;
-          gen_.increment(false, gen_p0_, rng);
-          ++tc; // remove
-        }
-      }
-      ++tc;
-      gen_.increment(true, 1.0 - gen_p0_, rng); // end of utterance
-    }
-    cerr << "TC: " << tc << endl;
-    cerr << "Initial LLH: " << llh() << endl;
-    cerr << "Sampling...\n";
-    cerr << gen_ << endl;
-    for (unsigned s = 1; s < samples; ++s) {
-      cerr << '.';
-      if (s % 10 == 0) {
-        cerr << " [" << s;
-        if (hyp_inf) ResampleHyperparameters(rng);
-        cerr << " LLH=" << llh() << "]\n";
-        vector<int> z(z_[0].size(), 0);
-        //for (int j = 0; j < z.size(); ++j) z[j] = z_[0][j];
-        //SegCorpus::Write(corpus_[0], z, d);
-      }
-      for (unsigned i = 0; i < corpus_.size(); ++i) {
-        const vector<int>& line = corpus_[i];
-        const int ls = line.size();
-        const int last_pos = ls - 1;
-        vector<bool>& z = z_[i];
-        int prev = 0;
-        for (int j = 0; j < last_pos; ++j) { // don't resample last position
-          int next = j+1;  while(!z[next]) { ++next; }
-          const vector<int> p1p2(line.begin() + prev, line.begin() + next + 1);
-          const vector<int> p1(line.begin() + prev, line.begin() + j + 1);
-          const vector<int> p2(line.begin() + j + 1, line.begin() + next + 1);
-
-          if (z[j]) {
-            phrases_.decrement(p1, rng);
-            phrases_.decrement(p2, rng);
-            gen_.decrement(false, rng);
-            gen_.decrement(false, rng);
-          } else {
-            phrases_.decrement(p1p2, rng);
-            gen_.decrement(false, rng);
-          }
-
-          const double d1 = phrases_.prob(p1p2, p0(p1p2)) * gen_.prob(false, gen_p0_);
-          double d2 = phrases_.prob(p1, p0(p1)) * gen_.prob(false, gen_p0_);
-          phrases_.increment(p1, p0(p1), rng);
-          gen_.increment(false, gen_p0_, rng);
-          d2 *= phrases_.prob(p2, p0(p2)) * gen_.prob(false, gen_p0_);
-          phrases_.decrement(p1, rng);
-          gen_.decrement(false, rng);
-          z[j] = rng->SelectSample(d1, d2);
-
-          if (z[j]) {
-            phrases_.increment(p1, p0(p1), rng);
-            phrases_.increment(p2, p0(p2), rng);
-            gen_.increment(false, gen_p0_, rng);
-            gen_.increment(false, gen_p0_, rng);
-            prev = j + 1;
-          } else {
-            phrases_.increment(p1p2, p0(p1p2), rng);
-            gen_.increment(false, gen_p0_, rng);
-          }
-        }
-      }
-    }
-//    cerr << endl << endl << gen_ << endl << phrases_ << endl;
-    cerr << gen_.prob(false, gen_p0_) << " " << gen_.prob(true, 1 - gen_p0_) << endl;
-  }
-
-  void WriteCdecGrammarForCurrentSample(ostream* os) const {
-    CCRP<vector<int> >::const_iterator it = phrases_.begin();
-    for (; it != phrases_.end(); ++it) {
-      (*os) << "[X] ||| " << Join(' ', it->first) << " ||| "
-                          << Join('_', it->first) << " ||| C=1 P=" 
-                          << log(phrases_.prob(it->first, p0(it->first))) << endl;
-    }
-  }
-
-  double OOVUnigramLogProb() const {
-    vector<int> x(1,99999999);
-    return log(phrases_.prob(x, p0(x)));
-  }
-
-  void ResampleHyperparameters(MT19937* rng) {
-    phrases_.resample_hyperparameters(rng);
-    gen_.resample_hyperparameters(rng);
-    cerr << " d=" << phrases_.discount() << ",s=" << phrases_.strength();
-  }
-
-  CCRP<vector<int> > phrases_;
-  CCRP<bool> gen_;
-  vector<vector<bool> > z_;   // z_[i] is there a phrase boundary after the ith word
-  const vector<vector<int> >& corpus_;
-  const double uniform_word_;
-  const double gen_p0_;
-  const double p_end_; // in base length distribution, p of the end of a phrase
-  const bool use_poisson_;
-};
-
-
-int main(int argc, char** argv) {
-  po::variables_map conf;
-  InitCommandLine(argc, argv, &conf);
-  boost::shared_ptr<MT19937> prng;
-  if (conf.count("random_seed"))
-    prng.reset(new MT19937(conf["random_seed"].as<uint32_t>()));
-  else
-    prng.reset(new MT19937);
-  MT19937& rng = *prng;
-
-  vector<vector<int> > corpus;
-  set<int> vocab;
-  ReadCorpus(conf["input"].as<string>(), &corpus, &vocab);
-  cerr << "Corpus size: " << corpus.size() << " sentences\n";
-  cerr << "Vocabulary size: " << vocab.size() << " types\n";
-
-  UniphraseLM ulm(corpus, vocab, conf);
-  ulm.Sample(conf["samples"].as<unsigned>(), conf.count("no_hyperparameter_inference") == 0, &rng);
-  cerr << "OOV unigram prob: " << ulm.OOVUnigramLogProb() << endl;
-
-  for (unsigned i = 0; i < corpus.size(); ++i)
-//    SegCorpus::Write(corpus[i], shmmlm.z_[i], d);
- ;
-  if (conf.count("write_cdec_grammar")) {
-    string fname = conf["write_cdec_grammar"].as<string>();
-    cerr << "Writing model to " << fname << " ...\n";
-    WriteFile wf(fname);
-    ulm.WriteCdecGrammarForCurrentSample(wf.stream());
-  }
-
-  if (conf.count("write_cdec_weights")) {
-    string fname = conf["write_cdec_weights"].as<string>();
-    cerr << "Writing weights to " << fname << " .\n";
-    WriteFile wf(fname);
-    ostream& os = *wf.stream();
-    os << "# make C smaller to use more phrases\nP 1\nPassThrough " << ulm.OOVUnigramLogProb() << "\nC -3\n";
-  }
-
-  return 0;
-}
-
diff --git a/phrasinator/gibbs_train_plm.notables.cc b/phrasinator/gibbs_train_plm.notables.cc
deleted file mode 100644
index 4526eaa6..00000000
--- a/phrasinator/gibbs_train_plm.notables.cc
+++ /dev/null
@@ -1,335 +0,0 @@
-#include <iostream>
-#include <tr1/memory>
-
-#include <boost/program_options.hpp>
-#include <boost/program_options/variables_map.hpp>
-
-#include "filelib.h"
-#include "dict.h"
-#include "sampler.h"
-#include "ccrp.h"
-#include "ccrp_nt.h"
-
-using namespace std;
-using namespace std::tr1;
-namespace po = boost::program_options;
-
-Dict d; // global dictionary
-
-string Join(char joiner, const vector<int>& phrase) {
-  ostringstream os;
-  for (unsigned i = 0; i < phrase.size(); ++i) {
-    if (i > 0) os << joiner;
-    os << d.Convert(phrase[i]);
-  }
-  return os.str();
-}
-
-template <typename BType>
-void WriteSeg(const vector<int>& line, const vector<BType>& label, const Dict& d) {
-  assert(line.size() == label.size());
-  assert(label.back());
-  unsigned prev = 0;
-  unsigned cur = 0;
-  while (cur < line.size()) {
-    if (label[cur]) {
-      if (prev) cout << ' ';
-      cout << "{{";
-      for (unsigned i = prev; i <= cur; ++i)
-        cout << (i == prev ? "" : " ") << d.Convert(line[i]);
-      cout << "}}:" << label[cur];
-      prev = cur + 1;
-    }
-    ++cur;
-  }
-  cout << endl;
-}
-
-ostream& operator<<(ostream& os, const vector<int>& phrase) {
-  for (unsigned i = 0; i < phrase.size(); ++i)
-    os << (i == 0 ? "" : " ") << d.Convert(phrase[i]);
-  return os;
-}
-
-struct UnigramLM {
-  explicit UnigramLM(const string& fname) {
-    ifstream in(fname.c_str());
-    assert(in);
-  }
-
-  double logprob(unsigned word) const {
-    assert(word < freqs_.size());
-    return freqs_[word];
-  }
-
-  vector<double> freqs_;
-};
-
-void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
-  po::options_description opts("Configuration options");
-  opts.add_options()
-        ("samples,s",po::value<unsigned>()->default_value(1000),"Number of samples")
-        ("input,i",po::value<string>(),"Read file from")
-        ("random_seed,S",po::value<uint32_t>(), "Random seed")
-        ("write_cdec_grammar,g", po::value<string>(), "Write cdec grammar to this file")
-        ("write_cdec_weights,w", po::value<string>(), "Write cdec weights to this file")
-        ("poisson_length,p", "Use a Poisson distribution as the length of a phrase in the base distribuion")
-        ("no_hyperparameter_inference,N", "Disable hyperparameter inference");
-  po::options_description clo("Command line options");
-  clo.add_options()
-        ("config", po::value<string>(), "Configuration file")
-        ("help,h", "Print this help message and exit");
-  po::options_description dconfig_options, dcmdline_options;
-  dconfig_options.add(opts);
-  dcmdline_options.add(opts).add(clo);
-  
-  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
-  if (conf->count("config")) {
-    ifstream config((*conf)["config"].as<string>().c_str());
-    po::store(po::parse_config_file(config, dconfig_options), *conf);
-  }
-  po::notify(*conf);
-
-  if (conf->count("help") || (conf->count("input") == 0)) {
-    cerr << dcmdline_options << endl;
-    exit(1);
-  }
-}
-
-void ReadCorpus(const string& filename, vector<vector<int> >* c, set<int>* vocab) {
-  c->clear();
-  istream* in;
-  if (filename == "-")
-    in = &cin;
-  else
-    in = new ifstream(filename.c_str());
-  assert(*in);
-  string line;
-  while(*in) {
-    getline(*in, line);
-    if (line.empty() && !*in) break;
-    c->push_back(vector<int>());
-    vector<int>& v = c->back();
-    d.ConvertWhitespaceDelimitedLine(line, &v);
-    for (unsigned i = 0; i < v.size(); ++i) vocab->insert(v[i]);
-  }
-  if (in != &cin) delete in;
-}
-
-double log_poisson(unsigned x, const double& lambda) {
-  assert(lambda > 0.0);
-  return log(lambda) * x - lgamma(x + 1) - lambda;
-}
-
-struct UniphraseLM {
-  UniphraseLM(const vector<vector<int> >& corpus,
-              const set<int>& vocab,
-              const po::variables_map& conf) :
-    phrases_(1,1),
-    gen_(1,1),
-    corpus_(corpus),
-    uniform_word_(1.0 / vocab.size()),
-    gen_p0_(0.5),
-    p_end_(0.5),
-    use_poisson_(conf.count("poisson_length") > 0) {}
-
-  double p0(const vector<int>& phrase) const {
-    static vector<double> p0s(10000, 0.0);
-    assert(phrase.size() < 10000);
-    double& p = p0s[phrase.size()];
-    if (p) return p;
-    p = exp(log_p0(phrase));
-    if (!p) {
-      cerr << "0 prob phrase: " << phrase << "\nAssigning std::numeric_limits<double>::min()\n";
-      p = std::numeric_limits<double>::min();
-    }
-    return p;
-  }
-
-  double log_p0(const vector<int>& phrase) const {
-    double len_logprob;
-    if (use_poisson_)
-      len_logprob = log_poisson(phrase.size(), 1.0);
-    else
-      len_logprob = log(1 - p_end_) * (phrase.size() -1) + log(p_end_);
-    return log(uniform_word_) * phrase.size() + len_logprob;
-  }
-
-  double llh() const {
-    double llh = gen_.log_crp_prob();
-    llh += log(gen_p0_) + log(1 - gen_p0_);
-    double llhr = phrases_.log_crp_prob();
-    for (CCRP_NoTable<vector<int> >::const_iterator it = phrases_.begin(); it != phrases_.end(); ++it) {
-      llhr += log_p0(it->first);
-      //llhr += log_p0(it->first);
-      if (!isfinite(llh)) {
-        cerr << it->first << endl;
-        cerr << log_p0(it->first) << endl;
-        abort();
-      }
-    }
-    return llh + llhr;
-  }
-
-  void Sample(unsigned int samples, bool hyp_inf, MT19937* rng) {
-    cerr << "Initializing...\n";
-    z_.resize(corpus_.size());
-    int tc = 0;
-    for (unsigned i = 0; i < corpus_.size(); ++i) {
-      const vector<int>& line = corpus_[i];
-      const int ls = line.size();
-      const int last_pos = ls - 1;
-      vector<bool>& z = z_[i];
-      z.resize(ls);
-      int prev = 0;
-      for (int j = 0; j < ls; ++j) {
-        z[j] = rng->next() < 0.5;
-        if (j == last_pos) z[j] = true;  // break phrase at the end of the sentence
-        if (z[j]) {
-          const vector<int> p(line.begin() + prev, line.begin() + j + 1);
-          phrases_.increment(p);
-          //cerr << p << ": " << p0(p) << endl;
-          prev = j + 1;
-          gen_.increment(false);
-          ++tc; // remove
-        }
-      }
-      ++tc;
-      gen_.increment(true); // end of utterance
-    }
-    cerr << "TC: " << tc << endl;
-    cerr << "Initial LLH: " << llh() << endl;
-    cerr << "Sampling...\n";
-    cerr << gen_ << endl;
-    for (unsigned s = 1; s < samples; ++s) {
-      cerr << '.';
-      if (s % 10 == 0) {
-        cerr << " [" << s;
-        if (hyp_inf) ResampleHyperparameters(rng);
-        cerr << " LLH=" << llh() << "]\n";
-        vector<int> z(z_[0].size(), 0);
-        //for (int j = 0; j < z.size(); ++j) z[j] = z_[0][j];
-        //SegCorpus::Write(corpus_[0], z, d);
-      }
-      for (unsigned i = 0; i < corpus_.size(); ++i) {
-        const vector<int>& line = corpus_[i];
-        const int ls = line.size();
-        const int last_pos = ls - 1;
-        vector<bool>& z = z_[i];
-        int prev = 0;
-        for (int j = 0; j < last_pos; ++j) { // don't resample last position
-          int next = j+1;  while(!z[next]) { ++next; }
-          const vector<int> p1p2(line.begin() + prev, line.begin() + next + 1);
-          const vector<int> p1(line.begin() + prev, line.begin() + j + 1);
-          const vector<int> p2(line.begin() + j + 1, line.begin() + next + 1);
-
-          if (z[j]) {
-            phrases_.decrement(p1);
-            phrases_.decrement(p2);
-            gen_.decrement(false);
-            gen_.decrement(false);
-          } else {
-            phrases_.decrement(p1p2);
-            gen_.decrement(false);
-          }
-
-          const double d1 = phrases_.prob(p1p2, p0(p1p2)) * gen_.prob(false, gen_p0_);
-          double d2 = phrases_.prob(p1, p0(p1)) * gen_.prob(false, gen_p0_);
-          phrases_.increment(p1);
-          gen_.increment(false);
-          d2 *= phrases_.prob(p2, p0(p2)) * gen_.prob(false, gen_p0_);
-          phrases_.decrement(p1);
-          gen_.decrement(false);
-          z[j] = rng->SelectSample(d1, d2);
-
-          if (z[j]) {
-            phrases_.increment(p1);
-            phrases_.increment(p2);
-            gen_.increment(false);
-            gen_.increment(false);
-            prev = j + 1;
-          } else {
-            phrases_.increment(p1p2);
-            gen_.increment(false);
-          }
-        }
-      }
-    }
-//    cerr << endl << endl << gen_ << endl << phrases_ << endl;
-    cerr << gen_.prob(false, gen_p0_) << " " << gen_.prob(true, 1 - gen_p0_) << endl;
-  }
-
-  void WriteCdecGrammarForCurrentSample(ostream* os) const {
-    CCRP_NoTable<vector<int> >::const_iterator it = phrases_.begin();
-    for (; it != phrases_.end(); ++it) {
-      (*os) << "[X] ||| " << Join(' ', it->first) << " ||| "
-                          << Join('_', it->first) << " ||| C=1 P=" 
-                          << log(phrases_.prob(it->first, p0(it->first))) << endl;
-    }
-  }
-
-  double OOVUnigramLogProb() const {
-    vector<int> x(1,99999999);
-    return log(phrases_.prob(x, p0(x)));
-  }
-
-  void ResampleHyperparameters(MT19937* rng) {
-    phrases_.resample_hyperparameters(rng);
-    gen_.resample_hyperparameters(rng);
-    cerr << " " << phrases_.alpha();
-  }
-
-  CCRP_NoTable<vector<int> > phrases_;
-  CCRP_NoTable<bool> gen_;
-  vector<vector<bool> > z_;   // z_[i] is there a phrase boundary after the ith word
-  const vector<vector<int> >& corpus_;
-  const double uniform_word_;
-  const double gen_p0_;
-  const double p_end_; // in base length distribution, p of the end of a phrase
-  const bool use_poisson_;
-};
-
-
-int main(int argc, char** argv) {
-  po::variables_map conf;
-  InitCommandLine(argc, argv, &conf);
-  boost::shared_ptr<MT19937> prng;
-  if (conf.count("random_seed"))
-    prng.reset(new MT19937(conf["random_seed"].as<uint32_t>()));
-  else
-    prng.reset(new MT19937);
-  MT19937& rng = *prng;
-
-  vector<vector<int> > corpus;
-  set<int> vocab;
-  ReadCorpus(conf["input"].as<string>(), &corpus, &vocab);
-  cerr << "Corpus size: " << corpus.size() << " sentences\n";
-  cerr << "Vocabulary size: " << vocab.size() << " types\n";
-
-  UniphraseLM ulm(corpus, vocab, conf);
-  ulm.Sample(conf["samples"].as<unsigned>(), conf.count("no_hyperparameter_inference") == 0, &rng);
-  cerr << "OOV unigram prob: " << ulm.OOVUnigramLogProb() << endl;
-
-  for (unsigned i = 0; i < corpus.size(); ++i)
-    WriteSeg(corpus[i], ulm.z_[i], d);
-
-  if (conf.count("write_cdec_grammar")) {
-    string fname = conf["write_cdec_grammar"].as<string>();
-    cerr << "Writing model to " << fname << " ...\n";
-    WriteFile wf(fname);
-    ulm.WriteCdecGrammarForCurrentSample(wf.stream());
-  }
-
-  if (conf.count("write_cdec_weights")) {
-    string fname = conf["write_cdec_weights"].as<string>();
-    cerr << "Writing weights to " << fname << " .\n";
-    WriteFile wf(fname);
-    ostream& os = *wf.stream();
-    os << "# make C smaller to use more phrases\nP 1\nPassThrough " << ulm.OOVUnigramLogProb() << "\nC -3\n";
-  }
-
-  
-
-  return 0;
-}
-
diff --git a/phrasinator/train-phrasinator.pl b/phrasinator/train-phrasinator.pl
deleted file mode 100755
index c50b8e68..00000000
--- a/phrasinator/train-phrasinator.pl
+++ /dev/null
@@ -1,89 +0,0 @@
-#!/usr/bin/perl -w
-use strict;
-my $script_dir; BEGIN { use Cwd qw/ abs_path cwd /; use File::Basename; $script_dir = dirname(abs_path($0)); push @INC, $script_dir; }
-use Getopt::Long;
-use File::Spec qw (rel2abs);
-
-my $DECODER = "$script_dir/../decoder/cdec";
-my $TRAINER = "$script_dir/gibbs_train_plm_notables";
-
-die "Can't find $TRAINER" unless -f $TRAINER;
-die "Can't execute $TRAINER" unless -x $TRAINER;
-
-if (!GetOptions(
-	"decoder=s" => \$DECODER,
-)) { usage(); }
-
-die "Can't find $DECODER" unless -f $DECODER;
-die "Can't execute $DECODER" unless -x $DECODER;
-if (scalar @ARGV != 2) { usage(); }
-my $INFILE = shift @ARGV;
-my $OUTDIR = shift @ARGV;
-$OUTDIR = File::Spec->rel2abs($OUTDIR);
-print STDERR "      Input file: $INFILE\n";
-print STDERR "Output directory: $OUTDIR\n";
-open F, "<$INFILE" or die "Failed to open $INFILE for reading: $!";
-close F;
-die "Please remove existing directory $OUTDIR\n" if (-f $OUTDIR || -d $OUTDIR);
-
-my $CMD = "mkdir $OUTDIR";
-safesystem($CMD) or die "Failed to create directory $OUTDIR\n$!";
-
-my $grammar="$OUTDIR/grammar.gz";
-my $weights="$OUTDIR/weights";
-$CMD = "$TRAINER -w $weights -g $grammar -i $INFILE";
-safesystem($CMD) or die "Failed to train model!\n";
-my $cdecini = "$OUTDIR/cdec.ini";
-open C, ">$cdecini" or die "Failed to open $cdecini for writing: $!";
-
-print C <<EOINI;
-quiet=true
-formalism=scfg
-grammar=$grammar
-add_pass_through_rules=true
-weights=$OUTDIR/weights
-EOINI
-
-close C;
-
-print <<EOT;
-
-Model trained successfully.  Text can be decoded into phrasal units with
-the following command:
-
-  $DECODER -c $OUTDIR/cdec.ini < FILE.TXT
-
-EOT
-exit(0);
-
-sub usage {
-  print <<EOT;
-Usage: $0 [options] INPUT.TXT OUTPUT-DIRECTORY
-
-  Infers a phrasal segmentation model from the tokenized text in INPUT.TXT
-  and writes it to OUTPUT-DIRECTORY/ so that it can be applied to other
-  text or have its granularity altered.
-
-EOT
-  exit(1);
-}
-
-sub safesystem {
-  print STDERR "Executing: @_\n";
-  system(@_);
-  if ($? == -1) {
-      print STDERR "ERROR: Failed to execute: @_\n  $!\n";
-      exit(1);
-  }
-  elsif ($? & 127) {
-      printf STDERR "ERROR: Execution of: @_\n  died with signal %d, %s coredump\n",
-          ($? & 127),  ($? & 128) ? 'with' : 'without';
-      exit(1);
-  }
-  else {
-    my $exitcode = $? >> 8;
-    print STDERR "Exit code: $exitcode\n" if $exitcode;
-    return ! $exitcode;
-  }
-}
-
diff --git a/python/README.md b/python/README.md
index da9f9387..bea6190a 100644
--- a/python/README.md
+++ b/python/README.md
@@ -12,6 +12,10 @@ Compile a parallel corpus and a word alignment into a suffix array representatio
 
 	python -m cdec.sa.compile -f f.txt -e e.txt -a a.txt -o output/ -c extract.ini
 
+Or, if your parallel corpus is in a single-file format (with source and target sentences on a single line, separated by a triple pipe `|||`), use:
+
+	python -m cdec.sa.compile -b f-e.txt -a a.txt -o output/ -c extract.ini
+
 Extract grammar rules from the compiled corpus:
 	
 	cat input.txt | python -m cdec.sa.extract -c extract.ini -g grammars/
diff --git a/python/examples/cdec-mt.py b/python/examples/cdec-mt.py
new file mode 100644
index 00000000..9621df80
--- /dev/null
+++ b/python/examples/cdec-mt.py
@@ -0,0 +1,41 @@
+#!/usr/bin/env python
+import sys
+import argparse
+import logging
+import multiprocessing as mp
+import cdec
+
+decoder = None
+def make_decoder(config, weights):
+    global decoder
+    decoder = cdec.Decoder(config)
+    decoder.read_weights(weights)
+
+def translate(sentence):
+    global decoder
+    return decoder.translate(sentence).viterbi()
+
+def main():
+    logging.basicConfig(level=logging.INFO, format='%(message)s')
+
+    parser = argparse.ArgumentParser(description='Run multiple decoders concurrentely')
+    parser.add_argument('-c', '--config', required=True,
+                        help='decoder configuration')
+    parser.add_argument('-w', '--weights', required=True,
+                        help='feature weights')
+    parser.add_argument('-j', '--jobs', type=int, default=mp.cpu_count(),
+                        help='number of decoder instances')
+    parser.add_argument('-s', '--chunksize', type=int, default=10,
+                        help='number of sentences / chunk')
+    args = parser.parse_args()
+
+    with open(args.config) as config:
+        config = config.read()
+    logging.info('Starting %d workers; chunk size: %d', args.jobs, args.chunksize)
+    pool = mp.Pool(args.jobs, make_decoder, (config, args.weights))
+    for output in pool.imap(translate, sys.stdin, args.chunksize):
+        print(output.encode('utf8'))
+    logging.info('Shutting down workers...')
+
+if __name__ == '__main__':
+    main()
diff --git a/python/examples/rampion.py b/python/examples/rampion.py
new file mode 100644
index 00000000..30244cf7
--- /dev/null
+++ b/python/examples/rampion.py
@@ -0,0 +1,76 @@
+import argparse
+import logging
+from itertools import izip
+import cdec, cdec.score
+
+def evaluate(hyp, ref):
+    """ Compute BLEU score for a set of hypotheses+references """
+    return sum(cdec.score.BLEU(r).evaluate(h) for h, r in izip(hyp, ref)).score
+
+T1, T2, T3 = 5, 10, 20 # number of iterations (global, CCCP, SSD)
+K = 500 # k-best list size
+C = 1 # regularization coefficient
+eta = 1e-4 # step size
+cost = lambda c: 10 * (1 - c.score) # cost definition
+
+def rampion(decoder, sources, references):
+    # Empty k-best lists
+    candidate_sets = [cdec.score.BLEU(refs).candidate_set() for refs in references]
+    # Weight vector -> sparse
+    w = decoder.weights.tosparse()
+    w0 = w.copy()
+
+    N = len(sources)
+    for t in range(T1):
+        logging.info('Iteration {0}: translating...'.format(t+1))
+        # Get the hypergraphs and extend the k-best lists
+        hgs = []
+        for src, candidates in izip(sources, candidate_sets):
+            hg = decoder.translate(src)
+            hgs.append(hg)
+            candidates.add_kbest(hg, K)
+        # BLEU score for the previous iteration
+        score = evaluate((hg.viterbi() for hg in hgs), references)
+        logging.info('BLEU: {:.2f}'.format(100 * score))
+        logging.info('Optimizing...')
+        for _ in range(T2):
+            # y_i^+, h_i^+; i=1..N
+            plus = [max(candidates, key=lambda c: w.dot(c.fmap) - cost(c)).fmap
+                    for candidates in candidate_sets]
+            for _ in range(T3):
+                for fp, candidates in izip(plus, candidate_sets):
+                    # y^-, h^-
+                    fm = max(candidates, key=lambda c: w.dot(c.fmap) + cost(c)).fmap
+                    # update weights (line 11-12)
+                    w += eta * ((fp - fm) - C/N * (w - w0))
+        logging.info('Updated weight vector: {0}'.format(dict(w)))
+        # Update decoder weights
+        decoder.weights = w
+
+def main():
+    logging.basicConfig(level=logging.INFO, format='%(message)s')
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-c', '--config', help='cdec config', required=True)
+    parser.add_argument('-w', '--weights', help='initial weights', required=True)
+    parser.add_argument('-r', '--reference', help='reference file', required=True)
+    parser.add_argument('-s', '--source', help='source file', required=True)
+    args = parser.parse_args()
+
+    with open(args.config) as fp:
+        config = fp.read()
+
+    decoder = cdec.Decoder(config)
+    decoder.read_weights(args.weights)
+    with open(args.reference) as fp:
+        references = fp.readlines()
+    with open(args.source) as fp:
+        sources = fp.readlines()
+    assert len(references) == len(sources)
+    rampion(decoder, sources, references)
+
+    for fname, fval in sorted(dict(decoder.weights).iteritems()):
+        print('{0}\t{1}'.format(fname, fval))
+
+if __name__ == '__main__':
+    main()
diff --git a/python/test.py b/python/examples/test.py
index eb9e6a95..eb9e6a95 100644
--- a/python/test.py
+++ b/python/examples/test.py
diff --git a/python/pkg/cdec/__init__.py b/python/pkg/cdec/__init__.py
index 531fea49..8e10f340 100644
--- a/python/pkg/cdec/__init__.py
+++ b/python/pkg/cdec/__init__.py
@@ -1 +1,2 @@
-from cdec._cdec import Decoder, Lattice, TRule, MRule, NT, NTRef, ParseFailed, InvalidConfig
+from cdec._cdec import Decoder, Lattice, TRule, MRule, NT, NTRef,\
+        ParseFailed, InvalidConfig, set_silent
diff --git a/python/pkg/cdec/sa/__init__.py b/python/pkg/cdec/sa/__init__.py
index fd4a4148..e0a344b7 100644
--- a/python/pkg/cdec/sa/__init__.py
+++ b/python/pkg/cdec/sa/__init__.py
@@ -1,4 +1,24 @@
-from cdec.sa._sa import sym_fromstring,\
+from cdec.sa._sa import make_lattice, decode_lattice, decode_sentence,\
         SuffixArray, DataArray, LCP, Precomputation, Alignment, BiLex,\
-        HieroCachingRuleFactory, Sampler
+        HieroCachingRuleFactory, Sampler, Scorer
 from cdec.sa.extractor import GrammarExtractor
+
+_SA_FEATURES = []
+_SA_ANNOTATORS = {}
+_SA_CONFIGURE = []
+
+def feature(fn):
+    _SA_FEATURES.append(fn)
+    return fn
+
+def annotator(fn):
+    _SA_ANNOTATORS[fn.__name__] = fn
+
+def annotate(sentence):
+    meta = {}
+    for name, fn in _SA_ANNOTATORS.iteritems():
+        meta[name] = fn(sentence)
+    return meta
+
+def configure(fn):
+    _SA_CONFIGURE.append(fn)
diff --git a/python/pkg/cdec/sa/extract.py b/python/pkg/cdec/sa/extract.py
index 875bf42e..10a81556 100644
--- a/python/pkg/cdec/sa/extract.py
+++ b/python/pkg/cdec/sa/extract.py
@@ -3,29 +3,72 @@ import sys
 import os
 import argparse
 import logging
+import multiprocessing as mp
+import signal
 import cdec.sa
 
+extractor, prefix = None, None
+def make_extractor(config, grammars, features):
+    global extractor, prefix
+    signal.signal(signal.SIGINT, signal.SIG_IGN) # Let parent process catch Ctrl+C
+    load_features(features)
+    extractor = cdec.sa.GrammarExtractor(config)
+    prefix = grammars
+
+def load_features(features):
+    for featdef in features:
+        logging.info('Loading additional feature definitions from %s', featdef)
+        prefix = os.path.dirname(featdef)
+        sys.path.append(prefix)
+        __import__(os.path.basename(featdef).replace('.py', ''))
+        sys.path.remove(prefix)
+
+def extract(inp):
+    global extractor, prefix
+    i, sentence = inp
+    sentence = sentence[:-1]
+    grammar_file = os.path.join(prefix, 'grammar.{0}'.format(i))
+    with open(grammar_file, 'w') as output:
+        for rule in extractor.grammar(sentence):
+            output.write(str(rule)+'\n')
+    grammar_file = os.path.abspath(grammar_file)
+    return '<seg grammar="{0}" id="{1}">{2}</seg>'.format(grammar_file, i, sentence)
+
 def main():
     logging.basicConfig(level=logging.INFO)
     parser = argparse.ArgumentParser(description='Extract grammars from a compiled corpus.')
     parser.add_argument('-c', '--config', required=True,
-                        help='Extractor configuration')
+                        help='extractor configuration')
     parser.add_argument('-g', '--grammars', required=True,
-                        help='Grammar output path')
+                        help='grammar output path')
+    parser.add_argument('-j', '--jobs', type=int, default=1,
+                        help='number of parallel extractors')
+    parser.add_argument('-s', '--chunksize', type=int, default=10,
+                        help='number of sentences / chunk')
+    parser.add_argument('-f', '--features', nargs='*', default=[],
+                        help='additional feature definitions')
     args = parser.parse_args()
 
     if not os.path.exists(args.grammars):
         os.mkdir(args.grammars)
-
-    extractor = cdec.sa.GrammarExtractor(args.config)
-    for i, sentence in enumerate(sys.stdin):
-        sentence = sentence[:-1]
-        grammar_file = os.path.join(args.grammars, 'grammar.{0}'.format(i))
-        with open(grammar_file, 'w') as output:
-            for rule in extractor.grammar(sentence):
-                output.write(str(rule)+'\n')
-        grammar_file = os.path.abspath(grammar_file)
-        print('<seg grammar="{0}" id="{1}">{2}</seg>'.format(grammar_file, i, sentence))
+    for featdef in args.features:
+        if not featdef.endswith('.py'):
+            sys.stderr.write('Error: feature definition file <{0}>'
+                    ' should be a python module\n'.format(featdef))
+            sys.exit(1)
+    
+    if args.jobs > 1:
+        logging.info('Starting %d workers; chunk size: %d', args.jobs, args.chunksize)
+        pool = mp.Pool(args.jobs, make_extractor, (args.config, args.grammars, args.features))
+        try:
+            for output in pool.imap(extract, enumerate(sys.stdin), args.chunksize):
+                print(output)
+        except KeyboardInterrupt:
+            pool.terminate()
+    else:
+        make_extractor(args.config, args.grammars, args.features)
+        for output in map(extract, enumerate(sys.stdin)):
+            print(output)
 
 if __name__ == '__main__':
     main()
diff --git a/python/pkg/cdec/sa/extractor.py b/python/pkg/cdec/sa/extractor.py
index bb912e16..a5ce8a68 100644
--- a/python/pkg/cdec/sa/extractor.py
+++ b/python/pkg/cdec/sa/extractor.py
@@ -9,7 +9,7 @@ import cdec.sa
 MAX_INITIAL_SIZE = 15
 
 class GrammarExtractor:
-    def __init__(self, config):
+    def __init__(self, config, features=None):
         if isinstance(config, str) or isinstance(config, unicode):
             if not os.path.exists(config):
                 raise IOError('cannot read configuration from {0}'.format(config))
@@ -57,8 +57,11 @@ class GrammarExtractor:
         # lexical weighting tables
         tt = cdec.sa.BiLex(from_binary=config['lex_file'])
 
-        self.models = (EgivenFCoherent, SampleCountF, CountEF, 
-                MaxLexFgivenE(tt), MaxLexEgivenF(tt), IsSingletonF, IsSingletonFE)
+        # TODO: use @cdec.sa.features decorator for standard features too
+        # + add a mask to disable features
+        scorer = cdec.sa.Scorer(EgivenFCoherent, SampleCountF, CountEF, 
+            MaxLexFgivenE(tt), MaxLexEgivenF(tt), IsSingletonF, IsSingletonFE,
+            *cdec.sa._SA_FEATURES)
 
         fsarray = cdec.sa.SuffixArray(from_binary=config['f_sa_file'])
         edarray = cdec.sa.DataArray(from_binary=config['e_file'])
@@ -67,12 +70,15 @@ class GrammarExtractor:
         # -1 = don't sample, use all data (VERY SLOW!)
         sampler = cdec.sa.Sampler(300, fsarray)
 
-        self.factory.configure(fsarray, edarray, sampler)
+        self.factory.configure(fsarray, edarray, sampler, scorer)
+        # Initialize feature definitions with configuration
+        for fn in cdec.sa._SA_CONFIGURE:
+            fn(config)
 
     def grammar(self, sentence):
         if isinstance(sentence, unicode):
             sentence = sentence.encode('utf8')
-        cnet = chain(('<s>',), sentence.split(), ('</s>',))
-        cnet = (cdec.sa.sym_fromstring(word, terminal=True) for word in cnet)
-        cnet = tuple(((word, None, 1), ) for word in cnet)
-        return self.factory.input(cnet, self.models)
+        words = tuple(chain(('<s>',), sentence.split(), ('</s>',)))
+        meta = cdec.sa.annotate(words)
+        cnet = cdec.sa.make_lattice(words)
+        return self.factory.input(cnet, meta)
diff --git a/python/pkg/cdec/sa/features.py b/python/pkg/cdec/sa/features.py
index 325b9e13..a4ae23e8 100644
--- a/python/pkg/cdec/sa/features.py
+++ b/python/pkg/cdec/sa/features.py
@@ -3,55 +3,55 @@ import math
 
 MAXSCORE = 99
 
-def EgivenF(fphrase, ephrase, paircount, fcount, fsample_count): # p(e|f)
-    return -math.log10(paircount/fcount)
+def EgivenF(ctx): # p(e|f) = c(e, f)/c(f)
+    return -math.log10(ctx.paircount/ctx.fcount)
 
-def CountEF(fphrase, ephrase, paircount, fcount, fsample_count):
-    return math.log10(1 + paircount)
+def CountEF(ctx): # c(e, f)
+    return math.log10(1 + ctx.paircount)
 
-def SampleCountF(fphrase, ephrase, paircount, fcount, fsample_count):
-    return math.log10(1 + fsample_count)
+def SampleCountF(ctx): # sample c(f)
+    return math.log10(1 + ctx.fsample_count)
 
-def EgivenFCoherent(fphrase, ephrase, paircount, fcount, fsample_count):
-    prob = paircount/fsample_count
+def EgivenFCoherent(ctx): # c(e, f) / sample c(f)
+    prob = ctx.paircount/ctx.fsample_count
     return -math.log10(prob) if prob > 0 else MAXSCORE
 
-def CoherenceProb(fphrase, ephrase, paircount, fcount, fsample_count):
-    return -math.log10(fcount/fsample_count)
+def CoherenceProb(ctx): # c(f) / sample c(f)
+    return -math.log10(ctx.fcount/ctx.fsample_count)
 
 def MaxLexEgivenF(ttable):
-    def feature(fphrase, ephrase, paircount, fcount, fsample_count):
-        fwords = fphrase.words
+    def MaxLexEgivenF(ctx):
+        fwords = ctx.fphrase.words
         fwords.append('NULL')
         def score():
-            for e in ephrase.words:
+            for e in ctx.ephrase.words:
               maxScore = max(ttable.get_score(f, e, 0) for f in fwords)
               yield -math.log10(maxScore) if maxScore > 0 else MAXSCORE
         return sum(score())
-    return feature
+    return MaxLexEgivenF
 
 def MaxLexFgivenE(ttable):
-    def feature(fphrase, ephrase, paircount, fcount, fsample_count):
-        ewords = ephrase.words
+    def MaxLexFgivenE(ctx):
+        ewords = ctx.ephrase.words
         ewords.append('NULL')
         def score():
-            for f in fphrase.words:
+            for f in ctx.fphrase.words:
               maxScore = max(ttable.get_score(f, e, 1) for e in ewords)
               yield -math.log10(maxScore) if maxScore > 0 else MAXSCORE
         return sum(score())
-    return feature
+    return MaxLexFgivenE
 
-def IsSingletonF(fphrase, ephrase, paircount, fcount, fsample_count):
-    return (fcount == 1)
+def IsSingletonF(ctx):
+    return (ctx.fcount == 1)
 
-def IsSingletonFE(fphrase, ephrase, paircount, fcount, fsample_count):
-    return (paircount == 1)
+def IsSingletonFE(ctx):
+    return (ctx.paircount == 1)
 
-def IsNotSingletonF(fphrase, ephrase, paircount, fcount, fsample_count):
-    return (fcount > 1)
+def IsNotSingletonF(ctx):
+    return (ctx.fcount > 1)
 
-def IsNotSingletonFE(fphrase, ephrase, paircount, fcount, fsample_count):
-    return (paircount > 1)
+def IsNotSingletonFE(ctx):
+    return (ctx.paircount > 1)
 
-def IsFEGreaterThanZero(fphrase, ephrase, paircount, fcount, fsample_count):
-    return (paircount > 0.01)
+def IsFEGreaterThanZero(ctx):
+    return (ctx.paircount > 0.01)
diff --git a/python/setup.py b/python/setup.py
deleted file mode 100644
index cced4c1a..00000000
--- a/python/setup.py
+++ /dev/null
@@ -1,53 +0,0 @@
-from distutils.core import setup
-from distutils.extension import Extension
-import sys
-import os
-import glob
-
-INC = ['..', 'src/', '../decoder', '../utils', '../mteval']
-LIB = ['../decoder', '../utils', '../mteval', '../training', '../klm/lm', '../klm/util']
-LINK_ARGS = ['-lz']
-
-# Detect Boost
-BOOST_ROOT = os.getenv('BOOST_ROOT')
-if BOOST_ROOT:
-    BOOST_INC = os.path.join(BOOST_ROOT, 'include')
-    BOOST_LIB = os.path.join(BOOST_ROOT, 'lib')
-    if not os.path.exists(BOOST_INC):
-        sys.stderr.write('Error: could not find Boost headers in <%s>\n' % BOOST_INC)
-        sys.exit(1)
-    if not os.path.exists(BOOST_LIB):
-        sys.stderr.write('Error: could not find Boost libraries in <%s>\n' % BOOST_LIB)
-        sys.exit(1)
-    INC.append(BOOST_INC)
-    LIB.append(BOOST_LIB)
-    LINK_ARGS += ['-Wl,-rpath', '-Wl,'+BOOST_LIB]
-else:
-    BOOST_LIB = '/usr/local/lib'
-
-# Detect -mt
-if glob.glob(os.path.join(BOOST_LIB, 'libboost_program_options-mt.*')):
-    BOOST_PROGRAM_OPTIONS = 'boost_program_options-mt'
-else:
-    BOOST_PROGRAM_OPTIONS = 'boost_program_options'
-
-ext_modules = [
-    Extension(name='cdec._cdec',
-        sources=['src/_cdec.cpp'],
-        include_dirs=INC,
-        library_dirs=LIB,
-        libraries=[BOOST_PROGRAM_OPTIONS, 'z',
-                   'cdec', 'utils', 'mteval', 'training', 'klm', 'klm_util'],
-        extra_compile_args=['-DHAVE_CONFIG_H'],
-        extra_link_args=LINK_ARGS),
-    Extension(name='cdec.sa._sa',
-        sources=['src/sa/_sa.c', 'src/sa/strmap.cc'])
-]
-
-setup(
-    name='cdec',
-    ext_modules=ext_modules,
-    requires=['configobj'],
-    packages=['cdec', 'cdec.sa'],
-    package_dir={'': 'pkg'}
-)
diff --git a/python/setup.py.in b/python/setup.py.in
new file mode 100644
index 00000000..f191ef8b
--- /dev/null
+++ b/python/setup.py.in
@@ -0,0 +1,33 @@
+from distutils.core import setup
+from distutils.extension import Extension
+import re
+
+INC = ['..', 'src/', '../decoder', '../utils', '../mteval']
+LIB = ['../decoder', '../utils', '../mteval', '../training', '../klm/lm', '../klm/util', '../klm/search']
+
+# Set automatically by configure
+LIBS = re.findall('-l([^\s]+)', '@LIBS@')
+CPPFLAGS = re.findall('-[^\s]+', '@CPPFLAGS@')
+LDFLAGS = re.findall('-[^\s]+', '@LDFLAGS@')
+# Make sure linker flags go only to the linker
+LDFLAGS = [opt.replace('-R', '-Wl,-rpath,') for opt in LDFLAGS]
+
+ext_modules = [
+    Extension(name='cdec._cdec',
+        sources=['src/_cdec.cpp'],
+        include_dirs=INC,
+        library_dirs=LIB,
+        libraries=LIBS + ['z', 'cdec', 'utils', 'mteval', 'training', 'klm', 'klm_util', 'ksearch'],
+        extra_compile_args=CPPFLAGS,
+        extra_link_args=LDFLAGS),
+    Extension(name='cdec.sa._sa',
+        sources=['src/sa/_sa.c', 'src/sa/strmap.cc'])
+]
+
+setup(
+    name='cdec',
+    ext_modules=ext_modules,
+    requires=['configobj'],
+    packages=['cdec', 'cdec.sa'],
+    package_dir={'': 'pkg'}
+)
diff --git a/python/src/_cdec.cpp b/python/src/_cdec.cpp
index dcd33448..c8d50a4f 100644
--- a/python/src/_cdec.cpp
+++ b/python/src/_cdec.cpp
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.17.beta1 on Sun Jul 29 23:00:27 2012 */
+/* Generated by Cython 0.17.1 on Tue Oct 16 01:04:11 2012 */
 
 #define PY_SSIZE_T_CLEAN
 #include "Python.h"
@@ -11,7 +11,6 @@
 #ifndef offsetof
 #define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
 #endif
-
 #if !defined(WIN32) && !defined(MS_WINDOWS)
   #ifndef __stdcall
     #define __stdcall
@@ -23,22 +22,18 @@
     #define __fastcall
   #endif
 #endif
-
 #ifndef DL_IMPORT
   #define DL_IMPORT(t) t
 #endif
 #ifndef DL_EXPORT
   #define DL_EXPORT(t) t
 #endif
-
 #ifndef PY_LONG_LONG
   #define PY_LONG_LONG LONG_LONG
 #endif
-
 #ifndef Py_HUGE_VAL
   #define Py_HUGE_VAL HUGE_VAL
 #endif
-
 #ifdef PYPY_VERSION
 #define CYTHON_COMPILING_IN_PYPY 1
 #define CYTHON_COMPILING_IN_CPYTHON 0
@@ -46,12 +41,12 @@
 #define CYTHON_COMPILING_IN_PYPY 0
 #define CYTHON_COMPILING_IN_CPYTHON 1
 #endif
-
 #if PY_VERSION_HEX < 0x02050000
   typedef int Py_ssize_t;
   #define PY_SSIZE_T_MAX INT_MAX
   #define PY_SSIZE_T_MIN INT_MIN
   #define PY_FORMAT_SIZE_T ""
+  #define CYTHON_FORMAT_SSIZE_T ""
   #define PyInt_FromSsize_t(z) PyInt_FromLong(z)
   #define PyInt_AsSsize_t(o)   __Pyx_PyInt_AsInt(o)
   #define PyNumber_Index(o)    ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
@@ -63,8 +58,8 @@
   #define __PYX_BUILD_PY_SSIZE_T "i"
 #else
   #define __PYX_BUILD_PY_SSIZE_T "n"
+  #define CYTHON_FORMAT_SSIZE_T "z"
 #endif
-
 #if PY_VERSION_HEX < 0x02060000
   #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
   #define Py_TYPE(ob)   (((PyObject*)(ob))->ob_type)
@@ -72,7 +67,6 @@
   #define PyVarObject_HEAD_INIT(type, size) \
           PyObject_HEAD_INIT(type) size,
   #define PyType_Modified(t)
-
   typedef struct {
      void *buf;
      PyObject *obj;
@@ -86,7 +80,6 @@
      Py_ssize_t *suboffsets;
      void *internal;
   } Py_buffer;
-
   #define PyBUF_SIMPLE 0
   #define PyBUF_WRITABLE 0x0001
   #define PyBUF_FORMAT 0x0004
@@ -98,11 +91,9 @@
   #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
   #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
   #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
-
   typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
   typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
 #endif
-
 #if PY_MAJOR_VERSION < 3
   #define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
   #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
@@ -112,21 +103,16 @@
   #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
           PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
 #endif
-
 #if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
   #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
 #endif
-
 #if PY_MAJOR_VERSION >= 3
   #define Py_TPFLAGS_CHECKTYPES 0
   #define Py_TPFLAGS_HAVE_INDEX 0
 #endif
-
 #if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
   #define Py_TPFLAGS_HAVE_NEWBUFFER 0
 #endif
-
-
 #if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
   #define CYTHON_PEP393_ENABLED 1
   #define __Pyx_PyUnicode_READY(op)       (likely(PyUnicode_IS_READY(op)) ? \
@@ -139,10 +125,8 @@
   #define __Pyx_PyUnicode_READY(op)       (0)
   #define __Pyx_PyUnicode_GET_LENGTH(u)   PyUnicode_GET_SIZE(u)
   #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
-
   #define __Pyx_PyUnicode_READ(k, d, i)   ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
 #endif
-
 #if PY_MAJOR_VERSION >= 3
   #define PyBaseString_Type            PyUnicode_Type
   #define PyStringObject               PyUnicodeObject
@@ -150,7 +134,6 @@
   #define PyString_Check               PyUnicode_Check
   #define PyString_CheckExact          PyUnicode_CheckExact
 #endif
-
 #if PY_VERSION_HEX < 0x02060000
   #define PyBytesObject                PyStringObject
   #define PyBytes_Type                 PyString_Type
@@ -169,7 +152,6 @@
   #define PyBytes_Concat               PyString_Concat
   #define PyBytes_ConcatAndDel         PyString_ConcatAndDel
 #endif
-
 #if PY_VERSION_HEX < 0x02060000
   #define PySet_Check(obj)             PyObject_TypeCheck(obj, &PySet_Type)
   #define PyFrozenSet_Check(obj)       PyObject_TypeCheck(obj, &PyFrozenSet_Type)
@@ -177,9 +159,7 @@
 #ifndef PySet_CheckExact
   #define PySet_CheckExact(obj)        (Py_TYPE(obj) == &PySet_Type)
 #endif
-
 #define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
-
 #if PY_MAJOR_VERSION >= 3
   #define PyIntObject                  PyLongObject
   #define PyInt_Type                   PyLong_Type
@@ -196,11 +176,9 @@
   #define PyInt_AsUnsignedLongMask     PyLong_AsUnsignedLongMask
   #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
 #endif
-
 #if PY_MAJOR_VERSION >= 3
   #define PyBoolObject                 PyLongObject
 #endif
-
 #if PY_VERSION_HEX < 0x03020000
   typedef long Py_hash_t;
   #define __Pyx_PyInt_FromHash_t PyInt_FromLong
@@ -209,7 +187,6 @@
   #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
   #define __Pyx_PyInt_AsHash_t   PyInt_AsSsize_t
 #endif
-
 #if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300)
   #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
   #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
@@ -228,11 +205,9 @@
         (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \
             (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1)))
 #endif
-
 #if PY_MAJOR_VERSION >= 3
   #define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
 #endif
-
 #if PY_VERSION_HEX < 0x02050000
   #define __Pyx_GetAttrString(o,n)   PyObject_GetAttrString((o),((char *)(n)))
   #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a))
@@ -242,7 +217,6 @@
   #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a))
   #define __Pyx_DelAttrString(o,n)   PyObject_DelAttrString((o),(n))
 #endif
-
 #if PY_VERSION_HEX < 0x02050000
   #define __Pyx_NAMESTR(n) ((char *)(n))
   #define __Pyx_DOCSTR(n)  ((char *)(n))
@@ -251,6 +225,7 @@
   #define __Pyx_DOCSTR(n)  (n)
 #endif
 
+
 #if PY_MAJOR_VERSION >= 3
   #define __Pyx_PyNumber_Divide(x,y)         PyNumber_TrueDivide(x,y)
   #define __Pyx_PyNumber_InPlaceDivide(x,y)  PyNumber_InPlaceTrueDivide(x,y)
@@ -275,6 +250,10 @@
 #define __PYX_HAVE_API___cdec
 #include "string.h"
 #include <string>
+#include "ios"
+#include "new"
+#include "stdexcept"
+#include "typeinfo"
 #include <vector>
 #include <utility>
 #include <iostream>
@@ -303,6 +282,7 @@
 #include "decoder/ff_register.h"
 #include "decoder/decoder.h"
 #include "observer.h"
+#include "stdio.h"
 #include "decoder/kbest.h"
 #include "mteval/ns.h"
 #include "py_scorer.h"
@@ -404,14 +384,17 @@ static const char *__pyx_f[] = {
 };
 
 /*--- Type declarations ---*/
-struct __pyx_obj_5_cdec_Scorer;
+struct __pyx_obj_4cdec_2sa_3_sa_FeatureVector;
+struct __pyx_obj_5_cdec___pyx_scope_struct_24___init__;
 struct __pyx_obj_5_cdec_NTRef;
-struct __pyx_obj_5_cdec___pyx_scope_struct_23___cinit__;
-struct __pyx_obj_5_cdec___pyx_scope_struct_24_genexpr;
+struct __pyx_obj_5_cdec_Scorer;
+struct __pyx_obj_4cdec_2sa_3_sa_IntList;
 struct __pyx_obj_4cdec_2sa_3_sa_Phrase;
+struct __pyx_obj_5_cdec___pyx_scope_struct_22___iter__;
 struct __pyx_obj_5_cdec_Grammar;
+struct __pyx_obj_5_cdec___pyx_scope_struct_20_lines;
+struct __pyx_obj_5_cdec___pyx_scope_struct_12_sample_trees;
 struct __pyx_obj_5_cdec___pyx_scope_struct_13___get__;
-struct __pyx_obj_5_cdec___pyx_scope_struct_18_todot;
 struct __pyx_obj_5_cdec___pyx_scope_struct_2__phrase;
 struct __pyx_obj_5_cdec_CandidateSet;
 struct __pyx_obj_5_cdec___pyx_scope_struct_14___get__;
@@ -419,18 +402,21 @@ struct __pyx_obj_5_cdec_TRule;
 struct __pyx_obj_4cdec_2sa_3_sa_Rule;
 struct __pyx_obj_5_cdec_MRule;
 struct __pyx_obj_5_cdec_SegmentEvaluator;
-struct __pyx_obj_5_cdec___pyx_scope_struct_20___iter__;
+struct __pyx_obj_5_cdec___pyx_scope_struct_25_genexpr;
+struct __pyx_obj_5_cdec___pyx_scope_struct_19_todot;
 struct __pyx_obj_5_cdec_Candidate;
 struct __pyx_obj_5_cdec___pyx_scope_struct_6_genexpr;
 struct __pyx_obj_5_cdec_NT;
+struct __pyx_obj_4cdec_2sa_3_sa_FloatList;
 struct __pyx_obj_5_cdec_HypergraphEdge;
 struct __pyx_obj_5_cdec___pyx_scope_struct_1___iter__;
 struct __pyx_obj_5_cdec___pyx_scope_struct_16___get__;
 struct __pyx_obj_5_cdec___pyx_scope_struct_4___get__;
+struct __pyx_obj_5_cdec___pyx_scope_struct_18___iter__;
 struct __pyx_obj_5_cdec_Decoder;
 struct __pyx_obj_5_cdec_HypergraphNode;
 struct __pyx_obj_5_cdec_SparseVector;
-struct __pyx_obj_5_cdec___pyx_scope_struct_17___iter__;
+struct __pyx_obj_5_cdec___pyx_scope_struct_17___get__;
 struct __pyx_obj_5_cdec___pyx_scope_struct____iter__;
 struct __pyx_obj_5_cdec___pyx_scope_struct_21___iter__;
 struct __pyx_obj_5_cdec_DenseVector;
@@ -446,16 +432,14 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_9_kbest_trees;
 struct __pyx_obj_5_cdec_Hypergraph;
 struct __pyx_obj_5_cdec_Lattice;
 struct __pyx_obj_5_cdec___pyx_scope_struct_11_sample;
-struct __pyx_obj_5_cdec___pyx_scope_struct_12___get__;
-struct __pyx_obj_5_cdec___pyx_scope_struct_22__make_config;
+struct __pyx_obj_5_cdec___pyx_scope_struct_23__make_config;
 struct __pyx_obj_5_cdec_TextGrammar;
-struct __pyx_obj_5_cdec___pyx_scope_struct_19_lines;
 struct __pyx_opt_args_5_cdec_as_str;
 
 /* "_cdec.pyx":6
  * cimport decoder
  * 
- * cdef char* as_str(data, char* error_msg='Cannot convert type %s to str'):             # <<<<<<<<<<<<<<
+ * cdef bytes as_str(data, char* error_msg='Cannot convert type %s to str'):             # <<<<<<<<<<<<<<
  *     cdef bytes ret
  *     if isinstance(data, unicode):
  */
@@ -464,21 +448,34 @@ struct __pyx_opt_args_5_cdec_as_str {
   char *error_msg;
 };
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":117
- *         return CandidateSet(self)
+/* "/home/vchahune/tools/cdec/python/src/cdec.sa._sa.pxd":25
+ *     cdef void read_handle(self, FILE* f)
  * 
- * cdef class Scorer:             # <<<<<<<<<<<<<<
- *     cdef string* name
- *     cdef mteval.EvaluationMetric* metric
+ * cdef class FeatureVector:             # <<<<<<<<<<<<<<
+ *     cdef IntList names
+ *     cdef FloatList values
  */
-struct __pyx_obj_5_cdec_Scorer {
+struct __pyx_obj_4cdec_2sa_3_sa_FeatureVector {
   PyObject_HEAD
-  std::string *name;
-  EvaluationMetric *metric;
+  struct __pyx_obj_4cdec_2sa_3_sa_IntList *names;
+  struct __pyx_obj_4cdec_2sa_3_sa_FloatList *values;
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":20
+/* "_cdec.pyx":47
+ *     cdef DenseVector weights
+ * 
+ *     def __init__(self, config_str=None, **config):             # <<<<<<<<<<<<<<
+ *         """Decoder('formalism = scfg') -> initialize from configuration string
+ *         Decoder(formalism='scfg') -> initialize from named parameters
+ */
+struct __pyx_obj_5_cdec___pyx_scope_struct_24___init__ {
+  PyObject_HEAD
+  PyObject *__pyx_v_config;
+};
+
+
+/* "/home/vchahune/tools/cdec/python/src/grammar.pxi":21
  *         return '[%s]' % self.cat
  * 
  * cdef class NTRef:             # <<<<<<<<<<<<<<
@@ -491,37 +488,40 @@ struct __pyx_obj_5_cdec_NTRef {
 };
 
 
-/* "_cdec.pyx":43
- *     cdef DenseVector weights
+/* "/home/vchahune/tools/cdec/python/src/mteval.pxi":121
+ *         return CandidateSet(self)
  * 
- *     def __cinit__(self, config_str=None, **config):             # <<<<<<<<<<<<<<
- *         """ Configuration can be given as a string:
- *                 Decoder('formalism = scfg')
+ * cdef class Scorer:             # <<<<<<<<<<<<<<
+ *     cdef string* name
+ *     cdef mteval.EvaluationMetric* metric
  */
-struct __pyx_obj_5_cdec___pyx_scope_struct_23___cinit__ {
+struct __pyx_obj_5_cdec_Scorer {
   PyObject_HEAD
-  PyObject *__pyx_v_config;
+  std::string *name;
+  EvaluationMetric *metric;
 };
 
 
-/* "_cdec.pyx":54
- *                     'csplit', 'tagger', 'lexalign'):
- *                 raise InvalidConfig('formalism "%s" unknown' % formalism)
- *             config_str = '\n'.join('%s = %s' % kv for kv in _make_config(config))             # <<<<<<<<<<<<<<
- *         cdef istringstream* config_stream = new istringstream(config_str)
- *         self.dec = new decoder.Decoder(config_stream)
+/* "/home/vchahune/tools/cdec/python/src/cdec.sa._sa.pxd":12
+ *     cdef void read_handle(self, FILE* f)
+ * 
+ * cdef class IntList:             # <<<<<<<<<<<<<<
+ *     cdef int size
+ *     cdef int increment
  */
-struct __pyx_obj_5_cdec___pyx_scope_struct_24_genexpr {
+struct __pyx_obj_4cdec_2sa_3_sa_IntList {
   PyObject_HEAD
-  struct __pyx_obj_5_cdec___pyx_scope_struct_23___cinit__ *__pyx_outer_scope;
-  PyObject *__pyx_v_kv;
-  PyObject *__pyx_t_0;
-  Py_ssize_t __pyx_t_1;
-  PyObject *(*__pyx_t_2)(PyObject *);
+  struct __pyx_vtabstruct_4cdec_2sa_3_sa_IntList *__pyx_vtab;
+  int size;
+  int increment;
+  int len;
+  int *arr;
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/cdec.sa._sa.pxd":1
+/* "/home/vchahune/tools/cdec/python/src/cdec.sa._sa.pxd":29
+ *     cdef FloatList values
+ * 
  * cdef class Phrase:             # <<<<<<<<<<<<<<
  *     cdef int *syms
  *     cdef int n, *varpos, n_vars
@@ -536,8 +536,24 @@ struct __pyx_obj_4cdec_2sa_3_sa_Phrase {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":181
- *         super(MRule, self).__init__(lhs, rhs, e, scores, a)
+/* "/home/vchahune/tools/cdec/python/src/mteval.pxi":90
+ *         return candidate
+ * 
+ *     def __iter__(self):             # <<<<<<<<<<<<<<
+ *         cdef unsigned i
+ *         for i in range(len(self)):
+ */
+struct __pyx_obj_5_cdec___pyx_scope_struct_22___iter__ {
+  PyObject_HEAD
+  unsigned int __pyx_v_i;
+  struct __pyx_obj_5_cdec_CandidateSet *__pyx_v_self;
+  Py_ssize_t __pyx_t_0;
+  unsigned int __pyx_t_1;
+};
+
+
+/* "/home/vchahune/tools/cdec/python/src/grammar.pxi":193
+ *         super(MRule, self).__init__(lhs, rhs, e, scores, None)
  * 
  * cdef class Grammar:             # <<<<<<<<<<<<<<
  *     cdef shared_ptr[grammar.Grammar]* grammar
@@ -549,36 +565,64 @@ struct __pyx_obj_5_cdec_Grammar {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":119
+/* "/home/vchahune/tools/cdec/python/src/lattice.pxi":63
+ *     def todot(self):
+ *         """lattice.todot() -> Representation of the lattice in GraphViz dot format."""
+ *         def lines():             # <<<<<<<<<<<<<<
+ *             yield 'digraph lattice {'
+ *             yield 'rankdir = LR;'
+ */
+struct __pyx_obj_5_cdec___pyx_scope_struct_20_lines {
+  PyObject_HEAD
+  struct __pyx_obj_5_cdec___pyx_scope_struct_19_todot *__pyx_outer_scope;
+  PyObject *__pyx_v_delta;
+  PyObject *__pyx_v_i;
+  PyObject *__pyx_v_label;
+  PyObject *__pyx_v_weight;
+  Py_ssize_t __pyx_t_0;
+  PyObject *__pyx_t_1;
+  PyObject *(*__pyx_t_2)(PyObject *);
+  PyObject *__pyx_t_3;
+  Py_ssize_t __pyx_t_4;
+  PyObject *(*__pyx_t_5)(PyObject *);
+};
+
+
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":103
+ *             del hypos
  * 
- *     property nodes:
- *         def __get__(self):             # <<<<<<<<<<<<<<
- *             cdef unsigned i
- *             for i in range(self.hg.nodes_.size()):
+ *     def sample_trees(self, unsigned n):             # <<<<<<<<<<<<<<
+ *        """hg.sample_trees(n) -> Sample of n trees from the hypergraph."""
+ *        cdef vector[string]* trees = new vector[string]()
  */
-struct __pyx_obj_5_cdec___pyx_scope_struct_13___get__ {
+struct __pyx_obj_5_cdec___pyx_scope_struct_12_sample_trees {
   PyObject_HEAD
-  unsigned int __pyx_v_i;
+  unsigned int __pyx_v_k;
+  unsigned int __pyx_v_n;
   struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self;
+  std::vector<std::string> *__pyx_v_trees;
   size_t __pyx_t_0;
   unsigned int __pyx_t_1;
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/lattice.pxi":57
- *             yield self[i]
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":156
  * 
- *     def todot(self):             # <<<<<<<<<<<<<<
- *         def lines():
- *             yield 'digraph lattice {'
+ *     property edges:
+ *         def __get__(self):             # <<<<<<<<<<<<<<
+ *             cdef unsigned i
+ *             for i in range(self.hg.edges_.size()):
  */
-struct __pyx_obj_5_cdec___pyx_scope_struct_18_todot {
+struct __pyx_obj_5_cdec___pyx_scope_struct_13___get__ {
   PyObject_HEAD
-  struct __pyx_obj_5_cdec_Lattice *__pyx_v_self;
+  unsigned int __pyx_v_i;
+  struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self;
+  size_t __pyx_t_0;
+  unsigned int __pyx_t_1;
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":5
+/* "/home/vchahune/tools/cdec/python/src/grammar.pxi":5
  * import cdec.sa._sa as _sa
  * 
  * def _phrase(phrase):             # <<<<<<<<<<<<<<
@@ -591,7 +635,7 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_2__phrase {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":65
+/* "/home/vchahune/tools/cdec/python/src/mteval.pxi":65
  *         return result
  * 
  * cdef class CandidateSet:             # <<<<<<<<<<<<<<
@@ -606,23 +650,23 @@ struct __pyx_obj_5_cdec_CandidateSet {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":167
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":162
  * 
- *     property tail_nodes:
+ *     property nodes:
  *         def __get__(self):             # <<<<<<<<<<<<<<
  *             cdef unsigned i
- *             for i in range(self.edge.tail_nodes_.size()):
+ *             for i in range(self.hg.nodes_.size()):
  */
 struct __pyx_obj_5_cdec___pyx_scope_struct_14___get__ {
   PyObject_HEAD
   unsigned int __pyx_v_i;
-  struct __pyx_obj_5_cdec_HypergraphEdge *__pyx_v_self;
-  unsigned int __pyx_t_0;
+  struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self;
+  size_t __pyx_t_0;
   unsigned int __pyx_t_1;
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":50
+/* "/home/vchahune/tools/cdec/python/src/grammar.pxi":49
  *     return TRule(lhs, f, e, scores, a)
  * 
  * cdef class TRule:             # <<<<<<<<<<<<<<
@@ -635,11 +679,11 @@ struct __pyx_obj_5_cdec_TRule {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/cdec.sa._sa.pxd":7
+/* "/home/vchahune/tools/cdec/python/src/cdec.sa._sa.pxd":35
  *     cdef public int chunklen(self, int k)
  * 
  * cdef class Rule:             # <<<<<<<<<<<<<<
- *     cdef public int lhs
+ *     cdef int lhs
  *     cdef readonly Phrase f, e
  */
 struct __pyx_obj_4cdec_2sa_3_sa_Rule {
@@ -647,25 +691,25 @@ struct __pyx_obj_4cdec_2sa_3_sa_Rule {
   int lhs;
   struct __pyx_obj_4cdec_2sa_3_sa_Phrase *f;
   struct __pyx_obj_4cdec_2sa_3_sa_Phrase *e;
-  float *cscores;
+  struct __pyx_obj_4cdec_2sa_3_sa_FeatureVector *scores;
   int n_scores;
   PyObject *word_alignments;
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":169
+/* "/home/vchahune/tools/cdec/python/src/grammar.pxi":177
  *                 _phrase(self.f), _phrase(self.e), scores)
  * 
  * cdef class MRule(TRule):             # <<<<<<<<<<<<<<
- *     def __init__(self, lhs, rhs, scores, a=None):
- *         cdef unsigned i = 1
+ *     def __init__(self, lhs, rhs, scores):
+ *         """MRule(lhs, rhs, scores, a=None) -> Monolingual rule.
  */
 struct __pyx_obj_5_cdec_MRule {
   struct __pyx_obj_5_cdec_TRule __pyx_base;
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":98
+/* "/home/vchahune/tools/cdec/python/src/mteval.pxi":100
  *         self.cs.AddKBestCandidates(hypergraph.hg[0], k, self.scorer.get())
  * 
  * cdef class SegmentEvaluator:             # <<<<<<<<<<<<<<
@@ -679,24 +723,37 @@ struct __pyx_obj_5_cdec_SegmentEvaluator {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":44
- *         return self.stats.size()
- * 
- *     def __iter__(self):             # <<<<<<<<<<<<<<
- *         for i in range(len(self)):
- *             yield self[i]
+/* "_cdec.pyx":56
+ *                     'csplit', 'tagger', 'lexalign'):
+ *                 raise InvalidConfig('formalism "%s" unknown' % formalism)
+ *             config_str = '\n'.join('%s = %s' % kv for kv in _make_config(config))             # <<<<<<<<<<<<<<
+ *         cdef istringstream* config_stream = new istringstream(config_str)
+ *         self.dec = new decoder.Decoder(config_stream)
  */
-struct __pyx_obj_5_cdec___pyx_scope_struct_20___iter__ {
+struct __pyx_obj_5_cdec___pyx_scope_struct_25_genexpr {
   PyObject_HEAD
-  PyObject *__pyx_v_i;
-  struct __pyx_obj_5_cdec_SufficientStats *__pyx_v_self;
-  Py_ssize_t __pyx_t_0;
-  PyObject *__pyx_t_1;
+  struct __pyx_obj_5_cdec___pyx_scope_struct_24___init__ *__pyx_outer_scope;
+  PyObject *__pyx_v_kv;
+  PyObject *__pyx_t_0;
+  Py_ssize_t __pyx_t_1;
   PyObject *(*__pyx_t_2)(PyObject *);
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":12
+/* "/home/vchahune/tools/cdec/python/src/lattice.pxi":61
+ *             yield self[i]
+ * 
+ *     def todot(self):             # <<<<<<<<<<<<<<
+ *         """lattice.todot() -> Representation of the lattice in GraphViz dot format."""
+ *         def lines():
+ */
+struct __pyx_obj_5_cdec___pyx_scope_struct_19_todot {
+  PyObject_HEAD
+  struct __pyx_obj_5_cdec_Lattice *__pyx_v_self;
+};
+
+
+/* "/home/vchahune/tools/cdec/python/src/mteval.pxi":12
  *         return stats
  * 
  * cdef class Candidate:             # <<<<<<<<<<<<<<
@@ -710,7 +767,7 @@ struct __pyx_obj_5_cdec_Candidate {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":165
+/* "/home/vchahune/tools/cdec/python/src/grammar.pxi":173
  * 
  *     def __str__(self):
  *         scores = ' '.join('%s=%s' % feat for feat in self.scores)             # <<<<<<<<<<<<<<
@@ -727,7 +784,7 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_6_genexpr {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":8
+/* "/home/vchahune/tools/cdec/python/src/grammar.pxi":8
  *     return ' '.join(w.encode('utf8') if isinstance(w, unicode) else str(w) for w in phrase)
  * 
  * cdef class NT:             # <<<<<<<<<<<<<<
@@ -741,7 +798,24 @@ struct __pyx_obj_5_cdec_NT {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":147
+/* "/home/vchahune/tools/cdec/python/src/cdec.sa._sa.pxd":3
+ * from libc.stdio cimport FILE
+ * 
+ * cdef class FloatList:             # <<<<<<<<<<<<<<
+ *     cdef int size
+ *     cdef int increment
+ */
+struct __pyx_obj_4cdec_2sa_3_sa_FloatList {
+  PyObject_HEAD
+  struct __pyx_vtabstruct_4cdec_2sa_3_sa_FloatList *__pyx_vtab;
+  int size;
+  int increment;
+  int len;
+  float *arr;
+};
+
+
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":191
  *         return vector
  * 
  * cdef class HypergraphEdge:             # <<<<<<<<<<<<<<
@@ -757,7 +831,7 @@ struct __pyx_obj_5_cdec_HypergraphEdge {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":67
+/* "/home/vchahune/tools/cdec/python/src/vectors.pxi":72
  *         self.vector.set_value(fid, value)
  * 
  *     def __iter__(self):             # <<<<<<<<<<<<<<
@@ -774,12 +848,12 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_1___iter__ {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":209
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":247
  * 
- *     property out_edges:
+ *     property in_edges:
  *         def __get__(self):             # <<<<<<<<<<<<<<
  *             cdef unsigned i
- *             for i in range(self.node.out_edges_.size()):
+ *             for i in range(self.node.in_edges_.size()):
  */
 struct __pyx_obj_5_cdec___pyx_scope_struct_16___get__ {
   PyObject_HEAD
@@ -790,7 +864,7 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_16___get__ {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":124
+/* "/home/vchahune/tools/cdec/python/src/grammar.pxi":131
  * 
  *     property a:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -807,8 +881,24 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_4___get__ {
 };
 
 
-/* "_cdec.pyx":39
- *             yield key, bytes(value)
+/* "/home/vchahune/tools/cdec/python/src/lattice.pxi":56
+ *         return unicode(str(self), 'utf8')
+ * 
+ *     def __iter__(self):             # <<<<<<<<<<<<<<
+ *         cdef unsigned i
+ *         for i in range(len(self)):
+ */
+struct __pyx_obj_5_cdec___pyx_scope_struct_18___iter__ {
+  PyObject_HEAD
+  unsigned int __pyx_v_i;
+  struct __pyx_obj_5_cdec_Lattice *__pyx_v_self;
+  Py_ssize_t __pyx_t_0;
+  unsigned int __pyx_t_1;
+};
+
+
+/* "_cdec.pyx":43
+ *             yield key, str(value)
  * 
  * cdef class Decoder:             # <<<<<<<<<<<<<<
  *     cdef decoder.Decoder* dec
@@ -821,7 +911,7 @@ struct __pyx_obj_5_cdec_Decoder {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":193
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":237
  *         raise NotImplemented('comparison not implemented for HypergraphEdge')
  * 
  * cdef class HypergraphNode:             # <<<<<<<<<<<<<<
@@ -836,7 +926,7 @@ struct __pyx_obj_5_cdec_HypergraphNode {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":45
+/* "/home/vchahune/tools/cdec/python/src/vectors.pxi":48
  *         return sparse
  * 
  * cdef class SparseVector:             # <<<<<<<<<<<<<<
@@ -849,23 +939,23 @@ struct __pyx_obj_5_cdec_SparseVector {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/lattice.pxi":52
- *         return hypergraph.AsPLF(self.lattice[0], True).c_str()
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":253
  * 
- *     def __iter__(self):             # <<<<<<<<<<<<<<
- *         cdef unsigned i
- *         for i in range(len(self)):
+ *     property out_edges:
+ *         def __get__(self):             # <<<<<<<<<<<<<<
+ *             cdef unsigned i
+ *             for i in range(self.node.out_edges_.size()):
  */
-struct __pyx_obj_5_cdec___pyx_scope_struct_17___iter__ {
+struct __pyx_obj_5_cdec___pyx_scope_struct_17___get__ {
   PyObject_HEAD
   unsigned int __pyx_v_i;
-  struct __pyx_obj_5_cdec_Lattice *__pyx_v_self;
-  Py_ssize_t __pyx_t_0;
+  struct __pyx_obj_5_cdec_HypergraphNode *__pyx_v_self;
+  size_t __pyx_t_0;
   unsigned int __pyx_t_1;
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":31
+/* "/home/vchahune/tools/cdec/python/src/vectors.pxi":32
  *         self.vector[0][fid] = value
  * 
  *     def __iter__(self):             # <<<<<<<<<<<<<<
@@ -881,23 +971,24 @@ struct __pyx_obj_5_cdec___pyx_scope_struct____iter__ {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":90
- *         return candidate
+/* "/home/vchahune/tools/cdec/python/src/mteval.pxi":44
+ *         return self.stats.size()
  * 
  *     def __iter__(self):             # <<<<<<<<<<<<<<
- *         cdef unsigned i
  *         for i in range(len(self)):
+ *             yield self[i]
  */
 struct __pyx_obj_5_cdec___pyx_scope_struct_21___iter__ {
   PyObject_HEAD
-  unsigned int __pyx_v_i;
-  struct __pyx_obj_5_cdec_CandidateSet *__pyx_v_self;
+  PyObject *__pyx_v_i;
+  struct __pyx_obj_5_cdec_SufficientStats *__pyx_v_self;
   Py_ssize_t __pyx_t_0;
-  unsigned int __pyx_t_1;
+  PyObject *__pyx_t_1;
+  PyObject *(*__pyx_t_2)(PyObject *);
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":3
+/* "/home/vchahune/tools/cdec/python/src/vectors.pxi":3
  * from cython.operator cimport preincrement as pinc
  * 
  * cdef class DenseVector:             # <<<<<<<<<<<<<<
@@ -911,7 +1002,7 @@ struct __pyx_obj_5_cdec_DenseVector {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":187
+/* "/home/vchahune/tools/cdec/python/src/grammar.pxi":199
  *         del self.grammar
  * 
  *     def __iter__(self):             # <<<<<<<<<<<<<<
@@ -930,7 +1021,7 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_7___iter__ {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":173
+/* "/home/vchahune/tools/cdec/python/src/mteval.pxi":176
  *         out.fields[i] = ss[i]
  * 
  * cdef class Metric:             # <<<<<<<<<<<<<<
@@ -943,7 +1034,7 @@ struct __pyx_obj_5_cdec_Metric {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":26
+/* "/home/vchahune/tools/cdec/python/src/mteval.pxi":26
  *             return fmap
  * 
  * cdef class SufficientStats:             # <<<<<<<<<<<<<<
@@ -957,12 +1048,12 @@ struct __pyx_obj_5_cdec_SufficientStats {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":31
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":44
  *         return unicode(hypergraph.JoshuaVisualizationString(self.hg[0]).c_str(), 'utf8')
  * 
  *     def kbest(self, size):             # <<<<<<<<<<<<<<
+ *         """hg.kbest(size) -> List of k-best hypotheses in the hypergraph."""
  *         cdef kbest.KBestDerivations[vector[WordID], kbest.ESentenceTraversal]* derivations = new kbest.KBestDerivations[vector[WordID], kbest.ESentenceTraversal](self.hg[0], size)
- *         cdef kbest.KBestDerivations[vector[WordID], kbest.ESentenceTraversal].Derivation* derivation
  */
 struct __pyx_obj_5_cdec___pyx_scope_struct_8_kbest {
   PyObject_HEAD
@@ -976,12 +1067,12 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_8_kbest {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":61
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":76
  *             del e_derivations
  * 
  *     def kbest_features(self, size):             # <<<<<<<<<<<<<<
+ *         """hg.kbest_trees(size) -> List of k-best feature vectors in the hypergraph."""
  *         cdef kbest.KBestDerivations[FastSparseVector[weight_t], kbest.FeatureVectorTraversal]* derivations = new kbest.KBestDerivations[FastSparseVector[weight_t], kbest.FeatureVectorTraversal](self.hg[0], size)
- *         cdef kbest.KBestDerivations[FastSparseVector[weight_t], kbest.FeatureVectorTraversal].Derivation* derivation
  */
 struct __pyx_obj_5_cdec___pyx_scope_struct_10_kbest_features {
   PyObject_HEAD
@@ -996,24 +1087,24 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_10_kbest_features {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":203
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":211
  * 
- *     property in_edges:
+ *     property tail_nodes:
  *         def __get__(self):             # <<<<<<<<<<<<<<
  *             cdef unsigned i
- *             for i in range(self.node.in_edges_.size()):
+ *             for i in range(self.edge.tail_nodes_.size()):
  */
 struct __pyx_obj_5_cdec___pyx_scope_struct_15___get__ {
   PyObject_HEAD
   unsigned int __pyx_v_i;
-  struct __pyx_obj_5_cdec_HypergraphNode *__pyx_v_self;
-  size_t __pyx_t_0;
+  struct __pyx_obj_5_cdec_HypergraphEdge *__pyx_v_self;
+  unsigned int __pyx_t_0;
   unsigned int __pyx_t_1;
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":164
- *             self.rule.get().lhs_ = -TDConvert(<char *>lhs.cat)
+/* "/home/vchahune/tools/cdec/python/src/grammar.pxi":172
+ *             self.rule.get().lhs_ = -TDConvert((<NT> lhs).cat)
  * 
  *     def __str__(self):             # <<<<<<<<<<<<<<
  *         scores = ' '.join('%s=%s' % feat for feat in self.scores)
@@ -1025,7 +1116,7 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_5___str__ {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":6
+/* "/home/vchahune/tools/cdec/python/src/grammar.pxi":6
  * 
  * def _phrase(phrase):
  *     return ' '.join(w.encode('utf8') if isinstance(w, unicode) else str(w) for w in phrase)             # <<<<<<<<<<<<<<
@@ -1042,12 +1133,12 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_3_genexpr {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":43
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":57
  *             del derivations
  * 
  *     def kbest_trees(self, size):             # <<<<<<<<<<<<<<
+ *         """hg.kbest_trees(size) -> List of k-best trees in the hypergraph."""
  *         cdef kbest.KBestDerivations[vector[WordID], kbest.FTreeTraversal]* f_derivations = new kbest.KBestDerivations[vector[WordID], kbest.FTreeTraversal](self.hg[0], size)
- *         cdef kbest.KBestDerivations[vector[WordID], kbest.FTreeTraversal].Derivation* f_derivation
  */
 struct __pyx_obj_5_cdec___pyx_scope_struct_9_kbest_trees {
   PyObject_HEAD
@@ -1065,7 +1156,7 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_9_kbest_trees {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":4
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":4
  * cimport kbest
  * 
  * cdef class Hypergraph:             # <<<<<<<<<<<<<<
@@ -1074,12 +1165,13 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_9_kbest_trees {
  */
 struct __pyx_obj_5_cdec_Hypergraph {
   PyObject_HEAD
+  struct __pyx_vtabstruct_5_cdec_Hypergraph *__pyx_vtab;
   Hypergraph *hg;
   MT19937 *rng;
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/lattice.pxi":3
+/* "/home/vchahune/tools/cdec/python/src/lattice.pxi":3
  * cimport lattice
  * 
  * cdef class Lattice:             # <<<<<<<<<<<<<<
@@ -1092,12 +1184,12 @@ struct __pyx_obj_5_cdec_Lattice {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":76
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":92
  *             del derivations
  * 
  *     def sample(self, unsigned n):             # <<<<<<<<<<<<<<
+ *         """hg.sample(n) -> Sample of n hypotheses from the hypergraph."""
  *         cdef vector[hypergraph.Hypothesis]* hypos = new vector[hypergraph.Hypothesis]()
- *         if self.rng == NULL:
  */
 struct __pyx_obj_5_cdec___pyx_scope_struct_11_sample {
   PyObject_HEAD
@@ -1110,30 +1202,14 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_11_sample {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":113
- * 
- *     property edges:
- *         def __get__(self):             # <<<<<<<<<<<<<<
- *             cdef unsigned i
- *             for i in range(self.hg.edges_.size()):
- */
-struct __pyx_obj_5_cdec___pyx_scope_struct_12___get__ {
-  PyObject_HEAD
-  unsigned int __pyx_v_i;
-  struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self;
-  size_t __pyx_t_0;
-  unsigned int __pyx_t_1;
-};
-
-
-/* "_cdec.pyx":28
- * class ParseFailed(Exception): pass
+/* "_cdec.pyx":32
+ *     SetSilent(yn)
  * 
  * def _make_config(config):             # <<<<<<<<<<<<<<
  *     for key, value in config.items():
  *         if isinstance(value, dict):
  */
-struct __pyx_obj_5_cdec___pyx_scope_struct_22__make_config {
+struct __pyx_obj_5_cdec___pyx_scope_struct_23__make_config {
   PyObject_HEAD
   PyObject *__pyx_v_config;
   PyObject *__pyx_v_info;
@@ -1149,43 +1225,86 @@ struct __pyx_obj_5_cdec___pyx_scope_struct_22__make_config {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":204
- *             self.grammar.get().SetGrammarName(string(<char *>name))
+/* "/home/vchahune/tools/cdec/python/src/grammar.pxi":217
+ *             self.grammar.get().SetGrammarName(name)
  * 
  * cdef class TextGrammar(Grammar):             # <<<<<<<<<<<<<<
- *     def __cinit__(self, rules):
- *         self.grammar = new shared_ptr[grammar.Grammar](new grammar.TextGrammar())
+ *     def __init__(self, rules):
+ *         """TextGrammar(rules) -> SCFG Grammar containing the rules."""
  */
 struct __pyx_obj_5_cdec_TextGrammar {
   struct __pyx_obj_5_cdec_Grammar __pyx_base;
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/lattice.pxi":58
+
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":4
+ * cimport kbest
  * 
- *     def todot(self):
- *         def lines():             # <<<<<<<<<<<<<<
- *             yield 'digraph lattice {'
- *             yield 'rankdir = LR;'
+ * cdef class Hypergraph:             # <<<<<<<<<<<<<<
+ *     cdef hypergraph.Hypergraph* hg
+ *     cdef MT19937* rng
  */
-struct __pyx_obj_5_cdec___pyx_scope_struct_19_lines {
-  PyObject_HEAD
-  struct __pyx_obj_5_cdec___pyx_scope_struct_18_todot *__pyx_outer_scope;
-  PyObject *__pyx_v_delta;
-  PyObject *__pyx_v_i;
-  PyObject *__pyx_v_label;
-  PyObject *__pyx_v_weight;
-  Py_ssize_t __pyx_t_0;
-  PyObject *__pyx_t_1;
-  PyObject *(*__pyx_t_2)(PyObject *);
-  PyObject *__pyx_t_3;
-  Py_ssize_t __pyx_t_4;
-  PyObject *(*__pyx_t_5)(PyObject *);
+
+struct __pyx_vtabstruct_5_cdec_Hypergraph {
+  MT19937 *(*_rng)(struct __pyx_obj_5_cdec_Hypergraph *);
 };
+static struct __pyx_vtabstruct_5_cdec_Hypergraph *__pyx_vtabptr_5_cdec_Hypergraph;
 
 
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":191
+ *         return vector
+ * 
+ * cdef class HypergraphEdge:             # <<<<<<<<<<<<<<
+ *     cdef hypergraph.Hypergraph* hg
+ *     cdef hypergraph.HypergraphEdge* edge
+ */
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/cdec.sa._sa.pxd":1
+struct __pyx_vtabstruct_5_cdec_HypergraphEdge {
+  PyObject *(*init)(struct __pyx_obj_5_cdec_HypergraphEdge *, Hypergraph *, unsigned int);
+};
+static struct __pyx_vtabstruct_5_cdec_HypergraphEdge *__pyx_vtabptr_5_cdec_HypergraphEdge;
+
+
+/* "/home/vchahune/tools/cdec/python/src/cdec.sa._sa.pxd":12
+ *     cdef void read_handle(self, FILE* f)
+ * 
+ * cdef class IntList:             # <<<<<<<<<<<<<<
+ *     cdef int size
+ *     cdef int increment
+ */
+
+struct __pyx_vtabstruct_4cdec_2sa_3_sa_IntList {
+  void (*set)(struct __pyx_obj_4cdec_2sa_3_sa_IntList *, int, int);
+  void (*_append)(struct __pyx_obj_4cdec_2sa_3_sa_IntList *, int);
+  void (*_extend)(struct __pyx_obj_4cdec_2sa_3_sa_IntList *, struct __pyx_obj_4cdec_2sa_3_sa_IntList *);
+  void (*_extend_arr)(struct __pyx_obj_4cdec_2sa_3_sa_IntList *, int *, int);
+  void (*_clear)(struct __pyx_obj_4cdec_2sa_3_sa_IntList *);
+  void (*write_handle)(struct __pyx_obj_4cdec_2sa_3_sa_IntList *, FILE *);
+  void (*read_handle)(struct __pyx_obj_4cdec_2sa_3_sa_IntList *, FILE *);
+};
+static struct __pyx_vtabstruct_4cdec_2sa_3_sa_IntList *__pyx_vtabptr_4cdec_2sa_3_sa_IntList;
+
+
+/* "/home/vchahune/tools/cdec/python/src/cdec.sa._sa.pxd":3
+ * from libc.stdio cimport FILE
+ * 
+ * cdef class FloatList:             # <<<<<<<<<<<<<<
+ *     cdef int size
+ *     cdef int increment
+ */
+
+struct __pyx_vtabstruct_4cdec_2sa_3_sa_FloatList {
+  void (*set)(struct __pyx_obj_4cdec_2sa_3_sa_FloatList *, int, float);
+  void (*write_handle)(struct __pyx_obj_4cdec_2sa_3_sa_FloatList *, FILE *);
+  void (*read_handle)(struct __pyx_obj_4cdec_2sa_3_sa_FloatList *, FILE *);
+};
+static struct __pyx_vtabstruct_4cdec_2sa_3_sa_FloatList *__pyx_vtabptr_4cdec_2sa_3_sa_FloatList;
+
+
+/* "/home/vchahune/tools/cdec/python/src/cdec.sa._sa.pxd":29
+ *     cdef FloatList values
+ * 
  * cdef class Phrase:             # <<<<<<<<<<<<<<
  *     cdef int *syms
  *     cdef int n, *varpos, n_vars
@@ -1198,7 +1317,7 @@ struct __pyx_vtabstruct_4cdec_2sa_3_sa_Phrase {
 static struct __pyx_vtabstruct_4cdec_2sa_3_sa_Phrase *__pyx_vtabptr_4cdec_2sa_3_sa_Phrase;
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":193
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":237
  *         raise NotImplemented('comparison not implemented for HypergraphEdge')
  * 
  * cdef class HypergraphNode:             # <<<<<<<<<<<<<<
@@ -1210,20 +1329,6 @@ struct __pyx_vtabstruct_5_cdec_HypergraphNode {
   PyObject *(*init)(struct __pyx_obj_5_cdec_HypergraphNode *, Hypergraph *, unsigned int);
 };
 static struct __pyx_vtabstruct_5_cdec_HypergraphNode *__pyx_vtabptr_5_cdec_HypergraphNode;
-
-
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":147
- *         return vector
- * 
- * cdef class HypergraphEdge:             # <<<<<<<<<<<<<<
- *     cdef hypergraph.Hypergraph* hg
- *     cdef hypergraph.HypergraphEdge* edge
- */
-
-struct __pyx_vtabstruct_5_cdec_HypergraphEdge {
-  PyObject *(*init)(struct __pyx_obj_5_cdec_HypergraphEdge *, Hypergraph *, unsigned int);
-};
-static struct __pyx_vtabstruct_5_cdec_HypergraphEdge *__pyx_vtabptr_5_cdec_HypergraphEdge;
 #ifndef CYTHON_REFNANNY
   #define CYTHON_REFNANNY 0
 #endif
@@ -1308,22 +1413,6 @@ static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \
     PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \
     const char* function_name); /*proto*/
 
-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) {
-    PyListObject* L = (PyListObject*) list;
-    Py_ssize_t len = Py_SIZE(list);
-    if (likely(L->allocated > len)) {
-        Py_INCREF(x);
-        PyList_SET_ITEM(list, len, x);
-        Py_SIZE(list) = len+1;
-        return 0;
-    }
-    return PyList_Append(list, x);
-}
-#else
-#define __Pyx_PyList_Append(L,x) PyList_Append(L,x)
-#endif
-
 static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
     if (likely(PyList_CheckExact(L))) {
         if (unlikely(PyList_Append(L, x) < 0)) return NULL;
@@ -1433,11 +1522,9 @@ static CYTHON_INLINE int __Pyx_IterFinish(void); /*proto*/
 
 static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /*proto*/
 
-static CYTHON_INLINE int __Pyx_NegateNonNeg(int b) {
-    return unlikely(b < 0) ? b : !b;
-}
-static CYTHON_INLINE PyObject* __Pyx_PyBoolOrNull_FromLong(long b) {
-    return unlikely(b < 0) ? NULL : __Pyx_PyBool_FromLong(b);
+static CYTHON_INLINE int __Pyx_PyDict_Contains(PyObject* item, PyObject* dict, int eq) {
+    int result = PyDict_Contains(dict, item);
+    return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
 }
 
 #define __Pyx_PyIter_Next(obj) __Pyx_PyIter_Next2(obj, NULL)
@@ -1552,18 +1639,6 @@ static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *m,
                                                             PyObject *tuple);
 static int __Pyx_CyFunction_init(void);
 
-#include <string.h>
-
-static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/
-
-static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/
-
-#if PY_MAJOR_VERSION >= 3
-#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals
-#else
-#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals
-#endif
-
 static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *);
 
 static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject *);
@@ -1596,9 +1671,6 @@ static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject *);
 
 static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *);
 
-static void __Pyx_WriteUnraisable(const char *name, int clineno,
-                                  int lineno, const char *filename); /*proto*/
-
 static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
 
 #define __Pyx_Generator_USED
@@ -1609,14 +1681,14 @@ typedef struct {
     PyObject_HEAD
     __pyx_generator_body_t body;
     PyObject *closure;
-    int is_running;
-    int resume_label;
     PyObject *exc_type;
     PyObject *exc_value;
     PyObject *exc_traceback;
     PyObject *gi_weakreflist;
     PyObject *classobj;
     PyObject *yieldfrom;
+    int resume_label;
+    char is_running;  // using T_BOOL for property below requires char value
 } __pyx_GeneratorObject;
 static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
                                                   PyObject *closure);
@@ -1628,6 +1700,9 @@ static int __Pyx_PyGen_FetchStopIterationValue(PyObject **pvalue);
 #define __Pyx_PyGen_FetchStopIterationValue(pvalue) PyGen_FetchStopIterationValue(pvalue)
 #endif
 
+static void __Pyx_WriteUnraisable(const char *name, int clineno,
+                                  int lineno, const char *filename); /*proto*/
+
 static int __Pyx_check_binary_version(void);
 
 static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
@@ -1640,10 +1715,10 @@ static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
 #endif
 #endif
 
-static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict);  /*proto*/
-
 static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
 
+static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict);  /*proto*/
+
 static void* __Pyx_GetVtable(PyObject *dict); /*proto*/
 
 static int __Pyx_ImportFunction(PyObject *module, const char *funcname, void (**f)(void), const char *sig); /*proto*/
@@ -1688,7 +1763,12 @@ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
 
 /* Module declarations from 'decoder' */
 
+/* Module declarations from 'libc.stdio' */
+
 /* Module declarations from 'cdec.sa._sa' */
+static PyTypeObject *__pyx_ptype_4cdec_2sa_3_sa_FloatList = 0;
+static PyTypeObject *__pyx_ptype_4cdec_2sa_3_sa_IntList = 0;
+static PyTypeObject *__pyx_ptype_4cdec_2sa_3_sa_FeatureVector = 0;
 static PyTypeObject *__pyx_ptype_4cdec_2sa_3_sa_Phrase = 0;
 static PyTypeObject *__pyx_ptype_4cdec_2sa_3_sa_Rule = 0;
 static char *(*__pyx_f_4cdec_2sa_3_sa_sym_tostring)(int); /*proto*/
@@ -1732,25 +1812,26 @@ static PyTypeObject *__pyx_ptype_5_cdec___pyx_scope_struct_8_kbest = 0;
 static PyTypeObject *__pyx_ptype_5_cdec___pyx_scope_struct_9_kbest_trees = 0;
 static PyTypeObject *__pyx_ptype_5_cdec___pyx_scope_struct_10_kbest_features = 0;
 static PyTypeObject *__pyx_ptype_5_cdec___pyx_scope_struct_11_sample = 0;
-static PyTypeObject *__pyx_ptype_5_cdec___pyx_scope_struct_12___get__ = 0;
+static PyTypeObject *__pyx_ptype_5_cdec___pyx_scope_struct_12_sample_trees = 0;
 static PyTypeObject *__pyx_ptype_5_cdec___pyx_scope_struct_13___get__ = 0;
 static PyTypeObject *__pyx_ptype_5_cdec___pyx_scope_struct_14___get__ = 0;
 static PyTypeObject *__pyx_ptype_5_cdec___pyx_scope_struct_15___get__ = 0;
 static PyTypeObject *__pyx_ptype_5_cdec___pyx_scope_struct_16___get__ = 0;
-static PyTypeObject *__pyx_ptype_5_cdec___pyx_scope_struct_17___iter__ = 0;
-static PyTypeObject *__pyx_ptype_5_cdec___pyx_scope_struct_18_todot = 0;
-static PyTypeObject *__pyx_ptype_5_cdec___pyx_scope_struct_19_lines = 0;
-static PyTypeObject *__pyx_ptype_5_cdec___pyx_scope_struct_20___iter__ = 0;
+static PyTypeObject *__pyx_ptype_5_cdec___pyx_scope_struct_17___get__ = 0;
+static PyTypeObject *__pyx_ptype_5_cdec___pyx_scope_struct_18___iter__ = 0;
+static PyTypeObject *__pyx_ptype_5_cdec___pyx_scope_struct_19_todot = 0;
+static PyTypeObject *__pyx_ptype_5_cdec___pyx_scope_struct_20_lines = 0;
 static PyTypeObject *__pyx_ptype_5_cdec___pyx_scope_struct_21___iter__ = 0;
-static PyTypeObject *__pyx_ptype_5_cdec___pyx_scope_struct_22__make_config = 0;
-static PyTypeObject *__pyx_ptype_5_cdec___pyx_scope_struct_23___cinit__ = 0;
-static PyTypeObject *__pyx_ptype_5_cdec___pyx_scope_struct_24_genexpr = 0;
-static char *__pyx_f_5_cdec_as_str(PyObject *, struct __pyx_opt_args_5_cdec_as_str *__pyx_optional_args); /*proto*/
+static PyTypeObject *__pyx_ptype_5_cdec___pyx_scope_struct_22___iter__ = 0;
+static PyTypeObject *__pyx_ptype_5_cdec___pyx_scope_struct_23__make_config = 0;
+static PyTypeObject *__pyx_ptype_5_cdec___pyx_scope_struct_24___init__ = 0;
+static PyTypeObject *__pyx_ptype_5_cdec___pyx_scope_struct_25_genexpr = 0;
+static PyObject *__pyx_f_5_cdec_as_str(PyObject *, struct __pyx_opt_args_5_cdec_as_str *__pyx_optional_args); /*proto*/
 static struct __pyx_obj_5_cdec_TRule *__pyx_f_5_cdec_convert_rule(struct __pyx_obj_4cdec_2sa_3_sa_Rule *); /*proto*/
 static struct __pyx_obj_5_cdec_SufficientStats *__pyx_f_5_cdec_as_stats(PyObject *, PyObject *); /*proto*/
 static float __pyx_f_5_cdec__compute_score(void *, SufficientStats *); /*proto*/
 static void __pyx_f_5_cdec__compute_sufficient_stats(void *, std::string *, std::vector<std::string> *, SufficientStats *); /*proto*/
-static PyObject *__pyx_convert_string_to_py_(const std::string &); /*proto*/
+static std::string __pyx_convert_string_from_py_(PyObject *); /*proto*/
 #define __Pyx_MODULE_NAME "_cdec"
 int __pyx_module_is_main__cdec = 0;
 
@@ -1762,6 +1843,7 @@ static PyObject *__pyx_builtin_range;
 static PyObject *__pyx_builtin_NotImplemented;
 static PyObject *__pyx_builtin_super;
 static PyObject *__pyx_builtin_ValueError;
+static PyObject *__pyx_builtin_basestring;
 static PyObject *__pyx_builtin_eval;
 static PyObject *__pyx_builtin_enumerate;
 static PyObject *__pyx_builtin_IndexError;
@@ -1799,7 +1881,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_37__div__(PyObject *__pyx_v_x, P
 #endif
 static PyObject *__pyx_pf_5_cdec_7_phrase_genexpr(PyObject *__pyx_self); /* proto */
 static PyObject *__pyx_pf_5_cdec__phrase(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_phrase); /* proto */
-static int __pyx_pf_5_cdec_2NT___init__(struct __pyx_obj_5_cdec_NT *__pyx_v_self, char *__pyx_v_cat, unsigned int __pyx_v_ref); /* proto */
+static int __pyx_pf_5_cdec_2NT___init__(struct __pyx_obj_5_cdec_NT *__pyx_v_self, PyObject *__pyx_v_cat, unsigned int __pyx_v_ref); /* proto */
 static PyObject *__pyx_pf_5_cdec_2NT_2__str__(struct __pyx_obj_5_cdec_NT *__pyx_v_self); /* proto */
 static PyObject *__pyx_pf_5_cdec_2NT_3cat___get__(struct __pyx_obj_5_cdec_NT *__pyx_v_self); /* proto */
 static int __pyx_pf_5_cdec_2NT_3cat_2__set__(struct __pyx_obj_5_cdec_NT *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
@@ -1825,12 +1907,12 @@ static PyObject *__pyx_pf_5_cdec_5TRule_3lhs___get__(struct __pyx_obj_5_cdec_TRu
 static int __pyx_pf_5_cdec_5TRule_3lhs_2__set__(struct __pyx_obj_5_cdec_TRule *__pyx_v_self, PyObject *__pyx_v_lhs); /* proto */
 static PyObject *__pyx_pf_5_cdec_5TRule_7__str___genexpr(PyObject *__pyx_self); /* proto */
 static PyObject *__pyx_pf_5_cdec_5TRule_4__str__(struct __pyx_obj_5_cdec_TRule *__pyx_v_self); /* proto */
-static int __pyx_pf_5_cdec_5MRule___init__(struct __pyx_obj_5_cdec_MRule *__pyx_v_self, PyObject *__pyx_v_lhs, PyObject *__pyx_v_rhs, PyObject *__pyx_v_scores, PyObject *__pyx_v_a); /* proto */
+static int __pyx_pf_5_cdec_5MRule___init__(struct __pyx_obj_5_cdec_MRule *__pyx_v_self, PyObject *__pyx_v_lhs, PyObject *__pyx_v_rhs, PyObject *__pyx_v_scores); /* proto */
 static void __pyx_pf_5_cdec_7Grammar___dealloc__(CYTHON_UNUSED struct __pyx_obj_5_cdec_Grammar *__pyx_v_self); /* proto */
 static PyObject *__pyx_pf_5_cdec_7Grammar_2__iter__(struct __pyx_obj_5_cdec_Grammar *__pyx_v_self); /* proto */
 static PyObject *__pyx_pf_5_cdec_7Grammar_4name___get__(struct __pyx_obj_5_cdec_Grammar *__pyx_v_self); /* proto */
 static int __pyx_pf_5_cdec_7Grammar_4name_2__set__(struct __pyx_obj_5_cdec_Grammar *__pyx_v_self, PyObject *__pyx_v_name); /* proto */
-static int __pyx_pf_5_cdec_11TextGrammar___cinit__(struct __pyx_obj_5_cdec_TextGrammar *__pyx_v_self, PyObject *__pyx_v_rules); /* proto */
+static int __pyx_pf_5_cdec_11TextGrammar___init__(struct __pyx_obj_5_cdec_TextGrammar *__pyx_v_self, PyObject *__pyx_v_rules); /* proto */
 static void __pyx_pf_5_cdec_10Hypergraph___dealloc__(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self); /* proto */
 static PyObject *__pyx_pf_5_cdec_10Hypergraph_2viterbi(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self); /* proto */
 static PyObject *__pyx_pf_5_cdec_10Hypergraph_4viterbi_trees(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self); /* proto */
@@ -1840,15 +1922,17 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_10kbest(struct __pyx_obj_5_cdec_Hy
 static PyObject *__pyx_pf_5_cdec_10Hypergraph_13kbest_trees(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self, PyObject *__pyx_v_size); /* proto */
 static PyObject *__pyx_pf_5_cdec_10Hypergraph_16kbest_features(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self, PyObject *__pyx_v_size); /* proto */
 static PyObject *__pyx_pf_5_cdec_10Hypergraph_19sample(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self, unsigned int __pyx_v_n); /* proto */
-static PyObject *__pyx_pf_5_cdec_10Hypergraph_22intersect(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self, struct __pyx_obj_5_cdec_Lattice *__pyx_v_lat); /* proto */
-static PyObject *__pyx_pf_5_cdec_10Hypergraph_24prune(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self, PyObject *__pyx_v_beam_alpha, PyObject *__pyx_v_density, PyObject *__pyx_v_kwargs); /* proto */
-static PyObject *__pyx_pf_5_cdec_10Hypergraph_26lattice(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5_cdec_10Hypergraph_28reweight(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self, PyObject *__pyx_v_weights); /* proto */
+static PyObject *__pyx_pf_5_cdec_10Hypergraph_22sample_trees(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self, unsigned int __pyx_v_n); /* proto */
+static PyObject *__pyx_pf_5_cdec_10Hypergraph_25intersect(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self, PyObject *__pyx_v_inp); /* proto */
+static PyObject *__pyx_pf_5_cdec_10Hypergraph_27prune(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self, PyObject *__pyx_v_beam_alpha, PyObject *__pyx_v_density, PyObject *__pyx_v_kwargs); /* proto */
+static PyObject *__pyx_pf_5_cdec_10Hypergraph_29lattice(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5_cdec_10Hypergraph_31plf(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5_cdec_10Hypergraph_33reweight(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self, PyObject *__pyx_v_weights); /* proto */
 static PyObject *__pyx_pf_5_cdec_10Hypergraph_5edges___get__(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self); /* proto */
 static PyObject *__pyx_pf_5_cdec_10Hypergraph_5nodes___get__(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self); /* proto */
 static PyObject *__pyx_pf_5_cdec_10Hypergraph_4goal___get__(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self); /* proto */
 static PyObject *__pyx_pf_5_cdec_10Hypergraph_6npaths___get__(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5_cdec_10Hypergraph_30inside_outside(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5_cdec_10Hypergraph_35inside_outside(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self); /* proto */
 static Py_ssize_t __pyx_pf_5_cdec_14HypergraphEdge___len__(struct __pyx_obj_5_cdec_HypergraphEdge *__pyx_v_self); /* proto */
 static PyObject *__pyx_pf_5_cdec_14HypergraphEdge_9head_node___get__(struct __pyx_obj_5_cdec_HypergraphEdge *__pyx_v_self); /* proto */
 static PyObject *__pyx_pf_5_cdec_14HypergraphEdge_10tail_nodes___get__(struct __pyx_obj_5_cdec_HypergraphEdge *__pyx_v_self); /* proto */
@@ -1864,15 +1948,18 @@ static PyObject *__pyx_pf_5_cdec_14HypergraphNode_9out_edges___get__(struct __py
 static PyObject *__pyx_pf_5_cdec_14HypergraphNode_4span___get__(struct __pyx_obj_5_cdec_HypergraphNode *__pyx_v_self); /* proto */
 static PyObject *__pyx_pf_5_cdec_14HypergraphNode_3cat___get__(struct __pyx_obj_5_cdec_HypergraphNode *__pyx_v_self); /* proto */
 static PyObject *__pyx_pf_5_cdec_14HypergraphNode___richcmp__(struct __pyx_obj_5_cdec_HypergraphNode *__pyx_v_x, struct __pyx_obj_5_cdec_HypergraphNode *__pyx_v_y, int __pyx_v_op); /* proto */
-static int __pyx_pf_5_cdec_7Lattice___cinit__(struct __pyx_obj_5_cdec_Lattice *__pyx_v_self, PyObject *__pyx_v_inp); /* proto */
-static void __pyx_pf_5_cdec_7Lattice_2__dealloc__(CYTHON_UNUSED struct __pyx_obj_5_cdec_Lattice *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5_cdec_7Lattice_4__getitem__(struct __pyx_obj_5_cdec_Lattice *__pyx_v_self, int __pyx_v_index); /* proto */
-static int __pyx_pf_5_cdec_7Lattice_6__setitem__(struct __pyx_obj_5_cdec_Lattice *__pyx_v_self, int __pyx_v_index, PyObject *__pyx_v_arcs); /* proto */
-static Py_ssize_t __pyx_pf_5_cdec_7Lattice_8__len__(struct __pyx_obj_5_cdec_Lattice *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5_cdec_7Lattice_10__str__(struct __pyx_obj_5_cdec_Lattice *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5_cdec_7Lattice_12__iter__(struct __pyx_obj_5_cdec_Lattice *__pyx_v_self); /* proto */
+static int __pyx_pf_5_cdec_7Lattice___cinit__(struct __pyx_obj_5_cdec_Lattice *__pyx_v_self); /* proto */
+static int __pyx_pf_5_cdec_7Lattice_2__init__(struct __pyx_obj_5_cdec_Lattice *__pyx_v_self, PyObject *__pyx_v_inp); /* proto */
+static void __pyx_pf_5_cdec_7Lattice_4__dealloc__(CYTHON_UNUSED struct __pyx_obj_5_cdec_Lattice *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5_cdec_7Lattice_6__getitem__(struct __pyx_obj_5_cdec_Lattice *__pyx_v_self, int __pyx_v_index); /* proto */
+static int __pyx_pf_5_cdec_7Lattice_8__setitem__(struct __pyx_obj_5_cdec_Lattice *__pyx_v_self, int __pyx_v_index, PyObject *__pyx_v_arcs); /* proto */
+static Py_ssize_t __pyx_pf_5_cdec_7Lattice_10__len__(struct __pyx_obj_5_cdec_Lattice *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5_cdec_7Lattice_12__str__(struct __pyx_obj_5_cdec_Lattice *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5_cdec_7Lattice_14__unicode__(struct __pyx_obj_5_cdec_Lattice *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5_cdec_7Lattice_16__iter__(struct __pyx_obj_5_cdec_Lattice *__pyx_v_self); /* proto */
 static PyObject *__pyx_pf_5_cdec_7Lattice_5todot_lines(PyObject *__pyx_self); /* proto */
-static PyObject *__pyx_pf_5_cdec_7Lattice_15todot(struct __pyx_obj_5_cdec_Lattice *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5_cdec_7Lattice_19todot(struct __pyx_obj_5_cdec_Lattice *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5_cdec_7Lattice_21as_hypergraph(struct __pyx_obj_5_cdec_Lattice *__pyx_v_self); /* proto */
 static PyObject *__pyx_pf_5_cdec_9Candidate_5words___get__(struct __pyx_obj_5_cdec_Candidate *__pyx_v_self); /* proto */
 static PyObject *__pyx_pf_5_cdec_9Candidate_4fmap___get__(struct __pyx_obj_5_cdec_Candidate *__pyx_v_self); /* proto */
 static PyObject *__pyx_pf_5_cdec_9Candidate_5score___get__(struct __pyx_obj_5_cdec_Candidate *__pyx_v_self); /* proto */
@@ -1902,9 +1989,10 @@ static int __pyx_pf_5_cdec_6Metric___cinit__(struct __pyx_obj_5_cdec_Metric *__p
 static PyObject *__pyx_pf_5_cdec_6Metric_2__call__(struct __pyx_obj_5_cdec_Metric *__pyx_v_self, PyObject *__pyx_v_refs); /* proto */
 static PyObject *__pyx_pf_5_cdec_6Metric_4score(CYTHON_UNUSED struct __pyx_obj_5_cdec_Metric *__pyx_v_stats); /* proto */
 static PyObject *__pyx_pf_5_cdec_6Metric_6evaluate(CYTHON_UNUSED struct __pyx_obj_5_cdec_Metric *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_hyp, CYTHON_UNUSED PyObject *__pyx_v_refs); /* proto */
-static PyObject *__pyx_pf_5_cdec_2_make_config(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_config); /* proto */
-static PyObject *__pyx_pf_5_cdec_7Decoder_9__cinit___genexpr(PyObject *__pyx_self); /* proto */
-static int __pyx_pf_5_cdec_7Decoder___cinit__(struct __pyx_obj_5_cdec_Decoder *__pyx_v_self, PyObject *__pyx_v_config_str, PyObject *__pyx_v_config); /* proto */
+static PyObject *__pyx_pf_5_cdec_2set_silent(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_yn); /* proto */
+static PyObject *__pyx_pf_5_cdec_4_make_config(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_config); /* proto */
+static PyObject *__pyx_pf_5_cdec_7Decoder_8__init___genexpr(PyObject *__pyx_self); /* proto */
+static int __pyx_pf_5_cdec_7Decoder___init__(struct __pyx_obj_5_cdec_Decoder *__pyx_v_self, PyObject *__pyx_v_config_str, PyObject *__pyx_v_config); /* proto */
 static void __pyx_pf_5_cdec_7Decoder_2__dealloc__(CYTHON_UNUSED struct __pyx_obj_5_cdec_Decoder *__pyx_v_self); /* proto */
 static PyObject *__pyx_pf_5_cdec_7Decoder_7weights___get__(struct __pyx_obj_5_cdec_Decoder *__pyx_v_self); /* proto */
 static int __pyx_pf_5_cdec_7Decoder_7weights_2__set__(struct __pyx_obj_5_cdec_Decoder *__pyx_v_self, PyObject *__pyx_v_weights); /* proto */
@@ -1921,40 +2009,42 @@ static char __pyx_k_10[] = "[%d]";
 static char __pyx_k_11[] = "%s=%s";
 static char __pyx_k_12[] = "%s ||| %s ||| %s ||| %s";
 static char __pyx_k_13[] = "the grammar should contain TRule objects";
-static char __pyx_k_15[] = "csplit_preserve_full_word";
-static char __pyx_k_16[] = "cannot reweight hypergraph with %s";
-static char __pyx_k_17[] = "comparison not implemented for HypergraphEdge";
-static char __pyx_k_19[] = "comparison not implemented for HypergraphNode";
-static char __pyx_k_22[] = "Cannot create lattice from %s";
+static char __pyx_k_15[] = "cannot intersect hypergraph with %s";
+static char __pyx_k_16[] = "csplit_preserve_full_word";
+static char __pyx_k_17[] = "cannot reweight hypergraph with %s";
+static char __pyx_k_18[] = "comparison not implemented for HypergraphEdge";
+static char __pyx_k_20[] = "comparison not implemented for HypergraphNode";
+static char __pyx_k_22[] = "cannot create lattice from %s";
 static char __pyx_k_23[] = "lattice index out of range";
-static char __pyx_k_27[] = "digraph lattice {";
-  static char __pyx_k_28[] = "rankdir = LR;";
-  static char __pyx_k_29[] = "node [shape=circle];";
-  static char __pyx_k_30[] = "%d -> %d [label=\"%s\"];";
-  static char __pyx_k_31[] = "\"";
-  static char __pyx_k_32[] = "\\\"";
-  static char __pyx_k_34[] = "%d [shape=doublecircle]";
-static char __pyx_k_35[] = "}";
-static char __pyx_k_38[] = "/Users/vchahun/Sandbox/cdec/python/src/lattice.pxi";
-static char __pyx_k_39[] = "\n";
-static char __pyx_k_41[] = "sufficient stats vector index out of range";
-static char __pyx_k_43[] = "candidate set index out of range";
-static char __pyx_k_45[] = "%s %s";
-static char __pyx_k_46[] = "%s = %s";
-static char __pyx_k_48[] = "formalism \"%s\" unknown";
-static char __pyx_k_49[] = "cannot initialize weights with %s";
-static char __pyx_k_50[] = "#";
-static char __pyx_k_53[] = "Cannot translate input type %s";
-static char __pyx_k_54[] = "cdec.sa._sa";
-static char __pyx_k_55[] = "*";
-static char __pyx_k_58[] = "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi";
-static char __pyx_k_64[] = "/Users/vchahun/Sandbox/cdec/python/src/_cdec.pyx";
+static char __pyx_k_26[] = "digraph lattice {";
+  static char __pyx_k_27[] = "rankdir = LR;";
+  static char __pyx_k_28[] = "node [shape=circle];";
+  static char __pyx_k_29[] = "%d -> %d [label=\"%s\"];";
+  static char __pyx_k_30[] = "\"";
+  static char __pyx_k_31[] = "\\\"";
+  static char __pyx_k_33[] = "%d [shape=doublecircle]";
+static char __pyx_k_34[] = "}";
+static char __pyx_k_37[] = "/home/vchahune/tools/cdec/python/src/lattice.pxi";
+static char __pyx_k_38[] = "\n";
+static char __pyx_k_40[] = "sufficient stats vector index out of range";
+static char __pyx_k_42[] = "candidate set index out of range";
+static char __pyx_k_44[] = "%s %s";
+static char __pyx_k_45[] = "%s = %s";
+static char __pyx_k_47[] = "formalism \"%s\" unknown";
+static char __pyx_k_48[] = "cannot initialize weights with %s";
+static char __pyx_k_49[] = "#";
+static char __pyx_k_52[] = "Cannot translate input type %s";
+static char __pyx_k_53[] = "cdec.sa._sa";
+static char __pyx_k_54[] = "*";
+static char __pyx_k_57[] = "/home/vchahune/tools/cdec/python/src/grammar.pxi";
+static char __pyx_k_63[] = "/home/vchahune/tools/cdec/python/src/_cdec.pyx";
 static char __pyx_k__a[] = "a";
 static char __pyx_k__e[] = "e";
 static char __pyx_k__f[] = "f";
 static char __pyx_k__i[] = "i";
 static char __pyx_k__k[] = "k";
 static char __pyx_k__pb[] = "pb";
+static char __pyx_k__yn[] = "yn";
 static char __pyx_k__CER[] = "CER";
 static char __pyx_k__TER[] = "TER";
 static char __pyx_k___sa[] = "_sa";
@@ -2027,12 +2117,14 @@ static char __pyx_k__evaluator[] = "evaluator";
 static char __pyx_k__formalism[] = "formalism";
 static char __pyx_k__IndexError[] = "IndexError";
 static char __pyx_k__ValueError[] = "ValueError";
+static char __pyx_k__alignments[] = "alignments";
+static char __pyx_k__basestring[] = "basestring";
 static char __pyx_k__beam_alpha[] = "beam_alpha";
 static char __pyx_k__config_str[] = "config_str";
 static char __pyx_k__hypergraph[] = "hypergraph";
+static char __pyx_k__set_silent[] = "set_silent";
 static char __pyx_k__startswith[] = "startswith";
 static char __pyx_k__ParseFailed[] = "ParseFailed";
-static char __pyx_k__PhraseModel_[] = "PhraseModel_";
 static char __pyx_k___make_config[] = "_make_config";
 static char __pyx_k__InvalidConfig[] = "InvalidConfig";
 static char __pyx_k__NotImplemented[] = "NotImplemented";
@@ -2040,36 +2132,37 @@ static PyObject *__pyx_kp_s_10;
 static PyObject *__pyx_kp_s_11;
 static PyObject *__pyx_kp_s_12;
 static PyObject *__pyx_kp_s_13;
-static PyObject *__pyx_n_s_15;
-static PyObject *__pyx_kp_s_16;
+static PyObject *__pyx_kp_s_15;
+static PyObject *__pyx_n_s_16;
 static PyObject *__pyx_kp_s_17;
-static PyObject *__pyx_kp_s_19;
+static PyObject *__pyx_kp_s_18;
+static PyObject *__pyx_kp_s_20;
 static PyObject *__pyx_kp_s_22;
 static PyObject *__pyx_kp_s_23;
+static PyObject *__pyx_kp_s_26;
 static PyObject *__pyx_kp_s_27;
 static PyObject *__pyx_kp_s_28;
 static PyObject *__pyx_kp_s_29;
 static PyObject *__pyx_kp_s_3;
 static PyObject *__pyx_kp_s_30;
 static PyObject *__pyx_kp_s_31;
-static PyObject *__pyx_kp_s_32;
+static PyObject *__pyx_kp_s_33;
 static PyObject *__pyx_kp_s_34;
-static PyObject *__pyx_kp_s_35;
+static PyObject *__pyx_kp_s_37;
 static PyObject *__pyx_kp_s_38;
-static PyObject *__pyx_kp_s_39;
 static PyObject *__pyx_kp_s_4;
-static PyObject *__pyx_kp_s_41;
-static PyObject *__pyx_kp_s_43;
+static PyObject *__pyx_kp_s_40;
+static PyObject *__pyx_kp_s_42;
+static PyObject *__pyx_kp_s_44;
 static PyObject *__pyx_kp_s_45;
-static PyObject *__pyx_kp_s_46;
+static PyObject *__pyx_kp_s_47;
 static PyObject *__pyx_kp_s_48;
 static PyObject *__pyx_kp_s_49;
-static PyObject *__pyx_kp_s_50;
-static PyObject *__pyx_kp_s_53;
+static PyObject *__pyx_kp_s_52;
+static PyObject *__pyx_n_s_53;
 static PyObject *__pyx_n_s_54;
-static PyObject *__pyx_n_s_55;
-static PyObject *__pyx_kp_s_58;
-static PyObject *__pyx_kp_s_64;
+static PyObject *__pyx_kp_s_57;
+static PyObject *__pyx_kp_s_63;
 static PyObject *__pyx_kp_s_7;
 static PyObject *__pyx_kp_s_8;
 static PyObject *__pyx_kp_s_9;
@@ -2082,7 +2175,6 @@ static PyObject *__pyx_n_s__InvalidConfig;
 static PyObject *__pyx_n_s__KeyError;
 static PyObject *__pyx_n_s__NotImplemented;
 static PyObject *__pyx_n_s__ParseFailed;
-static PyObject *__pyx_n_s__PhraseModel_;
 static PyObject *__pyx_n_s__TER;
 static PyObject *__pyx_n_s__TypeError;
 static PyObject *__pyx_n_s__ValueError;
@@ -2098,6 +2190,8 @@ static PyObject *__pyx_n_s___make_config;
 static PyObject *__pyx_n_s___phrase;
 static PyObject *__pyx_n_s___sa;
 static PyObject *__pyx_n_s__a;
+static PyObject *__pyx_n_s__alignments;
+static PyObject *__pyx_n_s__basestring;
 static PyObject *__pyx_n_s__beam_alpha;
 static PyObject *__pyx_n_s__cat;
 static PyObject *__pyx_n_s__config;
@@ -2151,6 +2245,7 @@ static PyObject *__pyx_n_s__score;
 static PyObject *__pyx_n_s__scores;
 static PyObject *__pyx_n_s__self;
 static PyObject *__pyx_n_s__sentence;
+static PyObject *__pyx_n_s__set_silent;
 static PyObject *__pyx_n_s__span;
 static PyObject *__pyx_n_s__split;
 static PyObject *__pyx_n_s__startswith;
@@ -2160,54 +2255,53 @@ static PyObject *__pyx_n_s__tagger;
 static PyObject *__pyx_n_s__utf8;
 static PyObject *__pyx_n_s__value;
 static PyObject *__pyx_n_s__weight;
+static PyObject *__pyx_n_s__yn;
 static PyObject *__pyx_int_0;
 static PyObject *__pyx_int_1;
-static PyObject *__pyx_int_65536;
 static PyObject *__pyx_k_tuple_2;
 static PyObject *__pyx_k_tuple_5;
 static PyObject *__pyx_k_tuple_6;
 static PyObject *__pyx_k_tuple_14;
-static PyObject *__pyx_k_tuple_18;
-static PyObject *__pyx_k_tuple_20;
+static PyObject *__pyx_k_tuple_19;
 static PyObject *__pyx_k_tuple_21;
 static PyObject *__pyx_k_tuple_24;
 static PyObject *__pyx_k_tuple_25;
-static PyObject *__pyx_k_tuple_26;
-static PyObject *__pyx_k_tuple_33;
-static PyObject *__pyx_k_tuple_36;
-static PyObject *__pyx_k_tuple_40;
-static PyObject *__pyx_k_tuple_42;
-static PyObject *__pyx_k_tuple_44;
-static PyObject *__pyx_k_tuple_47;
+static PyObject *__pyx_k_tuple_32;
+static PyObject *__pyx_k_tuple_35;
+static PyObject *__pyx_k_tuple_39;
+static PyObject *__pyx_k_tuple_41;
+static PyObject *__pyx_k_tuple_43;
+static PyObject *__pyx_k_tuple_46;
+static PyObject *__pyx_k_tuple_50;
 static PyObject *__pyx_k_tuple_51;
-static PyObject *__pyx_k_tuple_52;
-static PyObject *__pyx_k_tuple_56;
+static PyObject *__pyx_k_tuple_55;
+static PyObject *__pyx_k_tuple_58;
 static PyObject *__pyx_k_tuple_59;
 static PyObject *__pyx_k_tuple_60;
 static PyObject *__pyx_k_tuple_61;
-static PyObject *__pyx_k_tuple_62;
-static PyObject *__pyx_k_codeobj_37;
-static PyObject *__pyx_k_codeobj_57;
-static PyObject *__pyx_k_codeobj_63;
+static PyObject *__pyx_k_tuple_64;
+static PyObject *__pyx_k_codeobj_36;
+static PyObject *__pyx_k_codeobj_56;
+static PyObject *__pyx_k_codeobj_62;
+static PyObject *__pyx_k_codeobj_65;
 
 /* "_cdec.pyx":6
  * cimport decoder
  * 
- * cdef char* as_str(data, char* error_msg='Cannot convert type %s to str'):             # <<<<<<<<<<<<<<
+ * cdef bytes as_str(data, char* error_msg='Cannot convert type %s to str'):             # <<<<<<<<<<<<<<
  *     cdef bytes ret
  *     if isinstance(data, unicode):
  */
 
-static char *__pyx_f_5_cdec_as_str(PyObject *__pyx_v_data, struct __pyx_opt_args_5_cdec_as_str *__pyx_optional_args) {
+static PyObject *__pyx_f_5_cdec_as_str(PyObject *__pyx_v_data, struct __pyx_opt_args_5_cdec_as_str *__pyx_optional_args) {
   char *__pyx_v_error_msg = ((char *)__pyx_k_1);
   PyObject *__pyx_v_ret = 0;
-  char *__pyx_r;
+  PyObject *__pyx_r = NULL;
   __Pyx_RefNannyDeclarations
   PyObject *__pyx_t_1 = NULL;
   int __pyx_t_2;
   PyObject *__pyx_t_3 = NULL;
   PyObject *__pyx_t_4 = NULL;
-  char *__pyx_t_5;
   int __pyx_lineno = 0;
   const char *__pyx_filename = NULL;
   int __pyx_clineno = 0;
@@ -2219,7 +2313,7 @@ static char *__pyx_f_5_cdec_as_str(PyObject *__pyx_v_data, struct __pyx_opt_args
   }
 
   /* "_cdec.pyx":8
- * cdef char* as_str(data, char* error_msg='Cannot convert type %s to str'):
+ * cdef bytes as_str(data, char* error_msg='Cannot convert type %s to str'):
  *     cdef bytes ret
  *     if isinstance(data, unicode):             # <<<<<<<<<<<<<<
  *         ret = data.encode('utf8')
@@ -2318,26 +2412,32 @@ static char *__pyx_f_5_cdec_as_str(PyObject *__pyx_v_data, struct __pyx_opt_args
  * 
  * include "vectors.pxi"
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 static int __pyx_pw_5_cdec_11DenseVector_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":28
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-  if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":33
+  /* "/home/vchahune/tools/cdec/python/src/vectors.pxi":34
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- *             yield FDConvert(fid).c_str(), self.vector[0][fid]
+ *             yield str(FDConvert(fid).c_str()), self.vector[0][fid]
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":34
+    /* "/home/vchahune/tools/cdec/python/src/vectors.pxi":35
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+    __pyx_t_3 = PyBytes_FromString(FD::Convert(__pyx_cur_scope->__pyx_v_fid).c_str()); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_t_3));
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+    __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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 /* Python wrapper */
 static PyObject *__pyx_pw_5_cdec_11DenseVector_14dot(PyObject *__pyx_v_self, PyObject *__pyx_v_other); /*proto*/
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 static PyObject *__pyx_pw_5_cdec_11DenseVector_14dot(PyObject *__pyx_v_self, PyObject *__pyx_v_other) {
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+  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_other), __pyx_ptype_5_cdec_SparseVector, 1, "other", 0))) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -2862,12 +2981,12 @@ static PyObject *__pyx_pw_5_cdec_11DenseVector_14dot(PyObject *__pyx_v_self, PyO
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":36
- *             yield FDConvert(fid).c_str(), self.vector[0][fid]
+/* "/home/vchahune/tools/cdec/python/src/vectors.pxi":37
+ *             yield str(FDConvert(fid).c_str()), self.vector[0][fid]
  * 
  *     def dot(self, SparseVector other):             # <<<<<<<<<<<<<<
+ *         """vector.dot(SparseVector other) -> Dot product of the two vectors."""
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- * 
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 static PyObject *__pyx_pf_5_cdec_11DenseVector_13dot(struct __pyx_obj_5_cdec_DenseVector *__pyx_v_self, struct __pyx_obj_5_cdec_SparseVector *__pyx_v_other) {
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":37
- * 
+  /* "/home/vchahune/tools/cdec/python/src/vectors.pxi":39
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+  __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_other), __pyx_n_s__dot); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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 /* Python wrapper */
 static PyObject *__pyx_pw_5_cdec_11DenseVector_16tosparse(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_5_cdec_11DenseVector_15tosparse[] = "vector.tosparse() -> Equivalent SparseVector.";
 static PyObject *__pyx_pw_5_cdec_11DenseVector_16tosparse(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":39
+/* "/home/vchahune/tools/cdec/python/src/vectors.pxi":41
  *         return other.dot(self)
  * 
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 static PyObject *__pyx_pf_5_cdec_11DenseVector_15tosparse(struct __pyx_obj_5_cdec_DenseVector *__pyx_v_self) {
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":40
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+  /* "/home/vchahune/tools/cdec/python/src/vectors.pxi":43
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+  __pyx_t_1 = __Pyx_tp_new(((PyObject*)__pyx_ptype_5_cdec_SparseVector)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  if (!(likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5_cdec_SparseVector)))) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":41
- *     def tosparse(self):
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":42
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":43
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 /* Python wrapper */
 static int __pyx_pw_5_cdec_12SparseVector_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
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-/* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":48
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 static int __pyx_pf_5_cdec_12SparseVector___init__(struct __pyx_obj_5_cdec_SparseVector *__pyx_v_self) {
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":49
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+  /* "/home/vchahune/tools/cdec/python/src/vectors.pxi":53
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-/* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":51
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":52
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 /* Python wrapper */
 static PyObject *__pyx_pw_5_cdec_12SparseVector_5copy(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
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 static PyObject *__pyx_pw_5_cdec_12SparseVector_5copy(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":54
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- * 
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":55
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+  /* "/home/vchahune/tools/cdec/python/src/vectors.pxi":60
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-/* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":57
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":58
+  /* "/home/vchahune/tools/cdec/python/src/vectors.pxi":63
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":59
+  /* "/home/vchahune/tools/cdec/python/src/vectors.pxi":64
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-    {__pyx_filename = __pyx_f[1]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":60
+  /* "/home/vchahune/tools/cdec/python/src/vectors.pxi":65
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+  __pyx_t_2 = PyFloat_FromDouble(__pyx_v_self->vector->value(__pyx_v_fid)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_v_fname = PyBytes_AsString(__pyx_arg_fname); if (unlikely((!__pyx_v_fname) && PyErr_Occurred())) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":62
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  *     def __setitem__(self, char* fname, float value):             # <<<<<<<<<<<<<<
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":63
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-  __pyx_v_fid = FD::Convert(((char *)__pyx_v_fname));
+  __pyx_v_fid = FD::Convert(__pyx_v_fname);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":64
+  /* "/home/vchahune/tools/cdec/python/src/vectors.pxi":69
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-    {__pyx_filename = __pyx_f[1]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":65
- *         cdef int fid = FDConvert(<char *>fname)
+  /* "/home/vchahune/tools/cdec/python/src/vectors.pxi":70
+ *         cdef int fid = FDConvert(fname)
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":67
+/* "/home/vchahune/tools/cdec/python/src/vectors.pxi":72
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+    __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_5_cdec_12SparseVector_12generator1, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":68
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":70
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- *                 yield (FDConvert(it[0].ptr().first).c_str(), it[0].ptr().second)
+ *                 yield (str(FDConvert(it[0].ptr().first).c_str()), it[0].ptr().second)
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":71
+    /* "/home/vchahune/tools/cdec/python/src/vectors.pxi":76
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  *             for i in range(self.vector.size()):             # <<<<<<<<<<<<<<
- *                 yield (FDConvert(it[0].ptr().first).c_str(), it[0].ptr().second)
+ *                 yield (str(FDConvert(it[0].ptr().first).c_str()), it[0].ptr().second)
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":72
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-      if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L5;}
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":73
+      /* "/home/vchahune/tools/cdec/python/src/vectors.pxi":78
  *             for i in range(self.vector.size()):
- *                 yield (FDConvert(it[0].ptr().first).c_str(), it[0].ptr().second)
+ *                 yield (str(FDConvert(it[0].ptr().first).c_str()), it[0].ptr().second)
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     }
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":75
+  /* "/home/vchahune/tools/cdec/python/src/vectors.pxi":80
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 /* Python wrapper */
 static PyObject *__pyx_pw_5_cdec_12SparseVector_14dot(PyObject *__pyx_v_self, PyObject *__pyx_v_other); /*proto*/
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 static PyObject *__pyx_pw_5_cdec_12SparseVector_14dot(PyObject *__pyx_v_self, PyObject *__pyx_v_other) {
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":77
+/* "/home/vchahune/tools/cdec/python/src/vectors.pxi":82
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":78
- * 
+  /* "/home/vchahune/tools/cdec/python/src/vectors.pxi":84
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":79
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+    /* "/home/vchahune/tools/cdec/python/src/vectors.pxi":85
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@@ -3594,7 +3728,7 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_13dot(struct __pyx_obj_5_cdec_Sp
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":80
+  /* "/home/vchahune/tools/cdec/python/src/vectors.pxi":86
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":81
+    /* "/home/vchahune/tools/cdec/python/src/vectors.pxi":87
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@@ -3624,26 +3758,26 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_13dot(struct __pyx_obj_5_cdec_Sp
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":82
+  /* "/home/vchahune/tools/cdec/python/src/vectors.pxi":88
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-  {__pyx_filename = __pyx_f[1]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_x), __pyx_ptype_5_cdec_SparseVector, 1, "x", 0))) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 90; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -3675,7 +3809,7 @@ static PyObject *__pyx_pw_5_cdec_12SparseVector_16__richcmp__(PyObject *__pyx_v_
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":84
+/* "/home/vchahune/tools/cdec/python/src/vectors.pxi":90
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":87
+  /* "/home/vchahune/tools/cdec/python/src/vectors.pxi":93
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":85
+    /* "/home/vchahune/tools/cdec/python/src/vectors.pxi":91
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":86
+    /* "/home/vchahune/tools/cdec/python/src/vectors.pxi":92
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":87
+    /* "/home/vchahune/tools/cdec/python/src/vectors.pxi":93
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":88
+    /* "/home/vchahune/tools/cdec/python/src/vectors.pxi":94
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@@ -3755,18 +3888,18 @@ static PyObject *__pyx_pf_5_cdec_12SparseVector_15__richcmp__(struct __pyx_obj_5
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":89
+  /* "/home/vchahune/tools/cdec/python/src/vectors.pxi":95
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-/* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":91
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-/* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":94
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":95
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-/* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":97
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":98
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":99
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":100
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":101
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@@ -3971,7 +4104,7 @@ static PyObject *__pyx_pw_5_cdec_12SparseVector_24__iadd__(PyObject *__pyx_v_sel
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-/* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":103
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":104
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":105
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-/* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":107
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":108
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":109
+  /* "/home/vchahune/tools/cdec/python/src/vectors.pxi":115
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-/* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":111
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":112
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":113
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-/* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":115
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":116
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":117
+  /* "/home/vchahune/tools/cdec/python/src/vectors.pxi":123
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":120
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":121
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":122
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":125
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+  __pyx_t_1 = __Pyx_tp_new(((PyObject*)__pyx_ptype_5_cdec_SparseVector)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":126
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":127
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-/* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":129
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":132
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":133
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":134
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":136
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":143
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+  if (!(likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5_cdec_SparseVector)))) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 149; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":144
+  /* "/home/vchahune/tools/cdec/python/src/vectors.pxi":150
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":145
+  /* "/home/vchahune/tools/cdec/python/src/vectors.pxi":151
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+static PyObject *__pyx_gb_5_cdec_7_phrase_2generator18(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":6
+/* "/home/vchahune/tools/cdec/python/src/grammar.pxi":6
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-static PyObject *__pyx_gb_5_cdec_7_phrase_2generator17(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value) /* generator body */
+static PyObject *__pyx_gb_5_cdec_7_phrase_2generator18(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value) /* generator body */
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":5
+/* "/home/vchahune/tools/cdec/python/src/grammar.pxi":5
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":6
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":6
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+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":13
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-  __Pyx_GIVEREF(((PyObject *)__pyx_t_1));
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-  __pyx_t_1 = 0;
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":13
- *     def __init__(self, char* cat, unsigned ref=0):
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":14
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  *         self.ref = ref             # <<<<<<<<<<<<<<
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   __pyx_r = 0;
-  goto __pyx_L0;
-  __pyx_L1_error:;
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   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":15
+/* "/home/vchahune/tools/cdec/python/src/grammar.pxi":16
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":16
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":17
+    /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":18
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":18
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":19
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+  __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_9), ((PyObject *)__pyx_v_self->cat)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 19; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":9
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  * 
  * cdef class NT:
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  *     cdef public unsigned ref
- *     def __init__(self, char* cat, unsigned ref=0):
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 static PyObject *__pyx_pf_5_cdec_2NT_3cat___get__(struct __pyx_obj_5_cdec_NT *__pyx_v_self) {
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":10
+/* "/home/vchahune/tools/cdec/python/src/grammar.pxi":10
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- *     def __init__(self, char* cat, unsigned ref=0):
- *         self.cat = cat
+ *     def __init__(self, bytes cat, unsigned ref=0):
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 static PyObject *__pyx_pf_5_cdec_2NT_3ref___get__(struct __pyx_obj_5_cdec_NT *__pyx_v_self) {
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 /* Python wrapper */
 static int __pyx_pw_5_cdec_5NTRef_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_5_cdec_5NTRef___init__[] = "NTRef(int ref) -> Non-terminal reference.";
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+struct wrapperbase __pyx_wrapperbase_5_cdec_5NTRef___init__;
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+  __Pyx_RaiseArgtupleInvalid("__init__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":22
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-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":25
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":26
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-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":21
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+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":32
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":35
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  *     f, e = [], []
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":38
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":42
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+  if (PyObject_SetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__scores, __pyx_v_scores) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":59
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":64
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":60
+    /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":65
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":61
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":66
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  *         self.rule.get().ComputeArity()             # <<<<<<<<<<<<<<
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-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":63
+/* "/home/vchahune/tools/cdec/python/src/grammar.pxi":68
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":64
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-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":67
+/* "/home/vchahune/tools/cdec/python/src/grammar.pxi":72
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":68
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":73
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+  __pyx_t_1 = PyInt_FromLong(__pyx_v_self->rule->get()->arity_); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 73; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":71
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":72
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":77
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":74
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":79
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+  __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":76
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":81
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":77
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":82
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  *             for i in range(f_.size()):             # <<<<<<<<<<<<<<
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":78
+    /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":83
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":79
+    /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":84
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":80
+      /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":85
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":81
+      /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":86
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- *                     f.append(NT(TDConvert(-w), idx))             # <<<<<<<<<<<<<<
+ *                     f.append(NT(TDConvert(-w).c_str(), idx))             # <<<<<<<<<<<<<<
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+      __pyx_t_1 = PyBytes_FromString(TD::Convert((-__pyx_v_w)).c_str()); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_5 = PyInt_FromLong(__pyx_v_idx); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":83
- *                     f.append(NT(TDConvert(-w), idx))
+      /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":88
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+      __pyx_t_6 = PyBytes_FromString(TD::Convert(__pyx_v_w).c_str()); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_6 = __Pyx_PyObject_Append(__pyx_v_f, __pyx_t_1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -6260,9 +6311,9 @@ static PyObject *__pyx_pf_5_cdec_5TRule_1f___get__(struct __pyx_obj_5_cdec_TRule
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":84
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":89
  *                 else:
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+ *                     f.append(unicode(TDConvert(w).c_str(), encoding='utf8'))
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  *         def __set__(self, f):
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":86
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   unsigned int __pyx_v_i;
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":87
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":88
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":93
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":90
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":95
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":91
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":96
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":95
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":101
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":103
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":104
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":105
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":107
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":108
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":111
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":115
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":121
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-  __pyx_t_1 = PyObject_Length(__pyx_v_e); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 115; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_Length(__pyx_v_e); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":117
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":123
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-  __pyx_t_1 = PyObject_Length(__pyx_v_e); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_Length(__pyx_v_e); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":118
+    /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":124
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":119
+      /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":125
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+      __pyx_t_6 = __Pyx_PyInt_from_py_WordID(__pyx_t_4); if (unlikely((__pyx_t_6 == (WordID)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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       goto __pyx_L5;
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":121
+      /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":127
  *                     e_[0][i] = 1-e[i].ref
  *                 else:
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+ *                     ei = as_str(e[i])             # <<<<<<<<<<<<<<
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-      __pyx_t_4 = __Pyx_GetItemInt(__pyx_v_e, __pyx_v_i, sizeof(unsigned int)+1, PyLong_FromUnsignedLong); if (!__pyx_t_4) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_4 = __Pyx_GetItemInt(__pyx_v_e, __pyx_v_i, sizeof(unsigned int)+1, PyLong_FromUnsignedLong); if (!__pyx_t_4) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 127; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      ((__pyx_v_e_[0])[__pyx_v_i]) = TD::Convert(((char *)__pyx_f_5_cdec_as_str(__pyx_t_4, NULL)));
+      __pyx_t_3 = ((PyObject *)__pyx_f_5_cdec_as_str(__pyx_t_4, NULL)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 127; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __Pyx_GOTREF(__pyx_t_3);
       __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+      __Pyx_XDECREF(((PyObject *)__pyx_v_ei));
+      __pyx_v_ei = ((PyObject*)__pyx_t_3);
+      __pyx_t_3 = 0;
+
+      /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":128
+ *                 else:
+ *                     ei = as_str(e[i])
+ *                     e_[0][i] = TDConvert(ei)             # <<<<<<<<<<<<<<
+ * 
+ *     property a:
+ */
+      __pyx_t_7 = PyBytes_AsString(((PyObject *)__pyx_v_ei)); if (unlikely((!__pyx_t_7) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 128; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      ((__pyx_v_e_[0])[__pyx_v_i]) = TD::Convert(__pyx_t_7);
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@@ -6738,6 +6818,7 @@ static int __pyx_pf_5_cdec_5TRule_1e_2__set__(struct __pyx_obj_5_cdec_TRule *__p
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 }
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":124
+/* "/home/vchahune/tools/cdec/python/src/grammar.pxi":131
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+    __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_5_cdec_5TRule_1a_2generator2, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -6817,9 +6898,9 @@ static PyObject *__pyx_gb_5_cdec_5TRule_1a_2generator2(__pyx_GeneratorObject *__
     return NULL;
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   __pyx_L3_first_run:;
-  if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":126
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":133
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":127
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":134
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  *             for i in range(a.size()):             # <<<<<<<<<<<<<<
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     __pyx_cur_scope->__pyx_v_i = __pyx_t_2;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":128
+    /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":135
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-    __pyx_t_3 = PyInt_FromLong(((__pyx_cur_scope->__pyx_v_a[0])[__pyx_cur_scope->__pyx_v_i]).s_); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 128; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_3 = PyInt_FromLong(((__pyx_cur_scope->__pyx_v_a[0])[__pyx_cur_scope->__pyx_v_i]).s_); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_4 = PyInt_FromLong(((__pyx_cur_scope->__pyx_v_a[0])[__pyx_cur_scope->__pyx_v_i]).t_); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 128; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -6898,7 +6979,7 @@ static int __pyx_pw_5_cdec_5TRule_1a_4__set__(PyObject *__pyx_v_self, PyObject *
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":130
+/* "/home/vchahune/tools/cdec/python/src/grammar.pxi":137
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":131
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":138
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":132
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":139
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-  __pyx_t_1 = PyObject_Length(__pyx_v_a); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_Length(__pyx_v_a); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_a_->resize(__pyx_t_1);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":135
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":142
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-  __pyx_t_1 = PyObject_Length(__pyx_v_a); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_Length(__pyx_v_a); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":136
+    /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":143
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+    __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_a, __pyx_v_i, sizeof(unsigned int)+1, PyLong_FromUnsignedLong); if (!__pyx_t_3) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 143; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-        {__pyx_filename = __pyx_f[2]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        {__pyx_filename = __pyx_f[2]; __pyx_lineno = 143; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_4 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 143; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      {__pyx_filename = __pyx_f[2]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":137
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":140
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":141
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+  __pyx_t_1 = __Pyx_tp_new(((PyObject*)__pyx_ptype_5_cdec_SparseVector)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 148; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":142
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":149
  *         def __get__(self):
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":143
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":150
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":145
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   int __pyx_v_fid;
   float __pyx_v_fval;
   PyObject *__pyx_v_fname = NULL;
+  PyObject *__pyx_v_fn = NULL;
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   PyObject *(*__pyx_t_8)(PyObject *);
   float __pyx_t_9;
-  int __pyx_t_10;
+  char *__pyx_t_10;
+  int __pyx_t_11;
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":146
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":153
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  *             cdef FastSparseVector[double]* scores_ = &self.rule.get().scores_             # <<<<<<<<<<<<<<
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  */
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":147
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":154
  *         def __set__(self, scores):
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":150
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":157
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  *             cdef float fval
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- *                 fid = FDConvert(<char *>as_str(fname))
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+ *                 fid = FDConvert(fn)
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+  __pyx_t_1 = PyObject_GetAttr(__pyx_v_scores, __pyx_n_s__items); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_2); __pyx_t_3++;
+      __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_2); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 150; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+      __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_2); __pyx_t_3++;
+      __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_2); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-          else {__pyx_filename = __pyx_f[2]; __pyx_lineno = 150; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -7238,7 +7321,7 @@ static int __pyx_pf_5_cdec_5TRule_6scores_2__set__(struct __pyx_obj_5_cdec_TRule
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         else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
-        {__pyx_filename = __pyx_f[2]; __pyx_lineno = 150; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        {__pyx_filename = __pyx_f[2]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -7251,14 +7334,14 @@ static int __pyx_pf_5_cdec_5TRule_6scores_2__set__(struct __pyx_obj_5_cdec_TRule
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+      __pyx_t_6 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      {__pyx_filename = __pyx_f[2]; __pyx_lineno = 150; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":151
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+ *                 fn = as_str(fname)             # <<<<<<<<<<<<<<
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+    __Pyx_GOTREF(__pyx_t_2);
+    __Pyx_XDECREF(((PyObject *)__pyx_v_fn));
+    __pyx_v_fn = ((PyObject*)__pyx_t_2);
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":152
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+ *                 fn = as_str(fname)
+ *                 fid = FDConvert(fn)             # <<<<<<<<<<<<<<
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+ *                 scores_.set_value(fid, fval)
+ */
+    __pyx_t_10 = PyBytes_AsString(((PyObject *)__pyx_v_fn)); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_v_fid = FD::Convert(__pyx_t_10);
+
+    /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":160
+ *                 fn = as_str(fname)
+ *                 fid = FDConvert(fn)
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+    __pyx_t_11 = (__pyx_v_fid < 0);
+    if (__pyx_t_11) {
+      __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_6 = PyObject_Call(__pyx_builtin_KeyError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      {__pyx_filename = __pyx_f[2]; __pyx_lineno = 152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      {__pyx_filename = __pyx_f[2]; __pyx_lineno = 160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":153
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+    /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":161
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":156
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":157
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+  __pyx_t_1 = PyBytes_FromString(TD::Convert((-__pyx_v_self->rule->get()->lhs_)).c_str()); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 165; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 165; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5_cdec_NT)), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 165; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":159
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":160
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":161
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":162
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-  __pyx_v_self->rule->get()->lhs_ = (-TD::Convert(((char *)__pyx_t_5)));
+  __pyx_t_5 = PyBytes_AsString(((PyObject *)((struct __pyx_obj_5_cdec_NT *)__pyx_v_lhs)->cat)); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 170; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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 }
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-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":165
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+    __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_5_cdec_5TRule_7__str___2generator19, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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 }
 
-static PyObject *__pyx_gb_5_cdec_5TRule_7__str___2generator18(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value) /* generator body */
+static PyObject *__pyx_gb_5_cdec_5TRule_7__str___2generator19(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value) /* generator body */
 {
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+  if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (unlikely(!__pyx_cur_scope->__pyx_outer_scope->__pyx_v_self)) { __Pyx_RaiseClosureNameError("self"); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
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+    __pyx_t_3 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++;
+      __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_1 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++;
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-          else {__pyx_filename = __pyx_f[2]; __pyx_lineno = 165; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_11), __pyx_cur_scope->__pyx_v_feat); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+/* "/home/vchahune/tools/cdec/python/src/grammar.pxi":172
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":165
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 /* Python wrapper */
 static int __pyx_pw_5_cdec_5MRule_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
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+/* "/home/vchahune/tools/cdec/python/src/grammar.pxi":178
+ * 
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+ *         """MRule(lhs, rhs, scores, a=None) -> Monolingual rule.
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+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":183
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":172
- *     def __init__(self, lhs, rhs, scores, a=None):
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":184
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":173
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  *         cdef unsigned i = 1
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-      __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++;
+      __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 185; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 185; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++;
+      __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 185; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 185; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-          else {__pyx_filename = __pyx_f[2]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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     __pyx_v_s = __pyx_t_4;
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":174
+    /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":186
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":175
+      /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":187
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+      __pyx_t_4 = PyLong_FromUnsignedLong(__pyx_v_i); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_4 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5_cdec_NTRef)), ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":176
+      /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":188
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":178
+      /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":190
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":179
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":191
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+  __pyx_t_4 = PyTuple_New(5); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 191; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __Pyx_INCREF(Py_None);
+  PyTuple_SET_ITEM(__pyx_t_4, 4, Py_None);
+  __Pyx_GIVEREF(Py_None);
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":184
+/* "/home/vchahune/tools/cdec/python/src/grammar.pxi":196
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":185
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":197
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":187
+/* "/home/vchahune/tools/cdec/python/src/grammar.pxi":199
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+    __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_5_cdec_7Grammar_4generator3, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 199; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 199; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":188
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":200
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":189
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":201
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":192
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":204
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":193
+    /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":205
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-    __pyx_t_3 = __Pyx_tp_new(((PyObject*)__pyx_ptype_5_cdec_TRule)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_3 = __Pyx_tp_new(((PyObject*)__pyx_ptype_5_cdec_TRule)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    if (!(likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5_cdec_TRule)))) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":194
+    /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":206
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":195
+    /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":207
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-    if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 207; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -8288,29 +8375,51 @@ static PyObject *__pyx_pw_5_cdec_7Grammar_4name_1__get__(PyObject *__pyx_v_self)
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":198
+/* "/home/vchahune/tools/cdec/python/src/grammar.pxi":210
  * 
  *     property name:
  *         def __get__(self):             # <<<<<<<<<<<<<<
- *             self.grammar.get().GetGrammarName().c_str()
+ *             str(self.grammar.get().GetGrammarName().c_str())
  * 
  */
 
 static PyObject *__pyx_pf_5_cdec_7Grammar_4name___get__(struct __pyx_obj_5_cdec_Grammar *__pyx_v_self) {
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   __Pyx_RefNannyDeclarations
+  PyObject *__pyx_t_1 = NULL;
+  PyObject *__pyx_t_2 = NULL;
+  int __pyx_lineno = 0;
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+  int __pyx_clineno = 0;
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":199
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":211
  *     property name:
  *         def __get__(self):
- *             self.grammar.get().GetGrammarName().c_str()             # <<<<<<<<<<<<<<
+ *             str(self.grammar.get().GetGrammarName().c_str())             # <<<<<<<<<<<<<<
  * 
  *         def __set__(self, name):
  */
-  __pyx_v_self->grammar->get()->GetGrammarName().c_str();
+  __pyx_t_1 = PyBytes_FromString(__pyx_v_self->grammar->get()->GetGrammarName().c_str()); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 211; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1));
+  __Pyx_GIVEREF(((PyObject *)__pyx_t_1));
+  __pyx_t_1 = 0;
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+  __Pyx_GOTREF(__pyx_t_1);
+  __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
   __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+  goto __pyx_L0;
+  __pyx_L1_error:;
+  __Pyx_XDECREF(__pyx_t_1);
+  __Pyx_XDECREF(__pyx_t_2);
+  __Pyx_AddTraceback("_cdec.Grammar.name.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+  __pyx_r = NULL;
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@@ -8327,50 +8436,71 @@ static int __pyx_pw_5_cdec_7Grammar_4name_3__set__(PyObject *__pyx_v_self, PyObj
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":201
- *             self.grammar.get().GetGrammarName().c_str()
+/* "/home/vchahune/tools/cdec/python/src/grammar.pxi":213
+ *             str(self.grammar.get().GetGrammarName().c_str())
  * 
  *         def __set__(self, name):             # <<<<<<<<<<<<<<
- *             self.grammar.get().SetGrammarName(string(<char *>name))
- * 
+ *             name = as_str(name)
+ *             self.grammar.get().SetGrammarName(name)
  */
 
 static int __pyx_pf_5_cdec_7Grammar_4name_2__set__(struct __pyx_obj_5_cdec_Grammar *__pyx_v_self, PyObject *__pyx_v_name) {
   int __pyx_r;
   __Pyx_RefNannyDeclarations
-  char *__pyx_t_1;
+  PyObject *__pyx_t_1 = NULL;
+  std::string __pyx_t_2;
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":202
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":214
  * 
  *         def __set__(self, name):
- *             self.grammar.get().SetGrammarName(string(<char *>name))             # <<<<<<<<<<<<<<
+ *             name = as_str(name)             # <<<<<<<<<<<<<<
+ *             self.grammar.get().SetGrammarName(name)
+ * 
+ */
+  __pyx_t_1 = ((PyObject *)__pyx_f_5_cdec_as_str(__pyx_v_name, NULL)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(__pyx_t_1);
+  __Pyx_DECREF(__pyx_v_name);
+  __pyx_v_name = __pyx_t_1;
+  __pyx_t_1 = 0;
+
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":215
+ *         def __set__(self, name):
+ *             name = as_str(name)
+ *             self.grammar.get().SetGrammarName(name)             # <<<<<<<<<<<<<<
  * 
  * cdef class TextGrammar(Grammar):
  */
-  __pyx_t_1 = PyBytes_AsString(__pyx_v_name); if (unlikely((!__pyx_t_1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_v_self->grammar->get()->SetGrammarName(std::string(((char *)__pyx_t_1)));
+  __pyx_t_2 = __pyx_convert_string_from_py_(__pyx_v_name); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_v_self->grammar->get()->SetGrammarName(__pyx_t_2);
 
   __pyx_r = 0;
   goto __pyx_L0;
   __pyx_L1_error:;
+  __Pyx_XDECREF(__pyx_t_1);
   __Pyx_AddTraceback("_cdec.Grammar.name.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
   __pyx_r = -1;
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+  __Pyx_XDECREF(__pyx_v_name);
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 /* Python wrapper */
-static int __pyx_pw_5_cdec_11TextGrammar_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_5_cdec_11TextGrammar_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static int __pyx_pw_5_cdec_11TextGrammar_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_5_cdec_11TextGrammar___init__[] = "TextGrammar(rules) -> SCFG Grammar containing the rules.";
+#if CYTHON_COMPILING_IN_CPYTHON
+struct wrapperbase __pyx_wrapperbase_5_cdec_11TextGrammar___init__;
+#endif
+static int __pyx_pw_5_cdec_11TextGrammar_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   PyObject *__pyx_v_rules = 0;
   int __pyx_r;
   __Pyx_RefNannyDeclarations
-  __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
+  __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
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     PyObject* values[1] = {0};
@@ -8389,7 +8519,7 @@ static int __pyx_pw_5_cdec_11TextGrammar_1__cinit__(PyObject *__pyx_v_self, PyOb
         else goto __pyx_L5_argtuple_error;
       }
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-        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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       goto __pyx_L5_argtuple_error;
@@ -8400,26 +8530,26 @@ static int __pyx_pw_5_cdec_11TextGrammar_1__cinit__(PyObject *__pyx_v_self, PyOb
   }
   goto __pyx_L4_argument_unpacking_done;
   __pyx_L5_argtuple_error:;
-  __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+  __Pyx_RaiseArgtupleInvalid("__init__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
   __pyx_L3_error:;
-  __Pyx_AddTraceback("_cdec.TextGrammar.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+  __Pyx_AddTraceback("_cdec.TextGrammar.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
   __Pyx_RefNannyFinishContext();
   return -1;
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-  __pyx_r = __pyx_pf_5_cdec_11TextGrammar___cinit__(((struct __pyx_obj_5_cdec_TextGrammar *)__pyx_v_self), __pyx_v_rules);
+  __pyx_r = __pyx_pf_5_cdec_11TextGrammar___init__(((struct __pyx_obj_5_cdec_TextGrammar *)__pyx_v_self), __pyx_v_rules);
   __Pyx_RefNannyFinishContext();
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":205
+/* "/home/vchahune/tools/cdec/python/src/grammar.pxi":218
  * 
  * cdef class TextGrammar(Grammar):
- *     def __cinit__(self, rules):             # <<<<<<<<<<<<<<
+ *     def __init__(self, rules):             # <<<<<<<<<<<<<<
+ *         """TextGrammar(rules) -> SCFG Grammar containing the rules."""
  *         self.grammar = new shared_ptr[grammar.Grammar](new grammar.TextGrammar())
- *         cdef grammar.TextGrammar* _g = <grammar.TextGrammar*> self.grammar.get()
  */
 
-static int __pyx_pf_5_cdec_11TextGrammar___cinit__(struct __pyx_obj_5_cdec_TextGrammar *__pyx_v_self, PyObject *__pyx_v_rules) {
+static int __pyx_pf_5_cdec_11TextGrammar___init__(struct __pyx_obj_5_cdec_TextGrammar *__pyx_v_self, PyObject *__pyx_v_rules) {
   TextGrammar *__pyx_v__g;
   PyObject *__pyx_v_trule = NULL;
   int __pyx_r;
@@ -8434,19 +8564,19 @@ static int __pyx_pf_5_cdec_11TextGrammar___cinit__(struct __pyx_obj_5_cdec_TextG
   int __pyx_lineno = 0;
   const char *__pyx_filename = NULL;
   int __pyx_clineno = 0;
-  __Pyx_RefNannySetupContext("__cinit__", 0);
+  __Pyx_RefNannySetupContext("__init__", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":206
- * cdef class TextGrammar(Grammar):
- *     def __cinit__(self, rules):
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":220
+ *     def __init__(self, rules):
+ *         """TextGrammar(rules) -> SCFG Grammar containing the rules."""
  *         self.grammar = new shared_ptr[grammar.Grammar](new grammar.TextGrammar())             # <<<<<<<<<<<<<<
  *         cdef grammar.TextGrammar* _g = <grammar.TextGrammar*> self.grammar.get()
  *         for trule in rules:
  */
   __pyx_v_self->__pyx_base.grammar = new boost::shared_ptr<Grammar>(new TextGrammar());
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":207
- *     def __cinit__(self, rules):
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":221
+ *         """TextGrammar(rules) -> SCFG Grammar containing the rules."""
  *         self.grammar = new shared_ptr[grammar.Grammar](new grammar.TextGrammar())
  *         cdef grammar.TextGrammar* _g = <grammar.TextGrammar*> self.grammar.get()             # <<<<<<<<<<<<<<
  *         for trule in rules:
@@ -8454,7 +8584,7 @@ static int __pyx_pf_5_cdec_11TextGrammar___cinit__(struct __pyx_obj_5_cdec_TextG
  */
   __pyx_v__g = ((TextGrammar *)__pyx_v_self->__pyx_base.grammar->get());
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":208
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":222
  *         self.grammar = new shared_ptr[grammar.Grammar](new grammar.TextGrammar())
  *         cdef grammar.TextGrammar* _g = <grammar.TextGrammar*> self.grammar.get()
  *         for trule in rules:             # <<<<<<<<<<<<<<
@@ -8465,7 +8595,7 @@ static int __pyx_pf_5_cdec_11TextGrammar___cinit__(struct __pyx_obj_5_cdec_TextG
     __pyx_t_1 = __pyx_v_rules; __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0;
     __pyx_t_3 = NULL;
   } else {
-    __pyx_t_2 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_rules); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_rules); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_1);
     __pyx_t_3 = Py_TYPE(__pyx_t_1)->tp_iternext;
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@@ -8473,23 +8603,23 @@ static int __pyx_pf_5_cdec_11TextGrammar___cinit__(struct __pyx_obj_5_cdec_TextG
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       if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_1)) break;
       #if CYTHON_COMPILING_IN_CPYTHON
-      __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++;
+      __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++;
+      __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+      __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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           if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
-          else {__pyx_filename = __pyx_f[2]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          else {__pyx_filename = __pyx_f[2]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -8499,7 +8629,7 @@ static int __pyx_pf_5_cdec_11TextGrammar___cinit__(struct __pyx_obj_5_cdec_TextG
     __pyx_v_trule = __pyx_t_4;
     __pyx_t_4 = 0;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":209
+    /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":223
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  *         for trule in rules:
  *             if isinstance(trule, _sa.Rule):             # <<<<<<<<<<<<<<
@@ -8512,17 +8642,17 @@ static int __pyx_pf_5_cdec_11TextGrammar___cinit__(struct __pyx_obj_5_cdec_TextG
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     if (__pyx_t_5) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":210
+      /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":224
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+      if (!(likely(((__pyx_v_trule) == Py_None) || likely(__Pyx_TypeTest(__pyx_v_trule, __pyx_ptype_4cdec_2sa_3_sa_Rule))))) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 224; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_6 = ((PyObject *)__pyx_f_5_cdec_convert_rule(((struct __pyx_obj_4cdec_2sa_3_sa_Rule *)__pyx_t_4))); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 224; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -8531,7 +8661,7 @@ static int __pyx_pf_5_cdec_11TextGrammar___cinit__(struct __pyx_obj_5_cdec_TextG
       goto __pyx_L5;
     }
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":211
+    /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":225
  *             if isinstance(trule, _sa.Rule):
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  *             elif not isinstance(trule, TRule):             # <<<<<<<<<<<<<<
@@ -8545,22 +8675,22 @@ static int __pyx_pf_5_cdec_11TextGrammar___cinit__(struct __pyx_obj_5_cdec_TextG
     __pyx_t_7 = (!__pyx_t_5);
     if (__pyx_t_7) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":212
+      /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":226
  *                 trule = convert_rule(trule)
  *             elif not isinstance(trule, TRule):
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-      {__pyx_filename = __pyx_f[2]; __pyx_lineno = 212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      {__pyx_filename = __pyx_f[2]; __pyx_lineno = 226; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       goto __pyx_L5;
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":213
+    /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":227
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-  __Pyx_AddTraceback("_cdec.TextGrammar.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+  __Pyx_AddTraceback("_cdec.TextGrammar.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":8
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  *     cdef MT19937* rng
  * 
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":9
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":10
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":10
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":11
+    /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":11
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  *             del self.rng             # <<<<<<<<<<<<<<
  * 
- *     def viterbi(self):
+ *     cdef MT19937* _rng(self):
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@@ -8639,8 +8769,70 @@ static void __pyx_pf_5_cdec_10Hypergraph___dealloc__(struct __pyx_obj_5_cdec_Hyp
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+
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+ *             self.rng = new MT19937()
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+ */
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+    /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":15
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+ * 
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+    __pyx_v_self->rng = __pyx_t_2;
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+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":16
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+ *         return self.rng             # <<<<<<<<<<<<<<
+ * 
+ *     def viterbi(self):
+ */
+  __pyx_r = __pyx_v_self->rng;
+  goto __pyx_L0;
+
+  __pyx_r = 0;
+  goto __pyx_L0;
+  __pyx_L1_error:;
+  __Pyx_WriteUnraisable("_cdec.Hypergraph._rng", __pyx_clineno, __pyx_lineno, __pyx_filename);
+  __pyx_r = 0;
+  __pyx_L0:;
+  __Pyx_RefNannyFinishContext();
+  return __pyx_r;
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+
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 static PyObject *__pyx_pw_5_cdec_10Hypergraph_3viterbi(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_5_cdec_10Hypergraph_2viterbi[] = "hg.viterbi() -> String for the best hypothesis in the hypergraph.";
 static PyObject *__pyx_pw_5_cdec_10Hypergraph_3viterbi(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":13
- *             del self.rng
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":18
+ *         return self.rng
  * 
  *     def viterbi(self):             # <<<<<<<<<<<<<<
+ *         """hg.viterbi() -> String for the best hypothesis in the hypergraph."""
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- *         hypergraph.ViterbiESentence(self.hg[0], &trans)
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 static PyObject *__pyx_pf_5_cdec_10Hypergraph_2viterbi(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self) {
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":15
- *     def viterbi(self):
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":21
+ *         """hg.viterbi() -> String for the best hypothesis in the hypergraph."""
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":16
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":22
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+  __pyx_t_1 = PyBytes_FromString(TD::GetString(__pyx_v_trans).c_str()); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)(&PyUnicode_Type))), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 16; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)(&PyUnicode_Type))), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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 /* Python wrapper */
 static PyObject *__pyx_pw_5_cdec_10Hypergraph_5viterbi_trees(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_5_cdec_10Hypergraph_4viterbi_trees[] = "hg.viterbi_trees() -> (f_tree, e_tree)\n        f_tree: Source tree for the best hypothesis in the hypergraph.\n        e_tree: Target tree for the best hypothesis in the hypergraph.\n        ";
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":18
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":24
  *         return unicode(GetString(trans).c_str(), 'utf8')
  * 
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- *         f_tree = unicode(hypergraph.ViterbiFTree(self.hg[0]).c_str(), 'utf8')
- *         e_tree = unicode(hypergraph.ViterbiETree(self.hg[0]).c_str(), 'utf8')
+ *         """hg.viterbi_trees() -> (f_tree, e_tree)
+ *         f_tree: Source tree for the best hypothesis in the hypergraph.
  */
 
 static PyObject *__pyx_pf_5_cdec_10Hypergraph_4viterbi_trees(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self) {
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":19
- * 
- *     def viterbi_trees(self):
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":29
+ *         e_tree: Target tree for the best hypothesis in the hypergraph.
+ *         """
  *         f_tree = unicode(hypergraph.ViterbiFTree(self.hg[0]).c_str(), 'utf8')             # <<<<<<<<<<<<<<
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+  __pyx_t_1 = PyBytes_FromString(ViterbiFTree((__pyx_v_self->hg[0])).c_str()); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __Pyx_GIVEREF(((PyObject *)__pyx_n_s__utf8));
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+  __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)(&PyUnicode_Type))), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":20
- *     def viterbi_trees(self):
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":30
+ *         """
  *         f_tree = unicode(hypergraph.ViterbiFTree(self.hg[0]).c_str(), 'utf8')
  *         e_tree = unicode(hypergraph.ViterbiETree(self.hg[0]).c_str(), 'utf8')             # <<<<<<<<<<<<<<
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+  __pyx_t_1 = PyBytes_FromString(ViterbiETree((__pyx_v_self->hg[0])).c_str()); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 30; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 30; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)(&PyUnicode_Type))), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 30; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":21
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":31
  *         f_tree = unicode(hypergraph.ViterbiFTree(self.hg[0]).c_str(), 'utf8')
  *         e_tree = unicode(hypergraph.ViterbiETree(self.hg[0]).c_str(), 'utf8')
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+  __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -8830,6 +9023,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_4viterbi_trees(struct __pyx_obj_5_
 
 /* Python wrapper */
 static PyObject *__pyx_pw_5_cdec_10Hypergraph_7viterbi_features(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_5_cdec_10Hypergraph_6viterbi_features[] = "hg.viterbi_features() -> SparseVector with the features corresponding\n        to the best derivation in the hypergraph.";
 static PyObject *__pyx_pw_5_cdec_10Hypergraph_7viterbi_features(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":23
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":33
  *         return (f_tree, e_tree)
  * 
  *     def viterbi_features(self):             # <<<<<<<<<<<<<<
- *         cdef SparseVector fmap = SparseVector.__new__(SparseVector)
- *         fmap.vector = new FastSparseVector[weight_t](hypergraph.ViterbiFeatures(self.hg[0]))
+ *         """hg.viterbi_features() -> SparseVector with the features corresponding
+ *         to the best derivation in the hypergraph."""
  */
 
 static PyObject *__pyx_pf_5_cdec_10Hypergraph_6viterbi_features(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self) {
@@ -8857,21 +9051,21 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_6viterbi_features(struct __pyx_obj
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("viterbi_features", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":24
- * 
- *     def viterbi_features(self):
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":36
+ *         """hg.viterbi_features() -> SparseVector with the features corresponding
+ *         to the best derivation in the hypergraph."""
  *         cdef SparseVector fmap = SparseVector.__new__(SparseVector)             # <<<<<<<<<<<<<<
  *         fmap.vector = new FastSparseVector[weight_t](hypergraph.ViterbiFeatures(self.hg[0]))
  *         return fmap
  */
-  __pyx_t_1 = __Pyx_tp_new(((PyObject*)__pyx_ptype_5_cdec_SparseVector)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 24; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = __Pyx_tp_new(((PyObject*)__pyx_ptype_5_cdec_SparseVector)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_1);
-  if (!(likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5_cdec_SparseVector)))) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 24; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (!(likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5_cdec_SparseVector)))) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_fmap = ((struct __pyx_obj_5_cdec_SparseVector *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":25
- *     def viterbi_features(self):
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":37
+ *         to the best derivation in the hypergraph."""
  *         cdef SparseVector fmap = SparseVector.__new__(SparseVector)
  *         fmap.vector = new FastSparseVector[weight_t](hypergraph.ViterbiFeatures(self.hg[0]))             # <<<<<<<<<<<<<<
  *         return fmap
@@ -8879,7 +9073,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_6viterbi_features(struct __pyx_obj
  */
   __pyx_v_fmap->vector = new FastSparseVector<weight_t>(ViterbiFeatures((__pyx_v_self->hg[0])));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":26
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":38
  *         cdef SparseVector fmap = SparseVector.__new__(SparseVector)
  *         fmap.vector = new FastSparseVector[weight_t](hypergraph.ViterbiFeatures(self.hg[0]))
  *         return fmap             # <<<<<<<<<<<<<<
@@ -8906,6 +9100,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_6viterbi_features(struct __pyx_obj
 
 /* Python wrapper */
 static PyObject *__pyx_pw_5_cdec_10Hypergraph_9viterbi_joshua(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_5_cdec_10Hypergraph_8viterbi_joshua[] = "hg.viterbi_joshua() -> Joshua representation of the best derivation.";
 static PyObject *__pyx_pw_5_cdec_10Hypergraph_9viterbi_joshua(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
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@@ -8915,12 +9110,12 @@ static PyObject *__pyx_pw_5_cdec_10Hypergraph_9viterbi_joshua(PyObject *__pyx_v_
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":28
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":40
  *         return fmap
  * 
  *     def viterbi_joshua(self):             # <<<<<<<<<<<<<<
+ *         """hg.viterbi_joshua() -> Joshua representation of the best derivation."""
  *         return unicode(hypergraph.JoshuaVisualizationString(self.hg[0]).c_str(), 'utf8')
- * 
  */
 
 static PyObject *__pyx_pf_5_cdec_10Hypergraph_8viterbi_joshua(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self) {
@@ -8933,17 +9128,17 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_8viterbi_joshua(struct __pyx_obj_5
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("viterbi_joshua", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":29
- * 
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":42
  *     def viterbi_joshua(self):
+ *         """hg.viterbi_joshua() -> Joshua representation of the best derivation."""
  *         return unicode(hypergraph.JoshuaVisualizationString(self.hg[0]).c_str(), 'utf8')             # <<<<<<<<<<<<<<
  * 
  *     def kbest(self, size):
  */
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-  __pyx_t_1 = PyBytes_FromString(JoshuaVisualizationString((__pyx_v_self->hg[0])).c_str()); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyBytes_FromString(JoshuaVisualizationString((__pyx_v_self->hg[0])).c_str()); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(((PyObject *)__pyx_t_1));
-  __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -8951,7 +9146,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_8viterbi_joshua(struct __pyx_obj_5
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   __Pyx_GIVEREF(((PyObject *)__pyx_n_s__utf8));
   __pyx_t_1 = 0;
-  __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)(&PyUnicode_Type))), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)(&PyUnicode_Type))), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -8974,6 +9169,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_12generator4(__pyx_GeneratorObject
 
 /* Python wrapper */
 static PyObject *__pyx_pw_5_cdec_10Hypergraph_11kbest(PyObject *__pyx_v_self, PyObject *__pyx_v_size); /*proto*/
+static char __pyx_doc_5_cdec_10Hypergraph_10kbest[] = "hg.kbest(size) -> List of k-best hypotheses in the hypergraph.";
 static PyObject *__pyx_pw_5_cdec_10Hypergraph_11kbest(PyObject *__pyx_v_self, PyObject *__pyx_v_size) {
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   __Pyx_RefNannyDeclarations
@@ -8983,12 +9179,12 @@ static PyObject *__pyx_pw_5_cdec_10Hypergraph_11kbest(PyObject *__pyx_v_self, Py
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":31
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":44
  *         return unicode(hypergraph.JoshuaVisualizationString(self.hg[0]).c_str(), 'utf8')
  * 
  *     def kbest(self, size):             # <<<<<<<<<<<<<<
+ *         """hg.kbest(size) -> List of k-best hypotheses in the hypergraph."""
  *         cdef kbest.KBestDerivations[vector[WordID], kbest.ESentenceTraversal]* derivations = new kbest.KBestDerivations[vector[WordID], kbest.ESentenceTraversal](self.hg[0], size)
- *         cdef kbest.KBestDerivations[vector[WordID], kbest.ESentenceTraversal].Derivation* derivation
  */
 
 static PyObject *__pyx_pf_5_cdec_10Hypergraph_10kbest(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self, PyObject *__pyx_v_size) {
@@ -9012,7 +9208,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_10kbest(struct __pyx_obj_5_cdec_Hy
   __Pyx_INCREF(__pyx_cur_scope->__pyx_v_size);
   __Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_size);
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-    __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_5_cdec_10Hypergraph_12generator4, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_5_cdec_10Hypergraph_12generator4, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -9049,19 +9245,19 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_12generator4(__pyx_GeneratorObject
     return NULL;
   }
   __pyx_L3_first_run:;
-  if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":32
- * 
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":46
  *     def kbest(self, size):
+ *         """hg.kbest(size) -> List of k-best hypotheses in the hypergraph."""
  *         cdef kbest.KBestDerivations[vector[WordID], kbest.ESentenceTraversal]* derivations = new kbest.KBestDerivations[vector[WordID], kbest.ESentenceTraversal](self.hg[0], size)             # <<<<<<<<<<<<<<
  *         cdef kbest.KBestDerivations[vector[WordID], kbest.ESentenceTraversal].Derivation* derivation
  *         cdef unsigned k
  */
-  __pyx_t_1 = __Pyx_PyInt_AsUnsignedInt(__pyx_cur_scope->__pyx_v_size); if (unlikely((__pyx_t_1 == (unsigned int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = __Pyx_PyInt_AsUnsignedInt(__pyx_cur_scope->__pyx_v_size); if (unlikely((__pyx_t_1 == (unsigned int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_cur_scope->__pyx_v_derivations = new KBest::KBestDerivations<std::vector<WordID>,ESentenceTraversal>((__pyx_cur_scope->__pyx_v_self->hg[0]), __pyx_t_1);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":35
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":49
  *         cdef kbest.KBestDerivations[vector[WordID], kbest.ESentenceTraversal].Derivation* derivation
  *         cdef unsigned k
  *         try:             # <<<<<<<<<<<<<<
@@ -9070,18 +9266,18 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_12generator4(__pyx_GeneratorObject
  */
   /*try:*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":36
+    /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":50
  *         cdef unsigned k
  *         try:
  *             for k in range(size):             # <<<<<<<<<<<<<<
  *                 derivation = derivations.LazyKthBest(self.hg.nodes_.size() - 1, k)
  *                 if not derivation: break
  */
-    __pyx_t_2 = __Pyx_PyInt_AsLong(__pyx_cur_scope->__pyx_v_size); if (unlikely((__pyx_t_2 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L5;}
+    __pyx_t_2 = __Pyx_PyInt_AsLong(__pyx_cur_scope->__pyx_v_size); if (unlikely((__pyx_t_2 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L5;}
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       __pyx_cur_scope->__pyx_v_k = __pyx_t_1;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":37
+      /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":51
  *         try:
  *             for k in range(size):
  *                 derivation = derivations.LazyKthBest(self.hg.nodes_.size() - 1, k)             # <<<<<<<<<<<<<<
@@ -9090,7 +9286,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_12generator4(__pyx_GeneratorObject
  */
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":38
+      /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":52
  *             for k in range(size):
  *                 derivation = derivations.LazyKthBest(self.hg.nodes_.size() - 1, k)
  *                 if not derivation: break             # <<<<<<<<<<<<<<
@@ -9104,16 +9300,16 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_12generator4(__pyx_GeneratorObject
       }
       __pyx_L9:;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":39
+      /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":53
  *                 derivation = derivations.LazyKthBest(self.hg.nodes_.size() - 1, k)
  *                 if not derivation: break
  *                 yield unicode(GetString(derivation._yield).c_str(), 'utf8')             # <<<<<<<<<<<<<<
  *         finally:
  *             del derivations
  */
-      __pyx_t_4 = PyBytes_FromString(TD::GetString(__pyx_cur_scope->__pyx_v_derivation->yield).c_str()); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L5;}
+      __pyx_t_4 = PyBytes_FromString(TD::GetString(__pyx_cur_scope->__pyx_v_derivation->yield).c_str()); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L5;}
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-      __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L5;}
+      __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L5;}
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       __Pyx_GIVEREF(((PyObject *)__pyx_t_4));
@@ -9121,7 +9317,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_12generator4(__pyx_GeneratorObject
       PyTuple_SET_ITEM(__pyx_t_5, 1, ((PyObject *)__pyx_n_s__utf8));
       __Pyx_GIVEREF(((PyObject *)__pyx_n_s__utf8));
       __pyx_t_4 = 0;
-      __pyx_t_4 = PyObject_Call(((PyObject *)((PyObject*)(&PyUnicode_Type))), ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L5;}
+      __pyx_t_4 = PyObject_Call(((PyObject *)((PyObject*)(&PyUnicode_Type))), ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L5;}
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@@ -9136,12 +9332,12 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_12generator4(__pyx_GeneratorObject
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       __pyx_t_2 = __pyx_cur_scope->__pyx_t_1;
-      if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L5;}
+      if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L5;}
     }
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":41
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":55
  *                 yield unicode(GetString(derivation._yield).c_str(), 'utf8')
  *         finally:
  *             del derivations             # <<<<<<<<<<<<<<
@@ -9192,6 +9388,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_15generator5(__pyx_GeneratorObject
 
 /* Python wrapper */
 static PyObject *__pyx_pw_5_cdec_10Hypergraph_14kbest_trees(PyObject *__pyx_v_self, PyObject *__pyx_v_size); /*proto*/
+static char __pyx_doc_5_cdec_10Hypergraph_13kbest_trees[] = "hg.kbest_trees(size) -> List of k-best trees in the hypergraph.";
 static PyObject *__pyx_pw_5_cdec_10Hypergraph_14kbest_trees(PyObject *__pyx_v_self, PyObject *__pyx_v_size) {
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@@ -9201,12 +9398,12 @@ static PyObject *__pyx_pw_5_cdec_10Hypergraph_14kbest_trees(PyObject *__pyx_v_se
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":43
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":57
  *             del derivations
  * 
  *     def kbest_trees(self, size):             # <<<<<<<<<<<<<<
+ *         """hg.kbest_trees(size) -> List of k-best trees in the hypergraph."""
  *         cdef kbest.KBestDerivations[vector[WordID], kbest.FTreeTraversal]* f_derivations = new kbest.KBestDerivations[vector[WordID], kbest.FTreeTraversal](self.hg[0], size)
- *         cdef kbest.KBestDerivations[vector[WordID], kbest.FTreeTraversal].Derivation* f_derivation
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 static PyObject *__pyx_pf_5_cdec_10Hypergraph_13kbest_trees(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self, PyObject *__pyx_v_size) {
@@ -9230,7 +9427,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_13kbest_trees(struct __pyx_obj_5_c
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+    __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_5_cdec_10Hypergraph_15generator5, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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     return NULL;
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-  if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":44
- * 
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":59
  *     def kbest_trees(self, size):
+ *         """hg.kbest_trees(size) -> List of k-best trees in the hypergraph."""
  *         cdef kbest.KBestDerivations[vector[WordID], kbest.FTreeTraversal]* f_derivations = new kbest.KBestDerivations[vector[WordID], kbest.FTreeTraversal](self.hg[0], size)             # <<<<<<<<<<<<<<
  *         cdef kbest.KBestDerivations[vector[WordID], kbest.FTreeTraversal].Derivation* f_derivation
  *         cdef kbest.KBestDerivations[vector[WordID], kbest.ETreeTraversal]* e_derivations = new kbest.KBestDerivations[vector[WordID], kbest.ETreeTraversal](self.hg[0], size)
  */
-  __pyx_t_1 = __Pyx_PyInt_AsUnsignedInt(__pyx_cur_scope->__pyx_v_size); if (unlikely((__pyx_t_1 == (unsigned int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = __Pyx_PyInt_AsUnsignedInt(__pyx_cur_scope->__pyx_v_size); if (unlikely((__pyx_t_1 == (unsigned int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_cur_scope->__pyx_v_f_derivations = new KBest::KBestDerivations<std::vector<WordID>,FTreeTraversal>((__pyx_cur_scope->__pyx_v_self->hg[0]), __pyx_t_1);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":46
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":61
  *         cdef kbest.KBestDerivations[vector[WordID], kbest.FTreeTraversal]* f_derivations = new kbest.KBestDerivations[vector[WordID], kbest.FTreeTraversal](self.hg[0], size)
  *         cdef kbest.KBestDerivations[vector[WordID], kbest.FTreeTraversal].Derivation* f_derivation
  *         cdef kbest.KBestDerivations[vector[WordID], kbest.ETreeTraversal]* e_derivations = new kbest.KBestDerivations[vector[WordID], kbest.ETreeTraversal](self.hg[0], size)             # <<<<<<<<<<<<<<
  *         cdef kbest.KBestDerivations[vector[WordID], kbest.ETreeTraversal].Derivation* e_derivation
  *         cdef unsigned k
  */
-  __pyx_t_1 = __Pyx_PyInt_AsUnsignedInt(__pyx_cur_scope->__pyx_v_size); if (unlikely((__pyx_t_1 == (unsigned int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = __Pyx_PyInt_AsUnsignedInt(__pyx_cur_scope->__pyx_v_size); if (unlikely((__pyx_t_1 == (unsigned int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_cur_scope->__pyx_v_e_derivations = new KBest::KBestDerivations<std::vector<WordID>,ETreeTraversal>((__pyx_cur_scope->__pyx_v_self->hg[0]), __pyx_t_1);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":49
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":64
  *         cdef kbest.KBestDerivations[vector[WordID], kbest.ETreeTraversal].Derivation* e_derivation
  *         cdef unsigned k
  *         try:             # <<<<<<<<<<<<<<
@@ -9300,18 +9497,18 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_15generator5(__pyx_GeneratorObject
  */
   /*try:*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":50
+    /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":65
  *         cdef unsigned k
  *         try:
  *             for k in range(size):             # <<<<<<<<<<<<<<
  *                 f_derivation = f_derivations.LazyKthBest(self.hg.nodes_.size() - 1, k)
  *                 e_derivation = e_derivations.LazyKthBest(self.hg.nodes_.size() - 1, k)
  */
-    __pyx_t_2 = __Pyx_PyInt_AsLong(__pyx_cur_scope->__pyx_v_size); if (unlikely((__pyx_t_2 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L5;}
+    __pyx_t_2 = __Pyx_PyInt_AsLong(__pyx_cur_scope->__pyx_v_size); if (unlikely((__pyx_t_2 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L5;}
     for (__pyx_t_1 = 0; __pyx_t_1 < __pyx_t_2; __pyx_t_1+=1) {
       __pyx_cur_scope->__pyx_v_k = __pyx_t_1;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":51
+      /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":66
  *         try:
  *             for k in range(size):
  *                 f_derivation = f_derivations.LazyKthBest(self.hg.nodes_.size() - 1, k)             # <<<<<<<<<<<<<<
@@ -9320,7 +9517,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_15generator5(__pyx_GeneratorObject
  */
       __pyx_cur_scope->__pyx_v_f_derivation = __pyx_cur_scope->__pyx_v_f_derivations->LazyKthBest((__pyx_cur_scope->__pyx_v_self->hg->nodes_.size() - 1), __pyx_cur_scope->__pyx_v_k);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":52
+      /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":67
  *             for k in range(size):
  *                 f_derivation = f_derivations.LazyKthBest(self.hg.nodes_.size() - 1, k)
  *                 e_derivation = e_derivations.LazyKthBest(self.hg.nodes_.size() - 1, k)             # <<<<<<<<<<<<<<
@@ -9329,7 +9526,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_15generator5(__pyx_GeneratorObject
  */
       __pyx_cur_scope->__pyx_v_e_derivation = __pyx_cur_scope->__pyx_v_e_derivations->LazyKthBest((__pyx_cur_scope->__pyx_v_self->hg->nodes_.size() - 1), __pyx_cur_scope->__pyx_v_k);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":53
+      /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":68
  *                 f_derivation = f_derivations.LazyKthBest(self.hg.nodes_.size() - 1, k)
  *                 e_derivation = e_derivations.LazyKthBest(self.hg.nodes_.size() - 1, k)
  *                 if not f_derivation or not e_derivation: break             # <<<<<<<<<<<<<<
@@ -9349,16 +9546,16 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_15generator5(__pyx_GeneratorObject
       }
       __pyx_L9:;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":54
+      /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":69
  *                 e_derivation = e_derivations.LazyKthBest(self.hg.nodes_.size() - 1, k)
  *                 if not f_derivation or not e_derivation: break
  *                 f_tree = unicode(GetString(f_derivation._yield).c_str(), 'utf8')             # <<<<<<<<<<<<<<
  *                 e_tree = unicode(GetString(e_derivation._yield).c_str(), 'utf8')
  *                 yield (f_tree, e_tree)
  */
-      __pyx_t_6 = PyBytes_FromString(TD::GetString(__pyx_cur_scope->__pyx_v_f_derivation->yield).c_str()); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L5;}
+      __pyx_t_6 = PyBytes_FromString(TD::GetString(__pyx_cur_scope->__pyx_v_f_derivation->yield).c_str()); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L5;}
       __Pyx_GOTREF(((PyObject *)__pyx_t_6));
-      __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L5;}
+      __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L5;}
       __Pyx_GOTREF(__pyx_t_7);
       PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_6));
       __Pyx_GIVEREF(((PyObject *)__pyx_t_6));
@@ -9366,7 +9563,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_15generator5(__pyx_GeneratorObject
       PyTuple_SET_ITEM(__pyx_t_7, 1, ((PyObject *)__pyx_n_s__utf8));
       __Pyx_GIVEREF(((PyObject *)__pyx_n_s__utf8));
       __pyx_t_6 = 0;
-      __pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)(&PyUnicode_Type))), ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L5;}
+      __pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)(&PyUnicode_Type))), ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L5;}
       __Pyx_GOTREF(__pyx_t_6);
       __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
       __Pyx_XGOTREF(((PyObject *)__pyx_cur_scope->__pyx_v_f_tree));
@@ -9375,16 +9572,16 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_15generator5(__pyx_GeneratorObject
       __pyx_cur_scope->__pyx_v_f_tree = ((PyObject*)__pyx_t_6);
       __pyx_t_6 = 0;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":55
+      /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":70
  *                 if not f_derivation or not e_derivation: break
  *                 f_tree = unicode(GetString(f_derivation._yield).c_str(), 'utf8')
  *                 e_tree = unicode(GetString(e_derivation._yield).c_str(), 'utf8')             # <<<<<<<<<<<<<<
  *                 yield (f_tree, e_tree)
  *         finally:
  */
-      __pyx_t_6 = PyBytes_FromString(TD::GetString(__pyx_cur_scope->__pyx_v_e_derivation->yield).c_str()); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L5;}
+      __pyx_t_6 = PyBytes_FromString(TD::GetString(__pyx_cur_scope->__pyx_v_e_derivation->yield).c_str()); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L5;}
       __Pyx_GOTREF(((PyObject *)__pyx_t_6));
-      __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L5;}
+      __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L5;}
       __Pyx_GOTREF(__pyx_t_7);
       PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_6));
       __Pyx_GIVEREF(((PyObject *)__pyx_t_6));
@@ -9392,7 +9589,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_15generator5(__pyx_GeneratorObject
       PyTuple_SET_ITEM(__pyx_t_7, 1, ((PyObject *)__pyx_n_s__utf8));
       __Pyx_GIVEREF(((PyObject *)__pyx_n_s__utf8));
       __pyx_t_6 = 0;
-      __pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)(&PyUnicode_Type))), ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L5;}
+      __pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)(&PyUnicode_Type))), ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L5;}
       __Pyx_GOTREF(__pyx_t_6);
       __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
       __Pyx_XGOTREF(((PyObject *)__pyx_cur_scope->__pyx_v_e_tree));
@@ -9401,14 +9598,14 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_15generator5(__pyx_GeneratorObject
       __pyx_cur_scope->__pyx_v_e_tree = ((PyObject*)__pyx_t_6);
       __pyx_t_6 = 0;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":56
+      /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":71
  *                 f_tree = unicode(GetString(f_derivation._yield).c_str(), 'utf8')
  *                 e_tree = unicode(GetString(e_derivation._yield).c_str(), 'utf8')
  *                 yield (f_tree, e_tree)             # <<<<<<<<<<<<<<
  *         finally:
  *             del f_derivations
  */
-      __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L5;}
+      __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L5;}
       __Pyx_GOTREF(__pyx_t_6);
       __Pyx_INCREF(((PyObject *)__pyx_cur_scope->__pyx_v_f_tree));
       PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_cur_scope->__pyx_v_f_tree));
@@ -9428,12 +9625,12 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_15generator5(__pyx_GeneratorObject
       __pyx_L10_resume_from_yield:;
       __pyx_t_1 = __pyx_cur_scope->__pyx_t_0;
       __pyx_t_2 = __pyx_cur_scope->__pyx_t_1;
-      if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L5;}
+      if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L5;}
     }
     __pyx_L8_break:;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":58
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":73
  *                 yield (f_tree, e_tree)
  *         finally:
  *             del f_derivations             # <<<<<<<<<<<<<<
@@ -9457,7 +9654,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_15generator5(__pyx_GeneratorObject
     __pyx_L6:;
     delete __pyx_cur_scope->__pyx_v_f_derivations;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":59
+    /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":74
  *         finally:
  *             del f_derivations
  *             del e_derivations             # <<<<<<<<<<<<<<
@@ -9493,6 +9690,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_18generator6(__pyx_GeneratorObject
 
 /* Python wrapper */
 static PyObject *__pyx_pw_5_cdec_10Hypergraph_17kbest_features(PyObject *__pyx_v_self, PyObject *__pyx_v_size); /*proto*/
+static char __pyx_doc_5_cdec_10Hypergraph_16kbest_features[] = "hg.kbest_trees(size) -> List of k-best feature vectors in the hypergraph.";
 static PyObject *__pyx_pw_5_cdec_10Hypergraph_17kbest_features(PyObject *__pyx_v_self, PyObject *__pyx_v_size) {
   PyObject *__pyx_r = 0;
   __Pyx_RefNannyDeclarations
@@ -9502,12 +9700,12 @@ static PyObject *__pyx_pw_5_cdec_10Hypergraph_17kbest_features(PyObject *__pyx_v
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":61
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":76
  *             del e_derivations
  * 
  *     def kbest_features(self, size):             # <<<<<<<<<<<<<<
+ *         """hg.kbest_trees(size) -> List of k-best feature vectors in the hypergraph."""
  *         cdef kbest.KBestDerivations[FastSparseVector[weight_t], kbest.FeatureVectorTraversal]* derivations = new kbest.KBestDerivations[FastSparseVector[weight_t], kbest.FeatureVectorTraversal](self.hg[0], size)
- *         cdef kbest.KBestDerivations[FastSparseVector[weight_t], kbest.FeatureVectorTraversal].Derivation* derivation
  */
 
 static PyObject *__pyx_pf_5_cdec_10Hypergraph_16kbest_features(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self, PyObject *__pyx_v_size) {
@@ -9531,7 +9729,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_16kbest_features(struct __pyx_obj_
   __Pyx_INCREF(__pyx_cur_scope->__pyx_v_size);
   __Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_size);
   {
-    __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_5_cdec_10Hypergraph_18generator6, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_5_cdec_10Hypergraph_18generator6, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_DECREF(__pyx_cur_scope);
     __Pyx_RefNannyFinishContext();
     return (PyObject *) gen;
@@ -9567,19 +9765,19 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_18generator6(__pyx_GeneratorObject
     return NULL;
   }
   __pyx_L3_first_run:;
-  if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":62
- * 
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":78
  *     def kbest_features(self, size):
+ *         """hg.kbest_trees(size) -> List of k-best feature vectors in the hypergraph."""
  *         cdef kbest.KBestDerivations[FastSparseVector[weight_t], kbest.FeatureVectorTraversal]* derivations = new kbest.KBestDerivations[FastSparseVector[weight_t], kbest.FeatureVectorTraversal](self.hg[0], size)             # <<<<<<<<<<<<<<
  *         cdef kbest.KBestDerivations[FastSparseVector[weight_t], kbest.FeatureVectorTraversal].Derivation* derivation
  *         cdef SparseVector fmap
  */
-  __pyx_t_1 = __Pyx_PyInt_AsUnsignedInt(__pyx_cur_scope->__pyx_v_size); if (unlikely((__pyx_t_1 == (unsigned int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = __Pyx_PyInt_AsUnsignedInt(__pyx_cur_scope->__pyx_v_size); if (unlikely((__pyx_t_1 == (unsigned int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_cur_scope->__pyx_v_derivations = new KBest::KBestDerivations<FastSparseVector<weight_t>,FeatureVectorTraversal>((__pyx_cur_scope->__pyx_v_self->hg[0]), __pyx_t_1);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":66
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":82
  *         cdef SparseVector fmap
  *         cdef unsigned k
  *         try:             # <<<<<<<<<<<<<<
@@ -9588,18 +9786,18 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_18generator6(__pyx_GeneratorObject
  */
   /*try:*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":67
+    /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":83
  *         cdef unsigned k
  *         try:
  *             for k in range(size):             # <<<<<<<<<<<<<<
  *                 derivation = derivations.LazyKthBest(self.hg.nodes_.size() - 1, k)
  *                 if not derivation: break
  */
-    __pyx_t_2 = __Pyx_PyInt_AsLong(__pyx_cur_scope->__pyx_v_size); if (unlikely((__pyx_t_2 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L5;}
+    __pyx_t_2 = __Pyx_PyInt_AsLong(__pyx_cur_scope->__pyx_v_size); if (unlikely((__pyx_t_2 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L5;}
     for (__pyx_t_1 = 0; __pyx_t_1 < __pyx_t_2; __pyx_t_1+=1) {
       __pyx_cur_scope->__pyx_v_k = __pyx_t_1;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":68
+      /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":84
  *         try:
  *             for k in range(size):
  *                 derivation = derivations.LazyKthBest(self.hg.nodes_.size() - 1, k)             # <<<<<<<<<<<<<<
@@ -9608,7 +9806,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_18generator6(__pyx_GeneratorObject
  */
       __pyx_cur_scope->__pyx_v_derivation = __pyx_cur_scope->__pyx_v_derivations->LazyKthBest((__pyx_cur_scope->__pyx_v_self->hg->nodes_.size() - 1), __pyx_cur_scope->__pyx_v_k);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":69
+      /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":85
  *             for k in range(size):
  *                 derivation = derivations.LazyKthBest(self.hg.nodes_.size() - 1, k)
  *                 if not derivation: break             # <<<<<<<<<<<<<<
@@ -9622,23 +9820,23 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_18generator6(__pyx_GeneratorObject
       }
       __pyx_L9:;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":70
+      /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":86
  *                 derivation = derivations.LazyKthBest(self.hg.nodes_.size() - 1, k)
  *                 if not derivation: break
  *                 fmap = SparseVector.__new__(SparseVector)             # <<<<<<<<<<<<<<
  *                 fmap.vector = new FastSparseVector[weight_t](derivation._yield)
  *                 yield fmap
  */
-      __pyx_t_4 = __Pyx_tp_new(((PyObject*)__pyx_ptype_5_cdec_SparseVector)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L5;}
+      __pyx_t_4 = __Pyx_tp_new(((PyObject*)__pyx_ptype_5_cdec_SparseVector)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L5;}
       __Pyx_GOTREF(__pyx_t_4);
-      if (!(likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5_cdec_SparseVector)))) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L5;}
+      if (!(likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5_cdec_SparseVector)))) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L5;}
       __Pyx_XGOTREF(((PyObject *)__pyx_cur_scope->__pyx_v_fmap));
       __Pyx_XDECREF(((PyObject *)__pyx_cur_scope->__pyx_v_fmap));
       __Pyx_GIVEREF(__pyx_t_4);
       __pyx_cur_scope->__pyx_v_fmap = ((struct __pyx_obj_5_cdec_SparseVector *)__pyx_t_4);
       __pyx_t_4 = 0;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":71
+      /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":87
  *                 if not derivation: break
  *                 fmap = SparseVector.__new__(SparseVector)
  *                 fmap.vector = new FastSparseVector[weight_t](derivation._yield)             # <<<<<<<<<<<<<<
@@ -9647,7 +9845,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_18generator6(__pyx_GeneratorObject
  */
       __pyx_cur_scope->__pyx_v_fmap->vector = new FastSparseVector<weight_t>(__pyx_cur_scope->__pyx_v_derivation->yield);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":72
+      /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":88
  *                 fmap = SparseVector.__new__(SparseVector)
  *                 fmap.vector = new FastSparseVector[weight_t](derivation._yield)
  *                 yield fmap             # <<<<<<<<<<<<<<
@@ -9666,12 +9864,12 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_18generator6(__pyx_GeneratorObject
       __pyx_L10_resume_from_yield:;
       __pyx_t_1 = __pyx_cur_scope->__pyx_t_0;
       __pyx_t_2 = __pyx_cur_scope->__pyx_t_1;
-      if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L5;}
+      if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L5;}
     }
     __pyx_L8_break:;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":74
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":90
  *                 yield fmap
  *         finally:
  *             del derivations             # <<<<<<<<<<<<<<
@@ -9720,13 +9918,14 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_21generator7(__pyx_GeneratorObject
 
 /* Python wrapper */
 static PyObject *__pyx_pw_5_cdec_10Hypergraph_20sample(PyObject *__pyx_v_self, PyObject *__pyx_arg_n); /*proto*/
+static char __pyx_doc_5_cdec_10Hypergraph_19sample[] = "hg.sample(n) -> Sample of n hypotheses from the hypergraph.";
 static PyObject *__pyx_pw_5_cdec_10Hypergraph_20sample(PyObject *__pyx_v_self, PyObject *__pyx_arg_n) {
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+    __pyx_v_n = __Pyx_PyInt_AsUnsignedInt(__pyx_arg_n); if (unlikely((__pyx_v_n == (unsigned int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 92; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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@@ -9739,12 +9938,12 @@ static PyObject *__pyx_pw_5_cdec_10Hypergraph_20sample(PyObject *__pyx_v_self, P
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":76
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":92
  *             del derivations
  * 
  *     def sample(self, unsigned n):             # <<<<<<<<<<<<<<
+ *         """hg.sample(n) -> Sample of n hypotheses from the hypergraph."""
  *         cdef vector[hypergraph.Hypothesis]* hypos = new vector[hypergraph.Hypothesis]()
- *         if self.rng == NULL:
  */
 
 static PyObject *__pyx_pf_5_cdec_10Hypergraph_19sample(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self, unsigned int __pyx_v_n) {
@@ -9766,7 +9965,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_19sample(struct __pyx_obj_5_cdec_H
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   __pyx_cur_scope->__pyx_v_n = __pyx_v_n;
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+    __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_5_cdec_10Hypergraph_21generator7, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 92; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -9788,67 +9987,44 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_21generator7(__pyx_GeneratorObject
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-  int __pyx_t_1;
-  MT19937 *__pyx_t_2;
-  size_t __pyx_t_3;
-  unsigned int __pyx_t_4;
+  std::vector<HypergraphSampler::Hypothesis> *__pyx_t_1;
+  size_t __pyx_t_2;
+  unsigned int __pyx_t_3;
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+    case 1: goto __pyx_L9_resume_from_yield;
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-  if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 92; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":77
- * 
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":94
  *     def sample(self, unsigned n):
+ *         """hg.sample(n) -> Sample of n hypotheses from the hypergraph."""
  *         cdef vector[hypergraph.Hypothesis]* hypos = new vector[hypergraph.Hypothesis]()             # <<<<<<<<<<<<<<
- *         if self.rng == NULL:
- *             self.rng = new MT19937()
- */
-  __pyx_cur_scope->__pyx_v_hypos = new std::vector<HypergraphSampler::Hypothesis>();
-
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":78
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- *         if self.rng == NULL:             # <<<<<<<<<<<<<<
- *             self.rng = new MT19937()
- *         hypergraph.sample_hypotheses(self.hg[0], n, self.rng, hypos)
- */
-  __pyx_t_1 = (__pyx_cur_scope->__pyx_v_self->rng == NULL);
-  if (__pyx_t_1) {
-
-    /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":79
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- *         if self.rng == NULL:
- *             self.rng = new MT19937()             # <<<<<<<<<<<<<<
- *         hypergraph.sample_hypotheses(self.hg[0], n, self.rng, hypos)
+ *         hypergraph.sample_hypotheses(self.hg[0], n, self._rng(), hypos)
  *         cdef unsigned k
  */
-    try {__pyx_t_2 = new MT19937();} catch(...) {__Pyx_CppExn2PyErr(); {__pyx_filename = __pyx_f[3]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;}}
-    __pyx_cur_scope->__pyx_v_self->rng = __pyx_t_2;
-    goto __pyx_L4;
-  }
-  __pyx_L4:;
+  try {__pyx_t_1 = new std::vector<HypergraphSampler::Hypothesis>();} catch(...) {__Pyx_CppExn2PyErr(); {__pyx_filename = __pyx_f[3]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;}}
+  __pyx_cur_scope->__pyx_v_hypos = __pyx_t_1;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":80
- *         if self.rng == NULL:
- *             self.rng = new MT19937()
- *         hypergraph.sample_hypotheses(self.hg[0], n, self.rng, hypos)             # <<<<<<<<<<<<<<
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":95
+ *         """hg.sample(n) -> Sample of n hypotheses from the hypergraph."""
+ *         cdef vector[hypergraph.Hypothesis]* hypos = new vector[hypergraph.Hypothesis]()
+ *         hypergraph.sample_hypotheses(self.hg[0], n, self._rng(), hypos)             # <<<<<<<<<<<<<<
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  *         try:
  */
-  HypergraphSampler::sample_hypotheses((__pyx_cur_scope->__pyx_v_self->hg[0]), __pyx_cur_scope->__pyx_v_n, __pyx_cur_scope->__pyx_v_self->rng, __pyx_cur_scope->__pyx_v_hypos);
+  HypergraphSampler::sample_hypotheses((__pyx_cur_scope->__pyx_v_self->hg[0]), __pyx_cur_scope->__pyx_v_n, ((struct __pyx_vtabstruct_5_cdec_Hypergraph *)__pyx_cur_scope->__pyx_v_self->__pyx_vtab)->_rng(__pyx_cur_scope->__pyx_v_self), __pyx_cur_scope->__pyx_v_hypos);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":82
- *         hypergraph.sample_hypotheses(self.hg[0], n, self.rng, hypos)
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":97
+ *         hypergraph.sample_hypotheses(self.hg[0], n, self._rng(), hypos)
  *         cdef unsigned k
  *         try:             # <<<<<<<<<<<<<<
  *             for k in range(hypos.size()):
@@ -9856,75 +10032,75 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_21generator7(__pyx_GeneratorObject
  */
   /*try:*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":83
+    /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":98
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  *         try:
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  *         finally:
  */
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-      __pyx_cur_scope->__pyx_v_k = __pyx_t_4;
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":84
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  *             del hypos
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":86
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- *     def intersect(self, Lattice lat):
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@@ -9940,8 +10116,8 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_21generator7(__pyx_GeneratorObject
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 /* Python wrapper */
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+static PyObject *__pyx_pw_5_cdec_10Hypergraph_28prune(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_5_cdec_10Hypergraph_27prune[] = "hg.prune(beam_alpha=0, density=0): Prune the hypergraph.\n        beam_alpha: use beam pruning\n        density: use density pruning";
+static PyObject *__pyx_pw_5_cdec_10Hypergraph_28prune(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
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@@ -10049,7 +10521,7 @@ static PyObject *__pyx_pw_5_cdec_10Hypergraph_25prune(PyObject *__pyx_v_self, Py
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+  __pyx_r = __pyx_pf_5_cdec_10Hypergraph_27prune(((struct __pyx_obj_5_cdec_Hypergraph *)__pyx_v_self), __pyx_v_beam_alpha, __pyx_v_density, __pyx_v_kwargs);
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-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":91
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":125
  *         return hypergraph.Intersect(lat.lattice[0], self.hg)
  * 
  *     def prune(self, beam_alpha=0, density=0, **kwargs):             # <<<<<<<<<<<<<<
- *         cdef hypergraph.EdgeMask* preserve_mask = NULL
- *         if 'csplit_preserve_full_word' in kwargs:
+ *         """hg.prune(beam_alpha=0, density=0): Prune the hypergraph.
+ *         beam_alpha: use beam pruning
  */
 
-static PyObject *__pyx_pf_5_cdec_10Hypergraph_24prune(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self, PyObject *__pyx_v_beam_alpha, PyObject *__pyx_v_density, PyObject *__pyx_v_kwargs) {
+static PyObject *__pyx_pf_5_cdec_10Hypergraph_27prune(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self, PyObject *__pyx_v_beam_alpha, PyObject *__pyx_v_density, PyObject *__pyx_v_kwargs) {
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":92
- * 
- *     def prune(self, beam_alpha=0, density=0, **kwargs):
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":129
+ *         beam_alpha: use beam pruning
+ *         density: use density pruning"""
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":93
- *     def prune(self, beam_alpha=0, density=0, **kwargs):
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":130
+ *         density: use density pruning"""
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":94
+    /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":131
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":95
+    /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":132
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":96
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":97
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":134
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":98
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-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":100
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- *         return Lattice(eval(plf))
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-static PyObject *__pyx_pf_5_cdec_10Hypergraph_26lattice(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self) {
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+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":140
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+  struct __pyx_obj_5_cdec___pyx_scope_struct_14___get__ *__pyx_cur_scope = ((struct __pyx_obj_5_cdec___pyx_scope_struct_14___get__ *)__pyx_generator->closure);
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   size_t __pyx_t_1;
   unsigned int __pyx_t_2;
@@ -10600,9 +11138,9 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_5nodes_2generator9(__pyx_Generator
     return NULL;
   }
   __pyx_L3_first_run:;
-  if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 119; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 162; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":121
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":164
  *         def __get__(self):
  *             cdef unsigned i
  *             for i in range(self.hg.nodes_.size()):             # <<<<<<<<<<<<<<
@@ -10613,16 +11151,16 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_5nodes_2generator9(__pyx_Generator
   for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) {
     __pyx_cur_scope->__pyx_v_i = __pyx_t_2;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":122
+    /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":165
  *             cdef unsigned i
  *             for i in range(self.hg.nodes_.size()):
  *                 yield HypergraphNode().init(self.hg, i)             # <<<<<<<<<<<<<<
  * 
  *     property goal:
  */
-    __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5_cdec_HypergraphNode)), ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 122; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5_cdec_HypergraphNode)), ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 165; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_3);
-    __pyx_t_4 = ((struct __pyx_vtabstruct_5_cdec_HypergraphNode *)((struct __pyx_obj_5_cdec_HypergraphNode *)__pyx_t_3)->__pyx_vtab)->init(((struct __pyx_obj_5_cdec_HypergraphNode *)__pyx_t_3), __pyx_cur_scope->__pyx_v_self->hg, __pyx_cur_scope->__pyx_v_i); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 122; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_4 = ((struct __pyx_vtabstruct_5_cdec_HypergraphNode *)((struct __pyx_obj_5_cdec_HypergraphNode *)__pyx_t_3)->__pyx_vtab)->init(((struct __pyx_obj_5_cdec_HypergraphNode *)__pyx_t_3), __pyx_cur_scope->__pyx_v_self->hg, __pyx_cur_scope->__pyx_v_i); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 165; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_4);
     __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
     __pyx_r = __pyx_t_4;
@@ -10637,7 +11175,7 @@ static PyObject *__pyx_gb_5_cdec_10Hypergraph_5nodes_2generator9(__pyx_Generator
     __pyx_L6_resume_from_yield:;
     __pyx_t_1 = __pyx_cur_scope->__pyx_t_0;
     __pyx_t_2 = __pyx_cur_scope->__pyx_t_1;
-    if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 122; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 165; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   }
   PyErr_SetNone(PyExc_StopIteration);
   goto __pyx_L0;
@@ -10664,7 +11202,7 @@ static PyObject *__pyx_pw_5_cdec_10Hypergraph_4goal_1__get__(PyObject *__pyx_v_s
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":125
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":168
  * 
  *     property goal:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -10682,7 +11220,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_4goal___get__(struct __pyx_obj_5_c
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__get__", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":126
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":169
  *     property goal:
  *         def __get__(self):
  *             return HypergraphNode().init(self.hg, self.hg.GoalNode())             # <<<<<<<<<<<<<<
@@ -10690,9 +11228,9 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_4goal___get__(struct __pyx_obj_5_c
  *     property npaths:
  */
   __Pyx_XDECREF(__pyx_r);
-  __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5_cdec_HypergraphNode)), ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 126; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5_cdec_HypergraphNode)), ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 169; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_1);
-  __pyx_t_2 = ((struct __pyx_vtabstruct_5_cdec_HypergraphNode *)((struct __pyx_obj_5_cdec_HypergraphNode *)__pyx_t_1)->__pyx_vtab)->init(((struct __pyx_obj_5_cdec_HypergraphNode *)__pyx_t_1), __pyx_v_self->hg, __pyx_v_self->hg->GoalNode()); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 126; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = ((struct __pyx_vtabstruct_5_cdec_HypergraphNode *)((struct __pyx_obj_5_cdec_HypergraphNode *)__pyx_t_1)->__pyx_vtab)->init(((struct __pyx_obj_5_cdec_HypergraphNode *)__pyx_t_1), __pyx_v_self->hg, __pyx_v_self->hg->GoalNode()); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 169; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_2);
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
   __pyx_r = __pyx_t_2;
@@ -10723,7 +11261,7 @@ static PyObject *__pyx_pw_5_cdec_10Hypergraph_6npaths_1__get__(PyObject *__pyx_v
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":129
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":172
  * 
  *     property npaths:
  *         def __get__(self):             # <<<<<<<<<<<<<<
@@ -10740,7 +11278,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_6npaths___get__(struct __pyx_obj_5
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__get__", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":130
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":173
  *     property npaths:
  *         def __get__(self):
  *             return self.hg.NumberOfPaths()             # <<<<<<<<<<<<<<
@@ -10748,7 +11286,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_6npaths___get__(struct __pyx_obj_5
  *     def inside_outside(self):
  */
   __Pyx_XDECREF(__pyx_r);
-  __pyx_t_1 = PyFloat_FromDouble(__pyx_v_self->hg->NumberOfPaths()); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 130; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyFloat_FromDouble(__pyx_v_self->hg->NumberOfPaths()); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_1);
   __pyx_r = __pyx_t_1;
   __pyx_t_1 = 0;
@@ -10767,25 +11305,26 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_6npaths___get__(struct __pyx_obj_5
 }
 
 /* Python wrapper */
-static PyObject *__pyx_pw_5_cdec_10Hypergraph_31inside_outside(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static PyObject *__pyx_pw_5_cdec_10Hypergraph_31inside_outside(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+static PyObject *__pyx_pw_5_cdec_10Hypergraph_36inside_outside(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_5_cdec_10Hypergraph_35inside_outside[] = "hg.inside_outside() -> SparseVector with inside-outside scores for each feature.";
+static PyObject *__pyx_pw_5_cdec_10Hypergraph_36inside_outside(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
   PyObject *__pyx_r = 0;
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("inside_outside (wrapper)", 0);
-  __pyx_r = __pyx_pf_5_cdec_10Hypergraph_30inside_outside(((struct __pyx_obj_5_cdec_Hypergraph *)__pyx_v_self));
+  __pyx_r = __pyx_pf_5_cdec_10Hypergraph_35inside_outside(((struct __pyx_obj_5_cdec_Hypergraph *)__pyx_v_self));
   __Pyx_RefNannyFinishContext();
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":132
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":175
  *             return self.hg.NumberOfPaths()
  * 
  *     def inside_outside(self):             # <<<<<<<<<<<<<<
+ *         """hg.inside_outside() -> SparseVector with inside-outside scores for each feature."""
  *         cdef FastSparseVector[prob_t]* result = new FastSparseVector[prob_t]()
- *         cdef prob_t z = hypergraph.InsideOutside(self.hg[0], result)
  */
 
-static PyObject *__pyx_pf_5_cdec_10Hypergraph_30inside_outside(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self) {
+static PyObject *__pyx_pf_5_cdec_10Hypergraph_35inside_outside(struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_self) {
   FastSparseVector<prob_t> *__pyx_v_result;
   prob_t __pyx_v_z;
   struct __pyx_obj_5_cdec_SparseVector *__pyx_v_vector = 0;
@@ -10801,17 +11340,17 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_30inside_outside(struct __pyx_obj_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("inside_outside", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":133
- * 
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":177
  *     def inside_outside(self):
+ *         """hg.inside_outside() -> SparseVector with inside-outside scores for each feature."""
  *         cdef FastSparseVector[prob_t]* result = new FastSparseVector[prob_t]()             # <<<<<<<<<<<<<<
  *         cdef prob_t z = hypergraph.InsideOutside(self.hg[0], result)
  *         result[0] /= z
  */
   __pyx_v_result = new FastSparseVector<prob_t>();
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":134
- *     def inside_outside(self):
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":178
+ *         """hg.inside_outside() -> SparseVector with inside-outside scores for each feature."""
  *         cdef FastSparseVector[prob_t]* result = new FastSparseVector[prob_t]()
  *         cdef prob_t z = hypergraph.InsideOutside(self.hg[0], result)             # <<<<<<<<<<<<<<
  *         result[0] /= z
@@ -10819,7 +11358,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_30inside_outside(struct __pyx_obj_
  */
   __pyx_v_z = InsideOutside<prob_t, EdgeProb, SparseVector<prob_t>, EdgeFeaturesAndProbWeightFunction>((__pyx_v_self->hg[0]), __pyx_v_result);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":135
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":179
  *         cdef FastSparseVector[prob_t]* result = new FastSparseVector[prob_t]()
  *         cdef prob_t z = hypergraph.InsideOutside(self.hg[0], result)
  *         result[0] /= z             # <<<<<<<<<<<<<<
@@ -10828,20 +11367,20 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_30inside_outside(struct __pyx_obj_
  */
   (__pyx_v_result[0]) /= __pyx_v_z;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":136
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":180
  *         cdef prob_t z = hypergraph.InsideOutside(self.hg[0], result)
  *         result[0] /= z
  *         cdef SparseVector vector = SparseVector.__new__(SparseVector)             # <<<<<<<<<<<<<<
  *         vector.vector = new FastSparseVector[double]()
  *         cdef FastSparseVector[prob_t].const_iterator* it = new FastSparseVector[prob_t].const_iterator(result[0], False)
  */
-  __pyx_t_1 = __Pyx_tp_new(((PyObject*)__pyx_ptype_5_cdec_SparseVector)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = __Pyx_tp_new(((PyObject*)__pyx_ptype_5_cdec_SparseVector)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_1);
-  if (!(likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5_cdec_SparseVector)))) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (!(likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5_cdec_SparseVector)))) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_vector = ((struct __pyx_obj_5_cdec_SparseVector *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":137
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":181
  *         result[0] /= z
  *         cdef SparseVector vector = SparseVector.__new__(SparseVector)
  *         vector.vector = new FastSparseVector[double]()             # <<<<<<<<<<<<<<
@@ -10850,7 +11389,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_30inside_outside(struct __pyx_obj_
  */
   __pyx_v_vector->vector = new FastSparseVector<double>();
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":138
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":182
  *         cdef SparseVector vector = SparseVector.__new__(SparseVector)
  *         vector.vector = new FastSparseVector[double]()
  *         cdef FastSparseVector[prob_t].const_iterator* it = new FastSparseVector[prob_t].const_iterator(result[0], False)             # <<<<<<<<<<<<<<
@@ -10859,7 +11398,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_30inside_outside(struct __pyx_obj_
  */
   __pyx_v_it = new FastSparseVector<prob_t>::const_iterator((__pyx_v_result[0]), 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":140
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":184
  *         cdef FastSparseVector[prob_t].const_iterator* it = new FastSparseVector[prob_t].const_iterator(result[0], False)
  *         cdef unsigned i
  *         for i in range(result.size()):             # <<<<<<<<<<<<<<
@@ -10870,7 +11409,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_30inside_outside(struct __pyx_obj_
   for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
     __pyx_v_i = __pyx_t_3;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":141
+    /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":185
  *         cdef unsigned i
  *         for i in range(result.size()):
  *             vector.vector.set_value(it[0].ptr().first, log(it[0].ptr().second))             # <<<<<<<<<<<<<<
@@ -10879,7 +11418,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_30inside_outside(struct __pyx_obj_
  */
     __pyx_v_vector->vector->set_value((__pyx_v_it[0]).operator->()->first, log((__pyx_v_it[0]).operator->()->second));
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":142
+    /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":186
  *         for i in range(result.size()):
  *             vector.vector.set_value(it[0].ptr().first, log(it[0].ptr().second))
  *             pinc(it[0]) # ++it             # <<<<<<<<<<<<<<
@@ -10889,7 +11428,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_30inside_outside(struct __pyx_obj_
     (++(__pyx_v_it[0]));
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":143
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":187
  *             vector.vector.set_value(it[0].ptr().first, log(it[0].ptr().second))
  *             pinc(it[0]) # ++it
  *         del it             # <<<<<<<<<<<<<<
@@ -10898,7 +11437,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_30inside_outside(struct __pyx_obj_
  */
   delete __pyx_v_it;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":144
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":188
  *             pinc(it[0]) # ++it
  *         del it
  *         del result             # <<<<<<<<<<<<<<
@@ -10907,7 +11446,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_30inside_outside(struct __pyx_obj_
  */
   delete __pyx_v_result;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":145
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":189
  *         del it
  *         del result
  *         return vector             # <<<<<<<<<<<<<<
@@ -10932,7 +11471,7 @@ static PyObject *__pyx_pf_5_cdec_10Hypergraph_30inside_outside(struct __pyx_obj_
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":152
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":196
  *     cdef public TRule trule
  * 
  *     cdef init(self, hypergraph.Hypergraph* hg, unsigned i):             # <<<<<<<<<<<<<<
@@ -10949,7 +11488,7 @@ static PyObject *__pyx_f_5_cdec_14HypergraphEdge_init(struct __pyx_obj_5_cdec_Hy
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("init", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":153
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":197
  * 
  *     cdef init(self, hypergraph.Hypergraph* hg, unsigned i):
  *         self.hg = hg             # <<<<<<<<<<<<<<
@@ -10958,7 +11497,7 @@ static PyObject *__pyx_f_5_cdec_14HypergraphEdge_init(struct __pyx_obj_5_cdec_Hy
  */
   __pyx_v_self->hg = __pyx_v_hg;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":154
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":198
  *     cdef init(self, hypergraph.Hypergraph* hg, unsigned i):
  *         self.hg = hg
  *         self.edge = &hg.edges_[i]             # <<<<<<<<<<<<<<
@@ -10967,23 +11506,23 @@ static PyObject *__pyx_f_5_cdec_14HypergraphEdge_init(struct __pyx_obj_5_cdec_Hy
  */
   __pyx_v_self->edge = (&(__pyx_v_hg->edges_[__pyx_v_i]));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":155
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":199
  *         self.hg = hg
  *         self.edge = &hg.edges_[i]
  *         self.trule = TRule.__new__(TRule)             # <<<<<<<<<<<<<<
  *         self.trule.rule = new shared_ptr[grammar.TRule](self.edge.rule_)
  *         return self
  */
-  __pyx_t_1 = __Pyx_tp_new(((PyObject*)__pyx_ptype_5_cdec_TRule)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = __Pyx_tp_new(((PyObject*)__pyx_ptype_5_cdec_TRule)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 199; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_1);
-  if (!(likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5_cdec_TRule)))) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (!(likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5_cdec_TRule)))) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 199; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":156
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":200
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":157
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":201
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":159
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":203
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":160
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":204
  * 
  *     def __len__(self):
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@@ -11067,7 +11606,7 @@ static PyObject *__pyx_pw_5_cdec_14HypergraphEdge_9head_node_1__get__(PyObject *
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":163
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":207
  * 
  *     property head_node:
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":164
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":208
  *     property head_node:
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@@ -11093,9 +11632,9 @@ static PyObject *__pyx_pf_5_cdec_14HypergraphEdge_9head_node___get__(struct __py
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-  __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5_cdec_HypergraphNode)), ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 164; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5_cdec_HypergraphNode)), ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __pyx_t_2 = ((struct __pyx_vtabstruct_5_cdec_HypergraphNode *)((struct __pyx_obj_5_cdec_HypergraphNode *)__pyx_t_1)->__pyx_vtab)->init(((struct __pyx_obj_5_cdec_HypergraphNode *)__pyx_t_1), __pyx_v_self->hg, __pyx_v_self->edge->head_node_); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 164; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = ((struct __pyx_vtabstruct_5_cdec_HypergraphNode *)((struct __pyx_obj_5_cdec_HypergraphNode *)__pyx_t_1)->__pyx_vtab)->init(((struct __pyx_obj_5_cdec_HypergraphNode *)__pyx_t_1), __pyx_v_self->hg, __pyx_v_self->edge->head_node_); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-static PyObject *__pyx_gb_5_cdec_14HypergraphEdge_10tail_nodes_2generator10(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
+static PyObject *__pyx_gb_5_cdec_14HypergraphEdge_10tail_nodes_2generator11(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
 
 /* Python wrapper */
 static PyObject *__pyx_pw_5_cdec_14HypergraphEdge_10tail_nodes_1__get__(PyObject *__pyx_v_self); /*proto*/
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":167
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  *     property tail_nodes:
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 static PyObject *__pyx_pf_5_cdec_14HypergraphEdge_10tail_nodes___get__(struct __pyx_obj_5_cdec_HypergraphEdge *__pyx_v_self) {
-  struct __pyx_obj_5_cdec___pyx_scope_struct_14___get__ *__pyx_cur_scope;
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+  __pyx_cur_scope = (struct __pyx_obj_5_cdec___pyx_scope_struct_15___get__ *)__pyx_ptype_5_cdec___pyx_scope_struct_15___get__->tp_new(__pyx_ptype_5_cdec___pyx_scope_struct_15___get__, __pyx_empty_tuple, NULL);
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+    __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_5_cdec_14HypergraphEdge_10tail_nodes_2generator11, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 211; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-static PyObject *__pyx_gb_5_cdec_14HypergraphEdge_10tail_nodes_2generator10(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value) /* generator body */
+static PyObject *__pyx_gb_5_cdec_14HypergraphEdge_10tail_nodes_2generator11(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value) /* generator body */
 {
-  struct __pyx_obj_5_cdec___pyx_scope_struct_14___get__ *__pyx_cur_scope = ((struct __pyx_obj_5_cdec___pyx_scope_struct_14___get__ *)__pyx_generator->closure);
+  struct __pyx_obj_5_cdec___pyx_scope_struct_15___get__ *__pyx_cur_scope = ((struct __pyx_obj_5_cdec___pyx_scope_struct_15___get__ *)__pyx_generator->closure);
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-  if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 167; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 211; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":169
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":170
+    /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":214
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  *     property span:
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+    __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5_cdec_HypergraphNode)), ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_4 = ((struct __pyx_vtabstruct_5_cdec_HypergraphNode *)((struct __pyx_obj_5_cdec_HypergraphNode *)__pyx_t_3)->__pyx_vtab)->init(((struct __pyx_obj_5_cdec_HypergraphNode *)__pyx_t_3), __pyx_cur_scope->__pyx_v_self->hg, (__pyx_cur_scope->__pyx_v_self->edge->tail_nodes_[__pyx_cur_scope->__pyx_v_i])); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 170; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":173
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":217
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":174
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":218
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+  __pyx_t_1 = PyInt_FromLong(__pyx_v_self->edge->i_); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_2 = PyInt_FromLong(__pyx_v_self->edge->j_); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_2);
-  __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":177
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":221
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  *     property feature_values:
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":178
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":222
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-  __pyx_t_1 = __Pyx_tp_new(((PyObject*)__pyx_ptype_5_cdec_SparseVector)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = __Pyx_tp_new(((PyObject*)__pyx_ptype_5_cdec_SparseVector)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  if (!(likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5_cdec_SparseVector)))) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":179
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":223
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":180
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":183
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":184
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":228
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+  __pyx_t_1 = PyFloat_FromDouble(__pyx_v_self->edge->edge_prob_.as_float()); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 228; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_x), __pyx_ptype_5_cdec_HypergraphEdge, 1, "x", 0))) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 230; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_y), __pyx_ptype_5_cdec_HypergraphEdge, 1, "y", 0))) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 230; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":186
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":230
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":189
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":233
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":187
+    /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":231
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":188
+    /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":232
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+    __pyx_t_1 = __Pyx_PyBool_FromLong((__pyx_v_x->edge == __pyx_v_y->edge)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":189
+    /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":233
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":190
+    /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":234
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+    __pyx_t_1 = PyObject_RichCompare(((PyObject *)__pyx_v_x), ((PyObject *)__pyx_v_y), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_1 = __Pyx_PyBool_FromLong((!__pyx_t_2)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -11537,18 +12075,18 @@ static PyObject *__pyx_pf_5_cdec_14HypergraphEdge_2__richcmp__(struct __pyx_obj_
     break;
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":191
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":235
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+  __pyx_t_1 = PyObject_Call(__pyx_builtin_NotImplemented, ((PyObject *)__pyx_k_tuple_19), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 235; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  {__pyx_filename = __pyx_f[3]; __pyx_lineno = 191; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  {__pyx_filename = __pyx_f[3]; __pyx_lineno = 235; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":150
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+  if (!(likely(((__pyx_v_value) == Py_None) || likely(__Pyx_TypeTest(__pyx_v_value, __pyx_ptype_5_cdec_TRule))))) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 194; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":197
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":241
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":198
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":199
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":243
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":200
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":244
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+static PyObject *__pyx_gb_5_cdec_14HypergraphNode_8in_edges_2generator12(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
 
 /* Python wrapper */
 static PyObject *__pyx_pw_5_cdec_14HypergraphNode_8in_edges_1__get__(PyObject *__pyx_v_self); /*proto*/
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":203
+/* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":247
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-  struct __pyx_obj_5_cdec___pyx_scope_struct_15___get__ *__pyx_cur_scope;
+  struct __pyx_obj_5_cdec___pyx_scope_struct_16___get__ *__pyx_cur_scope;
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+  __pyx_cur_scope = (struct __pyx_obj_5_cdec___pyx_scope_struct_16___get__ *)__pyx_ptype_5_cdec___pyx_scope_struct_16___get__->tp_new(__pyx_ptype_5_cdec___pyx_scope_struct_16___get__, __pyx_empty_tuple, NULL);
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+    __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_5_cdec_14HypergraphNode_8in_edges_2generator12, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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 }
 
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+static PyObject *__pyx_gb_5_cdec_14HypergraphNode_8in_edges_2generator12(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value) /* generator body */
 {
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+  struct __pyx_obj_5_cdec___pyx_scope_struct_16___get__ *__pyx_cur_scope = ((struct __pyx_obj_5_cdec___pyx_scope_struct_16___get__ *)__pyx_generator->closure);
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":205
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":206
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+    __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5_cdec_HypergraphEdge)), ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_4 = ((struct __pyx_vtabstruct_5_cdec_HypergraphEdge *)((struct __pyx_obj_5_cdec_HypergraphEdge *)__pyx_t_3)->__pyx_vtab)->init(((struct __pyx_obj_5_cdec_HypergraphEdge *)__pyx_t_3), __pyx_cur_scope->__pyx_v_self->hg, (__pyx_cur_scope->__pyx_v_self->node->in_edges_[__pyx_cur_scope->__pyx_v_i])); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 206; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-static PyObject *__pyx_gb_5_cdec_14HypergraphNode_9out_edges_2generator12(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
+static PyObject *__pyx_gb_5_cdec_14HypergraphNode_9out_edges_2generator13(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
 
 /* Python wrapper */
 static PyObject *__pyx_pw_5_cdec_14HypergraphNode_9out_edges_1__get__(PyObject *__pyx_v_self); /*proto*/
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 }
 
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+  __pyx_cur_scope = (struct __pyx_obj_5_cdec___pyx_scope_struct_17___get__ *)__pyx_ptype_5_cdec___pyx_scope_struct_17___get__->tp_new(__pyx_ptype_5_cdec___pyx_scope_struct_17___get__, __pyx_empty_tuple, NULL);
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 }
 
-static PyObject *__pyx_gb_5_cdec_14HypergraphNode_9out_edges_2generator12(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value) /* generator body */
+static PyObject *__pyx_gb_5_cdec_14HypergraphNode_9out_edges_2generator13(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value) /* generator body */
 {
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+  struct __pyx_obj_5_cdec___pyx_scope_struct_17___get__ *__pyx_cur_scope = ((struct __pyx_obj_5_cdec___pyx_scope_struct_17___get__ *)__pyx_generator->closure);
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-  if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 253; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":211
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":255
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":212
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-    if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":215
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":216
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":219
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":220
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":221
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-/* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":223
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":226
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":224
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":225
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":226
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":227
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":228
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+  __pyx_t_1 = PyObject_Call(__pyx_builtin_NotImplemented, ((PyObject *)__pyx_k_tuple_21), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  {__pyx_filename = __pyx_f[3]; __pyx_lineno = 228; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  {__pyx_filename = __pyx_f[3]; __pyx_lineno = 272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
   __pyx_r = Py_None; __Pyx_INCREF(Py_None);
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@@ -12212,10 +12759,55 @@ static PyObject *__pyx_pf_5_cdec_14HypergraphNode___richcmp__(struct __pyx_obj_5
 /* Python wrapper */
 static int __pyx_pw_5_cdec_7Lattice_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
 static int __pyx_pw_5_cdec_7Lattice_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
-  PyObject *__pyx_v_inp = 0;
   int __pyx_r;
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   __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
+  if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
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+  if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__cinit__", 0))) return -1;
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+  __Pyx_RefNannyFinishContext();
+  return __pyx_r;
+}
+
+/* "/home/vchahune/tools/cdec/python/src/lattice.pxi":6
+ *     cdef lattice.Lattice* lattice
+ * 
+ *     def __cinit__(self):             # <<<<<<<<<<<<<<
+ *         self.lattice = new lattice.Lattice()
+ * 
+ */
+
+static int __pyx_pf_5_cdec_7Lattice___cinit__(struct __pyx_obj_5_cdec_Lattice *__pyx_v_self) {
+  int __pyx_r;
+  __Pyx_RefNannyDeclarations
+  __Pyx_RefNannySetupContext("__cinit__", 0);
+
+  /* "/home/vchahune/tools/cdec/python/src/lattice.pxi":7
+ * 
+ *     def __cinit__(self):
+ *         self.lattice = new lattice.Lattice()             # <<<<<<<<<<<<<<
+ * 
+ *     def __init__(self, inp):
+ */
+  __pyx_v_self->lattice = new Lattice();
+
+  __pyx_r = 0;
+  __Pyx_RefNannyFinishContext();
+  return __pyx_r;
+}
+
+/* Python wrapper */
+static int __pyx_pw_5_cdec_7Lattice_3__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_5_cdec_7Lattice_2__init__[] = "Lattice(tuple) -> Lattice from node list.\n        Lattice(string) -> Lattice from PLF representation.";
+#if CYTHON_COMPILING_IN_CPYTHON
+struct wrapperbase __pyx_wrapperbase_5_cdec_7Lattice_2__init__;
+#endif
+static int __pyx_pw_5_cdec_7Lattice_3__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+  PyObject *__pyx_v_inp = 0;
+  int __pyx_r;
+  __Pyx_RefNannyDeclarations
+  __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
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+        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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@@ -12245,26 +12837,26 @@ static int __pyx_pw_5_cdec_7Lattice_1__cinit__(PyObject *__pyx_v_self, PyObject
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+  __Pyx_RaiseArgtupleInvalid("__init__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[4]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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-  __Pyx_AddTraceback("_cdec.Lattice.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+  __Pyx_AddTraceback("_cdec.Lattice.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
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-  __pyx_r = __pyx_pf_5_cdec_7Lattice___cinit__(((struct __pyx_obj_5_cdec_Lattice *)__pyx_v_self), __pyx_v_inp);
+  __pyx_r = __pyx_pf_5_cdec_7Lattice_2__init__(((struct __pyx_obj_5_cdec_Lattice *)__pyx_v_self), __pyx_v_inp);
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-/* "/Users/vchahun/Sandbox/cdec/python/src/lattice.pxi":6
- *     cdef lattice.Lattice* lattice
+/* "/home/vchahune/tools/cdec/python/src/lattice.pxi":9
+ *         self.lattice = new lattice.Lattice()
  * 
- *     def __cinit__(self, inp):             # <<<<<<<<<<<<<<
- *         if isinstance(inp, tuple):
- *             self.lattice = new lattice.Lattice(len(inp))
+ *     def __init__(self, inp):             # <<<<<<<<<<<<<<
+ *         """Lattice(tuple) -> Lattice from node list.
+ *         Lattice(string) -> Lattice from PLF representation."""
  */
 
-static int __pyx_pf_5_cdec_7Lattice___cinit__(struct __pyx_obj_5_cdec_Lattice *__pyx_v_self, PyObject *__pyx_v_inp) {
+static int __pyx_pf_5_cdec_7Lattice_2__init__(struct __pyx_obj_5_cdec_Lattice *__pyx_v_self, PyObject *__pyx_v_inp) {
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@@ -12275,19 +12867,17 @@ static int __pyx_pf_5_cdec_7Lattice___cinit__(struct __pyx_obj_5_cdec_Lattice *_
   PyObject *__pyx_t_4 = NULL;
   PyObject *(*__pyx_t_5)(PyObject *);
   PyObject *__pyx_t_6 = NULL;
-  int __pyx_t_7;
-  char *__pyx_t_8;
+  std::string __pyx_t_7;
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-  __Pyx_RefNannySetupContext("__cinit__", 0);
-  __Pyx_INCREF(__pyx_v_inp);
+  __Pyx_RefNannySetupContext("__init__", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/lattice.pxi":7
- * 
- *     def __cinit__(self, inp):
+  /* "/home/vchahune/tools/cdec/python/src/lattice.pxi":12
+ *         """Lattice(tuple) -> Lattice from node list.
+ *         Lattice(string) -> Lattice from PLF representation."""
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- *             self.lattice = new lattice.Lattice(len(inp))
+ *             self.lattice.resize(len(inp))
  *             for i, arcs in enumerate(inp):
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@@ -12296,22 +12886,22 @@ static int __pyx_pf_5_cdec_7Lattice___cinit__(struct __pyx_obj_5_cdec_Lattice *_
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/lattice.pxi":8
- *     def __cinit__(self, inp):
+    /* "/home/vchahune/tools/cdec/python/src/lattice.pxi":13
+ *         Lattice(string) -> Lattice from PLF representation."""
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- *             self.lattice = new lattice.Lattice(len(inp))             # <<<<<<<<<<<<<<
+ *             self.lattice.resize(len(inp))             # <<<<<<<<<<<<<<
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-    __pyx_v_self->lattice = new Lattice(__pyx_t_3);
+    __pyx_t_3 = PyObject_Length(__pyx_v_inp); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 13; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_v_self->lattice->resize(__pyx_t_3);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/lattice.pxi":9
+    /* "/home/vchahune/tools/cdec/python/src/lattice.pxi":14
  *         if isinstance(inp, tuple):
- *             self.lattice = new lattice.Lattice(len(inp))
+ *             self.lattice.resize(len(inp))
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  *                 self[i] = arcs
- *         else:
+ *         elif isinstance(inp, basestring):
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+      __pyx_t_3 = -1; __pyx_t_4 = PyObject_GetIter(__pyx_v_inp); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -12327,23 +12917,23 @@ static int __pyx_pf_5_cdec_7Lattice___cinit__(struct __pyx_obj_5_cdec_Lattice *_
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-        __pyx_t_6 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++;
+        __pyx_t_6 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+        __pyx_t_6 = PySequence_ITEM(__pyx_t_4, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-        __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++;
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/lattice.pxi":10
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+      /* "/home/vchahune/tools/cdec/python/src/lattice.pxi":15
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/lattice.pxi":12
+  /* "/home/vchahune/tools/cdec/python/src/lattice.pxi":16
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  *                 self[i] = arcs
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/lattice.pxi":13
+    /* "/home/vchahune/tools/cdec/python/src/lattice.pxi":17
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@@ -12473,38 +13023,37 @@ static int __pyx_pf_5_cdec_7Lattice___cinit__(struct __pyx_obj_5_cdec_Lattice *_
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-static void __pyx_pf_5_cdec_7Lattice_2__dealloc__(CYTHON_UNUSED struct __pyx_obj_5_cdec_Lattice *__pyx_v_self) {
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/lattice.pxi":20
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/lattice.pxi":24
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/lattice.pxi":25
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+  __pyx_t_4 = PyList_New(0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/lattice.pxi":26
+  /* "/home/vchahune/tools/cdec/python/src/lattice.pxi":28
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/lattice.pxi":29
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/lattice.pxi":30
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/lattice.pxi":31
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 }
 
 /* Python wrapper */
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-static int __pyx_pw_5_cdec_7Lattice_7__setitem__(PyObject *__pyx_v_self, PyObject *__pyx_arg_index, PyObject *__pyx_v_arcs) {
+static int __pyx_pw_5_cdec_7Lattice_9__setitem__(PyObject *__pyx_v_self, PyObject *__pyx_arg_index, PyObject *__pyx_v_arcs); /*proto*/
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+  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_arcs), (&PyTuple_Type), 1, "arcs", 1))) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_r = __pyx_pf_5_cdec_7Lattice_8__setitem__(((struct __pyx_obj_5_cdec_Lattice *)__pyx_v_self), ((int)__pyx_v_index), ((PyObject*)__pyx_v_arcs));
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/lattice.pxi":35
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/lattice.pxi":36
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/lattice.pxi":37
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/lattice.pxi":39
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-    {__pyx_filename = __pyx_f[4]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    {__pyx_filename = __pyx_f[4]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      {__pyx_filename = __pyx_f[4]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/lattice.pxi":40
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+    /* "/home/vchahune/tools/cdec/python/src/lattice.pxi":44
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+  __pyx_cur_scope = (struct __pyx_obj_5_cdec___pyx_scope_struct_21___iter__ *)__pyx_ptype_5_cdec___pyx_scope_struct_21___iter__->tp_new(__pyx_ptype_5_cdec___pyx_scope_struct_21___iter__, __pyx_empty_tuple, NULL);
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 {
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+  struct __pyx_obj_5_cdec___pyx_scope_struct_21___iter__ *__pyx_cur_scope = ((struct __pyx_obj_5_cdec___pyx_scope_struct_21___iter__ *)__pyx_generator->closure);
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":45
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-      __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_1); __Pyx_INCREF(__pyx_t_2); __pyx_t_1++;
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+      __pyx_t_2 = PySequence_ITEM(__pyx_t_3, __pyx_t_1); __pyx_t_1++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":46
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":48
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":49
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":50
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":51
+  /* "/home/vchahune/tools/cdec/python/src/mteval.pxi":51
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":53
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":54
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":55
+  /* "/home/vchahune/tools/cdec/python/src/mteval.pxi":55
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-/* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":57
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":58
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":59
+  /* "/home/vchahune/tools/cdec/python/src/mteval.pxi":59
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":60
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":61
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":62
+  /* "/home/vchahune/tools/cdec/python/src/mteval.pxi":62
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":63
+  /* "/home/vchahune/tools/cdec/python/src/mteval.pxi":63
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-/* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":70
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":71
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":72
+  /* "/home/vchahune/tools/cdec/python/src/mteval.pxi":72
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":73
+  /* "/home/vchahune/tools/cdec/python/src/mteval.pxi":73
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":76
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":77
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-/* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":79
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":80
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-/* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":82
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":83
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":84
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":85
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   __pyx_t_3 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":86
+  /* "/home/vchahune/tools/cdec/python/src/mteval.pxi":86
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  *         candidate.candidate = &self.cs[0][k]             # <<<<<<<<<<<<<<
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":87
+  /* "/home/vchahune/tools/cdec/python/src/mteval.pxi":87
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":88
+  /* "/home/vchahune/tools/cdec/python/src/mteval.pxi":88
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  *         candidate.score = self.metric.ComputeScore(self.cs[0][k].eval_feats)
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+static PyObject *__pyx_gb_5_cdec_12CandidateSet_10generator16(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
 
 /* Python wrapper */
 static PyObject *__pyx_pw_5_cdec_12CandidateSet_9__iter__(PyObject *__pyx_v_self); /*proto*/
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   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":90
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 static PyObject *__pyx_pf_5_cdec_12CandidateSet_8__iter__(struct __pyx_obj_5_cdec_CandidateSet *__pyx_v_self) {
-  struct __pyx_obj_5_cdec___pyx_scope_struct_21___iter__ *__pyx_cur_scope;
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+  __pyx_cur_scope = (struct __pyx_obj_5_cdec___pyx_scope_struct_22___iter__ *)__pyx_ptype_5_cdec___pyx_scope_struct_22___iter__->tp_new(__pyx_ptype_5_cdec___pyx_scope_struct_22___iter__, __pyx_empty_tuple, NULL);
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+    __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_5_cdec_12CandidateSet_10generator16, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 90; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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 }
 
-static PyObject *__pyx_gb_5_cdec_12CandidateSet_10generator15(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value) /* generator body */
+static PyObject *__pyx_gb_5_cdec_12CandidateSet_10generator16(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value) /* generator body */
 {
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+  struct __pyx_obj_5_cdec___pyx_scope_struct_22___iter__ *__pyx_cur_scope = ((struct __pyx_obj_5_cdec___pyx_scope_struct_22___iter__ *)__pyx_generator->closure);
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":92
+  /* "/home/vchahune/tools/cdec/python/src/mteval.pxi":92
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":93
+    /* "/home/vchahune/tools/cdec/python/src/mteval.pxi":93
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 static PyObject *__pyx_pw_5_cdec_12CandidateSet_12add_kbest(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_5_cdec_12CandidateSet_11add_kbest[] = "cs.add_kbest(Hypergraph hypergraph, int k) -> Extract K-best hypotheses \n        from the hypergraph and add them to the candidate set.";
 static PyObject *__pyx_pw_5_cdec_12CandidateSet_12add_kbest(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
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   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":95
+/* "/home/vchahune/tools/cdec/python/src/mteval.pxi":95
  *             yield self[i]
  * 
  *     def add_kbest(self, Hypergraph hypergraph, unsigned k):             # <<<<<<<<<<<<<<
- *         self.cs.AddKBestCandidates(hypergraph.hg[0], k, self.scorer.get())
- * 
+ *         """cs.add_kbest(Hypergraph hypergraph, int k) -> Extract K-best hypotheses
+ *         from the hypergraph and add them to the candidate set."""
  */
 
 static PyObject *__pyx_pf_5_cdec_12CandidateSet_11add_kbest(struct __pyx_obj_5_cdec_CandidateSet *__pyx_v_self, struct __pyx_obj_5_cdec_Hypergraph *__pyx_v_hypergraph, unsigned int __pyx_v_k) {
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":96
- * 
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+  /* "/home/vchahune/tools/cdec/python/src/mteval.pxi":98
+ *         """cs.add_kbest(Hypergraph hypergraph, int k) -> Extract K-best hypotheses
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-/* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":102
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":103
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 /* Python wrapper */
 static PyObject *__pyx_pw_5_cdec_16SegmentEvaluator_3evaluate(PyObject *__pyx_v_self, PyObject *__pyx_v_sentence); /*proto*/
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 static PyObject *__pyx_pw_5_cdec_16SegmentEvaluator_3evaluate(PyObject *__pyx_v_self, PyObject *__pyx_v_sentence) {
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-/* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":105
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  * 
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":109
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":110
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":111
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- *         ConvertSentence(string(as_str(sentence.strip())), &hyp)
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":112
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+  /* "/home/vchahune/tools/cdec/python/src/mteval.pxi":115
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 /* Python wrapper */
 static PyObject *__pyx_pw_5_cdec_16SegmentEvaluator_5candidate_set(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
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 static PyObject *__pyx_pw_5_cdec_16SegmentEvaluator_5candidate_set(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
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 static PyObject *__pyx_pf_5_cdec_16SegmentEvaluator_4candidate_set(struct __pyx_obj_5_cdec_SegmentEvaluator *__pyx_v_self) {
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":115
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":138
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":139
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+    /* "/home/vchahune/tools/cdec/python/src/mteval.pxi":142
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":141
+  /* "/home/vchahune/tools/cdec/python/src/mteval.pxi":144
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+  __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5_cdec_SegmentEvaluator)), ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 144; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":142
+  /* "/home/vchahune/tools/cdec/python/src/mteval.pxi":145
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":143
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":145
+  /* "/home/vchahune/tools/cdec/python/src/mteval.pxi":148
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":146
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-/* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":148
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":149
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-  __pyx_r = ((PyObject *)__pyx_t_1);
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+  __Pyx_XDECREF(__pyx_t_2);
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-/* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":151
- *         return self.name.c_str()
+/* "/home/vchahune/tools/cdec/python/src/mteval.pxi":154
+ *         return str(self.name.c_str())
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  * cdef float _compute_score(void* metric_, mteval.SufficientStats* stats):             # <<<<<<<<<<<<<<
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":152
+  /* "/home/vchahune/tools/cdec/python/src/mteval.pxi":155
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":153
+  /* "/home/vchahune/tools/cdec/python/src/mteval.pxi":156
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":155
+  /* "/home/vchahune/tools/cdec/python/src/mteval.pxi":158
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":156
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":157
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+  __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_6 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_7 = __pyx_PyFloat_AsFloat(__pyx_t_6); if (unlikely((__pyx_t_7 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":159
+/* "/home/vchahune/tools/cdec/python/src/mteval.pxi":162
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":163
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":164
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":166
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+      __pyx_t_5 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_6 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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       __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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     {
       Py_ssize_t index = -1;
-      __pyx_t_7 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_7 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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       __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
       __pyx_t_8 = Py_TYPE(__pyx_t_7)->tp_iternext;
@@ -16682,7 +17519,7 @@ static PyObject *__pyx_gb_5_cdec_4generator16(__pyx_GeneratorObject *__pyx_gener
       __Pyx_GOTREF(__pyx_t_5);
       index = 1; __pyx_t_6 = __pyx_t_8(__pyx_t_7); if (unlikely(!__pyx_t_6)) goto __pyx_L6_unpacking_failed;
       __Pyx_GOTREF(__pyx_t_6);
-      if (__Pyx_IternextUnpackEndCheck(__pyx_t_8(__pyx_t_7), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      if (__Pyx_IternextUnpackEndCheck(__pyx_t_8(__pyx_t_7), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __pyx_t_8 = NULL;
       __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
       goto __pyx_L7_unpacking_done;
@@ -16690,7 +17527,7 @@ static PyObject *__pyx_gb_5_cdec_4generator16(__pyx_GeneratorObject *__pyx_gener
       __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
       __pyx_t_8 = NULL;
       if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
-      {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __pyx_L7_unpacking_done:;
     }
     __Pyx_XGOTREF(__pyx_cur_scope->__pyx_v_key);
@@ -16704,7 +17541,7 @@ static PyObject *__pyx_gb_5_cdec_4generator16(__pyx_GeneratorObject *__pyx_gener
     __pyx_cur_scope->__pyx_v_value = __pyx_t_6;
     __pyx_t_6 = 0;
 
-    /* "_cdec.pyx":30
+    /* "_cdec.pyx":34
  * def _make_config(config):
  *     for key, value in config.items():
  *         if isinstance(value, dict):             # <<<<<<<<<<<<<<
@@ -16717,23 +17554,23 @@ static PyObject *__pyx_gb_5_cdec_4generator16(__pyx_GeneratorObject *__pyx_gener
     __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
     if (__pyx_t_9) {
 
-      /* "_cdec.pyx":31
+      /* "_cdec.pyx":35
  *     for key, value in config.items():
  *         if isinstance(value, dict):
  *             for name, info in value.items():             # <<<<<<<<<<<<<<
  *                 yield key, '%s %s' % (name, info)
  *         elif isinstance(value, list):
  */
-      __pyx_t_2 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_value, __pyx_n_s__items); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_2 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_value, __pyx_n_s__items); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_2);
-      __pyx_t_6 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_6 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_6);
       __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
       if (PyList_CheckExact(__pyx_t_6) || PyTuple_CheckExact(__pyx_t_6)) {
         __pyx_t_2 = __pyx_t_6; __Pyx_INCREF(__pyx_t_2); __pyx_t_10 = 0;
         __pyx_t_11 = NULL;
       } else {
-        __pyx_t_10 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_10 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_2);
         __pyx_t_11 = Py_TYPE(__pyx_t_2)->tp_iternext;
       }
@@ -16742,23 +17579,23 @@ static PyObject *__pyx_gb_5_cdec_4generator16(__pyx_GeneratorObject *__pyx_gener
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           if (__pyx_t_10 >= PyList_GET_SIZE(__pyx_t_2)) break;
           #if CYTHON_COMPILING_IN_CPYTHON
-          __pyx_t_6 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_10); __Pyx_INCREF(__pyx_t_6); __pyx_t_10++;
+          __pyx_t_6 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_10); __Pyx_INCREF(__pyx_t_6); __pyx_t_10++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           #else
-          __pyx_t_6 = PySequence_ITEM(__pyx_t_2, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+          __pyx_t_6 = PySequence_ITEM(__pyx_t_2, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           #endif
         } else if (!__pyx_t_11 && PyTuple_CheckExact(__pyx_t_2)) {
           if (__pyx_t_10 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
           #if CYTHON_COMPILING_IN_CPYTHON
-          __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_10); __Pyx_INCREF(__pyx_t_6); __pyx_t_10++;
+          __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_10); __Pyx_INCREF(__pyx_t_6); __pyx_t_10++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           #else
-          __pyx_t_6 = PySequence_ITEM(__pyx_t_2, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+          __pyx_t_6 = PySequence_ITEM(__pyx_t_2, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           #endif
         } else {
           __pyx_t_6 = __pyx_t_11(__pyx_t_2);
           if (unlikely(!__pyx_t_6)) {
             if (PyErr_Occurred()) {
               if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
-              else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             }
             break;
           }
@@ -16774,7 +17611,7 @@ static PyObject *__pyx_gb_5_cdec_4generator16(__pyx_GeneratorObject *__pyx_gener
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             if (size > 2) __Pyx_RaiseTooManyValuesError(2);
             else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
-            {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           }
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@@ -16787,14 +17624,14 @@ static PyObject *__pyx_gb_5_cdec_4generator16(__pyx_GeneratorObject *__pyx_gener
           __Pyx_INCREF(__pyx_t_5);
           __Pyx_INCREF(__pyx_t_7);
           #else
-          __pyx_t_5 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-          __pyx_t_7 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __pyx_t_5 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __pyx_t_7 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           #endif
           __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
         } else
         {
           Py_ssize_t index = -1;
-          __pyx_t_12 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __pyx_t_12 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           __Pyx_GOTREF(__pyx_t_12);
           __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
           __pyx_t_8 = Py_TYPE(__pyx_t_12)->tp_iternext;
@@ -16802,7 +17639,7 @@ static PyObject *__pyx_gb_5_cdec_4generator16(__pyx_GeneratorObject *__pyx_gener
           __Pyx_GOTREF(__pyx_t_5);
           index = 1; __pyx_t_7 = __pyx_t_8(__pyx_t_12); if (unlikely(!__pyx_t_7)) goto __pyx_L11_unpacking_failed;
           __Pyx_GOTREF(__pyx_t_7);
-          if (__Pyx_IternextUnpackEndCheck(__pyx_t_8(__pyx_t_12), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          if (__Pyx_IternextUnpackEndCheck(__pyx_t_8(__pyx_t_12), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           __pyx_t_8 = NULL;
           __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
           goto __pyx_L12_unpacking_done;
@@ -16810,7 +17647,7 @@ static PyObject *__pyx_gb_5_cdec_4generator16(__pyx_GeneratorObject *__pyx_gener
           __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
           __pyx_t_8 = NULL;
           if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
-          {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           __pyx_L12_unpacking_done:;
         }
         __Pyx_XGOTREF(__pyx_cur_scope->__pyx_v_name);
@@ -16824,14 +17661,14 @@ static PyObject *__pyx_gb_5_cdec_4generator16(__pyx_GeneratorObject *__pyx_gener
         __pyx_cur_scope->__pyx_v_info = __pyx_t_7;
         __pyx_t_7 = 0;
 
-        /* "_cdec.pyx":32
+        /* "_cdec.pyx":36
  *         if isinstance(value, dict):
  *             for name, info in value.items():
  *                 yield key, '%s %s' % (name, info)             # <<<<<<<<<<<<<<
  *         elif isinstance(value, list):
  *             for name in value:
  */
-        __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_6);
         __Pyx_INCREF(__pyx_cur_scope->__pyx_v_name);
         PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_cur_scope->__pyx_v_name);
@@ -16839,10 +17676,10 @@ static PyObject *__pyx_gb_5_cdec_4generator16(__pyx_GeneratorObject *__pyx_gener
         __Pyx_INCREF(__pyx_cur_scope->__pyx_v_info);
         PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_cur_scope->__pyx_v_info);
         __Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_info);
-        __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_45), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_44), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(((PyObject *)__pyx_t_7));
         __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
-        __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_6);
         __Pyx_INCREF(__pyx_cur_scope->__pyx_v_key);
         PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_cur_scope->__pyx_v_key);
@@ -16876,13 +17713,13 @@ static PyObject *__pyx_gb_5_cdec_4generator16(__pyx_GeneratorObject *__pyx_gener
         __pyx_t_4 = __pyx_cur_scope->__pyx_t_3;
         __pyx_t_10 = __pyx_cur_scope->__pyx_t_4;
         __pyx_t_11 = __pyx_cur_scope->__pyx_t_5;
-        if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       }
       __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
       goto __pyx_L8;
     }
 
-    /* "_cdec.pyx":33
+    /* "_cdec.pyx":37
  *             for name, info in value.items():
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  *         elif isinstance(value, list):             # <<<<<<<<<<<<<<
@@ -16895,7 +17732,7 @@ static PyObject *__pyx_gb_5_cdec_4generator16(__pyx_GeneratorObject *__pyx_gener
     __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
     if (__pyx_t_9) {
 
-      /* "_cdec.pyx":34
+      /* "_cdec.pyx":38
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  *         elif isinstance(value, list):
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         __pyx_t_11 = NULL;
       } else {
-        __pyx_t_10 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_value); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_10 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_value); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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         __pyx_t_11 = Py_TYPE(__pyx_t_2)->tp_iternext;
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@@ -16914,23 +17751,23 @@ static PyObject *__pyx_gb_5_cdec_4generator16(__pyx_GeneratorObject *__pyx_gener
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           #if CYTHON_COMPILING_IN_CPYTHON
-          __pyx_t_6 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_10); __Pyx_INCREF(__pyx_t_6); __pyx_t_10++;
+          __pyx_t_6 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_10); __Pyx_INCREF(__pyx_t_6); __pyx_t_10++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+          __pyx_t_6 = PySequence_ITEM(__pyx_t_2, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-          __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_10); __Pyx_INCREF(__pyx_t_6); __pyx_t_10++;
+          __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_10); __Pyx_INCREF(__pyx_t_6); __pyx_t_10++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-          __pyx_t_6 = PySequence_ITEM(__pyx_t_2, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+          __pyx_t_6 = PySequence_ITEM(__pyx_t_2, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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             if (PyErr_Occurred()) {
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-              else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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         __pyx_cur_scope->__pyx_v_name = __pyx_t_6;
         __pyx_t_6 = 0;
 
-        /* "_cdec.pyx":35
+        /* "_cdec.pyx":39
  *         elif isinstance(value, list):
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  *                 yield key, name             # <<<<<<<<<<<<<<
  *         else:
- *             yield key, bytes(value)
+ *             yield key, str(value)
  */
-        __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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         __pyx_t_11 = __pyx_cur_scope->__pyx_t_5;
-        if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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       __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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     }
     /*else*/ {
 
-      /* "_cdec.pyx":37
+      /* "_cdec.pyx":41
  *                 yield key, name
  *         else:
- *             yield key, bytes(value)             # <<<<<<<<<<<<<<
+ *             yield key, str(value)             # <<<<<<<<<<<<<<
  * 
  * cdef class Decoder:
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-      __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_6);
       __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
-      __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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       __pyx_t_4 = __pyx_cur_scope->__pyx_t_3;
-      if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -17054,25 +17891,29 @@ static PyObject *__pyx_gb_5_cdec_4generator16(__pyx_GeneratorObject *__pyx_gener
 }
 
 /* Python wrapper */
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-static int __pyx_pw_5_cdec_7Decoder_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static int __pyx_pw_5_cdec_7Decoder_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_5_cdec_7Decoder___init__[] = "Decoder('formalism = scfg') -> initialize from configuration string\n        Decoder(formalism='scfg') -> initialize from named parameters\n        Create a decoder using a given configuration. Formalism is required.";
+#if CYTHON_COMPILING_IN_CPYTHON
+struct wrapperbase __pyx_wrapperbase_5_cdec_7Decoder___init__;
+#endif
+static int __pyx_pw_5_cdec_7Decoder_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   PyObject *__pyx_v_config_str = 0;
   PyObject *__pyx_v_config = 0;
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-  __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
+  __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
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     static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__config_str,0};
     PyObject* values[1] = {0};
 
-    /* "_cdec.pyx":43
+    /* "_cdec.pyx":47
  *     cdef DenseVector weights
  * 
- *     def __cinit__(self, config_str=None, **config):             # <<<<<<<<<<<<<<
- *         """ Configuration can be given as a string:
- *                 Decoder('formalism = scfg')
+ *     def __init__(self, config_str=None, **config):             # <<<<<<<<<<<<<<
+ *         """Decoder('formalism = scfg') -> initialize from configuration string
+ *         Decoder(formalism='scfg') -> initialize from named parameters
  */
     values[0] = ((PyObject *)Py_None);
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@@ -17092,7 +17933,7 @@ static int __pyx_pw_5_cdec_7Decoder_1__cinit__(PyObject *__pyx_v_self, PyObject
         }
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-        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_config, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_config, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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       switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -17105,21 +17946,21 @@ static int __pyx_pw_5_cdec_7Decoder_1__cinit__(PyObject *__pyx_v_self, PyObject
   }
   goto __pyx_L4_argument_unpacking_done;
   __pyx_L5_argtuple_error:;
-  __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 0, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+  __Pyx_RaiseArgtupleInvalid("__init__", 0, 0, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
   __pyx_L3_error:;
   __Pyx_CLEAR(__pyx_v_config);
-  __Pyx_AddTraceback("_cdec.Decoder.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+  __Pyx_AddTraceback("_cdec.Decoder.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
   __Pyx_RefNannyFinishContext();
   return -1;
   __pyx_L4_argument_unpacking_done:;
-  __pyx_r = __pyx_pf_5_cdec_7Decoder___cinit__(((struct __pyx_obj_5_cdec_Decoder *)__pyx_v_self), __pyx_v_config_str, __pyx_v_config);
+  __pyx_r = __pyx_pf_5_cdec_7Decoder___init__(((struct __pyx_obj_5_cdec_Decoder *)__pyx_v_self), __pyx_v_config_str, __pyx_v_config);
   __Pyx_XDECREF(__pyx_v_config);
   __Pyx_RefNannyFinishContext();
   return __pyx_r;
 }
-static PyObject *__pyx_gb_5_cdec_7Decoder_9__cinit___2generator20(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
+static PyObject *__pyx_gb_5_cdec_7Decoder_8__init___2generator21(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
 
-/* "_cdec.pyx":54
+/* "_cdec.pyx":56
  *                     'csplit', 'tagger', 'lexalign'):
  *                 raise InvalidConfig('formalism "%s" unknown' % formalism)
  *             config_str = '\n'.join('%s = %s' % kv for kv in _make_config(config))             # <<<<<<<<<<<<<<
@@ -17127,25 +17968,25 @@ static PyObject *__pyx_gb_5_cdec_7Decoder_9__cinit___2generator20(__pyx_Generato
  *         self.dec = new decoder.Decoder(config_stream)
  */
 
-static PyObject *__pyx_pf_5_cdec_7Decoder_9__cinit___genexpr(PyObject *__pyx_self) {
-  struct __pyx_obj_5_cdec___pyx_scope_struct_24_genexpr *__pyx_cur_scope;
+static PyObject *__pyx_pf_5_cdec_7Decoder_8__init___genexpr(PyObject *__pyx_self) {
+  struct __pyx_obj_5_cdec___pyx_scope_struct_25_genexpr *__pyx_cur_scope;
   PyObject *__pyx_r = NULL;
   __Pyx_RefNannyDeclarations
   int __pyx_lineno = 0;
   const char *__pyx_filename = NULL;
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("genexpr", 0);
-  __pyx_cur_scope = (struct __pyx_obj_5_cdec___pyx_scope_struct_24_genexpr *)__pyx_ptype_5_cdec___pyx_scope_struct_24_genexpr->tp_new(__pyx_ptype_5_cdec___pyx_scope_struct_24_genexpr, __pyx_empty_tuple, NULL);
+  __pyx_cur_scope = (struct __pyx_obj_5_cdec___pyx_scope_struct_25_genexpr *)__pyx_ptype_5_cdec___pyx_scope_struct_25_genexpr->tp_new(__pyx_ptype_5_cdec___pyx_scope_struct_25_genexpr, __pyx_empty_tuple, NULL);
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     __Pyx_RefNannyFinishContext();
     return NULL;
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-  __pyx_cur_scope->__pyx_outer_scope = (struct __pyx_obj_5_cdec___pyx_scope_struct_23___cinit__ *) __pyx_self;
+  __pyx_cur_scope->__pyx_outer_scope = (struct __pyx_obj_5_cdec___pyx_scope_struct_24___init__ *) __pyx_self;
   __Pyx_INCREF(((PyObject *)__pyx_cur_scope->__pyx_outer_scope));
   __Pyx_GIVEREF(__pyx_cur_scope->__pyx_outer_scope);
   {
-    __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_5_cdec_7Decoder_9__cinit___2generator20, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_5_cdec_7Decoder_8__init___2generator21, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -17154,7 +17995,7 @@ static PyObject *__pyx_pf_5_cdec_7Decoder_9__cinit___genexpr(PyObject *__pyx_sel
   __pyx_r = Py_None; __Pyx_INCREF(Py_None);
   goto __pyx_L0;
   __pyx_L1_error:;
-  __Pyx_AddTraceback("_cdec.Decoder.__cinit__.genexpr", __pyx_clineno, __pyx_lineno, __pyx_filename);
+  __Pyx_AddTraceback("_cdec.Decoder.__init__.genexpr", __pyx_clineno, __pyx_lineno, __pyx_filename);
   __pyx_r = NULL;
   __pyx_L0:;
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@@ -17163,9 +18004,9 @@ static PyObject *__pyx_pf_5_cdec_7Decoder_9__cinit___genexpr(PyObject *__pyx_sel
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 }
 
-static PyObject *__pyx_gb_5_cdec_7Decoder_9__cinit___2generator20(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value) /* generator body */
+static PyObject *__pyx_gb_5_cdec_7Decoder_8__init___2generator21(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value) /* generator body */
 {
-  struct __pyx_obj_5_cdec___pyx_scope_struct_24_genexpr *__pyx_cur_scope = ((struct __pyx_obj_5_cdec___pyx_scope_struct_24_genexpr *)__pyx_generator->closure);
+  struct __pyx_obj_5_cdec___pyx_scope_struct_25_genexpr *__pyx_cur_scope = ((struct __pyx_obj_5_cdec___pyx_scope_struct_25_genexpr *)__pyx_generator->closure);
   PyObject *__pyx_r = NULL;
   PyObject *__pyx_t_1 = NULL;
   PyObject *__pyx_t_2 = NULL;
@@ -17182,16 +18023,16 @@ static PyObject *__pyx_gb_5_cdec_7Decoder_9__cinit___2generator20(__pyx_Generato
     return NULL;
   }
   __pyx_L3_first_run:;
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-  __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s___make_config); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s___make_config); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_1);
-  if (unlikely(!__pyx_cur_scope->__pyx_outer_scope->__pyx_v_config)) { __Pyx_RaiseClosureNameError("config"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
-  __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (unlikely(!__pyx_cur_scope->__pyx_outer_scope->__pyx_v_config)) { __Pyx_RaiseClosureNameError("config"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
+  __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_4 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_3 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_3); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_3 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      __pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_3); __pyx_t_4++;
+      __pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_3); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_3 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-          else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   return NULL;
 }
 
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  * 
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- *         """ Configuration can be given as a string:
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+ *     def __init__(self, config_str=None, **config):             # <<<<<<<<<<<<<<
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+ *         Decoder(formalism='scfg') -> initialize from named parameters
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-  struct __pyx_obj_5_cdec___pyx_scope_struct_23___cinit__ *__pyx_cur_scope;
+static int __pyx_pf_5_cdec_7Decoder___init__(struct __pyx_obj_5_cdec_Decoder *__pyx_v_self, PyObject *__pyx_v_config_str, PyObject *__pyx_v_config) {
+  struct __pyx_obj_5_cdec___pyx_scope_struct_24___init__ *__pyx_cur_scope;
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   const char *__pyx_filename = NULL;
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+  __Pyx_RefNannySetupContext("__init__", 0);
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   __Pyx_INCREF(__pyx_v_config_str);
 
-  /* "_cdec.pyx":49
- *                 Decoder(formalism='scfg')
- *         """
+  /* "_cdec.pyx":51
+ *         Decoder(formalism='scfg') -> initialize from named parameters
+ *         Create a decoder using a given configuration. Formalism is required."""
  *         if config_str is None:             # <<<<<<<<<<<<<<
  *             formalism = config.get('formalism', None)
  *             if formalism not in ('scfg', 'fst', 'lextrans', 'pb',
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   __pyx_t_1 = (__pyx_v_config_str == Py_None);
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-    /* "_cdec.pyx":50
- *         """
+    /* "_cdec.pyx":52
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+    __pyx_t_2 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_config, __pyx_n_s__get); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "_cdec.pyx":51
+    /* "_cdec.pyx":53
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+      __pyx_t_2 = PyObject_RichCompare(__pyx_t_3, ((PyObject *)__pyx_n_s__lexalign), Py_NE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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     __pyx_t_4 = __pyx_t_1;
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-      /* "_cdec.pyx":53
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-    /* "_cdec.pyx":54
+    /* "_cdec.pyx":56
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+  __pyx_t_7 = PyBytes_AsString(__pyx_v_config_str); if (unlikely((!__pyx_t_7) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "_cdec.pyx":56
+  /* "_cdec.pyx":58
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-  /* "_cdec.pyx":57
+  /* "_cdec.pyx":59
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-  /* "_cdec.pyx":58
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-  __pyx_t_6 = __Pyx_tp_new(((PyObject*)__pyx_ptype_5_cdec_DenseVector)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_6 = __Pyx_tp_new(((PyObject*)__pyx_ptype_5_cdec_DenseVector)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  if (!(likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5_cdec_DenseVector)))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __pyx_v_self->weights = ((struct __pyx_obj_5_cdec_DenseVector *)__pyx_t_6);
   __pyx_t_6 = 0;
 
-  /* "_cdec.pyx":59
+  /* "_cdec.pyx":61
  *         del config_stream
  *         self.weights = DenseVector.__new__(DenseVector)
  *         self.weights.vector = &self.dec.CurrentWeightVector()             # <<<<<<<<<<<<<<
@@ -17490,7 +18345,7 @@ static int __pyx_pf_5_cdec_7Decoder___cinit__(struct __pyx_obj_5_cdec_Decoder *_
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-  /* "_cdec.pyx":60
+  /* "_cdec.pyx":62
  *         self.weights = DenseVector.__new__(DenseVector)
  *         self.weights.vector = &self.dec.CurrentWeightVector()
  *         self.weights.owned = True             # <<<<<<<<<<<<<<
@@ -17505,7 +18360,7 @@ static int __pyx_pf_5_cdec_7Decoder___cinit__(struct __pyx_obj_5_cdec_Decoder *_
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-  __Pyx_AddTraceback("_cdec.Decoder.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+  __Pyx_AddTraceback("_cdec.Decoder.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
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 }
 
-/* "_cdec.pyx":62
+/* "_cdec.pyx":64
  *         self.weights.owned = True
  * 
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@@ -17536,7 +18391,7 @@ static void __pyx_pf_5_cdec_7Decoder_2__dealloc__(CYTHON_UNUSED struct __pyx_obj
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-  /* "_cdec.pyx":63
+  /* "_cdec.pyx":65
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  *     def __dealloc__(self):
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@@ -17559,7 +18414,7 @@ static PyObject *__pyx_pw_5_cdec_7Decoder_7weights_1__get__(PyObject *__pyx_v_se
   return __pyx_r;
 }
 
-/* "_cdec.pyx":66
+/* "_cdec.pyx":68
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  *     property weights:
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-  /* "_cdec.pyx":67
+  /* "_cdec.pyx":69
  *     property weights:
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@@ -17602,7 +18457,7 @@ static int __pyx_pw_5_cdec_7Decoder_7weights_3__set__(PyObject *__pyx_v_self, Py
   return __pyx_r;
 }
 
-/* "_cdec.pyx":69
+/* "_cdec.pyx":71
  *             return self.weights
  * 
  *         def __set__(self, weights):             # <<<<<<<<<<<<<<
@@ -17629,7 +18484,7 @@ static int __pyx_pf_5_cdec_7Decoder_7weights_2__set__(struct __pyx_obj_5_cdec_De
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-  /* "_cdec.pyx":70
+  /* "_cdec.pyx":72
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  *         def __set__(self, weights):
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@@ -17642,7 +18497,7 @@ static int __pyx_pf_5_cdec_7Decoder_7weights_2__set__(struct __pyx_obj_5_cdec_De
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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-    /* "_cdec.pyx":71
+    /* "_cdec.pyx":73
  *         def __set__(self, weights):
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  *                 self.weights.vector[0] = (<DenseVector> weights).vector[0]             # <<<<<<<<<<<<<<
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     goto __pyx_L3;
   }
 
-  /* "_cdec.pyx":72
+  /* "_cdec.pyx":74
  *             if isinstance(weights, DenseVector):
  *                 self.weights.vector[0] = (<DenseVector> weights).vector[0]
  *             elif isinstance(weights, SparseVector):             # <<<<<<<<<<<<<<
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   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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-    /* "_cdec.pyx":73
+    /* "_cdec.pyx":75
  *                 self.weights.vector[0] = (<DenseVector> weights).vector[0]
  *             elif isinstance(weights, SparseVector):
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@@ -17675,7 +18530,7 @@ static int __pyx_pf_5_cdec_7Decoder_7weights_2__set__(struct __pyx_obj_5_cdec_De
  */
     __pyx_v_self->weights->vector->clear();
 
-    /* "_cdec.pyx":74
+    /* "_cdec.pyx":76
  *             elif isinstance(weights, SparseVector):
  *                 self.weights.vector.clear()
  *                 ((<SparseVector> weights).vector[0]).init_vector(self.weights.vector)             # <<<<<<<<<<<<<<
@@ -17686,7 +18541,7 @@ static int __pyx_pf_5_cdec_7Decoder_7weights_2__set__(struct __pyx_obj_5_cdec_De
     goto __pyx_L3;
   }
 
-  /* "_cdec.pyx":75
+  /* "_cdec.pyx":77
  *                 self.weights.vector.clear()
  *                 ((<SparseVector> weights).vector[0]).init_vector(self.weights.vector)
  *             elif isinstance(weights, dict):             # <<<<<<<<<<<<<<
@@ -17699,7 +18554,7 @@ static int __pyx_pf_5_cdec_7Decoder_7weights_2__set__(struct __pyx_obj_5_cdec_De
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
   if (__pyx_t_2) {
 
-    /* "_cdec.pyx":76
+    /* "_cdec.pyx":78
  *                 ((<SparseVector> weights).vector[0]).init_vector(self.weights.vector)
  *             elif isinstance(weights, dict):
  *                 self.weights.vector.clear()             # <<<<<<<<<<<<<<
@@ -17708,23 +18563,23 @@ static int __pyx_pf_5_cdec_7Decoder_7weights_2__set__(struct __pyx_obj_5_cdec_De
  */
     __pyx_v_self->weights->vector->clear();
 
-    /* "_cdec.pyx":77
+    /* "_cdec.pyx":79
  *             elif isinstance(weights, dict):
  *                 self.weights.vector.clear()
  *                 for fname, fval in weights.items():             # <<<<<<<<<<<<<<
  *                     self.weights[fname] = fval
  *             else:
  */
-    __pyx_t_1 = PyObject_GetAttr(__pyx_v_weights, __pyx_n_s__items); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_1 = PyObject_GetAttr(__pyx_v_weights, __pyx_n_s__items); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_3);
     __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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       __pyx_t_1 = __pyx_t_3; __Pyx_INCREF(__pyx_t_1); __pyx_t_4 = 0;
       __pyx_t_5 = NULL;
     } else {
-      __pyx_t_4 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_4 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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       __pyx_t_5 = Py_TYPE(__pyx_t_1)->tp_iternext;
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@@ -17733,23 +18588,23 @@ static int __pyx_pf_5_cdec_7Decoder_7weights_2__set__(struct __pyx_obj_5_cdec_De
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         if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_1)) break;
         #if CYTHON_COMPILING_IN_CPYTHON
-        __pyx_t_3 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_3); __pyx_t_4++;
+        __pyx_t_3 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_3); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         #else
-        __pyx_t_3 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+        __pyx_t_3 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         #endif
       } else if (!__pyx_t_5 && PyTuple_CheckExact(__pyx_t_1)) {
         if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
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-        __pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_3); __pyx_t_4++;
+        __pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_3); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-        __pyx_t_3 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+        __pyx_t_3 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-            else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           }
           break;
         }
@@ -17765,7 +18620,7 @@ static int __pyx_pf_5_cdec_7Decoder_7weights_2__set__(struct __pyx_obj_5_cdec_De
         if (unlikely(size != 2)) {
           if (size > 2) __Pyx_RaiseTooManyValuesError(2);
           else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
-          {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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         #if CYTHON_COMPILING_IN_CPYTHON
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@@ -17778,14 +18633,14 @@ static int __pyx_pf_5_cdec_7Decoder_7weights_2__set__(struct __pyx_obj_5_cdec_De
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         __Pyx_INCREF(__pyx_t_7);
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-        __pyx_t_6 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-        __pyx_t_7 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_6 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_7 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+        __pyx_t_8 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -17793,7 +18648,7 @@ static int __pyx_pf_5_cdec_7Decoder_7weights_2__set__(struct __pyx_obj_5_cdec_De
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-        if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_8), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_8), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -17801,7 +18656,7 @@ static int __pyx_pf_5_cdec_7Decoder_7weights_2__set__(struct __pyx_obj_5_cdec_De
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-        {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      /* "_cdec.pyx":78
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-    /* "_cdec.pyx":80
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+    __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_48), ((PyObject *)Py_TYPE(__pyx_v_weights))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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 }
 
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- *             return conf[0]['formalism'].as_str()
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 static PyObject *__pyx_pf_5_cdec_7Decoder_9formalism___get__(struct __pyx_obj_5_cdec_Decoder *__pyx_v_self) {
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+  PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1));
+  __Pyx_GIVEREF(((PyObject *)__pyx_t_1));
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 /* Python wrapper */
 static PyObject *__pyx_pw_5_cdec_7Decoder_5read_weights(PyObject *__pyx_v_self, PyObject *__pyx_v_weights); /*proto*/
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 static PyObject *__pyx_pw_5_cdec_7Decoder_5read_weights(PyObject *__pyx_v_self, PyObject *__pyx_v_weights) {
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  *     def read_weights(self, weights):             # <<<<<<<<<<<<<<
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-              {__pyx_filename = __pyx_f[0]; __pyx_lineno = 91; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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-            /* "_cdec.pyx":92
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+            __pyx_t_1 = PyObject_Call(__pyx_t_11, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 95; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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-        /* "_cdec.pyx":88
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+        /* "_cdec.pyx":91
  *     def read_weights(self, weights):
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-            {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
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-        if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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 /* Python wrapper */
 static PyObject *__pyx_pw_5_cdec_7Decoder_7translate(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
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 static PyObject *__pyx_pw_5_cdec_7Decoder_7translate(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
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-    /* "_cdec.pyx":94
+    /* "_cdec.pyx":97
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@@ -18324,7 +19191,7 @@ static PyObject *__pyx_pw_5_cdec_7Decoder_7translate(PyObject *__pyx_v_self, PyO
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+  __Pyx_RaiseArgtupleInvalid("translate", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 97; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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  *         cdef bytes input_str
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-  if (__pyx_t_4) {
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 }
 
 static PyMethodDef __pyx_methods_5_cdec_DenseVector[] = {
-  {__Pyx_NAMESTR("dot"), (PyCFunction)__pyx_pw_5_cdec_11DenseVector_14dot, METH_O, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("tosparse"), (PyCFunction)__pyx_pw_5_cdec_11DenseVector_16tosparse, METH_NOARGS, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("dot"), (PyCFunction)__pyx_pw_5_cdec_11DenseVector_14dot, METH_O, __Pyx_DOCSTR(__pyx_doc_5_cdec_11DenseVector_13dot)},
+  {__Pyx_NAMESTR("tosparse"), (PyCFunction)__pyx_pw_5_cdec_11DenseVector_16tosparse, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5_cdec_11DenseVector_15tosparse)},
   {0, 0, 0, 0}
 };
 
@@ -18905,8 +19751,8 @@ static int __pyx_mp_ass_subscript_5_cdec_SparseVector(PyObject *o, PyObject *i,
 }
 
 static PyMethodDef __pyx_methods_5_cdec_SparseVector[] = {
-  {__Pyx_NAMESTR("copy"), (PyCFunction)__pyx_pw_5_cdec_12SparseVector_5copy, METH_NOARGS, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("dot"), (PyCFunction)__pyx_pw_5_cdec_12SparseVector_14dot, METH_O, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("copy"), (PyCFunction)__pyx_pw_5_cdec_12SparseVector_5copy, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5_cdec_12SparseVector_4copy)},
+  {__Pyx_NAMESTR("dot"), (PyCFunction)__pyx_pw_5_cdec_12SparseVector_14dot, METH_O, __Pyx_DOCSTR(__pyx_doc_5_cdec_12SparseVector_13dot)},
   {0, 0, 0, 0}
 };
 
@@ -19075,7 +19921,7 @@ static PyObject *__pyx_tp_new_5_cdec_NT(PyTypeObject *t, CYTHON_UNUSED PyObject
 
 static void __pyx_tp_dealloc_5_cdec_NT(PyObject *o) {
   struct __pyx_obj_5_cdec_NT *p = (struct __pyx_obj_5_cdec_NT *)o;
-  Py_XDECREF(((PyObject *)p->cat));
+  Py_CLEAR(p->cat);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -20103,9 +20949,6 @@ static PyTypeObject __pyx_type_5_cdec_Grammar = {
 static PyObject *__pyx_tp_new_5_cdec_TextGrammar(PyTypeObject *t, PyObject *a, PyObject *k) {
   PyObject *o = __pyx_tp_new_5_cdec_Grammar(t, a, k);
   if (!o) return 0;
-  if (__pyx_pw_5_cdec_11TextGrammar_1__cinit__(o, a, k) < 0) {
-    Py_DECREF(o); o = 0;
-  }
   return o;
 }
 
@@ -20255,7 +21098,7 @@ static PyTypeObject __pyx_type_5_cdec_TextGrammar = {
   0, /*tp_descr_get*/
   0, /*tp_descr_set*/
   0, /*tp_dictoffset*/
-  0, /*tp_init*/
+  __pyx_pw_5_cdec_11TextGrammar_1__init__, /*tp_init*/
   0, /*tp_alloc*/
   __pyx_tp_new_5_cdec_TextGrammar, /*tp_new*/
   0, /*tp_free*/
@@ -20270,10 +21113,14 @@ static PyTypeObject __pyx_type_5_cdec_TextGrammar = {
   0, /*tp_version_tag*/
   #endif
 };
+static struct __pyx_vtabstruct_5_cdec_Hypergraph __pyx_vtable_5_cdec_Hypergraph;
 
 static PyObject *__pyx_tp_new_5_cdec_Hypergraph(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+  struct __pyx_obj_5_cdec_Hypergraph *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
+  p = ((struct __pyx_obj_5_cdec_Hypergraph *)o);
+  p->__pyx_vtab = __pyx_vtabptr_5_cdec_Hypergraph;
   return o;
 }
 
@@ -20307,19 +21154,21 @@ static PyObject *__pyx_getprop_5_cdec_10Hypergraph_npaths(PyObject *o, CYTHON_UN
 }
 
 static PyMethodDef __pyx_methods_5_cdec_Hypergraph[] = {
-  {__Pyx_NAMESTR("viterbi"), (PyCFunction)__pyx_pw_5_cdec_10Hypergraph_3viterbi, METH_NOARGS, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("viterbi_trees"), (PyCFunction)__pyx_pw_5_cdec_10Hypergraph_5viterbi_trees, METH_NOARGS, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("viterbi_features"), (PyCFunction)__pyx_pw_5_cdec_10Hypergraph_7viterbi_features, METH_NOARGS, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("viterbi_joshua"), (PyCFunction)__pyx_pw_5_cdec_10Hypergraph_9viterbi_joshua, METH_NOARGS, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("kbest"), (PyCFunction)__pyx_pw_5_cdec_10Hypergraph_11kbest, METH_O, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("kbest_trees"), (PyCFunction)__pyx_pw_5_cdec_10Hypergraph_14kbest_trees, METH_O, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("kbest_features"), (PyCFunction)__pyx_pw_5_cdec_10Hypergraph_17kbest_features, METH_O, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("sample"), (PyCFunction)__pyx_pw_5_cdec_10Hypergraph_20sample, METH_O, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("intersect"), (PyCFunction)__pyx_pw_5_cdec_10Hypergraph_23intersect, METH_O, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("prune"), (PyCFunction)__pyx_pw_5_cdec_10Hypergraph_25prune, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("lattice"), (PyCFunction)__pyx_pw_5_cdec_10Hypergraph_27lattice, METH_NOARGS, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("reweight"), (PyCFunction)__pyx_pw_5_cdec_10Hypergraph_29reweight, METH_O, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("inside_outside"), (PyCFunction)__pyx_pw_5_cdec_10Hypergraph_31inside_outside, METH_NOARGS, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("viterbi"), (PyCFunction)__pyx_pw_5_cdec_10Hypergraph_3viterbi, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5_cdec_10Hypergraph_2viterbi)},
+  {__Pyx_NAMESTR("viterbi_trees"), (PyCFunction)__pyx_pw_5_cdec_10Hypergraph_5viterbi_trees, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5_cdec_10Hypergraph_4viterbi_trees)},
+  {__Pyx_NAMESTR("viterbi_features"), (PyCFunction)__pyx_pw_5_cdec_10Hypergraph_7viterbi_features, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5_cdec_10Hypergraph_6viterbi_features)},
+  {__Pyx_NAMESTR("viterbi_joshua"), (PyCFunction)__pyx_pw_5_cdec_10Hypergraph_9viterbi_joshua, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5_cdec_10Hypergraph_8viterbi_joshua)},
+  {__Pyx_NAMESTR("kbest"), (PyCFunction)__pyx_pw_5_cdec_10Hypergraph_11kbest, METH_O, __Pyx_DOCSTR(__pyx_doc_5_cdec_10Hypergraph_10kbest)},
+  {__Pyx_NAMESTR("kbest_trees"), (PyCFunction)__pyx_pw_5_cdec_10Hypergraph_14kbest_trees, METH_O, __Pyx_DOCSTR(__pyx_doc_5_cdec_10Hypergraph_13kbest_trees)},
+  {__Pyx_NAMESTR("kbest_features"), (PyCFunction)__pyx_pw_5_cdec_10Hypergraph_17kbest_features, METH_O, __Pyx_DOCSTR(__pyx_doc_5_cdec_10Hypergraph_16kbest_features)},
+  {__Pyx_NAMESTR("sample"), (PyCFunction)__pyx_pw_5_cdec_10Hypergraph_20sample, METH_O, __Pyx_DOCSTR(__pyx_doc_5_cdec_10Hypergraph_19sample)},
+  {__Pyx_NAMESTR("sample_trees"), (PyCFunction)__pyx_pw_5_cdec_10Hypergraph_23sample_trees, METH_O, __Pyx_DOCSTR(__pyx_doc_5_cdec_10Hypergraph_22sample_trees)},
+  {__Pyx_NAMESTR("intersect"), (PyCFunction)__pyx_pw_5_cdec_10Hypergraph_26intersect, METH_O, __Pyx_DOCSTR(__pyx_doc_5_cdec_10Hypergraph_25intersect)},
+  {__Pyx_NAMESTR("prune"), (PyCFunction)__pyx_pw_5_cdec_10Hypergraph_28prune, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5_cdec_10Hypergraph_27prune)},
+  {__Pyx_NAMESTR("lattice"), (PyCFunction)__pyx_pw_5_cdec_10Hypergraph_30lattice, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5_cdec_10Hypergraph_29lattice)},
+  {__Pyx_NAMESTR("plf"), (PyCFunction)__pyx_pw_5_cdec_10Hypergraph_32plf, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5_cdec_10Hypergraph_31plf)},
+  {__Pyx_NAMESTR("reweight"), (PyCFunction)__pyx_pw_5_cdec_10Hypergraph_34reweight, METH_O, __Pyx_DOCSTR(__pyx_doc_5_cdec_10Hypergraph_33reweight)},
+  {__Pyx_NAMESTR("inside_outside"), (PyCFunction)__pyx_pw_5_cdec_10Hypergraph_36inside_outside, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5_cdec_10Hypergraph_35inside_outside)},
   {0, 0, 0, 0}
 };
 
@@ -20498,7 +21347,7 @@ static PyObject *__pyx_tp_new_5_cdec_HypergraphEdge(PyTypeObject *t, CYTHON_UNUS
 
 static void __pyx_tp_dealloc_5_cdec_HypergraphEdge(PyObject *o) {
   struct __pyx_obj_5_cdec_HypergraphEdge *p = (struct __pyx_obj_5_cdec_HypergraphEdge *)o;
-  Py_XDECREF(((PyObject *)p->trule));
+  Py_CLEAR(p->trule);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -20917,10 +21766,10 @@ static PyTypeObject __pyx_type_5_cdec_HypergraphNode = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_5_cdec_Lattice(PyTypeObject *t, PyObject *a, PyObject *k) {
+static PyObject *__pyx_tp_new_5_cdec_Lattice(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
-  if (__pyx_pw_5_cdec_7Lattice_1__cinit__(o, a, k) < 0) {
+  if (__pyx_pw_5_cdec_7Lattice_1__cinit__(o, __pyx_empty_tuple, NULL) < 0) {
     Py_DECREF(o); o = 0;
   }
   return o;
@@ -20931,7 +21780,7 @@ static void __pyx_tp_dealloc_5_cdec_Lattice(PyObject *o) {
     PyObject *etype, *eval, *etb;
     PyErr_Fetch(&etype, &eval, &etb);
     ++Py_REFCNT(o);
-    __pyx_pw_5_cdec_7Lattice_3__dealloc__(o);
+    __pyx_pw_5_cdec_7Lattice_5__dealloc__(o);
     if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
     --Py_REFCNT(o);
     PyErr_Restore(etype, eval, etb);
@@ -20948,7 +21797,7 @@ static PyObject *__pyx_sq_item_5_cdec_Lattice(PyObject *o, Py_ssize_t i) {
 
 static int __pyx_mp_ass_subscript_5_cdec_Lattice(PyObject *o, PyObject *i, PyObject *v) {
   if (v) {
-    return __pyx_pw_5_cdec_7Lattice_7__setitem__(o, i, v);
+    return __pyx_pw_5_cdec_7Lattice_9__setitem__(o, i, v);
   }
   else {
     PyErr_Format(PyExc_NotImplementedError,
@@ -20958,7 +21807,9 @@ static int __pyx_mp_ass_subscript_5_cdec_Lattice(PyObject *o, PyObject *i, PyObj
 }
 
 static PyMethodDef __pyx_methods_5_cdec_Lattice[] = {
-  {__Pyx_NAMESTR("todot"), (PyCFunction)__pyx_pw_5_cdec_7Lattice_16todot, METH_NOARGS, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("__unicode__"), (PyCFunction)__pyx_pw_5_cdec_7Lattice_15__unicode__, METH_NOARGS, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("todot"), (PyCFunction)__pyx_pw_5_cdec_7Lattice_20todot, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5_cdec_7Lattice_19todot)},
+  {__Pyx_NAMESTR("as_hypergraph"), (PyCFunction)__pyx_pw_5_cdec_7Lattice_22as_hypergraph, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5_cdec_7Lattice_21as_hypergraph)},
   {0, 0, 0, 0}
 };
 
@@ -21021,7 +21872,7 @@ static PyNumberMethods __pyx_tp_as_number_Lattice = {
 };
 
 static PySequenceMethods __pyx_tp_as_sequence_Lattice = {
-  __pyx_pw_5_cdec_7Lattice_9__len__, /*sq_length*/
+  __pyx_pw_5_cdec_7Lattice_11__len__, /*sq_length*/
   0, /*sq_concat*/
   0, /*sq_repeat*/
   __pyx_sq_item_5_cdec_Lattice, /*sq_item*/
@@ -21034,8 +21885,8 @@ static PySequenceMethods __pyx_tp_as_sequence_Lattice = {
 };
 
 static PyMappingMethods __pyx_tp_as_mapping_Lattice = {
-  __pyx_pw_5_cdec_7Lattice_9__len__, /*mp_length*/
-  __pyx_pw_5_cdec_7Lattice_5__getitem__, /*mp_subscript*/
+  __pyx_pw_5_cdec_7Lattice_11__len__, /*mp_length*/
+  __pyx_pw_5_cdec_7Lattice_7__getitem__, /*mp_subscript*/
   __pyx_mp_ass_subscript_5_cdec_Lattice, /*mp_ass_subscript*/
 };
 
@@ -21080,7 +21931,7 @@ static PyTypeObject __pyx_type_5_cdec_Lattice = {
   &__pyx_tp_as_mapping_Lattice, /*tp_as_mapping*/
   0, /*tp_hash*/
   0, /*tp_call*/
-  __pyx_pw_5_cdec_7Lattice_11__str__, /*tp_str*/
+  __pyx_pw_5_cdec_7Lattice_13__str__, /*tp_str*/
   0, /*tp_getattro*/
   0, /*tp_setattro*/
   &__pyx_tp_as_buffer_Lattice, /*tp_as_buffer*/
@@ -21090,7 +21941,7 @@ static PyTypeObject __pyx_type_5_cdec_Lattice = {
   0, /*tp_clear*/
   0, /*tp_richcompare*/
   0, /*tp_weaklistoffset*/
-  __pyx_pw_5_cdec_7Lattice_13__iter__, /*tp_iter*/
+  __pyx_pw_5_cdec_7Lattice_17__iter__, /*tp_iter*/
   0, /*tp_iternext*/
   __pyx_methods_5_cdec_Lattice, /*tp_methods*/
   0, /*tp_members*/
@@ -21100,7 +21951,7 @@ static PyTypeObject __pyx_type_5_cdec_Lattice = {
   0, /*tp_descr_get*/
   0, /*tp_descr_set*/
   0, /*tp_dictoffset*/
-  0, /*tp_init*/
+  __pyx_pw_5_cdec_7Lattice_3__init__, /*tp_init*/
   0, /*tp_alloc*/
   __pyx_tp_new_5_cdec_Lattice, /*tp_new*/
   0, /*tp_free*/
@@ -21541,7 +22392,7 @@ static PyObject *__pyx_sq_item_5_cdec_CandidateSet(PyObject *o, Py_ssize_t i) {
 }
 
 static PyMethodDef __pyx_methods_5_cdec_CandidateSet[] = {
-  {__Pyx_NAMESTR("add_kbest"), (PyCFunction)__pyx_pw_5_cdec_12CandidateSet_12add_kbest, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("add_kbest"), (PyCFunction)__pyx_pw_5_cdec_12CandidateSet_12add_kbest, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5_cdec_12CandidateSet_11add_kbest)},
   {0, 0, 0, 0}
 };
 
@@ -21719,8 +22570,8 @@ static void __pyx_tp_dealloc_5_cdec_SegmentEvaluator(PyObject *o) {
 }
 
 static PyMethodDef __pyx_methods_5_cdec_SegmentEvaluator[] = {
-  {__Pyx_NAMESTR("evaluate"), (PyCFunction)__pyx_pw_5_cdec_16SegmentEvaluator_3evaluate, METH_O, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("candidate_set"), (PyCFunction)__pyx_pw_5_cdec_16SegmentEvaluator_5candidate_set, METH_NOARGS, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("evaluate"), (PyCFunction)__pyx_pw_5_cdec_16SegmentEvaluator_3evaluate, METH_O, __Pyx_DOCSTR(__pyx_doc_5_cdec_16SegmentEvaluator_2evaluate)},
+  {__Pyx_NAMESTR("candidate_set"), (PyCFunction)__pyx_pw_5_cdec_16SegmentEvaluator_5candidate_set, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5_cdec_16SegmentEvaluator_4candidate_set)},
   {0, 0, 0, 0}
 };
 
@@ -22072,7 +22923,7 @@ static PyObject *__pyx_tp_new_5_cdec_Metric(PyTypeObject *t, CYTHON_UNUSED PyObj
 
 static void __pyx_tp_dealloc_5_cdec_Metric(PyObject *o) {
   struct __pyx_obj_5_cdec_Metric *p = (struct __pyx_obj_5_cdec_Metric *)o;
-  Py_XDECREF(((PyObject *)p->scorer));
+  Py_CLEAR(p->scorer);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -22254,15 +23105,12 @@ static PyTypeObject __pyx_type_5_cdec_Metric = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_5_cdec_Decoder(PyTypeObject *t, PyObject *a, PyObject *k) {
+static PyObject *__pyx_tp_new_5_cdec_Decoder(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
   struct __pyx_obj_5_cdec_Decoder *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
   p = ((struct __pyx_obj_5_cdec_Decoder *)o);
   p->weights = ((struct __pyx_obj_5_cdec_DenseVector *)Py_None); Py_INCREF(Py_None);
-  if (__pyx_pw_5_cdec_7Decoder_1__cinit__(o, a, k) < 0) {
-    Py_DECREF(o); o = 0;
-  }
   return o;
 }
 
@@ -22277,7 +23125,7 @@ static void __pyx_tp_dealloc_5_cdec_Decoder(PyObject *o) {
     --Py_REFCNT(o);
     PyErr_Restore(etype, eval, etb);
   }
-  Py_XDECREF(((PyObject *)p->weights));
+  Py_CLEAR(p->weights);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -22318,8 +23166,8 @@ static PyObject *__pyx_getprop_5_cdec_7Decoder_formalism(PyObject *o, CYTHON_UNU
 }
 
 static PyMethodDef __pyx_methods_5_cdec_Decoder[] = {
-  {__Pyx_NAMESTR("read_weights"), (PyCFunction)__pyx_pw_5_cdec_7Decoder_5read_weights, METH_O, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("translate"), (PyCFunction)__pyx_pw_5_cdec_7Decoder_7translate, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("read_weights"), (PyCFunction)__pyx_pw_5_cdec_7Decoder_5read_weights, METH_O, __Pyx_DOCSTR(__pyx_doc_5_cdec_7Decoder_4read_weights)},
+  {__Pyx_NAMESTR("translate"), (PyCFunction)__pyx_pw_5_cdec_7Decoder_7translate, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5_cdec_7Decoder_6translate)},
   {0, 0, 0, 0}
 };
 
@@ -22467,7 +23315,7 @@ static PyTypeObject __pyx_type_5_cdec_Decoder = {
   0, /*tp_descr_get*/
   0, /*tp_descr_set*/
   0, /*tp_dictoffset*/
-  0, /*tp_init*/
+  __pyx_pw_5_cdec_7Decoder_1__init__, /*tp_init*/
   0, /*tp_alloc*/
   __pyx_tp_new_5_cdec_Decoder, /*tp_new*/
   0, /*tp_free*/
@@ -22494,7 +23342,7 @@ static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct____iter__(PyTypeObject *
 
 static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct____iter__(PyObject *o) {
   struct __pyx_obj_5_cdec___pyx_scope_struct____iter__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct____iter__ *)o;
-  Py_XDECREF(((PyObject *)p->__pyx_v_self));
+  Py_CLEAR(p->__pyx_v_self);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -22685,7 +23533,7 @@ static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_1___iter__(PyTypeObject
 
 static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_1___iter__(PyObject *o) {
   struct __pyx_obj_5_cdec___pyx_scope_struct_1___iter__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_1___iter__ *)o;
-  Py_XDECREF(((PyObject *)p->__pyx_v_self));
+  Py_CLEAR(p->__pyx_v_self);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -22876,7 +23724,7 @@ static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_2__phrase(PyTypeObject *
 
 static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_2__phrase(PyObject *o) {
   struct __pyx_obj_5_cdec___pyx_scope_struct_2__phrase *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_2__phrase *)o;
-  Py_XDECREF(p->__pyx_v_phrase);
+  Py_CLEAR(p->__pyx_v_phrase);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -23069,9 +23917,9 @@ static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_3_genexpr(PyTypeObject *
 
 static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_3_genexpr(PyObject *o) {
   struct __pyx_obj_5_cdec___pyx_scope_struct_3_genexpr *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_3_genexpr *)o;
-  Py_XDECREF(((PyObject *)p->__pyx_outer_scope));
-  Py_XDECREF(p->__pyx_v_w);
-  Py_XDECREF(p->__pyx_t_0);
+  Py_CLEAR(p->__pyx_outer_scope);
+  Py_CLEAR(p->__pyx_v_w);
+  Py_CLEAR(p->__pyx_t_0);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -23274,7 +24122,7 @@ static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_4___get__(PyTypeObject *
 
 static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_4___get__(PyObject *o) {
   struct __pyx_obj_5_cdec___pyx_scope_struct_4___get__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_4___get__ *)o;
-  Py_XDECREF(((PyObject *)p->__pyx_v_self));
+  Py_CLEAR(p->__pyx_v_self);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -23465,7 +24313,7 @@ static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_5___str__(PyTypeObject *
 
 static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_5___str__(PyObject *o) {
   struct __pyx_obj_5_cdec___pyx_scope_struct_5___str__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_5___str__ *)o;
-  Py_XDECREF(((PyObject *)p->__pyx_v_self));
+  Py_CLEAR(p->__pyx_v_self);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -23658,9 +24506,9 @@ static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_6_genexpr(PyTypeObject *
 
 static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_6_genexpr(PyObject *o) {
   struct __pyx_obj_5_cdec___pyx_scope_struct_6_genexpr *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_6_genexpr *)o;
-  Py_XDECREF(((PyObject *)p->__pyx_outer_scope));
-  Py_XDECREF(p->__pyx_v_feat);
-  Py_XDECREF(p->__pyx_t_0);
+  Py_CLEAR(p->__pyx_outer_scope);
+  Py_CLEAR(p->__pyx_v_feat);
+  Py_CLEAR(p->__pyx_t_0);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -23864,8 +24712,8 @@ static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_7___iter__(PyTypeObject
 
 static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_7___iter__(PyObject *o) {
   struct __pyx_obj_5_cdec___pyx_scope_struct_7___iter__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_7___iter__ *)o;
-  Py_XDECREF(((PyObject *)p->__pyx_v_self));
-  Py_XDECREF(((PyObject *)p->__pyx_v_trule));
+  Py_CLEAR(p->__pyx_v_self);
+  Py_CLEAR(p->__pyx_v_trule);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -24063,8 +24911,8 @@ static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_8_kbest(PyTypeObject *t,
 
 static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_8_kbest(PyObject *o) {
   struct __pyx_obj_5_cdec___pyx_scope_struct_8_kbest *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_8_kbest *)o;
-  Py_XDECREF(((PyObject *)p->__pyx_v_self));
-  Py_XDECREF(p->__pyx_v_size);
+  Py_CLEAR(p->__pyx_v_self);
+  Py_CLEAR(p->__pyx_v_size);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -24264,10 +25112,10 @@ static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_9_kbest_trees(PyTypeObje
 
 static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_9_kbest_trees(PyObject *o) {
   struct __pyx_obj_5_cdec___pyx_scope_struct_9_kbest_trees *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_9_kbest_trees *)o;
-  Py_XDECREF(((PyObject *)p->__pyx_v_e_tree));
-  Py_XDECREF(((PyObject *)p->__pyx_v_f_tree));
-  Py_XDECREF(((PyObject *)p->__pyx_v_self));
-  Py_XDECREF(p->__pyx_v_size);
+  Py_CLEAR(p->__pyx_v_e_tree);
+  Py_CLEAR(p->__pyx_v_f_tree);
+  Py_CLEAR(p->__pyx_v_self);
+  Py_CLEAR(p->__pyx_v_size);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -24478,9 +25326,9 @@ static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_10_kbest_features(PyType
 
 static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_10_kbest_features(PyObject *o) {
   struct __pyx_obj_5_cdec___pyx_scope_struct_10_kbest_features *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_10_kbest_features *)o;
-  Py_XDECREF(((PyObject *)p->__pyx_v_fmap));
-  Py_XDECREF(((PyObject *)p->__pyx_v_self));
-  Py_XDECREF(p->__pyx_v_size);
+  Py_CLEAR(p->__pyx_v_fmap);
+  Py_CLEAR(p->__pyx_v_self);
+  Py_CLEAR(p->__pyx_v_size);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -24683,7 +25531,7 @@ static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_11_sample(PyTypeObject *
 
 static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_11_sample(PyObject *o) {
   struct __pyx_obj_5_cdec___pyx_scope_struct_11_sample *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_11_sample *)o;
-  Py_XDECREF(((PyObject *)p->__pyx_v_self));
+  Py_CLEAR(p->__pyx_v_self);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -24863,32 +25711,32 @@ static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_11_sample = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_12___get__(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
-  struct __pyx_obj_5_cdec___pyx_scope_struct_12___get__ *p;
+static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_12_sample_trees(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+  struct __pyx_obj_5_cdec___pyx_scope_struct_12_sample_trees *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
-  p = ((struct __pyx_obj_5_cdec___pyx_scope_struct_12___get__ *)o);
+  p = ((struct __pyx_obj_5_cdec___pyx_scope_struct_12_sample_trees *)o);
   p->__pyx_v_self = 0;
   return o;
 }
 
-static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_12___get__(PyObject *o) {
-  struct __pyx_obj_5_cdec___pyx_scope_struct_12___get__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_12___get__ *)o;
-  Py_XDECREF(((PyObject *)p->__pyx_v_self));
+static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_12_sample_trees(PyObject *o) {
+  struct __pyx_obj_5_cdec___pyx_scope_struct_12_sample_trees *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_12_sample_trees *)o;
+  Py_CLEAR(p->__pyx_v_self);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
-static int __pyx_tp_traverse_5_cdec___pyx_scope_struct_12___get__(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_5_cdec___pyx_scope_struct_12_sample_trees(PyObject *o, visitproc v, void *a) {
   int e;
-  struct __pyx_obj_5_cdec___pyx_scope_struct_12___get__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_12___get__ *)o;
+  struct __pyx_obj_5_cdec___pyx_scope_struct_12_sample_trees *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_12_sample_trees *)o;
   if (p->__pyx_v_self) {
     e = (*v)(((PyObject*)p->__pyx_v_self), a); if (e) return e;
   }
   return 0;
 }
 
-static int __pyx_tp_clear_5_cdec___pyx_scope_struct_12___get__(PyObject *o) {
-  struct __pyx_obj_5_cdec___pyx_scope_struct_12___get__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_12___get__ *)o;
+static int __pyx_tp_clear_5_cdec___pyx_scope_struct_12_sample_trees(PyObject *o) {
+  struct __pyx_obj_5_cdec___pyx_scope_struct_12_sample_trees *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_12_sample_trees *)o;
   PyObject* tmp;
   tmp = ((PyObject*)p->__pyx_v_self);
   p->__pyx_v_self = ((struct __pyx_obj_5_cdec_Hypergraph *)Py_None); Py_INCREF(Py_None);
@@ -24896,11 +25744,11 @@ static int __pyx_tp_clear_5_cdec___pyx_scope_struct_12___get__(PyObject *o) {
   return 0;
 }
 
-static PyMethodDef __pyx_methods_5_cdec___pyx_scope_struct_12___get__[] = {
+static PyMethodDef __pyx_methods_5_cdec___pyx_scope_struct_12_sample_trees[] = {
   {0, 0, 0, 0}
 };
 
-static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_12___get__ = {
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_12_sample_trees = {
   0, /*nb_add*/
   0, /*nb_subtract*/
   0, /*nb_multiply*/
@@ -24958,7 +25806,7 @@ static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_12___get__ = {
   #endif
 };
 
-static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_12___get__ = {
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_12_sample_trees = {
   0, /*sq_length*/
   0, /*sq_concat*/
   0, /*sq_repeat*/
@@ -24971,13 +25819,13 @@ static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_12___get__ = {
   0, /*sq_inplace_repeat*/
 };
 
-static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_12___get__ = {
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_12_sample_trees = {
   0, /*mp_length*/
   0, /*mp_subscript*/
   0, /*mp_ass_subscript*/
 };
 
-static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_12___get__ = {
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_12_sample_trees = {
   #if PY_MAJOR_VERSION < 3
   0, /*bf_getreadbuffer*/
   #endif
@@ -24998,12 +25846,12 @@ static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_12___get__ = {
   #endif
 };
 
-static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_12___get__ = {
+static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_12_sample_trees = {
   PyVarObject_HEAD_INIT(0, 0)
-  __Pyx_NAMESTR("_cdec.__pyx_scope_struct_12___get__"), /*tp_name*/
-  sizeof(struct __pyx_obj_5_cdec___pyx_scope_struct_12___get__), /*tp_basicsize*/
+  __Pyx_NAMESTR("_cdec.__pyx_scope_struct_12_sample_trees"), /*tp_name*/
+  sizeof(struct __pyx_obj_5_cdec___pyx_scope_struct_12_sample_trees), /*tp_basicsize*/
   0, /*tp_itemsize*/
-  __pyx_tp_dealloc_5_cdec___pyx_scope_struct_12___get__, /*tp_dealloc*/
+  __pyx_tp_dealloc_5_cdec___pyx_scope_struct_12_sample_trees, /*tp_dealloc*/
   0, /*tp_print*/
   0, /*tp_getattr*/
   0, /*tp_setattr*/
@@ -25013,24 +25861,24 @@ static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_12___get__ = {
   0, /*reserved*/
   #endif
   0, /*tp_repr*/
-  &__pyx_tp_as_number___pyx_scope_struct_12___get__, /*tp_as_number*/
-  &__pyx_tp_as_sequence___pyx_scope_struct_12___get__, /*tp_as_sequence*/
-  &__pyx_tp_as_mapping___pyx_scope_struct_12___get__, /*tp_as_mapping*/
+  &__pyx_tp_as_number___pyx_scope_struct_12_sample_trees, /*tp_as_number*/
+  &__pyx_tp_as_sequence___pyx_scope_struct_12_sample_trees, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping___pyx_scope_struct_12_sample_trees, /*tp_as_mapping*/
   0, /*tp_hash*/
   0, /*tp_call*/
   0, /*tp_str*/
   0, /*tp_getattro*/
   0, /*tp_setattro*/
-  &__pyx_tp_as_buffer___pyx_scope_struct_12___get__, /*tp_as_buffer*/
+  &__pyx_tp_as_buffer___pyx_scope_struct_12_sample_trees, /*tp_as_buffer*/
   Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
   0, /*tp_doc*/
-  __pyx_tp_traverse_5_cdec___pyx_scope_struct_12___get__, /*tp_traverse*/
-  __pyx_tp_clear_5_cdec___pyx_scope_struct_12___get__, /*tp_clear*/
+  __pyx_tp_traverse_5_cdec___pyx_scope_struct_12_sample_trees, /*tp_traverse*/
+  __pyx_tp_clear_5_cdec___pyx_scope_struct_12_sample_trees, /*tp_clear*/
   0, /*tp_richcompare*/
   0, /*tp_weaklistoffset*/
   0, /*tp_iter*/
   0, /*tp_iternext*/
-  __pyx_methods_5_cdec___pyx_scope_struct_12___get__, /*tp_methods*/
+  __pyx_methods_5_cdec___pyx_scope_struct_12_sample_trees, /*tp_methods*/
   0, /*tp_members*/
   0, /*tp_getset*/
   0, /*tp_base*/
@@ -25040,7 +25888,7 @@ static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_12___get__ = {
   0, /*tp_dictoffset*/
   0, /*tp_init*/
   0, /*tp_alloc*/
-  __pyx_tp_new_5_cdec___pyx_scope_struct_12___get__, /*tp_new*/
+  __pyx_tp_new_5_cdec___pyx_scope_struct_12_sample_trees, /*tp_new*/
   0, /*tp_free*/
   0, /*tp_is_gc*/
   0, /*tp_bases*/
@@ -25065,7 +25913,7 @@ static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_13___get__(PyTypeObject
 
 static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_13___get__(PyObject *o) {
   struct __pyx_obj_5_cdec___pyx_scope_struct_13___get__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_13___get__ *)o;
-  Py_XDECREF(((PyObject *)p->__pyx_v_self));
+  Py_CLEAR(p->__pyx_v_self);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -25256,7 +26104,7 @@ static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_14___get__(PyTypeObject
 
 static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_14___get__(PyObject *o) {
   struct __pyx_obj_5_cdec___pyx_scope_struct_14___get__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_14___get__ *)o;
-  Py_XDECREF(((PyObject *)p->__pyx_v_self));
+  Py_CLEAR(p->__pyx_v_self);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -25273,7 +26121,7 @@ static int __pyx_tp_clear_5_cdec___pyx_scope_struct_14___get__(PyObject *o) {
   struct __pyx_obj_5_cdec___pyx_scope_struct_14___get__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_14___get__ *)o;
   PyObject* tmp;
   tmp = ((PyObject*)p->__pyx_v_self);
-  p->__pyx_v_self = ((struct __pyx_obj_5_cdec_HypergraphEdge *)Py_None); Py_INCREF(Py_None);
+  p->__pyx_v_self = ((struct __pyx_obj_5_cdec_Hypergraph *)Py_None); Py_INCREF(Py_None);
   Py_XDECREF(tmp);
   return 0;
 }
@@ -25447,7 +26295,7 @@ static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_15___get__(PyTypeObject
 
 static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_15___get__(PyObject *o) {
   struct __pyx_obj_5_cdec___pyx_scope_struct_15___get__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_15___get__ *)o;
-  Py_XDECREF(((PyObject *)p->__pyx_v_self));
+  Py_CLEAR(p->__pyx_v_self);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -25464,7 +26312,7 @@ static int __pyx_tp_clear_5_cdec___pyx_scope_struct_15___get__(PyObject *o) {
   struct __pyx_obj_5_cdec___pyx_scope_struct_15___get__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_15___get__ *)o;
   PyObject* tmp;
   tmp = ((PyObject*)p->__pyx_v_self);
-  p->__pyx_v_self = ((struct __pyx_obj_5_cdec_HypergraphNode *)Py_None); Py_INCREF(Py_None);
+  p->__pyx_v_self = ((struct __pyx_obj_5_cdec_HypergraphEdge *)Py_None); Py_INCREF(Py_None);
   Py_XDECREF(tmp);
   return 0;
 }
@@ -25638,7 +26486,7 @@ static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_16___get__(PyTypeObject
 
 static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_16___get__(PyObject *o) {
   struct __pyx_obj_5_cdec___pyx_scope_struct_16___get__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_16___get__ *)o;
-  Py_XDECREF(((PyObject *)p->__pyx_v_self));
+  Py_CLEAR(p->__pyx_v_self);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -25818,32 +26666,223 @@ static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_16___get__ = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_17___iter__(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
-  struct __pyx_obj_5_cdec___pyx_scope_struct_17___iter__ *p;
+static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_17___get__(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+  struct __pyx_obj_5_cdec___pyx_scope_struct_17___get__ *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
-  p = ((struct __pyx_obj_5_cdec___pyx_scope_struct_17___iter__ *)o);
+  p = ((struct __pyx_obj_5_cdec___pyx_scope_struct_17___get__ *)o);
   p->__pyx_v_self = 0;
   return o;
 }
 
-static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_17___iter__(PyObject *o) {
-  struct __pyx_obj_5_cdec___pyx_scope_struct_17___iter__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_17___iter__ *)o;
-  Py_XDECREF(((PyObject *)p->__pyx_v_self));
+static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_17___get__(PyObject *o) {
+  struct __pyx_obj_5_cdec___pyx_scope_struct_17___get__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_17___get__ *)o;
+  Py_CLEAR(p->__pyx_v_self);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
-static int __pyx_tp_traverse_5_cdec___pyx_scope_struct_17___iter__(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_5_cdec___pyx_scope_struct_17___get__(PyObject *o, visitproc v, void *a) {
   int e;
-  struct __pyx_obj_5_cdec___pyx_scope_struct_17___iter__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_17___iter__ *)o;
+  struct __pyx_obj_5_cdec___pyx_scope_struct_17___get__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_17___get__ *)o;
   if (p->__pyx_v_self) {
     e = (*v)(((PyObject*)p->__pyx_v_self), a); if (e) return e;
   }
   return 0;
 }
 
-static int __pyx_tp_clear_5_cdec___pyx_scope_struct_17___iter__(PyObject *o) {
-  struct __pyx_obj_5_cdec___pyx_scope_struct_17___iter__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_17___iter__ *)o;
+static int __pyx_tp_clear_5_cdec___pyx_scope_struct_17___get__(PyObject *o) {
+  struct __pyx_obj_5_cdec___pyx_scope_struct_17___get__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_17___get__ *)o;
+  PyObject* tmp;
+  tmp = ((PyObject*)p->__pyx_v_self);
+  p->__pyx_v_self = ((struct __pyx_obj_5_cdec_HypergraphNode *)Py_None); Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  return 0;
+}
+
+static PyMethodDef __pyx_methods_5_cdec___pyx_scope_struct_17___get__[] = {
+  {0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_17___get__ = {
+  0, /*nb_add*/
+  0, /*nb_subtract*/
+  0, /*nb_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_divide*/
+  #endif
+  0, /*nb_remainder*/
+  0, /*nb_divmod*/
+  0, /*nb_power*/
+  0, /*nb_negative*/
+  0, /*nb_positive*/
+  0, /*nb_absolute*/
+  0, /*nb_nonzero*/
+  0, /*nb_invert*/
+  0, /*nb_lshift*/
+  0, /*nb_rshift*/
+  0, /*nb_and*/
+  0, /*nb_xor*/
+  0, /*nb_or*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_coerce*/
+  #endif
+  0, /*nb_int*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_long*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*nb_float*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_oct*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_hex*/
+  #endif
+  0, /*nb_inplace_add*/
+  0, /*nb_inplace_subtract*/
+  0, /*nb_inplace_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_inplace_divide*/
+  #endif
+  0, /*nb_inplace_remainder*/
+  0, /*nb_inplace_power*/
+  0, /*nb_inplace_lshift*/
+  0, /*nb_inplace_rshift*/
+  0, /*nb_inplace_and*/
+  0, /*nb_inplace_xor*/
+  0, /*nb_inplace_or*/
+  0, /*nb_floor_divide*/
+  0, /*nb_true_divide*/
+  0, /*nb_inplace_floor_divide*/
+  0, /*nb_inplace_true_divide*/
+  #if PY_VERSION_HEX >= 0x02050000
+  0, /*nb_index*/
+  #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_17___get__ = {
+  0, /*sq_length*/
+  0, /*sq_concat*/
+  0, /*sq_repeat*/
+  0, /*sq_item*/
+  0, /*sq_slice*/
+  0, /*sq_ass_item*/
+  0, /*sq_ass_slice*/
+  0, /*sq_contains*/
+  0, /*sq_inplace_concat*/
+  0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_17___get__ = {
+  0, /*mp_length*/
+  0, /*mp_subscript*/
+  0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_17___get__ = {
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getreadbuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getwritebuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getsegcount*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getcharbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_getbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_releasebuffer*/
+  #endif
+};
+
+static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_17___get__ = {
+  PyVarObject_HEAD_INIT(0, 0)
+  __Pyx_NAMESTR("_cdec.__pyx_scope_struct_17___get__"), /*tp_name*/
+  sizeof(struct __pyx_obj_5_cdec___pyx_scope_struct_17___get__), /*tp_basicsize*/
+  0, /*tp_itemsize*/
+  __pyx_tp_dealloc_5_cdec___pyx_scope_struct_17___get__, /*tp_dealloc*/
+  0, /*tp_print*/
+  0, /*tp_getattr*/
+  0, /*tp_setattr*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*tp_compare*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*tp_repr*/
+  &__pyx_tp_as_number___pyx_scope_struct_17___get__, /*tp_as_number*/
+  &__pyx_tp_as_sequence___pyx_scope_struct_17___get__, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping___pyx_scope_struct_17___get__, /*tp_as_mapping*/
+  0, /*tp_hash*/
+  0, /*tp_call*/
+  0, /*tp_str*/
+  0, /*tp_getattro*/
+  0, /*tp_setattro*/
+  &__pyx_tp_as_buffer___pyx_scope_struct_17___get__, /*tp_as_buffer*/
+  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+  0, /*tp_doc*/
+  __pyx_tp_traverse_5_cdec___pyx_scope_struct_17___get__, /*tp_traverse*/
+  __pyx_tp_clear_5_cdec___pyx_scope_struct_17___get__, /*tp_clear*/
+  0, /*tp_richcompare*/
+  0, /*tp_weaklistoffset*/
+  0, /*tp_iter*/
+  0, /*tp_iternext*/
+  __pyx_methods_5_cdec___pyx_scope_struct_17___get__, /*tp_methods*/
+  0, /*tp_members*/
+  0, /*tp_getset*/
+  0, /*tp_base*/
+  0, /*tp_dict*/
+  0, /*tp_descr_get*/
+  0, /*tp_descr_set*/
+  0, /*tp_dictoffset*/
+  0, /*tp_init*/
+  0, /*tp_alloc*/
+  __pyx_tp_new_5_cdec___pyx_scope_struct_17___get__, /*tp_new*/
+  0, /*tp_free*/
+  0, /*tp_is_gc*/
+  0, /*tp_bases*/
+  0, /*tp_mro*/
+  0, /*tp_cache*/
+  0, /*tp_subclasses*/
+  0, /*tp_weaklist*/
+  0, /*tp_del*/
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*tp_version_tag*/
+  #endif
+};
+
+static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_18___iter__(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+  struct __pyx_obj_5_cdec___pyx_scope_struct_18___iter__ *p;
+  PyObject *o = (*t->tp_alloc)(t, 0);
+  if (!o) return 0;
+  p = ((struct __pyx_obj_5_cdec___pyx_scope_struct_18___iter__ *)o);
+  p->__pyx_v_self = 0;
+  return o;
+}
+
+static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_18___iter__(PyObject *o) {
+  struct __pyx_obj_5_cdec___pyx_scope_struct_18___iter__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_18___iter__ *)o;
+  Py_CLEAR(p->__pyx_v_self);
+  (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_5_cdec___pyx_scope_struct_18___iter__(PyObject *o, visitproc v, void *a) {
+  int e;
+  struct __pyx_obj_5_cdec___pyx_scope_struct_18___iter__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_18___iter__ *)o;
+  if (p->__pyx_v_self) {
+    e = (*v)(((PyObject*)p->__pyx_v_self), a); if (e) return e;
+  }
+  return 0;
+}
+
+static int __pyx_tp_clear_5_cdec___pyx_scope_struct_18___iter__(PyObject *o) {
+  struct __pyx_obj_5_cdec___pyx_scope_struct_18___iter__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_18___iter__ *)o;
   PyObject* tmp;
   tmp = ((PyObject*)p->__pyx_v_self);
   p->__pyx_v_self = ((struct __pyx_obj_5_cdec_Lattice *)Py_None); Py_INCREF(Py_None);
@@ -25851,11 +26890,11 @@ static int __pyx_tp_clear_5_cdec___pyx_scope_struct_17___iter__(PyObject *o) {
   return 0;
 }
 
-static PyMethodDef __pyx_methods_5_cdec___pyx_scope_struct_17___iter__[] = {
+static PyMethodDef __pyx_methods_5_cdec___pyx_scope_struct_18___iter__[] = {
   {0, 0, 0, 0}
 };
 
-static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_17___iter__ = {
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_18___iter__ = {
   0, /*nb_add*/
   0, /*nb_subtract*/
   0, /*nb_multiply*/
@@ -25913,7 +26952,7 @@ static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_17___iter__ = {
   #endif
 };
 
-static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_17___iter__ = {
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_18___iter__ = {
   0, /*sq_length*/
   0, /*sq_concat*/
   0, /*sq_repeat*/
@@ -25926,13 +26965,13 @@ static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_17___iter__ = {
   0, /*sq_inplace_repeat*/
 };
 
-static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_17___iter__ = {
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_18___iter__ = {
   0, /*mp_length*/
   0, /*mp_subscript*/
   0, /*mp_ass_subscript*/
 };
 
-static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_17___iter__ = {
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_18___iter__ = {
   #if PY_MAJOR_VERSION < 3
   0, /*bf_getreadbuffer*/
   #endif
@@ -25953,12 +26992,12 @@ static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_17___iter__ = {
   #endif
 };
 
-static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_17___iter__ = {
+static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_18___iter__ = {
   PyVarObject_HEAD_INIT(0, 0)
-  __Pyx_NAMESTR("_cdec.__pyx_scope_struct_17___iter__"), /*tp_name*/
-  sizeof(struct __pyx_obj_5_cdec___pyx_scope_struct_17___iter__), /*tp_basicsize*/
+  __Pyx_NAMESTR("_cdec.__pyx_scope_struct_18___iter__"), /*tp_name*/
+  sizeof(struct __pyx_obj_5_cdec___pyx_scope_struct_18___iter__), /*tp_basicsize*/
   0, /*tp_itemsize*/
-  __pyx_tp_dealloc_5_cdec___pyx_scope_struct_17___iter__, /*tp_dealloc*/
+  __pyx_tp_dealloc_5_cdec___pyx_scope_struct_18___iter__, /*tp_dealloc*/
   0, /*tp_print*/
   0, /*tp_getattr*/
   0, /*tp_setattr*/
@@ -25968,24 +27007,24 @@ static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_17___iter__ = {
   0, /*reserved*/
   #endif
   0, /*tp_repr*/
-  &__pyx_tp_as_number___pyx_scope_struct_17___iter__, /*tp_as_number*/
-  &__pyx_tp_as_sequence___pyx_scope_struct_17___iter__, /*tp_as_sequence*/
-  &__pyx_tp_as_mapping___pyx_scope_struct_17___iter__, /*tp_as_mapping*/
+  &__pyx_tp_as_number___pyx_scope_struct_18___iter__, /*tp_as_number*/
+  &__pyx_tp_as_sequence___pyx_scope_struct_18___iter__, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping___pyx_scope_struct_18___iter__, /*tp_as_mapping*/
   0, /*tp_hash*/
   0, /*tp_call*/
   0, /*tp_str*/
   0, /*tp_getattro*/
   0, /*tp_setattro*/
-  &__pyx_tp_as_buffer___pyx_scope_struct_17___iter__, /*tp_as_buffer*/
+  &__pyx_tp_as_buffer___pyx_scope_struct_18___iter__, /*tp_as_buffer*/
   Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
   0, /*tp_doc*/
-  __pyx_tp_traverse_5_cdec___pyx_scope_struct_17___iter__, /*tp_traverse*/
-  __pyx_tp_clear_5_cdec___pyx_scope_struct_17___iter__, /*tp_clear*/
+  __pyx_tp_traverse_5_cdec___pyx_scope_struct_18___iter__, /*tp_traverse*/
+  __pyx_tp_clear_5_cdec___pyx_scope_struct_18___iter__, /*tp_clear*/
   0, /*tp_richcompare*/
   0, /*tp_weaklistoffset*/
   0, /*tp_iter*/
   0, /*tp_iternext*/
-  __pyx_methods_5_cdec___pyx_scope_struct_17___iter__, /*tp_methods*/
+  __pyx_methods_5_cdec___pyx_scope_struct_18___iter__, /*tp_methods*/
   0, /*tp_members*/
   0, /*tp_getset*/
   0, /*tp_base*/
@@ -25995,7 +27034,7 @@ static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_17___iter__ = {
   0, /*tp_dictoffset*/
   0, /*tp_init*/
   0, /*tp_alloc*/
-  __pyx_tp_new_5_cdec___pyx_scope_struct_17___iter__, /*tp_new*/
+  __pyx_tp_new_5_cdec___pyx_scope_struct_18___iter__, /*tp_new*/
   0, /*tp_free*/
   0, /*tp_is_gc*/
   0, /*tp_bases*/
@@ -26009,32 +27048,32 @@ static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_17___iter__ = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_18_todot(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
-  struct __pyx_obj_5_cdec___pyx_scope_struct_18_todot *p;
+static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_19_todot(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+  struct __pyx_obj_5_cdec___pyx_scope_struct_19_todot *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
-  p = ((struct __pyx_obj_5_cdec___pyx_scope_struct_18_todot *)o);
+  p = ((struct __pyx_obj_5_cdec___pyx_scope_struct_19_todot *)o);
   p->__pyx_v_self = 0;
   return o;
 }
 
-static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_18_todot(PyObject *o) {
-  struct __pyx_obj_5_cdec___pyx_scope_struct_18_todot *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_18_todot *)o;
-  Py_XDECREF(((PyObject *)p->__pyx_v_self));
+static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_19_todot(PyObject *o) {
+  struct __pyx_obj_5_cdec___pyx_scope_struct_19_todot *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_19_todot *)o;
+  Py_CLEAR(p->__pyx_v_self);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
-static int __pyx_tp_traverse_5_cdec___pyx_scope_struct_18_todot(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_5_cdec___pyx_scope_struct_19_todot(PyObject *o, visitproc v, void *a) {
   int e;
-  struct __pyx_obj_5_cdec___pyx_scope_struct_18_todot *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_18_todot *)o;
+  struct __pyx_obj_5_cdec___pyx_scope_struct_19_todot *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_19_todot *)o;
   if (p->__pyx_v_self) {
     e = (*v)(((PyObject*)p->__pyx_v_self), a); if (e) return e;
   }
   return 0;
 }
 
-static int __pyx_tp_clear_5_cdec___pyx_scope_struct_18_todot(PyObject *o) {
-  struct __pyx_obj_5_cdec___pyx_scope_struct_18_todot *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_18_todot *)o;
+static int __pyx_tp_clear_5_cdec___pyx_scope_struct_19_todot(PyObject *o) {
+  struct __pyx_obj_5_cdec___pyx_scope_struct_19_todot *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_19_todot *)o;
   PyObject* tmp;
   tmp = ((PyObject*)p->__pyx_v_self);
   p->__pyx_v_self = ((struct __pyx_obj_5_cdec_Lattice *)Py_None); Py_INCREF(Py_None);
@@ -26042,11 +27081,11 @@ static int __pyx_tp_clear_5_cdec___pyx_scope_struct_18_todot(PyObject *o) {
   return 0;
 }
 
-static PyMethodDef __pyx_methods_5_cdec___pyx_scope_struct_18_todot[] = {
+static PyMethodDef __pyx_methods_5_cdec___pyx_scope_struct_19_todot[] = {
   {0, 0, 0, 0}
 };
 
-static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_18_todot = {
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_19_todot = {
   0, /*nb_add*/
   0, /*nb_subtract*/
   0, /*nb_multiply*/
@@ -26104,7 +27143,7 @@ static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_18_todot = {
   #endif
 };
 
-static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_18_todot = {
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_19_todot = {
   0, /*sq_length*/
   0, /*sq_concat*/
   0, /*sq_repeat*/
@@ -26117,13 +27156,13 @@ static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_18_todot = {
   0, /*sq_inplace_repeat*/
 };
 
-static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_18_todot = {
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_19_todot = {
   0, /*mp_length*/
   0, /*mp_subscript*/
   0, /*mp_ass_subscript*/
 };
 
-static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_18_todot = {
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_19_todot = {
   #if PY_MAJOR_VERSION < 3
   0, /*bf_getreadbuffer*/
   #endif
@@ -26144,12 +27183,12 @@ static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_18_todot = {
   #endif
 };
 
-static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_18_todot = {
+static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_19_todot = {
   PyVarObject_HEAD_INIT(0, 0)
-  __Pyx_NAMESTR("_cdec.__pyx_scope_struct_18_todot"), /*tp_name*/
-  sizeof(struct __pyx_obj_5_cdec___pyx_scope_struct_18_todot), /*tp_basicsize*/
+  __Pyx_NAMESTR("_cdec.__pyx_scope_struct_19_todot"), /*tp_name*/
+  sizeof(struct __pyx_obj_5_cdec___pyx_scope_struct_19_todot), /*tp_basicsize*/
   0, /*tp_itemsize*/
-  __pyx_tp_dealloc_5_cdec___pyx_scope_struct_18_todot, /*tp_dealloc*/
+  __pyx_tp_dealloc_5_cdec___pyx_scope_struct_19_todot, /*tp_dealloc*/
   0, /*tp_print*/
   0, /*tp_getattr*/
   0, /*tp_setattr*/
@@ -26159,24 +27198,24 @@ static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_18_todot = {
   0, /*reserved*/
   #endif
   0, /*tp_repr*/
-  &__pyx_tp_as_number___pyx_scope_struct_18_todot, /*tp_as_number*/
-  &__pyx_tp_as_sequence___pyx_scope_struct_18_todot, /*tp_as_sequence*/
-  &__pyx_tp_as_mapping___pyx_scope_struct_18_todot, /*tp_as_mapping*/
+  &__pyx_tp_as_number___pyx_scope_struct_19_todot, /*tp_as_number*/
+  &__pyx_tp_as_sequence___pyx_scope_struct_19_todot, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping___pyx_scope_struct_19_todot, /*tp_as_mapping*/
   0, /*tp_hash*/
   0, /*tp_call*/
   0, /*tp_str*/
   0, /*tp_getattro*/
   0, /*tp_setattro*/
-  &__pyx_tp_as_buffer___pyx_scope_struct_18_todot, /*tp_as_buffer*/
+  &__pyx_tp_as_buffer___pyx_scope_struct_19_todot, /*tp_as_buffer*/
   Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
   0, /*tp_doc*/
-  __pyx_tp_traverse_5_cdec___pyx_scope_struct_18_todot, /*tp_traverse*/
-  __pyx_tp_clear_5_cdec___pyx_scope_struct_18_todot, /*tp_clear*/
+  __pyx_tp_traverse_5_cdec___pyx_scope_struct_19_todot, /*tp_traverse*/
+  __pyx_tp_clear_5_cdec___pyx_scope_struct_19_todot, /*tp_clear*/
   0, /*tp_richcompare*/
   0, /*tp_weaklistoffset*/
   0, /*tp_iter*/
   0, /*tp_iternext*/
-  __pyx_methods_5_cdec___pyx_scope_struct_18_todot, /*tp_methods*/
+  __pyx_methods_5_cdec___pyx_scope_struct_19_todot, /*tp_methods*/
   0, /*tp_members*/
   0, /*tp_getset*/
   0, /*tp_base*/
@@ -26186,7 +27225,7 @@ static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_18_todot = {
   0, /*tp_dictoffset*/
   0, /*tp_init*/
   0, /*tp_alloc*/
-  __pyx_tp_new_5_cdec___pyx_scope_struct_18_todot, /*tp_new*/
+  __pyx_tp_new_5_cdec___pyx_scope_struct_19_todot, /*tp_new*/
   0, /*tp_free*/
   0, /*tp_is_gc*/
   0, /*tp_bases*/
@@ -26200,11 +27239,11 @@ static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_18_todot = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_19_lines(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
-  struct __pyx_obj_5_cdec___pyx_scope_struct_19_lines *p;
+static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_20_lines(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+  struct __pyx_obj_5_cdec___pyx_scope_struct_20_lines *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
-  p = ((struct __pyx_obj_5_cdec___pyx_scope_struct_19_lines *)o);
+  p = ((struct __pyx_obj_5_cdec___pyx_scope_struct_20_lines *)o);
   p->__pyx_outer_scope = 0;
   p->__pyx_v_delta = 0;
   p->__pyx_v_i = 0;
@@ -26215,21 +27254,21 @@ static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_19_lines(PyTypeObject *t
   return o;
 }
 
-static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_19_lines(PyObject *o) {
-  struct __pyx_obj_5_cdec___pyx_scope_struct_19_lines *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_19_lines *)o;
-  Py_XDECREF(((PyObject *)p->__pyx_outer_scope));
-  Py_XDECREF(p->__pyx_v_delta);
-  Py_XDECREF(p->__pyx_v_i);
-  Py_XDECREF(p->__pyx_v_label);
-  Py_XDECREF(p->__pyx_v_weight);
-  Py_XDECREF(p->__pyx_t_1);
-  Py_XDECREF(p->__pyx_t_3);
+static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_20_lines(PyObject *o) {
+  struct __pyx_obj_5_cdec___pyx_scope_struct_20_lines *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_20_lines *)o;
+  Py_CLEAR(p->__pyx_outer_scope);
+  Py_CLEAR(p->__pyx_v_delta);
+  Py_CLEAR(p->__pyx_v_i);
+  Py_CLEAR(p->__pyx_v_label);
+  Py_CLEAR(p->__pyx_v_weight);
+  Py_CLEAR(p->__pyx_t_1);
+  Py_CLEAR(p->__pyx_t_3);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
-static int __pyx_tp_traverse_5_cdec___pyx_scope_struct_19_lines(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_5_cdec___pyx_scope_struct_20_lines(PyObject *o, visitproc v, void *a) {
   int e;
-  struct __pyx_obj_5_cdec___pyx_scope_struct_19_lines *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_19_lines *)o;
+  struct __pyx_obj_5_cdec___pyx_scope_struct_20_lines *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_20_lines *)o;
   if (p->__pyx_outer_scope) {
     e = (*v)(((PyObject*)p->__pyx_outer_scope), a); if (e) return e;
   }
@@ -26254,11 +27293,11 @@ static int __pyx_tp_traverse_5_cdec___pyx_scope_struct_19_lines(PyObject *o, vis
   return 0;
 }
 
-static int __pyx_tp_clear_5_cdec___pyx_scope_struct_19_lines(PyObject *o) {
-  struct __pyx_obj_5_cdec___pyx_scope_struct_19_lines *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_19_lines *)o;
+static int __pyx_tp_clear_5_cdec___pyx_scope_struct_20_lines(PyObject *o) {
+  struct __pyx_obj_5_cdec___pyx_scope_struct_20_lines *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_20_lines *)o;
   PyObject* tmp;
   tmp = ((PyObject*)p->__pyx_outer_scope);
-  p->__pyx_outer_scope = ((struct __pyx_obj_5_cdec___pyx_scope_struct_18_todot *)Py_None); Py_INCREF(Py_None);
+  p->__pyx_outer_scope = ((struct __pyx_obj_5_cdec___pyx_scope_struct_19_todot *)Py_None); Py_INCREF(Py_None);
   Py_XDECREF(tmp);
   tmp = ((PyObject*)p->__pyx_v_delta);
   p->__pyx_v_delta = Py_None; Py_INCREF(Py_None);
@@ -26281,11 +27320,11 @@ static int __pyx_tp_clear_5_cdec___pyx_scope_struct_19_lines(PyObject *o) {
   return 0;
 }
 
-static PyMethodDef __pyx_methods_5_cdec___pyx_scope_struct_19_lines[] = {
+static PyMethodDef __pyx_methods_5_cdec___pyx_scope_struct_20_lines[] = {
   {0, 0, 0, 0}
 };
 
-static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_19_lines = {
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_20_lines = {
   0, /*nb_add*/
   0, /*nb_subtract*/
   0, /*nb_multiply*/
@@ -26343,7 +27382,7 @@ static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_19_lines = {
   #endif
 };
 
-static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_19_lines = {
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_20_lines = {
   0, /*sq_length*/
   0, /*sq_concat*/
   0, /*sq_repeat*/
@@ -26356,13 +27395,13 @@ static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_19_lines = {
   0, /*sq_inplace_repeat*/
 };
 
-static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_19_lines = {
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_20_lines = {
   0, /*mp_length*/
   0, /*mp_subscript*/
   0, /*mp_ass_subscript*/
 };
 
-static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_19_lines = {
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_20_lines = {
   #if PY_MAJOR_VERSION < 3
   0, /*bf_getreadbuffer*/
   #endif
@@ -26383,12 +27422,12 @@ static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_19_lines = {
   #endif
 };
 
-static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_19_lines = {
+static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_20_lines = {
   PyVarObject_HEAD_INIT(0, 0)
-  __Pyx_NAMESTR("_cdec.__pyx_scope_struct_19_lines"), /*tp_name*/
-  sizeof(struct __pyx_obj_5_cdec___pyx_scope_struct_19_lines), /*tp_basicsize*/
+  __Pyx_NAMESTR("_cdec.__pyx_scope_struct_20_lines"), /*tp_name*/
+  sizeof(struct __pyx_obj_5_cdec___pyx_scope_struct_20_lines), /*tp_basicsize*/
   0, /*tp_itemsize*/
-  __pyx_tp_dealloc_5_cdec___pyx_scope_struct_19_lines, /*tp_dealloc*/
+  __pyx_tp_dealloc_5_cdec___pyx_scope_struct_20_lines, /*tp_dealloc*/
   0, /*tp_print*/
   0, /*tp_getattr*/
   0, /*tp_setattr*/
@@ -26398,24 +27437,24 @@ static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_19_lines = {
   0, /*reserved*/
   #endif
   0, /*tp_repr*/
-  &__pyx_tp_as_number___pyx_scope_struct_19_lines, /*tp_as_number*/
-  &__pyx_tp_as_sequence___pyx_scope_struct_19_lines, /*tp_as_sequence*/
-  &__pyx_tp_as_mapping___pyx_scope_struct_19_lines, /*tp_as_mapping*/
+  &__pyx_tp_as_number___pyx_scope_struct_20_lines, /*tp_as_number*/
+  &__pyx_tp_as_sequence___pyx_scope_struct_20_lines, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping___pyx_scope_struct_20_lines, /*tp_as_mapping*/
   0, /*tp_hash*/
   0, /*tp_call*/
   0, /*tp_str*/
   0, /*tp_getattro*/
   0, /*tp_setattro*/
-  &__pyx_tp_as_buffer___pyx_scope_struct_19_lines, /*tp_as_buffer*/
+  &__pyx_tp_as_buffer___pyx_scope_struct_20_lines, /*tp_as_buffer*/
   Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
   0, /*tp_doc*/
-  __pyx_tp_traverse_5_cdec___pyx_scope_struct_19_lines, /*tp_traverse*/
-  __pyx_tp_clear_5_cdec___pyx_scope_struct_19_lines, /*tp_clear*/
+  __pyx_tp_traverse_5_cdec___pyx_scope_struct_20_lines, /*tp_traverse*/
+  __pyx_tp_clear_5_cdec___pyx_scope_struct_20_lines, /*tp_clear*/
   0, /*tp_richcompare*/
   0, /*tp_weaklistoffset*/
   0, /*tp_iter*/
   0, /*tp_iternext*/
-  __pyx_methods_5_cdec___pyx_scope_struct_19_lines, /*tp_methods*/
+  __pyx_methods_5_cdec___pyx_scope_struct_20_lines, /*tp_methods*/
   0, /*tp_members*/
   0, /*tp_getset*/
   0, /*tp_base*/
@@ -26425,7 +27464,7 @@ static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_19_lines = {
   0, /*tp_dictoffset*/
   0, /*tp_init*/
   0, /*tp_alloc*/
-  __pyx_tp_new_5_cdec___pyx_scope_struct_19_lines, /*tp_new*/
+  __pyx_tp_new_5_cdec___pyx_scope_struct_20_lines, /*tp_new*/
   0, /*tp_free*/
   0, /*tp_is_gc*/
   0, /*tp_bases*/
@@ -26439,28 +27478,28 @@ static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_19_lines = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_20___iter__(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
-  struct __pyx_obj_5_cdec___pyx_scope_struct_20___iter__ *p;
+static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_21___iter__(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+  struct __pyx_obj_5_cdec___pyx_scope_struct_21___iter__ *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
-  p = ((struct __pyx_obj_5_cdec___pyx_scope_struct_20___iter__ *)o);
+  p = ((struct __pyx_obj_5_cdec___pyx_scope_struct_21___iter__ *)o);
   p->__pyx_v_i = 0;
   p->__pyx_v_self = 0;
   p->__pyx_t_1 = 0;
   return o;
 }
 
-static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_20___iter__(PyObject *o) {
-  struct __pyx_obj_5_cdec___pyx_scope_struct_20___iter__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_20___iter__ *)o;
-  Py_XDECREF(p->__pyx_v_i);
-  Py_XDECREF(((PyObject *)p->__pyx_v_self));
-  Py_XDECREF(p->__pyx_t_1);
+static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_21___iter__(PyObject *o) {
+  struct __pyx_obj_5_cdec___pyx_scope_struct_21___iter__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_21___iter__ *)o;
+  Py_CLEAR(p->__pyx_v_i);
+  Py_CLEAR(p->__pyx_v_self);
+  Py_CLEAR(p->__pyx_t_1);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
-static int __pyx_tp_traverse_5_cdec___pyx_scope_struct_20___iter__(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_5_cdec___pyx_scope_struct_21___iter__(PyObject *o, visitproc v, void *a) {
   int e;
-  struct __pyx_obj_5_cdec___pyx_scope_struct_20___iter__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_20___iter__ *)o;
+  struct __pyx_obj_5_cdec___pyx_scope_struct_21___iter__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_21___iter__ *)o;
   if (p->__pyx_v_i) {
     e = (*v)(p->__pyx_v_i, a); if (e) return e;
   }
@@ -26473,8 +27512,8 @@ static int __pyx_tp_traverse_5_cdec___pyx_scope_struct_20___iter__(PyObject *o,
   return 0;
 }
 
-static int __pyx_tp_clear_5_cdec___pyx_scope_struct_20___iter__(PyObject *o) {
-  struct __pyx_obj_5_cdec___pyx_scope_struct_20___iter__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_20___iter__ *)o;
+static int __pyx_tp_clear_5_cdec___pyx_scope_struct_21___iter__(PyObject *o) {
+  struct __pyx_obj_5_cdec___pyx_scope_struct_21___iter__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_21___iter__ *)o;
   PyObject* tmp;
   tmp = ((PyObject*)p->__pyx_v_i);
   p->__pyx_v_i = Py_None; Py_INCREF(Py_None);
@@ -26488,11 +27527,11 @@ static int __pyx_tp_clear_5_cdec___pyx_scope_struct_20___iter__(PyObject *o) {
   return 0;
 }
 
-static PyMethodDef __pyx_methods_5_cdec___pyx_scope_struct_20___iter__[] = {
+static PyMethodDef __pyx_methods_5_cdec___pyx_scope_struct_21___iter__[] = {
   {0, 0, 0, 0}
 };
 
-static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_20___iter__ = {
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_21___iter__ = {
   0, /*nb_add*/
   0, /*nb_subtract*/
   0, /*nb_multiply*/
@@ -26550,7 +27589,7 @@ static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_20___iter__ = {
   #endif
 };
 
-static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_20___iter__ = {
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_21___iter__ = {
   0, /*sq_length*/
   0, /*sq_concat*/
   0, /*sq_repeat*/
@@ -26563,13 +27602,13 @@ static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_20___iter__ = {
   0, /*sq_inplace_repeat*/
 };
 
-static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_20___iter__ = {
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_21___iter__ = {
   0, /*mp_length*/
   0, /*mp_subscript*/
   0, /*mp_ass_subscript*/
 };
 
-static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_20___iter__ = {
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_21___iter__ = {
   #if PY_MAJOR_VERSION < 3
   0, /*bf_getreadbuffer*/
   #endif
@@ -26590,12 +27629,12 @@ static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_20___iter__ = {
   #endif
 };
 
-static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_20___iter__ = {
+static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_21___iter__ = {
   PyVarObject_HEAD_INIT(0, 0)
-  __Pyx_NAMESTR("_cdec.__pyx_scope_struct_20___iter__"), /*tp_name*/
-  sizeof(struct __pyx_obj_5_cdec___pyx_scope_struct_20___iter__), /*tp_basicsize*/
+  __Pyx_NAMESTR("_cdec.__pyx_scope_struct_21___iter__"), /*tp_name*/
+  sizeof(struct __pyx_obj_5_cdec___pyx_scope_struct_21___iter__), /*tp_basicsize*/
   0, /*tp_itemsize*/
-  __pyx_tp_dealloc_5_cdec___pyx_scope_struct_20___iter__, /*tp_dealloc*/
+  __pyx_tp_dealloc_5_cdec___pyx_scope_struct_21___iter__, /*tp_dealloc*/
   0, /*tp_print*/
   0, /*tp_getattr*/
   0, /*tp_setattr*/
@@ -26605,24 +27644,24 @@ static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_20___iter__ = {
   0, /*reserved*/
   #endif
   0, /*tp_repr*/
-  &__pyx_tp_as_number___pyx_scope_struct_20___iter__, /*tp_as_number*/
-  &__pyx_tp_as_sequence___pyx_scope_struct_20___iter__, /*tp_as_sequence*/
-  &__pyx_tp_as_mapping___pyx_scope_struct_20___iter__, /*tp_as_mapping*/
+  &__pyx_tp_as_number___pyx_scope_struct_21___iter__, /*tp_as_number*/
+  &__pyx_tp_as_sequence___pyx_scope_struct_21___iter__, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping___pyx_scope_struct_21___iter__, /*tp_as_mapping*/
   0, /*tp_hash*/
   0, /*tp_call*/
   0, /*tp_str*/
   0, /*tp_getattro*/
   0, /*tp_setattro*/
-  &__pyx_tp_as_buffer___pyx_scope_struct_20___iter__, /*tp_as_buffer*/
+  &__pyx_tp_as_buffer___pyx_scope_struct_21___iter__, /*tp_as_buffer*/
   Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
   0, /*tp_doc*/
-  __pyx_tp_traverse_5_cdec___pyx_scope_struct_20___iter__, /*tp_traverse*/
-  __pyx_tp_clear_5_cdec___pyx_scope_struct_20___iter__, /*tp_clear*/
+  __pyx_tp_traverse_5_cdec___pyx_scope_struct_21___iter__, /*tp_traverse*/
+  __pyx_tp_clear_5_cdec___pyx_scope_struct_21___iter__, /*tp_clear*/
   0, /*tp_richcompare*/
   0, /*tp_weaklistoffset*/
   0, /*tp_iter*/
   0, /*tp_iternext*/
-  __pyx_methods_5_cdec___pyx_scope_struct_20___iter__, /*tp_methods*/
+  __pyx_methods_5_cdec___pyx_scope_struct_21___iter__, /*tp_methods*/
   0, /*tp_members*/
   0, /*tp_getset*/
   0, /*tp_base*/
@@ -26632,7 +27671,7 @@ static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_20___iter__ = {
   0, /*tp_dictoffset*/
   0, /*tp_init*/
   0, /*tp_alloc*/
-  __pyx_tp_new_5_cdec___pyx_scope_struct_20___iter__, /*tp_new*/
+  __pyx_tp_new_5_cdec___pyx_scope_struct_21___iter__, /*tp_new*/
   0, /*tp_free*/
   0, /*tp_is_gc*/
   0, /*tp_bases*/
@@ -26646,32 +27685,32 @@ static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_20___iter__ = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_21___iter__(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
-  struct __pyx_obj_5_cdec___pyx_scope_struct_21___iter__ *p;
+static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_22___iter__(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+  struct __pyx_obj_5_cdec___pyx_scope_struct_22___iter__ *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
-  p = ((struct __pyx_obj_5_cdec___pyx_scope_struct_21___iter__ *)o);
+  p = ((struct __pyx_obj_5_cdec___pyx_scope_struct_22___iter__ *)o);
   p->__pyx_v_self = 0;
   return o;
 }
 
-static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_21___iter__(PyObject *o) {
-  struct __pyx_obj_5_cdec___pyx_scope_struct_21___iter__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_21___iter__ *)o;
-  Py_XDECREF(((PyObject *)p->__pyx_v_self));
+static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_22___iter__(PyObject *o) {
+  struct __pyx_obj_5_cdec___pyx_scope_struct_22___iter__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_22___iter__ *)o;
+  Py_CLEAR(p->__pyx_v_self);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
-static int __pyx_tp_traverse_5_cdec___pyx_scope_struct_21___iter__(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_5_cdec___pyx_scope_struct_22___iter__(PyObject *o, visitproc v, void *a) {
   int e;
-  struct __pyx_obj_5_cdec___pyx_scope_struct_21___iter__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_21___iter__ *)o;
+  struct __pyx_obj_5_cdec___pyx_scope_struct_22___iter__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_22___iter__ *)o;
   if (p->__pyx_v_self) {
     e = (*v)(((PyObject*)p->__pyx_v_self), a); if (e) return e;
   }
   return 0;
 }
 
-static int __pyx_tp_clear_5_cdec___pyx_scope_struct_21___iter__(PyObject *o) {
-  struct __pyx_obj_5_cdec___pyx_scope_struct_21___iter__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_21___iter__ *)o;
+static int __pyx_tp_clear_5_cdec___pyx_scope_struct_22___iter__(PyObject *o) {
+  struct __pyx_obj_5_cdec___pyx_scope_struct_22___iter__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_22___iter__ *)o;
   PyObject* tmp;
   tmp = ((PyObject*)p->__pyx_v_self);
   p->__pyx_v_self = ((struct __pyx_obj_5_cdec_CandidateSet *)Py_None); Py_INCREF(Py_None);
@@ -26679,11 +27718,11 @@ static int __pyx_tp_clear_5_cdec___pyx_scope_struct_21___iter__(PyObject *o) {
   return 0;
 }
 
-static PyMethodDef __pyx_methods_5_cdec___pyx_scope_struct_21___iter__[] = {
+static PyMethodDef __pyx_methods_5_cdec___pyx_scope_struct_22___iter__[] = {
   {0, 0, 0, 0}
 };
 
-static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_21___iter__ = {
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_22___iter__ = {
   0, /*nb_add*/
   0, /*nb_subtract*/
   0, /*nb_multiply*/
@@ -26741,7 +27780,7 @@ static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_21___iter__ = {
   #endif
 };
 
-static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_21___iter__ = {
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_22___iter__ = {
   0, /*sq_length*/
   0, /*sq_concat*/
   0, /*sq_repeat*/
@@ -26754,13 +27793,13 @@ static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_21___iter__ = {
   0, /*sq_inplace_repeat*/
 };
 
-static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_21___iter__ = {
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_22___iter__ = {
   0, /*mp_length*/
   0, /*mp_subscript*/
   0, /*mp_ass_subscript*/
 };
 
-static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_21___iter__ = {
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_22___iter__ = {
   #if PY_MAJOR_VERSION < 3
   0, /*bf_getreadbuffer*/
   #endif
@@ -26781,12 +27820,12 @@ static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_21___iter__ = {
   #endif
 };
 
-static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_21___iter__ = {
+static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_22___iter__ = {
   PyVarObject_HEAD_INIT(0, 0)
-  __Pyx_NAMESTR("_cdec.__pyx_scope_struct_21___iter__"), /*tp_name*/
-  sizeof(struct __pyx_obj_5_cdec___pyx_scope_struct_21___iter__), /*tp_basicsize*/
+  __Pyx_NAMESTR("_cdec.__pyx_scope_struct_22___iter__"), /*tp_name*/
+  sizeof(struct __pyx_obj_5_cdec___pyx_scope_struct_22___iter__), /*tp_basicsize*/
   0, /*tp_itemsize*/
-  __pyx_tp_dealloc_5_cdec___pyx_scope_struct_21___iter__, /*tp_dealloc*/
+  __pyx_tp_dealloc_5_cdec___pyx_scope_struct_22___iter__, /*tp_dealloc*/
   0, /*tp_print*/
   0, /*tp_getattr*/
   0, /*tp_setattr*/
@@ -26796,24 +27835,24 @@ static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_21___iter__ = {
   0, /*reserved*/
   #endif
   0, /*tp_repr*/
-  &__pyx_tp_as_number___pyx_scope_struct_21___iter__, /*tp_as_number*/
-  &__pyx_tp_as_sequence___pyx_scope_struct_21___iter__, /*tp_as_sequence*/
-  &__pyx_tp_as_mapping___pyx_scope_struct_21___iter__, /*tp_as_mapping*/
+  &__pyx_tp_as_number___pyx_scope_struct_22___iter__, /*tp_as_number*/
+  &__pyx_tp_as_sequence___pyx_scope_struct_22___iter__, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping___pyx_scope_struct_22___iter__, /*tp_as_mapping*/
   0, /*tp_hash*/
   0, /*tp_call*/
   0, /*tp_str*/
   0, /*tp_getattro*/
   0, /*tp_setattro*/
-  &__pyx_tp_as_buffer___pyx_scope_struct_21___iter__, /*tp_as_buffer*/
+  &__pyx_tp_as_buffer___pyx_scope_struct_22___iter__, /*tp_as_buffer*/
   Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
   0, /*tp_doc*/
-  __pyx_tp_traverse_5_cdec___pyx_scope_struct_21___iter__, /*tp_traverse*/
-  __pyx_tp_clear_5_cdec___pyx_scope_struct_21___iter__, /*tp_clear*/
+  __pyx_tp_traverse_5_cdec___pyx_scope_struct_22___iter__, /*tp_traverse*/
+  __pyx_tp_clear_5_cdec___pyx_scope_struct_22___iter__, /*tp_clear*/
   0, /*tp_richcompare*/
   0, /*tp_weaklistoffset*/
   0, /*tp_iter*/
   0, /*tp_iternext*/
-  __pyx_methods_5_cdec___pyx_scope_struct_21___iter__, /*tp_methods*/
+  __pyx_methods_5_cdec___pyx_scope_struct_22___iter__, /*tp_methods*/
   0, /*tp_members*/
   0, /*tp_getset*/
   0, /*tp_base*/
@@ -26823,7 +27862,7 @@ static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_21___iter__ = {
   0, /*tp_dictoffset*/
   0, /*tp_init*/
   0, /*tp_alloc*/
-  __pyx_tp_new_5_cdec___pyx_scope_struct_21___iter__, /*tp_new*/
+  __pyx_tp_new_5_cdec___pyx_scope_struct_22___iter__, /*tp_new*/
   0, /*tp_free*/
   0, /*tp_is_gc*/
   0, /*tp_bases*/
@@ -26837,11 +27876,11 @@ static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_21___iter__ = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_22__make_config(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
-  struct __pyx_obj_5_cdec___pyx_scope_struct_22__make_config *p;
+static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_23__make_config(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+  struct __pyx_obj_5_cdec___pyx_scope_struct_23__make_config *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
-  p = ((struct __pyx_obj_5_cdec___pyx_scope_struct_22__make_config *)o);
+  p = ((struct __pyx_obj_5_cdec___pyx_scope_struct_23__make_config *)o);
   p->__pyx_v_config = 0;
   p->__pyx_v_info = 0;
   p->__pyx_v_key = 0;
@@ -26852,21 +27891,21 @@ static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_22__make_config(PyTypeOb
   return o;
 }
 
-static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_22__make_config(PyObject *o) {
-  struct __pyx_obj_5_cdec___pyx_scope_struct_22__make_config *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_22__make_config *)o;
-  Py_XDECREF(p->__pyx_v_config);
-  Py_XDECREF(p->__pyx_v_info);
-  Py_XDECREF(p->__pyx_v_key);
-  Py_XDECREF(p->__pyx_v_name);
-  Py_XDECREF(p->__pyx_v_value);
-  Py_XDECREF(p->__pyx_t_0);
-  Py_XDECREF(p->__pyx_t_1);
+static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_23__make_config(PyObject *o) {
+  struct __pyx_obj_5_cdec___pyx_scope_struct_23__make_config *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_23__make_config *)o;
+  Py_CLEAR(p->__pyx_v_config);
+  Py_CLEAR(p->__pyx_v_info);
+  Py_CLEAR(p->__pyx_v_key);
+  Py_CLEAR(p->__pyx_v_name);
+  Py_CLEAR(p->__pyx_v_value);
+  Py_CLEAR(p->__pyx_t_0);
+  Py_CLEAR(p->__pyx_t_1);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
-static int __pyx_tp_traverse_5_cdec___pyx_scope_struct_22__make_config(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_5_cdec___pyx_scope_struct_23__make_config(PyObject *o, visitproc v, void *a) {
   int e;
-  struct __pyx_obj_5_cdec___pyx_scope_struct_22__make_config *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_22__make_config *)o;
+  struct __pyx_obj_5_cdec___pyx_scope_struct_23__make_config *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_23__make_config *)o;
   if (p->__pyx_v_config) {
     e = (*v)(p->__pyx_v_config, a); if (e) return e;
   }
@@ -26891,8 +27930,8 @@ static int __pyx_tp_traverse_5_cdec___pyx_scope_struct_22__make_config(PyObject
   return 0;
 }
 
-static int __pyx_tp_clear_5_cdec___pyx_scope_struct_22__make_config(PyObject *o) {
-  struct __pyx_obj_5_cdec___pyx_scope_struct_22__make_config *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_22__make_config *)o;
+static int __pyx_tp_clear_5_cdec___pyx_scope_struct_23__make_config(PyObject *o) {
+  struct __pyx_obj_5_cdec___pyx_scope_struct_23__make_config *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_23__make_config *)o;
   PyObject* tmp;
   tmp = ((PyObject*)p->__pyx_v_config);
   p->__pyx_v_config = Py_None; Py_INCREF(Py_None);
@@ -26918,11 +27957,11 @@ static int __pyx_tp_clear_5_cdec___pyx_scope_struct_22__make_config(PyObject *o)
   return 0;
 }
 
-static PyMethodDef __pyx_methods_5_cdec___pyx_scope_struct_22__make_config[] = {
+static PyMethodDef __pyx_methods_5_cdec___pyx_scope_struct_23__make_config[] = {
   {0, 0, 0, 0}
 };
 
-static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_22__make_config = {
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_23__make_config = {
   0, /*nb_add*/
   0, /*nb_subtract*/
   0, /*nb_multiply*/
@@ -26980,7 +28019,7 @@ static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_22__make_config = {
   #endif
 };
 
-static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_22__make_config = {
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_23__make_config = {
   0, /*sq_length*/
   0, /*sq_concat*/
   0, /*sq_repeat*/
@@ -26993,13 +28032,13 @@ static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_22__make_config
   0, /*sq_inplace_repeat*/
 };
 
-static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_22__make_config = {
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_23__make_config = {
   0, /*mp_length*/
   0, /*mp_subscript*/
   0, /*mp_ass_subscript*/
 };
 
-static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_22__make_config = {
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_23__make_config = {
   #if PY_MAJOR_VERSION < 3
   0, /*bf_getreadbuffer*/
   #endif
@@ -27020,12 +28059,12 @@ static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_22__make_config = {
   #endif
 };
 
-static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_22__make_config = {
+static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_23__make_config = {
   PyVarObject_HEAD_INIT(0, 0)
-  __Pyx_NAMESTR("_cdec.__pyx_scope_struct_22__make_config"), /*tp_name*/
-  sizeof(struct __pyx_obj_5_cdec___pyx_scope_struct_22__make_config), /*tp_basicsize*/
+  __Pyx_NAMESTR("_cdec.__pyx_scope_struct_23__make_config"), /*tp_name*/
+  sizeof(struct __pyx_obj_5_cdec___pyx_scope_struct_23__make_config), /*tp_basicsize*/
   0, /*tp_itemsize*/
-  __pyx_tp_dealloc_5_cdec___pyx_scope_struct_22__make_config, /*tp_dealloc*/
+  __pyx_tp_dealloc_5_cdec___pyx_scope_struct_23__make_config, /*tp_dealloc*/
   0, /*tp_print*/
   0, /*tp_getattr*/
   0, /*tp_setattr*/
@@ -27035,24 +28074,24 @@ static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_22__make_config = {
   0, /*reserved*/
   #endif
   0, /*tp_repr*/
-  &__pyx_tp_as_number___pyx_scope_struct_22__make_config, /*tp_as_number*/
-  &__pyx_tp_as_sequence___pyx_scope_struct_22__make_config, /*tp_as_sequence*/
-  &__pyx_tp_as_mapping___pyx_scope_struct_22__make_config, /*tp_as_mapping*/
+  &__pyx_tp_as_number___pyx_scope_struct_23__make_config, /*tp_as_number*/
+  &__pyx_tp_as_sequence___pyx_scope_struct_23__make_config, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping___pyx_scope_struct_23__make_config, /*tp_as_mapping*/
   0, /*tp_hash*/
   0, /*tp_call*/
   0, /*tp_str*/
   0, /*tp_getattro*/
   0, /*tp_setattro*/
-  &__pyx_tp_as_buffer___pyx_scope_struct_22__make_config, /*tp_as_buffer*/
+  &__pyx_tp_as_buffer___pyx_scope_struct_23__make_config, /*tp_as_buffer*/
   Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
   0, /*tp_doc*/
-  __pyx_tp_traverse_5_cdec___pyx_scope_struct_22__make_config, /*tp_traverse*/
-  __pyx_tp_clear_5_cdec___pyx_scope_struct_22__make_config, /*tp_clear*/
+  __pyx_tp_traverse_5_cdec___pyx_scope_struct_23__make_config, /*tp_traverse*/
+  __pyx_tp_clear_5_cdec___pyx_scope_struct_23__make_config, /*tp_clear*/
   0, /*tp_richcompare*/
   0, /*tp_weaklistoffset*/
   0, /*tp_iter*/
   0, /*tp_iternext*/
-  __pyx_methods_5_cdec___pyx_scope_struct_22__make_config, /*tp_methods*/
+  __pyx_methods_5_cdec___pyx_scope_struct_23__make_config, /*tp_methods*/
   0, /*tp_members*/
   0, /*tp_getset*/
   0, /*tp_base*/
@@ -27062,7 +28101,7 @@ static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_22__make_config = {
   0, /*tp_dictoffset*/
   0, /*tp_init*/
   0, /*tp_alloc*/
-  __pyx_tp_new_5_cdec___pyx_scope_struct_22__make_config, /*tp_new*/
+  __pyx_tp_new_5_cdec___pyx_scope_struct_23__make_config, /*tp_new*/
   0, /*tp_free*/
   0, /*tp_is_gc*/
   0, /*tp_bases*/
@@ -27076,32 +28115,32 @@ static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_22__make_config = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_23___cinit__(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
-  struct __pyx_obj_5_cdec___pyx_scope_struct_23___cinit__ *p;
+static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_24___init__(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+  struct __pyx_obj_5_cdec___pyx_scope_struct_24___init__ *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
-  p = ((struct __pyx_obj_5_cdec___pyx_scope_struct_23___cinit__ *)o);
+  p = ((struct __pyx_obj_5_cdec___pyx_scope_struct_24___init__ *)o);
   p->__pyx_v_config = 0;
   return o;
 }
 
-static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_23___cinit__(PyObject *o) {
-  struct __pyx_obj_5_cdec___pyx_scope_struct_23___cinit__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_23___cinit__ *)o;
-  Py_XDECREF(p->__pyx_v_config);
+static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_24___init__(PyObject *o) {
+  struct __pyx_obj_5_cdec___pyx_scope_struct_24___init__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_24___init__ *)o;
+  Py_CLEAR(p->__pyx_v_config);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
-static int __pyx_tp_traverse_5_cdec___pyx_scope_struct_23___cinit__(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_5_cdec___pyx_scope_struct_24___init__(PyObject *o, visitproc v, void *a) {
   int e;
-  struct __pyx_obj_5_cdec___pyx_scope_struct_23___cinit__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_23___cinit__ *)o;
+  struct __pyx_obj_5_cdec___pyx_scope_struct_24___init__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_24___init__ *)o;
   if (p->__pyx_v_config) {
     e = (*v)(p->__pyx_v_config, a); if (e) return e;
   }
   return 0;
 }
 
-static int __pyx_tp_clear_5_cdec___pyx_scope_struct_23___cinit__(PyObject *o) {
-  struct __pyx_obj_5_cdec___pyx_scope_struct_23___cinit__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_23___cinit__ *)o;
+static int __pyx_tp_clear_5_cdec___pyx_scope_struct_24___init__(PyObject *o) {
+  struct __pyx_obj_5_cdec___pyx_scope_struct_24___init__ *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_24___init__ *)o;
   PyObject* tmp;
   tmp = ((PyObject*)p->__pyx_v_config);
   p->__pyx_v_config = Py_None; Py_INCREF(Py_None);
@@ -27109,11 +28148,11 @@ static int __pyx_tp_clear_5_cdec___pyx_scope_struct_23___cinit__(PyObject *o) {
   return 0;
 }
 
-static PyMethodDef __pyx_methods_5_cdec___pyx_scope_struct_23___cinit__[] = {
+static PyMethodDef __pyx_methods_5_cdec___pyx_scope_struct_24___init__[] = {
   {0, 0, 0, 0}
 };
 
-static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_23___cinit__ = {
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_24___init__ = {
   0, /*nb_add*/
   0, /*nb_subtract*/
   0, /*nb_multiply*/
@@ -27171,7 +28210,7 @@ static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_23___cinit__ = {
   #endif
 };
 
-static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_23___cinit__ = {
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_24___init__ = {
   0, /*sq_length*/
   0, /*sq_concat*/
   0, /*sq_repeat*/
@@ -27184,13 +28223,13 @@ static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_23___cinit__ =
   0, /*sq_inplace_repeat*/
 };
 
-static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_23___cinit__ = {
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_24___init__ = {
   0, /*mp_length*/
   0, /*mp_subscript*/
   0, /*mp_ass_subscript*/
 };
 
-static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_23___cinit__ = {
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_24___init__ = {
   #if PY_MAJOR_VERSION < 3
   0, /*bf_getreadbuffer*/
   #endif
@@ -27211,12 +28250,12 @@ static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_23___cinit__ = {
   #endif
 };
 
-static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_23___cinit__ = {
+static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_24___init__ = {
   PyVarObject_HEAD_INIT(0, 0)
-  __Pyx_NAMESTR("_cdec.__pyx_scope_struct_23___cinit__"), /*tp_name*/
-  sizeof(struct __pyx_obj_5_cdec___pyx_scope_struct_23___cinit__), /*tp_basicsize*/
+  __Pyx_NAMESTR("_cdec.__pyx_scope_struct_24___init__"), /*tp_name*/
+  sizeof(struct __pyx_obj_5_cdec___pyx_scope_struct_24___init__), /*tp_basicsize*/
   0, /*tp_itemsize*/
-  __pyx_tp_dealloc_5_cdec___pyx_scope_struct_23___cinit__, /*tp_dealloc*/
+  __pyx_tp_dealloc_5_cdec___pyx_scope_struct_24___init__, /*tp_dealloc*/
   0, /*tp_print*/
   0, /*tp_getattr*/
   0, /*tp_setattr*/
@@ -27226,24 +28265,24 @@ static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_23___cinit__ = {
   0, /*reserved*/
   #endif
   0, /*tp_repr*/
-  &__pyx_tp_as_number___pyx_scope_struct_23___cinit__, /*tp_as_number*/
-  &__pyx_tp_as_sequence___pyx_scope_struct_23___cinit__, /*tp_as_sequence*/
-  &__pyx_tp_as_mapping___pyx_scope_struct_23___cinit__, /*tp_as_mapping*/
+  &__pyx_tp_as_number___pyx_scope_struct_24___init__, /*tp_as_number*/
+  &__pyx_tp_as_sequence___pyx_scope_struct_24___init__, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping___pyx_scope_struct_24___init__, /*tp_as_mapping*/
   0, /*tp_hash*/
   0, /*tp_call*/
   0, /*tp_str*/
   0, /*tp_getattro*/
   0, /*tp_setattro*/
-  &__pyx_tp_as_buffer___pyx_scope_struct_23___cinit__, /*tp_as_buffer*/
+  &__pyx_tp_as_buffer___pyx_scope_struct_24___init__, /*tp_as_buffer*/
   Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
   0, /*tp_doc*/
-  __pyx_tp_traverse_5_cdec___pyx_scope_struct_23___cinit__, /*tp_traverse*/
-  __pyx_tp_clear_5_cdec___pyx_scope_struct_23___cinit__, /*tp_clear*/
+  __pyx_tp_traverse_5_cdec___pyx_scope_struct_24___init__, /*tp_traverse*/
+  __pyx_tp_clear_5_cdec___pyx_scope_struct_24___init__, /*tp_clear*/
   0, /*tp_richcompare*/
   0, /*tp_weaklistoffset*/
   0, /*tp_iter*/
   0, /*tp_iternext*/
-  __pyx_methods_5_cdec___pyx_scope_struct_23___cinit__, /*tp_methods*/
+  __pyx_methods_5_cdec___pyx_scope_struct_24___init__, /*tp_methods*/
   0, /*tp_members*/
   0, /*tp_getset*/
   0, /*tp_base*/
@@ -27253,7 +28292,7 @@ static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_23___cinit__ = {
   0, /*tp_dictoffset*/
   0, /*tp_init*/
   0, /*tp_alloc*/
-  __pyx_tp_new_5_cdec___pyx_scope_struct_23___cinit__, /*tp_new*/
+  __pyx_tp_new_5_cdec___pyx_scope_struct_24___init__, /*tp_new*/
   0, /*tp_free*/
   0, /*tp_is_gc*/
   0, /*tp_bases*/
@@ -27267,28 +28306,28 @@ static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_23___cinit__ = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_24_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
-  struct __pyx_obj_5_cdec___pyx_scope_struct_24_genexpr *p;
+static PyObject *__pyx_tp_new_5_cdec___pyx_scope_struct_25_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+  struct __pyx_obj_5_cdec___pyx_scope_struct_25_genexpr *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
-  p = ((struct __pyx_obj_5_cdec___pyx_scope_struct_24_genexpr *)o);
+  p = ((struct __pyx_obj_5_cdec___pyx_scope_struct_25_genexpr *)o);
   p->__pyx_outer_scope = 0;
   p->__pyx_v_kv = 0;
   p->__pyx_t_0 = 0;
   return o;
 }
 
-static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_24_genexpr(PyObject *o) {
-  struct __pyx_obj_5_cdec___pyx_scope_struct_24_genexpr *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_24_genexpr *)o;
-  Py_XDECREF(((PyObject *)p->__pyx_outer_scope));
-  Py_XDECREF(p->__pyx_v_kv);
-  Py_XDECREF(p->__pyx_t_0);
+static void __pyx_tp_dealloc_5_cdec___pyx_scope_struct_25_genexpr(PyObject *o) {
+  struct __pyx_obj_5_cdec___pyx_scope_struct_25_genexpr *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_25_genexpr *)o;
+  Py_CLEAR(p->__pyx_outer_scope);
+  Py_CLEAR(p->__pyx_v_kv);
+  Py_CLEAR(p->__pyx_t_0);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
-static int __pyx_tp_traverse_5_cdec___pyx_scope_struct_24_genexpr(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_5_cdec___pyx_scope_struct_25_genexpr(PyObject *o, visitproc v, void *a) {
   int e;
-  struct __pyx_obj_5_cdec___pyx_scope_struct_24_genexpr *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_24_genexpr *)o;
+  struct __pyx_obj_5_cdec___pyx_scope_struct_25_genexpr *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_25_genexpr *)o;
   if (p->__pyx_outer_scope) {
     e = (*v)(((PyObject*)p->__pyx_outer_scope), a); if (e) return e;
   }
@@ -27301,11 +28340,11 @@ static int __pyx_tp_traverse_5_cdec___pyx_scope_struct_24_genexpr(PyObject *o, v
   return 0;
 }
 
-static int __pyx_tp_clear_5_cdec___pyx_scope_struct_24_genexpr(PyObject *o) {
-  struct __pyx_obj_5_cdec___pyx_scope_struct_24_genexpr *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_24_genexpr *)o;
+static int __pyx_tp_clear_5_cdec___pyx_scope_struct_25_genexpr(PyObject *o) {
+  struct __pyx_obj_5_cdec___pyx_scope_struct_25_genexpr *p = (struct __pyx_obj_5_cdec___pyx_scope_struct_25_genexpr *)o;
   PyObject* tmp;
   tmp = ((PyObject*)p->__pyx_outer_scope);
-  p->__pyx_outer_scope = ((struct __pyx_obj_5_cdec___pyx_scope_struct_23___cinit__ *)Py_None); Py_INCREF(Py_None);
+  p->__pyx_outer_scope = ((struct __pyx_obj_5_cdec___pyx_scope_struct_24___init__ *)Py_None); Py_INCREF(Py_None);
   Py_XDECREF(tmp);
   tmp = ((PyObject*)p->__pyx_v_kv);
   p->__pyx_v_kv = Py_None; Py_INCREF(Py_None);
@@ -27316,11 +28355,11 @@ static int __pyx_tp_clear_5_cdec___pyx_scope_struct_24_genexpr(PyObject *o) {
   return 0;
 }
 
-static PyMethodDef __pyx_methods_5_cdec___pyx_scope_struct_24_genexpr[] = {
+static PyMethodDef __pyx_methods_5_cdec___pyx_scope_struct_25_genexpr[] = {
   {0, 0, 0, 0}
 };
 
-static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_24_genexpr = {
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_25_genexpr = {
   0, /*nb_add*/
   0, /*nb_subtract*/
   0, /*nb_multiply*/
@@ -27378,7 +28417,7 @@ static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_24_genexpr = {
   #endif
 };
 
-static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_24_genexpr = {
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_25_genexpr = {
   0, /*sq_length*/
   0, /*sq_concat*/
   0, /*sq_repeat*/
@@ -27391,13 +28430,13 @@ static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_24_genexpr = {
   0, /*sq_inplace_repeat*/
 };
 
-static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_24_genexpr = {
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_25_genexpr = {
   0, /*mp_length*/
   0, /*mp_subscript*/
   0, /*mp_ass_subscript*/
 };
 
-static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_24_genexpr = {
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_25_genexpr = {
   #if PY_MAJOR_VERSION < 3
   0, /*bf_getreadbuffer*/
   #endif
@@ -27418,12 +28457,12 @@ static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_24_genexpr = {
   #endif
 };
 
-static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_24_genexpr = {
+static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_25_genexpr = {
   PyVarObject_HEAD_INIT(0, 0)
-  __Pyx_NAMESTR("_cdec.__pyx_scope_struct_24_genexpr"), /*tp_name*/
-  sizeof(struct __pyx_obj_5_cdec___pyx_scope_struct_24_genexpr), /*tp_basicsize*/
+  __Pyx_NAMESTR("_cdec.__pyx_scope_struct_25_genexpr"), /*tp_name*/
+  sizeof(struct __pyx_obj_5_cdec___pyx_scope_struct_25_genexpr), /*tp_basicsize*/
   0, /*tp_itemsize*/
-  __pyx_tp_dealloc_5_cdec___pyx_scope_struct_24_genexpr, /*tp_dealloc*/
+  __pyx_tp_dealloc_5_cdec___pyx_scope_struct_25_genexpr, /*tp_dealloc*/
   0, /*tp_print*/
   0, /*tp_getattr*/
   0, /*tp_setattr*/
@@ -27433,24 +28472,24 @@ static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_24_genexpr = {
   0, /*reserved*/
   #endif
   0, /*tp_repr*/
-  &__pyx_tp_as_number___pyx_scope_struct_24_genexpr, /*tp_as_number*/
-  &__pyx_tp_as_sequence___pyx_scope_struct_24_genexpr, /*tp_as_sequence*/
-  &__pyx_tp_as_mapping___pyx_scope_struct_24_genexpr, /*tp_as_mapping*/
+  &__pyx_tp_as_number___pyx_scope_struct_25_genexpr, /*tp_as_number*/
+  &__pyx_tp_as_sequence___pyx_scope_struct_25_genexpr, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping___pyx_scope_struct_25_genexpr, /*tp_as_mapping*/
   0, /*tp_hash*/
   0, /*tp_call*/
   0, /*tp_str*/
   0, /*tp_getattro*/
   0, /*tp_setattro*/
-  &__pyx_tp_as_buffer___pyx_scope_struct_24_genexpr, /*tp_as_buffer*/
+  &__pyx_tp_as_buffer___pyx_scope_struct_25_genexpr, /*tp_as_buffer*/
   Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
   0, /*tp_doc*/
-  __pyx_tp_traverse_5_cdec___pyx_scope_struct_24_genexpr, /*tp_traverse*/
-  __pyx_tp_clear_5_cdec___pyx_scope_struct_24_genexpr, /*tp_clear*/
+  __pyx_tp_traverse_5_cdec___pyx_scope_struct_25_genexpr, /*tp_traverse*/
+  __pyx_tp_clear_5_cdec___pyx_scope_struct_25_genexpr, /*tp_clear*/
   0, /*tp_richcompare*/
   0, /*tp_weaklistoffset*/
   0, /*tp_iter*/
   0, /*tp_iternext*/
-  __pyx_methods_5_cdec___pyx_scope_struct_24_genexpr, /*tp_methods*/
+  __pyx_methods_5_cdec___pyx_scope_struct_25_genexpr, /*tp_methods*/
   0, /*tp_members*/
   0, /*tp_getset*/
   0, /*tp_base*/
@@ -27460,7 +28499,7 @@ static PyTypeObject __pyx_type_5_cdec___pyx_scope_struct_24_genexpr = {
   0, /*tp_dictoffset*/
   0, /*tp_init*/
   0, /*tp_alloc*/
-  __pyx_tp_new_5_cdec___pyx_scope_struct_24_genexpr, /*tp_new*/
+  __pyx_tp_new_5_cdec___pyx_scope_struct_25_genexpr, /*tp_new*/
   0, /*tp_free*/
   0, /*tp_is_gc*/
   0, /*tp_bases*/
@@ -27497,36 +28536,37 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
   {&__pyx_kp_s_11, __pyx_k_11, sizeof(__pyx_k_11), 0, 0, 1, 0},
   {&__pyx_kp_s_12, __pyx_k_12, sizeof(__pyx_k_12), 0, 0, 1, 0},
   {&__pyx_kp_s_13, __pyx_k_13, sizeof(__pyx_k_13), 0, 0, 1, 0},
-  {&__pyx_n_s_15, __pyx_k_15, sizeof(__pyx_k_15), 0, 0, 1, 1},
-  {&__pyx_kp_s_16, __pyx_k_16, sizeof(__pyx_k_16), 0, 0, 1, 0},
+  {&__pyx_kp_s_15, __pyx_k_15, sizeof(__pyx_k_15), 0, 0, 1, 0},
+  {&__pyx_n_s_16, __pyx_k_16, sizeof(__pyx_k_16), 0, 0, 1, 1},
   {&__pyx_kp_s_17, __pyx_k_17, sizeof(__pyx_k_17), 0, 0, 1, 0},
-  {&__pyx_kp_s_19, __pyx_k_19, sizeof(__pyx_k_19), 0, 0, 1, 0},
+  {&__pyx_kp_s_18, __pyx_k_18, sizeof(__pyx_k_18), 0, 0, 1, 0},
+  {&__pyx_kp_s_20, __pyx_k_20, sizeof(__pyx_k_20), 0, 0, 1, 0},
   {&__pyx_kp_s_22, __pyx_k_22, sizeof(__pyx_k_22), 0, 0, 1, 0},
   {&__pyx_kp_s_23, __pyx_k_23, sizeof(__pyx_k_23), 0, 0, 1, 0},
+  {&__pyx_kp_s_26, __pyx_k_26, sizeof(__pyx_k_26), 0, 0, 1, 0},
   {&__pyx_kp_s_27, __pyx_k_27, sizeof(__pyx_k_27), 0, 0, 1, 0},
   {&__pyx_kp_s_28, __pyx_k_28, sizeof(__pyx_k_28), 0, 0, 1, 0},
   {&__pyx_kp_s_29, __pyx_k_29, sizeof(__pyx_k_29), 0, 0, 1, 0},
   {&__pyx_kp_s_3, __pyx_k_3, sizeof(__pyx_k_3), 0, 0, 1, 0},
   {&__pyx_kp_s_30, __pyx_k_30, sizeof(__pyx_k_30), 0, 0, 1, 0},
   {&__pyx_kp_s_31, __pyx_k_31, sizeof(__pyx_k_31), 0, 0, 1, 0},
-  {&__pyx_kp_s_32, __pyx_k_32, sizeof(__pyx_k_32), 0, 0, 1, 0},
+  {&__pyx_kp_s_33, __pyx_k_33, sizeof(__pyx_k_33), 0, 0, 1, 0},
   {&__pyx_kp_s_34, __pyx_k_34, sizeof(__pyx_k_34), 0, 0, 1, 0},
-  {&__pyx_kp_s_35, __pyx_k_35, sizeof(__pyx_k_35), 0, 0, 1, 0},
+  {&__pyx_kp_s_37, __pyx_k_37, sizeof(__pyx_k_37), 0, 0, 1, 0},
   {&__pyx_kp_s_38, __pyx_k_38, sizeof(__pyx_k_38), 0, 0, 1, 0},
-  {&__pyx_kp_s_39, __pyx_k_39, sizeof(__pyx_k_39), 0, 0, 1, 0},
   {&__pyx_kp_s_4, __pyx_k_4, sizeof(__pyx_k_4), 0, 0, 1, 0},
-  {&__pyx_kp_s_41, __pyx_k_41, sizeof(__pyx_k_41), 0, 0, 1, 0},
-  {&__pyx_kp_s_43, __pyx_k_43, sizeof(__pyx_k_43), 0, 0, 1, 0},
+  {&__pyx_kp_s_40, __pyx_k_40, sizeof(__pyx_k_40), 0, 0, 1, 0},
+  {&__pyx_kp_s_42, __pyx_k_42, sizeof(__pyx_k_42), 0, 0, 1, 0},
+  {&__pyx_kp_s_44, __pyx_k_44, sizeof(__pyx_k_44), 0, 0, 1, 0},
   {&__pyx_kp_s_45, __pyx_k_45, sizeof(__pyx_k_45), 0, 0, 1, 0},
-  {&__pyx_kp_s_46, __pyx_k_46, sizeof(__pyx_k_46), 0, 0, 1, 0},
+  {&__pyx_kp_s_47, __pyx_k_47, sizeof(__pyx_k_47), 0, 0, 1, 0},
   {&__pyx_kp_s_48, __pyx_k_48, sizeof(__pyx_k_48), 0, 0, 1, 0},
   {&__pyx_kp_s_49, __pyx_k_49, sizeof(__pyx_k_49), 0, 0, 1, 0},
-  {&__pyx_kp_s_50, __pyx_k_50, sizeof(__pyx_k_50), 0, 0, 1, 0},
-  {&__pyx_kp_s_53, __pyx_k_53, sizeof(__pyx_k_53), 0, 0, 1, 0},
+  {&__pyx_kp_s_52, __pyx_k_52, sizeof(__pyx_k_52), 0, 0, 1, 0},
+  {&__pyx_n_s_53, __pyx_k_53, sizeof(__pyx_k_53), 0, 0, 1, 1},
   {&__pyx_n_s_54, __pyx_k_54, sizeof(__pyx_k_54), 0, 0, 1, 1},
-  {&__pyx_n_s_55, __pyx_k_55, sizeof(__pyx_k_55), 0, 0, 1, 1},
-  {&__pyx_kp_s_58, __pyx_k_58, sizeof(__pyx_k_58), 0, 0, 1, 0},
-  {&__pyx_kp_s_64, __pyx_k_64, sizeof(__pyx_k_64), 0, 0, 1, 0},
+  {&__pyx_kp_s_57, __pyx_k_57, sizeof(__pyx_k_57), 0, 0, 1, 0},
+  {&__pyx_kp_s_63, __pyx_k_63, sizeof(__pyx_k_63), 0, 0, 1, 0},
   {&__pyx_kp_s_7, __pyx_k_7, sizeof(__pyx_k_7), 0, 0, 1, 0},
   {&__pyx_kp_s_8, __pyx_k_8, sizeof(__pyx_k_8), 0, 0, 1, 0},
   {&__pyx_kp_s_9, __pyx_k_9, sizeof(__pyx_k_9), 0, 0, 1, 0},
@@ -27539,7 +28579,6 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
   {&__pyx_n_s__KeyError, __pyx_k__KeyError, sizeof(__pyx_k__KeyError), 0, 0, 1, 1},
   {&__pyx_n_s__NotImplemented, __pyx_k__NotImplemented, sizeof(__pyx_k__NotImplemented), 0, 0, 1, 1},
   {&__pyx_n_s__ParseFailed, __pyx_k__ParseFailed, sizeof(__pyx_k__ParseFailed), 0, 0, 1, 1},
-  {&__pyx_n_s__PhraseModel_, __pyx_k__PhraseModel_, sizeof(__pyx_k__PhraseModel_), 0, 0, 1, 1},
   {&__pyx_n_s__TER, __pyx_k__TER, sizeof(__pyx_k__TER), 0, 0, 1, 1},
   {&__pyx_n_s__TypeError, __pyx_k__TypeError, sizeof(__pyx_k__TypeError), 0, 0, 1, 1},
   {&__pyx_n_s__ValueError, __pyx_k__ValueError, sizeof(__pyx_k__ValueError), 0, 0, 1, 1},
@@ -27555,6 +28594,8 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
   {&__pyx_n_s___phrase, __pyx_k___phrase, sizeof(__pyx_k___phrase), 0, 0, 1, 1},
   {&__pyx_n_s___sa, __pyx_k___sa, sizeof(__pyx_k___sa), 0, 0, 1, 1},
   {&__pyx_n_s__a, __pyx_k__a, sizeof(__pyx_k__a), 0, 0, 1, 1},
+  {&__pyx_n_s__alignments, __pyx_k__alignments, sizeof(__pyx_k__alignments), 0, 0, 1, 1},
+  {&__pyx_n_s__basestring, __pyx_k__basestring, sizeof(__pyx_k__basestring), 0, 0, 1, 1},
   {&__pyx_n_s__beam_alpha, __pyx_k__beam_alpha, sizeof(__pyx_k__beam_alpha), 0, 0, 1, 1},
   {&__pyx_n_s__cat, __pyx_k__cat, sizeof(__pyx_k__cat), 0, 0, 1, 1},
   {&__pyx_n_s__config, __pyx_k__config, sizeof(__pyx_k__config), 0, 0, 1, 1},
@@ -27608,6 +28649,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
   {&__pyx_n_s__scores, __pyx_k__scores, sizeof(__pyx_k__scores), 0, 0, 1, 1},
   {&__pyx_n_s__self, __pyx_k__self, sizeof(__pyx_k__self), 0, 0, 1, 1},
   {&__pyx_n_s__sentence, __pyx_k__sentence, sizeof(__pyx_k__sentence), 0, 0, 1, 1},
+  {&__pyx_n_s__set_silent, __pyx_k__set_silent, sizeof(__pyx_k__set_silent), 0, 0, 1, 1},
   {&__pyx_n_s__span, __pyx_k__span, sizeof(__pyx_k__span), 0, 0, 1, 1},
   {&__pyx_n_s__split, __pyx_k__split, sizeof(__pyx_k__split), 0, 0, 1, 1},
   {&__pyx_n_s__startswith, __pyx_k__startswith, sizeof(__pyx_k__startswith), 0, 0, 1, 1},
@@ -27617,20 +28659,22 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
   {&__pyx_n_s__utf8, __pyx_k__utf8, sizeof(__pyx_k__utf8), 0, 0, 1, 1},
   {&__pyx_n_s__value, __pyx_k__value, sizeof(__pyx_k__value), 0, 0, 1, 1},
   {&__pyx_n_s__weight, __pyx_k__weight, sizeof(__pyx_k__weight), 0, 0, 1, 1},
+  {&__pyx_n_s__yn, __pyx_k__yn, sizeof(__pyx_k__yn), 0, 0, 1, 1},
   {0, 0, 0, 0, 0, 0, 0}
 };
 static int __Pyx_InitCachedBuiltins(void) {
   __pyx_builtin_Exception = __Pyx_GetName(__pyx_b, __pyx_n_s__Exception); if (!__pyx_builtin_Exception) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_builtin_TypeError = __Pyx_GetName(__pyx_b, __pyx_n_s__TypeError); if (!__pyx_builtin_TypeError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 13; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_builtin_KeyError = __Pyx_GetName(__pyx_b, __pyx_n_s__KeyError); if (!__pyx_builtin_KeyError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_builtin_range = __Pyx_GetName(__pyx_b, __pyx_n_s__range); if (!__pyx_builtin_range) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_builtin_NotImplemented = __Pyx_GetName(__pyx_b, __pyx_n_s__NotImplemented); if (!__pyx_builtin_NotImplemented) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_builtin_super = __Pyx_GetName(__pyx_b, __pyx_n_s__super); if (!__pyx_builtin_super) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 179; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_builtin_ValueError = __Pyx_GetName(__pyx_b, __pyx_n_s__ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_builtin_eval = __Pyx_GetName(__pyx_b, __pyx_n_s__eval); if (!__pyx_builtin_eval) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 102; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_builtin_enumerate = __Pyx_GetName(__pyx_b, __pyx_n_s__enumerate); if (!__pyx_builtin_enumerate) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_builtin_IndexError = __Pyx_GetName(__pyx_b, __pyx_n_s__IndexError); if (!__pyx_builtin_IndexError) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 24; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_builtin_open = __Pyx_GetName(__pyx_b, __pyx_n_s__open); if (!__pyx_builtin_open) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_builtin_KeyError = __Pyx_GetName(__pyx_b, __pyx_n_s__KeyError); if (!__pyx_builtin_KeyError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_builtin_range = __Pyx_GetName(__pyx_b, __pyx_n_s__range); if (!__pyx_builtin_range) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_builtin_NotImplemented = __Pyx_GetName(__pyx_b, __pyx_n_s__NotImplemented); if (!__pyx_builtin_NotImplemented) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 95; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_builtin_super = __Pyx_GetName(__pyx_b, __pyx_n_s__super); if (!__pyx_builtin_super) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 191; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_builtin_ValueError = __Pyx_GetName(__pyx_b, __pyx_n_s__ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 226; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_builtin_basestring = __Pyx_GetName(__pyx_b, __pyx_n_s__basestring); if (!__pyx_builtin_basestring) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 119; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_builtin_eval = __Pyx_GetName(__pyx_b, __pyx_n_s__eval); if (!__pyx_builtin_eval) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_builtin_enumerate = __Pyx_GetName(__pyx_b, __pyx_n_s__enumerate); if (!__pyx_builtin_enumerate) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_builtin_IndexError = __Pyx_GetName(__pyx_b, __pyx_n_s__IndexError); if (!__pyx_builtin_IndexError) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_builtin_open = __Pyx_GetName(__pyx_b, __pyx_n_s__open); if (!__pyx_builtin_open) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 91; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   return 0;
   __pyx_L1_error:;
   return -1;
@@ -27654,21 +28698,21 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_n_s__utf8));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_2));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/vectors.pxi":89
+  /* "/home/vchahune/tools/cdec/python/src/vectors.pxi":95
  *         elif op == 3: # !=
  *             return not (x == y)
  *         raise NotImplemented('comparison not implemented for SparseVector')             # <<<<<<<<<<<<<<
  * 
  *     def __len__(self):
  */
-  __pyx_k_tuple_5 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_k_tuple_5 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 95; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_k_tuple_5);
   __Pyx_INCREF(((PyObject *)__pyx_kp_s_4));
   PyTuple_SET_ITEM(__pyx_k_tuple_5, 0, ((PyObject *)__pyx_kp_s_4));
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_4));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_5));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":6
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":6
  * 
  * def _phrase(phrase):
  *     return ' '.join(w.encode('utf8') if isinstance(w, unicode) else str(w) for w in phrase)             # <<<<<<<<<<<<<<
@@ -27682,319 +28726,308 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_n_s__utf8));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_6));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":212
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":226
  *                 trule = convert_rule(trule)
  *             elif not isinstance(trule, TRule):
  *                 raise ValueError('the grammar should contain TRule objects')             # <<<<<<<<<<<<<<
  *             _g.AddRule((<TRule> trule).rule[0])
  */
-  __pyx_k_tuple_14 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_14)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_k_tuple_14 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_14)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 226; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_k_tuple_14);
   __Pyx_INCREF(((PyObject *)__pyx_kp_s_13));
   PyTuple_SET_ITEM(__pyx_k_tuple_14, 0, ((PyObject *)__pyx_kp_s_13));
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_13));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_14));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":191
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":235
  *         elif op == 3: # !=
  *             return not (x == y)
  *         raise NotImplemented('comparison not implemented for HypergraphEdge')             # <<<<<<<<<<<<<<
  * 
  * cdef class HypergraphNode:
  */
-  __pyx_k_tuple_18 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_18)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 191; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  PyTuple_SET_ITEM(__pyx_k_tuple_18, 0, ((PyObject *)__pyx_kp_s_17));
-  __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_17));
-  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_18));
+  __pyx_k_tuple_19 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_19)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 235; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(__pyx_k_tuple_19);
+  __Pyx_INCREF(((PyObject *)__pyx_kp_s_18));
+  PyTuple_SET_ITEM(__pyx_k_tuple_19, 0, ((PyObject *)__pyx_kp_s_18));
+  __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_18));
+  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_19));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/hypergraph.pxi":228
+  /* "/home/vchahune/tools/cdec/python/src/hypergraph.pxi":272
  *         elif op == 3: # !=
  *             return not (x == y)
  *         raise NotImplemented('comparison not implemented for HypergraphNode')             # <<<<<<<<<<<<<<
  */
-  __pyx_k_tuple_20 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_20)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 228; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  PyTuple_SET_ITEM(__pyx_k_tuple_20, 0, ((PyObject *)__pyx_kp_s_19));
-  __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_19));
-  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_20));
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/lattice.pxi":13
- *         else:
- *             if isinstance(inp, unicode):
- *                 inp = inp.encode('utf8')             # <<<<<<<<<<<<<<
- *             if not isinstance(inp, str):
- *                 raise TypeError('Cannot create lattice from %s' % type(inp))
- */
-  __pyx_k_tuple_21 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_21)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 13; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_k_tuple_21 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_21)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __Pyx_GIVEREF(((PyObject *)__pyx_n_s__utf8));
+  __Pyx_INCREF(((PyObject *)__pyx_kp_s_20));
+  PyTuple_SET_ITEM(__pyx_k_tuple_21, 0, ((PyObject *)__pyx_kp_s_20));
+  __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_20));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_21));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/lattice.pxi":24
+  /* "/home/vchahune/tools/cdec/python/src/lattice.pxi":26
  *     def __getitem__(self, int index):
  *         if not 0 <= index < len(self):
  *             raise IndexError('lattice index out of range')             # <<<<<<<<<<<<<<
  *         arcs = []
  *         cdef vector[lattice.LatticeArc] arc_vector = self.lattice[0][index]
  */
-  __pyx_k_tuple_24 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_24)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 24; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_k_tuple_24 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_24)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_24));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/lattice.pxi":37
+  /* "/home/vchahune/tools/cdec/python/src/lattice.pxi":39
  *     def __setitem__(self, int index, tuple arcs):
  *         if not 0 <= index < len(self):
  *             raise IndexError('lattice index out of range')             # <<<<<<<<<<<<<<
  *         cdef lattice.LatticeArc* arc
  *         for (label, cost, dist2next) in arcs:
  */
-  __pyx_k_tuple_25 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_25)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_k_tuple_25 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_25)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- *             if isinstance(label, unicode):
- *                 label = label.encode('utf8')             # <<<<<<<<<<<<<<
- *             arc = new lattice.LatticeArc(TDConvert(<char *>label), cost, dist2next)
- *             self.lattice[0][index].push_back(arc[0])
- */
-  __pyx_k_tuple_26 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_26)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_26));
-
-  /* "/Users/vchahun/Sandbox/cdec/python/src/lattice.pxi":64
+  /* "/home/vchahune/tools/cdec/python/src/lattice.pxi":69
  *             for i in range(len(self)):
  *                 for label, weight, delta in self[i]:
  *                     yield '%d -> %d [label="%s"];' % (i, i+delta, label.replace('"', '\\"'))             # <<<<<<<<<<<<<<
  *             yield '%d [shape=doublecircle]' % len(self)
  *             yield '}'
  */
-  __pyx_k_tuple_33 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_33)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_GOTREF(__pyx_k_tuple_33);
+  __pyx_k_tuple_32 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_32)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  PyTuple_SET_ITEM(__pyx_k_tuple_32, 0, ((PyObject *)__pyx_kp_s_30));
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   __Pyx_INCREF(((PyObject *)__pyx_kp_s_31));
-  PyTuple_SET_ITEM(__pyx_k_tuple_33, 0, ((PyObject *)__pyx_kp_s_31));
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-  __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_32));
-  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_33));
+  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_32));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/lattice.pxi":58
- * 
+  /* "/home/vchahune/tools/cdec/python/src/lattice.pxi":63
  *     def todot(self):
+ *         """lattice.todot() -> Representation of the lattice in GraphViz dot format."""
  *         def lines():             # <<<<<<<<<<<<<<
  *             yield 'digraph lattice {'
  *             yield 'rankdir = LR;'
  */
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-  __Pyx_GOTREF(__pyx_k_tuple_36);
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   __Pyx_INCREF(((PyObject *)__pyx_n_s__i));
-  PyTuple_SET_ITEM(__pyx_k_tuple_36, 0, ((PyObject *)__pyx_n_s__i));
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-  PyTuple_SET_ITEM(__pyx_k_tuple_36, 2, ((PyObject *)__pyx_n_s__weight));
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   __Pyx_INCREF(((PyObject *)__pyx_n_s__delta));
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+  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_35));
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/lattice.pxi":67
+  /* "/home/vchahune/tools/cdec/python/src/lattice.pxi":72
  *             yield '%d [shape=doublecircle]' % len(self)
  *             yield '}'
  *         return '\n'.join(lines()).encode('utf8')             # <<<<<<<<<<<<<<
+ * 
+ *     def as_hypergraph(self):
  */
-  __pyx_k_tuple_40 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_40)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_GOTREF(__pyx_k_tuple_40);
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   __Pyx_INCREF(((PyObject *)__pyx_n_s__utf8));
-  PyTuple_SET_ITEM(__pyx_k_tuple_40, 0, ((PyObject *)__pyx_n_s__utf8));
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   __Pyx_GIVEREF(((PyObject *)__pyx_n_s__utf8));
-  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_40));
+  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_39));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":50
+  /* "/home/vchahune/tools/cdec/python/src/mteval.pxi":50
  *     def __getitem__(self, int index):
  *         if not 0 <= index < len(self):
  *             raise IndexError('sufficient stats vector index out of range')             # <<<<<<<<<<<<<<
  *         return self.stats[0][index]
  * 
  */
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-  __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_41));
-  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_42));
+  __pyx_k_tuple_41 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_41)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(__pyx_k_tuple_41);
+  __Pyx_INCREF(((PyObject *)__pyx_kp_s_40));
+  PyTuple_SET_ITEM(__pyx_k_tuple_41, 0, ((PyObject *)__pyx_kp_s_40));
+  __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_40));
+  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_41));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":84
+  /* "/home/vchahune/tools/cdec/python/src/mteval.pxi":84
  *     def __getitem__(self,int k):
  *         if not 0 <= k < self.cs.size():
  *             raise IndexError('candidate set index out of range')             # <<<<<<<<<<<<<<
  *         cdef Candidate candidate = Candidate()
  *         candidate.candidate = &self.cs[0][k]
  */
-  __pyx_k_tuple_44 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_44)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  PyTuple_SET_ITEM(__pyx_k_tuple_44, 0, ((PyObject *)__pyx_kp_s_43));
-  __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_43));
-  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_44));
+  __pyx_k_tuple_43 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_43)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __Pyx_INCREF(((PyObject *)__pyx_kp_s_42));
+  PyTuple_SET_ITEM(__pyx_k_tuple_43, 0, ((PyObject *)__pyx_kp_s_42));
+  __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_42));
+  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_43));
 
-  /* "_cdec.pyx":50
- *         """
+  /* "_cdec.pyx":52
+ *         Create a decoder using a given configuration. Formalism is required."""
  *         if config_str is None:
  *             formalism = config.get('formalism', None)             # <<<<<<<<<<<<<<
  *             if formalism not in ('scfg', 'fst', 'lextrans', 'pb',
  *                     'csplit', 'tagger', 'lexalign'):
  */
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-  __Pyx_GOTREF(__pyx_k_tuple_47);
+  __pyx_k_tuple_46 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_46)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(__pyx_k_tuple_46);
   __Pyx_INCREF(((PyObject *)__pyx_n_s__formalism));
-  PyTuple_SET_ITEM(__pyx_k_tuple_47, 0, ((PyObject *)__pyx_n_s__formalism));
+  PyTuple_SET_ITEM(__pyx_k_tuple_46, 0, ((PyObject *)__pyx_n_s__formalism));
   __Pyx_GIVEREF(((PyObject *)__pyx_n_s__formalism));
   __Pyx_INCREF(Py_None);
-  PyTuple_SET_ITEM(__pyx_k_tuple_47, 1, Py_None);
+  PyTuple_SET_ITEM(__pyx_k_tuple_46, 1, Py_None);
   __Pyx_GIVEREF(Py_None);
-  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_47));
+  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_46));
 
-  /* "_cdec.pyx":90
+  /* "_cdec.pyx":93
  *         with open(weights) as fp:
  *             for line in fp:
  *                 if line.strip().startswith('#'): continue             # <<<<<<<<<<<<<<
  *                 fname, value = line.split()
  *                 self.weights[fname.strip()] = float(value)
  */
-  __pyx_k_tuple_51 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_51)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 90; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __Pyx_INCREF(((PyObject *)__pyx_kp_s_50));
-  PyTuple_SET_ITEM(__pyx_k_tuple_51, 0, ((PyObject *)__pyx_kp_s_50));
-  __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_50));
-  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_51));
+  __pyx_k_tuple_50 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_50)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 93; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(__pyx_k_tuple_50);
+  __Pyx_INCREF(((PyObject *)__pyx_kp_s_49));
+  PyTuple_SET_ITEM(__pyx_k_tuple_50, 0, ((PyObject *)__pyx_kp_s_49));
+  __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_49));
+  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_50));
 
-  /* "_cdec.pyx":88
- * 
+  /* "_cdec.pyx":91
  *     def read_weights(self, weights):
+ *         """decoder.read_weights(filename): Read decoder weights from a file."""
  *         with open(weights) as fp:             # <<<<<<<<<<<<<<
  *             for line in fp:
  *                 if line.strip().startswith('#'): continue
  */
-  __pyx_k_tuple_52 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_52)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_GOTREF(__pyx_k_tuple_52);
+  __pyx_k_tuple_51 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_51)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 91; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(__pyx_k_tuple_51);
   __Pyx_INCREF(Py_None);
-  PyTuple_SET_ITEM(__pyx_k_tuple_52, 0, Py_None);
+  PyTuple_SET_ITEM(__pyx_k_tuple_51, 0, Py_None);
   __Pyx_GIVEREF(Py_None);
   __Pyx_INCREF(Py_None);
-  PyTuple_SET_ITEM(__pyx_k_tuple_52, 1, Py_None);
+  PyTuple_SET_ITEM(__pyx_k_tuple_51, 1, Py_None);
   __Pyx_GIVEREF(Py_None);
   __Pyx_INCREF(Py_None);
-  PyTuple_SET_ITEM(__pyx_k_tuple_52, 2, Py_None);
+  PyTuple_SET_ITEM(__pyx_k_tuple_51, 2, Py_None);
   __Pyx_GIVEREF(Py_None);
-  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_52));
+  __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_51));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":5
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":5
  * import cdec.sa._sa as _sa
  * 
  * def _phrase(phrase):             # <<<<<<<<<<<<<<
  *     return ' '.join(w.encode('utf8') if isinstance(w, unicode) else str(w) for w in phrase)
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+  if (__Pyx_SetAttrString(__pyx_m, "TRule", (PyObject *)&__pyx_type_5_cdec_TRule) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_5_cdec_TRule = &__pyx_type_5_cdec_TRule;
   __pyx_type_5_cdec_MRule.tp_base = __pyx_ptype_5_cdec_TRule;
-  if (PyType_Ready(&__pyx_type_5_cdec_MRule) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 169; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  if (__Pyx_SetAttrString(__pyx_m, "MRule", (PyObject *)&__pyx_type_5_cdec_MRule) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 169; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_5_cdec_MRule) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 177; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  #if CYTHON_COMPILING_IN_CPYTHON
+  {
+    PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5_cdec_MRule, "__init__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 177; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
+      __pyx_wrapperbase_5_cdec_5MRule___init__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+      __pyx_wrapperbase_5_cdec_5MRule___init__.doc = __pyx_doc_5_cdec_5MRule___init__;
+      ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5_cdec_5MRule___init__;
+    }
+  }
+  #endif
+  if (__Pyx_SetAttrString(__pyx_m, "MRule", (PyObject *)&__pyx_type_5_cdec_MRule) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 177; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_5_cdec_MRule = &__pyx_type_5_cdec_MRule;
-  if (PyType_Ready(&__pyx_type_5_cdec_Grammar) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  if (__Pyx_SetAttrString(__pyx_m, "Grammar", (PyObject *)&__pyx_type_5_cdec_Grammar) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_5_cdec_Grammar) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (__Pyx_SetAttrString(__pyx_m, "Grammar", (PyObject *)&__pyx_type_5_cdec_Grammar) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_5_cdec_Grammar = &__pyx_type_5_cdec_Grammar;
   __pyx_type_5_cdec_TextGrammar.tp_base = __pyx_ptype_5_cdec_Grammar;
-  if (PyType_Ready(&__pyx_type_5_cdec_TextGrammar) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 204; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  if (__Pyx_SetAttrString(__pyx_m, "TextGrammar", (PyObject *)&__pyx_type_5_cdec_TextGrammar) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 204; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_5_cdec_TextGrammar) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  #if CYTHON_COMPILING_IN_CPYTHON
+  {
+    PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5_cdec_TextGrammar, "__init__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
+      __pyx_wrapperbase_5_cdec_11TextGrammar___init__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+      __pyx_wrapperbase_5_cdec_11TextGrammar___init__.doc = __pyx_doc_5_cdec_11TextGrammar___init__;
+      ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5_cdec_11TextGrammar___init__;
+    }
+  }
+  #endif
+  if (__Pyx_SetAttrString(__pyx_m, "TextGrammar", (PyObject *)&__pyx_type_5_cdec_TextGrammar) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_5_cdec_TextGrammar = &__pyx_type_5_cdec_TextGrammar;
+  __pyx_vtabptr_5_cdec_Hypergraph = &__pyx_vtable_5_cdec_Hypergraph;
+  __pyx_vtable_5_cdec_Hypergraph._rng = (MT19937 *(*)(struct __pyx_obj_5_cdec_Hypergraph *))__pyx_f_5_cdec_10Hypergraph__rng;
   if (PyType_Ready(&__pyx_type_5_cdec_Hypergraph) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 4; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (__Pyx_SetVtable(__pyx_type_5_cdec_Hypergraph.tp_dict, __pyx_vtabptr_5_cdec_Hypergraph) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 4; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   if (__Pyx_SetAttrString(__pyx_m, "Hypergraph", (PyObject *)&__pyx_type_5_cdec_Hypergraph) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 4; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_5_cdec_Hypergraph = &__pyx_type_5_cdec_Hypergraph;
   __pyx_vtabptr_5_cdec_HypergraphEdge = &__pyx_vtable_5_cdec_HypergraphEdge;
   __pyx_vtable_5_cdec_HypergraphEdge.init = (PyObject *(*)(struct __pyx_obj_5_cdec_HypergraphEdge *, Hypergraph *, unsigned int))__pyx_f_5_cdec_14HypergraphEdge_init;
-  if (PyType_Ready(&__pyx_type_5_cdec_HypergraphEdge) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 147; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  if (__Pyx_SetVtable(__pyx_type_5_cdec_HypergraphEdge.tp_dict, __pyx_vtabptr_5_cdec_HypergraphEdge) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 147; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  if (__Pyx_SetAttrString(__pyx_m, "HypergraphEdge", (PyObject *)&__pyx_type_5_cdec_HypergraphEdge) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 147; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_5_cdec_HypergraphEdge) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 191; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (__Pyx_SetVtable(__pyx_type_5_cdec_HypergraphEdge.tp_dict, __pyx_vtabptr_5_cdec_HypergraphEdge) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 191; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (__Pyx_SetAttrString(__pyx_m, "HypergraphEdge", (PyObject *)&__pyx_type_5_cdec_HypergraphEdge) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 191; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_5_cdec_HypergraphEdge = &__pyx_type_5_cdec_HypergraphEdge;
   __pyx_vtabptr_5_cdec_HypergraphNode = &__pyx_vtable_5_cdec_HypergraphNode;
   __pyx_vtable_5_cdec_HypergraphNode.init = (PyObject *(*)(struct __pyx_obj_5_cdec_HypergraphNode *, Hypergraph *, unsigned int))__pyx_f_5_cdec_14HypergraphNode_init;
-  if (PyType_Ready(&__pyx_type_5_cdec_HypergraphNode) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  if (__Pyx_SetVtable(__pyx_type_5_cdec_HypergraphNode.tp_dict, __pyx_vtabptr_5_cdec_HypergraphNode) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  if (__Pyx_SetAttrString(__pyx_m, "HypergraphNode", (PyObject *)&__pyx_type_5_cdec_HypergraphNode) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_5_cdec_HypergraphNode) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 237; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (__Pyx_SetVtable(__pyx_type_5_cdec_HypergraphNode.tp_dict, __pyx_vtabptr_5_cdec_HypergraphNode) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 237; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (__Pyx_SetAttrString(__pyx_m, "HypergraphNode", (PyObject *)&__pyx_type_5_cdec_HypergraphNode) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 237; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_5_cdec_HypergraphNode = &__pyx_type_5_cdec_HypergraphNode;
   if (PyType_Ready(&__pyx_type_5_cdec_Lattice) < 0) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 3; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  #if CYTHON_COMPILING_IN_CPYTHON
+  {
+    PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5_cdec_Lattice, "__init__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 3; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
+      __pyx_wrapperbase_5_cdec_7Lattice_2__init__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+      __pyx_wrapperbase_5_cdec_7Lattice_2__init__.doc = __pyx_doc_5_cdec_7Lattice_2__init__;
+      ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5_cdec_7Lattice_2__init__;
+    }
+  }
+  #endif
   if (__Pyx_SetAttrString(__pyx_m, "Lattice", (PyObject *)&__pyx_type_5_cdec_Lattice) < 0) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 3; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_5_cdec_Lattice = &__pyx_type_5_cdec_Lattice;
   if (PyType_Ready(&__pyx_type_5_cdec_Candidate) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 12; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -28136,72 +29247,89 @@ PyMODINIT_FUNC PyInit__cdec(void)
   if (PyType_Ready(&__pyx_type_5_cdec_CandidateSet) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   if (__Pyx_SetAttrString(__pyx_m, "CandidateSet", (PyObject *)&__pyx_type_5_cdec_CandidateSet) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_5_cdec_CandidateSet = &__pyx_type_5_cdec_CandidateSet;
-  if (PyType_Ready(&__pyx_type_5_cdec_SegmentEvaluator) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 98; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  if (__Pyx_SetAttrString(__pyx_m, "SegmentEvaluator", (PyObject *)&__pyx_type_5_cdec_SegmentEvaluator) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 98; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_5_cdec_SegmentEvaluator) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 100; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (__Pyx_SetAttrString(__pyx_m, "SegmentEvaluator", (PyObject *)&__pyx_type_5_cdec_SegmentEvaluator) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 100; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_5_cdec_SegmentEvaluator = &__pyx_type_5_cdec_SegmentEvaluator;
-  if (PyType_Ready(&__pyx_type_5_cdec_Scorer) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  if (__Pyx_SetAttrString(__pyx_m, "Scorer", (PyObject *)&__pyx_type_5_cdec_Scorer) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_5_cdec_Scorer) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (__Pyx_SetAttrString(__pyx_m, "Scorer", (PyObject *)&__pyx_type_5_cdec_Scorer) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_5_cdec_Scorer = &__pyx_type_5_cdec_Scorer;
-  if (PyType_Ready(&__pyx_type_5_cdec_Metric) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  if (__Pyx_SetAttrString(__pyx_m, "Metric", (PyObject *)&__pyx_type_5_cdec_Metric) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_5_cdec_Metric) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 176; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (__Pyx_SetAttrString(__pyx_m, "Metric", (PyObject *)&__pyx_type_5_cdec_Metric) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 176; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_5_cdec_Metric = &__pyx_type_5_cdec_Metric;
-  if (PyType_Ready(&__pyx_type_5_cdec_Decoder) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  if (__Pyx_SetAttrString(__pyx_m, "Decoder", (PyObject *)&__pyx_type_5_cdec_Decoder) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_5_cdec_Decoder) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  #if CYTHON_COMPILING_IN_CPYTHON
+  {
+    PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5_cdec_Decoder, "__init__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
+      __pyx_wrapperbase_5_cdec_7Decoder___init__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+      __pyx_wrapperbase_5_cdec_7Decoder___init__.doc = __pyx_doc_5_cdec_7Decoder___init__;
+      ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5_cdec_7Decoder___init__;
+    }
+  }
+  #endif
+  if (__Pyx_SetAttrString(__pyx_m, "Decoder", (PyObject *)&__pyx_type_5_cdec_Decoder) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_5_cdec_Decoder = &__pyx_type_5_cdec_Decoder;
-  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct____iter__) < 0) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct____iter__) < 0) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_5_cdec___pyx_scope_struct____iter__ = &__pyx_type_5_cdec___pyx_scope_struct____iter__;
-  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_1___iter__) < 0) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_1___iter__) < 0) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_5_cdec___pyx_scope_struct_1___iter__ = &__pyx_type_5_cdec___pyx_scope_struct_1___iter__;
   if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_2__phrase) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 5; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_5_cdec___pyx_scope_struct_2__phrase = &__pyx_type_5_cdec___pyx_scope_struct_2__phrase;
   if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_3_genexpr) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_5_cdec___pyx_scope_struct_3_genexpr = &__pyx_type_5_cdec___pyx_scope_struct_3_genexpr;
-  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_4___get__) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_4___get__) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_5_cdec___pyx_scope_struct_4___get__ = &__pyx_type_5_cdec___pyx_scope_struct_4___get__;
-  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_5___str__) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 164; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_5___str__) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_5_cdec___pyx_scope_struct_5___str__ = &__pyx_type_5_cdec___pyx_scope_struct_5___str__;
-  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_6_genexpr) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 165; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_6_genexpr) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_5_cdec___pyx_scope_struct_6_genexpr = &__pyx_type_5_cdec___pyx_scope_struct_6_genexpr;
-  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_7___iter__) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_7___iter__) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 199; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_5_cdec___pyx_scope_struct_7___iter__ = &__pyx_type_5_cdec___pyx_scope_struct_7___iter__;
-  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_8_kbest) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_8_kbest) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_5_cdec___pyx_scope_struct_8_kbest = &__pyx_type_5_cdec___pyx_scope_struct_8_kbest;
-  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_9_kbest_trees) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_9_kbest_trees) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_5_cdec___pyx_scope_struct_9_kbest_trees = &__pyx_type_5_cdec___pyx_scope_struct_9_kbest_trees;
-  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_10_kbest_features) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_10_kbest_features) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_5_cdec___pyx_scope_struct_10_kbest_features = &__pyx_type_5_cdec___pyx_scope_struct_10_kbest_features;
-  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_11_sample) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_11_sample) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 92; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_12___get__) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 113; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_ptype_5_cdec___pyx_scope_struct_12___get__ = &__pyx_type_5_cdec___pyx_scope_struct_12___get__;
-  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_13___get__) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 119; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_12_sample_trees) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_5_cdec___pyx_scope_struct_12_sample_trees = &__pyx_type_5_cdec___pyx_scope_struct_12_sample_trees;
+  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_13___get__) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_14___get__) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 167; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_14___get__) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 162; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_15___get__) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_15___get__) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 211; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_5_cdec___pyx_scope_struct_15___get__ = &__pyx_type_5_cdec___pyx_scope_struct_15___get__;
-  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_16___get__) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_16___get__) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __pyx_ptype_5_cdec___pyx_scope_struct_19_lines = &__pyx_type_5_cdec___pyx_scope_struct_19_lines;
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-  __pyx_ptype_5_cdec___pyx_scope_struct_20___iter__ = &__pyx_type_5_cdec___pyx_scope_struct_20___iter__;
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+  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_17___get__) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 253; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_5_cdec___pyx_scope_struct_17___get__ = &__pyx_type_5_cdec___pyx_scope_struct_17___get__;
+  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_18___iter__) < 0) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_5_cdec___pyx_scope_struct_18___iter__ = &__pyx_type_5_cdec___pyx_scope_struct_18___iter__;
+  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_19_todot) < 0) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_5_cdec___pyx_scope_struct_19_todot = &__pyx_type_5_cdec___pyx_scope_struct_19_todot;
+  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_20_lines) < 0) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_5_cdec___pyx_scope_struct_20_lines = &__pyx_type_5_cdec___pyx_scope_struct_20_lines;
+  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_21___iter__) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_22__make_config) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_ptype_5_cdec___pyx_scope_struct_22__make_config = &__pyx_type_5_cdec___pyx_scope_struct_22__make_config;
-  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_23___cinit__) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_ptype_5_cdec___pyx_scope_struct_23___cinit__ = &__pyx_type_5_cdec___pyx_scope_struct_23___cinit__;
-  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_24_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_ptype_5_cdec___pyx_scope_struct_24_genexpr = &__pyx_type_5_cdec___pyx_scope_struct_24_genexpr;
+  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_22___iter__) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 90; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_5_cdec___pyx_scope_struct_22___iter__ = &__pyx_type_5_cdec___pyx_scope_struct_22___iter__;
+  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_23__make_config) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_5_cdec___pyx_scope_struct_23__make_config = &__pyx_type_5_cdec___pyx_scope_struct_23__make_config;
+  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_24___init__) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_5_cdec___pyx_scope_struct_24___init__ = &__pyx_type_5_cdec___pyx_scope_struct_24___init__;
+  if (PyType_Ready(&__pyx_type_5_cdec___pyx_scope_struct_25_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_5_cdec___pyx_scope_struct_25_genexpr = &__pyx_type_5_cdec___pyx_scope_struct_25_genexpr;
   /*--- Type import code ---*/
-  __pyx_ptype_4cdec_2sa_3_sa_Phrase = __Pyx_ImportType("cdec.sa._sa", "Phrase", sizeof(struct __pyx_obj_4cdec_2sa_3_sa_Phrase), 1); if (unlikely(!__pyx_ptype_4cdec_2sa_3_sa_Phrase)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __pyx_ptype_4cdec_2sa_3_sa_Rule = __Pyx_ImportType("cdec.sa._sa", "Rule", sizeof(struct __pyx_obj_4cdec_2sa_3_sa_Rule), 1); if (unlikely(!__pyx_ptype_4cdec_2sa_3_sa_Rule)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_4cdec_2sa_3_sa_FloatList = __Pyx_ImportType("cdec.sa._sa", "FloatList", sizeof(struct __pyx_obj_4cdec_2sa_3_sa_FloatList), 1); if (unlikely(!__pyx_ptype_4cdec_2sa_3_sa_FloatList)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 3; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_vtabptr_4cdec_2sa_3_sa_FloatList = (struct __pyx_vtabstruct_4cdec_2sa_3_sa_FloatList*)__Pyx_GetVtable(__pyx_ptype_4cdec_2sa_3_sa_FloatList->tp_dict); if (unlikely(!__pyx_vtabptr_4cdec_2sa_3_sa_FloatList)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 3; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_4cdec_2sa_3_sa_IntList = __Pyx_ImportType("cdec.sa._sa", "IntList", sizeof(struct __pyx_obj_4cdec_2sa_3_sa_IntList), 1); if (unlikely(!__pyx_ptype_4cdec_2sa_3_sa_IntList)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 12; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_vtabptr_4cdec_2sa_3_sa_IntList = (struct __pyx_vtabstruct_4cdec_2sa_3_sa_IntList*)__Pyx_GetVtable(__pyx_ptype_4cdec_2sa_3_sa_IntList->tp_dict); if (unlikely(!__pyx_vtabptr_4cdec_2sa_3_sa_IntList)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 12; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_4cdec_2sa_3_sa_FeatureVector = __Pyx_ImportType("cdec.sa._sa", "FeatureVector", sizeof(struct __pyx_obj_4cdec_2sa_3_sa_FeatureVector), 1); if (unlikely(!__pyx_ptype_4cdec_2sa_3_sa_FeatureVector)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_4cdec_2sa_3_sa_Phrase = __Pyx_ImportType("cdec.sa._sa", "Phrase", sizeof(struct __pyx_obj_4cdec_2sa_3_sa_Phrase), 1); if (unlikely(!__pyx_ptype_4cdec_2sa_3_sa_Phrase)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_vtabptr_4cdec_2sa_3_sa_Phrase = (struct __pyx_vtabstruct_4cdec_2sa_3_sa_Phrase*)__Pyx_GetVtable(__pyx_ptype_4cdec_2sa_3_sa_Phrase->tp_dict); if (unlikely(!__pyx_vtabptr_4cdec_2sa_3_sa_Phrase)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_4cdec_2sa_3_sa_Rule = __Pyx_ImportType("cdec.sa._sa", "Rule", sizeof(struct __pyx_obj_4cdec_2sa_3_sa_Rule), 1); if (unlikely(!__pyx_ptype_4cdec_2sa_3_sa_Rule)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -28212,7 +29340,7 @@ PyMODINIT_FUNC PyInit__cdec(void)
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   /*--- Execution code ---*/
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":3
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":3
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  * import cdec.sa._sa as _sa             # <<<<<<<<<<<<<<
@@ -28221,16 +29349,16 @@ PyMODINIT_FUNC PyInit__cdec(void)
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-  __Pyx_INCREF(((PyObject *)__pyx_n_s_55));
-  PyList_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_n_s_55));
-  __Pyx_GIVEREF(((PyObject *)__pyx_n_s_55));
-  __pyx_t_3 = __Pyx_Import(((PyObject *)__pyx_n_s_54), ((PyObject *)__pyx_t_2), -1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 3; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_INCREF(((PyObject *)__pyx_n_s_54));
+  PyList_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_n_s_54));
+  __Pyx_GIVEREF(((PyObject *)__pyx_n_s_54));
+  __pyx_t_3 = __Pyx_Import(((PyObject *)__pyx_n_s_53), ((PyObject *)__pyx_t_2), -1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 3; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/grammar.pxi":5
+  /* "/home/vchahune/tools/cdec/python/src/grammar.pxi":5
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  * 
  * def _phrase(phrase):             # <<<<<<<<<<<<<<
@@ -28242,37 +29370,37 @@ PyMODINIT_FUNC PyInit__cdec(void)
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   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":190
+  /* "/home/vchahune/tools/cdec/python/src/mteval.pxi":194
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  * BLEU = Scorer('IBM_BLEU')             # <<<<<<<<<<<<<<
  * TER = Scorer('TER')
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-  __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5_cdec_Scorer)), ((PyObject *)__pyx_k_tuple_59), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 190; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5_cdec_Scorer)), ((PyObject *)__pyx_k_tuple_58), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 194; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  if (PyObject_SetAttr(__pyx_m, __pyx_n_s__BLEU, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 190; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyObject_SetAttr(__pyx_m, __pyx_n_s__BLEU, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 194; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":191
+  /* "/home/vchahune/tools/cdec/python/src/mteval.pxi":195
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  * CER = Scorer('CER')
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-  __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5_cdec_Scorer)), ((PyObject *)__pyx_k_tuple_60), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 191; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5_cdec_Scorer)), ((PyObject *)__pyx_k_tuple_59), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_3);
-  if (PyObject_SetAttr(__pyx_m, __pyx_n_s__TER, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 191; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyObject_SetAttr(__pyx_m, __pyx_n_s__TER, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/mteval.pxi":192
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-  __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5_cdec_Scorer)), ((PyObject *)__pyx_k_tuple_61), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 192; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5_cdec_Scorer)), ((PyObject *)__pyx_k_tuple_60), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_3);
-  if (PyObject_SetAttr(__pyx_m, __pyx_n_s__CER, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 192; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyObject_SetAttr(__pyx_m, __pyx_n_s__CER, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
   /* "_cdec.pyx":22
@@ -28319,7 +29447,7 @@ PyMODINIT_FUNC PyInit__cdec(void)
  * class InvalidConfig(Exception): pass
  * class ParseFailed(Exception): pass             # <<<<<<<<<<<<<<
  * 
- * def _make_config(config):
+ * def set_silent(yn):
  */
   __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(((PyObject *)__pyx_t_3));
@@ -28338,13 +29466,25 @@ PyMODINIT_FUNC PyInit__cdec(void)
   /* "_cdec.pyx":28
  * class ParseFailed(Exception): pass
  * 
+ * def set_silent(yn):             # <<<<<<<<<<<<<<
+ *     """set_silent(bool): Configure the verbosity of cdec."""
+ *     SetSilent(yn)
+ */
+  __pyx_t_3 = PyCFunction_NewEx(&__pyx_mdef_5_cdec_3set_silent, NULL, __pyx_n_s___cdec); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(__pyx_t_3);
+  if (PyObject_SetAttr(__pyx_m, __pyx_n_s__set_silent, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+
+  /* "_cdec.pyx":32
+ *     SetSilent(yn)
+ * 
  * def _make_config(config):             # <<<<<<<<<<<<<<
  *     for key, value in config.items():
  *         if isinstance(value, dict):
  */
-  __pyx_t_3 = PyCFunction_NewEx(&__pyx_mdef_5_cdec_3_make_config, NULL, __pyx_n_s___cdec); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = PyCFunction_NewEx(&__pyx_mdef_5_cdec_5_make_config, NULL, __pyx_n_s___cdec); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_3);
-  if (PyObject_SetAttr(__pyx_m, __pyx_n_s___make_config, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyObject_SetAttr(__pyx_m, __pyx_n_s___make_config, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
   /* "_cdec.pyx":1
@@ -28357,11 +29497,11 @@ PyMODINIT_FUNC PyInit__cdec(void)
   if (PyObject_SetAttr(__pyx_m, __pyx_n_s____test__, ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
 
-  /* "string.to_py":25
+  /* "string.from_py":11
  * 
- * @cname("__pyx_convert_string_to_py_")
- * cdef object __pyx_convert_string_to_py_(string& s):             # <<<<<<<<<<<<<<
- *     return s.data()[:s.size()]
+ * @cname("__pyx_convert_string_from_py_")
+ * cdef string __pyx_convert_string_from_py_(object o) except *:             # <<<<<<<<<<<<<<
+ *     return string(<char*>o, len(o))
  * 
  */
   goto __pyx_L0;
@@ -28452,33 +29592,38 @@ static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyOb
 static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
                         CYTHON_UNUSED PyObject *cause) {
     Py_XINCREF(type);
-    Py_XINCREF(value);
-    Py_XINCREF(tb);
-    if (tb == Py_None) {
-        Py_DECREF(tb);
-        tb = 0;
-    }
-    else if (tb != NULL && !PyTraceBack_Check(tb)) {
-        PyErr_SetString(PyExc_TypeError,
-            "raise: arg 3 must be a traceback or None");
-        goto raise_error;
-    }
-    if (value == NULL) {
-        value = Py_None;
+    if (!value || value == Py_None)
+        value = NULL;
+    else
         Py_INCREF(value);
+    if (!tb || tb == Py_None)
+        tb = NULL;
+    else {
+        Py_INCREF(tb);
+        if (!PyTraceBack_Check(tb)) {
+            PyErr_SetString(PyExc_TypeError,
+                "raise: arg 3 must be a traceback or None");
+            goto raise_error;
+        }
     }
     #if PY_VERSION_HEX < 0x02050000
-    if (!PyClass_Check(type))
+    if (PyClass_Check(type)) {
     #else
-    if (!PyType_Check(type))
+    if (PyType_Check(type)) {
     #endif
-    {
-        if (value != Py_None) {
+#if CYTHON_COMPILING_IN_PYPY
+        if (!value) {
+            Py_INCREF(Py_None);
+            value = Py_None;
+        }
+#endif
+        PyErr_NormalizeException(&type, &value, &tb);
+    } else {
+        if (value) {
             PyErr_SetString(PyExc_TypeError,
                 "instance exception may not have a separate value");
             goto raise_error;
         }
-        Py_DECREF(value);
         value = type;
         #if PY_VERSION_HEX < 0x02050000
             if (PyInstance_Check(type)) {
@@ -28511,6 +29656,7 @@ raise_error:
 }
 #else /* Python 3+ */
 static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
+    PyObject* owned_instance = NULL;
     if (tb == Py_None) {
         tb = 0;
     } else if (tb && !PyTraceBack_Check(tb)) {
@@ -28528,12 +29674,36 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
         }
         value = type;
         type = (PyObject*) Py_TYPE(value);
-    } else if (!PyExceptionClass_Check(type)) {
+    } else if (PyExceptionClass_Check(type)) {
+        PyObject *args;
+        if (!value)
+            args = PyTuple_New(0);
+        else if (PyTuple_Check(value)) {
+            Py_INCREF(value);
+            args = value;
+        }
+        else
+            args = PyTuple_Pack(1, value);
+        if (!args)
+            goto bad;
+        owned_instance = PyEval_CallObject(type, args);
+        Py_DECREF(args);
+        if (!owned_instance)
+            goto bad;
+        value = owned_instance;
+        if (!PyExceptionInstance_Check(value)) {
+            PyErr_Format(PyExc_TypeError,
+                         "calling %R should have returned an instance of "
+                         "BaseException, not %R",
+                         type, Py_TYPE(value));
+            goto bad;
+        }
+    } else {
         PyErr_SetString(PyExc_TypeError,
             "raise: exception class must be a subclass of BaseException");
         goto bad;
     }
-    if (cause) {
+    if (cause && cause != Py_None) {
         PyObject *fixed_cause;
         if (PyExceptionClass_Check(cause)) {
             fixed_cause = PyObject_CallObject(cause, NULL);
@@ -28550,9 +29720,6 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
                             "BaseException");
             goto bad;
         }
-        if (!value) {
-            value = PyObject_CallObject(type, NULL);
-        }
         PyException_SetCause(value, fixed_cause);
     }
     PyErr_SetObject(type, value);
@@ -28566,6 +29733,7 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
         }
     }
 bad:
+    Py_XDECREF(owned_instance);
     return;
 }
 #endif
@@ -28590,7 +29758,7 @@ static void __Pyx_RaiseArgtupleInvalid(
         more_or_less = "exactly";
     }
     PyErr_Format(PyExc_TypeError,
-                 "%s() takes %s %" PY_FORMAT_SIZE_T "d positional argument%s (%" PY_FORMAT_SIZE_T "d given)",
+                 "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" CYTHON_FORMAT_SSIZE_T "d given)",
                  func_name, more_or_less, num_expected,
                  (num_expected == 1) ? "" : "s", num_found);
 }
@@ -28610,10 +29778,9 @@ static CYTHON_INLINE int __Pyx_CheckKeywordStrings(
     while (PyDict_Next(kwdict, &pos, &key, 0)) {
         #if PY_MAJOR_VERSION < 3
         if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key)))
-        #else
-        if (unlikely(!PyUnicode_Check(key)))
         #endif
-            goto invalid_keyword_type;
+            if (unlikely(!PyUnicode_Check(key)))
+                goto invalid_keyword_type;
     }
     if ((!kw_allowed) && unlikely(key))
         goto invalid_keyword;
@@ -28680,7 +29847,7 @@ static void __Pyx_RaiseDoubleKeywordsError(
         "%s() got multiple values for keyword argument '%U'", func_name, kw_name);
         #else
         "%s() got multiple values for keyword argument '%s'", func_name,
-        PyString_AS_STRING(kw_name));
+        PyString_AsString(kw_name));
         #endif
 }
 
@@ -28701,48 +29868,72 @@ static int __Pyx_ParseOptionalKeywords(
         while (*name && (**name != key)) name++;
         if (*name) {
             values[name-argnames] = value;
-        } else {
-            #if PY_MAJOR_VERSION < 3
-            if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) {
-            #else
-            if (unlikely(!PyUnicode_Check(key))) {
-            #endif
-                goto invalid_keyword_type;
-            } else {
-                for (name = first_kw_arg; *name; name++) {
-                    #if PY_MAJOR_VERSION >= 3
-                    if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
-                        PyUnicode_Compare(**name, key) == 0) break;
-                    #else
-                    if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
-                        _PyString_Eq(**name, key)) break;
-                    #endif
-                }
-                if (*name) {
+            continue;
+        }
+        name = first_kw_arg;
+        #if PY_MAJOR_VERSION < 3
+        if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) {
+            while (*name) {
+                if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key))
+                        && _PyString_Eq(**name, key)) {
                     values[name-argnames] = value;
-                } else {
-                    for (name=argnames; name != first_kw_arg; name++) {
-                        if (**name == key) goto arg_passed_twice;
-                        #if PY_MAJOR_VERSION >= 3
-                        if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
-                            PyUnicode_Compare(**name, key) == 0) goto arg_passed_twice;
-                        #else
-                        if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
-                            _PyString_Eq(**name, key)) goto arg_passed_twice;
-                        #endif
-                    }
-                    if (kwds2) {
-                        if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
-                    } else {
-                        goto invalid_keyword;
+                    break;
+                }
+                name++;
+            }
+            if (*name) continue;
+            else {
+                PyObject*** argname = argnames;
+                while (argname != first_kw_arg) {
+                    if ((**argname == key) || (
+                            (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key))
+                             && _PyString_Eq(**argname, key))) {
+                        goto arg_passed_twice;
                     }
+                    argname++;
+                }
+            }
+        } else
+        #endif
+        if (likely(PyUnicode_Check(key))) {
+            while (*name) {
+                int cmp = (**name == key) ? 0 :
+                #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
+                    (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
+                #endif
+                    PyUnicode_Compare(**name, key);
+                if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
+                if (cmp == 0) {
+                    values[name-argnames] = value;
+                    break;
                 }
+                name++;
             }
+            if (*name) continue;
+            else {
+                PyObject*** argname = argnames;
+                while (argname != first_kw_arg) {
+                    int cmp = (**argname == key) ? 0 :
+                    #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
+                        (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
+                    #endif
+                        PyUnicode_Compare(**argname, key);
+                    if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
+                    if (cmp == 0) goto arg_passed_twice;
+                    argname++;
+                }
+            }
+        } else
+            goto invalid_keyword_type;
+        if (kwds2) {
+            if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
+        } else {
+            goto invalid_keyword;
         }
     }
     return 0;
 arg_passed_twice:
-    __Pyx_RaiseDoubleKeywordsError(function_name, **name);
+    __Pyx_RaiseDoubleKeywordsError(function_name, key);
     goto bad;
 invalid_keyword_type:
     PyErr_Format(PyExc_TypeError,
@@ -28763,12 +29954,12 @@ bad:
 
 static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
     PyErr_Format(PyExc_ValueError,
-                 "too many values to unpack (expected %" PY_FORMAT_SIZE_T "d)", expected);
+                 "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected);
 }
 
 static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
     PyErr_Format(PyExc_ValueError,
-                 "need more than %" PY_FORMAT_SIZE_T "d value%s to unpack",
+                 "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack",
                  index, (index == 1) ? "" : "s");
 }
 
@@ -29136,9 +30327,8 @@ static CYTHON_INLINE WordID __Pyx_PyInt_from_py_WordID(PyObject* x) {
     }
 }
 
-static PyObject* __Pyx_Globals() {
+static PyObject* __Pyx_Globals(void) {
     Py_ssize_t i;
-    /*PyObject *d;*/
     PyObject *names = NULL;
     PyObject *globals = PyObject_GetAttrString(__pyx_m, "__dict__");
     if (!globals) {
@@ -29149,25 +30339,36 @@ static PyObject* __Pyx_Globals() {
     names = PyObject_Dir(__pyx_m);
     if (!names)
         goto bad;
-    for (i = 0; i < PyList_GET_SIZE(names); i++) {
+    for (i = PyList_GET_SIZE(names)-1; i >= 0; i--) {
+#if CYTHON_COMPILING_IN_PYPY
+        PyObject* name = PySequence_GetItem(names, i);
+        if (!name)
+            goto bad;
+#else
         PyObject* name = PyList_GET_ITEM(names, i);
+#endif
         if (!PyDict_Contains(globals, name)) {
-            PyObject* value = PyObject_GetAttr(__pyx_m, PyList_GET_ITEM(names, i));
-            if (!value)
+            PyObject* value = PyObject_GetAttr(__pyx_m, name);
+            if (!value) {
+#if CYTHON_COMPILING_IN_PYPY
+                Py_DECREF(name);
+#endif
                 goto bad;
+            }
             if (PyDict_SetItem(globals, name, value) < 0) {
+#if CYTHON_COMPILING_IN_PYPY
+                Py_DECREF(name);
+#endif
                 Py_DECREF(value);
                 goto bad;
             }
         }
+#if CYTHON_COMPILING_IN_PYPY
+        Py_DECREF(name);
+#endif
     }
     Py_DECREF(names);
     return globals;
-    /*
-    d = PyDictProxy_New(globals);
-    Py_DECREF(globals);
-    return d;
-    */
 bad:
     Py_XDECREF(names);
     Py_XDECREF(globals);
@@ -29583,86 +30784,6 @@ static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyOb
     Py_INCREF(tuple);
 }
 
-static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) {
-#if CYTHON_COMPILING_IN_PYPY
-    return PyObject_RichCompareBool(s1, s2, equals);
-#else
-    if (s1 == s2) {
-        return (equals == Py_EQ);
-    } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) {
-        if (PyBytes_GET_SIZE(s1) != PyBytes_GET_SIZE(s2)) {
-            return (equals == Py_NE);
-        } else if (PyBytes_GET_SIZE(s1) == 1) {
-            if (equals == Py_EQ)
-                return (PyBytes_AS_STRING(s1)[0] == PyBytes_AS_STRING(s2)[0]);
-            else
-                return (PyBytes_AS_STRING(s1)[0] != PyBytes_AS_STRING(s2)[0]);
-        } else {
-            int result = memcmp(PyBytes_AS_STRING(s1), PyBytes_AS_STRING(s2), (size_t)PyBytes_GET_SIZE(s1));
-            return (equals == Py_EQ) ? (result == 0) : (result != 0);
-        }
-    } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) {
-        return (equals == Py_NE);
-    } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) {
-        return (equals == Py_NE);
-    } else {
-        int result;
-        PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
-        if (!py_result)
-            return -1;
-        result = __Pyx_PyObject_IsTrue(py_result);
-        Py_DECREF(py_result);
-        return result;
-    }
-#endif
-}
-
-static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
-#if CYTHON_COMPILING_IN_PYPY
-    return PyObject_RichCompareBool(s1, s2, equals);
-#else
-    if (s1 == s2) {
-        return (equals == Py_EQ);
-    } else if (PyUnicode_CheckExact(s1) & PyUnicode_CheckExact(s2)) {
-        #if CYTHON_PEP393_ENABLED
-        if ((PyUnicode_READY(s1) < 0) || (PyUnicode_READY(s2) < 0))
-            return -1;
-        if (PyUnicode_GET_LENGTH(s1) != PyUnicode_GET_LENGTH(s2)) {
-            return (equals == Py_NE);
-        } else if (PyUnicode_GET_LENGTH(s1) == 1) {
-            Py_UCS4 ch1 = PyUnicode_READ_CHAR(s1, 0);
-            Py_UCS4 ch2 = PyUnicode_READ_CHAR(s2, 0);
-            return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2);
-        #else
-        if (PyUnicode_GET_SIZE(s1) != PyUnicode_GET_SIZE(s2)) {
-            return (equals == Py_NE);
-        } else if (PyUnicode_GET_SIZE(s1) == 1) {
-            Py_UNICODE ch1 = PyUnicode_AS_UNICODE(s1)[0];
-            Py_UNICODE ch2 = PyUnicode_AS_UNICODE(s2)[0];
-            return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2);
-        #endif
-        } else {
-            int result = PyUnicode_Compare(s1, s2);
-            if ((result == -1) && unlikely(PyErr_Occurred()))
-                return -1;
-            return (equals == Py_EQ) ? (result == 0) : (result != 0);
-        }
-    } else if ((s1 == Py_None) & PyUnicode_CheckExact(s2)) {
-        return (equals == Py_NE);
-    } else if ((s2 == Py_None) & PyUnicode_CheckExact(s1)) {
-        return (equals == Py_NE);
-    } else {
-        int result;
-        PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
-        if (!py_result)
-            return -1;
-        result = __Pyx_PyObject_IsTrue(py_result);
-        Py_DECREF(py_result);
-        return result;
-    }
-#endif
-}
-
 static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) {
     const unsigned char neg_one = (unsigned char)-1, const_zero = 0;
     const int is_unsigned = neg_one > const_zero;
@@ -30063,25 +31184,6 @@ static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject*
     }
 }
 
-static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno,
-                                  CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename) {
-    PyObject *old_exc, *old_val, *old_tb;
-    PyObject *ctx;
-    __Pyx_ErrFetch(&old_exc, &old_val, &old_tb);
-    #if PY_MAJOR_VERSION < 3
-    ctx = PyString_FromString(name);
-    #else
-    ctx = PyUnicode_FromString(name);
-    #endif
-    __Pyx_ErrRestore(old_exc, old_val, old_tb);
-    if (!ctx) {
-        PyErr_WriteUnraisable(Py_None);
-    } else {
-        PyErr_WriteUnraisable(ctx);
-        Py_DECREF(ctx);
-    }
-}
-
 static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) {
     PyObject *tmp_type, *tmp_value, *tmp_tb;
 #if CYTHON_COMPILING_IN_CPYTHON
@@ -30504,7 +31606,7 @@ static PyMemberDef __pyx_Generator_memberlist[] = {
 #if PY_VERSION_HEX >= 0x02060000
      T_BOOL,
 #else
-     T_INT,
+     T_BYTE,
 #endif
      offsetof(__pyx_GeneratorObject, is_running),
      READONLY,
@@ -30602,6 +31704,25 @@ static int __pyx_Generator_init(void) {
     return 0;
 }
 
+static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno,
+                                  CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename) {
+    PyObject *old_exc, *old_val, *old_tb;
+    PyObject *ctx;
+    __Pyx_ErrFetch(&old_exc, &old_val, &old_tb);
+    #if PY_MAJOR_VERSION < 3
+    ctx = PyString_FromString(name);
+    #else
+    ctx = PyUnicode_FromString(name);
+    #endif
+    __Pyx_ErrRestore(old_exc, old_val, old_tb);
+    if (!ctx) {
+        PyErr_WriteUnraisable(Py_None);
+    } else {
+        PyErr_WriteUnraisable(ctx);
+        Py_DECREF(ctx);
+    }
+}
+
 static int __Pyx_check_binary_version(void) {
     char ctversion[4], rtversion[4];
     PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
@@ -30638,6 +31759,23 @@ bad:
     return -1;
 }
 
+#ifndef __PYX_HAVE_RT_ImportModule
+#define __PYX_HAVE_RT_ImportModule
+static PyObject *__Pyx_ImportModule(const char *name) {
+    PyObject *py_name = 0;
+    PyObject *py_module = 0;
+    py_name = __Pyx_PyIdentifier_FromString(name);
+    if (!py_name)
+        goto bad;
+    py_module = PyImport_Import(py_name);
+    Py_DECREF(py_name);
+    return py_module;
+bad:
+    Py_XDECREF(py_name);
+    return 0;
+}
+#endif
+
 #ifndef __PYX_HAVE_RT_ImportType
 #define __PYX_HAVE_RT_ImportType
 static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
@@ -30690,23 +31828,6 @@ bad:
 }
 #endif
 
-#ifndef __PYX_HAVE_RT_ImportModule
-#define __PYX_HAVE_RT_ImportModule
-static PyObject *__Pyx_ImportModule(const char *name) {
-    PyObject *py_name = 0;
-    PyObject *py_module = 0;
-    py_name = __Pyx_PyIdentifier_FromString(name);
-    if (!py_name)
-        goto bad;
-    py_module = PyImport_Import(py_name);
-    Py_DECREF(py_name);
-    return py_module;
-bad:
-    Py_XDECREF(py_name);
-    return 0;
-}
-#endif
-
 static void* __Pyx_GetVtable(PyObject *dict) {
     void* ptr;
     PyObject *ob = PyMapping_GetItemString(dict, (char *)"__pyx_vtable__");
@@ -30745,7 +31866,7 @@ static int __Pyx_ImportFunction(PyObject *module, const char *funcname, void (**
                 PyModule_GetName(module), funcname);
         goto bad;
     }
-#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
+#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3 && PY_MINOR_VERSION==0)
     if (!PyCapsule_IsValid(cobj, sig)) {
         PyErr_Format(PyExc_TypeError,
             "C function %s.%s has wrong signature (expected %s, got %s)",
diff --git a/python/src/_cdec.pyx b/python/src/_cdec.pyx
index e93474fe..71e083e4 100644
--- a/python/src/_cdec.pyx
+++ b/python/src/_cdec.pyx
@@ -3,7 +3,7 @@ from libcpp.vector cimport vector
 from utils cimport *
 cimport decoder
 
-cdef char* as_str(data, char* error_msg='Cannot convert type %s to str'):
+cdef bytes as_str(data, char* error_msg='Cannot convert type %s to str'):
     cdef bytes ret
     if isinstance(data, unicode):
         ret = data.encode('utf8')
@@ -25,6 +25,10 @@ decoder.register_feature_functions()
 class InvalidConfig(Exception): pass
 class ParseFailed(Exception): pass
 
+def set_silent(yn):
+    """set_silent(bool): Configure the verbosity of cdec."""
+    SetSilent(yn)
+
 def _make_config(config):
     for key, value in config.items():
         if isinstance(value, dict):
@@ -34,18 +38,16 @@ def _make_config(config):
             for name in value:
                 yield key, name
         else:
-            yield key, bytes(value)
+            yield key, str(value)
 
 cdef class Decoder:
     cdef decoder.Decoder* dec
     cdef DenseVector weights
 
-    def __cinit__(self, config_str=None, **config):
-        """ Configuration can be given as a string:
-                Decoder('formalism = scfg')
-            or using keyword arguments:
-                Decoder(formalism='scfg')
-        """
+    def __init__(self, config_str=None, **config):
+        """Decoder('formalism = scfg') -> initialize from configuration string
+        Decoder(formalism='scfg') -> initialize from named parameters
+        Create a decoder using a given configuration. Formalism is required."""
         if config_str is None:
             formalism = config.get('formalism', None)
             if formalism not in ('scfg', 'fst', 'lextrans', 'pb',
@@ -82,9 +84,10 @@ cdef class Decoder:
     property formalism:
         def __get__(self):
             cdef variables_map* conf = &self.dec.GetConf()
-            return conf[0]['formalism'].as_str()
+            return str(conf[0]['formalism'].as_str().c_str())
 
     def read_weights(self, weights):
+        """decoder.read_weights(filename): Read decoder weights from a file."""
         with open(weights) as fp:
             for line in fp:
                 if line.strip().startswith('#'): continue
@@ -92,20 +95,22 @@ cdef class Decoder:
                 self.weights[fname.strip()] = float(value)
 
     def translate(self, sentence, grammar=None):
+        """decoder.translate(sentence, grammar=None) -> Hypergraph
+        Translate a sentence (string/Lattice) with a grammar (string/list of rules)."""
         cdef bytes input_str
-        if isinstance(sentence, unicode) or isinstance(sentence, str):
+        if isinstance(sentence, basestring):
             input_str = as_str(sentence.strip())
         elif isinstance(sentence, Lattice):
             input_str = str(sentence) # PLF format
         else:
             raise TypeError('Cannot translate input type %s' % type(sentence))
         if grammar:
-            if isinstance(grammar, str) or isinstance(grammar, unicode):
-                self.dec.AddSupplementalGrammarFromString(string(as_str(grammar)))
+            if isinstance(grammar, basestring):
+                self.dec.AddSupplementalGrammarFromString(as_str(grammar))
             else:
                 self.dec.AddSupplementalGrammar(TextGrammar(grammar).grammar[0])
         cdef decoder.BasicObserver observer = decoder.BasicObserver()
-        self.dec.Decode(string(input_str), &observer)
+        self.dec.Decode(input_str, &observer)
         if observer.hypergraph == NULL:
             raise ParseFailed()
         cdef Hypergraph hg = Hypergraph()
diff --git a/python/src/decoder.pxd b/python/src/decoder.pxd
index a66166a2..b68b836e 100644
--- a/python/src/decoder.pxd
+++ b/python/src/decoder.pxd
@@ -15,9 +15,8 @@ cdef extern from "decoder/decoder.h":
         DecoderObserver()
 
     cdef cppclass Decoder:
-        Decoder(int argc, char** argv)
-        Decoder(istream* config_file)
-        bint Decode(string& inp, DecoderObserver* observer)
+        Decoder(istream* config_file) nogil
+        bint Decode(string& inp, DecoderObserver* observer) nogil
 
         # access this to either *read* or *write* to the decoder's last
         # weight vector (i.e., the weights of the finest past)
@@ -27,8 +26,8 @@ cdef extern from "decoder/decoder.h":
         variables_map& GetConf()
 
         # add grammar rules (currently only supported by SCFG decoders)
-        void AddSupplementalGrammarFromString(string& grammar_str)
-        void AddSupplementalGrammar(shared_ptr[Grammar] grammar)
+        void AddSupplementalGrammarFromString(string& grammar_str) nogil
+        void AddSupplementalGrammar(shared_ptr[Grammar] grammar) nogil
 
 cdef extern from "observer.h":
     cdef cppclass BasicObserver(DecoderObserver):
diff --git a/python/src/grammar.pxd b/python/src/grammar.pxd
index 833de2e3..0ffe80fa 100644
--- a/python/src/grammar.pxd
+++ b/python/src/grammar.pxd
@@ -35,11 +35,9 @@ cdef extern from "decoder/grammar.h":
 
     cdef cppclass Grammar:
         const_GrammarIter* GetRoot()
-        bint HasRuleForSpan(int i, int j, int distance)
-        unsigned GetCTFLevels()
         string GetGrammarName()
         void SetGrammarName(string)
 
     cdef cppclass TextGrammar(Grammar):
         TextGrammar()
-        void AddRule(shared_ptr[TRule]& rule)
+        void AddRule(shared_ptr[TRule]& rule) nogil
diff --git a/python/src/grammar.pxi b/python/src/grammar.pxi
index a9a5ea14..d523e4d2 100644
--- a/python/src/grammar.pxi
+++ b/python/src/grammar.pxi
@@ -8,7 +8,8 @@ def _phrase(phrase):
 cdef class NT:
     cdef public bytes cat
     cdef public unsigned ref
-    def __init__(self, char* cat, unsigned ref=0):
+    def __init__(self, bytes cat, unsigned ref=0):
+        """NT(bytes cat, int ref=0) -> Non-terminal from category `cat`."""
         self.cat = cat
         self.ref = ref
 
@@ -20,17 +21,15 @@ cdef class NT:
 cdef class NTRef:
     cdef public unsigned ref
     def __init__(self, unsigned ref):
+        """NTRef(int ref) -> Non-terminal reference."""
         self.ref = ref
 
     def __str__(self):
         return '[%d]' % self.ref
 
 cdef TRule convert_rule(_sa.Rule rule):
-    cdef unsigned i
-    cdef lhs = _sa.sym_tocat(rule.lhs)
-    cdef scores = {}
-    for i in range(rule.n_scores):
-        scores['PhraseModel_'+str(i)] = rule.cscores[i]
+    lhs = _sa.sym_tocat(rule.lhs)
+    scores = dict(rule.scores)
     f, e = [], []
     cdef int* fsyms = rule.f.syms
     for i in range(rule.f.n):
@@ -44,13 +43,19 @@ cdef TRule convert_rule(_sa.Rule rule):
             e.append(NTRef(_sa.sym_getindex(esyms[i])))
         else:
             e.append(_sa.sym_tostring(esyms[i]))
-    cdef a = [(point/65536, point%65536) for point in rule.word_alignments]
+    a = list(rule.alignments())
     return TRule(lhs, f, e, scores, a)
 
 cdef class TRule:
     cdef shared_ptr[grammar.TRule]* rule
 
     def __init__(self, lhs, f, e, scores, a=None):
+        """TRule(lhs, f, e, scores, a=None) -> Translation rule.
+        lhs: left hand side non-terminal
+        f: source phrase (list of words/NT)
+        e: target phrase (list of words/NTRef)
+        scores: dictionary of feature scores
+        a: optional list of alignment points"""
         self.rule = new shared_ptr[grammar.TRule](new grammar.TRule())
         self.lhs = lhs
         self.e = e
@@ -78,9 +83,9 @@ cdef class TRule:
                 w = f_[0][i]
                 if w < 0:
                     idx += 1
-                    f.append(NT(TDConvert(-w), idx))
+                    f.append(NT(TDConvert(-w).c_str(), idx))
                 else:
-                    f.append(unicode(TDConvert(w), encoding='utf8'))
+                    f.append(unicode(TDConvert(w).c_str(), encoding='utf8'))
             return f
 
         def __set__(self, f):
@@ -90,9 +95,10 @@ cdef class TRule:
             cdef int idx = 0
             for i in range(len(f)):
                 if isinstance(f[i], NT):
-                    f_[0][i] = -TDConvert(<char *>f[i].cat)
+                    f_[0][i] = -TDConvert((<NT> f[i]).cat)
                 else:
-                    f_[0][i] = TDConvert(<char *>as_str(f[i]))
+                    fi = as_str(f[i])
+                    f_[0][i] = TDConvert(fi)
 
     property e:
         def __get__(self):
@@ -107,7 +113,7 @@ cdef class TRule:
                     idx += 1
                     e.append(NTRef(1-w))
                 else:
-                    e.append(unicode(TDConvert(w), encoding='utf8'))
+                    e.append(unicode(TDConvert(w).c_str(), encoding='utf8'))
             return e
 
         def __set__(self, e):
@@ -118,7 +124,8 @@ cdef class TRule:
                 if isinstance(e[i], NTRef):
                     e_[0][i] = 1-e[i].ref
                 else:
-                    e_[0][i] = TDConvert(<char *>as_str(e[i]))
+                    ei = as_str(e[i])
+                    e_[0][i] = TDConvert(ei)
 
     property a:
         def __get__(self):
@@ -148,18 +155,19 @@ cdef class TRule:
             cdef int fid
             cdef float fval
             for fname, fval in scores.items():
-                fid = FDConvert(<char *>as_str(fname))
+                fn = as_str(fname)
+                fid = FDConvert(fn)
                 if fid < 0: raise KeyError(fname)
                 scores_.set_value(fid, fval)
 
     property lhs:
         def __get__(self):
-            return NT(TDConvert(-self.rule.get().lhs_))
+            return NT(TDConvert(-self.rule.get().lhs_).c_str())
 
         def __set__(self, lhs):
             if not isinstance(lhs, NT):
                 lhs = NT(lhs)
-            self.rule.get().lhs_ = -TDConvert(<char *>lhs.cat)
+            self.rule.get().lhs_ = -TDConvert((<NT> lhs).cat)
 
     def __str__(self):
         scores = ' '.join('%s=%s' % feat for feat in self.scores)
@@ -167,7 +175,11 @@ cdef class TRule:
                 _phrase(self.f), _phrase(self.e), scores)
 
 cdef class MRule(TRule):
-    def __init__(self, lhs, rhs, scores, a=None):
+    def __init__(self, lhs, rhs, scores):
+        """MRule(lhs, rhs, scores, a=None) -> Monolingual rule.
+        lhs: left hand side non-terminal
+        rhs: right hand side phrase (list of words/NT)
+        scores: dictionary of feature scores"""
         cdef unsigned i = 1
         e = []
         for s in rhs:
@@ -176,7 +188,7 @@ cdef class MRule(TRule):
                 i += 1
             else:
                 e.append(s)
-        super(MRule, self).__init__(lhs, rhs, e, scores, a)
+        super(MRule, self).__init__(lhs, rhs, e, scores, None)
 
 cdef class Grammar:
     cdef shared_ptr[grammar.Grammar]* grammar
@@ -196,13 +208,15 @@ cdef class Grammar:
 
     property name:
         def __get__(self):
-            self.grammar.get().GetGrammarName().c_str()
+            str(self.grammar.get().GetGrammarName().c_str())
 
         def __set__(self, name):
-            self.grammar.get().SetGrammarName(string(<char *>name))
+            name = as_str(name)
+            self.grammar.get().SetGrammarName(name)
 
 cdef class TextGrammar(Grammar):
-    def __cinit__(self, rules):
+    def __init__(self, rules):
+        """TextGrammar(rules) -> SCFG Grammar containing the rules."""
         self.grammar = new shared_ptr[grammar.Grammar](new grammar.TextGrammar())
         cdef grammar.TextGrammar* _g = <grammar.TextGrammar*> self.grammar.get()
         for trule in rules:
diff --git a/python/src/hypergraph.pxd b/python/src/hypergraph.pxd
index 886660bf..dd3d39cc 100644
--- a/python/src/hypergraph.pxd
+++ b/python/src/hypergraph.pxd
@@ -31,41 +31,45 @@ cdef extern from "decoder/hg.h":
     ctypedef HypergraphNode const_HypergraphNode "const Hypergraph::Node"
 
     cdef cppclass Hypergraph:
-        Hypergraph(Hypergraph)
+        Hypergraph()
+        Hypergraph(Hypergraph) nogil
         vector[HypergraphNode] nodes_
         vector[HypergraphEdge] edges_
         int GoalNode()
         double NumberOfPaths()
-        void Reweight(vector[weight_t]& weights)
-        void Reweight(FastSparseVector& weights)
+        void Reweight(vector[weight_t]& weights) nogil
+        void Reweight(FastSparseVector[weight_t]& weights) nogil
         bint PruneInsideOutside(double beam_alpha,
                                 double density,
                                 EdgeMask* preserve_mask,
                                 bint use_sum_prod_semiring,
                                 double scale,
-                                bint safe_inside)
+                                bint safe_inside) nogil
 
 cdef extern from "decoder/viterbi.h":
-    prob_t ViterbiESentence(Hypergraph& hg, vector[WordID]* trans)
-    string ViterbiETree(Hypergraph& hg)
-    prob_t ViterbiFSentence(Hypergraph& hg, vector[WordID]* trans)
-    string ViterbiFTree(Hypergraph& hg)
-    FastSparseVector[weight_t] ViterbiFeatures(Hypergraph& hg)
+    prob_t ViterbiESentence(Hypergraph& hg, vector[WordID]* trans) nogil
+    string ViterbiETree(Hypergraph& hg) nogil
+    prob_t ViterbiFSentence(Hypergraph& hg, vector[WordID]* trans) nogil
+    string ViterbiFTree(Hypergraph& hg) nogil
+    FastSparseVector[weight_t] ViterbiFeatures(Hypergraph& hg) nogil
     FastSparseVector[weight_t] ViterbiFeatures(Hypergraph& hg, 
             FastSparseVector[weight_t]* weights,
-            bint fatal_dotprod_disagreement)
-    string JoshuaVisualizationString(Hypergraph& hg)
+            bint fatal_dotprod_disagreement) nogil
+    string JoshuaVisualizationString(Hypergraph& hg) nogil
 
 cdef extern from "decoder/hg_io.h" namespace "HypergraphIO":
+    # Hypergraph JSON I/O
     bint ReadFromJSON(istream* inp, Hypergraph* out)
     bint WriteToJSON(Hypergraph& hg, bint remove_rules, ostream* out)
-    void ReadFromPLF(string& inp, Hypergraph* out, int line)
+    # Hypergraph PLF I/O
+    void ReadFromPLF(string& inp, Hypergraph* out)
     string AsPLF(Hypergraph& hg, bint include_global_parentheses)
+    # Lattice PLF I/O
     void PLFtoLattice(string& plf, Lattice* pl)
     string AsPLF(Lattice& lat, bint include_global_parentheses)
 
 cdef extern from "decoder/hg_intersect.h" namespace "HG":
-    bint Intersect(Lattice& target, Hypergraph* hg)
+    bint Intersect(Lattice& target, Hypergraph* hg) nogil
 
 cdef extern from "decoder/hg_sampler.h" namespace "HypergraphSampler":
     cdef cppclass Hypothesis:
@@ -75,10 +79,14 @@ cdef extern from "decoder/hg_sampler.h" namespace "HypergraphSampler":
     void sample_hypotheses(Hypergraph& hg, 
                            unsigned n, 
                            MT19937* rng, 
-                           vector[Hypothesis]* hypos)
+                           vector[Hypothesis]* hypos) nogil
+    void sample_trees(Hypergraph& hg, 
+                      unsigned n, 
+                      MT19937* rng, 
+                      vector[string]* trees) nogil
 
 cdef extern from "decoder/csplit.h" namespace "CompoundSplit":
     int GetFullWordEdgeIndex(Hypergraph& forest)
 
 cdef extern from "decoder/inside_outside.h":
-    prob_t InsideOutside "InsideOutside<prob_t, EdgeProb, SparseVector<prob_t>, EdgeFeaturesAndProbWeightFunction>" (Hypergraph& hg, FastSparseVector[prob_t]* result)
+    prob_t InsideOutside "InsideOutside<prob_t, EdgeProb, SparseVector<prob_t>, EdgeFeaturesAndProbWeightFunction>" (Hypergraph& hg, FastSparseVector[prob_t]* result) nogil
diff --git a/python/src/hypergraph.pxi b/python/src/hypergraph.pxi
index b210f440..5b675531 100644
--- a/python/src/hypergraph.pxi
+++ b/python/src/hypergraph.pxi
@@ -10,25 +10,39 @@ cdef class Hypergraph:
         if self.rng != NULL:
             del self.rng
 
+    cdef MT19937* _rng(self):
+        if self.rng == NULL:
+            self.rng = new MT19937()
+        return self.rng
+
     def viterbi(self):
+        """hg.viterbi() -> String for the best hypothesis in the hypergraph."""
         cdef vector[WordID] trans
         hypergraph.ViterbiESentence(self.hg[0], &trans)
         return unicode(GetString(trans).c_str(), 'utf8')
 
     def viterbi_trees(self):
+        """hg.viterbi_trees() -> (f_tree, e_tree)
+        f_tree: Source tree for the best hypothesis in the hypergraph.
+        e_tree: Target tree for the best hypothesis in the hypergraph.
+        """
         f_tree = unicode(hypergraph.ViterbiFTree(self.hg[0]).c_str(), 'utf8')
         e_tree = unicode(hypergraph.ViterbiETree(self.hg[0]).c_str(), 'utf8')
         return (f_tree, e_tree)
     
     def viterbi_features(self):
+        """hg.viterbi_features() -> SparseVector with the features corresponding
+        to the best derivation in the hypergraph."""
         cdef SparseVector fmap = SparseVector.__new__(SparseVector)
         fmap.vector = new FastSparseVector[weight_t](hypergraph.ViterbiFeatures(self.hg[0]))
         return fmap
 
     def viterbi_joshua(self):
+        """hg.viterbi_joshua() -> Joshua representation of the best derivation."""
         return unicode(hypergraph.JoshuaVisualizationString(self.hg[0]).c_str(), 'utf8')
 
     def kbest(self, size):
+        """hg.kbest(size) -> List of k-best hypotheses in the hypergraph."""
         cdef kbest.KBestDerivations[vector[WordID], kbest.ESentenceTraversal]* derivations = new kbest.KBestDerivations[vector[WordID], kbest.ESentenceTraversal](self.hg[0], size)
         cdef kbest.KBestDerivations[vector[WordID], kbest.ESentenceTraversal].Derivation* derivation
         cdef unsigned k
@@ -41,6 +55,7 @@ cdef class Hypergraph:
             del derivations
 
     def kbest_trees(self, size):
+        """hg.kbest_trees(size) -> List of k-best trees in the hypergraph."""
         cdef kbest.KBestDerivations[vector[WordID], kbest.FTreeTraversal]* f_derivations = new kbest.KBestDerivations[vector[WordID], kbest.FTreeTraversal](self.hg[0], size)
         cdef kbest.KBestDerivations[vector[WordID], kbest.FTreeTraversal].Derivation* f_derivation
         cdef kbest.KBestDerivations[vector[WordID], kbest.ETreeTraversal]* e_derivations = new kbest.KBestDerivations[vector[WordID], kbest.ETreeTraversal](self.hg[0], size)
@@ -59,6 +74,7 @@ cdef class Hypergraph:
             del e_derivations
 
     def kbest_features(self, size):
+        """hg.kbest_trees(size) -> List of k-best feature vectors in the hypergraph."""
         cdef kbest.KBestDerivations[FastSparseVector[weight_t], kbest.FeatureVectorTraversal]* derivations = new kbest.KBestDerivations[FastSparseVector[weight_t], kbest.FeatureVectorTraversal](self.hg[0], size)
         cdef kbest.KBestDerivations[FastSparseVector[weight_t], kbest.FeatureVectorTraversal].Derivation* derivation
         cdef SparseVector fmap
@@ -74,10 +90,9 @@ cdef class Hypergraph:
             del derivations
 
     def sample(self, unsigned n):
+        """hg.sample(n) -> Sample of n hypotheses from the hypergraph."""
         cdef vector[hypergraph.Hypothesis]* hypos = new vector[hypergraph.Hypothesis]()
-        if self.rng == NULL:
-            self.rng = new MT19937()
-        hypergraph.sample_hypotheses(self.hg[0], n, self.rng, hypos)
+        hypergraph.sample_hypotheses(self.hg[0], n, self._rng(), hypos)
         cdef unsigned k
         try:
             for k in range(hypos.size()):
@@ -85,10 +100,32 @@ cdef class Hypergraph:
         finally:
             del hypos
 
-    def intersect(self, Lattice lat):
+    def sample_trees(self, unsigned n):
+       """hg.sample_trees(n) -> Sample of n trees from the hypergraph."""
+       cdef vector[string]* trees = new vector[string]()
+       hypergraph.sample_trees(self.hg[0], n, self._rng(), trees)
+       cdef unsigned k
+       try:
+           for k in range(trees.size()):
+               yield unicode(trees[0][k].c_str(), 'utf8')
+       finally:
+           del trees
+
+    def intersect(self, inp):
+        """hg.intersect(Lattice/string): Intersect the hypergraph with the provided reference."""
+        cdef Lattice lat
+        if isinstance(inp, Lattice):
+            lat = <Lattice> inp
+        elif isinstance(inp, basestring):
+            lat = Lattice(inp)
+        else:
+            raise TypeError('cannot intersect hypergraph with %s' % type(inp))
         return hypergraph.Intersect(lat.lattice[0], self.hg)
 
     def prune(self, beam_alpha=0, density=0, **kwargs):
+        """hg.prune(beam_alpha=0, density=0): Prune the hypergraph.
+        beam_alpha: use beam pruning
+        density: use density pruning"""
         cdef hypergraph.EdgeMask* preserve_mask = NULL
         if 'csplit_preserve_full_word' in kwargs:
              preserve_mask = new hypergraph.EdgeMask(self.hg.edges_.size())
@@ -98,10 +135,16 @@ cdef class Hypergraph:
             del preserve_mask
 
     def lattice(self): # TODO direct hg -> lattice conversion in cdec
-        cdef str plf = hypergraph.AsPLF(self.hg[0], True).c_str()
+        """hg.lattice() -> Lattice corresponding to the hypergraph."""
+        cdef bytes plf = hypergraph.AsPLF(self.hg[0], True).c_str()
         return Lattice(eval(plf))
 
+    def plf(self):
+        """hg.plf() -> Lattice PLF representation corresponding to the hypergraph."""
+        return bytes(hypergraph.AsPLF(self.hg[0], True).c_str())
+
     def reweight(self, weights):
+        """hg.reweight(SparseVector/DenseVector): Reweight the hypergraph with a new vector."""
         if isinstance(weights, SparseVector):
             self.hg.Reweight((<SparseVector> weights).vector[0])
         elif isinstance(weights, DenseVector):
@@ -130,6 +173,7 @@ cdef class Hypergraph:
             return self.hg.NumberOfPaths()
 
     def inside_outside(self):
+        """hg.inside_outside() -> SparseVector with inside-outside scores for each feature."""
         cdef FastSparseVector[prob_t]* result = new FastSparseVector[prob_t]()
         cdef prob_t z = hypergraph.InsideOutside(self.hg[0], result)
         result[0] /= z
@@ -218,7 +262,7 @@ cdef class HypergraphNode:
     property cat:
         def __get__(self):
             if self.node.cat_:
-                return TDConvert(-self.node.cat_)
+                return str(TDConvert(-self.node.cat_).c_str())
 
     def __richcmp__(HypergraphNode x, HypergraphNode y, int op):
         if op == 2: # ==
diff --git a/python/src/kbest.pxd b/python/src/kbest.pxd
index cef42bd3..44ecfbab 100644
--- a/python/src/kbest.pxd
+++ b/python/src/kbest.pxd
@@ -16,5 +16,5 @@ cdef extern from "decoder/kbest.h" namespace "KBest":
     cdef cppclass KBestDerivations[T, Traversal]:
         cppclass Derivation:
             T _yield "yield"
-        KBestDerivations(Hypergraph& hg, unsigned k)
-        Derivation* LazyKthBest(unsigned v, unsigned k)
+        KBestDerivations(Hypergraph& hg, unsigned k) nogil
+        Derivation* LazyKthBest(unsigned v, unsigned k) nogil
diff --git a/python/src/lattice.pxd b/python/src/lattice.pxd
index 3a4bc22f..8ad710e5 100644
--- a/python/src/lattice.pxd
+++ b/python/src/lattice.pxd
@@ -12,10 +12,9 @@ cdef extern from "decoder/lattice.h":
 
     cdef cppclass Lattice(vector): # (vector[vector[LatticeArc]])
         Lattice()
-        Lattice(unsigned t)
-        Lattice(unsigned t, vector[LatticeArc]& v)
         bint IsSentence()
         vector[LatticeArc]& operator[](unsigned)
+        void resize(unsigned)
 
 cdef extern from "decoder/lattice.h" namespace "LatticeTools":
-    void ConvertTextToLattice(string& text, Lattice* pl)
+    void ConvertTextOrPLF(string& text, Lattice* pl)
diff --git a/python/src/lattice.pxi b/python/src/lattice.pxi
index 14864549..8000b61e 100644
--- a/python/src/lattice.pxi
+++ b/python/src/lattice.pxi
@@ -3,18 +3,20 @@ cimport lattice
 cdef class Lattice:
     cdef lattice.Lattice* lattice
 
-    def __cinit__(self, inp):
+    def __cinit__(self):
+        self.lattice = new lattice.Lattice()
+
+    def __init__(self, inp):
+        """Lattice(tuple) -> Lattice from node list.
+        Lattice(string) -> Lattice from PLF representation."""
         if isinstance(inp, tuple):
-            self.lattice = new lattice.Lattice(len(inp))
+            self.lattice.resize(len(inp))
             for i, arcs in enumerate(inp):
                 self[i] = arcs
+        elif isinstance(inp, basestring):
+            lattice.ConvertTextOrPLF(as_str(inp), self.lattice)
         else:
-            if isinstance(inp, unicode):
-                inp = inp.encode('utf8')
-            if not isinstance(inp, str):
-                raise TypeError('Cannot create lattice from %s' % type(inp))
-            self.lattice = new lattice.Lattice()
-            lattice.ConvertTextToLattice(string(<char *>inp), self.lattice)
+            raise TypeError('cannot create lattice from %s' % type(inp))
 
     def __dealloc__(self):
         del self.lattice
@@ -28,7 +30,7 @@ cdef class Lattice:
         cdef unsigned i
         for i in range(arc_vector.size()):
             arc = &arc_vector[i]
-            label = unicode(TDConvert(arc.label), 'utf8')
+            label = unicode(TDConvert(arc.label).c_str(), 'utf8')
             arcs.append((label, arc.cost, arc.dist2next))
         return tuple(arcs)
 
@@ -37,9 +39,8 @@ cdef class Lattice:
             raise IndexError('lattice index out of range')
         cdef lattice.LatticeArc* arc
         for (label, cost, dist2next) in arcs:
-            if isinstance(label, unicode):
-                label = label.encode('utf8')
-            arc = new lattice.LatticeArc(TDConvert(<char *>label), cost, dist2next)
+            label_str = as_str(label)
+            arc = new lattice.LatticeArc(TDConvert(label_str), cost, dist2next)
             self.lattice[0][index].push_back(arc[0])
             del arc
 
@@ -47,7 +48,10 @@ cdef class Lattice:
         return self.lattice.size()
 
     def __str__(self):
-        return hypergraph.AsPLF(self.lattice[0], True).c_str()
+        return str(hypergraph.AsPLF(self.lattice[0], True).c_str())
+
+    def __unicode__(self):
+        return unicode(str(self), 'utf8')
 
     def __iter__(self):
         cdef unsigned i
@@ -55,6 +59,7 @@ cdef class Lattice:
             yield self[i]
 
     def todot(self):
+        """lattice.todot() -> Representation of the lattice in GraphViz dot format."""
         def lines():
             yield 'digraph lattice {'
             yield 'rankdir = LR;'
@@ -65,3 +70,11 @@ cdef class Lattice:
             yield '%d [shape=doublecircle]' % len(self)
             yield '}'
         return '\n'.join(lines()).encode('utf8')
+
+    def as_hypergraph(self):
+        """lattice.as_hypergraph() -> Hypergraph representation of the lattice."""
+        cdef Hypergraph result = Hypergraph.__new__(Hypergraph)
+        result.hg = new hypergraph.Hypergraph()
+        cdef bytes plf = str(self)
+        hypergraph.ReadFromPLF(plf, result.hg)
+        return result
diff --git a/python/src/mteval.pxi b/python/src/mteval.pxi
index cd1c3c81..f3bec393 100644
--- a/python/src/mteval.pxi
+++ b/python/src/mteval.pxi
@@ -36,7 +36,7 @@ cdef class SufficientStats:
 
     property detail:
         def __get__(self):
-            return self.metric.DetailedScore(self.stats[0]).c_str()
+            return str(self.metric.DetailedScore(self.stats[0]).c_str())
 
     def __len__(self):
         return self.stats.size()
@@ -93,6 +93,8 @@ cdef class CandidateSet:
             yield self[i]
 
     def add_kbest(self, Hypergraph hypergraph, unsigned k):
+        """cs.add_kbest(Hypergraph hypergraph, int k) -> Extract K-best hypotheses 
+        from the hypergraph and add them to the candidate set."""
         self.cs.AddKBestCandidates(hypergraph.hg[0], k, self.scorer.get())
 
 cdef class SegmentEvaluator:
@@ -103,15 +105,17 @@ cdef class SegmentEvaluator:
         del self.scorer
 
     def evaluate(self, sentence):
+        """se.evaluate(sentence) -> SufficientStats for the given hypothesis."""
         cdef vector[WordID] hyp
         cdef SufficientStats sf = SufficientStats()
         sf.metric = self.metric
         sf.stats = new mteval.SufficientStats()
-        ConvertSentence(string(as_str(sentence.strip())), &hyp)
+        ConvertSentence(as_str(sentence.strip()), &hyp)
         self.scorer.get().Evaluate(hyp, sf.stats)
         return sf
 
     def candidate_set(self):
+        """se.candidate_set() -> Candidate set using this segment evaluator for scoring."""
         return CandidateSet(self)
 
 cdef class Scorer:
@@ -127,14 +131,13 @@ cdef class Scorer:
         del self.name
     
     def __call__(self, refs):
-        if isinstance(refs, unicode) or isinstance(refs, str):
+        if isinstance(refs, basestring):
             refs = [refs]
         cdef vector[vector[WordID]]* refsv = new vector[vector[WordID]]()
         cdef vector[WordID]* refv
-        cdef bytes ref_str
         for ref in refs:
             refv = new vector[WordID]()
-            ConvertSentence(string(as_str(ref.strip())), refv)
+            ConvertSentence(as_str(ref.strip()), refv)
             refsv.push_back(refv[0])
             del refv
         cdef unsigned i
@@ -146,7 +149,7 @@ cdef class Scorer:
         return evaluator
 
     def __str__(self):
-        return self.name.c_str()
+        return str(self.name.c_str())
 
 cdef float _compute_score(void* metric_, mteval.SufficientStats* stats):
     cdef Metric metric = <Metric> metric_
@@ -164,8 +167,8 @@ cdef void _compute_sufficient_stats(void* metric_,
     cdef list refs_ = []
     cdef unsigned i
     for i in range(refs.size()):
-        refs_.append(refs[0][i].c_str())
-    cdef list ss = metric.evaluate(hyp.c_str(), refs_)
+        refs_.append(str(refs[0][i].c_str()))
+    cdef list ss = metric.evaluate(str(hyp.c_str()), refs_)
     out.fields.resize(len(ss))
     for i in range(len(ss)):
         out.fields[i] = ss[i]
@@ -174,7 +177,8 @@ cdef class Metric:
     cdef Scorer scorer
     def __cinit__(self):
         self.scorer = Scorer()
-        self.scorer.name = new string(as_str(self.__class__.__name__))
+        cdef bytes class_name = self.__class__.__name__
+        self.scorer.name = new string(class_name)
         self.scorer.metric = mteval.PyMetricInstance(self.scorer.name[0],
                 <void*> self, _compute_sufficient_stats, _compute_score)
 
diff --git a/python/src/sa/_sa.c b/python/src/sa/_sa.c
index 0f9b0d22..5b47fe8a 100644
--- a/python/src/sa/_sa.c
+++ b/python/src/sa/_sa.c
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.17.beta1 on Sat Jul 28 17:07:03 2012 */
+/* Generated by Cython 0.17 on Thu Sep  6 14:56:12 2012 */
 
 #define PY_SSIZE_T_CLEAN
 #include "Python.h"
@@ -11,7 +11,6 @@
 #ifndef offsetof
 #define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
 #endif
-
 #if !defined(WIN32) && !defined(MS_WINDOWS)
   #ifndef __stdcall
     #define __stdcall
@@ -23,22 +22,18 @@
     #define __fastcall
   #endif
 #endif
-
 #ifndef DL_IMPORT
   #define DL_IMPORT(t) t
 #endif
 #ifndef DL_EXPORT
   #define DL_EXPORT(t) t
 #endif
-
 #ifndef PY_LONG_LONG
   #define PY_LONG_LONG LONG_LONG
 #endif
-
 #ifndef Py_HUGE_VAL
   #define Py_HUGE_VAL HUGE_VAL
 #endif
-
 #ifdef PYPY_VERSION
 #define CYTHON_COMPILING_IN_PYPY 1
 #define CYTHON_COMPILING_IN_CPYTHON 0
@@ -46,12 +41,12 @@
 #define CYTHON_COMPILING_IN_PYPY 0
 #define CYTHON_COMPILING_IN_CPYTHON 1
 #endif
-
 #if PY_VERSION_HEX < 0x02050000
   typedef int Py_ssize_t;
   #define PY_SSIZE_T_MAX INT_MAX
   #define PY_SSIZE_T_MIN INT_MIN
   #define PY_FORMAT_SIZE_T ""
+  #define CYTHON_FORMAT_SSIZE_T ""
   #define PyInt_FromSsize_t(z) PyInt_FromLong(z)
   #define PyInt_AsSsize_t(o)   __Pyx_PyInt_AsInt(o)
   #define PyNumber_Index(o)    ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
@@ -63,8 +58,8 @@
   #define __PYX_BUILD_PY_SSIZE_T "i"
 #else
   #define __PYX_BUILD_PY_SSIZE_T "n"
+  #define CYTHON_FORMAT_SSIZE_T "z"
 #endif
-
 #if PY_VERSION_HEX < 0x02060000
   #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
   #define Py_TYPE(ob)   (((PyObject*)(ob))->ob_type)
@@ -72,7 +67,6 @@
   #define PyVarObject_HEAD_INIT(type, size) \
           PyObject_HEAD_INIT(type) size,
   #define PyType_Modified(t)
-
   typedef struct {
      void *buf;
      PyObject *obj;
@@ -86,7 +80,6 @@
      Py_ssize_t *suboffsets;
      void *internal;
   } Py_buffer;
-
   #define PyBUF_SIMPLE 0
   #define PyBUF_WRITABLE 0x0001
   #define PyBUF_FORMAT 0x0004
@@ -98,11 +91,9 @@
   #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
   #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
   #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
-
   typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
   typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
 #endif
-
 #if PY_MAJOR_VERSION < 3
   #define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
   #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
@@ -112,21 +103,16 @@
   #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
           PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
 #endif
-
 #if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
   #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
 #endif
-
 #if PY_MAJOR_VERSION >= 3
   #define Py_TPFLAGS_CHECKTYPES 0
   #define Py_TPFLAGS_HAVE_INDEX 0
 #endif
-
 #if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
   #define Py_TPFLAGS_HAVE_NEWBUFFER 0
 #endif
-
-
 #if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
   #define CYTHON_PEP393_ENABLED 1
   #define __Pyx_PyUnicode_READY(op)       (likely(PyUnicode_IS_READY(op)) ? \
@@ -139,10 +125,8 @@
   #define __Pyx_PyUnicode_READY(op)       (0)
   #define __Pyx_PyUnicode_GET_LENGTH(u)   PyUnicode_GET_SIZE(u)
   #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
-
   #define __Pyx_PyUnicode_READ(k, d, i)   ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
 #endif
-
 #if PY_MAJOR_VERSION >= 3
   #define PyBaseString_Type            PyUnicode_Type
   #define PyStringObject               PyUnicodeObject
@@ -150,7 +134,6 @@
   #define PyString_Check               PyUnicode_Check
   #define PyString_CheckExact          PyUnicode_CheckExact
 #endif
-
 #if PY_VERSION_HEX < 0x02060000
   #define PyBytesObject                PyStringObject
   #define PyBytes_Type                 PyString_Type
@@ -169,7 +152,6 @@
   #define PyBytes_Concat               PyString_Concat
   #define PyBytes_ConcatAndDel         PyString_ConcatAndDel
 #endif
-
 #if PY_VERSION_HEX < 0x02060000
   #define PySet_Check(obj)             PyObject_TypeCheck(obj, &PySet_Type)
   #define PyFrozenSet_Check(obj)       PyObject_TypeCheck(obj, &PyFrozenSet_Type)
@@ -177,9 +159,7 @@
 #ifndef PySet_CheckExact
   #define PySet_CheckExact(obj)        (Py_TYPE(obj) == &PySet_Type)
 #endif
-
 #define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
-
 #if PY_MAJOR_VERSION >= 3
   #define PyIntObject                  PyLongObject
   #define PyInt_Type                   PyLong_Type
@@ -196,11 +176,9 @@
   #define PyInt_AsUnsignedLongMask     PyLong_AsUnsignedLongMask
   #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
 #endif
-
 #if PY_MAJOR_VERSION >= 3
   #define PyBoolObject                 PyLongObject
 #endif
-
 #if PY_VERSION_HEX < 0x03020000
   typedef long Py_hash_t;
   #define __Pyx_PyInt_FromHash_t PyInt_FromLong
@@ -209,7 +187,6 @@
   #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
   #define __Pyx_PyInt_AsHash_t   PyInt_AsSsize_t
 #endif
-
 #if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300)
   #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
   #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
@@ -228,11 +205,9 @@
         (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \
             (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1)))
 #endif
-
 #if PY_MAJOR_VERSION >= 3
   #define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
 #endif
-
 #if PY_VERSION_HEX < 0x02050000
   #define __Pyx_GetAttrString(o,n)   PyObject_GetAttrString((o),((char *)(n)))
   #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a))
@@ -242,7 +217,6 @@
   #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a))
   #define __Pyx_DelAttrString(o,n)   PyObject_DelAttrString((o),(n))
 #endif
-
 #if PY_VERSION_HEX < 0x02050000
   #define __Pyx_NAMESTR(n) ((char *)(n))
   #define __Pyx_DOCSTR(n)  ((char *)(n))
@@ -251,6 +225,7 @@
   #define __Pyx_DOCSTR(n)  (n)
 #endif
 
+
 #if PY_MAJOR_VERSION >= 3
   #define __Pyx_PyNumber_Divide(x,y)         PyNumber_TrueDivide(x,y)
   #define __Pyx_PyNumber_InPlaceDivide(x,y)  PyNumber_InPlaceTrueDivide(x,y)
@@ -375,15 +350,17 @@ static const char *__pyx_f[] = {
   "rulefactory.pxi",
   "lcp.pxi",
   "sym.pxi",
-  "_sa.pxd",
   "precomputation.pxi",
   "suffix_array.pxi",
+  "features.pxi",
   "str_map.pxi",
 };
 
 /*--- Type declarations ---*/
 struct __pyx_obj_3_sa_HieroCachingRuleFactory;
-struct __pyx_obj_3_sa___pyx_scope_struct_2_compute_stats;
+struct __pyx_obj_3_sa___pyx_scope_struct_9_decode_sentence;
+struct __pyx_obj_3_sa___pyx_scope_struct_3_compute_stats;
+struct __pyx_obj_3_sa___pyx_scope_struct_18_genexpr;
 struct __pyx_obj_3_sa_IntList;
 struct __pyx_obj_3_sa_VEBIterator;
 struct __pyx_obj_3_sa_BiLex;
@@ -391,24 +368,38 @@ struct __pyx_obj_3_sa_VEB;
 struct __pyx_obj_3_sa_LCP;
 struct __pyx_obj_3_sa_DataArray;
 struct __pyx_obj_3_sa_BitSetIterator;
-struct __pyx_obj_3_sa___pyx_scope_struct__read_bitext;
+struct __pyx_obj_3_sa___pyx_scope_struct_14_alignments;
 struct __pyx_obj_3_sa_Precomputation;
 struct __pyx_obj_3_sa_SuffixArray;
-struct __pyx_obj_3_sa___pyx_scope_struct_4_input;
 struct __pyx_obj_3_sa_Alphabet;
 struct __pyx_obj_3_sa_Rule;
+struct __pyx_obj_3_sa___pyx_scope_struct_6_genexpr;
+struct __pyx_obj_3_sa___pyx_scope_struct_2_genexpr;
 struct __pyx_obj_3_sa_PhraseLocation;
-struct __pyx_obj_3_sa___pyx_scope_struct_3___iter__;
+struct __pyx_obj_3_sa___pyx_scope_struct_16___iter__;
+struct __pyx_obj_3_sa___pyx_scope_struct_1_read_bitext;
+struct __pyx_obj_3_sa_FeatureVector;
+struct __pyx_obj_3_sa___pyx_scope_struct_7_decode_lattice;
+struct __pyx_obj_3_sa_Scorer;
 struct __pyx_obj_3_sa_Alignment;
 struct __pyx_obj_3_sa_BitSet;
 struct __pyx_obj_3_sa_Sampler;
 struct __pyx_obj_3_sa_StringMap;
+struct __pyx_obj_3_sa___pyx_scope_struct_17___str__;
 struct __pyx_obj_3_sa_TrieNode;
 struct __pyx_obj_3_sa_ExtendedTrieNode;
 struct __pyx_obj_3_sa_TrieMap;
+struct __pyx_obj_3_sa___pyx_scope_struct_8_genexpr;
+struct __pyx_obj_3_sa___pyx_scope_struct_4_make_lattice;
+struct __pyx_obj_3_sa___pyx_scope_struct_12___str__;
+struct __pyx_obj_3_sa___pyx_scope_struct_15_input;
+struct __pyx_obj_3_sa___pyx_scope_struct_13_genexpr;
 struct __pyx_obj_3_sa_Phrase;
+struct __pyx_obj_3_sa___pyx_scope_struct____iter__;
 struct __pyx_obj_3_sa_TrieTable;
-struct __pyx_obj_3_sa___pyx_scope_struct_1_genexpr;
+struct __pyx_obj_3_sa___pyx_scope_struct_11___iter__;
+struct __pyx_obj_3_sa___pyx_scope_struct_5_genexpr;
+struct __pyx_obj_3_sa___pyx_scope_struct_10_genexpr;
 struct __pyx_obj_3_sa_FloatList;
 struct __pyx_t_3_sa__node;
 struct __pyx_t_3_sa__BitSet;
@@ -418,8 +409,8 @@ struct __pyx_t_3_sa__Trie_Node;
 struct __pyx_t_3_sa_match_node;
 struct __pyx_t_3_sa_Matching;
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":9
- * from libc.string cimport memset, strcpy, strlen
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":9
+ * from libc.string cimport memset, strcpy
  * 
  * cdef struct _node:             # <<<<<<<<<<<<<<
  *     _node* smaller
@@ -432,7 +423,7 @@ struct __pyx_t_3_sa__node {
   int val;
 };
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":30
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":30
  * _init_lower_mask()
  * 
  * cdef struct _BitSet:             # <<<<<<<<<<<<<<
@@ -446,7 +437,7 @@ struct __pyx_t_3_sa__BitSet {
   int size;
 };
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":168
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":168
  *     return result
  * 
  * cdef struct _VEB:             # <<<<<<<<<<<<<<
@@ -463,7 +454,7 @@ struct __pyx_t_3_sa__VEB {
   void **bottom;
 };
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":10
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":10
  * cdef struct _Trie_Node    # forward decl
  * 
  * cdef struct _Trie_Edge:             # <<<<<<<<<<<<<<
@@ -477,7 +468,7 @@ struct __pyx_t_3_sa__Trie_Edge {
   struct __pyx_t_3_sa__Trie_Edge *smaller;
 };
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":8
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":8
  * from libc.string cimport memset, memcpy
  * 
  * cdef struct _Trie_Node    # forward decl             # <<<<<<<<<<<<<<
@@ -490,7 +481,7 @@ struct __pyx_t_3_sa__Trie_Node {
   int arr_len;
 };
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":48
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":66
  * 
  * # linked list structure for storing matches in BaselineRuleFactory
  * cdef struct match_node:             # <<<<<<<<<<<<<<
@@ -502,7 +493,7 @@ struct __pyx_t_3_sa_match_node {
   struct __pyx_t_3_sa_match_node *next;
 };
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":145
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":162
  * 
  * # struct used to encapsulate a single matching
  * cdef struct Matching:             # <<<<<<<<<<<<<<
@@ -517,7 +508,7 @@ struct __pyx_t_3_sa_Matching {
   int size;
 };
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":201
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":218
  * 
  * 
  * cdef class HieroCachingRuleFactory:             # <<<<<<<<<<<<<<
@@ -529,6 +520,7 @@ struct __pyx_obj_3_sa_HieroCachingRuleFactory {
   struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *__pyx_vtab;
   struct __pyx_obj_3_sa_TrieTable *rules;
   struct __pyx_obj_3_sa_Sampler *sampler;
+  struct __pyx_obj_3_sa_Scorer *scorer;
   int max_chunks;
   int max_target_chunks;
   int max_length;
@@ -565,14 +557,26 @@ struct __pyx_obj_3_sa_HieroCachingRuleFactory {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":36
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":115
+ *             for arc in node for node in lattice)
+ * 
+ * def decode_sentence(lattice):             # <<<<<<<<<<<<<<
+ *     return tuple(sym_tostring(sym) for ((sym, _, _),) in lattice)
+ */
+struct __pyx_obj_3_sa___pyx_scope_struct_9_decode_sentence {
+  PyObject_HEAD
+  PyObject *__pyx_v_lattice;
+};
+
+
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":36
  *         logger.info("LCP array completed")
  * 
  *     def compute_stats(self, int max_n):             # <<<<<<<<<<<<<<
  *         """Note: the output of this function is not exact.  In
  *         particular, the frequency associated with each word is
  */
-struct __pyx_obj_3_sa___pyx_scope_struct_2_compute_stats {
+struct __pyx_obj_3_sa___pyx_scope_struct_3_compute_stats {
   PyObject_HEAD
   int __pyx_v_N;
   int __pyx_v_freq;
@@ -596,8 +600,25 @@ struct __pyx_obj_3_sa___pyx_scope_struct_2_compute_stats {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":9
- * from libc.string cimport memset, memcpy
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/features.pxi":21
+ * 
+ *     def __str__(self):
+ *         return ' '.join('%s=%s' % feat for feat in self)             # <<<<<<<<<<<<<<
+ * 
+ * cdef class Scorer:
+ */
+struct __pyx_obj_3_sa___pyx_scope_struct_18_genexpr {
+  PyObject_HEAD
+  struct __pyx_obj_3_sa___pyx_scope_struct_17___str__ *__pyx_outer_scope;
+  PyObject *__pyx_v_feat;
+  PyObject *__pyx_t_0;
+  Py_ssize_t __pyx_t_1;
+  PyObject *(*__pyx_t_2)(PyObject *);
+};
+
+
+/* "_sa.pxd":12
+ *     cdef void read_handle(self, FILE* f)
  * 
  * cdef class IntList:             # <<<<<<<<<<<<<<
  *     cdef int size
@@ -613,7 +634,7 @@ struct __pyx_obj_3_sa_IntList {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":340
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":340
  * 
  * 
  * cdef class VEBIterator:             # <<<<<<<<<<<<<<
@@ -627,7 +648,7 @@ struct __pyx_obj_3_sa_VEBIterator {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":47
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":47
  * 
  * 
  * cdef class BiLex:             # <<<<<<<<<<<<<<
@@ -648,7 +669,7 @@ struct __pyx_obj_3_sa_BiLex {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":354
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":354
  * 
  * 
  * cdef class VEB:             # <<<<<<<<<<<<<<
@@ -662,7 +683,7 @@ struct __pyx_obj_3_sa_VEB {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":5
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":5
  * as k most frequent n-grams"""
  * 
  * cdef class LCP:             # <<<<<<<<<<<<<<
@@ -676,12 +697,12 @@ struct __pyx_obj_3_sa_LCP {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":9
- * from libc.string cimport memset, strcpy, strlen
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/data_array.pxi":9
+ * from libc.string cimport memset, strcpy
  * 
  * cdef class DataArray:             # <<<<<<<<<<<<<<
- *     cdef word2id
- *     cdef id2word
+ *     cdef public word2id
+ *     cdef public id2word
  */
 struct __pyx_obj_3_sa_DataArray {
   PyObject_HEAD
@@ -695,7 +716,7 @@ struct __pyx_obj_3_sa_DataArray {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":100
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":100
  * 
  * 
  * cdef class BitSetIterator:             # <<<<<<<<<<<<<<
@@ -709,21 +730,24 @@ struct __pyx_obj_3_sa_BitSetIterator {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":71
- *             self.read_text_data(fp)
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":190
+ *         return ' ||| '.join(fields)
  * 
- *     def read_bitext(self, char* filename, int side):             # <<<<<<<<<<<<<<
- *         with gzip_or_text(filename) as fp:
- *             data = (line.split(' ||| ')[side] for line in fp)
+ *     def alignments(self):             # <<<<<<<<<<<<<<
+ *         for point in self.word_alignments:
+ *             yield point/65536, point%65536
  */
-struct __pyx_obj_3_sa___pyx_scope_struct__read_bitext {
+struct __pyx_obj_3_sa___pyx_scope_struct_14_alignments {
   PyObject_HEAD
-  PyObject *__pyx_v_fp;
-  int __pyx_v_side;
+  PyObject *__pyx_v_point;
+  struct __pyx_obj_3_sa_Rule *__pyx_v_self;
+  PyObject *__pyx_t_0;
+  Py_ssize_t __pyx_t_1;
+  PyObject *(*__pyx_t_2)(PyObject *);
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":188
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":188
  * 
  * 
  * cdef class Precomputation:             # <<<<<<<<<<<<<<
@@ -744,7 +768,7 @@ struct __pyx_obj_3_sa_Precomputation {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":6
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":6
  * from libc.stdio cimport FILE, fclose, fopen
  * 
  * cdef class SuffixArray:             # <<<<<<<<<<<<<<
@@ -760,93 +784,7 @@ struct __pyx_obj_3_sa_SuffixArray {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":919
- *         return sorted(result);
- * 
- *     def input(self, fwords, models):             # <<<<<<<<<<<<<<
- *         '''When this function is called on the RuleFactory,
- *         it looks up all of the rules that can be used to translate
- */
-struct __pyx_obj_3_sa___pyx_scope_struct_4_input {
-  PyObject_HEAD
-  PyObject *__pyx_v_alignment;
-  PyObject *__pyx_v_als;
-  PyObject *__pyx_v_alslist;
-  int __pyx_v_alt;
-  int __pyx_v_alt_id;
-  int __pyx_v_arity;
-  struct __pyx_obj_3_sa_IntList *__pyx_v_chunklen;
-  PyObject *__pyx_v_count;
-  PyObject *__pyx_v_currcount;
-  PyObject *__pyx_v_e;
-  PyObject *__pyx_v_elist;
-  PyObject *__pyx_v_extract;
-  PyObject *__pyx_v_extract_start;
-  PyObject *__pyx_v_extract_stop;
-  PyObject *__pyx_v_extracts;
-  PyObject *__pyx_v_f;
-  PyObject *__pyx_v_f_margin;
-  PyObject *__pyx_v_fals;
-  PyObject *__pyx_v_fcount;
-  int __pyx_v_flen;
-  PyObject *__pyx_v_fphrases;
-  PyObject *__pyx_v_frontier;
-  PyObject *__pyx_v_frontier_nodes;
-  PyObject *__pyx_v_fwords;
-  struct __pyx_obj_3_sa_Phrase *__pyx_v_hiero_phrase;
-  long __pyx_v_hit;
-  int __pyx_v_i;
-  PyObject *__pyx_v_is_shadow_path;
-  int __pyx_v_j;
-  int __pyx_v_k;
-  PyObject *__pyx_v_key;
-  int __pyx_v_lookup_required;
-  struct __pyx_t_3_sa_Matching __pyx_v_matching;
-  PyObject *__pyx_v_model;
-  PyObject *__pyx_v_models;
-  PyObject *__pyx_v_new_frontier;
-  PyObject *__pyx_v_new_node;
-  PyObject *__pyx_v_next_states;
-  PyObject *__pyx_v_node;
-  PyObject *__pyx_v_nodes_isteps_away_buffer;
-  int __pyx_v_nualt;
-  int __pyx_v_num_samples;
-  int __pyx_v_num_subpatterns;
-  PyObject *__pyx_v_pathlen;
-  PyObject *__pyx_v_phrase;
-  struct __pyx_obj_3_sa_PhraseLocation *__pyx_v_phrase_location;
-  PyObject *__pyx_v_prefix;
-  PyObject *__pyx_v_reachable_buffer;
-  PyObject *__pyx_v_sa_range;
-  struct __pyx_obj_3_sa_IntList *__pyx_v_sample;
-  PyObject *__pyx_v_scores;
-  struct __pyx_obj_3_sa_HieroCachingRuleFactory *__pyx_v_self;
-  PyObject *__pyx_v_spanlen;
-  float __pyx_v_start_time;
-  PyObject *__pyx_v_stop_time;
-  PyObject *__pyx_v_suffix_link;
-  int __pyx_v_suffix_link_xcat;
-  PyObject *__pyx_v_suffix_link_xcat_index;
-  PyObject *__pyx_v_word_id;
-  int __pyx_v_x1;
-  int __pyx_v_xcat;
-  PyObject *__pyx_v_xcat_index;
-  PyObject *__pyx_v_xnode;
-  PyObject *__pyx_v_xroot;
-  Py_ssize_t __pyx_t_0;
-  PyObject *__pyx_t_1;
-  Py_ssize_t __pyx_t_2;
-  int __pyx_t_3;
-  PyObject *__pyx_t_4;
-  PyObject *__pyx_t_5;
-  int __pyx_t_6;
-  Py_ssize_t __pyx_t_7;
-  Py_ssize_t __pyx_t_8;
-  Py_ssize_t __pyx_t_9;
-};
-
-
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":7
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":7
  * cdef int INDEX_MASK = (1<<INDEX_SHIFT)-1
  * 
  * cdef class Alphabet:             # <<<<<<<<<<<<<<
@@ -863,24 +801,58 @@ struct __pyx_obj_3_sa_Alphabet {
   PyObject *id2sym;
 };
 
+
+/* "_sa.pxd":35
+ *     cdef public int chunklen(self, int k)
+ * 
+ * cdef class Rule:             # <<<<<<<<<<<<<<
+ *     cdef int lhs
+ *     cdef readonly Phrase f, e
+ */
 struct __pyx_obj_3_sa_Rule {
   PyObject_HEAD
   int lhs;
   struct __pyx_obj_3_sa_Phrase *f;
   struct __pyx_obj_3_sa_Phrase *e;
-  float *cscores;
+  struct __pyx_obj_3_sa_FeatureVector *scores;
   int n_scores;
   PyObject *word_alignments;
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":56
- * # in the suffix array; if discontiguous, it is the set of
- * # actual locations (packed into an array)
- * cdef class PhraseLocation:             # <<<<<<<<<<<<<<
- *     cdef int sa_low
- *     cdef int sa_high
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":109
+ * def make_lattice(words):
+ *     word_ids = (sym_fromstring(word, True) for word in words)
+ *     return tuple(((word, None, 1), ) for word in word_ids)             # <<<<<<<<<<<<<<
+ * 
+ * def decode_lattice(lattice):
+ */
+struct __pyx_obj_3_sa___pyx_scope_struct_6_genexpr {
+  PyObject_HEAD
+  struct __pyx_obj_3_sa___pyx_scope_struct_4_make_lattice *__pyx_outer_scope;
+  PyObject *__pyx_v_word;
+  PyObject *__pyx_t_0;
+  Py_ssize_t __pyx_t_1;
+  PyObject *(*__pyx_t_2)(PyObject *);
+};
+
+
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/data_array.pxi":74
+ *     def read_bitext(self, char* filename, int side):
+ *         with gzip_or_text(filename) as fp:
+ *             data = (line.split(' ||| ')[side] for line in fp)             # <<<<<<<<<<<<<<
+ *             self.read_text_data(data)
+ * 
  */
+struct __pyx_obj_3_sa___pyx_scope_struct_2_genexpr {
+  PyObject_HEAD
+  struct __pyx_obj_3_sa___pyx_scope_struct_1_read_bitext *__pyx_outer_scope;
+  PyObject *__pyx_v_line;
+  PyObject *__pyx_t_0;
+  Py_ssize_t __pyx_t_1;
+  PyObject *(*__pyx_t_2)(PyObject *);
+};
+
 struct __pyx_obj_3_sa_PhraseLocation {
   PyObject_HEAD
   struct __pyx_vtabstruct_3_sa_PhraseLocation *__pyx_vtab;
@@ -893,22 +865,78 @@ struct __pyx_obj_3_sa_PhraseLocation {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":141
- *         return self.syms[i]
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/features.pxi":15
+ *         self.values.append(value)
  * 
  *     def __iter__(self):             # <<<<<<<<<<<<<<
- *         cdef int i
- *         for i from 0 <= i < self.n:
+ *         cdef unsigned i
+ *         for i in range(self.names.len):
  */
-struct __pyx_obj_3_sa___pyx_scope_struct_3___iter__ {
+struct __pyx_obj_3_sa___pyx_scope_struct_16___iter__ {
   PyObject_HEAD
-  int __pyx_v_i;
-  struct __pyx_obj_3_sa_Phrase *__pyx_v_self;
+  unsigned int __pyx_v_i;
+  struct __pyx_obj_3_sa_FeatureVector *__pyx_v_self;
   int __pyx_t_0;
+  unsigned int __pyx_t_1;
+};
+
+
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/data_array.pxi":72
+ *             self.read_text_data(fp)
+ * 
+ *     def read_bitext(self, char* filename, int side):             # <<<<<<<<<<<<<<
+ *         with gzip_or_text(filename) as fp:
+ *             data = (line.split(' ||| ')[side] for line in fp)
+ */
+struct __pyx_obj_3_sa___pyx_scope_struct_1_read_bitext {
+  PyObject_HEAD
+  PyObject *__pyx_v_fp;
+  int __pyx_v_side;
+};
+
+
+/* "_sa.pxd":25
+ *     cdef void read_handle(self, FILE* f)
+ * 
+ * cdef class FeatureVector:             # <<<<<<<<<<<<<<
+ *     cdef IntList names
+ *     cdef FloatList values
+ */
+struct __pyx_obj_3_sa_FeatureVector {
+  PyObject_HEAD
+  struct __pyx_obj_3_sa_IntList *names;
+  struct __pyx_obj_3_sa_FloatList *values;
+};
+
+
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":111
+ *     return tuple(((word, None, 1), ) for word in word_ids)
+ * 
+ * def decode_lattice(lattice):             # <<<<<<<<<<<<<<
+ *     return tuple((sym_tostring(sym), weight, dist) for (sym, weight, dist) in arc
+ *             for arc in node for node in lattice)
+ */
+struct __pyx_obj_3_sa___pyx_scope_struct_7_decode_lattice {
+  PyObject_HEAD
+  PyObject *__pyx_v_lattice;
+};
+
+
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/features.pxi":23
+ *         return ' '.join('%s=%s' % feat for feat in self)
+ * 
+ * cdef class Scorer:             # <<<<<<<<<<<<<<
+ *     cdef models
+ *     def __init__(self, *models):
+ */
+struct __pyx_obj_3_sa_Scorer {
+  PyObject_HEAD
+  struct __pyx_vtabstruct_3_sa_Scorer *__pyx_vtab;
+  PyObject *models;
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":8
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":8
  * # May need to revisit if things get really tight, though.
  * 
  * cdef class Alignment:             # <<<<<<<<<<<<<<
@@ -923,7 +951,7 @@ struct __pyx_obj_3_sa_Alignment {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":118
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":118
  * # (entirely C-implemented) _BitSet struct.
  * # Very slow; use only for debugging
  * cdef class BitSet:             # <<<<<<<<<<<<<<
@@ -936,7 +964,7 @@ struct __pyx_obj_3_sa_BitSet {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":79
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":96
  * 
  * 
  * cdef class Sampler:             # <<<<<<<<<<<<<<
@@ -950,7 +978,7 @@ struct __pyx_obj_3_sa_Sampler {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/str_map.pxi":8
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/str_map.pxi":8
  *     char* stringmap_word(StrMap *vocab, int i)
  * 
  * cdef class StringMap:             # <<<<<<<<<<<<<<
@@ -964,7 +992,20 @@ struct __pyx_obj_3_sa_StringMap {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":18
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/features.pxi":20
+ *             yield (FD.word(self.names[i]), self.values[i])
+ * 
+ *     def __str__(self):             # <<<<<<<<<<<<<<
+ *         return ' '.join('%s=%s' % feat for feat in self)
+ * 
+ */
+struct __pyx_obj_3_sa___pyx_scope_struct_17___str__ {
+  PyObject_HEAD
+  struct __pyx_obj_3_sa_FeatureVector *__pyx_v_self;
+};
+
+
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":36
  * cdef int EPSILON = sym_fromstring('*EPS*', True)
  * 
  * cdef class TrieNode:             # <<<<<<<<<<<<<<
@@ -977,7 +1018,7 @@ struct __pyx_obj_3_sa_TrieNode {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":24
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":42
  *         self.children = {}
  * 
  * cdef class ExtendedTrieNode(TrieNode):             # <<<<<<<<<<<<<<
@@ -992,7 +1033,7 @@ struct __pyx_obj_3_sa_ExtendedTrieNode {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":109
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":109
  *         trie_node_to_map(edge.node, result, prefix, include_zeros)
  * 
  * cdef class TrieMap:             # <<<<<<<<<<<<<<
@@ -1007,7 +1048,166 @@ struct __pyx_obj_3_sa_TrieMap {
 };
 
 
-/* "_sa.pxd":1
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":112
+ * 
+ * def decode_lattice(lattice):
+ *     return tuple((sym_tostring(sym), weight, dist) for (sym, weight, dist) in arc             # <<<<<<<<<<<<<<
+ *             for arc in node for node in lattice)
+ * 
+ */
+struct __pyx_obj_3_sa___pyx_scope_struct_8_genexpr {
+  PyObject_HEAD
+  struct __pyx_obj_3_sa___pyx_scope_struct_7_decode_lattice *__pyx_outer_scope;
+  PyObject *__pyx_v_arc;
+  PyObject *__pyx_v_dist;
+  PyObject *__pyx_v_node;
+  PyObject *__pyx_v_sym;
+  PyObject *__pyx_v_weight;
+  PyObject *__pyx_t_0;
+  Py_ssize_t __pyx_t_1;
+  PyObject *(*__pyx_t_2)(PyObject *);
+  PyObject *__pyx_t_3;
+  PyObject *__pyx_t_4;
+  Py_ssize_t __pyx_t_5;
+  PyObject *(*__pyx_t_6)(PyObject *);
+  Py_ssize_t __pyx_t_7;
+  PyObject *(*__pyx_t_8)(PyObject *);
+};
+
+
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":107
+ *     return ALPHABET.fromstring(string, terminal)
+ * 
+ * def make_lattice(words):             # <<<<<<<<<<<<<<
+ *     word_ids = (sym_fromstring(word, True) for word in words)
+ *     return tuple(((word, None, 1), ) for word in word_ids)
+ */
+struct __pyx_obj_3_sa___pyx_scope_struct_4_make_lattice {
+  PyObject_HEAD
+  PyObject *__pyx_v_word_ids;
+  PyObject *__pyx_v_words;
+};
+
+
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":183
+ *         return self.f.arity()
+ * 
+ *     def __str__(self):             # <<<<<<<<<<<<<<
+ *         cdef unsigned i
+ *         fields = [sym_tostring(self.lhs), str(self.f), str(self.e), str(self.scores)]
+ */
+struct __pyx_obj_3_sa___pyx_scope_struct_12___str__ {
+  PyObject_HEAD
+  struct __pyx_obj_3_sa_Rule *__pyx_v_self;
+};
+
+
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":939
+ *         return sorted(result);
+ * 
+ *     def input(self, fwords, meta):             # <<<<<<<<<<<<<<
+ *         '''When this function is called on the RuleFactory,
+ *         it looks up all of the rules that can be used to translate
+ */
+struct __pyx_obj_3_sa___pyx_scope_struct_15_input {
+  PyObject_HEAD
+  PyObject *__pyx_v_alignment;
+  PyObject *__pyx_v_als;
+  PyObject *__pyx_v_alslist;
+  int __pyx_v_alt;
+  int __pyx_v_alt_id;
+  int __pyx_v_arity;
+  struct __pyx_obj_3_sa_IntList *__pyx_v_chunklen;
+  PyObject *__pyx_v_count;
+  PyObject *__pyx_v_e;
+  PyObject *__pyx_v_elist;
+  PyObject *__pyx_v_extract;
+  PyObject *__pyx_v_extract_start;
+  PyObject *__pyx_v_extract_stop;
+  PyObject *__pyx_v_extracts;
+  PyObject *__pyx_v_f;
+  PyObject *__pyx_v_fcount;
+  int __pyx_v_flen;
+  PyObject *__pyx_v_fphrases;
+  PyObject *__pyx_v_frontier;
+  PyObject *__pyx_v_frontier_nodes;
+  PyObject *__pyx_v_fwords;
+  struct __pyx_obj_3_sa_Phrase *__pyx_v_hiero_phrase;
+  long __pyx_v_hit;
+  int __pyx_v_i;
+  PyObject *__pyx_v_input_match;
+  PyObject *__pyx_v_is_shadow_path;
+  int __pyx_v_j;
+  int __pyx_v_k;
+  PyObject *__pyx_v_key;
+  PyObject *__pyx_v_loc;
+  PyObject *__pyx_v_locs;
+  int __pyx_v_lookup_required;
+  struct __pyx_t_3_sa_Matching __pyx_v_matching;
+  PyObject *__pyx_v_max_locs;
+  PyObject *__pyx_v_meta;
+  PyObject *__pyx_v_new_frontier;
+  PyObject *__pyx_v_new_node;
+  PyObject *__pyx_v_next_states;
+  PyObject *__pyx_v_node;
+  PyObject *__pyx_v_nodes_isteps_away_buffer;
+  int __pyx_v_nualt;
+  int __pyx_v_num_samples;
+  int __pyx_v_num_subpatterns;
+  PyObject *__pyx_v_pathlen;
+  PyObject *__pyx_v_phrase;
+  struct __pyx_obj_3_sa_PhraseLocation *__pyx_v_phrase_location;
+  PyObject *__pyx_v_prefix;
+  PyObject *__pyx_v_reachable_buffer;
+  PyObject *__pyx_v_sa_range;
+  struct __pyx_obj_3_sa_IntList *__pyx_v_sample;
+  struct __pyx_obj_3_sa_FeatureVector *__pyx_v_scores;
+  struct __pyx_obj_3_sa_HieroCachingRuleFactory *__pyx_v_self;
+  PyObject *__pyx_v_spanlen;
+  float __pyx_v_start_time;
+  PyObject *__pyx_v_stop_time;
+  PyObject *__pyx_v_suffix_link;
+  int __pyx_v_suffix_link_xcat;
+  PyObject *__pyx_v_suffix_link_xcat_index;
+  PyObject *__pyx_v_word_id;
+  int __pyx_v_x1;
+  int __pyx_v_xcat;
+  PyObject *__pyx_v_xcat_index;
+  PyObject *__pyx_v_xnode;
+  PyObject *__pyx_v_xroot;
+  Py_ssize_t __pyx_t_0;
+  PyObject *__pyx_t_1;
+  Py_ssize_t __pyx_t_2;
+  int __pyx_t_3;
+  PyObject *__pyx_t_4;
+  PyObject *__pyx_t_5;
+  int __pyx_t_6;
+  Py_ssize_t __pyx_t_7;
+  Py_ssize_t __pyx_t_8;
+  Py_ssize_t __pyx_t_9;
+};
+
+
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":187
+ *         fields = [sym_tostring(self.lhs), str(self.f), str(self.e), str(self.scores)]
+ *         if self.word_alignments is not None:
+ *             fields.append(' '.join('%d-%d' % a for a in self.alignments()))             # <<<<<<<<<<<<<<
+ *         return ' ||| '.join(fields)
+ * 
+ */
+struct __pyx_obj_3_sa___pyx_scope_struct_13_genexpr {
+  PyObject_HEAD
+  struct __pyx_obj_3_sa___pyx_scope_struct_12___str__ *__pyx_outer_scope;
+  PyObject *__pyx_v_a;
+  PyObject *__pyx_t_0;
+  Py_ssize_t __pyx_t_1;
+  PyObject *(*__pyx_t_2)(PyObject *);
+};
+
+
+/* "_sa.pxd":29
+ *     cdef FloatList values
+ * 
  * cdef class Phrase:             # <<<<<<<<<<<<<<
  *     cdef int *syms
  *     cdef int n, *varpos, n_vars
@@ -1022,7 +1222,23 @@ struct __pyx_obj_3_sa_Phrase {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":35
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/int_list.pxi":81
+ *         free(self.arr)
+ * 
+ *     def __iter__(self):             # <<<<<<<<<<<<<<
+ *         cdef int i
+ *         for i in range(self.len):
+ */
+struct __pyx_obj_3_sa___pyx_scope_struct____iter__ {
+  PyObject_HEAD
+  int __pyx_v_i;
+  struct __pyx_obj_3_sa_IntList *__pyx_v_self;
+  int __pyx_t_0;
+  int __pyx_t_1;
+};
+
+
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":53
  * 
  * 
  * cdef class TrieTable:             # <<<<<<<<<<<<<<
@@ -1037,25 +1253,56 @@ struct __pyx_obj_3_sa_TrieTable {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":73
- *     def read_bitext(self, char* filename, int side):
- *         with gzip_or_text(filename) as fp:
- *             data = (line.split(' ||| ')[side] for line in fp)             # <<<<<<<<<<<<<<
- *             self.read_text_data(data)
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":141
+ *         return self.syms[i]
  * 
+ *     def __iter__(self):             # <<<<<<<<<<<<<<
+ *         cdef int i
+ *         for i from 0 <= i < self.n:
  */
-struct __pyx_obj_3_sa___pyx_scope_struct_1_genexpr {
+struct __pyx_obj_3_sa___pyx_scope_struct_11___iter__ {
   PyObject_HEAD
-  struct __pyx_obj_3_sa___pyx_scope_struct__read_bitext *__pyx_outer_scope;
-  PyObject *__pyx_v_line;
+  int __pyx_v_i;
+  struct __pyx_obj_3_sa_Phrase *__pyx_v_self;
+  int __pyx_t_0;
+};
+
+
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":108
+ * 
+ * def make_lattice(words):
+ *     word_ids = (sym_fromstring(word, True) for word in words)             # <<<<<<<<<<<<<<
+ *     return tuple(((word, None, 1), ) for word in word_ids)
+ * 
+ */
+struct __pyx_obj_3_sa___pyx_scope_struct_5_genexpr {
+  PyObject_HEAD
+  struct __pyx_obj_3_sa___pyx_scope_struct_4_make_lattice *__pyx_outer_scope;
+  PyObject *__pyx_v_word;
   PyObject *__pyx_t_0;
   Py_ssize_t __pyx_t_1;
   PyObject *(*__pyx_t_2)(PyObject *);
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":9
- * from libc.string cimport memset, strcpy, strlen
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":116
+ * 
+ * def decode_sentence(lattice):
+ *     return tuple(sym_tostring(sym) for ((sym, _, _),) in lattice)             # <<<<<<<<<<<<<<
+ */
+struct __pyx_obj_3_sa___pyx_scope_struct_10_genexpr {
+  PyObject_HEAD
+  struct __pyx_obj_3_sa___pyx_scope_struct_9_decode_sentence *__pyx_outer_scope;
+  PyObject *__pyx_v__;
+  PyObject *__pyx_v_sym;
+  PyObject *__pyx_t_0;
+  Py_ssize_t __pyx_t_1;
+  PyObject *(*__pyx_t_2)(PyObject *);
+};
+
+
+/* "_sa.pxd":3
+ * from libc.stdio cimport FILE
  * 
  * cdef class FloatList:             # <<<<<<<<<<<<<<
  *     cdef int size
@@ -1072,7 +1319,7 @@ struct __pyx_obj_3_sa_FloatList {
 
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/str_map.pxi":8
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/str_map.pxi":8
  *     char* stringmap_word(StrMap *vocab, int i)
  * 
  * cdef class StringMap:             # <<<<<<<<<<<<<<
@@ -1087,12 +1334,12 @@ struct __pyx_vtabstruct_3_sa_StringMap {
 static struct __pyx_vtabstruct_3_sa_StringMap *__pyx_vtabptr_3_sa_StringMap;
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":9
- * from libc.string cimport memset, strcpy, strlen
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/data_array.pxi":9
+ * from libc.string cimport memset, strcpy
  * 
  * cdef class DataArray:             # <<<<<<<<<<<<<<
- *     cdef word2id
- *     cdef id2word
+ *     cdef public word2id
+ *     cdef public id2word
  */
 
 struct __pyx_vtabstruct_3_sa_DataArray {
@@ -1102,7 +1349,7 @@ struct __pyx_vtabstruct_3_sa_DataArray {
 static struct __pyx_vtabstruct_3_sa_DataArray *__pyx_vtabptr_3_sa_DataArray;
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":109
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":109
  *         trie_node_to_map(edge.node, result, prefix, include_zeros)
  * 
  * cdef class TrieMap:             # <<<<<<<<<<<<<<
@@ -1117,7 +1364,7 @@ struct __pyx_vtabstruct_3_sa_TrieMap {
 static struct __pyx_vtabstruct_3_sa_TrieMap *__pyx_vtabptr_3_sa_TrieMap;
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":8
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":8
  * # May need to revisit if things get really tight, though.
  * 
  * cdef class Alignment:             # <<<<<<<<<<<<<<
@@ -1133,7 +1380,7 @@ struct __pyx_vtabstruct_3_sa_Alignment {
 static struct __pyx_vtabstruct_3_sa_Alignment *__pyx_vtabptr_3_sa_Alignment;
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":47
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":47
  * 
  * 
  * cdef class BiLex:             # <<<<<<<<<<<<<<
@@ -1152,12 +1399,12 @@ struct __pyx_vtabstruct_3_sa_BiLex {
 static struct __pyx_vtabstruct_3_sa_BiLex *__pyx_vtabptr_3_sa_BiLex;
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":9
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/int_list.pxi":9
  * from libc.string cimport memset, memcpy
  * 
  * cdef class IntList:             # <<<<<<<<<<<<<<
- *     cdef int size
- *     cdef int increment
+ * 
+ *     def __cinit__(self, int size=0, int increment=1, int initial_len=0):
  */
 
 struct __pyx_vtabstruct_3_sa_IntList {
@@ -1172,7 +1419,7 @@ struct __pyx_vtabstruct_3_sa_IntList {
 static struct __pyx_vtabstruct_3_sa_IntList *__pyx_vtabptr_3_sa_IntList;
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":4
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":4
  * from libc.string cimport strsep, strcpy, strlen
  * 
  * cdef class Phrase:             # <<<<<<<<<<<<<<
@@ -1187,7 +1434,7 @@ struct __pyx_vtabstruct_3_sa_Phrase {
 static struct __pyx_vtabstruct_3_sa_Phrase *__pyx_vtabptr_3_sa_Phrase;
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":56
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":74
  * # in the suffix array; if discontiguous, it is the set of
  * # actual locations (packed into an array)
  * cdef class PhraseLocation:             # <<<<<<<<<<<<<<
@@ -1201,7 +1448,7 @@ struct __pyx_vtabstruct_3_sa_PhraseLocation {
 static struct __pyx_vtabstruct_3_sa_PhraseLocation *__pyx_vtabptr_3_sa_PhraseLocation;
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":188
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":188
  * 
  * 
  * cdef class Precomputation:             # <<<<<<<<<<<<<<
@@ -1216,12 +1463,26 @@ struct __pyx_vtabstruct_3_sa_Precomputation {
 static struct __pyx_vtabstruct_3_sa_Precomputation *__pyx_vtabptr_3_sa_Precomputation;
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":9
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/features.pxi":23
+ *         return ' '.join('%s=%s' % feat for feat in self)
+ * 
+ * cdef class Scorer:             # <<<<<<<<<<<<<<
+ *     cdef models
+ *     def __init__(self, *models):
+ */
+
+struct __pyx_vtabstruct_3_sa_Scorer {
+  struct __pyx_obj_3_sa_FeatureVector *(*score)(struct __pyx_obj_3_sa_Scorer *, PyObject *);
+};
+static struct __pyx_vtabstruct_3_sa_Scorer *__pyx_vtabptr_3_sa_Scorer;
+
+
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/float_list.pxi":9
  * from libc.string cimport memset, strcpy, strlen
  * 
  * cdef class FloatList:             # <<<<<<<<<<<<<<
- *     cdef int size
- *     cdef int increment
+ * 
+ *     def __cinit__(self, int size=0, int increment=1, int initial_len=0):
  */
 
 struct __pyx_vtabstruct_3_sa_FloatList {
@@ -1232,7 +1493,7 @@ struct __pyx_vtabstruct_3_sa_FloatList {
 static struct __pyx_vtabstruct_3_sa_FloatList *__pyx_vtabptr_3_sa_FloatList;
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":354
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":354
  * 
  * 
  * cdef class VEB:             # <<<<<<<<<<<<<<
@@ -1248,7 +1509,7 @@ struct __pyx_vtabstruct_3_sa_VEB {
 static struct __pyx_vtabstruct_3_sa_VEB *__pyx_vtabptr_3_sa_VEB;
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":7
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":7
  * cdef int INDEX_MASK = (1<<INDEX_SHIFT)-1
  * 
  * cdef class Alphabet:             # <<<<<<<<<<<<<<
@@ -1271,7 +1532,7 @@ struct __pyx_vtabstruct_3_sa_Alphabet {
 static struct __pyx_vtabstruct_3_sa_Alphabet *__pyx_vtabptr_3_sa_Alphabet;
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":201
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":218
  * 
  * 
  * cdef class HieroCachingRuleFactory:             # <<<<<<<<<<<<<<
@@ -1293,13 +1554,13 @@ struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory {
   PyObject *(*find_projection)(struct __pyx_obj_3_sa_HieroCachingRuleFactory *, int, int, int *, int *, int *, int *);
   int *(*int_arr_extend)(struct __pyx_obj_3_sa_HieroCachingRuleFactory *, int *, int *, int *, int);
   PyObject *(*extract_phrases)(struct __pyx_obj_3_sa_HieroCachingRuleFactory *, int, int, int *, int *, int *, int, int, int, int *, int *, int *, int, int, int);
-  PyObject *(*create_alignments)(struct __pyx_obj_3_sa_HieroCachingRuleFactory *, int *, int, PyObject *, PyObject *);
+  struct __pyx_obj_3_sa_IntList *(*create_alignments)(struct __pyx_obj_3_sa_HieroCachingRuleFactory *, int *, int, PyObject *, PyObject *);
   PyObject *(*extract)(struct __pyx_obj_3_sa_HieroCachingRuleFactory *, struct __pyx_obj_3_sa_Phrase *, struct __pyx_t_3_sa_Matching *, int *, int);
 };
 static struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *__pyx_vtabptr_3_sa_HieroCachingRuleFactory;
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":6
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":6
  * from libc.stdio cimport FILE, fclose, fopen
  * 
  * cdef class SuffixArray:             # <<<<<<<<<<<<<<
@@ -1430,11 +1691,18 @@ static int __Pyx_PyBytes_Tailmatch(PyObject* self, PyObject* substr, Py_ssize_t
                                    Py_ssize_t end, int direction)
 {
     if (unlikely(PyTuple_Check(substr))) {
-        int result;
-        Py_ssize_t i;
-        for (i = 0; i < PyTuple_GET_SIZE(substr); i++) {
+        Py_ssize_t i, count = PyTuple_GET_SIZE(substr);
+        for (i = 0; i < count; i++) {
+            int result;
+#if CYTHON_COMPILING_IN_CPYTHON
             result = __Pyx_PyBytes_SingleTailmatch(self, PyTuple_GET_ITEM(substr, i),
                                                    start, end, direction);
+#else
+            PyObject* sub = PySequence_GetItem(substr, i);
+            if (unlikely(!sub)) return -1;
+            result = __Pyx_PyBytes_SingleTailmatch(self, sub, start, end, direction);
+            Py_DECREF(sub);
+#endif
             if (result) {
                 return result;
             }
@@ -1548,11 +1816,9 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i)
     return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
 }
 
-static CYTHON_INLINE int __Pyx_NegateNonNeg(int b) {
-    return unlikely(b < 0) ? b : !b;
-}
-static CYTHON_INLINE PyObject* __Pyx_PyBoolOrNull_FromLong(long b) {
-    return unlikely(b < 0) ? NULL : __Pyx_PyBool_FromLong(b);
+static CYTHON_INLINE int __Pyx_PySequence_Contains(PyObject* item, PyObject* seq, int eq) {
+    int result = PySequence_Contains(seq, item);
+    return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
 }
 
 static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
@@ -1663,6 +1929,11 @@ static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) {
 #define __Pyx_PyList_Append(L,x) PyList_Append(L,x)
 #endif
 
+static CYTHON_INLINE int __Pyx_PyDict_Contains(PyObject* item, PyObject* dict, int eq) {
+    int result = PyDict_Contains(dict, item);
+    return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
+}
+
 static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void);
 
 static void __Pyx_UnpackTupleError(PyObject *, Py_ssize_t index); /*proto*/
@@ -1744,54 +2015,54 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_Pop(PyObject* L) {
     return PyObject_CallMethod(L, (char*)"pop", NULL);
 }
 
-static PyObject *__Pyx_PyDict_SetDefault(PyObject *d, PyObject *key, PyObject *default_value) {
-    PyObject* value;
-#if PY_MAJOR_VERSION >= 3
-    value = PyDict_GetItemWithError(d, key);
-    if (unlikely(!value)) {
-        if (unlikely(PyErr_Occurred()))
-            return NULL;
-        if (unlikely(PyDict_SetItem(d, key, default_value) == -1))
-            return NULL;
-        value = default_value;
-    }
-    Py_INCREF(value);
-#else
-    if (PyString_CheckExact(key) || PyUnicode_CheckExact(key) || PyInt_CheckExact(key)) {
-        value = PyDict_GetItem(d, key);
-        if (unlikely(!value)) {
-            if (unlikely(PyDict_SetItem(d, key, default_value) == -1))
-                return NULL;
-            value = default_value;
-        }
-        Py_INCREF(value);
-    } else {
-        PyObject *m;
-        m = __Pyx_GetAttrString(d, "setdefault");
-        if (!m) return NULL;
-        value = PyObject_CallFunctionObjArgs(m, key, default_value, NULL);
-        Py_DECREF(m);
-    }
-#endif
-    return value;
-}
-
 static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
 static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
 
 static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level); /*proto*/
 
-#include <string.h>
-
-static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/
+static CYTHON_INLINE void __Pyx_RaiseImportError(PyObject *name);
 
-static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/
-
-#if PY_MAJOR_VERSION >= 3
-#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals
-#else
-#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals
-#endif
+#define __Pyx_CyFunction_USED 1
+#include <structmember.h>
+#define __Pyx_CYFUNCTION_STATICMETHOD  0x01
+#define __Pyx_CYFUNCTION_CLASSMETHOD   0x02
+#define __Pyx_CYFUNCTION_CCLASS        0x04
+#define __Pyx_CyFunction_GetClosure(f) \
+    (((__pyx_CyFunctionObject *) (f))->func_closure)
+#define __Pyx_CyFunction_GetClassObj(f) \
+    (((__pyx_CyFunctionObject *) (f))->func_classobj)
+#define __Pyx_CyFunction_Defaults(type, f) \
+    ((type *)(((__pyx_CyFunctionObject *) (f))->defaults))
+#define __Pyx_CyFunction_SetDefaultsGetter(f, g) \
+    ((__pyx_CyFunctionObject *) (f))->defaults_getter = (g)
+typedef struct {
+    PyCFunctionObject func;
+    int flags;
+    PyObject *func_dict;
+    PyObject *func_weakreflist;
+    PyObject *func_name;
+    PyObject *func_doc;
+    PyObject *func_code;
+    PyObject *func_closure;
+    PyObject *func_classobj; /* No-args super() class cell */
+    void *defaults;
+    int defaults_pyobjects;
+    PyObject *defaults_tuple; /* Const defaults tuple */
+    PyObject *(*defaults_getter)(PyObject *);
+} __pyx_CyFunctionObject;
+static PyTypeObject *__pyx_CyFunctionType = 0;
+#define __Pyx_CyFunction_NewEx(ml, flags, self, module, code) \
+    __Pyx_CyFunction_New(__pyx_CyFunctionType, ml, flags, self, module, code)
+static PyObject *__Pyx_CyFunction_New(PyTypeObject *,
+                                      PyMethodDef *ml, int flags,
+                                      PyObject *self, PyObject *module,
+                                      PyObject* code);
+static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *m,
+                                                         size_t size,
+                                                         int pyobjects);
+static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *m,
+                                                            PyObject *tuple);
+static int __Pyx_CyFunction_init(void);
 
 static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *);
 
@@ -1838,14 +2109,14 @@ typedef struct {
     PyObject_HEAD
     __pyx_generator_body_t body;
     PyObject *closure;
-    int is_running;
-    int resume_label;
     PyObject *exc_type;
     PyObject *exc_value;
     PyObject *exc_traceback;
     PyObject *gi_weakreflist;
     PyObject *classobj;
     PyObject *yieldfrom;
+    int resume_label;
+    char is_running;  // using T_BOOL for property below requires char value
 } __pyx_GeneratorObject;
 static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
                                                   PyObject *closure);
@@ -1892,10 +2163,11 @@ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
 /* Module declarations from 'libc.math' */
 
 /* Module declarations from '_sa' */
-static PyTypeObject *__pyx_ptype_3_sa_Phrase = 0;
-static PyTypeObject *__pyx_ptype_3_sa_Rule = 0;
 static PyTypeObject *__pyx_ptype_3_sa_FloatList = 0;
 static PyTypeObject *__pyx_ptype_3_sa_IntList = 0;
+static PyTypeObject *__pyx_ptype_3_sa_FeatureVector = 0;
+static PyTypeObject *__pyx_ptype_3_sa_Phrase = 0;
+static PyTypeObject *__pyx_ptype_3_sa_Rule = 0;
 static PyTypeObject *__pyx_ptype_3_sa_StringMap = 0;
 static PyTypeObject *__pyx_ptype_3_sa_DataArray = 0;
 static PyTypeObject *__pyx_ptype_3_sa_Alignment = 0;
@@ -1915,11 +2187,26 @@ static PyTypeObject *__pyx_ptype_3_sa_TrieTable = 0;
 static PyTypeObject *__pyx_ptype_3_sa_PhraseLocation = 0;
 static PyTypeObject *__pyx_ptype_3_sa_Sampler = 0;
 static PyTypeObject *__pyx_ptype_3_sa_HieroCachingRuleFactory = 0;
-static PyTypeObject *__pyx_ptype_3_sa___pyx_scope_struct__read_bitext = 0;
-static PyTypeObject *__pyx_ptype_3_sa___pyx_scope_struct_1_genexpr = 0;
-static PyTypeObject *__pyx_ptype_3_sa___pyx_scope_struct_2_compute_stats = 0;
-static PyTypeObject *__pyx_ptype_3_sa___pyx_scope_struct_3___iter__ = 0;
-static PyTypeObject *__pyx_ptype_3_sa___pyx_scope_struct_4_input = 0;
+static PyTypeObject *__pyx_ptype_3_sa_Scorer = 0;
+static PyTypeObject *__pyx_ptype_3_sa___pyx_scope_struct____iter__ = 0;
+static PyTypeObject *__pyx_ptype_3_sa___pyx_scope_struct_1_read_bitext = 0;
+static PyTypeObject *__pyx_ptype_3_sa___pyx_scope_struct_2_genexpr = 0;
+static PyTypeObject *__pyx_ptype_3_sa___pyx_scope_struct_3_compute_stats = 0;
+static PyTypeObject *__pyx_ptype_3_sa___pyx_scope_struct_4_make_lattice = 0;
+static PyTypeObject *__pyx_ptype_3_sa___pyx_scope_struct_5_genexpr = 0;
+static PyTypeObject *__pyx_ptype_3_sa___pyx_scope_struct_6_genexpr = 0;
+static PyTypeObject *__pyx_ptype_3_sa___pyx_scope_struct_7_decode_lattice = 0;
+static PyTypeObject *__pyx_ptype_3_sa___pyx_scope_struct_8_genexpr = 0;
+static PyTypeObject *__pyx_ptype_3_sa___pyx_scope_struct_9_decode_sentence = 0;
+static PyTypeObject *__pyx_ptype_3_sa___pyx_scope_struct_10_genexpr = 0;
+static PyTypeObject *__pyx_ptype_3_sa___pyx_scope_struct_11___iter__ = 0;
+static PyTypeObject *__pyx_ptype_3_sa___pyx_scope_struct_12___str__ = 0;
+static PyTypeObject *__pyx_ptype_3_sa___pyx_scope_struct_13_genexpr = 0;
+static PyTypeObject *__pyx_ptype_3_sa___pyx_scope_struct_14_alignments = 0;
+static PyTypeObject *__pyx_ptype_3_sa___pyx_scope_struct_15_input = 0;
+static PyTypeObject *__pyx_ptype_3_sa___pyx_scope_struct_16___iter__ = 0;
+static PyTypeObject *__pyx_ptype_3_sa___pyx_scope_struct_17___str__ = 0;
+static PyTypeObject *__pyx_ptype_3_sa___pyx_scope_struct_18_genexpr = 0;
 static int __pyx_v_3_sa_MIN_BOTTOM_SIZE;
 static int __pyx_v_3_sa_MIN_BOTTOM_BITS;
 static int __pyx_v_3_sa_LOWER_MASK[32];
@@ -1930,6 +2217,7 @@ static int __pyx_v_3_sa_PRECOMPUTE;
 static int __pyx_v_3_sa_MERGE;
 static int __pyx_v_3_sa_BAEZA_YATES;
 static int __pyx_v_3_sa_EPSILON;
+static struct __pyx_obj_3_sa_StringMap *__pyx_v_3_sa_FD = 0;
 static char *__pyx_f_3_sa_sym_tostring(int); /*proto*/
 static int __pyx_f_3_sa_sym_isvar(int); /*proto*/
 static int __pyx_f_3_sa_sym_getindex(int); /*proto*/
@@ -1949,6 +2237,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *); /*proto*/
 static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *, int); /*proto*/
 static int __pyx_f_3_sa_VEB_contains(struct __pyx_t_3_sa__VEB *, int); /*proto*/
 static int __pyx_f_3_sa_sym_setindex(int, int); /*proto*/
+static int __pyx_f_3_sa_sym_fromstring(char *, int); /*proto*/
 static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_new_trie_node(void); /*proto*/
 static struct __pyx_t_3_sa__Trie_Edge *__pyx_f_3_sa_new_trie_edge(int); /*proto*/
 static PyObject *__pyx_f_3_sa_free_trie_node(struct __pyx_t_3_sa__Trie_Node *); /*proto*/
@@ -1977,8 +2266,8 @@ static PyObject *__pyx_builtin_Exception;
 static PyObject *__pyx_builtin_zip;
 static PyObject *__pyx_builtin_StopIteration;
 static PyObject *__pyx_builtin_cmp;
-static PyObject *__pyx_builtin_ValueError;
 static PyObject *__pyx_builtin_sorted;
+static PyObject *__pyx_builtin_max;
 static PyObject *__pyx_pf_3_sa_gzip_or_text(CYTHON_UNUSED PyObject *__pyx_self, char *__pyx_v_filename); /* proto */
 static int __pyx_pf_3_sa_9FloatList___cinit__(struct __pyx_obj_3_sa_FloatList *__pyx_v_self, int __pyx_v_size, int __pyx_v_increment, int __pyx_v_initial_len); /* proto */
 static void __pyx_pf_3_sa_9FloatList_2__dealloc__(struct __pyx_obj_3_sa_FloatList *__pyx_v_self); /* proto */
@@ -1996,23 +2285,24 @@ static PyObject *__pyx_pf_3_sa_7IntList_8_doquicksort(struct __pyx_obj_3_sa_IntL
 static PyObject *__pyx_pf_3_sa_7IntList_10sort(struct __pyx_obj_3_sa_IntList *__pyx_v_self); /* proto */
 static PyObject *__pyx_pf_3_sa_7IntList_12reset(struct __pyx_obj_3_sa_IntList *__pyx_v_self); /* proto */
 static void __pyx_pf_3_sa_7IntList_14__dealloc__(struct __pyx_obj_3_sa_IntList *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_3_sa_7IntList_16__getitem__(struct __pyx_obj_3_sa_IntList *__pyx_v_self, PyObject *__pyx_v_index); /* proto */
-static int __pyx_pf_3_sa_7IntList_18__setitem__(struct __pyx_obj_3_sa_IntList *__pyx_v_self, PyObject *__pyx_v_i, PyObject *__pyx_v_val); /* proto */
-static Py_ssize_t __pyx_pf_3_sa_7IntList_20__len__(struct __pyx_obj_3_sa_IntList *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_3_sa_7IntList_22getSize(struct __pyx_obj_3_sa_IntList *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_3_sa_7IntList_24append(struct __pyx_obj_3_sa_IntList *__pyx_v_self, int __pyx_v_val); /* proto */
-static PyObject *__pyx_pf_3_sa_7IntList_26extend(struct __pyx_obj_3_sa_IntList *__pyx_v_self, PyObject *__pyx_v_other); /* proto */
-static PyObject *__pyx_pf_3_sa_7IntList_28write(struct __pyx_obj_3_sa_IntList *__pyx_v_self, char *__pyx_v_filename); /* proto */
-static PyObject *__pyx_pf_3_sa_7IntList_30read(struct __pyx_obj_3_sa_IntList *__pyx_v_self, char *__pyx_v_filename); /* proto */
+static PyObject *__pyx_pf_3_sa_7IntList_16__iter__(struct __pyx_obj_3_sa_IntList *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_3_sa_7IntList_19__getitem__(struct __pyx_obj_3_sa_IntList *__pyx_v_self, PyObject *__pyx_v_index); /* proto */
+static int __pyx_pf_3_sa_7IntList_21__setitem__(struct __pyx_obj_3_sa_IntList *__pyx_v_self, PyObject *__pyx_v_i, PyObject *__pyx_v_val); /* proto */
+static Py_ssize_t __pyx_pf_3_sa_7IntList_23__len__(struct __pyx_obj_3_sa_IntList *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_3_sa_7IntList_25get_size(struct __pyx_obj_3_sa_IntList *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_3_sa_7IntList_27append(struct __pyx_obj_3_sa_IntList *__pyx_v_self, int __pyx_v_val); /* proto */
+static PyObject *__pyx_pf_3_sa_7IntList_29extend(struct __pyx_obj_3_sa_IntList *__pyx_v_self, PyObject *__pyx_v_other); /* proto */
+static PyObject *__pyx_pf_3_sa_7IntList_31write(struct __pyx_obj_3_sa_IntList *__pyx_v_self, char *__pyx_v_filename); /* proto */
+static PyObject *__pyx_pf_3_sa_7IntList_33read(struct __pyx_obj_3_sa_IntList *__pyx_v_self, char *__pyx_v_filename); /* proto */
 static int __pyx_pf_3_sa_9StringMap___cinit__(struct __pyx_obj_3_sa_StringMap *__pyx_v_self); /* proto */
 static void __pyx_pf_3_sa_9StringMap_2__dealloc__(struct __pyx_obj_3_sa_StringMap *__pyx_v_self); /* proto */
 static int __pyx_pf_3_sa_9DataArray___cinit__(struct __pyx_obj_3_sa_DataArray *__pyx_v_self, PyObject *__pyx_v_from_binary, PyObject *__pyx_v_from_text, PyObject *__pyx_v_side, int __pyx_v_use_sent_id); /* proto */
 static Py_ssize_t __pyx_pf_3_sa_9DataArray_2__len__(struct __pyx_obj_3_sa_DataArray *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_3_sa_9DataArray_4getSentId(struct __pyx_obj_3_sa_DataArray *__pyx_v_self, PyObject *__pyx_v_i); /* proto */
-static PyObject *__pyx_pf_3_sa_9DataArray_6getSent(struct __pyx_obj_3_sa_DataArray *__pyx_v_self, PyObject *__pyx_v_i); /* proto */
-static PyObject *__pyx_pf_3_sa_9DataArray_8getSentPos(struct __pyx_obj_3_sa_DataArray *__pyx_v_self, PyObject *__pyx_v_loc); /* proto */
-static PyObject *__pyx_pf_3_sa_9DataArray_10get_id(struct __pyx_obj_3_sa_DataArray *__pyx_v_self, PyObject *__pyx_v_word); /* proto */
-static PyObject *__pyx_pf_3_sa_9DataArray_12get_word(struct __pyx_obj_3_sa_DataArray *__pyx_v_self, PyObject *__pyx_v_id); /* proto */
+static PyObject *__pyx_pf_3_sa_9DataArray_4get_sentence_id(struct __pyx_obj_3_sa_DataArray *__pyx_v_self, PyObject *__pyx_v_i); /* proto */
+static PyObject *__pyx_pf_3_sa_9DataArray_6get_sentence(struct __pyx_obj_3_sa_DataArray *__pyx_v_self, PyObject *__pyx_v_i); /* proto */
+static PyObject *__pyx_pf_3_sa_9DataArray_8get_id(struct __pyx_obj_3_sa_DataArray *__pyx_v_self, PyObject *__pyx_v_word); /* proto */
+static PyObject *__pyx_pf_3_sa_9DataArray_10__getitem__(struct __pyx_obj_3_sa_DataArray *__pyx_v_self, PyObject *__pyx_v_loc); /* proto */
+static PyObject *__pyx_pf_3_sa_9DataArray_12get_sentence_bounds(struct __pyx_obj_3_sa_DataArray *__pyx_v_self, PyObject *__pyx_v_loc); /* proto */
 static PyObject *__pyx_pf_3_sa_9DataArray_14write_text(struct __pyx_obj_3_sa_DataArray *__pyx_v_self, char *__pyx_v_filename); /* proto */
 static PyObject *__pyx_pf_3_sa_9DataArray_16read_text(struct __pyx_obj_3_sa_DataArray *__pyx_v_self, char *__pyx_v_filename); /* proto */
 static PyObject *__pyx_pf_3_sa_9DataArray_11read_bitext_genexpr(PyObject *__pyx_self); /* proto */
@@ -2022,6 +2312,21 @@ static PyObject *__pyx_pf_3_sa_9DataArray_22read_binary(struct __pyx_obj_3_sa_Da
 static PyObject *__pyx_pf_3_sa_9DataArray_24write_binary(struct __pyx_obj_3_sa_DataArray *__pyx_v_self, char *__pyx_v_filename); /* proto */
 static PyObject *__pyx_pf_3_sa_9DataArray_26write_enhanced_handle(struct __pyx_obj_3_sa_DataArray *__pyx_v_self, PyObject *__pyx_v_f); /* proto */
 static PyObject *__pyx_pf_3_sa_9DataArray_28write_enhanced(struct __pyx_obj_3_sa_DataArray *__pyx_v_self, char *__pyx_v_filename); /* proto */
+static PyObject *__pyx_pf_3_sa_9DataArray_7word2id___get__(struct __pyx_obj_3_sa_DataArray *__pyx_v_self); /* proto */
+static int __pyx_pf_3_sa_9DataArray_7word2id_2__set__(struct __pyx_obj_3_sa_DataArray *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static int __pyx_pf_3_sa_9DataArray_7word2id_4__del__(struct __pyx_obj_3_sa_DataArray *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_3_sa_9DataArray_7id2word___get__(struct __pyx_obj_3_sa_DataArray *__pyx_v_self); /* proto */
+static int __pyx_pf_3_sa_9DataArray_7id2word_2__set__(struct __pyx_obj_3_sa_DataArray *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static int __pyx_pf_3_sa_9DataArray_7id2word_4__del__(struct __pyx_obj_3_sa_DataArray *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_3_sa_9DataArray_4data___get__(struct __pyx_obj_3_sa_DataArray *__pyx_v_self); /* proto */
+static int __pyx_pf_3_sa_9DataArray_4data_2__set__(struct __pyx_obj_3_sa_DataArray *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static int __pyx_pf_3_sa_9DataArray_4data_4__del__(struct __pyx_obj_3_sa_DataArray *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_3_sa_9DataArray_7sent_id___get__(struct __pyx_obj_3_sa_DataArray *__pyx_v_self); /* proto */
+static int __pyx_pf_3_sa_9DataArray_7sent_id_2__set__(struct __pyx_obj_3_sa_DataArray *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static int __pyx_pf_3_sa_9DataArray_7sent_id_4__del__(struct __pyx_obj_3_sa_DataArray *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_3_sa_9DataArray_10sent_index___get__(struct __pyx_obj_3_sa_DataArray *__pyx_v_self); /* proto */
+static int __pyx_pf_3_sa_9DataArray_10sent_index_2__set__(struct __pyx_obj_3_sa_DataArray *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static int __pyx_pf_3_sa_9DataArray_10sent_index_4__del__(struct __pyx_obj_3_sa_DataArray *__pyx_v_self); /* proto */
 static PyObject *__pyx_pf_3_sa_9Alignment_unlink(CYTHON_UNUSED struct __pyx_obj_3_sa_Alignment *__pyx_v_self, PyObject *__pyx_v_link); /* proto */
 static PyObject *__pyx_pf_3_sa_9Alignment_2get_sent_links(struct __pyx_obj_3_sa_Alignment *__pyx_v_self, int __pyx_v_sent_id); /* proto */
 static int __pyx_pf_3_sa_9Alignment_4__cinit__(struct __pyx_obj_3_sa_Alignment *__pyx_v_self, PyObject *__pyx_v_from_binary, PyObject *__pyx_v_from_text); /* proto */
@@ -2065,7 +2370,13 @@ static int __pyx_pf_3_sa_8Alphabet___cinit__(struct __pyx_obj_3_sa_Alphabet *__p
 static void __pyx_pf_3_sa_8Alphabet_2__dealloc__(CYTHON_UNUSED struct __pyx_obj_3_sa_Alphabet *__pyx_v_self); /* proto */
 static PyObject *__pyx_pf_3_sa_8Alphabet_9terminals___get__(struct __pyx_obj_3_sa_Alphabet *__pyx_v_self); /* proto */
 static PyObject *__pyx_pf_3_sa_8Alphabet_12nonterminals___get__(struct __pyx_obj_3_sa_Alphabet *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_3_sa_2sym_fromstring(CYTHON_UNUSED PyObject *__pyx_self, char *__pyx_v_string, int __pyx_v_terminal); /* proto */
+static PyObject *__pyx_pf_3_sa_12make_lattice_genexpr(PyObject *__pyx_self); /* proto */
+static PyObject *__pyx_pf_3_sa_12make_lattice_3genexpr(PyObject *__pyx_self); /* proto */
+static PyObject *__pyx_pf_3_sa_2make_lattice(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_words); /* proto */
+static PyObject *__pyx_pf_3_sa_14decode_lattice_genexpr(PyObject *__pyx_self); /* proto */
+static PyObject *__pyx_pf_3_sa_4decode_lattice(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_lattice); /* proto */
+static PyObject *__pyx_pf_3_sa_15decode_sentence_genexpr(PyObject *__pyx_self); /* proto */
+static PyObject *__pyx_pf_3_sa_6decode_sentence(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_lattice); /* proto */
 static int __pyx_pf_3_sa_6Phrase___cinit__(struct __pyx_obj_3_sa_Phrase *__pyx_v_self, PyObject *__pyx_v_words); /* proto */
 static void __pyx_pf_3_sa_6Phrase_2__dealloc__(struct __pyx_obj_3_sa_Phrase *__pyx_v_self); /* proto */
 static PyObject *__pyx_pf_3_sa_6Phrase_4__str__(struct __pyx_obj_3_sa_Phrase *__pyx_v_self); /* proto */
@@ -2086,24 +2397,17 @@ static PyObject *__pyx_pf_3_sa_6Phrase_28__iter__(struct __pyx_obj_3_sa_Phrase *
 static PyObject *__pyx_pf_3_sa_6Phrase_31subst(struct __pyx_obj_3_sa_Phrase *__pyx_v_self, PyObject *__pyx_v_start, PyObject *__pyx_v_children); /* proto */
 static PyObject *__pyx_pf_3_sa_6Phrase_5words___get__(struct __pyx_obj_3_sa_Phrase *__pyx_v_self); /* proto */
 static int __pyx_pf_3_sa_4Rule___cinit__(struct __pyx_obj_3_sa_Rule *__pyx_v_self, int __pyx_v_lhs, struct __pyx_obj_3_sa_Phrase *__pyx_v_f, struct __pyx_obj_3_sa_Phrase *__pyx_v_e, PyObject *__pyx_v_scores, PyObject *__pyx_v_word_alignments); /* proto */
-static void __pyx_pf_3_sa_4Rule_2__dealloc__(struct __pyx_obj_3_sa_Rule *__pyx_v_self); /* proto */
-static Py_hash_t __pyx_pf_3_sa_4Rule_4__hash__(struct __pyx_obj_3_sa_Rule *__pyx_v_self); /* proto */
+static Py_hash_t __pyx_pf_3_sa_4Rule_2__hash__(struct __pyx_obj_3_sa_Rule *__pyx_v_self); /* proto */
 #if PY_MAJOR_VERSION < 3
-static int __pyx_pf_3_sa_4Rule_6__cmp__(struct __pyx_obj_3_sa_Rule *__pyx_v_self, struct __pyx_obj_3_sa_Rule *__pyx_v_other); /* proto */
+static int __pyx_pf_3_sa_4Rule_4__cmp__(struct __pyx_obj_3_sa_Rule *__pyx_v_self, struct __pyx_obj_3_sa_Rule *__pyx_v_other); /* proto */
 #endif
-static PyObject *__pyx_pf_3_sa_4Rule_8__iadd__(struct __pyx_obj_3_sa_Rule *__pyx_v_self, struct __pyx_obj_3_sa_Rule *__pyx_v_other); /* proto */
-static PyObject *__pyx_pf_3_sa_4Rule_10fmerge(struct __pyx_obj_3_sa_Rule *__pyx_v_self, struct __pyx_obj_3_sa_Phrase *__pyx_v_f); /* proto */
-static PyObject *__pyx_pf_3_sa_4Rule_12arity(struct __pyx_obj_3_sa_Rule *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_3_sa_4Rule_14__str__(struct __pyx_obj_3_sa_Rule *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_3_sa_4Rule_6scores___get__(struct __pyx_obj_3_sa_Rule *__pyx_v_self); /* proto */
-static int __pyx_pf_3_sa_4Rule_6scores_2__set__(struct __pyx_obj_3_sa_Rule *__pyx_v_self, PyObject *__pyx_v_s); /* proto */
-static PyObject *__pyx_pf_3_sa_4Rule_3lhs___get__(struct __pyx_obj_3_sa_Rule *__pyx_v_self); /* proto */
-static int __pyx_pf_3_sa_4Rule_3lhs_2__set__(struct __pyx_obj_3_sa_Rule *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static PyObject *__pyx_pf_3_sa_4Rule_6fmerge(struct __pyx_obj_3_sa_Rule *__pyx_v_self, struct __pyx_obj_3_sa_Phrase *__pyx_v_f); /* proto */
+static PyObject *__pyx_pf_3_sa_4Rule_8arity(struct __pyx_obj_3_sa_Rule *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_3_sa_4Rule_7__str___genexpr(PyObject *__pyx_self); /* proto */
+static PyObject *__pyx_pf_3_sa_4Rule_10__str__(struct __pyx_obj_3_sa_Rule *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_3_sa_4Rule_12alignments(struct __pyx_obj_3_sa_Rule *__pyx_v_self); /* proto */
 static PyObject *__pyx_pf_3_sa_4Rule_1f___get__(struct __pyx_obj_3_sa_Rule *__pyx_v_self); /* proto */
 static PyObject *__pyx_pf_3_sa_4Rule_1e___get__(struct __pyx_obj_3_sa_Rule *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_3_sa_4Rule_15word_alignments___get__(struct __pyx_obj_3_sa_Rule *__pyx_v_self); /* proto */
-static int __pyx_pf_3_sa_4Rule_15word_alignments_2__set__(struct __pyx_obj_3_sa_Rule *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_3_sa_4Rule_15word_alignments_4__del__(struct __pyx_obj_3_sa_Rule *__pyx_v_self); /* proto */
 static int __pyx_pf_3_sa_7TrieMap___cinit__(struct __pyx_obj_3_sa_TrieMap *__pyx_v_self, int __pyx_v_alphabet_size); /* proto */
 static void __pyx_pf_3_sa_7TrieMap_2__dealloc__(struct __pyx_obj_3_sa_TrieMap *__pyx_v_self); /* proto */
 static PyObject *__pyx_pf_3_sa_7TrieMap_4insert(struct __pyx_obj_3_sa_TrieMap *__pyx_v_self, PyObject *__pyx_v_pattern); /* proto */
@@ -2115,16 +2419,13 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_4write_binary(struct __pyx_obj_3
 static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_sa_Precomputation *__pyx_v_self, PyObject *__pyx_v_stats, struct __pyx_obj_3_sa_SuffixArray *__pyx_v_sarray); /* proto */
 static int __pyx_pf_3_sa_11SuffixArray___cinit__(struct __pyx_obj_3_sa_SuffixArray *__pyx_v_self, PyObject *__pyx_v_from_binary, PyObject *__pyx_v_from_text, PyObject *__pyx_v_side); /* proto */
 static PyObject *__pyx_pf_3_sa_11SuffixArray_2__getitem__(struct __pyx_obj_3_sa_SuffixArray *__pyx_v_self, PyObject *__pyx_v_i); /* proto */
-static PyObject *__pyx_pf_3_sa_11SuffixArray_4getSentId(struct __pyx_obj_3_sa_SuffixArray *__pyx_v_self, PyObject *__pyx_v_i); /* proto */
-static PyObject *__pyx_pf_3_sa_11SuffixArray_6getSent(struct __pyx_obj_3_sa_SuffixArray *__pyx_v_self, PyObject *__pyx_v_i); /* proto */
-static PyObject *__pyx_pf_3_sa_11SuffixArray_8getSentPos(struct __pyx_obj_3_sa_SuffixArray *__pyx_v_self, PyObject *__pyx_v_loc); /* proto */
-static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_SuffixArray *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_side); /* proto */
-static PyObject *__pyx_pf_3_sa_11SuffixArray_12q3sort(struct __pyx_obj_3_sa_SuffixArray *__pyx_v_self, int __pyx_v_i, int __pyx_v_j, int __pyx_v_h, struct __pyx_obj_3_sa_IntList *__pyx_v_isa, PyObject *__pyx_v_pad); /* proto */
-static PyObject *__pyx_pf_3_sa_11SuffixArray_14write_text(struct __pyx_obj_3_sa_SuffixArray *__pyx_v_self, char *__pyx_v_filename); /* proto */
-static PyObject *__pyx_pf_3_sa_11SuffixArray_16read_binary(struct __pyx_obj_3_sa_SuffixArray *__pyx_v_self, char *__pyx_v_filename); /* proto */
-static PyObject *__pyx_pf_3_sa_11SuffixArray_18write_binary(struct __pyx_obj_3_sa_SuffixArray *__pyx_v_self, char *__pyx_v_filename); /* proto */
-static PyObject *__pyx_pf_3_sa_11SuffixArray_20write_enhanced(struct __pyx_obj_3_sa_SuffixArray *__pyx_v_self, char *__pyx_v_filename); /* proto */
-static PyObject *__pyx_pf_3_sa_11SuffixArray_22lookup(struct __pyx_obj_3_sa_SuffixArray *__pyx_v_self, PyObject *__pyx_v_word, int __pyx_v_offset, int __pyx_v_low, int __pyx_v_high); /* proto */
+static PyObject *__pyx_pf_3_sa_11SuffixArray_4read_text(struct __pyx_obj_3_sa_SuffixArray *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_side); /* proto */
+static PyObject *__pyx_pf_3_sa_11SuffixArray_6q3sort(struct __pyx_obj_3_sa_SuffixArray *__pyx_v_self, int __pyx_v_i, int __pyx_v_j, int __pyx_v_h, struct __pyx_obj_3_sa_IntList *__pyx_v_isa, PyObject *__pyx_v_pad); /* proto */
+static PyObject *__pyx_pf_3_sa_11SuffixArray_8write_text(struct __pyx_obj_3_sa_SuffixArray *__pyx_v_self, char *__pyx_v_filename); /* proto */
+static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_binary(struct __pyx_obj_3_sa_SuffixArray *__pyx_v_self, char *__pyx_v_filename); /* proto */
+static PyObject *__pyx_pf_3_sa_11SuffixArray_12write_binary(struct __pyx_obj_3_sa_SuffixArray *__pyx_v_self, char *__pyx_v_filename); /* proto */
+static PyObject *__pyx_pf_3_sa_11SuffixArray_14write_enhanced(struct __pyx_obj_3_sa_SuffixArray *__pyx_v_self, char *__pyx_v_filename); /* proto */
+static PyObject *__pyx_pf_3_sa_11SuffixArray_16lookup(struct __pyx_obj_3_sa_SuffixArray *__pyx_v_self, PyObject *__pyx_v_word, int __pyx_v_offset, int __pyx_v_low, int __pyx_v_high); /* proto */
 static int __pyx_pf_3_sa_8TrieNode___cinit__(struct __pyx_obj_3_sa_TrieNode *__pyx_v_self); /* proto */
 static PyObject *__pyx_pf_3_sa_8TrieNode_8children___get__(struct __pyx_obj_3_sa_TrieNode *__pyx_v_self); /* proto */
 static int __pyx_pf_3_sa_8TrieNode_8children_2__set__(struct __pyx_obj_3_sa_TrieNode *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
@@ -2151,7 +2452,7 @@ static int __pyx_pf_3_sa_14PhraseLocation___cinit__(struct __pyx_obj_3_sa_Phrase
 static int __pyx_pf_3_sa_7Sampler___cinit__(struct __pyx_obj_3_sa_Sampler *__pyx_v_self, int __pyx_v_sample_size, struct __pyx_obj_3_sa_SuffixArray *__pyx_v_fsarray); /* proto */
 static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *__pyx_v_self, struct __pyx_obj_3_sa_PhraseLocation *__pyx_v_phrase_location); /* proto */
 static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_sa_HieroCachingRuleFactory *__pyx_v_self, struct __pyx_obj_3_sa_Alignment *__pyx_v_alignment, float __pyx_v_by_slack_factor, char *__pyx_v_category, PyObject *__pyx_v_max_chunks, unsigned int __pyx_v_max_initial_size, unsigned int __pyx_v_max_length, unsigned int __pyx_v_max_nonterminals, PyObject *__pyx_v_max_target_chunks, PyObject *__pyx_v_max_target_length, unsigned int __pyx_v_min_gap_size, PyObject *__pyx_v_precompute_file, unsigned int __pyx_v_precompute_secondary_rank, unsigned int __pyx_v_precompute_rank, int __pyx_v_require_aligned_terminal, int __pyx_v_require_aligned_chunks, unsigned int __pyx_v_train_max_initial_size, unsigned int __pyx_v_train_min_gap_size, int __pyx_v_tight_phrases, int __pyx_v_use_baeza_yates, int __pyx_v_use_collocations, int __pyx_v_use_index); /* proto */
-static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_2configure(struct __pyx_obj_3_sa_HieroCachingRuleFactory *__pyx_v_self, struct __pyx_obj_3_sa_SuffixArray *__pyx_v_fsarray, struct __pyx_obj_3_sa_DataArray *__pyx_v_edarray, struct __pyx_obj_3_sa_Sampler *__pyx_v_sampler); /* proto */
+static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_2configure(struct __pyx_obj_3_sa_HieroCachingRuleFactory *__pyx_v_self, struct __pyx_obj_3_sa_SuffixArray *__pyx_v_fsarray, struct __pyx_obj_3_sa_DataArray *__pyx_v_edarray, struct __pyx_obj_3_sa_Sampler *__pyx_v_sampler, struct __pyx_obj_3_sa_Scorer *__pyx_v_scorer); /* proto */
 static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_4pattern2phrase(struct __pyx_obj_3_sa_HieroCachingRuleFactory *__pyx_v_self, PyObject *__pyx_v_pattern); /* proto */
 static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_6pattern2phrase_plus(struct __pyx_obj_3_sa_HieroCachingRuleFactory *__pyx_v_self, PyObject *__pyx_v_pattern); /* proto */
 static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_8precompute(struct __pyx_obj_3_sa_HieroCachingRuleFactory *__pyx_v_self); /* proto */
@@ -2161,7 +2462,16 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_14get_all_nodes_isteps_
 static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_16reachable(struct __pyx_obj_3_sa_HieroCachingRuleFactory *__pyx_v_self, PyObject *__pyx_v_fwords, PyObject *__pyx_v_ifrom, PyObject *__pyx_v_dist); /* proto */
 static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_18shortest(struct __pyx_obj_3_sa_HieroCachingRuleFactory *__pyx_v_self, PyObject *__pyx_v_fwords, PyObject *__pyx_v_ifrom, PyObject *__pyx_v_ito); /* proto */
 static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_20get_next_states(struct __pyx_obj_3_sa_HieroCachingRuleFactory *__pyx_v_self, PyObject *__pyx_v__columns, PyObject *__pyx_v_curr_idx, PyObject *__pyx_v_min_dist); /* proto */
-static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_22input(struct __pyx_obj_3_sa_HieroCachingRuleFactory *__pyx_v_self, PyObject *__pyx_v_fwords, PyObject *__pyx_v_models); /* proto */
+static PyObject *__pyx_lambda_funcdef_lambda2(CYTHON_UNUSED PyObject *__pyx_self); /* proto */
+static PyObject *__pyx_lambda_funcdef_lambda1(CYTHON_UNUSED PyObject *__pyx_self); /* proto */
+static PyObject *__pyx_lambda_funcdef_lambda3(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_x); /* proto */
+static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_22input(struct __pyx_obj_3_sa_HieroCachingRuleFactory *__pyx_v_self, PyObject *__pyx_v_fwords, PyObject *__pyx_v_meta); /* proto */
+static int __pyx_pf_3_sa_13FeatureVector___cinit__(struct __pyx_obj_3_sa_FeatureVector *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_3_sa_13FeatureVector_2set(struct __pyx_obj_3_sa_FeatureVector *__pyx_v_self, unsigned int __pyx_v_name, float __pyx_v_value); /* proto */
+static PyObject *__pyx_pf_3_sa_13FeatureVector_4__iter__(struct __pyx_obj_3_sa_FeatureVector *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_3_sa_13FeatureVector_7__str___genexpr(PyObject *__pyx_self); /* proto */
+static PyObject *__pyx_pf_3_sa_13FeatureVector_7__str__(struct __pyx_obj_3_sa_FeatureVector *__pyx_v_self); /* proto */
+static int __pyx_pf_3_sa_6Scorer___init__(struct __pyx_obj_3_sa_Scorer *__pyx_v_self, PyObject *__pyx_v_models); /* proto */
 static char __pyx_k_1[] = ".gz";
 static char __pyx_k_2[] = "Requested index %d of %d-length FloatList";
 static char __pyx_k_3[] = "IntList[";
@@ -2254,10 +2564,11 @@ static char __pyx_k_130[] = "Inside edges of following subphrase are not tight";
 static char __pyx_k_131[] = "Subphrase [%d, %d] failed integrity check";
 static char __pyx_k_132[] = "Didn't extract anything from [%d, %d] -> [%d, %d]";
 static char __pyx_k_133[] = "Unable to extract basic phrase";
-static char __pyx_k_136[] = "/Users/vchahun/Sandbox/cdec/python/src/sa/_sa.pyx";
-static char __pyx_k_137[] = "cdec.sa";
-static char __pyx_k_141[] = "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi";
-static char __pyx_k_142[] = "*EPS*";
+static char __pyx_k_134[] = "%s=%s";
+static char __pyx_k_137[] = "/home/hltcoe/alopez/dev/cdec/python/src/sa/_sa.pyx";
+static char __pyx_k_138[] = "cdec.sa";
+static char __pyx_k_142[] = "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi";
+static char __pyx_k_147[] = "*EPS*";
 static char __pyx_k__gc[] = "gc";
 static char __pyx_k__sa[] = "sa";
 static char __pyx_k___sa[] = "_sa";
@@ -2267,11 +2578,14 @@ static char __pyx_k__col[] = "col";
 static char __pyx_k__end[] = "end";
 static char __pyx_k__isa[] = "isa";
 static char __pyx_k__ito[] = "ito";
+static char __pyx_k__key[] = "key";
 static char __pyx_k__lhs[] = "lhs";
 static char __pyx_k__low[] = "low";
 static char __pyx_k__map[] = "map";
+static char __pyx_k__max[] = "max";
 static char __pyx_k__pad[] = "pad";
 static char __pyx_k__res[] = "res";
+static char __pyx_k__set[] = "set";
 static char __pyx_k__zip[] = "zip";
 static char __pyx_k__NULL[] = "NULL";
 static char __pyx_k__dist[] = "dist";
@@ -2279,6 +2593,8 @@ static char __pyx_k__gzip[] = "gzip";
 static char __pyx_k__high[] = "high";
 static char __pyx_k__info[] = "info";
 static char __pyx_k__join[] = "join";
+static char __pyx_k__meta[] = "meta";
+static char __pyx_k__name[] = "name";
 static char __pyx_k__open[] = "open";
 static char __pyx_k__seek[] = "seek";
 static char __pyx_k__side[] = "side";
@@ -2289,6 +2605,7 @@ static char __pyx_k__warn[] = "warn";
 static char __pyx_k__word[] = "word";
 static char __pyx_k___SEP_[] = "_SEP_";
 static char __pyx_k__arity[] = "arity";
+static char __pyx_k__chain[] = "chain";
 static char __pyx_k__debug[] = "debug";
 static char __pyx_k__eword[] = "eword";
 static char __pyx_k__fword[] = "fword";
@@ -2301,34 +2618,42 @@ static char __pyx_k__split[] = "split";
 static char __pyx_k__start[] = "start";
 static char __pyx_k__stats[] = "stats";
 static char __pyx_k__toMap[] = "toMap";
+static char __pyx_k__value[] = "value";
 static char __pyx_k__words[] = "words";
 static char __pyx_k__write[] = "write";
+static char __pyx_k__e_text[] = "e_text";
 static char __pyx_k__earray[] = "earray";
 static char __pyx_k__extend[] = "extend";
+static char __pyx_k__f_text[] = "f_text";
+static char __pyx_k__fcount[] = "fcount";
 static char __pyx_k__fwords[] = "fwords";
 static char __pyx_k__get_id[] = "get_id";
 static char __pyx_k__insert[] = "insert";
 static char __pyx_k__logger[] = "logger";
 static char __pyx_k__lookup[] = "lookup";
-static char __pyx_k__models[] = "models";
 static char __pyx_k__offset[] = "offset";
 static char __pyx_k__phrase[] = "phrase";
 static char __pyx_k__q3sort[] = "q3sort";
 static char __pyx_k__sa_low[] = "sa_low";
 static char __pyx_k__sample[] = "sample";
 static char __pyx_k__sarray[] = "sarray";
+static char __pyx_k__scorer[] = "scorer";
 static char __pyx_k__scores[] = "scores";
 static char __pyx_k__sorted[] = "sorted";
 static char __pyx_k__source[] = "source";
-static char __pyx_k__string[] = "string";
 static char __pyx_k__unlink[] = "unlink";
+static char __pyx_k__Counter[] = "Counter";
 static char __pyx_k__advance[] = "advance";
 static char __pyx_k__arr_low[] = "arr_low";
 static char __pyx_k__collect[] = "collect";
 static char __pyx_k__edarray[] = "edarray";
+static char __pyx_k__ephrase[] = "ephrase";
+static char __pyx_k__fphrase[] = "fphrase";
 static char __pyx_k__fsarray[] = "fsarray";
-static char __pyx_k__getSent[] = "getSent";
+static char __pyx_k__genexpr[] = "genexpr";
+static char __pyx_k__lattice[] = "lattice";
 static char __pyx_k__logging[] = "logging";
+static char __pyx_k__matches[] = "matches";
 static char __pyx_k__pathlen[] = "pathlen";
 static char __pyx_k__sa_high[] = "sa_high";
 static char __pyx_k__sampler[] = "sampler";
@@ -2336,6 +2661,7 @@ static char __pyx_k__spanlen[] = "spanlen";
 static char __pyx_k__GzipFile[] = "GzipFile";
 static char __pyx_k____exit__[] = "__exit__";
 static char __pyx_k____main__[] = "__main__";
+static char __pyx_k____name__[] = "__name__";
 static char __pyx_k____test__[] = "__test__";
 static char __pyx_k___columns[] = "_columns";
 static char __pyx_k__arr_high[] = "arr_high";
@@ -2354,8 +2680,9 @@ static char __pyx_k__resource[] = "resource";
 static char __pyx_k__ru_stime[] = "ru_stime";
 static char __pyx_k__ru_utime[] = "ru_utime";
 static char __pyx_k__shortest[] = "shortest";
-static char __pyx_k__terminal[] = "terminal";
+static char __pyx_k__word_ids[] = "word_ids";
 static char __pyx_k__Exception[] = "Exception";
+static char __pyx_k__INCREMENT[] = "INCREMENT";
 static char __pyx_k__TypeError[] = "TypeError";
 static char __pyx_k____enter__[] = "__enter__";
 static char __pyx_k__alignment[] = "alignment";
@@ -2363,28 +2690,33 @@ static char __pyx_k__enumerate[] = "enumerate";
 static char __pyx_k__from_data[] = "from_data";
 static char __pyx_k__from_text[] = "from_text";
 static char __pyx_k__getLogger[] = "getLogger";
-static char __pyx_k__getSentId[] = "getSentId";
 static char __pyx_k__getrusage[] = "getrusage";
 static char __pyx_k__increment[] = "increment";
 static char __pyx_k__iteritems[] = "iteritems";
+static char __pyx_k__itertools[] = "itertools";
+static char __pyx_k__paircount[] = "paircount";
 static char __pyx_k__partition[] = "partition";
 static char __pyx_k__reachable[] = "reachable";
 static char __pyx_k__read_text[] = "read_text";
 static char __pyx_k__use_index[] = "use_index";
 static char __pyx_k__IndexError[] = "IndexError";
-static char __pyx_k__ValueError[] = "ValueError";
+static char __pyx_k__alignments[] = "alignments";
 static char __pyx_k__from_stats[] = "from_stats";
-static char __pyx_k__getSentPos[] = "getSentPos";
+static char __pyx_k__input_span[] = "input_span";
+static char __pyx_k__itervalues[] = "itervalues";
 static char __pyx_k__max_chunks[] = "max_chunks";
 static char __pyx_k__max_length[] = "max_length";
+static char __pyx_k__namedtuple[] = "namedtuple";
 static char __pyx_k__precompute[] = "precompute";
-static char __pyx_k__setdefault[] = "setdefault";
 static char __pyx_k__write_text[] = "write_text";
 static char __pyx_k__END_OF_FILE[] = "END_OF_FILE";
 static char __pyx_k__END_OF_LINE[] = "END_OF_LINE";
 static char __pyx_k__RUSAGE_SELF[] = "RUSAGE_SELF";
+static char __pyx_k__collections[] = "collections";
+static char __pyx_k__defaultdict[] = "defaultdict";
 static char __pyx_k__from_binary[] = "from_binary";
 static char __pyx_k__initial_len[] = "initial_len";
+static char __pyx_k__input_match[] = "input_match";
 static char __pyx_k__next_states[] = "next_states";
 static char __pyx_k__precomputed[] = "precomputed";
 static char __pyx_k__read_binary[] = "read_binary";
@@ -2394,14 +2726,20 @@ static char __pyx_k__suffix_link[] = "suffix_link";
 static char __pyx_k__use_sent_id[] = "use_sent_id";
 static char __pyx_k___doquicksort[] = "_doquicksort";
 static char __pyx_k__gzip_or_text[] = "gzip_or_text";
+static char __pyx_k__make_lattice[] = "make_lattice";
 static char __pyx_k__min_gap_size[] = "min_gap_size";
 static char __pyx_k__StopIteration[] = "StopIteration";
 static char __pyx_k__alphabet_size[] = "alphabet_size";
+static char __pyx_k__from_iterable[] = "from_iterable";
+static char __pyx_k__fsample_count[] = "fsample_count";
+static char __pyx_k__test_sentence[] = "test_sentence";
 static char __pyx_k__tight_phrases[] = "tight_phrases";
+static char __pyx_k__FeatureContext[] = "FeatureContext";
+static char __pyx_k__decode_lattice[] = "decode_lattice";
 static char __pyx_k__pattern2phrase[] = "pattern2phrase";
 static char __pyx_k__read_text_data[] = "read_text_data";
-static char __pyx_k__sym_fromstring[] = "sym_fromstring";
 static char __pyx_k__by_slack_factor[] = "by_slack_factor";
+static char __pyx_k__decode_sentence[] = "decode_sentence";
 static char __pyx_k__get_next_states[] = "get_next_states";
 static char __pyx_k__num_subpatterns[] = "num_subpatterns";
 static char __pyx_k__phrase_location[] = "phrase_location";
@@ -2409,6 +2747,7 @@ static char __pyx_k__precompute_file[] = "precompute_file";
 static char __pyx_k__precompute_rank[] = "precompute_rank";
 static char __pyx_k__use_baeza_yates[] = "use_baeza_yates";
 static char __pyx_k__word_alignments[] = "word_alignments";
+static char __pyx_k__INITIAL_CAPACITY[] = "INITIAL_CAPACITY";
 static char __pyx_k__max_initial_size[] = "max_initial_size";
 static char __pyx_k__max_nonterminals[] = "max_nonterminals";
 static char __pyx_k__reachable_buffer[] = "reachable_buffer";
@@ -2449,10 +2788,10 @@ static PyObject *__pyx_kp_s_130;
 static PyObject *__pyx_kp_s_131;
 static PyObject *__pyx_kp_s_132;
 static PyObject *__pyx_kp_s_133;
-static PyObject *__pyx_kp_s_136;
+static PyObject *__pyx_kp_s_134;
 static PyObject *__pyx_kp_s_137;
+static PyObject *__pyx_kp_s_138;
 static PyObject *__pyx_kp_s_14;
-static PyObject *__pyx_kp_s_141;
 static PyObject *__pyx_kp_s_142;
 static PyObject *__pyx_kp_s_18;
 static PyObject *__pyx_kp_s_2;
@@ -2505,25 +2844,30 @@ static PyObject *__pyx_kp_s_94;
 static PyObject *__pyx_kp_s_95;
 static PyObject *__pyx_kp_s__0;
 static PyObject *__pyx_kp_s__1;
+static PyObject *__pyx_n_s__Counter;
 static PyObject *__pyx_n_s__END_OF_FILE;
 static PyObject *__pyx_n_s__END_OF_LINE;
 static PyObject *__pyx_n_s__Exception;
+static PyObject *__pyx_n_s__FeatureContext;
 static PyObject *__pyx_n_s__GzipFile;
+static PyObject *__pyx_n_s__INCREMENT;
+static PyObject *__pyx_n_s__INITIAL_CAPACITY;
 static PyObject *__pyx_n_s__IndexError;
 static PyObject *__pyx_n_s__NULL;
 static PyObject *__pyx_n_s__RUSAGE_SELF;
 static PyObject *__pyx_n_s__StopIteration;
 static PyObject *__pyx_n_s__TypeError;
-static PyObject *__pyx_n_s__ValueError;
 static PyObject *__pyx_n_s____enter__;
 static PyObject *__pyx_n_s____exit__;
 static PyObject *__pyx_n_s____main__;
+static PyObject *__pyx_n_s____name__;
 static PyObject *__pyx_n_s____test__;
 static PyObject *__pyx_n_s___columns;
 static PyObject *__pyx_n_s___doquicksort;
 static PyObject *__pyx_n_s___sa;
 static PyObject *__pyx_n_s__advance;
 static PyObject *__pyx_n_s__alignment;
+static PyObject *__pyx_n_s__alignments;
 static PyObject *__pyx_n_s__alphabet_size;
 static PyObject *__pyx_n_s__arity;
 static PyObject *__pyx_n_s__arr;
@@ -2531,36 +2875,46 @@ static PyObject *__pyx_n_s__arr_high;
 static PyObject *__pyx_n_s__arr_low;
 static PyObject *__pyx_n_s__by_slack_factor;
 static PyObject *__pyx_n_s__category;
+static PyObject *__pyx_n_s__chain;
 static PyObject *__pyx_n_s__children;
 static PyObject *__pyx_n_s__cmp;
 static PyObject *__pyx_n_s__col;
 static PyObject *__pyx_n_s__collect;
+static PyObject *__pyx_n_s__collections;
 static PyObject *__pyx_n_s__curr_idx;
 static PyObject *__pyx_n_s__debug;
+static PyObject *__pyx_n_s__decode_lattice;
+static PyObject *__pyx_n_s__decode_sentence;
+static PyObject *__pyx_n_s__defaultdict;
 static PyObject *__pyx_n_s__dist;
 static PyObject *__pyx_n_s__e;
+static PyObject *__pyx_n_s__e_text;
 static PyObject *__pyx_n_s__earray;
 static PyObject *__pyx_n_s__edarray;
 static PyObject *__pyx_n_s__end;
 static PyObject *__pyx_n_s__enumerate;
+static PyObject *__pyx_n_s__ephrase;
 static PyObject *__pyx_n_s__eword;
 static PyObject *__pyx_n_s__extend;
 static PyObject *__pyx_n_s__extended;
 static PyObject *__pyx_n_s__f;
+static PyObject *__pyx_n_s__f_text;
+static PyObject *__pyx_n_s__fcount;
 static PyObject *__pyx_n_s__filename;
+static PyObject *__pyx_n_s__fphrase;
 static PyObject *__pyx_n_s__from_binary;
 static PyObject *__pyx_n_s__from_data;
+static PyObject *__pyx_n_s__from_iterable;
 static PyObject *__pyx_n_s__from_stats;
 static PyObject *__pyx_n_s__from_text;
 static PyObject *__pyx_n_s__frontier;
+static PyObject *__pyx_n_s__fsample_count;
 static PyObject *__pyx_n_s__fsarray;
 static PyObject *__pyx_n_s__fword;
 static PyObject *__pyx_n_s__fwords;
 static PyObject *__pyx_n_s__gc;
+static PyObject *__pyx_n_s__genexpr;
 static PyObject *__pyx_n_s__getLogger;
-static PyObject *__pyx_n_s__getSent;
-static PyObject *__pyx_n_s__getSentId;
-static PyObject *__pyx_n_s__getSentPos;
 static PyObject *__pyx_n_s__get_e_id;
 static PyObject *__pyx_n_s__get_f_id;
 static PyObject *__pyx_n_s__get_id;
@@ -2578,18 +2932,27 @@ static PyObject *__pyx_n_s__increment;
 static PyObject *__pyx_n_s__index;
 static PyObject *__pyx_n_s__info;
 static PyObject *__pyx_n_s__initial_len;
+static PyObject *__pyx_n_s__input_match;
+static PyObject *__pyx_n_s__input_span;
 static PyObject *__pyx_n_s__insert;
 static PyObject *__pyx_n_s__isa;
 static PyObject *__pyx_n_s__iteritems;
+static PyObject *__pyx_n_s__itertools;
+static PyObject *__pyx_n_s__itervalues;
 static PyObject *__pyx_n_s__ito;
 static PyObject *__pyx_n_s__j;
 static PyObject *__pyx_n_s__join;
+static PyObject *__pyx_n_s__key;
+static PyObject *__pyx_n_s__lattice;
 static PyObject *__pyx_n_s__lhs;
 static PyObject *__pyx_n_s__logger;
 static PyObject *__pyx_n_s__logging;
 static PyObject *__pyx_n_s__lookup;
 static PyObject *__pyx_n_s__low;
+static PyObject *__pyx_n_s__make_lattice;
 static PyObject *__pyx_n_s__map;
+static PyObject *__pyx_n_s__matches;
+static PyObject *__pyx_n_s__max;
 static PyObject *__pyx_n_s__max_chunks;
 static PyObject *__pyx_n_s__max_initial_size;
 static PyObject *__pyx_n_s__max_length;
@@ -2597,14 +2960,17 @@ static PyObject *__pyx_n_s__max_nonterminals;
 static PyObject *__pyx_n_s__max_target_chunks;
 static PyObject *__pyx_n_s__max_target_length;
 static PyObject *__pyx_n_s__merge;
+static PyObject *__pyx_n_s__meta;
 static PyObject *__pyx_n_s__min_dist;
 static PyObject *__pyx_n_s__min_gap_size;
-static PyObject *__pyx_n_s__models;
+static PyObject *__pyx_n_s__name;
+static PyObject *__pyx_n_s__namedtuple;
 static PyObject *__pyx_n_s__next_states;
 static PyObject *__pyx_n_s__num_subpatterns;
 static PyObject *__pyx_n_s__offset;
 static PyObject *__pyx_n_s__open;
 static PyObject *__pyx_n_s__pad;
+static PyObject *__pyx_n_s__paircount;
 static PyObject *__pyx_n_s__partition;
 static PyObject *__pyx_n_s__pathlen;
 static PyObject *__pyx_n_s__pattern2phrase;
@@ -2635,9 +3001,10 @@ static PyObject *__pyx_n_s__sample;
 static PyObject *__pyx_n_s__sample_size;
 static PyObject *__pyx_n_s__sampler;
 static PyObject *__pyx_n_s__sarray;
+static PyObject *__pyx_n_s__scorer;
 static PyObject *__pyx_n_s__scores;
 static PyObject *__pyx_n_s__seek;
-static PyObject *__pyx_n_s__setdefault;
+static PyObject *__pyx_n_s__set;
 static PyObject *__pyx_n_s__shortest;
 static PyObject *__pyx_n_s__side;
 static PyObject *__pyx_n_s__size;
@@ -2649,10 +3016,8 @@ static PyObject *__pyx_n_s__split;
 static PyObject *__pyx_n_s__start;
 static PyObject *__pyx_n_s__stats;
 static PyObject *__pyx_n_s__stop;
-static PyObject *__pyx_n_s__string;
 static PyObject *__pyx_n_s__suffix_link;
-static PyObject *__pyx_n_s__sym_fromstring;
-static PyObject *__pyx_n_s__terminal;
+static PyObject *__pyx_n_s__test_sentence;
 static PyObject *__pyx_n_s__tight_phrases;
 static PyObject *__pyx_n_s__toMap;
 static PyObject *__pyx_n_s__train_min_gap_size;
@@ -2661,10 +3026,12 @@ static PyObject *__pyx_n_s__use_baeza_yates;
 static PyObject *__pyx_n_s__use_collocations;
 static PyObject *__pyx_n_s__use_index;
 static PyObject *__pyx_n_s__use_sent_id;
+static PyObject *__pyx_n_s__value;
 static PyObject *__pyx_n_s__w;
 static PyObject *__pyx_n_s__warn;
 static PyObject *__pyx_n_s__word;
 static PyObject *__pyx_n_s__word_alignments;
+static PyObject *__pyx_n_s__word_ids;
 static PyObject *__pyx_n_s__words;
 static PyObject *__pyx_n_s__write;
 static PyObject *__pyx_n_s__write_text;
@@ -2673,6 +3040,7 @@ static PyObject *__pyx_int_0;
 static PyObject *__pyx_int_1;
 static PyObject *__pyx_int_2;
 static PyObject *__pyx_int_5;
+static PyObject *__pyx_int_7;
 static PyObject *__pyx_int_neg_1;
 static PyObject *__pyx_int_10;
 static PyObject *__pyx_int_20;
@@ -2728,11 +3096,15 @@ static PyObject *__pyx_k_tuple_98;
 static PyObject *__pyx_k_tuple_102;
 static PyObject *__pyx_k_tuple_107;
 static PyObject *__pyx_k_tuple_122;
-static PyObject *__pyx_k_tuple_134;
-static PyObject *__pyx_k_tuple_138;
+static PyObject *__pyx_k_tuple_135;
 static PyObject *__pyx_k_tuple_139;
-static PyObject *__pyx_k_codeobj_135;
-static PyObject *__pyx_k_codeobj_140;
+static PyObject *__pyx_k_tuple_140;
+static PyObject *__pyx_k_tuple_143;
+static PyObject *__pyx_k_tuple_145;
+static PyObject *__pyx_k_codeobj_136;
+static PyObject *__pyx_k_codeobj_141;
+static PyObject *__pyx_k_codeobj_144;
+static PyObject *__pyx_k_codeobj_146;
 
 /* "_sa.pyx":5
  * import gzip
@@ -3002,7 +3374,7 @@ static int __pyx_pw_3_sa_9FloatList_1__cinit__(PyObject *__pyx_v_self, PyObject
         }
       }
       if (unlikely(kw_args > 0)) {
-        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
       }
     } else {
       switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -3014,24 +3386,24 @@ static int __pyx_pw_3_sa_9FloatList_1__cinit__(PyObject *__pyx_v_self, PyObject
       }
     }
     if (values[0]) {
-      __pyx_v_size = __Pyx_PyInt_AsInt(values[0]); if (unlikely((__pyx_v_size == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+      __pyx_v_size = __Pyx_PyInt_AsInt(values[0]); if (unlikely((__pyx_v_size == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
     } else {
       __pyx_v_size = ((int)0);
     }
     if (values[1]) {
-      __pyx_v_increment = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_increment == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+      __pyx_v_increment = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_increment == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
     } else {
       __pyx_v_increment = ((int)1);
     }
     if (values[2]) {
-      __pyx_v_initial_len = __Pyx_PyInt_AsInt(values[2]); if (unlikely((__pyx_v_initial_len == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+      __pyx_v_initial_len = __Pyx_PyInt_AsInt(values[2]); if (unlikely((__pyx_v_initial_len == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
     } else {
       __pyx_v_initial_len = ((int)0);
     }
   }
   goto __pyx_L4_argument_unpacking_done;
   __pyx_L5_argtuple_error:;
-  __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 0, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[1]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+  __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 0, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[1]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
   __pyx_L3_error:;
   __Pyx_AddTraceback("_sa.FloatList.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
   __Pyx_RefNannyFinishContext();
@@ -3042,8 +3414,8 @@ static int __pyx_pw_3_sa_9FloatList_1__cinit__(PyObject *__pyx_v_self, PyObject
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":15
- *     cdef float* arr
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/float_list.pxi":11
+ * cdef class FloatList:
  * 
  *     def __cinit__(self, int size=0, int increment=1, int initial_len=0):             # <<<<<<<<<<<<<<
  *         if initial_len > size:
@@ -3056,7 +3428,7 @@ static int __pyx_pf_3_sa_9FloatList___cinit__(struct __pyx_obj_3_sa_FloatList *_
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   __Pyx_RefNannySetupContext("__cinit__", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":16
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/float_list.pxi":12
  * 
  *     def __cinit__(self, int size=0, int increment=1, int initial_len=0):
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@@ -3066,7 +3438,7 @@ static int __pyx_pf_3_sa_9FloatList___cinit__(struct __pyx_obj_3_sa_FloatList *_
   __pyx_t_1 = (__pyx_v_initial_len > __pyx_v_size);
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":17
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/float_list.pxi":13
  *     def __cinit__(self, int size=0, int increment=1, int initial_len=0):
  *         if initial_len > size:
  *             size = initial_len             # <<<<<<<<<<<<<<
@@ -3078,7 +3450,7 @@ static int __pyx_pf_3_sa_9FloatList___cinit__(struct __pyx_obj_3_sa_FloatList *_
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":18
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/float_list.pxi":14
  *         if initial_len > size:
  *             size = initial_len
  *         self.size = size             # <<<<<<<<<<<<<<
@@ -3087,7 +3459,7 @@ static int __pyx_pf_3_sa_9FloatList___cinit__(struct __pyx_obj_3_sa_FloatList *_
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":19
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/float_list.pxi":15
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  *         self.size = size
  *         self.increment = increment             # <<<<<<<<<<<<<<
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":20
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/float_list.pxi":16
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  *         self.increment = increment
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":21
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/float_list.pxi":17
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":22
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/float_list.pxi":18
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":25
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":27
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":28
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":29
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":30
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+    __pyx_v_val = __pyx_PyFloat_AsFloat(__pyx_arg_val); if (unlikely((__pyx_v_val == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":49
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/float_list.pxi":45
  *         return self.len
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@@ -3576,7 +3945,7 @@ static PyObject *__pyx_pf_3_sa_9FloatList_10append(struct __pyx_obj_3_sa_FloatLi
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":50
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/float_list.pxi":46
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@@ -3586,7 +3955,7 @@ static PyObject *__pyx_pf_3_sa_9FloatList_10append(struct __pyx_obj_3_sa_FloatLi
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":51
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/float_list.pxi":47
  *     def append(self, float val):
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  *             self.size = self.size + self.increment             # <<<<<<<<<<<<<<
@@ -3595,7 +3964,7 @@ static PyObject *__pyx_pf_3_sa_9FloatList_10append(struct __pyx_obj_3_sa_FloatLi
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":52
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/float_list.pxi":48
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  *             self.arr = <float*> realloc(self.arr, self.size*sizeof(float))             # <<<<<<<<<<<<<<
@@ -3607,7 +3976,7 @@ static PyObject *__pyx_pf_3_sa_9FloatList_10append(struct __pyx_obj_3_sa_FloatLi
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":53
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/float_list.pxi":49
  *             self.size = self.size + self.increment
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  *         self.arr[self.len] = val             # <<<<<<<<<<<<<<
@@ -3616,7 +3985,7 @@ static PyObject *__pyx_pf_3_sa_9FloatList_10append(struct __pyx_obj_3_sa_FloatLi
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":54
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/float_list.pxi":50
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  *         self.len = self.len + 1             # <<<<<<<<<<<<<<
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":56
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/float_list.pxi":52
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":57
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/float_list.pxi":53
  * 
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@@ -3652,7 +4021,7 @@ static void __pyx_f_3_sa_9FloatList_write_handle(struct __pyx_obj_3_sa_FloatList
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   fwrite((&__pyx_v_self->len), (sizeof(float)), 1, __pyx_v_f);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":58
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/float_list.pxi":54
  *     cdef void write_handle(self, FILE* f):
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  *         fwrite(self.arr, sizeof(float), self.len, f)             # <<<<<<<<<<<<<<
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+    __pyx_v_filename = PyBytes_AsString(__pyx_arg_filename); if (unlikely((!__pyx_v_filename) && PyErr_Occurred())) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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@@ -3685,7 +4054,7 @@ static PyObject *__pyx_pw_3_sa_9FloatList_13write(PyObject *__pyx_v_self, PyObje
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":60
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/float_list.pxi":56
  *         fwrite(self.arr, sizeof(float), self.len, f)
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":62
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/float_list.pxi":58
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   __pyx_v_f = fopen(__pyx_v_filename, __pyx_k__w);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":63
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/float_list.pxi":59
  *         cdef FILE* f
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   ((struct __pyx_vtabstruct_3_sa_FloatList *)__pyx_v_self->__pyx_vtab)->write_handle(__pyx_v_self, __pyx_v_f);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":64
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/float_list.pxi":60
  *         f = fopen(filename, "w")
  *         self.write_handle(f)
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@@ -3732,7 +4101,7 @@ static PyObject *__pyx_pf_3_sa_9FloatList_12write(struct __pyx_obj_3_sa_FloatLis
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":66
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/float_list.pxi":62
  *         fclose(f)
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  *     cdef void read_handle(self, FILE* f):             # <<<<<<<<<<<<<<
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":67
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/float_list.pxi":63
  * 
  *     cdef void read_handle(self, FILE* f):
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@@ -3753,7 +4122,7 @@ static void __pyx_f_3_sa_9FloatList_read_handle(struct __pyx_obj_3_sa_FloatList
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   free(__pyx_v_self->arr);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":68
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/float_list.pxi":64
  *     cdef void read_handle(self, FILE* f):
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  *         fread(&(self.len), sizeof(float), 1, f)             # <<<<<<<<<<<<<<
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   fread((&__pyx_v_self->len), (sizeof(float)), 1, __pyx_v_f);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":69
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/float_list.pxi":65
  *         free(self.arr)
  *         fread(&(self.len), sizeof(float), 1, f)
  *         self.arr = <float*> malloc(self.len * sizeof(float))             # <<<<<<<<<<<<<<
@@ -3771,7 +4140,7 @@ static void __pyx_f_3_sa_9FloatList_read_handle(struct __pyx_obj_3_sa_FloatList
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   __pyx_v_self->arr = ((float *)malloc((__pyx_v_self->len * (sizeof(float)))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":70
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/float_list.pxi":66
  *         fread(&(self.len), sizeof(float), 1, f)
  *         self.arr = <float*> malloc(self.len * sizeof(float))
  *         self.size = self.len             # <<<<<<<<<<<<<<
@@ -3780,7 +4149,7 @@ static void __pyx_f_3_sa_9FloatList_read_handle(struct __pyx_obj_3_sa_FloatList
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   __pyx_v_self->size = __pyx_v_self->len;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":71
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/float_list.pxi":67
  *         self.arr = <float*> malloc(self.len * sizeof(float))
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  *         fread(self.arr, sizeof(float), self.len, f)             # <<<<<<<<<<<<<<
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+    __pyx_v_filename = PyBytes_AsString(__pyx_arg_filename); if (unlikely((!__pyx_v_filename) && PyErr_Occurred())) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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@@ -3813,7 +4182,7 @@ static PyObject *__pyx_pw_3_sa_9FloatList_15read(PyObject *__pyx_v_self, PyObjec
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":73
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/float_list.pxi":69
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":75
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/float_list.pxi":71
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":76
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/float_list.pxi":72
  *         cdef FILE* f
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  *         self.read_handle(f)             # <<<<<<<<<<<<<<
@@ -3844,7 +4213,7 @@ static PyObject *__pyx_pf_3_sa_9FloatList_14read(struct __pyx_obj_3_sa_FloatList
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":77
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/float_list.pxi":73
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@@ -3898,7 +4267,7 @@ static int __pyx_pw_3_sa_7IntList_1__cinit__(PyObject *__pyx_v_self, PyObject *_
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+        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+      __pyx_v_size = __Pyx_PyInt_AsInt(values[0]); if (unlikely((__pyx_v_size == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+      __pyx_v_increment = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_increment == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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     if (values[2]) {
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+      __pyx_v_initial_len = __Pyx_PyInt_AsInt(values[2]); if (unlikely((__pyx_v_initial_len == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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-  __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 0, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+  __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 0, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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@@ -3938,8 +4307,8 @@ static int __pyx_pw_3_sa_7IntList_1__cinit__(PyObject *__pyx_v_self, PyObject *_
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":15
- *     cdef int* arr
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/int_list.pxi":11
+ * cdef class IntList:
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":16
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/int_list.pxi":12
  * 
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":17
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/int_list.pxi":13
  *     def __cinit__(self, int size=0, int increment=1, int initial_len=0):
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":18
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/int_list.pxi":14
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":19
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/int_list.pxi":15
  *             size = initial_len
  *         self.size = size
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   __pyx_v_self->increment = __pyx_v_increment;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":20
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/int_list.pxi":16
  *         self.size = size
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  *         self.len = initial_len             # <<<<<<<<<<<<<<
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   __pyx_v_self->len = __pyx_v_initial_len;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":21
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/int_list.pxi":17
  *         self.increment = increment
  *         self.len = initial_len
  *         self.arr = <int*> malloc(size*sizeof(int))             # <<<<<<<<<<<<<<
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":22
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/int_list.pxi":18
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":26
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/int_list.pxi":22
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":27
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":28
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":29
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":30
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":31
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":32
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/int_list.pxi":28
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":33
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/int_list.pxi":29
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+  __pyx_t_4 = PyNumber_InPlaceAdd(__pyx_v_ret, __pyx_t_5); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":34
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/int_list.pxi":30
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-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":36
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/int_list.pxi":32
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":38
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/int_list.pxi":34
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":39
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/int_list.pxi":35
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":40
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":41
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/int_list.pxi":37
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":44
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":45
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":46
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":49
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":50
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":53
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":54
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":55
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":56
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":57
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":58
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":59
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":60
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/int_list.pxi":56
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":61
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":63
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+        __pyx_t_5 = __Pyx_PyIndex_AsSsize_t(__pyx_v_bottom); if (unlikely((__pyx_t_5 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":65
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+  __pyx_t_1 = __Pyx_PyIndex_AsSsize_t(__pyx_v_top); if (unlikely((__pyx_t_1 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":66
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+          __Pyx_RaiseArgtupleInvalid("_doquicksort", 1, 2, 2, 1); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_doquicksort") < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":106
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":108
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-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":110
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":111
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":112
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":113
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":169
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":20
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/data_array.pxi":20
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  *         self.id2word = ["END_OF_FILE", "END_OF_LINE"]
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":21
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/data_array.pxi":21
  *         self.id2word = ["END_OF_FILE", "END_OF_LINE"]
  *         self.data = IntList(1000,1000)
  *         self.sent_id = IntList(1000,1000)             # <<<<<<<<<<<<<<
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":22
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/data_array.pxi":22
  *         self.data = IntList(1000,1000)
  *         self.sent_id = IntList(1000,1000)
  *         self.sent_index = IntList(1000,1000)             # <<<<<<<<<<<<<<
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":23
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/data_array.pxi":23
  *         self.sent_id = IntList(1000,1000)
  *         self.sent_index = IntList(1000,1000)
  *         self.use_sent_id = use_sent_id             # <<<<<<<<<<<<<<
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":24
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/data_array.pxi":24
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  *         self.use_sent_id = use_sent_id
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":25
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/data_array.pxi":25
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":26
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/data_array.pxi":26
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  *             self.read_binary(from_binary)
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":27
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/data_array.pxi":27
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":28
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/data_array.pxi":28
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":30
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/data_array.pxi":30
  *                 self.read_bitext(from_text, (0 if side == 'source' else 1))
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  *                 self.read_text(from_text)             # <<<<<<<<<<<<<<
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-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":32
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  * 
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":33
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  * 
  *     def __len__(self):
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- *     def getSentId(self, i):
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-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":35
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  *         return len(self.data)
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- *     def getSentId(self, i):             # <<<<<<<<<<<<<<
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-static PyObject *__pyx_pf_3_sa_9DataArray_4getSentId(struct __pyx_obj_3_sa_DataArray *__pyx_v_self, PyObject *__pyx_v_i) {
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":36
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/data_array.pxi":36
  * 
- *     def getSentId(self, i):
+ *     def get_sentence_id(self, i):
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  * 
- *     def getSent(self, i):
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 /* Python wrapper */
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-static PyObject *__pyx_pw_3_sa_9DataArray_7getSent(PyObject *__pyx_v_self, PyObject *__pyx_v_i) {
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-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":38
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-static PyObject *__pyx_pf_3_sa_9DataArray_6getSent(struct __pyx_obj_3_sa_DataArray *__pyx_v_self, PyObject *__pyx_v_i) {
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":41
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":42
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":43
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":44
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":43
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":45
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":83
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":84
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":87
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":96
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":97
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":106
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":107
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":147
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@@ -9829,7 +10782,7 @@ static int *__pyx_f_3_sa_9Alignment__get_sent_links(struct __pyx_obj_3_sa_Alignm
   __pyx_t_1 = (__pyx_v_num_links[0]);
   for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_1; __pyx_v_i++) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":42
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":42
  *         sent_links = <int*> malloc(2*num_links[0]*sizeof(int))
  *         for i from 0 <= i < num_links[0]:
  *             self._unlink(self.links.arr[start + i], sent_links + (2*i), sent_links + (2*i) + 1)             # <<<<<<<<<<<<<<
@@ -9841,7 +10794,7 @@ static int *__pyx_f_3_sa_9Alignment__get_sent_links(struct __pyx_obj_3_sa_Alignm
     __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":43
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":43
  *         for i from 0 <= i < num_links[0]:
  *             self._unlink(self.links.arr[start + i], sent_links + (2*i), sent_links + (2*i) + 1)
  *         return sent_links             # <<<<<<<<<<<<<<
@@ -9874,7 +10827,7 @@ static int __pyx_pw_3_sa_9Alignment_5__cinit__(PyObject *__pyx_v_self, PyObject
     static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__from_binary,&__pyx_n_s__from_text,0};
     PyObject* values[2] = {0,0};
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":45
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":45
  *         return sent_links
  * 
  *     def __cinit__(self, from_binary=None, from_text=None):             # <<<<<<<<<<<<<<
@@ -9944,7 +10897,7 @@ static int __pyx_pf_3_sa_9Alignment_4__cinit__(struct __pyx_obj_3_sa_Alignment *
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__cinit__", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":46
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":46
  * 
  *     def __cinit__(self, from_binary=None, from_text=None):
  *         self.links = IntList(1000,1000)             # <<<<<<<<<<<<<<
@@ -9959,7 +10912,7 @@ static int __pyx_pf_3_sa_9Alignment_4__cinit__(struct __pyx_obj_3_sa_Alignment *
   __pyx_v_self->links = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":47
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":47
  *     def __cinit__(self, from_binary=None, from_text=None):
  *         self.links = IntList(1000,1000)
  *         self.sent_index = IntList(1000,1000)             # <<<<<<<<<<<<<<
@@ -9974,7 +10927,7 @@ static int __pyx_pf_3_sa_9Alignment_4__cinit__(struct __pyx_obj_3_sa_Alignment *
   __pyx_v_self->sent_index = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":48
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":48
  *         self.links = IntList(1000,1000)
  *         self.sent_index = IntList(1000,1000)
  *         if from_binary:             # <<<<<<<<<<<<<<
@@ -9984,7 +10937,7 @@ static int __pyx_pf_3_sa_9Alignment_4__cinit__(struct __pyx_obj_3_sa_Alignment *
   __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_from_binary); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   if (__pyx_t_2) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":49
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":49
  *         self.sent_index = IntList(1000,1000)
  *         if from_binary:
  *             self.read_binary(from_binary)             # <<<<<<<<<<<<<<
@@ -10006,7 +10959,7 @@ static int __pyx_pf_3_sa_9Alignment_4__cinit__(struct __pyx_obj_3_sa_Alignment *
     goto __pyx_L3;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":50
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":50
  *         if from_binary:
  *             self.read_binary(from_binary)
  *         elif from_text:             # <<<<<<<<<<<<<<
@@ -10016,7 +10969,7 @@ static int __pyx_pf_3_sa_9Alignment_4__cinit__(struct __pyx_obj_3_sa_Alignment *
   __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_from_text); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   if (__pyx_t_2) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":51
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":51
  *             self.read_binary(from_binary)
  *         elif from_text:
  *             self.read_text(from_text)             # <<<<<<<<<<<<<<
@@ -10073,7 +11026,7 @@ static PyObject *__pyx_pw_3_sa_9Alignment_7read_text(PyObject *__pyx_v_self, PyO
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":53
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":53
  *             self.read_text(from_text)
  * 
  *     def read_text(self, char* filename):             # <<<<<<<<<<<<<<
@@ -10115,7 +11068,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_6read_text(struct __pyx_obj_3_sa_Align
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   __Pyx_RefNannySetupContext("read_text", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":54
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":54
  * 
  *     def read_text(self, char* filename):
  *         with gzip_or_text(filename) as f:             # <<<<<<<<<<<<<<
@@ -10155,7 +11108,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_6read_text(struct __pyx_obj_3_sa_Align
           __pyx_v_f = __pyx_t_1;
           __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":55
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":55
  *     def read_text(self, char* filename):
  *         with gzip_or_text(filename) as f:
  *             for line in f:             # <<<<<<<<<<<<<<
@@ -10174,16 +11127,16 @@ static PyObject *__pyx_pf_3_sa_9Alignment_6read_text(struct __pyx_obj_3_sa_Align
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               if (__pyx_t_8 >= PyList_GET_SIZE(__pyx_t_1)) break;
               #if CYTHON_COMPILING_IN_CPYTHON
-              __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_8); __Pyx_INCREF(__pyx_t_2); __pyx_t_8++;
+              __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_8); __Pyx_INCREF(__pyx_t_2); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
               #else
-              __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L7_error;};
+              __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
               #endif
             } else if (!__pyx_t_9 && PyTuple_CheckExact(__pyx_t_1)) {
               if (__pyx_t_8 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
               #if CYTHON_COMPILING_IN_CPYTHON
-              __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_8); __Pyx_INCREF(__pyx_t_2); __pyx_t_8++;
+              __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_8); __Pyx_INCREF(__pyx_t_2); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
               #else
-              __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L7_error;};
+              __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
               #endif
             } else {
               __pyx_t_2 = __pyx_t_9(__pyx_t_1);
@@ -10200,7 +11153,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_6read_text(struct __pyx_obj_3_sa_Align
             __pyx_v_line = __pyx_t_2;
             __pyx_t_2 = 0;
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":56
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":56
  *         with gzip_or_text(filename) as f:
  *             for line in f:
  *                 self.sent_index.append(len(self.links))             # <<<<<<<<<<<<<<
@@ -10218,7 +11171,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_6read_text(struct __pyx_obj_3_sa_Align
             __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
             __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":57
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":57
  *             for line in f:
  *                 self.sent_index.append(len(self.links))
  *                 pairs = line.split()             # <<<<<<<<<<<<<<
@@ -10234,7 +11187,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_6read_text(struct __pyx_obj_3_sa_Align
             __pyx_v_pairs = __pyx_t_2;
             __pyx_t_2 = 0;
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":58
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":58
  *                 self.sent_index.append(len(self.links))
  *                 pairs = line.split()
  *                 for pair in pairs:             # <<<<<<<<<<<<<<
@@ -10253,16 +11206,16 @@ static PyObject *__pyx_pf_3_sa_9Alignment_6read_text(struct __pyx_obj_3_sa_Align
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                 if (__pyx_t_10 >= PyList_GET_SIZE(__pyx_t_2)) break;
                 #if CYTHON_COMPILING_IN_CPYTHON
-                __pyx_t_3 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_10); __Pyx_INCREF(__pyx_t_3); __pyx_t_10++;
+                __pyx_t_3 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_10); __Pyx_INCREF(__pyx_t_3); __pyx_t_10++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
                 #else
-                __pyx_t_3 = PySequence_ITEM(__pyx_t_2, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L7_error;};
+                __pyx_t_3 = PySequence_ITEM(__pyx_t_2, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
                 #endif
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                 if (__pyx_t_10 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
                 #if CYTHON_COMPILING_IN_CPYTHON
-                __pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_10); __Pyx_INCREF(__pyx_t_3); __pyx_t_10++;
+                __pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_10); __Pyx_INCREF(__pyx_t_3); __pyx_t_10++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
                 #else
-                __pyx_t_3 = PySequence_ITEM(__pyx_t_2, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L7_error;};
+                __pyx_t_3 = PySequence_ITEM(__pyx_t_2, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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                 __pyx_t_3 = __pyx_t_11(__pyx_t_2);
@@ -10279,7 +11232,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_6read_text(struct __pyx_obj_3_sa_Align
               __pyx_v_pair = __pyx_t_3;
               __pyx_t_3 = 0;
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":59
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":59
  *                 pairs = line.split()
  *                 for pair in pairs:
  *                     (i, j) = map(int, pair.split('-'))             # <<<<<<<<<<<<<<
@@ -10358,7 +11311,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_6read_text(struct __pyx_obj_3_sa_Align
               __pyx_v_j = __pyx_t_13;
               __pyx_t_13 = 0;
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":60
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":60
  *                 for pair in pairs:
  *                     (i, j) = map(int, pair.split('-'))
  *                     self.links.append(self.link(i, j))             # <<<<<<<<<<<<<<
@@ -10378,7 +11331,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_6read_text(struct __pyx_obj_3_sa_Align
           }
           __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":61
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":61
  *                     (i, j) = map(int, pair.split('-'))
  *                     self.links.append(self.link(i, j))
  *             self.sent_index.append(len(self.links))             # <<<<<<<<<<<<<<
@@ -10408,7 +11361,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_6read_text(struct __pyx_obj_3_sa_Align
         __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
         __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":54
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":54
  * 
  *     def read_text(self, char* filename):
  *         with gzip_or_text(filename) as f:             # <<<<<<<<<<<<<<
@@ -10532,7 +11485,7 @@ static PyObject *__pyx_pw_3_sa_9Alignment_9read_binary(PyObject *__pyx_v_self, P
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":63
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":63
  *             self.sent_index.append(len(self.links))
  * 
  *     def read_binary(self, char* filename):             # <<<<<<<<<<<<<<
@@ -10546,7 +11499,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_8read_binary(struct __pyx_obj_3_sa_Ali
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("read_binary", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":65
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":65
  *     def read_binary(self, char* filename):
  *         cdef FILE* f
  *         f = fopen(filename, "r")             # <<<<<<<<<<<<<<
@@ -10555,7 +11508,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_8read_binary(struct __pyx_obj_3_sa_Ali
  */
   __pyx_v_f = fopen(__pyx_v_filename, __pyx_k__r);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":66
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":66
  *         cdef FILE* f
  *         f = fopen(filename, "r")
  *         self.links.read_handle(f)             # <<<<<<<<<<<<<<
@@ -10564,7 +11517,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_8read_binary(struct __pyx_obj_3_sa_Ali
  */
   ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_self->links->__pyx_vtab)->read_handle(__pyx_v_self->links, __pyx_v_f);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":67
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":67
  *         f = fopen(filename, "r")
  *         self.links.read_handle(f)
  *         self.sent_index.read_handle(f)             # <<<<<<<<<<<<<<
@@ -10573,7 +11526,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_8read_binary(struct __pyx_obj_3_sa_Ali
  */
   ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_self->sent_index->__pyx_vtab)->read_handle(__pyx_v_self->sent_index, __pyx_v_f);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":68
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":68
  *         self.links.read_handle(f)
  *         self.sent_index.read_handle(f)
  *         fclose(f)             # <<<<<<<<<<<<<<
@@ -10609,7 +11562,7 @@ static PyObject *__pyx_pw_3_sa_9Alignment_11write_text(PyObject *__pyx_v_self, P
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":70
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":70
  *         fclose(f)
  * 
  *     def write_text(self, char* filename):             # <<<<<<<<<<<<<<
@@ -10644,7 +11597,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_10write_text(struct __pyx_obj_3_sa_Ali
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   __Pyx_RefNannySetupContext("write_text", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":71
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":71
  * 
  *     def write_text(self, char* filename):
  *         with open(filename, "w") as f:             # <<<<<<<<<<<<<<
@@ -10684,7 +11637,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_10write_text(struct __pyx_obj_3_sa_Ali
           __pyx_v_f = __pyx_t_4;
           __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":72
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":72
  *     def write_text(self, char* filename):
  *         with open(filename, "w") as f:
  *             sent_num = 0             # <<<<<<<<<<<<<<
@@ -10694,7 +11647,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_10write_text(struct __pyx_obj_3_sa_Ali
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           __pyx_v_sent_num = __pyx_int_0;
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":73
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":73
  *         with open(filename, "w") as f:
  *             sent_num = 0
  *             for i, link in enumerate(self.links):             # <<<<<<<<<<<<<<
@@ -10715,16 +11668,16 @@ static PyObject *__pyx_pf_3_sa_9Alignment_10write_text(struct __pyx_obj_3_sa_Ali
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               if (__pyx_t_8 >= PyList_GET_SIZE(__pyx_t_1)) break;
               #if CYTHON_COMPILING_IN_CPYTHON
-              __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_8); __Pyx_INCREF(__pyx_t_2); __pyx_t_8++;
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-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":75
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-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":77
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":78
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":71
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":83
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":84
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":85
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-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":87
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":89
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":90
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-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":91
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":92
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":93
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-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":94
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":95
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":88
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":101
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":102
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":102
  *         result = []
  *         start = self.sent_index.arr[i]
  *         end = self.sent_index.arr[i+1]             # <<<<<<<<<<<<<<
@@ -11485,7 +12437,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_16alignment(struct __pyx_obj_3_sa_Alig
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
   __pyx_v_end = (__pyx_v_self->sent_index->arr[__pyx_t_2]);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":103
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":103
  *         start = self.sent_index.arr[i]
  *         end = self.sent_index.arr[i+1]
  *         for j from start <= j < end:             # <<<<<<<<<<<<<<
@@ -11495,7 +12447,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_16alignment(struct __pyx_obj_3_sa_Alig
   __pyx_t_3 = __pyx_v_end;
   for (__pyx_v_j = __pyx_v_start; __pyx_v_j < __pyx_t_3; __pyx_v_j++) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":104
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":104
  *         end = self.sent_index.arr[i+1]
  *         for j from start <= j < end:
  *             result.append(self.unlink(self.links.arr[j]))             # <<<<<<<<<<<<<<
@@ -11518,7 +12470,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_16alignment(struct __pyx_obj_3_sa_Alig
     __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":105
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":105
  *         for j from start <= j < end:
  *             result.append(self.unlink(self.links.arr[j]))
  *         return result             # <<<<<<<<<<<<<<
@@ -11543,7 +12495,7 @@ static PyObject *__pyx_pf_3_sa_9Alignment_16alignment(struct __pyx_obj_3_sa_Alig
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":15
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":15
  *     int val
  * 
  * cdef _node* new_node(int key):             # <<<<<<<<<<<<<<
@@ -11557,7 +12509,7 @@ static struct __pyx_t_3_sa__node *__pyx_f_3_sa_new_node(int __pyx_v_key) {
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("new_node", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":17
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":17
  * cdef _node* new_node(int key):
  *     cdef _node* n
  *     n = <_node*> malloc(sizeof(_node))             # <<<<<<<<<<<<<<
@@ -11566,7 +12518,7 @@ static struct __pyx_t_3_sa__node *__pyx_f_3_sa_new_node(int __pyx_v_key) {
  */
   __pyx_v_n = ((struct __pyx_t_3_sa__node *)malloc((sizeof(struct __pyx_t_3_sa__node))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":18
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":18
  *     cdef _node* n
  *     n = <_node*> malloc(sizeof(_node))
  *     n.smaller = NULL             # <<<<<<<<<<<<<<
@@ -11575,7 +12527,7 @@ static struct __pyx_t_3_sa__node *__pyx_f_3_sa_new_node(int __pyx_v_key) {
  */
   __pyx_v_n->smaller = NULL;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":19
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":19
  *     n = <_node*> malloc(sizeof(_node))
  *     n.smaller = NULL
  *     n.bigger = NULL             # <<<<<<<<<<<<<<
@@ -11584,7 +12536,7 @@ static struct __pyx_t_3_sa__node *__pyx_f_3_sa_new_node(int __pyx_v_key) {
  */
   __pyx_v_n->bigger = NULL;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":20
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":20
  *     n.smaller = NULL
  *     n.bigger = NULL
  *     n.key = key             # <<<<<<<<<<<<<<
@@ -11593,7 +12545,7 @@ static struct __pyx_t_3_sa__node *__pyx_f_3_sa_new_node(int __pyx_v_key) {
  */
   __pyx_v_n->key = __pyx_v_key;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":21
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":21
  *     n.bigger = NULL
  *     n.key = key
  *     n.val = 0             # <<<<<<<<<<<<<<
@@ -11602,7 +12554,7 @@ static struct __pyx_t_3_sa__node *__pyx_f_3_sa_new_node(int __pyx_v_key) {
  */
   __pyx_v_n->val = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":22
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":22
  *     n.key = key
  *     n.val = 0
  *     return n             # <<<<<<<<<<<<<<
@@ -11618,7 +12570,7 @@ static struct __pyx_t_3_sa__node *__pyx_f_3_sa_new_node(int __pyx_v_key) {
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":25
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":25
  * 
  * 
  * cdef del_node(_node* n):             # <<<<<<<<<<<<<<
@@ -11636,7 +12588,7 @@ static PyObject *__pyx_f_3_sa_del_node(struct __pyx_t_3_sa__node *__pyx_v_n) {
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("del_node", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":26
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":26
  * 
  * cdef del_node(_node* n):
  *     if n.smaller != NULL:             # <<<<<<<<<<<<<<
@@ -11646,7 +12598,7 @@ static PyObject *__pyx_f_3_sa_del_node(struct __pyx_t_3_sa__node *__pyx_v_n) {
   __pyx_t_1 = (__pyx_v_n->smaller != NULL);
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":27
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":27
  * cdef del_node(_node* n):
  *     if n.smaller != NULL:
  *         del_node(n.smaller)             # <<<<<<<<<<<<<<
@@ -11660,7 +12612,7 @@ static PyObject *__pyx_f_3_sa_del_node(struct __pyx_t_3_sa__node *__pyx_v_n) {
   }
   __pyx_L3:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":28
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":28
  *     if n.smaller != NULL:
  *         del_node(n.smaller)
  *     if n.bigger != NULL:             # <<<<<<<<<<<<<<
@@ -11670,7 +12622,7 @@ static PyObject *__pyx_f_3_sa_del_node(struct __pyx_t_3_sa__node *__pyx_v_n) {
   __pyx_t_1 = (__pyx_v_n->bigger != NULL);
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":29
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":29
  *         del_node(n.smaller)
  *     if n.bigger != NULL:
  *         del_node(n.bigger)             # <<<<<<<<<<<<<<
@@ -11684,7 +12636,7 @@ static PyObject *__pyx_f_3_sa_del_node(struct __pyx_t_3_sa__node *__pyx_v_n) {
   }
   __pyx_L4:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":30
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":30
  *     if n.bigger != NULL:
  *         del_node(n.bigger)
  *     free(n)             # <<<<<<<<<<<<<<
@@ -11705,7 +12657,7 @@ static PyObject *__pyx_f_3_sa_del_node(struct __pyx_t_3_sa__node *__pyx_v_n) {
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":32
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":32
  *     free(n)
  * 
  * cdef int* get_val(_node* n, int key):             # <<<<<<<<<<<<<<
@@ -11719,7 +12671,7 @@ static int *__pyx_f_3_sa_get_val(struct __pyx_t_3_sa__node *__pyx_v_n, int __pyx
   int __pyx_t_1;
   __Pyx_RefNannySetupContext("get_val", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":33
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":33
  * 
  * cdef int* get_val(_node* n, int key):
  *     if key == n.key:             # <<<<<<<<<<<<<<
@@ -11729,7 +12681,7 @@ static int *__pyx_f_3_sa_get_val(struct __pyx_t_3_sa__node *__pyx_v_n, int __pyx
   __pyx_t_1 = (__pyx_v_key == __pyx_v_n->key);
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":34
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":34
  * cdef int* get_val(_node* n, int key):
  *     if key == n.key:
  *         return &n.val             # <<<<<<<<<<<<<<
@@ -11741,7 +12693,7 @@ static int *__pyx_f_3_sa_get_val(struct __pyx_t_3_sa__node *__pyx_v_n, int __pyx
     goto __pyx_L3;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":35
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":35
  *     if key == n.key:
  *         return &n.val
  *     elif key < n.key:             # <<<<<<<<<<<<<<
@@ -11751,7 +12703,7 @@ static int *__pyx_f_3_sa_get_val(struct __pyx_t_3_sa__node *__pyx_v_n, int __pyx
   __pyx_t_1 = (__pyx_v_key < __pyx_v_n->key);
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":36
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":36
  *         return &n.val
  *     elif key < n.key:
  *         if n.smaller == NULL:             # <<<<<<<<<<<<<<
@@ -11761,7 +12713,7 @@ static int *__pyx_f_3_sa_get_val(struct __pyx_t_3_sa__node *__pyx_v_n, int __pyx
     __pyx_t_1 = (__pyx_v_n->smaller == NULL);
     if (__pyx_t_1) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":37
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":37
  *     elif key < n.key:
  *         if n.smaller == NULL:
  *             n.smaller = new_node(key)             # <<<<<<<<<<<<<<
@@ -11770,7 +12722,7 @@ static int *__pyx_f_3_sa_get_val(struct __pyx_t_3_sa__node *__pyx_v_n, int __pyx
  */
       __pyx_v_n->smaller = __pyx_f_3_sa_new_node(__pyx_v_key);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":38
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":38
  *         if n.smaller == NULL:
  *             n.smaller = new_node(key)
  *             return &(n.smaller.val)             # <<<<<<<<<<<<<<
@@ -11783,7 +12735,7 @@ static int *__pyx_f_3_sa_get_val(struct __pyx_t_3_sa__node *__pyx_v_n, int __pyx
     }
     __pyx_L4:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":39
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":39
  *             n.smaller = new_node(key)
  *             return &(n.smaller.val)
  *         return get_val(n.smaller, key)             # <<<<<<<<<<<<<<
@@ -11796,7 +12748,7 @@ static int *__pyx_f_3_sa_get_val(struct __pyx_t_3_sa__node *__pyx_v_n, int __pyx
   }
   /*else*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":41
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":41
  *         return get_val(n.smaller, key)
  *     else:
  *         if n.bigger == NULL:             # <<<<<<<<<<<<<<
@@ -11806,7 +12758,7 @@ static int *__pyx_f_3_sa_get_val(struct __pyx_t_3_sa__node *__pyx_v_n, int __pyx
     __pyx_t_1 = (__pyx_v_n->bigger == NULL);
     if (__pyx_t_1) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":42
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":42
  *     else:
  *         if n.bigger == NULL:
  *             n.bigger = new_node(key)             # <<<<<<<<<<<<<<
@@ -11815,7 +12767,7 @@ static int *__pyx_f_3_sa_get_val(struct __pyx_t_3_sa__node *__pyx_v_n, int __pyx
  */
       __pyx_v_n->bigger = __pyx_f_3_sa_new_node(__pyx_v_key);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":43
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":43
  *         if n.bigger == NULL:
  *             n.bigger = new_node(key)
  *             return &(n.bigger.val)             # <<<<<<<<<<<<<<
@@ -11828,7 +12780,7 @@ static int *__pyx_f_3_sa_get_val(struct __pyx_t_3_sa__node *__pyx_v_n, int __pyx
     }
     __pyx_L5:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":44
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":44
  *             n.bigger = new_node(key)
  *             return &(n.bigger.val)
  *         return get_val(n.bigger, key)             # <<<<<<<<<<<<<<
@@ -11862,7 +12814,7 @@ static int __pyx_pw_3_sa_5BiLex_1__cinit__(PyObject *__pyx_v_self, PyObject *__p
     static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__from_text,&__pyx_n_s__from_data,&__pyx_n_s__from_binary,&__pyx_n_s__earray,&__pyx_n_s__fsarray,&__pyx_n_s__alignment,0};
     PyObject* values[6] = {0,0,0,0,0,0};
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":54
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":54
  *     cdef id2eword, id2fword, eword2id, fword2id
  * 
  *     def __cinit__(self, from_text=None, from_data=False, from_binary=None,             # <<<<<<<<<<<<<<
@@ -11873,7 +12825,7 @@ static int __pyx_pw_3_sa_5BiLex_1__cinit__(PyObject *__pyx_v_self, PyObject *__p
     values[1] = __pyx_k_41;
     values[2] = ((PyObject *)Py_None);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":55
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":55
  * 
  *     def __cinit__(self, from_text=None, from_data=False, from_binary=None,
  *             earray=None, fsarray=None, alignment=None):             # <<<<<<<<<<<<<<
@@ -11964,7 +12916,7 @@ static int __pyx_pw_3_sa_5BiLex_1__cinit__(PyObject *__pyx_v_self, PyObject *__p
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":54
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":54
  *     cdef id2eword, id2fword, eword2id, fword2id
  * 
  *     def __cinit__(self, from_text=None, from_data=False, from_binary=None,             # <<<<<<<<<<<<<<
@@ -11985,7 +12937,7 @@ static int __pyx_pf_3_sa_5BiLex___cinit__(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__cinit__", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":56
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":56
  *     def __cinit__(self, from_text=None, from_data=False, from_binary=None,
  *             earray=None, fsarray=None, alignment=None):
  *         self.id2eword = []             # <<<<<<<<<<<<<<
@@ -12000,7 +12952,7 @@ static int __pyx_pf_3_sa_5BiLex___cinit__(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
   __pyx_v_self->id2eword = ((PyObject *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":57
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":57
  *             earray=None, fsarray=None, alignment=None):
  *         self.id2eword = []
  *         self.id2fword = []             # <<<<<<<<<<<<<<
@@ -12015,7 +12967,7 @@ static int __pyx_pf_3_sa_5BiLex___cinit__(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
   __pyx_v_self->id2fword = ((PyObject *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":58
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":58
  *         self.id2eword = []
  *         self.id2fword = []
  *         self.eword2id = {}             # <<<<<<<<<<<<<<
@@ -12030,7 +12982,7 @@ static int __pyx_pf_3_sa_5BiLex___cinit__(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
   __pyx_v_self->eword2id = ((PyObject *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":59
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":59
  *         self.id2fword = []
  *         self.eword2id = {}
  *         self.fword2id = {}             # <<<<<<<<<<<<<<
@@ -12045,7 +12997,7 @@ static int __pyx_pf_3_sa_5BiLex___cinit__(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
   __pyx_v_self->fword2id = ((PyObject *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":60
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":60
  *         self.eword2id = {}
  *         self.fword2id = {}
  *         self.e_index = IntList()             # <<<<<<<<<<<<<<
@@ -12060,7 +13012,7 @@ static int __pyx_pf_3_sa_5BiLex___cinit__(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
   __pyx_v_self->e_index = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":61
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":61
  *         self.fword2id = {}
  *         self.e_index = IntList()
  *         self.f_index = IntList()             # <<<<<<<<<<<<<<
@@ -12075,7 +13027,7 @@ static int __pyx_pf_3_sa_5BiLex___cinit__(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
   __pyx_v_self->f_index = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":62
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":62
  *         self.e_index = IntList()
  *         self.f_index = IntList()
  *         self.col1 = FloatList()             # <<<<<<<<<<<<<<
@@ -12090,7 +13042,7 @@ static int __pyx_pf_3_sa_5BiLex___cinit__(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
   __pyx_v_self->col1 = ((struct __pyx_obj_3_sa_FloatList *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":63
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":63
  *         self.f_index = IntList()
  *         self.col1 = FloatList()
  *         self.col2 = FloatList()             # <<<<<<<<<<<<<<
@@ -12105,7 +13057,7 @@ static int __pyx_pf_3_sa_5BiLex___cinit__(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
   __pyx_v_self->col2 = ((struct __pyx_obj_3_sa_FloatList *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":64
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":64
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  *         self.col2 = FloatList()
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   if (__pyx_t_2) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":65
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":65
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     goto __pyx_L3;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":66
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":66
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":67
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":67
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":69
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":69
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":72
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  * 
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   int *__pyx_v_emargin;
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-  PyObject *__pyx_v_word = 0;
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   PyObject *__pyx_v_num_sents = NULL;
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":80
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":79
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":81
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":80
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-      __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++;
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+      __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-          else {__pyx_filename = __pyx_f[5]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    __Pyx_XDECREF(((PyObject *)__pyx_v_word));
-    __pyx_v_word = ((PyObject*)__pyx_t_4);
+    __Pyx_XDECREF(__pyx_v_word);
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":82
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":81
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  *         for word in fsa.darray.id2word: # I miss list comprehensions
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+    __pyx_t_4 = __Pyx_PyObject_Append(__pyx_v_self->id2fword, __pyx_v_word); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":83
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":82
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":84
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":83
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  *         self.id2fword[null_word] = "NULL"
  *         for id, word in enumerate(self.id2fword):             # <<<<<<<<<<<<<<
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+    __pyx_t_2 = -1; __pyx_t_4 = PyObject_GetIter(__pyx_v_self->id2fword); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      __pyx_t_5 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_2); __Pyx_INCREF(__pyx_t_5); __pyx_t_2++;
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+      __pyx_t_5 = PySequence_ITEM(__pyx_t_4, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_2); __Pyx_INCREF(__pyx_t_5); __pyx_t_2++;
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-          else {__pyx_filename = __pyx_f[5]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    __Pyx_XDECREF(((PyObject *)__pyx_v_word));
-    __pyx_v_word = ((PyObject*)__pyx_t_5);
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":85
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":84
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":87
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":86
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":88
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":89
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":90
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":91
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":93
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":95
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":96
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":97
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":96
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":98
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":99
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":98
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":100
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":102
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":103
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":105
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":106
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":108
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":107
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@@ -12671,7 +13619,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
     __pyx_v_fsent = (__pyx_v_fsa->darray->data->arr + (__pyx_v_fsa->darray->sent_index->arr[__pyx_v_sent_id]));
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":109
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":108
  * 
  *             fsent = fsa.darray.data.arr + fsa.darray.sent_index.arr[sent_id]
  *             I = fsa.darray.sent_index.arr[sent_id+1] - fsa.darray.sent_index.arr[sent_id] - 1             # <<<<<<<<<<<<<<
@@ -12680,7 +13628,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
     __pyx_v_I = (((__pyx_v_fsa->darray->sent_index->arr[(__pyx_v_sent_id + 1)]) - (__pyx_v_fsa->darray->sent_index->arr[__pyx_v_sent_id])) - 1);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":110
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":109
  *             fsent = fsa.darray.data.arr + fsa.darray.sent_index.arr[sent_id]
  *             I = fsa.darray.sent_index.arr[sent_id+1] - fsa.darray.sent_index.arr[sent_id] - 1
  *             faligned = <int*> malloc(I*sizeof(int))             # <<<<<<<<<<<<<<
@@ -12689,7 +13637,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
     __pyx_v_faligned = ((int *)malloc((__pyx_v_I * (sizeof(int)))));
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":111
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":110
  *             I = fsa.darray.sent_index.arr[sent_id+1] - fsa.darray.sent_index.arr[sent_id] - 1
  *             faligned = <int*> malloc(I*sizeof(int))
  *             memset(faligned, 0, I*sizeof(int))             # <<<<<<<<<<<<<<
@@ -12698,7 +13646,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
     memset(__pyx_v_faligned, 0, (__pyx_v_I * (sizeof(int))));
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":113
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":112
  *             memset(faligned, 0, I*sizeof(int))
  * 
  *             esent = eda.data.arr + eda.sent_index.arr[sent_id]             # <<<<<<<<<<<<<<
@@ -12707,7 +13655,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
     __pyx_v_esent = (__pyx_v_eda->data->arr + (__pyx_v_eda->sent_index->arr[__pyx_v_sent_id]));
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":114
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":113
  * 
  *             esent = eda.data.arr + eda.sent_index.arr[sent_id]
  *             J = eda.sent_index.arr[sent_id+1] - eda.sent_index.arr[sent_id] - 1             # <<<<<<<<<<<<<<
@@ -12716,7 +13664,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
     __pyx_v_J = (((__pyx_v_eda->sent_index->arr[(__pyx_v_sent_id + 1)]) - (__pyx_v_eda->sent_index->arr[__pyx_v_sent_id])) - 1);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":115
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":114
  *             esent = eda.data.arr + eda.sent_index.arr[sent_id]
  *             J = eda.sent_index.arr[sent_id+1] - eda.sent_index.arr[sent_id] - 1
  *             ealigned = <int*> malloc(J*sizeof(int))             # <<<<<<<<<<<<<<
@@ -12725,7 +13673,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
     __pyx_v_ealigned = ((int *)malloc((__pyx_v_J * (sizeof(int)))));
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":116
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":115
  *             J = eda.sent_index.arr[sent_id+1] - eda.sent_index.arr[sent_id] - 1
  *             ealigned = <int*> malloc(J*sizeof(int))
  *             memset(ealigned, 0, J*sizeof(int))             # <<<<<<<<<<<<<<
@@ -12734,7 +13682,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
     memset(__pyx_v_ealigned, 0, (__pyx_v_J * (sizeof(int))));
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":118
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":117
  *             memset(ealigned, 0, J*sizeof(int))
  * 
  *             links = aa._get_sent_links(sent_id, &num_links)             # <<<<<<<<<<<<<<
@@ -12743,7 +13691,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
     __pyx_v_links = ((struct __pyx_vtabstruct_3_sa_Alignment *)__pyx_v_aa->__pyx_vtab)->_get_sent_links(__pyx_v_aa, __pyx_v_sent_id, (&__pyx_v_num_links));
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":120
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":119
  *             links = aa._get_sent_links(sent_id, &num_links)
  * 
  *             for l from 0 <= l < num_links:             # <<<<<<<<<<<<<<
@@ -12753,7 +13701,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
     __pyx_t_7 = __pyx_v_num_links;
     for (__pyx_v_l = 0; __pyx_v_l < __pyx_t_7; __pyx_v_l++) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":121
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":120
  * 
  *             for l from 0 <= l < num_links:
  *                 i = links[l*2]             # <<<<<<<<<<<<<<
@@ -12762,7 +13710,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
       __pyx_v_i = (__pyx_v_links[(__pyx_v_l * 2)]);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":122
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":121
  *             for l from 0 <= l < num_links:
  *                 i = links[l*2]
  *                 j = links[l*2+1]             # <<<<<<<<<<<<<<
@@ -12771,7 +13719,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
       __pyx_v_j = (__pyx_v_links[((__pyx_v_l * 2) + 1)]);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":123
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":122
  *                 i = links[l*2]
  *                 j = links[l*2+1]
  *                 if i >= I or j >= J:             # <<<<<<<<<<<<<<
@@ -12787,24 +13735,24 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
       }
       if (__pyx_t_10) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":124
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":123
  *                 j = links[l*2+1]
  *                 if i >= I or j >= J:
  *                     raise Exception("%d-%d out of bounds (I=%d,J=%d) in line %d\n" % (i,j,I,J,sent_id+1))             # <<<<<<<<<<<<<<
  *                 f_i = fsent[i]
  *                 e_j = esent[j]
  */
-        __pyx_t_1 = PyInt_FromLong(__pyx_v_i); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_1 = PyInt_FromLong(__pyx_v_i); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_1);
-        __pyx_t_4 = PyInt_FromLong(__pyx_v_j); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_4 = PyInt_FromLong(__pyx_v_j); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_4);
-        __pyx_t_5 = PyInt_FromLong(__pyx_v_I); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_5 = PyInt_FromLong(__pyx_v_I); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_5);
-        __pyx_t_11 = PyInt_FromLong(__pyx_v_J); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_11 = PyInt_FromLong(__pyx_v_J); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_11);
-        __pyx_t_12 = PyInt_FromLong((__pyx_v_sent_id + 1)); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_12 = PyInt_FromLong((__pyx_v_sent_id + 1)); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_12);
-        __pyx_t_13 = PyTuple_New(5); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_13 = PyTuple_New(5); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_13);
         PyTuple_SET_ITEM(__pyx_t_13, 0, __pyx_t_1);
         __Pyx_GIVEREF(__pyx_t_1);
@@ -12821,25 +13769,25 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
         __pyx_t_5 = 0;
         __pyx_t_11 = 0;
         __pyx_t_12 = 0;
-        __pyx_t_12 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_42), ((PyObject *)__pyx_t_13)); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_12 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_42), ((PyObject *)__pyx_t_13)); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(((PyObject *)__pyx_t_12));
         __Pyx_DECREF(((PyObject *)__pyx_t_13)); __pyx_t_13 = 0;
-        __pyx_t_13 = PyTuple_New(1); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_13 = PyTuple_New(1); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_13);
         PyTuple_SET_ITEM(__pyx_t_13, 0, ((PyObject *)__pyx_t_12));
         __Pyx_GIVEREF(((PyObject *)__pyx_t_12));
         __pyx_t_12 = 0;
-        __pyx_t_12 = PyObject_Call(__pyx_builtin_Exception, ((PyObject *)__pyx_t_13), NULL); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_12 = PyObject_Call(__pyx_builtin_Exception, ((PyObject *)__pyx_t_13), NULL); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_12);
         __Pyx_DECREF(((PyObject *)__pyx_t_13)); __pyx_t_13 = 0;
         __Pyx_Raise(__pyx_t_12, 0, 0, 0);
         __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
-        {__pyx_filename = __pyx_f[5]; __pyx_lineno = 124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        {__pyx_filename = __pyx_f[5]; __pyx_lineno = 123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         goto __pyx_L15;
       }
       __pyx_L15:;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":125
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":124
  *                 if i >= I or j >= J:
  *                     raise Exception("%d-%d out of bounds (I=%d,J=%d) in line %d\n" % (i,j,I,J,sent_id+1))
  *                 f_i = fsent[i]             # <<<<<<<<<<<<<<
@@ -12848,7 +13796,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
       __pyx_v_f_i = (__pyx_v_fsent[__pyx_v_i]);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":126
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":125
  *                     raise Exception("%d-%d out of bounds (I=%d,J=%d) in line %d\n" % (i,j,I,J,sent_id+1))
  *                 f_i = fsent[i]
  *                 e_j = esent[j]             # <<<<<<<<<<<<<<
@@ -12857,7 +13805,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
       __pyx_v_e_j = (__pyx_v_esent[__pyx_v_j]);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":127
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":126
  *                 f_i = fsent[i]
  *                 e_j = esent[j]
  *                 fmargin[f_i] = fmargin[f_i]+1             # <<<<<<<<<<<<<<
@@ -12866,7 +13814,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
       (__pyx_v_fmargin[__pyx_v_f_i]) = ((__pyx_v_fmargin[__pyx_v_f_i]) + 1);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":128
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":127
  *                 e_j = esent[j]
  *                 fmargin[f_i] = fmargin[f_i]+1
  *                 emargin[e_j] = emargin[e_j]+1             # <<<<<<<<<<<<<<
@@ -12875,7 +13823,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
       (__pyx_v_emargin[__pyx_v_e_j]) = ((__pyx_v_emargin[__pyx_v_e_j]) + 1);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":129
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":128
  *                 fmargin[f_i] = fmargin[f_i]+1
  *                 emargin[e_j] = emargin[e_j]+1
  *                 if dict[f_i] == NULL:             # <<<<<<<<<<<<<<
@@ -12885,7 +13833,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
       __pyx_t_10 = ((__pyx_v_dict[__pyx_v_f_i]) == NULL);
       if (__pyx_t_10) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":130
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":129
  *                 emargin[e_j] = emargin[e_j]+1
  *                 if dict[f_i] == NULL:
  *                     dict[f_i] = new_node(e_j)             # <<<<<<<<<<<<<<
@@ -12894,7 +13842,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
         (__pyx_v_dict[__pyx_v_f_i]) = __pyx_f_3_sa_new_node(__pyx_v_e_j);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":131
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":130
  *                 if dict[f_i] == NULL:
  *                     dict[f_i] = new_node(e_j)
  *                     dict[f_i].val = 1             # <<<<<<<<<<<<<<
@@ -12903,7 +13851,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
         (__pyx_v_dict[__pyx_v_f_i])->val = 1;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":132
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":131
  *                     dict[f_i] = new_node(e_j)
  *                     dict[f_i].val = 1
  *                     num_pairs = num_pairs + 1             # <<<<<<<<<<<<<<
@@ -12915,7 +13863,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
       }
       /*else*/ {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":134
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":133
  *                     num_pairs = num_pairs + 1
  *                 else:
  *                     count = get_val(dict[f_i], e_j)             # <<<<<<<<<<<<<<
@@ -12924,7 +13872,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
         __pyx_v_count = __pyx_f_3_sa_get_val((__pyx_v_dict[__pyx_v_f_i]), __pyx_v_e_j);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":135
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":134
  *                 else:
  *                     count = get_val(dict[f_i], e_j)
  *                     if count[0] == 0:             # <<<<<<<<<<<<<<
@@ -12934,7 +13882,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
         __pyx_t_10 = ((__pyx_v_count[0]) == 0);
         if (__pyx_t_10) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":136
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":135
  *                     count = get_val(dict[f_i], e_j)
  *                     if count[0] == 0:
  *                         num_pairs = num_pairs + 1             # <<<<<<<<<<<<<<
@@ -12946,7 +13894,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
         }
         __pyx_L17:;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":137
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":136
  *                     if count[0] == 0:
  *                         num_pairs = num_pairs + 1
  *                     count[0] = count[0] + 1             # <<<<<<<<<<<<<<
@@ -12957,7 +13905,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
       }
       __pyx_L16:;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":139
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":138
  *                     count[0] = count[0] + 1
  *                 # add count
  *                 faligned[i] = 1             # <<<<<<<<<<<<<<
@@ -12966,7 +13914,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
       (__pyx_v_faligned[__pyx_v_i]) = 1;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":140
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":139
  *                 # add count
  *                 faligned[i] = 1
  *                 ealigned[j] = 1             # <<<<<<<<<<<<<<
@@ -12976,7 +13924,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
       (__pyx_v_ealigned[__pyx_v_j]) = 1;
     }
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":141
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":140
  *                 faligned[i] = 1
  *                 ealigned[j] = 1
  *             for i from 0 <= i < I:             # <<<<<<<<<<<<<<
@@ -12986,7 +13934,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
     __pyx_t_7 = __pyx_v_I;
     for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_7; __pyx_v_i++) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":142
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":141
  *                 ealigned[j] = 1
  *             for i from 0 <= i < I:
  *                 if faligned[i] == 0:             # <<<<<<<<<<<<<<
@@ -12996,7 +13944,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
       __pyx_t_10 = ((__pyx_v_faligned[__pyx_v_i]) == 0);
       if (__pyx_t_10) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":143
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":142
  *             for i from 0 <= i < I:
  *                 if faligned[i] == 0:
  *                     f_i = fsent[i]             # <<<<<<<<<<<<<<
@@ -13005,7 +13953,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
         __pyx_v_f_i = (__pyx_v_fsent[__pyx_v_i]);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":144
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":143
  *                 if faligned[i] == 0:
  *                     f_i = fsent[i]
  *                     fmargin[f_i] = fmargin[f_i] + 1             # <<<<<<<<<<<<<<
@@ -13014,7 +13962,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
         (__pyx_v_fmargin[__pyx_v_f_i]) = ((__pyx_v_fmargin[__pyx_v_f_i]) + 1);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":145
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":144
  *                     f_i = fsent[i]
  *                     fmargin[f_i] = fmargin[f_i] + 1
  *                     emargin[null_word] = emargin[null_word] + 1             # <<<<<<<<<<<<<<
@@ -13023,7 +13971,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
         (__pyx_v_emargin[__pyx_v_null_word]) = ((__pyx_v_emargin[__pyx_v_null_word]) + 1);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":146
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":145
  *                     fmargin[f_i] = fmargin[f_i] + 1
  *                     emargin[null_word] = emargin[null_word] + 1
  *                     if dict[f_i] == NULL:             # <<<<<<<<<<<<<<
@@ -13033,7 +13981,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
         __pyx_t_10 = ((__pyx_v_dict[__pyx_v_f_i]) == NULL);
         if (__pyx_t_10) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":147
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":146
  *                     emargin[null_word] = emargin[null_word] + 1
  *                     if dict[f_i] == NULL:
  *                         dict[f_i] = new_node(null_word)             # <<<<<<<<<<<<<<
@@ -13042,7 +13990,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
           (__pyx_v_dict[__pyx_v_f_i]) = __pyx_f_3_sa_new_node(__pyx_v_null_word);
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":148
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":147
  *                     if dict[f_i] == NULL:
  *                         dict[f_i] = new_node(null_word)
  *                         dict[f_i].val = 1             # <<<<<<<<<<<<<<
@@ -13051,7 +13999,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
           (__pyx_v_dict[__pyx_v_f_i])->val = 1;
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":149
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":148
  *                         dict[f_i] = new_node(null_word)
  *                         dict[f_i].val = 1
  *                         num_pairs = num_pairs + 1             # <<<<<<<<<<<<<<
@@ -13063,7 +14011,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
         }
         /*else*/ {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":151
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":150
  *                         num_pairs = num_pairs + 1
  *                     else:
  *                         count = get_val(dict[f_i], null_word)             # <<<<<<<<<<<<<<
@@ -13072,7 +14020,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
           __pyx_v_count = __pyx_f_3_sa_get_val((__pyx_v_dict[__pyx_v_f_i]), __pyx_v_null_word);
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":152
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":151
  *                     else:
  *                         count = get_val(dict[f_i], null_word)
  *                         if count[0] == 0:             # <<<<<<<<<<<<<<
@@ -13082,7 +14030,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
           __pyx_t_10 = ((__pyx_v_count[0]) == 0);
           if (__pyx_t_10) {
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":153
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":152
  *                         count = get_val(dict[f_i], null_word)
  *                         if count[0] == 0:
  *                             num_pairs = num_pairs + 1             # <<<<<<<<<<<<<<
@@ -13094,7 +14042,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
           }
           __pyx_L22:;
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":154
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":153
  *                         if count[0] == 0:
  *                             num_pairs = num_pairs + 1
  *                         count[0] = count[0] + 1             # <<<<<<<<<<<<<<
@@ -13109,7 +14057,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
       __pyx_L20:;
     }
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":155
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":154
  *                             num_pairs = num_pairs + 1
  *                         count[0] = count[0] + 1
  *             for j from 0 <= j < J:             # <<<<<<<<<<<<<<
@@ -13119,7 +14067,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
     __pyx_t_7 = __pyx_v_J;
     for (__pyx_v_j = 0; __pyx_v_j < __pyx_t_7; __pyx_v_j++) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":156
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":155
  *                         count[0] = count[0] + 1
  *             for j from 0 <= j < J:
  *                 if ealigned[j] == 0:             # <<<<<<<<<<<<<<
@@ -13129,7 +14077,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
       __pyx_t_10 = ((__pyx_v_ealigned[__pyx_v_j]) == 0);
       if (__pyx_t_10) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":157
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":156
  *             for j from 0 <= j < J:
  *                 if ealigned[j] == 0:
  *                     e_j = esent[j]             # <<<<<<<<<<<<<<
@@ -13138,7 +14086,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
         __pyx_v_e_j = (__pyx_v_esent[__pyx_v_j]);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":158
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":157
  *                 if ealigned[j] == 0:
  *                     e_j = esent[j]
  *                     fmargin[null_word] = fmargin[null_word] + 1             # <<<<<<<<<<<<<<
@@ -13147,7 +14095,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
         (__pyx_v_fmargin[__pyx_v_null_word]) = ((__pyx_v_fmargin[__pyx_v_null_word]) + 1);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":159
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":158
  *                     e_j = esent[j]
  *                     fmargin[null_word] = fmargin[null_word] + 1
  *                     emargin[e_j] = emargin[e_j] + 1             # <<<<<<<<<<<<<<
@@ -13156,7 +14104,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
         (__pyx_v_emargin[__pyx_v_e_j]) = ((__pyx_v_emargin[__pyx_v_e_j]) + 1);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":160
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":159
  *                     fmargin[null_word] = fmargin[null_word] + 1
  *                     emargin[e_j] = emargin[e_j] + 1
  *                     if dict[null_word] == NULL:             # <<<<<<<<<<<<<<
@@ -13166,7 +14114,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
         __pyx_t_10 = ((__pyx_v_dict[__pyx_v_null_word]) == NULL);
         if (__pyx_t_10) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":161
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":160
  *                     emargin[e_j] = emargin[e_j] + 1
  *                     if dict[null_word] == NULL:
  *                         dict[null_word] = new_node(e_j)             # <<<<<<<<<<<<<<
@@ -13175,7 +14123,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
           (__pyx_v_dict[__pyx_v_null_word]) = __pyx_f_3_sa_new_node(__pyx_v_e_j);
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":162
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":161
  *                     if dict[null_word] == NULL:
  *                         dict[null_word] = new_node(e_j)
  *                         dict[null_word].val = 1             # <<<<<<<<<<<<<<
@@ -13184,7 +14132,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
           (__pyx_v_dict[__pyx_v_null_word])->val = 1;
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":163
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":162
  *                         dict[null_word] = new_node(e_j)
  *                         dict[null_word].val = 1
  *                         num_pairs = num_pairs + 1             # <<<<<<<<<<<<<<
@@ -13196,7 +14144,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
         }
         /*else*/ {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":165
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":164
  *                         num_pairs = num_pairs + 1
  *                     else:
  *                         count = get_val(dict[null_word], e_j)             # <<<<<<<<<<<<<<
@@ -13205,7 +14153,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
           __pyx_v_count = __pyx_f_3_sa_get_val((__pyx_v_dict[__pyx_v_null_word]), __pyx_v_e_j);
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":166
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":165
  *                     else:
  *                         count = get_val(dict[null_word], e_j)
  *                         if count[0] == 0:             # <<<<<<<<<<<<<<
@@ -13215,7 +14163,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
           __pyx_t_10 = ((__pyx_v_count[0]) == 0);
           if (__pyx_t_10) {
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":167
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":166
  *                         count = get_val(dict[null_word], e_j)
  *                         if count[0] == 0:
  *                             num_pairs = num_pairs + 1             # <<<<<<<<<<<<<<
@@ -13227,7 +14175,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
           }
           __pyx_L27:;
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":168
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":167
  *                         if count[0] == 0:
  *                             num_pairs = num_pairs + 1
  *                         count[0] = count[0] + 1             # <<<<<<<<<<<<<<
@@ -13242,7 +14190,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
       __pyx_L25:;
     }
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":169
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":168
  *                             num_pairs = num_pairs + 1
  *                         count[0] = count[0] + 1
  *             free(links)             # <<<<<<<<<<<<<<
@@ -13251,7 +14199,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
     free(__pyx_v_links);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":170
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":169
  *                         count[0] = count[0] + 1
  *             free(links)
  *             free(faligned)             # <<<<<<<<<<<<<<
@@ -13260,7 +14208,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
     free(__pyx_v_faligned);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":171
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":170
  *             free(links)
  *             free(faligned)
  *             free(ealigned)             # <<<<<<<<<<<<<<
@@ -13270,20 +14218,20 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
     free(__pyx_v_ealigned);
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":172
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":171
  *             free(faligned)
  *             free(ealigned)
  *         self.f_index = IntList(initial_len=V_F)             # <<<<<<<<<<<<<<
  *         self.e_index = IntList(initial_len=num_pairs)
  *         self.col1 = FloatList(initial_len=num_pairs)
  */
-  __pyx_t_12 = PyDict_New(); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_12 = PyDict_New(); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 171; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(((PyObject *)__pyx_t_12));
-  __pyx_t_13 = PyInt_FromLong(__pyx_v_V_F); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_13 = PyInt_FromLong(__pyx_v_V_F); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 171; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_13);
-  if (PyDict_SetItem(__pyx_t_12, ((PyObject *)__pyx_n_s__initial_len), __pyx_t_13) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyDict_SetItem(__pyx_t_12, ((PyObject *)__pyx_n_s__initial_len), __pyx_t_13) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 171; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
-  __pyx_t_13 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_IntList)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_12)); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_13 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_IntList)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_12)); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 171; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_13);
   __Pyx_DECREF(((PyObject *)__pyx_t_12)); __pyx_t_12 = 0;
   __Pyx_GIVEREF(__pyx_t_13);
@@ -13292,20 +14240,20 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
   __pyx_v_self->f_index = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_13);
   __pyx_t_13 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":173
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":172
  *             free(ealigned)
  *         self.f_index = IntList(initial_len=V_F)
  *         self.e_index = IntList(initial_len=num_pairs)             # <<<<<<<<<<<<<<
  *         self.col1 = FloatList(initial_len=num_pairs)
  *         self.col2 = FloatList(initial_len=num_pairs)
  */
-  __pyx_t_13 = PyDict_New(); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_13 = PyDict_New(); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(((PyObject *)__pyx_t_13));
-  __pyx_t_12 = PyInt_FromLong(__pyx_v_num_pairs); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_12 = PyInt_FromLong(__pyx_v_num_pairs); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_12);
-  if (PyDict_SetItem(__pyx_t_13, ((PyObject *)__pyx_n_s__initial_len), __pyx_t_12) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyDict_SetItem(__pyx_t_13, ((PyObject *)__pyx_n_s__initial_len), __pyx_t_12) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
-  __pyx_t_12 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_IntList)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_13)); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_12 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_IntList)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_13)); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_12);
   __Pyx_DECREF(((PyObject *)__pyx_t_13)); __pyx_t_13 = 0;
   __Pyx_GIVEREF(__pyx_t_12);
@@ -13314,20 +14262,20 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
   __pyx_v_self->e_index = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_12);
   __pyx_t_12 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":174
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":173
  *         self.f_index = IntList(initial_len=V_F)
  *         self.e_index = IntList(initial_len=num_pairs)
  *         self.col1 = FloatList(initial_len=num_pairs)             # <<<<<<<<<<<<<<
  *         self.col2 = FloatList(initial_len=num_pairs)
  * 
  */
-  __pyx_t_12 = PyDict_New(); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_12 = PyDict_New(); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(((PyObject *)__pyx_t_12));
-  __pyx_t_13 = PyInt_FromLong(__pyx_v_num_pairs); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_13 = PyInt_FromLong(__pyx_v_num_pairs); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_13);
-  if (PyDict_SetItem(__pyx_t_12, ((PyObject *)__pyx_n_s__initial_len), __pyx_t_13) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyDict_SetItem(__pyx_t_12, ((PyObject *)__pyx_n_s__initial_len), __pyx_t_13) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
-  __pyx_t_13 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_FloatList)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_12)); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_13 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_FloatList)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_12)); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_13);
   __Pyx_DECREF(((PyObject *)__pyx_t_12)); __pyx_t_12 = 0;
   __Pyx_GIVEREF(__pyx_t_13);
@@ -13336,20 +14284,20 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
   __pyx_v_self->col1 = ((struct __pyx_obj_3_sa_FloatList *)__pyx_t_13);
   __pyx_t_13 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":175
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":174
  *         self.e_index = IntList(initial_len=num_pairs)
  *         self.col1 = FloatList(initial_len=num_pairs)
  *         self.col2 = FloatList(initial_len=num_pairs)             # <<<<<<<<<<<<<<
  * 
  *         num_pairs = 0
  */
-  __pyx_t_13 = PyDict_New(); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_13 = PyDict_New(); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(((PyObject *)__pyx_t_13));
-  __pyx_t_12 = PyInt_FromLong(__pyx_v_num_pairs); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_12 = PyInt_FromLong(__pyx_v_num_pairs); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_12);
-  if (PyDict_SetItem(__pyx_t_13, ((PyObject *)__pyx_n_s__initial_len), __pyx_t_12) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyDict_SetItem(__pyx_t_13, ((PyObject *)__pyx_n_s__initial_len), __pyx_t_12) < 0) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
-  __pyx_t_12 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_FloatList)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_13)); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_12 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_FloatList)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_13)); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_12);
   __Pyx_DECREF(((PyObject *)__pyx_t_13)); __pyx_t_13 = 0;
   __Pyx_GIVEREF(__pyx_t_12);
@@ -13358,7 +14306,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
   __pyx_v_self->col2 = ((struct __pyx_obj_3_sa_FloatList *)__pyx_t_12);
   __pyx_t_12 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":177
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":176
  *         self.col2 = FloatList(initial_len=num_pairs)
  * 
  *         num_pairs = 0             # <<<<<<<<<<<<<<
@@ -13367,7 +14315,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
   __pyx_v_num_pairs = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":178
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":177
  * 
  *         num_pairs = 0
  *         for i from 0 <= i < V_F:             # <<<<<<<<<<<<<<
@@ -13377,7 +14325,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
   __pyx_t_6 = __pyx_v_V_F;
   for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_6; __pyx_v_i++) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":180
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":179
  *         for i from 0 <= i < V_F:
  *             #self.f_index[i] = num_pairs
  *             self.f_index.set(i, num_pairs)             # <<<<<<<<<<<<<<
@@ -13386,7 +14334,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
     ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_self->f_index->__pyx_vtab)->set(__pyx_v_self->f_index, __pyx_v_i, __pyx_v_num_pairs);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":181
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":180
  *             #self.f_index[i] = num_pairs
  *             self.f_index.set(i, num_pairs)
  *             if dict[i] != NULL:             # <<<<<<<<<<<<<<
@@ -13396,25 +14344,25 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
     __pyx_t_10 = ((__pyx_v_dict[__pyx_v_i]) != NULL);
     if (__pyx_t_10) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":182
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":181
  *             self.f_index.set(i, num_pairs)
  *             if dict[i] != NULL:
  *                 self._add_node(dict[i], &num_pairs, float(fmargin[i]), emargin)             # <<<<<<<<<<<<<<
  *                 del_node(dict[i])
  *         free(fmargin)
  */
-      __pyx_t_12 = ((struct __pyx_vtabstruct_3_sa_BiLex *)__pyx_v_self->__pyx_vtab)->_add_node(__pyx_v_self, (__pyx_v_dict[__pyx_v_i]), (&__pyx_v_num_pairs), ((double)(__pyx_v_fmargin[__pyx_v_i])), __pyx_v_emargin); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 182; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_12 = ((struct __pyx_vtabstruct_3_sa_BiLex *)__pyx_v_self->__pyx_vtab)->_add_node(__pyx_v_self, (__pyx_v_dict[__pyx_v_i]), (&__pyx_v_num_pairs), ((double)(__pyx_v_fmargin[__pyx_v_i])), __pyx_v_emargin); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_12);
       __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":183
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":182
  *             if dict[i] != NULL:
  *                 self._add_node(dict[i], &num_pairs, float(fmargin[i]), emargin)
  *                 del_node(dict[i])             # <<<<<<<<<<<<<<
  *         free(fmargin)
  *         free(emargin)
  */
-      __pyx_t_12 = __pyx_f_3_sa_del_node((__pyx_v_dict[__pyx_v_i])); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_12 = __pyx_f_3_sa_del_node((__pyx_v_dict[__pyx_v_i])); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 182; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_12);
       __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
       goto __pyx_L30;
@@ -13422,7 +14370,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
     __pyx_L30:;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":184
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":183
  *                 self._add_node(dict[i], &num_pairs, float(fmargin[i]), emargin)
  *                 del_node(dict[i])
  *         free(fmargin)             # <<<<<<<<<<<<<<
@@ -13431,7 +14379,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
   free(__pyx_v_fmargin);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":185
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":184
  *                 del_node(dict[i])
  *         free(fmargin)
  *         free(emargin)             # <<<<<<<<<<<<<<
@@ -13440,7 +14388,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
   free(__pyx_v_emargin);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":186
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":185
  *         free(fmargin)
  *         free(emargin)
  *         free(dict)             # <<<<<<<<<<<<<<
@@ -13449,7 +14397,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
  */
   free(__pyx_v_dict);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":187
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":186
  *         free(emargin)
  *         free(dict)
  *         return             # <<<<<<<<<<<<<<
@@ -13480,7 +14428,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_compute_from_data(struct __pyx_obj_3_sa_BiL
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":190
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":189
  * 
  * 
  *     cdef _add_node(self, _node* n, int* num_pairs, float fmargin, int* emargin):             # <<<<<<<<<<<<<<
@@ -13499,7 +14447,7 @@ static PyObject *__pyx_f_3_sa_5BiLex__add_node(struct __pyx_obj_3_sa_BiLex *__py
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("_add_node", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":192
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":191
  *     cdef _add_node(self, _node* n, int* num_pairs, float fmargin, int* emargin):
  *         cdef int loc
  *         if n.smaller != NULL:             # <<<<<<<<<<<<<<
@@ -13509,21 +14457,21 @@ static PyObject *__pyx_f_3_sa_5BiLex__add_node(struct __pyx_obj_3_sa_BiLex *__py
   __pyx_t_1 = (__pyx_v_n->smaller != NULL);
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":193
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":192
  *         cdef int loc
  *         if n.smaller != NULL:
  *             self._add_node(n.smaller, num_pairs, fmargin, emargin)             # <<<<<<<<<<<<<<
  *         loc = num_pairs[0]
  *         self.e_index.set(loc, n.key)
  */
-    __pyx_t_2 = ((struct __pyx_vtabstruct_3_sa_BiLex *)__pyx_v_self->__pyx_vtab)->_add_node(__pyx_v_self, __pyx_v_n->smaller, __pyx_v_num_pairs, __pyx_v_fmargin, __pyx_v_emargin); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = ((struct __pyx_vtabstruct_3_sa_BiLex *)__pyx_v_self->__pyx_vtab)->_add_node(__pyx_v_self, __pyx_v_n->smaller, __pyx_v_num_pairs, __pyx_v_fmargin, __pyx_v_emargin); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 192; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_2);
     __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
     goto __pyx_L3;
   }
   __pyx_L3:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":194
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":193
  *         if n.smaller != NULL:
  *             self._add_node(n.smaller, num_pairs, fmargin, emargin)
  *         loc = num_pairs[0]             # <<<<<<<<<<<<<<
@@ -13532,7 +14480,7 @@ static PyObject *__pyx_f_3_sa_5BiLex__add_node(struct __pyx_obj_3_sa_BiLex *__py
  */
   __pyx_v_loc = (__pyx_v_num_pairs[0]);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":195
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":194
  *             self._add_node(n.smaller, num_pairs, fmargin, emargin)
  *         loc = num_pairs[0]
  *         self.e_index.set(loc, n.key)             # <<<<<<<<<<<<<<
@@ -13541,7 +14489,7 @@ static PyObject *__pyx_f_3_sa_5BiLex__add_node(struct __pyx_obj_3_sa_BiLex *__py
  */
   ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_self->e_index->__pyx_vtab)->set(__pyx_v_self->e_index, __pyx_v_loc, __pyx_v_n->key);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":196
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":195
  *         loc = num_pairs[0]
  *         self.e_index.set(loc, n.key)
  *         self.col1.set(loc, float(n.val)/fmargin)             # <<<<<<<<<<<<<<
@@ -13550,11 +14498,11 @@ static PyObject *__pyx_f_3_sa_5BiLex__add_node(struct __pyx_obj_3_sa_BiLex *__py
  */
   if (unlikely(__pyx_v_fmargin == 0)) {
     PyErr_Format(PyExc_ZeroDivisionError, "float division");
-    {__pyx_filename = __pyx_f[5]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    {__pyx_filename = __pyx_f[5]; __pyx_lineno = 195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   }
   ((struct __pyx_vtabstruct_3_sa_FloatList *)__pyx_v_self->col1->__pyx_vtab)->set(__pyx_v_self->col1, __pyx_v_loc, (((double)__pyx_v_n->val) / __pyx_v_fmargin));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":197
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":196
  *         self.e_index.set(loc, n.key)
  *         self.col1.set(loc, float(n.val)/fmargin)
  *         self.col2.set(loc, float(n.val)/float(emargin[n.key]))             # <<<<<<<<<<<<<<
@@ -13563,11 +14511,11 @@ static PyObject *__pyx_f_3_sa_5BiLex__add_node(struct __pyx_obj_3_sa_BiLex *__py
  */
   if (unlikely(((double)(__pyx_v_emargin[__pyx_v_n->key])) == 0)) {
     PyErr_Format(PyExc_ZeroDivisionError, "float division");
-    {__pyx_filename = __pyx_f[5]; __pyx_lineno = 197; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    {__pyx_filename = __pyx_f[5]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   }
   ((struct __pyx_vtabstruct_3_sa_FloatList *)__pyx_v_self->col2->__pyx_vtab)->set(__pyx_v_self->col2, __pyx_v_loc, (((double)__pyx_v_n->val) / ((double)(__pyx_v_emargin[__pyx_v_n->key]))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":198
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":197
  *         self.col1.set(loc, float(n.val)/fmargin)
  *         self.col2.set(loc, float(n.val)/float(emargin[n.key]))
  *         num_pairs[0] = loc + 1             # <<<<<<<<<<<<<<
@@ -13576,7 +14524,7 @@ static PyObject *__pyx_f_3_sa_5BiLex__add_node(struct __pyx_obj_3_sa_BiLex *__py
  */
   (__pyx_v_num_pairs[0]) = (__pyx_v_loc + 1);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":199
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":198
  *         self.col2.set(loc, float(n.val)/float(emargin[n.key]))
  *         num_pairs[0] = loc + 1
  *         if n.bigger != NULL:             # <<<<<<<<<<<<<<
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":200
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":199
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+    __pyx_t_2 = ((struct __pyx_vtabstruct_3_sa_BiLex *)__pyx_v_self->__pyx_vtab)->_add_node(__pyx_v_self, __pyx_v_n->bigger, __pyx_v_num_pairs, __pyx_v_fmargin, __pyx_v_emargin); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 199; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -13620,7 +14568,7 @@ static PyObject *__pyx_pw_3_sa_5BiLex_3write_binary(PyObject *__pyx_v_self, PyOb
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+    __pyx_v_filename = PyBytes_AsString(__pyx_arg_filename); if (unlikely((!__pyx_v_filename) && PyErr_Occurred())) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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@@ -13633,7 +14581,7 @@ static PyObject *__pyx_pw_3_sa_5BiLex_3write_binary(PyObject *__pyx_v_self, PyOb
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":203
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":202
  * 
  * 
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":205
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":204
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  *         cdef FILE* f
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":206
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":205
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":207
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":206
  *         f = fopen(filename, "w")
  *         self.f_index.write_handle(f)
  *         self.e_index.write_handle(f)             # <<<<<<<<<<<<<<
@@ -13679,7 +14627,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_2write_binary(struct __pyx_obj_3_sa_BiLex
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":208
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":207
  *         self.f_index.write_handle(f)
  *         self.e_index.write_handle(f)
  *         self.col1.write_handle(f)             # <<<<<<<<<<<<<<
@@ -13688,7 +14636,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_2write_binary(struct __pyx_obj_3_sa_BiLex
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":209
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":208
  *         self.e_index.write_handle(f)
  *         self.col1.write_handle(f)
  *         self.col2.write_handle(f)             # <<<<<<<<<<<<<<
@@ -13697,7 +14645,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_2write_binary(struct __pyx_obj_3_sa_BiLex
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   ((struct __pyx_vtabstruct_3_sa_FloatList *)__pyx_v_self->col2->__pyx_vtab)->write_handle(__pyx_v_self->col2, __pyx_v_f);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":210
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":209
  *         self.col1.write_handle(f)
  *         self.col2.write_handle(f)
  *         self.write_wordlist(self.id2fword, f)             # <<<<<<<<<<<<<<
@@ -13706,12 +14654,12 @@ static PyObject *__pyx_pf_3_sa_5BiLex_2write_binary(struct __pyx_obj_3_sa_BiLex
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+  __pyx_t_2 = ((struct __pyx_vtabstruct_3_sa_BiLex *)__pyx_v_self->__pyx_vtab)->write_wordlist(__pyx_v_self, __pyx_t_1, __pyx_v_f); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":211
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":210
  *         self.col2.write_handle(f)
  *         self.write_wordlist(self.id2fword, f)
  *         self.write_wordlist(self.id2eword, f)             # <<<<<<<<<<<<<<
@@ -13720,12 +14668,12 @@ static PyObject *__pyx_pf_3_sa_5BiLex_2write_binary(struct __pyx_obj_3_sa_BiLex
  */
   __pyx_t_2 = __pyx_v_self->id2eword;
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-  __pyx_t_1 = ((struct __pyx_vtabstruct_3_sa_BiLex *)__pyx_v_self->__pyx_vtab)->write_wordlist(__pyx_v_self, __pyx_t_2, __pyx_v_f); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 211; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = ((struct __pyx_vtabstruct_3_sa_BiLex *)__pyx_v_self->__pyx_vtab)->write_wordlist(__pyx_v_self, __pyx_t_2, __pyx_v_f); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 210; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":212
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":211
  *         self.write_wordlist(self.id2fword, f)
  *         self.write_wordlist(self.id2eword, f)
  *         fclose(f)             # <<<<<<<<<<<<<<
@@ -13747,7 +14695,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_2write_binary(struct __pyx_obj_3_sa_BiLex
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":215
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":214
  * 
  * 
  *     cdef write_wordlist(self, wordlist, FILE* f):             # <<<<<<<<<<<<<<
@@ -13758,7 +14706,6 @@ static PyObject *__pyx_pf_3_sa_5BiLex_2write_binary(struct __pyx_obj_3_sa_BiLex
 static PyObject *__pyx_f_3_sa_5BiLex_write_wordlist(CYTHON_UNUSED struct __pyx_obj_3_sa_BiLex *__pyx_v_self, PyObject *__pyx_v_wordlist, FILE *__pyx_v_f) {
   int __pyx_v_word_len;
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-  char *__pyx_v_c_word;
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@@ -13766,43 +14713,44 @@ static PyObject *__pyx_f_3_sa_5BiLex_write_wordlist(CYTHON_UNUSED struct __pyx_o
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   PyObject *(*__pyx_t_3)(PyObject *);
   PyObject *__pyx_t_4 = NULL;
-  char *__pyx_t_5;
+  Py_ssize_t __pyx_t_5;
+  char *__pyx_t_6;
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   const char *__pyx_filename = NULL;
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":220
- *         cdef char* c_word
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":218
+ *         cdef int num_words
  * 
  *         num_words = len(wordlist)             # <<<<<<<<<<<<<<
  *         fwrite(&(num_words), sizeof(int), 1, f)
  *         for word in wordlist:
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-  __pyx_t_1 = PyObject_Length(__pyx_v_wordlist); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_Length(__pyx_v_wordlist); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_num_words = __pyx_t_1;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":221
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":219
  * 
  *         num_words = len(wordlist)
  *         fwrite(&(num_words), sizeof(int), 1, f)             # <<<<<<<<<<<<<<
  *         for word in wordlist:
- *             c_word = word
+ *             word_len = len(word) + 1
  */
   fwrite((&__pyx_v_num_words), (sizeof(int)), 1, __pyx_v_f);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":222
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":220
  *         num_words = len(wordlist)
  *         fwrite(&(num_words), sizeof(int), 1, f)
  *         for word in wordlist:             # <<<<<<<<<<<<<<
- *             c_word = word
- *             word_len = strlen(c_word) + 1
+ *             word_len = len(word) + 1
+ *             fwrite(&(word_len), sizeof(int), 1, f)
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   if (PyList_CheckExact(__pyx_v_wordlist) || PyTuple_CheckExact(__pyx_v_wordlist)) {
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-    __pyx_t_1 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_v_wordlist); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_1 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_v_wordlist); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_2);
     __pyx_t_3 = Py_TYPE(__pyx_t_2)->tp_iternext;
   }
@@ -13810,23 +14758,23 @@ static PyObject *__pyx_f_3_sa_5BiLex_write_wordlist(CYTHON_UNUSED struct __pyx_o
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       if (__pyx_t_1 >= PyList_GET_SIZE(__pyx_t_2)) break;
       #if CYTHON_COMPILING_IN_CPYTHON
-      __pyx_t_4 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_1); __Pyx_INCREF(__pyx_t_4); __pyx_t_1++;
+      __pyx_t_4 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_1); __Pyx_INCREF(__pyx_t_4); __pyx_t_1++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       #else
-      __pyx_t_4 = PySequence_ITEM(__pyx_t_2, __pyx_t_1); __pyx_t_1++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+      __pyx_t_4 = PySequence_ITEM(__pyx_t_2, __pyx_t_1); __pyx_t_1++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       #endif
     } else if (!__pyx_t_3 && PyTuple_CheckExact(__pyx_t_2)) {
       if (__pyx_t_1 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
       #if CYTHON_COMPILING_IN_CPYTHON
-      __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_1); __Pyx_INCREF(__pyx_t_4); __pyx_t_1++;
+      __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_1); __Pyx_INCREF(__pyx_t_4); __pyx_t_1++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       #else
-      __pyx_t_4 = PySequence_ITEM(__pyx_t_2, __pyx_t_1); __pyx_t_1++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+      __pyx_t_4 = PySequence_ITEM(__pyx_t_2, __pyx_t_1); __pyx_t_1++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       #endif
     } else {
       __pyx_t_4 = __pyx_t_3(__pyx_t_2);
       if (unlikely(!__pyx_t_4)) {
         if (PyErr_Occurred()) {
           if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
-          else {__pyx_filename = __pyx_f[5]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          else {__pyx_filename = __pyx_f[5]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         }
         break;
       }
@@ -13836,42 +14784,34 @@ static PyObject *__pyx_f_3_sa_5BiLex_write_wordlist(CYTHON_UNUSED struct __pyx_o
     __pyx_v_word = __pyx_t_4;
     __pyx_t_4 = 0;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":223
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":221
  *         fwrite(&(num_words), sizeof(int), 1, f)
  *         for word in wordlist:
- *             c_word = word             # <<<<<<<<<<<<<<
- *             word_len = strlen(c_word) + 1
+ *             word_len = len(word) + 1             # <<<<<<<<<<<<<<
  *             fwrite(&(word_len), sizeof(int), 1, f)
+ *             fwrite(<char *>word, sizeof(char), word_len, f)
  */
-    __pyx_t_5 = PyBytes_AsString(__pyx_v_word); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-    __pyx_v_c_word = __pyx_t_5;
+    __pyx_t_5 = PyObject_Length(__pyx_v_word); if (unlikely(__pyx_t_5 == -1)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_v_word_len = (__pyx_t_5 + 1);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":224
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":222
  *         for word in wordlist:
- *             c_word = word
- *             word_len = strlen(c_word) + 1             # <<<<<<<<<<<<<<
- *             fwrite(&(word_len), sizeof(int), 1, f)
- *             fwrite(c_word, sizeof(char), word_len, f)
- */
-    __pyx_v_word_len = (strlen(__pyx_v_c_word) + 1);
-
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":225
- *             c_word = word
- *             word_len = strlen(c_word) + 1
+ *             word_len = len(word) + 1
  *             fwrite(&(word_len), sizeof(int), 1, f)             # <<<<<<<<<<<<<<
- *             fwrite(c_word, sizeof(char), word_len, f)
+ *             fwrite(<char *>word, sizeof(char), word_len, f)
  * 
  */
     fwrite((&__pyx_v_word_len), (sizeof(int)), 1, __pyx_v_f);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":226
- *             word_len = strlen(c_word) + 1
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":223
+ *             word_len = len(word) + 1
  *             fwrite(&(word_len), sizeof(int), 1, f)
- *             fwrite(c_word, sizeof(char), word_len, f)             # <<<<<<<<<<<<<<
+ *             fwrite(<char *>word, sizeof(char), word_len, f)             # <<<<<<<<<<<<<<
  * 
  * 
  */
-    fwrite(__pyx_v_c_word, (sizeof(char)), __pyx_v_word_len, __pyx_v_f);
+    __pyx_t_6 = PyBytes_AsString(__pyx_v_word); if (unlikely((!__pyx_t_6) && PyErr_Occurred())) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    fwrite(((char *)__pyx_t_6), (sizeof(char)), __pyx_v_word_len, __pyx_v_f);
   }
   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
@@ -13889,7 +14829,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_write_wordlist(CYTHON_UNUSED struct __pyx_o
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":229
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":226
  * 
  * 
  *     cdef read_wordlist(self, word2id, id2word, FILE* f):             # <<<<<<<<<<<<<<
@@ -13900,21 +14840,21 @@ static PyObject *__pyx_f_3_sa_5BiLex_write_wordlist(CYTHON_UNUSED struct __pyx_o
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   int __pyx_v_num_words;
   int __pyx_v_word_len;
-  char *__pyx_v_c_word;
-  PyObject *__pyx_v_py_word = 0;
+  char *__pyx_v_word;
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":236
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":237
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- *             fread(c_word, sizeof(char), word_len, f)
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":238
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":239
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":248
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-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":281
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":276
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-                {__pyx_filename = __pyx_f[5]; __pyx_lineno = 281; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":282
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-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":283
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-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":284
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-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":285
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-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":286
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":289
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":290
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":291
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":292
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":298
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":302
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-              __pyx_t_12 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_8); __Pyx_INCREF(__pyx_t_12); __pyx_t_8++;
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-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":304
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-                {__pyx_filename = __pyx_f[5]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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-              {__pyx_filename = __pyx_f[5]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":305
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-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":306
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-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":307
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-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":308
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@@ -15386,7 +16318,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_swap(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
   int __pyx_t_1;
   __Pyx_RefNannySetupContext("swap", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":324
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":319
  *         cdef float ftmp
  * 
  *         if i == j:             # <<<<<<<<<<<<<<
@@ -15396,7 +16328,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_swap(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
   __pyx_t_1 = (__pyx_v_i == __pyx_v_j);
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":325
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":320
  * 
  *         if i == j:
  *             return             # <<<<<<<<<<<<<<
@@ -15410,7 +16342,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_swap(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
   }
   __pyx_L3:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":327
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":322
  *             return
  * 
  *         itmp = self.e_index.arr[i]             # <<<<<<<<<<<<<<
@@ -15419,7 +16351,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_swap(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
  */
   __pyx_v_itmp = (__pyx_v_self->e_index->arr[__pyx_v_i]);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":328
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":323
  * 
  *         itmp = self.e_index.arr[i]
  *         self.e_index.arr[i] = self.e_index.arr[j]             # <<<<<<<<<<<<<<
@@ -15428,7 +16360,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_swap(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
  */
   (__pyx_v_self->e_index->arr[__pyx_v_i]) = (__pyx_v_self->e_index->arr[__pyx_v_j]);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":329
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":324
  *         itmp = self.e_index.arr[i]
  *         self.e_index.arr[i] = self.e_index.arr[j]
  *         self.e_index.arr[j] = itmp             # <<<<<<<<<<<<<<
@@ -15437,7 +16369,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_swap(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
  */
   (__pyx_v_self->e_index->arr[__pyx_v_j]) = __pyx_v_itmp;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":331
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":326
  *         self.e_index.arr[j] = itmp
  * 
  *         ftmp = self.col1.arr[i]             # <<<<<<<<<<<<<<
@@ -15446,7 +16378,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_swap(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
  */
   __pyx_v_ftmp = (__pyx_v_self->col1->arr[__pyx_v_i]);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":332
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":327
  * 
  *         ftmp = self.col1.arr[i]
  *         self.col1.arr[i] = self.col1.arr[j]             # <<<<<<<<<<<<<<
@@ -15455,7 +16387,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_swap(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
  */
   (__pyx_v_self->col1->arr[__pyx_v_i]) = (__pyx_v_self->col1->arr[__pyx_v_j]);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":333
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":328
  *         ftmp = self.col1.arr[i]
  *         self.col1.arr[i] = self.col1.arr[j]
  *         self.col1.arr[j] = ftmp             # <<<<<<<<<<<<<<
@@ -15464,7 +16396,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_swap(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
  */
   (__pyx_v_self->col1->arr[__pyx_v_j]) = __pyx_v_ftmp;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":335
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":330
  *         self.col1.arr[j] = ftmp
  * 
  *         ftmp = self.col2.arr[i]             # <<<<<<<<<<<<<<
@@ -15473,7 +16405,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_swap(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
  */
   __pyx_v_ftmp = (__pyx_v_self->col2->arr[__pyx_v_i]);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":336
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":331
  * 
  *         ftmp = self.col2.arr[i]
  *         self.col2.arr[i] = self.col2.arr[j]             # <<<<<<<<<<<<<<
@@ -15482,7 +16414,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_swap(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
  */
   (__pyx_v_self->col2->arr[__pyx_v_i]) = (__pyx_v_self->col2->arr[__pyx_v_j]);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":337
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":332
  *         ftmp = self.col2.arr[i]
  *         self.col2.arr[i] = self.col2.arr[j]
  *         self.col2.arr[j] = ftmp             # <<<<<<<<<<<<<<
@@ -15498,7 +16430,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_swap(struct __pyx_obj_3_sa_BiLex *__pyx_v_s
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":340
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":335
  * 
  * 
  *     cdef qsort(self, int i, int j, pad):             # <<<<<<<<<<<<<<
@@ -15521,7 +16453,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_qsort(struct __pyx_obj_3_sa_BiLex *__pyx_v_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("qsort", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":343
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":338
  *         cdef int pval, p
  * 
  *         if i > j:             # <<<<<<<<<<<<<<
@@ -15531,23 +16463,23 @@ static PyObject *__pyx_f_3_sa_5BiLex_qsort(struct __pyx_obj_3_sa_BiLex *__pyx_v_
   __pyx_t_1 = (__pyx_v_i > __pyx_v_j);
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":344
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":339
  * 
  *         if i > j:
  *             raise Exception("Sort error in CLex")             # <<<<<<<<<<<<<<
  *         if i == j: #empty interval
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-    __pyx_t_2 = PyObject_Call(__pyx_builtin_Exception, ((PyObject *)__pyx_k_tuple_47), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = PyObject_Call(__pyx_builtin_Exception, ((PyObject *)__pyx_k_tuple_47), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 339; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_2);
     __Pyx_Raise(__pyx_t_2, 0, 0, 0);
     __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
-    {__pyx_filename = __pyx_f[5]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    {__pyx_filename = __pyx_f[5]; __pyx_lineno = 339; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     goto __pyx_L3;
   }
   __pyx_L3:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":345
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":340
  *         if i > j:
  *             raise Exception("Sort error in CLex")
  *         if i == j: #empty interval             # <<<<<<<<<<<<<<
@@ -15557,7 +16489,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_qsort(struct __pyx_obj_3_sa_BiLex *__pyx_v_
   __pyx_t_1 = (__pyx_v_i == __pyx_v_j);
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":346
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":341
  *             raise Exception("Sort error in CLex")
  *         if i == j: #empty interval
  *             return             # <<<<<<<<<<<<<<
@@ -15571,7 +16503,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_qsort(struct __pyx_obj_3_sa_BiLex *__pyx_v_
   }
   __pyx_L4:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":347
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":342
  *         if i == j: #empty interval
  *             return
  *         if i == j-1: # singleton interval             # <<<<<<<<<<<<<<
@@ -15581,7 +16513,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_qsort(struct __pyx_obj_3_sa_BiLex *__pyx_v_
   __pyx_t_1 = (__pyx_v_i == (__pyx_v_j - 1));
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":348
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":343
  *             return
  *         if i == j-1: # singleton interval
  *             return             # <<<<<<<<<<<<<<
@@ -15595,7 +16527,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_qsort(struct __pyx_obj_3_sa_BiLex *__pyx_v_
   }
   __pyx_L5:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":350
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":345
  *             return
  * 
  *         p = (i+j)/2             # <<<<<<<<<<<<<<
@@ -15604,7 +16536,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_qsort(struct __pyx_obj_3_sa_BiLex *__pyx_v_
  */
   __pyx_v_p = __Pyx_div_long((__pyx_v_i + __pyx_v_j), 2);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":351
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":346
  * 
  *         p = (i+j)/2
  *         pval = self.e_index.arr[p]             # <<<<<<<<<<<<<<
@@ -15613,18 +16545,18 @@ static PyObject *__pyx_f_3_sa_5BiLex_qsort(struct __pyx_obj_3_sa_BiLex *__pyx_v_
  */
   __pyx_v_pval = (__pyx_v_self->e_index->arr[__pyx_v_p]);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":352
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":347
  *         p = (i+j)/2
  *         pval = self.e_index.arr[p]
  *         self.swap(i, p)             # <<<<<<<<<<<<<<
  *         p = i
  *         for k from i+1 <= k < j:
  */
-  __pyx_t_2 = ((struct __pyx_vtabstruct_3_sa_BiLex *)__pyx_v_self->__pyx_vtab)->swap(__pyx_v_self, __pyx_v_i, __pyx_v_p); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 352; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = ((struct __pyx_vtabstruct_3_sa_BiLex *)__pyx_v_self->__pyx_vtab)->swap(__pyx_v_self, __pyx_v_i, __pyx_v_p); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_2);
   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":353
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":348
  *         pval = self.e_index.arr[p]
  *         self.swap(i, p)
  *         p = i             # <<<<<<<<<<<<<<
@@ -15633,7 +16565,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_qsort(struct __pyx_obj_3_sa_BiLex *__pyx_v_
  */
   __pyx_v_p = __pyx_v_i;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":354
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":349
  *         self.swap(i, p)
  *         p = i
  *         for k from i+1 <= k < j:             # <<<<<<<<<<<<<<
@@ -15643,7 +16575,7 @@ static PyObject *__pyx_f_3_sa_5BiLex_qsort(struct __pyx_obj_3_sa_BiLex *__pyx_v_
   __pyx_t_3 = __pyx_v_j;
   for (__pyx_v_k = (__pyx_v_i + 1); __pyx_v_k < __pyx_t_3; __pyx_v_k++) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":355
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":350
  *         p = i
  *         for k from i+1 <= k < j:
  *             if pval >= self.e_index.arr[k]:             # <<<<<<<<<<<<<<
@@ -15653,29 +16585,29 @@ static PyObject *__pyx_f_3_sa_5BiLex_qsort(struct __pyx_obj_3_sa_BiLex *__pyx_v_
     __pyx_t_1 = (__pyx_v_pval >= (__pyx_v_self->e_index->arr[__pyx_v_k]));
     if (__pyx_t_1) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":356
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":351
  *         for k from i+1 <= k < j:
  *             if pval >= self.e_index.arr[k]:
  *                 self.swap(p+1, k)             # <<<<<<<<<<<<<<
  *                 self.swap(p, p+1)
  *                 p = p + 1
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-      __pyx_t_2 = ((struct __pyx_vtabstruct_3_sa_BiLex *)__pyx_v_self->__pyx_vtab)->swap(__pyx_v_self, (__pyx_v_p + 1), __pyx_v_k); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_2 = ((struct __pyx_vtabstruct_3_sa_BiLex *)__pyx_v_self->__pyx_vtab)->swap(__pyx_v_self, (__pyx_v_p + 1), __pyx_v_k); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 351; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_2);
       __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":357
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":352
  *             if pval >= self.e_index.arr[k]:
  *                 self.swap(p+1, k)
  *                 self.swap(p, p+1)             # <<<<<<<<<<<<<<
  *                 p = p + 1
  *         self.qsort(i,p, pad+"    ")
  */
-      __pyx_t_2 = ((struct __pyx_vtabstruct_3_sa_BiLex *)__pyx_v_self->__pyx_vtab)->swap(__pyx_v_self, __pyx_v_p, (__pyx_v_p + 1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_2 = ((struct __pyx_vtabstruct_3_sa_BiLex *)__pyx_v_self->__pyx_vtab)->swap(__pyx_v_self, __pyx_v_p, (__pyx_v_p + 1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 352; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_2);
       __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":358
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":353
  *                 self.swap(p+1, k)
  *                 self.swap(p, p+1)
  *                 p = p + 1             # <<<<<<<<<<<<<<
@@ -15688,30 +16620,30 @@ static PyObject *__pyx_f_3_sa_5BiLex_qsort(struct __pyx_obj_3_sa_BiLex *__pyx_v_
     __pyx_L8:;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":359
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":354
  *                 self.swap(p, p+1)
  *                 p = p + 1
  *         self.qsort(i,p, pad+"    ")             # <<<<<<<<<<<<<<
  *         self.qsort(p+1,j, pad+"    ")
  * 
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-  __pyx_t_2 = PyNumber_Add(__pyx_v_pad, ((PyObject *)__pyx_kp_s_48)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = PyNumber_Add(__pyx_v_pad, ((PyObject *)__pyx_kp_s_48)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_2);
-  __pyx_t_4 = ((struct __pyx_vtabstruct_3_sa_BiLex *)__pyx_v_self->__pyx_vtab)->qsort(__pyx_v_self, __pyx_v_i, __pyx_v_p, __pyx_t_2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_4 = ((struct __pyx_vtabstruct_3_sa_BiLex *)__pyx_v_self->__pyx_vtab)->qsort(__pyx_v_self, __pyx_v_i, __pyx_v_p, __pyx_t_2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_4);
   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
   __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":360
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":355
  *                 p = p + 1
  *         self.qsort(i,p, pad+"    ")
  *         self.qsort(p+1,j, pad+"    ")             # <<<<<<<<<<<<<<
  * 
  * 
  */
-  __pyx_t_4 = PyNumber_Add(__pyx_v_pad, ((PyObject *)__pyx_kp_s_48)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_4 = PyNumber_Add(__pyx_v_pad, ((PyObject *)__pyx_kp_s_48)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 355; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_4);
-  __pyx_t_2 = ((struct __pyx_vtabstruct_3_sa_BiLex *)__pyx_v_self->__pyx_vtab)->qsort(__pyx_v_self, (__pyx_v_p + 1), __pyx_v_j, __pyx_t_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = ((struct __pyx_vtabstruct_3_sa_BiLex *)__pyx_v_self->__pyx_vtab)->qsort(__pyx_v_self, (__pyx_v_p + 1), __pyx_v_j, __pyx_t_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 355; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_2);
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   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":363
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-                {__pyx_filename = __pyx_f[5]; __pyx_lineno = 368; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
+                {__pyx_filename = __pyx_f[5]; __pyx_lineno = 363; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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-              {__pyx_filename = __pyx_f[5]; __pyx_lineno = 368; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":369
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":370
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":371
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-              __pyx_t_11 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_11); __pyx_t_8++;
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-              __pyx_t_11 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_11); __pyx_t_8++;
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+              __pyx_t_11 = PySequence_ITEM(__pyx_t_2, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 366; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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-              __pyx_t_10 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_8); __Pyx_INCREF(__pyx_t_10); __pyx_t_8++;
+              __pyx_t_10 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_8); __Pyx_INCREF(__pyx_t_10); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 369; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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-              __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_8); __Pyx_INCREF(__pyx_t_10); __pyx_t_8++;
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+              __pyx_t_10 = PySequence_ITEM(__pyx_t_1, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 369; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":375
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":376
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@@ -16299,7 +17231,7 @@ static PyObject *__pyx_pf_3_sa_5BiLex_12write_enhanced(struct __pyx_obj_3_sa_BiL
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":364
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":383
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":384
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":385
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":386
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":387
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":388
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":389
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":390
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":392
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":41
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  *     b.bitset = 0
  *     b.min_val = -1
  *     b.max_val = -1             # <<<<<<<<<<<<<<
@@ -17298,7 +18223,7 @@ static struct __pyx_t_3_sa__BitSet *__pyx_f_3_sa_new_BitSet(void) {
  */
   __pyx_v_b->max_val = -1;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":44
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":44
  *     b.min_val = -1
  *     b.max_val = -1
  *     b.size = 0             # <<<<<<<<<<<<<<
@@ -17307,7 +18232,7 @@ static struct __pyx_t_3_sa__BitSet *__pyx_f_3_sa_new_BitSet(void) {
  */
   __pyx_v_b->size = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":45
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":45
  *     b.max_val = -1
  *     b.size = 0
  *     return b             # <<<<<<<<<<<<<<
@@ -17323,7 +18248,7 @@ static struct __pyx_t_3_sa__BitSet *__pyx_f_3_sa_new_BitSet(void) {
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":48
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":48
  * 
  * 
  * cdef int bitset_findsucc(_BitSet* b, int i):             # <<<<<<<<<<<<<<
@@ -17344,7 +18269,7 @@ static int __pyx_f_3_sa_bitset_findsucc(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
   int __pyx_t_3;
   __Pyx_RefNannySetupContext("bitset_findsucc", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":52
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":52
  *     cdef int low, high, mid
  * 
  *     if b.max_val == -1 or i >= b.max_val:             # <<<<<<<<<<<<<<
@@ -17360,7 +18285,7 @@ static int __pyx_f_3_sa_bitset_findsucc(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
   }
   if (__pyx_t_3) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":53
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":53
  * 
  *     if b.max_val == -1 or i >= b.max_val:
  *         return -1             # <<<<<<<<<<<<<<
@@ -17373,7 +18298,7 @@ static int __pyx_f_3_sa_bitset_findsucc(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
   }
   __pyx_L3:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":54
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":54
  *     if b.max_val == -1 or i >= b.max_val:
  *         return -1
  *     if i < b.min_val:             # <<<<<<<<<<<<<<
@@ -17383,7 +18308,7 @@ static int __pyx_f_3_sa_bitset_findsucc(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
   __pyx_t_3 = (__pyx_v_i < __pyx_v_b->min_val);
   if (__pyx_t_3) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":55
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":55
  *         return -1
  *     if i < b.min_val:
  *         return b.min_val             # <<<<<<<<<<<<<<
@@ -17396,7 +18321,7 @@ static int __pyx_f_3_sa_bitset_findsucc(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
   }
   __pyx_L4:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":57
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":57
  *         return b.min_val
  * 
  *     bitset = b.bitset & ~LOWER_MASK[i]             # <<<<<<<<<<<<<<
@@ -17405,7 +18330,7 @@ static int __pyx_f_3_sa_bitset_findsucc(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
  */
   __pyx_v_bitset = (__pyx_v_b->bitset & (~(__pyx_v_3_sa_LOWER_MASK[__pyx_v_i])));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":58
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":58
  * 
  *     bitset = b.bitset & ~LOWER_MASK[i]
  *     low = i+1             # <<<<<<<<<<<<<<
@@ -17414,7 +18339,7 @@ static int __pyx_f_3_sa_bitset_findsucc(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
  */
   __pyx_v_low = (__pyx_v_i + 1);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":59
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":59
  *     bitset = b.bitset & ~LOWER_MASK[i]
  *     low = i+1
  *     high = b.max_val+1             # <<<<<<<<<<<<<<
@@ -17423,7 +18348,7 @@ static int __pyx_f_3_sa_bitset_findsucc(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
  */
   __pyx_v_high = (__pyx_v_b->max_val + 1);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":60
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":60
  *     low = i+1
  *     high = b.max_val+1
  *     while low < high-1:             # <<<<<<<<<<<<<<
@@ -17434,7 +18359,7 @@ static int __pyx_f_3_sa_bitset_findsucc(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
     __pyx_t_3 = (__pyx_v_low < (__pyx_v_high - 1));
     if (!__pyx_t_3) break;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":61
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":61
  *     high = b.max_val+1
  *     while low < high-1:
  *         mid = (high + low)/2             # <<<<<<<<<<<<<<
@@ -17443,7 +18368,7 @@ static int __pyx_f_3_sa_bitset_findsucc(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
  */
     __pyx_v_mid = __Pyx_div_long((__pyx_v_high + __pyx_v_low), 2);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":62
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":62
  *     while low < high-1:
  *         mid = (high + low)/2
  *         mask = ~(LOWER_MASK[high-1] ^ LOWER_MASK[mid-1])             # <<<<<<<<<<<<<<
@@ -17452,7 +18377,7 @@ static int __pyx_f_3_sa_bitset_findsucc(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
  */
     __pyx_v_mask = (~((__pyx_v_3_sa_LOWER_MASK[(__pyx_v_high - 1)]) ^ (__pyx_v_3_sa_LOWER_MASK[(__pyx_v_mid - 1)])));
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":63
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":63
  *         mid = (high + low)/2
  *         mask = ~(LOWER_MASK[high-1] ^ LOWER_MASK[mid-1])
  *         if bitset & mask == 0:             # <<<<<<<<<<<<<<
@@ -17462,7 +18387,7 @@ static int __pyx_f_3_sa_bitset_findsucc(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
     __pyx_t_3 = ((__pyx_v_bitset & __pyx_v_mask) == 0);
     if (__pyx_t_3) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":64
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":64
  *         mask = ~(LOWER_MASK[high-1] ^ LOWER_MASK[mid-1])
  *         if bitset & mask == 0:
  *             low = mid             # <<<<<<<<<<<<<<
@@ -17474,7 +18399,7 @@ static int __pyx_f_3_sa_bitset_findsucc(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
     }
     /*else*/ {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":66
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":66
  *             low = mid
  *         else:
  *             bitset = bitset & mask             # <<<<<<<<<<<<<<
@@ -17483,7 +18408,7 @@ static int __pyx_f_3_sa_bitset_findsucc(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
  */
       __pyx_v_bitset = (__pyx_v_bitset & __pyx_v_mask);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":67
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":67
  *         else:
  *             bitset = bitset & mask
  *             high = mid             # <<<<<<<<<<<<<<
@@ -17495,7 +18420,7 @@ static int __pyx_f_3_sa_bitset_findsucc(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
     __pyx_L7:;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":68
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":68
  *             bitset = bitset & mask
  *             high = mid
  *     return low             # <<<<<<<<<<<<<<
@@ -17511,7 +18436,7 @@ static int __pyx_f_3_sa_bitset_findsucc(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":71
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":71
  * 
  * 
  * cdef int bitset_insert(_BitSet* b, int i):             # <<<<<<<<<<<<<<
@@ -17526,7 +18451,7 @@ static int __pyx_f_3_sa_bitset_insert(struct __pyx_t_3_sa__BitSet *__pyx_v_b, in
   int __pyx_t_1;
   __Pyx_RefNannySetupContext("bitset_insert", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":74
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":74
  *     cdef int val
  * 
  *     val = 1 << i             # <<<<<<<<<<<<<<
@@ -17535,7 +18460,7 @@ static int __pyx_f_3_sa_bitset_insert(struct __pyx_t_3_sa__BitSet *__pyx_v_b, in
  */
   __pyx_v_val = (1 << __pyx_v_i);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":75
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":75
  * 
  *     val = 1 << i
  *     if b.bitset & val == 0:             # <<<<<<<<<<<<<<
@@ -17545,7 +18470,7 @@ static int __pyx_f_3_sa_bitset_insert(struct __pyx_t_3_sa__BitSet *__pyx_v_b, in
   __pyx_t_1 = ((__pyx_v_b->bitset & __pyx_v_val) == 0);
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":76
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":76
  *     val = 1 << i
  *     if b.bitset & val == 0:
  *         b.bitset = b.bitset | val             # <<<<<<<<<<<<<<
@@ -17554,7 +18479,7 @@ static int __pyx_f_3_sa_bitset_insert(struct __pyx_t_3_sa__BitSet *__pyx_v_b, in
  */
     __pyx_v_b->bitset = (__pyx_v_b->bitset | __pyx_v_val);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":77
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":77
  *     if b.bitset & val == 0:
  *         b.bitset = b.bitset | val
  *         if b.size == 0:             # <<<<<<<<<<<<<<
@@ -17564,7 +18489,7 @@ static int __pyx_f_3_sa_bitset_insert(struct __pyx_t_3_sa__BitSet *__pyx_v_b, in
     __pyx_t_1 = (__pyx_v_b->size == 0);
     if (__pyx_t_1) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":78
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":78
  *         b.bitset = b.bitset | val
  *         if b.size == 0:
  *             b.min_val = i             # <<<<<<<<<<<<<<
@@ -17573,7 +18498,7 @@ static int __pyx_f_3_sa_bitset_insert(struct __pyx_t_3_sa__BitSet *__pyx_v_b, in
  */
       __pyx_v_b->min_val = __pyx_v_i;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":79
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":79
  *         if b.size == 0:
  *             b.min_val = i
  *             b.max_val = i             # <<<<<<<<<<<<<<
@@ -17585,7 +18510,7 @@ static int __pyx_f_3_sa_bitset_insert(struct __pyx_t_3_sa__BitSet *__pyx_v_b, in
     }
     /*else*/ {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":81
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":81
  *             b.max_val = i
  *         else:
  *             if i < b.min_val:             # <<<<<<<<<<<<<<
@@ -17595,7 +18520,7 @@ static int __pyx_f_3_sa_bitset_insert(struct __pyx_t_3_sa__BitSet *__pyx_v_b, in
       __pyx_t_1 = (__pyx_v_i < __pyx_v_b->min_val);
       if (__pyx_t_1) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":82
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":82
  *         else:
  *             if i < b.min_val:
  *                 b.min_val = i             # <<<<<<<<<<<<<<
@@ -17607,7 +18532,7 @@ static int __pyx_f_3_sa_bitset_insert(struct __pyx_t_3_sa__BitSet *__pyx_v_b, in
       }
       __pyx_L5:;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":83
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":83
  *             if i < b.min_val:
  *                 b.min_val = i
  *             if i > b.max_val:             # <<<<<<<<<<<<<<
@@ -17617,7 +18542,7 @@ static int __pyx_f_3_sa_bitset_insert(struct __pyx_t_3_sa__BitSet *__pyx_v_b, in
       __pyx_t_1 = (__pyx_v_i > __pyx_v_b->max_val);
       if (__pyx_t_1) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":84
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":84
  *                 b.min_val = i
  *             if i > b.max_val:
  *                 b.max_val = i             # <<<<<<<<<<<<<<
@@ -17631,7 +18556,7 @@ static int __pyx_f_3_sa_bitset_insert(struct __pyx_t_3_sa__BitSet *__pyx_v_b, in
     }
     __pyx_L4:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":85
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":85
  *             if i > b.max_val:
  *                 b.max_val = i
  *         b.size = b.size + 1             # <<<<<<<<<<<<<<
@@ -17640,7 +18565,7 @@ static int __pyx_f_3_sa_bitset_insert(struct __pyx_t_3_sa__BitSet *__pyx_v_b, in
  */
     __pyx_v_b->size = (__pyx_v_b->size + 1);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":86
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":86
  *                 b.max_val = i
  *         b.size = b.size + 1
  *         return 1             # <<<<<<<<<<<<<<
@@ -17653,7 +18578,7 @@ static int __pyx_f_3_sa_bitset_insert(struct __pyx_t_3_sa__BitSet *__pyx_v_b, in
   }
   __pyx_L3:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":87
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":87
  *         b.size = b.size + 1
  *         return 1
  *     return 0             # <<<<<<<<<<<<<<
@@ -17669,7 +18594,7 @@ static int __pyx_f_3_sa_bitset_insert(struct __pyx_t_3_sa__BitSet *__pyx_v_b, in
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":90
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":90
  * 
  * 
  * cdef int bitset_contains(_BitSet* b, int i):             # <<<<<<<<<<<<<<
@@ -17684,7 +18609,7 @@ static int __pyx_f_3_sa_bitset_contains(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
   int __pyx_t_1;
   __Pyx_RefNannySetupContext("bitset_contains", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":93
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":93
  *     cdef int val
  * 
  *     val = 1 << i             # <<<<<<<<<<<<<<
@@ -17693,7 +18618,7 @@ static int __pyx_f_3_sa_bitset_contains(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
  */
   __pyx_v_val = (1 << __pyx_v_i);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":94
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":94
  * 
  *     val = 1 << i
  *     if b.bitset & val == 0:             # <<<<<<<<<<<<<<
@@ -17703,7 +18628,7 @@ static int __pyx_f_3_sa_bitset_contains(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
   __pyx_t_1 = ((__pyx_v_b->bitset & __pyx_v_val) == 0);
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":95
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":95
  *     val = 1 << i
  *     if b.bitset & val == 0:
  *         return 0             # <<<<<<<<<<<<<<
@@ -17716,7 +18641,7 @@ static int __pyx_f_3_sa_bitset_contains(struct __pyx_t_3_sa__BitSet *__pyx_v_b,
   }
   /*else*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":97
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":97
  *         return 0
  *     else:
  *         return 1             # <<<<<<<<<<<<<<
@@ -17745,7 +18670,7 @@ static PyObject *__pyx_pw_3_sa_14BitSetIterator_1__next__(PyObject *__pyx_v_self
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":104
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":104
  *     cdef int next_val
  * 
  *     def __next__(self):             # <<<<<<<<<<<<<<
@@ -17764,7 +18689,7 @@ static PyObject *__pyx_pf_3_sa_14BitSetIterator___next__(struct __pyx_obj_3_sa_B
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__next__", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":107
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":107
  *         cdef int ret_val
  * 
  *         if self.next_val == -1:             # <<<<<<<<<<<<<<
@@ -17774,7 +18699,7 @@ static PyObject *__pyx_pf_3_sa_14BitSetIterator___next__(struct __pyx_obj_3_sa_B
   __pyx_t_1 = (__pyx_v_self->next_val == -1);
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":108
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":108
  * 
  *         if self.next_val == -1:
  *             raise StopIteration()             # <<<<<<<<<<<<<<
@@ -17790,7 +18715,7 @@ static PyObject *__pyx_pf_3_sa_14BitSetIterator___next__(struct __pyx_obj_3_sa_B
   }
   __pyx_L3:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":109
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":109
  *         if self.next_val == -1:
  *             raise StopIteration()
  *         ret_val = self.next_val             # <<<<<<<<<<<<<<
@@ -17799,7 +18724,7 @@ static PyObject *__pyx_pf_3_sa_14BitSetIterator___next__(struct __pyx_obj_3_sa_B
  */
   __pyx_v_ret_val = __pyx_v_self->next_val;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":110
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":110
  *             raise StopIteration()
  *         ret_val = self.next_val
  *         self.next_val = bitset_findsucc(self.b, ret_val)             # <<<<<<<<<<<<<<
@@ -17808,7 +18733,7 @@ static PyObject *__pyx_pf_3_sa_14BitSetIterator___next__(struct __pyx_obj_3_sa_B
  */
   __pyx_v_self->next_val = __pyx_f_3_sa_bitset_findsucc(__pyx_v_self->b, __pyx_v_ret_val);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":111
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":111
  *         ret_val = self.next_val
  *         self.next_val = bitset_findsucc(self.b, ret_val)
  *         return ret_val             # <<<<<<<<<<<<<<
@@ -17848,7 +18773,7 @@ static int __pyx_pw_3_sa_6BitSet_1__cinit__(PyObject *__pyx_v_self, PyObject *__
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":122
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":122
  *     cdef _BitSet* b
  * 
  *     def __cinit__(self):             # <<<<<<<<<<<<<<
@@ -17861,7 +18786,7 @@ static int __pyx_pf_3_sa_6BitSet___cinit__(struct __pyx_obj_3_sa_BitSet *__pyx_v
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__cinit__", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":123
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":123
  * 
  *     def __cinit__(self):
  *         self.b = new_BitSet()             # <<<<<<<<<<<<<<
@@ -17884,7 +18809,7 @@ static void __pyx_pw_3_sa_6BitSet_3__dealloc__(PyObject *__pyx_v_self) {
   __Pyx_RefNannyFinishContext();
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":125
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":125
  *         self.b = new_BitSet()
  * 
  *     def __dealloc__(self):             # <<<<<<<<<<<<<<
@@ -17896,7 +18821,7 @@ static void __pyx_pf_3_sa_6BitSet_2__dealloc__(struct __pyx_obj_3_sa_BitSet *__p
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__dealloc__", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":126
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":126
  * 
  *     def __dealloc__(self):
  *         free(self.b)             # <<<<<<<<<<<<<<
@@ -17919,7 +18844,7 @@ static PyObject *__pyx_pw_3_sa_6BitSet_5__iter__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":128
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":128
  *         free(self.b)
  * 
  *     def __iter__(self):             # <<<<<<<<<<<<<<
@@ -17937,7 +18862,7 @@ static PyObject *__pyx_pf_3_sa_6BitSet_4__iter__(struct __pyx_obj_3_sa_BitSet *_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__iter__", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":130
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":130
  *     def __iter__(self):
  *         cdef BitSetIterator it
  *         it = BitSetIterator()             # <<<<<<<<<<<<<<
@@ -17949,7 +18874,7 @@ static PyObject *__pyx_pf_3_sa_6BitSet_4__iter__(struct __pyx_obj_3_sa_BitSet *_
   __pyx_v_it = ((struct __pyx_obj_3_sa_BitSetIterator *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":131
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":131
  *         cdef BitSetIterator it
  *         it = BitSetIterator()
  *         it.b = self.b             # <<<<<<<<<<<<<<
@@ -17958,7 +18883,7 @@ static PyObject *__pyx_pf_3_sa_6BitSet_4__iter__(struct __pyx_obj_3_sa_BitSet *_
  */
   __pyx_v_it->b = __pyx_v_self->b;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":132
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":132
  *         it = BitSetIterator()
  *         it.b = self.b
  *         it.next_val = self.b.min_val             # <<<<<<<<<<<<<<
@@ -17967,7 +18892,7 @@ static PyObject *__pyx_pf_3_sa_6BitSet_4__iter__(struct __pyx_obj_3_sa_BitSet *_
  */
   __pyx_v_it->next_val = __pyx_v_self->b->min_val;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":133
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":133
  *         it.b = self.b
  *         it.next_val = self.b.min_val
  *         return it             # <<<<<<<<<<<<<<
@@ -18003,7 +18928,7 @@ static PyObject *__pyx_pw_3_sa_6BitSet_7insert(PyObject *__pyx_v_self, PyObject
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":135
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":135
  *         return it
  * 
  *     def insert(self, i):             # <<<<<<<<<<<<<<
@@ -18021,7 +18946,7 @@ static PyObject *__pyx_pf_3_sa_6BitSet_6insert(struct __pyx_obj_3_sa_BitSet *__p
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("insert", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":136
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":136
  * 
  *     def insert(self, i):
  *         return bitset_insert(self.b, i)             # <<<<<<<<<<<<<<
@@ -18059,7 +18984,7 @@ static PyObject *__pyx_pw_3_sa_6BitSet_9findsucc(PyObject *__pyx_v_self, PyObjec
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":138
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":138
  *         return bitset_insert(self.b, i)
  * 
  *     def findsucc(self, i):             # <<<<<<<<<<<<<<
@@ -18077,7 +19002,7 @@ static PyObject *__pyx_pf_3_sa_6BitSet_8findsucc(struct __pyx_obj_3_sa_BitSet *_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("findsucc", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":139
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":139
  * 
  *     def findsucc(self, i):
  *         return bitset_findsucc(self.b, i)             # <<<<<<<<<<<<<<
@@ -18115,7 +19040,7 @@ static PyObject *__pyx_pw_3_sa_6BitSet_11__str__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":141
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":141
  *         return bitset_findsucc(self.b, i)
  * 
  *     def __str__(self):             # <<<<<<<<<<<<<<
@@ -18134,7 +19059,7 @@ static PyObject *__pyx_pf_3_sa_6BitSet_10__str__(struct __pyx_obj_3_sa_BitSet *_
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__str__", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":142
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":142
  * 
  *     def __str__(self):
  *         return dec2bin(self.b.bitset)+"  ("+str(self.b.size)+","+str(self.b.min_val)+","+str(self.b.max_val)+")"             # <<<<<<<<<<<<<<
@@ -18227,7 +19152,7 @@ static PyObject *__pyx_pw_3_sa_6BitSet_13min(PyObject *__pyx_v_self, CYTHON_UNUS
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":144
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":144
  *         return dec2bin(self.b.bitset)+"  ("+str(self.b.size)+","+str(self.b.min_val)+","+str(self.b.max_val)+")"
  * 
  *     def min(self):             # <<<<<<<<<<<<<<
@@ -18244,7 +19169,7 @@ static PyObject *__pyx_pf_3_sa_6BitSet_12min(struct __pyx_obj_3_sa_BitSet *__pyx
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("min", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":145
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":145
  * 
  *     def min(self):
  *         return self.b.min_val             # <<<<<<<<<<<<<<
@@ -18281,7 +19206,7 @@ static PyObject *__pyx_pw_3_sa_6BitSet_15max(PyObject *__pyx_v_self, CYTHON_UNUS
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":147
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":147
  *         return self.b.min_val
  * 
  *     def max(self):             # <<<<<<<<<<<<<<
@@ -18298,7 +19223,7 @@ static PyObject *__pyx_pf_3_sa_6BitSet_14max(struct __pyx_obj_3_sa_BitSet *__pyx
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("max", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":148
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":148
  * 
  *     def max(self):
  *         return self.b.max_val             # <<<<<<<<<<<<<<
@@ -18335,7 +19260,7 @@ static Py_ssize_t __pyx_pw_3_sa_6BitSet_17__len__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":150
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":150
  *         return self.b.max_val
  * 
  *     def __len__(self):             # <<<<<<<<<<<<<<
@@ -18348,7 +19273,7 @@ static Py_ssize_t __pyx_pf_3_sa_6BitSet_16__len__(struct __pyx_obj_3_sa_BitSet *
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   __Pyx_RefNannySetupContext("__len__", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":151
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":151
  * 
  *     def __len__(self):
  *         return self.b.size             # <<<<<<<<<<<<<<
@@ -18375,7 +19300,7 @@ static int __pyx_pw_3_sa_6BitSet_19__contains__(PyObject *__pyx_v_self, PyObject
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":153
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":153
  *         return self.b.size
  * 
  *     def __contains__(self, i):             # <<<<<<<<<<<<<<
@@ -18394,7 +19319,7 @@ static int __pyx_pf_3_sa_6BitSet_18__contains__(struct __pyx_obj_3_sa_BitSet *__
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__contains__", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":154
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":154
  * 
  *     def __contains__(self, i):
  *         return bool(bitset_contains(self.b, i))             # <<<<<<<<<<<<<<
@@ -18420,7 +19345,7 @@ static int __pyx_pf_3_sa_6BitSet_18__contains__(struct __pyx_obj_3_sa_BitSet *__
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":157
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":157
  * 
  * 
  * cdef str dec2bin(long i):             # <<<<<<<<<<<<<<
@@ -18442,7 +19367,7 @@ static PyObject *__pyx_f_3_sa_dec2bin(long __pyx_v_i) {
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("dec2bin", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":158
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":158
  * 
  * cdef str dec2bin(long i):
  *     cdef str result = ""             # <<<<<<<<<<<<<<
@@ -18452,7 +19377,7 @@ static PyObject *__pyx_f_3_sa_dec2bin(long __pyx_v_i) {
   __Pyx_INCREF(((PyObject *)__pyx_kp_s_45));
   __pyx_v_result = __pyx_kp_s_45;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":160
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":160
  *     cdef str result = ""
  *     cdef unsigned d
  *     for d in range(MIN_BOTTOM_SIZE):             # <<<<<<<<<<<<<<
@@ -18463,7 +19388,7 @@ static PyObject *__pyx_f_3_sa_dec2bin(long __pyx_v_i) {
   for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) {
     __pyx_v_d = __pyx_t_2;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":161
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":161
  *     cdef unsigned d
  *     for d in range(MIN_BOTTOM_SIZE):
  *         if i & LOWER_MASK[0] == 0:             # <<<<<<<<<<<<<<
@@ -18473,7 +19398,7 @@ static PyObject *__pyx_f_3_sa_dec2bin(long __pyx_v_i) {
     __pyx_t_3 = ((__pyx_v_i & (__pyx_v_3_sa_LOWER_MASK[0])) == 0);
     if (__pyx_t_3) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":162
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":162
  *     for d in range(MIN_BOTTOM_SIZE):
  *         if i & LOWER_MASK[0] == 0:
  *             result = "0"+result             # <<<<<<<<<<<<<<
@@ -18489,7 +19414,7 @@ static PyObject *__pyx_f_3_sa_dec2bin(long __pyx_v_i) {
     }
     /*else*/ {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":164
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":164
  *             result = "0"+result
  *         else:
  *             result = "1"+result             # <<<<<<<<<<<<<<
@@ -18504,7 +19429,7 @@ static PyObject *__pyx_f_3_sa_dec2bin(long __pyx_v_i) {
     }
     __pyx_L5:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":165
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":165
  *         else:
  *             result = "1"+result
  *         i = i >> 1             # <<<<<<<<<<<<<<
@@ -18514,7 +19439,7 @@ static PyObject *__pyx_f_3_sa_dec2bin(long __pyx_v_i) {
     __pyx_v_i = (__pyx_v_i >> 1);
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":166
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":166
  *             result = "1"+result
  *         i = i >> 1
  *     return result             # <<<<<<<<<<<<<<
@@ -18539,7 +19464,7 @@ static PyObject *__pyx_f_3_sa_dec2bin(long __pyx_v_i) {
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":177
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":177
  *     void** bottom
  * 
  * cdef _VEB* new_VEB(int n):             # <<<<<<<<<<<<<<
@@ -18560,7 +19485,7 @@ static struct __pyx_t_3_sa__VEB *__pyx_f_3_sa_new_VEB(int __pyx_v_n) {
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   __Pyx_RefNannySetupContext("new_VEB", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":181
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":181
  *     cdef int num_bits, num_top_bits, i
  * 
  *     veb = <_VEB*> malloc(sizeof(_VEB))             # <<<<<<<<<<<<<<
@@ -18569,7 +19494,7 @@ static struct __pyx_t_3_sa__VEB *__pyx_f_3_sa_new_VEB(int __pyx_v_n) {
  */
   __pyx_v_veb = ((struct __pyx_t_3_sa__VEB *)malloc((sizeof(struct __pyx_t_3_sa__VEB))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":183
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":183
  *     veb = <_VEB*> malloc(sizeof(_VEB))
  * 
  *     num_bits = int(ceil(log(n) / log(2)))             # <<<<<<<<<<<<<<
@@ -18584,7 +19509,7 @@ static struct __pyx_t_3_sa__VEB *__pyx_f_3_sa_new_VEB(int __pyx_v_n) {
   }
   __pyx_v_num_bits = ((int)ceil((__pyx_t_1 / __pyx_t_2)));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":184
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":184
  * 
  *     num_bits = int(ceil(log(n) / log(2)))
  *     veb.num_bottom_bits = num_bits/2             # <<<<<<<<<<<<<<
@@ -18593,7 +19518,7 @@ static struct __pyx_t_3_sa__VEB *__pyx_f_3_sa_new_VEB(int __pyx_v_n) {
  */
   __pyx_v_veb->num_bottom_bits = __Pyx_div_long(__pyx_v_num_bits, 2);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":185
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":185
  *     num_bits = int(ceil(log(n) / log(2)))
  *     veb.num_bottom_bits = num_bits/2
  *     if veb.num_bottom_bits < MIN_BOTTOM_BITS:             # <<<<<<<<<<<<<<
@@ -18603,7 +19528,7 @@ static struct __pyx_t_3_sa__VEB *__pyx_f_3_sa_new_VEB(int __pyx_v_n) {
   __pyx_t_3 = (__pyx_v_veb->num_bottom_bits < __pyx_v_3_sa_MIN_BOTTOM_BITS);
   if (__pyx_t_3) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":186
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":186
  *     veb.num_bottom_bits = num_bits/2
  *     if veb.num_bottom_bits < MIN_BOTTOM_BITS:
  *         veb.num_bottom_bits = MIN_BOTTOM_BITS             # <<<<<<<<<<<<<<
@@ -18615,7 +19540,7 @@ static struct __pyx_t_3_sa__VEB *__pyx_f_3_sa_new_VEB(int __pyx_v_n) {
   }
   __pyx_L3:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":187
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":187
  *     if veb.num_bottom_bits < MIN_BOTTOM_BITS:
  *         veb.num_bottom_bits = MIN_BOTTOM_BITS
  *     veb.top_universe_size = (n >> veb.num_bottom_bits) + 1             # <<<<<<<<<<<<<<
@@ -18624,7 +19549,7 @@ static struct __pyx_t_3_sa__VEB *__pyx_f_3_sa_new_VEB(int __pyx_v_n) {
  */
   __pyx_v_veb->top_universe_size = ((__pyx_v_n >> __pyx_v_veb->num_bottom_bits) + 1);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":189
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":189
  *     veb.top_universe_size = (n >> veb.num_bottom_bits) + 1
  * 
  *     veb.bottom = <void**> malloc(veb.top_universe_size * sizeof(void*))             # <<<<<<<<<<<<<<
@@ -18633,7 +19558,7 @@ static struct __pyx_t_3_sa__VEB *__pyx_f_3_sa_new_VEB(int __pyx_v_n) {
  */
   __pyx_v_veb->bottom = ((void **)malloc((__pyx_v_veb->top_universe_size * (sizeof(void *)))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":190
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":190
  * 
  *     veb.bottom = <void**> malloc(veb.top_universe_size * sizeof(void*))
  *     memset(veb.bottom, 0, veb.top_universe_size * sizeof(void*))             # <<<<<<<<<<<<<<
@@ -18642,7 +19567,7 @@ static struct __pyx_t_3_sa__VEB *__pyx_f_3_sa_new_VEB(int __pyx_v_n) {
  */
   memset(__pyx_v_veb->bottom, 0, (__pyx_v_veb->top_universe_size * (sizeof(void *))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":192
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":192
  *     memset(veb.bottom, 0, veb.top_universe_size * sizeof(void*))
  * 
  *     if veb.top_universe_size > MIN_BOTTOM_SIZE:             # <<<<<<<<<<<<<<
@@ -18652,7 +19577,7 @@ static struct __pyx_t_3_sa__VEB *__pyx_f_3_sa_new_VEB(int __pyx_v_n) {
   __pyx_t_3 = (__pyx_v_veb->top_universe_size > __pyx_v_3_sa_MIN_BOTTOM_SIZE);
   if (__pyx_t_3) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":193
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":193
  * 
  *     if veb.top_universe_size > MIN_BOTTOM_SIZE:
  *         veb.top = new_VEB(veb.top_universe_size)             # <<<<<<<<<<<<<<
@@ -18664,7 +19589,7 @@ static struct __pyx_t_3_sa__VEB *__pyx_f_3_sa_new_VEB(int __pyx_v_n) {
   }
   /*else*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":195
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":195
  *         veb.top = new_VEB(veb.top_universe_size)
  *     else:
  *         veb.top = new_BitSet()             # <<<<<<<<<<<<<<
@@ -18675,7 +19600,7 @@ static struct __pyx_t_3_sa__VEB *__pyx_f_3_sa_new_VEB(int __pyx_v_n) {
   }
   __pyx_L4:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":197
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":197
  *         veb.top = new_BitSet()
  * 
  *     veb.max_val = -1             # <<<<<<<<<<<<<<
@@ -18684,7 +19609,7 @@ static struct __pyx_t_3_sa__VEB *__pyx_f_3_sa_new_VEB(int __pyx_v_n) {
  */
   __pyx_v_veb->max_val = -1;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":198
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":198
  * 
  *     veb.max_val = -1
  *     veb.min_val = -1             # <<<<<<<<<<<<<<
@@ -18693,7 +19618,7 @@ static struct __pyx_t_3_sa__VEB *__pyx_f_3_sa_new_VEB(int __pyx_v_n) {
  */
   __pyx_v_veb->min_val = -1;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":199
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":199
  *     veb.max_val = -1
  *     veb.min_val = -1
  *     veb.size = 0             # <<<<<<<<<<<<<<
@@ -18702,7 +19627,7 @@ static struct __pyx_t_3_sa__VEB *__pyx_f_3_sa_new_VEB(int __pyx_v_n) {
  */
   __pyx_v_veb->size = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":200
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":200
  *     veb.min_val = -1
  *     veb.size = 0
  *     return veb             # <<<<<<<<<<<<<<
@@ -18722,7 +19647,7 @@ static struct __pyx_t_3_sa__VEB *__pyx_f_3_sa_new_VEB(int __pyx_v_n) {
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":203
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":203
  * 
  * 
  * cdef int VEB_insert(_VEB* veb, int i):             # <<<<<<<<<<<<<<
@@ -18743,7 +19668,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
   int __pyx_t_3;
   __Pyx_RefNannySetupContext("VEB_insert", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":208
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":208
  *     cdef int a, b, tmp
  * 
  *     if veb.size == 0:             # <<<<<<<<<<<<<<
@@ -18753,7 +19678,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
   __pyx_t_1 = (__pyx_v_veb->size == 0);
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":209
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":209
  * 
  *     if veb.size == 0:
  *         veb.min_val = i             # <<<<<<<<<<<<<<
@@ -18762,7 +19687,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
  */
     __pyx_v_veb->min_val = __pyx_v_i;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":210
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":210
  *     if veb.size == 0:
  *         veb.min_val = i
  *         veb.max_val = i             # <<<<<<<<<<<<<<
@@ -18773,7 +19698,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
     goto __pyx_L3;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":211
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":211
  *         veb.min_val = i
  *         veb.max_val = i
  *     elif i == veb.min_val or i == veb.max_val:             # <<<<<<<<<<<<<<
@@ -18789,7 +19714,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
   }
   if (__pyx_t_3) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":212
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":212
  *         veb.max_val = i
  *     elif i == veb.min_val or i == veb.max_val:
  *         return 0             # <<<<<<<<<<<<<<
@@ -18802,7 +19727,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
   }
   /*else*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":214
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":214
  *         return 0
  *     else:
  *         if i < veb.min_val:             # <<<<<<<<<<<<<<
@@ -18812,7 +19737,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
     __pyx_t_3 = (__pyx_v_i < __pyx_v_veb->min_val);
     if (__pyx_t_3) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":215
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":215
  *     else:
  *         if i < veb.min_val:
  *             tmp = i             # <<<<<<<<<<<<<<
@@ -18821,7 +19746,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
  */
       __pyx_v_tmp = __pyx_v_i;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":216
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":216
  *         if i < veb.min_val:
  *             tmp = i
  *             i = veb.min_val             # <<<<<<<<<<<<<<
@@ -18830,7 +19755,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
  */
       __pyx_v_i = __pyx_v_veb->min_val;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":217
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":217
  *             tmp = i
  *             i = veb.min_val
  *             veb.min_val = tmp             # <<<<<<<<<<<<<<
@@ -18842,7 +19767,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
     }
     __pyx_L4:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":218
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":218
  *             i = veb.min_val
  *             veb.min_val = tmp
  *         a = i >> veb.num_bottom_bits             # <<<<<<<<<<<<<<
@@ -18851,7 +19776,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
  */
     __pyx_v_a = (__pyx_v_i >> __pyx_v_veb->num_bottom_bits);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":219
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":219
  *             veb.min_val = tmp
  *         a = i >> veb.num_bottom_bits
  *         b = i & LOWER_MASK[veb.num_bottom_bits-1]             # <<<<<<<<<<<<<<
@@ -18860,7 +19785,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
  */
     __pyx_v_b = (__pyx_v_i & (__pyx_v_3_sa_LOWER_MASK[(__pyx_v_veb->num_bottom_bits - 1)]));
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":220
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":220
  *         a = i >> veb.num_bottom_bits
  *         b = i & LOWER_MASK[veb.num_bottom_bits-1]
  *         if veb.bottom[a] == NULL:             # <<<<<<<<<<<<<<
@@ -18870,7 +19795,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
     __pyx_t_3 = ((__pyx_v_veb->bottom[__pyx_v_a]) == NULL);
     if (__pyx_t_3) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":221
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":221
  *         b = i & LOWER_MASK[veb.num_bottom_bits-1]
  *         if veb.bottom[a] == NULL:
  *             if veb.top_universe_size > MIN_BOTTOM_SIZE:             # <<<<<<<<<<<<<<
@@ -18880,7 +19805,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
       __pyx_t_3 = (__pyx_v_veb->top_universe_size > __pyx_v_3_sa_MIN_BOTTOM_SIZE);
       if (__pyx_t_3) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":222
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":222
  *         if veb.bottom[a] == NULL:
  *             if veb.top_universe_size > MIN_BOTTOM_SIZE:
  *                 subv = <_VEB*> veb.top             # <<<<<<<<<<<<<<
@@ -18889,7 +19814,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
  */
         __pyx_v_subv = ((struct __pyx_t_3_sa__VEB *)__pyx_v_veb->top);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":223
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":223
  *             if veb.top_universe_size > MIN_BOTTOM_SIZE:
  *                 subv = <_VEB*> veb.top
  *                 VEB_insert(subv, a)             # <<<<<<<<<<<<<<
@@ -18901,7 +19826,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
       }
       /*else*/ {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":225
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":225
  *                 VEB_insert(subv, a)
  *             else:
  *                 subb = <_BitSet*> veb.top             # <<<<<<<<<<<<<<
@@ -18910,7 +19835,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
  */
         __pyx_v_subb = ((struct __pyx_t_3_sa__BitSet *)__pyx_v_veb->top);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":226
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":226
  *             else:
  *                 subb = <_BitSet*> veb.top
  *                 bitset_insert(subb, a)             # <<<<<<<<<<<<<<
@@ -18921,7 +19846,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
       }
       __pyx_L6:;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":227
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":227
  *                 subb = <_BitSet*> veb.top
  *                 bitset_insert(subb, a)
  *             if veb.num_bottom_bits > MIN_BOTTOM_BITS:             # <<<<<<<<<<<<<<
@@ -18931,7 +19856,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
       __pyx_t_3 = (__pyx_v_veb->num_bottom_bits > __pyx_v_3_sa_MIN_BOTTOM_BITS);
       if (__pyx_t_3) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":228
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":228
  *                 bitset_insert(subb, a)
  *             if veb.num_bottom_bits > MIN_BOTTOM_BITS:
  *                 veb.bottom[a] = new_VEB(1 << veb.num_bottom_bits)             # <<<<<<<<<<<<<<
@@ -18943,7 +19868,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
       }
       /*else*/ {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":230
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":230
  *                 veb.bottom[a] = new_VEB(1 << veb.num_bottom_bits)
  *             else:
  *                 veb.bottom[a] = new_BitSet()             # <<<<<<<<<<<<<<
@@ -18957,7 +19882,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
     }
     __pyx_L5:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":231
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":231
  *             else:
  *                 veb.bottom[a] = new_BitSet()
  *         if veb.num_bottom_bits > MIN_BOTTOM_BITS:             # <<<<<<<<<<<<<<
@@ -18967,7 +19892,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
     __pyx_t_3 = (__pyx_v_veb->num_bottom_bits > __pyx_v_3_sa_MIN_BOTTOM_BITS);
     if (__pyx_t_3) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":232
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":232
  *                 veb.bottom[a] = new_BitSet()
  *         if veb.num_bottom_bits > MIN_BOTTOM_BITS:
  *             subv = <_VEB*> veb.bottom[a]             # <<<<<<<<<<<<<<
@@ -18976,7 +19901,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
  */
       __pyx_v_subv = ((struct __pyx_t_3_sa__VEB *)(__pyx_v_veb->bottom[__pyx_v_a]));
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":233
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":233
  *         if veb.num_bottom_bits > MIN_BOTTOM_BITS:
  *             subv = <_VEB*> veb.bottom[a]
  *             if VEB_insert(subv, b) == 0:             # <<<<<<<<<<<<<<
@@ -18986,7 +19911,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
       __pyx_t_3 = (__pyx_f_3_sa_VEB_insert(__pyx_v_subv, __pyx_v_b) == 0);
       if (__pyx_t_3) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":234
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":234
  *             subv = <_VEB*> veb.bottom[a]
  *             if VEB_insert(subv, b) == 0:
  *                 return 0             # <<<<<<<<<<<<<<
@@ -19002,7 +19927,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
     }
     /*else*/ {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":236
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":236
  *                 return 0
  *         else:
  *             subb = <_BitSet*> veb.bottom[a]             # <<<<<<<<<<<<<<
@@ -19011,7 +19936,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
  */
       __pyx_v_subb = ((struct __pyx_t_3_sa__BitSet *)(__pyx_v_veb->bottom[__pyx_v_a]));
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":237
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":237
  *         else:
  *             subb = <_BitSet*> veb.bottom[a]
  *             if bitset_insert(subb, b) == 0:             # <<<<<<<<<<<<<<
@@ -19021,7 +19946,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
       __pyx_t_3 = (__pyx_f_3_sa_bitset_insert(__pyx_v_subb, __pyx_v_b) == 0);
       if (__pyx_t_3) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":238
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":238
  *             subb = <_BitSet*> veb.bottom[a]
  *             if bitset_insert(subb, b) == 0:
  *                 return 0             # <<<<<<<<<<<<<<
@@ -19036,7 +19961,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
     }
     __pyx_L8:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":240
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":240
  *                 return 0
  * 
  *         if i > veb.max_val:             # <<<<<<<<<<<<<<
@@ -19046,7 +19971,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
     __pyx_t_3 = (__pyx_v_i > __pyx_v_veb->max_val);
     if (__pyx_t_3) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":241
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":241
  * 
  *         if i > veb.max_val:
  *             veb.max_val = i             # <<<<<<<<<<<<<<
@@ -19060,7 +19985,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
   }
   __pyx_L3:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":242
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":242
  *         if i > veb.max_val:
  *             veb.max_val = i
  *     veb.size = veb.size + 1             # <<<<<<<<<<<<<<
@@ -19069,7 +19994,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
  */
   __pyx_v_veb->size = (__pyx_v_veb->size + 1);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":243
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":243
  *             veb.max_val = i
  *     veb.size = veb.size + 1
  *     return 1             # <<<<<<<<<<<<<<
@@ -19085,7 +20010,7 @@ static int __pyx_f_3_sa_VEB_insert(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int __
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":246
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":246
  * 
  * 
  * cdef del_VEB(_VEB* veb):             # <<<<<<<<<<<<<<
@@ -19104,7 +20029,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *__pyx_v_veb) {
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("del_VEB", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":249
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":249
  *     cdef int i
  * 
  *     if veb.top_universe_size > MIN_BOTTOM_SIZE:             # <<<<<<<<<<<<<<
@@ -19114,7 +20039,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *__pyx_v_veb) {
   __pyx_t_1 = (__pyx_v_veb->top_universe_size > __pyx_v_3_sa_MIN_BOTTOM_SIZE);
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":250
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":250
  * 
  *     if veb.top_universe_size > MIN_BOTTOM_SIZE:
  *         i = (<_VEB*> veb.top).min_val             # <<<<<<<<<<<<<<
@@ -19126,7 +20051,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *__pyx_v_veb) {
   }
   /*else*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":252
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":252
  *         i = (<_VEB*> veb.top).min_val
  *     else:
  *         i = (<_BitSet*> veb.top).min_val             # <<<<<<<<<<<<<<
@@ -19137,7 +20062,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *__pyx_v_veb) {
   }
   __pyx_L3:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":254
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":254
  *         i = (<_BitSet*> veb.top).min_val
  * 
  *     while i != -1:             # <<<<<<<<<<<<<<
@@ -19148,7 +20073,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *__pyx_v_veb) {
     __pyx_t_1 = (__pyx_v_i != -1);
     if (!__pyx_t_1) break;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":255
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":255
  * 
  *     while i != -1:
  *         if veb.num_bottom_bits > MIN_BOTTOM_BITS:             # <<<<<<<<<<<<<<
@@ -19158,7 +20083,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *__pyx_v_veb) {
     __pyx_t_1 = (__pyx_v_veb->num_bottom_bits > __pyx_v_3_sa_MIN_BOTTOM_BITS);
     if (__pyx_t_1) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":256
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":256
  *     while i != -1:
  *         if veb.num_bottom_bits > MIN_BOTTOM_BITS:
  *             del_VEB(<_VEB*> veb.bottom[i])             # <<<<<<<<<<<<<<
@@ -19172,7 +20097,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *__pyx_v_veb) {
     }
     /*else*/ {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":258
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":258
  *             del_VEB(<_VEB*> veb.bottom[i])
  *         else:
  *             free(<_BitSet*> veb.bottom[i])             # <<<<<<<<<<<<<<
@@ -19183,7 +20108,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *__pyx_v_veb) {
     }
     __pyx_L6:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":260
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":260
  *             free(<_BitSet*> veb.bottom[i])
  * 
  *         if veb.top_universe_size > MIN_BOTTOM_SIZE:             # <<<<<<<<<<<<<<
@@ -19193,7 +20118,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *__pyx_v_veb) {
     __pyx_t_1 = (__pyx_v_veb->top_universe_size > __pyx_v_3_sa_MIN_BOTTOM_SIZE);
     if (__pyx_t_1) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":261
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":261
  * 
  *         if veb.top_universe_size > MIN_BOTTOM_SIZE:
  *             i = VEB_findsucc(<_VEB*> veb.top, i)             # <<<<<<<<<<<<<<
@@ -19205,7 +20130,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *__pyx_v_veb) {
     }
     /*else*/ {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":263
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":263
  *             i = VEB_findsucc(<_VEB*> veb.top, i)
  *         else:
  *             i = bitset_findsucc(<_BitSet*> veb.top, i)             # <<<<<<<<<<<<<<
@@ -19217,7 +20142,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *__pyx_v_veb) {
     __pyx_L7:;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":265
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":265
  *             i = bitset_findsucc(<_BitSet*> veb.top, i)
  * 
  *     if veb.top_universe_size > MIN_BOTTOM_SIZE:             # <<<<<<<<<<<<<<
@@ -19227,7 +20152,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *__pyx_v_veb) {
   __pyx_t_1 = (__pyx_v_veb->top_universe_size > __pyx_v_3_sa_MIN_BOTTOM_SIZE);
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":266
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":266
  * 
  *     if veb.top_universe_size > MIN_BOTTOM_SIZE:
  *         del_VEB(<_VEB*> veb.top)             # <<<<<<<<<<<<<<
@@ -19241,7 +20166,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *__pyx_v_veb) {
   }
   /*else*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":268
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":268
  *         del_VEB(<_VEB*> veb.top)
  *     else:
  *         free(<_BitSet*> veb.top)             # <<<<<<<<<<<<<<
@@ -19252,7 +20177,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *__pyx_v_veb) {
   }
   __pyx_L8:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":269
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":269
  *     else:
  *         free(<_BitSet*> veb.top)
  *     free(veb.bottom)             # <<<<<<<<<<<<<<
@@ -19261,7 +20186,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *__pyx_v_veb) {
  */
   free(__pyx_v_veb->bottom);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":270
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":270
  *         free(<_BitSet*> veb.top)
  *     free(veb.bottom)
  *     free(veb)             # <<<<<<<<<<<<<<
@@ -19282,7 +20207,7 @@ static PyObject *__pyx_f_3_sa_del_VEB(struct __pyx_t_3_sa__VEB *__pyx_v_veb) {
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":273
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":273
  * 
  * 
  * cdef int VEB_findsucc(_VEB* veb, int i):             # <<<<<<<<<<<<<<
@@ -19305,7 +20230,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   int __pyx_t_3;
   __Pyx_RefNannySetupContext("VEB_findsucc", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":278
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":278
  *     cdef int a, b, j, c, found
  * 
  *     if veb.max_val == -1 or i>=veb.max_val:             # <<<<<<<<<<<<<<
@@ -19321,7 +20246,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   }
   if (__pyx_t_3) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":279
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":279
  * 
  *     if veb.max_val == -1 or i>=veb.max_val:
  *         return -1             # <<<<<<<<<<<<<<
@@ -19334,7 +20259,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   }
   __pyx_L3:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":280
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":280
  *     if veb.max_val == -1 or i>=veb.max_val:
  *         return -1
  *     if i < veb.min_val:             # <<<<<<<<<<<<<<
@@ -19344,7 +20269,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   __pyx_t_3 = (__pyx_v_i < __pyx_v_veb->min_val);
   if (__pyx_t_3) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":281
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":281
  *         return -1
  *     if i < veb.min_val:
  *         return veb.min_val             # <<<<<<<<<<<<<<
@@ -19357,7 +20282,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   }
   __pyx_L4:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":283
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":283
  *         return veb.min_val
  * 
  *     a = i >> veb.num_bottom_bits             # <<<<<<<<<<<<<<
@@ -19366,7 +20291,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
  */
   __pyx_v_a = (__pyx_v_i >> __pyx_v_veb->num_bottom_bits);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":284
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":284
  * 
  *     a = i >> veb.num_bottom_bits
  *     b = i & LOWER_MASK[veb.num_bottom_bits-1]             # <<<<<<<<<<<<<<
@@ -19375,7 +20300,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
  */
   __pyx_v_b = (__pyx_v_i & (__pyx_v_3_sa_LOWER_MASK[(__pyx_v_veb->num_bottom_bits - 1)]));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":285
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":285
  *     a = i >> veb.num_bottom_bits
  *     b = i & LOWER_MASK[veb.num_bottom_bits-1]
  *     found = 0             # <<<<<<<<<<<<<<
@@ -19384,7 +20309,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
  */
   __pyx_v_found = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":286
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":286
  *     b = i & LOWER_MASK[veb.num_bottom_bits-1]
  *     found = 0
  *     if veb.bottom[a] != NULL:             # <<<<<<<<<<<<<<
@@ -19394,7 +20319,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   __pyx_t_3 = ((__pyx_v_veb->bottom[__pyx_v_a]) != NULL);
   if (__pyx_t_3) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":287
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":287
  *     found = 0
  *     if veb.bottom[a] != NULL:
  *         if veb.num_bottom_bits > MIN_BOTTOM_BITS:             # <<<<<<<<<<<<<<
@@ -19404,7 +20329,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
     __pyx_t_3 = (__pyx_v_veb->num_bottom_bits > __pyx_v_3_sa_MIN_BOTTOM_BITS);
     if (__pyx_t_3) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":288
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":288
  *     if veb.bottom[a] != NULL:
  *         if veb.num_bottom_bits > MIN_BOTTOM_BITS:
  *             subv = <_VEB*> veb.bottom[a]             # <<<<<<<<<<<<<<
@@ -19413,7 +20338,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
  */
       __pyx_v_subv = ((struct __pyx_t_3_sa__VEB *)(__pyx_v_veb->bottom[__pyx_v_a]));
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":289
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":289
  *         if veb.num_bottom_bits > MIN_BOTTOM_BITS:
  *             subv = <_VEB*> veb.bottom[a]
  *             if subv.max_val > b:             # <<<<<<<<<<<<<<
@@ -19423,7 +20348,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
       __pyx_t_3 = (__pyx_v_subv->max_val > __pyx_v_b);
       if (__pyx_t_3) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":290
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":290
  *             subv = <_VEB*> veb.bottom[a]
  *             if subv.max_val > b:
  *                 j = (a << veb.num_bottom_bits) + VEB_findsucc(subv, b)             # <<<<<<<<<<<<<<
@@ -19432,7 +20357,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
  */
         __pyx_v_j = ((__pyx_v_a << __pyx_v_veb->num_bottom_bits) + __pyx_f_3_sa_VEB_findsucc(__pyx_v_subv, __pyx_v_b));
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":291
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":291
  *             if subv.max_val > b:
  *                 j = (a << veb.num_bottom_bits) + VEB_findsucc(subv, b)
  *                 found = 1             # <<<<<<<<<<<<<<
@@ -19447,7 +20372,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
     }
     /*else*/ {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":293
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":293
  *                 found = 1
  *         else:
  *             subb = <_BitSet*> veb.bottom[a]             # <<<<<<<<<<<<<<
@@ -19456,7 +20381,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
  */
       __pyx_v_subb = ((struct __pyx_t_3_sa__BitSet *)(__pyx_v_veb->bottom[__pyx_v_a]));
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":294
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":294
  *         else:
  *             subb = <_BitSet*> veb.bottom[a]
  *             if subb.max_val > b:             # <<<<<<<<<<<<<<
@@ -19466,7 +20391,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
       __pyx_t_3 = (__pyx_v_subb->max_val > __pyx_v_b);
       if (__pyx_t_3) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":295
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":295
  *             subb = <_BitSet*> veb.bottom[a]
  *             if subb.max_val > b:
  *                 j = (a << veb.num_bottom_bits) + bitset_findsucc(subb, b)             # <<<<<<<<<<<<<<
@@ -19475,7 +20400,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
  */
         __pyx_v_j = ((__pyx_v_a << __pyx_v_veb->num_bottom_bits) + __pyx_f_3_sa_bitset_findsucc(__pyx_v_subb, __pyx_v_b));
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":296
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":296
  *             if subb.max_val > b:
  *                 j = (a << veb.num_bottom_bits) + bitset_findsucc(subb, b)
  *                 found = 1             # <<<<<<<<<<<<<<
@@ -19492,7 +20417,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   }
   __pyx_L5:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":297
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":297
  *                 j = (a << veb.num_bottom_bits) + bitset_findsucc(subb, b)
  *                 found = 1
  *     if found==0:             # <<<<<<<<<<<<<<
@@ -19502,7 +20427,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   __pyx_t_3 = (__pyx_v_found == 0);
   if (__pyx_t_3) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":298
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":298
  *                 found = 1
  *     if found==0:
  *         if veb.top_universe_size > MIN_BOTTOM_SIZE:             # <<<<<<<<<<<<<<
@@ -19512,7 +20437,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
     __pyx_t_3 = (__pyx_v_veb->top_universe_size > __pyx_v_3_sa_MIN_BOTTOM_SIZE);
     if (__pyx_t_3) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":299
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":299
  *     if found==0:
  *         if veb.top_universe_size > MIN_BOTTOM_SIZE:
  *             subv = <_VEB*> veb.top             # <<<<<<<<<<<<<<
@@ -19521,7 +20446,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
  */
       __pyx_v_subv = ((struct __pyx_t_3_sa__VEB *)__pyx_v_veb->top);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":300
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":300
  *         if veb.top_universe_size > MIN_BOTTOM_SIZE:
  *             subv = <_VEB*> veb.top
  *             c = VEB_findsucc(subv, a)             # <<<<<<<<<<<<<<
@@ -19533,7 +20458,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
     }
     /*else*/ {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":302
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":302
  *             c = VEB_findsucc(subv, a)
  *         else:
  *             subb = <_BitSet*> veb.top             # <<<<<<<<<<<<<<
@@ -19542,7 +20467,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
  */
       __pyx_v_subb = ((struct __pyx_t_3_sa__BitSet *)__pyx_v_veb->top);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":303
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":303
  *         else:
  *             subb = <_BitSet*> veb.top
  *             c = bitset_findsucc(subb, a)             # <<<<<<<<<<<<<<
@@ -19553,7 +20478,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
     }
     __pyx_L10:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":304
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":304
  *             subb = <_BitSet*> veb.top
  *             c = bitset_findsucc(subb, a)
  *         if veb.num_bottom_bits > MIN_BOTTOM_BITS:             # <<<<<<<<<<<<<<
@@ -19563,7 +20488,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
     __pyx_t_3 = (__pyx_v_veb->num_bottom_bits > __pyx_v_3_sa_MIN_BOTTOM_BITS);
     if (__pyx_t_3) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":305
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":305
  *             c = bitset_findsucc(subb, a)
  *         if veb.num_bottom_bits > MIN_BOTTOM_BITS:
  *             subv = <_VEB*> veb.bottom[c]             # <<<<<<<<<<<<<<
@@ -19572,7 +20497,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
  */
       __pyx_v_subv = ((struct __pyx_t_3_sa__VEB *)(__pyx_v_veb->bottom[__pyx_v_c]));
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":306
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":306
  *         if veb.num_bottom_bits > MIN_BOTTOM_BITS:
  *             subv = <_VEB*> veb.bottom[c]
  *             j = (c << veb.num_bottom_bits) + subv.min_val             # <<<<<<<<<<<<<<
@@ -19584,7 +20509,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
     }
     /*else*/ {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":308
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":308
  *             j = (c << veb.num_bottom_bits) + subv.min_val
  *         else:
  *             subb = <_BitSet*> veb.bottom[c]             # <<<<<<<<<<<<<<
@@ -19593,7 +20518,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
  */
       __pyx_v_subb = ((struct __pyx_t_3_sa__BitSet *)(__pyx_v_veb->bottom[__pyx_v_c]));
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":309
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":309
  *         else:
  *             subb = <_BitSet*> veb.bottom[c]
  *             j = (c << veb.num_bottom_bits) + subb.min_val             # <<<<<<<<<<<<<<
@@ -19607,7 +20532,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   }
   __pyx_L9:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":310
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":310
  *             subb = <_BitSet*> veb.bottom[c]
  *             j = (c << veb.num_bottom_bits) + subb.min_val
  *     return j             # <<<<<<<<<<<<<<
@@ -19623,7 +20548,7 @@ static int __pyx_f_3_sa_VEB_findsucc(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":313
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":313
  * 
  * 
  * cdef int VEB_contains(_VEB* veb, int i):             # <<<<<<<<<<<<<<
@@ -19644,7 +20569,7 @@ static int __pyx_f_3_sa_VEB_contains(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   int __pyx_t_4;
   __Pyx_RefNannySetupContext("VEB_contains", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":318
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":318
  *     cdef int a, b
  * 
  *     if veb.size == 0 or i < veb.min_val or i > veb.max_val:             # <<<<<<<<<<<<<<
@@ -19666,7 +20591,7 @@ static int __pyx_f_3_sa_VEB_contains(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   }
   if (__pyx_t_2) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":319
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":319
  * 
  *     if veb.size == 0 or i < veb.min_val or i > veb.max_val:
  *         return 0             # <<<<<<<<<<<<<<
@@ -19679,7 +20604,7 @@ static int __pyx_f_3_sa_VEB_contains(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   }
   __pyx_L3:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":321
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":321
  *         return 0
  * 
  *     if veb.min_val == i:             # <<<<<<<<<<<<<<
@@ -19689,7 +20614,7 @@ static int __pyx_f_3_sa_VEB_contains(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   __pyx_t_2 = (__pyx_v_veb->min_val == __pyx_v_i);
   if (__pyx_t_2) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":322
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":322
  * 
  *     if veb.min_val == i:
  *         return 1             # <<<<<<<<<<<<<<
@@ -19702,7 +20627,7 @@ static int __pyx_f_3_sa_VEB_contains(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   }
   /*else*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":324
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":324
  *         return 1
  *     else:
  *         if veb.size == 1:             # <<<<<<<<<<<<<<
@@ -19712,7 +20637,7 @@ static int __pyx_f_3_sa_VEB_contains(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
     __pyx_t_2 = (__pyx_v_veb->size == 1);
     if (__pyx_t_2) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":325
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":325
  *     else:
  *         if veb.size == 1:
  *             return 0             # <<<<<<<<<<<<<<
@@ -19727,7 +20652,7 @@ static int __pyx_f_3_sa_VEB_contains(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   }
   __pyx_L4:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":327
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":327
  *             return 0
  * 
  *     a = i >> veb.num_bottom_bits             # <<<<<<<<<<<<<<
@@ -19736,7 +20661,7 @@ static int __pyx_f_3_sa_VEB_contains(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
  */
   __pyx_v_a = (__pyx_v_i >> __pyx_v_veb->num_bottom_bits);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":328
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":328
  * 
  *     a = i >> veb.num_bottom_bits
  *     b = i & LOWER_MASK[veb.num_bottom_bits-1]             # <<<<<<<<<<<<<<
@@ -19745,7 +20670,7 @@ static int __pyx_f_3_sa_VEB_contains(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
  */
   __pyx_v_b = (__pyx_v_i & (__pyx_v_3_sa_LOWER_MASK[(__pyx_v_veb->num_bottom_bits - 1)]));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":329
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":329
  *     a = i >> veb.num_bottom_bits
  *     b = i & LOWER_MASK[veb.num_bottom_bits-1]
  *     if veb.bottom[a] == NULL:             # <<<<<<<<<<<<<<
@@ -19755,7 +20680,7 @@ static int __pyx_f_3_sa_VEB_contains(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   __pyx_t_2 = ((__pyx_v_veb->bottom[__pyx_v_a]) == NULL);
   if (__pyx_t_2) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":330
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":330
  *     b = i & LOWER_MASK[veb.num_bottom_bits-1]
  *     if veb.bottom[a] == NULL:
  *         return 0             # <<<<<<<<<<<<<<
@@ -19768,7 +20693,7 @@ static int __pyx_f_3_sa_VEB_contains(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
   }
   /*else*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":332
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":332
  *         return 0
  *     else:
  *         if veb.num_bottom_bits > MIN_BOTTOM_BITS:             # <<<<<<<<<<<<<<
@@ -19778,7 +20703,7 @@ static int __pyx_f_3_sa_VEB_contains(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
     __pyx_t_2 = (__pyx_v_veb->num_bottom_bits > __pyx_v_3_sa_MIN_BOTTOM_BITS);
     if (__pyx_t_2) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":333
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":333
  *     else:
  *         if veb.num_bottom_bits > MIN_BOTTOM_BITS:
  *             subv = <_VEB*> veb.bottom[a]             # <<<<<<<<<<<<<<
@@ -19787,7 +20712,7 @@ static int __pyx_f_3_sa_VEB_contains(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
  */
       __pyx_v_subv = ((struct __pyx_t_3_sa__VEB *)(__pyx_v_veb->bottom[__pyx_v_a]));
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":334
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":334
  *         if veb.num_bottom_bits > MIN_BOTTOM_BITS:
  *             subv = <_VEB*> veb.bottom[a]
  *             return VEB_contains(subv, b)             # <<<<<<<<<<<<<<
@@ -19800,7 +20725,7 @@ static int __pyx_f_3_sa_VEB_contains(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
     }
     /*else*/ {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":336
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":336
  *             return VEB_contains(subv, b)
  *         else:
  *             subb = <_BitSet*> veb.bottom[a]             # <<<<<<<<<<<<<<
@@ -19809,7 +20734,7 @@ static int __pyx_f_3_sa_VEB_contains(struct __pyx_t_3_sa__VEB *__pyx_v_veb, int
  */
       __pyx_v_subb = ((struct __pyx_t_3_sa__BitSet *)(__pyx_v_veb->bottom[__pyx_v_a]));
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":337
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":337
  *         else:
  *             subb = <_BitSet*> veb.bottom[a]
  *             return bitset_contains(subb, b)             # <<<<<<<<<<<<<<
@@ -19840,7 +20765,7 @@ static PyObject *__pyx_pw_3_sa_11VEBIterator_1__next__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":344
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":344
  *     cdef int next_val
  * 
  *     def __next__(self):             # <<<<<<<<<<<<<<
@@ -19859,7 +20784,7 @@ static PyObject *__pyx_pf_3_sa_11VEBIterator___next__(struct __pyx_obj_3_sa_VEBI
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__next__", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":347
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":347
  *         cdef int ret_val
  * 
  *         if self.next_val == -1:             # <<<<<<<<<<<<<<
@@ -19869,7 +20794,7 @@ static PyObject *__pyx_pf_3_sa_11VEBIterator___next__(struct __pyx_obj_3_sa_VEBI
   __pyx_t_1 = (__pyx_v_self->next_val == -1);
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":348
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":348
  * 
  *         if self.next_val == -1:
  *             raise StopIteration()             # <<<<<<<<<<<<<<
@@ -19885,7 +20810,7 @@ static PyObject *__pyx_pf_3_sa_11VEBIterator___next__(struct __pyx_obj_3_sa_VEBI
   }
   __pyx_L3:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":349
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":349
  *         if self.next_val == -1:
  *             raise StopIteration()
  *         ret_val = self.next_val             # <<<<<<<<<<<<<<
@@ -19894,7 +20819,7 @@ static PyObject *__pyx_pf_3_sa_11VEBIterator___next__(struct __pyx_obj_3_sa_VEBI
  */
   __pyx_v_ret_val = __pyx_v_self->next_val;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":350
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":350
  *             raise StopIteration()
  *         ret_val = self.next_val
  *         self.next_val = VEB_findsucc(self.v, ret_val)             # <<<<<<<<<<<<<<
@@ -19903,7 +20828,7 @@ static PyObject *__pyx_pf_3_sa_11VEBIterator___next__(struct __pyx_obj_3_sa_VEBI
  */
   __pyx_v_self->next_val = __pyx_f_3_sa_VEB_findsucc(__pyx_v_self->v, __pyx_v_ret_val);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":351
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":351
  *         ret_val = self.next_val
  *         self.next_val = VEB_findsucc(self.v, ret_val)
  *         return ret_val             # <<<<<<<<<<<<<<
@@ -19976,7 +20901,7 @@ static int __pyx_pw_3_sa_3VEB_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":360
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":360
  *     cdef int _first(self)
  * 
  *     def __cinit__(self, int size):             # <<<<<<<<<<<<<<
@@ -19989,7 +20914,7 @@ static int __pyx_pf_3_sa_3VEB___cinit__(struct __pyx_obj_3_sa_VEB *__pyx_v_self,
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__cinit__", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":361
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":361
  * 
  *     def __cinit__(self, int size):
  *         self.veb = new_VEB(size)             # <<<<<<<<<<<<<<
@@ -20012,7 +20937,7 @@ static void __pyx_pw_3_sa_3VEB_3__dealloc__(PyObject *__pyx_v_self) {
   __Pyx_RefNannyFinishContext();
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":363
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":363
  *         self.veb = new_VEB(size)
  * 
  *     def __dealloc__(self):             # <<<<<<<<<<<<<<
@@ -20028,7 +20953,7 @@ static void __pyx_pf_3_sa_3VEB_2__dealloc__(struct __pyx_obj_3_sa_VEB *__pyx_v_s
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__dealloc__", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":364
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":364
  * 
  *     def __dealloc__(self):
  *         del_VEB(self.veb)             # <<<<<<<<<<<<<<
@@ -20058,7 +20983,7 @@ static PyObject *__pyx_pw_3_sa_3VEB_5__iter__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":366
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":366
  *         del_VEB(self.veb)
  * 
  *     def __iter__(self):             # <<<<<<<<<<<<<<
@@ -20076,7 +21001,7 @@ static PyObject *__pyx_pf_3_sa_3VEB_4__iter__(struct __pyx_obj_3_sa_VEB *__pyx_v
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__iter__", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":368
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":368
  *     def __iter__(self):
  *         cdef VEBIterator it
  *         it = VEBIterator()             # <<<<<<<<<<<<<<
@@ -20088,7 +21013,7 @@ static PyObject *__pyx_pf_3_sa_3VEB_4__iter__(struct __pyx_obj_3_sa_VEB *__pyx_v
   __pyx_v_it = ((struct __pyx_obj_3_sa_VEBIterator *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":369
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":369
  *         cdef VEBIterator it
  *         it = VEBIterator()
  *         it.v = self.veb             # <<<<<<<<<<<<<<
@@ -20097,7 +21022,7 @@ static PyObject *__pyx_pf_3_sa_3VEB_4__iter__(struct __pyx_obj_3_sa_VEB *__pyx_v
  */
   __pyx_v_it->v = __pyx_v_self->veb;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":370
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":370
  *         it = VEBIterator()
  *         it.v = self.veb
  *         it.next_val = self.veb.min_val             # <<<<<<<<<<<<<<
@@ -20106,7 +21031,7 @@ static PyObject *__pyx_pf_3_sa_3VEB_4__iter__(struct __pyx_obj_3_sa_VEB *__pyx_v
  */
   __pyx_v_it->next_val = __pyx_v_self->veb->min_val;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":371
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":371
  *         it.v = self.veb
  *         it.next_val = self.veb.min_val
  *         return it             # <<<<<<<<<<<<<<
@@ -20142,7 +21067,7 @@ static PyObject *__pyx_pw_3_sa_3VEB_7insert(PyObject *__pyx_v_self, PyObject *__
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":373
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":373
  *         return it
  * 
  *     def insert(self, i):             # <<<<<<<<<<<<<<
@@ -20160,7 +21085,7 @@ static PyObject *__pyx_pf_3_sa_3VEB_6insert(struct __pyx_obj_3_sa_VEB *__pyx_v_s
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("insert", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":374
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":374
  * 
  *     def insert(self, i):
  *         return VEB_insert(self.veb, i)             # <<<<<<<<<<<<<<
@@ -20187,7 +21112,7 @@ static PyObject *__pyx_pf_3_sa_3VEB_6insert(struct __pyx_obj_3_sa_VEB *__pyx_v_s
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":376
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":376
  *         return VEB_insert(self.veb, i)
  * 
  *     cdef int _insert(self, int i):             # <<<<<<<<<<<<<<
@@ -20200,7 +21125,7 @@ static int __pyx_f_3_sa_3VEB__insert(struct __pyx_obj_3_sa_VEB *__pyx_v_self, in
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("_insert", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":377
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":377
  * 
  *     cdef int _insert(self, int i):
  *         return VEB_insert(self.veb, i)             # <<<<<<<<<<<<<<
@@ -20227,7 +21152,7 @@ static PyObject *__pyx_pw_3_sa_3VEB_9findsucc(PyObject *__pyx_v_self, PyObject *
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":379
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":379
  *         return VEB_insert(self.veb, i)
  * 
  *     def findsucc(self, i):             # <<<<<<<<<<<<<<
@@ -20245,7 +21170,7 @@ static PyObject *__pyx_pf_3_sa_3VEB_8findsucc(struct __pyx_obj_3_sa_VEB *__pyx_v
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("findsucc", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":380
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":380
  * 
  *     def findsucc(self, i):
  *         return VEB_findsucc(self.veb, i)             # <<<<<<<<<<<<<<
@@ -20272,7 +21197,7 @@ static PyObject *__pyx_pf_3_sa_3VEB_8findsucc(struct __pyx_obj_3_sa_VEB *__pyx_v
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":382
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":382
  *         return VEB_findsucc(self.veb, i)
  * 
  *     cdef int _first(self):             # <<<<<<<<<<<<<<
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   __Pyx_RefNannySetupContext("_first", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":383
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":383
  * 
  *     cdef int _first(self):
  *         return self.veb.min_val             # <<<<<<<<<<<<<<
@@ -20301,7 +21226,7 @@ static int __pyx_f_3_sa_3VEB__first(struct __pyx_obj_3_sa_VEB *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":385
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":385
  *         return self.veb.min_val
  * 
  *     cdef int _findsucc(self, int i):             # <<<<<<<<<<<<<<
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   __Pyx_RefNannySetupContext("_findsucc", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":386
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":386
  * 
  *     cdef int _findsucc(self, int i):
  *         return VEB_findsucc(self.veb, i)             # <<<<<<<<<<<<<<
@@ -20341,7 +21266,7 @@ static Py_ssize_t __pyx_pw_3_sa_3VEB_11__len__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":388
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":388
  *         return VEB_findsucc(self.veb, i)
  * 
  *     def __len__(self):             # <<<<<<<<<<<<<<
@@ -20354,7 +21279,7 @@ static Py_ssize_t __pyx_pf_3_sa_3VEB_10__len__(struct __pyx_obj_3_sa_VEB *__pyx_
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   __Pyx_RefNannySetupContext("__len__", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":389
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":389
  * 
  *     def __len__(self):
  *         return self.veb.size             # <<<<<<<<<<<<<<
@@ -20381,7 +21306,7 @@ static int __pyx_pw_3_sa_3VEB_13__contains__(PyObject *__pyx_v_self, PyObject *_
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":391
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":391
  *         return self.veb.size
  * 
  *     def __contains__(self, i):             # <<<<<<<<<<<<<<
@@ -20397,7 +21322,7 @@ static int __pyx_pf_3_sa_3VEB_12__contains__(struct __pyx_obj_3_sa_VEB *__pyx_v_
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   __Pyx_RefNannySetupContext("__contains__", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":392
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":392
  * 
  *     def __contains__(self, i):
  *         return VEB_contains(self.veb, i)             # <<<<<<<<<<<<<<
@@ -20468,7 +21393,7 @@ static int __pyx_pw_3_sa_3LCP_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":9
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":9
  *     cdef IntList lcp
  * 
  *     def __cinit__(self, SuffixArray sa):             # <<<<<<<<<<<<<<
@@ -20497,7 +21422,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
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   __Pyx_RefNannySetupContext("__cinit__", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":13
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":13
  *         cdef IntList rank
  * 
  *         logger.info("Constructing LCP array")             # <<<<<<<<<<<<<<
@@ -20514,7 +21439,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":14
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":14
  * 
  *         logger.info("Constructing LCP array")
  *         self.sa = sa             # <<<<<<<<<<<<<<
@@ -20527,7 +21452,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
   __Pyx_DECREF(((PyObject *)__pyx_v_self->sa));
   __pyx_v_self->sa = __pyx_v_sa;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":15
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":15
  *         logger.info("Constructing LCP array")
  *         self.sa = sa
  *         n = self.sa.sa.len             # <<<<<<<<<<<<<<
@@ -20536,7 +21461,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
  */
   __pyx_v_n = __pyx_v_self->sa->sa->len;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":16
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":16
  *         self.sa = sa
  *         n = self.sa.sa.len
  *         self.lcp = IntList(initial_len=n)             # <<<<<<<<<<<<<<
@@ -20558,7 +21483,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
   __pyx_v_self->lcp = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_2);
   __pyx_t_2 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":18
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":18
  *         self.lcp = IntList(initial_len=n)
  * 
  *         rank = IntList(initial_len=n)             # <<<<<<<<<<<<<<
@@ -20577,7 +21502,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
   __pyx_v_rank = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":19
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":19
  * 
  *         rank = IntList(initial_len=n)
  *         for i from 0 <= i < n:             # <<<<<<<<<<<<<<
@@ -20587,7 +21512,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
   __pyx_t_3 = __pyx_v_n;
   for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_3; __pyx_v_i++) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":20
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":20
  *         rank = IntList(initial_len=n)
  *         for i from 0 <= i < n:
  *             rank.arr[sa.sa.arr[i]] = i             # <<<<<<<<<<<<<<
@@ -20597,7 +21522,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
     (__pyx_v_rank->arr[(__pyx_v_sa->sa->arr[__pyx_v_i])]) = __pyx_v_i;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":22
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":22
  *             rank.arr[sa.sa.arr[i]] = i
  * 
  *         h = 0             # <<<<<<<<<<<<<<
@@ -20606,7 +21531,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
  */
   __pyx_v_h = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":23
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":23
  * 
  *         h = 0
  *         for i from 0 <= i < n:             # <<<<<<<<<<<<<<
@@ -20616,7 +21541,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
   __pyx_t_3 = __pyx_v_n;
   for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_3; __pyx_v_i++) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":24
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":24
  *         h = 0
  *         for i from 0 <= i < n:
  *             k = rank.arr[i]             # <<<<<<<<<<<<<<
@@ -20625,7 +21550,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
  */
     __pyx_v_k = (__pyx_v_rank->arr[__pyx_v_i]);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":25
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":25
  *         for i from 0 <= i < n:
  *             k = rank.arr[i]
  *             if k == 0:             # <<<<<<<<<<<<<<
@@ -20635,7 +21560,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
     __pyx_t_4 = (__pyx_v_k == 0);
     if (__pyx_t_4) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":26
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":26
  *             k = rank.arr[i]
  *             if k == 0:
  *                 self.lcp.arr[k] = -1             # <<<<<<<<<<<<<<
@@ -20647,7 +21572,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
     }
     /*else*/ {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":28
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":28
  *                 self.lcp.arr[k] = -1
  *             else:
  *                 j = sa.sa.arr[k-1]             # <<<<<<<<<<<<<<
@@ -20656,7 +21581,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
  */
       __pyx_v_j = (__pyx_v_sa->sa->arr[(__pyx_v_k - 1)]);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":29
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":29
  *             else:
  *                 j = sa.sa.arr[k-1]
  *                 while i+h < n and j+h < n and sa.darray.data.arr[i+h] == sa.darray.data.arr[j+h]:             # <<<<<<<<<<<<<<
@@ -20679,7 +21604,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
         }
         if (!__pyx_t_5) break;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":30
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":30
  *                 j = sa.sa.arr[k-1]
  *                 while i+h < n and j+h < n and sa.darray.data.arr[i+h] == sa.darray.data.arr[j+h]:
  *                     h = h+1             # <<<<<<<<<<<<<<
@@ -20689,7 +21614,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
         __pyx_v_h = (__pyx_v_h + 1);
       }
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":31
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":31
  *                 while i+h < n and j+h < n and sa.darray.data.arr[i+h] == sa.darray.data.arr[j+h]:
  *                     h = h+1
  *                 self.lcp.arr[k] = h             # <<<<<<<<<<<<<<
@@ -20700,7 +21625,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
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     __pyx_L7:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":32
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":32
  *                     h = h+1
  *                 self.lcp.arr[k] = h
  *             if h > 0:             # <<<<<<<<<<<<<<
@@ -20710,7 +21635,7 @@ static int __pyx_pf_3_sa_3LCP___cinit__(struct __pyx_obj_3_sa_LCP *__pyx_v_self,
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     if (__pyx_t_5) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":33
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":33
  *                 self.lcp.arr[k] = h
  *             if h > 0:
  *                 h = h-1             # <<<<<<<<<<<<<<
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     __pyx_L10:;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":34
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":34
  *             if h > 0:
  *                 h = h-1
  *         logger.info("LCP array completed")             # <<<<<<<<<<<<<<
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   return __pyx_r;
 }
-static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
+static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
 
 /* Python wrapper */
 static PyObject *__pyx_pw_3_sa_3LCP_3compute_stats(PyObject *__pyx_v_self, PyObject *__pyx_arg_max_n); /*proto*/
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   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":36
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":36
  *         logger.info("LCP array completed")
  * 
  *     def compute_stats(self, int max_n):             # <<<<<<<<<<<<<<
@@ -20785,14 +21710,14 @@ static PyObject *__pyx_pw_3_sa_3LCP_3compute_stats(PyObject *__pyx_v_self, PyObj
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 static PyObject *__pyx_pf_3_sa_3LCP_2compute_stats(struct __pyx_obj_3_sa_LCP *__pyx_v_self, int __pyx_v_max_n) {
-  struct __pyx_obj_3_sa___pyx_scope_struct_2_compute_stats *__pyx_cur_scope;
+  struct __pyx_obj_3_sa___pyx_scope_struct_3_compute_stats *__pyx_cur_scope;
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+  __pyx_cur_scope = (struct __pyx_obj_3_sa___pyx_scope_struct_3_compute_stats *)__pyx_ptype_3_sa___pyx_scope_struct_3_compute_stats->tp_new(__pyx_ptype_3_sa___pyx_scope_struct_3_compute_stats, __pyx_empty_tuple, NULL);
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   __pyx_cur_scope->__pyx_v_max_n = __pyx_v_max_n;
   {
-    __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_3_sa_3LCP_4generator, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[9]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_3_sa_3LCP_4generator1, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[9]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   return __pyx_r;
 }
 
-static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value) /* generator body */
+static PyObject *__pyx_gb_3_sa_3LCP_4generator1(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value) /* generator body */
 {
-  struct __pyx_obj_3_sa___pyx_scope_struct_2_compute_stats *__pyx_cur_scope = ((struct __pyx_obj_3_sa___pyx_scope_struct_2_compute_stats *)__pyx_generator->closure);
+  struct __pyx_obj_3_sa___pyx_scope_struct_3_compute_stats *__pyx_cur_scope = ((struct __pyx_obj_3_sa___pyx_scope_struct_3_compute_stats *)__pyx_generator->closure);
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   PyObject *__pyx_t_1 = NULL;
   int __pyx_t_2;
@@ -20847,7 +21772,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
   __pyx_L3_first_run:;
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":48
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":48
  *         cdef VEB veb
  * 
  *         N = self.sa.sa.len             # <<<<<<<<<<<<<<
@@ -20856,7 +21781,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
  */
   __pyx_cur_scope->__pyx_v_N = __pyx_cur_scope->__pyx_v_self->sa->sa->len;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":50
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":50
  *         N = self.sa.sa.len
  * 
  *         ngram_starts = []             # <<<<<<<<<<<<<<
@@ -20869,7 +21794,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
   __pyx_cur_scope->__pyx_v_ngram_starts = __pyx_t_1;
   __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":51
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":51
  * 
  *         ngram_starts = []
  *         for n from 0 <= n < max_n:             # <<<<<<<<<<<<<<
@@ -20879,7 +21804,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
   __pyx_t_2 = __pyx_cur_scope->__pyx_v_max_n;
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":52
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":52
  *         ngram_starts = []
  *         for n from 0 <= n < max_n:
  *             ngram_starts.append(IntList(initial_len=N))             # <<<<<<<<<<<<<<
@@ -20899,7 +21824,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
     __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":54
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":54
  *             ngram_starts.append(IntList(initial_len=N))
  * 
  *         run_start = IntList(initial_len=max_n)             # <<<<<<<<<<<<<<
@@ -20919,7 +21844,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
   __pyx_cur_scope->__pyx_v_run_start = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":55
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":55
  * 
  *         run_start = IntList(initial_len=max_n)
  *         veb = VEB(N)             # <<<<<<<<<<<<<<
@@ -20940,7 +21865,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
   __pyx_cur_scope->__pyx_v_veb = ((struct __pyx_obj_3_sa_VEB *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":57
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":57
  *         veb = VEB(N)
  * 
  *         for i from 0 <= i < N:             # <<<<<<<<<<<<<<
@@ -20950,7 +21875,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
   __pyx_t_2 = __pyx_cur_scope->__pyx_v_N;
   for (__pyx_cur_scope->__pyx_v_i = 0; __pyx_cur_scope->__pyx_v_i < __pyx_t_2; __pyx_cur_scope->__pyx_v_i++) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":58
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":58
  * 
  *         for i from 0 <= i < N:
  *             h = self.lcp.arr[i]             # <<<<<<<<<<<<<<
@@ -20959,7 +21884,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
  */
     __pyx_cur_scope->__pyx_v_h = (__pyx_cur_scope->__pyx_v_self->lcp->arr[__pyx_cur_scope->__pyx_v_i]);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":59
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":59
  *         for i from 0 <= i < N:
  *             h = self.lcp.arr[i]
  *             if h < 0:             # <<<<<<<<<<<<<<
@@ -20969,7 +21894,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
     __pyx_t_5 = (__pyx_cur_scope->__pyx_v_h < 0);
     if (__pyx_t_5) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":60
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":60
  *             h = self.lcp.arr[i]
  *             if h < 0:
  *                 h = 0             # <<<<<<<<<<<<<<
@@ -20981,7 +21906,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
     }
     __pyx_L8:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":61
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":61
  *             if h < 0:
  *                 h = 0
  *             for n from h <= n < max_n:             # <<<<<<<<<<<<<<
@@ -20991,7 +21916,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
     __pyx_t_6 = __pyx_cur_scope->__pyx_v_max_n;
     for (__pyx_cur_scope->__pyx_v_n = __pyx_cur_scope->__pyx_v_h; __pyx_cur_scope->__pyx_v_n < __pyx_t_6; __pyx_cur_scope->__pyx_v_n++) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":62
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":62
  *                 h = 0
  *             for n from h <= n < max_n:
  *                 rs = run_start.arr[n]             # <<<<<<<<<<<<<<
@@ -21000,7 +21925,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
  */
       __pyx_cur_scope->__pyx_v_rs = (__pyx_cur_scope->__pyx_v_run_start->arr[__pyx_cur_scope->__pyx_v_n]);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":63
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":63
  *             for n from h <= n < max_n:
  *                 rs = run_start.arr[n]
  *                 run_start.arr[n] = i             # <<<<<<<<<<<<<<
@@ -21009,7 +21934,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
  */
       (__pyx_cur_scope->__pyx_v_run_start->arr[__pyx_cur_scope->__pyx_v_n]) = __pyx_cur_scope->__pyx_v_i;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":64
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":64
  *                 rs = run_start.arr[n]
  *                 run_start.arr[n] = i
  *                 freq = i - rs             # <<<<<<<<<<<<<<
@@ -21018,7 +21943,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
  */
       __pyx_cur_scope->__pyx_v_freq = (__pyx_cur_scope->__pyx_v_i - __pyx_cur_scope->__pyx_v_rs);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":65
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":65
  *                 run_start.arr[n] = i
  *                 freq = i - rs
  *                 if freq > 1000: # arbitrary, but see note below             # <<<<<<<<<<<<<<
@@ -21028,7 +21953,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
       __pyx_t_5 = (__pyx_cur_scope->__pyx_v_freq > 1000);
       if (__pyx_t_5) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":66
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":66
  *                 freq = i - rs
  *                 if freq > 1000: # arbitrary, but see note below
  *                     veb._insert(freq)             # <<<<<<<<<<<<<<
@@ -21037,7 +21962,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
  */
         ((struct __pyx_vtabstruct_3_sa_VEB *)__pyx_cur_scope->__pyx_v_veb->__pyx_vtab)->_insert(__pyx_cur_scope->__pyx_v_veb, __pyx_cur_scope->__pyx_v_freq);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":67
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":67
  *                 if freq > 1000: # arbitrary, but see note below
  *                     veb._insert(freq)
  *                     ngram_start = ngram_starts[n]             # <<<<<<<<<<<<<<
@@ -21053,7 +21978,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
         __pyx_cur_scope->__pyx_v_ngram_start = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_1);
         __pyx_t_1 = 0;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":68
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":68
  *                     veb._insert(freq)
  *                     ngram_start = ngram_starts[n]
  *                     while ngram_start.arr[freq] > 0:             # <<<<<<<<<<<<<<
@@ -21064,7 +21989,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
           __pyx_t_5 = ((__pyx_cur_scope->__pyx_v_ngram_start->arr[__pyx_cur_scope->__pyx_v_freq]) > 0);
           if (!__pyx_t_5) break;
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":69
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":69
  *                     ngram_start = ngram_starts[n]
  *                     while ngram_start.arr[freq] > 0:
  *                         freq = freq + 1 # cheating a bit, should be ok for sparse histogram             # <<<<<<<<<<<<<<
@@ -21074,7 +21999,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
           __pyx_cur_scope->__pyx_v_freq = (__pyx_cur_scope->__pyx_v_freq + 1);
         }
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":70
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":70
  *                     while ngram_start.arr[freq] > 0:
  *                         freq = freq + 1 # cheating a bit, should be ok for sparse histogram
  *                     ngram_start.arr[freq] = rs             # <<<<<<<<<<<<<<
@@ -21088,7 +22013,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
     }
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":71
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":71
  *                         freq = freq + 1 # cheating a bit, should be ok for sparse histogram
  *                     ngram_start.arr[freq] = rs
  *         i = veb.veb.min_val             # <<<<<<<<<<<<<<
@@ -21097,7 +22022,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
  */
   __pyx_cur_scope->__pyx_v_i = __pyx_cur_scope->__pyx_v_veb->veb->min_val;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":72
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":72
  *                     ngram_start.arr[freq] = rs
  *         i = veb.veb.min_val
  *         while i != -1:             # <<<<<<<<<<<<<<
@@ -21108,7 +22033,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
     __pyx_t_5 = (__pyx_cur_scope->__pyx_v_i != -1);
     if (!__pyx_t_5) break;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":73
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":73
  *         i = veb.veb.min_val
  *         while i != -1:
  *             ii = veb._findsucc(i)             # <<<<<<<<<<<<<<
@@ -21117,7 +22042,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
  */
     __pyx_cur_scope->__pyx_v_ii = ((struct __pyx_vtabstruct_3_sa_VEB *)__pyx_cur_scope->__pyx_v_veb->__pyx_vtab)->_findsucc(__pyx_cur_scope->__pyx_v_veb, __pyx_cur_scope->__pyx_v_i);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":74
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":74
  *         while i != -1:
  *             ii = veb._findsucc(i)
  *             for n from 0 <= n < max_n:             # <<<<<<<<<<<<<<
@@ -21127,7 +22052,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
     __pyx_t_2 = __pyx_cur_scope->__pyx_v_max_n;
     for (__pyx_cur_scope->__pyx_v_n = 0; __pyx_cur_scope->__pyx_v_n < __pyx_t_2; __pyx_cur_scope->__pyx_v_n++) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":75
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":75
  *             ii = veb._findsucc(i)
  *             for n from 0 <= n < max_n:
  *                 ngram_start = ngram_starts[n]             # <<<<<<<<<<<<<<
@@ -21143,7 +22068,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
       __pyx_cur_scope->__pyx_v_ngram_start = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_1);
       __pyx_t_1 = 0;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":76
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":76
  *             for n from 0 <= n < max_n:
  *                 ngram_start = ngram_starts[n]
  *                 iii = i             # <<<<<<<<<<<<<<
@@ -21152,7 +22077,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
  */
       __pyx_cur_scope->__pyx_v_iii = __pyx_cur_scope->__pyx_v_i;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":77
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":77
  *                 ngram_start = ngram_starts[n]
  *                 iii = i
  *                 rs = ngram_start.arr[iii]             # <<<<<<<<<<<<<<
@@ -21161,7 +22086,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
  */
       __pyx_cur_scope->__pyx_v_rs = (__pyx_cur_scope->__pyx_v_ngram_start->arr[__pyx_cur_scope->__pyx_v_iii]);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":78
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":78
  *                 iii = i
  *                 rs = ngram_start.arr[iii]
  *                 while (ii==-1 or iii < ii) and rs != 0:             # <<<<<<<<<<<<<<
@@ -21184,7 +22109,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
         }
         if (!__pyx_t_7) break;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":79
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":79
  *                 rs = ngram_start.arr[iii]
  *                 while (ii==-1 or iii < ii) and rs != 0:
  *                     j = self.sa.sa.arr[rs]             # <<<<<<<<<<<<<<
@@ -21193,7 +22118,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
  */
         __pyx_cur_scope->__pyx_v_j = (__pyx_cur_scope->__pyx_v_self->sa->sa->arr[__pyx_cur_scope->__pyx_v_rs]);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":80
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":80
  *                 while (ii==-1 or iii < ii) and rs != 0:
  *                     j = self.sa.sa.arr[rs]
  *                     valid = 1             # <<<<<<<<<<<<<<
@@ -21202,7 +22127,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
  */
         __pyx_cur_scope->__pyx_v_valid = 1;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":81
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":81
  *                     j = self.sa.sa.arr[rs]
  *                     valid = 1
  *                     for k from 0 <= k < n+1:             # <<<<<<<<<<<<<<
@@ -21212,7 +22137,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
         __pyx_t_9 = (__pyx_cur_scope->__pyx_v_n + 1);
         for (__pyx_cur_scope->__pyx_v_k = 0; __pyx_cur_scope->__pyx_v_k < __pyx_t_9; __pyx_cur_scope->__pyx_v_k++) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":82
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":82
  *                     valid = 1
  *                     for k from 0 <= k < n+1:
  *                         if self.sa.darray.data.arr[j+k] < 2:             # <<<<<<<<<<<<<<
@@ -21222,7 +22147,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
           __pyx_t_7 = ((__pyx_cur_scope->__pyx_v_self->sa->darray->data->arr[(__pyx_cur_scope->__pyx_v_j + __pyx_cur_scope->__pyx_v_k)]) < 2);
           if (__pyx_t_7) {
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":83
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":83
  *                     for k from 0 <= k < n+1:
  *                         if self.sa.darray.data.arr[j+k] < 2:
  *                             valid = 0             # <<<<<<<<<<<<<<
@@ -21235,7 +22160,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
           __pyx_L22:;
         }
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":84
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":84
  *                         if self.sa.darray.data.arr[j+k] < 2:
  *                             valid = 0
  *                     if valid:             # <<<<<<<<<<<<<<
@@ -21244,7 +22169,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
  */
         if (__pyx_cur_scope->__pyx_v_valid) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":85
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":85
  *                             valid = 0
  *                     if valid:
  *                         ngram = tuple([self.sa.darray.data.arr[j+k] for k in range(n+1)])             # <<<<<<<<<<<<<<
@@ -21270,7 +22195,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
           __pyx_cur_scope->__pyx_v_ngram = __pyx_t_3;
           __pyx_t_3 = 0;
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":86
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":86
  *                     if valid:
  *                         ngram = tuple([self.sa.darray.data.arr[j+k] for k in range(n+1)])
  *                         yield i, n+1, ngram             # <<<<<<<<<<<<<<
@@ -21307,7 +22232,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
         }
         __pyx_L23:;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":87
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":87
  *                         ngram = tuple([self.sa.darray.data.arr[j+k] for k in range(n+1)])
  *                         yield i, n+1, ngram
  *                     iii = iii + 1             # <<<<<<<<<<<<<<
@@ -21316,7 +22241,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
  */
         __pyx_cur_scope->__pyx_v_iii = (__pyx_cur_scope->__pyx_v_iii + 1);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":88
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":88
  *                         yield i, n+1, ngram
  *                     iii = iii + 1
  *                     rs = ngram_start.arr[iii]             # <<<<<<<<<<<<<<
@@ -21326,7 +22251,7 @@ static PyObject *__pyx_gb_3_sa_3LCP_4generator(__pyx_GeneratorObject *__pyx_gene
       }
     }
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":89
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":89
  *                     iii = iii + 1
  *                     rs = ngram_start.arr[iii]
  *             i = ii             # <<<<<<<<<<<<<<
@@ -21362,7 +22287,7 @@ static int __pyx_pw_3_sa_8Alphabet_1__cinit__(PyObject *__pyx_v_self, PyObject *
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":12
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":12
  *     cdef dict id2sym
  * 
  *     def __cinit__(self):             # <<<<<<<<<<<<<<
@@ -21379,7 +22304,7 @@ static int __pyx_pf_3_sa_8Alphabet___cinit__(struct __pyx_obj_3_sa_Alphabet *__p
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__cinit__", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":13
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":13
  * 
  *     def __cinit__(self):
  *         self.terminals = StringMap()             # <<<<<<<<<<<<<<
@@ -21394,7 +22319,7 @@ static int __pyx_pf_3_sa_8Alphabet___cinit__(struct __pyx_obj_3_sa_Alphabet *__p
   __pyx_v_self->terminals = ((struct __pyx_obj_3_sa_StringMap *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":14
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":14
  *     def __cinit__(self):
  *         self.terminals = StringMap()
  *         self.nonterminals = StringMap()             # <<<<<<<<<<<<<<
@@ -21409,7 +22334,7 @@ static int __pyx_pf_3_sa_8Alphabet___cinit__(struct __pyx_obj_3_sa_Alphabet *__p
   __pyx_v_self->nonterminals = ((struct __pyx_obj_3_sa_StringMap *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":15
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":15
  *         self.terminals = StringMap()
  *         self.nonterminals = StringMap()
  *         self.id2sym = {}             # <<<<<<<<<<<<<<
@@ -21424,7 +22349,7 @@ static int __pyx_pf_3_sa_8Alphabet___cinit__(struct __pyx_obj_3_sa_Alphabet *__p
   __pyx_v_self->id2sym = __pyx_t_1;
   __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":16
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":16
  *         self.nonterminals = StringMap()
  *         self.id2sym = {}
  *         self.first_nonterminal = -1             # <<<<<<<<<<<<<<
@@ -21453,7 +22378,7 @@ static void __pyx_pw_3_sa_8Alphabet_3__dealloc__(PyObject *__pyx_v_self) {
   __Pyx_RefNannyFinishContext();
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":18
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":18
  *         self.first_nonterminal = -1
  * 
  *     def __dealloc__(self):             # <<<<<<<<<<<<<<
@@ -21468,7 +22393,7 @@ static void __pyx_pf_3_sa_8Alphabet_2__dealloc__(CYTHON_UNUSED struct __pyx_obj_
   __Pyx_RefNannyFinishContext();
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":21
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":21
  *         pass
  * 
  *     cdef int isvar(self, int sym):             # <<<<<<<<<<<<<<
@@ -21481,7 +22406,7 @@ static int __pyx_f_3_sa_8Alphabet_isvar(CYTHON_UNUSED struct __pyx_obj_3_sa_Alph
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("isvar", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":22
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":22
  * 
  *     cdef int isvar(self, int sym):
  *         return sym < 0             # <<<<<<<<<<<<<<
@@ -21497,7 +22422,7 @@ static int __pyx_f_3_sa_8Alphabet_isvar(CYTHON_UNUSED struct __pyx_obj_3_sa_Alph
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":24
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":24
  *         return sym < 0
  * 
  *     cdef int isword(self, int sym):             # <<<<<<<<<<<<<<
@@ -21510,7 +22435,7 @@ static int __pyx_f_3_sa_8Alphabet_isword(CYTHON_UNUSED struct __pyx_obj_3_sa_Alp
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("isword", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":25
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":25
  * 
  *     cdef int isword(self, int sym):
  *         return sym >= 0             # <<<<<<<<<<<<<<
@@ -21526,7 +22451,7 @@ static int __pyx_f_3_sa_8Alphabet_isword(CYTHON_UNUSED struct __pyx_obj_3_sa_Alp
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":27
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":27
  *         return sym >= 0
  * 
  *     cdef int getindex(self, int sym):             # <<<<<<<<<<<<<<
@@ -21539,7 +22464,7 @@ static int __pyx_f_3_sa_8Alphabet_getindex(CYTHON_UNUSED struct __pyx_obj_3_sa_A
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("getindex", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":28
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":28
  * 
  *     cdef int getindex(self, int sym):
  *         return -sym & INDEX_MASK             # <<<<<<<<<<<<<<
@@ -21555,7 +22480,7 @@ static int __pyx_f_3_sa_8Alphabet_getindex(CYTHON_UNUSED struct __pyx_obj_3_sa_A
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":30
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":30
  *         return -sym & INDEX_MASK
  * 
  *     cdef int setindex(self, int sym, int ind):             # <<<<<<<<<<<<<<
@@ -21568,7 +22493,7 @@ static int __pyx_f_3_sa_8Alphabet_setindex(CYTHON_UNUSED struct __pyx_obj_3_sa_A
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("setindex", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":31
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":31
  * 
  *     cdef int setindex(self, int sym, int ind):
  *         return -(-sym & ~INDEX_MASK | ind)             # <<<<<<<<<<<<<<
@@ -21584,7 +22509,7 @@ static int __pyx_f_3_sa_8Alphabet_setindex(CYTHON_UNUSED struct __pyx_obj_3_sa_A
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":33
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":33
  *         return -(-sym & ~INDEX_MASK | ind)
  * 
  *     cdef int clearindex(self, int sym):             # <<<<<<<<<<<<<<
@@ -21597,7 +22522,7 @@ static int __pyx_f_3_sa_8Alphabet_clearindex(CYTHON_UNUSED struct __pyx_obj_3_sa
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("clearindex", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":34
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":34
  * 
  *     cdef int clearindex(self, int sym):
  *         return -(-sym& ~INDEX_MASK)             # <<<<<<<<<<<<<<
@@ -21613,7 +22538,7 @@ static int __pyx_f_3_sa_8Alphabet_clearindex(CYTHON_UNUSED struct __pyx_obj_3_sa
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":36
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":36
  *         return -(-sym& ~INDEX_MASK)
  * 
  *     cdef int match(self, int sym1, int sym2):             # <<<<<<<<<<<<<<
@@ -21626,7 +22551,7 @@ static int __pyx_f_3_sa_8Alphabet_match(struct __pyx_obj_3_sa_Alphabet *__pyx_v_
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("match", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":37
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":37
  * 
  *     cdef int match(self, int sym1, int sym2):
  *         return self.clearindex(sym1) == self.clearindex(sym2);             # <<<<<<<<<<<<<<
@@ -21642,7 +22567,7 @@ static int __pyx_f_3_sa_8Alphabet_match(struct __pyx_obj_3_sa_Alphabet *__pyx_v_
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":39
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":39
  *         return self.clearindex(sym1) == self.clearindex(sym2);
  * 
  *     cdef char* tocat(self, int sym):             # <<<<<<<<<<<<<<
@@ -21655,7 +22580,7 @@ static char *__pyx_f_3_sa_8Alphabet_tocat(struct __pyx_obj_3_sa_Alphabet *__pyx_
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("tocat", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":40
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":40
  * 
  *     cdef char* tocat(self, int sym):
  *         return self.nonterminals.word((-sym >> INDEX_SHIFT)-1)             # <<<<<<<<<<<<<<
@@ -21671,7 +22596,7 @@ static char *__pyx_f_3_sa_8Alphabet_tocat(struct __pyx_obj_3_sa_Alphabet *__pyx_
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":42
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":42
  *         return self.nonterminals.word((-sym >> INDEX_SHIFT)-1)
  * 
  *     cdef int fromcat(self, char *s):             # <<<<<<<<<<<<<<
@@ -21686,7 +22611,7 @@ static int __pyx_f_3_sa_8Alphabet_fromcat(struct __pyx_obj_3_sa_Alphabet *__pyx_
   int __pyx_t_1;
   __Pyx_RefNannySetupContext("fromcat", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":44
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":44
  *     cdef int fromcat(self, char *s):
  *         cdef int i
  *         i = self.nonterminals.index(s)             # <<<<<<<<<<<<<<
@@ -21695,7 +22620,7 @@ static int __pyx_f_3_sa_8Alphabet_fromcat(struct __pyx_obj_3_sa_Alphabet *__pyx_
  */
   __pyx_v_i = ((struct __pyx_vtabstruct_3_sa_StringMap *)__pyx_v_self->nonterminals->__pyx_vtab)->index(__pyx_v_self->nonterminals, __pyx_v_s);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":45
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":45
  *         cdef int i
  *         i = self.nonterminals.index(s)
  *         if self.first_nonterminal == -1:             # <<<<<<<<<<<<<<
@@ -21705,7 +22630,7 @@ static int __pyx_f_3_sa_8Alphabet_fromcat(struct __pyx_obj_3_sa_Alphabet *__pyx_
   __pyx_t_1 = (__pyx_v_self->first_nonterminal == -1);
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":46
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":46
  *         i = self.nonterminals.index(s)
  *         if self.first_nonterminal == -1:
  *             self.first_nonterminal = i             # <<<<<<<<<<<<<<
@@ -21717,7 +22642,7 @@ static int __pyx_f_3_sa_8Alphabet_fromcat(struct __pyx_obj_3_sa_Alphabet *__pyx_
   }
   __pyx_L3:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":47
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":47
  *         if self.first_nonterminal == -1:
  *             self.first_nonterminal = i
  *         if i > self.last_nonterminal:             # <<<<<<<<<<<<<<
@@ -21727,7 +22652,7 @@ static int __pyx_f_3_sa_8Alphabet_fromcat(struct __pyx_obj_3_sa_Alphabet *__pyx_
   __pyx_t_1 = (__pyx_v_i > __pyx_v_self->last_nonterminal);
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":48
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":48
  *             self.first_nonterminal = i
  *         if i > self.last_nonterminal:
  *             self.last_nonterminal = i             # <<<<<<<<<<<<<<
@@ -21739,7 +22664,7 @@ static int __pyx_f_3_sa_8Alphabet_fromcat(struct __pyx_obj_3_sa_Alphabet *__pyx_
   }
   __pyx_L4:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":49
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":49
  *         if i > self.last_nonterminal:
  *             self.last_nonterminal = i
  *         return -(i+1 << INDEX_SHIFT)             # <<<<<<<<<<<<<<
@@ -21755,7 +22680,7 @@ static int __pyx_f_3_sa_8Alphabet_fromcat(struct __pyx_obj_3_sa_Alphabet *__pyx_
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":51
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":51
  *         return -(i+1 << INDEX_SHIFT)
  * 
  *     cdef char* tostring(self, int sym):             # <<<<<<<<<<<<<<
@@ -21778,7 +22703,7 @@ static char *__pyx_f_3_sa_8Alphabet_tostring(struct __pyx_obj_3_sa_Alphabet *__p
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("tostring", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":53
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":53
  *     cdef char* tostring(self, int sym):
  *         cdef int ind
  *         if self.isvar(sym):             # <<<<<<<<<<<<<<
@@ -21788,7 +22713,7 @@ static char *__pyx_f_3_sa_8Alphabet_tostring(struct __pyx_obj_3_sa_Alphabet *__p
   __pyx_t_1 = ((struct __pyx_vtabstruct_3_sa_Alphabet *)__pyx_v_self->__pyx_vtab)->isvar(__pyx_v_self, __pyx_v_sym);
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":54
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":54
  *         cdef int ind
  *         if self.isvar(sym):
  *             if sym in self.id2sym:             # <<<<<<<<<<<<<<
@@ -21801,11 +22726,11 @@ static char *__pyx_f_3_sa_8Alphabet_tostring(struct __pyx_obj_3_sa_Alphabet *__p
       PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
       {__pyx_filename = __pyx_f[10]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     }
-    __pyx_t_3 = ((PyDict_Contains(((PyObject *)__pyx_v_self->id2sym), __pyx_t_2))); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_3 = (__Pyx_PyDict_Contains(__pyx_t_2, ((PyObject *)__pyx_v_self->id2sym), Py_EQ)); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
     if (__pyx_t_3) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":55
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":55
  *         if self.isvar(sym):
  *             if sym in self.id2sym:
  *                 return self.id2sym[sym]             # <<<<<<<<<<<<<<
@@ -21826,7 +22751,7 @@ static char *__pyx_f_3_sa_8Alphabet_tostring(struct __pyx_obj_3_sa_Alphabet *__p
     }
     __pyx_L4:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":56
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":56
  *             if sym in self.id2sym:
  *                 return self.id2sym[sym]
  *             ind = self.getindex(sym)             # <<<<<<<<<<<<<<
@@ -21835,7 +22760,7 @@ static char *__pyx_f_3_sa_8Alphabet_tostring(struct __pyx_obj_3_sa_Alphabet *__p
  */
     __pyx_v_ind = ((struct __pyx_vtabstruct_3_sa_Alphabet *)__pyx_v_self->__pyx_vtab)->getindex(__pyx_v_self, __pyx_v_sym);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":57
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":57
  *                 return self.id2sym[sym]
  *             ind = self.getindex(sym)
  *             if ind > 0:             # <<<<<<<<<<<<<<
@@ -21845,7 +22770,7 @@ static char *__pyx_f_3_sa_8Alphabet_tostring(struct __pyx_obj_3_sa_Alphabet *__p
     __pyx_t_3 = (__pyx_v_ind > 0);
     if (__pyx_t_3) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":58
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":58
  *             ind = self.getindex(sym)
  *             if ind > 0:
  *                 self.id2sym[sym] = "[%s,%d]" % (self.tocat(sym), ind)             # <<<<<<<<<<<<<<
@@ -21877,7 +22802,7 @@ static char *__pyx_f_3_sa_8Alphabet_tostring(struct __pyx_obj_3_sa_Alphabet *__p
     }
     /*else*/ {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":60
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":60
  *                 self.id2sym[sym] = "[%s,%d]" % (self.tocat(sym), ind)
  *             else:
  *                 self.id2sym[sym] = "[%s]" % self.tocat(sym)             # <<<<<<<<<<<<<<
@@ -21898,7 +22823,7 @@ static char *__pyx_f_3_sa_8Alphabet_tostring(struct __pyx_obj_3_sa_Alphabet *__p
     }
     __pyx_L5:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":61
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":61
  *             else:
  *                 self.id2sym[sym] = "[%s]" % self.tocat(sym)
  *             return self.id2sym[sym]             # <<<<<<<<<<<<<<
@@ -21919,7 +22844,7 @@ static char *__pyx_f_3_sa_8Alphabet_tostring(struct __pyx_obj_3_sa_Alphabet *__p
   }
   /*else*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":63
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":63
  *             return self.id2sym[sym]
  *         else:
  *             return self.terminals.word(sym)             # <<<<<<<<<<<<<<
@@ -21944,7 +22869,7 @@ static char *__pyx_f_3_sa_8Alphabet_tostring(struct __pyx_obj_3_sa_Alphabet *__p
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":65
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":65
  *             return self.terminals.word(sym)
  * 
  *     cdef int fromstring(self, char *s, bint terminal):             # <<<<<<<<<<<<<<
@@ -21972,7 +22897,7 @@ static int __pyx_f_3_sa_8Alphabet_fromstring(struct __pyx_obj_3_sa_Alphabet *__p
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("fromstring", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":69
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":69
  *         cdef char *comma
  *         cdef int n
  *         n = strlen(s)             # <<<<<<<<<<<<<<
@@ -21981,7 +22906,7 @@ static int __pyx_f_3_sa_8Alphabet_fromstring(struct __pyx_obj_3_sa_Alphabet *__p
  */
   __pyx_v_n = strlen(__pyx_v_s);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":71
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":71
  *         n = strlen(s)
  *         cdef char *sep
  *         sep = strstr(s,"_SEP_")             # <<<<<<<<<<<<<<
@@ -21990,7 +22915,7 @@ static int __pyx_f_3_sa_8Alphabet_fromstring(struct __pyx_obj_3_sa_Alphabet *__p
  */
   __pyx_v_sep = strstr(__pyx_v_s, __pyx_k___SEP_);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":72
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":72
  *         cdef char *sep
  *         sep = strstr(s,"_SEP_")
  *         if n >= 3 and s[0] == c'[' and s[n-1] == c']' and sep == NULL:             # <<<<<<<<<<<<<<
@@ -22018,7 +22943,7 @@ static int __pyx_f_3_sa_8Alphabet_fromstring(struct __pyx_obj_3_sa_Alphabet *__p
   }
   if (__pyx_t_2) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":73
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":73
  *         sep = strstr(s,"_SEP_")
  *         if n >= 3 and s[0] == c'[' and s[n-1] == c']' and sep == NULL:
  *             if terminal:             # <<<<<<<<<<<<<<
@@ -22027,7 +22952,7 @@ static int __pyx_f_3_sa_8Alphabet_fromstring(struct __pyx_obj_3_sa_Alphabet *__p
  */
     if (__pyx_v_terminal) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":74
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":74
  *         if n >= 3 and s[0] == c'[' and s[n-1] == c']' and sep == NULL:
  *             if terminal:
  *                 s1 = "\\"+s             # <<<<<<<<<<<<<<
@@ -22042,7 +22967,7 @@ static int __pyx_f_3_sa_8Alphabet_fromstring(struct __pyx_obj_3_sa_Alphabet *__p
       __pyx_v_s1 = __pyx_t_7;
       __pyx_t_7 = 0;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":75
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":75
  *             if terminal:
  *                 s1 = "\\"+s
  *                 return self.terminals.index(s1)             # <<<<<<<<<<<<<<
@@ -22056,7 +22981,7 @@ static int __pyx_f_3_sa_8Alphabet_fromstring(struct __pyx_obj_3_sa_Alphabet *__p
     }
     __pyx_L4:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":76
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":76
  *                 s1 = "\\"+s
  *                 return self.terminals.index(s1)
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":80
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":81
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":39
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":41
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":43
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":43
  *         i = 1
  *         j = 0
  *         for j from 0 <= j < self.n:             # <<<<<<<<<<<<<<
@@ -22928,7 +24945,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_6handle(struct __pyx_obj_3_sa_Phrase *__p
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   for (__pyx_v_j = 0; __pyx_v_j < __pyx_t_2; __pyx_v_j++) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":44
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":44
  *         j = 0
  *         for j from 0 <= j < self.n:
  *             s = self.syms[j]             # <<<<<<<<<<<<<<
@@ -22937,7 +24954,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_6handle(struct __pyx_obj_3_sa_Phrase *__p
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     __pyx_v_s = (__pyx_v_self->syms[__pyx_v_j]);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":45
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":45
  *         for j from 0 <= j < self.n:
  *             s = self.syms[j]
  *             if sym_isvar(s):             # <<<<<<<<<<<<<<
@@ -22947,7 +24964,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_6handle(struct __pyx_obj_3_sa_Phrase *__p
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     if (__pyx_t_3) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":46
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":46
  *             s = self.syms[j]
  *             if sym_isvar(s):
  *                 s = sym_setindex(s,i)             # <<<<<<<<<<<<<<
@@ -22956,7 +24973,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_6handle(struct __pyx_obj_3_sa_Phrase *__p
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       __pyx_v_s = __pyx_f_3_sa_sym_setindex(__pyx_v_s, __pyx_v_i);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":47
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":47
  *             if sym_isvar(s):
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@@ -22968,7 +24985,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_6handle(struct __pyx_obj_3_sa_Phrase *__p
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     __pyx_L5:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":48
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":48
  *                 s = sym_setindex(s,i)
  *                 i = i + 1
  *             norm.append(s)             # <<<<<<<<<<<<<<
@@ -22981,7 +24998,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_6handle(struct __pyx_obj_3_sa_Phrase *__p
     __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":49
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":49
  *                 i = i + 1
  *             norm.append(s)
  *         return tuple(norm)             # <<<<<<<<<<<<<<
@@ -23019,7 +25036,7 @@ static PyObject *__pyx_pw_3_sa_6Phrase_9strhandle(PyObject *__pyx_v_self, CYTHON
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":51
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":51
  *         return tuple(norm)
  * 
  *     def strhandle(self):             # <<<<<<<<<<<<<<
@@ -23046,7 +25063,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_8strhandle(struct __pyx_obj_3_sa_Phrase *
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":52
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":52
  * 
  *     def strhandle(self):
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@@ -23058,7 +25075,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_8strhandle(struct __pyx_obj_3_sa_Phrase *
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":53
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":53
  *     def strhandle(self):
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@@ -23070,7 +25087,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_8strhandle(struct __pyx_obj_3_sa_Phrase *
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":55
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":55
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":56
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":56
  *         cdef int i, j, s
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  *         j = 0             # <<<<<<<<<<<<<<
@@ -23088,7 +25105,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_8strhandle(struct __pyx_obj_3_sa_Phrase *
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":57
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":57
  *         i = 1
  *         j = 0
  *         for j from 0 <= j < self.n:             # <<<<<<<<<<<<<<
@@ -23098,7 +25115,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_8strhandle(struct __pyx_obj_3_sa_Phrase *
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":58
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":58
  *         j = 0
  *         for j from 0 <= j < self.n:
  *             s = self.syms[j]             # <<<<<<<<<<<<<<
@@ -23107,7 +25124,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_8strhandle(struct __pyx_obj_3_sa_Phrase *
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":59
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":59
  *         for j from 0 <= j < self.n:
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@@ -23117,7 +25134,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_8strhandle(struct __pyx_obj_3_sa_Phrase *
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":60
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":60
  *             s = self.syms[j]
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@@ -23126,23 +25143,23 @@ static PyObject *__pyx_pf_3_sa_6Phrase_8strhandle(struct __pyx_obj_3_sa_Phrase *
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":61
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":61
  *             if sym_isvar(s):
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  *                 i = i + 1             # <<<<<<<<<<<<<<
  *             norm.append(sym_tostring(s))
- *         return " ".join(norm)
+ *         return ' '.join(norm)
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":62
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":62
  *                 s = sym_setindex(s,i)
  *                 i = i + 1
  *             norm.append(sym_tostring(s))             # <<<<<<<<<<<<<<
- *         return " ".join(norm)
+ *         return ' '.join(norm)
  * 
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     __pyx_t_1 = PyBytes_FromString(__pyx_f_3_sa_sym_tostring(__pyx_v_s)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -23151,10 +25168,10 @@ static PyObject *__pyx_pf_3_sa_6Phrase_8strhandle(struct __pyx_obj_3_sa_Phrase *
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":63
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":63
  *                 i = i + 1
  *             norm.append(sym_tostring(s))
- *         return " ".join(norm)             # <<<<<<<<<<<<<<
+ *         return ' '.join(norm)             # <<<<<<<<<<<<<<
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-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":65
- *         return " ".join(norm)
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":65
+ *         return ' '.join(norm)
  * 
  *     def arity(self):             # <<<<<<<<<<<<<<
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":66
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":66
  * 
  *     def arity(self):
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   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":68
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":68
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  * 
  *     def getvarpos(self, i):             # <<<<<<<<<<<<<<
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":69
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":69
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-  __pyx_t_1 = PyObject_RichCompare(__pyx_int_0, __pyx_v_i, Py_LE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_GOTREF(__pyx_t_1);
+  __pyx_t_1 = PyObject_RichCompare(__pyx_int_0, __pyx_v_i, Py_LE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    __pyx_t_1 = PyObject_RichCompare(__pyx_v_i, __pyx_t_2, Py_LT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-    __Pyx_GOTREF(__pyx_t_1);
+    __pyx_t_1 = PyObject_RichCompare(__pyx_v_i, __pyx_t_2, Py_LT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":70
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":70
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@@ -23314,7 +25329,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_12getvarpos(struct __pyx_obj_3_sa_Phrase
   }
   /*else*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":72
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":72
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  *         else:
  *             raise IndexError             # <<<<<<<<<<<<<<
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-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":74
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":74
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  *     def getvar(self, i):             # <<<<<<<<<<<<<<
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":75
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":75
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  *     def getvar(self, i):
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-  __pyx_t_1 = PyObject_RichCompare(__pyx_int_0, __pyx_v_i, Py_LE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_GOTREF(__pyx_t_1);
+  __pyx_t_1 = PyObject_RichCompare(__pyx_int_0, __pyx_v_i, Py_LE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    __pyx_t_1 = PyObject_RichCompare(__pyx_v_i, __pyx_t_2, Py_LT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-    __Pyx_GOTREF(__pyx_t_1);
+    __pyx_t_1 = PyObject_RichCompare(__pyx_v_i, __pyx_t_2, Py_LT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":76
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":76
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   }
   /*else*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":78
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":78
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  *             raise IndexError             # <<<<<<<<<<<<<<
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":80
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":80
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":81
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":81
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  *     cdef int chunkpos(self, int k):
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":82
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":82
  *     cdef int chunkpos(self, int k):
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   /*else*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":84
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":84
  *             return 0
  *         else:
  *             return self.varpos[k-1]+1             # <<<<<<<<<<<<<<
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":86
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":86
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  *     cdef int chunklen(self, int k):             # <<<<<<<<<<<<<<
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":87
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":87
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  *     cdef int chunklen(self, int k):
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   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":88
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":88
  *     cdef int chunklen(self, int k):
  *         if self.n_vars == 0:
  *             return self.n             # <<<<<<<<<<<<<<
@@ -23525,7 +25538,7 @@ int __pyx_f_3_sa_6Phrase_chunklen(struct __pyx_obj_3_sa_Phrase *__pyx_v_self, in
     goto __pyx_L3;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":89
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":89
  *         if self.n_vars == 0:
  *             return self.n
  *         elif k == 0:             # <<<<<<<<<<<<<<
@@ -23535,7 +25548,7 @@ int __pyx_f_3_sa_6Phrase_chunklen(struct __pyx_obj_3_sa_Phrase *__pyx_v_self, in
   __pyx_t_1 = (__pyx_v_k == 0);
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":90
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":90
  *             return self.n
  *         elif k == 0:
  *             return self.varpos[0]             # <<<<<<<<<<<<<<
@@ -23547,7 +25560,7 @@ int __pyx_f_3_sa_6Phrase_chunklen(struct __pyx_obj_3_sa_Phrase *__pyx_v_self, in
     goto __pyx_L3;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":91
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":91
  *         elif k == 0:
  *             return self.varpos[0]
  *         elif k == self.n_vars:             # <<<<<<<<<<<<<<
@@ -23557,7 +25570,7 @@ int __pyx_f_3_sa_6Phrase_chunklen(struct __pyx_obj_3_sa_Phrase *__pyx_v_self, in
   __pyx_t_1 = (__pyx_v_k == __pyx_v_self->n_vars);
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":92
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":92
  *             return self.varpos[0]
  *         elif k == self.n_vars:
  *             return self.n-self.varpos[k-1]-1             # <<<<<<<<<<<<<<
@@ -23570,7 +25583,7 @@ int __pyx_f_3_sa_6Phrase_chunklen(struct __pyx_obj_3_sa_Phrase *__pyx_v_self, in
   }
   /*else*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":94
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":94
  *             return self.n-self.varpos[k-1]-1
  *         else:
  *             return self.varpos[k]-self.varpos[k-1]-1             # <<<<<<<<<<<<<<
@@ -23599,7 +25612,7 @@ static PyObject *__pyx_pw_3_sa_6Phrase_17clen(PyObject *__pyx_v_self, PyObject *
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":96
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":96
  *             return self.varpos[k]-self.varpos[k-1]-1
  * 
  *     def clen(self, k):             # <<<<<<<<<<<<<<
@@ -23617,7 +25630,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_16clen(struct __pyx_obj_3_sa_Phrase *__py
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("clen", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":97
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":97
  * 
  *     def clen(self, k):
  *          return self.chunklen(k)             # <<<<<<<<<<<<<<
@@ -23655,7 +25668,7 @@ static PyObject *__pyx_pw_3_sa_6Phrase_19getchunk(PyObject *__pyx_v_self, PyObje
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":99
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":99
  *          return self.chunklen(k)
  * 
  *     def getchunk(self, ci):             # <<<<<<<<<<<<<<
@@ -23678,7 +25691,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_18getchunk(struct __pyx_obj_3_sa_Phrase *
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("getchunk", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":101
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":101
  *     def getchunk(self, ci):
  *         cdef int start, stop
  *         start = self.chunkpos(ci)             # <<<<<<<<<<<<<<
@@ -23688,7 +25701,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_18getchunk(struct __pyx_obj_3_sa_Phrase *
   __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_ci); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 101; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_start = ((struct __pyx_vtabstruct_3_sa_Phrase *)__pyx_v_self->__pyx_vtab)->chunkpos(__pyx_v_self, __pyx_t_1);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":102
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":102
  *         cdef int start, stop
  *         start = self.chunkpos(ci)
  *         stop = start+self.chunklen(ci)             # <<<<<<<<<<<<<<
@@ -23698,7 +25711,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_18getchunk(struct __pyx_obj_3_sa_Phrase *
   __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_ci); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 102; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_stop = (__pyx_v_start + ((struct __pyx_vtabstruct_3_sa_Phrase *)__pyx_v_self->__pyx_vtab)->chunklen(__pyx_v_self, __pyx_t_1));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":103
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":103
  *         start = self.chunkpos(ci)
  *         stop = start+self.chunklen(ci)
  *         chunk = []             # <<<<<<<<<<<<<<
@@ -23710,7 +25723,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_18getchunk(struct __pyx_obj_3_sa_Phrase *
   __pyx_v_chunk = __pyx_t_2;
   __pyx_t_2 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":104
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":104
  *         stop = start+self.chunklen(ci)
  *         chunk = []
  *         for i from start <= i < stop:             # <<<<<<<<<<<<<<
@@ -23720,7 +25733,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_18getchunk(struct __pyx_obj_3_sa_Phrase *
   __pyx_t_1 = __pyx_v_stop;
   for (__pyx_v_i = __pyx_v_start; __pyx_v_i < __pyx_t_1; __pyx_v_i++) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":105
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":105
  *         chunk = []
  *         for i from start <= i < stop:
  *             chunk.append(self.syms[i])             # <<<<<<<<<<<<<<
@@ -23733,7 +25746,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_18getchunk(struct __pyx_obj_3_sa_Phrase *
     __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":106
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":106
  *         for i from start <= i < stop:
  *             chunk.append(self.syms[i])
  *         return chunk             # <<<<<<<<<<<<<<
@@ -23771,7 +25784,7 @@ static int __pyx_pw_3_sa_6Phrase_21__cmp__(PyObject *__pyx_v_self, PyObject *__p
 }
 #endif /*!(#if PY_MAJOR_VERSION < 3)*/
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":108
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":108
  *         return chunk
  * 
  *     def __cmp__(self, other):             # <<<<<<<<<<<<<<
@@ -23794,7 +25807,7 @@ static int __pyx_pf_3_sa_6Phrase_20__cmp__(struct __pyx_obj_3_sa_Phrase *__pyx_v
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__cmp__", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":111
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":111
  *         cdef Phrase otherp
  *         cdef int i
  *         otherp = other             # <<<<<<<<<<<<<<
@@ -23805,7 +25818,7 @@ static int __pyx_pf_3_sa_6Phrase_20__cmp__(struct __pyx_obj_3_sa_Phrase *__pyx_v
   __Pyx_INCREF(__pyx_v_other);
   __pyx_v_otherp = ((struct __pyx_obj_3_sa_Phrase *)__pyx_v_other);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":112
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":112
  *         cdef int i
  *         otherp = other
  *         for i from 0 <= i < min(self.n, otherp.n):             # <<<<<<<<<<<<<<
@@ -23822,7 +25835,7 @@ static int __pyx_pf_3_sa_6Phrase_20__cmp__(struct __pyx_obj_3_sa_Phrase *__pyx_v
   __pyx_t_1 = __pyx_t_3;
   for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_1; __pyx_v_i++) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":113
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":113
  *         otherp = other
  *         for i from 0 <= i < min(self.n, otherp.n):
  *             if self.syms[i] < otherp.syms[i]:             # <<<<<<<<<<<<<<
@@ -23832,7 +25845,7 @@ static int __pyx_pf_3_sa_6Phrase_20__cmp__(struct __pyx_obj_3_sa_Phrase *__pyx_v
     __pyx_t_4 = ((__pyx_v_self->syms[__pyx_v_i]) < (__pyx_v_otherp->syms[__pyx_v_i]));
     if (__pyx_t_4) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":114
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":114
  *         for i from 0 <= i < min(self.n, otherp.n):
  *             if self.syms[i] < otherp.syms[i]:
  *                 return -1             # <<<<<<<<<<<<<<
@@ -23844,7 +25857,7 @@ static int __pyx_pf_3_sa_6Phrase_20__cmp__(struct __pyx_obj_3_sa_Phrase *__pyx_v
       goto __pyx_L5;
     }
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":115
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":115
  *             if self.syms[i] < otherp.syms[i]:
  *                 return -1
  *             elif self.syms[i] > otherp.syms[i]:             # <<<<<<<<<<<<<<
@@ -23854,7 +25867,7 @@ static int __pyx_pf_3_sa_6Phrase_20__cmp__(struct __pyx_obj_3_sa_Phrase *__pyx_v
     __pyx_t_4 = ((__pyx_v_self->syms[__pyx_v_i]) > (__pyx_v_otherp->syms[__pyx_v_i]));
     if (__pyx_t_4) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":116
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":116
  *                 return -1
  *             elif self.syms[i] > otherp.syms[i]:
  *                 return 1             # <<<<<<<<<<<<<<
@@ -23868,7 +25881,7 @@ static int __pyx_pf_3_sa_6Phrase_20__cmp__(struct __pyx_obj_3_sa_Phrase *__pyx_v
     __pyx_L5:;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":117
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":117
  *             elif self.syms[i] > otherp.syms[i]:
  *                 return 1
  *         if self.n < otherp.n:             # <<<<<<<<<<<<<<
@@ -23878,7 +25891,7 @@ static int __pyx_pf_3_sa_6Phrase_20__cmp__(struct __pyx_obj_3_sa_Phrase *__pyx_v
   __pyx_t_4 = (__pyx_v_self->n < __pyx_v_otherp->n);
   if (__pyx_t_4) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":118
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":118
  *                 return 1
  *         if self.n < otherp.n:
  *             return -1             # <<<<<<<<<<<<<<
@@ -23890,7 +25903,7 @@ static int __pyx_pf_3_sa_6Phrase_20__cmp__(struct __pyx_obj_3_sa_Phrase *__pyx_v
     goto __pyx_L6;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":119
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":119
  *         if self.n < otherp.n:
  *             return -1
  *         elif self.n > otherp.n:             # <<<<<<<<<<<<<<
@@ -23900,7 +25913,7 @@ static int __pyx_pf_3_sa_6Phrase_20__cmp__(struct __pyx_obj_3_sa_Phrase *__pyx_v
   __pyx_t_4 = (__pyx_v_self->n > __pyx_v_otherp->n);
   if (__pyx_t_4) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":120
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":120
  *             return -1
  *         elif self.n > otherp.n:
  *             return 1             # <<<<<<<<<<<<<<
@@ -23913,7 +25926,7 @@ static int __pyx_pf_3_sa_6Phrase_20__cmp__(struct __pyx_obj_3_sa_Phrase *__pyx_v
   }
   /*else*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":122
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":122
  *             return 1
  *         else:
  *             return 0             # <<<<<<<<<<<<<<
@@ -23948,7 +25961,7 @@ static Py_hash_t __pyx_pw_3_sa_6Phrase_23__hash__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":124
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":124
  *             return 0
  * 
  *     def __hash__(self):             # <<<<<<<<<<<<<<
@@ -23965,7 +25978,7 @@ static Py_hash_t __pyx_pf_3_sa_6Phrase_22__hash__(struct __pyx_obj_3_sa_Phrase *
   int __pyx_t_2;
   __Pyx_RefNannySetupContext("__hash__", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":127
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":127
  *         cdef int i
  *         cdef unsigned h
  *         h = 0             # <<<<<<<<<<<<<<
@@ -23974,7 +25987,7 @@ static Py_hash_t __pyx_pf_3_sa_6Phrase_22__hash__(struct __pyx_obj_3_sa_Phrase *
  */
   __pyx_v_h = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":128
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":128
  *         cdef unsigned h
  *         h = 0
  *         for i from 0 <= i < self.n:             # <<<<<<<<<<<<<<
@@ -23984,7 +25997,7 @@ static Py_hash_t __pyx_pf_3_sa_6Phrase_22__hash__(struct __pyx_obj_3_sa_Phrase *
   __pyx_t_1 = __pyx_v_self->n;
   for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_1; __pyx_v_i++) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":129
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":129
  *         h = 0
  *         for i from 0 <= i < self.n:
  *             if self.syms[i] > 0:             # <<<<<<<<<<<<<<
@@ -23994,7 +26007,7 @@ static Py_hash_t __pyx_pf_3_sa_6Phrase_22__hash__(struct __pyx_obj_3_sa_Phrase *
     __pyx_t_2 = ((__pyx_v_self->syms[__pyx_v_i]) > 0);
     if (__pyx_t_2) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":130
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":130
  *         for i from 0 <= i < self.n:
  *             if self.syms[i] > 0:
  *                 h = (h << 1) + self.syms[i]             # <<<<<<<<<<<<<<
@@ -24006,7 +26019,7 @@ static Py_hash_t __pyx_pf_3_sa_6Phrase_22__hash__(struct __pyx_obj_3_sa_Phrase *
     }
     /*else*/ {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":132
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":132
  *                 h = (h << 1) + self.syms[i]
  *             else:
  *                 h = (h << 1) + -self.syms[i]             # <<<<<<<<<<<<<<
@@ -24018,7 +26031,7 @@ static Py_hash_t __pyx_pf_3_sa_6Phrase_22__hash__(struct __pyx_obj_3_sa_Phrase *
     __pyx_L5:;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":133
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":133
  *             else:
  *                 h = (h << 1) + -self.syms[i]
  *         return h             # <<<<<<<<<<<<<<
@@ -24046,7 +26059,7 @@ static Py_ssize_t __pyx_pw_3_sa_6Phrase_25__len__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":135
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":135
  *         return h
  * 
  *     def __len__(self):             # <<<<<<<<<<<<<<
@@ -24059,7 +26072,7 @@ static Py_ssize_t __pyx_pf_3_sa_6Phrase_24__len__(struct __pyx_obj_3_sa_Phrase *
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__len__", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":136
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":136
  * 
  *     def __len__(self):
  *         return self.n             # <<<<<<<<<<<<<<
@@ -24086,7 +26099,7 @@ static PyObject *__pyx_pw_3_sa_6Phrase_27__getitem__(PyObject *__pyx_v_self, PyO
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":138
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":138
  *         return self.n
  * 
  *     def __getitem__(self, i):             # <<<<<<<<<<<<<<
@@ -24104,7 +26117,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_26__getitem__(struct __pyx_obj_3_sa_Phras
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__getitem__", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":139
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":139
  * 
  *     def __getitem__(self, i):
  *         return self.syms[i]             # <<<<<<<<<<<<<<
@@ -24130,7 +26143,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_26__getitem__(struct __pyx_obj_3_sa_Phras
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   return __pyx_r;
 }
-static PyObject *__pyx_gb_3_sa_6Phrase_30generator1(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
+static PyObject *__pyx_gb_3_sa_6Phrase_30generator2(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
 
 /* Python wrapper */
 static PyObject *__pyx_pw_3_sa_6Phrase_29__iter__(PyObject *__pyx_v_self); /*proto*/
@@ -24143,7 +26156,7 @@ static PyObject *__pyx_pw_3_sa_6Phrase_29__iter__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":141
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":141
  *         return self.syms[i]
  * 
  *     def __iter__(self):             # <<<<<<<<<<<<<<
@@ -24152,14 +26165,14 @@ static PyObject *__pyx_pw_3_sa_6Phrase_29__iter__(PyObject *__pyx_v_self) {
  */
 
 static PyObject *__pyx_pf_3_sa_6Phrase_28__iter__(struct __pyx_obj_3_sa_Phrase *__pyx_v_self) {
-  struct __pyx_obj_3_sa___pyx_scope_struct_3___iter__ *__pyx_cur_scope;
+  struct __pyx_obj_3_sa___pyx_scope_struct_11___iter__ *__pyx_cur_scope;
   PyObject *__pyx_r = NULL;
   __Pyx_RefNannyDeclarations
   int __pyx_lineno = 0;
   const char *__pyx_filename = NULL;
   int __pyx_clineno = 0;
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+  __pyx_cur_scope = (struct __pyx_obj_3_sa___pyx_scope_struct_11___iter__ *)__pyx_ptype_3_sa___pyx_scope_struct_11___iter__->tp_new(__pyx_ptype_3_sa___pyx_scope_struct_11___iter__, __pyx_empty_tuple, NULL);
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+    __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_3_sa_6Phrase_30generator2, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-static PyObject *__pyx_gb_3_sa_6Phrase_30generator1(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value) /* generator body */
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":143
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":143
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":144
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":144
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   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":146
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":146
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":148
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":148
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":149
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":149
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":150
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":150
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@@ -24368,7 +26381,7 @@ static PyObject *__pyx_pf_3_sa_6Phrase_31subst(struct __pyx_obj_3_sa_Phrase *__p
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":152
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":152
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  *             else:
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":153
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":153
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   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":156
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":156
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":157
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":157
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-      __pyx_t_5 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_5); __pyx_t_3++;
+      __pyx_t_5 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_5); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_5 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_5); __pyx_t_3++;
+      __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_5); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_5 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -24548,12 +26561,12 @@ static int __pyx_pw_3_sa_4Rule_1__cinit__(PyObject *__pyx_v_self, PyObject *__py
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":162
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":161
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- *         cdef int i, n
- *         cdef char *rest
+ *     def __cinit__(self, int lhs, Phrase f, Phrase e, scores=None, word_alignments=None):             # <<<<<<<<<<<<<<
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+ *         self.lhs = lhs
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     values[3] = ((PyObject *)Py_None);
     values[4] = ((PyObject *)Py_None);
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":161
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 static int __pyx_pf_3_sa_4Rule___cinit__(struct __pyx_obj_3_sa_Rule *__pyx_v_self, int __pyx_v_lhs, struct __pyx_obj_3_sa_Phrase *__pyx_v_f, struct __pyx_obj_3_sa_Phrase *__pyx_v_e, PyObject *__pyx_v_scores, PyObject *__pyx_v_word_alignments) {
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- *             raise Exception('Invalid LHS symbol: %d' % lhs)
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":162
  * 
+ *     def __cinit__(self, int lhs, Phrase f, Phrase e, scores=None, word_alignments=None):
+ *         if not sym_isvar(lhs): raise Exception('Invalid LHS symbol: %d' % lhs)             # <<<<<<<<<<<<<<
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+ *         self.f = f
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":167
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+    {__pyx_filename = __pyx_f[7]; __pyx_lineno = 162; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":169
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- * 
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":170
- * 
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":164
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  *         self.f = f             # <<<<<<<<<<<<<<
  *         self.e = e
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+ *         self.word_alignments = word_alignments
  */
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   __pyx_v_self->f = __pyx_v_f;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":171
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":165
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  *         self.f = f
  *         self.e = e             # <<<<<<<<<<<<<<
- * 
  *         self.word_alignments = word_alignments
+ *         self.scores = scores
  */
   __Pyx_INCREF(((PyObject *)__pyx_v_e));
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@@ -24730,12 +26722,12 @@ static int __pyx_pf_3_sa_4Rule___cinit__(struct __pyx_obj_3_sa_Rule *__pyx_v_sel
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   __pyx_v_self->e = __pyx_v_e;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":173
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":166
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  *         self.e = e
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  *         self.word_alignments = word_alignments             # <<<<<<<<<<<<<<
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+ *         self.scores = scores
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":174
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":175
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rule.pxi":167
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rule.pxi":176
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-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":38
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":38
  *     return edge
  * 
  * cdef free_trie_node(_Trie_Node* node):             # <<<<<<<<<<<<<<
@@ -26160,7 +27794,7 @@ static PyObject *__pyx_f_3_sa_free_trie_node(struct __pyx_t_3_sa__Trie_Node *__p
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("free_trie_node", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":39
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":39
  * 
  * cdef free_trie_node(_Trie_Node* node):
  *     if node != NULL:             # <<<<<<<<<<<<<<
@@ -26170,18 +27804,18 @@ static PyObject *__pyx_f_3_sa_free_trie_node(struct __pyx_t_3_sa__Trie_Node *__p
   __pyx_t_1 = (__pyx_v_node != NULL);
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":40
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":40
  * cdef free_trie_node(_Trie_Node* node):
  *     if node != NULL:
  *         free_trie_edge(node.root)             # <<<<<<<<<<<<<<
  *         free(node.arr)
  * 
  */
-    __pyx_t_2 = __pyx_f_3_sa_free_trie_edge(__pyx_v_node->root); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 40; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = __pyx_f_3_sa_free_trie_edge(__pyx_v_node->root); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 40; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_2);
     __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":41
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":41
  *     if node != NULL:
  *         free_trie_edge(node.root)
  *         free(node.arr)             # <<<<<<<<<<<<<<
@@ -26205,7 +27839,7 @@ static PyObject *__pyx_f_3_sa_free_trie_node(struct __pyx_t_3_sa__Trie_Node *__p
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":43
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":43
  *         free(node.arr)
  * 
  * cdef free_trie_edge(_Trie_Edge* edge):             # <<<<<<<<<<<<<<
@@ -26223,7 +27857,7 @@ static PyObject *__pyx_f_3_sa_free_trie_edge(struct __pyx_t_3_sa__Trie_Edge *__p
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("free_trie_edge", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":44
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":44
  * 
  * cdef free_trie_edge(_Trie_Edge* edge):
  *     if edge != NULL:             # <<<<<<<<<<<<<<
@@ -26233,36 +27867,36 @@ static PyObject *__pyx_f_3_sa_free_trie_edge(struct __pyx_t_3_sa__Trie_Edge *__p
   __pyx_t_1 = (__pyx_v_edge != NULL);
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":45
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":45
  * cdef free_trie_edge(_Trie_Edge* edge):
  *     if edge != NULL:
  *         free_trie_node(edge.node)             # <<<<<<<<<<<<<<
  *         free_trie_edge(edge.bigger)
  *         free_trie_edge(edge.smaller)
  */
-    __pyx_t_2 = __pyx_f_3_sa_free_trie_node(__pyx_v_edge->node); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = __pyx_f_3_sa_free_trie_node(__pyx_v_edge->node); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_2);
     __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":46
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":46
  *     if edge != NULL:
  *         free_trie_node(edge.node)
  *         free_trie_edge(edge.bigger)             # <<<<<<<<<<<<<<
  *         free_trie_edge(edge.smaller)
  * 
  */
-    __pyx_t_2 = __pyx_f_3_sa_free_trie_edge(__pyx_v_edge->bigger); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = __pyx_f_3_sa_free_trie_edge(__pyx_v_edge->bigger); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_2);
     __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":47
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":47
  *         free_trie_node(edge.node)
  *         free_trie_edge(edge.bigger)
  *         free_trie_edge(edge.smaller)             # <<<<<<<<<<<<<<
  * 
  * cdef _Trie_Node* trie_find(_Trie_Node* node, int val):
  */
-    __pyx_t_2 = __pyx_f_3_sa_free_trie_edge(__pyx_v_edge->smaller); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = __pyx_f_3_sa_free_trie_edge(__pyx_v_edge->smaller); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_2);
     __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
     goto __pyx_L3;
@@ -26281,7 +27915,7 @@ static PyObject *__pyx_f_3_sa_free_trie_edge(struct __pyx_t_3_sa__Trie_Edge *__p
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":49
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":49
  *         free_trie_edge(edge.smaller)
  * 
  * cdef _Trie_Node* trie_find(_Trie_Node* node, int val):             # <<<<<<<<<<<<<<
@@ -26298,7 +27932,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_find(struct __pyx_t_3_s
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   __Pyx_RefNannySetupContext("trie_find", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":51
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":51
  * cdef _Trie_Node* trie_find(_Trie_Node* node, int val):
  *     cdef _Trie_Edge* cur
  *     cur = node.root             # <<<<<<<<<<<<<<
@@ -26307,7 +27941,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_find(struct __pyx_t_3_s
  */
   __pyx_v_cur = __pyx_v_node->root;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":52
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":52
  *     cdef _Trie_Edge* cur
  *     cur = node.root
  *     while cur != NULL and cur.val != val:             # <<<<<<<<<<<<<<
@@ -26324,7 +27958,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_find(struct __pyx_t_3_s
     }
     if (!__pyx_t_3) break;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":53
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":53
  *     cur = node.root
  *     while cur != NULL and cur.val != val:
  *         if val > cur.val:             # <<<<<<<<<<<<<<
@@ -26334,7 +27968,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_find(struct __pyx_t_3_s
     __pyx_t_3 = (__pyx_v_val > __pyx_v_cur->val);
     if (__pyx_t_3) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":54
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":54
  *     while cur != NULL and cur.val != val:
  *         if val > cur.val:
  *             cur = cur.bigger             # <<<<<<<<<<<<<<
@@ -26345,7 +27979,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_find(struct __pyx_t_3_s
       goto __pyx_L5;
     }
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":55
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":55
  *         if val > cur.val:
  *             cur = cur.bigger
  *         elif val < cur.val:             # <<<<<<<<<<<<<<
@@ -26355,7 +27989,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_find(struct __pyx_t_3_s
     __pyx_t_3 = (__pyx_v_val < __pyx_v_cur->val);
     if (__pyx_t_3) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":56
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":56
  *             cur = cur.bigger
  *         elif val < cur.val:
  *             cur = cur.smaller             # <<<<<<<<<<<<<<
@@ -26368,7 +28002,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_find(struct __pyx_t_3_s
     __pyx_L5:;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":57
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":57
  *         elif val < cur.val:
  *             cur = cur.smaller
  *     if cur == NULL:             # <<<<<<<<<<<<<<
@@ -26378,7 +28012,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_find(struct __pyx_t_3_s
   __pyx_t_3 = (__pyx_v_cur == NULL);
   if (__pyx_t_3) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":58
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":58
  *             cur = cur.smaller
  *     if cur == NULL:
  *         return NULL             # <<<<<<<<<<<<<<
@@ -26391,7 +28025,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_find(struct __pyx_t_3_s
   }
   /*else*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":60
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":60
  *         return NULL
  *     else:
  *         return cur.node             # <<<<<<<<<<<<<<
@@ -26409,7 +28043,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_find(struct __pyx_t_3_s
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":62
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":62
  *         return cur.node
  * 
  * cdef trie_node_data_append(_Trie_Node* node, int val):             # <<<<<<<<<<<<<<
@@ -26423,7 +28057,7 @@ static PyObject *__pyx_f_3_sa_trie_node_data_append(struct __pyx_t_3_sa__Trie_No
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("trie_node_data_append", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":64
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":64
  * cdef trie_node_data_append(_Trie_Node* node, int val):
  *     cdef int new_len
  *     new_len = node.arr_len + 1             # <<<<<<<<<<<<<<
@@ -26432,7 +28066,7 @@ static PyObject *__pyx_f_3_sa_trie_node_data_append(struct __pyx_t_3_sa__Trie_No
  */
   __pyx_v_new_len = (__pyx_v_node->arr_len + 1);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":65
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":65
  *     cdef int new_len
  *     new_len = node.arr_len + 1
  *     node.arr = <int*> realloc(node.arr, new_len*sizeof(int))             # <<<<<<<<<<<<<<
@@ -26441,7 +28075,7 @@ static PyObject *__pyx_f_3_sa_trie_node_data_append(struct __pyx_t_3_sa__Trie_No
  */
   __pyx_v_node->arr = ((int *)realloc(__pyx_v_node->arr, (__pyx_v_new_len * (sizeof(int)))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":66
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":66
  *     new_len = node.arr_len + 1
  *     node.arr = <int*> realloc(node.arr, new_len*sizeof(int))
  *     node.arr[node.arr_len] = val             # <<<<<<<<<<<<<<
@@ -26450,7 +28084,7 @@ static PyObject *__pyx_f_3_sa_trie_node_data_append(struct __pyx_t_3_sa__Trie_No
  */
   (__pyx_v_node->arr[__pyx_v_node->arr_len]) = __pyx_v_val;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":67
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":67
  *     node.arr = <int*> realloc(node.arr, new_len*sizeof(int))
  *     node.arr[node.arr_len] = val
  *     node.arr_len = new_len             # <<<<<<<<<<<<<<
@@ -26465,7 +28099,7 @@ static PyObject *__pyx_f_3_sa_trie_node_data_append(struct __pyx_t_3_sa__Trie_No
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":69
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":69
  *     node.arr_len = new_len
  * 
  * cdef trie_node_data_extend(_Trie_Node* node, int* vals, int num_vals):             # <<<<<<<<<<<<<<
@@ -26479,7 +28113,7 @@ static PyObject *__pyx_f_3_sa_trie_node_data_extend(struct __pyx_t_3_sa__Trie_No
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("trie_node_data_extend", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":71
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":71
  * cdef trie_node_data_extend(_Trie_Node* node, int* vals, int num_vals):
  *     cdef int new_len
  *     new_len = node.arr_len + num_vals             # <<<<<<<<<<<<<<
@@ -26488,7 +28122,7 @@ static PyObject *__pyx_f_3_sa_trie_node_data_extend(struct __pyx_t_3_sa__Trie_No
  */
   __pyx_v_new_len = (__pyx_v_node->arr_len + __pyx_v_num_vals);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":72
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":72
  *     cdef int new_len
  *     new_len = node.arr_len + num_vals
  *     node.arr = <int*> realloc(node.arr, new_len*sizeof(int))             # <<<<<<<<<<<<<<
@@ -26497,7 +28131,7 @@ static PyObject *__pyx_f_3_sa_trie_node_data_extend(struct __pyx_t_3_sa__Trie_No
  */
   __pyx_v_node->arr = ((int *)realloc(__pyx_v_node->arr, (__pyx_v_new_len * (sizeof(int)))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":73
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":73
  *     new_len = node.arr_len + num_vals
  *     node.arr = <int*> realloc(node.arr, new_len*sizeof(int))
  *     memcpy(node.arr + node.arr_len, vals, num_vals*sizeof(int))             # <<<<<<<<<<<<<<
@@ -26506,7 +28140,7 @@ static PyObject *__pyx_f_3_sa_trie_node_data_extend(struct __pyx_t_3_sa__Trie_No
  */
   memcpy((__pyx_v_node->arr + __pyx_v_node->arr_len), __pyx_v_vals, (__pyx_v_num_vals * (sizeof(int))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":74
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":74
  *     node.arr = <int*> realloc(node.arr, new_len*sizeof(int))
  *     memcpy(node.arr + node.arr_len, vals, num_vals*sizeof(int))
  *     node.arr_len = new_len             # <<<<<<<<<<<<<<
@@ -26521,7 +28155,7 @@ static PyObject *__pyx_f_3_sa_trie_node_data_extend(struct __pyx_t_3_sa__Trie_No
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":77
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":77
  * 
  * 
  * cdef _Trie_Node* trie_insert(_Trie_Node* node, int val):             # <<<<<<<<<<<<<<
@@ -26538,7 +28172,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_insert(struct __pyx_t_3
   int __pyx_t_3;
   __Pyx_RefNannySetupContext("trie_insert", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":79
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":79
  * cdef _Trie_Node* trie_insert(_Trie_Node* node, int val):
  *     cdef _Trie_Edge** cur
  *     cur = &node.root             # <<<<<<<<<<<<<<
@@ -26547,7 +28181,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_insert(struct __pyx_t_3
  */
   __pyx_v_cur = (&__pyx_v_node->root);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":80
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":80
  *     cdef _Trie_Edge** cur
  *     cur = &node.root
  *     while cur[0] != NULL and cur[0].val != val:             # <<<<<<<<<<<<<<
@@ -26564,7 +28198,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_insert(struct __pyx_t_3
     }
     if (!__pyx_t_3) break;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":81
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":81
  *     cur = &node.root
  *     while cur[0] != NULL and cur[0].val != val:
  *         if val > cur[0].val:             # <<<<<<<<<<<<<<
@@ -26574,7 +28208,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_insert(struct __pyx_t_3
     __pyx_t_3 = (__pyx_v_val > (__pyx_v_cur[0])->val);
     if (__pyx_t_3) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":82
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":82
  *     while cur[0] != NULL and cur[0].val != val:
  *         if val > cur[0].val:
  *             cur = &cur[0].bigger             # <<<<<<<<<<<<<<
@@ -26585,7 +28219,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_insert(struct __pyx_t_3
       goto __pyx_L5;
     }
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":83
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":83
  *         if val > cur[0].val:
  *             cur = &cur[0].bigger
  *         elif val < cur[0].val:             # <<<<<<<<<<<<<<
@@ -26595,7 +28229,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_insert(struct __pyx_t_3
     __pyx_t_3 = (__pyx_v_val < (__pyx_v_cur[0])->val);
     if (__pyx_t_3) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":84
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":84
  *             cur = &cur[0].bigger
  *         elif val < cur[0].val:
  *             cur = &cur[0].smaller             # <<<<<<<<<<<<<<
@@ -26608,7 +28242,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_insert(struct __pyx_t_3
     __pyx_L5:;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":85
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":85
  *         elif val < cur[0].val:
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  *     if cur[0] == NULL:             # <<<<<<<<<<<<<<
@@ -26618,7 +28252,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_insert(struct __pyx_t_3
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":86
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":86
  *             cur = &cur[0].smaller
  *     if cur[0] == NULL:
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@@ -26630,7 +28264,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_insert(struct __pyx_t_3
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":87
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":87
  *     if cur[0] == NULL:
  *         cur[0] = new_trie_edge(val)
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@@ -26646,7 +28280,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_trie_insert(struct __pyx_t_3
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":89
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":89
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":92
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":92
  *     cdef IntList arr
  * 
  *     if include_zeros or node.arr_len > 0:             # <<<<<<<<<<<<<<
@@ -26681,19 +28315,19 @@ static PyObject *__pyx_f_3_sa_trie_node_to_map(struct __pyx_t_3_sa__Trie_Node *_
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":93
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":93
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":94
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":94
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":95
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":95
  *         arr = IntList()
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  *         arr.arr = <int*> malloc(node.arr_len * sizeof(int))             # <<<<<<<<<<<<<<
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":96
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":96
  *         free(arr.arr)
  *         arr.arr = <int*> malloc(node.arr_len * sizeof(int))
  *         memcpy(arr.arr, node.arr, node.arr_len * sizeof(int))             # <<<<<<<<<<<<<<
@@ -26720,7 +28354,7 @@ static PyObject *__pyx_f_3_sa_trie_node_to_map(struct __pyx_t_3_sa__Trie_Node *_
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     memcpy(__pyx_v_arr->arr, __pyx_v_node->arr, (__pyx_v_node->arr_len * (sizeof(int))));
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":97
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":97
  *         arr.arr = <int*> malloc(node.arr_len * sizeof(int))
  *         memcpy(arr.arr, node.arr, node.arr_len * sizeof(int))
  *         arr.len = node.arr_len             # <<<<<<<<<<<<<<
@@ -26729,7 +28363,7 @@ static PyObject *__pyx_f_3_sa_trie_node_to_map(struct __pyx_t_3_sa__Trie_Node *_
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     __pyx_v_arr->len = __pyx_v_node->arr_len;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":98
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":98
  *         memcpy(arr.arr, node.arr, node.arr_len * sizeof(int))
  *         arr.len = node.arr_len
  *         arr.size = node.arr_len             # <<<<<<<<<<<<<<
@@ -26738,26 +28372,26 @@ static PyObject *__pyx_f_3_sa_trie_node_to_map(struct __pyx_t_3_sa__Trie_Node *_
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     __pyx_v_arr->size = __pyx_v_node->arr_len;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":99
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":99
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  *         arr.size = node.arr_len
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+    if (PyObject_SetItem(__pyx_v_result, __pyx_v_prefix, ((PyObject *)__pyx_v_arr)) < 0) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 99; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":100
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":100
  *         arr.size = node.arr_len
  *         result[prefix] = arr
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  * cdef trie_edge_to_map(_Trie_Edge* edge, result, prefix, int include_zeros):
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-  __pyx_t_3 = __pyx_f_3_sa_trie_edge_to_map(__pyx_v_node->root, __pyx_v_result, __pyx_v_prefix, __pyx_v_include_zeros); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 100; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = __pyx_f_3_sa_trie_edge_to_map(__pyx_v_node->root, __pyx_v_result, __pyx_v_prefix, __pyx_v_include_zeros); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 100; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -26774,7 +28408,7 @@ static PyObject *__pyx_f_3_sa_trie_node_to_map(struct __pyx_t_3_sa__Trie_Node *_
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":102
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":102
  *     trie_edge_to_map(node.root, result, prefix, include_zeros)
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  * cdef trie_edge_to_map(_Trie_Edge* edge, result, prefix, int include_zeros):             # <<<<<<<<<<<<<<
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":103
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":103
  * 
  * cdef trie_edge_to_map(_Trie_Edge* edge, result, prefix, int include_zeros):
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":104
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":104
  * cdef trie_edge_to_map(_Trie_Edge* edge, result, prefix, int include_zeros):
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+    __pyx_t_2 = __pyx_f_3_sa_trie_edge_to_map(__pyx_v_edge->smaller, __pyx_v_result, __pyx_v_prefix, __pyx_v_include_zeros); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 104; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":105
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":105
  *     if edge != NULL:
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-    __pyx_t_2 = __pyx_f_3_sa_trie_edge_to_map(__pyx_v_edge->bigger, __pyx_v_result, __pyx_v_prefix, __pyx_v_include_zeros); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 105; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = __pyx_f_3_sa_trie_edge_to_map(__pyx_v_edge->bigger, __pyx_v_result, __pyx_v_prefix, __pyx_v_include_zeros); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 105; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":106
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":106
  *         trie_edge_to_map(edge.smaller, result, prefix, include_zeros)
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+    __pyx_t_2 = PyNumber_Add(__pyx_v_prefix, ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 106; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":107
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":107
  *         trie_edge_to_map(edge.bigger, result, prefix, include_zeros)
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+    __pyx_t_2 = __pyx_f_3_sa_trie_node_to_map(__pyx_v_edge->node, __pyx_v_result, __pyx_v_prefix, __pyx_v_include_zeros); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 114; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+    __pyx_v_alphabet_size = __Pyx_PyInt_AsInt(values[0]); if (unlikely((__pyx_v_alphabet_size == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 114; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+  __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[11]; __pyx_lineno = 114; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":114
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":114
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":115
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":115
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  *     def __cinit__(self, int alphabet_size):
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   __pyx_v_self->V = __pyx_v_alphabet_size;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":116
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":116
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":117
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":117
  *         self.V = alphabet_size
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-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":120
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":120
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  * 
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":122
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":122
  *     def __dealloc__(self):
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  *         for i from 0 <= i < self.V:             # <<<<<<<<<<<<<<
@@ -27005,7 +28639,7 @@ static void __pyx_pf_3_sa_7TrieMap_2__dealloc__(struct __pyx_obj_3_sa_TrieMap *_
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   for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_1; __pyx_v_i++) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":123
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":123
  *         cdef int i
  *         for i from 0 <= i < self.V:
  *             if self.root[i] != NULL:             # <<<<<<<<<<<<<<
@@ -27015,14 +28649,14 @@ static void __pyx_pf_3_sa_7TrieMap_2__dealloc__(struct __pyx_obj_3_sa_TrieMap *_
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     if (__pyx_t_2) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":124
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":124
  *         for i from 0 <= i < self.V:
  *             if self.root[i] != NULL:
  *                 free_trie_node(self.root[i])             # <<<<<<<<<<<<<<
  *         free(self.root)
  * 
  */
-      __pyx_t_3 = __pyx_f_3_sa_free_trie_node((__pyx_v_self->root[__pyx_v_i])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_3 = __pyx_f_3_sa_free_trie_node((__pyx_v_self->root[__pyx_v_i])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -27030,7 +28664,7 @@ static void __pyx_pf_3_sa_7TrieMap_2__dealloc__(struct __pyx_obj_3_sa_TrieMap *_
     __pyx_L5:;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":125
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":125
  *             if self.root[i] != NULL:
  *                 free_trie_node(self.root[i])
  *         free(self.root)             # <<<<<<<<<<<<<<
@@ -27058,7 +28692,7 @@ static PyObject *__pyx_pw_3_sa_7TrieMap_5insert(PyObject *__pyx_v_self, PyObject
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":128
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":128
  * 
  * 
  *     def insert(self, pattern):             # <<<<<<<<<<<<<<
@@ -27081,17 +28715,17 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_4insert(struct __pyx_obj_3_sa_TrieMap *_
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   __Pyx_RefNannySetupContext("insert", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":131
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":131
  *         cdef int* p
  *         cdef int i, l
  *         l = len(pattern)             # <<<<<<<<<<<<<<
  *         p = <int*> malloc(l*sizeof(int))
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-  __pyx_t_1 = PyObject_Length(__pyx_v_pattern); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_Length(__pyx_v_pattern); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_l = __pyx_t_1;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":132
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":132
  *         cdef int i, l
  *         l = len(pattern)
  *         p = <int*> malloc(l*sizeof(int))             # <<<<<<<<<<<<<<
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   __pyx_v_p = ((int *)malloc((__pyx_v_l * (sizeof(int)))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":133
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":133
  *         l = len(pattern)
  *         p = <int*> malloc(l*sizeof(int))
  *         for i from 0 <= i < l:             # <<<<<<<<<<<<<<
@@ -27110,21 +28744,21 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_4insert(struct __pyx_obj_3_sa_TrieMap *_
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":134
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":134
  *         p = <int*> malloc(l*sizeof(int))
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-    __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_pattern, __pyx_v_i, sizeof(int), PyInt_FromLong); if (!__pyx_t_3) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 134; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_pattern, __pyx_v_i, sizeof(int), PyInt_FromLong); if (!__pyx_t_3) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 134; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_4 = __Pyx_PyInt_AsInt(__pyx_t_3); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 134; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":135
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":135
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  *             p[i] = pattern[i]
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@@ -27133,7 +28767,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_4insert(struct __pyx_obj_3_sa_TrieMap *_
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":136
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":136
  *             p[i] = pattern[i]
  *         self._insert(p,l)
  *         free(p)             # <<<<<<<<<<<<<<
@@ -27154,7 +28788,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_4insert(struct __pyx_obj_3_sa_TrieMap *_
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":139
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":139
  * 
  * 
  *     cdef _Trie_Node* _insert(self, int* pattern, int pattern_len):             # <<<<<<<<<<<<<<
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":142
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":142
  *         cdef int i
  *         cdef _Trie_Node* node
  *         if self.root[pattern[0]] == NULL:             # <<<<<<<<<<<<<<
@@ -27181,7 +28815,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_7TrieMap__insert(struct __py
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   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":143
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":143
  *         cdef _Trie_Node* node
  *         if self.root[pattern[0]] == NULL:
  *             self.root[pattern[0]] = new_trie_node()             # <<<<<<<<<<<<<<
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   }
   __pyx_L3:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":144
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":144
  *         if self.root[pattern[0]] == NULL:
  *             self.root[pattern[0]] = new_trie_node()
  *         node = self.root[pattern[0]]             # <<<<<<<<<<<<<<
@@ -27202,7 +28836,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_7TrieMap__insert(struct __py
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   __pyx_v_node = (__pyx_v_self->root[(__pyx_v_pattern[0])]);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":145
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":145
  *             self.root[pattern[0]] = new_trie_node()
  *         node = self.root[pattern[0]]
  *         for i from 1 <= i < pattern_len:             # <<<<<<<<<<<<<<
@@ -27212,7 +28846,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_7TrieMap__insert(struct __py
   __pyx_t_2 = __pyx_v_pattern_len;
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":146
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":146
  *         node = self.root[pattern[0]]
  *         for i from 1 <= i < pattern_len:
  *             node = trie_insert(node, pattern[i])             # <<<<<<<<<<<<<<
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":147
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":147
  *         for i from 1 <= i < pattern_len:
  *             node = trie_insert(node, pattern[i])
  *         return node             # <<<<<<<<<<<<<<
@@ -27249,7 +28883,7 @@ static PyObject *__pyx_pw_3_sa_7TrieMap_7contains(PyObject *__pyx_v_self, PyObje
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":149
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":149
  *         return node
  * 
  *     def contains(self, pattern):             # <<<<<<<<<<<<<<
@@ -27274,17 +28908,17 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_6contains(struct __pyx_obj_3_sa_TrieMap
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":153
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":153
  *         cdef int i, l
  *         cdef _Trie_Node* node
  *         l = len(pattern)             # <<<<<<<<<<<<<<
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  *         for i from 0 <= i < l:
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-  __pyx_t_1 = PyObject_Length(__pyx_v_pattern); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_Length(__pyx_v_pattern); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_l = __pyx_t_1;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":154
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":154
  *         cdef _Trie_Node* node
  *         l = len(pattern)
  *         p = <int*> malloc(l*sizeof(int))             # <<<<<<<<<<<<<<
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   __pyx_v_p = ((int *)malloc((__pyx_v_l * (sizeof(int)))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":155
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":155
  *         l = len(pattern)
  *         p = <int*> malloc(l*sizeof(int))
  *         for i from 0 <= i < l:             # <<<<<<<<<<<<<<
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":156
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":156
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":157
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":157
  *         for i from 0 <= i < l:
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":158
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":158
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   free(__pyx_v_p);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":159
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":159
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":160
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":160
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+    __pyx_t_3 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -27362,7 +28996,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_6contains(struct __pyx_obj_3_sa_TrieMap
   }
   /*else*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":162
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":162
  *             return False
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  *             return True             # <<<<<<<<<<<<<<
@@ -27370,7 +29004,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_6contains(struct __pyx_obj_3_sa_TrieMap
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+    __pyx_t_3 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 162; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -27390,7 +29024,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_6contains(struct __pyx_obj_3_sa_TrieMap
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":164
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":164
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  *     cdef _Trie_Node* _contains(self, int* pattern, int pattern_len):             # <<<<<<<<<<<<<<
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":167
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":167
  *         cdef int i
  *         cdef _Trie_Node* node
  *         node = self.root[pattern[0]]             # <<<<<<<<<<<<<<
@@ -27417,7 +29051,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_7TrieMap__contains(struct __
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   __pyx_v_node = (__pyx_v_self->root[(__pyx_v_pattern[0])]);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":168
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":168
  *         cdef _Trie_Node* node
  *         node = self.root[pattern[0]]
  *         i = 1             # <<<<<<<<<<<<<<
@@ -27426,7 +29060,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_7TrieMap__contains(struct __
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":169
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":169
  *         node = self.root[pattern[0]]
  *         i = 1
  *         while node != NULL and i < pattern_len:             # <<<<<<<<<<<<<<
@@ -27443,7 +29077,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_7TrieMap__contains(struct __
     }
     if (!__pyx_t_3) break;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":170
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":170
  *         i = 1
  *         while node != NULL and i < pattern_len:
  *             node = trie_find(node, pattern[i])             # <<<<<<<<<<<<<<
@@ -27452,7 +29086,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_7TrieMap__contains(struct __
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":171
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":171
  *         while node != NULL and i < pattern_len:
  *             node = trie_find(node, pattern[i])
  *             i = i+1             # <<<<<<<<<<<<<<
@@ -27462,7 +29096,7 @@ static struct __pyx_t_3_sa__Trie_Node *__pyx_f_3_sa_7TrieMap__contains(struct __
     __pyx_v_i = (__pyx_v_i + 1);
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":172
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":172
  *             node = trie_find(node, pattern[i])
  *             i = i+1
  *         return node             # <<<<<<<<<<<<<<
@@ -27489,7 +29123,7 @@ static PyObject *__pyx_pw_3_sa_7TrieMap_9toMap(PyObject *__pyx_v_self, PyObject
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":174
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":174
  *         return node
  * 
  *     def toMap(self, flag):             # <<<<<<<<<<<<<<
@@ -27512,17 +29146,17 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_8toMap(struct __pyx_obj_3_sa_TrieMap *__
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":177
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":177
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-  __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_flag); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 177; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_flag); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 177; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":178
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":178
  * 
  *         if flag:
  *             include_zeros=1             # <<<<<<<<<<<<<<
@@ -27534,7 +29168,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_8toMap(struct __pyx_obj_3_sa_TrieMap *__
   }
   /*else*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":180
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":180
  *             include_zeros=1
  *         else:
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@@ -27545,19 +29179,19 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_8toMap(struct __pyx_obj_3_sa_TrieMap *__
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":181
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":181
  *         else:
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-  __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":182
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":182
  *             include_zeros=0
  *         result = {}
  *         for i from 0 <= i < self.V:             # <<<<<<<<<<<<<<
@@ -27567,7 +29201,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_8toMap(struct __pyx_obj_3_sa_TrieMap *__
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":183
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":183
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":184
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":184
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+      __pyx_t_2 = PyInt_FromLong(__pyx_v_i); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      __pyx_t_2 = __pyx_f_3_sa_trie_node_to_map((__pyx_v_self->root[__pyx_v_i]), ((PyObject *)__pyx_v_result), ((PyObject *)__pyx_t_4), __pyx_v_include_zeros); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_2 = __pyx_f_3_sa_trie_node_to_map((__pyx_v_self->root[__pyx_v_i]), ((PyObject *)__pyx_v_result), ((PyObject *)__pyx_t_4), __pyx_v_include_zeros); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -27600,7 +29234,7 @@ static PyObject *__pyx_pf_3_sa_7TrieMap_8toMap(struct __pyx_obj_3_sa_TrieMap *__
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":185
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":185
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  *                 trie_node_to_map(self.root[i], result, (i,), include_zeros)
  *         return result             # <<<<<<<<<<<<<<
@@ -27645,7 +29279,7 @@ static int __pyx_pw_3_sa_14Precomputation_1__cinit__(PyObject *__pyx_v_self, PyO
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":200
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":200
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+        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 200; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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@@ -27755,7 +29389,7 @@ static int __pyx_pw_3_sa_14Precomputation_1__cinit__(PyObject *__pyx_v_self, PyO
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-  __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 0, 9, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[12]; __pyx_lineno = 200; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+  __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 0, 9, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[11]; __pyx_lineno = 200; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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@@ -27779,91 +29413,91 @@ static int __pyx_pf_3_sa_14Precomputation___cinit__(struct __pyx_obj_3_sa_Precom
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":204
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":204
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-  __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_precompute_rank); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 204; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_precompute_rank); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 204; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_self->precompute_rank = __pyx_t_1;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":205
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":205
  *             train_max_initial_size=10, train_min_gap_size=2):
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-  __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_precompute_secondary_rank); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_precompute_secondary_rank); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_self->precompute_secondary_rank = __pyx_t_1;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":206
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":206
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  *         self.precompute_secondary_rank = precompute_secondary_rank
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-  __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_max_length); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 206; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_max_length); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 206; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_self->max_length = __pyx_t_1;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":207
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":207
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  *         self.max_nonterminals = max_nonterminals             # <<<<<<<<<<<<<<
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  *         self.train_min_gap_size = train_min_gap_size
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-  __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_max_nonterminals); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 207; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_max_nonterminals); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 207; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_self->max_nonterminals = __pyx_t_1;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":208
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":208
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  *         self.max_nonterminals = max_nonterminals
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-  __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_train_max_initial_size); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_train_max_initial_size); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_self->train_max_initial_size = __pyx_t_1;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":209
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":209
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  *         self.train_max_initial_size = train_max_initial_size
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-  __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_train_min_gap_size); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_train_min_gap_size); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_self->train_min_gap_size = __pyx_t_1;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":210
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":210
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+  __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_from_binary); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 210; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":211
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":211
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+    __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 211; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_5 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 211; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -27871,26 +29505,26 @@ static int __pyx_pf_3_sa_14Precomputation___cinit__(struct __pyx_obj_3_sa_Precom
     goto __pyx_L3;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":212
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":212
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+  __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_from_stats); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   if (__pyx_t_2) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":213
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":213
  *             self.read_binary(from_binary)
  *         elif from_stats:
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  * 
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-    __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__precompute); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__precompute); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -27898,7 +29532,7 @@ static int __pyx_pf_3_sa_14Precomputation___cinit__(struct __pyx_obj_3_sa_Precom
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     PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_v_fsarray);
     __Pyx_GIVEREF(__pyx_v_fsarray);
-    __pyx_t_3 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_3 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -27928,7 +29562,7 @@ static PyObject *__pyx_pw_3_sa_14Precomputation_3read_binary(PyObject *__pyx_v_s
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-    __pyx_v_filename = PyBytes_AsString(__pyx_arg_filename); if (unlikely((!__pyx_v_filename) && PyErr_Occurred())) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+    __pyx_v_filename = PyBytes_AsString(__pyx_arg_filename); if (unlikely((!__pyx_v_filename) && PyErr_Occurred())) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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@@ -27941,7 +29575,7 @@ static PyObject *__pyx_pw_3_sa_14Precomputation_3read_binary(PyObject *__pyx_v_s
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":216
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":216
  * 
  * 
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":218
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":218
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   __pyx_v_f = fopen(__pyx_v_filename, __pyx_k__r);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":219
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":219
  *         cdef FILE* f
  *         f = fopen(filename, "r")
  *         fread(&(self.precompute_rank), sizeof(int), 1, f)             # <<<<<<<<<<<<<<
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   fread((&__pyx_v_self->precompute_rank), (sizeof(int)), 1, __pyx_v_f);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":220
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":220
  *         f = fopen(filename, "r")
  *         fread(&(self.precompute_rank), sizeof(int), 1, f)
  *         fread(&(self.precompute_secondary_rank), sizeof(int), 1, f)             # <<<<<<<<<<<<<<
@@ -27986,7 +29620,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_2read_binary(struct __pyx_obj_3_
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   fread((&__pyx_v_self->precompute_secondary_rank), (sizeof(int)), 1, __pyx_v_f);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":221
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":221
  *         fread(&(self.precompute_rank), sizeof(int), 1, f)
  *         fread(&(self.precompute_secondary_rank), sizeof(int), 1, f)
  *         fread(&(self.max_length), sizeof(int), 1, f)             # <<<<<<<<<<<<<<
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   fread((&__pyx_v_self->max_length), (sizeof(int)), 1, __pyx_v_f);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":222
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":222
  *         fread(&(self.precompute_secondary_rank), sizeof(int), 1, f)
  *         fread(&(self.max_length), sizeof(int), 1, f)
  *         fread(&(self.max_nonterminals), sizeof(int), 1, f)             # <<<<<<<<<<<<<<
@@ -28004,7 +29638,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_2read_binary(struct __pyx_obj_3_
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   fread((&__pyx_v_self->max_nonterminals), (sizeof(int)), 1, __pyx_v_f);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":223
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":223
  *         fread(&(self.max_length), sizeof(int), 1, f)
  *         fread(&(self.max_nonterminals), sizeof(int), 1, f)
  *         fread(&(self.train_max_initial_size), sizeof(int), 1, f)             # <<<<<<<<<<<<<<
@@ -28013,7 +29647,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_2read_binary(struct __pyx_obj_3_
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   fread((&__pyx_v_self->train_max_initial_size), (sizeof(int)), 1, __pyx_v_f);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":224
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":224
  *         fread(&(self.max_nonterminals), sizeof(int), 1, f)
  *         fread(&(self.train_max_initial_size), sizeof(int), 1, f)
  *         fread(&(self.train_min_gap_size), sizeof(int), 1, f)             # <<<<<<<<<<<<<<
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   fread((&__pyx_v_self->train_min_gap_size), (sizeof(int)), 1, __pyx_v_f);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":225
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":225
  *         fread(&(self.train_max_initial_size), sizeof(int), 1, f)
  *         fread(&(self.train_min_gap_size), sizeof(int), 1, f)
  *         self.precomputed_index = self.read_map(f)             # <<<<<<<<<<<<<<
  *         self.precomputed_collocations = self.read_map(f)
  *         fclose(f)
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-  __pyx_t_1 = ((struct __pyx_vtabstruct_3_sa_Precomputation *)__pyx_v_self->__pyx_vtab)->read_map(__pyx_v_self, __pyx_v_f); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 225; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = ((struct __pyx_vtabstruct_3_sa_Precomputation *)__pyx_v_self->__pyx_vtab)->read_map(__pyx_v_self, __pyx_v_f); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 225; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":226
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":226
  *         fread(&(self.train_min_gap_size), sizeof(int), 1, f)
  *         self.precomputed_index = self.read_map(f)
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-  __pyx_t_1 = ((struct __pyx_vtabstruct_3_sa_Precomputation *)__pyx_v_self->__pyx_vtab)->read_map(__pyx_v_self, __pyx_v_f); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 226; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = ((struct __pyx_vtabstruct_3_sa_Precomputation *)__pyx_v_self->__pyx_vtab)->read_map(__pyx_v_self, __pyx_v_f); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 226; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -28052,7 +29686,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_2read_binary(struct __pyx_obj_3_
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   __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":227
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":227
  *         self.precomputed_index = self.read_map(f)
  *         self.precomputed_collocations = self.read_map(f)
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+    __pyx_v_filename = PyBytes_AsString(__pyx_arg_filename); if (unlikely((!__pyx_v_filename) && PyErr_Occurred())) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 230; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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@@ -28094,7 +29728,7 @@ static PyObject *__pyx_pw_3_sa_14Precomputation_5write_binary(PyObject *__pyx_v_
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":230
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":230
  * 
  * 
  *     def write_binary(self, char* filename):             # <<<<<<<<<<<<<<
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":232
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":232
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   __pyx_v_f = fopen(__pyx_v_filename, __pyx_k__w);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":233
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":233
  *         cdef FILE* f
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  *         fwrite(&(self.precompute_rank), sizeof(int), 1, f)             # <<<<<<<<<<<<<<
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   fwrite((&__pyx_v_self->precompute_rank), (sizeof(int)), 1, __pyx_v_f);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":234
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":234
  *         f = fopen(filename, "w")
  *         fwrite(&(self.precompute_rank), sizeof(int), 1, f)
  *         fwrite(&(self.precompute_secondary_rank), sizeof(int), 1, f)             # <<<<<<<<<<<<<<
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   fwrite((&__pyx_v_self->precompute_secondary_rank), (sizeof(int)), 1, __pyx_v_f);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":235
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":235
  *         fwrite(&(self.precompute_rank), sizeof(int), 1, f)
  *         fwrite(&(self.precompute_secondary_rank), sizeof(int), 1, f)
  *         fwrite(&(self.max_length), sizeof(int), 1, f)             # <<<<<<<<<<<<<<
@@ -28149,7 +29783,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_4write_binary(struct __pyx_obj_3
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   fwrite((&__pyx_v_self->max_length), (sizeof(int)), 1, __pyx_v_f);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":236
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":236
  *         fwrite(&(self.precompute_secondary_rank), sizeof(int), 1, f)
  *         fwrite(&(self.max_length), sizeof(int), 1, f)
  *         fwrite(&(self.max_nonterminals), sizeof(int), 1, f)             # <<<<<<<<<<<<<<
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   fwrite((&__pyx_v_self->max_nonterminals), (sizeof(int)), 1, __pyx_v_f);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":237
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":237
  *         fwrite(&(self.max_length), sizeof(int), 1, f)
  *         fwrite(&(self.max_nonterminals), sizeof(int), 1, f)
  *         fwrite(&(self.train_max_initial_size), sizeof(int), 1, f)             # <<<<<<<<<<<<<<
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   fwrite((&__pyx_v_self->train_max_initial_size), (sizeof(int)), 1, __pyx_v_f);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":238
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":238
  *         fwrite(&(self.max_nonterminals), sizeof(int), 1, f)
  *         fwrite(&(self.train_max_initial_size), sizeof(int), 1, f)
  *         fwrite(&(self.train_min_gap_size), sizeof(int), 1, f)             # <<<<<<<<<<<<<<
@@ -28176,7 +29810,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_4write_binary(struct __pyx_obj_3
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   fwrite((&__pyx_v_self->train_min_gap_size), (sizeof(int)), 1, __pyx_v_f);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":239
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":239
  *         fwrite(&(self.train_max_initial_size), sizeof(int), 1, f)
  *         fwrite(&(self.train_min_gap_size), sizeof(int), 1, f)
  *         self.write_map(self.precomputed_index, f)             # <<<<<<<<<<<<<<
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-  __pyx_t_2 = ((struct __pyx_vtabstruct_3_sa_Precomputation *)__pyx_v_self->__pyx_vtab)->write_map(__pyx_v_self, __pyx_t_1, __pyx_v_f); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 239; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = ((struct __pyx_vtabstruct_3_sa_Precomputation *)__pyx_v_self->__pyx_vtab)->write_map(__pyx_v_self, __pyx_t_1, __pyx_v_f); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 239; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":240
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":240
  *         fwrite(&(self.train_min_gap_size), sizeof(int), 1, f)
  *         self.write_map(self.precomputed_index, f)
  *         self.write_map(self.precomputed_collocations, f)             # <<<<<<<<<<<<<<
@@ -28199,12 +29833,12 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_4write_binary(struct __pyx_obj_3
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-  __pyx_t_1 = ((struct __pyx_vtabstruct_3_sa_Precomputation *)__pyx_v_self->__pyx_vtab)->write_map(__pyx_v_self, __pyx_t_2, __pyx_v_f); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = ((struct __pyx_vtabstruct_3_sa_Precomputation *)__pyx_v_self->__pyx_vtab)->write_map(__pyx_v_self, __pyx_t_2, __pyx_v_f); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":241
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-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":244
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":248
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":249
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":250
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":250
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-    {__pyx_filename = __pyx_f[12]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":251
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":251
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+    __pyx_t_8 = PyObject_Length(__pyx_v_pattern); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 251; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":252
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":252
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":253
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":253
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":254
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":255
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":255
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":256
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":257
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":257
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-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":260
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":264
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":264
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+  __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 264; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":265
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":265
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":266
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":266
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":267
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":267
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":268
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":268
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":269
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":270
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":271
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":272
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":272
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":273
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":273
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":274
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":274
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+    if (PyDict_SetItem(((PyObject *)__pyx_v_m), ((PyObject *)__pyx_v_key), ((PyObject *)__pyx_v_arr)) < 0) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 274; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":275
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":275
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  *             m[key] = arr
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+          __Pyx_RaiseArgtupleInvalid("precompute", 1, 2, 2, 1); {__pyx_filename = __pyx_f[11]; __pyx_lineno = 278; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+  __Pyx_RaiseArgtupleInvalid("precompute", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[11]; __pyx_lineno = 278; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_sarray), __pyx_ptype_3_sa_SuffixArray, 1, "sarray", 0))) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 278; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":278
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":278
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  * 
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":280
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":280
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":285
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":285
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  * 
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@@ -28778,7 +30412,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":287
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":287
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  *         frequent_patterns = TrieMap(len(darray.id2word))             # <<<<<<<<<<<<<<
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+  __pyx_t_2 = PyObject_Length(__pyx_t_1); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_1 = PyInt_FromSsize_t(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_TrieMap)), ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":288
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":288
  * 
  *         frequent_patterns = TrieMap(len(darray.id2word))
  *         super_frequent_patterns = TrieMap(len(darray.id2word))             # <<<<<<<<<<<<<<
@@ -28811,22 +30445,22 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
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+  __pyx_t_2 = PyObject_Length(__pyx_t_1); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 288; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_1 = PyInt_FromSsize_t(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 288; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 288; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_TrieMap)), ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 288; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":289
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":289
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@@ -28835,99 +30469,99 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
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+  __pyx_t_2 = PyObject_Length(__pyx_t_1); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __pyx_t_1 = PyInt_FromSsize_t(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyInt_FromSsize_t(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_TrieMap)), ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_TrieMap)), ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":291
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":291
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-  __pyx_t_1 = PySet_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 291; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PySet_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 291; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":292
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":292
  * 
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-  __pyx_t_1 = PySet_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PySet_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":293
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":293
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  *         J_set = set()
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-  __pyx_t_1 = PySet_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 293; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PySet_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 293; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(((PyObject *)__pyx_t_1));
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":294
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":294
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-  __pyx_t_1 = PySet_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 294; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PySet_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 294; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":295
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":295
  *         J2_set = set()
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+  __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 295; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":297
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":297
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":298
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":298
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  *         logger.info("Precomputing frequent intersections")
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":300
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":300
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":301
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":301
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  *         max_pattern_len = 0
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-        {__pyx_filename = __pyx_f[12]; __pyx_lineno = 301; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_8 = PySequence_ITEM(sequence, 2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 301; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_9 = PyObject_GetIter(__pyx_t_5); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 301; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      {__pyx_filename = __pyx_f[12]; __pyx_lineno = 301; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":302
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":302
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+    __pyx_t_5 = PyInt_FromLong(__pyx_v_self->precompute_rank); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 302; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":303
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":304
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":305
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":306
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":307
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":308
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":308
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-    __pyx_t_7 = PyInt_FromLong(__pyx_v_self->precompute_secondary_rank); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_7 = PyInt_FromLong(__pyx_v_self->precompute_secondary_rank); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    __pyx_t_5 = PyObject_RichCompare(__pyx_v_rank, __pyx_t_7, Py_LT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-    __Pyx_GOTREF(__pyx_t_5);
+    __pyx_t_5 = PyObject_RichCompare(__pyx_v_rank, __pyx_t_7, Py_LT); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":309
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":309
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-      __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_super_frequent_patterns), __pyx_n_s__insert); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 309; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_super_frequent_patterns), __pyx_n_s__insert); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 309; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 309; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      __pyx_t_8 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 309; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_8 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 309; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":310
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":310
  *             if rank < self.precompute_secondary_rank:
  *                 super_frequent_patterns.insert(phrase)
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  *         queue = IntList(increment=1000)
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-      __pyx_t_15 = PySet_Add(__pyx_v_J_set, __pyx_v_phrase); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 310; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_15 = PySet_Add(__pyx_v_J_set, __pyx_v_phrase); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 310; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       goto __pyx_L8;
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@@ -29195,50 +30827,50 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
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   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":312
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":312
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  * 
  *         queue = IntList(increment=1000)             # <<<<<<<<<<<<<<
  * 
  *         logger.info("    Computing inverted indexes...")
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-  __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 312; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 312; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(((PyObject *)__pyx_t_1));
-  if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__increment), __pyx_int_1000) < 0) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 312; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_IntList)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 312; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__increment), __pyx_int_1000) < 0) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 312; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_IntList)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 312; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":314
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":314
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  *         logger.info("    Computing inverted indexes...")             # <<<<<<<<<<<<<<
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-  __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__logger); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__logger); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_75), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":315
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":315
  * 
  *         logger.info("    Computing inverted indexes...")
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-  __pyx_t_2 = PyObject_Length(((PyObject *)__pyx_v_data)); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = PyObject_Length(((PyObject *)__pyx_v_data)); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_N = __pyx_t_2;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":316
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":316
  *         logger.info("    Computing inverted indexes...")
  *         N = len(data)
  *         for i from 0 <= i < N:             # <<<<<<<<<<<<<<
@@ -29248,7 +30880,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":317
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":317
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@@ -29257,7 +30889,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":318
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":318
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@@ -29267,7 +30899,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":319
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":319
  *             sa_word_id = data.arr[i]
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@@ -29279,7 +30911,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
     }
     /*else*/ {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":321
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":321
  *                 queue._append(-1)
  *             else:
  *                 for l from 1 <= l <= max_pattern_len:             # <<<<<<<<<<<<<<
@@ -29289,7 +30921,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":322
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":322
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@@ -29298,7 +30930,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":323
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":323
  *                 for l from 1 <= l <= max_pattern_len:
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@@ -29308,7 +30940,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
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         if (__pyx_t_11) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":324
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":324
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@@ -29320,7 +30952,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":325
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":325
  *                     if node == NULL:
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@@ -29329,7 +30961,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":326
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":326
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@@ -29338,14 +30970,14 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":327
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":327
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+        __pyx_t_3 = __pyx_f_3_sa_trie_node_data_append(__pyx_v_node, __pyx_v_i); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 327; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":329
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":329
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+  __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__logger); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__info); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_77), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":330
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":330
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+  __pyx_t_2 = PyObject_Length(((PyObject *)__pyx_v_queue)); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_N = __pyx_t_2;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":331
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":331
  *         logger.info("    Computing collocations...")
  *         N = len(queue)
  *         ptr1 = 0             # <<<<<<<<<<<<<<
@@ -29390,7 +31022,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
   __pyx_v_ptr1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":332
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":332
  *         N = len(queue)
  *         ptr1 = 0
  *         sent_count = 0             # <<<<<<<<<<<<<<
@@ -29399,7 +31031,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
   __pyx_v_sent_count = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":333
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":333
  *         ptr1 = 0
  *         sent_count = 0
  *         while ptr1 < N:    # main loop             # <<<<<<<<<<<<<<
@@ -29410,7 +31042,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
     __pyx_t_11 = (__pyx_v_ptr1 < __pyx_v_N);
     if (!__pyx_t_11) break;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":334
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":334
  *         sent_count = 0
  *         while ptr1 < N:    # main loop
  *             i1 = queue.arr[ptr1]             # <<<<<<<<<<<<<<
@@ -29419,7 +31051,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
     __pyx_v_i1 = (__pyx_v_queue->arr[__pyx_v_ptr1]);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":335
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":335
  *         while ptr1 < N:    # main loop
  *             i1 = queue.arr[ptr1]
  *             if i1 > -1:             # <<<<<<<<<<<<<<
@@ -29429,7 +31061,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
     __pyx_t_11 = (__pyx_v_i1 > -1);
     if (__pyx_t_11) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":336
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":336
  *             i1 = queue.arr[ptr1]
  *             if i1 > -1:
  *                 l1 = queue.arr[ptr1+1]             # <<<<<<<<<<<<<<
@@ -29438,7 +31070,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
       __pyx_v_l1 = (__pyx_v_queue->arr[(__pyx_v_ptr1 + 1)]);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":337
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":337
  *             if i1 > -1:
  *                 l1 = queue.arr[ptr1+1]
  *                 ptr2 = ptr1 + 2             # <<<<<<<<<<<<<<
@@ -29447,7 +31079,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
       __pyx_v_ptr2 = (__pyx_v_ptr1 + 2);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":338
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":338
  *                 l1 = queue.arr[ptr1+1]
  *                 ptr2 = ptr1 + 2
  *                 while ptr2 < N:             # <<<<<<<<<<<<<<
@@ -29458,7 +31090,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
         __pyx_t_11 = (__pyx_v_ptr2 < __pyx_v_N);
         if (!__pyx_t_11) break;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":339
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":339
  *                 ptr2 = ptr1 + 2
  *                 while ptr2 < N:
  *                     i2 = queue.arr[ptr2]             # <<<<<<<<<<<<<<
@@ -29467,7 +31099,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
         __pyx_v_i2 = (__pyx_v_queue->arr[__pyx_v_ptr2]);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":340
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":340
  *                 while ptr2 < N:
  *                     i2 = queue.arr[ptr2]
  *                     if i2 == -1 or i2 - i1 >= self.train_max_initial_size:             # <<<<<<<<<<<<<<
@@ -29483,7 +31115,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
         }
         if (__pyx_t_18) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":341
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":341
  *                     i2 = queue.arr[ptr2]
  *                     if i2 == -1 or i2 - i1 >= self.train_max_initial_size:
  *                         break             # <<<<<<<<<<<<<<
@@ -29495,7 +31127,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
         }
         __pyx_L20:;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":342
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":342
  *                     if i2 == -1 or i2 - i1 >= self.train_max_initial_size:
  *                         break
  *                     l2 = queue.arr[ptr2+1]             # <<<<<<<<<<<<<<
@@ -29504,7 +31136,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
         __pyx_v_l2 = (__pyx_v_queue->arr[(__pyx_v_ptr2 + 1)]);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":343
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":343
  *                         break
  *                     l2 = queue.arr[ptr2+1]
  *                     if (i2 - i1 - l1 >= self.train_min_gap_size and             # <<<<<<<<<<<<<<
@@ -29514,7 +31146,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
         __pyx_t_18 = (((__pyx_v_i2 - __pyx_v_i1) - __pyx_v_l1) >= __pyx_v_self->train_min_gap_size);
         if (__pyx_t_18) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":344
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":344
  *                     l2 = queue.arr[ptr2+1]
  *                     if (i2 - i1 - l1 >= self.train_min_gap_size and
  *                             i2 + l2 - i1 <= self.train_max_initial_size and             # <<<<<<<<<<<<<<
@@ -29524,7 +31156,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
           __pyx_t_11 = (((__pyx_v_i2 + __pyx_v_l2) - __pyx_v_i1) <= __pyx_v_self->train_max_initial_size);
           if (__pyx_t_11) {
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":345
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":345
  *                     if (i2 - i1 - l1 >= self.train_min_gap_size and
  *                             i2 + l2 - i1 <= self.train_max_initial_size and
  *                             l1+l2+1 <= self.max_length):             # <<<<<<<<<<<<<<
@@ -29542,7 +31174,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
         }
         if (__pyx_t_11) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":346
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":346
  *                             i2 + l2 - i1 <= self.train_max_initial_size and
  *                             l1+l2+1 <= self.max_length):
  *                         node = collocations._insert(data.arr+i1, l1)             # <<<<<<<<<<<<<<
@@ -29551,7 +31183,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
           __pyx_v_node = ((struct __pyx_vtabstruct_3_sa_TrieMap *)__pyx_v_collocations->__pyx_vtab)->_insert(__pyx_v_collocations, (__pyx_v_data->arr + __pyx_v_i1), __pyx_v_l1);
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":347
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":347
  *                             l1+l2+1 <= self.max_length):
  *                         node = collocations._insert(data.arr+i1, l1)
  *                         node = trie_insert(node, -1)             # <<<<<<<<<<<<<<
@@ -29560,7 +31192,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
           __pyx_v_node = __pyx_f_3_sa_trie_insert(__pyx_v_node, -1);
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":348
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":348
  *                         node = collocations._insert(data.arr+i1, l1)
  *                         node = trie_insert(node, -1)
  *                         for i from i2 <= i < i2+l2:             # <<<<<<<<<<<<<<
@@ -29570,7 +31202,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
           __pyx_t_13 = (__pyx_v_i2 + __pyx_v_l2);
           for (__pyx_v_i = __pyx_v_i2; __pyx_v_i < __pyx_t_13; __pyx_v_i++) {
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":349
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":349
  *                         node = trie_insert(node, -1)
  *                         for i from i2 <= i < i2+l2:
  *                             node = trie_insert(node, data.arr[i])             # <<<<<<<<<<<<<<
@@ -29580,29 +31212,29 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
             __pyx_v_node = __pyx_f_3_sa_trie_insert(__pyx_v_node, (__pyx_v_data->arr[__pyx_v_i]));
           }
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":350
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":350
  *                         for i from i2 <= i < i2+l2:
  *                             node = trie_insert(node, data.arr[i])
  *                         trie_node_data_append(node, i1)             # <<<<<<<<<<<<<<
  *                         trie_node_data_append(node, i2)
  *                         if super_frequent_patterns._contains(data.arr+i2, l2) != NULL:
  */
-          __pyx_t_3 = __pyx_f_3_sa_trie_node_data_append(__pyx_v_node, __pyx_v_i1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 350; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __pyx_t_3 = __pyx_f_3_sa_trie_node_data_append(__pyx_v_node, __pyx_v_i1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 350; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           __Pyx_GOTREF(__pyx_t_3);
           __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":351
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":351
  *                             node = trie_insert(node, data.arr[i])
  *                         trie_node_data_append(node, i1)
  *                         trie_node_data_append(node, i2)             # <<<<<<<<<<<<<<
  *                         if super_frequent_patterns._contains(data.arr+i2, l2) != NULL:
  *                             if super_frequent_patterns._contains(data.arr+i1, l1) != NULL:
  */
-          __pyx_t_3 = __pyx_f_3_sa_trie_node_data_append(__pyx_v_node, __pyx_v_i2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 351; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __pyx_t_3 = __pyx_f_3_sa_trie_node_data_append(__pyx_v_node, __pyx_v_i2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 351; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           __Pyx_GOTREF(__pyx_t_3);
           __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":352
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":352
  *                         trie_node_data_append(node, i1)
  *                         trie_node_data_append(node, i2)
  *                         if super_frequent_patterns._contains(data.arr+i2, l2) != NULL:             # <<<<<<<<<<<<<<
@@ -29612,7 +31244,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
           __pyx_t_11 = (((struct __pyx_vtabstruct_3_sa_TrieMap *)__pyx_v_super_frequent_patterns->__pyx_vtab)->_contains(__pyx_v_super_frequent_patterns, (__pyx_v_data->arr + __pyx_v_i2), __pyx_v_l2) != NULL);
           if (__pyx_t_11) {
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":353
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":353
  *                         trie_node_data_append(node, i2)
  *                         if super_frequent_patterns._contains(data.arr+i2, l2) != NULL:
  *                             if super_frequent_patterns._contains(data.arr+i1, l1) != NULL:             # <<<<<<<<<<<<<<
@@ -29622,7 +31254,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
             __pyx_t_11 = (((struct __pyx_vtabstruct_3_sa_TrieMap *)__pyx_v_super_frequent_patterns->__pyx_vtab)->_contains(__pyx_v_super_frequent_patterns, (__pyx_v_data->arr + __pyx_v_i1), __pyx_v_l1) != NULL);
             if (__pyx_t_11) {
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":354
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":354
  *                         if super_frequent_patterns._contains(data.arr+i2, l2) != NULL:
  *                             if super_frequent_patterns._contains(data.arr+i1, l1) != NULL:
  *                                 is_super = 1             # <<<<<<<<<<<<<<
@@ -29634,7 +31266,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
             }
             /*else*/ {
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":356
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":356
  *                                 is_super = 1
  *                             else:
  *                                 is_super = 0             # <<<<<<<<<<<<<<
@@ -29645,7 +31277,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
             }
             __pyx_L25:;
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":357
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":357
  *                             else:
  *                                 is_super = 0
  *                             ptr3 = ptr2 + 2             # <<<<<<<<<<<<<<
@@ -29654,7 +31286,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
             __pyx_v_ptr3 = (__pyx_v_ptr2 + 2);
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":358
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":358
  *                                 is_super = 0
  *                             ptr3 = ptr2 + 2
  *                             while ptr3 < N:             # <<<<<<<<<<<<<<
@@ -29665,7 +31297,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
               __pyx_t_11 = (__pyx_v_ptr3 < __pyx_v_N);
               if (!__pyx_t_11) break;
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":359
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":359
  *                             ptr3 = ptr2 + 2
  *                             while ptr3 < N:
  *                                 i3 = queue.arr[ptr3]             # <<<<<<<<<<<<<<
@@ -29674,7 +31306,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
               __pyx_v_i3 = (__pyx_v_queue->arr[__pyx_v_ptr3]);
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":360
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":360
  *                             while ptr3 < N:
  *                                 i3 = queue.arr[ptr3]
  *                                 if i3 == -1 or i3 - i1 >= self.train_max_initial_size:             # <<<<<<<<<<<<<<
@@ -29690,7 +31322,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
               }
               if (__pyx_t_19) {
 
-                /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":361
+                /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":361
  *                                 i3 = queue.arr[ptr3]
  *                                 if i3 == -1 or i3 - i1 >= self.train_max_initial_size:
  *                                     break             # <<<<<<<<<<<<<<
@@ -29702,7 +31334,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
               }
               __pyx_L28:;
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":362
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":362
  *                                 if i3 == -1 or i3 - i1 >= self.train_max_initial_size:
  *                                     break
  *                                 l3 = queue.arr[ptr3+1]             # <<<<<<<<<<<<<<
@@ -29711,7 +31343,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
               __pyx_v_l3 = (__pyx_v_queue->arr[(__pyx_v_ptr3 + 1)]);
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":363
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":363
  *                                     break
  *                                 l3 = queue.arr[ptr3+1]
  *                                 if (i3 - i2 - l2 >= self.train_min_gap_size and             # <<<<<<<<<<<<<<
@@ -29721,7 +31353,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
               __pyx_t_19 = (((__pyx_v_i3 - __pyx_v_i2) - __pyx_v_l2) >= __pyx_v_self->train_min_gap_size);
               if (__pyx_t_19) {
 
-                /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":364
+                /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":364
  *                                 l3 = queue.arr[ptr3+1]
  *                                 if (i3 - i2 - l2 >= self.train_min_gap_size and
  *                                         i3 + l3 - i1 <= self.train_max_initial_size and             # <<<<<<<<<<<<<<
@@ -29731,7 +31363,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
                 __pyx_t_11 = (((__pyx_v_i3 + __pyx_v_l3) - __pyx_v_i1) <= __pyx_v_self->train_max_initial_size);
                 if (__pyx_t_11) {
 
-                  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":365
+                  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":365
  *                                 if (i3 - i2 - l2 >= self.train_min_gap_size and
  *                                         i3 + l3 - i1 <= self.train_max_initial_size and
  *                                         l1+l2+l3+2 <= self.max_length):             # <<<<<<<<<<<<<<
@@ -29749,7 +31381,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
               }
               if (__pyx_t_11) {
 
-                /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":366
+                /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":366
  *                                         i3 + l3 - i1 <= self.train_max_initial_size and
  *                                         l1+l2+l3+2 <= self.max_length):
  *                                     if is_super or super_frequent_patterns._contains(data.arr+i3, l3) != NULL:             # <<<<<<<<<<<<<<
@@ -29764,7 +31396,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
                 }
                 if (__pyx_t_19) {
 
-                  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":367
+                  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":367
  *                                         l1+l2+l3+2 <= self.max_length):
  *                                     if is_super or super_frequent_patterns._contains(data.arr+i3, l3) != NULL:
  *                                         node = collocations._insert(data.arr+i1, l1)             # <<<<<<<<<<<<<<
@@ -29773,7 +31405,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
                   __pyx_v_node = ((struct __pyx_vtabstruct_3_sa_TrieMap *)__pyx_v_collocations->__pyx_vtab)->_insert(__pyx_v_collocations, (__pyx_v_data->arr + __pyx_v_i1), __pyx_v_l1);
 
-                  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":368
+                  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":368
  *                                     if is_super or super_frequent_patterns._contains(data.arr+i3, l3) != NULL:
  *                                         node = collocations._insert(data.arr+i1, l1)
  *                                         node = trie_insert(node, -1)             # <<<<<<<<<<<<<<
@@ -29782,7 +31414,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
                   __pyx_v_node = __pyx_f_3_sa_trie_insert(__pyx_v_node, -1);
 
-                  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":369
+                  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":369
  *                                         node = collocations._insert(data.arr+i1, l1)
  *                                         node = trie_insert(node, -1)
  *                                         for i from i2 <= i < i2+l2:             # <<<<<<<<<<<<<<
@@ -29792,7 +31424,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
                   __pyx_t_13 = (__pyx_v_i2 + __pyx_v_l2);
                   for (__pyx_v_i = __pyx_v_i2; __pyx_v_i < __pyx_t_13; __pyx_v_i++) {
 
-                    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":370
+                    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":370
  *                                         node = trie_insert(node, -1)
  *                                         for i from i2 <= i < i2+l2:
  *                                             node = trie_insert(node, data.arr[i])             # <<<<<<<<<<<<<<
@@ -29802,7 +31434,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
                     __pyx_v_node = __pyx_f_3_sa_trie_insert(__pyx_v_node, (__pyx_v_data->arr[__pyx_v_i]));
                   }
 
-                  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":371
+                  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":371
  *                                         for i from i2 <= i < i2+l2:
  *                                             node = trie_insert(node, data.arr[i])
  *                                         node = trie_insert(node, -1)             # <<<<<<<<<<<<<<
@@ -29811,7 +31443,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
                   __pyx_v_node = __pyx_f_3_sa_trie_insert(__pyx_v_node, -1);
 
-                  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":372
+                  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":372
  *                                             node = trie_insert(node, data.arr[i])
  *                                         node = trie_insert(node, -1)
  *                                         for i from i3 <= i < i3+l3:             # <<<<<<<<<<<<<<
@@ -29821,7 +31453,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
                   __pyx_t_13 = (__pyx_v_i3 + __pyx_v_l3);
                   for (__pyx_v_i = __pyx_v_i3; __pyx_v_i < __pyx_t_13; __pyx_v_i++) {
 
-                    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":373
+                    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":373
  *                                         node = trie_insert(node, -1)
  *                                         for i from i3 <= i < i3+l3:
  *                                             node = trie_insert(node, data.arr[i])             # <<<<<<<<<<<<<<
@@ -29831,36 +31463,36 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
                     __pyx_v_node = __pyx_f_3_sa_trie_insert(__pyx_v_node, (__pyx_v_data->arr[__pyx_v_i]));
                   }
 
-                  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":374
+                  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":374
  *                                         for i from i3 <= i < i3+l3:
  *                                             node = trie_insert(node, data.arr[i])
  *                                         trie_node_data_append(node, i1)             # <<<<<<<<<<<<<<
  *                                         trie_node_data_append(node, i2)
  *                                         trie_node_data_append(node, i3)
  */
-                  __pyx_t_3 = __pyx_f_3_sa_trie_node_data_append(__pyx_v_node, __pyx_v_i1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 374; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  __pyx_t_3 = __pyx_f_3_sa_trie_node_data_append(__pyx_v_node, __pyx_v_i1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 374; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                   __Pyx_GOTREF(__pyx_t_3);
                   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
-                  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":375
+                  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":375
  *                                             node = trie_insert(node, data.arr[i])
  *                                         trie_node_data_append(node, i1)
  *                                         trie_node_data_append(node, i2)             # <<<<<<<<<<<<<<
  *                                         trie_node_data_append(node, i3)
  *                                 ptr3 = ptr3 + 2
  */
-                  __pyx_t_3 = __pyx_f_3_sa_trie_node_data_append(__pyx_v_node, __pyx_v_i2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  __pyx_t_3 = __pyx_f_3_sa_trie_node_data_append(__pyx_v_node, __pyx_v_i2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                   __Pyx_GOTREF(__pyx_t_3);
                   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
-                  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":376
+                  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":376
  *                                         trie_node_data_append(node, i1)
  *                                         trie_node_data_append(node, i2)
  *                                         trie_node_data_append(node, i3)             # <<<<<<<<<<<<<<
  *                                 ptr3 = ptr3 + 2
  *                     ptr2 = ptr2 + 2
  */
-                  __pyx_t_3 = __pyx_f_3_sa_trie_node_data_append(__pyx_v_node, __pyx_v_i3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 376; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  __pyx_t_3 = __pyx_f_3_sa_trie_node_data_append(__pyx_v_node, __pyx_v_i3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 376; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                   __Pyx_GOTREF(__pyx_t_3);
                   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
                   goto __pyx_L30;
@@ -29870,7 +31502,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
               }
               __pyx_L29:;
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":377
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":377
  *                                         trie_node_data_append(node, i2)
  *                                         trie_node_data_append(node, i3)
  *                                 ptr3 = ptr3 + 2             # <<<<<<<<<<<<<<
@@ -29887,7 +31519,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
         }
         __pyx_L21:;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":378
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":378
  *                                         trie_node_data_append(node, i3)
  *                                 ptr3 = ptr3 + 2
  *                     ptr2 = ptr2 + 2             # <<<<<<<<<<<<<<
@@ -29898,7 +31530,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
       }
       __pyx_L19_break:;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":379
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":379
  *                                 ptr3 = ptr3 + 2
  *                     ptr2 = ptr2 + 2
  *                 ptr1 = ptr1 + 2             # <<<<<<<<<<<<<<
@@ -29910,7 +31542,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
     }
     /*else*/ {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":381
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":381
  *                 ptr1 = ptr1 + 2
  *             else:
  *                 sent_count = sent_count + 1             # <<<<<<<<<<<<<<
@@ -29919,7 +31551,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
  */
       __pyx_v_sent_count = (__pyx_v_sent_count + 1);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":382
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":382
  *             else:
  *                 sent_count = sent_count + 1
  *                 if sent_count % 10000 == 0:             # <<<<<<<<<<<<<<
@@ -29929,21 +31561,21 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
       __pyx_t_19 = (__Pyx_mod_long(__pyx_v_sent_count, 10000) == 0);
       if (__pyx_t_19) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":383
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":383
  *                 sent_count = sent_count + 1
  *                 if sent_count % 10000 == 0:
  *                     logger.debug("        %d sentences", sent_count)             # <<<<<<<<<<<<<<
  *                 ptr1 = ptr1 + 1
  * 
  */
-        __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__logger); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 383; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__logger); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 383; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_3);
-        __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__debug); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 383; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__debug); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 383; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_1);
         __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
-        __pyx_t_3 = PyInt_FromLong(__pyx_v_sent_count); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 383; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_3 = PyInt_FromLong(__pyx_v_sent_count); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 383; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_3);
-        __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 383; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 383; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_8);
         __Pyx_INCREF(((PyObject *)__pyx_kp_s_78));
         PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_kp_s_78));
@@ -29951,7 +31583,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
         PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_3);
         __Pyx_GIVEREF(__pyx_t_3);
         __pyx_t_3 = 0;
-        __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 383; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 383; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_3);
         __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
         __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
@@ -29960,7 +31592,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
       }
       __pyx_L35:;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":384
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":384
  *                 if sent_count % 10000 == 0:
  *                     logger.debug("        %d sentences", sent_count)
  *                 ptr1 = ptr1 + 1             # <<<<<<<<<<<<<<
@@ -29972,23 +31604,23 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
     __pyx_L17:;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":386
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":386
  *                 ptr1 = ptr1 + 1
  * 
  *         self.precomputed_collocations = collocations.toMap(False)             # <<<<<<<<<<<<<<
  *         self.precomputed_index = frequent_patterns.toMap(True)
  * 
  */
-  __pyx_t_3 = PyObject_GetAttr(((PyObject *)__pyx_v_collocations), __pyx_n_s__toMap); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = PyObject_GetAttr(((PyObject *)__pyx_v_collocations), __pyx_n_s__toMap); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_3);
-  __pyx_t_8 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_8 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_8);
-  __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_1);
   PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_8);
   __Pyx_GIVEREF(__pyx_t_8);
   __pyx_t_8 = 0;
-  __pyx_t_8 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_8 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_8);
   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
   __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
@@ -29998,23 +31630,23 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
   __pyx_v_self->precomputed_collocations = __pyx_t_8;
   __pyx_t_8 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":387
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":387
  * 
  *         self.precomputed_collocations = collocations.toMap(False)
  *         self.precomputed_index = frequent_patterns.toMap(True)             # <<<<<<<<<<<<<<
  * 
  *         x = 0
  */
-  __pyx_t_8 = PyObject_GetAttr(((PyObject *)__pyx_v_frequent_patterns), __pyx_n_s__toMap); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 387; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_8 = PyObject_GetAttr(((PyObject *)__pyx_v_frequent_patterns), __pyx_n_s__toMap); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 387; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_8);
-  __pyx_t_1 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 387; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 387; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_1);
-  __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 387; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 387; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_3);
   PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
   __Pyx_GIVEREF(__pyx_t_1);
   __pyx_t_1 = 0;
-  __pyx_t_1 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 387; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 387; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_1);
   __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
   __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
@@ -30024,7 +31656,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
   __pyx_v_self->precomputed_index = __pyx_t_1;
   __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":389
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":389
  *         self.precomputed_index = frequent_patterns.toMap(True)
  * 
  *         x = 0             # <<<<<<<<<<<<<<
@@ -30034,14 +31666,14 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
   __Pyx_INCREF(__pyx_int_0);
   __pyx_v_x = __pyx_int_0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":390
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":390
  * 
  *         x = 0
  *         for pattern1 in J_set:             # <<<<<<<<<<<<<<
  *             for pattern2 in J_set:
  *                 if len(pattern1) + len(pattern2) + 1 < self.max_length:
  */
-  __pyx_t_1 = PyObject_GetIter(((PyObject *)__pyx_v_J_set)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_GetIter(((PyObject *)__pyx_v_J_set)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_1);
   __pyx_t_4 = Py_TYPE(__pyx_t_1)->tp_iternext;
   for (;;) {
@@ -30050,7 +31682,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
       if (unlikely(!__pyx_t_3)) {
         if (PyErr_Occurred()) {
           if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
-          else {__pyx_filename = __pyx_f[12]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          else {__pyx_filename = __pyx_f[11]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         }
         break;
       }
@@ -30060,14 +31692,14 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
     __pyx_v_pattern1 = __pyx_t_3;
     __pyx_t_3 = 0;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":391
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":391
  *         x = 0
  *         for pattern1 in J_set:
  *             for pattern2 in J_set:             # <<<<<<<<<<<<<<
  *                 if len(pattern1) + len(pattern2) + 1 < self.max_length:
  *                     combined_pattern = pattern1 + (-1,) + pattern2
  */
-    __pyx_t_3 = PyObject_GetIter(((PyObject *)__pyx_v_J_set)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_3 = PyObject_GetIter(((PyObject *)__pyx_v_J_set)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_3);
     __pyx_t_20 = Py_TYPE(__pyx_t_3)->tp_iternext;
     for (;;) {
@@ -30076,7 +31708,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
         if (unlikely(!__pyx_t_8)) {
           if (PyErr_Occurred()) {
             if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
-            else {__pyx_filename = __pyx_f[12]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            else {__pyx_filename = __pyx_f[11]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           }
           break;
         }
@@ -30086,42 +31718,42 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
       __pyx_v_pattern2 = __pyx_t_8;
       __pyx_t_8 = 0;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":392
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":392
  *         for pattern1 in J_set:
  *             for pattern2 in J_set:
  *                 if len(pattern1) + len(pattern2) + 1 < self.max_length:             # <<<<<<<<<<<<<<
  *                     combined_pattern = pattern1 + (-1,) + pattern2
  *                     J2_set.add(combined_pattern)
  */
-      __pyx_t_2 = PyObject_Length(__pyx_v_pattern1); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 392; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      __pyx_t_14 = PyObject_Length(__pyx_v_pattern2); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 392; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_2 = PyObject_Length(__pyx_v_pattern1); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 392; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_14 = PyObject_Length(__pyx_v_pattern2); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 392; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __pyx_t_19 = (((__pyx_t_2 + __pyx_t_14) + 1) < __pyx_v_self->max_length);
       if (__pyx_t_19) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":393
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":393
  *             for pattern2 in J_set:
  *                 if len(pattern1) + len(pattern2) + 1 < self.max_length:
  *                     combined_pattern = pattern1 + (-1,) + pattern2             # <<<<<<<<<<<<<<
  *                     J2_set.add(combined_pattern)
  * 
  */
-        __pyx_t_8 = PyNumber_Add(__pyx_v_pattern1, ((PyObject *)__pyx_k_tuple_79)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 393; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_8 = PyNumber_Add(__pyx_v_pattern1, ((PyObject *)__pyx_k_tuple_79)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 393; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_8);
-        __pyx_t_7 = PyNumber_Add(__pyx_t_8, __pyx_v_pattern2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 393; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_7 = PyNumber_Add(__pyx_t_8, __pyx_v_pattern2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 393; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_7);
         __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
         __Pyx_XDECREF(__pyx_v_combined_pattern);
         __pyx_v_combined_pattern = __pyx_t_7;
         __pyx_t_7 = 0;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":394
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":394
  *                 if len(pattern1) + len(pattern2) + 1 < self.max_length:
  *                     combined_pattern = pattern1 + (-1,) + pattern2
  *                     J2_set.add(combined_pattern)             # <<<<<<<<<<<<<<
  * 
  *         for pattern1 in I_set:
  */
-        __pyx_t_15 = PySet_Add(__pyx_v_J2_set, __pyx_v_combined_pattern); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 394; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_15 = PySet_Add(__pyx_v_J2_set, __pyx_v_combined_pattern); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 394; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         goto __pyx_L40;
       }
       __pyx_L40:;
@@ -30130,14 +31762,14 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
   }
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":396
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":396
  *                     J2_set.add(combined_pattern)
  * 
  *         for pattern1 in I_set:             # <<<<<<<<<<<<<<
  *             for pattern2 in I_set:
  *                 x = x+1
  */
-  __pyx_t_1 = PyObject_GetIter(((PyObject *)__pyx_v_I_set)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 396; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_GetIter(((PyObject *)__pyx_v_I_set)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 396; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_1);
   __pyx_t_4 = Py_TYPE(__pyx_t_1)->tp_iternext;
   for (;;) {
@@ -30146,7 +31778,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
       if (unlikely(!__pyx_t_3)) {
         if (PyErr_Occurred()) {
           if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
-          else {__pyx_filename = __pyx_f[12]; __pyx_lineno = 396; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          else {__pyx_filename = __pyx_f[11]; __pyx_lineno = 396; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         }
         break;
       }
@@ -30156,14 +31788,14 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
     __pyx_v_pattern1 = __pyx_t_3;
     __pyx_t_3 = 0;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":397
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":397
  * 
  *         for pattern1 in I_set:
  *             for pattern2 in I_set:             # <<<<<<<<<<<<<<
  *                 x = x+1
  *                 if len(pattern1) + len(pattern2) + 1 <= self.max_length:
  */
-    __pyx_t_3 = PyObject_GetIter(((PyObject *)__pyx_v_I_set)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_3 = PyObject_GetIter(((PyObject *)__pyx_v_I_set)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_3);
     __pyx_t_20 = Py_TYPE(__pyx_t_3)->tp_iternext;
     for (;;) {
@@ -30172,7 +31804,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
         if (unlikely(!__pyx_t_7)) {
           if (PyErr_Occurred()) {
             if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
-            else {__pyx_filename = __pyx_f[12]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            else {__pyx_filename = __pyx_f[11]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           }
           break;
         }
@@ -30182,55 +31814,55 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
       __pyx_v_pattern2 = __pyx_t_7;
       __pyx_t_7 = 0;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":398
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":398
  *         for pattern1 in I_set:
  *             for pattern2 in I_set:
  *                 x = x+1             # <<<<<<<<<<<<<<
  *                 if len(pattern1) + len(pattern2) + 1 <= self.max_length:
  *                     combined_pattern = pattern1 + (-1,) + pattern2
  */
-      __pyx_t_7 = PyNumber_Add(__pyx_v_x, __pyx_int_1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_7 = PyNumber_Add(__pyx_v_x, __pyx_int_1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_7);
       __Pyx_DECREF(__pyx_v_x);
       __pyx_v_x = __pyx_t_7;
       __pyx_t_7 = 0;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":399
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":399
  *             for pattern2 in I_set:
  *                 x = x+1
  *                 if len(pattern1) + len(pattern2) + 1 <= self.max_length:             # <<<<<<<<<<<<<<
  *                     combined_pattern = pattern1 + (-1,) + pattern2
  *                     IJ_set.add(combined_pattern)
  */
-      __pyx_t_14 = PyObject_Length(__pyx_v_pattern1); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      __pyx_t_2 = PyObject_Length(__pyx_v_pattern2); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_14 = PyObject_Length(__pyx_v_pattern1); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_2 = PyObject_Length(__pyx_v_pattern2); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __pyx_t_19 = (((__pyx_t_14 + __pyx_t_2) + 1) <= __pyx_v_self->max_length);
       if (__pyx_t_19) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":400
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":400
  *                 x = x+1
  *                 if len(pattern1) + len(pattern2) + 1 <= self.max_length:
  *                     combined_pattern = pattern1 + (-1,) + pattern2             # <<<<<<<<<<<<<<
  *                     IJ_set.add(combined_pattern)
  * 
  */
-        __pyx_t_7 = PyNumber_Add(__pyx_v_pattern1, ((PyObject *)__pyx_k_tuple_80)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 400; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_7 = PyNumber_Add(__pyx_v_pattern1, ((PyObject *)__pyx_k_tuple_80)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 400; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_7);
-        __pyx_t_8 = PyNumber_Add(__pyx_t_7, __pyx_v_pattern2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 400; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_8 = PyNumber_Add(__pyx_t_7, __pyx_v_pattern2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 400; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_8);
         __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
         __Pyx_XDECREF(__pyx_v_combined_pattern);
         __pyx_v_combined_pattern = __pyx_t_8;
         __pyx_t_8 = 0;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":401
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":401
  *                 if len(pattern1) + len(pattern2) + 1 <= self.max_length:
  *                     combined_pattern = pattern1 + (-1,) + pattern2
  *                     IJ_set.add(combined_pattern)             # <<<<<<<<<<<<<<
  * 
  *         for pattern1 in I_set:
  */
-        __pyx_t_15 = PySet_Add(__pyx_v_IJ_set, __pyx_v_combined_pattern); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 401; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_15 = PySet_Add(__pyx_v_IJ_set, __pyx_v_combined_pattern); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 401; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         goto __pyx_L45;
       }
       __pyx_L45:;
@@ -30239,14 +31871,14 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
   }
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":403
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":403
  *                     IJ_set.add(combined_pattern)
  * 
  *         for pattern1 in I_set:             # <<<<<<<<<<<<<<
  *             for pattern2 in J2_set:
  *                 x = x+2
  */
-  __pyx_t_1 = PyObject_GetIter(((PyObject *)__pyx_v_I_set)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 403; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_GetIter(((PyObject *)__pyx_v_I_set)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 403; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_1);
   __pyx_t_4 = Py_TYPE(__pyx_t_1)->tp_iternext;
   for (;;) {
@@ -30255,7 +31887,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
       if (unlikely(!__pyx_t_3)) {
         if (PyErr_Occurred()) {
           if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
-          else {__pyx_filename = __pyx_f[12]; __pyx_lineno = 403; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          else {__pyx_filename = __pyx_f[11]; __pyx_lineno = 403; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         }
         break;
       }
@@ -30265,14 +31897,14 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
     __pyx_v_pattern1 = __pyx_t_3;
     __pyx_t_3 = 0;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":404
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":404
  * 
  *         for pattern1 in I_set:
  *             for pattern2 in J2_set:             # <<<<<<<<<<<<<<
  *                 x = x+2
  *                 if len(pattern1) + len(pattern2) + 1<= self.max_length:
  */
-    __pyx_t_3 = PyObject_GetIter(((PyObject *)__pyx_v_J2_set)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 404; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_3 = PyObject_GetIter(((PyObject *)__pyx_v_J2_set)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 404; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_3);
     __pyx_t_20 = Py_TYPE(__pyx_t_3)->tp_iternext;
     for (;;) {
@@ -30281,7 +31913,7 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
         if (unlikely(!__pyx_t_8)) {
           if (PyErr_Occurred()) {
             if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
-            else {__pyx_filename = __pyx_f[12]; __pyx_lineno = 404; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            else {__pyx_filename = __pyx_f[11]; __pyx_lineno = 404; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           }
           break;
         }
@@ -30291,80 +31923,80 @@ static PyObject *__pyx_pf_3_sa_14Precomputation_6precompute(struct __pyx_obj_3_s
       __pyx_v_pattern2 = __pyx_t_8;
       __pyx_t_8 = 0;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":405
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":405
  *         for pattern1 in I_set:
  *             for pattern2 in J2_set:
  *                 x = x+2             # <<<<<<<<<<<<<<
  *                 if len(pattern1) + len(pattern2) + 1<= self.max_length:
  *                     combined_pattern = pattern1 + (-1,) + pattern2
  */
-      __pyx_t_8 = PyNumber_Add(__pyx_v_x, __pyx_int_2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 405; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_8 = PyNumber_Add(__pyx_v_x, __pyx_int_2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 405; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_8);
       __Pyx_DECREF(__pyx_v_x);
       __pyx_v_x = __pyx_t_8;
       __pyx_t_8 = 0;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":406
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":406
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":407
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":407
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+        __pyx_t_7 = PyNumber_Add(__pyx_t_8, __pyx_v_pattern2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 407; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":408
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":408
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":409
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":409
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+        __pyx_t_7 = PyNumber_Add(__pyx_v_pattern2, ((PyObject *)__pyx_k_tuple_82)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+        __pyx_t_8 = PyNumber_Add(__pyx_t_7, __pyx_v_pattern1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":410
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":410
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+        __pyx_t_15 = PySet_Add(__pyx_v_IJ_set, __pyx_v_combined_pattern); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":412
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":412
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+  __pyx_t_14 = PyDict_Size(((PyObject *)__pyx_v_pattern_rank)); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":413
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":413
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-  __pyx_t_3 = PyInt_FromLong(__pyx_v_N); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 413; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":414
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":414
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-  __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_IntList)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":415
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":415
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-    {__pyx_filename = __pyx_f[12]; __pyx_lineno = 415; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    {__pyx_filename = __pyx_f[11]; __pyx_lineno = 415; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":416
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":416
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":417
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":417
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":418
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":418
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-              else {__pyx_filename = __pyx_f[12]; __pyx_lineno = 418; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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         __pyx_t_3 = 0;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":419
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":419
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+        __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 419; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":420
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":420
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":422
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":423
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":423
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":425
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":425
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":426
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":426
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":427
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":427
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":428
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":428
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":429
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":446
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":446
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":447
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":448
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":449
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":451
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":452
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":453
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":453
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":454
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":11
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+  __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_IntList)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -31810,20 +33237,20 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
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   __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":43
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":34
  * 
  *         self.sa = IntList(initial_len=N)
  *         self.ha = IntList(initial_len=V+1)             # <<<<<<<<<<<<<<
  * 
  *         isa = IntList(initial_len=N)
  */
-  __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __pyx_t_2 = PyInt_FromLong((__pyx_v_V + 1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = PyInt_FromLong((__pyx_v_V + 1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__initial_len), __pyx_t_2) < 0) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__initial_len), __pyx_t_2) < 0) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
-  __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_IntList)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_IntList)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_2);
   __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
   __Pyx_GIVEREF(__pyx_t_2);
@@ -31832,45 +33259,45 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
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   __pyx_t_2 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":45
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":36
  *         self.ha = IntList(initial_len=V+1)
  * 
  *         isa = IntList(initial_len=N)             # <<<<<<<<<<<<<<
  *         word_count = IntList(initial_len=V+1)
  * 
  */
-  __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(((PyObject *)__pyx_t_2));
-  __pyx_t_1 = PyInt_FromLong(__pyx_v_N); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyInt_FromLong(__pyx_v_N); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_1);
-  if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__initial_len), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__initial_len), __pyx_t_1) < 0) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
-  __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_IntList)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_IntList)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_1);
   __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
   __pyx_v_isa = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":46
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":37
  * 
  *         isa = IntList(initial_len=N)
  *         word_count = IntList(initial_len=V+1)             # <<<<<<<<<<<<<<
  * 
  *         '''Step 1: bucket sort data'''
  */
-  __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(((PyObject *)__pyx_t_1));
-  __pyx_t_2 = PyInt_FromLong((__pyx_v_V + 1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = PyInt_FromLong((__pyx_v_V + 1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_2);
-  if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__initial_len), __pyx_t_2) < 0) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__initial_len), __pyx_t_2) < 0) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
-  __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_IntList)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_IntList)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_2);
   __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
   __pyx_v_word_count = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_2);
   __pyx_t_2 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":49
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":40
  * 
  *         '''Step 1: bucket sort data'''
  *         cdef float sort_start_time = monitor_cpu()             # <<<<<<<<<<<<<<
@@ -31879,7 +33306,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
  */
   __pyx_v_sort_start_time = __pyx_f_3_sa_monitor_cpu();
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":50
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":41
  *         '''Step 1: bucket sort data'''
  *         cdef float sort_start_time = monitor_cpu()
  *         cdef float start_time = sort_start_time             # <<<<<<<<<<<<<<
@@ -31888,7 +33315,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
  */
   __pyx_v_start_time = __pyx_v_sort_start_time;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":51
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":42
  *         cdef float sort_start_time = monitor_cpu()
  *         cdef float start_time = sort_start_time
  *         for i from 0 <= i < N:             # <<<<<<<<<<<<<<
@@ -31898,7 +33325,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
   __pyx_t_4 = __pyx_v_N;
   for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_4; __pyx_v_i++) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":52
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":43
  *         cdef float start_time = sort_start_time
  *         for i from 0 <= i < N:
  *             a_i = self.darray.data.arr[i]             # <<<<<<<<<<<<<<
@@ -31907,7 +33334,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
  */
     __pyx_v_a_i = (__pyx_v_self->darray->data->arr[__pyx_v_i]);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":53
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":44
  *         for i from 0 <= i < N:
  *             a_i = self.darray.data.arr[i]
  *             word_count.arr[a_i] = word_count.arr[a_i] + 1             # <<<<<<<<<<<<<<
@@ -31917,7 +33344,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
     (__pyx_v_word_count->arr[__pyx_v_a_i]) = ((__pyx_v_word_count->arr[__pyx_v_a_i]) + 1);
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":55
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":46
  *             word_count.arr[a_i] = word_count.arr[a_i] + 1
  * 
  *         n = 0             # <<<<<<<<<<<<<<
@@ -31926,7 +33353,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
  */
   __pyx_v_n = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":56
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":47
  * 
  *         n = 0
  *         for i from 0 <= i < V+1:             # <<<<<<<<<<<<<<
@@ -31936,7 +33363,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
   __pyx_t_5 = (__pyx_v_V + 1);
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":57
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":48
  *         n = 0
  *         for i from 0 <= i < V+1:
  *             self.ha.arr[i] = n             # <<<<<<<<<<<<<<
@@ -31945,7 +33372,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
  */
     (__pyx_v_self->ha->arr[__pyx_v_i]) = __pyx_v_n;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":58
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":49
  *         for i from 0 <= i < V+1:
  *             self.ha.arr[i] = n
  *             n = n + word_count.arr[i]             # <<<<<<<<<<<<<<
@@ -31954,7 +33381,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
  */
     __pyx_v_n = (__pyx_v_n + (__pyx_v_word_count->arr[__pyx_v_i]));
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":59
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":50
  *             self.ha.arr[i] = n
  *             n = n + word_count.arr[i]
  *             word_count.arr[i] = 0             # <<<<<<<<<<<<<<
@@ -31964,7 +33391,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
     (__pyx_v_word_count->arr[__pyx_v_i]) = 0;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":61
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":52
  *             word_count.arr[i] = 0
  * 
  *         for i from 0 <= i < N:             # <<<<<<<<<<<<<<
@@ -31974,7 +33401,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
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   for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_4; __pyx_v_i++) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":62
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":53
  * 
  *         for i from 0 <= i < N:
  *             a_i = self.darray.data.arr[i]             # <<<<<<<<<<<<<<
@@ -31983,7 +33410,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
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     __pyx_v_a_i = (__pyx_v_self->darray->data->arr[__pyx_v_i]);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":63
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":54
  *         for i from 0 <= i < N:
  *             a_i = self.darray.data.arr[i]
  *             self.sa.arr[self.ha.arr[a_i] + word_count.arr[a_i]] = i             # <<<<<<<<<<<<<<
@@ -31992,7 +33419,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
  */
     (__pyx_v_self->sa->arr[((__pyx_v_self->ha->arr[__pyx_v_a_i]) + (__pyx_v_word_count->arr[__pyx_v_a_i]))]) = __pyx_v_i;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":64
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":55
  *             a_i = self.darray.data.arr[i]
  *             self.sa.arr[self.ha.arr[a_i] + word_count.arr[a_i]] = i
  *             isa.arr[i] = self.ha.arr[a_i + 1] - 1 # bucket pointer is last index in bucket             # <<<<<<<<<<<<<<
@@ -32001,7 +33428,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
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     (__pyx_v_isa->arr[__pyx_v_i]) = ((__pyx_v_self->ha->arr[(__pyx_v_a_i + 1)]) - 1);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":65
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":56
  *             self.sa.arr[self.ha.arr[a_i] + word_count.arr[a_i]] = i
  *             isa.arr[i] = self.ha.arr[a_i + 1] - 1 # bucket pointer is last index in bucket
  *             word_count.arr[a_i] = word_count.arr[a_i] + 1             # <<<<<<<<<<<<<<
@@ -32011,7 +33438,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
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   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":68
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":59
  * 
  *         '''Determine size of initial runs'''
  *         current_run = 0             # <<<<<<<<<<<<<<
@@ -32020,7 +33447,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
  */
   __pyx_v_current_run = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":69
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":60
  *         '''Determine size of initial runs'''
  *         current_run = 0
  *         for i from 0 <= i < V+1:             # <<<<<<<<<<<<<<
@@ -32030,7 +33457,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":70
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":61
  *         current_run = 0
  *         for i from 0 <= i < V+1:
  *             if i < V and self.ha.arr[i+1] - self.ha.arr[i] == 1:             # <<<<<<<<<<<<<<
@@ -32046,7 +33473,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
     }
     if (__pyx_t_8) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":71
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":62
  *         for i from 0 <= i < V+1:
  *             if i < V and self.ha.arr[i+1] - self.ha.arr[i] == 1:
  *                 current_run = current_run + 1             # <<<<<<<<<<<<<<
@@ -32058,7 +33485,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
     }
     /*else*/ {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":73
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":64
  *                 current_run = current_run + 1
  *             else:
  *                 if current_run > 0:             # <<<<<<<<<<<<<<
@@ -32068,7 +33495,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
       __pyx_t_8 = (__pyx_v_current_run > 0);
       if (__pyx_t_8) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":74
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":65
  *             else:
  *                 if current_run > 0:
  *                     self.sa.arr[self.ha.arr[i] - current_run] = -current_run             # <<<<<<<<<<<<<<
@@ -32077,7 +33504,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":75
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":66
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":77
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":68
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  *         logger.info("    Bucket sort took %f seconds", (monitor_cpu() - sort_start_time))             # <<<<<<<<<<<<<<
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+  __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__logger); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__info); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_2 = PyFloat_FromDouble((__pyx_f_3_sa_monitor_cpu() - __pyx_v_sort_start_time)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":80
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":71
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@@ -32129,7 +33556,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":81
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":72
  *         '''Step 2: prefix-doubling sort'''
  *         h = 1
  *         while self.sa.arr[0] != -N:             # <<<<<<<<<<<<<<
@@ -32140,7 +33567,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
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     if (!__pyx_t_8) break;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":82
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":73
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  *             sort_start_time = monitor_cpu()             # <<<<<<<<<<<<<<
@@ -32149,21 +33576,21 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
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     __pyx_v_sort_start_time = __pyx_f_3_sa_monitor_cpu();
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":83
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":74
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+    __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__logger); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_9 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__debug); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_2 = PyInt_FromLong(__pyx_v_h); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_2 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":84
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":75
  *             sort_start_time = monitor_cpu()
  *             logger.debug("    Refining, sort depth = %d", h)
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@@ -32186,7 +33613,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":85
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":76
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  *             skip = 0             # <<<<<<<<<<<<<<
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":86
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":77
  *             i = 0
  *             skip = 0
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@@ -32206,7 +33633,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":87
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":78
  *             skip = 0
  *             while i < N:
  *                 if self.sa.arr[i] < 0:             # <<<<<<<<<<<<<<
@@ -32216,7 +33643,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
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       if (__pyx_t_8) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":88
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":79
  *             while i < N:
  *                 if self.sa.arr[i] < 0:
  *                     skip = skip + self.sa.arr[i]             # <<<<<<<<<<<<<<
@@ -32225,7 +33652,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":89
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":80
  *                 if self.sa.arr[i] < 0:
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  *                     i = i - self.sa.arr[i]             # <<<<<<<<<<<<<<
@@ -32237,7 +33664,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
       }
       /*else*/ {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":91
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":82
  *                     i = i - self.sa.arr[i]
  *                 else:
  *                     if skip < 0:             # <<<<<<<<<<<<<<
@@ -32247,7 +33674,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
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         if (__pyx_t_8) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":92
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":83
  *                 else:
  *                     if skip < 0:
  *                         self.sa.arr[i+skip] = skip             # <<<<<<<<<<<<<<
@@ -32256,7 +33683,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":93
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":84
  *                     if skip < 0:
  *                         self.sa.arr[i+skip] = skip
  *                         skip = 0             # <<<<<<<<<<<<<<
@@ -32268,7 +33695,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":94
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":85
  *                         self.sa.arr[i+skip] = skip
  *                         skip = 0
  *                     j = isa.arr[self.sa.arr[i]]             # <<<<<<<<<<<<<<
@@ -32277,22 +33704,22 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":95
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":86
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-        __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__q3sort); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 95; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__q3sort); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+        __pyx_t_1 = PyInt_FromLong(__pyx_v_i); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+        __pyx_t_9 = PyInt_FromLong(__pyx_v_j); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+        __pyx_t_10 = PyInt_FromLong(__pyx_v_h); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+        __pyx_t_11 = PyTuple_New(4); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+        __pyx_t_10 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_11), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":96
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":87
  *                     j = isa.arr[self.sa.arr[i]]
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@@ -32324,7 +33751,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":97
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":88
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@@ -32334,7 +33761,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
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     if (__pyx_t_8) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":98
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":89
  *                     i = j+1
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@@ -32346,7 +33773,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":99
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":90
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  *                 self.sa.arr[i+skip] = skip
  *             h = h * 2             # <<<<<<<<<<<<<<
@@ -32355,21 +33782,21 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_10read_text(struct __pyx_obj_3_sa_S
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     __pyx_v_h = (__pyx_v_h * 2);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":100
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":91
  *                 self.sa.arr[i+skip] = skip
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":103
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":104
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":105
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":106
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":107
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+    __pyx_v_i = __Pyx_PyInt_AsInt(values[0]); if (unlikely((__pyx_v_i == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 100; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+    __pyx_v_j = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_j == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 100; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+  __Pyx_RaiseArgtupleInvalid("q3sort", 0, 4, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[12]; __pyx_lineno = 100; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_isa), __pyx_ptype_3_sa_IntList, 1, "isa", 0))) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 100; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_r = __pyx_pf_3_sa_11SuffixArray_6q3sort(((struct __pyx_obj_3_sa_SuffixArray *)__pyx_v_self), __pyx_v_i, __pyx_v_j, __pyx_v_h, __pyx_v_isa, __pyx_v_pad);
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@@ -32568,7 +33995,7 @@ static PyObject *__pyx_pw_3_sa_11SuffixArray_13q3sort(PyObject *__pyx_v_self, Py
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":109
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":116
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":117
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  *             return
  */
-    __pyx_t_2 = PyInt_FromLong(__pyx_v_i); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = PyInt_FromLong(__pyx_v_i); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 108; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_2);
-    __pyx_t_3 = PyInt_FromLong(__pyx_v_j); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_3 = PyInt_FromLong(__pyx_v_j); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 108; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_3);
-    __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 108; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_4);
     PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_2);
     __Pyx_GIVEREF(__pyx_t_2);
@@ -32627,25 +34054,25 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12q3sort(struct __pyx_obj_3_sa_Suff
     __Pyx_GIVEREF(__pyx_t_3);
     __pyx_t_2 = 0;
     __pyx_t_3 = 0;
-    __pyx_t_3 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_95), ((PyObject *)__pyx_t_4)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_3 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_95), ((PyObject *)__pyx_t_4)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 108; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(((PyObject *)__pyx_t_3));
     __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
-    __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 108; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_4);
     PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)__pyx_t_3));
     __Pyx_GIVEREF(((PyObject *)__pyx_t_3));
     __pyx_t_3 = 0;
-    __pyx_t_3 = PyObject_Call(__pyx_builtin_Exception, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_3 = PyObject_Call(__pyx_builtin_Exception, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 108; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_3);
     __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
     __Pyx_Raise(__pyx_t_3, 0, 0, 0);
     __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
-    {__pyx_filename = __pyx_f[13]; __pyx_lineno = 117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    {__pyx_filename = __pyx_f[12]; __pyx_lineno = 108; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     goto __pyx_L3;
   }
   __pyx_L3:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":118
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":109
  *         if j-i < -1:
  *             raise Exception("Unexpected condition found in q3sort: sort from %d to %d" % (i,j))
  *         if j-i == -1:    # recursive base case -- empty interval             # <<<<<<<<<<<<<<
@@ -32655,7 +34082,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12q3sort(struct __pyx_obj_3_sa_Suff
   __pyx_t_1 = ((__pyx_v_j - __pyx_v_i) == -1);
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":119
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":110
  *             raise Exception("Unexpected condition found in q3sort: sort from %d to %d" % (i,j))
  *         if j-i == -1:    # recursive base case -- empty interval
  *             return             # <<<<<<<<<<<<<<
@@ -32669,7 +34096,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12q3sort(struct __pyx_obj_3_sa_Suff
   }
   __pyx_L4:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":120
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":111
  *         if j-i == -1:    # recursive base case -- empty interval
  *             return
  *         if (j-i == 0):    # recursive base case -- singleton interval             # <<<<<<<<<<<<<<
@@ -32679,7 +34106,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12q3sort(struct __pyx_obj_3_sa_Suff
   __pyx_t_1 = ((__pyx_v_j - __pyx_v_i) == 0);
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":121
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":112
  *             return
  *         if (j-i == 0):    # recursive base case -- singleton interval
  *             isa.arr[self.sa.arr[i]] = i             # <<<<<<<<<<<<<<
@@ -32688,7 +34115,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12q3sort(struct __pyx_obj_3_sa_Suff
  */
     (__pyx_v_isa->arr[(__pyx_v_self->sa->arr[__pyx_v_i])]) = __pyx_v_i;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":122
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":113
  *         if (j-i == 0):    # recursive base case -- singleton interval
  *             isa.arr[self.sa.arr[i]] = i
  *             self.sa.arr[i] = -1             # <<<<<<<<<<<<<<
@@ -32697,7 +34124,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12q3sort(struct __pyx_obj_3_sa_Suff
  */
     (__pyx_v_self->sa->arr[__pyx_v_i]) = -1;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":123
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":114
  *             isa.arr[self.sa.arr[i]] = i
  *             self.sa.arr[i] = -1
  *             return             # <<<<<<<<<<<<<<
@@ -32711,7 +34138,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12q3sort(struct __pyx_obj_3_sa_Suff
   }
   __pyx_L5:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":132
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":123
  *         # If the method of assigning word_id's is changed, this method
  *         # may need to be reconsidered as well.
  *         midpoint = (i+j)/2             # <<<<<<<<<<<<<<
@@ -32720,7 +34147,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12q3sort(struct __pyx_obj_3_sa_Suff
  */
   __pyx_v_midpoint = __Pyx_div_long((__pyx_v_i + __pyx_v_j), 2);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":133
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":124
  *         # may need to be reconsidered as well.
  *         midpoint = (i+j)/2
  *         pval = isa.arr[self.sa.arr[midpoint] + h]             # <<<<<<<<<<<<<<
@@ -32729,7 +34156,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12q3sort(struct __pyx_obj_3_sa_Suff
  */
   __pyx_v_pval = (__pyx_v_isa->arr[((__pyx_v_self->sa->arr[__pyx_v_midpoint]) + __pyx_v_h)]);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":134
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":125
  *         midpoint = (i+j)/2
  *         pval = isa.arr[self.sa.arr[midpoint] + h]
  *         if i != midpoint:             # <<<<<<<<<<<<<<
@@ -32739,7 +34166,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12q3sort(struct __pyx_obj_3_sa_Suff
   __pyx_t_1 = (__pyx_v_i != __pyx_v_midpoint);
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":135
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":126
  *         pval = isa.arr[self.sa.arr[midpoint] + h]
  *         if i != midpoint:
  *             tmp = self.sa.arr[midpoint]             # <<<<<<<<<<<<<<
@@ -32748,7 +34175,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12q3sort(struct __pyx_obj_3_sa_Suff
  */
     __pyx_v_tmp = (__pyx_v_self->sa->arr[__pyx_v_midpoint]);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":136
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":127
  *         if i != midpoint:
  *             tmp = self.sa.arr[midpoint]
  *             self.sa.arr[midpoint] = self.sa.arr[i]             # <<<<<<<<<<<<<<
@@ -32757,7 +34184,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12q3sort(struct __pyx_obj_3_sa_Suff
  */
     (__pyx_v_self->sa->arr[__pyx_v_midpoint]) = (__pyx_v_self->sa->arr[__pyx_v_i]);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":137
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":128
  *             tmp = self.sa.arr[midpoint]
  *             self.sa.arr[midpoint] = self.sa.arr[i]
  *             self.sa.arr[i] = tmp             # <<<<<<<<<<<<<<
@@ -32769,7 +34196,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12q3sort(struct __pyx_obj_3_sa_Suff
   }
   __pyx_L6:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":138
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":129
  *             self.sa.arr[midpoint] = self.sa.arr[i]
  *             self.sa.arr[i] = tmp
  *         phead = i             # <<<<<<<<<<<<<<
@@ -32778,7 +34205,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12q3sort(struct __pyx_obj_3_sa_Suff
  */
   __pyx_v_phead = __pyx_v_i;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":139
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":130
  *             self.sa.arr[i] = tmp
  *         phead = i
  *         ptail = i             # <<<<<<<<<<<<<<
@@ -32787,7 +34214,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12q3sort(struct __pyx_obj_3_sa_Suff
  */
   __pyx_v_ptail = __pyx_v_i;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":143
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":134
  *         # find the three partitions.    phead marks the first element
  *         # of the middle partition, and ptail marks the last element
  *         for k from i+1 <= k < j+1:             # <<<<<<<<<<<<<<
@@ -32797,7 +34224,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12q3sort(struct __pyx_obj_3_sa_Suff
   __pyx_t_5 = (__pyx_v_j + 1);
   for (__pyx_v_k = (__pyx_v_i + 1); __pyx_v_k < __pyx_t_5; __pyx_v_k++) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":144
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":135
  *         # of the middle partition, and ptail marks the last element
  *         for k from i+1 <= k < j+1:
  *             if isa.arr[self.sa.arr[k] + h] < pval:             # <<<<<<<<<<<<<<
@@ -32807,7 +34234,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12q3sort(struct __pyx_obj_3_sa_Suff
     __pyx_t_1 = ((__pyx_v_isa->arr[((__pyx_v_self->sa->arr[__pyx_v_k]) + __pyx_v_h)]) < __pyx_v_pval);
     if (__pyx_t_1) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":145
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":136
  *         for k from i+1 <= k < j+1:
  *             if isa.arr[self.sa.arr[k] + h] < pval:
  *                 if k > ptail+1:             # <<<<<<<<<<<<<<
@@ -32817,7 +34244,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12q3sort(struct __pyx_obj_3_sa_Suff
       __pyx_t_1 = (__pyx_v_k > (__pyx_v_ptail + 1));
       if (__pyx_t_1) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":146
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":137
  *             if isa.arr[self.sa.arr[k] + h] < pval:
  *                 if k > ptail+1:
  *                     tmp = self.sa.arr[phead]             # <<<<<<<<<<<<<<
@@ -32826,7 +34253,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12q3sort(struct __pyx_obj_3_sa_Suff
  */
         __pyx_v_tmp = (__pyx_v_self->sa->arr[__pyx_v_phead]);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":147
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":138
  *                 if k > ptail+1:
  *                     tmp = self.sa.arr[phead]
  *                     self.sa.arr[phead] = self.sa.arr[k]             # <<<<<<<<<<<<<<
@@ -32835,7 +34262,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12q3sort(struct __pyx_obj_3_sa_Suff
  */
         (__pyx_v_self->sa->arr[__pyx_v_phead]) = (__pyx_v_self->sa->arr[__pyx_v_k]);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":148
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":139
  *                     tmp = self.sa.arr[phead]
  *                     self.sa.arr[phead] = self.sa.arr[k]
  *                     self.sa.arr[k] = self.sa.arr[ptail+1]             # <<<<<<<<<<<<<<
@@ -32844,7 +34271,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12q3sort(struct __pyx_obj_3_sa_Suff
  */
         (__pyx_v_self->sa->arr[__pyx_v_k]) = (__pyx_v_self->sa->arr[(__pyx_v_ptail + 1)]);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":149
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":140
  *                     self.sa.arr[phead] = self.sa.arr[k]
  *                     self.sa.arr[k] = self.sa.arr[ptail+1]
  *                     self.sa.arr[ptail+1] = tmp             # <<<<<<<<<<<<<<
@@ -32856,7 +34283,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12q3sort(struct __pyx_obj_3_sa_Suff
       }
       /*else*/ {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":151
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":142
  *                     self.sa.arr[ptail+1] = tmp
  *                 else: # k == ptail+1
  *                     tmp = self.sa.arr[phead]             # <<<<<<<<<<<<<<
@@ -32865,7 +34292,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12q3sort(struct __pyx_obj_3_sa_Suff
  */
         __pyx_v_tmp = (__pyx_v_self->sa->arr[__pyx_v_phead]);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":152
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":143
  *                 else: # k == ptail+1
  *                     tmp = self.sa.arr[phead]
  *                     self.sa.arr[phead] = self.sa.arr[k]             # <<<<<<<<<<<<<<
@@ -32874,7 +34301,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12q3sort(struct __pyx_obj_3_sa_Suff
  */
         (__pyx_v_self->sa->arr[__pyx_v_phead]) = (__pyx_v_self->sa->arr[__pyx_v_k]);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":153
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":144
  *                     tmp = self.sa.arr[phead]
  *                     self.sa.arr[phead] = self.sa.arr[k]
  *                     self.sa.arr[k] = tmp             # <<<<<<<<<<<<<<
@@ -32885,7 +34312,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12q3sort(struct __pyx_obj_3_sa_Suff
       }
       __pyx_L10:;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":154
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":145
  *                     self.sa.arr[phead] = self.sa.arr[k]
  *                     self.sa.arr[k] = tmp
  *                 phead = phead + 1             # <<<<<<<<<<<<<<
@@ -32894,7 +34321,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12q3sort(struct __pyx_obj_3_sa_Suff
  */
       __pyx_v_phead = (__pyx_v_phead + 1);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":155
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":146
  *                     self.sa.arr[k] = tmp
  *                 phead = phead + 1
  *                 ptail = ptail + 1             # <<<<<<<<<<<<<<
@@ -32906,7 +34333,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12q3sort(struct __pyx_obj_3_sa_Suff
     }
     /*else*/ {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":157
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":148
  *                 ptail = ptail + 1
  *             else:
  *                 if isa.arr[self.sa.arr[k] + h] == pval:             # <<<<<<<<<<<<<<
@@ -32916,7 +34343,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12q3sort(struct __pyx_obj_3_sa_Suff
       __pyx_t_1 = ((__pyx_v_isa->arr[((__pyx_v_self->sa->arr[__pyx_v_k]) + __pyx_v_h)]) == __pyx_v_pval);
       if (__pyx_t_1) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":158
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":149
  *             else:
  *                 if isa.arr[self.sa.arr[k] + h] == pval:
  *                     if k > ptail+1:             # <<<<<<<<<<<<<<
@@ -32926,7 +34353,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12q3sort(struct __pyx_obj_3_sa_Suff
         __pyx_t_1 = (__pyx_v_k > (__pyx_v_ptail + 1));
         if (__pyx_t_1) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":159
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":150
  *                 if isa.arr[self.sa.arr[k] + h] == pval:
  *                     if k > ptail+1:
  *                         tmp = self.sa.arr[ptail+1]             # <<<<<<<<<<<<<<
@@ -32935,7 +34362,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12q3sort(struct __pyx_obj_3_sa_Suff
  */
           __pyx_v_tmp = (__pyx_v_self->sa->arr[(__pyx_v_ptail + 1)]);
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":160
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":151
  *                     if k > ptail+1:
  *                         tmp = self.sa.arr[ptail+1]
  *                         self.sa.arr[ptail+1] = self.sa.arr[k]             # <<<<<<<<<<<<<<
@@ -32944,7 +34371,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_12q3sort(struct __pyx_obj_3_sa_Suff
  */
           (__pyx_v_self->sa->arr[(__pyx_v_ptail + 1)]) = (__pyx_v_self->sa->arr[__pyx_v_k]);
 
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-                  else {__pyx_filename = __pyx_f[13]; __pyx_lineno = 200; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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@@ -33516,23 +34943,23 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_20write_enhanced(struct __pyx_obj_3
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-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":201
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+            __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_21), __pyx_v_a_i); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 192; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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+            __pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 192; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":202
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-          __pyx_t_2 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__write); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":203
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":194
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+            __pyx_t_8 = -1; __pyx_t_4 = PyObject_GetIter(((PyObject *)__pyx_v_self->ha)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 194; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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-              __pyx_t_2 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_8); __Pyx_INCREF(__pyx_t_2); __pyx_t_8++;
+              __pyx_t_2 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_8); __Pyx_INCREF(__pyx_t_2); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 194; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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+              __pyx_t_2 = PySequence_ITEM(__pyx_t_4, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 194; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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-              __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_8); __Pyx_INCREF(__pyx_t_2); __pyx_t_8++;
+              __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_8); __Pyx_INCREF(__pyx_t_2); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 194; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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+              __pyx_t_2 = PySequence_ITEM(__pyx_t_4, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 194; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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-                  else {__pyx_filename = __pyx_f[13]; __pyx_lineno = 203; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":204
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":195
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-            __pyx_t_2 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__write); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 204; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
+            __pyx_t_2 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__write); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 195; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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-            __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 204; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
+            __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 195; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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-            __pyx_t_10 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 204; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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@@ -33623,16 +35050,16 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_20write_enhanced(struct __pyx_obj_3
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":205
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":196
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+          __pyx_t_4 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__write); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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+          __pyx_t_10 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_k_tuple_97), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
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@@ -33647,7 +35074,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_20write_enhanced(struct __pyx_obj_3
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":198
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":189
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@@ -33673,11 +35100,11 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_20write_enhanced(struct __pyx_obj_3
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-            {__pyx_filename = __pyx_f[13]; __pyx_lineno = 198; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
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 }
 
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":210
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":201
  *         cdef int midpoint
  * 
  *         if low >= high:             # <<<<<<<<<<<<<<
@@ -33770,7 +35197,7 @@ static int __pyx_f_3_sa_11SuffixArray___search_high(struct __pyx_obj_3_sa_Suffix
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   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":211
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":202
  * 
  *         if low >= high:
  *             return high             # <<<<<<<<<<<<<<
@@ -33783,7 +35210,7 @@ static int __pyx_f_3_sa_11SuffixArray___search_high(struct __pyx_obj_3_sa_Suffix
   }
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":212
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":203
  *         if low >= high:
  *             return high
  *         midpoint = (high + low) / 2             # <<<<<<<<<<<<<<
@@ -33792,7 +35219,7 @@ static int __pyx_f_3_sa_11SuffixArray___search_high(struct __pyx_obj_3_sa_Suffix
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":213
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":204
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":214
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":205
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   }
   /*else*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":216
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":207
  *             return self.__search_high(word_id, offset, midpoint+1, high)
  *         else:
  *             return self.__search_high(word_id, offset, low, midpoint)             # <<<<<<<<<<<<<<
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   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":218
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":209
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":221
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":212
  *         cdef int midpoint
  * 
  *         if low >= high:             # <<<<<<<<<<<<<<
@@ -33858,7 +35285,7 @@ static int __pyx_f_3_sa_11SuffixArray___search_low(struct __pyx_obj_3_sa_SuffixA
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":222
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":213
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  *         if low >= high:
  *             return high             # <<<<<<<<<<<<<<
@@ -33871,7 +35298,7 @@ static int __pyx_f_3_sa_11SuffixArray___search_low(struct __pyx_obj_3_sa_SuffixA
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":223
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":214
  *         if low >= high:
  *             return high
  *         midpoint = (high + low) / 2             # <<<<<<<<<<<<<<
@@ -33880,7 +35307,7 @@ static int __pyx_f_3_sa_11SuffixArray___search_low(struct __pyx_obj_3_sa_SuffixA
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":224
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":215
  *             return high
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  *         if self.darray.data.arr[self.sa.arr[midpoint] + offset] == word_id:             # <<<<<<<<<<<<<<
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":225
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":216
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":227
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":218
  *             return self.__search_low(word_id, offset, low, midpoint)
  *         else:
  *             return self.__search_low(word_id, offset, midpoint+1, high)             # <<<<<<<<<<<<<<
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   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":229
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":220
  *             return self.__search_low(word_id, offset, midpoint+1, high)
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  *     cdef __get_range(self, int word_id, int offset, int low, int high, int midpoint):             # <<<<<<<<<<<<<<
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":230
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":221
  * 
  *     cdef __get_range(self, int word_id, int offset, int low, int high, int midpoint):
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+  __pyx_t_1 = PyInt_FromLong(((struct __pyx_vtabstruct_3_sa_SuffixArray *)__pyx_v_self->__pyx_vtab)->__pyx___search_low(__pyx_v_self, __pyx_v_word_id, __pyx_v_offset, __pyx_v_low, __pyx_v_midpoint)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":231
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":222
  *     cdef __get_range(self, int word_id, int offset, int low, int high, int midpoint):
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+  __pyx_t_2 = PyInt_FromLong(((struct __pyx_vtabstruct_3_sa_SuffixArray *)__pyx_v_self->__pyx_vtab)->__pyx___search_high(__pyx_v_self, __pyx_v_word_id, __pyx_v_offset, __pyx_v_midpoint, __pyx_v_high)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":233
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":224
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  *     cdef __lookup_helper(self, int word_id, int offset, int low, int high):             # <<<<<<<<<<<<<<
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":236
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":227
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":237
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":228
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  *         if offset == 0:
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+    __pyx_t_2 = PyInt_FromLong((__pyx_v_self->ha->arr[__pyx_v_word_id])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 228; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 228; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":238
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":229
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":239
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":230
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":241
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":232
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  * 
  *         midpoint = (high + low) / 2             # <<<<<<<<<<<<<<
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":242
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":233
  * 
  *         midpoint = (high + low) / 2
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":243
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":234
  *         midpoint = (high + low) / 2
  *         if self.darray.data.arr[self.sa.arr[midpoint] + offset] == word_id:
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@@ -34096,7 +35523,7 @@ static PyObject *__pyx_f_3_sa_11SuffixArray___lookup_helper(struct __pyx_obj_3_s
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+    __pyx_t_4 = ((struct __pyx_vtabstruct_3_sa_SuffixArray *)__pyx_v_self->__pyx_vtab)->__pyx___get_range(__pyx_v_self, __pyx_v_word_id, __pyx_v_offset, __pyx_v_low, __pyx_v_high, __pyx_v_midpoint); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -34105,7 +35532,7 @@ static PyObject *__pyx_f_3_sa_11SuffixArray___lookup_helper(struct __pyx_obj_3_s
   }
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":244
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":235
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":245
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":236
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+    __pyx_t_4 = ((struct __pyx_vtabstruct_3_sa_SuffixArray *)__pyx_v_self->__pyx_vtab)->__pyx___lookup_helper(__pyx_v_self, __pyx_v_word_id, __pyx_v_offset, __pyx_v_low, __pyx_v_midpoint); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 236; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":247
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":238
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  *         else:
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+    __pyx_t_4 = ((struct __pyx_vtabstruct_3_sa_SuffixArray *)__pyx_v_self->__pyx_vtab)->__pyx___lookup_helper(__pyx_v_self, __pyx_v_word_id, __pyx_v_offset, (__pyx_v_midpoint + 1), __pyx_v_high); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 238; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_4);
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@@ -34163,8 +35590,8 @@ static PyObject *__pyx_f_3_sa_11SuffixArray___lookup_helper(struct __pyx_obj_3_s
 }
 
 /* Python wrapper */
-static PyObject *__pyx_pw_3_sa_11SuffixArray_23lookup(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static PyObject *__pyx_pw_3_sa_11SuffixArray_23lookup(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pw_3_sa_11SuffixArray_17lookup(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static PyObject *__pyx_pw_3_sa_11SuffixArray_17lookup(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
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   int __pyx_v_offset;
   int __pyx_v_low;
@@ -34194,21 +35621,21 @@ static PyObject *__pyx_pw_3_sa_11SuffixArray_23lookup(PyObject *__pyx_v_self, Py
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-          __Pyx_RaiseArgtupleInvalid("lookup", 1, 4, 4, 1); {__pyx_filename = __pyx_f[13]; __pyx_lineno = 249; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("lookup", 1, 4, 4, 1); {__pyx_filename = __pyx_f[12]; __pyx_lineno = 240; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+          __Pyx_RaiseArgtupleInvalid("lookup", 1, 4, 4, 2); {__pyx_filename = __pyx_f[12]; __pyx_lineno = 240; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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         if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__high)) != 0)) kw_args--;
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-          __Pyx_RaiseArgtupleInvalid("lookup", 1, 4, 4, 3); {__pyx_filename = __pyx_f[13]; __pyx_lineno = 249; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("lookup", 1, 4, 4, 3); {__pyx_filename = __pyx_f[12]; __pyx_lineno = 240; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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       if (unlikely(kw_args > 0)) {
-        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "lookup") < 0)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 249; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "lookup") < 0)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 240; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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@@ -34219,24 +35646,24 @@ static PyObject *__pyx_pw_3_sa_11SuffixArray_23lookup(PyObject *__pyx_v_self, Py
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+    __pyx_v_offset = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_offset == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 240; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+    __pyx_v_low = __Pyx_PyInt_AsInt(values[2]); if (unlikely((__pyx_v_low == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 240; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+    __pyx_v_high = __Pyx_PyInt_AsInt(values[3]); if (unlikely((__pyx_v_high == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 240; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+  __Pyx_RaiseArgtupleInvalid("lookup", 1, 4, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[12]; __pyx_lineno = 240; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+  __pyx_r = __pyx_pf_3_sa_11SuffixArray_16lookup(((struct __pyx_obj_3_sa_SuffixArray *)__pyx_v_self), __pyx_v_word, __pyx_v_offset, __pyx_v_low, __pyx_v_high);
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":249
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  *             return self.__lookup_helper(word_id, offset, midpoint+1, high)
  * 
  *     def lookup(self, word, int offset, int low, int high):             # <<<<<<<<<<<<<<
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-static PyObject *__pyx_pf_3_sa_11SuffixArray_22lookup(struct __pyx_obj_3_sa_SuffixArray *__pyx_v_self, PyObject *__pyx_v_word, int __pyx_v_offset, int __pyx_v_low, int __pyx_v_high) {
+static PyObject *__pyx_pf_3_sa_11SuffixArray_16lookup(struct __pyx_obj_3_sa_SuffixArray *__pyx_v_self, PyObject *__pyx_v_word, int __pyx_v_offset, int __pyx_v_low, int __pyx_v_high) {
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@@ -34257,7 +35684,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_22lookup(struct __pyx_obj_3_sa_Suff
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":251
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":242
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@@ -34267,7 +35694,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_22lookup(struct __pyx_obj_3_sa_Suff
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":252
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":243
  *         cdef int wordid
  *         if low == -1:
  *             low = 0             # <<<<<<<<<<<<<<
@@ -34279,7 +35706,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_22lookup(struct __pyx_obj_3_sa_Suff
   }
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":253
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":244
  *         if low == -1:
  *             low = 0
  *         if high == -1:             # <<<<<<<<<<<<<<
@@ -34289,7 +35716,7 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_22lookup(struct __pyx_obj_3_sa_Suff
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":254
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":245
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  *         if high == -1:
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@@ -34298,36 +35725,36 @@ static PyObject *__pyx_pf_3_sa_11SuffixArray_22lookup(struct __pyx_obj_3_sa_Suff
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-    __pyx_t_3 = PyObject_Length(__pyx_t_2); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 254; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_3 = PyObject_Length(__pyx_t_2); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 245; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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     goto __pyx_L4;
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":255
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":246
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-  __pyx_t_1 = ((PySequence_Contains(__pyx_v_self->darray->word2id, __pyx_v_word))); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 255; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = (__Pyx_PySequence_Contains(__pyx_v_word, __pyx_v_self->darray->word2id, Py_EQ)); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 246; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":256
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":247
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+    __pyx_t_2 = PyObject_GetItem(__pyx_v_self->darray->word2id, __pyx_v_word); if (!__pyx_t_2) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":257
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":248
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-    __pyx_t_2 = ((struct __pyx_vtabstruct_3_sa_SuffixArray *)__pyx_v_self->__pyx_vtab)->__pyx___lookup_helper(__pyx_v_self, __pyx_t_4, __pyx_v_offset, __pyx_v_low, __pyx_v_high); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_4 = __Pyx_PyInt_AsInt(__pyx_v_word_id); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = ((struct __pyx_vtabstruct_3_sa_SuffixArray *)__pyx_v_self->__pyx_vtab)->__pyx___lookup_helper(__pyx_v_self, __pyx_t_4, __pyx_v_offset, __pyx_v_low, __pyx_v_high); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   }
   /*else*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":259
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":250
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   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":21
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":22
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":40
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  *     def __cinit__(self):
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  * cdef class ExtendedTrieNode(TrieNode):
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-  __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 40; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(((PyObject *)__pyx_t_1));
   __Pyx_GIVEREF(((PyObject *)__pyx_t_1));
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@@ -34438,7 +35865,7 @@ static PyObject *__pyx_pw_3_sa_8TrieNode_8children_1__get__(PyObject *__pyx_v_se
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":19
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":37
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     PyObject* values[3] = {0,0,0};
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":29
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":47
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@@ -34566,7 +35993,7 @@ static int __pyx_pw_3_sa_16ExtendedTrieNode_1__cinit__(PyObject *__pyx_v_self, P
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+        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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@@ -34583,7 +36010,7 @@ static int __pyx_pw_3_sa_16ExtendedTrieNode_1__cinit__(PyObject *__pyx_v_self, P
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-  __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 0, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+  __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 0, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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@@ -34599,7 +36026,7 @@ static int __pyx_pf_3_sa_16ExtendedTrieNode___cinit__(struct __pyx_obj_3_sa_Exte
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":30
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":48
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   __pyx_v_self->phrase = __pyx_v_phrase;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":31
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":49
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":32
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-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":25
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-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":26
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":40
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":41
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":45
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-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":65
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":66
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":71
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":89
  *             arr=None, int num_subpatterns=1):
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  *         self.sa_high = sa_high             # <<<<<<<<<<<<<<
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":72
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":90
  *         self.sa_low = sa_low
  *         self.sa_high = sa_high
  *         self.arr_low = arr_low             # <<<<<<<<<<<<<<
@@ -35490,7 +36917,7 @@ static int __pyx_pf_3_sa_14PhraseLocation___cinit__(struct __pyx_obj_3_sa_Phrase
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   __pyx_v_self->arr_low = __pyx_v_arr_low;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":73
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":91
  *         self.sa_high = sa_high
  *         self.arr_low = arr_low
  *         self.arr_high = arr_high             # <<<<<<<<<<<<<<
@@ -35499,21 +36926,21 @@ static int __pyx_pf_3_sa_14PhraseLocation___cinit__(struct __pyx_obj_3_sa_Phrase
  */
   __pyx_v_self->arr_high = __pyx_v_arr_high;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":74
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":92
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  *         self.arr_high = arr_high
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+  if (!(likely(((__pyx_v_arr) == Py_None) || likely(__Pyx_TypeTest(__pyx_v_arr, __pyx_ptype_3_sa_IntList))))) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 92; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":75
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":93
  *         self.arr_high = arr_high
  *         self.arr = arr
  *         self.num_subpatterns = num_subpatterns             # <<<<<<<<<<<<<<
@@ -35560,11 +36987,11 @@ static int __pyx_pw_3_sa_7Sampler_1__cinit__(PyObject *__pyx_v_self, PyObject *_
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         if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fsarray)) != 0)) kw_args--;
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-          __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 2, 2, 1); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 2, 2, 1); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 103; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 103; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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@@ -35572,18 +36999,18 @@ static int __pyx_pw_3_sa_7Sampler_1__cinit__(PyObject *__pyx_v_self, PyObject *_
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-    __pyx_v_sample_size = __Pyx_PyInt_AsInt(values[0]); if (unlikely((__pyx_v_sample_size == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+    __pyx_v_sample_size = __Pyx_PyInt_AsInt(values[0]); if (unlikely((__pyx_v_sample_size == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 103; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
     __pyx_v_fsarray = ((struct __pyx_obj_3_sa_SuffixArray *)values[1]);
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   goto __pyx_L4_argument_unpacking_done;
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-  __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+  __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 103; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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-  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_fsarray), __pyx_ptype_3_sa_SuffixArray, 1, "fsarray", 0))) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_fsarray), __pyx_ptype_3_sa_SuffixArray, 1, "fsarray", 0))) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   goto __pyx_L0;
   __pyx_L1_error:;
@@ -35593,7 +37020,7 @@ static int __pyx_pw_3_sa_7Sampler_1__cinit__(PyObject *__pyx_v_self, PyObject *_
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":86
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":103
  *     cdef IntList sa
  * 
  *     def __cinit__(self, int sample_size, SuffixArray fsarray):             # <<<<<<<<<<<<<<
@@ -35613,7 +37040,7 @@ static int __pyx_pf_3_sa_7Sampler___cinit__(struct __pyx_obj_3_sa_Sampler *__pyx
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   __Pyx_RefNannySetupContext("__cinit__", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":87
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":104
  * 
  *     def __cinit__(self, int sample_size, SuffixArray fsarray):
  *         self.sample_size = sample_size             # <<<<<<<<<<<<<<
@@ -35622,7 +37049,7 @@ static int __pyx_pf_3_sa_7Sampler___cinit__(struct __pyx_obj_3_sa_Sampler *__pyx
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   __pyx_v_self->sample_size = __pyx_v_sample_size;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":88
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":105
  *     def __cinit__(self, int sample_size, SuffixArray fsarray):
  *         self.sample_size = sample_size
  *         self.sa = fsarray.sa             # <<<<<<<<<<<<<<
@@ -35635,7 +37062,7 @@ static int __pyx_pf_3_sa_7Sampler___cinit__(struct __pyx_obj_3_sa_Sampler *__pyx
   __Pyx_DECREF(((PyObject *)__pyx_v_self->sa));
   __pyx_v_self->sa = __pyx_v_fsarray->sa;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":89
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":106
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  *         self.sa = fsarray.sa
  *         if sample_size > 0:             # <<<<<<<<<<<<<<
@@ -35645,21 +37072,21 @@ static int __pyx_pf_3_sa_7Sampler___cinit__(struct __pyx_obj_3_sa_Sampler *__pyx
   __pyx_t_1 = (__pyx_v_sample_size > 0);
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":90
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":107
  *         self.sa = fsarray.sa
  *         if sample_size > 0:
  *             logger.info("Sampling strategy: uniform, max sample size = %d", sample_size)             # <<<<<<<<<<<<<<
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  *             logger.info("Sampling strategy: no sampling")
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-    __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__logger); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 90; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__logger); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    __pyx_t_3 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__info); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 90; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_3 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__info); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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     __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
-    __pyx_t_2 = PyInt_FromLong(__pyx_v_sample_size); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 90; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = PyInt_FromLong(__pyx_v_sample_size); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 90; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -35667,7 +37094,7 @@ static int __pyx_pf_3_sa_7Sampler___cinit__(struct __pyx_obj_3_sa_Sampler *__pyx
     PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_2);
     __Pyx_GIVEREF(__pyx_t_2);
     __pyx_t_2 = 0;
-    __pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 90; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -35676,19 +37103,19 @@ static int __pyx_pf_3_sa_7Sampler___cinit__(struct __pyx_obj_3_sa_Sampler *__pyx
   }
   /*else*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":92
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":109
  *             logger.info("Sampling strategy: uniform, max sample size = %d", sample_size)
  *         else:
  *             logger.info("Sampling strategy: no sampling")             # <<<<<<<<<<<<<<
  * 
  *     def sample(self, PhraseLocation phrase_location):
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-    __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__logger); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 92; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__logger); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    __pyx_t_4 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__info); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 92; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_4 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__info); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_4);
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-    __pyx_t_2 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_k_tuple_102), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 92; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_k_tuple_102), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_2);
     __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
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@@ -35715,7 +37142,7 @@ static PyObject *__pyx_pw_3_sa_7Sampler_3sample(PyObject *__pyx_v_self, PyObject
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   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("sample (wrapper)", 0);
-  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_phrase_location), __pyx_ptype_3_sa_PhraseLocation, 1, "phrase_location", 0))) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_phrase_location), __pyx_ptype_3_sa_PhraseLocation, 1, "phrase_location", 0))) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   goto __pyx_L0;
   __pyx_L1_error:;
@@ -35725,7 +37152,7 @@ static PyObject *__pyx_pw_3_sa_7Sampler_3sample(PyObject *__pyx_v_self, PyObject
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":94
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":111
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@@ -35752,19 +37179,19 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
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   __Pyx_RefNannySetupContext("sample", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":107
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":124
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  *         sample = IntList()             # <<<<<<<<<<<<<<
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-  __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_IntList)), ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_IntList)), ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":108
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":125
  * 
  *         sample = IntList()
  *         if phrase_location.arr is None:             # <<<<<<<<<<<<<<
@@ -35774,7 +37201,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
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   if (__pyx_t_2) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":109
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":126
  *         sample = IntList()
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@@ -35783,7 +37210,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":110
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":127
  *         if phrase_location.arr is None:
  *             num_locations = phrase_location.sa_high - phrase_location.sa_low
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@@ -35799,7 +37226,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
     }
     if (__pyx_t_4) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":111
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":128
  *             num_locations = phrase_location.sa_high - phrase_location.sa_low
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  *                 sample._extend_arr(self.sa.arr + phrase_location.sa_low, num_locations)             # <<<<<<<<<<<<<<
@@ -35811,7 +37238,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
     }
     /*else*/ {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":113
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":130
  *                 sample._extend_arr(self.sa.arr + phrase_location.sa_low, num_locations)
  *             else:
  *                 stepsize = float(num_locations)/float(self.sample_size)             # <<<<<<<<<<<<<<
@@ -35820,11 +37247,11 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
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       if (unlikely(((double)__pyx_v_self->sample_size) == 0)) {
         PyErr_Format(PyExc_ZeroDivisionError, "float division");
-        {__pyx_filename = __pyx_f[8]; __pyx_lineno = 113; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        {__pyx_filename = __pyx_f[8]; __pyx_lineno = 130; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       }
       __pyx_v_stepsize = (((double)__pyx_v_num_locations) / ((double)__pyx_v_self->sample_size));
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":114
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":131
  *             else:
  *                 stepsize = float(num_locations)/float(self.sample_size)
  *                 i = phrase_location.sa_low             # <<<<<<<<<<<<<<
@@ -35833,7 +37260,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
  */
       __pyx_v_i = __pyx_v_phrase_location->sa_low;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":115
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":132
  *                 stepsize = float(num_locations)/float(self.sample_size)
  *                 i = phrase_location.sa_low
  *                 while i < phrase_location.sa_high and sample.len < self.sample_size:             # <<<<<<<<<<<<<<
@@ -35850,7 +37277,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
         }
         if (!__pyx_t_3) break;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":118
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":135
  *                     '''Note: int(i) not guaranteed to have the desired
  *                     effect, according to the python documentation'''
  *                     if fmod(i,1.0) > 0.5:             # <<<<<<<<<<<<<<
@@ -35860,7 +37287,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
         __pyx_t_3 = (fmod(__pyx_v_i, 1.0) > 0.5);
         if (__pyx_t_3) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":119
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":136
  *                     effect, according to the python documentation'''
  *                     if fmod(i,1.0) > 0.5:
  *                         val = int(ceil(i))             # <<<<<<<<<<<<<<
@@ -35872,7 +37299,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
         }
         /*else*/ {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":121
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":138
  *                         val = int(ceil(i))
  *                     else:
  *                         val = int(floor(i))             # <<<<<<<<<<<<<<
@@ -35883,7 +37310,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
         }
         __pyx_L7:;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":122
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":139
  *                     else:
  *                         val = int(floor(i))
  *                     sample._append(self.sa.arr[val])             # <<<<<<<<<<<<<<
@@ -35892,7 +37319,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
  */
         ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_sample->__pyx_vtab)->_append(__pyx_v_sample, (__pyx_v_self->sa->arr[__pyx_v_val]));
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":123
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":140
  *                         val = int(floor(i))
  *                     sample._append(self.sa.arr[val])
  *                     i = i + stepsize             # <<<<<<<<<<<<<<
@@ -35907,7 +37334,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
   }
   /*else*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":125
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":142
  *                     i = i + stepsize
  *         else:
  *             num_locations = (phrase_location.arr_high - phrase_location.arr_low) / phrase_location.num_subpatterns             # <<<<<<<<<<<<<<
@@ -35917,15 +37344,15 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
     __pyx_t_5 = (__pyx_v_phrase_location->arr_high - __pyx_v_phrase_location->arr_low);
     if (unlikely(__pyx_v_phrase_location->num_subpatterns == 0)) {
       PyErr_Format(PyExc_ZeroDivisionError, "integer division or modulo by zero");
-      {__pyx_filename = __pyx_f[8]; __pyx_lineno = 125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      {__pyx_filename = __pyx_f[8]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     }
     else if (sizeof(int) == sizeof(long) && unlikely(__pyx_v_phrase_location->num_subpatterns == -1) && unlikely(UNARY_NEG_WOULD_OVERFLOW(__pyx_t_5))) {
       PyErr_Format(PyExc_OverflowError, "value too large to perform division");
-      {__pyx_filename = __pyx_f[8]; __pyx_lineno = 125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      {__pyx_filename = __pyx_f[8]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     }
     __pyx_v_num_locations = __Pyx_div_int(__pyx_t_5, __pyx_v_phrase_location->num_subpatterns);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":126
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":143
  *         else:
  *             num_locations = (phrase_location.arr_high - phrase_location.arr_low) / phrase_location.num_subpatterns
  *             if self.sample_size == -1 or num_locations <= self.sample_size:             # <<<<<<<<<<<<<<
@@ -35941,7 +37368,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
     }
     if (__pyx_t_2) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":127
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":144
  *             num_locations = (phrase_location.arr_high - phrase_location.arr_low) / phrase_location.num_subpatterns
  *             if self.sample_size == -1 or num_locations <= self.sample_size:
  *                 sample = phrase_location.arr             # <<<<<<<<<<<<<<
@@ -35955,7 +37382,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
     }
     /*else*/ {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":129
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":146
  *                 sample = phrase_location.arr
  *             else:
  *                 stepsize = float(num_locations)/float(self.sample_size)             # <<<<<<<<<<<<<<
@@ -35964,11 +37391,11 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
  */
       if (unlikely(((double)__pyx_v_self->sample_size) == 0)) {
         PyErr_Format(PyExc_ZeroDivisionError, "float division");
-        {__pyx_filename = __pyx_f[8]; __pyx_lineno = 129; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        {__pyx_filename = __pyx_f[8]; __pyx_lineno = 146; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       }
       __pyx_v_stepsize = (((double)__pyx_v_num_locations) / ((double)__pyx_v_self->sample_size));
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":130
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":147
  *             else:
  *                 stepsize = float(num_locations)/float(self.sample_size)
  *                 i = phrase_location.arr_low             # <<<<<<<<<<<<<<
@@ -35977,7 +37404,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
  */
       __pyx_v_i = __pyx_v_phrase_location->arr_low;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":131
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":148
  *                 stepsize = float(num_locations)/float(self.sample_size)
  *                 i = phrase_location.arr_low
  *                 while i < num_locations and sample.len < self.sample_size * phrase_location.num_subpatterns:             # <<<<<<<<<<<<<<
@@ -35994,7 +37421,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
         }
         if (!__pyx_t_4) break;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":134
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":151
  *                     '''Note: int(i) not guaranteed to have the desired
  *                     effect, according to the python documentation'''
  *                     if fmod(i,1.0) > 0.5:             # <<<<<<<<<<<<<<
@@ -36004,7 +37431,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
         __pyx_t_4 = (fmod(__pyx_v_i, 1.0) > 0.5);
         if (__pyx_t_4) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":135
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":152
  *                     effect, according to the python documentation'''
  *                     if fmod(i,1.0) > 0.5:
  *                         val = int(ceil(i))             # <<<<<<<<<<<<<<
@@ -36016,7 +37443,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
         }
         /*else*/ {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":137
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":154
  *                         val = int(ceil(i))
  *                     else:
  *                         val = int(floor(i))             # <<<<<<<<<<<<<<
@@ -36027,7 +37454,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
         }
         __pyx_L11:;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":138
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":155
  *                     else:
  *                         val = int(floor(i))
  *                     j = phrase_location.arr_low + (val*phrase_location.num_subpatterns)             # <<<<<<<<<<<<<<
@@ -36036,7 +37463,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
  */
         __pyx_v_j = (__pyx_v_phrase_location->arr_low + (__pyx_v_val * __pyx_v_phrase_location->num_subpatterns));
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":139
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":156
  *                         val = int(floor(i))
  *                     j = phrase_location.arr_low + (val*phrase_location.num_subpatterns)
  *                     sample._extend_arr(phrase_location.arr.arr + j, phrase_location.num_subpatterns)             # <<<<<<<<<<<<<<
@@ -36045,7 +37472,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
  */
         ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_sample->__pyx_vtab)->_extend_arr(__pyx_v_sample, (__pyx_v_phrase_location->arr->arr + __pyx_v_j), __pyx_v_phrase_location->num_subpatterns);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":140
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":157
  *                     j = phrase_location.arr_low + (val*phrase_location.num_subpatterns)
  *                     sample._extend_arr(phrase_location.arr.arr + j, phrase_location.num_subpatterns)
  *                     i = i + stepsize             # <<<<<<<<<<<<<<
@@ -36059,7 +37486,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
   }
   __pyx_L3:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":141
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":158
  *                     sample._extend_arr(phrase_location.arr.arr + j, phrase_location.num_subpatterns)
  *                     i = i + stepsize
  *         return sample             # <<<<<<<<<<<<<<
@@ -36084,7 +37511,7 @@ static PyObject *__pyx_pf_3_sa_7Sampler_2sample(struct __pyx_obj_3_sa_Sampler *_
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":153
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":170
  * 
  * 
  * cdef void assign_matching(Matching* m, int* arr, int start, int step, int* sent_id_arr):             # <<<<<<<<<<<<<<
@@ -36096,7 +37523,7 @@ static void __pyx_f_3_sa_assign_matching(struct __pyx_t_3_sa_Matching *__pyx_v_m
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("assign_matching", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":154
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":171
  * 
  * cdef void assign_matching(Matching* m, int* arr, int start, int step, int* sent_id_arr):
  *     m.arr = arr             # <<<<<<<<<<<<<<
@@ -36105,7 +37532,7 @@ static void __pyx_f_3_sa_assign_matching(struct __pyx_t_3_sa_Matching *__pyx_v_m
  */
   __pyx_v_m->arr = __pyx_v_arr;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":155
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":172
  * cdef void assign_matching(Matching* m, int* arr, int start, int step, int* sent_id_arr):
  *     m.arr = arr
  *     m.start = start             # <<<<<<<<<<<<<<
@@ -36114,7 +37541,7 @@ static void __pyx_f_3_sa_assign_matching(struct __pyx_t_3_sa_Matching *__pyx_v_m
  */
   __pyx_v_m->start = __pyx_v_start;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":156
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":173
  *     m.arr = arr
  *     m.start = start
  *     m.end = start + step             # <<<<<<<<<<<<<<
@@ -36123,7 +37550,7 @@ static void __pyx_f_3_sa_assign_matching(struct __pyx_t_3_sa_Matching *__pyx_v_m
  */
   __pyx_v_m->end = (__pyx_v_start + __pyx_v_step);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":157
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":174
  *     m.start = start
  *     m.end = start + step
  *     m.sent_id = sent_id_arr[arr[start]]             # <<<<<<<<<<<<<<
@@ -36132,7 +37559,7 @@ static void __pyx_f_3_sa_assign_matching(struct __pyx_t_3_sa_Matching *__pyx_v_m
  */
   __pyx_v_m->sent_id = (__pyx_v_sent_id_arr[(__pyx_v_arr[__pyx_v_start])]);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":158
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":175
  *     m.end = start + step
  *     m.sent_id = sent_id_arr[arr[start]]
  *     m.size = step             # <<<<<<<<<<<<<<
@@ -36144,7 +37571,7 @@ static void __pyx_f_3_sa_assign_matching(struct __pyx_t_3_sa_Matching *__pyx_v_m
   __Pyx_RefNannyFinishContext();
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":161
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":178
  * 
  * 
  * cdef int* append_combined_matching(int* arr, Matching* loc1, Matching* loc2,             # <<<<<<<<<<<<<<
@@ -36161,7 +37588,7 @@ static int *__pyx_f_3_sa_append_combined_matching(int *__pyx_v_arr, struct __pyx
   int __pyx_t_2;
   __Pyx_RefNannySetupContext("append_combined_matching", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":165
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":182
  *     cdef int i, new_len
  * 
  *     new_len = result_len[0] + num_subpatterns             # <<<<<<<<<<<<<<
@@ -36170,7 +37597,7 @@ static int *__pyx_f_3_sa_append_combined_matching(int *__pyx_v_arr, struct __pyx
  */
   __pyx_v_new_len = ((__pyx_v_result_len[0]) + __pyx_v_num_subpatterns);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":166
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":183
  * 
  *     new_len = result_len[0] + num_subpatterns
  *     arr = <int*> realloc(arr, new_len*sizeof(int))             # <<<<<<<<<<<<<<
@@ -36179,7 +37606,7 @@ static int *__pyx_f_3_sa_append_combined_matching(int *__pyx_v_arr, struct __pyx
  */
   __pyx_v_arr = ((int *)realloc(__pyx_v_arr, (__pyx_v_new_len * (sizeof(int)))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":168
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":185
  *     arr = <int*> realloc(arr, new_len*sizeof(int))
  * 
  *     for i from 0 <= i < loc1.size:             # <<<<<<<<<<<<<<
@@ -36189,7 +37616,7 @@ static int *__pyx_f_3_sa_append_combined_matching(int *__pyx_v_arr, struct __pyx
   __pyx_t_1 = __pyx_v_loc1->size;
   for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_1; __pyx_v_i++) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":169
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":186
  * 
  *     for i from 0 <= i < loc1.size:
  *         arr[result_len[0]+i] = loc1.arr[loc1.start+i]             # <<<<<<<<<<<<<<
@@ -36199,7 +37626,7 @@ static int *__pyx_f_3_sa_append_combined_matching(int *__pyx_v_arr, struct __pyx
     (__pyx_v_arr[((__pyx_v_result_len[0]) + __pyx_v_i)]) = (__pyx_v_loc1->arr[(__pyx_v_loc1->start + __pyx_v_i)]);
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":170
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":187
  *     for i from 0 <= i < loc1.size:
  *         arr[result_len[0]+i] = loc1.arr[loc1.start+i]
  *     if num_subpatterns > loc1.size:             # <<<<<<<<<<<<<<
@@ -36209,7 +37636,7 @@ static int *__pyx_f_3_sa_append_combined_matching(int *__pyx_v_arr, struct __pyx
   __pyx_t_2 = (__pyx_v_num_subpatterns > __pyx_v_loc1->size);
   if (__pyx_t_2) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":171
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":188
  *         arr[result_len[0]+i] = loc1.arr[loc1.start+i]
  *     if num_subpatterns > loc1.size:
  *         arr[new_len-1] = loc2.arr[loc2.end-1]             # <<<<<<<<<<<<<<
@@ -36221,7 +37648,7 @@ static int *__pyx_f_3_sa_append_combined_matching(int *__pyx_v_arr, struct __pyx
   }
   __pyx_L5:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":172
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":189
  *     if num_subpatterns > loc1.size:
  *         arr[new_len-1] = loc2.arr[loc2.end-1]
  *     result_len[0] = new_len             # <<<<<<<<<<<<<<
@@ -36230,7 +37657,7 @@ static int *__pyx_f_3_sa_append_combined_matching(int *__pyx_v_arr, struct __pyx
  */
   (__pyx_v_result_len[0]) = __pyx_v_new_len;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":173
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":190
  *         arr[new_len-1] = loc2.arr[loc2.end-1]
  *     result_len[0] = new_len
  *     return arr             # <<<<<<<<<<<<<<
@@ -36246,7 +37673,7 @@ static int *__pyx_f_3_sa_append_combined_matching(int *__pyx_v_arr, struct __pyx
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":176
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":193
  * 
  * 
  * cdef int* extend_arr(int* arr, int* arr_len, int* appendix, int appendix_len):             # <<<<<<<<<<<<<<
@@ -36260,7 +37687,7 @@ static int *__pyx_f_3_sa_extend_arr(int *__pyx_v_arr, int *__pyx_v_arr_len, int
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("extend_arr", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":179
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":196
  *     cdef int new_len
  * 
  *     new_len = arr_len[0] + appendix_len             # <<<<<<<<<<<<<<
@@ -36269,7 +37696,7 @@ static int *__pyx_f_3_sa_extend_arr(int *__pyx_v_arr, int *__pyx_v_arr_len, int
  */
   __pyx_v_new_len = ((__pyx_v_arr_len[0]) + __pyx_v_appendix_len);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":180
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":197
  * 
  *     new_len = arr_len[0] + appendix_len
  *     arr = <int*> realloc(arr, new_len*sizeof(int))             # <<<<<<<<<<<<<<
@@ -36278,7 +37705,7 @@ static int *__pyx_f_3_sa_extend_arr(int *__pyx_v_arr, int *__pyx_v_arr_len, int
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   __pyx_v_arr = ((int *)realloc(__pyx_v_arr, (__pyx_v_new_len * (sizeof(int)))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":181
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":198
  *     new_len = arr_len[0] + appendix_len
  *     arr = <int*> realloc(arr, new_len*sizeof(int))
  *     memcpy(arr+arr_len[0], appendix, appendix_len*sizeof(int))             # <<<<<<<<<<<<<<
@@ -36287,7 +37714,7 @@ static int *__pyx_f_3_sa_extend_arr(int *__pyx_v_arr, int *__pyx_v_arr_len, int
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   memcpy((__pyx_v_arr + (__pyx_v_arr_len[0])), __pyx_v_appendix, (__pyx_v_appendix_len * (sizeof(int))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":182
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":199
  *     arr = <int*> realloc(arr, new_len*sizeof(int))
  *     memcpy(arr+arr_len[0], appendix, appendix_len*sizeof(int))
  *     arr_len[0] = new_len             # <<<<<<<<<<<<<<
@@ -36296,7 +37723,7 @@ static int *__pyx_f_3_sa_extend_arr(int *__pyx_v_arr, int *__pyx_v_arr_len, int
  */
   (__pyx_v_arr_len[0]) = __pyx_v_new_len;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":183
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":200
  *     memcpy(arr+arr_len[0], appendix, appendix_len*sizeof(int))
  *     arr_len[0] = new_len
  *     return arr             # <<<<<<<<<<<<<<
@@ -36312,7 +37739,7 @@ static int *__pyx_f_3_sa_extend_arr(int *__pyx_v_arr, int *__pyx_v_arr_len, int
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":185
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":202
  *     return arr
  * 
  * cdef int median(int low, int high, int step):             # <<<<<<<<<<<<<<
@@ -36329,7 +37756,7 @@ static int __pyx_f_3_sa_median(int __pyx_v_low, int __pyx_v_high, int __pyx_v_st
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("median", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":186
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":203
  * 
  * cdef int median(int low, int high, int step):
  *     return low + (((high - low)/step)/2)*step             # <<<<<<<<<<<<<<
@@ -36339,11 +37766,11 @@ static int __pyx_f_3_sa_median(int __pyx_v_low, int __pyx_v_high, int __pyx_v_st
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-    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 186; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   else if (sizeof(int) == sizeof(long) && unlikely(__pyx_v_step == -1) && unlikely(UNARY_NEG_WOULD_OVERFLOW(__pyx_t_1))) {
     PyErr_Format(PyExc_OverflowError, "value too large to perform division");
-    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 186; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   }
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@@ -36358,7 +37785,7 @@ static int __pyx_f_3_sa_median(int __pyx_v_low, int __pyx_v_high, int __pyx_v_st
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":189
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":206
  * 
  * 
  * cdef void find_comparable_matchings(int low, int high, int* arr, int step, int loc, int* loc_minus, int* loc_plus):             # <<<<<<<<<<<<<<
@@ -36373,7 +37800,7 @@ static void __pyx_f_3_sa_find_comparable_matchings(int __pyx_v_low, int __pyx_v_
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   __Pyx_RefNannySetupContext("find_comparable_matchings", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":193
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":210
  *     # in which all matchings have the same first index as the one
  *     # starting at loc
  *     loc_plus[0] = loc + step             # <<<<<<<<<<<<<<
@@ -36382,7 +37809,7 @@ static void __pyx_f_3_sa_find_comparable_matchings(int __pyx_v_low, int __pyx_v_
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   (__pyx_v_loc_plus[0]) = (__pyx_v_loc + __pyx_v_step);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":194
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":211
  *     # starting at loc
  *     loc_plus[0] = loc + step
  *     while loc_plus[0] < high and arr[loc_plus[0]] == arr[loc]:             # <<<<<<<<<<<<<<
@@ -36399,7 +37826,7 @@ static void __pyx_f_3_sa_find_comparable_matchings(int __pyx_v_low, int __pyx_v_
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":195
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":212
  *     loc_plus[0] = loc + step
  *     while loc_plus[0] < high and arr[loc_plus[0]] == arr[loc]:
  *         loc_plus[0] = loc_plus[0] + step             # <<<<<<<<<<<<<<
@@ -36409,7 +37836,7 @@ static void __pyx_f_3_sa_find_comparable_matchings(int __pyx_v_low, int __pyx_v_
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   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":196
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":213
  *     while loc_plus[0] < high and arr[loc_plus[0]] == arr[loc]:
  *         loc_plus[0] = loc_plus[0] + step
  *     loc_minus[0] = loc             # <<<<<<<<<<<<<<
@@ -36418,7 +37845,7 @@ static void __pyx_f_3_sa_find_comparable_matchings(int __pyx_v_low, int __pyx_v_
  */
   (__pyx_v_loc_minus[0]) = __pyx_v_loc;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":197
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":214
  *         loc_plus[0] = loc_plus[0] + step
  *     loc_minus[0] = loc
  *     while loc_minus[0]-step >= low and arr[loc_minus[0]-step] == arr[loc]:             # <<<<<<<<<<<<<<
@@ -36435,7 +37862,7 @@ static void __pyx_f_3_sa_find_comparable_matchings(int __pyx_v_low, int __pyx_v_
     }
     if (!__pyx_t_2) break;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":198
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":215
  *     loc_minus[0] = loc
  *     while loc_minus[0]-step >= low and arr[loc_minus[0]-step] == arr[loc]:
  *         loc_minus[0] = loc_minus[0] - step             # <<<<<<<<<<<<<<
@@ -36479,7 +37906,7 @@ static int __pyx_pw_3_sa_23HieroCachingRuleFactory_1__cinit__(PyObject *__pyx_v_
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":257
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":275
  *             char* category="[X]",
  *             # maximum number of contiguous chunks of terminal symbols in RHS of a rule. If None, defaults to max_nonterminals+1
  *             max_chunks=None,             # <<<<<<<<<<<<<<
@@ -36488,7 +37915,7 @@ static int __pyx_pw_3_sa_23HieroCachingRuleFactory_1__cinit__(PyObject *__pyx_v_
  */
     values[3] = ((PyObject *)Py_None);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":265
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":283
  *             unsigned max_nonterminals=2,
  *             # maximum number of contiguous chunks of terminal symbols in target-side RHS of a rule. If None, defaults to max_nonterminals+1
  *             max_target_chunks=None,             # <<<<<<<<<<<<<<
@@ -36497,7 +37924,7 @@ static int __pyx_pw_3_sa_23HieroCachingRuleFactory_1__cinit__(PyObject *__pyx_v_
  */
     values[7] = ((PyObject *)Py_None);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":267
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":285
  *             max_target_chunks=None,
  *             # maximum number of target side symbols (both T and NT) allowed in a rule. If None, defaults to max_initial_size
  *             max_target_length=None,             # <<<<<<<<<<<<<<
@@ -36506,7 +37933,7 @@ static int __pyx_pw_3_sa_23HieroCachingRuleFactory_1__cinit__(PyObject *__pyx_v_
  */
     values[8] = ((PyObject *)Py_None);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":271
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":289
  *             unsigned min_gap_size=2,
  *             # filename of file containing precomputed collocations
  *             precompute_file=None,             # <<<<<<<<<<<<<<
@@ -36649,7 +38076,7 @@ static int __pyx_pw_3_sa_23HieroCachingRuleFactory_1__cinit__(PyObject *__pyx_v_
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-        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 249; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 267; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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       switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -36680,10 +38107,10 @@ static int __pyx_pw_3_sa_23HieroCachingRuleFactory_1__cinit__(PyObject *__pyx_v_
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-      __pyx_v_by_slack_factor = __pyx_PyFloat_AsFloat(values[1]); if (unlikely((__pyx_v_by_slack_factor == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 253; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+      __pyx_v_by_slack_factor = __pyx_PyFloat_AsFloat(values[1]); if (unlikely((__pyx_v_by_slack_factor == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 271; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":253
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":271
  *             Alignment alignment,
  *             # parameter for double-binary search; doesn't seem to matter much
  *             float by_slack_factor=1.0,             # <<<<<<<<<<<<<<
@@ -36693,49 +38120,49 @@ static int __pyx_pw_3_sa_23HieroCachingRuleFactory_1__cinit__(PyObject *__pyx_v_
       __pyx_v_by_slack_factor = ((float)1.0);
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-      __pyx_v_category = PyBytes_AsString(values[2]); if (unlikely((!__pyx_v_category) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 255; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+      __pyx_v_category = PyBytes_AsString(values[2]); if (unlikely((!__pyx_v_category) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 273; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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       __pyx_v_category = ((char *)__pyx_k_105);
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     __pyx_v_max_chunks = values[3];
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-      __pyx_v_max_initial_size = __Pyx_PyInt_AsUnsignedInt(values[4]); if (unlikely((__pyx_v_max_initial_size == (unsigned int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 259; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+      __pyx_v_max_initial_size = __Pyx_PyInt_AsUnsignedInt(values[4]); if (unlikely((__pyx_v_max_initial_size == (unsigned int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 277; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+      __pyx_v_max_length = __Pyx_PyInt_AsUnsignedInt(values[5]); if (unlikely((__pyx_v_max_length == (unsigned int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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-      __pyx_v_max_nonterminals = __Pyx_PyInt_AsUnsignedInt(values[6]); if (unlikely((__pyx_v_max_nonterminals == (unsigned int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 263; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+      __pyx_v_max_nonterminals = __Pyx_PyInt_AsUnsignedInt(values[6]); if (unlikely((__pyx_v_max_nonterminals == (unsigned int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 281; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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     __pyx_v_max_target_chunks = values[7];
     __pyx_v_max_target_length = values[8];
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-      __pyx_v_min_gap_size = __Pyx_PyInt_AsUnsignedInt(values[9]); if (unlikely((__pyx_v_min_gap_size == (unsigned int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 269; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+      __pyx_v_min_gap_size = __Pyx_PyInt_AsUnsignedInt(values[9]); if (unlikely((__pyx_v_min_gap_size == (unsigned int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 287; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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-      __pyx_v_precompute_secondary_rank = __Pyx_PyInt_AsUnsignedInt(values[11]); if (unlikely((__pyx_v_precompute_secondary_rank == (unsigned int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 273; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+      __pyx_v_precompute_secondary_rank = __Pyx_PyInt_AsUnsignedInt(values[11]); if (unlikely((__pyx_v_precompute_secondary_rank == (unsigned int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 291; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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     if (values[12]) {
-      __pyx_v_precompute_rank = __Pyx_PyInt_AsUnsignedInt(values[12]); if (unlikely((__pyx_v_precompute_rank == (unsigned int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 275; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+      __pyx_v_precompute_rank = __Pyx_PyInt_AsUnsignedInt(values[12]); if (unlikely((__pyx_v_precompute_rank == (unsigned int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 293; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
     } else {
       __pyx_v_precompute_rank = ((unsigned int)100);
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     if (values[13]) {
-      __pyx_v_require_aligned_terminal = __Pyx_PyObject_IsTrue(values[13]); if (unlikely((__pyx_v_require_aligned_terminal == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 277; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+      __pyx_v_require_aligned_terminal = __Pyx_PyObject_IsTrue(values[13]); if (unlikely((__pyx_v_require_aligned_terminal == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 295; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
     } else {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":277
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":295
  *             unsigned precompute_rank=100,
  *             # require extracted rules to have at least one aligned word
  *             bint require_aligned_terminal=True,             # <<<<<<<<<<<<<<
@@ -36745,10 +38172,10 @@ static int __pyx_pw_3_sa_23HieroCachingRuleFactory_1__cinit__(PyObject *__pyx_v_
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     if (values[14]) {
-      __pyx_v_require_aligned_chunks = __Pyx_PyObject_IsTrue(values[14]); if (unlikely((__pyx_v_require_aligned_chunks == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+      __pyx_v_require_aligned_chunks = __Pyx_PyObject_IsTrue(values[14]); if (unlikely((__pyx_v_require_aligned_chunks == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 297; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
     } else {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":279
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":297
  *             bint require_aligned_terminal=True,
  *             # require each contiguous chunk of extracted rules to have at least one aligned word
  *             bint require_aligned_chunks=False,             # <<<<<<<<<<<<<<
@@ -36758,20 +38185,20 @@ static int __pyx_pw_3_sa_23HieroCachingRuleFactory_1__cinit__(PyObject *__pyx_v_
       __pyx_v_require_aligned_chunks = ((int)0);
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     if (values[15]) {
-      __pyx_v_train_max_initial_size = __Pyx_PyInt_AsUnsignedInt(values[15]); if (unlikely((__pyx_v_train_max_initial_size == (unsigned int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 281; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+      __pyx_v_train_max_initial_size = __Pyx_PyInt_AsUnsignedInt(values[15]); if (unlikely((__pyx_v_train_max_initial_size == (unsigned int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 299; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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       __pyx_v_train_max_initial_size = ((unsigned int)10);
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     if (values[16]) {
-      __pyx_v_train_min_gap_size = __Pyx_PyInt_AsUnsignedInt(values[16]); if (unlikely((__pyx_v_train_min_gap_size == (unsigned int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 283; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+      __pyx_v_train_min_gap_size = __Pyx_PyInt_AsUnsignedInt(values[16]); if (unlikely((__pyx_v_train_min_gap_size == (unsigned int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 301; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
     } else {
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+      __pyx_v_tight_phrases = __Pyx_PyObject_IsTrue(values[17]); if (unlikely((__pyx_v_tight_phrases == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 303; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":285
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":303
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+      __pyx_v_use_baeza_yates = __Pyx_PyObject_IsTrue(values[18]); if (unlikely((__pyx_v_use_baeza_yates == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 305; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":287
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":305
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+      __pyx_v_use_collocations = __Pyx_PyObject_IsTrue(values[19]); if (unlikely((__pyx_v_use_collocations == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 307; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":289
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":307
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+      __pyx_v_use_index = __Pyx_PyObject_IsTrue(values[20]); if (unlikely((__pyx_v_use_index == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 309; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":291
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":309
  *             bint use_collocations=True,
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+  __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 1, 21, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 267; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_alignment), __pyx_ptype_3_sa_Alignment, 1, "alignment", 0))) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 269; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -36838,7 +38265,7 @@ static int __pyx_pw_3_sa_23HieroCachingRuleFactory_1__cinit__(PyObject *__pyx_v_
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":249
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":267
  *     cdef IntList findexes1
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  *     def __cinit__(self,             # <<<<<<<<<<<<<<
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-  PyObject *__pyx_t_4 = NULL;
-  PyObject *__pyx_t_5 = NULL;
-  int __pyx_t_6;
+  int __pyx_t_4;
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":297
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":315
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+  __pyx_t_1 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_TrieTable)), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 297; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_TrieTable)), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -36883,20 +38308,20 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":298
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":316
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-  __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 298; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_PhraseLocation)), ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__phrase_location), __pyx_t_2) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_ExtendedTrieNode)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 298; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_ExtendedTrieNode)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -36905,7 +38330,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":299
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":317
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":300
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":318
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+    __pyx_t_2 = PyObject_Call(__pyx_builtin_Exception, ((PyObject *)__pyx_k_tuple_107), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 318; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 300; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 318; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":301
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":319
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   __pyx_v_self->alignment = __pyx_v_alignment;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":305
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":323
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":306
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":324
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":307
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":325
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   __pyx_v_self->max_initial_size = __pyx_v_max_initial_size;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":308
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":326
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":309
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":327
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":310
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":328
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":311
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-  __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
-  __pyx_t_6 = __Pyx_PyInt_AsInt(__pyx_t_4); if (unlikely((__pyx_t_6 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 311; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
-  __pyx_v_self->category = __pyx_t_6;
+  __pyx_v_self->category = __pyx_f_3_sa_sym_fromstring(__pyx_v_category, 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":313
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":331
  *         self.category = sym_fromstring(category, False)
  * 
  *         if max_chunks is None:             # <<<<<<<<<<<<<<
@@ -37037,7 +38442,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
   __pyx_t_3 = (__pyx_v_max_chunks == Py_None);
   if (__pyx_t_3) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":314
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":332
  * 
  *         if max_chunks is None:
  *             self.max_chunks = self.max_nonterminals + 1             # <<<<<<<<<<<<<<
@@ -37049,19 +38454,19 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
   }
   /*else*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":316
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":334
  *             self.max_chunks = self.max_nonterminals + 1
  *         else:
  *             self.max_chunks = max_chunks             # <<<<<<<<<<<<<<
  * 
  *         if max_target_chunks is None:
  */
-    __pyx_t_6 = __Pyx_PyInt_AsInt(__pyx_v_max_chunks); if (unlikely((__pyx_t_6 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-    __pyx_v_self->max_chunks = __pyx_t_6;
+    __pyx_t_4 = __Pyx_PyInt_AsInt(__pyx_v_max_chunks); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_v_self->max_chunks = __pyx_t_4;
   }
   __pyx_L4:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":318
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":336
  *             self.max_chunks = max_chunks
  * 
  *         if max_target_chunks is None:             # <<<<<<<<<<<<<<
@@ -37071,7 +38476,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
   __pyx_t_3 = (__pyx_v_max_target_chunks == Py_None);
   if (__pyx_t_3) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":319
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":337
  * 
  *         if max_target_chunks is None:
  *             self.max_target_chunks = self.max_nonterminals + 1             # <<<<<<<<<<<<<<
@@ -37083,19 +38488,19 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
   }
   /*else*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":321
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":339
  *             self.max_target_chunks = self.max_nonterminals + 1
  *         else:
  *             self.max_target_chunks = max_target_chunks             # <<<<<<<<<<<<<<
  * 
  *         if max_target_length is None:
  */
-    __pyx_t_6 = __Pyx_PyInt_AsInt(__pyx_v_max_target_chunks); if (unlikely((__pyx_t_6 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-    __pyx_v_self->max_target_chunks = __pyx_t_6;
+    __pyx_t_4 = __Pyx_PyInt_AsInt(__pyx_v_max_target_chunks); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 339; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_v_self->max_target_chunks = __pyx_t_4;
   }
   __pyx_L5:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":323
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":341
  *             self.max_target_chunks = max_target_chunks
  * 
  *         if max_target_length is None:             # <<<<<<<<<<<<<<
@@ -37105,7 +38510,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
   __pyx_t_3 = (__pyx_v_max_target_length == Py_None);
   if (__pyx_t_3) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":324
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":342
  * 
  *         if max_target_length is None:
  *             self.max_target_length = max_initial_size             # <<<<<<<<<<<<<<
@@ -37117,49 +38522,49 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
   }
   /*else*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":326
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":344
  *             self.max_target_length = max_initial_size
  *         else:
  *             self.max_target_length = max_target_length             # <<<<<<<<<<<<<<
  * 
  *         # algorithmic parameters and settings
  */
-    __pyx_t_6 = __Pyx_PyInt_AsInt(__pyx_v_max_target_length); if (unlikely((__pyx_t_6 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-    __pyx_v_self->max_target_length = __pyx_t_6;
+    __pyx_t_4 = __Pyx_PyInt_AsInt(__pyx_v_max_target_length); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_v_self->max_target_length = __pyx_t_4;
   }
   __pyx_L6:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":329
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":347
  * 
  *         # algorithmic parameters and settings
  *         self.precomputed_collocations = {}             # <<<<<<<<<<<<<<
  *         self.precomputed_index = {}
  *         self.use_index = use_index
  */
-  __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_GOTREF(((PyObject *)__pyx_t_4));
-  __Pyx_GIVEREF(((PyObject *)__pyx_t_4));
+  __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+  __Pyx_GIVEREF(((PyObject *)__pyx_t_2));
   __Pyx_GOTREF(__pyx_v_self->precomputed_collocations);
   __Pyx_DECREF(__pyx_v_self->precomputed_collocations);
-  __pyx_v_self->precomputed_collocations = ((PyObject *)__pyx_t_4);
-  __pyx_t_4 = 0;
+  __pyx_v_self->precomputed_collocations = ((PyObject *)__pyx_t_2);
+  __pyx_t_2 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":330
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":348
  *         # algorithmic parameters and settings
  *         self.precomputed_collocations = {}
  *         self.precomputed_index = {}             # <<<<<<<<<<<<<<
  *         self.use_index = use_index
  *         self.use_collocations = use_collocations
  */
-  __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_GOTREF(((PyObject *)__pyx_t_4));
-  __Pyx_GIVEREF(((PyObject *)__pyx_t_4));
+  __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 348; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+  __Pyx_GIVEREF(((PyObject *)__pyx_t_2));
   __Pyx_GOTREF(__pyx_v_self->precomputed_index);
   __Pyx_DECREF(__pyx_v_self->precomputed_index);
-  __pyx_v_self->precomputed_index = ((PyObject *)__pyx_t_4);
-  __pyx_t_4 = 0;
+  __pyx_v_self->precomputed_index = ((PyObject *)__pyx_t_2);
+  __pyx_t_2 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":331
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":349
  *         self.precomputed_collocations = {}
  *         self.precomputed_index = {}
  *         self.use_index = use_index             # <<<<<<<<<<<<<<
@@ -37168,7 +38573,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
  */
   __pyx_v_self->use_index = __pyx_v_use_index;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":332
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":350
  *         self.precomputed_index = {}
  *         self.use_index = use_index
  *         self.use_collocations = use_collocations             # <<<<<<<<<<<<<<
@@ -37177,22 +38582,22 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
  */
   __pyx_v_self->use_collocations = __pyx_v_use_collocations;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":333
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":351
  *         self.use_index = use_index
  *         self.use_collocations = use_collocations
  *         self.max_rank = {}             # <<<<<<<<<<<<<<
  *         self.precompute_file = precompute_file
  *         self.precompute_rank = precompute_rank
  */
-  __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 333; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_GOTREF(((PyObject *)__pyx_t_4));
-  __Pyx_GIVEREF(((PyObject *)__pyx_t_4));
+  __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 351; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+  __Pyx_GIVEREF(((PyObject *)__pyx_t_2));
   __Pyx_GOTREF(__pyx_v_self->max_rank);
   __Pyx_DECREF(__pyx_v_self->max_rank);
-  __pyx_v_self->max_rank = ((PyObject *)__pyx_t_4);
-  __pyx_t_4 = 0;
+  __pyx_v_self->max_rank = ((PyObject *)__pyx_t_2);
+  __pyx_t_2 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":334
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":352
  *         self.use_collocations = use_collocations
  *         self.max_rank = {}
  *         self.precompute_file = precompute_file             # <<<<<<<<<<<<<<
@@ -37205,7 +38610,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
   __Pyx_DECREF(__pyx_v_self->precompute_file);
   __pyx_v_self->precompute_file = __pyx_v_precompute_file;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":335
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":353
  *         self.max_rank = {}
  *         self.precompute_file = precompute_file
  *         self.precompute_rank = precompute_rank             # <<<<<<<<<<<<<<
@@ -37214,7 +38619,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
  */
   __pyx_v_self->precompute_rank = __pyx_v_precompute_rank;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":336
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":354
  *         self.precompute_file = precompute_file
  *         self.precompute_rank = precompute_rank
  *         self.precompute_secondary_rank = precompute_secondary_rank             # <<<<<<<<<<<<<<
@@ -37223,7 +38628,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
  */
   __pyx_v_self->precompute_secondary_rank = __pyx_v_precompute_secondary_rank;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":337
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":355
  *         self.precompute_rank = precompute_rank
  *         self.precompute_secondary_rank = precompute_secondary_rank
  *         self.use_baeza_yates = use_baeza_yates             # <<<<<<<<<<<<<<
@@ -37232,7 +38637,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
  */
   __pyx_v_self->use_baeza_yates = __pyx_v_use_baeza_yates;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":338
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":356
  *         self.precompute_secondary_rank = precompute_secondary_rank
  *         self.use_baeza_yates = use_baeza_yates
  *         self.by_slack_factor = by_slack_factor             # <<<<<<<<<<<<<<
@@ -37241,7 +38646,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
  */
   __pyx_v_self->by_slack_factor = __pyx_v_by_slack_factor;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":339
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":357
  *         self.use_baeza_yates = use_baeza_yates
  *         self.by_slack_factor = by_slack_factor
  *         if tight_phrases:             # <<<<<<<<<<<<<<
@@ -37250,7 +38655,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
  */
   if (__pyx_v_tight_phrases) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":340
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":358
  *         self.by_slack_factor = by_slack_factor
  *         if tight_phrases:
  *             self.tight_phrases = 1             # <<<<<<<<<<<<<<
@@ -37262,7 +38667,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
   }
   /*else*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":342
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":360
  *             self.tight_phrases = 1
  *         else:
  *             self.tight_phrases = 0             # <<<<<<<<<<<<<<
@@ -37273,7 +38678,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
   }
   __pyx_L7:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":344
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":362
  *             self.tight_phrases = 0
  * 
  *         if require_aligned_chunks:             # <<<<<<<<<<<<<<
@@ -37282,7 +38687,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
  */
   if (__pyx_v_require_aligned_chunks) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":346
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":364
  *         if require_aligned_chunks:
  *             # one condition is a stronger version of the other.
  *             self.require_aligned_chunks = 1             # <<<<<<<<<<<<<<
@@ -37291,7 +38696,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
  */
     __pyx_v_self->require_aligned_chunks = 1;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":347
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":365
  *             # one condition is a stronger version of the other.
  *             self.require_aligned_chunks = 1
  *             self.require_aligned_terminal = 1             # <<<<<<<<<<<<<<
@@ -37302,7 +38707,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
     goto __pyx_L8;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":348
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":366
  *             self.require_aligned_chunks = 1
  *             self.require_aligned_terminal = 1
  *         elif require_aligned_terminal:             # <<<<<<<<<<<<<<
@@ -37311,7 +38716,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
  */
   if (__pyx_v_require_aligned_terminal) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":349
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":367
  *             self.require_aligned_terminal = 1
  *         elif require_aligned_terminal:
  *             self.require_aligned_chunks = 0             # <<<<<<<<<<<<<<
@@ -37320,7 +38725,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
  */
     __pyx_v_self->require_aligned_chunks = 0;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":350
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":368
  *         elif require_aligned_terminal:
  *             self.require_aligned_chunks = 0
  *             self.require_aligned_terminal = 1             # <<<<<<<<<<<<<<
@@ -37332,7 +38737,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
   }
   /*else*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":352
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":370
  *             self.require_aligned_terminal = 1
  *         else:
  *             self.require_aligned_chunks = 0             # <<<<<<<<<<<<<<
@@ -37341,7 +38746,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
  */
     __pyx_v_self->require_aligned_chunks = 0;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":353
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":371
  *         else:
  *             self.require_aligned_chunks = 0
  *             self.require_aligned_terminal = 0             # <<<<<<<<<<<<<<
@@ -37352,7 +38757,7 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
   }
   __pyx_L8:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":357
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":375
  * 
  *         # diagnostics
  *         self.prev_norm_prefix = ()             # <<<<<<<<<<<<<<
@@ -37365,51 +38770,49 @@ static int __pyx_pf_3_sa_23HieroCachingRuleFactory___cinit__(struct __pyx_obj_3_
   __Pyx_DECREF(__pyx_v_self->prev_norm_prefix);
   __pyx_v_self->prev_norm_prefix = ((PyObject *)__pyx_empty_tuple);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":359
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":377
  *         self.prev_norm_prefix = ()
  * 
  *         self.findexes = IntList(initial_len=10)             # <<<<<<<<<<<<<<
  *         self.findexes1 = IntList(initial_len=10)
  * 
  */
-  __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":367
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":383
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":425
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":426
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":427
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":428
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+      __pyx_t_4 = PyInt_FromLong(__pyx_v_pre->train_max_initial_size); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      __pyx_t_2 = PyInt_FromLong(__pyx_v_self->train_max_initial_size); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 430; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_2 = PyInt_FromLong(__pyx_v_self->train_max_initial_size); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -38552,25 +39912,25 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_8precompute(struct __py
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+      __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_111), ((PyObject *)__pyx_t_5)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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       __Pyx_GIVEREF(((PyObject *)__pyx_t_2));
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+      __pyx_t_2 = PyObject_Call(__pyx_builtin_Exception, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_2);
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-      {__pyx_filename = __pyx_f[8]; __pyx_lineno = 430; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      {__pyx_filename = __pyx_f[8]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       goto __pyx_L6;
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":431
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":451
  *             if pre.train_max_initial_size != self.train_max_initial_size:
  *                 raise Exception("Precomputation done with max initial size %d, decoder uses %d" % (pre.train_max_initial_size, self.train_max_initial_size))
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@@ -38580,18 +39940,18 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_8precompute(struct __py
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     if (__pyx_t_1) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":432
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":452
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+      __pyx_t_2 = PyInt_FromLong(__pyx_v_pre->train_min_gap_size); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 452; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      __pyx_t_5 = PyInt_FromLong(__pyx_v_self->train_min_gap_size); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_5 = PyInt_FromLong(__pyx_v_self->train_min_gap_size); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 452; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 452; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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       PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_2);
       __Pyx_GIVEREF(__pyx_t_2);
@@ -38599,25 +39959,25 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_8precompute(struct __py
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+      __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_112), ((PyObject *)__pyx_t_4)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 452; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 452; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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       __Pyx_GIVEREF(((PyObject *)__pyx_t_5));
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-      __pyx_t_5 = PyObject_Call(__pyx_builtin_Exception, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_5 = PyObject_Call(__pyx_builtin_Exception, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 452; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      {__pyx_filename = __pyx_f[8]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      {__pyx_filename = __pyx_f[8]; __pyx_lineno = 452; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       goto __pyx_L7;
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":433
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":453
  *             if pre.train_min_gap_size != self.train_min_gap_size:
  *                 raise Exception("Precomputation done with min gap size %d, decoder uses %d" % (pre.train_min_gap_size, self.train_min_gap_size))
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@@ -38626,25 +39986,25 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_8precompute(struct __py
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     if (__pyx_v_self->use_index) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":434
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":454
  *                 raise Exception("Precomputation done with min gap size %d, decoder uses %d" % (pre.train_min_gap_size, self.train_min_gap_size))
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-      __pyx_t_5 = __Pyx_GetName(__pyx_m, __pyx_n_s__logger); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_5 = __Pyx_GetName(__pyx_m, __pyx_n_s__logger); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_4 = PyObject_GetAttr(__pyx_t_5, __pyx_n_s__info); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_6 = PyObject_Length(__pyx_t_5); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      __pyx_t_5 = PyInt_FromSsize_t(__pyx_t_6); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_5 = PyInt_FromSsize_t(__pyx_t_6); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -38652,13 +40012,13 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_8precompute(struct __py
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+      __pyx_t_5 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":435
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":455
  *             if self.use_index:
  *                 logger.info("Converting %d hash keys on precomputed inverted index... ", len(pre.precomputed_index))
  *                 for pattern, arr in pre.precomputed_index.iteritems():             # <<<<<<<<<<<<<<
@@ -38668,9 +40028,9 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_8precompute(struct __py
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-        {__pyx_filename = __pyx_f[8]; __pyx_lineno = 435; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        {__pyx_filename = __pyx_f[8]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_2 = __Pyx_dict_iterator(__pyx_v_pre->precomputed_index, 0, ((PyObject *)__pyx_n_s__iteritems), (&__pyx_t_7), (&__pyx_t_8)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -38678,7 +40038,7 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_8precompute(struct __py
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-        if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 435; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -38688,21 +40048,21 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_8precompute(struct __py
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":436
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":456
  *                 logger.info("Converting %d hash keys on precomputed inverted index... ", len(pre.precomputed_index))
  *                 for pattern, arr in pre.precomputed_index.iteritems():
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-        __pyx_t_4 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__pattern2phrase_plus); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_4 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__pattern2phrase_plus); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 456; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-        __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 456; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+        __pyx_t_3 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 456; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -38710,7 +40070,7 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_8precompute(struct __py
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":437
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":457
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+          __pyx_t_10 = -1; __pyx_t_3 = PyObject_GetIter(__pyx_v_phrases); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 457; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-            __pyx_t_2 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_10); __Pyx_INCREF(__pyx_t_2); __pyx_t_10++;
+            __pyx_t_2 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_10); __Pyx_INCREF(__pyx_t_2); __pyx_t_10++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 457; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+            __pyx_t_2 = PySequence_ITEM(__pyx_t_3, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 457; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-            __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_10); __Pyx_INCREF(__pyx_t_2); __pyx_t_10++;
+            __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_10); __Pyx_INCREF(__pyx_t_2); __pyx_t_10++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 457; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+            __pyx_t_2 = PySequence_ITEM(__pyx_t_3, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 457; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-                else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 437; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 457; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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           __pyx_t_2 = 0;
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":438
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":458
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  *                         self.precomputed_index[phrase] = arr             # <<<<<<<<<<<<<<
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+          if (PyObject_SetItem(__pyx_v_self->precomputed_index, __pyx_v_phrase, __pyx_v_arr) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 458; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -38771,7 +40131,7 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_8precompute(struct __py
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":439
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":459
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  *                         self.precomputed_index[phrase] = arr
  *             if self.use_collocations:             # <<<<<<<<<<<<<<
@@ -38780,25 +40140,25 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_8precompute(struct __py
  */
     if (__pyx_v_self->use_collocations) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":440
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":460
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  *                 logger.info("Converting %d hash keys on precomputed collocations... ", len(pre.precomputed_collocations))             # <<<<<<<<<<<<<<
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+      __pyx_t_5 = __Pyx_GetName(__pyx_m, __pyx_n_s__logger); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 460; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      __pyx_t_3 = PyObject_GetAttr(__pyx_t_5, __pyx_n_s__info); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 440; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_3 = PyObject_GetAttr(__pyx_t_5, __pyx_n_s__info); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 460; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_7 = PyObject_Length(__pyx_t_5); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 460; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_5 = PyInt_FromSsize_t(__pyx_t_7); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 460; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 460; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_5 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 460; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":441
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":461
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  *                 logger.info("Converting %d hash keys on precomputed collocations... ", len(pre.precomputed_collocations))
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-        {__pyx_filename = __pyx_f[8]; __pyx_lineno = 441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        {__pyx_filename = __pyx_f[8]; __pyx_lineno = 461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_2 = __Pyx_dict_iterator(__pyx_v_pre->precomputed_collocations, 0, ((PyObject *)__pyx_n_s__iteritems), (&__pyx_t_6), (&__pyx_t_8)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -38832,7 +40192,7 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_8precompute(struct __py
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+        if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -38842,21 +40202,21 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_8precompute(struct __py
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         __pyx_t_3 = 0;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":442
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":462
  *                 logger.info("Converting %d hash keys on precomputed collocations... ", len(pre.precomputed_collocations))
  *                 for pattern, arr in pre.precomputed_collocations.iteritems():
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+        __pyx_t_3 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__pattern2phrase); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 462; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+        __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 462; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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         PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_pattern);
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+        __pyx_t_4 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 462; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -38864,47 +40224,47 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_8precompute(struct __py
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         __pyx_t_4 = 0;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":443
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":463
  *                 for pattern, arr in pre.precomputed_collocations.iteritems():
  *                     phrase = self.pattern2phrase(pattern)
  *                     self.precomputed_collocations[phrase] = arr             # <<<<<<<<<<<<<<
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-        if (PyObject_SetItem(__pyx_v_self->precomputed_collocations, __pyx_v_phrase, __pyx_v_arr) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 443; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        if (PyObject_SetItem(__pyx_v_self->precomputed_collocations, __pyx_v_phrase, __pyx_v_arr) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 463; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":444
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":464
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  *                     self.precomputed_collocations[phrase] = arr
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-    __pyx_t_5 = PyFloat_FromDouble(__pyx_f_3_sa_monitor_cpu()); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 444; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_5 = PyFloat_FromDouble(__pyx_f_3_sa_monitor_cpu()); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":445
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":465
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  *             stop_time = monitor_cpu()
  *             logger.info("Processing precomputations took %f seconds", stop_time - start_time)             # <<<<<<<<<<<<<<
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+    __pyx_t_5 = __Pyx_GetName(__pyx_m, __pyx_n_s__logger); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_4 = PyObject_GetAttr(__pyx_t_5, __pyx_n_s__info); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_5 = PyNumber_Subtract(__pyx_v_stop_time, __pyx_v_start_time); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -38912,7 +40272,7 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_8precompute(struct __py
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+    __pyx_t_5 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -38954,7 +40314,7 @@ static PyObject *__pyx_pw_3_sa_23HieroCachingRuleFactory_11get_precomputed_collo
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":448
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":468
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  *     def get_precomputed_collocation(self, phrase):             # <<<<<<<<<<<<<<
@@ -38976,29 +40336,29 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_10get_precomputed_collo
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":449
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":469
  * 
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":450
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":470
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  *             arr = self.precomputed_collocations[phrase]             # <<<<<<<<<<<<<<
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  */
-    __pyx_t_2 = PyObject_GetItem(__pyx_v_self->precomputed_collocations, __pyx_v_phrase); if (!__pyx_t_2) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = PyObject_GetItem(__pyx_v_self->precomputed_collocations, __pyx_v_phrase); if (!__pyx_t_2) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":451
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":471
  *         if phrase in self.precomputed_collocations:
  *             arr = self.precomputed_collocations[phrase]
  *             return PhraseLocation(arr=arr, arr_low=0, arr_high=len(arr), num_subpatterns=phrase.arity()+1)             # <<<<<<<<<<<<<<
@@ -39006,26 +40366,26 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_10get_precomputed_collo
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+    __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__arr_low), __pyx_int_0) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 451; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    __pyx_t_4 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 451; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__arr), __pyx_v_arr) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__arr_low), __pyx_int_0) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_4 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__arr_high), __pyx_t_4) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    __pyx_t_4 = PyObject_GetAttr(__pyx_v_phrase, __pyx_n_s__arity); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 451; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_4 = PyObject_GetAttr(__pyx_v_phrase, __pyx_n_s__arity); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    __pyx_t_5 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 451; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_5 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    __pyx_t_4 = PyNumber_Add(__pyx_t_5, __pyx_int_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 451; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_4 = PyNumber_Add(__pyx_t_5, __pyx_int_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_4);
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-    if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__num_subpatterns), __pyx_t_4) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 451; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__num_subpatterns), __pyx_t_4) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    __pyx_t_4 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_PhraseLocation)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 451; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_4 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_PhraseLocation)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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     __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
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@@ -39035,7 +40395,7 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_10get_precomputed_collo
   }
   __pyx_L3:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":452
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":472
  *             arr = self.precomputed_collocations[phrase]
  *             return PhraseLocation(arr=arr, arr_low=0, arr_high=len(arr), num_subpatterns=phrase.arity()+1)
  *         return None             # <<<<<<<<<<<<<<
@@ -39062,7 +40422,7 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_10get_precomputed_collo
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":455
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":475
  * 
  * 
  *     cdef int* baeza_yates_helper(self, int low1, int high1, int* arr1, int step1,             # <<<<<<<<<<<<<<
@@ -39108,7 +40468,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":468
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":488
  *         cdef Matching loc1, loc2
  * 
  *         result = <int*> malloc(0*sizeof(int*))             # <<<<<<<<<<<<<<
@@ -39117,7 +40477,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   __pyx_v_result = ((int *)malloc((0 * (sizeof(int *)))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":470
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":490
  *         result = <int*> malloc(0*sizeof(int*))
  * 
  *         d_first = 0             # <<<<<<<<<<<<<<
@@ -39126,7 +40486,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   __pyx_v_d_first = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":471
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":491
  * 
  *         d_first = 0
  *         if high1 - low1 > high2 - low2:             # <<<<<<<<<<<<<<
@@ -39136,7 +40496,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   __pyx_t_1 = ((__pyx_v_high1 - __pyx_v_low1) > (__pyx_v_high2 - __pyx_v_low2));
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":472
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":492
  *         d_first = 0
  *         if high1 - low1 > high2 - low2:
  *             d_first = 1             # <<<<<<<<<<<<<<
@@ -39148,7 +40508,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   }
   __pyx_L3:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":476
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":496
  *         # First, check to see if we are at any of the recursive base cases
  *         # Case 1: one of the sets is empty
  *         if low1 >= high1 or low2 >= high2:             # <<<<<<<<<<<<<<
@@ -39164,7 +40524,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   }
   if (__pyx_t_3) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":477
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":497
  *         # Case 1: one of the sets is empty
  *         if low1 >= high1 or low2 >= high2:
  *             return result             # <<<<<<<<<<<<<<
@@ -39177,7 +40537,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   }
   __pyx_L4:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":480
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":500
  * 
  *         # Case 2: sets are non-overlapping
  *         assign_matching(&loc1, arr1, high1-step1, step1, self.fda.sent_id.arr)             # <<<<<<<<<<<<<<
@@ -39186,7 +40546,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
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   __pyx_f_3_sa_assign_matching((&__pyx_v_loc1), __pyx_v_arr1, (__pyx_v_high1 - __pyx_v_step1), __pyx_v_step1, __pyx_v_self->fda->sent_id->arr);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":481
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":501
  *         # Case 2: sets are non-overlapping
  *         assign_matching(&loc1, arr1, high1-step1, step1, self.fda.sent_id.arr)
  *         assign_matching(&loc2, arr2, low2, step2, self.fda.sent_id.arr)             # <<<<<<<<<<<<<<
@@ -39195,7 +40555,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   __pyx_f_3_sa_assign_matching((&__pyx_v_loc2), __pyx_v_arr2, __pyx_v_low2, __pyx_v_step2, __pyx_v_self->fda->sent_id->arr);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":482
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":502
  *         assign_matching(&loc1, arr1, high1-step1, step1, self.fda.sent_id.arr)
  *         assign_matching(&loc2, arr2, low2, step2, self.fda.sent_id.arr)
  *         if self.compare_matchings(&loc1, &loc2, offset_by_one, len_last) == -1:             # <<<<<<<<<<<<<<
@@ -39205,7 +40565,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   __pyx_t_3 = (((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->compare_matchings(__pyx_v_self, (&__pyx_v_loc1), (&__pyx_v_loc2), __pyx_v_offset_by_one, __pyx_v_len_last) == -1);
   if (__pyx_t_3) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":483
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":503
  *         assign_matching(&loc2, arr2, low2, step2, self.fda.sent_id.arr)
  *         if self.compare_matchings(&loc1, &loc2, offset_by_one, len_last) == -1:
  *             return result             # <<<<<<<<<<<<<<
@@ -39218,7 +40578,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   }
   __pyx_L5:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":485
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":505
  *             return result
  * 
  *         assign_matching(&loc1, arr1, low1, step1, self.fda.sent_id.arr)             # <<<<<<<<<<<<<<
@@ -39227,7 +40587,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
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   __pyx_f_3_sa_assign_matching((&__pyx_v_loc1), __pyx_v_arr1, __pyx_v_low1, __pyx_v_step1, __pyx_v_self->fda->sent_id->arr);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":486
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":506
  * 
  *         assign_matching(&loc1, arr1, low1, step1, self.fda.sent_id.arr)
  *         assign_matching(&loc2, arr2, high2-step2, step2, self.fda.sent_id.arr)             # <<<<<<<<<<<<<<
@@ -39236,7 +40596,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   __pyx_f_3_sa_assign_matching((&__pyx_v_loc2), __pyx_v_arr2, (__pyx_v_high2 - __pyx_v_step2), __pyx_v_step2, __pyx_v_self->fda->sent_id->arr);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":487
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":507
  *         assign_matching(&loc1, arr1, low1, step1, self.fda.sent_id.arr)
  *         assign_matching(&loc2, arr2, high2-step2, step2, self.fda.sent_id.arr)
  *         if self.compare_matchings(&loc1, &loc2, offset_by_one, len_last) == 1:             # <<<<<<<<<<<<<<
@@ -39246,7 +40606,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   __pyx_t_3 = (((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->compare_matchings(__pyx_v_self, (&__pyx_v_loc1), (&__pyx_v_loc2), __pyx_v_offset_by_one, __pyx_v_len_last) == 1);
   if (__pyx_t_3) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":488
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":508
  *         assign_matching(&loc2, arr2, high2-step2, step2, self.fda.sent_id.arr)
  *         if self.compare_matchings(&loc1, &loc2, offset_by_one, len_last) == 1:
  *             return result             # <<<<<<<<<<<<<<
@@ -39259,7 +40619,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   }
   __pyx_L6:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":492
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":512
  *         # Case 3: query set and data set do not meet size mismatch constraints;
  *         # We use mergesort instead in this case
  *         qsetsize = (high1-low1) / step1             # <<<<<<<<<<<<<<
@@ -39269,15 +40629,15 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   __pyx_t_4 = (__pyx_v_high1 - __pyx_v_low1);
   if (unlikely(__pyx_v_step1 == 0)) {
     PyErr_Format(PyExc_ZeroDivisionError, "integer division or modulo by zero");
-    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 492; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   }
   else if (sizeof(int) == sizeof(long) && unlikely(__pyx_v_step1 == -1) && unlikely(UNARY_NEG_WOULD_OVERFLOW(__pyx_t_4))) {
     PyErr_Format(PyExc_OverflowError, "value too large to perform division");
-    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 492; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   }
   __pyx_v_qsetsize = __Pyx_div_int(__pyx_t_4, __pyx_v_step1);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":493
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":513
  *         # We use mergesort instead in this case
  *         qsetsize = (high1-low1) / step1
  *         dsetsize = (high2-low2) / step2             # <<<<<<<<<<<<<<
@@ -39287,15 +40647,15 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   __pyx_t_4 = (__pyx_v_high2 - __pyx_v_low2);
   if (unlikely(__pyx_v_step2 == 0)) {
     PyErr_Format(PyExc_ZeroDivisionError, "integer division or modulo by zero");
-    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 493; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 513; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   }
   else if (sizeof(int) == sizeof(long) && unlikely(__pyx_v_step2 == -1) && unlikely(UNARY_NEG_WOULD_OVERFLOW(__pyx_t_4))) {
     PyErr_Format(PyExc_OverflowError, "value too large to perform division");
-    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 493; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 513; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   }
   __pyx_v_dsetsize = __Pyx_div_int(__pyx_t_4, __pyx_v_step2);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":494
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":514
  *         qsetsize = (high1-low1) / step1
  *         dsetsize = (high2-low2) / step2
  *         if d_first:             # <<<<<<<<<<<<<<
@@ -39304,7 +40664,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   if (__pyx_v_d_first) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":495
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":515
  *         dsetsize = (high2-low2) / step2
  *         if d_first:
  *             tmp = qsetsize             # <<<<<<<<<<<<<<
@@ -39313,7 +40673,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_v_tmp = __pyx_v_qsetsize;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":496
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":516
  *         if d_first:
  *             tmp = qsetsize
  *             qsetsize = dsetsize             # <<<<<<<<<<<<<<
@@ -39322,7 +40682,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_v_qsetsize = __pyx_v_dsetsize;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":497
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":517
  *             tmp = qsetsize
  *             qsetsize = dsetsize
  *             dsetsize = tmp             # <<<<<<<<<<<<<<
@@ -39334,7 +40694,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   }
   __pyx_L7:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":499
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":519
  *             dsetsize = tmp
  * 
  *         if self.by_slack_factor * qsetsize * log(dsetsize) / log(2) > dsetsize:             # <<<<<<<<<<<<<<
@@ -39345,12 +40705,12 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   __pyx_t_6 = log(2.0);
   if (unlikely(__pyx_t_6 == 0)) {
     PyErr_Format(PyExc_ZeroDivisionError, "float division");
-    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 499; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 519; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   }
   __pyx_t_3 = ((__pyx_t_5 / __pyx_t_6) > __pyx_v_dsetsize);
   if (__pyx_t_3) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":500
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":520
  * 
  *         if self.by_slack_factor * qsetsize * log(dsetsize) / log(2) > dsetsize:
  *             free(result)             # <<<<<<<<<<<<<<
@@ -39359,7 +40719,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     free(__pyx_v_result);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":501
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":521
  *         if self.by_slack_factor * qsetsize * log(dsetsize) / log(2) > dsetsize:
  *             free(result)
  *             return self.merge_helper(low1, high1, arr1, step1, low2, high2, arr2, step2, offset_by_one, len_last, num_subpatterns, result_len)             # <<<<<<<<<<<<<<
@@ -39372,7 +40732,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   }
   __pyx_L8:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":505
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":525
  *         # binary search.    There are two flavors, depending on
  *         # whether the queryset or dataset is first
  *         if d_first:             # <<<<<<<<<<<<<<
@@ -39381,7 +40741,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   if (__pyx_v_d_first) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":506
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":526
  *         # whether the queryset or dataset is first
  *         if d_first:
  *             med2 = median(low2, high2, step2)             # <<<<<<<<<<<<<<
@@ -39390,7 +40750,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_v_med2 = __pyx_f_3_sa_median(__pyx_v_low2, __pyx_v_high2, __pyx_v_step2);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":507
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":527
  *         if d_first:
  *             med2 = median(low2, high2, step2)
  *             assign_matching(&loc2, arr2, med2, step2, self.fda.sent_id.arr)             # <<<<<<<<<<<<<<
@@ -39399,7 +40759,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_f_3_sa_assign_matching((&__pyx_v_loc2), __pyx_v_arr2, __pyx_v_med2, __pyx_v_step2, __pyx_v_self->fda->sent_id->arr);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":509
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":529
  *             assign_matching(&loc2, arr2, med2, step2, self.fda.sent_id.arr)
  * 
  *             search_low = low1             # <<<<<<<<<<<<<<
@@ -39408,7 +40768,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_v_search_low = __pyx_v_low1;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":510
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":530
  * 
  *             search_low = low1
  *             search_high = high1             # <<<<<<<<<<<<<<
@@ -39417,7 +40777,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_v_search_high = __pyx_v_high1;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":511
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":531
  *             search_low = low1
  *             search_high = high1
  *             while search_low < search_high:             # <<<<<<<<<<<<<<
@@ -39428,7 +40788,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
       __pyx_t_3 = (__pyx_v_search_low < __pyx_v_search_high);
       if (!__pyx_t_3) break;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":512
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":532
  *             search_high = high1
  *             while search_low < search_high:
  *                 med1 = median(search_low, search_high, step1)             # <<<<<<<<<<<<<<
@@ -39437,7 +40797,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
       __pyx_v_med1 = __pyx_f_3_sa_median(__pyx_v_search_low, __pyx_v_search_high, __pyx_v_step1);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":513
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":533
  *             while search_low < search_high:
  *                 med1 = median(search_low, search_high, step1)
  *                 find_comparable_matchings(low1, high1, arr1, step1, med1, &med1_minus, &med1_plus)             # <<<<<<<<<<<<<<
@@ -39446,7 +40806,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
       __pyx_f_3_sa_find_comparable_matchings(__pyx_v_low1, __pyx_v_high1, __pyx_v_arr1, __pyx_v_step1, __pyx_v_med1, (&__pyx_v_med1_minus), (&__pyx_v_med1_plus));
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":514
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":534
  *                 med1 = median(search_low, search_high, step1)
  *                 find_comparable_matchings(low1, high1, arr1, step1, med1, &med1_minus, &med1_plus)
  *                 comparison = self.compare_matchings_set(med1_minus, med1_plus, arr1, step1, &loc2, offset_by_one, len_last)             # <<<<<<<<<<<<<<
@@ -39455,7 +40815,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
       __pyx_v_comparison = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->compare_matchings_set(__pyx_v_self, __pyx_v_med1_minus, __pyx_v_med1_plus, __pyx_v_arr1, __pyx_v_step1, (&__pyx_v_loc2), __pyx_v_offset_by_one, __pyx_v_len_last);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":517
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":537
  *                 if comparison == -1:
  *                     search_low = med1_plus
  *                 elif comparison == 1:             # <<<<<<<<<<<<<<
@@ -39464,7 +40824,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
       switch (__pyx_v_comparison) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":515
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":535
  *                 find_comparable_matchings(low1, high1, arr1, step1, med1, &med1_minus, &med1_plus)
  *                 comparison = self.compare_matchings_set(med1_minus, med1_plus, arr1, step1, &loc2, offset_by_one, len_last)
  *                 if comparison == -1:             # <<<<<<<<<<<<<<
@@ -39473,7 +40833,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
         case -1:
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":516
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":536
  *                 comparison = self.compare_matchings_set(med1_minus, med1_plus, arr1, step1, &loc2, offset_by_one, len_last)
  *                 if comparison == -1:
  *                     search_low = med1_plus             # <<<<<<<<<<<<<<
@@ -39483,7 +40843,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
         __pyx_v_search_low = __pyx_v_med1_plus;
         break;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":517
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":537
  *                 if comparison == -1:
  *                     search_low = med1_plus
  *                 elif comparison == 1:             # <<<<<<<<<<<<<<
@@ -39492,7 +40852,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
         case 1:
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":518
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":538
  *                     search_low = med1_plus
  *                 elif comparison == 1:
  *                     search_high = med1_minus             # <<<<<<<<<<<<<<
@@ -39503,7 +40863,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
         break;
         default:
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":520
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":540
  *                     search_high = med1_minus
  *                 else:
  *                     break             # <<<<<<<<<<<<<<
@@ -39519,7 +40879,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   }
   /*else*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":522
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":542
  *                     break
  *         else:
  *             med1 = median(low1, high1, step1)             # <<<<<<<<<<<<<<
@@ -39528,7 +40888,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_v_med1 = __pyx_f_3_sa_median(__pyx_v_low1, __pyx_v_high1, __pyx_v_step1);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":523
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":543
  *         else:
  *             med1 = median(low1, high1, step1)
  *             find_comparable_matchings(low1, high1, arr1, step1, med1, &med1_minus, &med1_plus)             # <<<<<<<<<<<<<<
@@ -39537,7 +40897,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_f_3_sa_find_comparable_matchings(__pyx_v_low1, __pyx_v_high1, __pyx_v_arr1, __pyx_v_step1, __pyx_v_med1, (&__pyx_v_med1_minus), (&__pyx_v_med1_plus));
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":525
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":545
  *             find_comparable_matchings(low1, high1, arr1, step1, med1, &med1_minus, &med1_plus)
  * 
  *             search_low = low2             # <<<<<<<<<<<<<<
@@ -39546,7 +40906,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_v_search_low = __pyx_v_low2;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":526
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":546
  * 
  *             search_low = low2
  *             search_high = high2             # <<<<<<<<<<<<<<
@@ -39555,7 +40915,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_v_search_high = __pyx_v_high2;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":527
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":547
  *             search_low = low2
  *             search_high = high2
  *             while search_low < search_high:             # <<<<<<<<<<<<<<
@@ -39566,7 +40926,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
       __pyx_t_3 = (__pyx_v_search_low < __pyx_v_search_high);
       if (!__pyx_t_3) break;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":528
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":548
  *             search_high = high2
  *             while search_low < search_high:
  *                 med2 = median(search_low, search_high, step2)             # <<<<<<<<<<<<<<
@@ -39575,7 +40935,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
       __pyx_v_med2 = __pyx_f_3_sa_median(__pyx_v_search_low, __pyx_v_search_high, __pyx_v_step2);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":529
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":549
  *             while search_low < search_high:
  *                 med2 = median(search_low, search_high, step2)
  *                 assign_matching(&loc2, arr2, med2, step2, self.fda.sent_id.arr)             # <<<<<<<<<<<<<<
@@ -39584,7 +40944,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
       __pyx_f_3_sa_assign_matching((&__pyx_v_loc2), __pyx_v_arr2, __pyx_v_med2, __pyx_v_step2, __pyx_v_self->fda->sent_id->arr);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":530
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":550
  *                 med2 = median(search_low, search_high, step2)
  *                 assign_matching(&loc2, arr2, med2, step2, self.fda.sent_id.arr)
  *                 comparison = self.compare_matchings_set(med1_minus, med1_plus, arr1, step1, &loc2, offset_by_one, len_last)             # <<<<<<<<<<<<<<
@@ -39593,7 +40953,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
       __pyx_v_comparison = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->compare_matchings_set(__pyx_v_self, __pyx_v_med1_minus, __pyx_v_med1_plus, __pyx_v_arr1, __pyx_v_step1, (&__pyx_v_loc2), __pyx_v_offset_by_one, __pyx_v_len_last);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":533
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":553
  *                 if comparison == -1:
  *                     search_high = med2
  *                 elif comparison == 1:             # <<<<<<<<<<<<<<
@@ -39602,7 +40962,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
       switch (__pyx_v_comparison) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":531
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":551
  *                 assign_matching(&loc2, arr2, med2, step2, self.fda.sent_id.arr)
  *                 comparison = self.compare_matchings_set(med1_minus, med1_plus, arr1, step1, &loc2, offset_by_one, len_last)
  *                 if comparison == -1:             # <<<<<<<<<<<<<<
@@ -39611,7 +40971,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
         case -1:
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":532
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":552
  *                 comparison = self.compare_matchings_set(med1_minus, med1_plus, arr1, step1, &loc2, offset_by_one, len_last)
  *                 if comparison == -1:
  *                     search_high = med2             # <<<<<<<<<<<<<<
@@ -39621,7 +40981,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
         __pyx_v_search_high = __pyx_v_med2;
         break;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":533
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":553
  *                 if comparison == -1:
  *                     search_high = med2
  *                 elif comparison == 1:             # <<<<<<<<<<<<<<
@@ -39630,7 +40990,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
         case 1:
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":534
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":554
  *                     search_high = med2
  *                 elif comparison == 1:
  *                     search_low = med2 + step2             # <<<<<<<<<<<<<<
@@ -39641,7 +41001,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
         break;
         default:
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":536
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":556
  *                     search_low = med2 + step2
  *                 else:
  *                     break             # <<<<<<<<<<<<<<
@@ -39656,7 +41016,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   }
   __pyx_L9:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":538
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":558
  *                     break
  * 
  *         med_result_len = 0             # <<<<<<<<<<<<<<
@@ -39665,7 +41025,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   __pyx_v_med_result_len = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":539
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":559
  * 
  *         med_result_len = 0
  *         med_result = <int*> malloc(0*sizeof(int*))             # <<<<<<<<<<<<<<
@@ -39674,7 +41034,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   __pyx_v_med_result = ((int *)malloc((0 * (sizeof(int *)))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":540
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":560
  *         med_result_len = 0
  *         med_result = <int*> malloc(0*sizeof(int*))
  *         if search_high > search_low:             # <<<<<<<<<<<<<<
@@ -39684,7 +41044,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   __pyx_t_3 = (__pyx_v_search_high > __pyx_v_search_low);
   if (__pyx_t_3) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":546
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":566
  *             # want to store the bindings for all of those elements.    We can
  *             # subsequently throw all of them away.
  *             med2_minus = med2             # <<<<<<<<<<<<<<
@@ -39693,7 +41053,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_v_med2_minus = __pyx_v_med2;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":547
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":567
  *             # subsequently throw all of them away.
  *             med2_minus = med2
  *             med2_plus = med2 + step2             # <<<<<<<<<<<<<<
@@ -39702,7 +41062,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_v_med2_plus = (__pyx_v_med2 + __pyx_v_step2);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":548
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":568
  *             med2_minus = med2
  *             med2_plus = med2 + step2
  *             i1 = med1_minus             # <<<<<<<<<<<<<<
@@ -39711,7 +41071,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_v_i1 = __pyx_v_med1_minus;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":549
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":569
  *             med2_plus = med2 + step2
  *             i1 = med1_minus
  *             while i1 < med1_plus:             # <<<<<<<<<<<<<<
@@ -39722,7 +41082,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
       __pyx_t_3 = (__pyx_v_i1 < __pyx_v_med1_plus);
       if (!__pyx_t_3) break;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":550
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":570
  *             i1 = med1_minus
  *             while i1 < med1_plus:
  *                 assign_matching(&loc1, arr1, i1, step1, self.fda.sent_id.arr)             # <<<<<<<<<<<<<<
@@ -39731,7 +41091,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
       __pyx_f_3_sa_assign_matching((&__pyx_v_loc1), __pyx_v_arr1, __pyx_v_i1, __pyx_v_step1, __pyx_v_self->fda->sent_id->arr);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":551
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":571
  *             while i1 < med1_plus:
  *                 assign_matching(&loc1, arr1, i1, step1, self.fda.sent_id.arr)
  *                 while med2_minus-step2 >= low2:             # <<<<<<<<<<<<<<
@@ -39742,7 +41102,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
         __pyx_t_3 = ((__pyx_v_med2_minus - __pyx_v_step2) >= __pyx_v_low2);
         if (!__pyx_t_3) break;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":552
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":572
  *                 assign_matching(&loc1, arr1, i1, step1, self.fda.sent_id.arr)
  *                 while med2_minus-step2 >= low2:
  *                     assign_matching(&loc2, arr2, med2_minus-step2, step2, self.fda.sent_id.arr)             # <<<<<<<<<<<<<<
@@ -39751,7 +41111,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
         __pyx_f_3_sa_assign_matching((&__pyx_v_loc2), __pyx_v_arr2, (__pyx_v_med2_minus - __pyx_v_step2), __pyx_v_step2, __pyx_v_self->fda->sent_id->arr);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":553
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":573
  *                 while med2_minus-step2 >= low2:
  *                     assign_matching(&loc2, arr2, med2_minus-step2, step2, self.fda.sent_id.arr)
  *                     if self.compare_matchings(&loc1, &loc2, offset_by_one, len_last) < 1:             # <<<<<<<<<<<<<<
@@ -39761,7 +41121,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
         __pyx_t_3 = (((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->compare_matchings(__pyx_v_self, (&__pyx_v_loc1), (&__pyx_v_loc2), __pyx_v_offset_by_one, __pyx_v_len_last) < 1);
         if (__pyx_t_3) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":554
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":574
  *                     assign_matching(&loc2, arr2, med2_minus-step2, step2, self.fda.sent_id.arr)
  *                     if self.compare_matchings(&loc1, &loc2, offset_by_one, len_last) < 1:
  *                         med2_minus = med2_minus - step2             # <<<<<<<<<<<<<<
@@ -39773,7 +41133,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
         }
         /*else*/ {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":556
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":576
  *                         med2_minus = med2_minus - step2
  *                     else:
  *                         break             # <<<<<<<<<<<<<<
@@ -39786,7 +41146,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
       }
       __pyx_L18_break:;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":557
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":577
  *                     else:
  *                         break
  *                 i2 = med2_minus             # <<<<<<<<<<<<<<
@@ -39795,7 +41155,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
       __pyx_v_i2 = __pyx_v_med2_minus;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":558
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":578
  *                         break
  *                 i2 = med2_minus
  *                 while i2 < high2:             # <<<<<<<<<<<<<<
@@ -39806,7 +41166,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
         __pyx_t_3 = (__pyx_v_i2 < __pyx_v_high2);
         if (!__pyx_t_3) break;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":559
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":579
  *                 i2 = med2_minus
  *                 while i2 < high2:
  *                     assign_matching(&loc2, arr2, i2, step2, self.fda.sent_id.arr)             # <<<<<<<<<<<<<<
@@ -39815,7 +41175,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
         __pyx_f_3_sa_assign_matching((&__pyx_v_loc2), __pyx_v_arr2, __pyx_v_i2, __pyx_v_step2, __pyx_v_self->fda->sent_id->arr);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":560
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":580
  *                 while i2 < high2:
  *                     assign_matching(&loc2, arr2, i2, step2, self.fda.sent_id.arr)
  *                     comparison = self.compare_matchings(&loc1, &loc2, offset_by_one, len_last)             # <<<<<<<<<<<<<<
@@ -39824,7 +41184,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
         __pyx_v_comparison = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->compare_matchings(__pyx_v_self, (&__pyx_v_loc1), (&__pyx_v_loc2), __pyx_v_offset_by_one, __pyx_v_len_last);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":561
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":581
  *                     assign_matching(&loc2, arr2, i2, step2, self.fda.sent_id.arr)
  *                     comparison = self.compare_matchings(&loc1, &loc2, offset_by_one, len_last)
  *                     if comparison == 0:             # <<<<<<<<<<<<<<
@@ -39834,7 +41194,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
         __pyx_t_3 = (__pyx_v_comparison == 0);
         if (__pyx_t_3) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":563
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":583
  *                     if comparison == 0:
  *                         pass
  *                         med_result = append_combined_matching(med_result, &loc1, &loc2, offset_by_one, num_subpatterns, &med_result_len)             # <<<<<<<<<<<<<<
@@ -39846,7 +41206,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
         }
         __pyx_L22:;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":564
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":584
  *                         pass
  *                         med_result = append_combined_matching(med_result, &loc1, &loc2, offset_by_one, num_subpatterns, &med_result_len)
  *                     if comparison == -1:             # <<<<<<<<<<<<<<
@@ -39856,7 +41216,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
         __pyx_t_3 = (__pyx_v_comparison == -1);
         if (__pyx_t_3) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":565
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":585
  *                         med_result = append_combined_matching(med_result, &loc1, &loc2, offset_by_one, num_subpatterns, &med_result_len)
  *                     if comparison == -1:
  *                         break             # <<<<<<<<<<<<<<
@@ -39868,7 +41228,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
         }
         __pyx_L23:;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":566
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":586
  *                     if comparison == -1:
  *                         break
  *                     i2 = i2 + step2             # <<<<<<<<<<<<<<
@@ -39879,7 +41239,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
       }
       __pyx_L21_break:;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":567
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":587
  *                         break
  *                     i2 = i2 + step2
  *                 if i2 > med2_plus:             # <<<<<<<<<<<<<<
@@ -39889,7 +41249,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
       __pyx_t_3 = (__pyx_v_i2 > __pyx_v_med2_plus);
       if (__pyx_t_3) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":568
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":588
  *                     i2 = i2 + step2
  *                 if i2 > med2_plus:
  *                     med2_plus = i2             # <<<<<<<<<<<<<<
@@ -39901,7 +41261,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
       }
       __pyx_L24:;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":569
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":589
  *                 if i2 > med2_plus:
  *                     med2_plus = i2
  *                 i1 = i1 + step1             # <<<<<<<<<<<<<<
@@ -39911,7 +41271,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
       __pyx_v_i1 = (__pyx_v_i1 + __pyx_v_step1);
     }
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":571
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":591
  *                 i1 = i1 + step1
  * 
  *             tmp = med1_minus             # <<<<<<<<<<<<<<
@@ -39920,7 +41280,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_v_tmp = __pyx_v_med1_minus;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":572
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":592
  * 
  *             tmp = med1_minus
  *             med1_minus = med1_plus             # <<<<<<<<<<<<<<
@@ -39929,7 +41289,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_v_med1_minus = __pyx_v_med1_plus;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":573
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":593
  *             tmp = med1_minus
  *             med1_minus = med1_plus
  *             med1_plus = tmp             # <<<<<<<<<<<<<<
@@ -39941,7 +41301,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   }
   /*else*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":576
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":596
  *         else:
  *             # No match; need to figure out the point of division in D and Q
  *             med2_minus = med2             # <<<<<<<<<<<<<<
@@ -39950,7 +41310,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_v_med2_minus = __pyx_v_med2;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":577
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":597
  *             # No match; need to figure out the point of division in D and Q
  *             med2_minus = med2
  *             med2_plus = med2             # <<<<<<<<<<<<<<
@@ -39959,7 +41319,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     __pyx_v_med2_plus = __pyx_v_med2;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":578
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":598
  *             med2_minus = med2
  *             med2_plus = med2
  *             if d_first:             # <<<<<<<<<<<<<<
@@ -39968,7 +41328,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
     if (__pyx_v_d_first) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":579
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":599
  *             med2_plus = med2
  *             if d_first:
  *                 med2_minus = med2_minus + step2             # <<<<<<<<<<<<<<
@@ -39977,7 +41337,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
       __pyx_v_med2_minus = (__pyx_v_med2_minus + __pyx_v_step2);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":580
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":600
  *             if d_first:
  *                 med2_minus = med2_minus + step2
  *                 if comparison == -1:             # <<<<<<<<<<<<<<
@@ -39987,7 +41347,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
       __pyx_t_3 = (__pyx_v_comparison == -1);
       if (__pyx_t_3) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":581
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":601
  *                 med2_minus = med2_minus + step2
  *                 if comparison == -1:
  *                     med1_minus = med1_plus             # <<<<<<<<<<<<<<
@@ -39999,7 +41359,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
       }
       __pyx_L26:;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":582
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":602
  *                 if comparison == -1:
  *                     med1_minus = med1_plus
  *                 if comparison == 1:             # <<<<<<<<<<<<<<
@@ -40009,7 +41369,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
       __pyx_t_3 = (__pyx_v_comparison == 1);
       if (__pyx_t_3) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":583
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":603
  *                     med1_minus = med1_plus
  *                 if comparison == 1:
  *                     med1_plus = med1_minus             # <<<<<<<<<<<<<<
@@ -40024,7 +41384,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
     }
     /*else*/ {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":585
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":605
  *                     med1_plus = med1_minus
  *             else:
  *                 tmp = med1_minus             # <<<<<<<<<<<<<<
@@ -40033,7 +41393,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
       __pyx_v_tmp = __pyx_v_med1_minus;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":586
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":606
  *             else:
  *                 tmp = med1_minus
  *                 med1_minus = med1_plus             # <<<<<<<<<<<<<<
@@ -40042,7 +41402,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
       __pyx_v_med1_minus = __pyx_v_med1_plus;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":587
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":607
  *                 tmp = med1_minus
  *                 med1_minus = med1_plus
  *                 med1_plus = tmp             # <<<<<<<<<<<<<<
@@ -40051,7 +41411,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
       __pyx_v_med1_plus = __pyx_v_tmp;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":588
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":608
  *                 med1_minus = med1_plus
  *                 med1_plus = tmp
  *                 if comparison == 1:             # <<<<<<<<<<<<<<
@@ -40061,7 +41421,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
       __pyx_t_3 = (__pyx_v_comparison == 1);
       if (__pyx_t_3) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":589
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":609
  *                 med1_plus = tmp
  *                 if comparison == 1:
  *                     med2_minus = med2_minus + step2             # <<<<<<<<<<<<<<
@@ -40070,7 +41430,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
         __pyx_v_med2_minus = (__pyx_v_med2_minus + __pyx_v_step2);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":590
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":610
  *                 if comparison == 1:
  *                     med2_minus = med2_minus + step2
  *                     med2_plus = med2_plus + step2             # <<<<<<<<<<<<<<
@@ -40086,7 +41446,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   }
   __pyx_L14:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":592
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":612
  *                     med2_plus = med2_plus + step2
  * 
  *         low_result_len = 0             # <<<<<<<<<<<<<<
@@ -40095,7 +41455,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   __pyx_v_low_result_len = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":593
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":613
  * 
  *         low_result_len = 0
  *         low_result = self.baeza_yates_helper(low1, med1_plus, arr1, step1, low2, med2_plus, arr2, step2, offset_by_one, len_last, num_subpatterns, &low_result_len)             # <<<<<<<<<<<<<<
@@ -40104,7 +41464,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   __pyx_v_low_result = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->baeza_yates_helper(__pyx_v_self, __pyx_v_low1, __pyx_v_med1_plus, __pyx_v_arr1, __pyx_v_step1, __pyx_v_low2, __pyx_v_med2_plus, __pyx_v_arr2, __pyx_v_step2, __pyx_v_offset_by_one, __pyx_v_len_last, __pyx_v_num_subpatterns, (&__pyx_v_low_result_len));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":594
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":614
  *         low_result_len = 0
  *         low_result = self.baeza_yates_helper(low1, med1_plus, arr1, step1, low2, med2_plus, arr2, step2, offset_by_one, len_last, num_subpatterns, &low_result_len)
  *         high_result_len = 0             # <<<<<<<<<<<<<<
@@ -40113,7 +41473,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   __pyx_v_high_result_len = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":595
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":615
  *         low_result = self.baeza_yates_helper(low1, med1_plus, arr1, step1, low2, med2_plus, arr2, step2, offset_by_one, len_last, num_subpatterns, &low_result_len)
  *         high_result_len = 0
  *         high_result = self.baeza_yates_helper(med1_minus, high1, arr1, step1, med2_minus, high2, arr2, step2, offset_by_one, len_last, num_subpatterns, &high_result_len)             # <<<<<<<<<<<<<<
@@ -40122,7 +41482,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   __pyx_v_high_result = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->baeza_yates_helper(__pyx_v_self, __pyx_v_med1_minus, __pyx_v_high1, __pyx_v_arr1, __pyx_v_step1, __pyx_v_med2_minus, __pyx_v_high2, __pyx_v_arr2, __pyx_v_step2, __pyx_v_offset_by_one, __pyx_v_len_last, __pyx_v_num_subpatterns, (&__pyx_v_high_result_len));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":597
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":617
  *         high_result = self.baeza_yates_helper(med1_minus, high1, arr1, step1, med2_minus, high2, arr2, step2, offset_by_one, len_last, num_subpatterns, &high_result_len)
  * 
  *         result = extend_arr(result, result_len, low_result, low_result_len)             # <<<<<<<<<<<<<<
@@ -40131,7 +41491,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   __pyx_v_result = __pyx_f_3_sa_extend_arr(__pyx_v_result, __pyx_v_result_len, __pyx_v_low_result, __pyx_v_low_result_len);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":598
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":618
  * 
  *         result = extend_arr(result, result_len, low_result, low_result_len)
  *         result = extend_arr(result, result_len, med_result, med_result_len)             # <<<<<<<<<<<<<<
@@ -40140,7 +41500,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   __pyx_v_result = __pyx_f_3_sa_extend_arr(__pyx_v_result, __pyx_v_result_len, __pyx_v_med_result, __pyx_v_med_result_len);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":599
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":619
  *         result = extend_arr(result, result_len, low_result, low_result_len)
  *         result = extend_arr(result, result_len, med_result, med_result_len)
  *         result = extend_arr(result, result_len, high_result, high_result_len)             # <<<<<<<<<<<<<<
@@ -40149,7 +41509,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   __pyx_v_result = __pyx_f_3_sa_extend_arr(__pyx_v_result, __pyx_v_result_len, __pyx_v_high_result, __pyx_v_high_result_len);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":600
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":620
  *         result = extend_arr(result, result_len, med_result, med_result_len)
  *         result = extend_arr(result, result_len, high_result, high_result_len)
  *         free(low_result)             # <<<<<<<<<<<<<<
@@ -40158,7 +41518,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   free(__pyx_v_low_result);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":601
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":621
  *         result = extend_arr(result, result_len, high_result, high_result_len)
  *         free(low_result)
  *         free(med_result)             # <<<<<<<<<<<<<<
@@ -40167,7 +41527,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   free(__pyx_v_med_result);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":602
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":622
  *         free(low_result)
  *         free(med_result)
  *         free(high_result)             # <<<<<<<<<<<<<<
@@ -40176,7 +41536,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
  */
   free(__pyx_v_high_result);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":604
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":624
  *         free(high_result)
  * 
  *         return result             # <<<<<<<<<<<<<<
@@ -40196,7 +41556,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_baeza_yates_helper(struct __p
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":608
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":628
  * 
  * 
  *     cdef long compare_matchings_set(self, int i1_minus, int i1_plus, int* arr1, int step1,             # <<<<<<<<<<<<<<
@@ -40215,7 +41575,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings_set(struct
   int __pyx_t_1;
   __Pyx_RefNannySetupContext("compare_matchings_set", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":619
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":639
  *         cdef Matching* loc1
  * 
  *         loc1 = &l1_stack             # <<<<<<<<<<<<<<
@@ -40224,7 +41584,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings_set(struct
  */
   __pyx_v_loc1 = (&__pyx_v_l1_stack);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":621
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":641
  *         loc1 = &l1_stack
  * 
  *         i1 = i1_minus             # <<<<<<<<<<<<<<
@@ -40233,7 +41593,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings_set(struct
  */
   __pyx_v_i1 = __pyx_v_i1_minus;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":622
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":642
  * 
  *         i1 = i1_minus
  *         while i1 < i1_plus:             # <<<<<<<<<<<<<<
@@ -40244,7 +41604,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings_set(struct
     __pyx_t_1 = (__pyx_v_i1 < __pyx_v_i1_plus);
     if (!__pyx_t_1) break;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":623
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":643
  *         i1 = i1_minus
  *         while i1 < i1_plus:
  *             assign_matching(loc1, arr1, i1, step1, self.fda.sent_id.arr)             # <<<<<<<<<<<<<<
@@ -40253,7 +41613,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings_set(struct
  */
     __pyx_f_3_sa_assign_matching(__pyx_v_loc1, __pyx_v_arr1, __pyx_v_i1, __pyx_v_step1, __pyx_v_self->fda->sent_id->arr);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":624
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":644
  *         while i1 < i1_plus:
  *             assign_matching(loc1, arr1, i1, step1, self.fda.sent_id.arr)
  *             comparison = self.compare_matchings(loc1, loc2, offset_by_one, len_last)             # <<<<<<<<<<<<<<
@@ -40262,7 +41622,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings_set(struct
  */
     __pyx_v_comparison = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->compare_matchings(__pyx_v_self, __pyx_v_loc1, __pyx_v_loc2, __pyx_v_offset_by_one, __pyx_v_len_last);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":625
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":645
  *             assign_matching(loc1, arr1, i1, step1, self.fda.sent_id.arr)
  *             comparison = self.compare_matchings(loc1, loc2, offset_by_one, len_last)
  *             if comparison == 0:             # <<<<<<<<<<<<<<
@@ -40272,7 +41632,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings_set(struct
     __pyx_t_1 = (__pyx_v_comparison == 0);
     if (__pyx_t_1) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":626
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":646
  *             comparison = self.compare_matchings(loc1, loc2, offset_by_one, len_last)
  *             if comparison == 0:
  *                 prev_comparison = 0             # <<<<<<<<<<<<<<
@@ -40281,7 +41641,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings_set(struct
  */
       __pyx_v_prev_comparison = 0;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":627
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":647
  *             if comparison == 0:
  *                 prev_comparison = 0
  *                 break             # <<<<<<<<<<<<<<
@@ -40292,7 +41652,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings_set(struct
       goto __pyx_L5;
     }
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":628
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":648
  *                 prev_comparison = 0
  *                 break
  *             elif i1 == i1_minus:             # <<<<<<<<<<<<<<
@@ -40302,7 +41662,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings_set(struct
     __pyx_t_1 = (__pyx_v_i1 == __pyx_v_i1_minus);
     if (__pyx_t_1) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":629
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":649
  *                 break
  *             elif i1 == i1_minus:
  *                 prev_comparison = comparison             # <<<<<<<<<<<<<<
@@ -40314,7 +41674,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings_set(struct
     }
     /*else*/ {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":631
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":651
  *                 prev_comparison = comparison
  *             else:
  *                 if comparison != prev_comparison:             # <<<<<<<<<<<<<<
@@ -40324,7 +41684,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings_set(struct
       __pyx_t_1 = (__pyx_v_comparison != __pyx_v_prev_comparison);
       if (__pyx_t_1) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":632
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":652
  *             else:
  *                 if comparison != prev_comparison:
  *                     prev_comparison = 0             # <<<<<<<<<<<<<<
@@ -40333,7 +41693,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings_set(struct
  */
         __pyx_v_prev_comparison = 0;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":633
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":653
  *                 if comparison != prev_comparison:
  *                     prev_comparison = 0
  *                     break             # <<<<<<<<<<<<<<
@@ -40347,7 +41707,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings_set(struct
     }
     __pyx_L5:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":634
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":654
  *                     prev_comparison = 0
  *                     break
  *             i1 = i1 + step1             # <<<<<<<<<<<<<<
@@ -40358,7 +41718,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings_set(struct
   }
   __pyx_L4_break:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":635
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":655
  *                     break
  *             i1 = i1 + step1
  *         return prev_comparison             # <<<<<<<<<<<<<<
@@ -40374,7 +41734,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings_set(struct
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":638
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":658
  * 
  * 
  *     cdef long compare_matchings(self, Matching* loc1, Matching* loc2, int offset_by_one, int len_last):             # <<<<<<<<<<<<<<
@@ -40392,7 +41752,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
   int __pyx_t_4;
   __Pyx_RefNannySetupContext("compare_matchings", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":641
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":661
  *         cdef int i
  * 
  *         if loc1.sent_id > loc2.sent_id:             # <<<<<<<<<<<<<<
@@ -40402,7 +41762,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
   __pyx_t_1 = (__pyx_v_loc1->sent_id > __pyx_v_loc2->sent_id);
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":642
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":662
  * 
  *         if loc1.sent_id > loc2.sent_id:
  *             return 1             # <<<<<<<<<<<<<<
@@ -40415,7 +41775,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
   }
   __pyx_L3:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":643
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":663
  *         if loc1.sent_id > loc2.sent_id:
  *             return 1
  *         if loc2.sent_id > loc1.sent_id:             # <<<<<<<<<<<<<<
@@ -40425,7 +41785,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
   __pyx_t_1 = (__pyx_v_loc2->sent_id > __pyx_v_loc1->sent_id);
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":644
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":664
  *             return 1
  *         if loc2.sent_id > loc1.sent_id:
  *             return -1             # <<<<<<<<<<<<<<
@@ -40438,7 +41798,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
   }
   __pyx_L4:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":646
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":666
  *             return -1
  * 
  *         if loc1.size == 1 and loc2.size == 1:             # <<<<<<<<<<<<<<
@@ -40454,7 +41814,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
   }
   if (__pyx_t_3) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":647
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":667
  * 
  *         if loc1.size == 1 and loc2.size == 1:
  *             if loc2.arr[loc2.start] - loc1.arr[loc1.start] <= self.train_min_gap_size:             # <<<<<<<<<<<<<<
@@ -40464,7 +41824,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
     __pyx_t_3 = (((__pyx_v_loc2->arr[__pyx_v_loc2->start]) - (__pyx_v_loc1->arr[__pyx_v_loc1->start])) <= __pyx_v_self->train_min_gap_size);
     if (__pyx_t_3) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":648
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":668
  *         if loc1.size == 1 and loc2.size == 1:
  *             if loc2.arr[loc2.start] - loc1.arr[loc1.start] <= self.train_min_gap_size:
  *                 return 1             # <<<<<<<<<<<<<<
@@ -40479,7 +41839,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
     goto __pyx_L5;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":650
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":670
  *                 return 1
  * 
  *         elif offset_by_one:             # <<<<<<<<<<<<<<
@@ -40488,7 +41848,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
  */
   if (__pyx_v_offset_by_one) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":651
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":671
  * 
  *         elif offset_by_one:
  *             for i from 1 <= i < loc1.size:             # <<<<<<<<<<<<<<
@@ -40498,7 +41858,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
     __pyx_t_4 = __pyx_v_loc1->size;
     for (__pyx_v_i = 1; __pyx_v_i < __pyx_t_4; __pyx_v_i++) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":652
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":672
  *         elif offset_by_one:
  *             for i from 1 <= i < loc1.size:
  *                 if loc1.arr[loc1.start+i] > loc2.arr[loc2.start+i-1]:             # <<<<<<<<<<<<<<
@@ -40508,7 +41868,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
       __pyx_t_3 = ((__pyx_v_loc1->arr[(__pyx_v_loc1->start + __pyx_v_i)]) > (__pyx_v_loc2->arr[((__pyx_v_loc2->start + __pyx_v_i) - 1)]));
       if (__pyx_t_3) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":653
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":673
  *             for i from 1 <= i < loc1.size:
  *                 if loc1.arr[loc1.start+i] > loc2.arr[loc2.start+i-1]:
  *                     return 1             # <<<<<<<<<<<<<<
@@ -40521,7 +41881,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
       }
       __pyx_L9:;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":654
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":674
  *                 if loc1.arr[loc1.start+i] > loc2.arr[loc2.start+i-1]:
  *                     return 1
  *                 if loc1.arr[loc1.start+i] < loc2.arr[loc2.start+i-1]:             # <<<<<<<<<<<<<<
@@ -40531,7 +41891,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
       __pyx_t_3 = ((__pyx_v_loc1->arr[(__pyx_v_loc1->start + __pyx_v_i)]) < (__pyx_v_loc2->arr[((__pyx_v_loc2->start + __pyx_v_i) - 1)]));
       if (__pyx_t_3) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":655
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":675
  *                     return 1
  *                 if loc1.arr[loc1.start+i] < loc2.arr[loc2.start+i-1]:
  *                     return -1             # <<<<<<<<<<<<<<
@@ -40548,7 +41908,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
   }
   /*else*/ {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":658
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":678
  * 
  *         else:
  *             if loc1.arr[loc1.start]+1 > loc2.arr[loc2.start]:             # <<<<<<<<<<<<<<
@@ -40558,7 +41918,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
     __pyx_t_3 = (((__pyx_v_loc1->arr[__pyx_v_loc1->start]) + 1) > (__pyx_v_loc2->arr[__pyx_v_loc2->start]));
     if (__pyx_t_3) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":659
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":679
  *         else:
  *             if loc1.arr[loc1.start]+1 > loc2.arr[loc2.start]:
  *                 return 1             # <<<<<<<<<<<<<<
@@ -40571,7 +41931,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
     }
     __pyx_L11:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":660
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":680
  *             if loc1.arr[loc1.start]+1 > loc2.arr[loc2.start]:
  *                 return 1
  *             if loc1.arr[loc1.start]+1 < loc2.arr[loc2.start]:             # <<<<<<<<<<<<<<
@@ -40581,7 +41941,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
     __pyx_t_3 = (((__pyx_v_loc1->arr[__pyx_v_loc1->start]) + 1) < (__pyx_v_loc2->arr[__pyx_v_loc2->start]));
     if (__pyx_t_3) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":661
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":681
  *                 return 1
  *             if loc1.arr[loc1.start]+1 < loc2.arr[loc2.start]:
  *                 return -1             # <<<<<<<<<<<<<<
@@ -40594,7 +41954,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
     }
     __pyx_L12:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":663
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":683
  *                 return -1
  * 
  *             for i from 1 <= i < loc1.size:             # <<<<<<<<<<<<<<
@@ -40604,7 +41964,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
     __pyx_t_4 = __pyx_v_loc1->size;
     for (__pyx_v_i = 1; __pyx_v_i < __pyx_t_4; __pyx_v_i++) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":664
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":684
  * 
  *             for i from 1 <= i < loc1.size:
  *                 if loc1.arr[loc1.start+i] > loc2.arr[loc2.start+i]:             # <<<<<<<<<<<<<<
@@ -40614,7 +41974,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
       __pyx_t_3 = ((__pyx_v_loc1->arr[(__pyx_v_loc1->start + __pyx_v_i)]) > (__pyx_v_loc2->arr[(__pyx_v_loc2->start + __pyx_v_i)]));
       if (__pyx_t_3) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":665
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":685
  *             for i from 1 <= i < loc1.size:
  *                 if loc1.arr[loc1.start+i] > loc2.arr[loc2.start+i]:
  *                     return 1             # <<<<<<<<<<<<<<
@@ -40627,7 +41987,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
       }
       __pyx_L15:;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":666
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":686
  *                 if loc1.arr[loc1.start+i] > loc2.arr[loc2.start+i]:
  *                     return 1
  *                 if loc1.arr[loc1.start+i] < loc2.arr[loc2.start+i]:             # <<<<<<<<<<<<<<
@@ -40637,7 +41997,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
       __pyx_t_3 = ((__pyx_v_loc1->arr[(__pyx_v_loc1->start + __pyx_v_i)]) < (__pyx_v_loc2->arr[(__pyx_v_loc2->start + __pyx_v_i)]));
       if (__pyx_t_3) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":667
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":687
  *                     return 1
  *                 if loc1.arr[loc1.start+i] < loc2.arr[loc2.start+i]:
  *                     return -1             # <<<<<<<<<<<<<<
@@ -40653,7 +42013,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
   }
   __pyx_L5:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":669
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":689
  *                     return -1
  * 
  *         if loc2.arr[loc2.end-1] + len_last - loc1.arr[loc1.start] > self.train_max_initial_size:             # <<<<<<<<<<<<<<
@@ -40663,7 +42023,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
   __pyx_t_3 = ((((__pyx_v_loc2->arr[(__pyx_v_loc2->end - 1)]) + __pyx_v_len_last) - (__pyx_v_loc1->arr[__pyx_v_loc1->start])) > __pyx_v_self->train_max_initial_size);
   if (__pyx_t_3) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":670
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":690
  * 
  *         if loc2.arr[loc2.end-1] + len_last - loc1.arr[loc1.start] > self.train_max_initial_size:
  *             return -1             # <<<<<<<<<<<<<<
@@ -40676,7 +42036,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
   }
   __pyx_L17:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":671
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":691
  *         if loc2.arr[loc2.end-1] + len_last - loc1.arr[loc1.start] > self.train_max_initial_size:
  *             return -1
  *         return 0             # <<<<<<<<<<<<<<
@@ -40692,7 +42052,7 @@ static long __pyx_f_3_sa_23HieroCachingRuleFactory_compare_matchings(struct __py
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":674
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":694
  * 
  * 
  *     cdef int* merge_helper(self, int low1, int high1, int* arr1, int step1,             # <<<<<<<<<<<<<<
@@ -40716,7 +42076,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
   int __pyx_t_3;
   __Pyx_RefNannySetupContext("merge_helper", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":682
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":702
  *         cdef Matching loc1, loc2
  * 
  *         result_len[0] = 0             # <<<<<<<<<<<<<<
@@ -40725,7 +42085,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
  */
   (__pyx_v_result_len[0]) = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":683
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":703
  * 
  *         result_len[0] = 0
  *         result = <int*> malloc(0*sizeof(int))             # <<<<<<<<<<<<<<
@@ -40734,7 +42094,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
  */
   __pyx_v_result = ((int *)malloc((0 * (sizeof(int)))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":685
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":705
  *         result = <int*> malloc(0*sizeof(int))
  * 
  *         i1 = low1             # <<<<<<<<<<<<<<
@@ -40743,7 +42103,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
  */
   __pyx_v_i1 = __pyx_v_low1;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":686
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":706
  * 
  *         i1 = low1
  *         i2 = low2             # <<<<<<<<<<<<<<
@@ -40752,7 +42112,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
  */
   __pyx_v_i2 = __pyx_v_low2;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":687
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":707
  *         i1 = low1
  *         i2 = low2
  *         while i1 < high1 and i2 < high2:             # <<<<<<<<<<<<<<
@@ -40769,7 +42129,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
     }
     if (!__pyx_t_3) break;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":690
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":710
  * 
  *             # First, pop all unneeded loc2's off the stack
  *             assign_matching(&loc1, arr1, i1, step1, self.fda.sent_id.arr)             # <<<<<<<<<<<<<<
@@ -40778,7 +42138,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
  */
     __pyx_f_3_sa_assign_matching((&__pyx_v_loc1), __pyx_v_arr1, __pyx_v_i1, __pyx_v_step1, __pyx_v_self->fda->sent_id->arr);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":691
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":711
  *             # First, pop all unneeded loc2's off the stack
  *             assign_matching(&loc1, arr1, i1, step1, self.fda.sent_id.arr)
  *             while i2 < high2:             # <<<<<<<<<<<<<<
@@ -40789,7 +42149,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
       __pyx_t_3 = (__pyx_v_i2 < __pyx_v_high2);
       if (!__pyx_t_3) break;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":692
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":712
  *             assign_matching(&loc1, arr1, i1, step1, self.fda.sent_id.arr)
  *             while i2 < high2:
  *                 assign_matching(&loc2, arr2, i2, step2, self.fda.sent_id.arr)             # <<<<<<<<<<<<<<
@@ -40798,7 +42158,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
  */
       __pyx_f_3_sa_assign_matching((&__pyx_v_loc2), __pyx_v_arr2, __pyx_v_i2, __pyx_v_step2, __pyx_v_self->fda->sent_id->arr);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":693
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":713
  *             while i2 < high2:
  *                 assign_matching(&loc2, arr2, i2, step2, self.fda.sent_id.arr)
  *                 if self.compare_matchings(&loc1, &loc2, offset_by_one, len_last) == 1:             # <<<<<<<<<<<<<<
@@ -40808,7 +42168,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
       __pyx_t_3 = (((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->compare_matchings(__pyx_v_self, (&__pyx_v_loc1), (&__pyx_v_loc2), __pyx_v_offset_by_one, __pyx_v_len_last) == 1);
       if (__pyx_t_3) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":694
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":714
  *                 assign_matching(&loc2, arr2, i2, step2, self.fda.sent_id.arr)
  *                 if self.compare_matchings(&loc1, &loc2, offset_by_one, len_last) == 1:
  *                     i2 = i2 + step2             # <<<<<<<<<<<<<<
@@ -40820,7 +42180,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
       }
       /*else*/ {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":696
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":716
  *                     i2 = i2 + step2
  *                 else:
  *                     break             # <<<<<<<<<<<<<<
@@ -40833,7 +42193,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
     }
     __pyx_L6_break:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":699
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":719
  * 
  *             # Next: process all loc1's with the same starting val
  *             j1 = i1             # <<<<<<<<<<<<<<
@@ -40842,7 +42202,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
  */
     __pyx_v_j1 = __pyx_v_i1;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":700
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":720
  *             # Next: process all loc1's with the same starting val
  *             j1 = i1
  *             while i1 < high1 and arr1[j1] == arr1[i1]:             # <<<<<<<<<<<<<<
@@ -40859,7 +42219,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
       }
       if (!__pyx_t_2) break;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":701
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":721
  *             j1 = i1
  *             while i1 < high1 and arr1[j1] == arr1[i1]:
  *                 assign_matching(&loc1, arr1, i1, step1, self.fda.sent_id.arr)             # <<<<<<<<<<<<<<
@@ -40868,7 +42228,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
  */
       __pyx_f_3_sa_assign_matching((&__pyx_v_loc1), __pyx_v_arr1, __pyx_v_i1, __pyx_v_step1, __pyx_v_self->fda->sent_id->arr);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":702
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":722
  *             while i1 < high1 and arr1[j1] == arr1[i1]:
  *                 assign_matching(&loc1, arr1, i1, step1, self.fda.sent_id.arr)
  *                 j2 = i2             # <<<<<<<<<<<<<<
@@ -40877,7 +42237,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
  */
       __pyx_v_j2 = __pyx_v_i2;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":703
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":723
  *                 assign_matching(&loc1, arr1, i1, step1, self.fda.sent_id.arr)
  *                 j2 = i2
  *                 while j2 < high2:             # <<<<<<<<<<<<<<
@@ -40888,7 +42248,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
         __pyx_t_2 = (__pyx_v_j2 < __pyx_v_high2);
         if (!__pyx_t_2) break;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":704
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":724
  *                 j2 = i2
  *                 while j2 < high2:
  *                     assign_matching(&loc2, arr2, j2, step2, self.fda.sent_id.arr)             # <<<<<<<<<<<<<<
@@ -40897,7 +42257,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
  */
         __pyx_f_3_sa_assign_matching((&__pyx_v_loc2), __pyx_v_arr2, __pyx_v_j2, __pyx_v_step2, __pyx_v_self->fda->sent_id->arr);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":705
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":725
  *                 while j2 < high2:
  *                     assign_matching(&loc2, arr2, j2, step2, self.fda.sent_id.arr)
  *                     comparison = self.compare_matchings(&loc1, &loc2, offset_by_one, len_last)             # <<<<<<<<<<<<<<
@@ -40906,7 +42266,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
  */
         __pyx_v_comparison = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->compare_matchings(__pyx_v_self, (&__pyx_v_loc1), (&__pyx_v_loc2), __pyx_v_offset_by_one, __pyx_v_len_last);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":706
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":726
  *                     assign_matching(&loc2, arr2, j2, step2, self.fda.sent_id.arr)
  *                     comparison = self.compare_matchings(&loc1, &loc2, offset_by_one, len_last)
  *                     if comparison == 0:             # <<<<<<<<<<<<<<
@@ -40916,7 +42276,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
         __pyx_t_2 = (__pyx_v_comparison == 0);
         if (__pyx_t_2) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":707
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":727
  *                     comparison = self.compare_matchings(&loc1, &loc2, offset_by_one, len_last)
  *                     if comparison == 0:
  *                         result = append_combined_matching(result, &loc1, &loc2, offset_by_one, num_subpatterns, result_len)             # <<<<<<<<<<<<<<
@@ -40928,7 +42288,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
         }
         __pyx_L12:;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":708
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":728
  *                     if comparison == 0:
  *                         result = append_combined_matching(result, &loc1, &loc2, offset_by_one, num_subpatterns, result_len)
  *                     if comparison == 1:             # <<<<<<<<<<<<<<
@@ -40941,7 +42301,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
         }
         __pyx_L13:;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":710
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":730
  *                     if comparison == 1:
  *                         pass
  *                     if comparison == -1:             # <<<<<<<<<<<<<<
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":711
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":731
  *                         pass
  *                     if comparison == -1:
  *                         break             # <<<<<<<<<<<<<<
@@ -40963,7 +42323,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
         }
         /*else*/ {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":713
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":733
  *                         break
  *                     else:
  *                         j2 = j2 + step2             # <<<<<<<<<<<<<<
@@ -40976,7 +42336,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
       }
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":714
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":734
  *                     else:
  *                         j2 = j2 + step2
  *                 i1 = i1 + step1             # <<<<<<<<<<<<<<
@@ -40987,7 +42347,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
     }
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":715
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":735
  *                         j2 = j2 + step2
  *                 i1 = i1 + step1
  *         return result             # <<<<<<<<<<<<<<
@@ -41003,7 +42363,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_merge_helper(struct __pyx_obj
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":718
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":738
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  * 
  *     cdef void sort_phrase_loc(self, IntList arr, PhraseLocation loc, Phrase phrase):             # <<<<<<<<<<<<<<
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":723
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":743
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-  __pyx_t_1 = ((PySequence_Contains(__pyx_v_self->precomputed_index, ((PyObject *)__pyx_v_phrase)))); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 723; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = (__Pyx_PySequence_Contains(((PyObject *)__pyx_v_phrase), __pyx_v_self->precomputed_index, Py_EQ)); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":724
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":744
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  *         if phrase in self.precomputed_index:
  *             loc.arr = self.precomputed_index[phrase]             # <<<<<<<<<<<<<<
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-    __pyx_t_2 = PyObject_GetItem(__pyx_v_self->precomputed_index, ((PyObject *)__pyx_v_phrase)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = PyObject_GetItem(__pyx_v_self->precomputed_index, ((PyObject *)__pyx_v_phrase)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_3_sa_IntList))))) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -41054,20 +42414,20 @@ static void __pyx_f_3_sa_23HieroCachingRuleFactory_sort_phrase_loc(struct __pyx_
   }
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":726
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":746
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-    __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 726; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    __pyx_t_3 = PyInt_FromLong((__pyx_v_loc->sa_high - __pyx_v_loc->sa_low)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 726; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_3 = PyInt_FromLong((__pyx_v_loc->sa_high - __pyx_v_loc->sa_low)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__initial_len), __pyx_t_3) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_IntList)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 726; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_IntList)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -41076,27 +42436,27 @@ static void __pyx_f_3_sa_23HieroCachingRuleFactory_sort_phrase_loc(struct __pyx_
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     __pyx_t_3 = 0;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":727
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":747
  *         else:
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-    __pyx_t_3 = PyInt_FromLong(__pyx_v_arr->len); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 727; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_3 = PyInt_FromLong(__pyx_v_arr->len); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 747; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 747; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_VEB)), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 747; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":728
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":748
  *             loc.arr = IntList(initial_len=loc.sa_high-loc.sa_low)
  *             veb = VEB(arr.len)
  *             for i from loc.sa_low <= i < loc.sa_high:             # <<<<<<<<<<<<<<
@@ -41106,7 +42466,7 @@ static void __pyx_f_3_sa_23HieroCachingRuleFactory_sort_phrase_loc(struct __pyx_
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":729
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":749
  *             veb = VEB(arr.len)
  *             for i from loc.sa_low <= i < loc.sa_high:
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@@ -41116,7 +42476,7 @@ static void __pyx_f_3_sa_23HieroCachingRuleFactory_sort_phrase_loc(struct __pyx_
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":730
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":750
  *             for i from loc.sa_low <= i < loc.sa_high:
  *                 veb._insert(arr.arr[i])
  *             i = veb.veb.min_val             # <<<<<<<<<<<<<<
@@ -41125,7 +42485,7 @@ static void __pyx_f_3_sa_23HieroCachingRuleFactory_sort_phrase_loc(struct __pyx_
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":731
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":751
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  *             for j from 0 <= j < loc.sa_high-loc.sa_low:             # <<<<<<<<<<<<<<
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":732
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":752
  *             i = veb.veb.min_val
  *             for j from 0 <= j < loc.sa_high-loc.sa_low:
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":733
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":753
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  *                 loc.arr.arr[j] = i
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":734
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":754
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  *         loc.arr_low = 0             # <<<<<<<<<<<<<<
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":735
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":755
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  *         loc.arr_high = loc.arr.len             # <<<<<<<<<<<<<<
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-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":738
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":758
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  * 
  *     cdef intersect_helper(self, Phrase prefix, Phrase suffix,             # <<<<<<<<<<<<<<
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":745
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":765
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":747
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":767
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+  __pyx_t_1 = __Pyx_GetItemInt(((PyObject *)__pyx_v_suffix), 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_2 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_2 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":748
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":768
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":750
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":770
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":752
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":772
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+  __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_suffix), __pyx_n_s__getchunk); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_5 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_5 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __pyx_t_6 = PyObject_Length(__pyx_t_5); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_6 = PyObject_Length(__pyx_t_5); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":754
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":774
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  * 
  *         if prefix_loc.arr is None:             # <<<<<<<<<<<<<<
@@ -41304,7 +42664,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
   __pyx_t_7 = (((PyObject *)__pyx_v_prefix_loc->arr) == Py_None);
   if (__pyx_t_7) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":755
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":775
  * 
  *         if prefix_loc.arr is None:
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@@ -41319,7 +42679,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":756
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":776
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  *         arr1 = prefix_loc.arr             # <<<<<<<<<<<<<<
@@ -41329,7 +42689,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
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   __pyx_v_arr1 = __pyx_v_prefix_loc->arr;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":757
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":777
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  *         arr1 = prefix_loc.arr
  *         low1 = prefix_loc.arr_low             # <<<<<<<<<<<<<<
@@ -41338,7 +42698,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
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   __pyx_v_low1 = __pyx_v_prefix_loc->arr_low;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":758
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":778
  *         arr1 = prefix_loc.arr
  *         low1 = prefix_loc.arr_low
  *         high1 = prefix_loc.arr_high             # <<<<<<<<<<<<<<
@@ -41347,7 +42707,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
  */
   __pyx_v_high1 = __pyx_v_prefix_loc->arr_high;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":759
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":779
  *         low1 = prefix_loc.arr_low
  *         high1 = prefix_loc.arr_high
  *         step1 = prefix_loc.num_subpatterns             # <<<<<<<<<<<<<<
@@ -41356,7 +42716,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
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   __pyx_v_step1 = __pyx_v_prefix_loc->num_subpatterns;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":761
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":781
  *         step1 = prefix_loc.num_subpatterns
  * 
  *         if suffix_loc.arr is None:             # <<<<<<<<<<<<<<
@@ -41366,7 +42726,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
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   if (__pyx_t_7) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":762
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":782
  * 
  *         if suffix_loc.arr is None:
  *             self.sort_phrase_loc(self.fsa.sa, suffix_loc, suffix)             # <<<<<<<<<<<<<<
@@ -41381,7 +42741,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
   }
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":763
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":783
  *         if suffix_loc.arr is None:
  *             self.sort_phrase_loc(self.fsa.sa, suffix_loc, suffix)
  *         arr2 = suffix_loc.arr             # <<<<<<<<<<<<<<
@@ -41391,7 +42751,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
   __Pyx_INCREF(((PyObject *)__pyx_v_suffix_loc->arr));
   __pyx_v_arr2 = __pyx_v_suffix_loc->arr;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":764
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":784
  *             self.sort_phrase_loc(self.fsa.sa, suffix_loc, suffix)
  *         arr2 = suffix_loc.arr
  *         low2 = suffix_loc.arr_low             # <<<<<<<<<<<<<<
@@ -41400,7 +42760,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
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   __pyx_v_low2 = __pyx_v_suffix_loc->arr_low;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":765
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":785
  *         arr2 = suffix_loc.arr
  *         low2 = suffix_loc.arr_low
  *         high2 = suffix_loc.arr_high             # <<<<<<<<<<<<<<
@@ -41409,7 +42769,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
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   __pyx_v_high2 = __pyx_v_suffix_loc->arr_high;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":766
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":786
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  *         high2 = suffix_loc.arr_high
  *         step2 = suffix_loc.num_subpatterns             # <<<<<<<<<<<<<<
@@ -41418,26 +42778,26 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":768
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":788
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":770
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":790
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  *         if algorithm == MERGE:             # <<<<<<<<<<<<<<
@@ -41447,7 +42807,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":773
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":793
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@@ -41459,7 +42819,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":777
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":797
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@@ -41470,7 +42830,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":779
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":799
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  *         if result_len == 0:             # <<<<<<<<<<<<<<
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":780
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":800
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  *         if result_len == 0:
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@@ -41489,7 +42849,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
  */
     free(__pyx_v_result_ptr);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":781
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":801
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":783
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":803
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+    __pyx_t_5 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_IntList)), ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":784
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":804
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@@ -41525,7 +42885,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
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     free(__pyx_v_result->arr);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":785
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":805
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  *             result.arr = result_ptr             # <<<<<<<<<<<<<<
@@ -41534,7 +42894,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_intersect_helper(struct
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     __pyx_v_result->arr = __pyx_v_result_ptr;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":786
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":806
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  *             result.arr = result_ptr
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     __pyx_v_result->len = __pyx_v_result_len;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":787
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":807
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  *             result.len = result_len
  *             result.size = result_len             # <<<<<<<<<<<<<<
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     __pyx_v_result->size = __pyx_v_result_len;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":788
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":808
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  *             result.size = result_len
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+    if (PyDict_SetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__arr_high), __pyx_t_4) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 808; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_4 = PyInt_FromLong(__pyx_v_num_subpatterns); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 808; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    if (PyDict_SetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__num_subpatterns), __pyx_t_4) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 808; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":790
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":810
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":792
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":812
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":793
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":813
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":794
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":814
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":795
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":815
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":796
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":816
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":797
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":817
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       __pyx_t_2 = 0;
     }
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":798
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":818
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+    __pyx_t_2 = PyNumber_Add(__pyx_v_result, ((PyObject *)__pyx_kp_s_59)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":799
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":819
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  *             i = i + loc.num_subpatterns             # <<<<<<<<<<<<<<
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   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":800
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":820
  *             result = result + ")"
  *             i = i + loc.num_subpatterns
  *         result = result + "}"             # <<<<<<<<<<<<<<
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+  __pyx_t_2 = PyNumber_Add(__pyx_v_result, ((PyObject *)__pyx_kp_s_118)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":801
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":821
  *             i = i + loc.num_subpatterns
  *         result = result + "}"
  *         return result             # <<<<<<<<<<<<<<
@@ -41756,7 +43116,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_loc2str(CYTHON_UNUSED st
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":803
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":823
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   __Pyx_RefNannySetupContext("intersect", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":807
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":827
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  *         prefix = prefix_node.phrase             # <<<<<<<<<<<<<<
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-  __pyx_t_1 = PyObject_GetAttr(__pyx_v_prefix_node, __pyx_n_s__phrase); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_GetAttr(__pyx_v_prefix_node, __pyx_n_s__phrase); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_3_sa_Phrase))))) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_3_sa_Phrase))))) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":808
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":828
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  *         prefix = prefix_node.phrase
  *         suffix = suffix_node.phrase             # <<<<<<<<<<<<<<
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  *         suffix_loc = suffix_node.phrase_location
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-  __pyx_t_1 = PyObject_GetAttr(__pyx_v_suffix_node, __pyx_n_s__phrase); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 808; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_GetAttr(__pyx_v_suffix_node, __pyx_n_s__phrase); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_3_sa_Phrase))))) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":809
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":829
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  *         suffix = suffix_node.phrase
  *         prefix_loc = prefix_node.phrase_location             # <<<<<<<<<<<<<<
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-  __pyx_t_1 = PyObject_GetAttr(__pyx_v_prefix_node, __pyx_n_s__phrase_location); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 809; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_GetAttr(__pyx_v_prefix_node, __pyx_n_s__phrase_location); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_3_sa_PhraseLocation))))) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":810
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":830
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  *         prefix_loc = prefix_node.phrase_location
  *         suffix_loc = suffix_node.phrase_location             # <<<<<<<<<<<<<<
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  *         result = self.get_precomputed_collocation(phrase)
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+  __pyx_t_1 = PyObject_GetAttr(__pyx_v_suffix_node, __pyx_n_s__phrase_location); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_3_sa_PhraseLocation))))) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":812
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":832
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+  __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s_119); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_3_sa_PhraseLocation))))) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":813
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":833
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":814
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":834
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":816
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  *         if result is None:             # <<<<<<<<<<<<<<
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":817
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  *         if result is None:
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":818
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":819
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":821
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":822
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":823
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 }
 
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-        {__pyx_filename = __pyx_f[8]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      {__pyx_filename = __pyx_f[8]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-        {__pyx_filename = __pyx_f[8]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":837
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":857
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":839
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+          __Pyx_RaiseArgtupleInvalid("get_all_nodes_isteps_away", 1, 7, 7, 1); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+          __Pyx_RaiseArgtupleInvalid("get_all_nodes_isteps_away", 1, 7, 7, 6); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+  __Pyx_RaiseArgtupleInvalid("get_all_nodes_isteps_away", 1, 7, 7, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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-  __Pyx_GOTREF(__pyx_t_4);
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+  __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":845
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":865
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":846
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":866
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+  __pyx_t_4 = PyList_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 866; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_1 = ((PyObject *)PyList_AsTuple(__pyx_t_4)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 866; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":847
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+  __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":848
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":868
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+  __pyx_t_5 = (__Pyx_PySequence_Contains(((PyObject *)__pyx_v_key), __pyx_v_reachable_buffer, Py_EQ)); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 868; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":849
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":869
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+    __pyx_t_1 = PyObject_GetItem(__pyx_v_reachable_buffer, ((PyObject *)__pyx_v_key)); if (!__pyx_t_1) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 869; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":851
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":852
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+    if (PyObject_SetItem(__pyx_v_reachable_buffer, ((PyObject *)__pyx_v_key), __pyx_v_reachable) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 872; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":853
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":873
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-      __pyx_t_4 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_4); __pyx_t_3++;
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-      __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_4); __pyx_t_3++;
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":854
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-        __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_7); __Pyx_INCREF(__pyx_t_4); __pyx_t_7++;
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+        __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 874; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":855
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":856
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-            __pyx_t_4 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_11); __Pyx_INCREF(__pyx_t_4); __pyx_t_11++;
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-            __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_11); __Pyx_INCREF(__pyx_t_4); __pyx_t_11++;
+            __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_11); __Pyx_INCREF(__pyx_t_4); __pyx_t_11++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-                else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":860
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-          __pyx_t_4 = PyObject_GetItem(__pyx_v_fwords, __pyx_v_next_id); if (!__pyx_t_4) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":861
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-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":862
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-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":863
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+              __pyx_t_10 = PyNumber_Add(__pyx_v_pathlen, __pyx_v_jump); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":864
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":884
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+          __Pyx_RaiseArgtupleInvalid("reachable", 1, 3, 3, 1); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 886; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "reachable") < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 886; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+  __Pyx_RaiseArgtupleInvalid("reachable", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 886; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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 }
 
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":868
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":888
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+  __pyx_t_2 = PyObject_Length(__pyx_v_fwords); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 888; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 894; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":875
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+        __pyx_t_4 = (__Pyx_PySequence_Contains(__pyx_v_ifrom, ((PyObject *)__pyx_v_ret), Py_NE)); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 895; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":876
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":878
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+        __pyx_t_7 = PyNumber_Add(__pyx_v_ifrom, __pyx_t_3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+        __pyx_t_3 = PyNumber_Subtract(__pyx_v_dist, __pyx_int_1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+        __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-        __pyx_t_3 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_3 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-          __pyx_t_10 = -1; __pyx_t_6 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __pyx_t_10 = -1; __pyx_t_6 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-            __pyx_t_3 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_10); __Pyx_INCREF(__pyx_t_3); __pyx_t_10++;
+            __pyx_t_3 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_10); __Pyx_INCREF(__pyx_t_3); __pyx_t_10++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-            __pyx_t_3 = PySequence_ITEM(__pyx_t_6, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 878; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+            __pyx_t_3 = PySequence_ITEM(__pyx_t_6, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-            __pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_6, __pyx_t_10); __Pyx_INCREF(__pyx_t_3); __pyx_t_10++;
+            __pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_6, __pyx_t_10); __Pyx_INCREF(__pyx_t_3); __pyx_t_10++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             #else
-            __pyx_t_3 = PySequence_ITEM(__pyx_t_6, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 878; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+            __pyx_t_3 = PySequence_ITEM(__pyx_t_6, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-                else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -43541,24 +44891,24 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_16reachable(struct __py
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":879
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":899
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  *                     for ifromchild in self.reachable(fwords,ifrom+fwords[ifrom][alt_id][2],dist-1):
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+          __pyx_t_4 = (__Pyx_PySequence_Contains(__pyx_v_ifromchild, ((PyObject *)__pyx_v_ret), Py_NE)); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           if (__pyx_t_4) {
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":880
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":900
  *                     for ifromchild in self.reachable(fwords,ifrom+fwords[ifrom][alt_id][2],dist-1):
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+            __pyx_t_9 = PyList_Append(__pyx_v_ret, __pyx_v_ifromchild); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 900; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -43571,7 +44921,7 @@ static PyObject *__pyx_pf_3_sa_23HieroCachingRuleFactory_16reachable(struct __py
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":882
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":902
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@@ -43632,16 +44982,16 @@ static PyObject *__pyx_pw_3_sa_23HieroCachingRuleFactory_19shortest(PyObject *__
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+          __Pyx_RaiseArgtupleInvalid("shortest", 1, 3, 3, 1); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 904; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+          __Pyx_RaiseArgtupleInvalid("shortest", 1, 3, 3, 2); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 904; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "shortest") < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 904; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+  __Pyx_RaiseArgtupleInvalid("shortest", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 904; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":884
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":904
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":886
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":906
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":887
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":907
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+  __pyx_t_1 = PyObject_RichCompare(__pyx_v_ifrom, __pyx_v_ito, Py_GT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":888
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":889
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":903
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":908
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":990
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1010
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-        __pyx_t_8 = (__pyx_t_15 == Py_None);
-        __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":992
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":994
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-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":995
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-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":997
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1017
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+              if (PyObject_SetItem(__pyx_t_3, __pyx_cur_scope->__pyx_v_word_id, Py_None) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1017; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":998
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1018
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-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1001
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1021
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@@ -45519,18 +47051,18 @@ static PyObject *__pyx_gb_3_sa_23HieroCachingRuleFactory_24generator2(__pyx_Gene
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-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1004
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1024
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-            {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1004; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1024; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1006
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1026
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1007
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1027
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1008
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1028
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1011
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         }
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1015
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-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1017
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-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1020
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-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1021
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-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1022
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1042
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-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1023
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-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1025
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1027
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1047
  *                                 phrase_location = None
  * 
  *                         if phrase_location is None:             # <<<<<<<<<<<<<<
@@ -45796,19 +47328,19 @@ static PyObject *__pyx_gb_3_sa_23HieroCachingRuleFactory_24generator2(__pyx_Gene
           __pyx_t_8 = (((PyObject *)__pyx_cur_scope->__pyx_v_phrase_location) == Py_None);
           if (__pyx_t_8) {
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1028
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1048
  * 
  *                         if phrase_location is None:
  *                             node.children[word_id] = None             # <<<<<<<<<<<<<<
  *                             # Search failed
  *                             continue
  */
-            __pyx_t_9 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_node, __pyx_n_s__children); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1028; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_9 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_node, __pyx_n_s__children); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1048; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_9);
-            if (PyObject_SetItem(__pyx_t_9, __pyx_cur_scope->__pyx_v_word_id, Py_None) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1028; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            if (PyObject_SetItem(__pyx_t_9, __pyx_cur_scope->__pyx_v_word_id, Py_None) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1048; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1030
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1050
  *                             node.children[word_id] = None
  *                             # Search failed
  *                             continue             # <<<<<<<<<<<<<<
@@ -45820,7 +47352,7 @@ static PyObject *__pyx_gb_3_sa_23HieroCachingRuleFactory_24generator2(__pyx_Gene
           }
           __pyx_L36:;
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1032
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1052
  *                             continue
  *                         # Search succeeded
  *                         suffix_link = self.rules.root             # <<<<<<<<<<<<<<
@@ -45833,34 +47365,34 @@ static PyObject *__pyx_gb_3_sa_23HieroCachingRuleFactory_24generator2(__pyx_Gene
           __Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_self->rules->root);
           __pyx_cur_scope->__pyx_v_suffix_link = __pyx_cur_scope->__pyx_v_self->rules->root;
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1033
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1053
  *                         # Search succeeded
  *                         suffix_link = self.rules.root
  *                         if node.suffix_link is not None:             # <<<<<<<<<<<<<<
  *                             suffix_link = node.suffix_link.children[word_id]
  *                         new_node = ExtendedTrieNode(phrase_location=phrase_location,
  */
-          __pyx_t_9 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_node, __pyx_n_s__suffix_link); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1033; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __pyx_t_9 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_node, __pyx_n_s__suffix_link); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1053; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           __Pyx_GOTREF(__pyx_t_9);
           __pyx_t_8 = (__pyx_t_9 != Py_None);
           __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
           if (__pyx_t_8) {
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1034
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1054
  *                         suffix_link = self.rules.root
  *                         if node.suffix_link is not None:
  *                             suffix_link = node.suffix_link.children[word_id]             # <<<<<<<<<<<<<<
  *                         new_node = ExtendedTrieNode(phrase_location=phrase_location,
  *                                 suffix_link=suffix_link,
  */
-            __pyx_t_9 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_node, __pyx_n_s__suffix_link); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1034; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_9 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_node, __pyx_n_s__suffix_link); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1054; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_9);
-            __pyx_t_10 = PyObject_GetAttr(__pyx_t_9, __pyx_n_s__children); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1034; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-            __Pyx_GOTREF(__pyx_t_10);
+            __pyx_t_11 = PyObject_GetAttr(__pyx_t_9, __pyx_n_s__children); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1054; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __Pyx_GOTREF(__pyx_t_11);
             __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
-            __pyx_t_9 = PyObject_GetItem(__pyx_t_10, __pyx_cur_scope->__pyx_v_word_id); if (!__pyx_t_9) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1034; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_9 = PyObject_GetItem(__pyx_t_11, __pyx_cur_scope->__pyx_v_word_id); if (!__pyx_t_9) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1054; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_9);
-            __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+            __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
             __Pyx_GOTREF(__pyx_cur_scope->__pyx_v_suffix_link);
             __Pyx_DECREF(__pyx_cur_scope->__pyx_v_suffix_link);
             __Pyx_GIVEREF(__pyx_t_9);
@@ -45870,58 +47402,58 @@ static PyObject *__pyx_gb_3_sa_23HieroCachingRuleFactory_24generator2(__pyx_Gene
           }
           __pyx_L37:;
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1035
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1055
  *                         if node.suffix_link is not None:
  *                             suffix_link = node.suffix_link.children[word_id]
  *                         new_node = ExtendedTrieNode(phrase_location=phrase_location,             # <<<<<<<<<<<<<<
  *                                 suffix_link=suffix_link,
  *                                 phrase=hiero_phrase)
  */
-          __pyx_t_9 = PyDict_New(); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1035; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __pyx_t_9 = PyDict_New(); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1055; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           __Pyx_GOTREF(((PyObject *)__pyx_t_9));
-          if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__phrase_location), ((PyObject *)__pyx_cur_scope->__pyx_v_phrase_location)) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1035; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__phrase_location), ((PyObject *)__pyx_cur_scope->__pyx_v_phrase_location)) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1055; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1036
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1056
  *                             suffix_link = node.suffix_link.children[word_id]
  *                         new_node = ExtendedTrieNode(phrase_location=phrase_location,
  *                                 suffix_link=suffix_link,             # <<<<<<<<<<<<<<
  *                                 phrase=hiero_phrase)
  *                     node.children[word_id] = new_node
  */
-          if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__suffix_link), __pyx_cur_scope->__pyx_v_suffix_link) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1035; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__suffix_link), __pyx_cur_scope->__pyx_v_suffix_link) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1055; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1037
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1057
  *                         new_node = ExtendedTrieNode(phrase_location=phrase_location,
  *                                 suffix_link=suffix_link,
  *                                 phrase=hiero_phrase)             # <<<<<<<<<<<<<<
  *                     node.children[word_id] = new_node
  *                     node = new_node
  */
-          if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__phrase), ((PyObject *)__pyx_cur_scope->__pyx_v_hiero_phrase)) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1035; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-          __pyx_t_10 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_ExtendedTrieNode)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_9)); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1035; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-          __Pyx_GOTREF(__pyx_t_10);
+          if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__phrase), ((PyObject *)__pyx_cur_scope->__pyx_v_hiero_phrase)) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1055; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __pyx_t_11 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_ExtendedTrieNode)), ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_9)); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1055; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __Pyx_GOTREF(__pyx_t_11);
           __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
           __Pyx_GOTREF(__pyx_cur_scope->__pyx_v_new_node);
           __Pyx_DECREF(__pyx_cur_scope->__pyx_v_new_node);
-          __Pyx_GIVEREF(__pyx_t_10);
-          __pyx_cur_scope->__pyx_v_new_node = __pyx_t_10;
-          __pyx_t_10 = 0;
+          __Pyx_GIVEREF(__pyx_t_11);
+          __pyx_cur_scope->__pyx_v_new_node = __pyx_t_11;
+          __pyx_t_11 = 0;
         }
         __pyx_L33:;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1038
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1058
  *                                 suffix_link=suffix_link,
  *                                 phrase=hiero_phrase)
  *                     node.children[word_id] = new_node             # <<<<<<<<<<<<<<
  *                     node = new_node
  * 
  */
-        __pyx_t_10 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_node, __pyx_n_s__children); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1038; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-        __Pyx_GOTREF(__pyx_t_10);
-        if (PyObject_SetItem(__pyx_t_10, __pyx_cur_scope->__pyx_v_word_id, __pyx_cur_scope->__pyx_v_new_node) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1038; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-        __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+        __pyx_t_11 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_node, __pyx_n_s__children); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1058; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __Pyx_GOTREF(__pyx_t_11);
+        if (PyObject_SetItem(__pyx_t_11, __pyx_cur_scope->__pyx_v_word_id, __pyx_cur_scope->__pyx_v_new_node) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1058; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1039
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1059
  *                                 phrase=hiero_phrase)
  *                     node.children[word_id] = new_node
  *                     node = new_node             # <<<<<<<<<<<<<<
@@ -45934,7 +47466,7 @@ static PyObject *__pyx_gb_3_sa_23HieroCachingRuleFactory_24generator2(__pyx_Gene
         __Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_new_node);
         __pyx_cur_scope->__pyx_v_node = __pyx_cur_scope->__pyx_v_new_node;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1044
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1064
  *                     This should happen before we get to extraction (so that
  *                     the node will exist if needed)'''
  *                     if arity < self.max_nonterminals:             # <<<<<<<<<<<<<<
@@ -45944,32 +47476,32 @@ static PyObject *__pyx_gb_3_sa_23HieroCachingRuleFactory_24generator2(__pyx_Gene
         __pyx_t_8 = (__pyx_cur_scope->__pyx_v_arity < __pyx_cur_scope->__pyx_v_self->max_nonterminals);
         if (__pyx_t_8) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1045
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1065
  *                     the node will exist if needed)'''
  *                     if arity < self.max_nonterminals:
  *                         xcat_index = arity+1             # <<<<<<<<<<<<<<
  *                         xcat = sym_setindex(self.category, xcat_index)
  *                         suffix_link_xcat_index = xcat_index
  */
-          __pyx_t_10 = PyInt_FromLong((__pyx_cur_scope->__pyx_v_arity + 1)); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1045; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-          __Pyx_GOTREF(__pyx_t_10);
+          __pyx_t_11 = PyInt_FromLong((__pyx_cur_scope->__pyx_v_arity + 1)); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1065; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __Pyx_GOTREF(__pyx_t_11);
           __Pyx_XGOTREF(__pyx_cur_scope->__pyx_v_xcat_index);
           __Pyx_XDECREF(__pyx_cur_scope->__pyx_v_xcat_index);
-          __Pyx_GIVEREF(__pyx_t_10);
-          __pyx_cur_scope->__pyx_v_xcat_index = __pyx_t_10;
-          __pyx_t_10 = 0;
+          __Pyx_GIVEREF(__pyx_t_11);
+          __pyx_cur_scope->__pyx_v_xcat_index = __pyx_t_11;
+          __pyx_t_11 = 0;
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1046
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1066
  *                     if arity < self.max_nonterminals:
  *                         xcat_index = arity+1
  *                         xcat = sym_setindex(self.category, xcat_index)             # <<<<<<<<<<<<<<
  *                         suffix_link_xcat_index = xcat_index
  *                         if is_shadow_path:
  */
-          __pyx_t_18 = __Pyx_PyInt_AsInt(__pyx_cur_scope->__pyx_v_xcat_index); if (unlikely((__pyx_t_18 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1046; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-          __pyx_cur_scope->__pyx_v_xcat = __pyx_f_3_sa_sym_setindex(__pyx_cur_scope->__pyx_v_self->category, __pyx_t_18);
+          __pyx_t_19 = __Pyx_PyInt_AsInt(__pyx_cur_scope->__pyx_v_xcat_index); if (unlikely((__pyx_t_19 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1066; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __pyx_cur_scope->__pyx_v_xcat = __pyx_f_3_sa_sym_setindex(__pyx_cur_scope->__pyx_v_self->category, __pyx_t_19);
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1047
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1067
  *                         xcat_index = arity+1
  *                         xcat = sym_setindex(self.category, xcat_index)
  *                         suffix_link_xcat_index = xcat_index             # <<<<<<<<<<<<<<
@@ -45982,206 +47514,206 @@ static PyObject *__pyx_gb_3_sa_23HieroCachingRuleFactory_24generator2(__pyx_Gene
           __Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_xcat_index);
           __pyx_cur_scope->__pyx_v_suffix_link_xcat_index = __pyx_cur_scope->__pyx_v_xcat_index;
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1048
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1068
  *                         xcat = sym_setindex(self.category, xcat_index)
  *                         suffix_link_xcat_index = xcat_index
  *                         if is_shadow_path:             # <<<<<<<<<<<<<<
  *                             suffix_link_xcat_index = xcat_index-1
  *                         suffix_link_xcat = sym_setindex(self.category, suffix_link_xcat_index)
  */
-          __pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_cur_scope->__pyx_v_is_shadow_path); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1048; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_cur_scope->__pyx_v_is_shadow_path); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1068; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           if (__pyx_t_8) {
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1049
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1069
  *                         suffix_link_xcat_index = xcat_index
  *                         if is_shadow_path:
  *                             suffix_link_xcat_index = xcat_index-1             # <<<<<<<<<<<<<<
  *                         suffix_link_xcat = sym_setindex(self.category, suffix_link_xcat_index)
  *                         node.children[xcat] = ExtendedTrieNode(phrase_location=node.phrase_location,
  */
-            __pyx_t_10 = PyNumber_Subtract(__pyx_cur_scope->__pyx_v_xcat_index, __pyx_int_1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1049; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-            __Pyx_GOTREF(__pyx_t_10);
+            __pyx_t_11 = PyNumber_Subtract(__pyx_cur_scope->__pyx_v_xcat_index, __pyx_int_1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1069; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __Pyx_GOTREF(__pyx_t_11);
             __Pyx_GOTREF(__pyx_cur_scope->__pyx_v_suffix_link_xcat_index);
             __Pyx_DECREF(__pyx_cur_scope->__pyx_v_suffix_link_xcat_index);
-            __Pyx_GIVEREF(__pyx_t_10);
-            __pyx_cur_scope->__pyx_v_suffix_link_xcat_index = __pyx_t_10;
-            __pyx_t_10 = 0;
+            __Pyx_GIVEREF(__pyx_t_11);
+            __pyx_cur_scope->__pyx_v_suffix_link_xcat_index = __pyx_t_11;
+            __pyx_t_11 = 0;
             goto __pyx_L39;
           }
           __pyx_L39:;
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1050
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1070
  *                         if is_shadow_path:
  *                             suffix_link_xcat_index = xcat_index-1
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           __Pyx_GOTREF(__pyx_t_3);
-          __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
+          __Pyx_DECREF(((PyObject *)__pyx_t_11)); __pyx_t_11 = 0;
           __Pyx_XGOTREF(((PyObject *)__pyx_cur_scope->__pyx_v_chunklen));
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1060
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1080
  *                         num_subpatterns = (<PhraseLocation> node.phrase_location).num_subpatterns
  *                         chunklen = IntList(initial_len=num_subpatterns)
  *                         for j from 0 <= j < num_subpatterns:             # <<<<<<<<<<<<<<
  *                             chunklen.arr[j] = hiero_phrase.chunklen(j)
  *                         extracts = []
  */
-          __pyx_t_18 = __pyx_cur_scope->__pyx_v_num_subpatterns;
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+          __pyx_t_19 = __pyx_cur_scope->__pyx_v_num_subpatterns;
+          for (__pyx_cur_scope->__pyx_v_j = 0; __pyx_cur_scope->__pyx_v_j < __pyx_t_19; __pyx_cur_scope->__pyx_v_j++) {
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1061
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1081
  *                         chunklen = IntList(initial_len=num_subpatterns)
  *                         for j from 0 <= j < num_subpatterns:
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1062
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1082
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1063
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1083
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1064
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1084
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  *                         j = 0
  *                         extract_start = monitor_cpu()             # <<<<<<<<<<<<<<
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  *                             extract = []
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1065
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1085
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-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1066
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1086
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-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1068
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-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1069
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  * 
  *                             assign_matching(&matching, sample.arr, j, num_subpatterns, self.fda.sent_id.arr)
+ *                             loc = tuple(sample[j:j+num_subpatterns])             # <<<<<<<<<<<<<<
+ *                             extract = self.extract(hiero_phrase, &matching, chunklen.arr, num_subpatterns)
+ *                             extracts.extend([(e, loc) for e in extract])
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+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1090
+ *                             assign_matching(&matching, sample.arr, j, num_subpatterns, self.fda.sent_id.arr)
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  *                             extract = self.extract(hiero_phrase, &matching, chunklen.arr, num_subpatterns)             # <<<<<<<<<<<<<<
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+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1091
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  *                             extract = self.extract(hiero_phrase, &matching, chunklen.arr, num_subpatterns)
- *                             extracts.extend(extract)             # <<<<<<<<<<<<<<
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1105
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1107
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1120
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1108
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+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1125
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1122
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1135
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1146
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1154
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1161
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   if (__pyx_t_5) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1162
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1175
  * 
  *         if e_high[0] - e_low[0] > max_e_len:
  *             return 0             # <<<<<<<<<<<<<<
@@ -47800,7 +49415,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     goto __pyx_L6;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1163
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1176
  *         if e_high[0] - e_low[0] > max_e_len:
  *             return 0
  *         elif e_in_high != -1 and e_high[0] != e_in_high:             # <<<<<<<<<<<<<<
@@ -47816,7 +49431,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
   }
   if (__pyx_t_4) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1164
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1177
  *             return 0
  *         elif e_in_high != -1 and e_high[0] != e_in_high:
  *             if e_high[0] - e_in_high < min_ex_size:             # <<<<<<<<<<<<<<
@@ -47826,7 +49441,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     __pyx_t_4 = (((__pyx_v_e_high[0]) - __pyx_v_e_in_high) < __pyx_v_min_ex_size);
     if (__pyx_t_4) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1165
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1178
  *         elif e_in_high != -1 and e_high[0] != e_in_high:
  *             if e_high[0] - e_in_high < min_ex_size:
  *                 e_high[0] = e_in_high + min_ex_size             # <<<<<<<<<<<<<<
@@ -47835,7 +49450,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
  */
       (__pyx_v_e_high[0]) = (__pyx_v_e_in_high + __pyx_v_min_ex_size);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1166
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1179
  *             if e_high[0] - e_in_high < min_ex_size:
  *                 e_high[0] = e_in_high + min_ex_size
  *                 if e_high[0] > e_sent_len:             # <<<<<<<<<<<<<<
@@ -47845,7 +49460,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
       __pyx_t_4 = ((__pyx_v_e_high[0]) > __pyx_v_e_sent_len);
       if (__pyx_t_4) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1167
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1180
  *                 e_high[0] = e_in_high + min_ex_size
  *                 if e_high[0] > e_sent_len:
  *                     return 0             # <<<<<<<<<<<<<<
@@ -47864,7 +49479,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
   }
   __pyx_L6:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1169
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1182
  *                     return 0
  * 
  *         f_back_low[0] = -1             # <<<<<<<<<<<<<<
@@ -47873,7 +49488,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
  */
   (__pyx_v_f_back_low[0]) = -1;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1170
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1183
  * 
  *         f_back_low[0] = -1
  *         f_back_high[0] = -1             # <<<<<<<<<<<<<<
@@ -47882,7 +49497,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
  */
   (__pyx_v_f_back_high[0]) = -1;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1171
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1184
  *         f_back_low[0] = -1
  *         f_back_high[0] = -1
  *         f_low_prev = f_low             # <<<<<<<<<<<<<<
@@ -47891,17 +49506,17 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
  */
   __pyx_v_f_low_prev = __pyx_v_f_low;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1172
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1185
  *         f_back_high[0] = -1
  *         f_low_prev = f_low
  *         f_high_prev = f_high             # <<<<<<<<<<<<<<
  *         new_x = 0
  *         new_low_x = 0
  */
-  __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_f_high); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_f_high); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1185; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_f_high_prev = __pyx_t_1;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1173
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1186
  *         f_low_prev = f_low
  *         f_high_prev = f_high
  *         new_x = 0             # <<<<<<<<<<<<<<
@@ -47910,7 +49525,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
  */
   __pyx_v_new_x = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1174
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1187
  *         f_high_prev = f_high
  *         new_x = 0
  *         new_low_x = 0             # <<<<<<<<<<<<<<
@@ -47919,7 +49534,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
  */
   __pyx_v_new_low_x = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1175
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1188
  *         new_x = 0
  *         new_low_x = 0
  *         new_high_x = 0             # <<<<<<<<<<<<<<
@@ -47928,7 +49543,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
  */
   __pyx_v_new_high_x = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1177
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1190
  *         new_high_x = 0
  * 
  *         while True:             # <<<<<<<<<<<<<<
@@ -47938,7 +49553,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
   while (1) {
     if (!1) break;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1179
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1192
  *         while True:
  * 
  *             if f_back_low[0] == -1:             # <<<<<<<<<<<<<<
@@ -47948,45 +49563,45 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     __pyx_t_4 = ((__pyx_v_f_back_low[0]) == -1);
     if (__pyx_t_4) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1180
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1193
  * 
  *             if f_back_low[0] == -1:
  *                 self.find_projection(e_low[0], e_high[0], e_links_low, e_links_high, f_back_low, f_back_high)             # <<<<<<<<<<<<<<
  *             else:
  *                 self.find_projection(e_low[0], e_low_prev, e_links_low, e_links_high, f_back_low, f_back_high)
  */
-      __pyx_t_2 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_projection(__pyx_v_self, (__pyx_v_e_low[0]), (__pyx_v_e_high[0]), __pyx_v_e_links_low, __pyx_v_e_links_high, __pyx_v_f_back_low, __pyx_v_f_back_high); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_2 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_projection(__pyx_v_self, (__pyx_v_e_low[0]), (__pyx_v_e_high[0]), __pyx_v_e_links_low, __pyx_v_e_links_high, __pyx_v_f_back_low, __pyx_v_f_back_high); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1193; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_2);
       __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
       goto __pyx_L11;
     }
     /*else*/ {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1182
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1195
  *                 self.find_projection(e_low[0], e_high[0], e_links_low, e_links_high, f_back_low, f_back_high)
  *             else:
  *                 self.find_projection(e_low[0], e_low_prev, e_links_low, e_links_high, f_back_low, f_back_high)             # <<<<<<<<<<<<<<
  *                 self.find_projection(e_high_prev, e_high[0], e_links_low, e_links_high, f_back_low, f_back_high)
  * 
  */
-      __pyx_t_2 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_projection(__pyx_v_self, (__pyx_v_e_low[0]), __pyx_v_e_low_prev, __pyx_v_e_links_low, __pyx_v_e_links_high, __pyx_v_f_back_low, __pyx_v_f_back_high); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1182; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_2 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_projection(__pyx_v_self, (__pyx_v_e_low[0]), __pyx_v_e_low_prev, __pyx_v_e_links_low, __pyx_v_e_links_high, __pyx_v_f_back_low, __pyx_v_f_back_high); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_2);
       __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1183
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1196
  *             else:
  *                 self.find_projection(e_low[0], e_low_prev, e_links_low, e_links_high, f_back_low, f_back_high)
  *                 self.find_projection(e_high_prev, e_high[0], e_links_low, e_links_high, f_back_low, f_back_high)             # <<<<<<<<<<<<<<
  * 
  *             if f_back_low[0] > f_low:
  */
-      __pyx_t_2 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_projection(__pyx_v_self, __pyx_v_e_high_prev, (__pyx_v_e_high[0]), __pyx_v_e_links_low, __pyx_v_e_links_high, __pyx_v_f_back_low, __pyx_v_f_back_high); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_2 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_projection(__pyx_v_self, __pyx_v_e_high_prev, (__pyx_v_e_high[0]), __pyx_v_e_links_low, __pyx_v_e_links_high, __pyx_v_f_back_low, __pyx_v_f_back_high); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_2);
       __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
     }
     __pyx_L11:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1185
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1198
  *                 self.find_projection(e_high_prev, e_high[0], e_links_low, e_links_high, f_back_low, f_back_high)
  * 
  *             if f_back_low[0] > f_low:             # <<<<<<<<<<<<<<
@@ -47996,7 +49611,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     __pyx_t_4 = ((__pyx_v_f_back_low[0]) > __pyx_v_f_low);
     if (__pyx_t_4) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1186
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1199
  * 
  *             if f_back_low[0] > f_low:
  *                 f_back_low[0] = f_low             # <<<<<<<<<<<<<<
@@ -48008,36 +49623,35 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     }
     __pyx_L12:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1188
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1201
  *                 f_back_low[0] = f_low
  * 
  *             if f_back_high[0] < f_high:             # <<<<<<<<<<<<<<
  *                 f_back_high[0] = f_high
  * 
  */
-    __pyx_t_2 = PyInt_FromLong((__pyx_v_f_back_high[0])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1188; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = PyInt_FromLong((__pyx_v_f_back_high[0])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_2);
-    __pyx_t_6 = PyObject_RichCompare(__pyx_t_2, __pyx_v_f_high, Py_LT); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1188; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-    __Pyx_GOTREF(__pyx_t_6);
+    __pyx_t_6 = PyObject_RichCompare(__pyx_t_2, __pyx_v_f_high, Py_LT); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
-    __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1188; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
     if (__pyx_t_4) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1189
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1202
  * 
  *             if f_back_high[0] < f_high:
  *                 f_back_high[0] = f_high             # <<<<<<<<<<<<<<
  * 
  *             if f_back_low[0] == f_low_prev and f_back_high[0] == f_high_prev:
  */
-      __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_f_high); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_f_high); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1202; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       (__pyx_v_f_back_high[0]) = __pyx_t_1;
       goto __pyx_L13;
     }
     __pyx_L13:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1191
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1204
  *                 f_back_high[0] = f_high
  * 
  *             if f_back_low[0] == f_low_prev and f_back_high[0] == f_high_prev:             # <<<<<<<<<<<<<<
@@ -48053,7 +49667,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     }
     if (__pyx_t_3) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1192
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1205
  * 
  *             if f_back_low[0] == f_low_prev and f_back_high[0] == f_high_prev:
  *                 return 1             # <<<<<<<<<<<<<<
@@ -48066,7 +49680,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     }
     __pyx_L14:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1194
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1207
  *                 return 1
  * 
  *             if allow_low_x == 0 and f_back_low[0] < f_low:             # <<<<<<<<<<<<<<
@@ -48082,7 +49696,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     }
     if (__pyx_t_5) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1196
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1209
  *             if allow_low_x == 0 and f_back_low[0] < f_low:
  *                 # FAIL: f phrase is not tight
  *                 return 0             # <<<<<<<<<<<<<<
@@ -48095,7 +49709,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     }
     __pyx_L15:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1198
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1211
  *                 return 0
  * 
  *             if f_back_high[0] - f_back_low[0] > max_f_len:             # <<<<<<<<<<<<<<
@@ -48105,7 +49719,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     __pyx_t_5 = (((__pyx_v_f_back_high[0]) - (__pyx_v_f_back_low[0])) > __pyx_v_max_f_len);
     if (__pyx_t_5) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1200
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1213
  *             if f_back_high[0] - f_back_low[0] > max_f_len:
  *                 # FAIL: f back projection is too wide
  *                 return 0             # <<<<<<<<<<<<<<
@@ -48118,7 +49732,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     }
     __pyx_L16:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1202
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1215
  *                 return 0
  * 
  *             if allow_high_x == 0 and f_back_high[0] > f_high:             # <<<<<<<<<<<<<<
@@ -48127,12 +49741,11 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
  */
     __pyx_t_5 = (__pyx_v_allow_high_x == 0);
     if (__pyx_t_5) {
-      __pyx_t_6 = PyInt_FromLong((__pyx_v_f_back_high[0])); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1202; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      __Pyx_GOTREF(__pyx_t_2);
+      __pyx_t_2 = PyObject_RichCompare(__pyx_t_6, __pyx_v_f_high, Py_GT); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -48140,7 +49753,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     }
     if (__pyx_t_4) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1204
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1217
  *             if allow_high_x == 0 and f_back_high[0] > f_high:
  *                 # FAIL: extension on high side not allowed
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@@ -48153,7 +49766,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     }
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1206
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1219
  *                 return 0
  * 
  *             if f_low != f_back_low[0]:             # <<<<<<<<<<<<<<
@@ -48163,7 +49776,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1207
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1220
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  *             if f_low != f_back_low[0]:
  *                 if new_low_x == 0:             # <<<<<<<<<<<<<<
@@ -48173,7 +49786,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1208
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1221
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  *                 if new_low_x == 0:
  *                     if new_x >= max_new_x:             # <<<<<<<<<<<<<<
@@ -48183,7 +49796,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1210
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1223
  *                     if new_x >= max_new_x:
  *                         # FAIL: extension required on low side violates max # of gaps
  *                         return 0             # <<<<<<<<<<<<<<
@@ -48196,7 +49809,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1212
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1225
  *                         return 0
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  *                         new_x = new_x + 1             # <<<<<<<<<<<<<<
@@ -48205,7 +49818,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1213
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1226
  *                     else:
  *                         new_x = new_x + 1
  *                         new_low_x = 1             # <<<<<<<<<<<<<<
@@ -48219,7 +49832,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1214
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1227
  *                         new_x = new_x + 1
  *                         new_low_x = 1
  *                 if f_low - f_back_low[0] < min_fx_size:             # <<<<<<<<<<<<<<
@@ -48229,7 +49842,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1215
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1228
  *                         new_low_x = 1
  *                 if f_low - f_back_low[0] < min_fx_size:
  *                     f_back_low[0] = f_low - min_fx_size             # <<<<<<<<<<<<<<
@@ -48238,7 +49851,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
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         (__pyx_v_f_back_low[0]) = (__pyx_v_f_low - __pyx_v_min_fx_size);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1216
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1229
  *                 if f_low - f_back_low[0] < min_fx_size:
  *                     f_back_low[0] = f_low - min_fx_size
  *                     if f_back_high[0] - f_back_low[0] > max_f_len:             # <<<<<<<<<<<<<<
@@ -48248,7 +49861,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1218
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1231
  *                     if f_back_high[0] - f_back_low[0] > max_f_len:
  *                         # FAIL: extension required on low side violates max initial length
  *                         return 0             # <<<<<<<<<<<<<<
@@ -48261,7 +49874,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1219
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1232
  *                         # FAIL: extension required on low side violates max initial length
  *                         return 0
  *                     if f_back_low[0] < 0:             # <<<<<<<<<<<<<<
@@ -48271,7 +49884,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1221
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1234
  *                     if f_back_low[0] < 0:
  *                         # FAIL: extension required on low side violates sentence boundary
  *                         return 0             # <<<<<<<<<<<<<<
@@ -48290,23 +49903,22 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1223
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1236
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  *             if f_high != f_back_high[0]:             # <<<<<<<<<<<<<<
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1224
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1237
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  *             if f_high != f_back_high[0]:
  *                 if new_high_x == 0:             # <<<<<<<<<<<<<<
@@ -48316,7 +49928,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1225
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1238
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  *                 if new_high_x == 0:
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@@ -48326,7 +49938,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1227
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1240
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1229
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1242
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  *                         new_x = new_x + 1             # <<<<<<<<<<<<<<
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1230
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1243
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  *                         new_x = new_x + 1
  *                         new_high_x = 1             # <<<<<<<<<<<<<<
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1231
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1244
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1232
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1245
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+        __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_t_6); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1245; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1233
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1246
  *                 if f_back_high[0] - f_high < min_fx_size:
  *                     f_back_high[0] = f_high + min_fx_size
  *                     if f_back_high[0] - f_back_low[0] > max_f_len:             # <<<<<<<<<<<<<<
@@ -48410,7 +50021,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1235
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1248
  *                     if f_back_high[0] - f_back_low[0] > max_f_len:
  *                         # FAIL: extension required on high side violates max initial length
  *                         return 0             # <<<<<<<<<<<<<<
@@ -48423,7 +50034,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
         }
         __pyx_L28:;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1236
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1249
  *                         # FAIL: extension required on high side violates max initial length
  *                         return 0
  *                     if f_back_high[0] > f_sent_len:             # <<<<<<<<<<<<<<
@@ -48433,7 +50044,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
         __pyx_t_4 = ((__pyx_v_f_back_high[0]) > __pyx_v_f_sent_len);
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-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1238
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1251
  *                     if f_back_high[0] > f_sent_len:
  *                         # FAIL: extension required on high side violates sentence boundary
  *                         return 0             # <<<<<<<<<<<<<<
@@ -48452,7 +50063,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     }
     __pyx_L24:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1240
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1253
  *                         return 0
  * 
  *             e_low_prev = e_low[0]             # <<<<<<<<<<<<<<
@@ -48461,7 +50072,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
  */
     __pyx_v_e_low_prev = (__pyx_v_e_low[0]);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1241
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1254
  * 
  *             e_low_prev = e_low[0]
  *             e_high_prev = e_high[0]             # <<<<<<<<<<<<<<
@@ -48470,29 +50081,29 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
  */
     __pyx_v_e_high_prev = (__pyx_v_e_high[0]);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1243
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1256
  *             e_high_prev = e_high[0]
  * 
  *             self.find_projection(f_back_low[0], f_low_prev, f_links_low, f_links_high, e_low, e_high)             # <<<<<<<<<<<<<<
  *             self.find_projection(f_high_prev, f_back_high[0], f_links_low, f_links_high, e_low, e_high)
  *             if e_low[0] == e_low_prev and e_high[0] == e_high_prev:
  */
-    __pyx_t_6 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_projection(__pyx_v_self, (__pyx_v_f_back_low[0]), __pyx_v_f_low_prev, __pyx_v_f_links_low, __pyx_v_f_links_high, __pyx_v_e_low, __pyx_v_e_high); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1243; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_6 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_projection(__pyx_v_self, (__pyx_v_f_back_low[0]), __pyx_v_f_low_prev, __pyx_v_f_links_low, __pyx_v_f_links_high, __pyx_v_e_low, __pyx_v_e_high); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_6);
     __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1244
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1257
  * 
  *             self.find_projection(f_back_low[0], f_low_prev, f_links_low, f_links_high, e_low, e_high)
  *             self.find_projection(f_high_prev, f_back_high[0], f_links_low, f_links_high, e_low, e_high)             # <<<<<<<<<<<<<<
  *             if e_low[0] == e_low_prev and e_high[0] == e_high_prev:
  *                 return 1
  */
-    __pyx_t_6 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_projection(__pyx_v_self, __pyx_v_f_high_prev, (__pyx_v_f_back_high[0]), __pyx_v_f_links_low, __pyx_v_f_links_high, __pyx_v_e_low, __pyx_v_e_high); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1244; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_6 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_projection(__pyx_v_self, __pyx_v_f_high_prev, (__pyx_v_f_back_high[0]), __pyx_v_f_links_low, __pyx_v_f_links_high, __pyx_v_e_low, __pyx_v_e_high); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1257; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_6);
     __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1245
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1258
  *             self.find_projection(f_back_low[0], f_low_prev, f_links_low, f_links_high, e_low, e_high)
  *             self.find_projection(f_high_prev, f_back_high[0], f_links_low, f_links_high, e_low, e_high)
  *             if e_low[0] == e_low_prev and e_high[0] == e_high_prev:             # <<<<<<<<<<<<<<
@@ -48508,7 +50119,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     }
     if (__pyx_t_3) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1246
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1259
  *             self.find_projection(f_high_prev, f_back_high[0], f_links_low, f_links_high, e_low, e_high)
  *             if e_low[0] == e_low_prev and e_high[0] == e_high_prev:
  *                 return 1             # <<<<<<<<<<<<<<
@@ -48521,7 +50132,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     }
     __pyx_L30:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1247
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1260
  *             if e_low[0] == e_low_prev and e_high[0] == e_high_prev:
  *                 return 1
  *             if allow_arbitrary_x == 0:             # <<<<<<<<<<<<<<
@@ -48531,7 +50142,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     __pyx_t_3 = (__pyx_v_allow_arbitrary_x == 0);
     if (__pyx_t_3) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1249
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1262
  *             if allow_arbitrary_x == 0:
  *                 # FAIL: arbitrary expansion not permitted
  *                 return 0             # <<<<<<<<<<<<<<
@@ -48544,7 +50155,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     }
     __pyx_L31:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1250
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1263
  *                 # FAIL: arbitrary expansion not permitted
  *                 return 0
  *             if e_high[0] - e_low[0] > max_e_len:             # <<<<<<<<<<<<<<
@@ -48554,7 +50165,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     __pyx_t_3 = (((__pyx_v_e_high[0]) - (__pyx_v_e_low[0])) > __pyx_v_max_e_len);
     if (__pyx_t_3) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1252
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1265
  *             if e_high[0] - e_low[0] > max_e_len:
  *                 # FAIL: re-projection violates sentence max phrase length
  *                 return 0             # <<<<<<<<<<<<<<
@@ -48567,7 +50178,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
     }
     __pyx_L32:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1253
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1266
  *                 # FAIL: re-projection violates sentence max phrase length
  *                 return 0
  *             f_low_prev = f_back_low[0]             # <<<<<<<<<<<<<<
@@ -48576,7 +50187,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
  */
     __pyx_v_f_low_prev = (__pyx_v_f_back_low[0]);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1254
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1267
  *                 return 0
  *             f_low_prev = f_back_low[0]
  *             f_high_prev = f_back_high[0]             # <<<<<<<<<<<<<<
@@ -48599,7 +50210,7 @@ static int __pyx_f_3_sa_23HieroCachingRuleFactory_find_fixpoint(struct __pyx_obj
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1257
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1270
  * 
  * 
  *     cdef find_projection(self, int in_low, int in_high, int* in_links_low, int* in_links_high,             # <<<<<<<<<<<<<<
@@ -48617,7 +50228,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_find_projection(CYTHON_U
   int __pyx_t_4;
   __Pyx_RefNannySetupContext("find_projection", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1260
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1273
  *                         int* out_low, int* out_high):
  *         cdef int i
  *         for i from in_low <= i < in_high:             # <<<<<<<<<<<<<<
@@ -48627,7 +50238,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_find_projection(CYTHON_U
   __pyx_t_1 = __pyx_v_in_high;
   for (__pyx_v_i = __pyx_v_in_low; __pyx_v_i < __pyx_t_1; __pyx_v_i++) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1261
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1274
  *         cdef int i
  *         for i from in_low <= i < in_high:
  *             if in_links_low[i] != -1:             # <<<<<<<<<<<<<<
@@ -48637,7 +50248,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_find_projection(CYTHON_U
     __pyx_t_2 = ((__pyx_v_in_links_low[__pyx_v_i]) != -1);
     if (__pyx_t_2) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1262
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1275
  *         for i from in_low <= i < in_high:
  *             if in_links_low[i] != -1:
  *                 if out_low[0] == -1 or in_links_low[i] < out_low[0]:             # <<<<<<<<<<<<<<
@@ -48653,7 +50264,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_find_projection(CYTHON_U
       }
       if (__pyx_t_4) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1263
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1276
  *             if in_links_low[i] != -1:
  *                 if out_low[0] == -1 or in_links_low[i] < out_low[0]:
  *                     out_low[0] = in_links_low[i]             # <<<<<<<<<<<<<<
@@ -48665,7 +50276,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_find_projection(CYTHON_U
       }
       __pyx_L6:;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1264
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1277
  *                 if out_low[0] == -1 or in_links_low[i] < out_low[0]:
  *                     out_low[0] = in_links_low[i]
  *                 if out_high[0] == -1 or in_links_high[i] > out_high[0]:             # <<<<<<<<<<<<<<
@@ -48681,7 +50292,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_find_projection(CYTHON_U
       }
       if (__pyx_t_3) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1265
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1278
  *                     out_low[0] = in_links_low[i]
  *                 if out_high[0] == -1 or in_links_high[i] > out_high[0]:
  *                     out_high[0] = in_links_high[i]             # <<<<<<<<<<<<<<
@@ -48703,7 +50314,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_find_projection(CYTHON_U
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1268
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1281
  * 
  * 
  *     cdef int* int_arr_extend(self, int* arr, int* arr_len, int* data, int data_len):             # <<<<<<<<<<<<<<
@@ -48717,7 +50328,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_int_arr_extend(CYTHON_UNUSED
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("int_arr_extend", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1270
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1283
  *     cdef int* int_arr_extend(self, int* arr, int* arr_len, int* data, int data_len):
  *         cdef int new_len
  *         new_len = arr_len[0] + data_len             # <<<<<<<<<<<<<<
@@ -48726,7 +50337,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_int_arr_extend(CYTHON_UNUSED
  */
   __pyx_v_new_len = ((__pyx_v_arr_len[0]) + __pyx_v_data_len);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1271
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1284
  *         cdef int new_len
  *         new_len = arr_len[0] + data_len
  *         arr = <int*> realloc(arr, new_len*sizeof(int))             # <<<<<<<<<<<<<<
@@ -48735,7 +50346,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_int_arr_extend(CYTHON_UNUSED
  */
   __pyx_v_arr = ((int *)realloc(__pyx_v_arr, (__pyx_v_new_len * (sizeof(int)))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1272
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1285
  *         new_len = arr_len[0] + data_len
  *         arr = <int*> realloc(arr, new_len*sizeof(int))
  *         memcpy(arr+arr_len[0], data, data_len*sizeof(int))             # <<<<<<<<<<<<<<
@@ -48744,7 +50355,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_int_arr_extend(CYTHON_UNUSED
  */
   memcpy((__pyx_v_arr + (__pyx_v_arr_len[0])), __pyx_v_data, (__pyx_v_data_len * (sizeof(int))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1273
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1286
  *         arr = <int*> realloc(arr, new_len*sizeof(int))
  *         memcpy(arr+arr_len[0], data, data_len*sizeof(int))
  *         arr_len[0] = new_len             # <<<<<<<<<<<<<<
@@ -48753,7 +50364,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_int_arr_extend(CYTHON_UNUSED
  */
   (__pyx_v_arr_len[0]) = __pyx_v_new_len;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1274
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1287
  *         memcpy(arr+arr_len[0], data, data_len*sizeof(int))
  *         arr_len[0] = new_len
  *         return arr             # <<<<<<<<<<<<<<
@@ -48769,7 +50380,7 @@ static int *__pyx_f_3_sa_23HieroCachingRuleFactory_int_arr_extend(CYTHON_UNUSED
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1277
+/* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1290
  * 
  * 
  *     cdef extract_phrases(self, int e_low, int e_high, int* e_gap_low, int* e_gap_high, int* e_links_low, int num_gaps,             # <<<<<<<<<<<<<<
@@ -48815,19 +50426,19 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("extract_phrases", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1285
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1298
  *         cdef result
  * 
  *         result = []             # <<<<<<<<<<<<<<
  *         len1 = 0
  *         e_gaps1 = <int*> malloc(0)
  */
-  __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1285; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1298; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_1);
   __pyx_v_result = ((PyObject *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1286
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1299
  * 
  *         result = []
  *         len1 = 0             # <<<<<<<<<<<<<<
@@ -48836,7 +50447,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
   __pyx_v_len1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1287
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1300
  *         result = []
  *         len1 = 0
  *         e_gaps1 = <int*> malloc(0)             # <<<<<<<<<<<<<<
@@ -48845,19 +50456,19 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
   __pyx_v_e_gaps1 = ((int *)malloc(0));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1288
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1301
  *         len1 = 0
  *         e_gaps1 = <int*> malloc(0)
  *         ephr_arr = IntList()             # <<<<<<<<<<<<<<
  * 
  *         e_gap_order = <int*> malloc(num_gaps*sizeof(int))
  */
-  __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_IntList)), ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1288; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_IntList)), ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1301; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_1);
   __pyx_v_ephr_arr = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1290
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1303
  *         ephr_arr = IntList()
  * 
  *         e_gap_order = <int*> malloc(num_gaps*sizeof(int))             # <<<<<<<<<<<<<<
@@ -48866,7 +50477,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
   __pyx_v_e_gap_order = ((int *)malloc((__pyx_v_num_gaps * (sizeof(int)))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1291
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1304
  * 
  *         e_gap_order = <int*> malloc(num_gaps*sizeof(int))
  *         if num_gaps > 0:             # <<<<<<<<<<<<<<
@@ -48876,7 +50487,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
   __pyx_t_2 = (__pyx_v_num_gaps > 0);
   if (__pyx_t_2) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1292
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1305
  *         e_gap_order = <int*> malloc(num_gaps*sizeof(int))
  *         if num_gaps > 0:
  *             e_gap_order[0] = 0             # <<<<<<<<<<<<<<
@@ -48885,7 +50496,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
     (__pyx_v_e_gap_order[0]) = 0;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1293
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1306
  *         if num_gaps > 0:
  *             e_gap_order[0] = 0
  *             for i from 1 <= i < num_gaps:             # <<<<<<<<<<<<<<
@@ -48895,7 +50506,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
     __pyx_t_3 = __pyx_v_num_gaps;
     for (__pyx_v_i = 1; __pyx_v_i < __pyx_t_3; __pyx_v_i++) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1294
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1307
  *             e_gap_order[0] = 0
  *             for i from 1 <= i < num_gaps:
  *                 for j from 0 <= j < i:             # <<<<<<<<<<<<<<
@@ -48905,7 +50516,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
       __pyx_t_4 = __pyx_v_i;
       for (__pyx_v_j = 0; __pyx_v_j < __pyx_t_4; __pyx_v_j++) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1295
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1308
  *             for i from 1 <= i < num_gaps:
  *                 for j from 0 <= j < i:
  *                     if e_gap_low[i] < e_gap_low[j]:             # <<<<<<<<<<<<<<
@@ -48915,7 +50526,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
         __pyx_t_2 = ((__pyx_v_e_gap_low[__pyx_v_i]) < (__pyx_v_e_gap_low[__pyx_v_j]));
         if (__pyx_t_2) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1296
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1309
  *                 for j from 0 <= j < i:
  *                     if e_gap_low[i] < e_gap_low[j]:
  *                         for k from j <= k < i:             # <<<<<<<<<<<<<<
@@ -48925,7 +50536,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
           __pyx_t_5 = __pyx_v_i;
           for (__pyx_v_k = __pyx_v_j; __pyx_v_k < __pyx_t_5; __pyx_v_k++) {
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1297
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1310
  *                     if e_gap_low[i] < e_gap_low[j]:
  *                         for k from j <= k < i:
  *                             e_gap_order[k+1] = e_gap_order[k]             # <<<<<<<<<<<<<<
@@ -48935,7 +50546,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
             (__pyx_v_e_gap_order[(__pyx_v_k + 1)]) = (__pyx_v_e_gap_order[__pyx_v_k]);
           }
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1298
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1311
  *                         for k from j <= k < i:
  *                             e_gap_order[k+1] = e_gap_order[k]
  *                         e_gap_order[j] = i             # <<<<<<<<<<<<<<
@@ -48944,7 +50555,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
           (__pyx_v_e_gap_order[__pyx_v_j]) = __pyx_v_i;
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1299
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1312
  *                             e_gap_order[k+1] = e_gap_order[k]
  *                         e_gap_order[j] = i
  *                         break             # <<<<<<<<<<<<<<
@@ -48958,7 +50569,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
       }
       /*else*/ {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1301
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1314
  *                         break
  *                 else:
  *                     e_gap_order[i] = i             # <<<<<<<<<<<<<<
@@ -48973,7 +50584,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
   }
   __pyx_L3:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1303
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1316
  *                     e_gap_order[i] = i
  * 
  *         e_x_low = e_low             # <<<<<<<<<<<<<<
@@ -48982,7 +50593,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
   __pyx_v_e_x_low = __pyx_v_e_low;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1304
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1317
  * 
  *         e_x_low = e_low
  *         e_x_high = e_high             # <<<<<<<<<<<<<<
@@ -48991,7 +50602,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
   __pyx_v_e_x_high = __pyx_v_e_high;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1305
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1318
  *         e_x_low = e_low
  *         e_x_high = e_high
  *         if self.tight_phrases == 0:             # <<<<<<<<<<<<<<
@@ -49001,7 +50612,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
   __pyx_t_2 = (__pyx_v_self->tight_phrases == 0);
   if (__pyx_t_2) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1306
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1319
  *         e_x_high = e_high
  *         if self.tight_phrases == 0:
  *             while e_x_low > 0 and e_high - e_x_low < self.train_max_initial_size and e_links_low[e_x_low-1] == -1:             # <<<<<<<<<<<<<<
@@ -49024,7 +50635,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
       }
       if (!__pyx_t_6) break;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1307
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1320
  *         if self.tight_phrases == 0:
  *             while e_x_low > 0 and e_high - e_x_low < self.train_max_initial_size and e_links_low[e_x_low-1] == -1:
  *                 e_x_low = e_x_low - 1             # <<<<<<<<<<<<<<
@@ -49034,7 +50645,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
       __pyx_v_e_x_low = (__pyx_v_e_x_low - 1);
     }
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1308
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1321
  *             while e_x_low > 0 and e_high - e_x_low < self.train_max_initial_size and e_links_low[e_x_low-1] == -1:
  *                 e_x_low = e_x_low - 1
  *             while e_x_high < e_sent_len and e_x_high - e_low < self.train_max_initial_size and e_links_low[e_x_high] == -1:             # <<<<<<<<<<<<<<
@@ -49057,7 +50668,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
       }
       if (!__pyx_t_2) break;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1309
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1322
  *                 e_x_low = e_x_low - 1
  *             while e_x_high < e_sent_len and e_x_high - e_low < self.train_max_initial_size and e_links_low[e_x_high] == -1:
  *                 e_x_high = e_x_high + 1             # <<<<<<<<<<<<<<
@@ -49070,7 +50681,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
   }
   __pyx_L11:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1311
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1324
  *                 e_x_high = e_x_high + 1
  * 
  *         for i from e_x_low <= i <= e_low:             # <<<<<<<<<<<<<<
@@ -49080,7 +50691,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
   __pyx_t_3 = __pyx_v_e_low;
   for (__pyx_v_i = __pyx_v_e_x_low; __pyx_v_i <= __pyx_t_3; __pyx_v_i++) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1312
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1325
  * 
  *         for i from e_x_low <= i <= e_low:
  *             e_gaps1 = self.int_arr_extend(e_gaps1, &len1, &i, 1)             # <<<<<<<<<<<<<<
@@ -49090,7 +50701,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
     __pyx_v_e_gaps1 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->int_arr_extend(__pyx_v_self, __pyx_v_e_gaps1, (&__pyx_v_len1), (&__pyx_v_i), 1);
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1314
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1327
  *             e_gaps1 = self.int_arr_extend(e_gaps1, &len1, &i, 1)
  * 
  *         for i from 0 <= i < num_gaps:             # <<<<<<<<<<<<<<
@@ -49100,7 +50711,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
   __pyx_t_3 = __pyx_v_num_gaps;
   for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_3; __pyx_v_i++) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1315
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1328
  * 
  *         for i from 0 <= i < num_gaps:
  *             e_gaps2 = <int*> malloc(0)             # <<<<<<<<<<<<<<
@@ -49109,7 +50720,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
     __pyx_v_e_gaps2 = ((int *)malloc(0));
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1316
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1329
  *         for i from 0 <= i < num_gaps:
  *             e_gaps2 = <int*> malloc(0)
  *             len2 = 0             # <<<<<<<<<<<<<<
@@ -49118,7 +50729,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
     __pyx_v_len2 = 0;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1318
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1331
  *             len2 = 0
  * 
  *             j = e_gap_order[i]             # <<<<<<<<<<<<<<
@@ -49127,7 +50738,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
     __pyx_v_j = (__pyx_v_e_gap_order[__pyx_v_i]);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1319
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1332
  * 
  *             j = e_gap_order[i]
  *             e_x_gap_low = e_gap_low[j]             # <<<<<<<<<<<<<<
@@ -49136,7 +50747,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
     __pyx_v_e_x_gap_low = (__pyx_v_e_gap_low[__pyx_v_j]);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1320
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1333
  *             j = e_gap_order[i]
  *             e_x_gap_low = e_gap_low[j]
  *             e_x_gap_high = e_gap_high[j]             # <<<<<<<<<<<<<<
@@ -49145,7 +50756,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
     __pyx_v_e_x_gap_high = (__pyx_v_e_gap_high[__pyx_v_j]);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1321
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1334
  *             e_x_gap_low = e_gap_low[j]
  *             e_x_gap_high = e_gap_high[j]
  *             if self.tight_phrases == 0:             # <<<<<<<<<<<<<<
@@ -49155,7 +50766,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
     __pyx_t_2 = (__pyx_v_self->tight_phrases == 0);
     if (__pyx_t_2) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1322
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1335
  *             e_x_gap_high = e_gap_high[j]
  *             if self.tight_phrases == 0:
  *                 while e_x_gap_low > e_x_low and e_links_low[e_x_gap_low-1] == -1:             # <<<<<<<<<<<<<<
@@ -49172,7 +50783,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
         }
         if (!__pyx_t_7) break;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1323
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1336
  *             if self.tight_phrases == 0:
  *                 while e_x_gap_low > e_x_low and e_links_low[e_x_gap_low-1] == -1:
  *                     e_x_gap_low = e_x_gap_low - 1             # <<<<<<<<<<<<<<
@@ -49182,7 +50793,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
         __pyx_v_e_x_gap_low = (__pyx_v_e_x_gap_low - 1);
       }
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1324
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1337
  *                 while e_x_gap_low > e_x_low and e_links_low[e_x_gap_low-1] == -1:
  *                     e_x_gap_low = e_x_gap_low - 1
  *                 while e_x_gap_high < e_x_high and e_links_low[e_x_gap_high] == -1:             # <<<<<<<<<<<<<<
@@ -49199,7 +50810,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
         }
         if (!__pyx_t_6) break;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1325
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1338
  *                     e_x_gap_low = e_x_gap_low - 1
  *                 while e_x_gap_high < e_x_high and e_links_low[e_x_gap_high] == -1:
  *                     e_x_gap_high = e_x_gap_high + 1             # <<<<<<<<<<<<<<
@@ -49212,7 +50823,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
     }
     __pyx_L20:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1327
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1340
  *                     e_x_gap_high = e_x_gap_high + 1
  * 
  *             k = 0             # <<<<<<<<<<<<<<
@@ -49221,7 +50832,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
     __pyx_v_k = 0;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1328
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1341
  * 
  *             k = 0
  *             step = 1+(i*2)             # <<<<<<<<<<<<<<
@@ -49230,7 +50841,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
     __pyx_v_step = (1 + (__pyx_v_i * 2));
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1329
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1342
  *             k = 0
  *             step = 1+(i*2)
  *             while k < len1:             # <<<<<<<<<<<<<<
@@ -49241,7 +50852,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
       __pyx_t_6 = (__pyx_v_k < __pyx_v_len1);
       if (!__pyx_t_6) break;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1330
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1343
  *             step = 1+(i*2)
  *             while k < len1:
  *                 for m from e_x_gap_low <= m <= e_gap_low[j]:             # <<<<<<<<<<<<<<
@@ -49251,7 +50862,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
       __pyx_t_4 = (__pyx_v_e_gap_low[__pyx_v_j]);
       for (__pyx_v_m = __pyx_v_e_x_gap_low; __pyx_v_m <= __pyx_t_4; __pyx_v_m++) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1331
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1344
  *             while k < len1:
  *                 for m from e_x_gap_low <= m <= e_gap_low[j]:
  *                     if m >= e_gaps1[k+step-1]:             # <<<<<<<<<<<<<<
@@ -49261,7 +50872,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
         __pyx_t_6 = (__pyx_v_m >= (__pyx_v_e_gaps1[((__pyx_v_k + __pyx_v_step) - 1)]));
         if (__pyx_t_6) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1332
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1345
  *                 for m from e_x_gap_low <= m <= e_gap_low[j]:
  *                     if m >= e_gaps1[k+step-1]:
  *                         for n from e_gap_high[j] <= n <= e_x_gap_high:             # <<<<<<<<<<<<<<
@@ -49271,7 +50882,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
           __pyx_t_5 = __pyx_v_e_x_gap_high;
           for (__pyx_v_n = (__pyx_v_e_gap_high[__pyx_v_j]); __pyx_v_n <= __pyx_t_5; __pyx_v_n++) {
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1333
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1346
  *                     if m >= e_gaps1[k+step-1]:
  *                         for n from e_gap_high[j] <= n <= e_x_gap_high:
  *                             if n-m >= 1:    # extractor.py doesn't restrict target-side gap length             # <<<<<<<<<<<<<<
@@ -49281,7 +50892,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
             __pyx_t_6 = ((__pyx_v_n - __pyx_v_m) >= 1);
             if (__pyx_t_6) {
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1334
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1347
  *                         for n from e_gap_high[j] <= n <= e_x_gap_high:
  *                             if n-m >= 1:    # extractor.py doesn't restrict target-side gap length
  *                                 e_gaps2 = self.int_arr_extend(e_gaps2, &len2, e_gaps1+k, step)             # <<<<<<<<<<<<<<
@@ -49290,7 +50901,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
               __pyx_v_e_gaps2 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->int_arr_extend(__pyx_v_self, __pyx_v_e_gaps2, (&__pyx_v_len2), (__pyx_v_e_gaps1 + __pyx_v_k), __pyx_v_step);
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1335
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1348
  *                             if n-m >= 1:    # extractor.py doesn't restrict target-side gap length
  *                                 e_gaps2 = self.int_arr_extend(e_gaps2, &len2, e_gaps1+k, step)
  *                                 e_gaps2 = self.int_arr_extend(e_gaps2, &len2, &m, 1)             # <<<<<<<<<<<<<<
@@ -49299,7 +50910,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
               __pyx_v_e_gaps2 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->int_arr_extend(__pyx_v_self, __pyx_v_e_gaps2, (&__pyx_v_len2), (&__pyx_v_m), 1);
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1336
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1349
  *                                 e_gaps2 = self.int_arr_extend(e_gaps2, &len2, e_gaps1+k, step)
  *                                 e_gaps2 = self.int_arr_extend(e_gaps2, &len2, &m, 1)
  *                                 e_gaps2 = self.int_arr_extend(e_gaps2, &len2, &n, 1)             # <<<<<<<<<<<<<<
@@ -49316,7 +50927,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
         __pyx_L29:;
       }
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1337
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1350
  *                                 e_gaps2 = self.int_arr_extend(e_gaps2, &len2, &m, 1)
  *                                 e_gaps2 = self.int_arr_extend(e_gaps2, &len2, &n, 1)
  *                 k = k + step             # <<<<<<<<<<<<<<
@@ -49326,7 +50937,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
       __pyx_v_k = (__pyx_v_k + __pyx_v_step);
     }
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1338
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1351
  *                                 e_gaps2 = self.int_arr_extend(e_gaps2, &len2, &n, 1)
  *                 k = k + step
  *             free(e_gaps1)             # <<<<<<<<<<<<<<
@@ -49335,7 +50946,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
     free(__pyx_v_e_gaps1);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1339
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1352
  *                 k = k + step
  *             free(e_gaps1)
  *             e_gaps1 = e_gaps2             # <<<<<<<<<<<<<<
@@ -49344,7 +50955,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
     __pyx_v_e_gaps1 = __pyx_v_e_gaps2;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1340
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1353
  *             free(e_gaps1)
  *             e_gaps1 = e_gaps2
  *             len1 = len2             # <<<<<<<<<<<<<<
@@ -49354,7 +50965,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
     __pyx_v_len1 = __pyx_v_len2;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1342
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1355
  *             len1 = len2
  * 
  *         step = 1+(num_gaps*2)             # <<<<<<<<<<<<<<
@@ -49363,7 +50974,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
   __pyx_v_step = (1 + (__pyx_v_num_gaps * 2));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1343
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1356
  * 
  *         step = 1+(num_gaps*2)
  *         e_gaps2 = <int*> malloc(0)             # <<<<<<<<<<<<<<
@@ -49372,7 +50983,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
   __pyx_v_e_gaps2 = ((int *)malloc(0));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1344
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1357
  *         step = 1+(num_gaps*2)
  *         e_gaps2 = <int*> malloc(0)
  *         len2 = 0             # <<<<<<<<<<<<<<
@@ -49381,7 +50992,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
   __pyx_v_len2 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1345
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1358
  *         e_gaps2 = <int*> malloc(0)
  *         len2 = 0
  *         for i from e_high <= i <= e_x_high:             # <<<<<<<<<<<<<<
@@ -49391,7 +51002,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
   __pyx_t_3 = __pyx_v_e_x_high;
   for (__pyx_v_i = __pyx_v_e_high; __pyx_v_i <= __pyx_t_3; __pyx_v_i++) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1346
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1359
  *         len2 = 0
  *         for i from e_high <= i <= e_x_high:
  *             j = 0             # <<<<<<<<<<<<<<
@@ -49400,7 +51011,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
     __pyx_v_j = 0;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1347
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1360
  *         for i from e_high <= i <= e_x_high:
  *             j = 0
  *             while j < len1:             # <<<<<<<<<<<<<<
@@ -49411,7 +51022,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
       __pyx_t_6 = (__pyx_v_j < __pyx_v_len1);
       if (!__pyx_t_6) break;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1348
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1361
  *             j = 0
  *             while j < len1:
  *                 if i - e_gaps1[j] <= self.train_max_initial_size and i >= e_gaps1[j+step-1]:             # <<<<<<<<<<<<<<
@@ -49427,7 +51038,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
       }
       if (__pyx_t_2) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1349
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1362
  *             while j < len1:
  *                 if i - e_gaps1[j] <= self.train_max_initial_size and i >= e_gaps1[j+step-1]:
  *                     e_gaps2 = self.int_arr_extend(e_gaps2, &len2, e_gaps1+j, step)             # <<<<<<<<<<<<<<
@@ -49436,7 +51047,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
         __pyx_v_e_gaps2 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->int_arr_extend(__pyx_v_self, __pyx_v_e_gaps2, (&__pyx_v_len2), (__pyx_v_e_gaps1 + __pyx_v_j), __pyx_v_step);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1350
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1363
  *                 if i - e_gaps1[j] <= self.train_max_initial_size and i >= e_gaps1[j+step-1]:
  *                     e_gaps2 = self.int_arr_extend(e_gaps2, &len2, e_gaps1+j, step)
  *                     e_gaps2 = self.int_arr_extend(e_gaps2, &len2, &i, 1)             # <<<<<<<<<<<<<<
@@ -49448,7 +51059,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
       }
       __pyx_L37:;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1351
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1364
  *                     e_gaps2 = self.int_arr_extend(e_gaps2, &len2, e_gaps1+j, step)
  *                     e_gaps2 = self.int_arr_extend(e_gaps2, &len2, &i, 1)
  *                 j = j + step             # <<<<<<<<<<<<<<
@@ -49459,7 +51070,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
     }
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1352
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1365
  *                     e_gaps2 = self.int_arr_extend(e_gaps2, &len2, &i, 1)
  *                 j = j + step
  *         free(e_gaps1)             # <<<<<<<<<<<<<<
@@ -49468,7 +51079,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
   free(__pyx_v_e_gaps1);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1353
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1366
  *                 j = j + step
  *         free(e_gaps1)
  *         e_gaps1 = e_gaps2             # <<<<<<<<<<<<<<
@@ -49477,7 +51088,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
   __pyx_v_e_gaps1 = __pyx_v_e_gaps2;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1354
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1367
  *         free(e_gaps1)
  *         e_gaps1 = e_gaps2
  *         len1 = len2             # <<<<<<<<<<<<<<
@@ -49486,7 +51097,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
   __pyx_v_len1 = __pyx_v_len2;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1356
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1369
  *         len1 = len2
  * 
  *         step = (num_gaps+1)*2             # <<<<<<<<<<<<<<
@@ -49495,7 +51106,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
   __pyx_v_step = ((__pyx_v_num_gaps + 1) * 2);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1357
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1370
  * 
  *         step = (num_gaps+1)*2
  *         i = 0             # <<<<<<<<<<<<<<
@@ -49504,7 +51115,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
   __pyx_v_i = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1359
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1372
  *         i = 0
  * 
  *         while i < len1:             # <<<<<<<<<<<<<<
@@ -49515,7 +51126,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
     __pyx_t_2 = (__pyx_v_i < __pyx_v_len1);
     if (!__pyx_t_2) break;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1360
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1373
  * 
  *         while i < len1:
  *             ephr_arr._clear()             # <<<<<<<<<<<<<<
@@ -49524,7 +51135,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
     ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_ephr_arr->__pyx_vtab)->_clear(__pyx_v_ephr_arr);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1361
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1374
  *         while i < len1:
  *             ephr_arr._clear()
  *             num_chunks = 0             # <<<<<<<<<<<<<<
@@ -49533,20 +51144,20 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  */
     __pyx_v_num_chunks = 0;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1362
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1375
  *             ephr_arr._clear()
  *             num_chunks = 0
  *             indexes = []             # <<<<<<<<<<<<<<
  *             for j from 0 <= j < num_gaps+1:
  *                 if e_gaps1[i+2*j] < e_gaps1[i+(2*j)+1]:
  */
-    __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_1);
     __Pyx_XDECREF(((PyObject *)__pyx_v_indexes));
     __pyx_v_indexes = __pyx_t_1;
     __pyx_t_1 = 0;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1363
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1376
  *             num_chunks = 0
  *             indexes = []
  *             for j from 0 <= j < num_gaps+1:             # <<<<<<<<<<<<<<
@@ -49556,7 +51167,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
     __pyx_t_9 = (__pyx_v_num_gaps + 1);
     for (__pyx_v_j = 0; __pyx_v_j < __pyx_t_9; __pyx_v_j++) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1364
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1377
  *             indexes = []
  *             for j from 0 <= j < num_gaps+1:
  *                 if e_gaps1[i+2*j] < e_gaps1[i+(2*j)+1]:             # <<<<<<<<<<<<<<
@@ -49566,7 +51177,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
       __pyx_t_2 = ((__pyx_v_e_gaps1[(__pyx_v_i + (2 * __pyx_v_j))]) < (__pyx_v_e_gaps1[((__pyx_v_i + (2 * __pyx_v_j)) + 1)]));
       if (__pyx_t_2) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1365
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1378
  *             for j from 0 <= j < num_gaps+1:
  *                 if e_gaps1[i+2*j] < e_gaps1[i+(2*j)+1]:
  *                     num_chunks = num_chunks + 1             # <<<<<<<<<<<<<<
@@ -49578,7 +51189,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
       }
       __pyx_L42:;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1366
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1379
  *                 if e_gaps1[i+2*j] < e_gaps1[i+(2*j)+1]:
  *                     num_chunks = num_chunks + 1
  *                 for k from e_gaps1[i+2*j] <= k < e_gaps1[i+(2*j)+1]:             # <<<<<<<<<<<<<<
@@ -49588,19 +51199,19 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
       __pyx_t_3 = (__pyx_v_e_gaps1[((__pyx_v_i + (2 * __pyx_v_j)) + 1)]);
       for (__pyx_v_k = (__pyx_v_e_gaps1[(__pyx_v_i + (2 * __pyx_v_j))]); __pyx_v_k < __pyx_t_3; __pyx_v_k++) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1367
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1380
  *                     num_chunks = num_chunks + 1
  *                 for k from e_gaps1[i+2*j] <= k < e_gaps1[i+(2*j)+1]:
  *                     indexes.append(k)             # <<<<<<<<<<<<<<
  *                     ephr_arr._append(self.eid2symid[self.eda.data.arr[e_sent_start+k]])
  *                 if j < num_gaps:
  */
-        __pyx_t_1 = PyInt_FromLong(__pyx_v_k); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_1 = PyInt_FromLong(__pyx_v_k); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1380; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_1);
-        __pyx_t_10 = PyList_Append(__pyx_v_indexes, __pyx_t_1); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_10 = PyList_Append(__pyx_v_indexes, __pyx_t_1); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1380; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1368
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1381
  *                 for k from e_gaps1[i+2*j] <= k < e_gaps1[i+(2*j)+1]:
  *                     indexes.append(k)
  *                     ephr_arr._append(self.eid2symid[self.eda.data.arr[e_sent_start+k]])             # <<<<<<<<<<<<<<
@@ -49608,14 +51219,14 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
  *                     indexes.append(sym_setindex(self.category, e_gap_order[j]+1))
  */
         __pyx_t_4 = (__pyx_v_self->eda->data->arr[(__pyx_v_e_sent_start + __pyx_v_k)]);
-        __pyx_t_1 = __Pyx_GetItemInt(((PyObject *)__pyx_v_self->eid2symid), __pyx_t_4, sizeof(int), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1368; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_1 = __Pyx_GetItemInt(((PyObject *)__pyx_v_self->eid2symid), __pyx_t_4, sizeof(int), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1381; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_1);
-        __pyx_t_4 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1368; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_4 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1381; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
         ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_ephr_arr->__pyx_vtab)->_append(__pyx_v_ephr_arr, __pyx_t_4);
       }
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1369
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1382
  *                     indexes.append(k)
  *                     ephr_arr._append(self.eid2symid[self.eda.data.arr[e_sent_start+k]])
  *                 if j < num_gaps:             # <<<<<<<<<<<<<<
@@ -49625,19 +51236,19 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases(struct _
       __pyx_t_2 = (__pyx_v_j < __pyx_v_num_gaps);
       if (__pyx_t_2) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1370
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1383
  *                     ephr_arr._append(self.eid2symid[self.eda.data.arr[e_sent_start+k]])
  *                 if j < num_gaps:
  *                     indexes.append(sym_setindex(self.category, e_gap_order[j]+1))             # <<<<<<<<<<<<<<
  *                     ephr_arr._append(sym_setindex(self.category, e_gap_order[j]+1))
  *             i = i + step
  */
-        __pyx_t_1 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, ((__pyx_v_e_gap_order[__pyx_v_j]) + 1))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1372
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-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1391
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1392
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1393
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1406
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-  __pyx_r = Py_None; __Pyx_INCREF(Py_None);
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-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1395
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-  PyObject *__pyx_v_als2 = NULL;
-  PyObject *__pyx_v_als3 = NULL;
-  PyObject *__pyx_v_als4 = NULL;
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1408
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1409
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1410
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1411
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1424
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1413
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1426
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1414
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1427
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1415
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1428
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1416
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1429
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1417
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1430
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1418
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1431
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1420
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1433
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+  __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes1), __pyx_n_s__reset); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1421
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1434
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1422
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1435
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1423
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1436
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1424
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1437
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  */
-      __pyx_t_2 = PyInt_FromLong((((__pyx_v_matching->arr[(__pyx_v_matching->start + __pyx_v_i)]) + __pyx_v_j) - __pyx_v_f_sent_start)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1424; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_2 = PyInt_FromLong((((__pyx_v_matching->arr[(__pyx_v_matching->start + __pyx_v_i)]) + __pyx_v_j) - __pyx_v_f_sent_start)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1437; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_2);
-      __pyx_t_1 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes1), __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1424; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_1 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes1), __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1437; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_1);
       __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
       __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1425
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1438
  *             for j in range(chunklen[i]):
  *                 self.findexes1.append(matching.arr[matching.start+i]+j-f_sent_start);
  *                 sofar += 1             # <<<<<<<<<<<<<<
  *             if (i+1<num_chunks):
  *                 self.findexes1.append(phrase[sofar])
  */
-      __pyx_t_1 = PyNumber_InPlaceAdd(__pyx_v_sofar, __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1425; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_1 = PyNumber_InPlaceAdd(__pyx_v_sofar, __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1438; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_1);
       __Pyx_DECREF(__pyx_v_sofar);
       __pyx_v_sofar = __pyx_t_1;
       __pyx_t_1 = 0;
     }
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1426
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1439
  *                 self.findexes1.append(matching.arr[matching.start+i]+j-f_sent_start);
  *                 sofar += 1
  *             if (i+1<num_chunks):             # <<<<<<<<<<<<<<
@@ -50255,28 +51863,28 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     __pyx_t_7 = ((__pyx_v_i + 1) < __pyx_v_num_chunks);
     if (__pyx_t_7) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1427
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1440
  *                 sofar += 1
  *             if (i+1<num_chunks):
  *                 self.findexes1.append(phrase[sofar])             # <<<<<<<<<<<<<<
  *                 sofar += 1
  * 
  */
-      __pyx_t_1 = PyObject_GetItem(((PyObject *)__pyx_v_phrase), __pyx_v_sofar); if (!__pyx_t_1) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1427; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_1 = PyObject_GetItem(((PyObject *)__pyx_v_phrase), __pyx_v_sofar); if (!__pyx_t_1) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1440; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_1);
-      __pyx_t_2 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes1), __pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1427; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_2 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes1), __pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1440; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_2);
       __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
       __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1428
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1441
  *             if (i+1<num_chunks):
  *                 self.findexes1.append(phrase[sofar])
  *                 sofar += 1             # <<<<<<<<<<<<<<
  * 
  * 
  */
-      __pyx_t_2 = PyNumber_InPlaceAdd(__pyx_v_sofar, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_2 = PyNumber_InPlaceAdd(__pyx_v_sofar, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_2);
       __Pyx_DECREF(__pyx_v_sofar);
       __pyx_v_sofar = __pyx_t_2;
@@ -50286,7 +51894,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     __pyx_L7:;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1431
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1444
  * 
  * 
  *         e_links_low = <int*> malloc(e_sent_len*sizeof(int))             # <<<<<<<<<<<<<<
@@ -50295,7 +51903,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   __pyx_v_e_links_low = ((int *)malloc((__pyx_v_e_sent_len * (sizeof(int)))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1432
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1445
  * 
  *         e_links_low = <int*> malloc(e_sent_len*sizeof(int))
  *         e_links_high = <int*> malloc(e_sent_len*sizeof(int))             # <<<<<<<<<<<<<<
@@ -50304,7 +51912,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   __pyx_v_e_links_high = ((int *)malloc((__pyx_v_e_sent_len * (sizeof(int)))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1433
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1446
  *         e_links_low = <int*> malloc(e_sent_len*sizeof(int))
  *         e_links_high = <int*> malloc(e_sent_len*sizeof(int))
  *         f_links_low = <int*> malloc(f_sent_len*sizeof(int))             # <<<<<<<<<<<<<<
@@ -50313,7 +51921,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   __pyx_v_f_links_low = ((int *)malloc((__pyx_v_f_sent_len * (sizeof(int)))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1434
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1447
  *         e_links_high = <int*> malloc(e_sent_len*sizeof(int))
  *         f_links_low = <int*> malloc(f_sent_len*sizeof(int))
  *         f_links_high = <int*> malloc(f_sent_len*sizeof(int))             # <<<<<<<<<<<<<<
@@ -50322,7 +51930,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   __pyx_v_f_links_high = ((int *)malloc((__pyx_v_f_sent_len * (sizeof(int)))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1435
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1448
  *         f_links_low = <int*> malloc(f_sent_len*sizeof(int))
  *         f_links_high = <int*> malloc(f_sent_len*sizeof(int))
  *         f_gap_low = <int*> malloc((num_chunks+1)*sizeof(int))             # <<<<<<<<<<<<<<
@@ -50331,7 +51939,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   __pyx_v_f_gap_low = ((int *)malloc(((__pyx_v_num_chunks + 1) * (sizeof(int)))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1436
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1449
  *         f_links_high = <int*> malloc(f_sent_len*sizeof(int))
  *         f_gap_low = <int*> malloc((num_chunks+1)*sizeof(int))
  *         f_gap_high = <int*> malloc((num_chunks+1)*sizeof(int))             # <<<<<<<<<<<<<<
@@ -50340,7 +51948,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   __pyx_v_f_gap_high = ((int *)malloc(((__pyx_v_num_chunks + 1) * (sizeof(int)))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1437
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1450
  *         f_gap_low = <int*> malloc((num_chunks+1)*sizeof(int))
  *         f_gap_high = <int*> malloc((num_chunks+1)*sizeof(int))
  *         e_gap_low = <int*> malloc((num_chunks+1)*sizeof(int))             # <<<<<<<<<<<<<<
@@ -50349,7 +51957,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   __pyx_v_e_gap_low = ((int *)malloc(((__pyx_v_num_chunks + 1) * (sizeof(int)))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1438
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1451
  *         f_gap_high = <int*> malloc((num_chunks+1)*sizeof(int))
  *         e_gap_low = <int*> malloc((num_chunks+1)*sizeof(int))
  *         e_gap_high = <int*> malloc((num_chunks+1)*sizeof(int))             # <<<<<<<<<<<<<<
@@ -50358,7 +51966,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   __pyx_v_e_gap_high = ((int *)malloc(((__pyx_v_num_chunks + 1) * (sizeof(int)))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1439
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1452
  *         e_gap_low = <int*> malloc((num_chunks+1)*sizeof(int))
  *         e_gap_high = <int*> malloc((num_chunks+1)*sizeof(int))
  *         memset(f_gap_low, 0, (num_chunks+1)*sizeof(int))             # <<<<<<<<<<<<<<
@@ -50367,7 +51975,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   memset(__pyx_v_f_gap_low, 0, ((__pyx_v_num_chunks + 1) * (sizeof(int))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1440
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1453
  *         e_gap_high = <int*> malloc((num_chunks+1)*sizeof(int))
  *         memset(f_gap_low, 0, (num_chunks+1)*sizeof(int))
  *         memset(f_gap_high, 0, (num_chunks+1)*sizeof(int))             # <<<<<<<<<<<<<<
@@ -50376,7 +51984,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   memset(__pyx_v_f_gap_high, 0, ((__pyx_v_num_chunks + 1) * (sizeof(int))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1441
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1454
  *         memset(f_gap_low, 0, (num_chunks+1)*sizeof(int))
  *         memset(f_gap_high, 0, (num_chunks+1)*sizeof(int))
  *         memset(e_gap_low, 0, (num_chunks+1)*sizeof(int))             # <<<<<<<<<<<<<<
@@ -50385,7 +51993,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   memset(__pyx_v_e_gap_low, 0, ((__pyx_v_num_chunks + 1) * (sizeof(int))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1442
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1455
  *         memset(f_gap_high, 0, (num_chunks+1)*sizeof(int))
  *         memset(e_gap_low, 0, (num_chunks+1)*sizeof(int))
  *         memset(e_gap_high, 0, (num_chunks+1)*sizeof(int))             # <<<<<<<<<<<<<<
@@ -50394,7 +52002,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   memset(__pyx_v_e_gap_high, 0, ((__pyx_v_num_chunks + 1) * (sizeof(int))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1444
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1457
  *         memset(e_gap_high, 0, (num_chunks+1)*sizeof(int))
  * 
  *         reason_for_failure = ""             # <<<<<<<<<<<<<<
@@ -50404,7 +52012,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
   __Pyx_INCREF(((PyObject *)__pyx_kp_s_45));
   __pyx_v_reason_for_failure = ((PyObject *)__pyx_kp_s_45);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1446
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1459
  *         reason_for_failure = ""
  * 
  *         for i from 0 <= i < e_sent_len:             # <<<<<<<<<<<<<<
@@ -50414,7 +52022,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
   __pyx_t_3 = __pyx_v_e_sent_len;
   for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_3; __pyx_v_i++) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1447
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1460
  * 
  *         for i from 0 <= i < e_sent_len:
  *             e_links_low[i] = -1             # <<<<<<<<<<<<<<
@@ -50423,7 +52031,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
     (__pyx_v_e_links_low[__pyx_v_i]) = -1;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1448
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1461
  *         for i from 0 <= i < e_sent_len:
  *             e_links_low[i] = -1
  *             e_links_high[i] = -1             # <<<<<<<<<<<<<<
@@ -50433,7 +52041,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     (__pyx_v_e_links_high[__pyx_v_i]) = -1;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1449
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1462
  *             e_links_low[i] = -1
  *             e_links_high[i] = -1
  *         for i from 0 <= i < f_sent_len:             # <<<<<<<<<<<<<<
@@ -50443,7 +52051,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
   __pyx_t_3 = __pyx_v_f_sent_len;
   for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_3; __pyx_v_i++) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1450
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1463
  *             e_links_high[i] = -1
  *         for i from 0 <= i < f_sent_len:
  *             f_links_low[i] = -1             # <<<<<<<<<<<<<<
@@ -50452,7 +52060,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
     (__pyx_v_f_links_low[__pyx_v_i]) = -1;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1451
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1464
  *         for i from 0 <= i < f_sent_len:
  *             f_links_low[i] = -1
  *             f_links_high[i] = -1             # <<<<<<<<<<<<<<
@@ -50462,7 +52070,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     (__pyx_v_f_links_high[__pyx_v_i]) = -1;
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1457
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1470
  *         # links that we care about (but then how to look up
  *         # when we want to check something on the e side?)
  *         i = 0             # <<<<<<<<<<<<<<
@@ -50471,7 +52079,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   __pyx_v_i = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1458
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1471
  *         # when we want to check something on the e side?)
  *         i = 0
  *         while i < num_links*2:             # <<<<<<<<<<<<<<
@@ -50482,7 +52090,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     __pyx_t_7 = (__pyx_v_i < (__pyx_v_num_links * 2));
     if (!__pyx_t_7) break;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1459
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1472
  *         i = 0
  *         while i < num_links*2:
  *             f_i = sent_links[i]             # <<<<<<<<<<<<<<
@@ -50491,7 +52099,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
     __pyx_v_f_i = (__pyx_v_sent_links[__pyx_v_i]);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1460
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1473
  *         while i < num_links*2:
  *             f_i = sent_links[i]
  *             e_i = sent_links[i+1]             # <<<<<<<<<<<<<<
@@ -50500,7 +52108,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
     __pyx_v_e_i = (__pyx_v_sent_links[(__pyx_v_i + 1)]);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1461
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1474
  *             f_i = sent_links[i]
  *             e_i = sent_links[i+1]
  *             if f_links_low[f_i] == -1 or f_links_low[f_i] > e_i:             # <<<<<<<<<<<<<<
@@ -50516,7 +52124,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     }
     if (__pyx_t_9) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1462
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1475
  *             e_i = sent_links[i+1]
  *             if f_links_low[f_i] == -1 or f_links_low[f_i] > e_i:
  *                 f_links_low[f_i] = e_i             # <<<<<<<<<<<<<<
@@ -50528,7 +52136,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     }
     __pyx_L14:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1463
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1476
  *             if f_links_low[f_i] == -1 or f_links_low[f_i] > e_i:
  *                 f_links_low[f_i] = e_i
  *             if f_links_high[f_i] == -1 or f_links_high[f_i] < e_i + 1:             # <<<<<<<<<<<<<<
@@ -50544,7 +52152,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     }
     if (__pyx_t_8) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1464
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1477
  *                 f_links_low[f_i] = e_i
  *             if f_links_high[f_i] == -1 or f_links_high[f_i] < e_i + 1:
  *                 f_links_high[f_i] = e_i + 1             # <<<<<<<<<<<<<<
@@ -50556,7 +52164,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     }
     __pyx_L15:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1465
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1478
  *             if f_links_high[f_i] == -1 or f_links_high[f_i] < e_i + 1:
  *                 f_links_high[f_i] = e_i + 1
  *             if e_links_low[e_i] == -1 or e_links_low[e_i] > f_i:             # <<<<<<<<<<<<<<
@@ -50572,7 +52180,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     }
     if (__pyx_t_7) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1466
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1479
  *                 f_links_high[f_i] = e_i + 1
  *             if e_links_low[e_i] == -1 or e_links_low[e_i] > f_i:
  *                 e_links_low[e_i] = f_i             # <<<<<<<<<<<<<<
@@ -50584,7 +52192,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     }
     __pyx_L16:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1467
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1480
  *             if e_links_low[e_i] == -1 or e_links_low[e_i] > f_i:
  *                 e_links_low[e_i] = f_i
  *             if e_links_high[e_i] == -1 or e_links_high[e_i] < f_i + 1:             # <<<<<<<<<<<<<<
@@ -50600,7 +52208,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     }
     if (__pyx_t_9) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1468
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1481
  *                 e_links_low[e_i] = f_i
  *             if e_links_high[e_i] == -1 or e_links_high[e_i] < f_i + 1:
  *                 e_links_high[e_i] = f_i + 1             # <<<<<<<<<<<<<<
@@ -50612,7 +52220,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     }
     __pyx_L17:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1469
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1482
  *             if e_links_high[e_i] == -1 or e_links_high[e_i] < f_i + 1:
  *                 e_links_high[e_i] = f_i + 1
  *             i = i + 2             # <<<<<<<<<<<<<<
@@ -50622,19 +52230,19 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     __pyx_v_i = (__pyx_v_i + 2);
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1471
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1484
  *             i = i + 2
  * 
  *         als = []             # <<<<<<<<<<<<<<
  *         for x in range(matching.start,matching.end):
  *             al = (matching.arr[x]-f_sent_start,f_links_low[matching.arr[x]-f_sent_start])
  */
-  __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_2);
   __pyx_v_als = __pyx_t_2;
   __pyx_t_2 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1472
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1485
  * 
  *         als = []
  *         for x in range(matching.start,matching.end):             # <<<<<<<<<<<<<<
@@ -50645,18 +52253,18 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
   for (__pyx_t_4 = __pyx_v_matching->start; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
     __pyx_v_x = __pyx_t_4;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1473
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1486
  *         als = []
  *         for x in range(matching.start,matching.end):
  *             al = (matching.arr[x]-f_sent_start,f_links_low[matching.arr[x]-f_sent_start])             # <<<<<<<<<<<<<<
  *             als.append(al)
  *         # check all source-side alignment constraints
  */
-    __pyx_t_2 = PyInt_FromLong(((__pyx_v_matching->arr[__pyx_v_x]) - __pyx_v_f_sent_start)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1473; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_2 = PyInt_FromLong(((__pyx_v_matching->arr[__pyx_v_x]) - __pyx_v_f_sent_start)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1486; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_2);
-    __pyx_t_1 = PyInt_FromLong((__pyx_v_f_links_low[((__pyx_v_matching->arr[__pyx_v_x]) - __pyx_v_f_sent_start)])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1473; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_1 = PyInt_FromLong((__pyx_v_f_links_low[((__pyx_v_matching->arr[__pyx_v_x]) - __pyx_v_f_sent_start)])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1486; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_1);
-    __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1473; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1486; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_10);
     PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_2);
     __Pyx_GIVEREF(__pyx_t_2);
@@ -50668,17 +52276,17 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     __pyx_v_al = __pyx_t_10;
     __pyx_t_10 = 0;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1474
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1487
  *         for x in range(matching.start,matching.end):
  *             al = (matching.arr[x]-f_sent_start,f_links_low[matching.arr[x]-f_sent_start])
  *             als.append(al)             # <<<<<<<<<<<<<<
  *         # check all source-side alignment constraints
  *         met_constraints = 1
  */
-    __pyx_t_11 = PyList_Append(__pyx_v_als, ((PyObject *)__pyx_v_al)); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1474; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_11 = PyList_Append(__pyx_v_als, ((PyObject *)__pyx_v_al)); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   }
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1476
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1489
  *             als.append(al)
  *         # check all source-side alignment constraints
  *         met_constraints = 1             # <<<<<<<<<<<<<<
@@ -50687,7 +52295,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   __pyx_v_met_constraints = 1;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1477
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1490
  *         # check all source-side alignment constraints
  *         met_constraints = 1
  *         if self.require_aligned_terminal:             # <<<<<<<<<<<<<<
@@ -50696,7 +52304,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   if (__pyx_v_self->require_aligned_terminal) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1478
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1491
  *         met_constraints = 1
  *         if self.require_aligned_terminal:
  *             num_aligned_chunks = 0             # <<<<<<<<<<<<<<
@@ -50705,7 +52313,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
     __pyx_v_num_aligned_chunks = 0;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1479
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1492
  *         if self.require_aligned_terminal:
  *             num_aligned_chunks = 0
  *             for i from 0 <= i < num_chunks:             # <<<<<<<<<<<<<<
@@ -50715,7 +52323,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     __pyx_t_3 = __pyx_v_num_chunks;
     for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_3; __pyx_v_i++) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1480
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1493
  *             num_aligned_chunks = 0
  *             for i from 0 <= i < num_chunks:
  *                 for j from 0 <= j < chunklen[i]:             # <<<<<<<<<<<<<<
@@ -50725,7 +52333,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
       __pyx_t_4 = (__pyx_v_chunklen[__pyx_v_i]);
       for (__pyx_v_j = 0; __pyx_v_j < __pyx_t_4; __pyx_v_j++) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1481
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1494
  *             for i from 0 <= i < num_chunks:
  *                 for j from 0 <= j < chunklen[i]:
  *                     if f_links_low[matching.arr[matching.start+i]+j-f_sent_start] > -1:             # <<<<<<<<<<<<<<
@@ -50735,7 +52343,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         __pyx_t_9 = ((__pyx_v_f_links_low[(((__pyx_v_matching->arr[(__pyx_v_matching->start + __pyx_v_i)]) + __pyx_v_j) - __pyx_v_f_sent_start)]) > -1);
         if (__pyx_t_9) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1482
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1495
  *                 for j from 0 <= j < chunklen[i]:
  *                     if f_links_low[matching.arr[matching.start+i]+j-f_sent_start] > -1:
  *                         num_aligned_chunks = num_aligned_chunks + 1             # <<<<<<<<<<<<<<
@@ -50744,7 +52352,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
           __pyx_v_num_aligned_chunks = (__pyx_v_num_aligned_chunks + 1);
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1483
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1496
  *                     if f_links_low[matching.arr[matching.start+i]+j-f_sent_start] > -1:
  *                         num_aligned_chunks = num_aligned_chunks + 1
  *                         break             # <<<<<<<<<<<<<<
@@ -50759,7 +52367,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
       __pyx_L24_break:;
     }
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1484
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1497
  *                         num_aligned_chunks = num_aligned_chunks + 1
  *                         break
  *             if num_aligned_chunks == 0:             # <<<<<<<<<<<<<<
@@ -50769,7 +52377,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     __pyx_t_9 = (__pyx_v_num_aligned_chunks == 0);
     if (__pyx_t_9) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1485
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1498
  *                         break
  *             if num_aligned_chunks == 0:
  *                 reason_for_failure = "No aligned terminals"             # <<<<<<<<<<<<<<
@@ -50780,7 +52388,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
       __Pyx_DECREF(__pyx_v_reason_for_failure);
       __pyx_v_reason_for_failure = ((PyObject *)__pyx_kp_s_126);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1486
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1499
  *             if num_aligned_chunks == 0:
  *                 reason_for_failure = "No aligned terminals"
  *                 met_constraints = 0             # <<<<<<<<<<<<<<
@@ -50792,7 +52400,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     }
     __pyx_L26:;
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1487
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1500
  *                 reason_for_failure = "No aligned terminals"
  *                 met_constraints = 0
  *             if self.require_aligned_chunks and num_aligned_chunks < num_chunks:             # <<<<<<<<<<<<<<
@@ -50807,7 +52415,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     }
     if (__pyx_t_7) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1488
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1501
  *                 met_constraints = 0
  *             if self.require_aligned_chunks and num_aligned_chunks < num_chunks:
  *                 reason_for_failure = "Unaligned chunk"             # <<<<<<<<<<<<<<
@@ -50818,7 +52426,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
       __Pyx_DECREF(__pyx_v_reason_for_failure);
       __pyx_v_reason_for_failure = ((PyObject *)__pyx_kp_s_127);
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1489
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1502
  *             if self.require_aligned_chunks and num_aligned_chunks < num_chunks:
  *                 reason_for_failure = "Unaligned chunk"
  *                 met_constraints = 0             # <<<<<<<<<<<<<<
@@ -50833,7 +52441,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
   }
   __pyx_L20:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1491
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1504
  *                 met_constraints = 0
  * 
  *         if met_constraints and self.tight_phrases:             # <<<<<<<<<<<<<<
@@ -50847,7 +52455,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
   }
   if (__pyx_t_7) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1493
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1506
  *         if met_constraints and self.tight_phrases:
  *             # outside edge constraints are checked later
  *             for i from 0 <= i < num_chunks-1:             # <<<<<<<<<<<<<<
@@ -50857,7 +52465,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     __pyx_t_12 = (__pyx_v_num_chunks - 1);
     for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_12; __pyx_v_i++) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1494
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1507
  *             # outside edge constraints are checked later
  *             for i from 0 <= i < num_chunks-1:
  *                 if f_links_low[matching.arr[matching.start+i]+chunklen[i]-f_sent_start] == -1:             # <<<<<<<<<<<<<<
@@ -50867,7 +52475,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
       __pyx_t_7 = ((__pyx_v_f_links_low[(((__pyx_v_matching->arr[(__pyx_v_matching->start + __pyx_v_i)]) + (__pyx_v_chunklen[__pyx_v_i])) - __pyx_v_f_sent_start)]) == -1);
       if (__pyx_t_7) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1495
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1508
  *             for i from 0 <= i < num_chunks-1:
  *                 if f_links_low[matching.arr[matching.start+i]+chunklen[i]-f_sent_start] == -1:
  *                     reason_for_failure = "Gaps are not tight phrases"             # <<<<<<<<<<<<<<
@@ -50878,7 +52486,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         __Pyx_DECREF(__pyx_v_reason_for_failure);
         __pyx_v_reason_for_failure = ((PyObject *)__pyx_kp_s_128);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1496
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1509
  *                 if f_links_low[matching.arr[matching.start+i]+chunklen[i]-f_sent_start] == -1:
  *                     reason_for_failure = "Gaps are not tight phrases"
  *                     met_constraints = 0             # <<<<<<<<<<<<<<
@@ -50887,7 +52495,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         __pyx_v_met_constraints = 0;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1497
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1510
  *                     reason_for_failure = "Gaps are not tight phrases"
  *                     met_constraints = 0
  *                     break             # <<<<<<<<<<<<<<
@@ -50899,7 +52507,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
       }
       __pyx_L31:;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1498
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1511
  *                     met_constraints = 0
  *                     break
  *                 if f_links_low[matching.arr[matching.start+i+1]-1-f_sent_start] == -1:             # <<<<<<<<<<<<<<
@@ -50909,7 +52517,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
       __pyx_t_7 = ((__pyx_v_f_links_low[(((__pyx_v_matching->arr[((__pyx_v_matching->start + __pyx_v_i) + 1)]) - 1) - __pyx_v_f_sent_start)]) == -1);
       if (__pyx_t_7) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1499
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1512
  *                     break
  *                 if f_links_low[matching.arr[matching.start+i+1]-1-f_sent_start] == -1:
  *                     reason_for_failure = "Gaps are not tight phrases"             # <<<<<<<<<<<<<<
@@ -50920,7 +52528,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         __Pyx_DECREF(__pyx_v_reason_for_failure);
         __pyx_v_reason_for_failure = ((PyObject *)__pyx_kp_s_128);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1500
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1513
  *                 if f_links_low[matching.arr[matching.start+i+1]-1-f_sent_start] == -1:
  *                     reason_for_failure = "Gaps are not tight phrases"
  *                     met_constraints = 0             # <<<<<<<<<<<<<<
@@ -50929,7 +52537,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         __pyx_v_met_constraints = 0;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1501
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1514
  *                     reason_for_failure = "Gaps are not tight phrases"
  *                     met_constraints = 0
  *                     break             # <<<<<<<<<<<<<<
@@ -50946,7 +52554,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
   }
   __pyx_L28:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1503
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1516
  *                     break
  * 
  *         f_low = matching.arr[matching.start] - f_sent_start             # <<<<<<<<<<<<<<
@@ -50955,7 +52563,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   __pyx_v_f_low = ((__pyx_v_matching->arr[__pyx_v_matching->start]) - __pyx_v_f_sent_start);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1504
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1517
  * 
  *         f_low = matching.arr[matching.start] - f_sent_start
  *         f_high = matching.arr[matching.start + matching.size - 1] + chunklen[num_chunks-1] - f_sent_start             # <<<<<<<<<<<<<<
@@ -50964,7 +52572,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   __pyx_v_f_high = (((__pyx_v_matching->arr[((__pyx_v_matching->start + __pyx_v_matching->size) - 1)]) + (__pyx_v_chunklen[(__pyx_v_num_chunks - 1)])) - __pyx_v_f_sent_start);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1505
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1518
  *         f_low = matching.arr[matching.start] - f_sent_start
  *         f_high = matching.arr[matching.start + matching.size - 1] + chunklen[num_chunks-1] - f_sent_start
  *         if met_constraints:             # <<<<<<<<<<<<<<
@@ -50973,17 +52581,17 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
   if (__pyx_v_met_constraints) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1507
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1520
  *         if met_constraints:
  * 
  *             if self.find_fixpoint(f_low, f_high, f_links_low, f_links_high, e_links_low, e_links_high,             # <<<<<<<<<<<<<<
  *                                 -1, -1, &e_low, &e_high, &f_back_low, &f_back_high, f_sent_len, e_sent_len,
  *                                 self.train_max_initial_size, self.train_max_initial_size,
  */
-    __pyx_t_10 = PyInt_FromLong(__pyx_v_f_high); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1507; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_10 = PyInt_FromLong(__pyx_v_f_high); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1520; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_10);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1511
+    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1524
  *                                 self.train_max_initial_size, self.train_max_initial_size,
  *                                 self.train_min_gap_size, 0,
  *                                 self.max_nonterminals - num_chunks + 1, 1, 1, 0, 0):             # <<<<<<<<<<<<<<
@@ -50994,7 +52602,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
     __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
     if (__pyx_t_3) {
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1512
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1525
  *                                 self.train_min_gap_size, 0,
  *                                 self.max_nonterminals - num_chunks + 1, 1, 1, 0, 0):
  *                 gap_error = 0             # <<<<<<<<<<<<<<
@@ -51003,7 +52611,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
       __pyx_v_gap_error = 0;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1513
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1526
  *                                 self.max_nonterminals - num_chunks + 1, 1, 1, 0, 0):
  *                 gap_error = 0
  *                 num_gaps = 0             # <<<<<<<<<<<<<<
@@ -51012,7 +52620,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
       __pyx_v_num_gaps = 0;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1515
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1528
  *                 num_gaps = 0
  * 
  *                 if f_back_low < f_low:             # <<<<<<<<<<<<<<
@@ -51022,7 +52630,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
       __pyx_t_7 = (__pyx_v_f_back_low < __pyx_v_f_low);
       if (__pyx_t_7) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1516
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1529
  * 
  *                 if f_back_low < f_low:
  *                     f_gap_low[0] = f_back_low             # <<<<<<<<<<<<<<
@@ -51031,7 +52639,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         (__pyx_v_f_gap_low[0]) = __pyx_v_f_back_low;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1517
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1530
  *                 if f_back_low < f_low:
  *                     f_gap_low[0] = f_back_low
  *                     f_gap_high[0] = f_low             # <<<<<<<<<<<<<<
@@ -51040,7 +52648,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         (__pyx_v_f_gap_high[0]) = __pyx_v_f_low;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1518
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1531
  *                     f_gap_low[0] = f_back_low
  *                     f_gap_high[0] = f_low
  *                     num_gaps = 1             # <<<<<<<<<<<<<<
@@ -51049,7 +52657,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         __pyx_v_num_gaps = 1;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1519
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1532
  *                     f_gap_high[0] = f_low
  *                     num_gaps = 1
  *                     gap_start = 0             # <<<<<<<<<<<<<<
@@ -51058,7 +52666,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         __pyx_v_gap_start = 0;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1520
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1533
  *                     num_gaps = 1
  *                     gap_start = 0
  *                     phrase_len = phrase_len+1             # <<<<<<<<<<<<<<
@@ -51067,7 +52675,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         __pyx_v_phrase_len = (__pyx_v_phrase_len + 1);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1521
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1534
  *                     gap_start = 0
  *                     phrase_len = phrase_len+1
  *                     if phrase_len > self.max_length:             # <<<<<<<<<<<<<<
@@ -51077,7 +52685,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         __pyx_t_7 = (__pyx_v_phrase_len > __pyx_v_self->max_length);
         if (__pyx_t_7) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1522
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1535
  *                     phrase_len = phrase_len+1
  *                     if phrase_len > self.max_length:
  *                         gap_error = 1             # <<<<<<<<<<<<<<
@@ -51089,7 +52697,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         }
         __pyx_L36:;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1523
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1536
  *                     if phrase_len > self.max_length:
  *                         gap_error = 1
  *                     if self.tight_phrases:             # <<<<<<<<<<<<<<
@@ -51098,7 +52706,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         if (__pyx_v_self->tight_phrases) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1524
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1537
  *                         gap_error = 1
  *                     if self.tight_phrases:
  *                         if f_links_low[f_back_low] == -1 or f_links_low[f_low-1] == -1:             # <<<<<<<<<<<<<<
@@ -51114,7 +52722,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
           }
           if (__pyx_t_8) {
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1525
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1538
  *                     if self.tight_phrases:
  *                         if f_links_low[f_back_low] == -1 or f_links_low[f_low-1] == -1:
  *                             gap_error = 1             # <<<<<<<<<<<<<<
@@ -51123,7 +52731,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             __pyx_v_gap_error = 1;
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1526
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1539
  *                         if f_links_low[f_back_low] == -1 or f_links_low[f_low-1] == -1:
  *                             gap_error = 1
  *                             reason_for_failure = "Inside edges of preceding subphrase are not tight"             # <<<<<<<<<<<<<<
@@ -51143,7 +52751,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
       }
       /*else*/ {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1528
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1541
  *                             reason_for_failure = "Inside edges of preceding subphrase are not tight"
  *                 else:
  *                     gap_start = 1             # <<<<<<<<<<<<<<
@@ -51152,7 +52760,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         __pyx_v_gap_start = 1;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1529
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1542
  *                 else:
  *                     gap_start = 1
  *                     if self.tight_phrases and f_links_low[f_low] == -1:             # <<<<<<<<<<<<<<
@@ -51167,7 +52775,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         }
         if (__pyx_t_7) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1532
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1545
  *                         # this is not a hard error.    we can't extract this phrase
  *                         # but we still might be able to extract a superphrase
  *                         met_constraints = 0             # <<<<<<<<<<<<<<
@@ -51181,7 +52789,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
       }
       __pyx_L35:;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1534
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1547
  *                         met_constraints = 0
  * 
  *                 for i from 0 <= i < matching.size - 1:             # <<<<<<<<<<<<<<
@@ -51191,7 +52799,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
       __pyx_t_12 = (__pyx_v_matching->size - 1);
       for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_12; __pyx_v_i++) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1535
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1548
  * 
  *                 for i from 0 <= i < matching.size - 1:
  *                     f_gap_low[1+i] = matching.arr[matching.start+i] + chunklen[i] - f_sent_start             # <<<<<<<<<<<<<<
@@ -51200,7 +52808,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         (__pyx_v_f_gap_low[(1 + __pyx_v_i)]) = (((__pyx_v_matching->arr[(__pyx_v_matching->start + __pyx_v_i)]) + (__pyx_v_chunklen[__pyx_v_i])) - __pyx_v_f_sent_start);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1536
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1549
  *                 for i from 0 <= i < matching.size - 1:
  *                     f_gap_low[1+i] = matching.arr[matching.start+i] + chunklen[i] - f_sent_start
  *                     f_gap_high[1+i] = matching.arr[matching.start+i+1] - f_sent_start             # <<<<<<<<<<<<<<
@@ -51209,7 +52817,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         (__pyx_v_f_gap_high[(1 + __pyx_v_i)]) = ((__pyx_v_matching->arr[((__pyx_v_matching->start + __pyx_v_i) + 1)]) - __pyx_v_f_sent_start);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1537
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1550
  *                     f_gap_low[1+i] = matching.arr[matching.start+i] + chunklen[i] - f_sent_start
  *                     f_gap_high[1+i] = matching.arr[matching.start+i+1] - f_sent_start
  *                     num_gaps = num_gaps + 1             # <<<<<<<<<<<<<<
@@ -51219,7 +52827,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         __pyx_v_num_gaps = (__pyx_v_num_gaps + 1);
       }
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1539
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1552
  *                     num_gaps = num_gaps + 1
  * 
  *                 if f_high < f_back_high:             # <<<<<<<<<<<<<<
@@ -51229,7 +52837,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
       __pyx_t_7 = (__pyx_v_f_high < __pyx_v_f_back_high);
       if (__pyx_t_7) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1540
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1553
  * 
  *                 if f_high < f_back_high:
  *                     f_gap_low[gap_start+num_gaps] = f_high             # <<<<<<<<<<<<<<
@@ -51238,7 +52846,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         (__pyx_v_f_gap_low[(__pyx_v_gap_start + __pyx_v_num_gaps)]) = __pyx_v_f_high;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1541
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1554
  *                 if f_high < f_back_high:
  *                     f_gap_low[gap_start+num_gaps] = f_high
  *                     f_gap_high[gap_start+num_gaps] = f_back_high             # <<<<<<<<<<<<<<
@@ -51247,7 +52855,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         (__pyx_v_f_gap_high[(__pyx_v_gap_start + __pyx_v_num_gaps)]) = __pyx_v_f_back_high;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1542
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1555
  *                     f_gap_low[gap_start+num_gaps] = f_high
  *                     f_gap_high[gap_start+num_gaps] = f_back_high
  *                     num_gaps = num_gaps + 1             # <<<<<<<<<<<<<<
@@ -51256,7 +52864,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         __pyx_v_num_gaps = (__pyx_v_num_gaps + 1);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1543
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1556
  *                     f_gap_high[gap_start+num_gaps] = f_back_high
  *                     num_gaps = num_gaps + 1
  *                     phrase_len = phrase_len+1             # <<<<<<<<<<<<<<
@@ -51265,7 +52873,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         __pyx_v_phrase_len = (__pyx_v_phrase_len + 1);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1544
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1557
  *                     num_gaps = num_gaps + 1
  *                     phrase_len = phrase_len+1
  *                     if phrase_len > self.max_length:             # <<<<<<<<<<<<<<
@@ -51275,7 +52883,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         __pyx_t_7 = (__pyx_v_phrase_len > __pyx_v_self->max_length);
         if (__pyx_t_7) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1545
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1558
  *                     phrase_len = phrase_len+1
  *                     if phrase_len > self.max_length:
  *                         gap_error = 1             # <<<<<<<<<<<<<<
@@ -51287,7 +52895,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         }
         __pyx_L43:;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1546
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1559
  *                     if phrase_len > self.max_length:
  *                         gap_error = 1
  *                     if self.tight_phrases:             # <<<<<<<<<<<<<<
@@ -51296,7 +52904,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         if (__pyx_v_self->tight_phrases) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1547
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1560
  *                         gap_error = 1
  *                     if self.tight_phrases:
  *                         if f_links_low[f_back_high-1] == -1 or f_links_low[f_high] == -1:             # <<<<<<<<<<<<<<
@@ -51312,7 +52920,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
           }
           if (__pyx_t_9) {
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1548
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1561
  *                     if self.tight_phrases:
  *                         if f_links_low[f_back_high-1] == -1 or f_links_low[f_high] == -1:
  *                             gap_error = 1             # <<<<<<<<<<<<<<
@@ -51321,7 +52929,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             __pyx_v_gap_error = 1;
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1549
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1562
  *                         if f_links_low[f_back_high-1] == -1 or f_links_low[f_high] == -1:
  *                             gap_error = 1
  *                             reason_for_failure = "Inside edges of following subphrase are not tight"             # <<<<<<<<<<<<<<
@@ -51341,7 +52949,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
       }
       /*else*/ {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1551
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1564
  *                             reason_for_failure = "Inside edges of following subphrase are not tight"
  *                 else:
  *                     if self.tight_phrases and f_links_low[f_high-1] == -1:             # <<<<<<<<<<<<<<
@@ -51356,7 +52964,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         }
         if (__pyx_t_7) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1552
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1565
  *                 else:
  *                     if self.tight_phrases and f_links_low[f_high-1] == -1:
  *                         met_constraints = 0             # <<<<<<<<<<<<<<
@@ -51370,7 +52978,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
       }
       __pyx_L42:;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1554
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1567
  *                         met_constraints = 0
  * 
  *                 if gap_error == 0:             # <<<<<<<<<<<<<<
@@ -51380,7 +52988,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
       __pyx_t_7 = (__pyx_v_gap_error == 0);
       if (__pyx_t_7) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1555
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1568
  * 
  *                 if gap_error == 0:
  *                     e_word_count = e_high - e_low             # <<<<<<<<<<<<<<
@@ -51389,7 +52997,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         __pyx_v_e_word_count = (__pyx_v_e_high - __pyx_v_e_low);
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1556
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1569
  *                 if gap_error == 0:
  *                     e_word_count = e_high - e_low
  *                     for i from 0 <= i < num_gaps: # check integrity of subphrases             # <<<<<<<<<<<<<<
@@ -51399,17 +53007,17 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         __pyx_t_3 = __pyx_v_num_gaps;
         for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_3; __pyx_v_i++) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1557
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1570
  *                     e_word_count = e_high - e_low
  *                     for i from 0 <= i < num_gaps: # check integrity of subphrases
  *                         if self.find_fixpoint(f_gap_low[gap_start+i], f_gap_high[gap_start+i],             # <<<<<<<<<<<<<<
  *                                             f_links_low, f_links_high, e_links_low, e_links_high,
  *                                             -1, -1, e_gap_low+gap_start+i, e_gap_high+gap_start+i,
  */
-          __pyx_t_10 = PyInt_FromLong((__pyx_v_f_gap_high[(__pyx_v_gap_start + __pyx_v_i)])); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1557; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __pyx_t_10 = PyInt_FromLong((__pyx_v_f_gap_high[(__pyx_v_gap_start + __pyx_v_i)])); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1570; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           __Pyx_GOTREF(__pyx_t_10);
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1562
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1575
  *                                             f_gap_low+gap_start+i, f_gap_high+gap_start+i,
  *                                             f_sent_len, e_sent_len,
  *                                             self.train_max_initial_size, self.train_max_initial_size,             # <<<<<<<<<<<<<<
@@ -51420,7 +53028,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
           __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
           if (__pyx_t_7) {
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1564
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1577
  *                                             self.train_max_initial_size, self.train_max_initial_size,
  *                                             0, 0, 0, 0, 0, 0, 0) == 0:
  *                             gap_error = 1             # <<<<<<<<<<<<<<
@@ -51429,18 +53037,18 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             __pyx_v_gap_error = 1;
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1565
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1578
  *                                             0, 0, 0, 0, 0, 0, 0) == 0:
  *                             gap_error = 1
  *                             reason_for_failure = "Subphrase [%d, %d] failed integrity check" % (f_gap_low[gap_start+i], f_gap_high[gap_start+i])             # <<<<<<<<<<<<<<
  *                             break
  * 
  */
-            __pyx_t_10 = PyInt_FromLong((__pyx_v_f_gap_low[(__pyx_v_gap_start + __pyx_v_i)])); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1565; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_10 = PyInt_FromLong((__pyx_v_f_gap_low[(__pyx_v_gap_start + __pyx_v_i)])); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_10);
-            __pyx_t_1 = PyInt_FromLong((__pyx_v_f_gap_high[(__pyx_v_gap_start + __pyx_v_i)])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1565; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_1 = PyInt_FromLong((__pyx_v_f_gap_high[(__pyx_v_gap_start + __pyx_v_i)])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_1);
-            __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1565; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_2);
             PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_10);
             __Pyx_GIVEREF(__pyx_t_10);
@@ -51448,14 +53056,14 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             __Pyx_GIVEREF(__pyx_t_1);
             __pyx_t_10 = 0;
             __pyx_t_1 = 0;
-            __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_131), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1565; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_131), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(((PyObject *)__pyx_t_1));
             __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
             __Pyx_DECREF(__pyx_v_reason_for_failure);
             __pyx_v_reason_for_failure = ((PyObject *)__pyx_t_1);
             __pyx_t_1 = 0;
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1566
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1579
  *                             gap_error = 1
  *                             reason_for_failure = "Subphrase [%d, %d] failed integrity check" % (f_gap_low[gap_start+i], f_gap_high[gap_start+i])
  *                             break             # <<<<<<<<<<<<<<
@@ -51472,7 +53080,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
       }
       __pyx_L47:;
 
-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1568
+      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1581
  *                             break
  * 
  *                 if gap_error == 0:             # <<<<<<<<<<<<<<
@@ -51482,7 +53090,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
       __pyx_t_7 = (__pyx_v_gap_error == 0);
       if (__pyx_t_7) {
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1569
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1582
  * 
  *                 if gap_error == 0:
  *                     i = 1             # <<<<<<<<<<<<<<
@@ -51491,21 +53099,21 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         __pyx_v_i = 1;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1570
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1583
  *                 if gap_error == 0:
  *                     i = 1
  *                     self.findexes.reset()             # <<<<<<<<<<<<<<
  *                     if f_back_low < f_low:
  *                         fphr_arr._append(sym_setindex(self.category, i))
  */
-        __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes), __pyx_n_s__reset); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1570; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes), __pyx_n_s__reset); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1583; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_1);
-        __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1570; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1583; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_2);
         __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
         __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1571
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1584
  *                     i = 1
  *                     self.findexes.reset()
  *                     if f_back_low < f_low:             # <<<<<<<<<<<<<<
@@ -51515,7 +53123,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         __pyx_t_7 = (__pyx_v_f_back_low < __pyx_v_f_low);
         if (__pyx_t_7) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1572
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1585
  *                     self.findexes.reset()
  *                     if f_back_low < f_low:
  *                         fphr_arr._append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
@@ -51524,7 +53132,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
           ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_fphr_arr->__pyx_vtab)->_append(__pyx_v_fphr_arr, __pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i));
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1573
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1586
  *                     if f_back_low < f_low:
  *                         fphr_arr._append(sym_setindex(self.category, i))
  *                         i = i+1             # <<<<<<<<<<<<<<
@@ -51533,16 +53141,16 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
           __pyx_v_i = (__pyx_v_i + 1);
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1574
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1587
  *                         fphr_arr._append(sym_setindex(self.category, i))
  *                         i = i+1
  *                         self.findexes.append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
  *                     self.findexes.extend(self.findexes1)
  *                     for j from 0 <= j < phrase.n:
  */
-          __pyx_t_2 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1574; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __pyx_t_2 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1587; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           __Pyx_GOTREF(__pyx_t_2);
-          __pyx_t_1 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes), __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1574; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __pyx_t_1 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes), __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1587; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           __Pyx_GOTREF(__pyx_t_1);
           __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
           __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -51550,27 +53158,27 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         }
         __pyx_L52:;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1575
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1588
  *                         i = i+1
  *                         self.findexes.append(sym_setindex(self.category, i))
  *                     self.findexes.extend(self.findexes1)             # <<<<<<<<<<<<<<
  *                     for j from 0 <= j < phrase.n:
  *                         if sym_isvar(phrase.syms[j]):
  */
-        __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes), __pyx_n_s__extend); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1575; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes), __pyx_n_s__extend); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1588; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_1);
-        __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1575; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1588; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_2);
         __Pyx_INCREF(((PyObject *)__pyx_v_self->findexes1));
         PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_self->findexes1));
         __Pyx_GIVEREF(((PyObject *)__pyx_v_self->findexes1));
-        __pyx_t_10 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1575; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_10 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1588; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_10);
         __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
         __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
         __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1576
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1589
  *                         self.findexes.append(sym_setindex(self.category, i))
  *                     self.findexes.extend(self.findexes1)
  *                     for j from 0 <= j < phrase.n:             # <<<<<<<<<<<<<<
@@ -51580,7 +53188,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         __pyx_t_3 = __pyx_v_phrase->n;
         for (__pyx_v_j = 0; __pyx_v_j < __pyx_t_3; __pyx_v_j++) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1577
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1590
  *                     self.findexes.extend(self.findexes1)
  *                     for j from 0 <= j < phrase.n:
  *                         if sym_isvar(phrase.syms[j]):             # <<<<<<<<<<<<<<
@@ -51590,7 +53198,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
           __pyx_t_4 = __pyx_f_3_sa_sym_isvar((__pyx_v_phrase->syms[__pyx_v_j]));
           if (__pyx_t_4) {
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1578
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1591
  *                     for j from 0 <= j < phrase.n:
  *                         if sym_isvar(phrase.syms[j]):
  *                             fphr_arr._append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
@@ -51599,7 +53207,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_fphr_arr->__pyx_vtab)->_append(__pyx_v_fphr_arr, __pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i));
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1579
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1592
  *                         if sym_isvar(phrase.syms[j]):
  *                             fphr_arr._append(sym_setindex(self.category, i))
  *                             i = i + 1             # <<<<<<<<<<<<<<
@@ -51611,7 +53219,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
           }
           /*else*/ {
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1581
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1594
  *                             i = i + 1
  *                         else:
  *                             fphr_arr._append(phrase.syms[j])             # <<<<<<<<<<<<<<
@@ -51623,7 +53231,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
           __pyx_L55:;
         }
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1582
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1595
  *                         else:
  *                             fphr_arr._append(phrase.syms[j])
  *                     if f_back_high > f_high:             # <<<<<<<<<<<<<<
@@ -51633,7 +53241,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         __pyx_t_7 = (__pyx_v_f_back_high > __pyx_v_f_high);
         if (__pyx_t_7) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1583
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1596
  *                             fphr_arr._append(phrase.syms[j])
  *                     if f_back_high > f_high:
  *                         fphr_arr._append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
@@ -51642,16 +53250,16 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
           ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_fphr_arr->__pyx_vtab)->_append(__pyx_v_fphr_arr, __pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i));
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1584
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1597
  *                     if f_back_high > f_high:
  *                         fphr_arr._append(sym_setindex(self.category, i))
  *                         self.findexes.append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
  * 
  *                     fphr = Phrase(fphr_arr)
  */
-          __pyx_t_10 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i)); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1584; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __pyx_t_10 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i)); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           __Pyx_GOTREF(__pyx_t_10);
-          __pyx_t_2 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes), __pyx_t_10); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1584; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __pyx_t_2 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes), __pyx_t_10); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           __Pyx_GOTREF(__pyx_t_2);
           __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
           __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -51659,25 +53267,25 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         }
         __pyx_L56:;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1586
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1599
  *                         self.findexes.append(sym_setindex(self.category, i))
  * 
  *                     fphr = Phrase(fphr_arr)             # <<<<<<<<<<<<<<
  *                     if met_constraints:
  *                         phrase_list = self.extract_phrases(e_low, e_high, e_gap_low + gap_start, e_gap_high + gap_start, e_links_low, num_gaps,
  */
-        __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1586; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1599; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_2);
         __Pyx_INCREF(((PyObject *)__pyx_v_fphr_arr));
         PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_fphr_arr));
         __Pyx_GIVEREF(((PyObject *)__pyx_v_fphr_arr));
-        __pyx_t_10 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_Phrase)), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1586; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_10 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_Phrase)), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1599; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_10);
         __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
         __pyx_v_fphr = ((struct __pyx_obj_3_sa_Phrase *)__pyx_t_10);
         __pyx_t_10 = 0;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1587
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1600
  * 
  *                     fphr = Phrase(fphr_arr)
  *                     if met_constraints:             # <<<<<<<<<<<<<<
@@ -51686,47 +53294,47 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
         if (__pyx_v_met_constraints) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1590
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1603
  *                         phrase_list = self.extract_phrases(e_low, e_high, e_gap_low + gap_start, e_gap_high + gap_start, e_links_low, num_gaps,
  *                                             f_back_low, f_back_high, f_gap_low + gap_start, f_gap_high + gap_start, f_links_low,
  *                                             matching.sent_id, e_sent_len, e_sent_start)             # <<<<<<<<<<<<<<
  *                         if len(phrase_list) > 0:
  *                             pair_count = 1.0 / len(phrase_list)
  */
-          __pyx_t_10 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->extract_phrases(__pyx_v_self, __pyx_v_e_low, __pyx_v_e_high, (__pyx_v_e_gap_low + __pyx_v_gap_start), (__pyx_v_e_gap_high + __pyx_v_gap_start), __pyx_v_e_links_low, __pyx_v_num_gaps, __pyx_v_f_back_low, __pyx_v_f_back_high, (__pyx_v_f_gap_low + __pyx_v_gap_start), (__pyx_v_f_gap_high + __pyx_v_gap_start), __pyx_v_f_links_low, __pyx_v_matching->sent_id, __pyx_v_e_sent_len, __pyx_v_e_sent_start); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1588; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __pyx_t_10 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->extract_phrases(__pyx_v_self, __pyx_v_e_low, __pyx_v_e_high, (__pyx_v_e_gap_low + __pyx_v_gap_start), (__pyx_v_e_gap_high + __pyx_v_gap_start), __pyx_v_e_links_low, __pyx_v_num_gaps, __pyx_v_f_back_low, __pyx_v_f_back_high, (__pyx_v_f_gap_low + __pyx_v_gap_start), (__pyx_v_f_gap_high + __pyx_v_gap_start), __pyx_v_f_links_low, __pyx_v_matching->sent_id, __pyx_v_e_sent_len, __pyx_v_e_sent_start); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1601; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           __Pyx_GOTREF(__pyx_t_10);
           __pyx_v_phrase_list = __pyx_t_10;
           __pyx_t_10 = 0;
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1591
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1604
  *                                             f_back_low, f_back_high, f_gap_low + gap_start, f_gap_high + gap_start, f_links_low,
  *                                             matching.sent_id, e_sent_len, e_sent_start)
  *                         if len(phrase_list) > 0:             # <<<<<<<<<<<<<<
  *                             pair_count = 1.0 / len(phrase_list)
  *                         else:
  */
-          __pyx_t_13 = PyObject_Length(__pyx_v_phrase_list); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1591; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          __pyx_t_13 = PyObject_Length(__pyx_v_phrase_list); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
           __pyx_t_7 = (__pyx_t_13 > 0);
           if (__pyx_t_7) {
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1592
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1605
  *                                             matching.sent_id, e_sent_len, e_sent_start)
  *                         if len(phrase_list) > 0:
  *                             pair_count = 1.0 / len(phrase_list)             # <<<<<<<<<<<<<<
  *                         else:
  *                             pair_count = 0
  */
-            __pyx_t_13 = PyObject_Length(__pyx_v_phrase_list); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1592; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_13 = PyObject_Length(__pyx_v_phrase_list); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1605; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             if (unlikely(__pyx_t_13 == 0)) {
               PyErr_Format(PyExc_ZeroDivisionError, "float division");
-              {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1592; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1605; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             }
             __pyx_v_pair_count = (1.0 / __pyx_t_13);
             goto __pyx_L58;
           }
           /*else*/ {
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1594
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1607
  *                             pair_count = 1.0 / len(phrase_list)
  *                         else:
  *                             pair_count = 0             # <<<<<<<<<<<<<<
@@ -51735,22 +53343,22 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             __pyx_v_pair_count = 0.0;
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1595
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1608
  *                         else:
  *                             pair_count = 0
  *                             reason_for_failure = "Didn't extract anything from [%d, %d] -> [%d, %d]" % (f_back_low, f_back_high, e_low, e_high)             # <<<<<<<<<<<<<<
  *                         for (phrase2,eindexes) in phrase_list:
  *                             als1 = self.create_alignments(sent_links,num_links,self.findexes,eindexes)
  */
-            __pyx_t_10 = PyInt_FromLong(__pyx_v_f_back_low); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1595; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_10 = PyInt_FromLong(__pyx_v_f_back_low); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_10);
-            __pyx_t_2 = PyInt_FromLong(__pyx_v_f_back_high); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1595; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_2 = PyInt_FromLong(__pyx_v_f_back_high); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_2);
-            __pyx_t_1 = PyInt_FromLong(__pyx_v_e_low); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1595; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_1 = PyInt_FromLong(__pyx_v_e_low); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_1);
-            __pyx_t_14 = PyInt_FromLong(__pyx_v_e_high); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1595; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_14 = PyInt_FromLong(__pyx_v_e_high); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_14);
-            __pyx_t_15 = PyTuple_New(4); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1595; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_15 = PyTuple_New(4); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_15);
             PyTuple_SET_ITEM(__pyx_t_15, 0, __pyx_t_10);
             __Pyx_GIVEREF(__pyx_t_10);
@@ -51764,7 +53372,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             __pyx_t_2 = 0;
             __pyx_t_1 = 0;
             __pyx_t_14 = 0;
-            __pyx_t_14 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_132), ((PyObject *)__pyx_t_15)); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1595; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_14 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_132), ((PyObject *)__pyx_t_15)); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(((PyObject *)__pyx_t_14));
             __Pyx_DECREF(((PyObject *)__pyx_t_15)); __pyx_t_15 = 0;
             __Pyx_DECREF(__pyx_v_reason_for_failure);
@@ -51773,7 +53381,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
           }
           __pyx_L58:;
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1596
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1609
  *                             pair_count = 0
  *                             reason_for_failure = "Didn't extract anything from [%d, %d] -> [%d, %d]" % (f_back_low, f_back_high, e_low, e_high)
  *                         for (phrase2,eindexes) in phrase_list:             # <<<<<<<<<<<<<<
@@ -51784,7 +53392,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
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             __pyx_t_16 = NULL;
           } else {
-            __pyx_t_13 = -1; __pyx_t_14 = PyObject_GetIter(__pyx_v_phrase_list); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1596; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_13 = -1; __pyx_t_14 = PyObject_GetIter(__pyx_v_phrase_list); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_14);
             __pyx_t_16 = Py_TYPE(__pyx_t_14)->tp_iternext;
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@@ -51792,23 +53400,23 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             if (!__pyx_t_16 && PyList_CheckExact(__pyx_t_14)) {
               if (__pyx_t_13 >= PyList_GET_SIZE(__pyx_t_14)) break;
               #if CYTHON_COMPILING_IN_CPYTHON
-              __pyx_t_15 = PyList_GET_ITEM(__pyx_t_14, __pyx_t_13); __Pyx_INCREF(__pyx_t_15); __pyx_t_13++;
+              __pyx_t_15 = PyList_GET_ITEM(__pyx_t_14, __pyx_t_13); __Pyx_INCREF(__pyx_t_15); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               #else
-              __pyx_t_15 = PySequence_ITEM(__pyx_t_14, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1596; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+              __pyx_t_15 = PySequence_ITEM(__pyx_t_14, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               #endif
             } else if (!__pyx_t_16 && PyTuple_CheckExact(__pyx_t_14)) {
               if (__pyx_t_13 >= PyTuple_GET_SIZE(__pyx_t_14)) break;
               #if CYTHON_COMPILING_IN_CPYTHON
-              __pyx_t_15 = PyTuple_GET_ITEM(__pyx_t_14, __pyx_t_13); __Pyx_INCREF(__pyx_t_15); __pyx_t_13++;
+              __pyx_t_15 = PyTuple_GET_ITEM(__pyx_t_14, __pyx_t_13); __Pyx_INCREF(__pyx_t_15); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               #else
-              __pyx_t_15 = PySequence_ITEM(__pyx_t_14, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1596; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+              __pyx_t_15 = PySequence_ITEM(__pyx_t_14, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               #endif
             } else {
               __pyx_t_15 = __pyx_t_16(__pyx_t_14);
               if (unlikely(!__pyx_t_15)) {
                 if (PyErr_Occurred()) {
                   if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
-                  else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1596; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 }
                 break;
               }
@@ -51824,7 +53432,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
               if (unlikely(size != 2)) {
                 if (size > 2) __Pyx_RaiseTooManyValuesError(2);
                 else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
-                {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1596; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               }
               #if CYTHON_COMPILING_IN_CPYTHON
               if (likely(PyTuple_CheckExact(sequence))) {
@@ -51837,14 +53445,14 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
               __Pyx_INCREF(__pyx_t_1);
               __Pyx_INCREF(__pyx_t_2);
               #else
-              __pyx_t_1 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1596; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-              __pyx_t_2 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1596; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_1 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_2 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               #endif
               __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
             } else
             {
               Py_ssize_t index = -1;
-              __pyx_t_10 = PyObject_GetIter(__pyx_t_15); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1596; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_10 = PyObject_GetIter(__pyx_t_15); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_10);
               __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
               __pyx_t_17 = Py_TYPE(__pyx_t_10)->tp_iternext;
@@ -51852,7 +53460,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
               __Pyx_GOTREF(__pyx_t_1);
               index = 1; __pyx_t_2 = __pyx_t_17(__pyx_t_10); if (unlikely(!__pyx_t_2)) goto __pyx_L61_unpacking_failed;
               __Pyx_GOTREF(__pyx_t_2);
-              if (__Pyx_IternextUnpackEndCheck(__pyx_t_17(__pyx_t_10), 2) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1596; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              if (__Pyx_IternextUnpackEndCheck(__pyx_t_17(__pyx_t_10), 2) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __pyx_t_17 = NULL;
               __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
               goto __pyx_L62_unpacking_done;
@@ -51860,7 +53468,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
               __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
               __pyx_t_17 = NULL;
               if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
-              {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1596; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __pyx_L62_unpacking_done:;
             }
             __Pyx_XDECREF(__pyx_v_phrase2);
@@ -51870,7 +53478,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             __pyx_v_eindexes = __pyx_t_2;
             __pyx_t_2 = 0;
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1597
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1610
  *                             reason_for_failure = "Didn't extract anything from [%d, %d] -> [%d, %d]" % (f_back_low, f_back_high, e_low, e_high)
  *                         for (phrase2,eindexes) in phrase_list:
  *                             als1 = self.create_alignments(sent_links,num_links,self.findexes,eindexes)             # <<<<<<<<<<<<<<
@@ -51879,31 +53487,31 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             __pyx_t_15 = ((PyObject *)__pyx_v_self->findexes);
             __Pyx_INCREF(__pyx_t_15);
-            __pyx_t_2 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->create_alignments(__pyx_v_self, __pyx_v_sent_links, __pyx_v_num_links, __pyx_t_15, __pyx_v_eindexes); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_2 = ((PyObject *)((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->create_alignments(__pyx_v_self, __pyx_v_sent_links, __pyx_v_num_links, __pyx_t_15, __pyx_v_eindexes)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_2);
             __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
-            __Pyx_XDECREF(__pyx_v_als1);
-            __pyx_v_als1 = __pyx_t_2;
+            __Pyx_XDECREF(((PyObject *)__pyx_v_als1));
+            __pyx_v_als1 = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_2);
             __pyx_t_2 = 0;
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1598
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1611
  *                         for (phrase2,eindexes) in phrase_list:
  *                             als1 = self.create_alignments(sent_links,num_links,self.findexes,eindexes)
  *                             extracts.append((fphr, phrase2, pair_count, tuple(als1)))             # <<<<<<<<<<<<<<
  * 
  *                     if (num_gaps < self.max_nonterminals and
  */
-            __pyx_t_2 = PyFloat_FromDouble(__pyx_v_pair_count); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_2 = PyFloat_FromDouble(__pyx_v_pair_count); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_2);
-            __pyx_t_15 = PyTuple_New(1); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_15 = PyTuple_New(1); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_15);
-            __Pyx_INCREF(__pyx_v_als1);
-            PyTuple_SET_ITEM(__pyx_t_15, 0, __pyx_v_als1);
-            __Pyx_GIVEREF(__pyx_v_als1);
-            __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)(&PyTuple_Type))), ((PyObject *)__pyx_t_15), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __Pyx_INCREF(((PyObject *)__pyx_v_als1));
+            PyTuple_SET_ITEM(__pyx_t_15, 0, ((PyObject *)__pyx_v_als1));
+            __Pyx_GIVEREF(((PyObject *)__pyx_v_als1));
+            __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)(&PyTuple_Type))), ((PyObject *)__pyx_t_15), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_1);
             __Pyx_DECREF(((PyObject *)__pyx_t_15)); __pyx_t_15 = 0;
-            __pyx_t_15 = PyTuple_New(4); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_15 = PyTuple_New(4); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_15);
             __Pyx_INCREF(((PyObject *)__pyx_v_fphr));
             PyTuple_SET_ITEM(__pyx_t_15, 0, ((PyObject *)__pyx_v_fphr));
@@ -51917,7 +53525,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             __Pyx_GIVEREF(__pyx_t_1);
             __pyx_t_2 = 0;
             __pyx_t_1 = 0;
-            __pyx_t_1 = __Pyx_PyObject_Append(__pyx_v_extracts, ((PyObject *)__pyx_t_15)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            __pyx_t_1 = __Pyx_PyObject_Append(__pyx_v_extracts, ((PyObject *)__pyx_t_15)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             __Pyx_GOTREF(__pyx_t_1);
             __Pyx_DECREF(((PyObject *)__pyx_t_15)); __pyx_t_15 = 0;
             __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -51927,7 +53535,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         }
         __pyx_L57:;
 
-        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1600
+        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1613
  *                             extracts.append((fphr, phrase2, pair_count, tuple(als1)))
  * 
  *                     if (num_gaps < self.max_nonterminals and             # <<<<<<<<<<<<<<
@@ -51937,7 +53545,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         __pyx_t_7 = (__pyx_v_num_gaps < __pyx_v_self->max_nonterminals);
         if (__pyx_t_7) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1601
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1614
  * 
  *                     if (num_gaps < self.max_nonterminals and
  *                         phrase_len < self.max_length and             # <<<<<<<<<<<<<<
@@ -51947,7 +53555,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
           __pyx_t_9 = (__pyx_v_phrase_len < __pyx_v_self->max_length);
           if (__pyx_t_9) {
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1602
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1615
  *                     if (num_gaps < self.max_nonterminals and
  *                         phrase_len < self.max_length and
  *                         f_back_high - f_back_low + self.train_min_gap_size <= self.train_max_initial_size):             # <<<<<<<<<<<<<<
@@ -51965,7 +53573,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
         }
         if (__pyx_t_9) {
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1603
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1616
  *                         phrase_len < self.max_length and
  *                         f_back_high - f_back_low + self.train_min_gap_size <= self.train_max_initial_size):
  *                         if (f_back_low == f_low and             # <<<<<<<<<<<<<<
@@ -51975,7 +53583,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
           __pyx_t_9 = (__pyx_v_f_back_low == __pyx_v_f_low);
           if (__pyx_t_9) {
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1604
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1617
  *                         f_back_high - f_back_low + self.train_min_gap_size <= self.train_max_initial_size):
  *                         if (f_back_low == f_low and
  *                                 f_low >= self.train_min_gap_size and             # <<<<<<<<<<<<<<
@@ -51985,7 +53593,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             __pyx_t_7 = (__pyx_v_f_low >= __pyx_v_self->train_min_gap_size);
             if (__pyx_t_7) {
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1605
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1618
  *                         if (f_back_low == f_low and
  *                                 f_low >= self.train_min_gap_size and
  *                                 ((not self.tight_phrases) or (f_links_low[f_low-1] != -1 and f_links_low[f_back_high-1] != -1))):             # <<<<<<<<<<<<<<
@@ -52015,7 +53623,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
           }
           if (__pyx_t_7) {
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1606
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1619
  *                                 f_low >= self.train_min_gap_size and
  *                                 ((not self.tight_phrases) or (f_links_low[f_low-1] != -1 and f_links_low[f_back_high-1] != -1))):
  *                             f_x_low = f_low-self.train_min_gap_size             # <<<<<<<<<<<<<<
@@ -52024,7 +53632,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             __pyx_v_f_x_low = (__pyx_v_f_low - __pyx_v_self->train_min_gap_size);
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1607
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1620
  *                                 ((not self.tight_phrases) or (f_links_low[f_low-1] != -1 and f_links_low[f_back_high-1] != -1))):
  *                             f_x_low = f_low-self.train_min_gap_size
  *                             met_constraints = 1             # <<<<<<<<<<<<<<
@@ -52033,7 +53641,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             __pyx_v_met_constraints = 1;
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1608
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1621
  *                             f_x_low = f_low-self.train_min_gap_size
  *                             met_constraints = 1
  *                             if self.tight_phrases:             # <<<<<<<<<<<<<<
@@ -52042,7 +53650,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             if (__pyx_v_self->tight_phrases) {
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1609
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1622
  *                             met_constraints = 1
  *                             if self.tight_phrases:
  *                                 while f_x_low >= 0 and f_links_low[f_x_low] == -1:             # <<<<<<<<<<<<<<
@@ -52059,7 +53667,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 }
                 if (!__pyx_t_18) break;
 
-                /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1610
+                /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1623
  *                             if self.tight_phrases:
  *                                 while f_x_low >= 0 and f_links_low[f_x_low] == -1:
  *                                     f_x_low = f_x_low - 1             # <<<<<<<<<<<<<<
@@ -52072,7 +53680,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             }
             __pyx_L65:;
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1611
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1624
  *                                 while f_x_low >= 0 and f_links_low[f_x_low] == -1:
  *                                     f_x_low = f_x_low - 1
  *                             if f_x_low < 0 or f_back_high - f_x_low > self.train_max_initial_size:             # <<<<<<<<<<<<<<
@@ -52088,7 +53696,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             }
             if (__pyx_t_9) {
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1612
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1625
  *                                     f_x_low = f_x_low - 1
  *                             if f_x_low < 0 or f_back_high - f_x_low > self.train_max_initial_size:
  *                                 met_constraints = 0             # <<<<<<<<<<<<<<
@@ -52100,7 +53708,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             }
             __pyx_L68:;
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1614
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1627
  *                                 met_constraints = 0
  * 
  *                             if (met_constraints and             # <<<<<<<<<<<<<<
@@ -52109,17 +53717,17 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             if (__pyx_v_met_constraints) {
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1615
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1628
  * 
  *                             if (met_constraints and
  *                                 self.find_fixpoint(f_x_low, f_back_high,             # <<<<<<<<<<<<<<
  *                                             f_links_low, f_links_high, e_links_low, e_links_high,
  *                                             e_low, e_high, &e_x_low, &e_x_high, &f_x_low, &f_x_high,
  */
-              __pyx_t_14 = PyInt_FromLong(__pyx_v_f_back_high); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1615; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_14 = PyInt_FromLong(__pyx_v_f_back_high); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_14);
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1619
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1632
  *                                             e_low, e_high, &e_x_low, &e_x_high, &f_x_low, &f_x_high,
  *                                             f_sent_len, e_sent_len,
  *                                             self.train_max_initial_size, self.train_max_initial_size,             # <<<<<<<<<<<<<<
@@ -52129,7 +53737,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
               if (((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_fixpoint(__pyx_v_self, __pyx_v_f_x_low, __pyx_t_14, __pyx_v_f_links_low, __pyx_v_f_links_high, __pyx_v_e_links_low, __pyx_v_e_links_high, __pyx_v_e_low, __pyx_v_e_high, (&__pyx_v_e_x_low), (&__pyx_v_e_x_high), (&__pyx_v_f_x_low), (&__pyx_v_f_x_high), __pyx_v_f_sent_len, __pyx_v_e_sent_len, __pyx_v_self->train_max_initial_size, __pyx_v_self->train_max_initial_size, 1, 1, 1, 1, 0, 1, 0)) {
                 __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
 
-                /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1621
+                /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1634
  *                                             self.train_max_initial_size, self.train_max_initial_size,
  *                                             1, 1, 1, 1, 0, 1, 0) and
  *                                 ((not self.tight_phrases) or f_links_low[f_x_low] != -1) and             # <<<<<<<<<<<<<<
@@ -52145,17 +53753,17 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 }
                 if (__pyx_t_7) {
 
-                  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1622
+                  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1635
  *                                             1, 1, 1, 1, 0, 1, 0) and
  *                                 ((not self.tight_phrases) or f_links_low[f_x_low] != -1) and
  *                                 self.find_fixpoint(f_x_low, f_low,    # check integrity of new subphrase             # <<<<<<<<<<<<<<
  *                                             f_links_low, f_links_high, e_links_low, e_links_high,
  *                                             -1, -1, e_gap_low, e_gap_high, f_gap_low, f_gap_high,
  */
-                  __pyx_t_1 = PyInt_FromLong(__pyx_v_f_low); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  __pyx_t_1 = PyInt_FromLong(__pyx_v_f_low); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1635; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                   __Pyx_GOTREF(__pyx_t_1);
 
-                  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1626
+                  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1639
  *                                             -1, -1, e_gap_low, e_gap_high, f_gap_low, f_gap_high,
  *                                             f_sent_len, e_sent_len,
  *                                             self.train_max_initial_size, self.train_max_initial_size,             # <<<<<<<<<<<<<<
@@ -52178,7 +53786,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             }
             if (__pyx_t_9) {
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1628
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1641
  *                                             self.train_max_initial_size, self.train_max_initial_size,
  *                                             0, 0, 0, 0, 0, 0, 0)):
  *                                 fphr_arr._clear()             # <<<<<<<<<<<<<<
@@ -52187,7 +53795,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
               ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_fphr_arr->__pyx_vtab)->_clear(__pyx_v_fphr_arr);
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1629
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1642
  *                                             0, 0, 0, 0, 0, 0, 0)):
  *                                 fphr_arr._clear()
  *                                 i = 1             # <<<<<<<<<<<<<<
@@ -52196,35 +53804,35 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
               __pyx_v_i = 1;
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1630
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1643
  *                                 fphr_arr._clear()
  *                                 i = 1
  *                                 self.findexes.reset()             # <<<<<<<<<<<<<<
  *                                 self.findexes.append(sym_setindex(self.category, i))
  *                                 fphr_arr._append(sym_setindex(self.category, i))
  */
-              __pyx_t_14 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes), __pyx_n_s__reset); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_14 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes), __pyx_n_s__reset); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1643; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_14);
-              __pyx_t_1 = PyObject_Call(__pyx_t_14, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_1 = PyObject_Call(__pyx_t_14, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1643; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_1);
               __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
               __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1631
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1644
  *                                 i = 1
  *                                 self.findexes.reset()
  *                                 self.findexes.append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
  *                                 fphr_arr._append(sym_setindex(self.category, i))
  *                                 i = i+1
  */
-              __pyx_t_1 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1631; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_1 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1644; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_1);
-              __pyx_t_14 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes), __pyx_t_1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1631; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_14 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes), __pyx_t_1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1644; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_14);
               __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
               __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1632
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1645
  *                                 self.findexes.reset()
  *                                 self.findexes.append(sym_setindex(self.category, i))
  *                                 fphr_arr._append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
@@ -52233,7 +53841,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
               ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_fphr_arr->__pyx_vtab)->_append(__pyx_v_fphr_arr, __pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i));
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1633
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1646
  *                                 self.findexes.append(sym_setindex(self.category, i))
  *                                 fphr_arr._append(sym_setindex(self.category, i))
  *                                 i = i+1             # <<<<<<<<<<<<<<
@@ -52242,27 +53850,27 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
               __pyx_v_i = (__pyx_v_i + 1);
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1634
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1647
  *                                 fphr_arr._append(sym_setindex(self.category, i))
  *                                 i = i+1
  *                                 self.findexes.extend(self.findexes1)             # <<<<<<<<<<<<<<
  *                                 for j from 0 <= j < phrase.n:
  *                                     if sym_isvar(phrase.syms[j]):
  */
-              __pyx_t_14 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes), __pyx_n_s__extend); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1634; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_14 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes), __pyx_n_s__extend); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_14);
-              __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1634; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_1);
               __Pyx_INCREF(((PyObject *)__pyx_v_self->findexes1));
               PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_v_self->findexes1));
               __Pyx_GIVEREF(((PyObject *)__pyx_v_self->findexes1));
-              __pyx_t_15 = PyObject_Call(__pyx_t_14, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1634; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_15 = PyObject_Call(__pyx_t_14, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_15);
               __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
               __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
               __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1635
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1648
  *                                 i = i+1
  *                                 self.findexes.extend(self.findexes1)
  *                                 for j from 0 <= j < phrase.n:             # <<<<<<<<<<<<<<
@@ -52272,7 +53880,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
               __pyx_t_3 = __pyx_v_phrase->n;
               for (__pyx_v_j = 0; __pyx_v_j < __pyx_t_3; __pyx_v_j++) {
 
-                /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1636
+                /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1649
  *                                 self.findexes.extend(self.findexes1)
  *                                 for j from 0 <= j < phrase.n:
  *                                     if sym_isvar(phrase.syms[j]):             # <<<<<<<<<<<<<<
@@ -52282,7 +53890,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 __pyx_t_4 = __pyx_f_3_sa_sym_isvar((__pyx_v_phrase->syms[__pyx_v_j]));
                 if (__pyx_t_4) {
 
-                  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1637
+                  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1650
  *                                 for j from 0 <= j < phrase.n:
  *                                     if sym_isvar(phrase.syms[j]):
  *                                         fphr_arr._append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
@@ -52291,7 +53899,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
                   ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_fphr_arr->__pyx_vtab)->_append(__pyx_v_fphr_arr, __pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i));
 
-                  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1638
+                  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1651
  *                                     if sym_isvar(phrase.syms[j]):
  *                                         fphr_arr._append(sym_setindex(self.category, i))
  *                                         i = i + 1             # <<<<<<<<<<<<<<
@@ -52303,7 +53911,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 }
                 /*else*/ {
 
-                  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1640
+                  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1653
  *                                         i = i + 1
  *                                     else:
  *                                         fphr_arr._append(phrase.syms[j])             # <<<<<<<<<<<<<<
@@ -52315,7 +53923,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 __pyx_L72:;
               }
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1641
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1654
  *                                     else:
  *                                         fphr_arr._append(phrase.syms[j])
  *                                 if f_back_high > f_high:             # <<<<<<<<<<<<<<
@@ -52325,7 +53933,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
               __pyx_t_9 = (__pyx_v_f_back_high > __pyx_v_f_high);
               if (__pyx_t_9) {
 
-                /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1642
+                /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1655
  *                                         fphr_arr._append(phrase.syms[j])
  *                                 if f_back_high > f_high:
  *                                     fphr_arr._append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
@@ -52334,16 +53942,16 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
                 ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_fphr_arr->__pyx_vtab)->_append(__pyx_v_fphr_arr, __pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i));
 
-                /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1643
+                /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1656
  *                                 if f_back_high > f_high:
  *                                     fphr_arr._append(sym_setindex(self.category, i))
  *                                     self.findexes.append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
  *                                 fphr = Phrase(fphr_arr)
  *                                 phrase_list = self.extract_phrases(e_x_low, e_x_high, e_gap_low, e_gap_high, e_links_low, num_gaps+1,
  */
-                __pyx_t_15 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i)); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1643; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_15 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i)); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1656; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_15);
-                __pyx_t_1 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes), __pyx_t_15); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1643; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_1 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes), __pyx_t_15); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1656; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_1);
                 __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
                 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -52351,67 +53959,67 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
               }
               __pyx_L73:;
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1644
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1657
  *                                     fphr_arr._append(sym_setindex(self.category, i))
  *                                     self.findexes.append(sym_setindex(self.category, i))
  *                                 fphr = Phrase(fphr_arr)             # <<<<<<<<<<<<<<
  *                                 phrase_list = self.extract_phrases(e_x_low, e_x_high, e_gap_low, e_gap_high, e_links_low, num_gaps+1,
  *                                                     f_x_low, f_x_high, f_gap_low, f_gap_high, f_links_low, matching.sent_id,
  */
-              __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1644; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1657; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_1);
               __Pyx_INCREF(((PyObject *)__pyx_v_fphr_arr));
               PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_v_fphr_arr));
               __Pyx_GIVEREF(((PyObject *)__pyx_v_fphr_arr));
-              __pyx_t_15 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_Phrase)), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1644; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_15 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_Phrase)), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1657; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_15);
               __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
               __Pyx_DECREF(((PyObject *)__pyx_v_fphr));
               __pyx_v_fphr = ((struct __pyx_obj_3_sa_Phrase *)__pyx_t_15);
               __pyx_t_15 = 0;
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1647
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1660
  *                                 phrase_list = self.extract_phrases(e_x_low, e_x_high, e_gap_low, e_gap_high, e_links_low, num_gaps+1,
  *                                                     f_x_low, f_x_high, f_gap_low, f_gap_high, f_links_low, matching.sent_id,
  *                                                     e_sent_len, e_sent_start)             # <<<<<<<<<<<<<<
  *                                 if len(phrase_list) > 0:
  *                                     pair_count = 1.0 / len(phrase_list)
  */
-              __pyx_t_15 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->extract_phrases(__pyx_v_self, __pyx_v_e_x_low, __pyx_v_e_x_high, __pyx_v_e_gap_low, __pyx_v_e_gap_high, __pyx_v_e_links_low, (__pyx_v_num_gaps + 1), __pyx_v_f_x_low, __pyx_v_f_x_high, __pyx_v_f_gap_low, __pyx_v_f_gap_high, __pyx_v_f_links_low, __pyx_v_matching->sent_id, __pyx_v_e_sent_len, __pyx_v_e_sent_start); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1645; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_15 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->extract_phrases(__pyx_v_self, __pyx_v_e_x_low, __pyx_v_e_x_high, __pyx_v_e_gap_low, __pyx_v_e_gap_high, __pyx_v_e_links_low, (__pyx_v_num_gaps + 1), __pyx_v_f_x_low, __pyx_v_f_x_high, __pyx_v_f_gap_low, __pyx_v_f_gap_high, __pyx_v_f_links_low, __pyx_v_matching->sent_id, __pyx_v_e_sent_len, __pyx_v_e_sent_start); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1658; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_15);
               __Pyx_XDECREF(__pyx_v_phrase_list);
               __pyx_v_phrase_list = __pyx_t_15;
               __pyx_t_15 = 0;
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1648
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1661
  *                                                     f_x_low, f_x_high, f_gap_low, f_gap_high, f_links_low, matching.sent_id,
  *                                                     e_sent_len, e_sent_start)
  *                                 if len(phrase_list) > 0:             # <<<<<<<<<<<<<<
  *                                     pair_count = 1.0 / len(phrase_list)
  *                                 else:
  */
-              __pyx_t_13 = PyObject_Length(__pyx_v_phrase_list); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1648; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_13 = PyObject_Length(__pyx_v_phrase_list); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1661; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __pyx_t_9 = (__pyx_t_13 > 0);
               if (__pyx_t_9) {
 
-                /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1649
+                /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1662
  *                                                     e_sent_len, e_sent_start)
  *                                 if len(phrase_list) > 0:
  *                                     pair_count = 1.0 / len(phrase_list)             # <<<<<<<<<<<<<<
  *                                 else:
  *                                     pair_count = 0
  */
-                __pyx_t_13 = PyObject_Length(__pyx_v_phrase_list); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1649; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_13 = PyObject_Length(__pyx_v_phrase_list); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1662; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 if (unlikely(__pyx_t_13 == 0)) {
                   PyErr_Format(PyExc_ZeroDivisionError, "float division");
-                  {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1649; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1662; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 }
                 __pyx_v_pair_count = (1.0 / __pyx_t_13);
                 goto __pyx_L74;
               }
               /*else*/ {
 
-                /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1651
+                /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1664
  *                                     pair_count = 1.0 / len(phrase_list)
  *                                 else:
  *                                     pair_count = 0             # <<<<<<<<<<<<<<
@@ -52422,7 +54030,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
               }
               __pyx_L74:;
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1652
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1665
  *                                 else:
  *                                     pair_count = 0
  *                                 for phrase2,eindexes in phrase_list:             # <<<<<<<<<<<<<<
@@ -52433,7 +54041,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 __pyx_t_15 = __pyx_v_phrase_list; __Pyx_INCREF(__pyx_t_15); __pyx_t_13 = 0;
                 __pyx_t_16 = NULL;
               } else {
-                __pyx_t_13 = -1; __pyx_t_15 = PyObject_GetIter(__pyx_v_phrase_list); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_13 = -1; __pyx_t_15 = PyObject_GetIter(__pyx_v_phrase_list); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1665; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_15);
                 __pyx_t_16 = Py_TYPE(__pyx_t_15)->tp_iternext;
               }
@@ -52441,23 +54049,23 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
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                   if (__pyx_t_13 >= PyList_GET_SIZE(__pyx_t_15)) break;
                   #if CYTHON_COMPILING_IN_CPYTHON
-                  __pyx_t_1 = PyList_GET_ITEM(__pyx_t_15, __pyx_t_13); __Pyx_INCREF(__pyx_t_1); __pyx_t_13++;
+                  __pyx_t_1 = PyList_GET_ITEM(__pyx_t_15, __pyx_t_13); __Pyx_INCREF(__pyx_t_1); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1665; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                   #else
-                  __pyx_t_1 = PySequence_ITEM(__pyx_t_15, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+                  __pyx_t_1 = PySequence_ITEM(__pyx_t_15, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1665; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                   #endif
                 } else if (!__pyx_t_16 && PyTuple_CheckExact(__pyx_t_15)) {
                   if (__pyx_t_13 >= PyTuple_GET_SIZE(__pyx_t_15)) break;
                   #if CYTHON_COMPILING_IN_CPYTHON
-                  __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_15, __pyx_t_13); __Pyx_INCREF(__pyx_t_1); __pyx_t_13++;
+                  __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_15, __pyx_t_13); __Pyx_INCREF(__pyx_t_1); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1665; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                   #else
-                  __pyx_t_1 = PySequence_ITEM(__pyx_t_15, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+                  __pyx_t_1 = PySequence_ITEM(__pyx_t_15, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1665; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                   #endif
                 } else {
                   __pyx_t_1 = __pyx_t_16(__pyx_t_15);
                   if (unlikely(!__pyx_t_1)) {
                     if (PyErr_Occurred()) {
                       if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
-                      else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                      else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1665; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                     }
                     break;
                   }
@@ -52473,7 +54081,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                   if (unlikely(size != 2)) {
                     if (size > 2) __Pyx_RaiseTooManyValuesError(2);
                     else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
-                    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1665; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                   }
                   #if CYTHON_COMPILING_IN_CPYTHON
                   if (likely(PyTuple_CheckExact(sequence))) {
@@ -52486,14 +54094,14 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                   __Pyx_INCREF(__pyx_t_14);
                   __Pyx_INCREF(__pyx_t_2);
                   #else
-                  __pyx_t_14 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-                  __pyx_t_2 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  __pyx_t_14 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1665; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  __pyx_t_2 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1665; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                   #endif
                   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
                 } else
                 {
                   Py_ssize_t index = -1;
-                  __pyx_t_10 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  __pyx_t_10 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1665; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                   __Pyx_GOTREF(__pyx_t_10);
                   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
                   __pyx_t_17 = Py_TYPE(__pyx_t_10)->tp_iternext;
@@ -52501,7 +54109,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                   __Pyx_GOTREF(__pyx_t_14);
                   index = 1; __pyx_t_2 = __pyx_t_17(__pyx_t_10); if (unlikely(!__pyx_t_2)) goto __pyx_L77_unpacking_failed;
                   __Pyx_GOTREF(__pyx_t_2);
-                  if (__Pyx_IternextUnpackEndCheck(__pyx_t_17(__pyx_t_10), 2) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  if (__Pyx_IternextUnpackEndCheck(__pyx_t_17(__pyx_t_10), 2) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1665; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                   __pyx_t_17 = NULL;
                   __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
                   goto __pyx_L78_unpacking_done;
@@ -52509,7 +54117,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                   __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
                   __pyx_t_17 = NULL;
                   if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
-                  {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1665; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                   __pyx_L78_unpacking_done:;
                 }
                 __Pyx_XDECREF(__pyx_v_phrase2);
@@ -52519,7 +54127,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 __pyx_v_eindexes = __pyx_t_2;
                 __pyx_t_2 = 0;
 
-                /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1653
+                /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1666
  *                                     pair_count = 0
  *                                 for phrase2,eindexes in phrase_list:
  *                                     als2 = self.create_alignments(sent_links,num_links,self.findexes,eindexes)             # <<<<<<<<<<<<<<
@@ -52528,31 +54136,31 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
                 __pyx_t_1 = ((PyObject *)__pyx_v_self->findexes);
                 __Pyx_INCREF(__pyx_t_1);
-                __pyx_t_2 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->create_alignments(__pyx_v_self, __pyx_v_sent_links, __pyx_v_num_links, __pyx_t_1, __pyx_v_eindexes); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_2 = ((PyObject *)((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->create_alignments(__pyx_v_self, __pyx_v_sent_links, __pyx_v_num_links, __pyx_t_1, __pyx_v_eindexes)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1666; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_2);
                 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
-                __Pyx_XDECREF(__pyx_v_als2);
-                __pyx_v_als2 = __pyx_t_2;
+                __Pyx_XDECREF(((PyObject *)__pyx_v_als2));
+                __pyx_v_als2 = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_2);
                 __pyx_t_2 = 0;
 
-                /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1654
+                /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1667
  *                                 for phrase2,eindexes in phrase_list:
  *                                     als2 = self.create_alignments(sent_links,num_links,self.findexes,eindexes)
  *                                     extracts.append((fphr, phrase2, pair_count, tuple(als2)))             # <<<<<<<<<<<<<<
  * 
  *                         if (f_back_high == f_high and
  */
-                __pyx_t_2 = PyFloat_FromDouble(__pyx_v_pair_count); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_2 = PyFloat_FromDouble(__pyx_v_pair_count); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1667; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_2);
-                __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1667; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_1);
-                __Pyx_INCREF(__pyx_v_als2);
-                PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_als2);
-                __Pyx_GIVEREF(__pyx_v_als2);
-                __pyx_t_14 = PyObject_Call(((PyObject *)((PyObject*)(&PyTuple_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __Pyx_INCREF(((PyObject *)__pyx_v_als2));
+                PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_v_als2));
+                __Pyx_GIVEREF(((PyObject *)__pyx_v_als2));
+                __pyx_t_14 = PyObject_Call(((PyObject *)((PyObject*)(&PyTuple_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1667; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_14);
                 __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
-                __pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1667; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_1);
                 __Pyx_INCREF(((PyObject *)__pyx_v_fphr));
                 PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_v_fphr));
@@ -52566,7 +54174,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 __Pyx_GIVEREF(__pyx_t_14);
                 __pyx_t_2 = 0;
                 __pyx_t_14 = 0;
-                __pyx_t_14 = __Pyx_PyObject_Append(__pyx_v_extracts, ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_14 = __Pyx_PyObject_Append(__pyx_v_extracts, ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1667; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_14);
                 __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
                 __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
@@ -52579,7 +54187,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
           }
           __pyx_L64:;
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1656
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1669
  *                                     extracts.append((fphr, phrase2, pair_count, tuple(als2)))
  * 
  *                         if (f_back_high == f_high and             # <<<<<<<<<<<<<<
@@ -52589,7 +54197,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
           __pyx_t_9 = (__pyx_v_f_back_high == __pyx_v_f_high);
           if (__pyx_t_9) {
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1657
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1670
  * 
  *                         if (f_back_high == f_high and
  *                             f_sent_len - f_high >= self.train_min_gap_size and             # <<<<<<<<<<<<<<
@@ -52599,7 +54207,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             __pyx_t_7 = ((__pyx_v_f_sent_len - __pyx_v_f_high) >= __pyx_v_self->train_min_gap_size);
             if (__pyx_t_7) {
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1658
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1671
  *                         if (f_back_high == f_high and
  *                             f_sent_len - f_high >= self.train_min_gap_size and
  *                             ((not self.tight_phrases) or (f_links_low[f_high] != -1 and f_links_low[f_back_low] != -1))):             # <<<<<<<<<<<<<<
@@ -52629,7 +54237,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
           }
           if (__pyx_t_7) {
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1659
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1672
  *                             f_sent_len - f_high >= self.train_min_gap_size and
  *                             ((not self.tight_phrases) or (f_links_low[f_high] != -1 and f_links_low[f_back_low] != -1))):
  *                             f_x_high = f_high+self.train_min_gap_size             # <<<<<<<<<<<<<<
@@ -52638,7 +54246,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             __pyx_v_f_x_high = (__pyx_v_f_high + __pyx_v_self->train_min_gap_size);
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1660
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1673
  *                             ((not self.tight_phrases) or (f_links_low[f_high] != -1 and f_links_low[f_back_low] != -1))):
  *                             f_x_high = f_high+self.train_min_gap_size
  *                             met_constraints = 1             # <<<<<<<<<<<<<<
@@ -52647,7 +54255,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             __pyx_v_met_constraints = 1;
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1661
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1674
  *                             f_x_high = f_high+self.train_min_gap_size
  *                             met_constraints = 1
  *                             if self.tight_phrases:             # <<<<<<<<<<<<<<
@@ -52656,7 +54264,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             if (__pyx_v_self->tight_phrases) {
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1662
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1675
  *                             met_constraints = 1
  *                             if self.tight_phrases:
  *                                 while f_x_high <= f_sent_len and f_links_low[f_x_high-1] == -1:             # <<<<<<<<<<<<<<
@@ -52673,7 +54281,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 }
                 if (!__pyx_t_18) break;
 
-                /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1663
+                /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1676
  *                             if self.tight_phrases:
  *                                 while f_x_high <= f_sent_len and f_links_low[f_x_high-1] == -1:
  *                                     f_x_high = f_x_high + 1             # <<<<<<<<<<<<<<
@@ -52686,7 +54294,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             }
             __pyx_L80:;
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1664
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1677
  *                                 while f_x_high <= f_sent_len and f_links_low[f_x_high-1] == -1:
  *                                     f_x_high = f_x_high + 1
  *                             if f_x_high > f_sent_len or f_x_high - f_back_low > self.train_max_initial_size:             # <<<<<<<<<<<<<<
@@ -52702,7 +54310,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             }
             if (__pyx_t_9) {
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1665
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1678
  *                                     f_x_high = f_x_high + 1
  *                             if f_x_high > f_sent_len or f_x_high - f_back_low > self.train_max_initial_size:
  *                                 met_constraints = 0             # <<<<<<<<<<<<<<
@@ -52714,7 +54322,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             }
             __pyx_L83:;
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1667
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1680
  *                                 met_constraints = 0
  * 
  *                             if (met_constraints and             # <<<<<<<<<<<<<<
@@ -52723,17 +54331,17 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             if (__pyx_v_met_constraints) {
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1668
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1681
  * 
  *                             if (met_constraints and
  *                                 self.find_fixpoint(f_back_low, f_x_high,             # <<<<<<<<<<<<<<
  *                                             f_links_low, f_links_high, e_links_low, e_links_high,
  *                                             e_low, e_high, &e_x_low, &e_x_high, &f_x_low, &f_x_high,
  */
-              __pyx_t_15 = PyInt_FromLong(__pyx_v_f_x_high); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1668; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_15 = PyInt_FromLong(__pyx_v_f_x_high); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1681; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_15);
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1672
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1685
  *                                             e_low, e_high, &e_x_low, &e_x_high, &f_x_low, &f_x_high,
  *                                             f_sent_len, e_sent_len,
  *                                             self.train_max_initial_size, self.train_max_initial_size,             # <<<<<<<<<<<<<<
@@ -52743,7 +54351,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
               if (((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_fixpoint(__pyx_v_self, __pyx_v_f_back_low, __pyx_t_15, __pyx_v_f_links_low, __pyx_v_f_links_high, __pyx_v_e_links_low, __pyx_v_e_links_high, __pyx_v_e_low, __pyx_v_e_high, (&__pyx_v_e_x_low), (&__pyx_v_e_x_high), (&__pyx_v_f_x_low), (&__pyx_v_f_x_high), __pyx_v_f_sent_len, __pyx_v_e_sent_len, __pyx_v_self->train_max_initial_size, __pyx_v_self->train_max_initial_size, 1, 1, 1, 0, 1, 1, 0)) {
                 __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
 
-                /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1674
+                /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1687
  *                                             self.train_max_initial_size, self.train_max_initial_size,
  *                                             1, 1, 1, 0, 1, 1, 0) and
  *                                 ((not self.tight_phrases) or f_links_low[f_x_high-1] != -1) and             # <<<<<<<<<<<<<<
@@ -52759,17 +54367,17 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 }
                 if (__pyx_t_7) {
 
-                  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1675
+                  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1688
  *                                             1, 1, 1, 0, 1, 1, 0) and
  *                                 ((not self.tight_phrases) or f_links_low[f_x_high-1] != -1) and
  *                                 self.find_fixpoint(f_high, f_x_high,             # <<<<<<<<<<<<<<
  *                                             f_links_low, f_links_high, e_links_low, e_links_high,
  *                                             -1, -1, e_gap_low+gap_start+num_gaps, e_gap_high+gap_start+num_gaps,
  */
-                  __pyx_t_14 = PyInt_FromLong(__pyx_v_f_x_high); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1675; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  __pyx_t_14 = PyInt_FromLong(__pyx_v_f_x_high); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1688; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                   __Pyx_GOTREF(__pyx_t_14);
 
-                  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1680
+                  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1693
  *                                             f_gap_low+gap_start+num_gaps, f_gap_high+gap_start+num_gaps,
  *                                             f_sent_len, e_sent_len,
  *                                             self.train_max_initial_size, self.train_max_initial_size,             # <<<<<<<<<<<<<<
@@ -52792,7 +54400,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             }
             if (__pyx_t_9) {
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1682
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1695
  *                                             self.train_max_initial_size, self.train_max_initial_size,
  *                                             0, 0, 0, 0, 0, 0, 0)):
  *                                 fphr_arr._clear()             # <<<<<<<<<<<<<<
@@ -52801,7 +54409,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
               ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_fphr_arr->__pyx_vtab)->_clear(__pyx_v_fphr_arr);
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1683
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1696
  *                                             0, 0, 0, 0, 0, 0, 0)):
  *                                 fphr_arr._clear()
  *                                 i = 1             # <<<<<<<<<<<<<<
@@ -52810,21 +54418,21 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
               __pyx_v_i = 1;
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1684
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1697
  *                                 fphr_arr._clear()
  *                                 i = 1
  *                                 self.findexes.reset()             # <<<<<<<<<<<<<<
  *                                 if f_back_low < f_low:
  *                                     fphr_arr._append(sym_setindex(self.category, i))
  */
-              __pyx_t_15 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes), __pyx_n_s__reset); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1684; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_15 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes), __pyx_n_s__reset); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_15);
-              __pyx_t_14 = PyObject_Call(__pyx_t_15, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1684; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_14 = PyObject_Call(__pyx_t_15, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_14);
               __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
               __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1685
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1698
  *                                 i = 1
  *                                 self.findexes.reset()
  *                                 if f_back_low < f_low:             # <<<<<<<<<<<<<<
@@ -52834,7 +54442,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
               __pyx_t_9 = (__pyx_v_f_back_low < __pyx_v_f_low);
               if (__pyx_t_9) {
 
-                /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1686
+                /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1699
  *                                 self.findexes.reset()
  *                                 if f_back_low < f_low:
  *                                     fphr_arr._append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
@@ -52843,7 +54451,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
                 ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_fphr_arr->__pyx_vtab)->_append(__pyx_v_fphr_arr, __pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i));
 
-                /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1687
+                /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1700
  *                                 if f_back_low < f_low:
  *                                     fphr_arr._append(sym_setindex(self.category, i))
  *                                     i = i+1             # <<<<<<<<<<<<<<
@@ -52852,16 +54460,16 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
                 __pyx_v_i = (__pyx_v_i + 1);
 
-                /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1688
+                /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1701
  *                                     fphr_arr._append(sym_setindex(self.category, i))
  *                                     i = i+1
  *                                     self.findexes.append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
  *                                 self.findexes.extend(self.findexes1)
  *                                 for j from 0 <= j < phrase.n:
  */
-                __pyx_t_14 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i)); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1688; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_14 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i)); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_14);
-                __pyx_t_15 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes), __pyx_t_14); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1688; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_15 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes), __pyx_t_14); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_15);
                 __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
                 __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
@@ -52869,27 +54477,27 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
               }
               __pyx_L85:;
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1689
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1702
  *                                     i = i+1
  *                                     self.findexes.append(sym_setindex(self.category, i))
  *                                 self.findexes.extend(self.findexes1)             # <<<<<<<<<<<<<<
  *                                 for j from 0 <= j < phrase.n:
  *                                     if sym_isvar(phrase.syms[j]):
  */
-              __pyx_t_15 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes), __pyx_n_s__extend); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_15 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes), __pyx_n_s__extend); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_15);
-              __pyx_t_14 = PyTuple_New(1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_14 = PyTuple_New(1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_14);
               __Pyx_INCREF(((PyObject *)__pyx_v_self->findexes1));
               PyTuple_SET_ITEM(__pyx_t_14, 0, ((PyObject *)__pyx_v_self->findexes1));
               __Pyx_GIVEREF(((PyObject *)__pyx_v_self->findexes1));
-              __pyx_t_1 = PyObject_Call(__pyx_t_15, ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_1 = PyObject_Call(__pyx_t_15, ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_1);
               __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
               __Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0;
               __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1690
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1703
  *                                     self.findexes.append(sym_setindex(self.category, i))
  *                                 self.findexes.extend(self.findexes1)
  *                                 for j from 0 <= j < phrase.n:             # <<<<<<<<<<<<<<
@@ -52899,7 +54507,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
               __pyx_t_3 = __pyx_v_phrase->n;
               for (__pyx_v_j = 0; __pyx_v_j < __pyx_t_3; __pyx_v_j++) {
 
-                /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1691
+                /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1704
  *                                 self.findexes.extend(self.findexes1)
  *                                 for j from 0 <= j < phrase.n:
  *                                     if sym_isvar(phrase.syms[j]):             # <<<<<<<<<<<<<<
@@ -52909,7 +54517,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 __pyx_t_4 = __pyx_f_3_sa_sym_isvar((__pyx_v_phrase->syms[__pyx_v_j]));
                 if (__pyx_t_4) {
 
-                  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1692
+                  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1705
  *                                 for j from 0 <= j < phrase.n:
  *                                     if sym_isvar(phrase.syms[j]):
  *                                         fphr_arr._append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
@@ -52918,7 +54526,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
                   ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_fphr_arr->__pyx_vtab)->_append(__pyx_v_fphr_arr, __pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i));
 
-                  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1693
+                  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1706
  *                                     if sym_isvar(phrase.syms[j]):
  *                                         fphr_arr._append(sym_setindex(self.category, i))
  *                                         i = i + 1             # <<<<<<<<<<<<<<
@@ -52930,7 +54538,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 }
                 /*else*/ {
 
-                  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1695
+                  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1708
  *                                         i = i + 1
  *                                     else:
  *                                         fphr_arr._append(phrase.syms[j])             # <<<<<<<<<<<<<<
@@ -52942,7 +54550,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 __pyx_L88:;
               }
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1696
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1709
  *                                     else:
  *                                         fphr_arr._append(phrase.syms[j])
  *                                 fphr_arr._append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
@@ -52951,81 +54559,81 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
               ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_fphr_arr->__pyx_vtab)->_append(__pyx_v_fphr_arr, __pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i));
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1697
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1710
  *                                         fphr_arr._append(phrase.syms[j])
  *                                 fphr_arr._append(sym_setindex(self.category, i))
  *                                 self.findexes.append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
  *                                 fphr = Phrase(fphr_arr)
  *                                 phrase_list = self.extract_phrases(e_x_low, e_x_high, e_gap_low+gap_start, e_gap_high+gap_start, e_links_low, num_gaps+1,
  */
-              __pyx_t_1 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_1 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1710; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_1);
-              __pyx_t_14 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes), __pyx_t_1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_14 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes), __pyx_t_1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1710; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_14);
               __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
               __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1698
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1711
  *                                 fphr_arr._append(sym_setindex(self.category, i))
  *                                 self.findexes.append(sym_setindex(self.category, i))
  *                                 fphr = Phrase(fphr_arr)             # <<<<<<<<<<<<<<
  *                                 phrase_list = self.extract_phrases(e_x_low, e_x_high, e_gap_low+gap_start, e_gap_high+gap_start, e_links_low, num_gaps+1,
  *                                                     f_x_low, f_x_high, f_gap_low+gap_start, f_gap_high+gap_start, f_links_low,
  */
-              __pyx_t_14 = PyTuple_New(1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_14 = PyTuple_New(1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_14);
               __Pyx_INCREF(((PyObject *)__pyx_v_fphr_arr));
               PyTuple_SET_ITEM(__pyx_t_14, 0, ((PyObject *)__pyx_v_fphr_arr));
               __Pyx_GIVEREF(((PyObject *)__pyx_v_fphr_arr));
-              __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_Phrase)), ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_Phrase)), ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_1);
               __Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0;
               __Pyx_DECREF(((PyObject *)__pyx_v_fphr));
               __pyx_v_fphr = ((struct __pyx_obj_3_sa_Phrase *)__pyx_t_1);
               __pyx_t_1 = 0;
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1701
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1714
  *                                 phrase_list = self.extract_phrases(e_x_low, e_x_high, e_gap_low+gap_start, e_gap_high+gap_start, e_links_low, num_gaps+1,
  *                                                     f_x_low, f_x_high, f_gap_low+gap_start, f_gap_high+gap_start, f_links_low,
  *                                                     matching.sent_id, e_sent_len, e_sent_start)             # <<<<<<<<<<<<<<
  *                                 if len(phrase_list) > 0:
  *                                     pair_count = 1.0 / len(phrase_list)
  */
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+              __pyx_t_1 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->extract_phrases(__pyx_v_self, __pyx_v_e_x_low, __pyx_v_e_x_high, (__pyx_v_e_gap_low + __pyx_v_gap_start), (__pyx_v_e_gap_high + __pyx_v_gap_start), __pyx_v_e_links_low, (__pyx_v_num_gaps + 1), __pyx_v_f_x_low, __pyx_v_f_x_high, (__pyx_v_f_gap_low + __pyx_v_gap_start), (__pyx_v_f_gap_high + __pyx_v_gap_start), __pyx_v_f_links_low, __pyx_v_matching->sent_id, __pyx_v_e_sent_len, __pyx_v_e_sent_start); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_1);
               __Pyx_XDECREF(__pyx_v_phrase_list);
               __pyx_v_phrase_list = __pyx_t_1;
               __pyx_t_1 = 0;
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1702
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1715
  *                                                     f_x_low, f_x_high, f_gap_low+gap_start, f_gap_high+gap_start, f_links_low,
  *                                                     matching.sent_id, e_sent_len, e_sent_start)
  *                                 if len(phrase_list) > 0:             # <<<<<<<<<<<<<<
  *                                     pair_count = 1.0 / len(phrase_list)
  *                                 else:
  */
-              __pyx_t_13 = PyObject_Length(__pyx_v_phrase_list); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_13 = PyObject_Length(__pyx_v_phrase_list); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1715; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __pyx_t_9 = (__pyx_t_13 > 0);
               if (__pyx_t_9) {
 
-                /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1703
+                /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1716
  *                                                     matching.sent_id, e_sent_len, e_sent_start)
  *                                 if len(phrase_list) > 0:
  *                                     pair_count = 1.0 / len(phrase_list)             # <<<<<<<<<<<<<<
  *                                 else:
  *                                     pair_count = 0
  */
-                __pyx_t_13 = PyObject_Length(__pyx_v_phrase_list); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1703; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_13 = PyObject_Length(__pyx_v_phrase_list); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1716; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 if (unlikely(__pyx_t_13 == 0)) {
                   PyErr_Format(PyExc_ZeroDivisionError, "float division");
-                  {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1703; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1716; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 }
                 __pyx_v_pair_count = (1.0 / __pyx_t_13);
                 goto __pyx_L89;
               }
               /*else*/ {
 
-                /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1705
+                /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1718
  *                                     pair_count = 1.0 / len(phrase_list)
  *                                 else:
  *                                     pair_count = 0             # <<<<<<<<<<<<<<
@@ -53036,7 +54644,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
               }
               __pyx_L89:;
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1706
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1719
  *                                 else:
  *                                     pair_count = 0
  *                                 for phrase2, eindexes in phrase_list:             # <<<<<<<<<<<<<<
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                 __pyx_t_16 = NULL;
               } else {
-                __pyx_t_13 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_phrase_list); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1706; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_13 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_phrase_list); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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                 __pyx_t_16 = Py_TYPE(__pyx_t_1)->tp_iternext;
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                   if (__pyx_t_13 >= PyList_GET_SIZE(__pyx_t_1)) break;
                   #if CYTHON_COMPILING_IN_CPYTHON
-                  __pyx_t_14 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_13); __Pyx_INCREF(__pyx_t_14); __pyx_t_13++;
+                  __pyx_t_14 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_13); __Pyx_INCREF(__pyx_t_14); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-                  __pyx_t_14 = PySequence_ITEM(__pyx_t_1, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1706; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+                  __pyx_t_14 = PySequence_ITEM(__pyx_t_1, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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                   if (__pyx_t_13 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
                   #if CYTHON_COMPILING_IN_CPYTHON
-                  __pyx_t_14 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_13); __Pyx_INCREF(__pyx_t_14); __pyx_t_13++;
+                  __pyx_t_14 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_13); __Pyx_INCREF(__pyx_t_14); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                   #else
-                  __pyx_t_14 = PySequence_ITEM(__pyx_t_1, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1706; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+                  __pyx_t_14 = PySequence_ITEM(__pyx_t_1, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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                 } else {
                   __pyx_t_14 = __pyx_t_16(__pyx_t_1);
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                     if (PyErr_Occurred()) {
                       if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
-                      else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1706; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                      else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -53087,7 +54695,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
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                     if (size > 2) __Pyx_RaiseTooManyValuesError(2);
                     else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
-                    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1706; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                    {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -53100,14 +54708,14 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
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                   __Pyx_INCREF(__pyx_t_2);
                   #else
-                  __pyx_t_15 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1706; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-                  __pyx_t_2 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1706; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  __pyx_t_15 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  __pyx_t_2 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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                 {
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-                  __pyx_t_10 = PyObject_GetIter(__pyx_t_14); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1706; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  __pyx_t_10 = PyObject_GetIter(__pyx_t_14); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -53115,7 +54723,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
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-                  if (__Pyx_IternextUnpackEndCheck(__pyx_t_17(__pyx_t_10), 2) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1706; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  if (__Pyx_IternextUnpackEndCheck(__pyx_t_17(__pyx_t_10), 2) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -53123,7 +54731,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
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-                  {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1706; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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                 __pyx_v_eindexes = __pyx_t_2;
                 __pyx_t_2 = 0;
 
-                /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1707
+                /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1720
  *                                     pair_count = 0
  *                                 for phrase2, eindexes in phrase_list:
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@@ -53142,31 +54750,31 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
                 __pyx_t_14 = ((PyObject *)__pyx_v_self->findexes);
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-                __pyx_t_2 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->create_alignments(__pyx_v_self, __pyx_v_sent_links, __pyx_v_num_links, __pyx_t_14, __pyx_v_eindexes); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1707; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_2 = ((PyObject *)((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->create_alignments(__pyx_v_self, __pyx_v_sent_links, __pyx_v_num_links, __pyx_t_14, __pyx_v_eindexes)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1720; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_2);
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-                __Pyx_XDECREF(__pyx_v_als3);
-                __pyx_v_als3 = __pyx_t_2;
+                __Pyx_XDECREF(((PyObject *)__pyx_v_als3));
+                __pyx_v_als3 = ((struct __pyx_obj_3_sa_IntList *)__pyx_t_2);
                 __pyx_t_2 = 0;
 
-                /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1708
+                /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1721
  *                                 for phrase2, eindexes in phrase_list:
  *                                     als3 = self.create_alignments(sent_links,num_links,self.findexes,eindexes)
  *                                     extracts.append((fphr, phrase2, pair_count, tuple(als3)))             # <<<<<<<<<<<<<<
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  *                             phrase_len+1 < self.max_length and
  */
-                __pyx_t_2 = PyFloat_FromDouble(__pyx_v_pair_count); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_2 = PyFloat_FromDouble(__pyx_v_pair_count); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1721; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-                __pyx_t_14 = PyTuple_New(1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_14 = PyTuple_New(1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1721; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_14);
-                __Pyx_INCREF(__pyx_v_als3);
-                PyTuple_SET_ITEM(__pyx_t_14, 0, __pyx_v_als3);
-                __Pyx_GIVEREF(__pyx_v_als3);
-                __pyx_t_15 = PyObject_Call(((PyObject *)((PyObject*)(&PyTuple_Type))), ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __Pyx_INCREF(((PyObject *)__pyx_v_als3));
+                PyTuple_SET_ITEM(__pyx_t_14, 0, ((PyObject *)__pyx_v_als3));
+                __Pyx_GIVEREF(((PyObject *)__pyx_v_als3));
+                __pyx_t_15 = PyObject_Call(((PyObject *)((PyObject*)(&PyTuple_Type))), ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1721; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_15);
                 __Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0;
-                __pyx_t_14 = PyTuple_New(4); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_14 = PyTuple_New(4); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1721; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_14);
                 __Pyx_INCREF(((PyObject *)__pyx_v_fphr));
                 PyTuple_SET_ITEM(__pyx_t_14, 0, ((PyObject *)__pyx_v_fphr));
@@ -53180,7 +54788,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 __Pyx_GIVEREF(__pyx_t_15);
                 __pyx_t_2 = 0;
                 __pyx_t_15 = 0;
-                __pyx_t_15 = __Pyx_PyObject_Append(__pyx_v_extracts, ((PyObject *)__pyx_t_14)); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_15 = __Pyx_PyObject_Append(__pyx_v_extracts, ((PyObject *)__pyx_t_14)); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1721; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_15);
                 __Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0;
                 __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
@@ -53193,7 +54801,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
           }
           __pyx_L79:;
 
-          /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1709
+          /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1722
  *                                     als3 = self.create_alignments(sent_links,num_links,self.findexes,eindexes)
  *                                     extracts.append((fphr, phrase2, pair_count, tuple(als3)))
  *                         if (num_gaps < self.max_nonterminals - 1 and             # <<<<<<<<<<<<<<
@@ -53203,7 +54811,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
           __pyx_t_9 = (__pyx_v_num_gaps < (__pyx_v_self->max_nonterminals - 1));
           if (__pyx_t_9) {
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1710
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1723
  *                                     extracts.append((fphr, phrase2, pair_count, tuple(als3)))
  *                         if (num_gaps < self.max_nonterminals - 1 and
  *                             phrase_len+1 < self.max_length and             # <<<<<<<<<<<<<<
@@ -53213,7 +54821,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             __pyx_t_7 = ((__pyx_v_phrase_len + 1) < __pyx_v_self->max_length);
             if (__pyx_t_7) {
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1711
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1724
  *                         if (num_gaps < self.max_nonterminals - 1 and
  *                             phrase_len+1 < self.max_length and
  *                             f_back_high == f_high and             # <<<<<<<<<<<<<<
@@ -53223,7 +54831,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
               __pyx_t_18 = (__pyx_v_f_back_high == __pyx_v_f_high);
               if (__pyx_t_18) {
 
-                /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1712
+                /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1725
  *                             phrase_len+1 < self.max_length and
  *                             f_back_high == f_high and
  *                             f_back_low == f_low and             # <<<<<<<<<<<<<<
@@ -53233,7 +54841,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 __pyx_t_8 = (__pyx_v_f_back_low == __pyx_v_f_low);
                 if (__pyx_t_8) {
 
-                  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1713
+                  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1726
  *                             f_back_high == f_high and
  *                             f_back_low == f_low and
  *                             f_back_high - f_back_low + (2*self.train_min_gap_size) <= self.train_max_initial_size and             # <<<<<<<<<<<<<<
@@ -53243,7 +54851,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                   __pyx_t_19 = (((__pyx_v_f_back_high - __pyx_v_f_back_low) + (2 * __pyx_v_self->train_min_gap_size)) <= __pyx_v_self->train_max_initial_size);
                   if (__pyx_t_19) {
 
-                    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1714
+                    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1727
  *                             f_back_low == f_low and
  *                             f_back_high - f_back_low + (2*self.train_min_gap_size) <= self.train_max_initial_size and
  *                             f_low >= self.train_min_gap_size and             # <<<<<<<<<<<<<<
@@ -53253,7 +54861,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                     __pyx_t_20 = (__pyx_v_f_low >= __pyx_v_self->train_min_gap_size);
                     if (__pyx_t_20) {
 
-                      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1715
+                      /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1728
  *                             f_back_high - f_back_low + (2*self.train_min_gap_size) <= self.train_max_initial_size and
  *                             f_low >= self.train_min_gap_size and
  *                             f_high <= f_sent_len - self.train_min_gap_size and             # <<<<<<<<<<<<<<
@@ -53263,7 +54871,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                       __pyx_t_21 = (__pyx_v_f_high <= (__pyx_v_f_sent_len - __pyx_v_self->train_min_gap_size));
                       if (__pyx_t_21) {
 
-                        /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1716
+                        /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1729
  *                             f_low >= self.train_min_gap_size and
  *                             f_high <= f_sent_len - self.train_min_gap_size and
  *                             ((not self.tight_phrases) or (f_links_low[f_low-1] != -1 and f_links_low[f_high] != -1))):             # <<<<<<<<<<<<<<
@@ -53313,7 +54921,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
           }
           if (__pyx_t_7) {
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1718
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1731
  *                             ((not self.tight_phrases) or (f_links_low[f_low-1] != -1 and f_links_low[f_high] != -1))):
  * 
  *                             met_constraints = 1             # <<<<<<<<<<<<<<
@@ -53322,7 +54930,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             __pyx_v_met_constraints = 1;
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1719
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1732
  * 
  *                             met_constraints = 1
  *                             f_x_low = f_low-self.train_min_gap_size             # <<<<<<<<<<<<<<
@@ -53331,7 +54939,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             __pyx_v_f_x_low = (__pyx_v_f_low - __pyx_v_self->train_min_gap_size);
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1720
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1733
  *                             met_constraints = 1
  *                             f_x_low = f_low-self.train_min_gap_size
  *                             if self.tight_phrases:             # <<<<<<<<<<<<<<
@@ -53340,7 +54948,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             if (__pyx_v_self->tight_phrases) {
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1721
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1734
  *                             f_x_low = f_low-self.train_min_gap_size
  *                             if self.tight_phrases:
  *                                 while f_x_low >= 0 and f_links_low[f_x_low] == -1:             # <<<<<<<<<<<<<<
@@ -53357,7 +54965,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 }
                 if (!__pyx_t_18) break;
 
-                /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1722
+                /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1735
  *                             if self.tight_phrases:
  *                                 while f_x_low >= 0 and f_links_low[f_x_low] == -1:
  *                                     f_x_low = f_x_low - 1             # <<<<<<<<<<<<<<
@@ -53370,7 +54978,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             }
             __pyx_L95:;
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1723
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1736
  *                                 while f_x_low >= 0 and f_links_low[f_x_low] == -1:
  *                                     f_x_low = f_x_low - 1
  *                             if f_x_low < 0:             # <<<<<<<<<<<<<<
@@ -53380,7 +54988,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             __pyx_t_18 = (__pyx_v_f_x_low < 0);
             if (__pyx_t_18) {
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1724
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1737
  *                                     f_x_low = f_x_low - 1
  *                             if f_x_low < 0:
  *                                 met_constraints = 0             # <<<<<<<<<<<<<<
@@ -53392,7 +55000,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             }
             __pyx_L98:;
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1726
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1739
  *                                 met_constraints = 0
  * 
  *                             f_x_high = f_high+self.train_min_gap_size             # <<<<<<<<<<<<<<
@@ -53401,7 +55009,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             __pyx_v_f_x_high = (__pyx_v_f_high + __pyx_v_self->train_min_gap_size);
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1727
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1740
  * 
  *                             f_x_high = f_high+self.train_min_gap_size
  *                             if self.tight_phrases:             # <<<<<<<<<<<<<<
@@ -53410,7 +55018,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             if (__pyx_v_self->tight_phrases) {
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1728
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1741
  *                             f_x_high = f_high+self.train_min_gap_size
  *                             if self.tight_phrases:
  *                                 while f_x_high <= f_sent_len and f_links_low[f_x_high-1] == -1:             # <<<<<<<<<<<<<<
@@ -53427,7 +55035,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 }
                 if (!__pyx_t_9) break;
 
-                /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1729
+                /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1742
  *                             if self.tight_phrases:
  *                                 while f_x_high <= f_sent_len and f_links_low[f_x_high-1] == -1:
  *                                     f_x_high = f_x_high + 1             # <<<<<<<<<<<<<<
@@ -53440,7 +55048,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             }
             __pyx_L99:;
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1730
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1743
  *                                 while f_x_high <= f_sent_len and f_links_low[f_x_high-1] == -1:
  *                                     f_x_high = f_x_high + 1
  *                             if f_x_high > f_sent_len or f_x_high - f_x_low > self.train_max_initial_size:             # <<<<<<<<<<<<<<
@@ -53456,7 +55064,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             }
             if (__pyx_t_7) {
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1731
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1744
  *                                     f_x_high = f_x_high + 1
  *                             if f_x_high > f_sent_len or f_x_high - f_x_low > self.train_max_initial_size:
  *                                 met_constraints = 0             # <<<<<<<<<<<<<<
@@ -53468,7 +55076,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             }
             __pyx_L102:;
 
-            /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1733
+            /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1746
  *                                 met_constraints = 0
  * 
  *                             if (met_constraints and             # <<<<<<<<<<<<<<
@@ -53477,17 +55085,17 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
             if (__pyx_v_met_constraints) {
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1734
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1747
  * 
  *                             if (met_constraints and
  *                                 self.find_fixpoint(f_x_low, f_x_high,             # <<<<<<<<<<<<<<
  *                                                 f_links_low, f_links_high, e_links_low, e_links_high,
  *                                                 e_low, e_high, &e_x_low, &e_x_high, &f_x_low, &f_x_high,
  */
-              __pyx_t_1 = PyInt_FromLong(__pyx_v_f_x_high); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1734; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_1 = PyInt_FromLong(__pyx_v_f_x_high); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1747; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_1);
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1738
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1751
  *                                                 e_low, e_high, &e_x_low, &e_x_high, &f_x_low, &f_x_high,
  *                                                 f_sent_len, e_sent_len,
  *                                                 self.train_max_initial_size, self.train_max_initial_size,             # <<<<<<<<<<<<<<
@@ -53497,7 +55105,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
               if (((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->find_fixpoint(__pyx_v_self, __pyx_v_f_x_low, __pyx_t_1, __pyx_v_f_links_low, __pyx_v_f_links_high, __pyx_v_e_links_low, __pyx_v_e_links_high, __pyx_v_e_low, __pyx_v_e_high, (&__pyx_v_e_x_low), (&__pyx_v_e_x_high), (&__pyx_v_f_x_low), (&__pyx_v_f_x_high), __pyx_v_f_sent_len, __pyx_v_e_sent_len, __pyx_v_self->train_max_initial_size, __pyx_v_self->train_max_initial_size, 1, 1, 2, 1, 1, 1, 1)) {
                 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-                /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1740
+                /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1753
  *                                                 self.train_max_initial_size, self.train_max_initial_size,
  *                                                 1, 1, 2, 1, 1, 1, 1) and
  *                                 ((not self.tight_phrases) or (f_links_low[f_x_low] != -1 and f_links_low[f_x_high-1] != -1)) and             # <<<<<<<<<<<<<<
@@ -53519,17 +55127,17 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 }
                 if (__pyx_t_9) {
 
-                  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1741
+                  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1754
  *                                                 1, 1, 2, 1, 1, 1, 1) and
  *                                 ((not self.tight_phrases) or (f_links_low[f_x_low] != -1 and f_links_low[f_x_high-1] != -1)) and
  *                                 self.find_fixpoint(f_x_low, f_low,             # <<<<<<<<<<<<<<
  *                                                 f_links_low, f_links_high, e_links_low, e_links_high,
  *                                                 -1, -1, e_gap_low, e_gap_high, f_gap_low, f_gap_high,
  */
-                  __pyx_t_15 = PyInt_FromLong(__pyx_v_f_low); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  __pyx_t_15 = PyInt_FromLong(__pyx_v_f_low); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                   __Pyx_GOTREF(__pyx_t_15);
 
-                  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1745
+                  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1758
  *                                                 -1, -1, e_gap_low, e_gap_high, f_gap_low, f_gap_high,
  *                                                 f_sent_len, e_sent_len,
  *                                                 self.train_max_initial_size, self.train_max_initial_size,             # <<<<<<<<<<<<<<
@@ -53540,17 +55148,17 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                   __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
                   if (__pyx_t_3) {
 
-                    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1747
+                    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1760
  *                                                 self.train_max_initial_size, self.train_max_initial_size,
  *                                                 0, 0, 0, 0, 0, 0, 0) and
  *                                 self.find_fixpoint(f_high, f_x_high,             # <<<<<<<<<<<<<<
  *                                                 f_links_low, f_links_high, e_links_low, e_links_high,
  *                                                 -1, -1, e_gap_low+1+num_gaps, e_gap_high+1+num_gaps,
  */
-                    __pyx_t_15 = PyInt_FromLong(__pyx_v_f_x_high); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1747; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                    __pyx_t_15 = PyInt_FromLong(__pyx_v_f_x_high); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                     __Pyx_GOTREF(__pyx_t_15);
 
-                    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1752
+                    /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1765
  *                                                 f_gap_low+1+num_gaps, f_gap_high+1+num_gaps,
  *                                                 f_sent_len, e_sent_len,
  *                                                 self.train_max_initial_size, self.train_max_initial_size,             # <<<<<<<<<<<<<<
@@ -53578,7 +55186,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
             }
             if (__pyx_t_8) {
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1754
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1767
  *                                                 self.train_max_initial_size, self.train_max_initial_size,
  *                                                 0, 0, 0, 0, 0, 0, 0)):
  *                                 fphr_arr._clear()             # <<<<<<<<<<<<<<
@@ -53587,7 +55195,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
               ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_fphr_arr->__pyx_vtab)->_clear(__pyx_v_fphr_arr);
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1755
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1768
  *                                                 0, 0, 0, 0, 0, 0, 0)):
  *                                 fphr_arr._clear()
  *                                 i = 1             # <<<<<<<<<<<<<<
@@ -53596,35 +55204,35 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
               __pyx_v_i = 1;
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1756
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1769
  *                                 fphr_arr._clear()
  *                                 i = 1
  *                                 self.findexes.reset()             # <<<<<<<<<<<<<<
  *                                 self.findexes.append(sym_setindex(self.category, i))
  *                                 fphr_arr._append(sym_setindex(self.category, i))
  */
-              __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes), __pyx_n_s__reset); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1756; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes), __pyx_n_s__reset); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_1);
-              __pyx_t_15 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1756; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_15 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_15);
               __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
               __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1757
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1770
  *                                 i = 1
  *                                 self.findexes.reset()
  *                                 self.findexes.append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
  *                                 fphr_arr._append(sym_setindex(self.category, i))
  *                                 i = i+1
  */
-              __pyx_t_15 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i)); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1757; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_15 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i)); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_15);
-              __pyx_t_1 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes), __pyx_t_15); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1757; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_1 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes), __pyx_t_15); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_1);
               __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
               __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1758
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1771
  *                                 self.findexes.reset()
  *                                 self.findexes.append(sym_setindex(self.category, i))
  *                                 fphr_arr._append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
@@ -53633,7 +55241,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
               ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_fphr_arr->__pyx_vtab)->_append(__pyx_v_fphr_arr, __pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i));
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1759
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1772
  *                                 self.findexes.append(sym_setindex(self.category, i))
  *                                 fphr_arr._append(sym_setindex(self.category, i))
  *                                 i = i+1             # <<<<<<<<<<<<<<
@@ -53642,27 +55250,27 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
               __pyx_v_i = (__pyx_v_i + 1);
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1760
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1773
  *                                 fphr_arr._append(sym_setindex(self.category, i))
  *                                 i = i+1
  *                                 self.findexes.extend(self.findexes1)             # <<<<<<<<<<<<<<
  *                                 for j from 0 <= j < phrase.n:
  *                                     if sym_isvar(phrase.syms[j]):
  */
-              __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes), __pyx_n_s__extend); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self->findexes), __pyx_n_s__extend); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_1);
-              __pyx_t_15 = PyTuple_New(1); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_15 = PyTuple_New(1); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_15);
               __Pyx_INCREF(((PyObject *)__pyx_v_self->findexes1));
               PyTuple_SET_ITEM(__pyx_t_15, 0, ((PyObject *)__pyx_v_self->findexes1));
               __Pyx_GIVEREF(((PyObject *)__pyx_v_self->findexes1));
-              __pyx_t_14 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_15), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_14 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_15), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_14);
               __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
               __Pyx_DECREF(((PyObject *)__pyx_t_15)); __pyx_t_15 = 0;
               __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1761
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1774
  *                                 i = i+1
  *                                 self.findexes.extend(self.findexes1)
  *                                 for j from 0 <= j < phrase.n:             # <<<<<<<<<<<<<<
@@ -53672,7 +55280,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
               __pyx_t_3 = __pyx_v_phrase->n;
               for (__pyx_v_j = 0; __pyx_v_j < __pyx_t_3; __pyx_v_j++) {
 
-                /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1762
+                /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1775
  *                                 self.findexes.extend(self.findexes1)
  *                                 for j from 0 <= j < phrase.n:
  *                                     if sym_isvar(phrase.syms[j]):             # <<<<<<<<<<<<<<
@@ -53682,7 +55290,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 __pyx_t_4 = __pyx_f_3_sa_sym_isvar((__pyx_v_phrase->syms[__pyx_v_j]));
                 if (__pyx_t_4) {
 
-                  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1763
+                  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1776
  *                                 for j from 0 <= j < phrase.n:
  *                                     if sym_isvar(phrase.syms[j]):
  *                                         fphr_arr._append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
@@ -53691,7 +55299,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
                   ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_fphr_arr->__pyx_vtab)->_append(__pyx_v_fphr_arr, __pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i));
 
-                  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1764
+                  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1777
  *                                     if sym_isvar(phrase.syms[j]):
  *                                         fphr_arr._append(sym_setindex(self.category, i))
  *                                         i = i + 1             # <<<<<<<<<<<<<<
@@ -53703,7 +55311,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 }
                 /*else*/ {
 
-                  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1766
+                  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1779
  *                                         i = i + 1
  *                                     else:
  *                                         fphr_arr._append(phrase.syms[j])             # <<<<<<<<<<<<<<
@@ -53715,7 +55323,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 __pyx_L106:;
               }
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1767
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1780
  *                                     else:
  *                                         fphr_arr._append(phrase.syms[j])
  *                                 fphr_arr._append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
@@ -53724,81 +55332,81 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
  */
               ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_fphr_arr->__pyx_vtab)->_append(__pyx_v_fphr_arr, __pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i));
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1768
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1781
  *                                         fphr_arr._append(phrase.syms[j])
  *                                 fphr_arr._append(sym_setindex(self.category, i))
  *                                 self.findexes.append(sym_setindex(self.category, i))             # <<<<<<<<<<<<<<
  *                                 fphr = Phrase(fphr_arr)
  *                                 phrase_list = self.extract_phrases(e_x_low, e_x_high, e_gap_low, e_gap_high, e_links_low, num_gaps+2,
  */
-              __pyx_t_14 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i)); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_14 = PyInt_FromLong(__pyx_f_3_sa_sym_setindex(__pyx_v_self->category, __pyx_v_i)); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_14);
-              __pyx_t_15 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes), __pyx_t_14); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_15 = __Pyx_PyObject_Append(((PyObject *)__pyx_v_self->findexes), __pyx_t_14); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_15);
               __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
               __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1769
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1782
  *                                 fphr_arr._append(sym_setindex(self.category, i))
  *                                 self.findexes.append(sym_setindex(self.category, i))
  *                                 fphr = Phrase(fphr_arr)             # <<<<<<<<<<<<<<
  *                                 phrase_list = self.extract_phrases(e_x_low, e_x_high, e_gap_low, e_gap_high, e_links_low, num_gaps+2,
  *                                                     f_x_low, f_x_high, f_gap_low, f_gap_high, f_links_low,
  */
-              __pyx_t_15 = PyTuple_New(1); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_15 = PyTuple_New(1); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1782; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_15);
               __Pyx_INCREF(((PyObject *)__pyx_v_fphr_arr));
               PyTuple_SET_ITEM(__pyx_t_15, 0, ((PyObject *)__pyx_v_fphr_arr));
               __Pyx_GIVEREF(((PyObject *)__pyx_v_fphr_arr));
-              __pyx_t_14 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_Phrase)), ((PyObject *)__pyx_t_15), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_14 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_3_sa_Phrase)), ((PyObject *)__pyx_t_15), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1782; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_14);
               __Pyx_DECREF(((PyObject *)__pyx_t_15)); __pyx_t_15 = 0;
               __Pyx_DECREF(((PyObject *)__pyx_v_fphr));
               __pyx_v_fphr = ((struct __pyx_obj_3_sa_Phrase *)__pyx_t_14);
               __pyx_t_14 = 0;
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1772
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1785
  *                                 phrase_list = self.extract_phrases(e_x_low, e_x_high, e_gap_low, e_gap_high, e_links_low, num_gaps+2,
  *                                                     f_x_low, f_x_high, f_gap_low, f_gap_high, f_links_low,
  *                                                     matching.sent_id, e_sent_len, e_sent_start)             # <<<<<<<<<<<<<<
  *                                 if len(phrase_list) > 0:
  *                                     pair_count = 1.0 / len(phrase_list)
  */
-              __pyx_t_14 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->extract_phrases(__pyx_v_self, __pyx_v_e_x_low, __pyx_v_e_x_high, __pyx_v_e_gap_low, __pyx_v_e_gap_high, __pyx_v_e_links_low, (__pyx_v_num_gaps + 2), __pyx_v_f_x_low, __pyx_v_f_x_high, __pyx_v_f_gap_low, __pyx_v_f_gap_high, __pyx_v_f_links_low, __pyx_v_matching->sent_id, __pyx_v_e_sent_len, __pyx_v_e_sent_start); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_14 = ((struct __pyx_vtabstruct_3_sa_HieroCachingRuleFactory *)__pyx_v_self->__pyx_vtab)->extract_phrases(__pyx_v_self, __pyx_v_e_x_low, __pyx_v_e_x_high, __pyx_v_e_gap_low, __pyx_v_e_gap_high, __pyx_v_e_links_low, (__pyx_v_num_gaps + 2), __pyx_v_f_x_low, __pyx_v_f_x_high, __pyx_v_f_gap_low, __pyx_v_f_gap_high, __pyx_v_f_links_low, __pyx_v_matching->sent_id, __pyx_v_e_sent_len, __pyx_v_e_sent_start); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __Pyx_GOTREF(__pyx_t_14);
               __Pyx_XDECREF(__pyx_v_phrase_list);
               __pyx_v_phrase_list = __pyx_t_14;
               __pyx_t_14 = 0;
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1773
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1786
  *                                                     f_x_low, f_x_high, f_gap_low, f_gap_high, f_links_low,
  *                                                     matching.sent_id, e_sent_len, e_sent_start)
  *                                 if len(phrase_list) > 0:             # <<<<<<<<<<<<<<
  *                                     pair_count = 1.0 / len(phrase_list)
  *                                 else:
  */
-              __pyx_t_13 = PyObject_Length(__pyx_v_phrase_list); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+              __pyx_t_13 = PyObject_Length(__pyx_v_phrase_list); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1786; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
               __pyx_t_8 = (__pyx_t_13 > 0);
               if (__pyx_t_8) {
 
-                /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1774
+                /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1787
  *                                                     matching.sent_id, e_sent_len, e_sent_start)
  *                                 if len(phrase_list) > 0:
  *                                     pair_count = 1.0 / len(phrase_list)             # <<<<<<<<<<<<<<
  *                                 else:
  *                                     pair_count = 0
  */
-                __pyx_t_13 = PyObject_Length(__pyx_v_phrase_list); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1774; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_13 = PyObject_Length(__pyx_v_phrase_list); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1787; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 if (unlikely(__pyx_t_13 == 0)) {
                   PyErr_Format(PyExc_ZeroDivisionError, "float division");
-                  {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1774; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                  {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1787; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 }
                 __pyx_v_pair_count = (1.0 / __pyx_t_13);
                 goto __pyx_L107;
               }
               /*else*/ {
 
-                /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1776
+                /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1789
  *                                     pair_count = 1.0 / len(phrase_list)
  *                                 else:
  *                                     pair_count = 0             # <<<<<<<<<<<<<<
@@ -53809,7 +55417,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
               }
               __pyx_L107:;
 
-              /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1777
+              /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":1790
  *                                 else:
  *                                     pair_count = 0
  *                                 for phrase2, eindexes in phrase_list:             # <<<<<<<<<<<<<<
@@ -53820,7 +55428,7 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 __pyx_t_14 = __pyx_v_phrase_list; __Pyx_INCREF(__pyx_t_14); __pyx_t_13 = 0;
                 __pyx_t_16 = NULL;
               } else {
-                __pyx_t_13 = -1; __pyx_t_14 = PyObject_GetIter(__pyx_v_phrase_list); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+                __pyx_t_13 = -1; __pyx_t_14 = PyObject_GetIter(__pyx_v_phrase_list); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                 __Pyx_GOTREF(__pyx_t_14);
                 __pyx_t_16 = Py_TYPE(__pyx_t_14)->tp_iternext;
               }
@@ -53828,23 +55436,23 @@ static PyObject *__pyx_f_3_sa_23HieroCachingRuleFactory_extract(struct __pyx_obj
                 if (!__pyx_t_16 && PyList_CheckExact(__pyx_t_14)) {
                   if (__pyx_t_13 >= PyList_GET_SIZE(__pyx_t_14)) break;
                   #if CYTHON_COMPILING_IN_CPYTHON
-                  __pyx_t_15 = PyList_GET_ITEM(__pyx_t_14, __pyx_t_13); __Pyx_INCREF(__pyx_t_15); __pyx_t_13++;
+                  __pyx_t_15 = PyList_GET_ITEM(__pyx_t_14, __pyx_t_13); __Pyx_INCREF(__pyx_t_15); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                   #else
-                  __pyx_t_15 = PySequence_ITEM(__pyx_t_14, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1777; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+                  __pyx_t_15 = PySequence_ITEM(__pyx_t_14, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                   #endif
                 } else if (!__pyx_t_16 && PyTuple_CheckExact(__pyx_t_14)) {
                   if (__pyx_t_13 >= PyTuple_GET_SIZE(__pyx_t_14)) break;
                   #if CYTHON_COMPILING_IN_CPYTHON
-                  __pyx_t_15 = PyTuple_GET_ITEM(__pyx_t_14, __pyx_t_13); __Pyx_INCREF(__pyx_t_15); __pyx_t_13++;
+                  __pyx_t_15 = PyTuple_GET_ITEM(__pyx_t_14, __pyx_t_13); __Pyx_INCREF(__pyx_t_15); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 1790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-                /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1778
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-                /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1779
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1793
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+    __Pyx_INCREF(__pyx_v_name);
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+    __Pyx_GIVEREF(__pyx_v_name);
+    PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_5);
+    __Pyx_GIVEREF(__pyx_t_5);
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+    __Pyx_GOTREF(__pyx_t_5);
+    __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+    __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+  }
+  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/features.pxi":33
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+ *             scores.set(name, model(ctx))
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+  __Pyx_INCREF(((PyObject *)__pyx_v_scores));
+  __pyx_r = __pyx_v_scores;
+  goto __pyx_L0;
+
+  __pyx_r = ((struct __pyx_obj_3_sa_FeatureVector *)Py_None); __Pyx_INCREF(Py_None);
+  goto __pyx_L0;
+  __pyx_L1_error:;
+  __Pyx_XDECREF(__pyx_t_1);
+  __Pyx_XDECREF(__pyx_t_4);
+  __Pyx_XDECREF(__pyx_t_5);
+  __Pyx_XDECREF(__pyx_t_6);
+  __Pyx_XDECREF(__pyx_t_7);
+  __Pyx_AddTraceback("_sa.Scorer.score", __pyx_clineno, __pyx_lineno, __pyx_filename);
+  __pyx_r = 0;
+  __pyx_L0:;
+  __Pyx_XDECREF((PyObject *)__pyx_v_scores);
+  __Pyx_XDECREF(__pyx_v_name);
+  __Pyx_XDECREF(__pyx_v_model);
+  __Pyx_XGIVEREF((PyObject *)__pyx_r);
+  __Pyx_RefNannyFinishContext();
+  return __pyx_r;
+}
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+
+static PyObject *__pyx_tp_new_3_sa_FloatList(PyTypeObject *t, PyObject *a, PyObject *k) {
+  struct __pyx_obj_3_sa_FloatList *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
-  p = ((struct __pyx_obj_3_sa_Phrase *)o);
-  p->__pyx_vtab = __pyx_vtabptr_3_sa_Phrase;
-  if (__pyx_pw_3_sa_6Phrase_1__cinit__(o, a, k) < 0) {
+  p = ((struct __pyx_obj_3_sa_FloatList *)o);
+  p->__pyx_vtab = __pyx_vtabptr_3_sa_FloatList;
+  if (__pyx_pw_3_sa_9FloatList_1__cinit__(o, a, k) < 0) {
     Py_DECREF(o); o = 0;
   }
   return o;
 }
 
-static void __pyx_tp_dealloc_3_sa_Phrase(PyObject *o) {
+static void __pyx_tp_dealloc_3_sa_FloatList(PyObject *o) {
   {
     PyObject *etype, *eval, *etb;
     PyErr_Fetch(&etype, &eval, &etb);
     ++Py_REFCNT(o);
-    __pyx_pw_3_sa_6Phrase_3__dealloc__(o);
+    __pyx_pw_3_sa_9FloatList_3__dealloc__(o);
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     --Py_REFCNT(o);
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   }
   (*Py_TYPE(o)->tp_free)(o);
 }
-static PyObject *__pyx_sq_item_3_sa_Phrase(PyObject *o, Py_ssize_t i) {
+static PyObject *__pyx_sq_item_3_sa_FloatList(PyObject *o, Py_ssize_t i) {
   PyObject *r;
   PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0;
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@@ -54145,28 +56640,25 @@ static PyObject *__pyx_sq_item_3_sa_Phrase(PyObject *o, Py_ssize_t i) {
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 }
 
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-  return __pyx_pw_3_sa_6Phrase_5words_1__get__(o);
+static int __pyx_mp_ass_subscript_3_sa_FloatList(PyObject *o, PyObject *i, PyObject *v) {
+  if (v) {
+    return __pyx_pw_3_sa_9FloatList_7__setitem__(o, i, v);
+  }
+  else {
+    PyErr_Format(PyExc_NotImplementedError,
+      "Subscript deletion not supported by %s", Py_TYPE(o)->tp_name);
+    return -1;
+  }
 }
 
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-  {__Pyx_NAMESTR("strhandle"), (PyCFunction)__pyx_pw_3_sa_6Phrase_9strhandle, METH_NOARGS, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("arity"), (PyCFunction)__pyx_pw_3_sa_6Phrase_11arity, METH_NOARGS, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("getvarpos"), (PyCFunction)__pyx_pw_3_sa_6Phrase_13getvarpos, METH_O, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("getvar"), (PyCFunction)__pyx_pw_3_sa_6Phrase_15getvar, METH_O, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("clen"), (PyCFunction)__pyx_pw_3_sa_6Phrase_17clen, METH_O, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("getchunk"), (PyCFunction)__pyx_pw_3_sa_6Phrase_19getchunk, METH_O, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("subst"), (PyCFunction)__pyx_pw_3_sa_6Phrase_32subst, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)},
+static PyMethodDef __pyx_methods_3_sa_FloatList[] = {
+  {__Pyx_NAMESTR("append"), (PyCFunction)__pyx_pw_3_sa_9FloatList_11append, METH_O, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("write"), (PyCFunction)__pyx_pw_3_sa_9FloatList_13write, METH_O, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("read"), (PyCFunction)__pyx_pw_3_sa_9FloatList_15read, METH_O, __Pyx_DOCSTR(0)},
   {0, 0, 0, 0}
 };
 
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-  {0, 0, 0, 0, 0}
-};
-
-static PyNumberMethods __pyx_tp_as_number_Phrase = {
+static PyNumberMethods __pyx_tp_as_number_FloatList = {
   0, /*nb_add*/
   0, /*nb_subtract*/
   0, /*nb_multiply*/
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 };
 
-static PySequenceMethods __pyx_tp_as_sequence_Phrase = {
-  __pyx_pw_3_sa_6Phrase_25__len__, /*sq_length*/
+static PySequenceMethods __pyx_tp_as_sequence_FloatList = {
+  __pyx_pw_3_sa_9FloatList_9__len__, /*sq_length*/
   0, /*sq_concat*/
   0, /*sq_repeat*/
-  __pyx_sq_item_3_sa_Phrase, /*sq_item*/
+  __pyx_sq_item_3_sa_FloatList, /*sq_item*/
   0, /*sq_slice*/
   0, /*sq_ass_item*/
   0, /*sq_ass_slice*/
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 };
 
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-  __pyx_pw_3_sa_6Phrase_25__len__, /*mp_length*/
-  __pyx_pw_3_sa_6Phrase_27__getitem__, /*mp_subscript*/
-  0, /*mp_ass_subscript*/
+static PyMappingMethods __pyx_tp_as_mapping_FloatList = {
+  __pyx_pw_3_sa_9FloatList_9__len__, /*mp_length*/
+  __pyx_pw_3_sa_9FloatList_5__getitem__, /*mp_subscript*/
+  __pyx_mp_ass_subscript_3_sa_FloatList, /*mp_ass_subscript*/
 };
 
-static PyBufferProcs __pyx_tp_as_buffer_Phrase = {
+static PyBufferProcs __pyx_tp_as_buffer_FloatList = {
   #if PY_MAJOR_VERSION < 3
   0, /*bf_getreadbuffer*/
   #endif
@@ -54264,41 +56756,41 @@ static PyBufferProcs __pyx_tp_as_buffer_Phrase = {
   #endif
 };
 
-static PyTypeObject __pyx_type_3_sa_Phrase = {
+static PyTypeObject __pyx_type_3_sa_FloatList = {
   PyVarObject_HEAD_INIT(0, 0)
-  __Pyx_NAMESTR("_sa.Phrase"), /*tp_name*/
-  sizeof(struct __pyx_obj_3_sa_Phrase), /*tp_basicsize*/
+  __Pyx_NAMESTR("_sa.FloatList"), /*tp_name*/
+  sizeof(struct __pyx_obj_3_sa_FloatList), /*tp_basicsize*/
   0, /*tp_itemsize*/
-  __pyx_tp_dealloc_3_sa_Phrase, /*tp_dealloc*/
+  __pyx_tp_dealloc_3_sa_FloatList, /*tp_dealloc*/
   0, /*tp_print*/
   0, /*tp_getattr*/
   0, /*tp_setattr*/
   #if PY_MAJOR_VERSION < 3
-  __pyx_pw_3_sa_6Phrase_21__cmp__, /*tp_compare*/
+  0, /*tp_compare*/
   #else
   0, /*reserved*/
   #endif
   0, /*tp_repr*/
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-  &__pyx_tp_as_sequence_Phrase, /*tp_as_sequence*/
-  &__pyx_tp_as_mapping_Phrase, /*tp_as_mapping*/
-  __pyx_pw_3_sa_6Phrase_23__hash__, /*tp_hash*/
+  &__pyx_tp_as_number_FloatList, /*tp_as_number*/
+  &__pyx_tp_as_sequence_FloatList, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping_FloatList, /*tp_as_mapping*/
+  0, /*tp_hash*/
   0, /*tp_call*/
-  __pyx_pw_3_sa_6Phrase_5__str__, /*tp_str*/
+  0, /*tp_str*/
   0, /*tp_getattro*/
   0, /*tp_setattro*/
-  &__pyx_tp_as_buffer_Phrase, /*tp_as_buffer*/
+  &__pyx_tp_as_buffer_FloatList, /*tp_as_buffer*/
   Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
   0, /*tp_doc*/
   0, /*tp_traverse*/
   0, /*tp_clear*/
   0, /*tp_richcompare*/
   0, /*tp_weaklistoffset*/
-  __pyx_pw_3_sa_6Phrase_29__iter__, /*tp_iter*/
+  0, /*tp_iter*/
   0, /*tp_iternext*/
-  __pyx_methods_3_sa_Phrase, /*tp_methods*/
+  __pyx_methods_3_sa_FloatList, /*tp_methods*/
   0, /*tp_members*/
-  __pyx_getsets_3_sa_Phrase, /*tp_getset*/
+  0, /*tp_getset*/
   0, /*tp_base*/
   0, /*tp_dict*/
   0, /*tp_descr_get*/
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   0, /*tp_init*/
   0, /*tp_alloc*/
-  __pyx_tp_new_3_sa_Phrase, /*tp_new*/
+  __pyx_tp_new_3_sa_FloatList, /*tp_new*/
   0, /*tp_free*/
   0, /*tp_is_gc*/
   0, /*tp_bases*/
@@ -54319,133 +56811,269 @@ static PyTypeObject __pyx_type_3_sa_Phrase = {
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 };
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-static PyObject *__pyx_tp_new_3_sa_Rule(PyTypeObject *t, PyObject *a, PyObject *k) {
-  struct __pyx_obj_3_sa_Rule *p;
+static PyObject *__pyx_tp_new_3_sa_IntList(PyTypeObject *t, PyObject *a, PyObject *k) {
+  struct __pyx_obj_3_sa_IntList *p;
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-  p->e = ((struct __pyx_obj_3_sa_Phrase *)Py_None); Py_INCREF(Py_None);
-  p->word_alignments = Py_None; Py_INCREF(Py_None);
-  if (__pyx_pw_3_sa_4Rule_1__cinit__(o, a, k) < 0) {
+  p = ((struct __pyx_obj_3_sa_IntList *)o);
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 }
 
-static void __pyx_tp_dealloc_3_sa_Rule(PyObject *o) {
-  struct __pyx_obj_3_sa_Rule *p = (struct __pyx_obj_3_sa_Rule *)o;
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     PyErr_Fetch(&etype, &eval, &etb);
     ++Py_REFCNT(o);
-    __pyx_pw_3_sa_4Rule_3__dealloc__(o);
+    __pyx_pw_3_sa_7IntList_15__dealloc__(o);
     if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
     --Py_REFCNT(o);
     PyErr_Restore(etype, eval, etb);
   }
-  Py_XDECREF(((PyObject *)p->f));
-  Py_XDECREF(((PyObject *)p->e));
-  Py_XDECREF(p->word_alignments);
   (*Py_TYPE(o)->tp_free)(o);
 }
-
-static int __pyx_tp_traverse_3_sa_Rule(PyObject *o, visitproc v, void *a) {
-  int e;
-  struct __pyx_obj_3_sa_Rule *p = (struct __pyx_obj_3_sa_Rule *)o;
-  if (p->f) {
-    e = (*v)(((PyObject*)p->f), a); if (e) return e;
-  }
-  if (p->e) {
-    e = (*v)(((PyObject*)p->e), a); if (e) return e;
-  }
-  if (p->word_alignments) {
-    e = (*v)(p->word_alignments, a); if (e) return e;
-  }
-  return 0;
-}
-
-static int __pyx_tp_clear_3_sa_Rule(PyObject *o) {
-  struct __pyx_obj_3_sa_Rule *p = (struct __pyx_obj_3_sa_Rule *)o;
-  PyObject* tmp;
-  tmp = ((PyObject*)p->f);
-  p->f = ((struct __pyx_obj_3_sa_Phrase *)Py_None); Py_INCREF(Py_None);
-  Py_XDECREF(tmp);
-  tmp = ((PyObject*)p->e);
-  p->e = ((struct __pyx_obj_3_sa_Phrase *)Py_None); Py_INCREF(Py_None);
-  Py_XDECREF(tmp);
-  tmp = ((PyObject*)p->word_alignments);
-  p->word_alignments = Py_None; Py_INCREF(Py_None);
-  Py_XDECREF(tmp);
-  return 0;
-}
-
-static PyObject *__pyx_getprop_3_sa_4Rule_scores(PyObject *o, CYTHON_UNUSED void *x) {
-  return __pyx_pw_3_sa_4Rule_6scores_1__get__(o);
+static PyObject *__pyx_sq_item_3_sa_IntList(PyObject *o, Py_ssize_t i) {
+  PyObject *r;
+  PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0;
+  r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x);
+  Py_DECREF(x);
+  return r;
 }
 
-static int __pyx_setprop_3_sa_4Rule_scores(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_mp_ass_subscript_3_sa_IntList(PyObject *o, PyObject *i, PyObject *v) {
   if (v) {
-    return __pyx_pw_3_sa_4Rule_6scores_3__set__(o, v);
+    return __pyx_pw_3_sa_7IntList_22__setitem__(o, i, v);
   }
   else {
-    PyErr_SetString(PyExc_NotImplementedError, "__del__");
+    PyErr_Format(PyExc_NotImplementedError,
+      "Subscript deletion not supported by %s", Py_TYPE(o)->tp_name);
     return -1;
   }
 }
 
-static PyObject *__pyx_getprop_3_sa_4Rule_lhs(PyObject *o, CYTHON_UNUSED void *x) {
-  return __pyx_pw_3_sa_4Rule_3lhs_1__get__(o);
-}
+static PyMethodDef __pyx_methods_3_sa_IntList[] = {
+  {__Pyx_NAMESTR("index"), (PyCFunction)__pyx_pw_3_sa_7IntList_5index, METH_O, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("partition"), (PyCFunction)__pyx_pw_3_sa_7IntList_7partition, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("_doquicksort"), (PyCFunction)__pyx_pw_3_sa_7IntList_9_doquicksort, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("sort"), (PyCFunction)__pyx_pw_3_sa_7IntList_11sort, METH_NOARGS, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("reset"), (PyCFunction)__pyx_pw_3_sa_7IntList_13reset, METH_NOARGS, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("get_size"), (PyCFunction)__pyx_pw_3_sa_7IntList_26get_size, METH_NOARGS, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("append"), (PyCFunction)__pyx_pw_3_sa_7IntList_28append, METH_O, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("extend"), (PyCFunction)__pyx_pw_3_sa_7IntList_30extend, METH_O, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("write"), (PyCFunction)__pyx_pw_3_sa_7IntList_32write, METH_O, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("read"), (PyCFunction)__pyx_pw_3_sa_7IntList_34read, METH_O, __Pyx_DOCSTR(0)},
+  {0, 0, 0, 0}
+};
 
-static int __pyx_setprop_3_sa_4Rule_lhs(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
-  if (v) {
-    return __pyx_pw_3_sa_4Rule_3lhs_3__set__(o, v);
-  }
-  else {
-    PyErr_SetString(PyExc_NotImplementedError, "__del__");
-    return -1;
-  }
-}
+static PyNumberMethods __pyx_tp_as_number_IntList = {
+  0, /*nb_add*/
+  0, /*nb_subtract*/
+  0, /*nb_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_divide*/
+  #endif
+  0, /*nb_remainder*/
+  0, /*nb_divmod*/
+  0, /*nb_power*/
+  0, /*nb_negative*/
+  0, /*nb_positive*/
+  0, /*nb_absolute*/
+  0, /*nb_nonzero*/
+  0, /*nb_invert*/
+  0, /*nb_lshift*/
+  0, /*nb_rshift*/
+  0, /*nb_and*/
+  0, /*nb_xor*/
+  0, /*nb_or*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_coerce*/
+  #endif
+  0, /*nb_int*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_long*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*nb_float*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_oct*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_hex*/
+  #endif
+  0, /*nb_inplace_add*/
+  0, /*nb_inplace_subtract*/
+  0, /*nb_inplace_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_inplace_divide*/
+  #endif
+  0, /*nb_inplace_remainder*/
+  0, /*nb_inplace_power*/
+  0, /*nb_inplace_lshift*/
+  0, /*nb_inplace_rshift*/
+  0, /*nb_inplace_and*/
+  0, /*nb_inplace_xor*/
+  0, /*nb_inplace_or*/
+  0, /*nb_floor_divide*/
+  0, /*nb_true_divide*/
+  0, /*nb_inplace_floor_divide*/
+  0, /*nb_inplace_true_divide*/
+  #if PY_VERSION_HEX >= 0x02050000
+  0, /*nb_index*/
+  #endif
+};
 
-static PyObject *__pyx_getprop_3_sa_4Rule_f(PyObject *o, CYTHON_UNUSED void *x) {
-  return __pyx_pw_3_sa_4Rule_1f_1__get__(o);
-}
+static PySequenceMethods __pyx_tp_as_sequence_IntList = {
+  __pyx_pw_3_sa_7IntList_24__len__, /*sq_length*/
+  0, /*sq_concat*/
+  0, /*sq_repeat*/
+  __pyx_sq_item_3_sa_IntList, /*sq_item*/
+  0, /*sq_slice*/
+  0, /*sq_ass_item*/
+  0, /*sq_ass_slice*/
+  0, /*sq_contains*/
+  0, /*sq_inplace_concat*/
+  0, /*sq_inplace_repeat*/
+};
 
-static PyObject *__pyx_getprop_3_sa_4Rule_e(PyObject *o, CYTHON_UNUSED void *x) {
-  return __pyx_pw_3_sa_4Rule_1e_1__get__(o);
+static PyMappingMethods __pyx_tp_as_mapping_IntList = {
+  __pyx_pw_3_sa_7IntList_24__len__, /*mp_length*/
+  __pyx_pw_3_sa_7IntList_20__getitem__, /*mp_subscript*/
+  __pyx_mp_ass_subscript_3_sa_IntList, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer_IntList = {
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getreadbuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getwritebuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getsegcount*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getcharbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_getbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_releasebuffer*/
+  #endif
+};
+
+static PyTypeObject __pyx_type_3_sa_IntList = {
+  PyVarObject_HEAD_INIT(0, 0)
+  __Pyx_NAMESTR("_sa.IntList"), /*tp_name*/
+  sizeof(struct __pyx_obj_3_sa_IntList), /*tp_basicsize*/
+  0, /*tp_itemsize*/
+  __pyx_tp_dealloc_3_sa_IntList, /*tp_dealloc*/
+  0, /*tp_print*/
+  0, /*tp_getattr*/
+  0, /*tp_setattr*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*tp_compare*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*tp_repr*/
+  &__pyx_tp_as_number_IntList, /*tp_as_number*/
+  &__pyx_tp_as_sequence_IntList, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping_IntList, /*tp_as_mapping*/
+  0, /*tp_hash*/
+  0, /*tp_call*/
+  __pyx_pw_3_sa_7IntList_3__str__, /*tp_str*/
+  0, /*tp_getattro*/
+  0, /*tp_setattro*/
+  &__pyx_tp_as_buffer_IntList, /*tp_as_buffer*/
+  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
+  0, /*tp_doc*/
+  0, /*tp_traverse*/
+  0, /*tp_clear*/
+  0, /*tp_richcompare*/
+  0, /*tp_weaklistoffset*/
+  __pyx_pw_3_sa_7IntList_17__iter__, /*tp_iter*/
+  0, /*tp_iternext*/
+  __pyx_methods_3_sa_IntList, /*tp_methods*/
+  0, /*tp_members*/
+  0, /*tp_getset*/
+  0, /*tp_base*/
+  0, /*tp_dict*/
+  0, /*tp_descr_get*/
+  0, /*tp_descr_set*/
+  0, /*tp_dictoffset*/
+  0, /*tp_init*/
+  0, /*tp_alloc*/
+  __pyx_tp_new_3_sa_IntList, /*tp_new*/
+  0, /*tp_free*/
+  0, /*tp_is_gc*/
+  0, /*tp_bases*/
+  0, /*tp_mro*/
+  0, /*tp_cache*/
+  0, /*tp_subclasses*/
+  0, /*tp_weaklist*/
+  0, /*tp_del*/
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*tp_version_tag*/
+  #endif
+};
+
+static PyObject *__pyx_tp_new_3_sa_FeatureVector(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+  struct __pyx_obj_3_sa_FeatureVector *p;
+  PyObject *o = (*t->tp_alloc)(t, 0);
+  if (!o) return 0;
+  p = ((struct __pyx_obj_3_sa_FeatureVector *)o);
+  p->names = ((struct __pyx_obj_3_sa_IntList *)Py_None); Py_INCREF(Py_None);
+  p->values = ((struct __pyx_obj_3_sa_FloatList *)Py_None); Py_INCREF(Py_None);
+  if (__pyx_pw_3_sa_13FeatureVector_1__cinit__(o, __pyx_empty_tuple, NULL) < 0) {
+    Py_DECREF(o); o = 0;
+  }
+  return o;
 }
 
-static PyObject *__pyx_getprop_3_sa_4Rule_word_alignments(PyObject *o, CYTHON_UNUSED void *x) {
-  return __pyx_pw_3_sa_4Rule_15word_alignments_1__get__(o);
+static void __pyx_tp_dealloc_3_sa_FeatureVector(PyObject *o) {
+  struct __pyx_obj_3_sa_FeatureVector *p = (struct __pyx_obj_3_sa_FeatureVector *)o;
+  Py_CLEAR(p->names);
+  Py_CLEAR(p->values);
+  (*Py_TYPE(o)->tp_free)(o);
 }
 
-static int __pyx_setprop_3_sa_4Rule_word_alignments(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
-  if (v) {
-    return __pyx_pw_3_sa_4Rule_15word_alignments_3__set__(o, v);
+static int __pyx_tp_traverse_3_sa_FeatureVector(PyObject *o, visitproc v, void *a) {
+  int e;
+  struct __pyx_obj_3_sa_FeatureVector *p = (struct __pyx_obj_3_sa_FeatureVector *)o;
+  if (p->names) {
+    e = (*v)(((PyObject*)p->names), a); if (e) return e;
   }
-  else {
-    return __pyx_pw_3_sa_4Rule_15word_alignments_5__del__(o);
+  if (p->values) {
+    e = (*v)(((PyObject*)p->values), a); if (e) return e;
   }
+  return 0;
 }
 
-static PyMethodDef __pyx_methods_3_sa_Rule[] = {
-  {__Pyx_NAMESTR("fmerge"), (PyCFunction)__pyx_pw_3_sa_4Rule_11fmerge, METH_O, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("arity"), (PyCFunction)__pyx_pw_3_sa_4Rule_13arity, METH_NOARGS, __Pyx_DOCSTR(0)},
-  {0, 0, 0, 0}
-};
+static int __pyx_tp_clear_3_sa_FeatureVector(PyObject *o) {
+  struct __pyx_obj_3_sa_FeatureVector *p = (struct __pyx_obj_3_sa_FeatureVector *)o;
+  PyObject* tmp;
+  tmp = ((PyObject*)p->names);
+  p->names = ((struct __pyx_obj_3_sa_IntList *)Py_None); Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->values);
+  p->values = ((struct __pyx_obj_3_sa_FloatList *)Py_None); Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  return 0;
+}
 
-static struct PyGetSetDef __pyx_getsets_3_sa_Rule[] = {
-  {(char *)"scores", __pyx_getprop_3_sa_4Rule_scores, __pyx_setprop_3_sa_4Rule_scores, 0, 0},
-  {(char *)"lhs", __pyx_getprop_3_sa_4Rule_lhs, __pyx_setprop_3_sa_4Rule_lhs, 0, 0},
-  {(char *)"f", __pyx_getprop_3_sa_4Rule_f, 0, 0, 0},
-  {(char *)"e", __pyx_getprop_3_sa_4Rule_e, 0, 0, 0},
-  {(char *)"word_alignments", __pyx_getprop_3_sa_4Rule_word_alignments, __pyx_setprop_3_sa_4Rule_word_alignments, 0, 0},
-  {0, 0, 0, 0, 0}
+static PyMethodDef __pyx_methods_3_sa_FeatureVector[] = {
+  {__Pyx_NAMESTR("set"), (PyCFunction)__pyx_pw_3_sa_13FeatureVector_3set, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)},
+  {0, 0, 0, 0}
 };
 
-static PyNumberMethods __pyx_tp_as_number_Rule = {
+static PyNumberMethods __pyx_tp_as_number_FeatureVector = {
   0, /*nb_add*/
   0, /*nb_subtract*/
   0, /*nb_multiply*/
@@ -54481,7 +57109,7 @@ static PyNumberMethods __pyx_tp_as_number_Rule = {
   #if PY_MAJOR_VERSION < 3
   0, /*nb_hex*/
   #endif
-  __pyx_pw_3_sa_4Rule_9__iadd__, /*nb_inplace_add*/
+  0, /*nb_inplace_add*/
   0, /*nb_inplace_subtract*/
   0, /*nb_inplace_multiply*/
   #if PY_MAJOR_VERSION < 3
@@ -54503,7 +57131,7 @@ static PyNumberMethods __pyx_tp_as_number_Rule = {
   #endif
 };
 
-static PySequenceMethods __pyx_tp_as_sequence_Rule = {
+static PySequenceMethods __pyx_tp_as_sequence_FeatureVector = {
   0, /*sq_length*/
   0, /*sq_concat*/
   0, /*sq_repeat*/
@@ -54516,13 +57144,13 @@ static PySequenceMethods __pyx_tp_as_sequence_Rule = {
   0, /*sq_inplace_repeat*/
 };
 
-static PyMappingMethods __pyx_tp_as_mapping_Rule = {
+static PyMappingMethods __pyx_tp_as_mapping_FeatureVector = {
   0, /*mp_length*/
   0, /*mp_subscript*/
   0, /*mp_ass_subscript*/
 };
 
-static PyBufferProcs __pyx_tp_as_buffer_Rule = {
+static PyBufferProcs __pyx_tp_as_buffer_FeatureVector = {
   #if PY_MAJOR_VERSION < 3
   0, /*bf_getreadbuffer*/
   #endif
@@ -54543,41 +57171,41 @@ static PyBufferProcs __pyx_tp_as_buffer_Rule = {
   #endif
 };
 
-static PyTypeObject __pyx_type_3_sa_Rule = {
+static PyTypeObject __pyx_type_3_sa_FeatureVector = {
   PyVarObject_HEAD_INIT(0, 0)
-  __Pyx_NAMESTR("_sa.Rule"), /*tp_name*/
-  sizeof(struct __pyx_obj_3_sa_Rule), /*tp_basicsize*/
+  __Pyx_NAMESTR("_sa.FeatureVector"), /*tp_name*/
+  sizeof(struct __pyx_obj_3_sa_FeatureVector), /*tp_basicsize*/
   0, /*tp_itemsize*/
-  __pyx_tp_dealloc_3_sa_Rule, /*tp_dealloc*/
+  __pyx_tp_dealloc_3_sa_FeatureVector, /*tp_dealloc*/
   0, /*tp_print*/
   0, /*tp_getattr*/
   0, /*tp_setattr*/
   #if PY_MAJOR_VERSION < 3
-  __pyx_pw_3_sa_4Rule_7__cmp__, /*tp_compare*/
+  0, /*tp_compare*/
   #else
   0, /*reserved*/
   #endif
   0, /*tp_repr*/
-  &__pyx_tp_as_number_Rule, /*tp_as_number*/
-  &__pyx_tp_as_sequence_Rule, /*tp_as_sequence*/
-  &__pyx_tp_as_mapping_Rule, /*tp_as_mapping*/
-  __pyx_pw_3_sa_4Rule_5__hash__, /*tp_hash*/
+  &__pyx_tp_as_number_FeatureVector, /*tp_as_number*/
+  &__pyx_tp_as_sequence_FeatureVector, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping_FeatureVector, /*tp_as_mapping*/
+  0, /*tp_hash*/
   0, /*tp_call*/
-  __pyx_pw_3_sa_4Rule_15__str__, /*tp_str*/
+  __pyx_pw_3_sa_13FeatureVector_8__str__, /*tp_str*/
   0, /*tp_getattro*/
   0, /*tp_setattro*/
-  &__pyx_tp_as_buffer_Rule, /*tp_as_buffer*/
+  &__pyx_tp_as_buffer_FeatureVector, /*tp_as_buffer*/
   Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
   0, /*tp_doc*/
-  __pyx_tp_traverse_3_sa_Rule, /*tp_traverse*/
-  __pyx_tp_clear_3_sa_Rule, /*tp_clear*/
+  __pyx_tp_traverse_3_sa_FeatureVector, /*tp_traverse*/
+  __pyx_tp_clear_3_sa_FeatureVector, /*tp_clear*/
   0, /*tp_richcompare*/
   0, /*tp_weaklistoffset*/
-  0, /*tp_iter*/
+  __pyx_pw_3_sa_13FeatureVector_5__iter__, /*tp_iter*/
   0, /*tp_iternext*/
-  __pyx_methods_3_sa_Rule, /*tp_methods*/
+  __pyx_methods_3_sa_FeatureVector, /*tp_methods*/
   0, /*tp_members*/
-  __pyx_getsets_3_sa_Rule, /*tp_getset*/
+  0, /*tp_getset*/
   0, /*tp_base*/
   0, /*tp_dict*/
   0, /*tp_descr_get*/
@@ -54585,7 +57213,7 @@ static PyTypeObject __pyx_type_3_sa_Rule = {
   0, /*tp_dictoffset*/
   0, /*tp_init*/
   0, /*tp_alloc*/
-  __pyx_tp_new_3_sa_Rule, /*tp_new*/
+  __pyx_tp_new_3_sa_FeatureVector, /*tp_new*/
   0, /*tp_free*/
   0, /*tp_is_gc*/
   0, /*tp_bases*/
@@ -54598,33 +57226,33 @@ static PyTypeObject __pyx_type_3_sa_Rule = {
   0, /*tp_version_tag*/
   #endif
 };
-static struct __pyx_vtabstruct_3_sa_FloatList __pyx_vtable_3_sa_FloatList;
+static struct __pyx_vtabstruct_3_sa_Phrase __pyx_vtable_3_sa_Phrase;
 
-static PyObject *__pyx_tp_new_3_sa_FloatList(PyTypeObject *t, PyObject *a, PyObject *k) {
-  struct __pyx_obj_3_sa_FloatList *p;
+static PyObject *__pyx_tp_new_3_sa_Phrase(PyTypeObject *t, PyObject *a, PyObject *k) {
+  struct __pyx_obj_3_sa_Phrase *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
-  p = ((struct __pyx_obj_3_sa_FloatList *)o);
-  p->__pyx_vtab = __pyx_vtabptr_3_sa_FloatList;
-  if (__pyx_pw_3_sa_9FloatList_1__cinit__(o, a, k) < 0) {
+  p = ((struct __pyx_obj_3_sa_Phrase *)o);
+  p->__pyx_vtab = __pyx_vtabptr_3_sa_Phrase;
+  if (__pyx_pw_3_sa_6Phrase_1__cinit__(o, a, k) < 0) {
     Py_DECREF(o); o = 0;
   }
   return o;
 }
 
-static void __pyx_tp_dealloc_3_sa_FloatList(PyObject *o) {
+static void __pyx_tp_dealloc_3_sa_Phrase(PyObject *o) {
   {
     PyObject *etype, *eval, *etb;
     PyErr_Fetch(&etype, &eval, &etb);
     ++Py_REFCNT(o);
-    __pyx_pw_3_sa_9FloatList_3__dealloc__(o);
+    __pyx_pw_3_sa_6Phrase_3__dealloc__(o);
     if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
     --Py_REFCNT(o);
     PyErr_Restore(etype, eval, etb);
   }
   (*Py_TYPE(o)->tp_free)(o);
 }
-static PyObject *__pyx_sq_item_3_sa_FloatList(PyObject *o, Py_ssize_t i) {
+static PyObject *__pyx_sq_item_3_sa_Phrase(PyObject *o, Py_ssize_t i) {
   PyObject *r;
   PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0;
   r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x);
@@ -54632,25 +57260,28 @@ static PyObject *__pyx_sq_item_3_sa_FloatList(PyObject *o, Py_ssize_t i) {
   return r;
 }
 
-static int __pyx_mp_ass_subscript_3_sa_FloatList(PyObject *o, PyObject *i, PyObject *v) {
-  if (v) {
-    return __pyx_pw_3_sa_9FloatList_7__setitem__(o, i, v);
-  }
-  else {
-    PyErr_Format(PyExc_NotImplementedError,
-      "Subscript deletion not supported by %s", Py_TYPE(o)->tp_name);
-    return -1;
-  }
+static PyObject *__pyx_getprop_3_sa_6Phrase_words(PyObject *o, CYTHON_UNUSED void *x) {
+  return __pyx_pw_3_sa_6Phrase_5words_1__get__(o);
 }
 
-static PyMethodDef __pyx_methods_3_sa_FloatList[] = {
-  {__Pyx_NAMESTR("append"), (PyCFunction)__pyx_pw_3_sa_9FloatList_11append, METH_O, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("write"), (PyCFunction)__pyx_pw_3_sa_9FloatList_13write, METH_O, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("read"), (PyCFunction)__pyx_pw_3_sa_9FloatList_15read, METH_O, __Pyx_DOCSTR(0)},
+static PyMethodDef __pyx_methods_3_sa_Phrase[] = {
+  {__Pyx_NAMESTR("handle"), (PyCFunction)__pyx_pw_3_sa_6Phrase_7handle, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_3_sa_6Phrase_6handle)},
+  {__Pyx_NAMESTR("strhandle"), (PyCFunction)__pyx_pw_3_sa_6Phrase_9strhandle, METH_NOARGS, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("arity"), (PyCFunction)__pyx_pw_3_sa_6Phrase_11arity, METH_NOARGS, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("getvarpos"), (PyCFunction)__pyx_pw_3_sa_6Phrase_13getvarpos, METH_O, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("getvar"), (PyCFunction)__pyx_pw_3_sa_6Phrase_15getvar, METH_O, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("clen"), (PyCFunction)__pyx_pw_3_sa_6Phrase_17clen, METH_O, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("getchunk"), (PyCFunction)__pyx_pw_3_sa_6Phrase_19getchunk, METH_O, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("subst"), (PyCFunction)__pyx_pw_3_sa_6Phrase_32subst, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)},
   {0, 0, 0, 0}
 };
 
-static PyNumberMethods __pyx_tp_as_number_FloatList = {
+static struct PyGetSetDef __pyx_getsets_3_sa_Phrase[] = {
+  {(char *)"words", __pyx_getprop_3_sa_6Phrase_words, 0, 0, 0},
+  {0, 0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number_Phrase = {
   0, /*nb_add*/
   0, /*nb_subtract*/
   0, /*nb_multiply*/
@@ -54708,11 +57339,11 @@ static PyNumberMethods __pyx_tp_as_number_FloatList = {
   #endif
 };
 
-static PySequenceMethods __pyx_tp_as_sequence_FloatList = {
-  __pyx_pw_3_sa_9FloatList_9__len__, /*sq_length*/
+static PySequenceMethods __pyx_tp_as_sequence_Phrase = {
+  __pyx_pw_3_sa_6Phrase_25__len__, /*sq_length*/
   0, /*sq_concat*/
   0, /*sq_repeat*/
-  __pyx_sq_item_3_sa_FloatList, /*sq_item*/
+  __pyx_sq_item_3_sa_Phrase, /*sq_item*/
   0, /*sq_slice*/
   0, /*sq_ass_item*/
   0, /*sq_ass_slice*/
@@ -54721,13 +57352,13 @@ static PySequenceMethods __pyx_tp_as_sequence_FloatList = {
   0, /*sq_inplace_repeat*/
 };
 
-static PyMappingMethods __pyx_tp_as_mapping_FloatList = {
-  __pyx_pw_3_sa_9FloatList_9__len__, /*mp_length*/
-  __pyx_pw_3_sa_9FloatList_5__getitem__, /*mp_subscript*/
-  __pyx_mp_ass_subscript_3_sa_FloatList, /*mp_ass_subscript*/
+static PyMappingMethods __pyx_tp_as_mapping_Phrase = {
+  __pyx_pw_3_sa_6Phrase_25__len__, /*mp_length*/
+  __pyx_pw_3_sa_6Phrase_27__getitem__, /*mp_subscript*/
+  0, /*mp_ass_subscript*/
 };
 
-static PyBufferProcs __pyx_tp_as_buffer_FloatList = {
+static PyBufferProcs __pyx_tp_as_buffer_Phrase = {
   #if PY_MAJOR_VERSION < 3
   0, /*bf_getreadbuffer*/
   #endif
@@ -54748,41 +57379,41 @@ static PyBufferProcs __pyx_tp_as_buffer_FloatList = {
   #endif
 };
 
-static PyTypeObject __pyx_type_3_sa_FloatList = {
+static PyTypeObject __pyx_type_3_sa_Phrase = {
   PyVarObject_HEAD_INIT(0, 0)
-  __Pyx_NAMESTR("_sa.FloatList"), /*tp_name*/
-  sizeof(struct __pyx_obj_3_sa_FloatList), /*tp_basicsize*/
+  __Pyx_NAMESTR("_sa.Phrase"), /*tp_name*/
+  sizeof(struct __pyx_obj_3_sa_Phrase), /*tp_basicsize*/
   0, /*tp_itemsize*/
-  __pyx_tp_dealloc_3_sa_FloatList, /*tp_dealloc*/
+  __pyx_tp_dealloc_3_sa_Phrase, /*tp_dealloc*/
   0, /*tp_print*/
   0, /*tp_getattr*/
   0, /*tp_setattr*/
   #if PY_MAJOR_VERSION < 3
-  0, /*tp_compare*/
+  __pyx_pw_3_sa_6Phrase_21__cmp__, /*tp_compare*/
   #else
   0, /*reserved*/
   #endif
   0, /*tp_repr*/
-  &__pyx_tp_as_number_FloatList, /*tp_as_number*/
-  &__pyx_tp_as_sequence_FloatList, /*tp_as_sequence*/
-  &__pyx_tp_as_mapping_FloatList, /*tp_as_mapping*/
-  0, /*tp_hash*/
+  &__pyx_tp_as_number_Phrase, /*tp_as_number*/
+  &__pyx_tp_as_sequence_Phrase, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping_Phrase, /*tp_as_mapping*/
+  __pyx_pw_3_sa_6Phrase_23__hash__, /*tp_hash*/
   0, /*tp_call*/
-  0, /*tp_str*/
+  __pyx_pw_3_sa_6Phrase_5__str__, /*tp_str*/
   0, /*tp_getattro*/
   0, /*tp_setattro*/
-  &__pyx_tp_as_buffer_FloatList, /*tp_as_buffer*/
+  &__pyx_tp_as_buffer_Phrase, /*tp_as_buffer*/
   Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
   0, /*tp_doc*/
   0, /*tp_traverse*/
   0, /*tp_clear*/
   0, /*tp_richcompare*/
   0, /*tp_weaklistoffset*/
-  0, /*tp_iter*/
+  __pyx_pw_3_sa_6Phrase_29__iter__, /*tp_iter*/
   0, /*tp_iternext*/
-  __pyx_methods_3_sa_FloatList, /*tp_methods*/
+  __pyx_methods_3_sa_Phrase, /*tp_methods*/
   0, /*tp_members*/
-  0, /*tp_getset*/
+  __pyx_getsets_3_sa_Phrase, /*tp_getset*/
   0, /*tp_base*/
   0, /*tp_dict*/
   0, /*tp_descr_get*/
@@ -54790,7 +57421,7 @@ static PyTypeObject __pyx_type_3_sa_FloatList = {
   0, /*tp_dictoffset*/
   0, /*tp_init*/
   0, /*tp_alloc*/
-  __pyx_tp_new_3_sa_FloatList, /*tp_new*/
+  __pyx_tp_new_3_sa_Phrase, /*tp_new*/
   0, /*tp_free*/
   0, /*tp_is_gc*/
   0, /*tp_bases*/
@@ -54803,66 +57434,89 @@ static PyTypeObject __pyx_type_3_sa_FloatList = {
   0, /*tp_version_tag*/
   #endif
 };
-static struct __pyx_vtabstruct_3_sa_IntList __pyx_vtable_3_sa_IntList;
 
-static PyObject *__pyx_tp_new_3_sa_IntList(PyTypeObject *t, PyObject *a, PyObject *k) {
-  struct __pyx_obj_3_sa_IntList *p;
+static PyObject *__pyx_tp_new_3_sa_Rule(PyTypeObject *t, PyObject *a, PyObject *k) {
+  struct __pyx_obj_3_sa_Rule *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
-  p = ((struct __pyx_obj_3_sa_IntList *)o);
-  p->__pyx_vtab = __pyx_vtabptr_3_sa_IntList;
-  if (__pyx_pw_3_sa_7IntList_1__cinit__(o, a, k) < 0) {
+  p = ((struct __pyx_obj_3_sa_Rule *)o);
+  p->f = ((struct __pyx_obj_3_sa_Phrase *)Py_None); Py_INCREF(Py_None);
+  p->e = ((struct __pyx_obj_3_sa_Phrase *)Py_None); Py_INCREF(Py_None);
+  p->scores = ((struct __pyx_obj_3_sa_FeatureVector *)Py_None); Py_INCREF(Py_None);
+  p->word_alignments = Py_None; Py_INCREF(Py_None);
+  if (__pyx_pw_3_sa_4Rule_1__cinit__(o, a, k) < 0) {
     Py_DECREF(o); o = 0;
   }
   return o;
 }
 
-static void __pyx_tp_dealloc_3_sa_IntList(PyObject *o) {
-  {
-    PyObject *etype, *eval, *etb;
-    PyErr_Fetch(&etype, &eval, &etb);
-    ++Py_REFCNT(o);
-    __pyx_pw_3_sa_7IntList_15__dealloc__(o);
-    if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
-    --Py_REFCNT(o);
-    PyErr_Restore(etype, eval, etb);
-  }
+static void __pyx_tp_dealloc_3_sa_Rule(PyObject *o) {
+  struct __pyx_obj_3_sa_Rule *p = (struct __pyx_obj_3_sa_Rule *)o;
+  Py_CLEAR(p->f);
+  Py_CLEAR(p->e);
+  Py_CLEAR(p->scores);
+  Py_CLEAR(p->word_alignments);
   (*Py_TYPE(o)->tp_free)(o);
 }
-static PyObject *__pyx_sq_item_3_sa_IntList(PyObject *o, Py_ssize_t i) {
-  PyObject *r;
-  PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0;
-  r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x);
-  Py_DECREF(x);
-  return r;
-}
 
-static int __pyx_mp_ass_subscript_3_sa_IntList(PyObject *o, PyObject *i, PyObject *v) {
-  if (v) {
-    return __pyx_pw_3_sa_7IntList_19__setitem__(o, i, v);
+static int __pyx_tp_traverse_3_sa_Rule(PyObject *o, visitproc v, void *a) {
+  int e;
+  struct __pyx_obj_3_sa_Rule *p = (struct __pyx_obj_3_sa_Rule *)o;
+  if (p->f) {
+    e = (*v)(((PyObject*)p->f), a); if (e) return e;
   }
-  else {
-    PyErr_Format(PyExc_NotImplementedError,
-      "Subscript deletion not supported by %s", Py_TYPE(o)->tp_name);
-    return -1;
+  if (p->e) {
+    e = (*v)(((PyObject*)p->e), a); if (e) return e;
+  }
+  if (p->scores) {
+    e = (*v)(((PyObject*)p->scores), a); if (e) return e;
+  }
+  if (p->word_alignments) {
+    e = (*v)(p->word_alignments, a); if (e) return e;
   }
+  return 0;
 }
 
-static PyMethodDef __pyx_methods_3_sa_IntList[] = {
-  {__Pyx_NAMESTR("index"), (PyCFunction)__pyx_pw_3_sa_7IntList_5index, METH_O, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("partition"), (PyCFunction)__pyx_pw_3_sa_7IntList_7partition, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("_doquicksort"), (PyCFunction)__pyx_pw_3_sa_7IntList_9_doquicksort, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("sort"), (PyCFunction)__pyx_pw_3_sa_7IntList_11sort, METH_NOARGS, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("reset"), (PyCFunction)__pyx_pw_3_sa_7IntList_13reset, METH_NOARGS, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("getSize"), (PyCFunction)__pyx_pw_3_sa_7IntList_23getSize, METH_NOARGS, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("append"), (PyCFunction)__pyx_pw_3_sa_7IntList_25append, METH_O, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("extend"), (PyCFunction)__pyx_pw_3_sa_7IntList_27extend, METH_O, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("write"), (PyCFunction)__pyx_pw_3_sa_7IntList_29write, METH_O, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("read"), (PyCFunction)__pyx_pw_3_sa_7IntList_31read, METH_O, __Pyx_DOCSTR(0)},
+static int __pyx_tp_clear_3_sa_Rule(PyObject *o) {
+  struct __pyx_obj_3_sa_Rule *p = (struct __pyx_obj_3_sa_Rule *)o;
+  PyObject* tmp;
+  tmp = ((PyObject*)p->f);
+  p->f = ((struct __pyx_obj_3_sa_Phrase *)Py_None); Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->e);
+  p->e = ((struct __pyx_obj_3_sa_Phrase *)Py_None); Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->scores);
+  p->scores = ((struct __pyx_obj_3_sa_FeatureVector *)Py_None); Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->word_alignments);
+  p->word_alignments = Py_None; Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  return 0;
+}
+
+static PyObject *__pyx_getprop_3_sa_4Rule_f(PyObject *o, CYTHON_UNUSED void *x) {
+  return __pyx_pw_3_sa_4Rule_1f_1__get__(o);
+}
+
+static PyObject *__pyx_getprop_3_sa_4Rule_e(PyObject *o, CYTHON_UNUSED void *x) {
+  return __pyx_pw_3_sa_4Rule_1e_1__get__(o);
+}
+
+static PyMethodDef __pyx_methods_3_sa_Rule[] = {
+  {__Pyx_NAMESTR("fmerge"), (PyCFunction)__pyx_pw_3_sa_4Rule_7fmerge, METH_O, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("arity"), (PyCFunction)__pyx_pw_3_sa_4Rule_9arity, METH_NOARGS, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("alignments"), (PyCFunction)__pyx_pw_3_sa_4Rule_13alignments, METH_NOARGS, __Pyx_DOCSTR(0)},
   {0, 0, 0, 0}
 };
 
-static PyNumberMethods __pyx_tp_as_number_IntList = {
+static struct PyGetSetDef __pyx_getsets_3_sa_Rule[] = {
+  {(char *)"f", __pyx_getprop_3_sa_4Rule_f, 0, 0, 0},
+  {(char *)"e", __pyx_getprop_3_sa_4Rule_e, 0, 0, 0},
+  {0, 0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number_Rule = {
   0, /*nb_add*/
   0, /*nb_subtract*/
   0, /*nb_multiply*/
@@ -54920,11 +57574,11 @@ static PyNumberMethods __pyx_tp_as_number_IntList = {
   #endif
 };
 
-static PySequenceMethods __pyx_tp_as_sequence_IntList = {
-  __pyx_pw_3_sa_7IntList_21__len__, /*sq_length*/
+static PySequenceMethods __pyx_tp_as_sequence_Rule = {
+  0, /*sq_length*/
   0, /*sq_concat*/
   0, /*sq_repeat*/
-  __pyx_sq_item_3_sa_IntList, /*sq_item*/
+  0, /*sq_item*/
   0, /*sq_slice*/
   0, /*sq_ass_item*/
   0, /*sq_ass_slice*/
@@ -54933,13 +57587,13 @@ static PySequenceMethods __pyx_tp_as_sequence_IntList = {
   0, /*sq_inplace_repeat*/
 };
 
-static PyMappingMethods __pyx_tp_as_mapping_IntList = {
-  __pyx_pw_3_sa_7IntList_21__len__, /*mp_length*/
-  __pyx_pw_3_sa_7IntList_17__getitem__, /*mp_subscript*/
-  __pyx_mp_ass_subscript_3_sa_IntList, /*mp_ass_subscript*/
+static PyMappingMethods __pyx_tp_as_mapping_Rule = {
+  0, /*mp_length*/
+  0, /*mp_subscript*/
+  0, /*mp_ass_subscript*/
 };
 
-static PyBufferProcs __pyx_tp_as_buffer_IntList = {
+static PyBufferProcs __pyx_tp_as_buffer_Rule = {
   #if PY_MAJOR_VERSION < 3
   0, /*bf_getreadbuffer*/
   #endif
@@ -54960,41 +57614,41 @@ static PyBufferProcs __pyx_tp_as_buffer_IntList = {
   #endif
 };
 
-static PyTypeObject __pyx_type_3_sa_IntList = {
+static PyTypeObject __pyx_type_3_sa_Rule = {
   PyVarObject_HEAD_INIT(0, 0)
-  __Pyx_NAMESTR("_sa.IntList"), /*tp_name*/
-  sizeof(struct __pyx_obj_3_sa_IntList), /*tp_basicsize*/
+  __Pyx_NAMESTR("_sa.Rule"), /*tp_name*/
+  sizeof(struct __pyx_obj_3_sa_Rule), /*tp_basicsize*/
   0, /*tp_itemsize*/
-  __pyx_tp_dealloc_3_sa_IntList, /*tp_dealloc*/
+  __pyx_tp_dealloc_3_sa_Rule, /*tp_dealloc*/
   0, /*tp_print*/
   0, /*tp_getattr*/
   0, /*tp_setattr*/
   #if PY_MAJOR_VERSION < 3
-  0, /*tp_compare*/
+  __pyx_pw_3_sa_4Rule_5__cmp__, /*tp_compare*/
   #else
   0, /*reserved*/
   #endif
   0, /*tp_repr*/
-  &__pyx_tp_as_number_IntList, /*tp_as_number*/
-  &__pyx_tp_as_sequence_IntList, /*tp_as_sequence*/
-  &__pyx_tp_as_mapping_IntList, /*tp_as_mapping*/
-  0, /*tp_hash*/
+  &__pyx_tp_as_number_Rule, /*tp_as_number*/
+  &__pyx_tp_as_sequence_Rule, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping_Rule, /*tp_as_mapping*/
+  __pyx_pw_3_sa_4Rule_3__hash__, /*tp_hash*/
   0, /*tp_call*/
-  __pyx_pw_3_sa_7IntList_3__str__, /*tp_str*/
+  __pyx_pw_3_sa_4Rule_11__str__, /*tp_str*/
   0, /*tp_getattro*/
   0, /*tp_setattro*/
-  &__pyx_tp_as_buffer_IntList, /*tp_as_buffer*/
-  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
+  &__pyx_tp_as_buffer_Rule, /*tp_as_buffer*/
+  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
   0, /*tp_doc*/
-  0, /*tp_traverse*/
-  0, /*tp_clear*/
+  __pyx_tp_traverse_3_sa_Rule, /*tp_traverse*/
+  __pyx_tp_clear_3_sa_Rule, /*tp_clear*/
   0, /*tp_richcompare*/
   0, /*tp_weaklistoffset*/
   0, /*tp_iter*/
   0, /*tp_iternext*/
-  __pyx_methods_3_sa_IntList, /*tp_methods*/
+  __pyx_methods_3_sa_Rule, /*tp_methods*/
   0, /*tp_members*/
-  0, /*tp_getset*/
+  __pyx_getsets_3_sa_Rule, /*tp_getset*/
   0, /*tp_base*/
   0, /*tp_dict*/
   0, /*tp_descr_get*/
@@ -55002,7 +57656,7 @@ static PyTypeObject __pyx_type_3_sa_IntList = {
   0, /*tp_dictoffset*/
   0, /*tp_init*/
   0, /*tp_alloc*/
-  __pyx_tp_new_3_sa_IntList, /*tp_new*/
+  __pyx_tp_new_3_sa_Rule, /*tp_new*/
   0, /*tp_free*/
   0, /*tp_is_gc*/
   0, /*tp_bases*/
@@ -55220,11 +57874,11 @@ static PyObject *__pyx_tp_new_3_sa_DataArray(PyTypeObject *t, PyObject *a, PyObj
 
 static void __pyx_tp_dealloc_3_sa_DataArray(PyObject *o) {
   struct __pyx_obj_3_sa_DataArray *p = (struct __pyx_obj_3_sa_DataArray *)o;
-  Py_XDECREF(p->word2id);
-  Py_XDECREF(p->id2word);
-  Py_XDECREF(((PyObject *)p->data));
-  Py_XDECREF(((PyObject *)p->sent_id));
-  Py_XDECREF(((PyObject *)p->sent_index));
+  Py_CLEAR(p->word2id);
+  Py_CLEAR(p->id2word);
+  Py_CLEAR(p->data);
+  Py_CLEAR(p->sent_id);
+  Py_CLEAR(p->sent_index);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -55269,13 +57923,84 @@ static int __pyx_tp_clear_3_sa_DataArray(PyObject *o) {
   Py_XDECREF(tmp);
   return 0;
 }
+static PyObject *__pyx_sq_item_3_sa_DataArray(PyObject *o, Py_ssize_t i) {
+  PyObject *r;
+  PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0;
+  r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x);
+  Py_DECREF(x);
+  return r;
+}
+
+static PyObject *__pyx_getprop_3_sa_9DataArray_word2id(PyObject *o, CYTHON_UNUSED void *x) {
+  return __pyx_pw_3_sa_9DataArray_7word2id_1__get__(o);
+}
+
+static int __pyx_setprop_3_sa_9DataArray_word2id(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+  if (v) {
+    return __pyx_pw_3_sa_9DataArray_7word2id_3__set__(o, v);
+  }
+  else {
+    return __pyx_pw_3_sa_9DataArray_7word2id_5__del__(o);
+  }
+}
+
+static PyObject *__pyx_getprop_3_sa_9DataArray_id2word(PyObject *o, CYTHON_UNUSED void *x) {
+  return __pyx_pw_3_sa_9DataArray_7id2word_1__get__(o);
+}
+
+static int __pyx_setprop_3_sa_9DataArray_id2word(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+  if (v) {
+    return __pyx_pw_3_sa_9DataArray_7id2word_3__set__(o, v);
+  }
+  else {
+    return __pyx_pw_3_sa_9DataArray_7id2word_5__del__(o);
+  }
+}
+
+static PyObject *__pyx_getprop_3_sa_9DataArray_data(PyObject *o, CYTHON_UNUSED void *x) {
+  return __pyx_pw_3_sa_9DataArray_4data_1__get__(o);
+}
+
+static int __pyx_setprop_3_sa_9DataArray_data(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+  if (v) {
+    return __pyx_pw_3_sa_9DataArray_4data_3__set__(o, v);
+  }
+  else {
+    return __pyx_pw_3_sa_9DataArray_4data_5__del__(o);
+  }
+}
+
+static PyObject *__pyx_getprop_3_sa_9DataArray_sent_id(PyObject *o, CYTHON_UNUSED void *x) {
+  return __pyx_pw_3_sa_9DataArray_7sent_id_1__get__(o);
+}
+
+static int __pyx_setprop_3_sa_9DataArray_sent_id(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+  if (v) {
+    return __pyx_pw_3_sa_9DataArray_7sent_id_3__set__(o, v);
+  }
+  else {
+    return __pyx_pw_3_sa_9DataArray_7sent_id_5__del__(o);
+  }
+}
+
+static PyObject *__pyx_getprop_3_sa_9DataArray_sent_index(PyObject *o, CYTHON_UNUSED void *x) {
+  return __pyx_pw_3_sa_9DataArray_10sent_index_1__get__(o);
+}
+
+static int __pyx_setprop_3_sa_9DataArray_sent_index(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+  if (v) {
+    return __pyx_pw_3_sa_9DataArray_10sent_index_3__set__(o, v);
+  }
+  else {
+    return __pyx_pw_3_sa_9DataArray_10sent_index_5__del__(o);
+  }
+}
 
 static PyMethodDef __pyx_methods_3_sa_DataArray[] = {
-  {__Pyx_NAMESTR("getSentId"), (PyCFunction)__pyx_pw_3_sa_9DataArray_5getSentId, METH_O, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("getSent"), (PyCFunction)__pyx_pw_3_sa_9DataArray_7getSent, METH_O, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("getSentPos"), (PyCFunction)__pyx_pw_3_sa_9DataArray_9getSentPos, METH_O, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("get_id"), (PyCFunction)__pyx_pw_3_sa_9DataArray_11get_id, METH_O, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("get_word"), (PyCFunction)__pyx_pw_3_sa_9DataArray_13get_word, METH_O, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("get_sentence_id"), (PyCFunction)__pyx_pw_3_sa_9DataArray_5get_sentence_id, METH_O, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("get_sentence"), (PyCFunction)__pyx_pw_3_sa_9DataArray_7get_sentence, METH_O, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("get_id"), (PyCFunction)__pyx_pw_3_sa_9DataArray_9get_id, METH_O, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("get_sentence_bounds"), (PyCFunction)__pyx_pw_3_sa_9DataArray_13get_sentence_bounds, METH_O, __Pyx_DOCSTR(0)},
   {__Pyx_NAMESTR("write_text"), (PyCFunction)__pyx_pw_3_sa_9DataArray_15write_text, METH_O, __Pyx_DOCSTR(0)},
   {__Pyx_NAMESTR("read_text"), (PyCFunction)__pyx_pw_3_sa_9DataArray_17read_text, METH_O, __Pyx_DOCSTR(0)},
   {__Pyx_NAMESTR("read_bitext"), (PyCFunction)__pyx_pw_3_sa_9DataArray_19read_bitext, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)},
@@ -55287,6 +58012,15 @@ static PyMethodDef __pyx_methods_3_sa_DataArray[] = {
   {0, 0, 0, 0}
 };
 
+static struct PyGetSetDef __pyx_getsets_3_sa_DataArray[] = {
+  {(char *)"word2id", __pyx_getprop_3_sa_9DataArray_word2id, __pyx_setprop_3_sa_9DataArray_word2id, 0, 0},
+  {(char *)"id2word", __pyx_getprop_3_sa_9DataArray_id2word, __pyx_setprop_3_sa_9DataArray_id2word, 0, 0},
+  {(char *)"data", __pyx_getprop_3_sa_9DataArray_data, __pyx_setprop_3_sa_9DataArray_data, 0, 0},
+  {(char *)"sent_id", __pyx_getprop_3_sa_9DataArray_sent_id, __pyx_setprop_3_sa_9DataArray_sent_id, 0, 0},
+  {(char *)"sent_index", __pyx_getprop_3_sa_9DataArray_sent_index, __pyx_setprop_3_sa_9DataArray_sent_index, 0, 0},
+  {0, 0, 0, 0, 0}
+};
+
 static PyNumberMethods __pyx_tp_as_number_DataArray = {
   0, /*nb_add*/
   0, /*nb_subtract*/
@@ -55349,7 +58083,7 @@ static PySequenceMethods __pyx_tp_as_sequence_DataArray = {
   __pyx_pw_3_sa_9DataArray_3__len__, /*sq_length*/
   0, /*sq_concat*/
   0, /*sq_repeat*/
-  0, /*sq_item*/
+  __pyx_sq_item_3_sa_DataArray, /*sq_item*/
   0, /*sq_slice*/
   0, /*sq_ass_item*/
   0, /*sq_ass_slice*/
@@ -55360,7 +58094,7 @@ static PySequenceMethods __pyx_tp_as_sequence_DataArray = {
 
 static PyMappingMethods __pyx_tp_as_mapping_DataArray = {
   __pyx_pw_3_sa_9DataArray_3__len__, /*mp_length*/
-  0, /*mp_subscript*/
+  __pyx_pw_3_sa_9DataArray_11__getitem__, /*mp_subscript*/
   0, /*mp_ass_subscript*/
 };
 
@@ -55419,7 +58153,7 @@ static PyTypeObject __pyx_type_3_sa_DataArray = {
   0, /*tp_iternext*/
   __pyx_methods_3_sa_DataArray, /*tp_methods*/
   0, /*tp_members*/
-  0, /*tp_getset*/
+  __pyx_getsets_3_sa_DataArray, /*tp_getset*/
   0, /*tp_base*/
   0, /*tp_dict*/
   0, /*tp_descr_get*/
@@ -55458,8 +58192,8 @@ static PyObject *__pyx_tp_new_3_sa_Alignment(PyTypeObject *t, PyObject *a, PyObj
 
 static void __pyx_tp_dealloc_3_sa_Alignment(PyObject *o) {
   struct __pyx_obj_3_sa_Alignment *p = (struct __pyx_obj_3_sa_Alignment *)o;
-  Py_XDECREF(((PyObject *)p->links));
-  Py_XDECREF(((PyObject *)p->sent_index));
+  Py_CLEAR(p->links);
+  Py_CLEAR(p->sent_index);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -55676,14 +58410,14 @@ static PyObject *__pyx_tp_new_3_sa_BiLex(PyTypeObject *t, PyObject *a, PyObject
 
 static void __pyx_tp_dealloc_3_sa_BiLex(PyObject *o) {
   struct __pyx_obj_3_sa_BiLex *p = (struct __pyx_obj_3_sa_BiLex *)o;
-  Py_XDECREF(((PyObject *)p->col1));
-  Py_XDECREF(((PyObject *)p->col2));
-  Py_XDECREF(((PyObject *)p->f_index));
-  Py_XDECREF(((PyObject *)p->e_index));
-  Py_XDECREF(p->id2eword);
-  Py_XDECREF(p->id2fword);
-  Py_XDECREF(p->eword2id);
-  Py_XDECREF(p->fword2id);
+  Py_CLEAR(p->col1);
+  Py_CLEAR(p->col2);
+  Py_CLEAR(p->f_index);
+  Py_CLEAR(p->e_index);
+  Py_CLEAR(p->id2eword);
+  Py_CLEAR(p->id2fword);
+  Py_CLEAR(p->eword2id);
+  Py_CLEAR(p->fword2id);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -56636,8 +59370,8 @@ static PyObject *__pyx_tp_new_3_sa_LCP(PyTypeObject *t, PyObject *a, PyObject *k
 
 static void __pyx_tp_dealloc_3_sa_LCP(PyObject *o) {
   struct __pyx_obj_3_sa_LCP *p = (struct __pyx_obj_3_sa_LCP *)o;
-  Py_XDECREF(((PyObject *)p->sa));
-  Py_XDECREF(((PyObject *)p->lcp));
+  Py_CLEAR(p->sa);
+  Py_CLEAR(p->lcp);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -56851,9 +59585,9 @@ static void __pyx_tp_dealloc_3_sa_Alphabet(PyObject *o) {
     --Py_REFCNT(o);
     PyErr_Restore(etype, eval, etb);
   }
-  Py_XDECREF(((PyObject *)p->terminals));
-  Py_XDECREF(((PyObject *)p->nonterminals));
-  Py_XDECREF(((PyObject *)p->id2sym));
+  Py_CLEAR(p->terminals);
+  Py_CLEAR(p->nonterminals);
+  Py_CLEAR(p->id2sym);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -57263,8 +59997,8 @@ static PyObject *__pyx_tp_new_3_sa_Precomputation(PyTypeObject *t, PyObject *a,
 
 static void __pyx_tp_dealloc_3_sa_Precomputation(PyObject *o) {
   struct __pyx_obj_3_sa_Precomputation *p = (struct __pyx_obj_3_sa_Precomputation *)o;
-  Py_XDECREF(p->precomputed_index);
-  Py_XDECREF(p->precomputed_collocations);
+  Py_CLEAR(p->precomputed_index);
+  Py_CLEAR(p->precomputed_collocations);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -57471,9 +60205,9 @@ static PyObject *__pyx_tp_new_3_sa_SuffixArray(PyTypeObject *t, PyObject *a, PyO
 
 static void __pyx_tp_dealloc_3_sa_SuffixArray(PyObject *o) {
   struct __pyx_obj_3_sa_SuffixArray *p = (struct __pyx_obj_3_sa_SuffixArray *)o;
-  Py_XDECREF(((PyObject *)p->darray));
-  Py_XDECREF(((PyObject *)p->sa));
-  Py_XDECREF(((PyObject *)p->ha));
+  Py_CLEAR(p->darray);
+  Py_CLEAR(p->sa);
+  Py_CLEAR(p->ha);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -57515,16 +60249,13 @@ static PyObject *__pyx_sq_item_3_sa_SuffixArray(PyObject *o, Py_ssize_t i) {
 }
 
 static PyMethodDef __pyx_methods_3_sa_SuffixArray[] = {
-  {__Pyx_NAMESTR("getSentId"), (PyCFunction)__pyx_pw_3_sa_11SuffixArray_5getSentId, METH_O, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("getSent"), (PyCFunction)__pyx_pw_3_sa_11SuffixArray_7getSent, METH_O, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("getSentPos"), (PyCFunction)__pyx_pw_3_sa_11SuffixArray_9getSentPos, METH_O, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("read_text"), (PyCFunction)__pyx_pw_3_sa_11SuffixArray_11read_text, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_3_sa_11SuffixArray_10read_text)},
-  {__Pyx_NAMESTR("q3sort"), (PyCFunction)__pyx_pw_3_sa_11SuffixArray_13q3sort, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_3_sa_11SuffixArray_12q3sort)},
-  {__Pyx_NAMESTR("write_text"), (PyCFunction)__pyx_pw_3_sa_11SuffixArray_15write_text, METH_O, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("read_binary"), (PyCFunction)__pyx_pw_3_sa_11SuffixArray_17read_binary, METH_O, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("write_binary"), (PyCFunction)__pyx_pw_3_sa_11SuffixArray_19write_binary, METH_O, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("write_enhanced"), (PyCFunction)__pyx_pw_3_sa_11SuffixArray_21write_enhanced, METH_O, __Pyx_DOCSTR(0)},
-  {__Pyx_NAMESTR("lookup"), (PyCFunction)__pyx_pw_3_sa_11SuffixArray_23lookup, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("read_text"), (PyCFunction)__pyx_pw_3_sa_11SuffixArray_5read_text, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_3_sa_11SuffixArray_4read_text)},
+  {__Pyx_NAMESTR("q3sort"), (PyCFunction)__pyx_pw_3_sa_11SuffixArray_7q3sort, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_3_sa_11SuffixArray_6q3sort)},
+  {__Pyx_NAMESTR("write_text"), (PyCFunction)__pyx_pw_3_sa_11SuffixArray_9write_text, METH_O, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("read_binary"), (PyCFunction)__pyx_pw_3_sa_11SuffixArray_11read_binary, METH_O, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("write_binary"), (PyCFunction)__pyx_pw_3_sa_11SuffixArray_13write_binary, METH_O, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("write_enhanced"), (PyCFunction)__pyx_pw_3_sa_11SuffixArray_15write_enhanced, METH_O, __Pyx_DOCSTR(0)},
+  {__Pyx_NAMESTR("lookup"), (PyCFunction)__pyx_pw_3_sa_11SuffixArray_17lookup, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)},
   {0, 0, 0, 0}
 };
 
@@ -57696,7 +60427,7 @@ static PyObject *__pyx_tp_new_3_sa_TrieNode(PyTypeObject *t, CYTHON_UNUSED PyObj
 
 static void __pyx_tp_dealloc_3_sa_TrieNode(PyObject *o) {
   struct __pyx_obj_3_sa_TrieNode *p = (struct __pyx_obj_3_sa_TrieNode *)o;
-  Py_XDECREF(p->children);
+  Py_CLEAR(p->children);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -57910,9 +60641,9 @@ static PyObject *__pyx_tp_new_3_sa_ExtendedTrieNode(PyTypeObject *t, PyObject *a
 
 static void __pyx_tp_dealloc_3_sa_ExtendedTrieNode(PyObject *o) {
   struct __pyx_obj_3_sa_ExtendedTrieNode *p = (struct __pyx_obj_3_sa_ExtendedTrieNode *)o;
-  Py_XDECREF(p->phrase);
-  Py_XDECREF(p->phrase_location);
-  Py_XDECREF(p->suffix_link);
+  Py_CLEAR(p->phrase);
+  Py_CLEAR(p->phrase_location);
+  Py_CLEAR(p->suffix_link);
   __pyx_tp_dealloc_3_sa_TrieNode(o);
 }
 
@@ -58166,7 +60897,7 @@ static PyObject *__pyx_tp_new_3_sa_TrieTable(PyTypeObject *t, PyObject *a, PyObj
 
 static void __pyx_tp_dealloc_3_sa_TrieTable(PyObject *o) {
   struct __pyx_obj_3_sa_TrieTable *p = (struct __pyx_obj_3_sa_TrieTable *)o;
-  Py_XDECREF(p->root);
+  Py_CLEAR(p->root);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -58410,7 +61141,7 @@ static PyObject *__pyx_tp_new_3_sa_PhraseLocation(PyTypeObject *t, PyObject *a,
 
 static void __pyx_tp_dealloc_3_sa_PhraseLocation(PyObject *o) {
   struct __pyx_obj_3_sa_PhraseLocation *p = (struct __pyx_obj_3_sa_PhraseLocation *)o;
-  Py_XDECREF(((PyObject *)p->arr));
+  Py_CLEAR(p->arr);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -58604,7 +61335,7 @@ static PyObject *__pyx_tp_new_3_sa_Sampler(PyTypeObject *t, PyObject *a, PyObjec
 
 static void __pyx_tp_dealloc_3_sa_Sampler(PyObject *o) {
   struct __pyx_obj_3_sa_Sampler *p = (struct __pyx_obj_3_sa_Sampler *)o;
-  Py_XDECREF(((PyObject *)p->sa));
+  Py_CLEAR(p->sa);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -58794,6 +61525,7 @@ static PyObject *__pyx_tp_new_3_sa_HieroCachingRuleFactory(PyTypeObject *t, PyOb
   p->__pyx_vtab = __pyx_vtabptr_3_sa_HieroCachingRuleFactory;
   p->rules = ((struct __pyx_obj_3_sa_TrieTable *)Py_None); Py_INCREF(Py_None);
   p->sampler = ((struct __pyx_obj_3_sa_Sampler *)Py_None); Py_INCREF(Py_None);
+  p->scorer = ((struct __pyx_obj_3_sa_Scorer *)Py_None); Py_INCREF(Py_None);
   p->precomputed_index = Py_None; Py_INCREF(Py_None);
   p->precomputed_collocations = Py_None; Py_INCREF(Py_None);
   p->precompute_file = Py_None; Py_INCREF(Py_None);
@@ -58815,21 +61547,22 @@ static PyObject *__pyx_tp_new_3_sa_HieroCachingRuleFactory(PyTypeObject *t, PyOb
 
 static void __pyx_tp_dealloc_3_sa_HieroCachingRuleFactory(PyObject *o) {
   struct __pyx_obj_3_sa_HieroCachingRuleFactory *p = (struct __pyx_obj_3_sa_HieroCachingRuleFactory *)o;
-  Py_XDECREF(((PyObject *)p->rules));
-  Py_XDECREF(((PyObject *)p->sampler));
-  Py_XDECREF(p->precomputed_index);
-  Py_XDECREF(p->precomputed_collocations);
-  Py_XDECREF(p->precompute_file);
-  Py_XDECREF(p->max_rank);
-  Py_XDECREF(p->prev_norm_prefix);
-  Py_XDECREF(((PyObject *)p->fsa));
-  Py_XDECREF(((PyObject *)p->fda));
-  Py_XDECREF(((PyObject *)p->eda));
-  Py_XDECREF(((PyObject *)p->alignment));
-  Py_XDECREF(((PyObject *)p->eid2symid));
-  Py_XDECREF(((PyObject *)p->fid2symid));
-  Py_XDECREF(((PyObject *)p->findexes));
-  Py_XDECREF(((PyObject *)p->findexes1));
+  Py_CLEAR(p->rules);
+  Py_CLEAR(p->sampler);
+  Py_CLEAR(p->scorer);
+  Py_CLEAR(p->precomputed_index);
+  Py_CLEAR(p->precomputed_collocations);
+  Py_CLEAR(p->precompute_file);
+  Py_CLEAR(p->max_rank);
+  Py_CLEAR(p->prev_norm_prefix);
+  Py_CLEAR(p->fsa);
+  Py_CLEAR(p->fda);
+  Py_CLEAR(p->eda);
+  Py_CLEAR(p->alignment);
+  Py_CLEAR(p->eid2symid);
+  Py_CLEAR(p->fid2symid);
+  Py_CLEAR(p->findexes);
+  Py_CLEAR(p->findexes1);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
@@ -58842,6 +61575,9 @@ static int __pyx_tp_traverse_3_sa_HieroCachingRuleFactory(PyObject *o, visitproc
   if (p->sampler) {
     e = (*v)(((PyObject*)p->sampler), a); if (e) return e;
   }
+  if (p->scorer) {
+    e = (*v)(((PyObject*)p->scorer), a); if (e) return e;
+  }
   if (p->precomputed_index) {
     e = (*v)(p->precomputed_index, a); if (e) return e;
   }
@@ -58893,6 +61629,9 @@ static int __pyx_tp_clear_3_sa_HieroCachingRuleFactory(PyObject *o) {
   tmp = ((PyObject*)p->sampler);
   p->sampler = ((struct __pyx_obj_3_sa_Sampler *)Py_None); Py_INCREF(Py_None);
   Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->scorer);
+  p->scorer = ((struct __pyx_obj_3_sa_Scorer *)Py_None); Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
   tmp = ((PyObject*)p->precomputed_index);
   p->precomputed_index = Py_None; Py_INCREF(Py_None);
   Py_XDECREF(tmp);
@@ -59103,33 +61842,417 @@ static PyTypeObject __pyx_type_3_sa_HieroCachingRuleFactory = {
   0, /*tp_version_tag*/
   #endif
 };
+static struct __pyx_vtabstruct_3_sa_Scorer __pyx_vtable_3_sa_Scorer;
+
+static PyObject *__pyx_tp_new_3_sa_Scorer(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+  struct __pyx_obj_3_sa_Scorer *p;
+  PyObject *o = (*t->tp_alloc)(t, 0);
+  if (!o) return 0;
+  p = ((struct __pyx_obj_3_sa_Scorer *)o);
+  p->__pyx_vtab = __pyx_vtabptr_3_sa_Scorer;
+  p->models = Py_None; Py_INCREF(Py_None);
+  return o;
+}
+
+static void __pyx_tp_dealloc_3_sa_Scorer(PyObject *o) {
+  struct __pyx_obj_3_sa_Scorer *p = (struct __pyx_obj_3_sa_Scorer *)o;
+  Py_CLEAR(p->models);
+  (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_3_sa_Scorer(PyObject *o, visitproc v, void *a) {
+  int e;
+  struct __pyx_obj_3_sa_Scorer *p = (struct __pyx_obj_3_sa_Scorer *)o;
+  if (p->models) {
+    e = (*v)(p->models, a); if (e) return e;
+  }
+  return 0;
+}
+
+static int __pyx_tp_clear_3_sa_Scorer(PyObject *o) {
+  struct __pyx_obj_3_sa_Scorer *p = (struct __pyx_obj_3_sa_Scorer *)o;
+  PyObject* tmp;
+  tmp = ((PyObject*)p->models);
+  p->models = Py_None; Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  return 0;
+}
+
+static PyMethodDef __pyx_methods_3_sa_Scorer[] = {
+  {0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number_Scorer = {
+  0, /*nb_add*/
+  0, /*nb_subtract*/
+  0, /*nb_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_divide*/
+  #endif
+  0, /*nb_remainder*/
+  0, /*nb_divmod*/
+  0, /*nb_power*/
+  0, /*nb_negative*/
+  0, /*nb_positive*/
+  0, /*nb_absolute*/
+  0, /*nb_nonzero*/
+  0, /*nb_invert*/
+  0, /*nb_lshift*/
+  0, /*nb_rshift*/
+  0, /*nb_and*/
+  0, /*nb_xor*/
+  0, /*nb_or*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_coerce*/
+  #endif
+  0, /*nb_int*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_long*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*nb_float*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_oct*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_hex*/
+  #endif
+  0, /*nb_inplace_add*/
+  0, /*nb_inplace_subtract*/
+  0, /*nb_inplace_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_inplace_divide*/
+  #endif
+  0, /*nb_inplace_remainder*/
+  0, /*nb_inplace_power*/
+  0, /*nb_inplace_lshift*/
+  0, /*nb_inplace_rshift*/
+  0, /*nb_inplace_and*/
+  0, /*nb_inplace_xor*/
+  0, /*nb_inplace_or*/
+  0, /*nb_floor_divide*/
+  0, /*nb_true_divide*/
+  0, /*nb_inplace_floor_divide*/
+  0, /*nb_inplace_true_divide*/
+  #if PY_VERSION_HEX >= 0x02050000
+  0, /*nb_index*/
+  #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence_Scorer = {
+  0, /*sq_length*/
+  0, /*sq_concat*/
+  0, /*sq_repeat*/
+  0, /*sq_item*/
+  0, /*sq_slice*/
+  0, /*sq_ass_item*/
+  0, /*sq_ass_slice*/
+  0, /*sq_contains*/
+  0, /*sq_inplace_concat*/
+  0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping_Scorer = {
+  0, /*mp_length*/
+  0, /*mp_subscript*/
+  0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer_Scorer = {
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getreadbuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getwritebuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getsegcount*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getcharbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_getbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_releasebuffer*/
+  #endif
+};
+
+static PyTypeObject __pyx_type_3_sa_Scorer = {
+  PyVarObject_HEAD_INIT(0, 0)
+  __Pyx_NAMESTR("_sa.Scorer"), /*tp_name*/
+  sizeof(struct __pyx_obj_3_sa_Scorer), /*tp_basicsize*/
+  0, /*tp_itemsize*/
+  __pyx_tp_dealloc_3_sa_Scorer, /*tp_dealloc*/
+  0, /*tp_print*/
+  0, /*tp_getattr*/
+  0, /*tp_setattr*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*tp_compare*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*tp_repr*/
+  &__pyx_tp_as_number_Scorer, /*tp_as_number*/
+  &__pyx_tp_as_sequence_Scorer, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping_Scorer, /*tp_as_mapping*/
+  0, /*tp_hash*/
+  0, /*tp_call*/
+  0, /*tp_str*/
+  0, /*tp_getattro*/
+  0, /*tp_setattro*/
+  &__pyx_tp_as_buffer_Scorer, /*tp_as_buffer*/
+  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+  0, /*tp_doc*/
+  __pyx_tp_traverse_3_sa_Scorer, /*tp_traverse*/
+  __pyx_tp_clear_3_sa_Scorer, /*tp_clear*/
+  0, /*tp_richcompare*/
+  0, /*tp_weaklistoffset*/
+  0, /*tp_iter*/
+  0, /*tp_iternext*/
+  __pyx_methods_3_sa_Scorer, /*tp_methods*/
+  0, /*tp_members*/
+  0, /*tp_getset*/
+  0, /*tp_base*/
+  0, /*tp_dict*/
+  0, /*tp_descr_get*/
+  0, /*tp_descr_set*/
+  0, /*tp_dictoffset*/
+  __pyx_pw_3_sa_6Scorer_1__init__, /*tp_init*/
+  0, /*tp_alloc*/
+  __pyx_tp_new_3_sa_Scorer, /*tp_new*/
+  0, /*tp_free*/
+  0, /*tp_is_gc*/
+  0, /*tp_bases*/
+  0, /*tp_mro*/
+  0, /*tp_cache*/
+  0, /*tp_subclasses*/
+  0, /*tp_weaklist*/
+  0, /*tp_del*/
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*tp_version_tag*/
+  #endif
+};
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct__read_bitext(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
-  struct __pyx_obj_3_sa___pyx_scope_struct__read_bitext *p;
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct____iter__(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+  struct __pyx_obj_3_sa___pyx_scope_struct____iter__ *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
-  p = ((struct __pyx_obj_3_sa___pyx_scope_struct__read_bitext *)o);
+  p = ((struct __pyx_obj_3_sa___pyx_scope_struct____iter__ *)o);
+  p->__pyx_v_self = 0;
+  return o;
+}
+
+static void __pyx_tp_dealloc_3_sa___pyx_scope_struct____iter__(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct____iter__ *p = (struct __pyx_obj_3_sa___pyx_scope_struct____iter__ *)o;
+  Py_CLEAR(p->__pyx_v_self);
+  (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_3_sa___pyx_scope_struct____iter__(PyObject *o, visitproc v, void *a) {
+  int e;
+  struct __pyx_obj_3_sa___pyx_scope_struct____iter__ *p = (struct __pyx_obj_3_sa___pyx_scope_struct____iter__ *)o;
+  if (p->__pyx_v_self) {
+    e = (*v)(((PyObject*)p->__pyx_v_self), a); if (e) return e;
+  }
+  return 0;
+}
+
+static int __pyx_tp_clear_3_sa___pyx_scope_struct____iter__(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct____iter__ *p = (struct __pyx_obj_3_sa___pyx_scope_struct____iter__ *)o;
+  PyObject* tmp;
+  tmp = ((PyObject*)p->__pyx_v_self);
+  p->__pyx_v_self = ((struct __pyx_obj_3_sa_IntList *)Py_None); Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  return 0;
+}
+
+static PyMethodDef __pyx_methods_3_sa___pyx_scope_struct____iter__[] = {
+  {0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct____iter__ = {
+  0, /*nb_add*/
+  0, /*nb_subtract*/
+  0, /*nb_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_divide*/
+  #endif
+  0, /*nb_remainder*/
+  0, /*nb_divmod*/
+  0, /*nb_power*/
+  0, /*nb_negative*/
+  0, /*nb_positive*/
+  0, /*nb_absolute*/
+  0, /*nb_nonzero*/
+  0, /*nb_invert*/
+  0, /*nb_lshift*/
+  0, /*nb_rshift*/
+  0, /*nb_and*/
+  0, /*nb_xor*/
+  0, /*nb_or*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_coerce*/
+  #endif
+  0, /*nb_int*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_long*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*nb_float*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_oct*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_hex*/
+  #endif
+  0, /*nb_inplace_add*/
+  0, /*nb_inplace_subtract*/
+  0, /*nb_inplace_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_inplace_divide*/
+  #endif
+  0, /*nb_inplace_remainder*/
+  0, /*nb_inplace_power*/
+  0, /*nb_inplace_lshift*/
+  0, /*nb_inplace_rshift*/
+  0, /*nb_inplace_and*/
+  0, /*nb_inplace_xor*/
+  0, /*nb_inplace_or*/
+  0, /*nb_floor_divide*/
+  0, /*nb_true_divide*/
+  0, /*nb_inplace_floor_divide*/
+  0, /*nb_inplace_true_divide*/
+  #if PY_VERSION_HEX >= 0x02050000
+  0, /*nb_index*/
+  #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct____iter__ = {
+  0, /*sq_length*/
+  0, /*sq_concat*/
+  0, /*sq_repeat*/
+  0, /*sq_item*/
+  0, /*sq_slice*/
+  0, /*sq_ass_item*/
+  0, /*sq_ass_slice*/
+  0, /*sq_contains*/
+  0, /*sq_inplace_concat*/
+  0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct____iter__ = {
+  0, /*mp_length*/
+  0, /*mp_subscript*/
+  0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct____iter__ = {
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getreadbuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getwritebuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getsegcount*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getcharbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_getbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_releasebuffer*/
+  #endif
+};
+
+static PyTypeObject __pyx_type_3_sa___pyx_scope_struct____iter__ = {
+  PyVarObject_HEAD_INIT(0, 0)
+  __Pyx_NAMESTR("_sa.__pyx_scope_struct____iter__"), /*tp_name*/
+  sizeof(struct __pyx_obj_3_sa___pyx_scope_struct____iter__), /*tp_basicsize*/
+  0, /*tp_itemsize*/
+  __pyx_tp_dealloc_3_sa___pyx_scope_struct____iter__, /*tp_dealloc*/
+  0, /*tp_print*/
+  0, /*tp_getattr*/
+  0, /*tp_setattr*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*tp_compare*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*tp_repr*/
+  &__pyx_tp_as_number___pyx_scope_struct____iter__, /*tp_as_number*/
+  &__pyx_tp_as_sequence___pyx_scope_struct____iter__, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping___pyx_scope_struct____iter__, /*tp_as_mapping*/
+  0, /*tp_hash*/
+  0, /*tp_call*/
+  0, /*tp_str*/
+  0, /*tp_getattro*/
+  0, /*tp_setattro*/
+  &__pyx_tp_as_buffer___pyx_scope_struct____iter__, /*tp_as_buffer*/
+  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+  0, /*tp_doc*/
+  __pyx_tp_traverse_3_sa___pyx_scope_struct____iter__, /*tp_traverse*/
+  __pyx_tp_clear_3_sa___pyx_scope_struct____iter__, /*tp_clear*/
+  0, /*tp_richcompare*/
+  0, /*tp_weaklistoffset*/
+  0, /*tp_iter*/
+  0, /*tp_iternext*/
+  __pyx_methods_3_sa___pyx_scope_struct____iter__, /*tp_methods*/
+  0, /*tp_members*/
+  0, /*tp_getset*/
+  0, /*tp_base*/
+  0, /*tp_dict*/
+  0, /*tp_descr_get*/
+  0, /*tp_descr_set*/
+  0, /*tp_dictoffset*/
+  0, /*tp_init*/
+  0, /*tp_alloc*/
+  __pyx_tp_new_3_sa___pyx_scope_struct____iter__, /*tp_new*/
+  0, /*tp_free*/
+  0, /*tp_is_gc*/
+  0, /*tp_bases*/
+  0, /*tp_mro*/
+  0, /*tp_cache*/
+  0, /*tp_subclasses*/
+  0, /*tp_weaklist*/
+  0, /*tp_del*/
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*tp_version_tag*/
+  #endif
+};
+
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_1_read_bitext(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_1_read_bitext *p;
+  PyObject *o = (*t->tp_alloc)(t, 0);
+  if (!o) return 0;
+  p = ((struct __pyx_obj_3_sa___pyx_scope_struct_1_read_bitext *)o);
   p->__pyx_v_fp = 0;
   return o;
 }
 
-static void __pyx_tp_dealloc_3_sa___pyx_scope_struct__read_bitext(PyObject *o) {
-  struct __pyx_obj_3_sa___pyx_scope_struct__read_bitext *p = (struct __pyx_obj_3_sa___pyx_scope_struct__read_bitext *)o;
-  Py_XDECREF(p->__pyx_v_fp);
+static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_1_read_bitext(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_1_read_bitext *p = (struct __pyx_obj_3_sa___pyx_scope_struct_1_read_bitext *)o;
+  Py_CLEAR(p->__pyx_v_fp);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
-static int __pyx_tp_traverse_3_sa___pyx_scope_struct__read_bitext(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_3_sa___pyx_scope_struct_1_read_bitext(PyObject *o, visitproc v, void *a) {
   int e;
-  struct __pyx_obj_3_sa___pyx_scope_struct__read_bitext *p = (struct __pyx_obj_3_sa___pyx_scope_struct__read_bitext *)o;
+  struct __pyx_obj_3_sa___pyx_scope_struct_1_read_bitext *p = (struct __pyx_obj_3_sa___pyx_scope_struct_1_read_bitext *)o;
   if (p->__pyx_v_fp) {
     e = (*v)(p->__pyx_v_fp, a); if (e) return e;
   }
   return 0;
 }
 
-static int __pyx_tp_clear_3_sa___pyx_scope_struct__read_bitext(PyObject *o) {
-  struct __pyx_obj_3_sa___pyx_scope_struct__read_bitext *p = (struct __pyx_obj_3_sa___pyx_scope_struct__read_bitext *)o;
+static int __pyx_tp_clear_3_sa___pyx_scope_struct_1_read_bitext(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_1_read_bitext *p = (struct __pyx_obj_3_sa___pyx_scope_struct_1_read_bitext *)o;
   PyObject* tmp;
   tmp = ((PyObject*)p->__pyx_v_fp);
   p->__pyx_v_fp = Py_None; Py_INCREF(Py_None);
@@ -59137,11 +62260,11 @@ static int __pyx_tp_clear_3_sa___pyx_scope_struct__read_bitext(PyObject *o) {
   return 0;
 }
 
-static PyMethodDef __pyx_methods_3_sa___pyx_scope_struct__read_bitext[] = {
+static PyMethodDef __pyx_methods_3_sa___pyx_scope_struct_1_read_bitext[] = {
   {0, 0, 0, 0}
 };
 
-static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct__read_bitext = {
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_1_read_bitext = {
   0, /*nb_add*/
   0, /*nb_subtract*/
   0, /*nb_multiply*/
@@ -59199,7 +62322,7 @@ static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct__read_bitext = {
   #endif
 };
 
-static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct__read_bitext = {
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_1_read_bitext = {
   0, /*sq_length*/
   0, /*sq_concat*/
   0, /*sq_repeat*/
@@ -59212,13 +62335,13 @@ static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct__read_bitext =
   0, /*sq_inplace_repeat*/
 };
 
-static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct__read_bitext = {
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_1_read_bitext = {
   0, /*mp_length*/
   0, /*mp_subscript*/
   0, /*mp_ass_subscript*/
 };
 
-static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct__read_bitext = {
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_1_read_bitext = {
   #if PY_MAJOR_VERSION < 3
   0, /*bf_getreadbuffer*/
   #endif
@@ -59239,12 +62362,12 @@ static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct__read_bitext = {
   #endif
 };
 
-static PyTypeObject __pyx_type_3_sa___pyx_scope_struct__read_bitext = {
+static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_1_read_bitext = {
   PyVarObject_HEAD_INIT(0, 0)
-  __Pyx_NAMESTR("_sa.__pyx_scope_struct__read_bitext"), /*tp_name*/
-  sizeof(struct __pyx_obj_3_sa___pyx_scope_struct__read_bitext), /*tp_basicsize*/
+  __Pyx_NAMESTR("_sa.__pyx_scope_struct_1_read_bitext"), /*tp_name*/
+  sizeof(struct __pyx_obj_3_sa___pyx_scope_struct_1_read_bitext), /*tp_basicsize*/
   0, /*tp_itemsize*/
-  __pyx_tp_dealloc_3_sa___pyx_scope_struct__read_bitext, /*tp_dealloc*/
+  __pyx_tp_dealloc_3_sa___pyx_scope_struct_1_read_bitext, /*tp_dealloc*/
   0, /*tp_print*/
   0, /*tp_getattr*/
   0, /*tp_setattr*/
@@ -59254,24 +62377,24 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct__read_bitext = {
   0, /*reserved*/
   #endif
   0, /*tp_repr*/
-  &__pyx_tp_as_number___pyx_scope_struct__read_bitext, /*tp_as_number*/
-  &__pyx_tp_as_sequence___pyx_scope_struct__read_bitext, /*tp_as_sequence*/
-  &__pyx_tp_as_mapping___pyx_scope_struct__read_bitext, /*tp_as_mapping*/
+  &__pyx_tp_as_number___pyx_scope_struct_1_read_bitext, /*tp_as_number*/
+  &__pyx_tp_as_sequence___pyx_scope_struct_1_read_bitext, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping___pyx_scope_struct_1_read_bitext, /*tp_as_mapping*/
   0, /*tp_hash*/
   0, /*tp_call*/
   0, /*tp_str*/
   0, /*tp_getattro*/
   0, /*tp_setattro*/
-  &__pyx_tp_as_buffer___pyx_scope_struct__read_bitext, /*tp_as_buffer*/
+  &__pyx_tp_as_buffer___pyx_scope_struct_1_read_bitext, /*tp_as_buffer*/
   Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
   0, /*tp_doc*/
-  __pyx_tp_traverse_3_sa___pyx_scope_struct__read_bitext, /*tp_traverse*/
-  __pyx_tp_clear_3_sa___pyx_scope_struct__read_bitext, /*tp_clear*/
+  __pyx_tp_traverse_3_sa___pyx_scope_struct_1_read_bitext, /*tp_traverse*/
+  __pyx_tp_clear_3_sa___pyx_scope_struct_1_read_bitext, /*tp_clear*/
   0, /*tp_richcompare*/
   0, /*tp_weaklistoffset*/
   0, /*tp_iter*/
   0, /*tp_iternext*/
-  __pyx_methods_3_sa___pyx_scope_struct__read_bitext, /*tp_methods*/
+  __pyx_methods_3_sa___pyx_scope_struct_1_read_bitext, /*tp_methods*/
   0, /*tp_members*/
   0, /*tp_getset*/
   0, /*tp_base*/
@@ -59281,7 +62404,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct__read_bitext = {
   0, /*tp_dictoffset*/
   0, /*tp_init*/
   0, /*tp_alloc*/
-  __pyx_tp_new_3_sa___pyx_scope_struct__read_bitext, /*tp_new*/
+  __pyx_tp_new_3_sa___pyx_scope_struct_1_read_bitext, /*tp_new*/
   0, /*tp_free*/
   0, /*tp_is_gc*/
   0, /*tp_bases*/
@@ -59295,28 +62418,28 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct__read_bitext = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_1_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
-  struct __pyx_obj_3_sa___pyx_scope_struct_1_genexpr *p;
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_2_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_2_genexpr *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
-  p = ((struct __pyx_obj_3_sa___pyx_scope_struct_1_genexpr *)o);
+  p = ((struct __pyx_obj_3_sa___pyx_scope_struct_2_genexpr *)o);
   p->__pyx_outer_scope = 0;
   p->__pyx_v_line = 0;
   p->__pyx_t_0 = 0;
   return o;
 }
 
-static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_1_genexpr(PyObject *o) {
-  struct __pyx_obj_3_sa___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_1_genexpr *)o;
-  Py_XDECREF(((PyObject *)p->__pyx_outer_scope));
-  Py_XDECREF(p->__pyx_v_line);
-  Py_XDECREF(p->__pyx_t_0);
+static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_2_genexpr(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_2_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_2_genexpr *)o;
+  Py_CLEAR(p->__pyx_outer_scope);
+  Py_CLEAR(p->__pyx_v_line);
+  Py_CLEAR(p->__pyx_t_0);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
-static int __pyx_tp_traverse_3_sa___pyx_scope_struct_1_genexpr(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_3_sa___pyx_scope_struct_2_genexpr(PyObject *o, visitproc v, void *a) {
   int e;
-  struct __pyx_obj_3_sa___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_1_genexpr *)o;
+  struct __pyx_obj_3_sa___pyx_scope_struct_2_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_2_genexpr *)o;
   if (p->__pyx_outer_scope) {
     e = (*v)(((PyObject*)p->__pyx_outer_scope), a); if (e) return e;
   }
@@ -59329,11 +62452,11 @@ static int __pyx_tp_traverse_3_sa___pyx_scope_struct_1_genexpr(PyObject *o, visi
   return 0;
 }
 
-static int __pyx_tp_clear_3_sa___pyx_scope_struct_1_genexpr(PyObject *o) {
-  struct __pyx_obj_3_sa___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_1_genexpr *)o;
+static int __pyx_tp_clear_3_sa___pyx_scope_struct_2_genexpr(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_2_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_2_genexpr *)o;
   PyObject* tmp;
   tmp = ((PyObject*)p->__pyx_outer_scope);
-  p->__pyx_outer_scope = ((struct __pyx_obj_3_sa___pyx_scope_struct__read_bitext *)Py_None); Py_INCREF(Py_None);
+  p->__pyx_outer_scope = ((struct __pyx_obj_3_sa___pyx_scope_struct_1_read_bitext *)Py_None); Py_INCREF(Py_None);
   Py_XDECREF(tmp);
   tmp = ((PyObject*)p->__pyx_v_line);
   p->__pyx_v_line = Py_None; Py_INCREF(Py_None);
@@ -59344,11 +62467,11 @@ static int __pyx_tp_clear_3_sa___pyx_scope_struct_1_genexpr(PyObject *o) {
   return 0;
 }
 
-static PyMethodDef __pyx_methods_3_sa___pyx_scope_struct_1_genexpr[] = {
+static PyMethodDef __pyx_methods_3_sa___pyx_scope_struct_2_genexpr[] = {
   {0, 0, 0, 0}
 };
 
-static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_1_genexpr = {
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_2_genexpr = {
   0, /*nb_add*/
   0, /*nb_subtract*/
   0, /*nb_multiply*/
@@ -59406,7 +62529,7 @@ static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_1_genexpr = {
   #endif
 };
 
-static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_1_genexpr = {
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_2_genexpr = {
   0, /*sq_length*/
   0, /*sq_concat*/
   0, /*sq_repeat*/
@@ -59419,13 +62542,13 @@ static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_1_genexpr = {
   0, /*sq_inplace_repeat*/
 };
 
-static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_1_genexpr = {
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_2_genexpr = {
   0, /*mp_length*/
   0, /*mp_subscript*/
   0, /*mp_ass_subscript*/
 };
 
-static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_1_genexpr = {
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_2_genexpr = {
   #if PY_MAJOR_VERSION < 3
   0, /*bf_getreadbuffer*/
   #endif
@@ -59446,12 +62569,12 @@ static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_1_genexpr = {
   #endif
 };
 
-static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_1_genexpr = {
+static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_2_genexpr = {
   PyVarObject_HEAD_INIT(0, 0)
-  __Pyx_NAMESTR("_sa.__pyx_scope_struct_1_genexpr"), /*tp_name*/
-  sizeof(struct __pyx_obj_3_sa___pyx_scope_struct_1_genexpr), /*tp_basicsize*/
+  __Pyx_NAMESTR("_sa.__pyx_scope_struct_2_genexpr"), /*tp_name*/
+  sizeof(struct __pyx_obj_3_sa___pyx_scope_struct_2_genexpr), /*tp_basicsize*/
   0, /*tp_itemsize*/
-  __pyx_tp_dealloc_3_sa___pyx_scope_struct_1_genexpr, /*tp_dealloc*/
+  __pyx_tp_dealloc_3_sa___pyx_scope_struct_2_genexpr, /*tp_dealloc*/
   0, /*tp_print*/
   0, /*tp_getattr*/
   0, /*tp_setattr*/
@@ -59461,24 +62584,24 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_1_genexpr = {
   0, /*reserved*/
   #endif
   0, /*tp_repr*/
-  &__pyx_tp_as_number___pyx_scope_struct_1_genexpr, /*tp_as_number*/
-  &__pyx_tp_as_sequence___pyx_scope_struct_1_genexpr, /*tp_as_sequence*/
-  &__pyx_tp_as_mapping___pyx_scope_struct_1_genexpr, /*tp_as_mapping*/
+  &__pyx_tp_as_number___pyx_scope_struct_2_genexpr, /*tp_as_number*/
+  &__pyx_tp_as_sequence___pyx_scope_struct_2_genexpr, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping___pyx_scope_struct_2_genexpr, /*tp_as_mapping*/
   0, /*tp_hash*/
   0, /*tp_call*/
   0, /*tp_str*/
   0, /*tp_getattro*/
   0, /*tp_setattro*/
-  &__pyx_tp_as_buffer___pyx_scope_struct_1_genexpr, /*tp_as_buffer*/
+  &__pyx_tp_as_buffer___pyx_scope_struct_2_genexpr, /*tp_as_buffer*/
   Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
   0, /*tp_doc*/
-  __pyx_tp_traverse_3_sa___pyx_scope_struct_1_genexpr, /*tp_traverse*/
-  __pyx_tp_clear_3_sa___pyx_scope_struct_1_genexpr, /*tp_clear*/
+  __pyx_tp_traverse_3_sa___pyx_scope_struct_2_genexpr, /*tp_traverse*/
+  __pyx_tp_clear_3_sa___pyx_scope_struct_2_genexpr, /*tp_clear*/
   0, /*tp_richcompare*/
   0, /*tp_weaklistoffset*/
   0, /*tp_iter*/
   0, /*tp_iternext*/
-  __pyx_methods_3_sa___pyx_scope_struct_1_genexpr, /*tp_methods*/
+  __pyx_methods_3_sa___pyx_scope_struct_2_genexpr, /*tp_methods*/
   0, /*tp_members*/
   0, /*tp_getset*/
   0, /*tp_base*/
@@ -59488,7 +62611,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_1_genexpr = {
   0, /*tp_dictoffset*/
   0, /*tp_init*/
   0, /*tp_alloc*/
-  __pyx_tp_new_3_sa___pyx_scope_struct_1_genexpr, /*tp_new*/
+  __pyx_tp_new_3_sa___pyx_scope_struct_2_genexpr, /*tp_new*/
   0, /*tp_free*/
   0, /*tp_is_gc*/
   0, /*tp_bases*/
@@ -59502,11 +62625,11 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_1_genexpr = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_2_compute_stats(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
-  struct __pyx_obj_3_sa___pyx_scope_struct_2_compute_stats *p;
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_3_compute_stats(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_3_compute_stats *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
-  p = ((struct __pyx_obj_3_sa___pyx_scope_struct_2_compute_stats *)o);
+  p = ((struct __pyx_obj_3_sa___pyx_scope_struct_3_compute_stats *)o);
   p->__pyx_v_ngram = 0;
   p->__pyx_v_ngram_start = 0;
   p->__pyx_v_ngram_starts = 0;
@@ -59516,20 +62639,20 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_2_compute_stats(PyTypeObje
   return o;
 }
 
-static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_2_compute_stats(PyObject *o) {
-  struct __pyx_obj_3_sa___pyx_scope_struct_2_compute_stats *p = (struct __pyx_obj_3_sa___pyx_scope_struct_2_compute_stats *)o;
-  Py_XDECREF(((PyObject *)p->__pyx_v_ngram));
-  Py_XDECREF(((PyObject *)p->__pyx_v_ngram_start));
-  Py_XDECREF(((PyObject *)p->__pyx_v_ngram_starts));
-  Py_XDECREF(((PyObject *)p->__pyx_v_run_start));
-  Py_XDECREF(((PyObject *)p->__pyx_v_self));
-  Py_XDECREF(((PyObject *)p->__pyx_v_veb));
+static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_3_compute_stats(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_3_compute_stats *p = (struct __pyx_obj_3_sa___pyx_scope_struct_3_compute_stats *)o;
+  Py_CLEAR(p->__pyx_v_ngram);
+  Py_CLEAR(p->__pyx_v_ngram_start);
+  Py_CLEAR(p->__pyx_v_ngram_starts);
+  Py_CLEAR(p->__pyx_v_run_start);
+  Py_CLEAR(p->__pyx_v_self);
+  Py_CLEAR(p->__pyx_v_veb);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
-static int __pyx_tp_traverse_3_sa___pyx_scope_struct_2_compute_stats(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_3_sa___pyx_scope_struct_3_compute_stats(PyObject *o, visitproc v, void *a) {
   int e;
-  struct __pyx_obj_3_sa___pyx_scope_struct_2_compute_stats *p = (struct __pyx_obj_3_sa___pyx_scope_struct_2_compute_stats *)o;
+  struct __pyx_obj_3_sa___pyx_scope_struct_3_compute_stats *p = (struct __pyx_obj_3_sa___pyx_scope_struct_3_compute_stats *)o;
   if (p->__pyx_v_ngram) {
     e = (*v)(p->__pyx_v_ngram, a); if (e) return e;
   }
@@ -59551,8 +62674,8 @@ static int __pyx_tp_traverse_3_sa___pyx_scope_struct_2_compute_stats(PyObject *o
   return 0;
 }
 
-static int __pyx_tp_clear_3_sa___pyx_scope_struct_2_compute_stats(PyObject *o) {
-  struct __pyx_obj_3_sa___pyx_scope_struct_2_compute_stats *p = (struct __pyx_obj_3_sa___pyx_scope_struct_2_compute_stats *)o;
+static int __pyx_tp_clear_3_sa___pyx_scope_struct_3_compute_stats(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_3_compute_stats *p = (struct __pyx_obj_3_sa___pyx_scope_struct_3_compute_stats *)o;
   PyObject* tmp;
   tmp = ((PyObject*)p->__pyx_v_ngram);
   p->__pyx_v_ngram = ((PyObject*)Py_None); Py_INCREF(Py_None);
@@ -59575,11 +62698,1476 @@ static int __pyx_tp_clear_3_sa___pyx_scope_struct_2_compute_stats(PyObject *o) {
   return 0;
 }
 
-static PyMethodDef __pyx_methods_3_sa___pyx_scope_struct_2_compute_stats[] = {
+static PyMethodDef __pyx_methods_3_sa___pyx_scope_struct_3_compute_stats[] = {
+  {0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_3_compute_stats = {
+  0, /*nb_add*/
+  0, /*nb_subtract*/
+  0, /*nb_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_divide*/
+  #endif
+  0, /*nb_remainder*/
+  0, /*nb_divmod*/
+  0, /*nb_power*/
+  0, /*nb_negative*/
+  0, /*nb_positive*/
+  0, /*nb_absolute*/
+  0, /*nb_nonzero*/
+  0, /*nb_invert*/
+  0, /*nb_lshift*/
+  0, /*nb_rshift*/
+  0, /*nb_and*/
+  0, /*nb_xor*/
+  0, /*nb_or*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_coerce*/
+  #endif
+  0, /*nb_int*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_long*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*nb_float*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_oct*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_hex*/
+  #endif
+  0, /*nb_inplace_add*/
+  0, /*nb_inplace_subtract*/
+  0, /*nb_inplace_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_inplace_divide*/
+  #endif
+  0, /*nb_inplace_remainder*/
+  0, /*nb_inplace_power*/
+  0, /*nb_inplace_lshift*/
+  0, /*nb_inplace_rshift*/
+  0, /*nb_inplace_and*/
+  0, /*nb_inplace_xor*/
+  0, /*nb_inplace_or*/
+  0, /*nb_floor_divide*/
+  0, /*nb_true_divide*/
+  0, /*nb_inplace_floor_divide*/
+  0, /*nb_inplace_true_divide*/
+  #if PY_VERSION_HEX >= 0x02050000
+  0, /*nb_index*/
+  #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_3_compute_stats = {
+  0, /*sq_length*/
+  0, /*sq_concat*/
+  0, /*sq_repeat*/
+  0, /*sq_item*/
+  0, /*sq_slice*/
+  0, /*sq_ass_item*/
+  0, /*sq_ass_slice*/
+  0, /*sq_contains*/
+  0, /*sq_inplace_concat*/
+  0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_3_compute_stats = {
+  0, /*mp_length*/
+  0, /*mp_subscript*/
+  0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_3_compute_stats = {
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getreadbuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getwritebuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getsegcount*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getcharbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_getbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_releasebuffer*/
+  #endif
+};
+
+static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_3_compute_stats = {
+  PyVarObject_HEAD_INIT(0, 0)
+  __Pyx_NAMESTR("_sa.__pyx_scope_struct_3_compute_stats"), /*tp_name*/
+  sizeof(struct __pyx_obj_3_sa___pyx_scope_struct_3_compute_stats), /*tp_basicsize*/
+  0, /*tp_itemsize*/
+  __pyx_tp_dealloc_3_sa___pyx_scope_struct_3_compute_stats, /*tp_dealloc*/
+  0, /*tp_print*/
+  0, /*tp_getattr*/
+  0, /*tp_setattr*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*tp_compare*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*tp_repr*/
+  &__pyx_tp_as_number___pyx_scope_struct_3_compute_stats, /*tp_as_number*/
+  &__pyx_tp_as_sequence___pyx_scope_struct_3_compute_stats, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping___pyx_scope_struct_3_compute_stats, /*tp_as_mapping*/
+  0, /*tp_hash*/
+  0, /*tp_call*/
+  0, /*tp_str*/
+  0, /*tp_getattro*/
+  0, /*tp_setattro*/
+  &__pyx_tp_as_buffer___pyx_scope_struct_3_compute_stats, /*tp_as_buffer*/
+  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+  0, /*tp_doc*/
+  __pyx_tp_traverse_3_sa___pyx_scope_struct_3_compute_stats, /*tp_traverse*/
+  __pyx_tp_clear_3_sa___pyx_scope_struct_3_compute_stats, /*tp_clear*/
+  0, /*tp_richcompare*/
+  0, /*tp_weaklistoffset*/
+  0, /*tp_iter*/
+  0, /*tp_iternext*/
+  __pyx_methods_3_sa___pyx_scope_struct_3_compute_stats, /*tp_methods*/
+  0, /*tp_members*/
+  0, /*tp_getset*/
+  0, /*tp_base*/
+  0, /*tp_dict*/
+  0, /*tp_descr_get*/
+  0, /*tp_descr_set*/
+  0, /*tp_dictoffset*/
+  0, /*tp_init*/
+  0, /*tp_alloc*/
+  __pyx_tp_new_3_sa___pyx_scope_struct_3_compute_stats, /*tp_new*/
+  0, /*tp_free*/
+  0, /*tp_is_gc*/
+  0, /*tp_bases*/
+  0, /*tp_mro*/
+  0, /*tp_cache*/
+  0, /*tp_subclasses*/
+  0, /*tp_weaklist*/
+  0, /*tp_del*/
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*tp_version_tag*/
+  #endif
+};
+
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_4_make_lattice(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_4_make_lattice *p;
+  PyObject *o = (*t->tp_alloc)(t, 0);
+  if (!o) return 0;
+  p = ((struct __pyx_obj_3_sa___pyx_scope_struct_4_make_lattice *)o);
+  p->__pyx_v_word_ids = 0;
+  p->__pyx_v_words = 0;
+  return o;
+}
+
+static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_4_make_lattice(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_4_make_lattice *p = (struct __pyx_obj_3_sa___pyx_scope_struct_4_make_lattice *)o;
+  Py_CLEAR(p->__pyx_v_word_ids);
+  Py_CLEAR(p->__pyx_v_words);
+  (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_3_sa___pyx_scope_struct_4_make_lattice(PyObject *o, visitproc v, void *a) {
+  int e;
+  struct __pyx_obj_3_sa___pyx_scope_struct_4_make_lattice *p = (struct __pyx_obj_3_sa___pyx_scope_struct_4_make_lattice *)o;
+  if (p->__pyx_v_word_ids) {
+    e = (*v)(p->__pyx_v_word_ids, a); if (e) return e;
+  }
+  if (p->__pyx_v_words) {
+    e = (*v)(p->__pyx_v_words, a); if (e) return e;
+  }
+  return 0;
+}
+
+static int __pyx_tp_clear_3_sa___pyx_scope_struct_4_make_lattice(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_4_make_lattice *p = (struct __pyx_obj_3_sa___pyx_scope_struct_4_make_lattice *)o;
+  PyObject* tmp;
+  tmp = ((PyObject*)p->__pyx_v_word_ids);
+  p->__pyx_v_word_ids = Py_None; Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->__pyx_v_words);
+  p->__pyx_v_words = Py_None; Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  return 0;
+}
+
+static PyMethodDef __pyx_methods_3_sa___pyx_scope_struct_4_make_lattice[] = {
+  {0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_4_make_lattice = {
+  0, /*nb_add*/
+  0, /*nb_subtract*/
+  0, /*nb_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_divide*/
+  #endif
+  0, /*nb_remainder*/
+  0, /*nb_divmod*/
+  0, /*nb_power*/
+  0, /*nb_negative*/
+  0, /*nb_positive*/
+  0, /*nb_absolute*/
+  0, /*nb_nonzero*/
+  0, /*nb_invert*/
+  0, /*nb_lshift*/
+  0, /*nb_rshift*/
+  0, /*nb_and*/
+  0, /*nb_xor*/
+  0, /*nb_or*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_coerce*/
+  #endif
+  0, /*nb_int*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_long*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*nb_float*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_oct*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_hex*/
+  #endif
+  0, /*nb_inplace_add*/
+  0, /*nb_inplace_subtract*/
+  0, /*nb_inplace_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_inplace_divide*/
+  #endif
+  0, /*nb_inplace_remainder*/
+  0, /*nb_inplace_power*/
+  0, /*nb_inplace_lshift*/
+  0, /*nb_inplace_rshift*/
+  0, /*nb_inplace_and*/
+  0, /*nb_inplace_xor*/
+  0, /*nb_inplace_or*/
+  0, /*nb_floor_divide*/
+  0, /*nb_true_divide*/
+  0, /*nb_inplace_floor_divide*/
+  0, /*nb_inplace_true_divide*/
+  #if PY_VERSION_HEX >= 0x02050000
+  0, /*nb_index*/
+  #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_4_make_lattice = {
+  0, /*sq_length*/
+  0, /*sq_concat*/
+  0, /*sq_repeat*/
+  0, /*sq_item*/
+  0, /*sq_slice*/
+  0, /*sq_ass_item*/
+  0, /*sq_ass_slice*/
+  0, /*sq_contains*/
+  0, /*sq_inplace_concat*/
+  0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_4_make_lattice = {
+  0, /*mp_length*/
+  0, /*mp_subscript*/
+  0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_4_make_lattice = {
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getreadbuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getwritebuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getsegcount*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getcharbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_getbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_releasebuffer*/
+  #endif
+};
+
+static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_4_make_lattice = {
+  PyVarObject_HEAD_INIT(0, 0)
+  __Pyx_NAMESTR("_sa.__pyx_scope_struct_4_make_lattice"), /*tp_name*/
+  sizeof(struct __pyx_obj_3_sa___pyx_scope_struct_4_make_lattice), /*tp_basicsize*/
+  0, /*tp_itemsize*/
+  __pyx_tp_dealloc_3_sa___pyx_scope_struct_4_make_lattice, /*tp_dealloc*/
+  0, /*tp_print*/
+  0, /*tp_getattr*/
+  0, /*tp_setattr*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*tp_compare*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*tp_repr*/
+  &__pyx_tp_as_number___pyx_scope_struct_4_make_lattice, /*tp_as_number*/
+  &__pyx_tp_as_sequence___pyx_scope_struct_4_make_lattice, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping___pyx_scope_struct_4_make_lattice, /*tp_as_mapping*/
+  0, /*tp_hash*/
+  0, /*tp_call*/
+  0, /*tp_str*/
+  0, /*tp_getattro*/
+  0, /*tp_setattro*/
+  &__pyx_tp_as_buffer___pyx_scope_struct_4_make_lattice, /*tp_as_buffer*/
+  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+  0, /*tp_doc*/
+  __pyx_tp_traverse_3_sa___pyx_scope_struct_4_make_lattice, /*tp_traverse*/
+  __pyx_tp_clear_3_sa___pyx_scope_struct_4_make_lattice, /*tp_clear*/
+  0, /*tp_richcompare*/
+  0, /*tp_weaklistoffset*/
+  0, /*tp_iter*/
+  0, /*tp_iternext*/
+  __pyx_methods_3_sa___pyx_scope_struct_4_make_lattice, /*tp_methods*/
+  0, /*tp_members*/
+  0, /*tp_getset*/
+  0, /*tp_base*/
+  0, /*tp_dict*/
+  0, /*tp_descr_get*/
+  0, /*tp_descr_set*/
+  0, /*tp_dictoffset*/
+  0, /*tp_init*/
+  0, /*tp_alloc*/
+  __pyx_tp_new_3_sa___pyx_scope_struct_4_make_lattice, /*tp_new*/
+  0, /*tp_free*/
+  0, /*tp_is_gc*/
+  0, /*tp_bases*/
+  0, /*tp_mro*/
+  0, /*tp_cache*/
+  0, /*tp_subclasses*/
+  0, /*tp_weaklist*/
+  0, /*tp_del*/
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*tp_version_tag*/
+  #endif
+};
+
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_5_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_5_genexpr *p;
+  PyObject *o = (*t->tp_alloc)(t, 0);
+  if (!o) return 0;
+  p = ((struct __pyx_obj_3_sa___pyx_scope_struct_5_genexpr *)o);
+  p->__pyx_outer_scope = 0;
+  p->__pyx_v_word = 0;
+  p->__pyx_t_0 = 0;
+  return o;
+}
+
+static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_5_genexpr(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_5_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_5_genexpr *)o;
+  Py_CLEAR(p->__pyx_outer_scope);
+  Py_CLEAR(p->__pyx_v_word);
+  Py_CLEAR(p->__pyx_t_0);
+  (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_3_sa___pyx_scope_struct_5_genexpr(PyObject *o, visitproc v, void *a) {
+  int e;
+  struct __pyx_obj_3_sa___pyx_scope_struct_5_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_5_genexpr *)o;
+  if (p->__pyx_outer_scope) {
+    e = (*v)(((PyObject*)p->__pyx_outer_scope), a); if (e) return e;
+  }
+  if (p->__pyx_v_word) {
+    e = (*v)(p->__pyx_v_word, a); if (e) return e;
+  }
+  if (p->__pyx_t_0) {
+    e = (*v)(p->__pyx_t_0, a); if (e) return e;
+  }
+  return 0;
+}
+
+static int __pyx_tp_clear_3_sa___pyx_scope_struct_5_genexpr(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_5_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_5_genexpr *)o;
+  PyObject* tmp;
+  tmp = ((PyObject*)p->__pyx_outer_scope);
+  p->__pyx_outer_scope = ((struct __pyx_obj_3_sa___pyx_scope_struct_4_make_lattice *)Py_None); Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->__pyx_v_word);
+  p->__pyx_v_word = Py_None; Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->__pyx_t_0);
+  p->__pyx_t_0 = Py_None; Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  return 0;
+}
+
+static PyMethodDef __pyx_methods_3_sa___pyx_scope_struct_5_genexpr[] = {
+  {0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_5_genexpr = {
+  0, /*nb_add*/
+  0, /*nb_subtract*/
+  0, /*nb_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_divide*/
+  #endif
+  0, /*nb_remainder*/
+  0, /*nb_divmod*/
+  0, /*nb_power*/
+  0, /*nb_negative*/
+  0, /*nb_positive*/
+  0, /*nb_absolute*/
+  0, /*nb_nonzero*/
+  0, /*nb_invert*/
+  0, /*nb_lshift*/
+  0, /*nb_rshift*/
+  0, /*nb_and*/
+  0, /*nb_xor*/
+  0, /*nb_or*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_coerce*/
+  #endif
+  0, /*nb_int*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_long*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*nb_float*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_oct*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_hex*/
+  #endif
+  0, /*nb_inplace_add*/
+  0, /*nb_inplace_subtract*/
+  0, /*nb_inplace_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_inplace_divide*/
+  #endif
+  0, /*nb_inplace_remainder*/
+  0, /*nb_inplace_power*/
+  0, /*nb_inplace_lshift*/
+  0, /*nb_inplace_rshift*/
+  0, /*nb_inplace_and*/
+  0, /*nb_inplace_xor*/
+  0, /*nb_inplace_or*/
+  0, /*nb_floor_divide*/
+  0, /*nb_true_divide*/
+  0, /*nb_inplace_floor_divide*/
+  0, /*nb_inplace_true_divide*/
+  #if PY_VERSION_HEX >= 0x02050000
+  0, /*nb_index*/
+  #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_5_genexpr = {
+  0, /*sq_length*/
+  0, /*sq_concat*/
+  0, /*sq_repeat*/
+  0, /*sq_item*/
+  0, /*sq_slice*/
+  0, /*sq_ass_item*/
+  0, /*sq_ass_slice*/
+  0, /*sq_contains*/
+  0, /*sq_inplace_concat*/
+  0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_5_genexpr = {
+  0, /*mp_length*/
+  0, /*mp_subscript*/
+  0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_5_genexpr = {
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getreadbuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getwritebuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getsegcount*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getcharbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_getbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_releasebuffer*/
+  #endif
+};
+
+static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_5_genexpr = {
+  PyVarObject_HEAD_INIT(0, 0)
+  __Pyx_NAMESTR("_sa.__pyx_scope_struct_5_genexpr"), /*tp_name*/
+  sizeof(struct __pyx_obj_3_sa___pyx_scope_struct_5_genexpr), /*tp_basicsize*/
+  0, /*tp_itemsize*/
+  __pyx_tp_dealloc_3_sa___pyx_scope_struct_5_genexpr, /*tp_dealloc*/
+  0, /*tp_print*/
+  0, /*tp_getattr*/
+  0, /*tp_setattr*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*tp_compare*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*tp_repr*/
+  &__pyx_tp_as_number___pyx_scope_struct_5_genexpr, /*tp_as_number*/
+  &__pyx_tp_as_sequence___pyx_scope_struct_5_genexpr, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping___pyx_scope_struct_5_genexpr, /*tp_as_mapping*/
+  0, /*tp_hash*/
+  0, /*tp_call*/
+  0, /*tp_str*/
+  0, /*tp_getattro*/
+  0, /*tp_setattro*/
+  &__pyx_tp_as_buffer___pyx_scope_struct_5_genexpr, /*tp_as_buffer*/
+  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+  0, /*tp_doc*/
+  __pyx_tp_traverse_3_sa___pyx_scope_struct_5_genexpr, /*tp_traverse*/
+  __pyx_tp_clear_3_sa___pyx_scope_struct_5_genexpr, /*tp_clear*/
+  0, /*tp_richcompare*/
+  0, /*tp_weaklistoffset*/
+  0, /*tp_iter*/
+  0, /*tp_iternext*/
+  __pyx_methods_3_sa___pyx_scope_struct_5_genexpr, /*tp_methods*/
+  0, /*tp_members*/
+  0, /*tp_getset*/
+  0, /*tp_base*/
+  0, /*tp_dict*/
+  0, /*tp_descr_get*/
+  0, /*tp_descr_set*/
+  0, /*tp_dictoffset*/
+  0, /*tp_init*/
+  0, /*tp_alloc*/
+  __pyx_tp_new_3_sa___pyx_scope_struct_5_genexpr, /*tp_new*/
+  0, /*tp_free*/
+  0, /*tp_is_gc*/
+  0, /*tp_bases*/
+  0, /*tp_mro*/
+  0, /*tp_cache*/
+  0, /*tp_subclasses*/
+  0, /*tp_weaklist*/
+  0, /*tp_del*/
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*tp_version_tag*/
+  #endif
+};
+
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_6_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_6_genexpr *p;
+  PyObject *o = (*t->tp_alloc)(t, 0);
+  if (!o) return 0;
+  p = ((struct __pyx_obj_3_sa___pyx_scope_struct_6_genexpr *)o);
+  p->__pyx_outer_scope = 0;
+  p->__pyx_v_word = 0;
+  p->__pyx_t_0 = 0;
+  return o;
+}
+
+static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_6_genexpr(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_6_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_6_genexpr *)o;
+  Py_CLEAR(p->__pyx_outer_scope);
+  Py_CLEAR(p->__pyx_v_word);
+  Py_CLEAR(p->__pyx_t_0);
+  (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_3_sa___pyx_scope_struct_6_genexpr(PyObject *o, visitproc v, void *a) {
+  int e;
+  struct __pyx_obj_3_sa___pyx_scope_struct_6_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_6_genexpr *)o;
+  if (p->__pyx_outer_scope) {
+    e = (*v)(((PyObject*)p->__pyx_outer_scope), a); if (e) return e;
+  }
+  if (p->__pyx_v_word) {
+    e = (*v)(p->__pyx_v_word, a); if (e) return e;
+  }
+  if (p->__pyx_t_0) {
+    e = (*v)(p->__pyx_t_0, a); if (e) return e;
+  }
+  return 0;
+}
+
+static int __pyx_tp_clear_3_sa___pyx_scope_struct_6_genexpr(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_6_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_6_genexpr *)o;
+  PyObject* tmp;
+  tmp = ((PyObject*)p->__pyx_outer_scope);
+  p->__pyx_outer_scope = ((struct __pyx_obj_3_sa___pyx_scope_struct_4_make_lattice *)Py_None); Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->__pyx_v_word);
+  p->__pyx_v_word = Py_None; Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->__pyx_t_0);
+  p->__pyx_t_0 = Py_None; Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  return 0;
+}
+
+static PyMethodDef __pyx_methods_3_sa___pyx_scope_struct_6_genexpr[] = {
+  {0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_6_genexpr = {
+  0, /*nb_add*/
+  0, /*nb_subtract*/
+  0, /*nb_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_divide*/
+  #endif
+  0, /*nb_remainder*/
+  0, /*nb_divmod*/
+  0, /*nb_power*/
+  0, /*nb_negative*/
+  0, /*nb_positive*/
+  0, /*nb_absolute*/
+  0, /*nb_nonzero*/
+  0, /*nb_invert*/
+  0, /*nb_lshift*/
+  0, /*nb_rshift*/
+  0, /*nb_and*/
+  0, /*nb_xor*/
+  0, /*nb_or*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_coerce*/
+  #endif
+  0, /*nb_int*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_long*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*nb_float*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_oct*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_hex*/
+  #endif
+  0, /*nb_inplace_add*/
+  0, /*nb_inplace_subtract*/
+  0, /*nb_inplace_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_inplace_divide*/
+  #endif
+  0, /*nb_inplace_remainder*/
+  0, /*nb_inplace_power*/
+  0, /*nb_inplace_lshift*/
+  0, /*nb_inplace_rshift*/
+  0, /*nb_inplace_and*/
+  0, /*nb_inplace_xor*/
+  0, /*nb_inplace_or*/
+  0, /*nb_floor_divide*/
+  0, /*nb_true_divide*/
+  0, /*nb_inplace_floor_divide*/
+  0, /*nb_inplace_true_divide*/
+  #if PY_VERSION_HEX >= 0x02050000
+  0, /*nb_index*/
+  #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_6_genexpr = {
+  0, /*sq_length*/
+  0, /*sq_concat*/
+  0, /*sq_repeat*/
+  0, /*sq_item*/
+  0, /*sq_slice*/
+  0, /*sq_ass_item*/
+  0, /*sq_ass_slice*/
+  0, /*sq_contains*/
+  0, /*sq_inplace_concat*/
+  0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_6_genexpr = {
+  0, /*mp_length*/
+  0, /*mp_subscript*/
+  0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_6_genexpr = {
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getreadbuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getwritebuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getsegcount*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getcharbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_getbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_releasebuffer*/
+  #endif
+};
+
+static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_6_genexpr = {
+  PyVarObject_HEAD_INIT(0, 0)
+  __Pyx_NAMESTR("_sa.__pyx_scope_struct_6_genexpr"), /*tp_name*/
+  sizeof(struct __pyx_obj_3_sa___pyx_scope_struct_6_genexpr), /*tp_basicsize*/
+  0, /*tp_itemsize*/
+  __pyx_tp_dealloc_3_sa___pyx_scope_struct_6_genexpr, /*tp_dealloc*/
+  0, /*tp_print*/
+  0, /*tp_getattr*/
+  0, /*tp_setattr*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*tp_compare*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*tp_repr*/
+  &__pyx_tp_as_number___pyx_scope_struct_6_genexpr, /*tp_as_number*/
+  &__pyx_tp_as_sequence___pyx_scope_struct_6_genexpr, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping___pyx_scope_struct_6_genexpr, /*tp_as_mapping*/
+  0, /*tp_hash*/
+  0, /*tp_call*/
+  0, /*tp_str*/
+  0, /*tp_getattro*/
+  0, /*tp_setattro*/
+  &__pyx_tp_as_buffer___pyx_scope_struct_6_genexpr, /*tp_as_buffer*/
+  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+  0, /*tp_doc*/
+  __pyx_tp_traverse_3_sa___pyx_scope_struct_6_genexpr, /*tp_traverse*/
+  __pyx_tp_clear_3_sa___pyx_scope_struct_6_genexpr, /*tp_clear*/
+  0, /*tp_richcompare*/
+  0, /*tp_weaklistoffset*/
+  0, /*tp_iter*/
+  0, /*tp_iternext*/
+  __pyx_methods_3_sa___pyx_scope_struct_6_genexpr, /*tp_methods*/
+  0, /*tp_members*/
+  0, /*tp_getset*/
+  0, /*tp_base*/
+  0, /*tp_dict*/
+  0, /*tp_descr_get*/
+  0, /*tp_descr_set*/
+  0, /*tp_dictoffset*/
+  0, /*tp_init*/
+  0, /*tp_alloc*/
+  __pyx_tp_new_3_sa___pyx_scope_struct_6_genexpr, /*tp_new*/
+  0, /*tp_free*/
+  0, /*tp_is_gc*/
+  0, /*tp_bases*/
+  0, /*tp_mro*/
+  0, /*tp_cache*/
+  0, /*tp_subclasses*/
+  0, /*tp_weaklist*/
+  0, /*tp_del*/
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*tp_version_tag*/
+  #endif
+};
+
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_7_decode_lattice(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_7_decode_lattice *p;
+  PyObject *o = (*t->tp_alloc)(t, 0);
+  if (!o) return 0;
+  p = ((struct __pyx_obj_3_sa___pyx_scope_struct_7_decode_lattice *)o);
+  p->__pyx_v_lattice = 0;
+  return o;
+}
+
+static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_7_decode_lattice(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_7_decode_lattice *p = (struct __pyx_obj_3_sa___pyx_scope_struct_7_decode_lattice *)o;
+  Py_CLEAR(p->__pyx_v_lattice);
+  (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_3_sa___pyx_scope_struct_7_decode_lattice(PyObject *o, visitproc v, void *a) {
+  int e;
+  struct __pyx_obj_3_sa___pyx_scope_struct_7_decode_lattice *p = (struct __pyx_obj_3_sa___pyx_scope_struct_7_decode_lattice *)o;
+  if (p->__pyx_v_lattice) {
+    e = (*v)(p->__pyx_v_lattice, a); if (e) return e;
+  }
+  return 0;
+}
+
+static int __pyx_tp_clear_3_sa___pyx_scope_struct_7_decode_lattice(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_7_decode_lattice *p = (struct __pyx_obj_3_sa___pyx_scope_struct_7_decode_lattice *)o;
+  PyObject* tmp;
+  tmp = ((PyObject*)p->__pyx_v_lattice);
+  p->__pyx_v_lattice = Py_None; Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  return 0;
+}
+
+static PyMethodDef __pyx_methods_3_sa___pyx_scope_struct_7_decode_lattice[] = {
+  {0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_7_decode_lattice = {
+  0, /*nb_add*/
+  0, /*nb_subtract*/
+  0, /*nb_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_divide*/
+  #endif
+  0, /*nb_remainder*/
+  0, /*nb_divmod*/
+  0, /*nb_power*/
+  0, /*nb_negative*/
+  0, /*nb_positive*/
+  0, /*nb_absolute*/
+  0, /*nb_nonzero*/
+  0, /*nb_invert*/
+  0, /*nb_lshift*/
+  0, /*nb_rshift*/
+  0, /*nb_and*/
+  0, /*nb_xor*/
+  0, /*nb_or*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_coerce*/
+  #endif
+  0, /*nb_int*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_long*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*nb_float*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_oct*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_hex*/
+  #endif
+  0, /*nb_inplace_add*/
+  0, /*nb_inplace_subtract*/
+  0, /*nb_inplace_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_inplace_divide*/
+  #endif
+  0, /*nb_inplace_remainder*/
+  0, /*nb_inplace_power*/
+  0, /*nb_inplace_lshift*/
+  0, /*nb_inplace_rshift*/
+  0, /*nb_inplace_and*/
+  0, /*nb_inplace_xor*/
+  0, /*nb_inplace_or*/
+  0, /*nb_floor_divide*/
+  0, /*nb_true_divide*/
+  0, /*nb_inplace_floor_divide*/
+  0, /*nb_inplace_true_divide*/
+  #if PY_VERSION_HEX >= 0x02050000
+  0, /*nb_index*/
+  #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_7_decode_lattice = {
+  0, /*sq_length*/
+  0, /*sq_concat*/
+  0, /*sq_repeat*/
+  0, /*sq_item*/
+  0, /*sq_slice*/
+  0, /*sq_ass_item*/
+  0, /*sq_ass_slice*/
+  0, /*sq_contains*/
+  0, /*sq_inplace_concat*/
+  0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_7_decode_lattice = {
+  0, /*mp_length*/
+  0, /*mp_subscript*/
+  0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_7_decode_lattice = {
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getreadbuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getwritebuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getsegcount*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getcharbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_getbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_releasebuffer*/
+  #endif
+};
+
+static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_7_decode_lattice = {
+  PyVarObject_HEAD_INIT(0, 0)
+  __Pyx_NAMESTR("_sa.__pyx_scope_struct_7_decode_lattice"), /*tp_name*/
+  sizeof(struct __pyx_obj_3_sa___pyx_scope_struct_7_decode_lattice), /*tp_basicsize*/
+  0, /*tp_itemsize*/
+  __pyx_tp_dealloc_3_sa___pyx_scope_struct_7_decode_lattice, /*tp_dealloc*/
+  0, /*tp_print*/
+  0, /*tp_getattr*/
+  0, /*tp_setattr*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*tp_compare*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*tp_repr*/
+  &__pyx_tp_as_number___pyx_scope_struct_7_decode_lattice, /*tp_as_number*/
+  &__pyx_tp_as_sequence___pyx_scope_struct_7_decode_lattice, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping___pyx_scope_struct_7_decode_lattice, /*tp_as_mapping*/
+  0, /*tp_hash*/
+  0, /*tp_call*/
+  0, /*tp_str*/
+  0, /*tp_getattro*/
+  0, /*tp_setattro*/
+  &__pyx_tp_as_buffer___pyx_scope_struct_7_decode_lattice, /*tp_as_buffer*/
+  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+  0, /*tp_doc*/
+  __pyx_tp_traverse_3_sa___pyx_scope_struct_7_decode_lattice, /*tp_traverse*/
+  __pyx_tp_clear_3_sa___pyx_scope_struct_7_decode_lattice, /*tp_clear*/
+  0, /*tp_richcompare*/
+  0, /*tp_weaklistoffset*/
+  0, /*tp_iter*/
+  0, /*tp_iternext*/
+  __pyx_methods_3_sa___pyx_scope_struct_7_decode_lattice, /*tp_methods*/
+  0, /*tp_members*/
+  0, /*tp_getset*/
+  0, /*tp_base*/
+  0, /*tp_dict*/
+  0, /*tp_descr_get*/
+  0, /*tp_descr_set*/
+  0, /*tp_dictoffset*/
+  0, /*tp_init*/
+  0, /*tp_alloc*/
+  __pyx_tp_new_3_sa___pyx_scope_struct_7_decode_lattice, /*tp_new*/
+  0, /*tp_free*/
+  0, /*tp_is_gc*/
+  0, /*tp_bases*/
+  0, /*tp_mro*/
+  0, /*tp_cache*/
+  0, /*tp_subclasses*/
+  0, /*tp_weaklist*/
+  0, /*tp_del*/
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*tp_version_tag*/
+  #endif
+};
+
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_8_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_8_genexpr *p;
+  PyObject *o = (*t->tp_alloc)(t, 0);
+  if (!o) return 0;
+  p = ((struct __pyx_obj_3_sa___pyx_scope_struct_8_genexpr *)o);
+  p->__pyx_outer_scope = 0;
+  p->__pyx_v_arc = 0;
+  p->__pyx_v_dist = 0;
+  p->__pyx_v_node = 0;
+  p->__pyx_v_sym = 0;
+  p->__pyx_v_weight = 0;
+  p->__pyx_t_0 = 0;
+  p->__pyx_t_3 = 0;
+  p->__pyx_t_4 = 0;
+  return o;
+}
+
+static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_8_genexpr(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_8_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_8_genexpr *)o;
+  Py_CLEAR(p->__pyx_outer_scope);
+  Py_CLEAR(p->__pyx_v_arc);
+  Py_CLEAR(p->__pyx_v_dist);
+  Py_CLEAR(p->__pyx_v_node);
+  Py_CLEAR(p->__pyx_v_sym);
+  Py_CLEAR(p->__pyx_v_weight);
+  Py_CLEAR(p->__pyx_t_0);
+  Py_CLEAR(p->__pyx_t_3);
+  Py_CLEAR(p->__pyx_t_4);
+  (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_3_sa___pyx_scope_struct_8_genexpr(PyObject *o, visitproc v, void *a) {
+  int e;
+  struct __pyx_obj_3_sa___pyx_scope_struct_8_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_8_genexpr *)o;
+  if (p->__pyx_outer_scope) {
+    e = (*v)(((PyObject*)p->__pyx_outer_scope), a); if (e) return e;
+  }
+  if (p->__pyx_v_arc) {
+    e = (*v)(p->__pyx_v_arc, a); if (e) return e;
+  }
+  if (p->__pyx_v_dist) {
+    e = (*v)(p->__pyx_v_dist, a); if (e) return e;
+  }
+  if (p->__pyx_v_node) {
+    e = (*v)(p->__pyx_v_node, a); if (e) return e;
+  }
+  if (p->__pyx_v_sym) {
+    e = (*v)(p->__pyx_v_sym, a); if (e) return e;
+  }
+  if (p->__pyx_v_weight) {
+    e = (*v)(p->__pyx_v_weight, a); if (e) return e;
+  }
+  if (p->__pyx_t_0) {
+    e = (*v)(p->__pyx_t_0, a); if (e) return e;
+  }
+  if (p->__pyx_t_3) {
+    e = (*v)(p->__pyx_t_3, a); if (e) return e;
+  }
+  if (p->__pyx_t_4) {
+    e = (*v)(p->__pyx_t_4, a); if (e) return e;
+  }
+  return 0;
+}
+
+static int __pyx_tp_clear_3_sa___pyx_scope_struct_8_genexpr(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_8_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_8_genexpr *)o;
+  PyObject* tmp;
+  tmp = ((PyObject*)p->__pyx_outer_scope);
+  p->__pyx_outer_scope = ((struct __pyx_obj_3_sa___pyx_scope_struct_7_decode_lattice *)Py_None); Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->__pyx_v_arc);
+  p->__pyx_v_arc = Py_None; Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->__pyx_v_dist);
+  p->__pyx_v_dist = Py_None; Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->__pyx_v_node);
+  p->__pyx_v_node = Py_None; Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->__pyx_v_sym);
+  p->__pyx_v_sym = Py_None; Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->__pyx_v_weight);
+  p->__pyx_v_weight = Py_None; Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->__pyx_t_0);
+  p->__pyx_t_0 = Py_None; Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->__pyx_t_3);
+  p->__pyx_t_3 = Py_None; Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->__pyx_t_4);
+  p->__pyx_t_4 = Py_None; Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  return 0;
+}
+
+static PyMethodDef __pyx_methods_3_sa___pyx_scope_struct_8_genexpr[] = {
+  {0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_8_genexpr = {
+  0, /*nb_add*/
+  0, /*nb_subtract*/
+  0, /*nb_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_divide*/
+  #endif
+  0, /*nb_remainder*/
+  0, /*nb_divmod*/
+  0, /*nb_power*/
+  0, /*nb_negative*/
+  0, /*nb_positive*/
+  0, /*nb_absolute*/
+  0, /*nb_nonzero*/
+  0, /*nb_invert*/
+  0, /*nb_lshift*/
+  0, /*nb_rshift*/
+  0, /*nb_and*/
+  0, /*nb_xor*/
+  0, /*nb_or*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_coerce*/
+  #endif
+  0, /*nb_int*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_long*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*nb_float*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_oct*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_hex*/
+  #endif
+  0, /*nb_inplace_add*/
+  0, /*nb_inplace_subtract*/
+  0, /*nb_inplace_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_inplace_divide*/
+  #endif
+  0, /*nb_inplace_remainder*/
+  0, /*nb_inplace_power*/
+  0, /*nb_inplace_lshift*/
+  0, /*nb_inplace_rshift*/
+  0, /*nb_inplace_and*/
+  0, /*nb_inplace_xor*/
+  0, /*nb_inplace_or*/
+  0, /*nb_floor_divide*/
+  0, /*nb_true_divide*/
+  0, /*nb_inplace_floor_divide*/
+  0, /*nb_inplace_true_divide*/
+  #if PY_VERSION_HEX >= 0x02050000
+  0, /*nb_index*/
+  #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_8_genexpr = {
+  0, /*sq_length*/
+  0, /*sq_concat*/
+  0, /*sq_repeat*/
+  0, /*sq_item*/
+  0, /*sq_slice*/
+  0, /*sq_ass_item*/
+  0, /*sq_ass_slice*/
+  0, /*sq_contains*/
+  0, /*sq_inplace_concat*/
+  0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_8_genexpr = {
+  0, /*mp_length*/
+  0, /*mp_subscript*/
+  0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_8_genexpr = {
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getreadbuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getwritebuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getsegcount*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getcharbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_getbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_releasebuffer*/
+  #endif
+};
+
+static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_8_genexpr = {
+  PyVarObject_HEAD_INIT(0, 0)
+  __Pyx_NAMESTR("_sa.__pyx_scope_struct_8_genexpr"), /*tp_name*/
+  sizeof(struct __pyx_obj_3_sa___pyx_scope_struct_8_genexpr), /*tp_basicsize*/
+  0, /*tp_itemsize*/
+  __pyx_tp_dealloc_3_sa___pyx_scope_struct_8_genexpr, /*tp_dealloc*/
+  0, /*tp_print*/
+  0, /*tp_getattr*/
+  0, /*tp_setattr*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*tp_compare*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*tp_repr*/
+  &__pyx_tp_as_number___pyx_scope_struct_8_genexpr, /*tp_as_number*/
+  &__pyx_tp_as_sequence___pyx_scope_struct_8_genexpr, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping___pyx_scope_struct_8_genexpr, /*tp_as_mapping*/
+  0, /*tp_hash*/
+  0, /*tp_call*/
+  0, /*tp_str*/
+  0, /*tp_getattro*/
+  0, /*tp_setattro*/
+  &__pyx_tp_as_buffer___pyx_scope_struct_8_genexpr, /*tp_as_buffer*/
+  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+  0, /*tp_doc*/
+  __pyx_tp_traverse_3_sa___pyx_scope_struct_8_genexpr, /*tp_traverse*/
+  __pyx_tp_clear_3_sa___pyx_scope_struct_8_genexpr, /*tp_clear*/
+  0, /*tp_richcompare*/
+  0, /*tp_weaklistoffset*/
+  0, /*tp_iter*/
+  0, /*tp_iternext*/
+  __pyx_methods_3_sa___pyx_scope_struct_8_genexpr, /*tp_methods*/
+  0, /*tp_members*/
+  0, /*tp_getset*/
+  0, /*tp_base*/
+  0, /*tp_dict*/
+  0, /*tp_descr_get*/
+  0, /*tp_descr_set*/
+  0, /*tp_dictoffset*/
+  0, /*tp_init*/
+  0, /*tp_alloc*/
+  __pyx_tp_new_3_sa___pyx_scope_struct_8_genexpr, /*tp_new*/
+  0, /*tp_free*/
+  0, /*tp_is_gc*/
+  0, /*tp_bases*/
+  0, /*tp_mro*/
+  0, /*tp_cache*/
+  0, /*tp_subclasses*/
+  0, /*tp_weaklist*/
+  0, /*tp_del*/
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*tp_version_tag*/
+  #endif
+};
+
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_9_decode_sentence(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_9_decode_sentence *p;
+  PyObject *o = (*t->tp_alloc)(t, 0);
+  if (!o) return 0;
+  p = ((struct __pyx_obj_3_sa___pyx_scope_struct_9_decode_sentence *)o);
+  p->__pyx_v_lattice = 0;
+  return o;
+}
+
+static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_9_decode_sentence(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_9_decode_sentence *p = (struct __pyx_obj_3_sa___pyx_scope_struct_9_decode_sentence *)o;
+  Py_CLEAR(p->__pyx_v_lattice);
+  (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_3_sa___pyx_scope_struct_9_decode_sentence(PyObject *o, visitproc v, void *a) {
+  int e;
+  struct __pyx_obj_3_sa___pyx_scope_struct_9_decode_sentence *p = (struct __pyx_obj_3_sa___pyx_scope_struct_9_decode_sentence *)o;
+  if (p->__pyx_v_lattice) {
+    e = (*v)(p->__pyx_v_lattice, a); if (e) return e;
+  }
+  return 0;
+}
+
+static int __pyx_tp_clear_3_sa___pyx_scope_struct_9_decode_sentence(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_9_decode_sentence *p = (struct __pyx_obj_3_sa___pyx_scope_struct_9_decode_sentence *)o;
+  PyObject* tmp;
+  tmp = ((PyObject*)p->__pyx_v_lattice);
+  p->__pyx_v_lattice = Py_None; Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  return 0;
+}
+
+static PyMethodDef __pyx_methods_3_sa___pyx_scope_struct_9_decode_sentence[] = {
+  {0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_9_decode_sentence = {
+  0, /*nb_add*/
+  0, /*nb_subtract*/
+  0, /*nb_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_divide*/
+  #endif
+  0, /*nb_remainder*/
+  0, /*nb_divmod*/
+  0, /*nb_power*/
+  0, /*nb_negative*/
+  0, /*nb_positive*/
+  0, /*nb_absolute*/
+  0, /*nb_nonzero*/
+  0, /*nb_invert*/
+  0, /*nb_lshift*/
+  0, /*nb_rshift*/
+  0, /*nb_and*/
+  0, /*nb_xor*/
+  0, /*nb_or*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_coerce*/
+  #endif
+  0, /*nb_int*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_long*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*nb_float*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_oct*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_hex*/
+  #endif
+  0, /*nb_inplace_add*/
+  0, /*nb_inplace_subtract*/
+  0, /*nb_inplace_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_inplace_divide*/
+  #endif
+  0, /*nb_inplace_remainder*/
+  0, /*nb_inplace_power*/
+  0, /*nb_inplace_lshift*/
+  0, /*nb_inplace_rshift*/
+  0, /*nb_inplace_and*/
+  0, /*nb_inplace_xor*/
+  0, /*nb_inplace_or*/
+  0, /*nb_floor_divide*/
+  0, /*nb_true_divide*/
+  0, /*nb_inplace_floor_divide*/
+  0, /*nb_inplace_true_divide*/
+  #if PY_VERSION_HEX >= 0x02050000
+  0, /*nb_index*/
+  #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_9_decode_sentence = {
+  0, /*sq_length*/
+  0, /*sq_concat*/
+  0, /*sq_repeat*/
+  0, /*sq_item*/
+  0, /*sq_slice*/
+  0, /*sq_ass_item*/
+  0, /*sq_ass_slice*/
+  0, /*sq_contains*/
+  0, /*sq_inplace_concat*/
+  0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_9_decode_sentence = {
+  0, /*mp_length*/
+  0, /*mp_subscript*/
+  0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_9_decode_sentence = {
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getreadbuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getwritebuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getsegcount*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getcharbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_getbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_releasebuffer*/
+  #endif
+};
+
+static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_9_decode_sentence = {
+  PyVarObject_HEAD_INIT(0, 0)
+  __Pyx_NAMESTR("_sa.__pyx_scope_struct_9_decode_sentence"), /*tp_name*/
+  sizeof(struct __pyx_obj_3_sa___pyx_scope_struct_9_decode_sentence), /*tp_basicsize*/
+  0, /*tp_itemsize*/
+  __pyx_tp_dealloc_3_sa___pyx_scope_struct_9_decode_sentence, /*tp_dealloc*/
+  0, /*tp_print*/
+  0, /*tp_getattr*/
+  0, /*tp_setattr*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*tp_compare*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*tp_repr*/
+  &__pyx_tp_as_number___pyx_scope_struct_9_decode_sentence, /*tp_as_number*/
+  &__pyx_tp_as_sequence___pyx_scope_struct_9_decode_sentence, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping___pyx_scope_struct_9_decode_sentence, /*tp_as_mapping*/
+  0, /*tp_hash*/
+  0, /*tp_call*/
+  0, /*tp_str*/
+  0, /*tp_getattro*/
+  0, /*tp_setattro*/
+  &__pyx_tp_as_buffer___pyx_scope_struct_9_decode_sentence, /*tp_as_buffer*/
+  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+  0, /*tp_doc*/
+  __pyx_tp_traverse_3_sa___pyx_scope_struct_9_decode_sentence, /*tp_traverse*/
+  __pyx_tp_clear_3_sa___pyx_scope_struct_9_decode_sentence, /*tp_clear*/
+  0, /*tp_richcompare*/
+  0, /*tp_weaklistoffset*/
+  0, /*tp_iter*/
+  0, /*tp_iternext*/
+  __pyx_methods_3_sa___pyx_scope_struct_9_decode_sentence, /*tp_methods*/
+  0, /*tp_members*/
+  0, /*tp_getset*/
+  0, /*tp_base*/
+  0, /*tp_dict*/
+  0, /*tp_descr_get*/
+  0, /*tp_descr_set*/
+  0, /*tp_dictoffset*/
+  0, /*tp_init*/
+  0, /*tp_alloc*/
+  __pyx_tp_new_3_sa___pyx_scope_struct_9_decode_sentence, /*tp_new*/
+  0, /*tp_free*/
+  0, /*tp_is_gc*/
+  0, /*tp_bases*/
+  0, /*tp_mro*/
+  0, /*tp_cache*/
+  0, /*tp_subclasses*/
+  0, /*tp_weaklist*/
+  0, /*tp_del*/
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*tp_version_tag*/
+  #endif
+};
+
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_10_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_10_genexpr *p;
+  PyObject *o = (*t->tp_alloc)(t, 0);
+  if (!o) return 0;
+  p = ((struct __pyx_obj_3_sa___pyx_scope_struct_10_genexpr *)o);
+  p->__pyx_outer_scope = 0;
+  p->__pyx_v__ = 0;
+  p->__pyx_v_sym = 0;
+  p->__pyx_t_0 = 0;
+  return o;
+}
+
+static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_10_genexpr(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_10_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_10_genexpr *)o;
+  Py_CLEAR(p->__pyx_outer_scope);
+  Py_CLEAR(p->__pyx_v__);
+  Py_CLEAR(p->__pyx_v_sym);
+  Py_CLEAR(p->__pyx_t_0);
+  (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_3_sa___pyx_scope_struct_10_genexpr(PyObject *o, visitproc v, void *a) {
+  int e;
+  struct __pyx_obj_3_sa___pyx_scope_struct_10_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_10_genexpr *)o;
+  if (p->__pyx_outer_scope) {
+    e = (*v)(((PyObject*)p->__pyx_outer_scope), a); if (e) return e;
+  }
+  if (p->__pyx_v__) {
+    e = (*v)(p->__pyx_v__, a); if (e) return e;
+  }
+  if (p->__pyx_v_sym) {
+    e = (*v)(p->__pyx_v_sym, a); if (e) return e;
+  }
+  if (p->__pyx_t_0) {
+    e = (*v)(p->__pyx_t_0, a); if (e) return e;
+  }
+  return 0;
+}
+
+static int __pyx_tp_clear_3_sa___pyx_scope_struct_10_genexpr(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_10_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_10_genexpr *)o;
+  PyObject* tmp;
+  tmp = ((PyObject*)p->__pyx_outer_scope);
+  p->__pyx_outer_scope = ((struct __pyx_obj_3_sa___pyx_scope_struct_9_decode_sentence *)Py_None); Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->__pyx_v__);
+  p->__pyx_v__ = Py_None; Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->__pyx_v_sym);
+  p->__pyx_v_sym = Py_None; Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->__pyx_t_0);
+  p->__pyx_t_0 = Py_None; Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  return 0;
+}
+
+static PyMethodDef __pyx_methods_3_sa___pyx_scope_struct_10_genexpr[] = {
   {0, 0, 0, 0}
 };
 
-static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_2_compute_stats = {
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_10_genexpr = {
   0, /*nb_add*/
   0, /*nb_subtract*/
   0, /*nb_multiply*/
@@ -59637,7 +64225,7 @@ static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_2_compute_stats = {
   #endif
 };
 
-static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_2_compute_stats = {
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_10_genexpr = {
   0, /*sq_length*/
   0, /*sq_concat*/
   0, /*sq_repeat*/
@@ -59650,13 +64238,13 @@ static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_2_compute_stats
   0, /*sq_inplace_repeat*/
 };
 
-static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_2_compute_stats = {
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_10_genexpr = {
   0, /*mp_length*/
   0, /*mp_subscript*/
   0, /*mp_ass_subscript*/
 };
 
-static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_2_compute_stats = {
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_10_genexpr = {
   #if PY_MAJOR_VERSION < 3
   0, /*bf_getreadbuffer*/
   #endif
@@ -59677,12 +64265,12 @@ static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_2_compute_stats = {
   #endif
 };
 
-static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_2_compute_stats = {
+static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_10_genexpr = {
   PyVarObject_HEAD_INIT(0, 0)
-  __Pyx_NAMESTR("_sa.__pyx_scope_struct_2_compute_stats"), /*tp_name*/
-  sizeof(struct __pyx_obj_3_sa___pyx_scope_struct_2_compute_stats), /*tp_basicsize*/
+  __Pyx_NAMESTR("_sa.__pyx_scope_struct_10_genexpr"), /*tp_name*/
+  sizeof(struct __pyx_obj_3_sa___pyx_scope_struct_10_genexpr), /*tp_basicsize*/
   0, /*tp_itemsize*/
-  __pyx_tp_dealloc_3_sa___pyx_scope_struct_2_compute_stats, /*tp_dealloc*/
+  __pyx_tp_dealloc_3_sa___pyx_scope_struct_10_genexpr, /*tp_dealloc*/
   0, /*tp_print*/
   0, /*tp_getattr*/
   0, /*tp_setattr*/
@@ -59692,24 +64280,24 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_2_compute_stats = {
   0, /*reserved*/
   #endif
   0, /*tp_repr*/
-  &__pyx_tp_as_number___pyx_scope_struct_2_compute_stats, /*tp_as_number*/
-  &__pyx_tp_as_sequence___pyx_scope_struct_2_compute_stats, /*tp_as_sequence*/
-  &__pyx_tp_as_mapping___pyx_scope_struct_2_compute_stats, /*tp_as_mapping*/
+  &__pyx_tp_as_number___pyx_scope_struct_10_genexpr, /*tp_as_number*/
+  &__pyx_tp_as_sequence___pyx_scope_struct_10_genexpr, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping___pyx_scope_struct_10_genexpr, /*tp_as_mapping*/
   0, /*tp_hash*/
   0, /*tp_call*/
   0, /*tp_str*/
   0, /*tp_getattro*/
   0, /*tp_setattro*/
-  &__pyx_tp_as_buffer___pyx_scope_struct_2_compute_stats, /*tp_as_buffer*/
+  &__pyx_tp_as_buffer___pyx_scope_struct_10_genexpr, /*tp_as_buffer*/
   Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
   0, /*tp_doc*/
-  __pyx_tp_traverse_3_sa___pyx_scope_struct_2_compute_stats, /*tp_traverse*/
-  __pyx_tp_clear_3_sa___pyx_scope_struct_2_compute_stats, /*tp_clear*/
+  __pyx_tp_traverse_3_sa___pyx_scope_struct_10_genexpr, /*tp_traverse*/
+  __pyx_tp_clear_3_sa___pyx_scope_struct_10_genexpr, /*tp_clear*/
   0, /*tp_richcompare*/
   0, /*tp_weaklistoffset*/
   0, /*tp_iter*/
   0, /*tp_iternext*/
-  __pyx_methods_3_sa___pyx_scope_struct_2_compute_stats, /*tp_methods*/
+  __pyx_methods_3_sa___pyx_scope_struct_10_genexpr, /*tp_methods*/
   0, /*tp_members*/
   0, /*tp_getset*/
   0, /*tp_base*/
@@ -59719,7 +64307,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_2_compute_stats = {
   0, /*tp_dictoffset*/
   0, /*tp_init*/
   0, /*tp_alloc*/
-  __pyx_tp_new_3_sa___pyx_scope_struct_2_compute_stats, /*tp_new*/
+  __pyx_tp_new_3_sa___pyx_scope_struct_10_genexpr, /*tp_new*/
   0, /*tp_free*/
   0, /*tp_is_gc*/
   0, /*tp_bases*/
@@ -59733,32 +64321,32 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_2_compute_stats = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_3___iter__(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
-  struct __pyx_obj_3_sa___pyx_scope_struct_3___iter__ *p;
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_11___iter__(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_11___iter__ *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
-  p = ((struct __pyx_obj_3_sa___pyx_scope_struct_3___iter__ *)o);
+  p = ((struct __pyx_obj_3_sa___pyx_scope_struct_11___iter__ *)o);
   p->__pyx_v_self = 0;
   return o;
 }
 
-static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_3___iter__(PyObject *o) {
-  struct __pyx_obj_3_sa___pyx_scope_struct_3___iter__ *p = (struct __pyx_obj_3_sa___pyx_scope_struct_3___iter__ *)o;
-  Py_XDECREF(((PyObject *)p->__pyx_v_self));
+static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_11___iter__(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_11___iter__ *p = (struct __pyx_obj_3_sa___pyx_scope_struct_11___iter__ *)o;
+  Py_CLEAR(p->__pyx_v_self);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
-static int __pyx_tp_traverse_3_sa___pyx_scope_struct_3___iter__(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_3_sa___pyx_scope_struct_11___iter__(PyObject *o, visitproc v, void *a) {
   int e;
-  struct __pyx_obj_3_sa___pyx_scope_struct_3___iter__ *p = (struct __pyx_obj_3_sa___pyx_scope_struct_3___iter__ *)o;
+  struct __pyx_obj_3_sa___pyx_scope_struct_11___iter__ *p = (struct __pyx_obj_3_sa___pyx_scope_struct_11___iter__ *)o;
   if (p->__pyx_v_self) {
     e = (*v)(((PyObject*)p->__pyx_v_self), a); if (e) return e;
   }
   return 0;
 }
 
-static int __pyx_tp_clear_3_sa___pyx_scope_struct_3___iter__(PyObject *o) {
-  struct __pyx_obj_3_sa___pyx_scope_struct_3___iter__ *p = (struct __pyx_obj_3_sa___pyx_scope_struct_3___iter__ *)o;
+static int __pyx_tp_clear_3_sa___pyx_scope_struct_11___iter__(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_11___iter__ *p = (struct __pyx_obj_3_sa___pyx_scope_struct_11___iter__ *)o;
   PyObject* tmp;
   tmp = ((PyObject*)p->__pyx_v_self);
   p->__pyx_v_self = ((struct __pyx_obj_3_sa_Phrase *)Py_None); Py_INCREF(Py_None);
@@ -59766,11 +64354,202 @@ static int __pyx_tp_clear_3_sa___pyx_scope_struct_3___iter__(PyObject *o) {
   return 0;
 }
 
-static PyMethodDef __pyx_methods_3_sa___pyx_scope_struct_3___iter__[] = {
+static PyMethodDef __pyx_methods_3_sa___pyx_scope_struct_11___iter__[] = {
+  {0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_11___iter__ = {
+  0, /*nb_add*/
+  0, /*nb_subtract*/
+  0, /*nb_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_divide*/
+  #endif
+  0, /*nb_remainder*/
+  0, /*nb_divmod*/
+  0, /*nb_power*/
+  0, /*nb_negative*/
+  0, /*nb_positive*/
+  0, /*nb_absolute*/
+  0, /*nb_nonzero*/
+  0, /*nb_invert*/
+  0, /*nb_lshift*/
+  0, /*nb_rshift*/
+  0, /*nb_and*/
+  0, /*nb_xor*/
+  0, /*nb_or*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_coerce*/
+  #endif
+  0, /*nb_int*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_long*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*nb_float*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_oct*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_hex*/
+  #endif
+  0, /*nb_inplace_add*/
+  0, /*nb_inplace_subtract*/
+  0, /*nb_inplace_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_inplace_divide*/
+  #endif
+  0, /*nb_inplace_remainder*/
+  0, /*nb_inplace_power*/
+  0, /*nb_inplace_lshift*/
+  0, /*nb_inplace_rshift*/
+  0, /*nb_inplace_and*/
+  0, /*nb_inplace_xor*/
+  0, /*nb_inplace_or*/
+  0, /*nb_floor_divide*/
+  0, /*nb_true_divide*/
+  0, /*nb_inplace_floor_divide*/
+  0, /*nb_inplace_true_divide*/
+  #if PY_VERSION_HEX >= 0x02050000
+  0, /*nb_index*/
+  #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_11___iter__ = {
+  0, /*sq_length*/
+  0, /*sq_concat*/
+  0, /*sq_repeat*/
+  0, /*sq_item*/
+  0, /*sq_slice*/
+  0, /*sq_ass_item*/
+  0, /*sq_ass_slice*/
+  0, /*sq_contains*/
+  0, /*sq_inplace_concat*/
+  0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_11___iter__ = {
+  0, /*mp_length*/
+  0, /*mp_subscript*/
+  0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_11___iter__ = {
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getreadbuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getwritebuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getsegcount*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getcharbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_getbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_releasebuffer*/
+  #endif
+};
+
+static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_11___iter__ = {
+  PyVarObject_HEAD_INIT(0, 0)
+  __Pyx_NAMESTR("_sa.__pyx_scope_struct_11___iter__"), /*tp_name*/
+  sizeof(struct __pyx_obj_3_sa___pyx_scope_struct_11___iter__), /*tp_basicsize*/
+  0, /*tp_itemsize*/
+  __pyx_tp_dealloc_3_sa___pyx_scope_struct_11___iter__, /*tp_dealloc*/
+  0, /*tp_print*/
+  0, /*tp_getattr*/
+  0, /*tp_setattr*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*tp_compare*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*tp_repr*/
+  &__pyx_tp_as_number___pyx_scope_struct_11___iter__, /*tp_as_number*/
+  &__pyx_tp_as_sequence___pyx_scope_struct_11___iter__, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping___pyx_scope_struct_11___iter__, /*tp_as_mapping*/
+  0, /*tp_hash*/
+  0, /*tp_call*/
+  0, /*tp_str*/
+  0, /*tp_getattro*/
+  0, /*tp_setattro*/
+  &__pyx_tp_as_buffer___pyx_scope_struct_11___iter__, /*tp_as_buffer*/
+  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+  0, /*tp_doc*/
+  __pyx_tp_traverse_3_sa___pyx_scope_struct_11___iter__, /*tp_traverse*/
+  __pyx_tp_clear_3_sa___pyx_scope_struct_11___iter__, /*tp_clear*/
+  0, /*tp_richcompare*/
+  0, /*tp_weaklistoffset*/
+  0, /*tp_iter*/
+  0, /*tp_iternext*/
+  __pyx_methods_3_sa___pyx_scope_struct_11___iter__, /*tp_methods*/
+  0, /*tp_members*/
+  0, /*tp_getset*/
+  0, /*tp_base*/
+  0, /*tp_dict*/
+  0, /*tp_descr_get*/
+  0, /*tp_descr_set*/
+  0, /*tp_dictoffset*/
+  0, /*tp_init*/
+  0, /*tp_alloc*/
+  __pyx_tp_new_3_sa___pyx_scope_struct_11___iter__, /*tp_new*/
+  0, /*tp_free*/
+  0, /*tp_is_gc*/
+  0, /*tp_bases*/
+  0, /*tp_mro*/
+  0, /*tp_cache*/
+  0, /*tp_subclasses*/
+  0, /*tp_weaklist*/
+  0, /*tp_del*/
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*tp_version_tag*/
+  #endif
+};
+
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_12___str__(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_12___str__ *p;
+  PyObject *o = (*t->tp_alloc)(t, 0);
+  if (!o) return 0;
+  p = ((struct __pyx_obj_3_sa___pyx_scope_struct_12___str__ *)o);
+  p->__pyx_v_self = 0;
+  return o;
+}
+
+static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_12___str__(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_12___str__ *p = (struct __pyx_obj_3_sa___pyx_scope_struct_12___str__ *)o;
+  Py_CLEAR(p->__pyx_v_self);
+  (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_3_sa___pyx_scope_struct_12___str__(PyObject *o, visitproc v, void *a) {
+  int e;
+  struct __pyx_obj_3_sa___pyx_scope_struct_12___str__ *p = (struct __pyx_obj_3_sa___pyx_scope_struct_12___str__ *)o;
+  if (p->__pyx_v_self) {
+    e = (*v)(((PyObject*)p->__pyx_v_self), a); if (e) return e;
+  }
+  return 0;
+}
+
+static int __pyx_tp_clear_3_sa___pyx_scope_struct_12___str__(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_12___str__ *p = (struct __pyx_obj_3_sa___pyx_scope_struct_12___str__ *)o;
+  PyObject* tmp;
+  tmp = ((PyObject*)p->__pyx_v_self);
+  p->__pyx_v_self = ((struct __pyx_obj_3_sa_Rule *)Py_None); Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  return 0;
+}
+
+static PyMethodDef __pyx_methods_3_sa___pyx_scope_struct_12___str__[] = {
   {0, 0, 0, 0}
 };
 
-static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_3___iter__ = {
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_12___str__ = {
   0, /*nb_add*/
   0, /*nb_subtract*/
   0, /*nb_multiply*/
@@ -59828,7 +64607,7 @@ static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_3___iter__ = {
   #endif
 };
 
-static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_3___iter__ = {
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_12___str__ = {
   0, /*sq_length*/
   0, /*sq_concat*/
   0, /*sq_repeat*/
@@ -59841,13 +64620,13 @@ static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_3___iter__ = {
   0, /*sq_inplace_repeat*/
 };
 
-static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_3___iter__ = {
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_12___str__ = {
   0, /*mp_length*/
   0, /*mp_subscript*/
   0, /*mp_ass_subscript*/
 };
 
-static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_3___iter__ = {
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_12___str__ = {
   #if PY_MAJOR_VERSION < 3
   0, /*bf_getreadbuffer*/
   #endif
@@ -59868,12 +64647,12 @@ static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_3___iter__ = {
   #endif
 };
 
-static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_3___iter__ = {
+static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_12___str__ = {
   PyVarObject_HEAD_INIT(0, 0)
-  __Pyx_NAMESTR("_sa.__pyx_scope_struct_3___iter__"), /*tp_name*/
-  sizeof(struct __pyx_obj_3_sa___pyx_scope_struct_3___iter__), /*tp_basicsize*/
+  __Pyx_NAMESTR("_sa.__pyx_scope_struct_12___str__"), /*tp_name*/
+  sizeof(struct __pyx_obj_3_sa___pyx_scope_struct_12___str__), /*tp_basicsize*/
   0, /*tp_itemsize*/
-  __pyx_tp_dealloc_3_sa___pyx_scope_struct_3___iter__, /*tp_dealloc*/
+  __pyx_tp_dealloc_3_sa___pyx_scope_struct_12___str__, /*tp_dealloc*/
   0, /*tp_print*/
   0, /*tp_getattr*/
   0, /*tp_setattr*/
@@ -59883,24 +64662,24 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_3___iter__ = {
   0, /*reserved*/
   #endif
   0, /*tp_repr*/
-  &__pyx_tp_as_number___pyx_scope_struct_3___iter__, /*tp_as_number*/
-  &__pyx_tp_as_sequence___pyx_scope_struct_3___iter__, /*tp_as_sequence*/
-  &__pyx_tp_as_mapping___pyx_scope_struct_3___iter__, /*tp_as_mapping*/
+  &__pyx_tp_as_number___pyx_scope_struct_12___str__, /*tp_as_number*/
+  &__pyx_tp_as_sequence___pyx_scope_struct_12___str__, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping___pyx_scope_struct_12___str__, /*tp_as_mapping*/
   0, /*tp_hash*/
   0, /*tp_call*/
   0, /*tp_str*/
   0, /*tp_getattro*/
   0, /*tp_setattro*/
-  &__pyx_tp_as_buffer___pyx_scope_struct_3___iter__, /*tp_as_buffer*/
+  &__pyx_tp_as_buffer___pyx_scope_struct_12___str__, /*tp_as_buffer*/
   Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
   0, /*tp_doc*/
-  __pyx_tp_traverse_3_sa___pyx_scope_struct_3___iter__, /*tp_traverse*/
-  __pyx_tp_clear_3_sa___pyx_scope_struct_3___iter__, /*tp_clear*/
+  __pyx_tp_traverse_3_sa___pyx_scope_struct_12___str__, /*tp_traverse*/
+  __pyx_tp_clear_3_sa___pyx_scope_struct_12___str__, /*tp_clear*/
   0, /*tp_richcompare*/
   0, /*tp_weaklistoffset*/
   0, /*tp_iter*/
   0, /*tp_iternext*/
-  __pyx_methods_3_sa___pyx_scope_struct_3___iter__, /*tp_methods*/
+  __pyx_methods_3_sa___pyx_scope_struct_12___str__, /*tp_methods*/
   0, /*tp_members*/
   0, /*tp_getset*/
   0, /*tp_base*/
@@ -59910,7 +64689,7 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_3___iter__ = {
   0, /*tp_dictoffset*/
   0, /*tp_init*/
   0, /*tp_alloc*/
-  __pyx_tp_new_3_sa___pyx_scope_struct_3___iter__, /*tp_new*/
+  __pyx_tp_new_3_sa___pyx_scope_struct_12___str__, /*tp_new*/
   0, /*tp_free*/
   0, /*tp_is_gc*/
   0, /*tp_bases*/
@@ -59924,17 +64703,430 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_3___iter__ = {
   #endif
 };
 
-static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_4_input(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
-  struct __pyx_obj_3_sa___pyx_scope_struct_4_input *p;
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_13_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_13_genexpr *p;
   PyObject *o = (*t->tp_alloc)(t, 0);
   if (!o) return 0;
-  p = ((struct __pyx_obj_3_sa___pyx_scope_struct_4_input *)o);
+  p = ((struct __pyx_obj_3_sa___pyx_scope_struct_13_genexpr *)o);
+  p->__pyx_outer_scope = 0;
+  p->__pyx_v_a = 0;
+  p->__pyx_t_0 = 0;
+  return o;
+}
+
+static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_13_genexpr(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_13_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_13_genexpr *)o;
+  Py_CLEAR(p->__pyx_outer_scope);
+  Py_CLEAR(p->__pyx_v_a);
+  Py_CLEAR(p->__pyx_t_0);
+  (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_3_sa___pyx_scope_struct_13_genexpr(PyObject *o, visitproc v, void *a) {
+  int e;
+  struct __pyx_obj_3_sa___pyx_scope_struct_13_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_13_genexpr *)o;
+  if (p->__pyx_outer_scope) {
+    e = (*v)(((PyObject*)p->__pyx_outer_scope), a); if (e) return e;
+  }
+  if (p->__pyx_v_a) {
+    e = (*v)(p->__pyx_v_a, a); if (e) return e;
+  }
+  if (p->__pyx_t_0) {
+    e = (*v)(p->__pyx_t_0, a); if (e) return e;
+  }
+  return 0;
+}
+
+static int __pyx_tp_clear_3_sa___pyx_scope_struct_13_genexpr(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_13_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_13_genexpr *)o;
+  PyObject* tmp;
+  tmp = ((PyObject*)p->__pyx_outer_scope);
+  p->__pyx_outer_scope = ((struct __pyx_obj_3_sa___pyx_scope_struct_12___str__ *)Py_None); Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->__pyx_v_a);
+  p->__pyx_v_a = Py_None; Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->__pyx_t_0);
+  p->__pyx_t_0 = Py_None; Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  return 0;
+}
+
+static PyMethodDef __pyx_methods_3_sa___pyx_scope_struct_13_genexpr[] = {
+  {0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_13_genexpr = {
+  0, /*nb_add*/
+  0, /*nb_subtract*/
+  0, /*nb_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_divide*/
+  #endif
+  0, /*nb_remainder*/
+  0, /*nb_divmod*/
+  0, /*nb_power*/
+  0, /*nb_negative*/
+  0, /*nb_positive*/
+  0, /*nb_absolute*/
+  0, /*nb_nonzero*/
+  0, /*nb_invert*/
+  0, /*nb_lshift*/
+  0, /*nb_rshift*/
+  0, /*nb_and*/
+  0, /*nb_xor*/
+  0, /*nb_or*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_coerce*/
+  #endif
+  0, /*nb_int*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_long*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*nb_float*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_oct*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_hex*/
+  #endif
+  0, /*nb_inplace_add*/
+  0, /*nb_inplace_subtract*/
+  0, /*nb_inplace_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_inplace_divide*/
+  #endif
+  0, /*nb_inplace_remainder*/
+  0, /*nb_inplace_power*/
+  0, /*nb_inplace_lshift*/
+  0, /*nb_inplace_rshift*/
+  0, /*nb_inplace_and*/
+  0, /*nb_inplace_xor*/
+  0, /*nb_inplace_or*/
+  0, /*nb_floor_divide*/
+  0, /*nb_true_divide*/
+  0, /*nb_inplace_floor_divide*/
+  0, /*nb_inplace_true_divide*/
+  #if PY_VERSION_HEX >= 0x02050000
+  0, /*nb_index*/
+  #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_13_genexpr = {
+  0, /*sq_length*/
+  0, /*sq_concat*/
+  0, /*sq_repeat*/
+  0, /*sq_item*/
+  0, /*sq_slice*/
+  0, /*sq_ass_item*/
+  0, /*sq_ass_slice*/
+  0, /*sq_contains*/
+  0, /*sq_inplace_concat*/
+  0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_13_genexpr = {
+  0, /*mp_length*/
+  0, /*mp_subscript*/
+  0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_13_genexpr = {
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getreadbuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getwritebuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getsegcount*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getcharbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_getbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_releasebuffer*/
+  #endif
+};
+
+static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_13_genexpr = {
+  PyVarObject_HEAD_INIT(0, 0)
+  __Pyx_NAMESTR("_sa.__pyx_scope_struct_13_genexpr"), /*tp_name*/
+  sizeof(struct __pyx_obj_3_sa___pyx_scope_struct_13_genexpr), /*tp_basicsize*/
+  0, /*tp_itemsize*/
+  __pyx_tp_dealloc_3_sa___pyx_scope_struct_13_genexpr, /*tp_dealloc*/
+  0, /*tp_print*/
+  0, /*tp_getattr*/
+  0, /*tp_setattr*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*tp_compare*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*tp_repr*/
+  &__pyx_tp_as_number___pyx_scope_struct_13_genexpr, /*tp_as_number*/
+  &__pyx_tp_as_sequence___pyx_scope_struct_13_genexpr, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping___pyx_scope_struct_13_genexpr, /*tp_as_mapping*/
+  0, /*tp_hash*/
+  0, /*tp_call*/
+  0, /*tp_str*/
+  0, /*tp_getattro*/
+  0, /*tp_setattro*/
+  &__pyx_tp_as_buffer___pyx_scope_struct_13_genexpr, /*tp_as_buffer*/
+  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+  0, /*tp_doc*/
+  __pyx_tp_traverse_3_sa___pyx_scope_struct_13_genexpr, /*tp_traverse*/
+  __pyx_tp_clear_3_sa___pyx_scope_struct_13_genexpr, /*tp_clear*/
+  0, /*tp_richcompare*/
+  0, /*tp_weaklistoffset*/
+  0, /*tp_iter*/
+  0, /*tp_iternext*/
+  __pyx_methods_3_sa___pyx_scope_struct_13_genexpr, /*tp_methods*/
+  0, /*tp_members*/
+  0, /*tp_getset*/
+  0, /*tp_base*/
+  0, /*tp_dict*/
+  0, /*tp_descr_get*/
+  0, /*tp_descr_set*/
+  0, /*tp_dictoffset*/
+  0, /*tp_init*/
+  0, /*tp_alloc*/
+  __pyx_tp_new_3_sa___pyx_scope_struct_13_genexpr, /*tp_new*/
+  0, /*tp_free*/
+  0, /*tp_is_gc*/
+  0, /*tp_bases*/
+  0, /*tp_mro*/
+  0, /*tp_cache*/
+  0, /*tp_subclasses*/
+  0, /*tp_weaklist*/
+  0, /*tp_del*/
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*tp_version_tag*/
+  #endif
+};
+
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_14_alignments(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_14_alignments *p;
+  PyObject *o = (*t->tp_alloc)(t, 0);
+  if (!o) return 0;
+  p = ((struct __pyx_obj_3_sa___pyx_scope_struct_14_alignments *)o);
+  p->__pyx_v_point = 0;
+  p->__pyx_v_self = 0;
+  p->__pyx_t_0 = 0;
+  return o;
+}
+
+static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_14_alignments(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_14_alignments *p = (struct __pyx_obj_3_sa___pyx_scope_struct_14_alignments *)o;
+  Py_CLEAR(p->__pyx_v_point);
+  Py_CLEAR(p->__pyx_v_self);
+  Py_CLEAR(p->__pyx_t_0);
+  (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_3_sa___pyx_scope_struct_14_alignments(PyObject *o, visitproc v, void *a) {
+  int e;
+  struct __pyx_obj_3_sa___pyx_scope_struct_14_alignments *p = (struct __pyx_obj_3_sa___pyx_scope_struct_14_alignments *)o;
+  if (p->__pyx_v_point) {
+    e = (*v)(p->__pyx_v_point, a); if (e) return e;
+  }
+  if (p->__pyx_v_self) {
+    e = (*v)(((PyObject*)p->__pyx_v_self), a); if (e) return e;
+  }
+  if (p->__pyx_t_0) {
+    e = (*v)(p->__pyx_t_0, a); if (e) return e;
+  }
+  return 0;
+}
+
+static int __pyx_tp_clear_3_sa___pyx_scope_struct_14_alignments(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_14_alignments *p = (struct __pyx_obj_3_sa___pyx_scope_struct_14_alignments *)o;
+  PyObject* tmp;
+  tmp = ((PyObject*)p->__pyx_v_point);
+  p->__pyx_v_point = Py_None; Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->__pyx_v_self);
+  p->__pyx_v_self = ((struct __pyx_obj_3_sa_Rule *)Py_None); Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->__pyx_t_0);
+  p->__pyx_t_0 = Py_None; Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  return 0;
+}
+
+static PyMethodDef __pyx_methods_3_sa___pyx_scope_struct_14_alignments[] = {
+  {0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_14_alignments = {
+  0, /*nb_add*/
+  0, /*nb_subtract*/
+  0, /*nb_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_divide*/
+  #endif
+  0, /*nb_remainder*/
+  0, /*nb_divmod*/
+  0, /*nb_power*/
+  0, /*nb_negative*/
+  0, /*nb_positive*/
+  0, /*nb_absolute*/
+  0, /*nb_nonzero*/
+  0, /*nb_invert*/
+  0, /*nb_lshift*/
+  0, /*nb_rshift*/
+  0, /*nb_and*/
+  0, /*nb_xor*/
+  0, /*nb_or*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_coerce*/
+  #endif
+  0, /*nb_int*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_long*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*nb_float*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_oct*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_hex*/
+  #endif
+  0, /*nb_inplace_add*/
+  0, /*nb_inplace_subtract*/
+  0, /*nb_inplace_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_inplace_divide*/
+  #endif
+  0, /*nb_inplace_remainder*/
+  0, /*nb_inplace_power*/
+  0, /*nb_inplace_lshift*/
+  0, /*nb_inplace_rshift*/
+  0, /*nb_inplace_and*/
+  0, /*nb_inplace_xor*/
+  0, /*nb_inplace_or*/
+  0, /*nb_floor_divide*/
+  0, /*nb_true_divide*/
+  0, /*nb_inplace_floor_divide*/
+  0, /*nb_inplace_true_divide*/
+  #if PY_VERSION_HEX >= 0x02050000
+  0, /*nb_index*/
+  #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_14_alignments = {
+  0, /*sq_length*/
+  0, /*sq_concat*/
+  0, /*sq_repeat*/
+  0, /*sq_item*/
+  0, /*sq_slice*/
+  0, /*sq_ass_item*/
+  0, /*sq_ass_slice*/
+  0, /*sq_contains*/
+  0, /*sq_inplace_concat*/
+  0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_14_alignments = {
+  0, /*mp_length*/
+  0, /*mp_subscript*/
+  0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_14_alignments = {
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getreadbuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getwritebuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getsegcount*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getcharbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_getbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_releasebuffer*/
+  #endif
+};
+
+static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_14_alignments = {
+  PyVarObject_HEAD_INIT(0, 0)
+  __Pyx_NAMESTR("_sa.__pyx_scope_struct_14_alignments"), /*tp_name*/
+  sizeof(struct __pyx_obj_3_sa___pyx_scope_struct_14_alignments), /*tp_basicsize*/
+  0, /*tp_itemsize*/
+  __pyx_tp_dealloc_3_sa___pyx_scope_struct_14_alignments, /*tp_dealloc*/
+  0, /*tp_print*/
+  0, /*tp_getattr*/
+  0, /*tp_setattr*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*tp_compare*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*tp_repr*/
+  &__pyx_tp_as_number___pyx_scope_struct_14_alignments, /*tp_as_number*/
+  &__pyx_tp_as_sequence___pyx_scope_struct_14_alignments, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping___pyx_scope_struct_14_alignments, /*tp_as_mapping*/
+  0, /*tp_hash*/
+  0, /*tp_call*/
+  0, /*tp_str*/
+  0, /*tp_getattro*/
+  0, /*tp_setattro*/
+  &__pyx_tp_as_buffer___pyx_scope_struct_14_alignments, /*tp_as_buffer*/
+  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+  0, /*tp_doc*/
+  __pyx_tp_traverse_3_sa___pyx_scope_struct_14_alignments, /*tp_traverse*/
+  __pyx_tp_clear_3_sa___pyx_scope_struct_14_alignments, /*tp_clear*/
+  0, /*tp_richcompare*/
+  0, /*tp_weaklistoffset*/
+  0, /*tp_iter*/
+  0, /*tp_iternext*/
+  __pyx_methods_3_sa___pyx_scope_struct_14_alignments, /*tp_methods*/
+  0, /*tp_members*/
+  0, /*tp_getset*/
+  0, /*tp_base*/
+  0, /*tp_dict*/
+  0, /*tp_descr_get*/
+  0, /*tp_descr_set*/
+  0, /*tp_dictoffset*/
+  0, /*tp_init*/
+  0, /*tp_alloc*/
+  __pyx_tp_new_3_sa___pyx_scope_struct_14_alignments, /*tp_new*/
+  0, /*tp_free*/
+  0, /*tp_is_gc*/
+  0, /*tp_bases*/
+  0, /*tp_mro*/
+  0, /*tp_cache*/
+  0, /*tp_subclasses*/
+  0, /*tp_weaklist*/
+  0, /*tp_del*/
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*tp_version_tag*/
+  #endif
+};
+
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_15_input(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_15_input *p;
+  PyObject *o = (*t->tp_alloc)(t, 0);
+  if (!o) return 0;
+  p = ((struct __pyx_obj_3_sa___pyx_scope_struct_15_input *)o);
   p->__pyx_v_alignment = 0;
   p->__pyx_v_als = 0;
   p->__pyx_v_alslist = 0;
   p->__pyx_v_chunklen = 0;
   p->__pyx_v_count = 0;
-  p->__pyx_v_currcount = 0;
   p->__pyx_v_e = 0;
   p->__pyx_v_elist = 0;
   p->__pyx_v_extract = 0;
@@ -59942,18 +65134,19 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_4_input(PyTypeObject *t, C
   p->__pyx_v_extract_stop = 0;
   p->__pyx_v_extracts = 0;
   p->__pyx_v_f = 0;
-  p->__pyx_v_f_margin = 0;
-  p->__pyx_v_fals = 0;
   p->__pyx_v_fcount = 0;
   p->__pyx_v_fphrases = 0;
   p->__pyx_v_frontier = 0;
   p->__pyx_v_frontier_nodes = 0;
   p->__pyx_v_fwords = 0;
   p->__pyx_v_hiero_phrase = 0;
+  p->__pyx_v_input_match = 0;
   p->__pyx_v_is_shadow_path = 0;
   p->__pyx_v_key = 0;
-  p->__pyx_v_model = 0;
-  p->__pyx_v_models = 0;
+  p->__pyx_v_loc = 0;
+  p->__pyx_v_locs = 0;
+  p->__pyx_v_max_locs = 0;
+  p->__pyx_v_meta = 0;
   p->__pyx_v_new_frontier = 0;
   p->__pyx_v_new_node = 0;
   p->__pyx_v_next_states = 0;
@@ -59982,64 +65175,64 @@ static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_4_input(PyTypeObject *t, C
   return o;
 }
 
-static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_4_input(PyObject *o) {
-  struct __pyx_obj_3_sa___pyx_scope_struct_4_input *p = (struct __pyx_obj_3_sa___pyx_scope_struct_4_input *)o;
-  Py_XDECREF(p->__pyx_v_alignment);
-  Py_XDECREF(p->__pyx_v_als);
-  Py_XDECREF(p->__pyx_v_alslist);
-  Py_XDECREF(((PyObject *)p->__pyx_v_chunklen));
-  Py_XDECREF(p->__pyx_v_count);
-  Py_XDECREF(p->__pyx_v_currcount);
-  Py_XDECREF(p->__pyx_v_e);
-  Py_XDECREF(p->__pyx_v_elist);
-  Py_XDECREF(p->__pyx_v_extract);
-  Py_XDECREF(p->__pyx_v_extract_start);
-  Py_XDECREF(p->__pyx_v_extract_stop);
-  Py_XDECREF(((PyObject *)p->__pyx_v_extracts));
-  Py_XDECREF(p->__pyx_v_f);
-  Py_XDECREF(p->__pyx_v_f_margin);
-  Py_XDECREF(((PyObject *)p->__pyx_v_fals));
-  Py_XDECREF(((PyObject *)p->__pyx_v_fcount));
-  Py_XDECREF(((PyObject *)p->__pyx_v_fphrases));
-  Py_XDECREF(((PyObject *)p->__pyx_v_frontier));
-  Py_XDECREF(p->__pyx_v_frontier_nodes);
-  Py_XDECREF(p->__pyx_v_fwords);
-  Py_XDECREF(((PyObject *)p->__pyx_v_hiero_phrase));
-  Py_XDECREF(p->__pyx_v_is_shadow_path);
-  Py_XDECREF(((PyObject *)p->__pyx_v_key));
-  Py_XDECREF(p->__pyx_v_model);
-  Py_XDECREF(p->__pyx_v_models);
-  Py_XDECREF(((PyObject *)p->__pyx_v_new_frontier));
-  Py_XDECREF(p->__pyx_v_new_node);
-  Py_XDECREF(((PyObject *)p->__pyx_v_next_states));
-  Py_XDECREF(p->__pyx_v_node);
-  Py_XDECREF(((PyObject *)p->__pyx_v_nodes_isteps_away_buffer));
-  Py_XDECREF(p->__pyx_v_pathlen);
-  Py_XDECREF(p->__pyx_v_phrase);
-  Py_XDECREF(((PyObject *)p->__pyx_v_phrase_location));
-  Py_XDECREF(p->__pyx_v_prefix);
-  Py_XDECREF(((PyObject *)p->__pyx_v_reachable_buffer));
-  Py_XDECREF(p->__pyx_v_sa_range);
-  Py_XDECREF(((PyObject *)p->__pyx_v_sample));
-  Py_XDECREF(((PyObject *)p->__pyx_v_scores));
-  Py_XDECREF(((PyObject *)p->__pyx_v_self));
-  Py_XDECREF(p->__pyx_v_spanlen);
-  Py_XDECREF(p->__pyx_v_stop_time);
-  Py_XDECREF(p->__pyx_v_suffix_link);
-  Py_XDECREF(p->__pyx_v_suffix_link_xcat_index);
-  Py_XDECREF(p->__pyx_v_word_id);
-  Py_XDECREF(p->__pyx_v_xcat_index);
-  Py_XDECREF(p->__pyx_v_xnode);
-  Py_XDECREF(p->__pyx_v_xroot);
-  Py_XDECREF(p->__pyx_t_1);
-  Py_XDECREF(p->__pyx_t_4);
-  Py_XDECREF(p->__pyx_t_5);
+static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_15_input(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_15_input *p = (struct __pyx_obj_3_sa___pyx_scope_struct_15_input *)o;
+  Py_CLEAR(p->__pyx_v_alignment);
+  Py_CLEAR(p->__pyx_v_als);
+  Py_CLEAR(p->__pyx_v_alslist);
+  Py_CLEAR(p->__pyx_v_chunklen);
+  Py_CLEAR(p->__pyx_v_count);
+  Py_CLEAR(p->__pyx_v_e);
+  Py_CLEAR(p->__pyx_v_elist);
+  Py_CLEAR(p->__pyx_v_extract);
+  Py_CLEAR(p->__pyx_v_extract_start);
+  Py_CLEAR(p->__pyx_v_extract_stop);
+  Py_CLEAR(p->__pyx_v_extracts);
+  Py_CLEAR(p->__pyx_v_f);
+  Py_CLEAR(p->__pyx_v_fcount);
+  Py_CLEAR(p->__pyx_v_fphrases);
+  Py_CLEAR(p->__pyx_v_frontier);
+  Py_CLEAR(p->__pyx_v_frontier_nodes);
+  Py_CLEAR(p->__pyx_v_fwords);
+  Py_CLEAR(p->__pyx_v_hiero_phrase);
+  Py_CLEAR(p->__pyx_v_input_match);
+  Py_CLEAR(p->__pyx_v_is_shadow_path);
+  Py_CLEAR(p->__pyx_v_key);
+  Py_CLEAR(p->__pyx_v_loc);
+  Py_CLEAR(p->__pyx_v_locs);
+  Py_CLEAR(p->__pyx_v_max_locs);
+  Py_CLEAR(p->__pyx_v_meta);
+  Py_CLEAR(p->__pyx_v_new_frontier);
+  Py_CLEAR(p->__pyx_v_new_node);
+  Py_CLEAR(p->__pyx_v_next_states);
+  Py_CLEAR(p->__pyx_v_node);
+  Py_CLEAR(p->__pyx_v_nodes_isteps_away_buffer);
+  Py_CLEAR(p->__pyx_v_pathlen);
+  Py_CLEAR(p->__pyx_v_phrase);
+  Py_CLEAR(p->__pyx_v_phrase_location);
+  Py_CLEAR(p->__pyx_v_prefix);
+  Py_CLEAR(p->__pyx_v_reachable_buffer);
+  Py_CLEAR(p->__pyx_v_sa_range);
+  Py_CLEAR(p->__pyx_v_sample);
+  Py_CLEAR(p->__pyx_v_scores);
+  Py_CLEAR(p->__pyx_v_self);
+  Py_CLEAR(p->__pyx_v_spanlen);
+  Py_CLEAR(p->__pyx_v_stop_time);
+  Py_CLEAR(p->__pyx_v_suffix_link);
+  Py_CLEAR(p->__pyx_v_suffix_link_xcat_index);
+  Py_CLEAR(p->__pyx_v_word_id);
+  Py_CLEAR(p->__pyx_v_xcat_index);
+  Py_CLEAR(p->__pyx_v_xnode);
+  Py_CLEAR(p->__pyx_v_xroot);
+  Py_CLEAR(p->__pyx_t_1);
+  Py_CLEAR(p->__pyx_t_4);
+  Py_CLEAR(p->__pyx_t_5);
   (*Py_TYPE(o)->tp_free)(o);
 }
 
-static int __pyx_tp_traverse_3_sa___pyx_scope_struct_4_input(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_3_sa___pyx_scope_struct_15_input(PyObject *o, visitproc v, void *a) {
   int e;
-  struct __pyx_obj_3_sa___pyx_scope_struct_4_input *p = (struct __pyx_obj_3_sa___pyx_scope_struct_4_input *)o;
+  struct __pyx_obj_3_sa___pyx_scope_struct_15_input *p = (struct __pyx_obj_3_sa___pyx_scope_struct_15_input *)o;
   if (p->__pyx_v_alignment) {
     e = (*v)(p->__pyx_v_alignment, a); if (e) return e;
   }
@@ -60055,9 +65248,6 @@ static int __pyx_tp_traverse_3_sa___pyx_scope_struct_4_input(PyObject *o, visitp
   if (p->__pyx_v_count) {
     e = (*v)(p->__pyx_v_count, a); if (e) return e;
   }
-  if (p->__pyx_v_currcount) {
-    e = (*v)(p->__pyx_v_currcount, a); if (e) return e;
-  }
   if (p->__pyx_v_e) {
     e = (*v)(p->__pyx_v_e, a); if (e) return e;
   }
@@ -60079,12 +65269,6 @@ static int __pyx_tp_traverse_3_sa___pyx_scope_struct_4_input(PyObject *o, visitp
   if (p->__pyx_v_f) {
     e = (*v)(p->__pyx_v_f, a); if (e) return e;
   }
-  if (p->__pyx_v_f_margin) {
-    e = (*v)(p->__pyx_v_f_margin, a); if (e) return e;
-  }
-  if (p->__pyx_v_fals) {
-    e = (*v)(p->__pyx_v_fals, a); if (e) return e;
-  }
   if (p->__pyx_v_fcount) {
     e = (*v)(p->__pyx_v_fcount, a); if (e) return e;
   }
@@ -60103,17 +65287,26 @@ static int __pyx_tp_traverse_3_sa___pyx_scope_struct_4_input(PyObject *o, visitp
   if (p->__pyx_v_hiero_phrase) {
     e = (*v)(((PyObject*)p->__pyx_v_hiero_phrase), a); if (e) return e;
   }
+  if (p->__pyx_v_input_match) {
+    e = (*v)(p->__pyx_v_input_match, a); if (e) return e;
+  }
   if (p->__pyx_v_is_shadow_path) {
     e = (*v)(p->__pyx_v_is_shadow_path, a); if (e) return e;
   }
   if (p->__pyx_v_key) {
     e = (*v)(p->__pyx_v_key, a); if (e) return e;
   }
-  if (p->__pyx_v_model) {
-    e = (*v)(p->__pyx_v_model, a); if (e) return e;
+  if (p->__pyx_v_loc) {
+    e = (*v)(p->__pyx_v_loc, a); if (e) return e;
+  }
+  if (p->__pyx_v_locs) {
+    e = (*v)(p->__pyx_v_locs, a); if (e) return e;
   }
-  if (p->__pyx_v_models) {
-    e = (*v)(p->__pyx_v_models, a); if (e) return e;
+  if (p->__pyx_v_max_locs) {
+    e = (*v)(p->__pyx_v_max_locs, a); if (e) return e;
+  }
+  if (p->__pyx_v_meta) {
+    e = (*v)(p->__pyx_v_meta, a); if (e) return e;
   }
   if (p->__pyx_v_new_frontier) {
     e = (*v)(p->__pyx_v_new_frontier, a); if (e) return e;
@@ -60152,7 +65345,7 @@ static int __pyx_tp_traverse_3_sa___pyx_scope_struct_4_input(PyObject *o, visitp
     e = (*v)(((PyObject*)p->__pyx_v_sample), a); if (e) return e;
   }
   if (p->__pyx_v_scores) {
-    e = (*v)(p->__pyx_v_scores, a); if (e) return e;
+    e = (*v)(((PyObject*)p->__pyx_v_scores), a); if (e) return e;
   }
   if (p->__pyx_v_self) {
     e = (*v)(((PyObject*)p->__pyx_v_self), a); if (e) return e;
@@ -60193,8 +65386,8 @@ static int __pyx_tp_traverse_3_sa___pyx_scope_struct_4_input(PyObject *o, visitp
   return 0;
 }
 
-static int __pyx_tp_clear_3_sa___pyx_scope_struct_4_input(PyObject *o) {
-  struct __pyx_obj_3_sa___pyx_scope_struct_4_input *p = (struct __pyx_obj_3_sa___pyx_scope_struct_4_input *)o;
+static int __pyx_tp_clear_3_sa___pyx_scope_struct_15_input(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_15_input *p = (struct __pyx_obj_3_sa___pyx_scope_struct_15_input *)o;
   PyObject* tmp;
   tmp = ((PyObject*)p->__pyx_v_alignment);
   p->__pyx_v_alignment = Py_None; Py_INCREF(Py_None);
@@ -60211,9 +65404,6 @@ static int __pyx_tp_clear_3_sa___pyx_scope_struct_4_input(PyObject *o) {
   tmp = ((PyObject*)p->__pyx_v_count);
   p->__pyx_v_count = Py_None; Py_INCREF(Py_None);
   Py_XDECREF(tmp);
-  tmp = ((PyObject*)p->__pyx_v_currcount);
-  p->__pyx_v_currcount = Py_None; Py_INCREF(Py_None);
-  Py_XDECREF(tmp);
   tmp = ((PyObject*)p->__pyx_v_e);
   p->__pyx_v_e = Py_None; Py_INCREF(Py_None);
   Py_XDECREF(tmp);
@@ -60235,17 +65425,11 @@ static int __pyx_tp_clear_3_sa___pyx_scope_struct_4_input(PyObject *o) {
   tmp = ((PyObject*)p->__pyx_v_f);
   p->__pyx_v_f = Py_None; Py_INCREF(Py_None);
   Py_XDECREF(tmp);
-  tmp = ((PyObject*)p->__pyx_v_f_margin);
-  p->__pyx_v_f_margin = Py_None; Py_INCREF(Py_None);
-  Py_XDECREF(tmp);
-  tmp = ((PyObject*)p->__pyx_v_fals);
-  p->__pyx_v_fals = ((PyObject*)Py_None); Py_INCREF(Py_None);
-  Py_XDECREF(tmp);
   tmp = ((PyObject*)p->__pyx_v_fcount);
-  p->__pyx_v_fcount = ((PyObject*)Py_None); Py_INCREF(Py_None);
+  p->__pyx_v_fcount = Py_None; Py_INCREF(Py_None);
   Py_XDECREF(tmp);
   tmp = ((PyObject*)p->__pyx_v_fphrases);
-  p->__pyx_v_fphrases = ((PyObject*)Py_None); Py_INCREF(Py_None);
+  p->__pyx_v_fphrases = Py_None; Py_INCREF(Py_None);
   Py_XDECREF(tmp);
   tmp = ((PyObject*)p->__pyx_v_frontier);
   p->__pyx_v_frontier = ((PyObject*)Py_None); Py_INCREF(Py_None);
@@ -60259,17 +65443,26 @@ static int __pyx_tp_clear_3_sa___pyx_scope_struct_4_input(PyObject *o) {
   tmp = ((PyObject*)p->__pyx_v_hiero_phrase);
   p->__pyx_v_hiero_phrase = ((struct __pyx_obj_3_sa_Phrase *)Py_None); Py_INCREF(Py_None);
   Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->__pyx_v_input_match);
+  p->__pyx_v_input_match = Py_None; Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
   tmp = ((PyObject*)p->__pyx_v_is_shadow_path);
   p->__pyx_v_is_shadow_path = Py_None; Py_INCREF(Py_None);
   Py_XDECREF(tmp);
   tmp = ((PyObject*)p->__pyx_v_key);
   p->__pyx_v_key = ((PyObject*)Py_None); Py_INCREF(Py_None);
   Py_XDECREF(tmp);
-  tmp = ((PyObject*)p->__pyx_v_model);
-  p->__pyx_v_model = Py_None; Py_INCREF(Py_None);
+  tmp = ((PyObject*)p->__pyx_v_loc);
+  p->__pyx_v_loc = Py_None; Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->__pyx_v_locs);
+  p->__pyx_v_locs = ((PyObject*)Py_None); Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->__pyx_v_max_locs);
+  p->__pyx_v_max_locs = Py_None; Py_INCREF(Py_None);
   Py_XDECREF(tmp);
-  tmp = ((PyObject*)p->__pyx_v_models);
-  p->__pyx_v_models = Py_None; Py_INCREF(Py_None);
+  tmp = ((PyObject*)p->__pyx_v_meta);
+  p->__pyx_v_meta = Py_None; Py_INCREF(Py_None);
   Py_XDECREF(tmp);
   tmp = ((PyObject*)p->__pyx_v_new_frontier);
   p->__pyx_v_new_frontier = ((PyObject*)Py_None); Py_INCREF(Py_None);
@@ -60308,7 +65501,7 @@ static int __pyx_tp_clear_3_sa___pyx_scope_struct_4_input(PyObject *o) {
   p->__pyx_v_sample = ((struct __pyx_obj_3_sa_IntList *)Py_None); Py_INCREF(Py_None);
   Py_XDECREF(tmp);
   tmp = ((PyObject*)p->__pyx_v_scores);
-  p->__pyx_v_scores = ((PyObject*)Py_None); Py_INCREF(Py_None);
+  p->__pyx_v_scores = ((struct __pyx_obj_3_sa_FeatureVector *)Py_None); Py_INCREF(Py_None);
   Py_XDECREF(tmp);
   tmp = ((PyObject*)p->__pyx_v_self);
   p->__pyx_v_self = ((struct __pyx_obj_3_sa_HieroCachingRuleFactory *)Py_None); Py_INCREF(Py_None);
@@ -60349,11 +65542,202 @@ static int __pyx_tp_clear_3_sa___pyx_scope_struct_4_input(PyObject *o) {
   return 0;
 }
 
-static PyMethodDef __pyx_methods_3_sa___pyx_scope_struct_4_input[] = {
+static PyMethodDef __pyx_methods_3_sa___pyx_scope_struct_15_input[] = {
+  {0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_15_input = {
+  0, /*nb_add*/
+  0, /*nb_subtract*/
+  0, /*nb_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_divide*/
+  #endif
+  0, /*nb_remainder*/
+  0, /*nb_divmod*/
+  0, /*nb_power*/
+  0, /*nb_negative*/
+  0, /*nb_positive*/
+  0, /*nb_absolute*/
+  0, /*nb_nonzero*/
+  0, /*nb_invert*/
+  0, /*nb_lshift*/
+  0, /*nb_rshift*/
+  0, /*nb_and*/
+  0, /*nb_xor*/
+  0, /*nb_or*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_coerce*/
+  #endif
+  0, /*nb_int*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_long*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*nb_float*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_oct*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_hex*/
+  #endif
+  0, /*nb_inplace_add*/
+  0, /*nb_inplace_subtract*/
+  0, /*nb_inplace_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_inplace_divide*/
+  #endif
+  0, /*nb_inplace_remainder*/
+  0, /*nb_inplace_power*/
+  0, /*nb_inplace_lshift*/
+  0, /*nb_inplace_rshift*/
+  0, /*nb_inplace_and*/
+  0, /*nb_inplace_xor*/
+  0, /*nb_inplace_or*/
+  0, /*nb_floor_divide*/
+  0, /*nb_true_divide*/
+  0, /*nb_inplace_floor_divide*/
+  0, /*nb_inplace_true_divide*/
+  #if PY_VERSION_HEX >= 0x02050000
+  0, /*nb_index*/
+  #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_15_input = {
+  0, /*sq_length*/
+  0, /*sq_concat*/
+  0, /*sq_repeat*/
+  0, /*sq_item*/
+  0, /*sq_slice*/
+  0, /*sq_ass_item*/
+  0, /*sq_ass_slice*/
+  0, /*sq_contains*/
+  0, /*sq_inplace_concat*/
+  0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_15_input = {
+  0, /*mp_length*/
+  0, /*mp_subscript*/
+  0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_15_input = {
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getreadbuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getwritebuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getsegcount*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getcharbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_getbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_releasebuffer*/
+  #endif
+};
+
+static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_15_input = {
+  PyVarObject_HEAD_INIT(0, 0)
+  __Pyx_NAMESTR("_sa.__pyx_scope_struct_15_input"), /*tp_name*/
+  sizeof(struct __pyx_obj_3_sa___pyx_scope_struct_15_input), /*tp_basicsize*/
+  0, /*tp_itemsize*/
+  __pyx_tp_dealloc_3_sa___pyx_scope_struct_15_input, /*tp_dealloc*/
+  0, /*tp_print*/
+  0, /*tp_getattr*/
+  0, /*tp_setattr*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*tp_compare*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*tp_repr*/
+  &__pyx_tp_as_number___pyx_scope_struct_15_input, /*tp_as_number*/
+  &__pyx_tp_as_sequence___pyx_scope_struct_15_input, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping___pyx_scope_struct_15_input, /*tp_as_mapping*/
+  0, /*tp_hash*/
+  0, /*tp_call*/
+  0, /*tp_str*/
+  0, /*tp_getattro*/
+  0, /*tp_setattro*/
+  &__pyx_tp_as_buffer___pyx_scope_struct_15_input, /*tp_as_buffer*/
+  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+  0, /*tp_doc*/
+  __pyx_tp_traverse_3_sa___pyx_scope_struct_15_input, /*tp_traverse*/
+  __pyx_tp_clear_3_sa___pyx_scope_struct_15_input, /*tp_clear*/
+  0, /*tp_richcompare*/
+  0, /*tp_weaklistoffset*/
+  0, /*tp_iter*/
+  0, /*tp_iternext*/
+  __pyx_methods_3_sa___pyx_scope_struct_15_input, /*tp_methods*/
+  0, /*tp_members*/
+  0, /*tp_getset*/
+  0, /*tp_base*/
+  0, /*tp_dict*/
+  0, /*tp_descr_get*/
+  0, /*tp_descr_set*/
+  0, /*tp_dictoffset*/
+  0, /*tp_init*/
+  0, /*tp_alloc*/
+  __pyx_tp_new_3_sa___pyx_scope_struct_15_input, /*tp_new*/
+  0, /*tp_free*/
+  0, /*tp_is_gc*/
+  0, /*tp_bases*/
+  0, /*tp_mro*/
+  0, /*tp_cache*/
+  0, /*tp_subclasses*/
+  0, /*tp_weaklist*/
+  0, /*tp_del*/
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*tp_version_tag*/
+  #endif
+};
+
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_16___iter__(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_16___iter__ *p;
+  PyObject *o = (*t->tp_alloc)(t, 0);
+  if (!o) return 0;
+  p = ((struct __pyx_obj_3_sa___pyx_scope_struct_16___iter__ *)o);
+  p->__pyx_v_self = 0;
+  return o;
+}
+
+static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_16___iter__(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_16___iter__ *p = (struct __pyx_obj_3_sa___pyx_scope_struct_16___iter__ *)o;
+  Py_CLEAR(p->__pyx_v_self);
+  (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_3_sa___pyx_scope_struct_16___iter__(PyObject *o, visitproc v, void *a) {
+  int e;
+  struct __pyx_obj_3_sa___pyx_scope_struct_16___iter__ *p = (struct __pyx_obj_3_sa___pyx_scope_struct_16___iter__ *)o;
+  if (p->__pyx_v_self) {
+    e = (*v)(((PyObject*)p->__pyx_v_self), a); if (e) return e;
+  }
+  return 0;
+}
+
+static int __pyx_tp_clear_3_sa___pyx_scope_struct_16___iter__(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_16___iter__ *p = (struct __pyx_obj_3_sa___pyx_scope_struct_16___iter__ *)o;
+  PyObject* tmp;
+  tmp = ((PyObject*)p->__pyx_v_self);
+  p->__pyx_v_self = ((struct __pyx_obj_3_sa_FeatureVector *)Py_None); Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  return 0;
+}
+
+static PyMethodDef __pyx_methods_3_sa___pyx_scope_struct_16___iter__[] = {
   {0, 0, 0, 0}
 };
 
-static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_4_input = {
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_16___iter__ = {
   0, /*nb_add*/
   0, /*nb_subtract*/
   0, /*nb_multiply*/
@@ -60411,7 +65795,7 @@ static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_4_input = {
   #endif
 };
 
-static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_4_input = {
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_16___iter__ = {
   0, /*sq_length*/
   0, /*sq_concat*/
   0, /*sq_repeat*/
@@ -60424,13 +65808,13 @@ static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_4_input = {
   0, /*sq_inplace_repeat*/
 };
 
-static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_4_input = {
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_16___iter__ = {
   0, /*mp_length*/
   0, /*mp_subscript*/
   0, /*mp_ass_subscript*/
 };
 
-static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_4_input = {
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_16___iter__ = {
   #if PY_MAJOR_VERSION < 3
   0, /*bf_getreadbuffer*/
   #endif
@@ -60451,12 +65835,12 @@ static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_4_input = {
   #endif
 };
 
-static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_4_input = {
+static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_16___iter__ = {
   PyVarObject_HEAD_INIT(0, 0)
-  __Pyx_NAMESTR("_sa.__pyx_scope_struct_4_input"), /*tp_name*/
-  sizeof(struct __pyx_obj_3_sa___pyx_scope_struct_4_input), /*tp_basicsize*/
+  __Pyx_NAMESTR("_sa.__pyx_scope_struct_16___iter__"), /*tp_name*/
+  sizeof(struct __pyx_obj_3_sa___pyx_scope_struct_16___iter__), /*tp_basicsize*/
   0, /*tp_itemsize*/
-  __pyx_tp_dealloc_3_sa___pyx_scope_struct_4_input, /*tp_dealloc*/
+  __pyx_tp_dealloc_3_sa___pyx_scope_struct_16___iter__, /*tp_dealloc*/
   0, /*tp_print*/
   0, /*tp_getattr*/
   0, /*tp_setattr*/
@@ -60466,24 +65850,24 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_4_input = {
   0, /*reserved*/
   #endif
   0, /*tp_repr*/
-  &__pyx_tp_as_number___pyx_scope_struct_4_input, /*tp_as_number*/
-  &__pyx_tp_as_sequence___pyx_scope_struct_4_input, /*tp_as_sequence*/
-  &__pyx_tp_as_mapping___pyx_scope_struct_4_input, /*tp_as_mapping*/
+  &__pyx_tp_as_number___pyx_scope_struct_16___iter__, /*tp_as_number*/
+  &__pyx_tp_as_sequence___pyx_scope_struct_16___iter__, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping___pyx_scope_struct_16___iter__, /*tp_as_mapping*/
   0, /*tp_hash*/
   0, /*tp_call*/
   0, /*tp_str*/
   0, /*tp_getattro*/
   0, /*tp_setattro*/
-  &__pyx_tp_as_buffer___pyx_scope_struct_4_input, /*tp_as_buffer*/
+  &__pyx_tp_as_buffer___pyx_scope_struct_16___iter__, /*tp_as_buffer*/
   Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
   0, /*tp_doc*/
-  __pyx_tp_traverse_3_sa___pyx_scope_struct_4_input, /*tp_traverse*/
-  __pyx_tp_clear_3_sa___pyx_scope_struct_4_input, /*tp_clear*/
+  __pyx_tp_traverse_3_sa___pyx_scope_struct_16___iter__, /*tp_traverse*/
+  __pyx_tp_clear_3_sa___pyx_scope_struct_16___iter__, /*tp_clear*/
   0, /*tp_richcompare*/
   0, /*tp_weaklistoffset*/
   0, /*tp_iter*/
   0, /*tp_iternext*/
-  __pyx_methods_3_sa___pyx_scope_struct_4_input, /*tp_methods*/
+  __pyx_methods_3_sa___pyx_scope_struct_16___iter__, /*tp_methods*/
   0, /*tp_members*/
   0, /*tp_getset*/
   0, /*tp_base*/
@@ -60493,7 +65877,405 @@ static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_4_input = {
   0, /*tp_dictoffset*/
   0, /*tp_init*/
   0, /*tp_alloc*/
-  __pyx_tp_new_3_sa___pyx_scope_struct_4_input, /*tp_new*/
+  __pyx_tp_new_3_sa___pyx_scope_struct_16___iter__, /*tp_new*/
+  0, /*tp_free*/
+  0, /*tp_is_gc*/
+  0, /*tp_bases*/
+  0, /*tp_mro*/
+  0, /*tp_cache*/
+  0, /*tp_subclasses*/
+  0, /*tp_weaklist*/
+  0, /*tp_del*/
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*tp_version_tag*/
+  #endif
+};
+
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_17___str__(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_17___str__ *p;
+  PyObject *o = (*t->tp_alloc)(t, 0);
+  if (!o) return 0;
+  p = ((struct __pyx_obj_3_sa___pyx_scope_struct_17___str__ *)o);
+  p->__pyx_v_self = 0;
+  return o;
+}
+
+static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_17___str__(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_17___str__ *p = (struct __pyx_obj_3_sa___pyx_scope_struct_17___str__ *)o;
+  Py_CLEAR(p->__pyx_v_self);
+  (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_3_sa___pyx_scope_struct_17___str__(PyObject *o, visitproc v, void *a) {
+  int e;
+  struct __pyx_obj_3_sa___pyx_scope_struct_17___str__ *p = (struct __pyx_obj_3_sa___pyx_scope_struct_17___str__ *)o;
+  if (p->__pyx_v_self) {
+    e = (*v)(((PyObject*)p->__pyx_v_self), a); if (e) return e;
+  }
+  return 0;
+}
+
+static int __pyx_tp_clear_3_sa___pyx_scope_struct_17___str__(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_17___str__ *p = (struct __pyx_obj_3_sa___pyx_scope_struct_17___str__ *)o;
+  PyObject* tmp;
+  tmp = ((PyObject*)p->__pyx_v_self);
+  p->__pyx_v_self = ((struct __pyx_obj_3_sa_FeatureVector *)Py_None); Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  return 0;
+}
+
+static PyMethodDef __pyx_methods_3_sa___pyx_scope_struct_17___str__[] = {
+  {0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_17___str__ = {
+  0, /*nb_add*/
+  0, /*nb_subtract*/
+  0, /*nb_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_divide*/
+  #endif
+  0, /*nb_remainder*/
+  0, /*nb_divmod*/
+  0, /*nb_power*/
+  0, /*nb_negative*/
+  0, /*nb_positive*/
+  0, /*nb_absolute*/
+  0, /*nb_nonzero*/
+  0, /*nb_invert*/
+  0, /*nb_lshift*/
+  0, /*nb_rshift*/
+  0, /*nb_and*/
+  0, /*nb_xor*/
+  0, /*nb_or*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_coerce*/
+  #endif
+  0, /*nb_int*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_long*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*nb_float*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_oct*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_hex*/
+  #endif
+  0, /*nb_inplace_add*/
+  0, /*nb_inplace_subtract*/
+  0, /*nb_inplace_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_inplace_divide*/
+  #endif
+  0, /*nb_inplace_remainder*/
+  0, /*nb_inplace_power*/
+  0, /*nb_inplace_lshift*/
+  0, /*nb_inplace_rshift*/
+  0, /*nb_inplace_and*/
+  0, /*nb_inplace_xor*/
+  0, /*nb_inplace_or*/
+  0, /*nb_floor_divide*/
+  0, /*nb_true_divide*/
+  0, /*nb_inplace_floor_divide*/
+  0, /*nb_inplace_true_divide*/
+  #if PY_VERSION_HEX >= 0x02050000
+  0, /*nb_index*/
+  #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_17___str__ = {
+  0, /*sq_length*/
+  0, /*sq_concat*/
+  0, /*sq_repeat*/
+  0, /*sq_item*/
+  0, /*sq_slice*/
+  0, /*sq_ass_item*/
+  0, /*sq_ass_slice*/
+  0, /*sq_contains*/
+  0, /*sq_inplace_concat*/
+  0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_17___str__ = {
+  0, /*mp_length*/
+  0, /*mp_subscript*/
+  0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_17___str__ = {
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getreadbuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getwritebuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getsegcount*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getcharbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_getbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_releasebuffer*/
+  #endif
+};
+
+static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_17___str__ = {
+  PyVarObject_HEAD_INIT(0, 0)
+  __Pyx_NAMESTR("_sa.__pyx_scope_struct_17___str__"), /*tp_name*/
+  sizeof(struct __pyx_obj_3_sa___pyx_scope_struct_17___str__), /*tp_basicsize*/
+  0, /*tp_itemsize*/
+  __pyx_tp_dealloc_3_sa___pyx_scope_struct_17___str__, /*tp_dealloc*/
+  0, /*tp_print*/
+  0, /*tp_getattr*/
+  0, /*tp_setattr*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*tp_compare*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*tp_repr*/
+  &__pyx_tp_as_number___pyx_scope_struct_17___str__, /*tp_as_number*/
+  &__pyx_tp_as_sequence___pyx_scope_struct_17___str__, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping___pyx_scope_struct_17___str__, /*tp_as_mapping*/
+  0, /*tp_hash*/
+  0, /*tp_call*/
+  0, /*tp_str*/
+  0, /*tp_getattro*/
+  0, /*tp_setattro*/
+  &__pyx_tp_as_buffer___pyx_scope_struct_17___str__, /*tp_as_buffer*/
+  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+  0, /*tp_doc*/
+  __pyx_tp_traverse_3_sa___pyx_scope_struct_17___str__, /*tp_traverse*/
+  __pyx_tp_clear_3_sa___pyx_scope_struct_17___str__, /*tp_clear*/
+  0, /*tp_richcompare*/
+  0, /*tp_weaklistoffset*/
+  0, /*tp_iter*/
+  0, /*tp_iternext*/
+  __pyx_methods_3_sa___pyx_scope_struct_17___str__, /*tp_methods*/
+  0, /*tp_members*/
+  0, /*tp_getset*/
+  0, /*tp_base*/
+  0, /*tp_dict*/
+  0, /*tp_descr_get*/
+  0, /*tp_descr_set*/
+  0, /*tp_dictoffset*/
+  0, /*tp_init*/
+  0, /*tp_alloc*/
+  __pyx_tp_new_3_sa___pyx_scope_struct_17___str__, /*tp_new*/
+  0, /*tp_free*/
+  0, /*tp_is_gc*/
+  0, /*tp_bases*/
+  0, /*tp_mro*/
+  0, /*tp_cache*/
+  0, /*tp_subclasses*/
+  0, /*tp_weaklist*/
+  0, /*tp_del*/
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*tp_version_tag*/
+  #endif
+};
+
+static PyObject *__pyx_tp_new_3_sa___pyx_scope_struct_18_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_18_genexpr *p;
+  PyObject *o = (*t->tp_alloc)(t, 0);
+  if (!o) return 0;
+  p = ((struct __pyx_obj_3_sa___pyx_scope_struct_18_genexpr *)o);
+  p->__pyx_outer_scope = 0;
+  p->__pyx_v_feat = 0;
+  p->__pyx_t_0 = 0;
+  return o;
+}
+
+static void __pyx_tp_dealloc_3_sa___pyx_scope_struct_18_genexpr(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_18_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_18_genexpr *)o;
+  Py_CLEAR(p->__pyx_outer_scope);
+  Py_CLEAR(p->__pyx_v_feat);
+  Py_CLEAR(p->__pyx_t_0);
+  (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_3_sa___pyx_scope_struct_18_genexpr(PyObject *o, visitproc v, void *a) {
+  int e;
+  struct __pyx_obj_3_sa___pyx_scope_struct_18_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_18_genexpr *)o;
+  if (p->__pyx_outer_scope) {
+    e = (*v)(((PyObject*)p->__pyx_outer_scope), a); if (e) return e;
+  }
+  if (p->__pyx_v_feat) {
+    e = (*v)(p->__pyx_v_feat, a); if (e) return e;
+  }
+  if (p->__pyx_t_0) {
+    e = (*v)(p->__pyx_t_0, a); if (e) return e;
+  }
+  return 0;
+}
+
+static int __pyx_tp_clear_3_sa___pyx_scope_struct_18_genexpr(PyObject *o) {
+  struct __pyx_obj_3_sa___pyx_scope_struct_18_genexpr *p = (struct __pyx_obj_3_sa___pyx_scope_struct_18_genexpr *)o;
+  PyObject* tmp;
+  tmp = ((PyObject*)p->__pyx_outer_scope);
+  p->__pyx_outer_scope = ((struct __pyx_obj_3_sa___pyx_scope_struct_17___str__ *)Py_None); Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->__pyx_v_feat);
+  p->__pyx_v_feat = Py_None; Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  tmp = ((PyObject*)p->__pyx_t_0);
+  p->__pyx_t_0 = Py_None; Py_INCREF(Py_None);
+  Py_XDECREF(tmp);
+  return 0;
+}
+
+static PyMethodDef __pyx_methods_3_sa___pyx_scope_struct_18_genexpr[] = {
+  {0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_18_genexpr = {
+  0, /*nb_add*/
+  0, /*nb_subtract*/
+  0, /*nb_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_divide*/
+  #endif
+  0, /*nb_remainder*/
+  0, /*nb_divmod*/
+  0, /*nb_power*/
+  0, /*nb_negative*/
+  0, /*nb_positive*/
+  0, /*nb_absolute*/
+  0, /*nb_nonzero*/
+  0, /*nb_invert*/
+  0, /*nb_lshift*/
+  0, /*nb_rshift*/
+  0, /*nb_and*/
+  0, /*nb_xor*/
+  0, /*nb_or*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_coerce*/
+  #endif
+  0, /*nb_int*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_long*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*nb_float*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_oct*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_hex*/
+  #endif
+  0, /*nb_inplace_add*/
+  0, /*nb_inplace_subtract*/
+  0, /*nb_inplace_multiply*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*nb_inplace_divide*/
+  #endif
+  0, /*nb_inplace_remainder*/
+  0, /*nb_inplace_power*/
+  0, /*nb_inplace_lshift*/
+  0, /*nb_inplace_rshift*/
+  0, /*nb_inplace_and*/
+  0, /*nb_inplace_xor*/
+  0, /*nb_inplace_or*/
+  0, /*nb_floor_divide*/
+  0, /*nb_true_divide*/
+  0, /*nb_inplace_floor_divide*/
+  0, /*nb_inplace_true_divide*/
+  #if PY_VERSION_HEX >= 0x02050000
+  0, /*nb_index*/
+  #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_18_genexpr = {
+  0, /*sq_length*/
+  0, /*sq_concat*/
+  0, /*sq_repeat*/
+  0, /*sq_item*/
+  0, /*sq_slice*/
+  0, /*sq_ass_item*/
+  0, /*sq_ass_slice*/
+  0, /*sq_contains*/
+  0, /*sq_inplace_concat*/
+  0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_18_genexpr = {
+  0, /*mp_length*/
+  0, /*mp_subscript*/
+  0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_18_genexpr = {
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getreadbuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getwritebuffer*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getsegcount*/
+  #endif
+  #if PY_MAJOR_VERSION < 3
+  0, /*bf_getcharbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_getbuffer*/
+  #endif
+  #if PY_VERSION_HEX >= 0x02060000
+  0, /*bf_releasebuffer*/
+  #endif
+};
+
+static PyTypeObject __pyx_type_3_sa___pyx_scope_struct_18_genexpr = {
+  PyVarObject_HEAD_INIT(0, 0)
+  __Pyx_NAMESTR("_sa.__pyx_scope_struct_18_genexpr"), /*tp_name*/
+  sizeof(struct __pyx_obj_3_sa___pyx_scope_struct_18_genexpr), /*tp_basicsize*/
+  0, /*tp_itemsize*/
+  __pyx_tp_dealloc_3_sa___pyx_scope_struct_18_genexpr, /*tp_dealloc*/
+  0, /*tp_print*/
+  0, /*tp_getattr*/
+  0, /*tp_setattr*/
+  #if PY_MAJOR_VERSION < 3
+  0, /*tp_compare*/
+  #else
+  0, /*reserved*/
+  #endif
+  0, /*tp_repr*/
+  &__pyx_tp_as_number___pyx_scope_struct_18_genexpr, /*tp_as_number*/
+  &__pyx_tp_as_sequence___pyx_scope_struct_18_genexpr, /*tp_as_sequence*/
+  &__pyx_tp_as_mapping___pyx_scope_struct_18_genexpr, /*tp_as_mapping*/
+  0, /*tp_hash*/
+  0, /*tp_call*/
+  0, /*tp_str*/
+  0, /*tp_getattro*/
+  0, /*tp_setattro*/
+  &__pyx_tp_as_buffer___pyx_scope_struct_18_genexpr, /*tp_as_buffer*/
+  Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+  0, /*tp_doc*/
+  __pyx_tp_traverse_3_sa___pyx_scope_struct_18_genexpr, /*tp_traverse*/
+  __pyx_tp_clear_3_sa___pyx_scope_struct_18_genexpr, /*tp_clear*/
+  0, /*tp_richcompare*/
+  0, /*tp_weaklistoffset*/
+  0, /*tp_iter*/
+  0, /*tp_iternext*/
+  __pyx_methods_3_sa___pyx_scope_struct_18_genexpr, /*tp_methods*/
+  0, /*tp_members*/
+  0, /*tp_getset*/
+  0, /*tp_base*/
+  0, /*tp_dict*/
+  0, /*tp_descr_get*/
+  0, /*tp_descr_set*/
+  0, /*tp_dictoffset*/
+  0, /*tp_init*/
+  0, /*tp_alloc*/
+  __pyx_tp_new_3_sa___pyx_scope_struct_18_genexpr, /*tp_new*/
   0, /*tp_free*/
   0, /*tp_is_gc*/
   0, /*tp_bases*/
@@ -60558,10 +66340,10 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
   {&__pyx_kp_s_131, __pyx_k_131, sizeof(__pyx_k_131), 0, 0, 1, 0},
   {&__pyx_kp_s_132, __pyx_k_132, sizeof(__pyx_k_132), 0, 0, 1, 0},
   {&__pyx_kp_s_133, __pyx_k_133, sizeof(__pyx_k_133), 0, 0, 1, 0},
-  {&__pyx_kp_s_136, __pyx_k_136, sizeof(__pyx_k_136), 0, 0, 1, 0},
+  {&__pyx_kp_s_134, __pyx_k_134, sizeof(__pyx_k_134), 0, 0, 1, 0},
   {&__pyx_kp_s_137, __pyx_k_137, sizeof(__pyx_k_137), 0, 0, 1, 0},
+  {&__pyx_kp_s_138, __pyx_k_138, sizeof(__pyx_k_138), 0, 0, 1, 0},
   {&__pyx_kp_s_14, __pyx_k_14, sizeof(__pyx_k_14), 0, 0, 1, 0},
-  {&__pyx_kp_s_141, __pyx_k_141, sizeof(__pyx_k_141), 0, 0, 1, 0},
   {&__pyx_kp_s_142, __pyx_k_142, sizeof(__pyx_k_142), 0, 0, 1, 0},
   {&__pyx_kp_s_18, __pyx_k_18, sizeof(__pyx_k_18), 0, 0, 1, 0},
   {&__pyx_kp_s_2, __pyx_k_2, sizeof(__pyx_k_2), 0, 0, 1, 0},
@@ -60614,25 +66396,30 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
   {&__pyx_kp_s_95, __pyx_k_95, sizeof(__pyx_k_95), 0, 0, 1, 0},
   {&__pyx_kp_s__0, __pyx_k__0, sizeof(__pyx_k__0), 0, 0, 1, 0},
   {&__pyx_kp_s__1, __pyx_k__1, sizeof(__pyx_k__1), 0, 0, 1, 0},
+  {&__pyx_n_s__Counter, __pyx_k__Counter, sizeof(__pyx_k__Counter), 0, 0, 1, 1},
   {&__pyx_n_s__END_OF_FILE, __pyx_k__END_OF_FILE, sizeof(__pyx_k__END_OF_FILE), 0, 0, 1, 1},
   {&__pyx_n_s__END_OF_LINE, __pyx_k__END_OF_LINE, sizeof(__pyx_k__END_OF_LINE), 0, 0, 1, 1},
   {&__pyx_n_s__Exception, __pyx_k__Exception, sizeof(__pyx_k__Exception), 0, 0, 1, 1},
+  {&__pyx_n_s__FeatureContext, __pyx_k__FeatureContext, sizeof(__pyx_k__FeatureContext), 0, 0, 1, 1},
   {&__pyx_n_s__GzipFile, __pyx_k__GzipFile, sizeof(__pyx_k__GzipFile), 0, 0, 1, 1},
+  {&__pyx_n_s__INCREMENT, __pyx_k__INCREMENT, sizeof(__pyx_k__INCREMENT), 0, 0, 1, 1},
+  {&__pyx_n_s__INITIAL_CAPACITY, __pyx_k__INITIAL_CAPACITY, sizeof(__pyx_k__INITIAL_CAPACITY), 0, 0, 1, 1},
   {&__pyx_n_s__IndexError, __pyx_k__IndexError, sizeof(__pyx_k__IndexError), 0, 0, 1, 1},
   {&__pyx_n_s__NULL, __pyx_k__NULL, sizeof(__pyx_k__NULL), 0, 0, 1, 1},
   {&__pyx_n_s__RUSAGE_SELF, __pyx_k__RUSAGE_SELF, sizeof(__pyx_k__RUSAGE_SELF), 0, 0, 1, 1},
   {&__pyx_n_s__StopIteration, __pyx_k__StopIteration, sizeof(__pyx_k__StopIteration), 0, 0, 1, 1},
   {&__pyx_n_s__TypeError, __pyx_k__TypeError, sizeof(__pyx_k__TypeError), 0, 0, 1, 1},
-  {&__pyx_n_s__ValueError, __pyx_k__ValueError, sizeof(__pyx_k__ValueError), 0, 0, 1, 1},
   {&__pyx_n_s____enter__, __pyx_k____enter__, sizeof(__pyx_k____enter__), 0, 0, 1, 1},
   {&__pyx_n_s____exit__, __pyx_k____exit__, sizeof(__pyx_k____exit__), 0, 0, 1, 1},
   {&__pyx_n_s____main__, __pyx_k____main__, sizeof(__pyx_k____main__), 0, 0, 1, 1},
+  {&__pyx_n_s____name__, __pyx_k____name__, sizeof(__pyx_k____name__), 0, 0, 1, 1},
   {&__pyx_n_s____test__, __pyx_k____test__, sizeof(__pyx_k____test__), 0, 0, 1, 1},
   {&__pyx_n_s___columns, __pyx_k___columns, sizeof(__pyx_k___columns), 0, 0, 1, 1},
   {&__pyx_n_s___doquicksort, __pyx_k___doquicksort, sizeof(__pyx_k___doquicksort), 0, 0, 1, 1},
   {&__pyx_n_s___sa, __pyx_k___sa, sizeof(__pyx_k___sa), 0, 0, 1, 1},
   {&__pyx_n_s__advance, __pyx_k__advance, sizeof(__pyx_k__advance), 0, 0, 1, 1},
   {&__pyx_n_s__alignment, __pyx_k__alignment, sizeof(__pyx_k__alignment), 0, 0, 1, 1},
+  {&__pyx_n_s__alignments, __pyx_k__alignments, sizeof(__pyx_k__alignments), 0, 0, 1, 1},
   {&__pyx_n_s__alphabet_size, __pyx_k__alphabet_size, sizeof(__pyx_k__alphabet_size), 0, 0, 1, 1},
   {&__pyx_n_s__arity, __pyx_k__arity, sizeof(__pyx_k__arity), 0, 0, 1, 1},
   {&__pyx_n_s__arr, __pyx_k__arr, sizeof(__pyx_k__arr), 0, 0, 1, 1},
@@ -60640,36 +66427,46 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
   {&__pyx_n_s__arr_low, __pyx_k__arr_low, sizeof(__pyx_k__arr_low), 0, 0, 1, 1},
   {&__pyx_n_s__by_slack_factor, __pyx_k__by_slack_factor, sizeof(__pyx_k__by_slack_factor), 0, 0, 1, 1},
   {&__pyx_n_s__category, __pyx_k__category, sizeof(__pyx_k__category), 0, 0, 1, 1},
+  {&__pyx_n_s__chain, __pyx_k__chain, sizeof(__pyx_k__chain), 0, 0, 1, 1},
   {&__pyx_n_s__children, __pyx_k__children, sizeof(__pyx_k__children), 0, 0, 1, 1},
   {&__pyx_n_s__cmp, __pyx_k__cmp, sizeof(__pyx_k__cmp), 0, 0, 1, 1},
   {&__pyx_n_s__col, __pyx_k__col, sizeof(__pyx_k__col), 0, 0, 1, 1},
   {&__pyx_n_s__collect, __pyx_k__collect, sizeof(__pyx_k__collect), 0, 0, 1, 1},
+  {&__pyx_n_s__collections, __pyx_k__collections, sizeof(__pyx_k__collections), 0, 0, 1, 1},
   {&__pyx_n_s__curr_idx, __pyx_k__curr_idx, sizeof(__pyx_k__curr_idx), 0, 0, 1, 1},
   {&__pyx_n_s__debug, __pyx_k__debug, sizeof(__pyx_k__debug), 0, 0, 1, 1},
+  {&__pyx_n_s__decode_lattice, __pyx_k__decode_lattice, sizeof(__pyx_k__decode_lattice), 0, 0, 1, 1},
+  {&__pyx_n_s__decode_sentence, __pyx_k__decode_sentence, sizeof(__pyx_k__decode_sentence), 0, 0, 1, 1},
+  {&__pyx_n_s__defaultdict, __pyx_k__defaultdict, sizeof(__pyx_k__defaultdict), 0, 0, 1, 1},
   {&__pyx_n_s__dist, __pyx_k__dist, sizeof(__pyx_k__dist), 0, 0, 1, 1},
   {&__pyx_n_s__e, __pyx_k__e, sizeof(__pyx_k__e), 0, 0, 1, 1},
+  {&__pyx_n_s__e_text, __pyx_k__e_text, sizeof(__pyx_k__e_text), 0, 0, 1, 1},
   {&__pyx_n_s__earray, __pyx_k__earray, sizeof(__pyx_k__earray), 0, 0, 1, 1},
   {&__pyx_n_s__edarray, __pyx_k__edarray, sizeof(__pyx_k__edarray), 0, 0, 1, 1},
   {&__pyx_n_s__end, __pyx_k__end, sizeof(__pyx_k__end), 0, 0, 1, 1},
   {&__pyx_n_s__enumerate, __pyx_k__enumerate, sizeof(__pyx_k__enumerate), 0, 0, 1, 1},
+  {&__pyx_n_s__ephrase, __pyx_k__ephrase, sizeof(__pyx_k__ephrase), 0, 0, 1, 1},
   {&__pyx_n_s__eword, __pyx_k__eword, sizeof(__pyx_k__eword), 0, 0, 1, 1},
   {&__pyx_n_s__extend, __pyx_k__extend, sizeof(__pyx_k__extend), 0, 0, 1, 1},
   {&__pyx_n_s__extended, __pyx_k__extended, sizeof(__pyx_k__extended), 0, 0, 1, 1},
   {&__pyx_n_s__f, __pyx_k__f, sizeof(__pyx_k__f), 0, 0, 1, 1},
+  {&__pyx_n_s__f_text, __pyx_k__f_text, sizeof(__pyx_k__f_text), 0, 0, 1, 1},
+  {&__pyx_n_s__fcount, __pyx_k__fcount, sizeof(__pyx_k__fcount), 0, 0, 1, 1},
   {&__pyx_n_s__filename, __pyx_k__filename, sizeof(__pyx_k__filename), 0, 0, 1, 1},
+  {&__pyx_n_s__fphrase, __pyx_k__fphrase, sizeof(__pyx_k__fphrase), 0, 0, 1, 1},
   {&__pyx_n_s__from_binary, __pyx_k__from_binary, sizeof(__pyx_k__from_binary), 0, 0, 1, 1},
   {&__pyx_n_s__from_data, __pyx_k__from_data, sizeof(__pyx_k__from_data), 0, 0, 1, 1},
+  {&__pyx_n_s__from_iterable, __pyx_k__from_iterable, sizeof(__pyx_k__from_iterable), 0, 0, 1, 1},
   {&__pyx_n_s__from_stats, __pyx_k__from_stats, sizeof(__pyx_k__from_stats), 0, 0, 1, 1},
   {&__pyx_n_s__from_text, __pyx_k__from_text, sizeof(__pyx_k__from_text), 0, 0, 1, 1},
   {&__pyx_n_s__frontier, __pyx_k__frontier, sizeof(__pyx_k__frontier), 0, 0, 1, 1},
+  {&__pyx_n_s__fsample_count, __pyx_k__fsample_count, sizeof(__pyx_k__fsample_count), 0, 0, 1, 1},
   {&__pyx_n_s__fsarray, __pyx_k__fsarray, sizeof(__pyx_k__fsarray), 0, 0, 1, 1},
   {&__pyx_n_s__fword, __pyx_k__fword, sizeof(__pyx_k__fword), 0, 0, 1, 1},
   {&__pyx_n_s__fwords, __pyx_k__fwords, sizeof(__pyx_k__fwords), 0, 0, 1, 1},
   {&__pyx_n_s__gc, __pyx_k__gc, sizeof(__pyx_k__gc), 0, 0, 1, 1},
+  {&__pyx_n_s__genexpr, __pyx_k__genexpr, sizeof(__pyx_k__genexpr), 0, 0, 1, 1},
   {&__pyx_n_s__getLogger, __pyx_k__getLogger, sizeof(__pyx_k__getLogger), 0, 0, 1, 1},
-  {&__pyx_n_s__getSent, __pyx_k__getSent, sizeof(__pyx_k__getSent), 0, 0, 1, 1},
-  {&__pyx_n_s__getSentId, __pyx_k__getSentId, sizeof(__pyx_k__getSentId), 0, 0, 1, 1},
-  {&__pyx_n_s__getSentPos, __pyx_k__getSentPos, sizeof(__pyx_k__getSentPos), 0, 0, 1, 1},
   {&__pyx_n_s__get_e_id, __pyx_k__get_e_id, sizeof(__pyx_k__get_e_id), 0, 0, 1, 1},
   {&__pyx_n_s__get_f_id, __pyx_k__get_f_id, sizeof(__pyx_k__get_f_id), 0, 0, 1, 1},
   {&__pyx_n_s__get_id, __pyx_k__get_id, sizeof(__pyx_k__get_id), 0, 0, 1, 1},
@@ -60687,18 +66484,27 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
   {&__pyx_n_s__index, __pyx_k__index, sizeof(__pyx_k__index), 0, 0, 1, 1},
   {&__pyx_n_s__info, __pyx_k__info, sizeof(__pyx_k__info), 0, 0, 1, 1},
   {&__pyx_n_s__initial_len, __pyx_k__initial_len, sizeof(__pyx_k__initial_len), 0, 0, 1, 1},
+  {&__pyx_n_s__input_match, __pyx_k__input_match, sizeof(__pyx_k__input_match), 0, 0, 1, 1},
+  {&__pyx_n_s__input_span, __pyx_k__input_span, sizeof(__pyx_k__input_span), 0, 0, 1, 1},
   {&__pyx_n_s__insert, __pyx_k__insert, sizeof(__pyx_k__insert), 0, 0, 1, 1},
   {&__pyx_n_s__isa, __pyx_k__isa, sizeof(__pyx_k__isa), 0, 0, 1, 1},
   {&__pyx_n_s__iteritems, __pyx_k__iteritems, sizeof(__pyx_k__iteritems), 0, 0, 1, 1},
+  {&__pyx_n_s__itertools, __pyx_k__itertools, sizeof(__pyx_k__itertools), 0, 0, 1, 1},
+  {&__pyx_n_s__itervalues, __pyx_k__itervalues, sizeof(__pyx_k__itervalues), 0, 0, 1, 1},
   {&__pyx_n_s__ito, __pyx_k__ito, sizeof(__pyx_k__ito), 0, 0, 1, 1},
   {&__pyx_n_s__j, __pyx_k__j, sizeof(__pyx_k__j), 0, 0, 1, 1},
   {&__pyx_n_s__join, __pyx_k__join, sizeof(__pyx_k__join), 0, 0, 1, 1},
+  {&__pyx_n_s__key, __pyx_k__key, sizeof(__pyx_k__key), 0, 0, 1, 1},
+  {&__pyx_n_s__lattice, __pyx_k__lattice, sizeof(__pyx_k__lattice), 0, 0, 1, 1},
   {&__pyx_n_s__lhs, __pyx_k__lhs, sizeof(__pyx_k__lhs), 0, 0, 1, 1},
   {&__pyx_n_s__logger, __pyx_k__logger, sizeof(__pyx_k__logger), 0, 0, 1, 1},
   {&__pyx_n_s__logging, __pyx_k__logging, sizeof(__pyx_k__logging), 0, 0, 1, 1},
   {&__pyx_n_s__lookup, __pyx_k__lookup, sizeof(__pyx_k__lookup), 0, 0, 1, 1},
   {&__pyx_n_s__low, __pyx_k__low, sizeof(__pyx_k__low), 0, 0, 1, 1},
+  {&__pyx_n_s__make_lattice, __pyx_k__make_lattice, sizeof(__pyx_k__make_lattice), 0, 0, 1, 1},
   {&__pyx_n_s__map, __pyx_k__map, sizeof(__pyx_k__map), 0, 0, 1, 1},
+  {&__pyx_n_s__matches, __pyx_k__matches, sizeof(__pyx_k__matches), 0, 0, 1, 1},
+  {&__pyx_n_s__max, __pyx_k__max, sizeof(__pyx_k__max), 0, 0, 1, 1},
   {&__pyx_n_s__max_chunks, __pyx_k__max_chunks, sizeof(__pyx_k__max_chunks), 0, 0, 1, 1},
   {&__pyx_n_s__max_initial_size, __pyx_k__max_initial_size, sizeof(__pyx_k__max_initial_size), 0, 0, 1, 1},
   {&__pyx_n_s__max_length, __pyx_k__max_length, sizeof(__pyx_k__max_length), 0, 0, 1, 1},
@@ -60706,14 +66512,17 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
   {&__pyx_n_s__max_target_chunks, __pyx_k__max_target_chunks, sizeof(__pyx_k__max_target_chunks), 0, 0, 1, 1},
   {&__pyx_n_s__max_target_length, __pyx_k__max_target_length, sizeof(__pyx_k__max_target_length), 0, 0, 1, 1},
   {&__pyx_n_s__merge, __pyx_k__merge, sizeof(__pyx_k__merge), 0, 0, 1, 1},
+  {&__pyx_n_s__meta, __pyx_k__meta, sizeof(__pyx_k__meta), 0, 0, 1, 1},
   {&__pyx_n_s__min_dist, __pyx_k__min_dist, sizeof(__pyx_k__min_dist), 0, 0, 1, 1},
   {&__pyx_n_s__min_gap_size, __pyx_k__min_gap_size, sizeof(__pyx_k__min_gap_size), 0, 0, 1, 1},
-  {&__pyx_n_s__models, __pyx_k__models, sizeof(__pyx_k__models), 0, 0, 1, 1},
+  {&__pyx_n_s__name, __pyx_k__name, sizeof(__pyx_k__name), 0, 0, 1, 1},
+  {&__pyx_n_s__namedtuple, __pyx_k__namedtuple, sizeof(__pyx_k__namedtuple), 0, 0, 1, 1},
   {&__pyx_n_s__next_states, __pyx_k__next_states, sizeof(__pyx_k__next_states), 0, 0, 1, 1},
   {&__pyx_n_s__num_subpatterns, __pyx_k__num_subpatterns, sizeof(__pyx_k__num_subpatterns), 0, 0, 1, 1},
   {&__pyx_n_s__offset, __pyx_k__offset, sizeof(__pyx_k__offset), 0, 0, 1, 1},
   {&__pyx_n_s__open, __pyx_k__open, sizeof(__pyx_k__open), 0, 0, 1, 1},
   {&__pyx_n_s__pad, __pyx_k__pad, sizeof(__pyx_k__pad), 0, 0, 1, 1},
+  {&__pyx_n_s__paircount, __pyx_k__paircount, sizeof(__pyx_k__paircount), 0, 0, 1, 1},
   {&__pyx_n_s__partition, __pyx_k__partition, sizeof(__pyx_k__partition), 0, 0, 1, 1},
   {&__pyx_n_s__pathlen, __pyx_k__pathlen, sizeof(__pyx_k__pathlen), 0, 0, 1, 1},
   {&__pyx_n_s__pattern2phrase, __pyx_k__pattern2phrase, sizeof(__pyx_k__pattern2phrase), 0, 0, 1, 1},
@@ -60744,9 +66553,10 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
   {&__pyx_n_s__sample_size, __pyx_k__sample_size, sizeof(__pyx_k__sample_size), 0, 0, 1, 1},
   {&__pyx_n_s__sampler, __pyx_k__sampler, sizeof(__pyx_k__sampler), 0, 0, 1, 1},
   {&__pyx_n_s__sarray, __pyx_k__sarray, sizeof(__pyx_k__sarray), 0, 0, 1, 1},
+  {&__pyx_n_s__scorer, __pyx_k__scorer, sizeof(__pyx_k__scorer), 0, 0, 1, 1},
   {&__pyx_n_s__scores, __pyx_k__scores, sizeof(__pyx_k__scores), 0, 0, 1, 1},
   {&__pyx_n_s__seek, __pyx_k__seek, sizeof(__pyx_k__seek), 0, 0, 1, 1},
-  {&__pyx_n_s__setdefault, __pyx_k__setdefault, sizeof(__pyx_k__setdefault), 0, 0, 1, 1},
+  {&__pyx_n_s__set, __pyx_k__set, sizeof(__pyx_k__set), 0, 0, 1, 1},
   {&__pyx_n_s__shortest, __pyx_k__shortest, sizeof(__pyx_k__shortest), 0, 0, 1, 1},
   {&__pyx_n_s__side, __pyx_k__side, sizeof(__pyx_k__side), 0, 0, 1, 1},
   {&__pyx_n_s__size, __pyx_k__size, sizeof(__pyx_k__size), 0, 0, 1, 1},
@@ -60758,10 +66568,8 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
   {&__pyx_n_s__start, __pyx_k__start, sizeof(__pyx_k__start), 0, 0, 1, 1},
   {&__pyx_n_s__stats, __pyx_k__stats, sizeof(__pyx_k__stats), 0, 0, 1, 1},
   {&__pyx_n_s__stop, __pyx_k__stop, sizeof(__pyx_k__stop), 0, 0, 1, 1},
-  {&__pyx_n_s__string, __pyx_k__string, sizeof(__pyx_k__string), 0, 0, 1, 1},
   {&__pyx_n_s__suffix_link, __pyx_k__suffix_link, sizeof(__pyx_k__suffix_link), 0, 0, 1, 1},
-  {&__pyx_n_s__sym_fromstring, __pyx_k__sym_fromstring, sizeof(__pyx_k__sym_fromstring), 0, 0, 1, 1},
-  {&__pyx_n_s__terminal, __pyx_k__terminal, sizeof(__pyx_k__terminal), 0, 0, 1, 1},
+  {&__pyx_n_s__test_sentence, __pyx_k__test_sentence, sizeof(__pyx_k__test_sentence), 0, 0, 1, 1},
   {&__pyx_n_s__tight_phrases, __pyx_k__tight_phrases, sizeof(__pyx_k__tight_phrases), 0, 0, 1, 1},
   {&__pyx_n_s__toMap, __pyx_k__toMap, sizeof(__pyx_k__toMap), 0, 0, 1, 1},
   {&__pyx_n_s__train_min_gap_size, __pyx_k__train_min_gap_size, sizeof(__pyx_k__train_min_gap_size), 0, 0, 1, 1},
@@ -60770,10 +66578,12 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
   {&__pyx_n_s__use_collocations, __pyx_k__use_collocations, sizeof(__pyx_k__use_collocations), 0, 0, 1, 1},
   {&__pyx_n_s__use_index, __pyx_k__use_index, sizeof(__pyx_k__use_index), 0, 0, 1, 1},
   {&__pyx_n_s__use_sent_id, __pyx_k__use_sent_id, sizeof(__pyx_k__use_sent_id), 0, 0, 1, 1},
+  {&__pyx_n_s__value, __pyx_k__value, sizeof(__pyx_k__value), 0, 0, 1, 1},
   {&__pyx_n_s__w, __pyx_k__w, sizeof(__pyx_k__w), 0, 0, 1, 1},
   {&__pyx_n_s__warn, __pyx_k__warn, sizeof(__pyx_k__warn), 0, 0, 1, 1},
   {&__pyx_n_s__word, __pyx_k__word, sizeof(__pyx_k__word), 0, 0, 1, 1},
   {&__pyx_n_s__word_alignments, __pyx_k__word_alignments, sizeof(__pyx_k__word_alignments), 0, 0, 1, 1},
+  {&__pyx_n_s__word_ids, __pyx_k__word_ids, sizeof(__pyx_k__word_ids), 0, 0, 1, 1},
   {&__pyx_n_s__words, __pyx_k__words, sizeof(__pyx_k__words), 0, 0, 1, 1},
   {&__pyx_n_s__write, __pyx_k__write, sizeof(__pyx_k__write), 0, 0, 1, 1},
   {&__pyx_n_s__write_text, __pyx_k__write_text, sizeof(__pyx_k__write_text), 0, 0, 1, 1},
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":21
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":65
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":60
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":68
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":73
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":72
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":145
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":148
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":151
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":154
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/data_array.pxi":157
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":46
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":47
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":59
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":54
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":75
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":78
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":78
  *                     sent_num = sent_num + 1
  *                 f.write("%d-%d " % self.unlink(link))
  *             f.write("\n")             # <<<<<<<<<<<<<<
@@ -61112,7 +66922,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_36));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":71
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":71
  * 
  *     def write_text(self, char* filename):
  *         with open(filename, "w") as f:             # <<<<<<<<<<<<<<
@@ -61132,7 +66942,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(Py_None);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_37));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":92
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":92
  *             for link in self.links:
  *                 f.write("%d " % link)
  *             f.write("\n")             # <<<<<<<<<<<<<<
@@ -61146,7 +66956,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_38));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":95
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":95
  *             for i in self.sent_index:
  *                 f.write("%d " % i)
  *             f.write("\n")             # <<<<<<<<<<<<<<
@@ -61160,7 +66970,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_39));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/alignment.pxi":88
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/alignment.pxi":88
  * 
  *     def write_enhanced(self, char* filename):
  *         with open(filename, "w") as f:             # <<<<<<<<<<<<<<
@@ -61180,28 +66990,28 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(Py_None);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_40));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":302
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":297
  * 
  *             # Re-read file, placing words into buckets
  *             f.seek(0)             # <<<<<<<<<<<<<<
  *             for line in f:
  *                 (fword, eword, score1, score2) = line.split()
  */
-  __pyx_k_tuple_43 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_43)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 302; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_k_tuple_43 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_43)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 297; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   PyTuple_SET_ITEM(__pyx_k_tuple_43, 0, __pyx_int_0);
   __Pyx_GIVEREF(__pyx_int_0);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_43));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":278
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":273
  * 
  *         fcount = IntList()
  *         with gzip_or_text(filename) as f:             # <<<<<<<<<<<<<<
  *             # first loop merely establishes size of array objects
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-  __pyx_k_tuple_44 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_44)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 278; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_k_tuple_44 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_44)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __Pyx_INCREF(Py_None);
   PyTuple_SET_ITEM(__pyx_k_tuple_44, 0, Py_None);
@@ -61214,84 +67024,84 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(Py_None);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_44));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":344
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":339
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  *         if i > j:
  *             raise Exception("Sort error in CLex")             # <<<<<<<<<<<<<<
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-  __pyx_k_tuple_47 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_47)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_k_tuple_47 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_47)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 339; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_46));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_47));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":367
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":362
  *             for i in self.f_index:
  *                 f.write("%d " % i)
  *             f.write("\n")             # <<<<<<<<<<<<<<
  *             for i, s1, s2 in zip(self.e_index, self.col1, self.col2):
  *                 f.write("%d %f %f " % (i, s1, s2))
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-  __pyx_k_tuple_49 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_49)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_k_tuple_49 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_49)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_49));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":370
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":365
  *             for i, s1, s2 in zip(self.e_index, self.col1, self.col2):
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  *             f.write("\n")             # <<<<<<<<<<<<<<
  *             for i, w in enumerate(self.id2fword):
  *                 f.write("%d %s " % (i, w))
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-  __pyx_k_tuple_51 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_51)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_k_tuple_51 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_51)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_51));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":373
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":368
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  *                 f.write("%d %s " % (i, w))
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-  __pyx_k_tuple_53 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_53)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 373; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_k_tuple_53 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_53)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 368; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_53));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":376
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":371
  *             for i, w in enumerate(self.id2eword):
  *                 f.write("%d %s " % (i, w))
  *             f.write("\n")             # <<<<<<<<<<<<<<
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  * 
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-  __pyx_k_tuple_54 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_54)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 376; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_k_tuple_54 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_54)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_54));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":364
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":359
  * 
  *     def write_enhanced(self, char* filename):
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  *             for i in self.f_index:
  *                 f.write("%d " % i)
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-  __pyx_k_tuple_55 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_55)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_k_tuple_55 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_55)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __Pyx_INCREF(Py_None);
   PyTuple_SET_ITEM(__pyx_k_tuple_55, 0, Py_None);
@@ -61304,14 +67114,14 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(Py_None);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_55));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":409
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":404
  *         cdef i, N, e_id, f_id
  * 
  *         with open(filename, "w") as f:             # <<<<<<<<<<<<<<
  *             N = len(self.e_index)
  *             f_id = 0
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-  __pyx_k_tuple_57 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_57)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_k_tuple_57 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_57)) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 404; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   PyTuple_SET_ITEM(__pyx_k_tuple_57, 0, Py_None);
@@ -61324,7 +67134,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(Py_None);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_57));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":13
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":13
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  * 
  *         logger.info("Constructing LCP array")             # <<<<<<<<<<<<<<
@@ -61338,7 +67148,7 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_60));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_61));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/lcp.pxi":34
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/lcp.pxi":34
  *             if h > 0:
  *                 h = h-1
  *         logger.info("LCP array completed")             # <<<<<<<<<<<<<<
@@ -61352,154 +67162,154 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_62));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_63));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":297
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":297
  *         pattern_rank = {}
  * 
  *         logger.info("Precomputing frequent intersections")             # <<<<<<<<<<<<<<
  *         cdef float start_time = monitor_cpu()
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-  __pyx_k_tuple_73 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_73)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 297; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_k_tuple_73 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_73)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 297; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_72));
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_73));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":314
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":314
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  * 
  *         logger.info("    Computing inverted indexes...")             # <<<<<<<<<<<<<<
  *         N = len(data)
  *         for i from 0 <= i < N:
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-  __pyx_k_tuple_75 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_75)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_k_tuple_75 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_75)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   PyTuple_SET_ITEM(__pyx_k_tuple_75, 0, ((PyObject *)__pyx_kp_s_74));
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   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_75));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":329
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":329
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  * 
  *         logger.info("    Computing collocations...")             # <<<<<<<<<<<<<<
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  *         ptr1 = 0
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-  __pyx_k_tuple_77 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_77)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_k_tuple_77 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_77)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_77));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":393
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":393
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-  __pyx_k_tuple_79 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_79)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 393; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_k_tuple_79 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_79)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 393; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_79));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":400
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":400
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-  __pyx_k_tuple_80 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_80)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 400; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_k_tuple_80 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_80)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 400; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_80));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":407
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":407
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-  __pyx_k_tuple_81 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_81)) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 407; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_k_tuple_81 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_81)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 407; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_81));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/precomputation.pxi":409
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/precomputation.pxi":409
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+  __pyx_k_tuple_82 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_82)) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":103
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":94
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":202
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/suffix_array.pxi":193
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":205
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/suffix_array.pxi":198
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":92
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":300
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":318
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":1004
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@@ -61636,7 +67498,6 @@ PyMODINIT_FUNC PyInit__sa(void)
   PyObject *__pyx_t_1 = NULL;
   PyObject *__pyx_t_2 = NULL;
   PyObject *__pyx_t_3 = NULL;
-  int __pyx_t_4;
   __Pyx_RefNannyDeclarations
   #if CYTHON_REFNANNY
   __Pyx_RefNanny = __Pyx_RefNannyImportAPI("refnanny");
@@ -61669,16 +67530,12 @@ PyMODINIT_FUNC PyInit__sa(void)
   #endif
   /*--- Module creation code ---*/
   #if PY_MAJOR_VERSION < 3
-  __pyx_m = Py_InitModule4(__Pyx_NAMESTR("_sa"), __pyx_methods, 0, 0, PYTHON_API_VERSION);
+  __pyx_m = Py_InitModule4(__Pyx_NAMESTR("_sa"), __pyx_methods, 0, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m);
   #else
   __pyx_m = PyModule_Create(&__pyx_moduledef);
   #endif
-  if (!__pyx_m) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
-  #if PY_MAJOR_VERSION < 3
-  Py_INCREF(__pyx_m);
-  #endif
-  __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME));
-  if (!__pyx_b) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+  if (unlikely(!__pyx_m)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME)); if (unlikely(!__pyx_b)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   #if CYTHON_COMPILING_IN_PYPY
   Py_INCREF(__pyx_b);
   #endif
@@ -61694,6 +67551,7 @@ PyMODINIT_FUNC PyInit__sa(void)
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   /*--- Global init code ---*/
   __pyx_v_3_sa_ALPHABET = ((struct __pyx_obj_3_sa_Alphabet *)Py_None); Py_INCREF(Py_None);
+  __pyx_v_3_sa_FD = ((struct __pyx_obj_3_sa_StringMap *)Py_None); Py_INCREF(Py_None);
   /*--- Variable export code ---*/
   /*--- Function export code ---*/
   if (__Pyx_ExportFunction("sym_tostring", (void (*)(void))__pyx_f_3_sa_sym_tostring, "char *(int)") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -61701,16 +67559,6 @@ PyMODINIT_FUNC PyInit__sa(void)
   if (__Pyx_ExportFunction("sym_isvar", (void (*)(void))__pyx_f_3_sa_sym_isvar, "int (int)") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   if (__Pyx_ExportFunction("sym_getindex", (void (*)(void))__pyx_f_3_sa_sym_getindex, "int (int)") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   /*--- Type init code ---*/
-  __pyx_vtabptr_3_sa_Phrase = &__pyx_vtable_3_sa_Phrase;
-  __pyx_vtable_3_sa_Phrase.chunkpos = (int (*)(struct __pyx_obj_3_sa_Phrase *, int))__pyx_f_3_sa_6Phrase_chunkpos;
-  __pyx_vtable_3_sa_Phrase.chunklen = (int (*)(struct __pyx_obj_3_sa_Phrase *, int))__pyx_f_3_sa_6Phrase_chunklen;
-  if (PyType_Ready(&__pyx_type_3_sa_Phrase) < 0) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 4; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  if (__Pyx_SetVtable(__pyx_type_3_sa_Phrase.tp_dict, __pyx_vtabptr_3_sa_Phrase) < 0) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 4; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  if (__Pyx_SetAttrString(__pyx_m, "Phrase", (PyObject *)&__pyx_type_3_sa_Phrase) < 0) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 4; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_ptype_3_sa_Phrase = &__pyx_type_3_sa_Phrase;
-  if (PyType_Ready(&__pyx_type_3_sa_Rule) < 0) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  if (__Pyx_SetAttrString(__pyx_m, "Rule", (PyObject *)&__pyx_type_3_sa_Rule) < 0) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_ptype_3_sa_Rule = &__pyx_type_3_sa_Rule;
   __pyx_vtabptr_3_sa_FloatList = &__pyx_vtable_3_sa_FloatList;
   __pyx_vtable_3_sa_FloatList.set = (void (*)(struct __pyx_obj_3_sa_FloatList *, int, float))__pyx_f_3_sa_9FloatList_set;
   __pyx_vtable_3_sa_FloatList.write_handle = (void (*)(struct __pyx_obj_3_sa_FloatList *, FILE *))__pyx_f_3_sa_9FloatList_write_handle;
@@ -61731,6 +67579,19 @@ PyMODINIT_FUNC PyInit__sa(void)
   if (__Pyx_SetVtable(__pyx_type_3_sa_IntList.tp_dict, __pyx_vtabptr_3_sa_IntList) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   if (__Pyx_SetAttrString(__pyx_m, "IntList", (PyObject *)&__pyx_type_3_sa_IntList) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_3_sa_IntList = &__pyx_type_3_sa_IntList;
+  if (PyType_Ready(&__pyx_type_3_sa_FeatureVector) < 0) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (__Pyx_SetAttrString(__pyx_m, "FeatureVector", (PyObject *)&__pyx_type_3_sa_FeatureVector) < 0) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_3_sa_FeatureVector = &__pyx_type_3_sa_FeatureVector;
+  __pyx_vtabptr_3_sa_Phrase = &__pyx_vtable_3_sa_Phrase;
+  __pyx_vtable_3_sa_Phrase.chunkpos = (int (*)(struct __pyx_obj_3_sa_Phrase *, int))__pyx_f_3_sa_6Phrase_chunkpos;
+  __pyx_vtable_3_sa_Phrase.chunklen = (int (*)(struct __pyx_obj_3_sa_Phrase *, int))__pyx_f_3_sa_6Phrase_chunklen;
+  if (PyType_Ready(&__pyx_type_3_sa_Phrase) < 0) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 4; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (__Pyx_SetVtable(__pyx_type_3_sa_Phrase.tp_dict, __pyx_vtabptr_3_sa_Phrase) < 0) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 4; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (__Pyx_SetAttrString(__pyx_m, "Phrase", (PyObject *)&__pyx_type_3_sa_Phrase) < 0) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 4; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_3_sa_Phrase = &__pyx_type_3_sa_Phrase;
+  if (PyType_Ready(&__pyx_type_3_sa_Rule) < 0) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (__Pyx_SetAttrString(__pyx_m, "Rule", (PyObject *)&__pyx_type_3_sa_Rule) < 0) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_3_sa_Rule = &__pyx_type_3_sa_Rule;
   __pyx_vtabptr_3_sa_StringMap = &__pyx_vtable_3_sa_StringMap;
   __pyx_vtable_3_sa_StringMap.word = (char *(*)(struct __pyx_obj_3_sa_StringMap *, int))__pyx_f_3_sa_9StringMap_word;
   __pyx_vtable_3_sa_StringMap.index = (int (*)(struct __pyx_obj_3_sa_StringMap *, char *))__pyx_f_3_sa_9StringMap_index;
@@ -61802,44 +67663,44 @@ PyMODINIT_FUNC PyInit__sa(void)
   __pyx_vtabptr_3_sa_TrieMap = &__pyx_vtable_3_sa_TrieMap;
   __pyx_vtable_3_sa_TrieMap._insert = (struct __pyx_t_3_sa__Trie_Node *(*)(struct __pyx_obj_3_sa_TrieMap *, int *, int))__pyx_f_3_sa_7TrieMap__insert;
   __pyx_vtable_3_sa_TrieMap._contains = (struct __pyx_t_3_sa__Trie_Node *(*)(struct __pyx_obj_3_sa_TrieMap *, int *, int))__pyx_f_3_sa_7TrieMap__contains;
-  if (PyType_Ready(&__pyx_type_3_sa_TrieMap) < 0) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  if (__Pyx_SetVtable(__pyx_type_3_sa_TrieMap.tp_dict, __pyx_vtabptr_3_sa_TrieMap) < 0) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  if (__Pyx_SetAttrString(__pyx_m, "TrieMap", (PyObject *)&__pyx_type_3_sa_TrieMap) < 0) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_3_sa_TrieMap) < 0) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (__Pyx_SetVtable(__pyx_type_3_sa_TrieMap.tp_dict, __pyx_vtabptr_3_sa_TrieMap) < 0) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (__Pyx_SetAttrString(__pyx_m, "TrieMap", (PyObject *)&__pyx_type_3_sa_TrieMap) < 0) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_3_sa_TrieMap = &__pyx_type_3_sa_TrieMap;
   __pyx_vtabptr_3_sa_Precomputation = &__pyx_vtable_3_sa_Precomputation;
   __pyx_vtable_3_sa_Precomputation.read_map = (PyObject *(*)(struct __pyx_obj_3_sa_Precomputation *, FILE *))__pyx_f_3_sa_14Precomputation_read_map;
   __pyx_vtable_3_sa_Precomputation.write_map = (PyObject *(*)(struct __pyx_obj_3_sa_Precomputation *, PyObject *, FILE *))__pyx_f_3_sa_14Precomputation_write_map;
-  if (PyType_Ready(&__pyx_type_3_sa_Precomputation) < 0) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  if (__Pyx_SetVtable(__pyx_type_3_sa_Precomputation.tp_dict, __pyx_vtabptr_3_sa_Precomputation) < 0) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  if (__Pyx_SetAttrString(__pyx_m, "Precomputation", (PyObject *)&__pyx_type_3_sa_Precomputation) < 0) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_3_sa_Precomputation) < 0) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (__Pyx_SetVtable(__pyx_type_3_sa_Precomputation.tp_dict, __pyx_vtabptr_3_sa_Precomputation) < 0) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (__Pyx_SetAttrString(__pyx_m, "Precomputation", (PyObject *)&__pyx_type_3_sa_Precomputation) < 0) {__pyx_filename = __pyx_f[11]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_3_sa_Precomputation = &__pyx_type_3_sa_Precomputation;
   __pyx_vtabptr_3_sa_SuffixArray = &__pyx_vtable_3_sa_SuffixArray;
   __pyx_vtable_3_sa_SuffixArray.__pyx___search_high = (int (*)(struct __pyx_obj_3_sa_SuffixArray *, int, int, int, int))__pyx_f_3_sa_11SuffixArray___search_high;
   __pyx_vtable_3_sa_SuffixArray.__pyx___search_low = (int (*)(struct __pyx_obj_3_sa_SuffixArray *, int, int, int, int))__pyx_f_3_sa_11SuffixArray___search_low;
   __pyx_vtable_3_sa_SuffixArray.__pyx___get_range = (PyObject *(*)(struct __pyx_obj_3_sa_SuffixArray *, int, int, int, int, int))__pyx_f_3_sa_11SuffixArray___get_range;
   __pyx_vtable_3_sa_SuffixArray.__pyx___lookup_helper = (PyObject *(*)(struct __pyx_obj_3_sa_SuffixArray *, int, int, int, int))__pyx_f_3_sa_11SuffixArray___lookup_helper;
-  if (PyType_Ready(&__pyx_type_3_sa_SuffixArray) < 0) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  if (__Pyx_SetVtable(__pyx_type_3_sa_SuffixArray.tp_dict, __pyx_vtabptr_3_sa_SuffixArray) < 0) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  if (__Pyx_SetAttrString(__pyx_m, "SuffixArray", (PyObject *)&__pyx_type_3_sa_SuffixArray) < 0) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_3_sa_SuffixArray) < 0) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (__Pyx_SetVtable(__pyx_type_3_sa_SuffixArray.tp_dict, __pyx_vtabptr_3_sa_SuffixArray) < 0) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (__Pyx_SetAttrString(__pyx_m, "SuffixArray", (PyObject *)&__pyx_type_3_sa_SuffixArray) < 0) {__pyx_filename = __pyx_f[12]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_3_sa_SuffixArray = &__pyx_type_3_sa_SuffixArray;
-  if (PyType_Ready(&__pyx_type_3_sa_TrieNode) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 18; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  if (__Pyx_SetAttrString(__pyx_m, "TrieNode", (PyObject *)&__pyx_type_3_sa_TrieNode) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 18; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_3_sa_TrieNode) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (__Pyx_SetAttrString(__pyx_m, "TrieNode", (PyObject *)&__pyx_type_3_sa_TrieNode) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_3_sa_TrieNode = &__pyx_type_3_sa_TrieNode;
   __pyx_type_3_sa_ExtendedTrieNode.tp_base = __pyx_ptype_3_sa_TrieNode;
-  if (PyType_Ready(&__pyx_type_3_sa_ExtendedTrieNode) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 24; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  if (__Pyx_SetAttrString(__pyx_m, "ExtendedTrieNode", (PyObject *)&__pyx_type_3_sa_ExtendedTrieNode) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 24; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_3_sa_ExtendedTrieNode) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (__Pyx_SetAttrString(__pyx_m, "ExtendedTrieNode", (PyObject *)&__pyx_type_3_sa_ExtendedTrieNode) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_3_sa_ExtendedTrieNode = &__pyx_type_3_sa_ExtendedTrieNode;
-  if (PyType_Ready(&__pyx_type_3_sa_TrieTable) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  if (__Pyx_SetAttrString(__pyx_m, "TrieTable", (PyObject *)&__pyx_type_3_sa_TrieTable) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_3_sa_TrieTable) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (__Pyx_SetAttrString(__pyx_m, "TrieTable", (PyObject *)&__pyx_type_3_sa_TrieTable) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_3_sa_TrieTable = &__pyx_type_3_sa_TrieTable;
   __pyx_vtabptr_3_sa_PhraseLocation = &__pyx_vtable_3_sa_PhraseLocation;
   __pyx_vtable_3_sa_PhraseLocation.contains = (int (*)(struct __pyx_obj_3_sa_PhraseLocation *, int))__pyx_f_3_sa_14PhraseLocation_contains;
-  if (PyType_Ready(&__pyx_type_3_sa_PhraseLocation) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  if (__Pyx_SetVtable(__pyx_type_3_sa_PhraseLocation.tp_dict, __pyx_vtabptr_3_sa_PhraseLocation) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  if (__Pyx_SetAttrString(__pyx_m, "PhraseLocation", (PyObject *)&__pyx_type_3_sa_PhraseLocation) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_3_sa_PhraseLocation) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (__Pyx_SetVtable(__pyx_type_3_sa_PhraseLocation.tp_dict, __pyx_vtabptr_3_sa_PhraseLocation) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (__Pyx_SetAttrString(__pyx_m, "PhraseLocation", (PyObject *)&__pyx_type_3_sa_PhraseLocation) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_3_sa_PhraseLocation = &__pyx_type_3_sa_PhraseLocation;
-  if (PyType_Ready(&__pyx_type_3_sa_Sampler) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  if (__Pyx_SetAttrString(__pyx_m, "Sampler", (PyObject *)&__pyx_type_3_sa_Sampler) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_3_sa_Sampler) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 96; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (__Pyx_SetAttrString(__pyx_m, "Sampler", (PyObject *)&__pyx_type_3_sa_Sampler) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 96; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_3_sa_Sampler = &__pyx_type_3_sa_Sampler;
   __pyx_vtabptr_3_sa_HieroCachingRuleFactory = &__pyx_vtable_3_sa_HieroCachingRuleFactory;
   __pyx_vtable_3_sa_HieroCachingRuleFactory.set_idmap = (PyObject *(*)(struct __pyx_obj_3_sa_HieroCachingRuleFactory *, struct __pyx_obj_3_sa_DataArray *))__pyx_f_3_sa_23HieroCachingRuleFactory_set_idmap;
@@ -61855,22 +67716,56 @@ PyMODINIT_FUNC PyInit__sa(void)
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   __pyx_vtable_3_sa_HieroCachingRuleFactory.int_arr_extend = (int *(*)(struct __pyx_obj_3_sa_HieroCachingRuleFactory *, int *, int *, int *, int))__pyx_f_3_sa_23HieroCachingRuleFactory_int_arr_extend;
   __pyx_vtable_3_sa_HieroCachingRuleFactory.extract_phrases = (PyObject *(*)(struct __pyx_obj_3_sa_HieroCachingRuleFactory *, int, int, int *, int *, int *, int, int, int, int *, int *, int *, int, int, int))__pyx_f_3_sa_23HieroCachingRuleFactory_extract_phrases;
-  __pyx_vtable_3_sa_HieroCachingRuleFactory.create_alignments = (PyObject *(*)(struct __pyx_obj_3_sa_HieroCachingRuleFactory *, int *, int, PyObject *, PyObject *))__pyx_f_3_sa_23HieroCachingRuleFactory_create_alignments;
+  __pyx_vtable_3_sa_HieroCachingRuleFactory.create_alignments = (struct __pyx_obj_3_sa_IntList *(*)(struct __pyx_obj_3_sa_HieroCachingRuleFactory *, int *, int, PyObject *, PyObject *))__pyx_f_3_sa_23HieroCachingRuleFactory_create_alignments;
   __pyx_vtable_3_sa_HieroCachingRuleFactory.extract = (PyObject *(*)(struct __pyx_obj_3_sa_HieroCachingRuleFactory *, struct __pyx_obj_3_sa_Phrase *, struct __pyx_t_3_sa_Matching *, int *, int))__pyx_f_3_sa_23HieroCachingRuleFactory_extract;
-  if (PyType_Ready(&__pyx_type_3_sa_HieroCachingRuleFactory) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  if (__Pyx_SetVtable(__pyx_type_3_sa_HieroCachingRuleFactory.tp_dict, __pyx_vtabptr_3_sa_HieroCachingRuleFactory) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  if (__Pyx_SetAttrString(__pyx_m, "HieroCachingRuleFactory", (PyObject *)&__pyx_type_3_sa_HieroCachingRuleFactory) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_3_sa_HieroCachingRuleFactory) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (__Pyx_SetVtable(__pyx_type_3_sa_HieroCachingRuleFactory.tp_dict, __pyx_vtabptr_3_sa_HieroCachingRuleFactory) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (__Pyx_SetAttrString(__pyx_m, "HieroCachingRuleFactory", (PyObject *)&__pyx_type_3_sa_HieroCachingRuleFactory) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  if (PyType_Ready(&__pyx_type_3_sa___pyx_scope_struct__read_bitext) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  if (PyType_Ready(&__pyx_type_3_sa___pyx_scope_struct_1_genexpr) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 73; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_ptype_3_sa___pyx_scope_struct_1_genexpr = &__pyx_type_3_sa___pyx_scope_struct_1_genexpr;
-  if (PyType_Ready(&__pyx_type_3_sa___pyx_scope_struct_2_compute_stats) < 0) {__pyx_filename = __pyx_f[9]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_ptype_3_sa___pyx_scope_struct_2_compute_stats = &__pyx_type_3_sa___pyx_scope_struct_2_compute_stats;
-  if (PyType_Ready(&__pyx_type_3_sa___pyx_scope_struct_3___iter__) < 0) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_ptype_3_sa___pyx_scope_struct_3___iter__ = &__pyx_type_3_sa___pyx_scope_struct_3___iter__;
-  if (PyType_Ready(&__pyx_type_3_sa___pyx_scope_struct_4_input) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 919; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_ptype_3_sa___pyx_scope_struct_4_input = &__pyx_type_3_sa___pyx_scope_struct_4_input;
+  __pyx_vtabptr_3_sa_Scorer = &__pyx_vtable_3_sa_Scorer;
+  __pyx_vtable_3_sa_Scorer.score = (struct __pyx_obj_3_sa_FeatureVector *(*)(struct __pyx_obj_3_sa_Scorer *, PyObject *))__pyx_f_3_sa_6Scorer_score;
+  if (PyType_Ready(&__pyx_type_3_sa_Scorer) < 0) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (__Pyx_SetVtable(__pyx_type_3_sa_Scorer.tp_dict, __pyx_vtabptr_3_sa_Scorer) < 0) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (__Pyx_SetAttrString(__pyx_m, "Scorer", (PyObject *)&__pyx_type_3_sa_Scorer) < 0) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_3_sa_Scorer = &__pyx_type_3_sa_Scorer;
+  if (PyType_Ready(&__pyx_type_3_sa___pyx_scope_struct____iter__) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_3_sa___pyx_scope_struct____iter__ = &__pyx_type_3_sa___pyx_scope_struct____iter__;
+  if (PyType_Ready(&__pyx_type_3_sa___pyx_scope_struct_1_read_bitext) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_3_sa___pyx_scope_struct_1_read_bitext = &__pyx_type_3_sa___pyx_scope_struct_1_read_bitext;
+  if (PyType_Ready(&__pyx_type_3_sa___pyx_scope_struct_2_genexpr) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_3_sa___pyx_scope_struct_2_genexpr = &__pyx_type_3_sa___pyx_scope_struct_2_genexpr;
+  if (PyType_Ready(&__pyx_type_3_sa___pyx_scope_struct_3_compute_stats) < 0) {__pyx_filename = __pyx_f[9]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_3_sa___pyx_scope_struct_3_compute_stats = &__pyx_type_3_sa___pyx_scope_struct_3_compute_stats;
+  if (PyType_Ready(&__pyx_type_3_sa___pyx_scope_struct_4_make_lattice) < 0) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_3_sa___pyx_scope_struct_4_make_lattice = &__pyx_type_3_sa___pyx_scope_struct_4_make_lattice;
+  if (PyType_Ready(&__pyx_type_3_sa___pyx_scope_struct_5_genexpr) < 0) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 108; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_3_sa___pyx_scope_struct_5_genexpr = &__pyx_type_3_sa___pyx_scope_struct_5_genexpr;
+  if (PyType_Ready(&__pyx_type_3_sa___pyx_scope_struct_6_genexpr) < 0) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_3_sa___pyx_scope_struct_6_genexpr = &__pyx_type_3_sa___pyx_scope_struct_6_genexpr;
+  if (PyType_Ready(&__pyx_type_3_sa___pyx_scope_struct_7_decode_lattice) < 0) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_3_sa___pyx_scope_struct_7_decode_lattice = &__pyx_type_3_sa___pyx_scope_struct_7_decode_lattice;
+  if (PyType_Ready(&__pyx_type_3_sa___pyx_scope_struct_8_genexpr) < 0) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_3_sa___pyx_scope_struct_8_genexpr = &__pyx_type_3_sa___pyx_scope_struct_8_genexpr;
+  if (PyType_Ready(&__pyx_type_3_sa___pyx_scope_struct_9_decode_sentence) < 0) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 115; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_3_sa___pyx_scope_struct_9_decode_sentence = &__pyx_type_3_sa___pyx_scope_struct_9_decode_sentence;
+  if (PyType_Ready(&__pyx_type_3_sa___pyx_scope_struct_10_genexpr) < 0) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_3_sa___pyx_scope_struct_10_genexpr = &__pyx_type_3_sa___pyx_scope_struct_10_genexpr;
+  if (PyType_Ready(&__pyx_type_3_sa___pyx_scope_struct_11___iter__) < 0) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_3_sa___pyx_scope_struct_11___iter__ = &__pyx_type_3_sa___pyx_scope_struct_11___iter__;
+  if (PyType_Ready(&__pyx_type_3_sa___pyx_scope_struct_12___str__) < 0) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_3_sa___pyx_scope_struct_12___str__ = &__pyx_type_3_sa___pyx_scope_struct_12___str__;
+  if (PyType_Ready(&__pyx_type_3_sa___pyx_scope_struct_13_genexpr) < 0) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_3_sa___pyx_scope_struct_13_genexpr = &__pyx_type_3_sa___pyx_scope_struct_13_genexpr;
+  if (PyType_Ready(&__pyx_type_3_sa___pyx_scope_struct_14_alignments) < 0) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 190; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_3_sa___pyx_scope_struct_14_alignments = &__pyx_type_3_sa___pyx_scope_struct_14_alignments;
+  if (PyType_Ready(&__pyx_type_3_sa___pyx_scope_struct_15_input) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 939; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_3_sa___pyx_scope_struct_15_input = &__pyx_type_3_sa___pyx_scope_struct_15_input;
+  if (PyType_Ready(&__pyx_type_3_sa___pyx_scope_struct_16___iter__) < 0) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_3_sa___pyx_scope_struct_16___iter__ = &__pyx_type_3_sa___pyx_scope_struct_16___iter__;
+  if (PyType_Ready(&__pyx_type_3_sa___pyx_scope_struct_17___str__) < 0) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 20; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_3_sa___pyx_scope_struct_17___str__ = &__pyx_type_3_sa___pyx_scope_struct_17___str__;
+  if (PyType_Ready(&__pyx_type_3_sa___pyx_scope_struct_18_genexpr) < 0) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_3_sa___pyx_scope_struct_18_genexpr = &__pyx_type_3_sa___pyx_scope_struct_18_genexpr;
   /*--- Type import code ---*/
   /*--- Variable import code ---*/
   /*--- Function import code ---*/
@@ -61933,13 +67828,13 @@ PyMODINIT_FUNC PyInit__sa(void)
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   __Pyx_GOTREF(__pyx_t_2);
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
-  __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_138), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_139), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/bilex.pxi":54
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/bilex.pxi":54
  *     cdef id2eword, id2fword, eword2id, fword2id
  * 
  *     def __cinit__(self, from_text=None, from_data=False, from_binary=None,             # <<<<<<<<<<<<<<
@@ -61952,7 +67847,7 @@ PyMODINIT_FUNC PyInit__sa(void)
   __Pyx_GIVEREF(__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":17
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":17
  * from libc.string cimport memset
  * 
  * cdef int MIN_BOTTOM_SIZE = 32             # <<<<<<<<<<<<<<
@@ -61961,7 +67856,7 @@ PyMODINIT_FUNC PyInit__sa(void)
  */
   __pyx_v_3_sa_MIN_BOTTOM_SIZE = 32;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":18
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":18
  * 
  * cdef int MIN_BOTTOM_SIZE = 32
  * cdef int MIN_BOTTOM_BITS = 5             # <<<<<<<<<<<<<<
@@ -61970,7 +67865,7 @@ PyMODINIT_FUNC PyInit__sa(void)
  */
   __pyx_v_3_sa_MIN_BOTTOM_BITS = 5;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/veb.pxi":28
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/veb.pxi":28
  *         LOWER_MASK[i] = mask
  * 
  * _init_lower_mask()             # <<<<<<<<<<<<<<
@@ -61979,7 +67874,7 @@ PyMODINIT_FUNC PyInit__sa(void)
  */
   __pyx_f_3_sa__init_lower_mask();
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":4
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":4
  * from libc.stdlib cimport malloc, realloc, strtol
  * 
  * cdef int INDEX_SHIFT = 3             # <<<<<<<<<<<<<<
@@ -61988,7 +67883,7 @@ PyMODINIT_FUNC PyInit__sa(void)
  */
   __pyx_v_3_sa_INDEX_SHIFT = 3;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":5
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":5
  * 
  * cdef int INDEX_SHIFT = 3
  * cdef int INDEX_MASK = (1<<INDEX_SHIFT)-1             # <<<<<<<<<<<<<<
@@ -61997,7 +67892,7 @@ PyMODINIT_FUNC PyInit__sa(void)
  */
   __pyx_v_3_sa_INDEX_MASK = ((1 << __pyx_v_3_sa_INDEX_SHIFT) - 1);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":87
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":87
  *             return self.terminals.index(s)
  * 
  * cdef Alphabet ALPHABET = Alphabet()             # <<<<<<<<<<<<<<
@@ -62012,39 +67907,192 @@ PyMODINIT_FUNC PyInit__sa(void)
   __pyx_v_3_sa_ALPHABET = ((struct __pyx_obj_3_sa_Alphabet *)__pyx_t_1);
   __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/sym.pxi":104
- *     return ALPHABET.setindex(sym, id)
- * 
- * def sym_fromstring(char* string, bint terminal):             # <<<<<<<<<<<<<<
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":107
  *     return ALPHABET.fromstring(string, terminal)
+ * 
+ * def make_lattice(words):             # <<<<<<<<<<<<<<
+ *     word_ids = (sym_fromstring(word, True) for word in words)
+ *     return tuple(((word, None, 1), ) for word in word_ids)
+ */
+  __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3_sa_3make_lattice, NULL, __pyx_n_s___sa); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(__pyx_t_1);
+  if (PyObject_SetAttr(__pyx_m, __pyx_n_s__make_lattice, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":111
+ *     return tuple(((word, None, 1), ) for word in word_ids)
+ * 
+ * def decode_lattice(lattice):             # <<<<<<<<<<<<<<
+ *     return tuple((sym_tostring(sym), weight, dist) for (sym, weight, dist) in arc
+ *             for arc in node for node in lattice)
  */
-  __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3_sa_3sym_fromstring, NULL, __pyx_n_s___sa); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 104; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3_sa_5decode_lattice, NULL, __pyx_n_s___sa); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_1);
-  if (PyObject_SetAttr(__pyx_m, __pyx_n_s__sym_fromstring, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 104; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyObject_SetAttr(__pyx_m, __pyx_n_s__decode_lattice, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":5
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/sym.pxi":115
+ *             for arc in node for node in lattice)
+ * 
+ * def decode_sentence(lattice):             # <<<<<<<<<<<<<<
+ *     return tuple(sym_tostring(sym) for ((sym, _, _),) in lattice)
+ */
+  __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3_sa_7decode_sentence, NULL, __pyx_n_s___sa); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 115; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(__pyx_t_1);
+  if (PyObject_SetAttr(__pyx_m, __pyx_n_s__decode_sentence, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 115; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":5
  * # Much faster than the Python numbers reported there.
  * # Note to reader: this code is closer to C than Python
  * import gc             # <<<<<<<<<<<<<<
+ * import itertools
  * 
- * from libc.stdlib cimport malloc, realloc, free
  */
   __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__gc), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 5; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":6
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+ * FeatureContext = namedtuple('FeatureContext',
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+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":14
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+ *      'ephrase',
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+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":15
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+ * FeatureContext = namedtuple('FeatureContext',
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+ *      'paircount',
+ */
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  * cdef int BAEZA_YATES = 2
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":12
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":30
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":13
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":31
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":16
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/rulefactory.pxi":34
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-  __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/rulefactory.pxi":39
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-  __pyx_k_99 = __pyx_t_2;
-  __Pyx_GIVEREF(__pyx_t_2);
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+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/features.pxi":3
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+
+  /* "/home/hltcoe/alopez/dev/cdec/python/src/sa/features.pxi":4
+ * 
+ * INITIAL_CAPACITY = 7 # default number of features
+ * INCREMENT = INITIAL_CAPACITY # double size             # <<<<<<<<<<<<<<
+ * 
+ * cdef class FeatureVector:
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   /* "_sa.pyx":1
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-  __Pyx_GOTREF(((PyObject *)__pyx_t_2));
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-  __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
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+  __Pyx_GOTREF(((PyObject *)__pyx_t_1));
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+  __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
   goto __pyx_L0;
   __pyx_L1_error:;
   __Pyx_XDECREF(__pyx_t_1);
@@ -62172,7 +68236,7 @@ static void __Pyx_RaiseDoubleKeywordsError(
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         #else
         "%s() got multiple values for keyword argument '%s'", func_name,
-        PyString_AS_STRING(kw_name));
+        PyString_AsString(kw_name));
         #endif
 }
 
@@ -62193,48 +68257,72 @@ static int __Pyx_ParseOptionalKeywords(
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         if (*name) {
             values[name-argnames] = value;
-        } else {
-            #if PY_MAJOR_VERSION < 3
-            if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) {
-            #else
-            if (unlikely(!PyUnicode_Check(key))) {
-            #endif
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-            } else {
-                for (name = first_kw_arg; *name; name++) {
-                    #if PY_MAJOR_VERSION >= 3
-                    if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
-                        PyUnicode_Compare(**name, key) == 0) break;
-                    #else
-                    if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
-                        _PyString_Eq(**name, key)) break;
-                    #endif
-                }
-                if (*name) {
+            continue;
+        }
+        name = first_kw_arg;
+        #if PY_MAJOR_VERSION < 3
+        if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) {
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                     values[name-argnames] = value;
-                } else {
-                    for (name=argnames; name != first_kw_arg; name++) {
-                        if (**name == key) goto arg_passed_twice;
-                        #if PY_MAJOR_VERSION >= 3
-                        if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
-                            PyUnicode_Compare(**name, key) == 0) goto arg_passed_twice;
-                        #else
-                        if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
-                            _PyString_Eq(**name, key)) goto arg_passed_twice;
-                        #endif
-                    }
-                    if (kwds2) {
-                        if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
-                    } else {
-                        goto invalid_keyword;
+                    break;
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+            }
+            if (*name) continue;
+            else {
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+                while (argname != first_kw_arg) {
+                    if ((**argname == key) || (
+                            (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key))
+                             && _PyString_Eq(**argname, key))) {
+                        goto arg_passed_twice;
                     }
+                    argname++;
                 }
             }
+        } else
+        #endif
+        if (likely(PyUnicode_Check(key))) {
+            while (*name) {
+                int cmp = (**name == key) ? 0 :
+                #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
+                    (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
+                #endif
+                    PyUnicode_Compare(**name, key);
+                if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
+                if (cmp == 0) {
+                    values[name-argnames] = value;
+                    break;
+                }
+                name++;
+            }
+            if (*name) continue;
+            else {
+                PyObject*** argname = argnames;
+                while (argname != first_kw_arg) {
+                    int cmp = (**argname == key) ? 0 :
+                    #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
+                        (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
+                    #endif
+                        PyUnicode_Compare(**argname, key);
+                    if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
+                    if (cmp == 0) goto arg_passed_twice;
+                    argname++;
+                }
+            }
+        } else
+            goto invalid_keyword_type;
+        if (kwds2) {
+            if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
+        } else {
+            goto invalid_keyword;
         }
     }
     return 0;
 arg_passed_twice:
-    __Pyx_RaiseDoubleKeywordsError(function_name, **name);
+    __Pyx_RaiseDoubleKeywordsError(function_name, key);
     goto bad;
 invalid_keyword_type:
     PyErr_Format(PyExc_TypeError,
@@ -62273,7 +68361,7 @@ static void __Pyx_RaiseArgtupleInvalid(
         more_or_less = "exactly";
     }
     PyErr_Format(PyExc_TypeError,
-                 "%s() takes %s %" PY_FORMAT_SIZE_T "d positional argument%s (%" PY_FORMAT_SIZE_T "d given)",
+                 "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" CYTHON_FORMAT_SSIZE_T "d given)",
                  func_name, more_or_less, num_expected,
                  (num_expected == 1) ? "" : "s", num_found);
 }
@@ -62313,33 +68401,38 @@ static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyOb
 static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
                         CYTHON_UNUSED PyObject *cause) {
     Py_XINCREF(type);
-    Py_XINCREF(value);
-    Py_XINCREF(tb);
-    if (tb == Py_None) {
-        Py_DECREF(tb);
-        tb = 0;
-    }
-    else if (tb != NULL && !PyTraceBack_Check(tb)) {
-        PyErr_SetString(PyExc_TypeError,
-            "raise: arg 3 must be a traceback or None");
-        goto raise_error;
-    }
-    if (value == NULL) {
-        value = Py_None;
+    if (!value || value == Py_None)
+        value = NULL;
+    else
         Py_INCREF(value);
+    if (!tb || tb == Py_None)
+        tb = NULL;
+    else {
+        Py_INCREF(tb);
+        if (!PyTraceBack_Check(tb)) {
+            PyErr_SetString(PyExc_TypeError,
+                "raise: arg 3 must be a traceback or None");
+            goto raise_error;
+        }
     }
     #if PY_VERSION_HEX < 0x02050000
-    if (!PyClass_Check(type))
+    if (PyClass_Check(type)) {
     #else
-    if (!PyType_Check(type))
+    if (PyType_Check(type)) {
     #endif
-    {
-        if (value != Py_None) {
+#if CYTHON_COMPILING_IN_PYPY
+        if (!value) {
+            Py_INCREF(Py_None);
+            value = Py_None;
+        }
+#endif
+        PyErr_NormalizeException(&type, &value, &tb);
+    } else {
+        if (value) {
             PyErr_SetString(PyExc_TypeError,
                 "instance exception may not have a separate value");
             goto raise_error;
         }
-        Py_DECREF(value);
         value = type;
         #if PY_VERSION_HEX < 0x02050000
             if (PyInstance_Check(type)) {
@@ -62372,6 +68465,7 @@ raise_error:
 }
 #else /* Python 3+ */
 static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
+    PyObject* owned_instance = NULL;
     if (tb == Py_None) {
         tb = 0;
     } else if (tb && !PyTraceBack_Check(tb)) {
@@ -62389,12 +68483,36 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
         }
         value = type;
         type = (PyObject*) Py_TYPE(value);
-    } else if (!PyExceptionClass_Check(type)) {
+    } else if (PyExceptionClass_Check(type)) {
+        PyObject *args;
+        if (!value)
+            args = PyTuple_New(0);
+        else if (PyTuple_Check(value)) {
+            Py_INCREF(value);
+            args = value;
+        }
+        else
+            args = PyTuple_Pack(1, value);
+        if (!args)
+            goto bad;
+        owned_instance = PyEval_CallObject(type, args);
+        Py_DECREF(args);
+        if (!owned_instance)
+            goto bad;
+        value = owned_instance;
+        if (!PyExceptionInstance_Check(value)) {
+            PyErr_Format(PyExc_TypeError,
+                         "calling %R should have returned an instance of "
+                         "BaseException, not %R",
+                         type, Py_TYPE(value));
+            goto bad;
+        }
+    } else {
         PyErr_SetString(PyExc_TypeError,
             "raise: exception class must be a subclass of BaseException");
         goto bad;
     }
-    if (cause) {
+    if (cause && cause != Py_None) {
         PyObject *fixed_cause;
         if (PyExceptionClass_Check(cause)) {
             fixed_cause = PyObject_CallObject(cause, NULL);
@@ -62411,9 +68529,6 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
                             "BaseException");
             goto bad;
         }
-        if (!value) {
-            value = PyObject_CallObject(type, NULL);
-        }
         PyException_SetCause(value, fixed_cause);
     }
     PyErr_SetObject(type, value);
@@ -62427,6 +68542,7 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
         }
     }
 bad:
+    Py_XDECREF(owned_instance);
     return;
 }
 #endif
@@ -62458,10 +68574,9 @@ static CYTHON_INLINE int __Pyx_CheckKeywordStrings(
     while (PyDict_Next(kwdict, &pos, &key, 0)) {
         #if PY_MAJOR_VERSION < 3
         if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key)))
-        #else
-        if (unlikely(!PyUnicode_Check(key)))
         #endif
-            goto invalid_keyword_type;
+            if (unlikely(!PyUnicode_Check(key)))
+                goto invalid_keyword_type;
     }
     if ((!kw_allowed) && unlikely(key))
         goto invalid_keyword;
@@ -62559,12 +68674,12 @@ static CYTHON_INLINE long __Pyx_mod_long(long a, long b) {
 
 static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
     PyErr_Format(PyExc_ValueError,
-                 "too many values to unpack (expected %" PY_FORMAT_SIZE_T "d)", expected);
+                 "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected);
 }
 
 static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
     PyErr_Format(PyExc_ValueError,
-                 "need more than %" PY_FORMAT_SIZE_T "d value%s to unpack",
+                 "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack",
                  index, (index == 1) ? "" : "s");
 }
 
@@ -62929,84 +69044,422 @@ bad:
     return module;
 }
 
-static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) {
-#if CYTHON_COMPILING_IN_PYPY
-    return PyObject_RichCompareBool(s1, s2, equals);
+static CYTHON_INLINE void __Pyx_RaiseImportError(PyObject *name) {
+#if PY_MAJOR_VERSION < 3
+    PyErr_Format(PyExc_ImportError, "cannot import name %.230s",
+                 PyString_AsString(name));
 #else
-    if (s1 == s2) {
-        return (equals == Py_EQ);
-    } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) {
-        if (PyBytes_GET_SIZE(s1) != PyBytes_GET_SIZE(s2)) {
-            return (equals == Py_NE);
-        } else if (PyBytes_GET_SIZE(s1) == 1) {
-            if (equals == Py_EQ)
-                return (PyBytes_AS_STRING(s1)[0] == PyBytes_AS_STRING(s2)[0]);
-            else
-                return (PyBytes_AS_STRING(s1)[0] != PyBytes_AS_STRING(s2)[0]);
-        } else {
-            int result = memcmp(PyBytes_AS_STRING(s1), PyBytes_AS_STRING(s2), (size_t)PyBytes_GET_SIZE(s1));
-            return (equals == Py_EQ) ? (result == 0) : (result != 0);
+    PyErr_Format(PyExc_ImportError, "cannot import name %S", name);
+#endif
+}
+
+static PyObject *
+__Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *closure)
+{
+    if (op->func_doc == NULL && op->func.m_ml->ml_doc) {
+#if PY_MAJOR_VERSION >= 3
+        op->func_doc = PyUnicode_FromString(op->func.m_ml->ml_doc);
+#else
+        op->func_doc = PyString_FromString(op->func.m_ml->ml_doc);
+#endif
+    }
+    if (op->func_doc == 0) {
+        Py_INCREF(Py_None);
+        return Py_None;
+    }
+    Py_INCREF(op->func_doc);
+    return op->func_doc;
+}
+static int
+__Pyx_CyFunction_set_doc(__pyx_CyFunctionObject *op, PyObject *value)
+{
+    PyObject *tmp = op->func_doc;
+    if (value == NULL)
+        op->func_doc = Py_None; /* Mark as deleted */
+    else
+        op->func_doc = value;
+    Py_INCREF(op->func_doc);
+    Py_XDECREF(tmp);
+    return 0;
+}
+static PyObject *
+__Pyx_CyFunction_get_name(__pyx_CyFunctionObject *op)
+{
+    if (op->func_name == NULL) {
+#if PY_MAJOR_VERSION >= 3
+        op->func_name = PyUnicode_InternFromString(op->func.m_ml->ml_name);
+#else
+        op->func_name = PyString_InternFromString(op->func.m_ml->ml_name);
+#endif
+    }
+    Py_INCREF(op->func_name);
+    return op->func_name;
+}
+static int
+__Pyx_CyFunction_set_name(__pyx_CyFunctionObject *op, PyObject *value)
+{
+    PyObject *tmp;
+#if PY_MAJOR_VERSION >= 3
+    if (value == NULL || !PyUnicode_Check(value)) {
+#else
+    if (value == NULL || !PyString_Check(value)) {
+#endif
+        PyErr_SetString(PyExc_TypeError,
+                        "__name__ must be set to a string object");
+        return -1;
+    }
+    tmp = op->func_name;
+    Py_INCREF(value);
+    op->func_name = value;
+    Py_XDECREF(tmp);
+    return 0;
+}
+static PyObject *
+__Pyx_CyFunction_get_self(__pyx_CyFunctionObject *m, CYTHON_UNUSED void *closure)
+{
+    PyObject *self;
+    self = m->func_closure;
+    if (self == NULL)
+        self = Py_None;
+    Py_INCREF(self);
+    return self;
+}
+static PyObject *
+__Pyx_CyFunction_get_dict(__pyx_CyFunctionObject *op)
+{
+    if (op->func_dict == NULL) {
+        op->func_dict = PyDict_New();
+        if (op->func_dict == NULL)
+            return NULL;
+    }
+    Py_INCREF(op->func_dict);
+    return op->func_dict;
+}
+static int
+__Pyx_CyFunction_set_dict(__pyx_CyFunctionObject *op, PyObject *value)
+{
+    PyObject *tmp;
+    if (value == NULL) {
+        PyErr_SetString(PyExc_TypeError,
+               "function's dictionary may not be deleted");
+        return -1;
+    }
+    if (!PyDict_Check(value)) {
+        PyErr_SetString(PyExc_TypeError,
+               "setting function's dictionary to a non-dict");
+        return -1;
+    }
+    tmp = op->func_dict;
+    Py_INCREF(value);
+    op->func_dict = value;
+    Py_XDECREF(tmp);
+    return 0;
+}
+static PyObject *
+__Pyx_CyFunction_get_globals(CYTHON_UNUSED __pyx_CyFunctionObject *op)
+{
+    PyObject* dict = PyModule_GetDict(__pyx_m);
+    Py_XINCREF(dict);
+    return dict;
+}
+static PyObject *
+__Pyx_CyFunction_get_closure(CYTHON_UNUSED __pyx_CyFunctionObject *op)
+{
+    Py_INCREF(Py_None);
+    return Py_None;
+}
+static PyObject *
+__Pyx_CyFunction_get_code(__pyx_CyFunctionObject *op)
+{
+    PyObject* result = (op->func_code) ? op->func_code : Py_None;
+    Py_INCREF(result);
+    return result;
+}
+static PyObject *
+__Pyx_CyFunction_get_defaults(__pyx_CyFunctionObject *op)
+{
+    if (op->defaults_tuple) {
+        Py_INCREF(op->defaults_tuple);
+        return op->defaults_tuple;
+    }
+    if (op->defaults_getter) {
+        PyObject *res = op->defaults_getter((PyObject *) op);
+        if (res) {
+            Py_INCREF(res);
+            op->defaults_tuple = res;
         }
-    } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) {
-        return (equals == Py_NE);
-    } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) {
-        return (equals == Py_NE);
-    } else {
-        int result;
-        PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
-        if (!py_result)
-            return -1;
-        result = __Pyx_PyObject_IsTrue(py_result);
-        Py_DECREF(py_result);
-        return result;
+        return res;
     }
+    Py_INCREF(Py_None);
+    return Py_None;
+}
+static PyGetSetDef __pyx_CyFunction_getsets[] = {
+    {(char *) "func_doc", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0},
+    {(char *) "__doc__",  (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0},
+    {(char *) "func_name", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0},
+    {(char *) "__name__", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0},
+    {(char *) "__self__", (getter)__Pyx_CyFunction_get_self, 0, 0, 0},
+    {(char *) "func_dict", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0},
+    {(char *) "__dict__", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0},
+    {(char *) "func_globals", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0},
+    {(char *) "__globals__", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0},
+    {(char *) "func_closure", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0},
+    {(char *) "__closure__", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0},
+    {(char *) "func_code", (getter)__Pyx_CyFunction_get_code, 0, 0, 0},
+    {(char *) "__code__", (getter)__Pyx_CyFunction_get_code, 0, 0, 0},
+    {(char *) "func_defaults", (getter)__Pyx_CyFunction_get_defaults, 0, 0, 0},
+    {(char *) "__defaults__", (getter)__Pyx_CyFunction_get_defaults, 0, 0, 0},
+    {0, 0, 0, 0, 0}
+};
+#ifndef PY_WRITE_RESTRICTED /* < Py2.5 */
+#define PY_WRITE_RESTRICTED WRITE_RESTRICTED
+#endif
+static PyMemberDef __pyx_CyFunction_members[] = {
+    {(char *) "__module__", T_OBJECT, offsetof(__pyx_CyFunctionObject, func.m_module), PY_WRITE_RESTRICTED, 0},
+    {0, 0, 0,  0, 0}
+};
+static PyObject *
+__Pyx_CyFunction_reduce(__pyx_CyFunctionObject *m, CYTHON_UNUSED PyObject *args)
+{
+#if PY_MAJOR_VERSION >= 3
+    return PyUnicode_FromString(m->func.m_ml->ml_name);
+#else
+    return PyString_FromString(m->func.m_ml->ml_name);
 #endif
 }
-
-static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
-#if CYTHON_COMPILING_IN_PYPY
-    return PyObject_RichCompareBool(s1, s2, equals);
+static PyMethodDef __pyx_CyFunction_methods[] = {
+    {__Pyx_NAMESTR("__reduce__"), (PyCFunction)__Pyx_CyFunction_reduce, METH_VARARGS, 0},
+    {0, 0, 0, 0}
+};
+static PyObject *__Pyx_CyFunction_New(PyTypeObject *type, PyMethodDef *ml, int flags,
+                                      PyObject *closure, PyObject *module, PyObject* code) {
+    __pyx_CyFunctionObject *op = PyObject_GC_New(__pyx_CyFunctionObject, type);
+    if (op == NULL)
+        return NULL;
+    op->flags = flags;
+    op->func_weakreflist = NULL;
+    op->func.m_ml = ml;
+    op->func.m_self = (PyObject *) op;
+    Py_XINCREF(closure);
+    op->func_closure = closure;
+    Py_XINCREF(module);
+    op->func.m_module = module;
+    op->func_dict = NULL;
+    op->func_name = NULL;
+    op->func_doc = NULL;
+    op->func_classobj = NULL;
+    Py_XINCREF(code);
+    op->func_code = code;
+    op->defaults_pyobjects = 0;
+    op->defaults = NULL;
+    op->defaults_tuple = NULL;
+    op->defaults_getter = NULL;
+    PyObject_GC_Track(op);
+    return (PyObject *) op;
+}
+static int
+__Pyx_CyFunction_clear(__pyx_CyFunctionObject *m)
+{
+    Py_CLEAR(m->func_closure);
+    Py_CLEAR(m->func.m_module);
+    Py_CLEAR(m->func_dict);
+    Py_CLEAR(m->func_name);
+    Py_CLEAR(m->func_doc);
+    Py_CLEAR(m->func_code);
+    Py_CLEAR(m->func_classobj);
+    Py_CLEAR(m->defaults_tuple);
+    if (m->defaults) {
+        PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m);
+        int i;
+        for (i = 0; i < m->defaults_pyobjects; i++)
+            Py_XDECREF(pydefaults[i]);
+        PyMem_Free(m->defaults);
+        m->defaults = NULL;
+    }
+    return 0;
+}
+static void __Pyx_CyFunction_dealloc(__pyx_CyFunctionObject *m)
+{
+    PyObject_GC_UnTrack(m);
+    if (m->func_weakreflist != NULL)
+        PyObject_ClearWeakRefs((PyObject *) m);
+    __Pyx_CyFunction_clear(m);
+    PyObject_GC_Del(m);
+}
+static int __Pyx_CyFunction_traverse(__pyx_CyFunctionObject *m, visitproc visit, void *arg)
+{
+    Py_VISIT(m->func_closure);
+    Py_VISIT(m->func.m_module);
+    Py_VISIT(m->func_dict);
+    Py_VISIT(m->func_name);
+    Py_VISIT(m->func_doc);
+    Py_VISIT(m->func_code);
+    Py_VISIT(m->func_classobj);
+    Py_VISIT(m->defaults_tuple);
+    if (m->defaults) {
+        PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m);
+        int i;
+        for (i = 0; i < m->defaults_pyobjects; i++)
+            Py_VISIT(pydefaults[i]);
+    }
+    return 0;
+}
+static PyObject *__Pyx_CyFunction_descr_get(PyObject *func, PyObject *obj, PyObject *type)
+{
+    __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
+    if (m->flags & __Pyx_CYFUNCTION_STATICMETHOD) {
+        Py_INCREF(func);
+        return func;
+    }
+    if (m->flags & __Pyx_CYFUNCTION_CLASSMETHOD) {
+        if (type == NULL)
+            type = (PyObject *)(Py_TYPE(obj));
+        return PyMethod_New(func,
+                            type, (PyObject *)(Py_TYPE(type)));
+    }
+    if (obj == Py_None)
+        obj = NULL;
+    return PyMethod_New(func, obj, type);
+}
+static PyObject*
+__Pyx_CyFunction_repr(__pyx_CyFunctionObject *op)
+{
+    PyObject *func_name = __Pyx_CyFunction_get_name(op);
+#if PY_MAJOR_VERSION >= 3
+    return PyUnicode_FromFormat("<cyfunction %U at %p>",
+                                func_name, (void *)op);
 #else
-    if (s1 == s2) {
-        return (equals == Py_EQ);
-    } else if (PyUnicode_CheckExact(s1) & PyUnicode_CheckExact(s2)) {
-        #if CYTHON_PEP393_ENABLED
-        if ((PyUnicode_READY(s1) < 0) || (PyUnicode_READY(s2) < 0))
-            return -1;
-        if (PyUnicode_GET_LENGTH(s1) != PyUnicode_GET_LENGTH(s2)) {
-            return (equals == Py_NE);
-        } else if (PyUnicode_GET_LENGTH(s1) == 1) {
-            Py_UCS4 ch1 = PyUnicode_READ_CHAR(s1, 0);
-            Py_UCS4 ch2 = PyUnicode_READ_CHAR(s2, 0);
-            return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2);
-        #else
-        if (PyUnicode_GET_SIZE(s1) != PyUnicode_GET_SIZE(s2)) {
-            return (equals == Py_NE);
-        } else if (PyUnicode_GET_SIZE(s1) == 1) {
-            Py_UNICODE ch1 = PyUnicode_AS_UNICODE(s1)[0];
-            Py_UNICODE ch2 = PyUnicode_AS_UNICODE(s2)[0];
-            return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2);
-        #endif
-        } else {
-            int result = PyUnicode_Compare(s1, s2);
-            if ((result == -1) && unlikely(PyErr_Occurred()))
-                return -1;
-            return (equals == Py_EQ) ? (result == 0) : (result != 0);
+    return PyString_FromFormat("<cyfunction %s at %p>",
+                               PyString_AsString(func_name), (void *)op);
+#endif
+}
+#if CYTHON_COMPILING_IN_PYPY
+static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
+    PyCFunctionObject* f = (PyCFunctionObject*)func;
+    PyCFunction meth = PyCFunction_GET_FUNCTION(func);
+    PyObject *self = PyCFunction_GET_SELF(func);
+    Py_ssize_t size;
+    switch (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST)) {
+    case METH_VARARGS:
+        if (likely(kw == NULL) || PyDict_Size(kw) == 0)
+            return (*meth)(self, arg);
+        break;
+    case METH_VARARGS | METH_KEYWORDS:
+        return (*(PyCFunctionWithKeywords)meth)(self, arg, kw);
+    case METH_NOARGS:
+        if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
+            size = PyTuple_GET_SIZE(arg);
+            if (size == 0)
+                return (*meth)(self, NULL);
+            PyErr_Format(PyExc_TypeError,
+                "%.200s() takes no arguments (%zd given)",
+                f->m_ml->ml_name, size);
+            return NULL;
         }
-    } else if ((s1 == Py_None) & PyUnicode_CheckExact(s2)) {
-        return (equals == Py_NE);
-    } else if ((s2 == Py_None) & PyUnicode_CheckExact(s1)) {
-        return (equals == Py_NE);
-    } else {
-        int result;
-        PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
-        if (!py_result)
-            return -1;
-        result = __Pyx_PyObject_IsTrue(py_result);
-        Py_DECREF(py_result);
-        return result;
+        break;
+    case METH_O:
+        if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
+            size = PyTuple_GET_SIZE(arg);
+            if (size == 1)
+                return (*meth)(self, PyTuple_GET_ITEM(arg, 0));
+            PyErr_Format(PyExc_TypeError,
+                "%.200s() takes exactly one argument (%zd given)",
+                f->m_ml->ml_name, size);
+            return NULL;
+        }
+        break;
+    default:
+        PyErr_SetString(PyExc_SystemError, "Bad call flags in "
+                        "__Pyx_CyFunction_Call. METH_OLDARGS is no "
+                        "longer supported!");
+        return NULL;
     }
+    PyErr_Format(PyExc_TypeError, "%.200s() takes no keyword arguments",
+                 f->m_ml->ml_name);
+    return NULL;
+}
+#else
+static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
+	return PyCFunction_Call(func, arg, kw);
+}
+#endif
+static PyTypeObject __pyx_CyFunctionType_type = {
+    PyVarObject_HEAD_INIT(0, 0)
+    __Pyx_NAMESTR("cython_function_or_method"), /*tp_name*/
+    sizeof(__pyx_CyFunctionObject),   /*tp_basicsize*/
+    0,                                  /*tp_itemsize*/
+    (destructor) __Pyx_CyFunction_dealloc, /*tp_dealloc*/
+    0,                                  /*tp_print*/
+    0,                                  /*tp_getattr*/
+    0,                                  /*tp_setattr*/
+#if PY_MAJOR_VERSION < 3
+    0,                                  /*tp_compare*/
+#else
+    0,                                  /*reserved*/
+#endif
+    (reprfunc) __Pyx_CyFunction_repr,   /*tp_repr*/
+    0,                                  /*tp_as_number*/
+    0,                                  /*tp_as_sequence*/
+    0,                                  /*tp_as_mapping*/
+    0,                                  /*tp_hash*/
+    __Pyx_CyFunction_Call,              /*tp_call*/
+    0,                                  /*tp_str*/
+    0,                                  /*tp_getattro*/
+    0,                                  /*tp_setattro*/
+    0,                                  /*tp_as_buffer*/
+    Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/
+    0,                                  /*tp_doc*/
+    (traverseproc) __Pyx_CyFunction_traverse,   /*tp_traverse*/
+    (inquiry) __Pyx_CyFunction_clear,   /*tp_clear*/
+    0,                                  /*tp_richcompare*/
+    offsetof(__pyx_CyFunctionObject, func_weakreflist), /* tp_weaklistoffse */
+    0,                                  /*tp_iter*/
+    0,                                  /*tp_iternext*/
+    __pyx_CyFunction_methods,           /*tp_methods*/
+    __pyx_CyFunction_members,           /*tp_members*/
+    __pyx_CyFunction_getsets,           /*tp_getset*/
+    0,                                  /*tp_base*/
+    0,                                  /*tp_dict*/
+    __Pyx_CyFunction_descr_get,         /*tp_descr_get*/
+    0,                                  /*tp_descr_set*/
+    offsetof(__pyx_CyFunctionObject, func_dict),/*tp_dictoffset*/
+    0,                                  /*tp_init*/
+    0,                                  /*tp_alloc*/
+    0,                                  /*tp_new*/
+    0,                                  /*tp_free*/
+    0,                                  /*tp_is_gc*/
+    0,                                  /*tp_bases*/
+    0,                                  /*tp_mro*/
+    0,                                  /*tp_cache*/
+    0,                                  /*tp_subclasses*/
+    0,                                  /*tp_weaklist*/
+    0,                                  /*tp_del*/
+#if PY_VERSION_HEX >= 0x02060000
+    0,                                  /*tp_version_tag*/
 #endif
+};
+static int __Pyx_CyFunction_init(void) {
+#if !CYTHON_COMPILING_IN_PYPY
+    __pyx_CyFunctionType_type.tp_call = PyCFunction_Call;
+#endif
+    if (PyType_Ready(&__pyx_CyFunctionType_type) < 0)
+        return -1;
+    __pyx_CyFunctionType = &__pyx_CyFunctionType_type;
+    return 0;
+}
+static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) {
+    __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
+    m->defaults = PyMem_Malloc(size);
+    if (!m->defaults)
+        return PyErr_NoMemory();
+    memset(m->defaults, 0, sizeof(size));
+    m->defaults_pyobjects = pyobjects;
+    return m->defaults;
+}
+static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) {
+    __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
+    m->defaults_tuple = tuple;
+    Py_INCREF(tuple);
 }
 
 static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) {
@@ -63850,7 +70303,7 @@ static PyMemberDef __pyx_Generator_memberlist[] = {
 #if PY_VERSION_HEX >= 0x02060000
      T_BOOL,
 #else
-     T_INT,
+     T_BYTE,
 #endif
      offsetof(__pyx_GeneratorObject, is_running),
      READONLY,
diff --git a/python/src/sa/_sa.pxd b/python/src/sa/_sa.pxd
index d390bfc5..f1cd8e29 100644
--- a/python/src/sa/_sa.pxd
+++ b/python/src/sa/_sa.pxd
@@ -1,3 +1,31 @@
+from libc.stdio cimport FILE
+
+cdef class FloatList:
+    cdef int size
+    cdef int increment
+    cdef int len
+    cdef float* arr
+    cdef void set(self, int i, float v)
+    cdef void write_handle(self, FILE* f)
+    cdef void read_handle(self, FILE* f)
+
+cdef class IntList:
+    cdef int size
+    cdef int increment
+    cdef int len
+    cdef int* arr
+    cdef void set(self, int i, int val)
+    cdef void _append(self, int val)
+    cdef void _extend(self, IntList other)
+    cdef void _extend_arr(self, int* other, int other_len)
+    cdef void _clear(self)
+    cdef void write_handle(self, FILE* f)
+    cdef void read_handle(self, FILE* f)
+
+cdef class FeatureVector:
+    cdef IntList names
+    cdef FloatList values
+
 cdef class Phrase:
     cdef int *syms
     cdef int n, *varpos, n_vars
@@ -5,11 +33,11 @@ cdef class Phrase:
     cdef public int chunklen(self, int k)
 
 cdef class Rule:
-    cdef public int lhs
+    cdef int lhs
     cdef readonly Phrase f, e
-    cdef float *cscores
+    cdef FeatureVector scores
     cdef int n_scores
-    cdef public word_alignments
+    cdef word_alignments
 
 cdef char* sym_tostring(int sym)
 cdef char* sym_tocat(int sym)
diff --git a/python/src/sa/_sa.pyx b/python/src/sa/_sa.pyx
index 710f8cb4..50da4235 100644
--- a/python/src/sa/_sa.pyx
+++ b/python/src/sa/_sa.pyx
@@ -27,3 +27,4 @@ include "rule.pxi"
 include "precomputation.pxi"
 include "suffix_array.pxi"
 include "rulefactory.pxi"
+include "features.pxi"
diff --git a/python/src/sa/bilex.pxi b/python/src/sa/bilex.pxi
index 27d1be49..44bc0ce6 100644
--- a/python/src/sa/bilex.pxi
+++ b/python/src/sa/bilex.pxi
@@ -4,7 +4,7 @@
 
 from libc.stdio cimport FILE, fopen, fread, fwrite, fclose
 from libc.stdlib cimport malloc, realloc, free
-from libc.string cimport memset, strcpy, strlen
+from libc.string cimport memset, strcpy
 
 cdef struct _node:
     _node* smaller
@@ -74,7 +74,6 @@ cdef class BiLex:
         cdef int *fsent, *esent, *alignment, *links, *ealigned, *faligned
         cdef _node** dict
         cdef int *fmargin, *emargin, *count
-        cdef bytes word
         cdef int null_word
 
         null_word = 0
@@ -215,32 +214,28 @@ cdef class BiLex:
     cdef write_wordlist(self, wordlist, FILE* f):
         cdef int word_len
         cdef int num_words
-        cdef char* c_word
 
         num_words = len(wordlist)
         fwrite(&(num_words), sizeof(int), 1, f)
         for word in wordlist:
-            c_word = word
-            word_len = strlen(c_word) + 1
+            word_len = len(word) + 1
             fwrite(&(word_len), sizeof(int), 1, f)
-            fwrite(c_word, sizeof(char), word_len, f)
+            fwrite(<char *>word, sizeof(char), word_len, f)
 
 
     cdef read_wordlist(self, word2id, id2word, FILE* f):
         cdef int num_words
         cdef int word_len
-        cdef char* c_word
-        cdef bytes py_word
+        cdef char* word
 
         fread(&(num_words), sizeof(int), 1, f)
         for i from 0 <= i < num_words:
             fread(&(word_len), sizeof(int), 1, f)
-            c_word = <char*> malloc (word_len * sizeof(char))
-            fread(c_word, sizeof(char), word_len, f)
-            py_word = c_word
-            free(c_word)
-            word2id[py_word] = len(id2word)
-            id2word.append(py_word)
+            word = <char*> malloc (word_len * sizeof(char))
+            fread(word, sizeof(char), word_len, f)
+            word2id[word] = len(id2word)
+            id2word.append(word)
+            free(word)
 
     def read_binary(self, char* filename):
         cdef FILE* f
diff --git a/python/src/sa/data_array.pxi b/python/src/sa/data_array.pxi
index 7a102a7e..2a8ea921 100644
--- a/python/src/sa/data_array.pxi
+++ b/python/src/sa/data_array.pxi
@@ -4,14 +4,14 @@
 
 from libc.stdio cimport FILE, fopen, fread, fwrite, fclose
 from libc.stdlib cimport malloc, realloc, free
-from libc.string cimport memset, strcpy, strlen
+from libc.string cimport memset, strcpy
 
 cdef class DataArray:
-    cdef word2id
-    cdef id2word
-    cdef IntList data
-    cdef IntList sent_id
-    cdef IntList sent_index
+    cdef public word2id
+    cdef public id2word
+    cdef public IntList data
+    cdef public IntList sent_id
+    cdef public IntList sent_index
     cdef bint use_sent_id
 
     def __cinit__(self, from_binary=None, from_text=None, side=None, bint use_sent_id=False):
@@ -32,10 +32,10 @@ cdef class DataArray:
     def __len__(self):
         return len(self.data)
 
-    def getSentId(self, i):
+    def get_sentence_id(self, i):
         return self.sent_id.arr[i]
 
-    def getSent(self, i):
+    def get_sentence(self, i):
         cdef int j, start, stop
         sent = []
         start = self.sent_index.arr[i]
@@ -44,17 +44,18 @@ cdef class DataArray:
             sent.append(self.id2word[self.data.arr[i]])
         return sent
 
-    def getSentPos(self, loc):
-        return loc - self.sent_index.arr[self.sent_id.arr[loc]]
-
     def get_id(self, word):
         if not word in self.word2id:
             self.word2id[word] = len(self.id2word)
             self.id2word.append(word)
         return self.word2id[word]
 
-    def get_word(self, id):
-        return self.id2word[id]
+    def __getitem__(self, loc):
+        return self.id2word[self.data.arr[loc]]
+
+    def get_sentence_bounds(self, loc):
+        cdef int sid = self.sent_id.arr[loc]
+        return (self.sent_index.arr[sid], self.sent_index.arr[sid+1])
 
     def write_text(self, char* filename):
         with open(filename, "w") as f:
@@ -99,20 +100,19 @@ cdef class DataArray:
     cdef void read_handle(self, FILE* f):
         cdef int num_words, word_len
         cdef unsigned i
-        cdef char* c_word
-        cdef bytes py_word
+        cdef char* word
+
         self.data.read_handle(f)
         self.sent_index.read_handle(f)
         self.sent_id.read_handle(f)
         fread(&(num_words), sizeof(int), 1, f)
         for i in range(num_words):
             fread(&(word_len), sizeof(int), 1, f)
-            c_word = <char*> malloc (word_len * sizeof(char))
-            fread(c_word, sizeof(char), word_len, f)
-            py_word = c_word
-            free(c_word)
-            self.word2id[py_word] = len(self.id2word)
-            self.id2word.append(py_word)
+            word = <char*> malloc (word_len * sizeof(char))
+            fread(word, sizeof(char), word_len, f)
+            self.word2id[word] = len(self.id2word)
+            self.id2word.append(word)
+            free(word)
         if len(self.sent_id) == 0:
             self.use_sent_id = False
         else:
@@ -121,17 +121,16 @@ cdef class DataArray:
     cdef void write_handle(self, FILE* f):
         cdef int word_len
         cdef int num_words
-        cdef char* c_word
+
         self.data.write_handle(f)
         self.sent_index.write_handle(f)
         self.sent_id.write_handle(f)
         num_words = len(self.id2word) - 2
         fwrite(&(num_words), sizeof(int), 1, f)
         for word in self.id2word[2:]:
-            c_word = word
-            word_len = strlen(c_word) + 1
+            word_len = len(word) + 1
             fwrite(&(word_len), sizeof(int), 1, f)
-            fwrite(c_word, sizeof(char), word_len, f)
+            fwrite(<char *>word, sizeof(char), word_len, f)
 
     def write_binary(self, char* filename):
         cdef FILE* f
diff --git a/python/src/sa/default_scorer.pxi b/python/src/sa/default_scorer.pxi
new file mode 100644
index 00000000..483f4743
--- /dev/null
+++ b/python/src/sa/default_scorer.pxi
@@ -0,0 +1,74 @@
+from libc.stdlib cimport malloc, realloc, free
+from libc.math cimport log10
+
+MAXSCORE = -99
+EgivenFCoherent = 0
+SampleCountF = 1
+CountEF = 2
+MaxLexFgivenE = 3
+MaxLexEgivenF = 4
+IsSingletonF = 5
+IsSingletonFE = 6
+NFEATURES = 7
+
+cdef class DefaultScorer(Scorer):
+    cdef BiLex ttable
+    cdef int* fid
+
+    def __dealloc__(self):
+        free(self.fid)
+
+    def __init__(self, BiLex ttable):
+        self.ttable = ttable
+        self.fid = <int*> malloc(NFEATURES*sizeof(int))
+        cdef unsigned i
+        for i, fnames in enumerate(('EgivenFCoherent', 'SampleCountF', 'CountEF',
+                'MaxLexFgivenE', 'MaxLexEgivenF', 'IsSingletonF', 'IsSingletonFE')):
+            self.fid[i] = FD.index(fnames)
+
+    cdef FeatureVector score(self, Phrase fphrase, Phrase ephrase,
+            unsigned paircount, unsigned fcount, unsigned fsample_count):
+        cdef FeatureVector scores = FeatureVector()
+
+        #  EgivenFCoherent
+        cdef float efc = <float>paircount/fsample_count
+        scores.set(self.fid[EgivenFCoherent], -log10(efc) if efc > 0 else MAXSCORE)
+
+        # SampleCountF
+        scores.set(self.fid[SampleCountF], log10(1 + fsample_count))
+
+        # CountEF
+        scores.set(self.fid[CountEF], log10(1 + paircount))
+
+        # MaxLexFgivenE TODO typify
+        ewords = ephrase.words
+        ewords.append('NULL')
+        cdef float mlfe = 0, max_score = -1
+        for f in fphrase.words:
+            for e in ewords:
+                score = self.ttable.get_score(f, e, 1)
+                if score > max_score:
+                    max_score = score
+            mlfe += -log10(max_score) if max_score > 0 else MAXSCORE
+        scores.set(self.fid[MaxLexFgivenE], mlfe)
+
+        # MaxLexEgivenF TODO same
+        fwords = fphrase.words
+        fwords.append('NULL')
+        cdef float mlef = 0
+        max_score = -1
+        for e in ephrase.words:
+            for f in fwords:
+                score = self.ttable.get_score(f, e, 0)
+                if score > max_score:
+                    max_score = score
+            mlef += -log10(max_score) if max_score > 0 else MAXSCORE
+        scores.set(self.fid[MaxLexEgivenF], mlef)
+
+        # IsSingletonF
+        scores.set(self.fid[IsSingletonF], (fcount == 1))
+
+        # IsSingletonFE
+        scores.set(self.fid[IsSingletonFE], (paircount == 1))
+
+        return scores
diff --git a/python/src/sa/features.pxi b/python/src/sa/features.pxi
new file mode 100644
index 00000000..9b9ecf3c
--- /dev/null
+++ b/python/src/sa/features.pxi
@@ -0,0 +1,33 @@
+cdef StringMap FD = StringMap() # Feature name dictionary
+
+INITIAL_CAPACITY = 7 # default number of features
+INCREMENT = INITIAL_CAPACITY # double size
+
+cdef class FeatureVector:
+    def __cinit__(self):
+        self.names = IntList(INITIAL_CAPACITY, INCREMENT)
+        self.values = FloatList(INITIAL_CAPACITY, INCREMENT)
+
+    def set(self, unsigned name, float value):
+        self.names.append(name)
+        self.values.append(value)
+
+    def __iter__(self):
+        cdef unsigned i
+        for i in range(self.names.len):
+            yield (FD.word(self.names[i]), self.values[i])
+
+    def __str__(self):
+        return ' '.join('%s=%s' % feat for feat in self)
+
+cdef class Scorer:
+    cdef models
+    def __init__(self, *models):
+        names = [FD.index(<char *>model.__name__) for model in models]
+        self.models = zip(names, models)
+
+    cdef FeatureVector score(self, ctx):
+        cdef FeatureVector scores = FeatureVector()
+        for name, model in self.models:
+            scores.set(name, model(ctx))
+        return scores
diff --git a/python/src/sa/float_list.pxi b/python/src/sa/float_list.pxi
index 88ffd5fc..b98e444f 100644
--- a/python/src/sa/float_list.pxi
+++ b/python/src/sa/float_list.pxi
@@ -7,10 +7,6 @@ from libc.stdlib cimport malloc, realloc, free
 from libc.string cimport memset, strcpy, strlen
 
 cdef class FloatList:
-    cdef int size
-    cdef int increment
-    cdef int len
-    cdef float* arr
 
     def __cinit__(self, int size=0, int increment=1, int initial_len=0):
         if initial_len > size:
diff --git a/python/src/sa/int_list.pxi b/python/src/sa/int_list.pxi
index ad14bc9c..55f5d174 100644
--- a/python/src/sa/int_list.pxi
+++ b/python/src/sa/int_list.pxi
@@ -7,10 +7,6 @@ from libc.stdlib cimport malloc, realloc, free
 from libc.string cimport memset, memcpy
 
 cdef class IntList:
-    cdef int size
-    cdef int increment
-    cdef int len
-    cdef int* arr
 
     def __cinit__(self, int size=0, int increment=1, int initial_len=0):
         if initial_len > size:
@@ -82,6 +78,11 @@ cdef class IntList:
     def __dealloc__(self):
         free(self.arr)
 
+    def __iter__(self):
+        cdef int i
+        for i in range(self.len):
+            yield self.arr[i]
+
     def __getitem__(self, index):
         cdef int i, j, k
         if isinstance(index, int):
@@ -121,7 +122,7 @@ cdef class IntList:
     def __len__(self):
         return self.len
 
-    def getSize(self):
+    def get_size(self):
         return self.size
 
     def append(self, int val):
diff --git a/python/src/sa/rule.pxi b/python/src/sa/rule.pxi
index bf1a83c6..98fbac76 100644
--- a/python/src/sa/rule.pxi
+++ b/python/src/sa/rule.pxi
@@ -31,7 +31,7 @@ cdef class Phrase:
         for i from 0 <= i < self.n:
             s = self.syms[i]
             strs.append(sym_tostring(s))
-        return " ".join(strs)
+        return ' '.join(strs)
 
     def handle(self):
         """return a hashable representation that normalizes the ordering
@@ -60,7 +60,7 @@ cdef class Phrase:
                 s = sym_setindex(s,i)
                 i = i + 1
             norm.append(sym_tostring(s))
-        return " ".join(norm)
+        return ' '.join(norm)
 
     def arity(self):
         return self.n_vars
@@ -158,45 +158,20 @@ cdef class Phrase:
 
 cdef class Rule:
 
-    def __cinit__(self, int lhs, Phrase f, Phrase e,
-            scores=None, word_alignments=None):
-        cdef int i, n
-        cdef char *rest
-
-        if not sym_isvar(lhs):
-            raise Exception('Invalid LHS symbol: %d' % lhs)
-
+    def __cinit__(self, int lhs, Phrase f, Phrase e, scores=None, word_alignments=None):
+        if not sym_isvar(lhs): raise Exception('Invalid LHS symbol: %d' % lhs)
         self.lhs = lhs
         self.f = f
         self.e = e
-
         self.word_alignments = word_alignments
-        if scores is None:
-            self.cscores = NULL
-            self.n_scores = 0
-        else:
-            n = len(scores)
-            self.cscores = <float *>malloc(n*sizeof(float))
-            self.n_scores = n
-            for i from 0 <= i < n:
-                self.cscores[i] = scores[i]
-
-    def __dealloc__(self):
-        if self.cscores != NULL:
-            free(self.cscores)
+        self.scores = scores
 
     def __hash__(self):
         return hash((self.lhs, self.f, self.e))
 
     def __cmp__(self, Rule other):
-        return cmp((self.lhs, self.f, self.e, self.word_alignments), (other.lhs, other.f, other.e, self.word_alignments))
-
-    def __iadd__(self, Rule other):
-        if self.n_scores != other.n_scores:
-            raise ValueError
-        for i from 0 <= i < self.n_scores:
-            self.cscores[i] = self.cscores[i] + other.cscores[i]
-        return self
+        return cmp((self.lhs, self.f, self.e, self.word_alignments),
+                (other.lhs, other.f, other.e, self.word_alignments))
 
     def fmerge(self, Phrase f):
         if self.f == f:
@@ -206,31 +181,12 @@ cdef class Rule:
         return self.f.arity()
 
     def __str__(self):
-        scorestrs = []
-        for i from 0 <= i < self.n_scores:
-            scorestrs.append(str(self.cscores[i]))
-        fields = [sym_tostring(self.lhs), str(self.f), str(self.e), " ".join(scorestrs)]
+        cdef unsigned i
+        fields = [sym_tostring(self.lhs), str(self.f), str(self.e), str(self.scores)]
         if self.word_alignments is not None:
-            alignstr = []
-            for i from 0 <= i < len(self.word_alignments):
-                alignstr.append("%d-%d" % (self.word_alignments[i]/65536, self.word_alignments[i]%65536))
-            #for s,t in self.word_alignments:
-                 #alignstr.append("%d-%d" % (s,t)) 
-            fields.append(" ".join(alignstr))
-        
-        return " ||| ".join(fields)
+            fields.append(' '.join('%d-%d' % a for a in self.alignments()))
+        return ' ||| '.join(fields)
 
-    property scores:
-        def __get__(self):
-            s = [None]*self.n_scores
-            for i from 0 <= i < self.n_scores:
-                s[i] = self.cscores[i]
-            return s
-
-        def __set__(self, s):
-            if self.cscores != NULL:
-                free(self.cscores)
-            self.cscores = <float *>malloc(len(s)*sizeof(float))
-            self.n_scores = len(s)
-            for i from 0 <= i < self.n_scores:
-                self.cscores[i] = s[i]
+    def alignments(self):
+        for point in self.word_alignments:
+            yield point/65536, point%65536
diff --git a/python/src/sa/rulefactory.pxi b/python/src/sa/rulefactory.pxi
index 1c8d25a4..5f6558b3 100644
--- a/python/src/sa/rulefactory.pxi
+++ b/python/src/sa/rulefactory.pxi
@@ -3,11 +3,29 @@
 # Much faster than the Python numbers reported there.
 # Note to reader: this code is closer to C than Python
 import gc
+import itertools
 
 from libc.stdlib cimport malloc, realloc, free
 from libc.string cimport memset, memcpy
 from libc.math cimport fmod, ceil, floor, log
 
+from collections import defaultdict, Counter, namedtuple
+
+FeatureContext = namedtuple('FeatureContext',
+    ['fphrase', 
+     'ephrase', 
+     'paircount', 
+     'fcount', 
+     'fsample_count',
+     'input_span',
+     'matches',
+     'input_match',
+     'test_sentence',
+     'f_text',
+     'e_text',
+     'meta'
+    ])
+
 cdef int PRECOMPUTE = 0
 cdef int MERGE = 1
 cdef int BAEZA_YATES = 2
@@ -73,8 +91,7 @@ cdef class PhraseLocation:
         self.arr_high = arr_high
         self.arr = arr
         self.num_subpatterns = num_subpatterns
-
-
+            
 
 cdef class Sampler:
     '''A Sampler implements a logic for choosing
@@ -208,6 +225,7 @@ cdef class HieroCachingRuleFactory:
 
     cdef TrieTable rules
     cdef Sampler sampler
+    cdef Scorer scorer
 
     cdef int max_chunks
     cdef int max_target_chunks
@@ -359,7 +377,8 @@ cdef class HieroCachingRuleFactory:
         self.findexes = IntList(initial_len=10)
         self.findexes1 = IntList(initial_len=10)
 
-    def configure(self, SuffixArray fsarray, DataArray edarray, Sampler sampler):
+    def configure(self, SuffixArray fsarray, DataArray edarray,
+            Sampler sampler, Scorer scorer):
         '''This gives the RuleFactory access to the Context object.
         Here we also use it to precompute the most expensive intersections
         in the corpus quickly.'''
@@ -370,6 +389,7 @@ cdef class HieroCachingRuleFactory:
         self.eid2symid = self.set_idmap(self.eda)
         self.precompute()
         self.sampler = sampler
+        self.scorer = scorer
 
     cdef set_idmap(self, DataArray darray):
         cdef int word_id, new_word_id, N
@@ -916,7 +936,7 @@ cdef class HieroCachingRuleFactory:
                     candidate.append([next_id,curr[1]+jump])
         return sorted(result);
 
-    def input(self, fwords, models):
+    def input(self, fwords, meta):
         '''When this function is called on the RuleFactory,
         it looks up all of the rules that can be used to translate
         the input sentence'''
@@ -941,7 +961,7 @@ cdef class HieroCachingRuleFactory:
         for i in range(len(fwords)):
             for alt in range(0, len(fwords[i])):
                 if fwords[i][alt][0] != EPSILON:
-                    frontier.append((i, i, alt, 0, self.rules.root, (), False))
+                    frontier.append((i, i, (i,), alt, 0, self.rules.root, (), False))
 
         xroot = None
         x1 = sym_setindex(self.category, 1)
@@ -954,7 +974,7 @@ cdef class HieroCachingRuleFactory:
         for i in range(self.min_gap_size, len(fwords)):
             for alt in range(0, len(fwords[i])):
                 if fwords[i][alt][0] != EPSILON:
-                    frontier.append((i-self.min_gap_size, i, alt, self.min_gap_size, xroot, (x1,), True))
+                    frontier.append((i-self.min_gap_size, i, (i,), alt, self.min_gap_size, xroot, (x1,), True))
 
         next_states = []
         for i in range(len(fwords)):
@@ -962,7 +982,7 @@ cdef class HieroCachingRuleFactory:
 
         while len(frontier) > 0:
             new_frontier = []
-            for k, i, alt, pathlen, node, prefix, is_shadow_path in frontier:
+            for k, i, input_match, alt, pathlen, node, prefix, is_shadow_path in frontier:
                 word_id = fwords[i][alt][0]
                 spanlen = fwords[i][alt][2]
                 # TODO get rid of k -- pathlen is replacing it
@@ -971,7 +991,7 @@ cdef class HieroCachingRuleFactory:
                     if i+spanlen >= len(fwords):
                         continue
                     for nualt in range(0,len(fwords[i+spanlen])):
-                        frontier.append((k, i+spanlen, nualt, pathlen, node, prefix, is_shadow_path))
+                        frontier.append((k, i+spanlen, input_match, nualt, pathlen, node, prefix, is_shadow_path))
                     continue
                 
                 phrase = prefix + (word_id,)
@@ -1066,42 +1086,35 @@ cdef class HieroCachingRuleFactory:
                             extract = []
 
                             assign_matching(&matching, sample.arr, j, num_subpatterns, self.fda.sent_id.arr)
+                            loc = tuple(sample[j:j+num_subpatterns])
                             extract = self.extract(hiero_phrase, &matching, chunklen.arr, num_subpatterns)
-                            extracts.extend(extract)
+                            extracts.extend([(e, loc) for e in extract])
                             j = j + num_subpatterns
 
                         num_samples = sample.len/num_subpatterns
                         extract_stop = monitor_cpu()
                         self.extract_time = self.extract_time + extract_stop - extract_start
                         if len(extracts) > 0:
-                            fphrases = {}
-                            fals = {}
-                            fcount = {}
-                            for f, e, count, als in extracts:
-                                fcount.setdefault(f, 0.0)
-                                fcount[f] = fcount[f] + count
-                                fphrases.setdefault(f, {})
-                                fphrases[f].setdefault(e, {})
-                                fphrases[f][e].setdefault(als,0.0)
-                                fphrases[f][e][als] = fphrases[f][e][als] + count
+                            fcount = Counter()
+                            fphrases = defaultdict(lambda: defaultdict(lambda: defaultdict(list)))
+                            for (f, e, count, als), loc in extracts:
+                                fcount[f] += count
+                                fphrases[f][e][als].append(loc)
                             for f, elist in fphrases.iteritems():
-                                f_margin = fcount[f]
                                 for e, alslist in elist.iteritems():
-                                    alignment = None
-                                    count = 0
-                                    for als, currcount in alslist.iteritems():
-                                        if currcount > count:
-                                            alignment = als
-                                            count = currcount 
-                                    scores = []
-                                    for model in models:
-                                        scores.append(model(f, e, count, fcount[f], num_samples))
-                                    yield Rule(self.category, f, e,
-                                            scores=scores, word_alignments=alignment)
+                                    alignment, max_locs = max(alslist.iteritems(), key=lambda x: len(x[1]))
+                                    locs = tuple(itertools.chain.from_iterable(alslist.itervalues()))
+                                    count = len(locs)
+                                    scores = self.scorer.score(FeatureContext(
+                                               f, e, count, fcount[f], num_samples,
+                                               (k,i+spanlen), locs, input_match, 
+                                               fwords, self.fda, self.eda,
+                                               meta))
+                                    yield Rule(self.category, f, e, scores, alignment)
 
                 if len(phrase) < self.max_length and i+spanlen < len(fwords) and pathlen+1 <= self.max_initial_size:
                     for alt_id in range(len(fwords[i+spanlen])):
-                        new_frontier.append((k, i+spanlen, alt_id, pathlen + 1, node, phrase, is_shadow_path))
+                        new_frontier.append((k, i+spanlen, input_match, alt_id, pathlen + 1, node, phrase, is_shadow_path))
                     num_subpatterns = arity
                     if not is_shadow_path:
                         num_subpatterns = num_subpatterns + 1
@@ -1118,7 +1131,7 @@ cdef class HieroCachingRuleFactory:
                             nodes_isteps_away_buffer[key] = frontier_nodes
                         
                         for (i, alt, pathlen) in frontier_nodes:
-                            new_frontier.append((k, i, alt, pathlen, xnode, phrase +(xcat,), is_shadow_path))
+                            new_frontier.append((k, i, input_match + (i,), alt, pathlen, xnode, phrase +(xcat,), is_shadow_path))
             frontier = new_frontier
                 
         stop_time = monitor_cpu()
@@ -1377,9 +1390,9 @@ cdef class HieroCachingRuleFactory:
         free(e_gap_order)
         return result
 
-    cdef create_alignments(self, int* sent_links, int num_links, findexes, eindexes):
+    cdef IntList create_alignments(self, int* sent_links, int num_links, findexes, eindexes):
         cdef unsigned i
-        ret = IntList()
+        cdef IntList ret = IntList()
         for i in range(len(findexes)):
             s = findexes[i]
             if (s<0):
diff --git a/python/src/sa/suffix_array.pxi b/python/src/sa/suffix_array.pxi
index d86e8ea6..de4adcd9 100644
--- a/python/src/sa/suffix_array.pxi
+++ b/python/src/sa/suffix_array.pxi
@@ -20,15 +20,6 @@ cdef class SuffixArray:
     def __getitem__(self, i):
         return self.sa.arr[i]
 
-    def getSentId(self, i):
-        return self.darray.getSentId(i)
-
-    def getSent(self, i):
-        return self.darray.getSent(i)
-
-    def getSentPos(self, loc):
-        return self.darray.getSentPos(loc)
-
     def read_text(self, filename, side):
         '''Constructs suffix array using the algorithm
         of Larsson & Sadahkane (1999)'''
diff --git a/python/src/sa/sym.pxi b/python/src/sa/sym.pxi
index 132925f6..f47599cf 100644
--- a/python/src/sa/sym.pxi
+++ b/python/src/sa/sym.pxi
@@ -101,5 +101,16 @@ cdef int sym_getindex(int sym):
 cdef int sym_setindex(int sym, int id):
     return ALPHABET.setindex(sym, id)
 
-def sym_fromstring(char* string, bint terminal):
+cdef int sym_fromstring(char* string, bint terminal):
     return ALPHABET.fromstring(string, terminal)
+
+def make_lattice(words):
+    word_ids = (sym_fromstring(word, True) for word in words)
+    return tuple(((word, None, 1), ) for word in word_ids)
+
+def decode_lattice(lattice):
+    return tuple((sym_tostring(sym), weight, dist) for (sym, weight, dist) in arc
+            for arc in node for node in lattice)
+
+def decode_sentence(lattice):
+    return tuple(sym_tostring(sym) for ((sym, _, _),) in lattice)
diff --git a/python/src/utils.pxd b/python/src/utils.pxd
index a1a4799b..687d3ac0 100644
--- a/python/src/utils.pxd
+++ b/python/src/utils.pxd
@@ -63,7 +63,7 @@ cdef extern from "utils/tdict.h" namespace "TD":
     string GetString(vector[WordID]& st)
     unsigned NumWords()
     WordID TDConvert "TD::Convert" (char*)
-    char* TDConvert "TD::Convert" (WordID)
+    string& TDConvert "TD::Convert" (WordID)
     void ConvertSentence(string& sent, vector[WordID]* ids)
 
 cdef extern from "utils/verbose.h":
diff --git a/python/src/vectors.pxi b/python/src/vectors.pxi
index 989a6a7c..46f58fd4 100644
--- a/python/src/vectors.pxi
+++ b/python/src/vectors.pxi
@@ -5,6 +5,7 @@ cdef class DenseVector:
     cdef bint owned # if True, do not manage memory
 
     def __init__(self):
+        """DenseVector() -> Dense weight/feature vector."""
         self.vector = new vector[weight_t]()
         self.owned = False
 
@@ -22,7 +23,7 @@ cdef class DenseVector:
         raise KeyError(fname)
     
     def __setitem__(self, char* fname, float value):
-        cdef int fid = FDConvert(<char *>fname)
+        cdef int fid = FDConvert(fname)
         if fid < 0: raise KeyError(fname)
         if self.vector.size() <= fid:
             self.vector.resize(fid + 1)
@@ -31,12 +32,14 @@ cdef class DenseVector:
     def __iter__(self):
         cdef unsigned fid
         for fid in range(1, self.vector.size()):
-            yield FDConvert(fid).c_str(), self.vector[0][fid]
+            yield str(FDConvert(fid).c_str()), self.vector[0][fid]
 
     def dot(self, SparseVector other):
+        """vector.dot(SparseVector other) -> Dot product of the two vectors."""
         return other.dot(self)
 
     def tosparse(self):
+        """vector.tosparse() -> Equivalent SparseVector."""
         cdef SparseVector sparse = SparseVector.__new__(SparseVector)
         sparse.vector = new FastSparseVector[weight_t]()
         InitSparseVector(self.vector[0], sparse.vector)
@@ -46,12 +49,14 @@ cdef class SparseVector:
     cdef FastSparseVector[weight_t]* vector
 
     def __init__(self):
+        """SparseVector() -> Sparse feature/weight vector."""
         self.vector = new FastSparseVector[weight_t]()
 
     def __dealloc__(self):
         del self.vector
 
     def copy(self):
+        """vector.copy() -> SparseVector copy."""
         return self * 1
 
     def __getitem__(self, char* fname):
@@ -60,7 +65,7 @@ cdef class SparseVector:
         return self.vector.value(fid)
     
     def __setitem__(self, char* fname, float value):
-        cdef int fid = FDConvert(<char *>fname)
+        cdef int fid = FDConvert(fname)
         if fid < 0: raise KeyError(fname)
         self.vector.set_value(fid, value)
 
@@ -69,12 +74,13 @@ cdef class SparseVector:
         cdef unsigned i
         try:
             for i in range(self.vector.size()):
-                yield (FDConvert(it[0].ptr().first).c_str(), it[0].ptr().second)
+                yield (str(FDConvert(it[0].ptr().first).c_str()), it[0].ptr().second)
                 pinc(it[0]) # ++it
         finally:
             del it
 
     def dot(self, other):
+        """vector.dot(SparseVector/DenseVector other) -> Dot product of the two vectors."""
         if isinstance(other, DenseVector):
             return self.vector.dot((<DenseVector> other).vector[0])
         elif isinstance(other, SparseVector):
diff --git a/rst_parser/Makefile.am b/rst_parser/Makefile.am
deleted file mode 100644
index 4977f584..00000000
--- a/rst_parser/Makefile.am
+++ /dev/null
@@ -1,17 +0,0 @@
-bin_PROGRAMS = \
-  mst_train rst_train rst_parse
-
-noinst_LIBRARIES = librst.a
-
-librst_a_SOURCES = arc_factored.cc arc_factored_marginals.cc rst.cc arc_ff.cc dep_training.cc global_ff.cc
-
-mst_train_SOURCES = mst_train.cc
-mst_train_LDADD = librst.a $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a ../klm/lm/libklm.a ../klm/util/libklm_util.a ../training/optimize.o -lz
-
-rst_train_SOURCES = rst_train.cc
-rst_train_LDADD = librst.a $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a ../klm/lm/libklm.a ../klm/util/libklm_util.a -lz
-
-rst_parse_SOURCES = rst_parse.cc
-rst_parse_LDADD = librst.a $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a ../klm/lm/libklm.a ../klm/util/libklm_util.a -lz
-
-AM_CPPFLAGS = -W -Wall -Wno-sign-compare $(GTEST_CPPFLAGS) -I$(top_srcdir)/decoder -I$(top_srcdir)/training -I$(top_srcdir)/utils -I$(top_srcdir)/mteval -I../klm
diff --git a/rst_parser/arc_factored.cc b/rst_parser/arc_factored.cc
deleted file mode 100644
index 74bf7516..00000000
--- a/rst_parser/arc_factored.cc
+++ /dev/null
@@ -1,151 +0,0 @@
-#include "arc_factored.h"
-
-#include <set>
-#include <tr1/unordered_set>
-
-#include <boost/pending/disjoint_sets.hpp>
-#include <boost/functional/hash.hpp>
-
-#include "arc_ff.h"
-
-using namespace std;
-using namespace std::tr1;
-using namespace boost;
-
-void EdgeSubset::ExtractFeatures(const TaggedSentence& sentence,
-                                 const ArcFeatureFunctions& ffs,
-                                 SparseVector<double>* features) const {
-  SparseVector<weight_t> efmap;
-  for (int j = 0; j < h_m_pairs.size(); ++j) {
-    efmap.clear();
-    ffs.EdgeFeatures(sentence, h_m_pairs[j].first,
-                     h_m_pairs[j].second,
-                     &efmap);
-    (*features) += efmap;
-  }
-  for (int j = 0; j < roots.size(); ++j) {
-    efmap.clear();
-    ffs.EdgeFeatures(sentence, -1, roots[j], &efmap);
-    (*features) += efmap;
-  }
-}
-
-void ArcFactoredForest::ExtractFeatures(const TaggedSentence& sentence,
-                                        const ArcFeatureFunctions& ffs) {
-  for (int m = 0; m < num_words_; ++m) {
-    for (int h = 0; h < num_words_; ++h) {
-      ffs.EdgeFeatures(sentence, h, m, &edges_(h,m).features);
-    }
-    ffs.EdgeFeatures(sentence, -1, m, &root_edges_[m].features);
-  }
-}
-
-void ArcFactoredForest::PickBestParentForEachWord(EdgeSubset* st) const {
-  for (int m = 0; m < num_words_; ++m) {
-    int best_head = -2;
-    prob_t best_score;
-    for (int h = -1; h < num_words_; ++h) {
-      const Edge& edge = (*this)(h,m);
-      if (best_head < -1 || edge.edge_prob > best_score) {
-        best_score = edge.edge_prob;
-        best_head = h;
-      }
-    }
-    assert(best_head >= -1);
-    if (best_head >= 0)
-      st->h_m_pairs.push_back(make_pair<short,short>(best_head, m));
-    else
-      st->roots.push_back(m);
-  }
-}
-
-struct WeightedEdge {
-  WeightedEdge() : h(), m(), weight() {}
-  WeightedEdge(short hh, short mm, float w) : h(hh), m(mm), weight(w) {}
-  short h, m;
-  float weight;
-  inline bool operator==(const WeightedEdge& o) const {
-    return h == o.h && m == o.m && weight == o.weight;
-  }
-  inline bool operator!=(const WeightedEdge& o) const {
-    return h != o.h || m != o.m || weight != o.weight;
-  }
-};
-inline bool operator<(const WeightedEdge& l, const WeightedEdge& o) { return l.weight < o.weight; }
-inline size_t hash_value(const WeightedEdge& e) { return reinterpret_cast<const size_t&>(e); }
-
-
-struct PriorityQueue {
-  void push(const WeightedEdge& e) {}
-  const WeightedEdge& top() const {
-    static WeightedEdge w(1,2,3);
-    return w;
-  }
-  void pop() {}
-  void increment_all(float p) {}
-};
-
-// based on Trajan 1977
-void ArcFactoredForest::MaximumSpanningTree(EdgeSubset* st) const {
-  typedef disjoint_sets_with_storage<identity_property_map, identity_property_map,
-      find_with_full_path_compression> DisjointSet;
-  DisjointSet strongly(num_words_ + 1);
-  DisjointSet weakly(num_words_ + 1);
-  set<unsigned> roots, rset;
-  unordered_set<WeightedEdge, boost::hash<WeightedEdge> > h;
-  vector<PriorityQueue> qs(num_words_ + 1);
-  vector<WeightedEdge> enter(num_words_ + 1);
-  vector<unsigned> mins(num_words_ + 1);
-  const WeightedEdge kDUMMY(0,0,0.0f);
-  for (unsigned i = 0; i <= num_words_; ++i) {
-    if (i > 0) {
-      // I(i) incidence on i -- all incoming edges
-      for (unsigned j = 0; j <= num_words_; ++j) {
-        qs[i].push(WeightedEdge(j, i, Weight(j,i)));
-      }
-    }
-    strongly.make_set(i);
-    weakly.make_set(i);
-    roots.insert(i);
-    enter[i] = kDUMMY;
-    mins[i] = i;
-  }
-  while(!roots.empty()) {
-    set<unsigned>::iterator it = roots.begin();
-    const unsigned k = *it;
-    roots.erase(it);
-    cerr << "k=" << k << endl;
-    WeightedEdge ij = qs[k].top();  // MAX(k)
-    qs[k].pop();
-    if (ij.weight <= 0) {
-      rset.insert(k);
-    } else {
-      if (strongly.find_set(ij.h) == k) {
-        roots.insert(k);
-      } else {
-        h.insert(ij);
-        if (weakly.find_set(ij.h) != weakly.find_set(ij.m)) {
-          weakly.union_set(ij.h, ij.m);
-          enter[k] = ij;
-        } else {
-          unsigned vertex = 0;
-          float val = 99999999999;
-          WeightedEdge xy = ij;
-          while(xy != kDUMMY) {
-            if (xy.weight < val) {
-              val = xy.weight;
-              vertex = strongly.find_set(xy.m);
-            }
-            xy = enter[strongly.find_set(xy.h)];
-          }
-          qs[k].increment_all(val - ij.weight);
-          mins[k] = mins[vertex];
-          xy = enter[strongly.find_set(ij.h)];
-          while (xy != kDUMMY) {
-          }
-        }
-      }
-    }
-  }
-}
-
diff --git a/rst_parser/arc_factored.h b/rst_parser/arc_factored.h
deleted file mode 100644
index c5481d80..00000000
--- a/rst_parser/arc_factored.h
+++ /dev/null
@@ -1,124 +0,0 @@
-#ifndef _ARC_FACTORED_H_
-#define _ARC_FACTORED_H_
-
-#include <iostream>
-#include <cassert>
-#include <vector>
-#include <utility>
-#include <boost/shared_ptr.hpp>
-#include "array2d.h"
-#include "sparse_vector.h"
-#include "prob.h"
-#include "weights.h"
-#include "wordid.h"
-
-struct TaggedSentence {
-  std::vector<WordID> words;
-  std::vector<WordID> pos;
-};
-
-struct ArcFeatureFunctions;
-struct EdgeSubset {
-  EdgeSubset() {}
-  std::vector<short> roots; // unless multiroot trees are supported, this
-                            // will have a single member
-  std::vector<std::pair<short, short> > h_m_pairs; // h,m start at 0
-  // assumes ArcFeatureFunction::PrepareForInput has already been called
-  void ExtractFeatures(const TaggedSentence& sentence,
-                       const ArcFeatureFunctions& ffs,
-                       SparseVector<double>* features) const;
-};
-
-class ArcFactoredForest {
- public:
-  ArcFactoredForest() : num_words_() {}
-  explicit ArcFactoredForest(short num_words) : num_words_(num_words) {
-    resize(num_words);
-  }
-
-  unsigned size() const { return num_words_; }
-
-  void resize(unsigned num_words) {
-    num_words_ = num_words;
-    root_edges_.clear();
-    edges_.clear();
-    root_edges_.resize(num_words);
-    edges_.resize(num_words, num_words);
-    for (int h = 0; h < num_words; ++h) {
-      for (int m = 0; m < num_words; ++m) {
-        edges_(h, m).h = h;
-        edges_(h, m).m = m;
-      }
-      root_edges_[h].h = -1;
-      root_edges_[h].m = h;
-    }
-  }
-
-  // compute the maximum spanning tree based on the current weighting
-  // using the O(n^2) CLE algorithm
-  void MaximumSpanningTree(EdgeSubset* st) const;
-
-  // Reweight edges so that edge_prob is the edge's marginals
-  // optionally returns log partition
-  void EdgeMarginals(prob_t* p_log_z = NULL);
-
-  // This may not return a tree
-  void PickBestParentForEachWord(EdgeSubset* st) const;
-
-  struct Edge {
-    Edge() : h(), m(), features(), edge_prob(prob_t::Zero()) {}
-    short h;
-    short m;
-    SparseVector<weight_t> features;
-    prob_t edge_prob;
-  };
-
-  // set eges_[*].features
-  void ExtractFeatures(const TaggedSentence& sentence,
-                       const ArcFeatureFunctions& ffs);
-
-  const Edge& operator()(short h, short m) const {
-    return h >= 0 ? edges_(h, m) : root_edges_[m];
-  }
-
-  Edge& operator()(short h, short m) {
-    return h >= 0 ? edges_(h, m) : root_edges_[m];
-  }
-
-  float Weight(short h, short m) const {
-    return log((*this)(h,m).edge_prob);
-  }
-
-  template <class V>
-  void Reweight(const V& weights) {
-    for (int m = 0; m < num_words_; ++m) {
-      for (int h = 0; h < num_words_; ++h) {
-        if (h != m) {
-          Edge& e = edges_(h, m);
-          e.edge_prob.logeq(e.features.dot(weights));
-        }
-      }
-      Edge& e = root_edges_[m];
-      e.edge_prob.logeq(e.features.dot(weights));
-    }
-  }
-
- private:
-  int num_words_;
-  std::vector<Edge> root_edges_;
-  Array2D<Edge> edges_;
-};
-
-inline std::ostream& operator<<(std::ostream& os, const ArcFactoredForest::Edge& edge) {
-  return os << "(" << edge.h << " < " << edge.m << ")";
-}
-
-inline std::ostream& operator<<(std::ostream& os, const EdgeSubset& ss) {
-  for (unsigned i = 0; i < ss.roots.size(); ++i)
-    os << "ROOT < " << ss.roots[i] << std::endl;
-  for (unsigned i = 0; i < ss.h_m_pairs.size(); ++i)
-    os << ss.h_m_pairs[i].first << " < " << ss.h_m_pairs[i].second << std::endl;
-  return os;
-}
-
-#endif
diff --git a/rst_parser/arc_factored_marginals.cc b/rst_parser/arc_factored_marginals.cc
deleted file mode 100644
index 3e8c9f86..00000000
--- a/rst_parser/arc_factored_marginals.cc
+++ /dev/null
@@ -1,58 +0,0 @@
-#include "arc_factored.h"
-
-#include <iostream>
-
-#include "config.h"
-
-using namespace std;
-
-#if HAVE_EIGEN
-
-#include <Eigen/Dense>
-typedef Eigen::Matrix<prob_t, Eigen::Dynamic, Eigen::Dynamic> ArcMatrix;
-typedef Eigen::Matrix<prob_t, Eigen::Dynamic, 1> RootVector;
-
-void ArcFactoredForest::EdgeMarginals(prob_t *plog_z) {
-  ArcMatrix A(num_words_,num_words_);
-  RootVector r(num_words_);
-  for (int h = 0; h < num_words_; ++h) {
-    for (int m = 0; m < num_words_; ++m) {
-      if (h != m)
-        A(h,m) = edges_(h,m).edge_prob;
-      else
-        A(h,m) = prob_t::Zero();
-    }
-    r(h) = root_edges_[h].edge_prob;
-  }
-
-  ArcMatrix L = -A;
-  L.diagonal() = A.colwise().sum();
-  L.row(0) = r;
-  ArcMatrix Linv = L.inverse();
-  if (plog_z) *plog_z = Linv.determinant();
-  RootVector rootMarginals = r.cwiseProduct(Linv.col(0));
-  static const prob_t ZERO(0);
-  static const prob_t ONE(1);
-//  ArcMatrix T = Linv;
-  for (int h = 0; h < num_words_; ++h) {
-    for (int m = 0; m < num_words_; ++m) {
-      const prob_t marginal = (m == 0 ? ZERO : ONE) * A(h,m) * Linv(m,m) -
-                              (h == 0 ? ZERO : ONE) * A(h,m) * Linv(m,h);
-      edges_(h,m).edge_prob = marginal;
-//      T(h,m) = marginal;
-    }
-    root_edges_[h].edge_prob = rootMarginals(h);
-  }
-//   cerr << "ROOT MARGINALS: " << rootMarginals.transpose() << endl;
-//  cerr << "M:\n" << T << endl;
-}
-
-#else
-
-void ArcFactoredForest::EdgeMarginals(prob_t *) {
-  cerr << "EdgeMarginals() requires --with-eigen!\n";
-  abort();
-}
-
-#endif
-
diff --git a/rst_parser/arc_ff.cc b/rst_parser/arc_ff.cc
deleted file mode 100644
index c4e5aa17..00000000
--- a/rst_parser/arc_ff.cc
+++ /dev/null
@@ -1,183 +0,0 @@
-#include "arc_ff.h"
-
-#include <iostream>
-#include <sstream>
-
-#include "stringlib.h"
-#include "tdict.h"
-#include "fdict.h"
-#include "sentence_metadata.h"
-
-using namespace std;
-
-struct ArcFFImpl {
-  ArcFFImpl() : kROOT("ROOT"), kLEFT_POS("LEFT"), kRIGHT_POS("RIGHT") {}
-  const string kROOT;
-  const string kLEFT_POS;
-  const string kRIGHT_POS;
-  map<WordID, vector<int> > pcs;
-
-  void PrepareForInput(const TaggedSentence& sent) {
-    pcs.clear();
-    for (int i = 0; i < sent.pos.size(); ++i)
-      pcs[sent.pos[i]].resize(1, 0);
-    pcs[sent.pos[0]][0] = 1;
-    for (int i = 1; i < sent.pos.size(); ++i) {
-      const WordID posi = sent.pos[i];
-      for (map<WordID, vector<int> >::iterator j = pcs.begin(); j != pcs.end(); ++j) {
-        const WordID posj = j->first;
-        vector<int>& cs = j->second;
-        cs.push_back(cs.back() + (posj == posi ? 1 : 0));
-      }
-    }
-  }
-
-  template <typename A>
-  static void Fire(SparseVector<weight_t>* v, const A& a) {
-    ostringstream os;
-    os << a;
-    v->set_value(FD::Convert(os.str()), 1);
-  }
-
-  template <typename A, typename B>
-  static void Fire(SparseVector<weight_t>* v, const A& a, const B& b) {
-    ostringstream os;
-    os << a << ':' << b;
-    v->set_value(FD::Convert(os.str()), 1);
-  }
-
-  template <typename A, typename B, typename C>
-  static void Fire(SparseVector<weight_t>* v, const A& a, const B& b, const C& c) {
-    ostringstream os;
-    os << a << ':' << b << '_' << c;
-    v->set_value(FD::Convert(os.str()), 1);
-  }
-
-  template <typename A, typename B, typename C, typename D>
-  static void Fire(SparseVector<weight_t>* v, const A& a, const B& b, const C& c, const D& d) {
-    ostringstream os;
-    os << a << ':' << b << '_' << c << '_' << d;
-    v->set_value(FD::Convert(os.str()), 1);
-  }
-
-  template <typename A, typename B, typename C, typename D, typename E>
-  static void Fire(SparseVector<weight_t>* v, const A& a, const B& b, const C& c, const D& d, const E& e) {
-    ostringstream os;
-    os << a << ':' << b << '_' << c << '_' << d << '_' << e;
-    v->set_value(FD::Convert(os.str()), 1);
-  }
-
-  static void AddConjoin(const SparseVector<double>& v, const string& feat, SparseVector<double>* pf) {
-    for (SparseVector<double>::const_iterator it = v.begin(); it != v.end(); ++it)
-      pf->set_value(FD::Convert(FD::Convert(it->first) + "_" + feat), it->second);
-  }
-
-  static inline string Fixup(const string& str) {
-    string res = LowercaseString(str);
-    if (res.size() < 6) return res;
-    return res.substr(0, 5) + "*";
-  }
-
-  static inline string Suffix(const string& str) {
-    if (str.size() < 4) return ""; else return str.substr(str.size() - 3);
-  }
-
-  void EdgeFeatures(const TaggedSentence& sent,
-                    short h,
-                    short m,
-                    SparseVector<weight_t>* features) const {
-    const bool is_root = (h == -1);
-    const string head_word = (is_root ? kROOT : Fixup(TD::Convert(sent.words[h])));
-    int num_words = sent.words.size();
-    const string& head_pos = (is_root ? kROOT : TD::Convert(sent.pos[h]));
-    const string mod_word = Fixup(TD::Convert(sent.words[m]));
-    const string& mod_pos = TD::Convert(sent.pos[m]);
-    const string& mod_pos_L = (m > 0 ? TD::Convert(sent.pos[m-1]) : kLEFT_POS);
-    const string& mod_pos_R = (m < sent.pos.size() - 1 ? TD::Convert(sent.pos[m]) : kRIGHT_POS);
-    const bool bdir = m < h;
-    const string dir = (bdir ? "MLeft" : "MRight");
-    int v = m - h;
-    if (v < 0) {
-      v= -1 - int(log(-v) / log(1.6));
-    } else {
-      v= int(log(v) / log(1.6)) + 1;
-    }
-    ostringstream os;
-    if (v < 0) os << "LenL" << -v; else os << "LenR" << v;
-    const string lenstr = os.str();
-    Fire(features, dir);
-    Fire(features, lenstr);
-    // dir, lenstr
-    if (is_root) {
-      Fire(features, "wROOT", mod_word);
-      Fire(features, "pROOT", mod_pos);
-      Fire(features, "wpROOT", mod_word, mod_pos);
-      Fire(features, "DROOT", mod_pos, lenstr);
-      Fire(features, "LROOT", mod_pos_L);
-      Fire(features, "RROOT", mod_pos_R);
-      Fire(features, "LROOT", mod_pos_L, mod_pos);
-      Fire(features, "RROOT", mod_pos_R, mod_pos);
-      Fire(features, "LDist", m);
-      Fire(features, "RDist", num_words - m);
-    } else { // not root
-      const string& head_pos_L = (h > 0 ? TD::Convert(sent.pos[h-1]) : kLEFT_POS);
-      const string& head_pos_R = (h < sent.pos.size() - 1 ? TD::Convert(sent.pos[h]) : kRIGHT_POS);
-      SparseVector<double> fv;
-      SparseVector<double>* f = &fv;
-      Fire(f, "H", head_pos);
-      Fire(f, "M", mod_pos);
-      Fire(f, "HM", head_pos, mod_pos);
-
-      // surrounders
-      Fire(f, "posLL", head_pos, mod_pos, head_pos_L, mod_pos_L);
-      Fire(f, "posRR", head_pos, mod_pos, head_pos_R, mod_pos_R);
-      Fire(f, "posLR", head_pos, mod_pos, head_pos_L, mod_pos_R);
-      Fire(f, "posRL", head_pos, mod_pos, head_pos_R, mod_pos_L);
-
-      // between features
-      int left = min(h,m);
-      int right = max(h,m);
-      if (right - left >= 2) {
-        if (bdir) --right; else ++left;
-        for (map<WordID, vector<int> >::const_iterator it = pcs.begin(); it != pcs.end(); ++it) {
-          if (it->second[left] != it->second[right]) {
-            Fire(f, "BT", head_pos, TD::Convert(it->first), mod_pos);
-          }
-        }
-      }
-
-      Fire(f, "wH", head_word);
-      Fire(f, "wM", mod_word);
-      Fire(f, "wpH", head_word, head_pos);
-      Fire(f, "wpM", mod_word, mod_pos);
-      Fire(f, "pHwM", head_pos, mod_word);
-      Fire(f, "wHpM", head_word, mod_pos);
-
-      Fire(f, "wHM", head_word, mod_word);
-      Fire(f, "pHMwH", head_pos, mod_pos, head_word);
-      Fire(f, "pHMwM", head_pos, mod_pos, mod_word);
-      Fire(f, "wHMpH", head_word, mod_word, head_pos);
-      Fire(f, "wHMpM", head_word, mod_word, mod_pos);
-      Fire(f, "wHMpHM", head_word, mod_word, head_pos, mod_pos);
-
-      AddConjoin(fv, dir, features);
-      AddConjoin(fv, lenstr, features);
-      (*features) += fv;
-    }
-  }
-};
-
-ArcFeatureFunctions::ArcFeatureFunctions() : pimpl(new ArcFFImpl) {}
-ArcFeatureFunctions::~ArcFeatureFunctions() { delete pimpl; }
-
-void ArcFeatureFunctions::PrepareForInput(const TaggedSentence& sentence) {
-  pimpl->PrepareForInput(sentence);
-}
-
-void ArcFeatureFunctions::EdgeFeatures(const TaggedSentence& sentence,
-                                       short h,
-                                       short m,
-                                       SparseVector<weight_t>* features) const {
-  pimpl->EdgeFeatures(sentence, h, m, features);
-}
-
diff --git a/rst_parser/arc_ff.h b/rst_parser/arc_ff.h
deleted file mode 100644
index 52f311d2..00000000
--- a/rst_parser/arc_ff.h
+++ /dev/null
@@ -1,28 +0,0 @@
-#ifndef _ARC_FF_H_
-#define _ARC_FF_H_
-
-#include <string>
-#include "sparse_vector.h"
-#include "weights.h"
-#include "arc_factored.h"
-
-struct TaggedSentence;
-struct ArcFFImpl;
-class ArcFeatureFunctions {
- public:
-  ArcFeatureFunctions();
-  ~ArcFeatureFunctions();
-
-  // called once, per input, before any calls to EdgeFeatures
-  // used to initialize sentence-specific data structures
-  void PrepareForInput(const TaggedSentence& sentence);
-
-  void EdgeFeatures(const TaggedSentence& sentence,
-                    short h,
-                    short m,
-                    SparseVector<weight_t>* features) const;
- private:
-  ArcFFImpl* pimpl;
-};
-
-#endif
diff --git a/rst_parser/dep_training.cc b/rst_parser/dep_training.cc
deleted file mode 100644
index ef97798b..00000000
--- a/rst_parser/dep_training.cc
+++ /dev/null
@@ -1,76 +0,0 @@
-#include "dep_training.h"
-
-#include <vector>
-#include <iostream>
-
-#include "stringlib.h"
-#include "filelib.h"
-#include "tdict.h"
-#include "picojson.h"
-
-using namespace std;
-
-static void ParseInstance(const string& line, int start, TrainingInstance* out, int lc = 0) {
-  picojson::value obj;
-  string err;
-  picojson::parse(obj, line.begin() + start, line.end(), &err);
-  if (err.size() > 0) { cerr << "JSON parse error in " << lc << ": " << err << endl; abort(); }
-  TrainingInstance& cur = *out;
-  TaggedSentence& ts = cur.ts;
-  EdgeSubset& tree = cur.tree;
-  ts.pos.clear();
-  ts.words.clear();
-  tree.roots.clear();
-  tree.h_m_pairs.clear();
-  assert(obj.is<picojson::object>());
-  const picojson::object& d = obj.get<picojson::object>();
-  const picojson::array& ta = d.find("tokens")->second.get<picojson::array>();
-  for (unsigned i = 0; i < ta.size(); ++i) {
-    ts.words.push_back(TD::Convert(ta[i].get<picojson::array>()[0].get<string>()));
-    ts.pos.push_back(TD::Convert(ta[i].get<picojson::array>()[1].get<string>()));
-  }
-  if (d.find("deps") != d.end()) {
-    const picojson::array& da = d.find("deps")->second.get<picojson::array>();
-    for (unsigned i = 0; i < da.size(); ++i) {
-      const picojson::array& thm = da[i].get<picojson::array>();
-      // get dep type here
-      short h = thm[2].get<double>();
-      short m = thm[1].get<double>();
-      if (h < 0)
-        tree.roots.push_back(m);
-      else
-        tree.h_m_pairs.push_back(make_pair(h,m));
-    }
-  }
-  //cerr << TD::GetString(ts.words) << endl << TD::GetString(ts.pos) << endl << tree << endl;
-}
-
-bool TrainingInstance::ReadInstance(std::istream* in, TrainingInstance* instance) {
-  string line;
-  if (!getline(*in, line)) return false;
-  size_t pos = line.rfind('\t');
-  assert(pos != string::npos);
-  static int lc = 0; ++lc;
-  ParseInstance(line, pos + 1, instance, lc);
-  return true;
-}
-
-void TrainingInstance::ReadTrainingCorpus(const string& fname, vector<TrainingInstance>* corpus, int rank, int size) {
-  ReadFile rf(fname);
-  istream& in = *rf.stream();
-  string line;
-  int lc = 0;
-  bool flag = false;
-  while(getline(in, line)) {
-    ++lc;
-    if ((lc-1) % size != rank) continue;
-    if (rank == 0 && lc % 10 == 0) { cerr << '.' << flush; flag = true; }
-    if (rank == 0 && lc % 400 == 0) { cerr << " [" << lc << "]\n"; flag = false; }
-    size_t pos = line.rfind('\t');
-    assert(pos != string::npos);
-    corpus->push_back(TrainingInstance());
-    ParseInstance(line, pos + 1, &corpus->back(), lc);
-  }
-  if (flag) cerr << "\nRead " << lc << " training instances\n";
-}
-
diff --git a/rst_parser/dep_training.h b/rst_parser/dep_training.h
deleted file mode 100644
index 3eeee22e..00000000
--- a/rst_parser/dep_training.h
+++ /dev/null
@@ -1,19 +0,0 @@
-#ifndef _DEP_TRAINING_H_
-#define _DEP_TRAINING_H_
-
-#include <iostream>
-#include <string>
-#include <vector>
-#include "arc_factored.h"
-#include "weights.h"
-
-struct TrainingInstance {
-  TaggedSentence ts;
-  EdgeSubset tree;
-  SparseVector<weight_t> features;
-  // reads a "Jsent" formatted dependency file
-  static bool ReadInstance(std::istream* in, TrainingInstance* instance); // returns false at EOF
-  static void ReadTrainingCorpus(const std::string& fname, std::vector<TrainingInstance>* corpus, int rank = 0, int size = 1);
-};
-
-#endif
diff --git a/rst_parser/global_ff.cc b/rst_parser/global_ff.cc
deleted file mode 100644
index ae410875..00000000
--- a/rst_parser/global_ff.cc
+++ /dev/null
@@ -1,44 +0,0 @@
-#include "global_ff.h"
-
-#include <iostream>
-#include <sstream>
-
-#include "tdict.h"
-
-using namespace std;
-
-struct GFFImpl {
-  void PrepareForInput(const TaggedSentence& sentence) {
-  }
-  void Features(const TaggedSentence& sentence,
-                const EdgeSubset& tree,
-                SparseVector<double>* feats) const {
-    const vector<WordID>& words = sentence.words;
-    const vector<WordID>& tags = sentence.pos;
-    const vector<pair<short,short> >& hms = tree.h_m_pairs;
-    assert(words.size() == tags.size());
-    vector<int> mods(words.size());
-    for (int i = 0; i < hms.size(); ++i) {
-      mods[hms[i].first]++;        // first = head, second = modifier
-    }
-    for (int i = 0; i < mods.size(); ++i) {
-      ostringstream os;
-      os << "NM:" << TD::Convert(tags[i]) << "_" << mods[i];
-      feats->add_value(FD::Convert(os.str()), 1.0);
-    }
-  }
-};
-
-GlobalFeatureFunctions::GlobalFeatureFunctions() : pimpl(new GFFImpl) {}
-GlobalFeatureFunctions::~GlobalFeatureFunctions() { delete pimpl; }
-
-void GlobalFeatureFunctions::PrepareForInput(const TaggedSentence& sentence) {
-  pimpl->PrepareForInput(sentence);
-}
-
-void GlobalFeatureFunctions::Features(const TaggedSentence& sentence,
-                                      const EdgeSubset& tree,
-                                      SparseVector<double>* feats) const {
-  pimpl->Features(sentence, tree, feats);
-}
-
diff --git a/rst_parser/global_ff.h b/rst_parser/global_ff.h
deleted file mode 100644
index d71d0fa1..00000000
--- a/rst_parser/global_ff.h
+++ /dev/null
@@ -1,18 +0,0 @@
-#ifndef _GLOBAL_FF_H_
-#define _GLOBAL_FF_H_
-
-#include "arc_factored.h"
-
-struct GFFImpl;
-struct GlobalFeatureFunctions {
-  GlobalFeatureFunctions();
-  ~GlobalFeatureFunctions();
-  void PrepareForInput(const TaggedSentence& sentence);
-  void Features(const TaggedSentence& sentence,
-                const EdgeSubset& tree,
-                SparseVector<double>* feats) const;
- private:
-  GFFImpl* pimpl;
-};
-
-#endif
diff --git a/rst_parser/mst_train.cc b/rst_parser/mst_train.cc
deleted file mode 100644
index a78df600..00000000
--- a/rst_parser/mst_train.cc
+++ /dev/null
@@ -1,228 +0,0 @@
-#include "arc_factored.h"
-
-#include <vector>
-#include <iostream>
-#include <boost/program_options.hpp>
-#include <boost/program_options/variables_map.hpp>
-// #define HAVE_THREAD 1
-#if HAVE_THREAD
-#include <boost/thread.hpp>
-#endif
-
-#include "arc_ff.h"
-#include "stringlib.h"
-#include "filelib.h"
-#include "tdict.h"
-#include "dep_training.h"
-#include "optimize.h"
-#include "weights.h"
-
-using namespace std;
-namespace po = boost::program_options;
-
-void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
-  po::options_description opts("Configuration options");
-  string cfg_file;
-  opts.add_options()
-        ("training_data,t",po::value<string>()->default_value("-"), "File containing training data (jsent format)")
-        ("weights,w",po::value<string>(), "Optional starting weights")
-        ("output_every_i_iterations,I",po::value<unsigned>()->default_value(1), "Write weights every I iterations")
-        ("regularization_strength,C",po::value<double>()->default_value(1.0), "Regularization strength")
-#ifdef HAVE_CMPH
-        ("cmph_perfect_feature_hash,h", po::value<string>(), "Load perfect hash function for features")
-#endif
-#if HAVE_THREAD
-        ("threads,T",po::value<unsigned>()->default_value(1), "Number of threads")
-#endif
-        ("correction_buffers,m", po::value<int>()->default_value(10), "LBFGS correction buffers");
-  po::options_description clo("Command line options");
-  clo.add_options()
-        ("config,c", po::value<string>(&cfg_file), "Configuration file")
-        ("help,?", "Print this help message and exit");
-
-  po::options_description dconfig_options, dcmdline_options;
-  dconfig_options.add(opts);
-  dcmdline_options.add(dconfig_options).add(clo);
-  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
-  if (cfg_file.size() > 0) {
-    ReadFile rf(cfg_file);
-    po::store(po::parse_config_file(*rf.stream(), dconfig_options), *conf);
-  }
-  if (conf->count("help")) {
-    cerr << dcmdline_options << endl;
-    exit(1);
-  }
-}
-
-void AddFeatures(double prob, const SparseVector<double>& fmap, vector<double>* g) {
-  for (SparseVector<double>::const_iterator it = fmap.begin(); it != fmap.end(); ++it)
-    (*g)[it->first] += it->second * prob;
-}
-
-double ApplyRegularizationTerms(const double C,
-                                const vector<double>& weights,
-                                vector<double>* g) {
-  assert(weights.size() == g->size());
-  double reg = 0;
-  for (size_t i = 0; i < weights.size(); ++i) {
-//    const double prev_w_i = (i < prev_weights.size() ? prev_weights[i] : 0.0);
-    const double& w_i = weights[i];
-    double& g_i = (*g)[i];
-    reg += C * w_i * w_i;
-    g_i += 2 * C * w_i;
-
-//    reg += T * (w_i - prev_w_i) * (w_i - prev_w_i);
-//    g_i += 2 * T * (w_i - prev_w_i);
-  }
-  return reg;
-}
-
-struct GradientWorker {
-  GradientWorker(int f,
-                 int t,
-                 vector<double>* w,
-                 vector<TrainingInstance>* c,
-                 vector<ArcFactoredForest>* fs) : obj(), weights(*w), from(f), to(t), corpus(*c), forests(*fs), g(w->size()) {}
-  void operator()() {
-    int every = (to - from) / 20;
-    if (!every) every++;
-    for (int i = from; i < to; ++i) {
-      if ((from == 0) && (i + 1) % every == 0) cerr << '.' << flush;
-      const int num_words = corpus[i].ts.words.size();
-      forests[i].Reweight(weights);
-      prob_t z;
-      forests[i].EdgeMarginals(&z);
-      obj -= log(z);
-      //cerr << " O = " << (-corpus[i].features.dot(weights)) << " D=" << -lz << "  OO= " << (-corpus[i].features.dot(weights) - lz) << endl;
-      //cerr << " ZZ = " << zz << endl;
-      for (int h = -1; h < num_words; ++h) {
-        for (int m = 0; m < num_words; ++m) {
-          if (h == m) continue;
-          const ArcFactoredForest::Edge& edge = forests[i](h,m);
-          const SparseVector<weight_t>& fmap = edge.features;
-          double prob = edge.edge_prob.as_float();
-          if (prob < -0.000001) { cerr << "Prob < 0: " << prob << endl; prob = 0; }
-          if (prob > 1.000001) { cerr << "Prob > 1: " << prob << endl; prob = 1; }
-          AddFeatures(prob, fmap, &g);
-          //mfm += fmap * prob;  // DE
-        }
-      }
-    }
-  }
-  double obj;
-  vector<double>& weights;
-  const int from, to;
-  vector<TrainingInstance>& corpus;
-  vector<ArcFactoredForest>& forests;
-  vector<double> g; // local gradient
-};
-
-int main(int argc, char** argv) {
-  int rank = 0;
-  int size = 1;
-  po::variables_map conf;
-  InitCommandLine(argc, argv, &conf);
-  if (conf.count("cmph_perfect_feature_hash")) {
-    cerr << "Loading perfect hash function from " << conf["cmph_perfect_feature_hash"].as<string>() << " ...\n";
-    FD::EnableHash(conf["cmph_perfect_feature_hash"].as<string>());
-    cerr << "  " << FD::NumFeats() << " features in map\n";
-  }
-  ArcFeatureFunctions ffs;
-  vector<TrainingInstance> corpus;
-  TrainingInstance::ReadTrainingCorpus(conf["training_data"].as<string>(), &corpus, rank, size);
-  vector<weight_t> weights;
-    Weights::InitFromFile(conf["weights"].as<string>(), &weights);
-  vector<ArcFactoredForest> forests(corpus.size());
-  SparseVector<double> empirical;
-  cerr << "Extracting features...\n";
-  bool flag = false;
-  for (int i = 0; i < corpus.size(); ++i) {
-    TrainingInstance& cur = corpus[i];
-    if (rank == 0 && (i+1) % 10 == 0) { cerr << '.' << flush; flag = true; }
-    if (rank == 0 && (i+1) % 400 == 0) { cerr << " [" << (i+1) << "]\n"; flag = false; }
-    ffs.PrepareForInput(cur.ts);
-    SparseVector<weight_t> efmap;
-    for (int j = 0; j < cur.tree.h_m_pairs.size(); ++j) {
-      efmap.clear();
-      ffs.EdgeFeatures(cur.ts, cur.tree.h_m_pairs[j].first,
-                       cur.tree.h_m_pairs[j].second,
-                       &efmap);
-      cur.features += efmap;
-    }
-    for (int j = 0; j < cur.tree.roots.size(); ++j) {
-      efmap.clear();
-      ffs.EdgeFeatures(cur.ts, -1, cur.tree.roots[j], &efmap);
-      cur.features += efmap;
-    }
-    empirical += cur.features;
-    forests[i].resize(cur.ts.words.size());
-    forests[i].ExtractFeatures(cur.ts, ffs);
-  }
-  if (flag) cerr << endl;
-  //cerr << "EMP: " << empirical << endl; //DE
-  weights.resize(FD::NumFeats(), 0.0);
-  vector<weight_t> g(FD::NumFeats(), 0.0);
-  cerr << "features initialized\noptimizing...\n";
-  boost::shared_ptr<BatchOptimizer> o;
-#if HAVE_THREAD
-  unsigned threads = conf["threads"].as<unsigned>();
-  if (threads > corpus.size()) threads = corpus.size();
-#else
-  const unsigned threads = 1;
-#endif
-  int chunk = corpus.size() / threads;
-  o.reset(new LBFGSOptimizer(g.size(), conf["correction_buffers"].as<int>()));
-  int iterations = 1000;
-  for (int iter = 0; iter < iterations; ++iter) {
-    cerr << "ITERATION " << iter << " " << flush;
-    fill(g.begin(), g.end(), 0.0);
-    for (SparseVector<double>::iterator it = empirical.begin(); it != empirical.end(); ++it)
-      g[it->first] = -it->second;
-    double obj = -empirical.dot(weights);
-    vector<boost::shared_ptr<GradientWorker> > jobs;
-    for (int from = 0; from < corpus.size(); from += chunk) {
-      int to = from + chunk;
-      if (to > corpus.size()) to = corpus.size();
-      jobs.push_back(boost::shared_ptr<GradientWorker>(new GradientWorker(from, to, &weights, &corpus, &forests)));
-    }
-#if HAVE_THREAD
-    boost::thread_group tg;
-    for (int i = 0; i < threads; ++i)
-      tg.create_thread(boost::ref(*jobs[i]));
-    tg.join_all();
-#else
-    (*jobs[0])();
-#endif
-    for (int i = 0; i < threads; ++i) {
-      obj += jobs[i]->obj;
-      vector<double>& tg = jobs[i]->g;
-      for (unsigned j = 0; j < g.size(); ++j)
-        g[j] += tg[j];
-    }
-    // SparseVector<double> mfm;  //DE
-    //cerr << endl << "E: " << empirical << endl;  // DE
-    //cerr << "M: " << mfm << endl;  // DE
-    double r = ApplyRegularizationTerms(conf["regularization_strength"].as<double>(), weights, &g);
-    double gnorm = 0;
-    for (int i = 0; i < g.size(); ++i)
-      gnorm += g[i]*g[i];
-    ostringstream ll;
-    ll << "ITER=" << (iter+1) << "\tOBJ=" << (obj+r) << "\t[F=" << obj << " R=" << r << "]\tGnorm=" << sqrt(gnorm);
-    cerr << ' ' << ll.str().substr(ll.str().find('\t')+1) << endl;
-    obj += r;
-    assert(obj >= 0);
-    o->Optimize(obj, g, &weights);
-    Weights::ShowLargestFeatures(weights);
-    const bool converged = o->HasConverged();
-    const char* ofname = converged ? "weights.final.gz" : "weights.cur.gz";
-    if (converged || ((iter+1) % conf["output_every_i_iterations"].as<unsigned>()) == 0) {
-      cerr << "writing..." << flush;
-      const string sl = ll.str();
-      Weights::WriteToFile(ofname, weights, true, &sl);
-      cerr << "done" << endl;
-    }
-    if (converged) { cerr << "CONVERGED\n"; break; }
-  }
-  return 0;
-}
-
diff --git a/rst_parser/picojson.h b/rst_parser/picojson.h
deleted file mode 100644
index bdb26057..00000000
--- a/rst_parser/picojson.h
+++ /dev/null
@@ -1,979 +0,0 @@
-/*
- * Copyright 2009-2010 Cybozu Labs, Inc.
- * Copyright 2011 Kazuho Oku
- * 
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- * 
- * 1. Redistributions of source code must retain the above copyright notice,
- *    this list of conditions and the following disclaimer.
- * 2. Redistributions in binary form must reproduce the above copyright notice,
- *    this list of conditions and the following disclaimer in the documentation
- *    and/or other materials provided with the distribution.
- * 
- * THIS SOFTWARE IS PROVIDED BY CYBOZU LABS, INC. ``AS IS'' AND ANY EXPRESS OR
- * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
- * MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
- * EVENT SHALL CYBOZU LABS, INC. OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
- * INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
- * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
- * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
- * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
- * THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- * 
- * The views and conclusions contained in the software and documentation are
- * those of the authors and should not be interpreted as representing official
- * policies, either expressed or implied, of Cybozu Labs, Inc.
- *
- */
-#ifndef picojson_h
-#define picojson_h
-
-#include <cassert>
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
-#include <iostream>
-#include <iterator>
-#include <map>
-#include <string>
-#include <vector>
-
-#ifdef _MSC_VER
-    #define SNPRINTF _snprintf_s
-    #pragma warning(push)
-    #pragma warning(disable : 4244) // conversion from int to char
-#else
-    #define SNPRINTF snprintf
-#endif
-
-namespace picojson {
-  
-  enum {
-    null_type,
-    boolean_type,
-    number_type,
-    string_type,
-    array_type,
-    object_type
-  };
-  
-  struct null {};
-  
-  class value {
-  public:
-    typedef std::vector<value> array;
-    typedef std::map<std::string, value> object;
-  protected:
-    int type_;
-    union {
-      bool boolean_;
-      double number_;
-      std::string* string_;
-      array* array_;
-      object* object_;
-    };
-  public:
-    value();
-    value(int type, bool);
-    explicit value(bool b);
-    explicit value(double n);
-    explicit value(const std::string& s);
-    explicit value(const array& a);
-    explicit value(const object& o);
-    explicit value(const char* s);
-    value(const char* s, size_t len);
-    ~value();
-    value(const value& x);
-    value& operator=(const value& x);
-    template <typename T> bool is() const;
-    template <typename T> const T& get() const;
-    template <typename T> T& get();
-    bool evaluate_as_boolean() const;
-    const value& get(size_t idx) const;
-    const value& get(const std::string& key) const;
-    bool contains(size_t idx) const;
-    bool contains(const std::string& key) const;
-    std::string to_str() const;
-    template <typename Iter> void serialize(Iter os) const;
-    std::string serialize() const;
-  private:
-    template <typename T> value(const T*); // intentionally defined to block implicit conversion of pointer to bool
-  };
-  
-  typedef value::array array;
-  typedef value::object object;
-  
-  inline value::value() : type_(null_type) {}
-  
-  inline value::value(int type, bool) : type_(type) {
-    switch (type) {
-#define INIT(p, v) case p##type: p = v; break
-      INIT(boolean_, false);
-      INIT(number_, 0.0);
-      INIT(string_, new std::string());
-      INIT(array_, new array());
-      INIT(object_, new object());
-#undef INIT
-    default: break;
-    }
-  }
-  
-  inline value::value(bool b) : type_(boolean_type) {
-    boolean_ = b;
-  }
-  
-  inline value::value(double n) : type_(number_type) {
-    number_ = n;
-  }
-  
-  inline value::value(const std::string& s) : type_(string_type) {
-    string_ = new std::string(s);
-  }
-  
-  inline value::value(const array& a) : type_(array_type) {
-    array_ = new array(a);
-  }
-  
-  inline value::value(const object& o) : type_(object_type) {
-    object_ = new object(o);
-  }
-  
-  inline value::value(const char* s) : type_(string_type) {
-    string_ = new std::string(s);
-  }
-  
-  inline value::value(const char* s, size_t len) : type_(string_type) {
-    string_ = new std::string(s, len);
-  }
-  
-  inline value::~value() {
-    switch (type_) {
-#define DEINIT(p) case p##type: delete p; break
-      DEINIT(string_);
-      DEINIT(array_);
-      DEINIT(object_);
-#undef DEINIT
-    default: break;
-    }
-  }
-  
-  inline value::value(const value& x) : type_(x.type_) {
-    switch (type_) {
-#define INIT(p, v) case p##type: p = v; break
-      INIT(boolean_, x.boolean_);
-      INIT(number_, x.number_);
-      INIT(string_, new std::string(*x.string_));
-      INIT(array_, new array(*x.array_));
-      INIT(object_, new object(*x.object_));
-#undef INIT
-    default: break;
-    }
-  }
-  
-  inline value& value::operator=(const value& x) {
-    if (this != &x) {
-      this->~value();
-      new (this) value(x);
-    }
-    return *this;
-  }
-  
-#define IS(ctype, jtype)			     \
-  template <> inline bool value::is<ctype>() const { \
-    return type_ == jtype##_type;		     \
-  }
-  IS(null, null)
-  IS(bool, boolean)
-  IS(int, number)
-  IS(double, number)
-  IS(std::string, string)
-  IS(array, array)
-  IS(object, object)
-#undef IS
-  
-#define GET(ctype, var)						\
-  template <> inline const ctype& value::get<ctype>() const {	\
-    assert("type mismatch! call vis<type>() before get<type>()" \
-	   && is<ctype>());				        \
-    return var;							\
-  }								\
-  template <> inline ctype& value::get<ctype>() {		\
-    assert("type mismatch! call is<type>() before get<type>()"	\
-	   && is<ctype>());					\
-    return var;							\
-  }
-  GET(bool, boolean_)
-  GET(double, number_)
-  GET(std::string, *string_)
-  GET(array, *array_)
-  GET(object, *object_)
-#undef GET
-  
-  inline bool value::evaluate_as_boolean() const {
-    switch (type_) {
-    case null_type:
-      return false;
-    case boolean_type:
-      return boolean_;
-    case number_type:
-      return number_ != 0;
-    case string_type:
-      return ! string_->empty();
-    default:
-      return true;
-    }
-  }
-  
-  inline const value& value::get(size_t idx) const {
-    static value s_null;
-    assert(is<array>());
-    return idx < array_->size() ? (*array_)[idx] : s_null;
-  }
-
-  inline const value& value::get(const std::string& key) const {
-    static value s_null;
-    assert(is<object>());
-    object::const_iterator i = object_->find(key);
-    return i != object_->end() ? i->second : s_null;
-  }
-
-  inline bool value::contains(size_t idx) const {
-    assert(is<array>());
-    return idx < array_->size();
-  }
-
-  inline bool value::contains(const std::string& key) const {
-    assert(is<object>());
-    object::const_iterator i = object_->find(key);
-    return i != object_->end();
-  }
-  
-  inline std::string value::to_str() const {
-    switch (type_) {
-    case null_type:      return "null";
-    case boolean_type:   return boolean_ ? "true" : "false";
-    case number_type:    {
-      char buf[256];
-      double tmp;
-      SNPRINTF(buf, sizeof(buf), modf(number_, &tmp) == 0 ? "%.f" : "%f", number_);
-      return buf;
-    }
-    case string_type:    return *string_;
-    case array_type:     return "array";
-    case object_type:    return "object";
-    default:             assert(0);
-#ifdef _MSC_VER
-      __assume(0);
-#endif
-    }
-  }
-  
-  template <typename Iter> void copy(const std::string& s, Iter oi) {
-    std::copy(s.begin(), s.end(), oi);
-  }
-  
-  template <typename Iter> void serialize_str(const std::string& s, Iter oi) {
-    *oi++ = '"';
-    for (std::string::const_iterator i = s.begin(); i != s.end(); ++i) {
-      switch (*i) {
-#define MAP(val, sym) case val: copy(sym, oi); break
-	MAP('"', "\\\"");
-	MAP('\\', "\\\\");
-	MAP('/', "\\/");
-	MAP('\b', "\\b");
-	MAP('\f', "\\f");
-	MAP('\n', "\\n");
-	MAP('\r', "\\r");
-	MAP('\t', "\\t");
-#undef MAP
-      default:
-	if ((unsigned char)*i < 0x20 || *i == 0x7f) {
-	  char buf[7];
-	  SNPRINTF(buf, sizeof(buf), "\\u%04x", *i & 0xff);
-	  copy(buf, buf + 6, oi);
-	  } else {
-	  *oi++ = *i;
-	}
-	break;
-      }
-    }
-    *oi++ = '"';
-  }
-  
-  template <typename Iter> void value::serialize(Iter oi) const {
-    switch (type_) {
-    case string_type:
-      serialize_str(*string_, oi);
-      break;
-    case array_type: {
-      *oi++ = '[';
-      for (array::const_iterator i = array_->begin(); i != array_->end(); ++i) {
-	if (i != array_->begin()) {
-	  *oi++ = ',';
-	}
-	i->serialize(oi);
-      }
-      *oi++ = ']';
-      break;
-    }
-    case object_type: {
-      *oi++ = '{';
-      for (object::const_iterator i = object_->begin();
-	   i != object_->end();
-	   ++i) {
-	if (i != object_->begin()) {
-	  *oi++ = ',';
-	}
-	serialize_str(i->first, oi);
-	*oi++ = ':';
-	i->second.serialize(oi);
-      }
-      *oi++ = '}';
-      break;
-    }
-    default:
-      copy(to_str(), oi);
-      break;
-    }
-  }
-  
-  inline std::string value::serialize() const {
-    std::string s;
-    serialize(std::back_inserter(s));
-    return s;
-  }
-  
-  template <typename Iter> class input {
-  protected:
-    Iter cur_, end_;
-    int last_ch_;
-    bool ungot_;
-    int line_;
-  public:
-    input(const Iter& first, const Iter& last) : cur_(first), end_(last), last_ch_(-1), ungot_(false), line_(1) {}
-    int getc() {
-      if (ungot_) {
-	ungot_ = false;
-	return last_ch_;
-      }
-      if (cur_ == end_) {
-	last_ch_ = -1;
-	return -1;
-      }
-      if (last_ch_ == '\n') {
-	line_++;
-      }
-      last_ch_ = *cur_++ & 0xff;
-      return last_ch_;
-    }
-    void ungetc() {
-      if (last_ch_ != -1) {
-	assert(! ungot_);
-	ungot_ = true;
-      }
-    }
-    Iter cur() const { return cur_; }
-    int line() const { return line_; }
-    void skip_ws() {
-      while (1) {
-	int ch = getc();
-	if (! (ch == ' ' || ch == '\t' || ch == '\n' || ch == '\r')) {
-	  ungetc();
-	  break;
-	}
-      }
-    }
-    int expect(int expect) {
-      skip_ws();
-      if (getc() != expect) {
-	ungetc();
-	return false;
-      }
-      return true;
-    }
-    bool match(const std::string& pattern) {
-      for (std::string::const_iterator pi(pattern.begin());
-	   pi != pattern.end();
-	   ++pi) {
-	if (getc() != *pi) {
-	  ungetc();
-	  return false;
-	}
-      }
-      return true;
-    }
-  };
-  
-  template<typename Iter> inline int _parse_quadhex(input<Iter> &in) {
-    int uni_ch = 0, hex;
-    for (int i = 0; i < 4; i++) {
-      if ((hex = in.getc()) == -1) {
-	return -1;
-      }
-      if ('0' <= hex && hex <= '9') {
-	hex -= '0';
-      } else if ('A' <= hex && hex <= 'F') {
-	hex -= 'A' - 0xa;
-      } else if ('a' <= hex && hex <= 'f') {
-	hex -= 'a' - 0xa;
-      } else {
-	in.ungetc();
-	return -1;
-      }
-      uni_ch = uni_ch * 16 + hex;
-    }
-    return uni_ch;
-  }
-  
-  template<typename String, typename Iter> inline bool _parse_codepoint(String& out, input<Iter>& in) {
-    int uni_ch;
-    if ((uni_ch = _parse_quadhex(in)) == -1) {
-      return false;
-    }
-    if (0xd800 <= uni_ch && uni_ch <= 0xdfff) {
-      if (0xdc00 <= uni_ch) {
-	// a second 16-bit of a surrogate pair appeared
-	return false;
-      }
-      // first 16-bit of surrogate pair, get the next one
-      if (in.getc() != '\\' || in.getc() != 'u') {
-	in.ungetc();
-	return false;
-      }
-      int second = _parse_quadhex(in);
-      if (! (0xdc00 <= second && second <= 0xdfff)) {
-	return false;
-      }
-      uni_ch = ((uni_ch - 0xd800) << 10) | ((second - 0xdc00) & 0x3ff);
-      uni_ch += 0x10000;
-    }
-    if (uni_ch < 0x80) {
-      out.push_back(uni_ch);
-    } else {
-      if (uni_ch < 0x800) {
-	out.push_back(0xc0 | (uni_ch >> 6));
-      } else {
-	if (uni_ch < 0x10000) {
-	  out.push_back(0xe0 | (uni_ch >> 12));
-	} else {
-	  out.push_back(0xf0 | (uni_ch >> 18));
-	  out.push_back(0x80 | ((uni_ch >> 12) & 0x3f));
-	}
-	out.push_back(0x80 | ((uni_ch >> 6) & 0x3f));
-      }
-      out.push_back(0x80 | (uni_ch & 0x3f));
-    }
-    return true;
-  }
-  
-  template<typename String, typename Iter> inline bool _parse_string(String& out, input<Iter>& in) {
-    while (1) {
-      int ch = in.getc();
-      if (ch < ' ') {
-	in.ungetc();
-	return false;
-      } else if (ch == '"') {
-	return true;
-      } else if (ch == '\\') {
-	if ((ch = in.getc()) == -1) {
-	  return false;
-	}
-	switch (ch) {
-#define MAP(sym, val) case sym: out.push_back(val); break
-	  MAP('"', '\"');
-	  MAP('\\', '\\');
-	  MAP('/', '/');
-	  MAP('b', '\b');
-	  MAP('f', '\f');
-	  MAP('n', '\n');
-	  MAP('r', '\r');
-	  MAP('t', '\t');
-#undef MAP
-	case 'u':
-	  if (! _parse_codepoint(out, in)) {
-	    return false;
-	  }
-	  break;
-	default:
-	  return false;
-	}
-      } else {
-	out.push_back(ch);
-      }
-    }
-    return false;
-  }
-  
-  template <typename Context, typename Iter> inline bool _parse_array(Context& ctx, input<Iter>& in) {
-    if (! ctx.parse_array_start()) {
-      return false;
-    }
-    if (in.expect(']')) {
-      return true;
-    }
-    size_t idx = 0;
-    do {
-      if (! ctx.parse_array_item(in, idx)) {
-	return false;
-      }
-      idx++;
-    } while (in.expect(','));
-    return in.expect(']');
-  }
-  
-  template <typename Context, typename Iter> inline bool _parse_object(Context& ctx, input<Iter>& in) {
-    if (! ctx.parse_object_start()) {
-      return false;
-    }
-    if (in.expect('}')) {
-      return true;
-    }
-    do {
-      std::string key;
-      if (! in.expect('"')
-	  || ! _parse_string(key, in)
-	  || ! in.expect(':')) {
-	return false;
-      }
-      if (! ctx.parse_object_item(in, key)) {
-	return false;
-      }
-    } while (in.expect(','));
-    return in.expect('}');
-  }
-  
-  template <typename Iter> inline bool _parse_number(double& out, input<Iter>& in) {
-    std::string num_str;
-    while (1) {
-      int ch = in.getc();
-      if (('0' <= ch && ch <= '9') || ch == '+' || ch == '-' || ch == '.'
-	  || ch == 'e' || ch == 'E') {
-	num_str.push_back(ch);
-      } else {
-	in.ungetc();
-	break;
-      }
-    }
-    char* endp;
-    out = strtod(num_str.c_str(), &endp);
-    return endp == num_str.c_str() + num_str.size();
-  }
-  
-  template <typename Context, typename Iter> inline bool _parse(Context& ctx, input<Iter>& in) {
-    in.skip_ws();
-    int ch = in.getc();
-    switch (ch) {
-#define IS(ch, text, op) case ch: \
-      if (in.match(text) && op) { \
-	return true; \
-      } else { \
-	return false; \
-      }
-      IS('n', "ull", ctx.set_null());
-      IS('f', "alse", ctx.set_bool(false));
-      IS('t', "rue", ctx.set_bool(true));
-#undef IS
-    case '"':
-      return ctx.parse_string(in);
-    case '[':
-      return _parse_array(ctx, in);
-    case '{':
-      return _parse_object(ctx, in);
-    default:
-      if (('0' <= ch && ch <= '9') || ch == '-') {
-	in.ungetc();
-	double f;
-	if (_parse_number(f, in)) {
-	  ctx.set_number(f);
-	  return true;
-	} else {
-	  return false;
-	}
-      }
-      break;
-    }
-    in.ungetc();
-    return false;
-  }
-  
-  class deny_parse_context {
-  public:
-    bool set_null() { return false; }
-    bool set_bool(bool) { return false; }
-    bool set_number(double) { return false; }
-    template <typename Iter> bool parse_string(input<Iter>&) { return false; }
-    bool parse_array_start() { return false; }
-    template <typename Iter> bool parse_array_item(input<Iter>&, size_t) {
-      return false;
-    }
-    bool parse_object_start() { return false; }
-    template <typename Iter> bool parse_object_item(input<Iter>&, const std::string&) {
-      return false;
-    }
-  };
-  
-  class default_parse_context {
-  protected:
-    value* out_;
-  public:
-    default_parse_context(value* out) : out_(out) {}
-    bool set_null() {
-      *out_ = value();
-      return true;
-    }
-    bool set_bool(bool b) {
-      *out_ = value(b);
-      return true;
-    }
-    bool set_number(double f) {
-      *out_ = value(f);
-      return true;
-    }
-    template<typename Iter> bool parse_string(input<Iter>& in) {
-      *out_ = value(string_type, false);
-      return _parse_string(out_->get<std::string>(), in);
-    }
-    bool parse_array_start() {
-      *out_ = value(array_type, false);
-      return true;
-    }
-    template <typename Iter> bool parse_array_item(input<Iter>& in, size_t) {
-      array& a = out_->get<array>();
-      a.push_back(value());
-      default_parse_context ctx(&a.back());
-      return _parse(ctx, in);
-    }
-    bool parse_object_start() {
-      *out_ = value(object_type, false);
-      return true;
-    }
-    template <typename Iter> bool parse_object_item(input<Iter>& in, const std::string& key) {
-      object& o = out_->get<object>();
-      default_parse_context ctx(&o[key]);
-      return _parse(ctx, in);
-    }
-  private:
-    default_parse_context(const default_parse_context&);
-    default_parse_context& operator=(const default_parse_context&);
-  };
-
-  class null_parse_context {
-  public:
-    struct dummy_str {
-      void push_back(int) {}
-    };
-  public:
-    null_parse_context() {}
-    bool set_null() { return true; }
-    bool set_bool(bool) { return true; }
-    bool set_number(double) { return true; }
-    template <typename Iter> bool parse_string(input<Iter>& in) {
-      dummy_str s;
-      return _parse_string(s, in);
-    }
-    bool parse_array_start() { return true; }
-    template <typename Iter> bool parse_array_item(input<Iter>& in, size_t) {
-      return _parse(*this, in);
-    }
-    bool parse_object_start() { return true; }
-    template <typename Iter> bool parse_object_item(input<Iter>& in, const std::string&) {
-      return _parse(*this, in);
-    }
-  private:
-    null_parse_context(const null_parse_context&);
-    null_parse_context& operator=(const null_parse_context&);
-  };
-  
-  // obsolete, use the version below
-  template <typename Iter> inline std::string parse(value& out, Iter& pos, const Iter& last) {
-    std::string err;
-    pos = parse(out, pos, last, &err);
-    return err;
-  }
-  
-  template <typename Context, typename Iter> inline Iter _parse(Context& ctx, const Iter& first, const Iter& last, std::string* err) {
-    input<Iter> in(first, last);
-    if (! _parse(ctx, in) && err != NULL) {
-      char buf[64];
-      SNPRINTF(buf, sizeof(buf), "syntax error at line %d near: ", in.line());
-      *err = buf;
-      while (1) {
-	int ch = in.getc();
-	if (ch == -1 || ch == '\n') {
-	  break;
-	} else if (ch >= ' ') {
-	  err->push_back(ch);
-	}
-      }
-    }
-    return in.cur();
-  }
-  
-  template <typename Iter> inline Iter parse(value& out, const Iter& first, const Iter& last, std::string* err) {
-    default_parse_context ctx(&out);
-    return _parse(ctx, first, last, err);
-  }
-  
-  inline std::string parse(value& out, std::istream& is) {
-    std::string err;
-    parse(out, std::istreambuf_iterator<char>(is.rdbuf()),
-	  std::istreambuf_iterator<char>(), &err);
-    return err;
-  }
-  
-  template <typename T> struct last_error_t {
-    static std::string s;
-  };
-  template <typename T> std::string last_error_t<T>::s;
-  
-  inline void set_last_error(const std::string& s) {
-    last_error_t<bool>::s = s;
-  }
-  
-  inline const std::string& get_last_error() {
-    return last_error_t<bool>::s;
-  }
-
-  inline bool operator==(const value& x, const value& y) {
-    if (x.is<null>())
-      return y.is<null>();
-#define PICOJSON_CMP(type)					\
-    if (x.is<type>())						\
-      return y.is<type>() && x.get<type>() == y.get<type>()
-    PICOJSON_CMP(bool);
-    PICOJSON_CMP(double);
-    PICOJSON_CMP(std::string);
-    PICOJSON_CMP(array);
-    PICOJSON_CMP(object);
-#undef PICOJSON_CMP
-    assert(0);
-#ifdef _MSC_VER
-    __assume(0);
-#endif
-    return false;
-  }
-  
-  inline bool operator!=(const value& x, const value& y) {
-    return ! (x == y);
-  }
-}
-
-inline std::istream& operator>>(std::istream& is, picojson::value& x)
-{
-  picojson::set_last_error(std::string());
-  std::string err = picojson::parse(x, is);
-  if (! err.empty()) {
-    picojson::set_last_error(err);
-    is.setstate(std::ios::failbit);
-  }
-  return is;
-}
-
-inline std::ostream& operator<<(std::ostream& os, const picojson::value& x)
-{
-  x.serialize(std::ostream_iterator<char>(os));
-  return os;
-}
-#ifdef _MSC_VER
-    #pragma warning(pop)
-#endif
-
-#endif
-#ifdef TEST_PICOJSON
-#ifdef _MSC_VER
-    #pragma warning(disable : 4127) // conditional expression is constant
-#endif
-
-using namespace std;
-  
-static void plan(int num)
-{
-  printf("1..%d\n", num);
-}
-
-static bool success = true;
-
-static void ok(bool b, const char* name = "")
-{
-  static int n = 1;
-  if (! b)
-    success = false;
-  printf("%s %d - %s\n", b ? "ok" : "ng", n++, name);
-}
-
-template <typename T> void is(const T& x, const T& y, const char* name = "")
-{
-  if (x == y) {
-    ok(true, name);
-  } else {
-    ok(false, name);
-  }
-}
-
-#include <algorithm>
-
-int main(void)
-{
-  plan(75);
-
-  // constructors
-#define TEST(expr, expected) \
-    is(picojson::value expr .serialize(), string(expected), "picojson::value" #expr)
-  
-  TEST( (true),  "true");
-  TEST( (false), "false");
-  TEST( (42.0),   "42");
-  TEST( (string("hello")), "\"hello\"");
-  TEST( ("hello"), "\"hello\"");
-  TEST( ("hello", 4), "\"hell\"");
-  
-#undef TEST
-  
-#define TEST(in, type, cmp, serialize_test) {				\
-    picojson::value v;							\
-    const char* s = in;							\
-    string err = picojson::parse(v, s, s + strlen(s));			\
-    ok(err.empty(), in " no error");					\
-    ok(v.is<type>(), in " check type");					\
-    is<type>(v.get<type>(), cmp, in " correct output");			\
-    is(*s, '\0', in " read to eof");					\
-    if (serialize_test) {						\
-      is(v.serialize(), string(in), in " serialize");			\
-    }									\
-  }
-  TEST("false", bool, false, true);
-  TEST("true", bool, true, true);
-  TEST("90.5", double, 90.5, false);
-  TEST("\"hello\"", string, string("hello"), true);
-  TEST("\"\\\"\\\\\\/\\b\\f\\n\\r\\t\"", string, string("\"\\/\b\f\n\r\t"),
-       true);
-  TEST("\"\\u0061\\u30af\\u30ea\\u30b9\"", string,
-       string("a\xe3\x82\xaf\xe3\x83\xaa\xe3\x82\xb9"), false);
-  TEST("\"\\ud840\\udc0b\"", string, string("\xf0\xa0\x80\x8b"), false);
-#undef TEST
-
-#define TEST(type, expr) {					       \
-    picojson::value v;						       \
-    const char *s = expr;					       \
-    string err = picojson::parse(v, s, s + strlen(s));		       \
-    ok(err.empty(), "empty " #type " no error");		       \
-    ok(v.is<picojson::type>(), "empty " #type " check type");	       \
-    ok(v.get<picojson::type>().empty(), "check " #type " array size"); \
-  }
-  TEST(array, "[]");
-  TEST(object, "{}");
-#undef TEST
-  
-  {
-    picojson::value v;
-    const char *s = "[1,true,\"hello\"]";
-    string err = picojson::parse(v, s, s + strlen(s));
-    ok(err.empty(), "array no error");
-    ok(v.is<picojson::array>(), "array check type");
-    is(v.get<picojson::array>().size(), size_t(3), "check array size");
-    ok(v.contains(0), "check contains array[0]");
-    ok(v.get(0).is<double>(), "check array[0] type");
-    is(v.get(0).get<double>(), 1.0, "check array[0] value");
-    ok(v.contains(1), "check contains array[1]");
-    ok(v.get(1).is<bool>(), "check array[1] type");
-    ok(v.get(1).get<bool>(), "check array[1] value");
-    ok(v.contains(2), "check contains array[2]");
-    ok(v.get(2).is<string>(), "check array[2] type");
-    is(v.get(2).get<string>(), string("hello"), "check array[2] value");
-    ok(!v.contains(3), "check not contains array[3]");
-  }
-  
-  {
-    picojson::value v;
-    const char *s = "{ \"a\": true }";
-    string err = picojson::parse(v, s, s + strlen(s));
-    ok(err.empty(), "object no error");
-    ok(v.is<picojson::object>(), "object check type");
-    is(v.get<picojson::object>().size(), size_t(1), "check object size");
-    ok(v.contains("a"), "check contains property");
-    ok(v.get("a").is<bool>(), "check bool property exists");
-    is(v.get("a").get<bool>(), true, "check bool property value");
-    is(v.serialize(), string("{\"a\":true}"), "serialize object");
-    ok(!v.contains("z"), "check not contains property");
-  }
-
-#define TEST(json, msg) do {				\
-    picojson::value v;					\
-    const char *s = json;				\
-    string err = picojson::parse(v, s, s + strlen(s));	\
-    is(err, string("syntax error at line " msg), msg);	\
-  } while (0)
-  TEST("falsoa", "1 near: oa");
-  TEST("{]", "1 near: ]");
-  TEST("\n\bbell", "2 near: bell");
-  TEST("\"abc\nd\"", "1 near: ");
-#undef TEST
-  
-  {
-    picojson::value v1, v2;
-    const char *s;
-    string err;
-    s = "{ \"b\": true, \"a\": [1,2,\"three\"], \"d\": 2 }";
-    err = picojson::parse(v1, s, s + strlen(s));
-    s = "{ \"d\": 2.0, \"b\": true, \"a\": [1,2,\"three\"] }";
-    err = picojson::parse(v2, s, s + strlen(s));
-    ok((v1 == v2), "check == operator in deep comparison");
-  }
-
-  {
-    picojson::value v1, v2;
-    const char *s;
-    string err;
-    s = "{ \"b\": true, \"a\": [1,2,\"three\"], \"d\": 2 }";
-    err = picojson::parse(v1, s, s + strlen(s));
-    s = "{ \"d\": 2.0, \"a\": [1,\"three\"], \"b\": true }";
-    err = picojson::parse(v2, s, s + strlen(s));
-    ok((v1 != v2), "check != operator for array in deep comparison");
-  }
-
-  {
-    picojson::value v1, v2;
-    const char *s;
-    string err;
-    s = "{ \"b\": true, \"a\": [1,2,\"three\"], \"d\": 2 }";
-    err = picojson::parse(v1, s, s + strlen(s));
-    s = "{ \"d\": 2.0, \"a\": [1,2,\"three\"], \"b\": false }";
-    err = picojson::parse(v2, s, s + strlen(s));
-    ok((v1 != v2), "check != operator for object in deep comparison");
-  }
-
-  {
-    picojson::value v1, v2;
-    const char *s;
-    string err;
-    s = "{ \"b\": true, \"a\": [1,2,\"three\"], \"d\": 2 }";
-    err = picojson::parse(v1, s, s + strlen(s));
-    picojson::object& o = v1.get<picojson::object>();
-    o.erase("b");
-    picojson::array& a = o["a"].get<picojson::array>();
-    picojson::array::iterator i;
-    i = std::remove(a.begin(), a.end(), picojson::value(std::string("three")));
-    a.erase(i, a.end());
-    s = "{ \"a\": [1,2], \"d\": 2 }";
-    err = picojson::parse(v2, s, s + strlen(s));
-    ok((v1 == v2), "check erase()");
-  }
-
-  ok(picojson::value(3.0).serialize() == "3",
-     "integral number should be serialized as a integer");
-  
-  {
-    const char* s = "{ \"a\": [1,2], \"d\": 2 }";
-    picojson::null_parse_context ctx;
-    string err;
-    picojson::_parse(ctx, s, s + strlen(s), &err);
-    ok(err.empty(), "null_parse_context");
-  }
-  
-  return success ? 0 : 1;
-}
-
-#endif
diff --git a/rst_parser/rst.cc b/rst_parser/rst.cc
deleted file mode 100644
index bc91330b..00000000
--- a/rst_parser/rst.cc
+++ /dev/null
@@ -1,82 +0,0 @@
-#include "rst.h"
-
-using namespace std;
-
-// David B. Wilson. Generating Random Spanning Trees More Quickly than the Cover Time.
-// this is an awesome algorithm
-TreeSampler::TreeSampler(const ArcFactoredForest& af) : forest(af), usucc(af.size() + 1) {
-  // edges are directed from modifiers to heads, and finally to the root
-  vector<double> p;
-  for (int m = 1; m <= forest.size(); ++m) {
-#if USE_ALIAS_SAMPLER
-    p.clear();
-#else
-    SampleSet<double>& ss = usucc[m];
-#endif
-    double z = 0;
-    for (int h = 0; h <= forest.size(); ++h) {
-      double u = forest(h-1,m-1).edge_prob.as_float();
-      z += u;
-#if USE_ALIAS_SAMPLER
-      p.push_back(u);
-#else
-      ss.add(u);
-#endif
-    }
-#if USE_ALIAS_SAMPLER
-    for (int i = 0; i < p.size(); ++i) { p[i] /= z; }
-    usucc[m].Init(p);
-#endif
-  }
-}
-
-void TreeSampler::SampleRandomSpanningTree(EdgeSubset* tree, MT19937* prng) {
-  MT19937& rng = *prng;
-  const int r = 0;
-  bool success = false;
-  while (!success) {
-    int roots = 0;
-    tree->h_m_pairs.clear();
-    tree->roots.clear();
-    vector<int> next(forest.size() + 1, -1);
-    vector<char> in_tree(forest.size() + 1, 0);
-    in_tree[r] = 1;
-    //cerr << "Forest size: " << forest.size() << endl;
-    for (int i = 0; i <= forest.size(); ++i) {
-      //cerr << "Sampling starting at u=" << i << endl;
-      int u = i;
-      if (in_tree[u]) continue;
-      while(!in_tree[u]) {
-#if USE_ALIAS_SAMPLER
-        next[u] = usucc[u].Draw(rng);
-#else
-        next[u] = rng.SelectSample(usucc[u]);
-#endif
-        u = next[u];
-      }
-      u = i;
-      //cerr << (u-1);
-      int prev = u-1;
-      while(!in_tree[u]) {
-        in_tree[u] = true;
-        u = next[u];
-        //cerr << " > " << (u-1);
-        if (u == r) {
-          ++roots;
-          tree->roots.push_back(prev);
-        } else {
-          tree->h_m_pairs.push_back(make_pair<short,short>(u-1,prev));
-        }
-        prev = u-1;
-      }
-      //cerr << endl;
-    }
-    assert(roots > 0);
-    if (roots > 1) {
-      //cerr << "FAILURE\n";
-    } else {
-      success = true;
-    }
-  }
-};
-
diff --git a/rst_parser/rst.h b/rst_parser/rst.h
deleted file mode 100644
index 8bf389f7..00000000
--- a/rst_parser/rst.h
+++ /dev/null
@@ -1,21 +0,0 @@
-#ifndef _RST_H_
-#define _RST_H_
-
-#include <vector>
-#include "sampler.h"
-#include "arc_factored.h"
-#include "alias_sampler.h"
-
-struct TreeSampler {
-  explicit TreeSampler(const ArcFactoredForest& af);
-  void SampleRandomSpanningTree(EdgeSubset* tree, MT19937* rng);
-  const ArcFactoredForest& forest;
-#define USE_ALIAS_SAMPLER 1
-#if USE_ALIAS_SAMPLER
-  std::vector<AliasSampler> usucc;
-#else
-  std::vector<SampleSet<double> > usucc;
-#endif
-};
-
-#endif
diff --git a/rst_parser/rst_parse.cc b/rst_parser/rst_parse.cc
deleted file mode 100644
index 9c42a8f4..00000000
--- a/rst_parser/rst_parse.cc
+++ /dev/null
@@ -1,111 +0,0 @@
-#include "arc_factored.h"
-
-#include <vector>
-#include <iostream>
-#include <boost/program_options.hpp>
-#include <boost/program_options/variables_map.hpp>
-
-#include "timing_stats.h"
-#include "arc_ff.h"
-#include "dep_training.h"
-#include "stringlib.h"
-#include "filelib.h"
-#include "tdict.h"
-#include "weights.h"
-#include "rst.h"
-#include "global_ff.h"
-
-using namespace std;
-namespace po = boost::program_options;
-
-void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
-  po::options_description opts("Configuration options");
-  string cfg_file;
-  opts.add_options()
-        ("input,i",po::value<string>()->default_value("-"), "File containing test data (jsent format)")
-        ("q_weights,q",po::value<string>(), "Arc-factored weights for proposal distribution (mandatory)")
-        ("p_weights,p",po::value<string>(), "Weights for target distribution (optional)")
-        ("samples,n",po::value<unsigned>()->default_value(1000), "Number of samples");
-  po::options_description clo("Command line options");
-  clo.add_options()
-        ("config,c", po::value<string>(&cfg_file), "Configuration file")
-        ("help,?", "Print this help message and exit");
-
-  po::options_description dconfig_options, dcmdline_options;
-  dconfig_options.add(opts);
-  dcmdline_options.add(dconfig_options).add(clo);
-  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
-  if (cfg_file.size() > 0) {
-    ReadFile rf(cfg_file);
-    po::store(po::parse_config_file(*rf.stream(), dconfig_options), *conf);
-  }
-  if (conf->count("help") || conf->count("q_weights") == 0) {
-    cerr << dcmdline_options << endl;
-    exit(1);
-  }
-}
-
-int main(int argc, char** argv) {
-  po::variables_map conf;
-  InitCommandLine(argc, argv, &conf);
-  vector<weight_t> qweights, pweights;
-  Weights::InitFromFile(conf["q_weights"].as<string>(), &qweights);
-  if (conf.count("p_weights"))
-    Weights::InitFromFile(conf["p_weights"].as<string>(), &pweights);
-  const bool global = pweights.size() > 0;
-  ArcFeatureFunctions ffs;
-  GlobalFeatureFunctions gff;
-  ReadFile rf(conf["input"].as<string>());
-  istream* in = rf.stream();
-  TrainingInstance sent;
-  MT19937 rng;
-  int samples = conf["samples"].as<unsigned>();
-  int totroot = 0, root_right = 0, tot = 0, cor = 0;
-  while(TrainingInstance::ReadInstance(in, &sent)) {
-    ffs.PrepareForInput(sent.ts);
-    if (global) gff.PrepareForInput(sent.ts);
-    ArcFactoredForest forest(sent.ts.pos.size());
-    forest.ExtractFeatures(sent.ts, ffs);
-    forest.Reweight(qweights);
-    TreeSampler ts(forest);
-    double best_score = -numeric_limits<double>::infinity();
-    EdgeSubset best_tree;
-    for (int n = 0; n < samples; ++n) {
-      EdgeSubset tree;
-      ts.SampleRandomSpanningTree(&tree, &rng);
-      SparseVector<double> qfeats, gfeats;
-      tree.ExtractFeatures(sent.ts, ffs, &qfeats);
-      double score = 0;
-      if (global) {
-        gff.Features(sent.ts, tree, &gfeats);
-        score = (qfeats + gfeats).dot(pweights);
-      } else {
-        score = qfeats.dot(qweights);
-      }
-      if (score > best_score) {
-        best_tree = tree;
-        best_score = score;
-      }
-    }
-    cerr << "BEST SCORE: " << best_score << endl;
-    cout << best_tree << endl;
-    const bool sent_has_ref = sent.tree.h_m_pairs.size() > 0;
-    if (sent_has_ref) {
-      map<pair<short,short>, bool> ref;
-      for (int i = 0; i < sent.tree.h_m_pairs.size(); ++i)
-        ref[sent.tree.h_m_pairs[i]] = true;
-      int ref_root = sent.tree.roots.front();
-      if (ref_root == best_tree.roots.front()) { ++root_right; }
-      ++totroot;
-      for (int i = 0; i < best_tree.h_m_pairs.size(); ++i) {
-        if (ref[best_tree.h_m_pairs[i]]) {
-          ++cor;
-        }
-        ++tot;
-      }
-    }
-  }
-  cerr << "F = " << (double(cor + root_right) / (tot + totroot)) << endl;
-  return 0;
-}
-
diff --git a/rst_parser/rst_train.cc b/rst_parser/rst_train.cc
deleted file mode 100644
index a8b8dd84..00000000
--- a/rst_parser/rst_train.cc
+++ /dev/null
@@ -1,144 +0,0 @@
-#include "arc_factored.h"
-
-#include <vector>
-#include <iostream>
-#include <boost/program_options.hpp>
-#include <boost/program_options/variables_map.hpp>
-
-#include "timing_stats.h"
-#include "arc_ff.h"
-#include "dep_training.h"
-#include "stringlib.h"
-#include "filelib.h"
-#include "tdict.h"
-#include "weights.h"
-#include "rst.h"
-#include "global_ff.h"
-
-using namespace std;
-namespace po = boost::program_options;
-
-void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
-  po::options_description opts("Configuration options");
-  string cfg_file;
-  opts.add_options()
-        ("training_data,t",po::value<string>()->default_value("-"), "File containing training data (jsent format)")
-        ("q_weights,q",po::value<string>(), "Arc-factored weights for proposal distribution")
-        ("samples,n",po::value<unsigned>()->default_value(1000), "Number of samples");
-  po::options_description clo("Command line options");
-  clo.add_options()
-        ("config,c", po::value<string>(&cfg_file), "Configuration file")
-        ("help,?", "Print this help message and exit");
-
-  po::options_description dconfig_options, dcmdline_options;
-  dconfig_options.add(opts);
-  dcmdline_options.add(dconfig_options).add(clo);
-  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
-  if (cfg_file.size() > 0) {
-    ReadFile rf(cfg_file);
-    po::store(po::parse_config_file(*rf.stream(), dconfig_options), *conf);
-  }
-  if (conf->count("help")) {
-    cerr << dcmdline_options << endl;
-    exit(1);
-  }
-}
-
-int main(int argc, char** argv) {
-  po::variables_map conf;
-  InitCommandLine(argc, argv, &conf);
-  vector<weight_t> qweights(FD::NumFeats(), 0.0);
-  Weights::InitFromFile(conf["q_weights"].as<string>(), &qweights);
-  vector<TrainingInstance> corpus;
-  ArcFeatureFunctions ffs;
-  GlobalFeatureFunctions gff;
-  TrainingInstance::ReadTrainingCorpus(conf["training_data"].as<string>(), &corpus);
-  vector<ArcFactoredForest> forests(corpus.size());
-  vector<prob_t> zs(corpus.size());
-  SparseVector<double> empirical;
-  bool flag = false;
-  for (int i = 0; i < corpus.size(); ++i) {
-    TrainingInstance& cur = corpus[i];
-    if ((i+1) % 10 == 0) { cerr << '.' << flush; flag = true; }
-    if ((i+1) % 400 == 0) { cerr << " [" << (i+1) << "]\n"; flag = false; }
-    SparseVector<weight_t> efmap;
-    ffs.PrepareForInput(cur.ts);
-    gff.PrepareForInput(cur.ts);
-    for (int j = 0; j < cur.tree.h_m_pairs.size(); ++j) {
-      efmap.clear();
-      ffs.EdgeFeatures(cur.ts, cur.tree.h_m_pairs[j].first,
-                       cur.tree.h_m_pairs[j].second,
-                       &efmap);
-      cur.features += efmap;
-    }
-    for (int j = 0; j < cur.tree.roots.size(); ++j) {
-      efmap.clear();
-      ffs.EdgeFeatures(cur.ts, -1, cur.tree.roots[j], &efmap);
-      cur.features += efmap;
-    }
-    efmap.clear();
-    gff.Features(cur.ts, cur.tree, &efmap);
-    cur.features += efmap;
-    empirical += cur.features;
-    forests[i].resize(cur.ts.words.size());
-    forests[i].ExtractFeatures(cur.ts, ffs);
-    forests[i].Reweight(qweights);
-    forests[i].EdgeMarginals(&zs[i]);
-    zs[i] = prob_t::One() / zs[i];
-    // cerr << zs[i] << endl;
-    forests[i].Reweight(qweights);    // EdgeMarginals overwrites edge_prob
-  }
-  if (flag) cerr << endl;
-  MT19937 rng;
-  SparseVector<double> model_exp;
-  SparseVector<double> weights;
-  Weights::InitSparseVector(qweights, &weights);
-  int samples = conf["samples"].as<unsigned>();
-  for (int i = 0; i < corpus.size(); ++i) {
-#if 0
-    forests[i].EdgeMarginals();
-    model_exp.clear();
-    for (int h = -1; h < num_words; ++h) {
-      for (int m = 0; m < num_words; ++m) {
-        if (h == m) continue;
-        const ArcFactoredForest::Edge& edge = forests[i](h,m);
-        const SparseVector<weight_t>& fmap = edge.features;
-        double prob = edge.edge_prob.as_float();
-        model_exp += fmap * prob;
-      }
-    }
-    cerr << "TRUE EXP: " << model_exp << endl;
-    forests[i].Reweight(weights);
-#endif
-
-    TreeSampler ts(forests[i]);
-    prob_t zhat = prob_t::Zero();
-    SparseVector<prob_t> sampled_exp;
-    for (int n = 0; n < samples; ++n) {
-      EdgeSubset tree;
-      ts.SampleRandomSpanningTree(&tree, &rng);
-      SparseVector<double> qfeats, gfeats;
-      tree.ExtractFeatures(corpus[i].ts, ffs, &qfeats);
-      prob_t u; u.logeq(qfeats.dot(qweights));
-      const prob_t q = u / zs[i];  // proposal mass
-      gff.Features(corpus[i].ts, tree, &gfeats);
-      SparseVector<double> tot_feats = qfeats + gfeats;
-      u.logeq(tot_feats.dot(weights));
-      prob_t w = u / q;
-      zhat += w;
-      for (SparseVector<double>::iterator it = tot_feats.begin(); it != tot_feats.end(); ++it)
-        sampled_exp.add_value(it->first, w * prob_t(it->second));
-    }
-    sampled_exp /= zhat;
-    SparseVector<double> tot_m;
-    for (SparseVector<prob_t>::iterator it = sampled_exp.begin(); it != sampled_exp.end(); ++it)
-      tot_m.add_value(it->first, it->second.as_float());
-    //cerr << "DIFF: " << (tot_m - corpus[i].features) << endl;
-    const double eta = 0.03;
-    weights -= (tot_m - corpus[i].features) * eta;
-  }
-  cerr << "WEIGHTS.\n";
-  cerr << weights << endl;
-  return 0;
-}
-
diff --git a/training/Jamfile b/training/Jamfile
deleted file mode 100644
index 073451fa..00000000
--- a/training/Jamfile
+++ /dev/null
@@ -1,25 +0,0 @@
-import testing ;
-import option ;
-
-lib training : 
-  ..//utils
-  ..//mteval
-  ..//decoder
-  ../klm/lm//kenlm
-  ..//boost_program_options
-  ttables.cc
-  : <include>.
-  : :
-  <library>..//decoder
-  <library>../klm/lm//kenlm
-  <library>..//utils
-  <library>..//mteval
-  <library>..//boost_program_options
-  ;
-
-exe model1 : model1.cc : <include>../decoder ;
-
-# // all_tests [ glob *_test.cc ] : ..//decoder : <testing.arg>$(TOP)/decoder/test_data ;
-
-alias programs : model1 ;
-
diff --git a/training/Makefile.am b/training/Makefile.am
index 4cef0d5b..f9c25391 100644
--- a/training/Makefile.am
+++ b/training/Makefile.am
@@ -1,5 +1,5 @@
 bin_PROGRAMS = \
-  model1 \
+  fast_align \
   lbl_model \
   test_ngram \
   mr_em_map_adapter \
@@ -32,60 +32,60 @@ libtraining_a_SOURCES = \
   risk.cc
 
 mpi_online_optimize_SOURCES = mpi_online_optimize.cc
-mpi_online_optimize_LDADD = libtraining.a $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a ../klm/lm/libklm.a ../klm/util/libklm_util.a -lz
+mpi_online_optimize_LDADD = libtraining.a $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/klm/search/libksearch.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a ../klm/lm/libklm.a ../klm/util/libklm_util.a -lz
 
 mpi_flex_optimize_SOURCES = mpi_flex_optimize.cc
-mpi_flex_optimize_LDADD = libtraining.a $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a ../klm/lm/libklm.a ../klm/util/libklm_util.a -lz
+mpi_flex_optimize_LDADD = libtraining.a $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/klm/search/libksearch.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a ../klm/lm/libklm.a ../klm/util/libklm_util.a -lz
 
 mpi_extract_reachable_SOURCES = mpi_extract_reachable.cc
-mpi_extract_reachable_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a ../klm/lm/libklm.a ../klm/util/libklm_util.a -lz
+mpi_extract_reachable_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/klm/search/libksearch.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a ../klm/lm/libklm.a ../klm/util/libklm_util.a -lz
 
 mpi_extract_features_SOURCES = mpi_extract_features.cc
-mpi_extract_features_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a ../klm/lm/libklm.a ../klm/util/libklm_util.a -lz
+mpi_extract_features_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/klm/search/libksearch.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a ../klm/lm/libklm.a ../klm/util/libklm_util.a -lz
 
 mpi_batch_optimize_SOURCES = mpi_batch_optimize.cc cllh_observer.cc
-mpi_batch_optimize_LDADD = libtraining.a $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a ../klm/lm/libklm.a ../klm/util/libklm_util.a -lz
+mpi_batch_optimize_LDADD = libtraining.a $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/klm/search/libksearch.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a ../klm/lm/libklm.a ../klm/util/libklm_util.a -lz
 
 mpi_compute_cllh_SOURCES = mpi_compute_cllh.cc cllh_observer.cc
-mpi_compute_cllh_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a ../klm/lm/libklm.a ../klm/util/libklm_util.a -lz
+mpi_compute_cllh_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/klm/search/libksearch.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a ../klm/lm/libklm.a ../klm/util/libklm_util.a -lz
 
 augment_grammar_SOURCES = augment_grammar.cc
-augment_grammar_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a ../klm/lm/libklm.a ../klm/util/libklm_util.a -lz
+augment_grammar_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/klm/search/libksearch.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a ../klm/lm/libklm.a ../klm/util/libklm_util.a -lz
 
 test_ngram_SOURCES = test_ngram.cc
-test_ngram_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a ../klm/lm/libklm.a ../klm/util/libklm_util.a -lz
+test_ngram_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/klm/search/libksearch.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a ../klm/lm/libklm.a ../klm/util/libklm_util.a -lz
 
-model1_SOURCES = model1.cc ttables.cc
-model1_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/utils/libutils.a -lz
+fast_align_SOURCES = fast_align.cc ttables.cc
+fast_align_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/klm/search/libksearch.a $(top_srcdir)/utils/libutils.a -lz
 
 lbl_model_SOURCES = lbl_model.cc
-lbl_model_LDADD = libtraining.a $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/utils/libutils.a -lz
+lbl_model_LDADD = libtraining.a $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/klm/search/libksearch.a $(top_srcdir)/utils/libutils.a -lz
 
 grammar_convert_SOURCES = grammar_convert.cc
-grammar_convert_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/utils/libutils.a -lz
+grammar_convert_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/klm/search/libksearch.a $(top_srcdir)/utils/libutils.a -lz
 
 optimize_test_SOURCES = optimize_test.cc
-optimize_test_LDADD = libtraining.a $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/utils/libutils.a -lz
+optimize_test_LDADD = libtraining.a $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/klm/search/libksearch.a $(top_srcdir)/utils/libutils.a -lz
 
 collapse_weights_SOURCES = collapse_weights.cc
-collapse_weights_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/utils/libutils.a -lz
+collapse_weights_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/klm/search/libksearch.a $(top_srcdir)/utils/libutils.a -lz
 
 lbfgs_test_SOURCES = lbfgs_test.cc
-lbfgs_test_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/utils/libutils.a -lz
+lbfgs_test_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/klm/search/libksearch.a $(top_srcdir)/utils/libutils.a -lz
 
 mr_optimize_reduce_SOURCES = mr_optimize_reduce.cc
-mr_optimize_reduce_LDADD = libtraining.a $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/utils/libutils.a -lz
+mr_optimize_reduce_LDADD = libtraining.a $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/klm/search/libksearch.a $(top_srcdir)/utils/libutils.a -lz
 
 mr_em_map_adapter_SOURCES = mr_em_map_adapter.cc
-mr_em_map_adapter_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/utils/libutils.a -lz
+mr_em_map_adapter_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/klm/search/libksearch.a $(top_srcdir)/utils/libutils.a -lz
 
 mr_reduce_to_weights_SOURCES = mr_reduce_to_weights.cc
-mr_reduce_to_weights_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/utils/libutils.a -lz
+mr_reduce_to_weights_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/klm/search/libksearch.a $(top_srcdir)/utils/libutils.a -lz
 
 mr_em_adapted_reduce_SOURCES = mr_em_adapted_reduce.cc
-mr_em_adapted_reduce_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/utils/libutils.a -lz
+mr_em_adapted_reduce_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/klm/search/libksearch.a $(top_srcdir)/utils/libutils.a -lz
 
 plftools_SOURCES = plftools.cc
-plftools_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/utils/libutils.a -lz
+plftools_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/klm/search/libksearch.a $(top_srcdir)/utils/libutils.a -lz
 
 AM_CPPFLAGS = -W -Wall -Wno-sign-compare $(GTEST_CPPFLAGS) -I$(top_srcdir)/decoder -I$(top_srcdir)/utils -I$(top_srcdir)/mteval -I../klm
diff --git a/training/cllh_observer.cc b/training/cllh_observer.cc
index 58232769..4ec2fa65 100644
--- a/training/cllh_observer.cc
+++ b/training/cllh_observer.cc
@@ -45,7 +45,7 @@ void ConditionalLikelihoodObserver::NotifyAlignmentForest(const SentenceMetadata
     cerr << "DIFF. ERR! log_model_z < log_ref_z: " << cur_obj << " " << log_ref_z << endl;
     exit(1);
   }
-  assert(!isnan(log_ref_z));
+  assert(!std::isnan(log_ref_z));
   acc_obj += (cur_obj - log_ref_z);
   trg_words += smeta.GetReference().size();
 }
diff --git a/training/collapse_weights.cc b/training/collapse_weights.cc
index dc480f6c..c03eb031 100644
--- a/training/collapse_weights.cc
+++ b/training/collapse_weights.cc
@@ -95,7 +95,7 @@ int main(int argc, char** argv) {
     if (line.empty()) continue;
     TRule tr(line, true);
     const double lp = tr.GetFeatureValues().dot(w);
-    if (isinf(lp)) { continue; }
+    if (std::isinf(lp)) { continue; }
     tr.scores_.clear();
 
     cout << tr.AsString() << " ||| F_and_E=" << lp - log(tot);
diff --git a/training/model1.cc b/training/fast_align.cc
index 19692b9a..7492d26f 100644
--- a/training/model1.cc
+++ b/training/fast_align.cc
@@ -17,18 +17,21 @@ using namespace std;
 bool InitCommandLine(int argc, char** argv, po::variables_map* conf) {
   po::options_description opts("Configuration options");
   opts.add_options()
-        ("iterations,i",po::value<unsigned>()->default_value(5),"Number of iterations of EM training")
-        ("beam_threshold,t",po::value<double>()->default_value(-4),"log_10 of beam threshold (-10000 to include everything, 0 max)")
-        ("bidir,b", "Run bidirectional alignment")
-        ("no_null_word,N","Do not generate from the null token")
-        ("write_alignments,A", "Write alignments instead of parameters")
+        ("input,i",po::value<string>(),"Parallel corpus input file")
+        ("reverse,r","Reverse estimation (swap source and target during training)")
+        ("iterations,I",po::value<unsigned>()->default_value(5),"Number of iterations of EM training")
+        //("bidir,b", "Run bidirectional alignment")
         ("favor_diagonal,d", "Use a static alignment distribution that assigns higher probabilities to alignments near the diagonal")
-        ("diagonal_tension,T", po::value<double>()->default_value(4.0), "How sharp or flat around the diagonal is the alignment distribution (<1 = flat >1 = sharp)")
         ("prob_align_null", po::value<double>()->default_value(0.08), "When --favor_diagonal is set, what's the probability of a null alignment?")
-        ("variational_bayes,v","Add a symmetric Dirichlet prior and infer VB estimate of weights")
-        ("testset,x", po::value<string>(), "After training completes, compute the log likelihood of this set of sentence pairs under the learned model")
+        ("diagonal_tension,T", po::value<double>()->default_value(4.0), "How sharp or flat around the diagonal is the alignment distribution (<1 = flat >1 = sharp)")
+        ("variational_bayes,v","Infer VB estimate of parameters under a symmetric Dirichlet prior")
         ("alpha,a", po::value<double>()->default_value(0.01), "Hyperparameter for optional Dirichlet prior")
-        ("no_add_viterbi,V","Do not add Viterbi alignment points (may generate a grammar where some training sentence pairs are unreachable)");
+        ("no_null_word,N","Do not generate from a null token")
+        ("output_parameters,p", "Write model parameters instead of alignments")
+        ("beam_threshold,t",po::value<double>()->default_value(-4),"When writing parameters, log_10 of beam threshold for writing parameter (-10000 to include everything, 0 max parameter only)")
+        ("hide_training_alignments,H", "Hide training alignments (only useful if you want to use -x option and just compute testset statistics)")
+        ("testset,x", po::value<string>(), "After training completes, compute the log likelihood of this set of sentence pairs under the learned model")
+        ("no_add_viterbi,V","When writing model parameters, do not add Viterbi alignment points (may generate a grammar where some training sentence pairs are unreachable)");
   po::options_description clo("Command line options");
   clo.add_options()
         ("config", po::value<string>(), "Configuration file")
@@ -44,36 +47,29 @@ bool InitCommandLine(int argc, char** argv, po::variables_map* conf) {
   }
   po::notify(*conf);
 
-  if (argc < 2 || conf->count("help")) {
-    cerr << "Usage " << argv[0] << " [OPTIONS] corpus.fr-en\n";
+  if (conf->count("help") || conf->count("input") == 0) {
+    cerr << "Usage " << argv[0] << " [OPTIONS] -i corpus.fr-en\n";
     cerr << dcmdline_options << endl;
     return false;
   }
   return true;
 }
 
-// src and trg are source and target strings, respectively (not really lattices)
-double PosteriorInference(const vector<WordID>& src, const vector<WordID>& trg) {
-  double llh = 0;
-  static vector<double> unnormed_a_i;
-  if (src.size() > unnormed_a_i.size())
-    unnormed_a_i.resize(src.size());
-  return llh;
-}
-
 int main(int argc, char** argv) {
   po::variables_map conf;
   if (!InitCommandLine(argc, argv, &conf)) return 1;
-  const string fname = argv[argc - 1];
+  const string fname = conf["input"].as<string>();
+  const bool reverse = conf.count("reverse") > 0;
   const int ITERATIONS = conf["iterations"].as<unsigned>();
   const double BEAM_THRESHOLD = pow(10.0, conf["beam_threshold"].as<double>());
   const bool use_null = (conf.count("no_null_word") == 0);
   const WordID kNULL = TD::Convert("<eps>");
   const bool add_viterbi = (conf.count("no_add_viterbi") == 0);
   const bool variational_bayes = (conf.count("variational_bayes") > 0);
-  const bool write_alignments = (conf.count("write_alignments") > 0);
+  const bool write_alignments = (conf.count("output_parameters") == 0);
   const double diagonal_tension = conf["diagonal_tension"].as<double>();
   const double prob_align_null = conf["prob_align_null"].as<double>();
+  const bool hide_training_alignments = (conf.count("hide_training_alignments") > 0);
   string testset;
   if (conf.count("testset")) testset = conf["testset"].as<string>();
   const double prob_align_not_null = 1.0 - prob_align_null;
@@ -100,14 +96,16 @@ int main(int argc, char** argv) {
     bool flag = false;
     string line;
     string ssrc, strg;
+    vector<WordID> src, trg;
     while(true) {
       getline(in, line);
       if (!in) break;
       ++lc;
       if (lc % 1000 == 0) { cerr << '.'; flag = true; }
       if (lc %50000 == 0) { cerr << " [" << lc << "]\n" << flush; flag = false; }
-      vector<WordID> src, trg;
+      src.clear(); trg.clear();
       CorpusTools::ReadLine(line, &src, &trg);
+      if (reverse) swap(src, trg);
       if (src.size() == 0 || trg.size() == 0) {
         cerr << "Error: " << lc << "\n" << line << endl;
         return 1;
@@ -160,10 +158,13 @@ int main(int argc, char** argv) {
                 max_i = src[i-1];
               }
             }
-            if (write_alignments) {
+            if (!hide_training_alignments && write_alignments) {
               if (max_index > 0) {
                 if (first_al) first_al = false; else cout << ' ';
-                cout << (max_index - 1) << "-" << j;
+                if (reverse)
+                  cout << j << '-' << (max_index - 1);
+                else
+                  cout << (max_index - 1) << '-' << j;
               }
             }
             s2t_viterbi[max_i][f_j] = 1.0;
@@ -176,7 +177,7 @@ int main(int argc, char** argv) {
         }
         likelihood += log(sum);
       }
-      if (write_alignments && final_iteration) cout << endl;
+      if (write_alignments && final_iteration && !hide_training_alignments) cout << endl;
     }
 
     // log(e) = 1.0
@@ -203,11 +204,13 @@ int main(int argc, char** argv) {
     istream& in = *rf.stream();
     int lc = 0;
     double tlp = 0;
-    string ssrc, strg, line;
+    string line;
     while (getline(in, line)) {
       ++lc;
       vector<WordID> src, trg;
       CorpusTools::ReadLine(line, &src, &trg);
+      cout << TD::GetString(src) << " ||| " << TD::GetString(trg) << " |||";
+      if (reverse) swap(src, trg);
       double log_prob = Md::log_poisson(trg.size(), 0.05 + src.size() * mean_srclen_multiplier);
       if (src.size() > unnormed_a_i.size())
         unnormed_a_i.resize(src.size());
@@ -216,11 +219,14 @@ int main(int argc, char** argv) {
       for (int j = 0; j < trg.size(); ++j) {
         const WordID& f_j = trg[j];
         double sum = 0;
+        int a_j = 0;
+        double max_pat = 0;
         const double j_over_ts = double(j) / trg.size();
         double prob_a_i = 1.0 / (src.size() + use_null);  // uniform (model 1)
         if (use_null) {
           if (favor_diagonal) prob_a_i = prob_align_null;
-          sum += s2t.prob(kNULL, f_j) * prob_a_i;
+          max_pat = s2t.prob(kNULL, f_j) * prob_a_i;
+          sum += max_pat;
         }
         double az = 0;
         if (favor_diagonal) {
@@ -233,13 +239,24 @@ int main(int argc, char** argv) {
         for (int i = 1; i <= src.size(); ++i) {
           if (favor_diagonal)
             prob_a_i = unnormed_a_i[i-1] / az;
-          sum += s2t.prob(src[i-1], f_j) * prob_a_i;
+          double pat = s2t.prob(src[i-1], f_j) * prob_a_i;
+          if (pat > max_pat) { max_pat = pat; a_j = i; }
+          sum += pat;
         }
         log_prob += log(sum);
+        if (write_alignments) {
+          if (a_j > 0) {
+            cout << ' ';
+            if (reverse)
+              cout << j << '-' << (a_j - 1);
+            else
+              cout << (a_j - 1) << '-' << j;
+          }
+        }
       }
       tlp += log_prob;
-      cerr << ssrc << " ||| " << strg << " ||| " << log_prob << endl;
-    }
+      cout << " ||| " << log_prob << endl << flush;
+    } // loop over test set sentences
     cerr << "TOTAL LOG PROB " << tlp << endl;
   }
 
diff --git a/training/lbfgs_test.cc b/training/lbfgs_test.cc
index c94682e9..9678e788 100644
--- a/training/lbfgs_test.cc
+++ b/training/lbfgs_test.cc
@@ -1,6 +1,7 @@
 #include <cassert>
 #include <iostream>
 #include <sstream>
+#include <cmath>
 #include "lbfgs.h"
 #include "sparse_vector.h"
 #include "fdict.h"
@@ -95,8 +96,9 @@ void TestSparseVector() {
   cout << data << endl;
   SparseVector<double> v;
   double obj;
-  assert(B64::Decode(&obj, &v, &data[0], data.size()));
+  bool decode_b64 = B64::Decode(&obj, &v, &data[0], data.size());
   cerr << obj << "\t" << v << endl;
+  assert(decode_b64);
   assert(obj == iobj);
   assert(g.size() == v.size());
 }
@@ -104,7 +106,7 @@ void TestSparseVector() {
 int main() {
   double o1 = TestOptimizer();
   double o2 = TestPersistentOptimizer();
-  if (o1 != o2) {
+  if (fabs(o1 - o2) > 1e-5) {
     cerr << "OPTIMIZERS PERFORMED DIFFERENTLY!\n" << o1 << " vs. " << o2 << endl;
     return 1;
   }
diff --git a/training/liblbfgs/Jamfile b/training/liblbfgs/Jamfile
deleted file mode 100644
index 49c82748..00000000
--- a/training/liblbfgs/Jamfile
+++ /dev/null
@@ -1,5 +0,0 @@
-import testing ;
-
-lib liblbfgs : lbfgs.c : <include>.. ;
-
-unit-test ll_test : ll_test.cc liblbfgs : <include>.. ;
diff --git a/training/mpi_batch_optimize.cc b/training/mpi_batch_optimize.cc
index 6432f4a2..2eff07e4 100644
--- a/training/mpi_batch_optimize.cc
+++ b/training/mpi_batch_optimize.cc
@@ -142,7 +142,7 @@ struct TrainingObserver : public DecoderObserver {
       cerr << "DIFF. ERR! log_model_z < log_ref_z: " << cur_obj << " " << log_ref_z << endl;
       exit(1);
     }
-    assert(!isnan(log_ref_z));
+    assert(!std::isnan(log_ref_z));
     ref_exp -= cur_model_exp;
     acc_grad -= ref_exp;
     acc_obj += (cur_obj - log_ref_z);
diff --git a/training/mpi_online_optimize.cc b/training/mpi_online_optimize.cc
index 993627f0..d6968848 100644
--- a/training/mpi_online_optimize.cc
+++ b/training/mpi_online_optimize.cc
@@ -143,7 +143,7 @@ struct TrainingObserver : public DecoderObserver {
       cerr << "DIFF. ERR! log_model_z < log_ref_z: " << cur_obj << " " << log_ref_z << endl;
       exit(1);
     }
-    assert(!isnan(log_ref_z));
+    assert(!std::isnan(log_ref_z));
     ref_exp -= cur_model_exp;
     acc_grad += ref_exp;
     acc_obj += (cur_obj - log_ref_z);
@@ -330,7 +330,7 @@ int main(int argc, char** argv) {
       if (rank == 0) {
         converged = (iter == max_iteration);
         Weights::SanityCheck(lambdas);
-        Weights::ShowLargestFeatures(lambdas);
+        static int cc = 0; ++cc; if (cc > 1) { Weights::ShowLargestFeatures(lambdas); }
         string fname = "weights.cur.gz";
         if (iter % write_weights_every_ith == 0) {
           ostringstream o; o << "weights.epoch_" << (ai+1) << '.' << iter << ".gz";
diff --git a/training/mr_optimize_reduce.cc b/training/mr_optimize_reduce.cc
index 461e6b5f..d490192f 100644
--- a/training/mr_optimize_reduce.cc
+++ b/training/mr_optimize_reduce.cc
@@ -19,8 +19,8 @@ namespace po = boost::program_options;
 
 void SanityCheck(const vector<double>& w) {
   for (int i = 0; i < w.size(); ++i) {
-    assert(!isnan(w[i]));
-    assert(!isinf(w[i]));
+    assert(!std::isnan(w[i]));
+    assert(!std::isinf(w[i]));
   }
 }
 
diff --git a/utils/Jamfile b/utils/Jamfile
deleted file mode 100644
index 4444b25f..00000000
--- a/utils/Jamfile
+++ /dev/null
@@ -1,32 +0,0 @@
-import testing ;
-import option ;
-
-additional = ;
-if [ option.get with-cmph ] {
-  additional += perfect_hash.cc ;
-}
-
-lib utils :
-  alignment_io.cc 
-  b64tools.cc 
-  corpus_tools.cc 
-  dict.cc 
-  tdict.cc 
-  fdict.cc 
-  gzstream.cc 
-  filelib.cc 
-  stringlib.cc 
-  sparse_vector.cc 
-  timing_stats.cc 
-  verbose.cc 
-  weights.cc
-  $(additional)
-  ..//z
-  : <include>.. <include>. : : <include>.. <include>. ;
-
-exe atools : atools.cc utils ..//boost_program_options ;
-exe reconstruct_weights : reconstruct_weights.cc utils ..//boost_program_options ;
-
-alias programs : reconstruct_weights atools ;
-
-all_tests [ glob *_test.cc phmt.cc ts.cc ] : utils : <testing.arg>$(TOP)/utils/test_data ;
diff --git a/utils/Makefile.am b/utils/Makefile.am
index 386344dd..3ad9d69e 100644
--- a/utils/Makefile.am
+++ b/utils/Makefile.am
@@ -3,15 +3,13 @@ bin_PROGRAMS = reconstruct_weights atools
 noinst_PROGRAMS = \
   ts \
   phmt \
-  mfcr_test \
-  crp_test \
   dict_test \
   m_test \
   weights_test \
   logval_test \
   small_vector_test
 
-TESTS = ts mfcr_test crp_test small_vector_test logval_test weights_test dict_test m_test
+TESTS = ts small_vector_test logval_test weights_test dict_test m_test
 
 noinst_LIBRARIES = libutils.a
 
@@ -47,12 +45,8 @@ m_test_SOURCES = m_test.cc
 m_test_LDADD = libutils.a $(BOOST_UNIT_TEST_FRAMEWORK_LDFLAGS) $(BOOST_UNIT_TEST_FRAMEWORK_LIBS) -lz
 dict_test_SOURCES = dict_test.cc
 dict_test_LDADD = libutils.a $(BOOST_UNIT_TEST_FRAMEWORK_LDFLAGS) $(BOOST_UNIT_TEST_FRAMEWORK_LIBS) -lz
-mfcr_test_SOURCES = mfcr_test.cc
-mfcr_test_LDADD = libutils.a $(BOOST_UNIT_TEST_FRAMEWORK_LDFLAGS) $(BOOST_UNIT_TEST_FRAMEWORK_LIBS) -lz
 weights_test_SOURCES = weights_test.cc
 weights_test_LDADD = libutils.a $(BOOST_UNIT_TEST_FRAMEWORK_LDFLAGS) $(BOOST_UNIT_TEST_FRAMEWORK_LIBS) -lz
-crp_test_SOURCES = crp_test.cc
-crp_test_LDADD = libutils.a $(BOOST_UNIT_TEST_FRAMEWORK_LDFLAGS) $(BOOST_UNIT_TEST_FRAMEWORK_LIBS) -lz
 logval_test_SOURCES = logval_test.cc
 logval_test_LDADD = libutils.a $(BOOST_UNIT_TEST_FRAMEWORK_LDFLAGS) $(BOOST_UNIT_TEST_FRAMEWORK_LIBS) -lz
 small_vector_test_SOURCES = small_vector_test.cc
diff --git a/utils/b64tools.cc b/utils/b64tools.cc
index 5512f975..78c1cb4e 100644
--- a/utils/b64tools.cc
+++ b/utils/b64tools.cc
@@ -10,9 +10,10 @@ static const char cd64[]="|$$$}rstuvwxyz{$$$$$$$>?@ABCDEFGHIJKLMNOPQRSTUVW$$$$$$
 
 static void encodeblock(const unsigned char* in, ostream* os, int len) {
   char out[4];
+  // cerr << len << endl;
   out[0] = cb64[ in[0] >> 2 ];
-  out[1] = cb64[ ((in[0] & 0x03) << 4) | ((in[1] & 0xf0) >> 4) ];
-  out[2] = (len > 1 ? cb64[ ((in[1] & 0x0f) << 2) | ((in[2] & 0xc0) >> 6) ] : '=');
+  out[1] = cb64[ ((in[0] & 0x03) << 4) | (len > 1 ? ((in[1] & 0xf0) >> 4) : static_cast<unsigned char>(0))];
+  out[2] = (len > 2 ? cb64[ ((in[1] & 0x0f) << 2) | ((in[2] & 0xc0) >> 6) ] : '=');
   out[3] = (len > 2 ? cb64[ in[2] & 0x3f ] : '=');
   os->write(out, 4);
 }
diff --git a/utils/ccrp.h b/utils/ccrp.h
deleted file mode 100644
index 1d41a3ef..00000000
--- a/utils/ccrp.h
+++ /dev/null
@@ -1,317 +0,0 @@
-#ifndef _CCRP_H_
-#define _CCRP_H_
-
-#include <numeric>
-#include <cassert>
-#include <cmath>
-#include <list>
-#include <iostream>
-#include <vector>
-#include <tr1/unordered_map>
-#include <boost/functional/hash.hpp>
-#include "sampler.h"
-#include "slice_sampler.h"
-#include "m.h"
-
-// Chinese restaurant process (Pitman-Yor parameters) with table tracking.
-
-template <typename Dish, typename DishHash = boost::hash<Dish> >
-class CCRP {
- public:
-  CCRP(double disc, double strength) :
-      num_tables_(),
-      num_customers_(),
-      discount_(disc),
-      strength_(strength),
-      discount_prior_strength_(std::numeric_limits<double>::quiet_NaN()),
-      discount_prior_beta_(std::numeric_limits<double>::quiet_NaN()),
-      strength_prior_shape_(std::numeric_limits<double>::quiet_NaN()),
-      strength_prior_rate_(std::numeric_limits<double>::quiet_NaN()) {
-    check_hyperparameters();
-  }
-
-  CCRP(double d_strength, double d_beta, double c_shape, double c_rate, double d = 0.9, double c = 1.0) :
-      num_tables_(),
-      num_customers_(),
-      discount_(d),
-      strength_(c),
-      discount_prior_strength_(d_strength),
-      discount_prior_beta_(d_beta),
-      strength_prior_shape_(c_shape),
-      strength_prior_rate_(c_rate) {
-    check_hyperparameters();
-  }
-
-  void check_hyperparameters() {
-    if (discount_ < 0.0 || discount_ >= 1.0) {
-      std::cerr << "Bad discount: " << discount_ << std::endl;
-      abort();
-    }
-    if (strength_ <= -discount_) {
-      std::cerr << "Bad strength: " << strength_ << " (discount=" << discount_ << ")" << std::endl;
-      abort();
-    }
-  }
-
-  double discount() const { return discount_; }
-  double strength() const { return strength_; }
-  void set_hyperparameters(double d, double s) {
-    discount_ = d; strength_ = s;
-    check_hyperparameters();
-  }
-  void set_discount(double d) { discount_ = d; check_hyperparameters(); }
-  void set_strength(double a) { strength_ = a; check_hyperparameters(); }
-
-  bool has_discount_prior() const {
-    return !std::isnan(discount_prior_strength_);
-  }
-
-  bool has_strength_prior() const {
-    return !std::isnan(strength_prior_shape_);
-  }
-
-  void clear() {
-    num_tables_ = 0;
-    num_customers_ = 0;
-    dish_locs_.clear();
-  }
-
-  unsigned num_tables() const {
-    return num_tables_;
-  }
-
-  unsigned num_tables(const Dish& dish) const {
-    const typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator it = dish_locs_.find(dish);
-    if (it == dish_locs_.end()) return 0;
-    return it->second.table_counts_.size();
-  }
-
-  unsigned num_customers() const {
-    return num_customers_;
-  }
-
-  unsigned num_customers(const Dish& dish) const {
-    const typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator it = dish_locs_.find(dish);
-    if (it == dish_locs_.end()) return 0;
-    return it->total_dish_count_;
-  }
-
-  // returns +1 or 0 indicating whether a new table was opened
-  //   p = probability with which the particular table was selected
-  //       excluding p0
-  template <typename T>
-  int increment(const Dish& dish, const T& p0, MT19937* rng, T* p = NULL) {
-    DishLocations& loc = dish_locs_[dish];
-    bool share_table = false;
-    if (loc.total_dish_count_) {
-      const T p_empty = T(strength_ + num_tables_ * discount_) * p0;
-      const T p_share = T(loc.total_dish_count_ - loc.table_counts_.size() * discount_);
-      share_table = rng->SelectSample(p_empty, p_share);
-    }
-    if (share_table) {
-      double r = rng->next() * (loc.total_dish_count_ - loc.table_counts_.size() * discount_);
-      for (typename std::list<unsigned>::iterator ti = loc.table_counts_.begin();
-           ti != loc.table_counts_.end(); ++ti) {
-        r -= (*ti - discount_);
-        if (r <= 0.0) {
-          if (p) { *p = T(*ti - discount_) / T(strength_ + num_customers_); }
-          ++(*ti);
-          break;
-        }
-      }
-      if (r > 0.0) {
-        std::cerr << "Serious error: r=" << r << std::endl;
-        Print(&std::cerr);
-        assert(r <= 0.0);
-      }
-    } else {
-      loc.table_counts_.push_back(1u);
-      if (p) { *p = T(strength_ + discount_ * num_tables_) / T(strength_ + num_customers_); }
-      ++num_tables_;
-    }
-    ++loc.total_dish_count_;
-    ++num_customers_;
-    return (share_table ? 0 : 1);
-  }
-
-  // returns -1 or 0, indicating whether a table was closed
-  int decrement(const Dish& dish, MT19937* rng) {
-    DishLocations& loc = dish_locs_[dish];
-    assert(loc.total_dish_count_);
-    if (loc.total_dish_count_ == 1) {
-      dish_locs_.erase(dish);
-      --num_tables_;
-      --num_customers_;
-      return -1;
-    } else {
-      int delta = 0;
-      // sample customer to remove UNIFORMLY. that is, do NOT use the discount
-      // here. if you do, it will introduce (unwanted) bias!
-      double r = rng->next() * loc.total_dish_count_;
-      --loc.total_dish_count_;
-      for (typename std::list<unsigned>::iterator ti = loc.table_counts_.begin();
-           ti != loc.table_counts_.end(); ++ti) {
-        r -= *ti;
-        if (r <= 0.0) {
-          if ((--(*ti)) == 0) {
-            --num_tables_;
-            delta = -1;
-            loc.table_counts_.erase(ti);
-          }
-          break;
-        }
-      }
-      if (r > 0.0) {
-        std::cerr << "Serious error: r=" << r << std::endl;
-        Print(&std::cerr);
-        assert(r <= 0.0);
-      }
-      --num_customers_;
-      return delta;
-    }
-  }
-
-  template <typename T>
-  T prob(const Dish& dish, const T& p0) const {
-    const typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator it = dish_locs_.find(dish);
-    const T r = T(num_tables_ * discount_ + strength_);
-    if (it == dish_locs_.end()) {
-      return r * p0 / T(num_customers_ + strength_);
-    } else {
-      return (T(it->second.total_dish_count_ - discount_ * it->second.table_counts_.size()) + r * p0) /
-               T(num_customers_ + strength_);
-    }
-  }
-
-  double log_crp_prob() const {
-    return log_crp_prob(discount_, strength_);
-  }
-
-  // taken from http://en.wikipedia.org/wiki/Chinese_restaurant_process
-  // does not include P_0's
-  double log_crp_prob(const double& discount, const double& strength) const {
-    double lp = 0.0;
-    if (has_discount_prior())
-      lp = Md::log_beta_density(discount, discount_prior_strength_, discount_prior_beta_);
-    if (has_strength_prior())
-      lp += Md::log_gamma_density(strength + discount, strength_prior_shape_, strength_prior_rate_);
-    assert(lp <= 0.0);
-    if (num_customers_) {
-      if (discount > 0.0) {
-        const double r = lgamma(1.0 - discount);
-        if (strength)
-          lp += lgamma(strength) - lgamma(strength / discount);
-        lp += - lgamma(strength + num_customers_)
-             + num_tables_ * log(discount) + lgamma(strength / discount + num_tables_);
-        assert(std::isfinite(lp));
-        for (typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator it = dish_locs_.begin();
-             it != dish_locs_.end(); ++it) {
-          const DishLocations& cur = it->second;
-          for (std::list<unsigned>::const_iterator ti = cur.table_counts_.begin(); ti != cur.table_counts_.end(); ++ti) {
-            lp += lgamma(*ti - discount) - r;
-          }
-        }
-      } else if (!discount) { // discount == 0.0
-        lp += lgamma(strength) + num_tables_ * log(strength) - lgamma(strength + num_tables_);
-        assert(std::isfinite(lp));
-        for (typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator it = dish_locs_.begin();
-             it != dish_locs_.end(); ++it) {
-          const DishLocations& cur = it->second;
-          lp += lgamma(cur.table_counts_.size());
-        }
-      } else {
-        assert(!"discount less than 0 detected!");
-      }
-    }
-    assert(std::isfinite(lp));
-    return lp;
-  }
-
-  void resample_hyperparameters(MT19937* rng, const unsigned nloop = 5, const unsigned niterations = 10) {
-    assert(has_discount_prior() || has_strength_prior());
-    if (num_customers() == 0) return;
-    DiscountResampler dr(*this);
-    StrengthResampler sr(*this);
-    for (unsigned iter = 0; iter < nloop; ++iter) {
-      if (has_strength_prior()) {
-        strength_ = slice_sampler1d(sr, strength_, *rng, -discount_ + std::numeric_limits<double>::min(),
-                               std::numeric_limits<double>::infinity(), 0.0, niterations, 100*niterations);
-      }
-      if (has_discount_prior()) {
-        double min_discount = std::numeric_limits<double>::min();
-        if (strength_ < 0.0) min_discount -= strength_;
-        discount_ = slice_sampler1d(dr, discount_, *rng, min_discount,
-                               1.0, 0.0, niterations, 100*niterations);
-      }
-    }
-    strength_ = slice_sampler1d(sr, strength_, *rng, -discount_,
-                             std::numeric_limits<double>::infinity(), 0.0, niterations, 100*niterations);
-  }
-
-  struct DiscountResampler {
-    DiscountResampler(const CCRP& crp) : crp_(crp) {}
-    const CCRP& crp_;
-    double operator()(const double& proposed_discount) const {
-      return crp_.log_crp_prob(proposed_discount, crp_.strength_);
-    }
-  };
-
-  struct StrengthResampler {
-    StrengthResampler(const CCRP& crp) : crp_(crp) {}
-    const CCRP& crp_;
-    double operator()(const double& proposed_strength) const {
-      return crp_.log_crp_prob(crp_.discount_, proposed_strength);
-    }
-  };
-
-  struct DishLocations {
-    DishLocations() : total_dish_count_() {}
-    unsigned total_dish_count_;        // customers at all tables with this dish
-    std::list<unsigned> table_counts_; // list<> gives O(1) deletion and insertion, which we want
-                                       // .size() is the number of tables for this dish
-  };
-
-  void Print(std::ostream* out) const {
-    std::cerr << "PYP(d=" << discount_ << ",c=" << strength_ << ") customers=" << num_customers_ << std::endl;
-    for (typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator it = dish_locs_.begin();
-         it != dish_locs_.end(); ++it) {
-      (*out) << it->first << " (" << it->second.total_dish_count_ << " on " << it->second.table_counts_.size() << " tables): ";
-      for (typename std::list<unsigned>::const_iterator i = it->second.table_counts_.begin();
-           i != it->second.table_counts_.end(); ++i) {
-        (*out) << " " << *i;
-      }
-      (*out) << std::endl;
-    }
-  }
-
-  typedef typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator const_iterator;
-  const_iterator begin() const {
-    return dish_locs_.begin();
-  }
-  const_iterator end() const {
-    return dish_locs_.end();
-  }
-
-  unsigned num_tables_;
-  unsigned num_customers_;
-  std::tr1::unordered_map<Dish, DishLocations, DishHash> dish_locs_;
-
-  double discount_;
-  double strength_;
-
-  // optional beta prior on discount_ (NaN if no prior)
-  double discount_prior_strength_;
-  double discount_prior_beta_;
-
-  // optional gamma prior on strength_ (NaN if no prior)
-  double strength_prior_shape_;
-  double strength_prior_rate_;
-};
-
-template <typename T,typename H>
-std::ostream& operator<<(std::ostream& o, const CCRP<T,H>& c) {
-  c.Print(&o);
-  return o;
-}
-
-#endif
diff --git a/utils/ccrp_nt.h b/utils/ccrp_nt.h
deleted file mode 100644
index 724b11bd..00000000
--- a/utils/ccrp_nt.h
+++ /dev/null
@@ -1,164 +0,0 @@
-#ifndef _CCRP_NT_H_
-#define _CCRP_NT_H_
-
-#include <numeric>
-#include <cassert>
-#include <cmath>
-#include <list>
-#include <iostream>
-#include <vector>
-#include <tr1/unordered_map>
-#include <boost/functional/hash.hpp>
-#include "sampler.h"
-#include "slice_sampler.h"
-#include "m.h"
-
-// Chinese restaurant process (1 parameter)
-template <typename Dish, typename DishHash = boost::hash<Dish> >
-class CCRP_NoTable {
- public:
-  explicit CCRP_NoTable(double conc) :
-    num_customers_(),
-    alpha_(conc),
-    alpha_prior_shape_(std::numeric_limits<double>::quiet_NaN()),
-    alpha_prior_rate_(std::numeric_limits<double>::quiet_NaN()) {}
-
-  CCRP_NoTable(double c_shape, double c_rate, double c = 10.0) :
-    num_customers_(),
-    alpha_(c),
-    alpha_prior_shape_(c_shape),
-    alpha_prior_rate_(c_rate) {}
-
-  double alpha() const { return alpha_; }
-  void set_alpha(const double& alpha) { alpha_ = alpha; assert(alpha_ > 0.0); }
-
-  bool has_alpha_prior() const {
-    return !std::isnan(alpha_prior_shape_);
-  }
-
-  void clear() {
-    num_customers_ = 0;
-    custs_.clear();
-  }
-
-  unsigned num_customers() const {
-    return num_customers_;
-  }
-
-  unsigned num_customers(const Dish& dish) const {
-    const typename std::tr1::unordered_map<Dish, unsigned, DishHash>::const_iterator it = custs_.find(dish);
-    if (it == custs_.end()) return 0;
-    return it->second;
-  }
-
-  int increment(const Dish& dish) {
-    int table_diff = 0;
-    if (++custs_[dish] == 1)
-      table_diff = 1;
-    ++num_customers_;
-    return table_diff;
-  }
-
-  int decrement(const Dish& dish) {
-    int table_diff = 0;
-    int nc = --custs_[dish];
-    if (nc == 0) {
-      custs_.erase(dish);
-      table_diff = -1;
-    } else if (nc < 0) {
-      std::cerr << "Dish counts dropped below zero for: " << dish << std::endl;
-      abort();
-    }
-    --num_customers_;
-    return table_diff;
-  }
-
-  template <typename F>
-  F prob(const Dish& dish, const F& p0) const {
-    const unsigned at_table = num_customers(dish);
-    return (F(at_table) + p0 * F(alpha_)) / F(num_customers_ + alpha_);
-  }
-
-  double logprob(const Dish& dish, const double& logp0) const {
-    const unsigned at_table = num_customers(dish);
-    return log(at_table + exp(logp0 + log(alpha_))) - log(num_customers_ + alpha_);
-  }
-
-  double log_crp_prob() const {
-    return log_crp_prob(alpha_);
-  }
-
-  // taken from http://en.wikipedia.org/wiki/Chinese_restaurant_process
-  // does not include P_0's
-  double log_crp_prob(const double& alpha) const {
-    double lp = 0.0;
-    if (has_alpha_prior())
-      lp += Md::log_gamma_density(alpha, alpha_prior_shape_, alpha_prior_rate_);
-    assert(lp <= 0.0);
-    if (num_customers_) {
-      lp += lgamma(alpha) - lgamma(alpha + num_customers_) +
-        custs_.size() * log(alpha);
-      assert(std::isfinite(lp));
-      for (typename std::tr1::unordered_map<Dish, unsigned, DishHash>::const_iterator it = custs_.begin();
-             it != custs_.end(); ++it) {
-          lp += lgamma(it->second);
-      }
-    }
-    assert(std::isfinite(lp));
-    return lp;
-  }
-
-  void resample_hyperparameters(MT19937* rng, const unsigned nloop = 5, const unsigned niterations = 10) {
-    assert(has_alpha_prior());
-    ConcentrationResampler cr(*this);
-    for (unsigned iter = 0; iter < nloop; ++iter) {
-        alpha_ = slice_sampler1d(cr, alpha_, *rng, 0.0,
-                               std::numeric_limits<double>::infinity(), 0.0, niterations, 100*niterations);
-    }
-  }
-
-  struct ConcentrationResampler {
-    ConcentrationResampler(const CCRP_NoTable& crp) : crp_(crp) {}
-    const CCRP_NoTable& crp_;
-    double operator()(const double& proposed_alpha) const {
-      return crp_.log_crp_prob(proposed_alpha);
-    }
-  };
-
-  void Print(std::ostream* out) const {
-    (*out) << "DP(alpha=" << alpha_ << ") customers=" << num_customers_ << std::endl;
-    int cc = 0;
-    for (typename std::tr1::unordered_map<Dish, unsigned, DishHash>::const_iterator it = custs_.begin();
-         it != custs_.end(); ++it) {
-      (*out) << " " << it->first << "(" << it->second << " eating)";
-      ++cc;
-      if (cc > 10) { (*out) << " ..."; break; }
-    }
-    (*out) << std::endl;
-  }
-
-  unsigned num_customers_;
-  std::tr1::unordered_map<Dish, unsigned, DishHash> custs_;
-
-  typedef typename std::tr1::unordered_map<Dish, unsigned, DishHash>::const_iterator const_iterator;
-  const_iterator begin() const {
-    return custs_.begin();
-  }
-  const_iterator end() const {
-    return custs_.end();
-  }
-
-  double alpha_;
-
-  // optional gamma prior on alpha_ (NaN if no prior)
-  double alpha_prior_shape_;
-  double alpha_prior_rate_;
-};
-
-template <typename T,typename H>
-std::ostream& operator<<(std::ostream& o, const CCRP_NoTable<T,H>& c) {
-  c.Print(&o);
-  return o;
-}
-
-#endif
diff --git a/utils/ccrp_onetable.h b/utils/ccrp_onetable.h
deleted file mode 100644
index abe399ea..00000000
--- a/utils/ccrp_onetable.h
+++ /dev/null
@@ -1,253 +0,0 @@
-#ifndef _CCRP_ONETABLE_H_
-#define _CCRP_ONETABLE_H_
-
-#include <numeric>
-#include <cassert>
-#include <cmath>
-#include <list>
-#include <iostream>
-#include <tr1/unordered_map>
-#include <boost/functional/hash.hpp>
-#include "sampler.h"
-#include "slice_sampler.h"
-
-// Chinese restaurant process (Pitman-Yor parameters) with one table approximation
-
-template <typename Dish, typename DishHash = boost::hash<Dish> >
-class CCRP_OneTable {
-  typedef std::tr1::unordered_map<Dish, unsigned, DishHash> DishMapType;
- public:
-  CCRP_OneTable(double disc, double conc) :
-    num_tables_(),
-    num_customers_(),
-    discount_(disc),
-    alpha_(conc),
-    discount_prior_alpha_(std::numeric_limits<double>::quiet_NaN()),
-    discount_prior_beta_(std::numeric_limits<double>::quiet_NaN()),
-    alpha_prior_shape_(std::numeric_limits<double>::quiet_NaN()),
-    alpha_prior_rate_(std::numeric_limits<double>::quiet_NaN()) {}
-
-  CCRP_OneTable(double d_alpha, double d_beta, double c_shape, double c_rate, double d = 0.9, double c = 1.0) :
-    num_tables_(),
-    num_customers_(),
-    discount_(d),
-    alpha_(c),
-    discount_prior_alpha_(d_alpha),
-    discount_prior_beta_(d_beta),
-    alpha_prior_shape_(c_shape),
-    alpha_prior_rate_(c_rate) {}
-
-  double discount() const { return discount_; }
-  double alpha() const { return alpha_; }
-  void set_alpha(double c) { alpha_ = c; }
-  void set_discount(double d) { discount_ = d; }
-
-  bool has_discount_prior() const {
-    return !std::isnan(discount_prior_alpha_);
-  }
-
-  bool has_alpha_prior() const {
-    return !std::isnan(alpha_prior_shape_);
-  }
-
-  void clear() {
-    num_tables_ = 0;
-    num_customers_ = 0;
-    dish_counts_.clear();
-  }
-
-  unsigned num_tables() const {
-    return num_tables_;
-  }
-
-  unsigned num_tables(const Dish& dish) const {
-    const typename DishMapType::const_iterator it = dish_counts_.find(dish);
-    if (it == dish_counts_.end()) return 0;
-    return 1;
-  }
-
-  unsigned num_customers() const {
-    return num_customers_;
-  }
-
-  unsigned num_customers(const Dish& dish) const {
-    const typename DishMapType::const_iterator it = dish_counts_.find(dish);
-    if (it == dish_counts_.end()) return 0;
-    return it->second;
-  }
-
-  // returns +1 or 0 indicating whether a new table was opened
-  int increment(const Dish& dish) {
-    unsigned& dc = dish_counts_[dish];
-    ++dc;
-    ++num_customers_;
-    if (dc == 1) {
-      ++num_tables_;
-      return 1;
-    } else {
-      return 0;
-    }
-  }
-
-  // returns -1 or 0, indicating whether a table was closed
-  int decrement(const Dish& dish) {
-    unsigned& dc = dish_counts_[dish];
-    assert(dc > 0);
-    if (dc == 1) {
-      dish_counts_.erase(dish);
-      --num_tables_;
-      --num_customers_;
-      return -1;
-    } else {
-      assert(dc > 1);
-      --dc;
-      --num_customers_;
-      return 0;
-    }
-  }
-
-  double prob(const Dish& dish, const double& p0) const {
-    const typename DishMapType::const_iterator it = dish_counts_.find(dish);
-    const double r = num_tables_ * discount_ + alpha_;
-    if (it == dish_counts_.end()) {
-      return r * p0 / (num_customers_ + alpha_);
-    } else {
-      return (it->second - discount_ + r * p0) /
-               (num_customers_ + alpha_);
-    }
-  }
-
-  template <typename T>
-  T probT(const Dish& dish, const T& p0) const {
-    const typename DishMapType::const_iterator it = dish_counts_.find(dish);
-    const T r(num_tables_ * discount_ + alpha_);
-    if (it == dish_counts_.end()) {
-      return r * p0 / T(num_customers_ + alpha_);
-    } else {
-      return (T(it->second - discount_) + r * p0) /
-               T(num_customers_ + alpha_);
-    }
-  }
-
-  double log_crp_prob() const {
-    return log_crp_prob(discount_, alpha_);
-  }
-
-  static double log_beta_density(const double& x, const double& alpha, const double& beta) {
-    assert(x > 0.0);
-    assert(x < 1.0);
-    assert(alpha > 0.0);
-    assert(beta > 0.0);
-    const double lp = (alpha-1)*log(x)+(beta-1)*log(1-x)+lgamma(alpha+beta)-lgamma(alpha)-lgamma(beta);
-    return lp;
-  }
-
-  static double log_gamma_density(const double& x, const double& shape, const double& rate) {
-    assert(x >= 0.0);
-    assert(shape > 0.0);
-    assert(rate > 0.0);
-    const double lp = (shape-1)*log(x) - shape*log(rate) - x/rate - lgamma(shape);
-    return lp;
-  }
-
-  // taken from http://en.wikipedia.org/wiki/Chinese_restaurant_process
-  // does not include P_0's
-  double log_crp_prob(const double& discount, const double& alpha) const {
-    double lp = 0.0;
-    if (has_discount_prior())
-      lp = log_beta_density(discount, discount_prior_alpha_, discount_prior_beta_);
-    if (has_alpha_prior())
-      lp += log_gamma_density(alpha, alpha_prior_shape_, alpha_prior_rate_);
-    assert(lp <= 0.0);
-    if (num_customers_) {
-      if (discount > 0.0) {
-        const double r = lgamma(1.0 - discount);
-        lp += lgamma(alpha) - lgamma(alpha + num_customers_)
-             + num_tables_ * log(discount) + lgamma(alpha / discount + num_tables_)
-             - lgamma(alpha / discount);
-        assert(std::isfinite(lp));
-        for (typename DishMapType::const_iterator it = dish_counts_.begin();
-             it != dish_counts_.end(); ++it) {
-          const unsigned& cur = it->second;
-          lp += lgamma(cur - discount) - r;
-        }
-      } else {
-        assert(!"not implemented yet");
-      }
-    }
-    assert(std::isfinite(lp));
-    return lp;
-  }
-
-  void resample_hyperparameters(MT19937* rng, const unsigned nloop = 5, const unsigned niterations = 10) {
-    assert(has_discount_prior() || has_alpha_prior());
-    DiscountResampler dr(*this);
-    ConcentrationResampler cr(*this);
-    for (unsigned iter = 0; iter < nloop; ++iter) {
-      if (has_alpha_prior()) {
-        alpha_ = slice_sampler1d(cr, alpha_, *rng, 0.0,
-                               std::numeric_limits<double>::infinity(), 0.0, niterations, 100*niterations);
-      }
-      if (has_discount_prior()) {
-        discount_ = slice_sampler1d(dr, discount_, *rng, std::numeric_limits<double>::min(),
-                               1.0, 0.0, niterations, 100*niterations);
-      }
-    }
-    alpha_ = slice_sampler1d(cr, alpha_, *rng, 0.0,
-                             std::numeric_limits<double>::infinity(), 0.0, niterations, 100*niterations);
-  }
-
-  struct DiscountResampler {
-    DiscountResampler(const CCRP_OneTable& crp) : crp_(crp) {}
-    const CCRP_OneTable& crp_;
-    double operator()(const double& proposed_discount) const {
-      return crp_.log_crp_prob(proposed_discount, crp_.alpha_);
-    }
-  };
-
-  struct ConcentrationResampler {
-    ConcentrationResampler(const CCRP_OneTable& crp) : crp_(crp) {}
-    const CCRP_OneTable& crp_;
-    double operator()(const double& proposed_alpha) const {
-      return crp_.log_crp_prob(crp_.discount_, proposed_alpha);
-    }
-  };
-
-  void Print(std::ostream* out) const {
-    (*out) << "PYP(d=" << discount_ << ",c=" << alpha_ << ") customers=" << num_customers_ << std::endl;
-    for (typename DishMapType::const_iterator it = dish_counts_.begin(); it != dish_counts_.end(); ++it) {
-      (*out) << "  " << it->first << " = " << it->second << std::endl;
-    }
-  }
-
-  typedef typename DishMapType::const_iterator const_iterator;
-  const_iterator begin() const {
-    return dish_counts_.begin();
-  }
-  const_iterator end() const {
-    return dish_counts_.end();
-  }
-
-  unsigned num_tables_;
-  unsigned num_customers_;
-  DishMapType dish_counts_;
-
-  double discount_;
-  double alpha_;
-
-  // optional beta prior on discount_ (NaN if no prior)
-  double discount_prior_alpha_;
-  double discount_prior_beta_;
-
-  // optional gamma prior on alpha_ (NaN if no prior)
-  double alpha_prior_shape_;
-  double alpha_prior_rate_;
-};
-
-template <typename T,typename H>
-std::ostream& operator<<(std::ostream& o, const CCRP_OneTable<T,H>& c) {
-  c.Print(&o);
-  return o;
-}
-
-#endif
diff --git a/utils/crp_test.cc b/utils/crp_test.cc
deleted file mode 100644
index 0cdb7afd..00000000
--- a/utils/crp_test.cc
+++ /dev/null
@@ -1,91 +0,0 @@
-#include <iostream>
-#include <vector>
-#include <string>
-
-#define BOOST_TEST_MODULE CrpTest
-#include <boost/test/unit_test.hpp>
-#include <boost/test/floating_point_comparison.hpp>
-
-#include "ccrp.h"
-#include "sampler.h"
-
-using namespace std;
-
-MT19937 rng;
-
-BOOST_AUTO_TEST_CASE(Dist) {
-  CCRP<string> crp(0.1, 5);
-  double un = 0.25;
-  int tt = 0;
-  tt += crp.increment("hi", un, &rng);
-  tt += crp.increment("foo", un, &rng);
-  tt += crp.increment("bar", un, &rng);
-  tt += crp.increment("bar", un, &rng);
-  tt += crp.increment("bar", un, &rng);
-  tt += crp.increment("bar", un, &rng);
-  tt += crp.increment("bar", un, &rng);
-  tt += crp.increment("bar", un, &rng);
-  tt += crp.increment("bar", un, &rng);
-  cout << "tt=" << tt << endl;
-  cout << crp << endl;
-  cout << "  P(bar)=" << crp.prob("bar", un) << endl;
-  cout << "  P(hi)=" << crp.prob("hi", un) << endl;
-  cout << "  P(baz)=" << crp.prob("baz", un) << endl;
-  cout << "  P(foo)=" << crp.prob("foo", un) << endl;
-  double x = crp.prob("bar", un) + crp.prob("hi", un) + crp.prob("baz", un) + crp.prob("foo", un);
-  cout << "    tot=" << x << endl;
-  BOOST_CHECK_CLOSE(1.0, x, 1e-6);
-  tt += crp.decrement("hi", &rng);
-  tt += crp.decrement("bar", &rng);
-  cout << crp << endl;
-  tt += crp.decrement("bar", &rng);
-  cout << crp << endl;
-  cout << "tt=" << tt << endl;
-}
-
-BOOST_AUTO_TEST_CASE(Exchangability) {
-    double tot = 0;
-    double xt = 0;
-    CCRP<int> crp(0.5, 1.0);
-    int cust = 10;
-    vector<int> hist(cust + 1, 0);
-    for (int i = 0; i < cust; ++i) { crp.increment(1, 1.0, &rng); }
-    const int samples = 100000;
-    const bool simulate = true;
-    for (int k = 0; k < samples; ++k) {
-      if (!simulate) {
-        crp.clear();
-        for (int i = 0; i < cust; ++i) { crp.increment(1, 1.0, &rng); }
-      } else {
-        int da = rng.next() * cust;
-        bool a = rng.next() < 0.5;
-        if (a) {
-          for (int i = 0; i < da; ++i) { crp.increment(1, 1.0, &rng); }
-          for (int i = 0; i < da; ++i) { crp.decrement(1, &rng); }
-          xt += 1.0;
-        } else {
-          for (int i = 0; i < da; ++i) { crp.decrement(1, &rng); }
-          for (int i = 0; i < da; ++i) { crp.increment(1, 1.0, &rng); }
-        }
-      }
-      int c = crp.num_tables(1);
-      ++hist[c];
-      tot += c;
-    }
-    BOOST_CHECK_EQUAL(cust, crp.num_customers());
-    cerr << "P(a) = " << (xt / samples) << endl;
-    cerr << "E[num tables] = " << (tot / samples) << endl;
-    double error = fabs((tot / samples) - 5.4);
-    cerr << "  error = " << error << endl;
-    BOOST_CHECK_MESSAGE(error < 0.1, "error is too big = " << error);  // it's possible for this to fail, but
-                            // very, very unlikely
-    for (int i = 1; i <= cust; ++i)
-      cerr << i << ' ' << (hist[i]) << endl;
-}
-
-BOOST_AUTO_TEST_CASE(LP) {
-  CCRP<string> crp(1,1,1,1,0.1,50.0);
-  crp.increment("foo", 1.0, &rng);
-  cerr << crp.log_crp_prob() << endl;
-}
-
diff --git a/utils/fast_sparse_vector.h b/utils/fast_sparse_vector.h
index 433a5cc5..590a60c4 100644
--- a/utils/fast_sparse_vector.h
+++ b/utils/fast_sparse_vector.h
@@ -13,6 +13,7 @@
 #include <map>
 #include <cassert>
 #include <vector>
+#include <limits>
 
 #ifdef HAVE_CONFIG_H
 #include "config.h"
@@ -192,28 +193,33 @@ class FastSparseVector {
     } else {
       is_remote_ = true;
       data_.rbmap = new SPARSE_HASH_MAP<unsigned, T>(first, last);
+      HASH_MAP_DELETED(*data_.rbmap, std::numeric_limits<unsigned>::max());
     }
   }
-  void erase(int k) {
+  void erase(unsigned k) {
     if (is_remote_) {
       data_.rbmap->erase(k);
     } else {
-      for (int i = 0; i < local_size_; ++i) {
+      for (unsigned i = 0; i < local_size_; ++i) {
         if (data_.local[i].first() == k) {
-          for (int j = i+1; j < local_size_; ++j) {
+          for (unsigned j = i+1; j < local_size_; ++j) {
             data_.local[j-1].first() = data_.local[j].first();
             data_.local[j-1].second() = data_.local[j].second();
           }
         }
       }
+      --local_size_;
     }
   }
   const FastSparseVector<T>& operator=(const FastSparseVector<T>& other) {
     if (&other == this) return *this;
     clear();
     std::memcpy(this, &other, sizeof(FastSparseVector));
-    if (is_remote_)
+    if (is_remote_) {
       data_.rbmap = new SPARSE_HASH_MAP<unsigned, T>(*data_.rbmap);
+      // TODO: do i need to set_deleted on a copy?
+      HASH_MAP_DELETED(*data_.rbmap, std::numeric_limits<unsigned>::max());
+    }
     return *this;
   }
   T const& get_singleton() const {
@@ -444,6 +450,7 @@ class FastSparseVector {
       SPARSE_HASH_MAP<unsigned, T>* m = new SPARSE_HASH_MAP<unsigned, T>(
          reinterpret_cast<std::pair<unsigned, T>*>(&data_.local[0]),
          reinterpret_cast<std::pair<unsigned, T>*>(&data_.local[local_size_]), local_size_ * 1.5 + 1);
+      HASH_MAP_DELETED(*m, std::numeric_limits<unsigned>::max());
       data_.rbmap = m;
       is_remote_ = true;
     }
@@ -515,7 +522,7 @@ const FastSparseVector<T> operator-(const FastSparseVector<T>& x, const FastSpar
 }
 
 template <class T>
-std::size_t hash_value(FastSparseVector<T> const& x) {
+std::size_t hash_value(FastSparseVector<T> const&) {
   assert(!"not implemented");
   return 0;
 }
diff --git a/utils/hash.h b/utils/hash.h
index 6d992086..189ed1ae 100644
--- a/utils/hash.h
+++ b/utils/hash.h
@@ -16,14 +16,16 @@
 # define SPARSE_HASH_MAP google::sparse_hash_map
 # define HASH_MAP google::dense_hash_map
 # define HASH_SET google::dense_hash_set
-# define HASH_MAP_RESERVED(h,empty,deleted) do { h.set_empty_key(empty); h.set_deleted_key(deleted); } while(0)
-# define HASH_MAP_EMPTY(h,empty) do { h.set_empty_key(empty); } while(0)
+# define HASH_MAP_DELETED(h,deleted) do { (h).set_deleted_key(deleted); } while(0)
+# define HASH_MAP_RESERVED(h,empty,deleted) do { (h).set_empty_key(empty); (h).set_deleted_key(deleted); } while(0)
+# define HASH_MAP_EMPTY(h,empty) do { (h).set_empty_key(empty); } while(0)
 #else
 # include <tr1/unordered_map>
 # include <tr1/unordered_set>
 # define SPARSE_HASH_MAP std::tr1::unordered_map
 # define HASH_MAP std::tr1::unordered_map
 # define HASH_SET std::tr1::unordered_set
+# define HASH_MAP_DELETED(h,deleted)
 # define HASH_MAP_RESERVED(h,empty,deleted)
 # define HASH_MAP_EMPTY(h,empty)
 #endif
diff --git a/utils/mfcr.h b/utils/mfcr.h
deleted file mode 100644
index 4aacb567..00000000
--- a/utils/mfcr.h
+++ /dev/null
@@ -1,370 +0,0 @@
-#ifndef _MFCR_H_
-#define _MFCR_H_
-
-#include <algorithm>
-#include <numeric>
-#include <cassert>
-#include <cmath>
-#include <list>
-#include <iostream>
-#include <vector>
-#include <iterator>
-#include <tr1/unordered_map>
-#include <boost/functional/hash.hpp>
-#include "sampler.h"
-#include "slice_sampler.h"
-#include "m.h"
-
-struct TableCount {
-  TableCount() : count(), floor() {}
-  TableCount(int c, int f) : count(c), floor(f) {
-    assert(f >= 0);
-  }
-  int count;               // count or delta (may be 0, <0, or >0)
-  unsigned char floor;     // from which floor?
-};
- 
-std::ostream& operator<<(std::ostream& o, const TableCount& tc) {
-  return o << "[c=" << tc.count << " floor=" << static_cast<unsigned int>(tc.floor) << ']';
-}
-
-// Multi-Floor Chinese Restaurant as proposed by Wood & Teh (AISTATS, 2009) to simulate
-// graphical Pitman-Yor processes.
-// http://jmlr.csail.mit.edu/proceedings/papers/v5/wood09a/wood09a.pdf
-//
-// Implementation is based on Blunsom, Cohn, Goldwater, & Johnson (ACL 2009) and code
-// referenced therein.
-// http://www.aclweb.org/anthology/P/P09/P09-2085.pdf
-//
-template <unsigned Floors, typename Dish, typename DishHash = boost::hash<Dish> >
-class MFCR {
- public:
-
-  MFCR(double d, double strength) :
-    num_tables_(),
-    num_customers_(),
-    discount_(d),
-    strength_(strength),
-    discount_prior_strength_(std::numeric_limits<double>::quiet_NaN()),
-    discount_prior_beta_(std::numeric_limits<double>::quiet_NaN()),
-    strength_prior_shape_(std::numeric_limits<double>::quiet_NaN()),
-    strength_prior_rate_(std::numeric_limits<double>::quiet_NaN()) { check_hyperparameters(); }
-
-  MFCR(double discount_strength, double discount_beta, double strength_shape, double strength_rate, double d = 0.9, double strength = 10.0) :
-    num_tables_(),
-    num_customers_(),
-    discount_(d),
-    strength_(strength),
-    discount_prior_strength_(discount_strength),
-    discount_prior_beta_(discount_beta),
-    strength_prior_shape_(strength_shape),
-    strength_prior_rate_(strength_rate) { check_hyperparameters(); }
-
-  void check_hyperparameters() {
-    if (discount_ < 0.0 || discount_ >= 1.0) {
-      std::cerr << "Bad discount: " << discount_ << std::endl;
-      abort();
-    }
-    if (strength_ <= -discount_) {
-      std::cerr << "Bad strength: " << strength_ << " (discount=" << discount_ << ")" << std::endl;
-      abort();
-    }
-  }
-
-  double discount() const { return discount_; }
-  double strength() const { return strength_; }
-  void set_hyperparameters(double d, double s) {
-    discount_ = d; strength_ = s;
-    check_hyperparameters();
-  }
-  void set_discount(double d) { discount_ = d; check_hyperparameters(); }
-  void set_strength(double a) { strength_ = a; check_hyperparameters(); }
-
-  bool has_discount_prior() const {
-    return !std::isnan(discount_prior_strength_);
-  }
-
-  bool has_strength_prior() const {
-    return !std::isnan(strength_prior_shape_);
-  }
-
-  void clear() {
-    num_tables_ = 0;
-    num_customers_ = 0;
-    dish_locs_.clear();
-  }
-
-  unsigned num_tables() const {
-    return num_tables_;
-  }
-
-  unsigned num_tables(const Dish& dish) const {
-    const typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator it = dish_locs_.find(dish);
-    if (it == dish_locs_.end()) return 0;
-    return it->second.table_counts_.size();
-  }
-
-  // this is not terribly efficient but it should not typically be necessary to execute this query
-  unsigned num_tables(const Dish& dish, const unsigned floor) const {
-    const typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator it = dish_locs_.find(dish);
-    if (it == dish_locs_.end()) return 0;
-    unsigned c = 0;
-    for (typename std::list<TableCount>::const_iterator i = it->second.table_counts_.begin();
-         i != it->second.table_counts_.end(); ++i) {
-      if (i->floor == floor) ++c;
-    }
-    return c;
-  }
-
-  unsigned num_customers() const {
-    return num_customers_;
-  }
-
-  unsigned num_customers(const Dish& dish) const {
-    const typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator it = dish_locs_.find(dish);
-    if (it == dish_locs_.end()) return 0;
-    return it->total_dish_count_;
-  }
-
-  // returns (delta, floor) indicating whether a new table (delta) was opened and on which floor
-  template <class InputIterator, class InputIterator2>
-  TableCount increment(const Dish& dish, InputIterator p0s, InputIterator2 lambdas, MT19937* rng) {
-    DishLocations& loc = dish_locs_[dish];
-    // marg_p0 = marginal probability of opening a new table on any floor with label dish
-    typedef typename std::iterator_traits<InputIterator>::value_type F;
-    const F marg_p0 = std::inner_product(p0s, p0s + Floors, lambdas, F(0.0));
-    assert(marg_p0 <= F(1.0001));
-    int floor = -1;
-    bool share_table = false;
-    if (loc.total_dish_count_) {
-      const F p_empty = F(strength_ + num_tables_ * discount_) * marg_p0;
-      const F p_share = F(loc.total_dish_count_ - loc.table_counts_.size() * discount_);
-      share_table = rng->SelectSample(p_empty, p_share);
-    }
-    if (share_table) {
-      // this can be done with doubles since P0 (which may be tiny) is not involved
-      double r = rng->next() * (loc.total_dish_count_ - loc.table_counts_.size() * discount_);
-      for (typename std::list<TableCount>::iterator ti = loc.table_counts_.begin();
-           ti != loc.table_counts_.end(); ++ti) {
-        r -= ti->count - discount_;
-        if (r <= 0.0) {
-          ++ti->count;
-          floor = ti->floor;
-          break;
-        }
-      }
-      if (r > 0.0) {
-        std::cerr << "Serious error: r=" << r << std::endl;
-        Print(&std::cerr);
-        assert(r <= 0.0);
-      }
-    } else { // sit at currently empty table -- must sample what floor
-      if (Floors == 1) {
-        floor = 0;
-      } else {
-        F r = F(rng->next()) * marg_p0;
-        for (unsigned i = 0; i < Floors; ++i) {
-          r -= (*p0s) * (*lambdas);
-          ++p0s;
-          ++lambdas;
-          if (r <= F(0.0)) {
-            floor = i;
-            break;
-          }
-        }
-      }
-      assert(floor >= 0);
-      loc.table_counts_.push_back(TableCount(1, floor));
-      ++num_tables_;
-    }
-    ++loc.total_dish_count_;
-    ++num_customers_;
-    return (share_table ? TableCount(0, floor) : TableCount(1, floor));
-  }
-
-  // returns first = -1 or 0, indicating whether a table was closed, and on what floor (second)
-  TableCount decrement(const Dish& dish, MT19937* rng) {
-    DishLocations& loc = dish_locs_[dish];
-    assert(loc.total_dish_count_);
-    int floor = -1;
-    int delta = 0;
-    if (loc.total_dish_count_ == 1) {
-      floor = loc.table_counts_.front().floor;
-      dish_locs_.erase(dish);
-      --num_tables_;
-      --num_customers_;
-      delta = -1;
-    } else {
-      // sample customer to remove UNIFORMLY. that is, do NOT use the d
-      // here. if you do, it will introduce (unwanted) bias!
-      double r = rng->next() * loc.total_dish_count_;
-      --loc.total_dish_count_;
-      --num_customers_;
-      for (typename std::list<TableCount>::iterator ti = loc.table_counts_.begin();
-           ti != loc.table_counts_.end(); ++ti) {
-        r -= ti->count;
-        if (r <= 0.0) {
-          floor = ti->floor;
-          if ((--ti->count) == 0) {
-            --num_tables_;
-            delta = -1;
-            loc.table_counts_.erase(ti);
-          }
-          break;
-        }
-      }
-      if (r > 0.0) {
-        std::cerr << "Serious error: r=" << r << std::endl;
-        Print(&std::cerr);
-        assert(r <= 0.0);
-      }
-    }
-    return TableCount(delta, floor);
-  }
-
-  template <class InputIterator, class InputIterator2>
-  typename std::iterator_traits<InputIterator>::value_type prob(const Dish& dish, InputIterator p0s, InputIterator2 lambdas) const {
-    typedef typename std::iterator_traits<InputIterator>::value_type F;
-    const F marg_p0 = std::inner_product(p0s, p0s + Floors, lambdas, F(0.0));
-    assert(marg_p0 <= F(1.0001));
-    const typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator it = dish_locs_.find(dish);
-    const F r = F(num_tables_ * discount_ + strength_);
-    if (it == dish_locs_.end()) {
-      return r * marg_p0 / F(num_customers_ + strength_);
-    } else {
-      return (F(it->second.total_dish_count_ - discount_ * it->second.table_counts_.size()) + F(r * marg_p0)) /
-               F(num_customers_ + strength_);
-    }
-  }
-
-  double log_crp_prob() const {
-    return log_crp_prob(discount_, strength_);
-  }
-
-  // taken from http://en.wikipedia.org/wiki/Chinese_restaurant_process
-  // does not include draws from G_w's
-  double log_crp_prob(const double& discount, const double& strength) const {
-    double lp = 0.0;
-    if (has_discount_prior())
-      lp = Md::log_beta_density(discount, discount_prior_strength_, discount_prior_beta_);
-    if (has_strength_prior())
-      lp += Md::log_gamma_density(strength + discount, strength_prior_shape_, strength_prior_rate_);
-    assert(lp <= 0.0);
-    if (num_customers_) {
-      if (discount > 0.0) {
-        const double r = lgamma(1.0 - discount);
-        if (strength)
-          lp += lgamma(strength) - lgamma(strength / discount);
-        lp += - lgamma(strength + num_customers_)
-             + num_tables_ * log(discount) + lgamma(strength / discount + num_tables_);
-        assert(std::isfinite(lp));
-        for (typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator it = dish_locs_.begin();
-             it != dish_locs_.end(); ++it) {
-          const DishLocations& cur = it->second;
-          for (std::list<TableCount>::const_iterator ti = cur.table_counts_.begin(); ti != cur.table_counts_.end(); ++ti) {
-            lp += lgamma(ti->count - discount) - r;
-          }
-        }
-      } else if (!discount) { // discount == 0.0
-        lp += lgamma(strength) + num_tables_ * log(strength) - lgamma(strength + num_tables_);
-        assert(std::isfinite(lp));
-        for (typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator it = dish_locs_.begin();
-             it != dish_locs_.end(); ++it) {
-          const DishLocations& cur = it->second;
-          lp += lgamma(cur.table_counts_.size());
-        }
-      } else {
-        assert(!"discount less than 0 detected!");
-      }
-    }
-    assert(std::isfinite(lp));
-    return lp;
-  }
-
-  void resample_hyperparameters(MT19937* rng, const unsigned nloop = 5, const unsigned niterations = 10) {
-    assert(has_discount_prior() || has_strength_prior());
-    DiscountResampler dr(*this);
-    StrengthResampler sr(*this);
-    for (int iter = 0; iter < nloop; ++iter) {
-      if (has_strength_prior()) {
-        strength_ = slice_sampler1d(sr, strength_, *rng, -discount_,
-                               std::numeric_limits<double>::infinity(), 0.0, niterations, 100*niterations);
-      }
-      if (has_discount_prior()) {
-        double min_discount = std::numeric_limits<double>::min();
-        if (strength_ < 0.0) min_discount -= strength_;
-        discount_ = slice_sampler1d(dr, discount_, *rng, min_discount,
-                               1.0, 0.0, niterations, 100*niterations);
-      }
-    }
-    strength_ = slice_sampler1d(sr, strength_, *rng, -discount_,
-                             std::numeric_limits<double>::infinity(), 0.0, niterations, 100*niterations);
-  }
-
-  struct DiscountResampler {
-    DiscountResampler(const MFCR& crp) : crp_(crp) {}
-    const MFCR& crp_;
-    double operator()(const double& proposed_d) const {
-      return crp_.log_crp_prob(proposed_d, crp_.strength_);
-    }
-  };
-
-  struct StrengthResampler {
-    StrengthResampler(const MFCR& crp) : crp_(crp) {}
-    const MFCR& crp_;
-    double operator()(const double& proposediscount_strength) const {
-      return crp_.log_crp_prob(crp_.discount_, proposediscount_strength);
-    }
-  };
-
-  struct DishLocations {
-    DishLocations() : total_dish_count_() {}
-    unsigned total_dish_count_;          // customers at all tables with this dish
-    std::list<TableCount> table_counts_; // list<> gives O(1) deletion and insertion, which we want
-                                         // .size() is the number of tables for this dish
-  };
-
-  void Print(std::ostream* out) const {
-    (*out) << "MFCR<" << Floors << ">(d=" << discount_ << ",strength=" << strength_ << ") customers=" << num_customers_ << std::endl;
-    for (typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator it = dish_locs_.begin();
-         it != dish_locs_.end(); ++it) {
-      (*out) << it->first << " (" << it->second.total_dish_count_ << " on " << it->second.table_counts_.size() << " tables): ";
-      for (typename std::list<TableCount>::const_iterator i = it->second.table_counts_.begin();
-           i != it->second.table_counts_.end(); ++i) {
-        (*out) << " " << *i;
-      }
-      (*out) << std::endl;
-    }
-  }
-
-  typedef typename std::tr1::unordered_map<Dish, DishLocations, DishHash>::const_iterator const_iterator;
-  const_iterator begin() const {
-    return dish_locs_.begin();
-  }
-  const_iterator end() const {
-    return dish_locs_.end();
-  }
-
-  unsigned num_tables_;
-  unsigned num_customers_;
-  std::tr1::unordered_map<Dish, DishLocations, DishHash> dish_locs_;
-
-  double discount_;
-  double strength_;
-
-  // optional beta prior on discount_ (NaN if no prior)
-  double discount_prior_strength_;
-  double discount_prior_beta_;
-
-  // optional gamma prior on strength_ (NaN if no prior)
-  double strength_prior_shape_;
-  double strength_prior_rate_;
-};
-
-template <unsigned N,typename T,typename H>
-std::ostream& operator<<(std::ostream& o, const MFCR<N,T,H>& c) {
-  c.Print(&o);
-  return o;
-}
-
-#endif
diff --git a/utils/mfcr_test.cc b/utils/mfcr_test.cc
deleted file mode 100644
index 29a1a2ce..00000000
--- a/utils/mfcr_test.cc
+++ /dev/null
@@ -1,72 +0,0 @@
-#include "mfcr.h"
-
-#include <iostream>
-#include <cassert>
-#include <cmath>
-
-#define BOOST_TEST_MODULE MFCRTest
-#include <boost/test/unit_test.hpp>
-#include <boost/test/floating_point_comparison.hpp>
-
-#include "sampler.h"
-
-using namespace std;
-
-BOOST_AUTO_TEST_CASE(Exchangability) {
-  MT19937 r;
-  MT19937* rng = &r;
-  MFCR<2, int> crp(0.5, 3.0);
-  vector<double> lambdas(2);
-  vector<double> p0s(2);
-  lambdas[0] = 0.2;
-  lambdas[1] = 0.8;
-  p0s[0] = 1.0;
-  p0s[1] = 1.0;
-
-  double tot = 0;
-  double tot2 = 0;
-  double xt = 0;
-  int cust = 10;
-  vector<int> hist(cust + 1, 0), hist2(cust + 1, 0);
-  for (int i = 0; i < cust; ++i) { crp.increment(1, p0s.begin(), lambdas.begin(), rng); }
-  const int samples = 100000;
-  const bool simulate = true;
-  for (int k = 0; k < samples; ++k) {
-    if (!simulate) {
-      crp.clear();
-      for (int i = 0; i < cust; ++i) { crp.increment(1, p0s.begin(), lambdas.begin(), rng); }
-    } else {
-      int da = rng->next() * cust;
-      bool a = rng->next() < 0.45;
-      if (a) {
-        for (int i = 0; i < da; ++i) { crp.increment(1, p0s.begin(), lambdas.begin(), rng); }
-        for (int i = 0; i < da; ++i) { crp.decrement(1, rng); }
-        xt += 1.0;
-      } else {
-        for (int i = 0; i < da; ++i) { crp.decrement(1, rng); }
-        for (int i = 0; i < da; ++i) { crp.increment(1, p0s.begin(), lambdas.begin(), rng); }
-      }
-    }
-    int c = crp.num_tables(1);
-    ++hist[c];
-    tot += c;
-    int c2 = crp.num_tables(1,0);  // tables on floor 0 with dish 1
-    ++hist2[c2];
-    tot2 += c2;
-  }
-  cerr << cust << " = " << crp.num_customers() << endl;
-  cerr << "P(a) = " << (xt / samples) << endl;
-  cerr << "E[num tables] = " << (tot / samples) << endl;
-  double error = fabs((tot / samples) - 6.894);
-  cerr << "   error = " << error << endl;
-  for (int i = 1; i <= cust; ++i)
-    cerr << i << ' ' << (hist[i]) << endl;
-  cerr << "E[num tables on floor 0] = " << (tot2 / samples) << endl;
-  double error2 = fabs((tot2 / samples) - 1.379);
-  cerr << "  error2 = " << error2 << endl;
-  for (int i = 1; i <= cust; ++i)
-    cerr << i << ' ' << (hist2[i]) << endl;
-  assert(error < 0.05);   // these can fail with very low probability
-  assert(error2 < 0.05);
-};
-
diff --git a/utils/sampler.h b/utils/sampler.h
index 3e4a4086..88e1856c 100644
--- a/utils/sampler.h
+++ b/utils/sampler.h
@@ -19,7 +19,7 @@
 
 #include "prob.h"
 
-template <typename F> struct SampleSet;
+template <typename F> class SampleSet;
 
 template <typename RNG>
 struct RandomNumberGenerator {
diff --git a/utils/slice_sampler.h b/utils/slice_sampler.h
deleted file mode 100644
index aa48a169..00000000
--- a/utils/slice_sampler.h
+++ /dev/null
@@ -1,191 +0,0 @@
-//! slice-sampler.h is an MCMC slice sampler
-//!
-//! Mark Johnson, 1st August 2008
-
-#ifndef SLICE_SAMPLER_H
-#define SLICE_SAMPLER_H
-
-#include <algorithm>
-#include <cassert>
-#include <cmath>
-#include <iostream>
-#include <limits>
-
-//! slice_sampler_rfc_type{} returns the value of a user-specified
-//! function if the argument is within range, or - infinity otherwise
-//
-template <typename F, typename Fn, typename U>
-struct slice_sampler_rfc_type {
-  F min_x, max_x;
-  const Fn& f;
-  U max_nfeval, nfeval;
-  slice_sampler_rfc_type(F min_x, F max_x, const Fn& f, U max_nfeval) 
-    : min_x(min_x), max_x(max_x), f(f), max_nfeval(max_nfeval), nfeval(0) { }
-    
-  F operator() (F x) {
-    if (min_x < x && x < max_x) {
-      assert(++nfeval <= max_nfeval);
-      F fx = f(x);
-      assert(std::isfinite(fx));
-      return fx;
-    }
-      return -std::numeric_limits<F>::infinity();
-  }
-};  // slice_sampler_rfc_type{}
-
-//! slice_sampler1d() implements the univariate "range doubling" slice sampler
-//! described in Neal (2003) "Slice Sampling", The Annals of Statistics 31(3), 705-767.
-//
-template <typename F, typename LogF, typename Uniform01>
-F slice_sampler1d(const LogF& logF0,               //!< log of function to sample
-		  F x,                             //!< starting point
-		  Uniform01& u01,                  //!< uniform [0,1) random number generator
-		  F min_x = -std::numeric_limits<F>::infinity(),  //!< minimum value of support
-		  F max_x = std::numeric_limits<F>::infinity(),   //!< maximum value of support
-		  F w = 0.0,                       //!< guess at initial width
-		  unsigned nsamples=1,             //!< number of samples to draw
-		  unsigned max_nfeval=200)         //!< max number of function evaluations
-{
-  typedef unsigned U;
-  slice_sampler_rfc_type<F,LogF,U> logF(min_x, max_x, logF0, max_nfeval);
-
-  assert(std::isfinite(x));
-
-  if (w <= 0.0) {                           // set w to a default width 
-    if (min_x > -std::numeric_limits<F>::infinity() && max_x < std::numeric_limits<F>::infinity())
-      w = (max_x - min_x)/4;
-    else
-      w = std::max(((x < 0.0) ? -x : x)/4, (F) 0.1);
-  }
-  assert(std::isfinite(w));
-
-  F logFx = logF(x);
-  for (U sample = 0; sample < nsamples; ++sample) {
-    F logY = logFx + log(u01()+1e-100);     //! slice logFx at this value
-    assert(std::isfinite(logY));
-
-    F xl = x - w*u01();                     //! lower bound on slice interval
-    F logFxl = logF(xl);
-    F xr = xl + w;                          //! upper bound on slice interval
-    F logFxr = logF(xr);
-
-    while (logY < logFxl || logY < logFxr)  // doubling procedure
-      if (u01() < 0.5) 
-	logFxl = logF(xl -= xr - xl);
-      else
-	logFxr = logF(xr += xr - xl);
-	
-    F xl1 = xl;
-    F xr1 = xr;
-    while (true) {                          // shrinking procedure
-      F x1 = xl1 + u01()*(xr1 - xl1);
-      if (logY < logF(x1)) {
-	F xl2 = xl;                         // acceptance procedure
-	F xr2 = xr; 
-	bool d = false;
-	while (xr2 - xl2 > 1.1*w) {
-	  F xm = (xl2 + xr2)/2;
-	  if ((x < xm && x1 >= xm) || (x >= xm && x1 < xm))
-	    d = true;
-	  if (x1 < xm)
-	    xr2 = xm;
-	  else
-	    xl2 = xm;
-	  if (d && logY >= logF(xl2) && logY >= logF(xr2))
-	    goto unacceptable;
-	}
-	x = x1;
-	goto acceptable;
-      }
-      goto acceptable;
-    unacceptable:
-      if (x1 < x)                           // rest of shrinking procedure
-	xl1 = x1;
-      else 
-	xr1 = x1;
-    }
-  acceptable:
-    w = (4*w + (xr1 - xl1))/5;              // update width estimate
-  }
-  return x;
-}
-
-/*
-//! slice_sampler1d() implements a 1-d MCMC slice sampler.
-//! It should be correct for unimodal distributions, but
-//! not for multimodal ones.
-//
-template <typename F, typename LogP, typename Uniform01>
-F slice_sampler1d(const LogP& logP,     //!< log of distribution to sample
-		  F x,                  //!< initial sample
-		  Uniform01& u01,       //!< uniform random number generator
-		  F min_x = -std::numeric_limits<F>::infinity(),  //!< minimum value of support
-		  F max_x = std::numeric_limits<F>::infinity(),   //!< maximum value of support
-		  F w = 0.0,            //!< guess at initial width
-		  unsigned nsamples=1,  //!< number of samples to draw
-		  unsigned max_nfeval=200)  //!< max number of function evaluations
-{
-  typedef unsigned U;
-  assert(std::isfinite(x));
-  if (w <= 0.0) {
-    if (min_x > -std::numeric_limits<F>::infinity() && max_x < std::numeric_limits<F>::infinity())
-      w = (max_x - min_x)/4;
-    else
-      w = std::max(((x < 0.0) ? -x : x)/4, 0.1);
-  }
-  // TRACE4(x, min_x, max_x, w);
-  F logPx = logP(x);
-  assert(std::isfinite(logPx));
-  U nfeval = 1;
-  for (U sample = 0; sample < nsamples; ++sample) {
-    F x0 = x;
-    F logU = logPx + log(u01()+1e-100);
-    assert(std::isfinite(logU));
-    F r = u01();
-    F xl = std::max(min_x, x - r*w);
-    F xr = std::min(max_x, x + (1-r)*w);
-    // TRACE3(x, logPx, logU);
-    while (xl > min_x && logP(xl) > logU) {
-      xl -= w;
-      w *= 2;
-      ++nfeval;
-      if (nfeval >= max_nfeval)
-	std::cerr << "## Error: nfeval = " << nfeval << ", max_nfeval = " << max_nfeval << ", sample = " << sample << ", nsamples = " << nsamples << ", r = " << r << ", w = " << w << ", xl = " << xl << std::endl;
-      assert(nfeval < max_nfeval);
-    }
-    xl = std::max(xl, min_x);
-    while (xr < max_x && logP(xr) > logU) {
-      xr += w;
-      w *= 2;
-      ++nfeval;
-      if (nfeval >= max_nfeval)
-	std::cerr << "## Error: nfeval = " << nfeval << ", max_nfeval = " << max_nfeval << ", sample = " << sample << ", nsamples = " << nsamples << ", r = " << r << ", w = " << w << ", xr = " << xr << std::endl;
-      assert(nfeval < max_nfeval);
-    }
-    xr = std::min(xr, max_x);
-    while (true) {
-      r = u01();
-      x = r*xl + (1-r)*xr;
-      assert(std::isfinite(x));
-      logPx = logP(x);
-      // TRACE4(logPx, x, xl, xr);
-      assert(std::isfinite(logPx));
-      ++nfeval;
-      if (nfeval >= max_nfeval)
-	std::cerr << "## Error: nfeval = " << nfeval << ", max_nfeval = " << max_nfeval << ", sample = " << sample << ", nsamples = " << nsamples << ", r = " << r << ", w = " << w << ", xl = " << xl << ", xr = " << xr << ", x = " << x << std::endl;
-      assert(nfeval < max_nfeval);
-      if (logPx > logU)
-        break;
-      else if (x > x0)
-          xr = x;
-        else
-          xl = x;
-    }
-    // w = (4*w + (xr-xl))/5;   // gradually adjust w
-  }
-  // TRACE2(logPx, x);
-  return x;
-}  // slice_sampler1d()
-*/
-
-#endif  // SLICE_SAMPLER_H
diff --git a/utils/small_vector.h b/utils/small_vector.h
index 894b1b32..c8a69927 100644
--- a/utils/small_vector.h
+++ b/utils/small_vector.h
@@ -66,7 +66,7 @@ class SmallVector {
   //TODO: figure out iterator traits to allow this to be selcted for any iterator range
   template <class I>
   SmallVector(I const* begin,I const* end) {
-    int s=end-begin;
+    unsigned s=end-begin;
     Alloc(s);
     if (s <= SV_MAX) {
       for (unsigned i = 0; i < s; ++i,++begin) data_.vals[i] = *begin;
diff --git a/utils/stringlib.h b/utils/stringlib.h
index 75772c4d..ff5dc89d 100644
--- a/utils/stringlib.h
+++ b/utils/stringlib.h
@@ -86,7 +86,7 @@ bool match_begin(Str const& str,Prefix const& prefix)
 // source will be returned as a string, target must be a sentence or
 // a lattice (in PLF format) and will be returned as a Lattice object
 void ParseTranslatorInput(const std::string& line, std::string* input, std::string* ref);
-struct Lattice;
+class Lattice;
 void ParseTranslatorInputLattice(const std::string& line, std::string* input, Lattice* ref);
 
 inline std::string Trim(const std::string& str, const std::string& dropChars = " \t") {
diff --git a/utils/tdict.cc b/utils/tdict.cc
index f33bd576..fd2b76cb 100644
--- a/utils/tdict.cc
+++ b/utils/tdict.cc
@@ -13,22 +13,6 @@ using namespace std;
 
 Dict TD::dict_;
 
-unsigned int TD::NumWords() {
-  return dict_.max();
-}
-
-WordID TD::Convert(const std::string& s) {
-  return dict_.Convert(s);
-}
-
-WordID TD::Convert(char const* s) {
-  return dict_.Convert(string(s));
-}
-
-const char* TD::Convert(WordID w) {
-  return dict_.Convert(w).c_str();
-}
-
 void TD::GetWordIDs(const std::vector<std::string>& strings, std::vector<WordID>* ids) {
   ids->clear();
   for (vector<string>::const_iterator i = strings.begin(); i != strings.end(); ++i)
@@ -57,7 +41,8 @@ std::string TD::GetString(WordID const* i,WordID const* e) {
 
 int TD::AppendString(const WordID& w, int pos, int bufsize, char* buffer)
 {
-  const char* word = TD::Convert(w);
+  const string& s = TD::Convert(w);
+  const char* word = s.c_str();
   const char* const end_buf = buffer + bufsize;
   char* dest = buffer + pos;
   while(dest < end_buf && *word) {
diff --git a/utils/tdict.h b/utils/tdict.h
index 393146fa..03afc2e6 100644
--- a/utils/tdict.h
+++ b/utils/tdict.h
@@ -3,10 +3,9 @@
 
 #include <string>
 #include <vector>
+#include <cassert>
 #include "wordid.h"
-#include <assert.h>
-
-class Dict;
+#include "dict.h"
 
 struct TD {
   static WordID end(); // next id to be assigned; [begin,end) give the non-reserved tokens seen so far
@@ -15,10 +14,18 @@ struct TD {
   static std::string GetString(const std::vector<WordID>& str);
   static std::string GetString(WordID const* i,WordID const* e);
   static int AppendString(const WordID& w, int pos, int bufsize, char* buffer);
-  static unsigned int NumWords();
-  static WordID Convert(const std::string& s);
-  static WordID Convert(char const* s);
-  static const char* Convert(WordID w);
+  static unsigned int NumWords() {
+    return dict_.max();
+  }
+  static WordID Convert(const std::string& s) {
+    return dict_.Convert(s);
+  }
+  static WordID Convert(char const* s) {
+    return dict_.Convert(std::string(s));
+  }
+  static const std::string& Convert(WordID w) {
+    return dict_.Convert(w);
+  }
  private:
   static Dict dict_;
 };
diff --git a/utils/unigram_pyp_lm.cc b/utils/unigram_pyp_lm.cc
deleted file mode 100644
index 510e8839..00000000
--- a/utils/unigram_pyp_lm.cc
+++ /dev/null
@@ -1,168 +0,0 @@
-#include <iostream>
-#include <tr1/memory>
-#include <queue>
-
-#include <boost/functional.hpp>
-#include <boost/program_options.hpp>
-#include <boost/program_options/variables_map.hpp>
-
-#include "corpus_tools.h"
-#include "m.h"
-#include "tdict.h"
-#include "sampler.h"
-#include "ccrp.h"
-
-// A not very memory-efficient implementation of an 1-gram LM based on PYPs
-// as described in Y.-W. Teh. (2006) A Hierarchical Bayesian Language Model
-// based on Pitman-Yor Processes. In Proc. ACL.
-
-using namespace std;
-using namespace tr1;
-namespace po = boost::program_options;
-
-boost::shared_ptr<MT19937> prng;
-
-void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
-  po::options_description opts("Configuration options");
-  opts.add_options()
-        ("samples,n",po::value<unsigned>()->default_value(50),"Number of samples")
-        ("train,i",po::value<string>(),"Training data file")
-        ("test,T",po::value<string>(),"Test data file")
-        ("discount_prior_a,a",po::value<double>()->default_value(1.0), "discount ~ Beta(a,b): a=this")
-        ("discount_prior_b,b",po::value<double>()->default_value(1.0), "discount ~ Beta(a,b): b=this")
-        ("strength_prior_s,s",po::value<double>()->default_value(1.0), "strength ~ Gamma(s,r): s=this")
-        ("strength_prior_r,r",po::value<double>()->default_value(1.0), "strength ~ Gamma(s,r): r=this")
-        ("random_seed,S",po::value<uint32_t>(), "Random seed");
-  po::options_description clo("Command line options");
-  clo.add_options()
-        ("config", po::value<string>(), "Configuration file")
-        ("help", "Print this help message and exit");
-  po::options_description dconfig_options, dcmdline_options;
-  dconfig_options.add(opts);
-  dcmdline_options.add(opts).add(clo);
-  
-  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
-  if (conf->count("config")) {
-    ifstream config((*conf)["config"].as<string>().c_str());
-    po::store(po::parse_config_file(config, dconfig_options), *conf);
-  }
-  po::notify(*conf);
-
-  if (conf->count("help") || (conf->count("train") == 0)) {
-    cerr << dcmdline_options << endl;
-    exit(1);
-  }
-}
-
-// uniform base distribution (0-gram model)
-struct UniformWordModel {
-  explicit UniformWordModel(unsigned vocab_size) : p0(1.0 / vocab_size), draws() {}
-  void increment() { ++draws; }
-  void decrement() { --draws; assert(draws >= 0); }
-  double prob(WordID) const { return p0; } // all words have equal prob
-  double log_likelihood() const { return draws * log(p0); }
-  const double p0;
-  int draws;
-};
-
-// represents an Unigram LM
-struct UnigramLM {
-  UnigramLM(unsigned vs, double da, double db, double ss, double sr) :
-      uniform_vocab(vs),
-      crp(da, db, ss, sr, 0.8, 1.0) {}
-  void increment(WordID w, MT19937* rng) {
-    const double backoff = uniform_vocab.prob(w);
-    if (crp.increment(w, backoff, rng))
-      uniform_vocab.increment();
-  }
-  void decrement(WordID w, MT19937* rng) {
-    if (crp.decrement(w, rng))
-      uniform_vocab.decrement();
-  }
-  double prob(WordID w) const {
-    const double backoff = uniform_vocab.prob(w);
-    return crp.prob(w, backoff);
-  }
-
-  double log_likelihood() const {
-    double llh = uniform_vocab.log_likelihood();
-    llh += crp.log_crp_prob();
-    return llh;
-  }
-
-  void resample_hyperparameters(MT19937* rng) {
-    crp.resample_hyperparameters(rng);
-  }
-
-  double discount_a, discount_b, strength_s, strength_r;
-  double d, strength;
-  UniformWordModel uniform_vocab;
-  CCRP<WordID> crp;
-};
-
-int main(int argc, char** argv) {
-  po::variables_map conf;
-
-  InitCommandLine(argc, argv, &conf);
-  const unsigned samples = conf["samples"].as<unsigned>();
-  if (conf.count("random_seed"))
-    prng.reset(new MT19937(conf["random_seed"].as<uint32_t>()));
-  else
-    prng.reset(new MT19937);
-  MT19937& rng = *prng;
-  vector<vector<WordID> > corpuse;
-  set<WordID> vocabe;
-  const WordID kEOS = TD::Convert("</s>");
-  cerr << "Reading corpus...\n";
-  CorpusTools::ReadFromFile(conf["train"].as<string>(), &corpuse, &vocabe);
-  cerr << "E-corpus size: " << corpuse.size() << " sentences\t (" << vocabe.size() << " word types)\n";
-  vector<vector<WordID> > test;
-  if (conf.count("test"))
-    CorpusTools::ReadFromFile(conf["test"].as<string>(), &test);
-  else
-    test = corpuse;
-  UnigramLM lm(vocabe.size(),
-               conf["discount_prior_a"].as<double>(),
-               conf["discount_prior_b"].as<double>(),
-               conf["strength_prior_s"].as<double>(),
-               conf["strength_prior_r"].as<double>());
-  for (int SS=0; SS < samples; ++SS) {
-    for (int ci = 0; ci < corpuse.size(); ++ci) {
-      const vector<WordID>& s = corpuse[ci];
-      for (int i = 0; i <= s.size(); ++i) {
-        WordID w = (i < s.size() ? s[i] : kEOS);
-        if (SS > 0) lm.decrement(w, &rng);
-        lm.increment(w, &rng);
-      }
-      if (SS > 0) lm.decrement(kEOS, &rng);
-      lm.increment(kEOS, &rng);
-    }
-    cerr << "LLH=" << lm.log_likelihood() << endl;
-    //if (SS % 10 == 9) lm.resample_hyperparameters(&rng);
-  }
-  double llh = 0;
-  unsigned cnt = 0;
-  unsigned oovs = 0;
-  for (int ci = 0; ci < test.size(); ++ci) {
-    const vector<WordID>& s = test[ci];
-    for (int i = 0; i <= s.size(); ++i) {
-      WordID w = (i < s.size() ? s[i] : kEOS);
-      double lp = log(lm.prob(w)) / log(2);
-      if (i < s.size() && vocabe.count(w) == 0) {
-        cerr << "**OOV ";
-        ++oovs;
-        lp = 0;
-      }
-      cerr << "p(" << TD::Convert(w) << ") = " << lp << endl;
-      llh -= lp;
-      cnt++;
-    }
-  }
-  cerr << "  Log_10 prob: " << (-llh * log(2) / log(10)) << endl;
-  cerr << "        Count: " << cnt << endl;
-  cerr << "         OOVs: " << oovs << endl;
-  cerr << "Cross-entropy: " << (llh / cnt) << endl;
-  cerr << "   Perplexity: " << pow(2, llh / cnt) << endl;
-  return 0;
-}
-
diff --git a/utils/weights.cc b/utils/weights.cc
index f56e2a20..575877b6 100644
--- a/utils/weights.cc
+++ b/utils/weights.cc
@@ -34,7 +34,7 @@ void Weights::InitFromFile(const string& filename,
     int weight_count = 0;
     bool fl = false;
     string buf;
-    weight_t val = 0;
+    double val = 0;
     while (in) {
       getline(in, buf);
       if (buf.size() == 0) continue;
@@ -53,7 +53,7 @@ void Weights::InitFromFile(const string& filename,
       if (feature_list) { feature_list->push_back(buf.substr(start, end - start)); }
       while(end < buf.size() && buf[end] == ' ') ++end;
       val = strtod(&buf.c_str()[end], NULL);
-      if (isnan(val)) {
+      if (std::isnan(val)) {
         cerr << FD::Convert(fid) << " has weight NaN!\n";
         abort();
       }
@@ -127,8 +127,8 @@ void Weights::InitSparseVector(const vector<weight_t>& dv,
 
 void Weights::SanityCheck(const vector<weight_t>& w) {
   for (unsigned i = 0; i < w.size(); ++i) {
-    assert(!isnan(w[i]));
-    assert(!isinf(w[i]));
+    assert(!std::isnan(w[i]));
+    assert(!std::isinf(w[i]));
   }
 }
 
diff --git a/word-aligner/makefiles/makefile.grammars b/word-aligner/makefiles/makefile.grammars
index 1a069abf..08ff33e1 100644
--- a/word-aligner/makefiles/makefile.grammars
+++ b/word-aligner/makefiles/makefile.grammars
@@ -16,7 +16,7 @@ STEM_E = $(SCRIPT_DIR)/stemmers/$(E_LANG).pl
 
 CLASSIFY = $(SUPPORT_DIR)/classify.pl
 MAKE_LEX_GRAMMAR = $(SUPPORT_DIR)/make_lex_grammar.pl
-MODEL1 = $(TRAINING_DIR)/model1
+MODEL1 = $(TRAINING_DIR)/fast_align
 MERGE_CORPUS = $(SUPPORT_DIR)/merge_corpus.pl
 
 e.voc: corpus.e
@@ -66,16 +66,16 @@ corpus.e-f: corpus.f corpus.e
 	$(MERGE_CORPUS) corpus.e corpus.f > $@
 
 corpus.f-e.model1: corpus.f-e
-	$(MODEL1) -v corpus.f-e > $@
+	$(MODEL1) -p -v -i corpus.f-e > $@
 
 corpus.e-f.model1: corpus.e-f
-	$(MODEL1) -v -V corpus.e-f > $@
+	$(MODEL1) -p -v -V -i corpus.e-f > $@
 
 corpus.f-e.full-model1: corpus.f-e
-	$(MODEL1) -t -999999 -v -V corpus.f-e > $@
+	$(MODEL1) -p -t -999999 -v -V -i corpus.f-e > $@
 
 corpus.e-f.full-model1: corpus.e-f
-	$(MODEL1) -t -999999 -v -V corpus.e-f > $@
+	$(MODEL1) -p -t -999999 -v -V -i corpus.e-f > $@
 
 corpus.f-e.lex-grammar.gz: corpus.f-e corpus.f-e.model1 corpus.e-f.model1
 	$(MAKE_LEX_GRAMMAR) corpus.f-e corpus.f-e.model1 corpus.e-f.model1 | $(GZIP) -9 > $@