13 files changed, 214 insertions, 11 deletions
diff --git a/configure.ac b/configure.ac
index eabb8645..dcd0a0d8 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,5 +1,6 @@
-AC_INIT
-AM_INIT_AUTOMAKE(cdec,0.1)
+AC_INIT([cdec],[1.0])
+AC_CONFIG_SRCDIR([decoder/cdec.cc])
+AM_INIT_AUTOMAKE
 AC_CONFIG_HEADERS(config.h)
 AC_PROG_LIBTOOL
 AC_PROG_LEX
diff --git a/decoder/Makefile.am b/decoder/Makefile.am
index 88a6116c..21187da8 100644
--- a/decoder/Makefile.am
+++ b/decoder/Makefile.am
@@ -26,7 +26,77 @@ rule_lexer.cc: rule_lexer.ll
 
 noinst_LIBRARIES = libcdec.a
 
+EXTRA_DIST = rule_lexer.ll
+
 libcdec_a_SOURCES = \
+  JSON_parser.h \
+  aligner.h \
+  apply_fsa_models.h \
+  apply_models.h \
+  bottom_up_parser.h \
+  cfg.h \
+  cfg_binarize.h \
+  cfg_format.h \
+  cfg_options.h \
+  csplit.h \
+  decoder.h \
+  dwarf.h \
+  earley_composer.h \
+  exp_semiring.h \
+  factored_lexicon_helper.h \
+  ff.h \
+  ff_basic.h \
+  ff_bleu.h \
+  ff_charset.h \
+  ff_context.h \
+  ff_csplit.h \
+  ff_dwarf.h \
+  ff_external.h \
+  ff_factory.h \
+  ff_klm.h \
+  ff_lm.h \
+  ff_ngrams.h \
+  ff_register.h \
+  ff_rules.h \
+  ff_ruleshape.h \
+  ff_sample_fsa.h \
+  ff_source_syntax.h \
+  ff_spans.h \
+  ff_tagger.h \
+  ff_wordalign.h \
+  ff_wordset.h \
+  ffset.h \
+  forest_writer.h \
+  freqdict.h \
+  grammar.h \
+  hg.h \
+  hg_cfg.h \
+  hg_intersect.h \
+  hg_io.h \
+  hg_remove_eps.h \
+  hg_sampler.h \
+  hg_test.h \
+  hg_union.h \
+  incremental.h \
+  inside_outside.h \
+  json_parse.h \
+  kbest.h \
+  lattice.h \
+  lexalign.h \
+  lextrans.h \
+  nt_span.h \
+  oracle_bleu.h \
+  phrasebased_translator.h \
+  phrasetable_fst.h \
+  program_options.h \
+  rule_lexer.h \
+  sentence_metadata.h \
+  sentences.h \
+  tagger.h \
+  translator.h \
+  tromble_loss.h \
+  trule.h \
+  viterbi.h \
   forest_writer.cc \
   maxtrans_blunsom.cc \
   cdec_ff.cc \
diff --git a/klm/lm/Makefile.am b/klm/lm/Makefile.am
index a12c5f03..436cfd08 100644
--- a/klm/lm/Makefile.am
+++ b/klm/lm/Makefile.am
@@ -12,6 +12,33 @@ build_binary_LDADD = libklm.a ../util/libklm_util.a -lz
 noinst_LIBRARIES = libklm.a
 
 libklm_a_SOURCES = \
+  bhiksha.hh \
+  binary_format.hh \
+  blank.hh \
+  config.hh \
+  enumerate_vocab.hh \
+  facade.hh \
+  left.hh \
+  lm_exception.hh \
+  max_order.hh \
+  model.hh \
+  model_type.hh \
+  ngram_query.hh \
+  partial.hh \
+  quantize.hh \
+  read_arpa.hh \
+  return.hh \
+  search_hashed.hh \
+  search_trie.hh \
+  state.hh \
+  trie.hh \
+  trie_sort.hh \
+  value.hh \
+  value_build.hh \
+  virtual_interface.hh \
+  vocab.hh \
+  weights.hh \
+  word_index.hh \
   bhiksha.cc \
   binary_format.cc \
   config.cc \
diff --git a/klm/search/Makefile.am b/klm/search/Makefile.am
index 5aea33c2..a34f6cea 100644
--- a/klm/search/Makefile.am
+++ b/klm/search/Makefile.am
@@ -1,11 +1,23 @@
 noinst_LIBRARIES = libksearch.a
 
 libksearch_a_SOURCES = \
+  applied.hh \
+  config.hh \
+  context.hh \
+  dedupe.hh \
+  edge.hh \
+  edge_generator.hh \
+  header.hh \
+  nbest.hh \
+  rule.hh \
+  types.hh \
+  vertex.hh \
+  vertex_generator.hh \
   edge_generator.cc \
 	nbest.cc \
   rule.cc \
   vertex.cc \
   vertex_generator.cc
 
-AM_CPPFLAGS = -W -Wall -Wno-sign-compare $(GTEST_CPPFLAGS) -I..
+AM_CPPFLAGS = -W -Wall -Wno-sign-compare -I..
 
diff --git a/klm/util/Makefile.am b/klm/util/Makefile.am
index a676bdb3..bb441432 100644
--- a/klm/util/Makefile.am
+++ b/klm/util/Makefile.am
@@ -19,6 +19,26 @@
 noinst_LIBRARIES = libklm_util.a
 
 libklm_util_a_SOURCES = \
+  bit_packing.hh \
+  ersatz_progress.hh \
+  exception.hh \
+  file.hh \
+  file_piece.hh \
+  getopt.hh \
+  have.hh \
+  joint_sort.hh \
+  mmap.hh \
+  murmur_hash.hh \
+  pool.hh \
+  probing_hash_table.hh \
+  proxy_iterator.hh \
+  read_compressed.hh \
+  scoped.hh \
+  sized_iterator.hh \
+  sorted_uniform.hh \
+  string_piece.hh \
+  tokenize_piece.hh \
+  usage.hh \
   ersatz_progress.cc \
   bit_packing.cc \
   exception.cc \
diff --git a/mteval/Makefile.am b/mteval/Makefile.am
index 4444285f..b19e4bb1 100644
--- a/mteval/Makefile.am
+++ b/mteval/Makefile.am
@@ -9,6 +9,17 @@ TESTS = scorer_test
 noinst_LIBRARIES = libmteval.a
 
 libmteval_a_SOURCES = \
+  aer_scorer.h \
+  comb_scorer.h \
+  external_scorer.h \
+  ns.h \
+  ns_cer.h \
+  ns_comb.h \
+  ns_docscorer.h \
+  ns_ext.h \
+  ns_ter.h \
+  scorer.h \
+  ter.h \
   aer_scorer.cc \
   comb_scorer.cc \
   external_scorer.cc \
diff --git a/training/crf/Makefile.am b/training/crf/Makefile.am
index d203df25..f72d8f92 100644
--- a/training/crf/Makefile.am
+++ b/training/crf/Makefile.am
@@ -18,10 +18,10 @@ mpi_extract_reachable_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/klm/
 mpi_extract_features_SOURCES = mpi_extract_features.cc
 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 $(top_srcdir)/klm/lm/libklm.a $(top_srcdir)/klm/util/libklm_util.a -lz
 
-mpi_batch_optimize_SOURCES = mpi_batch_optimize.cc cllh_observer.cc
+mpi_batch_optimize_SOURCES = mpi_batch_optimize.cc cllh_observer.cc cllh_observer.h
 mpi_batch_optimize_LDADD = $(top_srcdir)/training/utils/libtraining_utils.a $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/klm/search/libksearch.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
 
-mpi_compute_cllh_SOURCES = mpi_compute_cllh.cc cllh_observer.cc
+mpi_compute_cllh_SOURCES = mpi_compute_cllh.cc cllh_observer.cc cllh_observer.h
 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 $(top_srcdir)/klm/lm/libklm.a $(top_srcdir)/klm/util/libklm_util.a -lz
 
 AM_CPPFLAGS = -DBOOST_TEST_DYN_LINK -W -Wall -Wno-sign-compare -I$(top_srcdir)/training -I$(top_srcdir)/training/utils -I$(top_srcdir)/utils -I$(top_srcdir)/decoder -I$(top_srcdir)/mteval
diff --git a/training/dpmert/Makefile.am b/training/dpmert/Makefile.am
index 3dbdfa69..e5f13944 100644
--- a/training/dpmert/Makefile.am
+++ b/training/dpmert/Makefile.am
@@ -13,13 +13,13 @@ mr_dpmert_generate_mapper_input_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_sr
 # nbest2hg_SOURCES = nbest2hg.cc
 # nbest2hg_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a -lfst
 
-mr_dpmert_map_SOURCES = mert_geometry.cc ces.cc error_surface.cc mr_dpmert_map.cc line_optimizer.cc
+mr_dpmert_map_SOURCES = mert_geometry.cc ces.cc error_surface.cc mr_dpmert_map.cc line_optimizer.cc ces.h error_surface.h line_optimizer.h mert_geometry.h
 mr_dpmert_map_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a
 
-mr_dpmert_reduce_SOURCES = error_surface.cc ces.cc mr_dpmert_reduce.cc line_optimizer.cc mert_geometry.cc
+mr_dpmert_reduce_SOURCES = error_surface.cc ces.cc mr_dpmert_reduce.cc line_optimizer.cc mert_geometry.cc ces.h error_surface.h line_optimizer.h mert_geometry.h
 mr_dpmert_reduce_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a
 
-lo_test_SOURCES = lo_test.cc ces.cc mert_geometry.cc error_surface.cc line_optimizer.cc
+lo_test_SOURCES = lo_test.cc ces.cc mert_geometry.cc error_surface.cc line_optimizer.cc ces.h error_surface.h line_optimizer.h mert_geometry.h
 lo_test_LDADD = $(BOOST_UNIT_TEST_FRAMEWORK_LDFLAGS) $(BOOST_UNIT_TEST_FRAMEWORK_LIBS) $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a
 
 AM_CPPFLAGS = -DBOOST_TEST_DYN_LINK -W -Wall -Wno-sign-compare $(GTEST_CPPFLAGS) -I$(top_srcdir)/utils -I$(top_srcdir)/decoder -I$(top_srcdir)/mteval
diff --git a/training/dtrain/Makefile.am b/training/dtrain/Makefile.am
index 4f51b0c8..ee337ca8 100644
--- a/training/dtrain/Makefile.am
+++ b/training/dtrain/Makefile.am
@@ -1,6 +1,6 @@
 bin_PROGRAMS = dtrain
 
-dtrain_SOURCES = dtrain.cc score.cc
+dtrain_SOURCES = dtrain.cc score.cc dtrain.h kbestget.h ksampler.h pairsampling.h score.h
 dtrain_LDADD   = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/klm/search/libksearch.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a $(top_srcdir)/klm/lm/libklm.a $(top_srcdir)/klm/util/libklm_util.a
 
 AM_CPPFLAGS = -W -Wall -Wno-sign-compare -I$(top_srcdir)/utils -I$(top_srcdir)/decoder -I$(top_srcdir)/mteval
diff --git a/training/liblbfgs/Makefile.am b/training/liblbfgs/Makefile.am
index 64a3794d..f0d5c8aa 100644
--- a/training/liblbfgs/Makefile.am
+++ b/training/liblbfgs/Makefile.am
@@ -6,10 +6,17 @@ ll_test_LDADD = liblbfgs.a -lz
 
 noinst_LIBRARIES = liblbfgs.a
 
-liblbfgs_a_SOURCES = lbfgs.c
+liblbfgs_a_SOURCES = \
+  lbfgs.c \
+  arithmetic_ansi.h \
+  arithmetic_sse_double.h \
+  arithmetic_sse_float.h \
+  lbfgs++.h \
+  lbfgs.h
 
 ################################################################
 # do NOT NOT NOT add any other -I includes NO NO NO NO NO ######
 AM_LDFLAGS = liblbfgs.a -lz
 AM_CPPFLAGS = -DBOOST_TEST_DYN_LINK -W -Wall -I. -I..
 ################################################################
+
diff --git a/training/utils/Makefile.am b/training/utils/Makefile.am
index d708a9f5..a2ab86fd 100644
--- a/training/utils/Makefile.am
+++ b/training/utils/Makefile.am
@@ -18,6 +18,13 @@ sentclient_LDFLAGS = -pthread
 TESTS = lbfgs_test optimize_test
 
 libtraining_utils_a_SOURCES = \
+  candidate_set.h \
+  entropy.h \
+  lbfgs.h \
+  online_optimizer.h \
+  optimize.h \
+  risk.h \
+  sentserver.h \
   candidate_set.cc \
   entropy.cc \
   optimize.cc \
diff --git a/utils/Makefile.am b/utils/Makefile.am
index 639c30b8..3177325b 100644
--- a/utils/Makefile.am
+++ b/utils/Makefile.am
@@ -14,6 +14,53 @@ TESTS = ts small_vector_test logval_test weights_test dict_test m_test
 noinst_LIBRARIES = libutils.a
 
 libutils_a_SOURCES = \
+  alias_sampler.h \
+  alignment_io.h \
+  array2d.h \
+  b64tools.h \
+  batched_append.h \
+  city.h \
+  citycrc.h \
+  corpus_tools.h \
+  dict.h \
+  fast_sparse_vector.h \
+  fdict.h \
+  feature_vector.h \
+  filelib.h \
+  gzstream.h \
+  hash.h \
+  have_64_bits.h \
+  indices_after.h \
+  kernel_string_subseq.h \
+  logval.h \
+  m.h \
+  murmur_hash.h \
+  named_enum.h \
+  null_deleter.h \
+  null_traits.h \
+  perfect_hash.h \
+  prob.h \
+  sampler.h \
+  semiring.h \
+  show.h \
+  small_vector.h \
+  sparse_vector.h \
+  static_utoa.h \
+  stringlib.h \
+  swap_pod.h \
+  tdict.h \
+  timing_stats.h \
+  utoa.h \
+  value_array.h \
+  verbose.h \
+  warning_compiler.h \
+  warning_pop.h \
+  warning_push.h \
+  weights.h \
+  wordid.h \
+  writer.h \
+  fast_lexical_cast.hpp \
+  intrusive_refcount.hpp \
   alignment_io.cc \
   b64tools.cc \
   corpus_tools.cc \
@@ -56,3 +103,4 @@ small_vector_test_LDADD = libutils.a $(BOOST_UNIT_TEST_FRAMEWORK_LDFLAGS) $(BOOS
 # do NOT NOT NOT add any other -I includes NO NO NO NO NO ######
 AM_CPPFLAGS = -DBOOST_TEST_DYN_LINK -W -Wall -I.
 ################################################################
+
diff --git a/word-aligner/Makefile.am b/word-aligner/Makefile.am
index 2dcb688e..e274b209 100644
--- a/word-aligner/Makefile.am
+++ b/word-aligner/Makefile.am
@@ -1,6 +1,6 @@
 bin_PROGRAMS = fast_align
 
-fast_align_SOURCES = fast_align.cc ttables.cc
+fast_align_SOURCES = fast_align.cc ttables.cc da.h ttables.h
 fast_align_LDADD = $(top_srcdir)/utils/libutils.a
 
 AM_CPPFLAGS = -W -Wall $(GTEST_CPPFLAGS) -I$(top_srcdir)/utils -I$(top_srcdir)/training