126 files changed, 10 insertions, 735 deletions

diff --git a/Jamroot b/Jamroot
index b1637e5ba..5a9f52b11 100644
--- a/Jamroot
+++ b/Jamroot
@@ -104,7 +104,7 @@ build-project scripts ;
 #Regression tests (only does anything if --with-regtest is passed)
 build-project regression-testing ;
 
-alias programs : lm//query lm//build_binary moses-chart-cmd/src//moses_chart moses-cmd/src//programs OnDiskPt//CreateOnDiskPt OnDiskPt//queryOnDiskPt mert//programs contrib/server//mosesserver misc//programs scripts//training//symal scripts//training//lexical-reordering scripts//training//phrase-extract scripts//training//phrase-extract//extract-ghkm scripts//training//phrase-extract//pcfg-extract scripts//training//phrase-extract//pcfg-score ;
+alias programs : lm//query lm//build_binary moses-chart-cmd/src//moses_chart moses-cmd/src//programs OnDiskPt//CreateOnDiskPt OnDiskPt//queryOnDiskPt mert//programs contrib/server//mosesserver misc//programs symal scripts//training//lexical-reordering phrase-extract phrase-extract//extract-ghkm phrase-extract//pcfg-extract phrase-extract//pcfg-score ;
 
 install-bin-libs programs ;
 install-headers headers-base : [ glob-tree *.h *.hh : jam-files dist bin lib include kenlm moses ] : . ;
diff --git a/scripts/training/phrase-extract/AlignmentPhrase.cpp b/phrase-extract/AlignmentPhrase.cpp
index 2d4439567..2d4439567 100644
--- a/scripts/training/phrase-extract/AlignmentPhrase.cpp
+++ b/phrase-extract/AlignmentPhrase.cpp
diff --git a/scripts/training/phrase-extract/AlignmentPhrase.h b/phrase-extract/AlignmentPhrase.h
index f77b44f36..f77b44f36 100644
--- a/scripts/training/phrase-extract/AlignmentPhrase.h
+++ b/phrase-extract/AlignmentPhrase.h
diff --git a/scripts/training/phrase-extract/ExtractedRule.cpp b/phrase-extract/ExtractedRule.cpp
index c566e842a..c566e842a 100644
--- a/scripts/training/phrase-extract/ExtractedRule.cpp
+++ b/phrase-extract/ExtractedRule.cpp
diff --git a/scripts/training/phrase-extract/ExtractedRule.h b/phrase-extract/ExtractedRule.h
index be6e30836..be6e30836 100644
--- a/scripts/training/phrase-extract/ExtractedRule.h
+++ b/phrase-extract/ExtractedRule.h
diff --git a/scripts/training/phrase-extract/Hole.h b/phrase-extract/Hole.h
index 31e928f6e..31e928f6e 100644
--- a/scripts/training/phrase-extract/Hole.h
+++ b/phrase-extract/Hole.h
diff --git a/scripts/training/phrase-extract/HoleCollection.cpp b/phrase-extract/HoleCollection.cpp
index 4cffab7fd..4cffab7fd 100644
--- a/scripts/training/phrase-extract/HoleCollection.cpp
+++ b/phrase-extract/HoleCollection.cpp
diff --git a/scripts/training/phrase-extract/HoleCollection.h b/phrase-extract/HoleCollection.h
index 355e825fb..355e825fb 100644
--- a/scripts/training/phrase-extract/HoleCollection.h
+++ b/phrase-extract/HoleCollection.h
diff --git a/scripts/training/phrase-extract/InputFileStream.cpp b/phrase-extract/InputFileStream.cpp
index d111903e6..d111903e6 100644
--- a/scripts/training/phrase-extract/InputFileStream.cpp
+++ b/phrase-extract/InputFileStream.cpp
diff --git a/scripts/training/phrase-extract/InputFileStream.h b/phrase-extract/InputFileStream.h
index e2a31bc82..e2a31bc82 100644
--- a/scripts/training/phrase-extract/InputFileStream.h
+++ b/phrase-extract/InputFileStream.h
diff --git a/scripts/training/phrase-extract/Jamfile b/phrase-extract/Jamfile
index 6fae90bb0..d834674b8 100644
--- a/scripts/training/phrase-extract/Jamfile
+++ b/phrase-extract/Jamfile
@@ -1,5 +1,5 @@
 obj InputFileStream.o : InputFileStream.cpp : <include>. ;
-alias InputFileStream : InputFileStream.o ../../..//z ;
+alias InputFileStream : InputFileStream.o ..//z ;
 
 obj tables-core.o : tables-core.cpp : <include>. ;
 obj AlignmentPhrase.o : AlignmentPhrase.cpp : <include>. ;
@@ -10,17 +10,17 @@ obj XmlTree.o : XmlTree.cpp : <include>. ;
 alias filestreams : InputFileStream.cpp OutputFileStream.cpp : : : <include>. ;
 alias trees : SyntaxTree.cpp tables-core.o XmlTree.o : : : <include>. ;
 
-exe extract : tables-core.o SentenceAlignment.o extract.cpp OutputFileStream.cpp InputFileStream ../../..//boost_iostreams ;
+exe extract : tables-core.o SentenceAlignment.o extract.cpp OutputFileStream.cpp InputFileStream ..//boost_iostreams ;
 
-exe extract-rules : tables-core.o SentenceAlignment.o SyntaxTree.o XmlTree.o SentenceAlignmentWithSyntax.cpp HoleCollection.cpp extract-rules.cpp ExtractedRule.cpp OutputFileStream.cpp InputFileStream ../../../moses/src//ThreadPool ../../..//boost_iostreams ;
+exe extract-rules : tables-core.o SentenceAlignment.o SyntaxTree.o XmlTree.o SentenceAlignmentWithSyntax.cpp HoleCollection.cpp extract-rules.cpp ExtractedRule.cpp OutputFileStream.cpp InputFileStream ../moses/src//ThreadPool ..//boost_iostreams ;
 
 exe extract-lex : extract-lex.cpp InputFileStream ;
 
-exe score : tables-core.o AlignmentPhrase.o score.cpp PhraseAlignment.cpp OutputFileStream.cpp InputFileStream ../../..//boost_iostreams ;
+exe score : tables-core.o AlignmentPhrase.o score.cpp PhraseAlignment.cpp OutputFileStream.cpp InputFileStream ..//boost_iostreams ;
 
-exe consolidate : consolidate.cpp tables-core.o OutputFileStream.cpp InputFileStream ../../..//boost_iostreams ;
+exe consolidate : consolidate.cpp tables-core.o OutputFileStream.cpp InputFileStream ..//boost_iostreams ;
 
-exe consolidate-direct : consolidate-direct.cpp OutputFileStream.cpp InputFileStream ../../..//boost_iostreams ;
+exe consolidate-direct : consolidate-direct.cpp OutputFileStream.cpp InputFileStream ..//boost_iostreams ;
 
 exe consolidate-reverse :  consolidate-reverse.cpp tables-core.o InputFileStream ;
 
diff --git a/scripts/training/phrase-extract/OutputFileStream.cpp b/phrase-extract/OutputFileStream.cpp
index 2cad33bb9..2cad33bb9 100644
--- a/scripts/training/phrase-extract/OutputFileStream.cpp
+++ b/phrase-extract/OutputFileStream.cpp
diff --git a/scripts/training/phrase-extract/OutputFileStream.h b/phrase-extract/OutputFileStream.h
index f52e36d76..f52e36d76 100644
--- a/scripts/training/phrase-extract/OutputFileStream.h
+++ b/phrase-extract/OutputFileStream.h
diff --git a/scripts/training/phrase-extract/PhraseAlignment.cpp b/phrase-extract/PhraseAlignment.cpp
index ceb74f04c..ceb74f04c 100644
--- a/scripts/training/phrase-extract/PhraseAlignment.cpp
+++ b/phrase-extract/PhraseAlignment.cpp
diff --git a/scripts/training/phrase-extract/PhraseAlignment.h b/phrase-extract/PhraseAlignment.h
index 8bd83503d..8bd83503d 100644
--- a/scripts/training/phrase-extract/PhraseAlignment.h
+++ b/phrase-extract/PhraseAlignment.h
diff --git a/scripts/training/phrase-extract/RuleExist.h b/phrase-extract/RuleExist.h
index cf7fae3cd..cf7fae3cd 100644
--- a/scripts/training/phrase-extract/RuleExist.h
+++ b/phrase-extract/RuleExist.h
diff --git a/scripts/training/phrase-extract/RuleExtractionOptions.h b/phrase-extract/RuleExtractionOptions.h
index 272af2c76..272af2c76 100644
--- a/scripts/training/phrase-extract/RuleExtractionOptions.h
+++ b/phrase-extract/RuleExtractionOptions.h
diff --git a/scripts/training/phrase-extract/SafeGetline.h b/phrase-extract/SafeGetline.h
index 0e03b8468..0e03b8468 100644
--- a/scripts/training/phrase-extract/SafeGetline.h
+++ b/phrase-extract/SafeGetline.h
diff --git a/scripts/training/phrase-extract/SentenceAlignment.cpp b/phrase-extract/SentenceAlignment.cpp
index 8b513cfb4..8b513cfb4 100644
--- a/scripts/training/phrase-extract/SentenceAlignment.cpp
+++ b/phrase-extract/SentenceAlignment.cpp
diff --git a/scripts/training/phrase-extract/SentenceAlignment.h b/phrase-extract/SentenceAlignment.h
index df3987198..df3987198 100644
--- a/scripts/training/phrase-extract/SentenceAlignment.h
+++ b/phrase-extract/SentenceAlignment.h
diff --git a/scripts/training/phrase-extract/SentenceAlignmentWithSyntax.cpp b/phrase-extract/SentenceAlignmentWithSyntax.cpp
index 06dc3919f..06dc3919f 100644
--- a/scripts/training/phrase-extract/SentenceAlignmentWithSyntax.cpp
+++ b/phrase-extract/SentenceAlignmentWithSyntax.cpp
diff --git a/scripts/training/phrase-extract/SentenceAlignmentWithSyntax.h b/phrase-extract/SentenceAlignmentWithSyntax.h
index a2c164655..a2c164655 100644
--- a/scripts/training/phrase-extract/SentenceAlignmentWithSyntax.h
+++ b/phrase-extract/SentenceAlignmentWithSyntax.h
diff --git a/scripts/training/phrase-extract/SyntaxTree.cpp b/phrase-extract/SyntaxTree.cpp
index f2783ffd2..f2783ffd2 100644
--- a/scripts/training/phrase-extract/SyntaxTree.cpp
+++ b/phrase-extract/SyntaxTree.cpp
diff --git a/scripts/training/phrase-extract/SyntaxTree.h b/phrase-extract/SyntaxTree.h
index 17c106b49..17c106b49 100644
--- a/scripts/training/phrase-extract/SyntaxTree.h
+++ b/phrase-extract/SyntaxTree.h
diff --git a/scripts/training/phrase-extract/XmlException.h b/phrase-extract/XmlException.h
index 15ee91f20..15ee91f20 100644
--- a/scripts/training/phrase-extract/XmlException.h
+++ b/phrase-extract/XmlException.h
diff --git a/scripts/training/phrase-extract/XmlTree.cpp b/phrase-extract/XmlTree.cpp
index 29c0d94aa..29c0d94aa 100644
--- a/scripts/training/phrase-extract/XmlTree.cpp
+++ b/phrase-extract/XmlTree.cpp
diff --git a/scripts/training/phrase-extract/XmlTree.h b/phrase-extract/XmlTree.h
index 7e6bbecea..7e6bbecea 100644
--- a/scripts/training/phrase-extract/XmlTree.h
+++ b/phrase-extract/XmlTree.h
diff --git a/scripts/training/phrase-extract/consolidate-direct.cpp b/phrase-extract/consolidate-direct.cpp
index e7e68e977..e7e68e977 100644
--- a/scripts/training/phrase-extract/consolidate-direct.cpp
+++ b/phrase-extract/consolidate-direct.cpp
diff --git a/scripts/training/phrase-extract/consolidate-direct.vcxproj b/phrase-extract/consolidate-direct.vcxproj
index a84d2cce6..a84d2cce6 100644
--- a/scripts/training/phrase-extract/consolidate-direct.vcxproj
+++ b/phrase-extract/consolidate-direct.vcxproj
diff --git a/scripts/training/phrase-extract/consolidate-reverse.cpp b/phrase-extract/consolidate-reverse.cpp
index c86d870c8..c86d870c8 100644
--- a/scripts/training/phrase-extract/consolidate-reverse.cpp
+++ b/phrase-extract/consolidate-reverse.cpp
diff --git a/scripts/training/phrase-extract/consolidate.cpp b/phrase-extract/consolidate.cpp
index 17aa11846..17aa11846 100644
--- a/scripts/training/phrase-extract/consolidate.cpp
+++ b/phrase-extract/consolidate.cpp
diff --git a/scripts/training/phrase-extract/consolidate.vcxproj b/phrase-extract/consolidate.vcxproj
index 1e77a90f0..1e77a90f0 100644
--- a/scripts/training/phrase-extract/consolidate.vcxproj
+++ b/phrase-extract/consolidate.vcxproj
diff --git a/scripts/training/phrase-extract/extract-ghkm/Alignment.cpp b/phrase-extract/extract-ghkm/Alignment.cpp
index fcd5e14e1..fcd5e14e1 100644
--- a/scripts/training/phrase-extract/extract-ghkm/Alignment.cpp
+++ b/phrase-extract/extract-ghkm/Alignment.cpp
diff --git a/scripts/training/phrase-extract/extract-ghkm/Alignment.h b/phrase-extract/extract-ghkm/Alignment.h
index bc42191e1..bc42191e1 100644
--- a/scripts/training/phrase-extract/extract-ghkm/Alignment.h
+++ b/phrase-extract/extract-ghkm/Alignment.h
diff --git a/scripts/training/phrase-extract/extract-ghkm/AlignmentGraph.cpp b/phrase-extract/extract-ghkm/AlignmentGraph.cpp
index 6bd32a13b..6bd32a13b 100644
--- a/scripts/training/phrase-extract/extract-ghkm/AlignmentGraph.cpp
+++ b/phrase-extract/extract-ghkm/AlignmentGraph.cpp
diff --git a/scripts/training/phrase-extract/extract-ghkm/AlignmentGraph.h b/phrase-extract/extract-ghkm/AlignmentGraph.h
index 94948758a..94948758a 100644
--- a/scripts/training/phrase-extract/extract-ghkm/AlignmentGraph.h
+++ b/phrase-extract/extract-ghkm/AlignmentGraph.h
diff --git a/scripts/training/phrase-extract/extract-ghkm/ComposedRule.cpp b/phrase-extract/extract-ghkm/ComposedRule.cpp
index 8bf3cfc72..8bf3cfc72 100644
--- a/scripts/training/phrase-extract/extract-ghkm/ComposedRule.cpp
+++ b/phrase-extract/extract-ghkm/ComposedRule.cpp
diff --git a/scripts/training/phrase-extract/extract-ghkm/ComposedRule.h b/phrase-extract/extract-ghkm/ComposedRule.h
index 65ce9ac70..65ce9ac70 100644
--- a/scripts/training/phrase-extract/extract-ghkm/ComposedRule.h
+++ b/phrase-extract/extract-ghkm/ComposedRule.h
diff --git a/scripts/training/phrase-extract/extract-ghkm/Exception.h b/phrase-extract/extract-ghkm/Exception.h
index 9928785f0..9928785f0 100644
--- a/scripts/training/phrase-extract/extract-ghkm/Exception.h
+++ b/phrase-extract/extract-ghkm/Exception.h
diff --git a/scripts/training/phrase-extract/extract-ghkm/ExtractGHKM.cpp b/phrase-extract/extract-ghkm/ExtractGHKM.cpp
index dae876116..dae876116 100644
--- a/scripts/training/phrase-extract/extract-ghkm/ExtractGHKM.cpp
+++ b/phrase-extract/extract-ghkm/ExtractGHKM.cpp
diff --git a/scripts/training/phrase-extract/extract-ghkm/ExtractGHKM.h b/phrase-extract/extract-ghkm/ExtractGHKM.h
index f16abc5f3..f16abc5f3 100644
--- a/scripts/training/phrase-extract/extract-ghkm/ExtractGHKM.h
+++ b/phrase-extract/extract-ghkm/ExtractGHKM.h
diff --git a/phrase-extract/extract-ghkm/Jamfile b/phrase-extract/extract-ghkm/Jamfile
new file mode 100644
index 000000000..1a81c5f87
--- /dev/null
+++ b/phrase-extract/extract-ghkm/Jamfile
@@ -0,0 +1 @@
+exe extract-ghkm : [ glob *.cpp ] ..//filestreams ..//trees ../..//boost_iostreams ../..//boost_program_options ../..//z ;
diff --git a/scripts/training/phrase-extract/extract-ghkm/Main.cpp b/phrase-extract/extract-ghkm/Main.cpp
index faf3230a6..faf3230a6 100644
--- a/scripts/training/phrase-extract/extract-ghkm/Main.cpp
+++ b/phrase-extract/extract-ghkm/Main.cpp
diff --git a/scripts/training/phrase-extract/extract-ghkm/Node.cpp b/phrase-extract/extract-ghkm/Node.cpp
index beb7470b8..beb7470b8 100644
--- a/scripts/training/phrase-extract/extract-ghkm/Node.cpp
+++ b/phrase-extract/extract-ghkm/Node.cpp
diff --git a/scripts/training/phrase-extract/extract-ghkm/Node.h b/phrase-extract/extract-ghkm/Node.h
index 775473362..775473362 100644
--- a/scripts/training/phrase-extract/extract-ghkm/Node.h
+++ b/phrase-extract/extract-ghkm/Node.h
diff --git a/scripts/training/phrase-extract/extract-ghkm/Options.h b/phrase-extract/extract-ghkm/Options.h
index 362fc95d2..362fc95d2 100644
--- a/scripts/training/phrase-extract/extract-ghkm/Options.h
+++ b/phrase-extract/extract-ghkm/Options.h
diff --git a/scripts/training/phrase-extract/extract-ghkm/ParseTree.cpp b/phrase-extract/extract-ghkm/ParseTree.cpp
index 052b8dee1..052b8dee1 100644
--- a/scripts/training/phrase-extract/extract-ghkm/ParseTree.cpp
+++ b/phrase-extract/extract-ghkm/ParseTree.cpp
diff --git a/scripts/training/phrase-extract/extract-ghkm/ParseTree.h b/phrase-extract/extract-ghkm/ParseTree.h
index 273e2e04e..273e2e04e 100644
--- a/scripts/training/phrase-extract/extract-ghkm/ParseTree.h
+++ b/phrase-extract/extract-ghkm/ParseTree.h
diff --git a/scripts/training/phrase-extract/extract-ghkm/ScfgRule.cpp b/phrase-extract/extract-ghkm/ScfgRule.cpp
index 5dc70052c..5dc70052c 100644
--- a/scripts/training/phrase-extract/extract-ghkm/ScfgRule.cpp
+++ b/phrase-extract/extract-ghkm/ScfgRule.cpp
diff --git a/scripts/training/phrase-extract/extract-ghkm/ScfgRule.h b/phrase-extract/extract-ghkm/ScfgRule.h
index 2405d8fa3..2405d8fa3 100644
--- a/scripts/training/phrase-extract/extract-ghkm/ScfgRule.h
+++ b/phrase-extract/extract-ghkm/ScfgRule.h
diff --git a/scripts/training/phrase-extract/extract-ghkm/ScfgRuleWriter.cpp b/phrase-extract/extract-ghkm/ScfgRuleWriter.cpp
index cd993d6e8..cd993d6e8 100644
--- a/scripts/training/phrase-extract/extract-ghkm/ScfgRuleWriter.cpp
+++ b/phrase-extract/extract-ghkm/ScfgRuleWriter.cpp
diff --git a/scripts/training/phrase-extract/extract-ghkm/ScfgRuleWriter.h b/phrase-extract/extract-ghkm/ScfgRuleWriter.h
index b92a432a1..b92a432a1 100644
--- a/scripts/training/phrase-extract/extract-ghkm/ScfgRuleWriter.h
+++ b/phrase-extract/extract-ghkm/ScfgRuleWriter.h
diff --git a/scripts/training/phrase-extract/extract-ghkm/Span.cpp b/phrase-extract/extract-ghkm/Span.cpp
index f0eccbdf2..f0eccbdf2 100644
--- a/scripts/training/phrase-extract/extract-ghkm/Span.cpp
+++ b/phrase-extract/extract-ghkm/Span.cpp
diff --git a/scripts/training/phrase-extract/extract-ghkm/Span.h b/phrase-extract/extract-ghkm/Span.h
index 003d1ef84..003d1ef84 100644
--- a/scripts/training/phrase-extract/extract-ghkm/Span.h
+++ b/phrase-extract/extract-ghkm/Span.h
diff --git a/scripts/training/phrase-extract/extract-ghkm/Subgraph.cpp b/phrase-extract/extract-ghkm/Subgraph.cpp
index e048f2c55..e048f2c55 100644
--- a/scripts/training/phrase-extract/extract-ghkm/Subgraph.cpp
+++ b/phrase-extract/extract-ghkm/Subgraph.cpp
diff --git a/scripts/training/phrase-extract/extract-ghkm/Subgraph.h b/phrase-extract/extract-ghkm/Subgraph.h
index ede1233e9..ede1233e9 100644
--- a/scripts/training/phrase-extract/extract-ghkm/Subgraph.h
+++ b/phrase-extract/extract-ghkm/Subgraph.h
diff --git a/scripts/training/phrase-extract/extract-ghkm/XmlTreeParser.cpp b/phrase-extract/extract-ghkm/XmlTreeParser.cpp
index cc961dc0c..cc961dc0c 100644
--- a/scripts/training/phrase-extract/extract-ghkm/XmlTreeParser.cpp
+++ b/phrase-extract/extract-ghkm/XmlTreeParser.cpp
diff --git a/scripts/training/phrase-extract/extract-ghkm/XmlTreeParser.h b/phrase-extract/extract-ghkm/XmlTreeParser.h
index 664ab11a3..664ab11a3 100644
--- a/scripts/training/phrase-extract/extract-ghkm/XmlTreeParser.h
+++ b/phrase-extract/extract-ghkm/XmlTreeParser.h
diff --git a/scripts/training/phrase-extract/extract-lex.cpp b/phrase-extract/extract-lex.cpp
index 9b03a6da0..9b03a6da0 100644
--- a/scripts/training/phrase-extract/extract-lex.cpp
+++ b/phrase-extract/extract-lex.cpp
diff --git a/scripts/training/phrase-extract/extract-lex.h b/phrase-extract/extract-lex.h
index e2225ecbc..e2225ecbc 100644
--- a/scripts/training/phrase-extract/extract-lex.h
+++ b/phrase-extract/extract-lex.h
diff --git a/scripts/training/phrase-extract/extract-lex.vcxproj b/phrase-extract/extract-lex.vcxproj
index a291d51aa..a291d51aa 100644
--- a/scripts/training/phrase-extract/extract-lex.vcxproj
+++ b/phrase-extract/extract-lex.vcxproj
diff --git a/scripts/training/phrase-extract/extract-rules.cpp b/phrase-extract/extract-rules.cpp
index 997038224..997038224 100644
--- a/scripts/training/phrase-extract/extract-rules.cpp
+++ b/phrase-extract/extract-rules.cpp
diff --git a/scripts/training/phrase-extract/extract-rules.vcxproj b/phrase-extract/extract-rules.vcxproj
index ecd36fe50..ecd36fe50 100644
--- a/scripts/training/phrase-extract/extract-rules.vcxproj
+++ b/phrase-extract/extract-rules.vcxproj
diff --git a/scripts/training/phrase-extract/extract.cpp b/phrase-extract/extract.cpp
index 16b413da9..16b413da9 100644
--- a/scripts/training/phrase-extract/extract.cpp
+++ b/phrase-extract/extract.cpp
diff --git a/scripts/training/phrase-extract/extract.vcxproj b/phrase-extract/extract.vcxproj
index 60a1128eb..60a1128eb 100644
--- a/scripts/training/phrase-extract/extract.vcxproj
+++ b/phrase-extract/extract.vcxproj
diff --git a/scripts/training/phrase-extract/extract.xcodeproj/project.pbxproj b/phrase-extract/extract.xcodeproj/project.pbxproj
index 1e02493cb..1e02493cb 100644
--- a/scripts/training/phrase-extract/extract.xcodeproj/project.pbxproj
+++ b/phrase-extract/extract.xcodeproj/project.pbxproj
diff --git a/scripts/training/phrase-extract/gzfilebuf.h b/phrase-extract/gzfilebuf.h
index b5b0ce87f..b5b0ce87f 100644
--- a/scripts/training/phrase-extract/gzfilebuf.h
+++ b/phrase-extract/gzfilebuf.h
diff --git a/scripts/training/phrase-extract/hierarchical.h b/phrase-extract/hierarchical.h
index 61c899013..61c899013 100644
--- a/scripts/training/phrase-extract/hierarchical.h
+++ b/phrase-extract/hierarchical.h
diff --git a/scripts/training/phrase-extract/pcfg-common/Jamfile b/phrase-extract/pcfg-common/Jamfile
index 3dc272a56..3dc272a56 100644
--- a/scripts/training/phrase-extract/pcfg-common/Jamfile
+++ b/phrase-extract/pcfg-common/Jamfile
diff --git a/scripts/training/phrase-extract/pcfg-common/exception.h b/phrase-extract/pcfg-common/exception.h
index 3dbd59d0e..3dbd59d0e 100644
--- a/scripts/training/phrase-extract/pcfg-common/exception.h
+++ b/phrase-extract/pcfg-common/exception.h
diff --git a/scripts/training/phrase-extract/pcfg-common/numbered_set.h b/phrase-extract/pcfg-common/numbered_set.h
index 15e768b4c..15e768b4c 100644
--- a/scripts/training/phrase-extract/pcfg-common/numbered_set.h
+++ b/phrase-extract/pcfg-common/numbered_set.h
diff --git a/scripts/training/phrase-extract/pcfg-common/pcfg.cc b/phrase-extract/pcfg-common/pcfg.cc
index 054e20a48..054e20a48 100644
--- a/scripts/training/phrase-extract/pcfg-common/pcfg.cc
+++ b/phrase-extract/pcfg-common/pcfg.cc
diff --git a/scripts/training/phrase-extract/pcfg-common/pcfg.h b/phrase-extract/pcfg-common/pcfg.h
index b87336584..b87336584 100644
--- a/scripts/training/phrase-extract/pcfg-common/pcfg.h
+++ b/phrase-extract/pcfg-common/pcfg.h
diff --git a/scripts/training/phrase-extract/pcfg-common/pcfg_tree.h b/phrase-extract/pcfg-common/pcfg_tree.h
index bdac64dfc..bdac64dfc 100644
--- a/scripts/training/phrase-extract/pcfg-common/pcfg_tree.h
+++ b/phrase-extract/pcfg-common/pcfg_tree.h
diff --git a/scripts/training/phrase-extract/pcfg-common/syntax_tree.h b/phrase-extract/pcfg-common/syntax_tree.h
index 89c6ec0c3..89c6ec0c3 100644
--- a/scripts/training/phrase-extract/pcfg-common/syntax_tree.h
+++ b/phrase-extract/pcfg-common/syntax_tree.h
diff --git a/scripts/training/phrase-extract/pcfg-common/tool.cc b/phrase-extract/pcfg-common/tool.cc
index bebd220e1..bebd220e1 100644
--- a/scripts/training/phrase-extract/pcfg-common/tool.cc
+++ b/phrase-extract/pcfg-common/tool.cc
diff --git a/scripts/training/phrase-extract/pcfg-common/tool.h b/phrase-extract/pcfg-common/tool.h
index 0af342569..0af342569 100644
--- a/scripts/training/phrase-extract/pcfg-common/tool.h
+++ b/phrase-extract/pcfg-common/tool.h
diff --git a/scripts/training/phrase-extract/pcfg-common/typedef.h b/phrase-extract/pcfg-common/typedef.h
index 49a12d681..49a12d681 100644
--- a/scripts/training/phrase-extract/pcfg-common/typedef.h
+++ b/phrase-extract/pcfg-common/typedef.h
diff --git a/scripts/training/phrase-extract/pcfg-common/xml_tree_parser.cc b/phrase-extract/pcfg-common/xml_tree_parser.cc
index fd9d11334..fd9d11334 100644
--- a/scripts/training/phrase-extract/pcfg-common/xml_tree_parser.cc
+++ b/phrase-extract/pcfg-common/xml_tree_parser.cc
diff --git a/scripts/training/phrase-extract/pcfg-common/xml_tree_parser.h b/phrase-extract/pcfg-common/xml_tree_parser.h
index 6b418c44e..6b418c44e 100644
--- a/scripts/training/phrase-extract/pcfg-common/xml_tree_parser.h
+++ b/phrase-extract/pcfg-common/xml_tree_parser.h
diff --git a/scripts/training/phrase-extract/pcfg-common/xml_tree_writer.h b/phrase-extract/pcfg-common/xml_tree_writer.h
index 6a9a3de05..6a9a3de05 100644
--- a/scripts/training/phrase-extract/pcfg-common/xml_tree_writer.h
+++ b/phrase-extract/pcfg-common/xml_tree_writer.h
diff --git a/phrase-extract/pcfg-extract/Jamfile b/phrase-extract/pcfg-extract/Jamfile
new file mode 100644
index 000000000..fc93f1a19
--- /dev/null
+++ b/phrase-extract/pcfg-extract/Jamfile
@@ -0,0 +1 @@
+exe pcfg-extract : [ glob *.cc ] ..//pcfg-common ../..//boost_program_options ;
diff --git a/scripts/training/phrase-extract/pcfg-extract/main.cc b/phrase-extract/pcfg-extract/main.cc
index 47b45afc3..47b45afc3 100644
--- a/scripts/training/phrase-extract/pcfg-extract/main.cc
+++ b/phrase-extract/pcfg-extract/main.cc
diff --git a/scripts/training/phrase-extract/pcfg-extract/options.h b/phrase-extract/pcfg-extract/options.h
index 3acb31b58..3acb31b58 100644
--- a/scripts/training/phrase-extract/pcfg-extract/options.h
+++ b/phrase-extract/pcfg-extract/options.h
diff --git a/scripts/training/phrase-extract/pcfg-extract/pcfg_extract.cc b/phrase-extract/pcfg-extract/pcfg_extract.cc
index 71c2e31c3..71c2e31c3 100644
--- a/scripts/training/phrase-extract/pcfg-extract/pcfg_extract.cc
+++ b/phrase-extract/pcfg-extract/pcfg_extract.cc
diff --git a/scripts/training/phrase-extract/pcfg-extract/pcfg_extract.h b/phrase-extract/pcfg-extract/pcfg_extract.h
index 1af6cb4fe..1af6cb4fe 100644
--- a/scripts/training/phrase-extract/pcfg-extract/pcfg_extract.h
+++ b/phrase-extract/pcfg-extract/pcfg_extract.h
diff --git a/scripts/training/phrase-extract/pcfg-extract/rule_collection.cc b/phrase-extract/pcfg-extract/rule_collection.cc
index 32b63e0ef..32b63e0ef 100644
--- a/scripts/training/phrase-extract/pcfg-extract/rule_collection.cc
+++ b/phrase-extract/pcfg-extract/rule_collection.cc
diff --git a/scripts/training/phrase-extract/pcfg-extract/rule_collection.h b/phrase-extract/pcfg-extract/rule_collection.h
index 452fa0e97..452fa0e97 100644
--- a/scripts/training/phrase-extract/pcfg-extract/rule_collection.h
+++ b/phrase-extract/pcfg-extract/rule_collection.h
diff --git a/scripts/training/phrase-extract/pcfg-extract/rule_extractor.cc b/phrase-extract/pcfg-extract/rule_extractor.cc
index 217574e7d..217574e7d 100644
--- a/scripts/training/phrase-extract/pcfg-extract/rule_extractor.cc
+++ b/phrase-extract/pcfg-extract/rule_extractor.cc
diff --git a/scripts/training/phrase-extract/pcfg-extract/rule_extractor.h b/phrase-extract/pcfg-extract/rule_extractor.h
index 6bcffbc61..6bcffbc61 100644
--- a/scripts/training/phrase-extract/pcfg-extract/rule_extractor.h
+++ b/phrase-extract/pcfg-extract/rule_extractor.h
diff --git a/phrase-extract/pcfg-score/Jamfile b/phrase-extract/pcfg-score/Jamfile
new file mode 100644
index 000000000..6b8c963ce
--- /dev/null
+++ b/phrase-extract/pcfg-score/Jamfile
@@ -0,0 +1 @@
+exe pcfg-score : [ glob *.cc ] ..//pcfg-common ../..//boost_program_options ;
diff --git a/scripts/training/phrase-extract/pcfg-score/main.cc b/phrase-extract/pcfg-score/main.cc
index da5392add..da5392add 100644
--- a/scripts/training/phrase-extract/pcfg-score/main.cc
+++ b/phrase-extract/pcfg-score/main.cc
diff --git a/scripts/training/phrase-extract/pcfg-score/options.h b/phrase-extract/pcfg-score/options.h
index e54b2a0b9..e54b2a0b9 100644
--- a/scripts/training/phrase-extract/pcfg-score/options.h
+++ b/phrase-extract/pcfg-score/options.h
diff --git a/scripts/training/phrase-extract/pcfg-score/pcfg_score.cc b/phrase-extract/pcfg-score/pcfg_score.cc
index 345d7fc60..345d7fc60 100644
--- a/scripts/training/phrase-extract/pcfg-score/pcfg_score.cc
+++ b/phrase-extract/pcfg-score/pcfg_score.cc
diff --git a/scripts/training/phrase-extract/pcfg-score/pcfg_score.h b/phrase-extract/pcfg-score/pcfg_score.h
index 5e506c39d..5e506c39d 100644
--- a/scripts/training/phrase-extract/pcfg-score/pcfg_score.h
+++ b/phrase-extract/pcfg-score/pcfg_score.h
diff --git a/scripts/training/phrase-extract/pcfg-score/tree_scorer.cc b/phrase-extract/pcfg-score/tree_scorer.cc
index f9ce97ae0..f9ce97ae0 100644
--- a/scripts/training/phrase-extract/pcfg-score/tree_scorer.cc
+++ b/phrase-extract/pcfg-score/tree_scorer.cc
diff --git a/scripts/training/phrase-extract/pcfg-score/tree_scorer.h b/phrase-extract/pcfg-score/tree_scorer.h
index 36f4e1e99..36f4e1e99 100644
--- a/scripts/training/phrase-extract/pcfg-score/tree_scorer.h
+++ b/phrase-extract/pcfg-score/tree_scorer.h
diff --git a/scripts/training/phrase-extract/phrase-extract.sln b/phrase-extract/phrase-extract.sln
index 800c26192..800c26192 100644
--- a/scripts/training/phrase-extract/phrase-extract.sln
+++ b/phrase-extract/phrase-extract.sln
diff --git a/scripts/training/phrase-extract/relax-parse.cpp b/phrase-extract/relax-parse.cpp
index 6e561b921..6e561b921 100644
--- a/scripts/training/phrase-extract/relax-parse.cpp
+++ b/phrase-extract/relax-parse.cpp
diff --git a/scripts/training/phrase-extract/relax-parse.h b/phrase-extract/relax-parse.h
index ae5994641..ae5994641 100644
--- a/scripts/training/phrase-extract/relax-parse.h
+++ b/phrase-extract/relax-parse.h
diff --git a/scripts/training/phrase-extract/score.cpp b/phrase-extract/score.cpp
index 5e0ade627..5e0ade627 100644
--- a/scripts/training/phrase-extract/score.cpp
+++ b/phrase-extract/score.cpp
diff --git a/scripts/training/phrase-extract/score.h b/phrase-extract/score.h
index 9faa144c5..9faa144c5 100644
--- a/scripts/training/phrase-extract/score.h
+++ b/phrase-extract/score.h
diff --git a/scripts/training/phrase-extract/score.vcxproj b/phrase-extract/score.vcxproj
index e5dc1df9a..e5dc1df9a 100644
--- a/scripts/training/phrase-extract/score.vcxproj
+++ b/phrase-extract/score.vcxproj
diff --git a/scripts/training/phrase-extract/statistics.cpp b/phrase-extract/statistics.cpp
index a39e98a5d..a39e98a5d 100644
--- a/scripts/training/phrase-extract/statistics.cpp
+++ b/phrase-extract/statistics.cpp
diff --git a/scripts/training/phrase-extract/tables-core.cpp b/phrase-extract/tables-core.cpp
index 93ad8b6a1..93ad8b6a1 100644
--- a/scripts/training/phrase-extract/tables-core.cpp
+++ b/phrase-extract/tables-core.cpp
diff --git a/scripts/training/phrase-extract/tables-core.h b/phrase-extract/tables-core.h
index 1899b4d77..1899b4d77 100644
--- a/scripts/training/phrase-extract/tables-core.h
+++ b/phrase-extract/tables-core.h
diff --git a/scripts/training/Jamfile b/scripts/training/Jamfile
index 8ca408d07..e290bb0cb 100644
--- a/scripts/training/Jamfile
+++ b/scripts/training/Jamfile
@@ -1,8 +1,3 @@
-build-project compact-rule-table ;
-build-project phrase-extract ;
-build-project lexical-reordering ;
-build-project symal ;
-
 if $(WITH-GIZA) != no || $(CLEANING) != no {
   make train-model.perl : train-model.perl.missing_bin_dir : @missing_bin_dir ;
   actions missing_bin_dir {
diff --git a/scripts/training/compact-rule-table/Compactify.cpp b/scripts/training/compact-rule-table/Compactify.cpp
deleted file mode 100644
index ceb7eb090..000000000
--- a/scripts/training/compact-rule-table/Compactify.cpp
+++ /dev/null
@@ -1,296 +0,0 @@
-#include "Compactify.h"
-
-#include "NumberedSet.h"
-#include "Options.h"
-#include "RuleTableParser.h"
-
-#include <boost/algorithm/string.hpp>
-#include <boost/program_options.hpp>
-#include <boost/unordered_map.hpp>
-
-#include <cstdlib>
-#include <fstream>
-#include <iostream>
-#include <set>
-#include <sstream>
-
-namespace moses {
-
-int Compactify::main(int argc, char *argv[]) {
-  // Process the command-line arguments.
-  Options options;
-  processOptions(argc, argv, options);
-
-  // Open the input stream.
-  std::istream *inputPtr;
-  std::ifstream inputFileStream;
-  if (options.inputFile.empty() || options.inputFile == "-") {
-    inputPtr = &(std::cin);
-  } else {
-    inputFileStream.open(options.inputFile.c_str());
-    if (!inputFileStream) {
-      std::ostringstream msg;
-      msg << "failed to open input file: " << options.inputFile;
-      error(msg.str());
-    }
-    inputPtr = &inputFileStream;
-  }
-  std::istream &input = *inputPtr;
-
-  // Open the output stream.
-  std::ostream *outputPtr;
-  std::ofstream outputFileStream;
-  if (options.outputFile.empty()) {
-    outputPtr = &(std::cout);
-  } else {
-    outputFileStream.open(options.outputFile.c_str());
-    if (!outputFileStream) {
-      std::ostringstream msg;
-      msg << "failed to open output file: " << options.outputFile;
-      error(msg.str());
-    }
-    outputPtr = &outputFileStream;
-  }
-  std::ostream &output = *outputPtr;
-
-  // Open a temporary file: the rule section must appear last in the output
-  // file, but we don't want to store the full set of rules in memory during
-  // processing, so instead they're written to a temporary file then copied to
-  // the output file as a final step.
-  std::fstream tempFileStream;
-  {
-    char fileNameTemplate[] = "/tmp/compact_XXXXXX";
-    int fd = mkstemp(fileNameTemplate);
-    if (fd == -1) {
-      std::ostringstream msg;
-      msg << "failed to open temporary file with pattern " << fileNameTemplate;
-      error(msg.str());
-    }
-    tempFileStream.open(fileNameTemplate);
-    if (!tempFileStream) {
-      std::ostringstream msg;
-      msg << "failed to open existing temporary file: " << fileNameTemplate;
-      error(msg.str());
-    }
-    // Close the original file descriptor.
-    close(fd);
-    // Unlink the file.  Its contents will be safe until tempFileStream is
-    // closed.
-    unlink(fileNameTemplate);
-  }
-
-  // Write the version number
-  output << "1" << '\n';
-
-  SymbolSet symbolSet;
-  PhraseSet sourcePhraseSet;
-  PhraseSet targetPhraseSet;
-  AlignmentSetSet alignmentSetSet;
-
-  SymbolPhrase symbolPhrase;
-
-  size_t ruleCount = 0;
-  RuleTableParser end;
-  try {
-    for (RuleTableParser parser(input); parser != end; ++parser) {
-      const RuleTableParser::Entry &entry = *parser;
-      ++ruleCount;
-
-      // Report progress in the same format as extract-rules.
-      if (ruleCount % 100000 == 0) {
-        std::cerr << "." << std::flush;
-      }
-      if (ruleCount % 1000000 == 0) {
-        std::cerr << " " << ruleCount << std::endl;
-      }
-
-      // Encode the source LHS + RHS as a vector of symbol IDs and insert into
-      // sourcePhraseSet.
-      encodePhrase(entry.sourceLhs, entry.sourceRhs, symbolSet, symbolPhrase);
-      SymbolIDType sourceId = sourcePhraseSet.insert(symbolPhrase);
-
-      // Encode the target LHS + RHS as a vector of symbol IDs and insert into
-      // targetPhraseSet.
-      encodePhrase(entry.targetLhs, entry.targetRhs, symbolSet, symbolPhrase);
-      SymbolIDType targetId = targetPhraseSet.insert(symbolPhrase);
-
-      // Insert the alignments into alignmentSetSet.
-      AlignmentSetIDType alignmentSetId = alignmentSetSet.insert(
-          entry.alignments);
-
-      // Write this rule to the temporary file.
-      tempFileStream << sourceId << " " << targetId << " " << alignmentSetId;
-      for (std::vector<std::string>::const_iterator p = entry.scores.begin();
-           p != entry.scores.end(); ++p) {
-        tempFileStream << " " << *p;
-      }
-      tempFileStream << " :";
-      for (std::vector<std::string>::const_iterator p = entry.counts.begin();
-           p != entry.counts.end(); ++p) {
-        tempFileStream << " " << *p;
-      }
-      tempFileStream << '\n';
-    }
-  } catch (Exception &e) {
-    std::ostringstream msg;
-    msg << "error processing line " << ruleCount+1 << ": " << e.getMsg();
-    error(msg.str());
-  }
-
-  // Report the counts.
-
-  if (ruleCount % 1000000 != 0) {
-    std::cerr << std::endl;
-  }
-  std::cerr << "Rule count:          " << ruleCount << std::endl;
-  std::cerr << "Symbol count:        " << symbolSet.size() << std::endl;
-  std::cerr << "Source phrase count: " << sourcePhraseSet.size() << std::endl;
-  std::cerr << "Target phrase count: " << targetPhraseSet.size() << std::endl;
-  std::cerr << "Alignment set count: " << alignmentSetSet.size() << std::endl;
-
-  // Write the symbol vocabulary.
-
-  output << symbolSet.size() << '\n';
-  for (SymbolSet::const_iterator p = symbolSet.begin();
-       p != symbolSet.end(); ++p) {
-    const std::string &str = **p;
-    output << str << '\n';
-  }
-
-  // Write the source phrases.
-
-  output << sourcePhraseSet.size() << '\n';
-  for (PhraseSet::const_iterator p = sourcePhraseSet.begin();
-       p != sourcePhraseSet.end(); ++p) {
-    const SymbolPhrase &sourcePhrase = **p;
-    for (SymbolPhrase::const_iterator q = sourcePhrase.begin();
-         q != sourcePhrase.end(); ++q) {
-      if (q != sourcePhrase.begin()) {
-        output << " ";
-      }
-      output << *q;
-    }
-    output << '\n';
-  }
-
-  // Write the target phrases.
-
-  output << targetPhraseSet.size() << '\n';
-  for (PhraseSet::const_iterator p = targetPhraseSet.begin();
-       p != targetPhraseSet.end(); ++p) {
-    const SymbolPhrase &targetPhrase = **p;
-    for (SymbolPhrase::const_iterator q = targetPhrase.begin();
-         q != targetPhrase.end(); ++q) {
-      if (q != targetPhrase.begin()) {
-        output << " ";
-      }
-      output << *q;
-    }
-    output << '\n';
-  }
-
-  // Write the alignment sets.
-
-  output << alignmentSetSet.size() << '\n';
-  for (AlignmentSetSet::const_iterator p = alignmentSetSet.begin();
-       p != alignmentSetSet.end(); ++p) {
-    const AlignmentSet &alignmentSet = **p;
-    for (AlignmentSet::const_iterator q = alignmentSet.begin();
-          q != alignmentSet.end(); ++q) {
-      if (q != alignmentSet.begin()) {
-        output << " ";
-      }
-      output << q->first << "-" << q->second;
-    }
-    output << '\n';
-  }
-
-  // Write the rule count.
-  output << ruleCount << '\n';
-
-  // Copy the rules from the temporary file.
-  tempFileStream.seekg(0);
-  std::string line;
-  while (std::getline(tempFileStream, line)) {
-    output << line << '\n';
-  }
-
-  return 0;
-}
-
-void Compactify::processOptions(int argc, char *argv[],
-                                Options &options) const {
-  namespace po = boost::program_options;
-
-  std::ostringstream usageMsg;
-  usageMsg << "usage: " << getName() << " [OPTION]... [FILE]";
-
-  // Declare the command line options that are visible to the user.
-  std::string caption = usageMsg.str() + std::string("\n\nAllowed options");
-  po::options_description visible(caption);
-  visible.add_options()
-    ("help", "print help message and exit")
-    ("output,o", po::value<std::string>(),
-                 "write rule table to arg instead of standard output")
-  ;
-
-  // Declare the command line options that are hidden from the user
-  // (these are used as positional options).
-  po::options_description hidden("Hidden options");
-  hidden.add_options()
-    ("input", po::value<std::string>(), "input file")
-  ;
-
-  // Compose the full set of command-line options.
-  po::options_description cmdLineOptions;
-  cmdLineOptions.add(visible).add(hidden);
-
-  // Register the positional options.
-  po::positional_options_description p;
-  p.add("input", 1);
-
-  // Process the command-line.
-  po::variables_map vm;
-  try {
-    po::store(po::command_line_parser(argc, argv).
-              options(cmdLineOptions).positional(p).run(), vm);
-    po::notify(vm);
-  } catch (const std::exception &e) {
-    std::ostringstream msg;
-    msg << e.what() << "\n\n" << visible;
-    error(msg.str());
-    std::exit(1);
-  }
-
-  if (vm.count("help")) {
-    std::cout << visible << std::endl;
-    std::exit(0);
-  }
-
-  // Process positional options.
-
-  if (vm.count("input")) {
-    options.inputFile = vm["input"].as<std::string>();
-  }
-
-  // Process remaining options.
-
-  if (vm.count("output")) {
-    options.outputFile = vm["output"].as<std::string>();
-  }
-}
-
-void Compactify::encodePhrase(const std::string &lhs, const StringPhrase &rhs,
-                              SymbolSet &symbolSet, SymbolPhrase &vec) const {
-  vec.clear();
-  vec.reserve(rhs.size()+1);
-  SymbolIDType id = symbolSet.insert(lhs);
-  vec.push_back(id);
-  for (std::vector<std::string>::const_iterator p = rhs.begin();
-       p != rhs.end(); ++p) {
-    SymbolIDType id = symbolSet.insert(*p);
-    vec.push_back(id);
-  }
-}
-
-}  // namespace moses
diff --git a/scripts/training/compact-rule-table/Compactify.h b/scripts/training/compact-rule-table/Compactify.h
deleted file mode 100644
index ef5c1d9ec..000000000
--- a/scripts/training/compact-rule-table/Compactify.h
+++ /dev/null
@@ -1,43 +0,0 @@
-#pragma once
-#ifndef COMPACTIFY_H_
-#define COMPACTIFY_H_
-
-#include "NumberedSet.h"
-#include "Tool.h"
-
-#include <set>
-#include <vector>
-
-namespace moses {
-
-struct Options;
-
-// Tool for converting a rule table into a more compact format.
-class Compactify : public Tool {
- public:
-  Compactify() : Tool("compactify") {}
-  virtual int main(int, char *[]);
- private:
-  typedef unsigned int SymbolIDType;
-  typedef unsigned int PhraseIDType;
-  typedef unsigned int AlignmentSetIDType;
-  typedef std::vector<std::string> StringPhrase;
-  typedef std::vector<SymbolIDType> SymbolPhrase;
-  typedef std::pair<int, int> AlignmentPair;
-  typedef std::set<AlignmentPair> AlignmentSet;
-  typedef NumberedSet<std::string, SymbolIDType> SymbolSet;
-  typedef NumberedSet<SymbolPhrase, PhraseIDType> PhraseSet;
-  typedef NumberedSet<AlignmentSet, AlignmentSetIDType> AlignmentSetSet;
-
-  void processOptions(int, char *[], Options &) const;
-
-  // Given the string representations of a source or target LHS and RHS, encode
-  // the symbols using the given SymbolSet and create a SymbolPhrase object.
-  // The LHS index is the first element of the SymbolPhrase.
-  void encodePhrase(const std::string &, const StringPhrase &,
-                    SymbolSet &, SymbolPhrase &) const;
-};
-
-}  // namespace moses
-
-#endif
diff --git a/scripts/training/compact-rule-table/Compactify_Main.cpp b/scripts/training/compact-rule-table/Compactify_Main.cpp
deleted file mode 100644
index 5ae8833c1..000000000
--- a/scripts/training/compact-rule-table/Compactify_Main.cpp
+++ /dev/null
@@ -1,6 +0,0 @@
-#include "Compactify.h"
-
-int main(int argc, char *argv[]) {
-  moses::Compactify tool;
-  return tool.main(argc, argv);
-}
diff --git a/scripts/training/compact-rule-table/Exception.h b/scripts/training/compact-rule-table/Exception.h
deleted file mode 100644
index 3868fcec5..000000000
--- a/scripts/training/compact-rule-table/Exception.h
+++ /dev/null
@@ -1,22 +0,0 @@
-#pragma once
-#ifndef EXCEPTION_H_
-#define EXCEPTION_H_
-
-#include <string>
-
-namespace moses {
-
-class Exception {
- public:
-  Exception(const char *msg) : m_msg(msg) {}
-  Exception(const std::string &msg) : m_msg(msg) {}
-
-  const std::string &getMsg() const { return m_msg; }
-
- private:
-  std::string m_msg;
-};
-
-}  // namespace moses
-
-#endif
diff --git a/scripts/training/compact-rule-table/Jamfile b/scripts/training/compact-rule-table/Jamfile
deleted file mode 100644
index 09f45d454..000000000
--- a/scripts/training/compact-rule-table/Jamfile
+++ /dev/null
@@ -1,3 +0,0 @@
-exe compactify : [ glob *.cpp ] ../../..//boost_program_options ;
-
-install tools : compactify : <install-type>EXE ;
diff --git a/scripts/training/compact-rule-table/NumberedSet.h b/scripts/training/compact-rule-table/NumberedSet.h
deleted file mode 100644
index 72c01cb30..000000000
--- a/scripts/training/compact-rule-table/NumberedSet.h
+++ /dev/null
@@ -1,79 +0,0 @@
-#pragma once
-#ifndef NUMBEREDSET_H_
-#define NUMBEREDSET_H_
-
-#include "Exception.h"
-
-#include <boost/unordered_map.hpp>
-
-#include <limits>
-#include <sstream>
-#include <vector>
-
-namespace moses {
-
-// Stores a set of elements of type T, each of which is allocated an integral
-// ID of type IdType.  IDs are contiguous starting at 0.  Elements cannot be
-// removed.
-template<typename T, typename IdType=size_t>
-class NumberedSet {
- private:
-  typedef boost::unordered_map<T, IdType> ElementToIdMap;
-  typedef std::vector<const T *> IdToElementMap;
-
- public:
-  typedef typename IdToElementMap::const_iterator const_iterator;
-
-  NumberedSet() {}
-
-  const_iterator begin() const { return m_idToElement.begin(); }
-  const_iterator end() const { return m_idToElement.end(); }
-
-  // Static value
-  static IdType nullID() { return std::numeric_limits<IdType>::max(); }
-
-  bool empty() const { return m_idToElement.empty(); }
-  size_t size() const { return m_idToElement.size(); }
-
-  IdType lookup(const T &) const;
-  const T &lookup(IdType) const;
-
-  // Insert the given object and return its ID.
-  IdType insert(const T &);
-
- private:
-  ElementToIdMap m_elementToId;
-  IdToElementMap m_idToElement;
-};
-
-template<typename T, typename IdType>
-IdType NumberedSet<T, IdType>::lookup(const T &s) const {
-  typename ElementToIdMap::const_iterator p = m_elementToId.find(s);
-  return (p == m_elementToId.end()) ? nullID() : p->second;
-}
-
-template<typename T, typename IdType>
-const T &NumberedSet<T, IdType>::lookup(IdType id) const {
-  if (id < 0 || id >= m_idToElement.size()) {
-    std::ostringstream msg;
-    msg << "Value not found: " << id;
-    throw Exception(msg.str());
-  }
-  return *(m_idToElement[id]);
-}
-
-template<typename T, typename IdType>
-IdType NumberedSet<T, IdType>::insert(const T &x) {
-  std::pair<T, IdType> value(x, m_idToElement.size());
-  std::pair<typename ElementToIdMap::iterator, bool> result =
-      m_elementToId.insert(value);
-  if (result.second) {
-    // x is a new element.
-    m_idToElement.push_back(&result.first->first);
-  }
-  return result.first->second;
-}
-
-}  // namespace moses
-
-#endif
diff --git a/scripts/training/compact-rule-table/Options.h b/scripts/training/compact-rule-table/Options.h
deleted file mode 100644
index f3fdb9139..000000000
--- a/scripts/training/compact-rule-table/Options.h
+++ /dev/null
@@ -1,18 +0,0 @@
-#pragma once
-#ifndef OPTIONS_H_
-#define OPTIONS_H_
-
-#include <string>
-
-namespace moses {
-
-struct Options {
- public:
-  Options() {}
-  std::string inputFile;
-  std::string outputFile;
-};
-
-}  // namespace moses
-
-#endif
diff --git a/scripts/training/compact-rule-table/RuleTableParser.cpp b/scripts/training/compact-rule-table/RuleTableParser.cpp
deleted file mode 100644
index 6272079fd..000000000
--- a/scripts/training/compact-rule-table/RuleTableParser.cpp
+++ /dev/null
@@ -1,168 +0,0 @@
-#include "RuleTableParser.h"
-
-#include "Exception.h"
-
-#include <boost/algorithm/string.hpp>
-#include <boost/lexical_cast.hpp>
-
-#include <iostream>
-
-#include <istream>
-#include <string>
-
-namespace moses {
-
-RuleTableParser::RuleTableParser()
-  : m_input(0) {
-}
-
-RuleTableParser::RuleTableParser(std::istream &input)
-  : m_input(&input) {
-  ++(*this);
-}
-
-RuleTableParser & RuleTableParser::operator++() {
-  if (!m_input) {
-    return *this;
-  }
-  if (!std::getline(*m_input, m_line)) {
-    m_input = 0;
-    return *this;
-  }
-  parseLine(m_line);
-  return *this;
-}
-
-RuleTableParser RuleTableParser::operator++(int) {
-  RuleTableParser tmp(*this);
-  ++(*this);
-  return tmp;
-}
-
-void RuleTableParser::parseLine(const std::string &line) {
-  // Source symbols
-  size_t pos = line.find("|||");
-  if (pos == std::string::npos) {
-    throw Exception("missing first delimiter");
-  }
-  std::string text = line.substr(0, pos);
-  boost::trim(text);
-  m_value.sourceRhs.clear();
-  boost::split(m_value.sourceRhs, text, boost::algorithm::is_space(),
-               boost::algorithm::token_compress_on);
-  m_value.sourceLhs = m_value.sourceRhs.back();
-  m_value.sourceRhs.pop_back();
-  std::for_each(m_value.sourceRhs.begin(), m_value.sourceRhs.end(),
-                trimPairedSymbolFromRight);
-
-  // Target symbols
-  size_t begin = pos+3;
-  pos = line.find("|||", begin);
-  if (pos == std::string::npos) {
-    throw Exception("missing second delimiter");
-  }
-  text = line.substr(begin, pos-begin);
-  boost::trim(text);
-  m_value.targetRhs.clear();
-  boost::split(m_value.targetRhs, text, boost::algorithm::is_space(),
-               boost::algorithm::token_compress_on);
-  m_value.targetLhs = m_value.targetRhs.back();
-  m_value.targetRhs.pop_back();
-  std::for_each(m_value.targetRhs.begin(), m_value.targetRhs.end(),
-                trimPairedSymbolFromLeft);
-
-  // Scores
-  begin = pos+3;
-  pos = line.find("|||", begin);
-  if (pos == std::string::npos) {
-    throw Exception("missing third delimiter");
-  }
-  text = line.substr(begin, pos-begin);
-  boost::trim(text);
-  m_value.scores.clear();
-  boost::split(m_value.scores, text, boost::algorithm::is_space(),
-               boost::algorithm::token_compress_on);
-
-  // Alignments
-  begin = pos+3;
-  pos = line.find("|||", begin);
-  if (pos == std::string::npos) {
-    throw Exception("missing fourth delimiter");
-  }
-  text = line.substr(begin, pos-begin);
-  m_value.alignments.clear();
-  boost::trim(text);
-  // boost::split behaves differently between versions on empry strings
-  if (!text.empty()) {
-    tmpStringVec.clear();
-    boost::split(tmpStringVec, text, boost::algorithm::is_space(),
-                 boost::algorithm::token_compress_on);
-    for (std::vector<std::string>::const_iterator p = tmpStringVec.begin();
-         p != tmpStringVec.end(); ++p) {
-      assert(!p->empty());
-      std::vector<std::string> tmpVec;
-      tmpVec.reserve(2);
-      boost::split(tmpVec, *p, boost::algorithm::is_any_of("-"));
-      if (tmpVec.size() != 2) {
-        throw Exception("bad alignment pair");
-      }
-      std::pair<int, int> alignmentPair;
-      alignmentPair.first = boost::lexical_cast<int>(tmpVec[0]);
-      alignmentPair.second = boost::lexical_cast<int>(tmpVec[1]);
-      m_value.alignments.insert(alignmentPair);
-    }
-  }
-
-  // Counts + everything else (the 'tail')
-  begin = pos+3;
-  pos = line.find("|||", begin);
-  if (pos == std::string::npos) {
-    text = line.substr(begin);
-    m_value.tail.clear();
-  } else {
-    text = line.substr(begin, pos-begin);
-    m_value.tail = line.substr(pos+3);
-  }
-  boost::trim(text);
-  m_value.counts.clear();
-  boost::split(m_value.counts, text, boost::algorithm::is_space(),
-               boost::algorithm::token_compress_on);
-}
-
-void RuleTableParser::trimPairedSymbolFromLeft(std::string &s) {
-  size_t len = s.size();
-  if (len < 2 || s[0] != '[' || s[len-1] != ']') {
-    return;
-  }
-  size_t pos = s.find('[', 1);
-  if (pos == std::string::npos) {
-    std::ostringstream msg;
-    msg << "malformed non-terminal pair: " << s;
-    throw Exception(msg.str());
-  }
-  s.erase(0, pos);
-}
-
-void RuleTableParser::trimPairedSymbolFromRight(std::string &s) {
-  size_t len = s.size();
-  if (len < 2 || s[0] != '[' || s[len-1] != ']') {
-    return;
-  }
-  size_t pos = s.find('[', 1);
-  if (pos == std::string::npos) {
-    std::ostringstream msg;
-    msg << "malformed non-terminal pair: " << s;
-    throw Exception(msg.str());
-  }
-  s.resize(pos);
-}
-
-bool operator==(const RuleTableParser &lhs, const RuleTableParser &rhs) {
-  return lhs.m_input == rhs.m_input;
-}
-
-bool operator!=(const RuleTableParser &lhs, const RuleTableParser &rhs) {
-  return !(lhs == rhs);
-}
-
-}  // namespace moses
diff --git a/scripts/training/compact-rule-table/RuleTableParser.h b/scripts/training/compact-rule-table/RuleTableParser.h
deleted file mode 100644
index 5599e63de..000000000
--- a/scripts/training/compact-rule-table/RuleTableParser.h
+++ /dev/null
@@ -1,51 +0,0 @@
-#pragma once
-#ifndef RULETABLEPARSER_H_INCLUDED_
-#define RULETABLEPARSER_H_INCLUDED_
-
-#include <istream>
-#include <set>
-#include <string>
-#include <utility>
-#include <vector>
-
-namespace moses {
-
-class RuleTableParser {
- public:
-  struct Entry {
-    std::string sourceLhs;
-    std::vector<std::string> sourceRhs;
-    std::string targetLhs;
-    std::vector<std::string> targetRhs;
-    std::vector<std::string> scores;
-    std::set<std::pair<int, int> > alignments;
-    std::vector<std::string> counts;
-    std::string tail;
-  };
-
-  RuleTableParser();
-  RuleTableParser(std::istream &);
-
-  const Entry &operator*() const { return m_value; }
-  const Entry *operator->() const { return &m_value; }
-
-  RuleTableParser &operator++();
-  RuleTableParser operator++(int);
-
-  friend bool operator==(const RuleTableParser &, const RuleTableParser &);
-  friend bool operator!=(const RuleTableParser &, const RuleTableParser &);
-
- private:
-  Entry m_value;
-  std::istream *m_input;
-  std::string m_line;
-  std::vector<std::string> tmpStringVec;
-
-  void parseLine(const std::string &);
-  static void trimPairedSymbolFromLeft(std::string &);
-  static void trimPairedSymbolFromRight(std::string &);
-};
-
-}  // namespace moses
-
-#endif
diff --git a/scripts/training/compact-rule-table/Tool.h b/scripts/training/compact-rule-table/Tool.h
deleted file mode 100644
index 4a7e1e0e1..000000000
--- a/scripts/training/compact-rule-table/Tool.h
+++ /dev/null
@@ -1,34 +0,0 @@
-#pragma once
-#ifndef TOOL_H_
-#define TOOL_H_
-
-#include <cstdlib>
-#include <iostream>
-#include <string>
-
-namespace moses {
-
-class Tool {
- public:
-  Tool(const std::string &name) : m_name(name) {}
-
-  const std::string &getName() const { return m_name; }
-
-  virtual int main(int argc, char *argv[]) = 0;
-
-  void warn(const std::string &msg) const {
-    std::cerr << m_name << ": warning: " << msg << std::endl;
-  }
-
-  void error(const std::string &msg) const {
-    std::cerr << m_name << ": error: " << msg << std::endl;
-    std::exit(1);
-  }
-
- private:
-  std::string m_name;
-};
-
-}  // namespace moses
-
-#endif
diff --git a/scripts/training/phrase-extract/extract-ghkm/Jamfile b/scripts/training/phrase-extract/extract-ghkm/Jamfile
deleted file mode 100644
index 92adc2126..000000000
--- a/scripts/training/phrase-extract/extract-ghkm/Jamfile
+++ /dev/null
@@ -1 +0,0 @@
-exe extract-ghkm : [ glob *.cpp ] ..//filestreams ..//trees ../../../..//boost_iostreams ../../../..//boost_program_options ../../../..//z ;
diff --git a/scripts/training/phrase-extract/pcfg-extract/Jamfile b/scripts/training/phrase-extract/pcfg-extract/Jamfile
deleted file mode 100644
index be91d6d2f..000000000
--- a/scripts/training/phrase-extract/pcfg-extract/Jamfile
+++ /dev/null
@@ -1 +0,0 @@
-exe pcfg-extract : [ glob *.cc ] ..//pcfg-common ../../../..//boost_program_options ;
diff --git a/scripts/training/phrase-extract/pcfg-score/Jamfile b/scripts/training/phrase-extract/pcfg-score/Jamfile
deleted file mode 100644
index 7225381c0..000000000
--- a/scripts/training/phrase-extract/pcfg-score/Jamfile
+++ /dev/null
@@ -1 +0,0 @@
-exe pcfg-score : [ glob *.cc ] ..//pcfg-common ../../../..//boost_program_options ;
diff --git a/scripts/training/symal/Jamfile b/symal/Jamfile
index 3ab564790..3ab564790 100644
--- a/scripts/training/symal/Jamfile
+++ b/symal/Jamfile
diff --git a/scripts/training/symal/cmd.c b/symal/cmd.c
index 149fc7290..149fc7290 100644
--- a/scripts/training/symal/cmd.c
+++ b/symal/cmd.c
diff --git a/scripts/training/symal/cmd.h b/symal/cmd.h
index 01a00abc0..01a00abc0 100644
--- a/scripts/training/symal/cmd.h
+++ b/symal/cmd.h
diff --git a/scripts/training/symal/giza2bal.pl b/symal/giza2bal.pl
index 553ff2b3e..553ff2b3e 100755
--- a/scripts/training/symal/giza2bal.pl
+++ b/symal/giza2bal.pl
diff --git a/scripts/training/symal/symal.cpp b/symal/symal.cpp
index da386d973..da386d973 100644
--- a/scripts/training/symal/symal.cpp
+++ b/symal/symal.cpp
diff --git a/scripts/training/symal/symal.vcproj b/symal/symal.vcproj
index 6eac62f4a..6eac62f4a 100644
--- a/scripts/training/symal/symal.vcproj
+++ b/symal/symal.vcproj