diff --git a/mira/Decoder.cpp b/mira/Decoder.cpp
index 3fc90b95e..67a1d5cbf 100644
--- a/mira/Decoder.cpp
+++ b/mira/Decoder.cpp
@@ -18,15 +18,15 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 ***********************************************************************/
 
 #include "Decoder.h"
-#include "Manager.h"
-#include "ChartManager.h"
-#include "Sentence.h"
-#include "InputType.h"
-#include "TranslationSystem.h"
-#include "Phrase.h"
-#include "TrellisPathList.h"
-#include "ChartTrellisPathList.h"
-#include "ChartTrellisPath.h"
+#include "moses/Manager.h"
+#include "moses/ChartManager.h"
+#include "moses/Sentence.h"
+#include "moses/InputType.h"
+#include "moses/TranslationSystem.h"
+#include "moses/Phrase.h"
+#include "moses/TrellisPathList.h"
+#include "moses/ChartTrellisPathList.h"
+#include "moses/ChartTrellisPath.h"
 
 using namespace std;
 using namespace Moses;
diff --git a/mira/Decoder.h b/mira/Decoder.h
index 48b261fac..cc037a4c7 100644
--- a/mira/Decoder.h
+++ b/mira/Decoder.h
@@ -24,13 +24,13 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 #include <sstream>
 
 
-#include "BleuScoreFeature.h"
-#include "ChartTrellisPathList.h"
-#include "Hypothesis.h"
-#include "Parameter.h"
-#include "SearchNormal.h"
-#include "Sentence.h"
-#include "StaticData.h"
+#include "moses/BleuScoreFeature.h"
+#include "moses/ChartTrellisPathList.h"
+#include "moses/Hypothesis.h"
+#include "moses/Parameter.h"
+#include "moses/SearchNormal.h"
+#include "moses/Sentence.h"
+#include "moses/StaticData.h"
 
 //
 // Wrapper functions and objects for the decoder.
diff --git a/mira/Hildreth.h b/mira/Hildreth.h
index 699115242..da52995aa 100644
--- a/mira/Hildreth.h
+++ b/mira/Hildreth.h
@@ -1,5 +1,5 @@
-#include "FeatureVector.h"
-#include "ScoreComponentCollection.h"
+#include "moses/FeatureVector.h"
+#include "moses/ScoreComponentCollection.h"
 
 namespace Mira {
 
diff --git a/mira/Main.cpp b/mira/Main.cpp
index c984bce1c..d1f76f181 100644
--- a/mira/Main.cpp
+++ b/mira/Main.cpp
@@ -33,20 +33,20 @@ namespace mpi = boost::mpi;
 #endif
 
 #include "Main.h"
-#include "FeatureVector.h"
-#include "StaticData.h"
-#include "ChartTrellisPathList.h"
-#include "ChartTrellisPath.h"
-#include "ScoreComponentCollection.h"
 #include "Optimiser.h"
 #include "Hildreth.h"
-#include "ThreadPool.h"
-#include "DummyScoreProducers.h"
-#include "LexicalReordering.h"
-#include "BleuScorer.h"
 #include "HypothesisQueue.h"
-#include "WordTranslationFeature.h"
-#include "PhrasePairFeature.h"
+#include "moses/FeatureVector.h"
+#include "moses/StaticData.h"
+#include "moses/ChartTrellisPathList.h"
+#include "moses/ChartTrellisPath.h"
+#include "moses/ScoreComponentCollection.h"
+#include "moses/ThreadPool.h"
+#include "moses/DummyScoreProducers.h"
+#include "moses/LexicalReordering.h"
+#include "moses/WordTranslationFeature.h"
+#include "moses/PhrasePairFeature.h"
+#include "mert/BleuScorer.h"
 
 using namespace Mira;
 using namespace std;
diff --git a/mira/Main.h b/mira/Main.h
index 23db36c36..60b239fd6 100644
--- a/mira/Main.h
+++ b/mira/Main.h
@@ -21,9 +21,9 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 
 #include <vector>
 
-#include "ScoreComponentCollection.h"
-#include "Word.h"
-#include "ScoreProducer.h"
+#include "moses/ScoreComponentCollection.h"
+#include "moses/Word.h"
+#include "moses/ScoreProducer.h"
 #include "Decoder.h"
 
 typedef std::map<const Moses::ScoreProducer*, std::vector< float > > ProducerWeightMap;
diff --git a/mira/MiraOptimiser.cpp b/mira/MiraOptimiser.cpp
index d77cef759..4cc7f3fc3 100644
--- a/mira/MiraOptimiser.cpp
+++ b/mira/MiraOptimiser.cpp
@@ -1,6 +1,6 @@
 #include "Optimiser.h"
 #include "Hildreth.h"
-#include "StaticData.h"
+#include "moses/StaticData.h"
 
 using namespace Moses;
 using namespace std;
diff --git a/mira/Optimiser.h b/mira/Optimiser.h
index 213ee054e..a610268f3 100644
--- a/mira/Optimiser.h
+++ b/mira/Optimiser.h
@@ -21,7 +21,7 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 
 #include <vector>
 
-#include "ScoreComponentCollection.h"
+#include "moses/ScoreComponentCollection.h"
 
 
 namespace Mira {
diff --git a/misc/GenerateTuples.cpp b/misc/GenerateTuples.cpp
index 58e9697fd..db483a948 100644
--- a/misc/GenerateTuples.cpp
+++ b/misc/GenerateTuples.cpp
@@ -8,11 +8,11 @@
 
 
 #include <numeric>
-#include "Word.h"
-#include "Phrase.h"
-#include "ConfusionNet.h"
-#include "WordsRange.h"
-#include "PhraseDictionaryTree.h"
+#include "moses/Word.h"
+#include "moses/Phrase.h"
+#include "moses/ConfusionNet.h"
+#include "moses/WordsRange.h"
+#include "moses/PhraseDictionaryTree.h"
 
 using namespace Moses;
 
diff --git a/misc/GenerateTuples.h b/misc/GenerateTuples.h
index 728f28823..b1aa2658d 100644
--- a/misc/GenerateTuples.h
+++ b/misc/GenerateTuples.h
@@ -1,7 +1,7 @@
 // $Id$
 #ifndef GENERATETUPLES_H_
 #define GENERATETUPLES_H_
-#include "PhraseDictionaryTree.h"
+#include "moses/PhraseDictionaryTree.h"
 
 class ConfusionNet;
 
diff --git a/misc/processLexicalTable.cpp b/misc/processLexicalTable.cpp
index a81c65965..be4928234 100644
--- a/misc/processLexicalTable.cpp
+++ b/misc/processLexicalTable.cpp
@@ -1,9 +1,9 @@
 #include <iostream>
 #include <string>
 
-#include "Timer.h"
-#include "InputFileStream.h"
-#include "LexicalReorderingTable.h"
+#include "moses/Timer.h"
+#include "moses/InputFileStream.h"
+#include "moses/LexicalReorderingTable.h"
 
 using namespace Moses;
 
diff --git a/misc/processLexicalTableMin.cpp b/misc/processLexicalTableMin.cpp
index 20183a3b6..fc9f582f7 100644
--- a/misc/processLexicalTableMin.cpp
+++ b/misc/processLexicalTableMin.cpp
@@ -5,7 +5,7 @@
 #include <boost/thread/thread.hpp>
 #endif
 
-#include "CompactPT/LexicalReorderingTableCreator.h"
+#include "moses/CompactPT/LexicalReorderingTableCreator.h"
 
 using namespace Moses;
 
diff --git a/misc/processPhraseTable.cpp b/misc/processPhraseTable.cpp
index 7eca79349..33b9c6200 100644
--- a/misc/processPhraseTable.cpp
+++ b/misc/processPhraseTable.cpp
@@ -6,13 +6,13 @@
 #include <iterator>
 #include <functional>
 #include <sys/stat.h>
-#include "TypeDef.h"
-#include "PhraseDictionaryTree.h"
-#include "ConfusionNet.h"
-#include "FactorCollection.h"
-#include "Phrase.h"
-#include "InputFileStream.h"
-#include "Timer.h"
+#include "moses/TypeDef.h"
+#include "moses/PhraseDictionaryTree.h"
+#include "moses/ConfusionNet.h"
+#include "moses/FactorCollection.h"
+#include "moses/Phrase.h"
+#include "moses/InputFileStream.h"
+#include "moses/Timer.h"
 
 using namespace std;
 using namespace Moses;
diff --git a/misc/processPhraseTableMin.cpp b/misc/processPhraseTableMin.cpp
index 084562562..2ec5db929 100644
--- a/misc/processPhraseTableMin.cpp
+++ b/misc/processPhraseTableMin.cpp
@@ -4,8 +4,8 @@
 #include <boost/thread/thread.hpp>
 #endif 
 
-#include "TypeDef.h"
-#include "CompactPT/PhraseTableCreator.h"
+#include "moses/TypeDef.h"
+#include "moses/CompactPT/PhraseTableCreator.h"
 
 using namespace Moses;
 
diff --git a/misc/queryLexicalTable.cpp b/misc/queryLexicalTable.cpp
index 45eb68867..18cd89fa1 100644
--- a/misc/queryLexicalTable.cpp
+++ b/misc/queryLexicalTable.cpp
@@ -1,11 +1,11 @@
 #include <iostream>
 #include <string>
 
-#include "Phrase.h"
-#include "FactorCollection.h"
-#include "Timer.h"
-#include "InputFileStream.h"
-#include "LexicalReorderingTable.h"
+#include "moses/Phrase.h"
+#include "moses/FactorCollection.h"
+#include "moses/Timer.h"
+#include "moses/InputFileStream.h"
+#include "moses/LexicalReorderingTable.h"
 
 using namespace Moses;
 
diff --git a/misc/queryPhraseTable.cpp b/misc/queryPhraseTable.cpp
index 02e1c29a1..d647cce66 100644
--- a/misc/queryPhraseTable.cpp
+++ b/misc/queryPhraseTable.cpp
@@ -6,8 +6,8 @@
 #include <string>
 #include <vector>
 
-#include "PhraseDictionaryTree.h"
-#include "Util.h"
+#include "moses/PhraseDictionaryTree.h"
+#include "moses/Util.h"
 
 void usage();
 
diff --git a/misc/queryPhraseTableMin.cpp b/misc/queryPhraseTableMin.cpp
index 8958017ea..6743774dd 100644
--- a/misc/queryPhraseTableMin.cpp
+++ b/misc/queryPhraseTableMin.cpp
@@ -6,9 +6,9 @@
 #include <string>
 #include <vector>
 
-#include "CompactPT/PhraseDictionaryCompact.h"
-#include "Util.h"
-#include "Phrase.h"
+#include "moses/CompactPT/PhraseDictionaryCompact.h"
+#include "moses/Util.h"
+#include "moses/Phrase.h"
 
 void usage();
 
diff --git a/moses/LM/LDHT.cpp b/moses/LM/LDHT.cpp
index 6da941b5e..bb4e0640a 100644
--- a/moses/LM/LDHT.cpp
+++ b/moses/LM/LDHT.cpp
@@ -4,10 +4,10 @@
 
 #include "LM/Base.h"
 #include "LM/LDHT.h"
-#include "../FFState.h"
-#include "../TypeDef.h"
-#include "../Hypothesis.h"
-#include "../StaticData.h"
+#include "moses/FFState.h"
+#include "moses/TypeDef.h"
+#include "moses/Hypothesis.h"
+#include "moses/StaticData.h"
 
 #include <LDHT/Client.h>
 #include <LDHT/ClientLocal.h>
diff --git a/moses/LM/LDHT.h b/moses/LM/LDHT.h
index dc60d0725..a8489c0e3 100644
--- a/moses/LM/LDHT.h
+++ b/moses/LM/LDHT.h
@@ -5,7 +5,7 @@
 #ifndef moses_LanguageModelLDHT_h
 #define moses_LanguageModelLDHT_h
 
-#include "../TypeDef.h"
+#include "moses/TypeDef.h"
 
 namespace Moses {
 
diff --git a/moses/LM/ParallelBackoff.cpp b/moses/LM/ParallelBackoff.cpp
index ec2fb2f78..ee8279aef 100644
--- a/moses/LM/ParallelBackoff.cpp
+++ b/moses/LM/ParallelBackoff.cpp
@@ -19,21 +19,21 @@ License along with this library; if not, write to the Free Software
 Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 ***********************************************************************/
 
-#include "LM/ParallelBackoff.h"
+#include "ParallelBackoff.h"
 
 #include <vector>
 #include <string>
 #include <sstream>
 #include <fstream>
 
-#include "LM/MultiFactor.h"
-#include "Word.h"
-#include "Factor.h"
-#include "FactorTypeSet.h"
-#include "FactorCollection.h"
-#include "Phrase.h"
-#include "TypeDef.h"
-#include "Util.h"
+#include "MultiFactor.h"
+#include "moses/Word.h"
+#include "moses/Factor.h"
+#include "moses/FactorTypeSet.h"
+#include "moses/FactorCollection.h"
+#include "moses/Phrase.h"
+#include "moses/TypeDef.h"
+#include "moses/Util.h"
 
 #include "FNgramSpecs.h"
 #include "FNgramStats.h"
diff --git a/moses/LM/Rand.cpp b/moses/LM/Rand.cpp
index 93411b8d3..4f0718b68 100644
--- a/moses/LM/Rand.cpp
+++ b/moses/LM/Rand.cpp
@@ -17,23 +17,22 @@ License along with this library; if not, write to the Free Software
 Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 ***********************************************************************/
 
-#include "util/check.hh"
 #include <limits>
 #include <iostream>
 #include <fstream>
 #include <string>
 #include <vector>
-#include "Factor.h"
-#include "Util.h"
-#include "LM/SingleFactor.h"
+
+#include "SingleFactor.h"
 #include "RandLM.h"
-
-
-#include "LM/Rand.h"
-#include "FactorCollection.h"
-#include "Phrase.h"
-#include "InputFileStream.h"
-#include "StaticData.h"
+#include "Rand.h"
+#include "moses/Factor.h"
+#include "moses/Util.h"
+#include "moses/FactorCollection.h"
+#include "moses/Phrase.h"
+#include "moses/InputFileStream.h"
+#include "moses/StaticData.h"
+#include "util/check.hh"
 
 
 namespace Moses