resolved merge conflicts

17 files changed, 44 insertions, 169 deletions

diff --git a/Jamroot b/Jamroot
index 98bca2c47..94c60793f 100644
--- a/Jamroot
+++ b/Jamroot
@@ -114,9 +114,9 @@ project : requirements
   ;
 
 #Add directories here if you want their incidental targets too (i.e. tests).
-build-projects lm util phrase-extract search moses mert moses-cmd moses-chart-cmd/src mira scripts regression-testing  ;
+build-projects lm util phrase-extract search moses mert moses-cmd moses-chart-cmd mira scripts regression-testing  ;
 
-alias programs : lm//programs moses-chart-cmd/src//moses_chart moses-cmd//programs OnDiskPt//CreateOnDiskPt OnDiskPt//queryOnDiskPt mert//programs misc//programs symal phrase-extract phrase-extract//lexical-reordering phrase-extract//extract-ghkm phrase-extract//pcfg-extract phrase-extract//pcfg-score biconcor mira//mira contrib/server//mosesserver  ;
+alias programs : lm//programs moses-chart-cmd//moses_chart moses-cmd//programs OnDiskPt//CreateOnDiskPt OnDiskPt//queryOnDiskPt mert//programs misc//programs symal phrase-extract phrase-extract//lexical-reordering phrase-extract//extract-ghkm phrase-extract//pcfg-extract phrase-extract//pcfg-score biconcor mira//mira contrib/server//mosesserver  ;
 
 install-bin-libs programs ;
 install-headers headers-base : [ path.glob-tree biconcor contrib lm mert misc moses-chart-cmd moses-cmd OnDiskPt phrase-extract symal util : *.hh *.h ] : . ;
diff --git a/contrib/other-builds/moses-chart-cmd/.project b/contrib/other-builds/moses-chart-cmd/.project
index 6b7f36ccd..350d0a71e 100644
--- a/contrib/other-builds/moses-chart-cmd/.project
+++ b/contrib/other-builds/moses-chart-cmd/.project
@@ -89,112 +89,47 @@
 		<link>
 			<name>IOWrapper.cpp</name>
 			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-chart-cmd/src/IOWrapper.cpp</locationURI>
+			<locationURI>PARENT-3-PROJECT_LOC/moses-chart-cmd/IOWrapper.cpp</locationURI>
 		</link>
 		<link>
 			<name>IOWrapper.h</name>
 			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-chart-cmd/src/IOWrapper.h</locationURI>
+			<locationURI>PARENT-3-PROJECT_LOC/moses-chart-cmd/IOWrapper.h</locationURI>
 		</link>
 		<link>
 			<name>Jamfile</name>
 			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-chart-cmd/src/Jamfile</locationURI>
+			<locationURI>PARENT-3-PROJECT_LOC/moses-chart-cmd/Jamfile</locationURI>
 		</link>
 		<link>
 			<name>Main.cpp</name>
 			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-chart-cmd/src/Main.cpp</locationURI>
+			<locationURI>PARENT-3-PROJECT_LOC/moses-chart-cmd/Main.cpp</locationURI>
 		</link>
 		<link>
 			<name>Main.h</name>
 			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-chart-cmd/src/Main.h</locationURI>
+			<locationURI>PARENT-3-PROJECT_LOC/moses-chart-cmd/Main.h</locationURI>
 		</link>
 		<link>
 			<name>TranslationAnalysis.cpp</name>
 			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-chart-cmd/src/TranslationAnalysis.cpp</locationURI>
+			<locationURI>PARENT-3-PROJECT_LOC/moses-chart-cmd/TranslationAnalysis.cpp</locationURI>
 		</link>
 		<link>
 			<name>TranslationAnalysis.h</name>
 			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-chart-cmd/src/TranslationAnalysis.h</locationURI>
-		</link>
-		<link>
-			<name>bin</name>
-			<type>2</type>
-			<locationURI>virtual:/virtual</locationURI>
+			<locationURI>PARENT-3-PROJECT_LOC/moses-chart-cmd/TranslationAnalysis.h</locationURI>
 		</link>
 		<link>
 			<name>mbr.cpp</name>
 			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-chart-cmd/src/mbr.cpp</locationURI>
+			<locationURI>PARENT-3-PROJECT_LOC/moses-chart-cmd/mbr.cpp</locationURI>
 		</link>
 		<link>
 			<name>mbr.h</name>
 			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-chart-cmd/src/mbr.h</locationURI>
-		</link>
-		<link>
-			<name>moses_chart</name>
-			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-chart-cmd/src/moses_chart</locationURI>
-		</link>
-		<link>
-			<name>bin/gcc-4.6</name>
-			<type>2</type>
-			<locationURI>virtual:/virtual</locationURI>
-		</link>
-		<link>
-			<name>bin/gcc-4.6/release</name>
-			<type>2</type>
-			<locationURI>virtual:/virtual</locationURI>
-		</link>
-		<link>
-			<name>bin/gcc-4.6/release/debug-symbols-on</name>
-			<type>2</type>
-			<locationURI>virtual:/virtual</locationURI>
-		</link>
-		<link>
-			<name>bin/gcc-4.6/release/debug-symbols-on/link-static</name>
-			<type>2</type>
-			<locationURI>virtual:/virtual</locationURI>
-		</link>
-		<link>
-			<name>bin/gcc-4.6/release/debug-symbols-on/link-static/threading-multi</name>
-			<type>2</type>
-			<locationURI>virtual:/virtual</locationURI>
-		</link>
-		<link>
-			<name>bin/gcc-4.6/release/debug-symbols-on/link-static/threading-multi/IOWrapper.o</name>
-			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-chart-cmd/src/bin/gcc-4.6/release/debug-symbols-on/link-static/threading-multi/IOWrapper.o</locationURI>
-		</link>
-		<link>
-			<name>bin/gcc-4.6/release/debug-symbols-on/link-static/threading-multi/Main.o</name>
-			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-chart-cmd/src/bin/gcc-4.6/release/debug-symbols-on/link-static/threading-multi/Main.o</locationURI>
-		</link>
-		<link>
-			<name>bin/gcc-4.6/release/debug-symbols-on/link-static/threading-multi/PhraseDictionary.o</name>
-			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-chart-cmd/src/bin/gcc-4.6/release/debug-symbols-on/link-static/threading-multi/PhraseDictionary.o</locationURI>
-		</link>
-		<link>
-			<name>bin/gcc-4.6/release/debug-symbols-on/link-static/threading-multi/TranslationAnalysis.o</name>
-			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-chart-cmd/src/bin/gcc-4.6/release/debug-symbols-on/link-static/threading-multi/TranslationAnalysis.o</locationURI>
-		</link>
-		<link>
-			<name>bin/gcc-4.6/release/debug-symbols-on/link-static/threading-multi/mbr.o</name>
-			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-chart-cmd/src/bin/gcc-4.6/release/debug-symbols-on/link-static/threading-multi/mbr.o</locationURI>
-		</link>
-		<link>
-			<name>bin/gcc-4.6/release/debug-symbols-on/link-static/threading-multi/moses_chart</name>
-			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-chart-cmd/src/bin/gcc-4.6/release/debug-symbols-on/link-static/threading-multi/moses_chart</locationURI>
+			<locationURI>PARENT-3-PROJECT_LOC/moses-chart-cmd/mbr.h</locationURI>
 		</link>
 	</linkedResources>
 </projectDescription>
diff --git a/contrib/other-builds/moses-cmd/.cproject b/contrib/other-builds/moses-cmd/.cproject
index 2c759e32b..bc01c4f37 100644
--- a/contrib/other-builds/moses-cmd/.cproject
+++ b/contrib/other-builds/moses-cmd/.cproject
@@ -83,6 +83,12 @@
 							</tool>
 						</toolChain>
 					</folderInfo>
+					<fileInfo id="cdt.managedbuild.config.gnu.exe.debug.461114338.1207454186" name="LatticeMBRGrid.cpp" rcbsApplicability="disable" resourcePath="LatticeMBRGrid.cpp" toolsToInvoke="cdt.managedbuild.tool.gnu.cpp.compiler.exe.debug.626095182.1072381674">
+						<tool id="cdt.managedbuild.tool.gnu.cpp.compiler.exe.debug.626095182.1072381674" name="GCC C++ Compiler" superClass="cdt.managedbuild.tool.gnu.cpp.compiler.exe.debug.626095182"/>
+					</fileInfo>
+					<sourceEntries>
+						<entry excluding="LatticeMBRGrid.cpp" flags="VALUE_WORKSPACE_PATH|RESOLVED" kind="sourcePath" name=""/>
+					</sourceEntries>
 				</configuration>
 			</storageModule>
 			<storageModule moduleId="org.eclipse.cdt.core.externalSettings"/>
diff --git a/contrib/other-builds/moses-cmd/.project b/contrib/other-builds/moses-cmd/.project
index 2207c4ca2..2bed79b3f 100644
--- a/contrib/other-builds/moses-cmd/.project
+++ b/contrib/other-builds/moses-cmd/.project
@@ -89,127 +89,62 @@
 		<link>
 			<name>IOWrapper.cpp</name>
 			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-cmd/src/IOWrapper.cpp</locationURI>
+			<locationURI>PARENT-3-PROJECT_LOC/moses-cmd/IOWrapper.cpp</locationURI>
 		</link>
 		<link>
 			<name>IOWrapper.h</name>
 			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-cmd/src/IOWrapper.h</locationURI>
+			<locationURI>PARENT-3-PROJECT_LOC/moses-cmd/IOWrapper.h</locationURI>
+		</link>
+		<link>
+			<name>Jamfile</name>
+			<type>1</type>
+			<locationURI>PARENT-3-PROJECT_LOC/moses-cmd/Jamfile</locationURI>
 		</link>
 		<link>
 			<name>LatticeMBR.cpp</name>
 			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-cmd/src/LatticeMBR.cpp</locationURI>
+			<locationURI>PARENT-3-PROJECT_LOC/moses-cmd/LatticeMBR.cpp</locationURI>
 		</link>
 		<link>
 			<name>LatticeMBR.h</name>
 			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-cmd/src/LatticeMBR.h</locationURI>
+			<locationURI>PARENT-3-PROJECT_LOC/moses-cmd/LatticeMBR.h</locationURI>
+		</link>
+		<link>
+			<name>LatticeMBRGrid.cpp</name>
+			<type>1</type>
+			<locationURI>PARENT-3-PROJECT_LOC/moses-cmd/LatticeMBRGrid.cpp</locationURI>
 		</link>
 		<link>
 			<name>Main.cpp</name>
 			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-cmd/src/Main.cpp</locationURI>
+			<locationURI>PARENT-3-PROJECT_LOC/moses-cmd/Main.cpp</locationURI>
 		</link>
 		<link>
 			<name>Main.h</name>
 			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-cmd/src/Main.h</locationURI>
+			<locationURI>PARENT-3-PROJECT_LOC/moses-cmd/Main.h</locationURI>
 		</link>
 		<link>
 			<name>TranslationAnalysis.cpp</name>
 			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-cmd/src/TranslationAnalysis.cpp</locationURI>
+			<locationURI>PARENT-3-PROJECT_LOC/moses-cmd/TranslationAnalysis.cpp</locationURI>
 		</link>
 		<link>
 			<name>TranslationAnalysis.h</name>
 			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-cmd/src/TranslationAnalysis.h</locationURI>
-		</link>
-		<link>
-			<name>bin</name>
-			<type>2</type>
-			<locationURI>virtual:/virtual</locationURI>
+			<locationURI>PARENT-3-PROJECT_LOC/moses-cmd/TranslationAnalysis.h</locationURI>
 		</link>
 		<link>
 			<name>mbr.cpp</name>
 			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-cmd/src/mbr.cpp</locationURI>
+			<locationURI>PARENT-3-PROJECT_LOC/moses-cmd/mbr.cpp</locationURI>
 		</link>
 		<link>
 			<name>mbr.h</name>
 			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-cmd/src/mbr.h</locationURI>
-		</link>
-		<link>
-			<name>bin/gcc-4.6</name>
-			<type>2</type>
-			<locationURI>virtual:/virtual</locationURI>
-		</link>
-		<link>
-			<name>bin/gcc-4.6/release</name>
-			<type>2</type>
-			<locationURI>virtual:/virtual</locationURI>
-		</link>
-		<link>
-			<name>bin/gcc-4.6/release/debug-symbols-on</name>
-			<type>2</type>
-			<locationURI>virtual:/virtual</locationURI>
-		</link>
-		<link>
-			<name>bin/gcc-4.6/release/debug-symbols-on/link-static</name>
-			<type>2</type>
-			<locationURI>virtual:/virtual</locationURI>
-		</link>
-		<link>
-			<name>bin/gcc-4.6/release/debug-symbols-on/link-static/threading-multi</name>
-			<type>2</type>
-			<locationURI>virtual:/virtual</locationURI>
-		</link>
-		<link>
-			<name>bin/gcc-4.6/release/debug-symbols-on/link-static/threading-multi/IOWrapper.o</name>
-			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-cmd/src/bin/gcc-4.6/release/debug-symbols-on/link-static/threading-multi/IOWrapper.o</locationURI>
-		</link>
-		<link>
-			<name>bin/gcc-4.6/release/debug-symbols-on/link-static/threading-multi/LatticeMBR.o</name>
-			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-cmd/src/bin/gcc-4.6/release/debug-symbols-on/link-static/threading-multi/LatticeMBR.o</locationURI>
-		</link>
-		<link>
-			<name>bin/gcc-4.6/release/debug-symbols-on/link-static/threading-multi/LatticeMBRGrid.o</name>
-			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-cmd/src/bin/gcc-4.6/release/debug-symbols-on/link-static/threading-multi/LatticeMBRGrid.o</locationURI>
-		</link>
-		<link>
-			<name>bin/gcc-4.6/release/debug-symbols-on/link-static/threading-multi/Main.o</name>
-			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-cmd/src/bin/gcc-4.6/release/debug-symbols-on/link-static/threading-multi/Main.o</locationURI>
-		</link>
-		<link>
-			<name>bin/gcc-4.6/release/debug-symbols-on/link-static/threading-multi/PhraseDictionary.o</name>
-			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-cmd/src/bin/gcc-4.6/release/debug-symbols-on/link-static/threading-multi/PhraseDictionary.o</locationURI>
-		</link>
-		<link>
-			<name>bin/gcc-4.6/release/debug-symbols-on/link-static/threading-multi/TranslationAnalysis.o</name>
-			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-cmd/src/bin/gcc-4.6/release/debug-symbols-on/link-static/threading-multi/TranslationAnalysis.o</locationURI>
-		</link>
-		<link>
-			<name>bin/gcc-4.6/release/debug-symbols-on/link-static/threading-multi/lmbrgrid</name>
-			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-cmd/src/bin/gcc-4.6/release/debug-symbols-on/link-static/threading-multi/lmbrgrid</locationURI>
-		</link>
-		<link>
-			<name>bin/gcc-4.6/release/debug-symbols-on/link-static/threading-multi/mbr.o</name>
-			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-cmd/src/bin/gcc-4.6/release/debug-symbols-on/link-static/threading-multi/mbr.o</locationURI>
-		</link>
-		<link>
-			<name>bin/gcc-4.6/release/debug-symbols-on/link-static/threading-multi/moses</name>
-			<type>1</type>
-			<locationURI>PARENT-3-PROJECT_LOC/moses-cmd/src/bin/gcc-4.6/release/debug-symbols-on/link-static/threading-multi/moses</locationURI>
+			<locationURI>PARENT-3-PROJECT_LOC/moses-cmd/mbr.h</locationURI>
 		</link>
 	</linkedResources>
 </projectDescription>
diff --git a/moses-chart-cmd/src/IOWrapper.cpp b/moses-chart-cmd/IOWrapper.cpp
index f8b12dc63..f8b12dc63 100644
--- a/moses-chart-cmd/src/IOWrapper.cpp
+++ b/moses-chart-cmd/IOWrapper.cpp
diff --git a/moses-chart-cmd/src/IOWrapper.h b/moses-chart-cmd/IOWrapper.h
index 6f1f7e046..6f1f7e046 100644
--- a/moses-chart-cmd/src/IOWrapper.h
+++ b/moses-chart-cmd/IOWrapper.h
diff --git a/moses-chart-cmd/src/Jamfile b/moses-chart-cmd/Jamfile
index d9f6042df..bdcacefec 100644
--- a/moses-chart-cmd/src/Jamfile
+++ b/moses-chart-cmd/Jamfile
@@ -1,2 +1,2 @@
-exe moses_chart : Main.cpp mbr.cpp IOWrapper.cpp TranslationAnalysis.cpp ../../moses//moses ;
+exe moses_chart : Main.cpp mbr.cpp IOWrapper.cpp TranslationAnalysis.cpp ../moses//moses ;
 
diff --git a/moses-chart-cmd/src/Main.cpp b/moses-chart-cmd/Main.cpp
index 08a89fd47..08a89fd47 100644
--- a/moses-chart-cmd/src/Main.cpp
+++ b/moses-chart-cmd/Main.cpp
diff --git a/moses-chart-cmd/src/Main.h b/moses-chart-cmd/Main.h
index 4f2765695..4f2765695 100644
--- a/moses-chart-cmd/src/Main.h
+++ b/moses-chart-cmd/Main.h
diff --git a/moses-chart-cmd/src/TranslationAnalysis.cpp b/moses-chart-cmd/TranslationAnalysis.cpp
index df8a9be5c..df8a9be5c 100644
--- a/moses-chart-cmd/src/TranslationAnalysis.cpp
+++ b/moses-chart-cmd/TranslationAnalysis.cpp
diff --git a/moses-chart-cmd/src/TranslationAnalysis.h b/moses-chart-cmd/TranslationAnalysis.h
index 7c8f1d545..7c8f1d545 100644
--- a/moses-chart-cmd/src/TranslationAnalysis.h
+++ b/moses-chart-cmd/TranslationAnalysis.h
diff --git a/moses-chart-cmd/src/mbr.cpp b/moses-chart-cmd/mbr.cpp
index 63130b276..63130b276 100644
--- a/moses-chart-cmd/src/mbr.cpp
+++ b/moses-chart-cmd/mbr.cpp
diff --git a/moses-chart-cmd/src/mbr.h b/moses-chart-cmd/mbr.h
index cd40a13b1..cd40a13b1 100644
--- a/moses-chart-cmd/src/mbr.h
+++ b/moses-chart-cmd/mbr.h
diff --git a/moses-cmd/Jamfile b/moses-cmd/Jamfile
index 93bd81dec..bc00cfaae 100644
--- a/moses-cmd/Jamfile
+++ b/moses-cmd/Jamfile
@@ -1,6 +1,6 @@
-alias deps : ../moses//moses ;
+alias deps : IOWrapper.cpp mbr.cpp LatticeMBR.cpp TranslationAnalysis.cpp ../moses//moses ;
 
-exe moses : Main.cpp mbr.cpp TranslationAnalysis.cpp deps : <include>. ;
+exe moses : Main.cpp deps : <include>. ;
 exe lmbrgrid : LatticeMBRGrid.cpp deps : <include>. ;
 
 alias programs : moses lmbrgrid ;
diff --git a/moses-cmd/LatticeMBRGrid.cpp b/moses-cmd/LatticeMBRGrid.cpp
index 83a0f3562..fe1bbca07 100644
--- a/moses-cmd/LatticeMBRGrid.cpp
+++ b/moses-cmd/LatticeMBRGrid.cpp
@@ -48,8 +48,8 @@ POSSIBILITY OF SUCH DAMAGE.
 
 #include "IOWrapper.h"
 #include "LatticeMBR.h"
-#include "Manager.h"
-#include "StaticData.h"
+#include "moses/Manager.h"
+#include "moses/StaticData.h"
 
 
 using namespace std;
diff --git a/moses-cmd/Main.cpp b/moses-cmd/Main.cpp
index 542bd580c..a7f63ebec 100644
--- a/moses-cmd/Main.cpp
+++ b/moses-cmd/Main.cpp
@@ -37,7 +37,6 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 
 #include "TranslationAnalysis.h"
 #include "IOWrapper.h"
-#include "LatticeMBR.h"
 #include "mbr.h"
 
 #include "moses/Hypothesis.h"
diff --git a/regression-testing/Jamfile b/regression-testing/Jamfile
index 998e46317..16110ad29 100644
--- a/regression-testing/Jamfile
+++ b/regression-testing/Jamfile
@@ -24,8 +24,8 @@ if $(with-regtest) {
   actions reg_test_decode {
     $(TOP)/regression-testing/run-single-test.perl --decoder=$(>) --test=$(<:B) --data-dir=$(with-regtest) --test-dir=$(test-dir) && touch $(<)
   }
-  reg_test phrase : [ glob $(test-dir)/phrase.* ] : ../moses-cmd/src//moses : @reg_test_decode ;
-  reg_test chart : [ glob $(test-dir)/chart.* ] : ../moses-chart-cmd/src//moses_chart : @reg_test_decode ;
+  reg_test phrase : [ glob $(test-dir)/phrase.* ] : ../moses-cmd//moses : @reg_test_decode ;
+  reg_test chart : [ glob $(test-dir)/chart.* ] : ../moses-chart-cmd//moses_chart : @reg_test_decode ;
   
   actions reg_test_score {
     $(TOP)/regression-testing/run-test-scorer.perl --scorer=$(>) --test=$(<:B) --data-dir=$(with-regtest) --test-dir=$(test-dir) && touch $(<)