diff --git a/moses-cmd/configure b/moses-cmd/configure
index d97725ad5..f0f5fbfe9 100755
--- a/moses-cmd/configure
+++ b/moses-cmd/configure
@@ -847,6 +847,7 @@ Optional Features:
   --enable-FEATURE[=ARG]  include FEATURE [ARG=yes]
   --disable-dependency-tracking  speeds up one-time build
   --enable-dependency-tracking   do not reject slow dependency extractors
+  --enable-profiling      moses will dump profiling info
   --enable-mysql          (optional) build in MySQL support]
 
 Optional Packages:
@@ -2603,6 +2604,13 @@ else
 
 fi;
 
+# Check whether --enable-profiling or --disable-profiling was given.
+if test "${enable_profiling+set}" = set; then
+  enableval="$enable_profiling"
+  CPPFLAGS="$CPPFLAGS -pg"; LDFLAGS="$LDFLAGS -pg"
+
+fi;
+
 # Check whether --enable-mysql or --disable-mysql was given.
 if test "${enable_mysql+set}" = set; then
   enableval="$enable_mysql"
@@ -2612,7 +2620,7 @@ else
 fi;
 if test "x$with_boost" != 'xno'
 then
-  CPPFLAGS="$CPPFLAGS -I${with_boost}"
+  CPPFLAGS="$CPPFLAGS -I${with_boost} -I${with_boost}/include"
   LDFLAGS="$LDFLAGS -L${with_boost}/lib -L${with_boost}/stage/lib"
 fi
 
diff --git a/moses-cmd/src/Main.cpp b/moses-cmd/src/Main.cpp
index 7b19a139b..eaf61136a 100644
--- a/moses-cmd/src/Main.cpp
+++ b/moses-cmd/src/Main.cpp
@@ -73,6 +73,10 @@ int main(int argc, char* argv[])
 {
 	timer.start("Starting...");
 
+#ifdef N_BEST
+    cerr << "N_BEST flag on\n";
+#endif
+
 	StaticData staticData;
 	if (!staticData.LoadParameters(argc, argv))
 		return EXIT_FAILURE;
@@ -152,14 +156,18 @@ InputOutput *GetInputOutput(StaticData &staticData)
 		list< Phrase >	inputPhraseList;
 		string filePath = staticData.GetParam("input-file")[0];
 
+		TRACE_ERR("About to create ioFile" << endl);
 		IOFile *ioFile = new IOFile(factorOrder, inputFactorUsed
 																	, staticData.GetFactorCollection()
 																	, staticData.GetNBestSize()
 																	, staticData.GetNBestFilePath()
 																	, filePath);
+		TRACE_ERR("About to GetInputPhrase" << endl);
 		ioFile->GetInputPhrase(inputPhraseList);
+		TRACE_ERR("After GetInputPhrase" << endl);
 		inputOutput = ioFile;
 		inputFileHash = GetMD5Hash(filePath);
+		TRACE_ERR("About to LoadPhraseTables" << endl);
 		staticData.LoadPhraseTables(true, inputFileHash, inputPhraseList);
 	}
 	else
diff --git a/moses/src/HypothesisCollection.cpp b/moses/src/HypothesisCollection.cpp
index 3cdc00aaf..b81ea4f6a 100755
--- a/moses/src/HypothesisCollection.cpp
+++ b/moses/src/HypothesisCollection.cpp
@@ -44,6 +44,8 @@ void HypothesisCollection::Add(Hypothesis *hypo)
 	if (hypo->GetScore(ScoreType::Total) > m_bestScore)
 	{
 		m_bestScore = hypo->GetScore(ScoreType::Total);
+        if ( m_bestScore + m_beamThreshold > m_worstScore )
+          m_worstScore = m_bestScore + m_beamThreshold;
 	}
 
 	if (size() > m_maxHypoStackSize)
@@ -59,9 +61,9 @@ float HypothesisCollection::getBestScore(){
 
 
 
-bool HypothesisCollection::Add(Hypothesis *hypo, float beamThreshold)
+bool HypothesisCollection::AddPrune(Hypothesis *hypo)
 {
-	if (hypo->GetScore(ScoreType::Total) < m_bestScore + beamThreshold)
+	if (hypo->GetScore(ScoreType::Total) < m_worstScore)
 		return false;
 
 	// over threshold		
@@ -138,6 +140,7 @@ void HypothesisCollection::PruneToSize(size_t newSize)
 				++iter;
 			}
 		}
+        m_worstScore = scoreThreshold;
 	}
 }
 
diff --git a/moses/src/HypothesisCollection.h b/moses/src/HypothesisCollection.h
index 749ac3154..375507fcc 100755
--- a/moses/src/HypothesisCollection.h
+++ b/moses/src/HypothesisCollection.h
@@ -64,7 +64,9 @@ class HypothesisCollection : public std::set< Hypothesis*, CompareHypothesisColl
 	friend std::ostream& operator<<(std::ostream&, const HypothesisCollection&);
 
 protected:
-	float m_bestScore, m_beamThreshold;
+	float m_bestScore;
+    float m_worstScore;
+    float m_beamThreshold;
 	size_t m_maxHypoStackSize;
 
 //	std::list<Arc> m_arc;
@@ -80,6 +82,7 @@ public:
 	inline HypothesisCollection()
 	{
 		m_bestScore = -std::numeric_limits<float>::infinity();
+		m_worstScore = -std::numeric_limits<float>::infinity();
 	}
 
 	inline void AddNoPrune(Hypothesis *hypothesis)
@@ -87,7 +90,8 @@ public:
 		//push_back(hypothesis);
 		insert(hypothesis);
 	}
-	bool Add(Hypothesis *hypothesis, float beamThreshold);
+	bool AddPrune(Hypothesis *hypothesis);
+      // AddPrune adds the hypo, but only if within thresholds (beamThr+stackSize)
 	inline void Detach(const HypothesisCollection::iterator &iter)
 	{
 		erase(iter);
diff --git a/moses/src/Makefile.in b/moses/src/Makefile.in
index 06a83d3fd..ba7edf78f 100644
--- a/moses/src/Makefile.in
+++ b/moses/src/Makefile.in
@@ -105,8 +105,6 @@ AUTOCONF = @AUTOCONF@
 AUTOHEADER = @AUTOHEADER@
 AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
-BUILD_MYSQL_SUPPORT_FALSE = @BUILD_MYSQL_SUPPORT_FALSE@
-BUILD_MYSQL_SUPPORT_TRUE = @BUILD_MYSQL_SUPPORT_TRUE@
 CPPFLAGS = @CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
@@ -131,9 +129,6 @@ LIBOBJS = @LIBOBJS@
 LIBS = @LIBS@
 LTLIBOBJS = @LTLIBOBJS@
 MAKEINFO = @MAKEINFO@
-MYSQLCLIENT_CPPFLAGS = @MYSQLCLIENT_CPPFLAGS@
-MYSQLCLIENT_LDFLAGS = @MYSQLCLIENT_LDFLAGS@
-MYSQLCLIENT_LIBS = @MYSQLCLIENT_LIBS@
 OBJEXT = @OBJEXT@
 PACKAGE = @PACKAGE@
 PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
@@ -203,9 +198,9 @@ $(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
 	      exit 1;; \
 	  esac; \
 	done; \
-	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu  src/Makefile'; \
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign  src/Makefile'; \
 	cd $(top_srcdir) && \
-	  $(AUTOMAKE) --gnu  src/Makefile
+	  $(AUTOMAKE) --foreign  src/Makefile
 .PRECIOUS: Makefile
 Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	@case '$?' in \
diff --git a/moses/src/Manager.cpp b/moses/src/Manager.cpp
index d73088d98..75bce4c2b 100755
--- a/moses/src/Manager.cpp
+++ b/moses/src/Manager.cpp
@@ -75,7 +75,7 @@ void Manager::ProcessSentence()
 	LMList allLM = m_staticData.GetAllLM();
 	hypo->ResizeComponentScore(allLM, decodeStepList);
 #endif
-	m_hypoStack[0].Add(hypo, m_staticData.GetBeamThreshold());
+	m_hypoStack[0].AddPrune(hypo);
 	}
 
 	// go thru each stack
@@ -181,7 +181,7 @@ void Manager::ProcessOneHypothesis(const list < DecodeStep > &decodeStepList
 		}
 		size_t wordsTranslated = hypo->GetWordsBitmap().GetWordsCount();
 
-		if (m_hypoStack[wordsTranslated].Add(hypo, m_staticData.GetBeamThreshold()))
+		if (m_hypoStack[wordsTranslated].AddPrune(hypo))
 		{
 			HypothesisCollectionIntermediate::iterator iterCurr = iterHypo++;
 			lastHypoColl.Detach(iterCurr);
diff --git a/moses/src/TypeDef.h b/moses/src/TypeDef.h
index b1115a042..f880ea159 100755
--- a/moses/src/TypeDef.h
+++ b/moses/src/TypeDef.h
@@ -43,7 +43,7 @@ const size_t DEFAULT_VERBOSE_LEVEL = 1;
 #include "config.h"
 
 #define TRACE_ENABLE 1		// REMOVE after we figure this out
-// #define N_BEST 1					// REMOVE
+#define N_BEST 1					// REMOVE
 
 #  ifdef HAVE_SRILM
 #    define LM_SRI 1