diff --git a/prism/Makefile b/prism/Makefile
index 16e92359..7f039e0e 100644
--- a/prism/Makefile
+++ b/prism/Makefile
@@ -150,19 +150,23 @@ export CC CXX LD JAVAC JAVACC
 # Flags etc. #
 ##############
 
+# Tell compiler to generate debug information?
+# (WARNING: must not contain a % symbol!)
 DEBUG = 
 #DEBUG = -g
 
+# Compiler optimisation level:
+# (WARNING: must not contain a % symbol!)
 OPTIMISE = -O3
 #OPTIMISE =
 
-# warnings we'd like to get
+# Compiler warnings to enable:
+# (WARNING: must not contain a % symbol!)
 WARNINGS = -Wformat
 
 # Flags for compilation/linking
 # Flags to generate shared libraries
 # Executable/library naming conventions
-# Option to pass to CUDD makefile
 # Suffix for binary distribution directory
 # Place to look for (JNI) headers
 # (requires GNU make for conditional evaluation)
@@ -171,25 +175,22 @@ WARNINGS = -Wformat
 ifeq ($(OSTYPE),linux)
 	ifeq ($(ARCH),amd64)
 		# Position Independent Code required on AMD64/Itanium
-		CUDD_XCFLAGS = -m64 -fPIC -DPIC -DHAVE_IEEE_754 -DBSD -DSIZEOF_VOID_P=8 -DSIZEOF_LONG=8 $(DEBUG) $(WARNINGS)
-		CFLAGS = $(CUDD_XCFLAGS) $(OPTIMISE)
-		CXXFLAGS = --std=c++11 $(CUDD_XCFLAGS) $(OPTIMISE)
-		LDFLAGS = $(CUDD_XCFLAGS) $(OPTIMISE)
+		CFLAGS = -m64 -fPIC -DPIC -DHAVE_IEEE_754 -DBSD -DSIZEOF_VOID_P=8 -DSIZEOF_LONG=8 $(DEBUG) $(OPTIMISE) $(WARNINGS)
+		CXXFLAGS = --std=c++11 $(CFLAGS)
+		LDFLAGS = $(CFLAGS)
 		BINDISTSUFFIX = linux64
 	else
 	ifeq ($(ARCH),ia64)
 		# Position Independent Code required on AMD64/Itanium
 		# Note: We omit the -m64 flag from here since it seems to be unsupported by gcc on IA64
-		CUDD_XCFLAGS = -fPIC -DPIC -DHAVE_IEEE_754 -DBSD -DSIZEOF_VOID_P=8 -DSIZEOF_LONG=8 $(DEBUG) $(WARNINGS)
-		CFLAGS = $(CUDD_XCFLAGS) $(OPTIMISE)
-		CXXFLAGS = --std=c++11 $(CUDD_XCFLAGS) $(OPTIMISE)
-		LDFLAGS = $(CUDD_XCFLAGS) $(OPTIMISE)
+		CFLAGS = -fPIC -DPIC -DHAVE_IEEE_754 -DBSD -DSIZEOF_VOID_P=8 -DSIZEOF_LONG=8 $(DEBUG) $(OPTIMISE) $(WARNINGS)
+		CXXFLAGS = --std=c++11 $(CFLAGS)
+		LDFLAGS = $(CFLAGS)
 		BINDISTSUFFIX = linux64
 	else
-		CUDD_XCFLAGS = -m32 -malign-double -DHAVE_IEEE_754 -DBSD $(DEBUG) $(WARNINGS)
-		CFLAGS = $(CUDD_XCFLAGS) $(OPTIMISE)
-		CXXFLAGS = --std=c++11 $(CUDD_XCFLAGS) $(OPTIMISE)
-		LDFLAGS = $(CUDD_XCFLAGS) $(OPTIMISE)
+		CFLAGS = -m32 -malign-double -DHAVE_IEEE_754 -DBSD $(DEBUG) $(OPTIMISE) $(WARNINGS)
+		CXXFLAGS = --std=c++11 $(CFLAGS)
+		LDFLAGS = $(CFLAGS)
 		BINDISTSUFFIX = linux32
 	endif
 	endif
@@ -205,10 +206,9 @@ ifeq ($(OSTYPE),linux)
 endif
 # Solaris
 ifeq ($(OSTYPE),solaris)
-	CUDD_XCFLAGS = -mcpu=ultrasparc -DHAVE_IEEE_754 -DUNIX100 -DEPD_BIG_ENDIAN $(DEBUG) $(WARNINGS)
-	CFLAGS = $(CUDD_XCFLAGS) $(OPTIMISE)
-	CXXFLAGS = --std=c++11 $(CUDD_XCFLAGS) $(OPTIMISE)
-	LDFLAGS = $(CUDD_XCFLAGS) $(OPTIMISE)
+	CFLAGS = -mcpu=ultrasparc -DHAVE_IEEE_754 -DUNIX100 -DEPD_BIG_ENDIAN $(DEBUG) $(OPTIMISE) $(WARNINGS)
+	CXXFLAGS = --std=c++11 $(CFLAGS)
+	LDFLAGS = $(CFLAGS)
 	BINDISTSUFFIX = solaris
 	BIN_TARGETS=prism.linux xprism.linux
 	JFLAGS = -encoding UTF8
@@ -222,18 +222,16 @@ endif
 # Cygwin
 ifeq ($(OSTYPE),cygwin)
 	ifeq ($(ARCH),x86_64)
-		CUDD_XCFLAGS = -malign-double -DHAVE_IEEE_754 -DHAVE_GETRLIMIT=0 -DRLIMIT_DATA_DEFAULT=268435456 -DHAVE_SYS_RESOURCE_H=0 -DHAVE_SYS_WAIT_H=0 -DSIZEOF_VOID_P=8 -DSIZEOF_LONG=4 $(DEBUG) $(WARNINGS) -static-libgcc -static-libstdc++
-		CFLAGS = $(CUDD_XCFLAGS) $(OPTIMISE)
+		CFLAGS = -malign-double -DHAVE_IEEE_754 -DHAVE_GETRLIMIT=0 -DRLIMIT_DATA_DEFAULT=268435456 -DHAVE_SYS_RESOURCE_H=0 -DHAVE_SYS_WAIT_H=0 -DSIZEOF_VOID_P=8 -DSIZEOF_LONG=4 $(DEBUG) $(OPTIMISE) $(WARNINGS) -static-libgcc -static-libstdc++
 		# need -DWIN32 for lpsolve (WIN32 is only defined by mingw/gcc without --std=c++11)
-		CXXFLAGS = --std=c++11 -DWIN32 $(CUDD_XCFLAGS) $(OPTIMISE)
-		LDFLAGS = $(CUDD_XCFLAGS) $(OPTIMISE) -Wl,--add-stdcall-alias -Wl,-Bstatic,--whole-archive -lpthread -Wl,-Bdynamic,--no-whole-archive
+		CXXFLAGS = --std=c++11 -DWIN32 $(CFLAGS)
+		LDFLAGS = $(CFLAGS) -Wl,--add-stdcall-alias -Wl,-Bstatic,--whole-archive -lpthread -Wl,-Bdynamic,--no-whole-archive
 		BINDISTSUFFIX = win64
 	else
-		CUDD_XCFLAGS = -march=i686 -malign-double -DHAVE_IEEE_754 -DHAVE_GETRLIMIT=0 -DRLIMIT_DATA_DEFAULT=268435456 -DHAVE_SYS_RESOURCE_H=0 -DHAVE_SYS_WAIT_H=0 $(DEBUG) $(WARNINGS) -static-libgcc -static-libstdc++
-		CFLAGS = $(CUDD_XCFLAGS) $(OPTIMISE)
+		CFLAGS = -march=i686 -malign-double -DHAVE_IEEE_754 -DHAVE_GETRLIMIT=0 -DRLIMIT_DATA_DEFAULT=268435456 -DHAVE_SYS_RESOURCE_H=0 -DHAVE_SYS_WAIT_H=0 $(DEBUG) $(OPTIMISE) $(WARNINGS) -static-libgcc -static-libstdc++
 		# need -DWIN32 for lpsolve (WIN32 is only defined by mingw/gcc without --std=c++11)
-		CXXFLAGS = --std=c++11 -DWIN32 $(CUDD_XCFLAGS) $(OPTIMISE)
-		LDFLAGS = $(CUDD_XCFLAGS) $(OPTIMISE) -Wl,--add-stdcall-alias -Wl,-Bstatic,--whole-archive -lpthread -Wl,-Bdynamic,--no-whole-archive
+		CXXFLAGS = --std=c++11 -DWIN32 $(CFLAGS)
+		LDFLAGS = $(CFLAGS) -Wl,--add-stdcall-alias -Wl,-Bstatic,--whole-archive -lpthread -Wl,-Bdynamic,--no-whole-archive
 		BINDISTSUFFIX = win32
 	endif
 	BIN_TARGETS=prism.cygwin xprism.linux prism.bat.win xprism.bat.win
@@ -249,17 +247,15 @@ endif
 # Darwin
 ifeq ($(OSTYPE),darwin)
 	ifeq ($(ARCH),x86_64)
-		CUDD_XCFLAGS = -arch x86_64 -fPIC -DPIC -DHAVE_IEEE_754 -DBSD -DSIZEOF_VOID_P=8 -DSIZEOF_LONG=8 -fno-common $(DEBUG) $(WARNINGS)
-		CFLAGS = $(CUDD_XCFLAGS) $(OPTIMISE)
-		CXXFLAGS = --std=c++11 $(CUDD_XCFLAGS) $(OPTIMISE)
-		LDFLAGS = $(CUDD_XCFLAGS) $(OPTIMISE) -Wl,-search_paths_first
+		CFLAGS = -arch x86_64 -fPIC -DPIC -DHAVE_IEEE_754 -DBSD -DSIZEOF_VOID_P=8 -DSIZEOF_LONG=8 -fno-common $(DEBUG) $(OPTIMISE) $(WARNINGS)
+		CXXFLAGS = --std=c++11 $(CFLAGS)
+		LDFLAGS = $(CFLAGS) -Wl,-search_paths_first
 		BINDISTSUFFIX = osx64
 		BIN_TARGETS=prism.darwin64 xprism.linux
 	else
-		CUDD_XCFLAGS = -arch i386 -DHAVE_IEEE_754 -DBSD -fno-common $(DEBUG) $(WARNINGS)
-		CFLAGS = $(CUDD_XCFLAGS) $(OPTIMISE)
-		CXXFLAGS = --std=c++11 $(CUDD_XCFLAGS) $(OPTIMISE)
-		LDFLAGS = $(CUDD_XCFLAGS) $(OPTIMISE) -Wl,-search_paths_first
+		CFLAGS = -arch i386 -DHAVE_IEEE_754 -DBSD -fno-common $(DEBUG) $(OPTIMISE) $(WARNINGS)
+		CXXFLAGS = --std=c++11 $(CFLAGS)
+		LDFLAGS = $(CFLAGS) -Wl,-search_paths_first
 		BINDISTSUFFIX = osx32
 		BIN_TARGETS=prism.darwin32 xprism.linux
 	endif
@@ -328,7 +324,7 @@ cuddpackage: checks
 	@(if [ ! -h $(CUDD_DIR) ]; then \
 	  echo Making cudd ...; \
 	  cd $(CUDD_DIR) && \
-	  $(MAKE) XCFLAGS="$(CUDD_XCFLAGS)"; \
+	  $(MAKE) ICFLAGS="$(DEBUG) $(OPTIMISE) $(WARNINGS)" XCFLAGS="$(filter-out $(DEBUG) $(OPTIMISE) $(WARNINGS),$(CFLAGS))"; \
 	else \
 	  echo Skipping cudd make since it is a symlink...; \
 	fi)
@@ -337,7 +333,7 @@ cuddpackage: checks
 cuddpackageforce: checks
 	  @echo Making cudd ...; \
 	  cd $(CUDD_DIR) && \
-	  $(MAKE) XCFLAGS="$(CUDD_XCFLAGS)";
+	  $(MAKE) ICFLAGS="$(DEBUG) $(OPTIMISE) $(WARNINGS)" XCFLAGS="$(filter-out $(DEBUG) $(OPTIMISE) $(WARNINGS),$(CFLAGS))"
 
 # Use this to force a rebuild (with javacc) of the main parser
 parser: