diff --git a/Cantera/clib/src/Makefile.in b/Cantera/clib/src/Makefile.in
index 7abe6dbbc..d42de7845 100755
--- a/Cantera/clib/src/Makefile.in
+++ b/Cantera/clib/src/Makefile.in
@@ -15,6 +15,8 @@
 INSTALL_TSC = ../../../bin/install_tsc
 do_ranlib = @DO_RANLIB@
 
+PURIFY=@PURIFY@
+
 PIC_FLAG=@PIC@
 
 CXX_FLAGS = @CXXFLAGS@ $(CXX_OPT) $(PIC_FLAG)
@@ -57,7 +59,7 @@ LCXX_FLAGS = -L$(CANTERA_LIBDIR) @CXXFLAGS@
 
 # how to compile C++ source files to object files
 .@CXX_EXT@.@OBJ_EXT@:
-	$(CXX) -c $< $(CXX_INCLUDES) $(CXX_FLAGS)
+	$(PURIFY) $(CXX) -c $< $(CXX_INCLUDES) $(CXX_FLAGS)
 
 %.d: Makefile %.o
 	@CXX_DEPENDS@ $(CXX_FLAGS) $(CXX_INCLUDES) $*.cpp > $*.d
@@ -75,7 +77,7 @@ all: $(CTLIB) .depends
 $(CTLIB): $(OBJS) $(LIB_DEPS)
 	$(RM)     $(CTLIB)
 ifeq ($(shared_ctlib),1)
-	$(CXX) -o $(CTLIB) $(OBJS) $(LCXX_FLAGS)\
+	$(PURIFY) $(CXX) -o $(CTLIB) $(OBJS) $(LCXX_FLAGS)\
                 @SHARED@ $(LINK_OPTIONS) \
                 $(EXT_LIBS) @LIBS@ $(FORT_LIBS)
 else
diff --git a/Cantera/cxx/demos/Makefile.in b/Cantera/cxx/demos/Makefile.in
index 1f8c94721..752cc0271 100644
--- a/Cantera/cxx/demos/Makefile.in
+++ b/Cantera/cxx/demos/Makefile.in
@@ -26,6 +26,9 @@ srcdirtree=1
 # Fortran libraries
 FORT_LIBS = @FLIBS@
 
+# Purify options
+PURIFY=@PURIFY@
+
 # the C++ compiler
 CXX = @CXX@
 
@@ -59,7 +62,7 @@ LCXX_FLAGS = -L$(CANTERA_LIBDIR) @LOCAL_LIB_DIRS@ @CXXFLAGS@
 
 # how to compile C++ source files to object files
 .@CXX_EXT@.@OBJ_EXT@:
-	$(CXX) -c $< -I$(CANTERA_INCDIR) $(CXX_FLAGS) $(LOCAL_DEFNS)
+	$(PURIFY) $(CXX) -c $< -I$(CANTERA_INCDIR) $(CXX_FLAGS) $(LOCAL_DEFNS)
 
 # how to create a dependency file
 .@CXX_EXT@.d:
@@ -72,7 +75,7 @@ DEPENDS = $(OBJS:.o=.d)
 all: $(PROGRAM) 
 
 $(PROGRAM): $(OBJS) 
-	$(CXX) -o $(PROGRAM) $(OBJS) $(LCXX_FLAGS) $(CANTERA_LIBS) \
+	$(PURIFY) $(CXX) -o $(PROGRAM) $(OBJS) $(LCXX_FLAGS) $(CANTERA_LIBS) \
                    $(LINK_OPTIONS) $(EXT_LIBS) @LIBS@ $(FORT_LIBS) \
                   $(LCXX_END_LIBS)
 
diff --git a/Cantera/cxx/include/Cantera.mak.in b/Cantera/cxx/include/Cantera.mak.in
index dce207e8f..4a0d009f9 100644
--- a/Cantera/cxx/include/Cantera.mak.in
+++ b/Cantera/cxx/include/Cantera.mak.in
@@ -95,7 +95,7 @@ endif
 CANTERA_build_lapack= @build_lapack@
 CANTERA_build_blas= @build_blas@
 
-CANTERA_BLAS_LAPACK_DIR= @BLAS_LAPACK_DIR@
+CANTERA_BLAS_LAPACK_DIR= @ct_libdir@
 
 CANTERA_BLAS_LAPACK_LIBS = -L$(CANTERA_BLAS_LAPACK_DIR) @BLAS_LAPACK_LIBS@
 
@@ -121,11 +121,11 @@ CANTERA_TOTAL_INCLUDES= $(CANTERA_CORE_INCLUDES) $(CANTERA_BOOST_INCLUDES) $(CAN
 #
 # LIBS and LIBS should be the same ...
 #
-CANTERA_TOTAL_LIBS2 = @LOCAL_LIB_DIRS@ @LOCAL_LIBS@
+CANTERA_TOTAL_LIBS2 =  -L$(CANTERA_LIBSDIR)  @LOCAL_LIBS@
 
 CANTERA_TOTAL_LIBS= $(CANTERA_CORE_LIBS) $(CANTERA_BOOST_LIBS) \
                     $(CANTERA_CVODE_LIBS) $(CANTERA_BLAS_LAPACK_LIBS) \
-                     $(CANTERA_F2C_LIBS)
+                    $(CANTERA_F2C_LIBS)
 
 #
 # Dependency Line
diff --git a/Cantera/cxx/src/Makefile.in b/Cantera/cxx/src/Makefile.in
index 7e46bbbe1..01e78a4ac 100644
--- a/Cantera/cxx/src/Makefile.in
+++ b/Cantera/cxx/src/Makefile.in
@@ -19,6 +19,8 @@ OBJS =  importPhase.o
 
 DEPENDS = $(OBJS:.o=.d)
 
+PURIFY=@PURIFY@
+
 PIC_FLAG=@PIC@
 CXX_FLAGS = @CXXFLAGS@ $(CXX_OPT) $(PIC_FLAG)
 
@@ -28,7 +30,7 @@ CXX_INCLUDES = -I../../src/base -I../../src/thermo @CXX_INCLUDES@
 
 # how to compile C++ source files to object files
 .cpp.o:
-	@CXX@ -c $< $(CXX_INCLUDES) $(CXX_FLAGS)
+	$(PURIFY) @CXX@ -c $< $(CXX_INCLUDES) $(CXX_FLAGS)
 
 %.d: Makefile %.o
 	@CXX_DEPENDS@ $(CXX_FLAGS) $(CXX_INCLUDES) $*.cpp > $*.d
diff --git a/Cantera/fortran/src/Makefile.in b/Cantera/fortran/src/Makefile.in
index 1b64ea989..7049d28ae 100644
--- a/Cantera/fortran/src/Makefile.in
+++ b/Cantera/fortran/src/Makefile.in
@@ -14,6 +14,7 @@
 CXX_FLAGS = @CXXFLAGS@ $(CXX_OPT)
 FORT_FLAGS = @F90BUILDFLAGS@
 
+PURIFY=@PURIFY@
 
 CXX_OBJS = fct.o fctxml.o
 
@@ -61,16 +62,16 @@ LCXX_FLAGS = -L$(CANTERA_LIBDIR) @CXXFLAGS@
 
 # how to compile C++ source files to object files
 %.o : %.cpp
-	$(CXX) -c $< $(CXX_INCLUDES) $(CXX_FLAGS)
+	$(PURIFY) $(CXX) -c $< $(CXX_INCLUDES) $(CXX_FLAGS)
 
 %.o : %.f90
-	$(F90) -c $< $(FORT_FLAGS)
+	$(PURIFY) $(F90) -c $< $(FORT_FLAGS)
 
 %.mod : %_interface.f90
-	$(F90) -c $< $(FORT_FLAGS)
+	$(PURIFY) $(F90) -c $< $(FORT_FLAGS)
 
 %.mod : %.f90
-	$(F90) -c $< $(FORT_FLAGS)
+	$(PURIFY) $(F90) -c $< $(FORT_FLAGS)
 
 LIB_NAME=libfct.a
 
@@ -98,9 +99,11 @@ win-install:
 %.d: %.cpp
 	@CXX_DEPENDS@ $(CXX_INCLUDES) $*.cpp > $*.d
 
-depends: $(DEPENDS)
+depends: 
+	$(MAKE) .depends
+
+.depends: $(DEPENDS)
 	cat *.d > .depends
-	$(RM) $(DEPENDS) 
 
 cantera_thermo.o: fct.mod cantera_xml.mod cantera_thermo.f90
 fct.mod: fct_interface.f90
diff --git a/Cantera/python/Makefile.in b/Cantera/python/Makefile.in
index 4309157bc..eede4a9c2 100755
--- a/Cantera/python/Makefile.in
+++ b/Cantera/python/Makefile.in
@@ -47,7 +47,7 @@ win: _winbuild
 _build: $(SRCS) $(LIB_DEPS) Makefile setup.py
 	touch src/pycantera.cpp 
 	/bin/rm -f _build
-	(CXX="@CXX@"; export CXX; CC="@CXX@"; export CC; @PYTHON_CMD@ setup.py build)
+	(CXX="@CXX@"; export CXX; CC="@CXX@"; export CC; PURIFY="@PURIFY@"; export PURIFY; @PYTHON_CMD@ setup.py build)
 	echo 'ok' > _build
 
 #
diff --git a/Cantera/src/base/Makefile.in b/Cantera/src/base/Makefile.in
index bb3dc57ee..f12b52bfd 100644
--- a/Cantera/src/base/Makefile.in
+++ b/Cantera/src/base/Makefile.in
@@ -22,6 +22,8 @@ else
    DEBUG_FLAG=
 endif
 
+PURIFY=@PURIFY@
+
 PIC_FLAG=@PIC@
 
 CXX_FLAGS = @CXXFLAGS@ $(LOCAL_DEFS) $(CXX_OPT) $(PIC_FLAG) $(DEBUG_FLAG)
@@ -49,7 +51,7 @@ all: $(LIB) .depends
 	@CXX_DEPENDS@ $(CXX_FLAGS) $(CXX_INCLUDES) $*.cpp > $*.d
 
 .cpp.o:
-	@CXX@ -c $< $(CXX_FLAGS) $(CXX_INCLUDES)
+	$(PURIFY) @CXX@ -c $< $(CXX_FLAGS) $(CXX_INCLUDES)
 
 $(LIB): $(BASE_OBJ) $(BASE_H)
 	@ARCHIVE@ $(LIB) $(BASE_OBJ) > /dev/null
diff --git a/Cantera/src/converters/Makefile.in b/Cantera/src/converters/Makefile.in
index f331ce0cb..d491f2f59 100644
--- a/Cantera/src/converters/Makefile.in
+++ b/Cantera/src/converters/Makefile.in
@@ -15,6 +15,8 @@ INCDIR = ../../../build/include/cantera/kernel/converters
 INSTALL_TSC = ../../../bin/install_tsc
 do_ranlib = @DO_RANLIB@
 
+PURIFY=@PURIFY@
+
 PIC_FLAG=@PIC@
 
 CXX_FLAGS = @CXXFLAGS@ $(CXX_OPT) $(PIC_FLAG)
@@ -43,7 +45,7 @@ all: .depends $(CONV_LIB)
 	@CXX_DEPENDS@ $(CXX_FLAGS) $(CXX_INCLUDES) $*.cpp > $*.d
 
 .cpp.o:
-	@CXX@ -c $< $(CXX_FLAGS) $(CXX_INCLUDES)
+	$(PURIFY) @CXX@ -c $< $(CXX_FLAGS) $(CXX_INCLUDES)
 
 $(CONV_LIB): $(OBJS)
 	@ARCHIVE@ $(CONV_LIB) $(OBJS) 
diff --git a/Cantera/src/equil/Makefile.in b/Cantera/src/equil/Makefile.in
index 4bca5f445..363c44348 100644
--- a/Cantera/src/equil/Makefile.in
+++ b/Cantera/src/equil/Makefile.in
@@ -16,7 +16,10 @@ INSTALL_TSC = ../../../bin/install_tsc
 do_ranlib = @DO_RANLIB@
 
 do_VCSnonideal = @COMPILE_VCSNONIDEAL@
-
+#
+# Purify Options - instrument code for debugging and quantitification
+#
+PURIFY=@PURIFY@
 #
 # Decide whether ot use the linear programmaing module lookalike
 # (from Goodwin's code). Both should produce the same results.
@@ -101,10 +104,10 @@ all: $(LIB) $(VLIB) .depends
 	@CXX_DEPENDS@ $(CXX_FLAGS) $(CXX_INCLUDES) -I../../../ext/f2c_libs $*.c > $*.d
 
 .cpp.o:
-	@CXX@ -c $< $(CXX_FLAGS) $(CXX_INCLUDES)
+	$(PURIFY) @CXX@ -c $< $(CXX_FLAGS) $(CXX_INCLUDES)
 
 .c.o:
-	@CC@ -c $< $(CXX_FLAGS) $(CXX_INCLUDES) -I../../../ext/f2c_libs
+	$(PURIFY) @CC@ -c $< $(CXX_FLAGS) $(CXX_INCLUDES) -I../../../ext/f2c_libs
 
 $(LIB): $(EQUIL_OBJ) $(EQUIL_H) $(VCSNONIDEAL_OBJ) $(VCSNONIDEAL_H)
 	@ARCHIVE@ $(LIB) $(EQUIL_OBJ) $(VCSNONIDEAL_OBJ) > /dev/null
diff --git a/Cantera/src/kinetics/Makefile.in b/Cantera/src/kinetics/Makefile.in
index 0780d7318..843bbf93a 100644
--- a/Cantera/src/kinetics/Makefile.in
+++ b/Cantera/src/kinetics/Makefile.in
@@ -26,6 +26,8 @@ else
    DEBUG_FLAG=
 endif
 
+PURIFY=@PURIFY@
+
 PIC_FLAG=@PIC@
 # LOCAL_DEFS = -DDEBUG_SOLVESP
 CXX_FLAGS = @CXXFLAGS@ $(LOCAL_DEFS) $(CXX_OPT) $(PIC_FLAG) $(DEBUG_FLAG)
@@ -79,7 +81,7 @@ all: $(LIB) .depends
 	@CXX_DEPENDS@ $(CXX_FLAGS) $(CXX_INCLUDES) $*.cpp > $*.d
 
 .cpp.o:
-	@CXX@ -c $< $(CXX_FLAGS) $(CXX_INCLUDES)
+	$(PURIFY) @CXX@ -c $< $(CXX_FLAGS) $(CXX_INCLUDES)
 
 $(LIB): $(ALLKINETICS_OBJ) $(ALLKINETICS_H)
 	@ARCHIVE@ $(LIB) $(ALLKINETICS_OBJ) > /dev/null
diff --git a/Cantera/src/numerics/Makefile.in b/Cantera/src/numerics/Makefile.in
index ae634ab73..a718f4235 100644
--- a/Cantera/src/numerics/Makefile.in
+++ b/Cantera/src/numerics/Makefile.in
@@ -23,6 +23,9 @@ else
 endif
 
 SUNDIALS_INC=@sundials_include@
+
+PURIFY=@PURIFY@ 
+
 PIC_FLAG=@PIC@
 
 CXX_FLAGS = @CXXFLAGS@ $(LOCAL_DEFS) $(CXX_OPT) $(PIC_FLAG) $(DEBUG_FLAG)
@@ -51,7 +54,7 @@ all: .depends $(LIB)
 	@CXX_DEPENDS@ $(CXX_FLAGS) $(CXX_INCLUDES) $*.cpp > $*.d
 
 .cpp.o:
-	@CXX@ -c $< $(CXX_FLAGS) $(CXX_INCLUDES)
+	$(PURIFY) @CXX@ -c $< $(CXX_FLAGS) $(CXX_INCLUDES)
 
 $(LIB): $(NUMERICS_OBJ) $(NUMERICS_H)
 	@ARCHIVE@ $(LIB) $(NUMERICS_OBJ) > /dev/null
@@ -60,14 +63,14 @@ ifeq ($(do_ranlib),1)
 endif
 
 ODE_integrators.o:
-	@CXX@ -c ODE_integrators.cpp $(CXX_INCLUDES) $(SUNDIALS_INC) \
+	$(PURIFY) @CXX@ -c ODE_integrators.cpp $(CXX_INCLUDES) $(SUNDIALS_INC) \
             $(CXX_FLAGS) 
 ODE_integrators.d: ODE_integrators.cpp Makefile
 	@CXX_DEPENDS@ $(CXX_FLAGS) ODE_integrators.cpp $(CXX_INCLUDES) $(SUNDIALS_INC) \
              > ODE_integrators.d 
 
 DAE_solvers.o: DAE_solvers.cpp
-	@CXX@ -c DAE_solvers.cpp $(CXX_INCLUDES) $(SUNDIALS_INC) $(CXX_FLAGS)
+	$(PURIFY) @CXX@ -c DAE_solvers.cpp $(CXX_INCLUDES) $(SUNDIALS_INC) $(CXX_FLAGS)
 DAE_solvers.d: DAE_solvers.cpp Makefile
 	@CXX_DEPENDS@ $(CXX_FLAGS) DAE_solvers.cpp $(CXX_INCLUDES) $(SUNDIALS_INC) \
              > DAE_solvers.d  
diff --git a/Cantera/src/oneD/Makefile.in b/Cantera/src/oneD/Makefile.in
index 93cf945a3..ad4c6a0a5 100644
--- a/Cantera/src/oneD/Makefile.in
+++ b/Cantera/src/oneD/Makefile.in
@@ -15,6 +15,8 @@ INCDIR = ../../../build/include/cantera/kernel
 INSTALL_TSC = ../../../bin/install_tsc                      
 do_ranlib = @DO_RANLIB@
 
+PURIFY=@PURIFY@
+
 PIC_FLAG=@PIC@
 
 CXX_FLAGS = @CXXFLAGS@ $(CXX_OPT) $(PIC_FLAG)
@@ -35,7 +37,7 @@ DEPENDS = $(OBJS:.o=.d)
 	@CXX_DEPENDS@ @DEFS@ $(CXX_FLAGS) $(CXX_INCLUDES) $*.cpp > $*.d
 
 .cpp.o:
-	@CXX@ -c $< @DEFS@ $(CXX_FLAGS) $(CXX_INCLUDES)
+	$(PURIFY) @CXX@ -c $< @DEFS@ $(CXX_FLAGS) $(CXX_INCLUDES)
 
 all: $(ONED_LIB) .depends
 	@(@INSTALL@ -d $(INCDIR))
diff --git a/Cantera/src/spectra/Makefile.in b/Cantera/src/spectra/Makefile.in
index 4c1282035..a92c3b85f 100644
--- a/Cantera/src/spectra/Makefile.in
+++ b/Cantera/src/spectra/Makefile.in
@@ -22,6 +22,8 @@ else
    DEBUG_FLAG=
 endif
 
+PURIFY=@PURIFY@
+
 PIC_FLAG=@PIC@
 
 CXX_FLAGS = @CXXFLAGS@ $(LOCAL_DEFS) $(CXX_OPT) $(PIC_FLAG) $(DEBUG_FLAG)
@@ -44,7 +46,7 @@ all: $(LIB) .depends
 	@CXX_DEPENDS@ $(CXX_FLAGS) $(CXX_INCLUDES) $*.cpp > $*.d
 
 .cpp.o:
-	@CXX@ -c $< $(CXX_FLAGS) $(CXX_INCLUDES)
+	$(PURIFY) @CXX@ -c $< $(CXX_FLAGS) $(CXX_INCLUDES)
 
 $(LIB): $(SPECTRA_OBJ) $(SPECTRA_H)
 	@ARCHIVE@ $(LIB) $(SPECTRA_OBJ) > /dev/null
diff --git a/Cantera/src/thermo/Makefile.in b/Cantera/src/thermo/Makefile.in
index 15871d082..993e57594 100644
--- a/Cantera/src/thermo/Makefile.in
+++ b/Cantera/src/thermo/Makefile.in
@@ -24,6 +24,9 @@ else
    DEBUG_FLAG=
 endif
 
+# Purify command - usually this is blank
+PURIFY=@PURIFY@
+
 #LOCAL_DEFS=-DDEBUG_MODE
 PIC_FLAG=@PIC@
 
@@ -98,7 +101,7 @@ all: $(LIB) .depends
 	@CXX_DEPENDS@ $(CXX_FLAGS) $(CXX_INCLUDES) $*.cpp > $*.d
 
 .cpp.o:
-	@CXX@ -c $< $(CXX_FLAGS) $(CXX_INCLUDES)
+	$(PURIFY) @CXX@ -c $< $(CXX_FLAGS) $(CXX_INCLUDES)
 
 $(LIB): $(CATHERMO_OBJ) $(CATHERMO_H)
 	@ARCHIVE@ $(LIB) $(CATHERMO_OBJ) > /dev/null
diff --git a/Cantera/src/transport/Makefile.in b/Cantera/src/transport/Makefile.in
index 436a76b5a..d61a6dfe4 100644
--- a/Cantera/src/transport/Makefile.in
+++ b/Cantera/src/transport/Makefile.in
@@ -15,6 +15,8 @@ INCDIR = ../../../build/include/cantera/kernel
 INSTALL_TSC = ../../../bin/install_tsc
 do_ranlib = @DO_RANLIB@
 
+PURIFY=@PURIFY@
+
 PIC_FLAG=@PIC@
 
 debug_mode = @CANTERA_DEBUG_MODE@
@@ -49,7 +51,7 @@ all:  $(LIB) .depends
 	@CXX_DEPENDS@ $(CXX_FLAGS) $(CXX_INCLUDES) $*.cpp > $*.d
 
 .cpp.o:
-	@CXX@ -c $< $(CXX_FLAGS) $(CXX_INCLUDES)
+	$(PURIFY) @CXX@ -c $< $(CXX_FLAGS) $(CXX_INCLUDES)
 
 $(LIB): $(OBJS) $(TRAN_H)
 	@ARCHIVE@ $(LIB) $(OBJS) > /dev/null
diff --git a/Cantera/src/zeroD/Makefile.in b/Cantera/src/zeroD/Makefile.in
index 9326c035d..8c3000018 100644
--- a/Cantera/src/zeroD/Makefile.in
+++ b/Cantera/src/zeroD/Makefile.in
@@ -15,6 +15,8 @@ INCDIR = ../../../build/include/cantera/kernel
 INSTALL_TSC = ../../../bin/install_tsc
 do_ranlib = @DO_RANLIB@
 
+PURIFY=@PURIFY@
+
 PIC_FLAG=@PIC@
 
 CXX_FLAGS = @CXXFLAGS@ $(CXX_OPT) $(PIC_FLAG)
@@ -41,7 +43,7 @@ all: $(ZEROD_LIB) .depends
 	@CXX_DEPENDS@  @DEFS@ $(CXX_FLAGS) $(CXX_INCLUDES) $*.cpp > $*.d
 
 .cpp.o:
-	@CXX@ -c $< @DEFS@ $(CXX_FLAGS) $(CXX_INCLUDES)
+	$(PURIFY) @CXX@ -c $< @DEFS@ $(CXX_FLAGS) $(CXX_INCLUDES)
 
 $(ZEROD_LIB): $(OBJS) $(ZEROD_H)
 	@ARCHIVE@ $(ZEROD_LIB) $(OBJS) > /dev/null
diff --git a/examples/cxx/Makefile.in b/examples/cxx/Makefile.in
index 465e5b77e..e74a9f8ee 100755
--- a/examples/cxx/Makefile.in
+++ b/examples/cxx/Makefile.in
@@ -27,6 +27,8 @@ LINK_OPTIONS = @EXTRA_LINK@
 # the Fortran compiler
 FORT = @F90@
 
+PURIFY=@PURIFY@
+
 # Fortran compile flags  
 FORT_FLAGS = @FFLAGS@ 
 
@@ -87,11 +89,11 @@ LCXX_FLAGS = -L$(CANTERA_LIBDIR) @LOCAL_LIB_DIRS@ @CXXFLAGS@
 
 # how to compile C++ source files to object files
 .@CXX_EXT@.@OBJ_EXT@:
-	$(CXX) -c $< $(CANTERA_INC) $(CXX_FLAGS)
+	$(PURIFY) $(CXX) -c $< $(CANTERA_INC) $(CXX_FLAGS)
 
 # how to compile Fortran source files to object files
 .@F77_EXT@.@OBJ_EXT@: 
-	$(FORT) -c $< $(FORT_FLAGS)
+	$(PURIFY) $(FORT) -c $< $(FORT_FLAGS)
 
 PROGRAM = ./$(PROG_NAME)$(EXE_EXT)
 
@@ -103,7 +105,7 @@ DEPENDS=$(OBJS:.o=.d)
 	@CXX_DEPENDS@ $(CANTERA_INC) $(CXX_FLAGS) $*.cpp > $*.d
 
 $(PROGRAM): $(OBJS) $(LIB_DEPS)
-	$(CXX) -o $(PROGRAM) $(OBJS) $(LCXX_FLAGS) $(CANTERA_LIBS) \
+	$(PURIFY) $(CXX) -o $(PROGRAM) $(OBJS) $(LCXX_FLAGS) $(CANTERA_LIBS) \
                    $(LINK_OPTIONS) $(EXT_LIBS) @LIBS@ \
                   $(LCXX_END_LIBS)
 
diff --git a/ext/blas/Makefile.in b/ext/blas/Makefile.in
index 1f8eda74c..e9417b30f 100755
--- a/ext/blas/Makefile.in
+++ b/ext/blas/Makefile.in
@@ -9,6 +9,8 @@ BLASLIB = @buildlib@/libctblas.a
 SUFFIXES=
 SUFFIXES= .f .o
 
+PURIFY=@PURIFY@
+
 PIC_FLAG=@PIC@
 
 F_FLAGS = @FFLAGS@ $(PIC_FLAG)
@@ -67,7 +69,7 @@ ifeq ($(do_ranlib),1)
 endif
 
 %.o : %.f
-	@F77@ -c $< $(F_FLAGS) 
+	$(PURIFY) @F77@ -c $< $(F_FLAGS) 
 
 clean:
 	$(RM) $(OBJS) $(BLASLIB)
diff --git a/ext/cvode/Makefile.in b/ext/cvode/Makefile.in
index 03d9b9b6c..9f13161b6 100755
--- a/ext/cvode/Makefile.in
+++ b/ext/cvode/Makefile.in
@@ -23,6 +23,8 @@ do_ranlib = @DO_RANLIB@
 
 all: @buildlib@/libcvode.a
 
+PURIFY=@PURIFY@
+
 PIC_FLAG=@PIC@
    
 COMPILER = @CC@
@@ -43,54 +45,54 @@ endif
 
 source/cvode.o: source/cvode.c include/cvode.h include/llnltyps.h \
                 include/nvector.h include/llnlmath.h
-	(cd source; $(COMPILER) $(OPTS) -c cvode.c)
+	(cd source; $(PURIFY) $(COMPILER) $(OPTS) -c cvode.c)
 
 source/cvdense.o: source/cvdense.c include/cvdense.h include/cvode.h \
                   include/dense.h include/llnltyps.h include/nvector.h \
                   include/llnlmath.h
-	(cd source; $(COMPILER) $(OPTS) -c cvdense.c)
+	(cd source; $(PURIFY) $(COMPILER) $(OPTS) -c cvdense.c)
  
 source/dense.o: source/dense.c include/dense.h include/llnltyps.h \
                 include/nvector.h include/llnlmath.h
-	(cd source; $(COMPILER) $(OPTS) -c dense.c)
+	(cd source; $(PURIFY) $(COMPILER) $(OPTS) -c dense.c)
  
 source/cvband.o: source/cvband.c include/cvband.h include/cvode.h \
                  include/band.h include/llnltyps.h include/nvector.h \
                  include/llnlmath.h
-	(cd source; $(COMPILER) $(OPTS) -c cvband.c)
+	(cd source; $(PURIFY) $(COMPILER) $(OPTS) -c cvband.c)
  
 source/band.o: source/band.c include/band.h include/llnltyps.h \
                include/nvector.h include/llnlmath.h
-	(cd source; $(COMPILER) $(OPTS) -c band.c)
+	(cd source; $(PURIFY) $(COMPILER) $(OPTS) -c band.c)
  
 source/cvdiag.o: source/cvdiag.c include/cvdiag.h  include/cvode.h \
                  include/llnltyps.h include/nvector.h
-	(cd source; $(COMPILER) $(OPTS) -c cvdiag.c)
+	(cd source; $(PURIFY) $(COMPILER) $(OPTS) -c cvdiag.c)
  
 source/cvspgmr.o: source/cvspgmr.c include/cvspgmr.h include/cvode.h \
                   include/llnltyps.h include/nvector.h include/llnlmath.h \
                   include/iterativ.h include/spgmr.h
-	(cd source; $(COMPILER) $(OPTS) -c cvspgmr.c)
+	(cd source; $(PURIFY) $(COMPILER) $(OPTS) -c cvspgmr.c)
  
 source/spgmr.o: source/spgmr.c include/spgmr.h include/iterativ.h \
                 include/llnltyps.h include/nvector.h include/llnlmath.h 
-	(cd source; $(COMPILER) $(OPTS) -c spgmr.c)
+	(cd source; $(PURIFY) $(COMPILER) $(OPTS) -c spgmr.c)
  
 source/iterativ.o: source/iterativ.c include/iterativ.h include/llnltyps.h \
                    include/nvector.h include/llnlmath.h
-	(cd source; $(COMPILER) $(OPTS) -c iterativ.c)
+	(cd source; $(PURIFY) $(COMPILER) $(OPTS) -c iterativ.c)
  
 source/cvbandpre.o: source/cvbandpre.c include/cvbandpre.h include/cvode.h \
                     include/nvector.h include/llnltyps.h include/llnlmath.h \
                     include/band.h 
-	(cd source; $(COMPILER) $(OPTS) -c cvbandpre.c)
+	(cd source; $(PURIFY) $(COMPILER) $(OPTS) -c cvbandpre.c)
  
 source/nvector.o: source/nvector.c include/nvector.h include/llnltyps.h \
                  include/llnlmath.h
-	(cd source; $(COMPILER) $(OPTS) -c nvector.c)
+	(cd source; $(PURIFY) $(COMPILER) $(OPTS) -c nvector.c)
  
 source/llnlmath.o: source/llnlmath.c include/llnlmath.h include/llnltyps.h
-	(cd source; $(COMPILER) $(OPTS) -c llnlmath.c)
+	(cd source; $(PURIFY) $(COMPILER) $(OPTS) -c llnlmath.c)
 
 $(OBJS): Makefile
 
diff --git a/ext/f2c_blas/Makefile.in b/ext/f2c_blas/Makefile.in
index eb0f1f731..4f97af69f 100755
--- a/ext/f2c_blas/Makefile.in
+++ b/ext/f2c_blas/Makefile.in
@@ -13,6 +13,8 @@
 
 do_ranlib = @DO_RANLIB@
 
+PURIFY=@PURIFY@
+
 # the directory where the Cantera libraries are located
 CANTERA_LIBDIR=@buildlib@
 
@@ -41,7 +43,7 @@ CXX_INCLUDES=-I../f2c_libs
 
 # How to compile a C file
 .c.o:
-	@CC@ -c $< @DEFS@ $(CFLAGS) $(CXX_INCLUDES)
+	$(PURIFY) @CC@ -c $< @DEFS@ $(CFLAGS) $(CXX_INCLUDES)
 
 
 # -----------------------------------------------
diff --git a/ext/f2c_lapack/Makefile.in b/ext/f2c_lapack/Makefile.in
index bb2292ad7..bc3c1cc5f 100755
--- a/ext/f2c_lapack/Makefile.in
+++ b/ext/f2c_lapack/Makefile.in
@@ -11,6 +11,8 @@
 
 do_ranlib = @DO_RANLIB@
 
+PURIFY=@PURIFY@
+
 # the directory where the Cantera libraries are located
 CANTERA_LIBDIR=@buildlib@
 
@@ -35,7 +37,7 @@ CXX_INCLUDES=-I../f2c_libs
 	@CXX_DEPENDS@  $(CFLAGS) $(CXX_INCLUDES) $*.c > $*.d
 
 .c.o:
-	@CC@ -c $< $(CFLAGS) $(CXX_INCLUDES)
+	$(PURIFY) @CC@ -c $< $(CFLAGS) $(CXX_INCLUDES)
 
 # -----------------------------------------------
 
diff --git a/ext/f2c_math/Makefile.in b/ext/f2c_math/Makefile.in
index b1bb0f125..ec0bf569b 100644
--- a/ext/f2c_math/Makefile.in
+++ b/ext/f2c_math/Makefile.in
@@ -10,6 +10,9 @@
 .SUFFIXES : .c .cpp .d .o
 
 do_ranlib = @DO_RANLIB@
+
+PURIFY=@PURIFY@
+
 # the directory where the Cantera libraries are located
 CANTERA_LIBDIR=@buildlib@
 
@@ -39,11 +42,11 @@ CXX_INCLUDES=-I../f2c_libs
 
 # How to compile a C file
 .c.o:
-	@CC@ -c $< @DEFS@ $(CFLAGS) $(CXX_INCLUDES)
+	$(PURIFY) @CC@ -c $< @DEFS@ $(CFLAGS) $(CXX_INCLUDES)
 
 # How to compile a Cpp file
 .cpp.o:
-	@CXX@ -c $< @DEFS@ $(CXX_FLAGS) $(CXX_INCLUDES)
+	$(PURIFY) @CXX@ -c $< @DEFS@ $(CXX_FLAGS) $(CXX_INCLUDES)
 
 
 # -----------------------------------------------
diff --git a/ext/f2c_recipes/Makefile.in b/ext/f2c_recipes/Makefile.in
index 098c0929e..c80c4e397 100644
--- a/ext/f2c_recipes/Makefile.in
+++ b/ext/f2c_recipes/Makefile.in
@@ -11,6 +11,8 @@
 
 do_ranlib = @DO_RANLIB@
 
+PURIFY=@PURIFY@
+
 # the directory where the Cantera libraries are located
 CANTERA_LIBDIR=@buildlib@
 
@@ -36,7 +38,7 @@ CXX_INCLUDES=-I../f2c_libs
 
 # How to compile a C file
 .c.o:
-	@CC@ -c $< @DEFS@ $(CXX_FLAGS) $(CXX_INCLUDES)
+	$(PURIFY) @CC@ -c $< @DEFS@ $(CXX_FLAGS) $(CXX_INCLUDES)
 
 # -----------------------------------------------
 
diff --git a/ext/lapack/Makefile.in b/ext/lapack/Makefile.in
index 3cc8c9944..cd8a109f9 100755
--- a/ext/lapack/Makefile.in
+++ b/ext/lapack/Makefile.in
@@ -10,6 +10,8 @@ LAPACKLIB = @buildlib@/libctlapack.a
 
 do_ranlib = @DO_RANLIB@
 
+PURIFY=@PURIFY@
+
 PIC_FLAG=@PIC@
 
 F_FLAGS = @FFLAGS@ $(PIC_FLAG)
@@ -78,7 +80,7 @@ ifeq ($(do_ranlib),1)
 endif
 
 %.o : %.f
-	@F77@ -c $<  $(F77_INCLUDES) $(F_FLAGS) 
+	$(PURIFY) @F77@ -c $<  $(F77_INCLUDES) $(F_FLAGS) 
 
 $(OBJS): Makefile
 
diff --git a/ext/math/Makefile.in b/ext/math/Makefile.in
index 41efc80ad..b952cefe8 100755
--- a/ext/math/Makefile.in
+++ b/ext/math/Makefile.in
@@ -13,6 +13,9 @@ do_ranlib = @DO_RANLIB@
 LIB = @buildlib@/libctmath.a
 
 all: $(LIB)
+
+PURIFY=@PURIFY@
+
 PIC_FLAG=@PIC@
 
 F_FLAGS = @FFLAGS@ $(PIC_FLAG)
@@ -50,13 +53,13 @@ ifeq ($(do_ranlib),1)
 endif
 
 %.o : %.c
-	@CXX@ -c $< @DEFS@  @CXXFLAGS@ @PIC@ -I../.. $(INCLUDES)
+	$(PURIFY) @CXX@ -c $< @DEFS@  @CXXFLAGS@ @PIC@ -I../.. $(INCLUDES)
 
 %.o : %.cpp
-	@CXX@ -c $< @DEFS@  @CXXFLAGS@ @PIC@ $(INCLUDES)
+	$(PURIFY) @CXX@ -c $< @DEFS@  @CXXFLAGS@ @PIC@ $(INCLUDES)
 
 %.o : %.f
-	@F77@ -c $< $(F_FLAGS)
+	$(PURIFY) @F77@ -c $< $(F_FLAGS)
 
 $(OBJS): Makefile
 
diff --git a/ext/recipes/Makefile.in b/ext/recipes/Makefile.in
index 6bd73bed1..54f8922fb 100755
--- a/ext/recipes/Makefile.in
+++ b/ext/recipes/Makefile.in
@@ -9,6 +9,9 @@
 LIB = @buildlib@/librecipes.a
 
 do_ranlib = @DO_RANLIB@
+
+PURIFY=@PURIFY@
+
 PIC_FLAG=@PIC@
 F_FLAGS = @FFLAGS@ $(PIC_FLAG)
 
@@ -25,7 +28,7 @@ ifeq ($(do_ranlib),1)
 endif
 
 %.o : %.f
-	@F77@ -c $< $(F_FLAGS)
+	$(PURIFY) @F77@ -c $< $(F_FLAGS)
 
 clean:
 	$(RM) $(OBJS) $(LIB)
diff --git a/ext/tpx/Makefile.in b/ext/tpx/Makefile.in
index d0330c02b..d849cd415 100755
--- a/ext/tpx/Makefile.in
+++ b/ext/tpx/Makefile.in
@@ -6,6 +6,9 @@
 .SUFFIXES : .cpp .d .o
 
 do_ranlib = @DO_RANLIB@
+
+PURIFY=@PURIFY@
+
 PIC_FLAG=@PIC@
 CXX_FLAGS = @CXXFLAGS@ $(CXX_OPT) $(PIC_FLAG)
 
@@ -24,10 +27,10 @@ all:  $(TPLIB) .depends
 	@CXX_DEPENDS@ $(CXX_INCLUDES) $*.cpp > $*.d
 
 .cpp.o:
-	@CXX@ -c $< @DEFS@ $(CXX_FLAGS) $(CXX_INCLUDES)
+	$(PURIFY) @CXX@ -c $< @DEFS@ $(CXX_FLAGS) $(CXX_INCLUDES)
 
 .f.o:
-	@F77@ -c $< $(F77_FLAGS) 
+	$(PURIFY) @F77@ -c $< $(F77_FLAGS) 
 
 $(TPLIB): $(COBJS) $(FOBJS)
 	@ARCHIVE@ $(TPLIB) $(COBJS) $(FOBJS) > /dev/null
diff --git a/test_problems/cathermo/HMW_graph_GvI/HMW_graph_GvI.cpp b/test_problems/cathermo/HMW_graph_GvI/HMW_graph_GvI.cpp
index 40f927a49..c58e27964 100644
--- a/test_problems/cathermo/HMW_graph_GvI/HMW_graph_GvI.cpp
+++ b/test_problems/cathermo/HMW_graph_GvI/HMW_graph_GvI.cpp
@@ -9,17 +9,11 @@
  *  $Revision$
  */
 
-#ifdef SRCDIRTREE
-#include "ct_defs.h"
-#include "logger.h"
-#include "HMWSoln.h"
-#else
 
 #include "Cantera.h"
 
 #include "kernel/logger.h"
 #include "HMWSoln.h"
-#endif
 
 #include <cstdio>
 
diff --git a/test_problems/fracCoeff/Makefile.in b/test_problems/fracCoeff/Makefile.in
index c232af0f6..275ee94ad 100644
--- a/test_problems/fracCoeff/Makefile.in
+++ b/test_problems/fracCoeff/Makefile.in
@@ -23,6 +23,8 @@ LINK_OPTIONS = @EXTRA_LINK@
 
 #############################################################################
 
+PURIFY=@PURIFY@
+
 # Check to see whether we are in the msvc++ environment
 os_is_win = @OS_IS_WIN@
 
@@ -56,7 +58,7 @@ LCXX_FLAGS = -L$(CANTERA_LIBDIR) @LOCAL_LIB_DIRS@ @CXXFLAGS@
 
 # How to compile C++ source files to object files
 .@CXX_EXT@.@OBJ_EXT@: Interface.h
-	$(CXX) -c $< -I$(CANTERA_INCDIR) $(CXX_FLAGS)
+	$(PURIFY) $(CXX) -c $< -I$(CANTERA_INCDIR) $(CXX_FLAGS)
 
 # How to compile the dependency file
 .cpp.d:
@@ -73,7 +75,7 @@ all: $(PROGRAM)
 
 # Rule to make the program
 $(PROGRAM): $(OBJS) $(CANTERA_LIBDIR)/libctbase.a 
-	$(CXX) -o $(PROGRAM) $(OBJS) $(LCXX_FLAGS) $(LINK_OPTIONS) \
+	$(PURIFY) $(CXX) -o $(PROGRAM) $(OBJS) $(LCXX_FLAGS) $(LINK_OPTIONS) \
                   $(CANTERA_LIBS) @LIBS@ $(FORT_LIBS) \
                   $(LCXX_END_LIBS)
 
diff --git a/test_problems/silane_equil/Makefile.in b/test_problems/silane_equil/Makefile.in
index 56662bfa4..9fb9af396 100644
--- a/test_problems/silane_equil/Makefile.in
+++ b/test_problems/silane_equil/Makefile.in
@@ -33,6 +33,8 @@ else
 FORT_LIBS =
 endif
 
+PURIFY=@PURIFY@
+
 # the C++ compiler
 CXX = @CXX@
 
@@ -56,7 +58,7 @@ LCXX_FLAGS = -L$(CANTERA_LIBDIR) @LOCAL_LIB_DIRS@ @CXXFLAGS@
 
 # How to compile C++ source files to object files
 .@CXX_EXT@.@OBJ_EXT@:
-	$(CXX) -c $< -I$(CANTERA_INCDIR) @CXX_INCLUDES@ $(CXX_FLAGS)
+	$(PURIFY) $(CXX) -c $< -I$(CANTERA_INCDIR) @CXX_INCLUDES@ $(CXX_FLAGS)
 
 # How to compile the dependency file
 .cpp.d:
@@ -68,10 +70,10 @@ DEPENDS=$(OBJS:.o=.d)
 # Program Name
 PROGRAM = $(PROG_NAME)$(EXE_EXT)
 
-all: $(PROGRAM)
+all: .depends $(PROGRAM)
 
 $(PROGRAM): $(OBJS) $(CANTERA_LIBDIR)/libctbase.a
-	$(CXX) -o $(PROGRAM) $(OBJS) $(LCXX_FLAGS) $(LINK_OPTIONS) \
+	$(PURIFY) $(CXX) -o $(PROGRAM) $(OBJS) $(LCXX_FLAGS) $(LINK_OPTIONS) \
                   $(CANTERA_LIBS) @LIBS@ $(FORT_LIBS) \
                   $(LCXX_END_LIBS)
 
diff --git a/tools/src/Makefile.in b/tools/src/Makefile.in
index 9829595ba..72b8cadb1 100755
--- a/tools/src/Makefile.in
+++ b/tools/src/Makefile.in
@@ -5,6 +5,8 @@ INCDIR = -I@ctroot@/Cantera/src/
 BINDIR = @buildbin@
 build_ck = @BUILD_CK@
 
+PURIFY=@PURIFY@
+
 LCXX_FLAGS = -L$(LIBDIR)  @LOCAL_LIB_DIRS@ @CXXFLAGS@
 LOCAL_LIBS = @LOCAL_LIBS@ #-lcantera -ltpx -lctcxx 
 #LOCAL_LIBS = -lcantera @math_libs@ @BLAS_LAPACK_LIBS@ -lctcxx 
@@ -26,7 +28,7 @@ exes = $(progs)
 endif
 
 .cpp.o:
-	@CXX@ -c $< @DEFS@  $(INCDIR)base $(INCDIR)converters @CXX_INCLUDES@ @CXXFLAGS@ $(CXX_FLAGS) 
+	$(PURIFY) @CXX@ -c $< @DEFS@  $(INCDIR)base $(INCDIR)converters @CXX_INCLUDES@ @CXXFLAGS@ $(CXX_FLAGS) 
 
 all: $(exes)
 
@@ -34,17 +36,17 @@ ck: $(BINDIR)/ck2cti
 
 $(BINDIR)/ck2cti: ck2cti.o $(CONVLIB_DEP) 
 	$(RM) $(BINDIR)/ck2cti
-	@CXX@ -o $(BINDIR)/ck2cti ck2cti.o $(LCXX_FLAGS) \
+	$(PURIFY) @CXX@ -o $(BINDIR)/ck2cti ck2cti.o $(LCXX_FLAGS) \
                -lconverters -lctbase -ltpx -lctcxx $(LOCAL_LIBS) $(LCXX_END_LIBS)
 
 $(BINDIR)/cti2ctml: cti2ctml.o 
 	$(RM) $(BINDIR)/cti2ctml
-	@CXX@ -o $(BINDIR)/cti2ctml cti2ctml.o $(LCXX_FLAGS) $(LOCAL_LIBS) \
+	$(PURIFY) @CXX@ -o $(BINDIR)/cti2ctml cti2ctml.o $(LCXX_FLAGS) $(LOCAL_LIBS) \
                $(LCXX_END_LIBS)
 
 $(BINDIR)/fixtext: fixtext.o 
 	$(RM) $(BINDIR)/fixtext
-	@CXX@ -o $(BINDIR)/fixtext fixtext.o $(LCXX_FLAGS) \
+	$(PURIFY) @CXX@ -o $(BINDIR)/fixtext fixtext.o $(LCXX_FLAGS) \
                $(LOCAL_LIBS) $(LCXX_END_LIBS)
 
 $(CONVLIB_DEP):
diff --git a/tools/testtools/Makefile.in b/tools/testtools/Makefile.in
index b0e688c5a..945b9857b 100644
--- a/tools/testtools/Makefile.in
+++ b/tools/testtools/Makefile.in
@@ -6,6 +6,8 @@ BINDIR = @ctroot@/bin
 BBINDIR = @buildbin@
 build_ck = @BUILD_CK@
 
+PURIFY=@PURIFY@
+
 LCXX_FLAGS = -L$(LIBDIR)  @LOCAL_LIB_DIRS@ @CXXFLAGS@
 LOCAL_LIBS = -lcantera -lckreader @math_libs@ @LAPACK_LIBRARY@ @BLAS_LIBRARY@ -lctcxx
 
@@ -22,12 +24,12 @@ CONFIGDEFS=@DEFS@
 # not be needed here anyway.
 
 .cpp.o:
-	@CXX@ -c $< -I$(INCDIR) @CXXFLAGS@ -O0
+	$(PURIFY) @CXX@ -c $< -I$(INCDIR) @CXXFLAGS@ -O0
 
 all: $(BINDIR)/csvdiff $(BBINDIR)/csvdiff
 
 $(BINDIR)/csvdiff: mdp_allo.o csvdiff.o tok_input_util.o
-	@CXX@ -o $(BINDIR)/csvdiff  mdp_allo.o csvdiff.o tok_input_util.o \
+	$(PURIFY) @CXX@ -o $(BINDIR)/csvdiff  mdp_allo.o csvdiff.o tok_input_util.o \
 	 $(LCXX_FLAGS) $(LCXX_END_LIBS) 
 
 $(BBINDIR)/csvdiff: $(BINDIR)/csvdiff