diff --git a/Cantera/Makefile.am b/Cantera/Makefile.am
index bc93f0db6..c9ac09f25 100644
--- a/Cantera/Makefile.am
+++ b/Cantera/Makefile.am
@@ -1,4 +1,4 @@
 # $Id: $
 
 # will need to add python and matlab 
-SUBDIRS                 = src
+SUBDIRS                 = src user
diff --git a/Cantera/user/Makefile.am b/Cantera/user/Makefile.am
new file mode 100644
index 000000000..f65351db9
--- /dev/null
+++ b/Cantera/user/Makefile.am
@@ -0,0 +1,17 @@
+cc_sources              = user.cpp
+
+INCLUDES                = -I$(top_builddir)/build/include/ -I$(top_builddir)/build/include/cantera
+AM_CXXFLAGS             = $(INCLUDES)
+
+lib_LTLIBRARIES         = $(top_builddir)/build/lib/libuser.la
+library_includedir      = $(top_builddir)/build/include
+library_include_HEADERS = $(h_sources)
+
+#-----------------------
+# Cantera Converters C/C++ library
+#-----------------------
+
+__top_builddir__build_lib_libuser_la_LDFLAGS      = $(all_libraries) -release $(GENERIC_RELEASE)
+__top_builddir__build_lib_libuser_la_SOURCES      = $(cc_sources) $(h_sources)
+
+CLEANFILES = *.o
diff --git a/Cantera/user/Makefile.in b/Cantera/user/Makefile.in
deleted file mode 100644
index 2160a2aa5..000000000
--- a/Cantera/user/Makefile.in
+++ /dev/null
@@ -1,66 +0,0 @@
-#/bin/sh
-###############################################################
-#  $Author: hkmoffa $
-#  $Date: 2008/01/01 19:19:50 $
-#  $Revision: 1.7 $
-#
-#  Copyright 2002 California Institute of Technology
-#
-###############################################################
-
-###############################################################
-# list your object files here
-# This is probably the only thing you need to change in this file.
-
-OBJS    = user.o
-
-###############################################################
-
-.SUFFIXES :
-.SUFFIXES : .cpp .d .o
-
-OBJDIR = .
-PIC_FLAG=@PIC@
-CXX_FLAGS = @CXXFLAGS@ $(CXX_OPT) $(PIC_FLAG)
-
-
-CXX_INCLUDES = -I../src/base
-
-LIB = @buildlib@/libuser.a
-
-DEPENDS = $(OBJS:.o=.d)
-
-%.d: Makefile %.o
-	@CXX_DEPENDS@ $(CXX_INCLUDES) $*.cpp > $*.d
-
-.cpp.o:
-	@CXX@ -c $< $(CXX_FLAGS) $(CXX_INCLUDES)
-
-.f.o:
-	@F77@ -c $< $(F77_FLAGS) 
-
-all lib: $(LIB)
-
-$(LIB): $(OBJS)
-	@ARCHIVE@ $(LIB) $(OBJS) > /dev/null
-
-clean:
-	$(RM) *.o *~ $(LIB)
-
-depends:
-	@MAKE@ .depends
-
-.depends: $(DEPENDS)
-	cat *.d > .depends
-
-$(OBJS): Makefile
-
-install:
-
-TAGS: 
-	etags *.h *.cpp
-
-ifeq ($(wildcard .depends), .depends)
-include .depends
-endif
-
diff --git a/configure.ac b/configure.ac
index f819c2875..c3436b96b 100644
--- a/configure.ac
+++ b/configure.ac
@@ -61,8 +61,11 @@ AC_OUTPUT(Makefile examples/Makefile                                       \
 		   ext/Makefile                                            \
 		   ext/tpx/Makefile                                        \
 		   ext/math/Makefile                                       \
+		   ext/cvode/Makefile                                      \
 		   Cantera/Makefile                                        \
-                   Cantera/src/Makefile Cantera/src/base/Makefile          \
+                   Cantera/user/Makefile                                   \
+                   Cantera/src/Makefile                                    \
+                   Cantera/src/base/Makefile                               \
                    Cantera/src/converters/Makefile                         \
 		   Cantera/src/kinetics/Makefile                           \
                    Cantera/src/numerics/Makefile Cantera/src/oneD/Makefile \
diff --git a/examples/cxx/Makefile.am b/examples/cxx/Makefile.am
index 33dc42f22..da8f90421 100644
--- a/examples/cxx/Makefile.am
+++ b/examples/cxx/Makefile.am
@@ -7,7 +7,8 @@ cc_sources = examples.cpp kinetics_example1.cpp kinetics_example2.cpp \
 
 LINK                 = -lkinetics -ltransport -lthermo -lctnumerics
 LINK                += -lctbase -ltpx -lctmath -lconverters 
-# -luser -lcvode -lctlapack -lctblas -lctf2c -lctcxx -luser -lstdc++
+LINK                += -luser
+# -lcvode -lctlapack -lctblas -lctf2c -lctcxx -luser -lstdc++
 
 LIBS                 = -L$(top_builddir)/build/lib/ $(LINK)
 
diff --git a/ext/CMakeLists.txt b/ext/CMakeLists.txt
deleted file mode 100644
index 42207b639..000000000
--- a/ext/CMakeLists.txt
+++ /dev/null
@@ -1,12 +0,0 @@
-SET (CMAKE_C_FLAGS  -DSkip_f2c_Undefs)
-
-INCLUDE_DIRECTORIES (${PROJECT_SOURCE_DIR}/ext/f2c_libs )
-
-add_subdirectory ( f2c_libs )
-add_subdirectory ( f2c_blas )
-add_subdirectory ( f2c_lapack )
-add_subdirectory ( f2c_math )
-add_subdirectory ( cvode )
-add_subdirectory ( tpx )
-
-
diff --git a/ext/Makefile.am b/ext/Makefile.am
index da562fe76..f6374a334 100644
--- a/ext/Makefile.am
+++ b/ext/Makefile.am
@@ -1,2 +1,2 @@
-SUBDIRS                 = tpx math
+SUBDIRS                 = tpx math cvode
 
diff --git a/ext/Makefile.in b/ext/Makefile.in
deleted file mode 100755
index f01d5573b..000000000
--- a/ext/Makefile.in
+++ /dev/null
@@ -1,593 +0,0 @@
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-
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-# This Makefile.in is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
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diff --git a/ext/cvode/Makefile.in b/ext/cvode/Makefile.in
deleted file mode 100755
index ef438dc2b..000000000
--- a/ext/cvode/Makefile.in
+++ /dev/null
@@ -1,104 +0,0 @@
-#
-# $Source: /cvsroot/cantera/cantera/ext/cvode/Makefile.in,v $
-# $Author: hkmoffa $
-# $Revision: 1.10 $
-# $Date: 2008/12/30 21:49:42 $
-#
-#----------------------------------------------------------------------------
-#                                CVODE                                      
-#----------------------------------------------------------------------------
-# This file will compile all the CVODE modules in order to make the Unix
-# library cvodelib.a. All object (.o) files are removed after the library
-# has been created. 
-#
-# The following variables are used:
-#
-# COMPILER - set to use the gcc compiler
-# OPTS     - list of compiler options
-# OBJS     - list of object files in cvodelib.a
-#
-# Modify the COMPILER and OPTS variables as needed.
-#
-do_ranlib = @DO_RANLIB@
-
-all: @buildlib@/libcvode.a
-
-PURIFY=@PURIFY@
-
-PIC_FLAG=@PIC@
-   
-COMPILER = @CC@
-
-OPTS = -I../include @CFLAGS@ $(CXX_OPT) $(PIC_FLAG)
-
-OBJS = source/cvode.o source/cvdense.o source/dense.o source/cvband.o \
-       source/band.o source/cvdiag.o source/cvspgmr.o source/spgmr.o  \
-       source/iterativ.o source/cvbandpre.o source/nvector.o source/llnlmath.o
-
-
-@buildlib@/libcvode.a: $(OBJS)
-	$(RM) @buildlib@/libcvode.a
-	(ar rcv @buildlib@/libcvode.a $(OBJS))
-ifeq ($(do_ranlib),1)
-	@RANLIB@ @buildlib@/libcvode.a
-endif
-
-source/cvode.o: source/cvode.c include/cvode.h include/llnltyps.h \
-                include/nvector.h include/llnlmath.h
-	(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; $(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; $(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; $(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; $(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; $(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; $(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; $(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; $(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; $(PURIFY) $(COMPILER) $(OPTS) -c cvbandpre.c)
- 
-source/nvector.o: source/nvector.c include/nvector.h include/llnltyps.h \
-                 include/llnlmath.h
-	(cd source; $(PURIFY) $(COMPILER) $(OPTS) -c nvector.c)
- 
-source/llnlmath.o: source/llnlmath.c include/llnlmath.h include/llnltyps.h
-	(cd source; $(PURIFY) $(COMPILER) $(OPTS) -c llnlmath.c)
-
-$(OBJS): Makefile
-
-clean:
-	$(RM)  @buildlib@/libcvode.a
-	$(RM)  $(OBJS)
-
-depends:
-