diff --git a/ChangeLog b/ChangeLog
deleted file mode 100644
index f30cbb68d..000000000
--- a/ChangeLog
+++ /dev/null
@@ -1 +0,0 @@
-6/14/12 Merging PECOS autotools branch with scons cantera 2.0
diff --git a/Makefile.am b/Makefile.am
deleted file mode 100644
index 5915a1bd9..000000000
--- a/Makefile.am
+++ /dev/null
@@ -1,16 +0,0 @@
-include $(top_srcdir)/doc/doxygen/aminclude.am
-
-# Build in these directories:
-SUBDIRS  = ext src test_problems
-SUBDIRS += doc
-
-# Distribute these directories:
-DISTDIRS = ext src test_problems doc include
-
-# generated documentation will be included in distributed archive
-EXTRA_DIST  = bootstrap $(DX_CONFIG)
-EXTRA_DIST += AUTHORS README
-
-# Support for pkgconfig
-pkgconfigdir   = $(libdir)/pkgconfig
-pkgconfig_DATA = cantera.pc
diff --git a/NEWS b/NEWS
deleted file mode 100644
index 5c6fb09ba..000000000
--- a/NEWS
+++ /dev/null
@@ -1,2 +0,0 @@
- 7/18/12 pecos development branch merged into 2.0 trunk
-11/10/11 cantera 2.0.0 development begins on autotools chain
\ No newline at end of file
diff --git a/bootstrap b/bootstrap
deleted file mode 100755
index 087348df3..000000000
--- a/bootstrap
+++ /dev/null
@@ -1,53 +0,0 @@
-#! /bin/sh
-#
-# bootstrap: Utility to easy autoconf/automake toolchain setup on
-#            checkout from revision control.
-#
-# Copyright (c) 2002  Daniel Elstner  <daniel.elstner@gmx.net>
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License VERSION 2 as
-# published by the Free Software Foundation.  You are not allowed to
-# use any other version of the license; unless you got the explicit
-# permission from the author to do so.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
-
-dir=`echo "$0" | sed 's,[^/]*$,,'`
-test "x${dir}" = "x" && dir='.'
-
-if test "x`cd "${dir}" 2>/dev/null && pwd`" != "x`pwd`"
-then
-    echo "This script must be executed directly from the source directory."
-    exit 1
-fi
-
-rm -f config.cache acconfig.h
-
-echo "- aclocal. (local)"     && \
-aclocal -I m4 -I m4/common    && \
-echo "- autoheader."          && \
-autoheader                    && \
-
-if type glibtoolize >/dev/null 2>&1; then
-    echo "- glibtool."
-    glibtoolize --automake --copy --force
-else
-    echo "- libtool."
-    libtoolize --automake --copy --force
-fi
-
-echo "- automake."            && \
-automake --add-missing --copy && \
-echo "- autoconf."            && \
-autoconf                      && \
-exit 0
-
-exit 1
diff --git a/cantera.pc.in b/cantera.pc.in
deleted file mode 100644
index 38c27adb9..000000000
--- a/cantera.pc.in
+++ /dev/null
@@ -1,24 +0,0 @@
-# cantera installation details
-prefix=/h2/topalian/workspace/cantera/install
-exec_prefix=${prefix}
-libdir=${exec_prefix}/lib
-includedir=${prefix}/include
-# Fortran compilation and linking information
-# Retrieve these using `pkg-config --variable=name cantera`
-#fflags=-I${exec_prefix}/lib
-#flibs=-L${exec_prefix}/lib -lfcantera -lcantera
-
-Name: cantera
-Description: An object-oriented software toolkit for chemical kinetics, thermodynamics, and transport processes.
-URL: http://code.google.com/p/cantera/
-Requires:
-Version: 2.0.1
-
-LINK  = -lctcxx -luser -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo  -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode -lctlapack -lctblas -lctf2c -lm -lstdc++
-
-#Libs: -L${libdir} ${LINK}
-#Cflags: -I${includedir}
-
-fflags=-I${exec_prefix}/lib -I${includedir}
-#fflags=-I${exec_prefix}/lib
-flibs=-L${exec_prefix}/lib ${LINK}
\ No newline at end of file
diff --git a/configure.ac b/configure.ac
deleted file mode 100644
index fc47622b5..000000000
--- a/configure.ac
+++ /dev/null
@@ -1,173 +0,0 @@
- -*- Autoconf -*-
-# Process this file with autoconf to produce a configure script.
-
-AC_PREREQ(2.61)
-AC_INIT([cantera], [2.2a], [nick@ices.utexas.edu])
-AC_CONFIG_HEADER(config.h)
-AC_CONFIG_AUX_DIR([build-aux])
-#AX_ENABLE_BUILDDIR
-AM_INIT_AUTOMAKE(-Wall -Werror -Wshadow)
-
-# snarf and provide versioning numbers
-AX_SPLIT_VERSION
-GENERIC_MAJOR_VERSION=$AX_MAJOR_VERSION
-GENERIC_MINOR_VERSION=$AX_MINOR_VERSION
-GENERIC_MICRO_VERSION=$AX_POINT_VERSION
-GENERIC_VERSION=$GENERIC_MAJOR_VERSION.$GENERIC_MINOR_VERSION.$GENERIC_MICRO_VERSION
-GENERIC_RELEASE=$GENERIC_MAJOR_VERSION.$GENERIC_MINOR_VERSION
-
-AC_SUBST(GENERIC_VERSION)
-AC_SUBST(GENERIC_MAJOR_VERSION)
-AC_SUBST(GENERIC_MINOR_VERSION)
-AC_SUBST(GENERIC_MICRO_VERSION)
-AC_SUBST(GENERIC_RELEASE)
-
-PACKAGE_DESCRIPTION="An object-oriented software toolkit for chemical kinetics, thermodynamics, and transport processes."
-AC_SUBST([PACKAGE_DESCRIPTION])
-PACKAGE_URL="http://code.google.com/p/cantera/"
-AC_SUBST([PACKAGE_URL])
-
-# add various Defines
-AC_DEFINE([LAPACK_FTN_TRAILING_UNDERSCORE],1,[Define to add underscore after fortran functions])
-LAPACK_FTN_TRAILING_UNDERSCORE=1
-AC_DEFINE([FTN_TRAILING_UNDERSCORE],1,[Define to add underscore after fortran functions])
-FTN_TRAILING_UNDERSCORE=1
-AC_DEFINE([LAPACK_NAMES_LOWERCASE],1,[Define to make lapack functions lowercase])
-LAPACK_NAMES_LOWERCASE=1
-AC_DEFINE([LAPACK_FTN_STRING_LEN_AT_END],1,[Define to add string to end of lapack functions])
-LAPACK_FTN_STRING_LEN_AT_END=1
-AC_DEFINE([INCL_PURE_FLUIDS],1,[Define to include pure fluids])
-INCL_PURE_FLUIDS=1
-AC_DEFINE([WITH_PURE_FLUIDS],1,[Define to include pure fluids])
-WITH_PURE_FLUIDS=1
-AC_DEFINE([WITH_LATTICE_SOLID],1,[Define to include Lattice Solids])
-WITH_LATTICE_SOLID=1
-AC_DEFINE([WITH_METAL],1,[Define to include metals])
-WITH_METAL=1
-AC_DEFINE([WITH_STOICH_SUBSTANCE],1,[Define to include stoichiometric substances])
-WITH_STOICH_SUBSTANCE=1
-AC_DEFINE([WITH_IDEAL_SOLUTIONS],1,[Define to include ideal solutions])
-WITH_IDEAL_SOLUTIONS=1
-
-AC_DEFINE_UNQUOTED([CANTERA_DATA], ["$prefix/data"],
-            [Default data directory])
-
-AC_CHECK_TYPES([uint8_t, uint16_t, uint32_t, int32_t, uint64_t, int64_t])
-AH_BOTTOM([
-typedef  double       doublereal;   // Fortran double precision
-typedef  int          integer;      // Fortran integer
-typedef  int          ftnlen;       // Fortran hidden string length type
-
-#define STRING_LEN_AT_END
-#define STORE_MOLE_FRACTIONS
-                                                                                                                                                            
-#ifdef DEBUG_MODE
-#define DEBUG_MODE_ENABLED 1
-#else
-#define DEBUG_MODE_ENABLED 0
-#endif
-])
-
-# ------------------------------
-# Checks for required programs
-# ------------------------------
-
-AC_PROG_CC
-AC_PROG_CXX
-AC_PROG_FC
-AC_PROG_F77
-
-AC_PROG_LIBTOOL
-AM_SANITY_CHECK
-
-# ----------------
-# Doxygen support 
-# ---------------- 
-
-DX_HTML_FEATURE(ON)
-DX_CHM_FEATURE(OFF)
-DX_CHI_FEATURE(OFF)
-
-DX_MAN_FEATURE(OFF)
-DX_RTF_FEATURE(OFF)
-DX_XML_FEATURE(OFF)
-DX_PDF_FEATURE(ON)
-DX_PS_FEATURE(OFF)
-DX_INIT_DOXYGEN(cantera, doc/doxygen/cantera.dox, docs) 
-
-# Generate Output Files
-AC_OUTPUT(Makefile                                                         \
-		   ext/Makefile                                            \
-		   ext/libexecstream/Makefile                              \
-                   ext/f2c_math/Makefile                                   \
-		   ext/f2c_libs/Makefile                                   \
-		   ext/f2c_libs/arithchk/Makefile                          \
-		   ext/f2c_blas/Makefile                                   \
-		   ext/f2c_lapack/Makefile                                 \
-		   ext/cvode/Makefile                                      \
-		   ext/cvode/source/Makefile                               \
-                   test_problems/Makefile                                  \
-                   test_problems/mixGasTransport/Makefile                  \
-                   test_problems/ChemEquil_gri_matrix/Makefile             \
-                   test_problems/ChemEquil_gri_pairs/Makefile              \
-                   test_problems/ChemEquil_ionizedGas/Makefile             \
-                   test_problems/ChemEquil_red1/Makefile                   \
-                   test_problems/CpJump/Makefile                           \
-                   test_problems/cxx_ex/Makefile                           \
-                   test_problems/diamondSurf/Makefile                      \
-                   test_problems/diamondSurf_dupl/Makefile                 \
-                   test_problems/fracCoeff/Makefile                        \
-                   test_problems/multiGasTransport/Makefile                \
-                   test_problems/negATest/Makefile                         \
-                   test_problems/NASA9poly_test/Makefile                   \
-                   test_problems/printUtilUnitTest/Makefile                \
-                   test_problems/pureFluidTest/Makefile                    \
-                   test_problems/silane_equil/Makefile                     \
-                   test_problems/spectroscopy/Makefile                     \
-                   test_problems/surfkin/Makefile                          \
-                   test_problems/surfSolverTest/Makefile                   \
-                   test_problems/VPsilane_test/Makefile                    \
-                   test_problems/VCSnonideal/Makefile                      \
-                   test_problems/cathermo/Makefile                         \
-                   test_problems/cathermo/DH_graph_1/Makefile              \
-                   test_problems/cathermo/HMW_dupl_test/Makefile           \
-                   test_problems/cathermo/HMW_graph_CpvT/Makefile          \
-                   test_problems/cathermo/HMW_graph_HvT/Makefile           \
-                   test_problems/cathermo/HMW_graph_GvI/Makefile           \
-                   test_problems/cathermo/HMW_graph_GvT/Makefile           \
-                   test_problems/cathermo/HMW_graph_VvT/Makefile           \
-                   test_problems/cathermo/HMW_test_1/Makefile              \
-                   test_problems/cathermo/HMW_test_3/Makefile              \
-                   test_problems/cathermo/ims/Makefile                     \
-                   test_problems/cathermo/issp/Makefile                    \
-                   test_problems/cathermo/stoichSubSSTP/Makefile           \
-                   test_problems/cathermo/testIAPWS/Makefile               \
-                   test_problems/cathermo/testIAPWSPres/Makefile           \
-                   test_problems/cathermo/testIAPWSTripP/Makefile          \
-                   test_problems/cathermo/testWaterPDSS/Makefile           \
-                   test_problems/cathermo/testWaterTP/Makefile             \
-                   test_problems/cathermo/VPissp/Makefile                  \
-                   test_problems/cathermo/wtWater/Makefile                 \
-                   test_problems/PecosTransport/Makefile                   \
-                   test_problems/statmech/Makefile                         \
-		   doc/Makefile                                            \
-		   doc/doxygen/Makefile                                    \
-		   src/Makefile                                            \
-                   src/fortran/Makefile                                    \
-                   src/base/Makefile                                       \
-		   src/kinetics/Makefile                                   \
-                   src/numerics/Makefile src/oneD/Makefile                 \
-                   src/thermo/Makefile                                     \
-		   src/transport/Makefile                                  \
-                   src/spectra/Makefile src/zeroD/Makefile                 \
-                   src/equil/Makefile                                      \
-                   src/tpx/Makefile                                        \
-		   cantera.pc)                                   
-
-# skipped tests
-#                   test_problems/rankine_democxx/Makefile                  
-#                   test_problems/VCSnonideal/NaCl_equil/Makefile           
-
-# FINAL SUMMARY
-AX_SUMMARIZE_CONFIG 
-
diff --git a/doc/Makefile.am b/doc/Makefile.am
deleted file mode 100644
index e234f652f..000000000
--- a/doc/Makefile.am
+++ /dev/null
@@ -1 +0,0 @@
-SUBDIR = doxygen
diff --git a/doc/doxygen/Makefile.am b/doc/doxygen/Makefile.am
deleted file mode 100644
index 33a820a45..000000000
--- a/doc/doxygen/Makefile.am
+++ /dev/null
@@ -1,7 +0,0 @@
-EXTRA_DIST  = Cantera.txt cantera.page cantera.doc cantera.sty cantera.dox Makefile.am
-
-DISTDIRS=txt_common
-
-dist-hook:
-	rm -rf `find $(distdir)/ -name .svn`
-	rm -rf `find $(distdir)/ -name .deps`
diff --git a/ext/Makefile.am b/ext/Makefile.am
deleted file mode 100644
index 40a6dbc8a..000000000
--- a/ext/Makefile.am
+++ /dev/null
@@ -1 +0,0 @@
-SUBDIRS =   libexecstream f2c_math f2c_libs f2c_blas f2c_lapack cvode
\ No newline at end of file
diff --git a/ext/cvode/Makefile.am b/ext/cvode/Makefile.am
deleted file mode 100644
index e5abaf427..000000000
--- a/ext/cvode/Makefile.am
+++ /dev/null
@@ -1 +0,0 @@
-SUBDIRS=source
diff --git a/ext/cvode/source/Makefile.am b/ext/cvode/source/Makefile.am
deleted file mode 100644
index 31f71f080..000000000
--- a/ext/cvode/source/Makefile.am
+++ /dev/null
@@ -1,24 +0,0 @@
-cc_sources              = band.c cvband.c cvbandpre.c cvdense.c cvdiag.c   \
-                          cvode.c cvspgmr.c dense.c iterativ.c llnlmath.c  \
-	                  nvector.c spgmr.c
-
-h_sources               = 
-AM_CPPFLAGS             = -I../include
-AM_CXXFLAGS             = $(AM_CPPFLAGS)
-AM_FCFLAGS              = $(AM_CPPFLAGS)
-
-lib_LTLIBRARIES         = $(top_builddir)/build/lib/libcvode.la
-library_includedir      = $(top_builddir)/include
-library_include_HEADERS = $(h_sources)
-
-#-----------------------
-# Cantera Converters C/C++ library
-#-----------------------
-
-__top_builddir__build_lib_libcvode_la_LDFLAGS      = $(all_libraries) -release $(GENERIC_RELEASE)
-__top_builddir__build_lib_libcvode_la_SOURCES      = $(fc_sources) $(cc_sources)
-
-__top_builddir__build_lib_libcvode_include_HEADERS = $(h_sources)
-__top_builddir__build_lib_libcvode_includedir = $(prefix)/include
-
-CLEANFILES = *.o
diff --git a/ext/f2c_blas/Makefile.am b/ext/f2c_blas/Makefile.am
deleted file mode 100644
index 140934079..000000000
--- a/ext/f2c_blas/Makefile.am
+++ /dev/null
@@ -1,63 +0,0 @@
-cc_sources = \
-dasum.c \
-daxpy.c \
-dcabs1.c \
-dcopy.c \
-ddot.c \
-dgbmv.c \
-dgemm.c \
-dgemv.c \
-dger.c \
-dnrm2.c \
-drot.c \
-drotg.c \
-drotm.c \
-drotmg.c \
-dsbmv.c \
-dscal.c \
-dsdot.c \
-dspmv.c \
-dspr.c \
-dspr2.c \
-dswap.c \
-dsymm.c \
-dsymv.c \
-dsyr.c \
-dsyr2.c \
-dsyr2k.c \
-dsyrk.c \
-dtbmv.c \
-dtbsv.c \
-dtpmv.c \
-dtpsv.c \
-dtrmm.c \
-dtrmv.c \
-dtrsm.c \
-dtrsv.c \
-dzasum.c \
-dznrm2.c \
-idamax.c \
-lsame.c \
-xerbla.c 
-
-h_sources               = blaswrap.h
-
-AM_CPPFLAGS             = -I../f2c_libs
-AM_CXXFLAGS             = $(AM_CPPFLAGS)
-AM_FCFLAGS              = $(AM_CPPFLAGS)
-
-lib_LTLIBRARIES         = $(top_builddir)/build/lib/libctblas.la
-library_includedir      = $(top_builddir)/include
-library_include_HEADERS = $(h_sources)
-
-#-----------------------
-# Cantera Converters C/C++ library
-#-----------------------
-
-__top_builddir__build_lib_libctblas_la_LDFLAGS      = $(all_libraries) -release $(GENERIC_RELEASE)
-__top_builddir__build_lib_libctblas_la_SOURCES      = $(cc_sources) $(h_sources)
-
-__top_builddir__build_lib_libctblas_include_HEADERS = $(h_sources)
-__top_builddir__build_lib_libctblas_includedir = $(prefix)/include
-
-CLEANFILES = *.o
diff --git a/ext/f2c_lapack/Makefile.am b/ext/f2c_lapack/Makefile.am
deleted file mode 100644
index 2771f586a..000000000
--- a/ext/f2c_lapack/Makefile.am
+++ /dev/null
@@ -1,38 +0,0 @@
-cc_sources = dbdsqr.c dgbtrf.c dgbtf2.c dgbtrs.c dgbsv.c dgebd2.c dgebrd.c  \
-             dgelq2.c dgelqf.c dgelss.c dgeqr2.c dgeqrf.c dgetf2.c dgetrf.c \
-             dgetri.c dgetrs.c dlabad.c dlabrd.c dlacpy.c dlamch.c dlange.c \
-             dlapy2.c dlarf.c dlarfb.c dlarfg.c dlarft.c dlartg.c dlas2.c   \
-             dlascl.c dlaset.c dlasq1.c dlasq2.c dlasq3.c dlasq4.c dlasq5.c \
-             dlasq6.c dlasr.c dlasrt.c dlassq.c dlasv2.c dlaswp.c dorg2r.c  \
-             dorgbr.c dorgl2.c dorglq.c dorgqr.c dorm2r.c dormbr.c dorml2.c \
-             dormlq.c dormqr.c drscl.c dtrtri.c dtrti2.c ieeeck.c ilaenv.c  \
-	     dpotrs.c dtrtrs.c dgbcon.c dgecon.c dlatrs.c dlatbs.c dlacon.c \
-             dtrcon.c dlantr.c dpotrf.c dpotf2.c
-
-h_sources               = blaswrap.h
-
-AM_CPPFLAGS             = -I../f2c_libs
-AM_CXXFLAGS             = $(AM_CPPFLAGS)
-AM_FCFLAGS              = $(AM_CPPFLAGS)
-
-lib_LTLIBRARIES         = $(top_builddir)/build/lib/libctlapack.la
-library_includedir      = $(top_builddir)/include
-library_include_HEADERS = $(h_sources)
-
-#-----------------------
-# Cantera Converters C/C++ library
-#-----------------------
-
-__top_builddir__build_lib_libctlapack_la_LDFLAGS      = $(all_libraries) -release $(GENERIC_RELEASE)
-__top_builddir__build_lib_libctlapack_la_SOURCES      = $(cc_sources) $(h_sources)
-
-__top_builddir__build_lib_libctlapack_include_HEADERS = $(h_sources)
-__top_builddir__build_lib_libctlapack_includedir = $(prefix)/include
-
-
-CLEANFILES = *.o
-
-# header file accumulation
-#all:
-#	@echo copying headers $<
-#	cp -p *.h $(top_builddir)/build/include/
diff --git a/ext/f2c_libs/Makefile.am b/ext/f2c_libs/Makefile.am
deleted file mode 100644
index 787d07786..000000000
--- a/ext/f2c_libs/Makefile.am
+++ /dev/null
@@ -1,66 +0,0 @@
-SUBDIRS = arithchk
-
-cc_sources              = abort_.c c_log.c d_atn2.c dfe.c d_prod.c \
-                          due.c exit_.c getenv_.c hl_le.c i_dim.c  \
-                          inquire.c lread.c pow_ii.c r_acos.c      \
-                          r_dim.c r_nint.c r_tan.c                 \
-                          uninit.c z_abs.c close.c                 \
-                          d_cnjg.c d_imag.c d_sign.c ef1asc_.c     \
-                          f77_aloc.c h_abs.c hl_lt.c i_dnnt.c      \
-                          i_sign.c lwrite.c r_asin.c               \
-                          rewind.c rsfe.c r_tanh.c util.c \
-                          z_cos.c backspac.c c_sin.c d_cos.c       \
-                          d_int.c d_sin.c ef1cmc_.c f77vers.c      \
-                          h_dim.c h_mod.c i_indx.c lbitbits.c      \
-                          pow_ri.c r_atan.c r_exp.c r_sign.c       \
-                          s_cat.c s_rnge.c wref.c z_div.c c_abs.c  \
-	                  c_sqrt.c d_cosh.c d_lg10.c d_sinh.c      \
-                          endfile.c fmt.c h_dnnt.c h_nint.c iio.c  \
-                          lbitshft.c open.c pow_zi.c r_atn2.c      \
-                          r_imag.c r_sin.c s_cmp.c s_stop.c        \
-                          wrtfmt.c z_exp.c cabs.c d_abs.c d_dim.c  \
-                          d_log.c d_sqrt.c fmtlib.c h_indx.c\
-                          h_sign.c i_len.c l_ge.c pow_ci.c pow_zz.c\
-                          r_cnjg.c r_int.c r_sinh.c s_copy.c sue.c \
-                          wsfe.c z_log.c c_cos.c d_acos.c \
-                          d_mod.c d_tan.c                   \
-                          h_len.c i77vers.c ilnw.c l_gt.c pow_dd.c \
-                          r_cos.c r_lg10.c rsli.c sfe.c \
-                          system_.c wsle.c z_sin.c c_div.c d_asin.c\
-                          d_nint.c d_tanh.c err.c ftell_.c\
-                          hl_ge.c i_abs.c i_mod.c l_le.c pow_di.c  \
-                          r_cosh.c r_log.c rsne.c                  \
-                          sig_die.c typesize.c wsne.c z_sqrt.c     \
-                          c_exp.c d_atan.c d_exp.c dolio.c dtime_.c\
-                          etime_.c hl_gt.c                         \
-                          i_nint.c l_lt.c pow_hh.c r_abs.c rdfmt.c \
-                          r_mod.c r_sqrt.c signal_.c uio.c xwsne.c 
-
-h_sources               = 
-
-AM_CPPFLAGS             = -I.
-AM_CXXFLAGS             = $(AM_CPPFLAGS)
-AM_FCFLAGS              = $(AM_CPPFLAGS)
-
-lib_LTLIBRARIES         = $(top_builddir)/build/lib/libctf2c.la
-library_includedir      = $(top_builddir)/include
-library_include_HEADERS = $(h_sources)
-
-#-----------------------
-# Cantera Converters C/C++ library
-#-----------------------
-
-__top_builddir__build_lib_libctf2c_la_LDFLAGS      = $(all_libraries) -release $(GENERIC_RELEASE)
-__top_builddir__build_lib_libctf2c_la_SOURCES      = $(cc_sources) $(h_sources)
-
-__top_builddir__build_lib_libctf2c_include_HEADERS = $(h_sources)
-__top_builddir__build_lib_libctf2c_includedir = $(prefix)/include
-
-
-# header file accumulation
-all:
-	@echo copying headers $<
-	cp -p sysdep1.h0 sysdep1.h
-	cp -p signal1.h0 signal1.h
-
-CLEANFILES = *.o
diff --git a/ext/f2c_libs/arithchk/Makefile.am b/ext/f2c_libs/arithchk/Makefile.am
deleted file mode 100644
index 37625ceb0..000000000
--- a/ext/f2c_libs/arithchk/Makefile.am
+++ /dev/null
@@ -1,24 +0,0 @@
-AM_CPPFLAGS             = -I. -I../
-AM_CXXFLAGS             = $(AM_CPPFLAGS) -Wno-deprecated-declarations -pthread
-AM_CFLAGS               = $(AM_CPPFLAGS) -Wno-deprecated-declarations -pthread -finline-functions -Wno-inline -g -Wno-format-security -DNO_FPINIT -DNDEBUG
-AM_FCFLAGS              = $(AM_CPPFLAGS)
-AM_LDFLAGS              = -L$(top_builddir)/build/lib/ -lm
-
-lib_LTLIBRARIES         =
-library_includedir      = 
-library_include_HEADERS = $(h_sources)
-
-bin_PROGRAMS         = arithchk
-
-#-----------------------
-# Cantera Arithchk 
-#-----------------------
-
-arithchk_SOURCES = arithchk.c
-
-# header file creation
-all:
-	@echo creating arithchk.h
-	./arithchk > ../arith.h
-
-CLEANFILES = *.o
diff --git a/ext/f2c_math/Makefile.am b/ext/f2c_math/Makefile.am
deleted file mode 100644
index b8fdf8dab..000000000
--- a/ext/f2c_math/Makefile.am
+++ /dev/null
@@ -1,54 +0,0 @@
-cc_sources = \
-daux.c   \
-mach.cpp \
-ddaspk.c \
-dgbefa.c \
-dgbsl.c \
-dgefa.c \
-dgesl.c \
-dp1vlu.c \
-dpcoef.c \
-dpolft.c \
-fdump.c \
-j4save.c \
-pcoef.c \
-polfit.c \
-pvalue.c \
-xercnt.c \
-xerhlt.c \
-xermsg.c \
-xerprn.c \
-xersve.c \
-xgetua.c \
-printstring.c
-
-h_sources               = cblas.h gmres.h
-
-AM_CPPFLAGS             = -I../f2c_libs
-AM_CXXFLAGS             = $(AM_CPPFLAGS)
-AM_FCFLAGS              = $(AM_CPPFLAGS)
-
-lib_LTLIBRARIES         = $(top_builddir)/build/lib/libctmath.la
-library_includedir      = $(top_builddir)/include
-library_include_HEADERS = $(h_sources)
-
-#-----------------------
-# Cantera Converters C/C++ library
-#-----------------------
-
-__top_builddir__build_lib_libctmath_la_LDFLAGS      = $(all_libraries) -release $(GENERIC_RELEASE)
-__top_builddir__build_lib_libctmath_la_SOURCES      = $(cc_sources) $(h_sources)
-
-__top_builddir__build_lib_libctmath_include_HEADERS = $(h_sources)
-__top_builddir__build_lib_libctmath_includedir = $(prefix)/include
-
-
-CLEANFILES = *.o
-
-# header file accumulation
-all:
-	@echo copying headers $<
-	cp -p ../f2c_libs/sysdep1.h0 ../f2c_libs/sysdep1.h
-	cp -p ../f2c_libs/signal1.h0 ../f2c_libs/signal1.h
-	@echo installing config.h 
-	cp -p ../../config.h ../../include/cantera/base/
diff --git a/ext/libexecstream/Makefile.am b/ext/libexecstream/Makefile.am
deleted file mode 100644
index 141ec3307..000000000
--- a/ext/libexecstream/Makefile.am
+++ /dev/null
@@ -1,19 +0,0 @@
-cc_sources              = exec-stream.cpp
-h_sources               = exec-stream.h
-
-AM_CPPFLAGS             = -I.
-AM_CXXFLAGS             = $(AM_CPPFLAGS)
-AM_FCFLAGS              = $(AM_CPPFLAGS)
-
-lib_LTLIBRARIES         = $(top_builddir)/build/lib/libexecstream.la
-library_includedir      = $(top_builddir)/include
-library_include_HEADERS = $(h_sources)
-
-#-----------------------
-# Execstream library
-#-----------------------
-
-__top_builddir__build_lib_libexecstream_la_LDFLAGS      = $(all_libraries) -release $(GENERIC_RELEASE)
-__top_builddir__build_lib_libexecstream_la_SOURCES      = $(cc_sources) $(h_sources)
-
-CLEANFILES = *.o
diff --git a/m4/common/ax_configure_args.m4 b/m4/common/ax_configure_args.m4
deleted file mode 100644
index 0726b1bc8..000000000
--- a/m4/common/ax_configure_args.m4
+++ /dev/null
@@ -1,70 +0,0 @@
-# ===========================================================================
-#     http://www.gnu.org/software/autoconf-archive/ax_configure_args.html
-# ===========================================================================
-#
-# SYNOPSIS
-#
-#   AX_CONFIGURE_ARGS
-#
-# DESCRIPTION
-#
-#   Helper macro for AX_ENABLE_BUILDDIR.
-#
-#   The traditional way of starting a subdir-configure is running the script
-#   with ${1+"$@"} but since autoconf 2.60 this is broken. Instead we have
-#   to rely on eval'ing $ac_configure_args however some old autoconf
-#   versions do not provide that. To ensure maximum portability of autoconf
-#   extension macros this helper can be AC_REQUIRE'd so that
-#   $ac_configure_args will alsways be present.
-#
-#   Sadly, the traditional "exec $SHELL" of the enable_builddir macros is
-#   spoiled now and must be replaced by "eval + exit $?".
-#
-#   Example:
-#
-#     AC_DEFUN([AX_ENABLE_SUBDIR],[dnl
-#       AC_REQUIRE([AX_CONFIGURE_ARGS])dnl
-#       eval $SHELL $ac_configure_args || exit $?
-#       ...])
-#
-# LICENSE
-#
-#   Copyright (c) 2008 Guido U. Draheim <guidod@gmx.de>
-#
-#   This program is free software; you can redistribute it and/or modify it
-#   under the terms of the GNU General Public License as published by the
-#   Free Software Foundation; either version 3 of the License, or (at your
-#   option) any later version.
-#
-#   This program is distributed in the hope that it will be useful, but
-#   WITHOUT ANY WARRANTY; without even the implied warranty of
-#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
-#   Public License for more details.
-#
-#   You should have received a copy of the GNU General Public License along
-#   with this program. If not, see <http://www.gnu.org/licenses/>.
-#
-#   As a special exception, the respective Autoconf Macro's copyright owner
-#   gives unlimited permission to copy, distribute and modify the configure
-#   scripts that are the output of Autoconf when processing the Macro. You
-#   need not follow the terms of the GNU General Public License when using
-#   or distributing such scripts, even though portions of the text of the
-#   Macro appear in them. The GNU General Public License (GPL) does govern
-#   all other use of the material that constitutes the Autoconf Macro.
-#
-#   This special exception to the GPL applies to versions of the Autoconf
-#   Macro released by the Autoconf Archive. When you make and distribute a
-#   modified version of the Autoconf Macro, you may extend this special
-#   exception to the GPL to apply to your modified version as well.
-
-#serial 9
-
-AC_DEFUN([AX_CONFIGURE_ARGS],[
-   # [$]@ is unsable in 2.60+ but earlier autoconf had no ac_configure_args
-   if test "${ac_configure_args+set}" != "set" ; then
-      ac_configure_args=
-      for ac_arg in ${1+"[$]@"}; do
-         ac_configure_args="$ac_configure_args '$ac_arg'"
-      done
-   fi
-])
diff --git a/m4/common/ax_enable_builddir.m4 b/m4/common/ax_enable_builddir.m4
deleted file mode 100644
index 3fb87317d..000000000
--- a/m4/common/ax_enable_builddir.m4
+++ /dev/null
@@ -1,300 +0,0 @@
-# ===========================================================================
-#    http://www.gnu.org/software/autoconf-archive/ax_enable_builddir.html
-# ===========================================================================
-#
-# SYNOPSIS
-#
-#   AX_ENABLE_BUILDDIR [(dirstring-or-command [,Makefile.mk [,-all]])]
-#
-# DESCRIPTION
-#
-#   If the current configure was run within the srcdir then we move all
-#   configure-files into a subdir and let the configure steps continue
-#   there. We provide an option --disable-builddir to suppress the move into
-#   a separate builddir.
-#
-#   Defaults:
-#
-#     $1 = $host (overridden with $HOST)
-#     $2 = Makefile.mk
-#     $3 = -all
-#
-#   This macro must be called before AM_INIT_AUTOMAKE. It creates a default
-#   toplevel srcdir Makefile from the information found in the created
-#   toplevel builddir Makefile. It just copies the variables and
-#   rule-targets, each extended with a default rule-execution that recurses
-#   into the build directory of the current "HOST". You can override the
-#   auto-dection through `config.guess` and build-time of course, as in
-#
-#     make HOST=i386-mingw-cross
-#
-#   which can of course set at configure time as well using
-#
-#     configure --host=i386-mingw-cross
-#
-#   After the default has been created, additional rules can be appended
-#   that will not just recurse into the subdirectories and only ever exist
-#   in the srcdir toplevel makefile - these parts are read from the $2 =
-#   Makefile.mk file
-#
-#   The automatic rules are usually scanning the toplevel Makefile for lines
-#   like '#### $host |$builddir' to recognize the place where to recurse
-#   into. Usually, the last one is the only one used. However, almost all
-#   targets have an additional "*-all" rule which makes the script to
-#   recurse into _all_ variants of the current HOST (!!) setting. The "-all"
-#   suffix can be overriden for the macro as well.
-#
-#   a special rule is only given for things like "dist" that will copy the
-#   tarball from the builddir to the sourcedir (or $(PUB)) for reason of
-#   convenience.
-#
-# LICENSE
-#
-#   Copyright (c) 2009 Guido U. Draheim <guidod@gmx.de>
-#   Copyright (c) 2009 Alan Jenkins <alan-jenkins@tuffmail.co.uk>
-#
-#   This program is free software; you can redistribute it and/or modify it
-#   under the terms of the GNU General Public License as published by the
-#   Free Software Foundation; either version 3 of the License, or (at your
-#   option) any later version.
-#
-#   This program is distributed in the hope that it will be useful, but
-#   WITHOUT ANY WARRANTY; without even the implied warranty of
-#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
-#   Public License for more details.
-#
-#   You should have received a copy of the GNU General Public License along
-#   with this program. If not, see <http://www.gnu.org/licenses/>.
-#
-#   As a special exception, the respective Autoconf Macro's copyright owner
-#   gives unlimited permission to copy, distribute and modify the configure
-#   scripts that are the output of Autoconf when processing the Macro. You
-#   need not follow the terms of the GNU General Public License when using
-#   or distributing such scripts, even though portions of the text of the
-#   Macro appear in them. The GNU General Public License (GPL) does govern
-#   all other use of the material that constitutes the Autoconf Macro.
-#
-#   This special exception to the GPL applies to versions of the Autoconf
-#   Macro released by the Autoconf Archive. When you make and distribute a
-#   modified version of the Autoconf Macro, you may extend this special
-#   exception to the GPL to apply to your modified version as well.
-
-#serial 23
-
-AC_DEFUN([AX_ENABLE_BUILDDIR],[
-AC_REQUIRE([AC_CANONICAL_HOST])[]dnl
-AC_REQUIRE([AX_CONFIGURE_ARGS])[]dnl
-AC_REQUIRE([AM_AUX_DIR_EXPAND])[]dnl
-AC_BEFORE([$0],[AM_INIT_AUTOMAKE])dnl
-AS_VAR_PUSHDEF([SUB],[ax_enable_builddir])dnl
-AS_VAR_PUSHDEF([AUX],[ax_enable_builddir_auxdir])dnl
-AS_VAR_PUSHDEF([SED],[ax_enable_builddir_sed])dnl
-SUB="."
-AC_ARG_ENABLE([builddir], AS_HELP_STRING(
-  [--disable-builddir],[disable automatic build in subdir of sources])
-  ,[SUB="$enableval"], [SUB="auto"])
-if test ".$ac_srcdir_defaulted" != ".no" ; then
-if test ".$srcdir" = ".." ; then
-  if test -f config.status ; then
-    AC_MSG_NOTICE(toplevel srcdir already configured... skipping subdir build)
-  else
-    test ".$SUB" = "."  && SUB="."
-    test ".$SUB" = ".no"  && SUB="."
-    test ".$TARGET" = "." && TARGET="$target"
-    test ".$SUB" = ".auto" && SUB="m4_ifval([$1], [$1],[$TARGET])"
-    if test ".$SUB" != ".." ; then    # we know where to go and
-      AS_MKDIR_P([$SUB])
-      echo __.$SUB.__ > $SUB/conftest.tmp
-      cd $SUB
-      if grep __.$SUB.__ conftest.tmp >/dev/null 2>/dev/null ; then
-        rm conftest.tmp
-        AC_MSG_RESULT([continue configure in default builddir "./$SUB"])
-      else
-        AC_MSG_ERROR([could not change to default builddir "./$SUB"])
-      fi
-      srcdir=`echo "$SUB" |
-              sed -e 's,^\./,,;s,[[^/]]$,&/,;s,[[^/]]*/,../,g;s,[[/]]$,,;'`
-      # going to restart from subdirectory location
-      test -f $srcdir/config.log   && mv $srcdir/config.log   .
-      test -f $srcdir/confdefs.h   && mv $srcdir/confdefs.h   .
-      test -f $srcdir/conftest.log && mv $srcdir/conftest.log .
-      test -f $srcdir/$cache_file  && mv $srcdir/$cache_file  .
-      AC_MSG_RESULT(....exec $SHELL $srcdir/[$]0 "--srcdir=$srcdir" "--enable-builddir=$SUB" ${1+"[$]@"})
-      case "[$]0" in # restart
-       [/\\]*) eval $SHELL "'[$]0'" "'--srcdir=$srcdir'" "'--enable-builddir=$SUB'" $ac_configure_args ;;
-       *) eval $SHELL "'$srcdir/[$]0'" "'--srcdir=$srcdir'" "'--enable-builddir=$SUB'" $ac_configure_args ;;
-      esac ; exit $?
-    fi
-  fi
-fi fi
-test ".$SUB" = ".auto" && SUB="."
-dnl ac_path_prog uses "set dummy" to override $@ which would defeat the "exec"
-AC_PATH_PROG(SED,gsed sed, sed)
-AUX="$am_aux_dir"
-AS_VAR_POPDEF([SED])dnl
-AS_VAR_POPDEF([AUX])dnl
-AS_VAR_POPDEF([SUB])dnl
-AC_CONFIG_COMMANDS([buildir],[dnl .............. config.status ..............
-AS_VAR_PUSHDEF([SUB],[ax_enable_builddir])dnl
-AS_VAR_PUSHDEF([TOP],[top_srcdir])dnl
-AS_VAR_PUSHDEF([SRC],[ac_top_srcdir])dnl
-AS_VAR_PUSHDEF([AUX],[ax_enable_builddir_auxdir])dnl
-AS_VAR_PUSHDEF([SED],[ax_enable_builddir_sed])dnl
-pushdef([END],[Makefile.mk])dnl
-pushdef([_ALL],[ifelse([$3],,[-all],[$3])])dnl
-  SRC="$ax_enable_builddir_srcdir"
-  if test ".$SUB" = ".." ; then
-    if test -f "$TOP/Makefile" ; then
-      AC_MSG_NOTICE([skipping TOP/Makefile - left untouched])
-    else
-      AC_MSG_NOTICE([skipping TOP/Makefile - not created])
-    fi
-  else
-    if test -f "$SRC/Makefile" ; then
-      a=`grep "^VERSION " "$SRC/Makefile"` ; b=`grep "^VERSION " Makefile`
-      test "$a" != "$b" && rm "$SRC/Makefile"
-    fi
-    if test -f "$SRC/Makefile" ; then
-	echo "$SRC/Makefile : $SRC/Makefile.in" > $tmp/conftemp.mk
-	echo "	[]@ echo 'REMOVED,,,' >\$[]@" >> $tmp/conftemp.mk
-      eval "${MAKE-make} -f $tmp/conftemp.mk 2>/dev/null >/dev/null"
-      if grep '^REMOVED,,,' "$SRC/Makefile" >/dev/null
-      then rm $SRC/Makefile ; fi
-      cp $tmp/conftemp.mk $SRC/makefiles.mk~      ## DEBUGGING
-    fi
-    if test ! -f "$SRC/Makefile" ; then
-      AC_MSG_NOTICE([create TOP/Makefile guessed from local Makefile])
-      x='`' ; cat >$tmp/conftemp.sed <<_EOF
-/^\$/n
-x
-/^\$/bS
-x
-/\\\\\$/{H;d;}
-{H;s/.*//;x;}
-bM
-:S
-x
-/\\\\\$/{h;d;}
-{h;s/.*//;x;}
-:M
-s/\\(\\n\\)	/\\1 /g
-/^	/d
-/^[[	 ]]*[[\\#]]/d
-/^VPATH *=/d
-s/^srcdir *=.*/srcdir = ./
-s/^top_srcdir *=.*/top_srcdir = ./
-/[[:=]]/!d
-/^\\./d
-dnl Now handle rules (i.e. lines containing ":" but not " = ").
-/ = /b
-/ .= /b
-/:/!b
-s/:.*/:/
-s/ /  /g
-s/ \\([[a-z]][[a-z-]]*[[a-zA-Z0-9]]\\)\\([[ :]]\\)/ \\1 \\1[]_ALL\\2/g
-s/^\\([[a-z]][[a-z-]]*[[a-zA-Z0-9]]\\)\\([[ :]]\\)/\\1 \\1[]_ALL\\2/
-s/  / /g
-/^all all[]_ALL[[ :]]/i\\
-all-configured : all[]_ALL
-dnl dist-all exists... and would make for dist-all-all
-s/ [[a-zA-Z0-9-]]*[]_ALL [[a-zA-Z0-9-]]*[]_ALL[]_ALL//g
-/[]_ALL[]_ALL/d
-a\\
-	@ HOST="\$(HOST)\" \\\\\\
-	; test ".\$\$HOST" = "." && HOST=$x sh $AUX/config.guess $x \\\\\\
-	; BUILD=$x grep "^#### \$\$HOST " Makefile | sed -e 's/.*|//' $x \\\\\\
-	; use=$x basename "\$\@" _ALL $x; n=$x echo \$\$BUILD | wc -w $x \\\\\\
-	; echo "MAKE \$\$HOST : \$\$n * \$\@"; if test "\$\$n" -eq "0" ; then : \\\\\\
-	; BUILD=$x grep "^####.*|" Makefile |tail -1| sed -e 's/.*|//' $x ; fi \\\\\\
-	; test ".\$\$BUILD" = "." && BUILD="." \\\\\\
-	; test "\$\$use" = "\$\@" && BUILD=$x echo "\$\$BUILD" | tail -1 $x \\\\\\
-	; for i in \$\$BUILD ; do test ".\$\$i" = "." && continue \\\\\\
-	; (cd "\$\$i" && test ! -f configure && \$(MAKE) \$\$use) || exit; done
-dnl special rule add-on: "dist" copies the tarball to $(PUB). (source tree)
-/dist[]_ALL *:/a\\
-	@ HOST="\$(HOST)\" \\\\\\
-	; test ".\$\$HOST" = "." && HOST=$x sh $AUX/config.guess $x \\\\\\
-	; BUILD=$x grep "^#### \$\$HOST " Makefile | sed -e 's/.*|//' $x \\\\\\
-	; found=$x echo \$\$BUILD | wc -w $x \\\\\\
-	; echo "MAKE \$\$HOST : \$\$found \$(PACKAGE)-\$(VERSION).tar.*" \\\\\\
-	; if test "\$\$found" -eq "0" ; then : \\\\\\
-	; BUILD=$x grep "^#### .*|" Makefile |tail -1| sed -e 's/.*|//' $x \\\\\\
-	; fi ; for i in \$\$BUILD ; do test ".\$\$i" = "." && continue \\\\\\
-	; for f in \$\$i/\$(PACKAGE)-\$(VERSION).tar.* \\\\\\
-	; do test -f "\$\$f" && mv "\$\$f" \$(PUB). ; done ; break ; done
-dnl special rule add-on: "dist-foo" copies all the archives to $(PUB). (source tree)
-/dist-[[a-zA-Z0-9]]*[]_ALL *:/a\\
-	@ HOST="\$(HOST)\" \\\\\\
-	; test ".\$\$HOST" = "." && HOST=$x sh ./config.guess $x \\\\\\
-	; BUILD=$x grep "^#### \$\$HOST " Makefile | sed -e 's/.*|//' $x \\\\\\
-	; found=$x echo \$\$BUILD | wc -w $x \\\\\\
-	; echo "MAKE \$\$HOST : \$\$found \$(PACKAGE)-\$(VERSION).*" \\\\\\
-	; if test "\$\$found" -eq "0" ; then : \\\\\\
-	; BUILD=$x grep "^#### .*|" Makefile |tail -1| sed -e 's/.*|//' $x \\\\\\
-	; fi ; for i in \$\$BUILD ; do test ".\$\$i" = "." && continue \\\\\\
-	; for f in \$\$i/\$(PACKAGE)-\$(VERSION).* \\\\\\
-	; do test -f "\$\$f" && mv "\$\$f" \$(PUB). ; done ; break ; done
-dnl special rule add-on: "distclean" removes all local builddirs completely
-/distclean[]_ALL *:/a\\
-	@ HOST="\$(HOST)\" \\\\\\
-	; test ".\$\$HOST" = "." && HOST=$x sh $AUX/config.guess $x \\\\\\
-	; BUILD=$x grep "^#### .*|" Makefile | sed -e 's/.*|//' $x \\\\\\
-	; use=$x basename "\$\@" _ALL $x; n=$x echo \$\$BUILD | wc -w $x \\\\\\
-	; echo "MAKE \$\$HOST : \$\$n * \$\@ (all local builds)" \\\\\\
-	; test ".\$\$BUILD" = "." && BUILD="." \\\\\\
-	; for i in \$\$BUILD ; do test ".\$\$i" = "." && continue \\\\\\
-	; echo "# rm -r \$\$i"; done ; echo "# (sleep 3)" ; sleep 3 \\\\\\
-	; for i in \$\$BUILD ; do test ".\$\$i" = "." && continue \\\\\\
-	; echo "\$\$i" | grep "^/" > /dev/null && continue \\\\\\
-	; echo "\$\$i" | grep "^../" > /dev/null && continue \\\\\\
-	; echo "rm -r \$\$i"; (rm -r "\$\$i") ; done ; rm Makefile
-_EOF
-      cp "$tmp/conftemp.sed" "$SRC/makefile.sed~"            ## DEBUGGING
-      $SED -f $tmp/conftemp.sed Makefile >$SRC/Makefile
-      if test -f "$SRC/m4_ifval([$2],[$2],[END])" ; then
-        AC_MSG_NOTICE([extend TOP/Makefile with TOP/m4_ifval([$2],[$2],[END])])
-        cat $SRC/END >>$SRC/Makefile
-      fi ; xxxx="####"
-      echo "$xxxx CONFIGURATIONS FOR TOPLEVEL MAKEFILE: " >>$SRC/Makefile
-      # sanity check
-      if grep '^; echo "MAKE ' $SRC/Makefile >/dev/null ; then
-        AC_MSG_NOTICE([buggy sed found - it deletes tab in "a" text parts])
-        $SED -e '/^@ HOST=/s/^/	/' -e '/^; /s/^/	/' $SRC/Makefile \
-          >$SRC/Makefile~
-        (test -s $SRC/Makefile~ && mv $SRC/Makefile~ $SRC/Makefile) 2>/dev/null
-      fi
-    else
-      xxxx="\\#\\#\\#\\#"
-      # echo "/^$xxxx *$ax_enable_builddir_host /d" >$tmp/conftemp.sed
-      echo "s!^$xxxx [[^|]]* | *$SUB *\$!$xxxx ...... $SUB!" >$tmp/conftemp.sed
-      $SED -f "$tmp/conftemp.sed" "$SRC/Makefile" >$tmp/mkfile.tmp
-        cp "$tmp/conftemp.sed" "$SRC/makefiles.sed~"         ## DEBUGGING
-        cp "$tmp/mkfile.tmp"   "$SRC/makefiles.out~"         ## DEBUGGING
-      if cmp -s "$SRC/Makefile" "$tmp/mkfile.tmp" 2>/dev/null ; then
-        AC_MSG_NOTICE([keeping TOP/Makefile from earlier configure])
-        rm "$tmp/mkfile.tmp"
-      else
-        AC_MSG_NOTICE([reusing TOP/Makefile from earlier configure])
-        mv "$tmp/mkfile.tmp" "$SRC/Makefile"
-      fi
-    fi
-    AC_MSG_NOTICE([build in $SUB (HOST=$ax_enable_builddir_host)])
-    xxxx="####"
-    echo "$xxxx" "$ax_enable_builddir_host" "|$SUB" >>$SRC/Makefile
-  fi
-popdef([END])dnl
-AS_VAR_POPDEF([SED])dnl
-AS_VAR_POPDEF([AUX])dnl
-AS_VAR_POPDEF([SRC])dnl
-AS_VAR_POPDEF([TOP])dnl
-AS_VAR_POPDEF([SUB])dnl
-],[dnl
-ax_enable_builddir_srcdir="$srcdir"                    # $srcdir
-ax_enable_builddir_host="$HOST"                        # $HOST / $host
-ax_enable_builddir_version="$VERSION"                  # $VERSION
-ax_enable_builddir_package="$PACKAGE"                  # $PACKAGE
-ax_enable_builddir_auxdir="$ax_enable_builddir_auxdir" # $AUX
-ax_enable_builddir_sed="$ax_enable_builddir_sed"       # $SED
-ax_enable_builddir="$ax_enable_builddir"               # $SUB
-])dnl
-])
diff --git a/m4/common/ax_prog_doxygen.m4 b/m4/common/ax_prog_doxygen.m4
deleted file mode 100644
index 458e3a633..000000000
--- a/m4/common/ax_prog_doxygen.m4
+++ /dev/null
@@ -1,536 +0,0 @@
-# ===========================================================================
-#         http://www.nongnu.org/autoconf-archive/ax_prog_doxygen.html
-# ===========================================================================
-#
-# SYNOPSIS
-#
-#   DX_INIT_DOXYGEN(PROJECT-NAME, DOXYFILE-PATH, [OUTPUT-DIR])
-#   DX_DOXYGEN_FEATURE(ON|OFF)
-#   DX_DOT_FEATURE(ON|OFF)
-#   DX_HTML_FEATURE(ON|OFF)
-#   DX_CHM_FEATURE(ON|OFF)
-#   DX_CHI_FEATURE(ON|OFF)
-#   DX_MAN_FEATURE(ON|OFF)
-#   DX_RTF_FEATURE(ON|OFF)
-#   DX_XML_FEATURE(ON|OFF)
-#   DX_PDF_FEATURE(ON|OFF)
-#   DX_PS_FEATURE(ON|OFF)
-#
-# DESCRIPTION
-#
-#   The DX_*_FEATURE macros control the default setting for the given
-#   Doxygen feature. Supported features are 'DOXYGEN' itself, 'DOT' for
-#   generating graphics, 'HTML' for plain HTML, 'CHM' for compressed HTML
-#   help (for MS users), 'CHI' for generating a seperate .chi file by the
-#   .chm file, and 'MAN', 'RTF', 'XML', 'PDF' and 'PS' for the appropriate
-#   output formats. The environment variable DOXYGEN_PAPER_SIZE may be
-#   specified to override the default 'a4wide' paper size.
-#
-#   By default, HTML, PDF and PS documentation is generated as this seems to
-#   be the most popular and portable combination. MAN pages created by
-#   Doxygen are usually problematic, though by picking an appropriate subset
-#   and doing some massaging they might be better than nothing. CHM and RTF
-#   are specific for MS (note that you can't generate both HTML and CHM at
-#   the same time). The XML is rather useless unless you apply specialized
-#   post-processing to it.
-#
-#   The macros mainly control the default state of the feature. The use can
-#   override the default by specifying --enable or --disable. The macros
-#   ensure that contradictory flags are not given (e.g.,
-#   --enable-doxygen-html and --enable-doxygen-chm,
-#   --enable-doxygen-anything with --disable-doxygen, etc.) Finally, each
-#   feature will be automatically disabled (with a warning) if the required
-#   programs are missing.
-#
-#   Once all the feature defaults have been specified, call DX_INIT_DOXYGEN
-#   with the following parameters: a one-word name for the project for use
-#   as a filename base etc., an optional configuration file name (the
-#   default is 'Doxyfile', the same as Doxygen's default), and an optional
-#   output directory name (the default is 'doxygen-doc').
-#
-#   Automake Support
-#
-#   The following is a template aminclude.am file for use with Automake.
-#   Make targets and variables values are controlled by the various
-#   DX_COND_* conditionals set by autoconf.
-#
-#   The provided targets are:
-#
-#     doxygen-doc: Generate all doxygen documentation.
-#
-#     doxygen-run: Run doxygen, which will generate some of the
-#                  documentation (HTML, CHM, CHI, MAN, RTF, XML)
-#                  but will not do the post processing required
-#                  for the rest of it (PS, PDF, and some MAN).
-#
-#     doxygen-man: Rename some doxygen generated man pages.
-#
-#     doxygen-ps:  Generate doxygen PostScript documentation.
-#
-#     doxygen-pdf: Generate doxygen PDF documentation.
-#
-#   Note that by default these are not integrated into the automake targets.
-#   If doxygen is used to generate man pages, you can achieve this
-#   integration by setting man3_MANS to the list of man pages generated and
-#   then adding the dependency:
-#
-#     $(man3_MANS): doxygen-doc
-#
-#   This will cause make to run doxygen and generate all the documentation.
-#
-#   The following variable is intended for use in Makefile.am:
-#
-#     DX_CLEANFILES = everything to clean.
-#
-#   Then add this variable to MOSTLYCLEANFILES.
-#
-#     ----- begin aminclude.am -------------------------------------
-#
-#     ## --------------------------------- ##
-#     ## Format-independent Doxygen rules. ##
-#     ## --------------------------------- ##
-#
-#     if DX_COND_doc
-#
-#     ## ------------------------------- ##
-#     ## Rules specific for HTML output. ##
-#     ## ------------------------------- ##
-#
-#     if DX_COND_html
-#
-#     DX_CLEAN_HTML = @DX_DOCDIR@/html
-#
-#     endif DX_COND_html
-#
-#     ## ------------------------------ ##
-#     ## Rules specific for CHM output. ##
-#     ## ------------------------------ ##
-#
-#     if DX_COND_chm
-#
-#     DX_CLEAN_CHM = @DX_DOCDIR@/chm
-#
-#     if DX_COND_chi
-#
-#     DX_CLEAN_CHI = @DX_DOCDIR@/@PACKAGE@.chi
-#
-#     endif DX_COND_chi
-#
-#     endif DX_COND_chm
-#
-#     ## ------------------------------ ##
-#     ## Rules specific for MAN output. ##
-#     ## ------------------------------ ##
-#
-#     if DX_COND_man
-#
-#     DX_CLEAN_MAN = @DX_DOCDIR@/man
-#
-#     endif DX_COND_man
-#
-#     ## ------------------------------ ##
-#     ## Rules specific for RTF output. ##
-#     ## ------------------------------ ##
-#
-#     if DX_COND_rtf
-#
-#     DX_CLEAN_RTF = @DX_DOCDIR@/rtf
-#
-#     endif DX_COND_rtf
-#
-#     ## ------------------------------ ##
-#     ## Rules specific for XML output. ##
-#     ## ------------------------------ ##
-#
-#     if DX_COND_xml
-#
-#     DX_CLEAN_XML = @DX_DOCDIR@/xml
-#
-#     endif DX_COND_xml
-#
-#     ## ----------------------------- ##
-#     ## Rules specific for PS output. ##
-#     ## ----------------------------- ##
-#
-#     if DX_COND_ps
-#
-#     DX_CLEAN_PS = @DX_DOCDIR@/@PACKAGE@.ps
-#
-#     DX_PS_GOAL = doxygen-ps
-#
-#     doxygen-ps: @DX_DOCDIR@/@PACKAGE@.ps
-#
-#     @DX_DOCDIR@/@PACKAGE@.ps: @DX_DOCDIR@/@PACKAGE@.tag
-#   	  cd @DX_DOCDIR@/latex; \
-#   	  rm -f *.aux *.toc *.idx *.ind *.ilg *.log *.out; \
-#   	  $(DX_LATEX) refman.tex; \
-#   	  $(MAKEINDEX_PATH) refman.idx; \
-#   	  $(DX_LATEX) refman.tex; \
-#   	  countdown=5; \
-#   	  while $(DX_EGREP) 'Rerun (LaTeX|to get cross-references right)' \
-#   			    refman.log > /dev/null 2>&1 \
-#   	     && test $$countdown -gt 0; do \
-#   	      $(DX_LATEX) refman.tex; \
-#   	      countdown=`expr $$countdown - 1`; \
-#   	  done; \
-#   	  $(DX_DVIPS) -o ../@PACKAGE@.ps refman.dvi
-#
-#     endif DX_COND_ps
-#
-#     ## ------------------------------ ##
-#     ## Rules specific for PDF output. ##
-#     ## ------------------------------ ##
-#
-#     if DX_COND_pdf
-#
-#     DX_CLEAN_PDF = @DX_DOCDIR@/@PACKAGE@.pdf
-#
-#     DX_PDF_GOAL = doxygen-pdf
-#
-#     doxygen-pdf: @DX_DOCDIR@/@PACKAGE@.pdf
-#
-#     @DX_DOCDIR@/@PACKAGE@.pdf: @DX_DOCDIR@/@PACKAGE@.tag
-#   	  cd @DX_DOCDIR@/latex; \
-#   	  rm -f *.aux *.toc *.idx *.ind *.ilg *.log *.out; \
-#   	  $(DX_PDFLATEX) refman.tex; \
-#   	  $(DX_MAKEINDEX) refman.idx; \
-#   	  $(DX_PDFLATEX) refman.tex; \
-#   	  countdown=5; \
-#   	  while $(DX_EGREP) 'Rerun (LaTeX|to get cross-references right)' \
-#   			    refman.log > /dev/null 2>&1 \
-#   	     && test $$countdown -gt 0; do \
-#   	      $(DX_PDFLATEX) refman.tex; \
-#   	      countdown=`expr $$countdown - 1`; \
-#   	  done; \
-#   	  mv refman.pdf ../@PACKAGE@.pdf
-#
-#     endif DX_COND_pdf
-#
-#     ## ------------------------------------------------- ##
-#     ## Rules specific for LaTeX (shared for PS and PDF). ##
-#     ## ------------------------------------------------- ##
-#
-#     if DX_COND_latex
-#
-#     DX_CLEAN_LATEX = @DX_DOCDIR@/latex
-#
-#     endif DX_COND_latex
-#
-#     .PHONY: doxygen-run doxygen-doc $(DX_PS_GOAL) $(DX_PDF_GOAL)
-#
-#     .INTERMEDIATE: doxygen-run $(DX_PS_GOAL) $(DX_PDF_GOAL)
-#
-#     doxygen-run: @DX_DOCDIR@/@PACKAGE@.tag
-#
-#     doxygen-doc: doxygen-run $(DX_PS_GOAL) $(DX_PDF_GOAL)
-#
-#     @DX_DOCDIR@/@PACKAGE@.tag: $(DX_CONFIG) $(pkginclude_HEADERS)
-#   	  rm -rf @DX_DOCDIR@
-#   	  $(DX_ENV) $(DX_DOXYGEN) $(srcdir)/$(DX_CONFIG)
-#
-#     DX_CLEANFILES = \
-#         @DX_DOCDIR@/@PACKAGE@.tag \
-#         -r \
-#         $(DX_CLEAN_HTML) \
-#         $(DX_CLEAN_CHM) \
-#         $(DX_CLEAN_CHI) \
-#         $(DX_CLEAN_MAN) \
-#         $(DX_CLEAN_RTF) \
-#         $(DX_CLEAN_XML) \
-#         $(DX_CLEAN_PS) \
-#         $(DX_CLEAN_PDF) \
-#         $(DX_CLEAN_LATEX)
-#
-#     endif DX_COND_doc
-#
-#     ----- end aminclude.am ---------------------------------------
-#
-# LICENSE
-#
-#   Copyright (c) 2009 Oren Ben-Kiki <oren@ben-kiki.org>
-#
-#   Copying and distribution of this file, with or without modification, are
-#   permitted in any medium without royalty provided the copyright notice
-#   and this notice are preserved.
-
-## ----------##
-## Defaults. ##
-## ----------##
-
-DX_ENV=""
-AC_DEFUN([DX_FEATURE_doc],  ON)
-AC_DEFUN([DX_FEATURE_dot],  ON)
-AC_DEFUN([DX_FEATURE_man],  OFF)
-AC_DEFUN([DX_FEATURE_html], ON)
-AC_DEFUN([DX_FEATURE_chm],  OFF)
-AC_DEFUN([DX_FEATURE_chi],  OFF)
-AC_DEFUN([DX_FEATURE_rtf],  OFF)
-AC_DEFUN([DX_FEATURE_xml],  OFF)
-AC_DEFUN([DX_FEATURE_pdf],  ON)
-AC_DEFUN([DX_FEATURE_ps],   ON)
-
-## --------------- ##
-## Private macros. ##
-## --------------- ##
-
-# DX_ENV_APPEND(VARIABLE, VALUE)
-# ------------------------------
-# Append VARIABLE="VALUE" to DX_ENV for invoking doxygen.
-AC_DEFUN([DX_ENV_APPEND], [AC_SUBST([DX_ENV], ["$DX_ENV $1='$2'"])])
-
-# DX_DIRNAME_EXPR
-# ---------------
-# Expand into a shell expression prints the directory part of a path.
-AC_DEFUN([DX_DIRNAME_EXPR],
-         [[expr ".$1" : '\(\.\)[^/]*$' \| "x$1" : 'x\(.*\)/[^/]*$']])
-
-# DX_IF_FEATURE(FEATURE, IF-ON, IF-OFF)
-# -------------------------------------
-# Expands according to the M4 (static) status of the feature.
-AC_DEFUN([DX_IF_FEATURE], [ifelse(DX_FEATURE_$1, ON, [$2], [$3])])
-
-# DX_REQUIRE_PROG(VARIABLE, PROGRAM)
-# ----------------------------------
-# Require the specified program to be found for the DX_CURRENT_FEATURE to work.
-AC_DEFUN([DX_REQUIRE_PROG], [
-AC_PATH_TOOL([$1], [$2])
-if test "$DX_FLAG_[]DX_CURRENT_FEATURE$$1" = 1; then
-    AC_MSG_WARN([$2 not found - will not DX_CURRENT_DESCRIPTION])
-    AC_SUBST(DX_FLAG_[]DX_CURRENT_FEATURE, 0)
-fi
-])
-
-# DX_TEST_FEATURE(FEATURE)
-# ------------------------
-# Expand to a shell expression testing whether the feature is active.
-AC_DEFUN([DX_TEST_FEATURE], [test "$DX_FLAG_$1" = 1])
-
-# DX_CHECK_DEPEND(REQUIRED_FEATURE, REQUIRED_STATE)
-# -------------------------------------------------
-# Verify that a required features has the right state before trying to turn on
-# the DX_CURRENT_FEATURE.
-AC_DEFUN([DX_CHECK_DEPEND], [
-test "$DX_FLAG_$1" = "$2" \
-|| AC_MSG_ERROR([doxygen-DX_CURRENT_FEATURE ifelse([$2], 1,
-                            requires, contradicts) doxygen-DX_CURRENT_FEATURE])
-])
-
-# DX_CLEAR_DEPEND(FEATURE, REQUIRED_FEATURE, REQUIRED_STATE)
-# ----------------------------------------------------------
-# Turn off the DX_CURRENT_FEATURE if the required feature is off.
-AC_DEFUN([DX_CLEAR_DEPEND], [
-test "$DX_FLAG_$1" = "$2" || AC_SUBST(DX_FLAG_[]DX_CURRENT_FEATURE, 0)
-])
-
-# DX_FEATURE_ARG(FEATURE, DESCRIPTION,
-#                CHECK_DEPEND, CLEAR_DEPEND,
-#                REQUIRE, DO-IF-ON, DO-IF-OFF)
-# --------------------------------------------
-# Parse the command-line option controlling a feature. CHECK_DEPEND is called
-# if the user explicitly turns the feature on (and invokes DX_CHECK_DEPEND),
-# otherwise CLEAR_DEPEND is called to turn off the default state if a required
-# feature is disabled (using DX_CLEAR_DEPEND). REQUIRE performs additional
-# requirement tests (DX_REQUIRE_PROG). Finally, an automake flag is set and
-# DO-IF-ON or DO-IF-OFF are called according to the final state of the feature.
-AC_DEFUN([DX_ARG_ABLE], [
-    AC_DEFUN([DX_CURRENT_FEATURE], [$1])
-    AC_DEFUN([DX_CURRENT_DESCRIPTION], [$2])
-    AC_ARG_ENABLE(doxygen-$1,
-                  [AS_HELP_STRING(DX_IF_FEATURE([$1], [--disable-doxygen-$1],
-                                                      [--enable-doxygen-$1]),
-                                  DX_IF_FEATURE([$1], [don't $2], [$2]))],
-                  [
-case "$enableval" in
-#(
-y|Y|yes|Yes|YES)
-    AC_SUBST([DX_FLAG_$1], 1)
-    $3
-;; #(
-n|N|no|No|NO)
-    AC_SUBST([DX_FLAG_$1], 0)
-;; #(
-*)
-    AC_MSG_ERROR([invalid value '$enableval' given to doxygen-$1])
-;;
-esac
-], [
-AC_SUBST([DX_FLAG_$1], [DX_IF_FEATURE([$1], 1, 0)])
-$4
-])
-if DX_TEST_FEATURE([$1]); then
-    $5
-    :
-fi
-if DX_TEST_FEATURE([$1]); then
-    AM_CONDITIONAL(DX_COND_$1, :)
-    $6
-    :
-else
-    AM_CONDITIONAL(DX_COND_$1, false)
-    $7
-    :
-fi
-])
-
-## -------------- ##
-## Public macros. ##
-## -------------- ##
-
-# DX_XXX_FEATURE(DEFAULT_STATE)
-# -----------------------------
-AC_DEFUN([DX_DOXYGEN_FEATURE], [AC_DEFUN([DX_FEATURE_doc],  [$1])])
-AC_DEFUN([DX_MAN_FEATURE],     [AC_DEFUN([DX_FEATURE_man],  [$1])])
-AC_DEFUN([DX_HTML_FEATURE],    [AC_DEFUN([DX_FEATURE_html], [$1])])
-AC_DEFUN([DX_CHM_FEATURE],     [AC_DEFUN([DX_FEATURE_chm],  [$1])])
-AC_DEFUN([DX_CHI_FEATURE],     [AC_DEFUN([DX_FEATURE_chi],  [$1])])
-AC_DEFUN([DX_RTF_FEATURE],     [AC_DEFUN([DX_FEATURE_rtf],  [$1])])
-AC_DEFUN([DX_XML_FEATURE],     [AC_DEFUN([DX_FEATURE_xml],  [$1])])
-AC_DEFUN([DX_XML_FEATURE],     [AC_DEFUN([DX_FEATURE_xml],  [$1])])
-AC_DEFUN([DX_PDF_FEATURE],     [AC_DEFUN([DX_FEATURE_pdf],  [$1])])
-AC_DEFUN([DX_PS_FEATURE],      [AC_DEFUN([DX_FEATURE_ps],   [$1])])
-
-# DX_INIT_DOXYGEN(PROJECT, [CONFIG-FILE], [OUTPUT-DOC-DIR])
-# ---------------------------------------------------------
-# PROJECT also serves as the base name for the documentation files.
-# The default CONFIG-FILE is "Doxyfile" and OUTPUT-DOC-DIR is "doxygen-doc".
-AC_DEFUN([DX_INIT_DOXYGEN], [
-
-# Files:
-AC_SUBST([DX_PROJECT], [$1])
-AC_SUBST([DX_CONFIG], [ifelse([$2], [], Doxyfile, [$2])])
-AC_SUBST([DX_DOCDIR], [ifelse([$3], [], doxygen-doc, [$3])])
-
-# Environment variables used inside doxygen.cfg:
-DX_ENV_APPEND(SRCDIR, $srcdir)
-DX_ENV_APPEND(PROJECT, $DX_PROJECT)
-DX_ENV_APPEND(DOCDIR, $DX_DOCDIR)
-DX_ENV_APPEND(VERSION, $PACKAGE_VERSION)
-
-# Additional variables for PECOS dev environment:
-DX_ENV_APPEND(BUILDDATE,$BUILD_DATE)
-DX_ENV_APPEND(BUILDHOST,$BUILD_HOST)
-DX_ENV_APPEND(BUILDUSER,$USER)
-DX_ENV_APPEND(BUILDDIR,$srcdir)
-
-# Doxygen itself:
-DX_ARG_ABLE(doc, [generate any doxygen documentation],
-            [],
-            [],
-            [DX_REQUIRE_PROG([DX_DOXYGEN], doxygen)
-             DX_REQUIRE_PROG([DX_PERL], perl)],
-            [DX_ENV_APPEND(PERL_PATH, $DX_PERL)])
-
-# Dot for graphics:
-DX_ARG_ABLE(dot, [generate graphics for doxygen documentation],
-            [DX_CHECK_DEPEND(doc, 1)],
-            [DX_CLEAR_DEPEND(doc, 1)],
-            [DX_REQUIRE_PROG([DX_DOT], dot)],
-            [DX_ENV_APPEND(HAVE_DOT, YES)
-             DX_ENV_APPEND(DOT_PATH, [`DX_DIRNAME_EXPR($DX_DOT)`])],
-            [DX_ENV_APPEND(HAVE_DOT, NO)])
-
-# Man pages generation:
-DX_ARG_ABLE(man, [generate doxygen manual pages],
-            [DX_CHECK_DEPEND(doc, 1)],
-            [DX_CLEAR_DEPEND(doc, 1)],
-            [],
-            [DX_ENV_APPEND(GENERATE_MAN, YES)],
-            [DX_ENV_APPEND(GENERATE_MAN, NO)])
-
-# RTF file generation:
-DX_ARG_ABLE(rtf, [generate doxygen RTF documentation],
-            [DX_CHECK_DEPEND(doc, 1)],
-            [DX_CLEAR_DEPEND(doc, 1)],
-            [],
-            [DX_ENV_APPEND(GENERATE_RTF, YES)],
-            [DX_ENV_APPEND(GENERATE_RTF, NO)])
-
-# XML file generation:
-DX_ARG_ABLE(xml, [generate doxygen XML documentation],
-            [DX_CHECK_DEPEND(doc, 1)],
-            [DX_CLEAR_DEPEND(doc, 1)],
-            [],
-            [DX_ENV_APPEND(GENERATE_XML, YES)],
-            [DX_ENV_APPEND(GENERATE_XML, NO)])
-
-# (Compressed) HTML help generation:
-DX_ARG_ABLE(chm, [generate doxygen compressed HTML help documentation],
-            [DX_CHECK_DEPEND(doc, 1)],
-            [DX_CLEAR_DEPEND(doc, 1)],
-            [DX_REQUIRE_PROG([DX_HHC], hhc)],
-            [DX_ENV_APPEND(HHC_PATH, $DX_HHC)
-             DX_ENV_APPEND(GENERATE_HTML, YES)
-             DX_ENV_APPEND(GENERATE_HTMLHELP, YES)],
-            [DX_ENV_APPEND(GENERATE_HTMLHELP, NO)])
-
-# Seperate CHI file generation.
-DX_ARG_ABLE(chi, [generate doxygen seperate compressed HTML help index file],
-            [DX_CHECK_DEPEND(chm, 1)],
-            [DX_CLEAR_DEPEND(chm, 1)],
-            [],
-            [DX_ENV_APPEND(GENERATE_CHI, YES)],
-            [DX_ENV_APPEND(GENERATE_CHI, NO)])
-
-# Plain HTML pages generation:
-DX_ARG_ABLE(html, [generate doxygen plain HTML documentation],
-            [DX_CHECK_DEPEND(doc, 1) DX_CHECK_DEPEND(chm, 0)],
-            [DX_CLEAR_DEPEND(doc, 1) DX_CLEAR_DEPEND(chm, 0)],
-            [],
-            [DX_ENV_APPEND(GENERATE_HTML, YES)],
-            [DX_TEST_FEATURE(chm) || DX_ENV_APPEND(GENERATE_HTML, NO)])
-
-# PostScript file generation:
-DX_ARG_ABLE(ps, [generate doxygen PostScript documentation],
-            [DX_CHECK_DEPEND(doc, 1)],
-            [DX_CLEAR_DEPEND(doc, 1)],
-            [DX_REQUIRE_PROG([DX_LATEX], latex)
-             DX_REQUIRE_PROG([DX_MAKEINDEX], makeindex)
-             DX_REQUIRE_PROG([DX_DVIPS], dvips)
-             DX_REQUIRE_PROG([DX_EGREP], egrep)])
-
-# PDF file generation:
-DX_ARG_ABLE(pdf, [generate doxygen PDF documentation],
-            [DX_CHECK_DEPEND(doc, 1)],
-            [DX_CLEAR_DEPEND(doc, 1)],
-            [DX_REQUIRE_PROG([DX_PDFLATEX], pdflatex)
-             DX_REQUIRE_PROG([DX_MAKEINDEX], makeindex)
-             DX_REQUIRE_PROG([DX_EGREP], egrep)])
-
-# LaTeX generation for PS and/or PDF:
-if DX_TEST_FEATURE(ps) || DX_TEST_FEATURE(pdf); then
-    AM_CONDITIONAL(DX_COND_latex, :)
-    DX_ENV_APPEND(GENERATE_LATEX, YES)
-else
-    AM_CONDITIONAL(DX_COND_latex, false)
-    DX_ENV_APPEND(GENERATE_LATEX, NO)
-fi
-
-# Paper size for PS and/or PDF:
-AC_ARG_VAR(DOXYGEN_PAPER_SIZE,
-           [a4wide (default), a4, letter, legal or executive])
-case "$DOXYGEN_PAPER_SIZE" in
-#(
-"")
-    AC_SUBST(DOXYGEN_PAPER_SIZE, "")
-;; #(
-a4wide|a4|letter|legal|executive)
-    DX_ENV_APPEND(PAPER_SIZE, $DOXYGEN_PAPER_SIZE)
-;; #(
-*)
-    AC_MSG_ERROR([unknown DOXYGEN_PAPER_SIZE='$DOXYGEN_PAPER_SIZE'])
-;;
-esac
-
-#For debugging:
-#echo DX_FLAG_doc=$DX_FLAG_doc
-#echo DX_FLAG_dot=$DX_FLAG_dot
-#echo DX_FLAG_man=$DX_FLAG_man
-#echo DX_FLAG_html=$DX_FLAG_html
-#echo DX_FLAG_chm=$DX_FLAG_chm
-#echo DX_FLAG_chi=$DX_FLAG_chi
-#echo DX_FLAG_rtf=$DX_FLAG_rtf
-#echo DX_FLAG_xml=$DX_FLAG_xml
-#echo DX_FLAG_pdf=$DX_FLAG_pdf
-#echo DX_FLAG_ps=$DX_FLAG_ps
-#echo DX_ENV=$DX_ENV
-])
diff --git a/m4/common/ax_split_version.m4 b/m4/common/ax_split_version.m4
deleted file mode 100644
index 02737c392..000000000
--- a/m4/common/ax_split_version.m4
+++ /dev/null
@@ -1,38 +0,0 @@
-# ===========================================================================
-#     http://www.gnu.org/software/autoconf-archive/ax_split_version.html
-# ===========================================================================
-#
-# SYNOPSIS
-#
-#   AX_SPLIT_VERSION
-#
-# DESCRIPTION
-#
-#   Splits a version number in the format MAJOR.MINOR.POINT into its
-#   separate components.
-#
-#   Sets the variables.
-#
-# LICENSE
-#
-#   Copyright (c) 2008 Tom Howard <tomhoward@users.sf.net>
-#
-#   Copying and distribution of this file, with or without modification, are
-#   permitted in any medium without royalty provided the copyright notice
-#   and this notice are preserved. This file is offered as-is, without any
-#   warranty.
-
-#serial 9
-
-AC_DEFUN([AX_SPLIT_VERSION],[
-    AC_REQUIRE([AC_PROG_SED])
-    AX_MAJOR_VERSION=`echo "$VERSION" | $SED 's/\([[^.]][[^.]]*\).*/\1/'`
-    AX_MINOR_VERSION=`echo "$VERSION" | $SED 's/[[^.]][[^.]]*.\([[^.]][[^.]]*\).*/\1/'`
-    AX_POINT_VERSION=`echo "$VERSION" | $SED 's/[[^.]][[^.]]*.[[^.]][[^.]]*.\(.*\)/\1/'`
-    AC_MSG_CHECKING([Major version])
-    AC_MSG_RESULT([$AX_MAJOR_VERSION])
-    AC_MSG_CHECKING([Minor version])
-    AC_MSG_RESULT([$AX_MINOR_VERSION])
-    AC_MSG_CHECKING([Point version])
-    AC_MSG_RESULT([$AX_POINT_VERSION])
-])
diff --git a/m4/config_summary.m4 b/m4/config_summary.m4
deleted file mode 100644
index b9cbf707e..000000000
--- a/m4/config_summary.m4
+++ /dev/null
@@ -1,42 +0,0 @@
-# SYNOPSIS
-#
-#   Summarizes configuration settings.
-#
-#   AX_SUMMARIZE_CONFIG([, ACTION-IF-FOUND [, ACTION-IF-NOT-FOUND]]])
-#
-# DESCRIPTION
-#
-#   Outputs a summary of relevant configuration settings.
-#
-
-AC_DEFUN([AX_SUMMARIZE_CONFIG],
-[
-
-echo
-echo '----------------------------------- SUMMARY -----------------------------------'
-echo
-echo Package version.................   : $PACKAGE-$VERSION
-echo
-echo C++ compiler....................   : $CXX
-echo C++ compiler flags..............   : $CXXFLAGS
-echo C compiler......................   : $CC
-echo C compiler flags................   : $CFLAGS
-echo Fortran compiler................   : $FC
-echo Fortran compiler flags..........   : $FCFLAGS
-echo Install dir.....................   : $prefix
-echo Build user......................   : $USER
-echo Build host......................   : $BUILD_HOST
-echo Configure date..................   : $BUILD_DATE
-echo Build architecture..............   : $BUILD_ARCH
-echo SVN revision number.............   : $BUILD_VERSION
-echo
-echo
-echo '-------------------------------------------------------------------------------'
-
-echo
-echo Configure complete, now type \'make\' and then \'make install\'.
-echo
-echo To verify your verification library, type \'make check\'
-echo to run a suite of regression tests.
-
-])
diff --git a/samples/Makefile.am b/samples/Makefile.am
deleted file mode 100644
index 9b5df6b24..000000000
--- a/samples/Makefile.am
+++ /dev/null
@@ -1,7 +0,0 @@
-SUBDIRS  = cxx
-
-EXTRA_DIST =
-
-dist-hook:
-	rm -rf `find $(distdir)/ -name .svn`
-	rm -rf `find $(distdir)/ -name .deps`
\ No newline at end of file
diff --git a/samples/cxx/Makefile.am b/samples/cxx/Makefile.am
deleted file mode 100644
index c289c6711..000000000
--- a/samples/cxx/Makefile.am
+++ /dev/null
@@ -1,24 +0,0 @@
-h_sources  = example_utils.h
-
-cc_sources = examples.cpp kinetics_example1.cpp \
-	     kinetics_example3.cpp  equil_example1.cpp                \
-	     transport_example1.cpp transport_example2.cpp            \
-	     rxnpath_example1.cpp 
-
-LINK                 = -lctcxx -luser -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++
-
-LIBS                 = -L$(top_builddir)/build/lib/ $(LINK)
-AM_CPPFLAGS          = -I. -I$(top_builddir)/build/include/
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-bin_PROGRAMS         = cxx_examples
-library_includedir   = $(includedir) -I$(top_builddir)/build/include/
-
-#-----------------------
-# Cantera cxx examples
-#-----------------------
-
-cxx_examples_LDFLAGS = $(all_libraries) -release $(GENERIC_RELEASE)
-cxx_examples_SOURCES = $(cc_sources) $(h_sources)
diff --git a/src/Makefile.am b/src/Makefile.am
deleted file mode 100644
index c62e8a5bf..000000000
--- a/src/Makefile.am
+++ /dev/null
@@ -1,5 +0,0 @@
-# will need to add python and matlab 
-SUBDIRS = base numerics thermo transport oneD zeroD kinetics spectra equil fortran tpx
-
-
-
diff --git a/src/apps/Makefile.am b/src/apps/Makefile.am
deleted file mode 100644
index 884cf1ef8..000000000
--- a/src/apps/Makefile.am
+++ /dev/null
@@ -1,15 +0,0 @@
-cc_sources = csvdiff.cpp mdp_allo.cpp tok_input_util.cpp
-h_sources  = mdp_allo.h
-
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LIBS                 =  $(LINK)
-bin_PROGRAMS         = $(top_builddir)/bin/csvdiff
-
-#---------------------------------------
-# Cantera comma sep value differ
-#---------------------------------------
-
-__top_builddir__bin_csvdiff_SOURCES = $(cc_sources)
-
diff --git a/src/base/Makefile.am b/src/base/Makefile.am
deleted file mode 100644
index 65f7d0876..000000000
--- a/src/base/Makefile.am
+++ /dev/null
@@ -1,46 +0,0 @@
-h_sources               = $(top_builddir)/include/cantera/base/utilities.h \
-                          $(top_builddir)/include/cantera/base/ct_defs.h \
-                          $(top_builddir)/include/cantera/base/ctexceptions.h \
-                          $(top_builddir)/include/cantera/base/logger.h  \
-                          $(top_builddir)/include/cantera/base/ctml.h \
-                          $(top_builddir)/include/cantera/base/plots.h \
-                          $(top_builddir)/include/cantera/base/stringUtils.h \
-                          $(top_builddir)/include/cantera/base/xml.h  \
-			  $(top_builddir)/include/cantera/base/Array.h \
-                          $(top_builddir)/include/cantera/base/vec_functions.h \
-                          $(top_builddir)/include/cantera/base/global.h \
-                          $(top_builddir)/include/cantera/base/XML_Writer.h  \
-                          $(top_builddir)/include/cantera/base/FactoryBase.h \
-                          $(top_builddir)/include/cantera/base/clockWC.h \
-	                  $(top_builddir)/include/cantera/base/PrintCtrl.h \
-			  LogPrintCtrl.h units.h application.h
-
-cc_sources              = ct2ctml.cpp ctml.cpp plots.cpp                   \
-			  stringUtils.cpp xml.cpp clockWC.cpp              \
-	                  PrintCtrl.cpp LogPrintCtrl.cpp       \
-			  checkFinite.cpp application.cpp ctexceptions.cpp \
-	                  global.cpp
-
-AM_LDFLAGS              = -L$(top_builddir)/build/lib/ 
-LIBS                    = -L$(top_builddir)/build/lib/ -lexecstream
-
-AM_CPPFLAGS             = -I$(top_builddir) -I$(top_builddir)/include -I$(top_builddir)/ext/libexecstream
-AM_CXXFLAGS             = $(AM_CPPFLAGS)
-
-lib_LTLIBRARIES         = $(top_builddir)/build/lib/libctbase.la
-library_includedir      = $(top_builddir)/build/include
-
-otherincludedir         = $(top_builddir)/build/include/cantera/kernel
-otherinclude_HEADERS    = $(h_sources)
-
-#-----------------------
-# Cantera Converters C/C++ library
-#-----------------------
-
-__top_builddir__build_lib_libctbase_la_LDFLAGS      = $(all_libraries) -release $(GENERIC_RELEASE)
-__top_builddir__build_lib_libctbase_la_SOURCES      = $(cc_sources) $(h_sources)
-
-__top_builddir__build_lib_libctbase_include_HEADERS = $(h_sources)
-__top_builddir__build_lib_libctbase_includedir = $(prefix)/include/cantera/base
-
-CLEANFILES = *.o
diff --git a/src/equil/Makefile.am b/src/equil/Makefile.am
deleted file mode 100644
index 39a7c5738..000000000
--- a/src/equil/Makefile.am
+++ /dev/null
@@ -1,46 +0,0 @@
-h_sources = $(top_builddir)/include/cantera/equil/ChemEquil.h \
-            $(top_builddir)/include/cantera/equil/vcs_internal.h \
-            $(top_builddir)/include/cantera/equil/equil.h \
-            $(top_builddir)/include/cantera/equil/vcs_defs.h \
-            $(top_builddir)/include/cantera/equil/vcs_IntStarStar.h \
-            $(top_builddir)/include/cantera/equil/MultiPhaseEquil.h \
-            $(top_builddir)/include/cantera/equil/vcs_DoubleStarStar.h \
-            $(top_builddir)/include/cantera/equil/vcs_MultiPhaseEquil.h \
-            $(top_builddir)/include/cantera/equil/MultiPhase.h \
-            $(top_builddir)/include/cantera/equil/vcs_prob.h \
-            $(top_builddir)/include/cantera/equil/vcs_VolPhase.h \
-            $(top_builddir)/include/cantera/equil/vcs_solve.h
-
-#            $(top_builddir)/include/cantera/equil/PropertyCalculator.h
-#            $(top_builddir)/include/cantera/equil/vcs_SpeciesProperties.h
-#            $(top_builddir)/include/cantera/equil/vcs_species_thermo.h 
-#            $(top_builddir)/include/cantera/equil/vcs_Exception.h 
-
-cc_sources = BasisOptimize.cpp vcs_Gibbs.cpp vcs_root1d.cpp \
-             ChemEquil.cpp vcs_rxnadj.cpp vcs_TP.cpp \
-             equilibrate.cpp vcs_IntStarStar.cpp vcs_setMolesLinProg.cpp \
-             MultiPhase.cpp  vcs_MultiPhaseEquil.cpp vcs_solve.cpp \
-             MultiPhaseEquil.cpp vcs_nondim.cpp  vcs_solve_TP.cpp \
-             vcs_DoubleStarStar.cpp  vcs_phaseStability.cpp vcs_SpeciesProperties.cpp \
-             vcs_elem.cpp vcs_prep.cpp vcs_species_thermo.cpp \
-             vcs_elem_rearrange.cpp  vcs_prob.cpp vcs_inest.cpp \
-             vcs_equilibrate.cpp vcs_rearrange.cpp vcs_util.cpp \
-             vcs_report.cpp vcs_VolPhase.cpp \
-             vcs_solve_phaseStability.cpp
-#vcs_Exception.cpp 
-
-AM_CPPFLAGS = -I$(top_builddir)/include -I$(top_builddir)/ext/f2c_libs/
-AM_CXXFLAGS = $(AM_CPPFLAGS)
-
-lib_LTLIBRARIES    = $(top_builddir)/build/lib/libequil.la
-library_includedir = $(includedir)
-
-#-----------------------
-# Cantera Equil C/C++ library
-#-----------------------
-
-__top_builddir__build_lib_libequil_la_LDFLAGS      = $(all_libraries) -release $(GENERIC_RELEASE)
-__top_builddir__build_lib_libequil_la_SOURCES      = $(cc_sources) $(h_sources)
-
-__top_builddir__build_lib_libequil_include_HEADERS = $(h_sources)
-__top_builddir__build_lib_libequil_includedir = $(prefix)/include/cantera/equil
diff --git a/src/fortran/Makefile.am b/src/fortran/Makefile.am
deleted file mode 100644
index 28aa444b8..000000000
--- a/src/fortran/Makefile.am
+++ /dev/null
@@ -1,34 +0,0 @@
-cc_sources = fct.cpp fctxml.cpp
-
-fc_sources = fct_interface.f90 fctxml_interface.f90 cantera_xml.f90 cantera_thermo.f90 \
-	     cantera_kinetics.f90 cantera_transport.f90 cantera_iface.f90              \
-	     cantera_funcs.f90 cantera.f90
-
-h_sources               = 
-
-INC                     = -I$(top_builddir)/include/ -I$(top_builddir)/src/
-AM_CPPFLAGS             = $(INC)
-AM_CXXFLAGS             = $(AM_CPPFLAGS)
-AM_FCFLAGS              = $(AM_CPPFLAGS)
-
-LINK                    = -luser -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo
-LINK                   += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode
-LINK                   += -lctlapack -lctblas -lctf2c -lctcxx -lm  -lctf2c -lstdc++
-
-AM_LDFLAGS              = -L$(top_builddir)/build/lib/
-
-lib_LTLIBRARIES         = $(top_builddir)/build/lib/libfct.la
-library_includedir      = $(top_builddir)/build/include
-library_include_HEADERS = $(h_sources)
-
-#-----------------------
-# Cantera Converters C/C++ library
-#-----------------------
-
-__top_builddir__build_lib_libfct_la_LDFLAGS      = $(all_libraries) -release $(GENERIC_RELEASE)
-__top_builddir__build_lib_libfct_la_SOURCES      = $(cc_sources) $(fc_sources) $(h_sources)
-
-__top_builddir__build_lib_libfct_include_HEADERS = $(h_sources)
-__top_builddir__build_lib_libfct_includedir      = $(prefix)/include
-
-CLEANFILES = *.o
diff --git a/src/kinetics/Makefile.am b/src/kinetics/Makefile.am
deleted file mode 100644
index 6907f98ee..000000000
--- a/src/kinetics/Makefile.am
+++ /dev/null
@@ -1,46 +0,0 @@
-
-h_sources  = $(top_builddir)/include/cantera/kinetics/importKinetics.h \
-             $(top_builddir)/include/cantera/kinetics/GRI_30_Kinetics.h \
-             $(top_builddir)/include/cantera/kinetics/KineticsFactory.h \
-             $(top_builddir)/include/cantera/kinetics/Kinetics.h \
-             $(top_builddir)/include/cantera/kinetics/GasKinetics.h  \
-             $(top_builddir)/include/cantera/kinetics/FalloffFactory.h \
-             $(top_builddir)/include/cantera/kinetics/ReactionStoichMgr.h \
-             $(top_builddir)/include/cantera/kinetics/reaction_defs.h \
-             $(top_builddir)/include/cantera/kinetics/FalloffMgr.h  \
-             $(top_builddir)/include/cantera/kinetics/ThirdBodyMgr.h  \
-             $(top_builddir)/include/cantera/kinetics/RateCoeffMgr.h \
-             $(top_builddir)/include/cantera/kinetics/ReactionData.h \
-             $(top_builddir)/include/cantera/kinetics/RxnRates.h \
-             $(top_builddir)/include/cantera/kinetics/Enhanced3BConc.h \
-             $(top_builddir)/include/cantera/kinetics/StoichManager.h \
-             $(top_builddir)/include/cantera/kinetics/AqueousKinetics.h \
-             $(top_builddir)/include/cantera/kinetics/InterfaceKinetics.h  \
-             $(top_builddir)/include/cantera/kinetics/Group.h \
-             $(top_builddir)/include/cantera/kinetics/ReactionPath.h \
-             $(top_builddir)/include/cantera/kinetics/EdgeKinetics.h
-
-#             $(top_builddir)/include/cantera/kinetics/solveSP.h 
-#             $(top_builddir)/include/cantera/kinetics/ImplicitSurfChem.h 
-
-cc_sources = AqueousKinetics.cpp FalloffFactory.cpp GRI_30_Kinetics.cpp \
-             GasKinetics.cpp Group.cpp ImplicitSurfChem.cpp InterfaceKinetics.cpp \
-             Kinetics.cpp KineticsFactory.cpp ReactionPath.cpp ReactionStoichMgr.cpp \
-             importKinetics.cpp solveSP.cpp
-
-
-AM_CPPFLAGS             = -I$(top_builddir)/include/
-AM_CXXFLAGS             = $(AM_CPPFLAGS)
-
-lib_LTLIBRARIES         = $(top_builddir)/build/lib/libkinetics.la
-library_includedir      = $(includedir)
-
-#-----------------------
-# Cantera Kinetics C/C++ library
-#-----------------------
-
-__top_builddir__build_lib_libkinetics_la_LDFLAGS      = $(all_libraries) -release $(GENERIC_RELEASE)
-__top_builddir__build_lib_libkinetics_la_SOURCES      = $(cc_sources) $(h_sources)
-
-__top_builddir__build_lib_libkinetics_include_HEADERS = $(h_sources)
-__top_builddir__build_lib_libkinetics_includedir = $(prefix)/include/cantera/base
\ No newline at end of file
diff --git a/src/numerics/Makefile.am b/src/numerics/Makefile.am
deleted file mode 100644
index 448ddba05..000000000
--- a/src/numerics/Makefile.am
+++ /dev/null
@@ -1,39 +0,0 @@
-h_sources  = $(top_builddir)/include/cantera/numerics/DenseMatrix.h \
-             $(top_builddir)/include/cantera/numerics/funcs.h \
-             $(top_builddir)/include/cantera/numerics/ctlapack.h \
-             $(top_builddir)/include/cantera/numerics/Func1.h \
-             $(top_builddir)/include/cantera/numerics/FuncEval.h \
-             $(top_builddir)/include/cantera/numerics/polyfit.h \
-             $(top_builddir)/include/cantera/numerics/BandMatrix.h \
-             $(top_builddir)/include/cantera/numerics/Integrator.h \
-             $(top_builddir)/include/cantera/numerics/DAE_Solver.h \
-             $(top_builddir)/include/cantera/numerics/ResidEval.h \
-             $(top_builddir)/include/cantera/numerics/SquareMatrix.h \
-             $(top_builddir)/include/cantera/numerics/ResidJacEval.h \
-             $(top_builddir)/include/cantera/numerics/NonlinearSolver.h 
-
-# $(top_builddir)/include/cantera/numerics/ArrayViewer.h
-#             $(top_builddir)/include/cantera/numerics/sort.h
-
-#            $(top_builddir)/include/cantera/numerics/CVodeInt.h
-
-cc_sources = BEulerInt.cpp DenseMatrix.cpp funcs.cpp Func1.cpp ODE_integrators.cpp \
-	     BandMatrix.cpp DAE_solvers.cpp CVodeInt.cpp GeneralMatrix.cpp   \
-	     SquareMatrix.cpp ResidJacEval.cpp NonlinearSolver.cpp IDA_Solver.cpp \
-	     RootFind.cpp solveProb.cpp 
-
-AM_CPPFLAGS             = -I$(top_builddir)/include/ -I$(top_builddir)
-AM_CXXFLAGS             = $(AM_CPPFLAGS)
-
-lib_LTLIBRARIES         = $(top_builddir)/build/lib/libctnumerics.la
-library_includedir      = $(includedir)
-
-#-----------------------
-# Cantera Numerics C/C++ library
-#-----------------------
-
-__top_builddir__build_lib_libctnumerics_la_LDFLAGS      = $(all_libraries) -release $(GENERIC_RELEASE)
-__top_builddir__build_lib_libctnumerics_la_SOURCES      = $(cc_sources) $(h_sources)
-
-__top_builddir__build_lib_libctnumerics_include_HEADERS = $(h_sources)
-__top_builddir__build_lib_libctnumerics_includedir = $(prefix)/include/cantera/numerics
diff --git a/src/oneD/Makefile.am b/src/oneD/Makefile.am
deleted file mode 100644
index 22874241c..000000000
--- a/src/oneD/Makefile.am
+++ /dev/null
@@ -1,31 +0,0 @@
-h_sources  = $(top_builddir)/include/cantera/oneD/Inlet1D.h \
-             $(top_builddir)/include/cantera/oneD/MultiJac.h \
-             $(top_builddir)/include/cantera/oneD/Sim1D.h \
-             $(top_builddir)/include/cantera/oneD/StFlow.h \
-             $(top_builddir)/include/cantera/oneD/Domain1D.h \
-             $(top_builddir)/include/cantera/oneD/MultiNewton.h \
-             $(top_builddir)/include/cantera/oneD/OneDim.h \
-             $(top_builddir)/include/cantera/oneD/refine.h
-
-#             $(top_builddir)/include/cantera/oneD/Surf1D.h  
-#             $(top_builddir)/include/cantera/oneD/Resid1D.h
-#             $(top_builddir)/include/cantera/oneD/Solid1D.h
-
-cc_sources = MultiJac.cpp MultiNewton.cpp newton_utils.cpp OneDim.cpp \
-             StFlow.cpp boundaries1D.cpp refine.cpp Sim1D.cpp Domain1D.cpp
-
-AM_CPPFLAGS             = -I$(top_builddir)/include
-AM_CXXFLAGS             = $(AM_CPPFLAGS) -fPIC
-
-lib_LTLIBRARIES         = $(top_builddir)/build/lib/liboneD.la
-library_includedir      = $(includedir)
-
-#-----------------------
-# Cantera OneD C/C++ library
-#-----------------------
-
-__top_builddir__build_lib_liboneD_la_LDFLAGS      = $(all_libraries) -release $(GENERIC_RELEASE)
-__top_builddir__build_lib_liboneD_la_SOURCES      = $(cc_sources) $(h_sources)
-
-__top_builddir__build_lib_liboneD_include_HEADERS = $(h_sources)
-__top_builddir__build_lib_liboneD_includedir = $(prefix)/include/cantera/oneD
diff --git a/src/spectra/Makefile.am b/src/spectra/Makefile.am
deleted file mode 100644
index e583df700..000000000
--- a/src/spectra/Makefile.am
+++ /dev/null
@@ -1,22 +0,0 @@
-
-h_sources  = $(top_builddir)/include/cantera/spectra/LineBroadener.h \
-             $(top_builddir)/include/cantera/spectra/rotor.h
-#             $(top_builddir)/include/cantera/spectra/spectralUtilities.h
-
-cc_sources = LineBroadener.cpp rotor.cpp spectralUtilities.cpp
-
-AM_CPPFLAGS             = -I$(top_builddir)/include
-AM_CXXFLAGS             = $(AM_CPPFLAGS)
-
-lib_LTLIBRARIES         = $(top_builddir)/build/lib/libctspectra.la
-library_includedir      = $(includedir)
-
-#-----------------------
-# Cantera Spectra C/C++ library
-#-----------------------
-
-__top_builddir__build_lib_libctspectra_la_LDFLAGS      = $(all_libraries) -release $(GENERIC_RELEASE)
-__top_builddir__build_lib_libctspectra_la_SOURCES      = $(cc_sources) $(h_sources)
-
-__top_builddir__build_lib_libctspectra_include_HEADERS = $(h_sources)
-__top_builddir__build_lib_libctspectra_includedir = $(prefix)/include/cantera/spectra
diff --git a/src/thermo/Makefile.am b/src/thermo/Makefile.am
deleted file mode 100644
index e7bdd2ac2..000000000
--- a/src/thermo/Makefile.am
+++ /dev/null
@@ -1,112 +0,0 @@
-h_sources  = $(top_builddir)/include/cantera/thermo/Elements.h \
-             $(top_builddir)/include/cantera/thermo/Phase.h \
-             $(top_builddir)/include/cantera/thermo/mix_defs.h  \
-             $(top_builddir)/include/cantera/thermo/ThermoPhase.h \
-             $(top_builddir)/include/cantera/thermo/IdealGasPhase.h \
-             $(top_builddir)/include/cantera/thermo/ConstDensityThermo.h \
-             $(top_builddir)/include/cantera/thermo/SpeciesThermoFactory.h \
-             $(top_builddir)/include/cantera/thermo/ThermoFactory.h \
-             $(top_builddir)/include/cantera/thermo/NasaPoly1.h \
-             $(top_builddir)/include/cantera/thermo/Nasa9Poly1.h \
-             $(top_builddir)/include/cantera/thermo/WaterPropsIAPWS.h\
-             $(top_builddir)/include/cantera/thermo/SimpleThermo.h \
-             $(top_builddir)/include/cantera/thermo/SpeciesThermoInterpType.h \
-             $(top_builddir)/include/cantera/thermo/VPSSMgr_Water_ConstVol.h \
-             $(top_builddir)/include/cantera/thermo/GeneralSpeciesThermo.h \
-             $(top_builddir)/include/cantera/thermo/Mu0Poly.h \
-             $(top_builddir)/include/cantera/thermo/speciesThermoTypes.h \
-             $(top_builddir)/include/cantera/thermo/SpeciesThermo.h \
-             $(top_builddir)/include/cantera/thermo/SurfPhase.h  \
-             $(top_builddir)/include/cantera/thermo/EdgePhase.h \
-             $(top_builddir)/include/cantera/thermo/IdealSolnGasVPSS.h \
-             $(top_builddir)/include/cantera/thermo/MolalityVPSSTP.h  \
-             $(top_builddir)/include/cantera/thermo/VPSSMgr.h \
-             $(top_builddir)/include/cantera/thermo/VPSSMgr_General.h \
-             $(top_builddir)/include/cantera/thermo/VPSSMgr_IdealGas.h \
-             $(top_builddir)/include/cantera/thermo/VPSSMgr_ConstVol.h \
-             $(top_builddir)/include/cantera/thermo/PDSS_ConstVol.h \
-             $(top_builddir)/include/cantera/thermo/PDSS_IdealGas.h \
-             $(top_builddir)/include/cantera/thermo/PDSS_SSVol.h \
-             $(top_builddir)/include/cantera/thermo/DebyeHuckel.h  \
-             $(top_builddir)/include/cantera/thermo/VPStandardStateTP.h \
-             $(top_builddir)/include/cantera/thermo/PDSS_Water.h \
-             $(top_builddir)/include/cantera/thermo/WaterProps.h   \
-             $(top_builddir)/include/cantera/thermo/WaterPropsIAPWSphi.h \
-             $(top_builddir)/include/cantera/thermo/VPSSMgr_Water_HKFT.h \
-             $(top_builddir)/include/cantera/thermo/PDSS_HKFT.h \
-             $(top_builddir)/include/cantera/thermo/PDSS_IonsFromNeutral.h \
-             $(top_builddir)/include/cantera/thermo/IonsFromNeutralVPSSTP.h \
-             $(top_builddir)/include/cantera/thermo/GibbsExcessVPSSTP.h \
-             $(top_builddir)/include/cantera/thermo/LatticePhase.h \
-             $(top_builddir)/include/cantera/thermo/IdealMolalSoln.h \
-             $(top_builddir)/include/cantera/thermo/PDSS.h \
-             $(top_builddir)/include/cantera/thermo/HMWSoln.h \
-             $(top_builddir)/include/cantera/thermo/WaterSSTP.h \
-             $(top_builddir)/include/cantera/thermo/MetalSHEelectrons.h  \
-             $(top_builddir)/include/cantera/thermo/IdealSolidSolnPhase.h \
-             $(top_builddir)/include/cantera/thermo/StoichSubstanceSSTP.h \
-             $(top_builddir)/include/cantera/thermo/SingleSpeciesTP.h \
-             $(top_builddir)/include/cantera/thermo/MineralEQ3.h \
-             $(top_builddir)/include/cantera/thermo/PseudoBinaryVPSSTP.h \
-             $(top_builddir)/include/cantera/thermo/MargulesVPSSTP.h \
-             $(top_builddir)/include/cantera/thermo/StoichSubstance.h \
-             $(top_builddir)/include/cantera/thermo/electrolytes.h     \
-             $(top_builddir)/include/cantera/thermo/PureFluidPhase.h \
-             $(top_builddir)/include/cantera/thermo/LatticeSolidPhase.h \
-             $(top_builddir)/include/cantera/thermo/MetalPhase.h     \
-             $(top_builddir)/include/cantera/thermo/SpeciesThermoMgr.h \
-             $(top_builddir)/include/cantera/thermo/StatMech.h
-
-#$(top_builddir)/include/cantera/thermo/State.h
-#             $(top_builddir)/include/cantera/thermo/Constituents.h
-#             $(top_builddir)/include/cantera/thermo/NasaPoly2.h 
-#             $(top_builddir)/include/cantera/thermo/NasaThermo.h 
-#             $(top_builddir)/include/cantera/thermo/Nasa9PolyMultiTempRegion.h 
-#             $(top_builddir)/include/cantera/thermo/ShomateThermo.h 
-#             $(top_builddir)/include/cantera/thermo/ShomatePoly.h 
-#             $(top_builddir)/include/cantera/thermo/ConstCpPoly.h  
-#             $(top_builddir)/include/cantera/thermo/VPSSMgrFactory.h
-#             $(top_builddir)/include/cantera/thermo/VPSSMgr_types.h
-#             $(top_builddir)/include/cantera/thermo/PecosGasPhase.h
-
-
-cc_sources = ConstCpPoly.cpp ConstDensityThermo.cpp DebyeHuckel.cpp        \
-             Elements.cpp FixedChemPotSSTP.cpp GeneralSpeciesThermo.cpp    \
-             GibbsExcessVPSSTP.cpp HMWSoln.cpp HMWSoln_input.cpp           \
-             IdealGasPhase.cpp IdealMolalSoln.cpp IdealSolidSolnPhase.cpp  \
-	     IdealSolnGasVPSS.cpp IonsFromNeutralVPSSTP.cpp                \
-             LatticePhase.cpp LatticeSolidPhase.cpp MargulesVPSSTP.cpp     \
-	     MetalSHEelectrons.cpp MineralEQ3.cpp                          \
-	     MixedSolventElectrolyte.cpp MixtureFugacityTP.cpp             \
-	     MolalityVPSSTP.cpp MolarityIonicVPSSTP.cpp Mu0Poly.cpp        \
-	     Nasa9Poly1.cpp Nasa9PolyMultiTempRegion.cpp PDSS.cpp          \
-             PDSS_ConstVol.cpp PDSS_HKFT.cpp PDSS_IdealGas.cpp             \
-	     PDSS_IonsFromNeutral.cpp PDSS_SSVol.cpp PDSS_Water.cpp        \
-	     Phase.cpp PhaseCombo_Interaction.cpp PseudoBinaryVPSSTP.cpp   \
-             PureFluidPhase.cpp RedlichKisterVPSSTP.cpp                    \
-             RedlichKwongMFTP.cpp SemiconductorPhase.cpp SingleSpeciesTP.cpp \
-             SpeciesThermoFactory.cpp SpeciesThermoInterpType.cpp          \
-             StoichSubstance.cpp SurfPhase.cpp ThermoPhase.cpp             \
-             StoichSubstanceSSTP.cpp ThermoFactory.cpp VPSSMgr.cpp         \
-             VPSSMgrFactory.cpp VPSSMgr_ConstVol.cpp VPSSMgr_General.cpp   \
-             VPSSMgr_IdealGas.cpp VPSSMgr_Water_ConstVol.cpp               \
-             VPSSMgr_Water_HKFT.cpp VPStandardStateTP.cpp WaterProps.cpp   \
-             WaterPropsIAPWS.cpp WaterPropsIAPWSphi.cpp WaterSSTP.cpp      \
-	     StatMech.cpp
-
-
-AM_CPPFLAGS  = -I$(top_builddir)/include
-AM_CXXFLAGS  = $(AM_CPPFLAGS)
-
-lib_LTLIBRARIES    = $(top_builddir)/build/lib/libthermo.la
-library_includedir = $(includedir)
-
-#-----------------------
-# Cantera thermo C/C++ library
-#-----------------------
-
-__top_builddir__build_lib_libthermo_la_LDFLAGS      = $(all_libraries) -release $(GENERIC_RELEASE)
-__top_builddir__build_lib_libthermo_la_SOURCES      = $(cc_sources) $(h_sources)
-
-__top_builddir__build_lib_libthermo_include_HEADERS = $(h_sources)
-__top_builddir__build_lib_libthermo_includedir = $(prefix)/include/cantera/thermo
diff --git a/src/tpx/Makefile.am b/src/tpx/Makefile.am
deleted file mode 100644
index 329fe029c..000000000
--- a/src/tpx/Makefile.am
+++ /dev/null
@@ -1,24 +0,0 @@
-h_sources = $(top_builddir)/include/cantera/tpx/Sub.h \
-            $(top_builddir)/include/cantera/tpx/utils.h 
-
-cc_sources = Methane.cpp Nitrogen.cpp Oxygen.cpp Water.cpp Hydrogen.cpp RedlichKwong.cpp \
-             CarbonDioxide.cpp Heptane.cpp lk.cpp Sub.cpp utils.cpp HFC134a.cpp
-
-AM_CPPFLAGS = -I$(top_builddir)/include
-AM_CXXFLAGS = $(AM_CPPFLAGS)
-
-lib_LTLIBRARIES         = $(top_builddir)/build/lib/libtpx.la
-library_includedir      = $(top_builddir)/build/include
-library_include_HEADERS = $(h_sources)
-
-#-----------------------
-# Cantera Converters C/C++ library
-#-----------------------
-
-__top_builddir__build_lib_libtpx_la_LDFLAGS      = $(all_libraries) -release $(GENERIC_RELEASE)
-__top_builddir__build_lib_libtpx_la_SOURCES      = $(cc_sources) $(h_sources)
-
-__top_builddir__build_lib_libtpx_include_HEADERS = $(h_sources)
-__top_builddir__build_lib_libtpx_includedir = $(prefix)/include/cantera/tpx
-
-
diff --git a/src/transport/Makefile.am b/src/transport/Makefile.am
deleted file mode 100644
index e100f27f6..000000000
--- a/src/transport/Makefile.am
+++ /dev/null
@@ -1,43 +0,0 @@
-h_sources  = $(top_builddir)/include/cantera/transport/AqueousTransport.h \
-             $(top_builddir)/include/cantera/transport/LiquidTransportData.h \
-             $(top_builddir)/include/cantera/transport/MultiTransport.h \
-             $(top_builddir)/include/cantera/transport/TransportBase.h \
-             $(top_builddir)/include/cantera/transport/WaterTransport.h    \
-             $(top_builddir)/include/cantera/transport/DustyGasTransport.h \
-             $(top_builddir)/include/cantera/transport/LiquidTransport.h \
-             $(top_builddir)/include/cantera/transport/MixTransport.h \
-             $(top_builddir)/include/cantera/transport/SimpleTransport.h \
-             $(top_builddir)/include/cantera/transport/TransportFactory.h \
-             $(top_builddir)/include/cantera/transport/LiquidTransportParams.h \
-             $(top_builddir)/include/cantera/transport/SolidTransport.h \
-             $(top_builddir)/include/cantera/transport/TransportParams.h \
-             $(top_builddir)/include/cantera/transport/PecosTransport.h
-
-#             $(top_builddir)/include/cantera/transport/L_matrix.h  
-#             $(top_builddir)/include/cantera/transport/FtnTransport.h
-#             $(top_builddir)/include/cantera/transport/MMCollisionInt.h 
-cc_sources = AqueousTransport.cpp LiquidTransport.cpp MMCollisionInt.cpp \
-             SimpleTransport.cpp  TransportBase.cpp WaterTransport.cpp   \
-             DustyGasTransport.cpp  MixTransport.cpp MultiTransport.cpp  \
-	     SolidTransport.cpp TransportFactory.cpp LTPspecies.cpp      \
-	     LiquidTranInteraction.cpp LiquidTransportData.cpp           \
-             LiquidTransportParams.cpp TortuosityBase.cpp                \
-             TortuosityBruggeman.cpp TortuosityMaxwell.cpp               \
-             TortuosityPercolation.cpp TransportParams.cpp               \
-	     GasTransport.cpp PecosTransport.cpp
-
-AM_CPPFLAGS             = -I$(top_builddir)/include
-AM_CXXFLAGS             = $(AM_CPPFLAGS)
-
-lib_LTLIBRARIES         = $(top_builddir)/build/lib/libtransport.la
-library_includedir      = $(includedir)
-
-#-----------------------
-# Cantera Transport C/C++ library
-#-----------------------
-
-__top_builddir__build_lib_libtransport_la_LDFLAGS      = $(all_libraries) -release $(GENERIC_RELEASE)
-__top_builddir__build_lib_libtransport_la_SOURCES      = $(cc_sources) $(h_sources)
-
-__top_builddir__build_lib_libtransport_include_HEADERS = $(h_sources)
-__top_builddir__build_lib_libtransport_includedir = $(prefix)/include/cantera/transport
diff --git a/src/zeroD/Makefile.am b/src/zeroD/Makefile.am
deleted file mode 100644
index 0281fd701..000000000
--- a/src/zeroD/Makefile.am
+++ /dev/null
@@ -1,30 +0,0 @@
-h_sources  = $(top_builddir)/include/cantera/zeroD/Reactor.h \
-             $(top_builddir)/include/cantera/zeroD/ReactorBase.h \
-             $(top_builddir)/include/cantera/zeroD/FlowDevice.h \
-             $(top_builddir)/include/cantera/zeroD/Wall.h \
-             $(top_builddir)/include/cantera/zeroD/ReactorNet.h \
-             $(top_builddir)/include/cantera/zeroD/flowControllers.h \
-             $(top_builddir)/include/cantera/zeroD/Reservoir.h \
-             $(top_builddir)/include/cantera/zeroD/FlowReactor.h \
-             $(top_builddir)/include/cantera/zeroD/ConstPressureReactor.h \
-             $(top_builddir)/include/cantera/zeroD/ReactorFactory.h
-
-cc_sources = Reactor.cpp ReactorBase.cpp FlowDevice.cpp Wall.cpp \
-             ReactorNet.cpp FlowReactor.cpp ConstPressureReactor.cpp \
-             ReactorFactory.cpp
-
-AM_CPPFLAGS             = -I$(top_builddir)/include
-AM_CXXFLAGS             = $(AM_CPPFLAGS)
-
-lib_LTLIBRARIES         = $(top_builddir)/build/lib/libzeroD.la
-library_includedir      = $(includedir)
-
-#-----------------------
-# Cantera OneD C/C++ library
-#-----------------------
-
-__top_builddir__build_lib_libzeroD_la_LDFLAGS      = $(all_libraries) -release $(GENERIC_RELEASE)
-__top_builddir__build_lib_libzeroD_la_SOURCES      = $(cc_sources) $(h_sources)
-
-__top_builddir__build_lib_libzeroD_include_HEADERS = $(h_sources)
-__top_builddir__build_lib_libzeroD_includedir = $(prefix)/include
diff --git a/test_problems/ChemEquil_gri_matrix/Makefile.am b/test_problems/ChemEquil_gri_matrix/Makefile.am
deleted file mode 100644
index 36f96e31f..000000000
--- a/test_problems/ChemEquil_gri_matrix/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = gri_matrix.cpp
-
-INC                  = -I. -I$(top_builddir)/include/
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm  -lctf2c -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = gri_matrix
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-gri_matrix_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/ChemEquil_gri_pairs/Makefile.am b/test_problems/ChemEquil_gri_pairs/Makefile.am
deleted file mode 100644
index e239e762b..000000000
--- a/test_problems/ChemEquil_gri_pairs/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = gri_pairs.cpp
-
-INC                  = -I. -I$(top_builddir)/include/
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm  -lctf2c -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = gri_pairs
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-gri_pairs_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/ChemEquil_ionizedGas/Makefile.am b/test_problems/ChemEquil_ionizedGas/Makefile.am
deleted file mode 100644
index 40bce3aac..000000000
--- a/test_problems/ChemEquil_ionizedGas/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = ionizedGasEquil.cpp
-
-INC                  = -I. -I$(top_builddir)/include/
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm  -lctf2c -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = ionizedGasEquil
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-ionizedGasEquil_SOURCES = $(cc_sources)
-
-#TESTS_ENVIRONMENT = 
-#TESTS             = runtest
diff --git a/test_problems/ChemEquil_red1/Makefile.am b/test_problems/ChemEquil_red1/Makefile.am
deleted file mode 100644
index 1c7808e1c..000000000
--- a/test_problems/ChemEquil_red1/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = basopt_red1.cpp
-
-INC                  = -I. -I$(top_builddir)/include/
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm  -lctf2c -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = basopt_red1
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-basopt_red1_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/CpJump/Makefile.am b/test_problems/CpJump/Makefile.am
deleted file mode 100644
index c6a566f7a..000000000
--- a/test_problems/CpJump/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = CpJump.cpp
-
-INC                  = -I. -I$(top_builddir)/include/
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm  -lctf2c -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = CpJump
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-CpJump_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/Makefile.am b/test_problems/Makefile.am
deleted file mode 100644
index 4dc91ad3c..000000000
--- a/test_problems/Makefile.am
+++ /dev/null
@@ -1,20 +0,0 @@
-
-SUBDIRS  = statmech cathermo mixGasTransport ChemEquil_gri_matrix ChemEquil_gri_pairs
-SUBDIRS += ChemEquil_ionizedGas ChemEquil_red1 CpJump cxx_ex diamondSurf 
-SUBDIRS += diamondSurf_dupl fracCoeff multiGasTransport NASA9poly_test
-SUBDIRS += negATest printUtilUnitTest pureFluidTest silane_equil 
-SUBDIRS += spectroscopy surfkin surfSolverTest VPsilane_test 
-SUBDIRS += VCSnonideal PecosTransport
-
-#f77test
-
-# skipped (uses ck2cti or python):
-# python
-# rankine_democxx
-# VCSnonideal (unsure of problem)
-
-EXTRA_DIST =
-
-dist-hook:
-	rm -rf `find $(distdir)/ -name .svn`
-	rm -rf `find $(distdir)/ -name .deps`
\ No newline at end of file
diff --git a/test_problems/NASA9poly_test/Makefile.am b/test_problems/NASA9poly_test/Makefile.am
deleted file mode 100644
index 3257d83ad..000000000
--- a/test_problems/NASA9poly_test/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = NASA9poly_test.cpp
-
-INC                  = -I. -I$(top_builddir)/include/
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm  -lctf2c -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = NASA9poly_test
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-NASA9poly_test_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/PecosTransport/Makefile.am b/test_problems/PecosTransport/Makefile.am
deleted file mode 100644
index ed9f321fe..000000000
--- a/test_problems/PecosTransport/Makefile.am
+++ /dev/null
@@ -1,26 +0,0 @@
-cc_sources = PecosTransport.cpp
-
-INC                  = -I. -I$(top_builddir)/include/ -g
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = PecosTransport
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera Pecos Transport test
-#-----------------------
-
-PecosTransport_SOURCES = $(cc_sources)
-
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
-
-EXTRA_DIST = runtest
\ No newline at end of file
diff --git a/test_problems/VCSnonideal/Makefile.am b/test_problems/VCSnonideal/Makefile.am
deleted file mode 100644
index ce5c90005..000000000
--- a/test_problems/VCSnonideal/Makefile.am
+++ /dev/null
@@ -1 +0,0 @@
-#SUBDIRS = NaCl_equil
\ No newline at end of file
diff --git a/test_problems/VCSnonideal/NaCl_equil/Makefile.am b/test_problems/VCSnonideal/NaCl_equil/Makefile.am
deleted file mode 100644
index 6d1ba9670..000000000
--- a/test_problems/VCSnonideal/NaCl_equil/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = nacl_equil.cpp
-
-INC                  = -I. -I$(top_builddir)/build/include/
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -luser -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lctcxx -lm  -lctf2c -lstdc++
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = nacl_equil
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-nacl_equil_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/VPsilane_test/Makefile.am b/test_problems/VPsilane_test/Makefile.am
deleted file mode 100644
index f297cc3e7..000000000
--- a/test_problems/VPsilane_test/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = silane_equil.cpp
-
-INC                  = -I. -I$(top_builddir)/include/
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm  -lctf2c -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         =VPsilane_test
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-VPsilane_test_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/cathermo/DH_graph_1/Makefile.am b/test_problems/cathermo/DH_graph_1/Makefile.am
deleted file mode 100644
index f05c35c16..000000000
--- a/test_problems/cathermo/DH_graph_1/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-INC                  = -I. -I$(top_builddir)/include -I$(top_builddir)/test_problems/shared
-INC                 += -I$(top_builddir)/ext/libexecstream
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++ -lexecstream -pthread
-#-lctcxx -luser 
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = DH_graph_1
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-DH_graph_1_SOURCES = DH_graph_1.cpp
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/cathermo/HMW_dupl_test/Makefile.am b/test_problems/cathermo/HMW_dupl_test/Makefile.am
deleted file mode 100644
index 8d8685f78..000000000
--- a/test_problems/cathermo/HMW_dupl_test/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = HMW_dupl_test.cpp
-
-INC                  = -I$(top_builddir)/include/ -I$(top_builddir)/test_problems/shared
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = HMW_dupl_test
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-HMW_dupl_test_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/cathermo/HMW_graph_CpvT/Makefile.am b/test_problems/cathermo/HMW_graph_CpvT/Makefile.am
deleted file mode 100644
index d0fcd6e04..000000000
--- a/test_problems/cathermo/HMW_graph_CpvT/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = HMW_graph_CpvT.cpp
-
-INC                  = -I$(top_builddir)/include/ -I$(top_builddir)/test_problems/shared
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = HMW_graph_CpvT
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-HMW_graph_CpvT_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/cathermo/HMW_graph_GvI/Makefile.am b/test_problems/cathermo/HMW_graph_GvI/Makefile.am
deleted file mode 100644
index aa65ffeb6..000000000
--- a/test_problems/cathermo/HMW_graph_GvI/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = HMW_graph_GvI.cpp 
-
-INC                  = -I$(top_builddir)/include/ 
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = HMW_graph_GvI
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-HMW_graph_GvI_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/cathermo/HMW_graph_GvT/Makefile.am b/test_problems/cathermo/HMW_graph_GvT/Makefile.am
deleted file mode 100644
index f67391227..000000000
--- a/test_problems/cathermo/HMW_graph_GvT/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = HMW_graph_GvT.cpp
-
-INC                  = -I$(top_builddir)/include/ -I$(top_builddir)/test_problems/shared
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = HMW_graph_GvT
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-HMW_graph_GvT_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/cathermo/HMW_graph_HvT/Makefile.am b/test_problems/cathermo/HMW_graph_HvT/Makefile.am
deleted file mode 100644
index 9bd88964d..000000000
--- a/test_problems/cathermo/HMW_graph_HvT/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = HMW_graph_HvT.cpp
-
-INC                  = -I$(top_builddir)/include/ -I$(top_builddir)/test_problems/shared
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = HMW_graph_HvT
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-HMW_graph_HvT_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/cathermo/HMW_graph_VvT/Makefile.am b/test_problems/cathermo/HMW_graph_VvT/Makefile.am
deleted file mode 100644
index 223f735f5..000000000
--- a/test_problems/cathermo/HMW_graph_VvT/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = HMW_graph_VvT.cpp
-
-INC                  = -I$(top_builddir)/include/ -I$(top_builddir)/test_problems/shared
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++ -lexecstream -pthread
-LIBS                 =  $(LINK)
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-
-bin_PROGRAMS         = HMW_graph_VvT
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-HMW_graph_VvT_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/cathermo/HMW_test_1/Makefile.am b/test_problems/cathermo/HMW_test_1/Makefile.am
deleted file mode 100644
index 4f68701ec..000000000
--- a/test_problems/cathermo/HMW_test_1/Makefile.am
+++ /dev/null
@@ -1,24 +0,0 @@
-cc_sources = HMW_test_1.cpp
-
-INC                  = -I$(top_builddir)/include/ 
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = HMW_test_1
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-HMW_test_1_SOURCES = $(cc_sources)
-
-# test needs to be repaired
-#TESTS_ENVIRONMENT = 
-#TESTS             = runtest
diff --git a/test_problems/cathermo/HMW_test_3/Makefile.am b/test_problems/cathermo/HMW_test_3/Makefile.am
deleted file mode 100644
index ddf4e2e27..000000000
--- a/test_problems/cathermo/HMW_test_3/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = HMW_test_3.cpp
-
-INC                  = -I$(top_builddir)/include/
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = HMW_test_3
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-HMW_test_3_SOURCES = $(cc_sources)
-
-#TESTS_ENVIRONMENT = 
-#TESTS             = runtest
diff --git a/test_problems/cathermo/Makefile.am b/test_problems/cathermo/Makefile.am
deleted file mode 100644
index 2b2438d21..000000000
--- a/test_problems/cathermo/Makefile.am
+++ /dev/null
@@ -1,4 +0,0 @@
-SUBDIRS  = DH_graph_1 HMW_dupl_test HMW_graph_CpvT
-SUBDIRS += HMW_graph_CpvT HMW_graph_GvT HMW_graph_VvT HMW_test_3 HMW_graph_GvI HMW_graph_HvT HMW_test_1    
-SUBDIRS += issp/ stoichSubSSTP/ testIAPWSPres/ testWaterPDSS/ VPissp/
-SUBDIRS += ims/ testIAPWS/ testIAPWSTripP/ testWaterTP/ wtWater/
diff --git a/test_problems/cathermo/VPissp/Makefile.am b/test_problems/cathermo/VPissp/Makefile.am
deleted file mode 100644
index 15c24b081..000000000
--- a/test_problems/cathermo/VPissp/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = ISSPTester.cpp
-
-INC                  = -I$(top_builddir)/include/
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = ISSPTester
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-ISSPTester_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/cathermo/ims/Makefile.am b/test_problems/cathermo/ims/Makefile.am
deleted file mode 100644
index 9afce991b..000000000
--- a/test_problems/cathermo/ims/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = IMSTester.cpp
-
-INC                  = -I$(top_builddir)/include/
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = IMSTester
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-IMSTester_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/cathermo/issp/Makefile.am b/test_problems/cathermo/issp/Makefile.am
deleted file mode 100644
index 15c24b081..000000000
--- a/test_problems/cathermo/issp/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = ISSPTester.cpp
-
-INC                  = -I$(top_builddir)/include/
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = ISSPTester
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-ISSPTester_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/cathermo/stoichSubSSTP/Makefile.am b/test_problems/cathermo/stoichSubSSTP/Makefile.am
deleted file mode 100644
index 131963f84..000000000
--- a/test_problems/cathermo/stoichSubSSTP/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = stoichSubSSTP.cpp
-
-INC                  = -I$(top_builddir)/include/ -I$(top_builddir)/test_problems/shared 
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = stoichSubSSTP
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-stoichSubSSTP_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/cathermo/testIAPWS/Makefile.am b/test_problems/cathermo/testIAPWS/Makefile.am
deleted file mode 100644
index f3bc9c83c..000000000
--- a/test_problems/cathermo/testIAPWS/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = testIAPWSphi.cpp
-
-INC                  = -I$(top_builddir)/include/
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = testIAPWSphi
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-testIAPWSphi_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/cathermo/testIAPWSPres/Makefile.am b/test_problems/cathermo/testIAPWSPres/Makefile.am
deleted file mode 100644
index 1e3da33fd..000000000
--- a/test_problems/cathermo/testIAPWSPres/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = testPress.cpp
-
-INC                  = -I$(top_builddir)/include/
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = testPress
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-testPress_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/cathermo/testIAPWSTripP/Makefile.am b/test_problems/cathermo/testIAPWSTripP/Makefile.am
deleted file mode 100644
index 595dfe03f..000000000
--- a/test_problems/cathermo/testIAPWSTripP/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = testTripleP.cpp
-
-INC                  = -I$(top_builddir)/include/
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = testTripleP
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-testTripleP_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/cathermo/testWaterPDSS/Makefile.am b/test_problems/cathermo/testWaterPDSS/Makefile.am
deleted file mode 100644
index 7058cda88..000000000
--- a/test_problems/cathermo/testWaterPDSS/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = testWaterPDSS.cpp
-
-INC                  = -I$(top_builddir)/include/ 
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = testWaterPDSS
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-testWaterPDSS_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/cathermo/testWaterTP/Makefile.am b/test_problems/cathermo/testWaterTP/Makefile.am
deleted file mode 100644
index 22147d819..000000000
--- a/test_problems/cathermo/testWaterTP/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = testWaterSSTP.cpp
-
-INC                  = -I$(top_builddir)/include/
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = testWaterSSTP
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera test
-#-----------------------
-
-testWaterSSTP_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/cathermo/wtWater/Makefile.am b/test_problems/cathermo/wtWater/Makefile.am
deleted file mode 100644
index e8a380517..000000000
--- a/test_problems/cathermo/wtWater/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = wtWater.cpp
-
-INC                  = -I$(top_builddir)/include/
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = wtWater
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera test
-#-----------------------
-
-wtWater_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/cxx_ex/Makefile.am b/test_problems/cxx_ex/Makefile.am
deleted file mode 100644
index 3bbcec84f..000000000
--- a/test_problems/cxx_ex/Makefile.am
+++ /dev/null
@@ -1 +0,0 @@
-#TESTS = runtest
\ No newline at end of file
diff --git a/test_problems/diamondSurf/Makefile.am b/test_problems/diamondSurf/Makefile.am
deleted file mode 100644
index a74efaef1..000000000
--- a/test_problems/diamondSurf/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = runDiamond.cpp
-
-INC                  = -I. -I$(top_builddir)/include/
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm  -lctf2c -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = runDiamond
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-runDiamond_SOURCES = $(cc_sources)
-
-#TESTS_ENVIRONMENT = 
-#TESTS             = runtest
diff --git a/test_problems/diamondSurf_dupl/Makefile.am b/test_problems/diamondSurf_dupl/Makefile.am
deleted file mode 100644
index 54fb6c1dc..000000000
--- a/test_problems/diamondSurf_dupl/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = runDiamondDupl.cpp
-
-INC                  = -I. -I$(top_builddir)/include/
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm  -lctf2c -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = runDiamondDupl
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-runDiamondDupl_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/fracCoeff/Makefile.am b/test_problems/fracCoeff/Makefile.am
deleted file mode 100644
index ecde56f51..000000000
--- a/test_problems/fracCoeff/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = fracCoeff.cpp
-
-INC                  = -I. -I$(top_builddir)/include/
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm  -lctf2c -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = fracCoeff
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera fraccoeff tests
-#-----------------------
-
-fracCoeff_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/mixGasTransport/Makefile.am b/test_problems/mixGasTransport/Makefile.am
deleted file mode 100644
index 451bc70f8..000000000
--- a/test_problems/mixGasTransport/Makefile.am
+++ /dev/null
@@ -1,24 +0,0 @@
-cc_sources = mixGasTransport.cpp
-
-INC                  = -I. -I$(top_builddir)/include/ -g
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = mixGasTransport
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-mixGasTransport_SOURCES = $(cc_sources)
-
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/multiGasTransport/Makefile.am b/test_problems/multiGasTransport/Makefile.am
deleted file mode 100644
index 282ad9cba..000000000
--- a/test_problems/multiGasTransport/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = multiGasTransport.cpp
-
-INC                  = -I. -I$(top_builddir)/include/
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm  -lctf2c -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = multiGasTransport
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-multiGasTransport_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/negATest/Makefile.am b/test_problems/negATest/Makefile.am
deleted file mode 100644
index f1c0e7e80..000000000
--- a/test_problems/negATest/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = negATest.cpp
-
-INC                  = -I. -I$(top_builddir)/include/ -g
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = negATest
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-negATest_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/printUtilUnitTest/Makefile.am b/test_problems/printUtilUnitTest/Makefile.am
deleted file mode 100644
index 52eed7040..000000000
--- a/test_problems/printUtilUnitTest/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = pUtest.cpp
-
-INC                  = -I. -I$(top_builddir)/include/ -I$(top_builddir)/src/
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm  -lctf2c -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = pUtest
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-pUtest_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/pureFluidTest/Makefile.am b/test_problems/pureFluidTest/Makefile.am
deleted file mode 100644
index 47ad20c72..000000000
--- a/test_problems/pureFluidTest/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = testPureWater.cpp
-
-INC                  = -I. -I$(top_builddir)/include/
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm  -lctf2c -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = testPureWater
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-testPureWater_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/rankine_democxx/Makefile.am b/test_problems/rankine_democxx/Makefile.am
deleted file mode 100644
index bbf9a47a3..000000000
--- a/test_problems/rankine_democxx/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = rankine.cpp
-
-INC                  = -I. -I$(top_builddir)/build/include/
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -luser -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lctcxx -lm  -lctf2c -lstdc++
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = rankine
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-rankine_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/silane_equil/Makefile.am b/test_problems/silane_equil/Makefile.am
deleted file mode 100644
index 461f79948..000000000
--- a/test_problems/silane_equil/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = silane_equil.cpp
-
-INC                  = -I. -I$(top_builddir)/include/
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm  -lctf2c -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = silane_equil
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-silane_equil_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest
diff --git a/test_problems/spectroscopy/Makefile.am b/test_problems/spectroscopy/Makefile.am
deleted file mode 100644
index 8807901ff..000000000
--- a/test_problems/spectroscopy/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = spectratest.cpp
-
-INC                  = -I. -I$(top_builddir)/include/ -I$(top_builddir)/src/
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm  -lctf2c -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = spectroscopy
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-spectroscopy_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = spectroscopy
diff --git a/test_problems/statmech/Makefile.am b/test_problems/statmech/Makefile.am
deleted file mode 100644
index ffaf5fa28..000000000
--- a/test_problems/statmech/Makefile.am
+++ /dev/null
@@ -1,33 +0,0 @@
-INC                  = -I. -I$(top_builddir)/include/
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm  -lctf2c -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-check_PROGRAMS         = statmech_test \
-                         statmech_test_poly \
-                         statmech_test_Fe   \
-	                 statmech_transport
-
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-statmech_test_SOURCES      = statmech_test.cpp
-statmech_test_poly_SOURCES = statmech_test_poly.cpp
-statmech_test_Fe_SOURCES   = statmech_test_Fe.cpp
-statmech_transport_SOURCES = statmech_transport.cpp
-
-TESTS_ENVIRONMENT = 	
-TESTS             = statmech_test \
-                    statmech_test_Fe \
-	            statmech_transport
-#                    statmech_test_poly
-
-EXTRA_DIST = runtest_stat 
\ No newline at end of file
diff --git a/test_problems/surfSolverTest/Makefile.am b/test_problems/surfSolverTest/Makefile.am
deleted file mode 100644
index cc061c9f1..000000000
--- a/test_problems/surfSolverTest/Makefile.am
+++ /dev/null
@@ -1,25 +0,0 @@
-cc_sources = surfaceSolver.cpp
-cc2_sources = surfaceSolver2.cpp
-
-INC                  = -I. -I$(top_builddir)/include/ -I$(top_builddir)/src/
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm  -lctf2c -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = surfaceSolver surfaceSolver2
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-surfaceSolver_SOURCES  = $(cc_sources)
-surfaceSolver2_SOURCES = $(cc2_sources)
-
-#TESTS_ENVIRONMENT = 
-#TESTS             = runtest runtest2
diff --git a/test_problems/surfkin/Makefile.am b/test_problems/surfkin/Makefile.am
deleted file mode 100644
index c4b817b01..000000000
--- a/test_problems/surfkin/Makefile.am
+++ /dev/null
@@ -1,23 +0,0 @@
-cc_sources = surfdemo.cpp
-
-INC                  = -I. -I$(top_builddir)/include/
-AM_CPPFLAGS          = $(INC)
-AM_CXXFLAGS          = $(AM_CPPFLAGS)
-
-LINK                 = -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo 
-LINK                += -lctnumerics -lctmath -ltpx -lctspectra -lctbase -lcvode 
-LINK                += -lctlapack -lctblas -lctf2c -lm  -lctf2c -lstdc++ -lexecstream -pthread
-AM_LDFLAGS           = -L$(top_builddir)/build/lib/ 
-LIBS                 =  $(LINK)
-
-bin_PROGRAMS         = surfdemo
-library_includedir   = $(INC)
-
-#-----------------------
-# Cantera DH graph test
-#-----------------------
-
-surfdemo_SOURCES = $(cc_sources)
-
-TESTS_ENVIRONMENT = 
-TESTS             = runtest