diff --git a/tools/doc/.cvsignore b/tools/doc/.cvsignore
new file mode 100644
index 000000000..f3c7a7c5d
--- /dev/null
+++ b/tools/doc/.cvsignore
@@ -0,0 +1 @@
+Makefile
diff --git a/tools/doc/Cantera.cfg b/tools/doc/Cantera.cfg.in
similarity index 95%
rename from tools/doc/Cantera.cfg
rename to tools/doc/Cantera.cfg.in
index ea0bfbd5c..9b2df247e 100755
--- a/tools/doc/Cantera.cfg
+++ b/tools/doc/Cantera.cfg.in
@@ -5,7 +5,7 @@
 #---------------------------------------------------------------------------
 PROJECT_NAME           = Cantera
 PROJECT_NUMBER         = 1.6
-OUTPUT_DIRECTORY       = /Users/dgg/kernel
+OUTPUT_DIRECTORY       = @ctroot@/tools/doc
 CREATE_SUBDIRS         = NO
 OUTPUT_LANGUAGE        = English
 USE_WINDOWS_ENCODING   = NO
@@ -22,7 +22,7 @@ ABBREVIATE_BRIEF       = "The $name class" \
                          a \
                          an \
                          the
-ALWAYS_DETAILED_SEC    = NO
+ALWAYS_DETAILED_SEC    = YES
 INLINE_INHERITED_MEMB  = NO
 FULL_PATH_NAMES        = NO
 STRIP_FROM_PATH        = 
@@ -81,7 +81,8 @@ WARN_LOGFILE           =
 #---------------------------------------------------------------------------
 # configuration options related to the input files
 #---------------------------------------------------------------------------
-INPUT                  = ../../Cantera/src \
+INPUT                  = ../../Cantera/src \ 
+                         ../../Cantera/src/thermo \
                          ../../Cantera/cxx/include \
                          doxyinput
 FILE_PATTERNS          = Kinetics.h \
@@ -90,6 +91,7 @@ FILE_PATTERNS          = Kinetics.h \
                          ct_defs.h \
                          logger.h \
                          global.h \
+                         units.h \
                          ctexceptions.h \
                          *.txt \
                          equilibrium.h \
@@ -100,11 +102,7 @@ FILE_PATTERNS          = Kinetics.h \
                          Phase.h \
                          utilities.h
 RECURSIVE              = NO
->>>>>>> 1.8.2.3
-EXCLUDE                = CVS \
-                         examples \
-                         converters \
-                         zeroD
+EXCLUDE                = CVS examples  converters zeroD
 EXCLUDE_SYMLINKS       = NO
 EXCLUDE_PATTERNS       = *old/* \
                          *old_src/* \
@@ -113,8 +111,8 @@ EXCLUDE_PATTERNS       = *old/* \
                          *examples/* \
                          *test/* \
                          *tests/*
-EXAMPLE_PATH           = examples \
-                         input
+EXAMPLE_PATH           = ../../examples \
+                         ../../data/inputs
 EXAMPLE_PATTERNS       = *.cpp \
                          *.h
 EXAMPLE_RECURSIVE      = NO
@@ -244,7 +242,7 @@ CALL_GRAPH             = NO
 GRAPHICAL_HIERARCHY    = YES
 DIRECTORY_GRAPH        = YES
 DOT_IMAGE_FORMAT       = png
-DOT_PATH               = /Applications/Graphviz.app/Contents/MacOS
+DOT_PATH               = @GRAPHVIZDIR@
 DOTFILE_DIRS           = 
 MAX_DOT_GRAPH_WIDTH    = 1024
 MAX_DOT_GRAPH_HEIGHT   = 1024
diff --git a/tools/doc/Makefile.in b/tools/doc/Makefile.in
new file mode 100644
index 000000000..56c31bc84
--- /dev/null
+++ b/tools/doc/Makefile.in
@@ -0,0 +1,25 @@
+#
+# $Revision$
+# $Author$
+# $Date$
+#
+build_ck=@BUILD_CK@
+
+all: docs
+
+install:
+
+
+
+man-install:
+
+uninstall:
+
+clean:
+	cd html; $(RM) * 
+
+docs doxygen:
+	doxygen Cantera.cfg
+
+depends:
+
diff --git a/tools/doc/README b/tools/doc/README
new file mode 100644
index 000000000..036298805
--- /dev/null
+++ b/tools/doc/README
@@ -0,0 +1,15 @@
+Doxygen information:
+
+
+The current version is 1.4.7: 
+I have version 1.3.9.1
+
+Support is provided in the following versions for the following features
+
+SEPARATE_MEMBER_PAGES = 1.4.2
+FILE_VERSION_FILTER   = 1.4.0
+WARN_NO_PARAMDOC      = 1.4.0
+GROUP_GRAPHS          = 1.4.0
+DIRECTORY_GRAPHS      = 1.4.0
+DOT_TRANSPARENT       = 1.4.0
+DOT_MULTI_TARGET      =1.4.0
diff --git a/tools/doc/html/.cvsignore b/tools/doc/html/.cvsignore
new file mode 100644
index 000000000..7164c30a3
--- /dev/null
+++ b/tools/doc/html/.cvsignore
@@ -0,0 +1,9 @@
+*.html
+*.md5
+*.png
+*.dot
+*.gif
+*.hhc
+*.hhk
+*.hhp
+*.map