diff -dur cvc3-2.2.ORIG/doc/Doxyfile.in cvc3-2.2/doc/Doxyfile.in
--- cvc3-2.2.ORIG/doc/Doxyfile.in	2007-09-11 11:31:56.000000000 -0600
+++ cvc3-2.2/doc/Doxyfile.in	2009-11-19 12:20:02.067998020 -0700
@@ -31,7 +31,7 @@
 # This could be handy for archiving the generated documentation or 
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         = 2.2
 
 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) 
 # base path where the generated documentation will be put. 
@@ -499,8 +499,7 @@
 # excluded from the INPUT source files. This way you can easily exclude a 
 # subdirectory from a directory tree whose root is specified with the INPUT tag.
 
-EXCLUDE                = devel.dox \
-                         theory_api.dox
+EXCLUDE                = devel.dox
 
 # The EXCLUDE_SYMLINKS tag can be used select whether or not files or 
 # directories that are symbolic links (a Unix filesystem feature) are excluded 
@@ -1042,8 +1041,7 @@
 # undefined via #undef or recursively expanded use the := operator 
 # instead of the = operator.
 
-PREDEFINED             = DEBUG \
-                         DOXYGEN
+PREDEFINED             = DOXYGEN
 
 # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then 
 # this tag can be used to specify a list of macro names that should be expanded. 
@@ -1137,6 +1135,24 @@
 
 HAVE_DOT               = @HAVE_DOT@
 
+# By default doxygen will write a font called FreeSans.ttf to the output 
+# directory and reference it in all dot files that doxygen generates. This 
+# font does not include all possible unicode characters however, so when you need 
+# these (or just want a differently looking font) you can specify the font name 
+# using DOT_FONTNAME. You need need to make sure dot is able to find the font, 
+# which can be done by putting it in a standard location or by setting the 
+# DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory 
+# containing the font.
+
+DOT_FONTNAME           = FreeSans
+
+# By default doxygen will tell dot to use the output directory to look for the 
+# FreeSans.ttf font (which doxygen will put there itself). If you specify a 
+# different font using DOT_FONTNAME you can set the path where dot 
+# can find it using this tag.
+
+DOT_FONTPATH           = /usr/share/fonts/gnu-free
+
 # If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen 
 # will generate a graph for each documented class showing the direct and 
 # indirect inheritance relations. Setting this tag to YES will force the 
@@ -1213,7 +1229,7 @@
 # generated by dot. Possible values are png, jpg, or gif
 # If left blank png will be used.
 
-DOT_IMAGE_FORMAT       = gif
+DOT_IMAGE_FORMAT       = png
 
 # The tag DOT_PATH can be used to specify the path where the dot tool can be 
 # found. If left blank, it is assumed the dot tool can be found in the path.
@@ -1247,7 +1263,7 @@
 # makes dot run faster, but since only newer versions of dot (>1.8.10) 
 # support this, this feature is disabled by default.
 
-DOT_MULTI_TARGETS      = NO
+DOT_MULTI_TARGETS      = YES
 
 # If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will 
 # generate a legend page explaining the meaning of the various boxes and