Updated doxygen autotools integration

Attempt to make the doxygen version filter works with git

configure.ac

 
 AC_CHECK_PROGS([DOXYGEN], [doxygen])
 if test -z "$DOXYGEN";
-	then AC_MSG_WARN([Doxygen not found - continuing without Doxygen support])
+then
+	AC_MSG_WARN([Doxygen not found - continuing without Doxygen support])
 fi
 
 AC_CHECK_PROGS([GIT], [git])
-if test -z "$DOXYGEN";
-	then AC_MSG_WARN([git not found - continuing without Doxygen support])
+if test -z "$GIT";
+then 
+	AC_MSG_WARN([git not found - continuing without Doxygen support])
+	AC_SUBST([DOXYFILE_FILE_VERSION_FILTER], [])
+else
+	
+	AC_SUBST([DOXYFILE_FILE_VERSION_FILTER], ["\"/bin/sh -c 'git log --pretty=\\\"format:%ci, author:%aN <%aE>, commit:%h\\\" -1 --'\""])
 fi
 
 # Checks for libraries.

docs/Doxyfile.in

 # by doxygen. Whatever the program writes to standard output is used as the file
 # version. For an example see the documentation.
 
-if HAVE_GIT
-FILE_VERSION_FILTER    = "/bin/sh -c 'git log --pretty=\"format:%ci, author:%aN <%aE>, commit:%h\" -1 \"${1}\" || echo no git'"
-else
-FILE_VERSION_FILTER    =
-fi
+FILE_VERSION_FILTER    = @DOXYFILE_FILE_VERSION_FILTER@
 
 # The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
 # by doxygen. The layout file controls the global structure of the generated
 # spaces.
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = @top_srcdir@
+INPUT                  = @top_builddir@/src
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses