Doxygen also has to look in the new directories for documentation.

doc/Doxyfile.in

@@ -759,7 +759,7 @@ WARN_LOGFILE           =
 # spaces.
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = @top_srcdir@ @top_srcdir@/src
+INPUT                  = @top_srcdir@ @top_srcdir@/src @top_srcdir@/src/hydro/Default @top_srcdir@/src/gravity/Default
 
 # 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