diff --git a/doc/Doxyfile.in b/doc/Doxyfile.in
index 3fa8ae3fc583f1489a8c1b1f06b22afe337706bd..7f8af2fc2679e8bab96f8dd1796794d8dbf6b5fd 100644
--- a/doc/Doxyfile.in
+++ b/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