diff --git a/Makefile.am b/Makefile.am
index 1507982c6c504c60e2fa436d5e6c2afe238e4038..af8f434a84ac59c74035d80dda668fdfdd40d9b8 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -3,7 +3,7 @@
 # we need the module file to be able to build via dunecontrol
 EXTRA_DIST=dune.module
 
-SUBDIRS = m4 src test
+SUBDIRS = m4 dune test
 
 # possible options
 LDADD = $(IPOPT_LDFLAGS) $(IPOPT_LIBS)
diff --git a/configure.ac b/configure.ac
index 7f2724a30a103d360cd94db6c83893cdd6c55cff..42fabec0882d82d67973ab650de0c59523720b34 100644
--- a/configure.ac
+++ b/configure.ac
@@ -16,10 +16,11 @@ AC_SUBST(AM_LDFLAGS, $DUNE_LDFLAGS)
 LIBS="$DUNE_LIBS"
 
 AC_CONFIG_FILES([Makefile
-                 src/Makefile
+                 dune/Makefile
+                 dune/gfe/Makefile
                  test/Makefile
                  m4/Makefile
-                 rods.pc
+                 dune-gfe.pc
                 ])
 AC_OUTPUT
 
diff --git a/dune/gfe/Makefile.am b/dune/gfe/Makefile.am
index 36a2c8cd68bd38999c935838cd4d0d8ec1823fa2..2b2188813aef1d4b1e36c7150810a677705ee107 100644
--- a/dune/gfe/Makefile.am
+++ b/dune/gfe/Makefile.am
@@ -1,4 +1,4 @@
-# $Id: Makefile.am 5716 2009-11-20 12:23:19Z dedner $
+# $Id: $
 
 SUBDIRS =
 
diff --git a/m4/Makefile.am b/m4/Makefile.am
index 0986fb229b8e38c96a38dbf23a8d8e28ac67f209..535bde10b106c72a740364308109f639ae4bd147 100644
--- a/m4/Makefile.am
+++ b/m4/Makefile.am
@@ -1,4 +1,4 @@
-ALLM4S = rods.m4
+ALLM4S = dune-gfe.m4
 
 aclocaldir = $(datadir)/aclocal
 aclocal_DATA = $(ALLM4S)