[autotools,bugfix] Remove deleted dirs from configure.ac

Some cmake specific dirs have been deleted in commit c66db5376e36eb369e0a67f8125789a62ae58070
but not removed from configure.ac resulting the build process to fail for the autotools.
(cherry picked from commit 9ecbfc6414f10ac8b846fa2fbe465bcda2b5f43c)

Signed-off-by: Christoph Grüninger <gruenich@dune-project.org>