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

Some cmake specific dirs have been deleted in commit f9f1e146bb260ca0f1fb5d69201ba4ced70d68a6
but not removed from configure.ac resulting the build process to fail for the autotools.
(cherry picked from commit 2f803ff781ed3360c14679927187370ca7beff42)

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