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

Some cmake specific dirs have been deleted in commit 1546b9a93cb5359bdac77c029564d0f8eb7acf45 but not removed from
configure.ac resulting the build process to fail for the autotools.
(cherry picked from commit ae8a6d5ff1d699fb60b76cd46c380f306c95e226)

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