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

Some cmake specific dirs have been deleted in commit 9bfc01e93d5ff6cea1bf11b4d430a3f72b11405a but not removed from
configure.ac resulting the build process to fail for the autotools.
(cherry picked from commit 03990eefc21ce4e9892ba4817f70f0a097d6ff79)

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