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

cmake/pkg was deleted in commit ...476b581544fb32 but not
removed from configure.ac resulting the build process to fail
for the autotools.
(cherry picked from commit 98273547bbfbf969dcaf143b0f3c308cc4678997)

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