[bugfix,buildsystem] Force searching for installed packages with pkg-config, again.

Somewhere along the many changes we stopped forcing usage of pkg-config when
testing for installed versions of modules during configure. Without using
pkg-config there is no way of detecting custom installation parts used by
the user. In my case, this broke finding modules installed via cmake from
modules that are to built with autotools.

This patch forces DUNE_CHECK_MODULE to use pkg-config to setup the paths for
installed modules by dunecontrol not provinding --with-module=<path> to configure
for installed modules.