unpack_trees: move submodule specific code into verify_clean_submodule()

Currently verify_clean_subdirectory() will call resolve_gitlink_ref() and
do the hashcmp() between the submodule's HEAD and the commit recorded in
the superproject to call verify_clean_submodule() afterwards.

But these are both submodule related operations, so lets move them into
the verify_clean_submodule() function.

Signed-off-by: Jens Lehmann <Jens.Lehmann@web.de>