submodule: don't access the .gitmodules cache entry after removing it

Commit 5fee995244e introduced the stage_updated_gitmodules() function to
add submodule configuration updates to the index. It assumed that even
after calling remove_cache_entry_at() the same cache entry would still be
valid. This was true in the old days, as cache entries could never be
freed, but that is not so sure in the present as there is ongoing work to
free removed cache entries, which makes this code segfault.

Fix that by calling add_file_to_cache() instead of open coding it. Also
remove the "could not find .gitmodules in index" warning, as that won't
happen in regular use cases (and by then just silently adding it to the
index we do the right thing).

Thanks-to: Karsten Blees <karsten.blees@gmail.com>
Signed-off-by: Jens Lehmann <Jens.Lehmann@web.de>