Don't remove .gitmodules if there're other modules

Consider that I have a repository with multiple submodules [like this](http://git.savannah.gnu.org/cgit/dotgnu-pnet.git/tree/).

After I run `git-submerge cscctest`, it deletes the `.gitmodules`, but there're other modules I also want to import!

I think that `git-submerge` should just remove a reference to the merged module from `.gitmodules`, and it should remove a `.gitmodules` after that only if it's empty.