libgit2 removes submodule directories on `reset --hard` and rebase

If you reset- or rebase-to a commit where a submodule doesn't exist, libgit2 will happily throw away unstaged changes. Even if there are no such changes, it's annoying to find submodules unexpectedly closed during a rebase.

`git reset --hard` will give a warning about being unable to remove the submodule's directory
`git rebase` will leave a submodule directory alone

I created https://github.com/twosigma/git-meta/issues/509 to work around the problem