Fix checkout of submodules with no .gitmodules

Fix checkout of submodules with no .gitmodules

It is possible for there to be a submodule in a repository with
no .gitmodules file (for example, if the user forgot to commit
the .gitmodules file).  In this case, core Git will just create
an empty directory as a placeholder for the submodule but
otherwise ignore it.  We were generating an error and stopping
the checkout.  This makes our behavior match that of core git.