Update treatment of submodule-like directories with tracked content in the parent

This is a strange corner case, but it seems that many people have abortive submodule setups and then just went ahead and added the files into the parent repository.  In this case, we should just treat the "submodule" as if it was a normal directory.

Libgit2 will still try to skip over real submodules and contained repositories that do not have tracked files inside them, but this adds some new handling for cases where the apparently submodule data is in conflict with the actual list of tracked files.