This updates how libgit2 treats submodule-like directories that
actually have tracked content inside of them.  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.