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.

`git_submodule` objects were already refcounted internally in case
the submodule name was different from the path at which it was
stored.  This makes that refcounting externally used as well, so
`git_submodule_lookup` and `git_submodule_add_setup` return an
object that requires a `git_submodule_free` when done.

Extend the "unmodified" submodule workdir test to include
uninitialized submodules, to prevent reporting submodules as
modified when they're not in the workdir at all.