Test that `git_submodule_update` can handle a submodule that is
freshly cloned and has a path differing from its name.

Test an initial submodule update, where we are trying to checkout
the submodule for the first time, and placing a file within the
submodule working directory with the same name as the submodule
(and consequently, the same name as the repository itself).

Submodule init should handle relative paths in .gitmodules files
and resolve these urls when updating the git config file.

There was a little bug where the submodule cache thought that the
index date was out of date even when it wasn't that was resulting
in some extra scans of index data even when not needed.

Mostly this commit adds a bunch of new tests including adding and
removing submodules in the index and in the HEAD and seeing if we
can automatically pick them up when refreshing.

`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.