Remove most submodule reloads from tests

With the new submodule cache validity checks, we generally don't
need to call git_submodule_reload_all to have up-to-date submodule
data.  Some tests are still calling it where I want to actually
test that it can be called safely and doesn't break anything, but
mostly it is not needed.

This also expands some of the existing submodule tests to cover
some variants on the behavior that was already being tested.
More tests and fix submodule index refresh

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index date was out of date even when it wasn't that was resulting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.