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.

Make submodules externally refcounted

When a directory containing a .git directory (or even just a plain
gitlink) was found, libgit2 was going out of its way to treat it
specially.  This seemed like it was necessary because the diff
code was not originally emulating Git's behavior for untracked
directories correctly (i.e. scanning for ignored vs untracked items
inside).  Now that libgit2 diff mimics Git's untracked directory
behavior, the special handling for contained Git repos is actually
incorrect and this commit rips it out.

`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.

It's hard or even impossible to correctly free the string buffer
allocated by git_patch_to_str in some circumstances. Drop the function
so people have to use git_patch_to_buf instead - git_buf has a dedicated
destructor.