t: convert tests to not write references via the filesystem

Some of our tests manually create, update or delete references by
writing the respective new values into the filesystem directly. While
this works with the current files reference backend, this will break
once we have a second reference backend implementation in our codebase.

Refactor these tests to instead use git-update-ref(1) or our `ref-store`
test tool. The latter is required in some cases where safety checks of
git-update-ref(1) would otherwise reject a reference update.

While at it, refactor some of the tests to schedule the cleanup command
via `test_when_finished` before modifying the repository.

Signed-off-by: Patrick Steinhardt <ps@pks.im>
Signed-off-by: Junio C Hamano <gitster@pobox.com>

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