Quite a many tests assumed that newly created refs are made as
loose refs using the files backend, which have been updated to use
proper plumbing like rev-parse and update-ref, to avoid breakage
once we start using different ref backends.

* cc/tests-without-assuming-ref-files-backend:
  t990X: use '.git/objects' as 'deep inside .git' path
  t: make many tests depend less on the refs being files