setup: don't apply "GIT_REFERENCE_BACKEND" without a repository

setup: don't apply "GIT_REFERENCE_BACKEND" without a repository

When discovering a repository we eventually also apply the
"GIT_REFERENCE_BACKEND" environment variable to the repository. There's
two problems with that:

  - We do this unconditionally, which is rather pointless: we really
    only have to configure the repository when we have found one.

  - We have already applied the repository format at that point in time,
    so we need to manually reapply it.

Move the logic around so that we only apply the environment variable
when a repository was discovered. This also allows us to drop the
explcit call to `repo_set_ref_storage_format()` because we now adjust
the format before we apply it via `apply_repository_format()`.

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