setup: deduplicate logic to apply repository format

setup: deduplicate logic to apply repository format

After having discovered the repository format we then apply it to the
repository so that it knows to use the proper repository extensions. The
logic to apply the format is duplicated across three callsites, which
makes it rather painfull to add new extensions.

Introduce a new function `apply_repository_format()` that takes a repo
and applies a given format to it and adapt all callsites to use it.
While at it, rename `check_repository_format()` to clarify that it
doesn't only _check_ the format, but that it also applies it.

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