setup: stop applying repository format twice

When discovering the repository in "setup.c" we apply the final repository format multiple times: - Once via `repository_format_configure()`, where we apply the hash algorithm and ref storage format to both `struct repository_format` and `struct repository`. - And once via `apply_repository_format()`, where we apply these two settings from `struct repository_format` to `struct repository`. With the current flow both of these are in fact necessary. But this is only because we call `repository_format_configure()` after we have called `apply_repository_format()`. Consequently, if we only changed the repository format in `repository_format_configure()` it would never propagate to the repository. Refactor the code so that we first configure the repository format before applying it to the repository so that we can stop setting the hash and reference storage format multiple times. Signed-off-by: Patrick Steinhardt <ps@pks.im> Signed-off-by: Junio C Hamano <gitster@pobox.com>