setup: stop using `the_repository` in `initialize_repository_version()`

setup: stop using `the_repository` in `initialize_repository_version()`

Stop using `the_repository` in `initialize_repository_version()` and
instead accept the repository as a parameter. The injection of
`the_repository` is thus bumped one level higher, where callers now pass
it in explicitly.

Signed-off-by: Patrick Steinhardt <redacted>
Signed-off-by: Junio C Hamano <redacted>