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

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

Stop using `the_repository` in `setup_git_directory_gently()` 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 <ps@pks.im>
Signed-off-by: Junio C Hamano <gitster@pobox.com>