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

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

Stop using `the_repository` in `prefix_path()` 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>