setup: replace use of `the_repository` in static functions

Replace the use of `the_repository` in "setup.c" for all static
functions. For now, we simply add `the_repository` to invocations of
these functions. This will be addressed in subsequent commits, where
we'll move up `the_repository` one more layer to callers of "setup.c".

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

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