diagnose: stop using `the_repository`

diagnose: stop using `the_repository`

Stop using `the_repository` in the "diagnose" subsystem by passing in a
repository when generating a diagnostics archive.

Adjust callers accordingly by using `the_repository`. While there may be
some callers that have a repository available in their context, this
trivial conversion allows for easier verification and bubbles up the use
of `the_repository` by one level.

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