run-command: wean auto_maintenance() functions off the_repository

run-command: wean auto_maintenance() functions off the_repository

The prepare_auto_maintenance() relies on the_repository to read
configurations. Since run_auto_maintenance() calls
prepare_auto_maintenance(), it also implicitly depends the_repository.

Add 'struct repository *' as a parameter to both functions and update
all callers to pass the_repository.

With no global repository dependencies left in this file, remove the
USE_THE_REPOSITORY_VARIABLE macro.

Suggested-by: Patrick Steinhardt <ps@pks.im>
Signed-off-by: Burak Kaan Karaçay <bkkaracay@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>