cocci: add missing "the_repository" macros to "pending"

cocci: add missing "the_repository" macros to "pending"

In the case of diff.h, rerere.h and revision.h the macros were added
in [1], [2] and [3] when "the_repository.pending.cocci" didn't
exist. None of the subsequently added migration rules covered
them. Let's add those missing rules.

In the case of macros in "cache.h", "commit.h", "packfile.h",
"promisor-remote.h" and "refs.h" those aren't guarded by
"NO_THE_REPOSITORY_COMPATIBILITY_MACROS", but they're also macros that
add "the_repository" as the first argument, so we should migrate away
from them.

1. 2abf3503854 (revision.c: remove implicit dependency on the_index,
   2018-09-21)
2. e6757652350 (diff.c: remove implicit dependency on the_index,
   2018-09-21)
3. 35843b1123e (rerere.c: remove implicit dependency on the_index,
   2018-09-21)

Signed-off-by: Ævar Arnfjörð Bjarmason <avarab@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>