submodule.c: remove some of the_repository references

submodule.c: remove some of the_repository references

Commit 174d131fc9 (submodule.c: remove implicit dependency on
the_index - 2018-09-21) makes collect_changed_submodules() take a
"struct index_state *" as argument even if it's not really used. My
bad.

Instead of deleting this argument and fixing up all call sites. Let's
take this opportunity to remove some the_repository instead because
there's one or two in this function (and two more in its callback).
The callers can also get rid of some the_repository.

Noticed-by: Jeff King <peff@peff.net>
Signed-off-by: Nguyễn Thái Ngọc Duy <pclouds@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>