libs: use "struct repository *" argument, not "the_repository"

As can easily be seen from grepping in our sources, we had these uses
of "the_repository" in various library code in cases where the
function in question was already getting a "struct repository *"
argument. Let's use that argument instead.

Out of these changes only the changes to "cache-tree.c",
"commit-reach.c", "shallow.c" and "upload-pack.c" would have cleanly
applied before the migration away from the "repo_*()" wrapper macros
in the preceding commits.

The rest aren't new, as we'd previously implicitly refer to
"the_repository", but it's now more obvious that we were doing the
wrong thing all along, and should have used the parameter instead.

The change to change "get_index_format_default(the_repository)" in
"read-cache.c" to use the "r" variable instead should arguably have
been part of [1], or in the subsequent cleanup in [2]. Let's do it
here, as can be seen from the initial code in [3] it's not important
that we use "the_repository" there, but would prefer to always use the
current repository.

This change excludes the "the_repository" use in "upload-pack.c"'s
upload_pack_advertise(), as the in-flight [4] makes that change.

1. ee1f0c242e (read-cache: add index.skipHash config option,
   2023-01-06)
2. 6269f8eaad (treewide: always have a valid "index_state.repo"
   member, 2023-01-17)
3. 7211b9e753 (repo-settings: consolidate some config settings,
   2019-08-13)
4. <Y/hbUsGPVNAxTdmS@coredump.intra.peff.net>

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

notes-utils.c

@@ -23,7 +23,7 @@ void create_notes_commit(struct repository *r,
 		struct object_id parent_oid;
 		if (!read_ref(t->ref, &parent_oid)) {
 			struct commit *parent = lookup_commit(r, &parent_oid);
-			if (repo_parse_commit(the_repository, parent))
+			if (repo_parse_commit(r, parent))
 				die("Failed to find/parse commit %s", t->ref);
 			commit_list_insert(parent, &parents);
 		}