cocci: apply the "object-store.h" part of "the_repository.pending"

Apply the part of "the_repository.pending.cocci" pertaining to
"object-store.h".

Signed-off-by: Ævar Arnfjörð Bjarmason <avarab@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>
diff --git a/cache-tree.c b/cache-tree.c
index 88c2c04..5961011 100644
--- a/cache-tree.c
+++ b/cache-tree.c
@@ -229,7 +229,7 @@ int cache_tree_fully_valid(struct cache_tree *it)
 	int i;
 	if (!it)
 		return 0;
-	if (it->entry_count < 0 || !has_object_file(&it->oid))
+	if (it->entry_count < 0 || !repo_has_object_file(the_repository, &it->oid))
 		return 0;
 	for (i = 0; i < it->subtree_nr; i++) {
 		if (!cache_tree_fully_valid(it->down[i]->cache_tree))
@@ -280,7 +280,7 @@ static int update_one(struct cache_tree *it,
 		}
 	}
 
-	if (0 <= it->entry_count && has_object_file(&it->oid))
+	if (0 <= it->entry_count && repo_has_object_file(the_repository, &it->oid))
 		return it->entry_count;
 
 	/*
@@ -386,7 +386,7 @@ static int update_one(struct cache_tree *it,
 		ce_missing_ok = mode == S_IFGITLINK || missing_ok ||
 			!must_check_existence(ce);
 		if (is_null_oid(oid) ||
-		    (!ce_missing_ok && !has_object_file(oid))) {
+		    (!ce_missing_ok && !repo_has_object_file(the_repository, oid))) {
 			strbuf_release(&buffer);
 			if (expected_missing)
 				return -1;
@@ -434,7 +434,7 @@ static int update_one(struct cache_tree *it,
 		struct object_id oid;
 		hash_object_file(the_hash_algo, buffer.buf, buffer.len,
 				 OBJ_TREE, &oid);
-		if (has_object_file_with_flags(&oid, OBJECT_INFO_SKIP_FETCH_OBJECT))
+		if (repo_has_object_file_with_flags(the_repository, &oid, OBJECT_INFO_SKIP_FETCH_OBJECT))
 			oidcpy(&it->oid, &oid);
 		else
 			to_invalidate = 1;