odb: properly close sources before freeing them

It is possible to hit a memory leak when reading data from a submodule
via git-grep(1):

  Direct leak of 192 byte(s) in 1 object(s) allocated from:
    #0 0x55555562e726 in calloc (git+0xda726)
    #1 0x555555964734 in xcalloc ../wrapper.c:154:8
    #2 0x555555835136 in load_multi_pack_index_one ../midx.c:135:2
    #3 0x555555834fd6 in load_multi_pack_index ../midx.c:382:6
    #4 0x5555558365b6 in prepare_multi_pack_index_one ../midx.c:716:17
    #5 0x55555586c605 in packfile_store_prepare ../packfile.c:1103:3
    #6 0x55555586c90c in packfile_store_reprepare ../packfile.c:1118:2
    #7 0x5555558546b3 in odb_reprepare ../odb.c:1106:2
    #8 0x5555558539e4 in do_oid_object_info_extended ../odb.c:715:4
    #9 0x5555558533d1 in odb_read_object_info_extended ../odb.c:862:8
    #10 0x5555558540bd in odb_read_object ../odb.c:920:6
    #11 0x55555580a330 in grep_source_load_oid ../grep.c:1934:12
    #12 0x55555580a13a in grep_source_load ../grep.c:1986:10
    #13 0x555555809103 in grep_source_is_binary ../grep.c:2014:7
    #14 0x555555807574 in grep_source_1 ../grep.c:1625:8
    #15 0x555555807322 in grep_source ../grep.c:1837:10
    #16 0x5555556a5c58 in run ../builtin/grep.c:208:10
    #17 0x55555562bb42 in void* ThreadStartFunc<false>(void*) lsan_interceptors.cpp.o
    #18 0x7ffff7a9a979 in start_thread (/nix/store/xx7cm72qy2c0643cm1ipngd87aqwkcdp-glibc-2.40-66/lib/libc.so.6+0x9a979) (BuildId: cddea92d6cba8333be952b5a02fd47d61054c5ab)
    #19 0x7ffff7b22d2b in __GI___clone3 (/nix/store/xx7cm72qy2c0643cm1ipngd87aqwkcdp-glibc-2.40-66/lib/libc.so.6+0x122d2b) (BuildId: cddea92d6cba8333be952b5a02fd47d61054c5ab)

The root caues of this leak is the way we set up and release the
submodule:

  1. We use `repo_submodule_init()` to initialize a new repository. This
     repository is stored in `repos_to_free`.

  2. We now read data from the submodule repository.

  3. We then call `repo_clear()` on the submodule repositories.

  4. `repo_clear()` calls `odb_free()`.

  5. `odb_free()` calls `odb_free_sources()` followed by `odb_close()`.

The issue here is the 5th step: we call `odb_free_sources()` _before_ we
call `odb_close()`. But `odb_free_sources()` already frees all sources,
so the logic that closes them in `odb_close()` now becomes a no-op. As a
consequence, we never explicitly close sources at all.

Fix the leak by closing the store before we free the sources.

Signed-off-by: Patrick Steinhardt <ps@pks.im>
Signed-off-by: Junio C Hamano <gitster@pobox.com>

odb.c

@@ -1132,13 +1132,13 @@ void odb_free(struct object_database *o)
 	oidmap_clear(&o->replace_map, 1);
 	pthread_mutex_destroy(&o->replace_mutex);
 
+	odb_close(o);
 	odb_free_sources(o);
 
 	for (size_t i = 0; i < o->cached_object_nr; i++)
 		free((char *) o->cached_objects[i].value.buf);
 	free(o->cached_objects);
 
-	odb_close(o);
 	packfile_store_free(o->packfiles);
 	string_list_clear(&o->submodule_source_paths, 0);