repack -ad: prune the list of shallow commits

`git repack` can drop unreachable commits without further warning,
making the corresponding entries in `.git/shallow` invalid, which causes
serious problems when deepening the branches.

One scenario where unreachable commits are dropped by `git repack` is
when a `git fetch --prune` (or even a `git fetch` when a ref was
force-pushed in the meantime) can make a commit unreachable that was
reachable before.

Therefore it is not safe to assume that a `git repack -adlf` will keep
unreachable commits alone (under the assumption that they had not been
packed in the first place, which is an assumption at least some of Git's
code seems to make).

This is particularly important to keep in mind when looking at the
`.git/shallow` file: if any commits listed in that file become
unreachable, it is not a problem, but if they go missing, it *is* a
problem. One symptom of this problem is that a deepening fetch may now
fail with

	fatal: error in object: unshallow <commit-hash>

To avoid this problem, let's prune the shallow list in `git repack` when
the `-d` option is passed, unless `-A` is passed, too (which would force
the now-unreachable objects to be turned into loose objects instead of
being deleted). Additionally, we also need to take `--keep-reachable`
and `--unpack-unreachable=<date>` into account.

Note: an alternative solution discussed during the review of this patch
was to teach `git fetch` to simply ignore entries in .git/shallow if the
corresponding commits do not exist locally. A quick test, however,
revealed that the .git/shallow file is written during a shallow *clone*,
in which case the commits do not exist, either, but the "shallow" line
*does* need to be sent. Therefore, this approach would be a lot more
finicky than the approach presented by the this patch.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Signed-off-by: Junio C Hamano <gitster@pobox.com>

builtin/repack.c

@@ -531,6 +531,12 @@ int cmd_repack(int argc, const char **argv, const char *prefix)
 		if (!po_args.quiet && isatty(2))
 			opts |= PRUNE_PACKED_VERBOSE;
 		prune_packed_objects(opts);
+
+		if (!keep_unreachable &&
+		    (!(pack_everything & LOOSEN_UNREACHABLE) ||
+		     unpack_unreachable) &&
+		    is_repository_shallow(the_repository))
+			prune_shallow(PRUNE_QUICK);
 	}
 
 	if (!no_update_server_info)

t/t5537-fetch-shallow.sh

@@ -186,7 +186,7 @@ EOF
 	test_cmp expect actual
 '
 
-test_expect_failure '.git/shallow is edited by repack' '
+test_expect_success '.git/shallow is edited by repack' '
 	git init shallow-server &&
 	test_commit -C shallow-server A &&
 	test_commit -C shallow-server B &&