diff-lib: honor override_submodule_config flag bit

When `diff.ignoreSubmodules = all` is set and submodule commits are
manually staged (e.g. via `git-update-index`), `git-commit` should
record the commit  with updated submodules.

`index_differs_from` is called from `prepare_to_commit` with flags set to
`override_submodule_config = 1`. `index_differs_from` then merges the
default diff flags and passed flags.

When `diff.ignoreSubmodules` is set to "all", `flags` ends up having
both `override_submodule_config` and `ignore_submodules` set to 1. This
results in `git-commit` ignoring staged commits.

This patch restores original `flags.ignore_submodule` if
`flags.override_submodule_config` is set.

Signed-off-by: Josip Sokcevic <sokcevic@google.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>

diff-lib.c

@@ -669,8 +669,15 @@ int index_differs_from(struct repository *r,
 	setup_revisions(0, NULL, &rev, &opt);
 	rev.diffopt.flags.quick = 1;
 	rev.diffopt.flags.exit_with_status = 1;
-	if (flags)
+	if (flags) {
 		diff_flags_or(&rev.diffopt.flags, flags);
+		/*
+		 * Now that flags are merged, honor override_submodule_config
+		 * and ignore_submodules from passed flags.
+		 */
+		if (flags->override_submodule_config)
+			rev.diffopt.flags.ignore_submodules = flags->ignore_submodules;
+	}
 	rev.diffopt.ita_invisible_in_index = ita_invisible_in_index;
 	run_diff_index(&rev, 1);
 	has_changes = rev.diffopt.flags.has_changes;

t/t7406-submodule-update.sh

@@ -1179,4 +1179,27 @@ test_expect_success 'submodule update --recursive skip submodules with strategy=
 	test_cmp expect.err actual.err
 '
 
+add_submodule_commit_and_validate () {
+	HASH=$(git rev-parse HEAD) &&
+	git update-index --add --cacheinfo 160000,$HASH,sub &&
+	git commit -m "create submodule" &&
+	echo "160000 commit $HASH	sub" >expect &&
+	git ls-tree HEAD -- sub >actual &&
+	test_cmp expect actual
+}
+
+test_expect_success 'commit with staged submodule change' '
+	add_submodule_commit_and_validate
+'
+
+test_expect_success 'commit with staged submodule change with ignoreSubmodules dirty' '
+	test_config diff.ignoreSubmodules dirty &&
+	add_submodule_commit_and_validate
+'
+
+test_expect_success 'commit with staged submodule change with ignoreSubmodules all' '
+	test_config diff.ignoreSubmodules all &&
+	add_submodule_commit_and_validate
+'
+
 test_done