Caleb-T-Owens · Oct 5, 2026 · Oct 6, 2026
diff --git a/src/libgit2/checkout.c b/src/libgit2/checkout.c
@@ -361,6 +361,31 @@ static int checkout_queue_remove(checkout_data *data, const char *path)
 	return git_vector_insert(&data->removes, copy);
 }
 
+static bool checkout_is_empty_dir(checkout_data *data, const char *path)
+{
+	git_str *fullpath;
+
+	if (checkout_target_fullpath(&fullpath, data, path) < 0)
+		return false;
+
+	return git_fs_path_is_empty_dir(fullpath->ptr);
+}
+
+static bool wd_only_tree_needs_descent(
+	checkout_data *data, git_iterator *workdir, const git_index_entry *wd)
+{
+	bool remove_untracked =
+		(data->strategy & GIT_CHECKOUT_REMOVE_UNTRACKED) != 0;
+	bool remove_ignored =
+		(data->strategy & GIT_CHECKOUT_REMOVE_IGNORED) != 0;
+
+	return wd->mode == GIT_FILEMODE_TREE &&
+		remove_untracked != remove_ignored &&
+		!git_iterator_current_is_ignored(workdir) &&
+		wd_item_is_removable(data, wd) &&
+		!checkout_is_empty_dir(data, wd->path);
+}
+
 /* note that this advances the iterator over the wd item */
 static int checkout_action_wd_only(
 	checkout_data *data,
@@ -410,6 +435,9 @@ static int checkout_action_wd_only(
 		}
 	}
 
+	if (wd_only_tree_needs_descent(data, workdir, wd))
+		return git_iterator_advance_into(wditem, workdir);
+
 	if (notify != GIT_CHECKOUT_NOTIFY_NONE) {
 		/* if we found something in the index, notify and advance */
 		if ((error = checkout_notify(data, notify, NULL, wd)) != 0)
@@ -478,16 +506,6 @@ static bool submodule_is_config_only(
 	return rval;
 }
 
-static bool checkout_is_empty_dir(checkout_data *data, const char *path)
-{
-	git_str *fullpath;
-
-	if (checkout_target_fullpath(&fullpath, data, path) < 0)
-		return false;
-
-	return git_fs_path_is_empty_dir(fullpath->ptr);
-}
-
 static int checkout_action_with_wd(
 	int *action,
 	checkout_data *data,

diff --git a/tests/libgit2/checkout/tree.c b/tests/libgit2/checkout/tree.c
@@ -242,6 +242,106 @@ void test_checkout_tree__can_remove_ignored(void)
 	cl_assert(!git_fs_path_isfile("testrepo/ignored_file"));
 }
 
+static void make_dir_with_ignored_and_untracked(const char *dir)
+{
+	git_str path = GIT_STR_INIT;
+
+	cl_git_pass(git_futils_mkdir_r(dir, 0777));
+
+	cl_git_pass(git_str_joinpath(&path, dir, "ignored.txt"));
+	cl_git_mkfile(path.ptr, "as you wish");
+
+	cl_git_pass(git_str_joinpath(&path, dir, "untracked.txt"));
+	cl_git_mkfile(path.ptr, "as you wish");
+
+	cl_git_pass(git_ignore_add_rule(g_repo, "ignored.txt\n"));
+
+	git_str_dispose(&path);
+}
+
+void test_checkout_tree__remove_untracked_keeps_ignored_sibling(void)
+{
+	git_checkout_options opts = GIT_CHECKOUT_OPTIONS_INIT;
+
+	opts.checkout_strategy = GIT_CHECKOUT_REMOVE_UNTRACKED;
+
+	make_dir_with_ignored_and_untracked("testrepo/dir");
+
+	cl_git_pass(git_checkout_head(g_repo, &opts));
+
+	cl_assert(git_fs_path_isfile("testrepo/dir/ignored.txt"));
+	cl_assert(!git_fs_path_exists("testrepo/dir/untracked.txt"));
+}
+
+void test_checkout_tree__remove_ignored_keeps_untracked_sibling(void)
+{
+	git_checkout_options opts = GIT_CHECKOUT_OPTIONS_INIT;
+
+	opts.checkout_strategy = GIT_CHECKOUT_REMOVE_IGNORED;
+
+	make_dir_with_ignored_and_untracked("testrepo/dir");
+
+	cl_git_pass(git_checkout_head(g_repo, &opts));
+
+	cl_assert(!git_fs_path_exists("testrepo/dir/ignored.txt"));
+	cl_assert(git_fs_path_isfile("testrepo/dir/untracked.txt"));
+}
+
+void test_checkout_tree__remove_untracked_keeps_ignored_in_subdir(void)
+{
+	git_checkout_options opts = GIT_CHECKOUT_OPTIONS_INIT;
+
+	opts.checkout_strategy = GIT_CHECKOUT_REMOVE_UNTRACKED;
+
+	make_dir_with_ignored_and_untracked("testrepo/dir/sub");
+	cl_git_mkfile("testrepo/dir/untracked.txt", "as you wish");
+
+	cl_git_pass(git_checkout_head(g_repo, &opts));
+
+	cl_assert(git_fs_path_isfile("testrepo/dir/sub/ignored.txt"));
+	cl_assert(!git_fs_path_exists("testrepo/dir/sub/untracked.txt"));
+	cl_assert(!git_fs_path_exists("testrepo/dir/untracked.txt"));
+}
+
+void test_checkout_tree__remove_untracked_keeps_ignored_beside_tracked(void)
+{
+	git_checkout_options opts = GIT_CHECKOUT_OPTIONS_INIT;
+	git_index *index;
+
+	opts.checkout_strategy = GIT_CHECKOUT_REMOVE_UNTRACKED;
+
+	make_dir_with_ignored_and_untracked("testrepo/dir");
+	cl_git_mkfile("testrepo/dir/tracked.txt", "as you wish");
+
+	cl_git_pass(git_repository_index(&index, g_repo));
+	cl_git_pass(git_index_add_bypath(index, "dir/tracked.txt"));
+	cl_git_pass(git_index_write(index));
+	git_index_free(index);
+
+	cl_git_pass(git_checkout_head(g_repo, &opts));
+
+	cl_assert(git_fs_path_isfile("testrepo/dir/tracked.txt"));
+	cl_assert(git_fs_path_isfile("testrepo/dir/ignored.txt"));
+	cl_assert(!git_fs_path_exists("testrepo/dir/untracked.txt"));
+}
+
+void test_checkout_tree__remove_untracked_keeps_ignored_dir(void)
+{
+	git_checkout_options opts = GIT_CHECKOUT_OPTIONS_INIT;
+
+	opts.checkout_strategy = GIT_CHECKOUT_REMOVE_UNTRACKED;
+
+	cl_must_pass(p_mkdir("testrepo/dir", 0777));
+	cl_git_mkfile("testrepo/dir/one.txt", "as you wish");
+	cl_git_mkfile("testrepo/dir/two.txt", "as you wish");
+	cl_git_pass(git_ignore_add_rule(g_repo, "dir/\n"));
+
+	cl_git_pass(git_checkout_head(g_repo, &opts));
+
+	cl_assert(git_fs_path_isfile("testrepo/dir/one.txt"));
+	cl_assert(git_fs_path_isfile("testrepo/dir/two.txt"));
+}
+
 static int checkout_tree_with_blob_ignored_in_workdir(int strategy, bool isdir)
 {
 	git_oid oid;

diff --git a/tests/libgit2/stash/save.c b/tests/libgit2/stash/save.c
@@ -186,6 +186,20 @@ void test_stash_save__untracked_skips_ignored(void)
 	cl_assert(git_fs_path_exists("stash/just.ignore"));
 }
 
+void test_stash_save__untracked_skips_ignored_sibling(void)
+{
+	cl_must_pass(p_mkdir("stash/dir", 0777));
+	cl_git_mkfile("stash/dir/untracked", "contents\n");
+	cl_git_mkfile("stash/dir/sibling.ignore", "contents\n");
+
+	cl_git_pass(git_stash_save(
+		&stash_tip_oid, repo, signature, NULL, GIT_STASH_INCLUDE_UNTRACKED));
+
+	cl_assert(!git_fs_path_exists("stash/dir/untracked"));
+	assert_blob_oid("refs/stash^3:dir/sibling.ignore", NULL);
+	cl_assert(git_fs_path_exists("stash/dir/sibling.ignore"));
+}
+
 void test_stash_save__can_include_untracked_and_ignored_files(void)
 {
 	cl_git_pass(git_stash_save(&stash_tip_oid, repo, signature, NULL, GIT_STASH_INCLUDE_UNTRACKED | GIT_STASH_INCLUDE_IGNORED));