stash: handle staged changes in skip-worktree files correctly

When calling `git stash` while changes were staged for files that are
marked with the `skip-worktree` bit (e.g. files that are excluded in a
sparse checkout), the files are recorded as _deleted_ instead.

The reason is that `git stash` tries to construct the tree reflecting
the worktree essentially by copying the index to a temporary one and
then updating the files from the worktree. Crucially, it calls `git
diff-index` to update also those files that are in the HEAD but have
been unstaged in the index.

However, when the temporary index is updated via `git update-index --add
--remove`, skip-worktree entries mark the files as deleted by mistake.

Let's use the newly-introduced `--ignore-skip-worktree-entries` option
of `git update-index` to prevent exactly this from happening.

Note that the regression test case deliberately avoids replicating the
scenario described above and instead tries to recreate just the symptom.

Reported by Dan Thompson.

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

builtin/stash.c

@@ -1082,8 +1082,9 @@ static int stash_working_tree(struct stash_info *info, const struct pathspec *ps
 	}
 
 	cp_upd_index.git_cmd = 1;
-	argv_array_pushl(&cp_upd_index.args, "update-index", "-z", "--add",
-			 "--remove", "--stdin", NULL);
+	argv_array_pushl(&cp_upd_index.args, "update-index",
+			 "--ignore-skip-worktree-entries",
+			 "-z", "--add", "--remove", "--stdin", NULL);
 	argv_array_pushf(&cp_upd_index.env_array, "GIT_INDEX_FILE=%s",
 			 stash_index_path.buf);
 

git-legacy-stash.sh

@@ -193,7 +193,8 @@ create_stash () {
 			GIT_INDEX_FILE="$TMPindex" &&
 			export GIT_INDEX_FILE &&
 			git diff-index --name-only -z HEAD -- "$@" >"$TMP-stagenames" &&
-			git update-index -z --add --remove --stdin <"$TMP-stagenames" &&
+			git update-index --ignore-skip-worktree-entries \
+				-z --add --remove --stdin <"$TMP-stagenames" &&
 			git write-tree &&
 			rm -f "$TMPindex"
 		) ) ||

t/t3903-stash.sh

@@ -1241,4 +1241,15 @@ test_expect_success 'stash --keep-index with file deleted in index does not resu
 	test_path_is_missing to-remove
 '
 
+test_expect_success 'stash handles skip-worktree entries nicely' '
+	test_commit A &&
+	echo changed >A.t &&
+	git add A.t &&
+	git update-index --skip-worktree A.t &&
+	rm A.t &&
+	git stash &&
+
+	git rev-parse --verify refs/stash:A.t
+'
+
 test_done