update-index: optionally leave skip-worktree entries alone

While `git update-index` mostly ignores paths referring to index entries
whose skip-worktree bit is set, in b4d1690df1 (Teach Git to respect
skip-worktree bit (reading part), 2009-08-20), for reasons that are not
entirely obvious, the `--remove` option was made special: it _does_
remove index entries even if their skip-worktree bit is set.

Seeing as this behavior has been in place for a decade now, it does not
make sense to change it.

However, in preparation for fixing a bug in `git stash` where it
pretends that skip-worktree entries have actually been removed, we need
a mode where `git update-index` leaves all skip-worktree entries alone,
even if the `--remove` option was passed.

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

Documentation/git-update-index.txt

@@ -16,6 +16,7 @@ SYNOPSIS
 	     [--chmod=(+|-)x]
 	     [--[no-]assume-unchanged]
 	     [--[no-]skip-worktree]
+	     [--[no-]ignore-skip-worktree-entries]
 	     [--[no-]fsmonitor-valid]
 	     [--ignore-submodules]
 	     [--[no-]split-index]
@@ -113,6 +114,11 @@ you will need to handle the situation manually.
 	set and unset the "skip-worktree" bit for the paths. See
 	section "Skip-worktree bit" below for more information.
 
+
+--[no-]ignore-skip-worktree-entries::
+	Do not remove skip-worktree (AKA "index-only") entries even when
+	the `--remove` option was specified.
+
 --[no-]fsmonitor-valid::
 	When one of these flags is specified, the object name recorded
 	for the paths are not updated. Instead, these options

builtin/update-index.c

@@ -35,6 +35,7 @@ static int verbose;
 static int mark_valid_only;
 static int mark_skip_worktree_only;
 static int mark_fsmonitor_only;
+static int ignore_skip_worktree_entries;
 #define MARK_FLAG 1
 #define UNMARK_FLAG 2
 static struct strbuf mtime_dir = STRBUF_INIT;
@@ -381,7 +382,8 @@ static int process_path(const char *path, struct stat *st, int stat_errno)
 		 * so updating it does not make sense.
 		 * On the other hand, removing it from index should work
 		 */
-		if (allow_remove && remove_file_from_cache(path))
+		if (!ignore_skip_worktree_entries && allow_remove &&
+		    remove_file_from_cache(path))
 			return error("%s: cannot remove from the index", path);
 		return 0;
 	}
@@ -1013,6 +1015,8 @@ int cmd_update_index(int argc, const char **argv, const char *prefix)
 		{OPTION_SET_INT, 0, "no-skip-worktree", &mark_skip_worktree_only, NULL,
 			N_("clear skip-worktree bit"),
 			PARSE_OPT_NOARG | PARSE_OPT_NONEG, NULL, UNMARK_FLAG},
+		OPT_BOOL(0, "ignore-skip-worktree-entries", &ignore_skip_worktree_entries,
+			 N_("do not touch index-only entries")),
 		OPT_SET_INT(0, "info-only", &info_only,
 			N_("add to index only; do not add content to object database"), 1),
 		OPT_SET_INT(0, "force-remove", &force_remove,

t/t7012-skip-worktree-writing.sh

@@ -134,6 +134,21 @@ test_expect_success 'git-clean, dirty case' '
 	test_i18ncmp expected result
 '
 
+test_expect_success '--ignore-skip-worktree-entries leaves worktree alone' '
+	test_commit keep-me &&
+	git update-index --skip-worktree keep-me.t &&
+	rm keep-me.t &&
+
+	: ignoring the worktree &&
+	git update-index --remove --ignore-skip-worktree-entries keep-me.t &&
+	git diff-index --cached --exit-code HEAD &&
+
+	: not ignoring the worktree, a deletion is staged &&
+	git update-index --remove keep-me.t &&
+	test_must_fail git diff-index --cached --exit-code HEAD \
+		--diff-filter=D -- keep-me.t
+'
+
 #TODO test_expect_failure 'git-apply adds file' false
 #TODO test_expect_failure 'git-apply updates file' false
 #TODO test_expect_failure 'git-apply removes file' false