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 b4d1690 (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 <[email protected]>

Author: dscho

t/t7012-skip-worktree-writing.sh

@@ -135,17 +135,18 @@ test_expect_success 'git-clean, dirty case' '
 '
 
 test_expect_success '--ignore-skip-worktree-entries leaves worktree alone' '
-	test_commit geroff-me &&
-	git update-index --skip-worktree geroff-me.t &&
-	rm geroff-me.t &&
+	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 geroff-me.t &&
+	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 geroff-me.t &&
-	test_must_fail git diff-index --cached --exit-code HEAD
+	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