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 b4d1690df11 (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>

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