unpack-trees: let read-tree -u remove index entries outside sparse area

unpack-trees: let read-tree -u remove index entries outside sparse area

To avoid touching the worktree outside a sparse checkout,
when the update flag is enabled unpack_trees() clears the
CE_UPDATE and CE_REMOVE flags on entries that do not match the
sparse pattern before actually committing any updates to the
index file or worktree.

The effect on the index was unintentional; sparse checkout was
never meant to prevent index updates outside the area checked
out.  And the result is very confusing: for example, after a
failed merge, currently "git reset --hard" does not reset the
state completely but an additional "git reset --mixed" will.

So stop clearing the CE_REMOVE flag.  Instead, maintain a
CE_WT_REMOVE flag to separately track whether a particular
file removal should apply to the worktree in addition to the
index or not.

The CE_WT_REMOVE flag is used already to mark files that
should be removed because of a narrowing checkout area.  That
usage will still apply; do not clear the CE_WT_REMOVE flag
in that case (detectable because the CE_REMOVE flag is not
set).

This bug masked some other bugs illustrated by the test
suite, which will be addressed by later patches.

Reported-by: Frédéric Brière <fbriere@fbriere.net>
Fixes: http://bugs.debian.org/583699

Signed-off-by: Nguyễn Thái Ngọc Duy <pclouds@gmail.com>
Reviewed-by: Jonathan Nieder <jrnieder@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>