merge-recursive takes any files marked as unmerged by unpack_trees,
tries to figure out whether they can be resolved (e.g. using renames
or a file-level merge), and then if they can be it will delete the old
cache entries and writes new ones.  This means that any ce_flags for
those cache entries are essentially cleared when merging.

Unfortunately, if a file was marked as skip_worktree and it needs a
file-level merge but the merge results in the same version of the file
that was found in HEAD, we skip updating the worktree (because the
file was unchanged) but clear the skip_worktree bit (because of the
delete-cache-entry-and-write-new-one).  This makes git treat the file
as having a local change in the working copy, namely a delete, when it
should appear as unchanged despite not being present.  Avoid this
problem by copying the skip_worktree flag in this case.
Signed-off-by: NElijah Newren <newren@gmail.com>
Signed-off-by: NJunio C Hamano <gitster@pobox.com>