stash: Don't overwrite files that have gone from the index

The use of git add -u in create_stash isn't always complete. In
particular, if a file has been removed from the index but changed in the
work tree it will not be added to the stash's saved work tree tree
object. When stash then resets the work tree to match HEAD, any changes
will be lost.

To be complete, any work tree file which differs from HEAD needs to be
saved, regardless of whether it still appears in the index or not.

This is achieved with a combination of a diff against HEAD and a call to
update-index with an explicit list of paths that have changed.

Signed-off-by: Charles Bailey <charles@hashpling.org>
Signed-off-by: Junio C Hamano <gitster@pobox.com>

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