Fix git rebase --continue to work with touched files

Fix git rebase --continue to work with touched files

When performing a non-interactive rebase, sometimes
"git rebase --continue" will fail if an unmodified file is
touched in the working directory:

    You must edit all merge conflicts and then
    mark them as resolved using git add

This is caused by "git diff-files" reporting a difference
between the index and the filesystem:

    :100644 100644 d00491...... 000000...... M	file

The fix is to run "git update-index --refresh" before
"git diff-files" as is done in git-rebase--interactive.

Signed-off-by: David D. Kilzer <ddkilzer@kilzer.net>
Acked-by: Johannes Schindelin <Johannes.Schindelin@gmx.de>
Signed-off-by: Junio C Hamano <gitster@pobox.com>