Teach ls-files --with-tree=<tree> to work with options other than -c

Teach ls-files --with-tree=<tree> to work with options other than -c

Originally --with-tree=<tree> was designed for the sole purpose of
checking if a given pathspec makes sense as a parameter to git-commit
using it in conjunction with --error-unmatch.  It had logic to avoid
showing the same entry (one came from the original index, another from the
overlayed tree) twice so that it works with -c (i.e. "show-cached"), but
otherwise it was not designed to work with the flags such as -m, -d, etc.

This teaches the same logic to cover the codepath for -m and -d.

Signed-off-by: Junio C Hamano <gitster@pobox.com>