difftool --dir-diff: allow changing any clean working tree file

The temporary directory prepared by "difftool --dir-diff" to
show the result of a change can be modified by the user via
the tree diff program, and we try hard not to lose changes
to them after tree diff program returns to us.

However, the set of files to be copied back is computed
differently between --symlinks and --no-symlinks modes.  The
former checks all paths that start out as identical to the
working tree file, while the latter checks paths that
already had a local modification in the working tree,
allowing changes made in the tree diff program to paths that
did not have any local change to be lost.

Signed-off-by: Kenichi Saita <nitoyon@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>