Somewhat belatedly I've just updgraded to v1.6 on our site and whilst most stuff is working OK I can't seem to find the shuffle pads option in the editor any more.
The documentation for it is still there, but no menu entry (beginner or expert).
Where did it go?
Shuffle pads is now in the main gap4 Edit menu. This means it cannot be done within the editor (the down side), but it means it's easy to script (bonus) and can be done on multiple contigs.
It's also a total rewrite, using ideas from Gene Myers' ReAligner program. I think it does a substantially better job now than before.