Yeah, I definitely agree about a debugging mode. It'd be quite a lot of work to add this seeing as I only started to figure out the way it was written a few days ago, but I'll email Mitani and see what he says.
As for a duplication tool, It looks like it was started, but never finished, so it shouldn't be much work to add that in. I'll see what I can do.
The idea of ordering the layers is a very good one. I think this is one of the biggest problems Oripa, interesting idea. What would be the best way to order them? i.e. numbering each 'polygon' (every space a crease incloses, I don't mean the type of polygons used in drafting crease patterns), or another way?
EDIT:

I just realised there already was a copy and paste feature in Oripa... Is this what you wanted (It's under the edit menu) or did you have a different idea in mind?