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I second this request.

I have a few graphs, whose nodes are all the same. Hence it makes sense to put the nodes on a shared layer. The edges of each graph differ, so I put those on a regular layer. This means I can't connect my edges (lines) to my nodes (boxes). That's mighty annoying.

I do understand the issue: if I re-arrange the nodes on one canvas, not only do the edges on this canvas move along, the edges on another canvas should also move along. This may not be trivial to implement, but if it is implemented, it sure would safe me a lot of work making diagrams!