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I'm afraid that the problem here is that OmniGraffle's layout engine just isn't capable of a diagram layout like the one you have here -- It can do hierarchical and force-directed or web layouts, but this kind of set/subset layout won't be able to automatically lay out as shown in your file.

I really like that style, we're thinking of adding the ability for more different layouts in the future, so I'd like to add this one to the mix, that okay?
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