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Your use puts me in mind of various charting software (flow-charts, organisational charts, network diagrams etc), which could also be used for this purpose. But that's the problem, put a software engineer in charge of developing the product and suddenly you get all this extra stuff that ends up just making it harder to use. In the end, I think the simplicity of Scapple is probably it's most attractive feature.
Good luck with it.
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