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> What I want is tools that take their last output into consideration and generate new diagrams that are both correct and as similar as possible to the last output they produced.

Something I've been struggling with as well. Now it sounds like a task for ChatGPT and dot, need to try that today.

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If you're not too fussy about results it might not be "that hard" to load a previous layout into dot, and optionally mark the nodes and edges that are allowed to be moved (or preferred not to be moved), and run the algorithms on that. It "just" needs someone to work on it, or pay for developers to do it. We wrote a paper about this in the mid 90s and Gordon Woodhull even got a successor of that to work, see dynagaph.org

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