I only use diagramming tools with automatic layout algos to generate visualizations programmatically to debug things. For documentation purpose, I largely prefer to draw them by hand using OmniGraffle, because making graphs look nice using tools like graphviz is very complex and you find yourself abusing features to hack your vision into reality
What's dearly needed in my opinion is a graph layout algo based on a machine learning model (so that it can take into account readability and aesthetics). Unfortunately what I found so far is mostly concerned with displaying large graphs, which is kind of another domain altogether.
I hope Mermaid is collecting every single edition point that happens on their UI, that would make for a nice dataset I guess.
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