Do you have any UI benchmarks you like (or just know of) for these kinds of modular articles / books?
Trying to wrap my mind around how to handle all that source referencing, switching versions, opening wikis etc...
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Nope. Brand new territory. Nothing like this exists on the planet, as far as I know.
That's why I've been watching these events so closely, but development has stalled and I want to publish, so here goes. 😅
Liminal is from the natural sciences, so he was inspired by this 
They're the basis for wikis, but wikis don't have stable content, so they're actually a different thing. The content of zettel isn't supposed to vary wildly or change 5 times per day. It's something you write down and keep, to use and rearrange later, like snippets cut out of paper.
Zettelkasten - Wikipedia