Wow, embark is very well done! I feel like there is some sort of solution space between notes, whiteboards, jupyter notebooks and Arcan FE that could make knowledge organization much easier, but it's such a huge space to even comprehend in the first place I can only ever hold part of the solution in my head.

I also enjoyed Muse[1], which was made available in the iOS app store, and is now being maintained as "Allume"[2] (an unnamed company bought the Muse name).

Essentially a digital pinboard, it was an interesting experiment in "designed for tablet" UX and was developed far enough to be an app. The gesture based UX, nested board, PDF reader, and transclusion of PDF fragments are all interesting ideas.

[1]: https://www.inkandswitch.com/muse/ [2]: https://allume.com/

I really love this one on dynamic documents as well:

Potluck: Dynamic documents as personal software https://www.inkandswitch.com/potluck/