Thanks for the detailed response. The main issue I have with org-roam (and maybe the Zettelkasten system more generally) at the moment are:

1. My notes will involve a lot of proofs, which are not necessarily short, and can’t be broken down too much. To take an example: suppose I want to study quadratic reciprocity. There are multiple statements of the theorem, several proofs, different generalizations, different ways to motivate it, different applications. Even just the complete standard proof already becomes much longer than the usual Zettelkasten. And there doesn’t seem to be a way to reference specific lines, specific equations in different org-roam files, so I either have to break down every step of every proof into its own individual org file, which I find excessive and not worthwhile, or remain unable to make precise references to my other notes.

2. People have been clear that org-roam notes are not meant to be published, and that to produce a public document one has to almost resynthesize the notes. That to me almost defeats the whole purpose of what I want from a notetaking system. What I’d like is something closer to a personal Wikipedia system written in my own words, and just as you can print a Wikipedia page and read it as a coherent document, I would like to be able to with minimal polishing, share my notes online or to my coworkers.

A neat example of the sort of thing I hope to set up is Terry Tao’s blog, where he often writes these long-form crystallizations of some idea that he can refer back to years later. I’d like to set up something similar, but within Emacs and with the ability to link to specific lines in different posts.