I used https://github.com/ctoth/research-papers-plugin to produce the annotations. The thing that's really cool is how they surface the cross-links in the collection, for instance look at https://github.com/ctoth/Qlatt/blob/master/papers/Fant_1988_...

Claude is much faster and better at reading papers than Codex (some of this is nested skill dispatch) but they both work quite incredibly for this. Compile your set of papers, queue it up and hit /ingest-collection and go sleep, and come back to a remarkable knowledge base :)