Honestly I think that Markdown with LateX code blocks would be the most efficient representation but when doing it with Pandoc I kept having issues with loss of information and sometimes even syntax error.
Reading all the papers once isn't the same as this. I find it very useful.
I can ask an LLM to do the basic implementations, then I can refine them (make the code better, faster, cut on memory use), then I can ask the LLM if I'm still implementing the algorithms as they're described in the paper.
Then something in your {CLAUDE,AGENTS}.md that says: when working on something with relevant context supplied by papers, read the papers before doing the work. You can find all papers plus their descriptions in ./papers/INDEX.md and papers by tag in ./papers/tagged