> I want a tool that gives programmers a place to record their thoughts. Developers need a place to draw and write, and also interleave blocks of code that automatically update to match the actual state of the code.

Sounds, like you already mention with org-mode or similar ones) like literate programming (https://en.wikipedia.org/wiki/Literate_programming) or jupyter notebook.

I think the solution is still code, just at a much higher level of abstraction. Maybe a start is kind of typed ADR or FSM that guides (constrains) the agents. I believe more type checking guarantees will be more and more important for agents.