Hi there. I wrote this as a bit of speculation since I'm seeing more and more agent based coding in my consulting.
One thing to say given some of the comments here: in this approach the stuff in /src/md would be treated as well as stuff in /src/java or whatever: it would need to be maintained as precisely as possible, not just be a stream of development record of what has happened.
I'm also happy to consider that Markdown might not be the right format for this, or that the whole thing is a terrible idea. But I see people saving content in other places (linear, etc.) that drive agents and it just seems like maybe we should keep that stuff close to the generated source.