> Why not put issues alongside the codebase?

That's the idea of Epiq: https://ljtn.github.io/epiq/

> In my view, the main obstacle here is that without serious dedication, the user experience for humans would be a major downgrade. This isn’t insurmountable, but it would be a lot of work.

I think Epiq does a decent job of addressing this.

Take a look at the second animation on the page above. It even lets you "scrub" your way through the timeline to very quickly glance at what an agent (or junior developer) did to your code recently.