> Whenever an agent is planning there are often architecture and product choices that it asks humans to make. None of this intent is captured in the code or comments.

It must be in order to have an effective AI-assisted software engineering workflow, but it's not something that's magically done for you (usually). Knowledge management of project context is everything. Even the little music app I'm building has >100 ADRs (https://en.wikipedia.org/wiki/Architectural_decision), and that's just one form of project memory.