This is going to be hard to fix.
If you use an LLM and agents to regenerate code, a minor change in the "specification" may result in huge changes to the code. Even if it's just due to forcing regeneration. OK, got that.
But there may be no "specification", just an ongoing discussion with an agentic system. "We don't write code any more, we just yell at the agents." Even if the entire sequence of events has been captured, it might not be very useful. It's like having a transcript of a design meeting.
There's a real question as to what the static reference of the design should be. Or what it should look like. This is going to be difficult.