You’re not doing anything wrong. This isn’t a bulletproof idea. It can work, and this is what a lot of people end up with to manage complexity, but there’s a critical point beyond which things collapse: the agent can’t keep the wiki up to date anymore, the developer can’t grok it anymore.
Managing complexity, modularity, separation of concerns, were already critical for ensuring humans could still hold enough of the system in their brains to do something useful.
People who do not understand that will continue to not understand that it also applies to AI right now. Maybe at some point in the future it won't, not sure. But my impression is that systems grow in complexity far past the point where the system is gummed up and no-one can do anything, unless it's actively managed.
If a human can understand 10 units of complexity and their LLM can do 20, then they might just build a system that's 30 complex and not understand the failure modes until it's too late.