I’m interested in any approaches or ideas for how to keep agent harness and code separate, like ideally separate repos.

Spec driven development is going really well for me, along with a swarm of agents and skills etc.

However, I’m seeing .Claude/memory/, docs/, .specify/*, hooks and extensions, context management tools etc becoming as much an overhead to manage as the codebase itself sometimes.

Also, it’s all mixed in together, in the same repo. Surely this is an anti-pattern.

Are there better ways to do this (yet)? Or is this the next AI frontier to evolve?