I have my agent run all docker commands in the main worktree. Sometimes this is awkward but mostly docker stuff is slow changing. I never run the stuff I’m developing in docker, I always run on the host directly.

For my current project (Postgres proxy like PGBouncer) I had Claude write a benchmark system that’s worktree aware. I have flags like -a-worktree=… -b-worktree =… so I can A/B benchmark between worktrees. Works great.