With agents, my go to is now have multiple of the same repository and each agents must work on a separate one.

Preventing dirty workspace by solving the co-work problem to start with. merges are much more trivial than trying to make agents remember which branch or which folder it is supposed to work on. Disk space is cheaper than mental anguish and token usage.

https://git-scm.com/docs/git-worktree

What's your naming scheme?