I haven’t hit these issues when using worktrees. But what’s a pain is having to compile from scratch every time, and not carrying over gitignored files.

Worktrees are the obvious pick, and I get why. One command, cheap, and if you're the only one driving, then sharing .git is the point rather than a compromise. I started there too.

An agent in a worktree can reach your hooks, your config, another worktree's stash. Probably not a common problem. But when it does happen you're not debugging your code, you're debugging git, and it's not obvious where to even start looking.

The one that actually bothers me is prompt injection. The agent reads an issue, or a dependency's README, or a web page, and what it's told to do is drop a file in the .git it can already write to. Next time you commit, that runs on your machine as you.

Separate thing - worktrees just get annoying to manage. Can't check out the same branch twice, so you're making up branch names to keep git happy. Every one is another directory to keep track of. Then something goes stale and you're back in git worktree prune.

So has any of it got to you? Or do you hit the annoying parts, shrug, and carry on?