It's a good point. Maybe I should add an option to make certain directories read-only even under the current working directory, so that you can make .git/ read-only without moving it out of the project directory.
You can already make CWD an overlay with "jai -D". The tricky part is how to merge the changes back into your main working directory.
It's great that you have -D built into the tool already. That's a step in the right direction.
I don't think the file sync is actually that hard. Famous last words though. :)
This is the problem yoloAI (see below comment) is built around. The merge step is `yoloai diff` / `yoloai apply`: the agent works against a copy of your project inside the container, you review the diff, you decide what lands.
jai's -D flag captures the right data; the missing piece is surfacing it ergonomically. yoloAI uses git for the diff/apply so it already feels natural to a dev.
One thing that's not fully solved yet: your point about .git/hooks and .venv being write vectors even within the project dir. They're filtered from the diff surface but the agent can still write them during the session. A read-only flag for those paths (what you're considering adding to jai) would be a cleaner fix.