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.
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.