macOS does this for select directories. You either give access to all of `Documents` or none. It's also not great for notification fatigue, as you get like 8 popups at once in iTerm2. If you choose not to give access to a directory, you'll need to go to system settings to change this.

So, for a "better" system, we'd need to ask for every directory and you better hope the program doesn't try to glob all files in every directory and overload the user in prompts. Or you can "Allow all" or something, and then we're back at square one where the program has too much access.