What do you propose? Even if they configure node's lowest level file APIs to block any access to paths outside the vault, plugins can still execute arbitrary shell commands who will have access to the entire OS.

And before you say it's useless and should be stopped too, well, that's a fine opinion! But then you lose plugins providing git integration, automated backups, document conversion using pandoc, etc. Many users might value that greatly.

A permission system for their plugins might be the only solution, annoying permission request popups and all.