What? You run emacs as root?

Anything an LLM does on your computer should happen it its own account. No sudo config of course, or at most one that is strictly limited to what you want to allow it to do (risk here, as many programs have non-obvious paths to general command execution).

It should have zero access to your private home directory or your system configs. You can have access to its files of course. That's the beauty of separate accounts and permissions.