the moving from a todo file to done file is something i still havent figured out in plaintext

You can move between headings and files with a few keystrokes in emacs/org-mode. This doc shows a fairly advanced way of doing gtd w/ org-mode. I use a stripped down workflow based on this. https://emacs.cafe/emacs/orgmode/gtd/2017/06/30/orgmode-gtd....