What ties all these notes and files together is Emacs Lisp: Write Lisp functions to automate most of what you do. - Previously I used Python for that, but Elisp is so much more fun to automate text-based workflows.
I would have to write a book to summarize all the ways this can transform your interactions and workflows with your computer and especially with everything text.
Edit:
After twenty years of using all sorts of text based databases and PIMs (AskSam, NetManages ECCOPro, various outliners, Outlook, Evernote, Omni{Focus,Outliner}, Bear Writer App, Ulysses App, and half a dozen other tools) I have come to realize that nothing beats Emacs + Org + Lisp.