Managing my org files with an agent

I don't know why, but every couple of years I get bitten by an "I should try Emacs bug." I have no idea why, it's just this like... recurring intrusive thought. Usually I try and launch head-first into trying to replace my IDE, which is kind of like Emacs on hard mode.

This time, though, I was allured by org mode. I am a list-maker. A journaler. A planner. I love that fresh notebook feeling. I live for setting up a new TODO tracker. That satisfying feeling of drawing a big fat X next to a completed item is just :chefs-kiss:. Lists and notebooks help me get all of the planning chaos out of my head and down somewhere without having to worry I'll forget it (unless I lose the notebook which... happens). All of this to say, org mode's promise of being A GNU Emacs major mode for keeping notes, authoring documents, computational notebooks, literate programming, maintaining to-do lists, planning projects, and more — in a fast and effective plain text system. was promising. I'm not sure why I'd previously written it off. I'd probably gotten a new notebook that day or something.

And I'll preface all of this by saying that I've only scratched the surface. There is a lot more you can do with org mode. There's also a lot less you can do with org mode. It's as much of a can of worms as you want it to be. This is just what I've started with for now.

An org file for todos is pretty simple!

#+TITLE: Inbox

* Inbox
* TODO do a really important thing                                  :work:
SCHEDULED: <2026-01-28 Wed>
- [ ] subtask 1
- [ ] subtask 2

* DONE write blog post intro                                        :writing:
CLOSED: [2026-01-27 Tue 14:30]

* TODO review PR by Friday                                          :work:
DEADLINE: <2026-01-30 Fri>

* Notes
Make sure you don't forget to tag your boss on important thing.

Which when viewed in org mode in Emacs looks something like:

The tags work as filters. If you click on :work: (if you're using the GUI version of Emacs) it will filter your list to just the work items.

I love it.

But I wanted to go a bit further. I've been playing with building agents using different frameworks and MCP capabilities. I wanted an agent to coalesce data from my work calendar, Linear, and Github to generate a todo list for me each morning. I also wanted the ability to add my own items.

I landed on generating separate org files for each source. In order to securely fetch the data without my credentials passing through the agent or LLM directly, I created an MCP gateway using Arcade. I granted the MCP gateway access to only the read tools that I wanted to leverage (Github, Linear, Google Calendar). No write access tools.

Then I wrote an agent using Mastra to glue it all together. It doesn't do anything too fancy, just tells the agent how I want files formatted, where they should live, how to deduplicate entries (like a PR that has a matching Linear entry). The code is here. Notice that there are no .env variables for any of the tool auth. My agent does not have direct access to any of my tokens -- that's all managed by Arcade like I mentioned before. The agent simply forwards me the URL elicitation link for each set of tools and I grant access via OAuth.

From there, I wrote up a little snippet in my config.el (note: I'm using Doom Emacs because I wanted some sane defaults set for me. If you're using vanilla Emacs ymmv!):

;;; Org Agenda on Startup (Doom Emacs)
  ;; Shows today's agenda in a side window when Emacs starts.

  (after! org-agenda
    ;; Prevent Doom's popup system from managing the agenda buffer
    (set-popup-rule! "^\\*Org Agenda\\*" :ignore t)

    ;; Show just today, starting from today
    (setq org-agenda-span 'day
          org-agenda-start-on-weekday nil
          org-agenda-start-day nil))

  (defun my/agenda-side ()
    "Open today's agenda in a side window."
    (interactive)
    (let ((orig-win (selected-window)))
      (save-window-excursion
        (org-agenda nil "a"))
      (when-let ((buf (get-buffer "*Org Agenda*")))
        (display-buffer-in-side-window
         buf '((side . right) (slot . 0) (window-width . 0.35)))
        (set-window-dedicated-p (get-buffer-window buf) t))
      (select-window orig-win)))

  (defun my/agenda-refresh ()
    "Refresh the agenda buffer if it exists."
    (when-let ((buf (get-buffer "*Org Agenda*")))
      (with-current-buffer buf
        (org-agenda-redo-all))))

  ;; Open agenda on startup
  (add-hook 'doom-init-ui-hook
            (lambda ()
              (when (display-graphic-p)
                (run-with-timer 0.3 nil #'my/agenda-side))))

  ;; Keybinding (optional)
  (map! :leader
        :desc "Agenda (side)" "o A" #'my/agenda-side)

Which gives me this (work tasks redacted ;)):

It's so good. I can view an individual item to get a link right to the Linear issue / Github, easily toggle between TODO/IN REVIEW/WAITING modes, filter by status or tag, etc.

I haven't migrated my writing or my code editing over to Emacs yet, so we'll see

UPDATE: As of March 2026, I have once again abandoned EMACS. I'm back on, believe it or not, pen and paper todo's/notes. A lot of cognitive research around the benefits of putting pen to paper! Will I go back to EMACS again soon? We'll see.