From 48e1c41198179bb1860ff585d4a402ecd5070702 Mon Sep 17 00:00:00 2001
From: Ray Andrew <rs@rs.ht>
Date: Fri, 26 Dec 2025 03:08:22 -0600
Subject: [PATCH] feat(org): fix agenda workflow

---
 config/emacs/post-init.el | 129 ++++++++++++++++++++++-----
 docs/emacs.md             | 177 ++++++++++++++++++++++++++++++++++++++
 docs/mu4e.md              |  97 ---------------------
 3 files changed, 284 insertions(+), 119 deletions(-)
 create mode 100644 docs/emacs.md
 delete mode 100644 docs/mu4e.md

diff --git a/config/emacs/post-init.el b/config/emacs/post-init.el
index 3689bcd..e99e12d 100644
--- a/config/emacs/post-init.el
+++ b/config/emacs/post-init.el
@@ -586,7 +586,7 @@ frame if FRAME is nil, and to 1 if AMT is nil."
 (setq org-directory "~/NPersonal/") ; Non-absolute paths for agenda and
                                     ; capture templates will look here.
 
-(setq org-agenda-files '("inbox.org" "work.org"))
+(setq org-agenda-files '("agenda.org"))
 
 ;; Default tags
 (setq org-tag-alist '(
@@ -609,13 +609,44 @@ frame if FRAME is nil, and to 1 if AMT is nil."
                       ("reading")))
 
 ;; Org-refile: where should org-refile look?
-(setq org-refile-targets 'FIXME)
+(setq org-refile-targets '(("agenda.org" :maxlevel . 2)
+                           ("archive.org" :level . 1)))
+
+;; Archive location
+(setq org-archive-location "archive.org::* Archived")
 
 ;;; Phase 3 variables
 
-;; Org-roam variables
-(setq org-roam-directory "~/NPersonal/roam/")
-(setq org-roam-index-file "~/NPersonal/roam/index.org")
+;; Denote (zettelkasten with markdown)
+(use-package denote
+  :ensure t
+  :custom
+  (denote-directory "~/NPersonal/")
+  (denote-file-type 'markdown-yaml)  ;; Use markdown with YAML front matter
+  (denote-known-keywords '("project" "idea" "ref" "meeting" "paper"))
+  (denote-prompts '(title keywords))
+  :bind
+  (("C-c n n" . denote)              ;; Create new note
+   ("C-c n f" . denote-open-or-create)
+   ("C-c n i" . denote-link)         ;; Insert link to note
+   ("C-c n l" . denote-backlinks)    ;; Show backlinks
+   ("C-c n r" . denote-rename-file)
+   ("C-c n k" . denote-keywords-add)
+   ("C-c n K" . denote-keywords-remove))
+  :config
+  ;; Enable denote links in org
+  (denote-rename-buffer-mode 1))
+
+;; Denote org extras (better org integration)
+(use-package denote-org-extras
+  :ensure nil
+  :after denote
+  :config
+  ;; Create org links to denote files
+  (denote-org-extras-dblock-backlinks-mode 1)
+  :bind
+  (("C-c n b" . denote-org-extras-backlinks-for-heading)
+   ("C-c n h" . denote-org-extras-link-to-heading)))
 
 ;;; Optional variables
 
@@ -629,12 +660,38 @@ frame if FRAME is nil, and to 1 if AMT is nil."
   :elpaca nil
   :hook ((org-mode . visual-line-mode)  ; wrap lines at word breaks
          (org-mode . flyspell-mode))    ; spell checking!
+  :init
+  ;; Load mu4e-org for email links (before org loads)
+  (with-eval-after-load 'org
+    (require 'mu4e-org nil t))
+
+  ;; Open agenda on startup (deferred)
+  (add-hook 'elpaca-after-init-hook
+            (lambda ()
+              (run-with-idle-timer 1 nil #'org-agenda nil "n")))
 
   :bind (:map global-map
+              ("C-c a" . org-agenda)                ; Agenda
+              ("C-c c" . org-capture)               ; Capture
               ("C-c l s" . org-store-link)          ; Mnemonic: link → store
               ("C-c l i" . org-insert-link-global)) ; Mnemonic: link → insert
+  :custom
+  (org-time-stamp-rounding-minutes '(0 5))  ;; Round to 5 min
+  (org-read-date-prefer-future t)
+  (org-return-follows-link t)               ;; RET follows links
+  ;; Agenda settings
+  (org-agenda-window-setup 'current-window)
+  (org-agenda-start-with-log-mode t)
+  (org-agenda-include-diary nil)
+  (org-agenda-tags-column -80)
+  (org-agenda-block-separator ?─)
+  (org-agenda-time-grid '((daily today require-timed)
+                          (800 1000 1200 1400 1600 1800 2000)
+                          " ┄┄┄┄┄ " "┄┄┄┄┄┄┄┄┄┄┄┄┄┄┄"))
+  (org-agenda-current-time-string "◀── now ──────────────────────────────────────")
   :config
   (require 'oc-csl)                     ; citation support
+
   (add-to-list 'org-export-backends 'md)
   (setf (cdr (assoc 'file org-link-frame-setup)) 'find-file)
   (setq org-export-with-smart-quotes t)
@@ -643,29 +700,54 @@ frame if FRAME is nil, and to 1 if AMT is nil."
   (setq org-outline-path-complete-in-steps nil)
   (setq org-refile-use-outline-path 'file)
   (setq org-capture-templates
-        '(("c" "Default Capture" entry (file "inbox.org")
-           "* TODO %?\n%U\n%i")
+        '(("c" "Quick Capture" entry (file+headline "agenda.org" "Inbox")
+           "** TODO %?\n%U\n%i")
           ;; Capture and keep an org-link to the thing we're currently working with
-          ("r" "Capture with Reference" entry (file "inbox.org")
-           "* TODO %?\n%U\n%i\n%a")
-          ;; Define a section
-          ("w" "Work")
-          ("wm" "Work meeting" entry (file+headline "work.org" "Meetings")
+          ("r" "Capture with Reference" entry (file+headline "agenda.org" "Inbox")
            "** TODO %?\n%U\n%i\n%a")
-          ("wr" "Work report" entry (file+headline "work.org" "Reports")
+          ("t" "Task" entry (file+headline "agenda.org" "Tasks")
+           "** TODO %?\n%U\n%i")
+          ("m" "Meeting" entry (file+headline "agenda.org" "Meetings")
            "** TODO %?\n%U\n%i\n%a")
           ;; Email capture
           ("e" "Email")
-          ("et" "Email TODO" entry (file "inbox.org")
-           "* TODO %:fromname: %:subject\n%U\n%a\n\n%?")
-          ("ef" "Email Follow-up" entry (file "inbox.org")
-           "* TODO Follow up: %:subject\nDEADLINE: %(org-insert-time-stamp (org-read-date nil t \"+2d\"))\n%U\n%a\n\n%?")))
+          ("ei" "Email to Inbox" entry (file+headline "agenda.org" "Inbox")
+           "** TODO %:subject\nFrom: %:fromname <%:fromaddress>\nEmail: %a\n%?")
+          ("et" "Email to Tasks" entry (file+headline "agenda.org" "Tasks")
+           "** TODO %:subject\nFrom: %:fromname <%:fromaddress>\nEmail: %a\n%?")
+          ("ef" "Email Follow-up" entry (file+headline "agenda.org" "Tasks")
+           "** TODO Follow up: %:subject\nDEADLINE: %(org-insert-time-stamp (org-read-date nil t \"+2d\"))\nFrom: %:fromname\nEmail: %a\n%?")))
   (setq org-agenda-custom-commands
-        '(("n" "Agenda and All Todos"
-           ((agenda)
-            (todo)))
-          ("w" "Work" agenda ""
-           ((org-agenda-files '("work.org")))))))
+        '(("n" "Dashboard"
+           ((tags-todo "+DEADLINE<\"<today>\""
+                       ((org-agenda-overriding-header "Overdue!")))
+            (agenda "" ((org-agenda-span 'day)
+                        (org-deadline-warning-days 7)
+                        (org-agenda-time-grid nil)
+                        (org-agenda-overriding-header "Today")))
+            (todo "STARTED"
+                  ((org-agenda-overriding-header "In Progress")))
+            (todo "WAITING"
+                  ((org-agenda-overriding-header "Waiting")))
+            (tags-todo "+DEADLINE>=\"<today>\"+DEADLINE<=\"<+7d>\""
+                       ((org-agenda-overriding-header "Due This Week")))
+            (tags-todo "inbox"
+                       ((org-agenda-overriding-header "Inbox")))
+            (agenda "" ((org-agenda-span 7)
+                        (org-agenda-start-day "+1d")
+                        (org-agenda-start-on-weekday nil)
+                        (org-agenda-show-all-dates t)
+                        (org-agenda-time-grid nil)
+                        (org-agenda-overriding-header "Next 7 Days")))
+            (alltodo ""
+                     ((org-agenda-skip-function
+                       '(org-agenda-skip-entry-if 'scheduled 'deadline 'todo '("STARTED" "WAITING")))
+                      (org-agenda-overriding-header "Backlog")))))
+          ("w" "Week View"
+           ((agenda "" ((org-agenda-span 'week)
+                        (org-deadline-warning-days 14)))))
+          ("i" "Inbox" tags-todo "inbox")
+          ("p" "Projects" tags-todo "project"))))
 
 ;; =========================
 ;; Email (mu4e)
@@ -686,6 +768,9 @@ frame if FRAME is nil, and to 1 if AMT is nil."
   (setq mu4e-mu-binary (or (executable-find "mu")
                            "/etc/profiles/per-user/rayandrew/bin/mu"))
 
+  ;; Enable org-mode link support
+  (require 'mu4e-org)
+
   ;; General settings
   (setq mu4e-maildir "~/mail")
   (setq mu4e-get-mail-command "~/dotfiles/bin/path-shim mbsync -a")
diff --git a/docs/emacs.md b/docs/emacs.md
new file mode 100644
index 0000000..12e1bcc
--- /dev/null
+++ b/docs/emacs.md
@@ -0,0 +1,177 @@
+# Emacs Configuration
+
+## Notes & Org
+
+### Directory Structure
+
+- `~/NPersonal/agenda.org` - All tasks (Inbox, Tasks, Meetings)
+- `~/NPersonal/archive.org` - Completed/archived items
+- `~/NPersonal/*.md` - Denote markdown notes
+
+### agenda.org Structure
+
+```org
+* Inbox      <- quick captures
+* Tasks      <- organized tasks
+* Meetings   <- meetings
+```
+
+### Org Agenda
+
+| Key | Action |
+|-----|--------|
+| `C-c a` | Open agenda dispatcher |
+| `C-c c` | Capture (quick note/todo) |
+
+#### In Agenda View
+
+| Key | Action |
+|-----|--------|
+| `n` / `p` | Next / previous item |
+| `t` | Cycle TODO state |
+| `RET` | Go to item |
+| `q` | Quit agenda |
+
+### Org Mode
+
+| Key | Action |
+|-----|--------|
+| `C-c C-t` | Cycle TODO state |
+| `C-c C-s` | Schedule |
+| `C-c C-d` | Set deadline |
+| `C-c C-w` | Refile to another file/heading |
+| `C-c C-x C-a` | Archive subtree |
+| `C-c l s` | Store link |
+| `C-c l i` | Insert link |
+
+### Capture Templates (`C-c c`)
+
+| Key | Action |
+|-----|--------|
+| `c` | Quick capture to Inbox |
+| `r` | Capture with reference |
+| `t` | Task |
+| `m` | Meeting |
+| `e i` | Email to Inbox |
+| `e t` | Email to Tasks |
+| `e f` | Email follow-up with deadline |
+
+### Denote (Markdown Notes)
+
+Notes are saved as: `20241226T123456--title__keyword1_keyword2.md`
+
+| Key | Action |
+|-----|--------|
+| `C-c n n` | Create new note |
+| `C-c n f` | Find or create note |
+| `C-c n i` | Insert link to note |
+| `C-c n l` | Show backlinks |
+| `C-c n r` | Rename file |
+| `C-c n k` | Add keyword |
+| `C-c n K` | Remove keyword |
+| `C-c n b` | Backlinks for org heading |
+| `C-c n h` | Link to org heading |
+
+### Archive
+
+Completed tasks go to `archive.org` under `* Archived` heading.
+
+- `C-c C-x C-a` - Archive current subtree
+- `C-c C-w` then select `archive.org` - Refile to archive
+
+---
+
+## Email (mu4e)
+
+### Launch
+
+| Key | Action |
+|-----|--------|
+| `C-c e` | Open mu4e |
+
+### Main View
+
+| Key | Action |
+|-----|--------|
+| `U` | Update mail (run mbsync) |
+| `j` | Jump to maildir |
+| `s` | Search |
+| `b` | Bookmarks |
+| `C` | Compose new message |
+| `;` | Switch context (account) |
+| `q` | Quit mu4e |
+
+### Headers View (Message List)
+
+| Key | Action |
+|-----|--------|
+| `n` / `p` | Next / previous message |
+| `RET` | View message |
+| `d` | Mark for trash |
+| `D` | Mark for delete |
+| `t` | Mark for action (prompts) |
+| `u` | Unmark |
+| `m` | Move to folder |
+| `e` | Refile (archive) |
+| `+` / `-` | Mark / unmark flag |
+| `!` | Mark as read |
+| `?` | Mark as unread |
+| `r` | Reply |
+| `R` | Reply all |
+| `F` | Forward |
+| `x` | Execute marked actions |
+| `U` | Unmark all |
+| `%` | Mark by pattern |
+| `T` | Mark thread |
+| `g` | Rerun search |
+| `q` | Quit to main view |
+
+### Message View
+
+| Key | Action |
+|-----|--------|
+| `n` / `p` | Next / previous message |
+| `SPC` / `DEL` | Scroll down / up |
+| `r` | Reply |
+| `R` | Reply all |
+| `F` | Forward |
+| `o` | Open attachment |
+| `e` | Save attachment |
+| `a` | View action (open in browser, etc.) |
+| `#` | Toggle citation folding |
+| `.` | Raw view |
+| `h` | Toggle headers |
+| `q` | Return to headers |
+
+### Compose
+
+| Key | Action |
+|-----|--------|
+| `C-c C-c` | Send message |
+| `C-c C-k` | Kill (discard) message |
+| `C-c C-d` | Save as draft |
+| `C-c C-a` | Attach file |
+| `C-c C-s` | GPG sign message |
+| `C-c C-e` | GPG encrypt message |
+
+### Bookmarks (from main view, press `b`)
+
+| Key | Action |
+|-----|--------|
+| `u` | Unread messages |
+| `t` | Today's messages |
+| `w` | Last 7 days |
+| `i` | UChicago Inbox |
+| `p` | Personal Inbox |
+
+### Search Tips
+
+- `from:john` - messages from john
+- `to:jane` - messages to jane
+- `subject:meeting` - subject contains meeting
+- `flag:unread` - unread messages
+- `flag:attach` - messages with attachments
+- `date:today..now` - today's messages
+- `date:7d..now` - last 7 days
+- `maildir:/uchicago/Inbox` - specific maildir
+- `AND`, `OR`, `NOT` - boolean operators
diff --git a/docs/mu4e.md b/docs/mu4e.md
deleted file mode 100644
index 31cb138..0000000
--- a/docs/mu4e.md
+++ /dev/null
@@ -1,97 +0,0 @@
-# mu4e Configuration
-
-## Launch
-
-| Key | Action |
-|-----|--------|
-| `C-c e` | Open mu4e |
-
-## Main View
-
-| Key | Action |
-|-----|--------|
-| `U` | Update mail (run mbsync) |
-| `j` | Jump to maildir |
-| `s` | Search |
-| `b` | Bookmarks |
-| `C` | Compose new message |
-| `;` | Switch context (account) |
-| `q` | Quit mu4e |
-
-## Headers View (Message List)
-
-| Key | Action |
-|-----|--------|
-| `n` / `p` | Next / previous message |
-| `RET` | View message |
-| `d` | Mark for trash |
-| `D` | Mark for delete |
-| `t` | Mark for action (prompts) |
-| `u` | Unmark |
-| `m` | Move to folder |
-| `e` | Refile (archive) |
-| `+` / `-` | Mark / unmark flag |
-| `!` | Mark as read |
-| `?` | Mark as unread |
-| `r` | Reply |
-| `R` | Reply all |
-| `F` | Forward |
-| `x` | Execute marked actions |
-| `u` | Unmark |
-| `U` | Unmark all |
-| `*` | Mark for something |
-| `#` | Mark for deferred trash |
-| `%` | Mark by pattern |
-| `T` | Mark thread |
-| `g` | Rerun search |
-| `q` | Quit to main view |
-
-## Message View
-
-| Key | Action |
-|-----|--------|
-| `n` / `p` | Next / previous message |
-| `SPC` / `DEL` | Scroll down / up |
-| `r` | Reply |
-| `R` | Reply all |
-| `F` | Forward |
-| `o` | Open attachment |
-| `e` | Save attachment |
-| `a` | View action (open in browser, etc.) |
-| `#` | Toggle citation folding |
-| `.` | Raw view |
-| `h` | Toggle headers |
-| `q` | Return to headers |
-
-## Compose
-
-| Key | Action |
-|-----|--------|
-| `C-c C-c` | Send message |
-| `C-c C-k` | Kill (discard) message |
-| `C-c C-d` | Save as draft |
-| `C-c C-a` | Attach file |
-| `C-c C-s` | GPG sign message (custom) |
-| `C-c C-e` | GPG encrypt message |
-
-## Bookmarks (from main view, press `b`)
-
-| Key | Action |
-|-----|--------|
-| `u` | Unread messages |
-| `t` | Today's messages |
-| `w` | Last 7 days |
-| `i` | UChicago Inbox |
-| `p` | Personal Inbox |
-
-## Search Tips
-
-- `from:john` - messages from john
-- `to:jane` - messages to jane
-- `subject:meeting` - subject contains meeting
-- `flag:unread` - unread messages
-- `flag:attach` - messages with attachments
-- `date:today..now` - today's messages
-- `date:7d..now` - last 7 days
-- `maildir:/uchicago/Inbox` - specific maildir
-- `AND`, `OR`, `NOT` - boolean operators