refactor: Move Emacs config from system/ to projects/dotemacs/

- Delete deprecated system/ configuration files
- Update projects/dotemacs/modules/ with reorganized config
- Add .opencode/ directory for agent state
- Clean up attachments and unused documentation files

projects/dotemacs/modules/emacs-org.org

@@ -1,7 +1,10 @@
-#+TITLE: Emacs Org-mode Configuration
-#+property: header-args :tangle ~/.emacs.d/modules/org.el
+#+TITLE: Org Mode Configuration
+#+PROPERTY: header-args :tangle yes
+
+* Org Mode
+
+** Basic setup
 
-* Core Org Setup
 #+begin_src elisp
   (use-package org
     :config
@@ -11,41 +14,130 @@
   	 ("C-c c" . org-capture)
   	 :map org-mode-map)
     )
-  (defvar org-directory (concat (getenv "HOME") "/org/"))
 #+end_src
 
-* Agenda
 #+begin_src elisp
-   (setq org-deadline-warning-days 7)
-   (setq org-agenda-skip-additional-timestamps-same-entry t)
-   (setq org-agenda-span 'fortnight)
-   (setq org-agenda-tags-column 'auto)
-   (setq org-agenda-skip-scheduled-if-deadline-is-shown t)
-   (setq org-agenda-files (list
-  			(concat org-directory "/0_inbox/inbox.org")
-  			(concat org-directory "/0_inbox/org-gtd-tasks.org")
-  			)
-        )
+  (setq org-directory (expand-file-name "~/memex/"))
 #+end_src
 
-* Capture and Protocol
+** Looks
+
+Basic 
+#+begin_src elisp
+  (defvar org-pretty-entities t) ; Improve org mode looks
+  (defvar org-hide-emphasis-markers t) ; Hide emphasis markup
+  (defvar org-num-mode nil)
+  (defvar org-startup-folded 'shw2levels)
+#+end_src
+
+Indentation of headers
+#+begin_src elisp
+  (defvar org-startup-indented t) ; Indent org heirarchy
+  (defvar org-adapt-indentation t)
+  (defvar org-hide-leading-stars t) ; Minimal Outline
+  (defvar org-odd-levels-only nil)
+#+end_src
+
+Indentation of lists
+#+begin_src elisp
+  (setq org-list-demote-modify-bullet t)
+#+end_src
+
+Org-modern
+#+begin_src elisp
+  (use-package org-modern
+    :ensure t
+    :config
+        ;; Choose some fonts
+    (set-face-attribute 'default nil :family "sans-serif")
+    (set-face-attribute 'variable-pitch nil :family "sans-serif")
+    (set-face-attribute 'org-modern-symbol nil :family "Iosevka")
+
+    ;; Edit settings
+    (defvar org-auto-align-tags nil)
+    (defvar org-tags-column 0)
+    (defvar org-catch-invisible-edits 'show-and-error)
+    (defvar org-special-ctrl-a/e t)
+    (defvar org-insert-heading-respect-content t)
+
+     ;; Org styling, hide markup etc.
+     (defvar org-hide-emphasis-markers t)
+     (defvar org-pretty-entities t)
+
+     ;; Agenda styling
+     (defvar org-agenda-tags-column 0)
+     (defvar org-agenda-block-separator ?─)
+     (defvar org-agenda-time-grid
+       '((daily today require-timed)
+         (800 1000 1200 1400 1600 1800 2000)
+         " ┄┄┄┄┄ " "┄┄┄┄┄┄┄┄┄┄┄┄┄┄┄"))
+     (defvar org-agenda-current-time-string
+       "◀── now ─────────────────────────────────────────────────")
+
+    ;; Ellipsis styling
+     (defvar org-ellipsis "…")
+     (set-face-attribute 'org-ellipsis nil :inherit 'default :box nil)
+    
+     (global-org-modern-mode)
+    )
+#+end_src
+
+Highlight Sourcecode Syntax
+#+begin_src elisp
+  (setq org-src-fontify-natively t)
+  (setq org-src-tab-acts-natively t)
+#+end_src
+
+Images
+#+begin_src elisp
+  (setq org-startup-with-inline-images t)
+  (setq org-image-actual-width '(300))
+#+end_src
+
+** Capture
+
+#+begin_src elisp
+  (defvar org-default-notes-file (concat org-directory "inbox.org"))
+#+end_src
+
+*** Org-protocol
+
+Linux configuration
+#+begin_src bash :tangle yes
+[Desktop Entry]
+Name=org-protocol
+Comment=Intercept calls from emacsclient to trigger custom actions
+Categories=Other;
+Keywords=org-protocol;
+Icon=emacs
+Type=Application
+Exec=emacsclient -- %u
+Terminal=false
+StartupWMClass=Emacs
+MimeType=x-scheme-handler/org-protocol;
+#+end_src
+
+#+begin_src bash :tangle yes
+update-desktop-database ~/.local/share/applications/
+#+end_src
+
+Basic configuration
 #+begin_src elisp
   (require 'org-protocol)
-  (setq org-protocol-default-buffer-for-file-links "*scratch*")
-  (defvar org-default-notes-file (concat org-directory "/0_inbox/inbox.org"))
-  (setq org-protocol-default-template-key "L")
+  (setq org-protocol-default-buffer-for-file-links "*scratch*") ; fixes 'no buffers remain to edit error for org-protocol capturer
 #+end_src
 
-#+begin_src elisp :tangle ~/.emacs.d/custom.el
-  (defvar org-capture-templates '(
+Org-protocol templates
+#+begin_src elisp :tangle yes
+  (setq org-capture-templates '(
                                 ("p" "Protocol"
                                  entry
-                                 (file "0_inbox/inbox.org")
+                                 (file "inbox.org")
                                  "* %^{Title}\nSource: %u, %c\n #+BEGIN_QUOTE\n%i\n#+END_QUOTE\n\n\n%?"
                                  )
                                 ("L" "Protocol Link"
                                  entry
-                                 (file "0_inbox/inbox.org")
+                                 (file "inbox.org")
                                  "* %? [[%:link][%:description]]\n:PROPERTIES:\n:TITLE: %:description\n:URI: %:link\n:CREATED: %U\n:END:"
                                  :prepend nil
                                  :empty-lines 1
@@ -56,14 +148,86 @@
         )
 #+end_src
 
-* TODO Settings
 #+begin_src elisp
-  (setq org-todo-keywords
-          '(
-            (sequence "TODO(t)" "NEXT(n)" "|" "DONE(d!)")
-            (sequence "WAIT(w@/!)" "|" "CNCL(c@)")
-            )
-          )
-  (setq org-enforce-todo-dependencies t)
-  (setq org-log-into-drawer "LOGBOOK")
+  (setq org-protocol-default-template-key "L")
 #+end_src
+
+Convert Orgzly captures to org-protocol captures standard
+#+begin_src elisp
+  (defun my/org-convert-orgzly-to-org-protocol ()
+    "Reformat Orgzly bookmark at point to org-protocol bookmark."
+    (interactive)
+    (when (org-at-heading-p)
+      (let ((headline (nth 4 (org-heading-components))))
+        ;; Find and store the link. Delete the link line.
+        (search-forward-regexp "^https?://\\S-*" nil t)
+        (let ((link (match-string 0)))
+          (beginning-of-line)
+          (kill-line)
+          ;; Delete any trailing blank spaces
+          (org-back-to-heading)
+          (end-of-line)
+          (when (not (org-on-heading-p))
+            (delete-char 1)
+            )
+          ;; Set new headline
+          (goto-char (org-entry-beginning-position))
+          (org-edit-headline (format "[[%s][%s]]" link headline))
+          ;; Set new properties
+          (org-set-property "TITLE" headline)
+          (org-set-property "URI" link)
+          (message "Reformatted Orgzly bookmark at point to org-protocol bookmark")
+          )
+        )
+      )
+    )
+#+end_src
+
+** Exporting
+
+#+begin_src elisp :tangle yes
+  (setq org-export-with-smart-quotes t)
+  (setq org-export-backends '(beamer html latex md))
+#+end_src
+
+Export to EPUB
+#+begin_src elisp :tangle yes
+  (use-package ox-epub)
+#+end_src
+
+** org-attach
+
+#+begin_src elisp
+  (setq org-attach-id-dir (concat org-directory "/library"))
+#+end_src
+
+** Enable shell scripting support in org-babel
+
+#+begin_src elisp
+  (defvar org-babel-do-load-languages  'org-babel-load-languages  '((shell . t)))
+#+end_src
+
+** Insert org-mode links from clipboard
+#+begin_src elisp :tangle yes
+  (use-package org-cliplink
+    :bind
+    (("C-x p i" . org-cliplink))
+    )
+#+end_src
+
+** Deft
+#+begin_src elisp :tangle yes
+  (use-package deft
+    :commands (deft)
+    :init
+    (defvar deft-extensions '("org"))
+    (defvar deft-recursive nil)
+    (defvar deft-use-filename-as-title t)
+    :config
+    (defvar deft-directory org-directory)
+    (defvar deft-recursive t)
+    (defvar deft-strip-summary-regexp ":PROPERTIES:\n\\(.+\n\\)+:END:\n")
+    (defvar deft-use-filename-as-title t)
+    :bind  ("C-c n d" . deft)
+    )
+#+end_src