feat(org): Remove and reformat org configuration

Remove a lot of extraneous org-mode config.
Remove a lot of doom modules not using.
Add several useful doom modules (nix, direnv, etc)
Reformat configuration

config.org

@@ -36,23 +36,13 @@ Relative line numbers don't seem to work, because of folding in Org-mode.
 #+begin_src emacs-lisp
 (setq doom-theme 'doom-xcode)
 (setq doom-font (font-spec :family "Hack Nerd Font Mono" :size 16 :weight 'medium))
-
 (setq auto-save-default nil) ;I don't like autosaving. Let me do it myself.
-#+end_src
-
-#+RESULTS:
-
-** Doom splash screen
-I really don't like the widgets, and I think it takes longer to load so I get rid of them
-#+begin_src emacs-lisp
 (remove-hook '+doom-dashboard-functions #'doom-dashboard-widget-shortmenu)
 (remove-hook '+doom-dashboard-functions #'doom-dashboard-widget-footer)
+(setq fancy-splash-image (concat doom-private-dir "emacs.png"))
+(add-hook 'term-mode-hook 'hide-mode-line-mode)
 #+end_src
 
-Set a sweet splash image
-#+begin_src emacs-lisp
-(setq fancy-splash-image (concat doom-private-dir "emacs.png"))
-#+end_src
 * Evil configuration
 I want a non-ESC way to get back to normal mode:
 #+begin_src emacs-lisp
@@ -62,44 +52,20 @@ I want a non-ESC way to get back to normal mode:
 (map! :desc "Decrement number below or after cursor" :n "C-x" #'evil-numbers/dec-at-pt)
 (map! :n "g j" #'evil-next-visual-line)
 (map! :n "g k" #'evil-previous-visual-line)
+(map!
+ :map org-agenda-keymap
+ "j" #'evil-next-line
+ "k" #'evil-previous-line)
+(map!
+ :map org-super-agenda-header-map
+ "j" #'evil-next-line
+ "k" #'evil-previous-line)
 #+end_src
 
 * Terminal setup
-I like to just use bash:
-#+begin_src emacs-lisp
-(defun bash nil
-  "Lauch term with /bin/bash"
-  (interactive)
-  (term "/bin/bash"))
-
-(defun dash nil
-  "Lauch term with /bin/dash"
-  (interactive)
-  (term "/bin/dash"))
-
-(defun zsh nil
-  "Lauch term with /bin/zsh"
-  (interactive)
-  (term "/bin/zsh"))
-
-#+end_src
-
-#+RESULTS:
-: zsh
-
 ** Shell mappings
 #+begin_src emacs-lisp
 (map! :leader (:prefix ("k" . "shell")
-
-      :desc "Start a bash shell"
-      :n "b" #'bash
-
-      :desc "Start a dash shell"
-      :n "d" #'dash
-
-      :desc "Start a zsh shell"
-      :n "z" #'zsh
-
       :desc "Start an elisp repl"
       :n "e" #'+emacs-lisp/open-repl
 
@@ -107,44 +73,13 @@ I like to just use bash:
       :n "j" #'+python/open-repl))
 #+end_src
 
-#+RESULTS:
-
-,#+RESULTS:
-
-I don't like the modeline in the terminal.
-,#+begin_src emacs-lisp
-(add-hook 'term-mode-hook 'hide-mode-line-mode)
-#+end_src
-* Sage-math
-#+begin_src emacs-lisp
-(use-package! sage-shell-mode
-  :defer)
-
-;; Ob-sagemath supports only evaluating with a session.
-(setq org-babel-default-header-args:sage '((:session . t)
-                                           (:results . "output")))
-
-;; C-c c for asynchronous evaluating (only for SageMath code blocks).
-(with-eval-after-load "org"
-  (define-key org-mode-map (kbd "C-c c") 'ob-sagemath-execute-async))
-#+end_src
 I like to have a shortcut for calc as well, for simpler calculations
 #+begin_src emacs-lisp
 (map! :leader
       :desc "The Emacs Calculator"
       "C" #'calc)
 #+end_src
-* Beancount
+
-** FavaGTK :outdated:
-I want to launch favagtk more easily. Let's do that here:
-#+begin_src emacs-lisp
-(defun fava ()
-  (interactive)
-  (async-shell-command "flatpak run org.gnome.gitlab.johannesjh.favagtk"))
-(map! :leader
- :desc "Start favagtk"
- "r b" #'fava)
-#+end_src
 * Useful Functions
 ** Get the date from the shell
 I want to grab the current date and put it in the buffer.
@@ -166,9 +101,7 @@ Because I sometimes use Fish or another shell, it's good to make sure bash is ru
       "m" #'insert-current-date-alt)))
 #+end_src
 
-#+RESULTS:
+** Convert regex strings to rx :COMMENT:
-: insert-current-date-alt
-** Convert regex strings to rx
 #+begin_src elisp :tangle packages.el
 (package! xr)
 #+end_src
@@ -176,9 +109,6 @@ Because I sometimes use Fish or another shell, it's good to make sure bash is ru
 #+begin_src elisp
 (use-package! xr)
 #+end_src
-* Creating Diagrams and graphs
-** TODO set default values using org-babel's features for that.
-
 * Securing Sensitive Files
 ** Age.el
 #+begin_src emacs-lisp :tangle "packages.el"
@@ -203,7 +133,7 @@ Because I sometimes use Fish or another shell, it's good to make sure bash is ru
 :END:
 This preprocessor script allows me to use Ripgrep with Age to filter agenda files.
 You can see the configuration for that in [[#agenda-efficient][this section]].
-#+begin_src zsh :tangle "/home/user/age-preprocessor.zsh"
+#+begin_src zsh :tangle "/home/judah/age-preprocessor.zsh"
 #!/usr/bin/env zsh
 
 case "$1" in
@@ -244,6 +174,7 @@ Emacs has better default values now, so it will ask to evaluate local variables.
     (setq templates/post-capture-title "#+TITLE: ${title}\n")
     (setq templates/post-capture-template (concat templates/post-capture-title templates/post-capture-props))
 #+end_src
+
 * Org-mode for a great todo list
 ** Making the Agenda features more efficient
 Using ripgrep we can automatically narrow org-agenda files.
@@ -256,7 +187,7 @@ This piece of code will allow us to capture all the agenda files using the prepr
 #+begin_src sh :exports code :tangle no
 rg --type-add 'aorg:*.org.age' \
     -torg -taorg \
-    --pre ~/age-preprocessor.zsh --pre-glob '*.age' -l TODO /home/user/org
+    --pre ~/age-preprocessor.zsh --pre-glob '*.age' -l TODO /home/judah/10-19-personal-projects/11-zettelkasten
 #+end_src
 
 Now, of course, this code is not useful as it is--after all, we can't tangle a ~.sh~ script into [[file:config.el]].
@@ -266,13 +197,10 @@ The rubber hits the road here.
 I'll call that shell command to set the agenda files correctly.
 #+begin_src emacs-lisp
 (defun set-org-agenda-files-ripgrep ()
-    (setq org-agenda-files (split-string (shell-command-to-string "rg --type-add \'aorg:*.org.age\' -torg -taorg --pre ~/age-preprocessor.zsh --pre-glob \'*.age\' -l TODO /home/user/org ")))
+    (setq org-agenda-files (split-string (shell-command-to-string "rg --type-add \'aorg:*.org.age\' -torg -taorg --pre ~/age-preprocessor.zsh --pre-glob \'*.age\' -l TODO /home/judah/10-19-personal-projects/11-zettelkasten/")))
-    (setq org-agenda-files (remove "/home/user/org/archive.sec.org.age" org-agenda-files)))
+    (setq org-agenda-files (remove "/home/judah/10-19-personal-projects/11-zettelkasten/archive.sec.org.age" org-agenda-files)))
 #+end_src
 
-#+RESULTS:
-: set-org-agenda-files-ripgrep
-
 And then we want to call this before building the agenda:
 #+begin_src emacs-lisp
 (add-hook 'org-agenda-mode-hook 'set-org-agenda-files-ripgrep)
@@ -302,21 +230,8 @@ I don't want scheduled items to duplicate if the deadline is up.
 #+end_src
 
 #+RESULTS:
-: ~/org/
+: ~/10-19-personal-projects/11-zettelkasten/
 
-*** Keymap
-#+begin_src emacs-lisp
-(map!
- :map org-agenda-keymap
- "j" #'evil-next-line
- "k" #'evil-previous-line)
-(map!
- :map org-super-agenda-header-map
- "j" #'evil-next-line
- "k" #'evil-previous-line)
-#+end_src
-
-#+RESULTS:
 
 ** Appearances
 *** Images Preferences
@@ -332,7 +247,7 @@ Super-agenda allows many nice configurations to the agenda buffer.
 #+begin_src emacs-lisp :tangle "packages.el"
 (package! org-super-agenda)
 #+end_src
-Is it working now? It sure seems to be, so IDK what was up with it earlier.
+
 #+begin_src emacs-lisp
 (use-package! org-super-agenda
   :after org-roam
@@ -340,6 +255,9 @@ Is it working now? It sure seems to be, so IDK what was up with it earlier.
 
 #+end_src
 
+#+RESULTS:
+: t
+
 Configure the Super Agenda to neatly organize everything.
 #+begin_src emacs-lisp
 (setq org-super-agenda-groups
@@ -410,11 +328,11 @@ Edna allows better dependency handling for todos and the like.
 #+begin_src emacs-lisp
 
 (use-package org-habit
-:custom
+  :custom
-(org-habit-graph-column 1)
+  (org-habit-graph-column 1)
-(org-habit-preceding-days 10)
+  (org-habit-preceding-days 10)
-(org-habit-following-days 1)
+  (org-habit-following-days 1)
-(org-habit-show-habits-only-for-today t))
+  (org-habit-show-habits-only-for-today t))
 
 #+end_src
 
@@ -457,20 +375,12 @@ This is okay, but I'd rather find something that isn't already used.
 #+end_src
 
 * Programming Items
-** Editorconfig
-I need to make sure some different files work with
-#+begin_src emacs-lisp
-(after! editorconfig-mode
-(add-to-list 'editorconfig-mode-alist
-             '(cpp-mode . "cpp")))
-#+end_src
 ** LSP
 In order for editorconfig to do its thing, indentation by the lsp must be disabled.
 #+begin_src emacs-lisp
 (setq lsp-enable-indentation nil)
 #+end_src emacs-lisp
 
-
 * Website
 ** Capture template
 #+begin_src emacs-lisp
@@ -479,17 +389,12 @@ In order for editorconfig to do its thing, indentation by the lsp must be disabl
 (setq templates/post-capture-template (concat templates/post-capture-title templates/post-capture-props))
 #+end_src
 
-
+* Crafting a Writing Environment :export:
-** Hugo base directory
-#+begin_src emacs-lisp
-(setq org-hugo-base-dir (concat org-directory (file-name-as-directory "website")))
-(setq org-hugo-default-section-directory "posts")
-#+end_src
-* Crafting a Writing Environment
 For writing I like to automate as much as possible.
 This means creating an environment that does citations and such /for/ me.
 ** Export settings
-*** Ox-latex
+*** \LaTeX
+**** Ox-latex
 #+begin_src emacs-lisp
 (after! org
   ;; Import ox-latex to get org-latex-classes and other funcitonality
@@ -507,17 +412,17 @@ This means creating an environment that does citations and such /for/ me.
       (setq org-latex-classes nil))))
 #+end_src
 
-*** Lualatex as PDF Processor
+**** Lualatex as PDF Processor
 I've found that lualatex does a good job processing PDFs. $hi$
 #+begin_src emacs-lisp
 (after! ox-latex
   (setq org-latex-pdf-process
-  '("lualatex --output-directory=/home/user/Documents -shell-escape -interaction nonstopmode %f"
+        '("lualatex --output-directory=%o -shell-escape -interaction nonstopmode %f"
-    "lualatex --output-directory=/home/user/Documents -shell-escape -interaction nonstopmode %f")))
+          "lualatex --output-directory=%o -shell-escape -interaction nonstopmode %f")))
 #+end_src
 
 #+RESULTS:
-| lualatex --output-directory=/home/user/Documents -shell-escape -interaction nonstopmode %f | lualatex --output-directory=/home/user/Documents -shell-escape -interaction nonstopmode %f |
+| lualatex --output-directory=/home/judah/Documents -shell-escape -interaction nonstopmode %f | lualatex --output-directory=/home/judah/Documents -shell-escape -interaction nonstopmode %f |
 
 $x + 1 = 3$
 #+RESULTS:
@@ -614,12 +519,8 @@ $x + 1 = 3$
 
 #+end_src
 
-#+RESULTS:
+**** COMMENT Fixing dvipng image handling
-| mcdowellcv | \documentclass[]{mcdowellcv} |
-
-*** COMMENT Fixing dvipng image handling
 #+begin_src emacs-lisp
-
 (defun +org-refresh-latex-images-previews-h ()
   (dolist (buffer (doom-buffers-in-mode 'org-mode (buffer-list)))
     (with-current-buffer buffer
@@ -630,38 +531,8 @@ $x + 1 = 3$
 
 (add-hook 'doom-load-theme-hook #'+org-refresh-latex-images-previews-h)
 #+end_src
-*** Export Function
-#+begin_src emacs-lisp
-(defun eww-open-this-file ()
-       (set 'directory (file-name-directory buffer-file-name))
-       (set 'filename (file-name-sans-extension buffer-file-name))
-       (set 'extension ".html")
-       (set 'filename (format "%s%s" filename extension))
-       (eww-open-file filename)
-       (evil-window-left)
-)
 
-(defun org-export-and-open-eww ()
+**** Delete links from inline anki
-    "Export current file to html and open in eww"
-    (interactive)
-
-    (org-html-export-to-html)
-    (if (equal (file-name-extension buffer-file-name) "org")
-         (eww-open-this-file)
-      (message "Failed")
-    )
-)
-#+end_src
-
-We'll want a handy shortcut for this.
-#+begin_src emacs-lisp
-            (map! :leader
-                    :desc "Export to html and diplay with eww"
-                    "r E" #'org-export-and-open-eww)
-#+end_src
-#+RESULTS:
-: /home/user/.config/doom/
-*** Delete links from inline anki
 #+begin_src elisp
 (defun inline-anki-link-filter (link backend info)
   "Rewrite links in export to preserve link text only"
@@ -758,7 +629,7 @@ First of all, we must configure citar.
          :padding "  "
          :tag "is:cited"))
 
-(setq citar-indicators
+  (setq citar-indicators
         (list citar-indicator-files-icons
               citar-indicator-links-icons
               citar-indicator-notes-icons
@@ -774,6 +645,7 @@ Let's use a package or two to set a decent document class:
                "\\documentclass[stu]{apa7}
 \\usepackage[]{multicol}
 \\usepackage{mathptmx}
+\\usepackage{times}
 [NO-DEFAULT-PACKAGES]
 [NO-PACKAGES]"
                ("\\section{%s}" . "\\section*{%s}")
@@ -808,7 +680,7 @@ Let's use a package or two to set a decent document class:
                ("\\paragraph{%s}" . "\\paragraph*{%s}")
                ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
 
-       ;; org-latex-compilers = ("pdflatex" "xelatex" "lualatex"), which are the possible values for %latex
+;; org-latex-compilers = ("pdflatex" "xelatex" "lualatex"), which are the possible values for %latex
 #+end_src
 
 *** Engraving Faces
@@ -914,10 +786,10 @@ I use =r= for this purpose. It is close and goes well with *roam*.
 
 (use-package! org-roam-ui
   :after org-roam ;; or :after org
-;;         normally we'd recommend hooking orui after org-roam, but since org-roam does not have
+  ;;         normally we'd recommend hooking orui after org-roam, but since org-roam does not have
-;;         a hookable mode anymore, you're advised to pick something yourself
+  ;;         a hookable mode anymore, you're advised to pick something yourself
-;;         if you don't care about startup time, use
+  ;;         if you don't care about startup time, use
-;;  :hook (after-init . org-roam-ui-mode)
+  ;;  :hook (after-init . org-roam-ui-mode)
   :config
   (setq org-roam-ui-sync-theme t
         org-roam-ui-follow t
@@ -937,11 +809,6 @@ I use =r= for this purpose. It is close and goes well with *roam*.
 
                                                            ))))
 #+END_SRC
-*** Default Browser for Export
-#+begin_src emacs-lisp
-(setq browse-url-browser-function 'browse-url-generic
-      browse-url-generic-program "surf")
-#+end_src
 
 ** Journal Environment with org-roam
 #+begin_src emacs-lisp
@@ -981,13 +848,13 @@ Adding up values for one key is supported."
                       (concat ret " " val)
                     val)))
     ret))
-
 #+end_src
+
 ** Resume setup for a stellar CV
 *** ox-extra for ":ignore:" tags
 I want to be able to ignore headings on export.
 #+begin_src emacs-lisp
-  (use-package! ox-extra
+(use-package! ox-extra
   :after (org)
   :config
   (ox-extras-activate '(latex-header-blocks ignore-headlines)))
@@ -1273,7 +1140,7 @@ I like to have all my config in one place.
        doom              ; what makes DOOM look the way it does
        doom-dashboard    ; a nifty splash screen for Emacs
        ;;doom-quit         ; DOOM quit-message prompts when you quit Emacs
-       ;;(emoji +unicode)  ; 🙂
+       (emoji +unicode)  ; 🙂
        hl-todo           ; highlight TODO/FIXME/NOTE/DEPRECATED/HACK/REVIEW
        ;;hydra
        indent-guides     ; highlighted indent columns
@@ -1300,7 +1167,7 @@ I like to have all my config in one place.
        (format )  ; automated prettiness
        ;;god               ; run Emacs commands without modifier keys
        ;;lispy             ; vim for lisp, for people who don't like vim
-       multiple-cursors  ; editing in many places at once
+       ;;multiple-cursors  ; editing in many places at once
        ;;objed             ; text object editing for the innocent
        ;;parinfer          ; turn lisp into python, sort of
        ;;rotate-text       ; cycle region at point between text candidates
@@ -1317,7 +1184,7 @@ I like to have all my config in one place.
        :term
        ;;eshell            ; the elisp shell that works everywhere
        ;;shell             ; simple shell REPL for Emacs
-       term              ; basic terminal emulator for Emacs
+       ;;term              ; basic terminal emulator for Emacs
        vterm             ; the best terminal emulation in Emacs
 
        :checkers
@@ -1326,10 +1193,10 @@ I like to have all my config in one place.
        grammar           ; tasing grammar mistake every you make
 
        :tools
-       ;;ansible
+       ansible
        (biblio +icons)            ; Writes a PhD for you (citation needed)
        ;;debugger          ; FIXME stepping through code, to help you add bugs
-       ;;direnv
+       direnv
        ;;docker
        editorconfig      ; let someone else argue about tabs vs spaces
        ;;ein               ; tame Jupyter notebooks with emacs
@@ -1346,7 +1213,7 @@ I like to have all my config in one place.
        ;;taskrunner        ; taskrunner for all your projects
        ;;terraform         ; infrastructure as code
        ;;tmux              ; an API for interacting with tmux
-       ;;tree-sitter       ; syntax and parsing, sitting in a tree...
+       tree-sitter       ; syntax and parsing, sitting in a tree...
        ;;upload            ; map local to remote projects via ssh/ftp
 
        :os
@@ -1355,10 +1222,10 @@ I like to have all my config in one place.
 
        :lang
        ;;agda              ; types of types of types of types...
-       (beancount +lsp)         ; mind the GAAP
+       ;;(beancount +lsp)         ; mind the GAAP
        (cc +lsp)         ; C > C++ == 1
        ;;clojure           ; java with a lisp
-       ;;common-lisp       ; if you've seen one lisp, you've seen them all
+       common-lisp       ; if you've seen one lisp, you've seen them all
        ;;coq               ; proofs-as-programs
        ;;crystal           ; ruby at the speed of c
        ;;csharp            ; unity, .NET, and mono shenanigans
@@ -1376,7 +1243,7 @@ I like to have all my config in one place.
        ;;fsharp            ; ML stands for Microsoft's Language
        ;;fstar             ; (dependent) types and (monadic) effects and Z3
        ;;gdscript          ; the language you waited for
-       ;;(go +lsp)         ; the hipster dialect
+       (go +lsp)         ; the hipster dialect
        ;;(graphql +lsp)    ; Give queries a REST
        ;;(haskell +lsp)    ; a language that's lazier than I am
        ;;hy                ; readability of scheme w/ speed of python
@@ -1392,7 +1259,7 @@ I like to have all my config in one place.
        lua               ; one-based indices? one-based indices
        markdown          ; writing docs for people to ignore
        ;;nim               ; python + lisp at the speed of c
-       ;;nix               ; I hereby declare "nix geht mehr!"
+       (nix +lsp +treesitter)               ; I hereby declare "nix geht mehr!"
        ;;ocaml             ; an objective camel
        (org +roam2 +gnuplot +pomodoro +noter +present +pretty)               ; organize your plain life in plain text
        ;;php               ; perl's insecure younger brother
@@ -1413,8 +1280,8 @@ I like to have all my config in one place.
        ;;solidity          ; do you need a blockchain? No.
        ;;swift             ; who asked for emoji variables?
        ;;terra             ; Earth and Moon in alignment for performance.
-       web               ; the tubes
+       (web +lsp)               ; the tubes
-       ;;yaml              ; JSON, but readable
+       yaml              ; JSON, but readable
                                         ;zig               ; C, but simpler
 
        :email
@@ -1433,22 +1300,20 @@ I like to have all my config in one place.
        :config
        literate
        (default +bindings +smartparens)
-
+       )
-)
 #+end_src
 
 * Footnotes
 [fn:1] Stolen from Tecosaur's [[https://git.tecosaur.net/tec/emacs-config][config]]
 * Other Editing
-** Lillypond
+** Lilypond :COMMENT:noexport:
-
+*** package
-*** ob-lilypond
-**** package
 #+begin_src emacs-lisp :tangle "packages.el"
 (package! ob-lilypond
   :recipe (:host github :type git :repo "mjago/ob-lilypond"))
 #+end_src
-**** config
+
+*** config
 #+begin_src emacs-lisp
 (use-package! ob-lilypond)
 (setq ly-arrange-mode t)