From 75669df3a514f41ab86c4acede4219972d5be9a5 Mon Sep 17 00:00:00 2001
From: david <davidcrompton@duck.com>
Date: Wed, 5 Jun 2024 15:09:36 -0400
Subject: [PATCH] Major Revisions, Much Cleaner

---
 custom.el | 161 +----------
 main.org  | 785 +++++++++++++++++++++++++++++-------------------------
 2 files changed, 423 insertions(+), 523 deletions(-)

diff --git a/custom.el b/custom.el
index 0dbc69a..4484fbb 100644
--- a/custom.el
+++ b/custom.el
@@ -3,167 +3,8 @@
  ;; If you edit it by hand, you could mess it up, so be careful.
  ;; Your init file should contain only one such instance.
  ;; If there is more than one, they won't work right.
- '(conda-anaconda-home "~/opt/anaconda3")
  '(custom-safe-themes
-   '("5f79df6b4c56021d173c178d90b5a600c678a192d78cc639553915985b67c4ea" "8cda1cfae8e393bfb23f1d448d4be10720835d086f7db080908a7c8d01566516" "a27f7b52fe66bacaec9059f8afd04d055a4ac3c2fba9eb9128c81e10152fc566" "1ba7196d8e7b883272ea8818a5163aec21b57023368febf55255816226f7b370" "8256e7e03444834d34915a226dc24933b0d680a0a1da568ec03f852be776f168" "4ac2f45e6b46e5bb50826d4250df71a57124169b82cc0ad75e436de6e70a9690" "29addd67feb95ca1179e60d476bb92c1f11835548e2efaec15c9ac6af2a8e6a8" "9b7a425c38c4894e161887c26381c2a6fc1de3c1407158507caaf469d76eb27b" "bce055e1681dd343659957710af77f7a6ad106677d42c61f86ebeedf637c4493" "f62c69472d3f506179d797131c014fe4095d9609dddf14542c50e0388f1e8d6d" "cf143bf23fa8160f87331893cdadc40b876556634621dfa373fcf93c4c97c444" "f459dfd377e9cb98d90e53383dcca7d73396cc0a22b31d39af24fb1cf3548fb5" "fcc14e1a22c99d77f7b1455b0c8a320f8afd0c1f4a9c5c50b45f676eb0c54ba2" "a6bae299481c3c0058e611d2c32ca169fa27203345a880806a5a8554cdd2e588" "feb9556e03558588e29e6659c8e01ea3d2a17a1e7a13e9bf9fc9e59cacba4b72" default))
- '(delete-selection-mode nil)
- '(dired-listing-switches "-alh")
- '(elpy-rpc-python-command "python3")
- '(lsp-dart-flutter-sdk-dir "~/flutter")
- '(lsp-file-watch-ignored-directories
-   '("[/\\\\]\\.git\\'" "[/\\\\]\\.github\\'" "[/\\\\]\\.circleci\\'" "[/\\\\]\\.hg\\'" "[/\\\\]\\.bzr\\'" "[/\\\\]_darcs\\'" "[/\\\\]\\.svn\\'" "[/\\\\]_FOSSIL_\\'" "[/\\\\]\\.idea\\'" "[/\\\\]\\.ensime_cache\\'" "[/\\\\]\\.eunit\\'" "[/\\\\]node_modules" "[/\\\\]\\.yarn\\'" "[/\\\\]\\.fslckout\\'" "[/\\\\]\\.tox\\'" "[/\\\\]dist\\'" "[/\\\\]dist-newstyle\\'" "[/\\\\]\\.stack-work\\'" "[/\\\\]\\.bloop\\'" "[/\\\\]\\.metals\\'" "[/\\\\]target\\'" "[/\\\\]\\.ccls-cache\\'" "[/\\\\]\\.vscode\\'" "[/\\\\]\\.venv\\'" "[/\\\\]\\.mypy_cache\\'" "[/\\\\]\\.deps\\'" "[/\\\\]build-aux\\'" "[/\\\\]autom4te.cache\\'" "[/\\\\]\\.reference\\'" "[/\\\\]\\.lsp\\'" "[/\\\\]\\.clj-kondo\\'" "[/\\\\]\\.shadow-cljs\\'" "[/\\\\]\\.babel_cache\\'" "[/\\\\]\\.cpcache\\'" "[/\\\\]\\checkouts\\'" "[/\\\\]\\.m2\\'" "[/\\\\]bin/Debug\\'" "[/\\\\]obj\\'" "[/\\\\]_opam\\'" "[/\\\\]_build\\'" "[/\\\\]\\.elixir_ls\\'" "[/\\\\]\\.direnv\\'" "[/\\\\]\\.tmp\\'"))
- '(lsp-java-format-on-type-enabled nil)
- '(lsp-java-format-settings-profile nil)
- '(lsp-pylsp-plugins-jedi-use-pyenv-environment t)
- '(org-agenda-files
-   '("/home/universe/Documents/research/DBS/TechnicalEvaluation/technicaldraft.org"))
- '(org-export-backends '(ascii beamer html icalendar latex odt))
- '(org-latex-classes
-   '(("beamer" "\\documentclass[presentation]{beamer}"
-      ("\\section{%s}" . "\\section*{%s}")
-      ("\\subsection{%s}" . "\\subsection*{%s}")
-      ("\\subsubsection{%s}" . "\\subsubsection*{%s}"))
-     ("article" "\\documentclass[11pt]{article}"
-      ("\\section{%s}" . "\\section*{%s}")
-      ("\\subsection{%s}" . "\\subsection*{%s}")
-      ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
-      ("\\paragraph{%s}" . "\\paragraph*{%s}")
-      ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
-     ("report" "\\documentclass[11pt]{report}"
-      ("\\part{%s}" . "\\part*{%s}")
-      ("\\chapter{%s}" . "\\chapter*{%s}")
-      ("\\section{%s}" . "\\section*{%s}")
-      ("\\subsection{%s}" . "\\subsection*{%s}")
-      ("\\subsubsection{%s}" . "\\subsubsection*{%s}"))
-     ("book" "\\documentclass[11pt]{book}"
-      ("\\part{%s}" . "\\part*{%s}")
-      ("\\chapter{%s}" . "\\chapter*{%s}")
-      ("\\section{%s}" . "\\section*{%s}")
-      ("\\subsection{%s}" . "\\subsection*{%s}")
-      ("\\subsubsection{%s}" . "\\subsubsection*{%s}"))
-     ("thesis" "\\documentclass[11pt]{ut-thesis}"
-      ("\\part{%s}" . "\\part*{%s}")
-      ("\\chapter{%s}" . "\\chapter*{%s}")
-      ("\\section{%s}" . "\\section*{%s}")
-      ("\\subsection{%s}" . "\\subsection*{%s}")
-      ("\\subsubsection{%s}" . "\\subsubsection*{%s}"))))
- '(org-preview-latex-process-alist
-   '((dvipng :programs
-	     ("latex" "dvipng")
-	     :description "dvi > png" :message "you need to install the programs: latex and dvipng." :image-input-type "dvi" :image-output-type "png" :image-size-adjust
-	     (2.0 . 2.0)
-	     :latex-compiler
-	     ("latex -interaction nonstopmode -output-directory %o %f")
-	     :image-converter
-	     ("dvipng -D %D -T tight -o %O %f")
-	     :transparent-image-converter
-	     ("dvipng -D %D -T tight -bg Transparent -o %O %f"))
-     (dvisvgm :programs
-	      ("latex" "dvisvgm")
-	      :description "dvi > svg" :message "you need to install the programs: latex and dvisvgm." :image-input-type "dvi" :image-output-type "svg" :image-size-adjust
-	      (1.7 . 1.5)
-	      :latex-compiler
-	      ("latex -interaction nonstopmode -output-directory %o %f")
-	      :image-converter
-	      ("dvisvgm %f -n -b min -c %S -o %O"))
-     (imagemagick :programs
-		  ("latex" "convert")
-		  :description "pdf > png" :message "you need to install the programs: latex and imagemagick." :image-input-type "pdf" :image-output-type "png" :image-size-adjust
-		  (1.0 . 1.0)
-		  :latex-compiler
-		  ("pdflatex -interaction nonstopmode -output-directory %o %f")
-		  :image-converter
-		  ("convert -density %D -trim -antialias %f -quality 100 %O"))))
- '(package-selected-packages
-   '(dockerfile-mode :ensure slint-mode ox-reveal lsp-dart dart-mode gnuplot auctex ox-pandoc pdf-tools org-ref helm-bibtex ivy-bibtex geiser-racket rainbow-delimiters rust-mode company-ghci lsp-haskell haskell-mode meson-mode company-c-headers company-ctags poetry python-mode which-key dap-mode helm-lsp lsp-treemacs flycheck lsp-ui lsp-mode company yaml-mode d2-mode php-mode web-mode nix-mode direnv magit esup ligature exec-path-from-shell transient-dwim leaf-convert leaf-tree blackout hydra el-get leaf-keywords leaf))
- '(python-shell-completion-native-enable nil)
- '(sql-sqlite-program "sqlite3")
- '(warning-suppress-types '((comp) (comp) (comp) (comp) (comp))))
-'(org-latex-classes
-  '(("thesis" "\\documentclass{ut-thesis}"
-     ("\\chapter{%s}" . "\\chapter*{%s}")
-     ("\\section{%s}" . "\\section*{%}")
-     ("\\subsection{%s}" . "\\subsection*{%s}")
-     ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
-     ("\\paragraph{%s}" . "\\paragraph*{%s}")
-     ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
-    ("labtemplate" "\\documentclass{labtemplate}"
-     ("\\section{%s}" . "\\section*{%s}")
-     ("\\subsection{%s}" . "\\subsection*{%s}")
-     ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
-     ("\\paragraph{%s}" . "\\paragraph*{%s}")
-     ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
-    ("beamer" "\\documentclass[presentation]{beamer}"
-     ("\\section{%s}" . "\\section*{%s}")
-     ("\\subsection{%s}" . "\\subsection*{%s}")
-     ("\\subsubsection{%s}" . "\\subsubsection*{%s}"))
-    ("article" "\\documentclass[11pt]{article}"
-     ("\\section{%s}" . "\\section*{%s}")
-     ("\\subsection{%s}" . "\\subsection*{%s}")
-     ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
-     ("\\paragraph{%s}" . "\\paragraph*{%s}")
-     ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
-    ("report" "\\documentclass[11pt]{report}"
-     ("\\part{%s}" . "\\part*{%s}")
-     ("\\chapter{%s}" . "\\chapter*{%s}")
-     ("\\section{%s}" . "\\section*{%s}")
-     ("\\subsection{%s}" . "\\subsection*{%s}")
-     ("\\subsubsection{%s}" . "\\subsubsection*{%s}"))
-    ("letter" "\\documentclass{letter}"
-     ("" . ""))
-    ("book" "\\documentclass[11pt]{book}"
-     ("\\part{%s}" . "\\part*{%s}")
-     ("\\chapter{%s}" . "\\chapter*{%s}")
-     ("\\section{%s}" . "\\section*{%s}")
-     ("\\subsection{%s}" . "\\subsection*{%s}")
-     ("\\subsubsection{%s}" . "\\subsubsection*{%s}"))))
-'(org-latex-default-packages-alist
-  '(("AUTO" "inputenc" t
-     ("pdflatex"))
-    ("T1" "fontenc" t
-     ("pdflatex"))
-    ("" "graphicx" t nil)
-    ("" "grffile" t nil)
-    ("" "longtable" nil nil)
-    ("" "wrapfig" nil nil)
-    ("" "rotating" nil nil)
-    ("normalem" "ulem" t nil)
-    ("" "amsmath" t nil)
-    ("" "textcomp" t nil)
-    ("" "amssymb" t nil)
-    ("" "capt-of" nil nil)
-    ("" "hyperref" nil nil)))
-'(org-pandoc-menu-entry
-  '((61 "to ms-pdf and open." org-pandoc-export-to-ms-pdf-and-open)
-    (45 "to ms-pdf." org-pandoc-export-to-ms-pdf)
-    (106 "to json and open." org-pandoc-export-to-json-and-open)
-    (74 "as json." org-pandoc-export-as-json)
-    (80 "to pptx." org-pandoc-export-to-pptx)
-    (120 "to docx and open." org-pandoc-export-to-docx-and-open)
-    (88 "to docx." org-pandoc-export-to-docx)))
-'(python-shell-completion-native-enable nil)
-'(warning-suppress-log-types
-  '((direnv)
-    (lsp-mode)
-    (comp)
-    (comp)
-    (comp)
-    (comp)
-    (comp)
-    (comp)
-    (comp)
-    (comp)))
-'(warning-suppress-types
-  '((lsp-mode)
-    (comp)
-    (comp)
-    (comp)
-    (comp)
-    (comp)
-    (comp)
-    (comp)
-    (comp)))
-
+   '("5f79df6b4c56021d173c178d90b5a600c678a192d78cc639553915985b67c4ea" "8cda1cfae8e393bfb23f1d448d4be10720835d086f7db080908a7c8d01566516" "a27f7b52fe66bacaec9059f8afd04d055a4ac3c2fba9eb9128c81e10152fc566" "1ba7196d8e7b883272ea8818a5163aec21b57023368febf55255816226f7b370" "8256e7e03444834d34915a226dc24933b0d680a0a1da568ec03f852be776f168" "4ac2f45e6b46e5bb50826d4250df71a57124169b82cc0ad75e436de6e70a9690" "29addd67feb95ca1179e60d476bb92c1f11835548e2efaec15c9ac6af2a8e6a8" "9b7a425c38c4894e161887c26381c2a6fc1de3c1407158507caaf469d76eb27b" "bce055e1681dd343659957710af77f7a6ad106677d42c61f86ebeedf637c4493" "f62c69472d3f506179d797131c014fe4095d9609dddf14542c50e0388f1e8d6d" "cf143bf23fa8160f87331893cdadc40b876556634621dfa373fcf93c4c97c444" "f459dfd377e9cb98d90e53383dcca7d73396cc0a22b31d39af24fb1cf3548fb5" "fcc14e1a22c99d77f7b1455b0c8a320f8afd0c1f4a9c5c50b45f676eb0c54ba2" "a6bae299481c3c0058e611d2c32ca169fa27203345a880806a5a8554cdd2e588" "feb9556e03558588e29e6659c8e01ea3d2a17a1e7a13e9bf9fc9e59cacba4b72" default)))
 (custom-set-faces
  ;; custom-set-faces was added by Custom.
  ;; If you edit it by hand, you could mess it up, so be careful.
diff --git a/main.org b/main.org
index d5d7d03..da81375 100644
--- a/main.org
+++ b/main.org
@@ -14,53 +14,56 @@
 We must initialize =leaf.el=, which we use as a use-package
 replacement for defining configs and relations between packages etc.
 
-#+begin_src elisp :tangle yes
-  (eval-and-compile
-    (customize-set-variable
-     'package-archives '(("org" . "https://orgmode.org/elpa/")
-			 ("melpa" . "https://melpa.org/packages/")
-			 ("gnu" . "https://elpa.gnu.org/packages/")))
-    (package-initialize)
-    (unless (package-installed-p 'leaf)
-      (package-refresh-contents)
-      (package-install 'leaf))
+#+begin_src elisp :tangle yes :exports code
+(eval-and-compile
+  (customize-set-variable
+   'package-archives '(("org" . "https://orgmode.org/elpa/")
+		       ("melpa" . "https://melpa.org/packages/")
+		       ("gnu" . "https://elpa.gnu.org/packages/")))
+  (package-initialize)
+  (unless (package-installed-p 'leaf)
+    (package-refresh-contents)
+    (package-install 'leaf))
 
-    (leaf leaf-keywords
-      :ensure t
-      :init
-      (leaf el-get :ensure t)
-      (leaf hydra :ensure t)
-      (leaf blackout :ensure t)
+  (leaf leaf-keywords
+    :ensure t
+    :init
+    (leaf el-get :ensure t)
+    (leaf hydra :ensure t)
+    (leaf blackout :ensure t)
 
-      :config
-      ;; initialize leaf-keywords.el
-      (leaf-keywords-init)))
+    :config
+    ;; initialize leaf-keywords.el
+    (leaf-keywords-init)))
 
-  (leaf leaf-tree :ensure t)
-  (leaf leaf-convert :ensure t)
-  (leaf transient-dwim :ensure t
-    :bind (("M-=" . transient-dwim-dispatch)))
+(leaf leaf-tree :ensure t)
+(leaf leaf-convert :ensure t)
+(leaf transient-dwim :ensure t
+  :bind (("M-=" . transient-dwim-dispatch)))
 #+end_src
 
 ** MacOS Specific
 
-#+begin_src elisp :tangle yes
-  (when (eq system-type 'darwin)
-    (setq mac-option-modifier 'meta))
+#+begin_src elisp :tangle yes :exports code
+(leaf macos
+  :hook (after-init hook)
+  :when (eq system-type 'darwin)
+  :init
+  (setq mac-option-modifier 'meta))
 #+end_src
 
 ** Performance
 
 *** Garbage Collection
 
-#+begin_src elisp :tangle yes
-  (leaf gcmh :ensure t
-    :hook (after-init-hook))
+#+begin_src elisp :tangle yes :exports code
+(leaf gcmh :ensure t
+  :hook (after-init-hook))
 #+end_src
 
 *** Profiling
-#+begin_src elisp :tangle yes
-  (leaf esup :disabled nil :ensure t)
+#+begin_src elisp :tangle yes :exports code
+(leaf esup :disabled nil :ensure t)
 #+end_src
 
 ** Emacs Paths
@@ -69,24 +72,24 @@ replacement for defining configs and relations between packages etc.
 
 Ensure that the =custom.el= resides in the users' emacs directory.
 
-#+begin_src elisp :tangle yes
-  (leaf custom-el
-    :config
-    ;; Ensure custom writes to specific file
-    (setq custom-file (expand-file-name "custom.el" user-emacs-directory))
-    (load custom-file 'noerror 'nomessage))
+#+begin_src elisp :tangle yes :exports code
+(leaf custom-el
+  :config
+  ;; Ensure custom writes to specific file
+  (setq custom-file (expand-file-name "custom.el" user-emacs-directory))
+  (load custom-file 'noerror 'nomessage))
 #+end_src
 
 *** Backups
 
 Set the backups directory to reside in the users' emacs directory.
 
-#+begin_src elisp :tangle yes
-  (leaf backup
-    :config
-    ;; Change the location of file backups/locks into the emacs.d/backups/
-    (setq backup-directory-alist
-	  `(("." . ,(concat user-emacs-directory "backups")))))
+#+begin_src elisp :tangle yes :exports code
+(leaf backup
+  :config
+  ;; Change the location of file backups/locks into the emacs.d/backups/
+  (setq backup-directory-alist
+	`(("." . ,(concat user-emacs-directory "backups")))))
 #+end_src
 
 ** Shell Path Preservation
@@ -94,382 +97,442 @@ Set the backups directory to reside in the users' emacs directory.
 Exec-path-from-shell ensures that path variable is preserved from
 shell.
 
-#+begin_src elisp :tangle yes
-  (leaf exec-path-from-shell :ensure t
-    :config
-    (exec-path-from-shell-initialize))
+#+begin_src elisp :tangle yes :exports code
+(leaf exec-path-from-shell :ensure t
+  :config
+  (exec-path-from-shell-initialize))
 #+end_src
 
 * Visual Customization
 
 Visual Theme of Emacs config: defined in the =themes= directory.
 
-#+begin_src elisp :tangle yes
-  (leaf visual
-    :doc "Visual Changes to Emacs"
-    :tag "builtin" "internal"
-    :custom ((menu-bar-mode . nil)
-	     (tool-bar-mode . nil)
-	     (scroll-bar-mode . nil))
-    :custom-face ((default . '((t (:family "JuliaMono"
-					   :height 150
-					   :weight normal)))))
-    :config
-    ;; Set location of custom theme dir
-    (setq custom-theme-directory (concat user-emacs-directory "themes"))
-    (load-theme 'UniverseHighContrast))
+#+begin_src elisp :tangle yes :exports code
+(leaf visual
+  :doc "Visual Changes to Emacs"
+  :tag "builtin" "internal"
+  :custom ((menu-bar-mode . nil)
+	   (tool-bar-mode . nil)
+	   (scroll-bar-mode . nil))
+  :custom-face ((default . '((t (:family "JuliaMono"
+					 :height 150
+					 :weight normal)))))
+  :config
+  ;; Set location of custom theme dir
+  (setq custom-theme-directory (concat user-emacs-directory "themes"))
+  (load-theme 'UniverseHighContrast))
 #+end_src
 
-** Font Related
-
-*** Ligature
-
-Font related ligatures, combining multiple characters into "one".
-
-#+begin_src elisp :tangle yes
-  (leaf ligature
-	:ensure t
-	:config
-	;; Enable the "www" ligature in every possible major mode
-	(ligature-set-ligatures 't '("www"))
-	;; Enable traditional ligature support in eww-mode, if the
-	;; `variable-pitch' face supports it
-	(ligature-set-ligatures 'eww-mode '("ff" "fi" "ffi"))
-	;; Enable all Cascadia Code ligatures in programming modes
-	(ligature-set-ligatures 'prog-mode '("|||>" "<|||" "<==>" "<!--" "####" "~~>" "***" "||=" "||>"
-					     ":::" "::=" "=:=" "===" "==>" "=!=" "=>>" "=<<" "=/=" "!=="
-					     "!!." ">=>" ">>=" ">>>" ">>-" ">->" "->>" "-->" "---" "-<<"
-					     "<~~" "<~>" "<*>" "<||" "<|>" "<$>" "<==" "<=>" "<=<" "<->"
-					     "<--" "<-<" "<<=" "<<-" "<<<" "<+>" "</>" "###" "#_(" "..<"
-					     "..." "+++" "/==" "///" "_|_" "www" "&&" "^=" "~~" "~@" "~="
-					     "~>" "~-" "**" "*>" "*/" "||" "|}" "|]" "|=" "|>" "|-" "{|"
-					     "[|" "]#" "::" ":=" ":>" ":<" "$>" "==" "=>" "!=" "!!" ">:"
-					     ">=" ">>" ">-" "-~" "-|" "->" "--" "-<" "<~" "<*" "<|" "<:"
-					     "<$" "<=" "<>" "<-" "<<" "<+" "</" "#{" "#[" "#:" "#=" "#!"
-					     "##" "#(" "#?" "#_" "%%" ".=" ".-" ".." ".?" "+>" "++" "?:"
-					     "?=" "?." "??" ";;" "/*" "/=" "/>" "//" "__" "~~" "(*" "*)"
-					     "\\\\" "://"))
-	;; Enables ligature checks globally in all buffers. You can also do it
-	;; per mode with `ligature-mode'.
-	(global-ligature-mode t))
+* Version Control
+#+begin_src elisp :tangle yes :exports code
+(leaf magit :ensure t :require t)
 #+end_src
 
-* Package Configuration
+* Nix Related
 
-** Version Control
-#+begin_src elisp :tangle yes
-  (leaf magit :ensure t :require t)
-#+end_src
-
-** Nix Related
-
-*** Direnv
+** Direnv
 
 In order to support direnv (loading =nix-shell= / =nix develop=)
-#+begin_src elisp :tangle yes
-  (leaf direnv
-	:ensure t
-	:config
-	(direnv-mode))
+#+begin_src elisp :tangle yes :exports code
+(leaf direnv
+  :ensure t
+  :config
+  (direnv-mode))
 #+end_src
 
-*** Nix-mode
+** Nix-mode
 
 =.nix= file mode
-#+begin_src elisp :tangle yes
-  (leaf nix-mode :ensure t)
+#+begin_src elisp :tangle yes :exports code
+(leaf nix-mode :ensure t)
 #+end_src
 
-** WEB
+* IDE Like Things
 
-We all know the web is the future, obviously, of course.
+** Which Key Again?
 
-#+begin_src elisp :tangle yes
-  (leaf web-mode
-	:ensure t
-	:mode
-	"\\.p?html?\\'"
-	"\\.djtml\\'"
-	"\\.jsx?\\'"
-	"\\.tsx?\\'")
-  (leaf php-mode
-	:ensure t)
+#+begin_src elisp :tangle yes :exports code
+(leaf which-key :ensure t
+  :config (which-key-mode))
 #+end_src
 
-** D2
-
-#+begin_src elisp :tangle yes
-  (leaf d2-mode :ensure t)
-#+end_src
-
-** YAML
-
-#+begin_src elisp :tangle yes
-  (leaf yaml-mode :ensure t)
-#+end_src
-
-** IDE Like Things
-*** Company Completion!
+** Company Completion!
 
 We like autocomplete, it... is nice, okay?
 
-#+begin_src elisp :tangle yes
-  (leaf company :ensure t
-    :bind
-    (("C-<tab>" . company-complete))
-    :hook after-init-hook
-    :config (global-company-mode))
+#+begin_src elisp :tangle yes :exports code
+(leaf company :ensure t
+  :bind
+  (("C-<tab>" . company-complete))
+  :hook after-init-hook
+  :config (global-company-mode))
 #+end_src
-*** Language Server Protocol
+
+** Language Server Protocol
 
 We love language features that make languages nice
 
-#+begin_src elisp :tangle yes
-  (leaf lsp-mode
-    :ensure t
-    :init
-    (setq lsp-keymap-prefix "C-c l")
-    :hook
-    ((dart-mode-hook . lsp)
-     (python-mode-hook . lsp)
-     (c-mode-hook . lsp)
-     (c++-mode-hook . lsp)
-     (haskell-mode-hook . lsp)
-     (java-mode-hook . lsp)
-     (rust-mode-hook . lsp)
-     ;; which key support v v v
-     (lsp-mode-hook . lsp-enable-which-key-integration))
-    :commands lsp
-    :config
-    (leaf lsp-ui :ensure t
-	  :commands lsp-ui-mode)
-    (leaf flycheck :ensure t)
-    (leaf lsp-treemacs :ensure t
-	  :commands lsp-treemacs-errors-list)
-    (leaf helm-lsp :ensure t
-	  :commands helm-lsp-workspace-symbol)
-    (leaf dap-mode :ensure t)
-    (leaf which-key :ensure t
-	  :config (which-key-mode)))
+#+begin_src elisp :tangle yes :exports code
+(leaf lsp-mode
+  :ensure t
+  :init
+  (setq lsp-keymap-prefix "C-c l")
+  :commands lsp lsp-deferred
+  :hook
+  ;; which key support v v v
+  ((lsp-mode-hook . lsp-enable-which-key-integration)
 #+end_src
-**** Projectile (Projects)
-#+begin_src elisp :tangle yes
-  (leaf projectile
-    :commands projectile-mode
-    :config
-    (projectile-mode +1))
+
+*** IDE Languages
+
+**** Dart/Flutter
+
+#+begin_src elisp :tangle yes :exports code
+(dart-mode . lsp-deferred)
 #+end_src
-** Python Things
-*** Python-mode
+
+**** Python
+
+#+begin_src elisp :tangle yes :exports code
+(python-mode . lsp-deferred)
+#+end_src
+
+**** C/C++
+
+#+begin_src elisp :tangle yes :exports code
+(c-mode-hook . lsp-deferred)
+(c++-mode-hook . lsp-deferred)
+#+end_src
+
+**** Haskell
+
+#+begin_src elisp :tangle yes :exports code
+(haskell-mode-hook . lsp-deferred)
+#+end_src
+
+**** Java
+
+#+begin_src elisp :tangle yes :exports code
+(java-mode-hook . lsp-deferred)
+#+end_src
+
+**** Rust
+
+#+begin_src elisp :tangle yes :exports code
+(rust-mode-hook . lsp-deferred))
+#+end_src
+
+#+begin_src elisp :tangle yes :exports code
+)
+#+end_src
+
+*** LSP Plugins:
+
+We do want some nice to haves of course
+
+- A pretty UI:
+#+begin_src elisp :tangle yes :exports code
+(leaf lsp-ui :ensure t
+  :commands lsp-ui-mode)
+#+end_src
+- Flycheck compat:
+#+begin_src elisp :tangle yes :exports code
+(leaf flycheck :ensure t)
+#+end_src
+- Debugger Compatibility
+#+begin_src elisp :tangle yes :exports code
+(leaf dap-mode :ensure t)
+#+end_src
+
+*** Projectile (Projects)
+
+#+begin_src elisp :tangle yes :exports code
+(leaf projectile
+  :commands projectile-mode
+  :config
+  (projectile-mode +1))
+#+end_src
+
+* WEB
+
+We all know the web is the future, obviously, of course.
+
+#+begin_src elisp :tangle yes :exports code
+(leaf web-mode
+  :ensure t
+  :mode
+  "\\.p?html?\\'"
+  "\\.djtml\\'"
+  "\\.jsx?\\'"
+  "\\.tsx?\\'")
+(leaf php-mode
+  :ensure t)
+#+end_src
+
+* D2
+
+#+begin_src elisp :tangle yes :exports code
+(leaf d2-mode :ensure t)
+#+end_src
+
+* YAML
+
+#+begin_src elisp :tangle yes :exports code
+(leaf yaml-mode :ensure t)
+#+end_src
+
+* Python Things
+
+** Python-mode
 
 Using python-mode is to have more up to date features (and
 highlighting) compared to builtin python-mode.
 
-#+begin_src elisp :tangle yes
-  (leaf python-mode :ensure t
-	:config
-	(setq python-shell-interpreter "ipython"
-	      python-shell-interpreter-args "-i --simple-prompt --InteractiveShell.display_page=True"))
+#+begin_src elisp :tangle yes :exports code
+(leaf python-mode :ensure t
+  :config
+  (setq python-shell-interpreter "ipython"
+	python-shell-interpreter-args "-i --simple-prompt --InteractiveShell.display_page=True"))
 #+end_src
-*** Poetry
+
+** Poetry
 
 For when we aren't nix'ing things, and want some nice poetry.
 
-#+begin_src elisp :tangle yes
-  (leaf poetry :ensure t)
+#+begin_src elisp :tangle yes :exports code
+(leaf poetry :ensure t)
 #+end_src
-** Java
 
-LSP for java is /nice/.
+* C
 
-#+begin_src elisp :tangle yes
-  (leaf lsp-java
-	:hook (java-mode-hook . lsp))
-#+end_src
-** C
 Who even needs C++, not me, no way, no how.
-#+begin_src elisp :tangle yes
+
+#+begin_src elisp :tangle yes :exports code
+(leaf c-config
+  :hook c-mode-hook c++-mode-hook
+  :config
   (leaf company-ctags :ensure t)
   (leaf company-c-headers :ensure t)
-  (leaf meson-mode :ensure t)
+  (leaf meson-mode :ensure t))
 #+end_src
-** Haskell
-#+begin_src elisp :tangle yes
-  (leaf haskell-mode :ensure t
-	:config
-	(leaf lsp-haskell :ensure t)
-	(leaf company-ghci :ensure t))
+
+* Haskell
+
+#+begin_src elisp :tangle yes :exports code
+(leaf haskell-mode :ensure t)
+(leaf lsp-haskell :ensure t)
+(leaf company-ghci :ensure t)
 #+end_src
-** Rust
-#+begin_src elisp :tangle yes
-  (leaf rust-mode :ensure t
-    (leaf slint-mode :ensure t))
+
+* Rust
+
+#+begin_src elisp :tangle yes :exports code
+(leaf rust-mode :ensure t
+  :init
+  (leaf slint-mode :ensure t))
 #+end_src
-** Minecraft??
+
+* Minecraft??
+
 Minecraft =mcfunction= support, because, it can be annoying to type
 this stuff otherwise.
-#+begin_src elisp :tangle yes
-  (leaf mcf-mode
-	:el-get rasensuihei/mcf)
+#+begin_src elisp :tangle yes :exports code
+(leaf mcf-mode
+  :el-get rasensuihei/mcf)
 #+end_src
-** Lisps
+
+* Lisps
 
 Gonna need to have pretty brackets
-#+begin_src elisp :tangle yes
-  (leaf rainbow-delimiters
-	:ensure t
-	:commands rainbow-delimiters-mode
-	:config
-	(leaf rainbow
-	      :hook (emacs-lisp-mode-hook . rainbow-delimiters-mode)
-	      (geiser-mode-hook . rainbow-delimiters-mode)))
+#+begin_src elisp :tangle yes :exports code
+(leaf rainbow-delimiters
+  :ensure t
+  :commands rainbow-delimiters-mode
+  :config
+  (leaf rainbow
+    :hook (emacs-lisp-mode-hook . rainbow-delimiters-mode)
+    (geiser-mode-hook . rainbow-delimiters-mode)))
 #+end_src
-*** Racket
+
+** Racket
 Makes using racket so much nicer
 
-#+begin_src elisp :tangle yes
-  (leaf geiser-racket :ensure t)
+#+begin_src elisp :tangle yes :exports code
+(leaf geiser-racket :ensure t)
 #+end_src
-** Org
+
+* Org
+
+We ensure that org is available (though it is builtin)
+
+#+begin_src elisp :tangle yes :exports code
+(leaf org :ensure t
+  :require t org-tempo
+  :hook
+  (org-mode-hook . auto-fill-mode)
+  :config
+  (setq document-dir (expand-file-name (if (eq system-type 'darwin) "~/Nextcloud" "~/Documents")))
+  (setq org-directory (concat document-dir "/org"))
+  (set-fill-column 100)
+  (setq org-src-fontify-natively t
+	org-confirm-babel-evaluate nil
+	org-src-preserve-indentation t))
+;; (tempo-define-template "Fig. Caption"
+;; 			   '("" (P "Image: " image t)
+;; 			     (P "Caption: " caption t)
+;; 			     (P "Figure Name: " name t)
+;; 			     "#+CAPTION: " (s caption) > n >
+;; 			     "#+NAME: fig:" (s name) > n >
+;; 			     "#+ATTR_LaTeX: :placement [H]" > n >
+;; 			     "[[" (s image) "]]" > n > p >)
+;; 			   "<fig" "Inserts Figure with Caption"))
+#+end_src
+
+We also want to set our document directory (which as it stands is OS
+dependent)
+
+** Citations/References
 
 We use org-ref because it provides some niceties, like doi-utils for
 updating our bibliography.
 
-#+begin_src elisp :tangle yes
-  (leaf ivy-bibtex :ensure t)
-  (leaf helm-bibtex :ensure t)
-  (leaf org-ref :ensure t
-	:after org
-	:init
-	(leaf pdf-tools :ensure t)
-	:config
-	(setq bibtex-completion-bibliography
-	      (list (expand-file-name "~/Nextcloud/Bibliography/references.bib")))
+#+begin_src elisp :tangle no :exports code
+(leaf org-ref :ensure t helm-bibtex
+  :after org
+  :init
+  (leaf pdf-tools :ensure t)
+  :bind
+  (("C-c ]" . org-ref-insert-link))
+  :config
+  (setq org-bib-dir (concat document-dir "/Bibliography"))
+  (setq org-bib-file (concat org-bib-dir "/references.bib"))
+  ;; Where should PDFs be stored
+  (setq bibtex-completion-library-path `(,(concat org-bib-dir "/bibtex-pdfs/"))
+	;; Where is the bibliography expected (org-ref & org-cite)
+	bibtex-completion-bibliography (list org-bib-file)
+	org-cite-global-bibliography org-bib-file
 
-	(setq org-ref-bibliography-notes "~/Nextcloud/Bibliography/notes.org"
-	      org-ref-default-bibliography '("~/Nextcloud/Bibliography/references.bib")
-	      org-ref-pdf-directory "~/Nextcloud/Bibliography/bibtex-pdfs/")
-	(when (eq system-type 'darwin)
-	  (setq bibtex-completion-bibliography
-		(list (expand-file-name "~/Nextcloud/Bibliography/references.bib")))
+	bibtex-completion-notes-path (concat org-bib-dir "/notes")
+	bibtex-completion-notes-template-multiple-files "* ${author-or-editor}, ${title}, ${journal}, (${year}) :${=type=}: \n\nSee [[cite:&${=key=}]]\n"
 
-	  (setq org-ref-bibliography-notes "~/Nextcloud/Bibliography/notes.org"
-		org-ref-default-bibliography '("~/Nextcloud/Bibliography/references.bib")
-		org-ref-pdf-directory "~/Nextcloud/Bibliography/bibtex-pdfs/")
-	  )
-
-
-	(setq org-ref-insert-link-function 'org-ref-insert-link-hydra/body
-	      org-ref-insert-cite-function 'org-ref-cite-insert-helm
-	      org-ref-insert-label-function 'org-ref-insert-label-link
-	      org-ref-insert-ref-function 'org-ref-insert-ref-link
-	      org-ref-cite-onclick-function (lambda (_) (org-ref-citation-hydra/body)))
-
-	:require org-ref org-ref-ivy org-ref-helm doi-utils)
+	bibtex-completion-additional-search-fields '(keywords)
+	bibtex-completion-display-formats
+	'((article       . "${=has-pdf=:1}${=has-note=:1} ${year:4} ${author:36} ${title:*} ${journal:40}")
+	  (inbook        . "${=has-pdf=:1}${=has-note=:1} ${year:4} ${author:36} ${title:*} Chapter ${chapter:32}")
+	  (incollection  . "${=has-pdf=:1}${=has-note=:1} ${year:4} ${author:36} ${title:*} ${booktitle:40}")
+	  (inproceedings . "${=has-pdf=:1}${=has-note=:1} ${year:4} ${author:36} ${title:*} ${booktitle:40}")
+	  (t             . "${=has-pdf=:1}${=has-note=:1} ${year:4} ${author:36} ${title:*}"))
+	bibtex-completion-pdf-open-function
+	(lambda (fpath)
+	  (call-process "open" nil 0 nil fpath)))
+  ;; For bibtex generated keys (in-org citation format)
+  (setq bibtex-autokey-year-length 4
+	bibtex-autokey-name-year-separator "-"
+	bibtex-autokey-year-title-separator "-"
+	bibtex-autokey-titleword-separator "-"
+	bibtex-autokey-titlewords 2
+	bibtex-autokey-titlewords-stretch 1
+	bibtex-autokey-titleword-length 5)
+  :require org-ref org-ref-helm oc-bibtex oc-bibtex oc-csl oc-natbib)
 #+end_src
 
+** Extra Export Options
+
+*** LaTeX (Obviously)
+
+We really do require latex
+
+#+begin_src elisp :tangle no :exports code
+(leaf ox-latex
+  :after org org-ref
+  :config
+  ;; (add-to-list 'org-export-backends 'latex)
+  (add-to-list 'org-latex-packages-alist '("" "minted"))
+  (setq org-latex-listings 'minted) 
+
+  (add-to-list 'org-latex-classes
+	       '("labtemplate" "\\documentclass{labtemplate}"
+		 ("\\section{%s}" . "\\section*{%s}")
+		 ("\\subsection{%s}" . "\\subsection*{%s}")
+		 ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
+		 ("\\paragraph{%s}" . "\\paragraph*{%s}")
+		 ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
+  (add-to-list 'org-latex-classes
+	       '("thesis" "\\documentclass[11pt]{ut-thesis}"
+		 ("\\part{%s}" . "\\part*{%s}")
+		 ("\\chapter{%s}" . "\\chapter*{%s}")
+		 ("\\section{%s}" . "\\section*{%s}")
+		 ("\\subsection{%s}" . "\\subsection*{%s}")
+		 ("\\subsubsection{%s}" . "\\subsubsection*{%s}")))
+
+  (setq org-latex-pdf-process
+	'("%latex -shell-escape -interaction nonstopmode -output-directory %o %f"
+	  "%latex -shell-escape -interaction nonstopmode -output-directory %o %f"
+	  "bibtex %b"
+	  "%latex -shell-escape -interaction nonstopmode -output-directory %o %f"
+	  "%latex -shell-escape -interaction nonstopmode -output-directory %o %f")))
+#+end_src
+
+*** Pandoc the Panacea of Exports
+
 For more export formats we use pandoc:
-#+begin_src elisp :tangle yes
-  (leaf ox-pandoc :ensure t
-	:after org)
+#+begin_src elisp :tangle no :exports code
+(leaf ox-pandoc :ensure t
+  :after org org-ref
+  :config)
+  ;; (add-to-list 'org-export-backends 'pandoc))
 #+end_src
 
+*** Slideshows
+
+**** Web based (reveal)
+
 Writing mockup presentations can be quicker when you focus on the text
 of the presentation first, and prettifying later. Reveal.js is a nice
 in between of these.
 
-TODO: I need to ensure [[https://gitlab.com/oer/emacs-reveal.git][emacs-reveal]] is installed properly via both nix
-& the git clone. Could use a submodule? Maybe. I don't know if that
-will work
-
-#+begin_src elisp :tangle yes
-  (leaf ox-reveal :ensure t
-    :require t
-    :after org
-    :config
-    (setq org-reveal-root "https://cdn.jsdelivr.net/npm/reveal.js"))
+#+begin_src elisp :tangle no :exports code
+(leaf ox-reveal :ensure t
+  :config
+  ;; (add-to-list 'org-export-backends 'reveal)
+  (setq org-reveal-root "https://cdn.jsdelivr.net/npm/reveal.js"))
 #+end_src
 
+** LaTeX: with AuCTeX
+
 Nicer LaTeX editing (AuCTeX):
 
-#+begin_src elisp :tangle yes
-  (leaf auctex :ensure t
-	:after org)
+#+begin_src elisp :tangle yes :exports code
+(leaf auctex :ensure t
+  :after org)
 #+end_src
 
 We also ma(k|d)e use of org-tempo for templating things, which can be
 nice. Should use the export based templating probably. Eventually.
 
-#+begin_src elisp :tangle yes
-  (leaf org-cfg
-	:after org
-	:require org-ref oc-csl org-tempo ox-latex ox-pandoc ox-reveal
-	:init
-	:bind*
-	("C-c ]" . org-ref-insert-link)
-	("s-[" . org-ref-insert-link-hydra/body)
-	:hook
-	(org-mode-hook . auto-fill-mode)
-	:config
-	(set-fill-column 100)
-	(setq org-src-fontify-natively t
-	      org-confirm-babel-evaluate nil
-	      org-src-preserve-indentation t)
-
-	(tempo-define-template "Fig. Caption"
-			       '("" (P "Image: " image t)
-				 (P "Caption: " caption t)
-				 (P "Figure Name: " name t)
-				 "#+CAPTION: " (s caption) > n >
-				 "#+NAME: fig:" (s name) > n >
-				 "#+ATTR_LaTeX: :placement [H]" > n >
-				 "[[" (s image) "]]" > n > p >)
-			       "<fig" "Inserts Figure with Caption")
-	(add-to-list 'org-latex-packages-alist '("" "minted"))
-	(setq org-latex-listings 'minted) 
-
-	(add-to-list 'org-latex-classes
-		     '("labtemplate" "\\documentclass{labtemplate}"
-		       ("\\section{%s}" . "\\section*{%s}")
-		       ("\\subsection{%s}" . "\\subsection*{%s}")
-		       ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
-		       ("\\paragraph{%s}" . "\\paragraph*{%s}")
-		       ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
-		     )
-
-	(setq org-latex-pdf-process
-	      '("%latex -shell-escape -interaction nonstopmode -output-directory %o %f"
-		"%latex -shell-escape -interaction nonstopmode -output-directory %o %f"
-		"bibtex %b"
-		"%latex -shell-escape -interaction nonstopmode -output-directory %o %f"
-		"%latex -shell-escape -interaction nonstopmode -output-directory %o %f")))
-#+end_src
-
 And in case we want to make some (GNU)?plots?
 
-#+begin_src elisp :tangle yes
-  (leaf gnuplot
-	:ensure t)
+#+begin_src elisp :tangle yes :exports code
+(leaf gnuplot
+  :ensure t)
 #+end_src
 
-*** Org Mode Agenda/Calendar Things
+** Org Mode Agenda/Calendar Things
 
-**** Agenda Location
-Make it so that all files in the src_elisp{org-agenda-files} variable
-(e.g. "=~/Documents=") will be included in the tablutation and
-collation of all the dates and todos etc.
+*** Agenda Location
 
-#+begin_src elisp :tangle yes
-  (leaf org-agenda-file
-    :after org
-    :config
-    (setq org-agenda-files '("~/Nextcloud/org")))
-    (when (eq system-type 'darwin)
-      (setq org-agenda-files '("~/Nextcloud/org"))
-      )
+Make it so that all files in the " src_elisp{org-agenda-files} " variable (e.g. "=~/Documents=") will be
+included in the tablutation and collation of all the dates and todos
+etc.
+
+#+begin_src elisp :tangle yes :exports code
+(leaf org-agenda :require t
+  :after org
+  :config
+  (setq org-agenda-files (concat org-directory "/MasterList.org")))
 #+end_src
 
-**** Capture Things
+*** Capture Things
 
 Unless specified otherwise, any captured note, date, meeting, idea,
 should be put into the src_elisp{org-directory}.
@@ -478,46 +541,42 @@ Similarly, we have a default file for notes that we capture, in there
 =note.org=, which is where all captured things go when they aren't
 told to go elsewhere.
 
-#+begin_src elisp :tangle yes
-  (leaf org-capture-cfg
-    :after org
-    :config
-    (setq org-directory "~/Nextcloud/org")
-    (when (eq system-type 'darwin)
-      (setq org-directory '("~/Nextcloud/org"))
-      )
-
-    (setq org-default-notes-file (concat org-directory "/notes.org")))
+#+begin_src elisp :tangle yes :exports code
+(leaf org-capture
+  :after org
+  :config
+  (setq org-default-notes-file (concat org-directory "/notes.org")))
 #+end_src
 
 We also want to configure what type of things we want to capture,
 e.g. meetings, deadlines and whatever else:
 
-#+begin_src elisp :tangle yes
-  (leaf org-capture-what
-    :after org
-    :config
-    (setq org-capture-templates
-	  '(("t" "Todo" entry (file+headline "todo.org" "Tasks")
-	     "* TODO %?\n  %i\n  %a")
-	    ("j" "Journal" entry (file+datetree "journal.org")
-	     "* %?\nEntered on %U\n  %i\n  %a")
-	    ("m" "Meeting" entry (file+headline "dates.org" "Meetings")
-	     "* %^{prompt}\n:PROPERTIES:\n:CATEGORY: Meeting\n:END:\nWhen: %^t\nAdded: %U\nTags: %^g\n%?"))))
+
+#+begin_src elisp :tangle yes :exports code
+(leaf org-capture
+  :after org-capture
+  :config
+  (setq org-capture-templates
+	'(("t" "Todo" entry (file+headline "todo.org" "Tasks")
+	   "* TODO %?\n  %i\n  %a")
+	  ("j" "Journal" entry (file+datetree "journal.org")
+	   "* %?\nEntered on %U\n  %i\n  %a")
+	  ("m" "Meeting" entry (file+headline "dates.org" "Meetings")
+	   "* %^{prompt}\n:PROPERTIES:\n:CATEGORY: Meeting\n:END:\nWhen: %^t\nAdded: %U\nTags: %^g\n%?"))))
 #+end_src
 
-** Flutter
-#+begin_src elisp :tangle yes
-  (leaf dart-mode :ensure t)
-  (leaf lsp-dart :ensure t)
+* Flutter
+
+#+begin_src elisp :tangle yes :exports code
+(leaf dart-mode :ensure t)
+(leaf lsp-dart :ensure t)
 #+end_src
-** BQN
-#+begin_src elisp :tangle yes
-  (leaf bqn-mode
-    :el-get "museoa/bqn-mode"
-    :config
-    (leaf bqn-font
-	  :after bqn-mode
-	  :config
-	  (set-face-attribute 'bqn-default nil :family 'unspecified)))
+
+* BQN
+
+#+begin_src elisp :tangle yes :exports code
+(leaf bqn-mode
+  :el-get "museoa/bqn-mode"
+  :defer-config
+  (set-face-attribute 'bqn-default nil :family 'unspecified))
 #+end_src