Ignore Cleanup & More ORG

.gitignore

@@ -14,3 +14,8 @@ tramp
 /result
 /transient/
 /BROWSE
+org-roam.db
+bookmarks
+.org-id-locations
+.lsp-session-v1
+.dap-breakpoints

custom.el

@@ -3,169 +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))
+   '("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
-   '(("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}"))
-     ("book" "\\documentclass[11pt]{book}"
-      ("\\part{%s}" . "\\part*{%s}")
-      ("\\chapter{%s}" . "\\chapter*{%s}")
-      ("\\section{%s}" . "\\section*{%s}")
-      ("\\subsection{%s}" . "\\subsection*{%s}")
-      ("\\subsubsection{%s}" . "\\subsubsection*{%s}"))
-     ("letter" "\\documentclass{letter}"
-      ("" . ""))))
- '(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
-   '(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)))
-
 (custom-set-faces
  ;; custom-set-faces was added by Custom.
  ;; If you edit it by hand, you could mess it up, so be careful.

main.org

@@ -14,7 +14,7 @@
 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
+#+begin_src elisp :tangle yes :exports code
 (eval-and-compile
   (customize-set-variable
    'package-archives '(("org" . "https://orgmode.org/elpa/")
@@ -38,22 +38,34 @@ replacement for defining configs and relations between packages etc.
 
 (leaf leaf-tree :ensure t)
 (leaf leaf-convert :ensure t)
-  (leaf transient-dwim
+(leaf transient-dwim :ensure t
-    :ensure t
   :bind (("M-=" . transient-dwim-dispatch)))
 #+end_src
 
+#+RESULTS:
+: transient-dwim
+
+** MacOS Specific
+
+#+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
+#+begin_src elisp :tangle yes :exports code
 (leaf gcmh :ensure t
   :hook (after-init-hook))
 #+end_src
 
 *** Profiling
-#+begin_src elisp :tangle yes
+#+begin_src elisp :tangle yes :exports code
 (leaf esup :disabled nil :ensure t)
 #+end_src
 
@@ -63,7 +75,7 @@ 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
+#+begin_src elisp :tangle yes :exports code
 (leaf custom-el
   :config
   ;; Ensure custom writes to specific file
@@ -75,7 +87,7 @@ Ensure that the =custom.el= resides in the users' emacs directory.
 
 Set the backups directory to reside in the users' emacs directory.
 
-#+begin_src elisp :tangle yes
+#+begin_src elisp :tangle yes :exports code
 (leaf backup
   :config
   ;; Change the location of file backups/locks into the emacs.d/backups/
@@ -83,12 +95,12 @@ Set the backups directory to reside in the users' emacs directory.
 	`(("." . ,(concat user-emacs-directory "backups")))))
 #+end_src
 
-** Path Preservation
+** Shell Path Preservation
 
 Exec-path-from-shell ensures that path variable is preserved from
 shell.
 
-#+begin_src elisp :tangle yes
+#+begin_src elisp :tangle yes :exports code
 (leaf exec-path-from-shell :ensure t
   :config
   (exec-path-from-shell-initialize))
@@ -98,7 +110,7 @@ shell.
 
 Visual Theme of Emacs config: defined in the =themes= directory.
 
-#+begin_src elisp :tangle yes
+#+begin_src elisp :tangle yes :exports code
 (leaf visual
   :doc "Visual Changes to Emacs"
   :tag "builtin" "internal"
@@ -114,71 +126,141 @@ Visual Theme of Emacs config: defined in the =themes= directory.
   (load-theme 'UniverseHighContrast))
 #+end_src
 
-** Font Related
+* Version Control
-
+#+begin_src elisp :tangle yes :exports code
-*** 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))
-#+end_src
-
-* Package Configuration
-
-** Version Control
-#+begin_src elisp :tangle yes
 (leaf magit :ensure t :require t)
 #+end_src
 
-** Nix Related
+* Nix Related
 
-*** Direnv
+** Direnv
 
 In order to support direnv (loading =nix-shell= / =nix develop=)
-#+begin_src elisp :tangle yes
+#+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
+#+begin_src elisp :tangle yes :exports code
 (leaf nix-mode :ensure t)
 #+end_src
 
-** WEB
+* IDE Like Things
+
+** Which Key Again?
+
+#+begin_src elisp :tangle yes :exports code
+(leaf which-key :ensure t
+  :config (which-key-mode))
+#+end_src
+
+** Company Completion!
+
+We like autocomplete, it... is nice, okay?
+
+#+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
+
+We love language features that make languages nice
+
+#+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
+
+*** IDE Languages
+
+**** Dart/Flutter
+
+#+begin_src elisp :tangle yes :exports code
+(dart-mode . lsp-deferred)
+#+end_src
+
+**** 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
+#+begin_src elisp :tangle yes :exports code
 (leaf web-mode
   :ensure t
   :mode
@@ -190,125 +272,82 @@ We all know the web is the future, obviously, of course.
   :ensure t)
 #+end_src
 
-** D2
+* D2
 
-#+begin_src elisp :tangle yes
+#+begin_src elisp :tangle yes :exports code
 (leaf d2-mode :ensure t)
 #+end_src
 
-** YAML
+* YAML
 
-#+begin_src elisp :tangle yes
+#+begin_src elisp :tangle yes :exports code
 (leaf yaml-mode :ensure t)
 #+end_src
 
-** IDE Like Things
+* Python Things
-*** Company Completion!
 
-We like autocomplete, it... is nice, okay?
+** Python-mode
-
-#+begin_src elisp :tangle yes
-  (leaf company :ensure t
-    :bind
-    (("C-<tab>" . company-complete))
-    :hook after-init-hook
-    :config (global-company-mode))
-#+end_src
-*** 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)))
-#+end_src
-**** Projectile (Projects)
-#+begin_src elisp :tangle yes
-  (leaf projectile
-    :commands projectile-mode
-    :config
-    (projectile-mode +1))
-#+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
+#+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
+#+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
+* Haskell
-  (leaf haskell-mode :ensure t
+
-	:config
+#+begin_src elisp :tangle yes :exports code
+(leaf haskell-mode :ensure t)
 (leaf lsp-haskell :ensure t)
-	(leaf company-ghci :ensure t))
+(leaf company-ghci :ensure t)
 #+end_src
-** Rust
+
-#+begin_src elisp :tangle yes
+* Rust
-  (leaf rust-mode :ensure t)
+
+#+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
+#+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
+#+begin_src elisp :tangle yes :exports code
 (leaf rainbow-delimiters
   :ensure t
   :commands rainbow-delimiters-mode
@@ -317,94 +356,97 @@ Gonna need to have pretty brackets
     :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
+#+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
+#+begin_src elisp :tangle yes :exports code
-  (leaf ivy-bibtex :ensure t)
+(leaf org-ref :ensure t helm-bibtex pdf-tools
-  (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 "~/Documents/Bibliography/references.bib")))
-
-	(setq org-ref-bibliography-notes "~/Documents/Bibliography/notes.org"
-	      org-ref-default-bibliography '("~/Documents/Bibliography/references.bib")
-	      org-ref-pdf-directory "~/Documents/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)
-#+end_src
-
-For more export formats we use pandoc:
-#+begin_src elisp :tangle yes
-  (leaf ox-pandoc :ensure t
-	:after org)
-#+end_src
-
-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.
-
-#+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"))
-#+end_src
-
-Nicer LaTeX editing (AuCTeX):
-
-#+begin_src elisp :tangle yes
-  (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-bib-dir (concat document-dir "/Bibliography"))
-	(setq org-src-fontify-natively t
+  (setq org-bib-file (concat org-bib-dir "/references.bib"))
-	      org-confirm-babel-evaluate nil
+  ;; Where should PDFs be stored
-	      org-src-preserve-indentation t)
+  (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 (list org-bib-file)
 
-	(tempo-define-template "Fig. Caption"
+	bibtex-completion-notes-path (concat org-bib-dir "/notes")
-			       '("" (P "Image: " image t)
+	bibtex-completion-notes-template-multiple-files "* ${author-or-editor}, ${title}, ${journal}, (${year}) :${=type=}: \n\nSee [[cite:&${=key=}]]\n"
-				 (P "Caption: " caption t)
+
-				 (P "Figure Name: " name t)
+	bibtex-completion-additional-search-fields '(keywords)
-				 "#+CAPTION: " (s caption) > n >
+	bibtex-completion-display-formats
-				 "#+NAME: fig:" (s name) > n >
+	'((article       . "${=has-pdf=:1}${=has-note=:1} ${year:4} ${author:36} ${title:*} ${journal:40}")
-				 "#+ATTR_LaTeX: :placement [H]" > n >
+	  (inbook        . "${=has-pdf=:1}${=has-note=:1} ${year:4} ${author:36} ${title:*} Chapter ${chapter:32}")
-				 "[[" (s image) "]]" > n > p >)
+	  (incollection  . "${=has-pdf=:1}${=has-note=:1} ${year:4} ${author:36} ${title:*} ${booktitle:40}")
-			       "<fig" "Inserts Figure with Caption")
+	  (inproceedings . "${=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 yes :exports code
+(leaf ox-latex :require t
+  :after org
+  :config
   (add-to-list 'org-latex-packages-alist '("" "minted"))
   (setq org-latex-listings 'minted) 
 
@@ -414,8 +456,14 @@ nice. Should use the export based templating probably. Eventually.
 		 ("\\subsection{%s}" . "\\subsection*{%s}")
 		 ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
 		 ("\\paragraph{%s}" . "\\paragraph*{%s}")
-		       ("\\subparagraph{%s}" . "\\subparagraph*{%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"
@@ -425,28 +473,85 @@ nice. Should use the export based templating probably. Eventually.
 	  "%latex -shell-escape -interaction nonstopmode -output-directory %o %f")))
 #+end_src
 
+*** HTML Export
+
+#+begin_src elisp :tangle yes :exports code
+(leaf ox-html
+  :after org
+  :config
+  (setq org-html-head "
+<style type=\"text/css\">
+  pre.src {
+      background-color: #000;
+      color: #ccc;
+      border-radius: 2ch;
+  }
+  pre.src:before {
+      background-color: #ccc;
+      color: #000;
+      border-radius: 0.5ch;
+  }
+</style>
+"))
+#+end_src
+
+*** Pandoc the Panacea of Exports
+
+For more export formats we use pandoc:
+#+begin_src elisp :tangle yes :exports code
+(leaf ox-pandoc :ensure t :require t
+  :after org)
+#+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.
+
+#+begin_src elisp :tangle yes :exports code
+(leaf ox-reveal :ensure t :require t
+  :config
+  (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 :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.
+
 And in case we want to make some (GNU)?plots?
 
-#+begin_src elisp :tangle yes
+#+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
+*** 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.
 
-#+begin_src elisp :tangle yes
+# Make it so that all files in the " src_elisp{org-agenda-files} " variable (e.g. "=~/Documents=") will be
-  (leaf org-agenda-file
+# included in the tablutation and collation of all the dates and todos
+# etc.
+
+#+begin_src elisp :tangle yes :exports code
+(leaf org-agenda
   :after org
   :config
-    (setq org-agenda-files '("~/Documents/org")))
+  (setq org-agenda-files `(,(concat org-directory))))
 #+end_src
 
-**** Capture Things
+*** Capture Things
 
 Unless specified otherwise, any captured note, date, meeting, idea,
 should be put into the src_elisp{org-directory}.
@@ -455,42 +560,92 @@ 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
+#+begin_src elisp :tangle yes :exports code
-  (leaf org-capture-cfg
+(leaf org-capture
   :after org
   :config
-    (setq org-directory "~/Documents/org")
   (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
+#+begin_src elisp :tangle yes :exports code
-    :after org
+(leaf org-capture
+  :after org-capture
   :config
+  (add-hook 'org-capture-mode-hook #'org-id-get-create)
   (setq org-capture-templates
 	'(("t" "Todo" entry (file+headline "todo.org" "Tasks")
-	     "* TODO %?\n  %i\n  %a")
+	   "* TODO %^{Todo?} %^G\nSCHEDULED: %^t\n:PROPERTIES:\n:ADDED: %U\n:END:\n  %i\n  %a \n%?\n")
+	  ("h" "Habit" entry (file+headline "todo.org" "Habits")
+	   "* TODO %^{Habit} %^G\nSCHEDULED: %^T\n:PROPERTIES:\n:STYLE: habit\n:ADDED: %U\n:END:\n%?\n")
 	  ("j" "Journal" entry (file+datetree "journal.org")
-	     "* %?\nEntered on %U\n  %i\n  %a")
+	   "* %^{Journal Entry:} %^G\nEntered on %U\n  %i\n:PROPERTIES:\n:ADDED: %U\n:END:\n  %a\n%?\n")
 	  ("m" "Meeting" entry (file+headline "dates.org" "Meetings")
-	     "* %^{prompt}\n:PROPERTIES:\n:CATEGORY: Meeting\n:END:\nWhen: %^t\nAdded: %U\nTags: %^g\n%?"))))
+	   "* %^{Meeting Title:} %^G\nSCHEDULED: %^t\n:PROPERTIES:\n:CATEGORY: Meeting\n:LOCATION: %^{LOCATION}\n:ADDED: %U\n:END:\n%?\n"))))
 #+end_src
 
-** Flutter
+*** Habits
-#+begin_src elisp :tangle yes
+
+#+begin_src elisp :tangle yes :exports code
+(leaf org-habit
+  :after org
+  :require t
+  :config
+  (add-to-list 'org-modules 'org-habit t)
+  (setq org-habit-graph-column 80))
+#+end_src
+
+*** Org Mobile
+
+So that we can edit and view things on the go. We could use the proper =org-mobile= module of org,
+instead we synchronize w/ Nextcloud, as to have it be the format we like when using =Orgzly Revived=
+
+** Org Notes (Roam)
+
+Let alone being able to maintain dates and times and journal entries: having notes for consolidating
+a personal wiki (separately) is also rather useful. For this we use Org-roam, a slip-note style note
+taking package.
+
+*** Org Roam
+
+#+begin_src elisp :tangle yes :exports code
+(leaf org-roam :ensure t
+  :after org
+  :require t
+  :config
+  (setq org-roam-directory (file-truename org-directory))
+  (org-roam-db-autosync-mode))
+#+end_src
+
+**** Org Roam Babel (ORB)
+
+** Org Babel
+
+#+begin_src elisp :tangle yes :exports code
+(leaf org-babel
+  :after org
+  :config
+  (org-babel-do-load-languages
+   'org-babel-load-languages
+   '((emacs-lisp . t)
+     (python . t))))
+#+end_src
+
+* 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
+* BQN
+
+#+begin_src elisp :tangle yes :exports code
 (leaf bqn-mode
   :el-get "museoa/bqn-mode"
-    :config
+  :defer-config
-    (leaf bqn-font
+  (set-face-attribute 'bqn-default nil :family 'unspecified))
-	  :after bqn-mode
-	  :config
-	  (set-face-attribute 'bqn-default nil :family 'unspecified)))
 #+end_src

src/nmodl.el

@@ -0,0 +1,79 @@
+(defvar nmodl-mode-hook nil)
+
+(defvar wpdl-mode-map
+  (let ((map (make-keymap)))
+    ; (define-key map "\C-j" 'newline-and-indent)
+    map)
+  "Keymap for NMODL major mode")
+
+;;;###autoload
+(add-to-list 'auto-mode-alist '("\\.mod\\'" . nmodl-mode))
+
+(setq nmodl-keywords
+      '(
+	"NEURON"
+	"UNITS"
+	"PARAMETER"
+	"ASSIGNED"
+	"STATE"
+	"INITIAL"
+	"BREAKPOINT"
+	"DERIVATIVE"
+	"PROCEDURE"
+	))
+
+(setq nmodl-neuron-keywords
+      '(
+	"TITLE"
+	"SUFFIX"
+	"POINT_PROCESS"
+	"RANGE"
+	"GLOBAL"
+	"POINTER"
+	"BBCOREPOINTER"
+	"USEION"
+	"NONSPECIFIC_CURRENT"
+	"SOLVE"
+	"METHOD"
+	))
+
+(defvar nmodl-font-lock-keywords
+  `(
+    ,(regexp-opt nmodl-keywords t) . 'font-lock-keyword-face
+   )
+  "Minimal highlighting expressions for NMODL mode")
+
+(setq nmodl-font-lock-keywords
+      `(
+	(,(regexp-opt nmodl-keywords t) . 'font-lock-keyword-face)
+	(,(regexp-opt nmodl-neuron-keywords t) . 'font-lock-constant-face)
+	("^[[:space:]]*\\([[:alpha:]][[:alnum:]_]*\\)" . 'font-lock-variable-name-face)
+	))
+
+(setq nmodl-syntax-rules
+      (syntax-propertize-rules
+       ("TITLE\\([^\n]\\)[^\n]*\\(\n\\)" (1 "|") (2 "|"))
+       ("\\<\\(COMMENT\\)\\>" (1 "<"))
+       ("\\<ENDCOMMEN\\(T\\)\\>" (1 ">"))
+       ("^[^:\n]*\\(:\\)[^\n]*\\(\n\\)" (1 "!") (2 "!"))
+       ("\\({\\)" (1 "("))
+       ("\\(}\\)" (1 ")"))
+       ))
+
+(defun nmodl-indent ()
+  (indent-relative-first-indent-point)
+  )
+
+(defun nmodl-mode ()
+  "Major mode for editing Workflow Process Description Language files"
+  (interactive)
+  (kill-all-local-variables)
+  (setq-local font-lock-defaults '(nmodl-font-lock-keywords))
+  (setq-local syntax-propertize-function nmodl-syntax-rules)
+  (setq-local c-syntactic-indentation t)
+  (setq-local indent-line-function 'nmodl-indent)
+  ;; (use-local-map wpdl-mode-map)
+  (setq major-mode 'nmodl-mode)
+  (setq mode-name "NMODL")
+  (run-hooks 'nmodl-mode-hook))
+