Fix Cross References

Flake lock file updates:

• Updated input 'emacs-overlay':
    'github:nix-community/emacs-overlay/7a4b5bbc06182e2f704630cd77a614ab0d9c2f2e?narHash=sha256-bvj/wfLLFTc8cWAwhN8tgShiy8ekPWt1%2BgWlEH7W4zY%3D' (2023-08-14)
  → 'github:nix-community/emacs-overlay/4ebe4c890e7c8662ae31192359a56b0505cf10ba?narHash=sha256-R1p2ZXOydII%2BMT/SpeOXBjo/dgfD/gIArge2YAgSw38%3D' (2025-01-25)
• Removed input 'emacs-overlay/flake-utils'
• Removed input 'emacs-overlay/flake-utils/systems'
• Updated input 'emacs-overlay/nixpkgs-stable':
    'github:NixOS/nixpkgs/720e61ed8de116eec48d6baea1d54469b536b985?narHash=sha256-iUNEeudc4dGjx%2BHsHccnGiuZUVE/nhjXuQ1DVCsHIUY%3D' (2023-08-13)
  → 'github:NixOS/nixpkgs/035f8c0853c2977b24ffc4d0a42c74f00b182cd8?narHash=sha256-YnHJJ19wqmibLQdUeq9xzE6CjrMA568KN/lFPuSVs4I%3D' (2025-01-23)
• Updated input 'flake-utils':
    'github:numtide/flake-utils/919d646de7be200f3bf08cb76ae1f09402b6f9b4?narHash=sha256-6ixXo3wt24N/melDWjq70UuHQLxGV8jZvooRanIHXw0%3D' (2023-07-11)
  → 'github:numtide/flake-utils/11707dc2f618dd54ca8739b309ec4fc024de578b?narHash=sha256-l0KFg5HjrsfsO/JpG%2Br7fRrqm12kzFHyUHqHCVpMMbI%3D' (2024-11-13)
• Updated input 'nixpkgs':
    'github:NixOS/nixpkgs/6e287913f7b1ef537c97aa301b67c34ea46b640f?narHash=sha256-gMbKOiX1HwClRP9lADaaV/lnZr93NEaOFe4ApDx/zd8%3D' (2023-08-14)
  → 'github:NixOS/nixpkgs/825479c345a7f806485b7f00dbe3abb50641b083?narHash=sha256-nU6AezEX4EuahTO1YopzueAXfjFfmCHylYEFCagduHU%3D' (2025-01-24)

.gitignore

@@ -1,7 +1,8 @@
 /auto-save-list/
 /backups/
 /etc/
-/straight/
+/straight/*
+!/straight/versions
 /tutorial/
 /var/
 tramp
@@ -14,3 +15,8 @@ tramp
 /result
 /transient/
 /BROWSE
+org-roam.db
+bookmarks
+.org-id-locations
+.lsp-session-v1
+.dap-breakpoints

custom.el

@@ -3,169 +3,10 @@
  ;; 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
-   '("~/Documents/research/DBS/TechnicalEvaluation/technicaldraft.org" "/Users/universelaptop/Documents/research/CommitteeMeetings/First/Report/David_Crompton_Masters_Supervisory_Committee_Meeting_Report.org" "/Users/universelaptop/Documents/research/thesis/Ideas/ModelDetails.org" "/Users/universelaptop/Documents/uoft/JPB1071/WrittenAssignment/Crompton_David_1004162434_JPB1071_Written_Assignment.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))
+   '(sage-shell-mode ess lsp-dart dart-mode org-roam-bibtex org-roam-ui org-roam gnuplot auctex ox-reveal ox-pandoc pdf-tools helm-bibtex org-ref org geiser-racket rainbow-delimiters slint-mode rust-mode company-ghci lsp-haskell haskell-mode poetry python-mode yaml-mode d2-mode php-mode web-mode dap-mode flycheck lsp-ui lsp-mode company which-key nix-mode direnv magit exec-path-from-shell esup gcmh transient-dwim leaf-convert leaf-tree blackout hydra el-get leaf-keywords)))
- '(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.

flake.lock

@@ -1,55 +1,15 @@
 {
   "nodes": {
-    "emacs-overlay": {
-      "inputs": {
-        "flake-utils": "flake-utils",
-        "nixpkgs": [
-          "nixpkgs"
-        ],
-        "nixpkgs-stable": "nixpkgs-stable"
-      },
-      "locked": {
-        "lastModified": 1692037570,
-        "narHash": "sha256-bvj/wfLLFTc8cWAwhN8tgShiy8ekPWt1+gWlEH7W4zY=",
-        "owner": "nix-community",
-        "repo": "emacs-overlay",
-        "rev": "7a4b5bbc06182e2f704630cd77a614ab0d9c2f2e",
-        "type": "github"
-      },
-      "original": {
-        "owner": "nix-community",
-        "repo": "emacs-overlay",
-        "type": "github"
-      }
-    },
     "flake-utils": {
       "inputs": {
         "systems": "systems"
       },
       "locked": {
-        "lastModified": 1689068808,
+        "lastModified": 1731533236,
-        "narHash": "sha256-6ixXo3wt24N/melDWjq70UuHQLxGV8jZvooRanIHXw0=",
+        "narHash": "sha256-l0KFg5HjrsfsO/JpG+r7fRrqm12kzFHyUHqHCVpMMbI=",
         "owner": "numtide",
         "repo": "flake-utils",
-        "rev": "919d646de7be200f3bf08cb76ae1f09402b6f9b4",
+        "rev": "11707dc2f618dd54ca8739b309ec4fc024de578b",
-        "type": "github"
-      },
-      "original": {
-        "owner": "numtide",
-        "repo": "flake-utils",
-        "type": "github"
-      }
-    },
-    "flake-utils_2": {
-      "inputs": {
-        "systems": "systems_2"
-      },
-      "locked": {
-        "lastModified": 1689068808,
-        "narHash": "sha256-6ixXo3wt24N/melDWjq70UuHQLxGV8jZvooRanIHXw0=",
-        "owner": "numtide",
-        "repo": "flake-utils",
-        "rev": "919d646de7be200f3bf08cb76ae1f09402b6f9b4",
         "type": "github"
       },
       "original": {
@@ -60,11 +20,11 @@
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1691990649,
+        "lastModified": 1737746512,
-        "narHash": "sha256-gMbKOiX1HwClRP9lADaaV/lnZr93NEaOFe4ApDx/zd8=",
+        "narHash": "sha256-nU6AezEX4EuahTO1YopzueAXfjFfmCHylYEFCagduHU=",
         "owner": "NixOS",
         "repo": "nixpkgs",
-        "rev": "6e287913f7b1ef537c97aa301b67c34ea46b640f",
+        "rev": "825479c345a7f806485b7f00dbe3abb50641b083",
         "type": "github"
       },
       "original": {
@@ -74,26 +34,9 @@
         "type": "github"
       }
     },
-    "nixpkgs-stable": {
-      "locked": {
-        "lastModified": 1691950488,
-        "narHash": "sha256-iUNEeudc4dGjx+HsHccnGiuZUVE/nhjXuQ1DVCsHIUY=",
-        "owner": "NixOS",
-        "repo": "nixpkgs",
-        "rev": "720e61ed8de116eec48d6baea1d54469b536b985",
-        "type": "github"
-      },
-      "original": {
-        "owner": "NixOS",
-        "ref": "nixos-23.05",
-        "repo": "nixpkgs",
-        "type": "github"
-      }
-    },
     "root": {
       "inputs": {
-        "emacs-overlay": "emacs-overlay",
+        "flake-utils": "flake-utils",
-        "flake-utils": "flake-utils_2",
         "nixpkgs": "nixpkgs"
       }
     },
@@ -111,21 +54,6 @@
         "repo": "default",
         "type": "github"
       }
-    },
-    "systems_2": {
-      "locked": {
-        "lastModified": 1681028828,
-        "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=",
-        "owner": "nix-systems",
-        "repo": "default",
-        "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
-        "type": "github"
-      },
-      "original": {
-        "owner": "nix-systems",
-        "repo": "default",
-        "type": "github"
-      }
     }
   },
   "root": "root",

flake.nix

@@ -1,23 +1,21 @@
 {
   inputs.nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";
-  inputs.emacs-overlay.url = "github:nix-community/emacs-overlay";
-  inputs.emacs-overlay.inputs.nixpkgs.follows = "nixpkgs";
   inputs.flake-utils.url = "github:numtide/flake-utils";
 
-  outputs = { self, nixpkgs, flake-utils, emacs-overlay }:
+  outputs = { self, nixpkgs, flake-utils }: let
-    flake-utils.lib.eachDefaultSystem (system: let
+  in (flake-utils.lib.eachDefaultSystem (system: let
       pkgs = import nixpkgs {
         inherit system;
-        overlays = [
-          emacs-overlay.overlays.default
-        ];
       };
     in {
       packages = {
-        emacs = pkgs.emacsWithPackagesFromUsePackage {
+        me-emacs = pkgs.emacs;
-          config = ./main.org;
+        me-emacs-wayland = pkgs.emacs-pgtk;
-          package = pkgs.emacs29;
-        };
       };
+    })) // {
+      overlays.default = final: prev: ({
+        me-emacs = final.emacs;
+        me-emacs-wayland = final.emacs-pgtk;
       });
+    };
 }

init.el

@@ -3,22 +3,31 @@
 ;; This file loads Org and then loads the rest of our Emacs initialization from Emacs lisp
 ;; embedded in literate Org files.
 
-;; Load up Org Mode and (now included) Org Babel for elisp embedded in Org Mode files
+(setq straight-check-for-modifications '(check-on-save find-when-checking))
-(setq dotfiles-dir (file-name-directory (or (buffer-file-name) load-file-name)))
       
-(let* ((org-dir (expand-file-name
+(defvar bootstrap-version)
-                 "lisp" (expand-file-name
+(let ((bootstrap-file
-                         "org" (expand-file-name
+       (expand-file-name
-                                "src" dotfiles-dir))))
+        "straight/repos/straight.el/bootstrap.el"
-       (org-contrib-dir (expand-file-name
+        (or (bound-and-true-p straight-base-dir)
-                         "lisp" (expand-file-name
+            user-emacs-directory)))
-                                 "contrib" (expand-file-name
+      (bootstrap-version 7))
-                                            ".." org-dir))))
+  (unless (file-exists-p bootstrap-file)
-       (load-path (append (list org-dir org-contrib-dir)
+    (with-current-buffer
-                          (or load-path nil))))
+        (url-retrieve-synchronously
-  ;; load up Org and Org-babel
+         "https://raw.githubusercontent.com/radian-software/straight.el/develop/install.el"
-  (require 'org)
+         'silent 'inhibit-cookies)
-  (require 'ob-tangle))
+      (goto-char (point-max))
+      (eval-print-last-sexp)))
+  (load bootstrap-file nil 'nomessage))
+
+(setq straight-vc-git-default-clone-depth '(1 single-branch))  ;; instead of the default 'full
+
+;; prebuild is broken in org-mode (TODO: FIX)
+;; (straight-override-recipe '(org :local-repo "/Users/universelaptop/tmp/org"))
+(straight-use-package 'org)
+
+(setq dotfiles-dir (file-name-directory (or (buffer-file-name) load-file-name)))  
 
 ;; load up all literate org-mode files in this directory
 (mapc #'org-babel-load-file (directory-files dotfiles-dir t "\\.org$"))

main.org

@@ -7,62 +7,137 @@
 #+author:
 #+language: en
 
-* Intialization
+* Initialization
+
+** Straight.el
+
+Package management to be a little more fien/precise and work outside
+of Nix (as much as it would be nice to work inside of Nix too). This
+is actually contained within =init.el=
+
+#+begin_src elisp :tangle no :exports code
+(defvar bootstrap-version)
+(let ((bootstrap-file
+       (expand-file-name
+        "straight/repos/straight.el/bootstrap.el"
+        (or (bound-and-true-p straight-base-dir)
+            user-emacs-directory)))
+      (bootstrap-version 7))
+  (unless (file-exists-p bootstrap-file)
+    (with-current-buffer
+        (url-retrieve-synchronously
+         "https://raw.githubusercontent.com/radian-software/straight.el/develop/install.el"
+         'silent 'inhibit-cookies)
+      (goto-char (point-max))
+      (eval-print-last-sexp)))
+  (load bootstrap-file nil 'nomessage))
+#+end_src
+
+This code block actually resides in init.el (so that we can perform
+some necessary pre-configuration)
+
+** Leaf.el
 
 We must initialize =leaf.el=, which we use as a use-package
-replacement for defining configs for different things.
+replacement for defining configs and relations between packages etc.
 
-#+begin_src elisp :tangle yes
+#+begin_src elisp :tangle yes :exports code
-  ;; <leaf-install-code>
   (eval-and-compile
-    (customize-set-variable
+    (straight-use-package 'leaf)
-     '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)
+      (straight-use-package 'leaf-keywords)
-      (leaf hydra :ensure t)
+      :custom
-      (leaf blackout :ensure t)
+      (leaf-alias-keyword-alist .'((:ensure . :straight)))
-
       :config
       ;; initialize leaf-keywords.el
       (leaf-keywords-init)))
-  ;; </leaf-install-code>
 
   (leaf leaf-tree :ensure t)
   (leaf leaf-convert :ensure t)
-  (leaf transient-dwim
+  (leaf transient-dwim :ensure t
-    :ensure t
+    :require t ;; Needed so that org-roam may unobstructively depend on this
     :bind (("M-=" . transient-dwim-dispatch)))
 #+end_src
 
-#+begin_src elisp :tangle yes
+** 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
+
+This makes the garbage collection thresholds variable based on emacs
+usage. I don't know how well this plays with LSPs or similarly RAM hungry
+features. This was useful when I used a very restricted netbook w/ ~2GiB of
+RAM.
+
+Disabled for now. (May add flags to enable on specific systems)
+
+#+begin_src elisp :tangle yes :exports code
+; (leaf gcmh :ensure t
+;  :hook (after-init-hook))
+#+end_src
+
+*** Profiling
+#+begin_src elisp :tangle yes :exports code
+(leaf esup :disabled nil :ensure t)
+#+end_src
+
+** Emacs Paths
+
+*** Custom.el
+
+Ensure that the =custom.el= resides in the users' emacs directory.
+
+#+begin_src elisp :tangle yes :exports code
 (leaf custom-el
+  :leaf-defer nil
   :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
 
-#+begin_src elisp :tangle yes
+*** Backups
+
+Set the backups directory to reside in the users' emacs directory.
+
+#+begin_src elisp :tangle yes :exports code
 (leaf backup
+  :leaf-defer nil
   :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
+
+Exec-path-from-shell ensures that path variable is preserved from
+shell.
+
+#+begin_src elisp :tangle yes :exports code
+(leaf exec-path-from-shell :ensure t
+  :config
+  (exec-path-from-shell-initialize))
+#+end_src
+
 * Visual Customization
 
-#+begin_src elisp :tangle yes
+Visual Theme of Emacs config: defined in the =themes= directory.
+
+#+begin_src elisp :tangle yes :exports code
 (leaf visual
+  :leaf-defer nil
   :doc "Visual Changes to Emacs"
   :tag "builtin" "internal"
   :custom ((menu-bar-mode . nil)
@@ -71,93 +146,161 @@ replacement for defining configs for different things.
   :custom-face ((default . '((t (:family "JuliaMono"
 					 :height 150
 					 :weight normal)))))
-  :config (prog1 'visual
+  :config
   ;; Set location of custom theme dir
   (setq custom-theme-directory (concat user-emacs-directory "themes"))
-	   (load-theme 'UniverseHighContrast)))
+  (load-theme 'UniverseHighContrast))
 #+end_src
 
-* Package Configuration
+* Version Control
-
+#+begin_src elisp :tangle yes :exports code
-** Path Preservation
+(leaf magit
-
+  :leaf-defer nil
-Exec-path-from-shell ensures that path variable is preserved from
+  :ensure t :require t)
-shell.
-
-#+begin_src elisp :tangle yes
-  (leaf exec-path-from-shell :ensure t
-    :config
-    (exec-path-from-shell-initialize))
 #+end_src
 
-** Font Related
+* Nix Related
 
-*** Ligature
+** Direnv
-
-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
-
-** Profiling
-#+begin_src elisp :tangle yes
-  (leaf esup :disabled nil :ensure t)
-#+end_src
-
-** Version Control
-#+begin_src elisp :tangle yes
-  (leaf magit :ensure t :require t)
-#+end_src
-
-** Nix Related
-
-*** 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
-	:hook
+  :global-minor-mode direnv-mode)
-	(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)
+(leaf nix-mode
+  :ensure t
+  :mode "\\.nix\\'")
 #+end_src
 
-** WEB
+* IDE Like Things
+
+** Which Key Again?
+
+#+begin_src elisp :tangle yes :exports code
+(leaf which-key
+  :ensure t
+  :global-minor-mode 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
+  :global-minor-mode 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
+
+#+begin_src elisp :tangle yes :exports code
+:init
+#+end_src
+
+- 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
+
+END LSP CONFIG
+
+#+begin_src elisp :tangle yes :exports code
+)
+#+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
@@ -166,128 +309,104 @@ We all know the web is the future, obviously, of course.
   "\\.jsx?\\'"
   "\\.tsx?\\'")
 (leaf php-mode
+  :mode "\\.php\\'"
+  :ensure t)
+(leaf rainbow-mode
+  :leaf-defer nil
   :ensure t)
 #+end_src
 
-** D2
+* D2
 
-#+begin_src elisp :tangle yes
+#+begin_src elisp :tangle yes :exports code
-  (leaf d2-mode :ensure t)
+(leaf d2-mode
-#+end_src
-
-** YAML
-
-#+begin_src elisp :tangle yes
-  (leaf yaml-mode :ensure t)
-#+end_src
-
-** IDE Like Things
-*** 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))
-#+end_src
-*** Language Server Protocol
-
-We love language features that make languages nice
-
-#+begin_src elisp :tangle yes
-  (leaf lsp-mode
   :ensure t
-    :init
+  :mode "\\.d2\\'"
-    (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
+* YAML
-  (leaf projectile
+
-    :commands projectile-mode
+#+begin_src elisp :tangle yes :exports code
-    :config
+(leaf yaml-mode
-    (projectile-mode +1))
+  :ensure t
+  :mode "\\.yaml\\'"
+  )
 #+end_src
-** Python Things
+
-*** Python-mode
+* 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
+(leaf python-mode
+  :ensure t
+  :mode "\\.py\\'"
   :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
+
-  (leaf company-ctags :ensure t)
+#+begin_src elisp :tangle no :exports code
-  (leaf company-c-headers :ensure t)
+(leaf c-config
-  (leaf meson-mode :ensure t)
-#+end_src
-** Haskell
-#+begin_src elisp :tangle yes
-  (leaf haskell-mode :ensure t
   :config
+;  (leaf company-ctags :ensure t
+;      :hook c-mode-hook c++-mode-hook)
+;  (leaf company-c-headers :ensure t
+;      :hook c-mode-hook c++-mode-hook)
+;  (leaf meson-mode :ensure t
+;      :hook c-mode-hook c++-mode-hook)
+  )
+#+end_src
+
+* Haskell
+
+#+begin_src elisp :tangle yes :exports code
+(leaf haskell-mode
+  :ensure t
+  :mode "\\.hs\\'"
+  :init
   (leaf lsp-haskell :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
+  :mode "\\.rs\\'"
+  :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)
+  :straight (mcf-mode :type git :host github :repo "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
@@ -296,37 +415,179 @@ 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
+
+** Clojure
+
+For using clojure, we use both [[https://github.com/clojure-emacs/clojure-mode][clojure-mode]] and for REPL we use [[https://github.com/clojure-emacs/cider][CIDER]].
+
+#+begin_src elisp :tangle yes :exports code
+(leaf clojure-mode :ensure t cider)
+#+end_src
+
+* Org
+
+We ensure that org is available (though it is builtin)
+
+For Version compatibility we actually install org in init.el (to not
+conflict with the builtin version of Org)
+
+#+begin_src elisp :tangle yes :exports code
+(leaf org
+  :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"))
+  (when (not (file-exists-p org-directory)) (mkdir org-directory))
+  (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
+  :bind*
-	(leaf pdf-tools :ensure t)
+  ("C-c ]" . org-ref-insert-link)
   :config
-	:require org-ref org-ref-ivy org-ref-helm doi-utils)
+  (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 (list org-bib-file)
+
+	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"
+
+	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)
+  (add-to-list 'org-export-before-parsing-functions 'org-ref-csl-preprocess-buffer)
+  (add-to-list 'org-export-before-parsing-functions 'org-ref-refproc)
+  :require org-ref org-ref-helm oc-bibtex oc-bibtex oc-csl oc-natbib org-ref-refproc)
 #+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) 
+  (setq org-latex-prefer-user-labels t)
+  (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}"))))
+#+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
+#+begin_src elisp :tangle yes :exports code
-  (leaf ox-pandoc :ensure t
+(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
+#+begin_src elisp :tangle yes :exports code
 (leaf auctex :ensure t
   :after org)
 #+end_src
@@ -334,81 +595,149 @@ Nicer LaTeX editing (AuCTeX):
 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
-	: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)
-
-	(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)))
-	(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
+#+begin_src elisp :tangle yes :exports code
 (leaf gnuplot
   :ensure t)
 #+end_src
-** Flutter
+
-#+begin_src elisp :tangle yes
+** 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.
+
+#+begin_src elisp :tangle yes :exports code
+(leaf org-agenda
+  :after org
+  :config
+  (setq org-agenda-files `(,(concat org-directory))))
+#+end_src
+
+*** Capture Things
+
+Unless specified otherwise, any captured note, date, meeting, idea,
+should be put into the src_elisp{org-directory}.
+
+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 :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 :exports code
+(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 "todos.org" "Tasks")
+	   "* TODO %^{Todo?} %^G\nSCHEDULED: %^t\n:PROPERTIES:\n:ADDED: %U\n:END:\n  %i\n  %a \n%?\n")
+	  ("h" "Habit" entry (file+headline "todos.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")
+	   "* %^{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")
+	   "* %^{Meeting Title:} %^G\nSCHEDULED: %^t\n:PROPERTIES:\n:CATEGORY: Meeting\n:LOCATION: %^{LOCATION}\n:ADDED: %U\n:END:\n%?\n"))))
+#+end_src
+
+*** Habits
+
+#+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 transient-dwim
+  :require t
+  :config
+  (setq org-roam-directory (file-truename org-directory))
+  (org-roam-db-autosync-mode)
+  (transient-define-prefix transient--org-roam ()
+    ["Org Roam"
+     ("M-c" "Capture Note" org-roam-capture)
+     ("M-i" "Insert Note" org-roam-node-insert)
+     ("M-f" "Find Note" org-roam-node-find)])
+  (transient-append-suffix 'transient-dwim-org "M-o" '("M-n" "roam" transient--org-roam))
+  (setq org-roam-capture-templates
+	'(("d" "default" plain "%?"
+	   :target (file+head "notes/%<%Y%m%d%H%M%S>-${slug}.org"
+			      "#+title: ${title}\n")
+	   :unnarrowed t))))
+#+end_src
+
+**** Org Roam UI
+
+#+begin_src elisp :tangle yes :exports code
+(leaf org-roam-ui :ensure t
+  :after org-roam)
+#+end_src
+
+**** Org Roam Bibtex (ORB)
+
+#+begin_src elisp :tangle yes :exports code
+(leaf org-roam-bibtex :ensure t
+  :after org-roam org-ref
+  :require t
+  :hook (after-init-hook . org-roam-bibtex-mode))
+#+end_src
+
+** 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)
+     (shell . 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"
+  :ensure (bqn-mode :type git :host github :repo "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))
+

straight/versions/default.el

@@ -0,0 +1,104 @@
+(("ace-window" . "77115afc1b0b9f633084cf7479c767988106c196")
+ ("auctex" . "a2809e4d7068aaa7fa9cbd51214606393d4ab9eb")
+ ("avy" . "933d1f36cca0f71e4acb5fac707e9ae26c536264")
+ ("biblio.el" . "bb9d6b4b962fb2a4e965d27888268b66d868766b")
+ ("bqn-mode" . "a253194d880e762a2886feac4745ae9cf967567b")
+ ("bui.el" . "f3a137628e112a91910fd33c0cff0948fa58d470")
+ ("cfrs" . "981bddb3fb9fd9c58aed182e352975bd10ad74c8")
+ ("cider" . "8a4405ca0d8dd02d1f35e287131838feec2a81c6")
+ ("citeproc-el" . "f5217b9fdbcb41a0381ecf92108390fc843090dd")
+ ("clojure-mode" . "28dc02114ae70db6bb68d537ea77985f272120bc")
+ ("company-ghci" . "a1d25652583ab4666c5a78cac18cd8039776b50d")
+ ("company-mode" . "ca045bc54411f274779057d94a1807efe7f8d2a6")
+ ("compat" . "97f24af413a38a7f1aaedb29f5aaaa333796a5b4")
+ ("d2-mode" . "e1fc7d6c1915acaf476060c0f79b8bdef6bd1952")
+ ("dap-mode" . "c81014ccc390e8994b061bd2d9f8b5dd84498a3d")
+ ("dart-mode" . "edb45cb7095b1e4f62eaae33e56fe9af5b010213")
+ ("dash.el" . "af5ea5d8a13735fa27d2c3e6f756d065639a7b45")
+ ("el-get" . "8d3edab760ff84baf4ce36c0b33bfb8668c6d212")
+ ("eldoc" . "5cba6bcbd3b3d3f1ae9668cf6a1f9e2d3ebb10df")
+ ("emacs-async" . "59f6ee68eb9bed8de12d71ca78a11dd8effbc2aa")
+ ("emacs-direnv" . "c0bf3b81c7a97e2a0d06d05495e86848254fcc1f")
+ ("emacs-htmlize" . "c9a8196a59973fabb3763b28069af9a4822a5260")
+ ("emacs-request" . "c22e3c23a6dd90f64be536e176ea0ed6113a5ba6")
+ ("emacs-web-server" . "3982c55e9061475038a3ccd61aecb2de3d407cec")
+ ("emacs-websocket" . "40c208eaab99999d7c1e4bea883648da24c03be3")
+ ("emacs-which-key" . "38d4308d1143b61e4004b6e7a940686784e51500")
+ ("emacsmirror-mirror" . "dc1c32049771890965c0d498be5cced13a65296a")
+ ("emacsql" . "bc6713fb763388f43111ba1488df9263d5dc505b")
+ ("eros" . "a9a92bdc6be0521a6a06eb464be55ed61946639c")
+ ("esup" . "4b49c8d599d4cc0fbf994e9e54a9c78e5ab62a5f")
+ ("exec-path-from-shell" . "4896a797252fbfdac32fb77508500ac7d220f717")
+ ("f.el" . "931b6d0667fe03e7bf1c6c282d6d8d7006143c52")
+ ("flycheck" . "8c0dbfaa463e69efb41ef2cda9c4e89b99e266a0")
+ ("geiser" . "c8b862f00e208f2c09bf2a2b2436af0a466a2531")
+ ("gnu-elpa-mirror" . "4809077cd69544e81d946c7bb64c3d7e33e24ff1")
+ ("gnuplot" . "43e9674b869475b1c2a32f045c167673eb2faae0")
+ ("haskell-mode" . "e5d32021ea30438fb957976760b94af66a55b53b")
+ ("helm" . "c8d147be4d89cb3355b89a645ba3703a46bad15d")
+ ("helm-bibtex" . "6064e8625b2958f34d6d40312903a85c173b5261")
+ ("ht.el" . "1c49aad1c820c86f7ee35bf9fff8429502f60fef")
+ ("hydra" . "59a2a45a35027948476d1d7751b0f0215b1e61aa")
+ ("imenu-list" . "76f2335ee6f2f066d87fe4e4729219d70c9bc70d")
+ ("jsonrpc" . "444cafedd091815e674b6c93458ba97a55a76928")
+ ("leaf-convert.el" . "da86654f1021445cc42c1a5a9195f15097352209")
+ ("leaf-keywords.el" . "82ec27e3441900daedeaaebca509181f964da81f")
+ ("leaf-tree.el" . "89c3b8842df067bba67663d309f43aa311acdccd")
+ ("leaf.el" . "69c9b057cdeee560450c1d04a9a058235ecff0f7")
+ ("let-alist" . "35a1dae3c540705433a510c13c8af80206b29b5f")
+ ("llama" . "5990ae7b5cba3425252f64b9377352c9a01690d5")
+ ("lsp-dart" . "34e2a1191f723792d5f366b314cd6b07de4f1566")
+ ("lsp-docker" . "ff41f4a76b640d39dc238bacba7f654c297827fa")
+ ("lsp-haskell" . "aa9b5bce355790de1fbdbe239650d704f46a19a0")
+ ("lsp-mode" . "c0cafd07ea7e0a2d82fcd0680eb36da10356d700")
+ ("lsp-treemacs" . "3e5550f278db74f15ebe34add0138b138207ec08")
+ ("lsp-ui" . "030d36960338fd633a98b332bc3734c412c25ca6")
+ ("magit" . "7de46ddeb30e095645d93d73bbbc5fe3e8565ac5")
+ ("map" . "6ac89e5dd1084afdc1d8fdd717de11c572212428")
+ ("markdown-mode" . "d51c469133d220823cc6ab50ff8e8743ed6e42fb")
+ ("mcf" . "4e44b6e24d9fe7a4ce7249df79f4473c0b473232")
+ ("melpa" . "06f8868ff6e2966b8482cd100271e1d1afc2ce79")
+ ("nix-mode" . "719feb7868fb567ecfe5578f6119892c771ac5e5")
+ ("nongnu-elpa" . "cdbf329f7dae98bbd39a3bf090bd01793f6d5947")
+ ("org" . "526a7d1cc65409d5546b009f54fed28726a9457d")
+ ("org-ref" . "6a22c20f863b997497b618507adbcc8cb10a9f86")
+ ("org-reveal" . "f55c851bf6aeb1bb2a7f6cf0f2b7bd0e79c4a5a0")
+ ("org-roam" . "89dfaef38b6caa3027f20f96a551dc8f194ac533")
+ ("org-roam-bibtex" . "b065198f2c3bc2a47ae520acd2b1e00e7b0171e6")
+ ("org-roam-ui" . "5ac74960231db0bf7783c2ba7a19a60f582e91ab")
+ ("ox-pandoc" . "5766c70b6db5a553829ccdcf52fcf3c6244e443d")
+ ("parsebib" . "7bfde4e4679413424a9a9af099203d5c23e32cd2")
+ ("parseclj" . "6af22372e0fe14df882dd300b22b12ba2d7e00b0")
+ ("parseedn" . "3407e4530a367b6c2b857dae261cdbb67a440aaa")
+ ("pdf-tools" . "30b50544e55b8dbf683c2d932d5c33ac73323a16")
+ ("pfuture" . "19b53aebbc0f2da31de6326c495038901bffb73c")
+ ("php-mode" . "40b8abed3079771e060dd99a56703520dabf5be4")
+ ("poetry.el" . "1dff0d4a51ea8aff5f6ce97b154ea799902639ad")
+ ("posframe" . "12f540c9ad5da09673b2bca1132b41f94c134e82")
+ ("ppp.el" . "d5d854c3006dfd268e62c7f91c2aad6f86a505b5")
+ ("project" . "a0ebb2e9cfda339d8ebda77447c9d822fe313c2d")
+ ("python-mode" . "fcff76c308b4409007c61492e4936e7c0b7d5aee")
+ ("pyvenv" . "31ea715f2164dd611e7fc77b26390ef3ca93509b")
+ ("queue" . "8df1334d54d4735d2f821790422a850dfaaa08ef")
+ ("racket" . "22e56ce80389544d3872cf4beb4008fb514b2218")
+ ("rainbow-delimiters" . "f40ece58df8b2f0fb6c8576b527755a552a5e763")
+ ("rainbow-mode" . "2e6b18609c2fdd1a2dc513937a64d276fd6cf24c")
+ ("rust-mode" . "9915b3a585a7a75e9126df9e0e9d1df8057ae3cf")
+ ("s.el" . "dda84d38fffdaf0c9b12837b504b402af910d01d")
+ ("seq" . "da86da9bf111f68fb81efd466d76d53af5aebc00")
+ ("sesman" . "7bca68dbbab0af26a6a23be1ff5fa97f9a18e022")
+ ("slint-mode" . "168a6cfb90b5e36360074c83f80d5bbac2f0287e")
+ ("spinner" . "fa117f0893788f3fe24673715a6b83bb34d238dd")
+ ("straight.el" . "b7da472452615dc44b4ce76c64a059d6db3b7017")
+ ("string-inflection" . "617df25e91351feffe6aff4d9e4724733449d608")
+ ("tablist" . "fcd37147121fabdf003a70279cf86fbe08cfac6f")
+ ("transient" . "07a104aa73b5d5e3168ba6e202ebfb60188af6ed")
+ ("transient-dwim.el" . "cb5e0d35729fc6448553b7a17fc5c843f00e8c1d")
+ ("treemacs" . "5fa84199501fd43e5573b1277a2b1699c7473cc1")
+ ("web-mode" . "1eb0abb1a9bffbb33db7bbfc6efe5b48bf416d57")
+ ("wfnames" . "164e4efa2a96bed201a0a5402e137ebeef15bcc6")
+ ("with-editor" . "7787e19764c1089390584ac17a80129ef9afaa14")
+ ("xref" . "63b5875528e9c8dba3abbc76dae1b49351273c1c")
+ ("yaml-mode" . "d91f878729312a6beed77e6637c60497c5786efa")
+ ("yaml.el" . "f99ef76c80e6fc3fcf650c4fe34e10726594a4c4"))
+:gamma