Fix Cross References

init.el

@@ -3,6 +3,8 @@
 ;; This file loads Org and then loads the rest of our Emacs initialization from Emacs lisp
 ;; embedded in literate Org files.
 
+(setq straight-check-for-modifications '(check-on-save find-when-checking))
+      
 (defvar bootstrap-version)
 (let ((bootstrap-file
        (expand-file-name
@@ -19,24 +21,13 @@
       (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)
 
-;; Load up Org Mode and (now included) Org Babel for elisp embedded in Org Mode files
-(setq dotfiles-dir (file-name-directory (or (buffer-file-name) load-file-name)))
-
-(let* ((org-dir (expand-file-name
-                 "lisp" (expand-file-name
-                         "org" (expand-file-name
-                                "src" dotfiles-dir))))
-       (org-contrib-dir (expand-file-name
-                         "lisp" (expand-file-name
-                                 "contrib" (expand-file-name
-                                            ".." org-dir))))
-       (load-path (append (list org-dir org-contrib-dir)
-                          (or load-path nil))))
-  ;; load up Org and Org-babel
-  (require 'org)
-  (require 'ob-tangle))
+(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

@@ -12,7 +12,8 @@
 ** 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)
+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)
@@ -448,8 +449,8 @@ conflict with the builtin version of 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))
+  	org-confirm-babel-evaluate nil
+  	org-src-preserve-indentation t))
 ;; (tempo-define-template "Fig. Caption"
 ;; 			   '("" (P "Image: " image t)
 ;; 			     (P "Caption: " caption t)
@@ -504,8 +505,9 @@ updating our bibliography.
 	bibtex-autokey-titlewords 2
 	bibtex-autokey-titlewords-stretch 1
 	bibtex-autokey-titleword-length 5)
-  (add-hook 'org-export-before-parsing-functions 'org-ref-csl-preprocess-buffer)
-  :require org-ref org-ref-helm oc-bibtex oc-bibtex oc-csl oc-natbib)
+  (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
@@ -520,28 +522,21 @@ We really do require latex
   :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}")))
+  	       '("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")))
+  	       '("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
@@ -611,9 +606,9 @@ And in case we want to make some (GNU)?plots?
 
 *** 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.
+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
@@ -648,9 +643,9 @@ e.g. meetings, deadlines and whatever else:
   :config
   (add-hook 'org-capture-mode-hook #'org-id-get-create)
   (setq org-capture-templates
-	'(("t" "Todo" entry (file+headline "todo.org" "Tasks")
+	'(("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 "todo.org" "Habits")
+	  ("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")
@@ -716,7 +711,6 @@ taking package.
   :after org-roam org-ref
   :require t
   :hook (after-init-hook . org-roam-bibtex-mode))
-  
 #+end_src
 
 ** Org Babel