Set up org agenda with refile, decrease ltximg size, indent org

init.el

@@ -527,6 +527,7 @@
   (org-mode . my-inhibit-hl-line-mode)
   (org-mode . my-double-space-sentence)
   :custom
+  (org-startup-indented t)
   (org-startup-with-inline-images t)
   (org-special-ctrl-a/e t)
   (org-insert-heading-respect-content t)
@@ -539,7 +540,25 @@
                               (shell . t)
                               (C . t)
                               (asymptote . t)))
-  (org-agenda-files '("~/Agenda"))
+  (org-default-notes-file (expand-file-name "notes.org" org-directory))
+  (org-agenda-files (list (expand-file-name "agenda/" org-directory)))
+  (org-refile-targets '((org-agenda-files :maxlevel . 1)
+                        (nil :maxlevel . 3)))
+  (org-agenda-include-diary t)
+  (org-capture-templates
+   (let ((todo (expand-file-name "todo.org" (car org-agenda-files))))
+     `(("t" "Todo" entry
+        (file+olp ,todo
+                  "Tasks"
+                  "General")
+        "* TODO %?\n  %i"
+        :refile-targets ((,todo :level . 2)))
+       ("T" "Todo with link" entry
+        (file+olp ,todo
+                  "Tasks"
+                  "General")
+        "* TODO %?\n  %i\n  %a"
+        :refile-targets ((,todo :level . 2))))))
   ;; NixOS minimal LaTeX setup
   (org-latex-compiler "lualatex")
   (org-preview-latex-default-process 'lua-dvisvgm)
@@ -548,8 +567,8 @@
                                        ".ltximg/"))
   (org-latex-src-block-backend 'engraved)
   :config
-  (setq org-format-latex-options (plist-put org-format-latex-options :scale 1.3)
-        org-modules (append '(org-tempo org-habit) org-modules))
+  (setf (plist-get org-format-latex-options :scale) 1.1)
+  (add-to-list 'org-modules 'org-tempo)
   ;; Preview with lualatex to prevent errors when trying to load fontspec and
   ;; others with pdflatex
   (add-to-list