Use `set-default-toplevel-value' in `defcustom' setters

* lisp/ob-lilypond.el (org-babel-lilypond-commands):
* lisp/ob-shell.el (org-babel-shell-names):
* lisp/org-capture.el (org-capture-templates):
* lisp/org-clock.el (org-clock-ask-before-exiting):
* lisp/org-duration.el (org-duration-units):
* lisp/org-faces.el (org-set-tag-faces):
* lisp/org-footnote.el (org-footnote-section):
* lisp/org-list.el (org-plain-list-ordered-item-terminator):
(org-list-allow-alphabetical):
* lisp/org.el (org-babel-do-load-languages):
(org-set-modules):
(org-export-backends):
(org-use-fast-todo-selection):
(org-enforce-todo-dependencies):
(org-enforce-todo-checkbox-dependencies):
(org-display-custom-times):
(org-set-packages-alist):
(org-set-emph-re):
* lisp/ox-odt.el (org-odt-schema-dir): Use
`set-default-toplevel-value' instead of `set' or `set-default' in
`defcustom' :set argument.

This commit fixes a bug that occurred when using an autoload function
inside a let-binding for a custom variable when the feature defining
both the function and the custom variable had not been loaded yet.

See bug#54399 and
https://lists.gnu.org/archive/html/emacs-orgmode/2022-03/msg00085.html,
https://lists.gnu.org/archive/html/emacs-orgmode/2022-06/msg00226.html

lisp/ob-lilypond.el

@@ -107,7 +107,7 @@ you can leave the string empty on this case."
   :package-version '(Org . "8.2.7")
   :set
   (lambda (symbol value)
-    (set symbol value)
+    (set-default-toplevel-value symbol value)
     (setq
      org-babel-lilypond-ly-command   (nth 0 value)
      org-babel-lilypond-pdf-command  (nth 1 value)

lisp/ob-shell.el

@@ -68,7 +68,7 @@ outside the Customize interface."
   :group 'org-babel
   :type '(repeat (string :tag "Shell name: "))
   :set (lambda (symbol value)
-	 (set-default symbol value)
+	 (set-default-toplevel-value symbol value)
 	 (org-babel-shell-initialize)))
 
 (defcustom org-babel-shell-results-defaults-to-output t

lisp/org-capture.el

@@ -376,7 +376,7 @@ When you need to insert a literal percent sign in the template,
 you can escape ambiguous cases with a backward slash, e.g., \\%i."
   :group 'org-capture
   :package-version '(Org . "9.5")
-  :set (lambda (s v) (set s (org-capture-upgrade-templates v)))
+  :set (lambda (s v) (set-default-toplevel-value s (org-capture-upgrade-templates v)))
   :type
   (let ((file-variants '(choice :tag "Filename       "
 				(file :tag "Literal")

lisp/org-clock.el

@@ -493,7 +493,7 @@ This variable only has effect if set with \\[customize]."
          (if value
              (add-hook 'kill-emacs-query-functions #'org-clock-kill-emacs-query)
            (remove-hook 'kill-emacs-query-functions #'org-clock-kill-emacs-query))
-         (set symbol value))
+         (set-default-toplevel-value symbol value))
   :type 'boolean
   :package-version '(Org . "9.5"))
 

lisp/org-duration.el

@@ -98,7 +98,7 @@ sure to call the following command:
   :version "26.1"
   :package-version '(Org . "9.1")
   :set (lambda (var val)
-         (set-default var val)
+         (set-default-toplevel-value var val)
          ;; Avoid recursive load at startup.
 	 (when (featurep 'org-duration)
            (org-duration-set-regexps)))

lisp/org-faces.el

@@ -338,7 +338,7 @@ determines if it is a foreground or a background color."
 
 (defvar org-tags-special-faces-re nil)
 (defun org-set-tag-faces (var value)
-  (set var value)
+  (set-default-toplevel-value var value)
   (if (not value)
       (setq org-tags-special-faces-re nil)
     (setq org-tags-special-faces-re

lisp/org-footnote.el

@@ -110,7 +110,7 @@ you will need to run the following command after the change:
   :group 'org-footnote
   :initialize 'custom-initialize-default
   :set (lambda (var val)
-	 (set var val)
+	 (set-default-toplevel-value var val)
 	 (when (fboundp 'org-element-cache-reset)
 	   (org-element-cache-reset 'all)))
   :type '(choice

lisp/org-list.el

@@ -235,7 +235,7 @@ interface or run the following code after updating it:
   :type '(choice (const :tag "dot like in \"2.\"" ?.)
 		 (const :tag "paren like in \"2)\"" ?\))
 		 (const :tag "both" t))
-  :set (lambda (var val) (set var val)
+  :set (lambda (var val) (set-default-toplevel-value var val)
 	 (when (featurep 'org-element) (org-element-update-syntax))))
 
 (defcustom org-list-allow-alphabetical nil
@@ -253,7 +253,7 @@ interface or run the following code after updating it:
   :group 'org-plain-lists
   :version "24.1"
   :type 'boolean
-  :set (lambda (var val) (set var val)
+  :set (lambda (var val) (set-default-toplevel-value var val)
 	 (when (featurep 'org-element) (org-element-update-syntax))))
 
 (defcustom org-list-two-spaces-after-bullet-regexp nil

lisp/org.el

@@ -231,7 +231,7 @@ Stars are put in group 1 and the trimmed body in group 2.")
 ;;;###autoload
 (defun org-babel-do-load-languages (sym value)
   "Load the languages defined in `org-babel-load-languages'."
-  (set-default sym value)
+  (set-default-toplevel-value sym value)
   (dolist (pair org-babel-load-languages)
     (let ((active (cdr pair)) (lang (symbol-name (car pair))))
       (if active
@@ -706,7 +706,7 @@ defined in org-duration.el.")
 
 (defun org-set-modules (var value)
   "Set VAR to VALUE and call `org-load-modules-maybe' with the force flag."
-  (set var value)
+  (set-default-toplevel-value var value)
   (when (featurep 'org)
     (org-load-modules-maybe 'force)
     (org-element-cache-reset 'all)))
@@ -837,7 +837,7 @@ depends on, if any."
   :package-version '(Org . "9.0")
   :initialize 'custom-initialize-set
   :set (lambda (var val)
-	 (if (not (featurep 'ox)) (set-default var val)
+	 (if (not (featurep 'ox)) (set-default-toplevel-value var val)
 	   ;; Any back-end not required anymore (not present in VAL and not
 	   ;; a parent of any back-end in the new value) is removed from the
 	   ;; list of registered back-ends.
@@ -862,7 +862,7 @@ depends on, if any."
 			  backend))
 		((not (memq backend new-list)) (push backend new-list))))
 	     ;; Set VAR to that list with fixed dependencies.
-	     (set-default var new-list))))
+	     (set-default-toplevel-value var new-list))))
   :type '(set :greedy t
 	      (const :tag "   ascii       Export buffer to ASCII format" ascii)
 	      (const :tag "   beamer      Export buffer to Beamer presentation" beamer)
@@ -1815,9 +1815,9 @@ are followed by a letter in parenthesis, like TODO(t)."
   :group 'org-todo
   :set (lambda (var val)
 	 (cond
-	  ((eq var t) (set var 'auto))
-	  ((eq var 'prefix) (set var nil))
-	  (t (set var val))))
+	  ((eq var t) (set-default-toplevel-value var 'auto))
+	  ((eq var 'prefix) (set-default-toplevel-value var nil))
+	  (t (set-default-toplevel-value var val))))
   :type '(choice
 	  (const :tag "Never" nil)
 	  (const :tag "Automatically, when key letter have been defined" auto)
@@ -1899,7 +1899,7 @@ be blocked if any prior sibling is not yet done.
 Finally, if the parent is blocked because of ordered siblings of its own,
 the child will also be blocked."
   :set (lambda (var val)
-	 (set var val)
+	 (set-default-toplevel-value var val)
 	 (if val
 	     (add-hook 'org-blocker-hook
 		       'org-block-todo-from-children-or-siblings-or-parent)
@@ -1917,7 +1917,7 @@ This variable needs to be set before org.el is loaded, and you need to
 restart Emacs after a change to make the change effective.  The only way
 to change it while Emacs is running is through the customize interface."
   :set (lambda (var val)
-	 (set var val)
+	 (set-default-toplevel-value var val)
 	 (if val
 	     (add-hook 'org-blocker-hook
 		       'org-block-todo-from-checkboxes)
@@ -2368,7 +2368,6 @@ The formats are defined through the variable `org-time-stamp-custom-formats'.
 To turn this on on a per-file basis, insert anywhere in the file:
    #+STARTUP: customtime"
   :group 'org-time
-  :set 'set-default
   :type 'sexp)
 (make-variable-buffer-local 'org-display-custom-times)
 
@@ -3275,7 +3274,7 @@ header, or they will be appended."
 
 (defun org-set-packages-alist (var val)
   "Set the packages alist and make sure it has 3 elements per entry."
-  (set var (mapcar (lambda (x)
+  (set-default-toplevel-value var (mapcar (lambda (x)
 		     (if (and (consp x) (= (length x) 2))
 			 (list (car x) (nth 1 x) t)
 		       x))
@@ -3548,7 +3547,7 @@ After a match, the match groups contain these elements:
 (defvar org-emphasis-alist) ; defined just below
 (defun org-set-emph-re (var val)
   "Set variable and compute the emphasis regular expression."
-  (set var val)
+  (set-default-toplevel-value var val)
   (when (and (boundp 'org-emphasis-alist)
 	     (boundp 'org-emphasis-regexp-components)
 	     org-emphasis-alist org-emphasis-regexp-components)

lisp/ox-odt.el

@@ -404,7 +404,7 @@ with GNU ELPA tar or standard Emacs distribution."
     "Set `org-odt-schema-dir'.
 Also add it to `rng-schema-locating-files'."
     (let ((schema-dir value))
-      (set var
+      (set-default-toplevel-value var
 	   (if (and
 		(file-expand-wildcards
 		 (expand-file-name "od-manifest-schema*.rnc" schema-dir))