custom-file = ~/.doom.d/config.el

custom-file is now set to your private config.el, because users may want
to be able to see what Customize is storing (and where) front and
center. Storing it away in ~/.emacs.d/.local makes it harder to notice.

Also, have enable-command (and disable-command) save their data to
custom-file instead of ~/.emacs.d (see #3379).

Fixes #3379

core/core-modules.el

@@ -119,8 +119,7 @@ non-nil."
       (unless no-config-p
         (maphash (doom-module-loader doom-module-config-file) doom-modules)
         (run-hook-wrapped 'doom-init-modules-hook #'doom-try-run-hook)
-        (load! "config" doom-private-dir t)
+        (load! "config" doom-private-dir t)))))
-        (load custom-file 'noerror (not doom-debug-mode))))))
 
 
 ;;

core/core.el

@@ -233,7 +233,7 @@ users).")
 (setq abbrev-file-name             (concat doom-local-dir "abbrev.el")
       async-byte-compile-log-file  (concat doom-etc-dir "async-bytecomp.log")
       bookmark-default-file        (concat doom-etc-dir "bookmarks")
-      custom-file                  (concat doom-local-dir "custom.el")
+      custom-file                  (concat doom-private-dir "config.el")
       custom-theme-directory       (concat doom-private-dir "themes/")
       desktop-dirname              (concat doom-etc-dir "desktop")
       desktop-base-file-name       "autosave"
@@ -253,6 +253,14 @@ users).")
   :override #'emacs-session-filename
   (concat doom-cache-dir "emacs-session." session-id))
 
+(defadvice! doom--save-enabled-commands-to-doomdir-a (orig-fn &rest args)
+  "When enabling a disabled command, the `put' call is written to
+~/.emacs.d/init.el, which causes issues for Doom, so write it to the user's
+config.el instead."
+  :around #'en/disable-command
+  (let ((user-init-file custom-file))
+    (apply orig-fn args)))
+
 
 ;;
 ;;; Optimizations