Added check to catch when org has already been loaded.

core/templates/.spacemacs.template

@@ -216,8 +216,8 @@ values."
 
 (defun dotspacemacs/user-init ()
   "Initialization function for user code.
-It is called immediately after `dotspacemacs/init'.  You are free to put any
-user code."
+It is called immediately after `dotspacemacs/init'.  You are free to put almost any
+user code here. The exception is org related code, which should be placed in dotspacemacs/user-config."
   )
 
 (defun dotspacemacs/user-config ()

layers/org/README.org

@@ -42,6 +42,8 @@ Since version 0.104, spacemacs uses the `org` version from the org ELPA
 repository instead of the one shipped with emacs. Then, any `org` related code
 should not be loaded before `dotspacemacs/user-config`, otherwise both versions
 will be loaded and will conflict.
+Org layer checks if this has occurred and signals an error if org features have
+been instantiated prior to org layer loading.
 
 * Install
 ** Layer

layers/org/packages.el

@@ -80,6 +80,11 @@
     :defer t
     :init
     (progn
+      (when (member 'org features)
+        (configuration-layer//set-error)
+        (spacemacs-buffer/append
+         "Org features have been loaded before the spacemacs org layer has initialised. \nTry removing org code from user initialisation and private layers." t
+         ))
       (setq org-clock-persist-file
             (concat spacemacs-cache-directory "org-clock-save.el")
             org-id-locations-file