General refactor for consistency & idempotency

Also updated comments

modules/lang/emacs-lisp/config.el

@@ -57,9 +57,7 @@
   (defun +emacs-lisp|init-flycheck ()
     "Initialize flycheck-mode if not in emacs.d."
     (when (and buffer-file-name
-               (not (cl-loop for dir in (append (list doom-emacs-dir)
-                                                doom-modules-dirs
-                                                doom-psuedo-module-dirs)
+               (not (cl-loop for dir in (list doom-emacs-dir doom-private-dir)
                              if (file-in-directory-p buffer-file-name dir)
                              return t)))
       (flycheck-mode +1))))