Hi Jay,

I keep all my notes out of the agenda, because it slows down building the 
agenda (at least with previous versions of org, it might have improved 
recently), which I do quite often.

Instead I keep all those notes files in the variable 
org-agenda-text-search-extra-files, so that I am able to search on them and add 
them as well to the org-refile-targets. If you keep all your notes in the 
directory ~/org/notes, then set:

     #+BEGIN_SRC emacs-lisp
       (setq org-agenda-text-search-extra-files (cddr
                                                 (directory-files
                                                  "~/org/notes"
                                                  t
                                                  nil)))
       (setq org-refile-targets (list '(org-agenda-files
                                        . (:maxlevel . 1))
                                      '(org-agenda-text-search-extra-files
                                        . (:maxlevel . 1))
                                      '(nil
                                        . (:maxlevel . 5))))
     #+END_SRC

Best,

Jorge.

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