Re: Emacs inserts hardwired org-agenda-files variable, overwriting user options

[Tom Gillespie]

Here is a workaround. Emacs klobbering settings in .emacs has caused
many issues for me in the past. The solution I finally came up with
was to ensure that custom variables are loaded before any of my
settings. Near the top of my .emacs (before any calls to setq) I have
the following:

;;;; custom set variables
;;; PLEASE MAKE YOUR WAY TO THE EXIT AND STAY OUT OF MY INIT FILE
;;; These come first so that they will be overwritten by settings in packages
;;; in order to prevent stale variables from klobbering new values
(setq custom-file (expand-file-name  "custom.el" user-emacs-directory))
(when (file-exists-p custom-file)
  (load custom-file))

If you have that then your list will be retained. However Emacs will
probably continue to ask you to remove the missing file until some
file exists at that path. Not sure about the org agenda behavior for
missing files since I populate org-agenda-files by scanning folders
for existing org files and then having a blacklist to exclude files I
do not want.

Best,
Tom