customize creates custom-set-faces unintentionally

Question

I just edited the variable org-M-RET-may-split-line with easy costumize, saved and applied. I checked my dotfile right afterwards and noticed that (custom-set-faces '(default ((t (:foreground "#DCDCCC" :background "#3F3F3F"))))) was added to my dotfile. This already happened a few times to me when using easy customize. Any idea how to prevent this?

EDIT: I'm able to reproduce the issue:

• start spacemacs with emacs
• open dotfile with SPC f e d
• SPC f1 python-shell-interpreter
• change value to python3
• apply and save
• bottom of dotfile, this is what was added:

;; Do not write anything past this comment. This is where Emacs will
;; auto-generate custom variable definitions.
(custom-set-variables
 ;; custom-set-variables was added by Custom.
 ;; If you edit it by hand, you could mess it up, so be careful.
 ;; Your init file should contain only one such instance.
 ;; If there is more than one, they won't work right.
 '(fci-rule-color "#383838" t)
 '(nrepl-message-colors
   (quote
    ("#CC9393" "#DFAF8F" "#F0DFAF" "#7F9F7F" "#BFEBBF" "#93E0E3" "#94BFF3" "#DC8CC3")))
 '(org-M-RET-may-split-line (quote ((default))))
 '(pdf-view-midnight-colors (quote ("#DCDCCC" . "#383838")))
 '(python-shell-interpreter "python3")
 '(vc-annotate-background "#2B2B2B")
 '(vc-annotate-color-map
   (quote
    ((20 . "#BC8383")
     (40 . "#CC9393")
     (60 . "#DFAF8F")
     (80 . "#D0BF8F")
     (100 . "#E0CF9F")
     (120 . "#F0DFAF")
     (140 . "#5F7F5F")
     (160 . "#7F9F7F")
     (180 . "#8FB28F")
     (200 . "#9FC59F")
     (220 . "#AFD8AF")
     (240 . "#BFEBBF")
     (260 . "#93E0E3")
     (280 . "#6CA0A3")
     (300 . "#7CB8BB")
     (320 . "#8CD0D3")
     (340 . "#94BFF3")
     (360 . "#DC8CC3"))))
 '(vc-annotate-very-old-color "#DC8CC3"))
(custom-set-faces
 ;; custom-set-faces was added by Custom.
 ;; If you edit it by hand, you could mess it up, so be careful.
 ;; Your init file should contain only one such instance.
 ;; If there is more than one, they won't work right.
 '(default ((t (:family "Office Code Pro" :foundry "NATH" :slant normal :weight normal :height 120 :width normal)))))

Answer 1

Do not touch the entries which customize inserts, thats all.

But you can also split the stuff which customize writes into another file with:

(setq custom-file "~/.emacs.d/custom.el")
(load custom-file)

in your init.el. Then customize will write only to that file.

Answer 2

I don't have Spacemacs, but I looked for the function that saves customize buffers and found custom-save-all. It calls both custom-save-variables and custom-save-faces. So any time you save all customizations, both get called.

Looking at custom-save-faces, it doesn't check to see if you've changed any faces before it inserts custom-set-faces into your init or custom file - it only deletes the one that's there and replaces it with a newly constructed sexp. What seems strange to me is that you have a default face set there, while I do not; I don't know if that's a difference in Emacs (I'm on 24.5.1) or if it's something added by Spacemacs.

In any event, the hacky solution would be to redefine custom-save-faces to just return nil. That should work, but you'd lose the ability to customize faces. I haven't tested this, though. A proper solution would be much more involved.