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Suppose I did some customization through M-x customize-mode or something similar

 '(org-agenda-custom-commands
   '(("n" "Agenda and all TODOs"
      ((agenda "" nil)
       (alltodo "" nil))
      nil)
     ("i" "Urgent things" tags "URGENT" nil)))

they are inserted inside (custom-set-variables

Can I just cut the lines and put them inside

(use-package org ?

Actually do I need to? I thought it would be aethetically pleasing to see well cleaned up init.el file..

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It's a matter of preference (or aesthetics) but if you are making frequent changes you'll appreciate having all the settings in one place. Using use-package can be helpful for keeping similar configs together and being explicit about how keyconfigs, hooks and dependencies (etc) are related to a package.

If you change something with the customize interface, you can just move it into your init.el file as needed.

With use-package you could try something like...

 (use-package org
  :config (setq org-agenda-custom-commands ... 
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0

I thought it would be aethetically pleasing to see well cleaned up init.el file

Yes, and in my case I don't use the customize UI at all, all my config is out of the custom-set-variables region. custom-set-variables only contains assignments written by the packages I use.

If your custom-set-variables region is still in your init file, you may want to move it to another file, copying from my config copied from Purcell's config:

(setq custom-file (expand-file-name "custom.el" user-emacs-directory))
(unless (file-exists-p custom-file)
  (write-region "" nil custom-file))
(when (file-exists-p custom-file)
  (load custom-file))

One thing to note is that custom-set-variables can trigger the custom set behavior written by the package author, while setq cannot. Such behavior is defined in :set when using defcustom (read the doc of defcustom for more). use-package's :custom, obviously does trigger that, as its name states.

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