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From: Artur Malabarba <bruce.connor.am@gmail.com>
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Subject: Re: Customizable modes and package.el
Date: Mon, 30 Mar 2015 15:31:09 +0100
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> That's not an option, because the user may need/want to run some Elisp
> code of his own choosing *before* package-initialize is called.
> E.g. in my case, I need to set package-load-list and
> package-directory-list before package-initialize runs.

`package-initialize' could look into some file like
~/.emacs.d/package-init.el and load that before initializing.