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From: Eli Zaretskii <eliz@is.elta.co.il>
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Subject: Re: Building emacs with and without X -- packaging question.
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On Mon, 24 Jun 2002, Stefan Monnier wrote:

> IIRC It's because cus-dep.el loads files and the load order is important.
> The set of preloaded files is different, so the load order is different
> so the resulting cus-load.el is different.

That's true, but some of the differences are not just order differences.  
For example, scroll-bar doesn't appear in one custom-load, and 
gnus-article-x-face-command doesn't appear in the non-X version at all.