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From: Richard Stallman <rms@gnu.org>
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Subject: Re: Building emacs with and without X -- packaging question.
Date: Tue, 25 Jun 2002 19:32:52 -0400
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    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.

How about if we make cus-load.el start by sorting the files by ASCII
order.  That would eliminate all differences that result from this
cause.

However, the cause of the other differences remains to be determined.