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From: Richard Stallman <rms@gnu.org>
Newsgroups: gmane.emacs.devel
Subject: Re: config.in
Date: Wed, 24 Apr 2002 11:55:19 -0600 (MDT)
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    I have now replaced the dependency on configure.in by a variable, which
    can be set to FRC or configure.in to force running autoconf and
    autoheader.

That is a good solution.  You can make your .bashrc set the variable,
so that configure and config.in will always be updated for you.

Thanks.