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From: Richard Stallman <rms@gnu.org>
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Subject: Re: config.in
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    |> Ordinary make has to fix the timestamps too, and touch the generated
    |> files, when you are building from CVS.  It should not attempt
    |> to run autoconf unless the user says `make configure' or `make config.in'.

    In neither cases the makefile caters for CVS timestamp issues at the
    moment.  Doing it right would require a script like gcc_update from the
    gcc repository, since make cannot know whether the timestamp difference
    comes from modifying configure.in or from CVS update.

If someone wants to "do it right", then by all means do so.
But unless and until that happens, we should do something simple:
Makefile.in should update configure and src/config.in
simply by touching them.

Since you made the change to update config.in automatically, could you
please do that?