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From: Richard Stallman <rms@gnu.org>
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Subject: Re: query-replace on region highlights too much
Date: Tue, 15 Feb 2005 01:18:46 -0500
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Xref: main.gmane.org gmane.emacs.devel:33455
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    The problem is that the highlighting of the search string is performed
    in the whole buffer, not only in the region where replacing is going
    to happen.

I wrote the code to handle this.  I will install it soon.