Or there is something missing from this passage:
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One of the drawbacks of the CGI version of PHP is its inability to use PHP-based authentication. Besides the overall performance hit, this would be the other glaring drawback. There's nothing, however, stopping you from using your normal Web server-based authentication; they're mutually exclusive.
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EDIT Aksherly, all I was thinking was that mebbe they meant to srtick a "not" in front of "mutually exclusive."