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Or is there a way to limit that cgi one that is every where to just search a specific folder and nothing beyond that or does it have to search the whole site?
Now, if you would be a little more specific, maybe you can get some 'real' help ;)
What kind of files? And how big are they?
Plain text, or otherwise formatted?
Which CGI script are you talking about?
What kind of searches do you want to perform?