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.htpasswd doesn't protect your script any better from prying eyes or local users than properly implemented encryption (whether using md5, crypt() or whatever) inside your CGI. Both are equally valid methods if done correctly. .htpasswd is often easier to use, but its harder to log a user out if you choose this route
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First of all any CGI script can send their header as text/html, so those password protection scripts would proably work (if you didn't understand that have a look at Ovid's Web Programming Course, esp. lesson 3 which is a good introduction to web security). Also, have you tried Super Search searching for passwords and CGI, it gives a huge amount of nodes (Website login/authentication, perl web store, and perl web store just to name the first 3)
"Cogito cogito ergo cogito sum - I think that I think, therefore I think that I am." Ambrose Bierce
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