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I know I can use htpasswd to create a password file for apache, but how do I configure it to use valid users or groups from the system?

+1  A: 

You'll need to use an appropriate authentication module. Here's an example with mod_authnz_external: http://blog.innerewut.de/2007/6/26/apache-2-2-authentication-with-mod_authnz_external

David Zaslavsky