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I'm not familiar with CodeIgniter, but this isn't terribly different from how Wordpress and other PHP-based CMSs manage permalinks. Currently you're simply forwarding shortened URLs (/contact/) to the actual URL (/site/contact/), which isn't ideal. It would be preferable to remove the base path (/site/) from the URL completely. This guide (http://www.web-and-development.com/codeigniter-remove-index-php-minimize-url/) has a good rundown on how to control this in .htaccess. I believe that the sections titled "Removing 1st URL segment" and "Routing automatically" are going to be the ones that are applicable to your case, because you're trying to change the controller. You should also take a look through the original documentation at http://ellislab.com/codeigniter/user-guide/general/urls.html. You're also going to want to make sure that any canonicals being used in the match the intended URL, and that any incorrect URLs (eg /site/contact/) are 301 redirecting to the proper URL (eg /contact/). Use wheregoes.com and type in the /site/contact/ version of the URL to test this - it should spit out "301 redirect" not "302" or anything else. If you're not really comfortable messing around with htaccess, I'd highly recommend trying this out on a development server and making sure it all works correctly before you move it to a live server.