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[eluser]danmontgomery[/eluser]
You can move the system folder above web root, and you just need to change the $system_folder to point to that absolute location...

For example, if you put the system folder at: /usr/home/codeigniter/system, you just need to change $system_folder in all of your index.php files to:

Code:

$system_folder = "/usr/home/codeigniter/system";