[eluser]t'mo[/eluser]
Alternatively, you could (some would say *should*) configure your CI deployment so that only index.php is in the webroot, and everything else is up and out.
Code:
1) /home/yourid/public_html
2) /home/yourid/public_html/index.php
3) /home/yourid/codeigniter
1. webroot
2. the only "page" people hitting your site see; in here you configure your $system_folder and $application_folder variables to refer to '/home/yourid/codeigniter'
3. where your application code resides
You don't even have to do the usual "codeigniter/system/application" thing; you could also add another directory so multiple applications could share the same copy of the codeigniter libraries:
Code:
4) /home/yourid/first_application
/home/yourid/second_application
...