[eluser]tonanbarbarian[/eluser]
the setup that i usually use is something like this
A CodeIgniter folder somewhere that contains everything you get when you unzip the downloaded codeigniter file.
i.e. /usr/share/CodeIgniter
this then contains 2 folders
/usr/share/CodeIgniter/system
/usr/share/CodeIgniter/userguide
This allows many sites on the server to use the same codeigniter core libraries
If you need to run multiple different versions of codeigniter you can
/usr/share/CodeIgniter_1.7.1
/usr/share/CodeIgniter_1.7.2
etc
Then in the user folders but outside of the webroot for the user I have an applications folder in which I place a renamed version of the system/application folder
i.e.
/home/myuser/applications/app1
/home/myuser/applications/app2
/home/myuser/applications/app3
Then finally in the webroot you can include your index.php file, and if you are running several CI apps on the same site you can change the index.php file to something different for each app and then change the index_page in the config.php and modify your htaccess as well
i.e.
/home/myuser/public_html/index.php (links to app1)
/home/myuser/public_html/app2.php (links to app2)
/home/myuser/public_html/app3.php (links to app3)
Or you can place the index.php files in separate folders if you have multiple apps as well
