[eluser]tonanbarbarian[/eluser]
i actually split things up in 3 ways
1. ci system files, /usr/share/CodeIgniter_1.7.2/system
2. application files
these i put outside the web root
/var/www/myapplication
3. index.php, images, css and js all go in the web root
/var/www/html/index.php
Now of course you need to adjust that to the location of your web root etc
This split is useful if you have multiple user accounts with separate webroots
i.e. /home/myuser/public_html
in that case I would put the applications in
/home/myuser/apps/myapplication
and the index.php etc is in /home/myuser/public_html
This separation gives you extra security because most of the code files are not in the webroot and cannot be accessed or modified if someone gains access to the server via php