[eluser]JoostV[/eluser]
Best way is to regroup CI folders as a whole anyway, is my experience.
Assuming your webroot is named public_html:
|-public_html
| |-css/
| |-gfx/
| |-etc/
| |-index.php
|
|-application
|-codeigniter1.7.1
This way, the only executable php file in your webroot is index.php. The rest is outside webroot and cannot be accessed directly. Your current CI installation is in its own folder so if you wish to upgrade, you just substitute codeigniter1.7.1 with whatever version you wish.
All that is required for this to work is tweaking two lines of code in index.php:
Code:
$system_folder = "../codeigniter1.7.1";
Code:
$application_folder = "../application";
Place you CSS in public_html in public_html/css and link to it like you always do.