[eluser]gRoberts[/eluser]
Because how CI is written, it's "harder" to extend or access code CI files unless they are loaded correctly.
This means, really, it makes no difference.
What I do however, if I can, is:
Code:
/
/htdocs
/htdocs/index.php
/system
/application
and then use, as you have:
Code:
$system_folder = '../system';
$application_folder = '../application';
This prevents anyone from accessing the files via the browser, making it a little more secure.