Questions

[eluser]m4rw3r[/eluser]
You could put CodeIgniter's system directory wherever you want, just make sure the bootstrap file (index.php) links to it correctly (with $system_folder) and that you have the right permissions set.

Example:

Code:

/home/m4rw3r/mysite/
  \
  |-system  -\
  |          |-cache
...        ...
  |
  |-wwwroot -\
             |-index.php
             |-application/
             \-public/

Index.php:

Code:

$system_folder = "../system";