Changing the way that your application works can be a good way to secure your application. With CodeIgniter you can rename your system folder and even place it above the web root, making it inaccessible from a browser window. You can rename your application folder and pull it out of the system folder. Doing this may keep your application more secure than by simply keeping the default structure. The main reason behind this is that if vulnerability were to be found in the CodeIgniter core then nobody could act upon it, because you would have renamed your system folder and it won't be accessible to him or her anyway. Renaming your application folder keeps people from easily identifying it as a CodeIgniter project, therefore limiting the ways they could try to breach the application.
Once you rename your application and system folders and move them both (application out of system, and system out of the web root), open up index.php
and change the following variables...