Codeigniter index.php in the subfolder

In the index.php you should change the $system_path and the $application_folder variables, and thats should do it.

In your case:

$system_path = '../system';
$application_folder = '../application';

And of course your document root must to point to your public folder. Hope it helps.

I'm not sure what you want to achieve;

if you want to remove index.php from the url so you have

example.com/controller/method instead of example.com/index.php/controller/method

You need to create a .htaccess file

Options +FollowSymlinks
RewriteEngine On
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php?r=$1 [L,QSA]

For me, if you want to make it safer... I advised you to rename

application folder and system folder

E.g:

application change to my_secret_application

and

system change to my_secret_system

And in your index.php

$system_path = 'my_secret_application';
$application_folder = 'my_secret_system';