Folders for the code igniter core.

• /var/www
  • ci
    • application
    • system

Folders for the custom application.

• /var/www
  • myapp
    • application
    • index.php

Change in /var/www/myapp/index.php :

  $system_path = '../ci/system';

<IfModule mod_rewrite.c>
    RewriteEngine on

    RewriteCond %{REQUEST_URI} ^system.*
    RewriteCond $1 !^(index\.php|images|robots\.txt|css)
    RewriteRule ^(.*)$   index.php?/$1  [L]

    RewriteCond %{REQUEST_FILENAME} !-f
    RewriteCond %{REQUEST_FILENAME} !-d
    RewriteRule ^(.*)$   index.php?/$1  [L]
</IfModule>