In Administration part (localhost:9090)

1. Go to Virtual Host → Choose the codeigniter host
2. Go to Behaviour Tab
3. Target: Default → Handler
4. Change Handle: Redirection
5. Type: internal Regular Expression: ^(.*)$ Substitution: /index.php/$1

Don't forget in system/application/config/config.php to modify $config['index_page'] = ””;

As an extra, add a directory rule with web directory: /media (or wherever do you store css and js files) and handler Static Content.