URLs don't work when application is in web root

[eluser]Aken[/eluser]
Not 100% sure I'm understanding your question exactly, but you'd use routes to direct a non-existant URL to a valid class/method/id URI. You can also use the URL helper functions site_url() or anchor() to generate URLs that include index.php automatically. Which is good for if you remove index.php via .htaccess in the future.