Build a CI application alongside EE 2 installation

[eluser]Monarobase[/eluser]
Good question !

At the moment www.nifootball.co.uk/ redirects to http://www.nifootball.co.uk/pages/home.html

Which before .htaccess re-link was :

http://www.nifootball.co.uk/index.php/pages/home.html

What you need now is to be able to access :

http://www.nifootball.co.uk/stats.php

Without the .htaccess re-link this would not have been a problem, but my guess (without being sure this is the best way around it, maybe CI provides a cleaner way I'm not aware of) would be to add a condition to your .htaccass file, something like this :

if URL doesn't contain stats.php then do this

You could do this using a RewriteCond before your Expression Engine rewrite rules.