So the index.php file has been renamed to somethingelse.php, and you’ve changed this in your ee settings as well?
Do you have an .htaccess file doing anything tricky?
Generally, all you’d need to do would be to change this setting: EE > Admin > General Configuration > Name of your site’s index page and CT will use the new URL the next time your reload the page. Keep an eye out for cached templates, or cached sql queries. There aren’t any paths hardcoded in CT, so it should just be using your sites’ default index page location.
Yep, index.php is site.php and that’s set in the general config options (I’m using Leevi Graham’s config bootstrap but I’ve tested without it and the problem’s the same). Disabling the .htaccess doesn’t affect it either.