Routing

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I am getting a large number of page load failures (404). When this happens php is still running, and the server is still responding, I know this because I have tried loading an static html page, and a php page that returns the phpinfo and both worked.

Accessing mysite.com/index.php returns the default page, however all the links are broken suggesting routing, in addition to this mysite.com fails to find index.php

I have removed the htaccess file and have looked through app.php and can find no routing defined, so the only thing pointing to index.php that I can find is the default page.

Any ideas as to where there might be routes defined (or anything else I can look at)?

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