It should be a file called wpad.dat not index.php
can you access it at wpad.exmaple.com/wpad.dat?
Have you configured your browser to automatically determine the proxy settings?
That is the default, so Yes.
Still does not resolve properly.
Problem seems to be outdated Howto documents that no one seems motivated to update.
The wpad.dat file should go into the /var/webconfig/htdocs on the ClearOS system.
As the above is clearly wrong, the user even when told the new directory location is still uncertain the location so long as said proper location does not produce the desired results.