rename .js files to .js.php

This, in theory, will help developers realize that the files are mixed php/js.  These files may, and some will, contain php calls to export configurable options.
Move js out of php src
Move includes out of src and into version specific files

Also, update 4.0 client to use new method for wdn plugins (require js).
require the analytics plugin
use WDN.get/setCookie

remove extra jquery dependency
use $ for jQuery

RequireJS allows us to import as $.  WDN.jQuery may not be defined.