There is a number of legacy JS files in 4.0.A1, like prototype or sarissa. They aren't used and will be removed. jQuery is the base library for 4.x.
window.RichFaces sometimes uses jsf.ajax and sometimes jQuery to perform ajax requests. Why is that?
a4j:push component uses HEAD requests for server pinging and jsf.ajax doesn't allow sending such types of requests. So we've employed jQuery for sending them. And if HEAD request initiated by jQuery returns with data availability flag, we trigger common AJAX request via jsf.ajax.