Move Application and ApplicationInstance creation into VM sandbox

Currently, we do a few things in the node process (instead of within the sandbox context):

* Require the application factory (`require('~fastboot/app-factory')`)
* Create the application factory (`AppFactory.default()`)
* Boot the application (`app.boot()`)
* Create an application instance instance (`app.buildInstance()`)
* Boot the application instance instance (`instance.boot()`)
* Invoke `instance.visit`

Everything in this list _except_ the last item should actually be done within the sandboxed VM context instead. This will allow these steps to be further optimized and shared across visits (since the VM scripts we evaluate share bytecode and compilation information), and it will also significantly improve the prototype extension compatibility (#170).