Split up vendor and appliation code.

Generate an `/assets/vendor.js` in addition to `/assets/my-package.js`.

Also, ensures that ES3SafeFilter is only ran on application code AFTER transpiling.
Merge pull request #949 from rjackson/split-vendor-and-app

Split up vendor and appliation code.
Provide EmberApp with registry access.

* Allows customizing registry within `Brocfile.js`.
* Provides registry with `EmberApp` instance.
* Makes each `Plugin` have a `toTree` method. This will allow plugins
  that take a different signature to work properly (assuming they
  implement a custom `toTree`).
* Provides `name` property that is provided to `EmberApp` to plugin.
  This allows the plugin to name the generated output file properly.