Adds JSDoc to the Application.

Still a WIP, but this adds JSDoc to the Application source.

I've never used JSDoc before, so feel free to give me feedback on the methods and properties that I've already added.

Thanx
```
@memberof Marionette
@param {} [options...] - Options to be available on the Application instance directly.
```

`Marionette` in this case would be a namespace.

`{}` specifies any type `{Function|Object}` specifies multiple. `[paramName]` specifies that it is optional.  There is no official way of supporting rest params, however `[paramName...]` seems to be the way most people are doing it.