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
```
@param {String} commandName - The command to be executed.
@param {} [args...] - Additional arguments to pass to the command callback.
@public
```

`@public` is the correct tag in v3. There's also `@private`, and `@protected`. You can also write it as `@access public`, however I think we should should always use the shorthands for consistency.