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
Since `@desc` is the first item, you don't need to even write it. http://usejsdoc.org/tags-description.html

We should also probably specify that it is an `@instance` variable. http://usejsdoc.org/tags-instance.html