I wrote that tutorial well before JSC ever existed. As far as your first question...
The tutorial says to "Run the deploy target in the ant script..(Build.xml) " but how could u do this? Where do u place the module/root folder or what (pprogram) do you run to target/deploy the war file? The tutorial assumed a knowledge of Ant. If you want to run the tutorial as is, you need to set up your project's folder structure identical to what I show in the tutorial. Otherwise, you will have to modify the build script or build it in your favorite IDE. If you downloaded all the files and don't want to setup the project the exact same way, just make sure you put the appropriate files where they should go in your structure, not necessarily where I put them.
From the tutorial:
I use IntelliJ 4.0 for all my Java development. You can use whatever you want, but for my example, you need to setup your directory structure just like mine in order for the ant build script to work correctly. That is unless you feel comfortable enough to adjust it to your liking.