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I've been wondering the same thing for some time - I've used this documentation as the standard for a lot of my enterprise applications and have even ported it over to other technologies, but I'm starting to feel it's less relevant than it once was - it would be great to get an update on this for Java EE 6.
Its a standard, its not like it is a big secret. Any article or book on JEE deployment will tell you the structure, just Google it. There is also the JEE tutorial:
although at first glance there is nothing specifically about deployment. Any IDE in existence today can also create the proper binaries though, even if you don't want to use an IDE you can create a test project in one and see what it produces. So many ways to know what you want to know on your own, without having to resurrect and hijack old threads.