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After much threatening and promising to do exactly this, we finally have Maven archetypes for creating XNAT modules available! If you're unfamiliar with Maven archetypes, this basically means we have a method that allows you to easily create a skeleton project for creating XNAT modules. This should help clarify a lot of the structure that goes into an XNAT module, which is not the most obvious thing in the world.
The documentation for this is located in the Developing Modules page in the XNAT 1.6 Developer Documentation. It includes instructions for generating modules from the command line, as well as within the IntelliJ IDEA and Eclipse development environments.
To get started really quickly, all you have do is run this command (this assumes you have Maven installed):
mvn archetype:generate -DarchetypeCatalog=http://maven.xnat.org/libs-release
There's more to the process, but this will get you started. If you have any issues, please consult the documentation page and/or feel free to add comments to the documentation or this post.