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I'd like to run Jackpot as a part of my build process, for example: - in a continuous build - before a release - on patch files from users
What are you trying to do with Jackpot? Since it gives you the ability to make potentially massive changes to a project, it is best used in an IDE where you can review and select which changes to make, plus undo the operation if necessary. The rule of thumb is Jackpot is best if you are modifying version-controlled source files, but use apt for error-checking and for creating files which are generated with every build. As of Java 6 (Mustang), apt shared the same model Jackpot uses, but cannot modify the model or apply its changes back to source files.
The old Jackpot module is no longer maintained. There is a rewrite in progress at: http://bitbucket.org/jlahoda/jackpot30/wiki/Home