People get very confused because they see the tables and data in the Database Explorer but they aren't there when they run their app. And I quote: "Don't be confused if you don't see the data (or even tables) when you run your application in spite of the fact that you can see them in Services window of NetBeans. Recall that Derby is looking for the DB in the working directory and the working directory of NetBeans is different from the working directory of your project."
http://wiki.netbeans.org/BestPracticesWithJPAAndBeansBinding
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