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If you forget to create your site dir and configure it, your app will not build. This is a common problem. See iJAG FAQ on checking out an Eclipse project for instructions on setting up your site dir and configuring it.
To run your app, just right click the project and select Run As > Run on Server. The first time you do this it will ask you to pick which server to run on. If you check the checkbox at the bottom it won't ask you this again. By default, it will go to the action EntryAction.do.
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