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Setting up your environment
In order to run Neptus, first you need to install a Java version 1.7 run time environment (JRE). Moreover, if you want to extend Neptus, you need to have a Java Development Kit (JDK) so that you can compile and package your code into a jar plug-in. So download the latest Java JDK from here.
After installing the JDK, you should install the latest Eclipse IDE (Kepler at the time of writing) from here.
If you have Eclipse Kepler or later, you can import a project from Git. Select import from URI and paste the following text into the URI: https://github.com/LSTS/neptus.git. You can hit Next and import the single project in that repository (Neptus).
After cloning the Neptus repository, if all went well, a new project should be added to Eclipse's Package Explorer. Open this project and select the class pt.up.fe.dceg.neptus.loader.NeptusMain. Right-click it and choose Run As...-->Java Application. Neptus should start using your developing environment.