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You can cleanly uninstalled GEP only if you have installed it cleanly. To do so, install your GEP by using Eclipse update manager. If your GEP was installed within WTP, reinstall it with Eclipse update manager to update some meta information so that a clean uninstallation can be preformed with the following steps:

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Uninstalling GEP using Eclipse update manager

You can also uninstall GEP with GEP by using Eclipse update manager with the following steps:

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