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EcoreUtil.delete() alone appears to be sufficient to persistently delete an EObject; however, it only removes the objects references, which means it can be re-attached. Hence, EcoreUtil.delete() can be used to temporarily detach an EObject, but also to persistently delete it. Both inside a command. To make it more clear how to use the framework, log a warning whenever EcoreUtil.delete() is called without a command being started. See: https://bugs.eclipse.org/bugs/show_bug.cgi?id=365530
*** This bug has been marked as a duplicate of bug 464274 ***