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I suppressed the deprecation warnings in org.eclipse.emf.facet.query.java.* on internal uses of EMF Facet deprecated (but still maintained) APIs. Committed in revision 1111.
The @SuppressWarnings("deprecation") on the class org.eclipse.emf.facet.query.java.core.IJavaQuery<T, R> is an error. It must be replaced by a deprecation of the interface. All the methods using a deprecated type in their signature must be deprecated and replaced by another one. The import of deprecated type must be removed and replaced by the use of qualified names. The interfaces containing a deprecated method must be deprecated if the interface is no marked @noimplement or @noextend. When a method, a class or an interface is deprecated the developer must explain in the javadoc how to get the same service by using a non deprecated API. The deprecation of a method, a class or an interface exposed in API must be tracked and in a bug named "[Deprecated] <qualified_name>", where <qualified_name> is the qualifed name of the depreacted element. The bug URL must be added in the deprecation part of the Javadoc.