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It seems that if a nature id has a ".", the default behavior of adding the plugin ID as a prefix for the the nature's id is not happening any more. The JET nature was defined this way <extension point="org.eclipse.core.resources.natures" id="jet.IJETNature"> <runtime> <run class="org.eclipse.emf.codegen.jet.JETNature" /> </runtime> </extension> and our code would look for "org.eclipse.emf.codegen.jet.IJETNature". In M5, this id became "jet.IJETNature" causing no end of problems. The fix is to manually add the plugin id as the prefix of the nature's id.
The fix was committed to CVS.
The fix is available in EMF 2.2.0M5.
Move to verified as per bug 206558.