I too use the new GWT Plugin, not the deprecated Google one. 
I had to downgrade Eclipse to be able to work and don't remember the exact 
complete stack trace, but the top was certainly something like
org.eclipse.jdt.internal.core.JavaProject.computePackageFragmentRoots([Lorg/eclipse/jdt/core/IClasspathEntry;ZLjava/util/Map;)[Lorg/eclipse/jdt/core/IPackageFragmentRoot;


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