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Using N20060425-0010 I checked out org.eclipse.core.runtime.compatibility.registry from CVS HEAD. The plugin has folder \classes that shows in the Resource view, but not in the Package Explorer. The folder used to show up in the PackageExplorer in the earlier builds.
'classes' is referenced from the PDE container (where it still can be seen as child). I guess it could still show up as non-java resource in the package explorer that should only hide direct class, source and output folders. This is decided by the Java model which doesn't return 'classes' as non-Java resource. Moving to jdt.core to decide if this is wanted or not.
Reproduced with 3.3 RC4
Since 'classes' is on the build path, it isn't a non-Java resource, but a library folder. Thus it appears as such under the 'Plug-in Dependencies' node. Works as designed.