Bug 65240 Hierarchical layout: Problems with inclusion filters [package explorer]
org.eclipse.jdt.ui/ui/org/eclipse/jdt/internal/ui/packageview/PackageExplorerContentProvider.java
IJavaProject project= (IJavaProject)parentElement;
				return rootsAndContainers(project, children);
			}
			else
				return children;
		} catch (CoreException e) {
			return NO_CHILDREN;
		}
	}
	private Object[] rootsAndContainers(IJavaProject project, Object[] roots) throws JavaModelException { 
		List result= new ArrayList(roots.length);
		Set containers= new HashSet(roots.length);
		Set containedRoots= new HashSet(roots.length); 
		
		IClasspathEntry[] entries= project.getRawClasspath();
		for (int i= 0; i < entries.length; i++) {
			IClasspathEntry entry= entries[i];
			if (entry != null && entry.getEntryKind() == IClasspathEntry.CPE_CONTAINER) { 
				IPackageFragmentRoot[] roots1= project.findPackageFragmentRoots(entry);
				containedRoots.addAll(Arrays.asList(roots1));
				containers.add(entry);
			}
		}
		for (int i= 0; i < roots.length; i++) {
			if (roots[i] instanceof IPackageFragmentRoot) {
				if (!containedRoots.contains(roots[i])) {
					result.add(roots[i]);
				}
			} else {
				result.add(roots[i]);