Bug 68011 [java search] "Search the JRE System Libraries" looks like a local preference but behaves as a global one... [search]
org.eclipse.jdt.ui/ui/org/eclipse/jdt/internal/ui/search/JavaSearchScopeFactory.java
if (workingSets.length > 0)
				return workingSets;
		}
		return null;
	}
	public IJavaSearchScope createJavaSearchScope(IWorkingSet[] workingSets, boolean includeJRE) {
		if (workingSets == null || workingSets.length < 1)
			return EMPTY_SCOPE;
		Set javaElements= new HashSet(workingSets.length * 10);
		for (int i= 0; i < workingSets.length; i++) {
			IWorkingSet workingSet= workingSets[i];
			if (workingSet.isEmpty() && workingSet.isAggregateWorkingSet()) {
				return createWorkspaceScope(includeJRE);
			}
			addJavaElements(javaElements, workingSet);
		}
		return createJavaSearchScope(javaElements, includeJRE);
	}
	
	public IJavaSearchScope createJavaSearchScope(IWorkingSet workingSet, boolean includeJRE) {
		Set javaElements= new HashSet(10);
		if (workingSet.isEmpty() && workingSet.isAggregateWorkingSet()) {
			return createWorkspaceScope(includeJRE);
		}
		addJavaElements(javaElements, workingSet);
		return createJavaSearchScope(javaElements, includeJRE);
	}
	public IJavaSearchScope createJavaSearchScope(IResource[] resources, boolean includeJRE) {
		if (resources == null)
			return EMPTY_SCOPE;