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/ui/actions/FindWriteReferencesInProjectAction.java
void init() {
		setText(SearchMessages.Search_FindWriteReferencesInProjectAction_label); 
		setToolTipText(SearchMessages.Search_FindWriteReferencesInProjectAction_tooltip); 
		setImageDescriptor(JavaPluginImages.DESC_OBJS_SEARCH_REF);
		PlatformUI.getWorkbench().getHelpSystem().setHelp(this, IJavaHelpContextIds.FIND_WRITE_REFERENCES_IN_PROJECT_ACTION);
	}
	
	IJavaSearchScope getScope(IJavaElement element) {
		JavaSearchScopeFactory instance= JavaSearchScopeFactory.getInstance();
		JavaEditor editor= getEditor();
		if (editor != null) {
			return instance.createJavaProjectSearchScope(editor.getEditorInput(), JavaSearchPage.getSearchJRE());
		} else {
			return instance.createJavaProjectSearchScope(element.getJavaProject(), JavaSearchPage.getSearchJRE());
		}
	}
	String getScopeDescription(IJavaElement element) {
		JavaSearchScopeFactory instance= JavaSearchScopeFactory.getInstance();
		JavaEditor editor= getEditor();
		if (editor != null) {
			return instance.getProjectScopeDescription(editor.getEditorInput());
		} else {
			return instance.getProjectScopeDescription(element.getJavaProject());
		}
	}
	protected JavaSearchQuery createJob(IJavaElement element) {
		return new JavaSearchQuery(new ElementQuerySpecification(element, getLimitTo(), getScope(element), getScopeDescription(element)));
	}
}