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/JavaSearchPage.java
private static class SearchPatternData {
		private int searchFor;
		private int limitTo;
		private String pattern;
		private boolean isCaseSensitive;
		private IJavaElement javaElement;
		private int scope;
		private IWorkingSet[] workingSets;
		
		public SearchPatternData(int searchFor, int limitTo, boolean isCaseSensitive, String pattern, IJavaElement element) {
			this(searchFor, limitTo, pattern, isCaseSensitive, element, ISearchPageContainer.WORKSPACE_SCOPE, null);
		}
		
		public SearchPatternData(int searchFor, int limitTo, String pattern, boolean isCaseSensitive, IJavaElement element, int scope, IWorkingSet[] workingSets) {
			this.searchFor= searchFor;
			this.limitTo= limitTo;
			this.pattern= pattern;
			this.isCaseSensitive= isCaseSensitive;
			this.scope= scope;
			this.workingSets= workingSets;
			
			setJavaElement(element);
		}
		
		public void setJavaElement(IJavaElement javaElement) {
			this.javaElement= javaElement;
		}