Back to THashMap, which is less memory hungry than LinkedHashMap and ensure locality by sorting things. Please note, actual VirtualFile implementation does have an effective hashCode implementation

java/java-impl/src/com/intellij/codeInspection/reference/RefJavaManagerImpl.java

@@ -33,8 +33,6 @@ import gnu.trove.THashMap;
 import org.jdom.Element;
 import org.jetbrains.annotations.Nullable;
 
-import java.util.Map;
-
 /**
  * @author anna
  * Date: 20-Dec-2007
@@ -135,8 +133,7 @@ public class RefJavaManagerImpl extends RefJavaManager {
         refPackage.accept(visitor);
       }
     }
-    final Map<PsiAnchor, RefElement> refTable = myRefManager.getRefTable();
-    for (RefElement refElement : refTable.values()) {
+    for (RefElement refElement : myRefManager.getSortedElements()) {
       if (refElement instanceof RefClass) {
         RefClass refClass = (RefClass)refElement;
         RefMethod refDefaultConstructor = refClass.getDefaultConstructor();