Program: 31065
Project: 31065
Buggy source:
public void Annotate(boolean ClearExistingLabels,FPGAReport reporter){
  if (Annotated) {
    reporter.AddInfo("String_Node_Str");
    return;
  }
  SortedSet<Component> comps=new TreeSet<Component>(new AnnotateComparator());
  HashMap<String,AutoLabel> lablers=new HashMap<String,AutoLabel>();
  Set<String> LabelNames=new HashSet<String>();
  for (  Component comp : getNonWires()) {
    if (comp.getFactory() instanceof Tunnel)     continue;
    AttributeSet attrs=comp.getAttributeSet();
    if (attrs.containsAttribute(StdAttr.LABEL)) {
      String label=attrs.getValue(StdAttr.LABEL);
      if (!label.isEmpty()) {
        if (LabelNames.contains(label.toUpperCase())) {
          SetAttributeAction act=new SetAttributeAction(this,Strings.getter("String_Node_Str"));
          act.set(comp,StdAttr.LABEL,"String_Node_Str");
          proj.doAction(act);
          reporter.AddSevereWarning("String_Node_Str" + this.getName() + "String_Node_Str"+ label);
        }
 else {
          LabelNames.add(label.toUpperCase());
        }
      }
    }
    if (comp.getFactory().RequiresNonZeroLabel()) {
      if (ClearExistingLabels) {
        reporter.AddInfo("String_Node_Str" + this.getName() + "String_Node_Str"+ comp.getAttributeSet().getValue(StdAttr.LABEL));
        comp.getAttributeSet().setValue(StdAttr.LABEL,"String_Node_Str");
      }
      if (comp.getAttributeSet().getValue(StdAttr.LABEL).isEmpty()) {
        comps.add(comp);
        String ComponentName=GetAnnotationName(comp);
        if (!lablers.containsKey(ComponentName)) {
          lablers.put(ComponentName,new AutoLabel(ComponentName + "String_Node_Str",this));
        }
      }
    }
    if (comp.getFactory() instanceof SubcircuitFactory) {
      SubcircuitFactory sub=(SubcircuitFactory)comp.getFactory();
      sub.getSubcircuit().Annotate(ClearExistingLabels,reporter);
    }
  }
  for (  Component comp : comps) {
    String ComponentName=GetAnnotationName(comp);
    if (!lablers.containsKey(ComponentName) || !lablers.get(ComponentName).hasNext(this)) {
      reporter.AddFatalError("String_Node_Str");
      return;
    }
 else {
      String NewLabel=lablers.get(ComponentName).GetNext(this,comp.getFactory());
      SetAttributeAction act=new SetAttributeAction(this,Strings.getter("String_Node_Str"));
      act.set(comp,StdAttr.LABEL,NewLabel);
      proj.doAction(act);
      reporter.AddInfo("String_Node_Str" + this.getName() + "String_Node_Str"+ NewLabel);
    }
  }
  Annotated=true;
}

Fixed version (ground truth):
public void Annotate(boolean ClearExistingLabels,FPGAReport reporter){
  if (Annotated) {
    reporter.AddInfo("String_Node_Str");
    return;
  }
  SortedSet<Component> comps=new TreeSet<Component>(new AnnotateComparator());
  HashMap<String,AutoLabel> lablers=new HashMap<String,AutoLabel>();
  Set<String> LabelNames=new HashSet<String>();
  Set<String> Subcircuits=new HashSet<String>();
  for (  Component comp : getNonWires()) {
    if (comp.getFactory() instanceof Tunnel)     continue;
    AttributeSet attrs=comp.getAttributeSet();
    if (attrs.containsAttribute(StdAttr.LABEL)) {
      String label=attrs.getValue(StdAttr.LABEL);
      if (!label.isEmpty()) {
        if (LabelNames.contains(label.toUpperCase())) {
          SetAttributeAction act=new SetAttributeAction(this,Strings.getter("String_Node_Str"));
          act.set(comp,StdAttr.LABEL,"String_Node_Str");
          proj.doAction(act);
          reporter.AddSevereWarning("String_Node_Str" + this.getName() + "String_Node_Str"+ label);
        }
 else {
          LabelNames.add(label.toUpperCase());
        }
      }
    }
    if (comp.getFactory().RequiresNonZeroLabel()) {
      if (ClearExistingLabels) {
        reporter.AddInfo("String_Node_Str" + this.getName() + "String_Node_Str"+ comp.getAttributeSet().getValue(StdAttr.LABEL));
        SetAttributeAction act=new SetAttributeAction(this,Strings.getter("String_Node_Str"));
        act.set(comp,StdAttr.LABEL,"String_Node_Str");
        proj.doAction(act);
      }
      if (comp.getAttributeSet().getValue(StdAttr.LABEL).isEmpty()) {
        comps.add(comp);
        String ComponentName=GetAnnotationName(comp);
        if (!lablers.containsKey(ComponentName)) {
          lablers.put(ComponentName,new AutoLabel(ComponentName + "String_Node_Str",this));
        }
      }
    }
    if (comp.getFactory() instanceof SubcircuitFactory) {
      SubcircuitFactory sub=(SubcircuitFactory)comp.getFactory();
      if (!Subcircuits.contains(sub.getName()))       Subcircuits.add(sub.getName());
    }
  }
  for (  Component comp : comps) {
    String ComponentName=GetAnnotationName(comp);
    if (!lablers.containsKey(ComponentName) || !lablers.get(ComponentName).hasNext(this)) {
      reporter.AddFatalError("String_Node_Str");
      return;
    }
 else {
      String NewLabel=lablers.get(ComponentName).GetNext(this,comp.getFactory());
      SetAttributeAction act=new SetAttributeAction(this,Strings.getter("String_Node_Str"));
      act.set(comp,StdAttr.LABEL,NewLabel);
      proj.doAction(act);
      reporter.AddInfo("String_Node_Str" + this.getName() + "String_Node_Str"+ NewLabel);
    }
  }
  Annotated=true;
  for (  String subs : Subcircuits) {
    Circuit circ=proj.getLogisimFile().getCircuit(subs);
    circ.Annotate(ClearExistingLabels,reporter);
  }
}