Program: 12264
Project: 12264
Buggy source:
private void synchronize(){
  if (sourceChanged) {
    removeAllWmes(io,memory);
    sourceChanged=false;
  }
  if (source == null) {
    return;
  }
  if (rootNode == null) {
    rootNode=new SoarMemoryNode(io.getInputLink());
  }
  Set<String> oldPaths=new HashSet<String>(memory.keySet());
  Set<String> newPaths=new HashSet<String>();
  Set<String> newInternalPaths=new HashSet<String>();
  for (  String fullPath : source.getPaths()) {
    String[] pathElements=fullPath.split("String_Node_Str");
    String tmp="String_Node_Str";
    for (int ix=0; ix < pathElements.length; ++ix) {
      if (ix > 0) {
        tmp+="String_Node_Str";
      }
      tmp+=pathElements[ix];
      newPaths.add(tmp);
      oldPaths.remove(tmp);
      if (ix < pathElements.length - 1) {
        newInternalPaths.add(tmp);
      }
    }
  }
  List<String> oldPathsByLength=new ArrayList<String>(oldPaths);
  Collections.sort(oldPathsByLength,decreasingLengthComparator);
  for (  String path : oldPathsByLength) {
    SoarMemoryNode oldNode=memory.remove(path);
    oldNode.remove(io);
  }
  List<String> newPathsByLength=new ArrayList<String>(newPaths);
  Collections.sort(newPathsByLength,increasingLengthComparator);
  for (  String path : newPathsByLength) {
    SoarMemoryNode oldNode=memory.get(path);
    SoarMemoryNode parentNode=memory.get(getParentPath(path));
    if (parentNode == null) {
      parentNode=rootNode;
    }
    String name=getNameFromPath(path);
    MemoryNode newNode;
    if (!newInternalPaths.contains(path)) {
      newNode=((DefaultQMemory)source).getNode(path);
    }
 else {
      newNode=new MemoryNode();
      newNode.clearValue();
    }
    if (oldNode == null) {
      oldNode=new SoarMemoryNode(name);
      memory.put(path,oldNode);
    }
    oldNode.setParentNode(parentNode);
    oldNode.synchronizeToMemoryNode(io,newNode);
  }
  io.asynchronousInputReady();
}

Fixed version (ground truth):
private void synchronize(){
  if (sourceChanged) {
    removeAllWmes(io,memory);
    sourceChanged=false;
  }
  if (source == null) {
    return;
  }
  if (rootNode == null) {
    rootNode=new SoarMemoryNode(io.getInputLink());
  }
  final Set<String> oldPaths=new HashSet<String>(memory.keySet());
  final Set<String> newPaths=new HashSet<String>();
  final Set<String> newInternalPaths=new HashSet<String>();
  for (  String fullPath : source.getPaths()) {
    final String[] pathElements=fullPath.split("String_Node_Str");
    String tmp="String_Node_Str";
    for (int ix=0; ix < pathElements.length; ++ix) {
      if (ix > 0) {
        tmp+="String_Node_Str";
      }
      tmp+=pathElements[ix];
      newPaths.add(tmp);
      oldPaths.remove(tmp);
      if (ix < pathElements.length - 1) {
        newInternalPaths.add(tmp);
      }
    }
  }
  final List<String> oldPathsByLength=new ArrayList<String>(oldPaths);
  Collections.sort(oldPathsByLength,decreasingLengthComparator);
  for (  String path : oldPathsByLength) {
    final SoarMemoryNode oldNode=memory.remove(path);
    oldNode.remove(io);
  }
  final List<String> newPathsByLength=new ArrayList<String>(newPaths);
  Collections.sort(newPathsByLength,increasingLengthComparator);
  for (  String path : newPathsByLength) {
    SoarMemoryNode oldNode=memory.get(path);
    SoarMemoryNode parentNode=memory.get(getParentPath(path));
    if (parentNode == null) {
      parentNode=rootNode;
    }
    final String name=getNameFromPath(path);
    final MemoryNode newNode;
    if (!newInternalPaths.contains(path)) {
      newNode=((DefaultQMemory)source).getNode(path);
    }
 else {
      newNode=new MemoryNode();
      newNode.clearValue();
    }
    if (oldNode == null) {
      oldNode=new SoarMemoryNode(name);
      memory.put(path,oldNode);
    }
    oldNode.setParentNode(parentNode);
    oldNode.synchronizeToMemoryNode(io,newNode);
  }
}