Program: 52552
Project: 52552
Buggy source:
public static void main(String[] argv) throws Exception {
  Context c=new Context();
  c.setIgnoreAuthorization(true);
  ItemIterator ii=Item.findAll(c);
  while (ii.hasNext()) {
    boolean skipItem=false;
    Item myItem=ii.next();
    int licenseBundleIndex=-1;
    int primaryBundleIndex=-1;
    System.out.println("String_Node_Str" + myItem.getID());
    Bundle[] myBundles=myItem.getBundles();
    for (int i=0; i < myBundles.length; i++) {
      Bitstream[] bitstreams=myBundles[i].getBitstreams();
      if (bitstreams.length > 1) {
        System.out.println("String_Node_Str");
        skipItem=true;
        break;
      }
      BitstreamFormat bf=bitstreams[0].getFormat();
      if (bf.getShortDescription().equals("String_Node_Str")) {
        System.out.println("String_Node_Str");
        if (licenseBundleIndex == -1) {
          licenseBundleIndex=i;
          System.out.println("String_Node_Str" + i);
        }
 else {
          System.out.println("String_Node_Str");
          skipItem=true;
          break;
        }
      }
 else {
        if (primaryBundleIndex == -1) {
          primaryBundleIndex=i;
          System.out.println("String_Node_Str" + i);
        }
      }
    }
    if (!skipItem) {
      if (primaryBundleIndex != -1) {
        myBundles[primaryBundleIndex].setName("String_Node_Str");
        myBundles[primaryBundleIndex].update();
      }
      if (licenseBundleIndex != -1) {
        myBundles[licenseBundleIndex].setName("String_Node_Str");
        myBundles[licenseBundleIndex].update();
      }
      for (int i=0; i < myBundles.length; i++) {
        Bitstream[] bitstreams=myBundles[i].getBitstreams();
        if (bitstreams.length > 0) {
          if ((i != primaryBundleIndex) && (i != licenseBundleIndex)) {
            myBundles[primaryBundleIndex].addBitstream(bitstreams[0]);
            myItem.removeBundle(myBundles[i]);
            System.out.println("String_Node_Str" + i + "String_Node_Str");
          }
        }
      }
    }
  }
  c.complete();
}

Fixed version (ground truth):
public static void main(String[] argv) throws Exception {
  Context c=new Context();
  c.setIgnoreAuthorization(true);
  ItemIterator ii=null;
  Collection[] collections=Collection.findAll(c);
  System.out.println("String_Node_Str");
  for (int q=0; q < collections.length; q++) {
    ii=collections[q].getItems();
    while (ii.hasNext()) {
      Item myItem=ii.next();
      if (myItem.getOwningCollection() == null) {
        myItem.setOwningCollection(collections[q]);
        myItem.update();
        System.out.println("String_Node_Str" + myItem.getID() + "String_Node_Str"+ collections[q].getID());
      }
    }
  }
  c.commit();
  ii=Item.findAll(c);
  while (ii.hasNext()) {
    boolean skipItem=false;
    Item myItem=ii.next();
    int licenseBundleIndex=-1;
    int primaryBundleIndex=-1;
    System.out.println("String_Node_Str" + myItem.getID());
    Bundle[] myBundles=myItem.getBundles();
    for (int i=0; i < myBundles.length; i++) {
      if (myBundles[i].getName() != null) {
        System.out.println("String_Node_Str");
        skipItem=true;
        break;
      }
      Bitstream[] bitstreams=myBundles[i].getBitstreams();
      if (bitstreams.length > 1) {
        System.out.println("String_Node_Str");
        skipItem=true;
        break;
      }
      BitstreamFormat bf=bitstreams[0].getFormat();
      if (bf.getShortDescription().equals("String_Node_Str")) {
        System.out.println("String_Node_Str");
        if (licenseBundleIndex == -1) {
          licenseBundleIndex=i;
          System.out.println("String_Node_Str" + i);
        }
 else {
          System.out.println("String_Node_Str");
          skipItem=true;
          break;
        }
      }
 else {
        if (primaryBundleIndex == -1) {
          primaryBundleIndex=i;
          System.out.println("String_Node_Str" + i);
        }
      }
    }
    if (!skipItem) {
      if (primaryBundleIndex != -1) {
        myBundles[primaryBundleIndex].setName("String_Node_Str");
        myBundles[primaryBundleIndex].update();
      }
      if (licenseBundleIndex != -1) {
        myBundles[licenseBundleIndex].setName("String_Node_Str");
        myBundles[licenseBundleIndex].update();
      }
      for (int i=0; i < myBundles.length; i++) {
        Bitstream[] bitstreams=myBundles[i].getBitstreams();
        if (bitstreams.length > 0) {
          if ((i != primaryBundleIndex) && (i != licenseBundleIndex)) {
            myBundles[primaryBundleIndex].addBitstream(bitstreams[0]);
            myItem.removeBundle(myBundles[i]);
            System.out.println("String_Node_Str" + i + "String_Node_Str");
          }
        }
      }
    }
  }
  c.complete();
}