Program: 64400
Project: 64400
Buggy source:
@Override protected Object doMainTask(TaskMonitor monitor,ObjectRepository repository){
  String streamCLI=this.streamOption.getValueAsCLIString();
  String fileCLI=this.arffFileOption.getValueAsCLIString();
  for (int i=0; i < this.numStreamsOption.getValue(); i++) {
    String s=streamCLI;
    if (this.randomFlagOne.isSet()) {
      s=s.concat("String_Node_Str" + randomOneOption.getValue() + "String_Node_Str"+ WriteMultipleStreamsToARFF.primesAndBiprimes[i]);
    }
    if (this.randomFlagTwo.isSet()) {
      System.out.println("String_Node_Str" + randomTwoOption.getValue());
      s=s.concat("String_Node_Str" + randomTwoOption.getValue() + "String_Node_Str"+ WriteMultipleStreamsToARFF.primesAndBiprimes[i / WriteMultipleStreamsToARFF.primesAndBiprimes.length]);
    }
    this.streamOption.setValueViaCLIString(s);
    s=fileCLI;
    if (s.substring(s.length() - 5,s.length()).equals("String_Node_Str")) {
      s=s.substring(0,s.length() - 5);
    }
    s=s.concat("String_Node_Str" + i + "String_Node_Str");
    this.arffFileOption.setValueViaCLIString(s);
    File destFile=this.arffFileOption.getFile();
    if (destFile != null) {
      try {
        Writer w=new BufferedWriter(new FileWriter(destFile));
        System.out.println("String_Node_Str" + this.streamOption.getValueAsCLIString() + "String_Node_Str"+ this.arffFileOption.getValueAsCLIString());
        monitor.setCurrentActivityDescription("String_Node_Str" + this.streamOption.getValueAsCLIString() + "String_Node_Str"+ this.arffFileOption.getValueAsCLIString());
        if (!this.suppressHeaderOption.isSet()) {
          w.write(stream.getHeader().toString());
          w.write("String_Node_Str");
        }
        int numWritten=0;
        while ((numWritten < this.maxInstancesOption.getValue()) && stream.hasMoreInstances()) {
          w.write(stream.nextInstance().getData().toString());
          w.write("String_Node_Str");
          numWritten++;
        }
        w.close();
      }
 catch (      Exception ex) {
        throw new RuntimeException("String_Node_Str" + destFile,ex);
      }
    }
  }
  return "String_Node_Str";
}

Fixed version (ground truth):
@Override protected Object doMainTask(TaskMonitor monitor,ObjectRepository repository){
  String streamCLI=this.streamOption.getValueAsCLIString();
  String fileCLI=this.arffFileOption.getValueAsCLIString();
  stream=(InstanceStream)getPreparedClassOption(this.streamOption);
  for (int i=0; i < this.numStreamsOption.getValue(); i++) {
    String s=streamCLI;
    if (this.randomFlagOne.isSet()) {
      s=s.concat("String_Node_Str" + randomOneOption.getValue() + "String_Node_Str"+ WriteMultipleStreamsToARFF.primesAndBiprimes[i]);
    }
    if (this.randomFlagTwo.isSet()) {
      System.out.println("String_Node_Str" + randomTwoOption.getValue());
      s=s.concat("String_Node_Str" + randomTwoOption.getValue() + "String_Node_Str"+ WriteMultipleStreamsToARFF.primesAndBiprimes[i / WriteMultipleStreamsToARFF.primesAndBiprimes.length]);
    }
    this.streamOption.setValueViaCLIString(s);
    s=fileCLI;
    if (s.substring(s.length() - 5,s.length()).equals("String_Node_Str")) {
      s=s.substring(0,s.length() - 5);
    }
    s=s.concat("String_Node_Str" + i + "String_Node_Str");
    this.arffFileOption.setValueViaCLIString(s);
    File destFile=this.arffFileOption.getFile();
    if (destFile != null) {
      try {
        Writer w=new BufferedWriter(new FileWriter(destFile));
        System.out.println("String_Node_Str" + this.streamOption.getValueAsCLIString() + "String_Node_Str"+ this.arffFileOption.getValueAsCLIString());
        monitor.setCurrentActivityDescription("String_Node_Str" + this.streamOption.getValueAsCLIString() + "String_Node_Str"+ this.arffFileOption.getValueAsCLIString());
        if (!this.suppressHeaderOption.isSet()) {
          w.write(stream.getHeader().toString());
          w.write("String_Node_Str");
        }
        int numWritten=0;
        while ((numWritten < this.maxInstancesOption.getValue()) && stream.hasMoreInstances()) {
          w.write(stream.nextInstance().getData().toString());
          w.write("String_Node_Str");
          numWritten++;
        }
        w.close();
      }
 catch (      Exception ex) {
        throw new RuntimeException("String_Node_Str" + destFile,ex);
      }
    }
  }
  return "String_Node_Str";
}