Program: 20601
Project: 20601
Buggy source:
/** 
 * @param args
 */
public static void main(String[] args) throws Exception {
  Arguments arguments=new Arguments(args);
  List<String> errors=new ArrayList<String>();
  if (arguments.exists("String_Node_Str","String_Node_Str")) {
    System.out.println("String_Node_Str");
    System.out.println("String_Node_Str");
    System.out.println();
    System.out.println("String_Node_Str");
    System.out.println("String_Node_Str");
    System.out.println();
    System.out.println("String_Node_Str");
    System.out.println("String_Node_Str");
    System.out.println("String_Node_Str");
    System.out.println("String_Node_Str");
    System.out.println("String_Node_Str");
    System.out.println("String_Node_Str");
    System.out.println("String_Node_Str");
    System.out.println("String_Node_Str");
    System.out.println("String_Node_Str");
    System.out.println("String_Node_Str");
    System.out.println("String_Node_Str");
    System.out.println("String_Node_Str");
    System.exit(0);
  }
  String source=arguments.value("String_Node_Str","String_Node_Str");
  if (source == null) {
    errors.add("String_Node_Str");
  }
  String springVersion=arguments.value("String_Node_Str","String_Node_Str","String_Node_Str");
  Collection<String> packages=arguments.valueList("String_Node_Str","String_Node_Str");
  if (packages == null) {
    errors.add("String_Node_Str");
  }
  if (!errors.isEmpty()) {
    for (    String error : errors) {
      System.err.println(error);
    }
    System.err.println("String_Node_Str");
    System.exit(1);
  }
  File sourceDir=new File(source);
  File packageDirs[]=new File[packages.size()];
  int i=0;
  for (  String packageStr : packages) {
    packageStr=packageStr.replaceAll("String_Node_Str",File.separator);
    packageDirs[i]=new File(sourceDir,packageStr);
  }
  ApplicationContextGenerator generator=new ApplicationContextGenerator(springVersion);
  JavaFileFilter javaFileFilter=new JavaFileFilter();
  for (  File directory : packageDirs) {
    File files[]=directory.listFiles(javaFileFilter);
    for (    File file : files) {
      generator.processSourceFile(new FileReader(file));
    }
  }
  Document document=generator.getDocument();
  String xmlString;
{
    TransformerFactory transfac=TransformerFactory.newInstance();
    Transformer trans=transfac.newTransformer();
    trans.setOutputProperty(OutputKeys.INDENT,"String_Node_Str");
    StringWriter sw=new StringWriter();
    StreamResult result=new StreamResult(sw);
    DOMSource domSource=new DOMSource(document);
    trans.transform(domSource,result);
    xmlString=sw.toString();
  }
  System.out.println(xmlString);
}

Fixed version (ground truth):
/** 
 * Runs this utility from the command line.
 * @param args the command line arguments
 */
public static void main(String[] args) throws Exception {
  Arguments arguments=new Arguments(args);
  List<String> errors=new ArrayList<String>();
  if (arguments.exists("String_Node_Str","String_Node_Str")) {
    System.out.println("String_Node_Str");
    System.out.println("String_Node_Str");
    System.out.println();
    System.out.println("String_Node_Str");
    System.out.println("String_Node_Str");
    System.out.println();
    System.out.println("String_Node_Str");
    System.out.println("String_Node_Str");
    System.out.println("String_Node_Str");
    System.out.println("String_Node_Str");
    System.out.println("String_Node_Str");
    System.out.println("String_Node_Str");
    System.out.println("String_Node_Str");
    System.out.println("String_Node_Str");
    System.out.println("String_Node_Str");
    System.out.println("String_Node_Str");
    System.out.println("String_Node_Str");
    System.out.println("String_Node_Str");
    System.exit(0);
  }
  String source=arguments.value("String_Node_Str","String_Node_Str");
  if (source == null) {
    errors.add("String_Node_Str");
  }
  String springVersion=arguments.value("String_Node_Str","String_Node_Str","String_Node_Str");
  Collection<String> packages=arguments.valueList("String_Node_Str","String_Node_Str");
  if (packages == null) {
    errors.add("String_Node_Str");
  }
  if (!errors.isEmpty()) {
    for (    String error : errors) {
      System.err.println(error);
    }
    System.err.println("String_Node_Str");
    System.exit(1);
  }
  File sourceDir=new File(source);
  File packageDirs[]=new File[packages.size()];
  int i=0;
  for (  String packageStr : packages) {
    packageStr=packageStr.replaceAll("String_Node_Str",File.separator);
    packageDirs[i]=new File(sourceDir,packageStr);
    i++;
  }
  ApplicationContextGenerator generator=new ApplicationContextGenerator(springVersion);
  JavaFileFilter javaFileFilter=new JavaFileFilter();
  for (  File directory : packageDirs) {
    File files[]=directory.listFiles(javaFileFilter);
    for (    File file : files) {
      generator.addBean(new FileReader(file));
    }
  }
  Document document=generator.getDocument();
  String xmlString;
{
    TransformerFactory transfac=TransformerFactory.newInstance();
    Transformer trans=transfac.newTransformer();
    trans.setOutputProperty(OutputKeys.INDENT,"String_Node_Str");
    StringWriter sw=new StringWriter();
    StreamResult result=new StreamResult(sw);
    DOMSource domSource=new DOMSource(document);
    trans.transform(domSource,result);
    xmlString=sw.toString();
  }
  System.out.println(xmlString);
}