Program: 8595
Project: 8595
Buggy source:
public static void main(String[] args) throws Exception {
  if (args.length < 1 || args.length > 3 || (args.length == 1 && args[0].contains("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(-1);
  }
  final String script;
  final String file;
  final Properties fileConfiguration=new Properties();
  final Properties commandLineConfiguration=new Properties();
  if (args.length == 1) {
    script=args[0];
    file="String_Node_Str";
  }
 else   if (args.length == 2) {
    if (args[1].startsWith("String_Node_Str")) {
      script=args[0];
      file="String_Node_Str";
      for (      final String property : args[1].substring(2).trim().split("String_Node_Str")) {
        final String key=property.split("String_Node_Str")[0];
        final String value=property.split("String_Node_Str")[1];
        commandLineConfiguration.put(key,value);
      }
    }
 else {
      file=args[0];
      script=args[1];
    }
  }
 else {
    file=args[0];
    script=args[1];
    for (    final String property : args[2].substring(2).trim().split("String_Node_Str")) {
      final String key=property.split("String_Node_Str")[0];
      final String value=property.split("String_Node_Str")[1];
      commandLineConfiguration.put(key,value);
    }
  }
  fileConfiguration.load(new FileInputStream(file));
  final Configuration conf=new Configuration();
  for (  Map.Entry<Object,Object> entry : fileConfiguration.entrySet()) {
    conf.set(entry.getKey().toString(),entry.getValue().toString());
  }
  for (  Map.Entry<Object,Object> entry : commandLineConfiguration.entrySet()) {
    conf.set(entry.getKey().toString(),entry.getValue().toString());
  }
  final FaunusPipeline faunusPipeline=new FaunusPipeline(script,conf);
  final GroovyScriptEngineImpl scriptEngine=new GroovyScriptEngineImpl();
  scriptEngine.eval("String_Node_Str" + Direction.class.getName() + "String_Node_Str");
  scriptEngine.eval("String_Node_Str" + Direction.class.getName() + "String_Node_Str");
  scriptEngine.eval("String_Node_Str" + Direction.class.getName() + "String_Node_Str");
  scriptEngine.eval("String_Node_Str" + Query.Compare.class.getName() + "String_Node_Str");
  scriptEngine.eval("String_Node_Str" + Query.Compare.class.getName() + "String_Node_Str");
  scriptEngine.eval("String_Node_Str" + Query.Compare.class.getName() + "String_Node_Str");
  scriptEngine.eval("String_Node_Str" + Query.Compare.class.getName() + "String_Node_Str");
  scriptEngine.eval("String_Node_Str" + Query.Compare.class.getName() + "String_Node_Str");
  scriptEngine.eval("String_Node_Str" + Query.Compare.class.getName() + "String_Node_Str");
  scriptEngine.eval("String_Node_Str" + Tokens.Order.class.getName() + "String_Node_Str");
  scriptEngine.eval("String_Node_Str" + Tokens.Order.class.getName() + "String_Node_Str");
  scriptEngine.put("String_Node_Str",faunusPipeline);
  final FaunusPipeline pipeline=((FaunusPipeline)scriptEngine.eval(script)).done();
  final FaunusCompiler compiler=pipeline.compiler;
  compiler.completeSequence();
  int result=ToolRunner.run(compiler,args);
  System.exit(result);
}

Fixed version (ground truth):
public static void main(String[] args) throws Exception {
  if (args.length < 1 || args.length > 3 || (args.length == 1 && args[0].contains("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(-1);
  }
  final String script;
  final String file;
  final Properties fileConfiguration=new Properties();
  final Properties commandLineConfiguration=new Properties();
  if (args.length == 1) {
    script=args[0];
    file="String_Node_Str";
  }
 else   if (args.length == 2) {
    if (args[1].startsWith("String_Node_Str")) {
      script=args[0];
      file="String_Node_Str";
      for (      final String property : args[1].substring(2).trim().split("String_Node_Str")) {
        commandLineConfiguration.put(property.split("String_Node_Str")[0],property.split("String_Node_Str")[1]);
      }
    }
 else {
      file=args[0];
      script=args[1];
    }
  }
 else {
    file=args[0];
    script=args[1];
    for (    final String property : args[2].substring(2).trim().split("String_Node_Str")) {
      commandLineConfiguration.put(property.split("String_Node_Str")[0],property.split("String_Node_Str")[1]);
    }
  }
  fileConfiguration.load(new FileInputStream(file));
  final Configuration conf=new Configuration();
  for (  Map.Entry<Object,Object> entry : fileConfiguration.entrySet()) {
    conf.set(entry.getKey().toString(),entry.getValue().toString());
  }
  for (  Map.Entry<Object,Object> entry : commandLineConfiguration.entrySet()) {
    conf.set(entry.getKey().toString(),entry.getValue().toString());
  }
  final FaunusPipeline faunusPipeline=new FaunusPipeline(script,conf);
  final GroovyScriptEngineImpl scriptEngine=new GroovyScriptEngineImpl();
  scriptEngine.eval("String_Node_Str" + Direction.class.getName() + "String_Node_Str");
  scriptEngine.eval("String_Node_Str" + Direction.class.getName() + "String_Node_Str");
  scriptEngine.eval("String_Node_Str" + Direction.class.getName() + "String_Node_Str");
  scriptEngine.eval("String_Node_Str" + Query.Compare.class.getName() + "String_Node_Str");
  scriptEngine.eval("String_Node_Str" + Query.Compare.class.getName() + "String_Node_Str");
  scriptEngine.eval("String_Node_Str" + Query.Compare.class.getName() + "String_Node_Str");
  scriptEngine.eval("String_Node_Str" + Query.Compare.class.getName() + "String_Node_Str");
  scriptEngine.eval("String_Node_Str" + Query.Compare.class.getName() + "String_Node_Str");
  scriptEngine.eval("String_Node_Str" + Query.Compare.class.getName() + "String_Node_Str");
  scriptEngine.eval("String_Node_Str" + Tokens.Order.class.getName() + "String_Node_Str");
  scriptEngine.eval("String_Node_Str" + Tokens.Order.class.getName() + "String_Node_Str");
  scriptEngine.put("String_Node_Str",faunusPipeline);
  final FaunusPipeline pipeline=((FaunusPipeline)scriptEngine.eval(script)).done();
  final FaunusCompiler compiler=pipeline.compiler;
  compiler.completeSequence();
  int result=ToolRunner.run(compiler,args);
  System.exit(result);
}