Program: 75548
Project: 75548
Buggy source:
/** 
 * Write out the C (.i, .h, interface Header) files. Sample option arguments: <code>-p wjtp.writeJimple1 outDir:jimple1</code>
 * @param phaseName The name of the phase, for example<code>wjtp.writeJimple2</code>.
 * @param options The options Map.  This method uses the<code>outdir</code> option to specify where the .jimple file should be written
 */
public void internalTransform(String phaseName,Map options){
  System.out.println("String_Node_Str" + phaseName + "String_Node_Str"+ options+ "String_Node_Str");
  String outDir=soot.Options.getString(options,"String_Node_Str");
  String mainFile=soot.Options.getString(options,"String_Node_Str") + "String_Node_Str";
  OverriddenMethodGenerator.init();
  ArrayList classList=new ArrayList();
  for (Iterator classes=Scene.v().getApplicationClasses().iterator(); classes.hasNext(); classList.add(classes.next()))   ;
  StringBuffer sourcesList=new StringBuffer();
  for (Iterator sootClasses=classList.iterator(); sootClasses.hasNext(); ) {
    SootClass sootClass=(SootClass)sootClasses.next();
    String fileName;
    if (!outDir.equals("String_Node_Str")) {
      File outDirFile=new File(outDir);
      if (!outDirFile.isDirectory()) {
        outDirFile.mkdirs();
      }
      fileName=outDir + System.getProperty("String_Node_Str");
    }
 else {
      fileName="String_Node_Str";
    }
    fileName+=sootClass.getName();
    HeaderFileGenerator hGenerator=new HeaderFileGenerator();
    CodeFileGenerator cGenerator=new CodeFileGenerator();
    StubFileGenerator sGenerator=new StubFileGenerator();
    CNames.setup();
    RequiredFileGenerator RFG=new RequiredFileGenerator();
    String classPath=Scene.v().getSootClassPath();
    System.out.println("String_Node_Str" + classPath);
    Options.v().put("String_Node_Str","String_Node_Str");
    Options.v().put("String_Node_Str","String_Node_Str");
    Options.v().put("String_Node_Str","String_Node_Str");
    RFG.init(classPath,sootClass.getName());
    System.out.println("String_Node_Str" + mainFile);
    System.out.println("String_Node_Str" + sootClass.getName());
    boolean isMainClass=false;
    MainFileGenerator mGenerator=null;
    if (mainFile.equals(sootClass.getName())) {
      isMainClass=true;
      mGenerator=new MainFileGenerator();
    }
    System.out.println("String_Node_Str" + fileName);
    String code=null;
    code=sGenerator.generate(sootClass);
    FileHandler.write(fileName + StubFileGenerator.stubFileNameSuffix(),code);
    code=hGenerator.generate(sootClass);
    FileHandler.write(fileName + "String_Node_Str",code);
    code=cGenerator.generate(sootClass);
    FileHandler.write(fileName + "String_Node_Str",code);
    sourcesList.append("String_Node_Str" + fileName + "String_Node_Str");
    try {
      RFG.generateTransitiveClosureOf(classPath,sootClass.getName());
    }
 catch (    IOException exception) {
      throw new RuntimeException("String_Node_Str" + "String_Node_Str");
    }
    if (isMainClass) {
      code=mGenerator.generate(sootClass);
      FileHandler.write(fileName + "String_Node_Str",code);
    }
    System.out.println("String_Node_Str" + fileName);
  }
  MakefileWriter.addMakefileSubstitution("String_Node_Str",sourcesList.toString());
  _completedTransform=true;
}

Fixed version (ground truth):
/** 
 * Write out the C (.i, .h, interface Header) files. Sample option arguments: <code>-p wjtp.writeJimple1 outDir:jimple1</code>
 * @param phaseName The name of the phase, for example<code>wjtp.writeJimple2</code>.
 * @param options The options Map.  This method uses the<code>outdir</code> option to specify where the .jimple file should be written
 */
public void internalTransform(String phaseName,Map options){
  System.out.println("String_Node_Str" + phaseName + "String_Node_Str"+ options+ "String_Node_Str");
  String outDir=soot.Options.getString(options,"String_Node_Str");
  String mainFile=soot.Options.getString(options,"String_Node_Str") + "String_Node_Str";
  OverriddenMethodGenerator.init();
  ArrayList classList=new ArrayList();
  for (Iterator classes=Scene.v().getApplicationClasses().iterator(); classes.hasNext(); classList.add(classes.next()))   ;
  StringBuffer sourcesList=new StringBuffer();
  for (Iterator sootClasses=classList.iterator(); sootClasses.hasNext(); ) {
    SootClass sootClass=(SootClass)sootClasses.next();
    String fileName;
    fileName=CNames.classNameToFileName(sootClass.getName());
    HeaderFileGenerator hGenerator=new HeaderFileGenerator();
    CodeFileGenerator cGenerator=new CodeFileGenerator();
    StubFileGenerator sGenerator=new StubFileGenerator();
    CNames.setup();
    RequiredFileGenerator RFG=new RequiredFileGenerator();
    String classPath=Scene.v().getSootClassPath();
    System.out.println("String_Node_Str" + classPath);
    Options.v().put("String_Node_Str","String_Node_Str");
    Options.v().put("String_Node_Str","String_Node_Str");
    Options.v().put("String_Node_Str","String_Node_Str");
    RFG.init(classPath,sootClass.getName());
    System.out.println("String_Node_Str" + mainFile);
    System.out.println("String_Node_Str" + sootClass.getName());
    boolean isMainClass=false;
    MainFileGenerator mGenerator=null;
    if (mainFile.equals(sootClass.getName())) {
      isMainClass=true;
      mGenerator=new MainFileGenerator();
    }
    System.out.println("String_Node_Str" + fileName);
    String code=null;
    code=sGenerator.generate(sootClass);
    FileHandler.write(fileName + StubFileGenerator.stubFileNameSuffix(),code);
    code=hGenerator.generate(sootClass);
    FileHandler.write(fileName + "String_Node_Str",code);
    code=cGenerator.generate(sootClass);
    FileHandler.write(fileName + "String_Node_Str",code);
    sourcesList.append("String_Node_Str" + fileName + "String_Node_Str");
    try {
      RFG.generateTransitiveClosureOf(classPath,sootClass.getName());
    }
 catch (    IOException exception) {
      throw new RuntimeException("String_Node_Str" + "String_Node_Str");
    }
    if (isMainClass) {
      code=mGenerator.generate(sootClass);
      FileHandler.write(fileName + "String_Node_Str",code);
    }
    System.out.println("String_Node_Str" + fileName);
  }
  MakefileWriter.addMakefileSubstitution("String_Node_Str",sourcesList.toString());
  _completedTransform=true;
}