Program: 28327
Project: 28327
Buggy source:
private File createZipFileIfNeeded(ArrayList<String> binDirFiles) throws IOException, ZipFileException {
  String baseRootValue=getSystemProperty(SystemPropertyConstants.PRODUCT_ROOT_PROPERTY);
  File installRoot=new File(baseRootValue);
  File zipFileLocation=null;
  File glassFishZipFile=null;
  if (archive != null) {
    archive=archive.replace('\\','/');
    archiveName=archive.substring(archive.lastIndexOf("String_Node_Str") + 1,archive.length());
    zipFileLocation=new File(archive.substring(0,archive.lastIndexOf("String_Node_Str")));
    glassFishZipFile=new File(archive);
    if (glassFishZipFile.exists() && !create) {
      logger.finer("String_Node_Str" + archive);
      delete=false;
      return glassFishZipFile;
    }
 else     if (!zipFileLocation.canWrite()) {
      throw new IOException("String_Node_Str" + archive);
    }
  }
 else {
    zipFileLocation=new File("String_Node_Str");
    if (!zipFileLocation.canWrite()) {
      zipFileLocation=new File(System.getProperty("String_Node_Str"));
    }
    glassFishZipFile=File.createTempFile("String_Node_Str","String_Node_Str",zipFileLocation);
    String filePath=glassFishZipFile.getCanonicalPath();
    filePath=filePath.replaceAll("String_Node_Str","String_Node_Str");
    archiveName=filePath.substring(filePath.lastIndexOf("String_Node_Str") + 1,filePath.length());
  }
  FileListerRelative lister=new FileListerRelative(installRoot);
  lister.keepEmptyDirectories();
  String[] files=lister.getFiles();
  List<String> resultFiles1=Arrays.asList(files);
  ArrayList<String> resultFiles=new ArrayList<String>(resultFiles1);
  logger.finer("String_Node_Str" + resultFiles.size());
  Iterator<String> iter=resultFiles.iterator();
  while (iter.hasNext()) {
    String fileName=iter.next();
    String fPath=fileName.substring(fileName.lastIndexOf("String_Node_Str") + 1);
    if (fPath.equals(glassFishZipFile.getName())) {
      logger.finer("String_Node_Str" + fileName);
      iter.remove();
      continue;
    }
    if (fileName.contains("String_Node_Str") || fileName.contains("String_Node_Str")) {
      iter.remove();
    }
 else     if (isFileWithinBinDirectory(fileName)) {
      binDirFiles.add(fileName);
    }
  }
  logger.finer("String_Node_Str" + resultFiles.size());
  String[] filesToZip=new String[resultFiles.size()];
  filesToZip=resultFiles.toArray(filesToZip);
  ZipWriter writer=new ZipWriter(FileUtils.safeGetCanonicalPath(glassFishZipFile),installRoot.toString(),filesToZip);
  writer.safeWrite();
  logger.info("String_Node_Str" + FileUtils.safeGetCanonicalPath(glassFishZipFile));
  return glassFishZipFile;
}

Fixed version (ground truth):
private File createZipFileIfNeeded(ArrayList<String> binDirFiles) throws IOException, ZipFileException {
  String baseRootValue=getSystemProperty(SystemPropertyConstants.PRODUCT_ROOT_PROPERTY);
  File installRoot=new File(baseRootValue);
  File zipFileLocation=null;
  File glassFishZipFile=null;
  if (archive != null) {
    archive=archive.replace('\\','/');
    archiveName=archive.substring(archive.lastIndexOf("String_Node_Str") + 1,archive.length());
    zipFileLocation=new File(archive.substring(0,archive.lastIndexOf("String_Node_Str")));
    glassFishZipFile=new File(archive);
    if (glassFishZipFile.exists() && !create) {
      if (logger.isLoggable(Level.FINER))       logger.finer("String_Node_Str" + archive);
      delete=false;
      return glassFishZipFile;
    }
 else     if (!zipFileLocation.canWrite()) {
      throw new IOException("String_Node_Str" + archive);
    }
  }
 else {
    zipFileLocation=new File("String_Node_Str");
    if (!zipFileLocation.canWrite()) {
      zipFileLocation=new File(System.getProperty("String_Node_Str"));
    }
    glassFishZipFile=File.createTempFile("String_Node_Str","String_Node_Str",zipFileLocation);
    String filePath=glassFishZipFile.getCanonicalPath();
    filePath=filePath.replaceAll("String_Node_Str","String_Node_Str");
    archiveName=filePath.substring(filePath.lastIndexOf("String_Node_Str") + 1,filePath.length());
  }
  FileListerRelative lister=new FileListerRelative(installRoot);
  lister.keepEmptyDirectories();
  String[] files=lister.getFiles();
  List<String> resultFiles1=Arrays.asList(files);
  ArrayList<String> resultFiles=new ArrayList<String>(resultFiles1);
  if (logger.isLoggable(Level.FINER))   logger.finer("String_Node_Str" + resultFiles.size());
  Iterator<String> iter=resultFiles.iterator();
  while (iter.hasNext()) {
    String fileName=iter.next();
    String fPath=fileName.substring(fileName.lastIndexOf("String_Node_Str") + 1);
    if (fPath.equals(glassFishZipFile.getName())) {
      if (logger.isLoggable(Level.FINER))       logger.finer("String_Node_Str" + fileName);
      iter.remove();
      continue;
    }
    if (fileName.contains("String_Node_Str") || fileName.contains("String_Node_Str")) {
      iter.remove();
    }
 else     if (isFileWithinBinDirectory(fileName)) {
      binDirFiles.add(fileName);
    }
  }
  if (logger.isLoggable(Level.FINER))   logger.finer("String_Node_Str" + resultFiles.size());
  String[] filesToZip=new String[resultFiles.size()];
  filesToZip=resultFiles.toArray(filesToZip);
  ZipWriter writer=new ZipWriter(FileUtils.safeGetCanonicalPath(glassFishZipFile),installRoot.toString(),filesToZip);
  writer.safeWrite();
  logger.info("String_Node_Str" + FileUtils.safeGetCanonicalPath(glassFishZipFile));
  return glassFishZipFile;
}