Program: 21346
Project: 21346
Buggy source:
@Override public void run(){
  int c=0;
  if (IS_RUNNING)   logger.warning("String_Node_Str");
  while (IS_RUNNING) {
    if (c++ == 1200)     IS_RUNNING=false;
    try {
      Thread.sleep(1000);
    }
 catch (    InterruptedException e) {
      e.printStackTrace();
    }
  }
  IS_RUNNING=true;
  JUnrar unrar=getUnrar();
  if (lastFinishedDownload == null) {
    LinkedList<String> folders=new LinkedList<String>();
    if (JDUtilities.getConfiguration().getBooleanProperty(Configuration.PARAM_USE_PACKETNAME_AS_SUBFOLDER,false)) {
      Iterator<DownloadLink> iter=JDUtilities.getController().getFinishedLinks().iterator();
      while (iter.hasNext()) {
        DownloadLink element=(DownloadLink)iter.next();
        logger.info("String_Node_Str" + element.getFileOutput());
        File folder=new File(element.getFileOutput()).getParentFile();
        logger.info("String_Node_Str" + folder);
        if (folder.exists()) {
          if (folders.indexOf(folder.getAbsolutePath()) == -1) {
            logger.info("String_Node_Str" + folder.getAbsolutePath());
            folders.add(folder.getAbsolutePath());
          }
        }
      }
    }
    folders.add(JDUtilities.getConfiguration().getDefaultDownloadDirectory());
    logger.info("String_Node_Str" + folders);
    unrar.setFolders(folders);
  }
  LinkedList<String> followingFiles=new LinkedList<String>();
  Iterator<DownloadLink> ff=JDUtilities.getController().getDownloadLinks().iterator();
  while (ff.hasNext()) {
    DownloadLink dl=ff.next();
    if (dl.getStatus() != DownloadLink.STATUS_DONE && dl.getStatus() != DownloadLink.STATUS_DONE) {
      followingFiles.add(dl.getName());
    }
  }
  unrar.followingFiles=followingFiles.toArray(new String[followingFiles.size()]);
  LinkedList<File> unpacked=unrar.unrar();
  Iterator<File> iter=unpacked.iterator();
  LinkedList<mergeFile> mergeFiles=new LinkedList<mergeFile>();
  while (iter.hasNext()) {
    File file=(File)iter.next();
    if (!mergeFiles.contains((mergeFile)file))     mergeFiles.add((mergeFile)file);
    if (JDUtilities.getController().isContainerFile(file)) {
      if (JDUtilities.getConfiguration().getBooleanProperty(Configuration.PARAM_RELOADCONTAINER,true))       JDUtilities.getController().loadContainerFile(file);
    }
  }
  Boolean DELETE_MERGEDFILES=JDUtilities.getConfiguration().getBooleanProperty(Unrar.PROPERTY_DELETE_MERGEDFILES,true);
  if (lastFinishedDownload != null && JDUtilities.getConfiguration().getBooleanProperty(Unrar.PROPERTY_USE_HJMERGE,true)) {
    Merge.mergeIt(new File(lastFinishedDownload.getFileOutput()),unrar.followingFiles,DELETE_MERGEDFILES,unrar.extractFolder);
    Iterator<mergeFile> miter=mergeFiles.iterator();
    while (miter.hasNext()) {
      mergeFile mergeFile=(mergeFile)miter.next();
      Merge.mergeIt(mergeFile,unrar.followingFiles,DELETE_MERGEDFILES,unrar.extractFolder);
    }
  }
  IS_RUNNING=false;
  this.setCallCode(Interaction.INTERACTION_CALL_SUCCESS);
  Interaction.handleInteraction(Interaction.INTERACTION_AFTER_UNRAR,null);
}

Fixed version (ground truth):
@Override public void run(){
  int c=0;
  if (IS_RUNNING)   logger.warning("String_Node_Str");
  while (IS_RUNNING) {
    if (c++ == 1200)     IS_RUNNING=false;
    try {
      Thread.sleep(1000);
    }
 catch (    InterruptedException e) {
      e.printStackTrace();
    }
  }
  IS_RUNNING=true;
  JUnrar unrar=getUnrar();
  if (lastFinishedDownload == null) {
    LinkedList<String> folders=new LinkedList<String>();
    if (JDUtilities.getConfiguration().getBooleanProperty(Configuration.PARAM_USE_PACKETNAME_AS_SUBFOLDER,false)) {
      Iterator<DownloadLink> iter=JDUtilities.getController().getFinishedLinks().iterator();
      while (iter.hasNext()) {
        DownloadLink element=(DownloadLink)iter.next();
        logger.info("String_Node_Str" + element.getFileOutput());
        File folder=new File(element.getFileOutput()).getParentFile();
        logger.info("String_Node_Str" + folder);
        if (folder.exists()) {
          if (folders.indexOf(folder.getAbsolutePath()) == -1) {
            logger.info("String_Node_Str" + folder.getAbsolutePath());
            folders.add(folder.getAbsolutePath());
          }
        }
      }
    }
    folders.add(JDUtilities.getConfiguration().getDefaultDownloadDirectory());
    logger.info("String_Node_Str" + folders);
    unrar.setFolders(folders);
  }
  LinkedList<String> followingFiles=new LinkedList<String>();
  Iterator<DownloadLink> ff=JDUtilities.getController().getDownloadLinks().iterator();
  while (ff.hasNext()) {
    DownloadLink dl=ff.next();
    if (dl.getStatus() != DownloadLink.STATUS_DONE && dl.getStatus() != DownloadLink.STATUS_DONE) {
      followingFiles.add(dl.getName());
    }
  }
  unrar.followingFiles=followingFiles.toArray(new String[followingFiles.size()]);
  LinkedList<File> unpacked=unrar.unrar();
  Iterator<File> iter=unpacked.iterator();
  LinkedList<mergeFile> mergeFiles=new LinkedList<mergeFile>();
  while (iter.hasNext()) {
    File file=(File)iter.next();
    mergeFile mergeFile=new mergeFile(file.getAbsolutePath());
    if (!mergeFiles.contains(mergeFile))     mergeFiles.add(mergeFile);
    if (JDUtilities.getController().isContainerFile(file)) {
      if (JDUtilities.getConfiguration().getBooleanProperty(Configuration.PARAM_RELOADCONTAINER,true))       JDUtilities.getController().loadContainerFile(file);
    }
  }
  Boolean DELETE_MERGEDFILES=JDUtilities.getConfiguration().getBooleanProperty(Unrar.PROPERTY_DELETE_MERGEDFILES,true);
  if (lastFinishedDownload != null && JDUtilities.getConfiguration().getBooleanProperty(Unrar.PROPERTY_USE_HJMERGE,true)) {
    Merge.mergeIt(new File(lastFinishedDownload.getFileOutput()),unrar.followingFiles,DELETE_MERGEDFILES,unrar.extractFolder);
    Iterator<mergeFile> miter=mergeFiles.iterator();
    while (miter.hasNext()) {
      mergeFile mergeFile=(mergeFile)miter.next();
      Merge.mergeIt(mergeFile,unrar.followingFiles,DELETE_MERGEDFILES,unrar.extractFolder);
    }
  }
  IS_RUNNING=false;
  this.setCallCode(Interaction.INTERACTION_CALL_SUCCESS);
  Interaction.handleInteraction(Interaction.INTERACTION_AFTER_UNRAR,null);
}