Program: 21112
Project: 21112
Buggy source:
public void confirmPackage(LinkGrabberFilePackage fpv2,String host,int index){
  if (fpv2 == null)   return;
  ArrayList<DownloadLink> linkList=fpv2.getDownloadLinks();
  if (linkList.isEmpty())   return;
  FilePackage fp=FilePackage.getInstance();
  fp.setName(fpv2.getName());
  fp.setComment(fpv2.getComment());
  fp.setPassword(fpv2.getPassword());
  fp.setExtractAfterDownload(fpv2.isExtractAfterDownload());
  addToDownloadDirs(fpv2.getDownloadDirectory(),fpv2.getName());
  if (fpv2.useSubDir()) {
    File file=new File(new File(fpv2.getDownloadDirectory()),fp.getName());
    if (JDUtilities.getConfiguration().getBooleanProperty(Configuration.PARAM_CREATE_SUBFOLDER_BEFORE_DOWNLOAD,false)) {
      if (!file.exists())       file.mkdirs();
    }
    fp.setDownloadDirectory(file.getAbsolutePath());
  }
 else {
    fp.setDownloadDirectory(fpv2.getDownloadDirectory());
  }
  int files=0;
  if (host == null) {
    files=linkList.size();
    fp.addLinks(linkList);
    for (    DownloadLink link : linkList) {
      boolean avail=true;
      if (link.isAvailabilityStatusChecked())       avail=link.isAvailable();
      link.getLinkStatus().reset();
      if (!avail)       link.getLinkStatus().addStatus(LinkStatus.ERROR_FILE_NOT_FOUND);
      link.setFilePackage(fp);
    }
    fpv2.setDownloadLinks(new ArrayList<DownloadLink>());
  }
 else {
    ArrayList<DownloadLink> linkListHost=new ArrayList<DownloadLink>();
    for (int i=fpv2.getDownloadLinks().size() - 1; i >= 0; --i) {
      if (linkList.get(i).getHost().compareTo(host) == 0) {
        DownloadLink link=linkList.remove(i);
        boolean avail=true;
        if (link.isAvailabilityStatusChecked())         avail=link.isAvailable();
        link.getLinkStatus().reset();
        if (!avail)         link.getLinkStatus().addStatus(LinkStatus.ERROR_FILE_NOT_FOUND);
        linkListHost.add(link);
        link.setFilePackage(fp);
        ++files;
      }
    }
    if (files == 0)     return;
    fp.addLinks(linkListHost);
    fpv2.setDownloadLinks(linkList);
  }
  if (!fpv2.isIgnored()) {
    if (SimpleGuiConstants.GUI_CONFIG.getBooleanProperty(SimpleGuiConstants.PARAM_INSERT_NEW_LINKS_AT,false)) {
      JDUtilities.getDownloadController().addPackageAt(fp,index);
    }
 else {
      JDUtilities.getDownloadController().addPackage(fp);
    }
  }
}

Fixed version (ground truth):
public void confirmPackage(LinkGrabberFilePackage fpv2,String host,int index){
  if (fpv2 == null)   return;
  ArrayList<DownloadLink> linkList=fpv2.getDownloadLinks();
  if (linkList.isEmpty())   return;
  FilePackage fp=FilePackage.getInstance();
  fp.setName(fpv2.getName());
  fp.setComment(fpv2.getComment());
  fp.setPassword(fpv2.getPassword());
  fp.setExtractAfterDownload(fpv2.isExtractAfterDownload());
  addToDownloadDirs(fpv2.getDownloadDirectory(),fpv2.getName());
  if (fpv2.useSubDir()) {
    File file=new File(new File(fpv2.getDownloadDirectory()),fp.getName());
    if (JDUtilities.getConfiguration().getBooleanProperty(Configuration.PARAM_CREATE_SUBFOLDER_BEFORE_DOWNLOAD,false)) {
      if (!file.exists())       file.mkdirs();
    }
    fp.setDownloadDirectory(file.getAbsolutePath());
  }
 else {
    fp.setDownloadDirectory(fpv2.getDownloadDirectory());
  }
  int files=0;
  if (host == null) {
    files=linkList.size();
    fp.addLinks(linkList);
    for (    DownloadLink link : linkList) {
      boolean avail=true;
      if (link.isAvailabilityStatusChecked())       avail=link.isAvailable();
      link.getLinkStatus().reset();
      if (!avail)       link.getLinkStatus().addStatus(LinkStatus.ERROR_FILE_NOT_FOUND);
      link.setFilePackage(fp);
    }
    fpv2.setDownloadLinks(new ArrayList<DownloadLink>());
  }
 else {
    ArrayList<DownloadLink> linkListHost=new ArrayList<DownloadLink>();
    for (int i=fpv2.getDownloadLinks().size() - 1; i >= 0; --i) {
      if (linkList.get(i).getHost().compareTo(host) == 0) {
        DownloadLink link=linkList.remove(i);
        boolean avail=true;
        if (link.isAvailabilityStatusChecked())         avail=link.isAvailable();
        link.getLinkStatus().reset();
        if (!avail)         link.getLinkStatus().addStatus(LinkStatus.ERROR_FILE_NOT_FOUND);
        linkListHost.add(link);
        link.setFilePackage(fp);
        ++files;
      }
    }
    if (files == 0)     return;
    fp.addLinks(linkListHost);
    fpv2.setDownloadLinks(linkList);
  }
  if (!fpv2.isIgnored()) {
    if (SimpleGuiConstants.GUI_CONFIG != null && SimpleGuiConstants.GUI_CONFIG.getBooleanProperty(SimpleGuiConstants.PARAM_INSERT_NEW_LINKS_AT,false)) {
      JDUtilities.getDownloadController().addPackageAt(fp,index);
    }
 else {
      JDUtilities.getDownloadController().addPackage(fp);
    }
  }
}