Program: 80966
Project: 80966
Buggy source:
/** 
 * Checks for updates. This loads Patch Notes and prompts the user if they want to update. If the user does update, it kills the PAXChecker.
 * @param startupOutput The Startup object to update with information as updates are loaded
 * @return True if updates were checked for successfully, false if not
 */
public boolean loadUpdates(Startup startupOutput){
  String notes=null;
  try {
    if (startupOutput != null) {
      startupOutput.setStatus("String_Node_Str");
    }
    PatchNotesDownloader notesDownloader=new PatchNotesDownloader(getPatchNotesLink());
    notesDownloader.downloadVersionNotes(programVersion);
    notes=notesDownloader.getVersionNotes();
    if (notesDownloader.updateAvailable()) {
      UpdateDownloader myDownloader=new UpdateDownloader(getUpdateLink(),getBetaUpdateLink());
      UpdatePrompt myPrompt=null;
      boolean shouldUpdate;
      if (!headless) {
        myPrompt=new UpdatePrompt("String_Node_Str",myDownloader.getUpdateSize(),notesDownloader.getUpdateLevel(),programVersion,notesDownloader.getVersionNotes(programVersion));
        if (startupOutput != null) {
          startupOutput.stop();
        }
        myPrompt.showWindow();
        try {
          myPrompt.waitForClose();
        }
 catch (        InterruptedException e) {
        }
        shouldUpdate=myPrompt.shouldUpdateProgram();
      }
 else {
        System.out.println("String_Node_Str");
        System.out.println("String_Node_Str" + programVersion);
        System.out.println("String_Node_Str" + notesDownloader.getUpdateLevel());
        System.out.println("String_Node_Str" + myDownloader.getUpdateSize());
        System.out.print("String_Node_Str");
        Scanner in=new Scanner(System.in);
        shouldUpdate=in.nextLine().toUpperCase().startsWith("String_Node_Str");
      }
      if (shouldUpdate) {
        if (notesDownloader.getUpdateLevel() == 1) {
          myDownloader.setUseBeta();
        }
        myDownloader.updateProgram(myPrompt,new File(PAXChecker.class.getProtectionDomain().getCodeSource().getLocation().toURI().getPath()));
        System.exit(0);
      }
 else       if (startupOutput != null) {
        startupOutput.start();
      }
    }
  }
 catch (  IOException|URISyntaxException e) {
    e.printStackTrace();
    return false;
  }
  patchNotes=notes;
  return true;
}

Fixed version (ground truth):
/** 
 * Checks for updates. This loads Patch Notes and prompts the user if they want to update. If the user does update, it kills the PAXChecker.
 * @param startupOutput The Startup object to update with information as updates are loaded
 * @return True if updates were checked for successfully, false if not
 */
public boolean loadUpdates(Startup startupOutput){
  String notes=null;
  try {
    if (startupOutput != null) {
      startupOutput.setStatus("String_Node_Str");
    }
    PatchNotesDownloader notesDownloader=new PatchNotesDownloader(getPatchNotesLink());
    if (beta) {
      notesDownloader.enableBetaDownload();
    }
    notesDownloader.downloadVersionNotes(programVersion);
    notes=notesDownloader.getVersionNotes();
    if (notesDownloader.updateAvailable()) {
      UpdateDownloader myDownloader=new UpdateDownloader(getUpdateLink(),getBetaUpdateLink());
      UpdatePrompt myPrompt=null;
      boolean shouldUpdate;
      if (!headless) {
        myPrompt=new UpdatePrompt("String_Node_Str",myDownloader.getUpdateSize(),notesDownloader.getUpdateLevel(),programVersion,notesDownloader.getVersionNotes(programVersion));
        if (startupOutput != null) {
          startupOutput.stop();
        }
        myPrompt.showWindow();
        try {
          myPrompt.waitForClose();
        }
 catch (        InterruptedException e) {
        }
        shouldUpdate=myPrompt.shouldUpdateProgram();
      }
 else {
        System.out.println("String_Node_Str");
        System.out.println("String_Node_Str" + programVersion);
        System.out.println("String_Node_Str" + notesDownloader.getUpdateLevel());
        System.out.println("String_Node_Str" + myDownloader.getUpdateSize());
        System.out.print("String_Node_Str");
        Scanner in=new Scanner(System.in);
        shouldUpdate=in.nextLine().toUpperCase().startsWith("String_Node_Str");
      }
      if (shouldUpdate) {
        if (notesDownloader.getUpdateLevel() == 1) {
          myDownloader.setUseBeta();
        }
        myDownloader.updateProgram(myPrompt,new File(PAXChecker.class.getProtectionDomain().getCodeSource().getLocation().toURI().getPath()));
        System.exit(0);
      }
 else       if (startupOutput != null) {
        startupOutput.start();
      }
    }
  }
 catch (  IOException|URISyntaxException e) {
    e.printStackTrace();
    return false;
  }
  patchNotes=notes;
  return true;
}