Program: 98650
Project: 98650
Buggy source:
/** 
 * Reorders and executes all the events for the current round. Note that commands can be executed in a different order than they appear in the command file!
 * @param currentRoundEvents The list of the current round's events that we should add to
 */
private void executeEvents(ArrayList<Event> currentRoundEvents){
  canceledTimeouts=new HashSet<Timeout>();
  if (userControl == FailureLvl.EVERYTHING) {
    boolean doAgain=false;
    do {
      try {
        for (int i=0; i < currentRoundEvents.size(); ++i) {
          System.out.println(i + "String_Node_Str" + currentRoundEvents.get(i).toString());
        }
        System.out.println("String_Node_Str");
        String input=m_prompt ? Replay.getLine().trim() : "String_Node_Str";
        if (input.equals("String_Node_Str")) {
          for (          Event ev : currentRoundEvents) {
            handleEvent(ev);
          }
        }
 else {
          String[] order=input.split("String_Node_Str");
          HashSet<Event> dupeMissCheck=new HashSet<Event>();
          for (          String s : order) {
            dupeMissCheck.add(currentRoundEvents.get(Integer.parseInt(s)));
          }
          if (dupeMissCheck.size() != currentRoundEvents.size()) {
            System.out.println("String_Node_Str");
            doAgain=true;
            continue;
          }
          for (          String s : order) {
            Event ev=currentRoundEvents.get(Integer.parseInt(s));
            handleEvent(ev);
          }
        }
      }
 catch (      IOException e) {
        e.printStackTrace();
        doAgain=true;
      }
    }
 while (doAgain);
  }
 else {
    Collections.shuffle(currentRoundEvents,Utility.getRNG());
    System.out.println("String_Node_Str");
    for (    Event ev : currentRoundEvents) {
      System.out.println(ev.toString());
      handleEvent(ev);
    }
  }
  waitingTOs.removeAll(canceledTimeouts);
}

Fixed version (ground truth):
/** 
 * Reorders and executes all the events for the current round. Note that commands can be executed in a different order than they appear in the command file!
 * @param currentRoundEvents The list of the current round's events that we should add to
 */
private void executeEvents(ArrayList<Event> currentRoundEvents){
  canceledTimeouts=new HashSet<Timeout>();
  if (userControl == FailureLvl.EVERYTHING) {
    boolean doAgain=false;
    do {
      try {
        for (int i=0; i < currentRoundEvents.size(); ++i) {
          System.out.println(i + "String_Node_Str" + currentRoundEvents.get(i).toString());
        }
        String input="String_Node_Str";
        if (m_prompt) {
          System.out.println("String_Node_Str");
          input=Replay.getLine().trim();
        }
        if (input.equals("String_Node_Str")) {
          for (          Event ev : currentRoundEvents) {
            handleEvent(ev);
          }
        }
 else {
          String[] order=input.split("String_Node_Str");
          HashSet<Event> dupeMissCheck=new HashSet<Event>();
          for (          String s : order) {
            dupeMissCheck.add(currentRoundEvents.get(Integer.parseInt(s)));
          }
          if (dupeMissCheck.size() != currentRoundEvents.size()) {
            System.out.println("String_Node_Str");
            doAgain=true;
            continue;
          }
          for (          String s : order) {
            Event ev=currentRoundEvents.get(Integer.parseInt(s));
            handleEvent(ev);
          }
        }
      }
 catch (      IOException e) {
        e.printStackTrace();
        doAgain=true;
      }
    }
 while (doAgain);
  }
 else {
    Collections.shuffle(currentRoundEvents,Utility.getRNG());
    System.out.println("String_Node_Str");
    for (    Event ev : currentRoundEvents) {
      System.out.println(ev.toString());
      handleEvent(ev);
    }
  }
  waitingTOs.removeAll(canceledTimeouts);
}