Program: 158320
Project: 158320
Buggy source:
@Override protected void readLine(String line,DeckCardLists deckList){
  if (line.isEmpty() || line.startsWith("String_Node_Str")) {
    return;
  }
  Matcher m=pattern.matcher(line);
  if (m.matches()) {
    boolean sideboard=false;
    if ("String_Node_Str".equals(m.group(1))) {
      sideboard=true;
    }
    int count=Integer.parseInt(m.group(2));
    String setCode=m.group(3);
    String cardNum=m.group(4);
    DeckCardInfo deckCardInfo=null;
    CardInfo cardInfo=CardRepository.instance.findCard(setCode,cardNum);
    if (cardInfo != null) {
      deckCardInfo=new DeckCardInfo(cardInfo.getName(),cardInfo.getCardNumber(),cardInfo.getSetCode());
    }
    if (deckCardInfo != null) {
      for (int i=0; i < count; i++) {
        if (!sideboard) {
          deckList.getCards().add(deckCardInfo);
        }
 else {
          deckList.getSideboard().add(deckCardInfo);
        }
      }
    }
 else {
      sbMessage.append("String_Node_Str").append("String_Node_Str").append(lineCount).append("String_Node_Str").append(line).append("String_Node_Str");
    }
  }
 else   if (line.startsWith("String_Node_Str")) {
    deckList.setName(line.substring(5,line.length()));
  }
 else   if (line.startsWith("String_Node_Str")) {
    deckList.setAuthor(line.substring(7,line.length()));
  }
 else   if (line.startsWith("String_Node_Str")) {
    Matcher m2=layoutPattern.matcher(line);
    if (m2.find()) {
      String target=m2.group(1);
      int rows=Integer.parseInt(m2.group(2));
      int cols=Integer.parseInt(m2.group(3));
      String settings=m2.group(4);
      String stackData=m2.group(5);
      Matcher stackMatcher=layoutStackPattern.matcher(stackData);
      List<List<List<DeckCardInfo>>> grid=new ArrayList<>();
      int totalCardCount=0;
      for (int row=0; row < rows; ++row) {
        List<List<DeckCardInfo>> rowData=new ArrayList<>();
        grid.add(rowData);
        for (int col=0; col < cols; ++col) {
          List<DeckCardInfo> stack=new ArrayList<>();
          rowData.add(stack);
          if (stackMatcher.find()) {
            String thisStackData=stackMatcher.group(1);
            Matcher stackEntries=layoutStackEntryPattern.matcher(thisStackData);
            while (stackEntries.find()) {
              ++totalCardCount;
              stack.add(new DeckCardInfo("String_Node_Str",stackEntries.group(2),stackEntries.group(1)));
            }
          }
 else {
            sbMessage.append("String_Node_Str");
          }
        }
      }
      DeckCardLayout layout=new DeckCardLayout(grid,settings);
      int expectedCount=0;
      if (target.equals("String_Node_Str")) {
        deckList.setCardLayout(layout);
        expectedCount=deckList.getCards().size();
      }
 else       if (target.equals("String_Node_Str")) {
        deckList.setSideboardLayout(layout);
        expectedCount=deckList.getSideboard().size();
      }
 else {
        sbMessage.append("String_Node_Str" + target + "String_Node_Str");
      }
      if (totalCardCount != expectedCount) {
        sbMessage.append("String_Node_Str" + expectedCount + "String_Node_Str"+ totalCardCount+ "String_Node_Str"+ target+ "String_Node_Str");
      }
    }
 else {
      sbMessage.append("String_Node_Str");
    }
  }
}

Fixed version (ground truth):
@Override protected void readLine(String line,DeckCardLists deckList){
  if (line.isEmpty() || line.startsWith("String_Node_Str")) {
    return;
  }
  Matcher m=pattern.matcher(line);
  if (m.matches()) {
    boolean sideboard=false;
    if ("String_Node_Str".equals(m.group(1))) {
      sideboard=true;
    }
    int count=Integer.parseInt(m.group(2));
    String setCode=m.group(3);
    String cardNum=m.group(4);
    DeckCardInfo deckCardInfo=null;
    CardInfo cardInfo=CardRepository.instance.findCard(setCode,cardNum);
    if (cardInfo != null) {
      deckCardInfo=new DeckCardInfo(cardInfo.getName(),cardInfo.getCardNumber(),cardInfo.getSetCode());
    }
    if (deckCardInfo != null) {
      for (int i=0; i < count; i++) {
        if (!sideboard) {
          deckList.getCards().add(deckCardInfo);
        }
 else {
          deckList.getSideboard().add(deckCardInfo);
        }
      }
    }
 else {
      sbMessage.append("String_Node_Str").append("String_Node_Str").append(lineCount).append("String_Node_Str").append(line).append("String_Node_Str");
    }
  }
 else   if (line.startsWith("String_Node_Str")) {
    deckList.setName(line.substring(5,line.length()));
  }
 else   if (line.startsWith("String_Node_Str")) {
    deckList.setAuthor(line.substring(7,line.length()));
  }
 else   if (line.startsWith("String_Node_Str")) {
    Matcher m2=layoutPattern.matcher(line);
    if (m2.find()) {
      String target=m2.group(1);
      int rows=Integer.parseInt(m2.group(2));
      int cols=Integer.parseInt(m2.group(3));
      String settings=m2.group(4);
      String stackData=m2.group(5);
      Matcher stackMatcher=layoutStackPattern.matcher(stackData);
      List<List<List<DeckCardInfo>>> grid=new ArrayList<>();
      int totalCardCount=0;
      for (int row=0; row < rows; ++row) {
        List<List<DeckCardInfo>> rowData=new ArrayList<>();
        grid.add(rowData);
        for (int col=0; col < cols; ++col) {
          List<DeckCardInfo> stack=new ArrayList<>();
          rowData.add(stack);
          if (stackMatcher.find()) {
            String thisStackData=stackMatcher.group(1);
            Matcher stackEntries=layoutStackEntryPattern.matcher(thisStackData);
            while (stackEntries.find()) {
              ++totalCardCount;
              stack.add(new DeckCardInfo("String_Node_Str",stackEntries.group(2),stackEntries.group(1)));
            }
          }
 else {
            sbMessage.append("String_Node_Str");
          }
        }
      }
      DeckCardLayout layout=new DeckCardLayout(grid,settings);
      int expectedCount=0;
switch (target) {
case "String_Node_Str":
        deckList.setCardLayout(layout);
      expectedCount=deckList.getCards().size();
    break;
case "String_Node_Str":
  deckList.setSideboardLayout(layout);
expectedCount=deckList.getSideboard().size();
break;
default :
sbMessage.append("String_Node_Str").append(target).append("String_Node_Str");
break;
}
if (totalCardCount != expectedCount) {
sbMessage.append("String_Node_Str").append(expectedCount).append("String_Node_Str").append(totalCardCount).append("String_Node_Str").append(target).append("String_Node_Str");
}
}
 else {
sbMessage.append("String_Node_Str");
}
}
}