Program: 61526
Project: 61526
Buggy source:
protected void finalProcess(List<GraphTargetItem> list,int level,FinalProcessLocalData localData) throws InterruptedException {
  boolean toDelete[]=new boolean[list.size()];
  for (int i=0; i < list.size(); i++) {
    if (Thread.currentThread().isInterrupted()) {
      throw new InterruptedException();
    }
    GraphTargetItem itemI=list.get(i);
    if (itemI instanceof ForItem) {
      ForItem fori=(ForItem)itemI;
      int exprLine=fori.getLine();
      if (exprLine > 0) {
        List<GraphTargetItem> forFirstCommands=new ArrayList<>();
        for (int j=i - 1; j >= 0; j--) {
          if (list.get(j).getLine() == exprLine && !(list.get(j) instanceof LoopItem)) {
            forFirstCommands.add(0,list.get(j));
            toDelete[j]=true;
          }
 else {
            break;
          }
        }
        fori.firstCommands.addAll(0,forFirstCommands);
      }
    }
    if (itemI instanceof WhileItem) {
      WhileItem whi=(WhileItem)itemI;
      int whileExprLine=whi.getLine();
      if (whileExprLine > 0) {
        List<GraphTargetItem> forFirstCommands=new ArrayList<>();
        List<GraphTargetItem> forFinalCommands=new ArrayList<>();
        for (int j=i - 1; j >= 0; j--) {
          GraphTargetItem itemJ=list.get(i);
          if (itemJ.getLine() == whileExprLine && !(itemJ instanceof LoopItem)) {
            forFirstCommands.add(0,itemJ);
            toDelete[j]=true;
          }
 else {
            break;
          }
        }
        for (int j=whi.commands.size() - 1; j >= 0; j--) {
          if (whi.commands.get(j).getLine() == whileExprLine && !(whi.commands.get(j) instanceof LoopItem)) {
            forFinalCommands.add(0,whi.commands.remove(j));
          }
 else {
            break;
          }
        }
        if (!forFirstCommands.isEmpty() || !forFinalCommands.isEmpty()) {
          if (forFirstCommands.size() > 2 || forFinalCommands.size() > 2) {
            for (int k=0; k < forFirstCommands.size(); k++) {
              toDelete[i - 1 - k]=false;
            }
            whi.commands.addAll(forFinalCommands);
          }
 else           if (whi.commands.isEmpty() && forFirstCommands.isEmpty()) {
            whi.commands.addAll(forFinalCommands);
          }
 else {
            GraphTargetItem lastExpr=whi.expression.remove(whi.expression.size() - 1);
            forFirstCommands.addAll(whi.expression);
            list.set(i,new ForItem(whi.getSrc(),whi.loop,forFirstCommands,lastExpr,forFinalCommands,whi.commands));
          }
        }
      }
    }
  }
  for (int i=toDelete.length - 1; i >= 0; i--) {
    if (toDelete[i]) {
      list.remove(i);
    }
  }
}

Fixed version (ground truth):
protected void finalProcess(List<GraphTargetItem> list,int level,FinalProcessLocalData localData) throws InterruptedException {
  boolean toDelete[]=new boolean[list.size()];
  for (int i=0; i < list.size(); i++) {
    if (Thread.currentThread().isInterrupted()) {
      throw new InterruptedException();
    }
    GraphTargetItem itemI=list.get(i);
    if (itemI instanceof ForItem) {
      ForItem fori=(ForItem)itemI;
      int exprLine=fori.getLine();
      if (exprLine > 0) {
        List<GraphTargetItem> forFirstCommands=new ArrayList<>();
        for (int j=i - 1; j >= 0; j--) {
          if (list.get(j).getLine() == exprLine && !(list.get(j) instanceof LoopItem)) {
            forFirstCommands.add(0,list.get(j));
            toDelete[j]=true;
          }
 else {
            break;
          }
        }
        fori.firstCommands.addAll(0,forFirstCommands);
      }
    }
    if (itemI instanceof WhileItem) {
      WhileItem whi=(WhileItem)itemI;
      int whileExprLine=whi.getLine();
      if (whileExprLine > 0) {
        List<GraphTargetItem> forFirstCommands=new ArrayList<>();
        List<GraphTargetItem> forFinalCommands=new ArrayList<>();
        for (int j=i - 1; j >= 0; j--) {
          GraphTargetItem itemJ=list.get(j);
          if (itemJ.getLine() == whileExprLine && !(itemJ instanceof LoopItem)) {
            forFirstCommands.add(0,itemJ);
            toDelete[j]=true;
          }
 else {
            break;
          }
        }
        for (int j=whi.commands.size() - 1; j >= 0; j--) {
          if (whi.commands.get(j).getLine() == whileExprLine && !(whi.commands.get(j) instanceof LoopItem)) {
            forFinalCommands.add(0,whi.commands.remove(j));
          }
 else {
            break;
          }
        }
        if (!forFirstCommands.isEmpty() || !forFinalCommands.isEmpty()) {
          if (forFirstCommands.size() > 2 || forFinalCommands.size() > 2) {
            for (int k=0; k < forFirstCommands.size(); k++) {
              toDelete[i - 1 - k]=false;
            }
            whi.commands.addAll(forFinalCommands);
          }
 else           if (whi.commands.isEmpty() && forFirstCommands.isEmpty()) {
            whi.commands.addAll(forFinalCommands);
          }
 else {
            GraphTargetItem lastExpr=whi.expression.remove(whi.expression.size() - 1);
            forFirstCommands.addAll(whi.expression);
            list.set(i,new ForItem(whi.getSrc(),whi.loop,forFirstCommands,lastExpr,forFinalCommands,whi.commands));
          }
        }
      }
    }
  }
  for (int i=toDelete.length - 1; i >= 0; i--) {
    if (toDelete[i]) {
      list.remove(i);
    }
  }
}