Program: 6717
Project: 6717
Buggy source:
public boolean onCommand(CommandSender sender,Command commandArg,String commandLabel,String[] arg){
  Player player=(Player)sender;
  PlayerInventory inventory=player.getInventory();
  String command=commandArg.getName().toLowerCase();
  ItemStack itemstack;
  if (command.equalsIgnoreCase("String_Node_Str")) {
    if (player.isOp() || gimme.Permissions.has(player,"String_Node_Str") || (gimme.Permissions.has(player,"String_Node_Str") || gimme.Permissions.has(player,"String_Node_Str"))) {
      if (arg.length >= 1 && arg.length <= 2) {
        Pattern p=Pattern.compile("String_Node_Str");
        Matcher m=p.matcher(arg[0]);
        if (m.matches()) {
          if (!(itemdeny(Integer.valueOf(arg[0])))) {
            itemstack=new ItemStack(Integer.parseInt(arg[0]));
            if (arg.length == 1) {
              itemstack.setAmount(amount);
            }
            if (arg.length == 2) {
              itemstack.setAmount(Integer.parseInt(arg[1]));
            }
            player.sendMessage("String_Node_Str");
            inventory.addItem(itemstack);
          }
 else {
            player.sendMessage(logPrefix + "String_Node_Str");
            log.info(logPrefix + player + "String_Node_Str"+ arg[0].toString());
          }
        }
 else {
          int itemid=items.get(arg[0].toLowerCase());
          if (!(itemdeny(itemid))) {
            itemstack=new ItemStack(itemid);
            if (arg.length == 1) {
              itemstack.setAmount(amount);
            }
            if (arg.length == 2) {
              itemstack.setAmount(Integer.parseInt(arg[1]));
            }
            player.sendMessage("String_Node_Str");
            inventory.addItem(itemstack);
          }
 else {
            player.sendMessage(logPrefix + "String_Node_Str");
            log.info(logPrefix + player + "String_Node_Str"+ arg[0].toString());
          }
        }
      }
 else {
        player.sendMessage("String_Node_Str");
      }
    }
 else {
      player.sendMessage("String_Node_Str");
      log.info(logPrefix + "String_Node_Str" + player.getDisplayName()+ "String_Node_Str"+ command+ "String_Node_Str");
    }
    return true;
  }
  return true;
}

Fixed version (ground truth):
public boolean onCommand(CommandSender sender,Command commandArg,String commandLabel,String[] arg){
  Player player=(Player)sender;
  PlayerInventory inventory=player.getInventory();
  String command=commandArg.getName().toLowerCase();
  ItemStack itemstack;
  if (command.equalsIgnoreCase("String_Node_Str")) {
    if (gimme.Permissions.has(player,"String_Node_Str") || gimme.Permissions.has(player,"String_Node_Str") || (gimme.Permissions.has(player,"String_Node_Str"))) {
      if (arg.length >= 1 && arg.length <= 2) {
        Pattern p=Pattern.compile("String_Node_Str");
        Matcher m=p.matcher(arg[0]);
        if (m.matches()) {
          itemstack=new ItemStack(Integer.parseInt(arg[0]));
          if (arg.length == 1) {
            itemstack.setAmount(amount);
          }
          if (arg.length == 2) {
            itemstack.setAmount(Integer.parseInt(arg[1]));
          }
          player.sendMessage("String_Node_Str");
          inventory.addItem(itemstack);
        }
 else {
          int itemid=items.get(arg[0].toLowerCase());
          if (!(itemdeny(itemid))) {
            itemstack=new ItemStack(itemid);
            if (arg.length == 1) {
              itemstack.setAmount(amount);
            }
            if (arg.length == 2) {
              itemstack.setAmount(Integer.parseInt(arg[1]));
            }
            player.sendMessage("String_Node_Str");
            inventory.addItem(itemstack);
          }
        }
      }
 else {
        player.sendMessage("String_Node_Str");
      }
    }
    if (player.isOp() || gimme.Permissions.has(player,"String_Node_Str")) {
      if (!gimme.Permissions.has(player,"String_Node_Str")) {
        if (arg.length >= 1 && arg.length <= 2) {
          Pattern p=Pattern.compile("String_Node_Str");
          Matcher m=p.matcher(arg[0]);
          if (m.matches()) {
            if (!(itemdeny(Integer.valueOf(arg[0])))) {
              itemstack=new ItemStack(Integer.parseInt(arg[0]));
              if (arg.length == 1) {
                itemstack.setAmount(amount);
              }
              if (arg.length == 2) {
                itemstack.setAmount(Integer.parseInt(arg[1]));
              }
              player.sendMessage("String_Node_Str");
              inventory.addItem(itemstack);
            }
 else {
              player.sendMessage(logPrefix + "String_Node_Str");
              log.info(logPrefix + player.getDisplayName() + "String_Node_Str"+ arg[0].toString());
            }
          }
 else {
            int itemid=items.get(arg[0].toLowerCase());
            if (!(itemdeny(itemid))) {
              itemstack=new ItemStack(itemid);
              if (arg.length == 1) {
                itemstack.setAmount(amount);
              }
              if (arg.length == 2) {
                itemstack.setAmount(Integer.parseInt(arg[1]));
              }
              player.sendMessage("String_Node_Str");
              inventory.addItem(itemstack);
            }
 else {
              player.sendMessage(logPrefix + "String_Node_Str");
              log.info(logPrefix + player.getDisplayName() + "String_Node_Str"+ arg[0].toString());
            }
          }
        }
 else {
          player.sendMessage("String_Node_Str");
        }
      }
    }
 else {
      player.sendMessage("String_Node_Str");
      log.info(logPrefix + "String_Node_Str" + player.getDisplayName()+ "String_Node_Str"+ command+ "String_Node_Str");
    }
    return true;
  }
  return true;
}