Program: 6710
Project: 6710
Buggy source:
public boolean onCommand(CommandSender sender,Command commandArg,String commandLabel,String[] arg){
  try {
    Player player=(Player)sender;
    PlayerInventory inventory=player.getInventory();
    String command=commandArg.getName().toLowerCase();
    ItemStack itemstack;
    MaterialData itemdata;
    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()) {
            if (arg[0].contains("String_Node_Str")) {
              String clone=arg[0];
              String[] split=clone.split("String_Node_Str");
              itemstack=new ItemStack(Integer.parseInt(split[0]));
              itemdata=new MaterialData(Integer.parseInt(split[1]));
              itemstack.setData(itemdata);
              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 {
              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 {
            if (arg[0].contains("String_Node_Str")) {
              String clone=arg[0];
              String[] split=clone.split("String_Node_Str");
              int itemid=items.get(split[0].toLowerCase());
              itemstack=new ItemStack(itemid);
              itemdata=new MaterialData(Integer.parseInt(split[1]));
              itemstack.setData(itemdata);
              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());
              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 (arg[0].contains("String_Node_Str")) {
                String clone=arg[0];
                String[] split=clone.split("String_Node_Str");
                if (!(itemdeny(Integer.valueOf(split[0])))) {
                  itemstack=new ItemStack(Integer.parseInt(split[0]));
                  itemdata=new MaterialData(Integer.parseInt(split[1]));
                  itemstack.setData(itemdata);
                  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 {
                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 {
              if (arg[0].contains("String_Node_Str")) {
                String clone=arg[0];
                String[] split=clone.split("String_Node_Str");
                int itemid=items.get(arg[0].toLowerCase());
                if (!(itemdeny(itemid))) {
                  itemstack=new ItemStack(itemid);
                  itemdata=new MaterialData(Integer.parseInt(split[1]));
                  itemstack.setData(itemdata);
                  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");
              }
            }
            return true;
          }
        }
      }
 else {
        player.sendMessage("String_Node_Str");
        log.info(logPrefix + "String_Node_Str" + player.getDisplayName()+ "String_Node_Str"+ command+ "String_Node_Str");
      }
      return true;
    }
  }
 catch (  CommandException e) {
    e.printStackTrace();
  }
  return true;
}

Fixed version (ground truth):
public boolean onCommand(CommandSender sender,Command commandArg,String commandLabel,String[] arg){
  try {
    Player player=(Player)sender;
    String command=commandArg.getName().toLowerCase();
    if (command.equalsIgnoreCase("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()) {
            giveItemId(arg[0],arg[1],player);
          }
 else {
            giveItemName(arg[0],arg[1],player);
          }
        }
 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(strip(arg[0]))))) {
                giveItemId(arg[0],arg[1],player);
              }
 else {
                player.sendMessage(logPrefix + "String_Node_Str");
                log.info(logPrefix + player.getDisplayName() + "String_Node_Str"+ arg[0].toString());
              }
            }
 else {
              if (!(itemdeny(Integer.valueOf(strip(arg[0]))))) {
                giveItemName(arg[0],arg[1],player);
              }
 else {
                player.sendMessage(logPrefix + "String_Node_Str");
                log.info(logPrefix + player.getDisplayName() + "String_Node_Str"+ arg[0].toString());
              }
            }
          }
 else {
            player.sendMessage("String_Node_Str");
            return false;
          }
        }
 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;
  }
 catch (  CommandException e) {
    e.printStackTrace();
  }
  return true;
}