Program: 6713
Project: 6713
Buggy source:
public boolean onCommand(CommandSender sender,Command commandArg,String commandLabel,String[] arg){
  try {
    Player player=(Player)sender;
    String command=commandArg.getName().toLowerCase();
    try {
      if (command.equalsIgnoreCase("String_Node_Str")) {
        if (player.isOp() || 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(strip(arg[0]));
            if (m.matches()) {
              if (arg.length == 2) {
                giveItemId(arg[0],arg[1],player);
              }
 else {
                giveItemId(arg[0],"String_Node_Str",player);
              }
            }
 else {
              if (arg.length == 2) {
                giveItemName(arg[0],arg[1],player);
              }
 else {
                giveItemName(arg[0],"String_Node_Str",player);
              }
            }
          }
 else {
            player.sendMessage("String_Node_Str");
          }
        }
        if (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])))) {
                  if (arg[1] != null) {
                    giveItemId(arg[0],arg[1],player);
                  }
 else {
                    giveItemId(arg[0],"String_Node_Str",player);
                  }
                }
 else {
                  player.sendMessage(logPrefix + "String_Node_Str");
                  log.info(logPrefix + player.getDisplayName() + "String_Node_Str"+ arg[0].toString());
                }
              }
 else {
                if (!(itemDeny(items.get(arg[0])))) {
                  if (arg[1] != null) {
                    giveItemName(arg[0],arg[1],player);
                  }
 else {
                    giveItemName(arg[0],"String_Node_Str",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;
            }
          }
        }
        if (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 (!(itemAllow(Integer.valueOf(arg[0])))) {
                  if (arg[1] != null) {
                    giveItemId(arg[0],arg[1],player);
                  }
 else {
                    giveItemId(arg[0],"String_Node_Str",player);
                  }
                }
 else {
                  player.sendMessage(logPrefix + "String_Node_Str");
                  log.info(logPrefix + player.getDisplayName() + "String_Node_Str"+ arg[0].toString());
                }
              }
 else {
                if (!(itemAllow(items.get(arg[0])))) {
                  if (arg[1] != null) {
                    giveItemName(arg[0],arg[1],player);
                  }
 else {
                    giveItemName(arg[0],"String_Node_Str",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;
            }
          }
        }
        return true;
      }
    }
 catch (    NumberFormatException e) {
      e.printStackTrace();
    }
    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();
    try {
      if (command.equalsIgnoreCase("String_Node_Str")) {
        if (player.isOp() || 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(strip(arg[0]));
            if (m.matches()) {
              if (arg.length == 2) {
                giveItemId(arg[0],arg[1],player);
              }
 else {
                giveItemId(arg[0],"String_Node_Str",player);
              }
            }
 else {
              if (arg.length == 2) {
                giveItemName(arg[0],arg[1],player);
              }
 else {
                giveItemName(arg[0],"String_Node_Str",player);
              }
            }
          }
 else {
            player.sendMessage("String_Node_Str");
          }
        }
        if (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])))) {
                  if (arg[1] != null) {
                    giveItemId(arg[0],arg[1],player);
                  }
 else {
                    giveItemId(arg[0],"String_Node_Str",player);
                  }
                }
 else {
                  player.sendMessage(logPrefix + "String_Node_Str");
                  log.info(logPrefix + player.getDisplayName() + "String_Node_Str"+ arg[0].toString());
                }
              }
 else {
                if (!(itemDeny(items.get(arg[0])))) {
                  if (arg[1] != null) {
                    giveItemName(arg[0],arg[1],player);
                  }
 else {
                    giveItemName(arg[0],"String_Node_Str",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;
            }
          }
        }
        if (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 (itemAllow(Integer.valueOf(arg[0]))) {
                  if (arg[1] != null) {
                    giveItemId(arg[0],arg[1],player);
                  }
 else {
                    giveItemId(arg[0],"String_Node_Str",player);
                  }
                }
 else {
                  player.sendMessage(logPrefix + "String_Node_Str");
                  log.info(logPrefix + player.getDisplayName() + "String_Node_Str"+ arg[0].toString());
                }
              }
 else {
                if (itemAllow(items.get(arg[0]))) {
                  if (arg[1] != null) {
                    giveItemName(arg[0],arg[1],player);
                  }
 else {
                    giveItemName(arg[0],"String_Node_Str",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;
            }
          }
        }
        return true;
      }
    }
 catch (    NumberFormatException e) {
      e.printStackTrace();
    }
    return true;
  }
 catch (  CommandException e) {
    e.printStackTrace();
  }
  return true;
}