Program: 6705
Project: 6705
Buggy source:
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 (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],strip(arg[1]),player);
            }
 else {
              giveItemId(arg[0],"String_Node_Str",player);
            }
          }
 else {
            giveItemName(arg[0],strip(arg[1]),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(strip(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(Integer.valueOf(strip(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(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 (!(itemAllow(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;
          }
        }
      }
      return true;
    }
    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 (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 {
            giveItemName(arg[0],arg[1],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(strip(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(Integer.valueOf(strip(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(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 (!(itemAllow(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;
          }
        }
      }
      return true;
    }
    return true;
  }
 catch (  CommandException e) {
    e.printStackTrace();
  }
  return true;
}