Program: 83883
Project: 83883
Buggy source:
@Override public boolean onCommand(CommandSender cs,Command cmd,String alias,String[] args){
  if (!(cs instanceof Player)) {
    plugin.log(plugin.getMessage("String_Node_Str"));
    return true;
  }
  if (args.length > 0) {
    if (args[0].equalsIgnoreCase("String_Node_Str"))     args[0]="String_Node_Str";
 else     if (args[0].equalsIgnoreCase("String_Node_Str"))     args[0]="String_Node_Str";
 else     if (args[0].equalsIgnoreCase("String_Node_Str"))     args[0]="String_Node_Str";
  }
  Player player=(Player)cs;
  if (args.length == 0 || args[0].equalsIgnoreCase("String_Node_Str")) {
    plugin.msg(player,"String_Node_Str");
    String s="String_Node_Str";
    for (    String sKey : CircuitManager.getValidCircuitTypes().keySet()) {
      s+=sKey + "String_Node_Str";
    }
    plugin.msg(player,ChatColor.YELLOW + plugin.getMessage("String_Node_Str") + ChatColor.WHITE+ s.substring(0,s.length() - 2));
  }
 else   if (args[0].equalsIgnoreCase("String_Node_Str") || args[0].equalsIgnoreCase("String_Node_Str")) {
    if (CircuitManager.hasPendingCircuit(player)) {
      CircuitManager.removePendingCircuit(player);
      plugin.msg(player,plugin.getMessage("String_Node_Str"));
    }
 else {
      plugin.msg(player,plugin.getMessage("String_Node_Str"));
    }
  }
 else   if (args[0].equalsIgnoreCase("String_Node_Str")) {
    if (CircuitManager.hasPendingCircuit(player)) {
      PendingCircuit pc=CircuitManager.getPendingCircuit(player);
      if (pc.hasSenderLocation()) {
        if (pc.hasReceiver()) {
          CircuitManager.addCircuit(pc);
          if (pc.getSenderLocation().getBlock().getType() == Material.WOODEN_DOOR || pc.getSenderLocation().getBlock().getType() == Material.SPRUCE_DOOR || pc.getSenderLocation().getBlock().getType() == Material.BIRCH_DOOR || pc.getSenderLocation().getBlock().getType() == Material.JUNGLE_DOOR || pc.getSenderLocation().getBlock().getType() == Material.ACACIA_DOOR || pc.getSenderLocation().getBlock().getType() == Material.DARK_OAK_DOOR) {
            Block bDoor=pc.getSenderLocation().getBlock();
            int iData=(int)bDoor.getData();
            Block bOtherPiece=bDoor.getRelative((iData & 0x08) == 0x08 ? BlockFace.DOWN : BlockFace.UP);
            CircuitManager.addCircuit(bOtherPiece.getLocation(),pc.getCircuit());
          }
          CircuitManager.removePendingCircuit(player);
          plugin.msg(player,plugin.getMessage("String_Node_Str"));
        }
 else {
          plugin.msg(player,plugin.getMessage("String_Node_Str"));
        }
      }
 else {
        plugin.msg(player,plugin.getMessage("String_Node_Str"));
      }
    }
 else {
      plugin.msg(player,plugin.getMessage("String_Node_Str"));
    }
  }
 else   if (CircuitManager.isValidCircuitType(args[0])) {
    if (player.hasPermission("String_Node_Str" + args[0])) {
      double dDelay=0;
      if (args.length > 1) {
        try {
          dDelay=Double.parseDouble(args[1]);
        }
 catch (        NumberFormatException e) {
          dDelay=-1;
        }
        if (dDelay < 0 || (dDelay > QuantumConnectors.MAX_DELAY_TIME && !player.hasPermission("String_Node_Str"))) {
          dDelay=0;
          plugin.msg(player,ChatColor.RED + plugin.getMessage("String_Node_Str").replaceAll("String_Node_Str",new Integer(QuantumConnectors.MAX_DELAY_TIME).toString()));
        }
      }
      String sDelayMsg="String_Node_Str" + args[0] + "String_Node_Str"+ dDelay+ "String_Node_Str";
      sDelayMsg="String_Node_Str";
      int iDelayTicks=(int)Math.round(dDelay * 20);
      if (!CircuitManager.hasPendingCircuit(player)) {
        CircuitManager.addPendingCircuit(player,CircuitManager.getCircuitType(args[0]),iDelayTicks);
        plugin.msg(player,plugin.getMessage("String_Node_Str").replace("String_Node_Str",args[0].toUpperCase()).replace("String_Node_Str",new Double(dDelay).toString()));
      }
 else {
        CircuitManager.getPendingCircuit(player).setCircuitType(CircuitManager.getCircuitType(args[0]),iDelayTicks);
        plugin.msg(player,plugin.getMessage("String_Node_Str").replace("String_Node_Str",args[0].toUpperCase()).replace("String_Node_Str",new Double(dDelay).toString()));
      }
    }
 else {
      plugin.msg(player,ChatColor.RED + plugin.getMessage("String_Node_Str").replace("String_Node_Str",args[0].toUpperCase()));
    }
  }
 else {
    plugin.msg(player,plugin.getMessage("String_Node_Str"));
  }
  return true;
}

Fixed version (ground truth):
@Override public boolean onCommand(CommandSender cs,Command cmd,String alias,String[] args){
  if (!(cs instanceof Player)) {
    plugin.log(plugin.getMessage("String_Node_Str"));
    return true;
  }
  if (args.length > 0) {
    if (args[0].equalsIgnoreCase("String_Node_Str"))     args[0]="String_Node_Str";
 else     if (args[0].equalsIgnoreCase("String_Node_Str"))     args[0]="String_Node_Str";
 else     if (args[0].equalsIgnoreCase("String_Node_Str"))     args[0]="String_Node_Str";
  }
  Player player=(Player)cs;
  if (args.length == 0 || args[0].equalsIgnoreCase("String_Node_Str")) {
    plugin.msg(player,plugin.getMessage("String_Node_Str"));
    String s="String_Node_Str";
    for (    String sKey : CircuitManager.getValidCircuitTypes().keySet()) {
      s+=sKey + "String_Node_Str";
    }
    plugin.msg(player,ChatColor.YELLOW + plugin.getMessage("String_Node_Str") + ChatColor.WHITE+ s.substring(0,s.length() - 2));
  }
 else   if (args[0].equalsIgnoreCase("String_Node_Str") || args[0].equalsIgnoreCase("String_Node_Str")) {
    if (CircuitManager.hasPendingCircuit(player)) {
      CircuitManager.removePendingCircuit(player);
      plugin.msg(player,plugin.getMessage("String_Node_Str"));
    }
 else {
      plugin.msg(player,plugin.getMessage("String_Node_Str"));
    }
  }
 else   if (args[0].equalsIgnoreCase("String_Node_Str")) {
    if (CircuitManager.hasPendingCircuit(player)) {
      PendingCircuit pc=CircuitManager.getPendingCircuit(player);
      if (pc.hasSenderLocation()) {
        if (pc.hasReceiver()) {
          CircuitManager.addCircuit(pc);
          if (pc.getSenderLocation().getBlock().getType() == Material.WOODEN_DOOR || pc.getSenderLocation().getBlock().getType() == Material.SPRUCE_DOOR || pc.getSenderLocation().getBlock().getType() == Material.BIRCH_DOOR || pc.getSenderLocation().getBlock().getType() == Material.JUNGLE_DOOR || pc.getSenderLocation().getBlock().getType() == Material.ACACIA_DOOR || pc.getSenderLocation().getBlock().getType() == Material.DARK_OAK_DOOR) {
            Block bDoor=pc.getSenderLocation().getBlock();
            int iData=(int)bDoor.getData();
            Block bOtherPiece=bDoor.getRelative((iData & 0x08) == 0x08 ? BlockFace.DOWN : BlockFace.UP);
            CircuitManager.addCircuit(bOtherPiece.getLocation(),pc.getCircuit());
          }
          CircuitManager.removePendingCircuit(player);
          plugin.msg(player,plugin.getMessage("String_Node_Str"));
        }
 else {
          plugin.msg(player,plugin.getMessage("String_Node_Str"));
        }
      }
 else {
        plugin.msg(player,plugin.getMessage("String_Node_Str"));
      }
    }
 else {
      plugin.msg(player,plugin.getMessage("String_Node_Str"));
    }
  }
 else   if (CircuitManager.isValidCircuitType(args[0])) {
    if (player.hasPermission("String_Node_Str" + args[0])) {
      double dDelay=0;
      if (args.length > 1) {
        try {
          dDelay=Double.parseDouble(args[1]);
        }
 catch (        NumberFormatException e) {
          dDelay=-1;
        }
        if (dDelay < 0 || (dDelay > QuantumConnectors.MAX_DELAY_TIME && !player.hasPermission("String_Node_Str"))) {
          dDelay=0;
          plugin.msg(player,ChatColor.RED + plugin.getMessage("String_Node_Str").replaceAll("String_Node_Str",new Integer(QuantumConnectors.MAX_DELAY_TIME).toString()));
        }
      }
      String sDelayMsg="String_Node_Str" + args[0] + "String_Node_Str"+ dDelay+ "String_Node_Str";
      sDelayMsg="String_Node_Str";
      int iDelayTicks=(int)Math.round(dDelay * 20);
      if (!CircuitManager.hasPendingCircuit(player)) {
        CircuitManager.addPendingCircuit(player,CircuitManager.getCircuitType(args[0]),iDelayTicks);
        plugin.msg(player,plugin.getMessage("String_Node_Str").replace("String_Node_Str",args[0].toUpperCase()).replace("String_Node_Str",new Double(dDelay).toString()));
      }
 else {
        CircuitManager.getPendingCircuit(player).setCircuitType(CircuitManager.getCircuitType(args[0]),iDelayTicks);
        plugin.msg(player,plugin.getMessage("String_Node_Str").replace("String_Node_Str",args[0].toUpperCase()).replace("String_Node_Str",new Double(dDelay).toString()));
      }
    }
 else {
      plugin.msg(player,ChatColor.RED + plugin.getMessage("String_Node_Str").replace("String_Node_Str",args[0].toUpperCase()));
    }
  }
 else {
    plugin.msg(player,plugin.getMessage("String_Node_Str"));
  }
  return true;
}