Program: 44742
Project: 44742
Buggy source:
@Override public boolean onCommand(CommandSender cs,Command cmd,String alias,String[] args){
  if (!(cs instanceof Player)) {
    plugin.log("String_Node_Str");
  }
  Player player=(Player)cs;
  if (args.length == 0 || args[0].equalsIgnoreCase("String_Node_Str")) {
    plugin.msg(player,"String_Node_Str");
    plugin.msg(player,ChatColor.YELLOW + "String_Node_Str" + ChatColor.WHITE+ CircuitManager.getValidSendersString());
  }
 else   if (args[0].equalsIgnoreCase("String_Node_Str")) {
    if (CircuitManager.hasPendingCircuit(player)) {
      CircuitManager.removePendingCircuit(player);
      plugin.msg(player,"String_Node_Str");
    }
 else {
      plugin.msg(player,"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) {
            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,"String_Node_Str");
        }
 else {
          plugin.msg(player,"String_Node_Str");
        }
      }
 else {
        plugin.msg(player,"String_Node_Str");
      }
    }
 else {
      plugin.msg(player,"String_Node_Str");
    }
  }
 else   if (CircuitManager.isValidCircuitType(args[0])) {
    if (player.hasPermission("String_Node_Str" + args[0])) {
      int iDelay=0;
      if (args.length > 1) {
        try {
          iDelay=Integer.parseInt(args[1]);
        }
 catch (        NumberFormatException e) {
          iDelay=-1;
        }
        if (iDelay < 0 || iDelay > QuantumConnectors.MAX_DELAY_TIME) {
          iDelay=0;
          plugin.msg(player,ChatColor.RED + "String_Node_Str" + QuantumConnectors.MAX_DELAY_TIME+ "String_Node_Str");
        }
      }
      if (!CircuitManager.hasPendingCircuit(player)) {
        CircuitManager.addPendingCircuit(player,CircuitManager.getCircuitType(args[0]),iDelay);
        plugin.msg(player,"String_Node_Str");
      }
 else {
        plugin.msg(player,"String_Node_Str" + args[0] + "String_Node_Str"+ (iDelay == 0 ? "String_Node_Str" : iDelay + "String_Node_Str")+ "String_Node_Str");
      }
    }
 else {
      plugin.msg(player,ChatColor.RED + "String_Node_Str" + args[0]+ "String_Node_Str");
    }
  }
 else {
    plugin.msg(player,"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("String_Node_Str");
  }
  Player player=(Player)cs;
  if (args.length == 0 || args[0].equalsIgnoreCase("String_Node_Str")) {
    plugin.msg(player,"String_Node_Str");
    plugin.msg(player,ChatColor.YELLOW + "String_Node_Str" + ChatColor.WHITE+ CircuitManager.getValidSendersString());
  }
 else   if (args[0].equalsIgnoreCase("String_Node_Str")) {
    if (CircuitManager.hasPendingCircuit(player)) {
      CircuitManager.removePendingCircuit(player);
      plugin.msg(player,"String_Node_Str");
    }
 else {
      plugin.msg(player,"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) {
            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,"String_Node_Str");
        }
 else {
          plugin.msg(player,"String_Node_Str");
        }
      }
 else {
        plugin.msg(player,"String_Node_Str");
      }
    }
 else {
      plugin.msg(player,"String_Node_Str");
    }
  }
 else   if (CircuitManager.isValidCircuitType(args[0])) {
    if (player.hasPermission("String_Node_Str" + args[0])) {
      int iDelay=0;
      if (args.length > 1) {
        try {
          iDelay=Integer.parseInt(args[1]);
        }
 catch (        NumberFormatException e) {
          iDelay=-1;
        }
        if (iDelay < 0 || iDelay > QuantumConnectors.MAX_DELAY_TIME) {
          iDelay=0;
          plugin.msg(player,ChatColor.RED + "String_Node_Str" + QuantumConnectors.MAX_DELAY_TIME+ "String_Node_Str");
        }
      }
      if (!CircuitManager.hasPendingCircuit(player)) {
        CircuitManager.addPendingCircuit(player,CircuitManager.getCircuitType(args[0]),iDelay);
        plugin.msg(player,"String_Node_Str");
      }
 else {
        CircuitManager.getPendingCircuit(player).setCircuitType(CircuitManager.getCircuitType(args[0]),iDelay);
        plugin.msg(player,"String_Node_Str" + args[0] + "String_Node_Str"+ (iDelay == 0 ? "String_Node_Str" : iDelay + "String_Node_Str")+ "String_Node_Str");
      }
    }
 else {
      plugin.msg(player,ChatColor.RED + "String_Node_Str" + args[0]+ "String_Node_Str");
    }
  }
 else {
    plugin.msg(player,"String_Node_Str");
  }
  return true;
}