Program: 5446
Project: 5446
Buggy source:
@Override public boolean onCommand(CommandSender sender,Command cmd,String commandLabel,String[] args){
  if (!(sender instanceof Player)) {
    return false;
  }
  Player player=(Player)sender;
  if (cmd.getName().compareToIgnoreCase("String_Node_Str") == 0) {
    Location loc=null;
    if (args.length > 0) {
      if (!this.Permissions.has(player,"String_Node_Str"))       return true;
      loc=getPlayerHomeLocation(player,args[0]);
    }
 else {
      if (!this.Permissions.has(player,"String_Node_Str"))       return true;
      loc=getPlayerHomeLocation(player,"String_Node_Str");
    }
    if (loc == null) {
      player.sendMessage(ChatColor.RED + "String_Node_Str");
    }
 else {
      if (loc.getWorld().getName().equals(player.getWorld().getName())) {
        player.teleportTo(loc);
      }
 else {
        Location playerLoc=player.getLocation();
        player.teleportTo(new Location(loc.getWorld(),playerLoc.getX(),playerLoc.getY(),playerLoc.getZ(),playerLoc.getPitch(),playerLoc.getYaw()));
        player.teleportTo(loc);
      }
    }
    return true;
  }
 else   if (cmd.getName().compareToIgnoreCase("String_Node_Str") == 0) {
    if (args.length > 0) {
      if (!this.Permissions.has(player,"String_Node_Str"))       return true;
      setPlayerHomeLocation(player,args[0],player.getLocation());
      player.sendMessage(ChatColor.RED + "String_Node_Str" + args[0]+ "String_Node_Str");
      log.info(player.getName() + "String_Node_Str" + args[0]+ "String_Node_Str");
    }
 else {
      if (!this.Permissions.has(player,"String_Node_Str"))       return true;
      setPlayerHomeLocation(player,"String_Node_Str",player.getLocation());
      player.sendMessage(ChatColor.RED + "String_Node_Str");
      log.info(player.getName() + "String_Node_Str");
    }
    saveHomes();
    return true;
  }
 else   if (cmd.getName().compareToIgnoreCase("String_Node_Str") == 0) {
    if (args.length > 0) {
      if (!this.Permissions.has(player,"String_Node_Str"))       return true;
      if (deletePlayerHomeLocation(player,args[0])) {
        player.sendMessage(ChatColor.RED + "String_Node_Str" + args[0]+ "String_Node_Str");
        log.info(player.getName() + "String_Node_Str" + args[0]+ "String_Node_Str");
      }
    }
 else {
      player.sendMessage(ChatColor.RED + "String_Node_Str");
    }
    saveHomes();
    return true;
  }
 else   if (cmd.getName().compareToIgnoreCase("String_Node_Str") == 0) {
    ArrayList<HomeLocation> listHomeLocations;
    if (args.length > 0) {
      if (!this.Permissions.has(player,"String_Node_Str"))       return true;
      listHomeLocations=listPlayerHomeLocations(args[0]);
      log.info(player.getName() + "String_Node_Str" + args[0]+ "String_Node_Str");
    }
 else {
      if (!this.Permissions.has(player,"String_Node_Str"))       return true;
      listHomeLocations=listPlayerHomeLocations(player.getName());
    }
    String userResponse="String_Node_Str";
    for (    HomeLocation thisLocation : listHomeLocations) {
      if (thisLocation.getHomeName().length() == 0) {
        userResponse=userResponse + "String_Node_Str";
      }
 else {
        userResponse=userResponse + "String_Node_Str" + thisLocation.getHomeName();
      }
    }
    if (!userResponse.isEmpty() && userResponse.length() > 2) {
      player.sendMessage(ChatColor.RED + "String_Node_Str" + userResponse.substring(2));
    }
 else {
      player.sendMessage(ChatColor.RED + "String_Node_Str");
    }
    return true;
  }
  return false;
}

Fixed version (ground truth):
@Override public boolean onCommand(CommandSender sender,Command cmd,String commandLabel,String[] args){
  if (!(sender instanceof Player)) {
    return false;
  }
  Player player=(Player)sender;
  if (cmd.getName().compareToIgnoreCase("String_Node_Str") == 0) {
    Location loc=null;
    if (args.length > 0) {
      if (!this.Permissions.has(player,"String_Node_Str"))       return true;
      loc=getPlayerHomeLocation(player,args[0]);
    }
 else {
      if (!this.Permissions.has(player,"String_Node_Str"))       return true;
      loc=getPlayerHomeLocation(player,"String_Node_Str");
    }
    if (loc == null) {
      player.sendMessage(ChatColor.RED + "String_Node_Str");
    }
 else {
      if (loc.getWorld().getName().equals(player.getWorld().getName())) {
        player.teleportTo(loc);
      }
 else {
        Location playerLoc=player.getLocation();
        player.teleportTo(new Location(loc.getWorld(),playerLoc.getX(),playerLoc.getY(),playerLoc.getZ(),playerLoc.getPitch(),playerLoc.getYaw()));
        player.teleportTo(loc);
      }
    }
    return true;
  }
 else   if (cmd.getName().compareToIgnoreCase("String_Node_Str") == 0) {
    if (args.length > 0) {
      if (!this.Permissions.has(player,"String_Node_Str"))       return true;
      setPlayerHomeLocation(player,args[0],player.getLocation());
      player.sendMessage(ChatColor.RED + "String_Node_Str" + args[0]+ "String_Node_Str");
      log.info(player.getName() + "String_Node_Str" + args[0]+ "String_Node_Str");
    }
 else {
      if (!this.Permissions.has(player,"String_Node_Str"))       return true;
      setPlayerHomeLocation(player,"String_Node_Str",player.getLocation());
      player.sendMessage(ChatColor.RED + "String_Node_Str");
      log.info(player.getName() + "String_Node_Str");
    }
    saveHomes();
    return true;
  }
 else   if (cmd.getName().compareToIgnoreCase("String_Node_Str") == 0) {
    if (args.length > 0) {
      if (!this.Permissions.has(player,"String_Node_Str"))       return true;
      if (deletePlayerHomeLocation(player,args[0])) {
        player.sendMessage(ChatColor.RED + "String_Node_Str" + args[0]+ "String_Node_Str");
        log.info(player.getName() + "String_Node_Str" + args[0]+ "String_Node_Str");
      }
 else {
        player.sendMessage(ChatColor.RED + "String_Node_Str");
      }
    }
 else {
      player.sendMessage(ChatColor.RED + "String_Node_Str");
    }
    saveHomes();
    return true;
  }
 else   if (cmd.getName().compareToIgnoreCase("String_Node_Str") == 0) {
    ArrayList<HomeLocation> listHomeLocations;
    if (args.length > 0) {
      if (!this.Permissions.has(player,"String_Node_Str"))       return true;
      listHomeLocations=listPlayerHomeLocations(args[0]);
      log.info(player.getName() + "String_Node_Str" + args[0]+ "String_Node_Str");
    }
 else {
      if (!this.Permissions.has(player,"String_Node_Str"))       return true;
      listHomeLocations=listPlayerHomeLocations(player.getName());
    }
    String userResponse="String_Node_Str";
    for (    HomeLocation thisLocation : listHomeLocations) {
      if (thisLocation.getHomeName().length() == 0) {
        userResponse=userResponse + "String_Node_Str";
      }
 else {
        userResponse=userResponse + "String_Node_Str" + thisLocation.getHomeName();
      }
    }
    if (!userResponse.isEmpty() && userResponse.length() > 2) {
      player.sendMessage(ChatColor.RED + "String_Node_Str" + userResponse.substring(2));
    }
 else {
      player.sendMessage(ChatColor.RED + "String_Node_Str");
    }
    return true;
  }
  return false;
}