Program: 58020
Project: 58020
Buggy source:
@Override public boolean execute(final PlotPlayer plr,final String... args){
  final Location loc=plr.getLocation();
  final Plot plot=MainUtil.getPlot(loc);
  if (plot == null) {
    return !sendMessage(plr,C.NOT_IN_PLOT);
  }
  if (!plot.hasOwner()) {
    sendMessage(plr,C.PLOT_NOT_CLAIMED);
    return false;
  }
  if (!plot.isAdded(plr.getUUID())) {
    if (!Permissions.hasPermission(plr,"String_Node_Str")) {
      MainUtil.sendMessage(plr,C.NO_PERMISSION,"String_Node_Str");
      return false;
    }
  }
  if (args.length < 1) {
    PlotManager manager=PS.get().getPlotManager(loc.getWorld());
    ArrayList<String> newValues=new ArrayList<String>();
    newValues.addAll(Arrays.asList(values));
    newValues.addAll(Arrays.asList(manager.getPlotComponents(PS.get().getPlotWorld(loc.getWorld()),plot.id)));
    MainUtil.sendMessage(plr,C.SUBCOMMAND_SET_OPTIONS_HEADER.s() + getArgumentList(newValues));
    return false;
  }
  for (int i=0; i < aliases.length; i++) {
    if (aliases[i].equalsIgnoreCase(args[0])) {
      args[0]=values[i];
      break;
    }
  }
  if (args[0].equalsIgnoreCase("String_Node_Str")) {
    if (args.length < 2) {
      final String message=StringUtils.join(FlagManager.getFlags(plr),"String_Node_Str");
      MainUtil.sendMessage(plr,C.NEED_KEY.s().replaceAll("String_Node_Str",message));
      return false;
    }
    AbstractFlag af;
    try {
      af=FlagManager.getFlag(args[1].toLowerCase());
    }
 catch (    final Exception e) {
      af=new AbstractFlag(args[1].toLowerCase());
    }
    if (!FlagManager.getFlags().contains(af) || FlagManager.isReserved(af.getKey())) {
      MainUtil.sendMessage(plr,C.NOT_VALID_FLAG);
      return false;
    }
    if (!Permissions.hasPermission(plr,"String_Node_Str" + args[1].toLowerCase())) {
      MainUtil.sendMessage(plr,C.NO_PERMISSION,"String_Node_Str" + args[1].toLowerCase());
      return false;
    }
    if (args.length == 2) {
      if (FlagManager.getPlotFlagAbs(plot,args[1].toLowerCase()) == null) {
        MainUtil.sendMessage(plr,C.FLAG_NOT_IN_PLOT);
        return false;
      }
      final boolean result=FlagManager.removePlotFlag(plot,args[1].toLowerCase());
      if (!result) {
        MainUtil.sendMessage(plr,C.FLAG_NOT_REMOVED);
        return false;
      }
      MainUtil.sendMessage(plr,C.FLAG_REMOVED);
      APlotListener.manager.plotEntry(plr,plot);
      return true;
    }
    try {
      final String value=StringUtils.join(Arrays.copyOfRange(args,2,args.length),"String_Node_Str");
      final Object parsed_value=af.parseValueRaw(value);
      if (parsed_value == null) {
        MainUtil.sendMessage(plr,af.getValueDesc());
        return false;
      }
      final Flag flag=new Flag(FlagManager.getFlag(args[1].toLowerCase(),true),parsed_value);
      final boolean result=FlagManager.addPlotFlag(plot,flag);
      if (!result) {
        MainUtil.sendMessage(plr,C.FLAG_NOT_ADDED);
        return false;
      }
      MainUtil.sendMessage(plr,C.FLAG_ADDED);
      APlotListener.manager.plotEntry(plr,plot);
      return true;
    }
 catch (    final Exception e) {
      MainUtil.sendMessage(plr,"String_Node_Str" + e.getMessage());
      return false;
    }
  }
  if (args[0].equalsIgnoreCase("String_Node_Str")) {
    if (!Permissions.hasPermission(plr,"String_Node_Str")) {
      MainUtil.sendMessage(plr,C.NO_PERMISSION,"String_Node_Str");
      return false;
    }
    if (args.length > 1) {
      if (args[1].equalsIgnoreCase("String_Node_Str")) {
        plot.setHome(null);
        return true;
      }
      return MainUtil.sendMessage(plr,C.HOME_ARGUMENT);
    }
    final String world=plr.getLocation().getWorld();
    final Location base=MainUtil.getPlotBottomLoc(world,plot.id);
    base.setY(0);
    final Location relative=plr.getLocation().subtract(base.getX(),base.getY(),base.getZ());
    final BlockLoc blockloc=new BlockLoc(relative.getX(),relative.getY(),relative.getZ(),relative.getYaw(),relative.getPitch());
    plot.setHome(blockloc);
    return MainUtil.sendMessage(plr,C.POSITION_SET);
  }
  if (args[0].equalsIgnoreCase("String_Node_Str")) {
    if (!Permissions.hasPermission(plr,"String_Node_Str")) {
      MainUtil.sendMessage(plr,C.NO_PERMISSION,"String_Node_Str");
      return false;
    }
    if (args.length < 2) {
      MainUtil.sendMessage(plr,C.MISSING_ALIAS);
      return false;
    }
    final String alias=args[1];
    if (alias.length() >= 50) {
      MainUtil.sendMessage(plr,C.ALIAS_TOO_LONG);
      return false;
    }
    for (    final Plot p : PS.get().getPlots(plr.getLocation().getWorld()).values()) {
      if (p.settings.getAlias().equalsIgnoreCase(alias)) {
        MainUtil.sendMessage(plr,C.ALIAS_IS_TAKEN);
        return false;
      }
      if (UUIDHandler.nameExists(new StringWrapper(alias))) {
        MainUtil.sendMessage(plr,C.ALIAS_IS_TAKEN);
        return false;
      }
    }
    plot.setAlias(alias);
    MainUtil.sendMessage(plr,C.ALIAS_SET_TO.s().replaceAll("String_Node_Str",alias));
    return true;
  }
  if (args[0].equalsIgnoreCase("String_Node_Str")) {
    if (!Permissions.hasPermission(plr,"String_Node_Str")) {
      MainUtil.sendMessage(plr,C.NO_PERMISSION,"String_Node_Str");
      return false;
    }
    if (args.length < 2) {
      MainUtil.sendMessage(plr,C.NEED_BIOME);
      return true;
    }
    if (args[1].length() < 2) {
      sendMessage(plr,C.NAME_LITTLE,"String_Node_Str",args[1].length() + "String_Node_Str","String_Node_Str");
      return true;
    }
    final int biome=BlockManager.manager.getBiomeFromString(args[1]);
    if (biome == -1) {
      MainUtil.sendMessage(plr,getBiomeList(BlockManager.manager.getBiomeList()));
      return true;
    }
    plot.setBiome(args[1].toUpperCase());
    MainUtil.sendMessage(plr,C.BIOME_SET_TO.s() + args[1].toLowerCase());
    return true;
  }
  final String world=plr.getLocation().getWorld();
  final PlotWorld plotworld=PS.get().getPlotWorld(world);
  final PlotManager manager=PS.get().getPlotManager(world);
  final String[] components=manager.getPlotComponents(plotworld,plot.id);
  for (  final String component : components) {
    if (component.equalsIgnoreCase(args[0])) {
      if (!Permissions.hasPermission(plr,"String_Node_Str" + component)) {
        MainUtil.sendMessage(plr,C.NO_PERMISSION,"String_Node_Str" + component);
      }
      PlotBlock[] blocks;
      try {
        if (args.length < 2) {
          MainUtil.sendMessage(plr,C.NEED_BLOCK);
          return true;
        }
        String[] split=args[1].split("String_Node_Str");
        blocks=Configuration.BLOCKLIST.parseString(args[1]);
        for (int i=0; i < blocks.length; i++) {
          PlotBlock block=blocks[i];
          if (block == null) {
            MainUtil.sendMessage(plr,C.NOT_VALID_BLOCK,split[i]);
            String name;
            if (split[i].contains("String_Node_Str")) {
              name=split[i].split("String_Node_Str")[1];
            }
 else {
              name=split[i];
            }
            StringComparison<PlotBlock>.ComparisonResult match=BlockManager.manager.getClosestBlock(name);
            if (match != null) {
              name=BlockManager.manager.getClosestMatchingName(match.best);
              if (name != null) {
                MainUtil.sendMessage(plr,C.DID_YOU_MEAN,name.toLowerCase());
              }
            }
            return false;
          }
 else           if (!BlockManager.manager.isBlockSolid(block)) {
            MainUtil.sendMessage(plr,C.NOT_ALLOWED_BLOCK,block.toString());
            return false;
          }
        }
        for (        PlotBlock block : blocks) {
          if (!BlockManager.manager.isBlockSolid(block)) {
            MainUtil.sendMessage(plr,C.NOT_ALLOWED_BLOCK,block.toString());
            return false;
          }
        }
      }
 catch (      final Exception e2) {
        MainUtil.sendMessage(plr,C.NOT_VALID_BLOCK,args[1]);
        return false;
      }
      if (MainUtil.runners.containsKey(plot)) {
        MainUtil.sendMessage(plr,C.WAIT_FOR_TIMER);
        return false;
      }
      MainUtil.runners.put(plot,1);
      manager.setComponent(plotworld,plot.id,component,blocks);
      MainUtil.sendMessage(plr,C.GENERATING_COMPONENT);
      SetBlockQueue.addNotify(new Runnable(){
        @Override public void run(){
          MainUtil.runners.remove(plot);
        }
      }
);
      return true;
    }
  }
{
    AbstractFlag af;
    try {
      af=new AbstractFlag(args[0].toLowerCase());
    }
 catch (    final Exception e) {
      af=new AbstractFlag("String_Node_Str");
    }
    if (FlagManager.getFlags().contains(af)) {
      final StringBuilder a=new StringBuilder();
      if (args.length > 1) {
        for (int x=1; x < args.length; x++) {
          a.append("String_Node_Str").append(args[x]);
        }
      }
      MainCommand.onCommand(plr,world,("String_Node_Str" + args[0] + a.toString()).split("String_Node_Str"));
      return true;
    }
  }
  ArrayList<String> newValues=new ArrayList<String>();
  newValues.addAll(Arrays.asList(values));
  newValues.addAll(Arrays.asList(manager.getPlotComponents(PS.get().getPlotWorld(loc.getWorld()),plot.id)));
  MainUtil.sendMessage(plr,C.SUBCOMMAND_SET_OPTIONS_HEADER.s() + getArgumentList(newValues));
  return false;
}

Fixed version (ground truth):
@Override public boolean execute(final PlotPlayer plr,final String... args){
  final Location loc=plr.getLocation();
  final Plot plot=MainUtil.getPlot(loc);
  if (plot == null) {
    return !sendMessage(plr,C.NOT_IN_PLOT);
  }
  if (!plot.hasOwner()) {
    sendMessage(plr,C.PLOT_NOT_CLAIMED);
    return false;
  }
  if (!plot.isAdded(plr.getUUID())) {
    if (!Permissions.hasPermission(plr,"String_Node_Str")) {
      MainUtil.sendMessage(plr,C.NO_PERMISSION,"String_Node_Str");
      return false;
    }
  }
  if (args.length < 1) {
    PlotManager manager=PS.get().getPlotManager(loc.getWorld());
    ArrayList<String> newValues=new ArrayList<String>();
    newValues.addAll(Arrays.asList(values));
    newValues.addAll(Arrays.asList(manager.getPlotComponents(PS.get().getPlotWorld(loc.getWorld()),plot.id)));
    MainUtil.sendMessage(plr,C.SUBCOMMAND_SET_OPTIONS_HEADER.s() + getArgumentList(newValues));
    return false;
  }
  for (int i=0; i < aliases.length; i++) {
    if (aliases[i].equalsIgnoreCase(args[0])) {
      args[0]=values[i];
      break;
    }
  }
  if (args[0].equalsIgnoreCase("String_Node_Str")) {
    if (args.length < 2) {
      final String message=StringMan.replaceFromMap("String_Node_Str" + (StringUtils.join(FlagManager.getFlags(plr),"String_Node_Str")),C.replacements);
      MainUtil.sendMessage(plr,C.NEED_KEY.s().replaceAll("String_Node_Str",message));
      return false;
    }
    AbstractFlag af;
    try {
      af=FlagManager.getFlag(args[1].toLowerCase());
    }
 catch (    final Exception e) {
      af=new AbstractFlag(args[1].toLowerCase());
    }
    if (!FlagManager.getFlags().contains(af) || FlagManager.isReserved(af.getKey())) {
      MainUtil.sendMessage(plr,C.NOT_VALID_FLAG);
      return false;
    }
    if (!Permissions.hasPermission(plr,"String_Node_Str" + args[1].toLowerCase())) {
      MainUtil.sendMessage(plr,C.NO_PERMISSION,"String_Node_Str" + args[1].toLowerCase());
      return false;
    }
    if (args.length == 2) {
      if (FlagManager.getPlotFlagAbs(plot,args[1].toLowerCase()) == null) {
        MainUtil.sendMessage(plr,C.FLAG_NOT_IN_PLOT);
        return false;
      }
      final boolean result=FlagManager.removePlotFlag(plot,args[1].toLowerCase());
      if (!result) {
        MainUtil.sendMessage(plr,C.FLAG_NOT_REMOVED);
        return false;
      }
      MainUtil.sendMessage(plr,C.FLAG_REMOVED);
      APlotListener.manager.plotEntry(plr,plot);
      return true;
    }
    try {
      final String value=StringUtils.join(Arrays.copyOfRange(args,2,args.length),"String_Node_Str");
      final Object parsed_value=af.parseValueRaw(value);
      if (parsed_value == null) {
        MainUtil.sendMessage(plr,af.getValueDesc());
        return false;
      }
      final Flag flag=new Flag(FlagManager.getFlag(args[1].toLowerCase(),true),parsed_value);
      final boolean result=FlagManager.addPlotFlag(plot,flag);
      if (!result) {
        MainUtil.sendMessage(plr,C.FLAG_NOT_ADDED);
        return false;
      }
      MainUtil.sendMessage(plr,C.FLAG_ADDED);
      APlotListener.manager.plotEntry(plr,plot);
      return true;
    }
 catch (    final Exception e) {
      MainUtil.sendMessage(plr,"String_Node_Str" + e.getMessage());
      return false;
    }
  }
  if (args[0].equalsIgnoreCase("String_Node_Str")) {
    if (!Permissions.hasPermission(plr,"String_Node_Str")) {
      MainUtil.sendMessage(plr,C.NO_PERMISSION,"String_Node_Str");
      return false;
    }
    if (args.length > 1) {
      if (args[1].equalsIgnoreCase("String_Node_Str")) {
        plot.setHome(null);
        return true;
      }
      return MainUtil.sendMessage(plr,C.HOME_ARGUMENT);
    }
    final String world=plr.getLocation().getWorld();
    final Location base=MainUtil.getPlotBottomLoc(world,plot.id);
    base.setY(0);
    final Location relative=plr.getLocation().subtract(base.getX(),base.getY(),base.getZ());
    final BlockLoc blockloc=new BlockLoc(relative.getX(),relative.getY(),relative.getZ(),relative.getYaw(),relative.getPitch());
    plot.setHome(blockloc);
    return MainUtil.sendMessage(plr,C.POSITION_SET);
  }
  if (args[0].equalsIgnoreCase("String_Node_Str")) {
    if (!Permissions.hasPermission(plr,"String_Node_Str")) {
      MainUtil.sendMessage(plr,C.NO_PERMISSION,"String_Node_Str");
      return false;
    }
    if (args.length < 2) {
      MainUtil.sendMessage(plr,C.MISSING_ALIAS);
      return false;
    }
    final String alias=args[1];
    if (alias.length() >= 50) {
      MainUtil.sendMessage(plr,C.ALIAS_TOO_LONG);
      return false;
    }
    for (    final Plot p : PS.get().getPlots(plr.getLocation().getWorld()).values()) {
      if (p.settings.getAlias().equalsIgnoreCase(alias)) {
        MainUtil.sendMessage(plr,C.ALIAS_IS_TAKEN);
        return false;
      }
      if (UUIDHandler.nameExists(new StringWrapper(alias))) {
        MainUtil.sendMessage(plr,C.ALIAS_IS_TAKEN);
        return false;
      }
    }
    plot.setAlias(alias);
    MainUtil.sendMessage(plr,C.ALIAS_SET_TO.s().replaceAll("String_Node_Str",alias));
    return true;
  }
  if (args[0].equalsIgnoreCase("String_Node_Str")) {
    if (!Permissions.hasPermission(plr,"String_Node_Str")) {
      MainUtil.sendMessage(plr,C.NO_PERMISSION,"String_Node_Str");
      return false;
    }
    if (args.length < 2) {
      MainUtil.sendMessage(plr,C.NEED_BIOME);
      return true;
    }
    if (args[1].length() < 2) {
      sendMessage(plr,C.NAME_LITTLE,"String_Node_Str",args[1].length() + "String_Node_Str","String_Node_Str");
      return true;
    }
    final int biome=BlockManager.manager.getBiomeFromString(args[1]);
    if (biome == -1) {
      MainUtil.sendMessage(plr,getBiomeList(BlockManager.manager.getBiomeList()));
      return true;
    }
    plot.setBiome(args[1].toUpperCase());
    MainUtil.sendMessage(plr,C.BIOME_SET_TO.s() + args[1].toLowerCase());
    return true;
  }
  final String world=plr.getLocation().getWorld();
  final PlotWorld plotworld=PS.get().getPlotWorld(world);
  final PlotManager manager=PS.get().getPlotManager(world);
  final String[] components=manager.getPlotComponents(plotworld,plot.id);
  for (  final String component : components) {
    if (component.equalsIgnoreCase(args[0])) {
      if (!Permissions.hasPermission(plr,"String_Node_Str" + component)) {
        MainUtil.sendMessage(plr,C.NO_PERMISSION,"String_Node_Str" + component);
      }
      PlotBlock[] blocks;
      try {
        if (args.length < 2) {
          MainUtil.sendMessage(plr,C.NEED_BLOCK);
          return true;
        }
        String[] split=args[1].split("String_Node_Str");
        blocks=Configuration.BLOCKLIST.parseString(args[1]);
        for (int i=0; i < blocks.length; i++) {
          PlotBlock block=blocks[i];
          if (block == null) {
            MainUtil.sendMessage(plr,C.NOT_VALID_BLOCK,split[i]);
            String name;
            if (split[i].contains("String_Node_Str")) {
              name=split[i].split("String_Node_Str")[1];
            }
 else {
              name=split[i];
            }
            StringComparison<PlotBlock>.ComparisonResult match=BlockManager.manager.getClosestBlock(name);
            if (match != null) {
              name=BlockManager.manager.getClosestMatchingName(match.best);
              if (name != null) {
                MainUtil.sendMessage(plr,C.DID_YOU_MEAN,name.toLowerCase());
              }
            }
            return false;
          }
 else           if (!BlockManager.manager.isBlockSolid(block)) {
            MainUtil.sendMessage(plr,C.NOT_ALLOWED_BLOCK,block.toString());
            return false;
          }
        }
        for (        PlotBlock block : blocks) {
          if (!BlockManager.manager.isBlockSolid(block)) {
            MainUtil.sendMessage(plr,C.NOT_ALLOWED_BLOCK,block.toString());
            return false;
          }
        }
      }
 catch (      final Exception e2) {
        MainUtil.sendMessage(plr,C.NOT_VALID_BLOCK,args[1]);
        return false;
      }
      if (MainUtil.runners.containsKey(plot)) {
        MainUtil.sendMessage(plr,C.WAIT_FOR_TIMER);
        return false;
      }
      MainUtil.runners.put(plot,1);
      manager.setComponent(plotworld,plot.id,component,blocks);
      MainUtil.sendMessage(plr,C.GENERATING_COMPONENT);
      SetBlockQueue.addNotify(new Runnable(){
        @Override public void run(){
          MainUtil.runners.remove(plot);
        }
      }
);
      return true;
    }
  }
{
    AbstractFlag af;
    try {
      af=new AbstractFlag(args[0].toLowerCase());
    }
 catch (    final Exception e) {
      af=new AbstractFlag("String_Node_Str");
    }
    if (FlagManager.getFlags().contains(af)) {
      final StringBuilder a=new StringBuilder();
      if (args.length > 1) {
        for (int x=1; x < args.length; x++) {
          a.append("String_Node_Str").append(args[x]);
        }
      }
      MainCommand.onCommand(plr,world,("String_Node_Str" + args[0] + a.toString()).split("String_Node_Str"));
      return true;
    }
  }
  ArrayList<String> newValues=new ArrayList<String>();
  newValues.addAll(Arrays.asList(values));
  newValues.addAll(Arrays.asList(manager.getPlotComponents(PS.get().getPlotWorld(loc.getWorld()),plot.id)));
  MainUtil.sendMessage(plr,C.SUBCOMMAND_SET_OPTIONS_HEADER.s() + getArgumentList(newValues));
  return false;
}