Program: 170048
Project: 170048
Buggy source:
@Override public void processCommand(ICommandSender sender,String[] args){
  if (args.length > 0) {
    EntityPlayer entityPlayer=(EntityPlayer)sender;
    FlagWorld flagWorld=this.modFlagData.getFlagWorld(entityPlayer.worldObj);
    String commandName=args[0].toLowerCase();
    if (commandName.equalsIgnoreCase("String_Node_Str")) {
      if (args.length > 1) {
        String regionName=args[1];
        if (regionName.equalsIgnoreCase("String_Node_Str")) {
          String msg="String_Node_Str";
          Iterator<FlagWorld> itWorlds=this.modFlagData.getFlagWorlds().iterator();
          while (itWorlds.hasNext()) {
            Iterator<FlagRegion> itRegion=itWorlds.next().getRegions().iterator();
            while (itRegion.hasNext()) {
              FlagRegion flagRegion=itRegion.next();
              msg=msg + "String_Node_Str" + flagRegion.name+ "String_Node_Str"+ flagRegion.region.min.x+ "String_Node_Str"+ flagRegion.region.min.z+ "String_Node_Str"+ "String_Node_Str";
            }
          }
          if (msg != "String_Node_Str") {
            msg="String_Node_Str" + msg;
          }
 else {
            msg="String_Node_Str";
          }
          sender.sendChatToPlayer(msg);
        }
 else         if (flagWorld.getRegion(regionName) != null) {
          String msg="String_Node_Str";
          Iterator<Flag> i=flagWorld.getRegion(regionName).getFlags().iterator();
          while (i.hasNext()) {
            Flag flag=i.next();
            msg=msg + "String_Node_Str" + flag.name+ "String_Node_Str"+ flag.value+ "String_Node_Str";
          }
          if (msg != "String_Node_Str") {
            msg="String_Node_Str" + regionName + "String_Node_Str"+ msg;
          }
 else {
            msg="String_Node_Str";
          }
          sender.sendChatToPlayer(msg);
        }
 else {
          String msg="String_Node_Str";
          Iterator<Flag> i=flagWorld.getFlagsInPosition(new Vector3(entityPlayer)).iterator();
          while (i.hasNext()) {
            Flag flag=i.next();
            msg=msg + "String_Node_Str" + flag.name+ "String_Node_Str"+ flag.value+ "String_Node_Str";
          }
          sender.sendChatToPlayer(msg);
        }
      }
 else {
        String msg="String_Node_Str";
        Iterator<FlagRegion> i=flagWorld.getRegions().iterator();
        while (i.hasNext()) {
          FlagRegion flagRegion=i.next();
          msg=msg + "String_Node_Str" + flagRegion.name+ "String_Node_Str"+ flagRegion.region.min.x+ "String_Node_Str"+ flagRegion.region.min.z+ "String_Node_Str"+ "String_Node_Str";
        }
        if (msg != "String_Node_Str") {
          msg="String_Node_Str" + msg;
        }
 else {
          msg="String_Node_Str";
        }
        sender.sendChatToPlayer(msg);
      }
      return;
    }
 else     if (commandName.equalsIgnoreCase("String_Node_Str")) {
      String regionName=args[1];
      if (regionName.equalsIgnoreCase(FlagWorld.GLOBAL_REGION)) {
        if (flagWorld.addRegion(regionName,new Vector3(entityPlayer),1)) {
          sender.sendChatToPlayer("String_Node_Str");
          return;
        }
      }
 else       if (args.length > 2) {
        int radius=0;
        try {
          radius=Integer.parseInt(args[2]);
        }
 catch (        Exception e) {
          throw new WrongUsageException("String_Node_Str");
        }
        if (radius > 0) {
          if (flagWorld.getRegion(regionName) == null) {
            if (flagWorld.addRegion(regionName,new Vector3(entityPlayer),radius)) {
              sender.sendChatToPlayer("String_Node_Str" + regionName + "String_Node_Str");
              return;
            }
          }
 else {
            throw new WrongUsageException("String_Node_Str");
          }
        }
 else {
          throw new WrongUsageException("String_Node_Str");
        }
      }
 else {
        throw new WrongUsageException("String_Node_Str" + this.getCommandName() + "String_Node_Str");
      }
    }
 else     if (commandName.equalsIgnoreCase("String_Node_Str")) {
      if (args.length > 1) {
        String regionName=args[1];
        if (flagWorld.removeRegion(regionName)) {
          sender.sendChatToPlayer("String_Node_Str" + regionName + "String_Node_Str");
        }
 else {
          throw new WrongUsageException("String_Node_Str");
        }
      }
 else {
        throw new WrongUsageException("String_Node_Str");
      }
      return;
    }
 else     if (commandName.equalsIgnoreCase("String_Node_Str")) {
      if (args.length > 2) {
        String regionName=args[1];
        String flagName=args[2];
        FlagRegion flagRegion=flagWorld.getRegion(regionName);
        if (flagRegion != null) {
          if (args.length > 3) {
            String flagValue=args[3];
            if (FlagRegistry.flags.contains(flagName)) {
              flagRegion.setFlag(flagName,flagValue);
              sender.sendChatToPlayer("String_Node_Str" + flagName + "String_Node_Str"+ flagValue+ "String_Node_Str"+ regionName+ "String_Node_Str");
            }
 else {
              String flags="String_Node_Str";
              for (              String registeredFlag : FlagRegistry.flags) {
                flags=flags + registeredFlag + "String_Node_Str";
              }
              throw new WrongUsageException(flags);
            }
          }
 else {
            flagRegion.removeFlag(flagName);
            sender.sendChatToPlayer("String_Node_Str" + flagName + "String_Node_Str");
          }
        }
 else {
          throw new WrongUsageException("String_Node_Str" + regionName + "String_Node_Str");
        }
      }
 else {
        throw new WrongUsageException("String_Node_Str" + this.getCommandName() + "String_Node_Str");
      }
      return;
    }
  }
  throw new WrongUsageException(this.getCommandUsage(sender));
}

Fixed version (ground truth):
@Override public void processCommand(ICommandSender sender,String[] args){
  if (args.length > 0) {
    EntityPlayer entityPlayer=(EntityPlayer)sender;
    FlagWorld flagWorld=this.modFlagData.getFlagWorld(entityPlayer.worldObj);
    String commandName=args[0].toLowerCase();
    if (commandName.equalsIgnoreCase("String_Node_Str")) {
      if (args.length > 1) {
        String regionName=args[1];
        if (regionName.equalsIgnoreCase("String_Node_Str")) {
          String msg="String_Node_Str";
          Iterator<FlagWorld> itWorlds=this.modFlagData.getFlagWorlds().iterator();
          while (itWorlds.hasNext()) {
            Iterator<FlagRegion> itRegion=itWorlds.next().getRegions().iterator();
            while (itRegion.hasNext()) {
              FlagRegion flagRegion=itRegion.next();
              msg=msg + "String_Node_Str" + flagRegion.name+ "String_Node_Str"+ flagRegion.region.min.x+ "String_Node_Str"+ flagRegion.region.min.z+ "String_Node_Str"+ "String_Node_Str";
            }
          }
          if (msg != "String_Node_Str") {
            msg="String_Node_Str" + msg;
          }
 else {
            msg="String_Node_Str";
          }
          sender.sendChatToPlayer(msg);
        }
 else         if (flagWorld.getRegion(regionName) != null) {
          String msg="String_Node_Str";
          Iterator<Flag> i=flagWorld.getRegion(regionName).getFlags().iterator();
          while (i.hasNext()) {
            Flag flag=i.next();
            msg=msg + "String_Node_Str" + flag.name+ "String_Node_Str"+ flag.value+ "String_Node_Str";
          }
          if (msg != "String_Node_Str") {
            msg="String_Node_Str" + regionName + "String_Node_Str"+ msg;
          }
 else {
            msg="String_Node_Str";
          }
          sender.sendChatToPlayer(msg);
        }
 else {
          String msg="String_Node_Str";
          Iterator<Flag> i=flagWorld.getFlagsInPosition(new Vector3(entityPlayer)).iterator();
          while (i.hasNext()) {
            Flag flag=i.next();
            msg=msg + "String_Node_Str" + flag.name+ "String_Node_Str"+ flag.value+ "String_Node_Str";
          }
          sender.sendChatToPlayer(msg);
        }
      }
 else {
        String msg="String_Node_Str";
        Iterator<FlagRegion> i=flagWorld.getRegions().iterator();
        while (i.hasNext()) {
          FlagRegion flagRegion=i.next();
          msg=msg + "String_Node_Str" + flagRegion.name+ "String_Node_Str"+ flagRegion.region.min.x+ "String_Node_Str"+ flagRegion.region.min.z+ "String_Node_Str"+ "String_Node_Str";
        }
        if (msg != "String_Node_Str") {
          msg="String_Node_Str" + msg;
        }
 else {
          msg="String_Node_Str";
        }
        sender.sendChatToPlayer(msg);
      }
      return;
    }
 else     if (commandName.equalsIgnoreCase("String_Node_Str") && args.length > 1) {
      String regionName=args[1];
      if (regionName.equalsIgnoreCase(FlagWorld.GLOBAL_REGION)) {
        if (flagWorld.addRegion(regionName,new Vector3(entityPlayer),1)) {
          sender.sendChatToPlayer("String_Node_Str");
          return;
        }
      }
 else       if (args.length > 2) {
        int radius=0;
        try {
          radius=Integer.parseInt(args[2]);
        }
 catch (        Exception e) {
          throw new WrongUsageException("String_Node_Str");
        }
        if (radius > 0) {
          if (flagWorld.getRegion(regionName) == null) {
            if (flagWorld.addRegion(regionName,new Vector3(entityPlayer),radius)) {
              sender.sendChatToPlayer("String_Node_Str" + regionName + "String_Node_Str");
              return;
            }
          }
 else {
            throw new WrongUsageException("String_Node_Str");
          }
        }
 else {
          throw new WrongUsageException("String_Node_Str");
        }
      }
 else {
        throw new WrongUsageException("String_Node_Str" + this.getCommandName() + "String_Node_Str");
      }
    }
 else     if (commandName.equalsIgnoreCase("String_Node_Str")) {
      if (args.length > 1) {
        String regionName=args[1];
        if (flagWorld.removeRegion(regionName)) {
          sender.sendChatToPlayer("String_Node_Str" + regionName + "String_Node_Str");
        }
 else {
          throw new WrongUsageException("String_Node_Str");
        }
      }
 else {
        throw new WrongUsageException("String_Node_Str");
      }
      return;
    }
 else     if (commandName.equalsIgnoreCase("String_Node_Str")) {
      if (args.length > 2) {
        String regionName=args[1];
        String flagName=args[2];
        FlagRegion flagRegion=flagWorld.getRegion(regionName);
        if (flagRegion != null) {
          if (FlagRegistry.flags.contains(flagName)) {
            if (args.length > 3) {
              String flagValue=args[3];
              flagRegion.setFlag(flagName,flagValue);
              sender.sendChatToPlayer("String_Node_Str" + flagName + "String_Node_Str"+ flagValue+ "String_Node_Str"+ regionName+ "String_Node_Str");
            }
 else {
              flagRegion.removeFlag(flagName);
              sender.sendChatToPlayer("String_Node_Str" + flagName + "String_Node_Str");
            }
          }
 else {
            String flags="String_Node_Str";
            for (            String registeredFlag : FlagRegistry.flags) {
              flags=flags + registeredFlag + "String_Node_Str";
            }
            throw new WrongUsageException(flags);
          }
        }
 else {
          throw new WrongUsageException("String_Node_Str" + regionName + "String_Node_Str");
        }
      }
 else {
        throw new WrongUsageException("String_Node_Str" + this.getCommandName() + "String_Node_Str");
      }
      return;
    }
  }
  throw new WrongUsageException(this.getCommandUsage(sender));
}