Example of new argument parsing for /clear!

New.java

	@CommandDescription(aliases = "clear", usage = "[player] [item] [data]", desc = "Clears the target's inventory", min = 0, max = 3)
	@Permissible("vanilla.command.clear")
	public void clear(CommandSource source, CommandArguments args) throws CommandException {
		Player player = args.popPlayerOrMe("player", source);
		Material filter = VanillaArgumentTypes.popMaterial("filter", args);
		Integer data = args.popInteger("data");


		PlayerInventory inv = player.get(PlayerInventory.class);
		if (inv == null) {
			throw new CommandException(player.getName() + " doesn't have a inventory!");
		} else {
			// Count the items and clear the inventory
			Inventory[] inventories = new Inventory[]{inv.getMain(), inv.getQuickbar(), inv.getArmor()};
			int cleared = 0;
			for (int k = 0; k < inventories.length; k++) {
				for (int i = 0; i < inventories[k].size(); i++) {
					if (inventories[k].get(i) != null && (filter == null || inventories[k].get(i).isMaterial(filter)) && (data == null || inventories[k].get(i).getData() == data)) {
						cleared += inventories[k].get(i).getAmount();
						inventories[k].set(i, null);
					}
				}
			}

			if (cleared == 0) {
				throw new CommandException("Inventory is already empty");
			}

			source.sendMessage(plugin.getPrefix() + ChatStyle.GREEN + "Cleared the inventory of " + player.getName() + ", removing " + cleared + " items.");
		}
	}

Old.java

	@Command(aliases = "clear", usage = "[player] [item] [data]", desc = "Clears the target's inventory", min = 0, max = 3)
	@CommandPermissions("vanilla.command.clear")
	public void clear(CommandSource source, CommandArguments args) throws CommandException {
		Player player;
		Material filter = null;
		Integer data = null;
		
		if (args.length() == 0) {
			if (!(source instanceof Player)) {
				throw new CommandException("You must be a player to clear your own inventory.");
			}
			player = (Player) source;
		} else if (args.length() == 3) { 
			if (getEngine() instanceof Client) {
				throw new CommandException("You cannot search for players unless you are in server mode.");
			}
			
			player = getEngine().getPlayer(args.getString(0), false);
			if (player == null) {
				throw new CommandException(args.getString(0) + " is not online.");
			}
			
			if (args.isInteger(1)) {
				filter = VanillaMaterials.getMaterial((short) args.getInteger(1));
			} else {
				filter = Material.get(args.getString(1));
			}
			
			data = args.getInteger(2);
		} else {
			if (args.isInteger(0)) {
				if (!(source instanceof Player)) {
					throw new CommandException("You must be a player to clear your own inventory.");
				}
				player = (Player) source;
				
				filter = VanillaMaterials.getMaterial((short) args.getInteger(0));
			} else {
				if (getEngine() instanceof Client) {
					throw new CommandException("You cannot search for players unless you are in server mode.");
				}
				
				player = getEngine().getPlayer(args.getString(0), false);
				if (player == null) {
					filter = Material.get(args.getString(0));
					if (filter == null) {
						throw new CommandException(args.getString(0) + " is not online.");
					}
					if (!(source instanceof Player)) {
						throw new CommandException("You must be a player to clear your own inventory.");
					}
					player = (Player) source;
				}
			}
			if (args.length() == 2) {
				if (args.isInteger(1)) {
					if (filter == null) {
						filter = VanillaMaterials.getMaterial((short) args.getInteger(1));
					} else {
						data = args.getInteger(1);
					}
				} else {
					if (filter == null) {
						filter = Material.get(args.getString(1));
					} else {
						throw new NumberFormatException();
					}
				}
			}
		}
		
		PlayerInventory inv = player.get(PlayerInventory.class);
		if (inv == null) {
			throw new CommandException(player.getName() + " doesn't have a inventory!");
		} else {
			// Count the items and clear the inventory
			Inventory[] inventories = new Inventory[] { inv.getMain(), inv.getQuickbar(), inv.getArmor() };
			int cleared = 0;
			for (int k = 0; k < inventories.length; k++) {
				for (int i = 0; i < inventories[k].size(); i++) {
					if (inventories[k].get(i) != null && (filter == null || inventories[k].get(i).isMaterial(filter)) && (data == null || inventories[k].get(i).getData() == data)) {
						cleared += inventories[k].get(i).getAmount();
						inventories[k].set(i, null);
					}
				}
			}
			
			if (cleared == 0) {
				throw new CommandException("Inventory is already empty");
			}
			
			source.sendMessage(plugin.getPrefix() + ChatStyle.GREEN + "Cleared the inventory of " + player.getName() + ", removing " + cleared + " items.");
		}	
	}

In New, Line 12, the else isn't needed because a CommandException would be thrown and the method wouldn't continue.
EDIT: see my fork