Group.java

package us.universalpvp.pp.managers;

import java.util.ArrayList;

import org.bukkit.Bukkit;
import org.bukkit.configuration.ConfigurationSection;
import org.bukkit.entity.Player;

public class Groups {

	private String name;
	private ArrayList<String> perms;

	public Groups(String name) {
		this.name = name;

		ConfigurationSection s = PermissionsManager.getInstance().getGroupSection(name);

		if (!s.contains("perms"))
			s.set("perms", new ArrayList<String>());

		this.perms = new ArrayList<String>(s.getStringList("perms"));
	}

	public String getName() {
		return name;
	}

	public boolean hasPerm(String perm) {
		return perms.contains(perm);
	}

	public void addPerm(String perm) {
		perms.add(perm);
		PermissionsManager.getInstance().getGroupSection(name).set("perms", perms);
		PermissionsManager.getInstance().save();

		for (Player players : Bukkit.getOnlinePlayers()) {
			PermissionsManager.getInstance().injectPlayer(players);
		}
	}

	public void removePerm(String perm) {
		perms.remove(perm);
		PermissionsManager.getInstance().getGroupSection(name).set("perms", perms);
		PermissionsManager.getInstance().save();

		for (Player players : Bukkit.getOnlinePlayers()) {
			PermissionsManager.getInstance().injectPlayer(players);
		}
	}

	public ArrayList<String> getPerms() {
		return perms;
	}
}

GroupCmds.java

package us.universalpvp.pp.cmds;

import org.bukkit.ChatColor;
import org.bukkit.command.CommandSender;

import us.universalpvp.pp.managers.PermissionsManager;

public class GroupCmd extends PermsCommand {

	public void run(CommandSender sender, String[] args) {
		if (args.length == 0) {
			sender.sendMessage(ChatColor.RED + "Please specify a group.");
			return;
		}
		String g = args[0];

		if (args.length < 2) {

			if (PermissionsManager.getInstance().getGroup(g) != null) {

				if (PermissionsManager.getInstance().getGroup(g).getPerms().size() == 0) {
					sender.sendMessage(ChatColor.GREEN + "No permissions for " + g);
					return;
				}

				for (String perm : PermissionsManager.getInstance().getGroup(g).getPerms()) {
					sender.sendMessage(ChatColor.BLUE + perm);
					return;
				}
			} else {
				sender.sendMessage(
						ChatColor.RED + "Group " + ChatColor.YELLOW + g + ChatColor.RED + " does not exist!");
				sender.sendMessage(ChatColor.GREEN + "Syntax to create a group is: " + "/perms group <group> create");
			}

		} else {

			if (args[1].equalsIgnoreCase("create")) {

				PermissionsManager.getInstance().createGroup(g);
				sender.sendMessage(ChatColor.GREEN + "Created group " + g + "!");
				return;

			} else if (args[1].equalsIgnoreCase("delete")) {
				if (args.length < 3) {
					sender.sendMessage(ChatColor.RED + "Please specify a group name!");
					return;
				} else {
					PermissionsManager.getInstance().removeGroup(null, g);
					sender.sendMessage(ChatColor.BLUE + "Removed group " + g);

					return;
				}
			} else if (args[1].equalsIgnoreCase("addperm")) {

				PermissionsManager.getInstance().getGroup(g).addPerm(args[2]);
				sender.sendMessage(ChatColor.GREEN + "Added " + args[2] + " to group " + g);
				return;

			} else if (args[1].equalsIgnoreCase("removeperm")) {

				PermissionsManager.getInstance().getGroup(g).removePerm(args[2]);
				sender.sendMessage(ChatColor.BLUE + "Removed " + args[2] + " from group " + g);
				return;

			}
		}

	}

	public GroupCmd() {
		super("group", "[<name | list>] [<create | delete | addperm | removeperm> <perm>]");
	}
}

PermissionsManager.java

package us.universalpvp.pp.managers;

import java.io.File;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map.Entry;

import org.bukkit.Bukkit;
import org.bukkit.configuration.ConfigurationSection;
import org.bukkit.configuration.file.FileConfiguration;
import org.bukkit.configuration.file.YamlConfiguration;
import org.bukkit.entity.Player;
import org.bukkit.permissions.PermissionAttachment;
import org.bukkit.plugin.Plugin;

public class PermissionsManager {

	private PermissionsManager() {
	}

	private static PermissionsManager instance = new PermissionsManager();

	public static PermissionsManager getInstance() {
		return instance;
	}

	private Plugin p;
	private FileConfiguration config;
	private File cfile;

	private HashMap<String, PermissionAttachment> attachments = new HashMap<String, PermissionAttachment>();
	private ArrayList<Groups> groups = new ArrayList<>();

	public void setup(Plugin p) {
		this.p = p;

		if (!p.getDataFolder().exists())
			p.getDataFolder().mkdir();

		cfile = new File(p.getDataFolder(), "perms.yml");

		if (!cfile.exists()) {
			try {
				cfile.createNewFile();
			} catch (Exception e) {
				e.printStackTrace();
			}
		}

		config = YamlConfiguration.loadConfiguration(cfile);

		if (!config.contains("groups"))
			config.createSection("groups");

		setupGroups();
	}

	public void addPerm(String player, String perm) {
		player = player.toLowerCase();

		Player p = Bukkit.getServer().getPlayer(player);

		if (p != null) {
			injectPlayer(p);
			attachments.get(p.getName()).setPermission(perm, true);
		}

		List<String> perms = getPerms(player);
		perms.add(perm);
		config.set("user." + player + ".perms", perm);

		save();
	}

	public void removePerm(String player, String perm) {
		player = player.toLowerCase();

		Player p = Bukkit.getServer().getPlayer(player);

		if (p != null) {
			injectPlayer(p);
			attachments.get(p.getName()).setPermission(perm, false);
		}

		List<String> perms = getPerms(player);
		perms.remove(perm);
		config.set("user." + player + ".perms", perm);

		save();
	}

	public List<String> getPerms(String player) {
		player = player.toLowerCase();

		if (!config.contains("user." + player + ".perms"))
			config.set("user." + player + ".perms", new ArrayList<String>());

		return config.getStringList("user." + player + ".perms");
	}

	public void addGroup(String player, String g) {
		player = player.toLowerCase();

		List<String> groups = getGroups(player);
		groups.add(g);
		config.set("user." + player + ".groups", groups);

		save();

		Player p = Bukkit.getServer().getPlayer(player);

		if (p != null) {
			injectPlayer(p);
		}
	}

	public void removeGroup(String player, String g) {
		player = player.toLowerCase();

		List<String> groups = getGroups(player);
		groups.remove(g);
		config.set("user." + player + ".groups", groups);

		save();

		Player p = Bukkit.getServer().getPlayer(player);

		if (p != null) {
			injectPlayer(p);
		}
	}

	public List<String> getGroups(String player) {
		player = player.toLowerCase();

		if (!config.contains("user." + player + ".groups"))
			config.set("user." + player + ".groups", new ArrayList<String>());

		return config.getStringList("user." + player + ".groups");
	}

	public void createGroup(String group) {
		config.getConfigurationSection("groups").set(group + ".perms", new ArrayList<String>());
		save();
		setupGroups();
	}

	private void setupGroups() {
		groups.clear();

		for (String groupName : config.getConfigurationSection("groups").getKeys(false)) {

			groups.add(new Groups(groupName));
		}
	}

	public void injectPlayer(Player... pl) {
		for (Player p : pl) {
			if (attachments.get(p.getName()) == null)
				attachments.put(p.getName(), p.addAttachment(getPlugin()));

			for (Entry<String, Boolean> perm : attachments.get(p.getName()).getPermissions().entrySet()) {
				if (getPerms(p.getName()).contains(perm.getKey()))
					attachments.get(p.getName()).setPermission(perm.getKey(), true);
				else
					attachments.get(p.getName()).setPermission(perm.getKey(), false);
			}

			if (!config.contains("user." + p.getName().toLowerCase() + ".groups"))
				config.set("user." + p.getName().toLowerCase() + ".groups", new ArrayList<String>());

			for (String gName : config.getStringList("user." + p.getName().toLowerCase() + ".groups")) {
				for (Groups g : groups) {
					if (g.getName().equals(gName)) {
						for (String perm : g.getPerms()) {
							System.out.println("Injecting " + perm + " from " + gName);
							attachments.get(p.getName()).setPermission(perm, true);
						}
					}
				}
			}
		}
	}

	public void uninjectPlayer(Player pl) {
		if (attachments.get(pl.getName()) == null)
			return;
		pl.removeAttachment(attachments.get(pl.getName()));
		attachments.remove(pl.getName());
	}

	public Groups getGroup(String name) {
		for (Groups g : groups) {
			if (g.getName().equals(name))
				return g;
		}

		return null;
	}

	public ConfigurationSection getGroupSection(String name) {
		return config.getConfigurationSection("groups." + name);
	}

	public void save() {
		try {
			config.save(cfile);
		} catch (Exception e) {
			e.printStackTrace();
		}
	}

	public Plugin getPlugin() {
		return p;
	}
}