Okay, lets fix everything that depended on Permissions

src/main/java/com/gmail/nossr50/commands/general/AddxpCommand.java

@@ -23,7 +23,12 @@ public class AddxpCommand implements CommandExecutor {
 
 	@Override
 	public boolean onCommand(CommandSender sender, Command command, String label, String[] args) {
-		if (!mcPermissions.permissionsEnabled) {
+		Player player = null;
+        if (sender instanceof Player) {
+            player = (Player) sender;
+        }
+        
+        if (player != null && !mcPermissions.getInstance().mmoedit(player)) {
 			sender.sendMessage("This command requires permissions.");
 			return true;
 		}
@@ -55,8 +60,6 @@ public class AddxpCommand implements CommandExecutor {
 			return true;
 		}
 
-		Player player = (Player) sender;
-
 		if (!mcPermissions.getInstance().mmoedit(player)) {
 			player.sendMessage(ChatColor.YELLOW + "[mcMMO] " + ChatColor.DARK_RED + mcLocale.getString("mcPlayerListener.NoPermission"));
 			return true;

src/main/java/com/gmail/nossr50/commands/general/MmoeditCommand.java

@@ -24,7 +24,7 @@ public class MmoeditCommand implements CommandExecutor {
 
 	@Override
 	public boolean onCommand(CommandSender sender, Command command, String label, String[] args) {
-		if (!mcPermissions.permissionsEnabled) {
+		if (!mcPermissions.getInstance().mmoedit((Player) sender)) {
 			sender.sendMessage("This command requires permissions.");
 			return true;
 		}

src/main/java/com/gmail/nossr50/commands/general/StatsCommand.java

@@ -33,8 +33,7 @@ public class StatsCommand implements CommandExecutor {
 
 		player.sendMessage(mcLocale.getString("mcPlayerListener.YourStats"));
 
-		if (mcPermissions.getEnabled())
-			player.sendMessage(mcLocale.getString("mcPlayerListener.NoSkillNote"));
+		player.sendMessage(mcLocale.getString("mcPlayerListener.NoSkillNote"));
 
 		ChatColor header = ChatColor.GOLD;
 

src/main/java/com/gmail/nossr50/commands/mc/McabilityCommand.java

@@ -6,7 +6,6 @@ import org.bukkit.command.CommandSender;
 import org.bukkit.entity.Player;
 
 import com.gmail.nossr50.Users;
-import com.gmail.nossr50.mcPermissions;
 import com.gmail.nossr50.config.LoadProperties;
 import com.gmail.nossr50.datatypes.PlayerProfile;
 import com.gmail.nossr50.locale.mcLocale;
@@ -14,7 +13,12 @@ import com.gmail.nossr50.locale.mcLocale;
 public class McabilityCommand implements CommandExecutor {
 	@Override
 	public boolean onCommand(CommandSender sender, Command command, String label, String[] args) {
-		if (!mcPermissions.permissionsEnabled) {
+        Player player = null;
+        if (sender instanceof Player) {
+            player = (Player) sender;
+        }
+
+		if (player != null && player.hasPermission("mcmmo.commands.ability")) {
 			sender.sendMessage("This command requires permissions.");
 			return true;
 		}
@@ -29,7 +33,6 @@ public class McabilityCommand implements CommandExecutor {
 			return true;
 		}
 
-		Player player = (Player) sender;
 		PlayerProfile PP = Users.getProfile(player);
 
 		if (PP.getAbilityUse()) {

src/main/java/com/gmail/nossr50/commands/mc/McgodCommand.java

@@ -28,12 +28,12 @@ public class McgodCommand implements CommandExecutor {
 		Player player = (Player) sender;
 		PlayerProfile PP = Users.getProfile(player);
 
-		if (mcPermissions.permissionsEnabled) {
-			if (!mcPermissions.getInstance().mcgod(player)) {
-				player.sendMessage(ChatColor.YELLOW + "[mcMMO] " + ChatColor.DARK_RED + mcLocale.getString("mcPlayerListener.NoPermission"));
-				return true;
-			}
+		if (!mcPermissions.getInstance().mcgod(player)) {
+			player.sendMessage(ChatColor.YELLOW + "[mcMMO] " + ChatColor.DARK_RED + mcLocale.getString("mcPlayerListener.NoPermission"));
+			return true;
+		}
 
+        if (mcPermissions.getInstance().mcgod(player)) {
 			if (PP.getGodMode()) {
 				player.sendMessage(mcLocale.getString("mcPlayerListener.GodModeDisabled"));
 				PP.toggleGodMode();

src/main/java/com/gmail/nossr50/commands/spout/XplockCommand.java

@@ -31,7 +31,7 @@ public class XplockCommand implements CommandExecutor {
 		Player player = (Player) sender;
 		PlayerProfile PP = Users.getProfile(player);
 
-		if (args.length >= 1 && Skills.isSkill(args[0]) && mcPermissions.permission(player, "mcmmo.skills." + Skills.getSkillType(args[0]).toString().toLowerCase())) {
+		if (args.length >= 1 && Skills.isSkill(args[0]) && mcPermissions.getInstance().permission(player, "mcmmo.skills." + Skills.getSkillType(args[0]).toString().toLowerCase())) {
 			if (PP.getXpBarLocked()) {
 				PP.setSkillLock(Skills.getSkillType(args[0]));
 				player.sendMessage(mcLocale.getString("Commands.xplock.locked", new Object[] { m.getCapitalized(PP.getSkillLock().toString()) }));
@@ -52,7 +52,7 @@ public class XplockCommand implements CommandExecutor {
 			}
 		} else if (args.length >= 1 && !Skills.isSkill(args[0])) {
 			player.sendMessage("Commands.xplock.invalid");
-		} else if (args.length >= 2 && Skills.isSkill(args[0]) && !mcPermissions.permission(player, "mcmmo.skills." + Skills.getSkillType(args[0]).toString().toLowerCase())) {
+		} else if (args.length >= 2 && Skills.isSkill(args[0]) && !mcPermissions.getInstance().permission(player, "mcmmo.skills." + Skills.getSkillType(args[0]).toString().toLowerCase())) {
 			player.sendMessage(ChatColor.YELLOW + "[mcMMO] " + ChatColor.DARK_RED + mcLocale.getString("mcPlayerListener.NoPermission"));
 			return true;
 		}

src/main/java/com/gmail/nossr50/mcPermissions.java

@@ -24,11 +24,9 @@ import org.bukkit.entity.Player;
 public class mcPermissions 
 {
     private static volatile mcPermissions instance;
-
-
-    public static void initialize(Server server) 
-    {
-        Logger log = Logger.getLogger("Minecraft");
+    
+    public boolean permission(Player player, String perm) {
+        return player.hasPermission(perm);
     }
 
     public boolean admin(Player player){