Importing Bukkit is usually bad.

src/main/java/com/gmail/nossr50/commands/player/McrankCommand.java

@@ -1,6 +1,5 @@
 package com.gmail.nossr50.commands.player;
 
-import org.bukkit.Bukkit;
 import org.bukkit.command.Command;
 import org.bukkit.command.CommandExecutor;
 import org.bukkit.command.CommandSender;
@@ -119,6 +118,6 @@ public class McrankCommand implements CommandExecutor {
     }
 
     private void sqlDisplay(CommandSender sender, String playerName) {
-        Bukkit.getScheduler().runTaskAsynchronously(mcMMO.p, new McrankCommandAsyncTask(playerName, sender));
+        mcMMO.p.getServer().getScheduler().runTaskAsynchronously(mcMMO.p, new McrankCommandAsyncTask(playerName, sender));
     }
 }

src/main/java/com/gmail/nossr50/commands/player/MctopCommand.java

@@ -1,6 +1,5 @@
 package com.gmail.nossr50.commands.player;
 
-import org.bukkit.Bukkit;
 import org.bukkit.ChatColor;
 import org.bukkit.command.Command;
 import org.bukkit.command.CommandExecutor;
@@ -124,6 +123,6 @@ public class MctopCommand implements CommandExecutor {
     }
 
     private void sqlDisplay(int page, String query, CommandSender sender, Command command) {
-        Bukkit.getScheduler().runTaskAsynchronously(mcMMO.p, new MctopCommandAsyncTask(page, query, sender, command));
+        mcMMO.p.getServer().getScheduler().runTaskAsynchronously(mcMMO.p, new MctopCommandAsyncTask(page, query, sender, command));
     }
 }

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

@@ -8,7 +8,6 @@ import java.util.List;
 
 import net.shatteredlands.shatt.backup.ZipLibrary;
 
-import org.bukkit.Bukkit;
 import org.bukkit.OfflinePlayer;
 import org.bukkit.entity.Player;
 import org.bukkit.event.HandlerList;
@@ -156,7 +155,7 @@ public class mcMMO extends JavaPlugin {
                 getLogger().info("Please do not replace the mcMMO jar while the server is running.");
             }
 
-            Bukkit.getPluginManager().disablePlugin(this);
+            getServer().getPluginManager().disablePlugin(this);
         }
     }
 

src/main/java/com/gmail/nossr50/runnables/commands/McrankCommandAsyncTask.java

@@ -2,7 +2,6 @@ package com.gmail.nossr50.runnables.commands;
 
 import java.util.Map;
 
-import org.bukkit.Bukkit;
 import org.bukkit.command.CommandSender;
 
 import com.gmail.nossr50.mcMMO;
@@ -24,7 +23,7 @@ public class McrankCommandAsyncTask implements Runnable {
     public void run() {
         final Map<String, Integer> skills = DatabaseManager.readSQLRank(playerName);
 
-        Bukkit.getScheduler().scheduleSyncDelayedTask(mcMMO.p, new Runnable() {
+        mcMMO.p.getServer().getScheduler().scheduleSyncDelayedTask(mcMMO.p, new Runnable() {
             @Override
             public void run() {
                 sender.sendMessage(LocaleLoader.getString("Commands.mcrank.Heading"));

src/main/java/com/gmail/nossr50/runnables/commands/MctopCommandAsyncTask.java

@@ -3,7 +3,6 @@ package com.gmail.nossr50.runnables.commands;
 import java.util.ArrayList;
 import java.util.HashMap;
 
-import org.bukkit.Bukkit;
 import org.bukkit.ChatColor;
 import org.bukkit.command.Command;
 import org.bukkit.command.CommandSender;
@@ -40,7 +39,7 @@ public class MctopCommandAsyncTask implements Runnable {
         }
         String tablePrefix = Config.getInstance().getMySQLTablePrefix();
         final HashMap<Integer, ArrayList<String>> userslist = DatabaseManager.read("SELECT " + query + ", user, NOW() FROM " + tablePrefix + "users JOIN " + tablePrefix + "skills ON (user_id = id) WHERE " + query + " > 0 ORDER BY " + query + " DESC, user LIMIT " + ((page * 10) - 10) + ",10");
-        Bukkit.getScheduler().scheduleSyncDelayedTask(mcMMO.p, new Runnable() {
+        mcMMO.p.getServer().getScheduler().scheduleSyncDelayedTask(mcMMO.p, new Runnable() {
             @Override
             public void run() {
                 if (query.equals("taming+mining+woodcutting+repair+unarmed+herbalism+excavation+archery+swords+axes+acrobatics+fishing")) {

src/main/java/com/gmail/nossr50/util/HolidayManager.java

@@ -12,7 +12,6 @@ import java.util.Date;
 import java.util.GregorianCalendar;
 import java.util.List;
 
-import org.bukkit.Bukkit;
 import org.bukkit.ChatColor;
 import org.bukkit.Color;
 import org.bukkit.FireworkEffect;
@@ -98,7 +97,7 @@ public final class HolidayManager {
                 final int firework_amount = 10;
                 for (int i = 0; i < firework_amount; i++) {
                     int delay = (int) (Math.random() * 3) + 4;
-                    Bukkit.getScheduler().scheduleSyncDelayedTask(mcMMO.p, new Runnable() {
+                    mcMMO.p.getServer().getScheduler().scheduleSyncDelayedTask(mcMMO.p, new Runnable() {
                         @Override
                         public void run() {
                             spawnFireworks((Player) sender);

src/main/java/com/gmail/nossr50/util/blockmeta/HashChunkletManager.java

@@ -11,10 +11,11 @@ import java.io.StreamCorruptedException;
 import java.io.UTFDataFormatException;
 import java.util.HashMap;
 
-import org.bukkit.Bukkit;
 import org.bukkit.World;
 import org.bukkit.block.Block;
 
+import com.gmail.nossr50.mcMMO;
+
 public class HashChunkletManager implements ChunkletManager {
     public HashMap<String, ChunkletStore> store = new HashMap<String, ChunkletStore>();
 
@@ -168,7 +169,7 @@ public class HashChunkletManager implements ChunkletManager {
 
     @Override
     public void saveAll() {
-        for (World world : Bukkit.getWorlds()) {
+        for (World world : mcMMO.p.getServer().getWorlds()) {
             saveWorld(world);
         }
     }
@@ -176,7 +177,7 @@ public class HashChunkletManager implements ChunkletManager {
     @Override
     public void unloadAll() {
         saveAll();
-        for (World world : Bukkit.getWorlds()) {
+        for (World world : mcMMO.p.getServer().getWorlds()) {
             unloadWorld(world);
         }
     }
@@ -276,7 +277,7 @@ public class HashChunkletManager implements ChunkletManager {
         for (String key : store.keySet()) {
             if (store.get(key).isEmpty()) {
                 String[] info = key.split(",");
-                File dataDir = new File(Bukkit.getWorld(info[0]).getWorldFolder(), "mcmmo_data");
+                File dataDir = new File(mcMMO.p.getServer().getWorld(info[0]).getWorldFolder(), "mcmmo_data");
 
                 File cxDir = new File(dataDir, "" + info[1]);
                 if (!cxDir.exists()) {

src/main/java/com/gmail/nossr50/util/blockmeta/chunkmeta/HashChunkManager.java

@@ -11,12 +11,12 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.UUID;
 
-import org.bukkit.Bukkit;
 import org.bukkit.World;
 import org.bukkit.block.Block;
 import org.bukkit.block.BlockState;
 import org.bukkit.entity.Entity;
 
+import com.gmail.nossr50.mcMMO;
 import com.gmail.nossr50.util.blockmeta.conversion.BlockStoreConversionZDirectory;
 
 public class HashChunkManager implements ChunkManager {
@@ -283,7 +283,7 @@ public class HashChunkManager implements ChunkManager {
     public synchronized void saveAll() {
         closeAll();
 
-        for (World world : Bukkit.getWorlds()) {
+        for (World world : mcMMO.p.getServer().getWorlds()) {
             saveWorld(world);
         }
     }
@@ -292,7 +292,7 @@ public class HashChunkManager implements ChunkManager {
     public synchronized void unloadAll() {
         closeAll();
 
-        for (World world : Bukkit.getWorlds()) {
+        for (World world : mcMMO.p.getServer().getWorlds()) {
             unloadWorld(world);
         }
     }