Let's try and load the jails from flatfile.

src/main/java/com/graywolf336/jail/JailIO.java

@@ -2,11 +2,13 @@ package com.graywolf336.jail;
 
 import java.io.File;
 import java.io.IOException;
+import java.util.Set;
 
 import org.bukkit.configuration.file.FileConfiguration;
 import org.bukkit.configuration.file.YamlConfiguration;
 
 import com.graywolf336.jail.beans.Jail;
+import com.graywolf336.jail.beans.SimpleLocation;
 
 public class JailIO {
 	private JailMain pl;
@@ -50,10 +52,22 @@ public class JailIO {
 				break;
 			default:
 				//load the jails from flatfile
-				if(flat.contains("jails"))
-					pl.getLogger().info("Jails exists");
+				if(flat.isConfigurationSection("jails")) {
+					Set<String> jails = flat.getConfigurationSection("jails").getKeys(false);
+					if(!jails.isEmpty()) {
+						pl.getLogger().info("Jails configuration section exists and there are " + jails.size() + ".");
+						for(String name : jails) {
+							loadJail(name);
+						}
+					}else {
+						pl.getLogger().warning("Jails configuration section exists but no jails are there.");
+					}
+				}
 				break;
 		}
+		
+		int s = pl.getJailManager().getJails().size();
+		pl.getLogger().info("Loaded " + s + (s == 1 ? " jail." : " jails."));
 	}
 	
 	public void saveJail(Jail j) {
@@ -66,6 +80,7 @@ public class JailIO {
 					String node = "jails." + j.getName() + ".";
 					
 					//Corners
+					flat.set(node + "world", j.getWorldName());
 					flat.set(node + "top.x", j.getMaxPoint().getBlockX());
 					flat.set(node + "top.y", j.getMaxPoint().getBlockY());
 					flat.set(node + "top.z", j.getMaxPoint().getBlockZ());
@@ -77,15 +92,16 @@ public class JailIO {
 					flat.set(node + "tps.in.x", j.getTeleportIn().getX());
 					flat.set(node + "tps.in.y", j.getTeleportIn().getY());
 					flat.set(node + "tps.in.z", j.getTeleportIn().getZ());
-					flat.set(node + "tps.in.pitch", j.getTeleportIn().getPitch());
 					flat.set(node + "tps.in.yaw", j.getTeleportIn().getYaw());
+					flat.set(node + "tps.in.pitch", j.getTeleportIn().getPitch());
 					
 					//Tele out
+					flat.set(node + "tps.free.world", j.getTeleportFree().getWorld().getName());
 					flat.set(node + "tps.free.x", j.getTeleportFree().getX());
 					flat.set(node + "tps.free.y", j.getTeleportFree().getY());
 					flat.set(node + "tps.free.z", j.getTeleportFree().getZ());
-					flat.set(node + "tps.free.pitch", j.getTeleportFree().getPitch());
 					flat.set(node + "tps.free.yaw", j.getTeleportFree().getYaw());
+					flat.set(node + "tps.free.pitch", j.getTeleportFree().getPitch());
 					
 					try {
 						flat.save(new File(pl.getDataFolder(), "data.yml"));
@@ -98,4 +114,37 @@ public class JailIO {
 				break;
 		}
 	}
+	
+	private void loadJail(String name) {
+		switch(storage) {
+			case 1:
+			case 2:
+				break;
+			default:
+				String node = "jails." + name + ".";
+				Jail j = new Jail(pl, name);
+				
+				j.setWorld(node + "world");
+				j.setMaxPoint(new int[] {flat.getInt(node + "top.x"), flat.getInt(node + "top.y"), flat.getInt(node + "top.z")});
+				j.setMinPoint(new int[] {flat.getInt(node + "bottom.x"), flat.getInt(node + "bottom.y"), flat.getInt(node + "bottom.z")});
+				
+				j.setTeleportIn(new SimpleLocation(
+						flat.getString(node + "world"),
+						flat.getDouble(node + "tps.in.x"),
+						flat.getDouble(node + "tps.in.y"),
+						flat.getDouble(node + "tps.in.z"),
+						(float) flat.getDouble(node + "tps.in.yaw"),
+						(float) flat.getDouble(node + "tps.in.pitch")));
+				j.setTeleportFree(new SimpleLocation(
+						flat.getString(node + "tps.free.world"),
+						flat.getDouble(node + "tps.free.x"),
+						flat.getDouble(node + "tps.free.y"),
+						flat.getDouble(node + "tps.free.z"),
+						(float) flat.getDouble(node + "tps.free.yaw"),
+						(float) flat.getDouble(node + "tps.free.pitch")));
+				
+				pl.getJailManager().addJail(j, false);
+				break;
+		}
+	}
 }

src/main/java/com/graywolf336/jail/JailMain.java

@@ -19,11 +19,11 @@ public class JailMain extends JavaPlugin {
 	public void onEnable() {
 		loadConfig();
 		
+		jm = new JailManager(this);
 		io = new JailIO(this);
 		io.prepareStorage();
 		io.loadJails();
 		
-		jm = new JailManager(this);
 		cmdHand = new CommandHandler(this);
 		
 		PluginManager pm = this.getServer().getPluginManager();

src/main/java/com/graywolf336/jail/beans/Jail.java

@@ -5,6 +5,7 @@ import java.util.HashSet;
 
 import org.bukkit.Bukkit;
 import org.bukkit.Location;
+import org.bukkit.World;
 import org.bukkit.entity.Player;
 
 import com.graywolf336.jail.JailMain;
@@ -13,7 +14,7 @@ import com.graywolf336.jail.JailMain;
  * 
  * @author graywolf336
  * @since 3.0.0
- * @version 1.0.2
+ * @version 1.0.3
  */
 public class Jail {
 	private JailMain plugin;
@@ -91,6 +92,21 @@ public class Jail {
 		this.maxZ = coords[2];
 	}
 	
+	/** Sets the name of the world this Jail is in. */
+	public void setWorld(String name) {
+		this.world = name;
+	}
+	
+	/** Gets the name of the world this Jail is in. */
+	public String getWorldName() {
+		return this.world;
+	}
+	
+	/** Gets the instance of the {@link World world} this Jail is in. */
+	public World getWorld() {
+		return plugin.getServer().getWorld(world);
+	}
+	
 	/** Sets the {@link SimpleLocation location} of the teleport <strong>in</strong>. */
 	public void setTeleportIn(SimpleLocation location) {
 		if(this.world.isEmpty()) this.world = location.getWorldName();

src/test/java/test/java/com/graywolf336/jail/util/MockPlayerInventory.java

@@ -277,6 +277,7 @@ public class MockPlayerInventory implements PlayerInventory {
 		return false;
 	}
 
+	@SuppressWarnings("deprecation")
 	private static Map<String, Object> makeMap(ItemStack[] items) {
 		Map<String, Object> contents = new LinkedHashMap<String, Object>(
 				items.length);

src/test/java/test/java/com/graywolf336/jail/util/MockWorldFactory.java

@@ -15,7 +15,6 @@ import org.bukkit.World;
 import org.bukkit.WorldType;
 import org.bukkit.block.Block;
 import org.bukkit.generator.ChunkGenerator;
-
 import org.mockito.invocation.InvocationOnMock;
 import org.mockito.stubbing.Answer;
 
@@ -97,6 +96,7 @@ public class MockWorldFactory {
             }
         });
         when(mockWorld.getBlockAt(any(Location.class))).thenAnswer(new Answer<Block>() {
+            @SuppressWarnings("deprecation")
 			public Block answer(InvocationOnMock invocation) throws Throwable {
                 Location loc;
                 try {
@@ -141,6 +141,7 @@ public class MockWorldFactory {
             }
         });
         when(mockWorld.getBlockAt(any(Location.class))).thenAnswer(new Answer<Block>() {
+            @SuppressWarnings("deprecation")
 			public Block answer(InvocationOnMock invocation) throws Throwable {
                 Location loc;
                 try {