The server loads all settings correctly as far as I can tell. This marks the end of stage 2. Stage 3 (testing of all features and commands) will start tomorrow.

CraftBukkit-Patches/0004-Spigot-Configuration.patch

@@ -1,4 +1,4 @@
-From fddd6adfdc0d19ca28245d4e3618a87b6185ec94 Mon Sep 17 00:00:00 2001
+From 6d02dec6b5b43138083f33d639e9769a6b4c54d0 Mon Sep 17 00:00:00 2001
 From: md_5 <md_5@live.com.au>
 Date: Fri, 21 Jun 2013 19:06:58 +1000
 Subject: [PATCH] Spigot Configuration
@@ -78,10 +78,10 @@ index 00326c1..24f1f39 100644
          pluginManager.clearPlugins();
 diff --git a/src/main/java/org/spigotmc/SpigotConfig.java b/src/main/java/org/spigotmc/SpigotConfig.java
 new file mode 100644
-index 0000000..f6d3bcb
+index 0000000..c6cf18e
 --- /dev/null
 +++ b/src/main/java/org/spigotmc/SpigotConfig.java
-@@ -0,0 +1,111 @@
+@@ -0,0 +1,112 @@
 +package org.spigotmc;
 +
 +import com.google.common.base.Throwables;
@@ -114,7 +114,7 @@ index 0000000..f6d3bcb
 +            + "join us at the IRC or drop by our forums and leave a post.\n"
 +            + "\n"
 +            + "IRC: #spigot @ irc.esper.net ( http://webchat.esper.net/?channel=spigot )\n"
-+            + "Forums: http://www.spigotmc.org/forum/";
++            + "Forums: http://www.spigotmc.org/forum/\n";
 +    /*========================================================================*/
 +    static YamlConfiguration config;
 +    static int version;
@@ -144,10 +144,11 @@ index 0000000..f6d3bcb
 +        {
 +            if ( Modifier.isPrivate( method.getModifiers() ) )
 +            {
-+                if ( method.getParameterTypes().length == 0 )
++                if ( method.getParameterTypes().length == 0 && method.getReturnType() == Void.TYPE )
 +                {
 +                    try
 +                    {
++                        method.setAccessible( true );
 +                        method.invoke( instance );
 +                    } catch ( InvocationTargetException ex )
 +                    {

CraftBukkit-Patches/0009-Proxy-IP-Filter.patch

@@ -1,4 +1,4 @@
-From d5c30151eab3d605a75a710a29237ffb26adf1f6 Mon Sep 17 00:00:00 2001
+From 3bb4fed2ec0758923220bcf21388d9f1a9f25377 Mon Sep 17 00:00:00 2001
 From: md_5 <md_5@live.com.au>
 Date: Tue, 23 Apr 2013 11:22:07 +1000
 Subject: [PATCH] Proxy IP Filter
@@ -67,10 +67,10 @@ index 0000000..55d8d12
 +    }
 +}
 diff --git a/src/main/java/org/spigotmc/SpigotConfig.java b/src/main/java/org/spigotmc/SpigotConfig.java
-index c532dc7..632f86a 100644
+index 0b81a86..b4656d4 100644
 --- a/src/main/java/org/spigotmc/SpigotConfig.java
 +++ b/src/main/java/org/spigotmc/SpigotConfig.java
-@@ -108,4 +108,10 @@ public class SpigotConfig
+@@ -109,4 +109,10 @@ public class SpigotConfig
          config.addDefault( path, def );
          return config.getString( path, config.getString( path ) );
      }

CraftBukkit-Patches/0017-Highly-Optimized-Tick-Loop.patch

@@ -1,4 +1,4 @@
-From c6c24ff3f2b9873b4f17444183e5c3eb11516eda Mon Sep 17 00:00:00 2001
+From 04e51665bd1ac94510c2eb76ef995bfb2dd40e05 Mon Sep 17 00:00:00 2001
 From: md_5 <md_5@live.com.au>
 Date: Sun, 3 Feb 2013 12:28:17 +1100
 Subject: [PATCH] Highly Optimized Tick Loop
@@ -117,7 +117,7 @@ index 0000000..f114a31
 +    }
 +}
 diff --git a/src/main/java/org/spigotmc/SpigotConfig.java b/src/main/java/org/spigotmc/SpigotConfig.java
-index 632f86a..5ebb19a 100644
+index b4656d4..66bf600 100644
 --- a/src/main/java/org/spigotmc/SpigotConfig.java
 +++ b/src/main/java/org/spigotmc/SpigotConfig.java
 @@ -15,6 +15,7 @@ import org.bukkit.Bukkit;
@@ -128,7 +128,7 @@ index 632f86a..5ebb19a 100644
  
  public class SpigotConfig
  {
-@@ -114,4 +115,9 @@ public class SpigotConfig
+@@ -115,4 +116,9 @@ public class SpigotConfig
      {
          preventProxies = getBoolean( "settings.prevent-proxies", false );
      }

CraftBukkit-Patches/0024-Watchdog-Thread.patch

@@ -1,4 +1,4 @@
-From 816df7314c4e568cef2591dfbb22ff3af869c4cb Mon Sep 17 00:00:00 2001
+From 62cef831a76dbfe52e85f86902931b43a6fd50a3 Mon Sep 17 00:00:00 2001
 From: md_5 <md_5@live.com.au>
 Date: Sat, 23 Feb 2013 12:33:20 +1100
 Subject: [PATCH] Watchdog Thread.
@@ -142,10 +142,10 @@ index 0000000..a5c4549
 +    }
 +}
 diff --git a/src/main/java/org/spigotmc/SpigotConfig.java b/src/main/java/org/spigotmc/SpigotConfig.java
-index 9459195..d8167f2 100644
+index fdab366..32140d1 100644
 --- a/src/main/java/org/spigotmc/SpigotConfig.java
 +++ b/src/main/java/org/spigotmc/SpigotConfig.java
-@@ -133,4 +133,16 @@ public class SpigotConfig
+@@ -134,4 +134,16 @@ public class SpigotConfig
      {
          commands.put( "tps", new TicksPerSecondCommand( "tps" ) );
      }

CraftBukkit-Patches/0025-Netty.patch

@@ -1,4 +1,4 @@
-From 4656aab62face984022317b27962aa188daa25dd Mon Sep 17 00:00:00 2001
+From ad431c66fd54963754e01d91185c0741474bdfe6 Mon Sep 17 00:00:00 2001
 From: md_5 <md_5@live.com.au>
 Date: Fri, 21 Jun 2013 18:23:00 +1000
 Subject: [PATCH] Netty
@@ -350,7 +350,7 @@ index 0000000..386c2f8
 +    }
 +}
 diff --git a/src/main/java/org/spigotmc/SpigotConfig.java b/src/main/java/org/spigotmc/SpigotConfig.java
-index d8167f2..9b74bf0 100644
+index 32140d1..e762527 100644
 --- a/src/main/java/org/spigotmc/SpigotConfig.java
 +++ b/src/main/java/org/spigotmc/SpigotConfig.java
 @@ -6,6 +6,8 @@ import java.io.IOException;
@@ -362,7 +362,7 @@ index d8167f2..9b74bf0 100644
  import java.util.HashMap;
  import java.util.List;
  import java.util.Map;
-@@ -145,4 +147,44 @@ public class SpigotConfig
+@@ -146,4 +148,44 @@ public class SpigotConfig
          commands.put( "restart", new RestartCommand( "restart" ) );
          WatchdogThread.doStart( timeoutTime, restartOnCrash );
      }

CraftBukkit-Patches/0030-BungeeCord-Support.patch

@@ -1,4 +1,4 @@
-From 8e61227e44fdc81f2c39ef5463a1013718175998 Mon Sep 17 00:00:00 2001
+From eae71452b63e57a58eff69db1b7d444bd5829120 Mon Sep 17 00:00:00 2001
 From: md_5 <md_5@live.com.au>
 Date: Sat, 23 Mar 2013 11:15:11 +1100
 Subject: [PATCH] BungeeCord Support
@@ -75,7 +75,7 @@ index 7cae665..21141f2 100644
  
      public Spigot spigot()
 diff --git a/src/main/java/org/spigotmc/SpigotConfig.java b/src/main/java/org/spigotmc/SpigotConfig.java
-index 9b74bf0..8150dd3 100644
+index e762527..6234dca 100644
 --- a/src/main/java/org/spigotmc/SpigotConfig.java
 +++ b/src/main/java/org/spigotmc/SpigotConfig.java
 @@ -7,6 +7,7 @@ import java.lang.reflect.InvocationTargetException;
@@ -86,7 +86,7 @@ index 9b74bf0..8150dd3 100644
  import java.util.Collections;
  import java.util.HashMap;
  import java.util.List;
-@@ -187,4 +188,14 @@ public class SpigotConfig
+@@ -188,4 +189,14 @@ public class SpigotConfig
              listeners.add( new Listener( host, port, netty, connectionThrottle ) );
          }
      }

CraftBukkit-Patches/0050-Spam-Filter-Exclusions.patch

@@ -1,4 +1,4 @@
-From 3ffbaeae0fd56278f77e8a8efdb9afc43588dcbd Mon Sep 17 00:00:00 2001
+From 7dbc12290307517690e119452320858103500a7f Mon Sep 17 00:00:00 2001
 From: md_5 <md_5@live.com.au>
 Date: Fri, 21 Jun 2013 17:59:22 +1000
 Subject: [PATCH] Spam Filter Exclusions
@@ -19,10 +19,10 @@ index 998ac8d..a292c1a 100644
                          Waitable waitable = new Waitable() {
                              @Override
 diff --git a/src/main/java/org/spigotmc/SpigotConfig.java b/src/main/java/org/spigotmc/SpigotConfig.java
-index 8150dd3..97e99aa 100644
+index 6234dca..3c32b08 100644
 --- a/src/main/java/org/spigotmc/SpigotConfig.java
 +++ b/src/main/java/org/spigotmc/SpigotConfig.java
-@@ -198,4 +198,13 @@ public class SpigotConfig
+@@ -199,4 +199,13 @@ public class SpigotConfig
          bungeeAddresses = getList( "settings.bungeecord-addresses", bungee );
          bungee = getBoolean( "settings.bungeecord", true );
      }

CraftBukkit-Patches/0051-Allow-Disabling-of-Command-Logging.patch

@@ -1,4 +1,4 @@
-From 13bb5c1c6f2533b7135286e1f3db3b3c6aa31bb5 Mon Sep 17 00:00:00 2001
+From 36f3fc0a1175cf0b6dc14b0253de6ed6eb67fd58 Mon Sep 17 00:00:00 2001
 From: md_5 <md_5@live.com.au>
 Date: Fri, 21 Jun 2013 18:01:29 +1000
 Subject: [PATCH] Allow Disabling of Command Logging
@@ -23,10 +23,10 @@ index a292c1a..0e8d292 100644
                  org.bukkit.craftbukkit.SpigotTimings.playerCommandTimer.stopTiming(); // Spigot
                  return;
 diff --git a/src/main/java/org/spigotmc/SpigotConfig.java b/src/main/java/org/spigotmc/SpigotConfig.java
-index 97e99aa..69695d2 100644
+index 3c32b08..e15bf25 100644
 --- a/src/main/java/org/spigotmc/SpigotConfig.java
 +++ b/src/main/java/org/spigotmc/SpigotConfig.java
-@@ -207,4 +207,10 @@ public class SpigotConfig
+@@ -208,4 +208,10 @@ public class SpigotConfig
              "/skill"
          } ) );
      }

CraftBukkit-Patches/0052-Allow-Disabling-of-Command-TabComplete.patch

@@ -1,4 +1,4 @@
-From f68dba495b59be99c881bc4085a0cf6530596ff0 Mon Sep 17 00:00:00 2001
+From 61994fd6edb1fc608e913d2008fb7ec602c3056e Mon Sep 17 00:00:00 2001
 From: md_5 <md_5@live.com.au>
 Date: Fri, 21 Jun 2013 18:05:54 +1000
 Subject: [PATCH] Allow Disabling of Command TabComplete
@@ -18,10 +18,10 @@ index 7534188..4d030b0 100644
              player.sendMessage(ChatColor.RED + "An internal error occurred while attempting to tab-complete this command");
              getLogger().log(Level.SEVERE, "Exception when " + player.getName() + " attempted to tab complete " + message, ex);
 diff --git a/src/main/java/org/spigotmc/SpigotConfig.java b/src/main/java/org/spigotmc/SpigotConfig.java
-index 69695d2..d07701e 100644
+index e15bf25..8ac5e41 100644
 --- a/src/main/java/org/spigotmc/SpigotConfig.java
 +++ b/src/main/java/org/spigotmc/SpigotConfig.java
-@@ -213,4 +213,10 @@ public class SpigotConfig
+@@ -214,4 +214,10 @@ public class SpigotConfig
      {
          logCommands = getBoolean( "commands.log", true );
      }