Clear plugin metadata only after onDisable()

Fixes GH-776

Spigot-Server-Patches/Remove-Metadata-on-reload.patch

@@ -7,22 +7,26 @@ Metadata is not meant to persist reload as things break badly with non primitive
 This will remove metadata on reload so it does not crash everything if a plugin uses it.
 
 diff --git a/src/main/java/org/bukkit/craftbukkit/CraftServer.java b/src/main/java/org/bukkit/craftbukkit/CraftServer.java
-index b8f907038..f7aa5fb8a 100644
+index b8f90703..d4de72c8 100644
 --- a/src/main/java/org/bukkit/craftbukkit/CraftServer.java
 +++ b/src/main/java/org/bukkit/craftbukkit/CraftServer.java
 @@ -0,0 +0,0 @@ public final class CraftServer implements Server {
              world.paperConfig.init(); // Paper
          }
  
++        Plugin[] pluginClone = pluginManager.getPlugins().clone(); // Paper
+         pluginManager.clearPlugins();
+         commandMap.clearCommands();
++
 +        // Paper start
-+        for (Plugin plugin : pluginManager.getPlugins()) {
++        for (Plugin plugin : pluginClone) {
 +            entityMetadata.removeAll(plugin);
 +            worldMetadata.removeAll(plugin);
 +            playerMetadata.removeAll(plugin);
 +        }
 +        // Paper end
 +
-         pluginManager.clearPlugins();
-         commandMap.clearCommands();
          resetRecipes();
+         reloadData();
+         org.spigotmc.SpigotConfig.registerCommands(); // Spigot
 --