Properly copy collection references in ItemMeta.clone(). Fixes BUKKIT-3913

When cloning an item, all references are copied to the new item. For
collections, this makes internal changes become visible in both the old and
new items.

In CraftMetaItem, clone was not making copies of the appropriate collections
and has been fixed for non-null values.

In CraftMetaEnchantedBook and CraftMetaPotion, clone was using possible empty
collection references and has been changed to explicitly null-check instead.