Remove CraftItemStack.hasMetadata

This is not redundant as it can't be done efficiently due to the need
to filter out well-known tags. I don't believe there's a good use case
for this method anyway, now that the other two versions of
ItemStack.hasMetadata are there.
Allow storing Booleans, they get stored as bytes

MetadataValueAdapter should take care of converting them back to
booleans as requested.
Store unknown NBT data in store. Fixes BUKKIT-4864
Implement ItemMeta.set/hasGlowEffect. Adds BUKKIT-4767