Often may butler primitives are deserialized at the same time, and
it is useful for these objects to share references to each other.
This reduces load time and memory usage.

Downstream code now depends on refs holding UUIDs. Have the yaml
loader convert old style integer ids to UUIDs early rather than
waiting for downstream cleanups.

MyPy seems to narrow types somehow when comparing Enum Flags
directly with equality operators. Compare by value instead.