Metadata schemas and top-level metadata not included in `asdict` and `fromdict`

[benjeffery]

I'm pretty sure they should be as other wise they will silently disappear in some workflows.

[benjeffery]

While doing this I'm coming across lots of places where asdict is being directly passed to set_columns so I'm adding metadata_schema as an argument to set_columns. Even though it isn't a column, as set_columns really seems to mean set_state.