`runme fmt` can mangle frontmatter when `--flatten` is false

[mxsdev]

The runme fmt command doesn't use the notebook serializer/deserializer unless --flatten is set. So, in particular, it doesn't do separation of frontmatter from document when parsing.

I am personally fine with setting --flatten as the default, and warn users of this behavior for now; this is what I've done in #310.