Persist solely Protocol Buffers.

An design question was open for me in the beginning was whether to
serialize other types to disk, but Protocol Buffers quickly won out,
which allows us to drop support for other types.  This is a good
start to cleaning up a lot of cruft in the storage stack and
can let us eventually decouple the various moving parts into
separate subsystems for easier reasoning.

This commit is not strictly required, but it is a start to making
the rest a lot more enjoyable to interact with.