This is much more incremental, and will help us to support remote
execution (where Directory protos are the lingua franca).

There are still several significant things to clean up here:
 * Some IsolatedProcess tests are disabled
 * We need to work out how to do input/output conversions for
   IsolatedProcess for real
 * Process execution is hard-coded to be local, synchronous, and a
   little panic-y

but as this is already a very large change, and the process execution
pieces aren't actually used in production codepaths, I'd like those to
be follow-ups.