Use cli for all operations instead of the API

We have to re-implement logic (like updating a workspace before starting it) and it would be better to just call out to the cli since it already accounts for all that.

It is a lot of surface area to cover (every plugin) any time a feature is added.

If the command errors, show whatever is in stderr as the error message.

An alternative would be to handle these things at the API layer, and maybe there is a case to be made for that.