Cleanups and re-organizations with the recent changes

* Moved `Manager` into the `CLI`. These go together; the `CLI`
  drives the `Manager` and is just a light-wrapper to it.
* `Manager` now chooses ENV vars over passed options, which are
  chosen over the host's configuration.
* Removed some no-longer needed logic from `HostData`. This logic
  has been handled elsewhere. Closes #50.