i.e. instead of taking a directory that must contain "root" and
"scratch", and treating "root" as the root, use the directory directly.

In element.py:
* __sandbox takes the `bare_sandbox` arg, to pass into the sandbox's constructor

In sandbox.py:
* If bare_sandbox, `_root` is the passed-in directory, and `__scratch`
  is None.
* Trying to use `__scratch` when bare_sandbox is True is a bug.

In _mount.py:
* Don't get the value of `__scratch` if it's not needed.

This is part of #539