Tidy relative workspace tests

They were moving the whole tmpdir to move the project repository.
This moves the cache directories etc. as well, meaning cli.run can't find them.
This was worked around by setting configure=False,
but this has the side-effect of making use of the user's caches,
which it should not be doing for reproducibility reasons.

By changing the tempdir layout to have the project in a subdirectory
we can move the project around for the relative workspace tests
without losing track of the configured state directories,
so we can leave configure=True and avoid touching the user's caches.