Consider use of tmp_dir

[thclark]

The original design allowed for a tmp_dir option in which to place working files, which would be cleared up afterward.

But, python 3.something introduced NamedTemporaryDirectories, which are a cleaner way of managing this, so we probably shouldn't be encouraging the use of tmp_dir.

It's possible, however, to introduce the concept of a cache_dir (for persisting intermediate results between analyses) but this requires much more thought.

Original tmp_dir option in the CLI was:

@click.option(
    "--tmp-dir",
    type=click.Path(),
    default="<data-dir>/tmp",
    show_default=True,
    help="Absolute or relative path to a folder where intermediate files should be saved. Will be cleaned up post-analysis",
)