resolve ariatools errors re directory behavior

[jtencer]

Some of the recent changes broke regression tests on the aria side. These changes were necessary to resolve those issues.

[eparish1]

@jtencer I'm fine with this; did you find the base directory useful for your stuff? Alternatively you could put the base directory into your prefix string. I got rid of it in the revision because I felt it was a little confusing to have the extra directory floating around and Patrick and Francesco mostly agreed, but I don't have strong feelings on this so am glad to keep it.

[jtencer]

The problem I ran into was that it was hardwired to use the current working directory and I needed a way to pass in a location. If there's a different way to handle that I'd be open to it.

[eparish1]

You can do, e.g., "run_directory_prefix = path_to_work/run_", and it will then put everything in "path_to_work". Do you like this, or do you prefer the base_dir concept?

[jtencer]

I think I might prefer having only one argument but need it to support absolute paths. This change didn't introduce the base directory stuff. It just exposed it so that it could be something other than cwd.

I can push a change tomorrow morning that rips out all the base directory stuff.

[jtencer]

I got rid of it in sampling. There are still references to base_directory in sampling_coupler_base.py and the greedy stuff but I'm guessing those will probably go away as we propagate the Model concept through.

[eparish1]

Looks good to me!