Add default output directory

[ElliottKasoar]

Changes default file_prefix to include ./janus_results/ (originally results, but this clashes with mace training outputs, meaning that output files will normally all be contained within this directory, as discussed in #359.

I initially thought we may want a dedicated option for the file directory, but since file_prefix directories are created anyway, something like --file-prefix ./alt_dir/prefix, or --file-prefix ./just-prefix (to avoid creating a new directory), which both already work, is just as effective.

One slight question mark on the dev side of things is currently this will create the janus_results directory if it doesn't exist, including when running tests, but I only clean up the files, not the directory itself, so running the tests may leave behind a new empty directory. I thought this was probably preferable to a lot of extra logic figuring out if it starts empty and so is safe to delete/potential test failures if it's not.

[oerc0122]

Why not just use pytest's tmp_path factory fixture?

[ElliottKasoar]

We do generally, but that doesn't test that the default file_prefix creates the files we expect. (Unless we did something like change directories into a temporary directory, and ran everything from there)

[oerc0122]

Could monkeypatch to check the directory it would create and then over-write the return to tmp_path

[ElliottKasoar]

We probably could, but the exact way the filenames are built varies a little, so I'm not sure how easy it would be in a completely general way, and I think we might risk missing unusual interactions.

Arguably the current form is more of an integration test, since we test the file builder separately anyway, which I think is practically what we'd be checking again if we don't write to the actual default location.

[oerc0122]

Yeah. That was one of my other thoughts. Leaving behind miscellaneous files (even empty folders) in the test suite just feels unpleasant. I think at the very least we want to delete them before attempting the test.