Support using directories that are not subdirectories of the SPRAS directory

[melliott432]

The input, output, and config files all have to be in the subdirectories of the SPRAS directory. Any input files have to be copied into the spras input subdirectory. Would it be possible to set a different working directory or use directories that are not SPRAS subdirectories for input, output, and config?

[agitter]

After the updates in #49, the container run interfaces now support input, output, and config files in arbitrary locations on the file system. However, we still need to update and test our dataset loading code if we want to use alternative working directories or absolute paths. My initial tests with absolute paths on Windows failed. It may be related to how Snakemake expects path components to be joined in Windows that differs from os.join.

[tristan-f-r]

While we still need to write tests, #49 did seem to make this work: the spras-benchmarking CI runs well despite using reconstruction settings in another directory.