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Adjust file paths for file transfer when using URLs

Patrick Godwin requested to merge url_paths into main

This resolves #2 (closed) where input files for jobs are not pointed to the right files within the directory of the job's sandbox.

Adds a new path module with a function provided by @duncanmmacleod to aid in this, and migrate another internal function from the options module here for more general use.

Add tests to cover this case.

Closes #2 (closed).

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