Adjust file paths for file transfer when using URLs
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).