Enable reverse lookup of files when returning JSON

[chapmanb]

This summarizes a local discussion with @tetron.

Currently when running a CWL workflow inside a Docker container, there is no reverse mapping of outputs back to the original file locations.

When you are re-shaping input this results in not being able to find returned output. For example, we have code that re-groups BAM files into batches for simultaneous variant calling but returning regrouped JSON with a path to the original file (inside the Docker container) results in errors downstream since the file is not remapped externally.

The implementation fix is to add reverse lookups to collect_output_ports. This requires adding a reversemap to DockerPathMapper and using it to remap with adjustFiles.