FIX: Construct MCFLIRT output paths relative to out_file

[effigies]

Summary

MCFLIRT creates optional outputs in the same directory as the out_file, regardless of whether that happens in the current working directory.

Fixes #2698.

List of changes proposed in this PR (pull-request)

• Determine output directory from out_file

Acknowledgment

• (Mandatory) I acknowledge that this contribution will be available under the Apache 2 license.

[abelalez]

For my own purpose, I've been trying something identical (abelalez@7eee9ff), just defining: cwd = os.path.dirname(output['out_file'])
I tested it with my data and it worked.

[effigies]

Cool. Thanks for the confirmation. I'll merge this if tests pass.