Add optional parameter for flatfield and darkfield filenames

[AlexBarbera]

This PR adds 2 optional command line options that act as the file name for the flatfield and darkfield output names.

Currently they share the inputs basename, but this adds more flexibility and works better for nextflow patterns.
It also remains backwards compatible if the parameters are not used.

[jmuhlich]

It would probably be better to make --output-flatfield and --output-darkfield provide the entire output paths, bypassing the -ffp/-dfp suffixes and --output-folder value. This also means you'd want to check that the user passes either both --output-flatfield and --output-darkfield or only --output-folder.