further rework of yaml file
further rework of yaml file

- add support for sample groups (making 'Samples' one such). This
  makes it easy to apply options to just a subset of samples.
- remove old, deprecated options
- improve various checks and error messages
- partial renaming of 'prefixes' to 'genomes'

MikkelSchubert/paleomix,MikkelSchubert/paleomix,MikkelSchubert/paleomix