Add support for phenix 1.21

[dennisbrookner]

The major change in this PR is that all matchmaps utilities now support phenix 1.21 as well as previous versions. Along the way, various other changes were made:

• refactoring phenix-calling methods out of _utils.py into the new file _phenix_utils.py
• Various other refactorings for efficiency and clarity
• Output script includes the phenix version that was used. This is notable because the analogous matchmaps calls with phenix 1.20 or 1.21 seem to produce slightly different results.
• The parameter --phenix-version allows the user to override the automatically detected phenix version from the environment. I don't know why one would need to do this, but it was easy to support.