Fixed

• Brought back a command line argument for protein comparison tool #1096
• Upgraded the log facade framework to slf4j2 #1094
• Code smell fixes (Sonar issues S2293, S1319) #1095 #1091
• Various small fixes

Removed

• Removed capability of automatic download/caching of PDB archive files in MMTF format, following deprecation
  by RCSB PDB. Code to encode/decode in MMTF format is still in place #1099