Adding KO scan capabilities and many other improvements

[AstrobioMike]

• KO searching now available
  • argument -K
• helper program for managing environment variables
  • gtt-data-locations
• ugly color codes no longer in output log file
• gtt-get-accessions-from-GTDB checks variable/path of where the GTDB data is supposed to be stored, and reports how to change if needed
• added seed setting to gtt-subset-GTDB-accessions, so can be done the same way if the same ref version is used
• removed pre-packaged HMMs from install and github, now they are downloaded if used