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- made ~/.checkm the default directory for CheckM reference data
- "checkm data setRoot <directory>" is no longer interactive and the directory must be given on the command line
- fixed CheckM data setRoot command to work from command line (thanks…
… to cbt for PR)
- added logging to files
- improved reporting of CheckM results to include timestamp
- removed "--force-overwrite" option and now allow output directories to already exist