Merge cleanup and updated dependencies to development

[trentzz]

Changes

• Moved mity and verchew.ini to mitylib/
• Moved tests to a better test folder structure
• Created build tools in tools/ for pushing to test pypi
• Updated dockerfile dependencies
  • Python version from 3.7.4 to 3.10.6
  • bcftools and htslib to 1.17
  • Freebayes to 1.3.6
  • python-openssl to python3-openssl
• Added debug flag under each subparser (call, normalise, etc)
• Added config file config.ini for paths to static/reference files
• Moved constants (such as P_VAL and blacklist positions) to constants at the top of each file
• Replaced pyvcf usage with pysam
• Edited setup.py to support files being moved and config file
• Removed files that were no longer used

Note: setup.py description strings still need to be changed for eventual release.