Update CLI and move code into VariantValidator

[Peter-J-Freeman]

The existing CLIs were out of date and untested. This commit introduces 3 new CLIs. variantvalidator, variantformatter and gene2transcripts. It removed batch_validator.py which is now covered by the variantvalidator CLI. It also removed a dangerous CLI which only deleted the VV database,
and adds functionality to the vv_configuration CLI. All CLIs are tested
and have help messages. The commit also restructures the VV logger
setup so it can be overridden by interfaces without touching the
config.ini

[codecov]

Codecov Report

❌ Patch coverage is 95.00924% with 27 lines in your changes missing coverage. Please review.
✅ Project coverage is 81.89%. Comparing base (489e873) to head (4ec6901).
⚠️ Report is 2 commits behind head on develop.

Files with missing lines	Patch %	Lines
VariantValidator/bin/variantvalidator.py	93.29%	13 Missing ⚠️
VariantValidator/bin/variantformatter.py	94.66%	8 Missing ⚠️
VariantValidator/bin/gene2transcripts.py	97.76%	3 Missing ⚠️
VariantValidator/modules/vvMixinInit.py	33.33%	2 Missing ⚠️
VariantValidator/bin/vv_configure.py	97.87%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #858      +/-   ##
===========================================
+ Coverage    81.10%   81.89%   +0.79%     
===========================================
  Files           37       41       +4     
  Lines        13208    13740     +532     
===========================================
+ Hits         10712    11253     +541     
+ Misses        2496     2487       -9     

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