BQSR: restore ability to specify custom covariates and to disable standard covariates. (Take 2)

[takutosato]

This PR continues @droazen's prior PR #4688 from circa 2018, where he restored the ability to add custom covariates, which I've been told was a feature in GATK3 but was removed from GATK4 for performance reasons. (@lbergelson please correct me if I'm wrong.) He also added a sample custom covariate, RepeatLengthCovariate.

I rebased the branch, added comments where needed, and added tests.

[gatk-bot]

Github actions tests reported job failures from actions build 15620149812 Failures in the following jobs:

Test Type	JDK	Job ID	Logs
cloud	17.0.6+10	15620149812.10	logs
integration	17.0.6+10	15620149812.11	logs
integration	17.0.6+10	15620149812.0	logs