Refactor/merge CCGP work

[tsackton]

This is a major update to refactor and integrate work done on the CCGP fork with the main snpArcher repository. Includes:

• Integration of sention-based cloud option via config
• Updates to improve interval operations and stability
• Major refactor in wildcards to improve DAG building time
• Changes to output structure
• Changes to coverage calculations that remove need for bugging d4 stat operation and make using d4/mosdepth optional
• Other quality of life improvements and bugfixes