Actions/builders converted to running via config & manifest

[dogversioning]

This PR makes the following changes:

• Renames the StudyManifestParser to StudyParser #246
• Moves cursor/schema to config object #225
• Changes most actions & builders to take config + manifest as the first two arguments
  • Eliminates a lot of commonly passed args (verbose etc etc) in favor of the study config

    Checklist

• [X] Consider if documentation (like in docs/) needs to be updated
• [X] Consider if tests should be added
• [X] Update template repo if there are changes to study configuration

[github-actions[bot]]

☂️ Python Coverage

current status: ✅

Overall Coverage

Lines	Covered	Coverage	Threshold	Status
1930	1881	97%	90%	🟢

New Files

No new covered files...

Modified Files

File	Coverage	Status
cumulus_library/init.py	100%	🟢
cumulus_library/actions/builder.py	96%	🟢
cumulus_library/actions/cleaner.py	97%	🟢
cumulus_library/actions/exporter.py	97%	🟢
cumulus_library/actions/file_generator.py	98%	🟢
cumulus_library/actions/importer.py	100%	🟢
cumulus_library/base_table_builder.py	100%	🟢
cumulus_library/base_utils.py	97%	🟢
cumulus_library/cli.py	96%	🟢
cumulus_library/databases.py	95%	🟢
cumulus_library/log_utils.py	100%	🟢
cumulus_library/protected_table_builder.py	100%	🟢
cumulus_library/statistics/counts.py	100%	🟢
cumulus_library/statistics/psm.py	96%	🟢
cumulus_library/studies/core/builder_prereq_tables.py	100%	🟢
cumulus_library/studies/core/count_core.py	96%	🟢
cumulus_library/studies/vocab/vocab_icd_builder.py	100%	🟢
TOTAL	98%	🟢

updated for commit: a74e72d by action🐍