Johnfreeman/file formats refactor

[jcfreeman2]

Description

This draft PR is needed for the primary draft PR, DUNE-DAQ/dfmodules#497, to build

Type of change

• Documentation (non-breaking change that adds or improves the documentation)
• New feature or enhancement (non-breaking change which adds functionality)
• Optimization (non-breaking change that improves code/performance)
• Bug fix (non-breaking change which fixes an issue)
• Breaking change (whatever its nature)

Testing checklist

• Unit tests pass (e.g. dbt-build --unittest)
• Minimal system quicktest passes (pytest -s minimal_system_quick_test.py)
• Full set of integration tests pass (dunedaq_integtest_bundle.sh)
• Python tests pass if applicable (e.g. python -m pytest)
• Pre-commit hooks run successfully if applicable (e.g. pre-commit run --all-files)

Comments here on the testing

Further checks

• Code is commented where needed, particularly in hard-to-understand areas
• Code style is correct (dbt-build --lint, and/or see https://dune-daq-sw.readthedocs.io/en/latest/packages/styleguide/)
• If applicable, new tests have been added or an issue has been opened to tackle that in the future.
  (Indicate issue here: # (issue))

[eflumerf]

Code looks fine, probably won't have a chance to run through the integration tests until August, though

[jcfreeman2]

This is to be merged in concert with the feature branches of the same name in appmodel and dfmodules.