Materialize mongo alldocs collection

[dwinston]

Description

Fixes #543

Type of change

Please delete options that are not relevant.

• [X] New feature (non-breaking change which adds functionality)
• [x] This change requires a documentation update

How Has This Been Tested?

• Tested manually in local instance of dagster

• added test_materialize_all_docs()

Configuration Details: none

Checklist:

• [x] My code follows the style guidelines of this project (have you run black nmdc_runtime/?)
• [x] I have performed a self-review of my code
• [x] I have commented my code, particularly in hard-to-understand areas
• [x] I have made corresponding changes to the documentation (in docs/ and in https://github.com/microbiomedata/NMDC_documentation/?)
• [x] I have added tests that prove my fix is effective or that my feature works, incl. considering downstream usage (e.g. https://github.com/microbiomedata/notebook_hackathons) if applicable.
• [x] New and existing unit and functional tests pass locally with my changes (make up-test && make test-run)

[PeopleMakeCulture]

TODO:

• [x] standardize alldocs vs all_docs usage
• [x] update documentation in notebook
• [ ] consider refactoring notebook to use op.py code and utils