Implement notebook that migrates Mongo database to "Berkeley" schema

[eecavanna]

This PR branch is still under construction. I have not filled out the PR template yet.

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Description

Please include a summary of the changes and the related issue. Please also include relevant motivation and context. List any dependencies that are required for this change.

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Fixes # (issue)

Type of change

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• [ ] Bug fix (non-breaking change which fixes an issue)
• [ ] New feature (non-breaking change which adds functionality)
• [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
• [ ] This change requires a documentation update

How Has This Been Tested?

Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration, if it is not simply make up-test && make test-run.

• [ ] Test A
• [ ] Test B

Configuration Details: none

Checklist:

• [ ] My code follows the style guidelines of this project (have you run black nmdc_runtime/?)
• [ ] I have performed a self-review of my code
• [ ] I have commented my code, particularly in hard-to-understand areas
• [ ] I have made corresponding changes to the documentation (in docs/ and in https://github.com/microbiomedata/NMDC_documentation/?)
• [ ] 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.
• [ ] New and existing unit and functional tests pass locally with my changes (make up-test && make test-run)