Implement notebook that migrates database from schema v11.1.0 to v11.2.0

[eecavanna]

In this branch, I did two main things: (a) I implemented a migration notebook for the December NMDC release and (b) I moved all the migration-related code to a different directory in the repo.

Details

The migration notebook can be used to migrate the Mongo database from conforming to nmdc-schema version 11.1.0 to conforming to nmdc-schema version 11.2.0.

I moved all the migration-related code from demo/metadata_migration/notebooks to db/migrations/notebooks (db is a new top-level directory—a name inspired by Ruby on Rails).

Related issue(s)

Fixes #808

Related subsystem(s)

• Runtime API (except the Minter)
• Minter
• Dagster
• Project documentation (in the docs directory)
• Translators (metadata ingest pipelines)
• MongoDB migrations
• Other

Testing

• I tested these changes (explain below)
• I did not test these changes

The destination schema has not been released yet. I'll test this once it has. The notebook is a copy/paste of the previous notebook, with a couple cells removed and a couple strings updated.

Documentation

• I have not checked for relevant documentation yet (e.g. in the docs directory)
• I have updated all relevant documentation so it will remain accurate
• Other (explain below)

Maintainability

• Every Python function I defined includes a docstring (test functions are exempt from this)
• Every Python function parameter I introduced includes a type hint (e.g. study_id: str)
• All "to do" or "fix me" Python comments I added begin with either # TODO or # FIXME
• I used black to format all the Python files I created/modified
• The PR title is in the imperative mood (e.g. "Do X") and not the declarative mood (e.g. "Does X" or "Did X")