Add migration framework and schema versioning to the portable database's schema

To make it easier to evolve the portable database, we should consider integrating a migration framework such as [alembic](https://alembic.sqlalchemy.org/en/latest/).

The issue names no files, tests, or entry points; first locate the portable database schema and its initialization path. Review how schema changes are currently handled and evaluate the proposed Alembic integration, but clarify the migration and versioning requirements before implementation can be considered done.

Written by the indexing model from the issue text.