Move Alembic configuration from `alembic.ini` to `pyproject.toml`

[zobweyt]

This issue tracks the progress of moving our Alembic configuration from alembic.ini to pyproject.toml to maintain consistency in our configuration management. This move is dependent on the resolution of sqlalchemy/alembic#1082.

Configuration

• All common project configuration for such tools as pdm, ruff, and babel is centralized in pyproject.toml.
• All security-sensitive information, including logging and database connection strings, has already been moved to an untracked file, config.yaml.

The best place to put the Alembic configuration is pyproject.toml. Based on sqlalchemy/alembic#1082 (comment).

Goals

• Move Alembic configuration from alembic.ini to pyproject.toml.