Fix empty database bootstrap to use Alembic

[Genmin]

Summary

• run alembic upgrade head for empty databases instead of creating ORM metadata directly and then stamping head
• keep the existing baseline-stamp compatibility path for already-created schemas
• update bootstrap unit coverage so empty databases assert migrations run and Base.metadata.create_all() is not called

Fixes #4555.

Validation

• uv run ruff check mcpgateway/bootstrap_db.py
• uv run pytest tests/unit/mcpgateway/test_bootstrap_db.py -q