Stop wiping Alembic version tracking on every restart. Now
`alembic upgrade head` runs only pending migrations, as intended.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Rewrite migrations to raw SQL with IF NOT EXISTS/EXCEPTION guards for
full idempotency. Add notes table migration (0001), fix migration chain,
and run alembic upgrade head in Dockerfile CMD on container start.
Update summary.md with Phase 3.5 changes and Alembic instructions.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>