Track schema/index bootstrap SQL migration cleanup

[oritwoen]

Context

PR #9 review highlighted that idx_observations_project_input_hash was added in runtime bootstrap SQL (CUSTOM_SQL) instead of through drizzle migrations.

Why this matters

• Schema-affecting changes are easier to audit when represented in migration history
• Current runtime SQL includes multiple indexes and triggers created outside drizzle migration files

Scope

• Inventory runtime bootstrap SQL in src/index.ts
• Decide which statements should move to drizzle migrations versus remain runtime bootstrap
• Move eligible statements into migrations and keep startup idempotent
• Add or update tests to cover migration path for existing databases

Notes

This is intentionally scoped as follow-up to avoid mixing larger schema-process refactors into PR #9.