fix: reconcile model index declarations

[Linxiushen]

Summary

• remove ORM declarations for five low-value automations single-column indexes that are absent in production
• remove the redundant automation_runs.timeout_at single-column index declaration while retaining the deployed (status, timeout_at) composite
• add an idempotent cross-database migration so fresh databases and existing deployments converge on the same index set
• extend SQLite migration coverage to assert the redundant indexes are absent and the required run-history/polling indexes remain

Testing

• ran alembic upgrade head against a fresh SQLite database
• verified resulting indexes:
  • automations: none of the five drifted single-column indexes
  • automation_runs: automation_id, status, (status, created_at), (status, timeout_at)
• ran Alembic compare_metadata; none of the six reconciled indexes appeared in the diff
• ruff check and ruff format --check
• python -m py_compile on changed Python files

Fixes #252

Disclosure: This change was prepared with AI assistance. I reviewed the migration and verified it against a fresh SQLite schema.