Fixes critical issue where migration 002 indexes already existed in SCHEMA_SQL,
causing 'index already exists' errors on databases created before v1.0.0-rc.1.
Changes:
- Removed duplicate index definitions from SCHEMA_SQL (database.py)
- Enhanced migration system to detect and handle indexes properly
- Added comprehensive documentation of the fix
Version bumped to 1.0.0-rc.2 with full changelog entry.
Refs: docs/reports/2025-11-24-migration-fix-v1.0.0-rc.2.md
