- Introduced a new method `runCustomMigrations` in `DbService` to execute custom SQL statements that Drizzle cannot manage, such as triggers and virtual tables.
- Updated `database-patterns.md` and `README.md` to document the handling of custom SQL and its importance in maintaining database integrity during migrations.
- Refactored `messageFts.ts` to define FTS5 virtual table and associated triggers as idempotent SQL statements for better migration management.
- Introduced a new SQL migration script to create the `__new_message` table with updated schema, including foreign key constraints and check constraints for `role` and `status`.
- Migrated existing data from the old `message` table to the new structure and renamed the table to `message`.
- Added indexes for improved query performance on `parent_id`, `topic_id`, and `trace_id`.
- Updated metadata to reflect the new migration version and breakpoints for debugging.
- Modified the `message` table to include `siblings_group_id` and `stats`, while removing `usage` and `metrics`.
- Renamed `response_group_id` to `siblings_group_id` for clarity.
- Enhanced the `topic` table by adding `active_node_id` and ensuring `sort_order` and `is_name_manually_edited` are defined correctly.
- Updated the database schema to reflect these changes and removed obsolete migration files.
- Removed outdated API model and schema files to simplify the structure.
- Consolidated API types and schemas for better organization and clarity.
- Updated import paths across the codebase to reflect the new structure.
- Enhanced documentation in related README files to guide usage of the new API schema organization.
- Changed migration command from `yarn run migrations:generate` to `yarn run db:migrations:generate` for consistency across the project.
- Updated related documentation in `CLAUDE.md`, `migrations/README.md`, and `src/main/data/README.md` to reflect the new command.
- Added a notice in `migrations/README.md` regarding potential database structure changes before the alpha release.
