fix: rename 000.sql to 000_migration.sql and wrap legacy conversion in transaction

- Rename bootstrap migration from 000.sql to 000_migration.sql per
  REPO_POLICIES.md naming convention (NNN_description.sql pattern)
- Update all hardcoded references in migrations.go
- Wrap rebuildMigrationsTable() DROP/CREATE/INSERT sequence in a
  single transaction for crash safety
- Update test case filename to match renamed file

internal/database/migrations/000_migration.sql

@@ -0,0 +1,9 @@
+-- Migration 000: Schema migrations tracking table
+-- Applied as a bootstrap step before the normal migration loop.
+
+CREATE TABLE IF NOT EXISTS schema_migrations (
+    version INTEGER PRIMARY KEY,
+    applied_at DATETIME DEFAULT CURRENT_TIMESTAMP
+);
+
+INSERT OR IGNORE INTO schema_migrations (version) VALUES (0);