ORM cleanup phase 2: delete more dead code

Dead files removed:
- StorageMigrationService.ts - not imported anywhere
- QueryBuilder.ts (daemons/data-daemon) - replaced by Rust ORM
- QueryBuilder.ts (system/data/query) - not imported anywhere
- query-builder.test.ts, querybuilder-debug.test.ts

Outdated docs removed:
- SQL-ADAPTER-DEBUGGING-RECOVERY-PLAN.md
- SQL-ADAPTER-REFACTOR-PLAN.md
- VECTOR-SEARCH-ARCHITECTURE.md (referenced deleted SqliteStorageAdapter)

Author: DeepSeek Assistant