fix: resolve walker crash, improve db transactions and refine indexing types

- walker: fix runtime crash by reverting ALWAYS_IGNORE to Set
- db: add transaction to removeOrphanedFiles and CASCADE delete to FTS
- store: add chunk_key to search results and limit support for embeddings
- types: add non-null assertions for strict indexing and ranking

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>