fix: complete knowledge-base audit phase 2

[knqiufan]

Summary

• fixes KB-005–KB-009 from the knowledge-base audit; resolves fix: complete knowledge-base audit phase 2 #19
• makes remote vector targets and index-producing configuration changes explicitly stale
• restores deterministic per-KB retrieval semantics, RRF de-duplication, and a 10-second observable retrieval deadline
• records the implementation and resolved findings in the audit report

Verification

• pytest -q — 623 passed
• ruff check misaka/
• mypy misaka/
• pip check
• python -m misaka.main --rag-smoke