Relocate RAG and diagnosis decision/E2E writeups from docs/ root into
mvp/engineering so architecture, issues, and engineering narrative stay
together. Update indexes and cross-links; leave docs/learning as legacy.
Persist provider reasoning and assistant text separately on agent_reasoning_audit
(DeepSeekAssistantMessage path), extract diagnosis_run.conclusion, enrich RAG
tool audit (step_id/query/qualityScore), gate empty mysql tools, drop devtools,
and align MVP docs after live E2E verification.
Preserve same-document multi-chunk evidence with evidenceKey identity,
per-document caps, retrieve-k/return-n split, and a dense KnowledgeSearchPort.
Archives Delivery 1 OpenSpec change as the foundation for hybrid retrieval.
zhuyongxin