feat(harness,rag): dual LLM audit fields, run conclusion, and hybrid quality

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.

openspec/changes/archive/2026-07-28-rag-quality-score-unify/brief.md

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+# Brief: rag-quality-score-unify
+
+## Background
+
+True BM25 hybrid retrieval is live, but post-processing still normalizes as if every score were dense L2 and re-ranks with L0 keyword contains boosts. That splits ranking authority from quality gates and double-counts lexical signal.
+
+## Goals
+
+- Unify score labels to `dense` | `hybrid`.
+- Single `toQualityScore`; label-agnostic post-process.
+- Preserve retrieval rank; remove boost re-rank.
+- Hybrid quality = pure rank mapping (slice 1).
+
+## Scope
+
+Internal RAG pipeline: store emission, normalizer, evidence post-process, tests, architecture docs.
+
+## Non-goals
+
+Fine re-rankers, query rewrite, neighbor chunks, schema rebuild, ACI field renames, removing dense comparison mode.