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.
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+# Brief: rag-eval-hybrid-baseline
+
+## Background
+
+Offline RAG eval (golden × fixture × key-field baseline) existed but generator/docs still used dead `retrieval.vector-store.mode=spring`. Fixtures lacked search meta and did not reflect hybrid main path.
+
+## Goals (knife-1 only)
+
+- Snapshot generation uses `retrieval.search.mode` (default hybrid; dense override).
+- Fixtures record `searchMode` / `kbScope`.
+- README documents hybrid-era offline vs live loop.
+- Best-effort live seed + regenerate fixtures + update baseline.
+
+## Non-goals
+
+Dense/hybrid dual fixture trees; golden mustNot/chunk/level hard gates; new eval frameworks.