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.

devflow/projects/2026-07-28-rag-eval-hybrid-baseline/acceptance.md

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+# Acceptance: rag-eval-hybrid-baseline
+
+## Tasks
+
+All tasks in OpenSpec `tasks.md` checked, including apply-discovered 6.x quality-gate fix.
+
+## 静态验证
+
+- Snapshot generator path: no required `retrieval.vector-store.mode`.
+- README documents hybrid generation and offline/live split.
+
+## 脚本验证
+
+```text
+.\scripts\prepare_rag_eval_seed.ps1
+.\scripts\generate_rag_lookup_snapshots.ps1 -SearchMode hybrid -SkipEval
+python scripts\eval_rag_retrieval.py --json-report eval/rag-retrieval/reports/baseline.json --markdown-report eval/rag-retrieval/reports/baseline.md
+# Result: Evaluated 7 cases: passRate=1.0, recall@5=1.0, failed=0
+
+mvn -Dtest=RetrievalScoreNormalizerTest,KnowledgeEvidencePostProcessorTest,LookupKnowledgeToolTest,VectorSearchServiceTest,VectorKnowledgeSearchAdapterHybridTest test
+# exit 0
+```
+
+Fixture sample meta: `searchMode=hybrid`, `kbScope=rag-eval`.  
+Fallback case: `UNFILTERED_VECTOR_RETRY` + `filtered_vector_low_quality`.
+
+## 浏览器/人工
+
+- 未做 UI 验证。
+
+## 未验证 / 后续
+
+- Dense vs hybrid dual-directory comparison report (knife-2).
+- CI wiring of offline eval as required gate (optional process).
+- Long-term calibration of hybrid PRECISE distribution under denseDistance quality.
+
+## Specs
+
+Main spec synced: `openspec/specs/rag-eval-offline-baseline/spec.md`.

devflow/projects/2026-07-28-rag-eval-hybrid-baseline/brief.md

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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.

devflow/projects/2026-07-28-rag-eval-hybrid-baseline/decisions.md

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+# Decisions: rag-eval-hybrid-baseline（最终版）
+
+## Process
+
+sm-flow standard-lean: Discover → Commit → Apply → Archive.
+
+## Key decisions
+
+1. Replace eval generator `vector-store.mode` with `retrieval.search.mode` (default hybrid).
+2. Fixture meta: `searchMode`, `kbScope` when set.
+3. Knife-2 (dual fixtures / mustNot golden) deferred.
+4. Live refresh succeeded in apply env; baseline updated to hybrid snapshots.
+5. **Quality gate refinement (apply-found):** hybrid absolute quality for `isLowQuality` / relevance uses optional dense L2 (`denseDistance`); does not overwrite hybrid scoreLabel or RRF order. Rank mapping remains fallback when dense missing.
+
+## Trade-offs
+
+- Extra dense ANN on hybrid path for gate calibration (latency) vs correct filter-fallback behavior.
+- relevance_level still not a hard golden assertion (ordinal vs absolute mix).

devflow/projects/2026-07-28-rag-eval-hybrid-baseline/evidence.md

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+# Evidence: rag-eval-hybrid-baseline
+
+## Pre-change
+
+- `generate_rag_lookup_snapshots.ps1` passed `-Dretrieval.vector-store.mode=spring`.
+- Fixtures had `caseId/query/retrievedAt/lookupResult` only.
+- Offline eval already supported Hit levels, recall@K, baseline diff.
+
+## User decisions
+
+- Scope: knife-1 only (no dual fixture dirs).
+- Acceptance: wiring required; fixture refresh best-effort (env allowed full refresh).
+
+## Apply-discovered
+
+- After hybrid refresh, `chat-l0-filter-fallback` failed: pure rank→quality made topSimilarity=1.0 on decoy-only filtered hits → no unfiltered retry.
+- Fix: optional `denseDistance` on hybrid hits; quality gate uses L2 when present; sort order remains RRF.