v0.20.4 refine antigravity research skills

.agents/agents.md

@@ -1,64 +1,88 @@
 # Deep Research Agent Team
 
-This file defines Antigravity roles. Do not put detailed skills or long process rules here; use `.agents/skills/` and `.agents/workflows/` for those.
+This file defines Antigravity roles only. Put persistent constraints in `.agents/rules/`, reusable capabilities in `.agents/skills/`, and phase sequencing in `.agents/workflows/`.
 
 ## Research Manager
 
 Primary model: Gemini 3 Flash.
 
-Responsibilities:
+Purpose:
 
-- Keep the phase task list current.
+- Manage the task list, phase transitions, model switches, and approval gates.
 - Load the relevant rules, skills, and workflow.
-- Ask the user to switch models before heavyweight phase work.
-- Ensure artifacts are written under `projects/<slug>/`.
-- Stop at Phase 1 and Phase 3 approval gates.
+- Keep all artifacts under `projects/<slug>/`.
 
 Must not:
 
-- Invent sources or claim searches without receipts.
+- Perform deep reasoning that belongs to a phase specialist.
+- Claim that search or verification happened without receipts.
 - Run Python model-worker commands unless the user explicitly approves external API/ZenMux usage.
-- Hide uncertainty or missing evidence.
 
 ## Phase 0-1 Strategist
 
 Primary model: Claude Opus 4.6 (Thinking).
 
-Responsibilities:
+Purpose:
 
-- Interpret user materials and intended audience.
-- Select the research method and success criteria.
-- Build the chapter architecture, hypotheses, and validation plan.
-- Produce `phase1/material_brief.md`, `framework.md`, `research_brief.md/json`, and search logs.
+- Interpret materials, audience, and decision purpose.
+- Select the most appropriate research method or method mix.
+- Build the framework, hypotheses, evidence plan, and falsification route.
+
+Required skills:
+
+- `method-selection`
+- `search-strategy`
+- `source-quality`
+- `research-quality-gates`
+- `length-budget`
 
 ## Evidence Analyst
 
 Primary model: Gemini 3.1 Pro (Low).
 
-Responsibilities:
+Purpose:
 
 - Execute task-card research.
-- Use approved search tools and maintain `phase2/search_log.jsonl`.
-- Write evidence packets with source IDs, source quality scores, counter-evidence, and unsupported claims.
-- Draft chapters only from approved chapter briefs and compressed findings.
+- Maintain search logs and source ledgers.
+- Write evidence packets, chapter briefs, compressed findings, and first drafts.
+
+Required skills:
+
+- `search-strategy`
+- `source-quality`
+- `evidence-table`
+- `research-quality-gates`
+- `citation-manager`
 
 ## Chief Reviewer
 
 Primary model: Gemini 3.1 Pro (High).
 
-Responsibilities:
+Purpose:
 
-- Audit logic, MECE structure, source quality, unsupported claims, and counter-evidence.
-- Sample at least 10 core facts and verify source IDs and original-source access.
-- Produce `phase3/critique.md` with a `go`, `rework`, or `fail` decision.
+- Audit method fit, logic, structure, evidence quality, counter-evidence, and unsupported claims.
+- Produce a clear go / rework / fail decision.
+
+Required skills:
+
+- `source-quality`
+- `evidence-table`
+- `research-quality-gates`
+- `output-hygiene`
 
 ## Final Editor
 
 Primary model: Claude Opus 4.6 (Thinking).
 
-Responsibilities:
+Purpose:
 
-- Assemble the final Chinese report from approved drafts and sources.
+- Produce the final Chinese report from approved drafts and verified sources.
 - Improve narrative clarity, executive summary, consistency, and professional tone.
-- Produce `phase4/final_zh.md`, `editorial_notes.md`, and `final_fact_check.md`.
-- Avoid adding new facts unless sources and search logs are added first.
+- Preserve source traceability and downgrade unsupported claims.
+
+Required skills:
+
+- `citation-manager`
+- `research-quality-gates`
+- `humanizer-cn`
+- `output-hygiene`

.agents/rules/deep-research-antigravity.md

@@ -14,11 +14,13 @@ When operating this repository from Google Antigravity, use Antigravity as the p
 ## Anti-Hallucination Contract
 
 - No tool receipt, no search claim. The agent may not write that it has searched, checked, verified, or confirmed anything unless a search/browser/terminal/MCP tool call actually happened and the result is logged.
-- No source ID, no factual claim. Every concrete fact in drafts must map to a `source_id` in `sources.jsonl` or the current phase ledger.
+- No source ID, no factual claim. Every concrete fact in drafts must map to a `source_id` in `sources.jsonl` and a row in `claims_ledger.jsonl`, or be visibly marked as unverified.
 - No snippet laundering. Search result snippets, AI summaries, and memory are only leads; they cannot support final claims.
 - Failed access must be explicit. If a page, PDF, registry, patent, or filing cannot be opened, mark it as inaccessible and do not quote exact values from it.
 - Each phase must maintain `phaseX/search_log.md` or `phaseX/search_log.jsonl`.
-- Each evidence packet must include `search_receipts`, `sources`, `counter_evidence`, and `unsupported_claims`.
+- Each evidence packet must include `search_receipts`, `sources`, `evidence_spans`, `counter_evidence`, and `unsupported_claims`.
+- Phase 2 must maintain `claims_ledger.jsonl`, `coverage_matrix.md`, and `rejected_sources.jsonl`.
+- Before resuming or handing off work, update `continuation_state.json`.
 - When evidence is thin, write "该观点证据不足，待进一步验证" rather than smoothing over the gap.
 
 ## Quota Discipline

.agents/skills/antigravity-surface-adapter/SKILL.md

@@ -16,19 +16,20 @@ The Deep Research method still comes from this repo:
 - Follow `AGENTS.md` for evidence, source tiers, word budgets, pause points, and output hygiene.
 - Load project skills from `.agents/skills/*` as needed.
 - Write all artifacts under `projects/<slug>/`.
-- Keep claims traceable to source IDs in `sources.jsonl`.
+- Keep claims traceable through search receipts, source IDs, and `claims_ledger.jsonl`.
 
 ## Anti-Hallucination Contract
 
 This project treats Gemini-family research as high risk for false confidence. Follow these rules mechanically:
 
 1. No tool receipt, no search claim. Do not write "I searched", "confirmed", "official data shows", or similar unless the tool call happened and is recorded.
-2. No source ID, no factual claim. Every concrete fact needs a `source_id`.
+2. No source ID, no factual claim. Every concrete fact needs a `source_id` and claim-ledger entry.
 3. Search snippets are leads, not evidence. Open the original paper, filing, registry, patent, guideline, or company disclosure before citing.
 4. Failed access is a finding. Write that the source could not be opened; do not infer exact numbers from inaccessible pages.
 5. Log all searches in `phaseX/search_log.md` or `phaseX/search_log.jsonl`.
 6. Keep an `unsupported_claims` list. It is better to expose uncertainty than to make the report look complete.
-7. Before finishing each phase, sample at least 10 factual claims and verify that each has a source ID and opened source.
+7. Keep `continuation_state.json` current so a resumed Antigravity session can continue from artifacts, not chat memory.
+8. Before finishing each phase, sample at least 10 factual claims and verify that each has a source ID, opened source, evidence locator, and claim-ledger record.
 
 ## Antigravity Model Plan
 
@@ -64,32 +65,39 @@ uv run python scripts/dr.py finalize <slug> --no-pdf --no-docx
 ## Native Runbook
 
 1. Open the repository root in Antigravity.
-2. Start with Gemini 3 Flash as Research Manager. Load `.agents/agents.md`, this skill, `AGENTS.md`, `mckinsey-method`, `search-strategy`, `source-quality`, `evidence-table`, `citation-manager`, `length-budget`, and `output-hygiene`.
+2. Start with Gemini 3 Flash as Research Manager. Load `.agents/agents.md`, this skill, `AGENTS.md`, `method-selection`, `search-strategy`, `source-quality`, `evidence-table`, `research-quality-gates`, `citation-manager`, `length-budget`, and `output-hygiene`.
 3. Create or confirm `projects/<slug>/` and the phase folders. Use Python `init` only for scaffolding if helpful.
 4. Phase 0-1: ask the user to switch to Claude Opus 4.6 (Thinking). Produce:
 
 - `phase1/material_brief.md`
 - `phase1/framework.md`
+- `phase1/method_decision.md`
 - `phase1/research_brief.md`
 - `phase1/research_brief.json`
 - `phase1/search_log.md`
+- `phase1/assumptions.md`
 - `phase1/unsupported_claims.md`
 
 5. Pause for user confirmation.
 6. Phase 2: ask the user to switch to Gemini 3.1 Pro (Low). Build evidence packets and chapter drafts without Python model workers:
 
 - `phase2/task_cards.json`
-- `phase2/packets/*.json`
+- `phase2/search_log.jsonl`
 - `phase2/sources.jsonl`
+- `phase2/rejected_sources.jsonl`
+- `phase2/claims_ledger.jsonl`
+- `phase2/coverage_matrix.md`
+- `phase2/packets/*.json`
 - `phase2/chapter_briefs/*.json`
 - `phase2/compressed_findings/*.json`
 - `phase2/drafts/chXX.md`
-- `phase2/search_log.jsonl`
 - `phase2/unsupported_claims.md`
 
-7. Phase 3: ask the user to switch to Gemini 3.1 Pro (High). Produce `phase3/critique.md`, with explicit go/rework/fail decision and a source-audit table for at least 10 core facts.
+If a claim lacks support, use delta retrieval: write the gap, run targeted searches, update sources and the claim ledger, then either verify or visibly caveat the claim.
+
+7. Phase 3: ask the user to switch to Gemini 3.1 Pro (High). Produce `phase3/critique.md`, with explicit go/rework/fail decision, claim-ledger audit, contradiction audit, and a source-audit table for at least 10 core facts.
 8. Pause for user decision.
-9. Phase 4: ask the user to switch to Claude Opus 4.6 (Thinking). Produce `phase4/final_zh.md`, `phase4/editorial_notes.md`, and `phase4/final_fact_check.md`. Use deterministic renderers afterward for PDF/DOCX.
+9. Phase 4: ask the user to switch to Claude Opus 4.6 (Thinking). Produce `phase4/final_zh.md`, `phase4/editorial_notes.md`, and `phase4/final_fact_check.md`. New facts require new receipts and claim-ledger rows. Use deterministic renderers afterward for PDF/DOCX.
 
 ## Search Strategy
 

.agents/skills/evidence-table/SKILL.md

@@ -9,6 +9,51 @@ description: 证据矩阵规范。规定每条核心结论必须有对应的证
 
 **每条结论必须可追溯**。报告中每一个有 [src_xxx] 标注的观点，都必须在对应章节的 evidence 文件中有一行记录。
 
+Antigravity native 模式下，证据不能只停留在模型上下文或章节草稿里。除章节 evidence markdown 外，还必须维护机器可审计的 claim ledger，让 Phase 3/4 可以逐条核验。
+
+---
+
+## Antigravity Native 证据落盘
+
+Phase 2 必须至少维护以下文件：
+
+- `projects/<slug>/phase2/search_log.jsonl`：检索、打开、抽取的回执
+- `projects/<slug>/phase2/sources.jsonl`：稳定 source registry
+- `projects/<slug>/phase2/claims_ledger.jsonl`：原子 claim 台账
+- `projects/<slug>/phase2/coverage_matrix.md`：章节/任务覆盖矩阵
+- `projects/<slug>/phase2/unsupported_claims.md`：未证实或仅弱证据支持的观点
+
+`claims_ledger.jsonl` 每行必须是一个原子事实或判断，字段至少包括：
+
+```json
+{
+  "claim_id": "ch03_C012",
+  "chapter": "ch03",
+  "claim_type": "fact|trend|comparison|causal|forecast|recommendation",
+  "claim": "...",
+  "supporting_source_ids": ["src_042", "src_087"],
+  "counter_source_ids": ["src_103"],
+  "evidence_spans": [
+    {
+      "source_id": "src_042",
+      "locator": "Table 2",
+      "summary": "..."
+    }
+  ],
+  "confidence": "high|medium|low|unsupported",
+  "verification_status": "verified|partially_verified|conflicted|unsupported",
+  "needs_delta_retrieve": false,
+  "visible_caveat_required": false
+}
+```
+
+正文、章节 evidence markdown、`claims_ledger.jsonl` 三者必须能互相对上：
+
+- 正文的 `Cxx/Fxx/Txx` ID 必须在 evidence markdown 和 `claims_ledger.jsonl` 中存在；
+- `claims_ledger.jsonl` 中 `verification_status=unsupported` 的 claim 必须进入 `unsupported_claims.md`；
+- `needs_delta_retrieve=true` 的 claim 必须补做定向检索，或在正文显式降级；
+- Phase 4 不得新增未进入 claim ledger 的事实。
+
 ---
 
 ## 证据矩阵文件格式

.agents/skills/method-selection/SKILL.md

@@ -0,0 +1,157 @@
+---
+name: method-selection
+description: Selects the appropriate research framework and analytical tools for biomedical, market, investment, CMC/GMP, clinical, R&D, BD, and management consulting topics instead of defaulting to MECE or McKinsey-style framing.
+---
+
+# Method Selection
+
+Use this skill before Phase 0-1 framing and whenever the user changes the report purpose.
+
+## Principle
+
+Do not default to McKinsey/MECE. MECE, SCQA, and pyramid writing are useful communication tools, not universal research methods.
+
+Select the method based on:
+
+- report purpose
+- audience
+- decision to support
+- available materials
+- evidence type
+- regulatory or scientific risk
+- output format
+
+## Method Router
+
+### Market, investment, or commercial strategy
+
+Use when the user asks about market opportunity, competition, investment thesis, BD opportunity, pricing, or commercialization.
+
+Methods and tools:
+
+- market sizing: TAM/SAM/SOM, bottom-up demand model, volume-price bridge
+- competitive landscape: segmentation, product differentiation, launch timing, share shifts
+- value chain: upstream supply, manufacturing bottlenecks, channel economics
+- investment: thesis tree, scenario analysis, sensitivity analysis, risk-adjusted NPV where feasible
+- transaction/BD: deal comps, licensing terms, patent cliff, strategic fit
+
+Outputs:
+
+- market map
+- competitor table
+- assumptions ledger
+- upside/base/downside scenarios
+
+### Clinical, translational, or evidence review
+
+Use when the topic is efficacy, safety, trial design, disease area, standard of care, biomarker, or clinical development.
+
+Methods and tools:
+
+- PICO or PICOTS framing
+- evidence hierarchy
+- endpoint and comparator analysis
+- trial design critique
+- TPP and go/no-go criteria
+- benefit-risk assessment
+
+Outputs:
+
+- clinical evidence matrix
+- trial landscape
+- endpoint comparability table
+- evidence gaps and patient-selection risks
+
+### CMC, GMP, quality, or manufacturing operations
+
+Use when the topic involves process development, tech transfer, validation, inspection readiness, deviations, CAPA, sterility assurance, supply chain, or manufacturing risk.
+
+Methods and tools:
+
+- ICH / FDA / EMA / NMPA regulatory baseline mapping
+- gap assessment
+- FMEA or risk matrix
+- process validation lifecycle
+- control strategy mapping
+- deviation/CAPA effectiveness review
+- data integrity assessment
+
+Outputs:
+
+- gap register
+- risk heatmap
+- CAPA prioritization
+- control strategy map
+- readiness scorecard
+
+### R&D feasibility or technology assessment
+
+Use when the topic asks whether a technology, target, modality, platform, assay, or process is feasible.
+
+Methods and tools:
+
+- technology readiness level
+- critical path analysis
+- mechanism and modality fit
+- experiment roadmap
+- scale-up risk assessment
+- IP and freedom-to-operate screening
+
+Outputs:
+
+- feasibility scorecard
+- key experiments
+- kill criteria
+- technical risk register
+
+### Management, organization, or operating model
+
+Use when the topic involves organization, governance, operating cadence, capability building, performance management, or transformation.
+
+Methods and tools:
+
+- issue tree
+- operating model design
+- RACI / decision rights
+- KPI tree
+- process maturity assessment
+- change management roadmap
+
+Outputs:
+
+- operating model options
+- capability gap assessment
+- implementation roadmap
+- KPI and governance model
+
+### Policy, regulation, or access environment
+
+Use when the topic asks about policy, reimbursement, regulatory pathways, pricing access, or regional rules.
+
+Methods and tools:
+
+- policy timeline
+- stakeholder map
+- regulatory pathway comparison
+- access and reimbursement framework
+- scenario analysis by jurisdiction
+
+Outputs:
+
+- jurisdiction comparison
+- policy impact map
+- regulatory milestone table
+- access risks
+
+## Phase 0-1 Output Requirements
+
+Write a method decision note in `phase1/research_brief.md`:
+
+- selected method
+- why it fits
+- methods rejected and why
+- evidence types needed
+- search routes
+- expected output artifacts
+
+If the topic spans multiple scenarios, combine methods explicitly and define which chapters use which method.

.agents/skills/research-quality-gates/SKILL.md

@@ -0,0 +1,212 @@
+---
+name: research-quality-gates
+description: Applies stage gates for Antigravity-native Deep Research: search receipts, source access, claims ledger, triangulation, contradiction search, continuation state, and final assembly checks.
+---
+
+# Research Quality Gates
+
+Use this skill after every phase boundary and before any user-facing "done" claim. It is designed for Antigravity-native runs where model work happens inside Antigravity, while this repository provides the evidence discipline.
+
+## Core Principle
+
+Evidence must persist outside the model context. A claim is not verified because the model remembers it, summarized it, or saw it in a search snippet. It is verified only when the artifact trail contains:
+
+1. a search receipt,
+2. an opened original source or explicit access failure,
+3. a registered `source_id`,
+4. an evidence span or data locator,
+5. a claim-ledger record linking the claim to supporting and counter evidence.
+
+## Required Artifacts
+
+Create these files when the relevant phase begins. Empty files are acceptable at creation time, but they must be populated before the phase gate passes.
+
+| Phase | Artifact | Purpose |
+|---|---|---|
+| Phase 1 | `phase1/method_decision.md` | Selected method, rejected methods, evidence types, and search routes. |
+| Phase 1 | `phase1/assumptions.md` | Material assumptions and scope assumptions that need validation. |
+| Phase 2 | `phase2/search_log.jsonl` | One row per search/open/extract action. |
+| Phase 2 | `phase2/sources.jsonl` | Stable source registry with scores and tiers. |
+| Phase 2 | `phase2/rejected_sources.jsonl` | Rejected or low-quality sources with reasons. |
+| Phase 2 | `phase2/claims_ledger.jsonl` | Atomic factual and analytical claims with verification status. |
+| Phase 2 | `phase2/coverage_matrix.md` | Coverage of questions, chapters, methods, and evidence gaps. |
+| Phase 2 | `phase2/unsupported_claims.md` | Claims that could not be verified or need user-visible caveats. |
+| All phases | `continuation_state.json` | Current phase, completed sections, artifact paths, open gaps, and next actions. |
+| Phase 4 | `phase4/final_fact_check.md` | Final audit showing each core fact exists in the verified claim ledger. |
+
+## Search Receipt Gate
+
+Every search or retrieval action must write a row to `search_log.jsonl`.
+
+Required fields:
+
+```json
+{
+  "receipt_id": "srch_0001",
+  "timestamp": "YYYY-MM-DDTHH:MM:SSZ",
+  "tool": "search-cli|browser|project-search|other",
+  "mode": "academic|scholar|patents|news|extract|general|deep",
+  "query_or_url": "...",
+  "purpose": "which task/card/chapter this supports",
+  "result_count": 10,
+  "opened_urls": ["https://..."],
+  "status": "ok|partial|failed",
+  "failure_reason": null
+}
+```
+
+Gate fails if a model says it searched, confirmed, checked, extracted, opened, or verified a fact without a corresponding receipt.
+
+## Source Access Gate
+
+For any source used as evidence, `sources.jsonl` must record access status.
+
+Required additional fields:
+
+```json
+{
+  "id": "src_042",
+  "search_receipt_ids": ["srch_0001"],
+  "raw_url": "https://...",
+  "canonical_url": "https://...",
+  "title": "...",
+  "publication_date": "YYYY-MM-DD",
+  "source_type": "paper|regulator|trial_registry|patent|filing|database|consulting|media|other",
+  "tier": 1,
+  "score": 8.6,
+  "access_status": "opened_original|opened_abstract|paywalled|failed|snippet_only",
+  "evidence_locator": "page/table/section/trial id/patent claim",
+  "independence_cluster": "cluster_...",
+  "notes": "..."
+}
+```
+
+`snippet_only` sources cannot support final claims. Paywalled or abstract-only sources can be used only with a visible caveat or a second opened source that carries the same fact.
+
+## Claim Ledger Gate
+
+Each chapter draft must be backed by `claims_ledger.jsonl`. Store atomic claims, not paragraphs.
+
+Required fields:
+
+```json
+{
+  "claim_id": "ch03_C012",
+  "chapter": "ch03",
+  "claim_type": "fact|trend|comparison|causal|forecast|recommendation",
+  "claim": "...",
+  "supporting_source_ids": ["src_042", "src_087"],
+  "counter_source_ids": ["src_103"],
+  "evidence_spans": [
+    {
+      "source_id": "src_042",
+      "locator": "Table 2",
+      "summary": "..."
+    }
+  ],
+  "independence_clusters": ["cluster_a", "cluster_b"],
+  "confidence": "high|medium|low|unsupported",
+  "verification_status": "verified|partially_verified|conflicted|unsupported",
+  "needs_delta_retrieve": false,
+  "visible_caveat_required": false
+}
+```
+
+Gate fails if:
+
+- a core claim has fewer than 2 independent Tier 1-2 supporting sources;
+- a claim has source IDs but no evidence locator;
+- supporting sources all come from the same independence cluster;
+- a conflicted or unsupported claim is written as a settled conclusion.
+
+## Triangulation Gate
+
+Counting URLs is not enough. Sources are independent only when they do not trace back to the same press release, same trial registry entry, same company deck, same sell-side note, or same syndicated article.
+
+For core conclusions, require at least two of these source families where available:
+
+- regulator / official registry,
+- peer-reviewed paper or systematic review,
+- company filing / annual report / exchange disclosure,
+- patent or legal record,
+- independent database,
+- reputable industry or consulting report,
+- independent expert or professional media analysis.
+
+If a field has only one source family available, mark the limitation explicitly in `unsupported_claims.md` and in the report limitations section.
+
+## Contradiction Gate
+
+Every chapter requires at least one deliberate counter-search or falsification pass. Record it in `search_log.jsonl` and summarize it in the chapter brief.
+
+Minimum counter-evidence record:
+
+```json
+{
+  "claim_id": "ch03_C012",
+  "counter_query": "...",
+  "counter_source_ids": ["src_103"],
+  "result": "none_found|weak_counter|material_counter",
+  "impact": "keep|qualify|rewrite|delete"
+}
+```
+
+Gate fails if the chapter contains no counter-evidence section, no counter-search receipt, or no decision about how contradictions affected the draft.
+
+## Coverage Gate
+
+Before drafting, create `phase2/coverage_matrix.md` with one row per chapter/task axis:
+
+| Chapter | Method | Core Question | Required Evidence | Found Evidence | Gaps | Decision |
+|---|---|---|---|---|---|---|
+
+Gate fails if a chapter is drafted while its method, required evidence, or gaps are blank.
+
+## Delta-Retrieve Protocol
+
+When a gap appears, do not patch it from memory. Create a targeted delta task:
+
+1. write the gap in `coverage_matrix.md` or `claims_ledger.jsonl`;
+2. run 1-3 targeted searches with explicit query purpose;
+3. register any usable sources;
+4. update the relevant claim record;
+5. if still unsupported, keep the caveat visible.
+
+Delta retrieval is mandatory when Phase 3 finds a critical evidence gap.
+
+## Continuation Protocol
+
+For long reports or interrupted runs, keep `projects/<slug>/continuation_state.json` current.
+
+Minimum fields:
+
+```json
+{
+  "version": "0.20",
+  "slug": "...",
+  "current_phase": "phase2",
+  "active_model": "Gemini 3.1 Pro (Low)",
+  "completed_artifacts": ["phase2/task_cards.json"],
+  "open_gates": ["claim_ledger_gate"],
+  "artifact_paths": {
+    "sources": "phase2/sources.jsonl",
+    "claims": "phase2/claims_ledger.jsonl",
+    "search_log": "phase2/search_log.jsonl"
+  },
+  "open_questions": [],
+  "next_actions": []
+}
+```
+
+Before resuming a project, read this state and the latest artifacts. Do not rely on chat history alone.
+
+## Final Assembly Gate
+
+Phase 4 must prove that final facts are a subset of verified claims:
+
+- Sample at least 20 high-impact facts or all core claims, whichever is smaller.
+- For each sampled fact, record `claim_id`, `source_ids`, verification status, and final wording decision in `phase4/final_fact_check.md`.
+- New facts introduced during editing require new search receipts and claim-ledger records.
+- Delete or caveat any unsupported factual claim before rendering PDF/DOCX.
+
+Do not render final deliverables until the final assembly gate passes.

.agents/skills/source-quality/SKILL.md

@@ -78,7 +78,52 @@ description: 信源质量评分系统（0-10 分制）与黑名单机制。规
 
 ---
 
-## 三、黑名单（直接拒绝入库）
+## 三、检索回执与原文访问
+
+Gemini / Antigravity 模式下，信源质量评分必须和检索回执绑定。任何来源进入 `sources.jsonl` 前，必须能追溯到 `search_log.jsonl` 中的至少一条记录。
+
+### search_log.jsonl 最低字段
+
+```json
+{
+  "receipt_id": "srch_0001",
+  "timestamp": "YYYY-MM-DDTHH:MM:SSZ",
+  "tool": "search-cli|browser|project-search|other",
+  "mode": "academic|scholar|patents|news|extract|general|deep",
+  "query_or_url": "...",
+  "purpose": "which task/card/chapter this supports",
+  "result_count": 10,
+  "opened_urls": ["https://..."],
+  "status": "ok|partial|failed",
+  "failure_reason": null
+}
+```
+
+### sources.jsonl 追加字段
+
+```json
+{
+  "id": "src_042",
+  "search_receipt_ids": ["srch_0001"],
+  "raw_url": "https://...",
+  "canonical_url": "https://...",
+  "source_type": "paper|regulator|trial_registry|patent|filing|database|consulting|media|other",
+  "access_status": "opened_original|opened_abstract|paywalled|failed|snippet_only",
+  "evidence_locator": "page/table/section/trial id/patent claim",
+  "independence_cluster": "cluster_..."
+}
+```
+
+硬规则：
+
+- `snippet_only` 只能作为发现线索，不能支撑正文事实。
+- `failed` 必须保留失败原因，不能根据标题或搜索摘要推断具体数据。
+- `paywalled` / `opened_abstract` 可以用于发现方向，但核心结论还需要至少一个可打开原文或官方记录支撑。
+- 同一公司新闻稿、同一试验登记、同一专利族、同一券商报告转载链，必须归入同一个 `independence_cluster`。
+
+---
+
+## 四、黑名单（直接拒绝入库）
 
 以下信源**无论评分多少都禁用**：
 
@@ -112,7 +157,7 @@ description: 信源质量评分系统（0-10 分制）与黑名单机制。规
 
 ---
 
-## 四、利益冲突检测要点
+## 五、利益冲突检测要点
 
 ### 常见利益冲突场景
 - 药企赞助的 RCT 对自家产品评价极高 → 查对比剂、盲法、样本量
@@ -130,7 +175,7 @@ description: 信源质量评分系统（0-10 分制）与黑名单机制。规
 
 ---
 
-## 五、评分执行流程（伪代码）
+## 六、评分执行流程（伪代码）
 
 ```
 for each candidate_source in search_results:
@@ -162,7 +207,7 @@ for each candidate_source in search_results:
 
 ---
 
-## 六、输出字段（写入 sources.jsonl）
+## 七、输出字段（写入 sources.jsonl）
 
 ```jsonl
 {
@@ -177,12 +222,16 @@ for each candidate_source in search_results:
   "conflict_of_interest": null,
   "blacklist_checked": true,
   "retraction_checked": true,
+  "search_receipt_ids": ["srch_0001"],
+  "access_status": "opened_original",
+  "evidence_locator": "Table 2",
+  "independence_cluster": "cluster_trial_001",
   "notes": "NEJM 2025 原文，RCT 独立研究"
 }
 ```
 
 ---
 
-## 七、审计留痕
+## 八、审计留痕
 
-所有被**拒绝**的信源，也要写入 `projects/<slug>/phase2/rejected-sources.jsonl`（注明原因）。这是事后复盘的关键，不要静默丢弃。
+所有被**拒绝**的信源，也要写入 `projects/<slug>/phase2/rejected_sources.jsonl`（注明原因、对应 `receipt_id`、拒绝规则）。这是事后复盘的关键，不要静默丢弃。

.agents/workflows/deep-research-native.md

@@ -1,56 +1,154 @@
+---
+description: Run native biomedical Deep Research in Antigravity using roles, rules, skills, workflows, source receipts, and explicit approval gates.
+---
+
 # Deep Research Native Workflow
 
-Description: Run a biomedical Deep Research project in Antigravity using Antigravity model quota, with explicit anti-hallucination gates and source receipts.
+Invoke as `/deep-research-native <topic or slug>`.
 
-## Step 0: Load Context
+## Step 0: Load Operating Context
 
 - Load `AGENTS.md`.
+- Load `GEMINI.md`.
 - Load `.agents/agents.md`.
 - Load `.agents/rules/deep-research-antigravity.md`.
 - Load `.agents/skills/antigravity-surface-adapter/SKILL.md`.
-- Load skills: `mckinsey-method`, `search-strategy`, `source-quality`, `evidence-table`, `citation-manager`, `length-budget`, `output-hygiene`.
-- Confirm topic, slug, report type, target audience, method, output length, and allowed search tools.
+- Load `.agents/skills/method-selection/SKILL.md`.
+- Load relevant quality skills: `search-strategy`, `source-quality`, `evidence-table`, `research-quality-gates`, `citation-manager`, `length-budget`, `output-hygiene`.
 
-Gate: do not proceed if the topic, slug, and report purpose are unclear.
+Gate: if the active model has not loaded the above files, stop and ask the user to restart or explicitly mention them.
 
-## Step 1: Phase 0-1 With Opus
+## Step 1: Define The Research Problem
 
-- Ask the user to switch the conversation model to Claude Opus 4.6 (Thinking).
-- Create project folders under `projects/<slug>/`.
-- Read user materials and write `phase1/material_brief.md`.
-- Run real searches and log them in `phase1/search_log.md`.
-- Write `phase1/framework.md`, `phase1/research_brief.md`, and `phase1/research_brief.json`.
-- Write `phase1/unsupported_claims.md` for hypotheses not yet evidenced.
+Act as Research Manager with Gemini 3 Flash.
 
-Gate: pause for user confirmation. Do not enter Phase 2 before approval.
+Confirm:
 
-## Step 2: Phase 2 With Gemini 3.1 Pro Low
+- topic and slug
+- report purpose
+- target reader
+- decision the report supports
+- report type and expected length
+- available input materials
+- allowed search tools
+- whether Python model-worker commands are forbidden or allowed
 
-- Ask the user to switch the conversation model to Gemini 3.1 Pro (Low).
-- Build `phase2/task_cards.json`.
-- For each task card, run real searches and append `phase2/search_log.jsonl`.
-- Write `phase2/packets/*.json`; every packet must contain `search_receipts`, `sources`, `counter_evidence`, and `unsupported_claims`.
-- Build `phase2/chapter_briefs/*.json` and `phase2/compressed_findings/*.json`.
-- Write `phase2/drafts/chXX.md` only from chapter briefs and compressed findings.
+Create or confirm `projects/<slug>/` and phase folders. Create or update `projects/<slug>/continuation_state.json`. Use Python only for scaffolding if helpful.
 
-Gate: do not draft a chapter from memory or snippets. Every concrete claim needs a source ID.
+Gate: do not continue if purpose, audience, and decision use are unclear.
 
-## Step 3: Phase 3 With Gemini 3.1 Pro High
+## Step 2: Select Method
 
-- Ask the user to switch the conversation model to Gemini 3.1 Pro (High).
-- Review framework, packets, sources, chapter briefs, and drafts.
-- Write `phase3/critique.md`.
-- Include a source-audit table for at least 10 core facts.
-- Mark decision as `go`, `rework`, or `fail`.
+Ask the user to switch to Claude Opus 4.6 (Thinking).
+
+Act as Phase 0-1 Strategist. Use `method-selection`.
+
+Write a method decision note covering:
+
+- selected method or method mix
+- why it fits the scenario
+- rejected methods and why
+- evidence types required
+- search routes by chapter or task axis
+- expected artifacts
+
+Save it as `phase1/method_decision.md` or embed the same content in `phase1/research_brief.md` with a clear heading.
+
+Gate: do not default to McKinsey, MECE, or SCQA. Use them only when they fit the decision problem.
+
+## Step 3: Phase 0-1 Framing
+
+Still using Claude Opus 4.6 (Thinking), produce:
+
+- `phase1/material_brief.md`
+- `phase1/search_log.md`
+- `phase1/method_decision.md`
+- `phase1/assumptions.md`
+- `phase1/framework.md`
+- `phase1/research_brief.md`
+- `phase1/research_brief.json`
+- `phase1/unsupported_claims.md`
+
+Rules:
+
+- Hypotheses without evidence must be labeled as hypotheses.
+- Every searched claim must have a search receipt.
+- Each chapter must state method, core question, likely evidence, and falsification route.
+
+Gate: pause for user approval before Phase 2.
+
+## Step 4: Phase 2 Evidence And Drafting
+
+Ask the user to switch to Gemini 3.1 Pro (Low).
+
+Act as Evidence Analyst.
+
+Produce:
+
+- `phase2/task_cards.json`
+- `phase2/search_log.jsonl`
+- `phase2/sources.jsonl`
+- `phase2/rejected_sources.jsonl`
+- `phase2/claims_ledger.jsonl`
+- `phase2/coverage_matrix.md`
+- `phase2/packets/*.json`
+- `phase2/chapter_briefs/*.json`
+- `phase2/compressed_findings/*.json`
+- `phase2/drafts/chXX.md`
+- `phase2/unsupported_claims.md`
+
+Rules:
+
+- No tool receipt, no search claim.
+- No source ID, no factual claim.
+- Search snippets and AI summaries are leads only.
+- Every packet must include `search_receipts`, `sources`, `evidence_spans`, `counter_evidence`, and `unsupported_claims`.
+- Every core claim must be represented in `claims_ledger.jsonl`.
+- Every chapter must pass a counter-search or falsification pass.
+- Evidence gaps trigger delta retrieval before drafting or visible caveats if still unresolved.
+- Draft chapters only from approved chapter briefs and compressed findings.
+
+Gate: run `research-quality-gates`. Do not move to Phase 3 if packet evidence is missing, claim-ledger records are incomplete, unsupported claims are hidden, source independence is not tracked, or counter-evidence is absent.
+
+## Step 5: Phase 3 Review
+
+Ask the user to switch to Gemini 3.1 Pro (High).
+
+Act as Chief Reviewer.
+
+Produce `phase3/critique.md` with:
+
+- go / rework / fail decision
+- structural critique
+- method fit critique
+- evidence gap list
+- counter-evidence critique
+- claim-ledger audit
+- coverage matrix audit
+- source-audit table for at least 10 core facts
+- rework task list if needed
+
+If the critique finds a critical evidence gap, create delta-retrieve tasks instead of asking Phase 4 to paper over the gap.
 
 Gate: pause for user decision after critique.
 
-## Step 4: Phase 4 With Opus
+## Step 6: Phase 4 Finalization
 
-- Ask the user to switch the conversation model to Claude Opus 4.6 (Thinking).
-- Write `phase4/final_zh.md` from approved drafts and sources only.
-- Write `phase4/editorial_notes.md`.
-- Write `phase4/final_fact_check.md`, listing any unresolved or downgraded claims.
-- Use deterministic renderer tools afterward for PDF/DOCX.
+Ask the user to switch to Claude Opus 4.6 (Thinking).
 
-Gate: final output cannot introduce new facts without adding sources and search logs first.
+Act as Final Editor.
+
+Produce:
+
+- `phase4/final_zh.md`
+- `phase4/editorial_notes.md`
+- `phase4/final_fact_check.md`
+
+Rules:
+
+- Do not introduce new facts unless new sources and search logs are added first.
+- Final facts must be a subset of verified or explicitly caveated `claims_ledger.jsonl` rows.
+- Downgrade or mark claims that remain unsupported.
+- Use deterministic rendering tools afterward for PDF/DOCX.
+
+Gate: final output must pass citation and unsupported-claim review before rendering.

AGENTS.md

@@ -1,252 +1,91 @@
-# AGENTS.md — 生物医药 Deep Research 系统规则
+# AGENTS.md — Deep Research Cross-Tool Rules
 
-> 本文件为跨平台项目级指令文件。Codex、OpenCode、Claude Code、Antigravity、Gemini CLI 均应以本文件为运行规则。
-> 所有平台 adapter / skill / command 必须遵循本文件定义的研究方法论、信源标准与输出规范。
+This file is the shared, cross-tool instruction layer for Codex, OpenCode, Claude Code, Gemini CLI, and Antigravity.
 
----
+Keep this file short. Do not put Antigravity roles, detailed workflows, or long skill manuals here.
 
-## 1. 项目使命
+## Project
 
-本项目通过**Python core + skills + 可选多模型角色**协作，以**麦肯锡、德勤等顶尖机构的研究方法**，对生物医药领域（研发、工艺、管理、投资）的指定主题进行深度研究，输出专业级报告（PDF + DOCX）。
+Deep Research produces professional biomedical research reports for R&D, CMC/GMP, management, market, and investment topics.
 
-本项目**不涉及业务代码开发**，所有"代码"都是为**研究流水线**服务（如 Python runtime、ReportLab/Quarto 模板、下载脚本、信源 API 调用）。
+This repository is not an application codebase. Its code supports the research pipeline: Python runtime, search utilities, evidence schemas, citation checks, and PDF/DOCX rendering.
 
-### 1.1 v0.20 架构原则
+## Instruction Layers
 
-- `scripts/dr.py` 与 `scripts/runtime/*` 是核心编排真源；OpenCode、Codex、Claude Code、Antigravity、Gemini CLI 只是表层入口。
-- 模型选择以 `configs/models.yaml` 为准，由 Python runtime 解析 role/task 映射。
-- Skills 以 `.agents/skills` 为 canonical registry；adapter skill 目录由 `uv run python scripts/dr.py skills sync` 同步。
-- 默认工作链路为中文主写作；英文只保留在检索关键词、原文摘录、source title、DOI/URL 与来源笔记中。
+- Cross-tool baseline: `AGENTS.md`
+- Gemini / Antigravity override: `GEMINI.md`
+- Antigravity roles: `.agents/agents.md`
+- Antigravity strong rules: `.agents/rules/`
+- Reusable skills: `.agents/skills/`
+- Antigravity workflows: `.agents/workflows/`
+- Implementation plan and changelog: `PLAN.md`
 
-## 2. 研究方法论（所有 agent 必须遵循）
+If instructions conflict, use the more specific layer. For Antigravity, `GEMINI.md` and `.agents/rules/` override this file.
 
-### 2.1 麦肯锡核心原则
+## Operating Modes
 
-1. **研究方法适配场景**：MECE 是常用方法之一，但 GMP/CMC/管理咨询/研发立项等场景必须选择匹配框架
-2. **SCQA 叙事**（Situation → Complication → Question → Answer）：每章节开头用此结构引入
-3. **金字塔原理**：结论先行，论据支撑，纵向深入，横向 MECE
-4. **"每个标题即一个观点"**：标题不能是"概述""现状"这类模糊词，必须包含判断
-5. **So What? 自检**：每写完一段问自己"所以呢？"，若无则删
+Python-core mode:
 
-### 2.2 证据铁律
+- Use `scripts/dr.py`, `scripts/runtime/**`, `configs/models.yaml`, and `.agents/skills`.
+- Platform agents should call the Python CLI rather than reimplement worker orchestration.
+- Model routing is resolved by the Python runtime.
 
-- **每条结论至少 2 个独立 Tier 1-2 信源**佐证（见 §4 信源分级）
-- 达不到则**必须在正文注明**"该观点仅有 X 个来源支持，待进一步验证"
-- **反方证据优先**：每个 chapter 的研究必须主动搜索证伪性论点，不能只找支持证据
-- **数据可追溯**：所有数字、百分比、日期必须有来源 ID（如 `[src_042]`）
+Antigravity native mode:
 
-### 2.3 字数配额（硬要求）
+- Use `.agents/agents.md`, `.agents/rules/`, `.agents/skills/`, and `.agents/workflows/`.
+- Antigravity uses its own model quota for research execution.
+- Python scripts are auxiliary for scaffolding, local material processing, deterministic checks, citation/report rendering, and status.
+- Do not run Python model-worker commands such as `dr.py run`, `research --execute-packets`, or `research --assemble-chapters` unless the user explicitly approves external API/ZenMux usage.
 
-| 报告类型 | 最小字数 | 建议章节数 |
-|---|---|---|
-| 综述类 | 10,000 字 | 8-10 章 |
-| 研究类 | 30,000 字 | 10-12 章 |
-| 投资报告 | 20,000 字 | 10-12 章 |
-| 管理/工艺类 | 15,000-25,000 字 | 9-11 章 |
-
-**字数分配原则**：
-- 每章字数差距不超过 ±30%（避免头重脚轻）
-- 每 section 最少 800 字（不够则合并）
-- 结论章不少于全文 10%
-
-### 2.4 报告不能只谈结论
-
-- 每个观点后必须紧跟**数据/事实/案例**佐证
-- 禁止空洞形容词（"巨大""快速""显著"）不带数据
-- 趋势判断必须给**量化依据**（年复合增长率、市场规模、成功率等）
-
----
-
-## 3. Phase 工作流（4 阶段）
-
-### Phase 1：框架规划
-- **驱动命令**：`uv run python scripts/dr.py init <topic>` → `uv run python scripts/dr.py frame <slug>`（`/dr-init`、`/dr-frame` 只是薄封装）
-- **主导入口**：Python core 生成项目骨架与 framework；dr-plan 可作为表层访谈增强
-- **产出**：`phase1/material_brief.md` + `phase1/framework.md` + `phase1/research_brief.md/json`
-- **暂停点**：用户确认材料解读、研究方法、任务切分、检索策略和章节框架
-- **硬规则**：clarification 不只是问范围；必须固化报告用途、基调、成功标准、任务拆分、每个任务轴的 prompt/skills/search route，让低成本 worker 也能独立执行
-
-### Phase 2：深度研究
-- **驱动命令**：`uv run python scripts/dr.py research <slug> --workers 6`
-- **主导入口**：Python core 生成 task cards 并控制并发
-- **产出**：`phase2/task_cards.json` + `packets/*.json` + `sources.jsonl` + `chapter_briefs/*.json` + `compressed_findings/*.json` + `drafts/chXX.md`
-- **不暂停**：全自动跑完
-- **防碎片化规则**：并发 worker 只写 evidence packet；`--build-briefs` 必须先收束为 chapter brief 和 compressed finding；章节正文必须从 compressed finding 写，不得把 packet 按顺序拼贴成报告
-
-### Phase 3：总编审校
-- **驱动命令**：`uv run python scripts/dr.py review <slug>`（`/dr-review` 只是薄封装）
-- **主导入口**：Python core deterministic review；dr-chief-editor/Gemini 可作为后续深度审校增强
-- **产出**：`projects/<slug>/phase3/critique.md`
-- **暂停点**：用户决策（修正 / 回炉 phase2 / 整体重来）
-
-### Phase 4：成稿
-- **驱动命令**：`uv run python scripts/dr.py finalize <slug>`
-- **主导入口**：Python core 中文原生成稿；OpenCode/Codex/Claude Code 只调用 CLI
-- **默认链路**：final_zh.md → glossary/check(optional) → polish(optional) → citation_check → build_report
-- **兼容链路**：仅显式 `--legacy-translate` 时使用 final_en.md → translate → polish
-- **产出**：`phase4/final_zh.md` + `phase4/final_zh_polished.md`（可选）+ `phase4/*.pdf` + `phase4/*.docx`
-
----
-
-## 4. 信源分级（Tier 系统）
-
-### Tier 1 — 一级信源（优先使用，评分权重 × 1.2）
-
-- **一手学术文献**：PubMed、Cochrane、顶刊原文（NEJM / Lancet / Nature / Science / Cell / JAMA）
-- **监管机构公告**：FDA、EMA、NMPA、PMDA 官网及 openFDA
-- **临床试验注册**：ClinicalTrials.gov、ChiCTR
-- **专利原文**：USPTO、EPO、CNIPA、Google Patents
-- **上市公司披露**：SEC 10-K/10-Q、招股书、交易所年报
-
-### Tier 2 — 二级信源（可用，标准权重）
-
-- **权威咨询报告**：麦肯锡、BCG、德勤、IQVIA、EvaluatePharma、弗若斯特沙利文
-- **学术综述**：系统综述（Systematic Review）、Meta 分析
-- **行业协会**：PhRMA、BIO、中国医药工业协会
-- **专业数据库**：Wind、东方财富、同花顺（金融侧）
-- **专业媒体**：BioSpace、Endpoints News、FiercePharma、医药魔方、Insight 数据库
-
-### Tier 3 — 三级信源（辅助，不得作为唯一支撑）
-
-- **预印本**：bioRxiv、medRxiv（需标注"未经同行评审"）
-- **券商研报**：中金、中信、高盛生物医药团队（需注意利益冲突）
-- **会议摘要**：AACR、ASCO、ASH 会议摘要（数据可能未完整发表）
-- **企业白皮书**（注明来源，降权使用）
-
-### Tier 4 — 四级信源（仅做发现入口）
-
-- Tavily / Brave / Exa 通用搜索返回的**普通网页**
-- 一般新闻报道
-- Wikipedia（**只做术语理解入口，结论不得引用**）
-
-### 黑名单（禁用）
-
-- 纯新闻聚合站（百家号、头条号、部分自媒体公众号）
-- 未署名作者的行业博客
-- 被 Retraction Watch 标记为撤稿的论文
-- 明显软文/PR 稿（如"某某 CEO 表示..."而无实质数据）
-- 超过 5 年的综述（除机制类研究可放宽）
-
-### 信源评分（0-10）
-
-每个进入 `sources.jsonl` 的信源必须打分，维度：
-- 权威性（期刊 IF、机构排名）0-3
-- 时效性（≤3 年满分，每老 1 年 -0.5） 0-2
-- 一手性（一手 > 综述 > 二次解读） 0-2
-- 可验证性（有 DOI / URL / 原始数据） 0-2
-- 利益冲突（厂商自发 -1） 0-1
-
-**硬规则**：评分 < 5 的信源不得作为结论唯一支撑。
-
----
-
-## 5. Python Role / Task 模型
-
-平台 agent 文件只保留兼容和展示意义；真实角色、任务类型、模型、温度、并发上限以 Python runtime 为准。
-
-查看当前模型配置：
+## Core Commands
 
 ```bash
-uv run python scripts/dr.py models --profile medium
-uv run python scripts/dr.py models --profile medium --json
-uv run python scripts/dr.py methods list
+uv run python scripts/dr.py init "研究主题" --slug <slug> --method <method>
+uv run python scripts/dr.py frame <slug>
+uv run python scripts/dr.py research <slug> --workers 6 --execute-packets
+uv run python scripts/dr.py review <slug>
+uv run python scripts/dr.py finalize <slug>
+uv run python scripts/deploy_adapters.py antigravity --target /path/to/workspace --dry-run
 ```
 
-核心任务类型：
+## Research Integrity
 
-| Task type | 默认角色 | 用途 |
-|---|---|---|
-| `source_discovery` | `dr_searcher` | 轻量信源发现 |
-| `evidence_packet` | `dr_analyst` | task card → evidence packet |
-| `chapter_assembly` | `dr_analyst` | chapter brief → 中文章节 |
-| `counter_verification` | `dr_verifier` | 反方证据与交叉模型验证 |
-| `phase3_review` | `dr_chief_editor` | 总编审校 |
-| `final_editorial` | `dr_editor_in_chief` | 中文终稿统稿 |
-| `report_render` | `dr_reporter` | PDF/DOCX 渲染 |
+- No fabricated data, URLs, DOIs, clinical results, regulatory status, patents, or market figures.
+- No factual claim without a source ID or a clearly marked "to verify" status.
+- No claim that a search or verification was performed unless there is a real tool receipt or search log.
+- Search snippets, AI summaries, and model memory are discovery leads, not final evidence.
+- Every major conclusion needs at least two independent Tier 1-2 sources. If not available, downgrade and mark uncertainty.
+- Counter-evidence is mandatory. Do not collect only supporting evidence.
+- Wikipedia is allowed for orientation only and must not support final conclusions.
+- Use Chinese for formal report writing. English may remain in search keywords, titles, DOI/URL, original excerpts, and raw notes.
 
-默认策略：
+## Method Selection
 
-- Codex/GPT 系列适合代码、schema、回归、review。
-- Claude/Opus/Sonnet 适合长文结构、中文表达、访谈增强。
-- Gemini 适合长上下文审校、多模态材料、替代框架评估。
-- ZenMux 混合模型仍由 `configs/models.yaml` 统一管理，平台当前会话模型不得覆盖 Python role/task 映射。
+Do not default to McKinsey/MECE for every topic.
 
-## 6. Platform Adapter 调用方式
+Choose the research method and tools based on the user's scenario. Use `.agents/skills/method-selection/SKILL.md` for Antigravity native work and `configs/research_methods.yaml` for Python-core mode.
 
-详见 `docs/platform-adapters.md`。摘要如下：
+## Source Quality
 
-| Platform | 项目指令/命令位置 | 推荐调用 |
-|---|---|---|
-| OpenCode | `.opencode/commands/*.md` | `/dr-run <slug-or-topic>` |
-| Codex | `AGENTS.md` + `$CODEX_HOME` adapter（由 `scripts/deploy_adapters.py codex` 部署） | `uv run python scripts/dr.py ...` 或 `codex exec "$(uv run python scripts/dr.py prompt dr-run '<topic>')"` |
-| Claude Code | `.claude/skills/*/SKILL.md` | `/dr-run <slug-or-topic>` |
-| Gemini CLI | `GEMINI.md` + `.gemini/commands/dr/*.toml` | `/dr:run <slug-or-topic>` |
-| Antigravity | `.agents/agents.md` + `.agents/rules` + `.agents/skills` + `.agents/workflows` | 角色定义在 agents，强约束在 rules，技能在 skills，流程在 workflows |
+Detailed scoring belongs in `.agents/skills/source-quality/SKILL.md`.
 
-跨平台硬规则：
+Baseline tiers:
 
-- 除 Antigravity native 模式外，平台只做 surface adapter，不承载核心调度。
-- Antigravity 的角色定义放在 `.agents/agents.md`；不要把角色、技能和流程继续堆进本文件。
-- 不在平台 prompt 中手工并发写章节。
-- 不把平台 subagent 当默认并发机制。
-- 真实并发由 `scripts/runtime/workers.py` 的 worker pool 执行。
-- 真实模型选择由 `configs/models.yaml` 和 `scripts/runtime/roles.py` 执行。
-- 信息检索默认走 `scripts/search.py` / `SearchClient` / `search-gateway` skill；不得把 Tavily MCP、browser MCP 或平台 web search 作为默认路径，除非用户明确授权。
-- 搜索路由必须按任务类型选择：`evidence`=Exa highlights 受控证据发现，`fda/scholar/patents/news`=专用信源路径，`general`=宽泛发现和兜底；Tavily Research 只能作为阶段性 scan/enrichment/rework 输入，不能直接替代 evidence packet 或章节正文。
+- Tier 1: original academic papers, systematic reviews where appropriate, regulator documents, clinical trial registries, patents, company filings.
+- Tier 2: authoritative consulting/industry reports, industry associations, reputable professional media and databases.
+- Tier 3: preprints, conference abstracts, brokerage research, company white papers. Use with caution.
+- Tier 4: general web pages, ordinary news, Wikipedia. Discovery only.
 
----
+## Safety
 
-## 7. 目录约定
+- Keep API keys only in `secrets.env`; never hardcode or commit secrets.
+- Do not read or expose secrets unless the user explicitly asks.
+- Do not overwrite user settings or existing workspace rule/skill/workflow files unless the user asks for `--force`.
+- Do not run destructive git commands such as `git reset --hard`, `git clean`, or broad file deletion without explicit approval.
+- Do not write outside the current workspace unless the user explicitly approves.
 
-- 每个研究主题放在 `projects/<topic-slug>/`，slug 用小写+连字符，如 `glp1-r-agonist-market-2026`
-- 所有中间产物（drafts、evidence、sources.jsonl）均为 Markdown 或 JSONL，便于 diff 与版本控制
-- `archive/` 存放已完成或废弃的研究，不再主动维护
+## Change Management
 
----
-
-## 8. 安全与权限
-
-- API 密钥**只存** `secrets.env`（已入 gitignore），禁止硬编码到任何 agent/skill/command
-- 字体文件（~140MB）不入 git，通过 `download-fonts.sh` 获取
-- `bash` 权限默认 `ask`，仅允许 `python *` / `pandoc *` / `ls *` / `cat *` / `curl *` 自动执行
-
----
-
-## 9. 如何判断是否走了 Python Core
-
-不要用“平台是否 spawn subagent”作为成功标准。Python-core 模式的验证锚点是 Python runtime 产物：
-
-1. `uv run python scripts/dr.py status <slug>` 能看到 phase 状态。
-2. Phase 2 存在 `phase2/task_cards.json`。
-3. Phase 1 存在 `phase1/research_brief.md` 和 `phase1/research_brief.json`。
-4. `--execute-packets` 后存在 `phase2/packets/*.json` 和必要时的 `phase2/packet_errors/*.json`。
-5. `--build-briefs` 后存在 `phase2/chapter_briefs/*.json` 与 `phase2/compressed_findings/*.json`。
-6. `--assemble-chapters` 后存在 `phase2/drafts/chXX.md` 和必要时的 `phase2/chapter_errors/*.json`。
-7. `scripts/v020_regression.py` 输出 `v0.20 regression PASS`。
-
-Antigravity native 模式的验收锚点由 `.agents/workflows/deep-research-native.md` 定义。
-
----
-
-## 10. 禁止事项（negative instructions）
-
-所有 agent 均禁止：
-
-1. ❌ 引用 Wikipedia 作为结论支撑（仅做术语理解）
-2. ❌ 在缺乏 2 个独立信源时仍给出绝对化结论
-3. ❌ 使用"据报道""有专家认为"等未指明来源的表述
-4. ❌ 编造或虚构数据、URL、DOI
-5. ❌ 声称"已搜索/已验证/官网显示"但没有工具回执和检索记录
-6. ❌ 用搜索摘要、AI summary、snippet 冒充原文证据
-7. ❌ 写空洞的套话（"随着科技的发展""在大数据时代"）
-8. ❌ 忽略反方观点，只收集支持证据
-9. ❌ 对输出字数"打折"（综述 <10000 字、研究 <30000 字必须返工）
-10. ❌ 在正文中使用未在术语表中定义的专业缩写（首次出现需全称+缩写）
-
----
-
-## 11. 变更管理
-
-- 本文件与 `PLAN.md` 是**双核**：PLAN.md 管实施进度与架构，AGENTS.md 管运行时规则
-- 修改本文件需同步更新 PLAN.md 的"变更记录"段
-- 所有 agent/skill 新增或重大调整必须在 PLAN.md §8 清单中标记完成状态
+- Treat `AGENTS.md`, `GEMINI.md`, `.agents/**`, and `PLAN.md` as production configuration.
+- Keep root rules short. Move roles to `.agents/agents.md`, constraints to `.agents/rules`, capabilities to `.agents/skills`, and phase sequencing to `.agents/workflows`.
+- When changing runtime rules or adapter behavior, update `PLAN.md` changelog.

GEMINI.md

@@ -1,34 +1,34 @@
-# Gemini CLI Project Instructions
+# GEMINI.md — Gemini / Antigravity Overrides
 
-This repository is Deep Research v0.20. Gemini must assume it is high-risk for hallucination and false confirmation in research tasks.
+This file has higher priority than `AGENTS.md` for Gemini CLI and Antigravity.
 
-## Load Order
+## Load The Right Layer
 
-- Treat `AGENTS.md` as the cross-platform rule source.
-- For Antigravity-native work, also follow `.agents/rules/deep-research-antigravity.md` and `.agents/skills/antigravity-surface-adapter/SKILL.md`.
-- Use `/memory show` or equivalent context inspection when behavior seems inconsistent.
+- Shared baseline: `AGENTS.md`
+- Antigravity roles: `.agents/agents.md`
+- Strong research rules: `.agents/rules/`
+- Skills: `.agents/skills/`
+- Workflows: `.agents/workflows/`
 
-## Non-Negotiable Research Integrity
+For Antigravity native research, load `.agents/agents.md`, `.agents/rules/deep-research-antigravity.md`, `.agents/skills/antigravity-surface-adapter/SKILL.md`, `.agents/skills/method-selection/SKILL.md`, `.agents/skills/research-quality-gates/SKILL.md`, and `.agents/workflows/deep-research-native.md`.
 
-- Never claim "searched", "verified", "confirmed", "officially shows", or "according to source" unless a tool was actually executed in this session or current phase and the result is logged.
-- Every factual claim with a number, date, company, product, clinical phase, regulatory status, market size, patent status, or quote needs a `source_id`.
-- Search snippets, AI summaries, and model memory are discovery aids only. They are not evidence.
-- If you cannot open the original source, write "未能访问原文，仅作为发现线索" and do not extract exact values from it.
-- Maintain a phase search log: query, tool, timestamp, URL/title, selected/rejected status, and reason.
-- Prefer saying "未找到足够证据" over filling gaps.
+Use `/memory show` or `/memory refresh` in Gemini CLI when the loaded context may be stale.
 
-## Platform Mode
+## Gemini Failure Modes
 
-- Gemini CLI is normally a Python-core surface adapter. Use `.gemini/commands/dr/*.toml` or run `uv run python scripts/dr.py ...`.
-- Antigravity is the exception: it should use its own model quota and skills to execute research natively; Python scripts are auxiliary unless the user explicitly approves model-worker/API usage.
-- Keep formal research outputs Chinese-first. Search keywords, source titles, excerpts, DOI/URL and raw notes may remain English.
-- Do not modify `projects/**` unless the user is intentionally running a research project.
+Treat Gemini-family models as high risk for false certainty in research.
 
-## Typical Python-Core Commands
+- Never say "searched", "verified", "confirmed", "officially shows", or "according to source" unless a real tool call happened in this session or phase and the result is logged.
+- Do not use model memory, snippets, or AI summaries as evidence.
+- Every concrete fact needs a `source_id`, claim-ledger row, or a clear "to verify" label.
+- If the original source cannot be opened, write "未能访问原文，仅作为发现线索" and do not extract exact values from it.
+- Keep `search_log.jsonl`, `claims_ledger.jsonl`, and `continuation_state.json` current in Antigravity native runs.
+- Prefer "未找到足够证据" over filling gaps.
 
-```bash
-uv run python scripts/dr.py run "研究主题" --slug <slug> --method mckinsey_market
-uv run python scripts/dr.py research <slug> --workers 6 --execute-packets
-uv run python scripts/dr.py review <slug>
-uv run python scripts/dr.py finalize <slug>
-```
+## Platform Boundary
+
+Gemini CLI normally uses Python-core mode through `.gemini/commands/dr/*.toml` or `uv run python scripts/dr.py ...`.
+
+Antigravity is different: use native mode and its model quota for research execution. Python scripts are auxiliary unless the user explicitly approves Python model-worker/API usage.
+
+Do not modify `projects/**` unless the user is intentionally running a research project.

PLAN.md

@@ -754,7 +754,7 @@ OpenCode 的坑：如果只是在主会话里装样子地写"让 X agent 做"，
   - Claude/Claude Code 最佳实践可借鉴：根指令要短、具体、可执行，长流程拆到 rules/skills/workflows，避免巨型上下文降低遵从性。
 
   **已落地**：
-  - `AGENTS.md` 新增 Antigravity native 例外、检索回执、source_id、search_log、unsupported_claims 等反幻觉硬规则。
+  - 初版曾在 `AGENTS.md` 中加入 Antigravity native 例外、检索回执、source_id、search_log、unsupported_claims 等反幻觉硬规则；v0.20.3/v0.20.4 已将这些内容迁入 `.agents/rules`、`.agents/skills` 与 `.agents/workflows`。
   - `GEMINI.md` 重写为短约束：禁止假搜索、禁止无 source_id 事实、要求 search log，并区分 Gemini CLI 与 Antigravity native。
   - `.agents/rules/deep-research-antigravity.md` 加入 Anti-Hallucination Contract。
   - `.agents/skills/antigravity-surface-adapter/SKILL.md` 加入 phase artifacts、fact-audit、权限建议和检索日志要求。
@@ -773,3 +773,20 @@ OpenCode 的坑：如果只是在主会话里装样子地写"让 X agent 做"，
   - 瘦身 `AGENTS.md`，只保留跨平台研究底线与分层指引。
   - `antigravity-surface-adapter` skill 和 `deep-research-native` workflow 改为引用 `.agents/agents.md`。
   - `scripts/deploy_adapters.py antigravity` 同步部署 `.agents/agents.md`，默认跳过已有文件，`--force` 才备份覆盖。
+
+- 2026-05-07 v0.20.4 AGENTS/GEMINI slimdown + method selection：**根规则瘦身，研究方法按场景选择**
+
+  **设计结论**：
+  - 根 `AGENTS.md` 只保留跨工具底线、命令入口、安全边界和分层索引；Phase 0-4 工作流、Antigravity 角色、长规则和技能细则全部迁出。
+  - `GEMINI.md` 只做 Gemini/Antigravity 高优先级覆盖，强调上下文加载和反假搜索。
+  - 麦肯锡/MECE/SCQA 只是候选表达和咨询工具，不再作为默认研究方法；不同研究场景必须选择匹配的分析框架。
+
+  **已落地**：
+  - 重写 `AGENTS.md`，缩短为跨工具规则和索引。
+  - 重写 `GEMINI.md`，保留 Gemini 反幻觉、平台边界和 context 加载指引。
+  - 新增 `.agents/skills/method-selection/SKILL.md`，覆盖市场/投资、临床、CMC/GMP、R&D、管理、政策等方法路由。
+  - 参考 `199-biotechnologies/claude-deep-research-skill` 的证据持久化、claim-level verification、delta retrieve、continuation state 和 final assembly gate 设计，新增 `.agents/skills/research-quality-gates/SKILL.md`。
+  - 强化 `source-quality` 与 `evidence-table`：要求 search receipt、原文访问状态、独立性 cluster、`claims_ledger.jsonl`、`coverage_matrix.md` 和不可证实 claim 显式落盘。
+  - 重写 `.agents/agents.md`，只保留角色定义和 required skills。
+  - 重写 `.agents/workflows/deep-research-native.md`，把方法选择设为独立 gate，加入 claim ledger、delta retrieve、coverage audit 和 continuation state gate。
+  - 文档与测试同步更新。

README.md

@@ -101,7 +101,7 @@ v0.20 后，OpenCode/Codex/Claude Code/Gemini CLI 都是 Python core 的 surface
 - Codex：使用 `AGENTS.md` + 部署到 `$CODEX_HOME` 的 adapter 文件，优先用 GPT 系列做代码/测试/审阅。
 - Claude Code：使用 `.claude/skills/*/SKILL.md`，优先用 Opus/Sonnet 做访谈、结构讨论和中文风格审阅。
 - Gemini CLI：使用 `GEMINI.md` 与 `.gemini/commands/dr/*.toml`，优先用 Gemini 做长上下文、多模态和替代框架审阅。
-- Antigravity：作为 Agent Manager 打开仓库，使用 `.agents/rules` + `.agents/skills` 指导其用 Antigravity 模型配额原生执行 Deep Research；Python core 只做脚手架、校验、引用和出稿辅助。
+- Antigravity：作为 Agent Manager 打开仓库，使用 `.agents/rules` + `.agents/skills` 指导其用 Antigravity 模型配额原生执行 Deep Research；Python core 只做脚手架、校验、引用和出稿辅助；质量门由 `method-selection`、`research-quality-gates`、`source-quality`、`evidence-table` 共同约束。
 
 部署 Codex adapter（不在仓库内创建 `.codex`）：
 
@@ -120,7 +120,7 @@ uv run python scripts/deploy_adapters.py antigravity --target /path/to/workspace
 uv run python scripts/deploy_adapters.py antigravity --target /path/to/workspace
 ```
 
-Antigravity 部署不会修改全局设置。若目标工作区已有同名 agents/rule/skill/workflow 文件，默认跳过；只有显式加 `--force` 时才会先生成 `.bak` 备份再覆盖。
+Antigravity 部署不会修改全局设置。若目标工作区已有同名 agents/rule/skill/workflow 文件，默认跳过；只有显式加 `--force` 时才会先生成 `.bak` 备份再覆盖。Antigravity 分层为：`.agents/agents.md` 定义角色，`.agents/rules` 放强约束，`.agents/skills` 放能力，`.agents/workflows` 放流程。关键 artifact 包括 `search_log.jsonl`、`sources.jsonl`、`claims_ledger.jsonl`、`coverage_matrix.md` 和 `continuation_state.json`。
 
 部署到新环境后自检：
 

docs/platform-adapters.md

@@ -136,6 +136,8 @@ gemini
 
 - `.agents/agents.md`：Antigravity 角色定义，只定义 Research Manager / Strategist / Analyst / Reviewer / Final Editor 等角色。
 - `.agents/skills/antigravity-surface-adapter/SKILL.md`：Antigravity 专用执行说明。
+- `.agents/skills/method-selection/SKILL.md`：按场景选择研究方法，避免默认套用麦肯锡/MECE。
+- `.agents/skills/research-quality-gates/SKILL.md`：把 search receipt、source access、claims ledger、delta retrieve、continuation state 和 final fact check 做成阶段质量门。
 - `.agents/rules/deep-research-antigravity.md`：workspace rule，约束其优先使用 Antigravity 模型配额，避免主流程落回 ZenMux。
 - `.agents/workflows/deep-research-native.md`：可按 slash workflow 执行的四阶段研究流程与反幻觉 gate。
 - `.agents/skills/*`：Antigravity 官方默认 skill 目录，直接复用本项目 canonical skill registry。
@@ -166,7 +168,7 @@ uv run python scripts/deploy_adapters.py antigravity --target /path/to/workspace
 4. 给 Agent Manager 一个明确任务：
 
 ```text
-请加载 .agents/agents.md、.agents/rules/deep-research-antigravity.md、.agents/skills/antigravity-surface-adapter/SKILL.md 和 AGENTS.md。
+请加载 .agents/agents.md、.agents/rules/deep-research-antigravity.md、.agents/skills/antigravity-surface-adapter/SKILL.md、.agents/skills/research-quality-gates/SKILL.md 和 AGENTS.md。
 用 Gemini 3 Flash 做流程管理，按 skill 要求在需要时提示我切换模型。
 研究主题："ADC 全球竞争格局"，slug: adc-global-landscape，method: mckinsey_market。
 请先创建/确认项目目录，然后进入 Phase 0-1，并在生成 phase1/framework.md 和 research_brief 后暂停。
@@ -179,6 +181,7 @@ uv run python scripts/deploy_adapters.py antigravity --target /path/to/workspace
 - 不要默认运行 `dr.py run`、`research --execute-packets`、`research --assemble-chapters`，这些会把主流程重新导向 Python/ZenMux。
 - Python core 可用于 `init/status/skills validate/finalize/render` 等辅助动作。
 - 若本机安装了 `paperfoot/search-cli` 的 `search` 命令，Antigravity Phase 0-2 可优先用 `search agent-info`、`search ... --json` 做统一检索入口。
+- Phase 2 不只产出章节草稿；必须维护 `search_log.jsonl`、`sources.jsonl`、`claims_ledger.jsonl`、`coverage_matrix.md` 和 `unsupported_claims.md`，否则 Phase 3/4 不得声称已验证。
 - 不建议依赖 SOUL.md：它不是 Antigravity 官方 Deep Research 约束入口。本项目用 `AGENTS.md`、`.agents/agents.md`、`.agents/rules`、`.agents/skills` 和 `.agents/workflows` 分层约束。
 
 ## Model Strategy Across Platforms

tests/test_v020_runtime.py

@@ -36,6 +36,8 @@ def test_skill_registry_uses_agents_skills_as_canonical() -> None:
     assert "document-ingest" in names
     assert "deep-research" in names
     assert "antigravity-surface-adapter" in names
+    assert "method-selection" in names
+    assert "research-quality-gates" in names
     assert registry.validate()["ok"] is True