v0.20.4 refine antigravity research skills

.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.