61 lines
4.1 KiB
Markdown
61 lines
4.1 KiB
Markdown
---
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name: deep-research
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description: Use when a user wants to run Deep Research, create a client-ready research report, analyze supplied audit/material files, compare evidence against regulations or best practices, or continue a phase-based research project.
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---
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# Deep Research
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## Principle
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Deep Research is driven by the repository Python core, not by chat context. Treat Codex, OpenCode, Claude Code, Antigravity, and Gemini CLI as surface interfaces that call `scripts/dr.py`; all durable state must be written under `projects/<slug>/`.
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## Required Flow
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1. Work from the repository root.
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2. Validate the skill/runtime registry before a serious run:
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`uv run python scripts/dr.py skills validate`
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3. For user-supplied materials, stop after Phase 0/1 material brief and interview:
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`uv run python scripts/dr.py init "<topic>" --slug <slug> --method <method> --input-material <path>`
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Review `phase1/material_brief.md` with the user before generating or approving the framework.
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4. If model calls will be used, probe the selected profile first:
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`uv run python scripts/dr.py models --profile medium --probe`
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5. Run Phase 1 and pause for framework review:
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`uv run python scripts/dr.py frame <slug> --method <method>`
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After user approval: `uv run python scripts/dr.py approve <slug>`
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6. Run Phase 2 with file-backed task cards and packets:
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`uv run python scripts/dr.py research <slug> --workers 6 --execute-packets --allow-search-fallback`
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7. Build briefs and chapters only from persisted packets:
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`uv run python scripts/dr.py sources cache <slug> --limit 50`
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`uv run python scripts/dr.py research <slug> --build-briefs`
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`uv run python scripts/dr.py research <slug> --assemble-chapters --workers 4`
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8. Review and finalize through Python:
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`uv run python scripts/dr.py review <slug>`
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`uv run python scripts/dr.py finalize <slug> --report-engine reportlab`
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## Research Rules
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- Chinese is the formal thinking and writing language by default; English is allowed for search keywords, source titles, abstracts, and raw excerpts.
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- Do not invent evidence when model/API access fails. Stop at the last durable artifact and report the exact blocker.
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- Phase 2 concurrency must use task cards and packet files, not platform subagents as the default mechanism.
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- Search must use the project Python gateway (`scripts/search.py` / `scripts.lib.search_client`) by default. Do not use Tavily MCP, browser MCP, or platform-native web search in subagents unless the user explicitly requests that escape hatch.
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- Key Tier 1-2 sources such as ICH Q9/Q10, EU GMP Annex 1, FDA guidance/warning letters, EMA/NMPA/WHO pages, and pharmacopeia materials should be cached as local Markdown snapshots under `phase2/source_cache/` before chapter assembly.
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- User materials are starting evidence, not final truth. Cross-check against authoritative sources such as NMPA, FDA, EMA, ICH, WHO, pharmacopeias, and recognized best-practice references.
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- For GMP/quality/operations diagnosis, prefer `--method gmp_quality_operations_diagnosis`.
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- Chapter drafts are not acceptable if they merely summarize principles. Each section must turn evidence into concrete findings, risk implications, and整改动作；otherwise return to Phase 2 enrichment.
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## Useful Commands
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- Status: `uv run python scripts/dr.py status <slug>`
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- List methods: `uv run python scripts/dr.py methods list`
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- Show method: `uv run python scripts/dr.py methods show <method>`
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- Dry-run task cards: `uv run python scripts/dr.py research <slug> --dry-run`
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- Sync adapter skills: `uv run python scripts/dr.py skills sync`
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## Common Failures
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- If Codex cannot write `~/.codex`, run `uv run python scripts/deploy_adapters.py codex --force` outside sandboxed mode.
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- The Codex deploy script does not copy `config.toml` by default; use `--include-config` only when the user explicitly wants the bundled Codex profile.
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- If `models --probe` returns subscription/model errors, do not launch packet workers; switch profile/key/provider first.
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- If a PDF has little embedded text, Phase 0 should call FireRed OCR. Default endpoint: `http://192.168.50.100:8001`.
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- If a subagent asks for MCP/web permissions during research, stop it and reroute the task through `search-gateway`.
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