Universal deep research agent team. 13-agent pipeline for rigorous academic research on any topic. 8 modes: full research, quick brief, paper review, lit-review, fact-check, three-way literature scan, Socratic guided research dialogue, and systematic review with optional meta-analysis. Covers resear

Deep Research — Universal Academic Research Agent Team Universal deep research tool — a domain agnostic 13 agent team for rigorous academic research on any topic. v2.4 adds writing quality improvements to the report compiler: Style Profile consumption (optional) — If a Style Profile is available from academic paper intake, the report compiler applies it as a soft guide for the Executive Summary and Synthesis sections. Discipline conventions and report objectivity take priority. Writing Quality Check — The report compiler uses academic paper/references/writing quality check.md as a diagnostic guide before finalizing (prompts for judgment subordinate to author and venue requirements, not quotas), and flags claims the cited sources do not support as [MATERIAL GAP] rather than hedging them ( 825). Routing discipline (v3.9.2): see .claude/CLAUDE.md "Routing Discipline (v3.9.2)" + shared/references/intent clarification protocol.md for cross skill routing rules. This skill assumes routing has already settled — ambiguous cross phase materials should have been clarified upstream. Quick Start Minimal command: Socratic mode: Execution: 1. Scoping — Research question + methodology blueprint 2. Investigation — Systematic literature search + source verification 3. Analysis — Cross source synthesis + bias check 4. Composition — Full APA 7.0 report 5. Review — Editorial + ethics + vulnerability scan 6. Revision — Final polished report Trigger Conditions Trigger Keywords English : research, deep research, literature review, systematic review, meta analysis, PRISMA, evidence synthesis, fact check, methodology, APA report, academic analysis, policy analysis, WHY HOW WHAT papers, 3W literature scan, guide my research, help me think through, monitor this topic, set up alerts 繁體中文 : 研究, 深度研究, 文獻回顧, 文獻探討, 系統性回顧, 後設分析, 證據綜整, 事實查核, 三段式文獻掃描, WHY HOW WHAT 論文比較, 研究方法, 學術分析, 政策分析, 引導我的研究, 幫我釐清, 監測這個主題, 設定追蹤 한국어 : 심층 연구, 문헌 조사, 문헌 고찰, 체계적 문헌고찰, 메타분석, 근거 종합, 사실 확인, 팩트체크, 연구 방법 설계, 학술 분석, 연구 방향을 잡아줘, 연구 주제 정하는 것을 도와줘, 무엇을 연구할지 모르겠어, 이 주제 계속 모니터링해줘 Socratic Mode Activation Activate socratic mode when the user's intent matches any of the following patterns, regardless of language . Detect meaning, not exact keywords. Intent signals (any one is sufficient): 1. User has no clear research question and wants guided thinking 2. User asks to be "led", "guided", or "mentored" through research 3. User expresses uncertainty about what to research or where to start 4. User wants to brainstorm, explore, or clarify a research direction 5. User describes a vague interest without a specific, answerable question Default rule : When intent is ambiguous between socratic and full , prefer socratic — it is safer to guide first than to produce an unwanted report. The user can always switch to full later. Example triggers (illustrative, not exhaustive): "guide my research", "help me think through", 「引導我的研究」「幫我釐清」, or equivalent in any language Does NOT Trigger Scenario Use Instead Writing a paper (not researching) academic paper Reviewing a paper (structured review) academic paper reviewer Full research to paper pipeline academic pipeline Quick Mode Selection Guide Your Situation 你的狀況 Recommended Mode Spectrum Vague idea, need guidance / 有模糊想法，需要引導 socratic originality Clear RQ, need comprehensive research / 有明確 RQ，需要完整研究 full balanced Need a quick brief (30 min) / 需要快速摘要 quick fidelity Have a paper to evaluate before citing / 有論文需要評估 review balanced Need literature review for a topic / 需要文獻回顧 lit review fidelity Need a fast paper comparison scan / 需要快速比較多篇論文 three way scan fidelity Need to verify specific claims / 需要查核特定事實 fact check fidelity Need systematic review / meta analysis / 系統性回顧或後設分析 systematic review fidelity Spectrum (v3.2): fidelity = template heavy, predictable output; balanced = default; originality = exploratory, template light. See shared/mode spectrum.md for the full cross skill spectrum table. Not sure? Start with socratic — it will help you figure out what you need. 不確定？先用 socratic 模式——它會幫你釐清你需要什麼。 Agent Team (13 Agents) Agent Role Phase 1 research question agent Transforms vague topics into precise, FINER scored research questions with scope boundaries Phase 1, Socratic Layer 1 2 research architect agent Designs methodology blueprint: paradigm, method, data strategy, analytical framework, validity criteria Phase 1 3 bibliography agent Systematic literature search, source screening, annotated bibliography in APA 7.0 Phase 2 4 source verification agent Fact checking, source grading (evidence hierarchy), predatory journal detection, conflict of interest flagging Phase 2 5 synthesis agent Cross source integration, contradiction resolution, thematic synthesis, gap analysis Phase 3 6 report compiler agent Drafts complete APA 7.0 report (Title Abstract Intro Method Findings Discussion References) Phase 4, 6 7 editor in chief agent Q1 journal editorial review: originality, rigor, evidence sufficiency, verdict (Accept/Revise/Reject) Phase 5 8 devils advocate agent Challenges assumptions, tests for logical fallacies, finds alternative explanations, confirmation bias checks Phase 1, 3, 5, Socratic Layer 2, 4 9 ethics review agent AI assisted research ethics, attribution integrity, dual use screening, fair representation Phase 5 10 socratic mentor agent Q1 journal editor persona; guides research thinking through Socratic questioning across 5 layers Socratic Mode (Layer 1 5) 11 risk of bias agent Assesses risk of bias using RoB 2 (RCTs) and ROBINS I (non randomized); traffic light visualization Systematic Review (Phase 2) 12 meta analysis agent Designs and executes meta analysis or narrative synthesis; effect sizes, heterogeneity, GRADE Systematic Review (Phase 3) 13 monitoring agent Post research literature monitoring: digests, retraction alerts, contradictory findings detection Optional (post pipeline) Mode Selection Guide See references/mode selection guide.md for the detailed guide. Orchestration Workflow (6 Phases) Checkpoint Rules 1. ⚠️ IRON RULE : Devil's Advocate has 3 mandatory checkpoints; Critical severity issues block progression 2. Revision loops capped at 2 iterations ; remaining issues become "acknowledged limitations" 3. ⚠️ IRON RULE : Ethics Review stops the user once to confirm a Critical integrity concern (fabrication / plagiarism / missing AI disclosure / source misrepresentation / concrete harm enabling specifics). Overridable with recorded reasoning — it confirms, it does not veto. Subject matter alone never blocks; dual use is advisory (Responsible Use Statement), not a block. 4. User confirmation required after Phase 1 before proceeding Phase by phase Invocation Contract (v3.9.2) ARS pipeline runs in 6 phases. Two invocation modes: Mode A — orchestrator driven (default): pipeline orchestrator agent (in academic pipeline skill) runs all phases end to end with state tracking via Material Passport. Mode B — phase by phase (cross session resume): User invokes one agent per phase across sessions for long running projects. Common pattern via ARS PASSPORT RESET=1 + resume from passport=<hash (see academic pipeline/references/passport as reset boundary.md ). In Mode B, single phase agents (Bucket A per docs/design/2026 05 18 ars v3.9.2 agent phase classification.md ) stay strictly within their assigned phase for writes . Reads from upstream phases are allowed. Multi phase agents (Bucket B: devils advocate agent , report compiler agent ) do exactly the work specified by the caller's invocation for that phase — no extension to other phases in the same call. Routing into Mode B requires explicit user signal — /ars <mode slash command or [direct mode] prefix. Ambiguous cross phase input defaults to clarification per .claude/CLAUDE.md Routing Discipline + shared/references/intent clarification protocol.md . Enforcement (v3.9.2): Phase Boundary blocks on Bucket A agents + advisory verifier ( scripts/check pipeline integrity.py ) + a deterministic PreToolUse write scope guard in hook enabled runtimes ( 134 rescope, PR 294). Multi phase envelope remains forward scope ( 134 Slices 3 5). Socratic Mode: Guided Research Dialogue 5 layer dialogue guiding users from vague ideas to concrete research questions. Core principle while non generation Socratic mode is active: ⚠️ IRON RULE : Never give direct answers. The explicit candidate generation exit below leaves that mode before any candidate is shown. Layers : Clarification Assumption Probing Evidence/Reasoning Viewpoint/Perspective Implication/Consequence Research question authorship boundary: Socratic mode is non generation by default. Non convergence may produce only a summary of directions the user has already expressed plus focused questions or a lit review suggestion; it never produces candidate RQs automatically. If the user explicitly asks the system to propose candidates, announce the exit from non generation Socratic mode and emit [SOCRATIC NON GENERATION EXIT: explicit user request] on a standalone line before any clearly labeled AI generated candidate. Never switch silently. See references/socratic mode protocol.md for the full 5 layer dialogue flow, management rules, and auto end conditions. Opt in Reading Probe (v3.5.1) Setting ARS SOCRATIC READING PROBE=1 enables a one time honesty probe during goal oriented Socratic sessions. When the user cites a specific paper, the Mentor asks them to paraphrase one passage. Decline is logged without penalty. Default OFF. See agents/socratic mentor agent.md §"Optional Reading Probe Layer". Systematic Review Mode PRISMA 2020 compliant systematic review with optional meta analysis. Follows 5 phase protocol: Protocol Registration Systematic Search Screening & Selection Data Extraction & RoB Synthesis & Reporting. v3.4.0 compliance: systematic review mode triggers compliance agent at Stage 2.5 (Methods items) and Stage 4.5 (remaining items + RAISE 8 role matrix). PRISMA trAIce Mandatory failures block the pipeline. See shared/compliance checkpoint protocol.md . See references/systematic review protocol.md for full PRISMA pipeline, checkpoint rules, and meta analysis procedures. Operational Modes Mode Agents Active Output Word Count full (default) All 9 core (excluding socratic mentor, RoB, meta analysis) Full APA 7.0 report 3,000 8,000 quick RQ + Biblio + Verification + Report Research brief 500 1,500 review Editor + Devil's Advocate + Ethics Reviewer report on provided text N/A lit review Biblio + Verification + Synthesis Annotated bibliography + synthesis 1,500 4,000 three way scan Biblio + Verification (retrieval + WHY/HOW/WHAT extract) Paper shortlist compared by WHY/HOW/WHAT + cross paper synthesis 800 2,000 fact check Source Verification only Verification report 300 800 socratic Socratic Mentor + RQ + Devil's Advocate Research Plan Summary (INSIGHT collection) N/A (iterative) systematic review RQ + Architect + Biblio + Verification + RoB + Meta Analysis + Synthesis + Report + Editor + Ethics + DA Full PRISMA 2020 report + forest plot data + GRADE table 5,000 15,000 Three Way Scan Mode (WHY / HOW / WHAT) Use three way scan when the user needs a disciplined shortlist of papers compared in a stable frame, but does not yet need a full literature review report. WHY : what problem or bottleneck the paper addresses and why it matters

deep-research