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 research question formulation, Socratic mentoring, methodology design, systematic literature search, source verification, cross-source synthesis, risk of bias assessment, meta-analysis, APA 7.0 report compilation, editorial review, devil's advocate challenges, ethics review, and post-research literature monitoring. Triggers on: research, deep research, literature review, systematic review, meta-analysis, PRISMA, evidence synthesis, fact-check, WHY HOW WHAT papers, 3W literature scan, guide my research, help me think through, 研究, 深度研究, 文獻回顧, 文獻探討, 系統性回顧, 後設分析, 事實查核, 三段式文獻掃描, 引導我的研究, 幫我釐清, 幫我想想, 我不確定要研究什麼, 研究方向, 研究主題, 심층 연구, 문헌 조사, 체계적 문헌고찰, 메타분석, 사실 확인, 연구 방향을 잡아줘, 연구 주제 정하는 것을 도와줘.
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 research question formulation, Socratic mentoring, methodology design, systematic literature search, source verification, cross-source synthesis, risk of bias assessment, meta-analysis, APA 7.0 report compilation, editorial review, devil's advocate challenges, ethics review, and post-research literature monitoring. Triggers on: research, deep research, literature review, systematic review, meta-analysis, PRISMA, evidence synthesis, fact-check, WHY HOW WHAT papers, 3W literature scan, guide my research, help me think through, 研究, 深度研究, 文獻回顧, 文獻探討, 系統性回顧, 後設分析, 事實查核, 三段式文獻掃描, 引導我的研究, 幫我釐清, 幫我想想, 我不確定要研究什麼, 研究方向, 研究主題, 심층 연구, 문헌 조사, 체계적 문헌고찰, 메타분석, 사실 확인, 연구 방향을 잡아줘, 연구 주제 정하는 것을 도와줘.
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 runs a writing quality checklist before finalizing: flags AI-typical overused terms, checks sentence/paragraph length variation, removes throat-clearing openers. See .
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:
Research the impact of AI on higher education quality assurance
Socratic mode:
Guide my research on the impact of declining birth rates on private universities
引導我的研究：少子化對私立大學的影響
幫我釐清我的研究方向，我對高教品保有興趣但還不太確定
Execution:
Scoping — Research question + methodology blueprint
Investigation — Systematic literature search + source verification
Analysis — Cross-source synthesis + bias check
Composition — Full APA 7.0 report
Review — Editorial + ethics + vulnerability scan
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
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):
User has no clear research question and wants guided thinking
User asks to be "led", "guided", or "mentored" through research
User expresses uncertainty about what to research or where to start
User wants to brainstorm, explore, or clarify a research direction
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
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.
User Input
|
+-- Already have a clear research question?
| +-- Yes --> Need PRISMA-compliant systematic review / meta-analysis?
| | +-- Yes --> systematic-review mode
| | +-- No --> Need a full report?
| | +-- Yes --> full mode
| | +-- No --> Only need literature?
| | +-- Yes --> Need rapid paper comparison?
| | +-- Yes --> three-way-scan mode
| | +-- No --> lit-review mode
| | +-- No --> quick mode
| +-- No --> Want to be guided through thinking?
| +-- Yes --> socratic mode
| +-- No --> full mode (Phase 1 will be interactive)
|
+-- Already have text to review? --> review mode
+-- Only need fact-checking? --> fact-check mode
⚠️ IRON RULE: Devil's Advocate has 3 mandatory checkpoints; Critical-severity issues block progression
Revision loops capped at 2 iterations; remaining issues become "acknowledged limitations"
⚠️ 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.
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.
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 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
HOW: what strategy, method, or technical route the paper uses
WHAT: what the paper found, built, or still leaves unresolved
This mode is intentionally lighter than lit-review. It prioritizes:
candidate retrieval
deduplication
compact per-paper extraction
cross-paper synthesis of shared WHY, divergent HOW, and remaining gaps
If the user later wants a broader evidence matrix, thematic synthesis, or PRISMA-like coverage, escalate from three-way-scan to lit-review or systematic-review.
Failure Paths
See references/failure_paths.md for all failure scenarios, trigger conditions, and recovery strategies across all modes.
Key failure path summary:
Failure Scenario
Trigger Condition
Recovery Strategy
RQ cannot converge
Phase 1 / Layer 1 exceeds multiple rounds while still vague
Full mode may use its candidate workflow; Socratic mode summarizes user-expressed directions or suggests lit-review, with no candidate generation unless the user explicitly exits non-generation mode
Insufficient literature
bibliography_agent finds < 5 sources
Expand search strategy, alternative keywords
Methodology mismatch
RQ type misaligned with method capability
Return to Phase 1, suggest 3 alternative methods
Devil's Advocate CRITICAL
Fatal logical flaw discovered
STOP, explain the issue, require correction
Ethics BLOCKED
Critical integrity issue (not subject matter)
Stop the user once to confirm; list issues + remediation path; overridable with recorded reasoning
Socratic non-convergence
> 10 rounds without convergence
Suggest switching to full mode
User abandons mid-process
Explicitly states they don't want to continue
Save progress, provide re-entry path
Only Chinese-language literature
English search returns empty
Switch to Chinese academic databases
Literature Monitoring (Optional Post-Pipeline)
Optional post-research monitoring for new publications in the research area.
See references/literature_monitoring_strategies.md for setup instructions across academic databases.
Handoff Protocol: deep-research → academic-paper
After research is complete, the following materials can be handed off to academic-paper:
Research Question Brief (from research_question_agent)
[If socratic mode] INSIGHT Collection and Research Plan Summary
Preregistration handoff — exactly one builder-produced
preregistration-artifact/1.0 sidecar (including an unavailable receipt) and,
when status=provided, its explicitly named companion bytes
Trigger: User says "now help me write a paper" or "write a paper based on this"
academic-paper's intake_agent will automatically detect available materials and skip redundant steps:
Has RQ Brief -> skip topic scoping
Has Bibliography -> skip literature search
Has Synthesis -> accelerate findings / discussion writing
Has preregistration sidecar -> strict-validate it and its named companion,
then carry both byte-for-byte; never rebuild it from prose or a template
The non-shell research_architect_agent supplies only the explicit caller
declaration and companion handle. Before handoff, a shell-capable dispatcher
must run the named deterministic build-preregistration-artifact subcommand in
scripts/build_cross_document_consistency_advisory.py, with caller-held RFC3339
declared_at. Only that builder may create or update the sidecar. A later
explicit user supply creates a new builder-produced sidecar; omission or silent
substitution is invalid.
See examples/handoff_to_paper.md for a detailed handoff example.
Full Academic Pipeline
See academic-pipeline/SKILL.md for the complete workflow.
Agent File References
Agent
Definition File
research_question_agent
agents/research_question_agent.md
research_architect_agent
agents/research_architect_agent.md
bibliography_agent
agents/bibliography_agent.md
source_verification_agent
agents/source_verification_agent.md
synthesis_agent
agents/synthesis_agent.md
report_compiler_agent
agents/report_compiler_agent.md
editor_in_chief_agent
agents/editor_in_chief_agent.md
devils_advocate_agent
agents/devils_advocate_agent.md
ethics_review_agent
agents/ethics_review_agent.md
socratic_mentor_agent
agents/socratic_mentor_agent.md
risk_of_bias_agent
agents/risk_of_bias_agent.md
meta_analysis_agent
agents/meta_analysis_agent.md
monitoring_agent
agents/monitoring_agent.md
Reference Files
Reference
Purpose
Used By
references/apa7_style_guide.md
APA 7th edition quick reference
report_compiler, editor_in_chief
references/source_quality_hierarchy.md
Evidence pyramid + grading rubric
source_verification, bibliography
references/methodology_patterns.md
Research design templates
research_architect
references/logical_fallacies.md
30+ fallacies catalog
devils_advocate
references/ethics_checklist.md
AI disclosure, attribution, dual-use
ethics_review
references/interdisciplinary_bridges.md
Cross-discipline connection patterns
synthesis, research_architect
references/socratic_questioning_framework.md
6 types of Socratic questions + 30+ prompt patterns
socratic_mentor
references/failure_paths.md
12 failure scenarios with triggers and recovery paths
all agents
references/mode_selection_guide.md
Mode selection flowchart and comparison table
orchestrator
references/irb_decision_tree.md
Portable human-subjects navigation aid; not an authority, universal taxonomy, or pathway determination
Cognitive framework for evaluating argument strength: Toulmin model, causal reasoning (Bradford Hill), inference to best explanation, epistemic status classification
⚠️ IRON RULE: Every claim must have a citation — no unsupported assertions
Evidence hierarchy — meta-analyses > RCTs > cohort studies > case reports > expert opinion (field-neutral baseline; grading is discipline-relative — a source meeting its own field's gold standard can reach Grade A even at a low design level. See references/source_quality_hierarchy.md §Grading Rubric + §Field-Specific Adjustments)
Contradiction disclosure — if sources disagree, report both sides with evidence quality comparison
Limitation transparency — every report must have an explicit limitations section
AI disclosure — all reports include a statement that AI-assisted research tools were used
Reproducibility — search strategies, inclusion criteria, and analytical methods must be documented for replication
Socratic integrity — while non-generation Socratic mode is active, never give direct answers; always guide through questions. A candidate response is lawful only after the explicit exit marker and is outside that mode.
Cross-Agent Quality Alignment
Unified definitions across all agents. ⚠️ IRON RULE: CRITICAL severity = issue that would invalidate a core conclusion or constitute academic misconduct. Requires immediate resolution.
See references/cross_agent_quality_definitions.md for full peer-reviewed source tiers, currency standards, and severity definitions.
Integration with Other Skills
This skill is domain-agnostic but can be combined with domain-specific skills:
deep-research + tw-hei-intelligence -> Evidence-based HEI policy research
deep-research + report-to-website -> Interactive research report
deep-research + podcast-script-generator -> Research podcast
deep-research + academic-paper -> Full research-to-publication pipeline
deep-research (socratic) + academic-paper (plan) -> Guided research + paper planning
deep-research (systematic-review) + academic-paper -> PRISMA systematic review paper
Model Tiering (#517, optional)
When ARS_MODEL_TIERING is set, the dispatching session routes this skill's agents per shared/model_tiering.md (canonical: the full 39-agent judgment/execution table + rules). Compact rule:
Unset (default): every agent inherits the session model — byte-equivalent pre-#517 behavior.
economy (frontier-tier session): execution-type agents dispatch ONE tier below the session model — floor Opus-class, never lower; judgment-type agents stay on the session model. No-op at or below the floor (announce once).
quality-boost (below-frontier session): judgment-type agents at the checkpoint surfaces (Stage 2.5/4.5 gates; the opt-in Stage 4→5 claim–ref audit; final review) jump UP to the frontier tier (however many tiers away — not a single increment); nothing is ever downgraded. No-op at the frontier (announce once).
Unknown values → warn once, behave as unset. Tiers are relative positions, never hard-pinned model ids. When a direction is active, route repeated same-stage calls to the SAME worker so its prompt cache accumulates; unset means dispatch shapes stay byte-equivalent too.
Version Info
Item
Content
Skill Version
2.12.1
Last Updated
2026-08-15
Maintainer
Cheng-I Wu
Dependent Skills
academic-paper v1.0+ (downstream)
Version History
See references/changelog.md for full version history.
