deep-research

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 academic-paper/references/writing_quality_check.md.

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:

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

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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, 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, 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

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 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。

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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)

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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 --> 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

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Orchestration Workflow (6 Phases)

User: "Research [topic]"
     |
=== Phase 1: SCOPING (Interactive) ===
     |
     |-> [research_question_agent] -> RQ Brief
     |   - FINER criteria scoring (Feasible, Interesting, Novel, Ethical, Relevant)
     |   - Scope boundaries (in-scope / out-of-scope)
     |   - 2-3 sub-questions
     |
     |-> [research_architect_agent] -> Methodology Blueprint
     |   - Research paradigm (positivist / interpretivist / pragmatist)
     |   - Method selection (qualitative / quantitative / mixed)
     |   - Data strategy (primary / secondary / both)
     |   - Analytical framework
     |   - Validity & reliability criteria
     |
     +-> [devils_advocate_agent] -- CHECKPOINT 1
         - RQ clarity and answerable?
         - Method appropriate for question?
         - Scope too broad or too narrow?
         - Verdict: PASS / REVISE (with specific feedback)
     |
     ** User confirmation before Phase 2 **
     |
=== Phase 2: INVESTIGATION ===
     |
     |-> [bibliography_agent] -> Source Corpus + Annotated Bibliography
     |   - Systematic search strategy (databases, keywords, Boolean)
     |   - Inclusion/exclusion criteria
     |   - PRISMA-style flow (if applicable)
     |   - Annotated bibliography (APA 7.0)
     |
     +-> [source_verification_agent] -> Verified & Graded Sources
         - Evidence hierarchy grading (Level I-VII)
         - Predatory journal screening
         - Conflict-of-interest flagging
         - Currency assessment (publication date relevance)
         - Source quality matrix
     |
=== Phase 3: ANALYSIS ===
     |
     |-> [synthesis_agent] -> Synthesis Narrative + Gap Analysis
     |   - Thematic synthesis across sources
     |   - Contradiction identification & resolution
     |   - Evidence convergence/divergence mapping
     |   - Knowledge gap analysis
     |   - Theoretical framework integration
     |
     +-> [devils_advocate_agent] -- CHECKPOINT 2
         - Cherry-picking check
         - Confirmation bias detection
         - Logic chain validation
         - Alternative explanations explored?
         - Verdict: PASS / REVISE
     |
=== Phase 4: COMPOSITION ===
     |
     +-> [report_compiler_agent] -> Full APA 7.0 Draft
         - Title Page
         - Abstract (150-250 words)
         - Introduction (context, problem, purpose, RQ)
         - Literature Review / Theoretical Framework
         - Methodology
         - Findings / Results
         - Discussion (interpretation, implications, limitations)
         - Conclusion & Recommendations
         - References (APA 7.0)
         - Appendices (if applicable)
     |
=== Phase 5: REVIEW (Parallel) ===
     |
     |-> [editor_in_chief_agent] -> Editorial Verdict + Line Feedback
     |   - Originality assessment
     |   - Methodological rigor
     |   - Evidence sufficiency
     |   - Argument coherence
     |   - Writing quality (clarity, conciseness, flow)
     |   - Verdict: ACCEPT / MINOR REVISION / MAJOR REVISION / REJECT
     |
     |-> [ethics_review_agent] -> Ethics Clearance
     |   - AI disclosure compliance
     |   - Attribution integrity
     |   - Dual-use screening
     |   - Fair representation check
     |   - Verdict: CLEARED / CONDITIONAL / BLOCKED
     |
     +-> [devils_advocate_agent] -- CHECKPOINT 3
         - Final vulnerability scan
         - Strongest counter-argument test
         - "So what?" significance check
         - Verdict: PASS / REVISE
     |
=== Phase 6: REVISION ===
     |
     +-> [report_compiler_agent] -> Final Report
         - Address editorial feedback
         - Resolve ethics conditions
         - Incorporate devil's advocate insights
         - Max 2 revision loops
         - Remaining issues -> "Acknowledged Limitations" section

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

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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): prompt-level via Phase Boundary blocks on Bucket A agents + advisory verifier (scripts/check_pipeline_integrity.py). Deterministic PreToolUse hook + multi-phase envelope deferred to v3.10 active conductor (#134).

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Socratic Mode: Guided Research Dialogue

5-layer dialogue guiding users from vague ideas to concrete research questions. Core principle: ⚠️ IRON RULE: Never give direct answers.

Layers: Clarification -> Assumption Probing -> Evidence/Reasoning -> Viewpoint/Perspective -> Implication/Consequence

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".

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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.

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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
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

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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	Provide 3 candidate RQs or suggest lit-review
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

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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.

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Handoff Protocol: deep-research → academic-paper

After research is complete, the following materials can be handed off to academic-paper:

1. Research Question Brief (from research_question_agent)
2. Methodology Blueprint (from research_architect_agent)
3. Annotated Bibliography (from bibliography_agent)
4. Synthesis Report (from synthesis_agent)
5. [If socratic mode] INSIGHT Collection and Research Plan Summary

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

See examples/handoff_to_paper.md for a detailed handoff example.

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Full Academic Pipeline

See academic-pipeline/SKILL.md for the complete workflow.

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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

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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	IRB decision tree + Taiwan process + HE quick reference	ethics_review, research_architect
references/equator_reporting_guidelines.md	EQUATOR reporting guideline mapping	research_architect, report_compiler
references/preregistration_guide.md	Preregistration decision tree + platforms + checklist	research_architect
references/systematic_review_toolkit.md	Cochrane v6.4, PRISMA 2020, RoB 2, ROBINS-I, I² guide, GRADE, protocol registration	risk_of_bias, meta_analysis, bibliography, report_compiler
references/literature_monitoring_strategies.md	Google Scholar alerts, PubMed alerts, RSS feeds, Retraction Watch, citation tracking, monitoring cadence	monitoring_agent
references/argumentation_reasoning_framework.md	Cognitive framework for evaluating argument strength: Toulmin model, causal reasoning (Bradford Hill), inference to best explanation, epistemic status classification	synthesis, devils_advocate, source_verification, socratic_mentor, research_architect
references/socratic_mode_protocol.md	Full 5-layer Socratic dialogue flow, management rules, auto-end conditions	socratic_mentor, research_question
references/systematic_review_protocol.md	Full PRISMA pipeline, checkpoint rules, meta-analysis procedures	risk_of_bias, meta_analysis, bibliography, report_compiler
references/cross_agent_quality_definitions.md	Peer-reviewed source tiers, currency standards, severity definitions	all agents
references/changelog.md	Full version history	—

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Templates

Template	Purpose
templates/research_brief_template.md	Quick mode output format
templates/literature_matrix_template.md	Source x Theme analysis matrix
templates/evidence_assessment_template.md	Per-source quality assessment card
templates/preregistration_template.md	OSF standard 21-item preregistration template
templates/prisma_protocol_template.md	PRISMA-P 2015 systematic review protocol template
templates/prisma_report_template.md	PRISMA 2020 systematic review report template (27 items)

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Examples

Example	Demonstrates
examples/exploratory_research.md	Full 6-phase pipeline walkthrough
examples/systematic_review.md	PRISMA-style literature review
examples/policy_analysis.md	Applied comparative policy research
examples/socratic_guided_research.md	Complete Socratic mode multi-turn dialogue (12 rounds)
examples/handoff_to_paper.md	deep-research full mode handoff to academic-paper
examples/review_mode.md	Review mode: 3-agent review pipeline for policy recommendation text
examples/fact_check_mode.md	Fact-check mode: source verification of HEI claims with per-claim verdicts
examples/idea_diversity_coverage_gap_advisory.md	#257 Socratic wording-pattern + lit-review distributional-skew advisories

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Output Language

Follows the user's language. Academic terminology kept in English. Socratic mode uses natural conversational style.

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Anti-Patterns

Explicit prohibitions to prevent common failure modes:

#	Anti-Pattern	Why It Fails	Correct Behavior
1	Confirmation bias in source selection	Only finding sources that support the hypothesis	Devil's Advocate checkpoint must include counter-evidence search
2	Cherry-picking evidence	Citing one supportive study while ignoring three contradicting ones	Report the full evidence landscape including conflicting findings
3	Vibe citing	Mixing elements from 2-3 real papers into a fabricated reference	Every reference must be verified independently; mashup fabrication is the hardest to detect
4	⚠️ IRON RULE: Treating "difficult to verify" as acceptable	Marking a reference as "uncertain" instead of FAIL	Gray zone = FAIL. If you cannot confirm it exists, it does not go in the report
5	Skipping phases	Jumping to synthesis before completing source verification	Complete each phase fully; Phase N output is Phase N+1 input
6	Shallow Socratic mode	Giving answers disguised as questions ("Wouldn't you say X is true?")	Ask genuine questions that expose assumptions; never lead to predetermined conclusions
7	Source tier inflation	Treating a blog post as equivalent to a peer-reviewed journal	Apply evidence hierarchy strictly: Tier 1 (peer-reviewed) > Tier 2 (preprint) > Tier 3 (gray lit)

Quality Standards

1. ⚠️ IRON RULE: Every claim must have a citation — no unsupported assertions
2. 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)
3. Contradiction disclosure — if sources disagree, report both sides with evidence quality comparison
4. Limitation transparency — every report must have an explicit limitations section
5. AI disclosure — all reports include a statement that AI-assisted research tools were used
6. Reproducibility — search strategies, inclusion criteria, and analytical methods must be documented for replication
7. Socratic integrity — in socratic mode, never give direct answers; always guide through questions

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.

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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

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Version Info

Item	Content
Skill Version	2.9.4
Last Updated	2026-05-18
Maintainer	Cheng-I Wu
Dependent Skills	academic-paper v1.0+ (downstream)

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Version History

See references/changelog.md for full version history.