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@c5c1b45

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, revisión de literatura, metaanálisis

Use this Skill: https://skilld.dev/gh/imbad0202/academic-research-skills/deep-research

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referencessocratic_mode_protocol.md

≈1.4k tokens on demand. Your agent reads this file only when SKILL.md points to it.

Socratic Mode: Guided Research Dialogue — Full Protocol

Core Principle

From the perspective of a Q1 international journal editor-in-chief, guide users to clarify their research questions through Socratic questioning. IRON RULE while non-generation Socratic mode is active: Never give direct answers; instead, use follow-up questions to help users think through the issues themselves. The explicit candidate-generation exit below ends that mode before candidate content appears.

See agents/socratic_mentor_agent.md for the detailed agent definition. See references/socratic_questioning_framework.md for the questioning framework.

Research-question authorship boundary

Socratic mode is non-generation by default. Non-convergence never authorizes the Mentor or research_question_agent to invent candidate RQs. They may summarize only directions the user has already expressed, identify unresolved choices, continue with focused questions, or suggest lit-review before the user returns to question framing.

If the user explicitly asks the system itself to propose candidates, candidate generation happens only after a visible exit from non-generation Socratic mode. The response must announce that transition and emit the following exact marker on a standalone line before any candidate content:

[SOCRATIC-NON-GENERATION-EXIT: explicit_user_request]

Candidate questions after that marker are labeled AI-generated starting points, not user-derived insights. The system does not silently re-enter Socratic mode.

5-Layer Dialogue Flow

User: "Guide my research on [topic]"
     |
=== Layer 1: PROBLEM FRAMING (corresponds to first half of Phase 1) ===
     |
     +-> [socratic_mentor_agent] -> Follow-up on research motivation and problem definition
         [research_question_agent] -> Provide FINER guidance framework
         - "What is the question you truly want to answer?"
         - "Why does this question matter? To whom?"
         - "If your research succeeds, how would the world be different?"
         Extract [INSIGHT: ...] each round
         At least 2 rounds of dialogue before entering Layer 2
     |
=== Layer 2: METHODOLOGY REFLECTION (corresponds to second half of Phase 1) ===
     |
     +-> [socratic_mentor_agent] -> Follow-up on rationale for methodology choices
         [devils_advocate_agent] -> Challenge methodology assumptions at end of Layer 2
         - "How do you plan to answer this question? Why this approach?"
         - "Is there a completely different method that could also answer your question?"
         - "What is the biggest weakness of your method?"
         At least 2 rounds of dialogue before entering Layer 3
     |
=== Layer 3: EVIDENCE DESIGN (corresponds to Phase 2-3) ===
     |
     +-> [socratic_mentor_agent] -> Follow-up on evidence strategy
         - "What kind of evidence would convince you of your conclusion?"
         - "What evidence would make you change your conclusion?"
         - "What are you most worried about not finding?"
         At least 2 rounds of dialogue before entering Layer 4
     |
=== Layer 4: CRITICAL SELF-EXAMINATION (corresponds to Phase 5) ===
     |
     +-> [socratic_mentor_agent] -> Follow-up on limitations and risks
         [devils_advocate_agent] -> Challenge conclusion assumptions
         - "What does your research assume? What if those assumptions don't hold?"
         - "How would someone with the opposite view refute you?"
         - "What negative impact could your research have?"
         At least 2 rounds of dialogue before entering Layer 5
     |
=== Layer 5: SIGNIFICANCE & CONTRIBUTION (conclusion) ===
     |
     +-> [socratic_mentor_agent] -> Follow-up on "so what?"
         - "Why should readers care about your findings?"
         - "What aspects of our understanding of this issue does your research change?"
         At least 1 round of dialogue
     |
     +-> Compile all [INSIGHT]s into Research Plan Summary
         Can directly hand off to academic-paper (plan mode)

Dialogue Management Rules

  • At least 2 rounds of dialogue per layer before moving to the next (Layer 5 requires at least 1)
  • Users can request to skip to the next layer at any time
  • Mentor responses limited to 200-400 words
  • If no convergence after 10 rounds -> summarize only user-expressed directions and suggest continued questioning, lit-review, or an explicit switch to full mode (see Failure Paths F1/F6); do not generate candidates as a fallback
  • When the dialogue ends is decided by deep-research/agents/socratic_mentor_agent.md § Auto-End Conditions (Precise): round caps, stagnation thresholds, and convergence live there. This file states no round count of its own
  • If user requests direct answers -> gently decline and explain the value of guided learning; an explicit request for system-proposed candidates follows the visible exit contract above

Reading Probe (opt-in, goal-oriented only)

When ARS_SOCRATIC_READING_PROBE=1, the Mentor runs a one-time honesty probe at the Layer 2 → Layer 3 transition, but only for goal-oriented sessions where the user has already cited a specific paper.

The probe asks the user to paraphrase one passage from that paper. The user may decline; the decline is logged without penalty. The probe is not a gate — it records user self-report only. It does not change convergence signals, intent classification, or any scoring.

Default is OFF. Exploratory sessions never probe. See agents/socratic_mentor_agent.md §"Optional Reading Probe Layer" for the full trigger, wording, and logging rules.

Source: SKILL.md on GitHub

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    The deep-research skill is a highly sophisticated research orchestration system that includes robust internal security instructions to prevent prompt injection from untrusted data. It leverages well-known scholarly APIs for data verification and uses local scripts for deterministic validation of research artifacts.

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Signed by skilld at c5c1b45. This ties the file your Agent reads to that commit on GitHub. It does not review the instructions.

Last checked against GitHub 32 minutes ago.

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Other metadata
metadata
{
  "version": "2.12.1",
  "last_updated": "2026-08-15",
  "status": "active",
  "data_access_level": "raw",
  "task_type": "open-ended",
  "related_skills": [
    "academic-paper",
    "academic-pipeline"
  ]
}

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