Skill: andyrenxu7255/ars-deep-research (version 2.9.6)

--- name: deep-research description: "Universal deep research with 13-agent pipeline on Hermes Agent. 7 modes: full research, quick brief, paper review, lit-review, fact-check, Socratic guided research dialogue, systematic review with meta-analysis. Uses delegate_task for each agent. Triggers on: research, deep research, literature review, systematic review, meta-analysis, PRISMA, evidence synthesis, fact-check, guide my research, help me think through, 研究, 深度研究, 文獻回顧, 系統性回顧, 後設分析, 事實查核, 引導我的研究, 幫我釐清." metadata: version: "2.9.3-hermes-1.0" last_updated: "2026-05-16" status: active adapted_from: "imbad0202/academic-research-skills v2.9.3" adapted_for: "Hermes Agent (deepseek-v4-pro)" task_type: open-ended license: "CC BY-NC 4.0" original_author: "Cheng-I Wu" original_license: "CC BY-NC 4.0" original_repo: "https://github.com/Imbad0202/academic-research-skills" copyright: "Copyright (c) 2026 Cheng-I Wu" --- # Deep Research — Universal Academic Research (Hermes Edition) 📄 **License:** [CC BY-NC 4.0](https://creativecommons.org/licenses/by-nc/4.0/) · Copyright (c) 2026 Cheng-I Wu 🔗 **Original:** [Imbad0202/academic-research-skills](https://github.com/Imbad0202/academic-research-skills) v2.9.3 🔄 **Adaptation:** Multi-agent pipeline implemented via `delegate_task` instead of Claude Code's internal agent system. All agent definitions, references, templates, and quality standards preserved unchanged from original. **This adaptation is distributed under the same CC BY-NC 4.0 license.** **Model**: Uses `deepseek-v4-pro` (1M context / 384K max_tokens) for all agent tasks. ## Quick Start ``` Research the impact of AI on higher education quality assurance ``` **Execution** (Hermes orchestrator + delegate_task): 1. Scoping — delegate_task(research_question_agent + research_architect_agent) 2. Investigation — delegate_task(bibliography_agent + source_verification_agent) 3. Analysis — delegate_task(synthesis_agent + devils_advocate_agent) 4. Composition — delegate_task(report_compiler_agent) 5. Review — delegate_task(editor_in_chief + ethics_review + devils_advocate) 6. Revision — delegate_task(report_compiler_agent) --- ## Hermes-Specific Execution Model **Core pattern**: The main Hermes agent is the ORCHESTRATOR. Each research phase spawns subagents via `delegate_task`. The orchestrator manages: - Phase sequencing and checkpoint gating - Context handoff between phases - Quality enforcement (failure = halt and get user input) - Mode selection (full/quick/socratic/etc.) **Agent files** at `agents/` contain specialized prompts loaded as `context` in `delegate_task`. **Reference files** at `references/` provide domain knowledge injected as-needed. --- ## Phase 1: SCOPING ### Step 1.1: Research Question ```python delegate_task( goal="Transform the research topic '[USER_TOPIC]' into a precise, FINER-scored research question with scope boundaries. Output: RQ Brief with 2-3 sub-questions.", context="Use the agent definition at agents/research_question_agent.md for the full methodology. Apply FINER criteria (Feasible, Interesting, Novel, Ethical, Relevant).", toolsets=["file", "web"] ) ``` ### Step 1.2: Methodology Blueprint ```python delegate_task( goal="Design a methodology blueprint for the research question: [RQ_FROM_STEP_1]. Include: research paradigm, method selection, data strategy, analytical framework, validity criteria.", context="Use agent definition at agents/research_architect_agent.md. Reference: references/methodology_patterns.md.", toolsets=["file", "web"] ) ``` ### Checkpoint 1 — Devil's Advocate ```python delegate_task( goal="Review the Research Question Brief and Methodology Blueprint. Test for: RQ clarity, method appropriateness, scope validity. Output verdict: PASS or REVISE with specific feedback.", context="You are the Devil's Advocate. Use agent definition at agents/devils_advocate_agent.md. Reference: references/logical_fallacies.md, references/cross_agent_quality_definitions.md.", toolsets=["file"] ) ``` ⚠️ **CRITICAL issues → HALT. Require user correction.** User must confirm before Phase 2. --- ## Phase 2: INVESTIGATION ### Step 2.1: Literature Search ```python delegate_task( goal="Conduct a systematic literature search for [RQ]. Output: search strategy, inclusion/exclusion criteria, PRISMA-style flow, annotated bibliography in APA 7.0.", context="Use agent definition at agents/bibliography_agent.md. Reference: references/apa7_style_guide.md, references/source_quality_hierarchy.md.", toolsets=["file", "web"] ) ``` ### Step 2.2: Source Verification ```python delegate_task( goal="Verify and grade all sources from the bibliography. Apply evidence hierarchy grading (Level I-VII), predatory journal screening, conflict-of-interest flagging. Output: Verified & Graded Sources + Source Quality Matrix.", context="Use agent definition at agents/source_verification_agent.md. Reference: references/source_quality_hierarchy.md, references/cross_agent_quality_definitions.md.", toolsets=["file", "web"] ) ``` --- ## Phase 3: ANALYSIS ### Step 3.1: Cross-Source Synthesis ```python delegate_task( goal="Synthesize findings across all verified sources. Identify themes, contradictions, knowledge gaps. Output: Synthesis Narrative + Gap Analysis with evidence convergence/divergence mapping.", context="Use agent definition at agents/synthesis_agent.md. Reference: references/argumentation_reasoning_framework.md, references/interdisciplinary_bridges.md.", toolsets=["file"] ) ``` ### Checkpoint 2 — Devil's Advocate ```python delegate_task( goal="Review the synthesis. Check for cherry-picking, confirmation bias, logic chain validity, alternative explanations. Output verdict: PASS or REVISE.", context="Use agent definition at agents/devils_advocate_agent.md. Reference: references/logical_fallacies.md.", toolsets=["file"] ) ``` --- ## Phase 4: COMPOSITION ```python delegate_task( goal="Compile a full APA 7.0 research report from all prior materials. Structure: Title → Abstract → Intro → Lit Review → Methodology → Findings → Discussion → Conclusion → References. Word count: 3,000-8,000.", context="Use agent definition at agents/report_compiler_agent.md. Reference: references/apa7_style_guide.md. Include all prior phase outputs as context.", toolsets=["file"] ) ``` --- ## Phase 5: REVIEW (3 agents in parallel) ```python # Run all three simultaneously delegate_task(tasks=[ { "goal": "Editorial review: assess originality, rigor, evidence sufficiency, argument coherence, writing quality. Verdict: ACCEPT/MINOR/MAJOR/REJECT with line feedback.", "context": "Use agent definition at agents/editor_in_chief_agent.md. Reference: references/apa7_style_guide.md.", "toolsets": ["file"] }, { "goal": "Ethics review: AI disclosure compliance, attribution integrity, dual-use screening, fair representation. Verdict: CLEARED/CONDITIONAL/BLOCKED.", "context": "Use agent definition at agents/ethics_review_agent.md. Reference: references/ethics_checklist.md, references/irb_decision_tree.md.", "toolsets": ["file"] }, { "goal": "Final vulnerability scan: strongest counter-argument test, significance check, alternative explanations. Verdict: PASS/REVISE.", "context": "Use agent definition at agents/devils_advocate_agent.md. Reference: references/logical_fallacies.md.", "toolsets": ["file"] } ]) ``` --- ## Phase 6: REVISION ```python delegate_task( goal="Revise the full report addressing all Phase 5 feedback. Incorporate editorial, ethics, and devil's advocate insights. Max 2 revision loops. Remaining issues → Acknowledged Limitations section.", context="Use agent definition at agents/report_compiler_agent.md. Include all Phase 5 review outputs and the current draft.", toolsets=["file"] ) ``` --- ## Mode Selection Before starting, determine the mode based on user intent: | Mode | Phases Active | Output | Word Count | |------|---------------|--------|------------| | `full` (default) | All 6 phases | Full APA 7.0 report | 3,000-8,000 | | `quick` | Phase 1(RQ) + 2(Biblio+Verification) + 4(Report) | Research brief | 500-1,500 | | `review` | Phase 5 only | Reviewer report on provided text | N/A | | `lit-review` | Phase 2 + 3 | Annotated bibliography + synthesis | 1,500-4,000 | | `fact-check` | Phase 2.2 only | Verification report | 300-800 | | `socratic` | Socratic Mentor (see below) | Research Plan Summary | N/A | | `systematic-review` | All phases + RoB + Meta-Analysis | PRISMA 2020 report | 5,000-15,000 | **Mode Selection Logic**: - User has clear RQ and needs full report → `full` - User has vague idea, needs guidance → `socratic` - User has paper to evaluate → `review` - User needs quick summary → `quick` - User only needs literature → `lit-review` - User needs to verify claims → `fact-check` - PRISMA-compliant review needed → `systematic-review` When ambiguous between `socratic` and `full`, prefer `socratic`. --- ## Socratic Mode 5-layer dialogue guiding users from vague ideas to concrete research questions. Core principle: ⚠️ **Never give direct answers.** Guide through questions. ### Agent (single delegate_task per layer): ```python delegate_task( goal="Layer [N] Socratic dialogue for research topic: [USER_TOPIC]. Previous layers: [LAYER_OUTPUTS]. Ask questions that probe [LAYER_FOCUS]. Never give answers.", context="Use agent definition at agents/socratic_mentor_agent.md. Reference: references/socratic_mode_protocol.md, references/socratic_questioning_framework.md.", toolsets=["file"] ) ``` **Layers**: Clarification → Assumption Probing → Evidence/Reasoning → Viewpoint/Perspective → Implication/Consequence Auto-end after 10 rounds without convergence → suggest switching to `full` mode. --- ## Systematic Review Mode PRISMA 2020-compliant. Adds two extra agents: ```python # After Phase 2 bibliography: delegate_task(goal="Assess risk of bias using RoB 2 (RCTs) and ROBINS-I (non-randomized). Traffic-light visualization.", context="Use agent definition at agents/risk_of_bias_agent.md. Reference: references/systematic_review_toolkit.md.", toolsets=["file"]) # After Phase 3 synthesis: delegate_task(goal="Design and execute meta-analysis or narrative synthesis. Effect sizes, heterogeneity (I²), GRADE assessment.", context="Use agent definition at agents/meta_analysis_agent.md. Reference: references/systematic_review_toolkit.md.", toolsets=["file"]) ``` --- ## Critical Rules (IRON RULES) 1. ⚠️ **Every claim must have a citation** — no unsupported assertions 2. ⚠️ **Gray zone = FAIL** — if you cannot confirm a reference exists, it does not go in the report 3. ⚠️ **Devil's Advocate CRITICAL → HALT** — explain the issue, require user correction 4. ⚠️ **Ethics BLOCKED → HALT** — list issues and remediation path 5. ⚠️ **Max 2 revision loops** — remaining issues become Acknowledged Limitations 6. ⚠️ **User confirmation after Phase 1** — do not auto-continue 7. **Vibe citing = forbidden** — every reference must be independently verifiable 8. **No phase skipping** — complete each phase fully before moving to next --- ## Orchestrator Checklist Before starting each phase, the orchestrator (main Hermes agent) MUST: 1. Verify the previous phase checkpoint passed 2. Load the relevant agent file via `read_file` 3. Pass all prior outputs as context to `delegate_task` 4. Review subagent output before proceeding 5. Respect HALT conditions (ask user, don't auto-fix) --- ## Failure Paths | Scenario | Recovery | |----------|----------| | RQ cannot converge | Provide 3 candidate RQs, suggest lit-review | | Insufficient literature (<5 sources) | Expand search strategy, suggest alternative keywords | | Devil's Advocate CRITICAL | HALT, explain, require correction | | Ethics BLOCKED | HALT, list issues | | Socratic non-convergence (>10 rounds) | Suggest switching to full mode | --- ## Agent File References | Agent | 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 | All agent files are the original v2.9.3 definitions with unchanged methodology. They are loaded as `context` in `delegate_task` calls. --- ## Output Language Follow user's language. Academic terminology kept in English. --- ## Anti-Patterns | # | Anti-Pattern | Correct Behavior | |---|-------------|-----------------| | 1 | Confirmation bias in source selection | Devil's Advocate checkpoint must include counter-evidence search | | 2 | Cherry-picking evidence | Report full evidence landscape including conflicting findings | | 3 | Vibe citing (mixing elements from 2-3 real papers into fake reference) | Every reference must be verified independently | | 4 | ⚠️ Treating "difficult to verify" as acceptable | Gray zone = FAIL | | 5 | Skipping phases | Complete each phase fully | | 6 | Shallow Socratic mode | Ask genuine questions, never lead to predetermined conclusions | | 7 | Source tier inflation | Apply evidence hierarchy strictly | --- ## Handoff to academic-paper After research complete, these materials can be handed off: 1. Research Question Brief 2. Methodology Blueprint 3. Annotated Bibliography 4. Synthesis Report 5. [If socratic] INSIGHT Collection and Research Plan Summary User says "now help me write a paper" → switch to `academic-paper` skill. ## Security & Privacy **Multi-agent design disclosure:** This skill delegates research tasks across multiple subagents via `delegate_task`. Research content and intermediate outputs are processed by these agents. Use only with research topics you are comfortable processing through the AI provider's delegated-agent workflow. **Tool access:** Subagents are granted `file` tools (for writing output) and `web` tools (for literature search only). No terminal or system tools are exposed during review/composition phases. **Agent files:** The `agents/` directory contains academic research prompt templates (role definitions, methodology guidelines, quality rubrics). These are task instructions loaded as `context` in `delegate_task` calls — NOT system prompt overrides. Frontmatter in agent files (e.g., `name:`, `description:`) is metadata only.


Security scan verdicts — ClawScan: suspicious | static analysis: clean | VirusTotal: clean | SkillSpector: suspicious (CRITICAL)