USP
Unlike fully autonomous AI research systems, ARS emphasizes a human-in-the-loop approach, integrating mandatory integrity gates and verification steps to mitigate common AI failure modes like hallucinations and fabricated results. It focus…
Use cases
- 01Conducting systematic literature reviews
- 02Drafting academic papers with style calibration
- 03Simulating multi-perspective peer reviews
- 04Verifying academic integrity of research outputs
- 05Orchestrating the full research-to-publication pipeline
Detected files (5)
academic-paper/SKILL.mdskillShow content (32779 bytes)
--- name: academic-paper description: "12-agent academic paper writing pipeline. 10 modes (full/plan/outline/revision/revision-coach/abstract/lit-review/format-convert/citation-check/disclosure). 6 paper types, 5 citation formats, bilingual abstracts, LaTeX/DOCX-via-Pandoc/PDF output. Style Calibration + Writing Quality Check + Anti-Patterns with IRON RULE markers. Triggers: write paper, academic paper, guide my paper, parse reviews, AI disclosure, 寫論文, 學術論文, 引導我寫論文, 審查意見." metadata: version: "3.1.1" last_updated: "2026-04-27" status: active data_access_level: redacted task_type: open-ended related_skills: - deep-research - academic-paper-reviewer - academic-pipeline --- # Academic Paper — Academic Paper Writing Agent Team A general-purpose academic paper writing tool — 12-agent pipeline covering all disciplines, with higher education domain as the default reference. **v2.5** adds two writing quality features: - **Style Calibration** (intake Step 10, optional) — Provide 3+ past papers and the pipeline learns your writing voice (sentence rhythm, vocabulary preferences, citation integration style). Applied as a soft guide during drafting; discipline conventions always take priority. See `shared/style_calibration_protocol.md`. - **Writing Quality Check** (`references/writing_quality_check.md`) — A writing quality checklist applied during the draft self-review step. Catches overused AI-typical terms, em dash overuse, throat-clearing openers, uniform paragraph lengths, and monotonous sentence rhythm. These are good writing rules, not detection evasion. ## Quick Start **Minimal command:** ``` Write a paper on the impact of AI on higher education quality assurance ``` ``` Write a paper on the impact of declining birth rates on private university management strategies ``` **Execution flow:** 1. Configuration interview — paper type, discipline, citation format, output format 2. Literature search — systematic search strategy, source screening 3. Architecture design — paper structure, outline, word count allocation 4. Argumentation construction — claim-evidence chains, logical flow 5. Full-text drafting — section-by-section draft, register adjustment 6. Citation compliance + bilingual abstract (parallel) 7. Peer review — five-dimension scoring, revision suggestions 8. Output formatting — LaTeX/DOCX (via Pandoc)/PDF/Markdown --- ## Trigger Conditions ### Trigger Keywords **English**: write paper, academic paper, paper outline, write abstract, revise paper, literature review paper, check citations, convert to LaTeX, convert format, format paper, conference paper, journal article, thesis chapter, research paper, guide my paper, help me plan my paper, step by step paper, draft manuscript, write methodology, write discussion, parse reviews, revision roadmap, help me with my revision, I got reviewer comments, convert citations **繁體中文**: 寫論文, 學術論文, 論文大綱, 寫摘要, 修改論文, 文獻回顧論文, 檢查引用, 轉 LaTeX, 轉換格式, 研討會論文, 期刊文章, 學位論文, 研究論文, 引導我寫論文, 幫我規劃論文, 逐步寫論文, 寫方法論, 寫討論, 審查意見, 修訂路線圖, 幫我修改, 我收到審查意見, 轉換引用格式 ### Plan Mode Activation Activate `plan` mode when the user wants guidance, step-by-step planning, or expresses uncertainty about paper structure. **Default rule**: when ambiguous between `plan` and `full`, prefer `plan`. > See `references/plan_mode_protocol.md` for full intent signals and activation rules. ### Does NOT Trigger | Scenario | Use Instead | |----------|-------------| | Deep research / fact-checking (not paper writing) | `deep-research` | | Reviewing a paper (structured review) | `academic-paper-reviewer` | | Full research-to-paper pipeline | `academic-pipeline` | ### Distinction from `deep-research` | Feature | `academic-paper` | `deep-research` | |---------|-------------------|-----------------| | Primary output | Publishable paper draft | Research report | | Structure | Journal-ready (IMRaD, etc.) | APA 7.0 report | | Citation | Multi-format (APA/Chicago/MLA/IEEE/Vancouver) | APA 7.0 only | | Abstract | Bilingual (zh-TW + EN) | Single language | | Peer review | Simulated 5-dimension review | Editorial review | | Output format | LaTeX/DOCX (via Pandoc)/PDF/Markdown | Markdown only | | Revision loop | Max 2 rounds with targeted feedback | Max 2 rounds | --- ## Agent Team (12 Agents) | # | Agent | Role | Phase | |---|-------|------|-------| | 1 | `intake_agent` | Configuration interview: paper type, discipline, journal, citation format, output format, language, word count; Handoff detection; Plan mode simplified interview | Phase 0 | | 2 | `literature_strategist_agent` | Search strategy design, source screening, annotated bibliography, literature matrix | Phase 1 | | 3 | `structure_architect_agent` | Paper structure selection, detailed outline, word count allocation, evidence mapping | Phase 2 | | 4 | `argument_builder_agent` | Argument construction, claim-evidence chains, logical flow, counter-argument handling; Plan mode argument stress test | Phase 3 / Plan Step 3 | | 5 | `draft_writer_agent` | Section-by-section full draft writing, discipline register adjustment, word count tracking | Phase 4 | | 6 | `citation_compliance_agent` | Citation format verification, reference list completeness, DOI checking | Phase 5a | | 7 | `abstract_bilingual_agent` | Bilingual abstract (zh-TW + EN), 5-7 keywords each | Phase 5b | | 8 | `peer_reviewer_agent` | Simulated double-blind review, five-dimension scoring, revision suggestions (max 2 rounds) | Phase 6 | | 9 | `formatter_agent` | Convert to LaTeX/DOCX (via Pandoc)/PDF/Markdown, journal formatting, cover letter, citation format conversion (APA 7 / Chicago / MLA / IEEE / Vancouver) | Phase 7 | | 10 | `socratic_mentor_agent` | Plan mode Socratic mentor: chapter-by-chapter guidance, convergence criteria (4 signals), question taxonomy (4 types), INSIGHT extraction | Plan Step 0-3 | | 11 | `visualization_agent` | Parse paper data and generate publication-quality figure code (Python matplotlib / R ggplot2) with APA 7.0 formatting, colorblind-safe palettes, and LaTeX integration | Phase 4 / Phase 7 | | 12 | `revision_coach_agent` | Parse unstructured reviewer comments into structured Revision Roadmap; classify, map, and prioritize comments; works standalone without prior pipeline execution | Revision-Coach mode | --- ## Output Formats ### Text Formats LaTeX (.tex + .bib), DOCX (via Pandoc), PDF (via LaTeX or Pandoc), Markdown. ### Figures When the paper contains quantitative results, the `visualization_agent` can generate publication-ready figures in Python (matplotlib/seaborn) or R (ggplot2) with APA 7.0 formatting and colorblind-safe palettes. Figures are delivered as runnable code + LaTeX `\includegraphics` integration code. See `references/statistical_visualization_standards.md` for chart type decision trees and code templates. ### Citation Formats APA 7.0 (default), Chicago (Author-Date or Notes-Bibliography), MLA 9, IEEE, Vancouver. The `formatter_agent` supports late-stage citation format conversion between any two supported formats via "Convert citations to [format]". --- ## Orchestration Workflow (8 Phases) ``` Phase 0: CONFIG -> [intake_agent] -> Paper Configuration Record Phase 1: RESEARCH -> [literature_strategist] -> Search Strategy + Source Corpus Phase 2: ARCHITECTURE -> [structure_architect] -> Paper Outline + Evidence Map Phase 3: ARGUMENTATION -> [argument_builder] -> Argument Blueprint Phase 4: DRAFTING -> [draft_writer] -> Complete Draft Phase 5a: CITATIONS -> [citation_compliance] ──┐ -> Citation Audit Report Phase 5b: ABSTRACT -> [abstract_bilingual] ─┘ -> Bilingual Abstract + Keywords (parallel) Phase 6: PEER REVIEW -> [peer_reviewer] -> Review Report (max 2 revision loops) Phase 7: FORMAT -> [formatter] -> Final Output Package ``` > See `references/workflow_phase_details.md` for detailed per-phase agent behavior and output descriptions. ### Checkpoint Rules 1. ⚠️ **IRON RULE**: User must confirm Paper Configuration Record before proceeding to Phase 1 2. **Phase 2 -> 3**: User must approve outline (can request restructuring) 3. ⚠️ **IRON RULE**: Max 2 revision loops; unresolved items -> "Acknowledged Limitations" 4. **Peer Review** Critical-severity issues block progression to Phase 7 5. User can skip Phase 1 (literature) if providing own sources --- > **v3.4.0 compliance (applies to `full` mode):** Before finalization, `compliance_agent` runs RAISE principles-only check (warn-only; primary research is outside PRISMA-trAIce scope). Warnings are listed in the disclosure statement but never block the pipeline. See `shared/raise_framework.md §Scope disclaimer`. ## v3.6.6 Generator-Evaluator Contract Protocol > Authoritative orchestration block for the v3.6.6 contract-gated phase splits inside `academic-paper full` mode. Schema 13.1 since v3.6.6 (`shared/sprint_contract.schema.json`). Templates: `shared/contracts/writer/full.json` + `shared/contracts/evaluator/full.json`. Design spec: `docs/design/2026-04-27-ars-v3.6.6-generator-evaluator-contract-design.md` §5. > > **Applies to `academic-paper full` mode only.** Nine non-full modes (`plan`, `outline-only`, `revision`, `revision-coach`, `abstract-only`, `lit-review`, `format-convert`, `citation-check`, `disclosure`) are byte-equivalent across v3.6.5 → v3.6.6 and do not invoke this protocol. Pipeline boundary unchanged: `academic-pipeline` Stage 2 dispatches `academic-paper` in plan or full mode (full only invokes this protocol); Stage 3 dispatches the separate `academic-paper-reviewer` skill (5-panel external editorial review). The in-pair Phase 6 evaluator under this protocol and the Stage 3 reviewer are different review layers — see design doc §5.1 audit conclusion 2. ### Overview v3.6.6 splits Phase 4 (writer drafting) and Phase 6 (in-pair evaluator review) into paper-blind / paper-visible call pairs gated by the `writer_full` and `evaluator_full` contracts. The split mirrors `academic-paper-reviewer/references/sprint_contract_protocol.md` (the v3.6.2 reviewer pattern) but adapts it for single-agent generator modes that have no panel and (for the writer) no scoring_plan. The load-bearing mechanism is the **physical separation of calls**: writer Phase 4a never sees the runtime drafting artefacts; evaluator Phase 6a never sees the writer Phase 4b draft. This destroys the "read the paper, then rationalise the standard" drift path on the in-pair self-quality gate. ### Four-call structure For each `academic-paper full` invocation, Phase 4 + Phase 6 expand from two single calls into four separate model calls. Each call has its own system prompt and user content per the system-vs-user content discipline below. 1. **Phase 4a — writer paper-blind pre-commitment.** - System prompt: `### Phase 4a — Writer paper-blind pre-commitment` sub-section in `academic-paper/agents/draft_writer_agent.md` § "v3.6.6 Generator-Evaluator Contract Protocol". - User content: `writer_full` contract JSON + paper metadata only (`title`, `field`, `word_count`). - Output: `## Acceptance Criteria Paraphrase` section + terminal `[PRE-COMMITMENT-ACKNOWLEDGED]` tag. - Lint: 3 structural checks (see § "Phase 4a / 6a output lint" below). 2. **Phase 4b — writer paper-visible drafting + self-scoring.** - System prompt: `### Phase 4b — Writer paper-visible drafting + self-scoring` sub-section in the same agent file. - User content: `writer_full` contract JSON (re-injected) + Phase 4a output wrapped in `<phase4a_output>...</phase4a_output>` data delimiter + upstream drafting artefacts (Paper Configuration Record, Paper Outline, Argument Blueprint, Annotated Bibliography, optional Style Profile, optional Knowledge Isolation Directive). - Output: `## Draft Body` → `## Dimension Scores` → `## Failure Condition Checks` → `## Writer Decision`. - Lint: 4 structural checks (see § "Phase 4b / 6b output lint" below). 3. **Phase 6a — evaluator paper-blind pre-commitment.** - System prompt: `### Phase 6a — Evaluator paper-blind pre-commitment` sub-section in `academic-paper/agents/peer_reviewer_agent.md` § "v3.6.6 Generator-Evaluator Contract Protocol". - User content: `evaluator_full` contract JSON + paper metadata + the writer's most recent `<phase4a_output>` (the writer artefact the evaluator must verify per `disagreement_handling.pre_commitment_check_protocol.check_writer_artifact`). - Output: `## Contract Paraphrase` + `## Scoring Plan` (per-dimension `dimension_id` / `what_to_look_for` / `what_triggers_block` / `what_triggers_warn`) + terminal `[PRE-COMMITMENT-ACKNOWLEDGED]` tag. - Lint: 5 structural checks. 4. **Phase 6b — evaluator paper-visible scoring + decision.** - System prompt: `### Phase 6b — Evaluator paper-visible scoring + decision` sub-section in the same agent file. - User content: `evaluator_full` contract JSON (re-injected) + Phase 6a output wrapped in `<phase6a_output>...</phase6a_output>` + the writer's `<phase4a_output>` (unconditional per `pre_commitment_check_protocol.check_writer_artifact`) + the writer Phase 4b draft (the artefact under review). - Output: `## Dimension Scores` → `## Failure Condition Checks` → `## Review Body` → `## Evaluator Decision`. - Lint: 5 structural checks. ### System prompt vs user content discipline Mirrors `sprint_contract_protocol.md` §2 reviewer pattern verbatim: - **System prompt carries invariant policy text only**: the phase sub-section instructions from the agent file's `## v3.6.6 Generator-Evaluator Contract Protocol` block, the lint description, and the phase-boundary tag conventions. - **User content carries the contract JSON (re-injected per call) plus the runtime inputs allowed at that phase**: paper metadata, `<phase4a_output>` / `<phase6a_output>` delimiter blocks, upstream drafting artefacts, the paper draft. All dynamic LLM output (Phase Na runtime emissions, paper content) lives in user content via data delimiters, never in the system prompt. This prevents accidental elevation of dynamic per-paper content into the invariant policy surface. ### Schema field name vs runtime emission distinction `pre_commitment_artifacts` (snake_case, backticks) is the schema field name in `shared/sprint_contract.schema.json` — a configuration declaration in the frozen contract baseline. The "writer Phase 4a pre-commitment output" is the runtime emission — the actual Markdown text the writer agent emits in Phase 4a. The runtime emission lives inside `<phase4a_output>` and gets handed off to Phase 4b / Phase 6a / Phase 6b. Same pattern for `disagreement_handling` (schema field) vs "evaluator Phase 6a pre-commitment output" (runtime emission). Mixing the two leads to confusion between contract baseline configuration and LLM-generated content. ### Phase 4a / 6a output lint Mode-specific structural check counts, per `sprint_contract_protocol.md` §4 enumeration convention: - **Writer Phase 4a (3 checks)**: required sections in order (`## Acceptance Criteria Paraphrase`, terminal `[PRE-COMMITMENT-ACKNOWLEDGED]`); paraphrase paragraph count ≥ `pre_commitment_artifacts.acceptance_criteria_paraphrase.minimum_dimensions`; Phase 4a content references contract JSON + paper metadata only. **No `## Scoring Plan` section** — `writer_full` carries no scoring_plan. - **Evaluator Phase 6a (5 checks)**: required sections in order (`## Contract Paraphrase`, `## Scoring Plan`, terminal `[PRE-COMMITMENT-ACKNOWLEDGED]`); paraphrase paragraph count ≥ `disagreement_handling.paraphrase_minimum_dimensions`; one `### <Dn>: <name>` subsection per acceptance dimension; each scoring_plan subsection contains `disagreement_handling.scoring_plan.per_dimension_criteria` four-field shape (`dimension_id`, `what_to_look_for`, `what_triggers_block`, `what_triggers_warn`); Phase 6a content references contract JSON + paper metadata + the writer's `<phase4a_output>` only (no full draft / paper content). Retry semantics: lint failure on the first attempt → retry once with the specific lint gap hinted in the system prompt; second failure → mark this role unusable per § "Single-agent generator unusable handling" below. ### Phase 4b / 6b output lint - **Writer Phase 4b (4 checks)**: required sections in order — `## Draft Body`, `## Dimension Scores`, `## Failure Condition Checks`, `## Writer Decision`; Dimension Scores one-to-one across the seven writer dimensions D1–D7 (per `shared/contracts/writer/full.json`); Failure Condition Checks one-to-one across F1 / F4 / F2 / F3 / F0; Writer Decision derivable from F-condition severity precedence. **No multi-dissent retry** (writer has no scoring_plan to dissent against). **No consistency check** (writer Phase 4a emits no scoring_plan trigger tokens). - **Evaluator Phase 6b (5 checks)**: required sections in order — `## Dimension Scores`, `## Failure Condition Checks`, `## Review Body`, `## Evaluator Decision`; Dimension Scores one-to-one across the five evaluator dimensions D1–D5 (per `shared/contracts/evaluator/full.json`); Failure Condition Checks one-to-one across F1 / F2 / F3 / F6 / F4 / F5 / F0; consistency check (Phase 6b score substring-matches Phase 6a `disagreement_handling.scoring_plan.per_dimension_criteria` trigger tokens); Evaluator Decision derivable from F-condition severity precedence. **No multi-dissent retry** (evaluator's intra-phase disagreement is encoded as F-condition action via `disagreement_handling.disagreement_resolution`, not as a retry trigger). Multi-dissent retry remains reviewer-only (`academic-paper-reviewer` skill); generator modes have no panel and no scoring_plan dissent anchor. Lint count summary across the three modes: | Phase | Reviewer (zero-touch) | Writer | Evaluator | |---|---|---|---| | Phase 1 / 4a / 6a | 5 | 3 | 5 | | Phase 2 / 4b / 6b | 6 | 4 | 5 | ### Single-agent generator unusable handling When a writer or evaluator phase becomes unusable (Phase Na lint twice fail OR Phase Nb lint fail), `academic-paper` emits a phase-level abort tag and routes to user intervention: - **Writer Phase 4 unusable** → `[GENERATOR-PHASE-ABORTED: role=writer, contract=<id>, reason=<lint_failure_kind>]` → abort `academic-paper` Phase 4 → user intervention decides retry / fallback / regression to Phase 3 (Argument Blueprint). - **Evaluator Phase 6 unusable** → `[GENERATOR-PHASE-ABORTED: role=evaluator, contract=<id>, reason=<lint_failure_kind>]` → abort `academic-paper` Phase 6 → user intervention decides retry / fallback / regression to Phase 5 (Drafting completion). `[GENERATOR-PHASE-ABORTED]` does **not** constitute a valid Phase 6b emission and cannot enter Stage 3 reviewer dispatch. Two valid Stage 3 entry paths exist (per design doc §5.1): - **Standard path**: evaluator Phase 6b emits F0 `evaluator_decision=accept` or F4 `evaluator_decision=accept_with_dissent_note`. - **Exceptional path**: evaluator Phase 6b emits F5 `evaluator_decision=flag_for_reviewer_stage` after the in-pair revision loop exhausts at round 2 with mandatory-dimension block recurring. `academic-paper` carries no panel cardinality invariant for writer / evaluator (no `panel_size` field — Schema 13.1 §3.3.5 reviewer-conditional). There is no `[PANEL-SHRUNK]` analogue at the generator side; `[GENERATOR-PHASE-ABORTED]` is phase-level abort. **Operational monitor**: track `[GENERATOR-PHASE-ABORTED]` rate over the first three months of v3.6.6 deployment. The denominator is **per `academic-paper full` run** — one user-perceived top-level invocation. The 5% threshold is `(runs_with_any_abort) / (total_runs)`. If the rate exceeds 5%, v3.6.7 introduces graceful-degradation fallback (see § "Known limitations" below). ### Cross-session resume scope The v3.6.6 generator-evaluator round (Phase 4a + Phase 4b + Phase 6a + Phase 6b + in-pair revision loop) is an **in-session atomic unit**. Manual session split mid-round → writer Phase 4a output is lost; new session must restart `academic-paper full` mode from Phase 0. The v3.6.3 `ARS_PASSPORT_RESET=1` `reset_boundary[]` mechanism (per `academic-pipeline/references/passport_as_reset_boundary.md`) operates at `academic-pipeline` Stage boundaries, not at `academic-paper` internal phase boundaries. `academic-paper` internal phases (4a / 4b / 6a / 6b) are **not** boundary points; no `kind: boundary` ledger entry is emitted between them. v3.6.7+ may introduce `pre_commitment_history[]` to persist writer Phase 4a artefacts across sessions if operational data warrants — see § "Known limitations" below. ## Known limitations - **No graceful-degradation fallback in v3.6.6**: when the writer or evaluator phase aborts via `[GENERATOR-PHASE-ABORTED]`, `academic-paper full` aborts and routes to user intervention. v3.6.7 may introduce a fallback that degrades the affected phase to v3.6.5 single-call behaviour and logs the degradation. v3.6.6 ships with abort-only behaviour. See § "Single-agent generator unusable handling" above for the operational 5% / three-month monitor. - **No cross-session resume mid-round**: the four-phase generator-evaluator round is an in-session atomic unit. Manual session split mid-round loses the writer Phase 4a artefact and forces restart from Phase 0. v3.6.7+ may introduce a `pre_commitment_history[]` ledger entry in Schema 9 to persist the writer Phase 4a artefact across session boundaries; v3.6.6 does not implement. - **In-pair Phase 6 evaluator vs `academic-paper-reviewer` external review**: the in-pair `peer_reviewer_agent` (Phase 6 evaluator with the v3.6.6 contract gate) and the standalone `academic-paper-reviewer` skill (Stage 3 5-panel external editorial review) serve different review layers and remain documented as known technical debt per design doc §1 known limitations. Routing / merge decisions are deferred to v3.7.x. ## Operational Modes (10 Modes) See `references/mode_selection_guide.md` for details. | Mode | Trigger | Agents | Output | |------|---------|--------|--------| | `full` | "Write a paper" | All 9 (+ 11 if quantitative) | Complete paper draft (with figures if applicable) | | `outline-only` | "Paper outline" | 1->2->3 | Detailed outline + evidence map | | `revision` | "Revise paper" | 8->5->6 | Revised draft with tracked changes (uses `templates/revision_tracking_template.md`) | | `abstract-only` | "Write abstract" | 1->7 | Bilingual abstract + keywords | | `lit-review` | "Literature review" | 1->2 | Annotated bibliography + synthesis | | `format-convert` | "Convert to LaTeX" / "Convert citations to [format]" | 9 only | Formatted document; includes citation format conversion (APA 7 / Chicago / MLA / IEEE / Vancouver) | | `citation-check` | "Check citations" | 6 only | Citation error report | | `plan` | "guide my paper" / "help me plan my paper" | 1->10->3->4 | Chapter Plan + INSIGHT Collection | | `revision-coach` | "parse reviews" / "revision roadmap" / "I got reviewer comments" | 12 only | Revision Roadmap + optional Tracking Template + Response Letter Skeleton | | **`disclosure`** (v3.2) | **"AI disclosure for Nature" / "generate AI usage statement"** | **9 only** | **Venue-specific AI-usage disclosure paragraph(s) + placement instructions** | ### Quick Mode Selection Guide | Your Situation | Recommended Mode | Spectrum | |----------------|-----------------|----------| | Starting from scratch with a clear RQ | `full` | balanced | | Need help planning before writing | `plan` | originality | | Just need an outline | `outline-only` | balanced | | Have a draft, received review feedback | `revision` | fidelity | | Have unstructured reviewer comments | `revision-coach` | balanced | | Just need an abstract | `abstract-only` | fidelity | | Need to check/fix citations | `citation-check` | fidelity | | Need to convert format (LaTeX, DOCX) or citation style | `format-convert` | fidelity | | Want a systematic literature review paper | `lit-review` | fidelity | | Need a venue-specific AI-usage disclosure statement for submission | `disclosure` | 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 `plan` — it will guide you step by step. `disclosure` is a finishing step — run it after the paper is drafted, targeting the venue you plan to submit to. ### Mode Selection Logic > See `references/mode_selection_guide.md` for trigger-to-mode mappings and the full selection flowchart. --- ## Plan Mode: Chapter-by-Chapter Guided Planning Socratic mode that guides users through paper planning one chapter at a time. Builds a complete Paper Blueprint through structured dialogue. > See `references/plan_mode_protocol.md` for the full chapter-by-chapter dialogue flow and Paper Blueprint structure. --- ## Handoff Protocol: deep-research -> academic-paper `intake_agent` automatically detects deep-research materials (RQ Brief / Bibliography / Synthesis / INSIGHT Collection) and skips redundant steps. See `deep-research/SKILL.md` Handoff Protocol for the complete handoff material format. --- ## Failure Paths See `references/failure_paths.md` for details. Quick reference: | Failure Scenario | Handling Strategy | |---------|---------| | Insufficient research foundation | Recommend running `deep-research` first | | Wrong paper structure selected | Return to Phase 2, suggest alternative structure | | Word count significantly over/under target | Identify problematic chapters, suggest trimming/expansion | | Citation format entirely wrong | Re-run the entire citation phase | | Peer review rejection | Analyze rejection reasons, suggest major revision or restructuring | | Plan mode not converging | Suggest switching to outline-only mode | | Incomplete handoff materials | List missing items, suggest supplementing or re-running | | User abandons midway | Save completed Chapter Plan | --- ## Full Academic Pipeline See `academic-pipeline/SKILL.md` for the complete workflow. --- ## Phase 0: Configuration Interview See `agents/intake_agent.md` for the complete field definitions of the Phase 0 configuration interview. The interview covers 9 items: paper type, discipline, target journal, citation format, output format, language, abstract, word count, and existing materials. Outputs a Paper Configuration Record, awaiting user confirmation. --- ## File Structure **Agent definitions**: `agents/{agent_name}.md` — one file per agent (12 total, matching Agent Team table above). **References** (19 files in `references/`): - Citation: `apa7_extended_guide`, `apa7_chinese_citation_guide`, `citation_format_switcher` - Writing: `academic_writing_style`, `writing_quality_check`, `writing_judgment_framework` - Structure: `paper_structure_patterns` (6 types), `abstract_writing_guide` - Domain: `hei_domain_glossary` (bilingual), `journal_submission_guide`, `latex_template_reference` - Process: `failure_paths` (12 scenarios), `mode_selection_guide` (10 modes), `plan_mode_protocol`, `workflow_phase_details` - Ethics: `credit_authorship_guide` (CRediT 14 roles), `funding_statement_guide`, `statistical_visualization_standards` - Disclosure (v3.2): `disclosure_mode_protocol` (venue-specific AI-usage statement generation), `venue_disclosure_policies` (v1 database: ICLR, NeurIPS, Nature, Science, ACL, EMNLP) - Also: `deep-research/references/apa7_style_guide.md` (base reference, extended here) **Templates** (11 files in `templates/`): `imrad`, `literature_review`, `case_study`, `theoretical_paper`, `policy_brief`, `conference_paper`, `latex_article_template.tex`, `bilingual_abstract`, `credit_statement`, `funding_statement`, `revision_tracking` (4 status types). **Examples** (5 files in `examples/`): `imrad_hei_example`, `literature_review_example`, `plan_mode_guided_writing`, `chinese_paper_example`, `revision_mode_example`. --- ## Anti-Patterns Explicit prohibitions to prevent common failure modes: | # | Anti-Pattern | Why It Fails | Correct Behavior | |---|-------------|-------------|-----------------| | 1 | **AI-typical overused terms** | "delve into", "crucial", "it is important to note" = instant AI detection | Use discipline-specific vocabulary; see `references/writing_quality_check.md` | | 2 | **Em dash abuse** | More than 2 em dashes per page signals AI writing | Use parentheses, commas, or restructure the sentence | | 3 | **Throat-clearing openers** | "In this section, we will discuss..." adds no information | Start with the claim or finding directly | | 4 | **Uniform paragraph lengths** | Every paragraph is 4-5 sentences = monotonous AI rhythm | Vary paragraph length naturally (2-8 sentences) | | 5 | **⚠️ IRON RULE: Fabricated citations** | Inventing plausible-sounding references that don't exist | Every citation must be verified via DOI or WebSearch; see `academic-pipeline/agents/integrity_verification_agent.md` | | 6 | **Sycophantic revision** | Accepting all reviewer feedback without critical evaluation | Use REVIEWER_DISAGREE status when reviewer is wrong; justify with evidence | | 7 | **Scope creep during revision** | Adding unrequested sections/analyses to "improve" the paper | Revision addresses reviewer concerns only; new content requires explicit user approval | | 8 | **Ignoring failure paths** | Continuing despite desk-reject signals or fatal methodology flaws | Check `references/failure_paths.md`; invoke F11 Desk-Reject Recovery when triggered | --- ## Quality Standards ### Writing Quality 1. **Every claim must have a citation** or be supported by the paper's own data 2. **Zero citation orphans** — in-text citations <-> reference list must perfectly match 3. **Consistent register** — academic tone appropriate for the discipline 4. **Logical flow** — clear transitions between paragraphs and sections 5. **Word count compliance** — within +/-10% of target ### Bilingual Abstract Quality 6. **Independent writing** — zh-TW and EN abstracts are independently composed, NOT mechanical translations 7. **Structural alignment** — both abstracts cover the same key points in the same order 8. **Keywords** — 5-7 per language, reflecting the paper's core concepts 9. **Word count** — EN: 150-300 words; zh-TW: 300-500 characters ### Citation Quality 10. **Format compliance** — 100% adherence to selected citation style 11. ⚠️ IRON RULE: **DOI inclusion** — every source with a DOI must include it; every citation must be verified via DOI or WebSearch 12. **Currency** — flag sources older than 10 years (unless seminal works) 13. **Self-citation ratio** — flag if >15% ### Peer Review 14. **Five dimensions** — Originality (20%), Methodological Rigor (25%), Evidence Sufficiency (25%), Argument Coherence (15%), Writing Quality (15%) 15. **Actionable feedback** — every criticism must include a specific suggestion 16. **Max 2 revision rounds** — unresolved items become Acknowledged Limitations ### Mandatory Inclusions ⚠️ **IRON RULE**: Every paper MUST include: Data Availability Statement, Ethics Declaration, Author Contributions (CRediT), Conflict of Interest Statement, Funding Acknowledgment. 17. **AI disclosure statement** — every paper must include a statement on AI tool usage 18. **Limitations section** — explicitly discuss study limitations 19. **Ethics statement** — when applicable (human subjects, sensitive data) --- ## Output Language Follows the user's language. Academic terminology is kept in English. Bilingual abstracts are always provided regardless of the main text language. --- ## Integration with Other Skills ``` academic-paper + tw-hei-intelligence -> Evidence-based HEI paper with real MOE data academic-paper + deep-research -> Deep research phase -> paper writing phase (auto-handoff) academic-paper + report-to-website -> Interactive web version of the paper academic-paper + notebooklm-slides-generator -> Presentation slides from paper academic-paper + academic-paper-reviewer -> Peer review -> revision loop ``` --- ## Version Info | Item | Content | |------|---------| | Skill Version | 3.1.1 | | Last Updated | 2026-04-27 | | Maintainer | Cheng-I Wu | | Dependent Skills | deep-research v1.0+ (upstream), academic-paper-reviewer v1.0+ (downstream) | --- ## Version History > See `references/changelog.md` for full version history.academic-pipeline/SKILL.mdskillShow content (32535 bytes)
--- name: academic-pipeline description: "Orchestrator for the full academic research pipeline: research -> write -> integrity check -> review -> revise -> re-review -> re-revise -> final integrity check -> finalize. Coordinates deep-research, academic-paper, and academic-paper-reviewer into a seamless 10-stage workflow with mandatory integrity verification, two-stage peer review, and reproducible quality gates. Triggers on: academic pipeline, research to paper, full paper workflow, paper pipeline, end-to-end paper, research-to-publication, complete paper workflow." metadata: version: "3.7.0" last_updated: "2026-05-05" depends_on: "deep-research, academic-paper, academic-paper-reviewer" status: active data_access_level: verified_only task_type: open-ended related_skills: - deep-research - academic-paper - academic-paper-reviewer --- # Academic Pipeline v3.7.0 — Full Academic Research Workflow Orchestrator A lightweight orchestrator that manages the complete academic pipeline from research exploration to final manuscript. It does not perform substantive work — it only detects stages, recommends modes, dispatches skills, manages transitions, and tracks state. **v3.6.3 (opt-in):** Set `ARS_PASSPORT_RESET=1` to promote FULL checkpoints to context-reset boundaries. Use `resume_from_passport=<hash>` in a fresh session to continue from the recorded stage. See [`references/passport_as_reset_boundary.md`](references/passport_as_reset_boundary.md). **v2.0 Core Improvements**: 1. **Mandatory user confirmation checkpoints** — Each stage completion requires user confirmation before proceeding to the next step 2. **Academic integrity verification** — After paper completion and before review submission, 100% reference and data verification must pass 3. **Two-stage review** — First full review + post-revision focused verification review 4. **Final integrity check** — After revision completion, re-verify all citations and data are 100% correct 5. **Reproducible** — Standardized workflow producing consistent quality assurance each time 6. **Process documentation** — After pipeline completion, automatically generates a "Paper Creation Process Record" PDF documenting the human-AI collaboration history ## Quick Start **Full workflow (from scratch):** ``` I want to write a research paper on the impact of AI on higher education quality assurance ``` --> academic-pipeline launches, starting from Stage 1 (RESEARCH) **Mid-entry (existing paper):** ``` I already have a paper, help me review it ``` --> academic-pipeline detects mid-entry, starting from Stage 2.5 (INTEGRITY) **Revision mode (received reviewer feedback):** ``` I received reviewer comments, help me revise ``` --> academic-pipeline detects, starting from Stage 4 (REVISE) **Resume from passport (cross-session context reset, opt-in):** ``` resume_from_passport=<hash> [stage=<n>] [mode=<m>] ``` --> Loads the Material Passport (Schema 9), locates the `kind: boundary` entry matching `<hash>`, and confirms it has no later `kind: resume` entry consuming it. If `pending_decision` is set, the decision prompt fires first to capture the user's branch choice for the audit ledger; the prompt is never skipped, even when the user supplies `stage=`. After the prompt (or immediately if no `pending_decision`), the next stage is determined by: (a) `stage=<n>` CLI override if provided, else (b) the matched option's `next_stage`, else (c) the `next` field recorded in the boundary entry. CLI `stage=`/`mode=` overrides win over option routing. - **Gate (emit)**: `ARS_PASSPORT_RESET=1` must be set in the emitting session. Without the flag, no `kind: boundary` entries are written and there is nothing to resume from. - **Gate (resume)**: No flag required. Any session can invoke `resume_from_passport=<hash>` against a passport that carries a valid boundary entry matching the hash. - **Intent**: Invoke in a *fresh* Claude Code session. Resuming within the same session that emitted the boundary provides no token savings and may drop still-live in-session context. - **Stage**: Any. Resumes at whatever stage the routing rules above determine. - **Reference**: [`references/passport_as_reset_boundary.md`](references/passport_as_reset_boundary.md) — see §"`resume_from_passport` mode contract". **Execution flow:** 1. Detect the user's current stage and available materials 2. Recommend the optimal mode for each stage 3. Dispatch the corresponding skill for each stage 4. **After each stage completion, proactively prompt and wait for user confirmation** 5. Track progress throughout; Pipeline Status Dashboard available at any time --- ## Trigger Conditions ### Trigger Keywords **English**: academic pipeline, research to paper, full paper workflow, paper pipeline, end-to-end paper, research-to-publication, complete paper workflow ### Non-Trigger Scenarios | Scenario | Skill to Use | |----------|-------------| | Only need to search materials or do a literature review | `deep-research` | | Only need to write a paper (no research phase needed) | `academic-paper` | | Only need to review a paper | `academic-paper-reviewer` | | Only need to check citation format | `academic-paper` (citation-check mode) | | Only need to convert paper format | `academic-paper` (format-convert mode) | ### Trigger Exclusions - If the user only needs a single function (just search materials, just check citations), no pipeline is needed — directly trigger the corresponding skill - If the user is already using a specific mode of a skill, respect that entry point; the pipeline is opt-in - The pipeline is optional, not mandatory --- ## Pipeline Stages (10 Stages) | Stage | Name | Skill / Agent Called | Available Modes | Deliverables | |-------|------|---------------------|----------------|-------------| | 1 | RESEARCH | `deep-research` | socratic, full, quick | RQ Brief, Methodology, Bibliography, Synthesis | | 2 | WRITE | `academic-paper` | plan, full | Paper Draft | | **2.5** | **INTEGRITY** | **`integrity_verification_agent`** | **pre-review** | **Integrity verification report + corrected paper** | | 3 | REVIEW | `academic-paper-reviewer` | full (incl. Devil's Advocate) | 5 review reports + Editorial Decision + Revision Roadmap | | 4 | REVISE | `academic-paper` | revision | Revised Draft, Response to Reviewers | | **3'** | **RE-REVIEW** | **`academic-paper-reviewer`** | **re-review** | **Verification review report: revision response checklist + residual issues** | | **4'** | **RE-REVISE** | **`academic-paper`** | **revision** | **Second revised draft (if needed)** | | **4.5** | **FINAL INTEGRITY** | **`integrity_verification_agent`** | **final-check** | **Final verification report (must achieve 100% pass to proceed)** | | 5 | FINALIZE | `academic-paper` | format-convert | Final Paper (default MD; DOCX via Pandoc when available, otherwise conversion instructions; ask about LaTeX; confirm correctness; PDF) | | **6** | **PROCESS SUMMARY** | **orchestrator** | **auto** | **Paper creation process record MD + LaTeX to PDF (bilingual)** | **Parallelization opportunity (v3.3)**: Within Stage 2, the `academic-paper` skill's Phase 1 (literature_strategist_agent) and the `visualization_agent` can operate in parallel after Phase 2 (structure_architect_agent) completes the outline. Specifically: - Once the outline includes a visualization plan, `visualization_agent` can begin figure generation - Simultaneously, `argument_builder_agent` can build CER chains - `draft_writer_agent` waits for both to complete before beginning Phase 4 This mirrors PaperOrchestra's parallel execution of Plot Generation (Step 2) and Literature Review (Step 3) after Outline (Step 1), which reduces overall pipeline latency. The parallelization is optional — sequential execution remains the default for simplicity. --- ## Pipeline State Machine 1. **Stage 1 RESEARCH** -> user confirmation -> Stage 2 2. **Stage 2 WRITE** -> user confirmation -> Stage 2.5 3. **Stage 2.5 INTEGRITY** -> PASS -> Stage 3 (FAIL -> fix and re-verify, max 3 rounds) 4. **Stage 3 REVIEW** -> Accept -> Stage 4.5 / Minor|Major -> Stage 4 / Reject -> Stage 2 or end 5. **Stage 4 REVISE** -> user confirmation -> Stage 3' 6. **Stage 3' RE-REVIEW** -> Accept|Minor -> Stage 4.5 / Major -> Stage 4' 7. **Stage 4' RE-REVISE** -> user confirmation -> Stage 4.5 (no return to review) 8. **Stage 4.5 FINAL INTEGRITY** -> PASS (zero issues) -> Stage 5 (FAIL -> fix and re-verify) 9. **Stage 5 FINALIZE** -> MD -> DOCX via Pandoc when available (otherwise instructions) -> ask about LaTeX -> confirm -> PDF -> Stage 6 10. **Stage 6 PROCESS SUMMARY** -> ask language version -> generate process record MD -> LaTeX -> PDF -> end See `references/pipeline_state_machine.md` for complete state transition definitions. --- ## Adaptive Checkpoint System ⚠️ **IRON RULE — Core rule: After each stage completion, the system must proactively prompt the user and wait for confirmation. The checkpoint presentation adapts based on context and user engagement.** ### Checkpoint Types | Type | When Used | Content | |------|-----------|---------| | FULL | First checkpoint; after integrity boundaries; before finalization | Full deliverables list + decision dashboard + all options | | SLIM | After 2+ consecutive "continue" responses on non-critical stages | One-line status + explicit continue/pause prompt | | MANDATORY | Integrity FAIL; Review decision; Stage 5 | Cannot be skipped; requires explicit user input | ### Decision Dashboard (shown at FULL checkpoints) ``` ━━━ Stage [X] [Name] Complete ━━━ Metrics: - Word count: [N] (target: [T] +/-10%) [OK/OVER/UNDER] - References: [N] (min: [M]) [OK/LOW] - Coverage: [N]/[T] sections drafted [COMPLETE/PARTIAL] - Quality indicators: [score if available] Deliverables: - [Material 1] - [Material 2] Flagged: [any issues detected, or "None"] Ready to proceed to Stage [Y]? You can also: 1. View progress (say "status") 2. Adjust settings 3. Pause pipeline ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ ``` ### Adaptive Rules 1. **First checkpoint**: always FULL 2. **After 2+ consecutive "continue" without review**: prompt user awareness ("You've continued [N] times in a row. Want to review progress?") 3. **Integrity boundaries (Stage 2.5, 4.5)**: always MANDATORY 4. **Review decisions (Stage 3, 3')**: always MANDATORY 5. **Before finalization (Stage 5)**: always MANDATORY 6. **All other stages**: start FULL, downgrade to SLIM if user says "just continue" ### Checkpoint Rules 1. ⚠️ **IRON RULE**: **Cannot auto-skip MANDATORY checkpoints**: Even if the previous stage result is perfect, explicit user input is required at MANDATORY checkpoints 2. **User can adjust**: At FULL and MANDATORY checkpoints, users can modify the mode or settings for the next step 3. **Pause-friendly**: Users can pause at any checkpoint and resume later 4. **SLIM mode**: If the user says "just continue" or "fully automatic," subsequent non-critical checkpoints switch to SLIM format (one-line status + explicit continue/pause prompt) 5. **Awareness guard**: After 4+ consecutive continue responses, the system inserts a FULL checkpoint regardless of stage type to ensure user remains engaged ### Self-Check Questions (at every FULL checkpoint) Before presenting the checkpoint to the user, the orchestrator asks itself: 1. **Citation integrity**: Are there any unverified citations in the latest output? 2. **Sycophantic concession**: Did the latest stage uncritically accept all feedback without pushback? 3. **Quality trajectory**: Is the latest output ≥ the quality of the previous stage? If declining, PAUSE and flag. 4. **Scope discipline**: Did the latest stage add content not requested by the user or the revision roadmap? 5. **Completeness**: Are all required deliverables for this stage present? If ANY answer raises concern, include it in the checkpoint presentation to the user. --- ## Agent Team (4 Agents) | # | Agent | Role | File | |---|-------|------|------| | 1 | `pipeline_orchestrator_agent` | Main orchestrator: detects stage, recommends mode, triggers skill, manages transitions | `agents/pipeline_orchestrator_agent.md` | | 2 | `state_tracker_agent` | State tracker: records completed stages, produced materials, revision loop count | `agents/state_tracker_agent.md` | | 3 | `integrity_verification_agent` | Integrity verifier: 100% reference/citation/data verification (blocking) | `agents/integrity_verification_agent.md` | | 4 | `collaboration_depth_agent` | **Observer (advisory only — never blocks).** Reads dialogue log and scores user-AI collaboration pattern against `shared/collaboration_depth_rubric.md`. Invoked at FULL/SLIM checkpoints and at pipeline completion. Based on Wang & Zhang (2026). | `agents/collaboration_depth_agent.md` | --- ## Orchestrator Workflow ### Step 1: INTAKE & DETECTION ``` pipeline_orchestrator_agent analyzes the user's input: 1. What materials does the user have? - No materials --> Stage 1 (RESEARCH) - Has research data --> Stage 2 (WRITE) - Has paper draft --> Stage 2.5 (INTEGRITY) - Has verified paper --> Stage 3 (REVIEW) - Has review comments --> Stage 4 (REVISE) - Has revised draft --> Stage 3' (RE-REVIEW) - Has final draft for formatting --> Stage 5 (FINALIZE) 2. What is the user's goal? - Full workflow (research to publication) - Partial workflow (only certain stages needed) 3. Determine entry point, confirm with user ``` ### Step 2: MODE RECOMMENDATION ``` Based on entry point and user preferences, recommend modes for each stage: User type determination: - Novice / wants guidance --> socratic (Stage 1) + plan (Stage 2) + guided (Stage 3) - Experienced / wants direct output --> full (Stage 1) + full (Stage 2) + full (Stage 3) - Time-limited --> quick (Stage 1) + full (Stage 2) + quick (Stage 3) Explain the differences between modes when recommending, letting the user choose ``` ### Step 3: STAGE EXECUTION ``` Call the corresponding skill (does not do work itself, purely dispatching): 1. Inform the user which Stage is about to begin 2. Load the corresponding skill's SKILL.md 3. Launch the skill with the recommended mode 4. Monitor stage completion status After completion: 1. Compile deliverables list 2. Update pipeline state (call state_tracker_agent) 3. [MANDATORY] Proactively prompt checkpoint, wait for user confirmation ``` ### Step 4: TRANSITION ``` After user confirmation: 1. Pass the previous stage's deliverables as input to the next stage 2. Trigger handoff protocol (defined in each skill's SKILL.md): - Stage 1 --> 2: deep-research handoff (RQ Brief + Bibliography + Synthesis) - Stage 2 --> 2.5: Pass complete paper to integrity_verification_agent - Stage 2.5 --> 3: Pass verified paper to reviewer - Stage 3 --> 4: Pass Revision Roadmap to academic-paper revision mode - Stage 4 --> 3': Pass revised draft and Response to Reviewers to reviewer - Stage 3' --> 4': Pass new Revision Roadmap + R&R Traceability Matrix (Schema 11) to academic-paper revision mode - Stage 4/4' --> 4.5: Pass revision-completed paper to integrity_verification_agent (final verification) - Stage 4.5 --> 5: Pass verified final draft to format-convert mode 3. Begin next stage ``` ### Mid-Conversation Reinforcement Protocol At every stage transition, the orchestrator MUST inject a brief core principles reminder. This prevents context rot in long conversations. **Template** (adapt to the upcoming stage): ```` --- STAGE TRANSITION: [Current] → [Next] --- 🔄 Core Principles Reinforcement: 1. [Most relevant IRON RULE for the next stage] 2. [Most relevant Anti-Pattern to avoid in the next stage] 3. Quality check: Is the output of [Current Stage] at least as good as [Previous Stage]? If not, PAUSE. Checkpoint: [MANDATORY/ADVISORY] — [What user needs to confirm] --- ```` **Stage-specific reinforcement content**: See `references/reinforcement_content.md` for the full transition → reinforcement focus table. --- ## Integrity Review Protocol Stage 2.5 (pre-review) and Stage 4.5 (post-revision) verification. 5-phase protocol: references → citation context → statistical data → originality → claims. ⚠️ **IRON RULE**: Stage 4.5 must PASS with zero issues to proceed to Stage 5. Stage 4.5 verifies from scratch independently. ⚠️ **IRON RULE (v3.2)**: Both Stage 2.5 and Stage 4.5 must also run the **AI Research Failure Mode Checklist** — a 7-mode taxonomy extending the citation hallucination checks into implementation bugs, hallucinated results, shortcut reliance, bug-as-insight, methodology fabrication, and pipeline-level frame-lock. If any of the 7 modes is `SUSPECTED`, or if Modes 1/3/5/6 are `INSUFFICIENT EVIDENCE`, the pipeline **blocks** and the user must acknowledge (confirm / override with reasoning / revise) before the pipeline proceeds. There is no `--no-block` escape hatch. Stage 6 PROCESS SUMMARY then reports the full failure-mode audit log as part of the AI Self-Reflection Report. > See `references/integrity_review_protocol.md` for the 5-phase citation/claim verification procedures. > See `references/ai_research_failure_modes.md` for the 7-mode AI research failure checklist and block/override logic. - [v3.4.0] `compliance_agent` runs mode-aware PRISMA-trAIce + RAISE compliance check; tier-based block semantics. See `shared/compliance_checkpoint_protocol.md`. --- ## Two-Stage Review Protocol Stage 3 (full review, 5 reviewers) → Revision Coaching → Stage 4 → Stage 3' (re-review) → optional Residual Coaching → Stage 4'. > See `references/two_stage_review_protocol.md` for detailed stage flows and coaching dialogue limits. --- ## Mid-Entry Protocol Users can enter from any stage. The orchestrator will: 1. **Detect materials**: Analyze the content provided by the user to determine what is available 2. **Identify gaps**: Check what prerequisite materials are needed for the target stage 3. **Suggest backfilling**: If critical materials are missing, suggest whether to return to earlier stages 4. **Direct entry**: If materials are sufficient, directly start the specified stage **Important: mid-entry cannot skip Stage 2.5** - If the user brings a paper and enters directly, go through Stage 2.5 (INTEGRITY) first before Stage 3 (REVIEW) - Only exception: User can provide a previous integrity verification report and content has not been modified --- ## External Review Protocol Handles external (human) reviewer feedback integration. 4-step workflow: Intake & Structuring → Strategic Revision Coaching → Revision & Response → Self-Verification. > See `references/external_review_protocol.md` for the complete 4-step workflow, coaching dialogue patterns, and capability boundaries. --- ## Progress Dashboard ASCII dashboard shown at FULL checkpoints to display pipeline progress. > See `references/progress_dashboard_template.md` for the dashboard template. --- ## Revision Loop Management - Stage 3 (first review) -> Stage 4 (revision) -> Stage 3' (verification review) -> Stage 4' (re-revision, if needed) -> Stage 4.5 (final verification) - **Maximum 1 round of RE-REVISE** (Stage 4'): If Stage 3' gives Major, enter Stage 4' for revision then proceed directly to Stage 4.5 (no return to review) - **Pipeline overrides academic-paper's max 2 revision rule**: In the pipeline, revisions are limited to Stage 4 + Stage 4' (one round each), replacing academic-paper's max 2 rounds rule - Mark unresolved issues as Acknowledged Limitations - Provide cumulative revision history (each round's decision, items addressed, unresolved items) ### Early-Stopping Criterion (v3.2) At the end of each revision round, if **delta < 3 points** on the 0-100 rubric AND **no P0 issues remain**, suggest stopping the revision loop ("converged"). User can override. Hard cap: 2 full revision loops (Stage 4 + Stage 4'). ### Budget Transparency (v3.2) At pipeline start, estimate token cost based on paper length, mode, and cross-model toggle. Present estimate and ask for user confirmation before Stage 1 begins. --- ## Reproducibility Every pipeline artifact is versioned, hashed, and auditable. > See `references/reproducibility_audit.md` for standardized workflow guarantees, audit trail format, and artifact tracking. --- ## Stage 6: Process Summary Protocol Produces the final process record: paper creation journey, collaboration quality evaluation (6 dimensions, 1-100), and AI self-reflection report. > See `references/process_summary_protocol.md` for full workflow, required content structure, scoring dimensions, and output specifications. --- ## Collaboration Depth Observer (v3.5.0, advisory only — never blocks) The `collaboration_depth_agent` observes the user's collaboration pattern with the pipeline. It is **advisory only** and **never blocks** progression at any checkpoint. It is `non-blocking` by design and carries `blocking: false` in its frontmatter as a structural guarantee. **When invoked**: every FULL checkpoint, every SLIM checkpoint, and after Stage 6 (pipeline completion). MANDATORY checkpoints (Stages 2.5 / 4.5 integrity gates) **do not** invoke the observer — those are integrity concerns and must not be diluted. **What it does**: reads the dialogue range for the just-completed stage (at checkpoints) or the whole pipeline (at completion), scores the pattern against the canonical rubric at `shared/collaboration_depth_rubric.md`, and emits an advisory block/chapter. Dimensions: Delegation Intensity, Cognitive Vigilance, Cognitive Reallocation, Zone Classification (Zone 1 / Zone 2 / Zone 3). Rubric is based on Wang & Zhang (2026) IJETHE 23:11 (DOI 10.1186/s41239-026-00585-x). **Distinction from existing mechanisms**: | Mechanism | What it evaluates | Blocking? | |---|---|---| | `integrity_verification_agent` (Stages 2.5 / 4.5) | Paper content — references, citations, data | Yes (blocking gate) | | Stage 6 Collaboration Quality Evaluation (6 dims, 1–100) | AI's self-reflection on its own behaviour | No, but produced once only | | `collaboration_depth_agent` (this observer) | The **user's** collaboration pattern (delegation intensity, vigilance, reallocation) | **No — never blocks. Advisory only.** | **Non-blocking guarantees**: - Observer output never appears on the "Flagged" line of any checkpoint. - The `Ready to proceed?` prompt is unchanged by observer output. - `blocked_by: collaboration_depth_agent` is never a legal state in `state_tracker`. - If observer frontmatter ever asserts `blocking: true`, the orchestrator must refuse to dispatch it. **Cross-model**: when `ARS_CROSS_MODEL` is set, the observer runs on both models and flags any dimension divergence > 2 points. Scores are never silently averaged across models. > See `agents/collaboration_depth_agent.md` for full scoring procedure and anti-sycophancy discipline; `shared/collaboration_depth_rubric.md` for the canonical 4-dimension rubric. --- ## Anti-Patterns Explicit prohibitions to prevent common failure modes: | # | Anti-Pattern | Why It Fails | Correct Behavior | |---|-------------|-------------|-----------------| | 1 | **Skipping integrity checks** | "The paper looks fine, skip Stage 2.5/4.5" | Integrity checks are MANDATORY; they cannot be auto-skipped regardless of perceived quality | | 2 | **Orchestrator doing substantive work** | Pipeline orchestrator writes content or reviews the paper | Orchestrator only dispatches and coordinates; substantive work belongs to the sub-skills | | 3 | **Auto-advancing past MANDATORY checkpoints** | Moving to next stage without user confirmation at FULL checkpoints | MANDATORY checkpoints require explicit user input before proceeding | | 4 | **Quality degradation across stages** | Stage 4 revision is worse than Stage 2 draft because context window is exhausted | If Stage N output quality < Stage N-1, PAUSE and reload core principles before continuing | | 5 | **Silently dropping reviewer concerns** | Revision addresses 8 of 10 concerns and hopes nobody notices | The R&R tracking table must account for every concern with explicit status | | 6 | **Re-verifying only known issues at Stage 4.5** | Final integrity check only re-checks Stage 2.5 findings | Stage 4.5 must verify from scratch independently; revision may introduce new issues | | 7 | **Inflating Collaboration Quality scores** | Giving 90/100 to avoid awkward self-criticism | Honesty first: no inflation, no pleasantries; cite specific evidence for every score | | 8 | **Bypassing the Failure Mode Checklist block** (v3.2) | "The 7-mode checklist is new, let's skip it this run" | Stage 2.5/4.5 Failure Mode Checklist is MANDATORY and BLOCKING; no `--no-block` flag exists; overrides require user reasoning recorded for Stage 6 | --- ## Quality Standards | Dimension | Requirement | |-----------|------------| | Stage detection | Correctly identify user's current stage and available materials | | Mode recommendation | Recommend appropriate mode based on user preferences and material status | | Material handoff | Stage-to-stage handoff materials are complete and correctly formatted | | State tracking | Pipeline state updated in real time; Progress Dashboard accurate | | **Mandatory checkpoint** | **User confirmation required after each stage completion** | | **Mandatory integrity check** | **Stage 2.5 and 4.5 cannot be skipped, must PASS** | | **Mandatory failure mode checklist** (v3.2) | **Stage 2.5 and 4.5 must run the 7-mode AI research failure checklist; suspected failures block; overrides require user reasoning** | | No overstepping | ⚠️ IRON RULE: Orchestrator does not perform substantive research/writing/reviewing, only dispatching | | No forcing | ⚠️ IRON RULE: User can pause or exit pipeline at any time (but cannot skip integrity checks) | | Reproducible | Same input follows the same workflow across different sessions | | **Convergence-aware stopping** (v3.2) | **If delta < 3 points AND no P0 issues, suggest stopping revision loop; user can override** | | **Budget transparency** (v3.2) | **Token cost estimate + user confirmation at pipeline start** | --- ## Error Recovery | Stage | Error | Handling | |-------|-------|---------| | Intake | Cannot determine entry point | Ask user what materials they have and their goal | | Stage 1 | deep-research not converging | Suggest mode switch (socratic -> full) or narrow scope | | Stage 2 | Missing research foundation | Suggest returning to Stage 1 to supplement research | | Stage 2.5 | Still FAIL after 3 correction rounds | List unverifiable items; user decides whether to continue | | Stage 3 | Review result is Reject | Provide options: major restructuring (Stage 2) or abandon | | Stage 4 | Revision incomplete on all items | List unaddressed items; ask whether to continue | | Stage 3' | Verification still has major issues | Enter Stage 4' for final revision | | Stage 4' | Issues remain after revision | Mark as Acknowledged Limitations; proceed to Stage 4.5 | | Stage 4.5 | Final verification FAIL | Fix and re-verify (max 3 rounds) | | Any | User leaves midway | Save pipeline state; can resume from breakpoint next time | | Any | Skill execution failure | Report error; suggest retry, pause, or mode switch. Do not skip mandatory integrity or failure-mode gates | --- ## Agent File References | Agent | Definition File | |-------|----------------| | pipeline_orchestrator_agent | `agents/pipeline_orchestrator_agent.md` | | state_tracker_agent | `agents/state_tracker_agent.md` | | integrity_verification_agent | `agents/integrity_verification_agent.md` | | collaboration_depth_agent | `agents/collaboration_depth_agent.md` | --- ## Reference Files | Reference | Purpose | |-----------|---------| | `references/pipeline_state_machine.md` | Complete state machine definition: all legal transitions, preconditions, actions | | `references/plagiarism_detection_protocol.md` | Phase D originality verification protocol + self-plagiarism + AI text characteristics | | `references/mode_advisor.md` | Unified cross-skill decision tree: maps user intent to optimal skill + mode | | `references/claim_verification_protocol.md` | Phase E claim verification protocol: claim extraction, source tracing, cross-referencing, verdict taxonomy | | `references/ai_research_failure_modes.md` | 7-mode AI research failure checklist (Lu 2026), run at Stage 2.5 + 4.5 with blocking behaviour, reported at Stage 6 | | `references/team_collaboration_protocol.md` | Multi-person team coordination: role definitions, handoff protocol, version control, conflict resolution | | `references/integrity_review_protocol.md` | Stage 2.5 + 4.5 integrity verification: 5-phase protocol details | | `references/two_stage_review_protocol.md` | Two-stage review: Stage 3 full review + Stage 3' verification review | | `references/external_review_protocol.md` | External (human) reviewer feedback: 4-step intake/coaching/revision/verification | | `references/process_summary_protocol.md` | Stage 6: collaboration quality evaluation + AI self-reflection report | | `references/reproducibility_audit.md` | Standardized workflow guarantees + audit trail format | | `references/progress_dashboard_template.md` | ASCII progress dashboard template | | `references/reinforcement_content.md` | Stage-specific reinforcement focus table for transitions | | `references/changelog.md` | Full version history | | `shared/handoff_schemas.md` | Cross-skill data contracts: 9 schemas for all inter-stage handoff artifacts | | `shared/collaboration_depth_rubric.md` | Collaboration Depth Observer rubric (v1.0): 4 dimensions based on Wang & Zhang (2026) IJETHE 23:11 | --- ## Templates | Template | Purpose | |----------|---------| | `templates/pipeline_status_template.md` | Progress Dashboard output template | --- ## Examples | Example | Demonstrates | |---------|-------------| | `examples/full_pipeline_example.md` | Complete pipeline conversation log (Stage 1-5, with integrity + 2-stage review) | | `examples/mid_entry_example.md` | Mid-entry example starting from Stage 2.5 (existing paper -> integrity check -> review -> revision -> finalization) | --- ## Output Language Follows user language. Academic terminology retained in English. --- ## Integration with Other Skills ``` academic-pipeline dispatches the following skills (does not do work itself): Stage 1: deep-research - socratic mode: Guided research exploration - full mode: Complete research report - quick mode: Quick research summary Stage 2: academic-paper - plan mode: Socratic chapter-by-chapter guidance - full mode: Complete paper writing Stage 2.5: integrity_verification_agent (Mode 1: pre-review) Stage 4.5: integrity_verification_agent (Mode 2: final-check) Stage 3: academic-paper-reviewer - full mode: Complete 5-person review (EIC + R1/R2/R3 + Devil's Advocate) Stage 3': academic-paper-reviewer - re-review mode: Verification review (focused on revision responses) Stage 4/4': academic-paper (revision mode) Stage 5: academic-paper (format-convert mode) - Step 1: Ask user which academic formatting style (APA 7.0 / Chicago / IEEE, etc.) - Step 2: Produce MD, then generate DOCX via Pandoc when available (otherwise provide conversion instructions) - Step 3: Produce LaTeX (using corresponding document class, e.g., apa7 class for APA 7.0) - Step 4: After user confirms content is correct, tectonic compiles PDF (final version) - Fonts: Times New Roman (English) + Source Han Serif TC VF (Chinese) + Courier New (monospace) - ⚠️ IRON RULE: PDF must be compiled from LaTeX (HTML-to-PDF is prohibited) ``` --- ## Related Skills | Skill | Relationship | |-------|-------------| | `deep-research` | Dispatched (Stage 1 research phase) | | `academic-paper` | Dispatched (Stage 2 writing, Stage 4/4' revision, Stage 5 formatting) | | `academic-paper-reviewer` | Dispatched (Stage 3 first review, Stage 3' verification review) | --- ## Version Info | Item | Content | |------|---------| | Skill Version | 3.7.0 | | Last Updated | 2026-05-05 | | Maintainer | Cheng-I Wu | | Dependent Skills | deep-research v2.0+, academic-paper v2.0+, academic-paper-reviewer v1.1+ | | Role | Full academic research workflow orchestrator | --- ## Changelog > See `references/changelog.md` for full version history.academic-paper-reviewer/SKILL.mdskillShow content (21965 bytes)
--- name: academic-paper-reviewer description: "Multi-perspective academic paper review with dynamic reviewer personas. Simulates 5 independent reviewers (EIC + 3 peer reviewers + Devil's Advocate) with field-specific expertise. Supports full review, re-review (verification), quick assessment, methodology focus, Socratic guided, and calibration modes. Triggers on: review paper, peer review, manuscript review, referee report, review my paper, critique paper, simulate review, editorial review, calibrate reviewer, reviewer calibration, measure reviewer accuracy." metadata: version: "1.9.0" last_updated: "2026-04-23" status: active data_access_level: verified_only task_type: open-ended related_skills: - academic-paper - academic-pipeline --- # Academic Paper Reviewer v1.9.0 — Multi-Perspective Academic Paper Review Agent Team Simulates a complete international journal peer review process: automatically identifies the paper's field, dynamically configures 5 reviewers (Editor-in-Chief + 3 peer reviewers + Devil's Advocate) who review from four non-overlapping perspectives — methodology, domain expertise, cross-disciplinary viewpoints, and core argument challenges — ultimately producing a structured Editorial Decision and Revision Roadmap. **v1.1 Improvements**: 1. Added Devil's Advocate Reviewer — specifically challenges core arguments, detects logical fallacies, and identifies the strongest counter-arguments 2. Added `re-review` mode — verification review, focused on checking whether revisions address the review comments 3. Expanded review team from 4 to 5 members --- ## Quick Start **Simplest command:** ``` Review this paper: [paste paper or provide file] ``` **Output:** 1. Automatically identifies the paper's field and methodology type 2. Dynamically configures the specific identities and expertise of 5 reviewers 3. 5 independent review reports (each from a different perspective) 4. 1 Editorial Decision Letter + Revision Roadmap --- ## Trigger Conditions ### Trigger Keywords **English**: review paper, peer review, manuscript review, referee report, review my paper, critique paper, simulate review, editorial review, calibrate reviewer, reviewer calibration, measure reviewer accuracy ### Non-Trigger Scenarios | Scenario | Skill to Use | |----------|-------------| | Need to write a paper (not review) | `academic-paper` | | Need in-depth investigation of a research topic | `deep-research` | | Need to revise a paper (already have review comments) | `academic-paper` (revision mode) | ### Quick Mode Selection Guide | Your Situation | Recommended Mode | Spectrum | |----------------|-----------------|----------| | Need comprehensive review (first submission) | full | balanced | | Checking if revisions addressed comments | re-review | fidelity | | Quick quality assessment (15 min) | quick | fidelity | | Focus only on methods/statistics | methodology-focus | fidelity | | Want to learn by doing (guided review) | guided | originality | | Want to know this reviewer's own error profile before trusting its scores | calibration | 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? Use `full` for pre-submission review, `re-review` for post-revision verification. `calibration` is opt-in — run it once per domain when you want to know the reviewer's FNR/FPR before relying on its rubric scores. --- ## Agent Team (7 Agents) | # | Agent | Role | Phase | |---|-------|------|-------| | 1 | `field_analyst_agent` | Analyzes the paper's field, dynamically configures 5 reviewer identities | Phase 0 | | 2 | `eic_agent` | Journal Editor-in-Chief — journal fit, originality, overall quality | Phase 1 | | 3 | `methodology_reviewer_agent` | Peer Reviewer 1 — research design, statistical validity, reproducibility | Phase 1 | | 4 | `domain_reviewer_agent` | Peer Reviewer 2 — literature coverage, theoretical framework, domain contribution | Phase 1 | | 5 | `perspective_reviewer_agent` | Peer Reviewer 3 — cross-disciplinary connections, practical impact, challenging fundamental assumptions | Phase 1 | | 6 | **`devils_advocate_reviewer_agent`** | **Devil's Advocate — core argument challenges, logical fallacy detection, strongest counter-arguments** | **Phase 1** | | 7 | `editorial_synthesizer_agent` | Synthesizes all reviews, identifies consensus and disagreements, makes editorial decision | Phase 2 | --- ## Orchestration Workflow (3 Phases) ``` User: "Review this paper" | === Phase 0: FIELD ANALYSIS & PERSONA CONFIGURATION === | +-> [field_analyst_agent] -> Reviewer Configuration Card (x5) - Reads the complete paper - Identifies: primary discipline, secondary discipline, research paradigm, methodology type, target journal tier, paper maturity - Dynamically generates specific identities for 5 reviewers: * EIC: Which journal's editor, area of expertise, review preferences * Reviewer 1 (Methodology): Methodological expertise, what they particularly focus on * Reviewer 2 (Domain): Domain expertise, research interests * Reviewer 3 (Perspective): Cross-disciplinary angle, what unique perspective they bring * Devil's Advocate: Specifically challenges core arguments, detects logical gaps | ** Presents Reviewer Configuration to user for confirmation (adjustable) ** | === Phase 1: PARALLEL MULTI-PERSPECTIVE REVIEW === | |-> [eic_agent] -------> EIC Review Report | - Journal fit, originality, significance, relevance to readership | - Does not go deep into methodology (that's Reviewer 1's job) | - Sets the review tone | |-> [methodology_reviewer_agent] -> Methodology Review Report | - Research design rigor, sampling strategy, data collection | - Analysis method selection, statistical validity, effect sizes | - Reproducibility, data transparency | |-> [domain_reviewer_agent] -------> Domain Review Report | - Literature review completeness, theoretical framework appropriateness | - Academic argument accuracy, incremental contribution to the field | - Missing key references | |-> [perspective_reviewer_agent] --> Perspective Review Report | - Cross-disciplinary connections and borrowing opportunities | - Practical applications and policy implications | - Broader social or ethical implications | +-> [devils_advocate_reviewer_agent] --> Devil's Advocate Report - Core argument challenges (strongest counter-arguments) - Cherry-picking detection - Confirmation bias detection - Logic chain validation - Overgeneralization detection - Alternative paths analysis - Stakeholder blind spots - "So what?" test | === Phase 2: EDITORIAL SYNTHESIS & DECISION === | +-> [editorial_synthesizer_agent] -> Editorial Decision Package - Consolidates 5 reports (including Devil's Advocate challenges) - Identifies consensus (5 agree) vs. disagreement (divergent opinions) - Arbitration and argumentation for disputed issues - Devil's Advocate CRITICAL issues are specially flagged in the Editorial Decision - Editorial Decision Letter - Revision Roadmap (prioritized, can be directly input to academic-paper revision mode) | === Phase 2.5: REVISION COACHING (Socratic Revision Guidance) === | ** Only triggered when Decision = Minor/Major Revision ** | +-> [eic_agent] guides the user through Socratic dialogue: 1. Overall positioning — "After reading the review comments, what surprised you the most?" 2. Core issue focus — Guides user to understand consensus issues 3. Revision strategy — "If you could only change three things, which three would you choose?" 4. Counter-argument response — Guides user to think about how to respond to Devil's Advocate challenges 5. Implementation planning — Helps prioritize revisions | +-> After dialogue ends, produces: - User's self-formulated revision strategy - Reprioritized Revision Roadmap | ** User can say "just fix it" to skip guidance ** ``` ### Checkpoint Rules 1. **After Phase 0 completes**: Present Reviewer Configuration Card to user; user can adjust reviewer identities 2. ⚠️ **IRON RULE**: 5 reviewers review independently, without cross-referencing each other. 3. ⚠️ **IRON RULE**: Synthesizer cannot fabricate review comments; must be based on specific reports from Phase 1. 4. ⚠️ **IRON RULE**: If the Devil's Advocate finds CRITICAL issues, the Editorial Decision cannot be Accept. 5. **Phase 2.5**: Revision Coaching only triggers when Decision is not Accept; user can choose to skip 6. ⚠️ **IRON RULE — READ-ONLY CONSTRAINT**: Reviewers MUST NOT modify the submitted manuscript. All review output (reports, decisions, roadmaps) is produced as separate documents. The reviewer examines the paper — it never rewrites it. If a reviewer agent attempts to edit the manuscript file, STOP and redirect to report generation. --- ## Operational Modes (6 Modes) | Mode | Trigger | Agents | Output | |------|---------|--------|--------| | `full` | Default / "full review" | All 7 agents | 5 review reports + Editorial Decision + Revision Roadmap | | **`re-review`** | **Pipeline Stage 3' / "verification review"** | **field_analyst + eic + editorial_synthesizer** | **Revision response checklist + residual issues + new Decision** | | `quick` | "quick review" | field_analyst + eic | EIC quick assessment + key issues list (15-minute version) | | `methodology-focus` | "check methodology" | field_analyst + eic + methodology_reviewer | In-depth methodology review report (panel 2 under v3.6.2 sprint contract: EIC + methodology) | | `guided` | "guide me" | All + Socratic dialogue | Socratic issue-by-issue guided review | | **`calibration`** (v3.2) | **"calibrate reviewer" / "measure reviewer accuracy"** | **All 7 agents, 5x per gold paper, cross-model default-on** | **Calibration Report: FNR/FPR/balanced accuracy/AUC + per-dimension calibration error + session-scoped confidence disclosure** | ### Mode Selection Logic ``` "Review this paper" -> full "Give me a quick look at this paper" -> quick "Help me check the methodology" -> methodology-focus "Does this paper have methodology issues"-> methodology-focus "Guide me to improve this paper" -> guided "Walk me through the issues in my paper" -> guided "Verification review" / "Check revisions"-> re-review "How accurate is your review scoring?" -> calibration "Calibrate against these 10 papers" -> calibration ``` --- ## Re-Review Mode (Verification Review) Dedicated mode for Pipeline Stage 3' — verifies whether revisions address first-round review comments. Uses R&R Traceability Matrix (Schema 11) with Author's Claim + Verified? columns. **Input**: Original Revision Roadmap + Revised manuscript + Response to Reviewers (optional) **Output**: Verification Review Report with traceability matrix + new issues + Decision > See `references/re_review_mode_protocol.md` for full verification logic, output format template, and Socratic guidance details. --- ## Guided Mode (Socratic Guided Review) Helps authors understand problems themselves through progressive revelation. EIC opens with strengths, then gradually introduces deeper issues from each reviewer perspective. > See `references/guided_mode_protocol.md` for dialogue flow, rules, and progressive revelation sequence. --- ## Calibration Mode (v3.2) Opt-in mode that measures this reviewer's FNR / FPR / balanced accuracy against a user-supplied gold set (5-20 papers with known outcomes). Runs `full` 5x per paper with fresh context, cross-model default-on. Produces a Calibration Report attached as a confidence disclosure to subsequent reviews in the session. > See `references/calibration_mode_protocol.md` for full spec: intake rules, ensembling methodology, output format, and failure cases this mode does not fix. --- ## Review Output Format Each reviewer's report structure is detailed in `templates/peer_review_report_template.md`. ### Devil's Advocate Report Structure (Special Format) The Devil's Advocate uses a dedicated format, not the standard reviewer template: - **Strongest Counter-Argument** (200-300 words) - **Issue List** (categorized as CRITICAL / MAJOR / MINOR, with dimension and location) - **Ignored Alternative Explanations/Paths** - **Missing Stakeholder Perspectives** - **Observations (Non-Defects)** --- ## Editorial Decision Format The Editorial Decision Letter structure is detailed in `templates/editorial_decision_template.md`. --- ## Integration ### Upstream/Downstream Relationships ``` deep-research --> academic-paper --> [integrity check] --> academic-paper-reviewer --> academic-paper (revision) --> academic-paper-reviewer (re-review) --> [final integrity] --> finalize (research) (writing) (integrity audit) (review) (revision) (verification review) (final verification) (finalization) ``` ### Specific Integration Methods | Integration Direction | Description | |----------------------|-------------| | **Upstream: academic-paper -> reviewer** | Receives the complete paper output from `academic-paper` full mode, directly enters Phase 0 | | **Upstream: integrity check -> reviewer** | In the Pipeline, the paper must pass integrity check before entering reviewer | | **Downstream: reviewer -> academic-paper** | The Revision Roadmap format can be directly used as reviewer feedback input for `academic-paper` revision mode | | **Downstream: reviewer (re-review) -> integrity** | After re-review completes, proceeds to final integrity verification | ### Pipeline Usage Example > See `references/integration_guide.md` for a complete 9-step pipeline usage example. --- ## Agent File References | Agent | Definition File | |-------|----------------| | field_analyst_agent | `agents/field_analyst_agent.md` | | eic_agent | `agents/eic_agent.md` | | methodology_reviewer_agent | `agents/methodology_reviewer_agent.md` | | domain_reviewer_agent | `agents/domain_reviewer_agent.md` | | perspective_reviewer_agent | `agents/perspective_reviewer_agent.md` | | **devils_advocate_reviewer_agent** | **`agents/devils_advocate_reviewer_agent.md`** | | editorial_synthesizer_agent | `agents/editorial_synthesizer_agent.md` | --- ## Reference Files | Reference | Purpose | Used By | |-----------|---------|---------| | `references/review_criteria_framework.md` | Structured review criteria framework (differentiated by paper type) | all reviewers | | `references/top_journals_by_field.md` | Top journal lists for major academic fields (EIC role calibration) | field_analyst, eic | | `references/editorial_decision_standards.md` | Accept/Minor/Major/Reject criteria and decision matrix | eic, editorial_synthesizer | | `references/statistical_reporting_standards.md` | Statistical reporting standards + APA 7.0 format quick reference + red flag list | methodology_reviewer | | `references/quality_rubrics.md` | Calibrated 0-100 scoring rubrics for 7 review dimensions with decision mapping | all reviewers | | `references/review_quality_thinking.md` | Cognitive framework for review quality: three lenses (internal validity, external validity, contribution), common reviewer traps, calibration questions | all reviewers | | `references/re_review_mode_protocol.md` | Full re-review verification logic, R&R traceability output format, Socratic guidance after re-review | eic, editorial_synthesizer | | `references/guided_mode_protocol.md` | Guided mode dialogue flow, progressive revelation sequence, dialogue rules | all reviewers | | `references/calibration_mode_protocol.md` | Calibration mode: FNR/FPR/balanced accuracy measurement against user-supplied gold set, 5x ensembling, session-scoped confidence disclosure (v3.2) | all reviewers | | `references/integration_guide.md` | Complete 9-step pipeline usage example | — | | `references/changelog.md` | Full version history | — | --- ## Templates | Template | Purpose | |----------|---------| | `templates/peer_review_report_template.md` | Review report template used by each reviewer | | `templates/editorial_decision_template.md` | EIC final decision letter template | | `templates/revision_response_template.md` | Revision response template for authors (R->A->C format) | --- ## Examples | Example | Demonstrates | |---------|-------------| | `examples/hei_paper_review_example.md` | Full review example: "Impact of Declining Birth Rates on Management Strategies of Taiwan's Private Universities" | | `examples/interdisciplinary_review_example.md` | Cross-disciplinary review example: "Using Machine Learning to Predict University Closure Risk in Taiwan" | --- ## Anti-Patterns Explicit prohibitions to prevent common failure modes, especially during long conversations: | # | Anti-Pattern | Why It Fails | Correct Behavior | |---|-------------|-------------|-----------------| | 1 | **Fabricating review comments** | Synthesizer invents critique not in any reviewer report | Every synthesis point must trace to a specific Phase 1 reviewer report | | 2 | **Duplicate criticisms across reviewers** | R1/R2/R3 raise identical points = fake diversity | Each reviewer has a distinct perspective; overlapping topics get different angles | | 3 | **Ignoring Devil's Advocate CRITICAL findings** | Editorial Decision says Accept despite DA flagging critical issues | If DA finds CRITICAL → Decision cannot be Accept (Checkpoint Rule #4) | | 4 | **Rubber-stamp re-review** | Re-review says "all addressed" without verification | Each concern must be independently verified against the revised manuscript | | 5 | **Sycophantic score inflation** | Giving 8/10 to mediocre work to avoid conflict | Scores must be evidence-based; a paper with methodology gaps cannot score >6 on rigor | | 6 | **Editing the manuscript** | Reviewer "helpfully" fixes the paper directly | READ-ONLY: produce reports, never modify the paper (Checkpoint Rule #6) | | 7 | **Generic feedback** | "The methodology could be stronger" without specifics | Every criticism must include: what's wrong, where it is, and a proposed fix | --- ## Quality Standards | Dimension | Requirement | |-----------|-------------| | Perspective differentiation | Each reviewer's review must come from a different angle; no duplicate criticisms | | Evidence-based | EIC's decision must be based on specific reviewer comments; no fabrication | | Specificity | Reviews must cite specific passages, data, or page numbers from the paper; no vague comments | | Balance | Strengths and Weaknesses must be balanced; cannot only criticize without affirming | | Professional tone | Review tone must be professional and constructive; avoid personal attacks or demeaning language | | Actionability | Each weakness must include specific improvement suggestions | | Format consistency | All reports must follow the template structure; no freestyle | | **Devil's Advocate completeness** | **Devil's Advocate must produce the strongest counter-argument; cannot be omitted** | | **CRITICAL threshold** | **⚠️ IRON RULE: Devil's Advocate CRITICAL issues cannot be ignored by the Editorial Decision** | --- ## Output Language Follows the paper's language. Academic terms remain in English. User can override (e.g., "review this Chinese paper in English"). --- ## Related Skills | Skill | Relationship | |-------|-------------| | `academic-paper` | Upstream (provides paper) + Downstream (receives revision roadmap) | | `deep-research` | Upstream (provides research foundation) | | `tw-hei-intelligence` | Auxiliary (verifies higher education data accuracy) | | `academic-pipeline` | Orchestrated by (Stage 3 + Stage 3') | --- ## v3.6.2 Sprint Contract Hard Gate - **Reviewer hard gate.** All reviewer modes that ship with contracts (`reviewer_full`, `reviewer_methodology_focus`) now run two-call Phase 1 (paper-content-blind) + Phase 2 (paper-visible) orchestration. See `references/sprint_contract_protocol.md`. - **Schema 13 sprint contract.** Template-driven acceptance criteria with `panel_size`, `acceptance_dimensions`, `failure_conditions` (with `severity` precedence + `cross_reviewer_quantifier` panel-relative thresholds), `measurement_procedure`, optional `override_ladder`, bounded `agent_amendments`. Validator: `scripts/check_sprint_contract.py`. Schema: `shared/sprint_contract.schema.json`. - **Synthesizer three-step mechanical protocol.** Build cross-reviewer matrix → evaluate each failure_condition with panel-relative quantifier + expression vocabulary → resolve precedence by severity. Forbidden operations explicit in `agents/editorial_synthesizer_agent.md`. - **methodology_focus reduced panel.** `reviewer_methodology_focus` mode runs a 2-reviewer panel (EIC + methodology only) instead of the default 5. - **Templates:** `shared/contracts/reviewer/full.json` (panel 5) and `shared/contracts/reviewer/methodology_focus.json` (panel 2). Reserved modes (`reviewer_re_review`, `reviewer_calibration`, `reviewer_guided`) keep pre-v3.6.2 behaviour until follow-up patch templates land. --- ## Version Info | Item | Content | |------|---------| | Skill Version | 1.9.0 | | Last Updated | 2026-04-23 | | Maintainer | Cheng-I Wu | | Dependent Skills | academic-paper v1.0+ (upstream/downstream integration) | | Role | Multi-perspective academic paper review simulator | --- ## Changelog > See `references/changelog.md` for full version history.deep-research/SKILL.mdskillShow content (25724 bytes)
--- name: deep-research description: "Universal deep research agent team. 13-agent pipeline for rigorous academic research on any topic. 7 modes: full research, quick brief, paper review, lit-review, fact-check, 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, 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, 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." metadata: version: "2.9.3" last_updated: "2026-04-30" status: active data_access_level: raw task_type: open-ended related_skills: - academic-paper - academic-pipeline --- # 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`. ## 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 --- ## 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。 --- ## 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. ``` 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 ``` --- ## 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** can halt delivery for Critical ethics concerns 4. User confirmation required after Phase 1 before proceeding --- ## 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". --- ## 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 | | `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 | --- ## 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 | Serious ethical issue | STOP, list issues and remediation path | | 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`: 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. --- ## 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` | 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 | — | --- ## 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) | --- ## 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 | --- ## Output Language Follows the user's language. Academic terminology kept in English. Socratic mode uses natural conversational style. --- ## 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 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. --- ## 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 ``` --- ## Version Info | Item | Content | |------|---------| | Skill Version | 2.9.3 | | Last Updated | 2026-04-30 | | Maintainer | Cheng-I Wu | | Dependent Skills | academic-paper v1.0+ (downstream) | --- ## Version History > See `references/changelog.md` for full version history..claude-plugin/marketplace.jsonmarketplaceShow content (578 bytes)
{ "name": "academic-research-skills", "owner": { "name": "Cheng-I Wu", "url": "https://github.com/Imbad0202" }, "description": "Academic Research Skills — production-grade research, writing, peer review, and pipeline orchestration for Claude Code.", "plugins": [ { "name": "academic-research-skills", "source": "./", "description": "4 skills + 35+ modes + Material Passport pipeline. Includes v3.6.7 cross-model audit gate and v3.6.8 generator-evaluator contract.", "version": "3.7.0", "license": "CC-BY-NC-4.0" } ] }
README
Academic Research Skills for Claude Code
A comprehensive suite of Claude Code skills for academic research, covering the full pipeline from research to publication.
Install in 30 seconds (Claude Code CLI / VS Code / JetBrains, v3.7.0+):
/plugin marketplace add Imbad0202/academic-research-skills
/plugin install academic-research-skills
Then try /ars-plan to walk through your paper structure via Socratic dialogue, or jump to Quick install for prerequisites and the traditional symlink flow.
AI is your copilot, not the pilot. This tool won't write your paper for you. It handles the grunt work — hunting down references, formatting citations, verifying data, checking logical consistency — so you can focus on the parts that actually require your brain: defining the question, choosing the method, interpreting what the data means, and writing the sentence after "I argue that."
Unlike a humanizer, this tool doesn't help you hide the fact that you used AI. It helps you write better. Style Calibration learns your voice from past work. Writing Quality Check catches the patterns that make prose feel machine-generated. The goal is quality, not cheating.
Why human-in-the-loop, not full automation?
Lu et al. (2026, Nature 651:914-919) built The AI Scientist — the first fully autonomous AI research system to publish a paper through blind peer review at a top-tier ML venue (ICLR 2025 workshop, score 6.33/10 vs workshop average 4.87). Their Limitations section enumerates the failure modes that any fully-autonomous AI research pipeline inherits: implementation bugs, hallucinated results, shortcut reliance, bug-as-insight reframing, methodology fabrication, frame-lock, citation hallucinations.
ARS is built on the premise that a human researcher augmented by AI avoids these failure modes better than either alone. Stage 2.5 and Stage 4.5 integrity gates run a 7-mode blocking checklist (see academic-pipeline/references/ai_research_failure_modes.md); the reviewer offers an opt-in calibration mode that measures its own FNR/FPR against a user-supplied gold set.
v3.3 was inspired by PaperOrchestra (Song, Song, Pfister & Yoon, 2026, Google): Semantic Scholar API verification, anti-leakage protocol, VLM figure verification, and score trajectory tracking.
Architecture & pipeline
👉 docs/ARCHITECTURE.md — the full pipeline view: flow diagram, stage-by-stage matrix, data-access flow, skill dependency graph, quality gates, and mode list.
The architecture doc supersedes the sprawling pipeline description that used to live here. Everything about what runs in which stage now lives in one place.
Quick install
Prerequisites
- Claude Code (latest; plugin packaging requires recent versions)
ANTHROPIC_API_KEYexported, or set on firstclauderun- Optional: Pandoc for DOCX, tectonic + Source Han Serif TC for APA 7.0 PDF (Markdown output works without either)
Plugin install (v3.7.0+, recommended):
/plugin marketplace add Imbad0202/academic-research-skills
/plugin install academic-research-skills
Verify it works: run /ars-plan and describe a paper you're working on — ARS will start a Socratic dialogue to map out chapter structure. For a single-shot test instead, try /ars-lit-review "your topic".
👉 docs/SETUP.md — full guide: install Claude Code, set up API keys, optional Pandoc/tectonic for DOCX/PDF, cross-model verification (ARS_CROSS_MODEL), and five installation methods (Plugin, project skills, global skills, claude.ai Project, repo-cloned).
Performance & cost
👉 docs/PERFORMANCE.md — per-mode token budgets, full-pipeline estimate (~$4–6 for a 15k-word paper), and recommended Claude Code settings (Skip Permissions; Agent Team optional).
Guides & articles
- Academic Writing Shouldn't Be a Solo Act — full pipeline walkthrough (English)
- 學術寫作不該是一個人的事：一套開源 AI 協作工具如何改變研究者的工作流 — 完整使用指南（繁體中文）
Features at a glance
- Deep Research — 13-agent research team with Socratic guided mode, PRISMA systematic review, intent detection, dialogue health monitoring, optional cross-model DA, Semantic Scholar API verification.
- Academic Paper — 12-agent paper writing with Style Calibration, Writing Quality Check, LaTeX hardening, visualization, revision coaching, citation conversion, anti-leakage protocol, and VLM figure verification.
- Academic Paper Reviewer — 7-agent multi-perspective peer review with 0–100 quality rubrics (EIC + 3 dynamic reviewers + Devil's Advocate), concession threshold protocol, attack intensity preservation, optional cross-model DA critique / calibration, R&R traceability matrix, read-only constraint.
- Academic Pipeline — 10-stage pipeline orchestrator with adaptive checkpoints, claim verification, Material Passport, optional
repro_lock, optional cross-model integrity verification, mid-conversation reinforcement, and score trajectory tracking. - Data Access Level Metadata (v3.3.2+) — every skill declares
data_access_level(raw/redacted/verified_only); enforced byscripts/check_data_access_level.py. Pattern adapted from Anthropic's automated-w2s-researcher (2026). Seeshared/ground_truth_isolation_pattern.md. - Task Type Annotation (v3.3.2+) — every skill declares
task_type(open-endedoroutcome-gradable). All current ARS skills areopen-ended. - Benchmark Report Schema (v3.3.5+) — JSON Schema + lint for honest benchmark comparisons. See
shared/benchmark_report_pattern.md. - Artifact Reproducibility Lockfile (v3.3.5+) — optional
repro_locksub-block on Material Passport. Configuration documentation, not replay guarantee — LLM outputs are not byte-reproducible. Seeshared/artifact_reproducibility_pattern.md.
Showcase: real pipeline output
See the complete artifacts from a real 10-stage pipeline run — peer review reports, integrity verification reports, and the final paper:
Browse all pipeline artifacts →
| Artifact | Description |
|---|---|
| Final Paper (EN) | APA 7.0 formatted, LaTeX-compiled |
| Final Paper (ZH) | Chinese version, APA 7.0 |
| Integrity Report — Pre-Review | Stage 2.5: caught 15 fabricated refs + 3 statistical errors |
| Integrity Report — Final | Stage 4.5: zero regressions confirmed |
| Peer Review Round 1 | EIC + 3 Reviewers + Devil's Advocate |
| Re-Review | Verification after revisions |
| Peer Review Round 2 | Follow-up review |
| Response to Reviewers | Point-by-point author response |
| Post-Publication Audit Report | Independent full-reference audit: found 21/68 issues missed by 3 rounds of integrity checks |
Companion: Experiment Agent
If your research involves running experiments (code or human studies) before writing, the Experiment Agent skill fills the gap between ARS Stage 1 (RESEARCH) and Stage 2 (WRITE).
ARS Stage 1 RESEARCH → RQ Brief + Methodology Blueprint
↓
experiment-agent → run/manage experiments → validate results
↓
ARS Stage 2 WRITE → write paper with verified experiment results
What it does: executes code experiments (Python, R, etc.) with real-time monitoring, manages human study protocols with IRB ethics checklist, interprets statistics with 11-type fallacy detection, and verifies reproducibility.
How to use together: pause the ARS pipeline after Stage 1, run experiments in a separate experiment-agent session, then bring the results (with Material Passport) back to ARS Stage 2. ARS requires zero modification. See the experiment-agent README for setup instructions.
Usage
Quick Start
# Start a full research pipeline
You: "I want to write a research paper on AI's impact on higher education QA"
# Start with Socratic guidance
You: "Guide my research on AI in educational evaluation"
# Write a paper with guided planning
You: "Guide me through writing a paper on demographic decline"
# Review an existing paper
You: "Review this paper" (then provide the paper)
# Check pipeline status
You: "status"
Individual Skills
Deep Research (7 modes)
"Research the impact of AI on higher education" → full mode
"Give me a quick brief on X" → quick mode
"Do a systematic review on X with PRISMA" → systematic-review mode
"Guide my research on X" → socratic mode (guided)
"Fact-check these claims" → fact-check mode
"Do a literature review on X" → lit-review mode
"Review this paper's research quality" → review mode
Academic Paper (10 modes)
"Write a paper on X" → full mode
"Guide me through writing a paper" → plan mode (guided)
"Build a paper outline" → outline-only mode
"I have a draft, here are reviewer comments" → revision mode
"Parse these reviewer comments into a roadmap" → revision-coach mode
"Write an abstract for this paper" → abstract-only mode
"Turn this into a literature review paper" → lit-review mode
"Convert to LaTeX" / "Convert citations to IEEE" → format-convert mode
"Check citations" → citation-check mode
"Generate an AI disclosure statement for NeurIPS" → disclosure mode
Academic Paper Reviewer (6 modes)
"Review this paper" → full mode (EIC + R1/R2/R3 + Devil's Advocate)
"Quick assessment of this paper" → quick mode
"Guide me to improve this paper" → guided mode
"Check the methodology" → methodology-focus mode
"Verify the revisions" → re-review mode
"Calibrate this reviewer against my gold set" → calibration mode
Academic Pipeline (Orchestrator)
"I want to write a complete research paper" → full pipeline from Stage 1
"I already have a paper, review it" → mid-entry at Stage 2.5 (integrity first)
"I received reviewer comments" → mid-entry at Stage 4
Pipeline ends with Stage 6: Process Summary — auto-generates a paper creation process record with 6-dimension Collaboration Quality Evaluation (1–100 scoring).
Supported Languages
- Traditional Chinese (繁體中文) — default when user writes in Chinese
- English — default when user writes in English
- Bilingual abstracts (Chinese + English) for academic papers
Using a different language? Socratic mode (deep-research) and Plan mode (academic-paper) use intent-based activation — they detect the meaning of your request, not specific keywords. This means they work in any language without modification.
However, the general
Trigger Keywordssection (which determines whether the skill is activated at all) still lists English and Traditional Chinese keywords. If you find the skill isn't activating reliably in your language, you can add your language's keywords to the### Trigger Keywordssection in eachSKILL.mdfile to improve matching confidence.
Supported Citation Formats
- APA 7.0 (default, including Chinese citation rules)
- Chicago (Notes & Author-Date)
- MLA
- IEEE
- Vancouver
Supported Paper Structures
- IMRaD (empirical research)
- Thematic Literature Review
- Theoretical Analysis
- Case Study
- Policy Brief
- Conference Paper
Skill Details
Per-agent responsibilities and per-stage artifacts now live in docs/ARCHITECTURE.md. Version numbers are anchored here so release metadata stays in one place.
Deep Research (v2.8)
13-agent research team. Modes: full, quick, review, lit-review, fact-check, socratic, systematic-review. Full agent roster and artifacts: see ARCHITECTURE.md §3.
Academic Paper (v3.0)
12-agent paper writing pipeline. Modes: full, plan, outline-only, revision, revision-coach, abstract-only, lit-review, format-convert, citation-check, disclosure. Output: MD + DOCX (via Pandoc when available) + LaTeX (APA 7.0 apa7 class / IEEE / Chicago) → PDF via tectonic. Full agent roster and per-phase responsibilities: see ARCHITECTURE.md §3.
Academic Paper Reviewer (v1.8)
7-agent multi-perspective review with 0-100 quality rubrics. Modes: full, re-review, quick, methodology-focus, guided, calibration. Decision mapping: ≥80 Accept, 65-79 Minor Revision, 50-64 Major Revision, <50 Reject. First-round review team vs. narrow re-review team boundary: see ARCHITECTURE.md §3 Stage 3 / Stage 3'.
Academic Pipeline (v3.7)
10-stage orchestrator with integrity verification, two-stage review, Socratic coaching, and collaboration evaluation. Pipeline guarantees: every stage requires user confirmation checkpoint; integrity verification (Stage 2.5 + 4.5) cannot be skipped; R&R Traceability Matrix (Schema 11) independently verifies author revision claims. v3.4 added the Compliance Agent (PRISMA-trAIce + RAISE) at Stage 2.5 / 4.5. v3.5 adds the Collaboration Depth Observer (collaboration_depth_agent, advisory only — never blocks) at every FULL/SLIM checkpoint and at pipeline completion. MANDATORY integrity gates (2.5 / 4.5) explicitly skip the observer so compliance checks are not diluted. Based on Wang & Zhang (2026), IJETHE 23:11. Stage-by-stage matrix with agents, artifacts, and gates: see ARCHITECTURE.md §3.
v3.0 Optimizations: What We Discovered About AI's Structural Limits
What happened
While using ARS to write a reflection article about AI in higher education, I ran into three structural problems that no amount of prompt engineering could fix:
-
Frame-lock: I asked the AI to run a devil's advocate debate against its own thesis. It did — four rounds, each more refined than the last. But every round stayed inside the frame I'd set. The DA attacked arguments, never premises. It never asked "are we even discussing the right question?" This is the same pattern that caused the 31% citation error rate in v2.7's stress test: the verifying AI and the generating AI share the same cognitive frame.
-
Sycophancy under pushback: Every time I challenged the DA's attacks, it conceded too quickly. It retracted findings faster than it launched them. The model's training rewards conversational harmony — so "the user pushed back" was treated as evidence that the attack was wrong, when often it just meant the user was persistent.
-
Intent misdetection: The Socratic Mentor kept trying to converge and produce deliverables ("Want me to write this up?") when I was still exploring. It couldn't distinguish "the user wants a deep philosophical discussion" from "the user wants an RQ brief." Both look like engagement, but they need opposite AI behaviors.
What we changed (v3.0)
Devil's Advocate — Concession Threshold Protocol (deep-research + academic-paper-reviewer)
- DA must now score every rebuttal on a 1-5 scale before responding
- Concession only allowed at score ≥4 (rebuttal directly addresses core attack with evidence)
- Score ≤3: hold position and restate the original attack
- Anti-sycophancy rules: no consecutive concessions, concession rate tracking, frame-lock detection after each checkpoint
Socratic Mentor — Intent Detection Layer (deep-research)
- Classifies user intent as exploratory vs. goal-oriented at dialogue start and every 3 turns
- Exploratory mode: disables auto-convergence, raises max rounds to 60, prohibits "want me to summarize?" prompts
- Goal-oriented mode: standard convergence behavior
- Anti-premature-closure rules: in exploratory mode, the user decides when to stop
Socratic Mentor — Dialogue Health Indicator (deep-research)
- Silent self-assessment every 5 turns on three dimensions: persistent agreement, conflict avoidance, premature convergence
- Auto-injects challenging questions when agreement pattern detected
- Invisible to user (to prevent gaming), but log available for post-session review
Why this matters
These optimizations don't solve AI's structural limits — they make the limits visible and manageable. The DA will still eventually concede if pushed hard enough. The Socratic Mentor will still have some convergence bias. But now there are explicit checkpoints that slow down the sycophancy, force the DA to justify concessions, and prevent the Mentor from wrapping up before the user is ready.
The deeper lesson: AI literacy isn't about learning to use AI as a tool, following ethics rules, or fearing AI risks. It's about engaging AI deeply enough to discover its structural limits yourself — and your own thinking limits in the process.
License
This work is licensed under CC-BY-NC 4.0.
You are free to:
- Share — copy and redistribute the material
- Adapt — remix, transform, and build upon the material
Under the following terms:
- Attribution — You must give appropriate credit
- NonCommercial — You may not use the material for commercial purposes
Attribution format:
Based on Academic Research Skills by Cheng-I Wu
https://github.com/Imbad0202/academic-research-skills
Contributors
Cheng-I Wu (吳政宜) — Author and maintainer
aspi6246 — Contributor. The v3.1 optimization was inspired by patterns from Claude-Code-Skills-for-Academics: read-only constraint pattern, anti-pattern codification as first-class design, cognitive framework approach (teaching "how to think" not just procedures), and lean skill size philosophy.
mchesbro1 — Contributor. Originally proposed and drafted the IS Basket of 8 journals for academic-paper-reviewer/references/top_journals_by_field.md (Issue #5).
cloudenochcsis — Contributor. Extended the IS section from the Basket of 8 to the full Senior Scholars' Basket of 11 — adding Decision Support Systems, Information & Management, and Information and Organization (Issue #7, PR #8). Sourced from the AIS Senior Scholars' List of Premier Journals.
Changelog
v3.7.0 (2026-05-05) — Claude Code Plugin Packaging
Plugin packaging upgrade: ARS now installs in one line on Claude Code CLI / VS Code / JetBrains via
/plugin marketplace add Imbad0202/academic-research-skills+/plugin install academic-research-skills. The traditionalgit clone + symlink to ~/.claude/skills/flow continues to work — both tracks are first-class.
- Plugin manifest + marketplace metadata (Phase 1, PR #68).
.claude-plugin/plugin.jsondeclares the suite (4 skills auto-discovered fromskills/directory via relative symlinks)..claude-plugin/marketplace.jsonregisters the plugin so a single GitHub-hosted endpoint serves both the marketplace listing and the plugin source. README +README.zh-TW.md+docs/SETUP.mdcarry dual-track install instructions. - 10 slash commands at
commands/ars-*.md(Phase 2.1, PR #69) mappingMODE_REGISTRY.mdentries to/ars-<mode>triggers. Model routing is pinned in each command's frontmatter —opusforfullandrevision-coach(architectural / review-interpretation depth),sonnetfor the other 8. No Haiku per project policy. - 3 plugin-shipped agents at
agents/*_agent.md(Phase 2.1, PR #69) as relative symlinks to the v3.6.7-hardened downstream agents indeep-research/agents/:synthesis_agent,research_architect_agent,report_compiler_agent. Underscore filenames preserved to keepscripts/check_v3_6_7_pattern_protection.pyhard-pinned paths and INV-3 manifest-confined Clause 1 invariant intact. Symlinks (not copies) preserve a single source of truth and prevent the Pattern C3 attack surface that v3.6.7 §6 inversion sweep + INV-1/2/3 lint closes. model: inheritadded to those three source agent frontmatters. Inherit chosen over pinningsonnetso an opus session running ARS full pipeline keeps opus agents (instead of being capped). The user's~/.claude/hooks/warn-agent-no-model.shPreToolUse hook gates Haiku at the dispatching boundary, soinheritresolves through an already-Haiku-free model.- SessionStart announce hook at
hooks/hooks.json+scripts/announce-ars-loaded.sh(Phase 2.2, PR #70). When the plugin loads, the hook injects anadditionalContextlisting the 10 slash commands, the 3 plugin agents, and a token-budget pointer into the LLM's first turn.startupandclearsource values get the full announce;resumeandcompactget a one-line ack to avoid burning context. Bash 3.2 compatible — runs on macOS stock/bin/bashwith nobrew install bashrequirement. - Phase 2.2 scope reduction: a
SubagentStop → run_codex_audit.shcodex audit hook was scoped out for v3.7.0 due to a contract gap (the SubagentStop payload carries no stage/deliverable info, so the wrapper would have to half-infer required arguments) and an invoker-class boundary (run_codex_audit.shlines 4–7 forbid same-session in-LLM invocation; PostToolUse fires inside the producing session). Real audit-hook integration deferred to a future release when ARS gains a stage/deliverable propagation contract. Seedocs/design/2026-04-30-ars-v3.7.0-plugin-packaging-roadmap.mdUpdate note 2026-05-05 (Phase 2.2 scope reduction). docs/PERFORMANCE.md+.zh-TW.mdgain a "v3.7.0 Plugin agents and model routing" subsection explaining the inherit semantics and current 3-agent scope boundary.- Codex review chain across the three PRs: 8 inline iterative rounds + 3 fresh PR-level rounds, all converging to 0 P0/P1/P2 findings before merge. The Phase 2.2 fresh PR review caught one P2 (unquoted
${CLAUDE_PLUGIN_ROOT}breaking install paths with spaces) that the inline rounds missed — confirms the value of separating implementation review (inline) from contract review (fresh). - What did NOT change: the four skill directories, all 25 modes, agent prompts, schema files, and lint contracts. Plugin packaging only adds new top-level surface (
commands/,agents/,hooks/,.claude-plugin/,skills/symlink dir, three plugin-agentmodel: inheritfrontmatter additions). Existing 4.3k clone-install users see no breaking change.
v3.6.8 (2026-05-03) — Generator-Evaluator Contract Gate (v3.6.6 spec ship)
Naming note: this release ships the v3.6.6 generator-evaluator contract spec and implementation. The v3.6.6 work landed after v3.6.7 due to project sequencing; the design doc retains the v3.6.6 internal naming for the contract gate version, while the suite release is tagged v3.6.8 to keep the CHANGELOG monotonic.
- Schema 13.1 (
shared/sprint_contract.schema.json) extends Schema 13 with two newmodeenum values (writer_full+evaluator_full), two new optional top-level fields (pre_commitment_artifactswriter-only,disagreement_handlingevaluator-only), and 12allOfbranches enforcing reviewer- / writer- / evaluator-conditional gates. Existing reviewer contracts validate byte-equivalent under Schema 13.1 (§3.6 zero-touch promise). - Two new shipped contract templates under
shared/contracts/writer/full.json(D1–D7, F1/F4/F2/F3/F0) andshared/contracts/evaluator/full.json(D1–D5, F1/F2/F3/F6/F4/F5/F0). Promoted from design-time artefacts on the spec branch to live shipped status atomically with the Schema 13.1 upgrade. - Two-phase orchestration inside
academic-paper full: Phase 4 splits into Phase 4a (writer paper-blind pre-commitment) + Phase 4b (writer paper-visible drafting + self-scoring); Phase 6 splits into Phase 6a (evaluator paper-blind pre-commitment) + Phase 6b (evaluator paper-visible scoring + decision). Phase-numbered<phase4a_output>/<phase6a_output>data delimiters mirror the v3.6.2 reviewer pattern. Lint count summary: writer 3+4 / evaluator 5+5 / reviewer 5+6 (reviewer remains zero-touch). academic-paperSKILL + agent files gain a verbatim## v3.6.6 Generator-Evaluator Contract Protocolblock (101 lines in SKILL.md plus 47 lines indraft_writer_agent.md+ 57 lines inpeer_reviewer_agent.md). SKILL.md also adds a new## Known limitationssection carrying graceful-degradation + cross-session resume forward notes for v3.6.7+.- Validator extensions:
scripts/check_sprint_contract.pySC-* mode-gating audit (SC-5 + SC-11 reviewer-only; SC-9 extended across all three mode families). 17 new tests bring the validator unit-test count from 54 to 71 (positive + 5 schema-branch negative + 2 §3.6 reviewer regression + 6 mode-gating tests). - Manifest CI lint:
scripts/check_v3_6_6_ab_manifest.pyenforces §6.2 manifest schema + §6.5 git-tracked invariants ontests/fixtures/v3.6.6-ab/manifest.yaml..github/workflows/spec-consistency.ymlextends the sprint contract validation loop to iterate writer + evaluator template directories alongside the existing reviewer loop, plus runs the new manifest CI lint. - A/B evidence fixture stub at
tests/fixtures/v3.6.6-ab/(30 files): manifest + README + 6 paper-A inputs/baseline + 1 paper-C inputs/baseline + Stage 3 reviewer excerpt + 6 codex-judge baseline placeholders. Real fixture data populates in follow-up commits before the implementation work fully completes.
v3.6.7 (2026-04-30) — Downstream-Agent Pattern Protection (Step 1+2)
- Three downstream agents hardened against 13 of 18 documented hallucination/drift patterns:
synthesis_agent(A1–A5 narrative-side), the survey-designer mode ofresearch_architect_agent(B1–B5 instrument-side), and the abstract-only mode ofreport_compiler_agent(C1–C3 publication-side). Each agent prompt now carries aPATTERN PROTECTION (v3.6.7)block. - Four reference files in
shared/references/:irb_terminology_glossary.md,psychometric_terminology_glossary.md,protected_hedging_phrases.md,word_count_conventions.md. The reference files carry operational contracts that the agent prompts cite by path. - Cross-model audit prompt template at
shared/templates/codex_audit_multifile_template.mdwith seven audit dimensions and a mandatory three-part Section 4(f) check forreport_compiler_agentbundles. Failure of any sub-check is a P1 finding. - Static lint + 29-test mutation suite:
scripts/check_v3_6_7_pattern_protection.pyenforces protection-clause presence and obligation-phrase shape;scripts/test_check_v3_6_7_pattern_protection.pypreserves codex review evidence so future checker regressions surface in CI. Both are wired into.github/workflows/spec-consistency.yml. - Codex review history: seven rounds of
gpt-5.5+xhighcross-model review reached SHIP-OK with zero P1+P2 findings. Step 6 (orchestrator runtime hooks) and Step 8 (synthetic eval case) ship in a follow-up PR.
v3.6.5 (2026-04-27) — Material Passport literature_corpus[] Consumer Integration
- Two Phase 1 literature consumers wired:
deep-research/agents/bibliography_agent.mdandacademic-paper/agents/literature_strategist_agent.md. Both follow the same five-step corpus-first, search-fills-gap flow when the passport carries a non-emptyliterature_corpus[]and the same four Iron Rules (Same criteria / No silent skip / No corpus mutation / Graceful fallback on parse failure). - PRE-SCREENED reproducibility block in Search Strategy reports: enumerates included / excluded / skipped corpus entries, with F3 zero-hit note and F4a–F4f provenance reporting that compose around partial declaration of
obtained_via/obtained_at.final_included = pre_screened_included[] ∪ external_included[]stays neutral — no provenance tags on bibliography entries or literature matrix rows. - Consumer protocol reference at
academic-pipeline/references/literature_corpus_consumers.mdwith the canonical PRE-SCREENED template, BAD/GOOD examples, four Iron Rules, and per-consumer reading instructions. - CI lint
scripts/check_corpus_consumer_protocol.pyenforcing nine protocol invariants with manifest-driven consumer list (scripts/corpus_consumer_manifest.json). - Schema 9 caveat retired:
shared/handoff_schemas.mdretired the v3.6.4 "Consumer-side integration deferred to v3.6.5+" caveat; replaced with backpointer to the consumer protocol. - Presence-based, no schema change, no new env flag. Parse failures fall back to external-DB-only flow with a
[CORPUS PARSE FAILURE]surface.citation_compliance_agentcorpus integration deferred to v3.6.6+. - No breaking changes. Existing user adapters work without modification.
v3.6.4 (2026-04-25) — Material Passport literature_corpus[] Input Port
literature_corpus[]field added to Schema 9 as an optional input port for user-owned literature. Each entry conforms toshared/contracts/passport/literature_corpus_entry.schema.json(CSL-JSON authors, year, title, source_pointer + private optionalabstract/user_notes).- Language-neutral adapter contract at
academic-pipeline/references/adapters/overview.md: any program (any language) reading a user corpus source can produce conformantpassport.yaml+rejection_log.yaml. Fail-soft entry-level errors, fail-loud adapter-level errors, deterministic ordering. - Three reference Python adapters under
scripts/adapters/:folder_scan.py(filesystem of PDFs),zotero.py(Better BibTeX JSON export),obsidian.py(vault frontmatter). Starting points only; users are expected to write their own adapters for non-reference sources. - Rejection log contract at
shared/contracts/passport/rejection_log.schema.jsonwith closed enum of categorical reason values; always emitted (empty when no rejections). - CI gates:
scripts/check_literature_corpus_schema.pyvalidates schemas + adapter examples;scripts/sync_adapter_docs.py --checkprevents schema→docs drift; newpytest.ymlworkflow runsscripts/adapters/tests/on path-filtered triggers. - Input-port-only at v3.6.4: v3.6.4 shipped the schema and adapter contract without consumer integration.
bibliography_agentandliterature_strategist_agentwere wired in v3.6.5. - No breaking changes.
v3.6.3 (2026-04-23) — Opt-in Passport Reset Boundary
- Opt-in passport reset boundary (
ARS_PASSPORT_RESET=1). Promotes every FULL checkpoint to a context-reset boundary. Newresume_from_passport=<hash>mode lets users resume in a fresh Claude Code session from the Material Passport ledger alone.systematic-reviewmode with the flag ON makes reset mandatory at every FULL checkpoint; other modes treat reset as the flag-gated default. Flag OFF preserves pre-v3.6.3 behavior byte-for-byte. - Schema 9 gains an append-only
reset_boundary[]ledger with two entry kinds (kind: boundary+kind: resume). Hash uses JSON Canonical Form + SHA-256 with canonical placeholder for self-reference safety. Optionalpending_decisionhandles MANDATORY branch choices. - New
scripts/check_passport_reset_contract.pyCI lint: every mention of the flag must co-locate a pointer to the authoritative protocol doc. - Protocol doc:
academic-pipeline/references/passport_as_reset_boundary.md. docs/PERFORMANCE.mdupdated with long-running-session guidance.- No breaking changes. Flag default is OFF.
v3.6.2 (2026-04-23) — Reviewer Sprint Contract Hard Gate
v3.6.2 introduces Schema 13 sprint contracts and a hard-gate orchestration that forces reviewers to pre-commit their scoring plan before reading the paper. Reviewer-only first test case; writer/evaluator deferred to v3.6.4. See CHANGELOG.
- Schema 13 sprint contract with
panel_size,acceptance_dimensions,failure_conditions(withseverityprecedence + panel-relativecross_reviewer_quantifier),measurement_procedure, optionaloverride_ladder, boundedagent_amendments. Validator:scripts/check_sprint_contract.py. - Two-call hard gate. Reviewers run paper-content-blind Phase 1 + paper-visible Phase 2; Phase 1 output is wrapped in
<phase1_output>...</phase1_output>data delimiter to narrow the self-injection surface. - Synthesizer three-step mechanical protocol. Build cross-reviewer matrix → evaluate each
failure_conditionwith panel-relative quantifier + recognised expression vocabulary → resolve precedence byseverity. Forbidden-ops list explicit ineditorial_synthesizer_agent. - Two reviewer templates ship (
shared/contracts/reviewer/full.jsonpanel 5;shared/contracts/reviewer/methodology_focus.jsonpanel 2).reviewer_re_review,reviewer_calibration,reviewer_guidedare reserved in the schema enum but ship without contract templates in v3.6.2; they retain pre-v3.6.2 behaviour.reviewer_quickis excluded from the enum entirely. academic-paper-reviewerSKILL version:1.8.1 → 1.9.0.academic-pipelineSKILL version:3.5.1 → 3.6.2(suite-version invariant). Suite version bumped to3.6.2.- See spec
docs/design/2026-04-23-ars-v3.6.2-sprint-contract-design.mdand protocolacademic-paper-reviewer/references/sprint_contract_protocol.md.
v3.5.1 (2026-04-22) — Opt-in Socratic Reading-Check Probe
v3.5.1 adds an opt-in honesty probe to the Socratic Mentor (ARS_SOCRATIC_READING_PROBE=1). Default off. See CHANGELOG.
- Opt-in reading-check probe: when
ARS_SOCRATIC_READING_PROBE=1is set, the Socratic Mentor fires a one-time honesty probe during goal-oriented sessions where the user has cited a specific paper. Decline is logged without penalty. Outcome flows into the Research Plan Summary and Stage 6 AI Self-Reflection Report. No new agent, no schema change. deep-researchSKILL version:2.9.0 → 2.9.1.academic-pipelineSKILL version:3.5.0 → 3.5.1. Suite version bumped to3.5.1.
v3.5.0 (2026-04-21) — Collaboration Depth Observer
- New agent:
collaboration_depth_agentinacademic-pipeline(Agent Team grows from 3 to 4). Invoked at every FULL/SLIM checkpoint and at pipeline completion; scores user-AI collaboration against a 4-dimension rubric. Advisory only — never blocks progression. MANDATORY checkpoints (Stages 2.5 / 4.5 integrity gates) do NOT invoke the observer. - New rubric:
shared/collaboration_depth_rubric.mdv1.0. Dimensions: Delegation Intensity, Cognitive Vigilance, Cognitive Reallocation, Zone Classification (Zone 1 / Zone 2 / Zone 3). Based on Wang, S., & Zhang, H. (2026). "Pedagogical partnerships with generative AI in higher education: how dual cognitive pathways paradoxically enable transformative learning." International Journal of Educational Technology in Higher Education, 23:11. DOI 10.1186/s41239-026-00585-x. - Cross-model divergence flagged, not averaged: when
ARS_CROSS_MODELis set the observer runs on both models; dimension disagreement > 2 points is reported rather than silently smoothed.ARS_CROSS_MODEL_SAMPLE_INTERVALescape hatch for cost trade-off. - Short-stage guard: stages with fewer than 5 user turns inject a static
insufficient_evidenceblock instead of dispatching the full-model observer. - Anti-sycophancy discipline: scores ≥ 7 require specific dialogue-turn citations; Zone 3 triggers re-audit; no motivational framing.
academic-pipelineSKILL version:3.3.0 → 3.4.0. Suite version bumped to3.5.0. New lintscripts/check_collaboration_depth_rubric.py+ 10 tests.
v3.4.0 (2026-04-20) — Compliance Agent + Schema 12
- Compliance Agent (shared): single mode-aware agent running PRISMA-trAIce 17 items (SR mode only) + RAISE 4 principles + 8-role matrix. Hooks existing Stage 2.5 / 4.5 Integrity Gates; tier-based block (Mandatory → block, HR → warn, R/O → info). Non-SR entries run principles-only, warn-only.
- Schema 12 compliance_report appended to Material Passport via
compliance_history[](append-only). - 3-round user-override ladder auto-injects
disclosure_addenduminto manuscript. No detection evasion possible. - Calibration with transparent reporting, no hard FNR/FPR gate — self-consistent with
task_type: open-ended. - Upstream freshness CI warns on PRISMA-trAIce drift (non-blocking).
- Long-running session docs: Material Passport as cross-session resume mechanism.
v3.3.6 (2026-04-15) — README Streamlining + ARCHITECTURE doc
- Added
docs/ARCHITECTURE.mdas the single source of truth for pipeline structure (flow, matrix, data-access, dependency graph, quality gates, modes). Merged into main via PR #18. - Added
docs/SETUP.md(prerequisites, API keys, Pandoc/tectonic, cross-model verification, installation methods) anddocs/PERFORMANCE.md(token budgets, recommended Claude Code settings). README links to both instead of inlining them. - Streamlined README: removed the ASCII pipeline diagram and 16-point key-feature list (superseded by ARCHITECTURE.md); Skill Details section now anchors version numbers and points readers to ARCHITECTURE.md §3 for per-agent rosters.
- Note: no functional change to any skill. Pure documentation reorganization. Suite version bumped to
3.3.6.
v3.3.5 (2026-04-15)
- Added
benchmark_report.schema.json+repro_lockoptional block on Material Passport. Both ship with pattern docs, lints, and examples. First formal Python dev dep manifest (requirements-dev.txt).
v3.3.4 (2026-04-15) — README Changelog Sync Patch
- Synced the embedded changelog sections in
README.mdandREADME.zh-TW.mdso they include the missingv3.3.3andv3.3.2release summaries. - Extended
scripts/check_spec_consistency.pyso future README changelog drift fails CI.
v3.3.3 (2026-04-15) — Release Prep + Lint Hardening
- Hardened SKILL frontmatter linting: missing closing
---fences now fail cleanly instead of being parsed as valid YAML. - Frontmatter that parses as valid YAML but not as a mapping now reports a readable error instead of crashing.
- Fixed the broken showcase link for the post-publication audit report in both READMEs.
- Added README relative-link validation to the spec consistency check so dead links fail CI.
- Aligned the DOCX output contract across the docs: direct
.docxgeneration is Pandoc-dependent, with Markdown + conversion instructions as fallback. - Prepared the
v3.3.3release: suite version bump,academic-paper-> v3.0.2,academic-pipeline-> v3.2.2.
v3.3.2 (2026-04-15) — Data Access Levels + Task Type Metadata
- Added
metadata.data_access_levelto all top-levelSKILL.mdfiles with enforced vocabulary:raw,redacted,verified_only. - Added
metadata.task_typeto all top-levelSKILL.mdfiles with enforced vocabulary:open-ended,outcome-gradable. - Added lint scripts and unit tests for both metadata fields, wired into the GitHub Actions spec consistency workflow.
- Added
shared/ground_truth_isolation_pattern.mdand linked the new vocabulary fromshared/handoff_schemas.md.
v3.3.1 (2026-04-14) — Spec Consistency Patch
- Synced README,
.claude/CLAUDE.md,MODE_REGISTRY.md, andSKILL.mdfiles to the current mode counts and published skill versions. - Corrected cross-model wording: integrity sample checks and independent DA critique are implemented today; sixth-reviewer peer review remains planned.
- Clarified adaptive checkpoint semantics so SLIM checkpoints still wait for explicit user confirmation.
- Reaffirmed that Stage 2.5 and Stage 4.5 integrity gates cannot be skipped.
- Added a lightweight spec consistency check and GitHub Actions workflow to catch future drift.
v3.3 (2026-04-09) — PaperOrchestra-Inspired Enhancements
Integrates techniques from PaperOrchestra (Song, Song, Pfister & Yoon, 2026, Google).
- Semantic Scholar API Verification — Tier 0 programmatic reference existence check via S2 API. Levenshtein >= 0.70 title matching, DOI mismatch detection, bibliography deduplication via S2 IDs. Graceful degradation if API unavailable.
- Anti-Leakage Protocol — Knowledge Isolation Directive prioritizes session materials over LLM parametric memory. Flags
[MATERIAL GAP]for missing content instead of filling from memory. Reduces Mode 5/6 failure risk. - VLM Figure Verification (optional) — Closed-loop verification of rendered figures using vision-capable LLM. 10-point checklist, max 2 refinement iterations.
- Score Trajectory Protocol — Per-dimension rubric score delta tracking across revision rounds (7 dimensions). Detects regressions (delta < -3) and triggers mandatory checkpoint.
- Stage 2 Parallelization — Visualization and argument building can run in parallel after outline completion.
- New versions: deep-research v2.8, academic-paper v3.0, academic-pipeline v3.2
v3.2 (2026-04-09) — Lu 2026 Nature Integration
Integrates insights from Lu et al. (2026, Nature 651:914-919) — the first end-to-end autonomous AI research system to pass blind peer review.
- 7-mode AI Research Failure Mode Checklist — blocks pipeline at Stage 2.5/4.5 on suspected implementation bugs, hallucinated results, shortcut reliance, bug-as-insight, methodology fabrication, frame-lock. Extends existing 5-type citation hallucination taxonomy.
- Reviewer Calibration Mode (academic-paper-reviewer v1.8) — opt-in FNR/FPR/balanced-accuracy measurement against user-supplied gold set. 5× ensembling, cross-model default-on, session-scoped confidence disclosure.
- Disclosure Mode (academic-paper v2.9) — venue-specific AI-usage statement generator. v1 covers ICLR, NeurIPS, Nature, Science, ACL, EMNLP.
- Early-Stopping Criterion (academic-pipeline v3.1) — convergence check + budget transparency at pipeline start.
- Fidelity-Originality Mode Spectrum — classifies all modes across 3 skills per Lu 2026 Fig 1c.
- New versions: academic-paper v2.9, academic-paper-reviewer v1.8, academic-pipeline v3.1
v3.1.1 (2026-04-09) — IS Senior Scholars' Basket of 11
External contributions: @mchesbro1 originally proposed and drafted the IS Basket of 8 journals (Issue #5); @cloudenochcsis extended it to the full Senior Scholars' Basket of 11 (Issue #7, PR #8). Updated academic-paper-reviewer/references/top_journals_by_field.md Section 7, adding Decision Support Systems, Information & Management, and Information and Organization. Source: AIS Senior Scholars' List of Premier Journals.
v3.1 (2026-04-06) — Anti-Context-Rot + Cognitive Frameworks + Lean Size
Inspired by patterns from aspi6246/Claude-Code-Skills-for-Academics.
Wave 1: Anti-Context-Rot Anchors
- 29 explicit Anti-Patterns across all 4 skills (7-8 per skill, tabular format with "Why It Fails" + "Correct Behavior")
- 22 IRON RULE markers on critical rules that must not be violated even in long conversations
- Read-only constraint on academic-paper-reviewer (reviewers cannot modify the manuscript)
Wave 2: Traceability + Cognitive Frameworks + Reinforcement
- R&R Traceability Matrix (Schema 11): adds "Author's Claim" and "Verified?" columns to re-review output, enabling independent verification of revision claims
- 3 cognitive framework reference files teaching agents "how to think" not just "what to do":
argumentation_reasoning_framework.md— Toulmin model, Bradford Hill causal reasoning, inference to best explanation, epistemic status classificationreview_quality_thinking.md— three lenses (internal validity, external validity, contribution), common reviewer traps, calibration questionswriting_judgment_framework.md— clarity test, reader's journey, discipline-specific voice, revision decision matrix
- Mid-conversation reinforcement protocol: stage-specific IRON RULE + Anti-Pattern reminders at every pipeline transition
- Self-check questions at every FULL checkpoint (citation integrity, sycophantic concession, quality trajectory, scope discipline, completeness)
Wave 3: Lean Skill Size
- SKILL.md total size reduced from 142KB to 85KB (−40%) by extracting detailed protocols to
references/files - ~15 new reference files created (re-review protocol, guided mode, systematic review, process summary, external review, etc.)
- All IRON RULE markers preserved in SKILL.md; detailed content loaded on demand
- New versions: deep-research v2.7, academic-paper v2.8, academic-paper-reviewer v1.7, academic-pipeline v3.0
v3.0 (2026-04-03) — Anti-Sycophancy + Intent Detection + Dialogue Health
- Devil's Advocate Concession Threshold (deep-research + academic-paper-reviewer): DA must score rebuttals 1-5 before responding. Concession only at ≥4. No consecutive concessions. Concession rate tracking. Frame-lock detection after each checkpoint.
- Attack Intensity Preservation (academic-paper-reviewer): DA does not soften under pushback. Rebuttal assessment protocol with explicit deflection detection. Anti-sycophancy rules prevent persistent pushback from being treated as valid evidence.
- Intent Detection Layer (deep-research socratic): Classifies user intent as exploratory vs. goal-oriented. Exploratory mode disables auto-convergence, raises max rounds, prohibits premature closure. Re-assesses every 3 turns.
- Dialogue Health Indicator (deep-research socratic): Silent self-check every 5 turns for persistent agreement, conflict avoidance, premature convergence. Auto-injects challenges when agreement pattern detected.
- Cross-Model Verification Protocol (shared, optional): Use GPT-5.4 Pro or Gemini 3.1 Pro for integrity verification sample cross-checks and independent DA critique. Sixth-reviewer peer review remains planned, not yet implemented. Activated by setting
ARS_CROSS_MODELenv var — without it, everything works as before. Seeshared/cross_model_verification.mdfor full setup guide, API patterns, and cost estimates. - AI Self-Reflection Report (academic-pipeline Stage 6): Post-pipeline self-assessment of AI behavioral patterns — DA concession rate, checkpoint skip rate, health alerts, sycophancy risk rating (LOW/MEDIUM/HIGH), frame-lock incidents, convergence pattern analysis. Includes irony caveat: "this self-reflection is itself produced by the same AI that may have been sycophantic."
- Origin: Discovered through a 4-round dialectic experiment where the DA conceded too quickly, the Socratic Mentor tried to converge prematurely, and the entire debate stayed locked in a frame the human set.
- Versions: deep-research v2.5, academic-paper-reviewer v1.5, academic-pipeline v2.8
v2.9 (2026-03-27) — Style Calibration + Writing Quality Check
- Style Calibration (academic-paper intake Step 10, optional): Provide 3+ past papers and the pipeline learns your writing voice — sentence rhythm, vocabulary preferences, citation integration style. Applied as a soft guide during drafting; discipline conventions always take priority. Priority system: discipline norms (hard) > journal conventions (strong) > personal style (soft). See
shared/style_calibration_protocol.md - Writing Quality Check (
academic-paper/references/writing_quality_check.md): Writing quality checklist applied during draft self-review. 5 categories: AI high-frequency term warnings (25 terms), punctuation pattern control (em dash ≤3), throat-clearing opener detection, structural pattern warnings (Rule of Three, uniform paragraphs, synonym cycling), and burstiness checks (sentence length variation). These are good writing rules — not detection evasion - Style Profile carried through academic-pipeline Material Passport (Schema 10 in
shared/handoff_schemas.md) - deep-research report compiler also consumes both features optionally
- Versions: academic-paper v2.5, deep-research v2.4, academic-pipeline v2.7
v2.8 (2026-03-22) — SCR Loop Phase 1: State-Challenge-Reflect
- Socratic Mentor Agent (deep-research + academic-paper): SCR (State-Challenge-Reflect) protocol integration
- Commitment Gates: Collect user predictions before presenting evidence at each layer/chapter transition
- Certainty-Triggered Contradiction: Detect high-confidence language ("obviously", "clearly") and introduce counterpoints
- Adaptive Intensity: Track commitment accuracy, dynamically adjust challenge frequency
- Self-Calibration Signal (S5): New convergence signal tracking user's self-calibration growth across dialogue
- SCR Switch: Users can say "skip the predictions" to disable or "turn predictions back on" to re-enable mid-dialogue; Socratic questioning continues normally
deep-research/references/socratic_questioning_framework.md: SCR Overlay Protocol mapping SCR phases to Socratic functions- Added
CHANGELOG.md
v2.7 (2026-03-09) — Integrity Verification v2.0: Anti-Hallucination Overhaul
- integrity_verification_agent v2.0: Anti-Hallucination Mandate (no AI memory verification), eliminated gray-zone classifications (VERIFIED/NOT_FOUND/MISMATCH only), mandatory WebSearch audit trail for every reference, Stage 4.5 fresh independent verification, Gray-Zone Prevention Rule
- Known Hallucination Patterns: 5-type taxonomy (TF/PAC/IH/PH/SH) from GPTZero × NeurIPS 2025 study, 5 compound deception patterns, real-world case study, literature statistics
- Post-publication audit: Full WebSearch verification of all 68 references found 21 issues (31% error rate) that passed 3 rounds of integrity checks — proving the necessity of external verification
- Paper corrections: Removed 4 fabricated references, fixed 6 author errors, corrected 7 metadata errors, fixed 2 format issues
v2.6.2 (2026-03-09) — Intent-Based Mode Activation
- deep-research: Socratic mode now uses intent-based activation instead of keyword matching. Works in any language — detects meaning (e.g., "user wants guided thinking") rather than matching specific strings.
- academic-paper: Plan mode now uses intent-based activation. Detects intent signals like "user is uncertain how to start" or "user wants step-by-step guidance" in any language.
- Both modes now have a default rule: when intent is ambiguous, prefer
socratic/planoverfull— safer to guide first. - Two-layer architecture: Layer 1 (skill activation) uses bilingual keywords for matching confidence; Layer 2 (mode routing) uses language-agnostic intent signals.
v2.6.1 (2026-03-09) — Bilingual Trigger Keywords
- deep-research: Added Traditional Chinese trigger keywords for general activation and Socratic mode.
- academic-paper: Added Traditional Chinese trigger keywords and Plan Mode trigger section.
- Both mode selection guides now include bilingual examples and Chinese-specific misselection scenarios.
v2.6 / v2.4 / v1.4 (2026-03-08) — 15+ Improvements
- deep-research v2.3: New systematic-review / PRISMA mode (7th); 3 new agents (risk_of_bias, meta_analysis, monitoring); PRISMA protocol/report templates; Socratic convergence criteria (4 signals + auto-end); Quick Mode Selection Guide
- academic-paper v2.4: 2 new agents (visualization, revision_coach); revision tracking template with 4 status types; citation format conversion (APA↔Chicago↔MLA↔IEEE↔Vancouver); statistical visualization standards; Socratic convergence criteria; revision recovery example; LaTeX output hardening — mandatory
apa7document class, text justification fix (ragged2e+etoolbox), table column width formula, bilingual abstract centering, standardized font stack (Times New Roman + Source Han Serif TC VF + Courier New), PDF via tectonic only - academic-paper-reviewer v1.4: Quality rubrics with 0-100 scoring and behavioral indicators; decision mapping (≥80 Accept, 65-79 Minor, 50-64 Major, <50 Reject); Quick Mode Selection Guide
- academic-pipeline v2.6: Adaptive checkpoint system (FULL/SLIM/MANDATORY); Phase E Claim Verification in integrity checks; Material Passport for mid-entry provenance; cross-skill mode advisor (14 scenarios); team collaboration protocol; enhanced handoff schemas (9 schemas); integrity failure recovery example
v2.4 / v1.3 (2026-03-08)
- academic-pipeline v2.4: New Stage 6 PROCESS SUMMARY — auto-generates structured paper creation process record (MD → LaTeX → PDF, bilingual); mandatory final chapter: Collaboration Quality Evaluation with 6 dimensions scored 1–100 (Direction Setting, Intellectual Contribution, Quality Gatekeeping, Iteration Discipline, Delegation Efficiency, Meta-Learning), honest feedback, and improvement recommendations; pipeline expanded from 9 to 10 stages
v2.3 / v1.3 (2026-03-08)
- academic-pipeline v2.3: Stage 5 FINALIZE now prompts for formatting style (APA 7.0 / Chicago / IEEE); PDF must compile from LaTeX via
tectonic(no HTML-to-PDF); APA 7.0 usesapa7document class (manmode) with XeCJK for bilingual CJK support; font stack: Times New Roman + Source Han Serif TC VF + Courier New
v2.2 / v1.3 (2025-03-05)
- Cross-Agent Quality Alignment: unified definitions (peer-reviewed, currency rule, CRITICAL severity, source tier) across all agents
- deep-research v2.2: synthesis anti-patterns, Socratic auto-end conditions, DOI+WebSearch verification, enhanced ethics integrity check, mode transition matrix
- academic-paper v2.2: 4-level argument scoring, plagiarism screening, 2 new failure paths (F11 Desk-Reject Recovery, F12 Conference-to-Journal), Plan→Full mode conversion
- academic-paper-reviewer v1.3: DA vs R3 role boundaries, CRITICAL finding criteria, consensus classification (4/3/SPLIT/DA-CRITICAL), confidence score weighting, Asian & Regional Journals reference
- academic-pipeline v2.2: checkpoint confirmation semantics, mode switching matrix, failure fallback matrix, state ownership protocol, material version control
v2.0.1 (2026-03)
- Simplify 4 SKILL.md (-371 lines, -16.5%): remove cross-skill duplication, inline templates → file references, redundant routing tables, duplicate mode selection sections
- Fix revision loop cap contradiction between academic-paper and academic-pipeline
v2.0 (2026-02)
- academic-pipeline v2.0: 5→9 stages, mandatory integrity verification, two-stage review, Socratic revision coaching, reproducibility guarantees
- academic-paper-reviewer v1.1: +Devil's Advocate Reviewer (7th agent), +re-review mode (verification), +post-review Socratic coaching
- New agent:
integrity_verification_agent— 100% reference/data verification with audit trail - New agent:
devils_advocate_reviewer_agent— 8-dimension thesis challenger - Output order: MD → DOCX via Pandoc when available (else instructions) → ask LaTeX → confirm → PDF
v1.0 (2026-02)
- Initial release
- deep-research v2.0 (10 agents, 6 modes including socratic)
- academic-paper v2.0 (10 agents, 8 modes including plan)
- academic-paper-reviewer v1.0 (6 agents, 4 modes including guided)
- academic-pipeline v1.0 (orchestrator)