Academic Paper

---
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: "3.1.2"
  last_updated: "2026-05-18"
  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.

> **Routing discipline (v3.9.2):** see `.claude/CLAUDE.md` "Routing Discipline (v3.9.2)" + `shared/references/intent_clarification_protocol.md` for cross-skill routing rules. This skill assumes routing has already settled — ambiguous cross-phase materials should have been clarified upstream.

## Quick Start

**Minimal command:**
```
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`.

## Phase-by-phase Invocation Contract (v3.9.2)

academic-paper pipeline runs in 8 phases (Phase 0 intake → 7 formatting). Two invocation modes:

**Mode A — orchestrator-driven (default):** `pipeline_orchestrator_agent` (in `academic-pipeline` skill) runs all phases end-to-end with state tracking via Material Passport.

**Mode B — phase-by-phase (cross-session resume):** User invokes one agent per phase across sessions for long-running projects. Common pattern: write the draft in one session, return next week to citation-check / abstract / peer-review independently.

In Mode B, **single-phase agents (Bucket A per `docs/design/2026-05-18-ars-v3.9.2-agent-phase-classification.md`) stay strictly within their assigned phase for writes**. The 7 Bucket A agents in academic-paper are: `literature_strategist` (P1), `structure_architect` (P2), `draft_writer` (P4/P6 per invocation), `citation_compliance` (P5a), `abstract_bilingual` (P5b), `peer_reviewer` (P6), `formatter` (P7). Reads from upstream phases are allowed.

Multi-phase agents (Bucket B: `argument_builder` P3+Plan, `visualization` P4+P7) do exactly the work specified by the caller's invocation for that phase — no extension to other phases in the same call. The v3.6.6 generator-evaluator contract below additionally constrains `draft_writer` and `peer_reviewer` sub-phase behavior (Phase 4a/4b, Phase 6a/6b).

Routing into Mode B requires explicit user signal — `/ars-<mode>` slash command or `[direct-mode]` prefix. Ambiguous cross-phase input defaults to clarification per `.claude/CLAUDE.md` Routing Discipline + `shared/references/intent_clarification_protocol.md`.

**Enforcement (v3.9.2):** prompt-level via Phase Boundary blocks on Bucket A agents + advisory verifier (`scripts/check_pipeline_integrity.py`). Deterministic PreToolUse hook + multi-phase envelope deferred to v3.10 active conductor (#134).

## 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** (8 files in `examples/`): `imrad_hei_example`, `literature_review_example`, `plan_mode_guided_writing`, `chinese_paper_example`, `revision_mode_example`, `revision_recovery_example`, `clinical_citation_verification_checklist`, `clinical_epistemic_status_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.