academic-paper

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

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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

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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

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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]".

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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

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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. (The later-added rebuttal-audit mode is likewise non-full and does 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 (11 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	Patch document + deterministically applied revised draft + apply report (#390; revision log via 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" / "should we push back" / "conference rebuttal" / "grant panel response"	12 only	Revision Roadmap + optional Tracking Template + Response Letter Skeleton (covers pushback/disagreement posture + journal / conference / grant-panel / transfer-after-review scopes)
disclosure (v3.2)	"AI disclosure for Nature" / "generate AI usage statement"	9 only	Venue-specific AI-usage disclosure paragraph(s) + placement instructions
rebuttal-audit	"audit my response" / "check my rebuttal" / "did I miss any reviewer comment" (requires BOTH reviewer comments AND an existing rebuttal draft)	12 only (parse-only)	Rebuttal QA report: per-comment coverage + gaps + risk flags. No new response generated; advisory only. Does NOT emit Schema 11 / Material Passport / verified status.

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
Have a written rebuttal draft to QA against reviewer comments	rebuttal-audit	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.

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Rebuttal-Audit Mode

rebuttal-audit evaluates an author's existing rebuttal / response-to-reviewers draft for coverage, tone, and evidence. It is advisory QA — it does not write or rewrite the response.

Input gate (routing): activate rebuttal-audit only when the user supplies BOTH (a) the reviewer comments / decision letter AND (b) an existing rebuttal/response draft to evaluate. If only (a) is present (no draft yet), route to revision-coach (which generates a response skeleton). If intent is ambiguous, clarify rather than guess.

What it produces:

• Per-comment coverage table — every reviewer concern marked addressed / partially / missing in the draft.
• Gap list — concerns the draft fails to answer.
• Risk flags — tone too combative, claims made without evidence, or a response that misreads the reviewer's actual point.
• Improvement suggestions (advisory).

IRON RULE — integrity boundary (no false certification): rebuttal-audit reuses revision_coach_agent's comment-parsing capability, but a standalone invocation runs outside the pipeline and therefore never passes Stage 4.5 final integrity. It MUST NOT emit a Schema 11 commitment_extracted ledger, MUST NOT write to the Material Passport, and MUST NOT mark the package ready_to_submit or any verified status. Producing a Schema 11 artifact would falsely imply the response entered the pipeline's traceability system. The output is an advisory QA report only.

Boundary vs re-review: academic-paper-reviewer's re-review mode verifies the revised manuscript (did the author's claimed changes actually appear in the paper) and runs inside the pipeline. rebuttal-audit verifies the response letter itself (does the rebuttal cover every comment, is its tone/evidence sound) and runs standalone, advisory. Different artifacts, different layers.

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Revision Mode Patch Protocol (#390)

In revision mode, draft_writer_agent does NOT re-emit the complete paper. The round runs anchorize → patch → deterministic apply → finalizer, confining the regeneration surface to the blocks the revision explicitly touches (DELEGATE-52 blast-radius containment; spec docs/design/2026-06-10-390-diff-patch-revision-mode-spec.md):

1. Anchorize the draft (scripts/ars_anchorize_draft.py — idempotent, content-neutral): every block gets a stable <!--block:BNNNN--> marker; a block manifest (base_draft_hash + per-block old_hash) is regenerated. Nothing may rewrite the draft between this step and apply.
2. The writer emits a patch document (shared/contracts/patch/revision_patch.schema.json) as a sidecar file in its phase6_*/ fence — block ops with hash preconditions copied from the manifest, each op tracing to roadmap_item_ids. See agents/draft_writer_agent.md § Patch-Document Revision Emission.
3. Deterministic apply (scripts/ars_apply_revision_patch.py): two-phase fail-closed — one stale hash rejects the whole patch with the base byte-untouched; untouched blocks are preserved byte-identical by construction. Structural shapes (heading rewrites/deletes, section-count change, touched-ratio > 0.6) refuse without an explicit acknowledge that only the §3.6 escalation checkpoint may grant. The apply report (preserved_ratio, ops, fresh block IDs, structural flags) is a required input to re-review alongside the revised draft.
4. Escalation, never silent fallback: restructure-demanding rounds go to a MANDATORY user checkpoint; a confirmed full re-emission round is provenance-stamped mode: full_reemission_escalated and the draft is re-anchorized afterwards (new ID generation).

Orchestrated runs follow pipeline_orchestrator_agent.md § Revision-Round Patch Sequencing; Mode B (phase-by-phase manual) users run the same scripts by hand — exact commands in references/revision_patch_protocol.md. Honest boundary, stated once: patch mode removes the silent-distortion channel for text the revision does not touch; it does not make the revision itself better. The academic-paper full in-pair Phase 6→4 loop is NOT patch-adopted (its Phase 4b lint requires a full ## Draft Body; Item 9 boundary, spec §5.2/§7).

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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.

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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.

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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

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Full Academic Pipeline

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

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Phase 0: Configuration Interview

See agents/intake_agent.md for the complete field definitions of the Phase 0 configuration interview. The interview covers 9 core items: paper type, discipline, target journal, citation format, output format, language, abstract, word count, and existing materials — plus co-authors, funding, optional style calibration, the domain evidence profile (Step 12), and the citation-verification level (Step 13, #392: mark only by default / strict opt-in, seeding terminal_policies.citation_existence). Outputs a Paper Configuration Record, awaiting user confirmation.

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File Structure

Agent definitions: agents/{agent_name}.md — one file per agent (12 total, matching Agent Team table above).

References (20 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 (11 modes), plan_mode_protocol, workflow_phase_details, revision_patch_protocol (#390 Mode B commands + marker lifecycle)
• 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 (9 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, version_family_reconciliation_example.

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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

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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)

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Output Language

Follows the user's language. Academic terminology is kept in English. Bilingual abstracts are always provided regardless of the main text language.

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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

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Version Info

Item	Content
Skill Version	3.2.0
Last Updated	2026-06-01
Maintainer	Cheng-I Wu
Dependent Skills	deep-research v1.0+ (upstream), academic-paper-reviewer v1.0+ (downstream)

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Version History

See references/changelog.md for full version history.