# Academic Paper Orchestrator

> Coordinate an end-to-end academic paper, thesis, dissertation, review paper, or manuscript workflow by routing work across research verification, PDF/DOCX parsing, writing, academic figures, de-AI polishing, post-draft review, and formatting skills. Use when the user asks to manage a full paper project, plan a thesis from source materials to final DOCX, decide which academic skill should handle a task, run gated human-AI paper production, coordinate evidence gaps, field confirmation, reviewer-comment revision planning, final polish handoffs, or default multi-agent/sub-agent parallel review, verification, QA, and action-plan decomposition for substantial paper workflows. Chinese triggers: 论文全流程, 毕业论文, 学位论文, 综述论文, 论文总控, 编排论文工作流, 多agent论文流程, 子agent并行审查, 多智能体论文审查, 并行论文核验, 待补证据流程, 评审意见流程, 最终润色流程.

- Skill: `cuimuxuan/academic-paper-orchestrator` (Agent Skill, multi-file: 13 files)
- Install (CLI): `npx skillmds@latest add cuimuxuan/academic-paper-orchestrator`
- Raw SKILL.md: https://api.skillmd.com/api/skills/cuimuxuan/academic-paper-orchestrator/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: AI & ML
- Author: CuiMuxuan (https://skillmd.com/u/cuimuxuan)
- Updated: 2026-09-22
- Page: https://skillmd.com/skills/cuimuxuan/academic-paper-orchestrator

---


# Academic Paper Orchestrator

Use this skill to coordinate a complete academic paper workflow. Do not do every specialized task inside this skill; route to the focused skill that owns the current stage.

## Routing Map

| User need | Route to |
|---|---|
| Search literature, verify DOI/title match, check citation authenticity | `$academic-research-verification` |
| Parse PDFs or DOCX files into structured notes, evidence, headings, comments, or revision data | `$pdf-docx-parsing-workflow` |
| Plan sections, draft chapters, revise academic prose, integrate evidence into claims | `$paper-writing-workflow` |
| Confirm research field, handle terminology gates, mark writing evidence gaps, or plan ordinary reviewer/supervisor-comment revisions | `$paper-writing-workflow` |
| Resolve `LIT_GAP` items, find needed literature, verify new evidence, or update the evidence register | `$academic-research-verification` |
| Create mechanism figures, SVG diagrams, draw.io engineering diagrams, or approved OpenAI generated images | `$academic-figure-workflow` |
| Apply school handbook, Word template, journal guide, or general academic formatting | `$academic-formatting-workflow` |
| Review a complete initial draft against 3-10 benchmark papers and plan the next revision | `$post-manuscript-benchmark-review` |
| Review language style, wording, grammar, AI-like phrasing, terminology, translation accuracy, figure/table wording, or citation sentence style without editing | `$language-style-review` |
| Manage formal sentence-level revision rounds, object libraries, pass/fail confirmations, latest sentence-review drafts, project standards, material dependencies, and upgrade plans | `$revision-control` |
| Polish stable manuscript prose, reduce AI-like cadence, or remove internal project/operation traces | `$academic-de-ai-polishing` |

If a focused skill is unavailable, follow the same ownership boundaries and tell the user which part was handled without the dedicated skill.

## Core Rules

1. Ask only the minimum startup questions needed to choose the next stage.
2. Maintain visible project state, current gate, confirmed artifacts, missing materials, risks, and next step.
3. Treat verified evidence as the source of truth for scholarly claims.
4. Treat real codebase, dataset, or experiment artifacts as the source of truth for implementation or result claims.
5. Keep research, parsing, writing, figures, formatting, and post-draft review as separate passes.
6. Stop for user confirmation at required gates before moving to the next major stage.
7. Never fabricate citations, DOI records, experiment results, repository behavior, figure contents, or formatting rules.
8. Stop main-text or rebuttal writing when required support is missing; request the missing material before continuing.
9. Treat formulas, superscripts/subscripts, citations, cross-references, figures, and tables as conversion-sensitive artifacts.
10. For substantial paper workflows, plan multi-agent parallel review, verification, QA, or action-plan decomposition by default, but start sub-agents only after user confirmation unless prior full or automatic-execution permission exists.
11. For combined post-draft quality and language review, run quality review first, language-style review second, then send the unified priority queue to `$revision-control`.

## Intake

Collect only what is missing:

- paper type, language target, and delivery target;
- research field and target venue/school field when terminology may matter;
- target standard: school handbook, Word template, journal guide, supervisor requirement, or provisional baseline;
- target examples: 3-10 accepted papers, approved theses, templates, author guidelines, or supervisor-approved chapters when available;
- current materials: topic, outline, draft, PDFs, DOCX files, data, codebase, figures, bibliography, and notes;
- constraints: deadline, citation style, word/page count, required chapters, and permitted tools.

Before routing work into execution, ask for materials that would materially improve quality:

```text
Required or high-value materials:
Missing materials:
Can proceed without them: yes/no
Fallback if unavailable:
```

## Workflow

1. Rebuild or create the project state.
2. Decide the current mode and route using the routing map.
3. Apply [workflow-protocol-index.md](../../shared/workflow-protocol-index.md) and [trigger-conflict-matrix.md](../../shared/trigger-conflict-matrix.md) when a request spans stages or the owner skill is ambiguous.
4. Apply [multi-agent-academic-workflow-gate.md](../../shared/multi-agent-academic-workflow-gate.md) before substantial review, verification, QA, or reviewer-comment decomposition work that can be split into independent checks.
5. Apply [orchestration-contract.md](references/orchestration-contract.md) for substantial projects, state files, material passports, and handoff packets.
6. Apply [project-gates-and-phases.md](references/project-gates-and-phases.md) for full-project phase sequencing and required gates.
7. Apply [integrity-gate-patterns.md](references/integrity-gate-patterns.md) before drafting, benchmark review, final polish, formatting, or any claim about code/data/results.
8. Apply [writing-chain-gates.md](references/writing-chain-gates.md) when the project is entering field confirmation, evidence-gap handling, reviewer-comment response, post-draft review, or final polish.
9. Apply [main-text-and-rebuttal-claim-support-gate.md](../../shared/main-text-and-rebuttal-claim-support-gate.md) before final main-text or rebuttal claims.
10. Apply [reviewer-comment-action-plan-gate.md](../../shared/reviewer-comment-action-plan-gate.md) when two or more reviewer, editor, committee, or supervisor comments are provided.
11. Apply [notation-and-conversion-integrity-gate.md](../../shared/notation-and-conversion-integrity-gate.md) before lossy manuscript, figure, table, formula, citation, or cross-reference conversion.
12. Apply [dependency-and-software-guide.md](references/dependency-and-software-guide.md) when a stage may need Pandoc, Word, PDF/OCR tools, draw.io, Matplotlib, Graphviz, Inkscape, network APIs, or project-specific Python packages.
13. Route execution to the focused skill that owns the current stage.
14. When quality review and language review are both requested, sequence `$post-manuscript-benchmark-review` then `$language-style-review`, mark suggestions that could roll back quality priorities, and hand the confirmed queue to `$revision-control`.
15. At each gate, report completed work, artifacts, decisions, risks, missing materials, and recommended next step.

For narrow requests, run only the relevant stage and state what was intentionally skipped.

## Evidence And Version Discipline

- Keep a single evidence register or literature master list for the project.
- Mark items as `candidate`, `verified`, `downloaded`, `parsed`, `cited`, `rejected`, or `unresolved`.
- Track major project inputs with material passports when multiple stages depend on them.
- Keep paired Markdown and DOCX outputs at the same semantic version when both exist.
- Save new outputs with explicit suffixes; do not overwrite the only working draft unless the user explicitly requests it.
- Validate `project_state.json` before moving from research/parsing into drafting, and before moving from writing into formatting.

## Fallbacks

- If literature verification requires network access and network is unavailable, create a manual verification queue with exact DOI/title/search strings.
- If PDF parsing fails, list failed pages and recommended manual recovery.
- If a DOCX needs Word-only features, explain what can be automated and what requires Word.
- If a requested figure cannot be drawn faithfully from evidence or code, decline the specific figure or mark it unresolved.
- If the user wants to skip a gate, comply only after stating the risk.

## Reference

Read [stage-map.md](references/stage-map.md) when a full project needs a compact stage checklist or when resuming a long-running thesis workflow.

Read [workflow-protocol-index.md](../../shared/workflow-protocol-index.md) before selecting shared protocol references for cross-skill coordination.

Read [multi-agent-academic-workflow-gate.md](../../shared/multi-agent-academic-workflow-gate.md) when planning default parallel checks for substantial paper workflows, including literature verification, draft review, sentence-level language review, figure/format QA, or reviewer-comment action decomposition.

Read [trigger-conflict-matrix.md](../../shared/trigger-conflict-matrix.md) when a request could trigger multiple academic skills or when deciding whether the orchestrator should own the task.

Read [revision-control-contract.md](../../shared/revision-control-contract.md) when routing formal revision work, sentence pass/fail state, object libraries, project standards, or upgrade plans.

Read [language-style-review-schema.md](../../shared/language-style-review-schema.md) when consuming a language-style review report or merging it with quality review findings.

Read [handoff-field-schema.md](../../shared/handoff-field-schema.md) when checking field names for workflow modes, material passports, claim anchors, literature gaps, writing-ready handoffs, or benchmark reports.

Read [main-text-and-rebuttal-claim-support-gate.md](../../shared/main-text-and-rebuttal-claim-support-gate.md) before drafting, revising, polishing, or approving supported main-text or rebuttal claims.

Read [reviewer-comment-action-plan-gate.md](../../shared/reviewer-comment-action-plan-gate.md) when a comment batch needs triage and concrete revision actions before editing.

Read [notation-and-conversion-integrity-gate.md](../../shared/notation-and-conversion-integrity-gate.md) when formulas, superscripts/subscripts, citations, cross-references, figures, tables, or captions are converted across formats.

Read [project-artifact-templates.md](references/project-artifact-templates.md) when creating a project state file, handoff packet, or target-baseline note.

Read [orchestration-contract.md](references/orchestration-contract.md) for project-state output, route plan, handoff packets, and state-file use.

Read [project-gates-and-phases.md](references/project-gates-and-phases.md) for standard phases, required gates, and stage execution notes.

Read [integrity-gate-patterns.md](references/integrity-gate-patterns.md) before accepting claims about sources, code, data, experiments, benchmarks, figures, or final deliverables.

Read [writing-chain-gates.md](references/writing-chain-gates.md) for field confirmation, `LIT_GAP` handling, reviewer-comment revision planning, post-draft review routing, and final de-AI polishing gates.

Read [dependency-and-software-guide.md](references/dependency-and-software-guide.md) when a workflow stage may require external software, Python packages, Word automation, Pandoc, draw.io, image conversion tools, or network APIs.

## Bundled Utilities

- `scripts/project_state_check.py`: create a JSON project-state template or validate project state, required handoff packets, gate consistency, evidence readiness, and formatting readiness.