/academic-pipeline

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 9-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: "2.7"
  last_updated: "2026-03-27"
  depends_on: "deep-research, academic-paper, academic-paper-reviewer"

Academic Pipeline v2.7 — 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.

**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)

**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

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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, do not force them into the pipeline
• The pipeline is optional, not mandatory

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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; ask about LaTeX; confirm correctness; PDF) | | **6** | **PROCESS SUMMARY** | **orchestrator** | **auto** | **Paper creation process record MD + LaTeX to PDF (bilingual)** |

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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 -> 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.

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Adaptive Checkpoint System

**Core rule: After