domains / research / academic-paper-pipeline / academic-pipeline

academic-pipeline

Skill card

combined

The two copies are different major versions of the same orchestrator. The Imbad0202 copy (v3.23.0) is a 10-stage workflow that includes a detailed routing core, escape-hatch handling, and opt-in audit/reset flags, but its text is truncated before the stage table. The brycewang-stanford copy (v2.7) is a 9-stage workflow that explicitly defines the stage table, state machine, and a final 'Process Summary' stage, but lacks the routing core and newer audit features. Because each copy contains material steps and constraints the other lacks (routing/audit vs. explicit stage table/process summary), crowning one would hide a real alternative.

Repositories

Other copies

Combined skill

---
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 workflow with mandatory integrity checks, two-stage peer review, and auditable quality-assurance artifacts."
metadata:
  version: "3.23.0"
  depends_on: "deep-research, academic-paper, academic-paper-reviewer"
---

# Academic Pipeline — 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.

## Routing Discipline

**Step 0 — Escape hatch check:** If the user's first message begins with `[direct-mode]`, strip the prefix and skip directly to explicit-intent handling. The token is not passed to the dispatched agent.

**Step 1 — Explicit clear intent:** If the user invokes a specific skill via slash command or unambiguous trigger keyword, route directly.

**Step 2 — Cross-phase materials:** If the user provides artifacts spanning ≥ 2 pipeline phases without naming a specific skill, clarify. List candidate workflows as options.

**Step 3 — Ambiguous intent:** If no artifacts or clear request are provided, clarify.

## Pipeline Stages

| Stage | Name | Skill / Agent Called | Deliverables |
|-------|------|---------------------|--------------|
| 1 | RESEARCH | `deep-research` | RQ Brief, Methodology, Bibliography, Synthesis |
| 2 | WRITE | `academic-paper` | Paper Draft |
| 2.5 | INTEGRITY | `integrity_verification_agent` | Integrity verification report + corrected paper |
| 3 | REVIEW | `academic-paper-reviewer` | 5 review reports + Editorial Decision + Revision Roadmap |
| 4 | REVISE | `academic-paper` | Revised Draft, Response to Reviewers |
| 3' | RE-REVIEW | `academic-paper-reviewer` | Verification review report |
| 4' | RE-REVISE | `academic-paper` | Second revised draft (if needed) |
| 4.5 | FINAL INTEGRITY | `integrity_verification_agent` | Final verification report (100% pass required) |
| 5 | FINALIZE | `academic-paper` | Final Paper (MD, DOCX, PDF) |
| 6 | PROCESS SUMMARY | orchestrator | Paper creation process record (MD + PDF) |

## 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
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** -> generate process record MD -> LaTeX -> PDF -> end

## Opt-in Features

- Set `ARS_PASSPORT_RESET=1` to promote checkpoints to context-reset boundaries.
- Set `ARS_AUDIT_ARTIFACT_GATE=1` to enable the Audit Artifact Gate for external audit scripts.

## Conflicts

- **Imbad0202/academic-research-skills** includes the routing core and audit/reset flags but does not explicitly list Stage 6 in the provided text.
- **brycewang-stanford/Auto-Empirical-Research-Skills** explicitly lists Stage 6 (Process Summary) and the full state machine but lacks the routing core and audit/reset flags.