Academic Pipeline

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 each stage completion, the system must proactively prompt the user and wait for confirmation. The checkpoint presentation adapts based on context and user engagement.

Checkpoint Types

| Type | When Used | Content | |------|-----------|---------| | FULL | First checkpoint; after integrity boundaries; before finalization | Full deliverables list + decision dashboard + all options | | SLIM | After 2+ consecutive "continue" responses on non-critical stages | One-line status + auto-continue in 5 seconds | | MANDATORY | Integrity FAIL; Review decision; Stage 5 | Cannot be skipped; requires explicit user input |

Decision Dashboard (shown at FULL checkpoints)

━━━ Stage [X] [Name] Complete ━━━

Metrics:
- Word count: [N] (target: [T] +/-10%)    [OK/OVER/UNDER]
- References: [N] (min: [M])              [OK/LOW]
- Coverage: [N]/[T] sections drafted       [COMPLETE/PARTIAL]
- Quality indicators: [score if available]

Deliverables:
- [Material 1]
- [Material 2]

Flagged: [any issues detected, or "None"]

Ready to proceed to Stage [Y]? You can also:
1. View progress (say "status")
2. Adjust settings
3. Pause pipeline
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━

Adaptive Rules

1. First checkpoint: always FULL
2. After 2+ consecutive "continue" without review: prompt user awareness ("You've auto-continued [N] times. Want to review progress?")
3. Integrity boundaries (Stage 2.5, 4.5): always MANDATORY
4. Review decisions (Stage 3, 3'): always MANDATORY
5. Before finalization (Stage 5): always MANDATORY
6. All other stages: start FULL, downgrade to SLIM if user says "just continue"

Checkpoint Rules

1. Cannot auto-skip MANDATORY checkpoints: Even if the previous stage result is perfect, explicit user input is required at MANDATORY checkpoints
2. User can adjust: At FULL and MANDATORY checkpoints, users can modify the mode or settings for the next step
3. Pause-friendly: Users can pause at any checkpoint and resume later
4. SLIM mode: If the user says "just continue" or "fully automatic," subsequent non-critical checkpoints switch to SLIM format (one-line status + auto-continue), but notifications are still sent
5. Awareness guard: After 4+ consecutive auto-continues, the system inserts a FULL checkpoint regardless of stage type to ensure user remains engaged

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Agent Team (3 Agents)

| # | Agent | Role | File | |---|-------|------|------| | 1 | pipeline_orchestrator_agent | Main orchestrator: detects stage, recommends mode, triggers skill, manages transitions | agents/pipeline_orchestrator_agent.md | | 2 | state_tracker_agent | State tracker: records completed stages, produced materials, revision loop count | agents/state_tracker_agent.md | | 3 | integrity_verification_agent | Integrity verifier: 100% reference/citation/data verification | agents/integrity_verification_agent.md |

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Orchestrator Workflow

Step 1: INTAKE & DETECTION

pipeline_orchestrator_agent analyzes the user's input:

1. What materials does the user have?
   - No materials           --> Stage 1 (RESEARCH)
   - Has research data      --> Stage 2 (WRITE)
   - Has paper draft        --> Stage 2.5 (INTEGRITY)
   - Has verified paper     --> Stage 3 (REVIEW)
   - Has review comments    --> Stage 4 (REVISE)
   - Has revised draft      --> Stage 3' (RE-REVIEW)
   - Has final draft for formatting --> Stage 5 (FINALIZE)

2. What is the user's goal?
   - Full workflow (research to publication)
   - Partial workflow (only certain stages needed)

3. Determine entry point, confirm with user

Step 2: MODE RECOMMENDATION

Based on entry point and user preferences, recommend modes for each stage:

User type determination:
- Novice / wants guidance --> socratic (Stage 1) + plan (Stage 2) + guided (Stage 3)
- Experienced / wants direct output --> full (Stage 1) + full (Stage 2) + full (Stage 3)
- Time-limited --> quick (Stage 1) + full (Stage 2) + quick (Stage 3)

Explain the differences between modes when recommending, letting the user choose

Step 3: STAGE EXECUTION

Call the corresponding skill (does not do work itself, purely dispatching):

1. Inform the user which Stage is about to begin
2. Load the corresponding skill's SKILL.md
3. Launch the skill with the recommended mode
4. Monitor stage completion status

After completion:
1. Compile deliverables list
2. Update pipeline state (call state_tracker_agent)
3. [MANDATORY] Proactively prompt checkpoint, wait for user confirmation

Step 4: TRANSITION

After user confirmation:

1. Pass the previous stage's deliverables as input to the next stage
2. Trigger handoff protocol (defined in each skill's SKILL.md):
   - Stage 1  --> 2: deep-research handoff (RQ Brief + Bibliography + Synthesis)
   - Stage 2  --> 2.5: Pass complete paper to integrity_verification_agent
   - Stage 2.5 --> 3: Pass verified paper to reviewer
   - Stage 3  --> 4: Pass Revision Roadmap to academic-paper revision mode
   - Stage 4  --> 3': Pass revised draft and Response to Reviewers to reviewer
   - Stage 3' --> 4': Pass new Revision Roadmap to academic-paper revision mode
   - Stage 4/4' --> 4.5: Pass revision-completed paper to integrity_verification_agent (final verification)
   - Stage 4.5 --> 5: Pass verified final draft to format-convert mode
3. Begin next stage

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Integrity Review Protocol (Added in v2.0)

Stage 2.5: First Integrity Check (Pre-Review Integrity)

Trigger: After Stage 2 (WRITE) completion, before Stage 3 (REVIEW) Purpose: Ensure all references and data are not fabricated or erroneous before submission for review

Execution steps:
1. integrity_verification_agent executes Mode 1 (initial verification) on the paper
2. Verification scope:
   - Phase A: 100% reference existence + bibliographic accuracy + ghost citations
   - Phase B: >= 30% citation context spot-check
   - Phase C: 100% statistical data verification
   - Phase D: >= 30% originality spot-check + self-plagiarism check
   - Phase E: 30% claim verification spot-check (minimum 10 claims)
3. Result handling:
   - PASS -> checkpoint -> Stage 3
   - FAIL -> produce correction list -> fix item by item -> re-verify corrected items
   - PASS after corrections -> checkpoint -> Stage 3
   - Still FAIL after 3 rounds -> notify user, list unverifiable items

Stage 4.5: Final Integrity Check (Post-Revision Final Check)

Trigger: After Stage 4' (RE-REVISE) or Stage 3' (RE-REVIEW, Accept) completion, before Stage 5 (FINALIZE) Purpose: Confirm the revised paper is 100% correct and ready for publication

Execution steps:
1. integrity_verification_agent executes Mode 2 (final verification) on the revised draft
2. Verification scope:
   - Phase A: 100% reference verification (including those added during revision)
   - Phase B: 100% citation context verification (not spot-check, full check)
   - Phase C: 100% statistical data verification
   - Phase D: >= 50% originality spot-check (100% for newly added/modified paragraphs)
   - Phase E: 100% claim verification (zero MAJOR_DISTORTION + zero UNVERIFIABLE required)
3. Special check: Compare with Stage 2.5 results to confirm all previous issues are resolved
4. Result handling:
   - PASS (zero issues) -> checkpoint -> Stage 5
   - FAIL -> fix -> re-verify -> PASS -> Stage 5
5. **Must PASS with zero issues to proceed to Stage 5**

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Two-Stage Review Protocol (Added in v2.0)

Stage 3: First Review (Full Review)

• Input: Paper that passed integrity check
• Review team: EIC + R1 (methodology) + R2 (domain) + R3 (interdisciplinary) + Devil's Advocate
• Output: 5 review reports + Editorial Decision + Revision Roadmap + Socratic Revision Coaching
• Decision branches: Accept -> Stage 4.5 / Minor|Major -> Revision Coaching -> Stage 4 / Reject -> Stage 2 or end

See academic-paper-reviewer/SKILL.md for review process details.

Stage 3 -> 4 Transition: Revision Coaching

EIC uses Socratic dialogue to guide the user in understanding review comments and planning revision strategy (max 8 rounds). User can say "just fix it for me" to skip.

Stage 3': Second Review (Verification Review)

• Input: Revised draft + Response to Reviewers + original Revision Roadmap
• Mode: academic-paper-reviewer re-review mode
• Output: Revision response comparison table + new issues list + new Editorial Decision
• Decision branches: Accept|Minor -> Stage 4.5 / Major -> Residual Coaching -> Stage 4'

See academic-paper-reviewer/SKILL.md Re-Review Mode for verification review process.

Stage 3' -> 4' Transition: Residual Coaching

EIC guides the user in understanding residual issues and making trade-offs (max 5 rounds). User can say "just fix it" to skip.

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Mid-Entry Protocol

Users can enter from any stage. The orchestrator will:

1. Detect materials: Analyze the content provided by the user to determine what is available
2. Identify gaps: Check what prerequisite materials are needed for the target stage
3. Suggest backfilling: If critical materials are missing, suggest whether to return to earlier stages
4. Direct entry: If materials are sufficient, directly start the specified stage

Important: mid-entry cannot skip Stage 2.5

• If the user brings a paper and enters directly, go through Stage 2.5 (INTEGRITY) first before Stage 3 (REVIEW)
• Only exception: User can provide a previous integrity verification report and content has not been modified

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External Review Protocol (Added in v2.5)

Scenario: The user submitted to a journal and received feedback from real human reviewers, bringing those comments into the pipeline.

Trigger: User says "I received reviewer comments," "reviewer comments," "revise and resubmit," etc.

Differences from Internal Review

| Aspect | Internal Review (Stage 3 simulation) | External Review (real journal) | |--------|-------------------------------------|-------------------------------| | Source of review comments | Pipeline's AI reviewers | Journal's human reviewers | | Comment format | Structured (Revision Roadmap) | Unstructured (free text, PDF, email) | | Comment quality | Consistent, predictable | Variable quality, may be vague or contradictory | | Revision strategy | Can accept wholesale | Need to judge which to accept/reject/negotiate | | Acceptance criteria | AI re-review suffices | Ultimately decided by human reviewers |

Step 1: Intake and Structuring

1. Receive reviewer comments (supported formats):
   - Directly pasted text
   - Provide PDF/DOCX file path
   - Copy from journal system review letter

2. Parse into structured list:

…

## Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

- **Author:** [ARAVINDAN20](https://github.com/ARAVINDAN20)
- **Source:** [ARAVINDAN20/Claude-Research-Paper-OS](https://github.com/ARAVINDAN20/Claude-Research-Paper-OS)
- **License:** Apache-2.0

Install and usage instructions live in the source repository linked above.