---
name: Academic Pipeline
slug: academic-pipeline
category: Automation
description: Academic Pipeline orchestrates the full academic research workflow from topic exploration to final manuscript, coordinating deep research, paper writing, integrity verification, and two-stage peer review with mandatory confirmation checkpoints. Use it when you need an end-to-end research-to-publication pipeline with quality gates.
github: "https://github.com/Imbad0202/academic-research-skills/tree/main/academic-pipeline"
language: Python
stars: 42257
forks: 3369
install: "npx degit https://github.com/Imbad0202/academic-research-skills/tree/main/academic-pipeline ~/.claude/skills/academic-pipeline"
installs_to: ~/.claude/skills/academic-pipeline
source_path: academic-pipeline/SKILL.md
collection_size: 4
category_size: 1523
collection_url: "https://dirskills.com/collections/Imbad0202/academic-research-skills"
added: 2026-08-13T07:36:58.860Z
last_synced: 2026-08-13T07:36:58.860Z
canonical_url: "https://dirskills.com/skills/academic-pipeline"
---

# Academic Pipeline

Academic Pipeline orchestrates the full academic research workflow from topic exploration to final manuscript, coordinating deep research, paper writing, integrity verification, and two-stage peer review with mandatory confirmation checkpoints. Use it when you need an end-to-end research-to-publication pipeline with quality gates.

**Install:**

```bash
npx degit https://github.com/Imbad0202/academic-research-skills/tree/main/academic-pipeline ~/.claude/skills/academic-pipeline
```

## README

# Academic Pipeline v3.15.0 — 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 (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.

**v3.6.3 (opt-in):** Set `ARS_PASSPORT_RESET=1` to promote FULL checkpoints to context-reset boundaries. Use `resume_from_passport=<hash>` in a fresh session to continue from the recorded stage. See [`references/passport_as_reset_boundary.md`](references/passport_as_reset_boundary.md).

**v3.8 (opt-in):** Set `ARS_CLAIM_AUDIT=1` to enable the L3 claim-faithfulness audit gate at the Stage 4 → Stage 5 transition. When the flag is set, the orchestrator dispatches `claim_ref_alignment_audit_agent` after the v3.7.1 Cite-Time Provenance Finalizer and before `formatter_agent`'s hard gate. The audit emits `claim_audit_results[]` + `uncited_assertions[]` + `claim_drifts[]` + `constraint_violations[]` + `audit_sampling_summaries[]` aggregates per the 8-row matrix; HIGH-WARN classes gate-refuse output via the formatter REFUSE rules 6-10. Default OFF for v3.8.0 — ramp-on plan deferred to post-calibration evidence (spec §5 mode flag rationale). See `agents/claim_ref_alignment_audit_agent.md` and the orchestrator §3.6 prose.

**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** — Stage 6 generates a "Paper Creation Process Record" PDF documenting the human-AI collaboration history (delivered before the terminal acknowledgement that completes the pipeline)

## 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)

**Resume from passport (cross-session context reset, opt-in):**
```
resume_from_passport=<hash> [stage=<n>] [mode=<m>]
```
--> Loads the Material Passport (Schema 9), locates the `kind: boundary` entry matching `<hash>`, and confirms it has no later `kind: resume` entry consuming it. If `pending_decision` is set, the decision prompt fires first to capture the user's branch choice for the audit ledger; the prompt is never skipped, even when the user supplies `stage=`. After the prompt (or immediately if no `pending_decision`), the next stage is determined by: (a) `stage=<n>` CLI override if provided, else (b) the matched option's `next_stage`, else (c) the `next` field recorded in the boundary entry. CLI `stage=`/`mode=` overrides win over option routing.
- **Gate (emit)**: `ARS_PASSPORT_RESET=1` must be set in the emitting session. Without the flag, no `kind: boundary` entries are written and there is nothing to resume from.
- **Gate (resume)**: No flag required. Any session can invoke `resume_from_passport=<hash>` against a passport that carries a valid boundary entry matching the hash.
- **Intent**: Invoke in a *fresh* Claude Code session. Resuming within the same session that emitted the boundary provides no token savings and may drop still-live in-session context.
- **Stage**: Any. Resumes at whatever stage the routing rules above determine.
- **Reference**: [`references/passport_as_reset_boundary.md`](references/passport_as_reset_boundary.md) — see §"`resume_from_passport` mode contract".

**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

---

## 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

**한국어**: 학술 파이프라인, 연구부터 논문까지, 논문 전체 워크플로, 연구 주제 설정부터 논문 완성까지, 연구-논문 전 과정

### 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, respect that entry point; the pipeline is opt-in
- The pipeline is optional, not mandatory

---

## 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 via Pandoc when available, otherwise conversion instructions; ask about LaTeX; confirm correctness; PDF) |
| **6** | **PROCESS SUMMARY** | **orchestrator** | **auto** | **Paper creation process record MD + LaTeX to PDF (bilingual)** |

**Parallelization opportunity (v3.3)**: Within Stage 2, the `academic-paper` skill's Phase 1 (literature_strategist_agent) and the `visualization_agent` can operate in parallel after Phase 2 (structure_architect_agent) completes the outline. Specifically:
- Once the outline includes a visualization plan, `visualization_agent` can begin figure generation
- Simultaneously, `argument_builder_agent` can build CER chains
- `draft_writer_agent` waits for both to complete before beginning Phase 4

This mirrors PaperOrchestra's parallel execution of Plot Generation (Step 2) and Literature Review (Step 3) after Outline (Step 1), which reduces overall pipeline latency. The parallelization is optional — sequential execution remains the default for simplicity.

---

## 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 via Pandoc when available (otherwise instructions) -> ask about LaTeX -> confirm -> PDF -> completion checkpoint (FULL) -> Stage 6 (user may decline Stage 6: marked `skipped`, pipeline goes directly to `completed`)
10. **Stage 6 PROCESS SUMMARY** -> ask language version -> generate process record MD -> LaTeX -> PDF -> terminal acknowledgement (`finish` / `end` / `done` / `confirm`, or an unambiguous natural-language equivalent) -> pipeline global state `completed`

See `references/pipeline_state_machine.md` for complete state transition definitions.

---

## Adaptive Checkpoint System

⚠️ **IRON RULE — 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; Stage 5 completion (final-deliverable acceptance) | Full deliverables list + decision dashboard + all options |
| SLIM | After 2+ consecutive "continue" responses on non-critical stages | One-line status + explicit continue/pause prompt |
| MANDATORY | Integrity FAIL; Review decision; Stage 5 entry gate (before finalization) | 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 continued [N] times in a row. 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 entry gate)**: always MANDATORY — this is the checkpoint between Stage 4.5 PASS and the Stage 5 dispatch, where the user explicitly confirms proceeding and makes the finalization-format decision (citation style); the in-stage LaTeX question and content confirmation stay inside Stage 5 execution. The Stage 5 completion checkpoint (Final Paper delivered, before Stage 6) is FULL — never SLIM. See `references/pipeline_state_machine.md` § Stage 5 boundary semantics
6. **All other stages**: start FULL, downgrade to SLIM if user says "just continue"

### Checkpoint Rules

1. ⚠️ **IRON RULE**: **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 + explicit continue/pause prompt)
5. **Awareness guard**: After 4+ consecutive continue responses, the system inserts a FULL checkpoint regardless of stage type to ensure user remains engaged

### Self-Check Questions (at every FULL checkpoint)

Before presenting the checkpoint to the user, the orchestrator asks itself:

1. **Citation integrity**: Are there any unverified citations in the latest output?
2. **Sycophantic concession**: Did the latest stage uncritically accept all feedback without pushback?
3. **Quality trajectory**: Is the latest output ≥ the quality of the previous stage? If declining, PAUSE and flag.
4. **Scope discipline**: Did the latest stage add content not requested by the user or the revision roadmap?
5. **Completeness**: Are all required deliverables for this stage present?

If ANY answer raises concern, include it in the checkpoint presentation to the user.

---

## Agent Team (5 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 (blocking) | `agents/integrity_verification_agent.md` |
| 4 | `collaboration_depth_agent` | **Observer (advisory only — never blocks).** Reads dialogue log and scores user-AI collaboration pattern against `shared/collaboration_depth_rubric.md`. Invoked at FULL/SLIM checkpoints and during Stage 6 record compilation (whole-pipeline pass, before the Process Record is delivered). Based on Wang & Zhang (2026). | `agents/collaboration_depth_agent.md` |
| 5 | `claim_ref_alignment_audit_agent` | **Opt-in claim faithfulness auditor (v3.8 #103).** Audits sampled citations for claim ↔ reference alignment + negative-constraint compliance; emits per-claim `claim_audit_results[]`, `claim_drift[]`, `uncited_assertions[]`, `constraint_violations[]`. Dispatched via orchestrator §3.6 when claim_audit mode is requested. | `agents/claim_ref_alignment_audit_agent.md` |

---

## 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 + Methodology Blueprint + Bibliography + Synthesis)
   - #672 cargo on every transition: exact builder-produced `preregistration-artifact/1.0` receipt and its named companion when provided; validate and carry byte-for-byte
   - 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, the hard-required original pre-revision draft (#576 current 1.1 §3.1 Phase 2A comparison base), exact author-adjudication sidecar, fully replayed Revision-Evidence Bundle, Response to Reviewers, Editorial Decision Letter, Round-1 findings, the immutable Roadmap, the exact ordered patch/report pairs projected by the bundle, and Round-1 Reviewer Configuration Cards. Missing original/roadmap/author/bundle is `manifest_incomplete`; this is the default contract re-review transfer. A user-requested fresh full review at 3' remains a separate full-mode branch.
   - Stage 3' --> 4': Pass new Revision Roadmap + R&R Traceability Matrix (Schema 11) to academic-paper revision mode; the traceability sidecar (frozen `previously_missed`/`indeterminate` records, #576 §8) rides through 4' toward Stage 4.5
   - Stage 3' --> 4.5 (Accept/Minor direct path): Pass verified revised draft + the traceability sidecar's frozen records to integrity_verification_agent as gate input
   - Stage 4/4' --> 4.5: Pass revision-completed paper to integrity_verification_agent (final verification); on the Major-via-4' path the Stage 3' traceability sidecar travels along as gate input
   - Stage 4.5 --> 5: Pass verified final draft to the one mandatory Stage-5 entry checkpoint; run #660 then #672 against that same accepted artifact ID/SHA-256 before format-convert dispatch
   - Stage 5  --> 6: Pass final deliverables list + the Process-Summary projection of pipeline state history, omitting the #673 activity projection of terminal root `run_id`, pending/sealed activity fields, selected-store data, renderer output, and diagnostics (user may decline Stage 6 at the Stage 5 completion checkpoint)
3. Begin next stage
```

### Mid-Conversation Reinforcement Protocol

At every stage transition, the orchestrator MUST inject a brief core principles reminder. This prevents context rot in long conversations.

**Template** (adapt to the upcoming stage):

````
--- STAGE TRANSITION: [Current] → [Next] ---

🔄 Core Principles Reinforcement:
1. [Most relevant IRON RULE for the next stage]
2. [Most relevant Anti-Pattern to avoid in the next stage]
3. Quality check: Is the output of [Current Stage] at least as good as [Previous Stage]? If not, PAUSE.

Checkpoint: [MANDATORY/ADVISORY] — [What user needs to confirm]
---
````

**Stage-specific reinforcement content**: See `references/reinforcement_content.md` for the full transition → reinforcement focus table.

---

## Phase-by-phase Invocation Contract (v3.9.2)

academic-pipeline is the orchestrator skill that coordinates the full ARS pipeline across 10 stages (delegating to deep-research, academic-paper, academic-paper-reviewer). Two invocation modes:

**Mode A — orchestrator-driven (default):** `pipeline_orchestrator_agent` runs all stages end-to-end with state tracking via Material Passport. `state_tracker_agent`, `integrity_verification_agent`, `collaboration_depth_agent`, and `claim_ref_alignment_audit_agent` are dispatched by the orchestrator at the appropriate checkpoints.

**Mode B — phase-by-phase (cross-session resume):** User invokes one phase agent at a time across sessions, typically via `ARS_PASSPORT_RESET=1` + `resume_from_passport=<hash>` (see `references/passport_as_reset_boundary.md`).

In Mode B, **single-phase agents (Bucket A per `do