---
name: academic-pipeline
description: Orchestrates the full academic research pipeline from exploration to final manuscript, coordinating research, writing, integrity verification, peer review, revision, and finalization stages with user confirmation checkpoints.
---

# 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** — 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)

**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

### 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 -> 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.

---

## 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; before finalization | 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 | 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)**: always MANDATORY
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 at pipeline completion. 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 + 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 + R&R Traceability Matrix (Schema 11) 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
```

### 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 `docs/design/2026-05-18-ars-v3.9.2-agent-phase-classification.md`) in the downstream skills (deep-research, academic-paper, academic-paper-reviewer) stay strictly within their assigned phase for writes**. The 5 agents in academic-pipeline itself are all cross-phase / meta by design (Bucket C/D) — they have no fence by design:

- `pipeline_orchestrator_agent` (D — orchestrator, full pipeline visibility)
- `state_tracker_agent` (D — meta state, all phases)
- `integrity_verification_agent` (C — Stage 2.5 / 4.5 cross-skill gate)
- `collaboration_depth_agent` (C — FULL/SLIM checkpoints + pipeline completion, advisory-only)
- `claim_ref_alignment_audit_agent` (C — opt-in claim audit, phase-orthogonal)

Routing into Mode B requires explicit user signal — `/ars-<mode>` slash command or `[direct-mode]` prefix. Ambiguous cross-phase input defaults to clarification per `.claude/CLAUDE.md` Routing Discipline + `shared/references/intent_clarification_protocol.md`. **Critically:** if `pipeline_orchestrator_agent` is dispatched on ambiguous cross-phase materials, the orchestrator itself currently cannot reconcile (this is the v3.10 conductor #134 work) — v3.9.2 routes such cases to clarification BEFORE the orchestrator runs.

**Enforcement (v3.9.2):** Phase Boundary blocks on downstream Bucket A agents + advisory verifier (`scripts/check_pipeline_integrity.py`) + a deterministic PreToolUse write-scope guard in hook-enabled runtimes (#134 rescope, PR #294). Multi-phase envelope + orchestrator structured intake remain forward-scope (#134 Slices 3-5).

---

## Integrity Review Protocol

Stage 2.5 (pre-review) and Stage 4.5 (post-revision) verification. 5-phase protocol: references → citation context → statistical data → originality → claims.

⚠️ **IRON RULE**: Stage 4.5 must PASS with zero issues to proceed to Stage 5. Stage 4.5 verifies from scratch independently.

⚠️ **IRON RULE (v3.2)**: Both Stage 2.5 and Stage 4.5 must also run the **AI Research Failure Mode Checklist** — a 7-mode taxonomy extending the citation hallucination checks into implementation bugs, hallucinated results, shortcut reliance, bug-as-insight, methodology fabrication, and pipeline-level frame-lock. If any of the 7 modes is `SUSPECTED`, or if Modes 1/3/5/6 are `INSUFFICIENT EVIDENCE`, the pipeline **blocks** and the user must acknowledge (confirm / override with reasoning / revise) before the pipeline proceeds. There is no `--no-block` escape hatch. Stage 6 PROCESS SUMMARY then reports the full failure-mode audit log as part of the AI Self-Reflection Report.

> See `references/integrity_review_protocol.md` for the 5-phase citation/claim verification procedures.
> See `references/ai_research_failure_modes.md` for the 7-mode AI research failure checklist and block/override logic.

- [v3.4.0] `compliance_agent` runs mode-aware PRISMA-trAIce + RAISE compliance check; tier-based block semantics. See `shared/compliance_checkpoint_protocol.md`.

---

## Two-Stage Review Protocol

Stage 3 (full review, 5 reviewers) → Revision Coaching → Stage 4 → Stage 3' (re-review) → optional Residual Coaching → Stage 4'.

> See `references/two_stage_review_protocol.md` for detailed stage flows and coaching dialogue limits.

---

## 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

---

## External Review Protocol

Handles external (human) reviewer feedback integration. 4-step workflow: Intake & Structuring → Strategic Revision Coaching → Revision & Response → Self-Verification.

> See `references/external_review_protocol.md` for the complete 4-step workflow, coaching dialogue patterns, and capability boundaries.

---

## Progress Dashboard

ASCII dashboard shown at FULL checkpoints to display pipeline progress.

> See `references/progress_dashboard_template.md` for the dashboard template.

---

## Revision Loop Management

- Stage 3 (first review) -> Stage 4 (revision) -> Stage 3' (verification review) -> Stage 4' (re-revision, if needed) -> Stage 4.5 (final verification)
- **Maximum 1 round of RE-REVISE** (Stage 4'): If Stage 3' gives Major, enter Stage 4' for revision then proceed directly to Stage 4.5 (no return to review)
- **Pipeline overrides academic-paper's max 2 revision rule**: In the pipeline, revisions are limited to Stage 4 + Stage 4' (one round each), replacing academic-paper's max 2 rounds rule
- Mark unresolved issues as Acknowledged Limitations
- Provide cumulative revision history (each round's decision, items addressed, unresolved items)

### Early-Stopping Criterion (v3.2)

At the end of each revision round, if **delta < 3 points** on the 0-100 rubric AND **no P0 issues remain**, suggest stopping the revision loop ("converged"). User can override. Hard cap: 2 full revision loops (Stage 4 + Stage 4').

### Budget Transparency (v3.2; interaction-count extension #89/#388)

At pipeline start, estimate token cost based on paper length, mode, and cross-model toggle. Present estimate and ask for user confirmation before Stage 1 begins.

Alongside the token estimate, present the **interaction-count budget**: long-horizon document corruption compounds with the number of document round-trips, not with token volume (DELEGATE-52, arXiv:2604.15597). Enumerate the round-trip caps the pipeline already enforces — 2 full revision loops (Early-Stopping above), 8 + 5 Socratic coaching rounds (Stage 3→4 / 3'→4'), and the integrity-gate fix→re-verify loop at Stages 2.5/4.5 — and state the worst-case round-trip total those caps imply for the chosen mode. At each stage checkpoint, report the accumulated round-trip count next to the stage status. **Advisory only**: the count never blocks; the per-loop caps remain the enforcement layer. A run that exceeds its stated worst case signals a loop the caps do not cover — surface that explicitly rather than silently continuing.

---

## Reproducibility

Every pipeline artifact is versioned, hashed, and auditable.

> See `references/reproducibility_audit.md` for standardized workflow guarantees, audit trail format, and artifact tracking.

---

## Stage 6: Process Summary Protocol

Produces the final process record: paper creation journey, collaboration quality evaluation (6 dimensions, 1-100), and AI self-reflection report.

> See `references/process_summary_protocol.md` for full workflow, required content structure, scoring dimensions, and output specifications.

---

## Collaboration Depth Observer (v3.5.0, advisory only — never blocks)

The `collaboration_depth_agent` observes the user's collaboration pattern with the pipeline. It is **advisory only** and **never blocks** progression at any checkpoint. It is `non-blocking` by design and carries `blocking: false` in its frontmatter as a structural guarantee.

**When invoked**: every FULL checkpoint, every SLIM checkpoint, and after Stage 6 (pipeline completion). MANDATORY checkpoints (Stages 2.5 / 4.5 integrity gates) **do not** invoke the observer — those are integrity concerns and must not be diluted.

**What it does**: reads the dialogue range for the just-completed stage (at checkpoints) or the whole pipeline (at completion), scores the pattern against the canonical rubric at `shared/collaboration_depth_rubric.md`, and emits an advisory block/chapter. Dimensions: Delegation Intensity, Cognitive Vigilance, Cognitive Reallocation, Zone Classification (Zone 1 / Zone 2 / Zone 3). Rubric is based on Wang & Zhang (2026) IJETHE 23:11 (DOI 10.1186/s41239-026-00585-x).

**Distinction from existing mechanisms**:

| Mechanism | What it evaluates | Blocking? |
|---|---|---|
| `integrity_verification_agent` (Stages 2.5 / 4.5) | Paper content — references, citations, data | Yes (blocking gate) |
| Stage 6 Collaboration Quality Evaluation (6 dims, 1–100) | AI's self-reflection on its own behaviour | No, but produced once only |
| `collaboration_depth_agent` (this observer) | The **user's** collaboration pattern (delegation intensity, vigilance, reallocation) | **No — never blocks. Advisory only.** |

**Non-blocking guarantees**:
- Observer output never appears on the "Flagged" line of any checkpoint.
- The `Ready to proceed?` prompt is unchanged by observer output.
- `blocked_by: collaboration_depth_agent` is never a legal state in `state_tracker`.
- If observer frontmatter ever asserts `blocking: true`, the orchestrator must refuse to dispatch it.

**Cross-model**: when `ARS_CROSS_MODEL` is set, the observer runs on both models and flags any dimension divergence > 2 points. Scores are never silently averaged across models.

> See `agents/collaboration_depth_agent.md` for full scoring procedure and anti-sycophancy discipline; `shared/collaboration_depth_rubric.md` for the canonical 4-dimension rubric.

---

## Anti-Patterns

Explicit prohibitions to prevent common failure modes:

| # | Anti-Pattern | Why It Fails | Correct Behavior |
|---|-------------|-------------|-----------------|
| 1 | **Skipping integrity checks** | "The paper looks fine, skip Stage 2.5/4.5" | Integrity checks are MANDATORY; they cannot be auto-skipped regardless of perceived quality |
| 2 | **Orchestrator doing substantive work** | Pipeline orchestrator writes content or reviews the paper | Orchestrator only dispatches and coordinates; substantive work belongs to the sub-skills |
| 3 | **Auto-advancing past MANDATORY checkpoints** | Moving to next stage without user confirmation at FULL checkpoints | MANDATORY checkpoints require explicit user input before proceeding |
| 4 | **Quality degradation across stages** | Stage 4 revision is worse than Stage 2 draft because context window is exhausted | If Stage N output quality < Stage N-1, PAUSE and reload core principles before continuing |
| 5 | **Silently dropping reviewer concerns** | Revision addresses 8 of 10 concerns and hopes nobody notices | The R&R tracking table must account for every concern with explicit status |
| 6 | **Re-verifying only known issues at Stage 4.5** | Final integrity check only re-checks Stage 2.5 findings | Stage 4.5 must verify from scratch independently; revision may introduce new issues |
| 7 | **Inflating Collaboration Quality scores** | Giving 90/100 to avoid awkward self-criticism | Honesty first: no inflation, no pleasantries; cite specific evidence for every score |
| 8 | **Bypassing the Failure Mode Checklist block** (v3.2) | "The 7-mode checklist is new, let's skip it this run" | Stage 2.5/4.5 Failure Mode Checklist is MANDATORY and BLOCKING; no `--no-block` flag exists; overrides require user reasoning recorded for Stage 6 |

---

## Quality Standards

| Dimension | Requirement |
|-----------|------------|
| Stage detection | Correctly identify user's current stage and available materials |
| Mode recommendation | Recommend appropriate mode based on user preferences and material status |
| Material handoff | Stage-to-stage handoff materials are complete and correctly formatted |
| State tracking | Pipeline state updated in real time; Progress Dashboard accurate |
| **Mandatory checkpoint** | **User confirmation required after each stage completion** |
| **Mandatory integrity check** | **Stage 2.5 and 4.5 cannot be skipped, must PASS** |
| **Mandatory failure mode checklist** (v3.2) | **Stage 2.5 and 4.5 must run the 7-mode AI research failure checklist; suspected failures block; overrides require user reasoning** |
| No overstepping | ⚠️ IRON RULE: Orchestrator does not perform substantive research/writing/reviewing, only dispatching |
| No forcing | ⚠️ IRON RULE: User can pause or exit pipeline at any time (but cannot skip integrity checks) |
| Reproducible | Same input follows the same workflow across different sessions |
| **Convergence-aware stopping** (v3.2) | **If delta < 3 points AND no P0 issues, suggest stopping revision loop; user can override** |
| **Budget transparency** (v3.2; #388) | **Token cost estimate + interaction-count budget (round-trip caps + accumulated count at checkpoints, advisory) + user confirmation at pipeline start** |

---

## Error Recovery

| Stage | Error | Handling |
|-------|-------|---------|
| Intake | Cannot determine entry point | Ask user what materials they have and their goal |
| Stage 1 | deep-research not converging | Suggest mode switch (socratic -> full) or narrow scope |
| Stage 2 | Missing research foundation | Suggest returning to Stage 1 to supplement research |
| Stage 2.5 | Still FAIL after 3 correction rounds | List unverifiable items; user decides whether to continue |
| Stage 3 | Review result is Reject | Provide options: major restructuring (Stage 2) or abandon |
| Stage 4 | Revision incomplete on all items | List unaddressed items; ask whether to continue |
| Stage 3' | Verification still has major issues | Enter Stage 4' for final revision |
| Stage 4' | Issues remain after revision | Mark as Acknowledged Limitations; proceed to Stage 4.5 |
| Stage 4.5 | Final verification FAIL | Fix and re-verify (max 3 rounds) |
| Any | User leaves midway | Save pipeline state; can resume from breakpoint next time |
| Any | Skill execution failure | Report error; suggest retry, pause, or mode switch. Do not skip mandatory integrity or failure-mode gates |

---

## Agent File References

| Agent | Definition File |
|-------|----------------|
| pipeline_orchestrator_agent | `agents/pipeline_orchestrator_agent.md` |
| state_tracker_agent | `agents/state_tracker_agent.md` |
| integrity_verification_agent | `agents/integrity_verification_agent.md` |
| collaboration_depth_agent | `agents/collaboration_depth_agent.md` |
| claim_ref_alignment_audit_agent | `agents/claim_ref_alignment_audit_agent.md` |

---

## Reference Files

| Reference | Purpose |
|-----------|---------|
| `references/pipeline_state_machine.md` | Complete state machine definition: all legal transitions, preconditions, actions |
| `references/plagiarism_detection_protocol.md` | Phase D originality verification protocol + self-plagiarism + AI text characteristics |
| `references/mode_advisor.md` | Unified cross-skill decision tree: maps user intent to optimal skill + mode |
| `references/claim_verification_protocol.md` | Phase E claim verification protocol: claim extraction, source tracing, cross-referencing, verdict taxonomy |
| `references/claim_audit_calibration_protocol.md` | v3.8 #103 claim_ref_alignment audit calibration: gold-set shape (T-C3), threshold gates FNR<0.15 / FPR<0.10 (T-C1), per-class FNR/FPR reporting (T-C2). Re-run via `PYTHONPATH=. python3 -m unittest scripts.test_claim_audit_calibration -v`. |
| `references/ai_research_failure_modes.md` | 7-mode AI research failure checklist (Lu 2026), run at Stage 2.5 + 4.5 with blocking behaviour, reported at Stage 6 |
| `references/team_collaboration_protocol.md` | Multi-person team coordination: role definitions, handoff protocol, version control, conflict resolution |
| `references/integrity_review_protocol.md` | Stage 2.5 + 4.5 integrity verification: 5-phase protocol details |
| `references/two_stage_review_protocol.md` | Two-stage review: Stage 3 full review + Stage 3' verification review |
| `references/external_review_protocol.md` | External (human) reviewer feedback: 4-step intake/coaching/revision/verification |
| `references/process_summary_protocol.md` | Stage 6: collaboration quality evaluation + AI self-reflection report |
| `references/reproducibility_audit.md` | Standardized workflow guarantees + audit trail format |
| `references/progress_dashboard_template.md` | ASCII progress dashboard template |
| `references/reinforcement_content.md` | Stage-specific reinforcement focus table for transitions |
| `references/changelog.md` | Full version history |
| `shared/handoff_schemas.md` | Cross-skill data contracts: 9 schemas for all inter-stage handoff artifacts |
| `shared/collaboration_depth_rubric.md` | Collaboration Depth Observer rubric (v1.0): 4 dimensions based on Wang & Zhang (2026) IJETHE 23:11 |

---

## Templates

| Template | Purpose |
|----------|---------|
| `templates/pipeline_status_template.md` | Progress Dashboard output template |

---

## Examples

| Example | Demonstrates |
|---------|-------------|
| `examples/full_pipeline_example.md` | Complete pipeline conversation log (Stage 1-5, with integrity + 2-stage review) |
| `examples/mid_entry_example.md` | Mid-entry example starting from Stage 2.5 (existing paper -> integrity check -> review -> revision -> finalization) |

---

## Output Language

Follows user language. Academic terminology retained in English.

---

## Integration with Other Skills

```
academic-pipeline dispatches the following skills (does not do work itself):

Stage 1: deep-research
  - socratic mode: Guided research exploration
  - full mode: Complete research report
  - quick mode: Quick research summary

Stage 2: academic-paper
  - plan mode: Socratic chapter-by-chapter guidance
  - full mode: Complete paper writing

Stage 2.5: integrity_verification_agent (Mode 1: pre-review)
Stage 4.5: integrity_verification_agent (Mode 2: final-check)

Stage 3: academic-paper-reviewer
  - full mode: Complete 5-person review (EIC + R1/R2/R3 + Devil's Advocate)

Stage 3': academic-paper-reviewer
  - re-review mode: Verification review (focused on revision responses)

Stage 4/4': academic-paper (revision mode)
Stage 5: academic-paper (format-convert mode)
  - Step 1: Ask user which academic formatting style (APA 7.0 / Chicago / IEEE, etc.)
  - Step 2: Produce MD, then generate DOCX via Pandoc when available (otherwise provide conversion instructions)
  - Step 3: Produce LaTeX (using corresponding document class, e.g., apa7 class for APA 7.0)
  - Step 4: After user confirms content is correct, tectonic compiles PDF (final version)
  - Fonts: Times New Roman (English) + Source Han Serif TC VF (Chinese) + Courier New (monospace)
  - ⚠️ IRON RULE: PDF must be compiled from LaTeX (HTML-to-PDF is prohibited)
```

---

## Related Skills

| Skill | Relationship |
|-------|-------------|
| `deep-research` | Dispatched (Stage 1 research phase) |
| `academic-paper` | Dispatched (Stage 2 writing, Stage 4/4' revision, Stage 5 formatting) |
| `academic-paper-reviewer` | Dispatched (Stage 3 first review, Stage 3' verification review) |

---

## Version Info

| Item | Content |
|------|---------|
| Skill Version | 3.15.0 |
| Last Updated | 2026-07-04 |
| Maintainer | Cheng-I Wu |
| Dependent Skills | deep-research v2.0+, academic-paper v2.0+, academic-paper-reviewer v1.1+ |
| Role | Full academic research workflow orchestrator |

---

## Changelog

> See `references/changelog.md` for full version history.