Academic Pipeline v3.0 — 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.

v2.0 Core Improvements:

Mandatory user confirmation checkpoints — Each stage completion requires user confirmation before proceeding to the next step
Academic integrity verification — After paper completion and before review submission, 100% reference and data verification must pass
Two-stage review — First full review + post-revision focused verification review
Final integrity check — After revision completion, re-verify all citations and data are 100% correct
Reproducible — Standardized workflow producing consistent quality assurance each time
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:

Detect the user's current stage and available materials
Recommend the optimal mode for each stage
Dispatch the corresponding skill for each stage
After each stage completion, proactively prompt and wait for user confirmation
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, do not force them into the pipeline
The pipeline is optional, not mandatory

Pipeline Stages (10 Stages)


deep-research
academic-paper
integrity_verification_agent
academic-paper-reviewer
academic-paper
academic-paper-reviewer
academic-paper
integrity_verification_agent
academic-paper


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)

Pipeline State Machine

Stage 1 RESEARCH -> user confirmation -> Stage 2
Stage 2 WRITE -> user confirmation -> Stage 2.5
Stage 2.5 INTEGRITY -> PASS -> Stage 3 (FAIL -> fix and re-verify, max 3 rounds)
Stage 3 REVIEW -> Accept -> Stage 4.5 / Minor|Major -> Stage 4 / Reject -> Stage 2 or end
Stage 4 REVISE -> user confirmation -> Stage 3'
Stage 3' RE-REVIEW -> Accept|Minor -> Stage 4.5 / Major -> Stage 4'
Stage 4' RE-REVISE -> user confirmation -> Stage 4.5 (no return to review)
Stage 4.5 FINAL INTEGRITY -> PASS (zero issues) -> Stage 5 (FAIL -> fix and re-verify)
Stage 5 FINALIZE -> MD + DOCX -> ask about LaTeX -> confirm -> PDF -> Stage 6
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 + 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

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

Checkpoint Rules

⚠️ IRON RULE: Cannot auto-skip MANDATORY checkpoints: Even if the previous stage result is perfect, explicit user input is required at MANDATORY checkpoints
User can adjust: At FULL and MANDATORY checkpoints, users can modify the mode or settings for the next step
Pause-friendly: Users can pause at any checkpoint and resume later
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
Awareness guard: After 4+ consecutive auto-continues, 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:

Citation integrity: Are there any unverified citations in the latest output?
Sycophantic concession: Did the latest stage uncritically accept all feedback without pushback?
Quality trajectory: Is the latest output ≥ the quality of the previous stage? If declining, PAUSE and flag.
Scope discipline: Did the latest stage add content not requested by the user or the revision roadmap?
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 (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`

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.

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.

See
references/integrity_review_protocol.md
for full 5-phase verification procedures.

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:

Detect materials: Analyze the content provided by the user to determine what is available
Identify gaps: Check what prerequisite materials are needed for the target stage
Suggest backfilling: If critical materials are missing, suggest whether to return to earlier stages
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)

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.

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

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
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

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 or skip

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`

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/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

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: Auto-produce MD + DOCX
  - 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	3.0
Last Updated	2026-04-06
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.