Academic Pipeline v3.5 — 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):

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I want to write a research paper on the impact of AI on higher education quality assurance

--> academic-pipeline launches, starting from Stage 2 (RESEARCH)

Mid-entry (existing paper):

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I already have a paper, help me review it

--> academic-pipeline detects mid-entry, starting from Stage 4 (INTEGRITY)

Revision mode (received reviewer feedback):

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I received reviewer comments, help me revise

--> academic-pipeline detects, starting from Stage 7 (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#

ScenarioSkill to UseOnly need to search materials or do a literature reviewdeep-researchOnly need to write a paper (no research phase needed)academic-paperOnly need to review a paperacademic-paper-reviewerOnly need to check citation formatacademic-paper (citation-check mode)Only need to convert paper formatacademic-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 (12 Stages)#

StageNameSkill / Agent CalledAvailable ModesDeliverables1LITERATURE SEARCHacademic-searchmulti-source, single-source, two-pass, query-expansionBibliography (BibTeX) + metadata (JSON) + CCF/venue level + optional PDFs2RESEARCHdeep-researchsocratic, full, quickRQ Brief, Methodology, Bibliography, Synthesis3WRITEacademic-paperplan, fullPaper Draft4INTEGRITYintegrity_verification_agentpre-reviewIntegrity verification report + corrected paper5REVIEWacademic-paper-reviewerfull (incl. Devil's Advocate)5 review reports + Editorial Decision + Revision Roadmap6RE-REVIEWacademic-paper-reviewerre-reviewVerification review report: revision response checklist + residual issues7REVISEacademic-paperrevisionRevised Draft, Response to Reviewers8RE-REVISEacademic-paperrevisionSecond revised draft (if needed)9FINAL INTEGRITY****integrity_verification_agentfinal-checkFinal verification report (must achieve 100% pass to proceed)10HUMANIZE****humanizer + humanizer-zh****full (双语互补)****De-AI 化论文全文 + 双语变更摘要11FINALIZEacademic-paperformat-convertFinal Paper (default MD + DOCX; ask about LaTeX; confirm correctness; PDF)12PROCESS SUMMARYorchestratorautoPaper creation process record MD + LaTeX to PDF (bilingual)

Parallelization opportunity (v3.3): Within Stage 3, 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.

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Pipeline State Machine#

1. Stage 1 LITERATURE SEARCH -> user confirmation -> Stage 2
2. Stage 2 RESEARCH -> user confirmation -> Stage 3
3. Stage 3 WRITE -> user confirmation -> Stage 4
4. Stage 4 INTEGRITY -> PASS -> Stage 5 (FAIL -> fix and re-verify, max 3 rounds)
5. Stage 5 REVIEW -> Accept -> Stage 9 / Minor|Major -> Stage 7 / Reject -> Stage 3 or end
6. Stage 7 REVISE -> user confirmation -> Stage 6
7. Stage 6 RE-REVIEW -> Accept|Minor -> Stage 9 / Major -> Stage 8
8. Stage 8 RE-REVISE -> user confirmation -> Stage 9 (no return to review)
9. Stage 9 FINAL INTEGRITY -> PASS (zero issues) -> Stage 10 (FAIL -> fix and re-verify)
10. Stage 10 HUMANIZE -> user confirmation -> Stage 11
11. Stage 11 FINALIZE -> MD + DOCX -> ask about LaTeX -> confirm -> PDF -> Stage 12
12. Stage 12 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#

⚠️ 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#

TypeWhen UsedContentFULLFirst checkpoint; after integrity boundaries; before finalizationFull deliverables list + decision dashboard + all optionsSLIMAfter 2+ consecutive "continue" responses on non-critical stagesOne-line status + auto-continue in 5 secondsMANDATORYIntegrity FAIL; Review decision; Stage 11Cannot be skipped; requires explicit user input

Decision Dashboard (shown at FULL checkpoints)#

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━━━ 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
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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 4, 9): always MANDATORY
4. Review decisions (Stage 5, 6'): always MANDATORY
5. Before finalization (Stage 11): 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 + 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

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.

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Agent Team (3 Agents)#

#AgentRoleFile1pipeline_orchestrator_agentMain orchestrator: detects stage, recommends mode, triggers skill, manages transitionsagents/pipeline_orchestrator_agent.md2state_tracker_agentState tracker: records completed stages, produced materials, revision loop countagents/state_tracker_agent.md3integrity_verification_agentIntegrity verifier: 100% reference/citation/data verificationagents/integrity_verification_agent.md

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Orchestrator Workflow#

Step 1: INTAKE & DETECTION#

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pipeline_orchestrator_agent analyzes the user's input:

1. What materials does the user have?
   - No materials           --> Stage 2 (RESEARCH)
   - Has research data      --> Stage 3 (WRITE)
   - Has paper draft        --> Stage 4 (INTEGRITY)
   - Has verified paper     --> Stage 5 (REVIEW)
   - Has review comments    --> Stage 7 (REVISE)
   - Has revised draft      --> Stage 6 (RE-REVIEW)
   - Has final draft for formatting --> Stage 11 (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#

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

User type determination:
- Novice / wants guidance --> socratic (Stage 2) + plan (Stage 3) + guided (Stage 5)
- Experienced / wants direct output --> full (Stage 2) + full (Stage 3) + full (Stage 5)
- Time-limited --> quick (Stage 2) + full (Stage 3) + quick (Stage 5)

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

Step 3: STAGE EXECUTION#

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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#

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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 2  --> 2: deep-research handoff (RQ Brief + Bibliography + Synthesis)
   - Stage 3  --> 4: Pass complete paper to integrity_verification_agent
   - Stage 4 --> 3: Pass verified paper to reviewer
   - Stage 5  --> 4: Pass Revision Roadmap to academic-paper revision mode
   - Stage 7  --> 6: Pass revised draft and Response to Reviewers to reviewer
   - Stage 6 --> 8: Pass new Revision Roadmap + R&R Traceability Matrix (Schema 11) to academic-paper revision mode
   - Stage 7/8 --> 9: Pass revision-completed paper to integrity_verification_agent (final verification)
   - Stage 9 --> 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):

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--- 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.

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Integrity Review Protocol#

Stage 4 (pre-review) and Stage 9 (post-revision) verification. 5-phase protocol: references → citation context → statistical data → originality → claims.

⚠️ IRON RULE: Stage 9 must PASS with zero issues to proceed to Stage 11. Stage 9 verifies from scratch independently.

⚠️ IRON RULE (v3.2): Both Stage 4 and Stage 9 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 12 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.

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Two-Stage Review Protocol#

Stage 5 (full review, 5 reviewers) → Revision Coaching → Stage 7 → Stage 6 (re-review) → optional Residual Coaching → Stage 8.

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

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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 4

• If the user brings a paper and enters directly, go through Stage 4 (INTEGRITY) first before Stage 5 (REVIEW)
• Only exception: User can provide a previous integrity verification report and content has not been modified

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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.

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Progress Dashboard#

ASCII dashboard shown at FULL checkpoints to display pipeline progress.

See references/progress_dashboard_template.md for the dashboard template.

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Revision Loop Management#

• Stage 5 (first review) -> Stage 7 (revision) -> Stage 6 (verification review) -> Stage 8 (re-revision, if needed) -> Stage 9 (final verification)
• Maximum 1 round of RE-REVISE (Stage 8): If Stage 6 gives Major, enter Stage 8 for revision then proceed directly to Stage 9 (no return to review)
• Pipeline overrides academic-paper's max 2 revision rule: In the pipeline, revisions are limited to Stage 7 + Stage 8 (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 7 + Stage 8).

Budget Transparency (v3.2)#

At pipeline start, estimate token cost based on paper length, mode, and cross-model toggle. Present estimate and ask for user confirmation before Stage 2 begins.

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Reproducibility#

Every pipeline artifact is versioned, hashed, and auditable.

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

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Stage 12: 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.

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Anti-Patterns#

Explicit prohibitions to prevent common failure modes:

#Anti-PatternWhy It FailsCorrect Behavior1Skipping integrity checks"The paper looks fine, skip Stage 4, 9"Integrity checks are MANDATORY; they cannot be auto-skipped regardless of perceived quality2Orchestrator doing substantive workPipeline orchestrator writes content or reviews the paperOrchestrator only dispatches and coordinates; substantive work belongs to the sub-skills3Auto-advancing past MANDATORY checkpointsMoving to next stage without user confirmation at FULL checkpointsMANDATORY checkpoints require explicit user input before proceeding4Quality degradation across stagesStage 7 revision is worse than Stage 3 draft because context window is exhaustedIf Stage N output quality < Stage N-1, PAUSE and reload core principles before continuing5Silently dropping reviewer concernsRevision addresses 8 of 10 concerns and hopes nobody noticesThe R&R tracking table must account for every concern with explicit status6Re-verifying only known issues at Stage 9Final integrity check only re-checks Stage 4 findingsStage 9 must verify from scratch independently; revision may introduce new issues7Inflating Collaboration Quality scoresGiving 90/100 to avoid awkward self-criticismHonesty first: no inflation, no pleasantries; cite specific evidence for every score8Bypassing the Failure Mode Checklist block (v3.2)"The 7-mode checklist is new, let's skip it this run"Stage 4, 9 Failure Mode Checklist is MANDATORY and BLOCKING; no --no-block flag exists; overrides require user reasoning recorded for Stage 12

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Quality Standards#

DimensionRequirementStage detectionCorrectly identify user's current stage and available materialsMode recommendationRecommend appropriate mode based on user preferences and material statusMaterial handoffStage-to-stage handoff materials are complete and correctly formattedState trackingPipeline state updated in real time; Progress Dashboard accurateMandatory checkpointUser confirmation required after each stage completionMandatory integrity checkStage 4 and 9 cannot be skipped, must PASSMandatory failure mode checklist (v3.2)Stage 4 and 9 must run the 7-mode AI research failure checklist; suspected failures block; overrides require user reasoningNo overstepping⚠️ IRON RULE: Orchestrator does not perform substantive research/writing/reviewing, only dispatchingNo forcing⚠️ IRON RULE: User can pause or exit pipeline at any time (but cannot skip integrity checks)ReproducibleSame input follows the same workflow across different sessionsConvergence-aware stopping (v3.2)If delta < 3 points AND no P0 issues, suggest stopping revision loop; user can override****Budget transparency (v3.2)Token cost estimate + user confirmation at pipeline start

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Error Recovery#

StageErrorHandlingIntakeCannot determine entry pointAsk user what materials they have and their goalStage 2deep-research not convergingSuggest mode switch (socratic -> full) or narrow scopeStage 3Missing research foundationSuggest returning to Stage 2 to supplement researchStage 4Still FAIL after 3 correction roundsList unverifiable items; user decides whether to continueStage 5Review result is RejectProvide options: major restructuring (Stage 3) or abandonStage 7Revision incomplete on all itemsList unaddressed items; ask whether to continueStage 6Verification still has major issuesEnter Stage 8 for final revisionStage 8Issues remain after revisionMark as Acknowledged Limitations; proceed to Stage 9Stage 9Final verification FAILFix and re-verify (max 3 rounds)AnyUser leaves midwaySave pipeline state; can resume from breakpoint next timeAnySkill execution failureReport error; suggest retry or skip

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Agent File References#

AgentDefinition Filepipeline_orchestrator_agentagents/pipeline_orchestrator_agent.mdstate_tracker_agentagents/state_tracker_agent.mdintegrity_verification_agentagents/integrity_verification_agent.md

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Reference Files#

ReferencePurposereferences/pipeline_state_machine.mdComplete state machine definition: all legal transitions, preconditions, actionsreferences/plagiarism_detection_protocol.mdPhase D originality verification protocol + self-plagiarism + AI text characteristicsreferences/mode_advisor.mdUnified cross-skill decision tree: maps user intent to optimal skill + modereferences/claim_verification_protocol.mdPhase E claim verification protocol: claim extraction, source tracing, cross-referencing, verdict taxonomyreferences/ai_research_failure_modes.md7-mode AI research failure checklist (Lu 2026), run at Stage 4 + 9 with blocking behaviour, reported at Stage 12references/team_collaboration_protocol.mdMulti-person team coordination: role definitions, handoff protocol, version control, conflict resolutionreferences/integrity_review_protocol.mdStage 4 + 9 integrity verification: 5-phase protocol detailsreferences/two_stage_review_protocol.mdTwo-stage review: Stage 5 full review + Stage 6 verification reviewreferences/external_review_protocol.mdExternal (human) reviewer feedback: 4-step intake/coaching/revision/verificationreferences/process_summary_protocol.mdStage 12: collaboration quality evaluation + AI self-reflection reportreferences/reproducibility_audit.mdStandardized workflow guarantees + audit trail formatreferences/progress_dashboard_template.mdASCII progress dashboard templatereferences/reinforcement_content.mdStage-specific reinforcement focus table for transitionsreferences/changelog.mdFull version historyshared/handoff_schemas.mdCross-skill data contracts: 9 schemas for all inter-stage handoff artifacts

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Templates#

TemplatePurposetemplates/pipeline_status_template.mdProgress Dashboard output template

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Examples#

ExampleDemonstratesexamples/full_pipeline_example.mdComplete pipeline conversation log (Stage 2-5, with integrity + 2-stage review)examples/mid_entry_example.mdMid-entry example starting from Stage 4 (existing paper -> integrity check -> review -> revision -> finalization)

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Output Language#

Follows user language. Academic terminology retained in English.

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Integration with Other Skills#

text

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

Stage 2: deep-research
  - socratic mode: Guided research exploration
  - full mode: Complete research report
  - quick mode: Quick research summary

Stage 3: academic-paper
  - plan mode: Socratic chapter-by-chapter guidance
  - full mode: Complete paper writing

Stage 4: integrity_verification_agent (Mode 1: pre-review)
Stage 9: integrity_verification_agent (Mode 2: final-check)

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

Stage 6: academic-paper-reviewer
  - re-review mode: Verification review (focused on revision responses)

Stage 7/8: academic-paper (revision mode)
Stage 11: 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)

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Related Skills#

SkillRelationshipdeep-researchDispatched (Stage 2 research phase)academic-paperDispatched (Stage 3 writing, Stage 7/8 revision, Stage 11 formatting)academic-paper-reviewerDispatched (Stage 5 first review, Stage 6 verification review)

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Version Info#

ItemContentSkill Version3.2Last Updated2026-04-09MaintainerCheng-I WuDependent Skillsdeep-research v2.0+, academic-paper v2.0+, academic-paper-reviewer v1.1+RoleFull academic research workflow orchestrator

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Changelog#

See references/changelog.md for full version history.