| name | academic-pipeline |
| description | Orchestrator for the full academic research pipeline: research -> write -> integrity check -> review -> revise -> re-review -> re-revise -> final integrity check -> finalize. Coordinates deep-research, academic-paper, and academic-paper-reviewer into a seamless 9-stage workflow with mandatory integrity verification, two-stage peer review, and reproducible quality gates. Triggers on: academic pipeline, research to paper, full paper workflow, paper pipeline, end-to-end paper, research-to-publication, complete paper workflow. |
| metadata | {"version":"2.6","last_updated":"2026-03-08","depends_on":"deep-research, academic-paper, academic-paper-reviewer"} |
Academic Pipeline v2.6 — 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)
| 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
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
- 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
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 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
Integrity Review Protocol (Added in v2.0)
Stage 2.5: First Integrity Check (Pre-Review Integrity)
Trigger: After Stage 2 (WRITE) completion, before Stage 3 (REVIEW)
Purpose: Ensure all references and data are not fabricated or erroneous before submission for review
Execution steps:
1. integrity_verification_agent executes Mode 1 (initial verification) on the paper
2. Verification scope:
- Phase A: 100% reference existence + bibliographic accuracy + ghost citations
- Phase B: >= 30% citation context spot-check
- Phase C: 100% statistical data verification
- Phase D: >= 30% originality spot-check + self-plagiarism check
- Phase E: 30% claim verification spot-check (minimum 10 claims)
3. Result handling:
- PASS -> checkpoint -> Stage 3
- FAIL -> produce correction list -> fix item by item -> re-verify corrected items
- PASS after corrections -> checkpoint -> Stage 3
- Still FAIL after 3 rounds -> notify user, list unverifiable items
Stage 4.5: Final Integrity Check (Post-Revision Final Check)
Trigger: After Stage 4' (RE-REVISE) or Stage 3' (RE-REVIEW, Accept) completion, before Stage 5 (FINALIZE)
Purpose: Confirm the revised paper is 100% correct and ready for publication
Execution steps:
1. integrity_verification_agent executes Mode 2 (final verification) on the revised draft
2. Verification scope:
- Phase A: 100% reference verification (including those added during revision)
- Phase B: 100% citation context verification (not spot-check, full check)
- Phase C: 100% statistical data verification
- Phase D: >= 50% originality spot-check (100% for newly added/modified paragraphs)
- Phase E: 100% claim verification (zero MAJOR_DISTORTION + zero UNVERIFIABLE required)
3. Special check: Compare with Stage 2.5 results to confirm all previous issues are resolved
4. Result handling:
- PASS (zero issues) -> checkpoint -> Stage 5
- FAIL -> fix -> re-verify -> PASS -> Stage 5
5. **Must PASS with zero issues to proceed to Stage 5**
Two-Stage Review Protocol (Added in v2.0)
Stage 3: First Review (Full Review)
- Input: Paper that passed integrity check
- Review team: EIC + R1 (methodology) + R2 (domain) + R3 (interdisciplinary) + Devil's Advocate
- Output: 5 review reports + Editorial Decision + Revision Roadmap + Socratic Revision Coaching
- Decision branches: Accept -> Stage 4.5 / Minor|Major -> Revision Coaching -> Stage 4 / Reject -> Stage 2 or end
See academic-paper-reviewer/SKILL.md for review process details.
Stage 3 -> 4 Transition: Revision Coaching
EIC uses Socratic dialogue to guide the user in understanding review comments and planning revision strategy (max 8 rounds). User can say "just fix it for me" to skip.
Stage 3': Second Review (Verification Review)
- Input: Revised draft + Response to Reviewers + original Revision Roadmap
- Mode:
academic-paper-reviewer re-review mode
- Output: Revision response comparison table + new issues list + new Editorial Decision
- Decision branches: Accept|Minor -> Stage 4.5 / Major -> Residual Coaching -> Stage 4'
See academic-paper-reviewer/SKILL.md Re-Review Mode for verification review process.
Stage 3' -> 4' Transition: Residual Coaching
EIC guides the user in understanding residual issues and making trade-offs (max 5 rounds). User can say "just fix it" to skip.
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 (Added in v2.5)
Scenario: The user submitted to a journal and received feedback from real human reviewers, bringing those comments into the pipeline.
Trigger: User says "I received reviewer comments," "reviewer comments," "revise and resubmit," etc.
Differences from Internal Review
| Aspect | Internal Review (Stage 3 simulation) | External Review (real journal) |
|---|
| Source of review comments | Pipeline's AI reviewers | Journal's human reviewers |
| Comment format | Structured (Revision Roadmap) | Unstructured (free text, PDF, email) |
| Comment quality | Consistent, predictable | Variable quality, may be vague or contradictory |
| Revision strategy | Can accept wholesale | Need to judge which to accept/reject/negotiate |
| Acceptance criteria | AI re-review suffices | Ultimately decided by human reviewers |
Step 1: Intake and Structuring
1. Receive reviewer comments (supported formats):
- Directly pasted text
- Provide PDF/DOCX file path
- Copy from journal system review letter
2. Parse into structured list:
For each comment, extract:
- Reviewer number (Reviewer 1/2/3 or R1/R2/R3)
- Comment type: Major / Minor / Editorial / Positive
- Core request (one-sentence summary)
- Original text quote
- Paper section involved
3. Produce External Review Summary:
+----------------------------------------+
| External Review Summary |
+----------------------------------------+
| Journal: [journal name] |
| Decision: [R&R / Major / Minor] |
| Reviewers: [N] |
| Total comments: [N] |
| Major: [n] Minor: [n] Editorial: [n]|
+----------------------------------------+
4. Confirm parsing results with user:
"I organized the reviewer comments into [N] items. Here is the summary — please confirm nothing was missed or misinterpreted."
Step 2: Strategic Revision Coaching (External Revision Coaching)
Unlike the Socratic coaching for internal review, external review coaching focuses more on strategic judgment:
For each Major comment, guide the user to think through:
1. Understanding layer
"What is this reviewer's core concern? Is it about methodology, theory, or presentation?"
2. Judgment layer
"Do you agree with this criticism?"
- Agree -> "How do you plan to revise?"
- Partially agree -> "Which parts do you agree with and which not? What is your basis for disagreement?"
- Disagree -> "What is your rebuttal argument? Can you support it with literature or data?"
3. Strategy layer
"How will you phrase this in the response letter?"
- Accept revision: Show specifically what was changed and where
- Partially accept: Explain the accepted parts + reasons for non-acceptance (must be persuasive)
- Reject: Provide sufficient scholarly rationale (literature, data, methodological argumentation)
4. Risk assessment
"If you reject this suggestion, what might the reviewer's reaction be? Is it worth the risk?"
Key principles:
- Do not default to "accept all": Real reviewer comments are not always correct — some may be based on misunderstanding or school-of-thought bias
- Encourage user to inject context: "What school of thought do you think this reviewer might come from? What context might they not be aware of?"
- User can say "just fix it for me" to skip: But when skipping strategic discussion, AI defaults to accepting all comments (conservative strategy)
- Maximum 8 rounds of dialogue, but at least 1 round per Major comment
Step 3: Revision and Response to Reviewers
Produce two documents:
1. Revised draft
- Track all modification locations (additions/deletions/rewrites)
- Revision content consistent with Response to Reviewers
2. Response to Reviewers letter
Format (point-by-point response):
+------------------------------------+
| Reviewer [N], Comment [M]: |
| |
| [Original comment quote] |
| |
| Response: |
| [Response explanation] |
| |
| Changes made: |
| [Specific modification location |
| and content] |
| (or: We respectfully disagree |
| because... [rationale]) |
+------------------------------------+
Step 4: Self-Verification (Completeness Check)
Stage 3' behavior adjustments in external review mode:
1. Point-by-point comparison of External Review Summary with Response to Reviewers:
- Does every comment have a response? (completeness)
- Is each response consistent with actual changes? (consistency)
- Were the places claimed as "modified" actually changed? (truthfulness)
2. New citation verification:
- New references added during revision enter Stage 4.5 integrity verification
3. Things NOT done (different from internal review):
- Do not reassess paper quality (that is the human reviewers' job)
- Do not issue a new Editorial Decision
- Do not raise new revision requests
Honest Capability Boundaries
- AI verification does not equal human reviewer satisfaction: Stage 3' can confirm revisions are "complete and consistent," but cannot predict whether human reviewers will accept your responses. Reviewers may have unstated expectations, school-of-thought preferences, or methodological insistence
- Unstructured comments may not parse perfectly: Some reviewers write vaguely (e.g., "the methodology needs more work"), and AI will do its best to parse but may miss implied intentions. After parsing, user confirmation is mandatory
- AI cannot make scholarly judgments for you: "Should I accept Reviewer 2's suggestion?" is your decision. AI can provide an analytical framework, but final judgment rests with the researcher
- Cross-cultural review convention differences: Response conventions differ across journals/academic circles (some require extreme deference, others accept direct rebuttal). AI defaults to neutral academic tone; the user can request adjustments
Progress Dashboard
Users can say "status" or "pipeline status" at any time to view:
+=============================================+
| Academic Pipeline v2.0 Status |
+=============================================+
| Topic: Impact of AI on Higher Education |
| Quality Assurance |
+---------------------------------------------+
Stage 1 RESEARCH [v] Completed
Stage 2 WRITE [v] Completed
Stage 2.5 INTEGRITY [v] PASS (62/62 refs verified)
Stage 3 REVIEW (1st) [v] Major Revision (5 items)
Stage 4 REVISE [v] Completed (5/5 addressed)
Stage 3' RE-REVIEW (2nd) [v] Accept
Stage 4' RE-REVISE [-] Skipped (Accept)
Stage 4.5 FINAL INTEGRITY [..] In Progress
Stage 5 FINALIZE [ ] Pending
Stage 6 PROCESS SUMMARY [ ] Pending
+---------------------------------------------+
| Integrity Verification: |
| Pre-review: PASS (0 issues) |
| Final: In progress... |
+---------------------------------------------+
| Review History: |
| Round 1: Major Revision (5 required) |
| Round 2: Accept |
+=============================================+
See templates/pipeline_status_template.md for the output 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
v2.0 design ensures consistent quality assurance with each execution:
Standardized Workflow
| Guarantee Item | Mechanism |
|---|
| Integrity check every time | Stage 2.5 + Stage 4.5 are mandatory stages, cannot be skipped |
| Consistent review angles | EIC + R1/R2/R3 + Devil's Advocate — five fixed perspectives |
| Consistent verification methods | integrity_verification_agent uses standardized search templates |
| Consistent quality thresholds | Integrity check PASS/FAIL criteria are explicit (zero SERIOUS + zero MEDIUM + zero MAJOR_DISTORTION + zero UNVERIFIABLE) |
| Traceable workflow | Every stage's deliverables are recorded, enabling retrospective audit |
Audit Trail
When the pipeline ends, state_tracker_agent produces a complete audit trail:
Pipeline Audit Trail
====================
Topic: [topic]
Started: [time]
Completed: [time]
Total Stages: [X/9]
Stage 1 RESEARCH: [mode] -> [output count]
Stage 2 WRITE: [mode] -> [word count]
Stage 2.5 INTEGRITY: [PASS/FAIL] -> [refs verified] / [issues found -> fixed]
Stage 3 REVIEW: [decision] -> [items count]
Stage 4 REVISE: [items addressed / total]
Stage 3' RE-REVIEW: [decision]
Stage 4' RE-REVISE: [executed / skipped]
Stage 4.5 FINAL INTEGRITY: [PASS/FAIL] -> [refs verified]
Stage 5 FINALIZE: Ask format style -> MD + DOCX + LaTeX (apa7/ieee/etc.) -> tectonic -> PDF
Stage 6 PROCESS SUMMARY: Ask language -> MD -> LaTeX -> PDF (zh/en)
Integrity Summary:
Pre-review: [X] refs checked, [Y] issues found, [Y] fixed
Final: [X] refs checked, [Y] issues found, [Y] fixed
Overall: [CLEAN / ISSUES NOTED]
Stage 6: Process Summary Protocol (Added in v2.4)
Trigger: After Stage 5 (FINALIZE) completion
Purpose: Document the complete human-AI collaboration history for the paper creation process, for user sharing, reporting, or reflection
Workflow
1. Ask user language preference:
"Which language version of the process record would you like to generate first?"
- Chinese (Traditional Chinese)
- English
- Both (default: generate the user's primary conversation language first)
2. Review session history and compile the following:
- User's initial instructions (verbatim quote)
- Key decision points and user interventions at each stage
- Direction correction moments and reasons
- Iteration count and review result summaries
- Intellectual insights raised by the user (e.g., questions that spawned new chapters)
- Quality requirement evolution (e.g., formatting, tone adjustments)
- Pipeline statistics (stage count, review rounds, integrity verification count, etc.)
3. Generate Markdown version (paper_creation_process.md / paper_creation_process_en.md)
4. Convert to LaTeX and compile PDF:
- pandoc MD -> LaTeX body
- Package complete LaTeX document (with cover page, table of contents, headers/footers)
- tectonic compile PDF
- Chinese version requires xeCJK + Source Han Serif TC VF
Required Content in Process Record
| Section | Content |
|---|
| Paper Information | Title, final deliverables list |
| Stage-by-Stage Process | Input/output/key decisions for each stage, with verbatim user quotes |
| Iteration Details | Review comment summaries, revision items, re-review results |
| Interaction Pattern Summary | User role, Claude role, intervention count, key turning points — statistics table |
| User Key Decisions | Chronological list of every important decision made by the user |
| Key Lessons | Reusable lessons learned from the process |
| Collaboration Quality Evaluation | Final chapter: 1-100 score + dimensional analysis + improvement suggestions (see below) |
Collaboration Quality Evaluation (Final Chapter, Mandatory)
The final chapter of the process record is a "Collaboration Quality Evaluation" that honestly and constructively assesses the user's performance in the human-AI collaboration. Format follows the Claude Code CLI /insight feature.
Scoring Dimensions (each 1-100, weighted average for overall score)
+--------------------------------------------------+
| Collaboration Quality Score: [XX]/100 |
+--------------------------------------------------+
| |
| Direction Setting [---------- ] XX |
| Clarity, timing, scope definition |
| |
| Intellectual Contribution [------------ ] XX |
| Insight depth, original questions, concept |
| challenges |
| |
| Quality Gatekeeping [--------- ] XX |
| Visual inspection, formatting requirements, |
| quality standards |
| |
| Iteration Discipline [---------- ] XX |
| Timely direction correction, willingness to |
| re-run pipeline, refusing to settle |
| |
| Delegation Efficiency [------- ] XX |
| When to intervene/when to let go, instruction |
| precision, checkpoint efficiency |
| |
| Meta-Learning [------------ ] XX |
| Feeding experience back to skills, requesting |
| lesson recording, process improvement awareness |
| |
+--------------------------------------------------+
Scoring Criteria
| Score Range | Meaning |
|---|
| 90-100 | Exceptional — User intervention significantly elevated the paper's intellectual quality beyond what AI could produce independently |
| 75-89 | Excellent — User made correct directional decisions and effectively leveraged the pipeline's iteration capabilities |
| 60-74 | Good — User completed necessary decisions but some opportunities were missed |
| 40-59 | Basic — User primarily served as a "continue" button with little substantive intervention |
| 1-39 | Needs Improvement — User intervention may have disrupted the workflow or lacked critical quality gatekeeping |
Required Subsections
- Overall Score: Total score + one-sentence evaluation
- What Worked Well: 2-4 specific behaviors, with verbatim user quotes
- Missed Opportunities: 1-3 things the user could have done but didn't
- Recommendations for Next Time: 3-5 specific, actionable improvement suggestions
- Human vs AI Value-Add: Clearly identify which aspects of the final paper quality came from user intervention (not achievable by AI independently)
Evaluation Principles
- Honesty first: No inflation, no pleasantries. If the user only pressed "continue," reflect that truthfully
- Evidence-based: Every score is supported by specific behaviors or conversation records
- Constructive: Every criticism must include actionable improvement suggestions
- Acknowledge uncertainty: If certain dimensions cannot be evaluated (e.g., mid-entry skipped the research stage), mark as N/A
- Bidirectional reflection: Also candidly point out Claude's shortcomings during the process (e.g., areas requiring multiple corrections)
Output Specifications
- Filename:
paper_creation_process.md (Chinese) / paper_creation_process_en.md (English)
- PDF:
paper_creation_process_zh.pdf / paper_creation_process_en.pdf
- LaTeX template:
article class, 12pt, A4, Times New Roman + Source Han Serif TC VF
- Includes table of contents:
\tableofcontents
- Header: left = document title (italic), right = date
- Compilation: tectonic (same toolchain as Stage 5)
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 | Orchestrator does not perform substantive research/writing/reviewing, only dispatching |
| No forcing | 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 |
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)
- 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 | 2.6 |
| Last Updated | 2026-03-08 |
| 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
| Version | Date | Changes |
|---|
| 2.6 | 2026-03-08 | Handoff Data Schema: Enhanced shared/handoff_schemas.md with 9 comprehensive schemas (RQ Brief, Bibliography, Synthesis, Paper Draft, Integrity Report, Review Report, Revision Roadmap, Response to Reviewers, Material Passport) with full field definitions, type constraints, and validation rules; orchestrator validates output against schemas before each transition. Adaptive Checkpoint System: Replaced static checkpoint template with 3-tier system (FULL/SLIM/MANDATORY) based on stage criticality and user engagement; FULL checkpoints include decision dashboard with metrics; SLIM auto-continues for experienced users; MANDATORY cannot be bypassed at integrity/review/finalization boundaries; awareness guard after 4+ auto-continues. Mode Advisor: New references/mode_advisor.md with unified cross-skill decision tree, common misconceptions table, user archetype recommendations, decision flowchart, and anti-patterns guide. Team Collaboration Protocol: New references/team_collaboration_protocol.md with 5 role definitions, per-transition handoff procedures, git branching/tagging strategy, conflict resolution matrix, and communication templates; state tracker extended with assigned_to, approval_gate, team_notes per stage and schema_validation_log. Phase E Claim Verification: New references/claim_verification_protocol.md with E1 claim extraction, E2 source tracing, E3 cross-referencing; verdict taxonomy (VERIFIED / MINOR_DISTORTION / MAJOR_DISTORTION / UNVERIFIABLE / UNVERIFIABLE_ACCESS); severity mapping (MAJOR_DISTORTION -> SERIOUS, UNVERIFIABLE -> SERIOUS, MINOR_DISTORTION -> MINOR, UNVERIFIABLE_ACCESS -> MEDIUM); integrated into integrity_verification_agent Mode 1 (30% spot-check) and Mode 2 (100%); pass/fail criteria updated to include Phase E verdicts. Mid-Entry Material Passport Check: Pipeline orchestrator now validates Material Passport on mid-entry; decision tree checks verification_status, freshness (< 24 hours), and content modification (version_label comparison); offers skip/spot-check/full re-verify options for Stage 2.5 when passport is valid; passport freshness validation rules added to shared/handoff_schemas.md |
| 2.5 | 2026-03-08 | External Review Protocol: structured intake of real journal reviewer feedback (text/PDF/DOCX); 4-step workflow (parse -> strategic coaching -> revise + Response to Reviewers -> completeness check); differentiated behavior from internal simulated review (no default "accept all", risk assessment per comment, user confirmation of parsed items); explicit capability boundaries (AI verification ≠ reviewer satisfaction) |
| 2.4 | 2026-03-08 | Stage 6 PROCESS SUMMARY: post-pipeline paper creation process record; asks user preferred language (zh/en/both); generates structured MD summarizing full human-AI collaboration history with user quotes, key decisions, iteration details, and lessons learned; mandatory final chapter: Collaboration Quality Evaluation (6 dimensions scored 1-100, bar chart visualization, What Worked Well / Missed Opportunities / Recommendations / Human vs AI Value-Add / Claude's Self-Reflection); compiles to PDF via LaTeX + tectonic; outputs paper_creation_process_zh.pdf + paper_creation_process_en.pdf |
| 2.3 | 2026-03-08 | Stage 5 FINALIZE: mandatory formatting style prompt (APA 7.0 / Chicago / IEEE); PDF must compile from LaTeX via tectonic (no HTML-to-PDF); APA 7.0 uses apa7 document class (man mode) with XeCJK for bilingual support; font stack: Times New Roman + Source Han Serif TC VF + Courier New |
| 2.2 | 2025-03-05 | Checkpoint confirmation semantics (6 user commands with precise actions); mode switching rules (safe/dangerous/prohibited matrix); skill failure fallback matrix (per-stage degradation strategies); state ownership protocol (single source of truth with write access control); material version control (versioned artifacts with audit trail); cross-skill reference to shared/handoff_schemas.md |
| 2.1 | 2026-03 | Added plagiarism detection protocol (Phase D); enhanced integrity_verification_agent with originality verification (D1 WebSearch, D2 self-plagiarism); updated both verification modes |
| 2.0 | 2026-02 | Added Stage 2.5/4.5 integrity checks, two-stage review, mandatory checkpoints, Devil's Advocate, reproducibility guarantees, integrity_verification_agent |
| 1.0 | 2026-02 | Initial version: 5+1 stage pipeline |
