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.
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:
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:
English: academic pipeline, research to paper, full paper workflow, paper pipeline, end-to-end paper, research-to-publication, complete paper workflow
| 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) |
| 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) |
See references/pipeline_state_machine.md for complete state transition definitions.
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.
| 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 |
━━━ 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
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
| # | 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 |
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
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
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
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
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
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**
See academic-paper-reviewer/SKILL.md for review process details.
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.
academic-paper-reviewer re-review modeSee academic-paper-reviewer/SKILL.md Re-Review Mode for verification review process.
EIC guides the user in understanding residual issues and making trade-offs (max 5 rounds). User can say "just fix it" to skip.
Users can enter from any stage. The orchestrator will:
Important: mid-entry cannot skip Stage 2.5
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.
| 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 |
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."
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:
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]) |
+------------------------------------+
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
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.
v2.0 design ensures consistent quality assurance with each execution:
| 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 |
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]
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
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
| 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) |
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.
+--------------------------------------------------+
| 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 |
| |
+--------------------------------------------------+
| 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 |
The second-to-last chapter of the process record is an "AI Self-Reflection Report" that honestly documents AI's own behavioral patterns during the pipeline. This complements the Collaboration Quality Evaluation (which assesses the user) by assessing the AI.
All metrics below are derived from existing agent logs ([DA-DECISION], [DA-REBUTTAL], [HEALTH-CHECK], state tracker JSON) — no additional per-stage instrumentation is required. The orchestrator aggregates these at Stage 6 by scanning the dialogue transcript:
+--------------------------------------------------+
| AI Self-Reflection Report |
+--------------------------------------------------+
| |
| DA Concession Rate X/Y (Z%) |
| (concessions / total rebuttals received) |
| |
| DA Consecutive Concessions [list if any] |
| (violations of no-consecutive rule) |
| |
| Checkpoints Skipped X/Y |
| (SLIM or user-skipped / total checkpoints) |
| |
| User Overrides X |
| (times user overruled AI recommendation) |
| |
| Dialogue Health Alerts X |
| (health check interventions triggered) |
| - Persistent Agreement: X |
| - Conflict Avoidance: X |
| - Premature Convergence: X |
| |
| Intent Mode Transitions X |
| (exploratory ↔ goal-oriented switches) |
| |
| Cross-Model Disagreements X (if enabled) |
| (integrity + DA combined) |
| |
+--------------------------------------------------+
[CROSS-MODEL-FINDING] that the primary DA missed (if cross-model was enabled), or any frame-lock detections triggered during checkpoints. If none, state "No frame-lock incidents detected — note this could mean either good coverage or undetected frame-lock."For dimensions with no findings, state the null result in one sentence. Expand only when issues are detected. The real risk is generating verbose "everything is fine" paragraphs for empty subsections — resist this.
paper_creation_process.md (Chinese) / paper_creation_process_en.md (English)paper_creation_process_zh.pdf / paper_creation_process_en.pdfarticle class, 12pt, A4, Times New Roman + Source Han Serif TC VF\tableofcontents| 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 |
| 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 | 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 | 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 |
| Template | Purpose |
|---|---|
templates/pipeline_status_template.md | Progress Dashboard output template |
| 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) |
Follows user language. Academic terminology retained in English.
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)
| 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) |
| 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 |
| Version | Date | Changes |
|---|---|---|
| 2.7 | 2026-03-27 | Style Profile in Material Passport: Pipeline orchestrator now carries optional Style Profile (Schema 10 in shared/handoff_schemas.md) through all stages. Produced by academic-paper intake Step 10 when user provides past writing samples. Consumed by draft_writer (Stage 2) and report_compiler (Stage 1) as soft writing voice guide. Does not affect integrity verification or review stages. Coordinates with deep-research v2.4 and academic-paper v2.5 |
| 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 |