academic-pipeline

仓库: imbad0202/academic-research-skills
安装量: 242
排名: #8552

安装

npx skills add https://github.com/imbad0202/academic-research-skills --skill academic-pipeline
Academic Pipeline v3.2.2 — 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 via Pandoc when available, otherwise conversion instructions; ask about LaTeX; confirm correctness; PDF)
6
PROCESS SUMMARY
orchestrator
auto
Paper creation process record MD + LaTeX to PDF (bilingual)
Parallelization opportunity (v3.3)
Within Stage 2, the
academic-paper
skill's Phase 1 (literature_strategist_agent) and the
visualization_agent
can operate in parallel after Phase 2 (structure_architect_agent) completes the outline. Specifically:
Once the outline includes a visualization plan,
visualization_agent
can begin figure generation
Simultaneously,
argument_builder_agent
can build CER chains
draft_writer_agent
waits for both to complete before beginning Phase 4
This mirrors PaperOrchestra's parallel execution of Plot Generation (Step 2) and Literature Review (Step 3) after Outline (Step 1), which reduces overall pipeline latency. The parallelization is optional — sequential execution remains the default for simplicity.
Pipeline State Machine
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 via Pandoc when available (otherwise instructions) -> ask about LaTeX -> confirm -> PDF -> Stage 6
Stage 6 PROCESS SUMMARY
-> ask language version -> generate process record MD -> LaTeX -> PDF -> end
See
references/pipeline_state_machine.md
for complete state transition definitions.
Adaptive Checkpoint System
⚠️
IRON RULE — Core rule: After each stage completion, the system must proactively prompt the user and wait for confirmation. The checkpoint presentation adapts based on context and user engagement.
Checkpoint Types
Type
When Used
Content
FULL
First checkpoint; after integrity boundaries; before finalization
Full deliverables list + decision dashboard + all options
SLIM
After 2+ consecutive "continue" responses on non-critical stages
One-line status + explicit continue/pause prompt
MANDATORY
Integrity FAIL; Review decision; Stage 5
Cannot be skipped; requires explicit user input
Decision Dashboard (shown at FULL checkpoints)
━━━ Stage [X] [Name] Complete ━━━
Metrics:
- Word count: [N] (target: [T] +/-10%) [OK/OVER/UNDER]
- References: [N] (min: [M]) [OK/LOW]
- Coverage: [N]/[T] sections drafted [COMPLETE/PARTIAL]
- Quality indicators: [score if available]
Deliverables:
- [Material 1]
- [Material 2]
Flagged: [any issues detected, or "None"]
Ready to proceed to Stage [Y]? You can also:
1. View progress (say "status")
2. Adjust settings
3. Pause pipeline
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Adaptive Rules
First checkpoint
always FULL
After 2+ consecutive "continue" without review
prompt user awareness ("You've continued [N] times in a row. Want to review progress?")
Integrity boundaries (Stage 2.5, 4.5)
always MANDATORY
Review decisions (Stage 3, 3')
always MANDATORY
Before finalization (Stage 5)
always MANDATORY
All other stages
start FULL, downgrade to SLIM if user says "just continue"
Checkpoint Rules
⚠️
IRON RULE
:
Cannot auto-skip MANDATORY checkpoints
Even if the previous stage result is perfect, explicit user input is required at MANDATORY checkpoints
User can adjust
At FULL and MANDATORY checkpoints, users can modify the mode or settings for the next step
Pause-friendly
Users can pause at any checkpoint and resume later
SLIM mode
If the user says "just continue" or "fully automatic," subsequent non-critical checkpoints switch to SLIM format (one-line status + explicit continue/pause prompt)
Awareness guard
After 4+ consecutive continue responses, the system inserts a FULL checkpoint regardless of stage type to ensure user remains engaged
Self-Check Questions (at every FULL checkpoint)
Before presenting the checkpoint to the user, the orchestrator asks itself:
Citation integrity
Are there any unverified citations in the latest output?
Sycophantic concession
Did the latest stage uncritically accept all feedback without pushback?
Quality trajectory
Is the latest output ≥ the quality of the previous stage? If declining, PAUSE and flag.
Scope discipline
Did the latest stage add content not requested by the user or the revision roadmap?
Completeness
Are all required deliverables for this stage present? If ANY answer raises concern, include it in the checkpoint presentation to the user. Agent Team (3 Agents)

Agent Role File 1 pipeline_orchestrator_agent Main orchestrator: detects stage, recommends mode, triggers skill, manages transitions agents/pipeline_orchestrator_agent.md 2 state_tracker_agent State tracker: records completed stages, produced materials, revision loop count agents/state_tracker_agent.md 3 integrity_verification_agent Integrity verifier: 100% reference/citation/data verification agents/integrity_verification_agent.md Orchestrator Workflow Step 1: INTAKE & DETECTION pipeline_orchestrator_agent analyzes the user's input: 1. What materials does the user have? - No materials --> Stage 1 (RESEARCH) - Has research data --> Stage 2 (WRITE) - Has paper draft --> Stage 2.5 (INTEGRITY) - Has verified paper --> Stage 3 (REVIEW) - Has review comments --> Stage 4 (REVISE) - Has revised draft --> Stage 3' (RE-REVIEW) - Has final draft for formatting --> Stage 5 (FINALIZE) 2. What is the user's goal? - Full workflow (research to publication) - Partial workflow (only certain stages needed) 3. Determine entry point, confirm with user Step 2: MODE RECOMMENDATION Based on entry point and user preferences, recommend modes for each stage: User type determination: - Novice / wants guidance --> socratic (Stage 1) + plan (Stage 2) + guided (Stage 3) - Experienced / wants direct output --> full (Stage 1) + full (Stage 2) + full (Stage 3) - Time-limited --> quick (Stage 1) + full (Stage 2) + quick (Stage 3) Explain the differences between modes when recommending, letting the user choose Step 3: STAGE EXECUTION Call the corresponding skill (does not do work itself, purely dispatching): 1. Inform the user which Stage is about to begin 2. Load the corresponding skill's SKILL.md 3. Launch the skill with the recommended mode 4. Monitor stage completion status After completion: 1. Compile deliverables list 2. Update pipeline state (call state_tracker_agent) 3. [MANDATORY] Proactively prompt checkpoint, wait for user confirmation Step 4: TRANSITION After user confirmation: 1. Pass the previous stage's deliverables as input to the next stage 2. Trigger handoff protocol (defined in each skill's SKILL.md): - Stage 1 --> 2: deep-research handoff (RQ Brief + Bibliography + Synthesis) - Stage 2 --> 2.5: Pass complete paper to integrity_verification_agent - Stage 2.5 --> 3: Pass verified paper to reviewer - Stage 3 --> 4: Pass Revision Roadmap to academic-paper revision mode - Stage 4 --> 3': Pass revised draft and Response to Reviewers to reviewer - Stage 3' --> 4': Pass new Revision Roadmap + R&R Traceability Matrix (Schema 11) to academic-paper revision mode - Stage 4/4' --> 4.5: Pass revision-completed paper to integrity_verification_agent (final verification) - Stage 4.5 --> 5: Pass verified final draft to format-convert mode 3. Begin next stage Mid-Conversation Reinforcement Protocol At every stage transition, the orchestrator MUST inject a brief core principles reminder. This prevents context rot in long conversations. Template (adapt to the upcoming stage): --- STAGE TRANSITION: [Current] → [Next] --- 🔄 Core Principles Reinforcement: 1. [Most relevant IRON RULE for the next stage] 2. [Most relevant Anti-Pattern to avoid in the next stage] 3. Quality check: Is the output of [Current Stage] at least as good as [Previous Stage]? If not, PAUSE. Checkpoint: [MANDATORY/ADVISORY] — [What user needs to confirm]

Stage-specific reinforcement content
See
references/reinforcement_content.md
for the full transition → reinforcement focus table.
Integrity Review Protocol
Stage 2.5 (pre-review) and Stage 4.5 (post-revision) verification. 5-phase protocol: references → citation context → statistical data → originality → claims.
⚠️
IRON RULE
Stage 4.5 must PASS with zero issues to proceed to Stage 5. Stage 4.5 verifies from scratch independently.
⚠️
IRON RULE (v3.2)
Both Stage 2.5 and Stage 4.5 must also run the
AI Research Failure Mode Checklist
— a 7-mode taxonomy extending the citation hallucination checks into implementation bugs, hallucinated results, shortcut reliance, bug-as-insight, methodology fabrication, and pipeline-level frame-lock. If any of the 7 modes is
SUSPECTED
, or if Modes 1/3/5/6 are
INSUFFICIENT EVIDENCE
, the pipeline
blocks
and the user must acknowledge (confirm / override with reasoning / revise) before the pipeline proceeds. There is no
--no-block
escape hatch. Stage 6 PROCESS SUMMARY then reports the full failure-mode audit log as part of the AI Self-Reflection Report.
See
references/integrity_review_protocol.md
for the 5-phase citation/claim verification procedures.
See
references/ai_research_failure_modes.md
for the 7-mode AI research failure checklist and block/override logic.
Two-Stage Review Protocol
Stage 3 (full review, 5 reviewers) → Revision Coaching → Stage 4 → Stage 3' (re-review) → optional Residual Coaching → Stage 4'.
See
references/two_stage_review_protocol.md
for detailed stage flows and coaching dialogue limits.
Mid-Entry Protocol
Users can enter from any stage. The orchestrator will:
Detect materials
Analyze the content provided by the user to determine what is available
Identify gaps
Check what prerequisite materials are needed for the target stage
Suggest backfilling
If critical materials are missing, suggest whether to return to earlier stages
Direct entry
If materials are sufficient, directly start the specified stage
Important: mid-entry cannot skip Stage 2.5
If the user brings a paper and enters directly, go through Stage 2.5 (INTEGRITY) first before Stage 3 (REVIEW)
Only exception: User can provide a previous integrity verification report and content has not been modified
External Review Protocol
Handles external (human) reviewer feedback integration. 4-step workflow: Intake & Structuring → Strategic Revision Coaching → Revision & Response → Self-Verification.
See
references/external_review_protocol.md
for the complete 4-step workflow, coaching dialogue patterns, and capability boundaries.
Progress Dashboard
ASCII dashboard shown at FULL checkpoints to display pipeline progress.
See
references/progress_dashboard_template.md
for the dashboard template.
Revision Loop Management
Stage 3 (first review) -> Stage 4 (revision) -> Stage 3' (verification review) -> Stage 4' (re-revision, if needed) -> Stage 4.5 (final verification)
Maximum 1 round of RE-REVISE
(Stage 4'): If Stage 3' gives Major, enter Stage 4' for revision then proceed directly to Stage 4.5 (no return to review)
Pipeline overrides academic-paper's max 2 revision rule
In the pipeline, revisions are limited to Stage 4 + Stage 4' (one round each), replacing academic-paper's max 2 rounds rule Mark unresolved issues as Acknowledged Limitations Provide cumulative revision history (each round's decision, items addressed, unresolved items) Early-Stopping Criterion (v3.2) At the end of each revision round, if delta < 3 points on the 0-100 rubric AND no P0 issues remain , suggest stopping the revision loop ("converged"). User can override. Hard cap: 2 full revision loops (Stage 4 + Stage 4'). Budget Transparency (v3.2) At pipeline start, estimate token cost based on paper length, mode, and cross-model toggle. Present estimate and ask for user confirmation before Stage 1 begins. Reproducibility Every pipeline artifact is versioned, hashed, and auditable. See references/reproducibility_audit.md for standardized workflow guarantees, audit trail format, and artifact tracking. Stage 6: Process Summary Protocol Produces the final process record: paper creation journey, collaboration quality evaluation (6 dimensions, 1-100), and AI self-reflection report. See references/process_summary_protocol.md for full workflow, required content structure, scoring dimensions, and output specifications. Anti-Patterns Explicit prohibitions to prevent common failure modes:

Anti-Pattern Why It Fails Correct Behavior 1 Skipping integrity checks "The paper looks fine, skip Stage 2.5/4.5" Integrity checks are MANDATORY; they cannot be auto-skipped regardless of perceived quality 2 Orchestrator doing substantive work Pipeline orchestrator writes content or reviews the paper Orchestrator only dispatches and coordinates; substantive work belongs to the sub-skills 3 Auto-advancing past MANDATORY checkpoints Moving to next stage without user confirmation at FULL checkpoints MANDATORY checkpoints require explicit user input before proceeding 4 Quality degradation across stages Stage 4 revision is worse than Stage 2 draft because context window is exhausted If Stage N output quality < Stage N-1, PAUSE and reload core principles before continuing 5 Silently dropping reviewer concerns Revision addresses 8 of 10 concerns and hopes nobody notices The R&R tracking table must account for every concern with explicit status 6 Re-verifying only known issues at Stage 4.5 Final integrity check only re-checks Stage 2.5 findings Stage 4.5 must verify from scratch independently; revision may introduce new issues 7 Inflating Collaboration Quality scores Giving 90/100 to avoid awkward self-criticism Honesty first: no inflation, no pleasantries; cite specific evidence for every score 8 Bypassing the Failure Mode Checklist block (v3.2) "The 7-mode checklist is new, let's skip it this run" Stage 2.5/4.5 Failure Mode Checklist is MANDATORY and BLOCKING; no --no-block flag exists; overrides require user reasoning recorded for Stage 6 Quality Standards Dimension Requirement Stage detection Correctly identify user's current stage and available materials Mode recommendation Recommend appropriate mode based on user preferences and material status Material handoff Stage-to-stage handoff materials are complete and correctly formatted State tracking Pipeline state updated in real time; Progress Dashboard accurate Mandatory checkpoint User confirmation required after each stage completion Mandatory integrity check Stage 2.5 and 4.5 cannot be skipped, must PASS Mandatory failure mode checklist (v3.2) Stage 2.5 and 4.5 must run the 7-mode AI research failure checklist; suspected failures block; overrides require user reasoning No overstepping ⚠️ IRON RULE: Orchestrator does not perform substantive research/writing/reviewing, only dispatching No forcing ⚠️ IRON RULE: User can pause or exit pipeline at any time (but cannot skip integrity checks) Reproducible Same input follows the same workflow across different sessions Convergence-aware stopping (v3.2) If delta < 3 points AND no P0 issues, suggest stopping revision loop; user can override Budget transparency (v3.2) Token cost estimate + user confirmation at pipeline start Error Recovery Stage Error Handling Intake Cannot determine entry point Ask user what materials they have and their goal Stage 1 deep-research not converging Suggest mode switch (socratic -> full) or narrow scope Stage 2 Missing research foundation Suggest returning to Stage 1 to supplement research Stage 2.5 Still FAIL after 3 correction rounds List unverifiable items; user decides whether to continue Stage 3 Review result is Reject Provide options: major restructuring (Stage 2) or abandon Stage 4 Revision incomplete on all items List unaddressed items; ask whether to continue Stage 3' Verification still has major issues Enter Stage 4' for final revision Stage 4' Issues remain after revision Mark as Acknowledged Limitations; proceed to Stage 4.5 Stage 4.5 Final verification FAIL Fix and re-verify (max 3 rounds) Any User leaves midway Save pipeline state; can resume from breakpoint next time Any Skill execution failure Report error; suggest retry, pause, or mode switch. Do not skip mandatory integrity or failure-mode gates Agent File References Agent Definition File pipeline_orchestrator_agent agents/pipeline_orchestrator_agent.md state_tracker_agent agents/state_tracker_agent.md integrity_verification_agent agents/integrity_verification_agent.md 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/ai_research_failure_modes.md 7-mode AI research failure checklist (Lu 2026), run at Stage 2.5 + 4.5 with blocking behaviour, reported at Stage 6 references/team_collaboration_protocol.md Multi-person team coordination: role definitions, handoff protocol, version control, conflict resolution references/integrity_review_protocol.md Stage 2.5 + 4.5 integrity verification: 5-phase protocol details references/two_stage_review_protocol.md Two-stage review: Stage 3 full review + Stage 3' verification review references/external_review_protocol.md External (human) reviewer feedback: 4-step intake/coaching/revision/verification references/process_summary_protocol.md Stage 6: collaboration quality evaluation + AI self-reflection report references/reproducibility_audit.md Standardized workflow guarantees + audit trail format references/progress_dashboard_template.md ASCII progress dashboard template references/reinforcement_content.md Stage-specific reinforcement focus table for transitions references/changelog.md Full version history shared/handoff_schemas.md Cross-skill data contracts: 9 schemas for all inter-stage handoff artifacts Templates Template Purpose templates/pipeline_status_template.md Progress Dashboard output template Examples Example Demonstrates examples/full_pipeline_example.md Complete pipeline conversation log (Stage 1-5, with integrity + 2-stage review) examples/mid_entry_example.md Mid-entry example starting from Stage 2.5 (existing paper -> integrity check -> review -> revision -> finalization) Output Language Follows user language. Academic terminology retained in English. Integration with Other Skills academic-pipeline dispatches the following skills (does not do work itself): Stage 1: deep-research - socratic mode: Guided research exploration - full mode: Complete research report - quick mode: Quick research summary Stage 2: academic-paper - plan mode: Socratic chapter-by-chapter guidance - full mode: Complete paper writing Stage 2.5: integrity_verification_agent (Mode 1: pre-review) Stage 4.5: integrity_verification_agent (Mode 2: final-check) Stage 3: academic-paper-reviewer - full mode: Complete 5-person review (EIC + R1/R2/R3 + Devil's Advocate) Stage 3': academic-paper-reviewer - re-review mode: Verification review (focused on revision responses) Stage 4/4': academic-paper (revision mode) Stage 5: academic-paper (format-convert mode) - Step 1: Ask user which academic formatting style (APA 7.0 / Chicago / IEEE, etc.) - Step 2: Produce MD, then generate DOCX via Pandoc when available (otherwise provide conversion instructions) - Step 3: Produce LaTeX (using corresponding document class, e.g., apa7 class for APA 7.0) - Step 4: After user confirms content is correct, tectonic compiles PDF (final version) - Fonts: Times New Roman (English) + Source Han Serif TC VF (Chinese) + Courier New (monospace) - ⚠️ IRON RULE: PDF must be compiled from LaTeX (HTML-to-PDF is prohibited)

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