academic-pipeline

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 10-stage workflow with mandatory, coverage-bounded integrity checks, two-stage peer review, and auditable quality-assurance artifacts. Triggers on: academic pipeline, research to paper, full paper workflow, paper pipeline, end-to-end paper, research-to-publication, complete paper workflow, 연구부터 논문까지, 연구 주제 설정부터 논문 완성까지, 논문 전체 워크플로. metadata {"version":"3.21.2","last_updated":"2026-09-06","depends_on":"deep-research, academic-paper, academic-paper-reviewer","status":"active","data_access_level":"raw","task_type":"open-ended","related_skills":["deep-research","academic-paper","academic-paper-reviewer"]} Academic Pipeline v3.21.2 — 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. Routing discipline (v3.9.2): see .claude/CLAUDE.md "Routing Discipline (v3.9.2)" + shared/references/intent_clarification_protocol.md for cross-skill routing rules. This skill assumes routing has already settled — ambiguous cross-phase materials should have been clarified upstream. v3.6.3 (opt-in): Set ARS_PASSPORT_RESET=1 to promote FULL checkpoints to context-reset boundaries. Use resume_from_passport=<hash> in a fresh session to continue from the recorded stage. See references/passport_as_reset_boundary.md . v3.8 (opt-in): Set ARS_CLAIM_AUDIT=1 to enable the L3 claim-faithfulness audit gate at the Stage 4 → Stage 5 transition. When the flag is set, the orchestrator dispatches claim_ref_alignment_audit_agent after the v3.7.1 Cite-Time Provenance Finalizer and before formatter_agent 's hard gate. The audit emits claim_audit_results[] + uncited_assertions[] + claim_drifts[] + constraint_violations[] + audit_sampling_summaries[] aggregates per the 8-row matrix; HIGH-WARN classes gate-refuse output via the formatter REFUSE rules 6-10. Default OFF for v3.8.0 — ramp-on plan deferred to post-calibration evidence (spec §5 mode flag rationale). See agents/claim_ref_alignment_audit_agent.md and the orchestrator §3.6 prose. v2.0 Core Improvements : Mandatory user confirmation checkpoints — Each stage completion requires user confirmation before proceeding to the next step Academic integrity checks — After paper completion and before review submission, run the declared reference, registered-claim, and reported-data checks; expose denominators, sampling, unknown states, and blocking verdicts Two-stage review — First full review + post-revision focused verification review Final integrity check — After revision completion, rerun the final-check contract from fresh inputs; 100% applies only where the named registered population is explicitly complete Auditable — Version, hash, and retain workflow artifacts; deterministic checks are replayable, while generative outputs are not promised byte-identical Process documentation — Stage 6 generates a "Paper Creation Process Record" PDF documenting the human-AI collaboration history (delivered before the terminal acknowledgement that completes the pipeline) 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) Resume from passport (cross-session context reset, opt-in): resume_from_passport=<hash> [stage=<n>] [mode=<m>] --> Loads the Material Passport (Schema 9), locates the kind: boundary entry matching <hash> , and confirms it has no later kind: resume entry consuming it. If pending_decision is set, the decision prompt fires first to capture the user's branch choice for the audit ledger; the prompt is never skipped, even when the user supplies stage= . After the prompt (or immediately if no pending_decision ), the next stage is determined by: (a) stage=<n> CLI override if provided, else (b) the matched option's next_stage , else (c) the next field recorded in the boundary entry. CLI stage= / mode= overrides win over option routing. Gate (emit) : ARS_PASSPORT_RESET=1 must be set in the emitting session. Without the flag, no kind: boundary entries are written and there is nothing to resume from. Gate (resume) : No flag required. Any session can invoke resume_from_passport=<hash> against a passport that carries a valid boundary entry matching the hash. Intent : Invoke in a fresh Claude Code session. Resuming within the same session that emitted the boundary provides no token savings and may drop still-live in-session context. Stage : Any. Resumes at whatever stage the routing rules above determine. Reference : references/passport_as_reset_boundary.md — see §" resume_from_passport mode contract". 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 한국어 : 학술 파이프라인, 연구부터 논문까지, 논문 전체 워크플로, 연구 주제 설정부터 논문 완성까지, 연구-논문 전 과정 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, respect that entry point; the pipeline is opt-in 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 (declared checks must PASS; registered denominators and unknown/out-of-scope states remain visible) 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; then Integrity Check FAIL Loop -> recorded user decision) 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; after 3 unresolved rounds -> Integrity Check FAIL Loop -> recorded user decision) Stage 5 FINALIZE -> MD -> DOCX via Pandoc when available (otherwise instructions) -> ask about LaTeX -> confirm -> PDF -> completion checkpoint (FULL) -> Stage 6 (user may decline Stage 6: marked skipped , pipeline goes directly to completed ) Stage 6 PROCESS SUMMARY -> ask language version -> generate process record MD -> LaTeX -> PDF -> terminal acknowledgement ( finish / end / done / confirm , or an unambiguous natural-language equivalent) -> pipeline global state completed 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; Stage 5 completion (final-deliverable acceptance) 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 entry gate (before finalization) 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] - Criterion status: [named criterion + evidence-anchored categorical judgement, or `NOT_COMPARABLE`] 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 entry gate) : always MANDATORY — this is the checkpoint between Stage 4.5 PASS and the Stage 5 dispatch, where the user explicitly confirms proceeding and makes the finalization-format decision (citation style); the in-stage LaTeX question and content confirmation stay inside Stage 5 execution. The Stage 5 completion checkpoint (Final Paper delivered, before Stage 6) is FULL — never SLIM. See references/pipeline_state_machine.md § Stage 5 boundary semantics 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? Criterion trajectory : For each applicable named criterion, did the evidence-anchored status improve, remain unchanged, regress, or become non-comparable? Never reduce this to a hidden scalar or latest >= previous . Pause and flag any unresolved decision-bearing regression; use NOT_COMPARABLE when the criterion or evidence base changed. 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 (5 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 checker: coverage-bounded reference, citation, registered-claim, and reported-data checks (blocking verdicts are explicit) agents/integrity_verification_agent.md 4 collaboration_depth_agent Observer (advisory only — never blocks). Reads dialogue log and scores user-AI collaboration pattern against shared/collaboration_depth_rubric.md . Invoked at FULL/SLIM checkpoints and during Stage 6 record compilation (whole-pipeline pass, before the Process Record is delivered). Based on Wang & Zhang (2026). agents/collaboration_depth_agent.md 5 claim_ref_alignment_audit_agent Opt-in claim faithfulness auditor (v3.8 #103). Audits sampled citations for claim ↔ reference alignment + negative-constraint compliance; emits per-claim claim_audit_results[] , claim_drift[] , uncited_assertions[] , constraint_violations[] . Dispatched via orchestrator §3.6 when claim_audit mode is requested. agents/claim_ref_alignment_audit_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)