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, cove

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 ](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 : 1. Mandatory user confirmation checkpoints — Each stage completion requires user confirmation before proceeding to the next step 2. 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 3. Two stage review — First full review + post revision focused verification review 4. 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 5. Auditable — Version, hash, and retain workflow artifacts; deterministic checks are replayable, while generative outputs are not promised byte identical 6. 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): academic pipeline launches, starting from Stage 1 (RESEARCH) Mid entry (existing paper): academic pipeline detects mid entry, starting from Stage 2.5 (INTEGRITY) Revision mode (received reviewer feedback): academic pipeline detects, starting from Stage 4 (REVISE) Resume from passport (cross session context reset, opt in): 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 ](references/passport as reset boundary.md) — see §" resume from passport mode contract". Execution flow: 1. Detect the user's current stage and available materials 2. Recommend the optimal mode for each stage 3. Dispatch the corresponding skill for each stage 4. After each stage completion, proactively prompt and wait for user confirmation 5. Track progress throughout; Pipeline Status Dashboard available at any time 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 1. Stage 1 RESEARCH user confirmation Stage 2 2. Stage 2 WRITE user confirmation Stage 2.5 3. Stage 2.5 INTEGRITY PASS Stage 3 (FAIL fix and re verify, max 3 rounds; then Integrity Check FAIL Loop recorded user decision) 4. Stage 3 REVIEW Accept Stage 4.5 / Minor Major Stage 4 / Reject Stage 2 or end 5. Stage 4 REVISE user confirmation Stage 3' 6. Stage 3' RE REVIEW Accept Minor Stage 4.5 / Major Stage 4' 7. Stage 4' RE REVISE user confirmation Stage 4.5 (no return to review) 8. 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) 9. 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 ) 10. 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) Adaptive Rules 1. First checkpoint : always FULL 2. After 2+ consecutive "continue" without review : prompt user awareness ("You've continued [N] times in a row. Want to review progress?") 3. Integrity boundaries (Stage 2.5, 4.5) : always MANDATORY 4. Review decisions (Stage 3, 3') : always MANDATORY 5. 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 6. All other stages : start FULL, downgrade to SLIM if user says "just continue" Checkpoint Rules 1. ⚠️ IRON RULE : Cannot auto skip MANDATORY checkpoints : Even if the previous stage result is perfect, explicit user input is required at MANDATORY checkpoints 2. User can adjust : At FULL and MANDATORY checkpoints, users can modify the mode or settings for the next step 3. Pause friendly : Users can pause at any checkpoint and resume later 4. SLIM mode : If the user says "just continue" or "fully automatic," subsequent non critical checkpoints switch to SLIM format (one line status + explicit continue/pause prompt) 5. 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: 1. Citation integrity : Are there any unverified citations in the latest output? 2. Sycophantic concession : Did the latest stage uncritically accept all feedback without pushback? 3. Criterion trajectory : For each applicable named criterion, d

academic-pipeline