academic-pipeline

# Academic Pipeline v3.22.0 — 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):** ``` 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`](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 **Español**: flujo de trabajo académico, investigación a artículo, pipeline de artículo completo, desde tema de investigación hasta artículo terminado, flujo completo de investigación-publicación **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) ``` ━━━ 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 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, 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. 4. **Scope discipline**: Did the latest stage add content not requested by the user or the revision roadmap? 5. **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?