Academic PipelineCAUTION

Academic Research Skills for Claude Code: research → write → review → revise → finalize

The instruction file, verbatim from the audited commit — this is the text the model reads, and the surface the audit's instruction layer examines. Quoted here so you can judge it without cloning anything.

---
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, flujo de trabajo académico, investigación a artículo, flujo completo de artículo, pipeline de investigación completa, publicación de investigación, flujo de trabajo completo del artículo."
metadata:
  version: "3.22.2"
  last_updated: "2026-09-25"
  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 v3.22.2 — 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):** plugin and skills-copy installs do not load this repository's `.claude/CLAUDE.md`, so its routing core is repeated below, identical to `shared/references/routing_core.md` (#892). If routing has not settled when this skill loads, apply the core before dispatching any agent.

<!-- routing-core:begin -->
**Step 0 — Escape hatch check (before any classification):** If the user's first message begins with `[direct-mode]` (case-insensitive byte-0 token, optionally preceded by whitespace/newlines that are stripped on parse), record this fact, strip the prefix and surrounding whitespace from the message, and skip directly to **Step 1 explicit-intent handling** on the stripped content. The literal `[direct-mode]` is NOT passed through to the dispatched agent. If the stripped message itself has no clear skill named, Step 1 falls through to Step 3 clarification (the escape hatch bypasses cross-phase clarification (Step 2), not all routing). When the token is honored and the named agent or skill needs inputs the message does not supply, read that agent's or skill's file and ask for what it requires, in its terms. Without the byte-0 token, naming an agent is not explicit intent: such a message goes through Steps 1-3 like any other, so cross-phase materials still get Step 2 clarification.

Otherwise, classify the user's input:

1. **Explicit clear intent** — user invokes a specific skill via `/ars-*` slash command, or uses an unambiguous trigger keyword that maps to a single skill (e.g., "lit-review this", "review my paper", "draft an abstract"):
   → Route directly; no clarification, no orchestrator detour.
   → The request stays explicit when the mode's usual input is absent or a word in it has other everyday senses. A revision request with no reviewer comments is revision mode's "feel certain sections need improvement" case, and "revisar artículo" is the reviewer's trigger. Route to that mode and let the mode handle what is missing; do not reopen the choice of workflow.

2. **Cross-phase materials detected** — user provides artifacts spanning ≥ 2 pipeline phases without naming a specific skill (e.g., pre-written abstract + pre-collected literature; full draft + reviewer comments + bibliography):
   → **Clarify**. Do NOT auto-route to a single-phase agent. List candidate workflows as a-d options in markdown body (NOT via AskUserQuestion tool). See `shared/references/intent_clarification_protocol.md` for the message template.
   → Reason: clarification is the safest action when materials don't unambiguously identify intent. (v3.10 active conductor (#134) will handle this via structured intake; v3.9.2 asks.)

3. **Ambiguous intent, no materials** — user provides no artifacts and no clear request:
   → Clarify per `shared/references/intent_clarification_protocol.md`.

**Anti-pattern (caused #133):** Receiving ambiguous cross-phase materials and silently auto-routing to a single-phase agent based on which phase the materials "look closest to." This bypasses orchestrator-level reconciliation and lets the subagent inherit the full ambiguity without independent oversight.
<!-- routing-core:end -->

**v3.6.3 (opt-in):** Set `ARS_PASSPORT_RESET=1` to promote FULL and MANDATORY 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).

**#925 (opt-in):** Set `ARS_AUDIT_ARTIFACT_GATE=1` to enable the v3.6.7 Audit Artifact Gate, which has you run `scripts/run_codex_audit.sh` outside the session at each transition after a `synthesis_agent`, `research_architect_agent` (survey-designer), or `report_compiler_agent` (abstract-only) deliverable; the wrapper sends that deliverable to an external model. The variable is configuration, not consent: the gate runs only after the user agrees for the run under the consent boundary in [`shared/cross_model_verification.md`](../shared/cross_model_verification.md). Off by default; the Stage 2.5 and 4.5 integrity gates run either way. See `agents/pipeline_orchestrator_agent.md` § 3.5.

**v3.8 (opt-in):** Set `ARS_CLAIM_AUDIT=1` to enable the L3 claim-faithfulness audit gate at the Stage 4 → Stage 5 transition (in pipeline runs it first runs at Stage 4.5, so a finding can still be corrected; #929). 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 har

CAUTIONgrade B · trust 89/100 Install with care. The audit found things worth knowing before you trust its output.

What the source does

Filesystem

none-observed

Network

none-observed

Shell

none-observed

Dependencies

pinned

Secrets in source

none-found

Findings (4)

skills/academic-paper

skills/academic-paper-reviewer

skills/academic-pipeline

skills/deep-research

Gates applied: no_behavioural_pass.