academic-pipeline

SKILL.md

Academic Pipeline v3.8.2 — 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 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