template-academic-pipeline

# Academic pipeline Template-native orchestrator for the full research-to-publication path. It coordinates existing skills and file-backed controls; it does not introduce an autonomous hidden approval loop. ## Natural invoke - "Run the complete research-to-paper workflow" - "I already have a paper; review and finalize it" - "I received reviewer comments; revise and verify" - "Prepare this manuscript for Zenodo or arXiv" ## Inputs to confirm - **Entry point** - new research, existing paper, reviewer comments, or finalization. - **Project** - active template project or private project path; preserve confidentiality boundaries. - **HITL mode** - full-auto, gate-only, checkpoint, or project policy from pipeline control. - **Required gates** - claim verification, reproducibility, validation, review, and publication package checks. ## Workflow 1. **Stage map** - research -> paper plan/draft -> claim verification -> read-only review -> revision -> re-review -> reproducibility -> validation -> final package. 2. **Material passport** - record handoffs as file paths and generated artifacts: search corpus, claim ledger, evidence registry, artifact manifest, snapshots, validation reports, and reviewer matrices. 3. **Human checkpoints** - use existing HITL controls for gate-only or checkpoint approvals; detached review files live under `output/hitl/`. 4. **Integrity gates** - run claim verification before review and finalization; run the deterministic reference-existence gate (no f...