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 fabricated/mismatched/anachronistic citations) and the prose-quality scan; run double-run reproducibility before release claims. These gates are file-backed and deterministic, mirroring the ARS mandatory integrity-check stages but as code, not a hidden agent loop.
5. Finalize - render from source, validate outputs, copy deliverables, and document residual risks. Never hand-edit output/ as the fix.

Deliverables

• Pipeline status table: stage, owner skill, inputs, outputs, gate, and next action.
• Material passport summary with artifact paths and verification status.
• Review and revision traceability matrix.
• Final readiness report with claim, reproducibility, validation, and publication checks.

Verification commands

bash
uv run python scripts/runner/execute_pipeline.py --project <project> --core-only
uv run python -m infrastructure.validation.cli evidence projects/<project> --fail-on-issues
uv run python -m infrastructure.reference.verification verify projects/<project>/manuscript/references.bib --live --as-of-year <year> --fail-on-issues
uv run python -m infrastructure.validation.cli prose-quality projects/<project>/manuscript
uv run python -m infrastructure.validation.cli integrity output/<project>/
uv run python -m infrastructure.core.pipeline.snapshot compare <left> <right> --output-dir projects/<project>/output

References

• MODE_REGISTRY.md
• deep-research
• academic-paper
• academic-paper-reviewer
• reproducibility-audit