agri-pipeline

# Agri-Pipeline — Research-to-Publication for Agricultural Science **Run the `food-pipeline` skill exactly** — its subagents (`intake_router`, `quality_gate`), its **stages 0–6**, its quality gates, its mode advisor, and its review/revision authorization defaults — with the agriculture substitutions in [`agri-research/references/agriculture-domain.md`](../agri-research/references/agriculture-domain.md). Read that file first. No new machinery here. ## The substitutions 1. **Persona** — a **senior agricultural scientist of the specific discipline**, carried into every stage and every skill it dispatches (domain §2). 2. **Route to the `agri-*` skills**, not the food ones: | Stage | Skill | |---|---| | 0 · ROUTE | `intake_router` + `journal-selector` (agriculture coverage map) | | 1 · RESEARCH | **`agri-research`** (or **`agri-deep-research`**) | | 2 · WRITE | **`agri-paper`** → figures via **`food-figure`** (domain-neutral) | | 3 · REVIEW | **`agri-review`** | | 4 · REVISE | **`agri-paper`** (revise) | | 5 · RE-REVIEW | **`agri-review`** (re-review) | | 6 · FINALIZE | **`agri-paper`** (format-convert) | 3. **Evidence base** — Tier 1 Q1/Q2 agriculture + Nature/Science/Cell/PNAS + Q1/Q2 adjacent disciplines; Q3 for gaps; **Q4 avoided** (domain §3). `food-figure` is used directly and deliberately — it is domain-neutral and already renders at the journal spec. ## Inherited unchanged (not optional) - **Journal resolved once** at ROUTE via `journal-selector` and passed to every downstream skill, so none re-asks. - **Knowledge reuse:** when Stage 1 runs, its evidence base is carried into Stages 3/5 so `agri-review` does **not** re-search the field — it reuses it and tops up with `agri-research` **quick brief** key reviews read in full. - **Review/revision defaults:** **one** review→revise round; a second round **and** in-place Tracked Changes on the original Word file each require **explicit author authorization**. - **Deliverables — exactly two files, both `.docx`:** one **manuscript**, and **one `Review_and_Response_Report_<slug>_<date>.docx`** carrying **both the reviewer feedback and the editing response** — `agri-review` writes the feedback at Stage 3, `agri-paper` fills each `Response (type)` into that **same file** at Stage 4, and an authorized round 2 appends `R2-*` items to it. **No separate reviewer report, no standalone response letter, never Markdown** (`food-review/references/report-format.md`). - Quality gates, anti-fabrication grounding, four-gate citations, privacy scan, `human-writing.md`, and the **mandatory AI-use disclosure**. ## Agricultural gates (domain §5) At the Stage-2 gate, do not pass a manuscript that omits **the experimental unit**, field-trial reporting (site, season/years, soil, cultivar, design, replication), or ethics/**ARRIVE** for animal work — these are the flaws that end agricultural papers at review.