Scientific Writing (orchestrator)

Overview

A three-stage pipeline from a code+results repo to a manuscript draft. Each stage owns a skill and a durable artifact under docs/writing/<story-slug>/ in the consuming repo. This skill routes to the right stage and resumes from whatever artifacts already exist.

Method backbone — the fifteen steps

The pipeline operationalizes Drake & Han's "How to write a scientific paper in fifteen steps" (PLOS Comput Biol, 2025). Its core discipline: finish the thinking before the phrasing, and write only after the research is done. Full detail — every step, with the caption/CARS/connector-test specifics each stage calls on — is in scientific-writing/fifteen-steps.md. Each stage owns a contiguous block:

Steps	Stage	Delivers
1–2	Story	main point + two-part narrative arc
3–12	Outline	method/result/finding lists → CARS intro, findings + problem/response discussion, closing thesis, per-paragraph purpose statements, figures
13–15	Draft	topic / supporting / concluding sentences

Cross-cutting, and true of this agent too: generative AI is a Steps-13–15 tool (phrasing), not a Steps-1–12 tool (thinking). Do the intellectual work of shaping each stage's artifact before smoothing prose; never let fluency stand in for a claim you haven't backed.