Scientific Writing — Stage 2: Outline

Overview

Turn story.md into a bulleted outline whose every claim is backed — by a concrete repo artifact (results bullets) or a web-verified citation (background bullets). Multi-pass, modeled on superpowers:executing-plans. Outputs outline.md + references.md in the story dir.

Foundational rule: no bullet without backing. Inventing a citation or a number to fill a bullet is the cardinal failure of this stage.

Step 0 — confirm the venue

Ask the user the target journal/format (e.g. Nature/Science/Cell biological article; CS conference; BMC-style software article). This selects the section scaffold. Record the choice + rationale in the outline.md header. Common scaffolds:

• Nature/Cell biological: Abstract, Intro, Results, Discussion, Methods.
• BMC software article: Background, Implementation, Results, Conclusions.
• CS conference: Abstract, Intro, Related Work, Method, Experiments, Conclusion.

Multi-pass loop (per block of ~3–8 bullets)

1. Implement — write the bullets for the current section block.
2. Story review — consistent with story.md's thesis/beats? Are non-result (background/motivation) bullets backed by literature?
3. Technical review — is each result bullet backed by a named repo artifact (script/result CSV/plot/notebook)? Is every "magic number" (e.g. an RNA-seq count threshold, an x-fold ratio) backed by a principled source — an in-repo empirical result or a citation? Add the pointer inline. Also name the figure panel each result bullet maps to (e.g. Fig. 2C) so Stage 3 can attach the callout without inventing one.
4. Citation web-check — for each new citation, dispatch a subagent (parallelize with superpowers:dispatching-parallel-agents) to verify via web: (a) does the paper exist (authors, venue, year)? (b) does its content support the specific claim? Log every verdict to references.md.