outline

name	outline
description	Create structured paper outlines using Ten Rules framework. Use when starting a new section, planning results, or restructuring content.
allowed-tools	Read, Glob, Grep, Edit, Write, AskUserQuestion

Paper Outlining Skill

Generate structured one-sentence-per-paragraph outlines following the "Ten Simple Rules for Structuring Papers" (Mensh & Kording) and writing conventions.

Usage

/outline [section]

Examples:
  /outline abstract
  /outline introduction
  /outline results
  /outline discussion
  /outline          # (asks which section)

Instructions

Phase 1: Survey Available Findings

Before asking any questions, read all available analysis results and present a summary.

1. Read docs/paper/analysis_checklist.md for analysis status
2. Check notebooks/ for completed analyses
3. Group findings into themes
4. Present a table summarizing available findings

Phase 2: Confirm Selection

Do not proceed until the user confirms.

1. Based on user input, list the selected findings explicitly
2. Ask: "Does this selection look right? Any changes before I generate the outline?"
3. Wait for explicit confirmation before proceeding.

Phase 3: Gather Section-Specific Context

Only after selection is confirmed, ask section-specific questions:

For Abstract: "What is the central claim in one sentence?" For Introduction: "What's the field-level gap?" For Results: "What logical order should these findings appear?" For Discussion: "Which limitations are most important to acknowledge?"

Phase 4: Generate Outline

Apply structure from TENRULES.md and style from STYLE.md.

Output format: Numbered sentences with annotations:

## [Section]: [Central claim]

### Subsection Title (if Results)

1. [Context] First sentence establishing context...
2. [Data] Second sentence with key finding/data...
3. [Conclusion] Third sentence interpreting the result...

Phase 5: Iterate

After presenting the outline:

• Ask if any sections need expansion or reordering
• Check against the relevant checklist in CHECKLISTS.md
• Offer to revise based on feedback

Files Referenced

File	Purpose
TENRULES.md	Condensed actionable rules
STYLE.md	Writing patterns and examples
CHECKLISTS.md	Section-specific verification
docs/paper/outline.md	Current paper outline
docs/paper/analysis_checklist.md	Analysis status tracking

Critical Rules

1. Never generate an outline without showing available findings first
2. Never proceed without explicit user confirmation on selection
3. Always show what you're including AND excluding
4. Outlines are one sentence per paragraph - no prose yet