write-paper

name	write-paper
description	Write LaTeX paper sections based on outline.md using citations from main.bib

Write Paper Command

Iteratively transform outline into LaTeX. Each section is drafted, reviewed, and saved before proceeding.

Input

$ARGUMENTS

Reference

@paper/main.bib @paper/outline.md @.claude/reference/venue-info.md @.claude/reference/writing-style.md @.claude/reference/latex-rules.md @.claude/reference/latex-template.md

---

Step 1: Validate Prerequisites

outline.md: If missing, error "No outline found. Run /develop-outline first." and stop.

main.bib: If missing, warn "No bibliography. Using (CITATION NEEDED) markers." If exists, load keys and report count.

---

Step 2: Parse Outline

Extract from paper/outline.md:

• Section titles (## lines)
• Core claims (**Core claim:**)
• Key points (bullet lists)
• Citation pointers (AuthorYearKey - ...)

---

Step 3: Determine Scope

If $ARGUMENTS empty or "all": Process all sections.

If section name: Fuzzy match against titles (case-insensitive, partial matches, keywords). If no match, list available sections and stop.

---

Step 4: Check main.tex

If exists: Read and preserve preamble, title, authors, abstract, back matter. Identify insertion points.

If missing: Create from @.claude/reference/latex-template.md. Inform user.

---

Step 5: Load Section Context

Classify the current section:

• literature: Introduction, Related Work, Background, Discussion
• artifact: Results, Materials and Methods
• other: Abstract, Conclusion, Significance Statement

For literature sections:

• Extract citation keys (AuthorYearKey entries) from the outline section
• For each key: check lit_review/paper_summaries/**/{Key}.md; if found, load for context; if not, use BibTeX metadata only
• For Discussion specifically: main.tex (loaded in Step 4) contains previously written sections — reference this already-written content when discussing results; do NOT load artifact files

For artifact sections:

• Extract [artifact: path - description] entries from the outline section
• If artifact pointers found: Read each referenced file; use content as primary context for writing
• If NO artifact pointers found: Use AskUserQuestion:

  "The [Section Name] section has no artifact pointers in the outline. To write this section accurately, I need your actual results or methods details. Please:

  1. Provide file paths to relevant reports, scripts, or data files (e.g., results/reports/stats.txt, code/analysis/model.py)
  2. Paste relevant content directly into the chat
  3. Type 'write anyway' to proceed with outline guidance only (accuracy not guaranteed)"

  • If option 1: read the provided files and use as context
  • If option 2: use pasted content as context
  • If option 3: proceed with outline only; add a warning comment % NOTE: written without artifact context — verify accuracy at the section start

For other sections:

• No special loading; use outline content only

---

Step 6: Iterative Section Writing

For each section:

6a. Generate Draft

Write section header with label:

\section*{Section Title}
\label{sec:concise_name}

Generate prose following @.claude/reference/venue-info.md (structure, tone, and PNAS section guidance), @.claude/reference/writing-style.md (sentence-level CSS style), and @.claude/reference/latex-rules.md (citation mechanics and LaTeX formatting) for:

• Section structure and tone appropriate for PNAS Research Articles
• Hedged language guidelines
• Citation format (natbib)
• Paragraph structure

6b. Review

Present draft with citations list. Ask: "Does this look good? Any changes before I save?"

6c. Iterate

Revise based on feedback until approved.

6d. Save

Insert/update in paper/main.tex:

• New sections: before back matter
• Existing: replace between \section*{Title} and next section
• Preserve % KEEP: marked content

Confirm save, proceed to next section.

---

Step 7: Final Report

Sections written: {count} - {list}
Citations used: {count} - {keys with counts}
Warnings: (CITATION NEEDED) count, sections without citations
Output: paper/main.tex
Next: compile command, review markers, /write-paper [section] to revise

---

Edge Cases

• Section in main.tex but not outline: Preserve, don't overwrite.
• Very long section: Suggest subsections.
• Missing summaries: Use BibTeX only, note in report.
• Conflicting content: Ask "Replace, merge, or skip?"
• User stops mid-iteration: Previous sections already saved. List remaining, explain resume with /write-paper [section].
• Compile check: Suggest cd paper && pdflatex main.tex && bibtex main && pdflatex main.tex && pdflatex main.tex