Respond to Referee Skill

Structured workflow for addressing referee comments. Operates in two modes:

1. Single-point mode: Draft a response paragraph + LaTeX edits for one referee point
2. Full-reply mode: Generate a complete standalone reply LaTeX document

Examples

• /respond-to-referee referee2.md point 3 -- address a specific point from a referee file
• /respond-to-referee referee2.md -- generate complete reply to all points in the file
• /respond-to-referee identification -- address a point by topic keyword

Input

The user provides:

• A referee report file (markdown or text)
• Either a specific point number, a topic keyword, or no argument (full reply)

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Core Principles

These principles, distilled from journal editor guidelines and published advice (Noble 2017, PLOS Comp Bio; Review of Finance "Tips for Authors"), govern all referee responses.

Tone

• Grateful but not obsequious: "We thank the referee for this suggestion" (good) vs. "We are deeply grateful for this invaluable insight" (too much)
• Accept blame for misunderstandings: If the referee misread something, it is our exposition failure. "We realize our original text was ambiguous and have revised it as follows..."
• Never dismissive: No bare "we respectfully disagree." Every disagreement must be backed by evidence, data, or a reference.
• Direct answers first: Start each response with what you did ("We have added...", "We agree and now show..."), then explain why.
• Remember the audience: You are writing to the editor, not (only) the referee.

Structure

• Respond to every point: No exceptions, including minor ones.
• Self-contained responses: Quote or paraphrase the revised manuscript text directly in the letter.
• Reference by section name: Not page numbers (which shift between drafts).
• Group related points: When two comments address the same underlying issue, respond jointly.

Substance

• Do what the referee asks, even if you disagree: Run the requested analysis, report results in the letter, then explain why you believe the main text should differ.
• Don't over-revise: Restrict changes to what is requested.
• Address general criticisms globally: If the referee cites two examples, fix the problem paper-wide.

Common Mistakes to Avoid

Mistake	Why it fails
Bare "we respectfully disagree"	Editor has no basis to overrule
Sarcasm or condescension	Poisons the review relationship
Fixing only the specific examples cited	Signals you missed the general point
Long defensive paragraphs before stating what you did	Buries the lede
Page-number references	Numbers shift between drafts
Over-revising (large unrequested changes)	Creates new attack surface
Em-dashes (---) in prose	AI hallmark; see academic-writing.md
Hard-banned words (delve, crucial, etc.)	LLM tells; see academic-writing.md Section 1
Hedge words (somewhat, quite, very, arguably)	Weaken claims; give magnitudes instead

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Mode 1: Single-Point Workflow

Step 1: Load Context

1. Read the referee report file
2. Read the project's CLAUDE.md for paper state and claims
3. Read .claude/rules/academic-writing.md for style rules
4. Identify the specific referee point

Step 2: Map to Affected Sections

1. Identify which section(s) in the .tex file are affected
2. Read the affected passage(s)
3. Check if the point has already been partially addressed

Step 3: Draft Response Letter Paragraph

\item[\textbf{Referee:}] \textit{``[abbreviated quote of referee comment]''}

\item[Reply:] [We thank the referee for... / We agree that...]
[1-2 sentences explaining what we did and where]
[If helpful: quote the revised text in a \begin{quote} block]
[1-2 sentences explaining the rationale]

Step 4: Draft LaTeX Edits

1. Write proposed edits using the paper's terminology
2. Follow all rules from academic-writing.md
3. Show old text -> new text for each edit

Step 5: Consistency Check

Verify proposed edits do not:

• Contradict claims in other sections
• Change quantitative results that appear elsewhere
• Introduce terminology violations
• Break cross-references

Step 6: Output

REFEREE RESPONSE: Point [N] -- [topic]
======================================

REFEREE SAID:
[brief summary]

RESPONSE LETTER TEXT:
[draft LaTeX paragraph]

PROPOSED EDITS:
  File: [filename]
  Location: Section [key], ~line [N]
  OLD: [existing text]
  NEW: [proposed replacement]

CONSISTENCY NOTES:
- [any cross-section impacts]

STATUS: [Ready / Needs human review on X]

---

Mode 2: Full-Reply Workflow

Step 1: Load Context

1. Read the referee report file (all points)
2. Read the project's CLAUDE.md and academic-writing.md

Step 2: Plan the Reply

1. Enumerate all referee points (substantive + minor)
2. Check which have already been addressed
3. Group related points
4. Flag any points where paper edits are still needed vs. reply-only

Step 3: Create Reply Document

1. Create _replies/reply_referee{N}.tex using the LaTeX template below
2. Point-by-point responses with \item[\textbf{Referee:}] / \item[Reply:]
3. Opening and closing paragraphs

Step 4: Compile and Verify

1. Run pdflatex + bibtex + pdflatex + pdflatex (paths from canonical local state reported by tools/bootstrap.py audit, or a repo-root compatibility shim if present)
2. Check for undefined citations or references
3. Read through for tone, completeness, accuracy

Step 5: Output

Report the compiled PDF location, page count, and any issues.

---

LaTeX Template (for full replies)

\documentclass[12pt,letterpaper]{article}
\usepackage[top=1.0in, bottom=1.0in, left=0.90in, right=0.90in]{geometry}
\usepackage{amsfonts,amsmath,amssymb}
\usepackage{setspace,titlesec,xcolor,booktabs,enumerate}
\usepackage{natbib}
\usepackage{hyperref}

\renewcommand{\baselinestretch}{1.10}
\titleformat{\section}{\centering\large\bfseries}{\thesection.}{1em}{}
\renewcommand{\thesection}{\Roman{section}}

\begin{document}

\noindent \textbf{{\large Reply to Referee [N] for ``{Paper Title}''}}
\medskip

\noindent Manuscript [ID]

\bigskip

\noindent [Opening paragraph: thank referee, brief overview of revision scope]

\section{Response to the Referee's comments}

\noindent
\begin{enumerate}

\item[\textbf{Referee:}] \textit{``[quoted comment]''}

\item[Reply:] [response]

% ... repeat for each point ...

\end{enumerate}

\bigskip
\noindent [Closing paragraph]

{\footnotesize
\singlespacing
\setlength{\bibsep}{6pt}
\bibliographystyle{jf}
\bibliography{../latex/references}
}

\end{document}