review-paper

name	review-paper
description	Comprehensive manuscript review covering argument structure, methodology, citation completeness, writing quality, and potential referee objections. Works with .docx, .tex, .pdf, and .md manuscripts.
disable-model-invocation	true
argument-hint	[paper filename in manuscripts/ or master_supporting_docs/, or full path]
allowed-tools	["Read","Grep","Glob","Write","Task"]

Manuscript Review

Produce a thorough, constructive review of an academic manuscript — the kind of report a top-journal referee would write.

Input: $ARGUMENTS — path to a paper (.docx, .tex, .pdf, .md), or a filename in manuscripts/ or master_supporting_docs/.

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Steps

1. Locate and read the manuscript. Check:

   • Direct path from $ARGUMENTS
   • manuscripts/$ARGUMENTS
   • master_supporting_docs/supporting_papers/$ARGUMENTS
   • outputs/ for formatted versions
   • Glob for partial matches

2. Read the full paper end-to-end. For long documents, read in sections.

3. Evaluate across 6 dimensions (see below).

4. Generate 3-5 "referee objections" — the tough questions a top referee would ask.

5. Produce the review report.

6. Save to quality_reports/paper_review_[sanitized_name].md

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Review Dimensions

1. Argument Structure

• Is the research question clearly stated?
• Does the introduction motivate the question effectively?
• Is the logical flow sound (question → method → results → conclusion)?
• Are the conclusions supported by the evidence?
• Are limitations acknowledged?

2. Study Design and Methods

• Is the study design appropriate for the research question?
• Are key methodological assumptions stated explicitly?
• Are there threats to validity (confounding, bias, measurement error)?
• Are statistical methods appropriate?
• Is sample size / power discussed?

3. Results and Interpretation

• Are results clearly reported with appropriate statistics?
• Are figures and tables well-designed and self-contained?
• Is interpretation appropriate (not over-claiming)?
• Are negative or null results handled appropriately?

4. Literature Positioning

• Are the key papers cited?
• Is prior work characterized accurately?
• Is the contribution clearly differentiated from existing work?
• Any missing citations that a referee would flag?

5. Writing Quality

• Clarity and concision
• Academic tone
• Consistent terminology throughout
• Abstract effectively summarizes the paper
• Tables and figures have clear labels, notes, sources

6. Formatting and Presentation

• Is the paper the right length for the contribution?
• Is notation / terminology consistent throughout?
• Are there any typos, grammatical errors, or formatting issues?
• Are headings appropriate for the journal type?

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Output Format

# Manuscript Review: [Paper Title]

**Date:** [YYYY-MM-DD]
**Reviewer:** review-paper skill
**File:** [path to manuscript]

## Summary Assessment

**Overall recommendation:** [Strong Accept / Accept / Revise & Resubmit / Reject]

[2-3 paragraph summary: main contribution, strengths, and key concerns]

## Strengths

1. [Strength 1]
2. [Strength 2]
3. [Strength 3]

## Major Concerns

### MC1: [Title]
- **Dimension:** [Argument / Methods / Results / Literature / Writing / Presentation]
- **Issue:** [Specific description]
- **Suggestion:** [How to address it]
- **Location:** [Section/page if applicable]

[Repeat for each major concern]

## Minor Concerns

### mc1: [Title]
- **Issue:** [Description]
- **Suggestion:** [Fix]

[Repeat]

## Referee Objections

These are the tough questions a top referee would likely raise:

### RO1: [Question]
**Why it matters:** [Why this could be fatal]
**How to address it:** [Suggested response or additional analysis]

[Repeat for 3-5 objections]

## Specific Comments

[Section-by-section comments, if any]

## Summary Ratings

| Dimension | Rating (1-5) |
|-----------|-------------|
| Argument Structure | [N] |
| Study Design / Methods | [N] |
| Results / Interpretation | [N] |
| Literature | [N] |
| Writing | [N] |
| Presentation | [N] |
| **Overall** | **[N]** |

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Principles

• Be constructive. Every criticism should come with a suggestion.
• Be specific. Reference exact sections, tables, figures.
• Distinguish fatal flaws from minor issues. Not everything is equally important.
• Acknowledge what's done well. Good research deserves recognition.
• Do NOT fabricate details. If you can't read a section clearly, say so.
• Do NOT alter scientific content. This is a review, not an edit.