revise-paper

name	revise-paper
description	Apply revisions from a review report to a manuscript. Reads the review, presents prioritized plan, applies fixes section-by-section with user approval. Use when systematically addressing review issues, not drafting a new paper or running a fresh review.
when_to_use	revise paper, apply review, fix issues from review, address referee comments, apply revisions, work through review report, fix what reviewer found, address major concerns
argument-hint	[review report path, or leave blank to auto-detect]
allowed-tools	["Read","Grep","Glob","Write","Edit","Task","AskUserQuestion"]

Revise Paper from Review Report

Systematically apply revisions from a review report to a manuscript. Follows Prose Track rules — never auto-edits without approval.

Input: $ARGUMENTS — path to a review report, or leave blank to auto-detect.

Step 1: Locate the Review Report

If $ARGUMENTS is provided, use that path. Otherwise glob for:

• quality_reports/paper_review_*.md
• quality_reports/*_substance_review.md
• quality_reports/*_proofread.md

If multiple reports found, use AskUserQuestion:

• header: "Review Report"
• question: "Multiple review reports found. Which should I use for revisions?"
• options: list found reports (label: filename, description: date and type). User can select one.

Step 2: Locate the Manuscript

Read the review report and extract the manuscript path from its File: field.

If the file doesn't exist at that path, glob for:

• manuscripts/**/*.tex
• manuscripts/**/*.qmd

If multiple manuscripts found, use AskUserQuestion to let the user pick.

Read the full manuscript.

Step 3: Parse the Review Report

Extract all actionable items and classify them:

Priority	Source Section	Action
Critical	Major Concerns with "CRITICAL" or "BLOCKING"	Must fix before any submission
Major	Major Concerns, Referee Objections	Should fix — a reviewer would flag these
Minor	Minor Concerns, Specific Comments	Polish — fix if time allows

For each item, extract:

• The issue description
• The suggested fix (if provided)
• The location in the manuscript (section, line, table)

Step 4: Present Revision Plan (WAIT FOR APPROVAL)

Present the revision plan grouped by priority:

## Revision Plan

### Critical (N items) — must fix
1. [MC1: Title] — Section X — [brief description of fix]
2. ...

### Major (N items) — should fix
1. [MC2: Title] — Section Y — [brief description of fix]
2. ...

### Minor (N items) — polish
1. [mc1: Title] — Section Z — [brief description of fix]
2. ...

Total: N revisions across M sections.

Do NOT start editing until the user approves the plan or selects which items to address.

Step 5: Apply Approved Revisions

Work through approved items in this order:

1. Critical items first
2. Major items second
3. Minor items last

For each revision:

1. Show the current text and the proposed replacement
2. Apply the edit using the Edit tool
3. Move to the next item

Prose Track rules apply: If the user deferred any items, skip them and note them in the summary.

Step 6: Post-Revision Review

After all approved revisions are applied, dispatch the proofreader agent via Task to catch any issues introduced by the edits:

Task prompt: "Review the manuscript at [path] for grammar, typos, layout issues,
and consistency. Focus on sections that were recently revised: [list changed sections].
Return your report — the calling skill handles saving."

Present any new issues found by the proofreader.

Step 7: Save Revision Summary

Save to quality_reports/revision_summary_[paper-name].md:

# Revision Summary: [Paper Name]

**Date:** [YYYY-MM-DD]
**Review report used:** [path]
**Manuscript:** [path]

## Revisions Applied

| # | Priority | Issue | Section | Status |
|---|----------|-------|---------|--------|
| 1 | Critical | [title] | Section X | APPLIED |
| 2 | Major | [title] | Section Y | APPLIED |
| 3 | Minor | [title] | Section Z | DEFERRED — user chose to skip |

## Issues Deferred

- [Item]: [reason deferred]

## Post-Revision Proofreader Findings

- [Any new issues introduced by edits]

## Recommended Next Steps

- **`/quality-gate`** — verify claim consistency after edits
- **`/validate-bib`** — check citations if references were added or changed
- **`/review-paper`** — run a fresh review to confirm issues are resolved

Key Rules

• Prose Track only. Never apply edits without user approval.
• Work from the review report. Don't invent new issues — address what the review found.
• Preserve author voice. When rewriting prose, maintain the manuscript's existing style and tone.
• Track everything. Every revision applied or deferred must appear in the summary.