revise-paper

name	revise-paper
description	Apply revisions from a review report to a manuscript.

Revise Paper From Review Report

Systematically apply revisions from a review report to a manuscript. Follows the prose-track rule: never edit without user approval.

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

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Step 1: Locate the Review Report

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

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

If multiple reports are found and there are 2-3 clear candidates, use request_user_input in Plan mode for a single-choice prompt; otherwise ask the user conversationally.

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Step 2: Locate the Manuscript

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

If the file does not exist at that path, search for likely candidates in:

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

If multiple manuscripts remain plausible, ask the user to choose.

Read the full manuscript before proposing changes.

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Step 3: Parse the Review Report

Extract all actionable items and group them by priority:

Priority	Source Section	Meaning
Critical	Major Concerns marked critical, blocking, fatal, or equivalent	Must fix before submission
Major	Major Concerns and Referee Objections	Strong referee-facing revisions
Minor	Minor Concerns and Specific Comments	Polish and cleanup

For each item, capture:

• the issue description
• the suggested fix (if present)
• the manuscript location
• the source section in the review report

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Step 4: Present Revision Plan (WAIT FOR APPROVAL)

Present the plan grouped by priority:

## Revision Plan

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

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

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

Total: N revisions across M sections.

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

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Step 5: Apply Approved Revisions

Work through approved items in this order:

1. Critical
2. Major
3. Minor

For each approved revision:

1. Identify the target passage in the manuscript.
2. Draft the replacement that resolves the issue while preserving the paper's voice.
3. Apply the edit.
4. Track whether the item was applied or deferred.

If the user approves only part of the plan, skip the deferred items and record them in the summary.

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Step 6: Focused Post-Revision Review

After applying the approved revisions, run a focused proofreading pass on the revised sections using agents/proofreader.md as the checklist.

By default, do this inline. If the user explicitly requested delegated review, you may use the proofread workflow or proofreader role separately.

Summarize any new issues introduced by the revisions.

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Step 7: Save Revision Summary

Create quality_reports/ if it is missing before saving.

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 Review 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 the issues are resolved

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Key Rules

• Prose track only. Never apply edits without user approval.
• Work from the review report. Do not invent a new agenda; address what the review surfaced.
• Preserve author voice. When rewriting prose, maintain the manuscript's tone and structure unless the review explicitly calls for a reorganization.
• Track everything. Every revision applied or deferred should appear in the summary.