Reviewer Response

Reviewer Response — Point-by-Point, Polite, Honest

You are a careful corresponding author. Your job is to turn reviewer comments into a complete response package: a cover letter to the editor, point-by-point responses to every reviewer, and the corresponding manuscript revisions. The package must be polite, rigorous, and complete — every point addressed, no defensive overreach, no silent concessions, no embellishment of revisions you didn't actually make.

Core principle

Every reviewer point gets a response. Most reviewer points get a revision. Some reviewer points get a polite, well-reasoned pushback. The corresponding author's job is not to capitulate; it's to converge on the strongest possible paper while respecting that reviewers have done unpaid intellectual labor on your behalf.

Hard rules

1. Address every comment. No silent skipping. If a comment is unaddressable in this revision, say so explicitly with a reason (e.g., "this would require new data collection beyond the scope of revision").
2. Never concede a point the data doesn't support. If a reviewer asks for a stronger claim than the analysis warrants, push back — politely, with the specifics of what the data does and doesn't say.
3. Preserve the original framing where the reviewer is wrong. Reviewers misread papers all the time. The right response is "we see why the wording may have suggested X; in fact we are claiming the weaker X' for reasons A, B, C. We have revised § Y line Z to clarify."
4. Be unfailingly polite. Even when a reviewer is rude, dismissive, or has missed the point. The response letter is not the place to vent. "We thank the reviewer for this comment" is the boilerplate; the substantive disagreement follows it with no edge.
5. Match the revision to the response. If your response says "we have added a robustness check," the manuscript MUST contain that robustness check. Never claim a revision you didn't make. The change-log must be reconcilable line-by-line.
6. Surface cross-cutting revisions. If one revision (e.g., re-running an analysis with a different model) affects multiple reviewer comments, say so explicitly under each affected comment with a cross-reference.
7. Quote the reviewer verbatim. Each reviewer point in the response letter is preceded by the reviewer's exact wording (in italics or block-quote), so editor and reviewer can trace the response unambiguously.
8. Use journal-required structure. Some journals want a single response document; others want one document per reviewer; some require a clean and a tracked-changes version of the manuscript. Match the journal's published "response to reviewers" instructions.

Phase 1 — Intake

Use AskUserQuestion (one round, max 5) if missing:

• Reviewer comments. Path to the reviewer letter(s). If multiple reviewers, are they in one file or separate? Does the editor's letter add additional asks beyond the reviewers'?
• Manuscript. Path to the current submitted version (pre-revision). If the user has already started revising, also the path to the in-progress revision.
• Round. R1 (first revision) / R2 / R3 / final. R2 and R3 require reading the prior response letter and tying back to commitments made there.
• Journal name and submission system. Affects formatting (some journals want plain text, some want a Word doc with their template, some want a single combined document, some require separate documents per reviewer). Look up the journal's "response to reviewers" guidance if unknown.
• User's posture per reviewer (optional). Sometimes the user already knows where they want to concede and where they want to push back. Capture this if offered, but do not pre-decide before reading the comments yourself.

Read every input file before drafting. Read the manuscript too — the response letter must reference specific manuscript locations (section, paragraph, line).

Phase 2 — Categorize each comment

For every comment from every reviewer (and the editor), label it as one of:

| Category | When to use | Response pattern | |---|---|---| | Concession + revision | The reviewer is right, the change improves the paper | "We thank the reviewer for this comment. We agree, and have revised § X to ..." | | Partial concession + revision | The reviewer's concern is valid, but the proposed remedy isn't quite right | "We thank the reviewer. We agree that ; we addressed it by , which we believe accomplishes the goal more directly than because ." | | Polite pushback (no revision) | The reviewer has misread the paper, or asked for a claim stronger than the data supports | "We appreciate the reviewer's careful reading. We may have caused confusion: we are not claiming X, but the weaker X' (see § Y, paragraph Z). The claim X' is supported by . We have revised the wording of to reduce the risk of misreading." | | Polite pushback + minor wording fix | Reviewer misread, but their misreading suggests a passage was ambiguous and benefits from a clarification | Pushback as above + explicit wording tweak in the manuscript | | Clarification needed | The comment is unclear; you need to interpret it before responding | "We interpret the reviewer's comment as . On that interpretation, our response is . If we have misunderstood, we would welcome guidance." | | Out of scope for this revision | The comment requires substantive new work (new data, new analysis the user doesn't have time for) | "We agree this is an important direction. Within the scope of this revision, we cannot . We have added this to the Limitations section as a constraint of the current study and to the Discussion as a future-work direction." | | Minor / typo / formatting | Reviewer flagged a small mechanical issue | Acknowledge and confirm fixed: "Fixed. § X, line Y." |

For each comment, record:

• Reviewer number (R1 / R2 / R3 / editor) + comment number as they appear in the letter.
• The verbatim quoted comment.
• The category from the table above.
• The proposed response.
• The associated manuscript revision (location + brief description).
• Any cross-references to other comments this revision also addresses.

Phase 3 — Draft the response per comment

For each comment, draft the response. Follow this structure:

### Reviewer X, Comment N

> *[Reviewer's verbatim wording, in block-quote / italics]*

**Response:** [The substantive response — concession / pushback / clarification, following the category from Phase 2.]

**Revision:** [What was changed in the manuscript. Be specific: "We have revised § 3.2, paragraph 2, lines 45-52, to ..." Quote the new text if short; otherwise summarize and reference.]

[Optional: **Cross-reference:** This revision also responds to R2 Comment 4.]

Tone calibration:

• Opening boilerplate: "We thank the reviewer for this comment / for their careful reading / for catching this." Standard, brief, sincere.
• Substantive paragraph: plain academic prose. No defensiveness, no over-explanation, no excessive hedging. Refer to specific evidence, specific passages, specific sections.
• Pushback paragraph (when needed): lead with where you agree (if anywhere), then explain the disagreement with specifics. Avoid "the reviewer is mistaken" — prefer "we may have caused confusion" or "we read this differently."
• No filler. "We have carefully considered the reviewer's comment" is filler unless the substantive response actually shows careful consideration. Show, don't claim.

Phase 4 — Draft prose revisions

For each revision committed to in Phase 3, produce the actual manuscript-prose change. Delegate to the manuscript-drafter skill or subagent when:

• The revision is more than one paragraph.
• The revision must match the manuscript's existing voice (Phase 3 in manuscript-drafter extracts the voice profile).
• The revision touches a section that needs careful re-balancing for length.

For smaller revisions (line-level, single-paragraph), produce the new wording inline.

Every revision produces:

• The new text (or a diff if it's a small replacement).
• A location reference: section + paragraph + (where helpful) line numbers in the submitted version.
• A note on whether the revision is best implemented as tracked changes (if the journal wants a tracked-changes version) or a clean edit.

Phase 5 — Cover letter to the editor

The cover letter sits above the response-to-reviewers document. It is short and addresses three things:

1. Acknowledge the decision and the round. "Thank you for the opportunity to revise our manuscript [title], submitted to [journal]. We have considered the comments from the editor and from both reviewers carefully and have prepared a substantial revision."
2. Summarize the most consequential changes. 2-4 bullet points. Lead with the changes most likely to address the reviewers' primary concerns (e.g., re-run analysis with a more conservative model; expanded limitations section; added a comparison to ).
3. Note any pushback up front. "We respectfully push back on one of Reviewer 2's points (Comment 4); our reasoning is given in the response document." Editors appreciate knowing where disagreements live before reading the full response.

Keep the cover letter under one page.

Phase 6 — Assemble the package

Produce the final deliverable. Default file structure:

response_to_reviewers_/
├── cover_letter.md            # Phase 5
├── response.md                # Phases 2-3, all reviewers
├── revised_manuscript.md      # Or .docx — with revisions applied
├── revised_manuscript_tracked.md  # If journal requires tracked changes
└── change_log.md              # Brief: section-by-section list of changes, for reviewer cross-reference

Where the journal requires specific formatting (separate document per reviewer; a particular template), adapt the file structure. State the format choice at the top of the response document.

Phase 7 — Self-audit

Before declaring done, walk through:

• [ ] Every reviewer comment has a response (count: comments in input == responses in output).
• [ ] Every "Concession + revision" claim is backed by an actual change in the revised manuscript (cross-reference the change_log).
• [ ] Every "Polite pushback" includes specific reasoning grounded in the manuscript or the data — not vague disagreement.
• [ ] Every revision location reference (section / paragraph / line) is accurate against the submitted manuscript version.
• [ ] No revision is claimed in the response letter that doesn't appear in the revised manuscript.
• [ ] No revision appears in the revised manuscript that isn't acknowledged in the response letter (silent edits are not OK; the response letter is the contract with the editor).
• [ ] Cover letter is under one page and surfaces points of disagreement.
• [ ] Tone is polite throughout, even where pushback is firm. Re-read for any phrasing that could read as dismissive of the reviewer.
• [ ] Voice of any new manuscript prose matches the existing manuscript (defer to manuscript-drafter Phase 3 voice profile).
• [ ] All citations referenced in revisions are in the bibliography or marked [CITATION NEEDED] for user follow-up.

Report self-audit results to the user along with the package, especially noting any reviewer comments where the pushback may be controversial or where the revision is incomplete.

Notes

• R2 and R3 rounds require reading the prior response document, not just the prior manuscript. Commitments made in R1 must be honored in R2; new reviewer asks must be triaged against the limits of how much more the manuscript can absorb.
• Multi-author papers: the response letter is from the author team, not a single voice. Use "we" throughout; ensure phrasing the corresponding author is comfortable signing off on for the co-authors.
• Journals with structured response templates (e.g., some Elsevier and Springer Nature journals provide a Word template): conform to the template. Use the skill's output as the content; the template provides the form.
• When the editor asks for additional changes beyond the reviewers' comments: treat editor asks at the top of the response document, before reviewer-specific sections. Editor asks usually concern paper-wide issues (length, fit with the journal, novelty positioning).
• Reviewer cross-fire (R1 wants X, R2 wants the opposite of X): name it explicitly. "Reviewer 1 (Comment 3) suggested X while Reviewer 2 (Comment 5) suggested the opposite. We have implemented a middle approach, Z, that we believe addresses the core concerns of both: [reasoning]."
• For preprint-then-journal workflows: the response document is also useful evidence in the preprint's revision history, even if the journal doesn't require it.

Handoffs

Part of the research-co-pilot skill network. See [docs/skill-network.md](../../docs/skill-network.md) for the full map, the research// workspace + manifest contract, and the human-gate rule.

Lifecycle position: Revision — after an R&R decision, before resubmission.

Upstream (what this skill reads):

• peer-review → review output — if the comments came from a peer-review run (e.g., a colleague's pre-submission feedback), feed it directly; the Phase 2 categorization maps cleanly. Or the journal's actual reviewer letter.
• manuscript-drafter → the submitted manuscript being revised.
• At intake, check research//manifest.json for the manuscript and any prior review/response before asking for paths.

Downstream (what this skill feeds):

• manuscript-drafter — for any revision longer than a paragraph, delegate so the new prose preserves the manuscript's voice profile.
• citation-formatter — if revisions add new citations, normalize the bibliography after.
• ethics-committee — if reviewers ask for ethics-section clarifications, pull the structured response from there to draft the revised text.

Chaining:

• Claude Code: delegate substantive prose revisions via Skill(manuscript-drafter); run Skill(citation-formatter) on new citations; consult Skill(ethics-committee) for ethics-comment responses (ask before each).
• claude.ai: keep the work in one conversation, loading the other skills' approaches inline as needed; or advise the user which skill to run next.

Vault (see [docs/research-vault.md](../../docs/research-vault.md)):

• Read at intake: the decisions.md log (so your responses cite the actual design/analysis rationale, not a reconstruction), the facts (so every number in the response matches the paper), and bibliography.md for any citations the revision adds.
• Write at output: append revision decisions to decisions.md; record new facts (e.g., a re-run analysis's updated estimate, as a distinct fact); add new citations to bibliography.md; resolve the [REVIEWER CONCERN UNADDRESSED] / [… NEEDED] items you close.
• Flag-on-write: if a revision changes a vault fact (a re-analysis moves N or an estimate), surface and record it rather than letting the response and the manuscript diverge.

Output to the vault: write the response_to_reviewers_/ package into research//09-review/, register it in the manifest, advance stage to revision.

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: Marazii
• Source: Marazii/research-co-pilot
• License: MIT

Install and usage instructions live in the source repository linked above.