Manuscript Writing

Manuscript Writing

Overview

Use this skill to improve academic and scientific writing without changing unsupported claims. It has two modes: revision, which edits the text or supplied document, and review, which comments on issues without changing the source.

Always use verified facts only. Do not invent citations, data, mechanisms, numerical values, novelty claims, or literature context. If verification requires sources or figures that are not available, flag the claim instead of rewriting it as fact.

Mode Selection

Use revision when the user asks to edit, revise, rewrite, polish, tighten, or improve the manuscript text directly. For pasted text, return revised text. For supplied document files, create a new revised document and keep the original unchanged.

Use review when the user asks for comments, feedback, suggestions, critique, audit, or review without changing the manuscript. For pasted text, return a listed set of actionable suggestions. For supplied document files, create a new commented document and keep the original unchanged.

If the user asks for both, run review first to identify issues, then ask before applying edits unless the user already clearly requested direct revision.

Shared Rules

• Preserve technical meaning. Do not change the scope, certainty, mechanism, temperature range, material system, causal relationship, baseline, or numerical interpretation unless the supplied evidence supports the change.
• Separate evidence from interpretation. Data, literature claims, limitations, and implications must not be merged into stronger claims than the evidence permits.
• Keep examples as rewrite patterns only. Do not insert an example's technical content into a manuscript unless the source document or cited evidence supports it.
• Maintain the author's intended contribution while removing vague language, redundancy, inflated certainty, unsupported novelty, and logical gaps.
• When facts cannot be verified from the provided text, citations, figures, tables, or user-supplied context, mark them as requiring verification.
• Before performing either revision or review, read references/revision-checklist.md and use it as the governing checklist.
• Execute the checklist phases in order. If a checklist item cannot be completed because required evidence, figures, tables, citations, equations, or constraints are unavailable, flag it under Needs Verification instead of skipping it silently.
• Never overwrite the user's original file. For document inputs, write a new output file with a clear suffix such as -reviewed, -commented, or -revised.

Document File Handling

For .doc, .docx, or .pdf inputs, preserve the user's original file and create a new document output.

In review mode, do not edit the manuscript body. Add comments or annotations at the relevant locations. Each comment should identify the checklist issue and include the suggested revision, verification step, or citation need in the comment text.

In revision mode, apply supported edits directly to the document body in the new output file. Use comments only for unresolved verification needs, rationale that the author must review, or questions that cannot be resolved from the supplied evidence. Do not put suggested edits in comments when the edit has already been applied in the text.

If the available tools cannot safely preserve layout, comments, or annotations for a source format, create the closest faithful new output artifact and state the limitation clearly. Do not modify the original file.

Revision Mode: Edit the Document

1. Identify the target audience, venue constraints, required tone, and whether edits should be in-place, returned as revised prose, or provided as a separate revised file.
2. Read the full relevant text before editing so terminology, claims, abbreviations, figures, and equations are handled consistently.
3. Apply references/revision-checklist.md sequentially: scope setup, precision, concision, tone, scientific rigor, and final audit.
4. Preserve citations and factual claims unless the user provides evidence for a correction. If a claim is unsupported, keep the text conservative or insert a visible verification note rather than fabricating support.
5. Prefer objective active voice with the data, model, method, or literature as the subject.
6. Remove orphan facts, redundant modifiers, unsupported hyperbole, repeated arguments, and transition words that do not mark a clear logical relationship.
7. Check numerical consistency, percentage logic, figure/table sequencing, equation-variable definitions, and citation specificity when the required materials are available.
8. Perform a final sentence-level, paragraph-level, and section-level flow audit so revised prose does not become a list of disconnected facts.
9. For document files, save the revised copy as a new file and keep comments limited to unresolved verification needs, rationale, or author questions.
10. Return a concise revision log after the edited text or edited file, noting major changes to claims, structure, terminology, and evidence support.

Review Mode: Comment or List Suggestions Only

Do not rewrite the source document. For pasted text, include short suggested replacements only when needed to make recommendations actionable. For document files, put suggested replacements inside comments or annotations, not in the manuscript body.

Use references/revision-checklist.md as the review rubric. Convert checklist failures into listed suggestions rather than editing the source document.

For each issue, whether listed in chat or inserted as a document comment, provide:

• Location: section, paragraph, sentence, heading, figure, table, or equation when identifiable.
• Issue: the specific problem, such as unsupported claim, vague term, overstatement, missing citation, inconsistent terminology, flawed comparison, or unclear causal logic.
• Why it matters: the precision, rigor, readability, or evidence problem created by the issue.
• Suggested action: a concrete edit, verification step, citation need, or structural move.
• Optional rewrite: one concise sentence when useful, clearly marked as suggested wording.

Prioritize high-impact issues first: unsupported novelty, incorrect certainty, data inconsistency, mathematical errors, missing citations for factual claims, and claims that exceed the evidence. Then address flow, concision, tone, and style.

Output Expectations

For revision, provide the revised document content or new edited file path, then a short revision log. If unresolved verification issues remain, list them separately under Needs Verification or as comments in the new document.

For review, provide grouped suggestions with clear labels such as Scientific Rigor, Evidence and Citations, Structure and Flow, and Style and Clarity. For document files, provide the new commented file path. Do not present stylistic preferences as factual requirements.

For either mode, keep all feedback actionable and grounded in the supplied manuscript, data, figures, tables, citations, or user-provided context.