manuscript-structure-auditor

name	manuscript-structure-auditor
description	Audits manuscript coherence, section flow, paragraph logic, repetition, contradictions, and claim threading. Use when the user asks whether a paper draft, section, abstract, introduction, related work, or conclusion is logically connected, non-redundant, and easy for reviewers to follow.

Manuscript Structure Auditor

Use this before detailed sentence-level polishing.

Inputs

• Manuscript, section, abstract, outline, or pasted paragraphs.
• Target venue or audience if known.
• User concern: coherence, repetition, paragraph logic, section order, claim thread, contradiction, or reviewer readability.
• Optional artifacts: claim-evidence map, citation audit, figure plan, or red-team review.
• Desired depth: quick, standard, or deep; default to quick for daily revision.

If only a short passage is provided, audit local paragraph logic and state that full-paper coherence is not checked.

Workflow

1. Identify the unit under review: full manuscript, section, subsection, paragraph cluster, or abstract.
2. Extract the intended claim thread: problem -> gap -> contribution -> method -> evidence -> limitation.
3. Check section and paragraph jobs against references/structure-checks.md for standard or deep audits.
4. Mark repeated, redundant, contradictory, misplaced, or unsupported material.
5. Propose structural moves before sentence rewrites.
6. Produce a concise audit with severity and repair actions.

Read references/structure-checks.md when auditing more than one paragraph or when the user asks about coherence, repetition, or flow.

Output

For quick daily revision, avoid full tables unless needed:

## Claim Thread

## Top Structure Fixes
1.
2.
3.

## Repetition to Cut

For standard or deep audits:

## Claim Thread

## Structure Findings
| Severity | Location | Issue | Why it hurts the paper | Repair action |
| --- | --- | --- | --- | --- |

## Repetition Map
| Repeated idea | Locations | Keep | Remove or merge |
| --- | --- | --- | --- |

## Suggested Order

## Residual Risk

Severity

• blocking: the argument is internally inconsistent or reviewers cannot identify the contribution.
• major: flow, repetition, or missing transitions materially weakens the paper.
• minor: local paragraph order or phrasing slows the reader.
• nit: small structural polish.

Rules

• Do not rewrite the science to make the structure smoother.
• Do not delete repeated material unless one location can preserve the needed claim.
• Do not move claims ahead of the evidence or definitions needed to understand them.
• Do not treat every repeated term as redundancy; technical consistency often requires repeated terms.

Validation

• In quick revision, top structure fixes have a location or quoted cue and the unchecked scope is explicit.
• In standard or deep audits, every structural issue has a location or quoted cue.
• Every proposed deletion or merge preserves the scientific claim.
• The audit separates structure problems from grammar/style problems.
• The proposed order follows the paper's evidence state, not just a preferred template.

Completion

Done means the chosen depth is explicit, the manuscript unit has a visible claim thread, major coherence breaks have repair actions, and sentence-level editing can proceed without hiding structural problems.