Reformat a finished manuscript for a chosen journal

Why use this

1. A journal change can require reorganizing sections and references while preserving the scientific argument and citation relationships. A manuscript that looks correct after conversion may still contain broken reference fields, misplaced supplements or instructions from an outdated journal template.

2. A formatting-review packet could identify the intended structural changes and preservation requirements before conversion. The author could inspect a copy against the selected journal's supplied requirements without treating a finished-looking PDF as submission-ready.

Why an agent / simpler alternative

Useful judgment

Map manuscript elements to target requirements and notice conflicts that need an author decision rather than silent rewriting.

Simpler alternative

Use the journal's template directly when the manuscript is short and the required changes are limited.

Unsuitable when

The task would alter scientific claims, authorship or submission declarations without author review.

Proposed inputs

1. Name

   Manuscript structure sample

   Owner

   Corresponding author

   Minimum scope

   Fictional headings, citation fields, figures and supplement references

   Quality check

   Identify fields and content that must remain unchanged.

2. Name

   Journal requirement packet

   Owner

   Author

   Minimum scope

   Selected journal, supplied instructions and template version

   Quality check

   Distinguish mandatory requirements from optional style preferences.

Access and setup — proposed or unknown

Proposed minimum

1. Offline document descriptors and a proposed formatting-change manifest.

Compatibility unknowns

1. Unknown: current runtime, citation-field preservation, conversion tooling and PDF rendering.

External actions requiring approval

1. Target-journal changes, external manuscript processing, scientific edits and any submission.

Expected deliverable and review checks

Proposed artifact

Structure and reference-change plan with citation-preservation checks and author questions.

Critical checks

1. All source sections, figures and references have a proposed destination or explicit review flag.

2. Formatting changes do not silently revise scientific content or declarations.

Missing output evidence

No new workflow run or output inspection was performed for this overlay; use the canonical source-outcome references.

Failure signals and proposed responses

1. Signal

   Reference conversion would replace live citation fields with plain text.

   Why it matters

   Later edits could break citation maintenance.

   Proposed response

   Flag the loss and require an author-approved preservation or export strategy.

2. Signal

   A required section has no clear counterpart in the manuscript.

   Why it matters

   Automatic rearrangement may invent missing scientific material.

   Proposed response

   Leave the section unresolved and ask the author what content should satisfy it.

Effort and cost — unknown

Setup work

1. Confirm journal requirements and document preservation rules.

Ongoing review

1. Inspect later rendered output and reference integrity.

Unknowns

1. Unknown: conversion effort, formatting tools and remaining author revisions.

First check — proposed, unexecuted

Status

proposed_unexecuted

Synthetic fixture

A fictional manuscript map includes live citation fields and lacks a counterpart for one required section.

Acceptance checks

1. Flag citation-field preservation.

2. Request an author decision for the missing section without inventing text.

Stop conditions

1. Real manuscript processing, rendering, scientific edits or submission is required.

Limits

1. A structural manifest check is not a rendered-document review or proof that a journal will accept the submission.