# Submission Package Audit

Use this file when the user provides a full or partial submission package rather
than only one manuscript file.

Typical files:

- `Manuscript.docx`
- `Supplementary Information.docx`
- `Highlights.docx`
- `CoverLetter.docx`
- `Figures.pptx`
- `Supplementary Information.pptx`
- `TOC.pptx`

## Core rule

Audit the files as one submission package. The main manuscript and main figures
define the story; all other files must be consistent with them.

Do not check files independently if cross-file consistency matters.

## Recommended order

1. `Manuscript.docx`
2. `Figures.pptx`
3. `Supplementary Information.docx`
4. `Supplementary Information.pptx`
5. `Highlights.docx`
6. `CoverLetter.docx`
7. `TOC.pptx`

Rationale: the manuscript and main figures establish the scientific story, the
SI documents support the claims, and the highlights, cover letter, and TOC must
then align with that story.

## File-specific checks

### 1. Manuscript.docx

Check:

- central claim, novelty, target-journal fit, and story order
- title, abstract, introduction gap, results logic, discussion boundary
- claim-evidence alignment with figures and SI
- DOI-only citation comment placement if requested
- terminology, sample names, abbreviations, units, and spelling consistency
- whether strong related papers expose missing evidence or weaker positioning

Default output:

- annotated copy with Word native comments when editing is requested
- Markdown reviewer report for global issues

### 2. Figures.pptx

Check:

- main figure sequence matches manuscript Results order
- each figure has one clear conclusion
- panel labels, scale bars, axis labels, legends, units, and error bars
- sample names and colors match manuscript and SI
- resolution, font size, line width, contrast, cropping, and alignment risks
- whether any panel lacks explanation in the text
- whether any key claim in the text lacks a main or SI figure

### 3. Supplementary Information.docx

Check:

- SI figure/table numbering and order
- methods completeness and reproducibility
- experimental details, controls, statistics, and raw/supporting data
- cross-references from manuscript to SI
- whether SI evidence actually supports main-text claims
- consistency with `Supplementary Information.pptx`

### 4. Supplementary Information.pptx

Check:

- SI figures match `Supplementary Information.docx`
- figure numbering, captions, sample names, and units are consistent
- control figures and supplementary mechanism evidence are present
- image quality and visual style match main figures where appropriate

### 5. Highlights.docx

Check:

- highlights reflect the manuscript's true novelty
- claims are concrete and evidence-backed
- no mismatch with abstract, cover letter, or target journal positioning
- no empty phrases such as `excellent performance` without specifics
- each highlight is short, distinct, and not redundant

### 6. CoverLetter.docx

Check:

- target journal and article type are correct
- novelty and significance match manuscript evidence
- claims are not stronger than the data
- relationship to strong related papers is clear without sounding defensive
- required declarations are present if the journal requires them
- tone is professional and concise

If target-journal rules may have changed, verify the current journal page before
final submission advice.

### 7. TOC.pptx

Check:

- graphical TOC communicates material design, mechanism, and application at a
  glance
- it is consistent with manuscript title, abstract, and main figures
- visual hierarchy is clear
- text is minimal and readable
- mechanism arrows, labels, material names, and device icons are accurate
- it does not introduce claims absent from the manuscript

## Cross-file consistency checks

Always check:

- title consistency across manuscript, cover letter, TOC, and highlights
- material names, sample labels, and abbreviations
- figure numbering and panel references
- SI numbering and manuscript callouts
- performance values and units
- target journal name and article type
- novelty wording across abstract, highlights, cover letter, and TOC
- terminology and spelling variants
- whether DOI citation suggestions align with the claims being cited

## Output package

Preferred outputs:

- `<manuscript-name>_comments.docx`: Word native comments for sentence-level
  issues and DOI-only citation suggestions when requested
- `<manuscript-name>_reviewer_report.md`: global review, comparative audit,
  figure/SI/package issues, and priority revision plan
- optional `<manuscript-name>_package_checklist.md`: concise cross-file checklist

Never overwrite original files unless the user explicitly asks.

## Report format

Use:

```text
Package inventory
- Manuscript:
- Main figures:
- SI document:
- SI figures:
- Highlights:
- Cover letter:
- TOC:

Priority issues
| ID | Severity | File | Location | Problem | Fix | Cross-file impact |
|---|---|---|---|---|---|---|

Cross-file consistency
- ...

File-by-file findings
- Manuscript:
- Figures:
- SI document:
- SI figures:
- Highlights:
- Cover letter:
- TOC:

Next revision order
1. ...
2. ...
3. ...
```