LaTeX Word Roundtrip Cleaner

Purpose

Clean formatting damage caused by moving manuscripts among LaTeX, Word, Markdown, PDFs, and journal submission portals while protecting scientific content and references.

Typical Inputs

• LaTeX text copied into Word or plain text.
• Word/PDF text with broken line breaks, hyphenation, symbols, or references.
• Markdown tables or figure legends needing manuscript-safe cleanup.
• Submission portal text that rejects or damages LaTeX commands.

Core Rules

• Do not change manuscript meaning.
• Do not alter citation keys, equation labels, figure/table labels, accession IDs, gene names, drug names, P values, or statistical values.
• Do not fabricate or invent references, data, methods, or results.
• Preserve math delimiters and complex equations unless the user explicitly asks for conversion.
• Flag conversions that may require manual checking.
• Recommend final human review, especially for equations and references.

Workflow

1. Identify source and target format:
   • LaTeX to Word/plain text
   • Word/plain text to LaTeX
   • Markdown to manuscript text
   • submission portal cleanup
2. Protect technical tokens:
   • \cite{}
   • \ref{}
   • \label{}
   • $...$, \(...\), and \[...\]
   • gene names, units, P values, accession IDs
3. Clean formatting:
   • broken line breaks
   • hyphenation artifacts
   • double spaces
   • malformed punctuation
   • inconsistent figure/table references
4. Return the cleaned target-format text.
5. List protected items and risky conversions only when useful.

Reference Cleanup

Normalize reference wording according to the user's target style:

• Fig. 1, Figure 1, or Fig 1
• Table 1
• Supplementary Figure S1

Never merge supplementary references with main-text references.

Output Modes

Default output:

• Cleaned text only.

For risky conversions:

• Cleaned text.
• Protected items.
• Potentially unsafe conversions needing manual review.

Quality Checklist

• Cross-references and citations are intact.
• Equations are not corrupted.
• Scientific values are unchanged.
• Formatting is cleaner but content is not rewritten.