Queelius Papermill Polish

Submission Polish

Perform a final quality check on a research paper before submission. This is the last line of defense -- catch everything that would annoy a reviewer or cause a desk rejection.

Step 1: Read Context

Read .papermill.md (Read tool) for:

• Venue: Target venue and its requirements.
• Format: Paper format (latex, markdown, rmarkdown).
• Review history: Outstanding issues from previous reviews.

If .papermill.md does not exist, the pre-flight check can still run — infer the format from the manuscript files and ask the user for the target venue. The checklist works regardless. Suggest running /papermill:init to capture venue and format persistently.

Read the complete manuscript (Read tool).

Step 2: Pre-Flight Checklist

Work through each category systematically. Report issues as they are found.

Formatting

• Paper compiles without errors
• No LaTeX warnings (especially undefined references, missing citations)
• Page count within venue limits
• Correct venue template/style file used
• Margins, font size, and spacing match requirements
• Line numbers included if required by venue
• Anonymous submission if required (no author names in text or metadata)

Abstract

• Word count within venue limits (typically 150-300 words)
• Self-contained (no citations, no undefined terms)
• States the problem, approach, main result, and significance
• Matches the paper's actual content

Citations and References

• All citations resolve (no "?" in the PDF)
• Bibliography is complete (no missing fields)
• Citation style matches venue requirements
• All references are cited in the text (no orphan bib entries that should be removed)
• All cited works are in the bibliography
• Self-citations are reasonable in number

Figures and Tables

• All figures are referenced in the text
• Figure captions are self-contained (reader should understand without reading the text)
• Resolution is sufficient for print (300+ DPI for raster images)
• Color is used accessibly (works in grayscale, colorblind-safe)
• Tables have clear headers and units

Mathematical Content

• All symbols are defined before use
• Notation is consistent throughout
• Equation numbering is correct and referenced
• Theorem/definition/proof environments are properly labeled
• No orphan proofs (every proof has a parent theorem/proposition)

Writing Quality

• No first-person narrative inconsistencies ("I" vs "we")
• Consistent tense usage
• No obvious typos or grammatical errors
• Acronyms defined on first use
• No overly long paragraphs (break up walls of text)

Metadata

• Author names and affiliations are correct
• ORCID identifiers included if venue supports them
• Keywords/subject classification provided
• Acknowledgments section present (funding, help, etc.)
• Data availability statement if required
• Code availability statement if applicable

Supplementary Material

• Appendices are referenced from the main text
• Supplementary files are in the required format
• Appendix content is not essential to understanding the main paper

Step 3: Build Verification

Run a clean build appropriate to the paper format (Bash tool). Use the manuscript path discovered in Step 1 (from .papermill.md or by scanning for .tex/.md/.Rmd files with Glob tool). Examples:

LaTeX papers:

latexmk -pdf <path-to-main.tex>

Markdown papers:

pandoc <path-to-paper.md> -o paper.pdf

R Markdown papers:

Rscript -e "rmarkdown::render('<path-to-paper.Rmd>')"

Report:

• Number of pages
• Number of warnings (LaTeX warnings, pandoc warnings, R warnings)
• Number of undefined references
• Number of overfull/underfull hbox warnings (LaTeX; prioritize overfull)

Step 4: Present Results

Present the checklist results:

Pre-Flight Report

Status: [Ready / Issues found]

Passing: N/M checks passed Issues:

1. [issue + suggested fix]
2. [issue + suggested fix] ...

Step 5: Fix Issues

Offer to fix issues directly:

• Formatting fixes: Apply them.
• Content fixes: Suggest specific changes and ask for approval.
• Style fixes: Propose rewording.

Step 6: Update State File

After all issues are resolved:

• Set stage to submission in .papermill.md (Edit tool).
• Append a timestamped note: "Pre-flight check passed. Ready for submission to [venue]."

Step 7: Suggest Next Steps

Paper is polished and ready. Final steps:

• Submit: Follow the venue's submission instructions.
• /papermill:venue: If you haven't selected a venue yet, do so now.
• Archive: Consider creating a git tag marking the submitted version.

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