PaperSpine

PaperSpine is a motivation-driven SKILL.md package for academic papers and paper-like writing tasks. It can be used with Codex-style skill folders and Claude Code skill folders. It is designed as a research-writing learning system rather than a prose polisher: it first studies the target venue or task genre, learns from strong exemplars, confirms the controlling motivation, builds section-level blueprints, and only then rewrites or integrates the manuscript.

In short: PaperSpine helps a manuscript grow around its central spine: motivation, evidence, section logic, and revision accountability.

What It Does

• Confirms the paper's controlling motivation before substantive writing.
• Researches target journals, conferences, or paper-like task genres.
• Learns rhetorical structure from strong exemplar papers or reports.
• Builds traceable artifacts such as confirmed_motivation.md, style_profile.md, section_blueprints.md, rewrite_matrix.md, and logic_transfer_audit.md.
• Preserves version-specific requirements through special_requirements.md.
• Guards LaTeX projects against broken citations, labels, figures, and environments.
• Audits revisions for shallow editing and addition-heavy rewrites.

Install

Install the whole folder, not only SKILL.md. PaperSpine uses references/ and scripts/ as part of the skill.

Codex

Clone or copy this repository into your Codex skills directory as paper-spine. The default Codex skills directory is usually ~/.codex/skills.

macOS/Linux:

git clone https://github.com/WUBING2023/PaperSpine.git ~/.codex/skills/paper-spine

Windows PowerShell:

git clone https://github.com/WUBING2023/PaperSpine.git "$HOME\.codex\skills\paper-spine"

If you use a custom CODEX_HOME, install to:

<CODEX_HOME>/skills/paper-spine

Restart Codex after installation so the new skill is loaded. Then invoke it with $paper-spine:

Use $paper-spine to diagnose and rewrite my manuscript for a target journal.

Claude Code

For a personal skill available across projects, clone or copy this repository to:

~/.claude/skills/paper-spine/SKILL.md

For a project-only skill, put it under the project:

<project>/.claude/skills/paper-spine/SKILL.md

Example:

git clone https://github.com/WUBING2023/PaperSpine.git ~/.claude/skills/paper-spine

In Claude Code, the skill directory name becomes the slash command:

/paper-spine

Claude Code may also invoke the skill automatically when your request matches the description in SKILL.md.

Claude.ai

Zip the paper-spine folder itself, with SKILL.md directly inside that folder, then upload it through Claude's Skills settings. Keep the folder structure intact so references/ and scripts/ remain available.

Troubleshooting

If Codex does not recognize the skill:

1. Check that this file exists: ~/.codex/skills/paper-spine/SKILL.md.
2. Check that references/ and scripts/ are next to SKILL.md, not one folder deeper.
3. Restart Codex after copying or cloning the skill.
4. Invoke the skill explicitly with $paper-spine.

Common mistake: downloading the GitHub ZIP and placing the extracted outer folder directly under skills/. Make sure the final layout is:

~/.codex/skills/paper-spine/SKILL.md
~/.codex/skills/paper-spine/references/
~/.codex/skills/paper-spine/scripts/

Quick Start

Use $paper-spine to diagnose and rewrite my manuscript for a target journal.

For Claude Code, use:

/paper-spine

Typical Workflow

1. Create source_map.md to classify the draft, data, figures, references, and exemplar sources.
2. Carry forward special_requirements.md when making numbered versions such as V8, V9, or V10.
3. Confirm the motivation in confirmed_motivation.md, or create motivation_options.md for user selection.
4. Research the target venue or task genre.
5. Learn from exemplar papers or reports.
6. Build the motivation thread, evidence bank, section blueprints, and rewrite matrix.
7. Rewrite from the blueprint, not by appending sentences to old paragraphs.
8. Run revision, logic-transfer, and LaTeX integrity audits.

Scripts

All scripts use only the Python standard library.

python scripts/style_metrics.py path/to/paper.tex --markdown
python scripts/revision_audit.py original.tex revised.tex --markdown
python scripts/latex_guard.py main.tex --bib references.bib --markdown

Repository Hygiene

This repository should contain only the reusable skill. Do not commit user manuscripts, generated paper versions, local paper_rewriting_output/ folders, compiled PDFs, or temporary one-off generation scripts.

Privacy And Integrity

The skill is designed to keep user data separate from exemplar papers. Exemplar papers may teach structure and rhetorical moves, but their scientific results must not be copied into the user's manuscript. The skill also forbids fabricating data, citations, metrics, p-values, or experimental claims.