Md To PDF
Mathews-Tom/armory
Convert Markdown to styled PDFs with Mermaid diagrams, LaTeX/KaTeX math, tables, and code highlighting.
Cleans a Quarto (.qmd) file by replacing LaTeX holdovers with proper Quarto/Pandoc syntax so the document renders correctly to HTML, PDF (Typst/LaTeX), and Word.
Install Quarto Clean
$ npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill quarto-clean -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills quarto-clean --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/22-christopherkenny-skills/skills/quarto-clean .claude/skills/quarto-clean && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "quarto-clean" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/22-christopherkenny-skills/skills/quarto-clean into .claude/skills/quarto-clean/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "quarto-clean", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/22-christopherkenny-skills/skills/quarto-cleanType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill quarto-clean -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills quarto-clean --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/22-christopherkenny-skills/skills/quarto-clean .agents/skills/quarto-clean && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "quarto-clean" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/22-christopherkenny-skills/skills/quarto-clean into .agents/skills/quarto-clean/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "quarto-clean", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill quarto-clean -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills quarto-clean --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/22-christopherkenny-skills/skills/quarto-clean .cursor/skills/quarto-clean && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "quarto-clean" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/22-christopherkenny-skills/skills/quarto-clean into .cursor/skills/quarto-clean/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "quarto-clean", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git --path skills/22-christopherkenny-skills/skills/quarto-clean--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill quarto-clean -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills quarto-clean --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/22-christopherkenny-skills/skills/quarto-clean .gemini/skills/quarto-clean && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "quarto-clean" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/22-christopherkenny-skills/skills/quarto-clean into .gemini/skills/quarto-clean/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "quarto-clean", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills quarto-cleanInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill quarto-clean -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/22-christopherkenny-skills/skills/quarto-clean .github/skills/quarto-clean && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "quarto-clean" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/22-christopherkenny-skills/skills/quarto-clean into .github/skills/quarto-clean/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "quarto-clean", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill quarto-clean -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills quarto-clean --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/22-christopherkenny-skills/skills/quarto-clean .opencode/skills/quarto-clean && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "quarto-clean" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/22-christopherkenny-skills/skills/quarto-clean into .opencode/skills/quarto-clean/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "quarto-clean", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
quarto-clean- GitHub stars
- 4.5k
- Token cost
- ~3.3k tokens
- SKILL.md length
- 1,210 words
- Files
- 1
- Skills in repo
- 383
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
Cleans a Quarto (.qmd) file by replacing LaTeX holdovers with proper Quarto/Pandoc syntax so the document renders correctly to HTML, PDF (Typst/LaTeX), and Word.
- Works in 5 steps: Parse Arguments → Read the File → Apply All Transformations → …
- R Markdown document
- SKILL.md covers Input Arguments, Step-by-Step Workflow, Transformation Reference and Patterns That Need Judgment, plus 1 more section
- Calls git
What it does
Quarto Clean is an agent skill from brycewang-stanford/Auto-Empirical-Research-Skills. Cleans a Quarto (.qmd) file by replacing LaTeX holdovers with proper Quarto/Pandoc syntax so the document renders correctly to HTML, PDF (Typst/LaTeX), and Word. Fixes citations (\citep → [@key]), cross-references (\ref → @label), figures (\includegraphics → markdown), tables, text formatting (\textbf → bold), inline math (\( \) → $ $), hyperlinks (\href → [text](url)), footnotes (\footnote → ^[]), list environments, section headings, and R Markdown chunk options (dot-style → | YAML). Use when asked to clean…
Its SKILL.md is about 3.3k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
It sits in Documents & Office, covering LaTeX, Citation management and Markdown. It works with LaTeX and Pandoc. The repository describes itself as: 🔬 A curated collection of 23,000+ agent skills for empirical research across 8 social science disciplines. | 精选 23,000+ AI Agent 技能库，覆盖8大社会科学学科的实证研究。CoPaper.AI…
When your agent uses it
- R Markdown document
- LaTeX commands appear in a .qmd file
- A document fails to render to Word
- Citations/cross-references do not appear in non-LaTeX output
Example prompts
- “Use the quarto-clean skill to clean a Quarto (.qmd) file by replacing LaTeX holdovers with proper Quarto/Pandoc syntax so the document renders…”
- “/quarto-clean”
Workflow steps
5 steps, taken from the step headings in SKILL.md.
- Parse Arguments
- Read the File
- Apply All Transformations
- Write the Cleaned File
- Report to the User
What it can do on your machine
Read from SKILL.md and the folder at commit 9fa87d8. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Shell commands in SKILL.md call:
git
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md. Its commands use git, which can reach the network depending on how they are called.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Quarto Clean loads about 3.3k tokens when it runs. Until then it costs about 188 tokens; SKILL.md has 1,210 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
Its licence (Custom licence) doesn't allow us to republish the file, so here is its outline and opening line. It has 1,210 words (~3,280 tokens).
“You clean a Quarto (.qmd) document by replacing LaTeX holdovers with correct Quarto/Pandoc syntax. Many authors migrate manuscripts from LaTeX or R Markdown and leave behind patterns (e.g., \citep{}, \ref{}, \textbf{}) that silently fail when rendering to Word or Typst…”
- name
- quarto-clean
- metadata.author
- Christopher T. Kenny
- metadata.version
- 1.1
Files
Just SKILL.md in skills/22-christopherkenny-skills/skills/quarto-clean of brycewang-stanford/Auto-Empirical-Research-Skills.
Open the folder on GitHubat commit 9fa87d8
Compare with similar skills
Quarto Clean next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Quarto Clean this skillbrycewang-stanford/Auto-Empirical-Research-Skills | 4.5k | — | ~3.3k | Automated safety check: Pass | Custom licence | |
| Md To PDFMathews-Tom/armory | 328 | — | ~2.4k | Automated safety check: Pass | MIT | |
| Md To PDF Academicwentorai/research-plugins | 298 | 1 repos | ~1.8k | Automated safety check: Notes | MIT | |
| Markdown Academic Guidewentorai/research-plugins | 298 | 1 repos | ~1.5k | Automated safety check: Pass | MIT | |
| Academic Paper Writing PipelineImbad0202/academic-research-skills | 51k | — | ~16k | Automated safety check: Pass | Custom licence | |
| Literature Surveyai4s-research/ai4s-skills | 237 | 2 repos | ~2k | Automated safety check: Pass | MIT |
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Related
Categories
Questions about Quarto Clean
What does Quarto Clean do?
Cleans a Quarto (.qmd) file by replacing LaTeX holdovers with proper Quarto/Pandoc syntax so the document renders correctly to HTML, PDF (Typst/LaTeX), and Word. Quarto Clean is an agent skill from brycewang-stanford/Auto-Empirical-Research-Skills.qmd) file by replacing LaTeX holdovers with proper Quarto/Pandoc syntax so the document renders correctly to HTML, PDF (Typst/LaTeX), and Word.
When should I use Quarto Clean?
Quarto Clean fits situations like: R Markdown document; laTeX commands appear in a .qmd file; A document fails to render to Word; citations/cross-references do not appear in non-LaTeX output.
How do I install Quarto Clean in Claude Code?
Run `npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill quarto-clean -a claude-code`. Or copy the skill folder (skills/22-christopherkenny-skills/skills/quarto-clean in brycewang-stanford/Auto-Empirical-Research-Skills) into .claude/skills/quarto-clean in your project. Claude Code loads it when a task matches its description.
How do I install Quarto Clean in Codex?
Run `npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill quarto-clean -a codex`. Or copy the skill folder (skills/22-christopherkenny-skills/skills/quarto-clean in brycewang-stanford/Auto-Empirical-Research-Skills) into .agents/skills/quarto-clean in your project. Codex loads it when a task matches its description.
Can I use Quarto Clean in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill quarto-clean -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/quarto-clean, .gemini/skills/quarto-clean, .github/skills/quarto-clean and .opencode/skills/quarto-clean in your project.
What does Quarto Clean need to run?
Going by SKILL.md and its folder, Quarto Clean needs the command-line tools its instructions call (git).
Does Quarto Clean access the network?
SKILL.md contains no URLs. Its commands use git, which can reach the network depending on how they are called. This is read from the text; nothing was executed.
Is Quarto Clean safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
What licence does Quarto Clean use?
Quarto Clean has a licence file (the repository's licence) that doesn't match a standard licence. Read it on GitHub before reusing the skill.
How many tokens does Quarto Clean use?
About 3.3k tokens (SKILL.md is roughly 13k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Quarto Clean?
Skills that share tags, products or a category with Quarto Clean: Md To PDF (Mathews-Tom/armory, 328 stars), Md To PDF Academic (wentorai/research-plugins, 298 stars), Markdown Academic Guide (wentorai/research-plugins, 298 stars) and Academic Paper Writing Pipeline (Imbad0202/academic-research-skills, 51k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Quarto Clean?
brycewang-stanford (a GitHub user) maintains it in brycewang-stanford/Auto-Empirical-Research-Skills, which has 4,542 GitHub stars. The repository holds 383 skills in this directory. The repository was last updated on October 5, 2026.
Source: brycewang-stanford/Auto-Empirical-Research-Skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.