quarto-clean
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, fix, modernize, or port a Quarto or R Markdown document; when LaTeX commands app
Profile →npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill quarto-clean --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Quarto Clean 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 PDF. This skill finds and fixes them all in a single pass. **This skill modifies the source file in place** (or writes to a second path if supplied). Before writing, tell the user what file will be changed and remind them that `git diff` or file history can recover the original. --- ## Input Arguments | Position | Required | Description | |----------|----------|-------------| | 1 | **Yes** | Path to the `.qmd` file to clean (e.g., `paper/paper.qmd`). Cleaned in place by default. | | 2 | No | Output path. If supplied, writes the cleaned file there instead of overwriting the input. | **Example invocations:** ``` /quarto-clean paper/paper.qmd /quarto-clean paper/paper.qmd drafts/paper-clean.qmd ``` --- ## Step-by-Step Workflow ### 1. Parse Arguments Identify the input `.qmd` path (arg 1) and output path (arg 2, or same as arg 1 if omitted). ### 2. Read the File Use the `Read` tool to load the enti
- Input Arguments
- Step-by-Step Workflow
- 1. Parse Arguments
- 2. Read the File
- 3. Apply All Transformations
What does the quarto-clean skill 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. 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, fix, modernize, or port a Quarto or R Markdown document; when LaTeX commands app
How do I install it?
Run `npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill quarto-clean --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From brycewang-stanford/Auto-Empirical-Research-Skills, a repository with 3,244 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.