quarto-manager

name	quarto-manager
description	Complete Quarto project manager (websites and books). Use this skill whenever the user is working with .qmd or .Rmd files, mentions Quarto, wants to create/check/compile a Quarto site or book, manage a BibTeX bibliography, convert Rmd files to qmd, or organize a Quarto project structure. Also triggers for: _quarto.yml, cross-references (@fig-, @tbl-, @eq-), R/Python chunks, quarto render, revealjs, beamer, or any Quarto syntax question.
triggers	["/quarto"]

Quarto Manager

End-to-end Quarto project management: syntax checking, Rmd→qmd conversion, directory organization, bibliography management, and compilation.

User preferences

• Inline math: $...$
• Display equations: $$...$$
• Style: precise and concise

Quarto best practices

• After editing Quarto files, always verify PDF compilation with quarto render.
• Be careful with special characters (---, |) in markdown cells — they break YAML parsing.
• When adding images or covers, ensure changes work for both HTML and PDF output, not just one.
• For multiline equations, use $$ delimiters with \begin{aligned} inside. Avoid \begin{align} directly in markdown cells — it can cause rendering issues in PDF output.

Commands

Five slash commands are available. Each has detailed documentation in references/. Read the corresponding reference file before executing the command.

Command	Action	Reference
/quarto:check	Check format and syntax	references/check.md
/quarto:convert	Convert .Rmd → .qmd	references/convert.md
/quarto:organize	Organize project structure	references/organize.md
/quarto:bib	Manage bibliography	references/bib.md
/quarto:render	Compile the project	references/render.md

General behavior

Caution and backups

Always ask for confirmation before modifying or deleting files. Create automatic backups before any conversion or reorganization (backup/ folder). Suggest corrections without ever forcing them.

Project type detection

Read _quarto.yml to determine the type:

• Presence of website: → website project
• Presence of book: → book project
• Absence of _quarto.yml → offer to create it by asking the type

Directory structures

Website:

project/
├── _quarto.yml
├── index.qmd
├── about.qmd
├── images/
├── css/
├── js/
├── references.bib
└── _site/           (generated)

Book:

project/
├── _quarto.yml
├── index.qmd
├── 01-introduction.qmd
├── 02-methods.qmd
├── references.bib
├── figures/
└── _book/           (generated)

Quarto expertise

YAML header

A valid header starts and ends with ---. Common fields:

---
title: "My document"
author: "Name"
date: today
format:
  html:
    toc: true
  pdf:
    documentclass: article
bibliography: references.bib
---

Cross-references

• Figures: @fig-label with #| label: fig-label
• Tables: @tbl-label with #| label: tbl-label
• Equations: @eq-label with $$ ... $$ {#eq-label}
• Sections: @sec-label with {#sec-label}

Code chunks (qmd format, hashpipe)

```{r}
#| label: fig-example
#| fig-cap: "Caption"
#| echo: false
plot(x, y)
```

Key differences Rmd → qmd

• Chunk options: {r, echo=FALSE} → #| echo: false
• Cross-references: \@ref(fig:label) → @fig-label
• YAML: output: → format:
• Callouts: ::: {.callout-note} (native pandoc divs)

Supported output formats

html, pdf, docx, revealjs, beamer, pptx, epub, gfm, hugo-md

Scripts

Python scripts are available in scripts/ for automated operations:

Script	Function
scripts/check_yaml.py	Validate YAML headers
scripts/check_math.py	Check $/$$ delimiters
scripts/convert_rmd.py	Convert .Rmd to .qmd
scripts/check_bib.py	Check citations vs .bib