Code annotations break with code linking AND embedded HTML #13216
Description
I have:
- searched the issue tracker for similar issues
- installed the latest version of Quarto CLI
- formatted my issue following the Bug Reports guide
Bug description
Code annotation support is broken in HTML documents with embedded HTML and code-link: true.
Removing the {=html} code block (and keeping code-link: true) returns styling to the code annotation. Alternatively, setting code-link: false (and keeping the {=html} code block) also returns styling to the code annotation. Behavior is the same whether code-annotations is set to below, hover, or select.
The issue seems related to #3945 where the solution was to automatically disable code linking when code annotations are enabled. In this case, adding an {=html} code block disrupts the exception.
Steps to reproduce
---
code-annotations: below
code-link: true
---
```{=html}
Embedded HTML breaks the styling of code annotations when <tt>code-link</tt> is true.
```
```{r}
2 + 2 # <1>
```
1. This should be styled as a popup.
Actual behavior
The annotation marker in the code is not displayed. Code annotations are presented without styling in a list after the code.
Expected behavior
The annotation marker in the code should be displayed. Code annotations should be presented in a styled list after the code.
Your environment
- IDEs: Positron 2025.08.0 build 130 and RStudio 2025.05.0 Build 496
- OS: MacOS Sequoia 15.4.1
Quarto check output
Quarto 1.7.33
[✓] Checking environment information...
Quarto cache location: ~/Library/Caches/quarto
[✓] Checking versions of quarto binary dependencies...
Pandoc version 3.6.3: OK
Dart Sass version 1.85.1: OK
Deno version 1.46.3: OK
Typst version 0.13.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
Version: 1.7.33
Path: /Applications/quarto/bin
[✓] Checking tools....................OK
TinyTeX: v2023.01
Chromium: (not installed)
[✓] Checking LaTeX....................OK
Using: TinyTex
Path: ~/Library/TinyTeX/bin/universal-darwin
Version: 2022
[✓] Checking Chrome Headless....................OK
Using: Chrome found on system
Path: /Applications/Google Chrome.app/Contents/MacOS/Google Chrome
Source: MacOS known location
[✓] Checking basic markdown render....OK
[✓] Checking Python 3 installation....OK
Version: 3.9.6
Path: ~/.virtualenvs/r-reticulate/bin/python3
Jupyter: 5.7.2
Kernels: python3
[✓] Checking Jupyter engine render....OK
[✓] Checking R installation...........OK
Version: 4.5.0
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library
knitr: 1.50
rmarkdown: 2.29
[✓] Checking Knitr engine render......OK