Heading inside `content-hidden when-format="llms-txt"` loses its `<section>` and id, breaking TOC scroll

[mcanouil]

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

In a website project with llms-txt: true, a heading placed inside
::: {.content-hidden when-format="llms-txt"} is rendered in the HTML as a bare
<h2 ... data-anchor-id="..."> with no wrapping <section id="..."> and no real id.
Top-level headings render correctly inside <section id="..." class="level2">.
Because the heading has no id, the auto-generated TOC link
(data-scroll-target="#the-slug") matches nothing, so clicking it does not scroll, and direct
anchors and the hover anchor link are broken too.

Root cause (confirmed from the filter pipeline and the website llms finalizer):

1. For a block that is visible in HTML but hidden from llms output, the
   pre-llms-conditional-content filter replaces the ConditionalBlock with a plain
   <div class="llms-hidden-content"> that wraps the inner content, keeping the heading nested
   inside that div for the rest of the pipeline.
2. sections() (pandoc.structure.make_sections) runs in the crossref phase while the heading is
   still nested inside the llms-hidden-content div, so the heading is not treated as a top-level
   block and gets no <section> wrapper or id (only data-anchor-id).
3. After rendering, the website llms HTML finalizer calls cleanupConditionalContent, which
   unwraps .llms-hidden-content in the HTML DOM (keeps the children, removes the wrapper div),
   leaving the heading as a bare <h2> with no enclosing section and no id.

Source references:

• quarto-cli/src/resources/filters/main.lua

  Line 326 in 5748ba2

  { name = "pre-llms-conditional-content",

  : the pre-llms-conditional-content filter is registered in the pre phase.

• quarto-cli/src/resources/filters/quarto-pre/llms-conditional-content.lua

  Lines 40 to 54 in 5748ba2

  	ConditionalBlock = function(tbl)
  	local llms_visible = is_llms_visible(tbl)
  	if llms_visible == nil then return nil end
  	local html_visible = is_visible(tbl) -- from content-hidden.lua
  	if llms_visible == html_visible then return nil end -- no intervention needed
  	local div = tbl.original_node:clone()
  	if llms_visible then
  	div.classes:insert("llms-conditional-content")
  	else
  	div.classes:insert("llms-hidden-content")
  	end
  	return div
  	end

  : the handler replaces the ConditionalBlock with a <div class="llms-hidden-content"> wrapping the content.

• quarto-cli/src/resources/filters/main.lua

  Line 680 in 5748ba2

  sections(),

  : sections() runs in the crossref phase, after the wrapper exists and before it is unwrapped.

• quarto-cli/src/project/types/website/website.ts

  Line 365 in 5748ba2

  llmsHtmlFinalizer(source, project, format),

  : the HTML finalizer llmsHtmlFinalizer is invoked.

• quarto-cli/src/project/types/website/website-llms.ts

  Lines 105 to 122 in 5748ba2

  	function cleanupConditionalContent(doc: Document): void {
  	// Remove llms-only content from HTML output
  	for (const el of doc.querySelectorAll(".llms-conditional-content")) {
  	(el as Element).remove();
  	}
  	// Unwrap llms-hidden markers (keep content, remove wrapper div)
  	for (const el of doc.querySelectorAll(".llms-hidden-content")) {
  	const parent = (el as Element).parentElement;
  	if (parent) {
  	const element = el as Element;
  	while (element.firstChild) {
  	parent.insertBefore(element.firstChild as Node, element as Node);
  	}
  	element.remove();
  	}
  	}
  	}

  : cleanupConditionalContent unwraps .llms-hidden-content in the DOM after section wrapping.

I discovered this issue with llms-txt and conditional content features on the Quarto Wizard website where I wanted to hide the LLM prompt from the llms-txt output:

• https://github.com/mcanouil/quarto-wizard/blob/43b66bb90bd45f6b4ffd2a29825195123afffc02/docs/reference/schema-specification.qmd#L596

From my testing, it's really specific to llms-txt feature which badly interacts with conditional content.

Steps to reproduce

Create a minimal website project with two files, then render the whole project.

_quarto.yml:

project:
  type: website
website:
  title: "llms-txt repro"
  llms-txt: true
format:
  html:
    toc: true

index.qmd:

---
title: "Home"
---

## Normal Section

{{< lipsum 3 >}}

## Another Section

{{< lipsum 3 >}}

::: {.content-hidden when-format="llms-txt"}

## Conditional Section

Content

:::

Render the project and inspect the output:

quarto render
grep -c 'id="normal-section" class="level2"' _site/index.html       # 1
grep -c 'id="another-section" class="level2"' _site/index.html      # 1
grep -c 'id="conditional-section" class="level2"' _site/index.html  # 0 (bug)

Actual behavior

Normal Section is wrapped:

<section id="normal-section" class="level2">
  <h2 class="anchored" data-anchor-id="normal-section">Normal Section</h2>
  ...
</section>

Conditional Section, although visible in HTML, has no section and no id:

<h2 class="anchored" data-anchor-id="conditional-section">Conditional Section</h2>
...

The TOC entry is generated with data-scroll-target="#conditional-section", which matches no
element, so the TOC link does not scroll.
A live example is the last TOC entry on
https://m.canouil.dev/quarto-wizard/reference/schema-specification.html.

Expected behavior

A heading visible in the HTML output is wrapped in its own <section id="..."> and receives an
id, even when it sits inside content-hidden when-format="llms-txt", so TOC links, direct
anchors, the hover anchor link, and cross-references all work.

Your environment

• IDE: VSCode.
• OS: macOS (Darwin 25.5.0).
• Quarto: 99.9.9 (local development build from source, commit 5748ba2).

Quarto check output

Quarto 99.9.9
[✓] Checking environment information...
      Quarto cache location: /Users/mcanouil/Library/Caches/quarto
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.8.3: OK
      Dart Sass version 1.87.0: OK
      Deno version 2.7.14: OK
      Typst version 0.14.2: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 99.9.9
      commit: 5748ba2eb171c4906ce124f5c61c3246045e44a7
      Path: /Users/mcanouil/Projects/quarto-dev/quarto-cli/package/dist/bin

[✓] Checking tools....................OK
      TinyTeX: v2026.05
      Chrome Headless Shell: (not installed)
      VeraPDF: (not installed)

[✓] Checking LaTeX....................OK
      Using: TinyTex
      Path: /Users/mcanouil/Library/TinyTeX/bin/universal-darwin
      Version: 2026

[✓] Checking Chrome Headless....................OK
      Using: Chrome from QUARTO_CHROMIUM
      Path: /Applications/Brave Browser.app/Contents/MacOS/Brave Browser

[✓] Checking basic markdown render....OK

(|) Checking R installation...........ℹ R version 4.6.0 (2026-04-24)
! Config '~/.Rprofile' was loaded!
[✓] Checking R installation...........OK
      Version: 4.6.0
      Path: /Library/Frameworks/R.framework/Resources
      LibPaths:
        - /Library/Frameworks/R.framework/Versions/4.6/Resources/library
      knitr: 1.51
      rmarkdown: 2.31

[✓] Checking Knitr engine render......OK

[✓] Checking Python 3 installation....OK
      Version: 3.14.5
      Path: /opt/homebrew/opt/python@3.14/bin/python3.14
      Jupyter: (None)

      Jupyter is not available in this Python installation.
      Install with python3 -m pip install jupyter

      There is an unactivated Python environment in .venv. Did you forget to activate it?

[✓] Checking Julia installation...

[mcanouil]

Workaround is to not use "llms-txt" as conditional target for now.

::: {.content-visible when-format="html"}

instead of

::: {.content-hidden when-format="llms-txt"}