[manuscript/html] column-margin code blocks overlaid by subsequent content in article notebook

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• searched the issue tracker for similar issues
• installed the latest version of Quarto CLI
• formatted my issue following the Bug Reports guide

Bug description

When using div containers with class .column-margin in index.qmd of manuscript projects, these containers are overlaid by subsequent content in the article notebook html output (i.e. the index-preview.html).

In the index.html, the respective container is properly moved to the margin, as expected. In the article notebook that contains the manuscript's computations (index-preview.html), the container is not moved to the margin but still has class="no-row-height", causing it to reside in the main content's column but with no row-height.

In essence, the respective <div> container has classes no-row-height column-margin column-container in the main index.html, but only no-row-height in the index-preview.html.

Same behavior for both quarto 1.8.26 and quarto 1.9.11.

index.html	index-preview.html

index.html

<div class="no-row-height column-margin column-container"><div class="">
<div class="cell">
<div class="cell-output cell-output-stdout">
<pre><code>[1] "Moved to margin. \n This is overlaid by following content in Article Notebook since it is not moved to margin there."</code></pre>
</div>
</div>
</div></div>

index-preview.html

<div class="no-row-height"><div class="">
<div class="cell-container"><div class="cell-decorator"><pre>In [2]:</pre></div><div class="cell">
<div class="code-copy-outer-scaffold"><div class="sourceCode cell-code" id="cb3"><pre class="sourceCode r code-overflow-wrap code-with-copy"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="fu">cat</span>(<span class="st">"Moved to margin.</span><span class="sc">\n</span><span class="st">This is overlaid by following content in Article Notebook since it is not moved to margin there."</span>)</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
<div class="cell-output cell-output-stdout">
<pre><code>Moved to margin.
This is overlaid by following content in Article Notebook since it is not moved to margin there.</code></pre>
</div>
</div></div>
</div></div>

Steps to reproduce

1. Create a blank manuscript project:

   quarto create project manuscript
   

2. index.qmd:

   ---
   title: manuscript-margin-reprex
   authors:
     - name: Norah Jones
       affiliation: The University
       roles: writing
       corresponding: true
   bibliography: references.bib
   ---
    
   ## Section
   This is a simple placeholder for the manuscript's main document [@knuth84].
    
   ```{r}
   cat("This is a code block")
   ```
   
   :::{.column-margin}
   ```{r}
   #| code-overflow: wrap
   cat("Moved to margin.\nThis is overlaid by following content in Article Notebook since it is not moved to margin there.")
   ```
   :::
   
   ```{r}
   cat("Not margin.")
   ```
   

3. _quarto.yml:

   project:
     type: manuscript
   
   manuscript:
     article: index.qmd
   
   format: html
   
   execute:
     freeze: true
   

Actual behavior

.column-margin containers are overlaid by subsequent content in the article notebook (i.e. the index-preview.html) of a manuscript project.

Expected behavior

No overlaid blocks:

• Either, respective blocks are actually moved to the margin
• Or, respective blocks are displayed in the regular content flow of quarto-document-content container, e.g. by removing class no-row-height for div-containers with .column-margin in article notebooks (index-preview.html):
  

Your environment

• IDE: Positron 2025.11.0 build 234
• OS: Windows 11
• quarto: 1.8.26 (also tested with 1.9.11)

Quarto check output

Quarto 1.8.26
[>] Checking environment information...
      Quarto cache location: C:\Users\redacted\AppData\Local\quarto
[>] Checking versions of quarto binary dependencies...
      Pandoc version 3.6.3: OK
      Dart Sass version 1.87.0: OK
      Deno version 2.3.1: OK
      Typst version 0.13.0: OK
[>] Checking versions of quarto dependencies......OK
[>] Checking Quarto installation......OK
      Version: 1.8.26
      Path: C:\Users\redacted\AppData\Local\Programs\Quarto\bin
      CodePage: 1252

[>] Checking tools....................OK
      TinyTeX: v2025.10
      Chromium: 869685

[>] Checking LaTeX....................OK
      Using: TinyTex
      Path: C:\Users\redacted\AppData\Roaming\TinyTeX\bin\windows\
      Version: 2025

[>] Checking Chrome Headless....................OK
      Using: Chrome found on system
      Path: C:\Program Files (x86)\Microsoft\Edge\Application\msedge.exe
      Source: Windows Registry

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

[>] Checking Python 3 installation....OK
      Version: 3.14.0
      Path: C:/Users/redacted/AppData/Local/Python/pythoncore-3.14-64/python.exe
      Jupyter: (None)

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

[>] Checking R installation...........OK
      Version: 4.5.0
      Path: C:/Users/redacted/AppData/Local/Programs/R/R-4.5.0
      LibPaths:
        - C:/Users/redacted/AppData/Local/Programs/R/R-4.5.0/library
      knitr: 1.50
      rmarkdown: 2.30

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

Reproduce the manuscript project from the issue using _index.qmd and _quarto.yml, then compare _index.html with _index-preview.html. Start by tracing how .column-margin and no-row-height are assigned in the article notebook output. Done means margin blocks are no longer overlaid, either by moving them to the margin or keeping them in normal content flow.