A website using `embed` and `freeze` is missing files on second render

[cwickham]

Bug description

In a website, _quarto.yml:

project:
  title: "freeze-embed"
  type: website

execute:
  freeze: auto

Where one file embeds another, the first render (after turning on freeze) works, but a second render without any changes results in a website that is missing the notebook preview file.

Steps to reproduce

With repo at: https://github.com/cwickham/freeze-embed

1. First quarto render:

   [1/2] index.qmd
   Rendering qmd embeds
   [1/1] r.qmd
   
   
   processing file: r.qmd
   1/3           
   2/3 [addition]
   3/3           
   output file: r.knit.md
   
   [2/2] r.qmd
   
   
   processing file: r.qmd
   1/3           
   2/3 [addition]
   3/3           
   output file: r.knit.md
   
   
   Output created: _site/index.html
   

   Open _site/index.html. WORKS

2. Second quarto render (with no changes):

   [1/2] index.qmd
   [2/2] r.qmd
   
   Output created: _site/index.html
   

   Open _site/index.html. Links to "Source: R" don't work. _site/r.embed-preview.html is no longer present.

Expected behavior

A second render after freezing (with no changes to files) should have the same outcome at the first render.

Actual behavior

The second render removes some necessary files from _site/, in particular _site/r.embed-preview.html

Your environment

OS: Mac OS Sonoma 14.5

Quarto check output

Quarto 99.9.9
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.2.0: OK
      Dart Sass version 1.70.0: OK
      Deno version 1.41.0: OK
      Typst version 0.11.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 99.9.9
      commit: 3cfdf0178848bce308be22c0fad0ca420add762c
      Path: /Users/charlottewickham/Documents/posit/quarto-cli/package/dist/bin

[✓] Checking tools....................OK
      TinyTeX: v2024.03.13
      Chromium: (not installed)

[✓] Checking LaTeX....................OK
      Using: TinyTex
      Path: /Users/charlottewickham/Library/TinyTeX/bin/universal-darwin
      Version: 2024

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

[✓] Checking Python 3 installation....OK
      Version: 3.12.2
      Path: /Users/charlottewickham/.pyenv/versions/3.12.2/bin/python
      Jupyter: 5.7.2
      Kernels: julia-1.10, ark, python3

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

[✓] Checking R installation...........OK
      Version: 4.3.3
      Path: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources
      LibPaths:
        - /Users/charlottewickham/Library/R/arm64/4.3/library
        - /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
      knitr: 1.45
      rmarkdown: 2.28

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