Embed-resources does not work with Quarto project and just errors

Bug description

Problem: quarto render fails when enabling self-contained or embed-resources in yaml.

Steps to reproduce:

1. In terminal:
   > quarto create project book testbook
2. Add the following to _quarto.yml (any of these options produce same error):

format:
  html:
    self-contained: true
    embed-resources: true

3. Add to any qmd file:

```{r } 
#| label: test-plot

plot(1:10, 1:10)

4. > quarto render

Result in error:

ERROR: 
compilation failed- error
Unable to load picture or PDF file 'intro_files/figure-pdf/test-plot-1.pdf'.

...and warning:

[WARNING] Could not fetch resource ./summary.html

Works when option quarto render --to html is used. Curiously, quarto render --to pdf also works if run separately.

System info:

quarto --version: 1.5.57 on Arch linux
This is XeTeX, Version 3.141592653-2.6-0.999995 (TeX Live 2023) (preloaded format=xelatex)

Steps to reproduce

No response

Expected behavior

quarto render should produce html and pdf book

Actual behavior

quarto render fails
quarto render --to html and quarto render --to pdf works

Your environment

Linux Version: 6.9.2.arch1-1
quarto --version: 1.5.57 on Arch linux
This is XeTeX, Version 3.141592653-2.6-0.999995 (TeX Live 2023) (preloaded format=xelatex)
R version 4.4.0

Quarto check output

> quarto check

Quarto 1.5.57
[✓] 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: 1.5.57
Path: /opt/quarto/bin

[✓] Checking tools....................OK
TinyTeX: v2023.12
Chromium: (not installed)

[✓] Checking LaTeX....................OK
Using: TinyTex
Path: /home/e/.TinyTeX/bin/x86_64-linux
Version: 2023

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

[✓] Checking Python 3 installation....OK
Version: 3.12.3
Path: /usr/bin/python3
Jupyter: 5.7.2
Kernels: python3

(/) Checking Jupyter engine render....Traceback (most recent call last):
File "/opt/quarto/share/jupyter/jupyter.py", line 21, in
from notebook import notebook_execute, RestartKernel
File "/opt/quarto/share/jupyter/notebook.py", line 15, in
from yaml import safe_load as parse_string
ModuleNotFoundError: No module named 'yaml'
[✓] Checking Jupyter engine render....OK

Reproduce the failure with the shown _quarto.yml and qmd example, then compare combined quarto render with separate HTML and PDF renders. Trace the self-contained/embed-resources handling for the generated PDF resource and the summary.html warning; done means the example renders both book formats without errors.