Quarto manuscript not rendering dynamic figures

[AlexLietard]

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

The file considered to be the article in a manuscript project is not rendering the dynamic figures that I create.

Steps to reproduce

Using Windows.

First, I created a manuscript project and modified _quarto.yml so that freeze was set to auto:

project:
  type: manuscript

manuscript:
  article: index.qmd

format:
  html:
    comments:
      hypothesis: true
  docx: default
  jats: default

  # (other formats)
  # pdf: default

execute:
  freeze: auto

Next, I added a simple plot to index.qmd:

---
title: Try
authors:
  - name: Norah Jones
    affiliation: The University
    roles: writing
    corresponding: true
bibliography: references.bib
---

```{r}
#| label: fig-test
#| fig-cap: "Bon"
plot(1:10)
```

Actual behavior

When I run quarto render . the figure is not displayed in the rendered manuscript. The generated HTML contains an tag pointing to index_files/figure-html/fig-test-1.png.

However, the index_files directory is not present in _manuscript after rendering, even though it appears to be generated during the render process.

If I instead run:

quarto render . --cache-refresh

the figure is displayed correctly.

Furthermore, after a successful render with --cache-refresh, running:

quarto render .

also works and the figure is displayed. However, if I delete the .quarto and _freeze directories and then run:

quarto render .

the problem reappears and the figure is no longer displayed.

Expected behavior

I would like to have the generation of the figure directly with quarto render . or if it's in the documentation to make it clearer.

Your environment

• Positron 2026.06.0 release on Windows 11

Quarto check output

Quarto 1.9.38
[>] Checking environment information...
      Quarto cache location: ~\AppData\Local\quarto
[>] Checking versions of quarto binary dependencies...
      Pandoc version 3.8.3: OK
      Dart Sass version 1.87.0: OK
      Deno version 2.4.5: OK
      Version: 1.9.38
      Path: c:\Program Files\Positron\resources\app\quarto\bin
      CodePage: 1252

[>] Checking tools....................OK
      TinyTeX: (not installed)
      Chromium: (not installed)
      Chrome Headless Shell: (not installed)
      VeraPDF: (not installed)

[>] Checking LaTeX....................OK
      Tex:  (not detected)

[>] Checking Chrome Headless....................OK
      Using: Chrome found on system
      Path: C:\Program Files\Google\Chrome\Application\chrome.exe
      Source: Windows Registry

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

[>] Checking R installation...........OK
      Version: 4.4.1
      Path: C:/PROGRA~1/R/R-44~1.1
      LibPaths:
        -~/AppData/Local/R/win-library/4.4
        - C:/Program Files/R/R-4.4.1/library
      knitr: 1.51
      rmarkdown: 2.31

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

[>] Checking Python 3 installation....OK
      Version: 3.10.6
      Path: ~/Python/Python310/python.exe
      Jupyter: 5.7.2
      Kernels: ark, ir, python3

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

[>] Checking Julia installation...