Changes in `include`d files don't trigger re-execution when `freeze: auto` is set

Bug description

If you set freeze: auto at the project level, changes in included .qmd files don't trigger re-execution. It seems like change must happen in one of the files listed in _quarto.yml for re-execution to be triggered.

Steps to reproduce

You can see this behavior in the commit history of https://github.com/mine-cetinkaya-rundel/freeze-include.

Alternatively, steps below.

1. Create a book project and add a .qmd file that is included in a chapter with the {{< include >}} short code, e.g. _section.qmd to be included with {{< include _section.qmd >}}.
2. Set freeze: auto at the project level in _quarto.yml.
3. Render the project.
4. Then, make a change in _section.qmd. Render book. Changes aren't in the rendered output.
5. Them, make a change in the chapter file. Render book. Changes are now reflected in the rendered output.

Expected behavior

I would have expected changes in the included file to trigger re-execution.

Actual behavior

They do not trigger re-execution.

Your environment

• RStudio: 2023.09.0 Build 380
• Mac OS: Ventura 13.5 (22G74)

Quarto check output

Quarto 1.4.346
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.1.6: OK
      Dart Sass version 1.55.0: OK
      Deno version 1.33.4: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.4.346
      Path: /Applications/quarto/bin

[✓] Checking tools....................OK
      TinyTeX: v2023.08
      Chromium: (not installed)

[✓] Checking LaTeX....................OK
      Using: TinyTex
      Path: /Users/mine/Library/TinyTeX/bin/universal-darwin
      Version: 2023

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

[✓] Checking Python 3 installation....OK
      Version: 3.9.6
      Path: /Library/Developer/CommandLineTools/usr/bin/python3
      Jupyter: 5.3.0
      Kernels: python3

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

[✓] Checking R installation...........OK
      Version: 4.3.1
      Path: /Library/Frameworks/R.framework/Resources
      LibPaths:
        - /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
      knitr: 1.43
      rmarkdown: 2.24

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

Reproduce the issue with a book project, _quarto.yml, a chapter .qmd, and an included _section.qmd using freeze: auto. Start by tracing how changes are detected during project rendering; done means changing _section.qmd causes the next render to re-execute and update the output, with a regression test covering the case.