Quarto projects don't share dependencies

Bug description

When rendering a project, I would expect HTML output to share dependencies, rather than each dependency getting a complete copy.

Steps to reproduce

1. Create a new directory
2. Make it a quarto project by adding _quarto.yaml and add two qmd files: touch _quarto.yaml file1.qmd file2.qmd
3. Run quarto render
4. Observe that both file1_files and file_files2 contain a copy of the same dependencies

Expected behavior

There should only be one copy of the dependencies.

Actual behavior

There are two copies of the dependencies

Your environment

No response

Quarto check output

Quarto 1.5.40
[✓] 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: 1.5.40
      Path: /Applications/quarto/bin

[✓] Checking tools....................OK
      TinyTeX: (external install)
      Chromium: (not installed)

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

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

[✓] Checking Python 3 installation....OK
      Version: 3.12.3
      Path: /opt/homebrew/opt/python@3.12/bin/python3.12
      Jupyter: (None)

      Jupyter is not available in this Python installation.
      Install with python3 -m pip install jupyter

[✓] Checking R installation...........OK
      Version: 4.4.0
      Path: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources
      LibPaths:
        - /Users/hadleywickham/Library/R/arm64/4.4/library
        - /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
      knitr: 1.47
      rmarkdown: 2.27

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