quarto update does not removed out-dated files

[ALanguillaume]

Bug description

When updating a quarto extension, quarto update does not delete out-dated files.

Considering this extension https://github.com/ThinkR-open/quakr/ as a reprex

The tmp branch contains one exta files coucou.truc compare to main

tmp

main

Steps to reproduce

Create a quarto project and add extension thinkr-open/quakr using the version from branch tmp

mkdir -p quarto-bug
cd quarto-bug/
quarto create-project
quarto add thinkr-open/quakr@tmp --no-prompt

As expected the file coucou.truc is present in the extension folder

$ ls _extensions/thinkr-open/thinkridentity/
background.png  coucou.truc  _extension.yml  logo.png  logo.svg  thinkridentity.scss

Now updating the extension switching to main. Mimicking the suppression of the file coucou.truc

quarto update thinkr-open/quakr --no-prompt

Expected behavior

The extension is updated and correspond to the version on main.

coucou.truc should be deleted.

$ ls _extensions/thinkr-open/thinkridentity/
background.png   _extension.yml  logo.png  logo.svg  thinkridentity.scss

Actual behavior

The extension is updated but the file coucou.truc is NOT deleted and remains in the extension directory.

$ ls _extensions/thinkr-open/thinkridentity/
background.png  coucou.truc  _extension.yml  logo.png  logo.svg  thinkridentity.scss

Your environment

OS: Ubuntu Jammy 22.04 LTS

Quarto check output

[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.1.1: OK
      Dart Sass version 1.55.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.3.361
      Path: /opt/quarto/bin

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

[✓] Checking Python 3 installation....OK
      Version: 3.10.12
      Path: /usr/bin/python3
      Jupyter: 4.11.1
      Kernels: python3

(/) Checking Jupyter engine render....Traceback (most recent call last):
  File "/opt/quarto/share/jupyter/jupyter.py", line 21, in <module>
    from notebook import notebook_execute, RestartKernel
  File "/opt/quarto/share/jupyter/notebook.py", line 17, in <module>
    import nbformat
ModuleNotFoundError: No module named 'nbformat'
[✓] Checking Jupyter engine render....OK