[5.x]: Updating Craft removes all plugins

What happened?

Description

Under Utilities > Updates I had two updates:
one for CraftCMS, and one for Datastar.

I pressed "Update All".
After updating Craft to version 5.8.19 I noticed all the plugins were removed, only Datastar was available (which also had an update). All the other plugins were completely removed and had to be re-installed.
Luckily, all the settings persisted, so no further configuration was required. After reinstalling the previously installed plugins, the website was working again.

(If I remember correctly I had 3 Craft updates, so that'd mean I was on Craft v5.8.16)

Steps to reproduce

1. Press "Update All" under Utilities > Updates

Expected behavior

Craft and plugins get updated

Actual behavior

Craft and plugins get updated, but not updated plugins got uninstalled.

Craft CMS version

5.8.19

PHP version

8.4.13

Operating system and version

Linux 6.5.0-45-generic

Database type and version

MariaDB 11.4.3

Image driver and version

Imagick (ImageMagick 7.1.1-47)

Installed plugins and versions

After reinstalling all the plugins:

• CKEditor 4.10.1
• Datastar 1.0.0-RC.9
• Contact Form 3.1.0
• Contact Form Extensions 5.0.0
• SEO 5.0.0

Start at Utilities > Updates and reproduce the Update All flow with the reported Craft CMS 5.8.19, PHP 8.4.13, and MariaDB 11.4.3 versions. Compare the installed plugin list before and after updating; done means Craft and plugins update together without uninstalled plugins.