Weird project config interaction when installing cloner + applying other changes from admin

[J-Protz]

Describe the bug

I have been losing my mind for days trying to figure out why every time I try to bring down a prod db locally and apply the changes to test things out and make sure the deployment will go smoothly, it would instead delete my changes and rebuild the config based off the database.

I finally tried using the cli today and weirdly enough, no issues there. I noticed when clicking apply from the admin, it'd install cloner then say 'all set!', so my worker suggested uninstalling cloner to see what happens. Once I uninstalled cloner, I was able to apply from the admin and everything was good to go again.

Steps to reproduce

1. Make a backup
2. Install Cloner
3. Create a new site
4. Clone a bunch of sections, volumes, filesystems
5. import the backup, and try to apply changes via admin section

Craft CMS version

4.14.4

Plugin version

2.0

Multi-site?

yes

Additional context

No response

[engram-design]

I don't think this would be related to Cloner as a plugin just being installed, as the plugin doesn't actively do anything, unless you clone something. So even if the plugin was uninstalled, you'll still have your cloned data.

I'll see what I can do about replicating this though!