(This happened with Pipeline Tool 188.8.131.525)
I'm not sure if this is a bug or intended behaviour, but it sure fooled me!
This is what happened:
For some easier access I decided to make a shortcut to the content file, and placed the shortcut on my desktop.
Then I wanted to replace a content item with a newer version of the file.
It defaulted to adding a link, instead of adding/replacing the file. I just pressed OK without seeing it.
Then it added a .. folder and a Desktop folder, probably because of some working/current directory bug because I opened from shortcut?
With my super smart brain, I thought "Oh that's just a virtual folder item, I can delete that"
Pipeline tool freezes, and I see my desktop slowly clear in the background
Here's a reconstruction, without actually deleting the .. folder because I don't want to delete it all again
(Deleted comment contained same gif as above, if anyone is curious)