The age-old "turn it off and on again" should fix this.

I had the same issue and found that it was dictated by time, where after a few hours .staging eventually was able to be deleted with no problems and no changes on my end. Some background process is creating a lock on the contents of .staging, even with node/your editor not running, and that process dies eventually. You can speed that process up by restarting your computer, at which point the lock on the folder is released and you can delete the folder with no qualms.