Our com_admin script has a method to delete unexisting files and folders which is triggered during updates and when using the "Fix" button in the "Extension: Database" view.
There are three folders and one file in this list which are no longer empty due to recent PRs.
Testing
Press the database fix button and navigate to the "Extension: Manage" view. You will get an error due a missing file ("JForm::getInstance could not load file").
Apply patch and try again. Works now.
PRs which introduced the files are #6958 (@bertmert) and #7706 (@pe7er).