File integrity checker now reports files found in the filesystem but not expected to be there (#11096)

* File integrity checker now reports files found in the filesystem but not expected to be there

fixes #11087

* Move file integrity logic to own class

* Fix bug in logic so that third party plugins are not listed

* fix up some comments

* Also report any hidden files not expected to be there

* Issue a warning when file integrity didn't run for any reason. Safer choice

* Ui tests