Currently there is no way for a site admin to have visibility over files that been uploaded into courses other than by going into each section of each course - this is painful.
We have seen sites that have files inside the files table which do not belong to any course or section, we suspect because the section was deleted. These files are "lost" inside Moodle, taking up space on disk and in the db but are never visible to the site admin to move or delete.
It would be really nice to see some kind of centralised file management area that a site admin can go to and see every file, where it was uploaded, who it was uploaded by and actions to remove the file.
The cloud team had a go at this, but we were limited in what we could do because there is no easy way in core to do this, and it really should be something that needs to be addressed in core.