Basically it comes down to a big MAYBE. Vanilla WordPress may or may not include a particular file anymore, but that doesn’t necessarily mean that it is not a file still in use by a particular plugin. I suspect this is the reason why WordPress doesn’t remove any deprecated content because tracking which of the 1000s of plugins are actually using it or not using it is too great of a task. I’ve done the bulk delete recommended and its broken a site and I’ve done it and it didn’t appear to break anything. The long and short of it is that the safest way to delete possible unused legacy files is to create a staging copy of it and delete the files one by one on the staging site and test your site’s functionality. This however doesn’t guarantee that a future plugin that you install doesn’t require something you delete. My recommendation is that unless there is a known security issue with the file, leave it alone and the next time you redesign your site with a new theme install a fresh copy of everything you need.
