Update FileUpload.php

[luisvivasb]

The $file->setPermanent() is already call when you use the file in media entity. If you call this function at this point you can't use tokens or filefield_paths to manipulate the image name and folder to be saved.

#357 You can see the problem with filefield_paths

[phenaproxima]

This looks like a nice win. I think we're going to need a test of it, though. That's going to be fairly involved, since we'll likely have to write a few new Behat step definitions. I can probably open a feature branch and work on this there, if you'd prefer. Because I'd definitely like to get this committed.