Consequently, the answer to Questions 1 to 5 is that Article 1(2) of Directive 91/250 must be interpreted as meaning that neither the functionality of a computer program nor the programming language and the format of data files used in a computer program in order to exploit certain of its functions constitute a form of expression of that program and, as such, are not protected by copyright in computer programs for the purposes of that directive.
That's interesting because it goes even further than I'd have expected: that file formats themselves aren't protected. I guess that isn't surprising, since you'd want a market where programs could all compete to operate on the same files, but I don't remember that being talked about before (at least in reference to Oracle vs Google). And that does go to the format of the Java .class files.
I wonder what the EU courts would have to say about an encrypted file format...
most important bit:
Consequently, the answer to Questions 1 to 5 is that Article 1(2) of Directive 91/250 must be interpreted as meaning that neither the functionality of a computer program nor the programming language and the format of data files used in a computer program in order to exploit certain of its functions constitute a form of expression of that program and, as such, are not protected by copyright in computer programs for the purposes of that directive.