Programs are mathematical proofs. If maths cannot be patented, software can't be, either.
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Judges and Justices are not that precise. They aim to preserved public order before anything else. If a whole industry is based on a questionable interpretation of patent, they is a lot of chances that judges would agree on it. Even in countries where you could not patent algorythm, industries patent the documentation, the "software design", the brand name, the illustrations used, and aggregates everything together, to say they own it. And it works.
TL;DR : Class Justice
AFAIK european laws only allow to patent "inventions". Software is considered to be a series of "words" in whatever programming language you're using and, like sentences, it's not an invention and can't be patented.
On the other hand, software-assisted inventions can be patented as a whole.
With that said, software can still be considered a "work" protected by copyright laws.
And that's fine. VLC does their own implementation of codecs so that's not an issue. It's the patents that make it an issue.
That’s not their stance, that’s French law
I think it both. Not all software or codec provider aim to apply the EU and French laws. Quite the contrary