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Indeed, the CLIENT may be open source but the protocols won't be. The protocols, according to Joltid, are still owned by a private corporation (Joltid)/founders of Skype and eBay didn't receive the rights to the protocols when it bought the Skype business.

There's a legal battle still broiling over the core of Skype, and nothing major will be happening until that's been settled or been to trial.

eBay's been working on writing new protocols since shortly after it bought Skype. Don't expect to see the protocols go open source anytime soon, if ever. If they did, Skype would no longer need to exist.