How exactly is one supposed to make a clean-room reverse engineering in the absence of any documentation and sophisticated obfuscation on Skype's part ?
So what? That's not a valid excuse to distribute modified binaries to the public. If the "first" team wants to look at binaries to do their documentation, they can download the official Skype client from skype.com. Why do they need to download a hacked binary from Github?
I understand the rationale behind it, I think it is wrong and has bad implications for the future.
No it doesn't.
The Wikipeda link[1] mentions the original IBM PC clean room implementation by Columbia Data Products.
It doesn't have the complete story of that, but from memory the way it worked was CDP had one team documenting how the BIOS responded to inputs, and then a totally independent team reimplementing that behaviour.
Most clean room implementation don't have access to a specification, let alone source code.
From the ruling: "Some works are closer to the core of intended copyright protection than others. Sony's BIOS lay at a distance from the core because it contains unprotected aspects that cannot be examined without copying. The court of appeal therefore accorded it a lower degree of protection than more traditional literary works."
Thus one could try to make the same case for Skype.
If I write a script that generates the Matrix movies from the binary file of, say, Elephant's Dream, I won't be allowed to distribute that.
http://recon.cx/en/f/vskype-part1.pdf http://recon.cx/en/f/vskype-part2.pdf
This was the method used by Compaq to implement the IBM BIOS, back in the day.
What part of A's work involves distributing deobfuscated binaries to the general public?
Team B should only have access to the specifications developed by Team A and nothing else from them. That's the whole point of isolating them.
For example, there is no reverse engineered libraries for Facetime and iOS API. If you use Apple's libraries, they can come after you for copyright infringement.
Linux is an independent implementation of the Posix interfaces.