They're using SHA1 to sign / identify programs. Finding and exploiting a hash collision would be fairly straightforward and could have really bad consequences, since I presume I could publish my "rogue" modified program to peers fairly easily.
The National Institute of Standards and Technology has urged Federal agencies to stop using SHA1 digital signatures by the end of 2010, and instead start transitioning to the SHA2 family[3].
[1] http://stackoverflow.com/questions/1147830/understanding-sha...
[2] http://www.schneier.com/blog/archives/2005/02/sha1_broken.ht...
Much of Skynet's core technology is actually designed for mobile platforms. Skynet essentially thinks of a desktop computer as a fancy phone with a different UI toolkit and without a cellular modem.
While switching to SHA-2 is on our to-do list, it's not as high as nailing a stellar experience for our users. Should SHA-1 erode more quickly than expected, we'll be sure to bump up the priority of that transition. We'll be sure to pivot the network before it's a real problem.