The cloud, in broadest terms, refers to the Internet in general. Cloud Computing refers to the practice of using remote computers and resources over the Internet to perform computing tasks one would usually perform locally on one's own computer.
In the pivot missions, the goal is to upload Desmond's memories into the Internet so that the public at large can access them. There's also speculation that it's not only his memories but his entire consciousness that's being uploaded, but that's very debatable. As for the numbers at the end, I will have to politely disagree with the contention that they're meaningless, since it's not like Ubisoft to add a little detail like that and make it meaningless. They put numbers with hidden meanings everywhere in these games, therefore the chances that this particular number has no significance is very low.
Seems like its just a way for you to get cheats, after the game.
Guys who are hacking the animus could be related to new game like all previous epilogues. But its hard to believe that Rebecca could be hacked, considering how much knowledge she has. Although its still a possibility that these guys are hackers not related to the Assassins. Perhaps the plot of the next game will involve a rise in Assassins throughout the world thanks to these hackers or something like that.
Basically, you (the hacker) are trying to create a torrent of the game disk (Desmond's memories) into the internet for the democracy of freedom. Instead of Lucy stealing the game disk, you merely create an iso of the disk and upload it into the internet for all to burn their own copy or straight up play it on their modded Animus consoles.