Mojang's between a rock and a hard place on the Bukkit situation. While they do own it, they have been very careful not to put any actual Minecraft code in it. They've tolerated the fact that CraftBukkit contains obfuscated Minecraft code decompiled from the JAR file, but if they put even a little bit of "real" Minecraft code in it, they would be forced to GPL it, and I'm sure MS wouldn't be the tiniest bit happy about that. I suspect the EULA change was actually made directly because of the Microsoft acquisition. Anyway, what Wolfe did was basically accuse Mojang of having real Minecraft code in CraftBukkit without GPLing the entire source, so he claimed they were in violation and sent the takedown notices. I am not sure that they actually are in violation. Unfortunately, neither Spigot nor the Bukkit folks can resolve this on their own. Most of the Bukkit staff jumped ship right after this happened, no doubt wanting to avoid any legal fallout for themselves. It's all really sad. I didn't expect Bukkit to go out that way.