Yes, you're right. It's weird, since Mojang actually owns Bukkit but apparently let it be community-run, and then one or two members of that community decided to throw a tantrum and DMCA'd their own project. What the hell. I don't even.
ETA: Finally pieced it together. Man, what a mess. So, the GPL requires that any linking code also be GPLed. Since CraftBukkit and Spigot contain obfuscated/decompiled code from the official Minecraft Server, which is
not GLPed, this makes all releases of CB and Spigot to be technically in violation of the license and thus afoul of copyright laws since, without the provisions of the GPL, CB and Spigot constitute unauthorized derivative works and are therefore infringing.
So, who is behind this? Wesley Wolfe, one of the original Bukkit developers. He did this in response to Mojang introducing a new EULA which forbids unauthorized use/distribution/linking with their software. The thing is, Minecraft owns Bukkit and they have a relationship, so they weren't going to hold Bukkit or even Spigot accountable for that EULA. But this wasn't good enough for Wolfe, who apparently took the EULA change as a personal betrayal and performed the legal equivalent of taking his ball and going home, which in this case means taking everyone's balls away.
There is no silver lining or ray of sunshine to this. Those projects are just dead.
As I said, I will look to see what our options are. Maybe the vanilla MC server is more moddable than it used to be. Who knows?