The modding community really needs to re-write Minecraft themselves. As a group, you are all WAY better than Mojang at programming. Of course, now that evil-big-corporation (as they all are) Microsoft has gotten their grubby paws all over it, there will surely be an army of their zombie lawyers at the ready for anyone who tries to re-write it. But it needs to be done, somehow, some way. Microsoft didn't buy Mojang to make the game better, they bought Mojang to make their evil-big-corporation even more obscenely richer than they already are.
Grow up.
Here are some of the reasons Microsoft bought Minecraft:
http://www.zdnet.com/microsoft-stra...r-minecraft-is-a-development-tool-7000036073/
According to this Minecraft was purchased as a mechanism to get more kids into programming, and coincidentally using Microsoft products to do so.
While this may seem an unfair advantage to Windows-dom and XBox, keep in mind that "evil" Microsoft:
1). Released ".Net" technology to Open Source like 3 weeks ago
2). Is making Visual Studio a cross-platform development environment (Currently supports Intel and Arm processors, they just need to build compatible libraries)
3). Already makes Visual Studio available for free in it's Express version
4). Has started "Visual Studio Community" which is also free but uses the shared workspace, version control and other features from Enterprise Visual Studio
Also, since the idea is to use Minecraft as a teaching environment for programmers, we can probably assume that Java is on the endangered list and Minecraft will be "converted" to Visual Studio (I say this because it doesn't matter if you use Basic, C++, C# or Javascript, it all compiles to interchangeable modules).
This may be a good or a bad thing, but it should result in less bloated code, the abolishment of Obfuscation and a usable API with full source code availability.