Why did the new beta build break plugins using CraftBukkit or Minecraft code?

When I got 1.4.6, I noticed right away that my plugin was broken. I tried to fix it right away, but when I set the 1.4.6 jar as the reference jar, all my craftbukkit and net.minecraft imports "Could not be found"

Later, in the post announcing the first 1.4.6 beta build, it was said that plugins using net.minecraft or craftbukkit codes would not work.

I'm new to bukkit and plugin development, I'm just wondering, is this permanent or not? If not, when should I expect to be able to use craftbukkit and net.minecraft again?

 

Yes, it is permanent. Yes it will break your plugins. Yes it is fixable, using certain methods (newly added ItemMeta, CraftItemStack.asNMSCopy(), etc for items, EntityEquipment for mobs, and more)

 

That's because of this commit.
Now, if you plugin uses NMS or OBC, you'll need to update with every new (minor) version of Minecraft. Enjoy.

So I would suggest you try to find Bukkit API method for what you're doing with NMS/OBC code instead. (if there are any yet)