They should be much more efficient now (this reduced the tick time of the CI Chamber by 3-4x in my testing), due to being able to just use the HashMap's get() instead of being limited to iterating through entries. NEI integration code now a lot more readable and type-safe as well.
I went for what seemed like a good level of organisation:
Java
__________
Mekanism
__________
Minecraft
Forge
FML
__________
Netty
LWJGL
__________
Other APIs
__________
Static Imports.