Automatically delete empty JAR-files left over from upgrades.
Don't reference classes by name - it is not safe.
Improved the fuzzy reflection system tremendously.

It is now possible to specify exactly what method or field you're
looking for, based on a number of different critera such as return
value, parameter count or parameter type, exceptions, modifiers, name -
all using a very fluent builder syntax.
Improve JavaDoc and add the ability to match declaring class.
Attempting to add support for MCPC.

Still have to track down a very elusive bug however.
Fix a serious bug that caused Blocks to inadvertanly be created.

Our custom IOC system (DefaultInstances) would call new Block(0) on a
MCPC based CraftBukkit system, causing air blocks to be treated as 
solid blocks. We prevented this by explicitly forbidding it from 
creating instances of ItemStack or Block in our structure modifier's
default field generator.

A second bug was caused by mismatched methods in WrappedDataWatcher,
which we solved by simply trying to use them, and then swapping them 
if we encounter any errors or weird state.