I do not know of an easy way to create .jars for Alice 2 projects as Alice 2 is not strictly Java based environment, but is actually Jython based, a combination of Java and Python.
The Alice.a2w flew are actually a collection of .xml files that contain the descriptions of the objects and commands that can be rebuilt within the Alice 2 environment. There are not standalone source files in the traditional sense.
However, Alice 3 is rolling out a system in which Alice projects can be exported into standalone apps.
http://www.alice.org/resources/how-t...-an-alice-app/
Let me know if you have any other questions...
All the best,
Don Slater
Alice Project