Build support tasks to enable Fat Jar to compile/build a jar from a versioning system like MKS directly.
This will require creation of new ANT tasks e.g. "mkscheckout" that will checkout files from MKS into a local build folder. Something similar to what <stcheckout> Task of StarTeam does.
Once the task is created, it can be integrated to the "build.xml" that Fat Jar uses and continue building a new jar out of the locally checked out files.