I am creating a Python script within which I am executing UNIX system commands. I have a war archive named Binaries.war which is within an ear archive named Portal.ear
Can't you just change working directory within the python script using os.chdir(target)? I agree, I can't see any way of doing it from the jar command itself.
If you don't want to permanently change directory, then store the current directory (using os.getcwd())in a variable and change back afterwards.