Hello,
The parameters are regular Java environment properties; that can be set from the CLI with the -D switch.
You'll want to use "org.guvnor.m2repo.dir" to change the default location of the Maven repository.
We don't use a $WORKING_DIRECTORY parameter. Reference in the documentation to "working directory" means whatever your container (AS, Tomcat etc) uses. AS7 puts things in /bin for example.
As for Tomcat specifically; I'm no expert but found this:
http://www.liferaysavvy.com/2012/09/setting-environment-variables-and.html which gives a potential (untested) solution. Tomcat's documentation might give more information.
With kind regards,
Mike