In all of my examples I've shown how to set the system properties from within your Java code, i.e., something like this:
If for some reason you don't like this approach you can also set these properties from the command-line when starting up your Java application, like this:
java -cp wikitex.jar:. \ -Dcom.apple.mrj.application.growbox.intrudes=false \ com.devdaily.wikitex.Main
I haven't tested this, but the effect should be the same regardless of the approach taken.