After building the SDK, if you run "ant clean" from the top-level it should cleanup all build files. Currently, it fails to clean rt/build/ which contains the following:

[rt]
I build/javafx-beans-dt.jar
I build/javafx-concurrent.jar
I build/javafx-designtime.jar
I build/javafx-ui-charts.jar
I build/javafx-ui-common.jar
I build/javafx-ui-controls.jar
I build/javafx-util-converter.jar
I build/test-stub-toolkit.jar

The solution is to delete the rt/build directory in the clean target of "rt-closed/build.xml"