When I'm trying to do deploy project with -makeall option it fails with result like classpath is ignored:
For example, some error lines:
/local/work/packagerTestsSuite/apps/HelloWorld/src/helloworld/HelloWorld.java:3: error: package javafx.application does not exist
import javafx.application.Application;

I invoke javafxpackager with correct options including jfxrt.jar in classpath.

I attach some HelloWorld project, in which you'll see the errors: to invoke javafxpackager as I do you're to type this:
javafxpackager -makeall -classpath $JAVA_HOME/jre/lib/jfxrt.jar -appclass helloworld.HelloWorld -name HelloWorld -width 100 -height 100