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You need the directories bin, lib, profiles and runtime. The lib needs the subdirectories desktop, mobile, prism, shared and tv. profiles just has one file in it. runtime has the subdirectory natives. You can run your program from a batch file that is in bin.
The batch file I use looks like this:
javafx -Xms1200m -Xmx1200m -jar ..\lib\MyApp.jar
Perhaps you can get it leaner, but I've found this configuration to work.
Unfortunately I can't help with the Webstart side of things.