RAM:Ganymed.info will be an icon of type "Drawer". When it is double-clicked, Workbench will look for a sub-directory in the same location as the icon, with the same name (sans '.info'). It if finds it, it will open it.
I can see why you want to start it using WBRun; simulating a double-click on the icon launches the game with all the tooltypes specified in the icon. You could try putting a dummy file galled "Ganymed" in the Ganymed directory. Then use "WBRun Ganymed". It will simulate a double-click on the icon belonging to the file "Ganymed", namely "Ganymed.info". Because this icon will be a project type, the dummy file "Ganymed" shouldn't actually be launched, rather the default tool of the icon (WHDLoad) will be launched. Using the example directory structure you posted above:
echo "foo" >ram:Gaymed/Ganymed
I have no idea whether that will actually work, or whether the dummy file will cause confusion.
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moto