I'm not sure if this is something I'm doing wrong, or if Spoon is doing it wrong (I think the latter), but adding an input resource from the file system results in the class comment being dropped. Not always, but often. For example, with this file:

/**
 * This is a comment!
 */
public class Test {}

Then this drops the class comment:

launcher.addInputResource(new FileSystemFile(pathToFile));

but this captures the class comment:

launcher.addInputResource(new VirtualFile(readFile(pathToFile)));

TODO: Work around for now, report on Spoon issue tracker if the latest build doesn't resolve it.