This is is strange.
Try to compare Eclipse command line with your one. To see what Eclipse exactly executes go to Window → Show view → Other → Debug → Debug. Then when you right click on the clover launch, there is Properties item in the context menu. You can see command line, that Eclipse executes to run the graph.
The problem is that my custom component class is in the same Java project. That’s why Eclipse may see it even if it’s not in the classpath of the command line.
But when I make the package with my custom component in plugin folder and execute it from command line the jvm doesn’t see it. I really have to put it in the classpath of the executable jar file’s manifest file to make it work.
Seems that loading of my custom component fails even if log output says “loaded” !