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I realised what the problem was.. its the Layout...
Now with other projects.. not a problem at all.. If I select "Flat" I get the 2nd structure (which I don't like) while if I select "Hierarchy" I get the 1st Structure (this is what I want)
However, this change in layout works fine for other projects. But for the project in question, changing the layout is not having any effect at all.
Can you describe better what you have and what you are looking for?
In case DEF package does not contain any classes that GHI will be brought one step higher. Try adding a class to DEF package and you will see the structure you want. (I hope this is what are you asking. If not please discard it).