Well, I was thinking about all those problems with uderstanding "package" concept and whether they are actually related to bad terminology (I am not native english). Maybe it is time to consider terminology change.
What about "package" -> "unit"? It would remind Deplhi "unit" which is +/- quite correct (AFAIK there is similarity with "uses", and dissimilarity with file vs directory).
What the "nest" should be I am not sure, maybe "folder" or "unit folder" would do.