DSM: avoid "overlapping dependencies"

[NicolasAnquetil]

example: When showing DSM for packages, one package P1.1 could be a sub-package of another P1
if another package P2 as dependencies to P1.1, they will currently show as dependencies to P1
(it could also happen if proposed solution to #1216 is implemented)

This is misleading.

We could check for inclusion of entities and remove from the parent (P1) the dependencies that go to the child (p1.1)