Drag&Drop + Insert hierarchy fixed in r1782:
http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=17582

Collapse/Expand Hierarchy:

1. Problem with adding new hierarchies:
   • Add Data -> add a model
   • Go to the models module
   • right click on Scene and Insert Hierarchy
   • click on the new hieararchy and change the colour in the display tab
   • drag the model into the new hierarchy (currently the tree view is too small for me to see more than one row at a time, so can't drag and drop in Models, but you can switch to the Displayable scene view in the Data module and drag it there)
   • the hierarchy is collapsed, but it's not updating the Expanded flag on the hierarchy node so the model doesn't get assigned the hierarchy display node colour

Julien suggested looking for the model reset or layout changed events on the tree view, as connecting the rowsInserted signal on the sort filter doesn't get the added slot called in qSlicerModelsModuleWidget.cxx:

connect(d->ModelHierarchyTreeView->sortFilterProxyModel(), SIGNAL(rowsInserted(const QModelIndex&, int, int)), this, SLOT(onRowsInserted(const QModelIndex&, int, int)));

Changing the visibility on the model hierarchy's display node while the hierarchy is collapsed does not hide/show the models in the hierarchy. Neither do changes to Selected/Clip/Slice Intersections Visible propagate.
It works when changing the elements in the Material Properties.

Also: look at exposing the bugs through tests in Slicer4/QTModules/Models/Testing/Cxx

Need to add the visibility column to the scene model for the hierarchy nodes.

Visibility should be fixed in svn 18069.

r18076:

• Add visibility icon for hierarchy nodes
  http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=18076

Using knee atlas and mac nightly 9-16:
-still no eye icon for parents in hierarchy
-The display section allows to check visibility for a parent, but this has no effect.
-When collapsing a branch of a hierarchy, the children become invisible. This is reversible upon uncollapsing. Try clicking on the plus to the left of the vascular system in the knee atlas.
-drag and drop results in dropping the structure twice. see screenshot

-the eye icon has appeared for parents, but it is still not doing anything.

Eye icons don't do anything for parent in the Models module or in the Data module ?

2+ level hierarchy checked against Slicer3 behaviour and it is the same. It will use the colour of the first collapsed parent node above the model, rather than the one highest in the tree (see the vessels hierarchy in the knee atlas).
Still tracking down visibility changes on hierarchy nodes (mrml nodes are changing, the displayable manager isn't reflecting it).

svn 18468 fixes the hierarchy visibility flag when it's expanded for the knee atlas when it's loaded while not in the Models module. More testing/debugging required to figure out why the tree doesn't render properly when in the Models module while loading a scene.
http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=18468

svn 20827 fixed the load knee atlas while the Models module is open