I think the "two roots" he's talking about is just the two skeletons you end up with in one project when you import the json data exported from the Photoshop script.
"Import Data..." adds the skeleton from a JSON into your current project. But the skeleton data from the Photoshop script doesn't have the default animation that the New Project/New Skeleton normally has. When you go to Animate mode, you can't move or key anything. I assume this is the behavior you intentionally programmed for when there aren't any animations selected. It's just that it's not immediately obvious because the list of animations is at the bottom of the tree pane.
It's not really a bug. But I guess it's a place for a non-modal warning that says "This skeleton needs animations before you can animate anything." if you go to animate mode in a skeleton without animations. Or something. Or a prompt to create one, which might be annoying if you wanted to purposefully make an animationless skeleton.
But this does factor into the main issue I suspect with the centralized Tree UI, which is that the transparency it gives by being relatively 1:1 to the storage model/object model/json (being just a list of lists of lists of lists of what's in it) might not be working for the best interests of the animator.
It's useful as a data-centric summary for geeky types; Spine shines in its backend transparency. But I don't think a list of lists should be the go-to place for manipulation or inspection— not for image swapping. Not for keying color changes. Not for changing draw order. Not for finding bones or slots or images or animations. Maybe not even for inspecting what slots are under the currently selected bone.— It might be a function of typography or visual styling, but it's just too hard to skim or read or find or reach anything in it. And that means it scales really poorly with even moderate complexity of the skeleton.
In fact, it kinda feels like some of the big categories— the bone hierarchy, bones' child slots, the available images, the skins, the list of animations— should be in their own panels or areas, each optimized for the task involving them. And some of them should be represented in some other task-centric part of the UI. (I for one could get behind a good, solid, inspector pane or overlay widget that helps me get a read on and do stuff really quickly to my current selection)
In Setup Mode, it would certainly make sense to be able to drag an image from the list of available images into slots without having to repeatedly scroll up and down to find "where the hell is that image/slot I needed?".
And in Animate Mode, it would certainly make sense to put the list of animations (especially the currently selected animation) in a more visible, easy to reach place.
I'm not sure what the current plan is for the slot image chooser though.
I have a number suggestions for possibly small things. I'll post them later. : p
