My main gripe with this approach is that new projects, or upgraded projects, will have this setting explicitly written in project.godot to set it to false forever. It's not a problem technically but it's a bit annoying to have remnants of a 4.6 compat change carried along in all Godot project (even ones not using skeletons at all) until we release 5.0.

Ok, I did the opposite. The setting still defaults to false, but its automatically set to true when opening an older project.

Code changes look fine to me.

I'm trying to first reproduce the issue to validate the PR, but it seems I get it in 4.6-dev3 and dev4 official builds, but not with my local dev build from master (ef34c3d). Any clue as to why?

Edit: Seems like the symptoms on the TPS demo were fixed somehow between 4.6-dev4 (bd2ca13) and master (ef34c3d). Bisecting.

Edit 2: So I bisected the change to afd12e3, but... nevermind, this is just a change to how animations are imported, so my .godot imported from master was just incompatible with dev4.

Edit 3: So my testing confusion comes from the fact that the glTF importer will set the skeleton path based on the information in the glTF. For the player in the TPS demo, it happens to be a structure with MeshInstance3Ds under the Skeleton3D, so when you import with 4.6-dev2 or earlier (before the compat breakage), it doesn't save the value for skeleton_path since it's default. Then when you open the pre-imported scene in 4.6-dev3 or later, it's broken as the skeleton path is empty. Reimporting the glTF fixes it.

But we still need to restore compatibility for manually created Skeleton/MeshInstance hierarchies, which can't be solved by simply re-importing.

So uh, do I need to change anything? How to test it?
The upgrade tool runs imports, so it can patch stuff when importing.

No change needed for now, I just got a better understanding of what cases should be tested.

The gltf import probably doesn't need any compat in the end, as the skeleton is looked up in the gltf nodes directly so the hierarchy is defined by the spec (I believe).

So it's mostly for Godot authored Skeleton/MeshInstance scenes that we need compat, and not ones imported from gltf. We should check that the compat doesn't break the latter but I don't expect it to.

Thanks!