Godot version:
3.1 Alpha 3 and Alpha 2
OS/device including version:
Win 7 x64
Issue description:
If the skeleton the bones are tied to is animated the bones will transform, but the shapes do not move from their original position.
Minimal reproduction project:
Here is a test scene with an animated hand model I made. All you have to do is generate a set of physical bones from the skeleton, set the scene as the root scene, and hit F5. It's already set up to loop the animation.
Hopefully this gets fixed before the stable build is released since this completely breaks the tool.
Ping @AndreaCatania
For the stability of the skeleton is not possible to move the shape of bones that are always at the origin.
Moving the shape from the origin mean change the COM, the result is a strange motion of the bone.
@AndreaCatania I'm not sure if I understand your comment as it's a bit of a mess. But I'm going to assume I'm doing something wrong.
So what extra should I do so that the collision shapes do animate?
It's been a month, anything?
They ARE suppose to animate, right? Because in the last gif in the article describing the bones you can clearly see them animate with the bones
I have the same issue with IK. Bone constraints also seem to either get lost on export (even with better collada export) or be plainly ignored by the physical bone generation feature.
This makes usage extremely cumbersome at best and impossible at worst. :(

Still reproducible in the current master branch.
The Physical Bones are not supposed to be animated currently since they are thought for ragdoll only. I should add the support for this feature, in the meanwhile is advised to use bone attachment.
Fixed by this: #36008
Any chance it'll be backported to a 3.2.x update? It's not a major change
but would be nice to have before 4.0 drops.
E: Nevermind, I see that it has the flair that show's it'll be cherry-picked for 3.2
Most helpful comment
Fixed by this: #36008