Re-add Skeleton3D::animate_physical_bones property

[TokageItLab]

• Closes Re-add Skeleton3D::animate_physical_bones property and Skeleton3D::bone_pose_updated signal #90880

The bone_pose_updated signal is very dangerous as described in #90575, so it is reimplemented as an alias of skeleton_updated. We cannot re-add a compatible signal that is not hazardous and has no performance problems, so bone_pose_changed signal should be eliminated.

• Follow-up Rework migration of animate_physical_bones for compatibility #93504

The internal PhysicalBoneSimulator3D is set after enter_tree, so that animate_physical_bones is updated once there.

However, the old configuration where PhysicalBone is directly a child of Skeleton3D without already having PhysicalBoneSimulator3D is deprecated, so it is placed under the group "Deprecated", to avoid confusion if the user follows the recommended new settings and has PhysicalBoneSimulator3D explicitly.

[TokageItLab]

#94291 (comment)

As the discussion, we cannot re-add a compatible signal that is not hazardous and has no performance problems, so bone_pose_changed signal should be eliminated.

[raulsntos]

The reasoning for not re-adding bone_pose_changed makes sense to me, hopefully it won't be too disruptive. I'll make a note to document the change in godotengine/godot-docs#9250.

[akien-mga]

Thanks!