Code maintenance, fix comments, reorder class methods in usage order, remove unused methods and rename some methods for more consistency.
Try to break some dependencies between classes.
Remove unneeded includes.
Fix implementation of Scene::{getRenderableCount|getLightCount}(), it
was completely busted.
- We were not setting the bones ubo staging buffer size correctly
- The bones UBO was never bound to the shader
- The default values for the bones ubo wasn’t identity
