Fix Transform initialization for children and refactor prepare.rs

[Jondolf]

Problem

Currently, the transforms of bodies and colliders that are children are initialized incorrectly by the PreparePlugin. The Transform is assumed to be the same as GlobalTransform when updating Transform based on Position and Rotation.

Solution

This PR fixes the issue by computing the correct local transform based on the difference between the parent's and child's global positions/rotations.

Other changes

• Moved the transform initialization, which was previously in both init_rigid_bodies and init_colliders, into a separate system init_transforms
• apply_deferred is now called before the initialization systems
• Transform propagation is run if either rigid bodies or colliders have been added instead of just for new rigid bodies
• Added more comments for systems
• Removed some separate type aliases of component bundles (like RigidBodyComponents) and added the component types to the systems themselves. Each type alias was only used for a specific system, so they were unnecessary and made things longer.