Internally, the linked list now uses shared_ptrs instead of raw
pointers. In addition, in the WPILib the notifier handle is now made
atomic. Then before the class is destructed, the handle is now set to 0.
This should help solve one of the existing race conditions. A 0 handle
is correctly handled down at the HAL level.
Rename the following folders:
hal/lib/Athena -> hal/lib/athena
hal/lib/Desktop -> hal/lib/sim
hal/lib/Shared -> hal/lib/shared
wpilibc/Athena -> wpilibc/athena
wpilibc/simulation -> wpilibc/sim
Windows users may need to run gradlew clean after updating.