The network communication headers were moved to the include directory of the HAL and their copies were removed from wpilibc. Also, symModuleLink.h was removed because the function which it prototypes hasn't been used in WPILib since the roboRIO switch.
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.