Also added scripts for EOF newline management and for removing trailing whitespace. configure.bat was rewritten to use CRLF line endings. Documentation for the existing scripts was also improved.
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.