[build] Upgrade Gradle plugins (#8166)

I upgraded all plugins I could see except org.ysb33r.doxygen. 2.0 made
breaking changes, and I couldn't figure out how to migrate.

Most of the changes are for suppressing new linter purification rites.

wpilibNewCommands/src/main/java/edu/wpi/first/wpilibj2/command/ParallelRaceGroup.java

@@ -42,7 +42,6 @@ public class ParallelRaceGroup extends Command {
    *
    * @param commands Commands to add to the group.
    */
-  @SuppressWarnings("PMD.UseArraysAsList")
   public final void addCommands(Command... commands) {
     if (!m_finished) {
       throw new IllegalStateException(