[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.

wpimath/src/generate/main/java/Nat.java.jinja

@@ -18,6 +18,7 @@ import edu.wpi.first.math.numbers.N{{ num }};
  *
  * @param <T> The {@link Num} this represents.
  */
+@SuppressWarnings("PMD.ImplicitFunctionalInterface")
 public interface Nat<T extends Num> {
   /**
    * The number this interface represents.