[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.

wpiutil/src/test/java/edu/wpi/first/util/cleanup/CleanupPoolTest.java

@@ -87,7 +87,6 @@ class CleanupPoolTest {
   }
 
   @Test
-  @SuppressWarnings("PMD.AvoidCatchingGenericException")
   void cleanupStackWithExceptionInCloseWorks() {
     List<AutoCloseableObject> objects = new ArrayList<>();
     objects.add(new AutoCloseableObject());