Revise include order using clang-format-6.0

Run the `clang-format.bash` script to update our C and C++ code to a new
include order `.clang-format`.  Use `clang-format` version 6.0.

Tests/JavaNativeHeaders/D.cpp

@@ -1,9 +1,9 @@
 
+#include "D.h"
+
 #include <jni.h>
 #include <stdio.h>
 
-#include "D.h"
-
 JNIEXPORT void JNICALL Java_D_printName(JNIEnv*, jobject)
 {
   printf("D\n");