First of all, to actually understand the concept behind clone
better I recommend the answer to the question: How to properly override clone method?
Regarding the source code you have put into your question:
native
means here, that this is a method which is not implemented with Java, but with another language, often C or C++. It's still part of the JVM, hence you can find the actual implementation in the OpenJDK™ Source Release in the
"openjdk/hotspot/src/share/vm/prims/jvm.cpp":539
JVM_ENTRY(jobject, JVM_Clone(JNIEnv* env, jobject handle))
JVMWrapper("JVM_Clone");
Handle obj(THREAD, JNIHandles::resolve_non_null(handle));
const KlassHandle klass (THREAD, obj->klass());
JvmtiVMObjectAllocEventCollector oam;
.
.
.
JVM_END