An example agent that intercepts a method of the bootstrap class loader.

BootstrapAgent.java

package net.bytebuddy;

import net.bytebuddy.agent.ByteBuddyAgent;
import net.bytebuddy.agent.builder.AgentBuilder;
import net.bytebuddy.description.type.TypeDescription;
import net.bytebuddy.dynamic.ClassFileLocator;
import net.bytebuddy.dynamic.DynamicType;
import net.bytebuddy.dynamic.loading.ClassInjector;
import net.bytebuddy.implementation.MethodDelegation;
import net.bytebuddy.implementation.bind.annotation.SuperCall;
import net.bytebuddy.matcher.ElementMatchers;

import java.io.File;
import java.lang.instrument.Instrumentation;
import java.net.HttpURLConnection;
import java.net.URL;
import java.nio.file.Files;
import java.util.Collections;
import java.util.concurrent.Callable;

public class BootstrapAgent {

    public static void main(String[] args) throws Exception {
        premain(null, ByteBuddyAgent.install());
        HttpURLConnection urlConnection = (HttpURLConnection) new URL("http://www.google.com").openConnection();
        System.out.println(urlConnection.getRequestMethod());
    }

    public static void premain(String arg, Instrumentation inst) throws Exception {
        File temp = Files.createTempDirectory("tmp").toFile();
        ClassInjector.UsingInstrumentation.of(temp, ClassInjector.UsingInstrumentation.Target.BOOTSTRAP, inst).inject(Collections.singletonMap(
                new TypeDescription.ForLoadedType(MyInterceptor.class),
                ClassFileLocator.ForClassLoader.read(MyInterceptor.class).resolve()));
        new AgentBuilder.Default()
                .ignore(ElementMatchers.nameStartsWith("net.bytebuddy."))
                .enableBootstrapInjection(temp, inst)
                .type(ElementMatchers.nameEndsWith(".HttpURLConnection"))
                .transform(new AgentBuilder.Transformer() {
                    @Override
                    public DynamicType.Builder<?> transform(DynamicType.Builder<?> builder, TypeDescription typeDescription, ClassLoader classLoader) {
                        return builder.method(ElementMatchers.named("getRequestMethod")).intercept(MethodDelegation.to(MyInterceptor.class));
                    }
                }).installOn(inst);
    }

    public static class MyInterceptor {

        public static String intercept(@SuperCall Callable<String> zuper) throws Exception {
            System.out.println("Intercepted!");
            return zuper.call();
        }
    }
}

Found the problem
The Class.forName works fine.
but both methods bellow don`t

Object clazz = org.nanotek.config.spring.BootstrapAgent.class.getClassLoader()
.getResourceAsStream("org/nanotek/config/spring/repositories/SimpleTableRepository.class");
System.err.println("clazz "+clazz);

Object resource = org.nanotek.config.spring.BootstrapAgent.class.getClassLoader()
.getResource("org/nanotek/config/spring/repositories/SimpleTableRepository.class");
System.err.println("resource "+resource);

Now, I understood that a "ClassLoader" need to be used to override the methods that SpringData uses to scan the packages,
and also "register" the instances of DynamicTypes manually but, using the sequence of registration used by the framework.