No entendí muy bien como funciona el @Autowired de Spring

<code>@SpringBootApplication
public class PruebaExamenApplication implements ApplicationRunner {
	@Autowired
	public PersonaRepository personaRepository;

	public static void main(String[] args) {
		SpringApplication.run(PruebaExamenApplication.class, args);
	}

	@Override
	public void run(ApplicationArguments arg0) throws Exception {
		// TODO Auto-generated method stub
		
		 System.out.println(personaRepository.findById(2L).getProfesion());
		 
		 for (int i = 0; i < personaRepository.listaProfesiones().size(); i++) {
			 System.out.println(personaRepository.listaProfesiones().get(i)); 
		 } 
		 for(Persona p : personaRepository.findAll()) {
			 System.out.println(p.getNombre()+ " " +p.getProfesion()); 
		 }
		 
		 personaRepository.deleteAllInBatch();
		 personaRepository.deletePersona("Marketing");
		 Persona p = new Persona(3L, "54848788f", 27, "Jose" , "Marketing");
		 personaRepository.save(p);
		 personaRepository.actualizaNif("77777777k", "48569515t");
		 personaRepository.actualizaNifyNombre("89857556j", "Rojo");
	}
}

<code>@Transactional
public interface PersonaRepository extends JpaRepository<Persona, Long> {

	@Query("Select p from Persona p where id = ?1")
	public Persona findById(Long id);

	@Query("Select p.profesion from Persona p")
	public List<Persona> listaProfesiones();

	@Modifying
	@Transactional
	@Query("delete from Persona p where p.profesion = ?1")
	public void deletePersona(String profesion);

	@Modifying
	@Transactional
	@Query("update Persona p set p.nif = ?1 where p.nif = ?2")
	public void actualizaNif(String nifO, String nifD);
	
	@Modifying
	@Transactional
	@Query("update Persona p set p.nif = ?1, p.nombre = ?2 where p.nif = '5785693k'")
	public void actualizaNifyNombre(String nif, String nombre);

}

<code>@Entity
@Getter
@Setter
@AllArgsConstructor
@NoArgsConstructor
@Table(name = "carcel")
public class Carcel {
	@Id
	@GeneratedValue
	private Integer idCarcel;
	private String Nombre;
	private String Ciudad;
}


@Entity
@Getter
@Setter
@AllArgsConstructor
@NoArgsConstructor
@Table(name = "condena")
public class Condena {
	@Id
	@GeneratedValue
	private Integer idCondena;

	@Column(name = "nombreCondena")
	private String nombreCondena;

	@Column(name = "anyos")
	private Integer anyos;
}

<code>@Entity
@Getter
@Setter
@AllArgsConstructor
@NoArgsConstructor
@Table(name = "telefono")
public class Telefono {
	@Id
	@GeneratedValue
	private Integer idTelefono;
	private Integer numeroTelefono;
	private String compañia;

	@ManyToOne
	@JoinColumn(name = "preso_id")
	private Preso preso;
}

<code>@Entity
@Getter
@Setter
@AllArgsConstructor
@NoArgsConstructor
@Table(name = "preso")
public class Preso {
	@Id
	@GeneratedValue
	private Integer idPreso;

	private String Nombre;
	private String Apeliido;

	@ManyToOne
	@JoinColumn(name = "id")
	private Carcel idCarcel;

	@OneToMany(mappedBy = "preso")
	@Column(name = "telefonos")
	private List<Telefono> ListTelefono;

	@ManyToMany
	@JoinTable(name = "presoCondena", joinColumns = {
			@JoinColumn(name = "idPreso", referencedColumnName = "idPreso") }, inverseJoinColumns = {
					@JoinColumn(name = "idCondena", referencedColumnName = "idCondena") })
	private List<Condena> condenas = new ArrayList<Condena>();

}

<code><dependencies>
	<dependency>
		<groupId>org.hibernate</groupId>
		<artifactId>hibernate-core</artifactId>
		<version>5.2.12.Final</version>
	</dependency>
	<dependency>
		<groupId>mysql</groupId>
		<artifactId>mysql-connector-java</artifactId>
		<version>5.1.16</version>
	</dependency>
	<dependency>
		<groupId>org.projectlombok</groupId>
		<artifactId>lombok</artifactId>
		<version>1.16.20</version>
		<scope>provided</scope>
	</dependency>
	<dependency>
		<groupId>junit</groupId>
		<artifactId>junit</artifactId>
		<version>3.8.1</version>
		<scope>test</scope>
	</dependency>
</dependencies>

<?xml version='1.0' encoding='utf-8'?>
<!DOCTYPE hibernate-configuration PUBLIC
"-//Hibernate/Hibernate Configuration DTD//EN"
"http://hibernate.sourceforge.net/hibernate-configuration-5.0.dtd">
<hibernate-configuration>
	<session-factory>
<property name="hibernate.connection.driver_class">com.mysql.jdbc.Driver</property>
<property name="hbm2ddl.auto">update</property>
<property name="hibernate.connection.url" jdbc:mysql://localhost:3306/accesodatos2017</property>
<property name="hibernate.connection.username">root</property>
<property name="hibernate.connection.password"></property>
<property name="hibernate.connection.pool_size">10</property>
<property name="show_sql">true</property>
<property name="dialect">org.hibernate.dialect.MySQL5Dialect</property>
<property name="hibernate.current_session_context_class">thread</property>
<!--Mapeo de todas las clases-->
<mapping class="es.fempa.test.hibernate.Car" />
</session-factory>
</hibernate-configuration>


public class HibernateUtil {
	private static final SessionFactory sessionFactory;
	static {
		try {
			StandardServiceRegistry standardRegistry = new StandardServiceRegistryBuilder()
					.configure("hibernate.cfg.xml").build();
			Metadata metaData = new MetadataSources(standardRegistry).getMetadataBuilder().build();
			sessionFactory = metaData.getSessionFactoryBuilder().build();
		} catch (Throwable th) {
			System.err.println("Enitial SessionFactory creation failed" + th);
			throw new ExceptionInInitializerError(th);
		}
	}
	public static SessionFactory getSessionFactory() {
		return sessionFactory;
	}
}
  
  
public class App {
	public static void main(String[] args) {
		SessionFactory sessFact = null;

		try {
			sessFact = HibernateUtil.getSessionFactory();
			Session session = sessFact.getCurrentSession();
			Transaction tr = session.beginTransaction();

			  //INSERTAR Y GUARDAR
			  List<Condena> lista = new ArrayList<Condena>();
			  Condena con = new Condena();
			  con.setNombreCondena("Atraco");
			  con.setAnyos(10);
			  // con.setIdCondena(7);
			  lista.add(con);
			 
			  Carcel c = new Carcel();
			  c.setNombre("Otra");
			  c.setCiudad("Barcelona");
			  //c.setIdCarcel(8);
			  
			  Preso p = new Preso();
			  // p.setIdPreso(14);
			  p.setNombre("Pepe");
			  p.setApeliido("Diaz"); p.setIdCarcel(c);
			  
			  p.setCondenas(lista);
			  
			  List<Telefono> listado = new ArrayList<Telefono>();
			  Telefono tel = new Telefono();
			  tel.setNumeroTelefono(648878959);
			  tel.setCompañia("Vodafone");
			  listado.add(tel); p.setListTelefono(listado);
			  
			  session.save(con);
			  session.save(c);
			  session.save(p);
			  session.save(tel);
			 

			//MODO 1 DELETE
			Carcel car = new Carcel();
			car.setIdCarcel(24);
			session.delete(car);
			 
			//UPDATE 1
			Carcel c = new Carcel();
			c.setIdCarcel(16);
			c.setNombre("Carcel 1");
			c.setCiudad("Asturias");
			session.update(c);
      
     
      //UPDATE 2 MAS OPTIMA
   		Carcel c = (Carcel)session.get(Carcel.class, 7);
  		c.setNombre("CACACITY");
  		session.update(c);

			//SACAR TODOS LOS PRESOS CON SUS DATOS
			String allPresos = "select p from Preso p inner join p.idCarcel c" +
			" inner join p.ListTelefono inner join p.condenas co";
			  
			List<Preso> presoList = session.createQuery(allPresos).getResultList();
			  
			for (Preso preso : presoList) { System.out.println("ID: " + preso.getIdPreso());
			System.out.println("Name: " + preso.getNombre());
			System.out.println("Apellido: " + preso.getApeliido());
			for (Condena co : preso.getCondenas())
			  	{ System.out.println("Condena: " + co.getNombreCondena() + ", " + co.getAnyos() + " años"); }
			  
			for (Telefono tel : preso.getListTelefono())
				  System.out.println("telefono: " + tel.getNumeroTelefono());
			  
			System.out.println("Carcel: " + preso.getIdCarcel().getNombre() + " " + "Ciudad: " + preso.getIdCarcel().getCiudad()); }
			 

//MODO 2 DELETE
Query borrarPreso10 = session.createQuery("delete Preso where idPreso = :idPreso");
		borrarPreso10.setParameter("idPreso", 9);
		borrarPreso10.executeUpdate();
			 

			tr.commit();
			sessFact.close();
		} catch (Exception ex) {
			ex.getMessage();
		} finally {
			sessFact.close();
		}
	}

}
//Spring
//Aplication.properties
spring.jpa.hibernate.ddl-auto=update
spring.datasource.url=jdbc:mysql://localhost:3306/accesodatos2017
spring.datasource.username=root
spring.datasource.password=
server.port=8787
<!--Para ver las querys en consola-->
logging.level.org.hibernate.SQL=DEBUG
logging.level.org.hibernate.type.descriptor.sql.BasicBinder=TRACE

He mirado este Link, y aún no me queda claro http://stackoverflow.com/questions/19414734/understanding-spring-autowired-usage