I have a use-case that I need to separate my Spring configuration into 2 completely separate applications.
Application #1 will contain DAO models with Hibernate Mappings, JPA Repositories, DTO models, and logic to convert from a DAO to a DTO.
Application #2 will contain the RESTful Controllers and Service classes that contain all the business logic.
Application #1 configuration:
// For application startup
package com.appone.pkg.one
@SpringBootApplication
public class Application {
    public static void main(String[] args) {
        SpringApplication.run(Application.class, args);
    }
}
// For global configuration files across numerous projects
package com.appone.pkg.two
@Configuration
public class GlobalAppConfig {
    @Bean
    MapperFacade mapperFacade() {
        MapperFactory factory = new DefaultMapperFactory.Builder().build();
        factory.classMap(Group.class, GroupDTO.class).byDefault().register();
        factory.classMap(Role.class, RoleDTO.class).byDefault().register();
        factory.classMap(User.class, UserDTO.class).byDefault().register();
        return factory.getMapperFacade();
    }
 }
// For configuration aspects important for 1 project in particular
package com.appone.pkg.three
@Configuration
@EnableJpaRepositories("com.pkg.three.jpa.repository")
public class AppTwoConfig {
    @Autowired
    private EntityManager em;
    private RepositoryFactorySupport factorySupport;
    private void initialize(){
        if(factorySupport == null){
            factorySupport = new JpaRepositoryFactory(em);
        }
    }
    @Bean
    GroupRepository groupRepository(){
        initialize();
        return factorySupport.getRepository(GroupRepository.class);
    }
    @Bean
    RoleRepository roleRepository(){
        initialize();
        return factorySupport.getRepository(RoleRepository.class);
    }
    @Bean
    UserRepository userRepository(){
        initialize();
        return factorySupport.getRepository(UserRepository.class);
    }
    @Bean
    GroupValidator groupValidator(){
        return new GroupValidator();
    }
    @Bean
    UserValidator userValidator(){
        return new UserValidator();
    }
    @Bean
    ResourceMapper resourceMapper(){
        return new ResourceMapper();
    }
}
Application #2 configuration:
package com.apptwo.pkg.one;
@SpringBootApplication
@EnableAutoConfiguration
@EntityScan(basePackageClasses = {com.appone.pkg.three.AppTwoConfig.class})
public class ApplicationTwo {
    public static void main(String[] args) {
        SpringApplication.run(ApplicationTwo.class, args);
    }
}
Application #2 data load:
package com.apptwo.pkg.two;
@Component
public class DataLoader implements ApplicationRunner {
    @Autowired
    private GroupRepository groupRepository;
    @Autowired
    private RoleRepository roleRepository;
    @Autowired
    private UserRepository userRepository;
    @Autowired
    private ResourceMapper resourceMapper;
    /**
     * Loads initial data into the h2 database.
     */
    public void run(ApplicationArguments args) {
        // Load the initial data ... 
    }
}
This is the exception I am getting when I try to launch Application #2. Application #1 starts up fine on it's own, but I am not using the Repositories there and believe it could throw errors if I tried. Ultimately I want the logic only in Application #2 though. Do you have any ideas on what I am doing wrong?
I need to initialize all the dependencies in Application #1 configuration and then run that configuration from inside Application #2 before I run the Application #2 configuration.
Description: Field groupRepository in com.apptwo.pkg.two.DataLoader required a bean of type 'com.appone.pkg.three.jpa.repository.GroupRepository' that could not be found.
Action: Consider defining a bean of type 'com.appone.pkg.three.jpa.repository.GroupRepository' in your configuration.