Spring Boot ConflictingBeanDefinitionException: Annotation-specified bean name for @Controller class

I keep getting the ConflictingBeanDefinitionException error in my Spring boot application. I am not entirely sure as to how to address it, I have several @Configuration annotated classes helping to set up Thymeleaf, Spring Security and Web. Why is the application trying to setup the homeController twice? (and where is it trying to do this?)

The error is:

org.springframework.beans.factory.BeanDefinitionStoreException: 
Failed to parse configuration class [org.kemri.wellcome.hie.Application]; nested exception is org.springframework.context.annotation.ConflictingBeanDefinitionException:
Annotation-specified bean name 'homeController' for bean class [org.kemri.wellcome.hie.HomeController] conflicts with existing, non-compatible bean definition of same name and class [org.kemri.wellcome.hie.controller.HomeController]

My spring boot main application initializer:

@EnableScheduling
@EnableAspectJAutoProxy
@EnableCaching
@Configuration
@ComponentScan
@EnableAutoConfiguration
public class Application extends SpringBootServletInitializer {

    public static void main(String[] args) {
        SpringApplication.run(Application.class, args);
    }
    
    @Override
    protected final SpringApplicationBuilder configure(final SpringApplicationBuilder application) {
        return application.sources(Application.class);
    }

}

My database config file:

@Configuration
@EnableTransactionManagement
@EnableJpaRepositories(basePackages="org.kemri.wellcome.hie.repositories")
@PropertySource("classpath:application.properties")
public class DatabaseConfig {

  @Autowired
  private Environment env;

  @Autowired
  private DataSource dataSource;

  @Autowired
  private LocalContainerEntityManagerFactoryBean entityManagerFactory;

   @Bean
  public DataSource dataSource() {
    DriverManagerDataSource dataSource = new DriverManagerDataSource();
    dataSource.setDriverClassName(env.getProperty("spring.datasource.driverClassName"));
    dataSource.setUrl(env.getProperty("spring.datasource.url"));
    dataSource.setUsername(env.getProperty("spring.datasource.username"));
    dataSource.setPassword(env.getProperty("spring.datasource.password"));
    return dataSource;
  }
  @Bean
  public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
    LocalContainerEntityManagerFactoryBean entityManagerFactory =
        new LocalContainerEntityManagerFactoryBean();
    
    entityManagerFactory.setDataSource(dataSource);
    
    // Classpath scanning of @Component, @Service, etc annotated class
    entityManagerFactory.setPackagesToScan(
        env.getProperty("spring.jpa.hibernate.entitymanager.packagesToScan"));
    
    // Vendor adapter
    HibernateJpaVendorAdapter vendorAdapter = new HibernateJpaVendorAdapter();
    entityManagerFactory.setJpaVendorAdapter(vendorAdapter);
    
    // Hibernate properties
    Properties additionalProperties = new Properties();
    additionalProperties.put(
        "hibernate.dialect", 
        env.getProperty("spring.jpa.hibernate.dialect"));
    additionalProperties.put(
        "hibernate.showsql", 
        env.getProperty("spring.jpa.hibernate.showsql"));
    additionalProperties.put(
        "hibernate.hbm2ddl.auto", 
        env.getProperty("spring.jpa.hibernate.hbm2ddl.auto"));
    entityManagerFactory.setJpaProperties(additionalProperties);
    
    return entityManagerFactory;
  }
  @Bean
  public JpaTransactionManager transactionManager() {
    JpaTransactionManager transactionManager = 
        new JpaTransactionManager();
    transactionManager.setEntityManagerFactory(
        entityManagerFactory.getObject());
    return transactionManager;
  }
  @Bean
  public PersistenceExceptionTranslationPostProcessor exceptionTranslation() {
    return new PersistenceExceptionTranslationPostProcessor();
  }

}

My Thymeleaf config file:

@Configuration
public class ThymeleafConfig {

@Bean
public ServletContextTemplateResolver templateResolver(){
    ServletContextTemplateResolver thymeTemplateResolver = new ServletContextTemplateResolver();
    thymeTemplateResolver.setPrefix("/WEB-INF/views/");
    thymeTemplateResolver.setSuffix(".html");
    thymeTemplateResolver.setTemplateMode("HTML5");
    return thymeTemplateResolver;
}   

@Bean
public SpringSecurityDialect springSecurityDialect(){
    SpringSecurityDialect dialect = new SpringSecurityDialect();
    return dialect;
}

@Bean
public SpringTemplateEngine templateEngine() {
    SpringTemplateEngine engine = new SpringTemplateEngine();   
    engine.addTemplateResolver(templateResolver());
    Set<IDialect> dialects = new HashSet<IDialect>();
    dialects.add(springSecurityDialect());
    engine.setAdditionalDialects(dialects);     
    return engine;
}

@Bean
public ThymeleafViewResolver thymeleafViewResolver() {
    ThymeleafViewResolver resolver = new ThymeleafViewResolver();
    resolver.setTemplateEngine(templateEngine());
    resolver.setViewClass(ThymeleafTilesView.class);
    resolver.setCharacterEncoding("UTF-8");
    return resolver;
}

}

My Web config class:

@Configuration
@PropertySource("classpath:application.properties")
public class WebConfig extends WebMvcAutoConfigurationAdapter  {
    
    @Autowired
    private Environment env;
    
    @Bean
    public JavaMailSenderImpl javaMailSenderImpl() {
        JavaMailSenderImpl mailSenderImpl = new JavaMailSenderImpl();
        mailSenderImpl.setHost(env.getProperty("smtp.host"));
        mailSenderImpl.setPort(env.getProperty("smtp.port", Integer.class));
        mailSenderImpl.setProtocol(env.getProperty("smtp.protocol"));
        mailSenderImpl.setUsername(env.getProperty("smtp.username"));
        mailSenderImpl.setPassword(env.getProperty("smtp.password"));
        Properties javaMailProps = new Properties();
        javaMailProps.put("mail.smtp.auth", true);
        javaMailProps.put("mail.smtp.starttls.enable", true);
        mailSenderImpl.setJavaMailProperties(javaMailProps);
        return mailSenderImpl;
    }

    @Bean
    public CacheManager cacheManager() {
        return new ConcurrentMapCacheManager();
    }
}

My controller (where there is an error setting up the controller)

@Controller
public class HomeController {
    
    private static final Logger logger = LoggerFactory.getLogger(HomeController.class);
    
    /**
     * Simply selects the home view to render by returning its name.
     */
    @RequestMapping(value = "/", method = RequestMethod.GET)
    public String home(Locale locale, Model model) {
        logger.info("Welcome home! The client locale is {}.", locale);
        
        Date date = new Date();
        DateFormat dateFormat = DateFormat.getDateTimeInstance(DateFormat.LONG, DateFormat.LONG, locale);
        
        String formattedDate = dateFormat.format(date);
        
        model.addAttribute("serverTime", formattedDate );
        
        return "index.html";
    }
}

What might be causing the ConflictingBeanDefinitionException error for my controller class?

The solution, as I found out, is to disable double initialization by including a filter in the component scan. In my case:

@EnableScheduling
@EnableAspectJAutoProxy
@EnableCaching
@Configuration
@ComponentScan(basePackages = { "org.kemri.wellcome.hie" }, 
    excludeFilters = {@Filter(value = Controller.class, type = FilterType.ANNOTATION)})
@EnableAutoConfiguration
@PropertySource("classpath:application.properties")
public class Application extends SpringBootServletInitializer {

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