java.lang.IllegalStateException: Cannot initialize context because there is already a root application context present

@Controller
@ComponentScan
@Configuration
@EnableScheduling
@EnableAutoConfiguration(exclude={DataSourceAutoConfiguration.class, DataSourceTransactionManagerAutoConfiguration.class, RedisAutoConfiguration.class, MybatisAutoConfiguration.class})
@ImportResource(locations = {"classpath*:app.xml"})
public class AppMain extends SpringBootServletInitializer implements ApplicationContextAware {

@Override
    protected SpringApplicationBuilder configure(SpringApplicationBuilder builder) {
//        return super.configure(builder);
        return builder.sources(AppMain.class);
    }    @Override
    public void onStartup(ServletContext servletContext) throws ServletException {
        servletContext.setInitParameter("logSystem","log4j,logback");
        servletContext.setInitParameter("loggingLevel", "INFO");
        servletContext.setInitParameter("loggingCharset", "UTF-8");
        servletContext.setInitParameter("contextConfigLocation", "<NONE>");
        super.onStartup(servletContext);
    }
}

For anyone with a similar problem – turns out that spring-jersey used in the project was setting up its own context. My context and the spring-jersey one were initialized in random order apparently. More info here: 
https://java.net/jira/browse/JERSEY-2038 
https://java.net/projects/jersey/lists/users/archive/2014-03/message/124 
The suggested solution of adding:

servletContext.setInitParameter("contextConfigLocation", "<NONE>");

In WebAppInitializer implementation didn’t work reliably due to initialization order. What solved the problem was adding its xml equivalent:

<context-param>
    <param-name>contextConfigLocation</param-name>
    <param-value></param-value>
</context-param>

as the firt parameter in web.xml, ensuring that its set before the context is initialized.