resources in a Spring Boot application are missing from jar file when using Spring Boot Maven Plugin

As described in the documentation mvn spring-boot:run adds src/main/resources in front of your classpath to support hot reload by default. You can turn this off easily

<build>
  ...
  <plugins>
    ...
    <plugin>
      <groupId>org.springframework.boot</groupId>
      <artifactId>spring-boot-maven-plugin</artifactId>
      <version>1.2.7.RELEASE</version>
      <configuration>
        <addResources>false</addResources>
      </configuration>
    </plugin>
    ...
  </plugins>
  ...
</build>