Spring Boot allows all of this at once [1]. You can specify a configuration file in your sources but if you set specific keys in the environment that configuration has a higher priority. I think this is a very good solution.

Particularly this allows you to package a general configuration file, a user can provide an external configuration file and can for a specific instance even overwrite that with env (or command line arguments).

[1] http://docs.spring.io/spring-boot/docs/current/reference/htm...