My experience using environment variables as recommended above has been positive. I currently maintain a Clojure web app (a REST server really) and have found

My experience using environment variables as recommended above has been positive. I currently maintain a Clojure web app (a REST server really) and have found that maintaining configuration options, like a keystore and keystore password, in environment variables is really nice. Having the exact same code base in dev, test, and production with separate configs specific to the environment simplifies dev life. The one issue that has popped up here with the env var approach is that our system administrators are not used to the idea and this creates friction when deploying new apps or updated certs.