"These kind of systems have their own configs, be it elasticsearch.yml or my.cnf. The Dockerfile format is completely fucking useless at this kind of thing."

A solution I like: use Docker and mount the config as a volume or add it to the image in an additional build step. (I.e. have a my-app:2.3.4-base and then when moving to prod, create a new image my-app:2.3.4-prod). The reason why 'Docker in production' is inevitable (as I can see it) is because it makes trivial to iterate on your whole setup, not just your application code. If you work with gcc version X and Java version y, then you change and test with new versions, then you want to version control these changes, and update them in production easily, within your normal development flow.

(By inevitable, I mean that it's going to happen. Images are the new packages.)