I would use them in two containers.
You can just create a dockerfile
in each folder and create a new docker image for each folder/service.
Once you have the images ready you can use e.g. docker-compose to start your containers. Each container can get the same volume to the config file so that each container can read the same config file.
https://docs.docker.com/engine/reference/builder/
https://docs.docker.com/compose/
Jens
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