Re-apply config changes

[sbliven]

One of the difficulties using scicatlive for development is that docker compose makes some changes to config files, resulting in a dirty working directory. Trying to change branches while preserving these changes is challenging and changes often get lost, leading to a broken configuration.

I'm not sure how exactly to mitigate this, but it might involve some combination of the following

1. Use environmental variables over files whenever possible
2. Keep config files as minimal as possible. Don't include default values, only modified values
3. Have a script that could be run inside the container to re-apply config changes. (Maybe merge_json.sh can already do this if you delete .finished?)