Since ppl might up/down docker containers frequently (on system restart for instance), they would loose any of the config changes they've made inside the container.

I'd recommend placing a template amass-config.ini file in the main repo, having the user edit that. Then you can modify the docker-compose.yml to include this mount:

    volumes:
      - ../reconnote-output/:/var/www/html
      - ${PWD}/amass-config.ini:/deksterecon/amass-config.ini

I think this would also help to close issue #4