What are the best practices to deploy and host artifacts for a Docker Multicontainer environment in Elasticbeanstalk for Scala Apps?

If you're willing to use a different SBT plugin for step 1, then you can automate step 2.

Although quay.io supports building your image from GitHub, they do not require it. (You can publish a local Docker image directly to your quay.io repository.)

1. Use the sbt-native-packager plugin in project/plugins.sbt.
2. Setup the plugin settings in build.sbt, like: dockerRespository := Some("quay.io/myaccount")
3. Your step 1 becomes: sbt docker:stage
4. Followed by: sbt docker:publishLocal
5. Check your image names and tags with docker images. The new image should have a name like quay.io/myaccount/app
6. Before you can publish to quay.io, you must docker login quay.io. Read their tutorial.
7. Your step 2 becomes sbt docker:publish. Now your quay.io account should contain the same IMAGE ID as your local Docker daemon.

Proceed with steps 3+ on the AWS side...

I am not really familiar with Scala however I believe the artifacts could be generated by Jenkins/CircleCI inside of your container that is built on Jenkins/CircleCI then the appropriate image tags referenced within your Dockerrun.aws.json.

Hope that helps.