rpi-deploy-manifest.json should be present. All artifacts are downloaded, so any code present in the supplied init or command command can assume all artifacts are present when running. init is used to install any dependencies, while command is used for running the application.
It should be easy to specify which files you want include as an artifact. You can use a zip file as an artifact, and then unzip it in the init command.
The manifest contains the actual bash commands you want to run, which ideally is a call to a script for each of init and command