This is a minimal boilerplate so that part was excluded but in the real setup this was extracted from we use AWS SSO from the CLI to authenticate against AWS (short-lived tokens) and the keys for other things are in the AWS SSM parameter store as secure strings (encrypted), locked down with IAM so that agents can only access specific (test) keys while developing.
The agents are running inside a docker container (this is part of the setup) and only share the workspace and tmp dirs with the host. They run under user permissions in the container, not root.