They seem to be serving the same purpose. They can both be broken down into steps, each step being a script. A Command or Automation document can also both be part of SSM Associations in the State Manager. So my question is simple. In which case would I need to create a Command document instead of an Automation document ?
From documentation:
Using Run Command, a capability of AWS Systems Manager, you can remotely and securely manage the configuration of your managed nodes.
So with command documents you are executing commands on your managed instances (i.e. yum update)
Automation, a capability of AWS Systems Manager, simplifies common maintenance, deployment, and remediation tasks for AWS services like Amazon Elastic Compute Cloud (Amazon EC2), Amazon Relational Database Service (Amazon RDS), Amazon Redshift, Amazon Simple Storage Service (Amazon S3), and many more.
With Automation document you can interact with any AWS service to execute some actions (i.e. launch EC2 instance, crate AMI from running instance, crate RDS snapshot etc.) Moreover you can define retries, crate process branches (i.e. when some step fails, go different path than when it success)