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Amazon SSM Agent on Fedora Container Linux

Use rpm-ostree to actually install the SSM agent where it wants to live.

Yes. rpm-ostree can write to those filesystems that are eventually mounted as read-only.

e.g. Manually it looks like this:

# install the desired os-arch rpm of amazon ssm agent from the offical amazon s3 location
# rpm-ostree works with most rpms that follow RHEL or Fedora (so Amazon linux is fine)
sudo rpm-ostree install https://s3.amazonaws.com/ec2-downloads-windows/SSMAgent/latest/linux_amd64/amazon-ssm-agent.rpm
sudo systemctl enable amazon-ssm-manager.service
sudo systemctl reboot # disconnects your ssh until sshd restarts also

Obviously you can do this inside user-data / an ignition config with a one-shot unit!