Docker
I'm using Docker Compose to manage my running apps on my server. I store all my docker config on GitHub.
That repository also includes a script to update the host's linux runtime and all containers.
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caution
The setup I've used does not automatically install updates. This is to reduce unexpected downtime due to breaking changes in updates.
As a tradeoff, you must manually (and reguarly) update both the docker containers and the server itself. Failure to do so may introduce vulnerabilities.