What I did was that I removed all locally installed applications and just installed Docker on the machine and then Portainer to manage it and now I do everything in Docker. except local network SSH access to the machine.

You don't need to restart per say, like you could migrate everything but it absolutely isn't necessary; and for a system that's productive id even avise you not to until you're more comfortable with docker.

There shouldn't be any issues with on metal services living together with docker, in fact I have some services running that way myself.

When you switch to #docker you will never want to boo back. It may be hard at the beginning but it is worth to do it.

You can migrate your services one by one. Docker is just another software in your server.

Main drawback of docker is that images and containers consume significantly more space, but SSD cost is cheap nowadays.

My advise when you learn docker is that you focus on docker compose.

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Yes that's entirely possible. Just do it :-)