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I bought a used machine a couple weeks ago and am setting it up (1st bare metal build), prox with debian vm running docker. I found it annoying that pm doesn't support it natively but the ability to do snapshots through pm is nice, and let's me fuck around more than I would otherwise, slowly build up a machine.
But almost all of the stuff I have running on other machines is just docker containers, so it would be nice if pm just added a checkbox during install or something. (I want to poke at and learn pm, plus mess around with other vms, that's why I didn't do straight Debian)
I am with you on the advantages of running it in a VM. The isolation a VM provides is really nice. Snapshots FTW.
LXCs let you get all the benifits of VMs with fewer drawbacks, I recommend that approach if you want some extra sandboxing than docker on bare metal provides.