You do need to have some way of managing package installs and upgrades, but that tooling can itself be checked into the annex, along with the packages and other blobs which it uses as source data - again, all versioned courtesy of git. If you're managing your machines sanely, you don't need to check in the entire root filesystem - most of it doesn't vary from one machine to another. This all acts like a low-speed, distributed, "admin filesystem", with version control, staging, and whatever checks and balances you want to put into how you're using git and git annex.
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