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apply: Use staged deployment on booted systems
When finalizing an OSTree deployment, the current `/etc` is merged with the new commit's `/usr/etc`. Any changes that happen in the current `/etc` after the deployment has been finalized will not appear in the new deployment. Since eos-updater is often run in the background, it's likely the user will make changes in `/etc` (such as creating a new user) long before the new deployment is booted into. To address this issue, OSTree has provided the concept of a staged deployment since 2018.5. The new deployment is initialized but not finalized during shutdown via the `ostree-finalize-staged.service` systemd unit. Since staged deployments only work on OSTree booted systems that can initiate systemd units, this can't really work in the current test suite. The old full deployment method is kept for that case. Note that staged deployment finalization depends on the `ostree-finalize-staged.path` systemd unit being activated. Currently, OSTree does this on demand but in the future it may require the OS to explicitly activate the unit via a systemd preset or similar mechanism. https://phabricator.endlessm.com/T5658
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