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Atomic updates and different kinds of config files in /etc can create quite some headache and confusion. I will try to list the problems here and possible solutions.

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atomic-updates_and_etc's Issues

Use something like etc-update to inform sysadmin of changes

Many of the proposed solutions have the need to inform a sysadmin of changes to config files introduced by packages

etc-update from Gentoo https://wiki.gentoo.org/wiki/Handbook:X86/Portage/Tools#etc-update is designed to let sysadmins know when package changes alter config files in /etc

etc-update has already been modified to support openSUSE and .rpmnew files and such:
https://build.opensuse.org/package/show/openSUSE:Factory/etc-update

This might be part of the solution to those sysadmin-notification requirements of those solutions

misalignment with ostree's use of /usr/etc

So OSTree has implemented /usr/etc for many years now.

It's not clear to me that this proposal is aligned with it currently.

As of today, /usr/etc on OSTree-managed systems is not something most software should look at, because the config files are copied to /etc.

Further today, rpm-ostree for example automatically rewrites RPM content to use /usr/etc in the commit. Having applications directly install things in /usr/etc gets into an ownership mess.

Or to say this all more clearly; I think the OSTree model has been working out quite well for years and by choosing a slightly different implementation plan here, you're creating potential for a clash.

It doesn't seem like it'd be too hard for the transactional-update project to match what OSTree is doing and do the 3-way merge of /usr/etc with /etc right?

Another question here; are you thinking of using this scheme only for transactional-update systems or also for "traditional" zypper installs?

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