Risking being totally offtopic, but would TCB solve all most of this issues? www.openwall.com/tcb/ or http://www.openwall.com/presentations/Owl/mgp00020.html
It helps a little, but the problem here is not exactly about the underlying data format, but more about the merge/upgrade logic, which TCB by itself doesn't quite solve.
We would still need logic somewhere (likely ostree), like today how it lives in RPM %post scripts to check whether users exist, and if not create them. The binding between that logic and how the files get created on disk is the hard problem.
Also I originally thought TCB was a good idea, but I got less excited about it when I realized they'd just shifted setuid binaries to setgid. To me it'd be far more valuable to go the whole way and have authentication/passwd talk to a system service. Then you could even implement stuff like rate limiting sanely.
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