Thus, there’s the /usr/etc folder containing the immutable version of configuration files, and /etc which is the mutable directory. If I modify a file in /etc and ask OSTree to compare with the new version, it will show me the differences and preserve my local modifications.
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There’s a whole ecosystem of secrets management tools — Doppler, Infisical, HashiCorp Vault, SOPS, dotenvx. They’re all good, and if you’re running a team of 50+ engineers you should probably be evaluating them.