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It's an SQLite database, so you wouldn't be able to merge changes made in different clones.

Ah, I see. Thanks. My initial prototype will use a flat text file (a serialized s-exp) instead.

Another issue is full paths to the nix config file encoded in the state file itself. The state file should not point to the config files used IMO.

Totally agreed. The user should pass the config file to the program each time.