Apparently this was never properly tested and never worked. When the IPFS repo needs upgrading, the first call to ipfs, which is run before running the migration, fails with the error message "Error: ipfs repo needs migration".
To fix this, simply run the migration before any `ipfs config` calls but don't run it when `dataDir` is empty and we need to call `ipfs init`.
Writing a NixOS test for this would require keeping at least two versions of IPFS in Nixpkgs, which we don't currently do.
faad370edc