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If the dimension configuration file and database differ in major version, they are incompatible and it may not be possible to initialize the Registry client at all (so a migration script will definitely be needed).
Modifications to dimension configuration already in repositories (as opposed to the defaults in daf_butler) are effectively forks of the main configuration in daf_butler, and should be versioned as X.Y.Z+dX.dY.dZ, where X.Y.Z is fixed at daf_butler version at which it diverged, and dX.dY.dZ is the version of the fork (starting at 0.0.0).
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