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Hi @pcousins
Unfortunately, this isn't possible and the defaults are pre-set in the software behind the scenes.
However, I have done some tests and what you can do is save and copy the ComparisonOptions.xml & Filter.scpf from one of your configured repositories and then place directly into the new repository and pull the changes and it will apply to that database.
Hope this helps!
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My question is this: can we set these as the default for SQL Source Code Control when we link a new database to a repository?