Git: merging public and private branches while while keeping certain files intact in both branches

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To be on the safe side, you can add a git attribute (see here for an example) for those private files.

That way, you can define a script (a “merge manager”) which will ensure the file including private informations will remain empty (or with a public content) if merged on the public branch, while keeping its local content if merged to the private branch.
It means you can merge/rebase without thinking about that file.

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