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Hello.
I don't think it is possible to create a non-default branch in CloudFormation.
So I think it is necessary to create it from the git command or management console after the CodeCommit repository is created.
https://docs.aws.amazon.com/codecommit/latest/userguide/how-to-create-branch.html
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Cloudformation stack would be account specific and can't be branched. You may want to leverage code pipeline where you create the webhooks in each aws Account(environment per say) and that particular branch from source repository would be sourced. Take a look at this blog post, if you want to consider branch based deployment.