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You can use a CodePipeline Deploy stage that uses CloudFromation Stacks as the deployment provider, which should be easier than using CodeDeploy.
Before the Deploy stage, create Build stage that has a CLI command like:
aws cloudformation package --template-file $TemplateName.yaml --s3-bucket $S3Bucket --s3-prefix $S3BuildsPrefix --output-template-file packaged-template.yaml
This allows your parent template to refer to nested stacks as relative paths in your source tree, and "cloudformation package" resolves these by uploading dependencies to S3 and changing references in your template to refer to them. It can deal with many types of dependencies - have a look at https://docs.aws.amazon.com/cli/latest/reference/cloudformation/package.html.
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