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There is also a middle ground. Treat configuration file like a template and inject the key configuration settings at runtime. Take a look at a sample lukaszbudnik/migrator configuration file:
If you host your Kubernetes cluster in a cloud then I would strongly encourage you to use godaddy/kubernetes-external-secrets project to sync your Kubernetes secrets with external secrets services. kubernetes-external-secrets supports the following backends: AWS Systems Manager Parameter Store, Hashicorp Vault, Azure Key Vault, Google Secret Manager, and Alibaba Cloud KMS Secret Manager.