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Storing configurations is source control
Halyard stores secrets prompted by hal commands in your Halyard configuration directory, typically
~/.hal/config.yml and other
For both Halyard and the Spinnaker Operator to deploy and manage Spinnaker, you need to separate secrets from the rest of the config. This is done by replacing secret values and secret files by
encryptedFile... references as described in Spinnaker Secrets. This allows you to store secret-free configuration files under source control. When you need to make any changes, you can download the files, change them, deploy the changes, and then upload the files again.
Deploying config changes using Spinnaker Operator
If you are using the Spinnaker Operator, you can use any standard Kubernetes mechanism to update and apply config changes, like
Deploying config changes using Halyard
If you are using Halyard you need to issue
hal commands to modify the configuration and then run
hal deploy apply to apply the changes to Spinnaker.