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When making changes to an app's manifest.yml that is already deployed, the changes do not take effect on republish, or "Push" or "Update and Restart" operations. It seems manifest.yml properties are loaded only when publishing an app for the first time, but not when republishing. This may make it difficult for users to update Cloud properties through manifest.yml, especially if there are no associated UI to allow them to do that. For example, a user cannot update health check, health check endpoint, disk quota, etc for an already deployed application.