We've recently found that as we develop more applications in Azure, we need to put safeguards on the deployment of the applications to ensure that they're configured correctly. Part of this means editing the application manifests to ensure that certain settings are always enforced on certain applications. Here's what Microsoft has to say about updating Application manifests.
Bottom line, if you want to automate anything to do with manifests, you'll have to write your own application to use the Azure Graph API libraries to retrieve the manifest / application settings and edit them.
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