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I have a large number of applications running in Azure that need to have some very specific values set in their Manifests in the Active Directory section of the old Azure Management portal. Is there a cmdlet or other way to retrieve and set manifests for such applications through PowerShell ?

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The manifest is not a physical file, but a way for the 'system' to set values using the Graph API. You can set these values yourself using your tenants graph api endpoint, see https://msdn.microsoft.com/Library/Azure/Ad/Graph/api/entity-and-complex-type-reference for further referencen to the api object

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