No appPermissions section in the Manifest

I'm following the sample at https://github.com/AzureADSamples/NativeClient-DotNet

When I download the application manifest, it does not have an "appPermissions" section. 

If I add one and upload the manifest, the upload succeeds but strips out the appPermissions section (If I download the manifest again there is no appPermissions section). 

I can change other values in the manifest and upload successfully, but my AAD doesn't want to know about "appPermissions".

I'm using an organisational account user with admin privileges to do this.

The manifest looks like this:

{
  "allowActAsForAllClients": null,
  "appId": "8bdccb2e-0971-xxxxxxxxxxxxxx",
  "appMetadata": null,
  "appRoles": [],
  "availableToOtherTenants": false,
  "displayName": "AppPermissionsTest2",
  "errorUrl": null,
  "groupMembershipClaims": null,
  "homepage": "https://localhost:44303/",
  "identifierUris": [
    "https://xxxxxxxxxxxxxxxxx"
  ],
  "keyCredentials": [],
  "knownClientApplications": [],
  "logoutUrl": null,
  "oauth2AllowImplicitFlow": false,
  "oauth2AllowUrlPathMatching": false,
  "oauth2Permissions": [],
  "oauth2RequirePostResponse": false,
  "passwordCredentials": [],
  "publicClient": null,
  "replyUrls": [
    "https://localhost:44303/"
  ],
  "requiredResourceAccess": [],
  "samlMetadataUrl": null,
  "defaultPolicy": [],
  "extensionProperties": [],
  "objectType": "Application",
  "objectId": "01162e45-0xxxxxxxxxxxxxxx62",
  "deletionTimestamp": null,
  "createdOnBehalfOf": null,
  "createdObjects": [],
  "manager": null,
  "directReports": [],
  "members": [],
  "memberOf": [],
  "owners": [],
  "ownedObjects": []
}

What am I doing wrong?

Thanks

John