• Get source control tokens

ARMClient.exe get /providers/Microsoft.Web/sourceControls?api-version=2014-11-01 ARMClient.exe get /providers/Microsoft.Web/sourceControls/GitHub?api-version=2014-11-01 

• Update source control token (for instance, GitHub).

ARMClient.exe put /providers/Microsoft.Web/sourceControls/GitHub?api-version=2014-11-01 '@payload.json' 

sample payload.json

{ "properties": { "token": "abcd1234" } }

Note that you'll need to have assigned the 'Windows Azure Service Management API' permissions to the service principal before making the call to update the 'SourceControlTokens'.