Is "governor in council" the same as "governor general" in Canada?
If not, what does the "governor in council" do?
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It's the Canadian variation on Queen-in-Council
An executive order is made by the executive, in the person of the Monarch (or their representative in Canada), on the advice of their ministers. The nominal source of the order is said to be the "Governor in Council". Formally it's the Governor General as advised by the Privy Council, but in practice it's the cabinet making an order which is then formally approved by the Governor General.
(based on comments made by ross ridge)