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from doc: "For JWT, a single entry that specifies where to extract the JSON Web Token (JWT) from inbound requests. Currently only header-based and query parameter-based selections are supported, for example $request.header.Authorization."
As a workaround you can use a Lambda authorizer that will get the full request and validate the token.
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I've stumbled upon https://stackoverflow.com/questions/60861268/ which references an archived AWS Forums post and says that there is a backlog request to support Cookies with Token-based authorizers. However, since the post is archived I cannot tell if it contained the link to that backlog request or not. Uri, do you happen to know if such request exists so we could +1 it?