The GraphQL API appears to have no non-deprecated way of specifying which commit new comments refer to. #114345
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aleppard
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API and Webhooks
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The GraphQL addPullRequestReviewThread is the current non-deprecated way of adding comment threads.
It appears that it always associates a request to create a comment with the latest commit of the file. There is no commitOID (https://docs.github.com/en/graphql/reference/input-objects#addpullrequestreviewthreadinput) argument to specify which commit is referenced. You can tie the comment to a pull request review (via the pullRequestReviewId) and you can specify a commit ID for that pull request review, but that commit ID is ignored by this method.
There are two problems here:
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