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We've also experienced this, and have traced it back to an additional "url" payload now being sent from the GHE commit hook. It appears that this eventually makes its way to https://github.com/kohsuke/github-api/blob/master/src/main/java/org/kohsuke/github/GHPullRequest.java#L198 , at which point the API server (that already has api/v3) is joined with the full path of that url payload (that also includes api/v3), resulting in the path doubling.
I haven't dug into the code extensively, but it seems like a possible workaround would be to use the GHRepository.getApiTailUrl method (https://github.com/kohsuke/github-api/blob/master/src/main/java/org/kohsuke/github/GHRepository.java#L999) rather than getApiURL().getPath