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Getting a pull request by id always return 404, but can be found using PullRequestService#getPullRequests(). On top of that PullRequestService#isMerged(repository, id) method works.
PullRequestService#merge() throws 404 as well
After making a couple of GitHub requests I figured it out. The doc states the parameter of PullRequestService#getPullRequest() is `id`, while should be `number`. Pull request id is a different notion and should not be confused with the number.
One more API issue, which may probably be addressed to GitHub itself, but is present in EGit. PullRequestService#getPullRequests() can incorrectly determine the merged flag. The reason is that JSON does not include `merged` attribute, but includes `merged at`!