The REST API would tell you if a file was added, modified or deleted: https://developer.github.com/v3/pulls/#list-pull-requests-files
The GraphQL API doesn't seem to have any way to do this - you can see how many additions/deletions were in a commit/PR overall, but there isn't a way (without separately querying the repo) to see which files are new vs simply had lines added. This is functionality we used in the REST API for some of our automation.
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