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You can increase the buffer size by passing something like -Dcom.amazonaws.sdk.s3.defaultStreamBufferSize=15728640 to the jenkins java command-line. (This raises the buffer to 15MB from 128KB, which means that errors in the first 15MB are recoverable.)
It would be nice, though, if it this were fully avoidable, but I guess since Jenkins supports uploads from other servers (not just local files) you can't just pass a File object to AmazonS3Client.putObject, and so there needs to be some buffering to make the InputStream repeatable.