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The Upstream repository has the fix for a deadlock issue (shyiko#321). This impacts our project and hence we need this fix and hence so the others. I have resolved the merge conflicts with the upstream project after going over the difference in the changes.
I have retained the greeting packet authentication as of before and nothing has changed with the authentication as it was before. There were conflicts in the first place because of many minor method signature changes which were conflicting with the authentication-related code. Apart from that, all the commits which have been missed from the upstream repository have been resolved of every merge conflict.