My initial feedback:
The build fails with proto buff errors. I already have protobuf installed for other reasons, can't mvn pull down the protobuf version it needs vs relying on the system wide libs?
Including the bk/zk jar files in server/lib is a really bad practice. Why do we have to do this vs using versions built from the current tree? If we have to do ths we should also indicate that this is not a release version - typically in mvn this means putting something like "SNAPSHOT" into the name of the jars.
The README should have a tiny bit of text describing, at a very high level, what hedwig is.
The contents of the scripts directory are not executable by default, we should either fix this in the patch or note it for committer to fix at commit time.
ZooKeeperTestBase.java has windows eol characters. Perhaps run dos2unix on all the files and refresh the patch? (looks like all the tests suffer from this?)
RAT identified the following files which seem like they should have license headers added: