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The methods get, getVer, getVerTs, atomicIncrement were deprecated back in HBASE-1304. My guess is this was because it wasn't distinguishing between column family and column qualifier but I'm not sure. Either way it's been in there for six years without documentation or a deprecation at the interface level so it adds to my confusion and I'll attach a patch to remove the deprecations.
I guess at one point the whole old Thrift server will be deprecated.