Job configuration is overwritten by hbase-default and hbase-site in TableMapReduceUtil.initTable(Mapper|Reducer)Job, causing unexpected behavior in the following code:
Configuration conf = HBaseConfiguration.create();
// change keyvalue size
Job job = new Job(conf, ...);
// the job doesn't have the option changed, uses it from hbase-site or hbase-default
Although in this case it could be fixed by moving the set() after initTableMapperJob(), in case where user wants to change some option using GenericOptionsParser and -D this is impossible, making this cool feature useless.
In the 0.20.x era this code behaved as expected. The solution of this problem should be that we don't overwrite the options, but just read them if they are missing.