Hadoop ignores old-style config options for enabling compressed output

Hadoop seems to ignore the config options even though they are printed as deprecation warnings in the log: mapred.output.compress and
mapred.output.compression.codec

• settings that work on 0.20 but not on 0.23
  mapred.output.compress=true
  mapred.output.compression.codec=org.apache.hadoop.io.compress.BZip2Codec

• settings that work on 0.23
  mapreduce.output.fileoutputformat.compress=true
  mapreduce.output.fileoutputformat.compress.codec=org.apache.hadoop.io.compress.BZip2Codec

This breaks backwards compatibility and causes existing jobs to fail.

This was found to happen due to the JobSubmitter writing out the job.xml file with the old-style configs and can be fixed by handdling deprecation before the file is written out.