[SPARK-5979][SPARK-6032] Smaller safer --packages fix #4802
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@pwendell @tdas
This is the safer parts of PR #4754:
org.apache.spark
passed through--packages
, were being excluded from the dependency tree on the assumption that they would be in the assembly jar. This is not the case, therefore the exclusion rules had to be defined more explicitly.System.out
. Moved the logging toSystem.err
.