Drop spark args and setting spark properties through code

This is similar to https://github.com/bigdatagenomics/adam/pull/374  Also drop SparkArgs since that will be removed from ADAM

Basically when we are using spark-submit, we want to use that to set spark-master and spark-jar properties, without need to respecify them in the app.  Doing so can lead to an issue like I had earlier: http://mail-archives.apache.org/mod_mbox/spark-user/201408.mbox

For now all the Kryo properties are defaulted, but those can also be specified through a config file.