[SPARK-2894] spark-shell doesn't accept flags

As @sryza reported, spark-shell doesn't accept any flags.
The root cause is wrong usage of spark-submit in spark-shell and it come to the surface by #1801
I still think it's inconsistent that we use `SUBMIT_*` somewhere, `SPARK_SUBMIT_*` elsewhere, and then `SUBMISSION_*` here. Note a huge deal, but the word "submission" actually has a different connotation that I don't think is intended.