[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
Yes, @sarutak could you remove this? I didn't realize we already had an IPYTHON_OPTS for this purpose, and any application argument provided here will only go to `py4j.JavaGateway`, which is clearly not interested in our ipython arguments.