[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 don't think `application_opts` is needed as explained [here](https://github.com/apache/spark/pull/1864#discussion_r16026126). But anyway we can leave it as is.