[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
We actually do need the application arguments here. Note that this code path is only for the pyspark shell, and in `bin/pyspark` we only handle the application arguments for the python file case.