[SPARK-2423] Clean up SparkSubmit for readability

It is currently non-trivial to trace through how different combinations of cluster managers (e.g. yarn) and deploy modes (e.g. cluster) are processed in SparkSubmit. Moving forward, it will be easier to extend SparkSubmit if we first re-organize the code by grouping related logic together.

This is a precursor to fixing standalone-cluster mode, which is currently broken (SPARK-2260).

Author: Andrew Or <andrewor14@gmail.com>

Closes #1349 from andrewor14/submit-cleanup and squashes the following commits:

8f99200 [Andrew Or] script -> program (minor)
30f2e65 [Andrew Or] Merge branch 'master' of github.com:apache/spark into submit-cleanup
fe484a1 [Andrew Or] Move deploy mode checks after yarn code
7167824 [Andrew Or] Re-order config options and update comments
0b01ff8 [Andrew Or] Clean up SparkSubmit for readability