Change firrtl.options API, add Phase

This breaks firrtl.options.Stage into a small type hierarchy:

  * Phase: something that transforms an AnnotationSeq
  * Stage extends Phase: a Phase with a Command Line Interface

Some of the old "common options" (input annotation file and target
directory) are moved into firrtl.options and provided as part of the Stage
class. Stage will automatically preprocess an input annotation sequence to
resolve all input annotation files and add a default target directory.

Minor changes:

  * Adds ViewException
  * Stops mixing in the DoNotTerminateOnExit trait into the default Shell
    parser
  * Add StageOptionsView

Signed-off-by: Schuyler Eldridge <schuyler.eldridge@ibm.com>