This patch refactors the commands that use the mitchellh/cli library to
populate the command line flag set in both the Run() and the Help()
method. Earlier versions of the mitchellh/cli library relied on the
Run() method to populuate the flagset for generating the usage screen.
This has changed in later versions and was previously solved with a
small monkey patch to the library to restore the old behavior.
However, this makes upgrading the library difficult since the patch has
to be restored every time.
This patch addresses this by moving the command line flags into an
initFlags() method where appropriate and also moving all variables for
the flags from the Run() method into the command itself.
Fixes#3536
Frank Schroeder