Make {Stage, FirrtlStage}.run protected (#1926)

* Make Stage.run protected

Change the access modifier of Stage.run from no modifier to protected.
This method is really an internal API that the user implements with
the main entry point for a Stage being "execute" or "transform". By
allowing users to access "run" they can bypass checks, mandatory file
reads/writes, and wrappers.

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

* Make FirrtlStage.run protected

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