Fix cycle test problem (#157)

* Updating to keep up with Direction mega PR
Fix several classes to use ActualDirection/DataMirror.directionOf API
Fixed up Flip and UInt literal api references in several tests

* Fix problem with --no-check-comb-loops and verilator
annotation was not being passed down
requires [Firrtl PR #619](https://github.com/freechipsproject/firrtl/pull/619) to be merged