Fix compiler errors due to firrtl emitter api changes (#125)

* Reworked the VerilatorCppHarnessCompiler stuff.  It seemed to be unnecessarily using Transforms to do a simple template substitution.
chiselMain had it's own hooks into the above.  Cleaned this up as much as I dared
Fix deprecated code
Reg(init -> RegInit(
log2Up -> Log2Ceil
Fixed up style (I needed this to debug this mess)

* Got rid of chisel2 Module references

* Incorporate Angie's Bundle -> Record changes for PeekPokeTesterUtils