configInstance is ignored when ChiselMain.apply is called

[sdtwigg]

It seems improper (or, at least, not properly documented) that the configuration object is only constructed when ChiselMain.run is used and not ChiselMain.apply.

The reason in code for this is that the configuration object is only constructed by executeUnwrapped (which is bypassed by ChiselMain.apply). I can see why as the parameters must be injected by the wrapping Module call; however, this was somewhat tricky to figure out.... (Issue #308 being addressed would help with this issue somewhat.)

[sdtwigg]

As an addendum, ChiselMainTest does not have a run method (although it is still possible to test a Parameter-ized Module by using the alternative syntax).