Use CustomFileEmission for ChiselCircuitAnnotation

Removes the explicit chisel3.phases.Emitter and instead does emission
with a CustomFileEmission mixin to ChiselCircuitAnnotation. This then
prevents the need for passing around DeletedAnnotations. As a
consequence, I removed an unnecessary run of a second Converter in the
Driver.

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