Don't run FIRRTL in FlattenSpec's ChiselStage (#1493)

Fix a bug in FlattenSpec where ChiselStage was running the FIRRTL
compiler in ChiselStage and then re-running the FIRRTL compiler. This
changes it to be like InlineSpec and to not run FIRRTL during
ChiselStage.

This was manually backported to 3.3.x.

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