Add unit tests and fix for #2794 , add unit tests for #2773 (backport #2792) (#2834)

* Fixup and unit tests for D/I of IOs without explicit Input/Output (#2792)

(cherry picked from commit f24a6248

)

# Conflicts:
#	core/src/main/scala/chisel3/Module.scala

* Resolve backport conflicts

Co-authored-by: Megan Wachs <megan@sifive.com>
Co-authored-by: Jack Koenig <koenig@sifive.com>