Fix CloneModuleAsRecord support for .toTarget (backport #1974) (#1985)

* Fix CloneModuleAsRecord support for .toTarget

(cherry picked from commit d3e13ce2)

# Conflicts:
#	core/src/main/scala/chisel3/Module.scala
#	core/src/main/scala/chisel3/RawModule.scala
#	core/src/main/scala/chisel3/internal/Builder.scala
#	core/src/main/scala/chisel3/internal/firrtl/Converter.scala

* Set refs for ModuleClone and ClonePorts in less hacky way

(cherry picked from commit b87107ad

)

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

* Fixup for backport

* Resolve merge conflicts
* Fix semantic meaning change of Module -> MultiIOModule on master
* Waive bincompat errors that cannot impact Scala users

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