Remove all Bundle cloneTypes and chiselRuntimeDeprecate its use (#2052)

* Remove all manual cloneTypes and make it chisel runtime deprecated to add one
* runtime deprecate cloneType with runtime reflection
* [Backport this commit] Bundle: add check that override def cloneType still works (will be made an error later)
* Plugin: make it an error to override cloneType and add a test for that
* Docs: can't compile the cloneType anymore
* BundleSpec: comment out failing test I cannot get to fail or ignore

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