cloneTypeFull and ClonePorts does not work as well as we need it to to recursively set

specifiedDirection that have been "fixed up" for assigning leaves to Input/Output
that have Unspecified/Flipped directions.
Explicitly fix them up when making a module clone.

Should probably investigate whether it is in general a problem that cloneTypeFull
does not recursively set specifiedDirection, only at the top level.

Add comment to module about why this is necessary