Fix for #20160719-1B69F57

These after clone methods in transformed resources are being too clever and behave very badly when the transformation itself is cloned.

The suggested approach is to stop initializing int index & reference when cloning transformed resources ("transformation lines"). This behavior is kept when adding new transformed resource. This become consistent with what we have, for example, with Sale Order Lines in Sale Orders.

/cc @luke @seb @gabriel @kazuhiko @romain @Nicolas

( see also !148 (closed) for more )