Manual merge of nitrogen changes for Intra_R_Add_Endocyclic family.

Retain Fariba's Cdd addition changes.  Add N to top nodes.  (now they
are also in L3 nodes.)  Keep Aaron's higher number starred atoms.  Retain
Aaron's removal of R5_allenic groups.
Manual merge of changes to Intra_R_Add_Exocyclic family.

Added nitrogen to top nodes (Beat's changes).  Expanded groups to Cdd (Fariba's changes).
Retain Aaron's additional starred atoms.
Manual merge of Oa_R_recombination family

Added Beat's addition of O related forbidden groups.
Manual merge of nitrogen changes for R_Recombination family.
Manual merge of nitrogen changes to Substitution_O family.
Manual merge of nitrogen changes to intra_OH_migration family.
Manual merge of nitrogen changes for Cyclic_Ether_Formation Family.

From Java- cyclic ether formation family was completely restructured.
Retained Beat's nitrogen allowance for top nodes, added them also
for new RNOOJ groups.  Added new nitrogen groups.