New estimates from GA method for Intra_R_Add_Endocyclic family.  Partial mirror of https://github.com/GreenGroup/RMG-Java/commit/baa353ec98ca193d608efe4528b134e3a144f3d2

Older method had problems with endo addition to conjugated
double/triple bonds as those were estimated from the exo-additions

The problem was that exo addition to conjugated bonds is faster
while a slowing effect is observed for endo.
The new Intra_R_Add_Endocyclic tree. Mirror of https://github.com/GreenGroup/RMG-Java/commit/3a7508818babf256aaef7de8be7e13ff157a822d

Reorganized the tree in order to allow the calculated values to get
priority level 5. I also added some estimates and calculated values
to block strained reactions.

Additional notes:  Had to make some of the groups more general to adapt to
RMG-Py's nitrogen inclusive nodes.  Also removed deprecated groups
so that the travis unit tests would pass.
Updates from RMG-Java for Intra_R_Add_Exocyclic family.  Now up to date with https://github.com/GreenGroup/RMG-Java/commit/bea900d9ee5d3a8a82baa3a4f9b8bd9472ee5217

A lot of new estimates from the GA method.  https://github.com/GreenGroup/RMG-Java/commit/baa353ec98ca193d608efe4528b134e3a144f3d2
older method had problems with endo addition to conjugated double/triple bonds as those were estimated from the exo-additions
The problem was that exo addition to conjugated bonds is faster while a slowing effect is observed for endo.

Added rate coefficients for the intramolecular exocyclic addition R6_SMS_D
https://github.com/GreenGroup/RMG-Java/commit/9e1669fa2525f192cac5b42898c43160d6f24436

Restructuring of tree. https://github.com/GreenGroup/RMG-Java/commit/bea900d9ee5d3a8a82baa3a4f9b8bd9472ee5217
in order to allow the tree to be filled up by estimates.
I added some estimates and calculated values to block some steric hindered reactions.
Fixes to groups in R_Addition_Multiple_Bond.  Mirror of https://github.com/GreenGroup/RMG-Java/commit/693c071e1f75e9fdda6bd38ab0cbd28e5011bbb6
and https://github.com/GreenGroup/RMG-Java/commit/45228e890af38dc3e3fbf8dc85cb5490e91f8eec

The ligands renamed to Ct and bonds were changed from double to triple.

SJ was made to be more general.