Adding subtree 'R5-SD-DD' in 'R5-SD' group to fix degeneracy calculation error, RMG-Py issue#69!
Add Cdd atom type to *3 in Intra-R-Add-Endocyclic reaction family.

Some of these have been added already in recent commits.
Now, we went through systematically and added them all.
Removed a node we recently added.
Added some comments to the longDesc fields.
Jobs crashed with this error message:
"ValueError: invalid literal for int() with base 10"
Fixing the error with deleting spaces in the braces.
Merge remote-tracking branch 'fariba/master' to fix Intra_R_Add_Endocyclic

This hopefully fixes all the remaining bugs in Intra_R_Add_Endocyclic
that were due to Cdd atom types being excluded from the list of
carbons with double bonds (Remember Cd means C with only one double bond.)

We also added some comments to the longDesc fields to help explain the tree.