Added missing rate rules for several families.

The rate rules were missing because they came from rules that shared an
index with a later rule in the same family. This was caused mainly by the
sulfur rules, many of which overlap with non-sulfur rules. In the long
term we should give each rule a unique index, but this works for now.
Merge remote-tracking branch 'fariba/master'
Fix to OCOO rule in HO2_Elimination_from_PeroxyRadical.

For some reason this rule was not properly imported from the RMG-Java
database before.
Changed definition of OJ in Substitution_O to allow adjacent biradical.

This avoids an error where the Substitution_O family could only identify
a reaction in one direction (this family is its own reverse, so you
should be able to identify it in both directions).
Imported polycyclic thermo groups from RMG-Java.
Merge branch 'master' of github.com:GreenGroup/RMG-database
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.
Added Polycyclic stuff to output/RMG_database/thermo_groups

I copied these files straight from the RMG-Java database.
Perhaps they should be exported from this RMG-database project 
to make them formatted prettily. Or perhaps something else.
All I know is that without these, the ".loadOld" methods fail.