Commiting some changes to disproportionation reactions (mainly with O2) and H_Abstraction reactions (for alcohols) before pulling from master

Conflicts:

	databases/RMG_database/kinetics_groups/Disproportionation/rateLibrary.txt
	databases/RMG_database/kinetics_groups/H_Abstraction/tree.txt
Changed the addition of H to a primary double bond
Modfying disproportionation rates for Allyl + rad reactions

This just a estimate, Tsang estimates seem too fast.
Adding a barrier of 6 kcal/mol
Add info on default gfortran-4.6 issue of Ubuntu-12.04 in documentation
Fixing missing thermo comments

Because we made a copy of the chemgraph to get the thermo and
were calling the comments from this new graph, there were cases - when the
molecule was not aromatic it would return an empty string.

We now only call the comments from the thermo_graph if the species is aromatic and not present in a thermo library.

Sigh another Sunday (10:00 pm) bug fix!
Merge branch 'master' of https://github.com/GreenGroup/RMG-Java
Made small changes to the thermolibraries.
a) Modified the Cd-(Cd)(Cd) thermo group which appears to be 7 kcal/mol too low
b) Added a HBI for indenyl
c) Added ring correction