Updated OCOO rule in HO2_Elimination_from_PeroxyRadical family.

The old rule was an estimate made by MRH made by generalization of a rule
for CH3CHO + HO2 = HOCH[OO]CH3. The new rule is from a paper by Hermans et
al. (2005), and is for CH3COCH3 + HO2 = CH3C(OH)(OO)CH3. The two rules are
actually within an order of magnitude or so anyway, so there's not a big
change here.
Adding rough rate rules for C(R1)(R2)=O + ROO

Earlier RMG is using rules for RO for adding to double
bond. Josh and Shamel think this must be much slower (different)
for ROO species. For now using a very rough estimate for these
reactions based on JWA calculation for Acetone + HO2.
This must be updated with better rules in the future.
Fixed bug with setting keepQM files option.

Also reordered some error messages so that they are printed to
logger.
Updating the restart condition file

Earlier the restart condition file would write in all
the species in the core. This would lead to unintentional
consequence of all species specified in the seed
reacting with each other and generating all possible reactions
(i.e restarting with GenerateReactions = on for all seeds).
The restart condition file now skips over the species specified
in the seed as they will be added in when the model is
initiated again in RMG.
Merge remote-tracking branch 'josh/master'
Fix initialization problem with InchifyCHEMKINusingDictionary class.

I don't know what InchifyCHEMKINusingDictionary does, but apparently it has stopped
working because of the new working directory environment variable system.

I have replaced the startup lines with a call to the universal
   RMG.globalInitializeSystemProperties(); 
which all the other utilities use to set up their system properties.
Hopefully this addresses issue #282.
Merge remote-tracking branch 'shamel/master'
Include QOOR in cyclic ether formation reactions.
Remove references to FileNotFoundException from ReactionModelGenerator.

Every occurrence was in a catch block that was immediately followed by another
catch block for IOException, with both blocks containing exactly the same code
(usually Logger.logStackTrace()). Since FileNotFoundException is a child of
IOException, this code is redundant. (A few instances were causing warnings to
appear during compilation, which motivated this change.)
Finish removing R2OOR_cyclic from new Cyclic_ether_formation family.

The new family is defined by QOOR -> cyclic_ether + OR. Previously @ajalan
had commented out the R2OOR_cyclic group from the dictionary, but left
references to it in the RnOOR top-level node, tree, and rate library. This
commit removes those references so that RMG can run again.
Some restructuring of the Cyclic_ether_formation tree.

The new tree makes R2OOH, R3OOH, etc. and R2OOR, R3OOR, etc. mutual siblings.
The motivation for this is that the previous definition of the tree made
when trying to allow for OR leaving groups in cyclic ether formation caused
a change in how the kinetics were estimated for the original OH leaving
groups. The particular reaction I noticed this for was

C(COO)(C)C(=O)[C](C)C -> C(CO1)(C)C(=O)C1(C)C + [OH]

For the above reaction the new kinetics averaging scheme is almost certainly
worse, as it now averages over R2OOH, R3OOH, and R4OOH ring sizes rather
than over the other functional group.

Probably we need to look more at why the previous change to the tree changed
the way the kinetics are estimated as well, but that is probably a
significant undertaking.