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.
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.
RMG style applied for all java source files.
Replaced all HashMaps with LinkedHashMap. (\bHashMap\b --> LinkedHashMap)
Replaced all HashSets with LinkedHashSet. (\bHashSet\b --> LinkedHashSet)
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.
Added test_all.sh script to scripts folder. It runs all the tests in examples/RMG.
Changed the name of 1,3-hexadine to hexadiene to make it more friendly with scripts
Relaxed the error tolerance to 0.5 in liquid_phase and butane_pruning examples and reduced the reaction time to 10 secs for liquid_phase
Added test_all option in Makefile
Updated documentation to include QMLibrary and KeepQMFiles
Some error messages are converted to warnings.

ERROR: Could not find a polycyclic ring strain correction.  --> warning
ERROR: Thermochemistry of polycyclic species does not contain
corrections for thepolyclic ring system. It is advised to review the
thermochemistry data of this species. --> warning
ERROR: Error in database --> warning
make.bat update

Added  checks for the executables.
Updating documentation for new restart feature

Documentation now has details how the new restartConditionFile
can be used for restarting a RMG job.
Modified Makefile and test_all.sh for a better output.
Modified test_all.sh to show CRITICAL errors as well.
Merge remote-tracking branch 'murat/retouch'

Conflicts:
	source/RMG/jing/rxnSys/ReactionModelGenerator.java
Merge remote-tracking branch 'murat/retouch'
Added diethylsulfide example.

This is intended to be a simple example of an RMG job that involves sulfur.
It was adapted from one of Caleb's diethylsulfide desulfurization in
supercritical water jobs. It should run in ~1-2 minutes on a reasonably modern
computer.