RMG style applied for all java source files.
Replaced all HashMaps with LinkedHashMap. (\bHashMap\b --> LinkedHashMap)
Replaced all HashSets with LinkedHashSet. (\bHashSet\b --> LinkedHashSet)
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.
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.
Fixed the bug about Final_Model generation, and update test_all.sh and Makefile
There is still a problem if QM environment is not set up properly when RMG tried to delete qmFoler
Merge remote-tracking branch 'nathan/master'
In ThermoDataEstimator, don't require other QM lines when using BensonOnly.

When using the BensonOnly option for estimating thermo, the other lines are
meaningless. After this commit, you should not specify those lines if using
the BensonOnly method. Note that, in some of the other main scripts, all of
these lines are optional, but in the current ThermoDataEstimator, you must
at least specify BensonOnly.
Only check for RDBASE environment variable when it is needed.

Previously this variable would be checked when the QMTP class was
instantiated. Since it follows the singleton pattern, this instantiation
always occurs, even for BensonOnly jobs. Since we don't need RDBASE in
this case, it is better to perform the check at the point of use of that
environment variable instead.

This also eliminates the appearance of the RDBASE warning when running
regular RMG jobs using BensonOnly for thermo estimation.

Closes #282.
Minor edit to ThermoDataEstimator documentation to reflect QMflag requirements.
Fixed double writing of species' concentrations for restart condition file.
Added diethylsulfide job to the rmg examples test script.
Additional fix for commit 01dc91f7 for ThermoDataEstimator documentation.