Updated comments in RMG example batch scripts to reflect latest release version.
Added RMG example bash script files for linux users.
Changes to documentation and web source to reflect v4.0.1 upgrade.
Adding rate rules for olefin + HO2 radical addition

Reference:
Rate rules, Branching Ratios, and Pressure Dependence of the HO2+Olefin Addition Channels
http://pubs.acs.org/doi/abs/10.1021/jp405262r
Paper uses CBS-QB3 energy w/1D-HR calculations, refer to Table 2 for the rules.
Adding rate rules for ROO = olefin + HO2

Reference:
High pressure rate rulesfor Alkuly+O2 reactions: 1
http://pubs.acs.org/doi/pdf/10.1021/jp2079204

Refer to Table 4 for rate rules
uses CBS-QB3 w/1D-HR calculations, since the sumathy
rates and rates calculated by stephanie villano are
using the same method for energy and hindered rotors
they have the same rank for now.
Fixed typo in the rate rules

Typo in rate rules for HO2 elimination from peroxy
Fixed incorrect definition for group "OJ" instead of having duplicate of "OsJ".
Adding rate rules for intra-H migration for alkoxy radicals

These rules are made from the butoxy and hydroxybutyl system calculated at
RQCISD(T)/CBS//B3LYP/6-311++G(d,p) level.

Ref Ab Initio Kinetics for the Decomposition of Hydroxybutyl and
Butoxy Radicals of n-Butanol.
by: Zhang P.,Klippenstein S.K.,Law C.K.
dx.doi.org/10.1021/jp400155z | J. Phys. Chem. A 2013, 117, 1890-1906

Note some of rate rules were given as sum of two Arrhenius,they were
refitted to single Arrhenius
Adding rate rules for Beta-scission of alkoxy radicals

These rules are made by reversing the rules from the butoxy and
hydroxybutyl system calculated at RQCISD(T)/CBS//B3LYP/6-311++G(d,p) level.
The thermochemistry used comes from n-butanol mechanism
dx.doi.org/10.1016/j.combustflame.2010.06.002.

Ref Ab Initio Kinetics for the Decomposition of Hydroxybutyl and
Butoxy Radicals of n-Butanol.
by: Zhang P.,Klippenstein S.K.,Law C.K.
dx.doi.org/10.1021/jp400155z | J. Phys. Chem. A 2013, 117, 1890-1906

Note: some of rate rules were given as sum of two Arrhenius,they were
refitted to single Arrhenius
Merge branch 'master' of github.com:GreenGroup/RMG-Java
Adding rate rules for water addition to alkene (reverse of dehydration)

These rate rules are reverse of pri-, sec- and tert- alcohol dehydration
rate. The thermochemistry used to reverse the rate coefficients comes from
butanol mechanism dx.doi.org/10.1016/j.combustflame.2010.06.002

The dehydration rates were measured at NIST using a single pulse shocktube.
Fixed typo in rate rule

Made a typo in earlier commit for this family
Understand that multiplicity of '{2S,2T}' is equivalent to '2'.

This is when reading adjacency lists, and makes it more compatible with RMG-Py.
However, I think I'm about to make the database exporter export it as '2' anyway,
so this may not be necessary.
This is a belt-and-braces approach to solve @GreenGroup/RMG-database#18
Understand thermo trees that start at level L1 instead of L0.

I am not sure why the thermo trees used to start with L0
whereas the kinetics trees all begin with L1. In RMG-Py they
all begin at L1, which made exported things incompatible.
Now we try L0, if that fails try L1, and if that fails throw 
an exception.