Remove hardcoding of max reactant/product numbers from JDAS.

Everybody ought to use Structure.MAX_REACTANT_NUMBER and
Structure.MAX_PRODUCT_NUMBER as much as possible. This is only a small step
toward making it easier to change the maximum reactant and product numbers.
Increment maximum product count from 3 to 4 in RMG.

This allows us to handle more non-elementary reactions in seed mechanisms
and reaction libraries. Whether we ought to be using such reactions is
another matter, but at least we now have the capability.
Updated DASSL to handle up to four products in reactions.

The reaction arrays for regular, third body, Lindemann, and Troe reactions
needed to be updated to include another element for the new product. (Aside:
why aren't these arrays two-dimensional?)

DASPK has not yet been updated, since it would be even more involved, and
I'm not set up to test it at the moment. However, the sorts of changes made
here should be similar to changes that would be needed there.

Note that the maximum number of reactants and products is still hardcoded in
many places.
Updated DASPK to handle up to four products in reactions.

The changes mirror those recently made to DASSL, although these have not yet
been tested. Also, there is way too much duplicate code in both our DASSL
and DASPK implementations.
Added global Initialize System Property

This function was not updated with Richard's changes
to specify working and scratch directories. Updated
function to call global.InitializeSystemProperties()
Merge branch 'master' of github.com:GreenGroup/RMG-Java
Added some release notes and documentation for 4.0.1 bug-fix release.

Download links, templates, settings file, etc. etc. have not been updated.
Updated comments in RMG example batch scripts to reflect latest release version.
Added RMG example bash script files for linux users.