Fix missing variable reference in rmgpy.data.kinetics.groups
Always add training reactions to the rate rules, unless explicitly told not to.

Unless the user specifies '!training' in the kineticsDepositories list within
the input file, always add training reactions to rate rules automatically.
Store entry history taken from training reaction when saving to rate rules.

Store the new rate rules directly with the original rate rules.  Not sure what
the previous saving to self.entries did, as when running RMG-Py jobs they would
not pick up the training reactions but instead picked up averaged rates,
see https://github.com/GreenGroup/RMG-Py/issues/150
Clean up kinetics comment for averaged rates.
Save the group objects of the training rate rules so they display on website.

Also save the products of rate rules as empty lists instead of None
to not mess up website.
Indicate the training reaction where the rate rule originated from.
Documentation: added features and credits pages to RMG section.
Documentation: input file creation for RMG-Py.
Added framework for RMG user's guide.
Documentation: Add RMG theory guide.
Documentation: Port over thermochemistry estimation section.
Documentation: Fix email links in main page.
Documentation: Species and group representations.
Documentation: Added notes about molecular oxygen representation.
Documentation: Started example input files page.
Documentation: Fix name for generate reactions.
Updating the documentation for the input file
Merge remote-tracking branch 'shamel/documentation' into documentation
Documentation: Port over model building guidelines.
Documentation: Using and adding training reactions to database.