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.