Modifying species constraints checks

Trying to tackle issue https://github.com/GreenGroup/RMG-Py/issues/187.

Add species constraint checks to input species, seed mechs, and rxn libraries (they were only checked in the families prior to this.)  Let the user be able to add input species, seed mechs, or rxn libraries to an allowed list to bypass the constraints if they want to, but otherwise throw an error.

I'm not sure how useful https://github.com/connie/RMG-Py/commit/648e1e38a3594fdc5cc8855ce83d525bc4bd160a is.  I just noticed that we are doing double duty by trying to generateReactions in the seed mechanisms.  Not sure how much time this commit will save.