Add and modify calls for generateTransportData()

- move call for seed species from initialize() to
addSeedMechanismToCore()
- call getTransportData() for reactions found in reaction libraries in
addReactionLibraryToEdge()
Store PDep networks in List *and* Dictionary.

This means we can use the list when we want them to be in the same order,
and use the dictionary when we want to look them up (quickly) by source.

Perhaps an "ordered dictionary" class would be better, rather than us having
to maintain two things (it'd be easy to not delete from or add to one of these
stores at some point, especially when pruning)….

This addresses #176
Change TransportData __repr__ function and fix pdep/network#_#.py files.

@enochd pointed out in a comment to commit
8a6d32441007649807e3137ba7da0e6c2dab9f6d
that RMG-py was creating cantherm/measure input files
(eg. pdep/network23_1.py) that were malformed.

This should fix it, I hope.