Correcting check for chemkin duplicate while writing output file

While checking for duplicate we also included in our list
the outputReaction list which consist of all librray reactions.

This caused the library reaction already included in the core
to be marked as duplicates and created invalid chemkin file

closes #161
Partially fix transportDataTest unit test (and add another that fails)

Fixed it so the testJoback test works, and then added a species that
makes it fail. It was because of missing R=C=R ring group, but is now
just because we don't know what the correct values should be!
The test could be rewritten to make it just "don't crash on this species"
Report what settings are and where they came from.
Transport unit tests load database from global setting location.