Save an annotated chemkin file in addition to clean chemkin files during rmg job.

Comments for some reactions are way too long and sometimes cause problems when
used in CHEMKIN, in addition to making files way too large. Now there a
`chem_annotated.inp` file is saved in addition to clean  `chem.inp` files.

Also added group addivity comments to the species thermo in output chemkin file
and prettified some formatting.