Getting rid of legacy `history` field in database entries.

This field does nothing useful and only creates useless commit differences
on github.  Its removal lets the database be cleaner.
For kinetics databases, write reference and referenceType fields only if not None.
Merge pull request #197 from connie/universalDatabase

Universal database progress.
Looks good to me, and I merged the RMG-database commit too.
(And after all that effort that went into preserving the history entries and detecting changes....)