Make smart default for write_fluxes

Make “smart defaults” for write_flux and write_flux_by_mode such that both default to true for nonlinear runs and false for linear runs.

This version to master is a bit hackier than the proper version to next in PR #211, because master uses ruby to generate diagnostics_config. The ruby gets deprecated in the next release, and is replaced by the contents of PR #211.

Fixes #86