Add `output:flush_frequency` for `OptionsNetCDF`

[ZedThree]

Sort of fixes #2878

Two things:

• output:flush_frequency can be used to reduce how often netCDF data is flushed to disk (maybe flush_period is a more accurate name?)
• the Options used to store data to be written to disk is now reset after writing

These two together can significantly cut the time spent in IO:

(absolute time from the io timer for conduction example for 500 timesteps, rolling average over 100 steps)

The red line is basically current next

I'm a bit concerned that we still get an increase over time, but this seems to unavoidable.

This PR also includes some drive-by fixes for some minor OptionsIO issues.