Do we need the user to set the autotroph silicifier flag?

[mnlevy1981]

One alternative would be to replace all if (silicifier) statements with if (kSiO3 > 0). This would also affect the python logic for parsing the diagnostics JSON file, since there are some blocks in the YAML like

((autotroph_sname))_SiO3_lim_surf :
   dependencies :
      ((autotroph_silicifier)) : true
   longname : ((autotroph_lname)) SiO3 Limitation, Surface
   units : 1
   vertical_grid : none
   frequency : medium
   operator : average

And the python code that determines ((autotroph_silicifier)) will need to be updated.

(This offers a different solution to part of #278 -- we would definitely not want to base the logical checks on the diagnostic indices, but perhaps some logical checks should be based on the value of r8 settings rather than logical settings)

At the very least, we should ensure that silicifier .eqv. (kSiO3 > 0) in marbl_settings_consistency_check()