Change name of 'jacobian mode' flag

[luciansmith]

Right now, there's a 'jacobian mode' flag that can be 'true' or 'false'. This is pretty opaque: it turns out that 'true' means 'use concentrations' and 'false' means 'use amounts'. We need to find a way to rename the flag (jacobian_calculations_use_concentrations? Change the values to 'amounts' vs. 'concentrations'?) And be backwards compatible.