Allow calculation of fluxes even when there are initial assignments

[luciansmith]

As discovered by @janisshin , roadrunner fails to calculate control coefficients in models with initial assignments:

import tellurium as te
import roadrunner
r = te.loada("""
   $Xo -> S1; k1*Xo - k2*S1
     S1 ->; k3*S1
     Xo = 5; k1 =0.45; k2 = 0.23; k3 = 0.6
     V1 = 2.3
     S1 = 5.6/V1
""")
r.steadyState()
print (r.getScaledFluxControlCoefficientMatrix())

yields:

RuntimeError: Could not set value for S1, as it is defined by an initial assignment rule and can not be set independently., at ?setValues@LLVMExecutableModel@rrllvm@@AEAAHP6A_NPEAULLVMModelData@2@HN@ZP812@EAA?AV?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@std@@_K@Z2PEBHPEBN_N@Z

If I recall correctly, we're using the initial state of the model as a sort of 'scratch pad' to perform these calculations, but this doesn't work when there's an initial assignment rule. Need to either find a better scratch pad, or a way around the restriction.