conserve internalized substrates on transform

[drbergman]

much like we chose to preserve volume on transform (#284) we should at least consider preserving internalized substrates on transform. within Cell::convert_to_cell_definition we could go with something like the following lines (specifically those reference Molecular)

void Cell::convert_to_cell_definition( Cell_Definition& cd )
{	
	Volume cell_volume = phenotype.volume;
	Geometry cell_geometry = phenotype.geometry;
	Molecular cell_molecular = phenotype.molecular;

	// use the cell defaults; 
	type = cd.type; 
	type_name = cd.name; 
	
	custom_data = cd.custom_data; // this is kinda risky since users may want to be updating custom_data throughout
	parameters = cd.parameters; 
	functions = cd.functions; 
	
	phenotype = cd.phenotype; 
	phenotype.volume = cell_volume; // leave the cell volume alone..
	// ..except for the following target values
	// phenotype.volume.target_solid_cytoplasmic = cd.phenotype.volume.target_solid_cytoplasmic; // gets set by standard_volume_update_function anyways
	phenotype.volume.target_solid_nuclear = cd.phenotype.volume.target_solid_nuclear;
	phenotype.volume.target_fluid_fraction = cd.phenotype.volume.target_fluid_fraction;
	phenotype.volume.target_cytoplasmic_to_nuclear_ratio = cd.phenotype.volume.target_cytoplasmic_to_nuclear_ratio;
	phenotype.volume.relative_rupture_volume = cd.phenotype.volume.relative_rupture_volume;
	
	phenotype.geometry = cell_geometry; // leave the geometry alone

	phenotype.molecular.internalized_total_substrates = cell_molecular.internalized_total_substrates;
	...