Change numbering the frames when restarting run

In the current setting, when a run is restarted by giving the solution initializer a frame
number instead of a Domain and State objects, the controller will start counting frames from zero (which might override previous frames if the input and output are in the same directory). 

In this pull request, I changed that to make the controller counts from the frame number till the number of output frames as a default behavior. The user can use the flag `count_from_zero` to change the default behavior.

I'd like to get your opinions if you thought of alternative settings that might be more reasonable..