Comment by mjlm

I think this persistent state is one of the main advantages of the notebook environment, or the Matlab workspace, which I guess it was inspired by. It allows you to quickly try alternative values for certain variables without having to re-calculate everything. Saving snapshots would not be feasible if the project contains large amounts of data. If you want to reset everything, just "run all" from the beginning, or use a conventional IDE with a debugger.