add an option to not export modified models in scoring modules

[mgiulini]

scoring modules can add modifications to the models to be scored. When using multiple scoring modules, users may want to apply the scoring to the input/refined models and not to those produced by the previous scoring modules.

As an example, the mdscoring module can produce substantial fluctuations at the interface, and users that want to run emscoring after it may like to score directly the input ensemble rather than the mdscored one.