restart R when bootstrapping or restoring

This adds a restart flag to the restore function which defaults to !dry.run. It's a big ugly as internal uses of restore now need to remember to pass restart = FALSE but I couldn't clearly see another way to get this done. Let me know what you think.
Do we want to pass any arguments down to `restart()`? It might make sense down the line if we want to restart, then execute some code (it would help us avoid the dance with `library.new`, `library.old`)