Add session file entries for implied options. Needs some testing before merging.

The Markov stuff is not 100% foolproof (if you change the john.conf Statsfile entry you are still screwed when resuming) but that goes for incremental as well (even in core).

I'm not particularly happy with this code in terms of "beauty" but it should do what's needed.

Is there any more implied options we need to save? I deliberately do not save platform/device for GPU formats.