Fix/508 for code review

I have a first version of the code. I've made a new base class for khmer exceptions that derives from std::exception. 

A couple of things, though: 
- I think the exceptions defined in ``khmer.hh`` should be moved to the new file ``khmer_exceptions.hh``.
- when grepping the cc files for ``std::exception``,  a few functions throw ``std::exception``'s instead of khmer derived exceptions. I think this should be changed in most cases.
Includes should all be at the top together