Extra Additions to CMFD

This PR should be merged into develop after PR #314. This PR adds:
- tally resetting now performed with sets and thus can be performed after any batch
- D_hat resetting and fix neutron balance options set from cmfd.xml
- Updated user's guide documentation
Add *iterations*

Also, should we combine atoli and rtoli into one option? Maybe a `gauss_seidel_tolerance` which takes two numbers specifying the absolute and relative tolerance? Just a thought...