R2S module

This PR implements a rigorous 2-step activation workflow for Cartesian mesh. I will add tet mesh capability soon, and perhaps a CLI, but this PR was getting pretty big as is. 

This is basically a big wrapper around everything I have done in the past 2 months.The gist is a user supplies an MCNP meshtal file, a DAGMC loadable geometry, and some ALARA input parameters and ```irradiation_setup``` generates all the necessary input files to perform an irradiation problem in ALARA. Then ```photon_sampling_setup``` can be used to tag ALARA photon source density output to a ```Mesh``` object for mesh-based photon source sampling (also to be implemented).

I had to clean a few things up in ```mesh```, ```alara```, and ```material``` to get things working, which I will elaborate on in-line. This also closes #373.