Updates to input file syntax and small modifications to full core geometry and source files

The modifications in this PR include:
- Modified all input files to be consistent with new OpenMOC input syntax (mainly has to do with setting up CMFD).
- Modified full core geometry model. The asymmetric bundles needed to be rotated and one bundle H-11 was misplaced.
- Cleaned up indentation and organization of source files.
- Added full core input file with domain decomposition.
- Added search for hdf5 cross section files before generating cross sections. The step of generating cross sections takes a long time and is not necessary if the cross sections have already been created.
- Removed unnecessary files.
- Added setup.py file.
- Modified README.
- Changed number of rings in burnable poison pin inner air region from 10 to 3.
Burnable poison, not guide tube. This is nitpicky, sorry! (I'll change this on my own, you don't have to. This is just to remind me)