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.
Instrument tube, not guide tube. This is nitpicky, sorry!