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Merge pull request #6 from MikeHeiber/development

Code Cleanup, Documentation, and Testing Update
- updated README with more information about installing and using Ising_OPV and details about the morphology analysis data that is generated
- performed major reorganization of the code and streamlined the API
- updated how users import morphology files or tomogram data so that all options are in the parameter file and not passed as command line arguments
- added Parameters class to handle importing parameters from the parameter file and checking the validity of the parameters
- added Version class to keep track of the current version and compare parameter files and morphology files from different versions
- updated format of output for many of the morphology analysis files to be more consistent
- added API documentation for all public functions and class members
- added tests for all functional features and many cases of users attempting to use invalid parameters or input data
- updated format of the parameter file
- corrected bugs in the calculation of histograms for the morphology analysis
- added and implemented new utility MPI functions to make it easier to gather result values from each processor
- simplified tomogram analysis options and now allow users to specify the mixed phase volume fraction
- updated treatment of imported morphologies; when importing morphologies and then modifying them, the final morphologies will overwrite the morphologies in the current working directory

2325 of 2381 relevant lines covered (97.65%)

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Source Files on job 42.1 (OPTIONS="GCC_VERSION=4.7 && MPI=openmpi && TARGET=test_coverage")