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Getting this merged in should get us back to making more manageable pull requests.  This has a litany of changes:\r\n\r\n- All changes/bugfixes added pre-refactor have been incorporated.\r\n- More name-mangling done to fit the naming scheme as I came across them.  There is more to do\r\n- All old tests have been added to the tests directory and all bugs discovered fixed. This is **NOT** integrated into the testing framework.  That will be done at a later date\r\n-  A lot of routines were added to the public API that were used by the test programs.  I don't think any new structures were exposed but several constructor/destructor/accessor functions were added to make objects usable outside of the core library.\r\n- Several structs were moved out of the API.  These just had a few references and could be easily converted to ptrs.\r\n- Resolves issue #126 and #127 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