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It's pretty bad form to have header files do 'using namespace' directives and pull in a lot of definitions that way. While it isn't too horrible in a private project it's just bad practice. This removes all the `using namespace std;` from the header files and declares the objects with explicit namespaces. For the .cpp files, if there were only a few uses of the namespace, just do the in-place explicit naming. If the cpp file used it in a lot of places, those are a much more common (and expected) place to add those sort of `using` directives. Also removed a couple of long-commented out functions.
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