#1 Improve code layout to be more C++.

[Jason McGuiness]

Try to reduce the amount of global variables and increase the use of polymorphism, class heirarchies, etc to improve the code layout. Create classes from typedefs and sets of functions that operate on the type introduced by the typedefs.

[Jason McGuiness]

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Also make greater use of the STL for more simple coding paradigms and style.