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First major pass over target_link_libraries.
This fixes the majority of #383. In order to do so, I began to reorder some of the include directives as specified in #788 to facillitate easier inspection of the dependencies. The work is not complete at all. Further, I broke several dependencies where trivially possible by changing uses of derived classes to base classes and moving virtual function definitions into source files from headers. The diff is unpleasant, I know :(
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