[Restructure] NifSkope pro/pri function improvements
[Restructure] Doxygen improvements
[Restructure] Move Doxyfile.in
[Restructure] Remove outdated doxygen .sh/.bat

doxytag is obsolete and doesn't work on the Qt5 docs anyway (I tried).
For the actual doxygen .sh/.bat, the Makefile generated by qmake has a
build target for running doxygen:  `jom release-docs` or `make
release-docs` (or nmake/mingw32-make)