[doxygen] Correct include file paths.

1. Before this PR, the doxygen pages specify the full local path of the header files used to generate the doxygen. Thus, we publish doxygen that has paths like "C:/Users/Kevin X..." or "/home/fitze/...". Now, those parts of the path are omitted.
2. The Doxyfile.in had a hard-coded OpenSim version number in it. Now, I use the version number as it is provided in the root CMakeLists. Ideally, in the future, the version number will be listed in only one place.