Make doxygen build always available via 'make docs'

Previously, doxygen builds had to be enabled via cmake option and were
only built once per complete project build (requiring us to do a
complete project rebuild every time we wanted to refresh documentation).
This change was made to improve the workflow involved with previewing
documentation.
Doxyfile.in: Update input list

* Remove TODO.md & add third-party/README.md
Fix several doxygen warnings