Clean up of the Doxygen documentation

Modified the Doxyfile to properly document the inline functions at the core of the algorithm. Also corrected some typos in the documentation of functions that were mentioned in #15 (closed).

The doxygen documentation can now be built cleanly.

The changelog is massive due to the update of the Doxyfile to 1.8.x from 1.6.x. All the changes to the source files are in commented sections.