CMake-ize documentum generation
Doxygen documentation was waaay out of date and it was still using the
old make system. updated:
 * documentation is generated via cmake i.e. `make doc`
 * outdated doxygen descriptions are removed
 * since doxygen 1.8.0 markdown is supported, i have added some of the markdown documentation to doxygen
 * changed some of the markdown documentations' style to standard markdown from GFM since only standard
  markdown is supported by doxygen
 * fixed some minor errors in the documentation