* allow doxygen to process applications/**.H
 * use @cond/@endcond to suppress documenting classes/variables in applications/

 - allows some access from applications to libraries
 - connection between application and local includes is still a bit weak,
   but is possible via the dirs.html navigation.

  * skip doxygen docs for local variables (treeBoundBox)
  * filter transforms 'Typedef' -> @typedef
  * added tools/find-retagged
  * manually changed some InClass tags to Typedef - still needs more attention