also edit the doxyfiles for the dot tool path

for consistency with other interface classes

    t = re.sub(r'(\W)(Simulation)(\W)', r'\1I\2\3', t)
    t = re.sub(r'(/)I(Simulation)', r'\1\2', t)

(to simplify; 2 flavors are enough)

- Documentation can now be built by command 'make doxyuser'
- configured doxy files now in build/doxygen (no longer under version
  control)
- html output now under html/build

This resolves issue http://apps.jcns.fz-juelich.de/redmine/issues/2385