Global doxygen cleanup and fixes

Current Contiki Doxygen documentation in many places is a collection of loose groupings in non-hierarchical order. The most obvious impact can be studied on the "Modules" page where many modules (some with unreadable titles) are listed in the first level.
Additionaly many more issues are caused by wrong usage of doxygen, copy&paste or inconsistent work.

Beside several local fixes the main goal of this PR is to gain a clean and readable tree structure for Contiki and its users. For those unwilling to run doxygen on this PR themselves, here is a preview of how the documentation would look like (actual appearance depends on Doxygen version ;) ) http://share.ejoerns.de/contiki-doxygen-html/modules.html

Note: It's definetly far from being perfect but maybe this PR can be another step to improve usability of Contiki documentation.