doc: fixed remaining doxygen warnings in core

Only one warning remains and will be fixed in a separate commit.
doc: exclude more CPU specific stuff from doxygen
SQUASH ME: use patterns instead of single file excludes
doc: fix doxygen warnings for color module

Also fixes the module name in API documentation.
doc: fix ambiguous file name warnings

doxygen does a good job itself, identifying the unique part of the path
to identify a file.
doc: fix naming for Cortex M3 common group
doc: put atmega cpu file into the right group
doc: fix vtimer documentation
doc: rename iot-lab_M3 group name
doc: add names to pca1000x boards
doc: improve doxygen cache size
doc: beautify HTML documentation

* add logo
* add description
* use RIOT specific color scheme
* add search functionality
* remove broken custom header, footer, and style sheet
SQUASH ME: change from green to red
doc: remove more CPU specific documentation