doc: rename doxygen configuration file and build from doc/

Rename file to zephyr.doxyfile to allow integration in eclipse and make
it build locally in the doc/ directory without have to change to ../
first.

Change-Id: Ib2c4c26f385b050ea3d0e814ebfc3509f31e5e12
Signed-off-by: Anas Nashif <anas.nashif@intel.com>