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Clean up the INPUT paths for doxygen scanning:

- directory scans include sub-directories so no need
  to include them explicitly
- remove excluded (legacy) includes that no longer exist

Sync directory changes in the CMakeLists.txt (as noted in the comments)

Add content to the home page of the doxygen-generated HTML, and add a
Zephyr branding theme.
Signed-off-by: David B. Kinder <david.b.kinder@intel.com>

Fixes: #6773