Changes conf.py and fine tunes doxygen.config for index & auto-generated files.

Improves previous patch that enabled doxygen GUI for Reference.
Navigate to forto-collab/docs/ html/index.html to view. Not
linked to main docs in this patch. Index changes to show a
collapsed view as default.

Change-Id: I4d0c23699f645c5c20ca3ad50c988a5729afa24f
Signed-off-by: Carol Lee <carol.lee@windriver.com>