doc: update Doxyfile template to one from newer version

doc: update Doxyfile template to one from newer version

We want to use the USE_MDFILE_AS_MAINPAGE option which was introduced in
doxygen 1.8.3 (released 2012-12).

Right now the new options are commented, otherwise older doxygen spews
these these warnings, which can be ignored:

warning: ignoring unsupported tag `USE_MDFILE_AS_MAINPAGE =' at line 794, file doc/Doxyfile
warning: ignoring unsupported tag `MATHJAX_FORMAT         =' at line 1210, file doc/Doxyfile
warning: ignoring unsupported tag `EXTERNAL_SEARCH        =' at line 1257, file doc/Doxyfile
warning: ignoring unsupported tag `SEARCHENGINE_URL       =' at line 1265, file doc/Doxyfile
warning: ignoring unsupported tag `SEARCHDATA_FILE        =' at line 1271, file doc/Doxyfile
warning: ignoring unsupported tag `EXTERNAL_SEARCH_ID     =' at line 1278, file doc/Doxyfile
warning: ignoring unsupported tag `EXTRA_SEARCH_MAPPINGS  =' at line 1287, file doc/Doxyfile

Signed-off-by: Ran Benita <ran234@gmail.com>