Regenerated doxygen docs.
The actual update of the dox,
Reworked way doxygen input is scanned. REmoved about a hundred doxygen warning but then included enough files in the documentation generation process to moved the total warning count to around 3000. for reference almost 1200 of those warnings are the UI system which Mako is still refactoring.
A few minor readabilty enhancements to the documentation.