Tutorial auto colouring, Man page and Make fixes

Completely fixes #1557 and the underlying Doxygen changes that caused
it. Should make fish docs simpler and more robust, more consistent and
generally prettier.

todo:
- trap unmarked text as arguments in context
- test & fix sed portability - see in particular. (so far tested on BSD
(Mac) and GNU sed).
- test Makefile changes
- last round of aesthetic changes and getting that ascii fish in there…