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…

doc_src/alias.txt

@@ -23,11 +23,9 @@ The following code will create `rmi`, which runs `rm` with additional arguments
 
 \fish
 alias rmi "rm -i"
-\endfish
 
-This is equivalent to entering the following function:
+# This is equivalent to entering the following function:
 
-\fish
 function rmi
     rm -i $argv
 end