Natural Docs 0.9 now includes the ability to generate indexes automatically.  You can add an index of everything, as well as indexes of just classes, functions, and files.  As with the source files, the indexes are only updated when they have to be, and you get prototype tooltips on every link to a function or variable with a prototype.  Take a look.

The other important change is a bug squashed.  The first line of a comment could be ignored in certain situations when stringing single line comments together.  If this line was the topic line, this could cause the topic to not appear in the documentation.  Now fixed.