And ember-cli addon used by https://github.com/trek/ember-api to preprocesses the JSON data emitted by YUIDoc, which is fairly tightly coupled to their page generation needs.
This takes a YUIDoc data JSON object and emits an directory/file structure like this:
// Containing a list of all classes, namespaces, and modules by name property.
index.json
// for every class/namespace:
KlassName.json
KlassName/
index.json
methods.json
properties.json
events.json
// for every module
modules/
module-name.json
other-module-name.json
This can then be read by a web application later.
Ideally some day we'd write a pluggable markdown-based documentation tool that only emits a sensible JSON structure and leave file generation up to the consumer (i.e. does on thing well).