Documentation is generated with JsDoc (http://usejsdoc.org/index.html)

**** Configure it to read lib files ****
In conf.json, set source.includePattern as ".+\\.(js|lib|jsdoc)?$"

**** Generate documentation ****
To generate the documentation of the API:
jsdoc -d <doc_destination> <js_files...>
Example:
jsdoc -d .\doc\API .\API.js .\API.Map.js


**** Run JsDoc from Eclipse ****
You can run jsdoc_toolkit from within eclipse or Aptana by setting up Run -> External Tools -> Open External Tools Dialog...

Location
C:\DirectoryToWhereJavaIsLocated\Java\jre1.6.0_07\bin\java.exe

Working Directory
C:\DirectoryToWhereJsDocToolkitIsLocated\jsdoc-toolkit

Arguments
-jar jsrun.jar app\run.js "C:\PathToSourceFiles" -t=templates\jsdoc -d="C:\PathToOutputDirectory"

Note: You need to enclose the paths in quotes if they contain spaces (at least on windows)