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JsDoc - Open Source toolkit for JavaScript Documentation

JsDoc,  this is a very nice and well documented Open Source Toolkit for Javascript documentation. This supports all javascript frame work(including YUI). 

So this will be a good solution to avoid and make our code very clear and structured way.

Have a look at it:

JsDoc Toolkit is an application, written in JavaScript, for automatically generating template-formatted, multi-page HTML (or XML, JSON, or any other text-based) documentation from commented JavaScript source code.

Based on the project, this was renamed "Jsdoc Toolkit" during development as it grew into more than a simple version upgrade.

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