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Web Application Development - What is Documentation Best Practices

I am building a web based learning application using HTML, PHP, jQuery and MySQL. As my application gets bigger and has more and more interactions, I'm starting to get confused and messy. So, I would like to know what are the best methods for documenting a web application: methodologies, software, etc.

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Use strict PHPDoc blocks in all of your classes and methods, and then use Reflection to create documentation on the fly.

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