Application Documentation

I am looking for a document that is a good example on documenting a custom application build, from the platform to the data routing, protocols, and the database, etc.  Does anyone know or have a good example for this?
Jack_son_Asked:
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Ray PaseurCommented:
There is no "one thing" here -- but some of these links may give you good starter ideas.  Make sure you incorporate the value of this work in your estimates and proposals, or incorporate it as a change order.  I often find that the time spent on this activity exceeds the time spent creating code and data bases!

http://en.wikipedia.org/wiki/Affinity_diagram
http://en.wikipedia.org/wiki/Comment_%28computer_programming%29
http://en.wikipedia.org/wiki/PHPDoc
http://en.wikipedia.org/wiki/Website_wireframe
http://en.wikipedia.org/wiki/Entity%E2%80%93relationship_model
http://en.wikipedia.org/wiki/API_documentation
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