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I like to use [Sequence Diagrams](https://en.wikipedia.org/wiki/Sequence_diagram) to document order of operations and the sequence of function calls in an app. This [template](https://dl.dropboxusercontent.com/u/1186808/afomi/sequence-diagram-template/sequence-diagram-template.pdf) can be used when creating sequence diagrams for your project.  Alternatively, checkout http://agile.pics which supports rendering Sequence Diagrams from a GitHub Gist, using javascript.
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