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Most people have been talking about cross-reference tools so far.
The only product with which I have any experience is Hawkeye. It's certainly better than nothing, but I'll agree with Eric that it is far from perfect.

Emily Smith wrote:
We're undergoing the task of creating documentation for our iseries programs. The number/size/complexity/god-awful spaghetti code of these programs makes this impossible to do manually.

It sounds like you're interested in documentation of the internal structure of your programs as well as the relationships between programs. As far as I know, Hawkeye doesn't provide any such functionality.

There is a function in the CODE Editor that comes with WDSC which provides an application diagram which can be useful for getting an overview of the internal structure of a program. See http://archive.midrange.com/wdsci-l/200905/msg00033.html for more detailed instructions on how to use it.

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