Nice post. I use a variation on this figuring out how to develop, assume control of or modify apps for scientists. Just out of curiosity, how much time do you spend talking to people? from your writing that is the one difference I would have with you - I usually find documentation to be sketchy at best. When I've done these types of projects I usually try to make time to talk to the developers, the dbas, IT support, the end users. Sometimes you can eliminate a lot of work with a couple of questions. And I've also found some of my interpretations based on analyzing code base were wrong - I corrected this by again looking at the data flow and asking the developers & users what was going on in that portion of the application. Of course if you're taking over a botched project or a closed app, most of this conversation is with the end users and IT support for the system.
yet another biologist hacking perl....
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