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The major difference with Paul's is that the heart of the tool is a scan and store engine that places all the information in a database. The presentation layers he provides (one in CGIDEV2 and one in PHP) are simply demonstrations of what can be done to customize the output. i.e. there is no fixed output (other than the database) you can do what you want. This means that if all you want to do is run queries over the data with SQL you can do so at any time.
It occurs to me as I write this, that one could simply generate "Javascript" ( or "C++" or whatever ) from Paul's database and then run whatever documentation tool-du-jour you happen to prefer from the available OS offerings.
From what I can gather, this is pretty close to the best-case scenariofor using Sphinx with RPG. But of course I'd check out Paul's included
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