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Due to contractual obligations to protect IP and client information, we unfortunately, cannot use Cloud or Mathematica Online for development in the development of our projects.

We are further required to use a source control system behind our firewall(s).

Are there any particularly good and recommended documents or white papers on application development in Mathematica?

Are there third party IDEs for Mathematica development (we did look at Workbench but it appears that it is still in development).

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Plenty of folks use workbench- I think v2 is in development, but v1 is in production. An alternative could be IntelliJIDEA which may not be a full IDE, but is third-party. Also 5184

Wolfram has a paper on just this: Building large software systems in Mathematica - however, this seems fairly generalized. (didn't link to Wolfram because they make you fill out a survey to access)

There have been some posts discussing how to tackle large problems strategically: 109888

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    $\begingroup$ v2 is available and v3 is in development. $\endgroup$ – Karsten 7. May 28 '16 at 1:11

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