I would like to thank everyone for their input. Even though I believe Mathematica is the future for programming, I found getting started was a large task. You have helped me greatly.

Brian Buchholz

There are large and complex packages that were written this way: use a notebook (including text cells and comments) and auto-save to an .m file. SciDraw is one example. One nice feature of notebook is hierarchical sectioning.

The reason why I don't like to do this personally (for packages!) is that it's hard to use a version control system with it. The missing piece is a good reliable notebook diff tool, I guess. There is in fact a diff tool in Mathematica, but in the end I found using plain text more convenient for packages.

I use the Mathematica plugin IntelliJ IDEA instead of Workbench for packages.

But interactive work is something entirely different. IDEs are just not suitable for it. Even when writing packages, I constantly have a notebook open to interactively test it, even put new functions together within the notebook before moving the code to the package file.

Unless something has changed recently, Workbench 2 will not work with Mathematica 11. However, a beta version which will work is available from tech support on request. Or have I missed something?