As a developer, one the main tools I worked with was one of the various iterations of Microsoft's Visual Studio; something referred to in the industry as an IDE, or integrated development environment.
These can be useful precisely because they can provide you, inside of one creation management system, a comprehensive way of not only creating the integrated bits -- the various objects, whether buttons, or list selectors, or control windows into other programs, like spreadsheets, or databases etc, as well as whatever coded specifics needed to accompany these objects (all of which, of course were simply abstracted bits of their own code), but of keeping them all organized into logical structures that were, hopefully, a great deal easier to keep track of.
In my mind, one the most wonderful aspects of virtual systems, will be the expansion of such integrated development environments way beyond the capacities of their two dimensional brethren of today. And this will of course apply to a great deal more than just application development systems. Just think what such things could do for mathematics development, or engineering development systems.
You've already seen some part of this displayed by the Tony Stark Character in the Iron Man, and Avenger movies, when he manipulates design constructs in any of his labs. Even that, however, is a limited presentation of what complete immersion into an unlimited 3D design space would allow; especially one tied to on demand simulation feedback. It's a breathtaking picture and one that makes me quite jealous of the fact that it wasn't available in my day.