Just to clarify once more, step.rc would be maintained in all its glory - of that much you can be sure. Themes are a nightmare currently. Unfortunately, themes aren't about to change. Nobody is going to go through all those themes and clean them up, and efforts to create a theme standard have all fallen flat. People want to do thing the way they want to do them, and nobody's going to change that.
All themes have a common hub around which they build their entire interface - step.rc.
Step.rc is the rich source of all information, and using the proper tool, it can be used to gain complete understanding of a given theme. Step.rc has structure - although it is often difficult to find. With that information, a theme becomes simple to understand. A theming app would know where files need to go, and could alter the theme's step.rc file to point at the locations where they actually are. It would know which modules the theme expects to run, and point to the updated or existing versions of those libraries.