Ok, I have all the skinning panels for Nexus done, as well as the Theme Builder panels, plus the Theme Browser.
I was having some difficulty figuring out how to tie everything together, e.g.; as you know even though WorkShelf is a single application, it has multiple skinnable objects that can be skinned independently and have independent configuration files: the docks, the Shelf, each of the desktop modules, etc... Add NextSTART themes to this, etc...
For instance, even if you have Winstep Xtreme, you might want to just make a quick Nexus-only theme instead of skinning the whole she-bang...
So, when you select New Theme from the menu, a Theme node gets added to the navigation panel at the left (at first you only have the Theme Builder node visible, consisting of various configuration panels related to the builder itself, nothing else).
In the Theme root panel you can define the theme's name, author, add a wallpaper specific to that theme, and here is the important part, you can also define which 'part' of Winstep Xtreme you want to skin. By default you have the whole thing, but if you want you can change a combo box in that panel from 'Winstep Themes' to just 'Nexus'.
If you do this, only the nodes related to the Nexus skinning panels are visible on the left navigation panel. When you Save the theme, only the Nexus configuration files are saved. When you Apply the theme to preview it in the applications themselves, only the Nexus related settings are applied to Winstep Xtreme (so only the docks will change).
Likewise, when you Open an existing theme, you have a combo box that allows you to select which part of an existing theme you want to skin/see themes for. If you select 'Clock', only the available Clock themes are shown (as it happens in the Themes panel of Nexus/WorkShelf Preferences now). If you press Ok at this point, only the nodes related to the clock module are shown in the navigation tree.
Once I have all this actually working (as I'm starting with Nexus, all other panels will be/are blank/haven't been made yet) I will release an alpha so you guys can 'feel' where this is going (plus you will at least be able to churn out Nexus dock skins using the Builder itself). I guess it will then be easier to give some sort of feedback.