That worked for me, but wasn't what I was going for - however, it did give me some ideas and I figured it out now.
So, for anyone else looking to do this, here's where it's controlled.
In the theme maintenance, there are two areas where you can import resources, icon resources and custom icons. The icon resources field controls the folders.
So, to get a MUCH better starting point for E10, I exported the default theme of Inspired, then created a new theme of a custom name, then imported the Inspired.isl. Then from the actions menu Import Icon Resources and select "SysBaseImages_Classic" and wella, you get back all the colored folders embedded with the default E10 color scheme.
That already looks much better to people here, so I'm going to tweak it a bit further and separate the colors for our test and live environments further.