Ok, so you can use the Clean Installer to re-organize your files, right? For example, take all your downloaded plants and stick them in a subfolder. You can do this with any type of file except those listed in the manual. The list seems to be anything that you would use in create a Sim.

Does that mean that clothing put into a subfolder won't work? Because when I downloaded some Harry Potter clothes, they were automatically put into a subfolder and they still worked. Should I not risk putting other clothes into a subfolder if I don't want them to stop working?

It's because your question pertains mor to a general game help than specifically to the Clean Installer; and who is expert in the usage of the CI might not be expert in general game help...

In reply to your question, I see from your profile that you have all the EPs: starting from Nightlife, you have the ability to put in sub-folders also BodyShop stuff.

Here is the full article where you can find the answer to your doubts: http://www.modthesims2.com/article.php?t=46633