how do I stop dropbox from administering a particular directory
Move it out of the Dropbox folder. Dropbox can only sync the files and folders located within its own folder. If this is referring to yoru Desktop, Documents and Downloads folders, turn off the computer backup feature.
It sounds like you have the computer backup feature enabled @vonbarth, so you'll need to disable this through the desktop app preferences on the device that's being backed up.
You can follow the steps outlined at the bottom of this article to disable the backup, and in step 6 just make sure to choose to keep the files on your computer rather than Dropbox if you don't want to keep the files in Dropbox.
If you have any trouble with this, please feel free to send me some screenshots excluding any personal info.
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