Good question.
The "lib" folder wasn't included because it is a folder that contains files that the TD uses, and that shouldn't be modified. You might argue that it's OK to modify the autoPrizes.xml and prizeSuggestions.xml files, but the right thing to do is really leave those files alone and make your own if you wish to customize them. Instead of editing autoPrizes.xml, for example, copy it to a new file and then point the TD to the new file. You can save the file anywhere you like, and in your data store is probably the best place. On the Preferences tab, press the Config Files button to point the TD at the new file.
I guess you could also argue that you may want to use different copies of these files in different data stores, but I didn't feel like this would be a common scenario at all, and didn't feel it warranted that much change to the way the TD currently works. So no matter where you place your autoPrizes.xml file, when you switch data stores the TD will still be looking at the same autoPrizes.xml file. You'll have to change the appropriate Config Files setting if you wish to point it to a new file.
