Why do I have .AppleDouble directories?
Any time you access your Home Directory on a Macintosh computer, the system automatcially creates .AppleDouble listings inside each directory you accessed. These do take up a small amount of your allotted storage space limit (about 2 percent). To save space when you’re not on a Mac, you may delete these directories without affecting your files stored on Home Directory. The next time, however, you access your Home Directory on a Mac, the system will recreate these directories. They are necessary for Home Directory to work with Macs.