When I browse into an iCloud Drive folder (specifically Preview.app's folder) via Finder on OS X 10.11.1, I see both the files I knowingly placed there and the ones I opened with the related app, Preview in this example, which got automatically aliased in there.
To me, it's just clutter, useless. I'm thinking perhaps a workaround script or toll running periodically as a cron jobs could wipe out the aliases in the specified locations?
Is there a (hidden/unofficial)way to turn-off this behaviour of iCloud Drive that it doesn't create aliases? If not, has anyone a tool/script that would be the start of something I could adopt to clean the folders?