I've noticed this on both OS X El Capitan and macOS Sierra. I'm setup Boxcryptor to use iCloud, and noticed that even when Boxcryptor is not running, it stores a complete copy of what should be my protected (I even have filename encryption turned on) files, completely unencrypted, in ~/Library/Mobile\ Documents/iCloud~com~boxcryptor/Documents
Here is a sequence of commands to verify that this is happening:
LIB_PATH=~/"Library/Mobile Documents/iCloud~com~boxcryptor/Documents"
BC_PATH="/Volumes/Secomba/<code>whoami</code>/Boxcryptor/iCloud"
# Verify this file does not exist in either location
ls -l "$LIB_PATH"/testing.random "$BC_PATH"/testing.random
# Now create a random file in the Boxcryptor mountpoint
dd if=/dev/random bs=2048 count=1 > "$BC_PATH"/testing.random 2>/dev/null
# You can now see this file in both locations
ls -l "$LIB_PATH"/testing.random "$BC_PATH"/testing.random
# You can see the sum is the same, so it is unencrypted in both locations
sum "$BC_PATH"/testing.random "$LIB_PATH"/testing.random
# Now quit Boxcryptor, wait a few minutes, reboot, whatever, then try this again
sum "$BC_PATH"/testing.random "$LIB_PATH"/testing.random
Is this a known issue?
Rob