CyanogenMod 13 activates disk encryption on Nexus devices per default, which is good. Unfortunately a default password is used, and there is currently no way to change this in the settings.
You need to start a terminal and become root to enter the following commands:
# vdc cryptfs changepw password default_password test1234 200 0 0
To verify if the new password got set correctly:
# vdc cryptfs verifypw test1234 200 0 0
200 0 0 is important.
When rebooting, the new password needs to be entered.
Update: Non-Nexus devices are not encrypted by default, so you have to enable
encryption manually, and replace
default_password with the lockscreen pin
in the above command.
Update 2: Just use SnooperStopper instead, the latest version works fine with CyanogenMod 13.