Still old configurations after updating CyanogenMod I installed CyanogenMod 13 (UNOFFICIAL-20160104-NIGHTLY) on my Sony Xperia M (nicki) and updated it to CyanogenMod 13 (stable-20160527-NIGHTLY) successfuly. The update had no change on the configurations like the wallpaper, applications menu style, notifications menu, etc.
I installed the exact version (CyanogenMod 13 (stable-20160527-NIGHTLY)) on my wife's Sony Xperia M (nicki) last day but I saw the wallpaper, applications menu style, notifications menu and some other things are changed.

In our Linux desktop (like Fedora, Ubuntu, etc.) usually there is a .config directory in the ~home that keeps the configuration and if you simply delete this directory, after starting the application, it will run with new default configurations.

How can I delete/change old just CyanogenMod configurations/preferences directory on my CyanogedMod to see the new face and new menus of CyanogenMod? (I have no special customize on CyanogenMod but I do not to wipe all of my data on the internal storage like applications, etc.1)
Did you first wipe the /system partition before you flashed the rom?
Chances are you didn't. You may want to reflash the rom preferrably after wiping /system and /data