Remove Documents,Downloads,Music directories from home directory How to remove those directories permanently? Not just to hide them, but delete. Every time system reboots they are recreated and I have to sudo rm -rf NastyDir*.
Is there anything I can change in system settings?
Trane is right. Love 'em or 'hate 'em the system will always recreate them when you delete them.

You might try hiding them like this using Terminal

chflags hidden ~/Documents/


That will hide (for example) the documents folder in your home directory.

Not sure if O/S X will then un-hide it for you but it might be worth a try...