* manual: Mark commands that require root
Mark every command that requires to be run as root by prefixing them
with '#' instead of '$'.
* manual: Add note about commands that require root
This command was useful when NixOS was spread across multiple
repositories, but now it's pretty pointless (and obfuscates what
happens, i.e. "git clone git://github.com/NixOS/nixpkgs.git").
