There are different ways to shutdown or reboot a linux computer.
All are front-ends to the /sbin/shutdown command (This
is also true for Linuxconf).
Depress those three magic keys on the console keyboard to reboot
your system. This is controlled by /sbin/init and the
file /etc/inittab.
/sbin/reboot is an alias (indeed a symlink) for
/sbin/shutdown -r NOW.
/sbin/halt is an alias (also a symlink) for
/sbin/shutdown -h NOW.