The last point is indeed a good reason for leaving the script in /etc/init.d . But i experienced problems in case of using several runlevel editors (bum, ksysv, sysv-rc-config etc )to configure runlevels. Since they all list all scripts within /etc/init.d, it is easy to missconfigure your system by activating scripts in runlevels, which are not ment for being activated within runlevels. But this might is a problem of the sysv-rc mechanismus. To me, i would prefere to remove the script from /etc/init.d to avoid confusion if using runlevel editors.
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