If you're adding something that needs to be started up and shut down gracefully, like a server daemon that keeps files open, creating an /etc/init. D-style script and then symlinking it into the /etc/rc?. D directory is the right thing to do.
Put your scripts n /etc/rc. D/init.d. There's a standard set of parameters the scripts should take, e.g. "myscript start", "myscript stop".
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