puppet runs as root, your rc script should do the right thing and run
the service as the right user
you should use su in your script to switch users to the one the service
should run as.
consider what will happen when your server starts up? the rc script runs
and then what? ask you for a password? thats not good.
the rc script has to do what it should without interaction, its not a puppet
problem.
all you should need to do is copy the working rc script into the init.d dir
and use the service resource to enable it and ensure its running.
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Actually, runuser is better than su for use in init scripts.