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I am wondering why not all scripts placed in init.d folder are in rc folders eg. system cups is in init.d but there is not in rc folders?

I don’t know if I understand it right. When I want to disable service I have to execute 

 update-rc.d -f something remove

but do I have to delete this service file from init.d folder too ? because when I check

 service --status-all

after update-rc.d -f something remove this service is still present in the list. How to interpret it right ?

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I guess that cups service is an upstart job that run /etc/init.d/cups script.

Check if is present /etc/init/cups.conf and if it exec /etc/init.d/cups.

Regarding the removal of links in rcX.d you should remove your script in /ect/init.d before you run update-rc.d command, indeed according to update-rc.d manual:

  When  invoked  with the remove option, update-rc.d removes any links in
  the /etc/rcrunlevel.d directories to the script /etc/init.d/name.   The
  script  must have been deleted already.  If the script is still present
  then update-rc.d aborts with an error message.
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    I have found this line in manual too. So the safest way is to disable not remove e.g. for testing purpose. So the best way to do this: sudo update-rc.d something disable
    – EdiD
    Sep 29, 2014 at 12:09

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