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The question's in the title!

What is the benefit/purpose of supplying a user when installing the certificate?

Is specifying a user of "nobody" less secure than "jon"?

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up vote 2 down vote accepted

Yes, actually; having files owned by the nobody user is a fairly major security risk, because many "untrusted" processes are run as nobody, and if an attacker manages to work out a way to compromise an untrusted, running-as-nobody process, then they now have write access to all your certificates -- which I assume I don't have to spell out the downsides of.

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