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I am running Tor via a PHP exec() and therefore its instance and data directory will be owned by 'www-data'. Is this OK to do or is there a better way I should be doing this?

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Supposing you're hosting other sites under the www-data user, it is not a very safe configuration. I'd suggest you deploy the PHP site via FastCGI so that it runs under a dedicated user account. You can also consider using sudo to launch the external command under different user (you'll need to configure /etc/sudoers with NOPASSWD switch for this particular command).

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