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So my issue is the following:

In CXS 8 the very first option is:

What to scan:
If scanning a user, only scan within in the web root (e.g. ~user/public_html/)

Now, WHM Teak Settings has:

"Restrict document roots to public_html" which we have set to "Disabled" on all 25 production servers.

Which means that Addon Domains are created in /home/user/wordpress2 instead of /home/user/public_html/wordpress2

Does this mean that CXS Watch will not scan the Addon Domains not created in the public_html?

Regards

cxs caters for this when scanning using --allusers or --user [account] on cPanel servers. It obtains the document root from the cPanel data files for the users domains and subdomains from /var/cpanel/userdata/[account]/[domain/subdomain]

Do I pass this parameter only when doing a scheduled scan or do I add --allusers in the cxswatch.conf file?

If you need help on how to setup cxs, please use the helpdesk.