- Remove anything that may conflict with WHMCS from your public_html directory.
- Login to your admin panel and change the system URL to http://www.yourdomain.com/directory/ (http://www.yourdomain.com/ for root) under Setup > General Settings > General > System Location.
- Move your files from inside your folder to the directory of your choice directory (File Manager in cPanel makes this easy).
- Re-issue your WHMCS and enter the new license code when it’s requested when you go to login to your admin panel.
- Delete & re-add any WHMCS related Cron jobs you have running. Most users will have the WHMCS automation cron setup (Setup > Automation Settings). In most cases, there is a cron job for domain registrars also.
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