Find the device and its filesystem type with lsblk -f. For ext4, unmount it and run fsck -n /dev/DEVICE to check, then fsck -y /dev/DEVICE to repair. For XFS, the default on AlmaLinux and Rocky Linux, use xfs_repair -n and xfs_repair instead, because fsck does nothing on XFS. The root filesystem cannot be unmounted, so repair it from rescue mode or force a check at the next boot.
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Set folders to 755 and files to 644, make sure every file is owned by your cPanel user, and never use 777. On cPanel, PHP runs as your account, so Joomla can write to its cache, tmp, logs and images folders without any world-writable permissions. Check the result in Joomla under System > System Information > Folder Permissions.
As root, run /scripts/pkgacct USERNAME /backup to package one cPanel account (files, databases, email and settings) into /backup/cpmove-USERNAME.tar.gz. Copy the file off the server. To restore it on the same or another cPanel server, put the file in /home and run /scripts/restorepkg /home/cpmove-USERNAME.tar.gz. Restoring over an existing account replaces its data, so test first.
Missing VirtualHost directives in your Apache configuration? Learn how to restore them in cPanel by rebuilding httpd.conf.