Upgrade Wizard: Files showing as owned by root?

When I try to use the Upgrade Wizard, after the system check, damn near every file shows permissions of 0644 and ownership by root.

This certainly is not the case. After I go into the directory and look at the permissions they are 0755 or 0775 and owned by the the owner of the virtual server (this is set up up in a box managed by Virtualmin, and everything runs under the user of that virtual server).

Which web-server (apache/nginx/etc…) use you virtual server?
For files you should set permission 0644.

Apache. But why would permissions be 0644? Doesn’t the documentation call for 0755/0775?

It’s for directories but for files should be 0644.

From the install documentation:

sudo chown -R www-data:www-data .
sudo chmod -R 755 .
sudo chmod -R 775 cache custom modules themes data upload
sudo chmod 775 config_override.php 2>/dev/null

Wouldn’t chmod -R recurse into all files and directories?

You right, but I know that should be 0644.