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You know that by default, servers like nginx and apache use standard directories for sites. Like "public_html", "www". And I noticed that on multi-user setups the sites are placed in the user's home directory

/home/username/public_html

I have such a setup, with nginx and php-fpm, and I want to have a custom directory holding all the sites, outside of the owner's home directory, like

/sites/www.example.org/

Is this a bad idea? Is there any advantage of using the home dir instead?

Obviously I would chown each sitedir so it belongs to the associated user.

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I would say it depends. If each user has its own private website, you could put those in /home/user/public_html but if the website is not personal like that, I would put them in a folder structure like you gave, with them being in /sites/domain/subdomain/.

Having all websites in a single directory makes it easier to give permissions, do backups, possibly put them on a different disk (mount point), etc.

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